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biosynthesis and molecular actions of specialized 1,4-naphthoquinone natural products produced by horticultural plants.the 1,4-naphthoquinones (1,4-nqs) are a diverse group of natural products found in every kingdom of life. plants, including many horticultural species, collectively synthesize hundreds of specialized 1,4-nqs with ecological roles in plant-plant (allelopathy), plant-insect and plant-microbe interactions. numerous horticultural plants producing 1,4-nqs have also served as sources of traditional medicines for hundreds of years. as a result, horticultural species have been at the forefront of many b ...201627688890
comprehensive genomic and phenotypic metal resistance profile of pseudomonas putida strain s13.1.2 isolated from a vineyard soil.trace metals are required in many cellular processes in bacteria but also induce toxic effects to cells when present in excess. as such, various forms of adaptive responses towards extracellular trace metal ions are essential for the survival and fitness of bacteria in their environment. a soil pseudomonas putida, strain s13.1.2 has been isolated from french vineyard soil samples, and shown to confer resistance to copper ions. further investigation revealed a high capacity to tolerate elevated c ...201627730570
molecular detection of acanthamoeba spp., naegleria fowleri and vermamoeba (hartmannella) vermiformis as vectors for legionella spp. in untreated and solar pasteurized harvested rainwater.legionella spp. employ multiple strategies to adapt to stressful environments including the proliferation in protective biofilms and the ability to form associations with free-living amoeba (fla). the aim of the current study was to identify legionella spp., acanthamoeba spp., vermamoeba (hartmannella) vermiformis and naegleria fowleri that persist in a harvested rainwater and solar pasteurization treatment system.201627724947
highly efficient and stable novel nanobiohybrid catalyst to avert 3,4-dihydroxybenzoic acid pollutant in water.the present study reported for the first time covalent immobilization of protocatechuate 3,4-dioxygenase (3,4-pod) onto functionalized multi-walled carbon nanotubes (f-mwcnt) for degrading the toxic 3,4-dihydroxybenzoic acid (3,4-dhba) pollutant in water. the f-mwcnts had a maximum 3,4-pod loading of 1060 μg/mg. immobilized 3,4 pod had 44% of relative structural changes to its free configurations. nevertheless, >90% of relative activity and about 50% of catalytic efficiency were retained to the ...201627721429
novel nad+-farnesal dehydrogenase from polygonum minus leaves. purification and characterization of enzyme in juvenile hormone iii biosynthetic pathway in plant.juvenile hormone iii is of great concern due to negative effects on major developmental and reproductive maturation in insect pests. thus, the elucidation of enzymes involved jh iii biosynthetic pathway has become increasing important in recent years. one of the enzymes in the jh iii biosynthetic pathway that remains to be isolated and characterized is farnesal dehydrogenase, an enzyme responsible to catalyze the oxidation of farnesal into farnesoic acid. a novel nad+-farnesal dehydrogenase of p ...201627560927
toxin yafq reduces escherichia coli growth at low temperatures.toxin/antitoxin (ta) systems reduce metabolism under stress; for example, toxin yafq of the yafq/dinj escherichia coli ta system reduces growth by cleaving transcripts with in-frame 5'-aaa-g/a-3' sites, and antitoxin dinj is a global regulator that represses its locus as well as controls levels of the stationary sigma factor rpos. here we investigated the influence on cell growth at various temperatures and found that deletion of the antitoxin gene, dinj, resulted in both reduced metabolism and ...201627557125
the diversity of mtdna rns introns among strains of ophiostoma piliferum, ophiostoma pluriannulatum and related species.based on previous studies, it was suspected that the mitochondrial rns gene within the ophiostomatales is rich in introns. this study focused on a collection of strains representing ophiostoma piliferum, ophiostoma pluriannulatum and related species that cause blue-stain; these fungi colonize the sapwood of trees and impart a dark stain. this reduces the value of the lumber. the goal was to examine the mtdna rns intron landscape for these important blue stain fungi in order to facilitate future ...201627610327
functional genomic analyses of enterobacter, anopheles and plasmodium reciprocal interactions that impact vector competence.malaria exerts a tremendous socioeconomic impact worldwide despite current control efforts, and novel disease transmission-blocking strategies are urgently needed. the enterobacter bacterium esp_z, which is naturally harboured in the mosquito midgut, can inhibit the development of plasmodium parasites prior to their invasion of the midgut epithelium through a mechanism that involves oxidative stress. here, a multifaceted approach is used to study the tripartite interactions between the mosquito, ...201627549662
mitochondrial carriers link the catabolism of hydroxyaromatic compounds to the central metabolism in candida parapsilosis.the pathogenic yeast candida parapsilosis metabolizes hydroxyderivatives of benzene and benzoic acid to compounds channeled into central metabolism, including the mitochondrially localized tricarboxylic acid cycle, via the 3-oxoadipate and gentisate pathways. the orchestration of both catabolic pathways with mitochondrial metabolism as well as their evolutionary origin is not fully understood. our results show that the enzymes involved in these two pathways operate in the cytoplasm with the exce ...201627707801
disruption of pseudomonas putida by high pressure homogenization: a comparison of the predictive capacity of three process models for the efficient release of arginine deiminase.disruption of pseudomonas putida kt2440 by high-pressure homogenization in a french press is discussed for the release of arginine deiminase (adi). the enzyme release response of the disruption process was modelled for the experimental factors of biomass concentration in the broth being disrupted, the homogenization pressure and the number of passes of the cell slurry through the homogenizer. for the same data, the response surface method (rsm), the artificial neural network (ann) and the suppor ...201627699703
comparison of the complete genome sequences of four γ-hexachlorocyclohexane-degrading bacterial strains: insights into the evolution of bacteria able to degrade a recalcitrant man-made pesticide.γ-hexachlorocyclohexane (γ-hch) is a recalcitrant man-made chlorinated pesticide. here, the complete genome sequences of four γ-hch-degrading sphingomonad strains, which are most unlikely to have been derived from one ancestral γ-hch degrader, were compared. together with several experimental data, we showed that (i) all the four strains carry almost identical lina to line genes for the conversion of γ-hch to maleylacetate (designated "specific" lin genes), (ii) considerably different genes are ...201627581378
