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production of a bioactive peptide (iiaek) in escherichia coli using soybean proglycinin a1ab1b as a carrier.to produce large amounts of a peptide of fewer than 10 amino acid residues, construction of a gene encoding multimers of the small peptide is necessary. for this study a method was developed to facilitate the gene construction of high multimers of a small peptide with one step of cloning. a hypocholesterolemic peptide, iiaek, from cow's milk beta-lactoglobulin was used as a model peptide for the construction of a gene encoding multimers of iiaek and for the production of the peptide. two systems ...200919298043
two newly proposed infectious encephalitis/encephalopathy syndromes.two newly proposed infectious encephalitis/encephalopathy syndromes, in which magnetic resonance imaging (mri) is essential for the diagnosis, have been reviewed. acute encephalopathy with biphasic seizures and late reduced diffusion (aesd) is reported only in east asian infants, characterized by a febrile seizure (usually >30 min) as the initial neurological symptom on day 1, followed by secondary seizures at day 4 to 6; affected children display variable levels of neurological sequelae. mri sh ...200919339128
catalytic properties of rnase bn/rnase z from escherichia coli: rnase bn is both an exo- and endoribonuclease.processing of the 3' terminus of trna in many organisms is carried out by an endoribonuclease termed rnase z or 3'-trnase, which cleaves after the discriminator nucleotide to allow addition of the universal -cca sequence. in some eubacteria, such as escherichia coli, the -cca sequence is encoded in all known trna genes. nevertheless, an rnase z homologue (rnase bn) is still present, even though its action is not needed for trna maturation. to help identify which rna molecules might be potential ...200919366704
membrane estrogen receptor-alpha-mediated nongenomic actions of phytoestrogens in gh3/b6/f10 pituitary tumor cells.abstract:200919400946
a family of kassinatuerin-2 related peptides from the skin secretion of the african hyperoliid frog, kassina maculata.we describe the isolation and structural characterization of a family of antimicrobial peptides related to kassinatuerin-2, from the skin secretion of the african hyperoliid frog, kassina maculata. all four peptides, designated kassinatuerin-2ma through md, are c-terminally-amidated 20-mers with the consensus sequence - fx(1)gaiaaalphvix(2)aiknal - where x(1)=l/f/v/i and x2=s/n. all four peptides are encoded by precursors of 69 amino acids. synthetic replicates of all kassinatuerin-2 related pep ...200919427345
inhibition of vaccinia virus replication by peptide aptamers.a20 protein is a major component of the vaccinia virus replication complex. it binds to the dna polymerase e9, the uracil dna glycosylase d4 and the primase/helicase d5, three proteins that are essential for viral dna synthesis. the identification of molecules able to interact with the replication complex and inhibit its activity is a promising strategy for the design of new anti-orthopoxvirus drugs. in this study, we used a yeast genetic approach to select, from combinatorial libraries, 8-mers ...200919428604
96 shrnas designed for maximal coverage of hiv-1 variants.the rna interference (rnai) pathway is a mechanism of gene-suppression with potential gene therapy applications for treating viral disease such as hiv-1. the most suitable inducer of rnai for this application is short hairpin rna (shrna) although it is limited to suppressing a single target. a successful anti-hiv-1 therapy will require combinations of multiple highly active, highly conserved shrnas to adequately counter the emergence of resistant strains.200919497094
delimiting subterritories of the human subthalamic nucleus by means of microelectrode recordings and a hidden markov model.positive therapeutic response without adverse side effects to subthalamic nucleus deep brain stimulation (stn dbs) for parkinson's disease (pd) depends to a large extent on electrode location within the stn. the sensorimotor region of the stn (seemingly the preferred location for stn dbs) lies dorsolaterally, in a region also marked by distinct beta (13-30 hz) oscillations in the parkinsonian state. in this study, we present a real-time method to accurately demarcate subterritories of the stn du ...200919533755
degradation of nanorna is performed by multiple redundant rnases in bacillus subtilis.escherichia coli possesses only one essential oligoribonuclease (orn), an enzyme that can degrade oligoribonucleotides of five residues and shorter in length (nanorna). firmicutes including bacillus subtilis do not have an orn homolog. we had previously identified ytqi (nrna) as functional analog of orn in b. subtilis. screening a genomic library from b. subtilis for genes that can complement a conditional orn mutant, we identify here yngd (nrnb) as a second nanornase in b. subtilis. like nrna, ...200919553197
development of a novel peptide microarray for large-scale epitope mapping of food allergens.the peptide microarray is a novel assay that facilitates high-throughput screening of peptides with a small quantity of sample.200919577281
the disruptive positions in human g-quadruplex motifs are less polymorphic and more conserved than their neutral counterparts.specific guanine-rich sequence motifs in the human genome have considerable potential to form four-stranded structures known as g-quadruplexes or g4 dna. the enrichment of these motifs in key chromosomal regions has suggested a functional role for the g-quadruplex structure in genomic regulation. in this work, we have examined the spectrum of nucleotide substitutions in g4 motifs, and related this spectrum to g4 prevalence. data collected from the large repository of human snps indicates that th ...200919617376
compacted dna nanoparticle gene transfer of gdnf to the rat striatum enhances the survival of grafted fetal dopamine neurons.previously it was established that infusion of glial cell line-derived neurotrophic factor (gdnf) protein into grafts of embryonic dopamine cells has a neurotrophic effect on the grafted cells. in this study we used a nonviral technique to transfer the gene encoding for gdnf to striatal cells. plasmid dna encoding for gdnf was compacted into dna nanoparticles (dnps) by 10 kda polyethylene glycol (peg)-substituted lysine 30-mers (ck(30)peg10k) and then injected into the denervated striatum of rat ...200919650971
ionically crosslinked chitosan/tripolyphosphate nanoparticles for oligonucleotide and plasmid dna delivery.ionically crosslinked nanoparticles based on high and low molecular weight chitosans (cs) were formulated with plasmid dna or dsdna oligomers using the ionic gelation technique with pentasodium tripolyphospate (tpp) as crosslinking agent. the resulting cs/tpp nanoparticles were investigated with regard to their physical-chemical properties, in vitro transfection efficiency, toxicity, cellular uptake, and in vivo gene expression following intratracheal administration to mice. the effects of co-fo ...200919660537
