bluuebunny/crossref_metadata_2025_split huggingface dataset:
NSMAP: A method for spliced isoforms identification and quantification from RNA-Seq
Authors: Xia Zheng , Wen Jianguo , Chang Chung-Che , Zhou Xiaobo 
Published: May 2011

Abstract

Background
The development of techniques for sequencing the messenger RNA (RNA-Seq) enables it to study the biological mechanisms such as alternative splicing and gene expression regulation more deeply and accurately. Most existing methods employ RNA-Seq to quantify the expression levels of already annotated isoforms from the reference genome. However, the current reference genome is very incomplete due to the complexity of the transcriptome which hiders the comprehensive investigation of transcriptome using RNA-Seq. Novel study on isoform inference and estimation purely from RNA-Seq without annotation information is desirable.

Results
A N onnegativity and S parsity constrained M aximum A
P osteriori (NSMAP) model has been proposed to estimate the expression levels of isoforms from RNA-Seq data without the annotation information. In contrast to previous methods, NSMAP performs identification of the structures of expressed isoforms and estimation of the expression levels of those expressed isoforms simultaneously, which enables better identification of isoforms. In the simulations parameterized by two real RNA-Seq data sets, more than 77% expressed isoforms are correctly identified and quantified. Then, we apply NSMAP on two RNA-Seq data sets of myelodysplastic syndromes (MDS) samples and one normal sample in order to identify differentially expressed known and novel isoforms in MDS disease.

Conclusions
NSMAP provides a good strategy to identify and quantify novel isoforms without the knowledge of annotated reference genome which can further realize the potential of RNA-Seq technique in transcriptome analysis. NSMAP package is freely available at https://sites.google.com/site/nsmapforrnaseq.
Identification of microRNA precursors based on random forest with network-level representation method of stem-loop structure
Authors: Xiao Jiamin , Tang Xiaojing , Li Yizhou , Fang Zheng , Ma Daichuan , He Yangzhige , Li Menglong 
Published: May 2011

Abstract

Background
MicroRNAs (miRNAs) play a key role in regulating various biological processes such as participating in the post-transcriptional pathway and affecting the stability and/or the translation of mRNA. Current methods have extracted feature information at different levels, among which the characteristic stem-loop structure makes the greatest contribution to the prediction of putative miRNA precursor (pre-miRNA). We find that none of these features alone is capable of identifying new pre-miRNA accurately.

Results
In the present work, a pre-miRNA stem-loop secondary structure is translated to a network, which provides a novel perspective for its structural analysis. Network parameters are used to construct prediction model, achieving an area under the receiver operating curves (AUC) value of 0.956. Moreover, by repeating the same method on two independent datasets, accuracies of 0.976 and 0.913 are achieved, respectively.

Conclusions
Network parameters effectively characterize pre-miRNA secondary structure, which improves our prediction model in both prediction ability and computation efficiency. Additionally, as a complement to feature extraction methods in previous studies, these multifaceted features can reflect natural properties of miRNAs and be used for comprehensive and systematic analysis on miRNA.
Tools for genetic manipulation of the plant growth-promoting bacterium Azospirillum amazonense
Authors: Sant'Anna Fernando H , Andrade Dieime S , Trentini Débora B , Weber Shana S , Schrank Irene S 
Published: May 2011

AbstractBackgroundAzospirillum amazonensehas potential to be used as agricultural inoculant since it promotes plant growth without causing pollution, unlike industrial fertilizers. Owing to this fact, the study of this species has gained interest. However, a detailed understanding of its genetics and physiology is limited by the absence of appropriate genetic tools for the study of this species.ResultsConjugation and electrotransformation methods were established utilizing vectors with broad host-replication origins (pVS1 and pBBR1). Two genes of interest -glnKandglnB, encoding PII regulatory proteins - were isolated. Furthermore,glnK-specificA. amazonensemutants were generated utilizing the pK19MOBSACB vector system. Finally, a promoter analysis protocol based on fluorescent protein expression was optimized to aid genetic regulation studies on this bacterium.ConclusionIn this work, genetic tools that can support the study ofA. amazonensewere described. These methods could provide a better understanding of the genetic mechanisms of this species that underlie its plant growth promotion.
GhMPK16, a novel stress-responsive group D MAPK gene from cotton, is involved in disease resistance and drought sensitivity
Authors: Shi Jing , Zhang Liang , An Hailong , Wu Changai , Guo Xingqi 
Published: May 2011

Abstract

Background
Mitogen-activated protein kinase (MAPK) cascades play pivotal roles in mediating biotic and abiotic stress responses. In plants, MAPKs are classified into four major groups (A-D) according to their sequence homology and conserved phosphorylation motifs. Members of group A and B have been extensively characterized, but little information on the group D MAPKs has been reported.

