Publications

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 ...	2006	17193570
description of carbo-oxocarbons and assessment of exchange-correlation functionals for the dft description of carbo-mers.	mono- and polycyclic valence isomers of carbo-[3]oxocarbon c(9)o(3) and carbo-[5]oxocarbon c(15)o(5) have been characterized on the singlet spin state potential energy surface. by contrast to their geometry, their relative stability is highly sensitive to the calculation level. the performance of lda, gga, meta-gga, and hybrid functionals is compared to that of hf, post-hf, and multiconfigurational calculations. the results obtained for c(9)o(3) are compared to those obtained for hydrocarbon ana ...	2007	17201396
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 ...	2007	17253656
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 ...	2006	17254309
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 ...	2007	17259312
separations of hydrophobic synthetic peptides in counter-current chromatography.	synthetic peptides with many aromatic, aliphatic and especially acidic amino acid residues are not very soluble and require strong solvents for useful partitioning. a chloroform-methanol-acidic solvent system fractionates neutral and basically charged 26-mers to provide high yields. an insoluble 15-mer with 5 trp residues and 60% overall hydrophobic amino acid content was purified in pyridine-acetic acid and in another basic t-butyl methyl ether-n-butanol-acetonitrile solvent system with high re ...	2007	17266970
synthetic 3-o-methylmannose-containing polysaccharides (smmps): design and synthesis.	with the hope of mimicking the chemical and biological properties of natural 3-o-methylmannose-containing polysaccharides (mmps), synthetic 3-o-methylmannose-containing polysaccharides (smmps) were designed and synthesized in a convergent manner. with little modification of the mukaiyama glycosidation, high alpha-selectivity (>50:1 approximately >20:1) and yields (79 approximately 74%) were achieved for the key glycosidation steps. the exceptionally high alpha-selectivity observed was shown to b ...	2007	17274657
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 ...	2007	17288540
identification of hitherto undefined b-cell epitopes by antibodies in the sera of vitiligo patients using phage-display peptide library.	a random 12 mers phage library was used to screen a pool of immunoglobulin fractions obtained from vitiligo patients. subsequent to panning experiments, a panel of affinity selected phage from vitiligo patients were obtained. this panel was tested using an elisa for their reactivity with pooled sera from patients and normal controls. among the 16 randomly selected clones, two of clones showed distinct positive reactivity with the patient's sera compared with controls. the peptides displayed by t ...	2003	17301381
molecular dynamics study of small pna molecules in lipid-water system.	we present the results of molecular dynamics simulations of small peptide nucleic acid (pna) molecules, synthetic analogs of dna, at a lipid bilayer in water. at neutral ph, without any salt, and in the np(n)gammat ensemble, two similar pna molecules (6-mers) with the same nucleic base sequence and different terminal groups are investigated at the interface between water and a 1-palmitoyl-2-oleoylphosphatidylcholine lipid bilayer. the results of our simulations suggest that at low ionic strength ...	2007	17307825
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 ...	2007	17320292
accuracy of the three-body fragment molecular orbital method applied to møller-plesset perturbation theory.	the three-body energy expansion in the fragment molecular orbital method (fmo) was applied to the 2nd order møller-plesset theory (mp2). the accuracy of both the two and three-body expansions was determined for water clusters, alanine n-mers (alpha-helices and beta-strands) and one synthetic protein, using the 6-31g* and 6-311g* basis sets. at the best level of theory (three-body, two molecules/residues per fragment), the absolute errors in energy relative to ab initio mp2 were at most 1.2 and 5 ...	2007	17330884
symmetry-adapted-cluster/symmetry-adapted-cluster configuration interaction methodology extended to giant molecular systems: ring molecular crystals.	the symmetry adapted cluster (sac)/symmetry adapted cluster configuration interaction (sac-ci) methodology for the ground, excited, ionized, and electron-attached states of molecules was extended to giant molecular systems. the size extensivity of energy and the size intensivity of excitation energy are very important for doing quantitative chemical studies of giant molecular systems and are designed to be satisfied in the present giant sac/sac-ci method. the first extension was made to giant mo ...	2007	17343437