global microsatellite content distinguishes humans, primates, animals, and plants.microsatellites are highly mutable, repetitive sequences commonly used as genetic markers, but they have never been studied en masse. using a custom microarray to measure hybridization intensities of every possible repetitive nucleotide motif from 1-mers to 6-mers, we examined 25 genomes. here, we show that global microsatellite content varies predictably by species, as measured by array hybridization signal intensities, correlating with established taxonomic relationships, and particular motifs ...200919717526
multiplex primer prediction software for divergent targets.we describe a multiplex primer prediction (mpp) algorithm to build multiplex compatible primer sets to amplify all members of large, diverse and unalignable sets of target sequences. the mpp algorithm is scalable to larger target sets than other available software, and it does not require a multiple sequence alignment. we applied it to questions in viral detection, and demonstrated that there are no universally conserved priming sequences among viruses and that it could require an unfeasibly lar ...200919759213
genomic dna k-mer spectra: models and modalities.the empirical frequencies of dna k-mers in whole genome sequences provide an interesting perspective on genomic complexity, and the availability of large segments of genomic sequence from many organisms means that analysis of k-mers with non-trivial lengths is now possible.200919814784
design and performance of a turbot (scophthalmus maximus) oligo-microarray based on ests from immune tissues.an expressed sequence tag database from immune tissues was used to design the first high-density turbot (scophthalmus maximus) oligo-microarray with the aim of identifying candidate genes for tolerance to pathogens. specific oligonucleotides (60 mers) were successfully designed for 2,716 out of 3,482 unique sequences of the database. an agilent custom oligo-microarray 8 x 15 k (five replicates/gene; eight microarrays/slide) was constructed. the performance of the microarray and the sources of va ...201019844759
oligonucleotide-based microarray for detection of plant viruses employing sequence-independent amplification of targets.the potential of dna microarrays for detection of plant viruses is hampered by underutilization of sequence-independent amplification methods for target nucleic acid enrichment. a microarray system is described for an unbiased detection of plant viruses using both short (30 nt) and long (50 and 70 nt) oligonucleotide probes. the assay involves amplification of target nucleic acid using random primers followed by in vitro transcription whose crna product is labeled chemically, fragmented and used ...201019850081
peptide microarray-based identification of mycobacterium tuberculosis epitope binding to hla-drb1*0101, drb1*1501, and drb1*0401.a more effective vaccine against mycobacterium tuberculosis is needed, and a number of m. tuberculosis vaccine candidates are currently in preclinical or clinical phase i and ii studies. one of the strategies to select m. tuberculosis (protein) targets to elicit a cd8(+) or cd4(+) t-cell response is to gauge the binding of candidate peptides to major histocompatibility complex (mhc) class i or class ii molecules, a prerequisite for successful peptide presentation and to expand antigen-specific t ...201019864486
characterization of full-length sequenced cdna inserts (flics) from atlantic salmon (salmo salar).sequencing of the atlantic salmon genome is now being planned by an international research consortium. full-length sequenced inserts from cdnas (flics) are an important tool for correct annotation and clustering of the genomic sequence in any species. the large amount of highly similar duplicate sequences caused by the relatively recent genome duplication in the salmonid ancestor represents a particular challenge for the genome project. flics will therefore be an extremely useful resource for th ...200919878547
exploring epitopes of antibodies toward the human tryptophanyl-trna synthetase.there is a need to characterize the epitopes of affinity reagents to develop high quality affinity reagents for research, diagnostics and therapy. here, we describe the analysis of epitopes of antibodies generated toward human tryptophanyl-trna synthetase (wars) using both combinatorial bacterial display and suspension bead array. the bacterial display revealed that the polyclonal antibody binds to three separate epitopes and peptide scanning using 15-mers revealed binding to a 13 amino acid con ...201019913117
chloroacetaldehyde-induced mutagenesis in escherichia coli: the role of alkb protein in repair of 3,n(4)-ethenocytosine and 3,n(4)-alpha-hydroxyethanocytosine.etheno (epsilon) adducts are formed in reaction of dna bases with various environmental carcinogens and endogenously created products of lipid peroxidation. chloroacetaldehyde (caa), a metabolite of carcinogen vinyl chloride, is routinely used to generate epsilon-adducts. we studied the role of alkb, along with alka and mug proteins, all engaged in repair of epsilon-adducts, in caa-induced mutagenesis. the test system used involved pif102 and pif104 plasmids bearing the lactose operon of cc102 o ...201019941873
genotype 1 and global hepatitis c t-cell vaccines designed to optimize coverage of genetic diversity.immunological control of hepatitis c virus (hcv) is possible and is probably mediated by host t-cell responses, but the genetic diversity of the virus poses a major challenge to vaccine development. we considered monovalent and polyvalent candidates for an hcv vaccine, including natural, consensus and synthetic 'mosaic' sequence cocktails. mosaic vaccine reagents were designed using a computational approach first applied to and demonstrated experimentally for human immunodeficiency virus type 1 ...201020053820
conservation and regulatory associations of a wide affinity range of mouse transcription factor binding sites.sequence-specific binding by transcription factors (tfs) interprets regulatory information encoded in the genome. using recently published universal protein binding microarray (pbm) data on the in vitro dna binding preferences of these proteins for all possible 8-base-pair sequences, we examined the evolutionary conservation and enrichment within putative regulatory regions of the binding sequences of a diverse library of 104 nonredundant mouse tfs spanning 22 different dna-binding domain struct ...201020079828
identification of clinically important anaerobic bacteria by an oligonucleotide array.anaerobic bacteria can cause a wide variety of infections, and some of these infections can be serious. conventional identification methods based on biochemical tests are often lengthy and can produce inconclusive results. an oligonucleotide array based on the 16s-23s rrna intergenic spacer (its) sequences was developed to identify 28 species of anaerobic bacteria and veillonella. the method consisted of pcr amplification of the its regions with universal primers, followed by hybridization of th ...201020129959
synthetic design of strong promoters.we have taken a synthetic biology approach to the generation and screening of transcription factor binding sites for activity in human cells. all possible 10-mer dna sequences were printed on microarrays as 100-mers containing 10 repeats of the same sequence in tandem, yielding an oligonucleotide library of 52,429 unique sequences. this library of potential enhancers was introduced into a retroviral vector and screened in multiple cell lines for the ability to activate gfp transcription from a m ...201020133776
