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Bacteria evolution

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https://www.readbyqxmd.com/read/28335406/factors-that-negatively-affect-the-prognosis-of-pediatric-community-acquired-pneumonia-in-district-hospital-in-tanzania
#1
Serena Caggiano, Nicola Ullmann, Elisa De Vitis, Marzia Trivelli, Chiara Mariani, Maria Podagrosi, Fabiana Ursitti, Chiara Bertolaso, Carolina Putotto, Marta Unolt, Andrea Pietravalle, Paola Pansa, Kajoro Mphayokulela, Maria Incoronata Lemmo, Michael Mkwambe, Joseph Kazaura, Marzia Duse, Francesco Nieddu, Chiara Azzari, Renato Cutrera
Community-acquired pneumonia (CAP) is still the most important cause of death in countries with scarce resources. All children (33 months ± 35 DS) discharged from the Pediatric Unit of Itigi Hospital, Tanzania, with a diagnosis of CAP from August 2014 to April 2015 were enrolled. Clinical data were gathered. Dried blood spot (DBS) samples for quantitative real-time polymerase chain reaction (PCR) for bacterial detection were collected in all 100 children included. Twenty-four percent of patients were identified with severe CAP and 11% died...
March 13, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28333307/formation-physiology-ecology-evolution-and-clinical-importance-of-bacterial-persisters
#2
Bram Van den Bergh, Maarten Fauvart, Jan Michiels
Persisters are transiently tolerant variants that allow populations to avoid eradication by antibiotic treatment. Their antibiotic tolerance is non-genetic, not inheritable and results from a phenotypic switch from the normal, sensitive cell type to the tolerant, persister state. Here we give a comprehensive overview on bacterial persistence. We first define persistence, summarize the various aspects of persister physiology and show their heterogeneous nature. We then focus on the role of key cellular processes and mechanisms controlling the formation of a subpopulation of tolerant cells...
February 15, 2017: FEMS Microbiology Reviews
https://www.readbyqxmd.com/read/28331600/bacterial-cell-to-cell-signaling-promotes-the-evolution-of-resistance-to-parasitic-bacteriophages
#3
Pierre Moreau, Stephen P Diggle, Ville-Petri Friman
The evolution of host-parasite interactions could be affected by intraspecies variation between different host and parasite genotypes. Here we studied how bacterial host cell-to-cell signaling affects the interaction with parasites using two bacteria-specific viruses (bacteriophages) and the host bacterium Pseudomonas aeruginosa that communicates by secreting and responding to quorum sensing (QS) signal molecules. We found that a QS-signaling proficient strain was able to evolve higher levels of resistance to phages during a short-term selection experiment...
March 2017: Ecology and Evolution
https://www.readbyqxmd.com/read/28330987/architecture-and-mechanism-of-the-central-gear-in-an-ancient-molecular-timer
#4
REVIEW
Martin Egli
Molecular clocks are the product of natural selection in organisms from bacteria to human and their appearance early in evolution such as in the prokaryotic cyanobacterium Synechococcus elongatus suggests that these timers served a crucial role in genetic fitness. Thus, a clock allows cyanobacteria relying on photosynthesis and nitrogen fixation to temporally space the two processes and avoid exposure of nitrogenase carrying out fixation to high levels of oxygen produced during photosynthesis. Fascinating properties of molecular clocks are the long time constant, their precision and temperature compensation...
March 2017: Journal of the Royal Society, Interface
https://www.readbyqxmd.com/read/28330764/lipid-sugar-carriers-at-the-extremes-the-phosphodolichols-archaea-use-in-n-glycosylation
#5
REVIEW
Jerry Eichler, Ziqiang Guan
N-glycosylation, a post-translational modification whereby glycans are covalently linked to select Asn residues of target proteins, occurs in all three domains of life. Across evolution, the N-linked glycans are initially assembled on phosphorylated cytoplasmically-oriented polyisoprenoids, with polyprenol (mainly C55 undecaprenol) fulfilling this role in Bacteria and dolichol assuming this function in Eukarya and Archaea. The eukaryal and archaeal versions of dolichol can, however, be distinguished on the basis of their length, degree of saturation and by other traits...
