scholarly journals Occurrence and diversity of CRISPRs in Laribacter hongkongensis isolates from animals, environment and diarrhea patients in southern China

2019 ◽  
Author(s):  
Li Wang ◽  
Ling Wang ◽  
Zhihua Liu ◽  
Huijie Guo ◽  
Youzhao Liu ◽  
...  
Keyword(s):  
Functional Unit ◽  
Southern China ◽  
Biological Functions ◽  
Genetic Barrier ◽  
Laribacter Hongkongensis ◽  
Cas Genes ◽  
Chromosomal Sequences ◽  
Epidemiological Characteristics ◽  
Different Levels ◽  
Cas Proteins

Abstract Background Clustered regularly interspaced short palindromic repeats (CRISPRs) and CRISPR-associated (Cas) proteins are functional elements of archaea and bacteria, and they form the genetic barrier that reduces the transformation of horizontal genes by an unknown mechanism. Results we searched for CRISPRs in 118 Laribacter hongkongensis strains isolated from patients, animals, and water reservoirs. Two CRISPR loci, designated CRISPR4.1 and CRISPR4.2, were identified in L. hongkongensis strains. A CRISPR4.1/cas system was detected in 91.5% (108/118) of the isolates and belonged to the I-F/Ypest subtype of CRISPR/cas systems, while the remaining ten strains only possessed cas genes without the CRISPR4.1 array. The CRISPR4.2 locus was an orphan locus and existed in 72.0% (85/118) L. hongkongensis strains. Meanwhile, a total of 2562 spacers and 980 unique spacers, arranged in 77 alleles, were found, including 1613 (579 unique, 40 alleles) for CRISPR4.1 and 949 (401 unique, 37 alleles) for CRISPR4.2. The results showed that limited spacers had matches in the plasmid (34), phage (19) and bacteria chromosomal sequences (4) from GenBank databases. Consequently, we found the diversity and activity of CRISPRs from human and frog isolates were closer and higher, respectively, than those of the fish isolates. Conclusions CRISPR4.1 and CRISPR4.2 exist extensively in L. hongkongensis and belong to the I-F/Ypest subtype. Our results indicate that the CRISPR4.1/cas system is a functional unit, and CRISPR4.2 is perhaps a degenerated and nonfunctional locus. Considering that the CRISPR4.1 locus is relatively active, diverse, and conserved at different levels, the biological functions, types, and epidemiological characteristics of CRISPR loci may be worth studying.

scholarly journals A Decade of Mighty Lipophagy: What We Know and What Facts We Need to Know?

2021 ◽  
Vol 2021 ◽  
pp. 1-18
Author(s):  
Muhammad Babar Khawar ◽  
Muddasir Hassan Abbasi ◽  
Mussarat Rafiq ◽  
Naila Naz ◽  
Rabia Mehmood ◽  
...  
Keyword(s):  
Cell Death ◽  
Lipid Droplets ◽  
Lysosomal Enzymes ◽  
Lipid Homeostasis ◽  
Cellular Lipid ◽  
Biological Functions ◽  
Lysosomal Function ◽  
Selective Autophagy ◽  
Cellular Components ◽  
Different Levels

Lipids are integral cellular components that act as substrates for energy provision, signaling molecules, and essential constituents of biological membranes along with a variety of other biological functions. Despite their significance, lipid accumulation may result in lipotoxicity, impair autophagy, and lysosomal function that may lead to certain diseases and metabolic syndromes like obesity and even cell death. Therefore, these lipids are continuously recycled and redistributed by the process of selective autophagy specifically termed as lipophagy. This selective form of autophagy employs lysosomes for the maintenance of cellular lipid homeostasis. In this review, we have reviewed the current literature about how lipid droplets (LDs) are recruited towards lysosomes, cross-talk between a variety of autophagy receptors present on LD surface and lysosomes, and lipid hydrolysis by lysosomal enzymes. In addition to it, we have tried to answer most of the possible questions related to lipophagy regulation at different levels. Moreover, in the last part of this review, we have discussed some of the pathological states due to the accumulation of these LDs and their possible treatments under the light of currently available findings.

