scholarly journals Application of maximum-likelihood models to selection pressure analysis of group I nucleopolyhedrovirus genes

2004 ◽  
Vol 85 (1) ◽  
pp. 197-210 ◽  
Author(s):  
R. L. Harrison
Keyword(s):  
Maximum Likelihood ◽  
Selection Pressure ◽  
Group I ◽  
Pressure Analysis

scholarly journals Whole-Genome Sequence Analysis of Pseudorabies Virus Clinical Isolates from Pigs in China between 2012 and 2017 in China

Viruses ◽  
2021 ◽  
Vol 13 (7) ◽  
pp. 1322
Author(s):  
Ruiming Hu ◽  
Leyi Wang ◽  
Qingyun Liu ◽  
Lin Hua ◽  
Xi Huang ◽  
...  
Keyword(s):  
Selection Pressure ◽  
Pseudorabies Virus ◽  
Viral Evolution ◽  
Infectious Agent ◽  
Genomic Diversity ◽  
Whole Genome Sequence ◽  
Evolutionary Constraint ◽  
The Novel ◽  
Novel Variants ◽  
Pressure Analysis

Pseudorabies virus (PRV) is an economically significant swine infectious agent. A PRV outbreak took place in China in 2011 with novel virulent variants. Although the association of viral genomic variability with pathogenicity is not fully confirmed, the knowledge concerning PRV genomic diversity and evolution is still limited. Here, we sequenced 54 genomes of novel PRV variants isolated in China from 2012 to 2017. Phylogenetic analysis revealed that China strains and US/Europe strains were classified into two separate genotypes. PRV strains isolated from 2012 to 2017 in China are highly related to each other and genetically close to classic China strains such as Ea, Fa, and SC. RDP analysis revealed 23 recombination events within novel PRV variants, indicating that recombination contributes significantly to the viral evolution. The selection pressure analysis indicated that most ORFs were under evolutionary constraint, and 19 amino acid residue sites in 15 ORFs were identified under positive selection. Additionally, 37 unique mutations were identified in 19 ORFs, which distinguish the novel variants from classic strains. Overall, our study suggested that novel PRV variants might evolve from classical PRV strains through point mutation and recombination mechanisms.

scholarly journals Mixing unmixables: Unexpected formation of Li-Cs alloys at low pressure

2015 ◽  
Vol 1 (9) ◽  
pp. e1500669 ◽  
Author(s):  
Serge Desgreniers ◽  
John S. Tse ◽  
Takahiro Matsuoka ◽  
Yasuo Ohishi ◽  
Justin J. Tse
Keyword(s):  
Thermal Expansion ◽  
Theoretical Prediction ◽  
Maximum Entropy Method ◽  
Coefficient Of Thermal Expansion ◽  
Low Pressure ◽  
Entropy Method ◽  
Unexpected Formation ◽  
High Coefficient ◽  
Group I ◽  
Pressure Analysis

Contrary to the empirical Miedema and Hume-Rothery rules and a recent theoretical prediction, we report experimental evidence on the formation of Li-Cs alloys at very low pressure (>0.1 GPa). We also succeeded in synthesizing a pure nonstoichiometric and ordered crystalline phase from an approximately equimolar mixture and resolved its structure using the maximum entropy method. The new alloy has a primitive cubic cell with the Li atom situated in the center and the Cs at the corners. This structure is stable to at least 10 GPa and has an anomalously high coefficient of thermal expansion at low pressure. Analysis of the valence charge density shows that electrons are donated from Cs to the Li “p”-orbitals, resulting in a rare formal oxidation state of −1 for Li. The observation indicates the diversity in the bonding of the seeming simple group I Li element.

The selection pressure analysis of chicken anemia virus structural protein gene VP1

Virus Genes ◽  
2009 ◽  
Vol 38 (2) ◽  
pp. 259-262 ◽  
Author(s):  
Dong Wang ◽  
Wei Fan ◽  
Guan-Zhu Han ◽  
Cheng-Qiang He
Keyword(s):  
Selection Pressure ◽  
Protein Gene ◽  
Chicken Anemia Virus ◽  
Structural Protein ◽  
Anemia Virus ◽  
Structural Protein Gene ◽  
Pressure Analysis

scholarly journals Subtype-specific gout susceptibility loci and enrichment of selection pressure on ABCG2 and ALDH2 identified by subtype genome-wide meta-analyses of clinically defined gout patients

2020 ◽  
Vol 79 (5) ◽  
pp. 657-665 ◽  
Author(s):  
Akiyoshi Nakayama ◽  
Masahiro Nakatochi ◽  
Yusuke Kawamura ◽  
Ken Yamamoto ◽  
Hirofumi Nakaoka ◽  
...  
Keyword(s):  
Selection Pressure ◽  
Association Studies ◽  
Genome Wide Association Studies ◽  
Nucleotide Polymorphisms ◽  
Susceptibility Loci ◽  
Normal Type ◽  
Genome Wide ◽  
A Genome ◽  
Meta Analyses ◽  
Pressure Analysis

