scholarly journals Attenuation of Mycoplasma hyopneumoniae Strain ES-2 and Comparative Genomic Analysis of ES-2 and Its Attenuated Form ES-2L

2021 ◽  
Vol 8 ◽  
Author(s):  
Zhenya Li ◽  
Yingxin Wang ◽  
Yanyan Zhang ◽  
Xibiao Tang ◽  
Xiangru Wang ◽  
...  
Keyword(s):  
Genomic Analysis ◽  
Mycoplasma Hyopneumoniae ◽  
Comparative Genomic ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Virulence Attenuation ◽  
Genomic Analyses ◽  
Single Nucleotide Variations ◽  
Highly Virulent

Mycoplasma hyopneumoniae causes swine respiratory disease worldwide. Due to the difficulty of isolating and cultivating M. hyopneumoniae, very few attenuated strains have been successfully isolated, which hampers the development of attenuated vaccines. In order to produce an attenuated M. hyopneumoniae strain, we used the highly virulent M. hyopneumoniae strain ES-2, which was serially passaged in vitro 200 times to produce the attenuated strain ES-2L, and its virulence was evidenced to be low in an animal experiment. In order to elucidate the mechanisms underlying virulence attenuation, we performed whole-genome sequencing of both strains and conducted comparative genomic analyses of strain ES-2 and its attenuated form ES-2L. Strain ES-2L showed three large fragment deletion regions including a total of 18 deleted genes, compared with strain ES-2. Analysis of single-nucleotide polymorphisms (SNPs) and indels indicated that 22 dels were located in 19 predicted coding sequences. In addition to these indels, 348 single-nucleotide variations (SNVs) were identified between strains ES-2L and ES-2. These SNVs mapped to 99 genes where they appeared to induce amino acid substitutions and translation stops. The deleted genes and SNVs may be associated with decreased virulence of strain ES-2L. Our work provides a foundation for further examining virulence factors of M. hyopneumoniae and for the development of attenuated vaccines.

scholarly journals Genomic Analysis of an Attenuated Chlamydia abortus Live Vaccine Strain Reveals Defects in Central Metabolism and Surface Proteins

2009 ◽  
Vol 77 (9) ◽  
pp. 4161-4167 ◽  
Author(s):  
L. S. Burall ◽  
A. Rodolakis ◽  
A. Rekiki ◽  
G. S. A. Myers ◽  
P. M. Bavoil
Keyword(s):  
Pyruvate Kinase ◽  
Vaccine Strain ◽  
Genomic Analysis ◽  
Live Vaccine ◽  
Surface Proteins ◽  
Comparative Genomic ◽  
Temperature Sensitive ◽  
Nucleotide Polymorphisms ◽  
Chlamydia Abortus ◽  
Virulence Attenuation

ABSTRACT Comparative genomic analysis of a wild-type strain of the ovine pathogen Chlamydia abortus and its nitrosoguanidine-induced, temperature-sensitive, virulence-attenuated live vaccine derivative identified 22 single nucleotide polymorphisms unique to the mutant, including nine nonsynonymous mutations, one leading to a truncation of pmpG, which encodes a polymorphic membrane protein, and two intergenic mutations potentially affecting promoter sequences. Other nonsynonymous mutations mapped to a pmpG pseudogene and to predicted coding sequences encoding a putative lipoprotein, a sigma-54-dependent response regulator, a PhoH-like protein, a putative export protein, two tRNA synthetases, and a putative serine hydroxymethyltransferase. One of the intergenic mutations putatively affects transcription of two divergent genes encoding pyruvate kinase and a putative SOS response nuclease, respectively. These observations suggest that the temperature-sensitive phenotype and associated virulence attenuation of the vaccine strain result from disrupted metabolic activity due to altered pyruvate kinase expression and/or alteration in the function of one or more membrane proteins, most notably PmpG and a putative lipoprotein.

scholarly journals It Is Not All about Single Nucleotide Polymorphisms: Comparison of Mobile Genetic Elements and Deletions in Listeria monocytogenes Genomes Links Cases of Hospital-Acquired Listeriosis to the Environmental Source