microfluidic reactor array device for massively parallel in-situ synthesis of oligonucleotides.we have designed and fabricated a microfluidic reactor array device for massively parallel in-situ synthesis of oligonucleotides (odna). the device is made of glass anodically bonded to silicon consisting of three level features: microreactors, microchannels and through inlet/outlet holes. main challenges in the design of this device include preventing diffusion of photogenerated reagents upon activation and achieving uniform reagent flow through thousands of parallel reactors. the device embodi ...200920161215
quantitative study of stereospecific binding of monoclonal antibody to anti-benzo(a)pyrene diol epoxide-n(2)-dg adducts by capillary electrophoresis immunoassay.the stereospecific binding of monoclonal antibody (mab) 8e11 to anti-benzo(a)pyrene diol epoxide (bpde)-dg adducts in single nucleoside, long oligonucleotide, and genomic dna were quantitatively evaluated using noncompetitive and competitive capillary electrophoresis (ce) immunoassays. two single-stranded tmr-bpde-90 mers containing a single anti-bpde-dg adduct with defined stereochemistry and a fluorescent label at 5'-end were used as fluorescent probes for competitive ce immunoassay. to quanti ...201020223464
impact of nature and length of linker incorporated in agonists on toll-like receptor 9-mediated immune responses.oligodeoxynucleotides containing unmethylated cpg motifs act as ligands of toll-like receptor 9 (tlr9). we previously reported a novel class of tlr9 agonists, referred to as immune-modulatory oligonucleotides (imos), in which two 11-mers of the same sequence are attached via their 3'-ends through a 1,2,3-propanetriol linker and contain a synthetic immune-stimulatory motif, cp7-deaza-dg. in the present study, we have examined the impact of length, nature, and stereochemistry of the linker incorpo ...201020361743
unsupervised binning of environmental genomic fragments based on an error robust selection of l-mers.with the rapid development of genome sequencing techniques, traditional research methods based on the isolation and cultivation of microorganisms are being gradually replaced by metagenomics, which is also known as environmental genomics. the first step, which is still a major bottleneck, of metagenomics is the taxonomic characterization of dna fragments (reads) resulting from sequencing a sample of mixed species. this step is usually referred as "binning". existing binning methods are based on ...201020406503
htra proteases have a conserved activation mechanism that can be triggered by distinct molecular cues.htra proteases are tightly regulated proteolytic assemblies that are essential for maintaining protein homeostasis in extracytosolic compartments. though htra proteases have been characterized in detail, their precise molecular mechanism for switching between different functional states is still unknown. to address this, we carried out biochemical and structural studies of degp from escherichia coli. we show that effector-peptide binding to the pdz domain of degp induces oligomer conversion from ...201020581825
short locked nucleic acid antisense oligonucleotides potently reduce apolipoprotein b mrna and serum cholesterol in mice and non-human primates.the potency and specificity of locked nucleic acid (lna) antisense oligonucleotides was investigated as a function of length and affinity. the oligonucleotides were designed to target apolipoprotein b (apob) and were investigated both in vitro and in vivo. the high affinity of lna enabled the design of short antisense oligonucleotides (12- to 13-mers) that possessed high affinity and increased potency both in vitro and in vivo compared to longer oligonucleotides. the short lna oligonucleotides w ...201020615897
unexpected diversity of cellular immune responses against nef and vif in hiv-1-infected patients who spontaneously control viral replication.hiv-1-infected individuals who spontaneously control viral replication represent an example of successful containment of the aids virus. understanding the anti-viral immune responses in these individuals may help in vaccine design. however, immune responses against hiv-1 are normally analyzed using hiv-1 consensus b 15-mers that overlap by 11 amino acids. unfortunately, this method may underestimate the real breadth of the cellular immune responses against the autologous sequence of the infectin ...201020625436
luminol encapsulated liposome as a signal generator for the detection of specific antigen-antibody reactions and nucleotide hybridization.liposomes prepared with biotinylated phospholipids and luminol entrapped were shown to be of 187 nm in size, 59% of which were unilamellar and with 43% luminol trapping efficiency. liposome prepared from biotinylated phospholipids with a longer hydrophilic peg2000 spacer, but not with the shorter hydrophobic caproyl one, bound efficiently and specifically with immobilized streptavidin in a microplate assay. the interactions of dinitrophenol and tobramycin with their respective antibodies, and th ...201020631437
scs: signal, context, and structure features for genome-wide human promoter recognition.this paper integrates the signal, context, and structure features for genome-wide human promoter recognition, which is important in improving genome annotation and analyzing transcriptional regulation without experimental supports of ests, cdnas, or mrnas. first, cpg islands are salient biological signals associated with approximately 50 percent of mammalian promoters. second, the genomic context of promoters may have biological significance, which is based on n-mers (sequences of n bases long) ...201020671324
a phenomenological model for predicting melting temperatures of dna sequences.we report here a novel method for predicting melting temperatures of dna sequences based on a molecular-level hypothesis on the phenomena underlying the thermal denaturation of dna. the model presented here attempts to quantify the energetic components stabilizing the structure of dna such as base pairing, stacking, and ionic environment which are partially disrupted during the process of thermal denaturation. the model gives a pearson product-moment correlation coefficient (r) of approximately ...201020865157
membrane estrogen receptors stimulate intracellular calcium release and progesterone synthesis in hypothalamic astrocytes.in hypothalamic astrocytes obtained from adult female rats, estradiol rapidly increased free cytoplasmic calcium concentrations ([ca(2+)](i)) that facilitate progesterone synthesis. the present study demonstrated that estradiol (1 nm) significantly and maximally stimulated progesterone synthesis within 5 min, supporting a rapid, nongenomic mechanism. the group i metabotropic glutamate receptor (mglur1a) antagonist ly 367385 [(s)-(+)-a-amino-4-carboxy-2-methylbenzeneacetic acid] attenuated both t ...201020881113
