Phylogenetic Relationships of Combretoideae (Combretaceae) Inferred from Plastid, Nuclear Gene and Spacer Sequences

Journal of Plant Research. Dec, 2002  |  Pubmed ID: 12579451

Phylogenetic relationships of the subfamily Combretoideae (Combretaceae) were studied based on DNA sequences of nuclear ribosomal internal transcribed spacer (ITS) regions, the plastid rbcL gene and the intergenic spacer between the psaA and ycf3 genes (PY-IGS), including 16 species of eight genera within two traditional tribes of Combretoideae, and two species of the subfamily Strephonematoideae of Combretaceae as outgroups. Phylogenetic trees based on the three data sets (ITS, rbcL, and PY-IGS) were generated by using maximum parsimony (MP) and maximum likelihood (ML) analyses. Partition-homogeneity tests indicated that the three data sets and the combined data set are homogeneous. In the combined phylogenetic trees, all ingroup taxa are divided into two main clades, which correspond to the two tribes Laguncularieae and Combreteae. In the Laguncularieae clade, two mangrove genera, Lumnitzera and Laguncularia, are shown to be sister taxa. In the tribe Combreteae, two major clades can be classified: one includes three genera Quisqualis, Combretumand Calycopteris, within which the monophyly of the tribe Combreteae sensu Engler and Diels including Quisqualis and Combretumis strongly supported, and this monophyly is then sister to the monotypic genus Calycopteris; another major clade includes three genera Anogeissus, Terminalia and Conocarpus. There is no support for the monophyly of Terminaliaas it forms a polytomy with Anogeissus. This clade is sister to Conocarpus.

A Strategy for the Synthesis of Aryl Alpha-ketoamides Based Upon the Acylation of Anions Derived from Cyanomethylamines Followed by Oxidative Cleavage

Organic Letters. Apr, 2002  |  Pubmed ID: 11922793

[reaction: see text] Cyanomethylamines, prepared by alkylation of amines with chloroacetonitrile, were deprotonated using NaHDMS in THF, reacted with heteroaryl or substitutedphenyl esters, and then oxidized by adding Clorox(TM) to afford aryl alpha-ketoamides in a single operation in good overall yields.

A General Method for the Preparation of 4- and 6-azaindoles

The Journal of Organic Chemistry. Apr, 2002  |  Pubmed ID: 11925251

Nitropyridines reacted with an excess of vinyl Grignard reagent to produce 4- or 6-azaindoles. Improved yields were obtained when a halogen atom was present at the position alpha to the nitrogen atom in the pyridine ring.

Composition of Volatile Oil of Primula Obconica in Central China

Natural Product Letters. Aug, 2002  |  Pubmed ID: 12168760

Primula obconica was introduced to Europe from Hubei, China in 1880, and has been cultivated worldwide as one of popular ornamental plants. The volatile oil of wild P. obconica collected from its original place, Yichang, Hubei was first investigated. A total of 43 compounds constituting 93.49% of the oil were identified by using GC and GC-MS. The major compounds were methyl 2,4-dihydroxy-5-methyl benzoate (30.41%), methyl 2,6-dihydroxy-4-methyl benzoate (29.27%), and hypnone (8.92%) etc. In comparison with the published data of some European cultivars, the native P. obconica seems to be allergen-free due to absence of primin and miconidin.

An Effective Procedure for the Acylation of Azaindoles at C-3

The Journal of Organic Chemistry. Aug, 2002  |  Pubmed ID: 12182666

Conditions for attachment of acetyl chloride, benzoyl chloride, and chloromethyl oxalate to the 3-position of 4-, 5-, 6-, or 7-azaindoles were explored. Best results were achieved with an excess of AlCl(3) in CH(2)Cl(2) followed by the addition of an acyl chloride at room temperature.

Duplication and Adaptive Evolution of the Chalcone Synthase Genes of Dendranthema (Asteraceae)

Molecular Biology and Evolution. Oct, 2002  |  Pubmed ID: 12270901

Chalcone synthase (CHS) is a key enzyme in the biosynthesis of flavonoids, which are important for the pigmentation of flowers and act as attractants to the pollinators. Genes encoding CHS constitute a multigene family in which the copy number varies among plant species and functional divergence appears to have occurred repeatedly. Plants of the Dendranthema genus have white, yellow, and pink flowers, exhibiting considerable variation in flower color. In this article, 18 CHS genes from six Dendranthema species were sequenced. Two of them were found to be pseudogenes. The functional Dendranthema CHS genes formed three well-supported subfamilies: SF1, SF2, and SF3. The inferred phylogeny of the CHS genes of Dendranthema and Gerbera suggests that those genes originated as a result of duplications before divergence of these two genera, and the function of Dendranthema CHS genes have diverged in a similar fashion to the Gerbera CHS genes; i.e., the genes of SF1 and SF3 code for typical CHS enzymes expressed during different stages of development, whereas the genes of SF2 code for another enzyme that is different from CHS in substrate specificity and reaction. Relative rate tests revealed that the Dendranthema CHS genes significantly deviated from clocklike evolution at nonsynonymous sites. Maximum likelihood analysis showed that the nonsynonymous-synonymous (omega = d(N)/d(S)) rate ratio for the lineage ancestral to SF2 was much higher than for other lineages, with some sites having a ratio well above one. Positive selective pressure appears to have driven the divergence of SF2 from SF1 and SF3.

Propofol Reduces Infarct Size and Striatal Dopamine Accumulation Following Transient Middle Cerebral Artery Occlusion: a Microdialysis Study

European Journal of Pharmacology. Oct, 2002  |  Pubmed ID: 12359271

Acute cerebral ischemia is associated with an increased extracellular dopamine accumulation. Attenuation or prevention of excessive dopamine accumulation alleviates the cerebral ischemic damage. Propofol, an intravenous anesthetic, has been suggested to have neuroprotective properties. The effect of propofol on dopaminergic neurotransmitters is unclear. The in vivo microdialysis technique was used in this study to examine the effect of propofol on infarct size and striatal dopamine accumulation in rat model of temporary middle cerebral artery occlusion. Sixteen rats were fitted with a right striatal microdialysis probe. Ischemia was induced by inserting a 4-0 monofilament nylon suture into the middle cerebral artery. Propofol was intravenously infused in eight rats during ischemia (60 min) and reperfusion (60 min) at an average dose of 36 mg/kg/h. Control rats (n=8) received vehicle infusion. The infarct size was determined at the end of the experiment. Propofol significantly reduced infarct size, the median (interquatile range) value was 6.84% (7.68%), significantly lower than that in the control group, which was 28.04% (32.28%) (p<0.01). The middle cerebral artery occlusion significantly increased dopamine accumulation in the striatum. Propofol infusion significantly attenuated this middle cerebral artery occlusion-induced dopamine accumulation. The data demonstrate that propofol, when administered during ischemia and reperfusion, provides neuroprotection in our middle cerebral artery occlusion in rat model. The data also suggest that attenuated dopamine accumulation may be one of the factors contributing to the neuroprotective property of propofol.

Genetic Diversity in Primula Obconica (Primulaceae) from Central and South-west China As Revealed by ISSR Markers

Annals of Botany. Feb, 2003  |  Pubmed ID: 12547685

Genetic diversity was investigated in 60 individuals of Primula obconica from four natural populations (from Hubei, central China, and Sichuan, south-west China) and from cultivated material. Inter-simple sequence repeat (ISSR) techniques produced 249 polymorphic bands and identified 60 ISSR genotypes. Based on Shannon's index and Nei's genetic diversity, the genetic diversity detected in all natural populations of P. obconica was much higher than that in the cultivated plants, and that in the three Dalaoling (Hubei) populations was higher than that in the Wawushan (Sichuan) population. UPGMA cluster analysis showed that there was no distinct genetic differentiation between populations from the Mt Dalaoling area and the Mt Wawushan area. This study provides a population-level genetic profile of P. obconica, which was previously poorly known but which is important for Primula breeding and cultivation.

Interpopulation Congruence in Chinese Primula Ovalifolia Revealed by Chemical and Molecular Markers Using Essential Oils and ISSRs

Zeitschrift Für Naturforschung. C, Journal of Biosciences. Jan-Feb, 2003  |  Pubmed ID: 12622227

The chemical composition of the essential oils of five natural populations of P. ovalifolia from central and southwest China and their interpopulation variability were first analyzed by using GC-MS. Twenty-two essential oil compounds were obtained, in which eighteen ones were identified and characterized representing 95%-96% of the oil composition. Three main chemotypes, i.e., the methyl-acetyl-hydroquinone-rich, hydroquinone-rich, and acetyl-hydroquinone-rich chemotypes, were then differentiated, corresponding to the three groups obtained from the cluster analysis based on the essential oil composition percentages. Genetic variations among the five populations were also investigated using the Inter-Simple Sequence Repeats (ISSR) markers. Finally, the Mantel test showed that there was a significant correlation between two distance matrices based on the chemical compounds of essential oils and ISSR markers, confirming the congruence of interpopulation relationships in the P. ovalifolia revealed by the chemical and molecular markers

Chemical Composition of the Essential Oils of Two Rhodiola Species from Tibet

Zeitschrift Für Naturforschung. C, Journal of Biosciences. Mar-Apr, 2003  |  Pubmed ID: 12710720

The essential oils from rhizomes of Rhodiola crenulata and R. fastigiata in eastern Tibet were analyzed by using GC-MS. The major constituents were geraniol (53.3%), n-octanol (13.4%), 2-methyl-3-buten-2-ol (10.8%), citronellol (5.3%), 3-methyl-2-buten-1-ol (4.0%), myteol (3.0%), and linalool (2.4%) for R. crenulata and geraniol (45.3%), n-octanol (12.3%), 2-methyl-3-buten-2-ol (8.0%), linalool (5.1%), isogeraniol (4.5%), citronellol (4.4%), and cis-sabinenehydrate (3.6%) for R. fastigiata.

CDNA Microarray Analysis of Gene Expression Profiles in Human Fibroblast Cells Irradiated with Red Light

The Journal of Investigative Dermatology. May, 2003  |  Pubmed ID: 12713592

In this paper, the cDNA microarray technique was used to investigate the gene expression profiles of human fibroblasts irradiated by low-intensity red light. Proliferation assays showed that the fibroblast HS27 cells responded with a curve effect to different doses of low-intensity red light irradiation at a wavelength of 628 nm. An optimal dose of 0.88 J per cm2 was chosen for subsequent cDNA microarray experiments. The gene expression profiles revealed that 111 genes were regulated by the red light irradiation and can be grouped into 10 functional categories. Most of these genes directly or indirectly play roles in the enhancement of cell proliferation and the suppression of apoptosis. Two signaling pathways, the p38 mitogen-activated protein kinase signaling pathway and the platelet-derived growth factor signaling pathway, were found to be involved in cell growth induced by irradiation of low-intensity red light. Several genes related to antioxidation and mitochondria energy metabolism were also found to express differentially upon irradiation. This study provides insight into the molecular mechanisms associated with the beneficial effects of red light irradiation in accelerating wound healing.

Fanwort in Eastern China: an Invasive Aquatic Plant and Potential Ecological Consequences

Ambio. Mar, 2003  |  Pubmed ID: 12733803

Effect of Antisense Oligonucleotide of Noggin on Spatial Learning and Memory of Rats

Acta Pharmacologica Sinica. May, 2003  |  Pubmed ID: 12740172

To investigate the effect of antisense oligonucleotide (ASODN) of noggin on rat spatial learning and memory.

Urbanization, Land Use, and Water Quality in Shanghai. 1947-1996

Environment International. Aug, 2003  |  Pubmed ID: 12742408

The paper undertakes a preliminary investigation into the relationship between water quality and urbanization as well as the changing patterns of land use within Shanghai. Longitudinal changes to water quality at various points along the course of the Huangpu River are analysed and compared to changes in the rates of urbanization and changes in land uses. The results reveal that rapid urbanization corresponds with rapid degradation of water quality. It also shows that urban land uses are positively correlated with the decline in water quality. A regression model shows that close to 94% of the variability in water quality classifications is explained by industrial land area. The paper concludes with the need for comprehensive land use planning as a way of protecting valuable water resources.

A Phylogeny of Chinese Species in the Genus Phrynocephalus (Agamidae) Inferred from Mitochondrial DNA Sequences

Molecular Phylogenetics and Evolution. Jun, 2003  |  Pubmed ID: 12742745

We investigated the phylogenetic relationships among most Chinese species of lizards in the genus Phrynocephalus (118 individuals collected from 56 populations of 14 well-defined species and several unidentified specimens) using four mitochondrial gene fragments (12S rRNA, 16S rRNA, cytochrome b, and ND4-tRNA(LEU)). The partition-homogeneity tests indicated that the combined dataset was homogeneous, and maximum-parsimony (MP), neighbor-joining (NJ), maximum-likelihood (ML) and Bayesian (BI) analyses were performed on this combined dataset (49 haplotypes including outgroups for 2058bp in total). The maximum-parsimony analysis resulted in 24 equally parsimonious trees, and their strict consensus tree shows that there are two major clades representing the Chinese Phrynocephalus species: the viviparous group (Clade A) and the oviparous group (Clade B). The trees derived from Bayesian, ML, and NJ analyses were topologically identical to the MP analysis except for the position of P. mystaceus. All analyses left the nodes for the oviparous group, the most basal clade within the oviparous group, and P. mystaceus unresolved. The phylogenies further suggest that the monophyly of the viviparous species may have resulted from vicariance, while recent dispersal may have been important in generating the pattern of variation among the oviparous species.

Putative HAPN Receptor Binding Sites in SARS_CoV Spike Protein

Acta Pharmacologica Sinica. Jun, 2003  |  Pubmed ID: 12791172

To obtain the information of ligand-receptor binding between the S protein of SARS-CoV and CD13, identify the possible interacting domains or motifs related to binding sites, and provide clues for studying the functions of SARS proteins and designing anti-SARS drugs and vaccines.

Identification of Probable Genomic Packaging Signal Sequence from SARS-CoV Genome by Bioinformatics Analysis

Acta Pharmacologica Sinica. Jun, 2003  |  Pubmed ID: 12791173

To predict the probable genomic packaging signal of SARS-CoV by bioinformatics analysis. The derived packaging signal may be used to design antisense RNA and RNA interfere (RNAi) drugs treating SARS.

Preliminary Investigation of a Sensitive Biomarker of Organotin Pollution in Chinese Coastal Aquatic Environment and Marine Organisms

Environmental Pollution (Barking, Essex : 1987). 2003  |  Pubmed ID: 12826407

In nine batches of sea bivalves collected from Chinese coastal cities during the year of 2000 to 2002, a special sample named Mya arenaria was found to have strong ability of butyltin accumulation compared with the other sampled bivalves in the corresponding batches. Tributyltin compound was the predominant pollutant with the detection rate high up to 100%. Special high levels of g Sn/g were detected in some Mya arenaria samples. The results obtained showed that Mya arenaria was potentially a biomarker to indicate organotin pollution in coastal aquatic environment.

Chemical Composition of the Essential Oils of Two Chinese Endemic Meconopsis Species

Zeitschrift Für Naturforschung. C, Journal of Biosciences. May-Jun, 2003  |  Pubmed ID: 12872920

The essential oils from two Chinese endemic Meconopsis species, i. e., M. punicea and M. delavayi, were analyzed by using GC-MS for the first time. The major constituents were hexadecanoic acid (16.8%), 1,2-dimethyl naphthalene (11.4%), 1,4-dimethyl naphthalene (6.6%), 1,3-dimethyl-5-ethyl naphthalene (5.9%), and 3-methyl biphenyl (5.6%) for M. punicea, and hexadecanoic acid (9.9%), 1,2-dimethyl naphthalene (7.9%), 1,3-dimethyl-5-ethyl naphthalene (6.2%), tetradecane (5.9%), and hexyl cinnamaldehyde (5.5%) for M. delavayi.

[Phylogenetic Diversity of Microbes and Its Perspectives in Conservation Biology]

Ying Yong Sheng Tai Xue Bao = The Journal of Applied Ecology / Zhongguo Sheng Tai Xue Xue Hui, Zhongguo Ke Xue Yuan Shenyang Ying Yong Sheng Tai Yan Jiu Suo Zhu Ban. Apr, 2003  |  Pubmed ID: 12920914

Molecular phylogenetic analysis plays a very important role in the study of microbial diversity. For both cultivated and uncultivated microbes, the comparative sequence analysis of 16S rRNA enabled the investigation of phylogenetic relationships among microorganisms in a manner that was not feasible through traditional microbiological methods. As a result, there are drastic revisions in our understanding of microbiology. The phylogenetic diversity based on the comparative sequence analysis of 16S rRNA produced new insights into the biodiversity conservation. It provides a method for biodiversity judgment and a guideline for biodiversity conservation. Also, it produces the aim of conservation, which is to keep the phylogenetic information as much as possible. In this review, some characters of microbial phylogenetic diversity and the perspectives in conservation biology are outlined.

Genetic Diversity of Hibiscus Tiliaceus (Malvaceae) in China Assessed Using AFLP Markers

Annals of Botany. Sep, 2003  |  Pubmed ID: 12930729

Amplified fragment length polymorphism (AFLP) markers were used to investigate the genetic variations within and among nine natural populations of Hibiscus tiliaceus in China. DNA from 145 individuals was amplified with eight primer pairs. No polymorphisms were found among the 20 samples of a marginal population of recent origin probably due to a founder effect. Across the other 125 individuals, 501 of 566 bands (88.5%) were polymorphic, and 125 unique AFLP phenotypes were observed. Estimates of genetic diversity agreed with life history traits of H. tiliaceus and geographical distribution. AMOVA analysis revealed that most genetic diversity resided within populations (84.8%), which corresponded to results reported for outcrossing plants. The indirect estimate of gene flow based on phiST was moderate (Nm=1.395). Long-distance dispersal of floating seeds and local environments may play an important role in shaping the genetic diversity of the population and the genetic structure of this species.

Spatial and Temporal Patterns of Expression of Noggin and BMP4 in Embryonic and Postnatal Rat Hippocampus

Brain Research. Developmental Brain Research. Dec, 2003  |  Pubmed ID: 14643011

Recent studies indicate that bone morphogenetic protein-4 (BMP4) and Noggin not only play an important role in the early development of the nervous system, but may also play a role in postnatal central nervous system (CNS) development. In this study, we examined the relative levels and localization of Noggin and BMP4 mRNA in the hippocampus of rats of different developmental stages with reverse transcriptase-polymerase chain reaction (RT-PCR) and in situ hybridization (ISH). RT-PCR showed that the temporal changes in the levels of expression of Noggin and BMP4 were different. The peak level of expression of Noggin mRNA was observed at embryonic day 13 (E13), subsequently gradually declined at 1-3 months (P1-3M) postnatal, and was detected only at a low level at P18M. In contrast, the expression of BMP4 mRNA increased gradually during embryonic development, reached a maximal level at 3 weeks (W) postnatal, and declined only slightly through P18M. In situ hybridization revealed that at embryonic stages, Noggin mRNA was localized throughout all hippocampal regions, whereas at early postnatal ages, Noggin mRNA was primarily localized in the anterior subiculum. At embryonic and early postnatal stages, no significant BMP4 mRNA expression was detectable in the hippocampus. At later postnatal ages, however, Noggin and BMP4 mRNA expression was observed in similar patterns. At 1-3 months postnatal, expression of BMP4 was observed mainly in the dentate gyrus and in the CA1-CA3 pyramidal cell layers. Lower hybridization signals were observed in the hilus and subiculum. Taken together, our results demonstrate that Noggin and BMP4 are expressed in embryonic and postnatal hippocampus, and that the temporal and spatial patterns of their expression are developmentally regulated. These data suggest that Noggin and BMP4 play important roles in hippocampal development.

