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Find video protocols related to scientific articles indexed in Pubmed.
The complete mitochondrial genome of the spinner shark Carcharhinus brevipinna.
Mitochondrial DNA
PUBLISHED: 10-01-2014
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Abstract The mitochondrial genome of the spinner shark (Carcharhinus brevipinna) was determined in this study. It was 16,706?bp in length with the typical genomic organization and gene order as most vertebrates. Whole nucleotide base composition was 31.3% A, 25.3% C, 13.2% G and 30.1% T. Among the protein-coding genes, there are three overlapping reading-frames on the same strand, while one of it on the opposite strand. Two start codons (ATG and GTG) and three stop codons (AGG, TAG and TAA/T) were used in 13 protein-coding genes. The 22 tRNA ranged from 67 (tRNA-Cys and tRNA-Ser2) to 75?bp (tRNA-Leu1) in length. Only the tRNA-Ser2 could not fold into the typical clover-leaf structure, which lost the dihydrouridine (DHU) arm and replaced by a simple loop. The control region was 1064?bp in length and showed a higher AT content (66.8%) than the average value of whole mitogenome (61.4%).
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Rice SPX1 and SPX2 inhibit phosphate starvation responses through interacting with PHR2 in a phosphate-dependent manner.
Proc. Natl. Acad. Sci. U.S.A.
PUBLISHED: 09-30-2014
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In plants, sensing the levels of external and internal nutrients is essential for reprogramming the transcriptome and adapting to the fluctuating environment. Phosphate (Pi) is a key plant nutrient, and a large proportion of Pi starvation-responsive genes are under the control of PHOSPHATE STARVATION RESPONSE REGULATOR 1 (PHR1) in Arabidopsis (AtPHR1) and its homologs, such as Oryza sativa (Os)PHR2 in rice. AtPHR1 and OsPHR2 expression is not very responsive to Pi starvation, raising the question as to how plants sense changes in cellular Pi levels to activate the central regulator. SPX [named after SYG1 (suppressor of yeast gpa1), Pho81 (CDK inhibitor in yeast PHO pathway), and XPR1 (xenotropic and polytropic retrovirus receptor)] proteins that harbor only the SPX domain are reported to be involved in the negative regulation of Pi starvation responses. Here, we show that the nuclear localized SPX proteins SPX1 and SPX2 are Pi-dependent inhibitors of the activity of OsPHR2 in rice. Indeed, SPX1 and SPX2 proteins interact with PHR2 through their SPX domain, inhibiting its binding to P1BS (the PHR1-binding sequence: GNATATNC). In vivo data, as well as results from in vitro experiments using purified SPX1, SPX2, and OsPHR2 proteins, showed that SPX1 and SPX2 inhibition of OsPHR2 activity is Pi-dependent. These data provide evidence to support the involvement of SPX1 and SPX2 in the Pi-sensing mechanism in plants.
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Land use influences arbuscular mycorrhizal fungal communities in the farming-pastoral ecotone of northern China.
New Phytol.
PUBLISHED: 08-08-2014
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We performed a landscape-scale investigation to compare the arbuscular mycorrhizal fungal (AMF) communities between grasslands and farmlands in the farming-pastoral ecotone of northern China. AMF richness and community composition were examined with 454 pyrosequencing. Structural equation modelling (SEM) and multivariate analyses were applied to disentangle the direct and indirect effects (mediated by multiple environmental factors) of land use on AMF. Land use conversion from grassland to farmland significantly reduced AMF richness and extraradical hyphal length density, and these land use types also differed significantly in AMF community composition. SEM showed that the effects of land use on AMF richness and hyphal length density in soil were primarily mediated by available phosphorus and soil structural quality. Soil texture was the strongest predictor of AMF community composition. Soil carbon, nitrogen and soil pH were also significantly correlated with AMF community composition, indicating that these abiotic variables could be responsible for some of the community composition differences among sites. Our study shows that land use has a partly predictable effect on AMF communities across this ecologically relevant area of China, and indicates that high soil phosphorus concentrations and poor soil structure are particularly detrimental to AMF in this fragile ecosystem.
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Complete mitochondrial genome of the Zebra bullhead shark Heterodontus zebra (Heterodontiformes: Heterodontidae).
Mitochondrial DNA
PUBLISHED: 07-16-2014
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The complete mitochondrial genome of the Zebra bullhead shark Heterodontus zebra was first presented in this study. It was 16,720 bp in length, encoding 37 genes and one control region. The gene order and translate orientation were identical to most vertebrates. Overall nucleotide base composition of H. zebra mitogenome was 31.6% A; 26.8% C; 13.1% G and 28.4% T. Total 27 bp overlaps and 20 bp short intergenic spaces were found in 17 gene junctions in the genome. Two start codons (ATG and GTG) and three terminate codons (TAG, TAA and T) were found in 13 protein-coding genes. Except for tRNA-Ser2, which lost the dihydrouridine (DHU) arm and formed one simple loop, the remaining tRNAs could fold into the typical clover-leaf secondary structures. The termination-associated sequences and three short conserved blocks (CBS I-III) were identified in the control region.
