Characterization of the Shewanella oneidensis Fur gene: roles in iron and acid tolerance response.

abstract：BACKGROUND:Bacteroides thetaiotaomicron, a predominant member of the human gut microbiota, is characterized by its ability to utilize a wide variety of polysaccharides using the extensive saccharolytic machinery that is controlled by an expanded repertoire of transcription factors (TFs). The availability of genomic seq...

journal_title：BMC genomics

authors： Ravcheev DA,Godzik A,Osterman AL,Rodionov DA

更新日期：2013-12-12 00:00:00

abstract：BACKGROUND:Numerous human genes encode potentially active DNA transposases or recombinases, but our understanding of their functions remains limited due to shortage of methods to profile their activities on endogenous genomic substrates. RESULTS:To enable functional analysis of human transposase-derived genes, we comb...

journal_title：BMC genomics

authors： Henssen AG,Jiang E,Zhuang J,Pinello L,Socci ND,Koche R,Gonen M,Villasante CM,Armstrong SA,Bauer DE,Weng Z,Kentsis A

更新日期：2016-08-04 00:00:00

abstract：BACKGROUND:Most published genome sequences are drafts, and most are dominated by computational gene prediction. Draft genomes typically incorporate considerable sequence data that are not assigned to chromosomes, and predicted genes without quality confidence measures. The current Actinidia chinensis (kiwifruit) 'Hongy...

journal_title：BMC genomics

authors： Pilkington SM,Crowhurst R,Hilario E,Nardozza S,Fraser L,Peng Y,Gunaseelan K,Simpson R,Tahir J,Deroles SC,Templeton K,Luo Z,Davy M,Cheng C,McNeilage M,Scaglione D,Liu Y,Zhang Q,Datson P,De Silva N,Gardiner SE,Bas

更新日期：2018-04-16 00:00:00

abstract：BACKGROUND:Bacterial spore germination is a developmental process during which all required metabolic pathways are restored to transfer cells from their dormant state into vegetative growth. Streptomyces are soil dwelling filamentous bacteria with complex life cycle, studied mostly for they ability to synthesize second...

journal_title：BMC genomics

authors： Bobek J,Strakova E,Zikova A,Vohradsky J

更新日期：2014-12-23 00:00:00

abstract：BACKGROUND:Nitrogen (N) is a key macronutrient required for plant growth and development. In this study, watermelon plants were grown under hydroponic conditions at 0.2 mM N, 4.5 mM N, and 9 mM N for 14 days. RESULTS:Dry weight and photosynthetic assimilation at low N (0.2 mM) was reduced by 29 and 74% compared with h...

journal_title：BMC genomics

authors： Nawaz MA,Chen C,Shireen F,Zheng Z,Sohail H,Afzal M,Ali MA,Bie Z,Huang Y

更新日期：2018-06-13 00:00:00

abstract：BACKGROUND:Glutamine is a major amino donor for the synthesis of amino acids, nucleotides, and other nitrogen-containing compounds in all organisms. In addition to its role in nutrition and metabolism, glutamine can also function as a signaling molecule in bacteria, yeast, and humans. By contrast, the functions of glut...

journal_title：BMC genomics

authors： Kan CC,Chung TY,Juo YA,Hsieh MH

更新日期：2015-09-25 00:00:00

abstract：BACKGROUND:Cadmium (Cd) is a serious heavy metal (HM) soil pollutant. To alleviate or even eliminate HM pollution in soil, environmental-friendly methods are applied. One is that special plants are cultivated to absorb the HM in the contaminated soil. As an excellent economical plant with ornamental value and sound ada...

journal_title：BMC genomics

authors： Wang MQ,Bai ZY,Xiao YF,Li Y,Liu QL,Zhang L,Pan YZ,Jiang BB,Zhang F

更新日期：2019-11-20 00:00:00

abstract：BACKGROUND:Single cell transcriptome sequencing has become an increasingly valuable technology for dissecting complex biology at a resolution impossible with bulk sequencing. However, the gap between the technical expertise required to effectively work with the resultant high dimensional data and the biological experti...

journal_title：BMC genomics

authors： Feng D,Whitehurst CE,Shan D,Hill JD,Yue YG

更新日期：2019-08-27 00:00:00

abstract：BACKGROUND:Common carp (Cyprinus carpio) is thought to have undergone one extra round of genome duplication compared to zebrafish. Transcriptome analysis has been used to study the existence and timing of genome duplication in species for which genome sequences are incomplete. Large-scale transcriptome data for the com...

journal_title：BMC genomics

authors： Wang JT,Li JT,Zhang XF,Sun XW

更新日期：2012-03-19 00:00:00

abstract：BACKGROUND:Quantitative trait locus (QTL) studies show that variation in salinity tolerance in Arctic charr and rainbow trout has a genetic basis, even though both these species have low to moderate salinity tolerance capacities. QTL were observed to localize to homologous linkage group segments within putative chromos...

