Abstract:
BACKGROUND:Ocean acidification (OA), a change in ocean chemistry due to the absorption of atmospheric CO2 into surface oceans, challenges biogenic calcification in many marine organisms. Ocean acidification is expected to rapidly progress in polar seas, with regions of the Southern Ocean expected to experience severe OA within decades. Biologically, the consequences of OA challenge calcification processes and impose an energetic cost. RESULTS:In order to better characterize the response of a polar calcifier to conditions of OA, we assessed differential gene expression in the Antarctic pteropod, Limacina helicina antarctica. Experimental levels of pCO2 were chosen to create both contemporary pH conditions, and to mimic future pH expected in OA scenarios. Significant changes in the transcriptome were observed when juvenile L. h. antarctica were acclimated for 21 days to low-pH (7.71), mid-pH (7.9) or high-pH (8.13) conditions. Differential gene expression analysis of individuals maintained in the low-pH treatment identified down-regulation of genes involved in cytoskeletal structure, lipid transport, and metabolism. High pH exposure led to increased expression and enrichment for genes involved in shell formation, calcium ion binding, and DNA binding. Significant differential gene expression was observed in four major cellular and physiological processes: shell formation, the cellular stress response, metabolism, and neural function. Across these functional groups, exposure to conditions that mimic ocean acidification led to rapid suppression of gene expression. CONCLUSIONS:Results of this study demonstrated that the transcriptome of the juvenile pteropod, L. h. antarctica, was dynamic and changed in response to different levels of pCO2. In a global change context, exposure of L. h. antarctica to the low pH, high pCO2 OA conditions resulted in a suppression of transcripts for genes involved in key physiological processes: calcification, metabolism, and the cellular stress response. The transcriptomic response at both acute and longer-term acclimation time frames indicated that contemporary L. h. antarctica may not have the physiological plasticity necessary for adaptation to OA conditions expected in future decades. Lastly, the differential gene expression results further support the role of shelled pteropods such as L. h. antarctica as sentinel organisms for the impacts of ocean acidification.
journal_name
BMC Genomicsjournal_title
BMC genomicsauthors
Johnson KM,Hofmann GEdoi
10.1186/s12864-017-4161-0subject
Has Abstractpub_date
2017-10-23 00:00:00pages
812issue
1issn
1471-2164pii
10.1186/s12864-017-4161-0journal_volume
18pub_type
杂志文章相关文献
BMC GENOMICS文献大全abstract:BACKGROUND:Ashbya gossypii is a filamentous Saccharomycete used for the industrial production of riboflavin that has been recently explored as a host system for recombinant protein production. To gain insight into the protein secretory pathway of this biotechnologically relevant fungus, we undertook genome-wide analyse...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-15-1137
更新日期:2014-12-18 00:00:00
abstract:BACKGROUND:The question of whether bacterial species objectively exist has long divided microbiologists. A major source of contention stems from the fact that bacteria regularly engage in horizontal gene transfer (HGT), making it difficult to ascertain relatedness and draw boundaries between taxa. A natural way to defi...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-018-5099-6
更新日期:2018-10-03 00:00:00
abstract:BACKGROUND:Infectious disease outbreaks form major setbacks to aquaculture production and to further development of this important sector. Cyprinid herpes virus-3 (CyHV-3) is a dsDNA virus widely hampering production of common carp (Cyprinus carpio), one of the most farmed fish species worldwide. Genetically disease re...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-019-6391-9
更新日期:2019-12-26 00:00:00
abstract:BACKGROUND:Natural accessions of Arabidopsis thaliana are characterized by a high level of phenotypic variation that can be used to investigate the extent and mode of selection on the primary metabolic traits. A collection of 54 A. thaliana natural accession-derived lines were subjected to deep genotyping through Singl...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-11-188
更新日期:2010-03-20 00:00:00
abstract:BACKGROUND:Obesity and phenotypic traits associated with this condition exhibit significant heritability in natural populations of most organisms. While a number of genes and genetic pathways have been implicated to play a role in obesity associated traits, the genetic architecture that underlies the natural variation ...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-11-297
更新日期:2010-05-11 00:00:00