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Complete mitochondrial genome of the blacktip reef shark Carcharhinus melanopterus (Carcharhiniformes: Carcharhinidae).
Mitochondrial DNA
PUBLISHED: 05-29-2014
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Abstract The complete mitochondrial genome of the blacktip reef shark Carcharhinus melanopterus is determined for the first time in this study. The gene composition and order in the mitogenome of C. melanopterus is identical to most vertebrates. The overall base composition is 31.3% A, 25.3% C, 13.3% G and 30.1% T. There are 29?bp overlaps and 21?bp short intergenic spaces in the mitogenome. Two start codons and three stop codons were found in protein-coding genes. The dihydrouridine arm of tRNA-Ser2 was replaced by a simple loop and the other tRNAs could be folded into the typical cloverleaf structure. The termination associated sequence (TAS) and the conserved sequence blocks (CSB1-3) are found in the control region.
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Mitochondrial genome of the longtail butterfly ray Gymnura poecilura (Myliobatiformes: Gymnuridae).
Mitochondrial DNA
PUBLISHED: 05-01-2014
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Abstract The complete mitogenome the longtail butterfly ray (Gymnura poecilura) was first presented in this study. It is 17,874?bp in length, contains 37 genes with the typical gene order and transcriptional direction in vertebrates. The overall base composition is: 28.5% A, 26.5% T, 15.0% G and 30.1% C. There are 26?bp overlaps and 41?bp short intergenic spaces located in 7 and 16 gene junctions, respectively. Two start codons (ATG and GTG) and two stop codons (TAG and TAA/T) were used in protein-coding genes. The origin of L-strand replication (OL) was found between tRNA-Asn and tRNA-Cys genes. The control region has the same A and C contents (28.8%).
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Complete mitochondrial genome of milk sole fish Aseraggodes kobensis (Pleuronectiformes: Soleidae).
Mitochondrial DNA
PUBLISHED: 04-15-2014
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Abstract The complete mitochondrial genome of the milk sole fish Aseraggodes kobensis was determined in this study. It is 16,944?bp in length, contains 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes and one putative control region with the typical gene order and transcriptional orientation in vertebrates. The nucleotide base content of A. kobensis mitochondrial genome is: 31.7% A, 27.3% C, 15.3% G and 25.8% T. There are 24?bp overlaps and 48?bp short intergenic spaces located in 6 and 12 gene junctions, respectively. Two start codons (ATG and GTG) and two stop codons (TAG and TAA/T) were found in protein-coding genes. The origin of L-strand replication sequence was found between the tRNA(Asn) and tRNA(Cys) genes, and could be folded into a hairpin structure. The control region is 1239?bp in length with the rich A+T (66.4%) and poor G (13.1%) content.
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Complete mitogenome of the peacock sole Pardachirus pavoninus (Pleuronectiformes: Soleidae).
Mitochondrial DNA
PUBLISHED: 03-26-2014
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Abstract The complete mitochondrial genome of the peacock sole Pardachirus pavoninus was firstly determined in this study. It is 16,537?bp in length, consisting of 13 protein-coding genes, two rRNA genes, 22 tRNA genes and one control region with the typical gene order in vertebrates. There are 26?bp overlaps and 28?bp short intergenic spaces located in 7 and 11 gene junctions, respectively. The overall nucleotide composition of the L-strand is 29.1% A, 29.5% C, 16.4% G and 25.0% T. The 22 tRNAs range from 65?bp (tRNA-Cys) to 74?bp (tRNA-Val, tRNA-Leu1, tRNA-Lys and tRNA-Thr) in length. Two start codons (ATG and GTG) and two stop codons (AGG and TAA/T) were found in 13 protein-coding genes.
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The complete mitochondrial genome of the wavyband sole Pseudaesopia japonica (Pleuronectiformes: Soleidae).
Mitochondrial DNA
PUBLISHED: 03-26-2014
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Abstract The wavyband sole Pseudaesopia japonica is the only known member of the genus Pseudaesopia. In this study, we firstly determined the complete mitochondrial genome of P. japonica. It is 16,789?bp in length and contains two rRNA genes, 22 tRNA genes, 13 protein-coding genes and one putative control region with the typical gene order and transcriptional direction in vertebrates. The overall base composition of mitogenome in P. japonica is 28.4% A, 30.3% C, 15.6% G and 25.7% T. Two start codons (ATG and GTG) and four stop codons (AGA, AGG, TAG and TAA) were found in 13 protein-coding genes. The 22 tRNAs range from 67?bp (tRNA-Cys and tRNA-Tyr) to 75?bp (tRNA-Lys) in length. The control region is 1120?bp in length, representing a higher proportion of A?+?T (65.3%) while lower of G (12.0%).
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Complete mitogenome of the brown guitarfish Rhinobatos schlegelii (Rajiformes, Rhinobatidae).
