Publications

biochar treatment resulted in a combined effect on soybean growth promotion and a shift in plant growth promoting rhizobacteria.	the application of biochar to soil is considered to have the potential for long-term soil carbon sequestration, as well as for improving plant growth and suppressing soil pathogens. in our study we evaluated the effect of biochar on the plant growth of soybeans, as well as on the community composition of root-associated bacteria with plant growth promoting traits. two types of biochar, namely, maize biochar (mbc), wood biochar (wbc), and hydrochar (htc) were used for pot experiments to monitor p ...	2016	26941730
carbon nanomaterials in agriculture: a critical review.	there has been great interest in the use of carbon nano-materials (cnms) in agriculture. however, the existing literature reveals mixed effects from cnm exposure on plants, ranging from enhanced crop yield to acute cytotoxicity and genetic alteration. these seemingly inconsistent research-outcomes, taken with the current technological limitations for in situ cnm detection, present significant hurdles to the wide scale use of cnms in agriculture. the objective of this review is to evaluate the cu ...	2016	26941751
targeting the trehalose utilization pathways of mycobacterium tuberculosis.	tuberculosis (tb) is an epidemic disease and the growing burden of multidrug-resistant (mdr) tb world wide underlines the need to discover new drugs to treat the disease. mycobacterium tuberculosis (mtb) is the etiological agent of most cases of tb. mtb is difficult to treat, in part, due to the presence of a sturdy hydrophobic barrier that prevents penetration of drugs through the cell wall. mtb can also survive in a non-replicative state for long periods of time avoiding the action of common a ...	2015	26941930
targeting the trehalose utilization pathways of mycobacterium tuberculosis.	tuberculosis (tb) is an epidemic disease and the growing burden of multidrug-resistant (mdr) tb world wide underlines the need to discover new drugs to treat the disease. mycobacterium tuberculosis (mtb) is the etiological agent of most cases of tb. mtb is difficult to treat, in part, due to the presence of a sturdy hydrophobic barrier that prevents penetration of drugs through the cell wall. mtb can also survive in a non-replicative state for long periods of time avoiding the action of common a ...	2015	26941930
the dualistic nature of integrative and conjugative elements.	integrative and conjugative elements (ices) are mobile genetic elements that play a key role in bacterial adaptation. such elements are found in almost every bacterial genera and species, and often code for adaptive traits conferring selective advantages to their host. ices maintain by integrating into and replicating along with a replicon of the host genome. ices can propagate by conjugative transfer toward a recipient cell following excision from the replicon as a circular covalently-closed mo ...	2015	26942046
biological manganese oxidation by pseudomonas putida in trickling filters.	biological oxidation has been researched as a viable alternative for treating waters with high manganese (mn) concentrations, typically found in mine drainage or in some geological formations. in this study, laboratory-scale trickling filters were constructed to compare the mn removal efficiency between filters inoculated with the mn oxidizing bacteria, pseudomonas putida, and filters without inoculation. manganese oxidation and removal was found to be significantly greater in trickling filters ...	2016	26943637
mycelium-like networks increase bacterial dispersal, growth, and biodegradation in a model ecosystem at various water potentials.	fungal mycelia serve as effective dispersal networks for bacteria in water-unsaturated environments, thereby allowing bacteria to maintain important functions, such as biodegradation. however, poor knowledge exists on the effects of dispersal networks at various osmotic (ψo) and matric (ψm) potentials, which contribute to the water potential mainly in terrestrial soil environments. here we studied the effects of artificial mycelium-like dispersal networks on bacterial dispersal dynamics and subs ...	2016	26944849
two superoxide dismutases from tnotchr are involved in detoxification of reactive oxygen species induced by chromate.	superoxide dismutases (sod) have been reported as the most relevant bacterial enzymes involved in cells protection from reactive oxygen species (ros). these toxic species are often the product of heavy metal stress.	2016	26944876
airborne toluene removal for minimizing occupational health exposure by means of a trickle-bed biofilter.	the paper presents the experimental results on a biotrickling pilot plant, with a water scrubber as pre-treatment, finalized to the treatment of an airborne toluene stream in a working place. the air stream was characterized by a very high variability of the inlet concentrations of toluene (range: 4.35-68.20 mg nm(-3)) with an average concentrations of 16.41 mg nm(-3). the pilot plant has proved its effectiveness in toluene removal, along a 90-day experimentation period, in steady-state conditio ...	2016	26946504
dynamic clustering of the bacterial sensory kinase baes.	several bacterial sensory-kinase receptors form clusters on the cell membrane. however, the dynamics of sensory-kinase clustering are largely unclear. using measurements of fluorescence anisotropy and time-lapse imaging of escherichia coli cells, we demonstrate that copper ions trigger self-association of baes receptors and lead to rapid formation of clusters, which can be reversibly dispersed by a metal chelator. copper ions did not trigger self-association of other fluorescently tagged sensory ...	2016	26950881
using mutability landscapes of a promiscuous tautomerase to guide the engineering of enantioselective michaelases.	the michael-type addition reaction is widely used in organic synthesis for carbon-carbon bond formation. however, biocatalytic methodologies for this type of reaction are scarce, which is related to the fact that enzymes naturally catalysing carbon-carbon bond-forming michael-type additions are rare. a promising template to develop new biocatalysts for carbon-carbon bond formation is the enzyme 4-oxalocrotonate tautomerase, which exhibits promiscuous michael-type addition activity. here we prese ...	2016	26952338
a phopq-regulated abc transporter system exports tetracycline in pseudomonas aeruginosa.	pseudomonas aeruginosa is an important human pathogen whose infections are difficult to treat due to its high intrinsic resistance to many antibiotics. here, we show that the disruption of pa4456, encoding the atp binding component of a putative atp-binding cassette (abc) transporter, increased the bacterium's susceptible to tetracycline and other antibiotics or toxic chemicals. fluorescence spectroscopy and antibiotic accumulation tests showed that the interruption of the abc transporter caused ...	2016	26953208
delineation of steroid-degrading microorganisms through comparative genomic analysis.	steroids are ubiquitous in natural environments and are a significant growth substrate for microorganisms. microbial steroid metabolism is also important for some pathogens and for biotechnical applications. this study delineated the distribution of aerobic steroid catabolism pathways among over 8,000 microorganisms whose genomes are available in the ncbi refseq database. combined analysis of bacterial, archaeal, and fungal genomes with both hidden markov models and reciprocal blast identified 2 ...	2016	26956583
