Abstract:
BACKGROUND:Genomic characterization of rotavirus (RoV) has not been adopted at large-scale due to the complexity of obtaining sequences for all 11 segments, particularly when feces are used as starting material. METHODS:To overcome these limitations, we developed a novel RoV capture and genome sequencing method combining commercial enzyme immunoassay plates and a set of routinely used reagents. RESULTS:Our approach had a 100% success rate, producing >90% genome coverage for diverse RoV present in fecal samples (Ct < 30). CONCLUSIONS:This method provides a novel, reproducible and comparatively simple approach for genomic RoV characterization and could be scaled-up for use in global RoV surveillance systems. TRIAL REGISTRATION (PROSPECTIVELY REGISTERED):Current Controlled Trials ISRCTN88101063 . Date of registration: 14/06/2012.
journal_name
BMC Genomicsjournal_title
BMC genomicsauthors
Dung TTN,Duy PT,Sessions OM,Sangumathi UK,Phat VV,Tam PTT,To NTN,Phuc TM,Hong Chau TT,Chau NNM,Minh NN,Thwaites GE,Rabaa MA,Baker Sdoi
10.1186/s12864-017-3714-6subject
Has Abstractpub_date
2017-04-24 00:00:00pages
324issue
1issn
1471-2164pii
10.1186/s12864-017-3714-6journal_volume
18pub_type
杂志文章相关文献
BMC GENOMICS文献大全abstract:BACKGROUND:MicroRNAs (miRNAs) post-transcriptionally regulate a variety of genes involved in eukaryotic cell growth, development, metabolism and other biological processes, and numerous miRNAs are implicated in the initiation and progression of cancer. Enzootic nasal adenocarcinoma (ENA), an epithelial tumor induced in...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-016-3238-5
更新日期:2016-11-08 00:00:00
abstract:BACKGROUND:The identification of cell type-specific genes (markers) is an essential step for the deconvolution of the cellular fractions, primarily, from the gene expression data of a bulk sample. However, the genes with significant changes identified by pair-wise comparisons cannot indeed represent the specificity of ...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-020-06888-1
更新日期:2020-09-23 00:00:00
abstract:BACKGROUND:CCCH type zinc finger proteins are RNA binding proteins with regulatory functions at all stages of mRNA metabolism. The best-characterized member, tritetraproline (TTP), binds to AU rich elements in 3' UTRs of unstable mRNAs, mediating their degradation. In kinetoplastids, CCCH type zinc finger proteins have...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-11-283
更新日期:2010-05-05 00:00:00
abstract:BACKGROUND:The orange pigmentation of the agar cultures of many Fusarium species is due to the production of carotenoids, terpenoid pigments whose synthesis is stimulated by light. The genes of the carotenoid pathway and their regulation have been investigated in detail in Fusarium fujikuroi. In this and other Fusarium...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-019-5430-x
更新日期:2019-01-21 00:00:00
abstract:BACKGROUND:Acquisition of external phosphorus (P) and optimisation of internal P are essential for plant growth and development, and insufficient availability of P in soils is a major challenge in agriculture. Members of the purple acid phosphatase (PAP) family of enzymes are candidates for increasing P use efficiency....