abstract:BACKGROUND:Streptococcus pneumoniae causes over one million deaths worldwide annually, despite recent developments in vaccine and antibiotic therapy. Host susceptibility to pneumococcal infection and disease is controlled by a combination of genetic and environmental influences, but current knowledge remains limited. ...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-14-242
更新日期:2013-04-11 00:00:00
abstract:BACKGROUND:CRISPR-Cas9 is a revolutionary genome editing technique that allows for efficient and directed alterations of the eukaryotic genome. This relatively new technology has already been used in a large number of 'loss of function' experiments in cultured cells. Despite its simplicity and efficiency, screening for...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-15-1002
更新日期:2014-11-20 00:00:00
abstract:BACKGROUND:Carrot (Daucus carota) is a major food crop in the US and worldwide. Its capacity for storage and its lifecycle as a biennial make it an attractive species for the introduction of foreign genes, especially for oral delivery of vaccines and other therapeutic proteins. Until recently efforts to express recombi...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-7-222
更新日期:2006-08-31 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:Progress in genetics and breeding in pea still suffers from the limited availability of molecular resources. SNP markers that can be identified through affordable sequencing processes, without the need for prior genome reduction or a reference genome to assemble sequencing data would allow the discovery and ...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-016-2447-2
更新日期:2016-02-18 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:Hard ticks (family Ixodidae) are obligatory hematophagous ectoparasites of worldwide medical and veterinary importance. The haploid genomes of multiple species of ixodid ticks exceed 1 Gbp, prompting questions regarding gene, segmental and whole genome duplication in this phyletic group. The availability of ...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-015-2350-2
更新日期:2016-03-16 00:00:00
abstract:BACKGROUND:Microsatellites are extremely common in plant genomes, and in particular, they are significantly enriched in the 5' noncoding regions. Although some 5' noncoding microsatellites involved in gene regulation have been described, the general properties of microsatellites as regulatory elements are still unknown...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-7-323
更新日期:2006-12-25 00:00:00
abstract:BACKGROUND:Tumor necrosis factor alpha (TNF) is able to induce a variety of biological responses in the nervous system including inflammation and neuroprotection. Human astrocytoma cells U373 have been widely used as a model for inflammatory cytokine actions in the nervous system. Here we used cDNA microarrays to analy...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-4-46
更新日期:2003-11-25 00:00:00
abstract:BACKGROUND:Single-cell (sc) sequencing performs unbiased profiling of individual cells and enables evaluation of less prevalent cellular populations, often missed using bulk sequencing. However, the scale and the complexity of the sc datasets poses a great challenge in its utility and this problem is further exacerbate...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-020-07300-8
更新日期:2021-01-06 00:00:00
abstract:BACKGROUND:Clostridium sticklandii belongs to a cluster of non-pathogenic proteolytic clostridia which utilize amino acids as carbon and energy sources. Isolated by T.C. Stadtman in 1954, it has been generally regarded as a "gold mine" for novel biochemical reactions and is used as a model organism for studying metabol...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-11-555
更新日期:2010-10-11 00:00:00
abstract:BACKGROUND:Post-translational modification (PTM) of proteins is central to many cellular processes across all domains of life, but despite decades of study and a wealth of genomic and proteomic data the biological function of many PTMs remains unknown. This is especially true for prokaryotic PTM systems, many of which ...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-017-3676-8
更新日期:2017-04-17 00:00:00
abstract:BACKGROUND:Despite the importance of chromosomal translocations in the initiation and/or progression of cancer, a comprehensive catalog of translocation breakpoints in which these are precisely located on the reference sequence of the human genome is not available at present. DESCRIPTION:We have created a database tha...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-8-33
更新日期:2007-01-26 00:00:00
abstract:BACKGROUND:In understanding the evolutionary process of vertebrates, cyclostomes (hagfishes and lamprey) occupy crucial positions. Resolving molecular phylogenetic relationships of cyclostome genes with gnathostomes (jawed vertebrates) genes is indispensable in deciphering both the species tree and gene trees. However,...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-12-325
