In JoVE (1)

Other Publications (59)

Articles by Tianming Wang in JoVE

Other articles by Tianming Wang on PubMed

[Landscape Ecological Evaluation of Fenglin Nature Reverse: Quantification and Interpretation]

Ying Yong Sheng Tai Xue Bao = The Journal of Applied Ecology. May, 2005  |  Pubmed ID: 16110653

Fenglin National Class Nature Reserve is the largest well-saved virginal Korean pine (Pinus koraiensis) forest area and a precious species gene bank in China. In this study, the indexes diversity, naturalness, representativity, rarity, area suitability, stability, and anthropogenic interference were selected to establish a ranking ecological evaluation system to estimate the ecological condition of the Reserve. The value of each index was determined by the evaluation system, and the weight percentage was decided by Analytical Hierarchy Process (AHP). In the Reserve, there were 568 higher plant species belonging to 113 families and 220 higher animal species, with score 3 of species diversity. The zonal "climax" vegetation type broad-leaved Korean pine forest and the intrazonal community type spruce-fir forest constituted the principal part of the Reserve forest, which was the epitome of the virgin broad-leaved Korean pine forest in Lesser Xing'an Mountains, with representativity score 3. During the past 20-30 years, the natural habitat in the Reserve was quite good, and secondary succession was obtained effective control with few natural or anthropogenic disturbance, with score 4 of naturalness and anthropogenic interference. There were a lot of ancient species of the tertiary period, such as Pinus koraiensis, Fraxinus mandsurica, Juglans mandshurica, Pellodendron amurense, Tilia amurensis and Acer mono, and Pinus koraiensis was listed as one of severe danger species by the FAO of UN, with rarity score 4. The Reserve covered an area of 18165 hm2, with an enough size to maintain the structure and function of the ecosystem. Accordingly, its area suitability score was 4. Broad-leaved Korean pine forest was the most typical and stable vegetation type in the Reserve, and thus, its stability score was 4. Finally, the composite evaluation index (CEI) was figured out as 0.87, showing that the ecological quality of the Reserve was very good, and the protection value was quite high. In conclusion, the present area, structure, and management of the Reserve could satisfy the requirement of sustainable development.

On Graphical and Numerical Representation of Protein Sequences

Journal of Biomolecular Structure & Dynamics. Apr, 2006  |  Pubmed ID: 16494503

A new approach using a 3-D Cartesian coordinate system to represent protein sequences has been derived. By the 3-D Graphical representation we make a comparison of sequences belonging to nine different proteins.

A Novel 2D Graphical Representation of DNA Sequences and Its Application

Journal of Molecular Graphics & Modelling. Nov, 2006  |  Pubmed ID: 16515870

In this paper, we introduce a novel 2D graphical representation of DNA sequences, the W-curve, which is embedded in two unit circles. We associate the W-curves with the classifications of the nucleotides according to their chemical properties. Then we obtain an 8-component vector with entries being the average sums of the abscissa and y-axis of A+C and T+G (A+T and C+G, A+G and T+C), respectively. The introduced vector results in simpler characterizations and comparisons of DNA sequences. The construction of the W-curve has some important advantages: (1) it avoids loss of information and the W-curve standing for DNA doesn't overlap or intersect itself; (2) the space the W-curve occupied is very small, just two unit circles. The utility of the approach can be illustrated by the examination of similarities/dissimilarities among the coding sequences of the first exon of beta-globin gene of eleven different species in Table 1.

A Weighted Measure for the Similarity Analysis of DNA Sequences

Journal of Molecular Modeling. Sep, 2006  |  Pubmed ID: 16568272

Here we propose a weighted measure for the similarity analysis of DNA sequences. It is based on LZ complexity and (0,1) characteristic sequences of DNA sequences. This weighted measure enables biologists to extract similarity information from biological sequences according to their requirements. For example, by this weighted measure, one can obtain either the full similarity information or a similarity analysis from a given biological aspect. Moreover, the length of DNA sequence is not problematic. The application of the weighted measure to the similarity analysis of beta-globin genes from nine species shows its flexibility.

2D Representation of Protein Secondary Structure Sequences and Its Applications

Journal of Computational Chemistry. Aug, 2006  |  Pubmed ID: 16721724

In terms of the classification of the protein secondary structures, we propose a 2D representation of protein secondary structure sequences. The representation are used to display, analyze, and compare the secondary structure sequences. Based on this representation, we assign the structural class to the protein, and verify the advantage or disadvantage of the methods of predicted protein second structure.

PNN-curve: a New 2D Graphical Representation of DNA Sequences and Its Application

Journal of Theoretical Biology. Dec, 2006  |  Pubmed ID: 16945387

We introduce a novel 2D graphical representation of DNA sequences based on the pairs of the neighboring nucleotides (PNNs). Then we get the PNNs' distributions and obtain a y-M. The construction of the PNN-curve has some important advantages (1) It avoids loss of information and the PNN-curve standing for DNA sequences does not overlap or intersect with itself. (2) The novel 2D representation is more sensitive. The utility of this method can be illustrated by the examination of similarities/dissimilarities among the coding sequences of the first exon of beta-globin gene of eleven different species in Table 2.

Protein-based Phylogenetic Analysis by Using Hydropathy Profile of Amino Acids

FEBS Letters. Oct, 2006  |  Pubmed ID: 16979630

So far, various approaches for phylogenetic analysis have been developed. Almost all of them put stress on analyzing nucleic acid sequences or protein primary structures. In this paper, we take the physicochemical properties of amino acids into account and introduce the hydropathy profile of amino acids into phylogenetic analysis. We find that this introduction is effectual and our method may be used to complement phylogenetic analysis.

A Method for Rapid Similarity Analysis of RNA Secondary Structures

BMC Bioinformatics. Nov, 2006  |  Pubmed ID: 17090331

Owing to the rapid expansion of RNA structure databases in recent years, efficient methods for structure comparison are in demand for function prediction and evolutionary analysis. Usually, the similarity of RNA secondary structures is evaluated based on tree models and dynamic programming algorithms. We present here a new method for the similarity analysis of RNA secondary structures.

A Simple Method for Protein Structural Classification

Journal of Molecular Graphics & Modelling. Mar, 2007  |  Pubmed ID: 16997588

Since the concept of structural classes of proteins was proposed, the problem of protein classification has been tackled by many groups. Most of their classification criteria are based only on the helix/strand contents of proteins. In this paper, we proposed a method for protein structural classification based on their secondary structure sequences. It is a classification scheme that can confirm existing classifications. Here a mathematical model is constructed to describe protein secondary structure sequences, in which each protein secondary structure sequence corresponds to a transition probability matrix that characterizes and differentiates protein structure numerically. Its application to a set of real data has indicated that our method can classify protein structures correctly. The final classification result is shown schematically. So it is visual to observe the structural classifications, which is different from traditional methods.

A Solid-phase Extraction Method for High-performance Liquid Chromatographic Determination of Salvianolic Acid B in Rabbit Plasma: Application to Pharmacokinetic Study

Biomedical Chromatography : BMC. Feb, 2007  |  Pubmed ID: 17221907

A sensitive solid-phase extraction/high-performance liquid chromatographic method with ultraviolet detection was established for the analysis of salvianolic acid B in rabbit plasma. The analyte was separated on a reversed-phase column with trifluoroacetic acid-methanol-acetonitrile (70:10:20, v/v/v) as mobile phase at a flow rate of 1 mL/min, and ultraviolet detection at 315 nm. The calibration curve for salvianolic acid B was linear over the range 35-1400 microg/L with coefficients of correlation >0.999. The inter-day and intra-day precisions of analysis were <15%, and assay accuracy ranged from 95.3 to 109.1%. This method is suitable for determining salvianolic acid B in plasma and thus investigating the pharmacokinetics of salvianolic acid B.