primary succession of nitrogen cycling microbial communities along the deglaciated forelands of tianshan mountain, china.structural succession and its driving factors for nitrogen (n) cycling microbial communities during the early stages of soil development (0-44 years) were studied along a chronosequence in the glacial forelands of the tianshan mountain no.1 glacier in the arid and semi-arid region of central asia. we assessed the abundance and population of functional genes affiliated with n-fixation (nifh), nitrification (bacterial and archaeal amoa), and denitrification (nirk/s and nosz) in a glacier foreland ...201627625641
engineering of tm1459 from thermotoga maritima for increased oxidative alkene cleavage activity.oxidative cleavage of alkenes is a widely employed process allowing oxyfunctionalization to corresponding carbonyl compounds. recently, a novel biocatalytic oxidative alkene cleavage activity on styrene derivatives was identified in tm1459 from thermotoga maritima. in this work we engineered the enzyme by site-saturation mutagenesis of active site amino acids to increase its activity and to broaden its substrate scope. a high-throughput assay for the detection of the ketone products was successf ...201627713741
triclosan in water, implications for human and environmental health.triclosan (tcs) is a broad spectrum antibacterial agent present as an active ingredient in some personal care products such as soaps, toothpastes and sterilizers. it is an endocrine disrupting compound and its increasing presence in water resources as well as in biosolid-amended soils used in farming, its potential for bioaccumulation in fatty tissues and toxicity in aquatic organisms are a cause for concern to human and environmental health. tcs has also been detected in blood, breast milk, uri ...201627722057
metabolic engineering of pseudomonas putida kt2440 for the production of para-hydroxy benzoic acid.para-hydroxy benzoic acid (phba) is the key component for preparing parabens, a common preservatives in food, drugs, and personal care products, as well as high-performance bioplastics such as liquid crystal polymers. pseudomonas putida kt2440 was engineered to produce phba from glucose via the shikimate pathway intermediate chorismate. to obtain the phba production strain, chorismate lyase ubic from escherichia coli and a feedback resistant 3-deoxy-d-arabino-heptulosonate-7-phosphate synthase e ...201627965953
recent advances on multi-parameter flow cytometry to characterize antimicrobial treatments.the investigation on antimicrobial mechanisms is a challenging and crucial issue in the fields of food or clinical microbiology, as it constitutes a prerequisite to the development of new antimicrobial processes or compounds, as well as to anticipate phenomenon of microbial resistance. nowadays it is accepted that a cells population exposed to a stress can cause the appearance of different cell populations and in particular sub-lethally compromised cells which could be defined as viable but non- ...201627551279
insights into the genome sequences of an n-acyl homoserine lactone molecule producing two pseudomonas spp. isolated from the arctic.we report for the first time the draft genome sequence of two psychrotrophic pseudomonas species, pseudomonas simiae rgcb 73 and pseudomonas brenneri rgcb 108, from the arctic that produce more than one acyl homoserine lactone molecule of varied n-acyl length. the study confirms the presence of a luxr-luxi (type) mediated quorum-sensing system in both the pseudomonas species and enables us to understand the role of quorum sensing in their survival in extremely cold environments.201627491995
from the lab to the farm: an industrial perspective of plant beneficial microorganisms.any successful strategy aimed at enhancing crop productivity with microbial products ultimately relies on the ability to scale at regional to global levels. microorganisms that show promise in the lab may lack key characteristics for widespread adoption in sustainable and productive agricultural systems. this paper provides an overview of critical considerations involved with taking a strain from discovery to the farmer's field. in addition, we review some of the most effective microbial product ...201627540383
expression of a grapevine nac transcription factor gene is induced in response to powdery mildew colonization in salicylic acid-independent manner.tissue colonization by grape powdery mildew (pm) pathogen erysiphe necator (schw.) burr triggers a major remodeling of the transcriptome in the susceptible grapevine vitis vinifera l. while changes in the expression of many genes bear the signature of salicylic acid (sa) mediated regulation, the breadth of pm-induced changes suggests the involvement of additional regulatory networks. to explore pm-associated gene regulation mediated by other sa-independent systems, we designed a microarray exper ...201627488171
new family of biosensors for monitoring btx in aquatic and edaphic environments.benzene, toluene, ethylbenzene and xylenes (btex) contamination is a serious threat to public health and the environment, and therefore, there is an urgent need to detect its presence in nature. the use of whole-cell reporters is an efficient, easy-to-use and low-cost approach to detect and follow contaminants outside specialized laboratories; this is especially important in oil spills that are frequent in marine environments. the aim of this study is the construction of a bioreporter system and ...201627484951
structure and catalytic mechanism of monodehydroascorbate reductase, mdhar, from oryza sativa l. japonica.ascorbic acid (asa) maintains redox homeostasis by scavenging reactive oxygen species from prokaryotes to eukaryotes, especially plants. the enzyme monodehydroascorbate reductase (mdhar) regenerates asa by catalysing the reduction of monodehydroascorbate, using nadh or nadph as an electron donor. the detailed recycling mechanism of mdhar remains unclear due to lack of structural information. here, we present the crystal structures of mdhar in the presence of cofactors, nicotinamide adenine dinuc ...201627652777
genome-based genetic tool development for bacillus methanolicus: theta- and rolling circle-replicating plasmids for inducible gene expression and application to methanol-based cadaverine production.bacillus methanolicus is a thermophilic methylotroph able to overproduce amino acids from methanol, a substrate not used for human or animal nutrition. based on our previous rna-seq analysis a mannitol inducible promoter and a putative mannitol activator gene mtlr were identified. the mannitol inducible promoter was applied for controlled gene expression using fluorescent reporter proteins and a flow cytometry analysis, and improved by changing the -35 promoter region and by co-expression of the ...201627713731
multiple and variable nhej-like genes are involved in resistance to dna damage in streptomyces ambofaciens.non-homologous end-joining (nhej) is a double strand break (dsb) repair pathway which does not require any homologous template and can ligate two dna ends together. the basic bacterial nhej machinery involves two partners: the ku protein, a dna end binding protein for dsb recognition and the multifunctional ligd protein composed a ligase, a nuclease and a polymerase domain, for end processing and ligation of the broken ends. in silico analyses performed in the 38 sequenced genomes of streptomyce ...201627965636
