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bacterial genetics

Mehak Zahoor Khan, Prabhjot Kaur, Vinay Kumar Nandicoori
The emergence of increasingly drug-resistant Mycobacterium tuberculosis strains has become a crucial public health concern. In order to effectively treat tuberculosis, it is imperative to find newer drug targets, which are important for the in vivo bacterial survival and persistence. Phosphorylation based signaling cascades modulated by eukaryotic-like serine/threonine protein kinases and phosphatase in M. tuberculosis, transduce extracellular stimuli to a cellular response ensuing pathogen's growth, persistence and pathogenesis...
June 22, 2018: IUBMB Life
Alec M Judd, Melinda K Matthews, Rachel Hughes, Madeline Veloz, Corinne E Sexton, John M Chaston
Animal-associated microorganisms ('microbiota') dramatically influence nutritional and physiological traits of their hosts. To expand our understanding of such influences, we predicted bacterial genes that influence a quantitative animal trait by a comparative genomic approach and extended these predictions via mutant analysis. We focus on D. melanogaster starvation resistance (SR). We first confirmed that D. melanogaster SR responds to the microbiota by demonstrating that bacteria-free flies have greater SR than flies bearing a standard 5-species microbial community, and extended this analysis by revealing species-specific influence of 38 genome-sequenced bacterial species on D...
June 22, 2018: Applied and Environmental Microbiology
Na Li, Ren-Lei Tong, Li Yao, Qing Chen, Xin Yan, De-Rong Ding, Ji-Guo Qiu, Jian He, Jian-Dong Jiang
The herbicide dicamba is initially demethylated to 3,6-dichlorosalicylate (3,6-DCSA) in Rhizorhabdus dicambivorans Ndbn-20 and is subsequently 5-hydroxylated to 3,6-dichlorogentisate (3,6-DCGA). In the present study, two glutathione-dependent 3,6-DCGA dehalogenases, DsmH1 and DsmH2, were identified in strain Ndbn-20. DsmH2 shared low identity (only 31%) with the tetrachlorohydroquinone (TCHQ) dehalogenase PcpC from Sphingobium chlorophenolicum ATCC 39723, while DsmH1 shared high identity (79%) with PcpC. In the phylogenetic tree of related glutathione S-transferases (GSTs), DsmH1 and DsmH2, together with PcpC and the 2,5-dichlorohydroquinone dehalogenase LinD, formed a separate clade...
June 22, 2018: Applied and Environmental Microbiology
Laura Santamaría, Inés Reverón, Félix López de Felipe, Blanca de Las Rivas, Rosario Muñoz
Ethylphenols are strong odorants produced by microbial activity and described as off-flavours in several foods. Lactobacillus plantarum is a lactic bacterial species able to produce ethylphenols by the reduction of vinylphenols during the metabolism of hydroxycinnamic acids. However, the reductase involved has not been yet uncovered. In this study, the involvement in vinylphenol reduction of a gene encoding a putative reductase ( lp_3125 ) was confirmed by the absence of reduction activity in the Δlp_3125 knockout mutant...
June 22, 2018: Applied and Environmental Microbiology
Filipa F Vale, Philippe Lehours
The review uses the Helicobacter pylori , the gastric bacterium that colonizes the human stomach, to address how to obtain information from bacterial genomes about prophage biology. In a time of continuous growing number of genomes available, this review provides tools to explore genomes for prophage presence, or other mobile genetic elements and virulence factors. The review starts by covering the genetic diversity of H. pylori and then moves to the biologic basis and the bioinformatics approaches used for studding the H...
June 21, 2018: International Journal of Molecular Sciences
Monika Mioduchowska, Michał Jan Czyż, Bartłomiej Gołdyn, Jarosław Kur, Jerzy Sell
The cytochrome c oxidase subunit I (cox1) gene is the main mitochondrial molecular marker playing a pivotal role in phylogenetic research and is a crucial barcode sequence. Folmer's "universal" primers designed to amplify this gene in metazoan invertebrates allowed quick and easy barcode and phylogenetic analysis. On the other hand, the increase in the number of studies on barcoding leads to more frequent publishing of incorrect sequences, due to amplification of non-target taxa, and insufficient analysis of the obtained sequences...
2018: PloS One
Shuyan Wu, Pak-Lam Yu, Dave Wheeler, Steve Flint
OBJECTIVES: The aim of this study was to determine the gene expression associated with the persistence of a Listeria monocytogenes stationary phase population when facing lethal nisin treatment METHODS: RNA Seq analysis was used for gene expression profiling of the persister cells in rich medium (persister TN) compared with untreated cells (non-persister).The results were confirmed using RT PCR. RESULTS: Functional genes associated with the persister populations were identified in multiple systems, such as heat shock related stress response, cell wall synthesis, ATP-binding cassette (ABC) transport system, phosphotransferase system (PTS system), and SOS/DNA repair...