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-018-5022-1
更新日期:2018-08-31 00:00:00
abstract:BACKGROUND:Soybean seed weight is not only a yield component, but also a critical trait for various soybean food products such as sprouts, edamame, soy nuts, natto and miso. Linkage analysis and genome-wide association study (GWAS) are two complementary and powerful tools to connect phenotypic differences to the underl...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-017-3922-0
更新日期:2017-07-12 00:00:00
abstract:BACKGROUND:The beta-defensin gene cluster (DEFB) at chromosome 8p23.1 is one of the most copy number (CN) variable regions of the human genome. Whereas individual DEFB CNs have been suggested as independent genetic risk factors for several diseases (e.g. psoriasis and Crohn's disease), the role of multisite sequence va...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-11-252
更新日期:2010-04-19 00:00:00
abstract:BACKGROUND:Sensory hair cells are exquisitely sensitive to mechanical stimuli and as such, are prone to damage and apoptosis during dissections or in vitro manipulations. Thiouracil (TU)-tagging is a noninvasive method to label cell type-specific transcripts in an intact organism, thereby meeting the challenge of how t...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-015-2072-5
更新日期:2015-10-23 00:00:00
abstract:BACKGROUND:Grass carp (Ctenopharyngodon idella) belongs to the family Cyprinidae which includes more than 2000 fish species. It is one of the most important freshwater food fish species in world aquaculture. A linkage map is an essential framework for mapping traits of interest and is often the first step towards under...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-11-135
更新日期:2010-02-24 00:00:00
abstract:BACKGROUND:Small bioinformatics databases, unlike institutionally funded large databases, are vulnerable to discontinuation and many reported in publications are no longer accessible. This leads to irreproducible scientific work and redundant effort, impeding the pace of scientific progress. RESULTS:We describe a Web-...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-14-S5-S13
更新日期:2013-01-01 00:00:00
abstract::As gene expression profile data from DNA microarrays accumulate rapidly, there is a natural need to compare data across labs and platforms. Comparisons of microarray data can be quite challenging due to data complexity and variability. Different labs may adopt different technology platforms. One may ask about the degr...
journal_title:BMC genomics
pub_type: 杂志文章,多中心研究
doi:10.1186/1471-2164-6-71
更新日期:2005-05-11 00:00:00
abstract:BACKGROUND:TEs pervade mammalian genomes. However, compared with mice, fewer studies have focused on the TE expression patterns in rat, particularly the comparisons across different organs, developmental stages and sexes. In addition, TEs can influence the expression of nearby genes. The temporal and spatial influences...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-017-4078-7
更新日期:2017-08-29 00:00:00
abstract:BACKGROUND:Every year, substantial crop loss occurs globally, as a result of bacterial, fungal, parasite and viral infections in rice. Here, we present an in-depth investigation of the transcriptomic response to infection with the destructive bacterial pathogen Xanthomonas oryzae pv. oryzae(Xoo) in both resistant and s...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-14-93
更新日期:2013-02-12 00:00:00
abstract:BACKGROUND:Mice of the genus Apodemus are one the most common mammals in the Palaearctic region. Despite their broad range and long history of ecological observations, there are no whole-genome data available for Apodemus, hindering our ability to further exploit the genus in evolutionary and ecological genomics contex...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-020-6603-3
更新日期:2020-03-18 00:00:00
abstract:BACKGROUND:High throughput molecular sequencing and increased biospecimen variety have introduced significant informatics challenges for research biorepository infrastructures. We applied a modular system integration approach to develop an operational biorepository management system. This method enables aggregation of ...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-016-2797-9
更新日期:2016-08-18 00:00:00
abstract:BACKGROUND:Dermatophytes are the primary causative agent of dermatophytoses, a disease that affects billions of individuals worldwide. Trichophyton rubrum is the most common of the superficial fungi. Although T. rubrum is a recognized pathogen for humans, little is known about how its transcriptional pattern is related...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-7-255
更新日期:2006-10-11 00:00:00
abstract:BACKGROUND:In higher eukaryotes, small RNAs play a role in regulating gene expression. Overexpression (OE) lines of Arabidopsis thaliana purple acid phosphatase 2 (AtPAP2) were shown to grow faster and exhibit higher ATP and sugar contents. Leaf microarray studies showed that many genes involved in microRNAs (miRNAs) a...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-15-116
更新日期:2014-02-10 00:00:00
