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interpolated variable order motifs for identification of horizontally acquired dna: revisiting the salmonella pathogenicity islands.there is a growing literature on the detection of horizontal gene transfer (hgt) events by means of parametric, non-comparative methods. such approaches rely only on sequence information and utilize different low and high order indices to capture compositional deviation from the genome backbone; the superiority of the latter over the former has been shown elsewhere. however even high order k-mers may be poor estimators of hgt, when insufficient information is available, e.g. in short sliding win ...200616837528
motifcut: regulatory motifs finding with maximum density subgraphs.dna motif finding is one of the core problems in computational biology, for which several probabilistic and discrete approaches have been developed. most existing methods formulate motif finding as an intractable optimization problem and rely either on expectation maximization (em) or on local heuristic searches. another challenge is the choice of motif model: simpler models such as the position-specific scoring matrix (pssm) impose biologically unrealistic assumptions such as independence of th ...200616873465
efficient identification of dna hybridization partners in a sequence database.the specific hybridization of complementary dna molecules underlies many widely used molecular biology assays, including the polymerase chain reaction and various types of microarray analysis. in order for such an assay to work well, the primer or probe must bind to its intended target, without also binding to additional sequences in the reaction mixture. for any given probe or primer, potential non-specific binding partners can be identified using state-of-the-art models of dna binding stabilit ...200616873493
a database of 9-mers from promoter regions of human protein-coding genes.discovery of lexical characteristics of specific sequence motifs in human genomic dna can help with predicting and classifying regulatory cis elements according to the genes they control. in lexical models, some "words" may serve as downstream targets of signaling systems, whereas other "words" may specify sequences that selectively control the expression of a subset of genes to produce the various cell types and tissues. to discover lexical features of potential regulatory "words," we have crea ...200616888355
a program toolkit for the analysis of regulatory regions of genes.a major challenge in systems biology is to discover and reconstruct the cis-regulatory networks through which the expression of genes is controlled. even though a variety of sequences have been shown to interact with the transcription factors that bind dna, extensive work is needed to discover and classify regulatory "codes" and to elucidate the role played by the sequence context of genomic dna in the regulation of genes. databases of sequence elements extracted from regulatory regions may faci ...200616888356
interpreting oligonucleotide microarray data to determine rna secondary structure: application to the 3' end of bombyx mori r2 rna.a method to deduce rna secondary structure on the basis of data from microarrays of 2'-o-methyl rna 9-mers immobilized in agarose film on glass slides is tested with a 249 nucleotide rna from the 3' end of the r2 retrotransposon from bombyx mori. various algorithms incorporating binding data and free-energy minimization calculations were compared for interpreting the data to provide possible secondary structures. two different methods give structures with 100 and 87% of the base pairs determined ...200616893182
elastogenic effects of exogenous hyaluronan oligosaccharides on vascular smooth muscle cells.prior studies suggest that hyaluronan (ha), a glycosaminoglycan, may upregulate innately poor elastin matrix synthesis by adult vascular smooth muscle cells (smcs). ha scaffolds could thus be useful to regenerate damaged vascular elastin. in an earlier study, we established that the elastogenic effects of non-oligomeric ha are fragment size- and/or dose-specific. we currently investigate the pro-elastogenic effects of exogenous ha oligomers on rat aortic smooth muscle cells (rasmcs). rasmcs were ...200616899292
antisense inhibition of rnase p: mechanistic aspects and application to live bacteria.we explored bacterial rnase p as a drug target using antisense oligomers against the p15 loop region of escherichia coli rnase p rna. an rna 14-mer, or locked nucleic acid (lna) and peptide nucleic acid (pna) versions thereof, disrupted local secondary structure in the catalytic core, forming hybrid duplexes over their entire length. binding of the pna and lna 14-mers to rnase p rna in vitro was essentially irreversible and even resisted denaturing page. association rates for the rna, lna, and p ...200616901906
selection of cc chemokine receptor 5-binding peptide from a phage display peptide library.human cc chemokine receptor (ccr) 5 is a g protein-coupled receptor involved in a broad range of human diseases that mediates hiv-1 viral entry into cells. certain small molecule receptor antagonists to ccr5 have been useful in therapy for these diseases. in this study, ccr5-expressing cho cells (cho/ccr5 cells) were used to select ccr5-binding peptides from a phage-displayed 12-mers peptide library. all of the 30 clones selected from the library showed specific binding to cho/ccr5 cells by enzy ...200616960395
serum ige reactive against small myelin protein-derived peptides is increased in multiple sclerosis patients.though independent findings suggest roles for the allergic arm of the immune system and myelin-reactive antibodies in ms, myelin-reactive ige has not been investigated. we have developed a radioimmunoassay that measures reactive ige, igg and iga against short (5-6-mers) myelin protein-derived peptides bearing little to no sequence identity with other human proteins, and which might therefore be targets of a cns-specific autoimmune attack. here we show that, irrespective of clinical subtype, ms p ...200616996143
compact, universal dna microarrays to comprehensively determine transcription-factor binding site specificities.transcription factors (tfs) interact with specific dna regulatory sequences to control gene expression throughout myriad cellular processes. however, the dna binding specificities of only a small fraction of tfs are sufficiently characterized to predict the sequences that they can and cannot bind. we present a maximally compact, synthetic dna sequence design for protein binding microarray (pbm) experiments that represents all possible dna sequence variants of a given length k (that is, all 'k-me ...200616998473
detection of oligosaccharide ligands for hepatocyte growth factor/scatter factor (hgf/sf), keratinocyte growth factor (kgf/fgf-7), rantes and heparin cofactor ii by neoglycolipid microarrays of glycosaminoglycan-derived oligosaccharide fragments.neoglycolipid technology is eminently adaptable for microarray design for high-throughput detection and specificity assignments of carbohydrate-protein interactions. dermatan sulfate (ds) is known to play an important role because of its ability to bind growth factors as well as chemokines and to modulate their biological activities during inflammation and response to injury. we prepared various iduronic acid-rich fragments from ds by complete digestion with chondroitinase aci, and investigated ...200617006643