the cryptic dsda gene encodes a functional d-serine dehydratase in pseudomonas aeruginosa pao1.	d-serine, an important neurotransmitter, also contributes to bacterial adaptation and virulence in humans. it was reported that pseudomonas aeruginosa pao1 can grow on d-serine as the sole nitrogen source, and growth was severely reduced in the dada mutant devoid of the d-alanine dehydrogenase with broad substrate specificity. in this study, the dsda gene (pa3357) encoding a putative d-serine dehydratase was subjected to further characterization. growth on d-serine as the sole source of nitrogen ...	2016	26957519
photoactivation reduces side-chain dynamics of a lov photoreceptor.	we used neutron-scattering experiments to probe the conformational dynamics of the light, oxygen, voltage (lov) photoreceptor ppsb1-lov from pseudomonas putida in both the dark and light states. global protein diffusion and internal macromolecular dynamics were measured using incoherent neutron time-of-flight and backscattering spectroscopy on the picosecond to nanosecond timescales. global protein diffusion of ppsb1-lov is not influenced by photoactivation. observation-time-dependent global dif ...	2016	26958884
rationally rewiring the connectivity of the xylr/pu regulatory node of the m-xylene degradation pathway in pseudomonas putida.	the xylr/pu regulatory node of the m-xylene biodegradation pathway of pseudomonas putida mt-2 is one of the most intricate cases of processing internal and external cues into a single controlling element. despite this complexity, the performance of the regulatory system is determined in vivo only by the occupation of pu by m-xylene-activated xylr and σ(54)-rnap. the stoichiometry between these three elements defines natural system boundaries that outline a specific functional space. this space c ...	2016	26961967
genomic islands 1 and 2 play key roles in the evolution of extensively drug-resistant st235 isolates of pseudomonas aeruginosa.	pseudomonas aeruginosa are noscomially acquired, opportunistic pathogens that pose a major threat to the health of burns patients and the immunocompromised. we sequenced the genomes of p. aeruginosa isolates rns_pa1, rns_pa46 and rns_pae05, which displayed resistance to almost all frontline antibiotics, including gentamicin, piperacillin, timentin, meropenem, ceftazidime and colistin. we provide evidence that the isolates are representatives of p. aeruginosa sequence type (st) 235 and carry tn61 ...	2016	26962050
matrix-assisted laser desorption ionization time-of-flight mass spectrometry for rapid identification of mold and yeast cultures of penicillium marneffei.	penicillium marneffei is the most important thermal dimorphic fungus causing systemic mycosis in hiv-infected and other immunocompromised patients in southeast asia. however, laboratory diagnosis of penicilliosis, which relies on microscopic morphology and mycelial-to-yeast conversion, is time-consuming and expertise-dependent, thus delaying diagnosis and treatment. although matrix -assisted laser desorption ionization time-of-flight mass spectrometry (maldi-tof ms) is useful for identification ...	2016	26965891
tactic response of bacteria to zero-valent iron nanoparticles.	the microbial assessment of pollutant toxicity rarely includes behavioral responses. in this study, we investigated the tactic response of pseudomonas putida g7, a representative of soil bacterium, towards engineered zero-valent iron nanoparticles (nzvis), as a new end-point assessment of toxicity. the study integrated the characterization of size distribution and charge of nzvis and tactic reaction response by means of inverted capillary assay and computer-assisted motion analysis of motility b ...	2016	26967351
biological low-ph mn(ii) oxidation in a manganese deposit influenced by metal-rich groundwater.	the mechanisms, key organisms, and geochemical significance of biological low-ph mn(ii) oxidation are largely unexplored. here, we investigated the structure of indigenous mn(ii)-oxidizing microbial communities in a secondary subsurface mn oxide deposit influenced by acidic (ph 4.8) metal-rich groundwater in a former uranium mining area. microbial diversity was highest in the mn deposit compared to the adjacent soil layers and included the majority of known mn(ii)-oxidizing bacteria (mob) and tw ...	2016	26969702
different transcriptional responses from slow and fast growth rate strains of listeria monocytogenes adapted to low temperature.	listeria monocytogenes has become one of the principal foodborne pathogens worldwide. the capacity of this bacterium to grow at low temperatures has opened an interesting field of study in terms of the identification and classification of new strains of l. monocytogenes with different growth capacities at low temperatures. we determined the growth rate at 8°c of 110 strains of l. monocytogenes isolated from different food matrices. we identified a group of slow and fast strains according to thei ...	2016	26973610
formaldehyde stress responses in bacterial pathogens.	formaldehyde is the simplest of all aldehydes and is highly cytotoxic. its use and associated dangers from environmental exposure have been well documented. detoxification systems for formaldehyde are found throughout the biological world and they are especially important in methylotrophic bacteria, which generate this compound as part of their metabolism of methanol. formaldehyde metabolizing systems can be divided into those dependent upon pterin cofactors, sugar phosphates and those dependent ...	2016	26973631
biocatalytic desulfurization capabilities of a mixed culture during non-destructive utilization of recalcitrant organosulfur compounds.	we investigated the biodesulfurization potential of a mixed culture ak6 enriched from petroleum hydrocarbons-polluted soil with dibenzothiophene (dbt) as a sulfur source. in addition to dbt, ak6 utilized the following compounds as sulfur sources: 4-methyldibenzothiophene (4-mdbt), benzothiophene (bt), and 4,6- dimethyldibenzothiophene (4,6-dm-dbt). none of these compounds supported the growth of ak6 as the sole carbon and sulfur source. ak6 could not grow on dibenzylsulfide (dbs) as a sulfur sou ...	2016	26973637
engineering modular viral scaffolds for targeted bacterial population editing.	bacteria are central to human health and disease, but existing tools to edit microbial consortia are limited. for example, broad-spectrum antibiotics are unable to accurately manipulate bacterial communities. bacteriophages can provide highly specific targeting of bacteria, but assembling well-defined phage cocktails solely with natural phages can be a time-, labor- and cost-intensive process. here, we present a synthetic-biology strategy to modulate phage host ranges by engineering phage genome ...	2015	26973885
linalool isomerase, a membrane-anchored enzyme in the anaerobic monoterpene degradation in thauera linaloolentis 47lol.	thauera linaloolentis 47lol uses the tertiary monoterpene alcohol (r,s)-linalool as sole carbon and energy source under denitrifying conditions. the conversion of linalool to geraniol had been observed in carbon-excess cultures, suggesting the presence of a 3,1-hydroxyl-δ(1)-δ(2)-mutase (linalool isomerase) as responsible enzyme. to date, only a single enzyme catalyzing such a reaction is described: the linalool dehydratase/isomerase (ldi) from castellaniella defragrans 65phen acting only on (s) ...	2016	26979141
whole-genome identification, phylogeny, and evolution of the cytochrome p450 family 2 (cyp2) subfamilies in birds.	the cytochrome p450 (cyp) superfamily defends organisms from endogenous and noxious environmental compounds, and thus is crucial for survival. however, beyond mammals the molecular evolution of cyp2 subfamilies is poorly understood. here, we characterized the cyp2 family across 48 avian whole genomes representing all major extant bird clades. overall, 12 cyp2 subfamilies were identified, including the first description of the cyp2f, cyp2g, and several cyp2af genes in avian genomes. some of the c ...	2016	26979796