Simultaneous Quantification of Three Alkaloids of Coptidis Rhizoma in Rat Urine by High-performance Liquid Chromatography: Application to Pharmacokinetic Study

Biopharmaceutics & Drug Disposition. Dec, 2007  |  Pubmed ID: 17891749

A high-performance liquid chromatographic method with ultraviolet detection was established and validated for quantification of three alkaloids (coptisine, palmatine and berberine) in rat urine. Following a single-step liquid-liquid extraction, the analytes were separated on a reversed-phase C(18) column with water-formic acid-triethylamine-methanol as the mobile phase at a flow rate of 1 ml/min. The linear ranges of the calibration curves were 1.6-160 ng/ml for all three alkaloids. The lower limit of quantification was 1.6 ng/ml for all three alkaloids. The within-batch accuracy was 90.4-108.3% for coptisine, 88.6-107.8% for berberine and 88.4-110.1% for palmatine. The between-batch accuracy was 99.3-100.3% for coptisine, 94.3-100.6% for berberine and 93.7-100.0% for palmatine. The within-batch and between-batch precisions were

Comparison of TOPS Strings Based on LZ Complexity

Journal of Theoretical Biology. Mar, 2008  |  Pubmed ID: 18166201

Topology of protein structure (TOPS) cartoons are simplified descriptions of structural topology of proteins in 2D. This is coarse level description of protein structure. The comparison of protein structures is very important for the study of protein functions, and for the analysis of possible evolutionary relationships. In this paper, we use LZ algorithm to compare TOPS strings.

Use of Linear Regression Model to Compare RNA Secondary Structures

Journal of Theoretical Biology. Aug, 2008  |  Pubmed ID: 18538347

With more and more ribonucleic acid (RNA) secondary structures accumulated, the need for comparing different RNA secondary structures often arises in function prediction and evolutionary analysis. Numerous efficient algorithms were developed for comparing different RNA secondary structures, but challenges remain. In this paper, six new models based on the linear regression model were proposed for the comparison of RNA secondary structures. The proposed models were tested on a mixed data, containing six secondary structures from RNase P RNAs, three secondary structures from SSU rRNA and five secondary structures from 16S ribosomal RNAs. The results have shown the effectiveness of the proposed models. Moreover, the time complexity of our models is favorable by comparing with that of the existing methods which solve the similar problem.

Markov Model Plus K-word Distributions: a Synergy That Produces Novel Statistical Measures for Sequence Comparison

Bioinformatics (Oxford, England). Oct, 2008  |  Pubmed ID: 18710871

Many proposed statistical measures can efficiently compare biological sequences to further infer their structures, functions and evolutionary information. They are related in spirit because all the ideas for sequence comparison try to use the information on the k-word distributions, Markov model or both. Motivated by adding k-word distributions to Markov model directly, we investigated two novel statistical measures for sequence comparison, called wre.k.r and S2.k.r.

Comparison Study on K-word Statistical Measures for Protein: from Sequence to 'sequence Space'

BMC Bioinformatics. Sep, 2008  |  Pubmed ID: 18811946

Many proposed statistical measures can efficiently compare protein sequence to further infer protein structure, function and evolutionary information. They share the same idea of using k-word frequencies of protein sequences. Given a protein sequence, the information on its related protein sequences hasn't been used for protein sequence comparison until now. This paper proposed a scheme to construct protein 'sequence space' which was associated with protein sequences related to the given protein, and the performances of statistical measures were compared when they explored the information on protein 'sequence space' or not. This paper also presented two statistical measures for protein: gre.k (generalized relative entropy) and gsm.k (gapped similarity measure).

Influence of Coptis Chinensis on Pharmacokinetics of Flavonoids After Oral Administration of Radix Scutellariae in Rats

Biopharmaceutics & Drug Disposition. Oct, 2009  |  Pubmed ID: 19688740

Radix Scutellariae (RS) and Coptis Chinensis (CC) are the most popular components in traditional Chinese medicine prescriptions. Flavonoids are the main effective ingredients in RS and berberine is the main effective ingredient in CC. The aim of this study was to determine the influence of CC on the pharmacokinetics of flavonoids following the administration of RS in rats and to investigate the effects of CC on the pharmacokinetic mechanism. Rats were administered RS or RS+CC by intragastric gavage (i.g.). Plasma concentrations of baicalin (baicalein 7-glucuronide) and wogonoside (wogonin 7-glucuronide) were measured by HPLC. Pharmacokinetic parameters were calculated from the plasma concentration time curve. The effect of CC on the metabolism of flavonoids in RS by rat intestinal flora was studied using rat fecal suspensions after ig administration of CC. The effect of berberine on the bi-directional transport of baicalein and baicalin was studied in Caco-2 monolayer models. The effect of CC on the metabolism of baicalein and baicalin by the liver was studied using rat liver microsomes after i.g. administration of CC. Compared to RS alone, RS+CC decreased AUC and C(max) of baicalin and wogonoside. CC decreased the hydrolyzation of baicalin and wogonoside by intestinal flora. Berberine decreased the amount of baicalein transported to the basolateral side and the amount of baicalin which appeared at the basolateral side. The results showed that CC may decrease the bioavailability of baicalin and wogonoside in RS and the mechanism was related to CC decreasing the transport of flavonoid aglycones from the mucosa side to the serosal side and the hydrolyzation of flavonoids by inhibiting intestinal flora.

The Burrows-Wheeler Similarity Distribution Between Biological Sequences Based on Burrows-Wheeler Transform

Journal of Theoretical Biology. Feb, 2010  |  Pubmed ID: 19903487

This work aims at the similarity of biological sequences. Based on the Burrows-Wheeler transform, a definition of Burrows-Wheeler similarity distribution of two sequences is proposed to compare two sequences. Some distance measures are naturally followed by the distribution. The expectation and entropy of the similarity distribution are used to construct phylogenetic trees on two independent data sets. The result demonstrates that the method is efficient and powerful.

Metallothionein and Superoxide Dismutase Responses to Sublethal Cadmium Exposure in the Clam Mactra Veneriformis

Comparative Biochemistry and Physiology. Toxicology & Pharmacology : CBP. Apr, 2010  |  Pubmed ID: 20044031

The objective of this study was to identify the relationship between cadmium (Cd) and stress responses in the clam Mactra veneriformis. Metallothionein (MT) and Cu-Zn superoxide dismutase (SOD) cDNAs from the clam were isolated and characterized. The full-length cDNA of MvMT and MvSOD contained 830 and 689 nucleotides encoding 59 and 159 amino acids, respectively. Multiple alignments indicated that deduced amino acid sequences of MvMT and MvSOD shared high homology with MT and SOD sequences of other mollusks. Clams were exposed to 0, 50, 100, and 200microg/L Cd for 21days. The mRNA transcripts of the two genes, MT protein content and SOD activity in the digestive gland were examined. Cd treatment significantly elevated MvMT and MvSOD mRNA expression in a dose-dependent manner and MT protein level in a dose- and time-dependent manner. SOD activity significantly increased at the start of Cd exposure, then decreased and finally returned to the normal level. These results indicate that MT and SOD play an important role in maintaining cellular metabolism homeostasis and protecting M. veneriformis from Cd toxicity. MT and SOD could be used as biomarkers of Cd pollution in aquatic environment for the studied species.