genetic variation in opisthorchis viverrini (trematoda: opisthorchiidae) from northeast thailand and laos pdr based on random amplified polymorphic dna analyses.genetic variation in opisthorchis viverrini adults originating from different locations in northeast thailand and laos, people's democratic republic (pdr), was examined using random amplified polymorphic dna (rapd) analyses. in an initial analysis, the genomic dna of one fluke from each of ten localities was amplified using 15 random primers (10-mers); however, genetic variation among o. viverrini specimens was detected reliably for only four primers. a more detailed rapd analysis using these fo ...200717016722
structural characterization of beta-sheeted oligomers formed on the pathway of oxidative prion protein aggregation in vitro.the pathology of transmissible spongiform encephalopathies (tses) is strongly associated with the structural conversion of the cellular prion protein (prpc) into a misfolded isoform (prpsc) that assembles into amyloid fibrils. since increased levels of oxidative stress have been linked to prion diseases, we investigated the metal-induced oxidation of human prp (90-231). a novel in vitro conversion assay based on aerobic incubation of prp in the presence of elemental copper pellets at ph 5 was es ...200717023178
a peptide inhibitor of mura udp-n-acetylglucosamine enolpyruvyl transferase: the first committed step in peptidoglycan biosynthesis.the mura enzyme from pseudomonas aeruginosa was purified to homogeneity and found to be biologically active as a udp-n-acetylglucosamine (unag) enolpyruvyl transferase in a coupled enzyme assay where atpase activity was measured by the release of inorganic phosphate. a microtiter plate assay coupled to competitive biopanning using the udp-n-acetylglucosamine was used to screen 10(9) c-7-c and 12-mers peptides from phage display libraries. from 60 phage-encoded peptides identified after the fourt ...200617030076
a graph-based motif detection algorithm models complex nucleotide dependencies in transcription factor binding sites.given a set of known binding sites for a specific transcription factor, it is possible to build a model of the transcription factor binding site, usually called a motif model, and use this model to search for other sites that bind the same transcription factor. typically, this search is performed using a position-specific scoring matrix (pssm), also known as a position weight matrix. in this paper we analyze a set of eukaryotic transcription factor binding sites and show that there is extensive ...200617041233
array-based identification of species of the genera abiotrophia, enterococcus, granulicatella, and streptococcus.some species of enterococci and streptococci are difficult to differentiate by phenotypic traits. the feasibility of using an oligonucleotide array for identification of 11 viridans group streptococci was previously established. the aim of this study was to expand the array to identify species of abiotrophia (1 species), enterococcus (18 species), granulicatella (3 species), and streptococcus (31 species and 6 subspecies). the method consisted of pcr amplification of the ribosomal dna intergenic ...200617065265
interactions of bovine serum albumin with aluminum polyoxocations and aluminum hydroxide.interactions of aqueous solutions of aluminum polyoxocations (al13-mers and al30-mers) and aluminum hydroxide suspensions of varying particle sizes (26, 55, and 82 nm) with a model protein, bovine serum albumin (bsa), have been investigated using potentiometry, conductometry, viscometry, 27al solution nmr, uv-vis spectroscopy, dynamic light scattering, zeta-potential measurements, thermogravimetry, x-ray diffraction, and scanning electron microscopy. increasing amounts of bsa partially convert a ...200617107003
heterotetramers formed by an s-layer-streptavidin fusion protein and core-streptavidin as a nanoarrayed template for biochip development.based on the s-layer protein sbpa of bacillus sphaericus ccm 2177, an s-layer-streptavidin fusion protein was constructed. after heterologous expression, isolation of the fusion protein, and refolding, functional heterotetramers were obtained that had retained the ability to recrystallize into the square-lattice structure on plain gold chips and on gold chips precoated with secondary cell wall polymer (scwp), which is the natural anchoring molecule for the s-layer protein in the bacterial cell w ...200617193570
dna-oligonucleotide encapsulating liposomes as a secondary signal amplification means.a novel liposome-based signal amplification system was developed by encapsulating dna oligonucleotides within antibody-tagged liposomes and subsequently detecting the oligonucleotide with dye-encapsulating liposomes for double signal enhancement. in this sandwich immunoassay, the model analyte, protective antigen protein from b. anthracis, was captured by one set of antibodies immobilized in microtiter plate wells and detected using a second antibody conjugated to oligonucleotide-encapsulating l ...200717253656
large-scale analysis of antigenic diversity of t-cell epitopes in dengue virus.antigenic diversity in dengue virus strains has been studied, but large-scale and detailed systematic analyses have not been reported. in this study, we report a bioinformatics method for analyzing viral antigenic diversity in the context of t-cell mediated immune responses. we applied this method to study the relationship between short-peptide antigenic diversity and protein sequence diversity of dengue virus. we also studied the effects of sequence determinants on viral antigenic diversity. sh ...200617254309
the iclr-type transcriptional repressor ltbr regulates the expression of leucine and tryptophan biosynthesis genes in the amino acid producer corynebacterium glutamicum.the transcriptional regulator cg1486 of corynebacterium glutamicum atcc 13032 is a member of the iclr protein family and belongs to the conserved set of regulatory proteins in corynebacteria. a defined deletion in the cg1486 gene, now designated ltbr (leucine and tryptophan biosynthesis regulator), led to the mutant strain c. glutamicum ib1486. according to whole-genome expression analysis by dna microarray hybridizations, transcription of the leub and leucd genes encoding enzymes of the leucine ...200717259312
mapping binding sites for the pde4d5 camp-specific phosphodiesterase to the n- and c-domains of beta-arrestin using spot-immobilized peptide arrays.beta2-ars (beta2-adrenoceptors) become desensitized rapidly upon recruitment of cytosolic beta-arrestin. pde4d5 (family 4 camp-specific phosphodiesterase, subfamily d, isoform 5) can be recruited in complex with beta-arrestin, whereupon it regulates pka (camp-dependent protein kinase) phosphorylation of the beta2-ar. in the present study, we have used novel technology, employing a library of overlapping peptides (25-mers) immobilized on cellulose membranes that scan the entire sequence of beta-a ...200717288540
crosslinking of the ner damage recognition proteins xpc-hr23b, xpa and rpa to photoreactive probes that mimic dna damages.a new assay to probe the mechanism of mammalian nucleotide excision repair (ner) was developed. photoreactive arylazido analogues of dnmp in dna were shown to be substrates for the human ner system. oligonucleotides carrying photoreactive "damages" were prepared using the multi-stage protocol including one-nucleotide gap filling by dna polymerase beta using photoreactive dctp or dutp analogues followed by ligation of the resulting nick. photoreactive 60-mers were annealed with single-stranded pb ...200717320292