March 18, 2017: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/28327641/sequential-displacement-of-type-vi-secretion-system-effector-genes-leads-to-evolution-of-diverse-immunity-gene-arrays-in-vibrio-cholerae
#6
Paul C Kirchberger, Daniel Unterweger, Daniele Provenzano, Stefan Pukatzki, Yan Boucher
Type VI secretion systems (T6SS) enable bacteria to engage neighboring cells in contact-dependent competition. In Vibrio cholerae, three chromosomal clusters each encode a pair of effector and immunity genes downstream of those encoding the T6SS structural machinery for effector delivery. Different combinations of effector-immunity proteins lead to competition between strains of V. cholerae, which are thought to be protected only from the toxicity of their own effectors. Screening of all publically available V...
March 22, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28326078/inside-out-archaeal-ectosymbionts-suggest-a-second-model-of-reduced-genome-evolution
#7
REVIEW
Trevor Nicks, Lilah Rahn-Lee
Reduced-genome symbionts and their organelle counterparts, which have even smaller genomes, are essential to the lives of many organisms. But how and why have these genomes become so small? Endosymbiotic genome reduction is a product of isolation within the host, followed by massive pseudogenization and gene loss often including DNA repair mechanisms. This phenomenon can be observed in insect endosymbionts such as the bacteria Carsonella ruddii and Buchnera aphidicola. Yet endosymbionts are not the only organisms with reduced genomes...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28325372/is-predominant-clonal-evolution-a-common-evolutionary-adaptation-to-parasitism-in-pathogenic-parasitic-protozoa-fungi-bacteria-and-viruses
#8
M Tibayrenc, F J Ayala
We propose that predominant clonal evolution (PCE) in microbial pathogens be defined as restrained recombination on an evolutionary scale, with genetic exchange scarce enough to not break the prevalent pattern of clonal population structure. The main features of PCE are (1) strong linkage disequilibrium, (2) the widespread occurrence of stable genetic clusters blurred by occasional bouts of genetic exchange ('near-clades'), (3) the existence of a "clonality threshold", beyond which recombination is efficiently countered by PCE, and near-clades irreversibly diverge...
2017: Advances in Parasitology
https://www.readbyqxmd.com/read/28323281/chance-and-necessity-in-the-genome-evolution-of-endosymbiotic-bacteria-of-insects
#9
Beatriz Sabater-Muñoz, Christina Toft, David Alvarez-Ponce, Mario A Fares
An open question in evolutionary biology is how does the selection-drift balance determine the fates of biological interactions. We searched for signatures of selection and drift in genomes of five endosymbiotic bacterial groups known to evolve under strong genetic drift. Although most genes in endosymbiotic bacteria showed evidence of relaxed purifying selection, many genes in these bacteria exhibited stronger selective constraints than their orthologs in free-living bacterial relatives. Remarkably, most of these highly constrained genes had no role in the host-symbiont interactions but were involved in either buffering the deleterious consequences of drift or other host-unrelated functions, suggesting that they have either acquired new roles or their role became more central in endosymbiotic bacteria...
March 21, 2017: ISME Journal
https://www.readbyqxmd.com/read/28321528/silver-nanoparticles-against-salmonella-enterica-serotype-typhimurium-role-of-inner-membrane-dysfunction
#10
Minju Seong, Dong Gun Lee
The evolution of antibiotics-resistant bacteria is considered a major concern. To explore promising antibacterial materials and clarify their unknown mechanisms, the mode of action of silver nanoparticles (AgNPs) against Salmonella enterica serotype typhimurium was investigated. We investigated the effect of AgNPs on the bacterial membrane. The N-phenyl-1-naphthylamine assay showed that the permeability of the outer membrane was not changed by treatment with AgNPs. The O-nitrophenyl-β-D-galactopyranoside assay showed that the inner membrane permeability increased as AgNPs concentration increased...
