Abstract:
BACKGROUND:In mammals, CEACAM1 and closely related members represent paired receptors with similar extracellular ligand-binding regions and cytoplasmic domains with opposing functions. Human CEACAM1 and CEACAM3 which have inhibitory ITIM/ITSM and activating ITAM-like motifs, respectively, in their cytoplasmic regions are such paired receptors. Various bacterial pathogens bind to CEACAM1 on epithelial and immune cells facilitating both entry into the host and down-regulation of the immune response whereas interaction with granulocyte-specific CEACAM3 leads to their uptake and destruction. It is unclear whether paired CEACAM receptors also exist in other vertebrate clades. RESULTS:We identified more than 80 ceacam genes in Xenopus tropicalis and X. laevis. They consist of two subgroups containing one or two putative paired receptor pairs each. Analysis of genomic sequences of paired receptors provide evidence that their highly similar ligand binding domains were adjusted by recent gene conversion events. In contrast, selection for diversification is observed among inhibitory receptor orthologs of the two frogs which split some 60 million years ago. The allotetraploid X. laevis arose later by hybridization of two closely related species. Interestingly, despite the conservation of the genomic landscape surrounding the homeologous ceacam loci only one locus resembles the one found in X. tropicalis. From the second X. laevis locus more than 80 % of the ceacam genes were lost including 5 of the 6 paired receptor genes. This suggests that once the gene for one of the paired receptors is lost the remaining gene cluster degrades rapidly probably due to lack of selection pressure exerted by pathogens. CONCLUSIONS:The presence of paired receptors and selection for diversification suggests that also in amphibians CEACAM1-related inhibitory proteins are or were used as pathogen receptors.
journal_name
BMC Genomicsjournal_title
BMC genomicsauthors
Zimmermann W,Kammerer Rdoi
10.1186/s12864-016-3279-9subject
Has Abstractpub_date
2016-11-16 00:00:00pages
928issue
1issn
1471-2164pii
10.1186/s12864-016-3279-9journal_volume
17pub_type
杂志文章相关文献
BMC GENOMICS文献大全abstract:BACKGROUND:The superior temporal gyrus (STG), which encompasses the primary auditory cortex, is believed to be a major anatomical substrate for speech, language and communication. The STG connects to the limbic system (hippocampus and amygdala), the thalamus and neocortical association areas in the prefrontal cortex, a...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-9-199
更新日期:2008-04-29 00:00:00
abstract:BACKGROUND:There is a large amount of inconsistency in gene structure annotations of bacterial strains. This inconsistency is a frustrating impedance to effective comparative genomic analysis of bacterial strains in promising applications such as gaining insights into bacterial drug resistance. RESULTS:Here, we propos...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-12-S2-S6
更新日期:2011-01-01 00:00:00
abstract:BACKGROUND:Burkholderia cenocepacia is an opportunistic pathogen causing life-threatening infections in patients with cystic fibrosis. The bacterium survives within macrophages by interfering with endocytic trafficking and delaying the maturation of the B. cenocepacia-containing phagosome. We hypothesize that B. cenoce...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-13-63
更新日期:2012-02-09 00:00:00
abstract:BACKGROUND:New and improved antimicrobial countermeasures are urgently needed to counteract increased resistance to existing antimicrobial treatments and to combat currently untreatable or new emerging infectious diseases. We demonstrate that computational comparative genomics, together with experimental screening, can...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-10-501
更新日期:2009-10-29 00:00:00
abstract:BACKGROUND:More accurate and complete reference genomes have improved understanding of gene function, biology, and evolutionary mechanisms. Hybrid genome assembly approaches leverage benefits of both long, relatively error-prone reads from third-generation sequencing technologies and short, accurate reads from second-g...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-021-07390-y
更新日期:2021-01-28 00:00:00
abstract:BACKGROUND:It has been shown previously that aminocoumarin antibiotics such as novobiocin lead to immediate downregulation of recA expression and thereby inhibit the SOS response, mutation frequency and recombination capacity in Staphylococcus aureus. Aminocoumarins function by inhibiting the ATPase activity of DNA gyr...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-15-291
更新日期:2014-04-16 00:00:00
