gebhart/patrepeval huggingface dataset:
Template-Directed Crosslinking of Oligonucleotides: Site-Specific Covalent Modification of dG-N7 within Duplex DNA (1995)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTTemplate-Directed Crosslinking of Oligonucleotides: Site-Specific Covalent Modification of dG-N7 within Duplex DNARobert S. Coleman and Edward A. KesickiCite this: J. Org. Chem. 1995, 60, 20, 6252–6253Publication Date (Print):October 1, 1995Publication History Published online1 May 2002Published inissue 1 October 1995https://pubs.acs.org/doi/10.1021/jo00125a004https://doi.org/10.1021/jo00125a004research-articleACS PublicationsRequest reuse permissionsArticle Views167Altmetric-Citations20LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
The Structure of the Glycopeptide of Human γG Myeloma Proteins (1971)

Abstract Glycopeptides were isolated from seven γG myeloma proteins and the γG-immunoglobulins of one normal individual. The composition of each glycopeptide was determined and the structure of the oligosaccharide portion of the molecule established as follows. Sequential enzymatic degradation of the oligosaccharide chains with purified glycosidases established the sequences of the sugars. Serial periodate oxidation and methylation of both intact and partially degraded glycopeptides followed by identification of the methylated sugars by gas chromatography and mass spectrometry established the linkages between sugars. The carbohydrate composition of the glycopeptides was found to be (in residues per mole of glycopeptide): sialic acid, 0 to 2; fucose, 0.6 to 1.2; galactose, 0.3 to 2.3; N-acetylglucosamine, 3.9 to 6.0; and mannose, 3. The variability in the number of sialic acid, fucose, and galactose residues was shown to be caused by microheterogeneity of the oligosaccharides while the variability in the number of N-acetylglucosamine residues reflects differences in the sequence of the sugars in the of the molecules. Two of the seven myeloma proteins had an additional oligosaccharide chain. All the glycopeptides are branched oligosaccharides containing two nonreducing termini with the sequence Gal (β1,6)/→ GlcNAc (β1,2)/→ Man. When sialic acid is present, it is linked α2,6 to the galactose residue. Both branches are connected to another mannose residue in the core, which also contains either 2 or 3 N-acetylglucosamine (GlcNAc) residues. The sequence of sugars in the core varied from one glycopeptide to another, being either Man→GlcNAc→ GlcNAc→Asn, Man→[GlcNAc→]GlcNAc→Asn, or Man→ GlcNAc→[GlcNAc→]GlcNAc→Asn. Di-N-acetylchitobiose was isolated from the core of one glycopeptide with a core structure of Man→GlcNAc→GlcNAc→Asn. These studies establish that homogeneous γG-immunoglobulins of man may have different sequences of sugars in their oligosaccharide chains. The data also show that microheterogeneity of oligosaccharides exists in homogeneous glycoproteins secreted by a single clone of cells.
Transcription Profiling-Based Identification of Staphylococcus aureus Genes Regulated by the agr and/or sarA Loci (2001)

The advent of transcription profiling technologies has provided researchers with an unprecedented ability to study biological processes. Accordingly, a custom-made Affymetrix GeneChip, constituting >86% of the Staphylococcus aureus genome, was used to identify open reading frames that are regulated by agr and/or SarA, the two best-studied regulators of the organism's virulence response. RNA extracted from wild-type cells and agr, sarA, and agr sarA mutant cells in the early-, mid-, and late-log and stationary phases of growth was analyzed. Open reading frames with transcription patterns expected of genes either up- or downregulated in an agr- and/or SarA-dependent manner were identified. Oligonucleotide microarray and Northern blot analyses confirmed that the transcription of several known virulence genes, including hla (alpha-toxin) and spa (protein A), is regulated by each effector and provided insights about the regulatory cascades involved in both alpha-hemolysin and protein A expression. Several putative virulence factors were also identified as regulated by agr and/or SarA. In addition, genes that are involved in several biological processes but which are difficult to reconcile as playing a direct role in the organism's pathogenesis also appeared to be regulated by each effector, suggesting that products of both the agr and the sarA locus are more-global transcription regulators than previously realized.
Influence of Controlled Quantum-Mechanical Charge and Phase Fluctuations on Josephson Tunneling (1995)

We study the interplay of controlled quantum-mechanical charge and phase fluctuations by measuring their influence on the supercurrent through a small superconducting grain. The grain is connected to leads by two small Josephson tunnel junctions. The phase fluctuations are controlled by the magnetic flux threading a SQUID that connects the grain to a large superconductor. The charge fluctuations are modulated by a voltage on a gate capacitor. As a function of gate voltage we observe a broadening of the Coulomb resonance of the supercurrent for decreasing phase fluctuations, in agreement with theoretical predictions.
Properties and Anti-Hiv Activity of Hairpin Antisense Oligonucleotides Containing 2′-Methoxynucleosides with Base-Pairing in the Stem Region at the 3′-End (1996)