March 21, 2017: Current Microbiology
https://www.readbyqxmd.com/read/28321417/technologies-for-proteome-wide-discovery-of-extracellular-host-pathogen-interactions
#11
REVIEW
Nadia Martinez-Martin
Pathogens have evolved unique mechanisms to breach the cell surface barrier and manipulate the host immune response to establish a productive infection. Proteins exposed to the extracellular environment, both cell surface-expressed receptors and secreted proteins, are essential targets for initial invasion and play key roles in pathogen recognition and subsequent immunoregulatory processes. The identification of the host and pathogen extracellular molecules and their interaction networks is fundamental to understanding tissue tropism and pathogenesis and to inform the development of therapeutic strategies...
2017: Journal of Immunology Research
https://www.readbyqxmd.com/read/28318058/nuclear-codon-reassignments-in-the-genomics-era-and-mechanisms-behind-their-evolution
#12
REVIEW
Martin Kollmar, Stefanie Mühlhausen
The canonical genetic code ubiquitously translates nucleotide into peptide sequence with several alterations known in viruses, bacteria, mitochondria, plastids, and single-celled eukaryotes. A new hypothesis to explain genetic code changes, termed tRNA loss driven codon reassignment, has been proposed recently when the polyphyly of the yeast codon reassignment events has been uncovered. According to this hypothesis, the driving force for genetic code changes are tRNA or translation termination factor loss-of-function mutations or loss-of-gene events...
March 20, 2017: BioEssays: News and Reviews in Molecular, Cellular and Developmental Biology
https://www.readbyqxmd.com/read/28316961/acute-delayed-or-late-infection-of-revision-total-hip-arthroplasty-treated-with-debridement-antibiotic-loaded-cement-beads-and-retention-of-the-prosthesis
#13
Jun-Dong Chang, In-Sung Kim, Sang-Soo Lee, Je-Hyun Yoo
PURPOSE: The treatment of infected revision total hip arthroplasty (THA) is very challenging due to retained revision prosthesis, poor bone stock and soft tissue condition derived from previous revision surgeries, and comorbidities. The purpose of this study was to investigate the effectiveness and short-term outcomes of aggressive debridement and use of antibiotic-loaded cement beads with retention of the prosthesis for acute delayed or late infection of revision THAs. MATERIALS AND METHODS: Ten consecutive patients with symptoms or signs of less than one-week evolution and well-fixed prostheses, were treated with this procedure and a postoperative course of organism-specific antibiotics for a minimum of 6 weeks...
March 2017: Hip & Pelvis
https://www.readbyqxmd.com/read/28316597/insights-of-phage-host-interaction-in-hypersaline-ecosystem-through-metagenomics-analyses
#14
Amir Mohaghegh Motlagh, Ananda S Bhattacharjee, Felipe H Coutinho, Bas E Dutilh, Sherwood R Casjens, Ramesh K Goel
Bacteriophages, as the most abundant biological entities on Earth, place significant predation pressure on their hosts. This pressure plays a critical role in the evolution, diversity, and abundance of bacteria. In addition, phages modulate the genetic diversity of prokaryotic communities through the transfer of auxiliary metabolic genes. Various studies have been conducted in diverse ecosystems to understand phage-host interactions and their effects on prokaryote metabolism and community composition. However, hypersaline environments remain among the least studied ecosystems and the interaction between the phages and prokaryotes in these habitats is poorly understood...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28303404/phylogenetic-analysis-of-proteins-involved-in-the-stringent-response-in-plant-cells
#15
Doshun Ito, Yuta Ihara, Hidenori Nishihara, Shinji Masuda
The nucleotide (p)ppGpp is a second messenger that controls the stringent response in bacteria. The stringent response modifies expression of a large number of genes and metabolic processes and allows bacteria to survive under fluctuating environmental conditions. Recent genome sequencing analyses have revealed that genes responsible for the stringent response are also found in plants. These include (p)ppGpp synthases and hydrolases, RelA/SpoT homologs (RSHs), and the pppGpp-specific phosphatase GppA/Ppx. However, phylogenetic relationship between enzymes involved in bacterial and plant stringent responses is as yet generally unclear...