chemical synthesis of the mouse mitochondrial genome.we describe a one-step, isothermal assembly method for synthesizing dna molecules from overlapping oligonucleotides. the method cycles between in vitro recombination and amplification until the desired length is reached. as a demonstration of its simplicity and robustness, we synthesized the entire 16.3-kilobase mouse mitochondrial genome from 600 overlapping 60-mers.201020935651
structural and thermodynamic characterization of metal ion binding in streptococcus suis dpr.the use of protein cages for the creation of novel inorganic nanomaterials has attracted considerable attention in recent years. ferritins are among the most commonly used protein cages in nanoscience. accordingly, the binding of various metals to ferritins has been studied extensively. dps (dna-binding protein from starved cells)-like proteins belong to the ferritin superfamily. in contrast to ferritins, dps-like proteins form 12-mers instead of 24-mers, have a different ferroxidase center, and ...201021056572
amino acid sequence of b-cell epitope of n-terminal region of esat-6 mycobacterium leprae role as specific antigen for diagnosis of leprosy.the objective of this study was to find a specific b-cell epitope of n-terminal region of antigen l-esat-6 from leprosy patients, healthy individuals and healthy nurses working for more than 10 years in the leprosy ward of dr. a. rivai abdullah leprosy hospital, palembang, indonesia. fifty subjects were enrolled in this study, comprising 10 subjects with ll type leprosy, 10 subjects with bb type leprosy, 10 subjects with tt type leprosy, 10 healthy nurses from leprosy ward and 10 healthy individ ...201021073037
studying the evolution of promoter sequences: a waiting time problem.to gain a better understanding of the evolutionary dynamics of regulatory dna sequences, we address the following questions: (1) how long does it take until a given transcription factor (tf) binding site emerges at random in a promoter sequence? and (2) how does the composition of a tf binding site affect this waiting time? using two different probabilistic models (an i.i.d. model and a neighbor dependent model), we can compute the expected waiting time for every k-mer, k ranging from 5 to 10, u ...201021128851
root cause analysis of transfusion error: identifying causes to implement changes.as part of ongoing efforts to improve transfusion safety, an error reporting system was implemented in our hospital-based transfusion medicine unit at a tertiary care medical institute. this system is based on medical event reporting system-transfusion medicine (mers-tm) and collects data on all near miss, no harm, and misadventures related to the transfusion process. root cause analyses of one such innocuous appearing error demonstrate how weaknesses in the system can be identified to make nece ...201021128948
visualization of fine-scale genomic structure by oligonucleotide-based high-resolution fish.the discovery of complex structural variations that exist within individual genomes has prompted a need to visualize chromosomes at a higher resolution than previously possible. to address this concern, we established a robust, high-resolution fluorescence in situ hybridization (fish) method that utilizes probes derived from high complexity libraries of long oligonucleotides (>150 mers) synthesized in massively parallel reactions. in silico selected oligonucleotides, targeted to only the most in ...201021178330
modulation of human estrogen receptor α activity by multivalent estradiol-peptidomimetic conjugates.estradiol-peptidomimetic conjugates (epcs) are linear, sequence-specific peptoid oligomers that site-specifically display multiple copies of 17β-estradiol (e2), a ligand for the human estrogen receptor α (herα). we evaluate the ability of multivalent epcs to activate herα-mediated transcription. epcs activated the herα in both a length- and valence-dependent manner, with the highest levels of activation generated by divalent peptoid 6-mers, divalent 18-mers, and trivalent 9-mers. hexavalent epcs ...201121218226
conserved generation of short products at pirna loci.the pirna pathway operates in animal germ lines to ensure genome integrity through retrotransposon silencing. the piwi protein-associated small rnas (pirnas) guide piwi proteins to retrotransposon transcripts, which are degraded and thereby post-transcriptionally silenced through a ping-pong amplification process. cleavage of the retrotransposon transcript defines at the same time the 5' end of a secondary pirna that will in turn guide a piwi protein to a primary pirna precursor, thereby amplify ...201121247452
wordcluster: detecting clusters of dna words and genomic elements. 201121261981
a case of clinically mild encephalitis with a reversible splenial lesion (mers) after mumps vaccination.we describe for the first time an 8-year-old male patient who demonstrated clinically mild encephalitis with a reversible splenial lesion after mumps vaccination. he suffered from transient hallucinations, nuchal rigidity, and inappropriate antidiuretic hormone secretion syndrome. on the 5th day of admission, his head mri showed symmetrical high-signal-intensity lesions on t2, flair, and diffusion-weighted images in the splenium of the corpus callosum and in the periventricular white matter, whi ...201121273018
improved protein-binding microarrays for the identification of dna-binding specificities of transcription factors.transcriptional regulation depends on the specificity of transcription factors (tfs) recognizing cis regulatory sequences in the promoters of target genes. current knowledge about dna-binding specificities of tfs is based mostly on low- to medium-throughput methodologies, revealing dna motifs bound by a tf with high affinity. these strategies are time-consuming and often fail to identify dna motifs recognized by a tf with lower affinity but retaining biological relevance. here we report on the d ...201121284757
two distinct amyloid beta-protein (abeta) assembly pathways leading to oligomers and fibrils identified by combined fluorescence correlation spectroscopy, morphology, and toxicity analyses.nonfibrillar assemblies of amyloid ß-protein (aß) are considered to play primary roles in alzheimer disease (ad). elucidating the assembly pathways of these specific aggregates is essential for understanding disease pathogenesis and developing knowledge-based therapies. however, these assemblies cannot be monitored in vivo, and there has been no reliable in vitro monitoring method at low protein concentration. we have developed a highly sensitive in vitro monitoring method using fluorescence cor ...201121292768
elastogenic inductability of smooth muscle cells from a rat model of late stage abdominal aortic aneurysms.although abdominal aortic aneurysms (aaa) can be potentially stabilized by inhibiting inflammatory cell recruitment and their release of proteolytic enzymes, active aaa regression is not possible without regeneration of new elastic matrix structures. unfortunately, postneonatal vascular smooth muscle cells (smcs), healthy, and likely more so, diseased cells, poorly synthesize or remodel elastic fibers, impeding any effort directed at regenerative aaa treatment. previously, we determined the elea ...201121341992