A new type of hairpin antisense oligodeoxyribo-nucleotide, containing 2′-methoxynucleosides with base-pairing in the stem region at the 3′-end, was tested for 3′-exonuclease resistance and anti-HIV activity. An increased resistance to nuclease degradation has been observed by incubation of the hairpin oligo-nucleotides with DNA polymerase and foetal bovine serum. Of particular interest is the hairpin antisense oligonucleotide containing 2′-methoxynucleosides with base-pairing in the stem region at the 3′-end, which has increased nuclease resistance and hybridizes effectively with a complementary RNA. Furthermore, these compounds were assayed for inhibition of virus replication in HIV-1 infected MT-4 cells. In the anti-HIV activity test, the hairpin oligonucleotide phosphorothioate derivatives showed higher anti-HIV activities compared to their linear counterparts.
Rat prostate adenocarcinoma cells disseminate to bone and adhere preferentially to bone marrow-derived endothelial cells. (1992)

Approximately 70% of patients with prostatic cancer develop bone metastases. Metastatic prostate adenocarcinomas are associated with high mortality rates and represent a leading cause of cancer-related deaths among males. To study the host-tumor interactions underlying the predilection of prostate cancer cells for skeletal bone, an experimental model was developed using rat Dunning carcinoma Mat-LyLu cells. Inoculations of these cells into the left ventricle of the heart led to the development of spinal metastases in 100% of inoculated animals. A subline of Mat-LyLu (Mat-LyLu-B5) was subsequently selected through the sequential inoculation of bone marrow-derived carcinoma cells into the left ventricle and was found to have an increased metastatic potential compared to the parental line. The possible role of tumor cell adhesion to host cells in the process of bone marrow colonization was then investigated in vitro using the metastatic line and primary cultures of rat bone marrow-derived stromal cells. It was found that the adhesion of the metastatic Mat-LyLu cells to a bone marrow stromal cell culture highly enriched for endothelial cells was significantly higher than the adhesion to other bone-derived cells, including nonendothelial bone marrow stromal cells (3.5x) and osteoblasts (1.7x). It was also significantly higher than the adhesion to rat fibroblasts (7x) and to hepatic endothelial cells (7.5x). The results suggest that the adhesion of prostate carcinoma cells to the bone marrow endothelium may play a role in their metastasis to bone.
Mouse model of subarachnoid hemorrhage associated cerebral vasospasm: Methodological analysis (2002)

The transgenic mouse has been used to study subarachnoid hemorrhage (SAH) induced delayed cerebral vasospasm (DCV). Methodological parameters have not been analyzed to validate this model and associated neurological deficits have not been described. We introduce a technique to quantify DCV and associated neurological deficits. C57BL/6J mice were subjected to SAH or sham surgery. Seventy-two hours later, the vasculature was cast in situ with India ink/gelatin at perfusion pressures of 40-60, 60-80, or 100-120 mmHg. Mice were perfused with and without microfiltration. Additional mice underwent grading of SAH size, measurement of vascular diameters, and neurological examination (score range 5-27; 27= normal). When cast at 60-80 mmHg, SAH was associated with an intraluminal cross-sectional diameter reduction in 3 of 7 ipsilateral vascular segments. At 40-60 mmHg, the diameter of only one segment was reduced. No changes were observed at 100-120 mmHg. Emboli prevented adequate perfusion of vascular segments in the absence of microfiltration. Median (interquartile range) neurologic score was reduced after SAH (sham, 27(27); SAH 11(7-17)). Deficits correlated with middle cerebral artery (MCA) diameter and SAH grade. MCA diameter also correlated with SAH grade. Only when utilizing microfiltration, controlling for hemorrhage size, and casting at perfusion pressures of 60-80 mmHg does India ink/gelatin vascular casting demonstrate consistent DCV that correspnds to neurological deficits. This allows measurement of both anatomical and clinical DCV in the mouse.
A Low-complexity NBI Suppression Algorithm in UWB Systems (2006)

In this paper, a novel low-complexity narrow-band interference (NBI) suppression scheme is proposed which is based on singular value decomposition (SVD) and segment technique. Simulation results show that the presented scheme can eliminate NBI effectively. And its computational complexity is lower than conventional methods.
Autoreactive T cells can be protected from tolerance induction through competition by flanking determinants for access to class II MHC (2003)

