Analysis of N-Glycosylation Sites in HIV glycoprotein 160

HIV infection is a condition caused by the human immunodeficiency virus. The condition gradually destroys the immune system, which makes it harder for the body to fight infections. HIV presents a complex knot for scientists to unravel. An envelope protein of the human HIV that is encoded by the env gene contains numerous glycosylation sites. It serves as a precursor for both the GP120 and the GP41. Here statistical investigation was done to study the sequential aspects of amino acids around the N-glycosylated protein from HIV virus. Sequences containing N-glycosylated asparagine were selected from the uniprot database of N-glycosylated proteins. The frequency of occurrence of amino acid residues around the glycosylated asparagine showed that there are increased numbers of isoleucine and threonine residues around the N-glycosylation sites in comparison with the nonglycosylated asparagine residues. Preferential occurrence
of amino acid residues around the glycosylation site shows that T has the maximum preference around the N-glycosylation site. T at 3 and/or -3 positions strongly favors glycosylation irrespective of other glycosylation sites. The data presented in the present work clearly indicate that there is a pronounced positional preference for the hydrophobic and neutral amino acids at various positions around the N-glycosylation site. In the future it will be of much interest to investigate further the possible structural and conformational implications of some
of these suggested positional preferences of the various amino acids around the site of glycosylation. This is a potentially important study, and such analyses will surely contribute an important part of our knowledge base in the future on HIV research. These results will be of interest to molecular biologists and protein engineers to identify N-glycosylation sites important in molecular recognition processes in HIV virus

Genetic factors affecting EBV Load in Transformed LCLs from the 1000 Genome Project: a GWAS on Transformation

Trabajo presentado en la Annual Meeting of the Society for Molecular Biology and Evolution (SMBE 2015), celebrada en Viena del 12 al 16 de julio de 2015.Worldwide, >90% of the adult population is infected by the Epstein-Barr virus (EBV), which has been an evolutionary companion of our lineage for millions of years. EBV remains within the host after primary infection and can cause mononucleosis. There is also evidence linking it with multiple sclerosis and different types of tumors. Although the EBV has been the focus of extensive research work, much remain s unknown about what makes some individuals more sensitive to EBV infection and to adverse outcomes as a result of infection. The EBV is used to transform B-cells into lymphoblastoid cell lines (LCLs). We hypothesized that differences among individual LCLs in the EBV load resulting from EBV transformation may reflect different genetic susceptibility to EBV infection. To test this hypothesis, we retrieved whole-genome sequenced LCL reads 2215 samples sequenced within the 1000 Genome Project and derived from 26 different populations worldwide. We subjected these samples to in silico viral load estimation, and the accuracy was validated by RT-PCR. Our results showed considerable differences in viral load among populations, while no significant difference was observed between males and females. The proper estimation of EBV load has made it possible to perform a genome wide association analysis (GWAS) between estimated EBV load and genetic variants determined within the 1000 genome project samples. GWAS yielded many putative candidate genes that necessitate further evaluation to reveal the biological mechanisms underlying EBV load and EBV associated diseases.N

Understanding interactions between EBV and human genomic variation

The EBV has been linked to multiple human disease phenotypes and has been associated with cancers and other infections. Recently single gene analysis and genome-wide analysis studies have been exploited to uncover the human genetic variants that are linked with EBV diseases. It also suggested the substantial role of individual host genetics and also provided a clue in understanding the interaction between virus and human. Furthermore, the outcome of the EBV infection is a complex phenomenon governs by the variation in the genetic architecture of the viral and human genomes and/or the interacting environmental factors. Therefore, this PhD work is mainly a large-scale effort towards the understanding of the human and EBV genetic architecture to uncover the role of genetic variation in EBV associated infections, disease susceptibility, immune recognition and invasion. Our results also provide a framework on the impact of human and EBV genetic variation and their unusual interactions that highlight the human genetic influence affecting viral load reflecting the clinical behavior of EBV in LCLs and the other side viral antigenic variation modulating immune response to sustain persistence infection. This EBV-human perturbation is essential to follow-up in the context of the susceptibility of individual populations to a specific EBV associated pathology