2015 ◽  
Vol 53 (11) ◽  
pp. 3492-3500 ◽  
Author(s):  
Qinning Wang ◽  
Nadine Holmes ◽  
Elena Martinez ◽  
Peter Howard ◽  
Grant Hill-Cawthorne ◽  
...  
Keyword(s):  
Listeria Monocytogenes ◽  
Genomic Analysis ◽  
Comparative Genomic ◽  
Snp Analysis ◽  
Nucleotide Polymorphisms ◽  
Environmental Isolates ◽  
Single Nucleotide ◽  
Content Type ◽  
Serotype 1 ◽  
Hospital Acquired

The control of food-borne outbreaks caused byListeria monocytogenesin humans relies on the timely identification of food or environmental sources and the differentiation of outbreak-related isolates from unrelated ones. This study illustrates the utility of whole-genome sequencing for examining the link between clinical and environmental isolates ofL. monocytogenesassociated with an outbreak of hospital-acquired listeriosis in Sydney, Australia. Comparative genomic analysis confirmed an epidemiological link between the three clinical and two environmental isolates. Single nucleotide polymorphism (SNP) analysis showed that only two SNPs separated the three human outbreak isolates, which differed by 19 to 20 SNPs from the environmental isolates and 71 to >10,000 SNPs from sporadicL. monocytogenesisolates. The chromosomes of all human outbreak isolates and the two suspected environmental isolates were syntenic. In contrast to the genomes of background sporadic isolates, all epidemiologically linked isolates contained two novel prophages and a previously unreported clustered regularly interspaced short palindromic repeat (CRISPR)-associated (Cas) locus subtype sequence. The mobile genetic element (MGE) profile of these isolates was distinct from that of the other serotype 1/2b reference strains and sporadic isolates. The identification of SNPs and clonally distinctive MGEs strengthened evidence to distinguish outbreak-related isolates ofL. monocytogenesfrom cocirculating endemic strains.

scholarly journals Somatic variants for seed and fruit set in grapevine

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Laura Costantini ◽  
Paula Moreno-Sanz ◽  
Chinedu Charles Nwafor ◽  
Silvia Lorenzi ◽  
Annarita Marrano ◽  
...  
Keyword(s):  
Single Nucleotide Polymorphisms ◽  
Fruit Set ◽  
Climatic Factors ◽  
Embryo Sac ◽  
Wine Industry ◽  
Nucleotide Polymorphisms ◽  
Wine Quality ◽  
Single Nucleotide ◽  
Germplasm Collections

Abstract Background Grapevine reproductive development has direct implications on yield. It also impacts on berry and wine quality by affecting traits like seedlessness, berry and bunch size, cluster compactness and berry skin to pulp ratio. Seasonal fluctuations in yield, fruit composition and wine attributes, which are largely driven by climatic factors, are major challenges for worldwide table grape and wine industry. Accordingly, a better understanding of reproductive processes such as gamete development, fertilization, seed and fruit set is of paramount relevance for managing yield and quality. With the aim of providing new insights into this field, we searched for clones with contrasting seed content in two germplasm collections. Results We identified eight variant pairs that seemingly differ only in seed-related characteristics while showing identical genotype when tested with the GrapeReSeq_Illumina_20K_SNP_chip and several microsatellites. We performed multi-year observations on seed and fruit set deriving from different pollination treatments, with special emphasis on the pair composed by Sangiovese and its seedless variant locally named Corinto Nero. The pollen of Corinto Nero failed to germinate in vitro and gave poor berry set when used to pollinate other varieties. Most berries from both open- and cross-pollinated Corinto Nero inflorescences did not contain seeds. The genetic analysis of seedlings derived from occasional Corinto Nero normal seeds revealed that the few Corinto Nero functional gametes are mostly unreduced. Moreover, three genotypes, including Sangiovese and Corinto Nero, were unexpectedly found to develop fruits without pollen contribution and occasionally showed normal-like seeds. Five missense single nucleotide polymorphisms were identified between Corinto Nero and Sangiovese from transcriptomic data. Conclusions Our observations allowed us to attribute a seedlessness type to some variants for which it was not documented in the literature. Interestingly, the VvAGL11 mutation responsible for Sultanina stenospermocarpy was also discovered in a seedless mutant of Gouais Blanc. We suggest that Corinto Nero parthenocarpy is driven by pollen and/or embryo sac defects, and both events likely arise from meiotic anomalies. The single nucleotide polymorphisms identified between Sangiovese and Corinto Nero are suitable for testing as traceability markers for propagated material and as functional candidates for the seedless phenotype.