abstract:BACKGROUND:Cultivated peanut (Arachis hypogaea) is an allotetraploid species whose ancestral genomes are most likely derived from the A-genome species, A. duranensis, and the B-genome species, A. ipaensis. The very recent (several millennia) evolutionary origin of A. hypogaea has imposed a bottleneck for allelic and ph...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-13-469
更新日期:2012-09-11 00:00:00
abstract:BACKGROUND:Copy number variants (CNVs) have been shown to increase risk for physical anomalies, developmental, psychiatric and medical disorders. Some of them have been associated with changes in weight, height, and other physical traits. As most studies have been performed on children and young people, these effects o...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-018-5292-7
更新日期:2018-12-04 00:00:00
abstract:BACKGROUND:The activity of the yeast activator protein 1 (Yap1p) increases under stress conditions, which leads to enhanced transcription of a number of genes encoding protective enzymes or other proteins. To obtain a global overview of changes in expression of Yap1p-targeted proteins, we compared a Yap1p-overexpressin...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-13-230
更新日期:2012-06-09 00:00:00
abstract:BACKGROUND:To develop evolutionary models for the free living bacterium Alteromonas the genome sequences of isolates of the genus have been extensively analyzed. However, the main genetic exchange drivers in these microbes, conjugative elements (CEs), have not been considered in detail thus far. In this work, CEs have ...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-016-3461-0
更新日期:2017-01-05 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
pub_type: 杂志文章
doi:10.1186/s12864-018-4783-x
更新日期:2018-05-30 00:00:00
abstract:BACKGROUND:The Spemann/Mangold organizer is a transient tissue critical for patterning the gastrula stage vertebrate embryo and formation of the three germ layers. Despite its important role during development, there are still relatively few genes with specific expression in the organizer and its derivatives. Foxa2 is ...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-9-511
更新日期:2008-10-30 00:00:00
abstract:BACKGROUND:Despite its relevance, almost no studies account for the genetic control in the early stages of tree development, i.e. from germination on. This study seeks to make a quite complete transcriptome for olive development and to elucidate the dynamic regulation of the transcriptomic response during the early-juv...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-018-5232-6
更新日期:2018-11-19 00:00:00
abstract:BACKGROUND:As crucial markers in identifying biological elements and processes in mammalian genomes, CpG islands (CGI) play important roles in DNA methylation, gene regulation, epigenetic inheritance, gene mutation, chromosome inactivation and nuclesome retention. The generally accepted criteria of CGI rely on: (a) %G+...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-017-3731-5
更新日期:2017-05-24 00:00:00
abstract:BACKGROUND:Phenomena such as incomplete lineage sorting, horizontal gene transfer, gene duplication and subsequent sub- and neo-functionalisation can result in distinct local phylogenetic relationships that are discordant with species phylogeny. In order to assess the possible biological roles for these subdivisions, t...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-14-347
更新日期:2013-05-24 00:00:00
abstract:BACKGROUND:Gene ontology analysis using the microarray database generated in a previous study by this laboratory was used to further evaluate how maternal dietary supplementation with pyridoxine combined with different sources of selenium (Se) affected global gene expression of expanded porcine blastocysts. Data were g...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-018-5237-1
更新日期:2018-11-21 00:00:00
abstract:BACKGROUND:Segmental duplications (SDs) commonly exist in plant and animal genomes, playing crucial roles in genomic rearrangement, gene innovation and the formation of copy number variants. However, they have received little attention in most livestock species. RESULTS:Aiming at characterizing SDs across the genomes ...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-017-3690-x
更新日期:2017-04-12 00:00:00
abstract:BACKGROUND:Artificial insemination and genetic selection are major factors contributing to population stratification in dairy cattle. In this study, we analyzed the effect of sample stratification and the effect of stratification correction on results of a dairy genome-wide association study (GWAS). Three methods for s...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-13-536
更新日期:2012-10-06 00:00:00
abstract::The reporting of the first draft of the human genome in 2000 brought with it much hope for the future in what was felt as a paradigm shift toward improved health outcomes. Indeed, we have now mapped the majority of variation across human populations with landmark projects such as 1000 Genomes; in cancer, we have catal...