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 ...	2007	17355152
[separation of phosphodiester oligodeoxynucleotides and phosphorothioate antisense oligodeoxynucleotides by capillary zone electrophoresis at low ph].	oligodeoxynucleotides (odns) may possess biological activity in vivo, and are used for the cancer therapeusis. synthesized odns contains many by-products, and so their purity check and resolution of single-base, i. e., the separation of odns differing by one nucleotide in length, become necessary. in this study, capillary zone electrophoresis (cze) method was developed for the separation of two sets of model compounds of single-stranded oligodeoxynucleotide mixtures (18 - 20 mers), phosphodieste ...	2007	17432586
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 ...	2007	17440927
is multiple-sequence alignment required for accurate inference of phylogeny?	the process of inferring phylogenetic trees from molecular sequences almost always starts with a multiple alignment of these sequences but can also be based on methods that do not involve multiple sequence alignment. very little is known about the accuracy with which such alignment-free methods recover the correct phylogeny or about the potential for increasing their accuracy. we conducted a large-scale comparison of ten alignment-free methods, among them one new approach that does not calculate ...	2007	17454975
h4 histone tail mediated dna-dna interaction and effects on dna structure, flexibility, and counterion binding: a molecular dynamics study.	all-atom molecular dynamics (md) simulations were performed during 30-45 ns for a system of three identical dna 22-mers, 14 short fragments of the charged h4 histone tail peptide fragment (amino acids 5-12, kggkglgk) with k(+) counterions, and explicit water. the simulation setup mimics the crowded conditions of dna in eukaryotic chromatin. to assess the influence of tail fragments on dna structure and dynamics, a "control" 20 ns md simulation was carried for a system with the same dna and water ...	2014	17471473
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 ...	2007	17482565
g-boxes, bigfoot genes, and environmental response: characterization of intragenomic conserved noncoding sequences in arabidopsis.	a tetraploidy left arabidopsis thaliana with 6358 pairs of homoeologs that, when aligned, generated 14,944 intragenomic conserved noncoding sequences (cnss). our previous work assembled these phylogenetic footprints into a database. we show that known transcription factor (tf) binding motifs, including the g-box, are overrepresented in these cnss. a total of 254 genes spanning long lengths of cns-rich chromosomes (bigfoot) dominate this database. therefore, we made subdatabases: one containing b ...	2007	17496117
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 ...	2007	17526797
development of a statistically robust quantification method for microorganisms in mixtures using oligonucleotide microarrays.	high-density oligonucleotide arrays can be extremely useful for identifying and quantifying specific targets (i.e., ribosomal rna of microorganisms) in mixtures. however, current array identification schemes are severely compromised by nonspecific hybridization, resulting in numerous false-positive and false-negative calls, they lack an adequate internal control for assessing the quality of identification, and are dependent on amplification of specific target sequences which introduce biases. we ...	2007	17553581
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 ...	2007	17555767
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- ...	2007	17569499
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 ...	2007	17573430
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 ...	2007	17574666
structural and conformational analysis of scorpion (buthus sindicus) hemocyanin using low resolution techniques.	blue oxygen binding protein hemocyanin from scorpion buthus sindicus has been investigated using low resolution techniques. the native protein is a polymer of eight different types of subunits arranged in four cubic hexameric form (4x6-mers) as previously annotated using a combination of various types of chromatographic and electrophoretic techniques. in addition, both "top face" as well as the "side view" of the native assembly has also been identified from the negatively stained specimens usin ...	2007	17584175