Mitochondrial DNA
PUBLISHED: 03-13-2014
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Abstract The complete mitochondrial genome of the brown guitarfish Rhinobatos schlegelii is presented for the first time in this study. It is 16,780?bp in length, consisting 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes and 1 putative control region with the typical gene order and direction of transcription in vertebrates. The overall base composition is 32.1% A, 26.3% C, 13.2% G and 28.3% T. Two start codon (GTG and ATG) and two stop codon patterns (TAG and TAA/T) were found in protein-coding genes. The 22 tRNA genes ranged from 67 (tRNA-Ser2) to 75 (tRNA-Leu1) bp in length. The origin of L-strand replication (OL) was between tRNA-Asn and tRNA-Cys genes within the WANCY region. The tRNA-Ser2 could not be fold into the typical cloverleaf secondary structure because of the replacement of its dihydrouridine arm by a simple loop. The control region was 1089?bp in length with high A?+?T content (64.0%).
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Real time monitoring uracil excision using uracil-containing molecular beacons.
Anal. Chim. Acta
PUBLISHED: 01-29-2014
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As a highly conserved damage repair protein, UDG excises uracil bases through its glycosylase activity. We report here an alternative fluorescence method for UDG assay with high accuracy and sensitivity by applying uracil-modified molecular beacons as substrates. The detection limit of UDG is 0.005 U mL(-1). The KM and kcat are 0.89±0.1 ?M and 210±10 min(-1), respectively. The method is applied to screening inhibitors and the results indicate that both of the 5-FU and cisplatin can inhibit UDG activity with the IC50 values of 6.1±0.52 mM and 3.2±0.24 mM, respectively. Furthermore, the combination of uracil-modified molecular beacons and nuclease inhibitor makes the new method possible to specifically detect UDG activity in cell-free extracts and serum. Taken together, the simple, rapid and sensitive method has potential relevance for a variety of applications, such as molecular diagnosis and screening of UDG inhibitors.
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Complete mitogenome of Hemiculter leucisculus (Cyprinidae: Cultrinae).
Mitochondrial DNA
PUBLISHED: 01-24-2014
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Abstract The complete mitogenome was first determined for a minnow Hemiculter leucisculus in this study. It is 16,622?bp in length and has 13 protein-coding genes, 2 rRNA genes, 22 tRNA genes and 1 control region. Overall nucleotide base composition is 30.4% A, 27.10% C, 17.10% G and 25.40% T. All the tRNA genes can fold into the typical clover-leaf secondary structures, except the tRNA-Ser2 which loses the dihydrouridine arm and is replaced with one 11?bp loop. The origin of light-strand replication (OL) was found between the tRNA-Asn and tRNA-Cys genes while the termination associated sequence (TAS) and the conserved sequence blocks (CSB1-3) were found in the control region.
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Complete mitochondrial genome of the mangrove whipray Himantura granulata (Myliobatiformes: Dasyatidae).
Mitochondrial DNA
PUBLISHED: 01-21-2014
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Abstract In this study, the complete mitogenome of mangrove whipray Himantura granulata was first determined. It is 17,657?bp in length and consists 22 tRNA genes, 2 rRNA genes, 13 protein-coding genes and 1 putative control region with the typical gene arrangement and transcriptional orientation in vertebrates. Two start codon patterns and two stop codon patterns were found in the protein-coding genes. The tRNA-Ser2 (GCU) could not form the typical clover-leafs structure for lacking the dihydrouridine arm. The control region is 1914?bp in length with poor G (14.9%) and high A?+?T (59.1%) content.
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Complete mitochondrial genome of the blue shark Prionace glauca (Elasmobranchii: Carcharhiniformes).
Mitochondrial DNA
PUBLISHED: 09-20-2013
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Abstract In this study, we first presented the complete mitochondrial genome of the blue shark Prionace Glauca, a pelagic and oceanic species. It is 16,705?bp in length and contains 2 rRNA genes, 22 tRNA genes, 13 protein-coding genes and 1 putative control region. The overall base composition is 31.6% A, 24.4% C, 13.1% G and 30.9% T. Overlaps and short inter-genic spaces are located in the genome. The tRNA-Ser2 loses the dihydrouridine arm and cannot be folded into the typical clover-leaf secondary structure. Two start codons (GTG and ATG) with two stop codons (TAG and TAA) or with one incomplete stop codon (T) are found in the 13 protein-coding genes. The control region contains high A?+?T (69.9%) and low G (12.0%).
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Complete mitochondrial genome of the scalloped hammerhead Sphyrna lewini (Carcharhiniformes: Sphyrnidae).