Use of the Burrows-Wheeler Similarity Distribution to the Comparison of the Proteins

Amino Acids. Aug, 2010  |  Pubmed ID: 20300789

In this paper, we present an approach based on Burrows-Wheeler transform to compare the protein sequences. The strings representing amino acid sequences do not reflect the chemical physical properties better, and it is very hard to extract any key features by reading these long character strings directly. The use of the Burrows-Wheeler similarity distribution needs a suitable representation which can reflect some interesting properties of the proteins. For the comparison of the primary protein sequences we convert the protein sequences into digital codes by the Ponnuswamy hydrophobicity index, and for the comparison of the structure of the proteins we adjust the topology of protein structure strings, which are simple but useful representation of the secondary structure of proteins to match the Burrows-Wheeler similarity distribution. At last, some experiments show that the approach proposed in this paper is a powerful and useful tool for the comparison of proteins.

Inkjet Delivery of Glucose Oxidase

Chemical Communications (Cambridge, England). Aug, 2010  |  Pubmed ID: 20490421

The activity of glucose oxidase is reduced by inkjet printing and is a function of the printing conditions. Standard characterisation methods show no significant change to enzyme molecular weight, secondary structure and general molecular shape as a function of printing parameters. This indicates that a more subtle alteration of the protein structure may occur during printing.

Ecologically Asynchronous Agricultural Practice Erodes Sustainability of the Loess Plateau of China

Ecological Applications : a Publication of the Ecological Society of America. Jun, 2010  |  Pubmed ID: 20597295

Sustainability of agricultural landscapes depends largely on land-use practices. As one of the most productive and widespread agricultural soils, loess is often deep and easily eroded, posing grand challenges for environmental sustainability around the world. One prime example is the Loess Plateau of China, which has been cultivated for more than 7500 years. Based on long-term data sets, this study demonstrates that the dominant agricultural practice, winter wheat cropping, continues to be the primary driver for the massive soil erosion and landscape modifications on the Loess Plateau. This traditional farming system is asynchronous with the dynamic rhythm between natural vegetation and climate in the region. In particular, the long summer fallow period for winter wheat fields is concurrent with the heavy-rainstorm season, which greatly accelerates soil erosion. Our finding indicates that common land-use practices that have lasted for thousands of years in China are not environmentally sustainable. Agriculture in this region has relied primarily on the continuous "mining" of the soil for the past several thousand years but does not have a one-thousand-year future because of myriad environmental and socioeconomic factors associated with soil erosion. To contain soil erosion and promote sustainability on the Loess Plateau, therefore, a change in the agricultural regime is needed to make sure that current and future agricultural practices follow the vegetation-climate rhythm. In addition, to achieve environmental, economic, and social sustainability in this region, multifunctional land-use planning is required to increase landscape diversity and functions (e.g., proper arrangement of crop fields, orchards, and protected areas).

A Complexity-based Method to Compare RNA Secondary Structures and Its Application

Journal of Biomolecular Structure & Dynamics. Oct, 2010  |  Pubmed ID: 20645657

With the rapid emergence of RNA structure databases recently, efficient methods for RNA structure comparison are in demand for function prediction and evolutionary analysis. In this paper, we transform the complex secondary structure into the linear characteristic sequence which contains the information on primary sequence and the base pairing, and introduce the linear characteristic sequences into similarity analysis and phylogenetic analysis by using conditional LZ complexity. The results obtained from the two sets of real data have shown that our proposed method is effectual and feasible.

A Simple Feature Representation Vector for Phylogenetic Analysis of DNA Sequences

Journal of Theoretical Biology. Aug, 2010  |  Pubmed ID: 20665972

In this study, a simple 4k-dimension feature representation vector is proposed to reconstruct phylogenetic trees, where k is the length of a word. The vector is composed of elements which characterize the relative difference of biological sequence from sequence generated by an independent random process. In addition, the variance of a vector which is obtained by averaging every column of feature representation matrix is employed to determine appropriate word length. In our experiments, reliable results can always be generated when word length is < 7 which appears to be of lower computational complexity. Phylogenetic trees of 24 transferrins and 48 Hepatitis E viruses reconstructed at word length 6 are in good agreements with previous study, it shows that our method is efficient and powerful.

Simultaneous Quantification of Multiple Active Components from Xiexin Decoction in Rat Plasma by LC-ESI-MS/MS: Application in Pharmacokinetics

Biomedical Chromatography : BMC. Jul, 2011  |  Pubmed ID: 20872909

A sensitive and specific liquid chromatography-electrospray ionization-tandem mass spectrometric (LC-ESI-MS/MS) method was developed and validated to simultaneously quantify 11 active compounds (coptisine, jatrorrhizine, berberine, palmatine, baicalin, baicalein, wogonoside, wogonin, rhein, emodin and aloeemodin) from Xiexin decoction (XXD) in rat plasma. Plasma samples extracted by a single-step protein precipitation procedure were separated using the gradient mode on a Dikma ODS-C₁₈ column. Selected reaction monitoring scanning was employed for quantification with switching electrospray ion source polarity between positive and negative modes in a single run. Calibration curves offered satisfactory linearity (r > 0.995) at linear range of 0.47-60 ng/mL for coptisine, jatrorrhizine, berberine and palmatine, 15-1930 ng/mL for baicalin, 20-2560 ng/mL for baicalein, 14-1790 ng/mL for wogonoside, 0.57-72.8 ng/mL for wogonin, 10-1280 ng/mL for rhein, 0.6-76.8 ng/mL for emodin and 3.0-384 ng/mL for aloeemodin. The intra- and interday precisions were less than 10.2% in terms of relative standard deviation (RSD), and the accuracies were within ±10.84% in terms of relative error (RE). It was successfully applied to the evaluation of pharmacokinetics after single oral doses of XXD were administered to rats.

Phylogenetic Analysis of DNA Sequences Based on the Generalized Pseudo-amino Acid Composition

Journal of Theoretical Biology. Jan, 2011  |  Pubmed ID: 21040733

The main work of this paper is to propose a new theory and method, which is based on the idea of the pseudo-amino acid composition, for phylogenetic analysis of DNA primary sequences. In our method, we revise the part of the occurrence frequency of 20 amino acids in the method of the pseudo-amino acid composition by replacing the frequency of 16 dinucleotides. And we select eight LZ complexity factors of eight (0,1) sequences of a DNA primary sequence as PseAA components. Finally, we characterize a DNA sequence with a 24-dimensional vector. We reconstruct the phylogenetic trees of two datasets. The results show that our method is efficient and significant.

Genome Analysis with the Conditional Multinomial Distribution Profile

Journal of Theoretical Biology. Feb, 2011  |  Pubmed ID: 21129383

The focus of the research is on the analysis of genome sequences. Based on the inter-nucleotide distance sequence, we propose the conditional multinomial distribution profile for the complete genomic sequence. These profiles can be used to define a very simple, computationally efficient, alignment-free, distance measure that reflects the evolutionary relationships between genomic sequences. We use this distance measure to classify chromosomes according to species of origin, to build the phylogenetic tree of 24 complete genome sequences of coronaviruses. Our results demonstrate the new method is powerful and efficient.

Weighted Relative Entropy for Alignment-free Sequence Comparison Based on Markov Model

Journal of Biomolecular Structure & Dynamics. Feb, 2011  |  Pubmed ID: 21142223

In this paper, we introduce a probabilistic measure for computing the similarity between two biological sequences without alignment. The computation of the similarity measure is based on the Kullback-Leibler divergence of two constructed Markov models. We firstly validate the method on clustering nine chromosomes from three species. Secondly, we give the result of similarity search based on our new method. We lastly apply the measure to the construction of phylogenetic tree of 48 HEV genome sequences. Our results indicate that the weighted relative entropy is an efficient and powerful alignment-free measure for the analysis of sequences in the genomic scale.

