scholarly journals Binning enables efficient host genome reconstruction in cnidarian holobionts

GigaScience ◽  
2018 ◽  
Vol 7 (7) ◽  
Author(s):  
Juan Sebastián Celis ◽  
Daniel Wibberg ◽  
Catalina Ramírez-Portilla ◽  
Oliver Rupp ◽  
Alexander Sczyrba ◽  
...  
Keyword(s):  
Host Genome ◽  
Genome Reconstruction

scholarly journals A gene co-association network regulating gut microbial communities in a Duroc pig population

Microbiome ◽  
2021 ◽  
Vol 9 (1) ◽  
Author(s):  
Antonio Reverter ◽  
Maria Ballester ◽  
Pamela A. Alexandre ◽  
Emilio Mármol-Sánchez ◽  
Antoni Dalmau ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Candidate Genes ◽  
Relative Abundance ◽  
Association Studies ◽  
Single Gene ◽  
Host Genome ◽  
Genome Wide Association Studies ◽  
Vaccine Response ◽  
Microbiome Composition ◽  
Host Genetic

Abstract Background Analyses of gut microbiome composition in livestock species have shown its potential to contribute to the regulation of complex phenotypes. However, little is known about the host genetic control over the gut microbial communities. In pigs, previous studies are based on classical “single-gene-single-trait” approaches and have evaluated the role of host genome controlling gut prokaryote and eukaryote communities separately. Results In order to determine the ability of the host genome to control the diversity and composition of microbial communities in healthy pigs, we undertook genome-wide association studies (GWAS) for 39 microbial phenotypes that included 2 diversity indexes, and the relative abundance of 31 bacterial and six commensal protist genera in 390 pigs genotyped for 70 K SNPs. The GWAS results were processed through a 3-step analytical pipeline comprised of (1) association weight matrix; (2) regulatory impact factor; and (3) partial correlation and information theory. The inferred gene regulatory network comprised 3561 genes (within a 5 kb distance from a relevant SNP–P < 0.05) and 738,913 connections (SNP-to-SNP co-associations). Our findings highlight the complexity and polygenic nature of the pig gut microbial ecosystem. Prominent within the network were 5 regulators, PRDM15, STAT1, ssc-mir-371, SOX9 and RUNX2 which gathered 942, 607, 588, 284 and 273 connections, respectively. PRDM15 modulates the transcription of upstream regulators of WNT and MAPK-ERK signaling to safeguard naive pluripotency and regulates the production of Th1- and Th2-type immune response. The signal transducer STAT1 has long been associated with immune processes and was recently identified as a potential regulator of vaccine response to porcine reproductive and respiratory syndrome. The list of regulators was enriched for immune-related pathways, and the list of predicted targets includes candidate genes previously reported as associated with microbiota profile in pigs, mice and human, such as SLIT3, SLC39A8, NOS1, IL1R2, DAB1, TOX3, SPP1, THSD7B, ELF2, PIANP, A2ML1, and IFNAR1. Moreover, we show the existence of host-genetic variants jointly associated with the relative abundance of butyrate producer bacteria and host performance. Conclusions Taken together, our results identified regulators, candidate genes, and mechanisms linked with microbiome modulation by the host. They further highlight the value of the proposed analytical pipeline to exploit pleiotropy and the crosstalk between bacteria and protists as significant contributors to host-microbiome interactions and identify genetic markers and candidate genes that can be incorporated in breeding program to improve host-performance and microbial traits.

scholarly journals Current recommendations for clinical surveillance and genetic testing in rhabdoid tumor predisposition: a report from the SIOPE Host Genome Working Group

2021 ◽  
Author(s):  
M. C. Frühwald ◽  
K. Nemes ◽  
H. Boztug ◽  
M. C. A. Cornips ◽  
D. G. Evans ◽  
...  
Keyword(s):  
Working Group ◽  
Soft Part ◽  
Genetic Disorders ◽  
Panel Discussion ◽  
Rhabdoid Tumor ◽  
Host Genome ◽  
Cancer Surveillance ◽  
Malignant Neoplasms ◽  
Pathogenic Variants ◽  
Increased Risk