bacterial dispersal promotes biodegradation in heterogeneous systems exposed to osmotic stress.contaminant biodegradation in soils is hampered by the heterogeneous distribution of degrading communities colonizing isolated microenvironments as a result of the soil architecture. over the last years, soil salinization was recognized as an additional problem especially in arid and semiarid ecosystems as it drastically reduces the activity and motility of bacteria. here, we studied the importance of different spatial processes for benzoate biodegradation at an environmentally relevant range of ...201627536297
two distinct cardiolipin synthases operate in agrobacterium tumefaciens.cardiolipin (cl) is a universal component of energy generating membranes. in most bacteria, it is synthesized via the condensation of two molecules phosphatidylglycerol (pg) by phospholipase d-type cardiolipin synthases (pld-type cls). in the plant pathogen and natural genetic engineer agrobacterium tumefaciens cl comprises up to 15% of all phospholipids in late stationary growth phase. a. tumefaciens harbors two genes, atu1630 (cls1) and atu2486 (cls2), coding for pld-type cls. heterologous exp ...201627472399
engineering salmonella as intracellular factory for effective killing of tumour cells.salmonella have many desirable properties as antitumour-agent due to its ability to proliferate inside tumours and induce tumour regression. additionally, this bacterium can be genetically engineered to deliver therapeutic proteins intratumourally. the main limitation of this approach is the efficient release of therapeutic molecules from intratumoural bacteria. here we have developed an inducible autolysis system based in the lysis operon of the lambda phage that, in response to anhydrotetracyc ...201627464652
the importance of integrons for development and propagation of resistance in shigella: the case of latin america.in latin america, the disease burden of shigellosis is found to coexist with the rapid and rampant spread of resistance to commonly used antibiotics. the molecular basis of antibiotic resistance lies within genetic elements such as plasmids, transposons, integrons, genomic islands, etc., which are found in the bacterial genome. integrons are known to acquire, exchange, and express genes within gene cassettes and it is hypothesized that they play a significant role in the transmission of multidru ...201627528086
identification of electrode respiring, hydrocarbonoclastic bacterial strain stenotrophomonas maltophilia mk2 highlights the untapped potential for environmental bioremediation.electrode respiring bacteria (erb) possess a great potential for many biotechnological applications such as microbial electrochemical remediation systems (mers) because of their exoelectrogenic capabilities to degrade xenobiotic pollutants. very few erb have been isolated from mers, those exhibited a bioremediation potential toward organic contaminants. here we report once such bacterial strain, stenotrophomonas maltophilia mk2, a facultative anaerobic bacterium isolated from a hydrocarbon fed m ...201628018304
functional characterization of aconitase x as a cis-3-hydroxy-l-proline dehydratase.in the aconitase superfamily, which includes the archetypical aconitase, homoaconitase, and isopropylmalate isomerase, only aconitase x is not functionally annotated. the corresponding gene (lhpi) was often located within the bacterial gene cluster involved in l-hydroxyproline metabolism. screening of a library of (hydroxy)proline analogues revealed that this protein catalyzes the dehydration of cis-3-hydroxy-l-proline to δ(1)-pyrroline-2-carboxylate. furthermore, electron paramagnetic resonance ...201627929065
matrix-assisted laser desorption/ionization time-of-flight mass-spectrometry (maldi-tof ms) based microbial identifications: challenges and scopes for microbial ecologists.matrix-assisted laser desorption/ionization time-of-flight mass-spectrometry (maldi-tof ms) based biotyping is an emerging technique for high-throughput and rapid microbial identification. due to its relatively higher accuracy, comprehensive database of clinically important microorganisms and low-cost compared to other microbial identification methods, maldi-tof ms has started replacing existing practices prevalent in clinical diagnosis. however, applicability of maldi-tof ms in the area of micr ...201627625644
molecular and structural considerations of tf-dna binding for the generation of biologically meaningful and accurate phylogenetic footprinting analysis: the lysr-type transcriptional regulator family as a study model.the goal of most programs developed to find transcription factor binding sites (tfbss) is the identification of discrete sequence motifs that are significantly over-represented in a given set of sequences where a transcription factor (tf) is expected to bind. these programs assume that the nucleotide conservation of a specific motif is indicative of a selective pressure required for the recognition of a tf for its corresponding tfbs. despite their extensive use, the accuracies reached with these ...201627567672
nitrogen regulation of the xyl genes of pseudomonas putida mt-2 propagates into a significant effect of nitrate on m-xylene mineralization in soil.the nitrogen species available in the growth medium are key factors determining expression of xyl genes for biodegradation of aromatic compounds by pseudomonas putida. nitrogen compounds are frequently amended to promote degradation at polluted sites, but it remains unknown how regulation observed in the test tube is propagated into actual catabolism of, e.g. m-xylene in soil, the natural habitat of this bacterium. to address this issue, we have developed a test-tube-to-soil model system that ex ...201627561962
fine-tuning of amino sugar homeostasis by eiia(ntr) in salmonella typhimurium.the nitrogen-metabolic phosphotransferase system, pts(ntr), consists of the enzymes i(ntr), npr and iia(ntr) that are encoded by ptsp, ptso, and ptsn, respectively. due to the proximity of ptso and ptsn to rpon, the pts(ntr) system has been postulated to be closely related with nitrogen metabolism. to define the correlation between pts(ntr) and nitrogen metabolism, we performed ligand fishing with eiia(ntr) as a bait and revealed that d-glucosamine-6-phosphate synthase (glms) directly interacted ...201627628932
immune modulation enables a specialist insect to benefit from antibacterial withanolides in its host plant.the development of novel plant chemical defenses and counter adaptations by herbivorous insect could continually drive speciation, producing more insect specialists than generalists. one approach to test this hypothesis is to compare closely related generalist and specialist species to reveal the associated costs and benefits of these different adaptive strategies. we use the specialized moth heliothis subflexa, which feeds exclusively on plants in the genus physalis, and its close generalist re ...201627561781
