Publications
| Title | Abstract | Year(sorted ascending) Filter | PMID Filter |
|---|
| identification and classification of the causes of events in transfusion medicine. | transfusion medicine lacks a standard method for the systematic collection and analysis of event reports. review of event reports from the food and drug administration (fda) showed a relative paucity of information on event causation. thus, a causal analysis method was developed as part of a prototype medical event reporting system for transfusion medicine (mers-tm). | 2007 | 9838940 |
| 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 |
| 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 |
| 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 |
| 1,1'-binaphthalene-2,2'-diyl hydrogen phosphate. | the title compound, racemic bnppa, c(20)h(13)o(4)p, crystallizes with four mol-ecules in the asymmetric unit. two independent centrosymmetric o-h⋯o hydrogen-bonded tetra-mers, each involving two of the symmetry-independent mol-ecules in the asymmetric unit generate the packing motif in the crystal structure. the hydro-phobic parts of the tetra-mers connect to their neighbours via c-h⋯π and π-π inter-actions [3.899 (2), 3.895 (2) and 3.803 (2) å within the symmetric unit, 3.851 (2), 4.000 (2), 3. ... | 2007 | 21200821 |
| 1,1'-(4-oxoheptane-1,7-di-yl)bis-(2-methyl-1h-benzimidazole) penta-hydrate. | the title compound, c(23)h(26)n(4)o·5h(2)o, has noncrystallographic twofold rotation symmetry in the solid state. it crystallizes with five solvent water mol-ecules in the asymmetric unit. four of these water mol-ecules are connected with each other via hydrogen-bonding inter-actions to form two types of centrosymmetric hexa-meric (h(2)o)(6) rings. via edge sharing of the hexa-mers, the water clusters thus build infinite chains that stretch parallel to the a axis. the fifth water mol-ecule provi ... | 2007 | 21200708 |
| 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 |
| [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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| stereoscopic viewing system for proteins using openrasmol: a tool for displaying a filament of proteins. | we have made a stereoscopic viewing system for a large assembly of proteins using openrasmol. the stable version 2.7.1 of openrasmol is modified for the system, which uses an eye-ware instead of trained bare-eyes. software rendering and other benefits in openrasmol are reserved. a 3-d graphic board is used just for the active stereo method, not for the acceleration of rendering. our modification is simple one. in the results, an actin filament of 16-mers, where one actin monomer has about 400 re ... | 2007 | 27857567 |
| theoretical simulation and focused ion beam fabrication of gold nanostructures for surface-enhanced raman scattering (sers). | this paper describes the fabrication of gold nanopillar and nanorod arrays and theoretical calculations of electromagnetic fields (emfs) around ordered arrangements of these nanostructures. the emfs of both single nanopillars and di-mers of nanopillars - having nanoscale gaps between the two adjacent nanopillars forming the di-mers - are simulated in this work by employing the finite difference time domain (fdtd) method. in the case of simulations for di-mers of nanopillars, the nano-scale gaps ... | 2007 | 23976888 |
| 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 |
| 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 |
| nanoscale patterning in crosslinked methacrylate copolymer networks: an atomic force microscopy study. | to understand the properties of materials, their phase structure must be established. it has been difficult in previous work to visualize the heterogeneous cross-linked structure of methacrylate-based networks. in this work, nano-sized phases with worm-like features were detected in the surfaces of model crosslinked methacrylate copolymer containing hydrophobic/hydrophilic co-mono-mers using tapping mode atomic force microscopy/phase imaging technique. the effects of different surface-contact co ... | 2007 | 19081742 |
| selectivity of montmorillonite catalyzed prebiotic reactions of d, l-nucleotides. | the montmorillonite-catalyzed reactions of the 5'-phosphorimidazolides of d, l-adenosine (d, l-impa) (figure 1a. n = a, r = h) and d, l-uridine (figure 1a., n = u, r = h) yields oligomers that were as long as 7 mers and 6 mers, respectively. the reactions of dilute solutions of d-impa and d-impu under the same conditions gave oligomers as long as 9 and 8 mers respectively. this demonstrated that oligomer formation is only partially inhibited by incorporation of both the d- and l-enantiomers. the ... | 2007 | 17160436 |