extracellular and intraneuronal hmw-abetaos represent a molecular basis of memory loss in alzheimer's disease model mouse. 201121375782
supervised learning and prediction of physical interactions between human and hiv proteins.infectious diseases result in millions of deaths each year. physical interactions between pathogen and host proteins often form the basis of such infections. while a number of methods have been proposed for predicting protein-protein interactions (ppis), they have primarily focused on intra-species protein-protein interactions.201121382517
transition from a plasmid to a chromosomal mode of replication entails additional regulators.plasmid origins of replication are rare in bacterial chromosomes, except in multichromosome bacteria. the replication origin of vibrio cholerae chromosome ii (chrii) closely resembles iteron-bearing plasmid origins. iterons are repeated initiator binding sites in plasmid origins and participate both in replication initiation and its control. the control is mediated primarily by coupling of iterons via the bound initiators ("handcuffing"), which causes steric hindrance to the origin. the control ...201121444815
increased breadth and depth of cytotoxic t lymphocytes responses against hiv-1-b nef by inclusion of epitope variant sequences.different vaccine approaches cope with hiv-1 diversity, ranging from centralized(1-4) to variability-encompassing(5-7) antigens. for all these strategies, a concern remains: how does hiv-1 diversity impact epitope recognition by the immune system? we studied the relationship between hiv-1 diversity and cd8(+) t lymphocytes (ctl) targeting of hiv-1 subtype b nef using 944 peptides (10-mers overlapping by nine amino acids (aa)) that corresponded to consensus peptides and their most common variants ...201121464919
genomic structure and expression analyses of the pygm gene in the thoroughbred horse.muscle glycogen phosphorylase (pygm) has been shown to catalyze the degradation of glycogen to glucose-1-phosphate. the pygm gene can contribute to providing energy to the body by disassembling the glycogen in muscle. here, we analyzed the genomic structure and expression of the pygm gene in the thoroughbred horse. the pygm gene, containing several transposable elements (mirs, lines, and mers), was highly conserved in mammalian genomes. in order to understand the expression of the horse pygm gen ...201121466345
deciphering the complexity of sainfoin ( onobrychis viciifolia ) proanthocyanidins by maldi-tof mass spectrometry with a judicious choice of isotope patterns and matrixes.use of superdihydroxybenzoic acid as the matrix enabled the analysis of highly complex mixtures of proanthocyanidins from sainfoin ( onobrychis viciifolia ) by maldi-tof mass spectrometry. proanthocyanidins contained predominantly b-type homopolymers and heteropolymers up to 12-mers (3400 da). use of another matrix, 2,6-dihydroxyacetophenone, revealed the presence of a-type glycosylated dimers. in addition, we report here how a comparison of the isotopic adduct patterns, which resulted from li a ...201121488615
membrane-associated degp in bordetella chaperones a repeat-rich secretory protein.the chaperone/protease degp belongs to the htra superfamily and is involved in protein quality control in the periplasm of gram-negative bacteria. in escherichia coli, typical substrates are unfolded or misfolded globular proteins that trigger the rearrangement of inactive degp hexamers into substrate-sequestering 12- or 24-mers 'cages' for refolding or degradation. in bordetella pertussis, degp(bp) facilitates, in addition, the secretion of fha, a long β-helical adhesin that passes through the ...201121518392
the multifaceted role of oestrogen in enhancing chlamydia trachomatis infection in polarized human endometrial epithelial cells.the oestrogen receptor (er) α-β+ hec-1b and the erα+β+ ishikawa (ik) cell lines were investigated to dissect the effects of oestrogen exposure on several parameters of chlamydia trachomatis infection. antibody blockage of erα or erβ alone or simultaneously significantly decreased c. trachomatis infectivity (45-68%). addition of the erβ antagonist, tamoxifen, to ik or hec-1b prior to or after chlamydial infection caused a 30-90% decrease in infectivity, the latter due to disrupted eukaryotic orga ...201121615662
a multiscale approach to characterize the early aggregation steps of the amyloid-forming peptide gnnqqny from the yeast prion sup-35.the self-organization of peptides into amyloidogenic oligomers is one of the key events for a wide range of molecular and degenerative diseases. atomic-resolution characterization of the mechanisms responsible for the aggregation process and the resulting structures is thus a necessary step to improve our understanding of the determinants of these pathologies. to address this issue, we combine the accelerated sampling properties of replica exchange molecular dynamics simulations based on the ope ...201121625573
characterization of oligomer formation of amyloid-{beta} peptide using a split-luciferase complementation assay.amyloid-β peptide (aβ) is the amyloid component of senile plaques in alzheimer disease (ad) brains. recently a soluble oliomeric form of aβ in aβ precursor protein transgenic mouse brains and ad brains was identified as a potential causative molecule for memory impairment, suggesting that soluble aβ oligomers cause neurodegeneration in ad. further characterization of this species has been hampered, however, because the concentrations are quite small and it is difficult to monitor aβ oligomers sp ...201121652708
quantitative evaluation of all hexamers as exonic splicing elements.we describe a comprehensive quantitative measure of the splicing impact of a complete set of rna 6-mer sequences by deep sequencing successfully spliced transcripts. all 4096 6-mers were substituted at five positions within two different internal exons in a 3-exon minigene, and millions of successfully spliced transcripts were sequenced after transfection of human cells. the results allowed the assignment of a relative splicing strength score to each mutant molecule. the effect of 6-mers on spli ...201121659425
the legionella htra homologue degq is a self-compartmentizing protease that forms large 12-meric assemblies.proteases of the htra family are key factors dealing with folding stress in the periplasmatic compartment of prokaryotes. in escherichia coli, the well-characterized htra family members degs and degp counteract the accumulation of unfolded outer-membrane proteins under stress conditions. whereas degs serves as a folding-stress sensor, degp is a chaperone-protease facilitating refolding or degradation of defective outer-membrane proteins. here, we report the 2.15-ôä½-resolution crystal structure ...201121670246
application of immunosignatures to the assessment of alzheimer's disease.accurate assessment of alzheimer's disease (ad), both presymptomatically and at different disease stages, will become increasingly important with the expanding elderly population. there are a number of indications that the immune system is engaged in ad. here we explore the ability of an antibody-profiling technology to characterize ad and screen for peptides that may be used for a simple diagnostic test.201121823156