Mitochondrial DNA
PUBLISHED: 09-20-2013
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Abstract The complete mitochondrial genome of the endangered scalloped hammerhead Sphyrna lewini was firstly determined in this study. It is 16,726?bp in length with the typical gene composition and orders in vertebrates. The overall base composition is 31.4% A, 26.3% C, 13.2% G and 29.1% T. Two start codon (ATG and GTG) and three stop codon (TAG, AGA and TAA/TA/T) patterns were found in protein-coding genes. Except for the tRNA-Ser2, the remaining 21 tRNAs can be folded into the typical cloverleaf structure. The control region possess the highest A?+?T content (66.1%) and lowest G content (12.6%) among all mitochondrial partitions.
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Complete mitochondrial genome of the pelagic thresher Alopias pelagicus (Lamniformes: Alopiidae).
Mitochondrial DNA
PUBLISHED: 09-20-2013
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Abstract The complete mitochondrial genome of the pelagic thresher Alopias pelagicus is first presented in this study. It is 16,692?bp in length and contains the 37 genes and 1 control region with the typical gene order and transcriptional direction in the vertebrates. The overall base composition is 32.1% A, 29.3% T, 25.3% C and 13.3% G. Totally, 27?bp overlaps and 25?bp short intergenic spaces are dispersal in the mitogenome. The tRNA-Ser2 (GCU) cannot be folded into the typical cloverleaf structure because of lacking the dihydrouridine arm. Two start codons (ATG and GTG) and three stop codons (AGG, TAG and TAA/T) were used in the 13 protein-coding genes.
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Complete mitochondrial genome of the Japanese wobbegong Orectolobus japonicus (Orectolobiformes: Orectolobidae).
Mitochondrial DNA
PUBLISHED: 08-08-2013
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Abstract The complete mitochondrial genome of the Japanese wobbegong Orectolobus japonicus was presented in this study. It is 16,706?bp in length with the typical gene composition and arrangement in the mitochondrial genome of vertebrates. The overall base composition is 32.6% A, 24.0% C, 13.3% G and 30.1% T. Two start codons (ATG and GTG) and two stop codons (TAG and TAA) were found in protein-coding genes. The tRNA-Ser2 lacks the dihydrouridine arm and cannot be folded into a typical cloverleaf structure. One termination associated sequence (TAS) and three conserved sequence blocks (CSB1-3) were found in the control region.
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Complete mitochodrial genome of Spinibarbus caldwelli (Cypriniformes, Cyprinidae).
Mitochondrial DNA
PUBLISHED: 08-02-2013
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Abstract The complete mitochondrial genome of S. caldwelli was determined in this study. The gene composition, arrangement and transcriptional orientation in S. caldwelli mitogenome were identical to most vertebrates. Two start codon patterns (ATG and GTG) and three stop codon patterns (TAG, TAA and T) were found in protein-coding genes. Only the tRNA-Ser2 could not fold into a typical clover-leaf secondary structure for lacking the dihydrouridine arm. Sequences alignment results suggest that the complete mitogenome of S. caldwelli is an efficient tool to check species identification by comparing different gene sequences.
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Complete mitochondrial genome of the red stingray Dasyatis akajei (Myliobatiformes: Dasyatidae).
Mitochondrial DNA
PUBLISHED: 07-10-2013
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Abstract We determined the complete mitochondrial genome of the red stingray Dasyatis akajei. It is 17,658?bp in length, including 13 protein-coding genes, 2 ribosomal RNA genes, 22 transfer RNA genes and a control region. The gene arrangement and transcriptional direction were the same as those of the typical vertebrate mitogenomes. The overall base composition of the heavy-strand is 28.8% T, 26.8% C, 30.9% A and 13.6% G, with a slight A?+?T bias of 59.7%. The origin of light-strand replication (OL) was identified between tRNA-Asn and tRNA-Cys genes. The termination-associated sequences (TAS) and the conserved sequence blocks (CSB1-3) were identified in the control region.
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Complete mitochondrial genome of Pseudolaubuca engraulis (Pisces: Cyprinidae, Cultrinae).
Mitochondrial DNA
PUBLISHED: 07-10-2013
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Abstract The complete mitogenome of Pseudolaubuca engraulis was determined using long-distance polymerase chain reaction and sequenced by primer walking method. It is 16,612?bp in length and contains 13 protein-coding genes, 2 ribosomal RNA genes, 22 transfer RNA (tRNA) genes and 1 A?+?T-rich control region. The gene arrangement and characterization of P. engraulis are similar to most vertebrates. The overall base composition of the heavy strand is 27.1% A, 27.5% C, 25.9% T and 19.5% G, with a slight A?+?T bias. The shortest tRNA-Ser2 lacks the dihydrouridine arm and is replaced with a simple loop. The termination-associated sequence and the conserved sequence blocks (1-3) are found in the control region.
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Complete mitochondrial genome of the blue-spotted stingray Neotrygon kuhlii (Myliobatiformes: Dasyatidae).