| genetic variation in opisthorchis viverrini (trematoda: opisthorchiidae) from northeast thailand and laos pdr based on random amplified polymorphic dna analyses. | genetic variation in opisthorchis viverrini adults originating from different locations in northeast thailand and laos, people's democratic republic (pdr), was examined using random amplified polymorphic dna (rapd) analyses. in an initial analysis, the genomic dna of one fluke from each of ten localities was amplified using 15 random primers (10-mers); however, genetic variation among o. viverrini specimens was detected reliably for only four primers. a more detailed rapd analysis using these fo ... | 2007 | 17016722 |
| structural characterization of beta-sheeted oligomers formed on the pathway of oxidative prion protein aggregation in vitro. | the pathology of transmissible spongiform encephalopathies (tses) is strongly associated with the structural conversion of the cellular prion protein (prpc) into a misfolded isoform (prpsc) that assembles into amyloid fibrils. since increased levels of oxidative stress have been linked to prion diseases, we investigated the metal-induced oxidation of human prp (90-231). a novel in vitro conversion assay based on aerobic incubation of prp in the presence of elemental copper pellets at ph 5 was es ... | 2007 | 17023178 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| machine learning for regulatory analysis and transcription factor target prediction in yeast. | high throughput technologies, including array-based chromatin immunoprecipitation, have rapidly increased our knowledge of transcriptional maps-the identity and location of regulatory binding sites within genomes. still, the full identification of sites, even in lower eukaryotes, remains largely incomplete. in this paper we develop a supervised learning approach to site identification using support vector machines (svms) to combine 26 different data types. a comparison with the standard approach ... | 2007 | 19003435 |
| 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 |
| antitumor effects of cationic synthetic peptides derived from lys49 phospholipase a2 homologues of snake venoms. | the effects of two cationic synthetic peptides, derived from the c-terminal region of lys49 phospholipase a2 homologues from snake venoms, upon various murine tumor cell lines (b16 melanoma, emt6 mammary carcinoma, s-180 sarcoma, p3x myeloma, tend endothelial cells) were evaluated. the peptides are 13-mers derived from agkistrodon piscivorus piscivorus lys49 pla2 (p-appk: kkykayfklkckk) and bothrops asper lys49 myotoxin ii (pem-2[d]: kkwrwwlkalakk), respectively, in the latter case with slight m ... | 2007 | 17178238 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| molecular appraisal of indian animal isolates of echinococcus granulosus. | cystic echinococcosis (ce) has a wide host range and distinct entities, not only reflected phenotypically but also by genotypic variation. considering this fact, this study was undertaken to characterize the indian isolates of echinococcus granulosus to find out difference between indian cattle, buffalo and sheep isolates on the basis of random amplification of polymorphic dna (rapd) pcr and pcr mediated restriction fragment length polymorphism (pcrrflp) of internal transcribed spacer gene 1 (it ... | 2008 | 18577794 |
| comparative genomic profiling of dutch clinical bordetella pertussis isolates using dna microarrays: identification of genes absent from epidemic strains. | whooping cough caused by bordetella pertussis in humans, is re-emerging in many countries despite vaccination. several studies have shown that significant shifts have occurred in the b. pertussis population resulting in antigenic divergence between vaccine strains and circulating strains and suggesting pathogen adaptation. in the netherlands, the resurgence of pertussis is associated with the rise of b. pertussis strains with an altered promoter region for pertussis toxin (ptxp3). | 2008 | 18590534 |
| estimation of neuronal firing rates with the three-state biological point process model. | in the subcortex of the human brain, neuronal firing events are stochastic and the inter-arrival times of action potentials (aps) are highly irregular. it has been shown that stimulation of the subthalamic nucleus (stn), a small subcortical structure located within the basal ganglia, can help ameliorate the motor symptoms associated with parkinson's disease (pd). however, success of image guided stereotactic surgery is reliant upon the refinement of the anatomic target (in this case the stn) bas ... | 2008 | 18598715 |
| ribosome performance is enhanced by a rich cluster of pseudouridines in the a-site finger region of the large subunit. | the large subunit rrna in eukaryotes contains an unusually dense cluster of 8-10 pseudouridine (psi) modifications located in a three-helix structure (h37-h39) implicated in several functions. this region is dominated by a long flexible helix (h38) known as the "a-site finger" (asf). the asf protrudes from the large subunit just above the a-site of trna binding, interacts with 5 s rrna and trna, and through the terminal loop, forms a bridge (b1a) with the small subunit. in yeast, the three-helix ... | 2008 | 18611858 |
