| report on the fifth international conference on natural products for health and beauty (natpro 5) held in thailand, 6-8th may, 2014. | | 2014 | 25310253 |
| tmrdb (tmrna database). | maintained at the university of texas health science center at tyler, texas, the tmrna database (tmrdb) is accessible at the url http://psyche.uthct.edu/dbs/tmrdb/tmrdb.html with mirror sites located at auburn university, auburn, alabama (http://www.ag.auburn.edu/mirror/tmrdb/) and the bioinformatics research center, aarhus, denmark (http://www.bioinf.au.dk/tmrdb/). the tmrdb collects and distributes information relevant to the study of tmrna. in trans-translation, this molecule combines propert ... | 2003 | 12520048 |
| the 2-hydroxycarboxylate transporter family: physiology, structure, and mechanism. | the 2-hydroxycarboxylate transporter family is a family of secondary transporters found exclusively in the bacterial kingdom. they function in the metabolism of the di- and tricarboxylates malate and citrate, mostly in fermentative pathways involving decarboxylation of malate or oxaloacetate. these pathways are found in the class bacillales of the low-cg gram-positive bacteria and in the gamma subdivision of the proteobacteria. the pathways have evolved into a remarkable diversity in terms of th ... | 2005 | 16339740 |
| a computational method to predict genetically encoded rare amino acids in proteins. | in several natural settings, the standard genetic code is expanded to incorporate two additional amino acids with distinct functionality, selenocysteine and pyrrolysine. these rare amino acids can be overlooked inadvertently, however, as they arise by recoding at certain stop codons. we report a method for such recoding prediction from genomic data, using read-through similarity evaluation. a survey across a set of microbial genomes identifies almost all the known cases as well as a number of no ... | 2005 | 16168086 |
| structural classification of bacterial response regulators: diversity of output domains and domain combinations. | chey-like phosphoacceptor (or receiver [rec]) domain is a common module in a variety of response regulators of the bacterial signal transduction systems. in this work, 4,610 response regulators, encoded in complete genomes of 200 bacterial and archaeal species, were identified and classified by their domain architectures. previously uncharacterized output domains were analyzed and, in some cases, assigned to known domain families. transcriptional regulators of the ompr, narl, and ntrc families w ... | 2006 | 16740923 |
| the crisprdb database and tools to display crisprs and to generate dictionaries of spacers and repeats. | in archeae and bacteria, the repeated elements called crisprs for "clustered regularly interspaced short palindromic repeats" are believed to participate in the defence against viruses. short sequences called spacers are stored in-between repeated elements. in the current model, motifs comprising spacers and repeats may target an invading dna and lead to its degradation through a proposed mechanism similar to rna interference. analysis of intra-species polymorphism shows that new motifs (one spa ... | 2007 | 17521438 |
| exploiting quorum sensing to confuse bacterial pathogens. | cell-cell communication, or quorum sensing, is a widespread phenomenon in bacteria that is used to coordinate gene expression among local populations. its use by bacterial pathogens to regulate genes that promote invasion, defense, and spread has been particularly well documented. with the ongoing emergence of antibiotic-resistant pathogens, there is a current need for development of alternative therapeutic strategies. an antivirulence approach by which quorum sensing is impeded has caught on as ... | 2013 | 23471618 |
| inflammasomes and host defenses against bacterial infections. | the inflammasome has emerged as an important molecular protein complex which initiates proteolytic processing of pro-il-1β and pro-il-18 into mature inflammatory cytokines. in addition, inflammasomes initiate pyroptotic cell death that may be independent of those cytokines. inflammasomes are central to elicit innate immune responses against many pathogens, and are key components in the induction of host defenses following bacterial infection. here, we review recent discoveries related to nlrp1, ... | 2013 | 23318142 |
| traditional uses, phytochemistry, and pharmacology of olea europaea (olive). | aim of the review. to grasp the fragmented information available on the botany, traditional uses, phytochemistry, pharmacology, and toxicology of olea europaea to explore its therapeutic potential and future research opportunities. material and methods. all the available information on o. europaea was collected via electronic search (using pubmed, scirus, google scholar, and web of science) and a library search. results. ethnomedical uses of o. europaea are recorded throughout the world where it ... | 2015 | 25802541 |
| bacterial syntenies: an exact approach with gene quorum. | the automatic identification of syntenies across multiple species is a key step in comparative genomics that helps biologists shed light both on evolutionary and functional problems. | 2011 | 21605461 |
| rsfa (ybeb) proteins are conserved ribosomal silencing factors. | the ybeb (duf143) family of uncharacterized proteins is encoded by almost all bacterial and eukaryotic genomes but not archaea. while they have been shown to be associated with ribosomes, their molecular function remains unclear. here we show that ybeb is a ribosomal silencing factor (rsfa) in the stationary growth phase and during the transition from rich to poor media. a knock-out of the rsfa gene shows two strong phenotypes: (i) the viability of the mutant cells are sharply impaired during st ... | 2012 | 22829778 |
| functional genes to assess nitrogen cycling and aromatic hydrocarbon degradation: primers and processing matter. | targeting sequencing to genes involved in key environmental processes, i.e., ecofunctional genes, provides an opportunity to sample nature's gene guilds to greater depth and help link community structure to process-level outcomes. vastly different approaches have been implemented for sequence processing and, ultimately, for taxonomic placement of these gene reads. the overall quality of next generation sequence analysis of functional genes is dependent on multiple steps and assumptions of unknow ... | 2013 | 24062736 |
| a computational approach for identifying pathogenicity islands in prokaryotic genomes. | pathogenicity islands (pais), distinct genomic segments of pathogens encoding virulence factors, represent a subgroup of genomic islands (gis) that have been acquired by horizontal gene transfer event. up to now, computational approaches for identifying pais have been focused on the detection of genomic regions which only differ from the rest of the genome in their base composition and codon usage. these approaches often lead to the identification of genomic islands, rather than pais. | 2005 | 16033657 |
| the tyra family of aromatic-pathway dehydrogenases in phylogenetic context. | the tyra protein family includes members that catalyze two dehydrogenase reactions in distinct pathways leading to l-tyrosine and a third reaction that is not part of tyrosine biosynthesis. family members share a catalytic core region of about 30 kda, where inhibitors operate competitively by acting as substrate mimics. this protein family typifies many that are challenging for bioinformatic analysis because of relatively modest sequence conservation and small size. | 2005 | 15888209 |