Results
In this study, we isolated and characterised GhMPK16, the first group D MAPK gene found in cotton. Southern blot analysis suggests GhMPK16 is single copy in the cotton genome, and RNA blot analysis indicates that GhMPK16 transcripts accumulate following pathogen infection and treatment with multiple defense-related signal molecules. The analysis of the promoter region of GhMPK16 revealed a group of putative cis-acting elements related to stress responses. Subcellular localization analysis suggests that GhMPK16 acts in the nucleus. Transgenic Arabidopsis overexpressing GhMPK16 displayed significant resistance to fungi (Colletotrichum nicotianae and Alternaria alternata) and bacteria (Pseudomonas solanacearum) pathogen, and the transcripts of pathogen-related (PR) genes were more rapidly and strongly induced in the transgenic plants. Furthermore, transgenic Arabidopsis showed reduced drought tolerance and rapid H2O2 accumulation.

Conclusion
These results suggest that GhMPK16 might be involved in multiple signal transduction pathways, including biotic and abiotic stress signaling pathways.
Membrane Sealant Poloxamer P188 Protects Against Isoproterenol Induced Cardiomyopathy in Dystrophin Deficient Mice
Authors: Spurney Christopher F , Guerron Alfredo D , Yu Qing , Sali Arpana , van der Meulen Jack H , Hoffman Eric P , Nagaraju Kanneboyina 
Published: May 2011

Abstract

Background
Cardiomyopathy in Duchenne muscular dystrophy (DMD) is an increasing cause of death in patients. The absence of dystrophin leads to loss of membrane integrity, cell death and fibrosis in cardiac muscle. Treatment of cardiomyocyte membrane instability could help prevent cardiomyopathy.

Methods
Three month old female mdx mice were exposed to the β1 receptor agonist isoproterenol subcutaneously and treated with the non-ionic tri-block copolymer Poloxamer P188 (P188) (460 mg/kg/dose i.p. daily). Cardiac function was assessed using high frequency echocardiography. Tissue was evaluated with Evans Blue Dye (EBD) and picrosirius red staining.

Results
BL10 control mice tolerated 30 mg/kg/day of isoproterenol for 4 weeks while death occurred in mdx mice at 30, 15, 10, 5 and 1 mg/kg/day within 24 hours. Mdx mice tolerated a low dose of 0.5 mg/kg/day. Isoproterenol exposed mdx mice showed significantly increased heart rates (p < 0.02) and cardiac fibrosis (p < 0.01) over 4 weeks compared to unexposed controls. P188 treatment of mdx mice significantly increased heart rate (median 593 vs. 667 bpm; p < 0.001) after 2 weeks and prevented a decrease in cardiac function in isoproterenol exposed mice (Shortening Fraction = 46 ± 6% vs. 35 ± 6%; p = 0.007) after 4 weeks. P188 treated mdx mice did not show significant differences in cardiac fibrosis, but demonstrated significantly increased EBD positive fibers.

Conclusions
This model suggests that chronic intermittent intraperitoneal P188 treatment can prevent isoproterenol induced cardiomyopathy in dystrophin deficient mdx mice.
Rapid screening for chromosomal aneuploidies using array-MLPA
Authors: Yan Jing-Bin , Xu Miao , Xiong Can , Zhou Da-Wen , Ren Zhao-Rui , Huang Ying , Mommersteeg Monique , van Beuningen Rinie , Wang Ying-Tai , Liao Shi-Xiu , Zeng Fanyi , Wu Ying , Zeng Yi-Tao 
Published: May 2011

Abstract

Background
Chromosome abnormalities, especially trisomy of chromosome 21, 13, or 18 as well as sex chromosome aneuploidy, are a well-established cause of pregnancy loss. Cultured cell karyotype analysis and FISH have been considered reliable detectors of fetal abnormality. However, results are usually not available for 3-4 days or more. Multiplex ligation-dependent probe amplification (MLPA) has emerged as an alternative rapid technique for detection of chromosome aneuploidies. However, conventional MLPA does not allow for relative quantification of more than 50 different target sequences in one reaction and does not detect mosaic trisomy. A multiplexed MLPA with more sensitive detection would be useful for fetal genetic screening.

