MIT Scientists Defend Controversial SARS-CoV-2 Genome Integration Results

2021 ◽  
Vol 41 (7) ◽  
pp. 16-16
Keyword(s):  
Genome Integration

scholarly journals Four chromosome scale genomes and a pan-genome annotation to accelerate pecan tree breeding

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
John T. Lovell ◽  
Nolan B. Bentley ◽  
Gaurab Bhattarai ◽  
Jerry W. Jenkins ◽  
Avinash Sreedasyam ◽  
...  
Keyword(s):  
Tree Breeding ◽  
Pathogen Resistance ◽  
Perennial Crop ◽  
Crop Species ◽  
Annotation Database ◽  
Pan Genome ◽  
Genome Integration ◽  
Transformative Potential ◽  
Genome Assemblies ◽  
Quantitative Genomics

AbstractGenome-enabled biotechnologies have the potential to accelerate breeding efforts in long-lived perennial crop species. Despite the transformative potential of molecular tools in pecan and other outcrossing tree species, highly heterozygous genomes, significant presence–absence gene content variation, and histories of interspecific hybridization have constrained breeding efforts. To overcome these challenges, here, we present diploid genome assemblies and annotations of four outbred pecan genotypes, including a PacBio HiFi chromosome-scale assembly of both haplotypes of the ‘Pawnee’ cultivar. Comparative analysis and pan-genome integration reveal substantial and likely adaptive interspecific genomic introgressions, including an over-retained haplotype introgressed from bitternut hickory into pecan breeding pedigrees. Further, by leveraging our pan-genome presence–absence and functional annotation database among genomes and within the two outbred haplotypes of the ‘Lakota’ genome, we identify candidate genes for pest and pathogen resistance. Combined, these analyses and resources highlight significant progress towards functional and quantitative genomics in highly diverse and outbred crops.

scholarly journals Pathogenic Role of Immune Evasion and Integration of Human Papillomavirus in Oropharyngeal Cancer

2021 ◽  
Vol 9 (5) ◽  
pp. 891
Author(s):  
Takashi Hatano ◽  
Daisuke Sano ◽  
Hideaki Takahashi ◽  
Nobuhiko Oridate
Keyword(s):  
Human Papillomavirus ◽  
Immune Evasion ◽  
Oropharyngeal Cancer ◽  
Current Knowledge ◽  
Immune Evasion Mechanism ◽  
Cell Cycle Activation ◽  
Genome Integration ◽  
Integration Mechanisms ◽  
E6 And E7

The incidence of oropharyngeal cancer (OPC) is increasing remarkably among all head and neck cancers, mainly due to its association with the human papillomavirus (HPV). Most HPVs are eliminated by the host’s immune system; however, because HPV has developed an effective immune evasion mechanism to complete its replication cycle, a small number of HPVs are not eliminated, leading to persistent infection. Moreover, during the oncogenic process, the extrachromosomal HPV genome often becomes integrated into the host genome. Integration involves the induction and high expression of E6 and E7, leading to cell cycle activation and increased genomic instability in the host. Therefore, integration is an important event in oncogenesis, although the associated mechanism remains unclear, especially in HPV-OPC. In this review, we summarize the current knowledge on HPV-mediated carcinogenesis, with special emphasis on immune evasion and integration mechanisms, which are crucial for oncogenesis.

scholarly journals The pIT5 Plasmid Series, an Improved Toolkit for Repeated Genome Integration in E. coli

2021 ◽  
Author(s):  
Nan Hao ◽  
Qinqin Chen ◽  
Ian B. Dodd ◽  
Keith E. Shearwin
Keyword(s):  
E Coli ◽  
Genome Integration

scholarly journals Host genome integration and giant virus-induced reactivation of the virophage mavirus

Nature ◽  
2016 ◽  
Vol 540 (7632) ◽  
pp. 288-291 ◽  
Author(s):  
Matthias G. Fischer ◽  
Thomas Hackl
Keyword(s):  
Host Genome ◽  
Giant Virus ◽  
Genome Integration

Concerted action of cellular JNK and Pin1 restricts HIV-1 genome integration to activated CD4+ T lymphocytes

2010 ◽  
Vol 16 (3) ◽  
pp. 329-333 ◽  
Author(s):  
Lara Manganaro ◽  
Marina Lusic ◽  
Maria Ines Gutierrez ◽  
Anna Cereseto ◽  
Giannino Del Sal ◽  
...  
Keyword(s):  
T Lymphocytes ◽  
Concerted Action ◽  
Genome Integration ◽  
Hiv 1
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