journal_title:BMC genomics
pub_type: 杂志文章,评审
doi:10.1186/s12864-018-4963-8
更新日期:2018-08-08 00:00:00
abstract:BACKGROUND:Cryptocaryon irritans is an obligate parasitic ciliate protozoan that can infect various commercially important mariculture fish species and cause high lethality and economic loss. Current methods of controlling this parasite with chemicals or antibiotics are widely considered to be environmentally harmful. ...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-018-4565-5
更新日期:2018-03-12 00:00:00
abstract:BACKGROUND:Anthocyanins are water-soluble colored flavonoids present in multiple organs of various plant species including flowers, fruits, leaves, stems and roots. DNA-binding R2R3-MYB transcription factors, basic helix-loop-helix (bHLH) transcription factors, and WD40 repeat proteins are known to form MYB-bHLH-WD rep...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-018-5135-6
更新日期:2018-11-08 00:00:00
abstract:BACKGROUND:Chronic Allograft Nephropathy (CAN) is a clinical entity of progressive kidney transplant injury. The defining histology is tubular atrophy with interstitial fibrosis (IFTA). Using a meta-analysis of microarrays from 84 kidney transplant biopsies, we revealed growth factor and integrin adhesion molecule path...
journal_title:BMC genomics
pub_type: 杂志文章,meta分析
doi:10.1186/1471-2164-14-275
更新日期:2013-04-23 00:00:00
abstract:BACKGROUND:The Hafnia genus is an opportunistic pathogen that has been implicated in both nosocomial and community-acquired infections. Although Hafnia is fairly often isolated from clinical material, its taxonomy has remained an unsolved riddle, and the involvement and importance of Hafnia in human disease is also unc...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-019-6123-1
更新日期:2019-10-23 00:00:00
abstract:BACKGROUND:One challenge of systems biology is the integration of new data into the preexisting, and then re-interpretation of the integrated data. Here we use readily available metaanalysis computational methods to integrate new data on the transcriptomic effects of EGF in primary human epidermal keratinocytes with pr...
journal_title:BMC genomics
pub_type: 杂志文章,meta分析
doi:10.1186/1471-2164-14-85
更新日期:2013-02-08 00:00:00
abstract:BACKGROUND:Habitats colonized by acidophiles as an ideal physical barrier may induce genetic exchange of microbial members within the common communities, but little is known about how species in extremely acidic environments diverge and evolve. RESULTS:Using the acidophilic sulfur-oxidizer Acidithiobacillus as a case ...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-019-5827-6
更新日期:2019-05-30 00:00:00
abstract:BACKGROUND:Though genomic-level data are becoming widely available, many of the metazoan species sequenced are laboratory systems whose natural history is not well documented. In contrast, the wide array of species with very well-characterized natural history have, until recently, lacked genomics tools. It is now possi...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-13-305
更新日期:2012-07-09 00:00:00
abstract:BACKGROUND:For centuries roses have been selected based on a number of traits. Little information exists on the genetic and molecular basis that contributes to these traits, mainly because information on expressed genes for this economically important ornamental plant is scarce. RESULTS:Here, we used a combination of ...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-13-638
更新日期:2012-11-20 00:00:00
abstract:BACKGROUND:Excretory/secretory proteins (ESPs) play a major role in parasitic infection as they are present at the host-parasite interface and regulate host immune system. In case of parasitic helminths, transcriptomics has been used extensively to understand the molecular basis of parasitism and for developing novel t...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-12-S3-S14
更新日期:2011-11-30 00:00:00
abstract:BACKGROUND:In research laboratories using DNA-microarrays, usually a number of researchers perform experiments, each generating possible sources of error. There is a need for a quick and robust method to assess data quality and sources of errors in DNA-microarray experiments. To this end, a novel and cost-effective val...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-6-77
更新日期:2005-05-20 00:00:00
abstract:BACKGROUND:Abnormalities of pre-mRNA splicing are increasingly recognized as an important mechanism through which gene mutations cause disease. However, apart from the mutations in the donor and acceptor sites, the effects on splicing of other sequence variations are difficult to predict. Loosely defined exonic and int...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-7-243
更新日期:2006-09-22 00:00:00