motifclick: prediction of cis-regulatory binding sites via merging cliques.although dozens of algorithms and tools have been developed to find a set of cis-regulatory binding sites called a motif in a set of intergenic sequences using various approaches, most of these tools focus on identifying binding sites that are significantly different from their background sequences. however, some motifs may have a similar nucleotide distribution to that of their background sequences. therefore, such binding sites can be missed by these tools.201121679436
molecular adaptation of the degq protease to exert protein quality control in the bacterial cell envelope.to react to distinct stress situations and to prevent the accumulation of misfolded proteins, all cells employ a number of proteases and chaperones, which together set up an efficient protein quality control system. the functionality of proteins in the cell envelope of escherichia coli is monitored by the htra proteases degs, degp, and degq. in contrast with degp and degs, the structure and function of degq has not been addressed in detail. here, we show that substrate binding triggers the conve ...201121685389
Identification and typing of human enterovirus: a genomic barcode approach.Identification and typing of human enterovirus (HEVs) are important to pathogen detection and therapy. Previous phylogeny-based typing methods are mainly based on multiple sequence alignments of specific genes in the HEVs, but the results are not stable with respect to different choices of genes. Here we report a novel method for identification and typing of HEVs based on information derived from their whole genomes. Specifically, we calculate the k-mer based barcode image for each genome, HEV o ...201122022592
Characterization of NrnA homologs from Mycobacterium tuberculosis and Mycoplasma pneumoniae.Processive RNases are unable to degrade efficiently very short oligonucleotides, and they are complemented by specific enzymes, nanoRNases, that assist in this process. We previously identified NrnA (YtqI) from Bacillus subtilis as a bifunctional protein with the ability to degrade nanoRNA (RNA oligos =5 nucleotides) and to dephosphorylate 3'-phosphoadenosine 5'-phosphate (pAp) to AMP. While the former activity is analogous to that of oligoribonuclease (Orn) from Escherichia coli, the latter cor ...201222114320
thymic stromal lymphopoietin exerts antimicrobial activities.thymic stromal lymphopoietin (tslp) is an interleukin-7-like cytokine expressed by epithelial cells and reported to be involved in allergic diseases and atopic eczema. the presence of several predicted α-helical regions in tspl, a structure characterizing many classical antimicrobial peptides (amps), prompted us to investigate whether tslp exerts antimicrobial activities. recombinant human tslp exerted antimicrobial activity, particularly against gram-negative bacteria. using synthetic overlappi ...201122092577
Mapping of IgE and IgG(4) Antibody-Binding Epitopes in Cyn d 1, the Major Allergen of Bermuda Grass Pollen.Background: Bermuda grass pollen (BGP) is an important seasonal aeroallergen worldwide which induces allergic disorders such as allergic rhinitis, conjunctivitis and asthma. Cyn d 1 is the major allergen of BGP. This study is aimed to map human IgE and IgG(4) antibody-binding sequential epitopes on Cyn d 1 by dot immunoblotting. Methods: Synthetic peptides (10-mers; 5 overlapping residues) spanning the full length of Cyn d 1 were used for dot immunoblotting to map human IgE and IgG(1-4) antibody ...201121985791
structural properties of dna oligomers containing (gacx)(n) and (gaxc)(n) tandem repeats.the antisense dna sequence of mature mouse micro rna, mir341, includes three repeats of the tetranucleotide (gacc). the -gac- repeat is known to form a parallel duplex, in acidic environments. the thermal melting profile of mir341 dna, at ph 4, 5, and 6 indicates the formation of a very stable structure, which loses its stability when ph is increased. thus, the addition of a cytosine at the 3' end of the (gac) motif preserves the molecule's potential to fold into an unusual structure at low ph. ...201221953019
the extracellular chaperone clusterin sequesters oligomeric forms of the amyloid-β(1-40) peptide.in recent genome-wide association studies, the extracellular chaperone protein, clusterin, has been identified as a newly-discovered risk factor in alzheimer's disease. we have examined the interactions between human clusterin and the alzheimer's disease-associated amyloid-β(1-40) peptide (aβ(1-40)), which is prone to aggregate into an ensemble of oligomeric intermediates implicated in both the proliferation of amyloid fibrils and in neuronal toxicity. using highly sensitive single-molecule fluo ...201122179788
characterization of the structure and function of escherichia coli degq as a representative of the degq-like proteases of bacterial htra family proteins.htra family proteins play a central role in protein quality control in the bacterial periplasmic space. degq-like proteases, a group of bacterial htra proteins, are characterized by a short la loop as compared with degp-like proteases, and are found in many bacterial species. as a representative of the degq-like proteases, we report that escherichia coli degq exists in vivo primarily as a trimer (substrate-free) or dodecamer (substrate-containing). biochemical analysis of degq dodecamers reveale ...201121893291
Epidemiology of acute encephalopathy in Japan, with emphasis on the association of viruses and syndromes.A research committee supported by the Japanese government conducted a nationwide survey on the epidemiology of acute encephalopathy in Japan using a questionnaire. A total of 983 cases reportedly had acute encephalopathy during the past 3years, 2007-2010. Among the pathogens of the preceding infection, influenza virus was the most common, followed by human herpesvirus-6 (HHV-6) and rotavirus. Among syndromes of acute encephalopathy, acute encephalopathy with biphasic seizures and late reduced di ...201121924570
Comment on "SCS: Signal, Context, and Structure Features for Genome-Wide Human Promoter Recognition"We comment on the flexibility profiles calculated by Zeng et al., and show that these profiles do not represent the local flexibility of the DNA molecule. If one takes into account the physics of elasticity, the averaged flexibility profile show an additional peak which is missed in the original calculation. We show that it is not possible to calculate the flexibility of a 6-mer using tetranucleotide elastic constants, the shortest sequence is a 7-mer. For 6-mers, dinucleotide or trinucleotide p ...201121968958
Proanthocyanidins and other flavonoids in relation to pancreatic cancer: a case-control study in Italy.BACKGROUND: Four cohort studies have examined the relation between flavonoids and pancreatic cancer risk providing inconsistent results. PATIENTS AND METHODS: We conducted a case-control study between 1991 and 2008 in Northern Italy. Subjects were 326 cases with incident pancreatic cancer and 652 frequency-matched controls (admitted to the same hospitals as cases for acute non-neoplastic conditions) who answered a reproducible and valid food-frequency questionnaire. We computed odds ratios (OR ...201122052986