Mitochondrial DNA
PUBLISHED: 07-02-2013
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Abstract The blue-spotted stingray Neotrygon kuhlii is a small stingray distributed in the Indian and West Pacific Ocean. It was considered a species complex by morphological and molecular evidences. In this study, we firstly presented the complete mitochondrial genome of N. kuhlii. It is 18,039?bp in length, including 13 protein-coding genes, two ribosomal RNA genes, 22 transfer RNA genes and 1 control region, with the typical gene order in the mitogenomes of vertebrates. The total base composition is 31.9% A, 26.4% C, 13.1% G and 28.6% T, with an A?+?T bias of 60.5%. Alignment results demonstrated that the mitochondrial sequences of N. kuhlii in this study were highly similar to the 12S, 16S, COI and Cyt b sequences of the specimens collected from the Chinese seas in other studies.
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Complete mitochondrial genome of the tiger shark Galeocerdo cuvier (Carcharhiniformes: Carcharhinidae).
Mitochondrial DNA
PUBLISHED: 07-02-2013
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Abstract The tiger shark Galeocerdo cuvier is the only member of the genus Galeocerdo. The complete mitochondrial genome of G. cuvier is presented for the first time in this study. The gene composition and arrangement in the mitogenome of G. cuvier is identical to most animal mitogenome. There are 22?bp short noncoding sequences and 44 bp overlaps in the mitogenome. The overall base composition is 31.8% A, 23.9% C, 13.0% G and 31.3% T. The dihydrouridine arm of tRNA-Ser2 was replaced by a simple loop and the other tRNAs could be folded into the typical cloverleaf structure.
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Calcium/calmodulin-dependent serine protein kinase is involved in exendin-4-induced insulin secretion in INS-1 cells.
Metab. Clin. Exp.
PUBLISHED: 06-04-2013
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Exendin-4 (Ex-4) is an anti-diabetic drug that is a potent agonist of the glucagon-like peptide-1 (GLP-1) receptor. It has already been approved for the treatment of type 2 diabetes mellitus, but its underlying mechanisms of action are not fully understood. Calcium/calmodulin-dependent serine protein kinase (CASK), which plays a vital role in the transport and release of neurotransmitters in neurons, is expressed in pancreatic islet cells and ?-cells. This study aimed to investigate whether CASK is involved in the insulin secretagogue action induced by Ex-4 in INS-1 cells.
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[Comparative study on effect of plum-blossom needle and western medication on follicular maldevelopment].
Zhongguo Zhen Jiu
PUBLISHED: 05-30-2013
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To observe clinical efficacy of plum-blossom needle for follicular maldevelopment (FM).
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Complete mitogenome of Pseudohemiculter dispar (Cyprinidae: Cultrinae).
Mitochondrial DNA
PUBLISHED: 04-25-2013
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The complete mitogenome was first determined for a minnow Pseudohemiculter dispar in this study. It is 16,621 bp in length, including 13 protein-coding genes, 2 rRNA genes, 22 tRNA genes, and 1 control region. Overall nucleotide base composition is 30.30% A, 27.10% C, 17.10% G, and 25.50% T, with a A+T bias. Except for the tRNA-Ser2 that lost the dihydrouridine arm and replaced with one 11-bp loop, the other 22 tRNA genes can fold into the typical cloverleaf secondary structures. The origin of light-strand replication (OL) was found between the tRNA-Asn and tRNA-Cys genes, while the termination-associated sequence (TAS) was found in the control region. Both OL and TAS can form the hairpin structure that acts as the signals participated in the mitochondrial DNA replication.
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Real time monitoring of junction ribonuclease activity of RNase H using chimeric molecular beacons.
Analyst
PUBLISHED: 04-24-2013
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As a highly conserved damage repair protein, except for hydrolysis of DNA-RNA heteroduplex endonucleolytically, RNase H can cleave RNA-DNA junctions in Okazaki fragment processing through its junction ribonuclease (JRNase) activity. We report here a real time fluorescence method for detecting JRNase activity of RNase H with high accuracy by applying chimeric molecular beacons as substrates. The detection limit of E. coli RNase H is 0.5 U ml(-1). The Km and kcat are 20 nM and 0.6 s(-1), respectively. In addition, we used the method to investigate the effect of chemical drugs on the enzyme and found that both penicillin and streptomycin sulfate inhibit its activity with the IC50 values of 0.2 and 0.07 mM, respectively. Finally, we applied the method to reliably detect the JRNase level in tumor cells. In summary, these data indicate that the simple, rapid and sensitive method can be hopefully applied for high-throughput detection of samples and drug screening in vitro.
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Mitochondrial genome of blotched fantail ray Taeniura meyeni (Myliobatiformes: Dasyatidae).
Mitochondrial DNA
PUBLISHED: 03-06-2013
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The complete mitogenome of the blotched fantail ray Taeniura meyeni (Myliobatiformes: Dasyatidae) was first presented. The mitogenome is 17,638 bp in length and contains 13 protein-coding genes, 2 rRNAs, 22 tRNAs and control region, with the typical gene order and direction of transcription in vertebrate. The overall nucleotide composition of the whole mitogenome is A 30.74%, C 28.16%, G 13.47% and T 27.63%. The termination-associated sequence and three conserved sequence blocks were identified in the control region.