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 ...	2007	17586819
no evidence for circulating hud-specific cd8+ t cells in patients with paraneoplastic neurological syndromes and hu antibodies.	in paraneoplastic neurological syndromes (pns) associated with small cell lung cancer (sclc) and hu antibodies (hu-pns), hu antigens expressed by the tumour hypothetically trigger an immune response that also reacts with hu antigens in the nervous system, resulting in tumour suppression and neuronal damage. to gain more insight into the hypothesized cd8(+ )t cell-mediated immune pathogenesis of these syndromes, we searched for circulating hud-specific cd8(+) t cells in a large cohort of hu-pns p ...	2007	17597332
on-line hplc/esi-ms separation and characterization of hyaluronan oligosaccharides from 2-mers to 40-mers.	a new method for the separation and identification of oligosaccharides obtained by enzymatic digestion of hyaluronic acid (ha) with hyaluronidase (ec 3.2.1.35) using on-line high-performance liquid chromatography/electrospray mass spectrometry (hplc/esi-ms) is presented. reversed-phase ion pairing-hplc, based on tributylamine salts and a volatile mobile phase, provided excellent chromatographic resolution and separation was achieved for ha oligosaccharides containing 2-40 monomers (from 2- to 40 ...	2007	17608452
performance characteristics of 65-mer oligonucleotide microarrays.	microarray fabrication using presynthesized long oligonucleotide is becoming increasingly important, but a study of large-scale array productions has not yet been published. we addressed the issue of fabricating oligonucleotide microarrays by spotting commercial presynthesized 65-mers with 5' amines representing 7500 murine genes. amine-modified oligonucleotides were immobilized on glass slides having aldehyde groups via transient schiff base formation followed by reduction to produce a covalent ...	2007	17617369
rankmotif++: a motif-search algorithm that accounts for relative ranks of k-mers in binding transcription factors.	the sequence specificity of dna-binding proteins is typically represented as a position weight matrix in which each base position contributes independently to relative affinity. assessment of the accuracy and broad applicability of this representation has been limited by the lack of extensive dna-binding data. however, new microarray techniques, in which preferences for all possible k-mers are measured, enable a broad comparison of both motif representation and methods for motif discovery. here, ...	2007	17646348
allosteric properties of g protein-coupled receptor oligomers.	allosteric regulation of ligand binding is a well-established mechanism regulating the function of g protein-coupled receptors (gpcr). allosteric modulators have been considered so far as molecules binding to an allosteric site, distinct from that of the reference ligand (orthosteric site), and able to modulate the binding affinity at the orthosteric site and/or the signaling properties resulting from orthosteric site occupancy. given that most gpcr are known to form dimers or higher order oligo ...	2007	17655934
practical and scalable synthesis of alpha-(1-->4)-linked polysaccharides composed of 6-o-methyl-d-glucose.	a second-generation synthesis of synthetic 6-o-methyl-d-glucose-containing polysaccharides (smgps) is reported. glycosidation acceptor a and donor b are prepared from alpha-, beta-, and gamma-cyclodextrins in high yields. the glycosidation of a and b, followed by deprotection, furnishes smgp 12-, 14-, and 16-mers. this synthesis has appealing features such as scalability, operational simplicity, and high overall yield.	2007	17658840
guanosine gel for sequence-dependent separation of polymorphic ssdna.	the separation of fluorescent-labeled ssdna fragments of equal length based on differences in sequence was achieved through the use of guanosine gels (g-gels) formed by guanosine-5'-monophosphate (gmp) in capillary gel electrokinetic chromatography (cgekc) with lif detection. baseline resolution was achieved for homodimers and homopentamers of a, t, and c. g-gel cgekc provided better resolution than cze, mekc, or a sieving gel in cge. resolution improved with increasing gmp, indicating that the ...	2007	17661319
