Identification and genomic characterization of bovine parvovirus 1 in yaks

2021 ◽  
pp. 104063872110296
Author(s):  
Guoqing Shao ◽  
Long Zhao ◽  
Cheng Tang ◽  
Hua Yue
Keyword(s):  
Amino Acid ◽  
Tibet Plateau ◽  
Molecular Characteristics ◽  
Amino Acid Substitutions ◽  
Ns1 Protein ◽  
Cattle Diseases ◽  
Genomic Characterization ◽  
Amino Acid Mutations ◽  
Bovine Parvovirus ◽  
Qinghai Tibet Plateau

Bovine parvovirus 1 (BPV1) is a causative agent of respiratory, gastrointestinal, and reproductive cattle diseases. We collected 149 yak diarrhea fecal samples from 9 farms in the Qinghai-Tibet Plateau. The samples were screened for BPV1 by PCR, and 2 samples were positive for BPV1. The complete genomes of these BPV1 isolates were sequenced successfully. The sequences of these 2 variants were both 5,515 bp in length and shared 96.5–96.8% identity with 2 previously reported BPV1 genomes (GenBank DQ335247, NC_001540). Twenty-six identical amino acid mutations were found in the 2 yak variants, including 7 amino acid substitutions in receptor-binding regions of the VP2 protein, and 5 amino acid substitutions in the NS1 protein C-terminal region that functions to activate transcription. The new genome sequences contribute to better understanding of the evolution and molecular characteristics of BPV1.

scholarly journals Divergent and parallel routes of biochemical adaptation in high-altitude passerine birds from the Qinghai-Tibet Plateau

2018 ◽  
Vol 115 (8) ◽  
pp. 1865-1870 ◽  
Author(s):  
Xiaojia Zhu ◽  
Yuyan Guan ◽  
Anthony V. Signore ◽  
Chandrasekhar Natarajan ◽  
Shane G. DuBay ◽  
...  
Keyword(s):  
Amino Acid ◽  
High Altitude ◽  
Site Directed Mutagenesis ◽  
Tibet Plateau ◽  
Amino Acid Substitutions ◽  
Passerine Birds ◽  
Biochemical Adaptation ◽  
Cpg Dinucleotide ◽  
Functional Mechanisms ◽  
Qinghai Tibet Plateau

When different species experience similar selection pressures, the probability of evolving similar adaptive solutions may be influenced by legacies of evolutionary history, such as lineage-specific changes in genetic background. Here we test for adaptive convergence in hemoglobin (Hb) function among high-altitude passerine birds that are native to the Qinghai-Tibet Plateau, and we examine whether convergent increases in Hb–O2 affinity have a similar molecular basis in different species. We documented that high-altitude parid and aegithalid species from the Qinghai-Tibet Plateau have evolved derived increases in Hb–O2 affinity in comparison with their closest lowland relatives in East Asia. However, convergent increases in Hb–O2 affinity and convergence in underlying functional mechanisms were seldom attributable to the same amino acid substitutions in different species. Using ancestral protein resurrection and site-directed mutagenesis, we experimentally confirmed two cases in which parallel substitutions contributed to convergent increases in Hb–O2 affinity in codistributed high-altitude species. In one case involving the ground tit (Parus humilis) and gray-crested tit (Lophophanes dichrous), parallel amino acid replacements with affinity-enhancing effects were attributable to nonsynonymous substitutions at a CpG dinucleotide, suggesting a possible role for mutation bias in promoting recurrent changes at the same site. Overall, most altitude-related changes in Hb function were caused by divergent amino acid substitutions, and a select few were caused by parallel substitutions that produced similar phenotypic effects on the divergent genetic backgrounds of different species.

scholarly journals MOLECULAR AND GENETIC CHARACTERISTICS OF SURFACE AND NONSTRUCTURE PROTEINS OF PANDEMIC INFLUENZA VIRUSES A(H1N1)PDM09 IN 2015-2016 EPIDEMIC SEASON

2016 ◽  
Vol 72 (2) ◽  
pp. 44-48
Author(s):  
O. Smutko ◽  
L. Radchenko ◽  
A. Mironenko
Keyword(s):  
Amino Acid ◽  
Pandemic Influenza ◽  
Influenza A ◽  
Phylogenetic Trees ◽  
Influenza Viruses ◽  
Amino Acid Substitutions ◽  
Ns1 Protein ◽  
Genetic Characteristics ◽  
Epidemic Season ◽  
Influenza A H1n1