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Allitridin inhibits human cytomegalovirus replication in vitro.
Mol Med Rep
PUBLISHED: 02-05-2013
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Human cytomegalovirus (HCMV) has been associated with a wide spectrum of diseases. There is currently no effective treatment for eliminating the virus. Garlic bulb extract has been reported to possess anti-viral efficacy. This study aimed to investigate the expression of the immediate?early (IE; ul122 and ul123), early (E; ul54) and late (L; ul83) genes of HCMV as well as the inhibitory effect of allitridin on the transcription levels of these genes. The results indicated that a HCMV gene expression cascade occurred, and that the deletion of IE72 had no influence on the transcription of the ul122 gene, while it led to significant reductions of ul54 and ul83 mRNA expression levels. Additionally, allitridin effectively suppressed the transcription of the HCMV IE, E and L genes; the inhibition rates of the transcription of the ul122 and ul123 genes were higher compared with those of ul54 and ul83 mRNA expression, while the expression of the IE genes was not significantly reduced by ganciclovir (GCV). Our results indicate that the HCMV IE72 deletion mutant strain affects the transcription of the virus downstream gene, allitridin inhibits HCMV infection in vitro, and that the IE genes may be the key target of allitridin in its action against HCMV.
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Changes of AM fungal abundance along environmental gradients in the arid and semi-arid grasslands of northern China.
PLoS ONE
PUBLISHED: 01-26-2013
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Arbuscular mycorrhizal (AM) fungi are ubiquitous symbionts of higher plants in terrestrial ecosystems, while the occurrence of the AM symbiosis is influenced by a complex set of abiotic and biotic factors. To reveal the regional distribution pattern of AM fungi as driven by multiple environmental factors, and to understand the ecological importance of AM fungi in natural ecosystems, we conducted a field investigation on AM fungal abundance along environmental gradients in the arid and semi-arid grasslands of northern China. In addition to plant parameters recorded in situ, soil samples were collected, and soil chemo-physical and biological parameters were measured in the lab. Statistical analyses were performed to reveal the relative contribution of climatic, edaphic and vegetation factors to AM fungal abundance, especially for extraradical hyphal length density (HLD) in the soil. The results indicated that HLD were positively correlated with mean annual temperature (MAT), soil clay content and soil pH, but negatively correlated with both soil organic carbon (SOC) and soil available N. The multiple regressions and structural equation model showed that MAT was the key positive contributor and soil fertility was the key negative contributor to HLD. Furthermore, both the intraradical AM colonization (IMC) and relative abundance of AM fungi, which was quantified by real-time PCR assay, tended to decrease along the increasing SOC content. With regard to the obvious negative correlation between MAT and SOC in the research area, the positive correlation between MAT and HLD implied that AM fungi could potentially mitigate soil carbon losses especially in infertile soils under global warming. However, direct evidence from long-term experiments is still expected to support the AM fungal contribution to soil carbon pools.
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Complete mitochondrial genome of the Sinibrama macrops (Cyprinidae: Cultrinae).
Mitochondrial DNA
PUBLISHED: 01-18-2013
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The complete mitochondrial genome of Sinibrama macrops was first determined in this study. The genome is 16,626 bp in length, including 13 protein-coding genes, 2 ribosomal RNA genes, 22 transfer RNA genes and 1 control region. Its gene arrangement and translation direction were identical to those of other typical vertebrates. The overall base composition is 30.7% A, 27.9% C, 16.7% G and 24.7% T, with the negative GC skew value ( - 0.251). In a long term, S. macrops was confused with Sinibrama wui, which was confirmed as an invalid species by recent morphological study. Therefore, the mitochondrial genome of S. macrops can contribute to the molecular identification of the species and further phylogenetic study of Cyprinidae.
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Activation of mammalian target of rapamycin complex 1 (mTORC1) and Raf/Pyk2 by growth factor-mediated Eph receptor 2 (EphA2) is required for cholangiocarcinoma growth and metastasis.
Hepatology
PUBLISHED: 01-15-2013
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Eph receptor 2 (EphA2) overexpression is frequently accompanied by the loss of its cognate ligand during tumor progression. However, the molecular mechanism of this ligand-independent promotion of tumor by EphA2 remains unclear in highly malignant and fatal cholangiocarcinoma (CC). We examined the biological role of EphA2 in tumor growth and metastasis in CC tissues and cells according to the degree of differentiation and we explored the downstream signaling pathways of EphA2. Growth factor-mediated EphA2 overexpression itself leads to the activation of the mammalian target of rapamycin complex 1 (mTORC1) and extracellular signal-regulated kinase (ERK) pathways through ligand-independent activation of EphA2 (phosphorylation of S897). An in vitro soft agar assay and in vivo orthotopic or subcutaneous tumor model showed that EphA2 enhanced colony formation and accelerated tumor growth, and which seemed to be mainly associated with Akt (T308)/mTORC1 activation. Aberrant expression and activation of EphA2 was also associated with poorer differentiation and higher metastatic ability. Enhanced metastatic ability was also observed in an orthotopic tumor model or lung metastasis model, correlating with Pyk2(Y402)/c-Src/ERK activation in addition to activation of the canonical Raf/MEK/ERK pathway. The mTORC1 and Raf/Pyk2 pathways also appeared to affect each other. These results suggest that growth factor-mediated EphA2 might be involved in tumor growth and metastasis through activation of the mTORC1 and Raf/Pyk2 pathways. Therapeutic strategies that target EphA2 and its downstream effectors may be useful to control CC. (HEPATOLOGY 2013;57:2248-2260).