Semantic Search Among Heterogeneous Biological Databases Based on Gene Ontology

Acta Biochimica Et Biophysica Sinica. May, 2004  |  Pubmed ID: 15156279

Semantic search is a key issue in integration of heterogeneous biological databases. In this paper, we present a methodology for implementing semantic search in BioDW, an integrated biological data warehouse. Two tables are presented: the DB2GO table to correlate Gene Ontology (GO) annotated entries from BioDW data sources with GO, and the semantic similarity table to record similarity scores derived from any pair of GO terms. Based on the two tables, multifarious ways for semantic search are provided and the corresponding entries in heterogeneous biological databases in semantic terms can be expediently searched.

Chemical Composition of the Essential Oils of Clausena Lansium from Hainan Island, China

Zeitschrift Für Naturforschung. C, Journal of Biosciences. Mar-Apr, 2004  |  Pubmed ID: 15241914

The essential oils of wild Clausena lansium collected in Hainan Island, China were extracted from leaves, flowers, sarcocarps and seeds, and then analyzed by using GC/MS. The main constituents of the essential oils were: beta-santalol (35.2%), bisabolol (13.7%), methyl santalol (6.9%), ledol (6.5%) and sinensal (5.6%) in the leaves; beta-santalol (50.6%), 9-octadecenamide (17.2%) and sinensal (4.1%) in the flowers; beta-santalol (52.0%), alpha-santalol (15.5%), farnesol (5.2%) and sinensal (4.0%) in the sarcocarps; and phellandrene (54.8%), limonene (23.6%), and p-menth-1-en-4-ol (7.5%) in the seeds.

Chemical Composition of the Essential Oils of Two Alpinia Species from Hainan Island, China

Zeitschrift Für Naturforschung. C, Journal of Biosciences. Mar-Apr, 2004  |  Pubmed ID: 15241915

The essential oils of two Alpinia species, ie. A. hainanensis and A. katsumadai, from Hainan Island, China were analyzed by using GC-MS. The major constituents in the leaf oil of A. hainanensis were ocimene (27.4%), beta-pinene (10.1%), 9-octadecenoic acid (6.5%), n-hexadecanoic acid (5.8%), 9,12-octadecadienoic acid (5.4%), and terpinen (4.3%). The oil constituents obtained from the flowers of A. hainanensis were ocimene (39.8%), beta-pinene (17.7%), terpinene (5.5%), p-menth-1-en-ol (4.9%), caryophyllene (4.9%), and phellandrene (4.4%). In A. katsumadai, the major constituents in the leaf oil were p-menth-1-en-ol (22.0%), terpinen (19.0%), 4-carene (9.1%), 1,8-cineole (8.3%), and camphor (5.6%). The major constituents in the flower oil were p-menth-1-en-ol (21.3%), 1,8-cineole (20.2%), terpinen (12.6%), phellandrene (7.0%), 4-carene (6.4%), and beta-pinene (5.2%).

A Molecular Phylogeny of Oxya (Orthoptera: Acridoidea) in China Inferred from Partial Cytochrome B Gene Sequences

Molecular Phylogenetics and Evolution. Nov, 2004  |  Pubmed ID: 15336683

The grasshoppers of the genus Oxya are well known to damage rice, sugar cane, and other crops, yet their phylogenetic relationships have not been examined with molecular data. In this study, we obtained the 432 bp DNA sequences of the mitochondrial cytochrome b gene from 91 individuals of nine Oxya species and two outgroups (Gesonula punctifrons and Acrida cinerea). Phylogenetic analyses for the molecular data set were then carried out using the maximum parsimony and neighbor-joining methods. The results showed that the nine Oxya species form four well-supported clades, which include (1) O. intricata and O. flavefemura; (2) O. japonica and O. bicingula; (3) O. agavisa; and (4) O. chinensis, O. brachyptera, O. adentata, and O. hainanensis, respectively. In particular, the monophyly of O. hainanensis and O. agavisa is strongly supported, respectively. However, O. flavefemura and O. intricata, O. bicingula, and O. japonica form paraphyletic groups, respectively, and O. chinensis, O. adentata, and O. brachyptera form a polyphyletic group, suggesting that they should be merged as few as three species.

Molecular Phylogenetic Relationships of Eastern Asian Cyprinidae (pisces: Cypriniformes) Inferred from Cytochrome B Sequences

Science in China. Series C, Life Sciences / Chinese Academy of Sciences. Apr, 2004  |  Pubmed ID: 15379245

Complete mitochondrial cytochrome b sequences of 54 species, including 18 newly sequenced, were analyzed to infer the phylogenetic relationships within the family Cyprinidae in East Asia. Phylogenetic trees were generated using various tree-building methods, including Neighbor-joining (NJ), Maximum Parsimony (MP) and Maximum Likelihood (ML) methods, with Myxocyprinus asiaticus (family Catostomidae) as the designated outgroup. The results from NJ and ML methods were mostly similar, supporting some existing subfamilies within Cyprinidae as monophyletic, such as Cultrinae, Xenocyprinae and Gobioninae (including Gobiobotinae). However, genera within the subfamily "Danioninae" did not form a monophyletic group. The subfamily Leuciscinae was divided into two unrelated groups: the "Leuciscinae" in East Asia forming as a monophyletic group together with Cultrinae and Xenocyprinae, while the Leucisciriae in Europe, Siberia, and North America as another monophyletic group. The monophyly of subfamily Cyprininae sensu Howes was supported by NJ and ML trees and is basal in the tree. The position of Acheilognathinae, a widely accepted monophyletic group represented by Rhodeus sericeus, was not resolved.

High-throughput S-SAP by Fluorescent Multiplex PCR and Capillary Electrophoresis in Plants

Journal of Biotechnology. Oct, 2004  |  Pubmed ID: 15464599

The inherent replicative mode of transposition endows retrotransposons with considerable advantages as genetic tools in plant genome analysis. Here we present a high-throughput sequence-specific amplification polymorphism (S-SAP) method based on copia-like retrotransposons to fulfill the increasing desire of screening large numbers of samples in plants. Classic approach for digestion, ligation and pre-amplification was combined with optimized fluorescent multiplex PCR for simultaneously selective amplifying S-SAP fragments, and multiple S-SAPs were subsequently detected by capillary electrophoresis using ABI PRISM 3700 capillary instruments. Comparisons of results from multiplex PCR with simplex PCR, and from capillary electrophoresis with slab-gel electrophoresis demonstrated that this method is an efficient, economical, and accurate means for high-throughput and large-scale genotyping retrotransposon variation in plants.

Molecular Genetic Variation in Chinese Populations of Three Subspecies of Hippophae Rhamnoides

Biochemical Genetics. Aug, 2004  |  Pubmed ID: 15487589

To provide a population-level genetic profile for investigation and conservation of genetic diversity of the sea buckthorn (Hippophae rhamnoides L.), 300 individuals of fifteen natural populations of sea buckthorn in China were analyzed by using ISSR (inter-simple sequence repeats) markers. On the basis of Shannon's index and Nei's genetic diversity, the mean genetic diversity detected in the natural populations of Hippophae rhamnoides ssp. yunnanensis, ssp. sinensis, and ssp. gyantsensis was 0.1944, 0.2169, and 0.1372, respectively. The coefficient of gene differentiation (Gst) of seven ssp. yunnanensis populations is 0.2790, and that of seven ssp. sinensis populations is 0.4184. This means that 28% of the total molecular variance of seven ssp. yunnanensis populations existed among populations, and 42% for seven ssp. sinensis populations, suggesting that the subspecies have different genetic structures. No significant correlation between genetic and geographic distances of the populations was found using ISSR markers.

[Intrathecal Implantable Infusion Pumps in the Treatment of Refractory Pain--report of 3 Cases]

Zhonghua Yi Xue Za Zhi. Oct, 2004  |  Pubmed ID: 15569443

[Clinical Study on Treatment of Advanced Stage Non-small Cell Lung Cancer by Guben Xiaoliu Capsule]

Zhongguo Zhong Xi Yi Jie He Za Zhi Zhongguo Zhongxiyi Jiehe Zazhi = Chinese Journal of Integrated Traditional and Western Medicine / Zhongguo Zhong Xi Yi Jie He Xue Hui, Zhongguo Zhong Yi Yan Jiu Yuan Zhu Ban. Nov, 2004  |  Pubmed ID: 15609595

To observe the therapeutic effect of Guben Xiaoliu Capsule (GXC) in treating advanced stage non-small cell lung cancer (NSCLC).

[Introduction to the Methods of Constructing Phylogenetic Trees with DNA Sequences]

Yi Chuan = Hereditas / Zhongguo Yi Chuan Xue Hui Bian Ji. Mar, 2004  |  Pubmed ID: 15639989

Construction of phylogenetic trees is a key means in molecular evolutionary studies. The methods of constructing phylogenetic trees include the distance-based methods, parsimony, maximum likelihood, and Bayesian inference methods. To resolve a special problem about phylogeny, several notices are necessary: first, to select the reasonable data at less bias as possible; second, to choose the proper method to reconstruct phylogenetic tree; third, to evaluate the conclusions and explain them on the field of evolution. The present paper provides a brief introduction of the principles of data selection and tree-construction methods, and discusses about their advantage and disadvantage points.

Chemical Composition of the Essential Oil of Elephantopus Scaber from Southern China

Zeitschrift Für Naturforschung. C, Journal of Biosciences. May-Jun, 2004  |  Pubmed ID: 18998395

The essential oil of Elephantopus scaber, a famous medicinal herb from Yangjiang County in Southern China was analyzed for the first time using GC-MS. The major constituents were hexadecanoic acid (42.3%), isopropyl dimethyl tetrahydronaphthalenol (14.1%), beta-sesquiphellandrene (8.3%), octadecadienoic acid (5.5%), and phytol (5.2%).

Assignment of Orthologous Genes Via Genome Rearrangement

IEEE/ACM Transactions on Computational Biology and Bioinformatics / IEEE, ACM. Oct-Dec, 2005  |  Pubmed ID: 17044168

The assignment of orthologous genes between a pair of genomes is a fundamental and challenging problem in comparative genomics. Existing methods that assign orthologs based on the similarity between DNA or protein sequences may make erroneous assignments when sequence similarity does not clearly delineate the evolutionary relationship among genes of the same families. In this paper, we present a new approach to ortholog assignment that takes into account both sequence similarity and evolutionary events at a genome level, where orthologous genes are assumed to correspond to each other in the most parsimonious evolving scenario under genome rearrangement. First, the problem is formulated as that of computing the signed reversal distance with duplicates between the two genomes of interest. Then, the problem is decomposed into two new optimization problems, called minimum common partition and maximum cycle decomposition, for which efficient heuristic algorithms are given. Following this approach, we have implemented a high-throughput system for assigning orthologs on a genome scale, called SOAR, and tested it on both simulated data and real genome sequence data. Compared to a recent ortholog assignment method based entirely on homology search (called INPARANOID), SOAR shows a marginally better performance in terms of sensitivity on the real data set because it is able to identify several correct orthologous pairs that are missed by INPARANOID. The simulation results demonstrate that SOAR, in general, performs better than the iterated exemplar algorithm in terms of computing the reversal distance and assigning correct orthologs.

MPSS: an Integrated Database System for Surveying a Set of Proteins

Bioinformatics (Oxford, England). May, 2005  |  Pubmed ID: 15699026

SUMMARY: We design and implement an integrated database system called 'multi-protein survey system' (MPSS), which provides a platform to retrieve information about many proteins at a time. This system integrates several important and widely used databases including SwissProt, TrEMBL, PDB and InterPro, plus useful references such as GO and KEGG to other databases. Users may submit a group of protein IDs, entry names, SwissProt/TrEMBL accession numbers or GenBank GIs through MPSS' web interface, and obtain protein annotation information from public databases and pre-computed molecular properties speedily. MPSS can also supply comprehensive information about query proteins, including 3D structures, domains, pathway, gene ontology and visual presentation of mapping to the GO tree and KEGG pathway, to provide an up-to-date view of available knowledge with regard to the structures and molecular functions of proteins under study. AVAILABILITY: MPSS is freely accessible at http://www.scbit.org/mpss/

Phylogenetic Relationships of Salangid Fishes (Osmeridae, Salanginae) with Comments on Phylogenetic Placement of the Salangids Based on Mitochondrial DNA Sequences

Molecular Phylogenetics and Evolution. Apr, 2005  |  Pubmed ID: 15737583

We used partial DNA sequences of cytochrome b and 16S mitochondrial genes to determine the phylogenetic placement of salangid fishes and the generic relationships within the salangids. Our molecular data strongly support the monophyly of salangid fishes, the inclusion of salangids in the Osmeridae, and the sister group relationship between salangids and osmerids. Our analyses suggest that Plecoglossus can be separated from all the other salangids and osmerids. Mallotus and Hypomesus are clustered within Osmerinae, rather than allied with Salanginae. As regards the relationships within the salangids, our analyses are incongruent with all previous classification hypotheses. Our phylogenetic analyses support the sister group relationships between Protosalanx and Neosalanx, and between Salanx and Hemisalanx. More evidences show that Leucosoma is more closely related to the Salanx-Hemisalanx clade, while Salangichthys forms part of an unresolved basal polytomy.

Effect of Preoperative Use of Long-acting Octreotide on Growth Hormone Secreting Pituitary Adenoma and Transsphenoidal Surgery

Chinese Medical Sciences Journal = Chung-kuo I Hsüeh K'o Hsüeh Tsa Chih / Chinese Academy of Medical Sciences. Mar, 2005  |  Pubmed ID: 15844307

To investigate whether somatostatin analog octreotide long acting release (LAR) shrinks growth hormone (GH) secreting adenomas, and improves the results of subsequent transsphenoidal surgery.

Expression and Characterization of the Carboxyl Esterase Rv3487c from Mycobacterium Tuberculosis

Protein Expression and Purification. Jul, 2005  |  Pubmed ID: 15939293

Rv3487c (lipF), a member of the lipase family of Mycobacterium tuberculosis, is related to virulence of this pathogen. Real-time RT-PCR analysis indicated that Rv3487c was induced at low pH in M. tuberculosis cultured in vitro. The gene of Rv3487c was cloned and expressed as fusion protein in Escherichia coli. After removal of the N-terminal domain of the fusion partner by enterokinase treatment, the effect of pH, temperature, and detergents on the purified enzyme activity and stability was characterized. Rv3487c could efficiently hydrolyze short chain esters. The catalytic triad of Rv3487c consists of residues Ser90, Glu189, and His219 as demonstrated by amino acid sequence alignment, three-dimensional modeling, and site-directed mutagenesis.

A Molecular Docking Model of SARS-CoV S1 Protein in Complex with Its Receptor, Human ACE2

Computational Biology and Chemistry. Jun, 2005  |  Pubmed ID: 15979045

The exact residues within severe acute respiratory syndrome coronavirus (SARS-CoV) S1 protein and its receptor, human ACE2, involved in their interaction still remain largely undetermined. Identification of exact amino acid residues that are crucial for the interaction of S1 with ACE2 could provide working hypotheses for experimental studies and might be helpful for the development of antiviral inhibitor. In this paper, a molecular docking model of SARS-CoV S1 protein in complex with human ACE2 was constructed. The interacting residue pairs within this complex model and their contact types were also identified. Our model, supported by significant biochemical evidence, suggested receptor-binding residues were concentrated in two segments of S1 protein. In contrast, the interfacial residues in ACE2, though close to each other in tertiary structure, were found to be widely scattered in the primary sequence. In particular, the S1 residue ARG453 and ACE2 residue LYS341 might be the key residues in the complex formation.

Detecting Correlation Between Sequence and Expression Divergences in a Comparative Analysis of Human Serpin Genes

Bio Systems. Dec, 2005  |  Pubmed ID: 16112386

Physiological functions and characteristic structures of the serpin gene superfamily have been studied extensively, yet the evolution of the serpin genes remains unclear. Gene duplication in this superfamily may shed light on this issue. Two models are used to predict the preservation of duplicated genes: the classical model and the duplication-degeneration-complementation (DDC) model. In this study, we analyzed the phylogenetic relationships of 33 human serpin genes and the expression data of some members of the serpin superfamily from a DNA microarray of human leukemia U937 cells with stably inducible expression of the leukemia-related AML1-ETO gene. We then determined the utility of the DDC model by mapping serpin superfamily expression data to the phylogenetic tree. The correlation between sequence and expression divergences as measured by the Pearson correlation coefficient indicated that human serpin genes evolved under the DDC model. Our study provides a new strategy for comparative analysis of gene sequences and microarray data.

Polypeptide Multilayer Films

Biomacromolecules. Nov-Dec, 2005  |  Pubmed ID: 16283705

Research on polypeptide multilayer films, coatings, and microcapsules is located at the intersection of several disciplines: synthetic polymer chemistry and physics, biomaterials science, and nanoscale engineering. The past few years have witnessed considerable growth in each of these areas. Unexplored territory has been found at the borders, and new possibilities for technology development are taking form from technological advances in polypeptide production, sequencing of the human genome, and the nature of peptides themselves. Most envisioned applications of polypeptide multilayers have a biomedical bent. Prospects seem no less positive, however, in fields ranging from food technology to environmental science. This review of the present state of polypeptide multilayer film research covers key points of polypeptides as materials, means of polymer production and film preparation, film characterization methods, focal points of current research in basic science, and the outlook for a few specific applications. In addition, it discusses how the study of polypeptide multilayer films could help to clarify the physical basis of assembly and stability of polyelectrolyte multilayers, and mention is made of similarities to protein folding studies.

Detecting Horizontal Gene Transfer with T-REX and RHOM Programs

Briefings in Bioinformatics. Dec, 2005  |  Pubmed ID: 16420738

As the Human Genome Project and other genome projects experience remarkable success and a flood of biological data is produced by means of high-throughout sequencing techniques, detection of horizontal gene transfer (HGT) becomes a promising field in bioinformatics. This review describes two freeware programs: T-REX for MS Windows and RHOM for Linux. T-REX is a graphical user interface program that offers functions to reconstruct the HGT network among the donor and receptor hosts from the gene and species distance matrices. RHOM is a set of command-line driven programs used to detect HGT in genomes. While T-REX impresses with a user-friendly interface and drawing of the reticulation network, the strength of RHOM is an extensive statistical framework of genome and the graphical display of the estimated sequence position probabilities for the candidate horizontally transferred genes.

Fine Tuning of Physical Properties of Designed Polypeptide Multilayer Films by Control of PH

Biotechnology Progress. Jan-Feb, 2006  |  Pubmed ID: 16454502

Adjustment of pH can alter the ensemble of three-dimensional structures of a polypeptide in solution by changing the distribution of charge and Coulombic interactions. The role of pH in layer-by-layer self-assembly (LbL) of designed 32mer peptides containing the amino acid cysteine has been investigated using a combination of physical methods. Results show that pH can have a substantial influence on the mass of adsorbed peptide, surface roughness, and film density over a range of 1.5 pH units. Peptide film thickness depends on the number of layers, as with "conventional" polyelectrolytes. Film density and morphology, however, vary more with pH than does thickness, translating into a change in density on the order of 70% over the pH range 7.4-8.9. Results of this work provide insight on the physical basis of LbL and suggest that peptides are a promising class of polyelectrolytes for the creation of designer thin films for applications in biotechnology and other areas.

Cytoplasmic Male Sterility of Rice with Boro II Cytoplasm is Caused by a Cytotoxic Peptide and is Restored by Two Related PPR Motif Genes Via Distinct Modes of MRNA Silencing

The Plant Cell. Mar, 2006  |  Pubmed ID: 16489123

Cytoplasmic male sterility (CMS) and nucleus-controlled fertility restoration are widespread plant reproductive features that provide useful tools to exploit heterosis in crops. However, the molecular mechanism underlying this kind of cytoplasmic-nuclear interaction remains unclear. Here, we show in rice (Oryza sativa) with Boro II cytoplasm that an abnormal mitochondrial open reading frame, orf79, is cotranscribed with a duplicated atp6 (B-atp6) gene and encodes a cytotoxic peptide. Expression of orf79 in CMS lines and transgenic rice plants caused gametophytic male sterility. Immunoblot analysis showed that the ORF79 protein accumulates specifically in microspores. Two fertility restorer genes, Rf1a and Rf1b, were identified at the classical locus Rf-1 as members of a multigene cluster that encode pentatricopeptide repeat proteins. RF1A and RF1B are both targeted to mitochondria and can restore male fertility by blocking ORF79 production via endonucleolytic cleavage (RF1A) or degradation (RF1B) of dicistronic B-atp6/orf79 mRNA. In the presence of both restorers, RF1A was epistatic over RF1B in the mRNA processing. We have also shown that RF1A plays an additional role in promoting the editing of atp6 mRNAs, independent of its cleavage function.