It is not clear why the N-terminal autoantigenic determinant of myelin basic protein (MBP), Ac1-9, is dominant in the B1O.PL (H-2(u)) mouse, given its weak I-A(u)-MHC binding affinity. Similarly, how do high-affinity T cells specific for this determinant avoid negative selection? Because the MBP:1-9 sequence is embryonically expressed uniquely in the context of Golli-MBP, determinants were sought within the contiguous N-terminal "Golli" region that could out-compete MBP:1-9 for MHC binding, and thereby prevent negative selection of the public response to Ac1-9, shown here to be comprised of a V beta 8.2J beta 2.7 and a V beta 8.2J beta 2.4 expansion. Specifically, we demonstrate that Ac1-9 itself can be an effective inducer of central tolerance induction; however, in the context of Golli-MBP, Ac1-9 is flanked by determinants which prevent its display to autoreactive T cells. Our data support competitive capture as a means of protecting high-affinity, autoreactive T cells from central tolerance induction.
Fermentation of d -Xylose to Ethanol by Genetically Modified Klebsiella planticola (1987)

d-Xylose is a plentiful pentose sugar derived from agricultural or forest residues. Enteric bacteria such as Klebsiella spp. ferment d-xylose to form mixed acids and butanediol in addition to ethanol. Thus the ethanol yield is normally low. Zymomonas spp. and most yeasts are unable to ferment xylose, but they do ferment hexose sugars to ethanol in high yield because they contain pyruvate decarboxylase (EC 4.1.1.1), a key enzyme that is absent from enteric bacteria. This report describes the fermentation of d-xylose by Klebsiella planticola ATCC 33531 bearing multicopy plasmids containing the pdc gene inserted from Zymomonas mobilis. Expression of the gene markedly increased the yield of ethanol to 1.3 mol/mol of xylose, or 25.1 g/liter. Concurrently, there were significant decreases in the yields of formate, acetate, lactate, and butanediol. Transconjugant Klebsiella spp. grew almost as fast as the wild type and tolerated up to 4% ethanol. The plasmid was retained by the cells during at least one batch culture, even in the absence of selective pressure by antibiotics to maintain the plasmid. Ethanol production was 31.6 g/liter from 79.6 g of mixed substrate per liter chosen to simulate hydrolyzed hemicellulose. The physiology of the wild-type of K. planticola is described in more detail than in the original report of its isolation.
MICROFIBRILLAR PROTEIN FROM ELASTIC TISSUE: A CRITICAL EVALUATION (1984)

Many workers have claimed to have isolated proteins which have been derived from the microfibrillar components of elastic tissue. Virtually all of these preparations have been derived from extracts made with strong solutions of guanidinium chloride (GuHCl) under reducing conditions following Ross and Bornstein (1969). The products have ranged from heterogeneous mixtures of proteins to discrete glycoproteins. In no case has identity between an individual protein and the elastin-associated microfibrils been confirmed by immunoelectron microscopy. We have undertaken a detailed re-examination of the extractability of elastin-associated microfibrils and of the composition of the extracts from foetal bovine nuchal ligament. Finely homogenized samples were subjected to a series of extractions (including cyclical treatments with GuHCl and purified bacterial collagenase) in the presence of inhibitors of protease activity. Under these conditions it has been shown that--(i) microfibrils were removed progressively by GuHCl, throughout the extraction schedule, without the need for reduction; (ii) all remaining microfibrils were removed by reductive GuHCl extraction; (iii) the product from this reductive extraction consisted of a heterogeneous mixture of proteins including several glycoproteins; (iv) a major antigenic constituent of the mixture of proteins localized to elastin-associated microfibrils, as shown by immunoelectron microscopy. It is concluded that, while reductive GuHCl extracts do contain components with antigenic activity that is localized on elastin-associated microfibrils, they have many non-microfibrillar components. We stress that claims that a macromolecule is microfibrillar must be substantiated by immunoelectron microscopy.
Detection of Thrombin Receptor by Alkaline Phosphatase Antialkaline Phosphatase Method (1998)

Aim To establish a immunocytochemistry method of detection to thrombin receptor(TR).Methods TR activated by thrombin can release a peptide that contain 41 amino acids(TR1-41)from N-terminal of TR.The TR1-41 was synthesized accord-ing to the amino acids sequence of TR,then mice were immunized utilizing the TR1-41,4 cell strains produc-ing TR-McAb were gotten.Preparations of atheroscle-rotic human left ventricular myocardium of four died patients were cut out.The preparations were made in-to paraffin sections.Results A immunocytochemistry method-alkaline phosphatase antialkaline phosphatase(APAAP)to de-tect the thrombin receptor was established and the TR of myocardium were detected successfully.Conclusion The method established can detect TR expression of tissue and organ.
Do “heavy” eaters live longer? (2007)

