Publisher: Elsevier

Journal description

Current impact factor: 2.14

Impact Factor Rankings

2015 Impact Factor Available summer 2016
2014 Impact Factor 2.138
2013 Impact Factor 2.082
2012 Impact Factor 2.196
2011 Impact Factor 2.341
2010 Impact Factor 2.266
2009 Impact Factor 2.416
2008 Impact Factor 2.578
2007 Impact Factor 2.871
2006 Impact Factor 2.721
2005 Impact Factor 2.694
2004 Impact Factor 2.705
2003 Impact Factor 2.754
2002 Impact Factor 2.778
2001 Impact Factor 3.041
2000 Impact Factor 2.461
1999 Impact Factor 2.258
1998 Impact Factor 2.007
1997 Impact Factor 1.838
1996 Impact Factor 1.931
1995 Impact Factor 2.16
1994 Impact Factor 2.305
1993 Impact Factor 2.407
1992 Impact Factor 2.569

Impact factor over time

Impact factor

Additional details

5-year impact 2.19
Cited half-life >10.0
Immediacy index 0.62
Eigenfactor 0.03
Article influence 0.61
ISSN 1879-0038

Publisher details


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    • Authors pre-print on any website, including arXiv and RePEC
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    • Publisher's version/PDF cannot be used
    • Must link to publisher version with DOI
    • Author's post-print must be released with a Creative Commons Attribution Non-Commercial No Derivatives License
    • Publisher last reviewed on 03/06/2015
  • Classification
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Publications in this journal

  • [Show abstract] [Hide abstract]
    ABSTRACT: Oomycetes are eukaryotic microorganisms, which are phylogenetically distinct from the true-fungi, which they resemble morphologically. While many oomycetes are pathogenic to plants, Pythium insidiosum is capable of infecting humans and animals. Mitochondrial (mt) genomes are valuable genetic resources for exploring the evolution of eukaryotes. During the course of 454-based nuclear genome sequencing, we identified a complete 54.9 kb mt genome sequence, containing 2 large inverted repeats, from P. insidiosum. It contains 65 different genes (including 2 ribosomal RNA genes, 25 transfer RNA genes and 38 genes encoding NADH dehydrogenases, cytochrome b, cytochrome c oxidases, ATP synthases, and ribosomal proteins). Thirty-nine of the 65 genes have two copies, giving a total of 104 genes. A set of 30 conserved protein-coding genes from the mt genomes of P. insidiosum, 11 other oomycetes, and 2 diatoms (outgroup) were used for phylogenetic analyses. The oomycetes can be classified into 2 phylogenetic groups, in relation to their taxonomic lineages: Saprolegnialean and Peronosporalean. P. insidiosum is more closely related to Pythium ultimum than other oomycetes. In conclusion, the complete mt genome of P. insidiosum was successfully sequenced, assembled, and annotated, providing a useful genetic resource for exploring the biology and evolution of P. insidiosum and other oomycetes. Copyright © 2015. Published by Elsevier B.V.
    Gene 12/2015; DOI:10.1016/j.gene.2015.08.036
  • Barry Wolf
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    ABSTRACT: Biotinidase is the enzyme that is necessary for the recycling of the vitamin, biotin. Biotinidase deficiency is an autosomal recessively inherited metabolic disorder. If untreated, individuals with biotinidase deficiency usually develop neurological and cutaneous symptoms that can result in coma or death. Symptomatic individuals can be markedly improved by treating them with pharmacological doses of biotin; however, some clinical features may be irreversible. Fortunately, essentially all symptoms can be prevented if treatment is initiated at birth or before the symptoms develop. Because of this, the disorder is currently screened for in newborns in all states in the United States and in many countries around the world. This is the story of one laboratory's work in bringing basic science research from the discovery of the disorder to its translation into clinical medicine and its impact on the individuals with the disorder and their families.
