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https://www.readbyqxmd.com/read/28935819/identification-of-truncated-form-of-nosp-as-a-transcription-factor-to-regulate-the-biosynthesis-of-nosiheptide
#1
Xuri Wu, Liang Jin, Hong Zhang, Ruinian Tong, Min Ma, Yijun Chen
Nosiheptide (NOS), a typical member of the thiopeptides, possesses strong activities against multidrug-resistant, gram-positive bacterial pathogens. Similar to other thiopeptides, the biosynthetic pathway of NOS belongs to a ribosomally synthesized and posttranslationally modified peptide system. Bioinformatics analysis of the NOS gene cluster suggests that nosP gene encodes a homologous protein of Streptomyces antibiotic regulatory protein (SARP) family. In the present study, the actual initiation codon of nosP was identified by comparison of potential initiation codons GUG and AUG...
September 21, 2017: FASEB Journal: Official Publication of the Federation of American Societies for Experimental Biology
https://www.readbyqxmd.com/read/28931430/global-proteomic-profiling-of-yersinia-ruckeri-strains
#2
Gokhlesh Kumar, Karin Hummel, Timothy J Welch, Ebrahim Razzazi-Fazeli, Mansour El-Matbouli
Yersinia ruckeri is the causative agent of enteric redmouth disease (ERM) of salmonids. There is little information regarding the proteomics of Y. ruckeri. Herein, we perform whole protein identification and quantification of biotype 1 and biotype 2 strains of Y. ruckeri grown under standard culture conditions using a shotgun proteomic approach. Proteins were extracted, digested and peptides were separated by a nano liquid chromatography system and analyzed with a high-resolution hybrid triple quadrupole time of flight mass spectrometer coupled via a nano ESI interface...
September 20, 2017: Veterinary Research
https://www.readbyqxmd.com/read/28924489/identification-of-an-enterovirus-recombinant-with-a-torovirus-like-gene-insertion-during-a-diarrhea-outbreak-in-fattening-pigs
#3
Nádia Conceição-Neto, Sebastiaan Theuns, Tingting Cui, Mark Zeller, Claude Kwe Yinda, Isaura Christiaens, Elisabeth Heylen, Marc Van Ranst, Sebastien Carpentier, Hans J Nauwynck, Jelle Matthijnssens
Diarrhea outbreaks in pig farms have raised major concerns in Europe and USA, as they can lead to dramatic pig losses. During a suspected outbreak in Belgium of porcine epidemic diarrhea virus (PEDV), we performed viral metagenomics to assess other potential viral pathogens. Although PEDV was detected, its low abundance indicated that other viruses were involved in the outbreak. Interestingly, a porcine bocavirus and several enteroviruses were most abundant in the sample. We also observed the presence of a porcine enterovirus genome with a gene insertion, resembling a C28 peptidase gene found in toroviruses, which was confirmed using re-sequencing, bioinformatics, and proteomics approaches...
July 2017: Virus Evolution
https://www.readbyqxmd.com/read/28893639/on-the-application-of-reverse-vaccinology-to-parasitic-diseases-a-perspective-on-feature-selection-and-ranking-of-vaccine-candidates
#4
Stephen J Goodswen, Paul J Kennedy, John T Ellis
Reverse vaccinology has the potential to rapidly advance vaccine development against parasites, but it is unclear which features studied in silico will advance vaccine development. Here we consider Neospora caninum which is a globally distributed protozoan parasite causing significant economic and reproductive loss to cattle industries worldwide. The aim of this study was to use a reverse vaccinology approach to compile a worthy vaccine candidate list for N. caninum, including proteins containing pathogen-associated molecular patterns to act as vaccine carriers...
September 8, 2017: International Journal for Parasitology
https://www.readbyqxmd.com/read/28871248/identification-and-functional-characterization-of-small-alarmone-synthetases-in-corynebacterium-glutamicum
#5
Matthias Ruwe, Jörn Kalinowski, Marcus Persicke
The hyperphosphorylated guanosine derivatives ppGpp and pppGpp represent global regulators of the bacterial stress response, as they act as central elements of the stringent response system. Although it was assumed that both, (p)ppGpp synthesis and hydrolysis, are catalyzed by one bifunctional RSH-protein in the actinobacterial model organism Corynebacterium glutamicum ATCC 13032, two putative short alarmone synthetases (SASs) were identified by bioinformatic analyses. The predicted sequences of both enzymes, designated as RelP(*)Cg and RelSCg, exhibit high similarities to the conserved (p)ppGpp synthetase catalytic domain...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28864458/optimizing-genomic-medicine-in-epilepsy-through-a-gene-customized-approach-to-missense-variant-interpretation
#6
Joshua Traynelis, Michael Silk, Quanli Wang, Samuel F Berkovic, Liping Liu, David B Ascher, David J Balding, Slavé Petrovski
Gene panel and exome sequencing have revealed a high rate of molecular diagnoses among diseases where the genetic architecture has proven suitable for sequencing approaches, with a large number of distinct and highly penetrant causal variants identified among a growing list of disease genes. The challenge is, given the DNA sequence of a new patient, to distinguish disease-causing from benign variants. Large samples of human standing variation data highlight regional variation in the tolerance to missense variation within the protein-coding sequence of genes...