site specific n6-(2-hydroxy-3,4-epoxybut-1-yl)adenine oligodeoxynucleotide adducts of 1,2,3,4-diepoxybutane: synthesis and stability at physiological ph.1,2,3,4-diepoxybutane (deb) is an important metabolite of 1,3-butadiene, a high volume industrial chemical classified as a human and animal carcinogen. deb is a bifunctional alkylating agent that exhibits both mutagenic and cytotoxic activity, presumably a result of its ability to form bifunctional dna adducts. initial reactions of deb with dna produce 2-hydroxy-3,4-epoxybut-1-yl (heb) lesions at guanine and adenine nucleobases. the epoxy group of the monoadduct is inherently reactive and can th ...200717355152
synergistic effects of multiple treatments, and both dna and rna direct bindings on, green tea catechins.this article reviews two main topics: (1) the synergistic effects of multiple treatments with green tea catechin and (2) the direct binding of (-)-epigallocatechin gallate (egcg) to both dna and rna molecules. japanese drink green tea throughout the day, so we studied whether multiple treatments of cells with egcg would enhance the expression of apoptosis-related genes, such as growth arrest and dna damage-inducible gene (gadd153) and cyclin-dependent kinase inhibitor gene (p21(waf1)): the resul ...200717440927
a randomized lentivirus shrna library construction.vector based shrna (short hairpin rna) expression library has been widely used to screen functional genes. for two main methods that have been used to generate short hairpin rna libraries, chemical synthesis is too expensive to be widely used and the low efficiency of enzymatic approach makes it difficult to construct. we have developed a protocol to construct a new kind of shrna library called randomized shrna library. within three steps chemically synthesized randomized 19-mers dna were effici ...200717482565
a general framework for designing and validating oligomer-based dna microarrays and its application to clostridium acetobutylicum.while dna microarray analysis is widely accepted as an essential tool for modern biology, its use still eludes many researchers for several reasons, especially when microarrays are not commercially available. in that case, the design, construction, and use of microarrays for a sequenced organism constitute substantial, time-consuming, and expensive tasks. recently, it has become possible to construct custom microarrays using industrial manufacturing processes, which offer several advantages, inc ...200717526797
the rate of trap binding to rna is crucial for transcription attenuation control of the b. subtilis trp operon.the trp rna-binding attenuation protein (trap) regulates expression of the tryptophan biosynthetic and transport genes in bacillus subtilis in response to changes in the levels of intracellular tryptophan. transcription of the trpedcfba operon is controlled by an attenuation mechanism involving two overlapping rna secondary structures in the 5' leader region of the trp transcript; trap binding promotes formation of a transcription terminator structure that halts transcription prior to the struct ...200717555767
5'-modified g-quadruplex forming oligonucleotides endowed with anti-hiv activity: synthesis and biophysical properties.oligodeoxyribonucleotides of sequence d(5'tgggag3') carrying bulky aromatic groups at the 5' end were found to exhibit potent anti-hiv activity [hotoda, h., et al. (1998) j. med. chem. 41, 3655-3663 and references therein]. structure-activity relationship investigations indicated that g-quadruplex formation, as well as the presence of large aromatic substituents at the 5'-end, were both essential for their antiviral activity. in this work, we synthesized some representative examples of the anti- ...200717569499
insight into the folding inhibition of the hiv-1 protease by a small peptide.it has recently been shown that the highly protected segments 24-34 (s2) and 83-93 (s8) of each of the two 99-mers of human immunodeficiency virus type 1 protease play an essential role in the folding of the monomers, giving rise to the so-called (postcritical) folding nucleus ((fn) minimum condensation unit ensuring folding) when they dock. this scenario received further support from model calculations that demonstrated that the peptide p-s8, displaying an amino acid sequence identical to the c ...200717573430
impact of delivery mode of hyaluronan oligomers on elastogenic responses of adult vascular smooth muscle cells.our prior studies demonstrated that exogenous supplements of pure hyaluronan (ha) tetramers (ha4) dramatically upregulate elastin matrix synthesis by adult vascular smooth muscle cells (smcs). some studies suggest that exogenous ha likely only transiently contacts and signals cells, and may elicit different cell responses when presented on a substrate (e.g., scaffold surface). to clarify such differences, we used a carbodiimide-based chemistry to tether ha4 onto glass, and compared elastin matri ...200717574666
ytqi from bacillus subtilis has both oligoribonuclease and pap-phosphatase activity.oligoribonuclease is the only rnase in escherichia coli that is able to degrade rna oligonucleotides five residues and shorter in length. firmicutes including bacillus subtilis do not have an oligoribonuclease (orn) homologous protein and it is not yet understood which proteins accomplish the equivalent function in these organisms. we had previously identified oligoribonucleases orn from e. coli and its human homolog sfn in a screen for proteins that are regulated by 3'-phosphoadenosine 5'-phosp ...200717586819
identification of dermatophytes by an oligonucleotide array.species of dermatophytes are classified into three anamorphic (asexual) genera, epidermophyton, microsporum, and trichophyton. conventional methods used to identify dermatophytes are often lengthy and may be inconclusive because of atypical microscopic or colony morphology. based on the internal transcribed spacer 1 (its-1) and its-2 sequences of the rrna genes, an oligonucleotide array was developed to identify 17 dermatophyte species. the method consisted of pcr amplification of the its region ...200717687010
chondroprotective effects of a proanthocyanidin rich amazonian genonutrient reflects direct inhibition of matrix metalloproteinases and upregulation of igf-1 production by human chondrocytes.abstract:200717697350
priming with sars cov s dna and boosting with sars cov s epitopes specific for cd4+ and cd8+ t cells promote cellular immune responses.cellular immune response plays an important role in antiviral immunity. in our previous study, immunization of mice with severe acute respiratory syndrome coronavirus (sars cov) spike (s) dna vaccine could induce both humoral and cellular immunity in response to a pool of entire overlapping s peptides. identification of functional dominant epitopes in sars cov s protein for t cells is crucial for further understanding of cellular immune responses elicited by sars cov s dna vaccine. in present st ...200717709158
effect of the nonreducing end of shigella dysenteriae type 1 o-specific oligosaccharides on their immunogenicity as conjugates in mice.endemic and epidemic shigellosis, an acute invasive disease of the lower intestines, afflicts millions of people worldwide with an estimated one million fatalities per annum at a low infectious dose. our approach to vaccine development against shigella is based on the hypothesis that serum igg antibodies to the o-specific polysaccharide (o-sp) domains of the lps of these organisms confer protection to infection. the synthetic oligosaccharides corresponding to the tetrasaccharide repeating unit o ...200717726093
