Publications

pharmacological potentials of premna integrifolia l.	premna integrifolia linn. (verbenaceae) is an important constituent of the formulation of ten roots of herbs known as daśamūla and is widely used for treating various ailments in the indian system of medicine. aim of this review is to provide comprehensive information on the pharmacological activities of various parts of p. integrifolia. all the relevant universally accepted electronic databases were searched with respect to the terms "agnimanthā", "headache tree", "premna integrifolia", "premna ...	2016	27143797
recent developments in using advanced sequencing technologies for the genomic studies of lignin and cellulose degrading microorganisms.	lignin is a complex polyphenyl aromatic compound which exists in tight associations with cellulose and hemicellulose to form plant primary and secondary cell wall. lignocellulose is an abundant renewable biomaterial present on the earth. it has gained much attention in the scientific community in recent years because of its potential applications in bio-based industries. microbial degradation of lignocellulose polymers was well studied in wood decaying fungi. based on the plant materials they de ...	2016	26884714
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
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
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
abstracts.		2016	27243148
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
molecular cloning and functional expression of a δ9- fatty acid desaturase from an antarctic pseudomonas sp. a3.	fatty acid desaturase enzymes play an essential role in the synthesis of unsaturated fatty acids. pseudomonas sp. a3 was found to produce a large amount of palmitoleic and oleic acids after incubation at low temperatures. using polymerase chain reaction (pcr), a novel δ9- fatty acid desaturase gene was isolated, cloned, and successfully expressed in escherichia coli. the gene was designated as pa3fad9 and has an open reading frame of 1,185 bp which codes for 394 amino acids with a predicted mole ...	2016	27494717
isolation of bdellovibrio sp. from soil samples in mexico and their potential applications in control of pathogens.	in this study, two strains of bdellovibrio were isolated from soil samples using the culture-dependent technique and two members of the family enterobacteriaceae (klebsiella sp. and salmonella sp.) as prey. the bdellovibrio strains were bacteriolytic, plaque-forming, and highly motile gram-negative bacteria. we identified and confirmed the bdellovibrio strains using microscopy, pcr amplification, and sequencing of the 16s rrna gene. they were observed to be different strains based on hit locus a ...	2016	27297185
functional exploration of the polysaccharide lyase family pl6.	alginate, the main cell-wall polysaccharide of brown algae, is composed of two residues: mannuronic acid (m-residues) and, its c5-epimer, guluronic acid (g-residues). alginate lyases define a class of enzymes that cleave the glycosidic bond of alginate by β-elimination. they are classified according to their ability to recognize the distribution of m- and g-residues and are named m-, g- or mg-lyases. in the cazy database, alginate lyases have been grouped by sequence similarity into seven distin ...	2016	27438604
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
a novel mva-mediated pathway for isoprene production in engineered e. coli.	to deal with the increasingly severe energy crisis and environmental consequences, biofuels and biochemicals generated from renewable resources could serve as a promising alternative for replacing petroleum as a source of fuel and chemicals, among which isoprene (2-methyl-1,3-butadiene) in particular is of great significance in that it is an important platform chemical, which has been used in industrial production of synthetic rubber for tires and coatings or aviation fuel.	2016	26786050
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
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
mechanistic insights into c-di-gmp-dependent control of the biofilm regulator fleq from pseudomonas aeruginosa.	bacterial biofilm formation during chronic infections confers increased fitness, antibiotic tolerance, and cytotoxicity. in many pathogens, the transition from a planktonic lifestyle to collaborative, sessile biofilms represents a regulated process orchestrated by the intracellular second-messenger c-di-gmp. a main effector for c-di-gmp signaling in the opportunistic pathogen pseudomonas aeruginosa is the transcription regulator fleq. fleq is a bacterial enhancer-binding protein (bebp) with a ce ...	2016	26712005
mechanistic insights into c-di-gmp-dependent control of the biofilm regulator fleq from pseudomonas aeruginosa.	bacterial biofilm formation during chronic infections confers increased fitness, antibiotic tolerance, and cytotoxicity. in many pathogens, the transition from a planktonic lifestyle to collaborative, sessile biofilms represents a regulated process orchestrated by the intracellular second-messenger c-di-gmp. a main effector for c-di-gmp signaling in the opportunistic pathogen pseudomonas aeruginosa is the transcription regulator fleq. fleq is a bacterial enhancer-binding protein (bebp) with a ce ...	2016	26712005
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
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
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
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
analysis of plant growth-promoting effects of fluorescent pseudomonas strains isolated from mentha piperita rhizosphere and effects of their volatile organic compounds on essential oil composition.	many species or strains of the genus pseudomonas have been characterized as plant growth promoting rhizobacteria (pgpr). we used a combination of phenotypic and genotypic techniques to analyze the community of fluorescent pseudomonas strains in the rhizosphere of commercially grown mentha piperita (peppermint). biochemical techniques, amplified rdna restriction analysis (ardra), and 16s rrna gene sequence analysis revealed that the majority of the isolated native fluorescent strains were p. puti ...	2016	27486441
bacteria with phosphate solubilizing capacity alter mycorrhizal fungal growth both inside and outside the root and in the presence of native microbial communities.	arbuscular mycorrhizal fungi (amf) and phosphate solubilizing pseudomonas bacteria (psb) could potentially interact synergistically because psb solubilize phosphate into a form that amf can absorb and transport to the plant. however, very little is known about the interactions between these two groups of microorganisms and how they influence the growth of each other. we tested whether different strains of bacteria, that have the capacity to solubilize phosphate, are able to grow along amf hyphae ...	2016	27253975
antagonistic control of the turnover pathway for the global regulatory srna csrb by the csra and csrd proteins.	the widely conserved protein csra (carbon storage regulator a) globally regulates bacterial gene expression at the post-transcriptional level. in many species, csra activity is governed by untranslated srnas, csrb and csrc in escherichia coli, which bind to multiple csra dimers, sequestering them from lower affinity mrna targets. both the synthesis and turnover of csrb/c are regulated. their turnover requires the housekeeping endonuclease rnase e and is activated by the presence of a preferred c ...	2016	27235416
biosynthesis, chemical structure, and structure-activity relationship of orfamide lipopeptides produced by pseudomonas protegens and related species.	orfamide-type cyclic lipopeptides (clps) are biosurfactants produced by pseudomonas and involved in lysis of oomycete zoospores, biocontrol of rhizoctonia and insecticidal activity against aphids. in this study, we compared the biosynthesis, structural diversity, in vitro and in planta activities of orfamides produced by rhizosphere-derived pseudomonas protegens and related pseudomonas species. genetic characterization together with chemical identification revealed that the main orfamide compoun ...	2016	27065956
temperature and redox effect on mineral colonization in juan de fuca ridge flank subsurface crustal fluids.	to examine microbe-mineral interactions in subsurface oceanic crust, we evaluated microbial colonization on crustal minerals that were incubated in borehole fluids for 1 year at the seafloor wellhead of a crustal borehole observatory (iodp hole u1301a, juan de fuca ridge flank) as compared to an experiment that was not exposed to subsurface crustal fluids (at nearby iodp hole u1301b). in comparison to previous studies at these same sites, this approach allowed assessment of the effects of temper ...	2016	27064928
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
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