[The Study of Ribosomal Protein L15 CDNA Sequences As a Molecular Marker in the Teleostei Phylogenetic Analysis]

Yi Chuan = Hereditas / Zhongguo Yi Chuan Xue Hui Bian Ji. Feb, 2006  |  Pubmed ID: 16520312

In this study, the full-length cDNAs of RPL15 (ribosomal protein L15) gene were cloned and sequenced from fifteen fishes of five orders under Teleostei. The complete ORF sequences were analyzed for phylogenetic reconstruction for the first time to evaluate the potential of RPL15 gene as a novel marker in resolving teleostean phylogenetic relationships. The resultant NJ, MP and ML trees with Anguilla japonica as the outgroup were generally resolved and largely congruent with the morphology-based tree though some incongruities were observed. The incongruities were then analyzed for some explanations. The results suggested that: (1) RPL15 gene was highly conserved during eukaryotic evolution; (2) RPL15 ORF might be a good phylogenetic marker for resolving teleostean relationships. It might be especially appropriate for the higher-level relationships (such as interordinal), and it was possibly suitable for lower-level relationships as well. The same can be true for other eukaryotes.

Drought Tolerance Genes in Rice

Functional & Integrative Genomics. Oct, 2006  |  Pubmed ID: 16552602

Quantitative trait loci (QTLs) for drought tolerance (DT) can be readily identified in available databases and in this paper, these QTLs were summarized in the form of a consensus map. An in silico strategy was then deployed to mine for candidate genes associated with DT QTLs using rice dbEST and rice genome databases. DT QTLs on rice chromosomes 1, 2, 4, 8, and 9 were selected to test the method. The result showed candidate genes associated with DT could be readily identified.

[Recent Advances on the Study Between Steroids and Brain Function]

Sheng Li Ke Xue Jin Zhan [Progress in Physiology]. Jan, 2006  |  Pubmed ID: 16683536

It is vital for steroid hormones synthesized in the gonad gland, adrenal gland and placenta to the development and physiological metabolism of the body. In particular, its regulatory effect on brain functions has attracted more and more attention, as nearly all the steroid hormones can be synthesized de novo in the brain. This means steroids derived from brain and peripheral gland can modulate the physiology and pathology of the brain reciprocally and importantly on many aspects such as learning and memory, synaptic transmission, neuroprotection, neurodegenerative diseases (especially Alzheimer's disease), emotion, stress, and menstrual-cycle-linked disorders. In the present review, some new advances are summarized.

Reconstruction and in Silico Analysis of the MAPK Signaling Pathways in the Human Blood Fluke, Schistosoma Japonicum

FEBS Letters. Jun, 2006  |  Pubmed ID: 16765950

At present, little is known about signal transduction mechanisms in schistosomes, which cause the disease of schistosomiasis. The mitogen-activated protein kinase (MAPK) signaling pathways, which are evolutionarily conserved from yeast to Homo sapiens, play key roles in multiple cellular processes. Here, we reconstructed the hypothetical MAPK signaling pathways in Schistosoma japonicum and compared the schistosome pathways with those of model eukaryote species. We identified 60 homologous components in the S. japonciumMAPK signaling pathways. Among these, 27 were predicted to be full-length sequences. Phylogenetic analysis of these proteins confirmed the evolutionary conservation of the MAPK signaling pathways. Remarkably, we identified S. japonicum homologues of GTP-binding protein beta and alpha-I subunits in the yeast mating pathway, which might be involved in the regulation of different life stages and female sexual maturation processes as well in schistosomes. In addition, several pathway member genes, including ERK, JNK, Sja-DSP, MRAS and RAS, were determined through quantitative PCR analysis to be expressed in a stage-specific manner, with ERK, JNK and their inhibitor Sja-DSP markedly upregulated in adult female schistosomes.

Solution Structure of Urm1 and Its Implications for the Origin of Protein Modifiers

Proceedings of the National Academy of Sciences of the United States of America. Aug, 2006  |  Pubmed ID: 16864801

Protein modifiers are involved in diverse biological processes and regulate the activity or function of target proteins by covalently conjugating to them. Although ubiquitin and a number of ubiquitin-like protein modifiers (Ubls) in eukaryotes have been identified, no protein modifier has been found in prokaryotes; thus, their evolutionary origin remains a puzzle. To infer the evolutionary relationships between the protein modifiers and sulfur carrier proteins, we solved the solution NMR structure of the Urm1 (ubiquitin-related modifier-1) protein from Saccharomyces cerevisiae. Both structural comparison and phylogenetic analysis of the ubiquitin superfamily, with emphasis on the Urm1 family, indicate that Urm1 is the unique "molecular fossil" that has the most conserved structural and sequence features of the common ancestor of the entire superfamily. The similarities of 3D structure and hydrophobic and electrostatic surface features between Urm1 and MoaD (molybdopterin synthase small subunit) suggest that they may interact with partners in a similar manner, and similarities between Urm1-Uba4 and MoaD-MoeB establish an evolutionary link between ATP-dependent protein conjugation in eukaryotes and ATP-dependent cofactor sulfuration.

Characterization of the Porcine Alpha Interferon Multigene Family

Gene. Nov, 2006  |  Pubmed ID: 16901658

The availability of data on the pig genome sequence prompted us to characterize the porcine IFN-alpha (PoIFN-alpha) multigene family. Fourteen functional PoIFN-alpha genes and two PoIFN-alpha pseudogenes were detected in the porcine genome. Multiple sequence alignment revealed a C-terminal deletion of eight residues in six subtypes. A phylogenetic tree of the porcine IFN-alpha gene family defined the evolutionary relationship of the various subtypes. In addition, analysis of the evolutionary rate and the effect of positive selection suggested that the C-terminal deletion is a strategy for preservation in the genome. Eight PoIFN-alpha subtypes were isolated from the porcine liver genome and expressed in BHK-21 cells line. We detected the level of transcription by real-time quantitative RT-PCR analysis. The antiviral activities of the products were determined by WISH cells/Vesicular Stomatitis Virus (VSV) and PK 15 cells/Pseudorabies Virus (PRV) respectively. We found the antiviral activities of intact PoIFN-alpha genes are approximately 2-50 times higher than those of the subtypes with C-terminal deletions in WISH cells and 15-55 times higher in PK 15 cells. There was no obvious difference between the subtypes with and without C-terminal deletion on acid susceptibility.

Identification and Genetic Mapping of a Novel Gene Involved in Pollen Development in Arabidopsis

Fen Zi Xi Bao Sheng Wu Xue Bao = Journal of Molecular Cell Biology / Zhongguo Xi Bao Sheng Wu Xue Xue Hui Zhu Ban. Apr, 2006  |  Pubmed ID: 16944588

With an aim of the genetic dissection of anther and pollen development, we identified an Arabidopsis mutant line named zy1511 by ethyl-methane sulphonate (EMS) mutagenesis. Genetic analysis indicated that the mutant phenotype was controlled by a single recessive nuclear gene zy1511. Cytological studies of anther at various developmental stages indicated that the mutant anther tapetum did not start degenerating after microspores released from the tetrads. Part of the mutant anther tapetum still existed at late stages of anther development, indicating that mutant tapetum degenerated later than that of the wild-type. So the mutant microspores could not develop into normal pollen grains in the anther. For the further genetic analysis and the map-based cloning of gene zy1511, we have mapped it to a region of 134 kb between molecular markers F25P12 and T8L23 on chromosome 1 using a map-based cloning strategy. As no male sterile genes have been reported in this region, we believe that zy1511 is an undiscovered key gene involved in pollen development.

[Vitrification of Mouse Blastocyst by Open Pulled Straw (OPS) Method at Different Temperature]

Fen Zi Xi Bao Sheng Wu Xue Bao = Journal of Molecular Cell Biology / Zhongguo Xi Bao Sheng Wu Xue Xue Hui Zhu Ban. Jun, 2006  |  Pubmed ID: 16944599

To examine the efficiency of EDFS and EFS for blastocyst cryopreservation and to provide information for preparation of vitrification medium at different temperature, the present investigation was conducted to establish a model for vitrification of domestic animal's blastocyst and human blastocyst using mouse blastocyst as a model and OPS (open pulled straw) as the container. When ambient temperature was 25 degrees C and heating plate temperature was 37 degrees C, mouse blastocysts were vitrified using 1-step OPS method, after thawing, the expanded blastocyst (EB) rates of EDFS40 and EFS40 group (92.31%, 92.30%) were not different from that of the control (97.26%) (P > 0.05), however, the hatched blastocyst (HB) rate of EDFS40 group (59.62%) was significantly lower than that of the control (83.56%); When 2-step method was adopted at the same temperature, mouse blastocyst was successfully cryopreserved with EDFS30 and EFS40, the post-thawing EB rate (95.69%, 95.05%) and HB rate(80.48%, 78.95%) of both EDFS30 and EFS40 groups did not differ from those of the control (P > 0.05). When ambient temperature was 25 degrees C and heating plate was free, the EB rate (85.96%) and HB (75.44%) of embryos vitrified with EDFS40 using 1-step OPS method were not statistically different from those of the control (96.05% and 82.89%, respectively) (P > 0.05); the EB and HB rates (92.03%-95.31%, 67.19%-76.76%) of embryos vitrified with EDFS30, EDFS40 and EFS40 using 2-step OPS method were similar to those of the control (P > 0.05). According to in vitro development of vitrified embryos, the promising group was chosen for embryo transfer to examine in vivo development of vitrified embryos. When vitrified blastocysts were transferred into uterus of pseudopregnant mouse, the pregnancy rate of receipts (90.90%) and birth rate of foster mother (37.33%) were similar to those of fresh embryos (91.67% and 42.33%) (P > 0.05). All data demonstrated that mouse blastocyst was successfully cryopreserved with EDFS30, EDFS40 and EFS40 at different temperature and using different procedures.

Near Homogeneous Variation of Potentials in Large Systems and the Electronic Structure of Molecular Quantum Dots

The Journal of Chemical Physics. Sep, 2006  |  Pubmed ID: 16965100

It is shown from Kohn-Sham (KS) density-functional theory that in a large molecular system, the Coulomb potential, molecular electrostatic potential, and KS effective potential may exhibit an approximately homogeneous variation in space, in response to a small change of the electron number. The homogeneous variation of potentials underlies the constant interaction (CI) model of quantum dots (QDs) and is related to the delocalization and invariance of KS orbitals, the identical shift of KS levels, and a natural definition of the QD capacitance. Calculation results of a fullerene C60 and a single-walled carbon nanotube are presented. Although the homogeneity of the potential variation is not perfect, it seems to lead to fairly good approximation of the CI model to the addition energy spectra of these systems.

Origin of Mitochondrial DNA Diversity of Domestic Yaks

BMC Evolutionary Biology. 2006  |  Pubmed ID: 16995938

The domestication of plants and animals was extremely important anthropologically. Previous studies have revealed a general tendency for populations of livestock species to include deeply divergent maternal lineages, indicating that they were domesticated in multiple, independent events from genetically discrete wild populations. However, in water buffalo, there are suggestions that a similar deep maternal bifurcation may have originated from a single population. These hypotheses have rarely been rigorously tested because of a lack of sufficient wild samples. To investigate the origin of the domestic yak (Poephagus grunnies), we analyzed 637 bp of maternal inherited mtDNA from 13 wild yaks (including eight wild yaks from a small population in west Qinghai) and 250 domesticated yaks from major herding regions.

Genetic Variation and Population Structure of Oriental Migratory Locust, Locusta Migratoria Manilensis, in China by Allozyme, SSRP-PCR, and AFLP Markers

Biochemical Genetics. Oct, 2006  |  Pubmed ID: 17028785

Allozyme analysis, microsatellite primer PCR (SSRP-PCR), and amplified fragment length polymorphism (AFLP) techniques were used to assess genetic diversity and population structure of the Chinese oriental migratory locust, Locusta migratoria manilensis. A total of 299 PCR markers (67 SSRPs and 232 AFLPs) were detected in eight populations, of which 98.7% were polymorphic markers. The proportion of polymorphic loci (95.5-98.8%) by SSRP+AFLP markers indicated no significant differences between populations, and all populations exhibited a similar level of variability; results of the allozyme analysis demonstrated that 19 loci gave rise to a lower level of polymorphism (55.6-66.7%). The genetic distances between the populations were relatively low. Shannon's index and Nei's gene diversity showed low differentiation among the populations. Allozyme analysis, however, reflected greater similarity and smaller differentiation between the populations than those shown by SSRP and AFLP markers. Neighbor-joining dendrograms derived from both the allozyme and SSRP+AFLP markers showed that the genetic distances among Chinese oriental migratory locust populations were not greatly influenced by geographic distance and breeding habitats.

Genetic Diversity and Population Structure of Lamiophlomis Rotata (Lamiaceae), an Endemic Species of Qinghai-Tibet Plateau

Genetica. Sep-Nov, 2006  |  Pubmed ID: 17028966

Lamiophlomis rotata (Lamiaceae), a perennial medicinal herb, is endemic to the Qinghai-Tibet Plateau. A total of 188 individuals from eight natural populations of L. rotata in Qinghai-Tibet Plateau (four from Tibet, two from Yunnan, and two from Qinghai) were analyzed using intersimple sequence repeats (ISSR) and randomly amplified polymorphic DNA (RAPD) techniques. Our results revealed that the level of genetic variation in L. rotata was relatively high (P = 94.85%, I = 0.440 +/- 0.220, H(T) = 0.289 +/- 0.028). Three genetic groups corresponding to the three geographic regions were detected, suggesting significant geographic structure. Our results suggest that the highly structured geographic pattern found in L. rotata might represent diverging evolutionary processes associated with the uplifting of the Qinghai-Tibet Plateau and Quaternary climatic oscillations. These findings imply that as many populations as possible should be preserved in situ for the conservation of this species. Given their genetic variability and peripheral distribution, Qinghai and Yunnan populations should be assigned priority for conservation. Optimal harvesting strategies, domestication and tissue culture of L. rotata should be developed as soon as possible to guarantee its sustainable use.

Full-length Genome Sequences of Two SARS-like Coronaviruses in Horseshoe Bats and Genetic Variation Analysis

The Journal of General Virology. Nov, 2006  |  Pubmed ID: 17030870

Bats were recently identified as natural reservoirs of SARS-like coronavirus (SL-CoV) or SARS coronavirus-like virus. These viruses, together with SARS coronaviruses (SARS-CoV) isolated from human and palm civet, form a distinctive cluster within the group 2 coronaviruses of the genus Coronavirus, tentatively named group 2b (G2b). In this study, complete genome sequences of two additional group 2b coronaviruses (G2b-CoVs) were determined from horseshoe bat Rhinolophus ferrumequinum (G2b-CoV Rf1) and Rhinolophus macrotis (G2b-CoV Rm1). The bat G2b-CoV isolates have an identical genome organization and share an overall genome sequence identity of 88-92 % among themselves and between them and the human/civet isolates. The most variable regions are located in the genes encoding nsp3, ORF3a, spike protein and ORF8 when bat and human/civet G2b-CoV isolates are compared. Genetic analysis demonstrated that a diverse G2b-CoV population exists in the bat habitat and has evolved from a common ancestor of SARS-CoV.

Koopmans' Theorem for Large Molecular Systems Within Density Functional Theory

The Journal of Physical Chemistry. A. Nov, 2006  |  Pubmed ID: 17064189

It is shown that in density functional theory (DFT), Koopmans' theorem for a large molecular system can be stated as follows: The ionization energy of the system equals the negative of the highest occupied molecular orbital (HOMO) energy plus the Coulomb electrostatic energy of removing an electron from the system, or equivalently, the ionization energy of an N-electron system is the negative of the arithmetic average of the HOMO energy of this system and the lowest unoccupied molecular orbital (LUMO) energy of the (N - 1)-electron system. Relations between this DFT Koopmans' theorem and its existing counterparts in the literature are discussed. Some of the previous results are generalized and some are simplified. DFT calculation results of a fullerene molecule, a finite single-walled carbon nanotube and a finite boron nitride nanotube are presented, indicating that this Koopmans' theorem approximately holds, even if the orbital relaxation is taken into consideration.

Genetic Diversity and Population Structure of Yellow Camellia (Camellia Nitidissima) in China As Revealed by RAPD and AFLP Markers

Biochemical Genetics. Oct, 2006  |  Pubmed ID: 17109218

Camellia nitidissima, a rare plant but a useful genetic resource for commercial cultivation of ornamental camellias, is distributed in a narrow region of South China and North Vietnam. In this study, RAPD and AFLP markers were used to assess the genetic diversity and population structure of six natural populations of C. nitidissima from Guangxi in South China. Twenty RAPD primers amplified 183 bands, of which 143 bands were polymorphic, and 8 AFLP primer pairs produced 502 bands, of which 364 were polymorphic. Independent as well as combined analyses of the cluster analyses of the RAPD and AFLP fragments showed that the six populations could be classified into two major genetic groups corresponding to the Nanning and Fangcheng areas. The Mantel test revealed significant correlation between the genetic and geographic distances of C. nitidissima populations (r = 0.953, p = 0.036). AMOVA analysis allowed the partitioning of the genetic variation between groups (36.09%), among populations within groups (25.78%), and within populations (38.14%). An understanding of both the genetic diversity and the population structure of C. nitidissima in China can also provide insight into the conservation and management of this endangered species.

[Functional Analysis of Rice P0491E01 Gene Regulating Anther Development]

Fen Zi Xi Bao Sheng Wu Xue Bao = Journal of Molecular Cell Biology / Zhongguo Xi Bao Sheng Wu Xue Xue Hui Zhu Ban. Oct, 2006  |  Pubmed ID: 17117558

The rice P0491E01 gene shares high similarity in amino acid sequence with Arabidopsis gene AtDAD1 (DEFECTIVE IN ANTHER DEHISCENCE1) which plays a key role in the biosynthesis of jasmonic acid. In this paper, we investigated the function of this gene in the anther development of rice using RNA interference strategy. An exon fragment of 263bp was cloned from genomic DNA of P0491E01 to construct RNAi vector pP0491RNAi. Then, pP0491RNAi was transformed into O. sativa japonica by Agrobacterium-mediated transformation and ten transgenic plants were obtained. GUS-staining and PCR analysis confirmed that T-DNA was integrated into rice genome. Three of the transgenic plants were male sterile, and the other transgenic plants showed reduced fertility. Cytological observation indicated that anther development in the early stage of male sterile transgenic plants was normal, however, the microspores could not develop into mature pollen grains. Further investigations of the expression of P0491E01 gene in these transgenic lines by RT-PCR revealed that its transcription was significantly reduced. The results suggest that P0491E01 may play an important role during the late stage of anther development.