| cohesion group approach for evolutionary analysis of tyra, a protein family with wide-ranging substrate specificities. | many enzymes and other proteins are difficult subjects for bioinformatic analysis because they exhibit variant catalytic, structural, regulatory, and fusion mode features within a protein family whose sequences are not highly conserved. however, such features reflect dynamic and interesting scenarios of evolutionary importance. the value of experimental data obtained from individual organisms is instantly magnified to the extent that given features of the experimental organism can be projected u ... | 2008 | 18322033 |
| quorum sensing in extreme environments. | microbial communication, particularly that of quorum sensing, plays an important role in regulating gene expression in a range of organisms. although this phenomenon has been well studied in relation to, for example, virulence gene regulation, the focus of this article is to review our understanding of the role of microbial communication in extreme environments. cell signaling regulates many important microbial processes and may play a pivotal role in driving microbial functional diversity and u ... | 2013 | 25371335 |
| electronic waste - an emerging threat to the environment of urban india. | electronic waste or e-waste is one of the emerging problems in developed and developing countries worldwide. it comprises of a multitude of components with valuable materials, some containing toxic substances, that can have an adverse impact on human health and the environment. previous studies show that india has generated 0.4 million tons of e-waste in 2010 which may increase to 0.5 to 0.6 million tons by 2013-2014. coupled with lack of appropriate infrastructural facilities and procedures for ... | 2014 | 24444377 |
| a bioinformatic survey of distribution, conservation, and probable functions of luxr solo regulators in bacteria. | luxr solo transcriptional regulators contain both an autoinducer binding domain (abd; n-terminal) and a dna binding helix-turn-helix domain (hth; c-terminal), but are not associated with a cognate n-acyl homoserine lactone (ahl) synthase coding gene in the same genome. although a few luxr solos have been characterized, their distributions as well as their role in bacterial signal perception and other processes are poorly understood. in this study we have carried out a systematic survey of distri ... | 2015 | 25759807 |
| ancient intron insertion sites and palindromic genomic duplication evolutionally shapes an elementally functioning membrane protein family. | in spite of the recent accumulation of genomic data, the evolutionary pathway in the individual genes of present-day living taxa is still elusive for most genes. among ion channels, inward k+ rectifier (irk) channels are the fundamental and well-defined protein group. we analyzed the genomic structures of this group and compared them among a phylogenetically wide range with our sequenced halocynthia roretzi, a tunicate, irk genomic genes. | 2007 | 17708769 |
| evolution of the chaperone/usher assembly pathway: fimbrial classification goes greek. | many proteobacteria use the chaperone/usher pathway to assemble proteinaceous filaments on the bacterial surface. these filaments can curl into fimbrial or nonfimbrial surface structures (e.g., a capsule or spore coat). this article reviews the phylogeny of operons belonging to the chaperone/usher assembly class to explore the utility of establishing a scheme for subdividing them into clades of phylogenetically related gene clusters. based on usher amino acid sequence comparisons, our analysis s ... | 2007 | 18063717 |
| oxygen and hydrogen peroxide in the early evolution of life on earth: in silico comparative analysis of biochemical pathways. | in the universe, oxygen is the third most widespread element, while on earth it is the most abundant one. moreover, oxygen is a major constituent of all biopolymers fundamental to living organisms. besides o(2), reactive oxygen species (ros), among them hydrogen peroxide (h(2)o(2)), are also important reactants in the present aerobic metabolism. according to a widely accepted hypothesis, aerobic metabolism and many other reactions/pathways involving o(2) appeared after the evolution of oxygenic ... | 2012 | 22970865 |
| evolution of bacterial trp operons and their regulation. | survival and replication of most bacteria require the ability to synthesize the amino acid l-tryptophan whenever it is not available from the environment. in this article we describe the genes, operons, proteins, and reactions involved in tryptophan biosynthesis in bacteria, and the mechanisms they use in regulating tryptophan formation. we show that although the reactions of tryptophan biosynthesis are essentially identical, gene organization varies among species--from whole-pathway operons to ... | 2008 | 18374625 |
| a genomic survey of reb homologs suggests widespread occurrence of r-bodies in proteobacteria. | bacteria and eukaryotes are involved in many types of interaction in nature, with important ecological consequences. however, the diversity, occurrence, and mechanisms of these interactions often are not fully known. the obligate bacterial endosymbionts of paramecium provide their hosts with the ability to kill sensitive paramecium strains through the production of r-bodies, highly insoluble coiled protein ribbons. r-bodies have been observed in a number of free-living bacteria, where their func ... | 2013 | 23450193 |
| novel conopeptides of largely unexplored indo pacific conus sp. | cone snails are predatory creatures using venom as a weapon for prey capture and defense. since this venom is neurotoxic, the venom gland is considered as an enormous collection of pharmacologically interesting compounds having a broad spectrum of targets. as such, cone snail peptides represent an interesting treasure for drug development. here, we report five novel peptides isolated from the venom of conus longurionis, conus asiaticus and conus australis. lo6/7a and lo6/7b were retrieved from c ... | 2016 | 27801785 |
| bacterial cellulose biosynthesis: diversity of operons, subunits, products, and functions. | recent studies of bacterial cellulose biosynthesis, including structural characterization of a functional cellulose synthase complex, provided the first mechanistic insight into this fascinating process. in most studied bacteria, just two subunits, bcsa and bcsb, are necessary and sufficient for the formation of the polysaccharide chain in vitro. other subunits - which differ among various taxa - affect the enzymatic activity and product yield in vivo by modulating (i) the expression of the bios ... | 2015 | 26077867 |
| distribution in microbial genomes of genes similar to loda and goxa which encode a novel family of quinoproteins with amino acid oxidase activity. | l-amino acid oxidases (laos) have been generally described as flavoproteins that oxidize amino acids releasing the corresponding ketoacid, ammonium and hydrogen peroxide. the generation of hydrogen peroxide gives to these enzymes antimicrobial characteristics. they are involved in processes such as biofilm development and microbial competition. laos are of great biotechnological interest in different applications such as the design of biosensors, biotransformations and biomedicine. the marine ba ... | 2015 | 25886995 |
