scholarly journals Pan-genome analysis reveals the molecular basis of niche adaptation ofStaphylococcus epidermidisstrains

2019 ◽  
Author(s):  
Fei Su ◽  
Rui Tian ◽  
Yi Yang ◽  
Lihui Zou ◽  
Xiaomao Xu ◽  
...  
Keyword(s):  
Large Scale ◽  
Evolutionary Process ◽  
Bloodstream Infections ◽  
Vital Role ◽  
Whole Genome Sequence ◽  
Host Bacterium ◽  
Pan Genome ◽  
Source Of Infection ◽  
Niche Adaptation ◽  
Core Proteins

AbstractStaphylococcus epidermidisis the most commonly isolated species from human skin and the second leading cause of bloodstream infections. Here, we performed a large-scale comparative study without any pre-assigned reference to identify genomic determinants associated with their diversity and adaptation as a “double-side spy”, a skin dominant colonization, and a successful pathogen. The pan-genome ofS. epidermidisis open with 435 core proteins and a pan-genome size of 8034 proteins. Genome-wide phylogenetic tree shows that whole genome sequence is a powerful tool to analyze the complex evolutionary process ofS. epidermidisand investigate the source of infection. Comparative genome analyses demonstrate the high diversity of antimicrobial resistances, especially mobile genetic elements. The complicated relationships of host-bacterium and bacterium-bacterium helpS. epidermidisto play a vital role in balancing the epithelial microflora. The highly variable and dynamic nature of theS. epidermidisgenome may be the result of its success in adapting to broad habitats, which is necessary to deal with complex environments. This study gives the general landscape ofS. epidermidispan-genome and provides valuable insights into mechanisms for genome evolution and lifestyle adaptation of this ecologically flexible species.

scholarly journals Why does the spread of COVID-19 vary greatly in different countries? Revealing the efficacy of face masks in epidemic prevention

2021 ◽  
Vol 149 ◽  
Author(s):  
Jincheng Wei ◽  
Shurui Guo ◽  
Enshen Long ◽  
Li Zhang ◽  
Bizhen Shu ◽  
...  
Keyword(s):  
Social Isolation ◽  
Large Scale ◽  
Experimental Studies ◽  
Weighted Average ◽  
Filtration Efficiency ◽  
Volume Distribution ◽  
Particle Sizes ◽  
Economic Activities ◽  
Protection Measure ◽  
Source Of Infection

Abstract The severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2) is highly contagious, and the coronavirus disease 2019 (COVID-19) pandemic caused by it has forced many countries to adopt ‘lockdown’ measures to prevent the spread of the epidemic through social isolation of citizens. Some countries proposed universal mask wearing as a protection measure of public health to strengthen national prevention efforts and to limit the wider spread of the epidemic. In order to reveal the epidemic prevention efficacy of masks, this paper systematically evaluates the experimental studies of various masks and filter materials, summarises the general characteristics of the filtration efficiency of isolation masks with particle size, and reveals the actual efficacy of masks by combining the volume distribution characteristics of human exhaled droplets with different particle sizes and the SARS-CoV-2 virus load of nasopharynx and throat swabs from patients. The existing measured data show that the filtration efficiency of all kinds of masks for large particles and extra-large droplets is close to 100%. From the perspective of filtering the total number of pathogens discharged in the environment and protecting vulnerable individuals from breathing live viruses, the mask has a higher protective effect. If considering the weighted average filtration efficiency with different particle sizes, the filtration efficiencies of the N95 mask and the ordinary mask are 99.4% and 98.5%, respectively. The mask can avoid releasing active viruses to the environment from the source of infection, thus maximising the protection of vulnerable individuals by reducing the probability of inhaling a virus. Therefore, if the whole society strictly implements the policy of publicly wearing masks, the risk of large-scale spread of the epidemic can be greatly reduced. Compared with the overall cost of social isolation, limited personal freedoms and forced suspension of economic activities, the inconvenience for citizens caused by wearing masks is perfectly acceptable.

scholarly journals Large-scale transcriptomics to dissect 2 years of the life of a fungal phytopathogen interacting with its host plant

BMC Biology ◽  
2021 ◽  
Vol 19 (1) ◽  
Author(s):  
Elise J. Gay ◽  
Jessica L. Soyer ◽  
Nicolas Lapalu ◽  
Juliette Linglin ◽  
Isabelle Fudal ◽  
...  
Keyword(s):  
Host Plant ◽  
Large Scale ◽  
Field Experiments ◽  
Plant Residues ◽  
Plant Infection ◽  
Effector Genes ◽  
Controlled Conditions ◽  
Niche Adaptation ◽  
Depth Analysis ◽  
Fungal Genes