September 1, 2017: Genome Research
https://www.readbyqxmd.com/read/28861920/higher-than-expected-population-prevalence-of-potentially-pathogenic-germline-tp53-variants-in-individuals-unselected-for-cancer-history
#7
Kelvin C de Andrade, Lisa Mirabello, Douglas R Stewart, Eric Karlins, Roelof Koster, Mingyi Wang, Susan M Gapstur, Mia M Gaudet, Neal D Freedman, Maria T Landi, Nathanaël Lemonnier, Pierre Hainaut, Sharon A Savage, Maria I Achatz
Li-Fraumeni syndrome (LFS) is an autosomal dominant cancer disorder associated with pathogenic germline variants in TP53, with a high penetrance over an individual's lifetime. The actual population prevalence of pathogenic germline TP53 mutations is still unclear. The aim of this study was to estimate the prevalence of potentially pathogenic TP53 exonic variants in three data sources, totaling 63,983 unrelated individuals from three sequencing databases. Potential pathogenicity was defined using an original algorithm combining bioinformatic prediction tools, clinical significance evidences, and functional data...
September 1, 2017: Human Mutation
https://www.readbyqxmd.com/read/28861346/identification-of-rare-paired-box-3-variant-in-strabismus-by-whole-exome-sequencing
#8
Hui-Min Gong, Jing Wang, Jing Xu, Zhan-Yu Zhou, Jing-Wen Li, Shu-Fang Chen
AIM: To identify the potentially pathogenic gene variants that contributes to the etiology of strabismus. METHODS: A Chinese pedigree with strabismus was collected and the exomes of two affected individuals were sequenced using the next-generation sequencing technology. The resulting variants from exome sequencing were filtered by subsequent bioinformatics methods and the candidate mutation was verified as heterozygous in the affected proposita and her mother by sanger sequencing...
2017: International Journal of Ophthalmology
https://www.readbyqxmd.com/read/28859442/emerging-multidrug-resistance-in-community-associated-staphylococcus-aureus-involved-in-skin-and-soft-tissue-infections-and-nasal-colonization
#9
Grace C Lee, Steven D Dallas, Yufeng Wang, Randall J Olsen, Kenneth A Lawson, James Wilson, Christopher R Frei
Background: Staphylococcus aureus is a major pathogen causing significant morbidity and mortality worldwide. The emergence of MDR S. aureus strains in the community setting has major implications in disease management. However, data regarding the occurrence and patterns of MDR community-associated S. aureus sub-clones is limited. Objectives: To use whole-genome sequences to describe the diversity and distribution of resistance mechanisms among community-associated S...
September 1, 2017: Journal of Antimicrobial Chemotherapy
https://www.readbyqxmd.com/read/28852470/investigation-of-host-pathogen-interaction-between-burkholderia-pseudomallei-and-autophagy-related-protein-lc3-using-hydrophobic-chromatography-based-technique
#10
Pattamaporn Joompa, Saranyoo Ponnikorn, Sittiruk Roytrakul, Sumalee Tungpradabkul
BACKGROUND: Burkholderia pseudomallei is an intracellular bacteria causing Melioidosis, the disease widely disseminates in Southeast Asia and Northern Australia. B. pseudomallei has ability to invade various types of host cell and to interfere with host defense mechanisms, such as nitric oxide (NO). Due to the cross-talk among alternative killing mechanisms in host immune response against invading microbes, autophagy is the molecular mechanism belonging to intracellular elimination of eukaryotic cells that has been widely discussed...
