Publications

new restriction endonucleases from flavobacterium okeanokoites (foki) and micrococcus luteus (mlui).	two new restriction endonucleases have been isolated from flavobacterium okeanokoites ifo12536 and micrococcus luteus ifo12992 and named foki and mlui, respectively. based on analysis of the sequences around the restriction sites, the recognition sequences and cleavage sites of these endonucleases were deduced as below: foki: (formula: see text). mlui introduces double-strand cleavages at unique sequences that are completely two-fold rotationally symmetric like most type ii restriction endonucle ...	1981	6282705
cloning of two type ii methylase genes that recognise asymmetric nucleotide sequences: foki and hgai.	the modification genes of flavobacterium okeanokoites and haemophilus galinarum have been cloned into the vector pbr322 and expressed in escherichia coli cells. foki methylase gene is contained on a 3.80 kb piece of f. okeanokoites dna. plasmid constructs carrying this fragment of dna are resistant to digestion by foki restriction endonuclease but are sensitive to cleavage by hindiii, ecori and psti. unmodified lambda dna molecules, exposed in vitro to cell extracts prepared from cells habouring ...	1987	2828884
purification and characterization of the foki restriction endonuclease.	the restriction endonuclease foki from flavobacterium okeanokoites was purified to homogeneity. based on gel filtration, sedimentation and sodium dodecyl sulfate-polyacrylamide-gel electrophoresis, the following properties of the enzyme were determined: foki exists in one active monomeric form, and has an mr of 64-65.4 x 10(3).foki is a strongly basic protein with an isoelectric point of 9.4. the enzyme exhibits restriction activity in the ph range 5.0 to 10.5 (maximum level at ph 7.0-8.5) and i ...	1989	2583511
nucleotide sequence of the foki restriction-modification system: separate strand-specificity domains in the methyltransferase.	the genes for foki, a type-iis restriction-modification system from flavobacterium okeanokoites (asymmetric recognition sequence: 5'-ggatg/3'-cctac), were cloned into escherichia coli. recombinants carrying the fokir and fokim genes were found to modify their dna completely, and to restrict lambdoid phages weakly. the nt sequences of the genes were determined, and the probable start codons were confirmed by aa sequencing. the foki endonuclease (r.foki) and methyltransferase (m.foki) are encoded ...	1989	2684765
the foki restriction-modification system. i. organization and nucleotide sequences of the restriction and modification genes.	a dna fragment that carried the genes coding for foki endonuclease and methylase was cloned from the chromosomal dna of flavobacterium okeanokoites, and the coding regions were assigned to the nucleotide sequence by deletion analysis. the methylase gene was 1,941 base pairs (bp) long, corresponding to a protein of 647 amino acid residues (mr = 75,622), and the endonuclease gene was 1,749 bp long, corresponding to a protein of 583 amino acid residues (mr = 66,216). the assignment of the methylase ...	1989	2784436
m.foki methylates adenine in both strands of its asymmetric recognition sequence.	m.foki, a type-iis modification enzyme from flavobacterium okeanokoites, was purified, and its activity was characterized in vitro. the enzyme was found to be a dna-adenine methyltransferase and to methylate both strands of the asymmetric foki recognition sequence: (formula; see text) m.foki does not methylate single-stranded dna, nor does it methylate double-stranded dna at sequences other than foki sites.	1989	2744483
[a study of substrate specificity of dna-methylases from flavobacterium okeanokoites].	the specificity of dna methylase m. foki towards oligonucleotides containing sequence 5'...ggatg.../3'...cctac... was investigated, and n6-methyladenine in the ggatg chain was shown to be the only product of the modification.	1989	2742622
functional domains in fok i restriction endonuclease.	the pcr was used to alter transcriptional and translational signals surrounding the flavobacterium okeanokoites restriction endonuclease (fokir) gene, so as to achieve high expression in escherichia coli. by changing the ribosome-binding site sequence preceding the fokir gene to match the consensus e. coli signal and by placing a positive retroregulator stem-loop sequence downstream of the gene, fok i yield was increased to 5-8% of total cellular protein. fok i was purified to homogeneity with p ...	1992	1584761
emendation of the genus planococcus and transfer of flavobacterium okeanokoites zobell and upham 1944 to the genus planococcus as planococcus okeanokoites comb. nov.	the taxonomic position of flavobacterium okeanokoites ifo 12536t (t = type strain) was determined by 16s rrna gene sequencing and chemotaxonomic methods. phylogenetic evidence derived from a 16s rrna sequence analysis indicated that f. okeanokoites, which forms rod-shaped cells, belongs to the genus planococcus, which forms spherical cells. a phylogenetically close relationship was supported by chemotaxonomic characteristics, such as the presence of menaquinone 7 and menaquinone 8 as major isopr ...	1996	8863410