[Acute High Altitude Hypoxia Causes Glial Activation Markedly in the Brain of Adult Rats]

Zhongguo Ying Yong Sheng Li Xue Za Zhi = Zhongguo Yingyong Shenglixue Zazhi = Chinese Journal of Applied Physiology. Nov, 2006  |  Pubmed ID: 21155257

PlantQTL-GE: a Database System for Identifying Candidate Genes in Rice and Arabidopsis by Gene Expression and QTL Information

Nucleic Acids Research. Jan, 2007  |  Pubmed ID: 17142239

We have designed and implemented a web-based database system, called PlantQTL-GE, to facilitate quantitatine traits locus (QTL) based candidate gene identification and gene function analysis. We collected a large number of genes, gene expression information in microarray data and expressed sequence tags (ESTs) and genetic markers from multiple sources of Oryza sativa and Arabidopsis thaliana. The system integrates these diverse data sources and has a uniform web interface for easy access. It supports QTL queries specifying QTL marker intervals or genomic loci, and displays, on rice or Arabidopsis genome, known genes, microarray data, ESTs and candidate genes and similar putative genes in the other plant. Candidate genes in QTL intervals are further annotated based on matching ESTs, microarray gene expression data and cis-elements in regulatory sequences. The system is freely available at http://www.scbit.org/qtl2gene/new/.

Computational Simulation of Interactions Between SARS Coronavirus Spike Mutants and Host Species-specific Receptors

Computational Biology and Chemistry. Apr, 2007  |  Pubmed ID: 17368104

As a critical adaptive mechanism, amino acid replacements on the severe acute respiratory syndrome coronavirus (SARS-CoV) spike protein could alter the receptor-binding specificity of this envelope glycoprotein and in turn lead to the emergence or reemergence of this viral zoonosis. Based on the X-ray structures of SARS-CoV spike receptor-binding domain (RBD) in complex with its functional receptor (angiotensin-converting enzyme 2, ACE2), we perform computational simulations of interactions between three representative RBD mutants and four host species-specific receptors. The comparisons between computational predictions and experimental evidences validate our structural bioinformatics approaches. And the predictions further indicate that some viral prototypes might utilize the rat ACE2 while rats might serve as a vector or reservoir of SARS-CoV.

Computational Characterization and Design of SARS Coronavirus Receptor Recognition and Antibody Neutralization

Computational Biology and Chemistry. Apr, 2007  |  Pubmed ID: 17374510

The sequential determination of crystal structures of the SARS coronavirus spike receptor-binding domain (RBD) in complex with its cellular receptor or neutralizing antibody opened a door for the design and development of antiviral competitive inhibitors. Based on those complex structures, we conduct computational characterization and design of RBD-mediated receptor recognition and antibody neutralization. The comparisons between computational predictions and experimental evidences validate our structural bioinformatics protocols. And the calculations predict a number of single substitutions on RBD, receptor or antibody that could remarkably elevate the binding affinities of those complexes. It is reasonable to anticipate our structure-based computation-derived hypotheses could be informative to the future biochemical and immunological tests.

Stimulated Release of Small Molecules from Polyelectrolyte Multilayer Nanocoatings

Chemical Communications (Cambridge, England). Apr, 2007  |  Pubmed ID: 17389977

Free thiol-containing polyelectrolytes serve simultaneously as a material for self-assembly of a multilayer nanocoating and as a carrier of small molecules for release from the coating in response to an environmental cue.

[Bioinformatic Identification and Analysis of Schistosoma Japonicum Adenine Phosphoribosyltransferase]

Nan Fang Yi Ke Da Xue Xue Bao = Journal of Southern Medical University. Mar, 2007  |  Pubmed ID: 17425969

To identify adenine phosphoribosyltransferases in Schistosoma japonicum and analyze their structural features.

[Effects of Spectral Pretreatment on the Prediction of Crystallinity of Wood Cellulose Using Near Infrared Spectroscopy]

Guang Pu Xue Yu Guang Pu Fen Xi = Guang Pu. Mar, 2007  |  Pubmed ID: 17554892

The crystallinity of wood has an important effect on the physical, mechanical and chemical properties of cellulose fibers. The aims of this study were to investigate the ability of near infrared spectroscopy (NIR) to predict the crystallinity of wood cellulose and the effect of spectral pretreatment on the prediction of crystallinity in wood cellulose using near infrared spectroscopy (NIR). Near infrared diffuse reflectance spectra were collected from wood powder with a fiber-optical probe and the crystallinity of wood was determined by X-ray diffractometer (XRD) in this experiment. The results showed that near infrared spectroscopy coupled with partial least square (PLS) regression could be correlated with the crystallinity of plantation wood, and the ability of NIR prediction based on original spectra was better than that based on the first derivative or second derivative treated spectra. There was a significant correlation between NIR spectra and XRD determined crystallinity with a correlationcoefficient of 0.950 and a low RMSEP. Near infrared spectroscopy coupled with multivariate data anlaysis has proven to be an accurate and fast method for rapid prediction of wood crystallinity.

Controlled Loading and Release of a Model Drug from Polypeptide Multilayer Nanofilms

Nanomedicine : Nanotechnology, Biology, and Medicine. Jun, 2007  |  Pubmed ID: 17572357

A major concern of medicine today is the sustained release of therapeutic compounds. Delivery vehicles for such compounds must be biocompatible. Ideally, loading a drug into the delivery vehicle will be a simple process, and vehicle properties will allow control over the drug release profile under desired conditions. Here, polypeptide multilayer nanofilms have been prepared by electrostatic layer-by-layer self-assembly to study the post-fabrication loading and release of a model therapeutic, methylene blue (MB). Drug loading and release have been characterized by optical spectroscopy for different peptide designs at different pH values, and film surface morphology has been characterized by atomic force microscopy (AFM). Differences in peptide structure have been found to influence MB loading and release under otherwise fixed conditions. Release is also influenced by pH, salt concentration, and number of "capping" layers. Although more research will be needed to exhaust the potential of polypeptide multilayer films, present results would suggest that the technology holds considerable promise for applications in medicine.

[Discrimination of Wood Biological Decay by Soft Independent Modeling of Class Analogy (SIMCA) Pattern Recognition Based on Principal Component Analysis]

Guang Pu Xue Yu Guang Pu Fen Xi = Guang Pu. Apr, 2007  |  Pubmed ID: 17608176

Wood, as a biomass materials, tends to be attacked by microorganisms, and its structure could be rapidly destroyed by biological decay. Therefore, it's significant to rapidly and accurately detect or identify biological decay in wood. Recently, extensive research has demonstrated that near infrared spectroscopy (NIR) and soft independent modeling of class analogy (SIMCA) can be used to discriminate or detect a wide variety of food, medicine and agricultural products. The use of NIR coupled with principal component analysis (PCA) and SIMCA pattern recognition to detect wood biological decay was investigated in the present paper. The results showed that NIR spectroscopy coupled with SIMCA pattern recognition could be used to rapidly detect the biological decay in wood. The discrimination accuracy by the SIMCA model based on the training set for the non-decay, white-rot and brown-rot decay samples were 100%, 82. 5% and 100%, respectively; and that for the samples for the test set were 100%, 85% and 100%, respectively. However, some white-rot decay samples were mis-discriminated as brown-rot decay, for which the main reasons might be that the training set does not have enough typical samples, and there's a slight difference between white-rot and brown-rot decay during the early stage of decay.

MSOAR: a High-throughput Ortholog Assignment System Based on Genome Rearrangement

Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. Nov, 2007  |  Pubmed ID: 17990975

The assignment of orthologous genes between a pair of genomes is a fundamental and challenging problem in comparative genomics, since many computational methods for solving various biological problems critically rely on bona fide orthologs as input. While it is usually done using sequence similarity search, we recently proposed a new combinatorial approach that combines sequence similarity and genome rearrangement. This paper continues the development of the approach and unites genome rearrangement events and (post-speciation) duplication events in a single framework under the parsimony principle. In this framework, orthologous genes are assumed to correspond to each other in the most parsimonious evolutionary scenario involving both genome rearrangement and (post-speciation) gene duplication. Besides several original algorithmic contributions, the enhanced method allows for the detection of inparalogs. Following this approach, we have implemented a high-throughput system for ortholog assignment on a genome scale, called MSOAR, and applied it to human and mouse genomes. As the result will show, MSOAR is able to find 99 more true orthologs than the INPARANOID program did. In comparison to the iterated exemplar algorithm on simulated data, MSOAR performed favorably in terms of assignment accuracy. We also validated our predicted main ortholog pairs between human and mouse using public ortholog assignment datasets, synteny information, and gene function classification. These test results indicate that our approach is very promising for genome-wide ortholog assignment. Supplemental material and MSOAR program are available at http://msoar.cs.ucr.edu.

A Probabilistic Framework for Tracking Deformable Soft Tissue in Minimally Invasive Surgery

Medical Image Computing and Computer-assisted Intervention : MICCAI ... International Conference on Medical Image Computing and Computer-Assisted Intervention. 2007  |  Pubmed ID: 18044550

The use of vision based algorithms in minimally invasive surgery has attracted significant attention in recent years due to its potential in providing in situ 3D tissue deformation recovery for intra-operative surgical guidance and robotic navigation. Thus far, a large number of feature descriptors have been proposed in computer vision but direct application of these techniques to minimally invasive surgery has shown significant problems due to free-form tissue deformation and varying visual appearances of surgical scenes. This paper evaluates the current state-of-the-art feature descriptors in computer vision and outlines their respective performance issues when used for deformation tracking. A novel probabilistic framework for selecting the most discriminative descriptors is presented and a Bayesian fusion method is used to boost the accuracy and temporal persistency of soft-tissue deformation tracking. The performance of the proposed method is evaluated with both simulated data with known ground truth, as well as in vivo video sequences recorded from robotic assisted MIS procedures.

Helminth Infections and Risk Factor Analysis Among Residents in Eryuan County, Yunnan Province, China

Acta Tropica. Oct, 2007  |  Pubmed ID: 17719553

Whilst infections with soil-transmitted helminths are common across China, the public-health significance of Schistosoma japonicum and food-borne helminths is more focalized. Only few studies have investigated the local epidemiology of helminth infections in rural China, including risk factor analysis. We collected stool and blood samples from 3220 individuals, aged 5-88 years, from 35 randomly selected villages in Eryuan county, Yunnan province, China. Stool samples were subjected to the Kato-Katz technique and examined for helminth eggs. Blood samples were tested for Trichinella spp., S. japonicum and cysticerci-specific antibodies. Data on individual and family-level risk factors were collected using questionnaires. The prevalence of Ascaris lumbricoides, Taenia spp., Trichuris trichiura and hookworms was 15.4%, 3.5%, 1.7% and 0.3%, respectively. The seroprevalence of Trichinella spp. was 58.8% and that of cysticercosis 18.5%. The egg positivity rate of S. japonicum in the 13 known endemic villages was 2.7%, and the corresponding seroprevalence was 49.5%. We observed a strong spatial heterogeneity in the families' economic status. S. japonicum infections were more prevalent among the Han than Bai nationality (odds ratio (OR)=3.77, 95% confidence interval (CI)=1.97-7.23) and tobacco growers (OR=3.66, 95% CI=1.77-7.60) and was only found at elevations below 2150 m above sea level. A. lumbricoides and Taenia spp. infections were more prevalent at altitudes above 2150 m when compared to lower settings (OR=1.51, 95% CI=1.24-1.84 and OR=5.32, 95% CI=3.42-8.28, respectively). The opposite was found for T. trichiura (OR=0.31, 95% CI=0.14-0.70). Our findings can guide the design and spatial targeting of control interventions against helminth infections in Eryuan county.

Spatial Risk Profiling of Schistosoma Japonicum in Eryuan County, Yunnan Province, China

Geospatial Health. Nov, 2007  |  Pubmed ID: 18686256

Bayesian spatial risk profiling holds promise to enhance our understanding of the epidemiology of parasitic diseases, and to target interventions in a cost-effective manner. Here, we present findings from a study using Bayesian variogram models to map and predict the seroprevalence of Schistosoma japonicum in Eryuan county, Yunnan province, China, including risk factor analysis. Questionnaire and serological data were obtained through a cross-sectional survey carried out in 35 randomly selected villages with 3,220 people enrolled. Remotely-sensed environmental data were derived from publicly available databases. Bivariate and non-spatial Bayesian multiple logistic regression models were used to identify associations between the local seroprevalence and demographic (i.e. age and sex), environmental (i.e. location of village, altitude, slope, land surface temperature and normalized difference vegetation index) and socio-economic factors. In the spatially-explicit Bayesian model, S. japonicum seroprevalence was significantly associated with sex, age and the location of the village. Males, those aged below 10 years and inhabitants of villages situated on steep slopes (inclination =20 degrees ) or on less precipitous slopes of >5 degrees above 2,150 m were at lower risk of seroconversion than their respective counterparts. Our final prediction model revealed an elevated risk for seroconversion in the plains of the eastern parts of Eryuan county. In conclusion, the prediction map can be utilized for spatial targeting of schistosomiasis control interventions in Eryuan county. Moreover, S. japonicum seroprevalence studies might offer a convenient means to assess the infection pressure experienced by local communities, and to improve risk profiling in areas where the prevalence and infection intensities have come down following repeated rounds of praziquantel administration.

[Construction and Identification of Rat GDNF Gene Recombinant Retroviral Vector and Gene Transfection to NSC]

Sheng Wu Yi Xue Gong Cheng Xue Za Zhi = Journal of Biomedical Engineering = Shengwu Yixue Gongchengxue Zazhi. Jun, 2008  |  Pubmed ID: 18693448

By genetic recombinant technique, the rat GDNF cDNA was recombinated to the retroviral vector pLXSN. The recombinant plasmid pLXSN-GDNF was verified by digestion with restriction endonucleases and PCR. Then neural stem cells (NSCs) were infected with pLXSN-GDNF. Immunocytochemistry, RT-PCR and western-blot were used to detect the transfection effect. Results showed that GDNF cDNA was cloned into retroviral vector pLXSN correctly, and the pLXSN-GDNF can infect NSCs efficiently. These results provide the possibility for transplantation and gene therapy with GDNF of nervous system diseases and injury.

MPSQ: a Web Tool for Protein-state Searching

Bioinformatics (Oxford, England). Oct, 2008  |  Pubmed ID: 18697766

MPSQ (multi-protein-states query) is a web-based tool for the discovery of protein states (e.g. biological interactions, covalent modifications, cellular localizations). In particular, large sets of genes can be used to search for enriched state transition network maps (NMs) and features facilitating the interpretation of genomic-scale experiments such as microarrays. One NM collects all the catalogued states of a protein as well as the mutual transitions between the states. For the returned NM, graph visualization is provided for easy understanding and to guide further analysis.

PBmice: an Integrated Database System of PiggyBac (PB) Insertional Mutations and Their Characterizations in Mice

Nucleic Acids Research. Jan, 2008  |  Pubmed ID: 17932058

DNA transposon piggyBac (PB) is a newly established mutagen for large-scale mutagenesis in mice. We have designed and implemented an integrated database system called PBmice (PB Mutagenesis Information CEnter) for storing, retrieving and displaying the information derived from PB insertions (INSERTs) in the mouse genome. This system is centered on INSERTs with information including their genomic locations and flanking genomic sequences, the expression levels of the hit genes, and the expression patterns of the trapped genes if a trapping vector was used. It also archives mouse phenotyping data linked to INSERTs, and allows users to conduct quick and advanced searches for genotypic and phenotypic information relevant to a particular or a set of INSERT(s). Sequence-based information can be cross-referenced with other genomic databases such as Ensembl, BLAST and GBrowse tools used in PBmice offer enhanced search and display for additional information relevant to INSERTs. The total number and genomic distribution of PB INSERTs, as well as the availability of each PB insertional LINE can also be viewed with user-friendly interfaces. PBmice is freely available at http://www.idmshanghai.cn/PBmice or http://www.scbit.org/PBmice/.

[Discrimination of Wood Biological Decay by NIR and Partial Least Squares Discriminant Analysis (PLS-DA)]

Guang Pu Xue Yu Guang Pu Fen Xi = Guang Pu. Apr, 2008  |  Pubmed ID: 18619300

Extensive research has demonstrated that near infrared spectroscopy (NIR) and partial least squares discriminant analysis (PLS-DA) can be used to rapidly discriminate or detect a wide variety of food, medicine and agricultural products. The use of NIR coupled with PLS-DA to detect wood biological decay was investigated in the present paper. The results showed that the correlation between the predicted category variable of calibration and validation and the measured category variable is significant with a correlation coefficient (r) over 0.94 and low SEC and SEP (< 0.17); the discriminant accuracy for the non-decay, white-rot and brown-rot decay samples are 100% (deviation < 0.5) by the PLS-DA model based on the test set of samples; the discriminant accuracy by PLS-DA model is better than that by SIMCA model. It's suggested that NIR spectroscopy coupled with PLS-DA could be used to rapidly detect wood biological decay.

Thermodynamic and Structural Properties of Methanol-water Solutions Using Nonadditive Interaction Models

Journal of Computational Chemistry. May, 2008  |  Pubmed ID: 18074339

We study bulk structural and thermodynamic properties of methanol-water solutions via molecular dynamics simulations using novel interaction potentials based on the charge equilibration (fluctuating charge) formalism to explicitly account for molecular polarization at the atomic level. The study uses the TIP4P-FQ potential for water-water interactions, and the CHARMM-based (Chemistry at HARvard Molecular Mechanics) fluctuating charge potential for methanol-methanol and methanol-water interactions. In terms of bulk solution properties, we discuss liquid densities, enthalpies of mixing, dielectric constants, self-diffusion constants, as well as structural properties related to local hydrogen bonding structure as manifested in radial distribution functions and cluster analysis. We further explore the electronic response of water and methanol in the differing local environments established by the interaction of each species predominantly with molecules of the other species. The current force field for the alcohol-water interaction performs reasonably well for most properties, with the greatest deviation from experiment observed for the excess mixing enthalpies, which are predicted to be too favorable. This is qualitatively consistent with the overestimation of the methanol-water gas-phase interaction energy for the lowest-energy conformer (methanol as proton donor). Hydration free energies for methanol in TIP4P-FQ water are predicted to be -5.6 +/- 0.2 kcal/mol, in respectable agreement with the experimental value of -5.1 kcal/mol. With respect to solution microstructure, the present cluster analysis suggests that the microscale environment for concentrations where select thermodynamic quantities reach extremal values is described by a bipercolating network structure.

Transsphenoidal Surgery in a Patient with Acromegaly and McCune-Albright Syndrome: Application of Neuronavigation

Journal of Neurosurgery. Jan, 2008  |  Pubmed ID: 18173327

The McCune-Albright syndrome (MAS) is characterized by a clinical triad of polyostotic fibrous dysplasia, café-au-lait hyperpigmented macules, and hypersecretory endocrinopathies. Acromegaly is an uncommon manifestation of the endocrine disturbance associated with MAS, and the role of surgery in managing these cases has been a topic of debate. The authors present the case of a 35-year-old man with MAS who was also diagnosed with acromegaly, hyperprolactinemia, and pituitary macroadenoma. The patient had an 18-year history of fibrous dysplasia involving the right frontal bone and ribs as well as multiple endocrinopathies, but no cutaneous hyperpigmented macules. An oral glucose tolerance test demonstrated partial suppression of plasma levels of growth hormone (GH). The patient underwent transsphenoidal resection of the pituitary tumor, performed with assistance of neuronavigation, and tolerated the procedure well. After the surgery, both prolactin and GH levels returned to normal. These results suggest that neuronavigation-assisted transsphenoidal surgery can safely remove pituitary adenomas associated with MAS and successfully treat the underlying endocrine abnormalities.

Tibet's Seeds Must Be Stored As Climate Changes

Nature. Mar, 2008  |  Pubmed ID: 18322501

[Impact of All-trans Retinoic Acid on Gene Expression Profile of Glioblastoma Cell Line SHG-44]

Ai Zheng = Aizheng = Chinese Journal of Cancer. May, 2008  |  Pubmed ID: 18479597

Astrocytoma has the trend of malignant progression. Differentiation-inducing therapy can induce tumor differentiation and make tumor cells become less malignant or even normal. This study was to investigate the impact of all-trans retinoic acid (ATRA) on the gene expression profile of glioblastoma cell line SHG-44, and to provide basic data for further research on gene therapy for human astrocytoma.