transcriptional profiling of klebsiella pneumoniae defines signatures for planktonic, sessile and biofilm-dispersed cells.	surface-associated communities of bacteria, known as biofilms, play a critical role in the persistence and dissemination of bacteria in various environments. biofilm development is a sequential dynamic process from an initial bacterial adhesion to a three-dimensional structure formation, and a subsequent bacterial dispersion. transitions between these different modes of growth are governed by complex and partially known molecular pathways.	2016	26979871
volatile compounds emitted by pseudomonas aeruginosa stimulate growth of the fungal pathogen aspergillus fumigatus.	chronic lung infections with opportunistic bacterial and fungal pathogens are a major cause of morbidity and mortality especially in patients with cystic fibrosis. pseudomonas aeruginosa is the most frequently colonizing bacterium in these patients, and it is often found in association with the filamentous fungus aspergillus fumigatus. p. aeruginosa is known to inhibit the growth of a. fumigatus in situations of direct contact, suggesting the existence of interspecies communication that may infl ...	2016	26980832
synthesis and evaluation of mannitol-based inhibitors for lipopolysaccharide biosynthesis.	antibiotic resistance is a serious threat against humankind and the need for new therapeutics is crucial. without working antibiotics, diseases that we thought were extinct will come back. in this paper two new mannitol bisphosphate analogs, 1,6-dideoxy-1,6-diphosphoramidate mannitol and 1,6-dideoxy-1,6-dimethansulfonamide mannitol, have been synthesized and evaluated as potential inhibitors of the enzyme gmhb in the biosynthesis of lipopolysaccharides. 1,6-dideoxy-1,6-diphosphoramidate mannitol ...	2016	26981280
cytokinin production by pseudomonas fluorescens g20-18 determines biocontrol activity against pseudomonas syringae in arabidopsis.	plant beneficial microbes mediate biocontrol of diseases by interfering with pathogens or via strengthening the host. although phytohormones, including cytokinins, are known to regulate plant development and physiology as well as plant immunity, their production by microorganisms has not been considered as a biocontrol mechanism. here we identify the ability of pseudomonas fluorescens g20-18 to efficiently control p. syringae infection in arabidopsis, allowing maintenance of tissue integrity and ...	2016	26984671
antibiotic resistance mechanisms of myroides sp.	bacteria of the genus myroides (myroides spp.) are rare opportunistic pathogens. myroides sp. infections have been reported mainly in china. myroides sp. is highly resistant to most available antibiotics, but the resistance mechanisms are not fully elucidated. current strain identification methods based on biochemical traits are unable to identify strains accurately at the species level. while 16s ribosomal rna (rrna) gene sequencing can accurately achieve this, it fails to give information on t ...	2016	26984839
understanding butanol tolerance and assimilation in pseudomonas putida bird-1: an integrated omics approach.	pseudomonas putida bird-1 has the potential to be used for the industrial production of butanol due to its solvent tolerance and ability to metabolize low-cost compounds. however, the strain has two major limitations: it assimilates butanol as sole carbon source and butanol concentrations above 1% (v/v) are toxic. with the aim of facilitating bird-1 strain design for industrial use, a genome-wide mini-tn5 transposon mutant library was screened for clones exhibiting increased butanol sensitivity ...	2016	26986205
the higb/higa toxin/antitoxin system of pseudomonas aeruginosa influences the virulence factors pyochelin, pyocyanin, and biofilm formation.	toxin/antitoxin (ta) systems are prevalent in most bacterial and archaeal genomes, and one of the emerging physiological roles of ta systems is to help regulate pathogenicity. although ta systems have been studied in several model organisms, few studies have investigated the role of ta systems in pseudomonads. here, we demonstrate that the previously uncharacterized proteins higb (unannotated) and higa (pa4674) of pseudomonas aeruginosa pa14 form a type ii ta system in which antitoxin higa masks ...	2016	26987441
unusual microorganisms and antimicrobial resistances in a group of syrian migrants: sentinel surveillance data from an asylum seekers centre in italy.	three years of civil war in syria have caused death and increase of communicable diseases. the suffering population has been forced to migrate creating a fertile condition for epidemic spread of infection within the refugee camps.	2017	26987764
recent advances in the elucidation of enzymatic function in natural product biosynthesis.	with the successful production of artemisinic acid in yeast, the promising potential of synthetic biology for natural product biosynthesis is now being realized. the recent total biosynthesis of opioids in microbes is considered to be another landmark in this field. the importance and significance of enzymes in natural product biosynthetic pathways have been re-emphasized by these advancements. therefore, the characterization and elucidation of enzymatic function in natural product biosynthesis ...	2015	26989472
recent advances in the elucidation of enzymatic function in natural product biosynthesis.	with the successful production of artemisinic acid in yeast, the promising potential of synthetic biology for natural product biosynthesis is now being realized. the recent total biosynthesis of opioids in microbes is considered to be another landmark in this field. the importance and significance of enzymes in natural product biosynthetic pathways have been re-emphasized by these advancements. therefore, the characterization and elucidation of enzymatic function in natural product biosynthesis ...	2015	26989472
comparative study of wastewater treatment and nutrient recycle via activated sludge, microalgae and combination systems.	algal-bacterial synergistic cultivation could be an optional wastewater treatment technology in temperate areas. in this study, a locally screened vigorous chlorella strain was characterized and then it was used in a comparative study of wastewater treatment and nutrient recycle assessment via activated sludge (as), microalgae and their combination systems. chlorella sp. cultured with as in light showed the best performance, in which case the removal efficiencies of cod, nh3-n and tp were 87.3%, ...	2016	26995615
biodegradation of phenol by bacteria strain acinetobacter calcoaceticus pa isolated from phenolic wastewater.	a phenol-degrading bacterium strain pa was successfully isolated from the effluent of petrochemical wastewater. based on its morphological, physiological and biochemical characteristics, the strain pa was characterized as a gram-negative, strictly aerobic, nonmotile and short rod-shaped bacterium that utilizes phenol as a sole carbon and energy source. 16s rdna sequence analysis revealed that this strain is affiliated to acinetobacter calcoaceticus in the group of gammaproteobacteria. the strain ...	2016	27005648
