356 results match your criteria strain-specific variations

Dynamical Differences in Respiratory Syncytial Virus.

Bull Math Biol 2021 Nov 30;84(1):11. Epub 2021 Nov 30.

Department of Mathematics, Statistics, and Actuarial Science, Butler University, 4600 Sunset Ave, Indianapolis, IN, 46208, USA.

Respiratory syncytial virus (RSV) is a leading viral cause of pediatric respiratory infections and early infant mortality. Despite extensive development efforts currently underway, there remain no vaccines available for the prevention of RSV. RSV is an enveloped, negative-strand RNA virus that utilizes two different proteins (G and F) to mediate attachment and entry into host cells. Read More

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November 2021

Strain-Specific Liver Metabolite Profiles in Medaka.

Metabolites 2021 Oct 29;11(11). Epub 2021 Oct 29.

Institute for Biological Interfaces 4 (IBG 4), Karlsruhe Institute of Technology, Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany.

The relationship between genetic variation and phenotypic traits is often poorly understood since specific genotypes do not always easily translate into associated phenotypes, especially for complex disorders. The genetic background has been shown to affect metabolic pathways and thus contribute to variations in the metabolome. Here, we tested the suitability of NMR metabolomics for comparative analysis of fish lines as a first step towards phenotype-genotype association studies. Read More

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October 2021

Mouse strain-specific polymorphic provirus functions as cis-regulatory element leading to epigenomic and transcriptomic variations.

Nat Commun 2021 11 9;12(1):6462. Epub 2021 Nov 9.

Division of Life Science, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, SAR, China.

Polymorphic integrations of endogenous retroviruses (ERVs) have been previously detected in mouse and human genomes. While most are inert, a subset can influence the activity of the host genes. However, the molecular mechanism underlying how such elements affect the epigenome and transcriptome and their roles in driving intra-specific variation remain unclear. Read More

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November 2021

Viral Strain-Specific Activation of Pathogen-Associated Molecular Pattern-Triggered Immunity Enhances Symptom Severity in Broad Bean Wilt Virus 2 Infection.

Front Plant Sci 2021 21;12:746543. Epub 2021 Sep 21.

Department of International Agricultural Technology, Seoul National University, Pyeongchang, South Korea.

Broad bean wilt virus 2 (BBWV2) is an emerging virus in various economically important crops, especially pepper ( L.), worldwide. Recently, the emergence of various BBWV2 strains that induce severe symptoms has increased damage to pepper crops. Read More

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September 2021

Emerging Mutations in Nsp1 of SARS-CoV-2 and Their Effect on the Structural Stability.

Pathogens 2021 Oct 6;10(10). Epub 2021 Oct 6.

Peng Cheng Laboratory, Vanke Cloud City Phase I Building 8, Xili Street, Nashan District, Shenzhen 518055, China.

The genome of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) encodes 16 non-structural (Nsp) and 4 structural proteins. Among the Nsps, Nsp1 inhibits host gene expression and also evades the immune system. This protein has been proposed as a target for vaccine development and also for drug design. Read More

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October 2021

Stimulation of L. In Vitro Shoot Growth by Endophytic Group Bacteria.

Microorganisms 2021 Sep 6;9(9). Epub 2021 Sep 6.

Institute of Horticulture, Lithuanian Research Centre for Agriculture and Forestry, Kaunas str. 30, Babtai, 54333 Kaunas reg., Lithuania.

In vitro plant tissue cultures face various unfavorable conditions, such as mechanical damage, osmotic shock, and phytohormone imbalance, which can be detrimental to culture viability, growth efficiency, and genetic stability. Recent studies have revealed a presence of diverse endophytic bacteria, suggesting that engineering of the endophytic microbiome of in vitro plant tissues has the potential to improve their acclimatization and growth. Therefore, the aim of this study was to identify cultivated tobacco ( L. Read More

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September 2021

Clinical Outcomes of Single vs. Two-Strain Probiotic Prophylaxis for Prevention of Necrotizing Enterocolitis in Preterm Infants.

Front Pediatr 2021 30;9:729535. Epub 2021 Aug 30.

Westmead Hospital Neonatal Intensive Care Unit, Sydney, NSW, Australia.