abstract:BACKGROUND:Crocodilians (Order Crocodylia) are an ancient vertebrate group of tremendous ecological, social, and evolutionary importance. They are the only extant reptilian members of Archosauria, a monophyletic group that also includes birds, dinosaurs, and pterosaurs. Consequently, crocodilian genomes represent a gat...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-10-S2-S9
更新日期:2009-07-14 00:00:00
abstract:BACKGROUND:Two-component systems (TCSs) are modular and diverse signalling pathways, involving a stimulus-responsive transfer of phosphoryl groups from transmitter to partner receiver domains. TCS gene and domain organisation are both potentially informative regarding biological function, interaction partnerships and m...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-11-720
更新日期:2010-12-20 00:00:00
abstract:BACKGROUND:Subtractive hybridization methods are valuable tools for identifying differentially regulated genes in a given tissue avoiding redundant sequencing of clones representing the same expressed genes, maximizing detection of low abundant transcripts and thus, affecting the efficiency and cost effectiveness of sm...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-4-40
更新日期:2003-09-30 00:00:00
abstract:BACKGROUND:Protein phosphorylation by kinases plays crucial roles in various biological processes including signal transduction and tumorigenesis, thus a better understanding of protein phosphorylation events in cells is fundamental for studying protein functions and designing drugs to treat diseases caused by the malf...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-020-06895-2
更新日期:2020-08-04 00:00:00
abstract:BACKGROUND:Endogenous α-synuclein (α-Syn) is involved in many pathophysiological processes in the secondary injury stage after acute spinal cord injury (SCI), and the mechanism governing these functions has not been thoroughly elucidated to date. This research aims to characterize the effect of α-Syn knockdown on trans...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-019-6244-6
更新日期:2019-11-14 00:00:00
abstract:BACKGROUND:Carolacton is a newly identified secondary metabolite causing altered cell morphology and death of Streptococcus mutans biofilm cells. To unravel key regulators mediating these effects, the transcriptional regulatory response network of S. mutans biofilms upon carolacton treatment was constructed and analyze...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-15-362
更新日期:2014-05-12 00:00:00
abstract:BACKGROUND:RNA-Seq has become increasingly popular in transcriptome profiling. One aspect of transcriptome research is to quantify the expression levels of genomic elements, such as genes, their transcripts and exons. Acquiring a transcriptome expression profile requires genomic elements to be defined in the context of...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-015-1308-8
更新日期:2015-02-18 00:00:00
abstract:BACKGROUND:Succinate is produced petrochemically from maleic anhydride to satisfy a small specialty chemical market. If succinate could be produced fermentatively at a price competitive with that of maleic anhydride, though, it could replace maleic anhydride as the precursor of many bulk chemicals, transforming a multi...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-11-680
更新日期:2010-11-30 00:00:00
abstract:BACKGROUND:Genome-wide association studies show that most human traits and diseases are caused by a combination of environmental and genetic causes, with each one of these having a relatively small effect. In contrast, most therapies based on macromolecules like antibodies, antisense oligonucleotides or peptides focus ...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-015-1727-6
更新日期:2015-07-18 00:00:00
abstract:BACKGROUND:Health traits are of significant economic importance to the dairy industry due to their effects on milk production and associated treatment costs. Genome-wide association studies (GWAS) provide a means to identify associated genomic variants and thus reveal insights into the genetic architecture of complex t...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-020-6461-z
更新日期:2020-01-13 00:00:00
abstract:BACKGROUND:The genome-wide association (GWA) approach represents an alternative to biparental linkage mapping for determining the genetic basis of trait variation. Both approaches rely on recombination to re-arrange the genome, and seek to establish correlations between phenotype and genotype. The major advantages of G...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-15-896
更新日期:2014-10-14 00:00:00
abstract:BACKGROUND:The mosquito species Aedes aegypti is the primary vector of many arboviral diseases, including dengue and yellow fevers, that are responsible for a large worldwide health burden. The biological rhythms of mosquitoes regulate many of the physiological processes and behaviors that influence the transmission of...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-15-1128
更新日期:2014-12-17 00:00:00
abstract:BACKGROUND:Technological advances have enabled transcriptome characterization of cell types at the single-cell level providing new biological insights. New methods that enable simple yet high-throughput single-cell expression profiling are highly desirable. RESULTS:Here we report a novel nanowell-based single-cell RNA...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-017-3893-1
更新日期:2017-07-07 00:00:00