towards an enhanced understanding of plant-microbiome interactions to improve phytoremediation: engineering the metaorganism.	phytoremediation is a promising technology to clean-up contaminated soils based on the synergistic actions of plants and microorganisms. however, to become a widely accepted, and predictable remediation alternative, a deeper understanding of the plant-microbe interactions is needed. a number of studies link the success of phytoremediation to the plant-associated microbiome functioning, though whether the microbiome can exist in alternative, functional states for soil remediation, is incompletely ...	2016	27014254
potential biotechnological strategies for the cleanup of heavy metals and metalloids.	global mechanization, urbanization, and various natural processes have led to the increased release of toxic compounds into the biosphere. these hazardous toxic pollutants include a variety of organic and inorganic compounds, which pose a serious threat to the ecosystem. the contamination of soil and water are the major environmental concerns in the present scenario. this leads to a greater need for remediation of contaminated soils and water with suitable approaches and mechanisms. the conventi ...	2016	27014323
epoxyalkane:coenzyme m transferase gene diversity and distribution in groundwater samples from chlorinated-ethene-contaminated sites.	epoxyalkane:coenzyme m transferase (eacomt) plays a critical role in the aerobic biodegradation and assimilation of alkenes, including ethene, propene, and the toxic chloroethene vinyl chloride (vc). to improve our understanding of the diversity and distribution of eacomt genes in the environment, novel eacomt-specific terminal-restriction fragment length polymorphism (t-rflp) and nested-pcr methods were developed and applied to groundwater samples from six different contaminated sites. t-rflp a ...	2016	27016563
relating carbon and nitrogen isotope effects to reaction mechanisms during aerobic or anaerobic degradation of rdx (hexahydro-1,3,5-trinitro-1,3,5-triazine) by pure bacterial cultures.	kinetic isotopic fractionation of carbon and nitrogen during rdx (hexahydro-1,3,5-trinitro-1,3,5-triazine) biodegradation was investigated with pure bacterial cultures under aerobic and anaerobic conditions. relatively large bulk enrichments in (15)n were observed during biodegradation of rdx via anaerobic ring cleavage (ε(15)n = -12.7‰ ± 0.8‰) and anaerobic nitro reduction (ε(15)n = -9.9‰ ± 0.7‰), in comparison to smaller effects during biodegradation via aerobic denitration (ε(15)n = -2.4‰ ± 0 ...	2016	27016566
potentiation of aminoglycoside activity in pseudomonas aeruginosa by targeting the amgrs envelope stress-responsive two-component system.	a screen for agents that potentiated the activity of paromomycin (par), a 4,5-linked aminoglycoside (ag), against wild-type pseudomonas aeruginosa identified the rna polymerase inhibitor rifampin (rif). rif potentiated additional 4,5-linked ags, such as neomycin and ribostamycin, but not the clinically important 4,6-linked ags amikacin and gentamicin. potentiation was absent in a mutant lacking the amgrs envelope stress response two-component system (tcs), which protects the organism from ag-gen ...	2016	27021319
going beyond the control of quorum-sensing to combat biofilm infections.	most bacteria attach to surfaces where they form a biofilm, cells embedded in a complex matrix of polymers. cells in biofilms are much better protected against noxious agents than free-living cells. as a consequence it is very difficult to control pathogens with antibiotics in biofilm infections and novel targets are urgently needed. one approach aims at the communication between cells to form and to maintain a biofilm, a process called quorum-sensing. water soluble small-sized molecules mediate ...	2016	27025518
metabolic inhibition of meloxicam by specific cyp2c9 inhibitors in cunninghamella blakesleeana ncim 687: in silico and in vitro studies.	specific inhibitors of cytochrome p4502c9 enzyme (cyp2c9) viz. clopidogrel, fenofibrate fluvoxamine and sertraline at concentration of 50, 100, 150 and 200 µm were employed to investigate the nature of enzyme involved in bioconversion of meloxicam to its main metabolite 5-oh methyl meloxicam by cunninghamella blakesleeana. virtual screening for interaction of specific cyp2c9 inhibitors with human cyp2c9 enzyme was performed by molecular docking using auto dock vina 4.2 version. the in silico stu ...	2016	27026863
multidrug efflux systems in helicobacter cinaedi.	helicobacter cinaedi causes infections, such as bacteremia, diarrhea and cellulitis in mainly immunocompromised patients. this pathogen is often problematic to analyze, and insufficient information is available, because it grows slowly and poorly in subculture under a microaerobic atmosphere. the first-choice therapy to eradicate h. cinaedi is antimicrobial chemotherapy; however, its use is linked to the development of resistance. although we need to understand the antimicrobial resistance mecha ...	2012	27029418
numerical modelling of biophysicochemical effects on multispecies reactive transport in porous media involving pseudomonas putida for potential microbial enhanced oil recovery application.	ph and resident time of injected slug plays a critical role in characterizing the reservoir for potential microbial enhanced oil recovery (meor) application. to investigate meor processes, a multispecies (microbes-nutrients) reactive transport model in porous media was developed by coupling kinetic and transport model. the present work differs from earlier works by explicitly determining parametric values required for kinetic model by experimental investigations using pseudomonas putida at diffe ...	2016	27030954
pseudomonas putida biofilm dynamics following a single pulse of silver nanoparticles.	pseudomonas putida mono-species biofilms were exposed to silver nanoparticles (ag nps) in artificial wastewater (aw) under hydrodynamic conditions. specifically, 48 h old biofilms received a single pulse of ag nps at 0, 0.01, 0.1, 1, 10 and 100 mg l(-1) for 24 h in confocal laser scanning microscopy (clsm) compatible flow-cells. the biofilm dynamics (in terms of morphology, viability and activity) were characterised at 48, 72 and 96 h. consistent patterns were found across flow-cells and experim ...	2016	27031799
constitutive expression of a nag-like dioxygenase gene through an internal promoter in the 2-chloronitrobenzene catabolism gene cluster of pseudomonas stutzeri zwlr2-1.	the gene cluster encoding the 2-chloronitrobenzene (2cnb) catabolism pathway in pseudomonas stutzeri zwlr2-1 is a patchwork assembly of a nag-like dioxygenase (dioxygenase belonging to the naphthalene dioxygenase nagaaabacad family from ralstonia sp. strain u2) gene cluster and a chlorocatechol catabolism cluster. however, the transcriptional regulator gene usually present in the nag-like dioxygenase gene cluster is missing, leaving it unclear how this cluster is expressed. the pattern of expres ...	2016	27037114
regulatory activities of four arsr proteins in agrobacterium tumefaciens 5a.	arsr is a well-studied transcriptional repressor that regulates microbe-arsenic interactions. most microorganisms have an arsr gene, but in cases where multiple copies exist, the respective roles or potential functional overlap have not been explored. we examined the repressors encoded by arsr1 and arsr2 (ars1 operon) and by arsr3 and arsr4 (ars2 operon) in agrobacterium tumefaciens 5a. arsr1 and arsr4 are very similar in their primary sequences and diverge phylogenetically from arsr2 and arsr3, ...	2016	27037117
effects of polycyclic aromatic hydrocarbon mixtures on degradation, gene expression, and metabolite production in four mycobacterium species.	polycyclic aromatic hydrocarbons (pahs) are widespread environmental contaminants that are hazardous to human health. it has been demonstrated that members of the mycobacterium genus are among the most effective degraders of pahs, but few studies have focused on the degradation of pah mixtures. in this study, single and mixed pah metabolism was investigated in four phylogenetically distinct mycobacterium species with respect to (i) parent compound degradation, (ii) bacterial growth, (iii) catabo ...	2016	27037123