| design of compact, universal dna microarrays for protein binding microarray experiments. | our group has recently developed a compact, universal protein binding microarray (pbm) that can be used to determine the binding preferences of transcription factors (tfs). this design represents all possible sequence variants of a given length k (i.e., all k-mers) on a single array, allowing a complete characterization of the binding specificities of a given tf. here, we present the mathematical foundations of this design based on de bruijn sequences generated by linear feedback shift registers ... | 2008 | 18651798 |
| specific mutations within the at-rich region of a plasmid replication origin affect either origin opening or helicase loading. | prokaryotic and eukaryotic replicons possess a distinctive region containing a higher than average number of adenine and thymine residues (the at-rich region) where, during the process of replication initiation, the initial destabilization (opening) of the double helix takes place. in many prokaryotic origins, this region consists of repeated 13-mer motifs whose function has not yet been specified. here we identify specific mutations within the 13-mer sequences of the broad-host-range plasmid rk ... | 2008 | 18685104 |
| activation of degp chaperone-protease via formation of large cage-like oligomers upon binding to substrate proteins. | cells use molecular chaperones and proteases to implement the essential quality control mechanism of proteins. the degp (htra) protein, essential for the survival of escherichia coli cells at elevated temperatures with homologues found in almost all organisms uniquely has both functions. here we report a mechanism for degp to activate both functions via formation of large cage-like 12- and 24-mers after binding to substrate proteins. cryo-electron microscopic and biochemical studies revealed tha ... | 2008 | 18697939 |
| contamination of synthetic hud protein spanning peptide pools with a cmv-encoded peptide. | to detect hud-specific t cells in patients with hu-antibody associated paraneoplastic neurological syndromes (hu-pns), we used short-term stimulation assays with hud protein spanning peptide pools (pspp) with purities of at least 70% and found reproducible false-positive cd8+ t-cell responses in three of 127 individuals (two healthy controls and one hu-pns patient), which all shared hla-a*2402 and hla-b*1801. after testing the 15-mer peptides of the hud antigen separately, we discovered that the ... | 2008 | 18727061 |
| effective delivery of antisense peptide nucleic acid oligomers into cells by anthrax protective antigen. | peptide nucleic acid (pna) is highly stable and binds to complementary rna and dna with high affinity, but it resists cellular uptake, thereby limiting its bioavailability. we investigated whether protectiveantigen (pa, a non-toxic component of anthrax toxin) could transport antisense pna oligomers into reporter cells that contain luciferase transgenes with mutant beta-globin ivs2 intronic inserts, which permit aberrant pre-mrna splicing and impair luciferase expression. pna oligomers antisense ... | 2008 | 18774771 |
| asymptomatic human cd4+ cytotoxic t-cell epitopes identified from herpes simplex virus glycoprotein b. | the identification of "asymptomatic" (i.e., protective) epitopes recognized by t cells from herpes simplex virus (hsv)-seropositive healthy individuals is a prerequisite for an effective vaccine. using the pepscan epitope mapping strategy, a library of 179 potential peptide epitopes (15-mers overlapping by 10 amino acids) was identified from hsv type 1 (hsv-1) glycoprotein b (gb), an antigen that induces protective immunity in both animal models and humans. eighteen groups (g1 to g18) of 10 adja ... | 2008 | 18799581 |
| gene expression profiling of listeria monocytogenes strain f2365 during growth in ultrahigh-temperature-processed skim milk. | to study how listeria monocytogenes survives and grows in ultrahigh-temperature-processed (uht) skim milk, microarray technology was used to monitor the gene expression profiles of strain f2365 in uht skim milk. total rna was isolated from strain f2365 in uht skim milk after 24 h of growth at 4 degrees c, labeled with fluorescent dyes, and hybridized to "custom-made" commercial oligonucleotide (35-mers) microarray chips containing the whole genome of l. monocytogenes strain f2365. compared to l. ... | 2008 | 18806004 |
| induction of immunity in sheep to fasciola hepatica with mimotopes of cathepsin l selected from a phage display library. | an m13 phage random 12-mers peptide library was used to screen cathepsin l mimotopes of fasciola hepatica and to evaluate their immunogenicity in sheep. seven clones showed positive reactivity to a rabbit anti-cathepsin l1/l2 antiserum in elisa, and their amino acid sequences deduced by dna sequencing were tentatively mapped on the protein. twenty sheep were randomly allocated into 4 groups of 5 animals each, for immunization with 1x10(14) phage particles of clones 1, 20, a mixture of 7 clones a ... | 2008 | 18812010 |