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Complete mitochondrial genome of Acrossocheilus wenchowensis (Cyprinidae, Barbinae).
Mitochondrial DNA
PUBLISHED: 01-11-2013
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We determined the complete mitochondrial genome (mitogenome) of Acrossocheilus wenchowensis. It is the first report of mitogenome in genus Acrossocheilus. The total length of A. wenchowensis is 16,591 bp, consisting of 13 protein-coding genes, 2 rRNA genes, 22 transfer RNA genes and a A+T rich control region. The gene order and transcriptional orientation are similar to most vertebrates. The overall base composition is 31.00% A, 27.70% C, 16.30% G and 25.00% T. The termination-associated sequence and conserved sequence blocks were identified in the control region.
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Genome-wide expression patterns associated with oncogenesis and sarcomatous transdifferentation of cholangiocarcinoma.
BMC Cancer
PUBLISHED: 02-19-2011
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The molecular mechanisms of CC (cholangiocarcinoma) oncogenesis and progression are poorly understood. This study aimed to determine the genome-wide expression of genes related to CC oncogenesis and sarcomatous transdifferentiation.
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Preparation of photocrosslinkable polystyrene methylene cinnamate nanofibers via electrospinning.
J Nanosci Nanotechnol
PUBLISHED: 01-22-2011
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Nanoscaled photocrosslinkable polystyrene methylene cinnamate (PSMC) nanofibers were fabricated by electrospinning. The PSMC was prepared by the modification of polystyrene as a starting material via a two-step reaction process, chloromethylation and esterification. The chemical structure of PSMC was confirmed by 1H NMR and Fourier transform infrared spectroscopy (FT-IR). The photosensitivity of the PSMC was investigated using ultraviolet (UV) spectroscopic methods. Electrospun PSMC nanofiber mat showed excellent solubility in many organic solvents. UV irradiation of the electrospun mats led to photodimerization to resist dissolving in organic solvents. The morphology of the nanofiber was observed by scanning electron microscopy (SEM) and the result indicated that the average diameter of nanofibers is 350 nm and the crosslinked nanofibers were not collapsed after dipping into organic solvent showing good solvent-stability. This photocrosslinked nanofibers has the potential application in filtration, catalyst carrier and protective coating.
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The inhibitory effect of celecoxib on mouse hepatoma H22 cell line on the arachidonic acid metabolic pathway.
Biochem. Cell Biol.
PUBLISHED: 07-24-2010
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Celecoxib is a selective inhibitor of cyclooxygenase-2 (COX-2). It may reduce the risk of cancer formation by affecting the metabolism of arachidonic acid (AA), which has been implicated in the development of cancer. Accordingly, this study was designed to determine the effects of celecoxib on the AA pathway in mouse hepatoma H22 cells. Celecoxib was found to inhibit the proliferation of H22 cells in a dose- and time-dependent manner. Low doses (50 and 100 micromol.L-1) of celecoxib caused an increase in the expression of cytosolic phospholipase A2 (cPLA2), but did not affect the expression of COX-2 in terms of the mRNA and protein levels. Surprisingly, the amount of AA was elevated and the level of prostaglandin E2 (PGE2) was unaltered in the culture supernatant. At higher celecoxib doses (200 and 400 micromol.L-1), the mRNA and protein of both COX-2 and cPLA2 were inhibited. The concentration of AA was increased, and PGE2 level was depressed in H22 cells. The ratio of AA to PGE2 was increased in a dose-dependent manner. Our findings suggest that the imbalance between AA and PGE2, characterized by increased AA at a low dosage and decreased PGE2 at a high dosage of celecoxib, was an important indicator of cytotoxicity of celecoxib on H22 cells.
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Measurements of degree of sensitization (DoS) in aluminum alloys using EMAT ultrasound.