| new weapons to fight old enemies: novel strategies for the (bio)control of bacterial biofilms in the food industry. | biofilms are microbial communities characterized by their adhesion to solid surfaces and the production of a matrix of exopolymeric substances, consisting of polysaccharides, proteins, dna and lipids, which surround the microorganisms lending structural integrity and a unique biochemical profile to the biofilm. biofilm formation enhances the ability of the producer/s to persist in a given environment. pathogenic and spoilage bacterial species capable of forming biofilms are a significant problem ... | 2016 | 27803696 |
| antimicrobial resistance and virulence: a successful or deleterious association in the bacterial world? | hosts and bacteria have coevolved over millions of years, during which pathogenic bacteria have modified their virulence mechanisms to adapt to host defense systems. although the spread of pathogens has been hindered by the discovery and widespread use of antimicrobial agents, antimicrobial resistance has increased globally. the emergence of resistant bacteria has accelerated in recent years, mainly as a result of increased selective pressure. however, although antimicrobial resistance and bacte ... | 2013 | 23554414 |
| the [fefe] hydrogenase of nyctotherus ovalis has a chimeric origin. | the hydrogenosomes of the anaerobic ciliate nyctotherus ovalis show how mitochondria can evolve into hydrogenosomes because they possess a mitochondrial genome and parts of an electron-transport chain on the one hand, and a hydrogenase on the other hand. the hydrogenase permits direct reoxidation of nadh because it consists of a [fefe] hydrogenase module that is fused to two modules, which are homologous to the 24 kda and the 51 kda subunits of a mitochondrial complex i. | 2007 | 18021395 |
| characterization and structure of the aquifex aeolicus protein duf752: a bacterial trna-methyltransferase (mnmc2) functioning without the usually fused oxidase domain (mnmc1). | post-transcriptional modifications of the wobble uridine (u34) of trnas play a critical role in reading nna/g codons belonging to split codon boxes. in a subset of escherichia coli trna, this wobble uridine is modified to 5-methylaminomethyluridine (mnm(5)u34) through sequential enzymatic reactions. uridine 34 is first converted to 5-carboxymethylaminomethyluridine (cmnm(5)u34) by the mnme-mnmg enzyme complex. the cmnm(5)u34 is further modified to mnm(5)u by the bifunctional mnmc protein. in the ... | 2012 | 23091054 |
| reactive oxygen species in the signaling and adaptation of multicellular microbial communities. | one of the universal traits of microorganisms is their ability to form multicellular structures, the cells of which differentiate and communicate via various signaling molecules. reactive oxygen species (ros), and hydrogen peroxide in particular, have recently become well-established signaling molecules in higher eukaryotes, but still little is known about the regulatory functions of ros in microbial structures. here we summarize current knowledge on the possible roles of ros during the developm ... | 2012 | 22829965 |
| recognition of extracellular bacteria by nlrs and its role in the development of adaptive immunity. | innate immune recognition of bacteria is the first requirement for mounting an effective immune response able to control infection. over the previous decade, the general paradigm was that extracellular bacteria were only sensed by cell surface-expressed toll-like receptors (tlrs), whereas cytoplasmic sensors, including members of the nod-like receptor (nlr) family, were specific to pathogens capable of breaching the host cell membrane. it has become apparent, however, that intracellular innate i ... | 2013 | 24155747 |
| identification of bacterial protein o-oligosaccharyltransferases and their glycoprotein substrates. | o-glycosylation of proteins in neisseria meningitidis is catalyzed by pgll, which belongs to a protein family including waal o-antigen ligases. we developed two hidden markov models that identify 31 novel candidate pgll homologs in diverse bacterial species, and describe several conserved sequence and structural features. most of these genes are adjacent to possible novel target proteins for glycosylation. we show that in the general glycosylation system of n. meningitidis, efficient glycosylati ... | 2013 | 23658772 |
| diagnosis and treatment of gastrointestinal disorders in patients with primary immunodeficiency. | gastrointestinal disorders such as chronic or acute diarrhea, malabsorption, abdominal pain, and inflammatory bowel diseases can indicate immune deficiency. the gastrointestinal tract is the largest lymphoid organ in the body, so it is not surprising that intestinal diseases are common among immunodeficient patients. gastroenterologists therefore must be able to diagnose and treat patients with primary immunodeficiency. immune-related gastrointestinal diseases can be classified as those that dev ... | 2013 | 23501398 |
| requirement of the flagellar protein export apparatus component flio for optimal expression of flagellar genes in helicobacter pylori. | flagellar biogenesis in helicobacter pylori involves the coordinated expression of flagellar genes with assembly of the flagellum. the h. pylori flagellar genes are organized into three regulons based on the sigma factor needed for their transcription (rpod [σ(80)], rpon [σ(54)], or flia [σ(28)]). transcription of rpon-dependent genes is activated by a two-component system consisting of the sensor kinase flgs and the response regulator flgr. while the cellular cues sensed by the flgs/flgr two-co ... | 2014 | 24837287 |
| metalloproteins containing cytochrome, iron-sulfur, or copper redox centers. | | 2014 | 24758379 |
| haemophilus influenzae: using comparative genomics to accurately identify a highly recombinogenic human pathogen. | haemophilus influenzae is an opportunistic bacterial pathogen that exclusively colonises humans and is associated with both acute and chronic disease. despite its clinical significance, accurate identification of h. influenzae is a non-trivial endeavour. h. haemolyticus can be misidentified as h. influenzae from clinical specimens using selective culturing methods, reflecting both the shared environmental niche and phenotypic similarities of these species. on the molecular level, frequent geneti ... | 2015 | 26311542 |
| quercetin influences quorum sensing in food borne bacteria: in-vitro and in-silico evidence. | quorum sensing (qs) plays a vital role in regulating the virulence factor of many food borne pathogens, which causes severe public health risk. therefore, interrupting the qs signaling pathway may be an attractive strategy to combat microbial infections. in the current study qs inhibitory activity of quercetin and its anti-biofilm property was assessed against food-borne pathogens using a bio-sensor strain. in addition in-silico techniques like molecular docking and molecular dynamics simulation ... | 2015 | 26248208 |