AbstractThe rhabdoid tumor (RT) predisposition syndromes 1 and 2 (RTPS1 and 2) are rare genetic conditions rendering young children vulnerable to an increased risk of RT, malignant neoplasms affecting the kidney, miscellaneous soft-part tissues, the liver and the central nervous system (Atypical Teratoid Rhabdoid Tumors, ATRT). Both, RTPS1&2 are due to pathogenic variants (PV) in genes encoding constituents of the BAF chromatin remodeling complex, i.e. SMARCB1 (RTPS1) and SMARCA4 (RTPS2). In contrast to other genetic disorders related to PVs in SMARCB1 and SMARCA4 such as Coffin-Siris Syndrome, RTPS1&2 are characterized by a predominance of truncating PVs, terminating transcription thus explaining a specific cancer risk. The penetrance of RTPS1 early in life is high and associated with a poor survival. However, few unaffected carriers may be encountered. Beyond RT, the tumor spectrum may be larger than initially suspected, and cancer surveillance offered to unaffected carriers (siblings or parents) and long-term survivors of RT is still a matter of discussion. RTPS2 exposes female carriers to an ill-defined risk of small cell carcinoma of the ovaries, hypercalcemic type (SCCOHT), which may appear in prepubertal females. RT surveillance protocols for these rare families have not been established. To address unresolved issues in the care of individuals with RTPS and to propose appropriate surveillance guidelines in childhood, the SIOPe Host Genome working group invited pediatric oncologists and geneticists to contribute to an expert meeting. The current manuscript summarizes conclusions of the panel discussion, including consented statements as well as non-evidence-based proposals for validation in the future.

scholarly journals Transcriptionally inactive hepatitis B virus episome DNA preferentially resides in the vicinity of chromosome 19 in 3D host genome upon infection

Cell Reports ◽  
2021 ◽  
Vol 35 (13) ◽  
pp. 109288
Author(s):  
Dingbin Tang ◽  
Hanqing Zhao ◽  
Yumeng Wu ◽  
Bo Peng ◽  
Zhenchao Gao ◽  
...  
Keyword(s):  
Hepatitis B Virus ◽  
Hepatitis B ◽  
Host Genome ◽  
Chromosome 19 ◽  
B Virus

scholarly journals HCMV-Infected Cells Maintain Efficient Nucleotide Excision Repair of the Viral Genome while Abrogating Repair of the Host Genome

2012 ◽  
Vol 8 (11) ◽  
pp. e1003038 ◽  
Author(s):  
John M. O'Dowd ◽  
Anamaria G. Zavala ◽  
Celeste J. Brown ◽  
Toshio Mori ◽  
Elizabeth A. Fortunato
Keyword(s):  
Nucleotide Excision Repair ◽  
Viral Genome ◽  
Excision Repair ◽  
Host Genome ◽  
Nucleotide Excision ◽  
Infected Cells

scholarly journals Selfish supernumerary chromosome reveals its origin as a mosaic of host genome and organellar sequences

2012 ◽  
Vol 109 (33) ◽  
pp. 13343-13346 ◽  
Author(s):  
M. M. Martis ◽  
S. Klemme ◽  
A. M. Banaei-Moghaddam ◽  
F. R. Blattner ◽  
J. Macas ◽  
...  
Keyword(s):  
Supernumerary Chromosome ◽  
Host Genome

scholarly journals Integration of Trypanosoma cruzi kDNA minicircle sequence in the host genome may be associated with autoimmune serum factors in Chagas disease patients

1999 ◽  
Vol 94 (suppl 1) ◽  
pp. 249-252 ◽  
Author(s):  
Augusto Simões-Barbosa ◽  
Ana Maria Barros ◽  
Nadjar Nitz ◽  
Enrique R Argañaraz ◽  
Antonio RL Teixeira
Keyword(s):  
Trypanosoma Cruzi ◽  
Chagas Disease ◽  
Host Genome ◽  
Serum Factors ◽  
Minicircle Sequence

scholarly journals Brown Planthopper Nudivirus DNA Integrated in Its Host Genome

2014 ◽  
Vol 88 (10) ◽  
pp. 5310-5318 ◽  
Author(s):  
R.-L. Cheng ◽  
Y. Xi ◽  
Y.-H. Lou ◽  
Z. Wang ◽  
J.-Y. Xu ◽  
...  
Keyword(s):  
Brown Planthopper ◽  
Host Genome
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