Methods
We developed a method of array-based MLPA to rapidly screen for common aneuploidies. We designed 116 universal tag-probes covering chromosomes 13, 18, 21, X, and Y, and 8 control autosomal genes. We performed MLPA and hybridized the products on a 4-well flow-through microarray system. We determined chromosome copy numbers by analyzing the relative signals of the chromosome-specific probes.

Results
In a blind study of 161 peripheral blood and 12 amniotic fluid samples previously karyotyped, 169 of 173 (97.7%) including all the amniotic fluid samples were correctly identified by array-MLPA. Furthermore, we detected two chromosome X monosomy mosaic cases in which the mosaism rates estimated by array-MLPA were basically consistent with the results from karyotyping. Additionally, we identified five Y chromosome abnormalities in which G-banding could not distinguish their origins for four of the five cases.

Conclusions
Our study demonstrates the successful application and strong potential of array-MLPA in clinical diagnosis and prenatal testing for rapid and sensitive chromosomal aneuploidy screening. Furthermore, we have developed a simple and rapid procedure for screening copy numbers on chromosomes 13, 18, 21, X, and Y using array-MLPA.
No association between polymorphisms/haplotypes of the vascular endothelial growth factor gene and preeclampsia
Authors: Garza-Veloz Idalia , Castruita-De la Rosa Claudia , Cortes-Flores Raul , Martinez-Gaytan Victoria , Rivera-Muñoz Jose E , Garcia-Mayorga Elda A , Meza-Lamas Esteban , Rojas-Martinez Augusto , Ortiz-Lopez Rocio , Martinez-Fierro Margarita L 
Published: May 2011

Abstract

Background
Preeclampsia (PE) is the first worldwide cause of death in pregnant women, intra-uterine growth retardation, and fetal prematurity. Some vascular endothelial grown factor gene (VEGF) polymorphisms have been associated to PE and other pregnancy disturbances. We evaluated the associations between VEGF genotypes/haplotypes and PE in Mexican women.

Methods
164 pregnant women were enrolled in a case-control study (78 cases and 86 normotensive pregnant controls). The rs699947 (-2578C/A), rs1570360 (-1154G/A), rs2010963 (+405G/C), and rs25648 (-7C/T), VEGF variants were discriminated using Polymerase Chain Reaction - Restriction Fragment Length Polymorphism (PCR-RFLP) methods or Taqman single nucleotide polymorphism (SNP) assays.

Results
The proportions of the minor allele for rs699947, rs1570360, rs2010963, and rs25648 VEGF SNPs were 0.33, 0.2, 0.39, and 0.17 in controls, and 0.39, 0.23, 0.41, and 0.15 in cases, respectively (P values > 0.05). The most frequent haplotypes of rs699947, rs1570360, rs2010963, and rs25648 VEGF SNPs, were C-G-C-C and C-G-G-C with frequencies of 0.39, 0.21 in cases and 0.37, 0.25 in controls, respectively (P values > 0.05)

Conclusion
There was no evidence of an association between VEGF alleles, genotypes, or haplotypes frequencies and PE in our study.
Analysis of the Mitogen-activated protein kinase kinase 4 (MAP2K4) tumor suppressor gene in ovarian cancer
Authors: Davis Sally J , Choong David YH , Ramakrishna Manasa , Ryland Georgina L , Campbell Ian G , Gorringe Kylie L 
Published: May 2011

Abstract

Background

MAP2K4 is a putative tumor and metastasis suppressor gene frequently found to be deleted in various cancer types. We aimed to conduct a comprehensive analysis of this gene to assess its involvement in ovarian cancer.

Methods
We screened for mutations in MAP2K4 using High Resolution Melt analysis of 149 primary ovarian tumors and methylation at the promoter using Methylation-Specific Single-Stranded Conformation Polymorphism analysis of 39 tumors. We also considered the clinical impact of changes in MAP2K4 using publicly available expression and copy number array data. Finally, we used siRNA to measure the effect of reducing MAP2K4 expression in cell lines.