loop-grafted old yellow enzymes in the bienzymatic cascade reduction of allylic alcohols.	the enzymatic reduction of c=c bonds in allylic alcohols with old yellow enzymes represents a challenging task, due to insufficient activation through the hydroxy group. in our work, we coupled an alcohol dehydrogenase with three wild-type ene reductases-namely nicotinamide-dependent cyclohex-2-en-1-one reductase (ncr) from zymomonas mobilis, oye1 from saccharomyces pastorianus and morphinone reductase (mr) from pseudomonas putida m10-and four rationally designed β/α loop variants of ncr in the ...	2016	27037735
multi-host environments select for host-generalist conjugative plasmids.	conjugative plasmids play an important role in bacterial evolution by transferring ecologically important genes within and between species. a key limit on interspecific horizontal gene transfer is plasmid host range. here, we experimentally test the effect of single and multi-host environments on the host-range evolution of a large conjugative mercury resistance plasmid, pqbr57. specifically, pqbr57 was conjugated between strains of a single host species, either p. fluorescens or p. putida, or a ...	2016	27039285
rice-field drowning-associated pneumonia in which pseudomonas spp., aspergillus fumigatus, and cunninghamella sp. are isolated.	we herein report the case of an 84-year-old who developed pneumonia after drowning in a rice field. besides aspergillus fumigatus, many pathogens previously not reported in drowning-associated pneumonia (such as pseudomonas fluorescens, pseudomonas putida, nocardia niigatensis, and cunninghamella sp.) were isolated from his sputum. he received sulbactam/ampicillin, trimethoprim/sulfamethoxazole, voriconazole, levofloxacin and liposomal amphotericin b, but died due to respiratory failure. because ...	2016	27041173
analysis of a spontaneous non-motile and avirulent mutant shows that flim is required for full endoflagella assembly in leptospira interrogans.	pathogenic leptospira strains are responsible for leptospirosis, a worldwide emerging zoonotic disease. these spirochetes are unique amongst bacteria because of their corkscrew-like cell morphology and their periplasmic flagella. motility is reported as an important virulence determinant, probably favoring entry and dissemination of pathogenic leptospira in the host. however, proteins constituting the periplasmic flagella and their role in cell shape, motility and virulence remain poorly describ ...	2016	27044038
convenient broad-host-range unstable vectors for studying stabilization cassettes in diverse bacteria.	low-copy-number vectors of potential wide application in biotechnology need to encode stabilization modules ensuring their stable inheritance. the efficiency of stabilization may vary depending on the plasmid host so a thorough analysis of stabilization functions is required before use.	2016	27044351
transcriptional kinetics of the cross-talk between the ortho-cleavage and tol pathways of toluene biodegradation in pseudomonas putida mt-2.	the tol plasmid promoters are activated by toluene leading to gene expression responsible for the degradation of the environmental signal. benzoate is formed as an intermediate, activating the benr protein of the chromosomal ortho-cleavage pathway that up-regulates the chromosomal pbena promoter and the tol pm promoter resulting in cross-talk between the two networks. herein, the transcriptional kinetics of the pbenr and pbena promoters in conjunction with tol promoters was monitored by real-tim ...	2016	27046069
zinc-induced transposition of insertion sequence elements contributes to increased adaptability of cupriavidus metallidurans.	bacteria can respond to adverse environments by increasing their genomic variability and subsequently facilitating adaptive evolution. to demonstrate this, the contribution of insertion sequence (is) elements to the genetic adaptation of cupriavidus metallidurans ae126 to toxic zinc concentrations was determined. this derivative of type strain ch34, devoid of its main zinc resistance determinant, is still able to increase its zinc resistance level. specifically, upon plating on medium supplement ...	2016	27047473
keeping the wolves at bay: antitoxins of prokaryotic type ii toxin-antitoxin systems.	in their initial stages of discovery, prokaryotic toxin-antitoxin (ta) systems were confined to bacterial plasmids where they function to mediate the maintenance and stability of usually low- to medium-copy number plasmids through the post-segregational killing of any plasmid-free daughter cells that developed. their eventual discovery as nearly ubiquitous and repetitive elements in bacterial chromosomes led to a wealth of knowledge and scientific debate as to their diversity and functionality i ...	2016	27047942
singly flagellated pseudomonas aeruginosa chemotaxes efficiently by unbiased motor regulation.	pseudomonas aeruginosais an opportunistic human pathogen that has long been known to chemotax. more recently, it has been established that chemotaxis is an important factor in the ability ofp. aeruginosato make biofilms. genes that allowp. aeruginosato chemotax are homologous with genes in the paradigmatic model organism for chemotaxis,escherichia coli however,p. aeruginosais singly flagellated ande. colihas multiple flagella. therefore, the regulation of counterclockwise/clockwise flagellar mot ...	2016	27048795
modulating the import of medium-chain alkanes in e. coli through tuned expression of fadl.	in recent years, there have been intensive efforts to develop synthetic microbial platforms for the production, biosensing and bio-remediation of fossil fuel constituents such as alkanes. building predictable engineered systems for these applications will require the ability to tightly control and modulate the rate of import of alkanes into the host cell. the native components responsible for the import of alkanes within these systems have yet to be elucidated. to shed further insights on this, ...	2016	27053948
ventosimonas gracilis gen. nov., sp. nov., a member of the gammaproteobacteria isolated from cephalotes varians ant guts representing a new family, ventosimonadaceae fam. nov., within the order 'pseudomonadales'.	cephalotes 'turtle' ants are known to harbor a core group of gut symbionts, including members belonging to the gammaproteobacteria. here, we describe the cultivation and characterization of strain cv58t, a novel member of the gammaproteobacteria order pseudomonadales isolated from the guts of the ant cephalotes varians. strain cv58t was rod-shaped, gram-stain-negative, non-motile and formed pale-yellow colonies on trypticase soy agar. optimum growth occurred under an atmosphere of 4-20 % (v/v) o ...	2016	27054961
draft genome sequences of three bacillus species from south african marine sponges.	the rise in antibiotic-resistant bacteria has spurred efforts to identify novel compounds with antimicrobial activity. this brief report describes the genome sequence of threebacillusspecies isolates from south african marine sponges, which produce compounds with antimicrobial activity. a search for secondary metabolite clusters revealed several secondary metabolite pathways in these genomes, which may hold promise as novel antibiotics.	2016	27056214