the flavobacterium okeanokoites adenine-n6-specific dna-methyltransferase m.foki is a tandem enzyme of two independent domains with very different kinetic properties.	the flavobacterium okeanokoites adenine-n6-specific dna-methyltransferase, m.foki, modifies both adenine residues within its asymmetric recognition sequence 5'-ggatg/catcc-3'. it is a fusion protein comprising two independent enzymes. we have cloned, overexpressed and purified full-length m.foki as well as both individual domains and analyzed their kinetics of dna methylation using unmethylated and hemimethylated oligodeoxynucleotide substrates. our data show that both domains of m.foki methylat ...	1998	9490066
kinetic bias in estimates of coastal picoplankton community structure obtained by measurements of small-subunit rrna gene pcr amplicon length heterogeneity	marine bacterioplankton diversity was examined by quantifying natural length variation in the 5' domain of small-subunit (ssu) rrna genes (rdna) amplified by pcr from a dna sample from the oregon coast. this new technique, length heterogeneity analysis by pcr (lh-pcr), determines the relative proportions of amplicons originating from different organisms by measuring the fluorescence emission of a labeled primer used in the amplification reaction. relationships between the sizes of amplicons and ...	1998	9797317
foki dimerization is required for dna cleavage.	foki is a type iis restriction endonuclease comprised of a dna recognition domain and a catalytic domain. the structural similarity of the foki catalytic domain to the type ii restriction endonuclease bamhi monomer suggested that the foki catalytic domains may dimerize. in addition, the foki structure, presented in an accompanying paper in this issue of proceedings, reveals a dimerization interface between catalytic domains. we provide evidence here that foki catalytic domain must dimerize for d ...	1998	9724744
structure of foki has implications for dna cleavage.	foki is a member an unusual class of restriction enzymes that recognize a specific dna sequence and cleave nonspecifically a short distance away from that sequence. foki consists of an n-terminal dna recognition domain and a c-terminal cleavage domain. the bipartite nature of foki has led to the development of artificial enzymes with novel specificities. we have solved the structure of foki to 2.3 a resolution. the structure reveals a dimer, in which the dimerization interface is mediated by the ...	1998	9724743
chimeric restriction enzymes: what is next?	chimeric restriction enzymes are a novel class of engineered nucleases in which the non-specific dna cleavage domain of fokl (a type iis restriction endonuclease) is fused to other dna-binding motifs. the latter include the three common eukaryotic dna-binding motifs, namely the helix-turn-helix motif, the zinc finger motif and the basic helix-loop-helix protein containing a leucine zipper motif. such chimeric nucleases have been shown to make specific cuts in vitro very close to the expected rec ...	1999	10494832
the foki methyltransferase from flavobacterium okeanokoites. purification and characterization of the enzyme and its truncated derivatives.	the gene encoding the foki methyltransferase from flavobacterium okeanokoites was cloned into an escherichia coli vector. the transcriptional start sites were mapped as well as putative -10 and -35 regions of the fokim promoter. enzyme overproduction was ensured by cloning the fokim gene under the phi 10 promoter of phase t7. m.foki was purified using a two-step chromatography procedure. m.foki is a monomeric protein with a m(r) = 76,000 +/- 1,500 under denaturing conditions. it contains 21 arg ...	1999	10934517
llafi, a type iii restriction and modification system in lactococcus lactis.	we describe a type iii restriction and modification (r/m) system, llafi, in lactococcus lactis. llafi is encoded by a 12-kb native plasmid, pnd801, harbored in l. lactis ll42-1. sequencing revealed two adjacent open reading frames (orfs). one orf encodes a 680-amino-acid polypeptide, and this orf is followed by a second orf which encodes an 873-amino-acid polypeptide. the two orfs appear to be organized in an operon. a homology search revealed that the two orfs exhibited significant similarity t ...	1999	9925601
purification and characterization of monovalent cation-activated levodione reductase from corynebacterium aquaticum m-13.	(6r)-2,2,6-trimethyl-1,4-cyclohexanedione (levodione) reductase was isolated from a cell extract of the soil isolate corynebacterium aquaticum m-13. this enzyme catalyzed regio- and stereoselective reduction of levodione to (4r,6r)-4-hydroxy-2,2, 6-trimethylcyclohexanone (actinol). the relative molecular mass of the enzyme was estimated to be 142,000 da by high-performance gel permeation chromatography and 36,000 da by sodium dodecyl sulfate-polyacrylamide gel electrophoresis. the enzyme require ...	1999	10508066