2017: Cell & Bioscience
https://www.readbyqxmd.com/read/28842611/evidence-based-tailoring-of-bioinformatics-approaches-to-optimize-methods-that-predict-the-effects-of-nonsynonymous-amino-acid-substitutions-in-glucokinase
#11
Daniela Šimčíková, Lucie Kocková, Kateřina Vackářová, Miroslav Těšínský, Petr Heneberg
Computational methods that allow predicting the effects of nonsynonymous substitutions are an integral part of exome studies. Here, we validated and improved their specificity by performing a comprehensive bioinformatics analysis combined with experimental and clinical data on a model of glucokinase (GCK): 8835 putative variations, including 515 disease-associated variations from 1596 families with diagnoses of monogenic diabetes (GCK-MODY) or persistent hyperinsulinemic hypoglycemia of infancy (PHHI), and 126 variations with available or newly reported (19 variations) data on enzyme kinetics...
August 25, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28841402/genome-wide-identification-and-analysis-of-the-basic-leucine-zipper-bzip-transcription-factor-gene-family-in-i-ustilaginoidea-virens-i
#12
Weixiao Yin, Peng Cui, Wei Wei, Yang Lin, Chaoxi Luo
The basic leucine zipper (bZIP) transcription factor (TF) family is one of the largest and most diverse TF families widely distributed across the eukaryotes. The bZIP TF family play important roles in growth, development, and response to abiotic or biotic stresses, which have been well characterized in plants, but not in plant pathogenic fungi. In this study, we performed genome-wide and systematic bioinformatics analysis of bZIP genes in the fungus <i>Ustilaginoidea virens</i>, the causal agent of rice false smut disease...
August 25, 2017: Genome Génome / Conseil National de Recherches Canada
https://www.readbyqxmd.com/read/28822547/bacterial-diversity-in-goat-milk-from-the-guanzhong-area-of-china
#13
Fuxin Zhang, Zhaoxia Wang, Feiyan Lei, Bini Wang, Shuaiming Jiang, Qiannan Peng, Jiachao Zhang, Yuyu Shao
In this study, the V3 and V4 regions of the 16S rRNA gene from metagenomic DNA were sequenced to identify differences in microbial diversity in raw milk of Saanen and Guanzhong goats from the Guanzhong area of China. The results showed that Proteobacteria was the predominant phylum, accounting for 71.31% of all phyla identified in milk from the 2 breeds, and Enterobacter was the predominant genus (24.69%) within the microbial community. Microbial alpha diversity from Saanen goat milk was significantly higher than that of Guanzhong goat milk based on bioinformatic analysis of indices of Chao1, Shannon, Simpson, observed species, and the abundance-based coverage estimator...
August 16, 2017: Journal of Dairy Science
https://www.readbyqxmd.com/read/28814302/ompa-protein-sequence-based-typing-and-virulence-associated-gene-profiles-of-pasteurella-multocida-isolates-associated-with-bovine-haemorrhagic-septicaemia-and-porcine-pneumonic-pasteurellosis-in-thailand
#14
Teerasak E-Kobon, Ratiporn Leeanan, Saengtian Pannoi, Pornchai Anuntasomboon, Pacharee Thongkamkoon, Arinthip Thamchaipenet
BACKGROUND: Pasteurella multocida is a Gram-negative bacterium that causes economically significant infections of a broad range of animal species. Pneumonic and septicaemic pasteurellosis caused by this bacterium remain important problems in pigs, cattle, and water buffaloes in Thailand. The aim of this study was to characterise the virulence-associated gene profiles and to develop an OmpA molecular typing scheme for classifying 191 bovine and porcine isolates of P. multocida collected between 1989 and 2012 in Thailand using polymerase chain reactions (PCRs), nucleotide sequencing, and sequence and structural bioinformatics analyses...
August 16, 2017: BMC Veterinary Research
https://www.readbyqxmd.com/read/28808155/roca-is-an-accessory-protein-to-the-virulence-regulating-covr-s-two-component-system-in-the-group-a-streptococcus
#15
Ira Jain, Eric W Miller, Jessica L Danger, Kathryn J Pflughoeft, Paul Sumby
Regulating gene expression during infection is critical to the ability of pathogens to circumvent the immune response and cause disease. This is true for the group A Streptococcus (GAS), a pathogen that causes both invasive (e.g. necrotizing fasciitis) and non-invasive (e.g. pharyngitis) diseases. The control of virulence (CovR/S) two-component system has a major role in regulating GAS virulence factor expression. The regulator of cov (RocA) protein, which is a predicted kinase, functions in an undetermined manner through CovR/S to alter gene expression and reduce invasive disease virulence...