The aim of the present study was identifying of molecular and genetic changes in hemaglutinin (HA), neuraminidase (NA) and non-structure protein (NS1) genes of pandemic influenza A(H1N1)pdm09 strains, that circulated in Ukraine during 2015-2016 epidemic season. Samples (nasopharyngeal swabs from patients) were analyzed using real-time polymerase chain reaction (RTPCR). Phylogenetic trees were constructed using MEGA 7 software. 3D structures were constructed in Chimera 1.11.2rc software. Viruses were collected in 2015-2016 season fell into genetic group 6B and in two emerging subgroups, 6B.1 and 6B.2 by gene of HA and NA. Subgroups 6B.1 and 6B.2 are defined by the following amino acid substitutions. In the NS1 protein were identified new amino acid substitutions D2E, N48S, and E125D in 2015-2016 epidemic season. Specific changes were observed in HA protein antigenic sites, but viruses saved similarity to vaccine strain. NS1 protein acquired substitution associated with increased virulence of the influenza virus.

scholarly journals Three amino acid substitutions in the NS1 protein change the virus replication of H5N1 influenza virus in human cells

Virology ◽  
2018 ◽  
Vol 519 ◽  
pp. 64-73 ◽  
Author(s):  
Jing Li ◽  
Kun Zhang ◽  
Quanjiao Chen ◽  
Xiaoshuang Zhang ◽  
Yeping Sun ◽  
...  
Keyword(s):  
Influenza Virus ◽  
Amino Acid ◽  
Virus Replication ◽  
Human Cells ◽  
Amino Acid Substitutions ◽  
Ns1 Protein ◽  
H5n1 Influenza Virus ◽  
H5n1 Influenza ◽  
Protein Change

scholarly journals A study on the effect of synthetic α-to-β3-amino acid mutations on the binding of phosphopeptides to 14-3-3 proteins

2019 ◽  
Vol 55 (98) ◽  
pp. 14809-14812 ◽  
Author(s):  
Sebastian A. Andrei ◽  
Vito Thijssen ◽  
Luc Brunsveld ◽  
Christian Ottmann ◽  
Lech-Gustav Milroy
Keyword(s):  
Amino Acid ◽  
Crucial Role ◽  
Amino Acid Substitutions ◽  
Binding Peptides ◽  
Amino Acid Mutations

Systematic α → β3 amino acid substitutions reveal a crucial role for native +2 proline residues in 14-3-3 binding peptides.

scholarly journals Rapid Determination of Amino Acids of Nitraria tangutorum Bobr. from the Qinghai-Tibet Plateau Using HPLC-FLD-MS/MS and a Highly Selective and Sensitive Pre-Column Derivatization Method

Molecules ◽  
2019 ◽  
Vol 24 (9) ◽  
pp. 1665 ◽  
Author(s):  
Wu Zhou ◽  
Yuwei Wang ◽  
Fang Yang ◽  
Qi Dong ◽  
Honglun Wang ◽  
...  
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Acid Content ◽  
Rapid Determination ◽  
Amino Acid Content ◽  
Tibet Plateau ◽  
Relative Standard ◽  
Nitraria Tangutorum ◽  
Qinghai Tibet Plateau

Amino acids are indispensable components of living organisms. The high amino acid content in Nitraria tangutorum Bobr. fruit distinguishes it from other berry plants and is of great significance to its nutritional value. Herein, using 10-ethyl-acridine-3-sulfonyl chloride as a fluorescent pre-column labeling reagent, a method for the efficient and rapid determination of amino acid content in N. tangutorum by pre-column fluorescence derivatization and on-line mass spectrometry was established and further validated. The limits of detection (signal-to-noise ratio = 3) were between 0.13 and 1.13 nmol/L, with a linear coefficient greater than 0.997 and a relative standard deviation between 1.37% and 2.64%. In addition, the method required a short analysis time, separating 19 amino acids within 20 min. Subsequently, the method was used to analyze the amino acid content of Nitraria tangutorum Bobr. from tissues retrieved from seven regions of the Qinghai-Tibet Plateau. Nitraria tangutorum Bobr. was shown to contain a large amount of amino acids, with the total content and main amino acid varying between the different tissues. This research supports the nutritional evaluation, quality control, and development and utilization of Nitraria tangutorum Bobr.