The administration of live microbiota (probiotic) via enteral route to preterm infants facilitates intestinal colonization with beneficial bacteria, resulting in competitive inhibition of the growth of pathogenic bacteria preventing gut microbiome dysbiosis. This dysbiosis is linked to the pathogenesis of necrotizing enterocolitis (NEC), an acquired multi-factorial intestinal disease characterized by microbial invasion of the gut mucosa, particularly affecting preterm infants. Probiotic prophylaxis reduces NEC; however, variations in strain-specific probiotic effects, differences in administration protocols, and synergistic interactions with the use of combination strains have all led to challenges in selecting the optimal probiotic for clinical use. Read More

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Natural variation in the consequences of gene overexpression and its implications for evolutionary trajectories.

Elife 2021 08 2;10. Epub 2021 Aug 2.

Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, United States.

Copy number variation through gene or chromosome amplification provides a route for rapid phenotypic variation and supports the long-term evolution of gene functions. Although the evolutionary importance of copy-number variation is known, little is understood about how genetic background influences its tolerance. Here, we measured fitness costs of over 4000 overexpressed genes in 15 strains representing different lineages, to explore natural variation in tolerating gene overexpression (OE). Read More

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Transcriptional responses in jejunum of two layer chicken strains following variations in dietary calcium and phosphorus levels.

BMC Genomics 2021 Jun 29;22(1):485. Epub 2021 Jun 29.

Leibniz Institute for Farm Animal Biology (FBN), Institute for Genome Biology, Wilhelm- Stahl-Allee 2, 18196, Dummerstorf, Germany.

Background: Calcium (Ca) and phosphorus (P) are essential nutrients that are linked to a large array of biological processes. Disturbances in Ca and P homeostasis in chickens are associated with a decline in growth and egg laying performance and environmental burden due to excessive P excretion rates. Improved utilization of minerals in particular of P sources contributes to healthy growth while preserving the finite resource of mineral P and mitigating environmental pollution. Read More

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The biological role of MutT in the pathogenesis of the zoonotic pathogen serotype 2.

Virulence 2021 12;12(1):1538-1549

MOE Joint International Research Laboratory of Animal Health and Food Safety, Key Lab of Animal Bacteriology, Ministry of Agriculture, OIE Reference Lab for Swine Streptococcosis, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China.

() is an important rising pathogen that causes serious diseases in humans and pigs. Although some putative virulence factors of have been identified, its pathogenic mechanisms are largely unclear. Here, we identified a putative virulence-associated factor MutT, which is unique to serotype 2 (SS2) virulent strains. Read More

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December 2021

A fattening factor to quantify the accumulation ability of microorganisms under N-starvation.

N Biotechnol 2021 Apr 17;66:70-78. Epub 2021 Apr 17.

Department of Chemistry, University Sapienza of Rome, Piazzale Aldo Moro 5, 00185, Rome, Italy. Electronic address:

Many microorganisms can accumulate biomass in the form of lipids and polysaccharides, which can be used for biofuels, bioplastics, food and feed. Some innovative bioprocesses exploit the competitive advantage provided by such accumulation ability, mainly under N-starvation, to select high-accumulating strains against biological contaminants, by using uncoupled nutrient feeding. However, there is no general and easily comparable parameter available to compare biomass accumulation ability among different microbial strains, which could measure the competitive advantage. Read More

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Increasing temperature alters the within-host competition of viral strains and influences virus genetic variability.

Virus Evol 2021 Jan 23;7(1):veab017. Epub 2021 Feb 23.

Departamento de Biología del Estrés y Patología Vegetal, Centro de Edafología y Biología Aplicada del Segura (CEBAS), CSIC, PO Box 164, 30100 Murcia, Spain.

Environmental conditions can affect viral accumulation, virulence and adaptation, which have implications in the disease outcomes and efficiency of control measures. Concurrently, mixed viral infections are relevant in plants, being their epidemiology shaped by within-host virus-virus interactions. However, the extent in which the combined effect of variations in abiotic components of the plant ecological niche and the prevalence of mixed infections affect the evolutionary dynamics of viral populations is not well understood. Read More

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January 2021

Viral infection of human neurons triggers strain-specific differences in host neuronal and viral transcriptomes.