ObjectivesGenome-wide meta-analyses of clinically defined gout were performed to identify subtype-specific susceptibility loci. Evaluation using selection pressure analysis with these loci was also conducted to investigate genetic risks characteristic of the Japanese population over the last 2000–3000 years.MethodsTwo genome-wide association studies (GWASs) of 3053 clinically defined gout cases and 4554 controls from Japanese males were performed using the Japonica Array and Illumina Array platforms. About 7.2 million single-nucleotide polymorphisms were meta-analysed after imputation. Patients were then divided into four clinical subtypes (the renal underexcretion type, renal overload type, combined type and normal type), and meta-analyses were conducted in the same manner. Selection pressure analyses using singleton density score were also performed on each subtype.ResultsIn addition to the eight loci we reported previously, two novel loci, PIBF1 and ACSM2B, were identified at a genome-wide significance level (p<5.0×10–8) from a GWAS meta-analysis of all gout patients, and other two novel intergenic loci, CD2-PTGFRN and SLC28A3-NTRK2, from normal type gout patients. Subtype-dependent patterns of Manhattan plots were observed with subtype GWASs of gout patients, indicating that these subtype-specific loci suggest differences in pathophysiology along patients’ gout subtypes. Selection pressure analysis revealed significant enrichment of selection pressure on ABCG2 in addition to ALDH2 loci for all subtypes except for normal type gout.ConclusionsOur findings on subtype GWAS meta-analyses and selection pressure analysis of gout will assist elucidation of the subtype-dependent molecular targets and evolutionary involvement among genotype, phenotype and subtype-specific tailor-made medicine/prevention of gout and hyperuricaemia.

Population structure and selection pressure analysis among Sugarcane yellow leaf virus isolates based on P0 and P1 sequences

2016 ◽  
Vol 41 (4) ◽  
pp. 237-245 ◽  
Author(s):  
Chun-Hui Zhao ◽  
Yi-Hua Lin ◽  
Yong-Bao Pan ◽  
Hua-Ying Fu ◽  
Ru-Kai Chen ◽  
...  
Keyword(s):  
Population Structure ◽  
Selection Pressure ◽  
Yellow Leaf ◽  
Sugarcane Yellow Leaf Virus ◽  
Leaf Virus ◽  
Virus Isolates ◽  
Pressure Analysis

Heritability of Systolic Blood Pressure. Analysis of Variance in MZ Twin Parents and Their Children

1980 ◽  
Vol 29 (2) ◽  
pp. 143-149 ◽  
Author(s):  
R. J. Rose ◽  
D. W. Fulker ◽  
J. Z. Miller ◽  
C. E. Grim ◽  
J. C. Christian
Keyword(s):  
Blood Pressure ◽  
Maximum Likelihood ◽  
Maximum Likelihood Estimation ◽  
Systolic Blood Pressure ◽  
Analysis Of Variance ◽  
Environmental Effects ◽  
Environmental Parameters ◽  
Likelihood Estimation ◽  
Age And Sex ◽  
Pressure Analysis

Systolic blood pressure, standardized for age and sex, was measured in 76 MZ twin pairs and their 341 children. Maximum likelihood estimation of genetical and environmental parameters from the independent parental and offspring ANOVAs indicated a complete absence of both maternal and shared environmental effects, together with a heritability of 63%. These results are shown to be reasonably consistent with those from previous studies.

scholarly journals In silico multi-epitope vaccine against covid19 showing effective interaction with HLA-B*15:03

2020 ◽  
Author(s):  
Muniba Faiza ◽  
Tariq Abdullah ◽  
Jose Franklin Calderon-Tantalean ◽  
Manish Ravindranath Upadhyay ◽  
Abdelrahman H. Abdelmoneim ◽  
...  
Keyword(s):  
Human Health ◽  
In Silico ◽  
Selection Pressure ◽  
Vaccine Candidate ◽  
Promising Result ◽  
Effective Interaction ◽  
Epitope Vaccine ◽  
Furin Cleavage Site ◽  
Viral Vaccine ◽  
Pressure Analysis

AbstractThe recent outbreak of severe acute respiratory syndrome (SARS) coronavirus (CoV)-2 (SARS-CoV-2) causing coronavirus disease (covid19) has posed a great threat to human health. Previous outbreaks of SARS-CoV and Middle East respiratory Syndrome CoV (MERS-CoV) from the same CoV family had posed similar threat to human health and economic growth. To date, not even a single drug specific to any of these CoVs has been developed nor any anti-viral vaccine is available for the treatment of diseases caused by CoVs. Subunits present in spike glycoproteins of SARS-CoV and SARS-CoV-2 are involved in binding to human ACE2 Receptor which is the primary method of viral invasion. As it has been observed in the previous studies that there are very minor differences in the spike glycoproteins of SARS-CoV and SARS-CoV-2. SARS-CoV-2 has an additional furin cleavage site that makes it different from SARS-CoV (Walls et al., 2020). In this study, we have analyzed spike glycoproteins of SARS-CoV-2 and SARS-CoV phylogenetically and subjected them to selection pressure analysis. Selection pressure analysis has revealed some important sites in SARS-CoV-2 and SARS-CoV spike glycoproteins that might be involved in their pathogenicity. Further, we have developed a potential multi-epitope vaccine candidate against SARS-CoV-2 by analyzing its interactions with HLA-B*15:03 subtype. This vaccine consists of multiple T-helper (TH) cells, B-cells, and Cytotoxic T-cells (CTL) epitopes joined by linkers and an adjuvant to increase its immunogenicity. Conservation of selected epitopes in SARS, MERS, and human hosts, suggests that the designed vaccine could provide cross-protection. The vaccine is designed in silico by following a reverse vaccinology method acknowledging its antigenicity, immunogenicity, toxicity, and allergenicity. The vaccine candidate that we have designed as a result of this work shows promising result indicating its potential capability of simulating an immune response.

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