Abstract:
BACKGROUND:The obligate intracellular parasite Toxoplasma gondii establishes a life-long chronic infection within any warm-blooded host. After ingestion of an encysted parasite, T. gondii disseminates throughout the body as a rapidly replicating form during acute infection. Over time and after stimulation of the host immune response, T. gondii differentiates into a slow growing, cyst form that is the hallmark of chronic infection. Global transcriptome analysis of both host and parasite during the establishment of chronic T. gondii infection has not yet been performed. Here, we conducted a dual RNA-seq analysis of T. gondii and its rodent host to better understand host and parasite responses during acute and chronic infection. RESULTS:We obtained nearly one billion paired-end RNA sequences from the forebrains of uninfected, acutely and chronically infected mice, then aligned them to the genomic reference files of both T. gondii and Mus musculus. Gene ontology (GO) analysis of the 100 most highly expressed T. gondii genes showed less than half were shared between acute and chronic infection. The majority of the highly expressed genes common in both acute and chronic infection were involved in transcription and translation, underscoring that parasites in both stages are actively synthesizing proteins. Similarly, most of the T. gondii genes highly expressed during chronic infection were involved in metabolic processes, again highlighting the activity of the cyst stage at 28 days post-infection. Comparative analyses of host genes using uninfected forebrain revealed over twice as many immune regulatory genes were more abundant during chronic infection compared to acute. This demonstrates the influence of parasite development on host gene transcription as well as the influence of the host environment on parasite gene transcription. CONCLUSIONS:RNA-seq is a valuable tool to simultaneously analyze host and microbe transcriptomes. Our data shows that T. gondii is metabolically active and synthesizing proteins at 28 days post-infection and that a distinct subset of host genes associated with the immune response are more abundant specifically during chronic infection. These data suggest host and pathogen interplay is still present during chronic infection and provides novel T. gondii targets for future drug and vaccine development.
journal_name
BMC Genomicsjournal_title
BMC genomicsauthors
Pittman KJ,Aliota MT,Knoll LJdoi
10.1186/1471-2164-15-806subject
Has Abstractpub_date
2014-09-20 00:00:00pages
806issn
1471-2164pii
1471-2164-15-806journal_volume
15pub_type
杂志文章相关文献
BMC GENOMICS文献大全abstract:BACKGROUND:Despite the recent identification of several prognostic gene signatures, the lack of common genes among experimental cohorts has posed a considerable challenge in uncovering the molecular basis underlying hepatocellular carcinoma (HCC) recurrence for application in clinical purposes. To overcome the limitati...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-015-1472-x
更新日期:2015-04-10 00:00:00
abstract:BACKGROUND:Many biological systems respond to the presence or absence of gravity. Since experiments performed in space are expensive and can only be undertaken infrequently, Earth-based simulation techniques are used to investigate the biological response to weightlessness. A high gradient magnetic field can be used to...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-13-52
更新日期:2012-02-01 00:00:00
abstract:BACKGROUND:Aspergillus arachidicola is an aflatoxigenic fungal species, first isolated from the leaves of a wild peanut species native to Argentina. It has since been reported in maize, Brazil nut and human sputum samples. This aflatoxigenic species is capable of secreting both B and G aflatoxins, similar to A. parasit...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-018-4576-2
更新日期:2018-03-09 00:00:00
abstract:BACKGROUND:As consumers continue to request food products that have health advantages, it will be important for the livestock industry to supply a product that meet these demands. One such nutrient is fatty acids, which have been implicated as playing a role in cardiovascular disease. Therefore, the objective of this s...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-14-730
更新日期:2013-10-25 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
pub_type: 杂志文章
doi:10.1186/s12864-019-6053-y
更新日期:2019-08-27 00:00:00
abstract:BACKGROUND:While the gargantuan multi-nation effort of sequencing T. aestivum gets close to completion, the annotation process for the vast number of wheat genes and proteins is in its infancy. Previous experimental studies carried out on model plant organisms such as A. thaliana and O. sativa provide a plethora of gen...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-015-1496-2
更新日期:2015-04-15 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: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:The nucleoli, including their proteomes, of higher eukaryotes have been extensively studied, while few studies about the nucleoli of the lower eukaryotes - protists were reported. Giardia lamblia, a protist with the controversy of whether it is an extreme primitive eukaryote or just a highly evolved parasite...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-020-6679-9
更新日期:2020-03-30 00:00:00
abstract:BACKGROUND:Shotgun sequencing of environmental DNA is an essential technique for characterizing uncultivated microbes in situ. However, the taxonomic and functional assignment of the obtained sequence fragments remains a pressing problem. RESULTS:Existing algorithms are largely optimized for speed and coverage; in con...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-11-461
更新日期:2010-08-05 00:00:00
abstract:BACKGROUND:Although the study of gene regulation via the action of specific microRNAs (miRNAs) has experienced a boom in recent years, the analysis of genome-wide interaction networks among miRNAs and respective targeted mRNAs has lagged behind. MicroRNAs simultaneously target many transcripts and fine-tune the express...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-14-725
更新日期:2013-10-22 00:00:00
abstract:BACKGROUND:Mapping DNaseI hypersensitive sites is commonly used to identify regulatory regions in the genome. However, currently available methods are either time consuming and laborious, expensive or require large numbers of cells. We aimed to develop a quick and straightforward method for the analysis of DNaseI hyper...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-10-412
更新日期:2009-09-04 00:00:00
abstract:BACKGROUND:In contrast to wild species, which have typically evolved phenotypes over long periods of natural selection, domesticates rapidly gained human-preferred agronomic traits in a relatively short-time frame via artificial selection. Under domesticated conditions, many traits can be observed that cannot only be d...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-14-646