highly active and stable large catalase isolated from a hydrocarbon degrading aspergillus terreus mtcc 6324.	a hydrocarbon degrading aspergillus terreus mtcc 6324 produces a high level of extremely active and stable cellular large catalase (cat) during growth on n-hexadecane to combat the oxidative stress caused by the hydrocarbon degrading metabolic machinery inside the cell. a 160-fold purification with specific activity of around 66 × 10(5) u mg(-1) protein was achieved. the native protein molecular mass was 368 ± 5 kda with subunit molecular mass of nearly 90 kda, which indicates that the native ca ...	2016	27057351
coordinated regulation of species-specific hydroxycinnamic acid degradation and siderophore biosynthesis pathways in agrobacterium fabrum.	the rhizosphere-inhabiting species agrobacterium fabrum (genomospecies g8 of the agrobacterium tumefaciens species complex) is known to degrade hydroxycinnamic acids (hcas), especially ferulic acid and p-coumaric acid, via the novel a. fabrum hca degradation pathway. gene expression profiles of a. fabrum strain c58 were investigated in the presence of hcas, using a c58 whole-genome oligoarray. both ferulic acid and p-coumaric acid caused variations in the expression of more than 10% of the c58 g ...	2016	27060117
species diversity of environmental gim-1-producing bacteria collected during a long-term outbreak.	reports of outbreaks concerning carbapenemase-producing gram-negative bacteria in which the main source of transmission is the hospital environment are increasing. this study describes the results of environmental sampling in a protracted polyspecies metallo-beta-lactamase gim-1 outbreak driven by plasmids and bacterial clones of enterobacter cloacae and pseudomonas aeruginosa in a tertiary care center. environmental sampling targeting wet locations (especially sinks) was carried out on a surgic ...	2016	27060121
variable effects of exposure to formulated microbicides on antibiotic susceptibility in firmicutes and proteobacteria.	microbicides are broad-spectrum antimicrobial agents that generally interact with multiple pharmacological targets. while they are widely deployed in disinfectant, antiseptic, and preservative formulations, data relating to their potential to select for microbicide or antibiotic resistance have been generated mainly by testing the compounds in much simpler aqueous solutions. in the current investigation, antibiotic susceptibility was determined for bacteria that had previously exhibited decrease ...	2016	27060123
exploring the modular nature of riboswitches and rna thermometers.	natural regulatory rnas like riboswitches and rna thermometers (rnat) have considerable potential in synthetic biology. they are located in the 5' untranslated region (utr) of bacterial mrnas and sense small molecules or changes in temperature, respectively. while riboswitches act on the level of transcription, translation or mrna stability, all currently known rnats regulate translation initiation. in this study, we explored the modularity of riboswitches and rnats and obtained regulatory devic ...	2016	27060146
rna-seq transcriptome analysis of a pseudomonas strain with diversified catalytic properties growth under different culture medium.	biocatalysis is an emerging strategy for the production of enantio-pure organic molecules. however, lacking of commercially available enzymes restricts the widespread application of biocatalysis. in this study, we report a pseudomonas strain which exhibited versatile oxidation activity to synthesize chiral sulfoxides when growing under m9-toluene medium and reduction activity to synthesize chiral alcohols when on luria-bertani (lb) medium, respectively. further comparative transcriptome analysis ...	2016	27061463
methylmercury degradation by pseudomonas putida v1.	environmental contamination of mercury (hg) has caused public health concerns with focuses on the neurotoxic substance methylmercury, due to its bioaccumulation and biomagnification in food chains. the goals of the present study were to examine: (i) the transformation of methylmercury, thimerosal, phenylmercuric acetate and mercuric chloride by cultures of pseudomonas putida v1, (ii) the presence of the genes mera and merb in p. putida v1, and (iii) the degradation pathways of methylmercury by p ...	2016	27062344
structural elucidation and toxicity assessment of degraded products of aflatoxin b1 and b2 by aqueous extracts of trachyspermum ammi.	in this study aqueous extract of seeds and leaves of trachyspermum ammi were evaluated for their ability to detoxify aflatoxin b1 and b2 (afb1; 100 μg l(-1) and afb2; 50 μg l(-1)) by in vitro and in vivo assays. results indicated that t. ammi seeds extract was found to be significant (p < 0.05) in degrading afb1 and afb2 i.e., 92.8 and 91.9% respectively. however, t. ammi leaves extract proved to be less efficient in degrading these aflatoxins, under optimized conditions i.e., ph 8, temperature ...	2016	27064492
spatio-temporal responses of arabidopsis leaves in photosynthetic performance and metabolite contents to burkholderia phytofirmans psjn.	a valuable strategy to improve crop yield consists in the use of plant growth-promoting rhizobacteria (pgprs). however, the influence of pgpr colonization on plant physiology is largely unknown. pgpr burkholderia phytofirmans strain psjn (bp psjn) colonized only arabidopsis thaliana roots after seed or soil inoculation. foliar bacteria were detected only after leaf infiltration. since, different bacterial times of presence and/or locations in host plant could lead to different plant physiologica ...	2016	27066045
rhizospheric bacteria of maize with potential for biocontrol of fusarium verticillioides.	the stalk, ear and root rot (serr) of maize caused by fusarium verticillioides (fv) severely impacts crop production in tropical and subtropical regions. the aim of the present work was to screen bacterial isolates in order to find novel native biocontrol agents against fv. a culturable bacterial collection consisting of 11,520 isolates enriched in firmicutes and proteobacteria was created from rhizosphere samples taken from serr symptomatic or asymptomatic maize plants. the complete collection ...	2016	27066355
comprehensive molecular characterization of methylobacterium extorquens am1 adapted for 1-butanol tolerance.	the toxicity of alcohols is one of the major roadblocks of biological fermentation for biofuels production. methylobacterium extorquens am1, a facultative methylotrophic α-proteobacterium, has been engineered to generate 1-butanol from cheap carbon feedstocks through a synthetic metabolic pathway. however, m. extorquens am1 is vulnerable to solvent stress, which impedes further development for 1-butanol production. only a few studies have reported the general stress response of m. extorquens am1 ...	2016	27069508
activity enhancement based on the chemical equilibrium of multiple-subunit nitrile hydratase from bordetella petrii.	the maturation mechanism of nitrile hydratase (nhase) of pseudomonas putida nrrl-18668 was discovered and named as "self-subunit swapping." since the nhase of bordetella petrii dsm 12804 is similar to that of p. putida, the nhase maturation of b. petrii is proposed to be the same as that of p. putida. however, there is no further information on the application of nhase according to these findings. we successfully rapidly purified nhase and its activator through affinity his tag, and found that t ...	2016	27075457
reduced expression of cytochrome oxidases largely explains camp inhibition of aerobic growth in shewanella oneidensis.	inhibition of bacterial growth under aerobic conditions by elevated levels of cyclic adenosine 3',5'-monophosphate (camp), first revealed more than 50 years ago, was attributed to accumulation of toxic methylglyoxal (mg). here, we report a crp-dependent mechanism rather than mg accumulation that accounts for the phenotype in shewanella oneidensis, an emerging research model for the bacterial physiology. we show that a similar phenotype can be obtained by removing cpda, a camp phosphodiesterase t ...	2016	27076065