identifying modifications in rna by maldi mass spectrometry.	posttranscriptional modifications on the base or sugar of ribonucleosides generally result in mass increases that can be measured by mass spectrometry. matrix-assisted laser desorption/ionization mass spectrometry (maldi-ms) is a direct and accurate means of determining the masses of rnas. mass spectra produced by maldi are relatively straightforward to interpret, because they are dominated by singly charged ions, making it possible to analyze complex mixtures of rna oligonucleotides ranging fro ...	2007	17673077
conformations of dna strands containing gagt, gaca, or gagc tetranucleotide repeats.	the (ga)(n) microsatellite has been known from previous studies to adopt unusual, ordered, cooperatively melting secondary structures in neutral aqueous solutions containing physiological concentrations of salts, at acid ph values or in aqueous ethanol solutions. to find more about the primary structure specificity of these structures, we performed parallel comparative studies of related tetranucleotide repeats (gagc)(5), (gagt)(5), and (gaca)(5). the general conclusion following from these comp ...	2007	17680700
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 ...	2007	17687010
chondroprotective effects of a proanthocyanidin rich amazonian genonutrient reflects direct inhibition of matrix metalloproteinases and upregulation of igf-1 production by human chondrocytes.	abstract:	2007	17697350
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 ...	2007	17709158
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 ...	2007	17726093
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.	2007	17786195
prediction of cis-regulatory elements: from high-information content analysis to motif identification.	one popular approach to prediction of binding motifs of transcription factors is to model the problem as to search for a group of l-mers (motifs), for some l > 0, one from each of the provided promoter regions of a group of co-expressed genes, that exhibit high information content when aligned without gaps. in our current work, we assume that these desired l-mers have evolved from a common ancestor, each of which has mutations in at most k-positions from the common ancestor, where k is substanti ...	2007	17787058
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 ...	2008	17847071
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 ...	2007	17877642
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 ...	2008	17902054
backbone-base inclination as a fundamental determinant of nucleic acid self- and cross-pairing.	the crystal structure of the duplex formed by oligo(2',3'-dideoxy-beta-d-glucopyranosyl)nucleotides (homo-dna) revealed strongly inclined backbone and base-pair axes [egli,m., pallan,p.s., pattanayek,r., wilds,c.j., lubini,p., minasov,g., dobler,m., leumann,c.j. and eschenmoser,a. (2006) crystal structure of homo-dna and nature's choice of pentose over hexose in the genetic system. j. am. chem. soc., 128, 10847-10856]. this inclination is easily perceived because homo-dna exhibits only a modest ...	2007	17905816
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 ...	2007	17922485
analysis and purification of peptide nucleic acids by denaturing page.	a flexible and convenient protocol for the analysis and purification of peptide nucleic acid (pna) oligomers and pna-peptide chimeras by denaturing page is described. vertical slab gel electrophoresis, 26% in polyacrylamide and 8 m urea at ph 3, was suitable for analysis of oligomers ranging in size from tetramers (4-mers) to tetradodecamers (24-mers). single-base resolution of oligomers was achieved and separations are generally superior to those given by standard rp-hplc techniques. the separa ...	2007	17922504
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 ...	2007	17929942
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 ...	2007	17951828
determination of the optimized conditions for coupling oligonucleotides with 16-mercaptohexadecanoic acid chemically adsorbed upon au.	a specific 5'-modified amino group oligonucleotide (primer 1), 15-mers in length, is selectively coupled with the carboxyl terminated 16-mercaptohexadecanoic acid (mhda) chemically adsorbed on au and subsequently hybridized with antisense primer. the amide-coupling process is of significance to create an intermediate structure for the purpose of adding primer 1, while the hybridization reaction is relevant to various diagnostic purposes to determine the presence in nucleic acids for a target seq ...	2007	17970584