transcriptome analysis of pseudomonas aeruginosa pao1 grown at both body and elevated temperatures.functional genomics research can give us valuable insights into bacterial gene function. rna sequencing (rna-seq) can generate information on transcript abundance in bacteria following abiotic stress treatments. in this study, we used the rna-seq technique to study the transcriptomes of the opportunistic nosocomial pathogen pseudomonas aeruginosa pao1 following heat shock. samples were grown at both the human body temperature (37 °c) and an arbitrarily-selected temperature of 46 °c. in this work ...201627547539
thusin, a novel two-component lantibiotic with potent antimicrobial activity against several gram-positive pathogens.due to the rapidly increasing prevalence of multidrug-resistant bacterial strains, the need for new antimicrobial drugs to treat infections has become urgent. bacteriocins, which are antimicrobial peptides of bacterial origin, are considered potential alternatives to conventional antibiotics and have attracted widespread attention in recent years. among these bacteriocins, lantibiotics, especially two-component lantibiotics, exhibit potent antimicrobial activity against some clinically relevant ...201627486447
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 ...201627486441
development of a quadruplex loop-mediated isothermal amplification assay for field detection of four vibrio species associated with fish disease.a quadruplex loop-mediated isothermal amplification (lamp) method was developed to detect four vibrio species, including vibrio ichthyoenteri, vibrio parahaemolyticus, vibrio scophthalmi, and vibrio vulnificus, simultaneously. four sets of species-specific primers were designed with different restriction sites contained in the inner primers. the quadruplex lamp method could distinguish four vibrio species via the subsequent restriction enzyme analysis. the sensitivity of the quadruplex lamp meth ...201627468405
efficient reconstruction of predictive consensus metabolic network models.understanding cellular function requires accurate, comprehensive representations of metabolism. genome-scale, constraint-based metabolic models (gsms) provide such representations, but their usability is often hampered by inconsistencies at various levels, in particular for concurrent models. commgen, our tool for consensus metabolic model generation, automatically identifies inconsistencies between concurrent models and semi-automatically resolves them, thereby contributing to consolidate knowl ...201627563720
comparative genomics and metabolic analysis reveals peculiar characteristics of rhodococcus opacus strain m213 particularly for naphthalene degradation.the genome of rhodococcus opacus strain m213, isolated from a fuel-oil contaminated soil, was sequenced and annotated which revealed a genome size of 9,194,165 bp encoding 8680 putative genes and a g+c content of 66.72%. among the protein coding genes, 71.77% were annotated as clusters of orthologous groups of proteins (cogs); 55% of the cogs were present as paralog clusters. pulsed field gel electrophoresis (pfge) analysis of m213 revealed the presence of three different sized replicons- a circ ...201627532207
folding analysis of the most complex stevedore's protein knot.dehi is a homodimeric haloacid dehalogenase from pseudomonas putida that contains the most complex 61 stevedore's protein knot within its folding topology. to examine how dehi attains such an intricate knotted topology we combined far-uv circular dichroism (cd), intrinsic fluorescence spectroscopy and small angle x-ray scattering (saxs) to investigate its folding mechanism. equilibrium unfolding of dehi by chemical denaturation indicated the presence of two highly populated folding intermediates ...201627527519
arabidopsis thaliana contains both ni2+ and zn2+ dependent glyoxalase i enzymes and ectopic expression of the latter contributes more towards abiotic stress tolerance in e. coli.the glyoxalase pathway is ubiquitously found in all the organisms ranging from prokaryotes to eukaryotes. it acts as a major pathway for detoxification of methylglyoxal (mg), which deleteriously affects the biological system in stress conditions. the first important enzyme of this system is glyoxalase i (glyi). it is a metalloenzyme which requires divalent metal ions for its activity. this divalent metal ion can be either zn2+ as found in most of eukaryotes or ni2+ as seen in prokaryotes. in the ...201627415831
structural analysis and biological toxicity of aflatoxins b1 and b2 degradation products following detoxification by ocimum basilicum and cassia fistula aqueous extracts.this study showed the comparison between ocimum basilicum and cassia fistula (leaves and branch) aqueous extracts for their ability to detoxify of aflatoxins b1 and b2 (afb1; 100 μg l(-1) and afb2; 50 μg l(-1)) by in vitro assays and decontamination studies. results indicated that o. basilicum leaves extract was found to be highly significant (p < 0.05) in degrading afb1 and afb2, i.e., 90.4 and 88.6%, respectively. however, o. basilicum branch, c. fistula leaves and branch extracts proved to be ...201627471501
listeria monocytogenes dna glycosylase adlp affects flagellar motility, biofilm formation, virulence, and stress responses.the temperature-dependent alteration of flagellar motility gene expression is critical for the foodborne pathogen listeria monocytogenes to respond to a changing environment. in this study, a genetic determinant, l. monocytogenes f2365_0220 (lmof2365_0220), encoding a putative protein that is structurally similar to the bacillus cereus alkyl base dna glycosylase (alkd), was identified. this determinant was involved in the transcriptional repression of flagellar motility genes and was named adlp ...201627316964
genomic, transcriptomic and proteomic analysis provide insights into the cold adaptation mechanism of the obligate psychrophilic fungus mrakia psychrophila.mrakia psychrophila is an obligate psychrophilic fungus. the cold adaptation mechanism of psychrophilic fungi remains unknown. comparative genomics analysis indicated that m. psychrophila had a specific codon usage preference, especially for codons of gly and arg and its major facilitator superfamily (mfs) transporter gene family was expanded. transcriptomic analysis revealed that genes involved in ribosome and energy metabolism were upregulated at 4°c, while genes involved in unfolded protein b ...201627633791
plant drought tolerance enhancement by trehalose production of desiccation-tolerant microorganisms.a collection of desiccation-tolerant xeroprotectant-producing microorganisms was screened for their ability to protect plants against drought, and their role as plant growth-promoting rhizobacteria was investigated in two different crops (tomato and pepper). the most commonly described biochemical mechanisms for plant protection against drought by microorganisms including the production of phytohormones, antioxidants and xeroprotectants were analyzed. in particular, the degree of plant protectio ...201627746776
