Publications

modestobacter lacusdianchii sp. nov., a phosphate-solubilizing actinobacterium with ability to promote microcystis growth.	a novel actinobacterium, designated strain jxj cy 19t, was isolated from a culture mat of microcystis aeruginosa fachb-905 collected from dianchi lake, south-west china. 16s rrna gene sequences comparison of strain jxj cy 19t and the available sequences in the genbank database showed that the strain was closely related to modestobacter marinus 42h12-1t (99.1% similarity) and modestobacter roseus klbmp 1279t (99.0%). the isolate had meso-diaminopimelic in the cell wall with whole-cell sugars of m ...	2016	27537546
specialized microbiome of a halophyte and its role in helping non-host plants to withstand salinity.	root microbiota is a crucial determinant of plant productivity and stress tolerance. here, we hypothesize that the superior halo-tolerance of seepweed suaeda salsa is tightly linked to a specialized belowground microbiome. to test this hypothesis, we performed a phylogenetic trait-based framework analysis based on bacterial 16s rrna gene and fungal nuclear rrna internal transcribed spacer profiling. data showed that the dominant α-proteobacteria and γ-proteobacteria communities in bulk soil and ...	2016	27572178
human contamination in public genome assemblies.	contamination in genome assembly can lead to wrong or confusing results when using such genome as reference in sequence comparison. although bacterial contamination is well known, the problem of human-originated contamination received little attention. in this study we surveyed 45,735 available genome assemblies for evidence of human contamination. we used lineage specificity to distinguish between contamination and conservation. we found that 154 genome assemblies contain fragments that with hi ...	2016	27611326
bacterial viability within dental calculus: an untrodden, inquisitive clinico-patho- microbiological research.	chronic inflammatory periodontal diseases i.e. gingivitis and periodontitis are one of the most common afflictions faced by human beings. dental plaque, which is a pool of pathogenic microorganisms, remains to be current mainstay in etiopathogenesis. dental calculus, which is a mineralized product of this plaque remains ignored and is considered merely as an ash heap of minor significance. however, the intriguing array in disease etiopathogenesis bulldozed researchers to suspect the role of calc ...	2016	27630958
frequency of hospital acquired pneumonia and its microbiological etiology in medical intensive care unit.	the objectives were to assess the frequency of hospital acquired pneumonia (hap) in patients admitted to intensive care unit (icu) and to determine the frequencies of different etiological organisms in these patients.	2016	27648021
flagellin flic phosphorylation affects type 2 protease secretion and biofilm dispersal in pseudomonas aeruginosa pao1.	protein phosphorylation has a major role in controlling the life-cycle and infection stages of bacteria. proteome-wide occurrence of s/t/y phosphorylation has been reported for many prokaryotic systems. previously, we reported the phosphoproteome of pseudomonas aeruginosa and pseudomonas putida. in this study, we show the role of s/t phosphorylation of one motility protein, flic, in regulating multiple surface-associated phenomena of p. aeruginosa pao1. this is the first report of occurrence of ...	2016	27701473
protein domain architectures provide a fast, efficient and scalable alternative to sequence-based methods for comparative functional genomics.	a functional comparative genome analysis is essential to understand the mechanisms underlying bacterial evolution and adaptation. detection of functional orthologs using standard global sequence similarity methods faces several problems; the need for defining arbitrary acceptance thresholds for similarity and alignment length, lateral gene acquisition and the high computational cost for finding bi-directional best matches at a large scale. we investigated the use of protein domain architectures ...	2016	27703668
genotyping and descriptive proteomics of a potential zoonotic canine strain of giardia duodenalis, infective to mice.	the zoonotic potential of giardiasis, as proposed by who since the late 70's, has been largely confirmed in this century. the genetic assemblages a and b of giardia duodenalis are frequently isolated from human and canine hosts. most of the assemblage a strains are not infective to adult mice, which can limit the range of studies regarding to biology of g. duodenalis, including virulence factors and the interaction with host immune system. this study aimed to determine the infectivity in mice of ...	2016	27760188
expression and characterization of thermotolerant lipase with broad ph profiles isolated from an antarctic pseudomonas sp strain ams3.	a gene encoding a thermotolerant lipase with broad ph was isolated from an antarctic pseudomonas strain ams3. the recombinant lipase ams3 was purified by single-step purification using affinity chromatography, yielding a purification fold of approximately 1.52 and a recovery of 50%. the molecular weight was approximately ∼60 kda including the strep and affinity tags. interestingly, the purified antarctic ams3 lipase exhibited broad temperature profile from 10-70 °c and stable over a broad ph ran ...	2016	27781152