characterization of a salt-tolerant family 42 beta-galactosidase from a psychrophilic antarctic planococcus isolate.	we isolated a gram-positive, halotolerant psychrophile from a hypersaline pond located on the mcmurdo ice shelf in antarctica. a phylogenetic analysis of the 16s rrna gene sequence of this organism showed that it is a member of the genus planococcus. this assignment is consistent with the morphology and physiological characteristics of the organism. a gene encoding a beta-galactosidase in this isolate was cloned in an escherichia coli host. sequence analysis of this gene placed it in glycosidase ...	2000	10831422
planomicrobium koreense gen. nov., sp. nov., a bacterium isolated from the korean traditional fermented seafood jeotgal, and transfer of planococcus okeanokoites (nakagawa et al. 1996) and planococcus mcmeekinii (junge et al. 1998) to the genus planomicrobium.	a bacterial strain, jg07t, isolated from the korean traditional fermented seafood jeotgal, was subjected to a polyphasic taxonomic study. cells of strain jg07t are cocci or short rods in the early growth phase but change to rods as the cultures age. the peptidoglycan type is a4alpha, based on l-lys-d-glu. the menaquinone profile is characterized by the predominance of mk-8 followed by mk-7 and mk-6. the cellular fatty acid profile contains major amounts of saturated, unsaturated and branched fat ...	2001	11491353
use of a packed-column bioreactor for isolation of diverse protease-producing bacteria from antarctic soil.	seventy-five aerobic heterotrophs have been isolated from a packed-column bioreactor inoculated with soil from antarctica. the column was maintained at 10 degrees c and continuously fed with a casein-containing medium to enrich protease producers. twenty-eight isolates were selected for further characterization on the basis of morphology and production of clearing zones on skim milk plates. phenotypic tests indicated that the strains were mainly psychrotrophs and presented a high morphological a ...	2003	12620829
strain-specific ureolytic microbial calcium carbonate precipitation.	during a study of ureolytic microbial calcium carbonate (caco(3)) precipitation by bacterial isolates collected from different environmental samples, morphological differences were observed in the large caco(3) crystal aggregates precipitated within bacterial colonies grown on agar. based on these differences, 12 isolates were selected for further study. we hypothesized that the striking differences in crystal morphology were the result of different microbial species or, alternatively, differenc ...	2003	12902285
in vitro selection of restriction endonucleases by in vitro compartmentalization.	restriction endonucleases are widely used in laboratory applications from recombinant dna technology to diagnostics, but engineering of restriction enzymes by structure-guided design and in vivo directed evolution is at an early stage. here, we report the use of an in vitro compartmentalization system for completely in vitro selection of restriction enzymes. compartmentalization of a single gene in a rabbit reticulocyte in vitro transcription/translation system serves to isolate individually syn ...	2004	15247328
planococcus stackebrandtii sp. nov., isolated from a cold desert of the himalayas, india.	the taxonomic position of a bacterium isolated from a cold desert of the himalayas, india, was analysed by using a polyphasic approach. the isolated strain, designated k22-03t, had phenotypic characteristics that matched those of the genus planococcus and it represents a novel species. the almost-complete 16s rrna gene sequence (1464 bases) of the novel strain was compared with those of previously studied planococcus type strains and confirmed that the strain belongs to the genus planococcus. 16 ...	2005	15653859
planomicrobium chinense sp. nov., isolated from coastal sediment, and transfer of planococcus psychrophilus and planococcus alkanoclasticus to planomicrobium as planomicrobium psychrophilum comb. nov. and planomicrobium alkanoclasticum comb. nov.	an aerobic, motile, gram-positive strain, dx3-12(t), was isolated from coastal sediment of the eastern china sea in fujian province, china, and was identified by means of polyphasic taxonomy. on the basis of 16s rrna gene sequence similarity, strain dx3-12(t) was closely related to members of the genera planomicrobium and planococcus. 16s rrna gene sequence similarities between strain dx3-12(t) and planomicrobium mcmeekinii, planomicrobium koreense, planomicrobium okeanokoites, planococcus psych ...	2005	15774646