| status, antimicrobial mechanism, and regulation of natural preservatives in livestock food systems. | this review discusses the status, antimicrobial mechanisms, application, and regulation of natural preservatives in livestock food systems. conventional preservatives are synthetic chemical substances including nitrates/nitrites, sulfites, sodium benzoate, propyl gallate, and potassium sorbate. the use of artificial preservatives is being reconsidered because of concerns relating to headache, allergies, and cancer. as the demand for biopreservation in food systems has increased, new natural anti ... | 2016 | 27621697 |
| gelc-ms-based proteomics of chromobacterium violaceum: comparison of proteome changes elicited by hydrogen peroxide. | chromobacterium violaceum is a free-living bacillus with several genes that enables it survival under different harsh environments such as oxidative and temperature stresses. here we performed a label-free quantitative proteomic study to unravel the molecular mechanisms that enable c. violaceum to survive oxidative stress. to achieve this, total proteins extracted from control and c. violaceum cultures exposed during two hours with 8 mm hydrogen peroxide were analyzed using gelc-ms proteomics. a ... | 2016 | 27321545 |
| protist-bacteria associations: gammaproteobacteria and alphaproteobacteria are prevalent as digestion-resistant bacteria in ciliated protozoa. | protistan bacterivory, a microbial process involving ingestion and digestion, is ecologically important in the microbial loop in aquatic and terrestrial ecosystems. while bacterial resistance to protistan ingestion has been relatively well understood, little is known about protistan digestion in which some ingested bacteria could not be digested in cells of major protistan grazers in the natural environment. here we report the phylogenetic identities of digestion-resistant bacteria (drb) that co ... | 2016 | 27148188 |
| metagenomics: application of genomics to uncultured microorganisms. | metagenomics (also referred to as environmental and community genomics) is the genomic analysis of microorganisms by direct extraction and cloning of dna from an assemblage of microorganisms. the development of metagenomics stemmed from the ineluctable evidence that as-yet-uncultured microorganisms represent the vast majority of organisms in most environments on earth. this evidence was derived from analyses of 16s rrna gene sequences amplified directly from the environment, an approach that avo ... | 2004 | 15590779 |
| comparative and evolutionary analysis of the bacterial homologous recombination systems. | homologous recombination is a housekeeping process involved in the maintenance of chromosome integrity and generation of genetic variability. although detailed biochemical studies have described the mechanism of action of its components in model organisms, there is no recent extensive assessment of this knowledge, using comparative genomics and taking advantage of available experimental data on recombination. using comparative genomics, we assessed the diversity of recombination processes among ... | 2005 | 16132081 |
| diversity and antibiograms of bacterial organisms isolated from samples of household drinking-water consumed by hiv-positive individuals in rural settings, south africa. | diarrhoea is a hallmark of hiv infections in developing countries, and many diarrhoea-causing agents are often transmitted through water. the objective of the study was to determine the diversity and antibiotic susceptibility profiles of bacterial organisms isolated from samples of household drinking-water consumed by hiv-infected and aids patients. in the present study, household water stored for use by hiv-positive patients was tested for microbial quality, and isolated bacterial organisms wer ... | 2012 | 23082625 |
| risk factors of organ failure in cholangitis with bacteriobilia. | to identify the risk factors for organ failure (of) in cholangitis with bacteriobilia. | 2015 | 26139997 |
| comprehensive laboratory evaluation of a highly specific lateral flow assay for the presumptive identification of bacillus anthracis spores in suspicious white powders and environmental samples. | we conducted a comprehensive, multiphase laboratory evaluation of the anthrax biothreat alert(®) test strip, a lateral flow immunoassay (lfa) for the rapid detection of bacillus anthracis spores. the study, conducted at 2 sites, evaluated this assay for the detection of spores from the ames and sterne strains of b. anthracis, as well as those from an additional 22 strains. phylogenetic near neighbors, environmental background organisms, white powders, and environmental samples were also tested. ... | 2016 | 27661796 |
| biodiversity of genes encoding anti-microbial traits within plant associated microbes. | the plant is an attractive versatile home for diverse associated microbes. a subset of these microbes produces a diversity of anti-microbial natural products including polyketides, non-ribosomal peptides, terpenoids, heterocylic nitrogenous compounds, volatile compounds, bacteriocins, and lytic enzymes. in recent years, detailed molecular analysis has led to a better understanding of the underlying genetic mechanisms. new genomic and bioinformatic tools have permitted comparisons of orthologous ... | 2015 | 25914708 |
| look who's talking: communication and quorum sensing in the bacterial world. | for many years bacteria were considered primarily as autonomous unicellular organisms with little capacity for collective behaviour. however, we now appreciate that bacterial cells are in fact, highly communicative. the generic term 'quorum sensing' has been adopted to describe the bacterial cell-to-cell communication mechanisms which co-ordinate gene expression usually, but not always, when the population has reached a high cell density. quorum sensing depends on the synthesis of small molecule ... | 2007 | 17360280 |
| quorum sensing and social networking in the microbial world. | for many years, bacterial cells were considered primarily as selfish individuals, but, in recent years, it has become evident that, far from operating in isolation, they coordinate collective behaviour in response to environmental challenges using sophisticated intercellular communication networks. cell-to-cell communication between bacteria is mediated by small diffusible signal molecules that trigger changes in gene expression in response to fluctuations in population density. this process, ge ... | 2009 | 19674996 |
| type i polyketide synthases that require discrete acyltransferases. | the diverse structures of polyketide natural products are reflected by the equally diverse polyketide biosynthetic enzymes, namely polyketide synthases (pkss). three major classes of pkss are known-noniterative type i pkss, iterative type ii pkss and acyl carrier protein-independent type iii pkss, each of which consists of additional variants. one such variant is the noniterative type i pks in which each pks module lacks the cognate acyltransferase (at) domain. the essential at activity is inste ... | 2009 | 19362640 |
| thiol dioxygenases: unique families of cupin proteins. | proteins in the cupin superfamily have a wide range of biological functions in archaea, bacteria and eukaryotes. although proteins in the cupin superfamily show very low overall sequence similarity, they all contain two short but partially conserved cupin sequence motifs separated by a less conserved intermotif region that varies both in length and amino acid sequence. furthermore, these proteins all share a common architecture described as a six-stranded β-barrel core, and this canonical cupin ... | 2010 | 20195658 |