Genetic Diversity of Relictual and Endangered Plant Abies Ziyuanensis (Pinaceae) Revealed by AFLP and SSR Markers

Genetica. May, 2008  |  Pubmed ID: 17661154

Abies ziyuanensis is a highly endangered fir species endemic to South China. Unlike other Abies species that are distributed in areas with cold climates, A. ziyuanensis is restricted to several isolated island-like localities at subtropical mountains. In this study, we used dominant amplified fragment length polymorphism (AFLP) and co-dominant simple sequence repeats (SSR) markers to infer the genetic structure of A. ziyuanensis. Seven populations consisting of 139 individuals were sampled across their whole distribution. A. ziyuanenesis has a relatively low level of genetic variation, with a mean genetic diversity per population (He) of 0.136 (AFLP) and 0.337 (SSR), which is lower than that of other reported endemic species based on the same kind of marker. We observed high population differentiation, with Gst = 0.482 (AFLP) and Fst = 0.250 (SSR), among the seven populations. AMOVA also detected significant differentiation among populations (Phist (AFLP) = 0.550 and Phist (SSR) = 0.289) and among regions (Phict (AFLP) = 0.139 and Phict (SSR) = 0.135) in both marker types. Both ongoing evolutionary forces (e.g., genetic drift resulting from small population size) and historical events (e.g., population contraction and fragmentation during and after the Quaternary glacial cycles) may have contributed to the genetic structure in A. ziyuanensis.

Comparative Population Structure of Chinese Sumac Aphid Schlechtendalia Chinensis and Its Primary Host-plant Rhus Chinensis

Genetica. Jan, 2008  |  Pubmed ID: 17503190

Most of our current understanding of comparative population structure has been come from studies of parasite-host systems, whereas the genetic comparison of gallnut-aphids and their host-plants remain poorly documented. Here, we examined the population genetic structure of the Chinese sumac aphid Schlechtendalia chinensis and its unique primary host-plant Rhus chinensis in a mountainous province in western China using inter-simple sequence repeat (ISSR) markers. Despite being sampled from a mountainous geographic range, analysis of molecular variance (AMOVA) showed that the majority of genetic variation occurred among individuals within populations of both the aphid and its host. The aphid populations were found to be structured similarly to their primary host populations (F (ST) values were 0.239 for the aphid and 0.209 for its host), suggesting that there are similar patterns of gene flow between the populations of the aphid and between populations of its host-plant. The genetic distances (F (ST)/1 - F (ST)) between the aphid populations and between its host-plant populations were uncorrelated, indicating that sites with genetically similar host-plant populations may not always have genetically similar aphid populations. The lack of relationships between genetic and geographical distance matrices suggested that isolation by distance (IBD) played a negligible role at this level. This may be mainly attributed to the founder effect, genetic drift and the relative small spatial scale between populations.

Catena-Poly[[bis-[2-chloro-6-(1H-1,2,4-triazol-1-yl-κN)pyridine]cadmium(II)]-di-μ-thio-cyanato-κN:S;κS:N]: a One-dimensional Coordination Polymer

Acta Crystallographica. Section E, Structure Reports Online. 2008  |  Pubmed ID: 21201062

In the crystal structure of the title complex, [Cd(NCS)(2)(C(7)H(5)ClN(4))(2)](n), the Cd(II) atom lies on a crystallographic inversion center and assumes a distorted octa-hedral geometry. The 2-chloro-6-(1H-1,2,4-triazol-1-yl)pyridine mol-ecule acts as a terminal ligand. The thio-cyanate ligands function as μ(1,3)-bridging units connecting adjacent Cd(II) atoms with a separation of 5.7525 (11) Å, forming a one-dimensional chain along the a axis.

Diaqua-bis[2-(2-pyridylmeth-oxy)pyrazine-κN]bis-(thio-cyanato-κN)cobalt(II)

Acta Crystallographica. Section E, Structure Reports Online. 2008  |  Pubmed ID: 21201079

In the title complex, [Co(NCS)(2)(C(10)H(9)N(3)O)(2)(H(2)O)(2)], the Co(II) ion is located on a crystallographic twofold rotation axis and is in a slightly distorted octa-hedral CoN(4)O(2) coordination environment. The dihedral angle between the pyridine and pyrazine rings is 85.86 (10)°. In the crystal structure, inter-molecular O-H⋯N and O-H⋯S hydrogen bonds link complex mol-ecules into a three-dimensional network.

A Preliminary Genetic Distinctness of Four Coilia Fishes (Clupeiformes: Engraulidae) Inferred from Mitochondrial DNA Sequences

Genetika. Mar, 2008  |  Pubmed ID: 18664145

In order to understand the genetic distinctness between four Coilia fishes,i.e., C. ectenes, C. e. taihuensis, C. mystus, and C. grayii, the combined cytochrome b (cytb), 12S rRNA and 16S rRNA gene sequences were obtained and analysed. The results are as follows: 1) neighbour-joining (NJ) and maximum parsimony (MP) trees were built with 1000 bootstrap replicates. They supported that Coilia fishes consisted of two clades: C. grayii form a monophyletic group, and the rest samples form the other monophyletic group; 2) the topological differences between the NJ tree and the MP tree are checked by Templeton test, indicating that their differences are insignificant (P > 0.05); and 3) Kimura-2-parameter distances between the samples of C. ectenes, C. e. taihuensis and C. mystus are all no bigger than 1.6%, and most of them are between 0.0% and 0.9%. C. ectenes, C. e. taihuensis and C. mystus are closely related and that their differences may be under subspecies.

Inhibition of All-trans Retinoic Acid on MDM2 Gene Expression in Astrocytoma Cell Line SHG-44

Neuroscience Bulletin. Oct, 2008  |  Pubmed ID: 18839023

To investigate the impact of all-trans retinoic acid (ATRA) on MDM2 gene expression in astrocytoma cell line SHG-44, and to provide basic data for further research on the progression mechanism and gene therapy of human astrocytoma.

[Transsphenoidal Microsurgical Results of Non-invasive Prolactinomas]

Zhonghua Wai Ke Za Zhi [Chinese Journal of Surgery]. Feb, 2008  |  Pubmed ID: 18683769

To analyze the transsphenoidal microsurgical results of non-invasive prolactinomas, in order to provide reference for their treatment choice.

Dichlorido(2,6-dipyrazol-1-ylpyridine)zinc(II)

Acta Crystallographica. Section E, Structure Reports Online. 2008  |  Pubmed ID: 21580830

In the title complex, [ZnCl(2)(C(11)H(9)N(5))], the Zn(II) ion assumes a distorted trigonal-bipyramidal ZnN(3)Cl(2) coordination geometry [Zn-N = 2.1397 (16)-2.2117 (17) Å, Zn-Cl = 2.2470 (6) and 2.2564 (6) Å]. The crystal packing exhibits π-π stacking inter-actions between the 2,6-dipyrazol-1-ylpyridine ligands of neighbouring mol-ecules.

Catena-Poly[[[2,6-bis-(pyrazol-1-yl-κN)pyridine-κN](nitrato-κO,O')cadmium(II)]-μ-thio-cyanato-κN:S]

Acta Crystallographica. Section E, Structure Reports Online. 2008  |  Pubmed ID: 21580839

In the title crystal structure, [Cd(NCS)(NO(3))(C(11)H(9)N(5))](n), the unique Cd(II) ion is coordinated in a distorted penta-gonal-bipyramidal environment. The axial thio-cyanate ligands act in a μ(1,3)-bridging mode to connect symmetry-related Cd(II) ions into one-dimensional chains along [010]. In addition, there are inter-molecular C-H⋯O contacts between chains.

[Correlation Between Activation of L5-S2 Spinal Cord Astrocytes and Effect of Substance P in Chronic Prostatitis Pain]

Zhonghua Nan Ke Xue = National Journal of Andrology. Nov, 2009  |  Pubmed ID: 20218316

To observe the expressions of the substance P (SP) mRNA and neurokinin-1 receptor (NK-1R) in the posterior horn of the L5 - S2 spinal cord in the rat model of chronic prostatitis pain, and to investigate the changes in the activation of astrocytes and influence of SP on this activation in rat spinal cord astrocytes cultured in vitro.

Complete Nucleotide Sequence and Gene Arrangement of the Mitochondrial Genome of the Crab-eating Frog Fejervarya Cancrivora and Evolutionary Implications

Gene. Jul, 2009  |  Pubmed ID: 18848608

The complete nucleotide sequence of the mitochondrial (mt) genome of the crab-eating frog, Fejervarya cancrivora Gravenhorst (Amphibia: Anura: Ranidae), was determined. The mt genome is 17,843 bp long and contains 13 protein-coding (ATP6, ATP8, COI-III, ND1-6 and 4L, and Cyt b) and two ribosomal RNA (12S and 16SrRNA) genes. Although metazoan mt genomes typically encode 22 transfer RNA genes (tRNAs), the F. cancrivora mtDNA contains 23 tRNAs due to the presence of an extra copy of tRNA(Met). A major noncoding region and a prominent intergenic spacer corresponding to the control region and light-strand replication origin were also found. To confirm the phylogenetic position of F. cancrivora, we compared the gene arrangement with that of other anurans and performed phylogenetic analyses based on mt genomic data. The genome organization of F. cancrivora mtDNA differs from that of typical vertebrates and neobatrachian frogs but is identical with that of F. limnocharis, suggesting that the unique gene arrangement occurred in the common ancestor of the genus. Phylogenetic analyses supported the monophyly of the Fejervarya species used here as well as the dicroglossini clade. Although the family Ranidae as previously recognized (= Ranidae, Discoglossidae, and some other natatanuran families; sensu Frost et al., 2006) is shown as a clade in the maximum parsimony analysis, the maximum likelihood and the Bayesian analyses suggest the paraphyly of the Ranidae with respect to the families, Mantellidae and Rhacophoridae. Three-tandem duplications of gene regions followed by subsequent deletions of supernumerary genes were proposed to explain the evolution of the extra tRNA(Met) and translocation of ND5 from the original neobatrachian gene order.

A Simple Method for Phylogenomic Inference Using the Information of Gene Content of Genomes

Gene. Jul, 2009  |  Pubmed ID: 18675889

Many studies have been contributed to the inferences of phylogenies. Some studies are based on a single-gene (family), and some are based on entire genome data. In this paper, we propose a total loss genome distance approach based on gene content information to inferring phylogenies. Through various simulations, we demonstrate and evaluate the proposed approach. We compare it with some other approaches built upon gene content or extended gene content. Overall, the proposed approach performs equally well as the other methods do and is more efficient than some of the methods. We apply our approach to 34 microbial complete genomes from COG. The reconstructed tree agrees with the results from other approaches and the tree supports the concept of universal trees.

Identification of a Putative Invertebrate Helical Cytokine Similar to the Ciliary Neurotrophic Factor/leukemia Inhibitory Factor Family by PSI-BLAST-based Approach

Journal of Interferon & Cytokine Research : the Official Journal of the International Society for Interferon and Cytokine Research. Aug, 2009  |  Pubmed ID: 19514841

Most of our knowledge of helical cytokine-like molecules in invertebrates relies on functional assays and similarities at the physicochemical level. It is hard to predict helical cytokines in invertebrates based on sequences from mammals and vertebrates, because of their long evolutionary divergence. In this article, we collected 12 kinds of fish cytokines and constructed their respective consensus sequences using hidden Markov models; then, the conserved domains region of each consensus sequence were further extracted by the SMART tool, and used as the query sequence for PSI-BLAST analysis in Drosophila melanogaster. After two filtering processes based on the properties of helical cytokines, we obtained one protein named CG14629, which shares 25% identities/46% positives to fish M17 cytokine in the half length of the N-terminus. Considering the homology between M17 and LIF/CNTF (leukemia inhibitory factor/ciliary neurotrophic factor), and the close relationship between Dome, the putative cytokine receptor in Drosophila cells, and LIFR/CNTFR (LIF receptor/CNTF receptor), the results suggest that CG14629 is a good candidate for the helical cytokine ortholog in D. melanogaster.

Inhibitors of Human Immunodeficiency Virus Type 1 (HIV-1) Attachment. 5. An Evolution from Indole to Azaindoles Leading to the Discovery of 1-(4-benzoylpiperazin-1-yl)-2-(4,7-dimethoxy-1H-pyrrolo[2,3-c]pyridin-3-yl)ethane-1,2-dione (BMS-488043), a Drug Candidate That Demonstrates Antiviral Activity in HIV-1-infected Subjects

Journal of Medicinal Chemistry. Dec, 2009  |  Pubmed ID: 19769332

Azaindole derivatives derived from the screening lead 1-(4-benzoylpiperazin-1-yl)-2-(1H-indol-3-yl)ethane-1,2-dione (1) were prepared and characterized to assess their potential as inhibitors of HIV-1 attachment. Systematic replacement of each of the unfused carbon atoms in the phenyl ring of the indole moiety by a nitrogen atom provided four different azaindole derivatives that displayed a clear SAR for antiviral activity and all of which displayed marked improvements in pharmaceutical properties. Optimization of these azaindole leads resulted in the identification of two compounds that were advanced to clinical studies: (R)-1-(4-benzoyl-2-methylpiperazin-1-yl)-2-(4-methoxy-1H-pyrrolo[2,3-b]pyridin-3-yl)ethane-1,2-dione (BMS-377806, 3) and 1-(4-benzoylpiperazin-1-yl)-2-(4,7-dimethoxy-1H-pyrrolo[2,3-c]pyridin-3-yl)ethane-1,2-dione (BMS-488043, 4). In a preliminary clinical study, 4 administered as monotherapy for 8 days, reduced viremia in HIV-1-infected subjects, providing proof of concept for this mechanistic class.

Adaptive Evolution of Chloroplast Genomes in Ancestral Grasses

Plant Signaling & Behavior. Jul, 2009  |  Pubmed ID: 19820316

The grass family, Poaceae, is one of the most successful families among angiosperms. Although it has long been suggested that the chloroplast genomes of the Poaceae have undergone an elevated evolutionary rate compared to other angiosperms, little was known about the details of this phenomenon. By using chloroplast genome data from 31 seed plants species, we recently showed that episodic rate acceleration occurred in the common ancestral branch of the core Poaceae (a clade formed by rice Oryza sativa, wheat Triticum aestivum, maize Zea mays and their allies) accompanied by elevated non-synonymous/synonymous rate ratio, while the rate and the non-synonymous/synonymous rate ratio reverted to the low level typical of most monocot species in the terminal branches. It was further shown that positive selection or adaptive evolution operated in several chloroplast proteins during the evolution of ancestral grasses, and the amino acid sites which putatively experienced positive selection have been identified. These findings illustrate the importance of future works of structural biological research of chloroplasts to understand the background of the evolution of the successful group, Poaceae.

[Application of a Prediction Model in Inclusion Body Refolding]

Nan Fang Yi Ke Da Xue Xue Bao = Journal of Southern Medical University. Nov, 2009  |  Pubmed ID: 19923054

To establish a prediction method for the refolding of inclusion bodies and classify refolding types of different inclusion bodies directly from their primary structure to improve the efficiency of high throughput refolding process.

MapNext: a Software Tool for Spliced and Unspliced Alignments and SNP Detection of Short Sequence Reads

BMC Genomics. 2009  |  Pubmed ID: 19958476

Next-generation sequencing technologies provide exciting avenues for studies of transcriptomics and population genomics. There is an increasing need to conduct spliced and unspliced alignments of short transcript reads onto a reference genome and estimate minor allele frequency from sequences of population samples.

Development of a Database System for Mapping Insertional Mutations Onto the Mouse Genome with Large-scale Experimental Data

BMC Genomics. 2009  |  Pubmed ID: 19958505

Insertional mutagenesis is an effective method for functional genomic studies in various organisms. It can rapidly generate easily tractable mutations. A large-scale insertional mutagenesis with the piggyBac (PB) transposon is currently performed in mice at the Institute of Developmental Biology and Molecular Medicine (IDM), Fudan University in Shanghai, China. This project is carried out via collaborations among multiple groups overseeing interconnected experimental steps and generates a large volume of experimental data continuously. Therefore, the project calls for an efficient database system for recording, management, statistical analysis, and information exchange.

Modeling of Protein Refolding from Inclusion Bodies

Acta Biochimica Et Biophysica Sinica. Dec, 2009  |  Pubmed ID: 20011979

Overexpression of foreign proteins in Escherichia coli often leads to the formation of inclusion bodies (IBs), which becomes the major bottleneck in the preparation of recombinant proteins and their applications. In the present study, 36 proteins from IBs were refolded using a simple refolding method. Refolding yields of these proteins were defined as the percentage of soluble proteins following dilution refolding in the amount of denatured proteins in the samples before diluting into refolding buffer. Furthermore, a mathematical model was deduced to evaluate the role of biochemical properties in the protein refolding. Our results indicated that under the experimental conditions, isoelectric point of proteins might be mostly contributing to the high efficacy of protein refolding since the increment of one unit resulted in a decrease of 14.83% in the refolding yield. Other important mediators were components of protein secondary structure and the molecular weight (R(2) = 0.98, P = 0.000, F-test). Six proteins with low efficiency in the protein refolding possessed relatively low isoelectric points. Furthermore, refolding yields of six additional proteins from IBs were predicted and further validated by refolding the proteins under the same conditions. Therefore, the model of protein refolding developed here could be used to predict the refolding yields of proteins from IBs through a simple method. Our study will be suggestive to optimize the methods for protein refolding from IBs according to their intrinsic properties.

Phylogeographic Analysis of Human Papillomavirus 58

Science in China. Series C, Life Sciences / Chinese Academy of Sciences. Dec, 2009  |  Pubmed ID: 20016974

Human papillomavirus 58 (HPV58) is one type of HPV with high risk of causing cervical cancer. Unusually high prevalence of HPV58 has been reported in Asia, Africa and some other areas. However, due to the scattered distribution of global data, in addition to the lack of data of some HPV58 high-incidence nations and regions, like Mainland China, a comprehensive analysis of the global geographical distribution of HPV58 remains blank so far. In this study, HPV58 from the human cervical cancer tissue was detected in Mainland China, and 14 new HPV58-E6/L1 gene sequences were obtained. Moreover, phylogeographic analysis has been conducted combining the HPV58 sequences that have been deposited in GenBank since 1985. The study result shows that the sequences detected from the Shanghai, Jiangsu and Sichuan areas are homologous with those found in the past from Hong Kong and Xi'an, China, as well as Japan and other Southeast Asian areas. Furthermore, Western Africa is considered to be the "root" source of the HPV58 variant, while Mainland China and Southeast Asia are "transit points" and the new sources of HPV58 after receiving the isolates from the "root" source; like HPV16 and HPV18, the HPV58 might also be one of the major HPV types associated with the development and spread of cervical cancer.

Fine- and Landscape-scale Spatial Genetic Structure of Cushion Rockjasmine, Androsace Tapete (Primulaceae), Across Southern Qinghai-Tibetan Plateau

Genetica. Apr, 2009  |  Pubmed ID: 18604631

The cushion rockjasmine, Androsace tapete (Primulaceae), is among the angiosperms with highest altitudal distribution in the world. Cushion rockjasmine is a prominent pioneer species in alpine deserts and alpine flowstone slope habitats up to 5,300 m on Qinghai-Tibetan Plateau. In this study, we use inter simple sequence repeat (ISSR) markers to investigate the spatial genetic structure of A. tapete at both fine-scale and landscape-scale, with emphasis on testing the hypothesis that the low-altitude valley of the Brahmaputra River, running from west to east across Qinghai-Tibetan Plateau, has significant effects on the spatial population structure of A. tapete. A total of 235 individuals were collected from five populations in disjunct ridges (i.e. two populations located in the north, and three in the south of the Brahmaputra River), including 158 individuals that were spatial explicitly sampled from a 30 m x 90 m plot. At fine scale, spatial autocorrelation analysis indicates a significant genetic structure within a short distance (less than 10 m), which is probably due to limited gene dispersal via pollen and/or seeds. At landscape scale, however, AMOVA suggests that most of the total genetic variation (85%) is among individuals within populations; and the Brahmaputra River plays a weak role in shaping the spatial population structure of A. tapete. In addition, the results of PCA and STRUCTURE assignment show significant genetic associations between the populations across the Brahmaputra River. The historical gene exchanges and slow genetic drift may be responsible for the lack of deep genetic differentiation among topographically separated populations in A. tapete.