High-accuracy Prediction of Protein Structural Class for Low-similarity Sequences Based on Predicted Secondary Structure

Biochimie. Apr, 2011  |  Pubmed ID: 21237245

Information on the structural classes of proteins has been proven to be important in many fields of bioinformatics. Prediction of protein structural class for low-similarity sequences is a challenge problem. In this study, 11 features (including 8 re-used features and 3 newly-designed features) are rationally utilized to reflect the general contents and spatial arrangements of the secondary structural elements of a given protein sequence. To evaluate the performance of the proposed method, jackknife cross-validation tests are performed on two widely used benchmark datasets, 1189 and 25PDB with sequence similarity lower than 40% and 25%, respectively. Comparison of our results with other methods shows that our proposed method is very promising and may provide a cost-effective alternative to predict protein structural class in particular for low-similarity datasets.

Phylogenetic Analysis of Protein Sequences Based on Distribution of Length About Common Sub-string

The Protein Journal. Mar, 2011  |  Pubmed ID: 21461804

Up to now, various approaches for phylogenetic analysis have been developed. Almost all of them put stress on analyzing nucleic acid sequences or protein primary sequences. In this paper, we propose a new sequence distance for efficient reconstruction of phylogenetic trees based on the distribution of length about common sub-sequences between two sequences. We describe some applications of this method, which not only show the validity of the method, but also suggest a number of novel phylogenetic insights.

The Molecular Characterization and Expression of Heat Shock Protein 90 (Hsp90) and 26 (Hsp26) CDNAs in Sea Cucumber (Apostichopus Japonicus)

Cell Stress & Chaperones. Sep, 2011  |  Pubmed ID: 21484287

The heat shock proteins (HSPs) are a family of proteins whose expression is enhanced in response to environmental stressors. The Apostichopus japonicus hsp90 and hsp26 genes were cloned using expressed sequence tag and rapid amplification of cDNA ends techniques. The full-length cDNA of Aphsp90 and Aphsp26 contains 3,458 and 1,688 nucleotides encoding 720 and 236 amino acids, respectively. Multiple alignments indicated that the deduced amino acid sequences of ApHsp90 and ApHsp26 shared a high level of identity with Hsp90 and small SHPs (sHSPs) sequences of zebrafish, ant, acorn worms, etc., and shared identical structural features with Hsp90 and sHSPs. The expression profiles of these two genes under heat treatment were investigated by real-time quantitative PCR. It was found that the messenger RNA (mRNA) transcripts of the two A. japonicus genes varied among different tissues under normal conditions and heat shock, and that the mRNA expression of the two genes was higher in the intestine compared to other tissues. Heat shock significantly elevated the expression of Aphsp90 and Aphsp26 mRNA in a temperature- and time-dependent manner. The results indicate that Aphsp90 and Aphsp26 played important roles in mediating the environmental stress in A. japonicus.

Large Scale Gene Expression Profiling During Intestine and Body Wall Regeneration in the Sea Cucumber Apostichopus Japonicus

Comparative Biochemistry and Physiology. Part D, Genomics & Proteomics. Jun, 2011  |  Pubmed ID: 21501978

Sea cucumbers are fascinating invertebrate organisms because of their ability to rapidly regenerate many organs and appendages. In this study 454 cDNA sequencing method was used to characterize transcriptome in Apostichopus japonicus in order to investigate genes that are active in regeneration. Based on sequence similarity with known genes, our analysis identified 6590 genes expressed in the early stages of regeneration of the intestine and body wall. Assembled sequences were annotated with gene names and gene ontology terms. The transcription of genes associated with structural molecule activity was abundant during regeneration compared with the control sample (based on tissues from an uninjured animal). Many important genes involved in major intercellular signaling pathways associated with regeneration were identified, based on a KEGG database search. Our investigation also indicated the expression profiles of many genes associated with development, muscle dedifferentiation, ECM remolding and epigenetic reprogramming. During the early stages of regeneration we found that 324 genes were significantly up-regulated and 80 genes were significantly down-regulated. The top 25 genes that demonstrated the most significant differential expression during regeneration were verified using real-time PCR, which identified 90% consistency between these two approaches. The new candidate gene sequences, discovered for the first time in this study, will greatly enable future research - using the sea cucumber model - into the molecular mechanisms associated with intestine and body wall regeneration.

A Novel Protein Structural Classes Prediction Method Based on Predicted Secondary Structure

Biochimie. May, 2012  |  Pubmed ID: 22353242

Knowledge of structural classes plays an important role in understanding protein folding patterns. In this paper, features based on the predicted secondary structure sequence and the corresponding E-H sequence are extracted. Then, an 11-dimensional feature vector is selected based on a wrapper feature selection algorithm and a support vector machine (SVM). Among the 11 selected features, 4 novel features are newly designed to model the differences between α/β class and α + β class, and other 7 rational features are proposed by previous researchers. To examine the performance of our method, a total of 5 datasets are used to design and test the proposed method. The results show that competitive prediction accuracies can be achieved by the proposed method compared to existing methods (SCPRED, RKS-PPSC and MODAS), and 4 new features are demonstrated essential to differentiate α/β and α + β classes. Standalone version of the proposed method is written in JAVA language and it can be downloaded from

A Simple K-word Interval Method for Phylogenetic Analysis of DNA Sequences

Journal of Theoretical Biology. Jan, 2013  |  Pubmed ID: 23085256

In this study, the normalized k-word average interval distance is proposed to extract phylogenetic information from DNA sequences. The phylogenetic trees of 30 mammalian species based on Euclidean distance measure are reconstructed with k ranging from 2 to 9. Comparison of our results with other methods shows that our method is efficient and powerful for phylogenetic analysis. In addition, for a fixed k, 4(k) distinct k-words are divided into n classes based on a new proposed indicator, where n is the number of DNA sequences. The effect of each k-word class on phylogeny is discussed.

A Novel Statistical Measure for Sequence Comparison on the Basis of K-word Counts

Journal of Theoretical Biology. Feb, 2013  |  Pubmed ID: 23147229

Numerous efficient methods based on word counts for sequence analysis have been proposed to characterize DNA sequences to help in comparison, retrieval from the databases and reconstructing evolutionary relations. However, most of them seem unrelated to any intrinsic characteristics of DNA. In this paper, we proposed a novel statistical measure for sequence comparison on the basis of k-word counts. This new measure removed the influence of sequences' lengths and uncovered bulk property of DNA sequences. The proposed measure was tested by similarity search and phylogenetic analysis. The experimental assessment demonstrated that our similarity measure was efficient.

Large Local Analysis of the Unaligned Genome and Its Application

Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. Jan, 2013  |  Pubmed ID: 23294269

We describe a novel method for the local analysis of complete genomes. A local distance measure called LODIST is proposed, which is based on the relationship between the longest common words and the shortest absent words of two genomes we compared. LODIST can perform better than local alignment when the local region is large enough to cover some recombination genes. A distance measure called SILD.k.t with resolution k and step t is derived by the integral LODISTs of whole genomes. It is shown that the algorithm for computing the LODISTs and SILD.k.t is linear, which is fast enough to consider the problem of the genome comparison. We verify this method by recognizing the subtypes of the HIV-1 complete genomes and genome segments.