creating surfactant nanoparticles for block copolymer composites through surface chemistry.	a simple strategy to tailor the surface of nanoparticles for their specific adsorption to and localization at block copolymer interfaces was explored. gold nanoparticles coated by a mixture of low molecular weight thiol end-functional polystyrene (ps-sh) (mn = 1.5 and 3.4 kg/mol) and poly(2-vinylpyridine) homopolymers (p2vp-sh) (mn = 1.5 and 3.0 kg/mol) were incorporated into a lamellar poly(styrene-b-2-vinylpyridine) diblock copolymer (ps-b-p2vp) (mn = 196 kg/mol). a library of nanoparticles wi ...	2007	17973409
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 ...	2007	17973982
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 ...	2008	17981583
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 ...	2007	17984517
design and fabrication of spotted long oligonucleotide microarrays for gene expression analysis.	dna microarray technology has advanced rapidly since the first use of cdna microarrays almost a decade ago. for gene expression studies on organisms, for which the genomes have been sequenced, cdna microarrays are being gradually replaced by gene-specific oligonucleotide microarrays. although, cdna microarrays give higher signal intensity than oligonucleotide microarrays, they cannot be used for the measurement of gene-specific expression, whereas, oligonucleotide microarrays can. to obtain both ...	2007	17984521
relative binding affinities of chlorophylls in peridinin-chlorophyll-protein reconstituted with heterochlorophyllous mixtures.	peridinin-chlorophyll-protein (pcp), containing differently absorbing chlorophyll derivatives, are good models with which to study energy transfer among monomeric chlorophylls (chls) by both bulk and single-molecule spectroscopy. they can be obtained by reconstituting the n-terminal domain of the protein (n-pcp) with peridinin and chlorophyll mixtures. upon dimerization of these "half-mers", homo- and heterochlorophyllous complexes are generated, that correspond structurally to monomeric protome ...	2008	17985210
identifications of conserved 7-mers in 3'-utrs and micrornas in drosophila.	micrornas (mirnas) are a class of endogenous regulatory small rnas which play an important role in posttranscriptional regulations by targeting mrnas for cleavage or translational repression. the base-pairing between the 5'-end of mirna and the target mrna 3'-utrs is essential for the mirna:mrna recognition. recent studies show that many seed matches in 3'-utrs, which are fully complementary to mirna 5'-ends, are highly conserved. based on these features, a two-stage strategy can be implemented ...	2007	17996040
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 ...	2008	18028413
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 ...	2007	18028446
studies on dna dynamics using 2-n-tert-butylaminoxylpurines.	2-n-tert-butylaminoxylpurines (1) and (2) were synthesized from 2'-deoxy-6-chloropurine derivative by lithiation strategy. effects of motion of 1 and 2 on epr spectra were studied by epr measurement in sucrose solution at various temperatures. the single stranded and duplexed 15-mers containing 1 showed the clear difference in the epr spectra to indicate 1 has the potential to accurately study the dynamics of purine residues.	2007	18029637
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 ...	2007	18040053
new strategies for cyclization and bicyclization of oligonucleotides by click chemistry assisted by microwaves.	the synthesis of cyclic, branched, and bicyclic oligonucleotides was performed by copper-catalyzed azide-alkyne cycloaddition assisted by microwaves in solution and on solid support. for that purpose, new phosphoramidite building blocks and new solid supports were designed to introduce alkyne and bromo functions into the same oligonucleotide by solid-phase synthesis on a dna synthesizer. the bromine atom was then substituted by sodium azide to yield azide oligonucleotides. cyclizations were foun ...	2008	18067317
managing the prevention of retained surgical instruments: what is the value of counting?	preventing retained foreign bodies is critical for patient safety. however, the value of counting surgical instruments and the reliability of the information provided have never been quantified. this study examines the diagnostic characteristics of counting and its impact on surgical costs.	2008	18156916