    Gene 10/2015; DOI:10.1016/j.gene.2015.10.010
  • Amit Das · Simanti Bhattacharya · Sanchari Bhattacharjee · Angshuman Bagchi · Rakhi Dasgupta
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    ABSTRACT: Formin binding protein 4 (FNBP4) interacts with formins and other proteins via its WW domains. Previously, we reported the structural and phylogenetic clustering of FNBP4 across a wide range of organisms from different taxonomic groups along with characterizing its plant variant (Arabidopsis thaliana F4JC80). Recently, the FNBP4 gene is reported to be associated with a congenital disorder Microphthalmia with Limb Anomalies. Except these reports, FNBP4 is mostly uncharacterized, especially the FNBP4 gene. In this context, we have attempted to characterize the FNBP4 gene in terms of its length and compositional variations across 10 different organisms from different taxonomic groups. Our findings highlight that the length of the FNBP4 gene varies greatly among different species. Introns, UTRs and the entire gene were AT rich while CDS and mRNAs were GC rich. The RSCU values were also different for the different organisms indicating a possible impact on translational efficiency of this protein. Comparative analyses highlight gene element and base proportions related characteristics specific to highly expression regulated genes like FNBP4.
    Gene 10/2015; DOI:10.1016/j.gene.2015.09.087
  • Cátia L Marques · M Leonor Cancela · Vincent Laizé
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    ABSTRACT: Bone morphogenetic protein (BMP) 2 belongs to the transforming growth factor β (TGFβ) superfamily of cytokines and growth factors. While it plays important roles in embryo morphogenesis and organogenesis, BMP2 is also critical to bone and cartilage formation. Protein structure and function have been remarkably conserved throughout evolution and BMP2 transcription has been proposed to be tightly regulated, although few data is available. In this work we report the cloning and functional analysis of gilthead seabream BMP2 promoter. As in other vertebrates, seabream BMP2 gene has a 5' non-coding exon, a feature already present in DPP gene, the fruit fly ortholog of vertebrate BMP2 gene, and maintained throughout evolution. In silico analysis of seabream BMP2 promoter revealed several binding sites for bone and cartilage related transcription factors (TFs) and their functionality was evaluated using promoter-luciferase constructions and TF-expressing vectors. Runt-related transcription factor 3 (RUNX3) was shown to negatively regulate BMP2 transcription and combination with the core binding factor β (CBFβ) further reduced transcriptional activity of the promoter. Although to a lesser extent, myocyte enhancer factor 2C (MEF2C) had also a negative effect on the regulation of BMP2 gene transcription, when associated with SRY (sex determining region Y)-box 9 (SOX9b). Finally, v-ets avian erythroblastosis virus E26 oncogene homolog 1 (ETS1) was able to slightly enhance BMP2 transcription. Data reported here provides new insights toward the better understanding of the transcriptional regulation of BMP2 gene in a bone and cartilage context.
    Gene 10/2015; DOI:10.1016/j.gene.2015.10.005
  • Neetu Singh · Dinesh Kumar Sahu · Archana Mishra · Preeti Agarwal · Madhumati Goel · Anil Chandra · Sunil Kumar Singh · Chhitij Srivastava · Bal Krishna Ojha · Devendra Kumar Gupta · Ravi Kant
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    ABSTRACT: Purpose: Based on copy number alterations and transcriptional profiles, the posterior fossa tumors (medulloblastoma (MB), ependymoma and pilocytic astrocytoma) have been classified into various subgroups. The study design was aimed to identify and catalogue genome-wide copy number alterations and differential gene expression in different types of North-Indian pediatric posterior fossa tumors and matched control tissue through Molecular Inversion Probe (MIP) based and Human Transcriptome Array. Experimental design: MIP based Oncoscan Array and Human Transcriptome Array 2.0 was were used to molecularly-categorize histopathologically and immunohistochemically proven tumor samples on the basis of copy number variations and altered gene expression patterns and/or alternative splicing events. Results: Based on molecular, histopathological/immunohistochemical and age dependent factors MB was sub-grouped into group-3 MB, Wnt and SHH; Ependymoma into balanced, numerical and structural/anaplastic; and Pilocytic Astrocytoma was stratified age-dependently. Compared to the vermis tissue of MB, the vermis tissue of ependymoma showed higher levels of gain and losses compared to their counter tumor parts implicating metastasis within the confined region. Group-3 MB and anaplastic ependymoma represented highest differentially expressed genes both at gene and exon level in the CN altered regions compared to other subgroups of MB and Ependymoma respectively. Conclusion: Multiomics approach based on CNVs and differential gene expression patterns, This multiomics approach based molecular characterization of posterior-fossa tumors together with clinical and histopathological factors may help us in the area of personalized medicine.