Abstract Background The fungus Leptosphaeria maculans has an exceptionally long and complex relationship with its host plant, Brassica napus, during which it switches between different lifestyles, including asymptomatic, biotrophic, necrotrophic, and saprotrophic stages. The fungus is also exemplary of “two-speed” genome organisms in the genome of which gene-rich and repeat-rich regions alternate. Except for a few stages of plant infection under controlled conditions, nothing is known about the genes mobilized by the fungus throughout its life cycle, which may last several years in the field. Results We performed RNA-seq on samples corresponding to all stages of the interaction of L. maculans with its host plant, either alive or dead (stem residues after harvest) in controlled conditions or in field experiments under natural inoculum pressure, over periods of time ranging from a few days to months or years. A total of 102 biological samples corresponding to 37 sets of conditions were analyzed. We show here that about 9% of the genes of this fungus are highly expressed during its interactions with its host plant. These genes are distributed into eight well-defined expression clusters, corresponding to specific infection lifestyles or to tissue-specific genes. All expression clusters are enriched in effector genes, and one cluster is specific to the saprophytic lifestyle on plant residues. One cluster, including genes known to be involved in the first phase of asymptomatic fungal growth in leaves, is re-used at each asymptomatic growth stage, regardless of the type of organ infected. The expression of the genes of this cluster is repeatedly turned on and off during infection. Whatever their expression profile, the genes of these clusters are enriched in heterochromatin regions associated with H3K9me3 or H3K27me3 repressive marks. These findings provide support for the hypothesis that part of the fungal genes involved in niche adaptation is located in heterochromatic regions of the genome, conferring an extreme plasticity of expression. Conclusion This work opens up new avenues for plant disease control, by identifying stage-specific effectors that could be used as targets for the identification of novel durable disease resistance genes, or for the in-depth analysis of chromatin remodeling during plant infection, which could be manipulated to interfere with the global expression of effector genes at crucial stages of plant infection.

scholarly journals A modular microfluidic system based on a multilayered configuration to generate large-scale perfusable microvascular networks

2021 ◽  
Vol 7 (1) ◽  
Author(s):  
Tao Yue ◽  
Da Zhao ◽  
Duc T. T. Phan ◽  
Xiaolin Wang ◽  
Joshua Jonghyun Park ◽  
...  
Keyword(s):  
Large Scale ◽  
Circulatory System ◽  
Vertical Direction ◽  
Microfluidic System ◽  
Vital Role ◽  
Microvascular Networks ◽  
Biological Studies ◽  
Wide Range ◽  
High Flexibility

AbstractThe vascular network of the circulatory system plays a vital role in maintaining homeostasis in the human body. In this paper, a novel modular microfluidic system with a vertical two-layered configuration is developed to generate large-scale perfused microvascular networks in vitro. The two-layer polydimethylsiloxane (PDMS) configuration allows the tissue chambers and medium channels not only to be designed and fabricated independently but also to be aligned and bonded accordingly. This method can produce a modular microfluidic system that has high flexibility and scalability to design an integrated platform with multiple perfused vascularized tissues with high densities. The medium channel was designed with a rhombic shape and fabricated to be semiclosed to form a capillary burst valve in the vertical direction, serving as the interface between the medium channels and tissue chambers. Angiogenesis and anastomosis at the vertical interface were successfully achieved by using different combinations of tissue chambers and medium channels. Various large-scale microvascular networks were generated and quantified in terms of vessel length and density. Minimal leakage of the perfused 70-kDa FITC-dextran confirmed the lumenization of the microvascular networks and the formation of tight vertical interconnections between the microvascular networks and medium channels in different structural layers. This platform enables the culturing of interconnected, large-scale perfused vascularized tissue networks with high density and scalability for a wide range of multiorgan-on-a-chip applications, including basic biological studies and drug screening.

scholarly journals On the relation between mini-halos and AGN feedback in clusters of galaxies

2020 ◽  
Vol 499 (2) ◽  
pp. 2934-2958
Author(s):  
A Richard-Laferrière ◽  
J Hlavacek-Larrondo ◽  
R S Nemmen ◽  
C L Rhea ◽  
G B Taylor ◽  
...  
Keyword(s):  
Large Scale ◽  
State Of The Art ◽  
Vital Role ◽  
Clusters Of Galaxies ◽  
Relativistic Jets ◽  
X Ray ◽  
Core Cluster ◽  
Central Galaxy ◽  
Central Regions ◽  
Radio Power