| thiol dioxygenases: unique families of cupin proteins. | proteins in the cupin superfamily have a wide range of biological functions in archaea, bacteria and eukaryotes. although proteins in the cupin superfamily show very low overall sequence similarity, they all contain two short but partially conserved cupin sequence motifs separated by a less conserved intermotif region that varies both in length and amino acid sequence. furthermore, these proteins all share a common architecture described as a six-stranded β-barrel core, and this canonical cupin ... | 2010 | 20195658 |
| ethanolamine utilization in vibrio alginolyticus. | ethanolamine is used as an energy source by phylogenetically diverse bacteria including pathogens, by the concerted action of proteins from the eut-operon. previous studies have revealed the presence of eutbc genes encoding ethanolamine-ammonia lyase, a key enzyme that breaks ethanolamine into acetaldehyde and ammonia, in about 100 bacterial genomes including members of gamma-proteobacteria. however, ethanolamine utilization has not been reported for any member of the vibrio genus. our comparati ... | 2012 | 23234435 |
| bacterial danger sensing. | here we propose that bacteria detect and respond to threats posed by other bacteria via an innate immune-like process that we term danger sensing. we find support for this contention by reexamining existing literature from the perspective that intermicrobial antagonism, not opportunistic pathogenesis, is the major evolutionary force shaping the defensive behaviors of most bacteria. we conclude that many bacteria possess danger sensing pathways composed of a danger signal receptor and correspondi ... | 2015 | 26434507 |
| quorum sensing control of type vi secretion factors restricts the proliferation of quorum-sensing mutants. | burkholderia thailandensis uses acyl-homoserine lactone-mediated quorum sensing systems to regulate hundreds of genes. here we show that cell-cell contact-dependent type vi secretion (t6s) toxin-immunity systems are among those activated by quorum sensing in b. thailandensis. we also demonstrate that t6s is required to constrain proliferation of quorum sensing mutants in colony cocultures of a btar1 quorum-sensing signal receptor mutant and its parent. however, the btar1 mutant is not constraine ... | 2016 | 27183270 |
| metagenomic approaches to natural products from free-living and symbiotic organisms. | | 2009 | 19844642 |
| α,β-dehydroamino acids in naturally occurring peptides. | α,β-dehydroamino acids are naturally occurring non-coded amino acids, found primarily in peptides. the review focuses on the type of α,β-dehydroamino acids, the structure of dehydropeptides, the source of their origin and bioactivity. dehydropeptides are isolated primarily from bacteria and less often from fungi, marine invertebrates or even higher plants. they reveal mainly antibiotic, antifungal, antitumour, and phytotoxic activity. more than 60 different structures were classified, which ofte ... | 2015 | 25323736 |
| α,β-dehydroamino acids in naturally occurring peptides. | α,β-dehydroamino acids are naturally occurring non-coded amino acids, found primarily in peptides. the review focuses on the type of α,β-dehydroamino acids, the structure of dehydropeptides, the source of their origin and bioactivity. dehydropeptides are isolated primarily from bacteria and less often from fungi, marine invertebrates or even higher plants. they reveal mainly antibiotic, antifungal, antitumour, and phytotoxic activity. more than 60 different structures were classified, which ofte ... | 2015 | 25323736 |
| metagenomic discovery of novel enzymes and biosurfactants in a slaughterhouse biofilm microbial community. | dna derived from environmental samples is a rich source of novel bioactive molecules. the choice of the habitat to be sampled predefines the properties of the biomolecules to be discovered due to the physiological adaptation of the microbial community to the prevailing environmental conditions. we have constructed a metagenomic library in escherichia coli dh10b with environmental dna (edna) isolated from the microbial community of a slaughterhouse drain biofilm consisting mainly of species from ... | 2016 | 27271534 |
| non-pathogenic microflora of a spring water with regenerative properties. | the comano spring water (comano, italy) has been demonstrated to improve skin regeneration, not only by increasing keratinocyte proliferation and migration, but also by modulating the regenerated collagen and elastic fibers in the dermis. however, such biological properties may not be entirely explained by its mineral composition only. as the non-pathogenic bacterial populations have demonstrated an active role in different biological processes, the potential presence of non-pathogenic bacterial ... | 2015 | 26623012 |
| characterization of n-acylhomoserine lactones produced by bacteria isolated from industrial cooling water systems. | the cooling water systems are used to remove heat generated in the various industries. biofouling of the cooling water systems causes blocking of condenser pipes and the heat exchanger tubes. in many gram-negative bacteria, n-acylhomoserine lactone (ahl) are used as quorum-sensing signal molecule and associated with biofilm formation. to investigate the relationship between quorum sensing and biofouling in the cooling water system, we isolated a total of 192 bacterial strains from the five cooli ... | 2016 | 26729121 |
| characterization of n-acylhomoserine lactones produced by bacteria isolated from industrial cooling water systems. | the cooling water systems are used to remove heat generated in the various industries. biofouling of the cooling water systems causes blocking of condenser pipes and the heat exchanger tubes. in many gram-negative bacteria, n-acylhomoserine lactone (ahl) are used as quorum-sensing signal molecule and associated with biofilm formation. to investigate the relationship between quorum sensing and biofouling in the cooling water system, we isolated a total of 192 bacterial strains from the five cooli ... | 2016 | 26729121 |
| dialects of the dna uptake sequence in neisseriaceae. | in all sexual organisms, adaptations exist that secure the safe reassortment of homologous alleles and prevent the intrusion of potentially hazardous alien dna. some bacteria engage in a simple form of sex known as transformation. in the human pathogen neisseria meningitidis and in related bacterial species, transformation by exogenous dna is regulated by the presence of a specific dna uptake sequence (dus), which is present in thousands of copies in the respective genomes. dus affects transform ... | 2013 | 23637627 |
| selection of the n-acylhomoserine lactone-degrading bacterium alteromonas stellipolaris pqq-42 and of its potential for biocontrol in aquaculture. | the production of virulence factors by many pathogenic microorganisms depends on the intercellular communication system called quorum sensing, which involves the production and release of signal molecules known as autoinducers. based on this, new-therapeutic strategies have emerged for the treatment of a variety of infections, such as the enzymatic degradation of signaling molecules, known as quorum quenching (qq). in this study, we present the screening of qq activity amongst 450 strains isolat ... | 2016 | 27242684 |