PLoS Pathog 2021 03 22;17(3):e1009441. Epub 2021 Mar 22.

Departments of Biology, Biochemistry and Molecular Biology, Center for Infectious Disease Dynamics, and the Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, Pennsylvania, United States of America.

Infection with herpes simplex virus 1 (HSV-1) occurs in over half the global population, causing recurrent orofacial and/or genital lesions. Individual strains of HSV-1 demonstrate differences in neurovirulence in vivo, suggesting that viral genetic differences may impact phenotype. Here differentiated SH-SY5Y human neuronal cells were infected with one of three HSV-1 strains known to differ in neurovirulence in vivo. Read More

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Strain-specific genome evolution in Trypanosoma cruzi, the agent of Chagas disease.

PLoS Pathog 2021 01 28;17(1):e1009254. Epub 2021 Jan 28.

Center for Tropical and Emerging Global Diseases, University of Georgia, Athens, Georgia, United States of America.

The protozoan Trypanosoma cruzi almost invariably establishes life-long infections in humans and other mammals, despite the development of potent host immune responses that constrain parasite numbers. The consistent, decades-long persistence of T. cruzi in human hosts arises at least in part from the remarkable level of genetic diversity in multiple families of genes encoding the primary target antigens of anti-parasite immune responses. Read More

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January 2021

Comparative Genomic Analysis of Reveals Horizontal Gene Transfer-Mediated Evolution of the CRISPR-Cas System in the Mycobacterium tuberculosis Complex.

mSystems 2021 Jan 19;6(1). Epub 2021 Jan 19.

Department of Zoology, University of Delhi, Delhi, India

Clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated (Cas) genes are conserved genetic elements in many prokaryotes, including , the causative agent of tuberculosis. Although knowledge of CRISPR locus variability has been utilized in strain genotyping, its evolutionary path in is not well understood. In this study, we have performed a comparative analysis of 141 mycobacterial genomes and identified the exclusive presence of the CRISPR-Cas type III-A system in complex (MTBC). Read More

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January 2021

Sub-genomic analysis of Chikungunya virus E2 mutations in Pakistani isolates potentially modulating B-cell & T-Cell immune response.

Pak J Med Sci 2021 Jan-Feb;37(1):93-98

Prof. Dr. Saeed Khan, Ph.D. Department of Pathology, Dow University of Health Sciences, Karachi, Pakistan.

Background & Objectives: The Chikungunya virus (CHIKV) transmitted to the humans through species of the mosquitoes. In December 2016, a severe outbreak reported from Pakistan. However, there is no vaccine or anti-viral treatment currently available so host immune response against CHIKV gained significant interest. Read More

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January 2021

CRAGE-mediated insertion of fluorescent chromosomal markers for accurate and scalable measurement of co-culture dynamics in .

Synth Biol (Oxf) 2020 3;5(1):ysaa015. Epub 2020 Sep 3.

Genome Science and Technology Program, University of British Columbia, Vancouver, BC V6T 1Z4, Canada.

Monitoring population dynamics in co-culture is necessary in engineering microbial consortia involved in distributed metabolic processes or biosensing applications. However, it remains difficult to measure strain-specific growth dynamics in high-throughput formats. This is especially vexing in plate-based functional screens leveraging whole-cell biosensors to detect specific metabolic signals. Read More

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September 2020

Improving the Predictive Value of Prion Inactivation Validation Methods to Minimize the Risks of Iatrogenic Transmission With Medical Instruments.

Front Bioeng Biotechnol 2020 1;8:591024. Epub 2020 Dec 1.

Université Paris Saclay, INRAE, UVSQ, VIM, Jouy-en-Josas, France.

Prions are pathogenic infectious agents responsible for fatal, incurable neurodegenerative diseases in animals and humans. Prions are composed exclusively of an aggregated and misfolded form (PrP ) of the cellular prion protein (PrP). During the propagation of the disease, PrP recruits and misfolds PrP into further PrP. Read More

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December 2020

Nitrogen metabolism in three non-conventional wine yeast species: A tool to modulate wine aroma profiles.