August 14, 2017: Infection and Immunity
https://www.readbyqxmd.com/read/28790983/nitrate-sensing-and-metabolism-inhibit-biofilm-formation-in-the-opportunistic-pathogen-burkholderia-pseudomallei-by-reducing-the-intracellular-concentration-of-c-di-gmp
#16
Mihnea R Mangalea, Brooke A Plumley, Bradley R Borlee
The opportunistic pathogen Burkholderia pseudomallei is a saprophytic bacterium and the causative agent of melioidosis, an emerging infectious disease associated with high morbidity and mortality. Although melioidosis is most prevalent during the rainy season in endemic areas, domestic gardens and farms can also serve as a reservoir for B. pseudomallei during the dry season, in part due to irrigation and fertilizer use. In the environment, B. pseudomallei forms biofilms and persists in soil near plant root zones...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28780406/novel-mutations-in-the-cdkl5-gene-in-complex-genotypes-associated-with-west-syndrome-with-variable-phenotype-first-description-of-somatic-mosaic-state
#17
Marwa Ben Jdila, Abir Ben Issa, Boudour Khabou, Bochra Ben Rhouma, Fatma Kamoun, Leila Ammar-Keskes, Chahnez Triki, Faiza Fakhfakh
INTRODUCTION: West syndrome is a rare epileptic encephalopathy of early infancy, characterized by epileptic spasms, hypsarrhythmia, and psychomotor retardation beginning in the first year of life. METHODS: The present study reports the clinical, molecular and bioinformatic investigation in the three studied West patients. RESULTS: The results revealed a complex genotype with more than one mutation in each patient including the known mutations c...
October 2017: Clinica Chimica Acta; International Journal of Clinical Chemistry
https://www.readbyqxmd.com/read/28749409/host-response-comparison-of-h1n1-and-h5n1-infected-mice-identifies-two-potential-death-mechanisms
#18
Olivier Leymarie, Léa Meyer, Pierre-Louis Hervé, Bruno Da Costa, Bernard Delmas, Christophe Chevalier, Ronan Le Goffic
Highly pathogenic influenza A viruses (IAV) infections represent a serious threat to humans due to their considerable morbidity and mortality capacities. A good understanding of the molecular mechanisms responsible for the acute lung injury observed during this kind of infection is essential to design adapted therapies. In the current study, using an unbiased transcriptomic approach, we compared the host-responses of mice infected with two different subtypes of IAV: H1N1 vs. H5N1. The host-response comparison demonstrated a clear difference between the transcriptomic profiles of H1N1- and H5N1-infected mice despite identical survival kinetics and similar viral replications...
July 27, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28733845/genome-wide-identification-in-silico-characterization-and-expression-analysis-of-zip-like-genes-from-trichomonas-vaginalis-in-response-to-zinc-and-iron
#19
K G Fernández-Martín, M E Alvarez-Sánchez, V E Arana-Argáez, L C Alvarez-Sánchez, J C Lara-Riegos, J C Torres-Romero
Trace elements such as Zinc and Iron are essential components of metalloproteins and serve as cofactors or structural elements for enzymes involved in several important biological processes in almost all organisms. Because either excess or insufficient levels of Zn and Fe can be harmful for the cells, the homeostatic levels of these trace minerals must be tightly regulated. The Zinc regulated transporter, Iron regulated transporter-like Proteins (ZIP) comprise a diverse family, with several paralogues in diverse organisms and are considered essential for the Zn and Fe uptake and homeostasis...
July 21, 2017: Biometals: An International Journal on the Role of Metal Ions in Biology, Biochemistry, and Medicine
https://www.readbyqxmd.com/read/28719833/in-silico-search-of-inhibitors-of-streptococcus-mutans-for-the-control-of-dental-plaque
#20
Rodrigo Ochoa, María Cecilia Martínez-Pabón, María Adelaida Arismendi-Echeverri, Willer Leandro Rendón-Osorio, Carlos Enrique Muskus-López
Biofilm is an extremely complex microbial community arranged in a matrix of polysaccharides and attached to a substrate. Its development is crucial in the pathophysiology of oral infections like dental caries, as well as in periodontal, pulp, and periapical diseases. Streptococcus mutans is one of the most effective microorganisms in lactic acid production of the dental biofilm. Identifying essential Streptococcus mutans proteins using bioinformatics methods helps to search for alternative therapies. To this end, the bacterial genomes of several Streptococcus mutans strains and representative strains of other cariogenic and non-cariogenic bacteria were analysed by identifying pathogenicity islands and alignments with other bacteria, and by detecting the exclusive genes of cariogenic species in comparison to the non-pathogenic ones...
July 1, 2017: Archives of Oral Biology
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