| identification and characterization of ribn, a novel family of riboflavin transporters from rhizobium leguminosarum and other proteobacteria. | rhizobia are symbiotic bacteria able to invade and colonize the roots of legume plants, inducing the formation of nodules, where bacteria reduce atmospheric nitrogen (n2) to ammonia (nh3). riboflavin availability influences the capacity of rhizobia to survive in the rhizosphere and to colonize roots. in this study, we identified the rl1692 gene of rhizobium leguminosarum downstream of a flavin mononucleotide (fmn) riboswitch. rl1692 encodes a putative transmembrane permease with two eama domains ... | 2013 | 23935051 |
| inactivation of the organic hydroperoxide stress resistance regulator ohrr enhances resistance to oxidative stress and isoniazid in mycobacterium smegmatis. | the organic hydroperoxide stress resistance regulator (ohrr) is a marr type of transcriptional regulator that primarily regulates the expression of organic hydroperoxide reductase (ohr) in bacteria. in mycobacteria, the genes encoding these proteins exist in only a few species, which include the fast-growing organism mycobacterium smegmatis. to delineate the roles of ohr and ohrr in defense against oxidative stress in m. smegmatis, strains lacking the expression of these proteins were constructe ... | 2014 | 25313389 |
| inactivation of the organic hydroperoxide stress resistance regulator ohrr enhances resistance to oxidative stress and isoniazid in mycobacterium smegmatis. | the organic hydroperoxide stress resistance regulator (ohrr) is a marr type of transcriptional regulator that primarily regulates the expression of organic hydroperoxide reductase (ohr) in bacteria. in mycobacteria, the genes encoding these proteins exist in only a few species, which include the fast-growing organism mycobacterium smegmatis. to delineate the roles of ohr and ohrr in defense against oxidative stress in m. smegmatis, strains lacking the expression of these proteins were constructe ... | 2014 | 25313389 |
| arginine deiminase pathway is far more important than urease for acid resistance and intracellular survival in laribacter hongkongensis: a possible result of arc gene cassette duplication. | laribacter hongkongensis is a gram-negative, urease-positive bacillus associated with invasive bacteremic infections in liver cirrhosis patients and fish-borne community-acquired gastroenteritis and traveler's diarrhea. its mechanisms of adaptation to various environmental niches and host defense evasion are largely unknown. during the process of analyzing the l. hongkongensis genome, a complete urease cassette and two adjacent arc gene cassettes were found. we hypothesize that the urease casset ... | 2014 | 24533585 |
| from environment to man: genome evolution and adaptation of human opportunistic bacterial pathogens. | environment is recognized as a huge reservoir for bacterial species and a source of human pathogens. some environmental bacteria have an extraordinary range of activities that include promotion of plant growth or disease, breakdown of pollutants, production of original biomolecules, but also multidrug resistance and human pathogenicity. the versatility of bacterial life-style involves adaptation to various niches. adaptation to both open environment and human specific niches is a major challenge ... | 2012 | 24704914 |
| performances and reliability of bruker microflex lt and vitek ms maldi-tof mass spectrometry systems for the identification of clinical microorganisms. | in clinical microbiology laboratories, routine microbial identification is mostly performed using culture based methodologies requiring 24 to 72 hours from culturing to identification. matrix assisted laser desorption ionization-time of flight mass spectrometry (maldi-tof ms) technology has been established as a cost effective, reliable, and faster alternative identification platform. in this study, we evaluated the reliability of the two available maldi-tof ms systems for their routine clinical ... | 2015 | 26793718 |
| pathogens in ornamental waters: a pilot study. | in parks, ornamental waters of easy access and populated with animals are quite attractive to children and yet might hide threats to human health. the present work focuses on the microbiota of the ornamental waters of a lisboa park, characterized during 2015. the results show a dynamic microbiota integrating human pathogens such as klebsiella pneumoniae, aeromonas spp. and enterobacter spp., and also antibiotic resistant bacteria. k. pneumoniae and aeromonas spp. were present as planktonic and b ... | 2016 | 26891309 |
| in search of alternative antibiotic drugs: quorum-quenching activity in sponges and their bacterial isolates. | owing to the extensive development of drug resistance in pathogens against the available antibiotic arsenal, antimicrobial resistance is now an emerging major threat to public healthcare. anti-virulence drugs are a new type of therapeutic agent aiming at virulence factors rather than killing the pathogen, thus providing less selective pressure for evolution of resistance. one promising example of this therapeutic concept targets bacterial quorum sensing (qs), because qs controls many virulence f ... | 2016 | 27092109 |
| emerging organisms in a tertiary healthcare set up. | one-tenth of all infectious diseases are attributable to emerging organisms. as emerging organisms sporadically affect a relatively small percentage of population they are not studied at large. this study was aimed at studying the characteristics of emerging organisms encountered from various clinical samples in an apex tertiary care multispeciality teaching and research hospital. | 2013 | 24843199 |
| emerging organisms in a tertiary healthcare set up. | one-tenth of all infectious diseases are attributable to emerging organisms. as emerging organisms sporadically affect a relatively small percentage of population they are not studied at large. this study was aimed at studying the characteristics of emerging organisms encountered from various clinical samples in an apex tertiary care multispeciality teaching and research hospital. | 2013 | 24843199 |
| aidc, a novel n-acylhomoserine lactonase from the potato root-associated cytophaga-flavobacteria-bacteroides (cfb) group bacterium chryseobacterium sp. strain strb126. | n-acylhomoserine lactones (ahls) are used as quorum-sensing (qs) signal molecules by many gram-negative bacteria. we have reported that chryseobacterium sp. strain strb126, which was isolated from the root surface of potato, has ahl-degrading activity. in this study, we cloned and characterized the aidc gene from the genomic library of strb126. aidc has ahl-degrading activity and shows homology to several metallo-β-lactamase proteins from bacteroidetes, although not to any known ahl-degrading en ... | 2012 | 22941089 |