common patterns in type ii restriction enzyme binding sites.	restriction enzymes are among the best studied examples of dna binding proteins. in order to find general patterns in dna recognition sites, which may reflect important properties of protein-dna interaction, we analyse the binding sites of all known type ii restriction endonucleases. we find a significantly enhanced gc content and discuss three explanations for this phenomenon. moreover, we study patterns of nucleotide order in recognition sites. our analysis reveals a striking accumulation of a ...	2005	15888729
16s rrna sequences and differences in bacteria isolated from the muztag ata glacier at increasing depths.	small subunit 16s rrna sequences, growth temperatures, and phylogenetic relationships have been established for 129 bacterial isolates recovered under aerobic growth conditions from different regions of a 22-m ice core from the muztag ata mountain glacier on the pamirs plateau (china). only 11% were psychrophiles (grew at 2 degrees c or -2 degrees c up to approximately 20 degrees c), although the majority (82%) were psychrotolerant (grew at 2 degrees c or -2 degrees c up to 37 degrees c). the ma ...	2005	16085856
zinc finger nucleases: custom-designed molecular scissors for genome engineering of plant and mammalian cells.	custom-designed zinc finger nucleases (zfns), proteins designed to cut at specific dna sequences, are becoming powerful tools in gene targeting--the process of replacing a gene within a genome by homologous recombination (hr). zfns that combine the non-specific cleavage domain (n) of foki endonuclease with zinc finger proteins (zfps) offer a general way to deliver a site-specific double-strand break (dsb) to the genome. the development of zfn-mediated gene targeting provides molecular biologists ...	2005	16251401
distance determination by giy-yig intron endonucleases: discrimination between repression and cleavage functions.	giy-yig homing endonucleases are modular proteins, with conserved n-terminal catalytic domains connected by linkers to c-terminal dna-binding domains. i-tevi, the t4 phage giy-yig intron endonuclease, functions both in promoting td intron homing, and in acting as a transcriptional autorepressor. repression is achieved by binding to an operator, which is cleaved at 100-fold reduced efficiency relative to the intronless homing site. the linker includes a zinc finger, which functions in distance de ...	2006	16582101
structure, function and mechanism of exocyclic dna methyltransferases.	dna mtases (methyltransferases) catalyse the transfer of methyl groups to dna from adomet (s-adenosyl-l-methionine) producing adohcy (s-adenosyl-l-homocysteine) and methylated dna. the c5 and n4 positions of cytosine and n6 position of adenine are the target sites for methylation. all three methylation patterns are found in prokaryotes, whereas cytosine at the c5 position is the only methylation reaction that is known to occur in eukaryotes. in general, mtases are two-domain proteins comprising ...	2006	16987108
creation of a type iis restriction endonuclease with a long recognition sequence.	type iis restriction endonucleases cleave dna outside their recognition sequences, and are therefore particularly useful in the assembly of dna from smaller fragments. a limitation of type iis restriction endonucleases in assembly of long dna sequences is the relative abundance of their target sites. to facilitate ligation-based assembly of extremely long pieces of dna, we have engineered a new type iis restriction endonuclease that combines the specificity of the homing endonuclease i-scei with ...	2009	19304757
targeted genome editing in human cells with zinc finger nucleases constructed via modular assembly.	broad applications of zinc finger nuclease (zfn) technology-which allows targeted genome editing-in research, medicine, and biotechnology are hampered by the lack of a convenient, rapid, and publicly available method for the synthesis of functional zfns. here we describe an efficient and easy-to-practice modular-assembly method using publicly available zinc fingers to make zfns that can modify the dna sequences of predetermined genomic sites in human cells. we synthesized and tested hundreds of ...	2009	19470664
zinc finger nucleases as tools to understand and treat human diseases.	recent work has shown that it is possible to target regulatory elements to dna sequences of an investigator's choosing, increasing the armamentarium for probing gene function. in this review, we discuss the development and use of designer zinc finger proteins (zfps) as sequence specific tools. while the main focus of this review is to discuss the attachment of the foki nuclease to zfps and the ability of the resulting fusion protein (termed zinc finger nucleases (zfns)) to genomically manipulate ...	2010	20594338