    Gene 10/2015; DOI:10.1016/j.gene.2015.09.078
  • Hala Chamieh · Hiba Ibrahim · Juliana Kozah
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    ABSTRACT: Archaea microorganisms have long been used as model organisms for the study of protein molecular machines. Archaeal proteins are particularly appealing to study since archaea, even though prokaryotic, possess eukaryotic-like cellular processes. Super Family I (SF1) and Super Family II (SF2) helicase families have been studied in many model organisms, little is known about their presence and distribution in archaea. We performed an exhaustive search of homologs of SF1 and SF2 helicase proteins in 95 complete archaeal genomes. In the present study, we identified the complete sets of SF1 and SF2 helicases in archaea. Comparative analysis between archaea, human and the bacteria E.coli SF1 and SF2 helicases, resulted in the identification of seven helicase families conserved among representatives of the domains of life. This analysis suggests that these helicase families are highly conserved throughout evolution. We highlight the conserved motifs of each family and characteristic domains of the detected families. Distribution of SF1/SF2 families show that Ski2-like, Lhr, Sfth and Rad3-like helicases are ubiquitous among archaeal genomes while the other families are specific to certain archaeal groups. We also report the presence of a novel SF2 helicase specific to archaea domain named Archaea Specific Helicase (ASH). Phylogenetic analysis indicated that ASH has evolved in Euryarchaoeta and is evolutionary related to the Ski2-like family with specific characteristic domains. Our study provides the first exhaustive analysis of SF1 and SF2 helicases from archaea. It expands the variety of SF1 and SF2 archaeal helicases known to exist to date and provides a starting point for new biochemical and genetic studies needed to validate their biological functions.
    Gene 10/2015; DOI:10.1016/j.gene.2015.10.007
  • Shelly Goomber · Arbind Kumar · Jagdeep Kaur
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    ABSTRACT: Cold adapted enzymes have applications in detergent, textile, food, bioremediation and biotechnology processes. Bacillus lipases are 'generally recognized as safe' (GRAS) and hence are industrially attractive. Bacillus lipase of 1.4 subfamily are of lowest molecular weight and are reversibly unfolded due to absence of disulphide bonds. Therefore these are largely used to study energetic of protein stability that represents unfolding of native protein to fully unfolded state. In present study, metagenomically isolated Bacillus LipJ was laboratory evolved for cold adaptation by error Prone PCR. Library of variants were screened for high relative activity at low temperature of 10°C compared to native protein LipJ. Point mutant sequenced as Phe19→Leu was determined to be active at cold and was selected for extensive biochemical, biophysical characterization. Variant F19L showed its maximum activity at 10°C where parent protein LipJ had 20% relative activity. Psychrophilic nature of F19L was established with about 50% relative active at 5°C where native protein was frozen to act. Variant F19L showed no activity at temperature 40°C and above, establishing its thermolabile nature. Thermostability studies determined mutant to be unstable above 20°C and three fold decrease in its half life at 30°C compared to native protein. Far UV-CD and intrinsic fluorescence study demonstrated unstable tertiary structure of point variant F19L leading to its unfolding at low temperature of 20°C. Cold adaptation of mutant F19L is accompanied with increased specific activity. Mutant was catalytically more efficient with 1.3 fold increase in kcat. Homologue structure modelling predicted disruption of intersecondary hydrophobic core formed by aromatic ring of Phe19 with non polar residues placed at β3, β4, β5, β6, αF. Increased local flexibility of variant F19L explains molecular basis of its psychrophilic nature.