Results
In addition to 4 previously detected homozygous deletions, we identified a homozygous 16 bp truncating deletion and a heterozygous 4 bp deletion, each in one ovarian tumor. No promoter methylation was detected. The frequency of MAP2K4 homozygous inactivation was 5.6% overall, and 9.8% in high-grade serous cases. Hemizygous deletion of MAP2K4 was observed in 38% of samples. There were significant correlations of copy number and expression in three microarray data sets. There was a significant correlation between MAP2K4 expression and overall survival in one expression array data set, but this was not confirmed in an independent set. Treatment of JAM and HOSE6.3 cell lines with MAP2K4 siRNA showed some reduction in proliferation.

Conclusions

MAP2K4 is targeted by genetic inactivation in ovarian cancer and restricted to high grade serous and endometrioid carcinomas in our cohort.
Genetic polymorphisms of DNA double strand break gene Ku70 and gastric cancer in Taiwan
Authors: Yang Mei-Due , Wang Hwei-Chung , Chang Wen-Shin , Tsai Chia-Wen , Bau Da-Tian 
Published: May 2011

Abstract

Background and aim
The DNA repair gene Ku70, an important member of non-homologous end-joining repair system, is thought to play an important role in the repairing of DNA double strand breaks. It is known that defects in double strand break repair capacity can lead to irreversible genomic instability. However, the polymorphic variants of Ku70, have never been reported about their association with gastric cancer susceptibility.

Methods
In this hospital-based case-control study, the associations of Ku70 promoter T-991C (rs5751129), promoter G-57C (rs2267437), promoter A-31G (rs132770), and intron 3 (rs132774) polymorphisms with gastric cancer risk in a Taiwanese population were investigated. In total, 136 patients with gastric cancer and 560 age- and gender-matched healthy controls recruited from the China Medical Hospital in Taiwan were genotyped.

Results
As for Ku70 promoter T-991C, the ORs after adjusted by age and gender of the people carrying TC and CC genotypes were 2.41 (95% CI = 1.53-3.88) and 3.21 (95% CI = 0.96-9.41) respectively, compared to those carrying TT wild-type genotype. The P for trend was significant (P < 0.0001). In the dominant model (TC plus CC versus TT), the association between Ku70 promoter T-991C polymorphism and the risk for gastric cancer was also significant (adjusted OR = 2.48, 95% CI = 1.74-3.92). When stratified by age and gender, the association was restricted to those at the age of 55 or elder of age (TC vs TT: adjusted OR = 2.52, 95% CI = 1.37-4.68, P = 0.0139) and male (TC vs TT: adjusted OR = 2.58, 95% CI = 1.33-4.47, P = 0.0085). As for the other three polymorphisms, there was no difference between both groups in the distributions of their genotype frequencies.

Conclusion
In conclusion, the Ku70 promoter T-991C (rs5751129), but not the Ku70 promoter C-57G (rs2267437), promoter A-31G (rs132770) or intron 3 (rs132774), is associated with gastric cancer susceptibility. This polymorphism may be a novel useful marker for gastric carcinogenesis.
G protein-coupled receptor kinase 5 mediates Tazarotene-induced gene 1-induced growth suppression of human colon cancer cells
Authors: Wu Chang-Chieh , Tsai Fu-Ming , Shyu Rong-Yaun , Tsai Ya-Ming , Wang Chun-Hua , Jiang Shun-Yuan 
Published: May 2011

Abstract

Background
Tazarotene-induced gene 1 (TIG1) is a retinoid-inducible type II tumour suppressor gene. The B isoform of TIG1 (TIG1B) inhibits growth and invasion of cancer cells. Expression of TIG1B is frequently downregulated in various cancer tissues; however, the expression and activities of the TIG1A isoform are yet to be reported. Therefore, this study investigated the effects of the TIG1A and TIG1B isoforms on cell growth and gene expression profiles using colon cancer cells.