journal_title：BMC genomics

authors： Norman JD,Robinson M,Glebe B,Ferguson MM,Danzmann RG

更新日期：2012-08-24 00:00:00

abstract：BACKGROUND:The completion of the Plasmodium falciparum genome represents a milestone in malaria research. The genome sequence allows for the development of genome-wide approaches such as microarray and proteomics that will greatly facilitate our understanding of the parasite biology and accelerate new drug and vaccine ...

journal_title：BMC genomics

authors： Lu F,Jiang H,Ding J,Mu J,Valenzuela JG,Ribeiro JM,Su XZ

更新日期：2007-07-27 00:00:00

abstract：BACKGROUND:Functional analysis of the catfish genome will be useful for the identification of genes controlling traits of economic importance, especially innate disease resistance. However, this species lacks a platform for global gene expression profiling, so we designed a first generation high-density oligonucleotide...

journal_title：BMC genomics

authors： Li RW,Waldbieser GC

更新日期：2006-06-01 00:00:00

abstract：BACKGROUND:JWB phytoplasma is a kind of insect-transmitted and uncultivable bacterial plant pathogen causeing a destructive Jujube disease. To date, no genome information about JWB phytoplasma has been published, which hindered its characterization at genomic level. To understand its pathogenicity and ecology, the geno...

journal_title：BMC genomics

authors： Wang J,Song L,Jiao Q,Yang S,Gao R,Lu X,Zhou G

更新日期：2018-09-19 00:00:00

abstract：BACKGROUND:RNA editing is an important mechanism that expands the diversity and complexity of genetic codes. The conversions of adenosine (A) to inosine (I) and cytosine (C) to uridine (U) are two prominent types of RNA editing in animals. The roles of RNA editing events have been implicated in important biological pat...

journal_title：BMC genomics

authors： Cao Y,Cao R,Huang Y,Zhou H,Liu Y,Li X,Zhong W,Hao P

更新日期：2018-01-19 00:00:00

abstract：BACKGROUND:The phylum Platyhelminthes (flatworms) contains an important group of bilaterian organisms responsible for many debilitating and chronic infectious diseases of human and animal populations inhabiting the planet today. In addition to their biomedical and veterinary relevance, some platyhelminths are also freq...

journal_title：BMC genomics

authors： Geyer KK,Chalmers IW,Mackintosh N,Hirst JE,Geoghegan R,Badets M,Brophy PM,Brehm K,Hoffmann KF

更新日期：2013-07-09 00:00:00

abstract：BACKGROUND:Lipoxygenases (LOXs), a type of non-haem iron-containing dioxygenase, are ubiquitous enzymes in plants and participate in the formation of fruit aroma which is a very important aspect of fruit quality. Amongst the various aroma volatiles, saturated and unsaturated alcohols and aldehydes provide the character...

journal_title：BMC genomics

authors： Li M,Li L,Dunwell JM,Qiao X,Liu X,Zhang S

更新日期：2014-06-07 00:00:00

abstract：BACKGROUND:High throughput genotyping of single nucleotide polymorphisms (SNPs) for genome-wide association requires technologies for generating millions of genotypes with relative ease but also at a reasonable cost and with high accuracy. In this work, we have developed a theoretical approach to estimate allele freque...

journal_title：BMC genomics

authors： Yin BC,Li H,Ye BC

更新日期：2008-12-16 00:00:00

abstract：BACKGROUND:The term pan-genome was proposed to denominate collections of genomic sequences jointly analyzed or used as a reference. The constant growth of genomic data intensifies development of data structures and algorithms to investigate pan-genomes efficiently. RESULTS:This work focuses on providing a tool for dis...

journal_title：BMC genomics

authors： Dziadkiewicz P,Dojer N

更新日期：2020-04-16 00:00:00

abstract：BACKGROUND:Long non-coding RNAs (lncRNAs) exhibit remarkable cell-type specificity and disease association. LncRNA's functional versatility includes epigenetic modification, nuclear domain organization, transcriptional control, regulation of RNA splicing and translation, and modulation of protein activity. However, mos...

journal_title：BMC genomics

authors： Pyfrom SC,Luo H,Payton JE

更新日期：2019-02-15 00:00:00

abstract：BACKGROUND:Meta-analysis of QTLs combines the results of several QTL detection studies and provides narrow confidence intervals for meta-QTLs, permitting easier positional candidate gene identification. It is usually applied to multiple mapping populations, but can be applied to one. Here, a meta-analysis of drought re...