ABSTRACT A variety of large-scale diffuse radio structures have been identified in many clusters with the advent of new state-of-the-art facilities in radio astronomy. Among these diffuse radio structures, radio mini-halos are found in the central regions of cool core clusters. Their origin is still unknown and they are challenging to discover; less than 30 have been published to date. Based on new VLA observations, we confirmed the mini-halo in the massive strong cool core cluster PKS 0745−191 (z = 0.1028) and discovered one in the massive cool core cluster MACS J1447.4+0827 (z = 0.3755). Furthermore, using a detailed analysis of all known mini-halos, we explore the relation between mini-halos and active galactic nucleus (AGN) feedback processes from the central galaxy. We find evidence of strong, previously unknown correlations between mini-halo radio power and X-ray cavity power, and between mini-halo and the central galaxy radio power related to the relativistic jets when spectrally decomposing the AGN radio emission into a component for past outbursts and one for ongoing accretion. Overall, our study indicates that mini-halos are directly connected to the central AGN in clusters, following previous suppositions. We hypothesize that AGN feedback may be one of the dominant mechanisms giving rise to mini-halos by injecting energy into the intra-cluster medium and reaccelerating an old population of particles, while sloshing motion may drive the overall shape of mini-halos inside cold fronts. AGN feedback may therefore not only play a vital role in offsetting cooling in cool core clusters, but may also play a fundamental role in re-energizing non-thermal particles in clusters.

scholarly journals The Sense of Smell and Aging: What We Have Learned From Population Studies

2020 ◽  
Vol 4 (Supplement_1) ◽  
pp. 810-811
Author(s):  
Jayant Pinto
Keyword(s):  
Mental Health ◽  
Older Adults ◽  
Social Life ◽  
Large Scale ◽  
Population Studies ◽  
Vital Role ◽  
Sensory Function ◽  
Physical And Mental Health ◽  
Sense Of Smell ◽  
Health Aging

Abstract Decline of the sense of smell with age causes a marked impact on older adults, markedly reducing quality of life. Olfactory dysfunction impairs nutrition, decreases the ability to experience pleasure, and results in depression, among other burdens. Large-scale population studies have identified impaired olfaction as a key heath indicator that predicts the development of decreased physical and mental health, reduced physical activity, weight loss, mild cognitive impairment and dementia, and mortality itself. These data have been generated via analyses of data from several aging cohorts, including the National Social Life, Health, and Aging Project (NSHAP); the Beaver Dam cohort; the Atherosclerosis Risk in Communities project; the Rush Memory and Aging Project; the Health, Aging, and Body Composition project; the Washington Heights/Inwood Columbia Aging Project; among others. In this presentation, we will review the close connection between olfaction, health, aging, including discussion of insights from these studies. We will also discuss emerging data from NSHAP on the effects of sensory function on cognition, mental health, and social interaction, which demonstrate that sensory function plays a vital role in the lives of older adults. Part of a symposium sponsored by Sensory Health Interest Group.

scholarly journals Whole-genome sequence data suggests environmental adaptation of Ethiopian sheep populations

2021 ◽  
Author(s):  
Pamela Wiener ◽  
Christelle Robert ◽  
Abulgasim Ahbara ◽  
Mazdak Salavati ◽  
Ayele Abebe ◽  
...  
Keyword(s):  
High Altitude ◽  
Environmental Variables ◽  
Large Scale ◽  
Sequence Data ◽  
Strong Association ◽  
Environmental Adaptation ◽  
Whole Genome Sequence ◽  
Single Nucleotide Variants ◽  
High Altitude Adaptation ◽  
Altitude Adaptation

Abstract Great progress has been made over recent years in the identification of selection signatures in the genomes of livestock species. This work has primarily been carried out in commercial breeds for which the dominant selection pressures, are associated with artificial selection. As agriculture and food security are likely to be strongly affected by climate change, a better understanding of environment-imposed selection on agricultural species is warranted. Ethiopia is an ideal setting to investigate environmental adaptation in livestock due to its wide variation in geo-climatic characteristics and the extensive genetic and phenotypic variation of its livestock. Here, we identified over three million single nucleotide variants across 12 Ethiopian sheep populations and applied landscape genomics approaches to investigate the association between these variants and environmental variables. Our results suggest that environmental adaptation for precipitation-related variables is stronger than that related to altitude or temperature, consistent with large-scale meta-analyses of selection pressure across species. The set of genes showing association with environmental variables was enriched for genes highly expressed in human blood and nerve tissues. There was also evidence of enrichment for genes associated with high-altitude adaptation although no strong association was identified with hypoxia-inducible-factor (HIF) genes. One of the strongest altitude-related signals was for a collagen gene, consistent with previous studies of high-altitude adaptation. Several altitude-associated genes also showed evidence of adaptation with temperature, suggesting a relationship between responses to these environmental factors. These results provide a foundation to investigate further the effects of climatic variables on small ruminant populations.

scholarly journals Evaluation of WGS-subtyping methods for epidemiological surveillance of foodborne salmonellosis.