A new hypothesis is put forward, linking cellular endurance with dietary consumption of stable heavy isotopes. Due to the isotope effect, biomolecules that incorporate heavier isotopes give rise to more stable molecular structures with increased resistance to damages associated with aging and age-related disease. The inclusion of heavy isotopes might be either active (selection for heavier isotopes) or passive (incorporation reflecting the existing abundance). The hypothesis links consumption of foods relatively rich in heavy isotopes (such as (13)C and D, derived from C4-plants), especially at the early stages of the organism's development, with enhanced longevity. Implications of diets and intestinal microflora are also discussed.
Brain aluminum, magnesium and phosphorus contents of control and Alzheimer-diseased patients (2005)

A study was undertaken to determine Al, Mg and P concentrations in 5 different brain regions of 3 control and 3 Alzheimer-diseased patients. One of the aims of this work was to evaluate the performance of applied analytical techniques. The digested samples were analyzed by inductively coupled plasma atomic emission spectrometry for Al, Mg and P. The dried samples were measured by instrumental neutron activation analysis for Al and Mg. The determination of human brain Al levels is complicated by the interfering reaction of P. We have previously worked out an analytical method which can eliminate this interference. The accuracy of the measured data was investigated by the analysis of biological standard reference materials. Our second goal was to study the possible elemental concentration changes in Alzheimer-diseased patients. Significantly higher Al and lower Mg and P values were found in some AD brain regions compared to the controls.
Genetically engineered antibodies: progress and prospects. (1992)

Techniques of genetic engineering and expression have been applied to the production of antibodies in a variety of expression systems. Novel antibodies have been produced with a variety of modifications: as chimeric antibodies, as "humanized" antibodies, with catalytic groups, as bifunctional or fusion proteins, and as functional fragments such as Fabs or Fvs. The domain structure of the antibody is favorable to such manipulation; the novel proteins often retain their antibody-derived activity and acquire new properties as well. Chimeric and complementarity-determining region (CDR)-grafted antibodies have been effective in immunotherapy, but problems of immunogenicity remain. Combinatorial libraries produced in bacteriophage may present an alternative to animal immunization as a source of antigen-binding specificities. Structural and mutational analysis of variable regions is providing useful information about the requirements of the variable region for antigen binding. Careful analysis and comparison of effector functions among immunoglobulin isotypes may be applied to the design of effective therapeutic antibodies.
Cyanobactins—ribosomal cyclic peptides produced by cyanobacteria (2010)

Cyanobactins are small cyclic peptides that are produced by a diverse selection of cyanobacteria living in symbioses as well as terrestrial, marine, or freshwater environments. They include compounds with antimalarial, antitumor, and multidrug reversing activities and potential as pharmaceutical leads. Cyanobactins are produced through the proteolytic cleavage and cyclization of precursor peptides coupled with further posttranslational modifications such as heterocyclization, oxidation, or prenylation of amino acids. Cyanobactin gene clusters encode two proteases which cleave and cyclisize the precursor peptide as well as proteins participating in posttranslational modifications. The bioinformatic mining of cyanobacterial genomes has led to the discovery of novel cyanobactins. Heterologous expression of these gene clusters provided insights into the role of the genes participating in the biosynthesis of cyanobactins and facilitated the rational design of novel peptides. Enzymes participating in the biosynthesis of cyanobactins may prove useful as catalysts for producing novel cyclic peptides in the future. The recent discovery of the cyanobactin biosynthetic pathway in cyanobacteria extends our knowledge of their potential as producers of interesting metabolites.
Mechanisms of regulation of CXCR4/SDF-1 (CXCL12)–dependent migration and homing in multiple myeloma (2006)

The mechanisms by which multiple myeloma (MM) cells migrate and home to the bone marrow are not well understood. In this study, we sought to determine the effect of the chemokine SDF-1 (CXCL12) and its receptor CXCR4 on the migration and homing of MM cells. We demonstrated that CXCR4 is differentially expressed at high levels in the peripheral blood and is down-regulated in the bone marrow in response to high levels of SDF-1. SDF-1 induced motility, internalization, and cytoskeletal rearrangement in MM cells evidenced by confocal microscopy. The specific CXCR4 inhibitor AMD3100 and the anti-CXCR4 antibody MAB171 inhibited the migration of MM cells in vitro. CXCR4 knockdown experiments demonstrated that SDF-1-dependent migration was regulated by the P13K and ERK/ MAPK pathways but not by p38 MAPK. In addition, we demonstrated that AMD3100 inhibited the homing of MM cells to the bone marrow niches using in vivo flow cytometry, in vivo confocal microscopy, and whole body bioluminescence imaging. This study, therefore, demonstrates that SDF-1/CXCR4 is a critical regulator of MM homing and that it provides the framework for inhibitors of this pathway to be used in future clinical trials to abrogate MM trafficking.