Molecular Cloning and Expression-profile Analysis of Sea Cucumber DNA (cytosine-5)-methyltransferase 1 and Methyl-CpG Binding Domain Type 2/3 Genes During Aestivation

Comparative Biochemistry and Physiology. Part B, Biochemistry & Molecular Biology. May, 2013  |  Pubmed ID: 23466393

The sea cucumber Apostichopus japonicus Selenka survives high summer temperature by entering aestivation, characterized by hypometabolism and global gene silencing. We investigated the hypothesis that aestivation is associated with DNA methylation-dependent epigenetic mechanisms by cloning, sequencing and measuring the transcript abundances of two genes dnmt1 and mbd2/3, which comprise the DNA methylation system in A. japonicus Selenka. The deduced amino acid sequences and characteristic motifs of sea cucumber DNMT1 and MBD2/3 showed high homology to those of their mammalian counterparts. Quantitative real-time RT-PCR analysis showed that dnmt1 and mbd2/3 genes were similarly expressed in all four tissues examined (intestine, respiratory tree, muscle and body wall). Dnmt1 expression in the intestine was up-regulated during deep aestivation (P<0.05), while mbd2/3 was over-expressed in both the intestine and respiratory tree during the same period (P<0.01). No differences in expression levels were observed between other tissues. The results of this study suggest that DNA methylation may be involved in transcriptional silencing, and that the intestine is the major site for epigenetic regulation during aestivation in the sea cucumber.

Linear Regression Model of Short K-word: a Similarity Distance Suitable for Biological Sequences with Various Lengths

Journal of Theoretical Biology. Nov, 2013  |  Pubmed ID: 23933105

Originating from sequences' length difference, both k-word based methods and graphical representation approaches have uncovered biological information in their distinct ways. However, it is less likely that the mechanisms of information storage vary with sequences' length. A similarity distance suitable for sequences with various lengths will be much near to the mechanisms of information storage. In this paper, new sub-sequences of k-word were extracted from biological sequences under a one-to-one mapping. The new sub-sequences were evaluated by a linear regression model. Moreover, a new distance was defined on the invariants from the linear regression model. With comparison to other alignment-free distances, the results of four experiments demonstrated that our similarity distance was more efficient.

Pharmacokinetics of Liposomal-encapsulated and Un-encapsulated Vincristine After Injection of Liposomal Vincristine Sulfate in Beagle Dogs

Cancer Chemotherapy and Pharmacology. Mar, 2014  |  Pubmed ID: 24362508

Vincristine sulfate (VCR) is a potent and widely used anti-tumor drug. Encapsulating VCR with liposomes improves its therapeutic index. However, there is little known about the pharmacokinetic features of un-encapsulated VCR (UE-VCR) and encapsulated VCR (E-VCR).

Involvement of Herb-herb Interactions in the Influences of Radix Scutellaria and Coptis Chinensis on the Bioavailability of the Anthraquinones Form Rhei Rhizoma in Rats

European Journal of Drug Metabolism and Pharmacokinetics. Mar, 2015  |  Pubmed ID: 24659524

Xiexin decoction (XXD) is composed of Rhei Rhizoma (DH), Radix Scutellaria (HQ), and Coptis Chinensis (HL). Free anthraquinones in DH are the basic effective constituents in XXD. Reportedly, HL decreases the bioavailability of the anthraquinones, while HQ antagonizes the effect of HL. In this study, we aimed to determine the underlying mechanisms. The metabolisms of anthraquinones by intestinal flora were studied using rat fecal suspension (RFS); the metabolisms of rhein (a typical anthraquinone in DH) by rat intestine and liver were studied using rat intestine microsomes (RIMs) and rat liver microsomes (RLMs), respectively; the intestinal transport of rhein was studied using everted gut sacs. The results showed that HL decreased the amount of the free anthraquinones after incubation in RFS and inhibited the intestinal transport of rhein, but HQ antagonized the effect of HL. On the other hand, HQ strongly inhibited the glucuronidation of rhein in both RIMs and RLMs. The results suggested that HL decreased the oral bioavailability of the anthraquinones due to inhibiting the conversion of conjugated anthraquinones to free anthraquinones by intestinal flora and decreasing the intestinal transport of the anthraquinones; HQ confronted the effect of HL by inhibiting the glucuronidation of the anthraquinones in intestine and weakening the inhibitory effects of HL.

Lab-scale Preparations of Candida Albicans and Dual Candida Albicans-Candida Glabrata Biofilms on the Surface of Medical-grade Polyvinyl Chloride (PVC) Perfusion Tube Using a Modified Gravity-supported Free-flow Biofilm Incubator (GS-FFBI)

Journal of Microbiological Methods. Feb, 2015  |  Pubmed ID: 25528294

The assembly of a man-made gravity-supported free-flow biofilm incubator (GS-FFBI) was described, which was composed of a gas cushion injector and four incubators. The GS-FFBI had the characteristics of (i) a bottom-up flow direction, and (ii) lab-scale biofilm preparation without the use of a multichannel pump. Two opportunistic fungal strains, namely Candida albicans and Candida glabrata, were employed to incubate C. albicans and dual C. albicans-C. glabrata biofilms on the surface of medical-grade polyvinyl chloride perfusion tube. In terms of the results from {2, 3-bis (2-methoxy-4-nitro-5-sulfo-phenyl)-2H-tetrazolium-5-carboxanilide} (XTT) assay, dry weight measurement, colony-forming unit counting, susceptibility test, and scanning electron microscopy, it was demonstrated that GS-FFBI could form both stable single and dual Candida biofilms with no significant variations among the four incubators or the three daily incubations within 21h, and could operate for at least 96h smoothly with no contamination of stock medium. The results also indicated, for the first time, that C. albicans and C. glabrata might be co-existent competitively and symbiotically in the dual biofilms with flowing media. GS-FFBI would be a useful device to study in vitro morphological and physiological features of microbial biofilms in the medical settings.

Interaction Between Oblongifolin C and UDP-glucuronosyltransferase Isoforms in Human Liver and Intestine Microsomes

Xenobiotica; the Fate of Foreign Compounds in Biological Systems. 2015  |  Pubmed ID: 25714435

1. Oblongifolin C (OC) is a potential natural anticancer candidate, and its metabolic profile has not yet been established. 2. One major OC glucuronidation metabolite (OCG) has been identified in a pool of human liver microsomes (HLMs). Chemical inhibition experiments suggested that OCG was mainly formed by UGT1A. A screen of recombinant UDP-glucuronosyltransferase isoforms (UGTs) indicated that UGT1A1 primarily mediates OC conjugation, with minor contributions from UGT1A3 and UGT1A8. Enzyme kinetic studies showed that UGT1A1 was the main UGT isoform involved in OCG in HLMs. 3. Further investigation suggested that OC is a broad inhibitor of UGTs. Additionally, OC competitively inhibited UGT1A6 with a Ki value of 3.49 ± 0.57 μM, whereas non-competitively inhibited UGT1A10 with a Ki value of 2.12 ± 0.18 μM. 4. Understanding the interaction between OC and UGTs will greatly contribute to future investigations regarding the inter-individual differences in OC metabolism in clinical trials and potential drug-drug interactions.