comparative single-cell analysis of different e. coli expression systems during microfluidic cultivation.recombinant protein production is mostly realized with large-scale cultivations and monitored at the level of the entire population. detailed knowledge of cell-to-cell variations with respect to cellular growth and product formation is limited, even though phenotypic heterogeneity may distinctly hamper overall production yields, especially for toxic or difficult-to-express proteins. unraveling phenotypic heterogeneity is thus a key aspect in understanding and optimizing recombinant protein produ ...201627525986
replisome assembly at bacterial chromosomes and iteron plasmids.the proper initiation and occurrence of dna synthesis depends on the formation and rearrangements of nucleoprotein complexes within the origin of dna replication. in this review article, we present the current knowledge on the molecular mechanism of replication complex assembly at the origin of bacterial chromosome and plasmid replicon containing direct repeats (iterons) within the origin sequence. we describe recent findings on chromosomal and plasmid replication initiators, dnaa and rep protei ...201627563644
unknown unknowns: essential genes in quest for function.the experimental design of a minimal synthetic genome revealed the presence of a large number of genes without ascribed function, in part because the abstract laws of life must be implemented within ad hoc material contraptions. creating a function needs recruitment of some pre-existing structure and this reveals kludges in their set-up and history. here, we show that looking for functions as an engineer would help in discovery of a significant number of those, proposed together with conceptual ...201627435445
overexpression of transport proteins improves the production of 5-aminovalerate from l-lysine in escherichia coli.bacterial transporters mediate the exchanges between intracellular and extracellular environments. modification of transport route could be applied to speed up the metabolic reactions and promote the production of aimed compounds. herein, lysine 2-monooxygenase (davb) and δ-aminovaleramidase (dava) were co-expressed in escherichia coli bl21(de3) to produce nylon-5 monomer 5-aminovalerate from l-lysine. then, pp2911 (4-aminobutyrate transporter in pseudomonas putida) and lysp (the lysine specific ...201627510748
modeling central metabolism and energy biosynthesis across microbial life.automatically generated bacterial metabolic models, and even some curated models, lack accuracy in predicting energy yields due to poor representation of key pathways in energy biosynthesis and the electron transport chain (etc). further compounding the problem, complex interlinking pathways in genome-scale metabolic models, and the need for extensive gapfilling to support complex biomass reactions, often results in predicting unrealistic yields or unrealistic physiological flux profiles.201627502787
harnessing host-vector microbiome for sustainable plant disease management of phloem-limited bacteria.plant health and productivity is strongly influenced by their intimate interaction with deleterious and beneficial organisms, including microbes, and insects. of the various plant diseases, insect-vectored diseases are of particular interest, including those caused by obligate parasites affecting plant phloem such as candidatus (ca.) phytoplasma species and several species of ca. liberibacter. recent studies on plant-microbe and plant-insect interactions of these pathogens have demonstrated that ...201627746788
draft genome sequences of four hospital-associated pseudomonas putida isolates.we present here the draft genome sequences of four pseudomonas putida isolates belonging to a single clone suspected for nosocomial transmission between patients and a bronchoscope in a tertiary hospital. the four genome sequences belong to a single lineage but contain differences in their mobile genetic elements.201627688339
metabolic pathway involved in 6-chloro-2-benzoxazolinone degradation by pigmentiphaga sp. strain dl-8 and identification of the novel metal-dependent hydrolase cbaa.6-chloro-2-benzoxazolinone (cdhb) is a precursor of herbicide, insecticide, and fungicide synthesis and has a broad spectrum of biological activity. pigmentiphaga sp. strain dl-8 can transform cdhb into 2-amino-5-chlorophenol (2a5cp), which it then utilizes as a carbon source for growth. the cdhb hydrolase (cbaa) was purified from strain dl-8, which can also hydrolyze 2-benzoxazolinone (boa), 5-chloro-2-boa, and benzamide. the specific activity of purified cbaa was 5,900 u · mg protein(-1) for c ...201627208123
environmental factors modulating the stability and enzymatic activity of the petrotoga mobilis esterase (pmest).enzymes isolated from thermophilic organisms found in oil reservoirs can find applications in many fields, including the oleochemical, pharmaceutical, bioenergy, and food/dairy industries. in this study, in silico identification and recombinant production of an esterase from the extremophile bacteria petrotoga mobilis (designated pmest) were performed. then biochemical, bioinformatics and structural characterizations were undertaken using a combination of synchrotron radiation circular dichroism ...201627351338
disk carbapenemase test for the rapid detection of kpc-, ndm-, and other metallo-β-lactamase-producing gram-negative bacilli.rapid detection of carbapenemase-producing gram-negative bacilli (gnb) is required for optimal treatment of infected patients. we developed and assessed a new disk carbapenemase test (dct).201627374708
plants rather than mineral fertilization shape microbial community structure and functional potential in legacy contaminated soil.plant-microbe interactions are of particular importance in polluted soils. this study sought to determine how selected plants (horseradish, black nightshade and tobacco) and npk mineral fertilization shape the structure of soil microbial communities in legacy contaminated soil and the resultant impact of treatment on the soil microbial community functional potential. to explore these objectives, we combined shotgun metagenomics and 16s rrna gene amplicon high throughput sequencing with data anal ...201627446035
acidobacteria strains from subdivision 1 act as plant growth-promoting bacteria.acidobacteria is one of the most abundant phyla in soils and has been detected in rhizosphere mainly based on cultivation-independent approaches such as 16s rrna gene survey. although putative interaction of acidobacteria with plants was suggested, so far no plant-bacterial interactions were shown. therefore, we performed several in vitro tests to evaluate acidobacteria-plant interactions and the possible mechanisms involved in such interaction. we observed that arabidopsis thaliana inoculated w ...201627339258
draft genome sequence of comamonas thiooxydans strain phe2-6 (nbrc 110656), a chlorinated-ethene-degrading bacterium.comamonas thiooxydans strain phe2-6 (nbrc 110656), which was isolated from a trichloroethene-contaminated site in japan, utilizes phenol as a sole source of carbon and cometabolizes cis- and trans-dichloroethenes. we report here the draft genome sequence of this strain, containing 5,309,680 bp, with 60.6% g+c content.201627340052