molecularly defined caprolactone oligomers and polymers: synthesis and characterization.	the synthesis of molecularly defined epsilon-caprolactone oligomers and polymers up to the 64-mer, via an exponential growth strategy, is described. by careful selection of orthogonal protecting groups, t-butyldimethylsilyl (tbdms) ether for the hydroxyl group and benzyl (bn) ester for the carboxylic acid group, a highly efficient synthetic strategy was developed with yields for both deprotection steps being essentially quantitative and for the coupling reactions using 1,3-dicyclohexylcarbodiimi ...	2008	18189397
crosslinking of nucleotide excision repair proteins with dna containing photoreactive damages.	photoreactive dna duplexes mimicking substrates of nucleotide excision repair (ner) system were used to analyze the interaction of xpc-hr23b, rpa, and xpa with damaged dna. photoreactive groups in one strand of dna duplex (arylazido-dcmp or 4-thio-dump) were combined with anthracenyl-dcmp residue at the opposite strand to analyze contacts of ner factors with damaged and undamaged strands. crosslinking of xpc-hr23b complex with photoreactive 48-mers results in modification of xpc subunit. xpc-hr2 ...	2008	18191172
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 ...	2008	18212089
prior pallidotomy reduces and modifies neuronal activity in the subthalamic nucleus of parkinson's disease patients.	parkinson's disease (pd) patients with prior radio-frequency lesions in the internal segment of the globus pallidus (gpi, pallidotomy), whose symptoms have deteriorated, may be candidates for further invasive treatment such as subthalamic deep brain stimulation (stn dbs). six patients with prior pallidotomy (five unilaterally; one bilaterally) underwent bilateral stn dbs. the microelectrode recordings (mers, used intraoperatively for stn verification), ipsilateral and contralateral to pallidotom ...	2008	18215242
a caenorhabditis motif compendium for studying transcriptional gene regulation.	controlling gene expression is fundamental to biological complexity. the nematode caenorhabditis elegans is an important model for studying principles of gene regulation in multi-cellular organisms. a comprehensive parts list of putative regulatory motifs was yet missing for this model system. in this study, we compile a set of putative regulatory motifs by combining evidence from conservation and expression data.	2008	18215260
quantitative fluorescence in situ hybridization (q-fish).	this unit describes a quantitative technique for measuring the lengths of telomere repeat sequences in individual chromosomes from single metaphase cells. the technique is based on fluorescence in situ hybridization (fish) adapted for use with peptide nucleic acid (pna) probes. pna is an example of novel synthetic oligonucleotide "mimetic" which has a higher affinity than regular oligonucleotide (rna or dna) probes for complementary single-strand (ss) dna sequences. pna oligonucleotides have exc ...	2001	18228343
label-free optical detection of peptide synthesis on a porous silicon scaffold/sensor.	mesoporous porous silicon (psi) microcavity sensors are used to conduct conventional solid-phase peptide synthesis. the sensor optical response provides a convenient means to monitor the synthesis reaction in a nondestructive manner. measurements indicate that peptide synthesis occurs only when the psi sensor/scaffold is amine-terminated using, for example, the amino silane or deprotected acid-labile rink linker. equivalent coupling efficiencies of the first amino acid to both amine terminations ...	2008	18247639
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.	2008	18252004
one-step formation of oligopeptide-like molecules from glu and asp in hydrothermal environments.	biopolymer accumulation in the absence of enzymes is an essential step for the chemical evolution of primitive life-like systems, and successful simulation experiments of prebiotic biopolymer formation have suggested that oligopeptides could have formed near submarine hydrothermal vent environments on primitive earth. however, the yield and length of oligopeptides -- typically limited to 6-mers -- seems to be inadequate. one reason is the rapid formation of diketopiperazines (dkps) from dipeptid ...	2008	18253712
aromaticity of ring carbo-mers of [n]annulenes and [n]cycloalkanes.	maps of current density induced by a perpendicular external magnetic field are calculated at the ipsocentric ctocd-dz/6-31g//b3pw91/6-31g level for ring carbo-mers of [n]-annulenes (closed-shell singlet states of c(3n)h, n = 3 to 7, with q = -1, 0, +1, 0, -1, respectively, and also the triplet ground state for n = 4) and of [n]-cycloalkanes (c(3n)h(qn), n = 3, 4, 5). strong four-electron diatropic ring currents indicate conventional pi aromaticity for all the singlet and triplet carbo-[n]ann ...	2008	18259634