scholarly journals Molecular Characteristics of Group B Streptococci Isolated from Adults with Invasive Infections in Japan

2016 ◽  
Vol 54 (11) ◽  
pp. 2695-2700 ◽  
Author(s):  
Miyuki Morozumi ◽  
Takeaki Wajima ◽  
Misako Takata ◽  
Satoshi Iwata ◽  
Kimiko Ubukata
Keyword(s):  
Amino Acid ◽  
Group B Streptococcus ◽  
Antibiotic Use ◽  
Molecular Characteristics ◽  
Amino Acid Substitutions ◽  
Group B Streptococci ◽  
Content Type ◽  
Invasive Infections ◽  
Primary Focus ◽  
Group B

Streptococcus agalactiae(group B streptococcus) isolates (n= 443) obtained from Japanese adults with invasive infections between April 2010 and March 2013 were analyzed for capsular serotype, multilocus sequence type (ST), antibiotic susceptibility, and resistance genes. Among these cases, bacteremia without primary focus was the most common variety of infection (49.9%), followed by cellulitis (12.9%) and pneumonia (9.0%). Concerning patient age (18 to 59, 60 to 69, 70 to 79, 80 to 89, and 90 years old or older), the incidence of pneumonia increased in patients in their 70s and 80s (P< 0.001), while younger patients (18 to 59 and 60 to 69 years old) were more likely to have abscesses (P< 0.05). The mortality rate was 10.2% for all ages. The most common capsular serotype was Ib (39.5%), followed by V (16.0%), III (13.8%), VI (9.5%), and Ia (8.6%). The main ST of serotype Ib strains was ST10, which belonged to clonal complex 10 (88.0%). The predominant clonal complexes of serotypes V and III, respectively, were 1 (78.9%) and 19 (75.4%). Among these isolates, 9 strains (2.0%) were identified as group B streptococci with reduced penicillin susceptibility, reflecting amino acid substitutions in penicillin-binding protein 2X (PBP2X). In addition, 19.2% of all strains possessedmef(A/E),erm(A), orerm(B) genes, which mediate macrolide resistance, while 40.2% of strains were resistant to quinolones resulting from amino acid substitutions in GyrA and ParC. Our data argue strongly for the continuous surveillance of microbial characteristics and judicious antibiotic use in clinical practice.

scholarly journals High prevalence and genomic characteristics of G6P[1] Bovine Rotavirus A in yak in China

2020 ◽  
Vol 101 (7) ◽  
pp. 701-711
Author(s):  
Nan Yan ◽  
Ran Li ◽  
Yuanwei Wang ◽  
Bin Zhang ◽  
Hua Yue ◽  
...  
Keyword(s):  
Phylogenetic Tree ◽  
Tibet Plateau ◽  
Rotavirus A ◽  
Bovine Rotavirus ◽  
Genotype Constellation ◽  
High Prevalence ◽  
Health Significance ◽  
Amino Acid Mutations ◽  
Qinghai Tibet Plateau ◽  
Unique Amino Acid

Yak is an iconic species of the Qinghai–Tibet Plateau, which is the world's highest plateau. Here, a total of 541 yak diarrhoeic samples were collected from 69 farms in four provinces in the Qinghai–Tibet Plateau from April 2015 to June 2018, and 73.6 % of samples were detected as Bovine Rotavirus A (BRVA) positive by RT-PCR assay. Two G genotypes (G6, G10) and two P genotypes (P[1], P[11]) were determined, in which G6P[1] BRVA was the predominant strain. Moreover, VP7 and VP4 of these G6P[1] strains showed unique amino acid mutations, such that they clustered into an independent branch in the phylogenetic tree. A strain of BRVA designated as RVA/Yak-tc/CHN/QH-1/2015/G6P[1] was isolated successfully using MA104 cells, and the virus titre was determined as 105.84 TCID50 ml–1. The genome of strain QH-1 had a G6-P[1]-I2-R2-C2-M2-A3-N3-T6-E2-H3 genotype constellation. QH-1 was identified as a reassortment strain of BRVA, human RVA and ovine RVA based on the nucleotide identity and phylogenetic tree of 11 gene segments, indicating its public health significance. To the best of our knowledge, this is the first report on the molecular prevalence and genome characteristics of BRVA in yak, contributing to further understanding of the epidemic and genetic evolution of BRVA.