[a case of legionnaires' pneumonia accompanied by clinically mild encephalitis/encephalopathy with a reversible splenial lesion (mers) with transient altered mental status and cerebellar symptoms, which responded to treatment by antibiotics and corticosteroid].a 60-year-old man was admitted because of fever, headache, and difficulty in walking. respiratory symptoms included only mild cough, but crackles were present on auscultation at the right lung base, the chest roentgenogram and computed tomography scans showed consolidation in the right lower lobe. laboratory findings revealed hyponatremia, elevated liver function test values and creatine phosphokinase, and legionella pneumophila antigen in urine. neurological examination revealed mild mental sta ...201122073610
a 29-mer site regulates transcription of the initiator gene as well as function of the replication origin of vibrio cholerae chromosome ii.the region responsible for replication of vibrio cholerae chromosome ii (chrii) resembles those of plasmids that have repeated initiator binding sites (iterons) and an autorepressed initiator gene. chrii has additional features: its iterons require full methylation for initiator (rctb) binding, which makes them inactive for a part of the cell cycle when they are hemi-methylated. rctb also binds to a second kind of site, called 39-mers, in a methylation independent manner. this binding is inhibit ...201222248922
2-oxo-2h-chromen-4-yl 4-meth-oxy-benzoate.in the title mol-ecule, c17h12o5, the chromen-2-one ring and the 4-meth-oxy-benzoate side chain are inclined to one another at a dihedral angle of 69.82 (9)°. the crystal structure features parallel sheets of centrosymmetric r2(2)(6) dimers joined by a c(7) chain, resulting in centrosymetric tetra-mers of hydrogen-bonded mol-ecules with graph-set motif r4(4)(40). these centrosymetric tetra-mers are connected by a pair of hydrogen bonds described by an r2(2)(8) ring motif and a c(7) chain via c-h ...201223476255
4,6-dimeth-oxy-2-(methyl-sulfan-yl)pyrimidine-4-hy-droxy-benzoic acid (1/1).the base mol-ecule of the title co-crystal, c7h10n2o2s·c7h6o3, is essentially planar, with a maximum deviation of 0.0806 (14) å for all non-h atoms. the acid mol-ecule is also nearly planar, with a dihedral angle of 8.12 (14)° between the benzene ring and the carb-oxy group. in the crystal, the acid mol-ecules form an inversion dimer through a pair of o-h⋯o hydrogen bonds with an r2(2)(8) ring motif. the pyrimidine mol-ecules are linked on both sides of the dimer into a heterotetra-mer via o-h⋯n ...201223476237
intraoperative monitoring of tibialis anterior muscle motor evoked responses to transcranial electrical stimulation during partial neuromuscular blockade.we studied the feasibility of recording motor evoked responses to transcranial electrical stimulation (tce-mers) during partial neuromuscular blockade (nmb). in 11 patients, compound muscle action potentials were recorded from the tibialis anterior muscle in response to transcranial electrical stimulation during various levels of vecuronium-induced nmb. the level of nmb was assessed by accelerometry of the adductor pollicis muscle after train-of-four stimulation of the ulnar nerve. the compound ...20051356320
distinguishing between functional monomeric and oligomeric complexes of the ca,mg-atpase in sarcoplasmic reticulum.techniques are described for using blocking agents to distinguish between enzymes which are functional monomers and oligomers. to achieve this distinction the blocking agent must react exclusively at the active site with a stoichiometry of one mole of site per mole enzyme. the effect of the blocking agent on enzymatic activity in oligomers of n = 2 and 4 are described and the optimal degree of blocking is considered for tests of enzyme activity at saturating and less than saturating substrate co ...20102945643
chemical consequences of incorporation of 5-fluorouracil into dna as studied by nmr.the cytotoxic analogue of thymine, 5-fluorouracil (uf), is known to be incorporated into dna in biological systems. this abnormal base has been synthetically incorporated into short dna oligomers. the ionization of the n-3 proton of this base within dna oligomers was measured by observation of the 19f chemical shift at varying ph values. the pka values for the uf ring of dtpdufpdt and dapdufpda were determined to be 7.84 and 7.9, respectively. the self-complementary 12-mers d(g-c-g-c-a-a-t-uf-g- ...20133828314
epitope identification from fixed-complexity random-sequence peptide microarrays.antibodies play an important role in modern science and medicine. they are essential in many biological assays and have emerged as an important class of therapeutics. unfortunately, current methods for mapping antibody epitopes require costly synthesis or enrichment steps, and no low-cost universal platform exists. in order to address this, we tested a random-sequence peptide microarray consisting of over 330,000 unique peptide sequences sampling 83% of all possible tetramers and 27% of pentamer ...201425368412
time for t? immunoinformatics addresses vaccine design for neglected tropical and emerging infectious diseases.vaccines have been invaluable for global health, saving lives and reducing healthcare costs, while also raising the quality of human life. however, newly emerging infectious diseases (eid) and more well-established tropical disease pathogens present complex challenges to vaccine developers; in particular, neglected tropical diseases, which are most prevalent among the world's poorest, include many pathogens with large sizes, multistage life cycles and a variety of nonhuman vectors. eid such as m ...201425193104
benchmarking of methods for genomic taxonomy.one of the first issues that emerges when a prokaryotic organism of interest is encountered is the question of what it is--that is, which species it is. the 16s rrna gene formed the basis of the first method for sequence-based taxonomy and has had a tremendous impact on the field of microbiology. nevertheless, the method has been found to have a number of shortcomings. in the current study, we trained and benchmarked five methods for whole-genome sequence-based prokaryotic species identification ...201424574292
communicable diseases prioritized according to their public health relevance, sweden, 2013.to establish strategic priorities for the public health agency of sweden we prioritized pathogens according to their public health relevance in sweden in order to guide resource allocation. we then compared the outcome to ongoing surveillance. we used a modified prioritization method developed at the robert koch institute in germany. in a delphi process experts scored pathogens according to ten variables. we ranked the pathogens according to the total score and divided them into four priority gr ...201526397699
towards high-throughput immunomics for infectious diseases: use of next-generation peptide microarrays for rapid discovery and mapping of antigenic determinants.complete characterization of antibody specificities associated to natural infections is expected to provide a rich source of serologic biomarkers with potential applications in molecular diagnosis, follow-up of chemotherapeutic treatments, and prioritization of targets for vaccine development. here, we developed a highly-multiplexed platform based on next-generation high-density peptide microarrays to map these specificities in chagas disease, an exemplar of a human infectious disease caused by ...201525922409