recognition of hiv-1 peptides by host ctl is related to hiv-1 similarity to human proteins.while human immunodeficiency virus type 1 (hiv-1)-specific cytotoxic t lymphocytes preferentially target specific regions of the viral proteome, hiv-1 features that contribute to immune recognition are not well understood. one hypothesis is that similarities between hiv and human proteins influence the host immune response, i.e., resemblance between viral and host peptides could preclude reactivity against certain hiv epitopes.200717786195
systematic studies on the paracellular permeation of model permeants and oligonucleotides in the rat small intestine with chenodeoxycholate as enhancer.the objective of this study was to mechanistically and quantitatively analyze chenodeoxycholate-enhanced paracellular transport of polar permeants and oligonucleotides in the rat jejunum and ileum. micellar chenodeoxycholate solutions were used to perturbate the tight junctions. supporting studies included assessment of the aqueous boundary layer (abl) with abl-controlled permeants, measurements of the permeability coefficients and fluxes of the bile acid in dilute and micellar concentrations, a ...200817847071
an oligoarray for the detection of human papillomavirus type 16 variants.on the basis of human papillomavirus (hpv) e6 gene mutations, there are more than five variants of hpv 16. we applied a sensitive and specific stacking hybridization assay using an oligoarray for the detection of asian-american (aa) and european (e) (e350g) hpv 16 variants. a simple glass slide was coated with capture probes consisting of short oligonucleotide dna sequences (7-9 mers) specific for aa and e variants. two different regions of the e6 hpv 16 gene were amplified with a set of two pri ...200717877642
chondroitin c lyase [4.2.2.] is unable to cleave fructosylated sequences inside the partially fructosylated escherichia coli k4 polymer.chondroitin c lyase was demonstrated to be unable to act on fructosylated sequences inside a partially fructosylated polysaccharide having the chondroitin backbone structure, the escherichia coli k4 polymer, using different analytical approaches. chondroitin c lyase produced various unsaturated oligosaccharides by acting on an approximately 27%-fructosylated k4 polymer. the online hplc-esi-ms approach showed the disaccharide nature of the main species produced by chondroitinase c as deltahexa-ga ...200817902054
mass spectrometry characterization of escherichia coli k4 oligosaccharides from 2-mers to more than 20-mers.the separation and characterization of oligosaccharides obtained by hyaluronidase [e.c. 3.2.1.35] digestion of escherichia coli k4 polysaccharide using online high-performance liquid chromatography/electrospray ionization mass spectrometry (hplc/esi-ms) are presented. complete identification and structural information for oligosaccharides containing 2-24 monomers (from 2- to 24-mers) were obtained. in particular, smaller k4 species, from 2-mers to 4-mers, exhibited mainly [m-h](-1) anions, where ...200717922485
linkage between substrate recognition and catalysis during cleavage of sarcin/ricin loop rna by restrictocin.restrictocin is a site-specific endoribonuclease that inactivates ribosomes by cleaving the sarcin/ricin loop (srl) of 23s-28s rrna. here we present a kinetic and thermodynamic analysis of the srl cleavage reaction based on monitoring the cleavage of rna oligonucleotides (2-27-mers). restrictocin binds to a 27-mer srl model substrate (designated wild-type srl) via electrostatic interactions to form a nonspecific ground state complex e:s. at ph 6.7, physical steps govern the reaction rate: the wi ...200717929942
mango: a new approach to multiple sequence alignment.multiple sequence alignment is a classical and challenging task for biological sequence analysis. the problem is np-hard. the full dynamic programming takes too much time. the progressive alignment heuristics adopted by most state of the art multiple sequence alignment programs suffer from the 'once a gap, always a gap' phenomenon. is there a radically new way to do multiple sequence alignment? this paper introduces a novel and orthogonal multiple sequence alignment method, using multiple optimi ...200717951828
large-scale validation of methods for cytotoxic t-lymphocyte epitope prediction.reliable predictions of cytotoxic t lymphocyte (ctl) epitopes are essential for rational vaccine design. most importantly, they can minimize the experimental effort needed to identify epitopes. netctl is a web-based tool designed for predicting human ctl epitopes in any given protein. it does so by integrating predictions of proteasomal cleavage, tap transport efficiency, and mhc class i affinity. at least four other methods have been developed recently that likewise attempt to predict ctl epito ...200717973982
targeted gene modification by oligonucleotides and small dna fragments in eukaryotes.targeted modification of genomic dna (gdna) in a cell permanently changes its phenotype. numerous methods to modify target portions of gdna in eukaryotes have been developed, and several have found practical application (e.g., homologous recombination-utilized modification in mouse es cells). the past decade has seen active research both in oligonucleotide-directed modifications (where the oligonucleotides can be chimeric rna/dna oligonucleotides, single-stranded oligonucleotides, or triple heli ...200817981583
evaluating the quality of data from dna microarray measurements.gene expression technology offers great potentials to generate new insights into human disease pathogenesis; however, the data quality remains a major obstacle for realizing its potentials. in the present study 60-mers oligonucleotide target immobilized on coated glass slides were utilized as a model system to investigate parameters, such as target concentration, retention, signal linearity, and fluorescence properties of fluorophores, which likely affect the quality of microarray results. an ar ...200717984517
design and testing of 'genome-proxy' microarrays to profile marine microbial communities.microarrays are useful tools for detecting and quantifying specific functional and phylogenetic genes in natural microbial communities. in order to track uncultivated microbial genotypes and their close relatives in an environmental context, we designed and implemented a 'genome-proxy' microarray that targets microbial genome fragments recovered directly from the environment. fragments consisted of sequenced clones from large-insert genomic libraries from microbial communities in monterey bay, t ...200818028413
structure-function relationship of novel x4 hiv-1 entry inhibitors - l- and d-arginine peptide-aminoglycoside conjugates.we present the design, synthesis, anti-hiv-1 and mode of action of neomycin and neamine conjugated at specific sites to arginine 6- and 9-mers d- and l-arginine peptides (apacs). the d-apacs inhibit the infectivity of x4 hiv-1 strains by one or two orders of magnitude more potently than their respective l-apacs. d-arginine conjugates exhibit significantly higher affinity towards cxc chemokine receptor type 4 (cxcr4) than their l-arginine analogs, as determined by their inhibition of monoclonal a ...200718028446
phage display screening of epithelial cell monolayers treated with egta: identification of peptide fdfwitp that modulates tight junction activity.phage display was used to screen for peptides that modulate the activity of epithelial cell tight junctions. panning with a phage library that displays random 7-mers was performed using monolayers of human bronchial epithelial cells (16hbe14o(-)) treated with a calcium chelator, ethylene glycol-bis(2-aminoethylether)- n, n, n', n'-tetraacetic acid (egta), to increase accessibility to the junctional complex/paracellular space, followed by subtractive panning. a novel peptide, fdfwitp, identified ...200718040053