flra, flrb and flrc regulate adhesion by controlling the expression of critical virulence genes in vibrio alginolyticus.adhesion is an important virulence trait of vibrio alginolyticus. bacterial adhesion is influenced by environmental conditions; however, the molecular mechanism underlying this effect remains unknown. the expression levels of flra, flrb and flrc were significantly downregulated in adhesion-deficient v. alginolyticus strains cultured under cu(2+), pb(2+), hg(2+) and low-ph stresses. silencing these genes led to deficiencies in adhesion, motility, flagellar assembly, biofilm formation and exopolys ...201627485498
activation of the glutamic acid-dependent acid resistance system in escherichia coli bl21(de3) leads to increase of the fatty acid biotransformation activity.the biosynthesis of carboxylic acids including fatty acids from biomass is central in envisaged biorefinery concepts. the productivities are often, however, low due to product toxicity that hamper whole-cell biocatalyst performance. here, we have investigated factors that influence the tolerance of escherichia coli to medium chain carboxylic acid (i.e., n-heptanoic acid)-induced stress. the metabolic and genomic responses of e. coli bl21(de3) and mg1655 grown in the presence of n-heptanoic acid ...201627681369
structural and histone binding ability characterization of the arb2 domain of a histone deacetylase hda1 from saccharomyces cerevisiae.hda1 is the catalytic core component of the h2b- and h3- specific histone deacetylase (hdac) complex from saccharomyces cerevisiae, which is involved in the epigenetic repression and plays a crucial role in transcriptional regulation and developmental events. though the n-terminal catalytic hdac domain of hda1 is well characterized, the function of the c-terminal arb2 domain remains unknown. in this study, we determine the crystal structure of the arb2 domain from s. cerevisiae hda1 at a resolut ...201627665728
mapping the patent landscape of synthetic biology for fine chemical production pathways.a goal of synthetic biology bio-foundries is to innovate through an iterative design/build/test/learn pipeline. in assessing the value of new chemical production routes, the intellectual property (ip) novelty of the pathway is important. exploratory studies can be carried using knowledge of the patent/ip landscape for synthetic biology and metabolic engineering. in this paper, we perform an assessment of pathways as potential targets for chemical production across the full catalogue of reachable ...201627489206
lactobacillus oligofermentans glucose, ribose and xylose transcriptomes show higher similarity between glucose and xylose catabolism-induced responses in the early exponential growth phase.lactobacillus oligofermentans has been mostly isolated from cold-stored packaged meat products in connection with their spoilage, but its precise role in meat spoilage is unknown. it belongs to the l. vaccinostercus group of obligate heterofermentative lactobacilli that generally ferment pentoses (e.g. xylose and ribose) more efficiently than hexoses (e.g. glucose). however, more efficient hexose utilization can be induced. the regulation mechanisms of the carbohydrate catabolism in such bacteri ...201627487841
gut microbiota profiling: metabolomics based approach to unravel compounds affecting human health.the gut microbiota is composed of a huge number of different bacteria, that produce a large amount of compounds playing a key role in microbe selection and in the construction of a metabolic signaling network. the microbial activities are affected by environmental stimuli leading to the generation of a wide number of compounds, that influence the host metabolome and human health. indeed, metabolite profiles related to the gut microbiota can offer deep insights on the impact of lifestyle and diet ...201627507964
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 ...201627090177
genomics of high molecular weight plasmids isolated from an on-farm biopurification system.the use of biopurification systems (bps) constitutes an efficient strategy to eliminate pesticides from polluted wastewaters from farm activities. bps environments contain a high microbial density and diversity facilitating the exchange of information among bacteria, mediated by mobile genetic elements (mges), which play a key role in bacterial adaptation and evolution in such environments. here we sequenced and characterized high-molecular-weight plasmids from a bacterial collection of an on-fa ...201627321040
matrix-assisted laser desorption ionization-time of flight mass spectrometry (maldi-tof ms) can precisely discriminate the lineages of listeria monocytogenes and species of listeria.the genetic lineages of listeria monocytogenes and other species of the genus listeria are correlated with pathogenesis in humans. although matrix-assisted laser desorption ionization-time of flight mass spectrometry (maldi-tof ms) has become a prevailing tool for rapid and reliable microbial identification, the precise discrimination of listeria species and lineages remains a crucial issue in clinical settings and for food safety. in this study, we constructed an accurate and reliable ms databa ...201627442502
physiological and transcriptomic analyses reveal mechanistic insight into the adaption of marine bacillus subtilis c01 to alumina nanoparticles.an increasing number of studies have investigated the effects of nanoparticles (nps) on microbial systems; however, few existing reports have focused on the defense mechanisms of bacteria against nps. whether secondary metabolism biosynthesis is a response to np stress and contributes to the adaption of bacteria to nps is unclear. here, a significant induction in the surfactin production and biofilm formation were detected by adding al2o3 nps to the b. subtilis fermentation broth. physiological ...201627440502
sepsis-induced takotsubo cardiomyopathy leading to torsades de pointes.background. takotsubo cardiomyopathy (tcm) is sudden and reversible myocardial dysfunction often attributable to physical or emotional triggers. case report. we describe a 51-year-old man presented to emergency department with sepsis from urinary tract infection (uti). he was placed on cefepime for uti and non-st-elevation myocardial infarction protocol given elevated troponins with chest pain. subsequently, patient was pulseless with torsades de pointes (tdp) and then converted to sinus rhythm ...201627525128
genetic dissection of the regulatory network associated with high c-di-gmp levels in pseudomonas putida kt2440.most bacteria grow in nature forming multicellular structures named biofilms. the bacterial second messenger cyclic diguanosine monophosphate (c-di-gmp) is a key player in the regulation of the transition from planktonic to sessile lifestyles and this regulation is crucial in the development of biofilms. in pseudomonas putida kt2440, rup4959, a multidomain response regulator with diguanylate cyclase activity, when overexpressed causes an increment in the intracellular levels of c-di-gmp that giv ...201627489550
phosphorus mobilizing consortium mammoth p(™) enhances plant growth.phosphorus (p) is a critical nutrient used to maximize plant growth and yield. current agriculture management practices commonly experience low plant p use efficiency due to natural chemical sorption and transformations when p fertilizer is applied to soils. a perplexing challenge facing agriculture production is finding sustainable solutions to deliver p more efficiently to plants. using prescribed applications of specific soil microbial assemblages to mobilize soil bound-p to improve crop nutr ...201627326379