更新日期:2013-09-23 00:00:00
abstract:BACKGROUND:Ras-related proteins in brain (Rab)-family proteins are key members of the membrane trafficking pathway in cells. In addition, these proteins have been identified to have diverse functions such as cross-talking with different kinases and playing a role in cellular signaling. However, only a few Rab proteins ...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-016-3145-9
更新日期:2016-10-10 00:00:00
abstract:BACKGROUND:Williams syndrome transcription factor (WSTF) is a multifaceted protein that is involved in several nuclear processes, including replication, transcription, and the DNA damage response. WSTF participates in a chromatin-remodeling complex with the ISWI ATPase, SNF2H, and is thought to contribute to the mainte...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-14-740
更新日期:2013-10-29 00:00:00
abstract:BACKGROUND:Polypyrimidine-tract binding proteins (PTBs) are ubiquitous RNA-binding proteins in plants and animals that play diverse role in RNA metabolic processes. PTB proteins bind to target RNAs through motifs rich in cytosine/uracil residues to fine-tune transcript metabolism. Among tuber and root crops, potato has...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-018-4502-7
更新日期:2018-02-07 00:00:00
abstract:BACKGROUND:Chemical bioavailability is an important dose metric in environmental risk assessment. Although many approaches have been used to evaluate bioavailability, not a single approach is free from limitations. Previously, we developed a new genomics-based approach that integrated microarray technology and regressi...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-016-2541-5
更新日期:2016-03-08 00:00:00
abstract:BACKGROUND:Alternative σ factors are important transcriptional regulators in bacteria. While σ(B) has been shown to control a large regulon and play important roles in stress response and virulence in the pathogen Listeria monocytogenes, the function of σ(H) has not yet been well defined in Listeria, even though σ(H) c...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-016-2432-9
更新日期:2016-02-16 00:00:00
abstract:BACKGROUND:DNA methylation at promoters is largely correlated with inhibition of gene expression. However, the role of DNA methylation at enhancers is not fully understood, although a crosstalk with chromatin marks is expected. Actually, there exist contradictory reports about positive and negative correlations between...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-017-4353-7
更新日期:2017-12-12 00:00:00
abstract:BACKGROUND:Coral reefs are hotspots of oceanic biodiversity, forming the foundation of ecosystems that are important both ecologically and for their direct practical impacts on humans. Corals are declining globally due to a number of stressors, including rising sea-surface temperatures and pollution; such stresses can ...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-13-271
更新日期:2012-06-22 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
pub_type: 杂志文章
doi:10.1186/1471-2164-13-96
更新日期:2012-03-19 00:00:00
abstract:BACKGROUND:The reconstruction of gene regulatory networks from high-throughput "omics" data has become a major goal in the modelling of living systems. Numerous approaches have been proposed, most of which attempt only "one-shot" reconstruction of the whole network with no intervention from the user, or offer only simp...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-10-S3-S17
更新日期:2009-12-03 00:00:00
abstract:BACKGROUND:Subtilisin/kexin-like proprotein convertase (PCSK) enzymes have important regulatory function in a wide variety of biological processes. PCSKs proteolytically process at a target sequence that contains basic amino acids arginine and lysine, which results in functional maturation of the target protein. In vit...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-12-618
更新日期:2011-12-20 00:00:00
abstract:BACKGROUND:A-to-I RNA editing is a co-/post-transcriptional modification catalyzed by ADAR enzymes, that deaminates Adenosines (A) into Inosines (I). Most of known editing events are located within inverted ALU repeats, but they also occur in coding sequences and may alter the function of encoded proteins. RNA editing ...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-018-5364-8
更新日期:2018-12-27 00:00:00
abstract:BACKGROUND:A critical step in the RT-qPCR workflow for studying gene expression is data normalization, one of the strategies being the use of reference genes. This study aimed to identify and validate a selection of reference genes for relative quantification in Talaromyces versatilis, a relevant industrial filamentous...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-015-1224-y
更新日期:2015-02-14 00:00:00
abstract:BACKGROUND:The MHC and KIR loci are clinically relevant regions of the genome. Typing the sequence of these loci has a wide range of applications including organ transplantation, drug discovery, pharmacogenomics and furthering fundamental research in immune genetics. Rapid advances in biochemical and next-generation se...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-015-1949-7
更新日期:2015-11-05 00:00:00
abstract:BACKGROUND:Designing sustainable animal production systems that better balance productivity and resistance to disease is a major concern. In order to address questions related to immunity and resistance to disease in pig, it is necessary to increase knowledge on its immune system and to produce efficient tools dedicate...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-11-292
更新日期:2010-05-11 00:00:00
abstract:BACKGROUND:Identification and classification of highly similar microbial strains is a challenging issue in microbiology, ecology and evolutionary biology. Among various available approaches, gene content analysis is also at the core of microbial taxonomy. However, no threshold has been determined for grouping microorgn...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-016-2991-9
更新日期:2016-08-17 00:00:00
abstract:BACKGROUND:The siRNA and piRNA pathways have been shown in insects to be essential for regulation of gene expression and defence against exogenous and endogenous genetic elements (viruses and transposable elements). The vast majority of endogenous small RNAs produced by the siRNA and piRNA pathways originate from repet...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-015-1436-1
更新日期:2015-04-10 00:00:00
abstract:BACKGROUND:The transcription factor SOX10 is essential for all stages of Schwann cell development including myelination. SOX10 cooperates with other transcription factors to activate the expression of key myelin genes in Schwann cells and is therefore a context-dependent, pro-myelination transcription factor. As such, ...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-016-3167-3
更新日期:2016-11-07 00:00:00