更新日期:2011-06-23 00:00:00
abstract:BACKGROUND:Aging is affected by genetic and environmental factors, and cigarette smoking is strongly associated with accumulation of senescent cells. In this study, we wanted to identify genes that may potentially be beneficial for cell survival in response to cigarette smoke and thereby may contribute to development o...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-018-5409-z
更新日期:2019-01-09 00:00:00
abstract:BACKGROUND:Compromised intestinal barrier (CIB) has been associated with many enteropathies, including colorectal cancer (CRC) and inflammatory bowel disease (IBD). We hypothesized that CIB could lead to increased host-derived contents including epithelial cells into the gut, change its physio-metabolic properties, and...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-020-6749-z
更新日期:2020-05-11 00:00:00
abstract:BACKGROUND:Citrus blight is a very important progressive decline disease of commercial citrus. The etiology is unknown, although the disease can be transmitted by root grafts, suggesting a viral etiology. Diagnosis is made by demonstrating physical blockage of xylem cells that prevents the movement of water. This test ...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-019-6339-0
更新日期:2019-12-11 00:00:00
abstract:BACKGROUND:Zoysia matrella, widely used in lawns and sports fields, is of great economic and ecological value. Z. matrella is an allotetraploid species (2n = 4x = 40) in the genus zoysia under the subfamily Chloridoideae. Despite its ecological impacts and economic importance, the subfamily Chloridoideae has received l...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-016-2969-7
更新日期:2016-08-08 00:00:00
abstract:BACKGROUND:The regenerative response of Schwann cells after peripheral nerve injury is a critical process directly related to the pathophysiology of a number of neurodegenerative diseases. This SC injury response is dependent on an intricate gene regulatory program coordinated by a number of transcription factors and m...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-14-84
更新日期:2013-02-06 00:00:00
abstract:BACKGROUND:Genomic approaches provide unique opportunities to study interactions of insects with their pathogens. We developed a cDNA microarray to analyze the gene transcription profile of the lepidopteran pest Spodoptera frugiperda in response to injection of the polydnavirus HdIV associated with the ichneumonid wasp...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-7-160
更新日期:2006-06-21 00:00:00
abstract:BACKGROUND:Modern broiler chickens exhibit very rapid growth and high feed efficiency compared to unselected chicken breeds. The improved production efficiency in modern broiler chickens was achieved by the intensive genetic selection for meat production. This study was designed to investigate the genetic alterations a...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-016-3471-y
更新日期:2017-01-13 00:00:00
abstract:BACKGROUND:About 6 million Americans suffer from heart failure and 70% of heart failure cases are caused by myocardial infarction (MI). Following myocardial infarction, increased cytokines induce two major types of macrophages: classically activated macrophages which contribute to extracellular matrix destruction and a...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-13-S6-S21
更新日期:2012-01-01 00:00:00
abstract:BACKGROUND:Homology-based comparisons of the genes involved in innate immunity across many insect taxa with fully sequenced genomes has revealed a striking pattern of gene gain and loss, particularly among genes that encode proteins involved in clearing pathogens (effectors). However, limited functional annotation in n...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-10-259
更新日期:2009-06-07 00:00:00
abstract:BACKGROUND:Petal nectar spurs, which facilitate pollination through animal attraction and pollen placement, represent a key innovation promoting diversification in the genus Aquilegia (Ranunculaceae). Identifying the genetic components that contribute to the development of these three-dimensional structures will inform...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-019-6002-9
更新日期:2019-08-22 00:00:00
abstract:BACKGROUND:Regulation of bacterial gene expression by small RNAs (sRNAs) have proved to be important for many biological processes. Francisella tularensis is a highly pathogenic Gram-negative bacterium that causes the disease tularaemia in humans and animals. Relatively little is known about the regulatory networks exi...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-11-625
更新日期:2010-11-10 00:00:00