Food Microbiol 2021 Apr 29;94:103650. Epub 2020 Sep 29.

South African Grape and Wine Research Institute, Faculty of AgriSciences, Stellenbosch University, Stellenbosch, South Africa. Electronic address:

The positive impact of certain non-Saccharomyces yeasts on the aromatic profile of wines has been well documented in literature and their industrial use in association with S. cerevisiae is now recommended. Competition between non-Saccharomyces species and Saccharomyces cerevisiae for various nutrients, especially nitrogen sources, greatly impacts the production of aroma compounds. Read More

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Contribution of Time, Taxonomy, and Selective Antimicrobials to Antibiotic and Multidrug Resistance in Wastewater Bacteria.

Environ Sci Technol 2020 12 1;54(24):15946-15957. Epub 2020 Dec 1.

Department of Environmental Health and Engineering, Whiting School of Engineering, Johns Hopkins University, 3400 North Charles Street, 313 Ames Hall, Baltimore, Maryland 21218, United States.

The use of nontherapeutic broad-spectrum antimicrobial agents triclosan (TCS) and benzalkonium chloride (BC) can contribute to bacterial resistance to clinically relevant antibiotics. Antimicrobial-resistant bacteria within wastewater may reflect the resistance burden within the human microbiome, as antibiotics and pathogens in wastewater can track with clinically relevant parameters during perturbations to the community. In this study, we monitored culturable and resistant wastewater bacteria and cross-resistance to clinically relevant antibiotics to gauge the impact of each antimicrobial and identify factors influencing cross-resistance profiles. Read More

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December 2020

A Strain-Specific Inhibitor of Receptor-Bound HIV-1 Targets a Pocket near the Fusion Peptide.

Cell Rep 2020 11;33(8):108428

Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA; Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, International AIDS Vaccine Initiative Neutralizing Antibody Center, and Collaboration for AIDS Vaccine Discovery, The Scripps Research Institute, La Jolla, CA 92037, USA. Electronic address:

Disruption of viral fusion represents a viable, albeit under-explored, target for HIV therapeutics. Here, while studying the receptor-bound envelope glycoprotein conformation by cryoelectron microscopy (cryo-EM), we identify a pocket near the base of the trimer containing a bound detergent molecule and perform in silico drug screening by using a library of drug-like and commercially available molecules. After down-selection, we solve cryo-EM structures that validate the binding of two small molecule hits in very similar manners to the predicted binding poses, including interactions with aromatic residues within the fusion peptide. Read More

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November 2020

Enteropathogenic Potential of Isolates from Soil, Animals, Food and Biopesticides.

Foods 2020 Oct 17;9(10). Epub 2020 Oct 17.

Department of Veterinary Sciences, Faculty of Veterinary Medicine, Ludwig-Maximilians-Universität München, Schönleutnerstr. 8, 85764 Oberschleißheim, Germany.

Despite its benefits as biological insecticide, bears enterotoxins, which can be responsible for a diarrhoeal type of food poisoning. Thus, all 24 isolates from foodstuffs, animals, soil and commercially used biopesticides tested in this study showed the genetic prerequisites necessary to provoke the disease. Moreover, though highly strain-specific, various isolates were able to germinate and also to actively move, which are further requirements for the onset of the disease. Read More

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October 2020

The polymorphism of Hydra microsatellite sequences provides strain-specific signatures.

PLoS One 2020 28;15(9):e0230547. Epub 2020 Sep 28.

Department of Genetics and Evolution, Institute of Genetics and Genomics in Geneva (iGE3), University of Geneva, Geneva, Switzerland.

Hydra are freshwater polyps widely studied for their amazing regenerative capacity, adult stem cell populations, low senescence and value as ecotoxicological marker. Many wild-type strains of H. vulgaris have been collected worldwide and maintained effectively under laboratory conditions by asexual reproduction, while stable transgenic lines have been continuously produced since 2006. Read More

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October 2020

Comparison of chitin-induced natural transformation in pandemic Vibrio cholerae O1 El Tor strains.

Environ Microbiol 2020 10 9;22(10):4149-4166. Epub 2020 Sep 9.

Laboratory of Molecular Microbiology, Global Health Institute, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, CH-1015, Switzerland.