2020 ◽  
Author(s):  
Manal Mohammed ◽  
Salina Thapa
Keyword(s):  
Salmonella Typhimurium ◽  
Multilocus Sequence Typing ◽  
Bacterial Infections ◽  
Outbreak Investigation ◽  
Whole Genome Sequence ◽  
Epidemiological Surveillance ◽  
Whole Genome ◽  
Salmonella Dublin ◽  
Source Of Infection ◽  
Investigation Methods

Abstract Background: Salmonellosis is one of the most common foodborne diseases worldwide. Although human infection by non-typhoidal Salmonella (NTS) enterica subspecies enterica is associated primarily with a self-limiting diarrhoeal illness, invasive bacterial infections (such as septicaemia, bacteraemia and meningitis) were also reported. Human outbreaks of NTS were reported in several countries all over the world including developing as well as high-income countries. Conventional laboratory methods such as pulsed field gel electrophoresis (PFGE) do not display adequate discrimination and have their limitations in epidemiological surveillance. It is therefore very crucial to use accurate, reliable and highly discriminative subtyping methods for epidemiological characterisation and outbreak investigation. Methods: Here, we used different whole genome sequence (WGS)-based subtyping methods for retrospective investigation of two different outbreaks of Salmonella Typhimurium and Salmonella Dublin that occurred in 2013 in UK and Ireland respectively. Results: Single nucleotide polymorphism (SNP)-based cluster analysis of Salmonella Typhimurium genomes revealed well supported clades, that were concordant with epidemiologically defined outbreak and confirmed the source of outbreak is due to consumption of contaminated mayonnaise. SNP-analyses of Salmonella Dublin genomes confirmed the outbreak however the source of infection could not be determined. The core genome multilocus sequence typing (cgMLST) was discriminatory and separated the outbreak strains of Salmonella Dublin from the non-outbreak strains that were concordant with the epidemiological data however cgMLST could neither discriminate between the outbreak and non-outbreak strains of Salmonella Typhimurium nor confirm that contaminated mayonnaise is the source of infection, On the other hand, other WGS-based subtyping methods including multilocus sequence typing (MLST), ribosomal MLST (rMLST), whole genome MLST (wgMLST), clustered regularly interspaced short palindromic repeats (CRISPRs), prophage sequence profiling, antibiotic resistance profile and plasmid typing methods were less discriminatory and could not confirm the source of the outbreak. Conclusions: Foodborne salmonellosis is an important concern for public health therefore, it is crucial to use accurate, reliable and highly discriminative subtyping methods for epidemiological surveillance and outbreak investigation. In this study, we showed that SNP-based analyses do not only have the ability to confirm the occurrence of the outbreak but also to provide definitive evidence of the source of the outbreak in real-time.

scholarly journals Phyletic distribution and diversification of the Phage Shock Protein stress response system in bacteria and archaea

2021 ◽  
Author(s):  
Philipp F. Popp ◽  
Vadim M. Gumerov ◽  
Ekaterina P. Andrianova ◽  
Lisa Bewersdorf ◽  
Thorsten Mascher ◽  
...  
Keyword(s):  
Stress Response ◽  
Large Scale ◽  
Cell Envelope ◽  
Model Organisms ◽  
Microbial World ◽  
Natural Classification ◽  
Response System ◽  
Core Proteins ◽  
Envelope Stress

AbstractThe bacterial cell envelope is an essential structure that protects the cell from environmental threats, while simultaneously serving as communication interface and diffusion barrier. Therefore, maintaining cell envelope integrity is of vital importance for all microorganisms. Not surprisingly, evolution has shaped conserved protection networks that connect stress perception, transmembrane signal transduction and mediation of cellular responses upon cell envelope stress. The phage shock protein (PSP) stress response is one of such conserved protection networks. Most of the knowledge about the Psp response comes from studies in the Gram-negative model bacterium, Escherichia coli where the Psp system consists of several well-defined protein components. Homologous systems were identified in representatives of Proteobacteria, Actinobacteria, and Firmicutes; however, the Psp system distribution in the microbial world remains largely unknown. By carrying out a large-scale, unbiased comparative genomics analysis, we found components of the Psp system in many bacterial and archaeal phyla and demonstrated that the PSP system deviates dramatically from the proteobacterial prototype. Two of its core proteins, PspA and PspC, have been integrated in various (often phylum-specifically) conserved protein networks during evolution. Based on protein sequence and gene neighborhood analyses of pspA and pspC homologs, we built a natural classification system of PSP networks in bacteria and archaea. We performed a comprehensive in vivo protein interaction screen for the PSP network newly identified in the Gram-positive model organism Bacillus subtilis and found a strong interconnected PSP response system, illustrating the validity of our approach. Our study highlights the diversity of PSP organization and function across many bacterial and archaeal phyla and will serve as foundation for future studies of this envelope stress response beyond model organisms.