    Gene 10/2015; DOI:10.1016/j.gene.2015.10.006
  • James C Barton · Corwin Q Edwards · Ronald T Acton
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    ABSTRACT: The hemochromatosis gene HFE was discovered in 1996, more than a century after clinical and pathologic manifestations of hemochromatosis were reported. Linked to the major histocompatibility complex (MHC) on chromosome 6p, HFE encodes the MHC class I-like protein HFE that binds beta-2 microglobulin. HFE influences iron absorption by modulating the expression of hepcidin, the main controller of iron metabolism. Common HFE mutations account for ~90% of hemochromatosis phenotypes in whites of western European descent. We review HFE mapping and cloning, structure, promoters and controllers, and coding region mutations, HFE protein structure, cell and tissue expression and function, mouse Hfe knockouts and knockins, and HFE mutations in other mammals with iron overload. We describe the pertinence of HFE and HFE to mechanisms of iron homeostasis, the origin and fixation of HFE polymorphisms in European and other populations, and the genetic and biochemical basis of HFE hemochromatosis and iron overload.
    Gene 10/2015; DOI:10.1016/j.gene.2015.10.009
  • V VenkatRao · R K Chaitanya · A Dutta-Gupta
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    ABSTRACT: Arylphorin hexamerins are one of the major insect storage proteins involved in diverse functions during metamorphosis. However, their regulation during developement is not elucidated so far. In the present study, we documented 20-hydroxyecdysone (20E)-mediated regulation of arylphorin expression in fat body of the stored grain pest, Corcyra cephalonica. Based on the differential developmental expression and 20E-induced transcriptional as well as translational level alterations of arylphorin, we isolated the 5' upstream region of the gene to analyse regulatory motifs. Promoter motif analysis revealed the presence of ecdysone response element (ERE). Transient transfection studies showed the functionality of the ERE. Enzyme mobility shift experiments with radiolabelled, cold and mutated probes indicate ERE-nuclear factor binding. This study is the first to report transcriptional regulation of arylphorins by 20E in lepdopteran insect species.
    Gene 10/2015; DOI:10.1016/j.gene.2015.09.074
  • Chanchal Mandal · Debasish Halder · Jin Choul Chai · Young Seek Lee · Kyoung Hwa Jung · Young Gyu Chai
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    ABSTRACT: Fetal alcohol spectrum disorder is a collective term that represents fetal abnormalities associated with maternal alcohol consumption. Prenatal alcohol exposure and related anomalies are well characterized, but the molecular mechanism behind this phenomenon is not yet understood. Few insights have been gained from genetic and epigenetic studies of fetal alcohol spectrum disorder. Our aim was to profile the important molecular regulators of ethanol-related alterations of the genome. For this purpose, we have analyzed the gene expression pattern of human carcinoma cell-derived embryoid bodies in the absence or presence of ethanol. A cDNA microarray analysis was used to profile mRNA expression in embryoid bodies at day 7 with or without ethanol treatment. A total of 493 differentially expressed genes were identified in response to 50mM ethanol exposure. Of these, 111 genes were up-regulated, and 382 were down-regulated. Gene ontology term enrichment analysis revealed that these genes are involved in important biological processes: neurological system processes, cognition, behavior, sensory perception of smell, taste and chemical stimuli and synaptic transmission. Similarly, the enrichment of disease-related genes included relevant categories such as neurological diseases, developmental disorders, skeletal and muscular disorders, and connective tissue disorders. Furthermore, we have identified a group of 26 genes that encode transcription factors. We validated the relative gene expression of several transcription factors using quantitative real time PCR. We hope that our study substantially contributes to the understanding of the molecular mechanisms underlying the pathology of alcohol-mediated anomalies and facilitates further research.