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 ...	2008	18265428
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 ...	2008	18281088
impact of the oxidized guanine lesion spiroiminodihydantoin on the conformation and thermodynamic stability of a 15-mer dna duplex.	spiroiminodihydantoin (sp) is a hyperoxidized guanine base produced from oxidation of the mutagenic dna lesion 7,8-dihydro-8-oxo-2'-deoxguanosine (8-oxog) by a variety of species including peroxynitrite, singlet oxygen, and the high-valent metals ir(iv) and cr(v). in this study, the conformation and thermodynamic stability of a 15-mer dna duplex containing an sp lesion are examined using spectroscopic techniques and differential scanning calorimetry (dsc). the sp lesion does not alter the global ...	2008	18281959
structural basis for recognition of co2+ by rna aptamers.	co(2+) binding rna aptamers were chosen as research models to reveal the structural basis underlying the recognition of co(2+) by rna, with the application of two distinct methods. using the nucleotide analog interference mapping assay, we found strong interference effects after incorporation of the 7-deaza guanosine phosphorotioate analog into the rna chain at equivalent positions g27 and g28 in aptamer no. 18 and g25 and g26 in aptamer no. 20. the results obtained by nucleotide analog interfer ...	2008	18312410
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 ...	2008	18349386
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 ...	2008	18350171
design, manufacture, and assay of the efficacy of sirnas for gene silencing.	small interfering rnas (sirnas) have been widely exploited for nucleotide-sequence-specific posttranscriptional gene silencing, as a tool to investigate gene function in eukaryotes, and they hold promise as potential therapeutic agents. conventionally designed sirnas are 21-mers with symmetric 2-nt 3' overhangs that mimic intermediates (micrornas or mirnas) of the natural processing of longer dsrna (double-stranded rna). sirnas are sequences with full complementarity to their target mrna and can ...	2008	18370118
application of supercritical fluid chromatography to the analysis of hydrophobic metabolites.	this review describes the usefulness of supercritical fluid chromatography (sfc) in the analysis of hydrophobic metabolites. the use of sfc for the analysis of naturally occurring polyprenols markedly improves the chromatographic resolution of polyprenol homologues and their geometric isomers as compared to conventional hplc. under optimized sfc conditions, individual homologues with 10-100-mers were separated. furthermore, we established an analytical system for the fingerprinting and profiling ...	2008	18384099
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 ...	2008	18420744
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 ...	2008	18439100
molecular dynamics studies of polyethylene oxide and polyethylene glycol: hydrodynamic radius and shape anisotropy.	a revision (c35r) to the charmm ether force field is shown to reproduce experimentally observed conformational populations of dimethoxyethane. molecular dynamics simulations of 9, 18, 27, and 36-mers of polyethylene oxide (peo) and 27-mers of polyethylene glycol (peg) in water based on c35r yield a persistence length lambda = 3.7 a, in quantitative agreement with experimentally obtained values of 3.7 a for peo and 3.8 a for peg; agreement with experimental values for hydrodynamic radii of compar ...	2008	18456821
flexible chain molecules in the marginal and concentrated regimes: universal static scaling laws and cross-over predictions.	we present predictions for the static scaling exponents and for the cross-over polymer volumetric fractions in the marginal and concentrated solution regimes. corrections for finite chain length are made. predictions are based on an analysis of correlated fluctuations in density and chain length, in a semigrand ensemble in which mers and solvent sites exchange identities. cross-over volumetric fractions are found to be chain length independent to first order, although reciprocal-n corrections ar ...	2008	18465938
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 ...	2008	18487307