high-throughput biochemical analysis of in vivo location data reveals novel distinct classes of pou5f1(oct4)/dna complexes.the transcription factor pou5f1 is a key regulator of embryonic stem (es) cell pluripotency and a known oncoprotein. we have developed a novel high-throughput binding assay called megashift (microarray evaluation of genomic aptamers by shift) that we use to pinpoint the exact location, affinity, and stoichiometry of the dna-protein complexes identified by chromatin immunoprecipitation studies. we consider all genomic regions identified as pou5f1-chip-enriched in both human and mouse. compared wi ...200818212089
all and only cpg containing sequences are enriched in promoters abundantly bound by rna polymerase ii in multiple tissues.the promoters of housekeeping genes are well-bound by rna polymerase ii (rnap) in different tissues. although the promoters of these genes are known to contain cpg islands, the specific dna sequences that are associated with high rnap binding to housekeeping promoters has not been described.200818252004
hyaluronic acid cues for functional endothelialization of vascular constructs.current vascular implant materials insufficiently recruit endothelial cells (ecs) to form a normally functional and confluent endothelium, a key challenge to reinstating vascular homeostasis at the surgical site. recent studies indicate that hyaluronan (ha), a connective tissue gag whose biological effects are often dictated by its fragment size, may inherently stimulate endothelialization. we previously showed that ecs respond poorly to large ha fragments (10 kda < mw < 1 mda), therefore, we cu ...200818265428
regeneration of abdominal wall musculofascial defects by a human acellular collagen matrix.this work studied the reconstruction of an abdominal wall defect by a human acellular collagen matrix. the abdominal wall defect was cured in 40 rats by implanting (i) polypropylene (pro), (ii) polyester (mers) meshes, and (iii) human acellular collagen matrix with two orientations: fibres in parallel (fascia lata longitudinal [fll]) or perpendicular (fascia lata transversal [flt]) to native rats' abdominal walls. hernia recurrence, adhesions, and histology (for inflammation and remodelling) wer ...200818281088
velvet: algorithms for de novo short read assembly using de bruijn graphs.we have developed a new set of algorithms, collectively called "velvet," to manipulate de bruijn graphs for genomic sequence assembly. a de bruijn graph is a compact representation based on short words (k-mers) that is ideal for high coverage, very short read (25-50 bp) data sets. applying velvet to very short reads and paired-ends information only, one can produce contigs of significant length, up to 50-kb n50 length in simulations of prokaryotic data and 3-kb n50 on simulated mammalian bacs. w ...200818349386
improving phrap-based assembly of the rat using "reliable" overlaps.the assembly methods used for whole-genome shotgun (wgs) data have a major impact on the quality of resulting draft genomes. we present a novel algorithm to generate a set of "reliable" overlaps based on identifying repeat k-mers. to demonstrate the benefits of using reliable overlaps, we have created a version of the phrap assembly program that uses only overlaps from a specific list. we call this version phrapumd. integrating phrapumd and our "reliable-overlap" algorithm with the baylor colleg ...200818350171
estrogen signaling characteristics of atlantic croaker g protein-coupled receptor 30 (gpr30) and evidence it is involved in maintenance of oocyte meiotic arrest.human g protein-coupled receptor 30 (gpr30) mediates estradiol-17beta (e2) activation of adenylyl cyclase in breast cancer cells and displays e2 binding typical of membrane estrogen receptors (mers). we identified a mer in atlantic croaker ovaries with characteristics similar to those of human gpr30. to confirm the proposed role of gpr30 as a mer in this distantly related vertebrate group, we cloned gpr30 from croaker ovaries and examined its distribution, steroid binding, and signaling characte ...200818420744
determinants of cytokine induction by small interfering rna in human peripheral blood mononuclear cells.synthetic small interfering rnas (sirnas) can trigger a strong innate immune response in mammalian cells. this nonspecific side effect may hinder the application of sirnas as tools in gene silencing. chemically synthesized sirnas, including traditional 19-mers with 2-nt 3' overhangs, longer duplexes with blunt or 3' overhangs, and asymmetric duplexes with a blunt end and a 2-nt 3' overhang, can evoke strong dose-dependent interferon-alpha (ifn-alpha) and tumor necrosis factor-alpha (tnf-alpha) r ...200818439100
quantitative characterization of the large-scale association of erbb1 and erbb2 by flow cytometric homo-fret measurements.the association of receptor tyrosine kinases is a key step in the initiation of growth factor-mediated signaling. although the ligand-induced dimerization of inactive, monomeric receptors was the central dogma of receptor tyrosine kinase activation for decades, the existence of larger oligomers is now accepted. both homoassociations and heteroassociations are of extreme importance in the epidermal growth factor (egf) receptor family, leading to diverse and robust signaling. we present a statisti ...200818487307
web-based design and evaluation of t-cell vaccine candidates.we present a suite of on-line tools to design candidate vaccine proteins, and to assess antigen potential, using coverage of k-mers (as proxies for potential t-cell epitopes) as a metric. the vaccine design tool uses the recently published 'mosaic' method to generate protein sequences optimized for coverage of high-frequency k-mers; the coverage-assessment tools facilitate coverage comparisons for any potential antigens. to demonstrate these tools, we designed mosaic protein sets for b-clade hiv ...200818515277
spectrum-based de novo repeat detection in genomic sequences.a novel approach to the detection of genomic repeats is presented in this paper. the technique, dubbed sagri (spectrum assisted genomic repeat identifier), is based on the spectrum (set of sequence k-mers, for some k) of the genomic sequence. specifically, the genome is scanned twice. the first scan (findhit) detects candidate pairs of repeat-segments, by effectively reconstructing portions of the euler path of the (k-1)-mer graph of the genome only in correspondence with likely repeat sites. th ...200818549302
microarray for molecular typing of salmonella enterica serovars.we describe the development of a spotted array for the delineation of the most common 14 disease-causing salmonella serovars in the united states. our array consists of 414 70 mers targeting core genes of salmonella enterica, subspecies i specific genes, fimbrial genes, pathogenicity islands, gifsy elements and other variable genes. using this array we were able to identify a unique gene presence/absence profile for each of the targeted serovar which was used as the serovar differentiating crite ...200818554865
thrombogenic collagen-mimetic peptides: self-assembly of triple helix-based fibrils driven by hydrophobic interactions.collagens are integral structural proteins in animal tissues and play key functional roles in cellular modulation. we sought to discover collagen model peptides (cmps) that would form triple helices and self-assemble into supramolecular fibrils exhibiting collagen-like biological activity without preorganizing the peptide chains by covalent linkages. this challenging objective was accomplished by placing aromatic groups on the ends of a representative 30-mer cmp, (gpo)(10), as with l-phenylalani ...200818559857