killing two birds with one stone: natural rice rhizospheric microbes reduce arsenic uptake and blast infections in rice.	our recent work has shown that a rice thizospheric natural isolate, a pantoea sp (hereafter ea106) attenuates arsenic (as) uptake in rice. in parallel, yet another natural rice rhizospheric isolate, a pseudomonas chlororaphis (hereafter ea105), was shown to inhibit rice blast pathogen magnaporthe oryzae. considering the above, we envisaged to evaluate the importance of mixed stress regime in rice plants subjected to both as toxicity and blast infections. plants subjected to as regime showed incr ...	2016	27790229
comparison of substrate specificity of escherichia coli p-aminobenzoyl-glutamate hydrolase with pseudomonas carboxypeptidase g.	reduced folic acid derivatives support biosynthesis of dna, rna and amino acids in bacteria as well as in eukaryotes, including humans. while the genes and steps for bacterial folic acid synthesis are known, those associated with folic acid catabolism are not well understood. a folate catabolite found in both humans and bacteria is p-aminobenzoyl-glutamate (paba-glu). the enzyme p-aminobenzoyl-glutamate hydrolase (pgh) breaks down paba-glu and is part of an apparent operon, the abg region, in e. ...	2014	27795973
new, hybrid pectin-based biosorbents.	in this work hybrid pectin-based biosorbents with secondary polysaccharide additives (gellan, carob and xanthan gum, ratio to pectin 1:1, 1:1 and 1:3, respectively) were obtained at two temperatures. the presence of these additives in prepared beads was confirmed by raman spectra. the sem micrographs show better homogeneity of blends and grater differences between structures of beads with various additives obtained at higher temperature. the sorption capacity of our hybrid biosorbents as well as ...	2016	27812233
moleculo long-read sequencing facilitates assembly and genomic binning from complex soil metagenomes.	soil metagenomics has been touted as the "grand challenge" for metagenomics, as the high microbial diversity and spatial heterogeneity of soils make them unamenable to current assembly platforms. here, we aimed to improve soil metagenomic sequence assembly by applying the moleculo synthetic long-read sequencing technology. in total, we obtained 267 gbp of raw sequence data from a native prairie soil; these data included 109.7 gbp of short-read data (~100 bp) from the joint genome institute (jgi) ...	2016	27822530
l-asparaginase production in the pseudomonas pseudoalcaligenes strain jhs-71 isolated from jooshan hot-spring.	l-asparaginase has lots of medical and industrial applications. ever since l-asparaginase anti-tumor activity was first demonstrated, its production using microbial systems has attracted considerable attention owing to their cost-effective and eco-friendly nature. the aim of this study is to obtain l-asparaginase producing bacteria and determining the enzyme activity. samples were picked up from jooshan hot springs located in the sirch, kerman. the l-asparaginase producing bacteria were screened ...	2016	27844015
structure and dynamics underlying elementary ligand binding events in human pacemaking channels.	although molecular recognition is crucial for cellular signaling, mechanistic studies have relied primarily on ensemble measures that average over and thereby obscure underlying steps. single-molecule observations that resolve these steps are lacking due to diffraction-limited resolution of single fluorophores at relevant concentrations. here, we combined zero-mode waveguides with fluorescence resonance energy transfer (fret) to directly observe binding at individual cyclic nucleotide-binding do ...	2016	27858593
trends of bacterial keratitis culture isolates in jerusalem; a 13- years analysis.	to describe the trends in pathogens and antibacterial resistance of corneal culture isolates in infectious keratitis during a period of 13 years at hadassah-hebrew university medical center.	2016	27893743
antagonistic effect of pseudomonas sp. cmi-1 on foodborne pathogenic listeria monocytogenes.	bacterial isolates derived from food or raw food materials of animal origin were screened for potential antagonistic activity against foodborne pathogenic listeria monocytogenes. using the agar spot method, ten out of the 94 tested bacteria showed antilisterial activity. all of the antagonistic isolates identified by sequence analysis as strains of the genus pseudomonas were able to inhibit the growth of all the examined listeria species including the ruminal pathogenic l. ivanovii and the oppor ...	2015	27904352
insights into functional and evolutionary analysis of carbaryl metabolic pathway from pseudomonas sp. strain c5pp.	carbaryl (1-naphthyl n-methylcarbamate) is a most widely used carbamate pesticide in the agriculture field. soil isolate, pseudomonas sp. strain c5pp mineralizes carbaryl via 1-naphthol, salicylate and gentisate, however the genetic organization and evolutionary events of acquisition and assembly of pathway have not yet been studied. the draft genome analysis of strain c5pp reveals that the carbaryl catabolic genes are organized into three putative operons, 'upper', 'middle' and 'lower'. the seq ...	2016	27924916
epidemiology and risk factors for pneumonia severity and mortality in bangladeshi children <5 years of age before 10-valent pneumococcal conjugate vaccine introduction.	pneumonia is the leading infectious cause of morbidity and mortality in young children in bangladesh. we present the epidemiology of pneumonia in bangladeshi children <5 years before 10-valent pneumococcal conjugate vaccine introduction and investigate factors associated with disease severity and mortality.	2016	27927201