cd-resistant strains of b. cereus s5 with endurance capacity and their capacities for cadmium removal from cadmium-polluted water.	the goal of this study was to identify cd-resistant bacterial strains with endurance capacity and to evaluate their ability to remove cadmium ions from cadmium-polluted water. the bacillus cereuss5 strain identified in this study had the closest genetic relationship with b. cereus sp. cp1 and performed well in the removal of cd2+ions from solution. the results showed that both the live and dead biomasses of the cd2+-tolerant b. cereus s5 strain could absorb cd2+ ions in solution but that the liv ...	2016	27077388
draft genome sequence of pseudomonas putida bw11m1, a banana rhizosphere isolate with a diversified antimicrobial armamentarium.	in this study, we report the draft genome ofpseudomonas putidabw11m1, a banana rhizosphere isolate producing various antimicrobial compounds, including a lectin-like bacteriocin, an r-type tailocin, the cyclic lipopeptide xantholysin, and the fatty acid-derived pseudopyronine.	2016	27081131
crystal structures of apo and liganded 4-oxalocrotonate decarboxylase uncover a structural basis for the metal-assisted decarboxylation of a vinylogous β-keto acid.	the enzymes in the catechol meta-fission pathway have been studied for more than 50 years in several species of bacteria capable of degrading a number of aromatic compounds. in a related pathway, naphthalene, a toxic polycyclic aromatic hydrocarbon, is fully degraded to intermediates of the tricarboxylic acid cycle by the soil bacteria pseudomonas putida g7. in this organism, the 83 kb nah7 plasmid carries several genes involved in this biotransformation process. one enzyme in this route, nahk, ...	2016	27082660
genome-wide analysis and expression profiling of glyoxalase gene families in soybean (glycine max) indicate their development and abiotic stress specific response.	glyoxalase pathway consists of two enzymes, glyoxalase i (glyi) and glyoxalase ii (glyii) which detoxifies a highly cytotoxic metabolite methylglyoxal (mg) to its non-toxic form. mg may form advanced glycation end products with various cellular macro-molecules such as proteins, dna and rna; that ultimately lead to their inactivation. role of glyoxalase enzymes has been extensively investigated in various plant species which showed their crucial role in salinity, drought and heavy metal stress to ...	2016	27083416
identification of a third mn(ii) oxidase enzyme in pseudomonas putida gb-1.	the oxidation of soluble mn(ii) to insoluble mn(iv) is a widespread bacterial activity found in a diverse array of microbes. in the mn(ii)-oxidizing bacterium pseudomonas putida gb-1, two mn(ii) oxidase genes, named mnxg and mcoa, were previously identified; each encodes a multicopper oxidase (mco)-type enzyme. expression of these two genes is positively regulated by the response regulator mnxr. preliminary investigation into putative additional regulatory pathways suggested that the flagellar r ...	2016	27084014
application of alkbgt and alkl from pseudomonas putida gpo1 for selective alkyl ester ω-oxyfunctionalization in escherichia coli.	the enzyme system alkbgt from pseudomonas putida gpo1 can efficiently ω-functionalize fatty acid methyl esters. outer membrane protein alkl boosts this ω-functionalization. in this report, it is shown that whole cells of escherichia coli expressing the alkbgt system can also ω-oxidize ethyl nonanoate (naee). coexpression of alkbgt and alkl resulted in 1.7-fold-higher ω-oxidation activity on naee. with this strain, initial activity on naee was 70 u/g (dry weight) of cells (gcdw), 67% of the initi ...	2016	27084021
symbiotic nitrogen fixation and the challenges to its extension to nonlegumes.	access to fixed or available forms of nitrogen limits the productivity of crop plants and thus food production. nitrogenous fertilizer production currently represents a significant expense for the efficient growth of various crops in the developed world. there are significant potential gains to be had from reducing dependence on nitrogenous fertilizers in agriculture in the developed world and in developing countries, and there is significant interest in research on biological nitrogen fixation ...	2016	27084023
a pseudomonas putida cbrb transposon insertion mutant displays a biofilm hyperproducing phenotype that is resistant to dispersal.	the cbrab two-component system in the pseudomonads controls a variety of metabolic and behavioural traits required for its adaptation to changing environmental conditions, including the uptake or assimilation of certain carbon sources, and processes such as chemotaxis or stress tolerance. in this work we characterise a minitn5-luxab-km transposon insertion mutant in cbrb (mpo406) in pseudomonas putida leading to a biofilm overproducing phenotype that is not dispersed when nutrients are depleted. ...	2016	27085034
design of inducible expression vectors for improved protein production in ralstonia eutropha h16 derived host strains.	ralstonia eutropha h16 (cupriavidus necator h16) is a gram-negative, facultative chemolithoautotrophic bacterium which can use h2 and co2 as sole energy and carbon sources in the absence of organic substrates. the biotechnological use of r. eutropha h16 on an industrial scale has already been established; however, only a small number of tools promoting inducible gene expression is available. within this study two systems promoting inducible expression were designed on the basis of the strong j5 ...	2016	27085887
engineering a predatory bacterium as a proficient killer agent for intracellular bio-products recovery: the case of the polyhydroxyalkanoates.	this work examines the potential of the predatory bacterium bdellovibrio bacteriovorus hd100, an obligate predator of other gram-negative bacteria, as an external cell-lytic agent for recovering valuable intracellular bio-products produced by prey cultures. the bio-product targets to be recovered were polyhydroxyalkanoates (phas) produced naturally by pseudomonas putida and cupriavidus necator, or by recombinant escherichia coli strains. b. bacteriovorus with a mutated pha depolymerase gene to p ...	2016	27087466
clinical efficacy of polymyxin monotherapy versus nonvalidated polymyxin combination therapy versus validated polymyxin combination therapy in extensively drug-resistant gram-negative bacillus infections.	polymyxins have emerged as a last-resort treatment of extensively drug-resistant (xdr) gram-negative bacillus (gnb) infections, which present a growing threat. individualized polymyxin-based antibiotic combinations selected on the basis of the results of in vitro combination testing may be required to optimize therapy. a retrospective cohort study of hospitalized patients receiving polymyxins for xdr gnb infections from 2009 to 2014 was conducted to compare the treatment outcomes between patient ...	2016	27090177
an enantio- and diastereoselective chemoenzymatic synthesis of α-fluoro β-hydroxy carboxylic esters.	the trans-o-hydroxybenzylidene pyruvate aldolase-catalysed reactions between fluoropyruvate and many (hetero)aromatic aldehydes yield aldol adducts without subsequent dehydration. treatment of the reaction products with hydrogen peroxide yields the corresponding syn-configured α-fluoro β-hydroxy carboxylic acids which have >98 % ee. the overall chemoenzymatic approach, in which fluoropyruvate serves as a fluoroacetate equivalent, may be exploited in the synthesis of polar building blocks and fra ...	2016	27090612