scholarly journals Estimating Total Factor Productivity and Its Components: Evidence from Major Manufacturing Industries of Pakistan

2008 ◽  
Vol 47 (4II) ◽  
pp. 677-694 ◽  
Author(s):  
Abdul Raheman ◽  
Talat Afza ◽  
Abdul Qayyum ◽  
Mahmood Ahmed Bodla
Keyword(s):  
Textile Industry ◽  
Large Scale ◽  
Manufacturing Sector ◽  
Vital Role ◽  
Fiscal Year ◽  
Cotton Production ◽  
Oil Refineries ◽  
Used Cars ◽  
In The Beginning ◽  
Textile Sector

Manufacturing sector of Pakistan accounts for 19.1 percent of GDP and is the second largest sector of the economy. It grew by 8.4 percent during 2007 as against 10 percent last year. In the manufacturing sector, large scale manufacturing (LSM), plays a vital role and accounts for approximately 70 percent of overall manufacturing [Economic Survey of Pakistan (2006-07)]. During 2006-07 relatively slower pace of expansion exhibits signs of moderation on accounts of higher capacity utilisation, difficulties in the textile sector and lower than expected scale of operations of oil refineries. A number of other factors have also contributed to the low pace of expansion in manufacturing including zero percent growth in raw cotton production which is a critical input for the textile industry, vegetable ghee and cooking oil which comprise about 5.5 percent of the LSM sector, showed uninspiring performance due to unparalleled rise in international palm and soybean oil prices. The performance of the automobile sector has been far less impressive this year as compared to previous five years due to a fall in domestic demand for cars on account of increasing auto financing rates. The higher imports of used cars in the beginning of fiscal year 2006-07 also affected the performance of domestic auto mobile sector.

scholarly journals The large-scale blast score ratio (LS-BSR) pipeline: a method to rapidly compare genetic content between bacterial genomes

2014 ◽  
Author(s):  
Jason W Sahl ◽  
Greg Caporaso ◽  
David A Rasko ◽  
Paul S Keim
Keyword(s):  
Large Scale ◽  
Sequence Data ◽  
Parallel Implementation ◽  
Genetic Relationships ◽  
Clinical Diagnostics ◽  
Whole Genome Sequence ◽  
Bacterial Isolates ◽  
Bacterial Genomes ◽  
E Coli ◽  
Blast Score

Background. As whole genome sequence data from bacterial isolates becomes cheaper to generate, computational methods are needed to correlate sequence data with biological observations. Here we present the large-scale BLAST score ratio (LS-BSR) pipeline, which rapidly compares the genetic content of hundreds to thousands of bacterial genomes, and returns a matrix that describes the relatedness of all coding sequences (CDSs) in all genomes surveyed. This matrix can be easily parsed in order to identify genetic relationships between bacterial genomes. Although pipelines have been published that group peptides by sequence similarity, no other software performs the large-scale, flexible, full-genome comparative analyses carried out by LS-BSR. Results. To demonstrate the utility of the method, the LS-BSR pipeline was tested on 96 Escherichia coli and Shigella genomes; the pipeline ran in 163 minutes using 16 processors, which is a greater than 7-fold speedup compared to using a single processor. The BSR values for each CDS, which indicate a relative level of relatedness, were then mapped to each genome on an independent core genome single nucleotide polymorphism (SNP) based phylogeny. Comparisons were then used to identify clade specific CDS markers and validate the LS-BSR pipeline based on molecular markers that delineate between classical E. coli pathogenic variant (pathovar) designations. Scalability tests demonstrated that the LS-BSR pipeline can process 1,000 E. coli genomes in ~60h using 16 processors. Conclusions. LS-BSR is an open-source, parallel implementation of the BSR algorithm, enabling rapid comparison of the genetic content of large numbers of genomes. The results of the pipeline can be used to identify specific markers between user-defined phylogenetic groups, and to identify the loss and/or acquisition of genetic information between bacterial isolates. Taxa-specific genetic markers can then be translated into clinical diagnostics, or can be used to identify broadly conserved putative therapeutic candidates.

Sign in / Sign up

Export Citation Format

Share Document