| quorum quenching in culturable phyllosphere bacteria from tobacco. | many gram-negative plant pathogenic bacteria employ a n-acylhomoserine lactone (ahl)-based quorum sensing (qs) system to regulate their virulence traits. a sustainable biocontrol strategy has been developed using quorum quenching (qq) bacteria to interfere with qs and protect plants from pathogens. here, the prevalence and the diversity of qq strains inhabiting tobacco leaf surfaces were explored. a total of 1177 leaf-associated isolates were screened for their ability to disrupt ahl-mediated qs ... | 2013 | 23857057 |
| clinical features and laboratory diagnosis of infection with the potential bioterrorism agents burkholderia mallei and burkholderia pseudomallei. | burkholderia mallei and burkholderia pseudomallei are the causative organisms of glanders and melioidosis, respectively. although now rare in western countries, both organisms have recently gained much interest because of their unique potential as bioterrorism agents. these organisms are less familiar to medical and laboratory personnel than other select bioterrorism bacterial agents and thus heightened awareness of glanders and melioidosis is crucial in order to enable adequate emergency prepar ... | 2007 | 23675037 |
| microbial nad metabolism: lessons from comparative genomics. | nad is a coenzyme for redox reactions and a substrate of nad-consuming enzymes, including adp-ribose transferases, sir2-related protein lysine deacetylases, and bacterial dna ligases. microorganisms that synthesize nad from as few as one to as many as five of the six identified biosynthetic precursors have been identified. de novo nad synthesis from aspartate or tryptophan is neither universal nor strictly aerobic. salvage nad synthesis from nicotinamide, nicotinic acid, nicotinamide riboside, a ... | 2009 | 19721089 |
| inter-kingdom signaling: chemical language between bacteria and host. | chemical communication between cells ensures coordination of behavior. in prokaryotes, this chemical communication is usually referred to as quorum sensing, while eukaryotic cells signal through hormones. in the past years, a growing number of reports have shown that bacterial quorum sensing signals, called autoinducers, signal to eukaryotic cells, mimicking hormones. conversely, host hormones can signal to bacterial cells through converging pathways to autoinducer signaling. this inter-kingdom ... | 2009 | 19318290 |
| medicinal chemistry as a conduit for the modulation of quorum sensing. | | 2010 | 20669927 |
| genomic insights to sar86, an abundant and uncultivated marine bacterial lineage. | bacteria in the 16s rrna clade sar86 are among the most abundant uncultivated constituents of microbial assemblages in the surface ocean for which little genomic information is currently available. bioinformatic techniques were used to assemble two nearly complete genomes from marine metagenomes and single-cell sequencing provided two more partial genomes. recruitment of metagenomic data shows that these sar86 genomes substantially increase our knowledge of non-photosynthetic bacteria in the sur ... | 2011 | 22170421 |
| genomic insights to sar86, an abundant and uncultivated marine bacterial lineage. | bacteria in the 16s rrna clade sar86 are among the most abundant uncultivated constituents of microbial assemblages in the surface ocean for which little genomic information is currently available. bioinformatic techniques were used to assemble two nearly complete genomes from marine metagenomes and single-cell sequencing provided two more partial genomes. recruitment of metagenomic data shows that these sar86 genomes substantially increase our knowledge of non-photosynthetic bacteria in the sur ... | 2011 | 22170421 |
| analysis of the organic hydroperoxide response of chromobacterium violaceum reveals that ohrr is a cys-based redox sensor regulated by thioredoxin. | organic hydroperoxides are oxidants generated during bacterial-host interactions. here, we demonstrate that the peroxidase ohra and its negative regulator ohrr comprise a major pathway for sensing and detoxifying organic hydroperoxides in the opportunistic pathogen chromobacterium violaceum. initially, we found that an ohra mutant was hypersensitive to organic hydroperoxides and that it displayed a low efficiency for decomposing these molecules. expression of ohra and ohrr was specifically induc ... | 2012 | 23071722 |
| dotu and vgrg, core components of type vi secretion systems, are essential for francisella lvs pathogenicity. | the gram-negative bacterium francisella tularensis causes tularemia, a disease which requires bacterial escape from phagosomes of infected macrophages. once in the cytosol, the bacterium rapidly multiplies, inhibits activation of the inflammasome and ultimately causes death of the host cell. of importance for these processes is a 33-kb gene cluster, the francisella pathogenicity island (fpi), which is believed to encode a type vi secretion system (t6ss). in this study, we analyzed the role of th ... | 2012 | 22514651 |
| regulation of inflammasome signaling. | innate immune responses have the ability to both combat infectious microbes and drive pathological inflammation. inflammasome complexes are a central component of these processes through their regulation of interleukin 1β (il-1β), il-18 and pyroptosis. inflammasomes recognize microbial products or endogenous molecules released from damaged or dying cells both through direct binding of ligands and indirect mechanisms. the potential of the il-1 family of cytokines to cause tissue damage and chroni ... | 2012 | 22430786 |
| nlrp7 and related inflammasome activating pattern recognition receptors and their function in host defense and disease. | host defense requires the maturation and release of the pro-inflammatory cytokines interleukin (il)-1β and il-18 and the induction of pyroptotic cell death, which depends on the activation of inflammatory caspases within inflammasomes by innate immune cells. several cytosolic pattern recognition receptors (prrs) have been implicated in this process in response to infectious and sterile agonists. here we summarize the current knowledge on inflammasome-organizing prrs, emphasizing the recently des ... | 2013 | 23618810 |
| phylogenomic reconstruction indicates mitochondrial ancestor was an energy parasite. | reconstruction of mitochondrial ancestor has great impact on our understanding of the origin of mitochondria. previous studies have largely focused on reconstructing the last common ancestor of all contemporary mitochondria (proto-mitochondria), but not on the more informative pre-mitochondria (the last common ancestor of mitochondria and their alphaproteobacterial sister clade). using a phylogenomic approach and leveraging on the increased taxonomic sampling of alphaproteobacterial and eukaryot ... | 2014 | 25333787 |
| regulation of inflammasome activation. | inflammasome biology is one of the most exciting and rapidly growing areas in immunology. over the past 10 years, inflammasomes have been recognized for their roles in the host defense against invading pathogens and in the development of cancer, auto-inflammatory, metabolic, and neurodegenerative diseases. assembly of an inflammasome complex requires cytosolic sensing of pathogen-associated molecular patterns or danger-associated molecular patterns by a nucleotide-binding domain and leucine-rich ... | 2015 | 25879280 |