structural flexibility allows the functional diversity of potyvirus genome-linked protein vpg.	several viral genome-linked proteins (vpgs) of plant viruses are intrinsically disordered and undergo folding transitions in the presence of partners. this property has been postulated to be one of the factors that enable the functional diversity of the protein. we created a homology model of potato virus a vpg and positioned the known functions and structural properties of potyviral vpgs on the novel structural model. the model suggests an elongated structure with a hydrophobic core composed of ...	2010	21177813
structural flexibility allows the functional diversity of potyvirus genome-linked protein vpg.	several viral genome-linked proteins (vpgs) of plant viruses are intrinsically disordered and undergo folding transitions in the presence of partners. this property has been postulated to be one of the factors that enable the functional diversity of the protein. we created a homology model of potato virus a vpg and positioned the known functions and structural properties of potyviral vpgs on the novel structural model. the model suggests an elongated structure with a hydrophobic core composed of ...	2010	21177813
tal nucleases (talns): hybrid proteins composed of tal effectors and foki dna-cleavage domain.	dna double-strand breaks enhance homologous recombination in cells and have been exploited for targeted genome editing through use of engineered endonucleases. here we report the creation and initial characterization of a group of rare-cutting, site-specific dna nucleases produced by fusion of the restriction enzyme foki endonuclease domain (fn) with the high-specificity dna-binding domains of avrxa7 and pthxo1. avrxa7 and pthxo1 are members of the transcription activator-like (tal) effector fam ...	2011	20699274
tal nucleases (talns): hybrid proteins composed of tal effectors and foki dna-cleavage domain.	dna double-strand breaks enhance homologous recombination in cells and have been exploited for targeted genome editing through use of engineered endonucleases. here we report the creation and initial characterization of a group of rare-cutting, site-specific dna nucleases produced by fusion of the restriction enzyme foki endonuclease domain (fn) with the high-specificity dna-binding domains of avrxa7 and pthxo1. avrxa7 and pthxo1 are members of the transcription activator-like (tal) effector fam ...	2011	20699274
de novo-engineered transcription activator-like effector (tale) hybrid nuclease with novel dna binding specificity creates double-strand breaks.	site-specific and rare cutting nucleases are valuable tools for genome engineering. the generation of double-strand dna breaks (dsbs) promotes homologous recombination in eukaryotes and can facilitate gene targeting, additions, deletions, and inactivation. zinc finger nucleases have been used to generate dsbs and subsequently, for genome editing but with low efficiency and reproducibility. the transcription activator-like family of type iii effectors (tales) contains a central domain of tandem r ...	2011	21262818
identity of zinc finger nucleases with specificity to herpes simplex virus type ii genomic dna: novel hsv-2 vaccine/therapy precursors.	herpes simplex type ii (hsv-2) is a member of the family herpesviridae. human infection with this double stranded linear dna virus causes genital ulcerative disease and existing treatment options only serve to resolve the symptomatology (ulcers) associated with active hsv-2 infection but do not eliminate latent virus. as a result, infection with hsv-2 follows a life-long relapsing (active versus latent) course. on the basis of a primitive bacterium anti-phage dna defense, the restriction modific ...	2011	21702927
comparative genetics: synergizing human and nod mouse studies for identifying genetic causation of type 1 diabetes.	although once widely anticipated to unlock how human type 1 diabetes (t1d) develops, extensive study of the nonobese diabetic (nod) mouse has failed to yield effective treatments for patients with the disease. this has led many to question the usefulness of this animal model. while criticism about the differences between nod and human t1d is legitimate, in many cases disease in both species results from perturbations modulated by the same genes or different genes that function within the same bi ...	2012	23804259
comparative genetics: synergizing human and nod mouse studies for identifying genetic causation of type 1 diabetes.	although once widely anticipated to unlock how human type 1 diabetes (t1d) develops, extensive study of the nonobese diabetic (nod) mouse has failed to yield effective treatments for patients with the disease. this has led many to question the usefulness of this animal model. while criticism about the differences between nod and human t1d is legitimate, in many cases disease in both species results from perturbations modulated by the same genes or different genes that function within the same bi ...	2012	23804259