a multi-enzymatic cascade reaction for the stereoselective production of γ-oxyfunctionalyzed amino acids.	a stereoselective three-enzyme cascade for synthesis of diasteromerically pure γ-oxyfunctionalized α-amino acids was developed. by coupling a dynamic kinetic resolution (dkr) using an n-acylamino acid racemase (naaar) and an l-selective aminoacylase from geobacillus thermoglucosidasius with a stereoselective isoleucine dioxygenase from bacillus thuringiensis, diastereomerically pure oxidized amino acids were produced from racemic n-acetylamino acids. the three enzymes differed in their optimal t ...	2016	27092111
broad-host-range prouser vectors enable fast characterization of inducible promoters and optimization of p-coumaric acid production in pseudomonas putida kt2440.	pseudomonas putida kt2440 has gained increasing interest as a host for the production of biochemicals. because of the lack of a systematic characterization of inducible promoters in this strain, we generated prouser broad-host-expression plasmids that facilitate fast uracil-based cloning. a set of prouser-reporter vectors was further created to characterize different inducible promoters. the prhab and pm promoters were orthogonal and showed titratable, high, and homogeneous expression. to optimi ...	2016	27092814
impact of the chromatin remodeling factor chd1 on gut microbiome composition of drosophila melanogaster.	the composition of the intestinal microbiota of drosophila has been studied in some detail in recent years. environmental, developmental and host-specific genetic factors influence microbiome composition in the fly. our previous work has indicated that intestinal bacterial load can be affected by chromatin-targeted regulatory mechanisms. here we studied a potential role of the conserved chromatin assembly and remodeling factor chd1 in the shaping of the gut microbiome in drosophila melanogaster. ...	2016	27093431
evaluation of a fully automated research prototype for the immediate identification of microorganisms from positive blood cultures under clinical conditions.	a clinical laboratory evaluation of an intrinsic fluorescence spectroscopy (ifs)-based identification system paired to a bact/alert virtuo microbial detection system (biomérieux, inc., durham, nc) was performed to assess the potential for fully automated identification of positive blood cultures. the prototype ifs system incorporates a novel method combining a simple microbial purification procedure with rapid in situ identification via spectroscopy. results were available within 15 min of a bot ...	2016	27094332
waste workers' exposure to airborne fungal and bacterial species in the truck cab and during waste collection.	a large number of people work with garbage collection, and exposure to microorganisms is considered an occupational health problem. however, knowledge on microbial exposure at species level is limited. the aim of the study was to achieve knowledge on waste collectors' exposure to airborne inhalable fungal and bacterial species during waste collection with focus on the transport of airborne microorganisms into the truck cab. airborne microorganisms were collected with samplers mounted in the truc ...	2016	27098185
human interleukin-2 and hen egg white lysozyme: screening for bacteriolytic activity against various bacterial cells.	the bacteriolytic activity of interleukin-2 and hen egg white lysozyme against 34 different species of microorganisms has been studied. it was found that 6 species of microorganisms are lysed in the presence of interleukin-2. all interleukin-2-sensitive microorganisms belong either to the enterobacteriaceae, bacillaceae, or the lactobacillaceae family. it was also found that 12 species of microorganisms are lysed in the presence of lysozyme, and 16 species of microorganisms are lysed in the pres ...	2016	27099789
clinical usefulness of arbekacin.	arbekacin is a broad-spectrum aminoglycoside used to treat methicillin-resistant staphylococcus aureus (mrsa). arbekacin has antibacterial activities against high-level gentamicin-resistant enterococci, multidrug-resistant pseudomonas aeruginosa, and acinetobacter baumannii et al. here, we reviewed in vitro data on arbekacin in staphylococci and gram-negative microorganisms. we also reviewed clinical studies for clinical efficacy and microbiologic efficacy data in patients with identified mrsa a ...	2016	27104010
a β-alanine catabolism pathway containing a highly promiscuous ω-transaminase in the 12-aminododecanate-degrading pseudomonas sp. strain aac.	we previously isolated the transaminase kes23458 from pseudomonas sp. strain aac as a promising biocatalyst for the production of 12-aminododecanoic acid, a constituent building block of nylon-12. here, we report the subsequent characterization of this transaminase. it exhibits activity with a broad substrate range which includes α-, β-, and ω-amino acids, as well as α,ω-diamines and a number of other industrially relevant compounds. it is therefore a prospective candidate for the biosynthesis o ...	2016	27107110
phosphotransferase-dependent accumulation of (p)ppgpp in response to glutamine deprivation in caulobacter crescentus.	the alarmone (p)ppgpp is commonly used by bacteria to quickly respond to nutrient starvation. although (p)ppgpp synthetases such as spot have been extensively studied, little is known about the molecular mechanisms stimulating alarmone synthesis upon starvation. here, we describe an essential role of the nitrogen-related phosphotransferase system (pts(ntr)) in controlling (p)ppgpp accumulation in caulobacter crescentus. we show that cells sense nitrogen starvation by way of detecting glutamine d ...	2016	27109061
in silico structure and sequence analysis of bacterial porins and specific diffusion channels for hydrophilic molecules: conservation, multimericity and multifunctionality.	diffusion channels are involved in the selective uptake of nutrients and form the largest outer membrane protein (omp) family in gram-negative bacteria. differences in pore size and amino acid composition contribute to the specificity. structure-based multiple sequence alignments shed light on the structure-function relations for all eight subclasses. entropy-variability analysis results are correlated to known structural and functional aspects, such as structural integrity, multimericity, speci ...	2016	27110766
genome-wide mapping of transcription start sites yields novel insights into the primary transcriptome of pseudomonas putida.	the environmental bacterium pseudomonas putida is an organism endowed with a versatile metabolism and stress tolerance traits that are desirable in an efficient production organism. in this work, differential rna sequencing was used to investigate the primary transcriptome and rna regulatory elements of p. putida strain kt2440. a total of 7937 putative transcription start sites (tsss) were identified, where over two-thirds were located either on the opposite strand or internal to annotated genes ...	2016	27111755
bioprospecting of plant growth promoting bacilli and related genera prevalent in soils of pristine sacred groves: biochemical and molecular approach.	bacillus spp. and related genera native to soils of the pristine sacred groves from meghalaya, india were characterized using biochemical and 16s rrna gene analysis which revealed dominance of bacillus, paenibacillus, lysinibacillus and viridibacillus in the groves. biochemical estimation was carried out for in vitro testing of plant growth promoting traits present in these isolates. pcr screening were performed for plant growth-promoting related genes involved in the biosynthesis of acid phosph ...	2016	27111883