    Gene 10/2015; DOI:10.1016/j.gene.2015.09.085
  • Wang Shen · Yan Chen · Huimin Yao · Canwei Du · Ning Luan · Xiuwen Yan
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    ABSTRACT: Defensins are one of the major families of antimicrobial peptides (AMPs), and have been reported from prokaryotic to eukaryotic kingdoms. But defensins are seldom found in amphibian which is a major resource of novel AMPs. A novel defensin-like AMP (defensin-TK) was isolated and characterized from skin secretions of the tree frog Theloderma kwangsiensis. The cDNA encoding defensin-TK precursor was cloned from the skin cDNA library of T. kwangsiensis. The deduced precursor of defensin-TK was composed of three domains, a signal peptide of 16 residues, a spacer peptide of 1 residues and a mature peptide of 42 residues. The mature peptide of defensin-TK shared the highest identity with the salamander (Cynops fudingensis) defensin CFBD-1. The six conserved cysteines which formed intramolecular disulfide bonds of defensins also exist in defensin-TK. Phylogenetic analysis indicated that defensin-TK was closely related to fish β-defensins. Defensin-TK showed potent and broad-spectrum antimicrobial activity. In addition, defensin-TK exerted a low hemolytic activity on human red cells. These results suggested defensin-TK might play an important role in defense the skin pathogenic microbes of tree frog T. kwangsiensis, and might be a promising candidate for development of novel antimicrobial agents.
    Gene 10/2015; DOI:10.1016/j.gene.2015.09.086
  • Hao Peng · Xiaojuan Xu · Lusi Zhang · Xuehong Zhang · Hexiang Peng · Yu Zheng · Sanchuan Luo · Hui Guo · Kun Xia · Jiada Li · Hongliang Yao · Zhengmao Hu
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    ABSTRACT: Fabry disease (FD) was an X-linked lysosomal storage disorder resulting from a deficiency in glycosphingolipid catabolism caused by mutations in the α-galactosidase A gene GLA. Variant FD patients did not present with classical symptoms during childhood and were undiagnosed or misdiagnosed with other kidney diseases, such as chronic glomerulonephritis (CGN). In this study, we utilized exome sequencing and Sanger sequencing identified the variation p.E66Q of GLA completely co-segregated with the disease phenotype in a Chinese family, which previously been diagnosed as possible CGN. Female patients exhibited preferential X-chromosome inactivation (XCI) of the normal p.E66 allele, as indicated by XCI analysis. By measuring α-Gal A activity, we found that male patients in the pedigree had just little enzymatic activity while female patients had residual enzymatic activity. These patients were diagnosed with renal variant FD in subsequent clinical review. Our results directly implicated the GLA mutation p.E66Q as the genetic etiology of the Chinese renal variant FD pedigree.
    Gene 10/2015; DOI:10.1016/j.gene.2015.09.088
  • Leila Azimi · Malihe Talebi · Parviz Owlia · Mohammad-Reza Pourshafie · Mohamad Najafi · Elnaz Rastegar Lari · Abdolaziz Rastegar Lari
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    ABSTRACT: Background: Carbapenemase production causes multi antibiotics resistant in Gram-negative bacteria. A simple rapid and accurate phenotypic test for detection of Gram-negative carbapenemase-producing bacteria is useful for the treatment of infections. The aim of this study was to track the negative results in carbapenemase phenotypic test by Real-time PCR. Materials and methods: In this study, 161 imipenem resistant Gram-negative bacteria were surveyed. Modified Hodge test (MHT), boronic acid (BA), EDTA and dipicolinic acid were used for detection of Klebsiella pneumoniae carbapenemase (KPC) and metallo-beta-lactamase (MBLs). Different phenotypic methods and PCR confirmation followed by Real-time PCR for determination of phenotypic false-negative results were used. Results: Our results indicated that 85, 51 and 112 strains were MHT, BA and dipicolinic acid positive, respectively. No synergistic effect was observed between imipenem and EDTA. Sixty-nine strains were confirmed as carbapenemase-producers according to the results of molecular tests. All of the isolates carried the gene and expressed carbapenemase. Conclusion: Comparison between the results of phenotypic and genotypic methods showed that the phenotypic methods could be used as the primary screening and the PCR remains as the gold standard for detection of carbapenemase positive strains.