mango: multiple alignment with n gapped oligos.multiple sequence alignment is a classical and challenging task. the problem is np-hard. the full dynamic programming takes too much time. the progressive alignment heuristics adopted by most state-of-the-art works suffer from the "once a gap, always a gap" phenomenon. is there a radically new way to do multiple sequence alignment? in this paper, we introduce a novel and orthogonal multiple sequence alignment method, using both multiple optimized spaced seeds and new algorithms to handle these s ...200818574861
molecular appraisal of indian animal isolates of echinococcus granulosus.cystic echinococcosis (ce) has a wide host range and distinct entities, not only reflected phenotypically but also by genotypic variation. considering this fact, this study was undertaken to characterize the indian isolates of echinococcus granulosus to find out difference between indian cattle, buffalo and sheep isolates on the basis of random amplification of polymorphic dna (rapd) pcr and pcr mediated restriction fragment length polymorphism (pcrrflp) of internal transcribed spacer gene 1 (it ...200818577794
comparative genomic profiling of dutch clinical bordetella pertussis isolates using dna microarrays: identification of genes absent from epidemic strains.whooping cough caused by bordetella pertussis in humans, is re-emerging in many countries despite vaccination. several studies have shown that significant shifts have occurred in the b. pertussis population resulting in antigenic divergence between vaccine strains and circulating strains and suggesting pathogen adaptation. in the netherlands, the resurgence of pertussis is associated with the rise of b. pertussis strains with an altered promoter region for pertussis toxin (ptxp3).200818590534
estimation of neuronal firing rates with the three-state biological point process model.in the subcortex of the human brain, neuronal firing events are stochastic and the inter-arrival times of action potentials (aps) are highly irregular. it has been shown that stimulation of the subthalamic nucleus (stn), a small subcortical structure located within the basal ganglia, can help ameliorate the motor symptoms associated with parkinson's disease (pd). however, success of image guided stereotactic surgery is reliant upon the refinement of the anatomic target (in this case the stn) bas ...200818598715
ribosome performance is enhanced by a rich cluster of pseudouridines in the a-site finger region of the large subunit.the large subunit rrna in eukaryotes contains an unusually dense cluster of 8-10 pseudouridine (psi) modifications located in a three-helix structure (h37-h39) implicated in several functions. this region is dominated by a long flexible helix (h38) known as the "a-site finger" (asf). the asf protrudes from the large subunit just above the a-site of trna binding, interacts with 5 s rrna and trna, and through the terminal loop, forms a bridge (b1a) with the small subunit. in yeast, the three-helix ...200818611858
design of compact, universal dna microarrays for protein binding microarray experiments.our group has recently developed a compact, universal protein binding microarray (pbm) that can be used to determine the binding preferences of transcription factors (tfs). this design represents all possible sequence variants of a given length k (i.e., all k-mers) on a single array, allowing a complete characterization of the binding specificities of a given tf. here, we present the mathematical foundations of this design based on de bruijn sequences generated by linear feedback shift registers ...200818651798
specific mutations within the at-rich region of a plasmid replication origin affect either origin opening or helicase loading.prokaryotic and eukaryotic replicons possess a distinctive region containing a higher than average number of adenine and thymine residues (the at-rich region) where, during the process of replication initiation, the initial destabilization (opening) of the double helix takes place. in many prokaryotic origins, this region consists of repeated 13-mer motifs whose function has not yet been specified. here we identify specific mutations within the 13-mer sequences of the broad-host-range plasmid rk ...200818685104
activation of degp chaperone-protease via formation of large cage-like oligomers upon binding to substrate proteins.cells use molecular chaperones and proteases to implement the essential quality control mechanism of proteins. the degp (htra) protein, essential for the survival of escherichia coli cells at elevated temperatures with homologues found in almost all organisms uniquely has both functions. here we report a mechanism for degp to activate both functions via formation of large cage-like 12- and 24-mers after binding to substrate proteins. cryo-electron microscopic and biochemical studies revealed tha ...200818697939
contamination of synthetic hud protein spanning peptide pools with a cmv-encoded peptide.to detect hud-specific t cells in patients with hu-antibody associated paraneoplastic neurological syndromes (hu-pns), we used short-term stimulation assays with hud protein spanning peptide pools (pspp) with purities of at least 70% and found reproducible false-positive cd8+ t-cell responses in three of 127 individuals (two healthy controls and one hu-pns patient), which all shared hla-a*2402 and hla-b*1801. after testing the 15-mer peptides of the hud antigen separately, we discovered that the ...200818727061
effective delivery of antisense peptide nucleic acid oligomers into cells by anthrax protective antigen.peptide nucleic acid (pna) is highly stable and binds to complementary rna and dna with high affinity, but it resists cellular uptake, thereby limiting its bioavailability. we investigated whether protectiveantigen (pa, a non-toxic component of anthrax toxin) could transport antisense pna oligomers into reporter cells that contain luciferase transgenes with mutant beta-globin ivs2 intronic inserts, which permit aberrant pre-mrna splicing and impair luciferase expression. pna oligomers antisense ...200818774771
asymptomatic human cd4+ cytotoxic t-cell epitopes identified from herpes simplex virus glycoprotein b.the identification of "asymptomatic" (i.e., protective) epitopes recognized by t cells from herpes simplex virus (hsv)-seropositive healthy individuals is a prerequisite for an effective vaccine. using the pepscan epitope mapping strategy, a library of 179 potential peptide epitopes (15-mers overlapping by 10 amino acids) was identified from hsv type 1 (hsv-1) glycoprotein b (gb), an antigen that induces protective immunity in both animal models and humans. eighteen groups (g1 to g18) of 10 adja ...200818799581
gene expression profiling of listeria monocytogenes strain f2365 during growth in ultrahigh-temperature-processed skim milk.to study how listeria monocytogenes survives and grows in ultrahigh-temperature-processed (uht) skim milk, microarray technology was used to monitor the gene expression profiles of strain f2365 in uht skim milk. total rna was isolated from strain f2365 in uht skim milk after 24 h of growth at 4 degrees c, labeled with fluorescent dyes, and hybridized to "custom-made" commercial oligonucleotide (35-mers) microarray chips containing the whole genome of l. monocytogenes strain f2365. compared to l. ...200818806004