zinc finger arrays binding human papillomavirus types 16 and 18 genomic dna: precursors of gene-therapeutics for in-situ reversal of associated cervical neoplasia.	human papillomavirus (hpv) types 16 and 18 are the high-risk, sexually transmitted infectious causes of most cervical intraepithelial neoplasias (cin) or cancers. while efficacious vaccines to reduce the sexual acquisition of these high-risk hpvs have recently been introduced, no virus-targeted therapies exist for those already exposed and infected. considering the oncogenic role of the transforming (e6 and e7) genes of high-risk hpvs in the slow pathogenesis of cervical cancer, we hypothesize t ...	2012	22840184
zinc finger nucleases for targeted mutagenesis and repair of the sickle-cell disease mutation: an in-silico study.	sickle cell disease (or simply, scd) is an inherited hemoglobinopathy which is mostly prevalent among persons of african descent. scd results from a monogenic (hemoglobin, beta) point-mutation (substitution of the base adenine with thymine at position six) that leads to replacement of the amino acid glutamic acid (e) with valine (v). management of scd within resource-poor settings is largely syndromic, since the option of cure offered by bone-marrow transplantation (bmt) is risky and unaffordabl ...	2012	22583379
diversity of marine bacteria producing beta-glucosidase inhibitors.	beta-glucosidase inhibitors are being extensively studied for use as anti-diabetics, anti-obesity and anti-tumour compounds. so far, these compounds have been reported in large numbers from plants, mushrooms, algae and fungi. there are very few reports of such inhibitors from bacteria in the open literature, particularly marine bacteria; although the best known inhibitor deoxynojirimycin was isolated from bacilli and actinomycete. through this study, we tried to discover the diversity of microbi ...	2013	23590573
endonuclease domain of the drosophila melanogaster r2 non-ltr retrotransposon and related retroelements: a new model for transposition.	the molecular mechanisms of the transposition of non-long terminal repeat (non-ltr) retrotransposons are not well understood; the key questions of how the 3'-ends of cdna copies integrate and how site-specific integration occurs remain unresolved. integration depends on properties of the endonuclease (en) domain of retrotransposons. using the en domain of the drosophila r2 retrotransposon as a model for other, closely related non-ltr retrotransposons, we investigated the en domain and found that ...	2013	23637706
bias problems in culture-independent analysis of environmental bacterial communities: a representative study on hydrocarbonoclastic bacteria.	culture-dependent methods for bacterial community analysis are currently considered obsolete; therefore, molecular techniques are usually used instead. the results of the current study on hydrocarbonoclastic bacteria in various oily habitats in kuwait showed however, that the bacterial identities varied dramatically according to the analytical approach used. for six desert and six seawater samples used in this study, the culture-independent and culture-dependent techniques each led to a unique b ...	2013	24040582
purification and characterization of a protease produced by a planomicrobium sp. l-2 from gut of octopus vulgaris.	protease widely exists in the digestive tract of animals and humans, playing a very important role in protein digestion and absorption. in this study, a high protease-producing strain planomicrobium sp. l-2 was isolated and identified from the digestive tract of octopus variabilis. the strain was identified by physiological and biochemical experiments and 16s rdna sequences analysis. a protease was obtained from the strain planomicrobium sp. l-2 through ammonium sulfate precipitation, dialysis a ...	2013	24551830
efficient talen construction for bombyx mori gene targeting.	engineered nucleases are artificial enzymes able to introduce double stranded breaks at desired genomic locations. the double stranded breaks start the error-prone repair process of non-homologous end-joining (nhej), which eventually leads to the induction of mutations at target sites. we showed earlier that zfns and talens are able to induce nhej mutations in the b. mori genome. in order to optimize our mutagenesis protocol, we modified one of the reported truncated talen scaffolds and optimize ...	2013	24058473
phylogenetic identification of marine bacteria isolated from deep-sea sediments of the eastern south atlantic ocean.	the deep-sea environments of the south atlantic ocean are less studied in comparison to the north atlantic and pacific oceans. with the aim of identifying the deep-sea bacteria in this less known ocean, 70 strains were isolated from eight sediment samples (depth range between 1905 to 5560 m) collected in the eastern part of the south atlantic, from the equatorial region to the cape abyssal plain, using three different culture media. the strains were classified into three phylogenetic groups, gam ...	2013	23565357