Understanding interactions between EBV and human genomic variation

The EBV has been linked to multiple human disease phenotypes and has been associated with cancers and other infections. Recently single gene analysis and genome-wide analysis studies have been exploited to uncover the human genetic variants that are linked with EBV diseases. It also suggested the substantial role of individual host genetics and also provided a clue in understanding the interaction between virus and human. Furthermore, the outcome of the EBV infection is a complex phenomenon governs by the variation in the genetic architecture of the viral and human genomes and/or the interacting environmental factors. Therefore, this PhD work is mainly a large-scale effort towards the understanding of the human and EBV genetic architecture to uncover the role of genetic variation in EBV associated infections, disease susceptibility, immune recognition and invasion. Our results also provide a framework on the impact of human and EBV genetic variation and their unusual interactions that highlight the human genetic influence affecting viral load reflecting the clinical behavior of EBV in LCLs and the other side viral antigenic variation modulating immune response to sustain persistence infection. This EBV-human perturbation is essential to follow-up in the context of the susceptibility of individual populations to a specific EBV associated pathology

Correction: Genetic factors affecting EBV copy number in lymphoblastoid cell lines derived from the 1000 Genome Project samples.

[This corrects the article DOI: 10.1371/journal.pone.0179446.]

Genetic factors affecting EBV copy number in lymphoblastoid cell lines derived from the 1000 Genome Project samples

Epstein-Barr virus (EBV), human herpes virus 4, has been classically associated with infectious mononucleosis, multiple sclerosis and several types of cancers. Many of these diseases show marked geographical differences in prevalence, which points to underlying genetic and/or environmental factors. Those factors may include a different susceptibility to EBV infection and viral copy number among human populations. Since EBV is commonly used to transform B-cells into lymphoblastoid cell lines (LCLs) we hypothesize that differences in EBV copy number among individual LCLs may reflect differential susceptibility to EBV infection. To test this hypothesis, we retrieved whole-genome sequenced EBV-mapping reads from 1,753 LCL samples derived from 19 populations worldwide that were sequenced within the context of the 1000 Genomes Project. An in silico methodology was developed to estimate the number of EBV copy number in LCLs and validated these estimations by real-time PCR. After experimentally confirming that EBV relative copy number remains stable over cell passages, we performed a genome wide association analysis (GWAS) to try detecting genetic variants of the host that may be associated with EBV copy number. Our GWAS has yielded several genomic regions suggestively associated with the number of EBV genomes per cell in LCLs, unraveling promising candidate genes such as CAND1, a known inhibitor of EBV replication. While this GWAS does not unequivocally establish the degree to which genetic makeup of individuals determine viral levels within their derived LCLs, for which a larger sample size will be needed, it potentially highlighted human genes affecting EBV-related processes, which constitute interesting candidates to follow up in the context of EBV related pathologiesThis work was supported by Instituto de Salud Carlos III (ES) (RD07/0060); Spanish Government Grants (BFU2012-38236); Departament d'Innovació, Universitats I Empresa, Generalitat de Catalunya (2014SGR1311); Instituto de Salud Carlos III (PT13/0001/0026); FEDER (Fondo Europeo de Desarrollo Regional)/FSE (Fondo Social Europeo)

Regional association plots.

<p>Regional association plot for Asian <b>(A)</b>, European <b>(B)</b>, American <b>(C)</b> and African population <b>(D)</b> subsets produced by Locuszoom showing top SNPs from each population subset (in purple) and surrounding SNPs in the region colored by LD (r²) with the top SNP. Lower panel shows genes annotated within this region. Solid blue lines represent recombination rates.</p

Top EBV copy number-associated regions in the different population subsets.

<p>Top EBV copy number-associated regions in the different population subsets.</p

GWAS results Manhattan plot.

<p>Manhattan plots for Asian, African American and European population subsets showing top hits from each continent. The blue line indicates p-value of 10⁻⁵ and red line indicates p-value of 10⁻⁸.</p