Duplication and Adaptive Evolution of the COR15 Genes Within the Highly Cold-tolerant Draba Lineage (Brassicaceae)

Gene. Jul, 2009  |  Pubmed ID: 18640249

Plants have evolved diverse adaptive mechanisms that enable them to tolerate abiotic stresses, to varying degrees, and such stresses may have strongly influenced evolutionary changes at levels ranging from molecular to morphological. Previous studies on these phenomena have focused on the adaptive evolution of stress-related orthologous genes in specific lineages. However, heterogenetic evolution of the paralogous genes following duplication has only been examined in a very limited number of stress-response gene families. The COR15 gene encodes a low molecular weight protein that plays an important role in protecting plants from cold stresses. Although two different copies of this gene have been found in the model species, Arabidopsis thaliana, evolutionary patterns of this small gene family in plants have not been previously explored. In this study, we cloned COR15-like sequences and performed evolutionary analyses of these sequences (including those previously reported) in the highly cold-tolerant Draba lineage and related lineages of Brassicaceae. Our phylogenetic analyses indicate that all COR15-like sequences clustered into four clades that corresponded well to the morphological lineages. Gene conversions were found to have probably occurred before/during the divergence of Brassica and Draba lineage. However, repeated, independent duplications of this gene have occurred in different lineages of Brassicaceae. Further comparisons of all sequences suggest that there have been significant inter-lineage differences in evolutionary rates between the duplicated and original genes. We assessed the likelihood that the differences between two well-supported gene subfamilies that appear to have originated from a single duplication, COR15a and COR15b, within the Draba lineage have been driven by adaptive evolution. Comparisons of their non-synonymous/synonymous substitution ratios and rates of predicted amino acid changes indicate that these two gene groups are evolving under different selective pressures and may be functionally divergent. This functional divergence was confirmed by comparing site-specific shifts in evolution indexes of the two groups of predicted proteins. The evidence of differential selection and possible functional divergence suggests that the duplication may be of adaptive significance, with possible implications for the explosive diversification of the Draba lineage during the cooling Quaternary stages and the following worldwide colonization of arid alpine and artic regions.

Effect of Site-specific Heterogeneous Evolution on Phylogenetic Reconstruction: a Simple Evaluation

Gene. Jul, 2009  |  Pubmed ID: 18778757

Recent studies have shown that heterogeneous evolution may mislead phylogenetic analysis, which has been neglected for a long time. We evaluate the effect of heterogeneous evolution on phylogenetic analysis, using 18 fish mitogenomic coding sequences as an example. Using the software DIVERGE, we identify 198 amino acid sites that have experienced heterogeneous evolution. After removing these sites, the rest of sites are shown to be virtually homogeneous in the evolutionary rate. There are some differences between phylogenetic trees built with heterogeneous sites ("before tree") and without heterogeneous sites ("after tree"). Our study demonstrates that for phylogenetic reconstruction, an effective approach is to identify and remove sites with heterogeneous evolution, and suggests that researchers can use the software DIVERGE to remove the influence of heterogeneous evolution before reconstructing phylogenetic trees.

Differentially Expressed Genes from the Glioblastoma Cell Line SHG-44 Treated with All-trans Retinoic Acid in Vitro

Journal of Clinical Neuroscience : Official Journal of the Neurosurgical Society of Australasia. Feb, 2009  |  Pubmed ID: 19091570

Morphology, immunocytochemistry, growth curve assay, and flow cytometry were used to investigate the effects of all-trans retinoic acid (RA) on cell proliferation, cell cycle progression and differentiation of the astrocytoma cell line SHG-44 from glioblastoma multiforme (World Health Organization grade IV). The differentially expressed genes from RA-treated and normal SHG-44 were identified by cDNA microarray after the cell line SHG-44 was treated with 10muM RA for 3 days. Validation of some differentially expressed genes was performed by Northern Blot analysis. The expression of glial fibrillary acidic protein (GFAP) was markedly increased in RA-treated SHG-44 cells. Other changes included a short shuttle shape, small nucleus, decreased karyoplasm proportion, the formation of increased thin cytoplasmic processes, reduced cell growth and a 15% increase in G0/G1 phase cell populations. In addition, 42 known genes were identified with altered expression in our cDNA microarray. There was stable down-regulation of MDM2 and UGB as well as overexpression of SOD2, CSTB, and G3BP when RA-treated SHG-44 was compared with normal SHG-44. RA simultaneously suppressed the proliferation of SHG-44 cells significantly as well as induced differentiation and altered gene expression.

Electrostatic Polarization Effects and Hydrophobic Hydration in Ethanol-water Solutions from Molecular Dynamics Simulations

The Journal of Physical Chemistry. B. Jan, 2009  |  Pubmed ID: 19115819

Nonadditive electrostatic force fields based on the charge equilibration formalism coupled with long time-scale molecular dynamics simulations are used to investigate the microscopic structural aspects of hydrophobic hydration in ethanol-water solutions. Employing a combination of polarizable ethanol and water force fields (developed independently), we find that solution properties are satisfactorily reproduced across the ethanol mole fraction range between 0.1 and 0.9. Solution densities are predicted within 3.6% of experimental measurements, while excess mixing enthalpies are overestimated as in earlier studies. The solvation free energy of ethanol in infinite dilution is determined via thermodynamic integration to be 5.70 +/- 0.23 kcal/mol, overestimating the free energetics of solvation relative to experiment (5.01 kcal/mol). Bulk solution dielectric constants and diffusion constants reproduce experimental trends and are in reasonable agreement across the ethanol concentration range studied. Because of explicit accounting of induction effects, ethanol and water exhibit varying molecular dipole moment distributions with concentration. The polarizable ethanol model, possessing higher condensed-phase polarizability relative to the TIP4P-FQ water model (4.54 A(3) versus 1.1 A(3), respectively), displays greater variation upon perturbation by the electric field of water. With regard to hydrophobic hydration, the current force fields indicate positive hydrogen bonding excess for water in the dilute ethanol concentration range, consistent with previous theoretical and experimental studies. Strikingly, we find that there are both positive and negative hydrogen bond excess contributions within the first hydration shell of both the ethanol hydroxyl oxygen and ethylene carbon atoms. The larger positive contributions dominate the overall hydrogen bonding patterns to yield overall net positive excesses. Moreover, we do not find evidence of excess hydrogen bonding vicinal to the nonpolar moieties as has been suggested based on the "iceberg"-like models proposed by Frank and Evans. The present results suggest negative excess in the regions surrounding the alkyl groups that vis-a-vis corresponds to a reduction in the average molecular dipole moment of resident water molecules due to smaller dipole induction in the weaker electrostatic fields of the nonpolar groups.

Photosynthetic Metabolism of C3 Plants Shows Highly Cooperative Regulation Under Changing Environments: a Systems Biological Analysis

Proceedings of the National Academy of Sciences of the United States of America. Jan, 2009  |  Pubmed ID: 19129487

We studied the robustness of photosynthetic metabolism in the chloroplasts of C(3) plants under drought stress and at high CO(2) concentration conditions by using a method called Minimization of Metabolic Adjustment Dynamic Flux Balance Analysis (M_DFBA). Photosynthetic metabolism in the chloroplasts of C(3) plants applies highly cooperative regulation to minimize the fluctuation of metabolite concentration profiles in the face of transient perturbations. Our work suggests that highly cooperative regulation assures the robustness of the biological system and that there is closer cooperation under perturbation conditions than under normal conditions. This results in minimizing fluctuations in the profiles of metabolite concentrations, which is the key to maintaining a system's function. Our methods help in understanding such phenomena and the mechanisms of robustness for complex metabolic networks in dynamic processes.

The Contribution of Cis-regulatory Elements to Head-to-head Gene Pairs' Co-expression Pattern

Science in China. Series C, Life Sciences / Chinese Academy of Sciences. Jan, 2009  |  Pubmed ID: 19152086

Transcription regulation is one of the most critical pipelines in biological process, in which cis-elements play the role as gene expression regulators. We attempt to deduce the principles underlying the co-expression of "head-to-head" gene pairs by analyzing activities or behaviors of the shared cis-elements. A network component analysis was performed to estimate the impact of cis-elements on gene promoters and their activities under different conditions. Our discoveries reveal how biological system uses those regulatory elements to control the expression pattern of "head-to-head" gene pairs and the whole transcription regulation system.

Human Gene Expression Sensitivity According to Large Scale Meta-analysis

BMC Bioinformatics. 2009  |  Pubmed ID: 19208159

Genes show different sensitivities in expression corresponding to various biological conditions. Systematical study of this concept is required because of its important implications in microarray analysis etc. J.H. Ohn et al. first studied this gene property with yeast transcriptional profiling data.

Differential Stepwise Evolution of SARS Coronavirus Functional Proteins in Different Host Species

BMC Evolutionary Biology. 2009  |  Pubmed ID: 19261195

SARS coronavirus (SARS-CoV) was identified as the etiological agent of SARS, and extensive investigations indicated that it originated from an animal source (probably bats) and was recently introduced into the human population via wildlife animals from wet markets in southern China. Previous studies revealed that the spike (S) protein of SARS had experienced adaptive evolution, but whether other functional proteins of SARS have undergone adaptive evolution is not known.

Dissolution Rate of Limestone for Wet Flue Gas Desulfurization in the Presence of Sulfite

Journal of Hazardous Materials. Sep, 2009  |  Pubmed ID: 19359093

Limestone dissolution rate was measured by a pH-stat method with CO(2) sparging and dissolved sulfite. The dissolution rate of limestone under these conditions was found to be controlled by mass transfer and surface kinetics. As can be seen from the results, in the presence of sulfite, limestone dissolution rate increases with increasing stirring speed, reaction temperature and CO(2) partial pressure. The crystallinity of limestone has a great impact on the dissolution rate: The lower the value of the crystallinity of limestone is, the higher the dissolution rate is. The presence of sulfite promotes the dissolution rate when pH value is below 5.5 but inhibits it when pH value is above 5.5.

Episodic Evolution and Adaptation of Chloroplast Genomes in Ancestral Grasses

PloS One. 2009  |  Pubmed ID: 19390686

It has been suggested that the chloroplast genomes of the grass family, Poaceae, have undergone an elevated evolutionary rate compared to most other angiosperms, yet the details of this phenomenon have remained obscure. To know how the rate change occurred during evolution, estimation of the time-scale with reliable calibrations is needed. The recent finding of 65 Ma grass phytoliths in Cretaceous dinosaur coprolites places the diversification of the grasses to the Cretaceous period, and provides a reliable calibration in studying the tempo and mode of grass chloroplast evolution.

Imaging Findings of Abdominal Peripheral Primitive Neuroectodermal Tumor: Report of Four Cases with Pathological Correlation

Clinical Imaging. May-Jun, 2009  |  Pubmed ID: 19411024

Peripheral primitive neuroectodermal tumors (peripheral PNETs) are rare in the abdomen. We report the imaging findings of four peripheral PNETs arising in the abdomen. Three were ill-demarcated tumors and one was a well-demarcated tumor, with extensive local invasion and lymph node metastasis in two cases, respectively. The tumors are of inhomogeneous attenuation and heterogeneous enhancement after intravenous administration of contrast materials. Although their imaging manifestations cannot distinguish them from other sarcomas, recognition of these imaging features may be helpful in suggesting the possibility of peripheral PNETs in some cases.

Interfacial Structure, Thermodynamics, and Electrostatics of Aqueous Methanol Solutions Via Molecular Dynamics Simulations Using Charge Equilibration Models

The Journal of Physical Chemistry. B. Jul, 2009  |  Pubmed ID: 19569724

We present results from molecular dynamics simulations of methanol-water solutions using charge equilibration force fields to explicitly account for nonadditive electronic interaction contributions to the potential energy. We study solutions across the concentration range from 0.1 to 0.9 methanol mole fraction. At dilute concentrations, methanol density is enhanced at the liquid-vapor interface, consistent with previous molecular dynamics and experimental studies. Interfacial thickness exhibits a monotonic increase with increasing methanol mole fraction, while surface tensions display monotonic decrease with methanol concentration, in qualitative agreement with experimental data and previous molecular dynamics predictions using polarizable force fields. In terms of interfacial structure, in keeping with predictions of traditional force fields, there is a unique preferential orientation of methanol molecules at the interface. Moreover, there is a free energetic preference for methanol molecules at the interface as evidenced by potential of mean force calculations. The pmf calculations suggest an interfacial state with 0.8 kcal/mol stability relative to the bulk, again in qualitative agreement with previous simulation and experimental studies. Interfacial potentials based on double integration of total charge density range from -610 to -330 mV over the dilute to concentrated regimes, respectively. The preponderance of methanol at the interface at all mole fractions gives rise to a dominant methanol contribution to the total interfacial potential. Interestingly, there is a transition of the water surface potential contribution from negative to positive upon the transition from methanol mole fraction of 0.1 to 0.2. The dipole and quadrupole contributions to the water component of the total interfacial potential are effectively of equal magnitude and opposite sign, thus cancelling one another. We compute the in-plane component of the dielectric permittivity along the interface normal. We observe a nonmonotonic behavior of the methanol in-plane dielectric permittivity that tracks the methanol density profiles at low methanol mole fractions. At higher methanol mole fractions, the total in-plane permittivity is dominated by methanol and displays a monotonic decrease from bulk to vapor. We finally probe the nature of hydration of water in the bulk versus interfacial regions for methanol mole fractions of 0.1 and 0.2. In the bulk, methanol perturbs water structure so as to give rise to water hydrogen bond excesses. Moreover, we observe negative hydrogen bond excess in the vicinity of the alkyl group, as reported by Zhong et al. for bulk ethanol-water solutions using charge equilibration force fields, and positive excess in regions hydrogen bonding to nearest-neighbor methanol molecules. Within the interfacial region, water and methanol density reduction lead to concomitant water hydrogen bond deficiencies (negative hydrogen-bond excess).

TGFB1 509 C/T Polymorphism and Colorectal Cancer Risk: a Meta-analysis

Medical Oncology (Northwood, London, England). Dec, 2010  |  Pubmed ID: 20012233

Transforming growth factor β (TGF-β) is a cytokine. The TGF-β signaling pathway plays an important role in controlling cell proliferation and differentiation involved in colorectal carcinogenesis. In mammalian cells, TGFB1 is the most abundant subtype of TGF-β. The 509 C/T polymorphism in TGFB1 has been implicated in colorectal cancer risk. However, published data remain conflicting. To derive a more precise estimation of the relationship, a meta-analysis of 994 cases and 2,335 controls from five published case-control studies was performed. Overall, significantly increased colorectal cancer risks were found for CC versus TT (OR=1.62; 95% CI: 1.30-2.02; Pheterogeneity=0.118), TC+CC versus TT (OR=1.30; 95% CI: 1.08-1.58; Pheterogeneity=0.259) and CC versus TC+TT (OR=1.48; 95% CI: 1.26-1.75; Pheterogeneity=0.244). In the subgroup analysis by ethnicity, significantly increased risks were also found among Asians for CC versus TT (OR=1.77; 95% CI: 1.40-2.24; Pheterogeneity=0.519), TC+CC versus TT (OR=1.38; 95% CI: 1.13-1.68; Pheterogeneity=0.679) and CC versus TC+TT (OR=1.58; 95% CI: 1.31-1.89; Pheterogeneity=0.340). However, no significant associations were found among Europeans for all genetic models. This meta-analysis showed that TGFB1 509 C allele is a risk factor for developing colorectal cancer in Asians.

No Association Between CYP1B1 Val432Leu Polymorphism and Breast Cancer Risk: a Meta-analysis Involving 40,303 Subjects

Breast Cancer Research and Treatment. Jul, 2010  |  Pubmed ID: 20033481

Breast cancer is the most common cancer in women. To date, many publications have evaluated the association between Cytochrome P450 1B1 (CYP1B1) Val432Leu polymorphism and breast cancer risk. However, the results remain inconclusive. In order to derive a more precise estimation of the association, a meta-analysis was performed in this study. By searching Medline, Pubmed, and ISI Web of Knowledge databases, 26 studies including 19,028 cases and 21,275 controls were collected for CYP1B1 Val432Leu polymorphism. Crude ORs with 95% CIs were used to assess the strength of association between CYP1B1 Val432Leu polymorphism and breast cancer risk. The pooled ORs were performed for codominant model, dominant model, and recessive model, respectively. Overall, no significant associations between CYP1B1 Val432Leu polymorphism and breast cancer susceptibility were found for Val/Val versus Leu/Leu (OR = 0.98; 95% CI: 0.90-1.06), Val/Leu versus Leu/Leu (OR = 1.01; 95% CI: 0.93-1.09), Val/Val + Val/Leu versus Leu/Leu (OR = 1.00; 95% CI: 0.93-1.08) and Val/Val versus Val/Leu + Leu/Leu (OR = 0.96; 95% CI: 0.91-1.01). In the stratified analysis by ethnicity, menopausal status and sources of controls, significant associations were still not observed in all genetic models. In conclusion, this meta-analysis provides strong evidence that CYP1B1 Val432Leu polymorphism is not associated with breast cancer risk.

Pharmacological and Toxicological Target Organelles and Safe Use of Single-walled Carbon Nanotubes As Drug Carriers in Treating Alzheimer Disease

Nanomedicine : Nanotechnology, Biology, and Medicine. Jun, 2010  |  Pubmed ID: 20056170

Identification of pharmacological and toxicological profiles is of critical importance for the use of nanoparticles as drug carriers in nanomedicine and for the biosafety evaluation of environmental nanoparticles in nanotoxicology. Here we show that lysosomes are the pharmacological target organelles for single-walled carbon nanotubes (SWCNTs) and that mitochondria are the target organelles for their cytotoxicity. The gastrointestinally absorbed SWCNTs were lysosomotropic but also entered mitochondria at large doses. Genes encoding phosphoinositide-3-kinase and lysosomal-associated membrane protein 2 were involved in such an organelle preference. SWCNT administration resulted in collapse of mitochondrial membrane potentials, giving rise to overproduction of reactive oxygen species, leading to damage of mitochondria, which was followed by lysosomal and cellular injury. Based on the dosage differences in target organelles, SWCNTs were successfully used to deliver acetylcholine into brain for treatment of experimentally induced Alzheimer disease with a moderate safety range by precisely controlling the doses, ensuring that SWCNTs preferentially enter lysosomes, the target organelles, and not mitochondria, the target organelles for SWCNT cytotoxicity. FROM THE CLINICAL EDITOR: Single wall carbon nanotubes (SWCNT) could make excellent targeted delivery systems for pharmaceuticals. Inside the cells, lysosomes are the pharmacological target organelles of SWCNT, but in large doses mitochondria also take up SWCNT and mitochondrial toxicity becomes the reason for overall toxicity of this approach. In this paper, SWCNT were successfully used to deliver acetylcholine in Alzheimer's disease brains with high safety range by controlling the doses to ensure lysosomal but not mitochondrial targeting.