    Gene 10/2015; DOI:10.1016/j.gene.2015.10.008
  • Tekcham Dinesh Singh · Sanjeev Gupta · Braj Raj Shrivastav · Pramod Kumar Tiwari
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    ABSTRACT: Background: As on today, the global mortality rate of gallbladder cancer is still very high. Both genetic and epigenetic alterations play pivotal roles in the development of cancer. We selected seven tumor associated genes, implicated in other cancers, to assess their methylation status in gallbladder cancer and gallstone diseases. Aim of study: To study the promoter methylation of certain tumor associated genes in the molecular pathogenesis of gallbladder cancer and gall stone diseases. Materials and methods: Methylation Specific PCR for seven tumor associated genes, viz., MASPIN, 14-3-3 sigma gene, THBS1, FLNC, HLTF, COX-2 and SOCS1, was performed in 50 gallbladder cancer (GBC), 30 gall stone diseases (GSD) and their respective adjacent control tissues. Semi-quantitative PCR and Immunohistochemistry was carried out to check the expression level. Student's t-test was carried out to compare the differences in the methylation and expression patterns between cases and control tissues. Results: We observed methylation of CpG islands in seven of the studied markers, but, the frequency of methylation was found varying among different samples. Of them, 14-33 sigma showed methylation in 45 GBC (90%;p=0.0001) and 25 GSD (86.66%; p=0.001), MASPIN in 35 GBC (70%; p=0.0008) and 18 GSD (51.43%; p=0.040), FLNC in 16 GBC (32%; p=0.0044) and 9 GSD (25.71%; p=ns), THBS1 in 26 GBC (52%; p=0.0009) and 10 GSD (28.57%; p=0.0505), HLTF in 8 GBC (16%; p=ns) and 2 GSD (5.71%; p=ns), COX2 in 10 GBC (20%; p=ns) and 6 GSD (17.14%; p=ns) and SOCS-1 in 3 GBC samples only (6%; p=ns), but not in GSD. Semi-quantitative PCR revealed down regulation was observed in MASPIN, 14-3-3 sigma, THBS1, HLTF, COX2 and SOCS1 in advanced gallbladder cases. Immunohistochemistry further confirmed the down-regulation of SOCS1 in GBC. Conclusion: The present study infers that accumulation of epigenetic alterations increases poor prognosis of GBC patients. Out of seven genes, MASPIN and THBS1 play key epigenetic role in GBC, but not in GSD. The reason for downregulation of SOCS1 only in GBC, and unaltered expression of 14-3-3 sigma protein in all the GBC and GSD tissue samples is not clear. Further investigation on the expression pattern of these genes in GBC cell lines may elucidate their likely functional role in gallbladder cancer.
    Gene 10/2015; DOI:10.1016/j.gene.2015.10.004
  • Gene 10/2015; DOI:10.1016/j.gene.2015.10.003
  • Yanjie Wang · Chunlan Dong · Zeyun Xue · Qijiang Jin · Yingchun Xu
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    ABSTRACT: Paeonia ostii, an important ornamental and medicinal plant, grows normally on copper (Cu) mines with widespread Cu contamination of soils, and it has the ability to lower Cu contents in the Cu-contaminated soils. However, very little molecular information concerned with Cu resistance of P. ostii is available. In this study, high-throughput de novo transcriptome sequencing was carried out for P. ostii with and without Cu treatment using Illumina HiSeq™ 2000 platform. A total of 77,704 All-unigenes were obtained with a mean length of 710bp. Of these unigenes, 47,461 were annotated with public databases based on sequence similarities. Comparative transcript profiling allowed the discovery of 4324 differentially expressed genes (DEGs), with 2207 up-regulated and 2117 down-regulated unigenes in Cu-treated library as compared to the control counterpart. Based on these DEGs, Gene Ontology (GO) enrichment analysis indicated Cu stress-relevant terms, such as 'membrane' and 'antioxidant activity'. Meanwhile, Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis uncovered some important pathways, including 'biosynthesis of secondary metabolites' and 'metabolic pathways'. In addition, expression patterns of 12 selected DEGs derived from quantitative real-time polymerase chain reaction (qRT-PCR) were consistent with their transcript abundance changes obtained by transcriptomic analyses, suggesting that all the 12 genes were authentically involved in Cu tolerance in P. ostii. This is the first report to identify genes related to Cu stress responses in P. ostii, which could offer valuable information on the molecular mechanisms of Cu resistance, and provide a basis for further genomics research on this and related ornamental species for phytoremediation.