June 19, 2018: Journal of Global Antimicrobial Resistance
Jan-Erik Hoffmann, Dmytro Dziuba, Frank Stein, Carsten Schultz
Mapping of weak and hence transient interactions between low-abundance interacting molecules is still a major challenge in systems biology and protein biochemistry. Therefore, additional system-wide acting tools are needed to determine protein interactomics. Most important are reagents that can be applied at any kind of protein interface and the possibility to enrich cross-linked fragments with high efficiency. In this study, we report the synthesis of a novel noncanonical amino acid that features a diazirine group for ultraviolet cross-linking as well as an alkyne group for labeling by click chemistry...
June 22, 2018: Biochemistry
Cosmika Goswami, Stephen Fox, Matthew Holden, Martin Connor, Alistair Leanord, Thomas J Evans
Bacteraemia caused by Escherichia coli is a growing problem with a significant mortality. The factors that influence the acquisition and outcome of these infections are not clear. Here, we have linked detailed genetic data from the whole-genome sequencing of 162 bacteraemic isolates collected in Scotland, UK, in 2013-2015, with clinical data in order to delineate bacterial and host factors that influence the acquisition in hospital or the community, outcome and antibiotic resistance. We identified four major sequence types (STs) in these isolates: ST131, ST69, ST73 and ST95...
June 22, 2018: Microbial Genomics
Serap Süzük Yildiz, Meltem Yalinay, Tarkan Karakan
Microbiota is a dynamic system showing individual differences in both the number and species of microorganisms. Dietary habits, lifestyle, age, genetic predisposition of the host and use of antibiotics are effective on microbiota. The aim of our research was to carry out a quantitative comparison of Bifidobacterium spp, Bacteroides fragilis, Lactobacillus spp, Akkermansia mucinophilia and Faecalibacterium prausnitzii, important bacterial microbiota species, before and after antibiotic therapy treated with tetracycline and metronidazole in patients who are diagnosed as positive for Helicobacter pylori (HP), and to determine the effects of antibiotic use on the microbiota...
June 1, 2018: Le Infezioni in Medicina
Edson R Rocha, Hector A Bergonia, Svetlana Gerdes, Charles Jeffrey Smith
The intestinal commensal and opportunistic anaerobic pathogen Bacteroides fragilis has an essential requirement for both heme and free iron to support growth in extraintestinal infections. In the absence of free iron, B. fragilis can utilize heme as the sole source of iron. However, the mechanisms to remove iron from heme are not completely understood. In this study, we show that the inner membrane ferrous iron transporter ∆feoAB mutant strain is no longer able to grow with heme as the sole source of iron...
June 21, 2018: MicrobiologyOpen
Lisa M Rogers, Jennifer A Gaddy, Shannon D Manning, David M Aronoff
Background: Group B Streptococcus (GBS) is an encapsulated Gram-positive coccus that is an important cause of infections in adults with chronic medical conditions, pregnant women, and neonates. GBS causes a range of clinical syndromes, from asymptomatic colonization to deep-seated invasive and highly lethal infections. Macrophages are important sentinels of innate immunity, protecting host tissues from infection when bacteria advance beyond cutaneous or mucosal barriers. We hypothesized that the capacity for macrophages to phagocytose unopsonized GBS would vary across distinct clinical strains, and such differences would reflect serotype diversity...
2018: Pathogens & Immunity
S Jiang, J Zeng, X Zhou, Y Li
Growing evidence suggests the existence of new antibiotic resistance mechanisms. Recent studies have revealed that quorum-quenching enzymes, such as MacQ, are involved in both antibiotic resistance and cell-cell communication. Furthermore, some small bacterial regulatory RNAs, classified into RNA attenuators and small RNAs, modulate the expression of resistance genes. For example, small RNA sprX, can shape bacterial resistance to glycopeptide antibiotics via specific downregulation of protein SpoVG. Moreover, some bacterial lipocalins capture antibiotics in the extracellular space, contributing to severe multidrug resistance...
