HIV Progression Depends on Codon and Amino Acid Usage Profile of Envelope Protein and Associated Host-Genetic Influence

Roy, Ayan; Banerjee, Rachana; Basak, Surajit

doi:10.3389/fmicb.2017.01083

Cited by 13 publications

(8 citation statements)

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“…For some proteins, the names of which had been extracted from the texts of publications relevant to the studies of HIV ECs, we found direct associations of these proteins with the HIV progression (Taylor et al, 2000 ; Oleksyk et al, 2009 ; Marras et al, 2013 ; Slavov et al, 2015 ; Roy et al, 2017 ; Parodi et al, 2019 ; Hersberger et al, 2020 ; Wendel et al, 2020 ). We provide a few examples of the association between biological processes known for the proteins identified and their possible role in HIV disease progression.…”

Section: Discussionmentioning

confidence: 91%

Automated Extraction of Information From Texts of Scientific Publications: Insights Into HIV Treatment Strategies

et al. 2020

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Text analysis can help to identify named entities (NEs) of small molecules, proteins, and genes. Such data are very important for the analysis of molecular mechanisms of disease progression and development of new strategies for the treatment of various diseases and pathological conditions. The texts of publications represent a primary source of information, which is especially important to collect the data of the highest quality due to the immediate obtaining information, in comparison with databases. In our study, we aimed at the development and testing of an approach to the named entity recognition in the abstracts of publications. More specifically, we have developed and tested an algorithm based on the conditional random fields, which provides recognition of NEs of (i) genes and proteins and (ii) chemicals. Careful selection of abstracts strictly related to the subject of interest leads to the possibility of extracting the NEs strongly associated with the subject. To test the applicability of our approach, we have applied it for the extraction of (i) potential HIV inhibitors and (ii) a set of proteins and genes potentially responsible for viremic control in HIV-positive patients. The computational experiments performed provide the estimations of evaluating the accuracy of recognition of chemical NEs and proteins (genes). The precision of the chemical NEs recognition is over 0.91; recall is 0.86, and the F1-score (harmonic mean of precision and recall) is 0.89; the precision of recognition of proteins and genes names is over 0.86; recall is 0.83; while F1-score is above 0.85. Evaluation of the algorithm on two case studies related to HIV treatment confirms our suggestion about the possibility of extracting the NEs strongly relevant to (i) HIV inhibitors and (ii) a group of patients i.e., the group of HIV-positive individuals with an ability to maintain an undetectable HIV-1 viral load overtime in the absence of antiretroviral therapy. Analysis of the results obtained provides insights into the function of proteins that can be responsible for viremic control. Our study demonstrated the applicability of the developed approach for the extraction of useful data on HIV treatment.

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Section: Discussionmentioning

confidence: 91%

Automated Extraction of Information From Texts of Scientific Publications: Insights Into HIV Treatment Strategies

et al. 2020

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“…Regarding the mechanisms of resistance linked to the virus, they depend mostly on the inoculum amount and the characteristics of the HIV strain. An unexpected association between the evolutionary rate of substitution in the envelope ( env ) gene and disease progression was reported 173 . The envelope glycoproteins experience intense selection (purifying selection) from the host immune system, leading to sequence variation of env .…”

Section: Resultsmentioning

confidence: 99%

Resistance to human immunodeficiency virus infection: a rare but neglected state

Tamalet

Devaux

Dubourg

et al. 2020

Annals of the New York Academy of Sciences

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The natural history of human immunodeficiency virus (HIV) infection is well understood. In most individuals sexually exposed to HIV, the risk of becoming infected depends on the viral load and on sexual practices and gender. However, a low percentage of individuals who practice frequent unprotected sexual intercourse with HIV‐infected partners remain uninfected. Although the systematic study of these individuals has made it possible to identify HIV resistance factors including protective genetic patterns, such epidemiological situations remain paradoxical and not fully understood. In vitro experiments have demonstrated that peripheral blood mononuclear cells (PBMCs) from HIV‐free, unexposed blood donors are not equally susceptible to HIV infection; in addition, PBMCs from highly exposed seronegative individuals are generally resistant to infection by primary HIV clinical isolates. We review the literature on permissiveness of PBMCs from healthy blood donors and uninfected hyperexposed individuals to sustained infection and replication of HIV‐1 in vitro. In addition, we focus on recent evidence indicating that the gut microbiota may either contribute to natural resistance to or delay replication of HIV infected individuals.

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“…21 CoA reveals major trends of variation in the dataset by arranging them along continuous axes where consecutive axis have been arranged to have diminishing effect gradually. 22 We used CoA available in Codon W for the analysis of amino acid usage of spike gene sequences. Hydrophobicity of each spike gene sequence is calculated using the method Kyte–Doolittle available in Codon W. 23 …”

Section: Methodsmentioning

confidence: 99%

“…Correspondence analysis was performed to assess the variations in amino acid usage of spike protein dataset 21 . CoA reveals major trends of variation in the dataset by arranging them along continuous axes where consecutive axis have been arranged to have diminishing effect gradually 22 . We used CoA available in Codon W for the analysis of amino acid usage of spike gene sequences.…”

Section: Methodsmentioning

confidence: 99%

Underlying selection for the diversity of spike protein sequences of SARS‐CoV‐2

Ghosh

Basak

2021

IUBMB Life

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The global spread of SARS‐CoV‐2 is fast moving and has caused a worldwide public health crisis. In the present article, we analyzed spike protein sequences of SARS‐CoV‐2 genomes to assess the impact of mutational diversity. We observed from amino acid usage patterns that spike proteins are associated with a diversity of mutational changes and most important underlying cause of variation of amino acid usage is the changes in hydrophobicity of spike proteins. The changing patterns of hydrophobicity of spike proteins over time and its influence on the receptor binding affinity provides crucial information on the SARS‐CoV‐2 interaction with human receptor. Our results also show that spike proteins have evolved to prefer more hydrophobic residues over time. The present study provides a comprehensive analysis of molecular sequence data to consider that mutational variants might play a crucial role in modulating the virulence and spread of the virus and has immediate implications for therapeutic strategies.

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HIV Progression Depends on Codon and Amino Acid Usage Profile of Envelope Protein and Associated Host-Genetic Influence

Cited by 13 publications

References 50 publications

Automated Extraction of Information From Texts of Scientific Publications: Insights Into HIV Treatment Strategies

Automated Extraction of Information From Texts of Scientific Publications: Insights Into HIV Treatment Strategies

Resistance to human immunodeficiency virus infection: a rare but neglected state

Underlying selection for the diversity of spike protein sequences of SARS‐CoV‐2

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