induction of immunity in sheep to fasciola hepatica with mimotopes of cathepsin l selected from a phage display library.an m13 phage random 12-mers peptide library was used to screen cathepsin l mimotopes of fasciola hepatica and to evaluate their immunogenicity in sheep. seven clones showed positive reactivity to a rabbit anti-cathepsin l1/l2 antiserum in elisa, and their amino acid sequences deduced by dna sequencing were tentatively mapped on the protein. twenty sheep were randomly allocated into 4 groups of 5 animals each, for immunization with 1x10(14) phage particles of clones 1, 20, a mixture of 7 clones a ...200818812010
computational search for over-represented 8-mers within the 5'-regulatory regions of 634 mouse testis-specific genes.accumulation of microarray data has enabled the computational analysis of gene expressions in various tissues. although the genes showing testis-specific expression are most abundant among the genes exhibiting tissue-specific expression, no systematic study has been conducted for over-represented motifs within their regulatory regions. we have identified 117 over-represented 8-mers that appeared 2648 times within the regulatory regions of 634 testis-specific genes. of these, 64 over-represented ...200818817858
the peripheral light-harvesting complexes from purple sulfur bacteria have different 'ring' sizes.the integral membrane light-harvesting (lh) proteins from purple photosynthetic bacteria form circular oligomers of an elementary unit that is composed of two very hydrophobic polypeptides, termed alpha and beta. these apoprotein dimers are known to associate into closed circular arrays of 8, 9 and 16 alpha/beta-mers. we report the existence of peripheral lh proteins purified from allochromatium vinosum with two intermediate ring sizes and postulate that one is a 13 alpha/beta-mer. this shows th ...200818840433
uniprobe: an online database of protein binding microarray data on protein-dna interactions.the uniprobe (universal pbm resource for oligonucleotide binding evaluation) database hosts data generated by universal protein binding microarray (pbm) technology on the in vitro dna-binding specificities of proteins. this initial release of the uniprobe database provides a centralized resource for accessing comprehensive pbm data on the preferences of proteins for all possible sequence variants ('words') of length k ('k-mers'), as well as position weight matrix (pwm) and graphical sequence log ...200918842628
mass spectrometry for the characterization of unsulfated chondroitin oligosaccharides from 2-mers to 16-mers. comparison with hyaluronic acid oligomers.this study reports for the first time the complete liquid chromatography/electrospray ionization mass spectrometry (lc/esi-ms) and tandem mass spectrometry (ms/ms) analyses performed in negative ion mode of saturated unsulfated chondroitin oligosaccharides up to 16-mers and comparison with hyaluronic acid (ha) oligomers differing only in the nature of the hexosamine residue. ms/ms of the chondroitin disaccharide on the singly charged precursor at m/z 396.1 afforded a glycosidic cleavage c1 produ ...200818853395
size and morphology of toxic oligomers of amyloidogenic proteins: a case study of human stefin b.amyloid-induced toxicity is a well-known phenomenon but the molecular background remains unclear. one hypothesis relates toxicity to amyloid-membrane interactions, predicting that amyloid oligomers make pores into membranes. therefore, the toxicity and membrane interaction of prefibrillar aggregates and individual oligomers of a non-pathological yet highly amyloidogenic protein human stefin b (cystatin b) was examined. by monitoring caspase-3 activity and by testing cell viability, we showed tha ...200818925453
experimental analysis of oligonucleotide microarray design criteria to detect deletions by comparative genomic hybridization.microarray comparative genomic hybridization (cgh) is currently one of the most powerful techniques to measure dna copy number in large genomes. in humans, microarray cgh is widely used to assess copy number variants in healthy individuals and copy number aberrations associated with various diseases, syndromes and disease susceptibility. in model organisms such as caenorhabditis elegans (c. elegans) the technique has been applied to detect mutations, primarily deletions, in strains of interest. ...200818940006
immunodominant epitopes in herpes simplex virus type 2 glycoprotein d are recognized by cd4 lymphocytes from both hsv-1 and hsv-2 seropositive subjects.in human recurrent cutaneous herpes simplex, there is a sequential infiltrate of cd4 and then cd8 lymphocytes into lesions. cd4 lymphocytes are the major producers of the key cytokine ifn-gamma in lesions. they recognize mainly structural proteins and especially glycoproteins d and b (gd and gb) when restimulated in vitro. recent human vaccine trials using recombinant gd showed partial protection of hsv seronegative women against genital herpes disease and also, in placebo recipients, showed pro ...200818941251
pheromone-related inhibitors of ustilago hordei mating and tilletia tritici teliospore germination.abstract ustilago hordei, the causal agent of barley covered smut, produces mating pheromones that break down to smaller peptide compounds that act as potent inhibitors of mating and germination in several fungi. the pheromones are members of the farnesylated family of proteins. synthetic peptide analogs of the pheromone derivatives, ranging in size from 4 mers to full length pheromones, were farnesylated, methyl esterified, or both and tested for mating or teliospore germination inhibition with ...200218943096
variation in genotype and aggressiveness of ralstonia solanacearum race 1 isolated from tomato in taiwan.abstract a population of ralstonia solanacearum race 1 from tomato (lycopersicon esculentum) was analyzed for genetic polymorphism and aggressiveness on tomato. the 46 strains were collected from main tomato-growing areas in taiwan. genetic analysis was achieved by two polymerase chain reaction (pcr)-based methods: rep-, eric-, and box-pcr (collectively as rep-pcr) and random amplified polymorphic dna (rapd) techniques. rapd (with three 10-mers) and rep-pcr revealed 35 and 30 haplotypes, respect ...199918944778
over-represented sequences located on 3' utrs are potentially involved in regulatory functions.eukaryotic gene expression must be coordinated for the proper functioning of biological processes. this coordination can be achieved both at the transcriptional and post-transcriptional levels. in both cases, regulatory sequences placed at either promoter regions or on utrs function as markers recognized by regulators that can then activate or repress different groups of genes according to necessity. while regulatory sequences involved in transcription are quite well documented, there is a lack ...200818971640
sequence space coverage, entropy of genomes and the potential to detect non-human dna in human samples.genomes store information for building and maintaining organisms. complete sequencing of many genomes provides the opportunity to study and compare global information properties of those genomes.200818973670
machine learning for regulatory analysis and transcription factor target prediction in yeast.high throughput technologies, including array-based chromatin immunoprecipitation, have rapidly increased our knowledge of transcriptional maps-the identity and location of regulatory binding sites within genomes. still, the full identification of sites, even in lower eukaryotes, remains largely incomplete. in this paper we develop a supervised learning approach to site identification using support vector machines (svms) to combine 26 different data types. a comparison with the standard approach ...200719003435