whole-proteome phylogeny of prokaryotes by feature frequency profiles: an alignment-free method with optimal feature resolution.we present a whole-proteome phylogeny of prokaryotes constructed by comparing feature frequency profiles (ffps) of whole proteomes. features are l-mers of amino acids, and each organism is represented by a profile of frequencies of all features. the selection of feature length is critical in the ffp method, and we have developed a procedure for identifying the optimal feature lengths for inferring the phylogeny of prokaryotes, strictly speaking, a proteome phylogeny. our ffp trees are constructe ...200920018669
hostphinder: a phage host prediction tool.the current dramatic increase of antibiotic resistant bacteria has revitalised the interest in bacteriophages as alternative antibacterial treatment. meanwhile, the development of bioinformatics methods for analysing genomic data places high-throughput approaches for phage characterization within reach. here, we present hostphinder, a tool aimed at predicting the bacterial host of phages by examining the phage genome sequence. using a reference database of 2196 phages with known hosts, hostphind ...201627153081
a dictionary based informational genome analysis.in the post-genomic era several methods of computational genomics are emerging to understand how the whole information is structured within genomes. literature of last five years accounts for several alignment-free methods, arisen as alternative metrics for dissimilarity of biological sequences. among the others, recent approaches are based on empirical frequencies of dna k-mers in whole genomes.201222985068
large-scale machine learning for metagenomics sequence classification.metagenomics characterizes the taxonomic diversity of microbial communities by sequencing dna directly from an environmental sample. one of the main challenges in metagenomics data analysis is the binning step, where each sequenced read is assigned to a taxonomic clade. because of the large volume of metagenomics datasets, binning methods need fast and accurate algorithms that can operate with reasonable computing requirements. while standard alignment-based methods provide state-of-the-art perf ...201526589281
the inhibitory effect of non-substrate and substrate dna on the ligation and self-adenylylation reactions catalyzed by t4 dna ligase.dna ligases are essential both to in vivo replication, repair and recombination processes, and in vitro molecular biology protocols. prior characterization of dna ligases through gel shift assays has shown the presence of a nick site to be essential for tight binding between the enzyme and its dsdna substrate, with no interaction evident on dsdna lacking a nick. in the current study, we observed a significant substrate inhibition effect, as well as the inhibition of both the self-adenylylation a ...201626954034
predicting peptide structures in native proteins from physical simulations of fragments.it has long been proposed that much of the information encoding how a protein folds is contained locally in the peptide chain. here we present a large-scale simulation study designed to examine the extent to which conformations of peptide fragments in water predict native conformations in proteins. we perform replica exchange molecular dynamics (remd) simulations of 872 8-mer, 12-mer, and 16-mer peptide fragments from 13 proteins using the amber 96 force field and the obc implicit solvent model. ...200919197352
chemical synthesis of the 5-taurinomethyl(-2-thio)uridine modified anticodon arm of the human mitochondrial trna(leu(uur)) and trna(lys).5-taurinomethyluridine (τm(5)u) and 5-taurinomethyl-2-thiouridine (τm(5)s(2)u) are located at the wobble position of human mitochondrial (hmt) trna(leu(uur)) and trna(lys), respectively. both hypermodified units restrict decoding of the third codon letter to a and g. pathogenic mutations in the genes encoding hmt-trna(leu(uur)) and hmt-trna(lys) are responsible for the loss of the discussed modifications and, as a consequence, for the occurrence of severe mitochondrial dysfunctions (melas, merrf ...201424757169
separating metagenomic short reads into genomes via clustering. 201223009059
identification of electrode respiring, hydrocarbonoclastic bacterial strain stenotrophomonas maltophilia mk2 highlights the untapped potential for environmental bioremediation.electrode respiring bacteria (erb) possess a great potential for many biotechnological applications such as microbial electrochemical remediation systems (mers) because of their exoelectrogenic capabilities to degrade xenobiotic pollutants. very few erb have been isolated from mers, those exhibited a bioremediation potential toward organic contaminants. here we report once such bacterial strain, stenotrophomonas maltophilia mk2, a facultative anaerobic bacterium isolated from a hydrocarbon fed m ...201628018304
de novo assembled wheat transcriptomes delineate differentially expressed host genes in response to leaf rust infection.pathogens like puccinia triticina, the causal organism for leaf rust, extensively damages wheat production. the interaction at molecular level between wheat and the pathogen is complex and less explored. the pathogen induced response was characterized using mock- or pathogen inoculated near-isogenic wheat lines (with or without seedling leaf rust resistance gene lr28). four serial analysis of gene expression libraries were prepared from mock- and pathogen inoculated plants and were subjected to ...201626840746
molecular phylogenetics before sequences: oligonucleotide catalogs as k-mer spectra.from 1971 to 1985, carl woese and colleagues generated oligonucleotide catalogs of 16s/18s rrnas from more than 400 organisms. using these incomplete and imperfect data, carl and his colleagues developed unprecedented insights into the structure, function, and evolution of the large rna components of the translational apparatus. they recognized a third domain of life, revealed the phylogenetic backbone of bacteria (and its limitations), delineated taxa, and explored the tempo and mode of microbi ...201424572375
enhanced mers coronavirus surveillance of travelers from the middle east to england.during the first year of enhanced mers coronavirus surveillance in england, 77 persons traveling from the middle east had acute respiratory illness and were tested for the virus. infection was confirmed in 2 travelers with acute respiratory distress syndrome and 2 of their contacts. patients with less severe manifestations tested negative.201425148267
clinical and laboratory findings of the first imported case of middle east respiratory syndrome coronavirus to the united states.the middle east respiratory syndrome coronavirus (mers-cov) was discovered september 2012 in the kingdom of saudi arabia (ksa). the first us case of mers-cov was confirmed on 2 may 2014.201425100864
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