June 1, 2018: Journal of Dental Research
Ge-Ah Kim, Nicholas J Ginga, Shuichi Takayama
The gastrointestinal (GI) tract regulates physiologic responses in complex ways beyond facilitating nutrient entry into the circulatory system. Because of the anatomic location of the GI tract, studying in vivo physiology of the human gut, including host cell interaction with the microbiota, is limited. GI organoids derived from human stem cells are gaining interest as they recapitulate in vivo cellular phenotypes and functions. An underdeveloped capability that would further enhance the utility of these miniature models of the GI tract is to use sensors to quantitatively characterize the organoid systems with high spatiotemporal resolution...
2018: Cellular and Molecular Gastroenterology and Hepatology
Marilou P Sison-Mangus, César M J A Metzger, Dieter Ebert
Host-associated microbiota have been claimed to play a role in hosts' responses to parasitic infections, often protecting the hosts from infection. We tested for such a role in the crustacean Daphnia and the parasitic bacterium Pasteuria ramosa, a widely used model system for host-parasite interactions. We first determined the infection phenotype (i.e., resistotype) of eight clonal D. magna genotypes against four strains of P. ramosa by attachment test, followed by 16 S rDNA amplicon sequencing to determine if their genotype or their parasite resistotype influences the composition of their microbiome...
June 20, 2018: Scientific Reports
Jeong Yoon Lee, Ji Sun Lee, Emma C Materne, Rahul Rajala, Ashrafali M Ismail, Donald Seto, David W Dyer, Jaya Rajaiya, James Chodosh
Adenovirus infections in humans are common and sometimes lethal. Adenovirus-derived vectors are also commonly chosen for gene therapy in human clinical trials. We have shown in previous work that homologous recombination between adenoviral genomes of human adenovirus species D (HAdV-D), the largest and fastest growing HAdV species, is responsible for the rapid evolution of this species. Because adenovirus infection initiates in mucosal epithelia, particularly at the gastrointestinal, respiratory, genitourinary, and ocular surfaces, we sought to determine a possible role for mucosal microbiota in adenovirus genome diversity...
June 27, 2018: MSphere
Edgar Ricardo Vázquez-Martínez, Elizabeth García-Gómez, Ignacio Camacho-Arroyo, Bertha González-Pedrajo
BACKGROUND: Sex differences are important epidemiological factors that impact in the frequency and severity of infectious diseases. A clear sexual dimorphism in bacterial infections has been reported in both humans and animal models. Nevertheless, the molecular mechanisms involved in this gender bias are just starting to be elucidated. In the present article, we aim to review the available data in the literature that report bacterial infections presenting a clear sexual dimorphism, without considering behavioral and social factors...
June 20, 2018: Biology of Sex Differences
R A Squires
Bacteriophages (or phages) are naturally-occurring viruses that can infect and kill bacteria. They are remarkably diverse, numerous and widespread. Each phage has a narrow host range yet a large majority of bacteria studied so far play host to bacteriophages, hence the remarkable phage diversity. Phages were discovered just over 100 years ago and they have been used for treatment of bacterial infections in humans and other animals since the 1920s. They have also been studied intensively and this has led to, and continues to lead to, major insights in the fields of molecular biology and recombinant DNA technology, including that DNA is the genetic material, nucleotides are arranged in triplets to make codons, and messenger RNA is needed for protein synthesis...
June 20, 2018: New Zealand Veterinary Journal
Michael B Burns, Emmanuel Montassier, Juan Abrahante, Sambhawa Priya, David E Niccum, Alexander Khoruts, Timothy K Starr, Dan Knights, Ran Blekhman
Variation in the gut microbiome has been linked to colorectal cancer (CRC), as well as to host genetic variation. However, we do not know whether, in addition to baseline host genetics, somatic mutational profiles in CRC tumors interact with the surrounding tumor microbiome, and if so, whether these changes can be used to understand microbe-host interactions with potential functional biological relevance. Here, we characterized the association between CRC microbial communities and tumor mutations using microbiome profiling and whole-exome sequencing in 44 pairs of tumors and matched normal tissues...
June 20, 2018: PLoS Genetics
Joanna Żur, Artur Piński, Ariel Marchlewicz, Katarzyna Hupert-Kocurek, Danuta Wojcieszyńska, Urszula Guzik
Currently, analgesics and nonsteroidal anti-inflammatory drugs (NSAIDs) are classified as one of the most emerging group of xenobiotics and have been detected in various natural matrices. Among them, monocyclic paracetamol and ibuprofen, widely used to treat mild and moderate pain are the most popular. Since long-term adverse effects of these xenobiotics and their biological and pharmacokinetic activity especially at environmentally relevant concentrations are better understood, degradation of such contaminants has become a major concern...
June 19, 2018: Environmental Science and Pollution Research International
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