| computational search for over-represented 8-mers within the 5'-regulatory regions of 634 mouse testis-specific genes. | accumulation of microarray data has enabled the computational analysis of gene expressions in various tissues. although the genes showing testis-specific expression are most abundant among the genes exhibiting tissue-specific expression, no systematic study has been conducted for over-represented motifs within their regulatory regions. we have identified 117 over-represented 8-mers that appeared 2648 times within the regulatory regions of 634 testis-specific genes. of these, 64 over-represented ... | 2008 | 18817858 |
| the peripheral light-harvesting complexes from purple sulfur bacteria have different 'ring' sizes. | the integral membrane light-harvesting (lh) proteins from purple photosynthetic bacteria form circular oligomers of an elementary unit that is composed of two very hydrophobic polypeptides, termed alpha and beta. these apoprotein dimers are known to associate into closed circular arrays of 8, 9 and 16 alpha/beta-mers. we report the existence of peripheral lh proteins purified from allochromatium vinosum with two intermediate ring sizes and postulate that one is a 13 alpha/beta-mer. this shows th ... | 2008 | 18840433 |
| over-represented sequences located on 3' utrs are potentially involved in regulatory functions. | eukaryotic gene expression must be coordinated for the proper functioning of biological processes. this coordination can be achieved both at the transcriptional and post-transcriptional levels. in both cases, regulatory sequences placed at either promoter regions or on utrs function as markers recognized by regulators that can then activate or repress different groups of genes according to necessity. while regulatory sequences involved in transcription are quite well documented, there is a lack ... | 2008 | 18971640 |
| sequence space coverage, entropy of genomes and the potential to detect non-human dna in human samples. | genomes store information for building and maintaining organisms. complete sequencing of many genomes provides the opportunity to study and compare global information properties of those genomes. | 2008 | 18973670 |
| mass spectrometry for the characterization of unsulfated chondroitin oligosaccharides from 2-mers to 16-mers. comparison with hyaluronic acid oligomers. | this study reports for the first time the complete liquid chromatography/electrospray ionization mass spectrometry (lc/esi-ms) and tandem mass spectrometry (ms/ms) analyses performed in negative ion mode of saturated unsulfated chondroitin oligosaccharides up to 16-mers and comparison with hyaluronic acid (ha) oligomers differing only in the nature of the hexosamine residue. ms/ms of the chondroitin disaccharide on the singly charged precursor at m/z 396.1 afforded a glycosidic cleavage c1 produ ... | 2008 | 18853395 |
| size and morphology of toxic oligomers of amyloidogenic proteins: a case study of human stefin b. | amyloid-induced toxicity is a well-known phenomenon but the molecular background remains unclear. one hypothesis relates toxicity to amyloid-membrane interactions, predicting that amyloid oligomers make pores into membranes. therefore, the toxicity and membrane interaction of prefibrillar aggregates and individual oligomers of a non-pathological yet highly amyloidogenic protein human stefin b (cystatin b) was examined. by monitoring caspase-3 activity and by testing cell viability, we showed tha ... | 2008 | 18925453 |
| experimental analysis of oligonucleotide microarray design criteria to detect deletions by comparative genomic hybridization. | microarray comparative genomic hybridization (cgh) is currently one of the most powerful techniques to measure dna copy number in large genomes. in humans, microarray cgh is widely used to assess copy number variants in healthy individuals and copy number aberrations associated with various diseases, syndromes and disease susceptibility. in model organisms such as caenorhabditis elegans (c. elegans) the technique has been applied to detect mutations, primarily deletions, in strains of interest. ... | 2008 | 18940006 |
| immunodominant epitopes in herpes simplex virus type 2 glycoprotein d are recognized by cd4 lymphocytes from both hsv-1 and hsv-2 seropositive subjects. | in human recurrent cutaneous herpes simplex, there is a sequential infiltrate of cd4 and then cd8 lymphocytes into lesions. cd4 lymphocytes are the major producers of the key cytokine ifn-gamma in lesions. they recognize mainly structural proteins and especially glycoproteins d and b (gd and gb) when restimulated in vitro. recent human vaccine trials using recombinant gd showed partial protection of hsv seronegative women against genital herpes disease and also, in placebo recipients, showed pro ... | 2008 | 18941251 |