efficient gene editing in tomato in the first generation using the clustered regularly interspaced short palindromic repeats/crispr-associated9 system.		2014	25225186
halophilic microorganisms are responsible for the rosy discolouration of saline environments in three historical buildings with mural paintings.	a number of mural paintings and building materials from monuments located in central and south europe are characterized by the presence of an intriguing rosy discolouration phenomenon. although some similarities were observed among the bacterial and archaeal microbiota detected in these monuments, their origin and nature is still unknown. in order to get a complete overview of this biodeterioration process, we investigated the microbial communities in saline environments causing the rosy discolo ...	2014	25084531
a primary assessment of the endophytic bacterial community in a xerophilous moss (grimmia montana) using molecular method and cultivated isolates.	investigating the endophytic bacterial community in special moss species is fundamental to understanding the microbial-plant interactions and discovering the bacteria with stresses tolerance. thus, the community structure of endophytic bacteria in the xerophilous moss grimmia montana were estimated using a 16s rdna library and traditional cultivation methods. in total, 212 sequences derived from the 16s rdna library were used to assess the bacterial diversity. sequence alignment showed that the ...	2014	24948927
planomicrobium soli sp. nov., isolated from soil.	a gram-staining-positive bacterium, designated strain xn13(t), was isolated from a soil sample collected from alashan national geological park in inner mongolia autonomous region, china and subjected to a taxonomic study using a polyphasic approach. strain xn13(t) was found to have a range of chemical and morphological properties consistent with its classification in the genus planomicrobium. phylogenetic analyses based on 16s rrna gene sequences revealed that strain xn13(t) was related to membe ...	2014	24854007
genome editing and its applications in model organisms.	technological advances are important for innovative biological research. development of molecular tools for dna manipulation, such as zinc finger nucleases (zfns), transcription activator-like effector nucleases (talens), and the clustered regularly-interspaced short palindromic repeat (crispr)/crispr-associated (cas), has revolutionized genome editing. these approaches can be used to develop potential therapeutic strategies to effectively treat heritable diseases. in the last few years, substan ...	2015	26762955
genome editing and its applications in model organisms.	technological advances are important for innovative biological research. development of molecular tools for dna manipulation, such as zinc finger nucleases (zfns), transcription activator-like effector nucleases (talens), and the clustered regularly-interspaced short palindromic repeat (crispr)/crispr-associated (cas), has revolutionized genome editing. these approaches can be used to develop potential therapeutic strategies to effectively treat heritable diseases. in the last few years, substan ...	2015	26762955
noncontiguous finished genome sequence and description of planococcus massiliensis sp. nov., a moderately halophilic bacterium isolated from the human gut.	we propose the main phenotypic characteristics and the complete genome sequence and annotation of planococcus massiliensis strain es2(t) (= csur p1103 = dsm 28915), the type strain of p. massiliensis sp. nov., isolated from a faeces sample collected from a healthy senegalese man. it is an aerobic, gram-positive, moderately halophilic, motile and rod-shaped bacterium. the 3 357 017 bp long genome exhibits a g+c content of 46.0% and contains 3357 protein-coding genes and 48 rna genes.	2015	27257487
noncontiguous finished genome sequence and description of planococcus massiliensis sp. nov., a moderately halophilic bacterium isolated from the human gut.	we propose the main phenotypic characteristics and the complete genome sequence and annotation of planococcus massiliensis strain es2(t) (= csur p1103 = dsm 28915), the type strain of p. massiliensis sp. nov., isolated from a faeces sample collected from a healthy senegalese man. it is an aerobic, gram-positive, moderately halophilic, motile and rod-shaped bacterium. the 3 357 017 bp long genome exhibits a g+c content of 46.0% and contains 3357 protein-coding genes and 48 rna genes.	2015	27257487