scholarly journals Comparative genomic analyses of a virulent pseudorabies virus and a series of its in vitro passaged strains

2018 ◽  
Vol 15 (1) ◽  
Author(s):  
Chao Ye ◽  
Jiqiang Wu ◽  
Wu Tong ◽  
Tongling Shan ◽  
Xuefei Cheng ◽  
...  
Keyword(s):  
Pseudorabies Virus ◽  
Comparative Genomic ◽  
Genomic Analyses

In-Silico and In-vitro Analysis of Human SOS1 Protein Causing Noonan Syndrome – A Novel Approach to Explore the Molecular Pathways

2021 ◽  
Vol 22 ◽  
Author(s):  
Vinoth Sigamani ◽  
Sheeja Rajasingh ◽  
Narasimman Gurusamy ◽  
Arunima Panda ◽  
Johnson Rajasingh
Keyword(s):  
Noonan Syndrome ◽  
In Silico ◽  
Genetic Disorder ◽  
In Vitro Study ◽  
Human Skin Fibroblast ◽  
Nucleotide Polymorphisms ◽  
Gene Expressions ◽  
Single Nucleotide ◽  
Nucleotide Mutation

Aims: Noonan syndrome (NS) is an autosomal dominant genetic disorder caused by single nucleotide mutation in PTPN11, SOS1, RAF1, and KRAS genes. Background: We hypothesize that in-silico analysis of human SOS1 mutations would be a promising predictor in identifying the pathogenic effect of NS. Methods: Here, we computationally analyzed the SOS1 gene to identify the pathogenic non-synonymous single nucleotide polymorphisms (nsSNPs) to cause NS. The variant information of SOS1 was collected from the SNP database (dbSNP). The variants were further analyzed by in-silico tools I-Mutant, iPTREE-STAB, and MutPred to elucidate their structural and functional characteristics. Results: We found that 11 nsSNPs of SOS1 were more pathogenic to cause NS. The 3D modeling of the wild-type and the 11 nsSNPs were performed using I-TASSER and validated via ERRAT and RAMPAGE. SOS1 interacting proteins were analysed through STRING, which showed that SOS1 interacted with cardiac proteins GATA4, TNNT2, and ACTN2. During these interactions, GRB2 and HRAS act as an intermediate molecules between SOS1 and cardiac proteins. These in-silico analyses were validated using induced cardiomyocytes (iCMCs) derived from NS patients carrying SOS1 gene variant c.1654A>G (NS-iCMCs) and compared with control human skin fibroblast-derived iCMCs (C-iCMCs). Our in vitro data further confirmed that the SOS1, GRB2 and HRAS gene expressions as well as the activated ERK protein, were significantly decreased in NS-iCMCs compared to C-iCMCs. Conclusion: This is the first in-silico and in vitro study demonstrating that 11 nsSNPs of SOS1 were playing a deleterious pathogenic role in causing NS.

Contribution of boars to reproductive performance and paternity after homospermic and heterospermic artificial insemination

2015 ◽  
Vol 27 (7) ◽  
pp. 1012 ◽  
Author(s):  
C. E. R. Ferreira ◽  
D. B. Sávio ◽  
A. C. Guarise ◽  
M. J. Flach ◽  
G. D. A. Gastal ◽  
...  
Keyword(s):  
Reproductive Performance ◽  
Artificial Insemination ◽  
Penetration Rate ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Blood Samples ◽  
Precise Evaluation ◽  
Umbilical Cords ◽  
Farrowing Rate