March 16, 2017: Journal of Plant Research
https://www.readbyqxmd.com/read/28298351/community-analysis-of-microbial-sharing-and-specialization-in-a-costa-rican-ant-plant-hemipteran-symbiosis
#16
Elizabeth G Pringle, Corrie S Moreau
Ants have long been renowned for their intimate mutualisms with trophobionts and plants and more recently appreciated for their widespread and diverse interactions with microbes. An open question in symbiosis research is the extent to which environmental influence, including the exchange of microbes between interacting macroorganisms, affects the composition and function of symbiotic microbial communities. Here we approached this question by investigating symbiosis within symbiosis. Ant-plant-hemipteran symbioses are hallmarks of tropical ecosystems that produce persistent close contact among the macroorganism partners, which then have substantial opportunity to exchange symbiotic microbes...
March 15, 2017: Proceedings. Biological Sciences
https://www.readbyqxmd.com/read/28298180/bacterial-protein-meta-interactomes-predict-cross-species-interactions-and-protein-function
#17
J Harry Caufield, Christopher Wimble, Semarjit Shary, Stefan Wuchty, Peter Uetz
BACKGROUND: Protein-protein interactions (PPIs) can offer compelling evidence for protein function, especially when viewed in the context of proteome-wide interactomes. Bacteria have been popular subjects of interactome studies: more than six different bacterial species have been the subjects of comprehensive interactome studies while several more have had substantial segments of their proteomes screened for interactions. The protein interactomes of several bacterial species have been completed, including several from prominent human pathogens...
March 16, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28294933/differences-in-sheep-and-goats-milk-microbiological-profile-between-conventional-and-organic-farming-systems-in-greece
#18
Eleni Malissiova, Theofilos Papadopoulos, Aikaterini Kyriazi, Maria Mparda, Christina Sakorafa, Antonios Katsioulis, Anna Katsiaflaka, Maria Kyritsi, Antonios Zdragas, Christos Hadjichristodoulou
The aim of this study was to examine differences in the microbiological profile and antimicrobial resistance of bacteria isolated from milk from organic and conventional sheep and goat farms. Twenty-five organic and 25 conventional sheep and goat farms in the region of Thessaly, Greece participated in this study. A standardised detailed questionnaire was used to describe farming practices. A total of 50 samples were collected and analysed for total viable count (TVC), total coliform count (TCC) and somatic cell count (SCC), while Staphylococcus aureus and Escherichia coli were isolated using standard methods...
March 15, 2017: Journal of Dairy Research
https://www.readbyqxmd.com/read/28294218/-13-c-labeling-the-carbon-fixation-pathway-of-a-highly-efficient-artificial-photosynthetic-system
#19
Chong Liu, Shannon N Nangle, Brendan C Colón, Pamela A Silver, Daniel G Nocera
Interfacing the CO2-fixing microorganism, Ralstonia eutropha, to the energy derived from hydrogen produced by water splitting is a viable approach to achieving renewable CO2 reduction at high efficiencies. We employ (13)C-labeling to report on the nature of CO2 reduction in the inorganic water splitting|R. eutropha hybrid system. Accumulated biomass in a reactor under a (13)C-enriched CO2 atmosphere may be sampled at different time points during CO2 reduction. Converting the sampled biomass into gaseous CO2 allows the (13)C/(12)C ratio to be determined by gas chromatography-mass spectrometry...
March 15, 2017: Faraday Discussions
https://www.readbyqxmd.com/read/28293682/genome-sequence-of-the-thermotolerant-foodborne-pathogen-salmonella-enterica-serovar-senftenberg-atcc-43845-and-phylogenetic-analysis-of-loci-encoding-increased-protein-quality-control-mechanisms
#20
Scott V Nguyen, Gregory P Harhay, James L Bono, Timothy P L Smith, Dayna M Harhay
Salmonella enterica subsp. enterica bacteria are important foodborne pathogens with major economic impact. Some isolates exhibit increased heat tolerance, a concern for food safety. Analysis of a finished-quality genome sequence of an isolate commonly used in heat resistance studies, S. enterica subsp. enterica serovar Senftenberg 775W (ATCC 43845), demonstrated an interesting observation that this strain contains not just one, but two horizontally acquired thermotolerance locus homologs. These two loci reside on a large 341...
January 2017: MSystems
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