efficient modification of ccr5 in primary human hematopoietic cells using a megatal nuclease and aav donor template.	genetic mutations or engineered nucleases that disrupt the hiv co-receptor ccr5 block hiv infection of cd4(+) t cells. these findings have motivated the engineering of ccr5-specific nucleases for application as hiv therapies. the efficacy of this approach relies on efficient biallelic disruption of ccr5, and the ability to efficiently target sequences that confer hiv resistance to the ccr5 locus has the potential to further improve clinical outcomes. we used rna-based nuclease expression paired ...	2015	26424571
paenibacillus larvae-directed bacteriophage hb10c2 and its application in american foulbrood-affected honey bee larvae.	paenibacillus larvae is the causative agent of american foulbrood (afb), the most serious honey bee brood bacterial disease. we isolated and characterized p. larvae-directed bacteriophages and developed criteria for safe phage therapy. whole-genome analysis of a highly lytic virus of the family siphoviridae (hb10c2) provided a detailed safety profile and uncovered its lysogenic nature and a putative beta-lactamase-like protein. to rate its antagonistic activity against the pathogens targeted and ...	2015	26048941
aerobic bacterial flora of biotic and abiotic compartments of a hyperendemic zoonotic cutaneous leishmaniasis (zcl) focus.	identification of the microflora of the sand fly gut and the environmental distribution of these bacteria are important components for paratransgenic control of leishmania transmission by sand flies.	2015	25630498
endonuclease specificity and sequence dependence of type iis restriction enzymes.	restriction enzymes that recognize specific sequences but cleave unknown sequence outside the recognition site are extensively utilized tools in molecular biology. despite this, systematic functional categorization of cleavage performance has largely been lacking. we established a simple and automatable model system to assay cleavage distance variation (termed slippage) and the sequence dependence thereof. we coupled this to massively parallel sequencing in order to provide sensitive and accurat ...	2015	25629514
n-acetyltransferase 2 (nat2) gene polymorphism as a predisposing factor for phenytoin intoxication in tuberculous meningitis or tuberculoma patients having seizures - a pilot study.	simultaneous administration of phenytoin and isoniazid (inh) in tuberculous meningitis (tbm) or tuberculoma patients with seizures results in higher plasma phenytoin level and thus phenytoin intoxication. n-acetyltransferase 2 (nat2) enzyme catalyses two acetylation reactions in inh metabolism and nat2 gene polymorphism leads to slow and rapid acetylators. the present study was aimed to evaluate the effect of allelic variants of n-acetyltransferase 2 (nat2) gene as a predisposing factor for phen ...	2016	27488001
in search of alternative antibiotic drugs: quorum-quenching activity in sponges and their bacterial isolates.	owing to the extensive development of drug resistance in pathogens against the available antibiotic arsenal, antimicrobial resistance is now an emerging major threat to public healthcare. anti-virulence drugs are a new type of therapeutic agent aiming at virulence factors rather than killing the pathogen, thus providing less selective pressure for evolution of resistance. one promising example of this therapeutic concept targets bacterial quorum sensing (qs), because qs controls many virulence f ...	2016	27092109
a simple test for the cleavage activity of customized endonucleases in plants.	although customized endonucleases [transcription activator-like effector nucleases (talens) and rna-guided endonucleases (rgens)] are known to be effective agents of mutagenesis in various host plants, newly designed endonuclease constructs require some pre-validation with respect to functionality before investing in the creation of stable transgenic plants.	2016	26962325
molecular diversity and multifarious plant growth promoting attributes of bacilli associated with wheat (triticum aestivum l.) rhizosphere from six diverse agro-ecological zones of india.	the diversity of culturable bacilli was investigated in six wheat cultivating agro-ecological zones of india viz: northern hills, north western plains, north eastern plains, central, peninsular, and southern hills. these agro-ecological regions are based on the climatic conditions such as ph, salinity, drought, and temperature. a total of 395 bacilli were isolated by heat enrichment and different growth media. amplified ribosomal dna restriction analysis using three restriction enzymes alui, msp ...	2016	26567901
the epigenomic landscape of prokaryotes.	dna methylation acts in concert with restriction enzymes to protect the integrity of prokaryotic genomes. studies in a limited number of organisms suggest that methylation also contributes to prokaryotic genome regulation, but the prevalence and properties of such non-restriction-associated methylation systems remain poorly understood. here, we used single molecule, real-time sequencing to map dna modifications including m6a, m4c, and m5c across the genomes of 230 diverse bacterial and archaeal ...	2016	26870957