Heterospermic AI is commonly used in swine despite preventing precise evaluation of individual boar fertility. The present study compared the contribution of four boars (A, B, C and D) for reproductive performance and for paternity using homospermic and heterospermic (AB, AC, AD, BC, BD and CD) AI (n = 204 for homospermic AI; n = 307 for heterospermic AI). Blood samples from the four boars, from all sows inseminated with heterospermic doses and from the umbilical cords of their piglets, as well as tissue smears from mummified fetuses, were genotyped using single nucleotide polymorphisms (SNPs). Differences among boars were detected for the in vitro oocyte penetration rate and for the number of spermatozoa per oocyte (P < 0.05), but not for sperm motility, mitochondrial functionality and integrity of the membrane, acrosome and DNA (P > 0.05). Homospermic and heterospermic AI resulted in similar (P > 0.05) farrowing rates (90.5% and 89.9%, respectively) and total litter size (12.4 ± 0.4 and 12.7 ± 0.7, respectively). Farrowing rate was lower for Boar B than for Boar C (P < 0.05), but no other differences in reproductive performance among boars were observed with homospermic AI. The SNPs determined the paternity of 94.2% of the piglets sired by heterospermic AI. In the AC pool, paternity contribution per boar was similar (P > 0.05), but differences between boars occurred in all other pools (P < 0.05). Boar D achieved the greatest paternity contribution in all pools and parity categories (nearly 60%), whereas Boar B sired the fewest piglets (at most 40%). Reproductive performance was similar with homospermic and heterospermic AI, but differences in performance among boars undetected with homospermic AI were only evident after genotyping the piglets sired through heterospermic AI.

scholarly journals Genomic surveillance of COVID-19 cases in Beijing

2020 ◽  
Vol 11 (1) ◽  
Author(s):  
Pengcheng Du ◽  
Nan Ding ◽  
Jiarui Li ◽  
Fujie Zhang ◽  
Qi Wang ◽  
...  
Keyword(s):  
Single Nucleotide Polymorphisms ◽  
High Frequency ◽  
Epidemiological Data ◽  
Genomic Diversity ◽  
Nucleotide Polymorphisms ◽  
Genomic Evolution ◽  
Single Nucleotide ◽  
Imported Cases ◽  
Single Nucleotide Variations ◽  
Local Transmission

Abstract The spread of SARS-CoV-2 in Beijing before May, 2020 resulted from transmission following both domestic and global importation of cases. Here we present genomic surveillance data on 102 imported cases, which account for 17.2% of the total cases in Beijing. Our data suggest that all of the cases in Beijing can be broadly classified into one of three groups: Wuhan exposure, local transmission and overseas imports. We classify all sequenced genomes into seven clusters based on representative high-frequency single nucleotide polymorphisms (SNPs). Genomic comparisons reveal higher genomic diversity in the imported group compared to both the Wuhan exposure and local transmission groups, indicating continuous genomic evolution during global transmission. The imported group show region-specific SNPs, while the intra-host single nucleotide variations present as random features, and show no significant differences among groups. Epidemiological data suggest that detection of cases at immigration with mandatory quarantine may be an effective way to prevent recurring outbreaks triggered by imported cases. Notably, we also identify a set of novel indels. Our data imply that SARS-CoV-2 genomes may have high mutational tolerance.

scholarly journals Normocyte-binding protein required for human erythrocyte invasion by the zoonotic malaria parasite Plasmodium knowlesi

2016 ◽  
Vol 113 (26) ◽  
pp. 7231-7236 ◽  
Author(s):  
Robert W. Moon ◽  
Hazem Sharaf ◽  
Claire H. Hastings ◽  
Yung Shwen Ho ◽  
Mridul B. Nair ◽  
...  
Keyword(s):  
Vaccine Development ◽  
Plasmodium Knowlesi ◽  
Binding Protein ◽  
Cynomolgus Macaque ◽  
Genomic Analysis ◽  
Human Infection ◽  
Comparative Genomic ◽  
Gene Encoding ◽  
Human Rbcs

The dominant cause of malaria in Malaysia is now Plasmodium knowlesi, a zoonotic parasite of cynomolgus macaque monkeys found throughout South East Asia. Comparative genomic analysis of parasites adapted to in vitro growth in either cynomolgus or human RBCs identified a genomic deletion that includes the gene encoding normocyte-binding protein Xa (NBPXa) in parasites growing in cynomolgus RBCs but not in human RBCs. Experimental deletion of the NBPXa gene in parasites adapted to growth in human RBCs (which retain the ability to grow in cynomolgus RBCs) restricted them to cynomolgus RBCs, demonstrating that this gene is selectively required for parasite multiplication and growth in human RBCs. NBPXa-null parasites could bind to human RBCs, but invasion of these cells was severely impaired. Therefore, NBPXa is identified as a key mediator of P. knowlesi human infection and may be a target for vaccine development against this emerging pathogen.

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