process-oriented review of bacterial quorum quenching for membrane biofouling mitigation in membrane bioreactors (mbrs).	quorum quenching (qq) has been developed over the last few years to overcome practical issues related to membrane biofouling, which is currently the major difficulty thwarting the extensive development of membrane bioreactors (mbrs). qq is the disruption of quorum sensing (qs), cell-to-cell communication enabling the bacteria to harmonize their behavior. the production of biofilm, which is recognized as a major part of the biocake formed on a membrane surface, and which leads to biofouling, has ...	2016	27983578
deciphering a survival strategy during the interspecific competition between bacillus cereus msm-s1 and pseudomonas sp. msm-m1.	interspecific competition in bacteria governs colony growth dynamics and pattern formation. here, we demonstrate an interesting phenomenon of interspecific competition between bacillus cereus msm-s1 and pseudomonas sp. msm-m1, where secretion of an inhibitor by pseudomonas sp. is used as a strategy for survival. although b. cereus grows faster than pseudomonas sp., in the presence of pseudomonas sp. the population of b. cereus reduces significantly, whereas pseudomonas sp. do not show any marked ...	2016	28018625
high levels of soluble c5b-9 complex in dialysis fluid may predict poor prognosis in peritonitis in peritoneal dialysis patients.	we searched for indicators to predict the prognosis of infectious peritonitis by measuring levels of complement proteins and activation products in peritoneal dialysis (pd) fluid (pdf) of patients at early stages of peritonitis. we retrospectively analyzed the relationship between the levels of sc5b-9, c3 and c4 in pdf and the subsequent clinical prognosis.	2017	28046064
metabolic pathway for a new strain pseudomonas synxantha lsh-7': from chemotaxis to uptake of n-hexadecane.	bacteria can use n-hexadecane as a carbon source, but it remains incompletely understood whether n-hexadecane is transformed into metabolic intermediates prior to cellular uptake or not. we newly isolated a strain identified as pseudomonas synxantha lsh-7' and conducted chemotaxis experiment of this bacterial strain towards n-hexadecane, hexadecanol and hexadecanoic acid with qualitative assays respectively. furthermore, we described the identification of extracellular alkane hydroxylase and alc ...	2017	28051099
adenylate cyclase acya regulates development, aflatoxin biosynthesis and fungal virulence in aspergillus flavus.	aspergillus flavus is one of the most important opportunistic pathogens of crops and animals. the carcinogenic mycotoxin, aflatoxins produced by this pathogen cause a health problem to human and animals. since cyclic amp signaling controls a range of physiological processes, like fungal development and infection when responding to extracellular stimuli in fungal pathogens, in this study, we investigated the function of adenylate cyclase, a core component of camp signaling, in aflatoxins biosynth ...	2016	28066725
tracing of two pseudomonas strains in the root and rhizoplane of maize, as related to their plant growth-promoting effect in contrasting soils.	taqman-based quantitative pcr (qpcr) assays were developed to study the persistence of two well-characterized strains of plant growth-promoting rhizobacteria (pgpr), pseudomonas fluorescens pf153 and pseudomonas sp. dsmz 13134, in the root and rhizoplane of inoculated maize plants. this was performed in pot experiments with three contrasting field soils (buus, le caron and dok-m). potential cross-reactivity of the qpcr assays was assessed with indigenous pseudomonas and related bacterial species ...	2016	28119675
tracing of two pseudomonas strains in the root and rhizoplane of maize, as related to their plant growth-promoting effect in contrasting soils.	taqman-based quantitative pcr (qpcr) assays were developed to study the persistence of two well-characterized strains of plant growth-promoting rhizobacteria (pgpr), pseudomonas fluorescens pf153 and pseudomonas sp. dsmz 13134, in the root and rhizoplane of inoculated maize plants. this was performed in pot experiments with three contrasting field soils (buus, le caron and dok-m). potential cross-reactivity of the qpcr assays was assessed with indigenous pseudomonas and related bacterial species ...	2016	28119675
mycobiome in the lower respiratory tract - a clinical perspective.	recently the paradigm that the healthy lung is sterile was challenged and it is now believed that the lungs harbor a diverse microbiota also contributing to the pathogenesis of various diseases. most of the research studies targeting the respiratory microbiome have focused on bacteria and their impact on lung health and lung diseases. recently, also the mycobiome has gained attention. lower respiratory tract (lrt) diseases (e.g., cystic fibrosis) and other diseases or conditions (e.g., hiv infec ...	2016	28119685
mycobiome in the lower respiratory tract - a clinical perspective.	recently the paradigm that the healthy lung is sterile was challenged and it is now believed that the lungs harbor a diverse microbiota also contributing to the pathogenesis of various diseases. most of the research studies targeting the respiratory microbiome have focused on bacteria and their impact on lung health and lung diseases. recently, also the mycobiome has gained attention. lower respiratory tract (lrt) diseases (e.g., cystic fibrosis) and other diseases or conditions (e.g., hiv infec ...	2016	28119685