Concurrent Gemcitabine and High-intensity Focused Ultrasound Therapy in Patients with Locally Advanced Pancreatic Cancer

Anti-cancer Drugs. Apr, 2010  |  Pubmed ID: 20075714

This phase II trial was conducted to evaluate the safety and efficacy of concurrent gemcitabine and high-intensity focused ultrasound (HIFU) therapy in patients with locally advanced pancreatic cancer. Patients with localized unresectable pancreatic adenocarcinoma in the head or body of the pancreas received gemcitabine (1000 mg/m) intravenously over 30 min on days 1, 8, and 15, and concurrent HIFU therapy on days 1, 3, and 5. The treatment was given every 28 days. Thirty-seven (94.9%) of the 39 patients were assessable for response, and two cases of complete response and 15 cases of partial response were confirmed, giving an overall response rate of 43.6% [95% confidence interval (CI), 28.0-59.2%]. The median follow-up period was 16.5 months (range: 8.0-28.5 months). The median time to progression and overall survival for all patients were 8.4 months (95% CI, 5.4-11.2 months) and 12.6 months (95% CI, 10.2-15.0 months), respectively. The estimates of overall survival at 12 and 24 months were 50.6% (95% CI, 36.7-64.5%) and 17.1% (95%CI, 5.9-28.3%), respectively. A total of 16.2% of patients experienced grade 3/4 neutropenia. Grade 3 thrombocytopaenia was documented in two (5.4%) patients. Grade 3 nausea/vomiting and diarrhea were observed in three (8.1%), and two (5.4%) patients, respectively. Grade 1 or 2 fever was detected in 70.3% of patients. Twenty-eight patients (71.8%) complained of abdominal pain consistent with tumor-related pain before HIFU therapy. Pain was relieved in 22 patients (78.6%). In conclusion, concurrent gemcitabine and HIFU is a tolerated treatment modality with promising activity in patients with previously untreated locally advanced pancreatic cancer.

The Association Between TA-repeat Polymorphism in the Promoter Region of UGT1A1 and Breast Cancer Risk: a Meta-analysis

Breast Cancer Research and Treatment. Aug, 2010  |  Pubmed ID: 20087647

Uridine diphospho-glucuronosyltransferase 1A1 (UGT1A1) plays an important role in breast cancer development. To date, many publications have evaluated the correlation between UGT1A1 TA-repeat polymorphism and breast cancer risk. However, the results remain inconclusive. In order to resolve this conflict, a meta-analysis was performed by searching Medline, PubMed, and ISI Web of Knowledge databases. Seven studies including 5,746 cases and 8,365 controls were collected for UGT1A1 TA-repeat polymorphism. The strength of association between UGT1A1 TA-repeat polymorphism and breast cancer risk was assessed by calculating crude ORs with 95% CIs. Overall, no significant associations between UGT1A1 TA-repeat polymorphism and breast cancer susceptibility were found. In the stratified analysis by ethnicity and source of controls, significant associations were only observed for 6/6 versus 7/7 (OR = 0.88; 95% CI: 0.77-0.99; P = 0.425 for heterogeneity) in Caucasians, but no in other genetic models. In conclusion, this meta-analysis suggests that UGT1A1 A(TA)(7)TAA allele is a potential risk factor for breast cancer in Caucasians.

In Vivo Fluorescence Imaging of Muscle Cell Regeneration by Transplanted EGFP-labeled Myoblasts

Molecular Therapy : the Journal of the American Society of Gene Therapy. Apr, 2010  |  Pubmed ID: 20125125

In vivo fluorescence imaging (FLI) enables monitoring fluorescent protein (FP)-labeled cells and proteins in living organisms noninvasively. Here, we examined whether this modality could reach a sufficient sensitivity to allow evaluation of the regeneration process of enhanced green fluorescent protein (eGFP)-labeled muscle precursors (myoblasts). Using a basic FLI station, we were able to detect clear fluorescence signals generated by 40,000 labeled cells injected into a tibialis anterior (TA) muscle of mouse. We observed that the signal declined to approximately 25% on the 48 hours of cell injection followed by a recovery starting at the second day and reached a peak of approximately 45% of the original signal by the 7th day, suggesting that the survived population underwent a limited run of proliferation before differentiation. To assess whether transplanted myoblasts could form satellite cells, we injured the transplanted muscles repeatedly with cardiotoxin. We observed a recovery of fluorescence signal following a disappearance of the signal after each cardiotoxin injection. Histology results showed donor-derived cells located underneath basal membrane and expressing Pax7, confirming that the regeneration observed by imaging was indeed mediated by donor-derived satellite cells. Our results show that FLI is a powerful tool that can extend our ability to unveil complicated biological processes such as stem cell-mediated regeneration.

The Association Between ERCC2 Asp312Asn Polymorphism and Breast Cancer Risk: a Meta-analysis Involving 22,766 Subjects

Breast Cancer Research and Treatment. Aug, 2010  |  Pubmed ID: 20127278

To date, many publications discussed the correlation between ERCC2 Asp312Asn polymorphism and breast cancer risk. However, the results were not unanimous. In order to derive a more precise conclusion, a meta-analysis was performed in this study by searching Medline, PubMed, and ISI Web of Knowledge databases. Finally, 17 studies including 12,019 cases and 10,747 controls were collected for this meta-analysis. The strength of association between ERCC2 Asp312Asn polymorphism and breast cancer risk was assessed by calculating crude ORs with 95% CIs. Overall, no significant associations between ERCC2 Asp312Asn polymorphism and breast cancer susceptibility were found. In the stratified analysis by ethnicity, significant associations were observed for Asn/Asn versus Asp/Asp (OR = 0.55; 95% CI 0.32-0.96) and Asn/Asn versus Asn/Asp + Asp/Asp (OR = 0.53; 95% CI 0.32-0.90) in Asians. In the stratified analysis by study design, significant associations were found for Asn/Asn versus Asp/Asp (OR = 0.79; 95% CI 0.64-0.98) and Asn/Asn versus Asn/Asp + Asp/Asp (OR = 0.82; 95% CI 0.68-0.99) in population-based studies. In conclusion, this meta-analysis provides an evidence that ERCC2 312Asn allele may have a protective effect for breast cancer development in Asians.

Treating Triple-negative Breast Cancer by a Combination of Rapamycin and Cyclophosphamide: an in Vivo Bioluminescence Imaging Study

European Journal of Cancer (Oxford, England : 1990). Apr, 2010  |  Pubmed ID: 20156674

Rapamycin, a mammalian target of rapamycin (mTOR) inhibitor, has been shown to inhibit the growth of oestrogen positive breast cancer. However, triple-negative (TN) breast cancer is resistant to rapamycin treatment in vitro. We set to test a combination treatment of rapamycin with DNA-damage agent, cyclophosphamide, in a TN breast cancer model. By binding to and disrupting cellular DNA, cyclophosphamide kills cells via interfering with their normal functions. We assessed the responses of nude mice bearing tumour xenografts of TN MDA-MB-231 cells to the combination of rapamycin and cyclophosphamide in both orthotopic mammary and lung-metastasis models. We tracked tumour growth and metastasis by bioluminescent imaging and examined the expression of Ki67, CD34 and HIF-1alpha in tumour tissues by immunohistochemistry and apoptosis index with TUNEL assay, and found that MDA-MB-231 cells are sensitive to rapamycin therapy in orthotopic mammary, but not in lung with metastasis. Rapamycin when combined with cyclophosphamide is found to have a more significant effect in reducing tumour volume and metastasis with a much improved survival rate. Our data also show that the sensitivity of TN tumours to rapamycin is associated with the microenvironment of the tumour cells. The data indicate that in a relatively hypoxic environment HIF-1alpha may play a role in mediating the anti-cancer effect of rapamycin and cyclophosphamide may prevent the feedback activation of Akt by rapamycin. Overall our results show that rapamycin plus cyclophosphamide can achieve an improved efficacy in suppressing tumour growth and metastasis, suggesting that the combination therapy can be a promising treatment option for TN cancer.

Effect of PH on the Coagulation Performance of Al-based Coagulants and Residual Aluminum Speciation During the Treatment of Humic Acid-kaolin Synthetic Water

Journal of Hazardous Materials. Jun, 2010  |  Pubmed ID: 20188465

The fractionation and measurement of residual aluminum was conducted during the treatment of humic (HA)-kaolin synthetic water with Al(2)(SO(4))(3), AlCl(3) and polyaluminum chloride (PAC) in order to investigate the effect of pH on the coagulation performance as well as residual aluminum speciation. Experimental results suggested that turbidity removal performance varied according to the following order: AlCl(3)>PAC>Al(2)(SO(4))(3). HA removal performance of PAC was better than that of AlCl(3) under acidic condition. The optimum pH range for AlCl(3) and Al(2)(SO(4))(3) was between 6.0 and 7.0 while PAC showed stable HA and UV(254) removal capacity with broader pH variation (5.0-8.0). For the three coagulants, majority of residual aluminum existed in the form of total dissolved Al (60-80%), which existed mostly in oligomers or complexes formed between Al and natural organic matter or polymeric colloidal materials. PAC exhibited the least concentration for each kind of residual aluminum species as well as their percentage in total residual aluminum, followed by AlCl(3) and Al(2)(SO(4))(3) (in increasing order). Moreover, PAC could effectively reduce the concentration of dissolved monomeric Al and its residual aluminum ratio was the least among the three coagulants and varied little at an initial pH between 7.0 and 9.0.

The Association Between Two Polymorphisms of ENOS and Breast Cancer Risk: a Meta-analysis

Breast Cancer Research and Treatment. Nov, 2010  |  Pubmed ID: 20204503

Breast cancer is one of the most common malignant tumors worldwide. Endothelial nitric oxide synthase (eNOS) plays a key role in breast cancer development. The associations between the two eNOS polymorphisms (E298D rs1799983, -786T>C rs2070744) and breast cancer risk are inconclusive. A meta-analysis was performed in this study. By searching Medline, ISI Web of Knowledge, ScienceDirect, EBSCO, CNKI, and SinoMed database, six case-control studies were collected for the eNOS E298D polymorphism (3,038 cases and 2,508 controls) and three case-control studies were eligible for the eNOS -786T>C polymorphism. Crude ORs with 95% CIs were used to assess the strength of association between the two eNOS polymorphisms and breast cancer risk. The pooled ORs were performed for codominant model, dominant model, and recessive model, respectively. Overall, significantly decreased risk was observed for E298D (for EE vs. DD: OR = 0.74, 95% CI = 0.59-0.94; for ED vs. DD: OR = 0.78, 95% CI = 0.61-0.98; for dominant model: OR = 0.77, 95% CI = 0.61-0.96) and -786T > C (for TT vs. CC: OR = 0.60, 95% CI = 0.42-0.86; for dominant model: OR = 0.66, 95% CI = 0.47-0.94). In the subgroup analysis by ethnicity, significant decreased risks were found for E298D (for EE vs. DD: OR = 0.75, 95% CI = 0.56-0.99) and -786T>C (for TT vs. CC: OR = 0.53, 95% CI = 0.35-0.81; for dominant model: OR = 0.61, 95% CI = 0.41-0.91; for recessive model: OR = 0.70, 95% CI = 0.55-0.91) among Caucasians; significant decreased risks were observed for E298D (for ED vs. DD: OR = 0.12, 95% CI = 0.02-0.96; for dominant model: OR = 0.13, 95% CI = 0.02-1.00) among Asians. In conclusion, this meta-analysis suggests that both eNOS E298D and -786T>C polymorphisms are associated with reduced breast cancer risk.

No Association Between CYP17 T-34C Polymorphism and Breast Cancer Risk: a Meta-analysis Involving 58,814 Subjects

Breast Cancer Research and Treatment. Jul, 2010  |  Pubmed ID: 20013047

Breast cancer is one of the most common malignant tumors worldwide. To date, many articles have evaluated the association between Cytochrome P450c17 (CYP17) T-34C polymorphism and breast cancer risk. However, the results remain inconclusive. In order to derive a more precise estimation of the association, a meta-analysis was performed in this study. By searching Medline, ISI Web of Knowledge, Cochrane, ScienceDirect, EBSCO, CNKI, and SinoMed databases, 43 studies including 26,008 cases and 32,806 controls were collected for CYP17 T-34C polymorphism. Crude ORs with 95% CIs were used to assess the strength of association between CYP17 T-34C polymorphism and breast cancer risk. The pooled ORs were performed for codominant model, dominant model, and recessive model, respectively. Overall, no significant associations between CYP17 T-34C polymorphism and breast cancer susceptibility were found for TT versus CC (OR = 0.96; 95% CI: 0.89-1.05), TC versus CC (OR = 0.97; 95% CI: 0.89-1.06), TT + TC versus CC (OR = 0.97; 95% CI: 0.89-1.05) and TT versus TC + CC (OR = 0.98; 95% CI: 0.93-1.03). In the stratified analysis by ethnicity, menopausal status, and sources of controls, significant associations were still not detected in all genetic models. In conclusion, this meta-analysis strongly suggests that CYP17 T-34C polymorphism is not associated with breast cancer risk.

Microsatellite Markers for the Cushion Rock Jasmine, Androsace Tapete (Primulaceae), a Species Endemic to the Qinghai-Tibetan Plateau

American Journal of Botany. Oct, 2010  |  Pubmed ID: 21616790

• Premise of the study: Microsatellite markers were developed in an alpine plant endemic to the Qinghai-Tibetan Plateau, Androsace tapete, to investigate its spatial genetic structure, gene flow, and mating patterns. • Methods and Results: Using the combined biotin capture method, 16 microsatellite primer sets were isolated and characterized. Fifteen of these markers showed polymorphism, and the number of alleles per locus ranged from three to 13 across 56 individuals from six Tibetan populations. • Conclusions: These markers provide a useful tool to investigate the spatial genetic structure, gene flow, and mating system of A. tapete.

Adult Muscle 'stem' Cells Can Be Sustained in Culture As Free-floating Myospheres

Experimental Cell Research. Jul, 2010  |  Pubmed ID: 20381487

The effectiveness of cell-based therapy to treat muscle disease has been hampered by difficulties in isolating, maintaining and propagating the stem cells that are needed for treatment. Here we report the isolation of muscle-derived stem cells from both young and old mice and their propagation over extended periods of time in culture as "free-floating" myospheres. Analysis of these sphere-forming cells showed that they express stem cell antigen-1 (Sca-1), beta1 integrin (CD29), Thy-1 (CD90), and CD34, but did not express CD45, CD31, or myogenic markers (Pax7, Myf5, and MyoD). We found that cells derived from myospheres and then grown adherently (MDACs) behaved similar to primary myoblasts, in that these cells expressed myogenic markers and were able to easily form multinucleated myotubes. Unlike the parental myospheres but analogous to primary myoblasts, MDACs expressed Pax7, Myf5, and MyoD, indicating that the parent myosphere cells were a more primitive type of cell. In support of this we demonstrated that myospheres were also able to differentiate into adipogenic and osteogenic cells in culture, as well as being able to contribute to injured muscle in vivo. In summary, we report that primitive adult muscle stem cells can be easily isolated and sustained in culture as myospheres.

The Position of Gnetales Among Seed Plants: Overcoming Pitfalls of Chloroplast Phylogenomics

Molecular Biology and Evolution. Dec, 2010  |  Pubmed ID: 20601411

The phylogenetic position of Gnetales is one of the most contentious issues in the seed plant systematics. To elucidate the Gnetales position, an improved amino acid substitution matrix was estimated based on 64 chloroplast (cp) genomes and was applied to cp genome data including all three lineages of Gnetales in maximum likelihood analyses of proteins. Although the initial analysis strongly supported the sister relation of Gnetales with Cryptomeria (Cupressophyta or non-Pinaceae conifers) (the "Gnecup" hypothesis), the support seems to be caused by a long-branch attraction (LBA) artifact. Indeed, by removing fastest evolving proteins that are most likely associated with the LBA, the support drastically declined. Furthermore, another analysis of partial genome data with dense taxon sampling of conifers showed that, in psbC, rpl2, and rps7 proteins, there are many parallel amino acid substitutions between the lineages leading to Gnetales and to Cryptomeria, and by further excluding these three genes, the sister relation of Gnetales with Pinaceae (the "Gnepine" hypothesis) became supported. Overall, our analyses indicate that the LBA and parallel substitutions cause a seriously biased inference of phylogenetic position of Gnetales with the cp genome data.

Nonadditive Empirical Force Fields for Short-chain Linear Alcohols: Methanol to Butanol. Hydration Free Energetics and Kirkwood-Buff Analysis Using Charge Equilibration Models

The Journal of Physical Chemistry. B. Sep, 2010  |  Pubmed ID: 20687517

Building upon the nonadditive electrostatic force field for alcohols based on the CHARMM charge equilibration (CHEQ) formalism, we introduce atom-pair specific solute-solvent Lennard-Jones (LJ) parameters for alcohol-water interaction force fields targeting improved agreement with experimental hydration free energies of a series of small molecule linear alcohols as well as ab initio water-alcohol geometries and energetics. We consider short-chain, linear alcohols from methanol to butanol as they are canonical small-molecule organic model compounds to represent the hydroxyl chemical functionality for parametrizing biomolecular force fields for proteins. We discuss molecular dynamics simulations of dilute aqueous solutions of methanol and ethanol in TIP4P-FQ water, with particular discussion of solution densities, structure defined in radial distribution functions, electrostatic properties (dipole moment distributions), hydrogen bonding patterns of water, as well as a Kirkwood-Buff (KB) integral analysis. Calculation of the latter provides an assessment of how well classical force fields parametrized to at least semiquantitatively match experimental hydration free energies capture the microscopic structures of dilute alcohol solutions; the latter translate into macroscopic thermodynamic properties through the application of KB analysis. We find that the CHEQ alcohol force fields of this work semiquantitatively match experimental KB integrals for methanol and ethanol mole fractions of 0.1 and 0.2. The force field combination qualitatively captures the concentration dependence of the alcohol-alcohol and water-water KB integrals, but due to inadequacies in the representation of the microscopic structures in such systems (which cannot be parametrized in any systematic fashion), a priori quantitative description of alcohol-water KB integrals remains elusive.

Neural Endoscopic Assisted Micro-invasive Management of Chiari I Malformation

Chinese Medical Journal. Jul, 2010  |  Pubmed ID: 20819571

In order to make posterior fossa decompression for the management of Chiari I malformation simple and less invasive while using direct visualization, a novel solely endoscopic procedure has been employed for the decompression of Chiari malformation type I. The objective of this study was to present neural endoscopic posterior fossa decompression and atlas laminectomy for Chiari type I patients.

Using Activated Carbon Nanoparticles to Decrease the Genotoxicity and Teratogenicity of Anticancer Therapeutic Agents

Journal of Nanoscience and Nanotechnology. Dec, 2010  |  Pubmed ID: 21121372

One of the key obstacles against the success in cancer chemotherapy is the toxic and side effects of the chemotherapeutic agents. The avoidance of these toxic and side effects will greatly improve the therapeutic effects of anticancer drugs while decrease the pains of the patients. Here we show that activated carbon nanoparticles (ACNP), one of the mesoporous nanoparticles, can decrease the genotoxicity and teratogenicity of mitomycin C (MMC). To study the effects of ACNP on genotoxicity and teratogenicity of MMC, methods of PCE micronucleus test, Chinese hamster lung cell chromosome aberration experiment and rat teratogenicity were employed to observe the differences in genotoxicity and teratogenicity between ACNP-adsorbed MMC (ACNP-MMC) and free MMC. Results demonstrated that free MMC 0.16-5.0 microg/kg significantly increased the positive rate of PCE micronucleus test, the chromosome aberration rate and rat teratogenecity, but ACNP-MMC did not increased these heredity and reproduction toxicological indexes in a dose range of 0.625-10.0 microg/kg. From these results, it can be concluded that ACNP-MMC have significant effects to decrease the genotoxicity and teratogenicity effects of MMC. These results will have a considerable impact on the strategy of anticancer chemotherapy.

DbDEMC: a Database of Differentially Expressed MiRNAs in Human Cancers

BMC Genomics. 2010  |  Pubmed ID: 21143814

MicroRNAs (miRNAs) are small noncoding RNAs about 22 nt long that negatively regulate gene expression at the post-transcriptional level. Their key effects on various biological processes, e.g., embryonic development, cell division, differentiation and apoptosis, are widely recognized. Evidence suggests that aberrant expression of miRNAs may contribute to many types of human diseases, including cancer. Here we present a database of differentially expressed miRNAs in human cancers (dbDEMC), to explore aberrantly expressed miRNAs among different cancers.