encephalopathy with a reversible splenial lesion is associated with hyponatremia.	we have encountered several patients with clinically mild encephalitis/encephalopathy with a reversible splenial lesion (mers) associated hyponatremia. in order to better understand this phenomenon, na levels were evaluated in a series of patients with mers. na was 131.8+/-4.1 mmol/l (mean+/-sd, range 121-140) in 30 patients with mers; 138.3+/-2.7 mmol/l (range 134-144) in age-matched 21 patients with upper respiratory infection; 136.6+/-2.5 mmol/l (range 132-140) in nine patients with other typ ...	2009	18490123
self-assembly of amyloid-forming peptides by molecular dynamics simulations.	protein aggregation is associated with many neurodegenerative diseases. understanding the aggregation mechanisms is a fundamental step in order to design rational drugs interfering with the toxic intermediates. this self-assembly process is however difficult to observe experimentally, which gives simulations an important role in resolving this problem. this study shows how we can proceed to gain knowledge about the first steps of aggregation. we first start by characterizing the free energy surf ...	2008	18508615
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 ...	2008	18515277
functional characterization of endogenous sirna target genes in caenorhabditis elegans.	small interfering rna (sirna) molecules mediate sequence specific silencing in rna interference (rnai), a gene regulatory phenomenon observed in almost all organisms. large scale sequencing of small rna libraries obtained from c. elegans has revealed that a broad spectrum of sirnas is endogenously transcribed from genomic sequences. the biological role and molecular diversity of c. elegans endogenous sirna (endo-sirna) molecules, nonetheless, remain poorly understood. in order to gain insight in ...	2008	18522735
critical behavior of long straight rigid rods on two-dimensional lattices: theory and monte carlo simulations.	the critical behavior of long straight rigid rods of length k (k-mers) on square and triangular lattices at intermediate density has been studied. a nematic phase, characterized by a big domain of parallel k-mers, was found. this ordered phase is separated from the isotropic state by a continuous transition occurring at an intermediate density theta(c). two analytical techniques were combined with monte carlo simulations to predict the dependence of theta(c) on k, being theta(c)(k) proportional ...	2008	18537446
h-shaped ope/opv oligomers: a new member of 2d-conjugated fluorophore cores.	a new class of two-dimensional (2d), pi-conjugated, skewed h-shaped co-oligomers of phenylene vinylene and phenylene ethynylene (11a- d, termed h-mers) were synthesized using sonogashira coupling and wittig-horner reactions as the key steps. electronic and spectroscopic properties of the h-mers were investigated by uv-vis absorption, fluorescence spectroscopic techniques, and ab initio calculations (hf/3-21g). two amino-containing functional h-mers (11b and 11d) were found to exhibit appealing f ...	2008	18549229
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 ...	2008	18549302
study of hopping transport in long oligothiophenes and oligoselenophenes: dependence of reorganization energy on chain length.	internal reorganization energies for self-exchange hole-transfer process were calculated at the b3lyp/6-31g(d) level of theory for a series of oligothiophenes and oligoselenophenes up to the 50-mers. this is the first study of reorganization energy in very long pi-conjugated systems. we observed a linear correlation between reorganization energy and the reciprocal chain length for these long pi-conjugated heterocyclic oligomers, which can be explained by the changes in bond length that occur bet ...	2008	18551687
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 ...	2008	18554865
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 ...	2008	18559857
properties of a concentrated minipool solvent-detergent treated cryoprecipitate processed in single-use bag systems.	cryoprecipitate is still used to treat factor viii (fviii), von willebrand factor (vwf) and/or fibrinogen deficiency. recently a solvent-detergent (s/d) process of minipools of cryoprecipitate performed in a closed bag system has been designed to improve its viral safety. still, cryoprecipitate has other drawbacks, including low concentration in active proteins, and presence of haemolytic isoagglutinins. we report here the biochemical evaluation of s/d-treated minipools of cryoprecipitates deple ...	2008	18565126
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 ...	2008	18574861