Assessing Vegetation Cover Dynamics Induced by Policy-Driven Ecological Restoration and Implication to Soil Erosion in Southern China

PloS One. 2015  |  Pubmed ID: 26115116

In the aftermath of the severe droughts and floods at the end of the 20th century, the Chinese government launched several ecological restoration projects, including the Natural Forest Protection Program in 1998 and the Grain-for-Green Program in 1999, to promote afforestation and reforestation to reduce surface runoff and consequent soil erosion nationwide. However, it is still unclear how vegetation has changed in southern China since the launch of these programs. In this study, we used the MODIS Enhanced Vegetation Index (EVI) to analyze the vegetation cover dynamics in southern China from 2000 to 2009 and evaluate the resulting effects of controlling soil erosion. Our observations indicate that 5.3% of the study area significantly increased and 0.98% significantly decreased in EVI value (p < 0.05). The spring EVI had largest increase in space. The conversions of croplands on steep slopes to forests resulting from national policies led to significant increases in EVI. The increase in EVI was not driven by annual average temperature and annual precipitation. By referencing ecological restoration statistical data and field observations, we showed that ecological restoration programs significantly improved vegetation cover in southern China. Increase in the area of farmland-converted forestlands has reduced soil erosion based upon monitoring sediment yields at hydrologic stations in the Yangtze River. This study displays the spatial patterns of trend in vegetation growth since the beginning of the 21st century in southern China and highlights the important role of China's afforestation program.

In Vitro Antifungal Activity of Baicalin Against Candida Albicans Biofilms Via Apoptotic Induction

Microbial Pathogenesis. Oct, 2015  |  Pubmed ID: 26169236

The aim of this study was to investigate the antifungal activity of baicalin and its potential mechanism of action against Candida albicans biofilms. The standard techniques including microdilution method and checkerboard assay were employed to evaluate the susceptibilities of baicalin alone and in combination with fluconazole against planktonic and biofilm cells of C. albicans. Transmission electron microscope (TEM), scanning electron microscope (SEM), fluorescent microscope and flow cytometry were used to assess the apoptotic incidences induced by baicalin in biofilm cells. The expressions of four genes (RAS1, CAP1, PDE2 and TPK1) related to Ras-cAMP-PKA pathway were also analyzed by quantitative reverse transcription polymerase chain reaction (qRT-PCR). The results showed that minimum inhibitory concentration (MIC) and sessile minimum inhibitory concentration (SMIC50) of baicalin were 500 and 2000 μg/mL with fractional inhibitory concentration indexs (FICIs) ranging from 0.28 to 0.75. A series of events related to apoptosis were observed in baicalin-treated C. albicans biofilms, including extensive chromatin condensation along the nuclear envelope, ROS accumulation, MMP reduction, PS externalization, nuclear fragmentation, chromatin condensation, metacaspase activation and Cyt C release. Additionally, the expressions of RAS1 and TPK1 were up-regulated by 3.2 and 2.9 folds respectively, while those of CAP1 and PDE2 were down-regulated by 3.3 and 6.6 folds respectively after exposure to baicalin in biofilm cells. In conclusion, baicalin can suppress the development of C. albicans biofilms most likely due to inducing cell death via apoptosis.

Rapid and Accurate Liquid Chromatography and Tandem Mass Spectrometry Method for the Simultaneous Quantification of Ten Metabolic Reactions Catalyzed by Hepatic Cytochrome P450 Enzymes

Journal of Separation Science. Oct, 2015  |  Pubmed ID: 26256777

The hepatic cytochrome P450 enzymes play a central role in the biotransformation of endogenous and exogenous substances. A sensitive high-throughput liquid chromatography with tandem mass spectrometry assay was developed and validated for the simultaneous quantification of the products of ten metabolic reactions catalyzed by hepatic cytochrome P450 enzymes. After the substrates were incubated separately, the samples were pooled and analyzed by liquid chromatography with tandem mass spectrometry using an electrospray ionization source in the positive and negative ion modes. The method exhibited linearity over a broad concentration range, insensitivity to matrix effects, and high accuracy, precision, and stability. The novel method was successfully applied to study the kinetics of phenacetin-O deethylation, coumarin-7 hydroxylation, bupropion hydroxylation, taxol-6 hydroxylation, omeprazole-5 hydroxylation, dextromethorphan-O demethylation, tolbutamide-4 hydroxylation, chlorzoxazone-6 hydroxylation, testosterone-6β hydroxylation, and midazolam-1 hydroxylation in rat liver microsomes.

Contributions of Multiple Refugia During the Last Glacial Period to Current Mainland Populations of Korean Pine (Pinus Koraiensis)

Scientific Reports. Dec, 2015  |  Pubmed ID: 26691230

The northern microrefugia that existed during the Last Glacial Maximum (LGM) are a key factor in the demographic history of species. Pinus koraiensis has a unique distribution in northeast Asia. The Changbai Mountains and the Korean peninsula (CM/KP) are usually considered to be the LGM refugia for P. koraiensis. However, the Xiaoxingan Range (XR), at the northern part of this species' distribution, is another possible refugium. We used chloroplast sequencing and ten nuclear single-copy gene loci to calculate the genetic diversity pattern of P. koraiensis. The probabilities of a single LGM refugium and of multiple LGM refugia were calculated based on approximate Bayesian computation. The effect of the latitudinal gradient on genetic diversity was not significant. However, unique alleles occurred at low frequencies in CM/KP and XR. A conservative estimate of the coalescence time between CM/KP and XR is 0.4 million years ago, a time prior to the LGM. Gene flow between CM/KP and XR was estimated to be more than one in per generation, an amount that may be sufficient to limit genetic divergence between the regions. Our study strongly supports the hypothesis that XR was another LGM refugium in addition to CM/KP.

The Complete Mitochondrial Genome of Capricornis Sp., Possible a New Species of Serow from Guizhou, China

Mitochondrial DNA. Part A, DNA Mapping, Sequencing, and Analysis. 2016  |  Pubmed ID: 24865899

The genus Capricornis was widely distributed in Asia. In the present study, the complete mitochondrial genome of Capricornis sp., possible a new species of Serow from Guizhou province of China, was sequenced for the first time. Sequence analysis showed it is 16,441 bp in length, consisting of 12S rRNA gene, 16S rRNA gene, 22 transfer RNA (tRNA) genes, 13 protein-coding genes and one control region (CR).

The Complete Mitochondrial Genome of the North Chinese Leopard (Panthera Pardus Japonensis)

Mitochondrial DNA. Part A, DNA Mapping, Sequencing, and Analysis. 2016  |  Pubmed ID: 25028790

The North Chinese Leopard (Panthera pardus japonensis) is an endemic subspecies of Panthera pardus to China, living in small and isolated populations with a severely fragmented distribution. Here we first sequenced and annotated its complete mitochondrial genome. The total length of the North Chinese Leopard is of 16,966 base pairs that consist of 2 rRNA gene, 22 tRNA genes, 13 protein-coding genes, 1 OLR and 1 control region (CR). The structures of the genomes were highly similar to other Felidae.

The Roles of CDR1, CDR2, and MDR1 in Kaempferol-induced Suppression with Fluconazole-resistant Candida Albicans

Pharmaceutical Biology. 2016  |  Pubmed ID: 26459663

Fungal infections caused by fluconazole-resistant Candida albicans are an intractable clinical problem, calling for new efficient antifungal drugs. Kaempferol, an active flavonoid, has been considered a potential candidate against Candida species.