crystal structure of orf12 from lactococcus lactis phage p2 identifies a tape measure protein chaperone.we report here the characterization of the nonstructural protein orf12 of the virulent lactococcal phage p2, which belongs to the siphoviridae family. orf12 was produced as a soluble protein, which forms large oligomers (6- to 15-mers) in solution. using anti-orf12 antibodies, we have confirmed that orf12 is not found in the virion structure but is detected in the second half of the lytic cycle, indicating that it is a late-expressed protein. the structure of orf12, solved by single anomalous di ...200919047351
a model of phenotypic susceptibility to tuberculosis: deficient in silico selection of mycobacterium tuberculosis epitopes by hla alleles.hla-dr allelic variants have been associated with tuberculosis (tb) susceptibility in different populations with risk ratios of 3.7 to 7.2. we hypothesized that the genetic susceptibility to tb depends upon the reduced capability of hla-class ii alleles of tb patients to bind and select peptide antigen from the mycobacterium tuberculosis (mtb) expressed genome. to test this hypothesis, we developed a software that can predict hla-dr restricted epitopes within the whole mtb genome based on quanti ...200819070257
discovering sequences with potential regulatory characteristics.we developed a computational model to explore the hypothesis that regulatory instructions are context dependent and conveyed through specific 'codes' in human genomic dna. we provide examples of correlation of computational predictions to reported mapped dnase i hypersensitive segments in the hoxa locus in human chromosome 7. the examples show that statistically significant 9-mers from promoter regions may occur in sequences near and upstream of transcription initiation sites, in intronic region ...200919084590
predicting the binding preference of transcription factors to individual dna k-mers.motivation: recognition of specific dna sequences is a central mechanism by which transcription factors (tfs) control gene expression. many tf-binding preferences, however, are unknown or poorly characterized, in part due to the difficulty associated with determining their specificity experimentally, and an incomplete understanding of the mechanisms governing sequence specificity. new techniques that estimate the affinity of tfs to all possible k-mers provide a new opportunity to study dna-prote ...200919088121
expanded breadth of the t-cell response to mosaic human immunodeficiency virus type 1 envelope dna vaccination.an effective aids vaccine must control highly diverse circulating strains of human immunodeficiency virus type 1 (hiv-1). among hiv-1 gene products, the envelope (env) protein contains variable as well as conserved regions. in this report, an informatic approach to the design of t-cell vaccines directed to hiv-1 env m group global sequences was tested. synthetic env antigens were designed to express mosaics that maximize the inclusion of common potential t-cell epitope (pte) 9-mers and minimize ...200919109395
phospholipids influence the aggregation of recombinant ovine prions. from rapid extensive aggregation to amyloidogenic conversion.the transformation of prion protein (prp) into its insoluble amyloid form correlates with neurodegeneration in transmissible spongiform encephalopathies. prp is connected to the neuronal membrane by a covalently-linked glycosylphosphatidylinositol (gpi) anchor. the current study demonstrates that phosphatidylinositol and phosphatidylethanolamine in low concentrations (0.5-50 mum) stimulate rapid unlimited aggregation of prp. at a higher concentration (500 mum), lipid particles prevent the format ...200919124088
estrogens exert a rapid apoptotic action in anterior pituitary cells.it is now accepted that estrogens not only stimulate lactotrope proliferation but also sensitize anterior pituitary cells to proapoptotic stimuli. in addition to their classical mechanism of action through binding to intracellular estrogen receptors (ers), there is increasing evidence that estrogens exert rapid actions mediated by cell membrane-localized ers (mers). in the present study, we examined the involvement of membrane-initiated steroid signaling in the proapoptotic action of estradiol i ...200919158323
high-resolution dna-binding specificity analysis of yeast transcription factors.transcription factors (tfs) regulate the expression of genes through sequence-specific interactions with dna-binding sites. however, despite recent progress in identifying in vivo tf binding sites by microarray readout of chromatin immunoprecipitation (chip-chip), nearly half of all known yeast tfs are of unknown dna-binding specificities, and many additional predicted tfs remain uncharacterized. to address these gaps in our knowledge of yeast tfs and their cis regulatory sequences, we have dete ...200919158363
circular dichroism spectra and electrophoretic mobility shift assays show that human replication protein a binds and melts intramolecular g-quadruplex structures.noncanonical dna structures such as g-quadruplexes might obstruct the binding of hrpa, compromising the accuracy of replication, and be a source of genomic instability. in this study, circular dichroism (cd) and electrophoretic mobility shift assay (emsa) experiments were used to show that hrpa can bind and melt nontelomeric, intramolecular dna g-quadruplexes under physiologically germane conditions. emsa results show that hrpa binds to a 58-mer that includes an embedded quadruplex with an affin ...200919187036
the expression of the kallikrein gene family in the rat pituitary: oestrogen effects and the expression of an additional family member in the neurointermediate lobe.abstract using a series of oligonucleotide probes (18 to 21 mers) specific for members of the rat kallikrein/tonin gene family (ps, s1, s2, s3, k1, p1), we have shown by northern blot analysis that the oestrogen-dependent kallikrein gene expressed in the male and female rat anterior pituitary is true kallikrein (ps). in addition, we have demonstrated that oestrogen treatment may also induce ps gene expression in the male and female rat neurointermediate lobe. none of the other five rat arginyl-e ...198919210455
identification of legionella species by use of an oligonucleotide array.the genus legionella contains a diverse group of motile, asaccharolytic, nutritionally fastidious gram-negative rods. legionella pneumophila is the most important human pathogen, followed by l. micdadei, l. longbeachae, l. dumoffii, and other rare species. accurate identification of legionella spp. other than l. pneumophila is difficult because of biochemical inertness and phenotypic identity of different species. the feasibility of using an oligonucleotide array for identification of 18 species ...200919261788
the adp-ribosylation of sulfolobus solfataricus sso7 modulates protein/dna interactions in vitro.the 7 kda sso7 is a basic protein particularly abundant in sulfolobus solfataricus and is involved in dna assembly. this protein undergoes in vitro adp-ribosylation by an endogenous poly(adp-ribose) polymerase-like enzyme. the circular dichroism spectrum of purified adp-ribosylated sso7 shows that this modification stabilizes the prevalent protein beta-conformation, as suggested by shifting of negative ellipticity minimum to 220 nm. moreover, a short adp-ribose chain (up to 6-mers) bound to sso7 ...200919272378
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