The human pathogen Vibrio cholerae serves as a model organism for many important processes ranging from pathogenesis to natural transformation, which has been extensively studied in this bacterium. Previous work has deciphered important regulatory circuits involved in natural competence induction as well as mechanistic details related to its DNA acquisition and uptake potential. However, since competence was first reported for V. Read More

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October 2020

Analysis of the Diversity of the AvBD Gene Region in Japanese Quail.

J Hered 2020 09;111(5):436-443

Department of Animal Science, Tokyo University of Agriculture, Atsugi, Japan.

The avian β-defensin (AvBD) gene region is an important component of the innate immune system, encoding a variety of antimicrobial peptides. The AvBD region forms a multigene cluster in a specific chromosomal region. Comparison of the AvBD region among various birds suggests the presence of defects, duplications, and pseudogenization at many loci. Read More

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September 2020

SARS-CoV-2 exhibits intra-host genomic plasticity and low-frequency polymorphic quasispecies.

J Clin Virol 2020 Oct 11;131:104585. Epub 2020 Aug 11.

Public Health Laboratories, Department of Microbiology, Hellenic Pasteur Institute, Athens, Greece.

In December 2019, an outbreak of atypical pneumonia (Coronavirus disease 2019 -COVID-19) associated with a novel coronavirus (SARS-CoV-2) was reported in Wuhan city, Hubei province, China. The outbreak was traced to a seafood wholesale market and human to human transmission was confirmed. The rapid spread and the death toll of the new epidemic warrants immediate intervention. Read More

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October 2020

Strain Differences in Responsiveness to Repeated Restraint Stress Affect Remote Contextual Fear Memory and Blood Transcriptomics.

Neuroscience 2020 09 5;444:76-91. Epub 2020 Aug 5.

Department of Psychiatry and Behavioral Sciences, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA. Electronic address:

The role of stress in altering fear memory is not well understood. Since individual variations in stress reactivity exist, and stress alters fear memory, exposing individuals with differing stress-reactivity to repeated stress would affect their fear memory to various degrees. We explored this question using the average stress-reactive Fisher 344 (F344) rat strain and the Wistar-Kyoto (WKY) strain with its heightened stress-reactivity. Read More

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September 2020

pH effect on strain-specific transcriptomes of the take-all fungus.

PLoS One 2020 30;15(7):e0236429. Epub 2020 Jul 30.

IGEPP, INRAE, Institut Agro, Univ Rennes, Le Rheu, France.

The soilborne fungus Gaeumannomyces tritici (G. tritici) causes the take-all disease on wheat roots. Ambient pH has been shown to be critical in different steps of G. Read More

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September 2020

Correlation of drug resistance with single nucleotide variations through genome analysis and experimental validation in a multi-drug resistant clinical isolate of M. tuberculosis.

BMC Microbiol 2020 07 25;20(1):223. Epub 2020 Jul 25.

Dr. B. R. Ambedkar Center for Biomedical Research (ACBR), University of Delhi, 110007, New Delhi, India.

Background: Genome sequencing and genetic polymorphism analysis of clinical isolates of M. tuberculosis is carried out to gain further insight into molecular pathogenesis and host-pathogen interaction. Therefore the functional evaluation of the effect of single nucleotide variation (SNV) is essential. Read More

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Phenotypic and Genotypic Comparison of a Live-Attenuated Genotype I Japanese Encephalitis Virus SD12-F120 Strain with Its Virulent Parental SD12 Strain.

Viruses 2020 05 16;12(5). Epub 2020 May 16.

Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai 200241, China.

The phenotypic and genotypic characteristics of a live-attenuated genotype I (GI) strain (SD12-F120) of Japanese encephalitis virus (JEV) were compared with its virulent parental SD12 strain to gain an insight into the genetic changes acquired during the attenuation process. SD12-F120 formed smaller plaque on BHK-21 cells and showed reduced replication in mouse brains compared with SD12. Mice inoculated with SD12-F120 via either intraperitoneal or intracerebral route showed no clinical symptoms, indicating a highly attenuated phenotype in terms of both neuroinvasiveness and neurovirulence. Read More

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