Ultrasonics
PUBLISHED: 06-30-2010
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Sensitization in 5XXX aluminum alloys is an insidious problem characterized by the gradual formation and growth of beta phase (Mg(2)Al(3)) at grain boundaries, which increases the susceptibility of alloys to intergranular corrosion (IGC) and intergranular stress-corrosion cracking (IGSCC). The degree of sensitization (DoS) is currently quantified by the ASTM G67 Nitric Acid Mass Loss Test, which is destructive and time consuming. A fast, reliable, and non-destructive method for rapid detection and the assessment of the condition of DoS in AA5XXX aluminum alloys in the field is highly desirable. In this paper, we describe a non-destructive method for measurements of DoS in aluminum alloys with an electromagnetic acoustic transducer (EMAT). AA5083 aluminum alloy samples were sensitized at 100°C with processing times varying from 7days to 30days. The DoS of sensitized samples was first quantified with the ASTM 67 test in the laboratory. Both ultrasonic velocity and attenuation in sensitized specimens were then measured using EMAT and the results were correlated with the DoS data. We found that the longitudinal wave velocity was almost a constant, independent of the sensitization, which suggests that the longitudinal wave can be used to determine the sample thickness. The shear wave velocity and especially the shear wave attenuation are sensitive to DoS. Relationships between DoS and the shear velocity, as well as the shear attenuation have been established. Finally, we performed the data mining to evaluate and improve the accuracy in the measurements of DoS in aluminum alloys with EMAT.
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[Clinical and medication characteristics of senior hospitalized patients with chronic constipation].
Zhonghua Yi Xue Za Zhi
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To analyze the clinical features, risk factors and drug uses of senior hospitalized patients with chronic constipation.
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Stabilization of G-quadruplex DNA by C-5-methyl-cytosine in bcl-2 promoter: implications for epigenetic regulation.
Biochem. Biophys. Res. Commun.
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The C-5-methylation of cytosine in the CpG islands is an important pattern for epigenetic modification of gene, which plays a key role in regulating gene transcription. G-quadruplex is an unusual DNA secondary structure formed in G-rich regions and is identified as a transcription repressor in some oncogenes, such as c-myc and bcl-2. In the present study, the results from CD spectrum and FRET assay showed that the methylation of cytosine in the CpG islands could induce a conformational change of the G-quadruplex in the P1 promoter of bcl-2, and greatly increase the thermal-stability of this DNA oligomer. Moreover, the methylation of cytosine in the G-quadruplex could protect the structure from the disruption by the complementary strand, showing with the increasing ability to arrest the polymerase in PCR stop assay. This data indicated that the stabilization of the G-quadruplex structure in the CpG islands might be involved in the epigenetical transcriptional regulation for specific genes through the C-5-methylation modification pattern.
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Complete mitogenome of the pale-edged stingray Dasyatis zugei (Myliobatiformes: Dasyatidae).
Mitochondrial DNA
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The complete mitogenome of the pale-edged stingray (Dasyatis zugei) was first confirmed in this study. The mitogenome is 18,264 bp in length and contains 13 protein-coding genes, 2 rRNAs, 22 tRNAs and 1 control region, with the typical gene order in vertebrates. Similar to nucleotide composition of most vertebrate mitogenomes, the nucleotide composition of the pale-edged stingray demonstrates low G and high A+T components. The control region of the pale-edged stingray is 2523 bp in length, the longest known in Chondrichthyes. The termination-associated sequence and two short conserved blocks (CSB II and CSB III) are found in the control region.
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[Morphologic diagnosis and onset characteristics of acute leukemia: a retrospective analysis of 233 cases in 10 years].
Zhongguo Shi Yan Xue Ye Xue Za Zhi
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The objective of this study was to evaluate the value of morphologic diagnosis for acute leukemia (AL), to explore the relation of morphologic diagnosis with immunology, cytogenetics and molecular biology diagnosis of AL and to analyze the onset characteristics of AL in 10 years. The samples of bone marrow and peripheral blood from 233 newly diagnosed cases of AL were collected during 2001-2011 years; the morphologic examination and immunologic, cytogenetic and molecular biologic examination (ICM) were carried out, the consistency of morphologic diagnosis with ICM diagnosis was compared, the onset characteristics of AL was analyzed. The results showed that: (1) the consistent rate of immunology, cytogenetics, molecular biology diagnosis with morphologic diagnosis was 84.3%. The order of consistent rat was AUL, M0 < M1 < HAL < M4 < M2 < M3 < M5 < ALL < M6, M7, AP; (2) Misdiagnosis always occurred among AUL, M0, M1, ALL and HAL or among M2a, M3v, M4 and M5. (3) In 233 cases, the highest ratio of blast was observed in M1 (92.5%), while the lowest ratio of blast was observed in M2 (49.5%). (4) AL occurred more frequently in males than that in female (147:86). (5) AL occurred in patients aged from 1 to 88 years. The median age was 41.5 for AUL, 40.8 for M0, 43.4 for M1, 46.3 for M2, 33.8 for M3, 42.6 for M4, 48.8 for M5, 77.3 for M6, 2.5 for M7, 65.0 for AP, 29.1 for ALL and 40.3 for HAL. (6) The number of patients in the later five years (139 cases) was significantly greater than that in the first five years (94 cases), especially the patients with M1, M2, M3, M4, and M5. It is concluded that morphologic diagnosis has important clinical value in the MICM diagnosis of AL. Attaching importance to the confusing cell morphology and onset characteristics of AL can improve the diagnostic accuracy.
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