Methods
TIG1A and TIG1B stable clones derived from HCT116 and SW620 colon cancer cells were established using the GeneSwitch system; TIG1 isoform expression was induced by mifepristone treatment. Cell growth was assessed using the WST-1 cell proliferation and colony formation assays. RNA interference was used to examine the TIG1 mediating changes in cell growth. Gene expression profiles were determined using microarray and validated using real-time polymerase chain reaction, and Western blot analyses.

Results
Both TIG1 isoforms were expressed at high levels in normal prostate and colon tissues and were downregulated in colon cancer cell lines. Both TIG1 isoforms significantly inhibited the growth of transiently transfected HCT116 cells and stably expressing TIG1A and TIG1B HCT116 and SW620 cells. Expression of 129 and 55 genes was altered upon induction of TIG1A and TIG1B expression, respectively, in stably expressing HCT116 cells. Of the genes analysed, 23 and 6 genes were upregulated and downregulated, respectively, in both TIG1A and TIG1B expressing cells. Upregulation of the G-protein-coupled receptor kinase 5 (GRK5) was confirmed using real-time polymerase chain reaction and Western blot analyses in both TIG1 stable cell lines. Silencing of TIG1A or GRK5 expression significantly decreased TIG1A-mediated cell growth suppression.

Conclusions
Expression of both TIG1 isoforms was observed in normal prostate and colon tissues and was downregulated in colon cancer cell lines. Both TIG1 isoforms suppressed cell growth and stimulated GRK5 expression in HCT116 and SW620 cells. Knockdown of GRK5 expression alleviated TIG1A-induced growth suppression of HCT116 cells, suggesting that GRK5 mediates cell growth suppression by TIG1A. Thus, TIG1 may participate in the downregulation of G-protein coupled signaling by upregulating GRK5 expression.
Cancer mortality in a Chinese population surrounding a multi-metal sulphide mine in Guangdong province: an ecologic study
Authors: Wang Mao , Song Hong , Chen Wei-Qing , Lu Ciyong , Hu Qianshen , Ren Zefang , Yang Yan , Xu Yanjun , Zhong Aiming , Ling Wenhua 
Published: May 2011

Abstract

Background
The Dabaoshan mine in the southeast of Guangdong Province, China, is at high risk of multi-metal pollutant discharge into a local river (Hengshihe) and the surrounding area. Following approximately 30 years of exposure to these metals, little is known regarding the subsequent health effects and risks for the local residents. In our present study, we have estimated the relationships between long-term environmental exposure to multiple heavy metals and the risk of cancer mortality in a Chinese population in the vicinity of Dabaoshan.

Methods
An ecologic study was performed. Between 2000-2007, a total population of 194,131 lived in the nine agricultural villages that surround the Hengshihe area. Heavy metals concentrations were determined in local environmental samples (water and crops) and whole blood taken from 1152 local residents of both a high-exposure area (HEA) and a low-exposure area (LEA). We calculated the rate ratio and standardized mortality ratios based on age- and gender-specific cancer mortality rates for the different reference populations (based on district, county and province). Simple, multiple linear and ridge regression models were used to evaluate the associations between exposure to multiple heavy metals and cancer mortality in the nine villages, after adjustment for age and sex.

Results
The geometric mean blood levels of cadmium and lead were measured at 24.10 μg/L and 38.91 μg/dL for subjects (n = 563) in the HEA and 1.87 μg/L and 4.46 μg/dL for subjects (n = 589) from the LEA, respectively (P < 0.001). The rate of mortality from all cancers in the HEA was substantially elevated in comparison with the corresponding mortality rate in the LEA for men (rate ratio = 2.13; 95% confidence intervals = 1.63 - 2.77) and women (2.83; 1.91 - 4.19); rates were also significantly elevated compared with the rate when compared to the entire Wengyuan County area, or the provincial reference population. In addition, mortality rates were significantly increased for stomach, lung and esophageal cancer in the HEA in comparison with the corresponding rates in the LEA, in Wengyuan County and the provincial reference population for men, women and both combined. Further analysis showed that there were significantly positive correlations between exposure to cadmium and lead and the risk of all-cancers and stomach cancer mortality among women and both sexes, whilst zinc exposure showed no association with the risk of site-specific cancer mortality in the nine villages evaluated.

Conclusions
The findings of this study reveal probable associations between long-term environmental exposure to both cadmium and lead and an increased risk of mortality from all cancer, as well as from stomach, esophageal and lung-cancers.