Simultaneous Quantification of Catechin, Epicatechin, Liquiritin, Isoliquiritin, Liquiritigenin, Isoliquiritigenin, Piperine and Glycyrrhetinic Acid in Rat Plasma by HPLC-MS/MS: Application to a Pharmacokinetic Study of Longhu Rendan Pills

Biomedical Chromatography : BMC. Aug, 2016  |  Pubmed ID: 26613237

A sensitive, specific, accurate HPLC-MS/MS method was developed and validated for the simultaneous quantification of catechin, epicatechin, liquiritin, isoliquiritin, liquiritigenin, isoliquiritigenin, piperine and glycyrrhetinic acid from Longhu Rendan pills in rat plasma. Chromatographic separation was performed with a Hypersil Gold C18 column using a gradient of methanol and 0.01% acetic acid containing 0.2 mm ammonium acetate as mobile phase. The analytes were quantified on a triple quadrupole mass spectrometer, operating in selected reaction monitoring mode and switching the electrospray ion source polarity between positive and negative modes in a single run. The calibration curves of catechin, epicatechin, liquiritin, isoliquiritin, liquiritigenin, isoliquiritigenin, piperine and glycyrrhetinic acid were linear over the concentration ranges of 5-2000, 5-2000, 0.5-200, 0.5-200, 0.25-100, 0.25-100, 0.025-10 and 0.50-200 ng mL(-1) , respectively. The intra- and inter-assay precisions and accuracies were <11.6 and 91.9-108.2%, respectively, for all analytes. Matrix effects for all analytes were between 88.2 and 114.2%. Stability testing showed that all analytes were stable in plasma at 24 °C for 3 h, at 4 °C for 24 h, after three freeze-thaw cycles, and at -80 °C for 15 days. The method was successfully applied to an in vivo study evaluating the pharmacokinetics of multiple nonvolatile compounds following intragastric administration of Longhu Rendan pills to rats. Copyright © 2016 John Wiley & Sons, Ltd.

Cathepsin L of the Sea Cucumber Apostichopus Japonicus-molecular Characterization and Transcriptional Response to Vibrio Splendidus Infection

Fish & Shellfish Immunology. Feb, 2016  |  Pubmed ID: 26777896

Cathepsin L, a lysosomal endopeptidase, has been noted for its involvement in the innate immune response in invertebrates. Here, the cathepsin L cDNA of the sea cucumber Apostichopus japonicus (AjCatL) is identified from an EST library and then cloned by the rapid amplification of the cDNA ends (RACE) PCR. The full-length cDNA is 1678 bp long containing an open reading frame (ORF) of 1002 bp, an 80 bp 5' UTR and a 599 bp 3' UTR. The cDNA encodes 333 amino acid residues with a predicted molecular mass of 37.07 kDa and a theoretical isoelectric point (pI) of 5.01. The full-length AjCatL contains three active sites of eukaryotic thiol (cysteine) protease at positions 133-144, 278-288 and 295-314. Analysis of the predicted tertiary structure of prepro-CatL (17-333 aa) and mature-CatL (116-333 aa) reveals that the propeptide region (17-115 aa) blocks access to the substrate-binding cleft. Phylogenetic analysis shows that the AjCatL is clustered together with two other CatLs from Strongylocentrotus purpuratus. The enzymatic activity of AjCatL was verified using a substrate hydrolyzing assay with recombinant mAjCatL. Further analysis of real time-PCR demonstrates that the expression of AjCatL mRNA is significantly up-regulated in the coelomocytes in cases of infection with the common bacterial pathogen, Vibrio splendidus. This suggests that the AjCatL is likely to be involved in the immune response.

[Pulsatilla Decoction Inhibits Vulvovaginal Candida Albicans Proliferation and Reduces Inflammatory Cytokine Levels in Vulvovaginal Candidiasis Mice]

Xi Bao Yu Fen Zi Mian Yi Xue Za Zhi = Chinese Journal of Cellular and Molecular Immunology. Feb, 2016  |  Pubmed ID: 26927371

To explore the possible regulatory effect of Pulsatilla decoction on Th17 cells and inflammatory cytokines of vulvovaginal candidiasis (VVC) mice.

De Novo Assembly and Comparison of the Ovarian Transcriptomes of the Common Chinese Cuttlefish (Sepiella Japonica) with Different Gonadal Development

Genomics Data. Mar, 2016  |  Pubmed ID: 26981395

The common Chinese cuttlefish (Sepiella japonica) has been considered one of the most economically important marine Cephalopod species in East Asia and seed breeding technology has been established for massive aquaculture and stock enhancement. In the present study, we used Illumina HiSeq2000 to sequence, assemble and annotate the transcriptome of the ovary tissues of S. japonica for the first time. A total of 53,116,650 and 53,446,640 reads were obtained from the immature and matured ovaries, respectively (NCBI SRA database SRX1409472 and SRX1409473), and 70,039 contigs (N50 = 1443 bp) were obtained after de novo assembling with Trinity software. Digital gene expression analysis reveals 47,288 contigs show differential expression profile and 793 contigs are highly expressed in the immature ovary, while 38 contigs are highly expressed in the mature ovary with FPKM > 100. We hope that the ovarian transcriptome and those stage-enriched transcripts of S. japonica can provide some insight into the understanding of genome-wide transcriptome profile of cuttlefish gonad tissue and give useful information in cuttlefish gonad development.

Estimating the Population Size and Genetic Diversity of Amur Tigers in Northeast China

PloS One. 2016  |  Pubmed ID: 27100387

Over the past century, the endangered Amur tiger (Panthera tigris altaica) has experienced a severe contraction in demography and geographic range because of habitat loss, poaching, and prey depletion. In its historical home in Northeast China, there appears to be a single tiger population that includes tigers in Southwest Primorye and Northeast China; however, the current demographic status of this population is uncertain. Information on the abundance, distribution and genetic diversity of this population for assessing the efficacy of conservation interventions are scarce. We used noninvasive genetic detection data from scats, capture-recapture models and an accumulation curve method to estimate the abundance of Amur tigers in Northeast China. We identified 11 individual tigers (6 females and 5 males) using 10 microsatellite loci in three nature reserves between April 2013 and May 2015. These tigers are confined primarily to a Hunchun Nature Reserve along the border with Russia, with an estimated population abundance of 9-11 tigers during the winter of 2014-2015. They showed a low level of genetic diversity. The mean number of alleles per locus was 2.60 and expected and observed heterozygosity were 0.42 and 0.49, respectively. We also documented long-distance dispersal (~270 km) of a male Amur tiger to Huangnihe Nature Reserve from the border, suggesting that the expansion of neighboring Russian populations may eventually help sustain Chinese populations. However, the small and isolated population recorded by this study demonstrate that there is an urgent need for more intensive regional management to create a tiger-permeable landscape and increased genetic connectivity with other populations.

Estimating Abundance and Density of Amur Tigers Along the Sino-Russian Border

Integrative Zoology. Jul, 2016  |  Pubmed ID: 27136188

As an apex predator the Amur tiger (Panthera tigris altaica) could play a pivotal role in maintaining the integrity of forest ecosystems in Northeast Asia. Due to habitat loss and harvest over the past century, tigers rapidly declined in China and are now restricted to the Russian Far East and bordering habitat in nearby China. To facilitate restoration of the tiger in its historical range, reliable estimates of population size are essential to assess effectiveness of conservation interventions. Here we used camera trap data collected in Hunchun National Nature Reserve from April to June 2013 and 2014 to estimate tiger density and abundance using both maximum likelihood and Bayesian spatially explicit capture-recapture (SECR) methods. A minimum of 8 individuals were detected in both sample periods and the documentation of marking behavior and reproduction suggests the presence of a resident population. Using Bayesian SECR modeling within the 11 400 km(2) state space, density estimates were 0.33 and 0.40 individuals/100 km(2) in 2013 and 2014, respectively, corresponding to an estimated abundance of 38 and 45 animals for this transboundary Sino-Russian population. In a maximum likelihood framework, we estimated densities of 0.30 and 0.24 individuals/100 km(2) corresponding to abundances of 34 and 27, in 2013 and 2014, respectively. These density estimates are comparable to other published estimates for resident Amur tiger populations in the Russian Far East. This study reveals promising signs of tiger recovery in Northeast China, and demonstrates the importance of connectivity between the Russian and Chinese populations for recovering tigers in Northeast China.