journal_title：BMC genomics

authors： Khowaja FS,Norton GJ,Courtois B,Price AH

更新日期：2009-06-22 00:00:00

abstract：BACKGROUND:The large amount of data produced by high-throughput sequencing poses new computational challenges. In the last decade, several tools have been developed for the identification of transcription and splicing factor binding sites. RESULTS:Here, we introduce the SeAMotE (Sequence Analysis of Motifs Enrichment)...

journal_title：BMC genomics

authors： Agostini F,Cirillo D,Ponti RD,Tartaglia GG

更新日期：2014-10-23 00:00:00

abstract：BACKGROUND:Chromosome 17q21.31 contains a common inversion polymorphism of approximately 900 kb in populations with European ancestry. Two divergent MAPT haplotypes, H1 and H2 are described with distinct linkage disequilibrium patterns across the region reflecting the inversion status at this locus. The MAPT H1 haploty...

journal_title：BMC genomics

authors： de Jong S,Chepelev I,Janson E,Strengman E,van den Berg LH,Veldink JH,Ophoff RA

更新日期：2012-09-06 00:00:00

abstract：BACKGROUND:Several methods have recently been developed to identify regions of the genome that have been exposed to strong selection. However, recent theoretical and empirical work suggests that polygenic models are required to identify the genomic regions that are more moderately responding to ongoing selection on com...

journal_title：BMC genomics

authors： Decker JE,Vasco DA,McKay SD,McClure MC,Rolf MM,Kim J,Northcutt SL,Bauck S,Woodward BW,Schnabel RD,Taylor JF

更新日期：2012-11-09 00:00:00

abstract：BACKGROUND:Interactions among transcription factors (TFs) and histone modifications (HMs) play an important role in the precise regulation of gene expression. The context specificity of those interactions and further its dynamics in normal and disease remains largely unknown. Recent development in genomics technology e...

journal_title：BMC genomics

authors： Zhang L,Xue G,Liu J,Li Q,Wang Y

更新日期：2018-12-31 00:00:00

abstract：BACKGROUND:Controlling gene expression is fundamental to biological complexity. The nematode Caenorhabditis elegans is an important model for studying principles of gene regulation in multi-cellular organisms. A comprehensive parts list of putative regulatory motifs was yet missing for this model system. In this study,...

journal_title：BMC genomics

authors： Dieterich C,Sommer RJ

更新日期：2008-01-23 00:00:00

abstract：BACKGROUND:Color polymorphism in the nacre of pteriomorphian bivalves is of great interest for the pearl culture industry. The nacreous layer of the Polynesian black-lipped pearl oyster Pinctada margaritifera exhibits a large array of color variation among individuals including reflections of blue, green, yellow and pi...

journal_title：BMC genomics

authors： Lemer S,Saulnier D,Gueguen Y,Planes S

更新日期：2015-08-01 00:00:00

abstract：BACKGROUND:In clinical and basic research custom panels for transcript profiling are gaining importance because only project specific informative genes are interrogated. This approach reduces costs and complexity of data analysis and allows multiplexing of samples. Polymerase-chain-reaction (PCR) based TaqMan assays ha...

journal_title：BMC genomics

authors： Zhang JD,Schindler T,Küng E,Ebeling M,Certa U

更新日期：2014-07-05 00:00:00

abstract：BACKGROUND:The Iberian lynx (Lynx pardinus) has been acknowledged as the most endangered felid species in the world. An intense contraction and fragmentation during the twentieth century left less than 100 individuals split in two isolated and genetically eroded populations by 2002. Genetic monitoring and management so...

journal_title：BMC genomics

authors： Kleinman-Ruiz D,Martínez-Cruz B,Soriano L,Lucena-Perez M,Cruz F,Villanueva B,Fernández J,Godoy JA

更新日期：2017-07-21 00:00:00

abstract：BACKGROUND:Parasitoid wasps are well-known natural enemies of major agricultural pests and arthropod borne diseases. The parasitoid wasp Macrocentrus cingulum (Hymenoptera: Braconidae) has been widely used to control the notorious insect pests Ostrinia furnacalis (Asian Corn Borer) and O. nubilalis (European corn borer...

journal_title：BMC genomics

authors： Yin C,Li M,Hu J,Lang K,Chen Q,Liu J,Guo D,He K,Dong Y,Luo J,Song Z,Walters JR,Zhang W,Li F,Chen X

更新日期：2018-05-30 00:00:00

abstract：BACKGROUND:DNA methylation is a key modulator of gene expression in mammalian development and cellular differentiation, including neurons. To date, the role of DNA modifications in long-term potentiation (LTP) has not been explored. RESULTS:To investigate the occurrence of DNA methylation changes in LTP, we undertook ...

journal_title：BMC genomics

authors： Maag JL,Kaczorowski DC,Panja D,Peters TJ,Bramham CR,Wibrand K,Dinger ME

更新日期：2017-03-23 00:00:00