highly regio- and enantioselective multiple oxy- and amino-functionalizations of alkenes by modular cascade biocatalysis.new types of asymmetric functionalizations of alkenes are highly desirable for chemical synthesis. here, we develop three novel types of regio- and enantioselective multiple oxy- and amino-functionalizations of terminal alkenes via cascade biocatalysis to produce chiral α-hydroxy acids, 1,2-amino alcohols and α-amino acids, respectively. basic enzyme modules 1-4 are developed to convert alkenes to (s)-1,2-diols, (s)-1,2-diols to (s)-α-hydroxyacids, (s)-1,2-diols to (s)-aminoalcohols and (s)-α-hy ...201627297777
methane-oxidizing enzymes: an upstream problem in biological gas-to-liquids conversion.biological conversion of natural gas to liquids (bio-gtl) represents an immense economic opportunity. in nature, aerobic methanotrophic bacteria and anaerobic archaea are able to selectively oxidize methane using methane monooxygenase (mmo) and methyl coenzyme m reductase (mcr) enzymes. although significant progress has been made toward genetically manipulating these organisms for biotechnological applications, the enzymes themselves are slow, complex, and not recombinantly tractable in traditio ...201627366961
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 ...201627084021
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 ...201627084014
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 ...201627084023
proof of concept for the simplified breakdown of cellulose by combining pseudomonas putida strains with surface displayed thermophilic endocellulase, exocellulase and β-glucosidase.the production and employment of cellulases still represents an economic bottleneck in the conversion of lignocellulosic biomass to biofuels and other biocommodities. this process could be simplified by displaying the necessary enzymes on a microbial cell surface. such an approach, however, requires an appropriate host organism which on the one hand can withstand the rough environment coming along with lignocellulose hydrolysis, and on the other hand does not consume the generated glucose so tha ...201627287198
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 ...201627107110
inter-sigmulon communication through topological promoter coupling.divergent transcription from within bacterial intergenic regions frequently involves promoters dependent on alternative σ-factors. this is the case for the non-overlapping σ(70)- and σ(54)-dependent promoters that control production of the substrate-responsive regulator and enzymes for (methyl)phenol catabolism. here, using an array of in vivo and in vitro assays, we identify transcription-driven supercoiling arising from the σ(54)-promoter as the mechanism underlying inter-promoter communicatio ...201627422872
engineering pseudomonas putida kt2440 for simultaneous degradation of carbofuran and chlorpyrifos.currently, chlorpyrifos (cp) and carbofuran are often applied together to control major agricultural pests in many developing countries, in most cases, they are simultaneously detected in agricultural soils. some cost-effective techniques are required for the remediation of combined pollution caused by multiple pesticides. in this work, we aim at constructing a detectable recombinant microorganism with the capacity to simultaneously degrade cp and carbofuran. to achieve this purpose, cp/carbofur ...201627418102
characterization of genome-reduced bacillus subtilis strains and their application for the production of guanosine and thymidine.genome streamlining has emerged as an effective strategy to boost the production efficiency of bio-based products. many efforts have been made to construct desirable chassis cells by reducing the genome size of microbes. it has been reported that the genome-reduced bacillus subtilis strain mbg874 showed clear advantages for the production of several heterologous enzymes including alkaline cellulase and protease. in addition to enzymes, b. subtilis is also used for the production of chemicals. to ...201627260256
thigh abscess and necrotizing fasciitis following an inside-out transobturator tape intervention: a case report.tension-free vaginal transobturator tapes are used worldwide in the treatment of urinary incontinence in women. very few severe complications have been described following this procedure, with no standard treatment yet established.201627256334
muts regulates access of the error-prone dna polymerase pol iv to replication sites: a novel mechanism for maintaining replication fidelity.translesion dna polymerases (pol) function in the bypass of template lesions to relieve stalled replication forks but also display potentially deleterious mutagenic phenotypes that contribute to antibiotic resistance in bacteria and lead to human disease. effective activity of these enzymes requires association with ring-shaped processivity factors, which dictate their access to sites of dna synthesis. here, we show for the first time that the mismatch repair protein muts plays a role in regulat ...201627257069
biological control of rice bakanae by an endophytic bacillus oryzicola yc7007.in our previous study, we reported that a novel endophytic bacterium bacillus oryzicola yc7007 has suppressed bacterial diseases of rice via induced systemic resistance and antibiotic production. this endophytic strain, b. oryzicola yc7007 was used as a biological control agent against bakanae disease of rice caused by fusarium fujikuroi, and its mechanism of interaction with the pathogen and the rice was further elucidated. root drenching with b. oryzicola yc7007 suspension reduced the disease ...201627298598
draft genome sequence of pseudomonas putida cbf10-2, a soil isolate with bioremediation potential in agricultural and industrial environmental settings.pseudomonas putida cbf10-2 is a microorganism isolated from farmland soil in fairchild, tx, found to degrade high-impact xenobiotics, including organophosphate insecticides, petroleum hydrocarbons, and both monocyclic and polycyclic aromatics. the versatility of cbf10-2 makes it useful for multipurpose bioremediation of contaminated sites in agricultural and industrial environments.201627417844
crystal structure of sgcj, an ntf2-like superfamily protein involved in biosynthesis of the nine-membered enediyne antitumor antibiotic c-1027.comparative analysis of the enediyne biosynthetic gene clusters revealed sets of conserved genes serving as outstanding candidates for the enediyne core. here we report the crystal structures of sgcj and its homologue ncs-orf16, together with gene inactivation and site-directed mutagenesis studies, to gain insight into enediyne core biosynthesis. gene inactivation in vivo establishes that sgcj is required for c-1027 production in streptomyces globisporus. sgcj and ncs-orf16 share a common struct ...201627406907