[The Preliminary Study of Using Neuro-endoscope Assisted Atlanto Occipital Decompression to Treat Chiari Type I Malformation with Syringomyelia]

Zhonghua Wai Ke Za Zhi [Chinese Journal of Surgery]. Oct, 2010  |  Pubmed ID: 21176650

To explore and evaluate the methodology of neuro-endoscope assisted atlanto occipital decompression in Chiari type I malformation with syringomyelia.

[Estimation of the Physical and Mechanical Properties of Neosinocalamus Affinins Using Near Infrared Spectroscopy]

Guang Pu Xue Yu Guang Pu Fen Xi = Guang Pu. Mar, 2011  |  Pubmed ID: 21595210

Near infrared spectroscopy was applied to rapidly predict density, modulus of rupture and tensile strength parallel to grain of neosinocalamus affinins. Backward interval partial least squares (BiPLS) was used to find the most informative spectrum ranges, and build models based on raw spectra and pretreated spectra, including first derivative spectra, second derivative spectra, Savitzky-Golay smoothing spectra and standard normalized variate spectra. And partial least squares (PLS) models were also developed in the whole wavelength range 350-2500 nm. The results show that compared with PLS models, BiPLS could effectively find the optimal spectrum regions and improve the predictive ability of models. The optimal models of density, modulus of rupture and tensile strength parallel to grain were obtained through BiPLS method that separated the whole spectra pretreated by standard normalized variate, second derivative and first derivative respectively into 20, 30 and 20 intervals. And the prediction models of density, modulus of rupture and tensile strength parallel to grain had correlation coefficient (r) 0.85, 0.88 and 0.88, as well as root mean standard error of prediction (RMSEP) 0.0524, 0.0185 and 0.0292, respectively. The relation between NIR predicted values and actual values was good in all cases. Therefore, the experimental results demonstrated that NIR spectroscopy was promising for predicting the physical and mechanical properties of neosinocalamus affinins.

Population Genetic Structure and Phylogeographical Pattern of Rice Grasshopper, Oxya Hyla Intricata, Across Southeast Asia

Genetica. Apr, 2011  |  Pubmed ID: 21505761

The rice grasshopper, Oxya hyla intricata, is a rice pest in Southeast Asia. In this study, population genetic diversity and structure of this Oxya species was examined using both DNA sequences and AFLP technology. The samples of 12 populations were collected from four Southeast Asian countries, among which 175 individuals were analysed using mitochondrial DNA cytochrome c oxidase subunit I (COI) sequences, and 232 individuals were examined using amplified fragment length polymorphisms (AFLP) to test whether the phylogeographical pattern and population genetics of this species are related to past geological events and/or climatic oscillations. No obvious trend of genetic diversity was found along a latitude/longitude gradient among different geographical groups. Phylogenetic analysis indicated three deep monophyletic clades that approximately correspond to three geographical regions separated by high mountains and a deep strait, and TCS analysis also revealed three disconnected networks, suggesting that spatial and temporal separations by vicariance, which were also supported by AMOVA as a source of the molecular variance presented among groups. Gene flow analysis showed that there had been frequent historical gene flow among local populations in different regions, but the networks exhibited no shared haplotype among populations. In conclusion, the past geological events and climatic fluctuations are the most important factor on the phylogeographical structure and genetic patterns of O. hyla intricata in Southeast Asia. Habitat, vegetation, and anthropogenic effect may also contribute to gene flow and introgression of this species. Moreover, temperature, abundant rainfall and a diversity of graminaceous species are beneficial for the migration of O. hyla intricata. High haplotype diversity, deep phylogenetic division, negative Fu's F (s) values and unimodal and multimodal distribution shapes all suggest a complicated demographic expansion pattern of these O. hyla intricata populations, which might have been caused by climatic oscillations during glacial periods in the Quaternary.

Genes Under Positive Selection in Mycobacterium Tuberculosis

Computational Biology and Chemistry. Oct, 2011  |  Pubmed ID: 22000803

We employed an evolutionary genomics approach to detect genes under lineage-specific positive selection for the two closely related Mycobacterium tuberculosis strains, the virulent H37Rv and the avirulent H37Ra, with the clinical isolate CDC1551 as the outgroup. We found six H37Rv-specific and six H37Ra-specific positively selected genes, among which the former comprised a flavoprotein, a RNA polymerase sigma factor SigM, two PPE family proteins, as well as two hypothetical proteins, while the latter consisted of a dehydrogenase, a (3R)-hydroxyacyl-ACP dehydratase subunit HadA, a PPE family protein, and three PE-PGRS family proteins. Obviously, the PE/PPE/PE-PGRS family proteins were the main targets of positive selection. The functional discussion of our findings implied that those positively selected genes were highly involved in antigen variations and immune evasions of Mycobacterium tuberculosis.

[Preliminary Application of 3.0 T Intraoperative Magnetic Resonance Imaging Neuronavigation System in China]

Zhonghua Wai Ke Za Zhi [Chinese Journal of Surgery]. Aug, 2011  |  Pubmed ID: 22168929

To report the preliminary experience in clinical application of 3.0 T intraoperative magnetic resonance imaging (iMRI) neuronavigation system in China.

Analysis of Embryo, Cytoplasmic and Maternal Genetic Correlations for Seven Essential Amino Acids in Rapeseed Meal (Brassica Napus L.)

Journal of Genetics. Apr, 2011  |  Pubmed ID: 21677390

Genetic correlations of nutrient quality traits including lysine, methionine, leucine, isoleucine, phenylalanine, valine and threonine contents in rapeseed meal were analysed by the genetic model for quantitative traits of diploid plants using a diallel design with nine parents of Brassica napus L. These results indicated that the genetic correlations of embryo, cytoplasm and/or maternal plant havemade different contribution to total genetic correlations of most pairwise nutrient quality traits. The genetic correlations among the amino acids in rapeseed meal were simultaneously controlled by genetic main correlations and genotype x environment (GE) interaction correlations, especially for the maternal dominance correlations. Most components of genetic main correlations and GE interaction correlations for the pairwise traits studied were significantly positive. Some of the pairwise traits had negative genetic correlations, especially between valine and other amino acid contents. Indirect selection for improving the quality traits of rapeseed meal could be expected in rape breeding according to the magnitude and direction of genetic correlation components.

[Study on the Wood Grading by Near Infrared Spectroscopy]

Guang Pu Xue Yu Guang Pu Fen Xi = Guang Pu. Apr, 2011  |  Pubmed ID: 21714241

The present paper discussed wood grading according to modulus of rupture (MOR) by near infrared (NIR) spectroscopy. The calibration model was built between MOR of wood and NIR data in the range of 1 000-1 400 nm with partial least square regression (PLS). The correlation coefficient (r) was 0.89 and the standard error of calibration (SEC) was 6.30 MPa. The MOR of 35 unknown samples was predicted using the model. Wood samples were graded according to their predicted values and true values. The rate of right prediction for A, B and C was 75.0%, 91.3% and 80.0% respectively, and the whole rate of right prediction was 88.6%. The result has proved that near infrared spectroscopy is a fast method for the determination of wood grade in the small clear samples.

Why Does the Giant Panda Eat Bamboo? A Comparative Analysis of Appetite-reward-related Genes Among Mammals

PloS One. 2011  |  Pubmed ID: 21818345

The giant panda has an interesting bamboo diet unlike the other species in the order of Carnivora. The umami taste receptor gene T1R1 has been identified as a pseudogene during its genome sequencing project and confirmed using a different giant panda sample. The estimated mutation time for this gene is about 4.2 Myr. Such mutation coincided with the giant panda's dietary change and also reinforced its herbivorous life style. However, as this gene is preserved in herbivores such as cow and horse, we need to look for other reasons behind the giant panda's diet switch.

Development and Characterization of Polymorphic Microsatellite Primers in Reaumuria Soongorica (Tamaricaceae)

American Journal of Botany. Aug, 2011  |  Pubmed ID: 21821585

• Premise of the study: Polymorphic microsatellite markers were developed in Reaumuria soongorica, a desert shrub occurring widely in western China, to investigate its genetic diversity and population genetic structure. • Methods and Results: Using the combined biotin capture technique, 10 novel polymorphic microsatellite loci primer sets were isolated and characterized in 90 individuals from six populations of R. soongorica. Five to 14 alleles per locus were identified for these microsatellites. Observed and expected heterozygosities ranged from 0.132 to 0.593, and 0.217 to 0.803, respectively. • Conclusions: These microsatellite markers provide a useful tool to assess the genetic variation and population structure of R. soongorica.

Highly Efficient Production of Soluble Proteins from Insoluble Inclusion Bodies by a Two-step-denaturing and Refolding Method

PloS One. 2011  |  Pubmed ID: 21829569

The production of recombinant proteins in a large scale is important for protein functional and structural studies, particularly by using Escherichia coli over-expression systems; however, approximate 70% of recombinant proteins are over-expressed as insoluble inclusion bodies. Here we presented an efficient method for generating soluble proteins from inclusion bodies by using two steps of denaturation and one step of refolding. We first demonstrated the advantages of this method over a conventional procedure with one denaturation step and one refolding step using three proteins with different folding properties. The refolded proteins were found to be active using in vitro tests and a bioassay. We then tested the general applicability of this method by analyzing 88 proteins from human and other organisms, all of which were expressed as inclusion bodies. We found that about 76% of these proteins were refolded with an average of >75% yield of soluble proteins. This "two-step-denaturing and refolding" (2DR) method is simple, highly efficient and generally applicable; it can be utilized to obtain active recombinant proteins for both basic research and industrial purposes.

Self-organizing Map of Gene Regulatory Networks for Cell Phenotypes During Reprogramming

Computational Biology and Chemistry. Aug, 2011  |  Pubmed ID: 21864790

The induced pluripotent cells (iPSCs) are derived from somatic cells by reprogramming their genetic profiles. Such a process requires coordinated dynamic expression of hundreds of genes and proteins. As both deterministic and stochastic elements control the reprogramming process, it is not easy to have a way to reflect the status of gene regulatory network in those reprogramming cells. In this study, we applied self-organizing maps (SOMs) on those complex gene expression data from different pluripotent cells, including partially reprogrammed and fully reprogrammed induced pluripotent cells (iPSCs), embryonic stem cells (ESCs), and adult stem cells came from different tissues. We showed that our SOMs have good correlation with the previously reported PluriNet of stem cells and they are pictorial diagrams which can reflect the intrinsic status of cells.

Solvation Properties of N-acetyl-β-glucosamine: Molecular Dynamics Study Incorporating Electrostatic Polarization

Journal of Computational Chemistry. Dec, 2011  |  Pubmed ID: 21898464

N-Acetyl-β-glucosamine (NAG) is an important moiety of glycoproteins and is involved in many biological functions. However, conformational and dynamical properties of NAG molecules in aqueous solution, the most common biological environment, remain ambiguous due to limitations of experimental methods. Increasing efforts are made to probe structural properties of NAG and NAG-containing macromolecules, like peptidoglycans and polymeric chitin, at the atomic level using molecular dynamics simulations. In this work, we develop a polarizable carbohydrate force field for NAG and contrast simulation results of various properties using this novel force field and an analogous nonpolarizable (fixed charge) model. Aqueous solutions of NAG and its oligomers are investigated; we explore conformational properties (rotatable bond geometry), electrostatic properties (dipole moment distribution), dynamical properties (self-diffusion coefficient), hydrogen bonding (water bridge structure and dynamics), and free energy of hydration. The fixed-charge carbohydrate force field exhibits deviations from the gas phase relative rotation energy of exocyclic hydroxymethyl side chain and of chair/boat ring distortion. The polarizable force field predicts conformational properties in agreement with corresponding first-principles results. NAG-water hydrogen bonding pattern is studied through radial distribution functions (RDFs) and correlation functions. Intermolecular hydrogen bonding between solute and solvent is found to stabilize NAG solution structures while intramolecular hydrogen bonds define glycosidic linkage geometry of NAG oligomers. The electrostatic component of hydration free energy is highly dependent on force field atomic partial charges, influencing a more favorable free energy of hydration in the fixed-charge model compared to the polarizable model.

Chemical Irritation of the Prostate Sensitizes P(2)X(3) Receptor-mediated Responses in Rat Dorsal Root Ganglion Neurons

Neurourology and Urodynamics. Apr, 2011  |  Pubmed ID: 21254200

P(2)X(3) (ATP-gated receptors) in nociceptive neurons of dorsal root ganglion (DRG) participate in transmission of pain signals from the periphery to the spinal cord. However, the role of P(2)X(3) receptors in chronic prostate pain and continued intractable pain remains unclear.

Phase-transfer Energetics of Small-molecule Alcohols Across the Water-hexane Interface: Molecular Dynamics Simulations Using Charge Equilibration Models

Journal of Molecular Graphics & Modelling. Apr, 2011  |  Pubmed ID: 21414823

We study the water-hexane interface using molecular dynamics (MD) and polarizable charge equilibration (CHEQ) force fields. Bulk densities for TIP4P-FQ water and hexane, 1.0086±0.0002 and 0.6378±0.0001 g/cm(3), demonstrate excellent agreement with experiment. Interfacial width and interfacial tension are consistent with previously reported values. The in-plane component of the dielectric permittivity (ɛ(||)) for water is shown to decrease from 81.7±0.04 to unity, transitioning longitudinally from bulk water to bulk hexane. ɛ(||) for hexane reaches a maximum in the interface, but this term represents only a small contribution to the total dielectric constant (as expected for a non-polar species). Structurally, net orientations of the molecules arise in the interfacial region such that hexane lies slightly parallel to the interface and water reorients to maximize hydrogen bonding. Interfacial potentials due to contributions of the water and hexane are calculated to be -567.9±0.13 and 198.7±0.01 mV, respectively, giving rise to a total potential in agreement with the range of values reported from previous simulations of similar systems. Potentials of mean force (PMF) calculated for methanol, ethanol, and 1-propanol for the transfer from water to hexane indicate an interfacial free energy minimum, corresponding to the amphiphilic nature of the molecules. The magnitudes of transfer free energies were further characterized from the solvation free energies of alcohols in water and hexane using thermodynamic integration. This analysis shows that solvation free energies for alcohols in hexane are 0.2-0.3 kcal/mol too unfavorable, whereas solvation of alcohols in water is approximately 1 kcal/mol too favorable. For the pure hexane-water interfacial simulations, we observe a monotonic decrease of the water dipole moment to near-vacuum values. This suggests that the electrostatic component of the desolvation free energy is not as severe for polarizable models than for fixed-charge force fields. The implications of such behavior pertain to the modeling of polar and charged solutes in lipidic environments.

Determination of Asperosaponin VI in Dog Plasma by High-performance Liquid Chromatography-tandem Mass Spectrometry and Its Application to a Pilot Pharmacokinetic Study

Biomedical Chromatography : BMC. Jan, 2012  |  Pubmed ID: 21465503

A sensitive and rapid liquid chromatography-tandem mass spectrometry (LC-MS/MS) method has been developed and validated for the determination of asperosaponin VI in beagle dog plasma using glycyrrhizic acid as the internal standard (IS). Plasma samples were simply pretreated with methanol for deproteinization. Chromatographic separation was performed on a Hedera ODS-2 column using mobile phase of methanol-10 mm ammonium acetate buffer solution containing 0.05% acetic acid (71:29, v/v) at a flow rate of 0.38 mL/min. Asperosaponin VI and the IS were eluted at 2.8 and 1.9 min, respectively, ionized in negative ion mode, and then detected by multiple reaction monitoring. The detection used the transitions of the deprotonated molecules at m/z 927.5 → 603.4 for asperosaponin VI and m/z 821.4 → 645.4 for glycyrrhizic acid (IS). The assay was linear over the concentration range of 0.15-700 ng/mL and was successfully applied to a pilot pharmacokinetic study in beagle dogs.

Enhancing Intrinsic Growth Capacity Promotes Adult CNS Regeneration

Journal of the Neurological Sciences. Jan, 2012  |  Pubmed ID: 21924742

In the adult mammalian central nervous system (CNS), the axons do not spontaneously regenerate after injury due to the inhibitory extrinsic environment and a diminished intrinsic regenerative capability. Many previous studies focus largely on characterizing the hostile growth inhibitory molecules in the CNS. In fact, blocking such inhibitory activities by either genetic or pharmacological approaches only allows limited sprouting, and majority of the adult neurons fail to regenerate their axons even provided with permissive substrates. Upon the neural circuits established during development, the intrinsic neuronal growth activity is gradually repressed. Little is known to the mechanisms for transition from the robust growth mode of the immature neurons to the poor growth mode of the mature neurons and the way to reactivate the intrinsic growth capacity after injury. The primary sensory neurons with cell bodies in the dorsal root ganglion (DRG) provide a useful model to develop strategies to enhance the intrinsic growth capacity of neurons. The centrally projecting axons in the adult spinal cord do not regenerate, while the peripheral branches regenerate robustly after injury. Regeneration of the central branches can be significantly enhanced after a prior peripheral branch injury, which is defined as conditioning lesion. We reviewed the mode of conditioning lesion reactivating the intrinsic growth program. Importantly, we summarized the intrinsic neuronal determinants for neurite growth such as cAMP, PTEN/mTOR, APC-Cdh1, KLF4, etc., the mechanisms underlying development-dependent decline of CNS neurons growth ability, and procedures to enhance the intrinsic growth potential.

CTCF and Cohesin Cooperatively Mediate the Cell-type Specific Interchromatin Interaction Between Bcl11b and Arhgap6 Loci

Molecular and Cellular Biochemistry. Jan, 2012  |  Pubmed ID: 21948239

CCCTC-binding factor (CTCF) is a master organizer of genome spatial organization and plays an important role in mediating extensive chromatin interactions. Circular chromosome conformation capture (4C) is a high-throughput approach that allows genome-wide screening for unknown potential interaction partners. Using a conserved CTCF binding site on the Bcl11b locus as bait, an interaction partner at the Arhgap6 locus on a different chromosome was identified by 4C. Additional experiments verified that the interchromatin interaction between the Bcl11b and Arhgap6 loci was cell-type specific, which was cooperatively mediated by CTCF and cohesin. Functional analysis showed that the interchromatin interaction partners were repressing regulatory elements. These results indicate that interaction chromatin loops regulate the expression of the relevant genes.

The Complete Mitochondrial Genome of the Butterfly Apatura Metis (Lepidoptera: Nymphalidae)

Molecular Biology Reports. Feb, 2012  |  Pubmed ID: 22311013

As an important pest in the Slender Leaved Willow (Salix alba), Apatura metis is called Freyer's purple emperor, and its mitochondrial genome is 15,236 bp long. The encoded genes for 22 tRNA genes, two ribosomal RNA (rrnL and rrnS) genes, and 13 protein-coding genes (PCGs), and a control region in the A. metis mitochondria are highly homologous to other lepidopteran species. The mitochondrial genome of A. metis is biased toward a high A + T content (A + T = 80.5%). All protein-coding genes, except for COI begins with the CGA codon as observed in other lepidopterans, start with a typical ATN initiation codon. All tRNAs show the classic clover-leaf structure, except that the dihydrouridine (DHU) arm of tRNA ( Ser(AGN)) forms a simple loop. The A. metis A + T-rich region contains some conserved structures including a structure combining the motif 'ATAGA' and 19 bp poly (T) stretch, which is similar to those found in other lepidopteran mitogenomes. The phylogenetic analyses of lepidopterans based on mitogenomes sequences demonstrate that each of the six superfamilies is monophyletic, and the relationship among them is (((Noctuoidea + (Geometroidea + Bombycoidea)) + Pyraloidea) + Papilionoidea) + Tortricoidea. In Papilionoidea group, our conclusion argues that ((Lycaenidae + Pieridae) + Nymphalidae) + Papilionidae.