scholarly journals Using the genetic characteristics of Neisseria gonorrhoeae strains with decreased susceptibility to cefixime to develop a molecular assay to predict cefixime susceptibility

Sexual Health ◽  
2019 ◽  
Vol 16 (5) ◽  
pp. 488 ◽  
Author(s):  
Xiaomeng Deng ◽  
Lao-Tzu Allan-Blitz ◽  
Jeffrey D. Klausner
Keyword(s):  
Amino Acid ◽  
Amino Acid Position ◽  
Molecular Characteristics ◽  
Amino Acid Substitutions ◽  
Penicillin Binding Protein ◽  
Molecular Assay ◽  
Genetic Characteristics ◽  
Molecular Alterations ◽  
Critical Amino Acid ◽  
Susceptibility Assay

Background: In the last two decades, gonococcal strains with decreased cefixime susceptibility and cases of clinical treatment failure have been reported worldwide. Gonococcal strains with a cefixime minimum inhibitory concentration (MIC) ≥0.12 µg mL−1 are significantly more likely to fail cefixime treatment than strains with an MIC &lt;0.12 µg mL−1. Various researchers have described the molecular characteristics of gonococcal strains with reduced cefixime susceptibility, and many have proposed critical molecular alterations that contribute to this decreased susceptibility. Methods: A systematic review of all published articles in PubMed through 1 November 2018 was conducted that report findings on the molecular characteristics and potential mechanisms of resistance for gonococcal strains with decreased cefixime susceptibility. The findings were summarised and suggestions were made for the development of a molecular-based cefixime susceptibility assay. Results: The penicillin-binding protein 2 (PBP2) encoded by the penA gene is the primary target of cefixime antimicrobial activity. Decreased cefixime susceptibility is conferred by altered penA genes with mosaic substitute sequences from other Neisseria (N.) species (identifiable by alterations at amino acid position 375–377) or by non-mosaic penA genes with at least one of the critical amino acid substitutions at positions 501, 542 and 551. Based on this review of 415 international cefixime decreased susceptible N. gonorrhoeae isolates, the estimated sensitivity for an assay detecting the aforementioned amino acid alterations would be 99.5% (413/415). Conclusions: Targeting mosaic penA and critical amino acid substitutions in non-mosaic penA are necessary and may be sufficient to produce a robust, universal molecular assay to predict cefixime susceptibility.

scholarly journals Comparative transcriptomics of 3 high-altitude passerine birds and their low-altitude relatives

2019 ◽  
pp. 201819657 ◽  
Author(s):  
Yan Hao ◽  
Ying Xiong ◽  
Yalin Cheng ◽  
Gang Song ◽  
Chenxi Jia ◽  
...  
Keyword(s):  
Amino Acid ◽  
High Altitude ◽  
Expression Profiles ◽  
Eastern China ◽  
Tibet Plateau ◽  
Amino Acid Substitutions ◽  
Passerine Birds ◽  
Specific Expression ◽  
Low Altitude ◽  
Specific Expression Pattern

High-altitude environments present strong stresses for living organisms, which have driven striking phenotypic and genetic adaptations. While previous studies have revealed multiple genetic adaptations in high-altitude species, how evolutionary history (i.e., phylogenetic background) contributes to similarity in genetic adaptations to high-altitude environments is largely unknown, in particular in a group of birds. We explored this in 3 high-altitude passerine birds from the Qinghai-Tibet Plateau and their low-altitude relatives in lowland eastern China. We generated transcriptomic data for 5 tissues across these species and compared sequence changes and expression shifts between high- and low-altitude pairs. Sequence comparison revealed that similarity in all 3 high-altitude species was high for genes under positive selection (218 genes) but low in amino acid substitutions (only 4 genes sharing identical amino acid substitutions). Expression profiles for all genes identified a tissue-specific expression pattern (i.e., all species clustered by tissue). By contrast, an altitude-related pattern was observed in genes differentially expressed between all 3 species pairs and genes associated with altitude, suggesting that the high-altitude environment may drive similar expression shifts in the 3 high-altitude species. Gene expression level, gene connectivity, and the interactions of these 2 factors with altitude were correlated with evolutionary rates. Our results provide evidence for how gene sequence changes and expression shifts work in a concerted way in a group of high-altitude birds, leading to similar evolution routes in response to high-altitude environmental stresses.

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