scholarly journals CasCollect: targeted assembly of CRISPR-associated operons from high-throughput sequencing data

2020 ◽  
Vol 2 (3) ◽  
Author(s):  
Joshua D Podlevsky ◽  
Corey M Hudson ◽  
Jerilyn A Timlin ◽  
Kelly P Williams
Keyword(s):  
High Throughput Sequencing ◽  
Markov Models ◽  
Adaptive Immune System ◽  
Metagenomic Data ◽  
Sequencing Data ◽  
Bacteriophage Therapy ◽  
High Throughput Sequencing Data ◽  
Assembly Pipeline ◽  
Cas Genes ◽  
Cas Proteins

Abstract CRISPR arrays and CRISPR-associated (Cas) proteins comprise a widespread adaptive immune system in bacteria and archaea. These systems function as a defense against exogenous parasitic mobile genetic elements that include bacteriophages, plasmids and foreign nucleic acids. With the continuous spread of antibiotic resistance, knowledge of pathogen susceptibility to bacteriophage therapy is becoming more critical. Additionally, gene-editing applications would benefit from the discovery of new cas genes with favorable properties. While next-generation sequencing has produced staggering quantities of data, transitioning from raw sequencing reads to the identification of CRISPR/Cas systems has remained challenging. This is especially true for metagenomic data, which has the highest potential for identifying novel cas genes. We report a comprehensive computational pipeline, CasCollect, for the targeted assembly and annotation of cas genes and CRISPR arrays—even isolated arrays—from raw sequencing reads. Benchmarking our targeted assembly pipeline demonstrates significantly improved timing by almost two orders of magnitude compared with conventional assembly and annotation, while retaining the ability to detect CRISPR arrays and cas genes. CasCollect is a highly versatile pipeline and can be used for targeted assembly of any specialty gene set, reconfigurable for user provided Hidden Markov Models and/or reference nucleotide sequences.

scholarly journals In silico comparative analysis of crispr-cas system structures of Yersinia pseudotuberculosis causing different clinical manifestations of pseudotuberculosis

2019 ◽  
Vol 11 (2) ◽  
pp. 80-87
Author(s):  
N. P. Peretolchina ◽  
Yu. P. Dzhioev ◽  
A. Yu. Borisenko ◽  
L. A. Stepanenko ◽  
E. A. Voskresenskaya ◽  
...  
Keyword(s):  
Comparative Analysis ◽  
Yersinia Pseudotuberculosis ◽  
Protein Structures ◽  
Clinical Manifestations ◽  
Systemic Infection ◽  
Complete Genomes ◽  
Nucleotide Database ◽  
Cas Genes ◽  
Species Variability ◽  
Cas Proteins

The aim of this research was to analyze and compare CRIPSR loci and cas-proteins of Yersinia pseudotuberculosis strains isolated in different territories from patients with various clinical manifestations of pseudotuberculosis.Materials and Methods. Complete genomes of Y. pseudotuberculosis IP329353 (NC_006155) and IP31758 (NC_009708) were obtained from NCBI Nucleotide Database. Strains were isolated from patients with gastroenteritis and systemic infection respectively. Search, identification, and analysis of CRISPR systems were carried out by onlinetools CRISPROne, CRISPRDetect, and CRISPRTarget.Results. Analyzed strains have CRISPR-Cas systems that include one set of cas-genes and arrays situated at the long distances from each other. We defined three CRISPR arrays in Y. pseudotuberculosis IP32953: array YP1 located near cas-genes, arrays YP2 and YP3. CRISPR-Cas system of Y. pseudotuberculosis IP31758 includes two arrays – YP1 and YP3. CRISPR systems do not share similar spacers.Conclusion. CRISPR systems of the analyzed strains differ in CRISPR loci and cas-protein structures that can be used as specific molecular marks of analyzed strains during the study of intra-species variability and evolution of Y. pseudotuberculosis.