| mechanisms of inflammasome activation: recent advances and novel insights. | inflammasomes are cytosolic multiprotein platforms assembled in response to invading pathogens and other danger signals. typically inflammasome complexes contain a sensor protein, an adaptor protein, and a zymogen - procaspase-1. formation of inflammasome assembly results in processing of inactive procaspase-1 into an active cysteine-protease enzyme, caspase-1, which subsequently activates the proinflammatory cytokines, interleukins il-1β and il-18, and induces pyroptosis, a highly-pyrogenic inf ... | 2015 | 25639489 |
| an integrated phylogenomic approach toward pinpointing the origin of mitochondria. | overwhelming evidence supports the endosymbiosis theory that mitochondria originated once from the alphaproteobacteria. however, its exact position in the tree of life remains highly debated. this is because systematic errors, including biased taxonomic sampling, high evolutionary rates and sequence composition bias have long plagued the mitochondrial phylogenetics. in this study, we address this issue by 1) increasing the taxonomic representation of alphaproteobacterial genomes by sequencing 18 ... | 2015 | 25609566 |
| inflammasomes coordinate pyroptosis and natural killer cell cytotoxicity to clear infection by a ubiquitous environmental bacterium. | defective neutrophils in patients with chronic granulomatous disease (cgd) cause susceptibility to extracellular and intracellular infections. microbes must first be ejected from intracellular niches to expose them to neutrophil attack, so we hypothesized that inflammasomes detect certain cgd pathogens upstream of neutrophil killing. here, we identified one such ubiquitous environmental bacterium, chromobacterium violaceum, whose extreme virulence was fully counteracted by the nlrc4 inflammasome ... | 2015 | 26572063 |
| bacterial recognition pathways that lead to inflammasome activation. | inflammasomes are multi-protein signaling platforms that upon activation trigger the maturation of the pro-inflammatory cytokines, interleukin-1β (il-1β) and il-18, and cell death. inflammasome sensors detect microbial and host-derived molecules. here, we review the mechanisms of inflammasome activation triggered by bacterial infection, primarily focusing on two model intracellular bacterial pathogens, francisella novicida and salmonella typhimurium. we discuss the complex relationship between b ... | 2015 | 25879288 |
| asymmetric preparation of prim-, sec-, and tert-amines employing selected biocatalysts. | this account focuses on the application of ω-transaminases, lyases, and oxidases for the preparation of amines considering mainly work from our own lab. examples are given to access α-chiral primary amines from the corresponding ketones as well as terminal amines from primary alcohols via a two-step biocascade. 2,6-disubstituted piperidines, as examples for secondary amines, are prepared by biocatalytical regioselective asymmetric monoamination of designated diketones followed by spontaneous rin ... | 2013 | 23794796 |
| crystal structure of an (r)-selective ω-transaminase from aspergillus terreus. | chiral amines are important building blocks for the synthesis of pharmaceutical products, fine chemicals, and agrochemicals. ω-transaminases are able to directly synthesize enantiopure chiral amines by catalysing the transfer of an amino group from a primary amino donor to a carbonyl acceptor with pyridoxal 5'-phosphate (plp) as cofactor. in nature, (s)-selective amine transaminases are more abundant than the (r)-selective enzymes, and therefore more information concerning their structures is av ... | 2014 | 24498081 |
| active-site engineering of ω-transaminase for production of unnatural amino acids carrying a side chain bulkier than an ethyl substituent. | ω-transaminase (ω-ta) is a promising enzyme for use in the production of unnatural amino acids from keto acids using cheap amino donors such as isopropylamine. the small substrate-binding pocket of most ω-tas permits entry of substituents no larger than an ethyl group, which presents a significant challenge to the preparation of structurally diverse unnatural amino acids. here we report on the engineering of an (s)-selective ω-ta from ochrobactrum anthropi (oata) to reduce the steric constraint ... | 2015 | 26231640 |
| de-orphaning the structural proteome through reciprocal comparison of evolutionarily important structural features. | function prediction frequently relies on comparing genes or gene products to search for relevant similarities. because the number of protein structures with unknown function is mushrooming, however, we asked here whether such comparisons could be improved by focusing narrowly on the key functional features of protein structures, as defined by the evolutionary trace (et). therefore a series of algorithms was built to (a) extract local motifs (3d templates) from protein structures based on et rank ... | 2008 | 18461181 |
| the substrate specificity, enantioselectivity and structure of the (r)-selective amine : pyruvate transaminase from nectria haematococca. | during the last decade the use of transaminases for the production of pharmaceutical and fine chemical intermediates has attracted a great deal of attention. transaminases are versatile biocatalysts for the efficient production of amine intermediates and many have (s)-enantiospecificity. transaminases with (r)-specificity are needed to expand the applications of these enzymes in biocatalysis. in this work we have identified a fungal putative (r)-specific transaminase from the eurotiomycetes nect ... | 2014 | 24618038 |
| structure of ribosomal silencing factor bound to mycobacterium tuberculosis ribosome. | the ribosomal silencing factor rsfs slows cell growth by inhibiting protein synthesis during periods of diminished nutrient availability. the crystal structure of mycobacterium tuberculosis (mtb) rsfs, together with the cryo-electron microscopy (em) structure of the large subunit 50s of mtb ribosome, reveals how inhibition of protein synthesis by rsfs occurs. rsfs binds to the 50s at l14, which, when occupied, blocks the association of the small subunit 30s. although mtb rsfs is a dimer in solut ... | 2015 | 26299947 |
| a metagenomic study highlights phylogenetic proximity of quorum-quenching and xenobiotic-degrading amidases of the as-family. | quorum-sensing (qs) signals of the n-acylhomoserine lactone (nahl) class are cleaved by quorum-quenching enzymes, collectively named nahlases. here, functional metagenomics allowed the discovery of a novel bacterial nahlase in a rhizosphere that was treated with γ-caprolactone. as revealed by rrs-dgge and rrs-pyrosequencing, this treatment increased the percentage of the nahl-degrading bacteria and strongly biased the structure of the bacterial community, among which azospirillum dominated. amon ... | 2013 | 23762380 |
| phylogenetic analysis of tmrna genes within a bacterial subgroup reveals a specific structural signature. | bacterial tmrna mediates a trans-translation reaction, which permits the recycling of stalled ribosomes and probably also contributes to the regulated expression of a subset of genes. its action results in the addition of a small number of c-terminal amino acids to protein whose synthesis had stalled and these constitute a proteolytic recognition tag for the degradation of these incompletely synthesized proteins. previous work has identified pseudoknots and stem-loops that are widely conserved i ... | 2001 | 11266563 |