    Gene 10/2015; DOI:10.1016/j.gene.2015.09.077
  • Lei Zhang · Junfeng Chen · Qing Li · Wansheng Chen
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    ABSTRACT: Jasmonates (JAs) act as conserved elicitors of plant secondary metabolism. JAs perception triggers extensive transcriptional reprogramming leading to activation of the entire metabolic pathways. The family of basic helix-loop-helix (bHLH) transcription factors (TFs) has essential roles in JA signaling; however, little is known about their roles in regulation of secondary metabolites in Isatis indigotica. In this study, we identified 78 putative IibHLH sequences using the annotation of I. indigotica transcriptome. The identified proteins were characterized based on phylogenetic and conserved motif analyses. Using RNA sequencing, 16 IibHLHs showed significant positive response to MeJA (methyl jasmonate) at 1h, indicating their roles as early signaling events of JA-mediated transcriptional reprogramming. Ten IibHLHs presented co-expression pattern with biosynthetic pathway genes, suggesting their regulating role in secondary metabolite synthesis. These gene expression profiling data indicate that bHLHs can be used as candidate genes in molecular breeding programs to improve metabolite production in I. indigotica.
    Gene 10/2015; DOI:10.1016/j.gene.2015.09.083
  • Qiao-Cheng Chang · Guo-Hua Liu · Jun-Feng Gao · Xu Zheng · Yan Zhang · Hong Duan · Dong-Mei Yue · Xue Fu · Xin Su · Yuan Gao · Chun-Ren Wang
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    ABSTRACT: The trematode Eurytrema pancreaticum is a parasite of ruminant pancreatic and bile ducts, and also occasionally infects humans, causing eurytremiasis. In spite of it being a common fluke of cattle and sheep in endemic regions, little is known about the genomic resources of the parasite. We sequenced the complete mitochondrial (mt) genome of E. pancreaticum. It is 15,031bp in size, and encodes 36 genes: 12 protein-coding genes, two ribosomal RNA genes, and 22 transfer RNA genes. The E. pancreaticum mt gene order is the same as that of Dicrocoelium chinensis and Dicrocoelium dendriticum, and all genes are transcribed in the same direction. Phylogenetic analysis based on the concatenated amino acid sequences of 12 protein-coding genes by Bayesian inference shows that E. pancreaticum is closely related to D. chinensis and other members of the family Dicrocoeliidae with strong posterior probability support. The E. pancreaticum mt genome should prove to be a useful resource for comparative mt genomic studies of digenetic trematodes, and will provide a rich source of DNA markers for studies into the systematics, epidemiology, and population genetics of this parasite and other digenean trematodes.
    Gene 10/2015; DOI:10.1016/j.gene.2015.09.081
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    ABSTRACT: Several reports suggest that non-synonymous single nucleotide polymorphisms affect the function of XRCC1 which impairs DNA repair capacity and thus increases risk to diseases like cancer. In our study, we predicted the most damaging nsSNPs using a computational approach and analysed its functional impact on the XRCC1 and LIG3 interaction. SNP rs2307166 was predicted to be deleterious using eight software programs: SIFT, PolyPhen, PANTHER, PhD-SNP, nsSNPAnalyzer, SNPS&GO, SNAP and I-Mutant. Protein structural analysis was performed using Swiss PDB viewer, and PyMOL. Xenoview was used for molecular dynamic simulation and energy minimisation. Finally, PatchDock and FireDock were used to analyse the interactions of XRCC1 and LIG3. By comparing the results we found that the mutant protein has less binding energy and the interacting amino acids than native protein. Insilico analysis predicted rs2307166 to be more damaging than three other extensively studied SNPs. Identification of this SNP will help in determining the susceptibility of the individual to cancer, their prognosis and further treatment.
    Gene 10/2015; DOI:10.1016/j.gene.2015.09.084