scholarly journals Contact network analysis of Covid-19 in tourist areas——Based on 333 confirmed cases in China

PLoS ONE ◽  
2021 ◽  
Vol 16 (12) ◽  
pp. e0261335
Author(s):  
Zhangbo Yang ◽  
Jingen Song ◽  
Shanxing Gao ◽  
Hui Wang ◽  
Yingfei Du ◽  
...  
Keyword(s):  
Network Analysis ◽  
Network Structure ◽  
Southern China ◽  
Virus Transmission ◽  
Dynamic Contact ◽  
Contact Network ◽  
Degree Centrality ◽  
Imported Cases ◽  
Epidemiological Characteristics ◽  
Human Networks

The spread of infectious diseases is highly related to the structure of human networks. Analyzing the contact network of patients can help clarify the path of virus transmission. Based on confirmed cases of COVID-19 in two major tourist provinces in southern China (Hainan and Yunnan), this study analyzed the epidemiological characteristics and dynamic contact network structure of patients in these two places. Results show that: (1) There are more female patients than males in these two districts and most are imported cases, with an average age of 45 years. Medical measures were given in less than 3 days after symptoms appeared. (2) The whole contact network of the two areas is disconnected. There are a small number of transmission chains in the network. The average values of degree centrality, betweenness centrality, and PageRank index are small. Few patients have a relatively high contact number. There is no superspreader in the network.

scholarly journals Epidemiological characteristics of asymptomatic Norovirus infection in a population from oyster (Ostrea rivularis Gould) farms in southern China

2018 ◽  
Vol 146 (15) ◽  
pp. 1955-1964 ◽  
Author(s):  
Anna Wang ◽  
Qiong Huang ◽  
Lin Qin ◽  
Xianwu Zhong ◽  
Hui Li ◽  
...  
Keyword(s):  
Infection Rate ◽  
Southern China ◽  
Early Stage ◽  
Quantitative Polymerase Chain Reaction ◽  
Asymptomatic Infection ◽  
Time Period ◽  
New Variant ◽  
Oyster Farm ◽  
Stool Samples ◽  
Epidemiological Characteristics

AbstractThe following paper investigates the prevalence and characteristics of asymptomatic norovirus infection in the population living around oyster farm sites. Two consecutive surveys were conducted from January 2014 to December 2014 and 4549 stool samples were screened during the same time period. The total asymptomatic infection rate was 4.04% (184/4549). Norovirus infection rate was 5.20% in oyster farming population which was significantly higher compared with non-farming population where the infection rate was 3.65% (χ2 = 5.49, P < 0.05). A total of 184 NoV positive samples were identified by real time-quantitative polymerase chain reaction (RT-qPCR) and semi-nested RT-PCR and 136 sequences were obtained. The sequences were clustered into 14 genotypes. GI strains were clustered into six genotypes, including GI.2, GI.3, GI.5, GI.6, GI.8 and GI.9; while GII strains were clustered into GII.2, GII.3, GII.4, GII.5, GII.6, GII.8 and GII.13. GI.9 and GII.17 were the predominant and most prevalent genotypes, respectively. The GII.17 genotype replaced GII.4 becoming the dominant genotype in the oyster farming area in 2014. To sum up, long-term monitoring of asymptomatic infection is crucial for the detection of new variant strains and for identifying outbreaks during the early stage.

scholarly journals Hemoglobinopathy: Molecular Epidemiological Characteristics and Health Effects on Hakka People in the Meizhou Region, Southern China

PLoS ONE ◽  
2013 ◽  
Vol 8 (2) ◽  
pp. e55024 ◽  
Author(s):  
Min Lin ◽  
Ying-Fang Wen ◽  
Jiao-Ren Wu ◽  
Qian Wang ◽  
Lei Zheng ◽  
...  
Keyword(s):  
Health Effects ◽  
Southern China ◽  
Epidemiological Characteristics
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