Understanding Mechanism of Sea Cucumber Apostichopus Japonicus Aestivation: Insights from TMT-based Proteomic Study

Comparative Biochemistry and Physiology. Part D, Genomics & Proteomics. Sep, 2016  |  Pubmed ID: 27376927

Marine invertebrate aestivation is a unique strategy for summer survival in response to hot marine conditions. The sea cucumber, Apostichopus japonicus, is an excellent model marine invertebrate for studies of environmentally-induced aestivation. In the present study, we used a tandem mass tag (TMT)-coupled LC-MS/MS approach to identify and quantify the global proteome expression profile over the aestivation-arousal cycle of A. japonicus. A total of 3920 proteins were identified from the intestine of sea cucumber. Among them, 630 proteins showed significant differential expression when comparing three conditions of sea cucumbers: non-aestivating (active), deep-aestivation (at least 15days of continuous aestivation), and arousal after aestivation (renewed moving and feeding). Sea cucumbers in deep aestivation showed substantial differentially expressed proteins (143 up-regulated and 267 down-regulated proteins compared with non-aestivating controls). These differentially expressed proteins suggested that protein and phospholipid probably are major fuel sources during hypometabolism and a general attenuation of carbohydrate metabolism was observed during deep aestivation. Differentially expressed proteins also provided the first global picture of a shift in protein synthesis, protein folding, DNA binding, apoptosis, cellular transport and signaling, and cytoskeletal proteins during deep aestivation in sea cucumbers. A comparison of arousal from aestivation with deep aestivation, revealed a general reversal of the changes that occurred in aestivation for most proteins. Western blot detection further validated the significant up-regulation of HSP70 and down-regulation of methyltransferase-like protein 7A-like in deep-aestivation. Our results suggest that there is substantial post-transcriptional regulation of proteins during the aestivation-arousal cycle in sea cucumbers.

Cyp3a11-mediated Testosterone-6β-hydroxylation Decreased, While UGT1a9-mediated Propofol O-glucuronidation Increased, in Mice with Diabetes Mellitus

Biopharmaceutics & Drug Disposition. Oct, 2016  |  Pubmed ID: 27514509

The db/db mouse is one of the most popular animal models for type 2 diabetes mellitus, but changes in the activities of important P450s and UGTs are still not completely clear. This study was designed to investigate the alterations of major hepatic cytochrome P450s and UDP-glucuronyltransferase enzymes in db/db mice. Mouse liver microsomes (MLMs) were obtained from male db/db mice and their wild type littermates. After incubation of the substrates separately with MLMs, the samples were pooled and analysed by high-throughput liquid chromatography-tandem mass spectrometry system for the simultaneous study of nine phase I metabolic reactions and three glucuronidation conjugation reactions to determine the activity of the metabolic enzymes. Compared with normal controls, the Clint estimate for testosterone-6β-hydroxylation was lower (46%) (p < 0.05), while the Vmax and Clint estimates for propofol O-glucuronidation were 5-fold higher (p < 0.01) in the liver microsomes from db/db mice. There was no significant difference in phase I metabolic reactions of phenacetin-O-deethylation, coumarin-7-hydroxylation, bupropion-hydroxylation, omeprazole-5-hydroxylation, dextromethorphan-O-demethylation, tolbutamide-4-hydroxylation, chlorzoxazone-6-hydroxylation and midazolam-1-hydroxylation and in glucuronidation reactions of estradiol 3-O-glucuronidation, and 3-azido-3-deoxythymidine glucuronidation. The data suggest that, in db/db mice, the activity of Cyp3a11, catalysing testosterone-6β-hydroxylation, decreased, while the activity of UGT1a9, catalysing propofol O-glucuronidation, increased. Copyright © 2016 John Wiley & Sons, Ltd.

Antiproliferation of Berberine in Combination with Fluconazole from the Perspectives of Reactive Oxygen Species, Ergosterol and Drug Efflux in a Fluconazole-Resistant Candida Tropicalis Isolate

Frontiers in Microbiology. 2016  |  Pubmed ID: 27721812

Candida tropicalis has emerged as an important pathogenic fungus in nosocomial infections due to its recalcitrant resistance to conventional antifungal agents, especially to fluconazole (FLC). Berberine (BBR) is a bioactive herbal-originated alkaloids and has been reported to possess antifungal functions against C. albicans. In this paper, we tried to figure out the antifungal mechanisms of BBR and/or FLC in a clinical C. tropicalis isolate 2006. In the microdilution test, the minimum inhibitory concentration (MIC) of BBR was found 16 μg/mL with fractional inhibitory concentration index (FICI) 0.13 in C. tropicalis 2006. The synergism of BBR and FLC was also confirmed microscopically. After the treatments of BBR and/or FLC, the studies revealed that (i) FLC facilitated BBR to increase reactive oxygen species (ROS), (ii) FLC enhanced the intranuclear accumulation of BBR, (iii) BBR decreased the extracellular rhodamine 123 (Rh123) via inhibiting efflux transporters, (iv) FLC assisted BBR to reduce ergosterol content, and (v) BBR in combined with FLC largely downregulated the expressions of Candida drug resistance 1 (CDR1) and CDR2 but impact slightly multidrug resistance 1 (MDR1), and upregulate the expression of ergosterol 11 (ERG11). These results suggested that BBR could become a potent antifungal drug to strengthen FLC efficacy in FLC-resistant C. tropicalis via ROS increase, intracellular BBR accumulation, ergosterol decrease and efflux inhibition.

Synergistic in Vitro Activity of Sodium Houttuyfonate with Fluconazole Against Clinical Candida Albicans Strains Under Planktonic Growing Conditions

Pharmaceutical Biology. Dec, 2017  |  Pubmed ID: 27931143

Fluconazole resistance is an intractable problem of treating Candida albicans, calling for more antifungal agents to enhance the activity of fluconazole.

Identification and Functional Characterisation of 5-HT4 Receptor in Sea Cucumber Apostichopus Japonicus (Selenka)

Scientific Reports. Jan, 2017  |  Pubmed ID: 28059140

Serotonin (5-HT) is an important neurotransmitter and neuromodulator that controls a variety of sensory and motor functions through 5-HT receptors (5-HTRs). The 5-HT4R subfamily is linked to Gs proteins, which activate adenylyl cyclases (ACs), and is involved in many responses in peripheral organs. In this study, the 5-HT4R from Apostichopus japonicus (Aj5-HT4R) was identified and characterised. The cloned full-length Aj5-HT4R cDNA is 1,544 bp long and contains an open reading frame 1,011 bp in length encoding 336 amino acid proteins. Bioinformatics analysis of the Aj5-HT4R protein indicated this receptor was a member of class A G protein coupled receptor (GPCR) family. Further experiments using Aj5-HT4R-transfected HEK293 cells demonstrated that treatment with 5-HT triggered a significant increase in intracellular cAMP level in a dose-dependent manner and induced a rapid internalisation of Aj5-HT4R fused with enhanced green fluorescent protein (Aj5-HT4R-EGFP) from the cell surface into the cytoplasm. In addition, the transcriptional profiles of Aj5-HT4R in aestivating A. japonicas and phosphofructokinase (AjPFK) in 5-HT administrated A. japonicus have been analysed by real-time PCR assays. Results have led to a basic understanding of Aj5-HT4R in A. japonicus, and provide a foundation for further exploration of the cell signaling and regulatory functions of this receptor.

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