cultural, transcriptomic, and proteomic analyses of water-stressed cells of actinobacterial strains isolated from compost: ecological implications in the fed-batch composting process.this study was undertaken to examine the effects of water activity (aw) on the viability of actinobacterial isolates from a fed-batch composting (fbc) process by comparing culturability and stainability with 5-cyano-2,3-ditoryl tetrazolium chloride (ctc). the fbc reactor as the source of these bacteria was operated with the daily loading of household biowaste for 70 d. during this period of composting, aw in the reactor decreased linearly with time and reached approximately 0.95 at the end of op ...201627246805
high production of 3-hydroxypropionic acid in klebsiella pneumoniae by systematic optimization of glycerol metabolism.3-hydroxypropionic acid (3-hp) is an important platform chemical proposed by the united states department of energy. 3-hp can be converted to a series of bulk chemicals. biological production of 3-hp has made great progress in recent years. however, low yield of 3-hp restricts its commercialization. in this study, systematic optimization was conducted towards high-yield production of 3-hp in klebsiella pneumoniae. we first investigated appropriate promoters for the key enzyme (aldehyde dehydroge ...201627230116
rapid classification and identification of microcystis aeruginosa strains using maldi-tof ms and polygenetic analysis.matrix-assisted laser desorption-ionization-time-of-flight mass spectrometry (maldi-tof ms) was used to establish a rapid, simple, and accurate method to differentiate among strains of microcystis aeruginosa, one of the most prevalent types of bloom-forming cyanobacteria. m. aeruginosa nies-843, for which a complete genome has been sequenced, was used to characterize ribosomal proteins as biomarkers and to optimize conditions for observing ribosomal proteins as major peaks in a given mass spectr ...201627227555
when genome-based approach meets the "old but good": revealing genes involved in the antibacterial activity of pseudomonas sp. p482 against soft rot pathogens.dickeya solani and pectobacterium carotovorum subsp. brasiliense are recently established species of bacterial plant pathogens causing black leg and soft rot of many vegetables and ornamental plants. pseudomonas sp. strain p482 inhibits the growth of these pathogens, a desired trait considering the limited measures to combat these diseases. in this study, we determined the genetic background of the antibacterial activity of p482, and established the phylogenetic position of this strain. pseudomo ...201627303376
sublethal concentrations of antibiotics cause shift to anaerobic metabolism in listeria monocytogenes and induce phenotypes linked to antibiotic tolerance.the human pathogenic bacterium listeria monocytogenes is exposed to antibiotics both during clinical treatment and in its saprophytic lifestyle. as one of the keys to successful treatment is continued antibiotic sensitivity, the purpose of this study was to determine if exposure to sublethal antibiotic concentrations would affect the bacterial physiology and induce antibiotic tolerance. transcriptomic analyses demonstrated that each of the four antibiotics tested caused an antibiotic-specific ge ...201627462313
mcsm-lig: quantifying the effects of mutations on protein-small molecule affinity in genetic disease and emergence of drug resistance.the ability to predict how a mutation affects ligand binding is an essential step in understanding, anticipating and improving the design of new treatments for drug resistance, and in understanding genetic diseases. here we present mcsm-lig, a structure-guided computational approach for quantifying the effects of single-point missense mutations on affinities of small molecules for proteins. mcsm-lig uses graph-based signatures to represent the wild-type environment of mutations, and small-molecu ...201627384129
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 ...201627021319
identification, characterization and molecular adaptation of class i redox systems for the production of hydroxylated diterpenoids.de novo production of multi-hydroxylated diterpenoids is challenging due to the lack of efficient redox systems.201627216162
interrupting peptidoglycan deacetylation during bdellovibrio predator-prey interaction prevents ultimate destruction of prey wall, liberating bacterial-ghosts.the peptidoglycan wall, located in the periplasm between the inner and outer membranes of the cell envelope in gram-negative bacteria, maintains cell shape and endows osmotic robustness. predatory bdellovibrio bacteria invade the periplasm of other bacterial prey cells, usually crossing the peptidoglycan layer, forming transient structures called bdelloplasts within which the predators replicate. prey peptidoglycan remains intact for several hours, but is modified and then degraded by escaping p ...201627211869
control of fluxes in metabolic networks.understanding the control of large-scale metabolic networks is central to biology and medicine. however, existing approaches either require specifying a cellular objective or can only be used for small networks. we introduce new coupling types describing the relations between reaction activities, and develop an efficient computational framework, which does not require any cellular objective for systematic studies of large-scale metabolism. we identify the driver reactions facilitating control of ...201627197218
genetic basis for hyper production of hyaluronic acid in natural and engineered microorganisms.hyaluronic acid, or ha, is a rigid and linear biopolymer belonging to the class of the glycosaminoglycans, and composed of repeating units of the monosaccharides glucuronic acid and n-acetylglucosamine. ha has multiple important functions in the human body, due to its properties such as bio-compatibility, lubricity and hydrophilicity, it is widely applied in the biomedical, food, health and cosmetic fields. the growing interest in this molecule has motivated the discovery of new ways of obtainin ...201627370777
the regulation of para-nitrophenol degradation in pseudomonas putida dll-e4.pseudomonas putida dll-e4 can efficiently degrade para-nitrophenol and its intermediate metabolite hydroquinone. the regulation of para-nitrophenol degradation was studied, and pnp induced a global change in the transcriptome of p. putida dll-e4. when grown on pnp, the wild-type strain exhibited significant downregulation of 2912 genes and upregulation of 845 genes, whereas 2927 genes were downregulated and 891 genes upregulated in a pnpr-deleted strain. genes related to two non-coding rnas (ins ...201627191401
evaluation of heavy metal removal from wastewater in a modified packed bed biofilm reactor.for the effective application of a modified packed bed biofilm reactor (pbbr) in wastewater industrial practice, it is essential to distinguish the tolerance of the system for heavy metals removal. the industrial contamination of wastewater from various sources (e.g. zn, cu, cd and ni) was studied to assess the impacts on a pbbr. this biological system was examined by evaluating the tolerance of different strengths of composite heavy metals at the optimum hydraulic retention time (hrt) of 2 hour ...201627186636
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