Academic literature on the topic 'Sequenced-Defined polymers'
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Journal articles on the topic "Sequenced-Defined polymers"
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Denton, PH, DM Fowlkes, ST Lord, and HM Reisner. "Hemophilia B Durham: a mutation in the first EGF-like domain of factor IX that is characterized by polymerase chain reaction." Blood 72, no. 4 (October 1, 1988): 1407–11. http://dx.doi.org/10.1182/blood.v72.4.1407.bloodjournal7241407.
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Two men with factor IX (FIX)antigen-positive (CRM+) hemophilia B were selected for study because of their abnormal expression of an immunologically defined epitope previously localized to the EGF-like domains of the molecule. Exons IV and V (coding for the first and second EGF-like domains) of FIX were amplified 10(7) times from the patients' genomic DNA by using polymerase chain reaction (PCR) technology and sequenced. Both patients had identical mutations which resulted in the highly conserved Gly 60 residue being changed to Ser. PCR-amplified exon IV from six normal males had the previously defined canonic sequence. The correlation between the mutation and defective epitope expression in the two patients suggests that a change in the tertiary structure of the EGF-like domain is likely to cause the mild hemophilia B.
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Denton, PH, DM Fowlkes, ST Lord, and HM Reisner. "Hemophilia B Durham: a mutation in the first EGF-like domain of factor IX that is characterized by polymerase chain reaction." Blood 72, no. 4 (October 1, 1988): 1407–11. http://dx.doi.org/10.1182/blood.v72.4.1407.1407.
Full textAbstract:
Abstract Two men with factor IX (FIX)antigen-positive (CRM+) hemophilia B were selected for study because of their abnormal expression of an immunologically defined epitope previously localized to the EGF-like domains of the molecule. Exons IV and V (coding for the first and second EGF-like domains) of FIX were amplified 10(7) times from the patients' genomic DNA by using polymerase chain reaction (PCR) technology and sequenced. Both patients had identical mutations which resulted in the highly conserved Gly 60 residue being changed to Ser. PCR-amplified exon IV from six normal males had the previously defined canonic sequence. The correlation between the mutation and defective epitope expression in the two patients suggests that a change in the tertiary structure of the EGF-like domain is likely to cause the mild hemophilia B.
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Hennessy, Bryan T. J., Kirsten M. Timms, Mark S. Carey, Alexander Gutin, Larissa A. Meyer, Darl D. Flake, Victor Abkevich, et al. "Somatic Mutations in BRCA1 and BRCA2 Could Expand the Number of Patients That Benefit From Poly (ADP Ribose) Polymerase Inhibitors in Ovarian Cancer." Journal of Clinical Oncology 28, no. 22 (August 1, 2010): 3570–76. http://dx.doi.org/10.1200/jco.2009.27.2997.
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Purpose The prevalence of BRCA½ mutations in germline DNA from unselected ovarian cancer patients is 11% to 15.3%. It is important to determine the frequency of somatic BRCA½ changes, given the sensitivity of BRCA-mutated cancers to poly (ADP ribose) polymerase-1 (PARP1) inhibitors and platinum analogs. Patients and Methods In 235 unselected ovarian cancers, BRCA½ was sequenced in 235, assessed by copy number analysis in 95, and tiling arrays in 65. 113 tumors were sequenced for TP53. BRCA½ transcript levels were assessed by quantitative polymerase chain reaction in 220. When available for tumors with BRCA½ mutations, germline DNA was sequenced. Results Forty-four mutations (19%) in BRCA1 (n = 31)/BRCA2 (n = 13) were detected, including one homozygous BRCA1 intragenic deletion. BRCA½ mutations were particularly common (23%) in high-grade serous cancers. In 28 patients with available germline DNA, nine (42.9%) of 21 and two (28.6%) of seven BRCA1 and BRCA2 mutations were demonstrated to be somatic, respectively. Five mutations not previously identified in germline DNA were more commonly somatic than germline (four of 11 v one of 17; P = .062). There was a positive association between BRCA1 and TP53 mutations (P = .012). BRCA½ mutations were associated with improved progression-free survival (PFS) after platinum-based chemotherapy in univariate (P = .032; hazard ratio [HR] = 0.65; 95% CI, 0.43 to 0.98) and multivariate (P = .019) analyses. BRCA½ deficiency, defined as BRCA½ mutations or expression loss (in 24 [13.3%] BRCA½–wild-type cancers), was present in 67 ovarian cancers (30%) and was also significantly associated with PFS in univariate (P = .026; HR = 0.67; 95% CI, 0.47 to 0.96) and multivariate (P = .008) analyses. Conclusion BRCA½ somatic and germline mutations and expression loss are sufficiently common in ovarian cancer to warrant assessment for prediction of benefit in clinical trials of PARP1 inhibitors.
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Flores, R., J. A. Navarro, M. de la Peña, B. Navarro, S. Ambrós, and A. Vera. "Viroids with Hammerhead Ribozymes: Some Unique Structural and Functional Aspects with Respect to Other Members of the Group." Biological Chemistry 380, no. 7-8 (July 1, 1999): 849–54. http://dx.doi.org/10.1515/bc.1999.104.
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AbstractViroids, subviral pathogens of plants, are composed of a single-stranded circular RNA of 246–399 nucleotides. Within the 27 viroids sequenced, avocado sunblotch, peach latent mosaic and chrysanthemum chlorotic mottle viroids (ASBVd, PLMVd and CChMVd, respectively) can form hammerhead structures in both of their polarity strands. These ribozymes mediate self-cleavage of the oligomeric RNAs generated in the replication through a rolling circle mechanism, whose two other steps are catalyzed by an RNA polymerase and an RNA ligase. ASBVd, and presumably PLMVd and CChMVd, replicate and accumulate in the chloroplast, whereas typical viroids replicate and accumulate in the nucleus. PLMVd and CChMVd do not adopt a rod-like or quasi rod-like secondary structure as typical viroids do but have a highly branched conformation. A pathogenicity determinant has been mapped in a defined region of the CChMVd molecule.
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Baum, Bernard R., and D. A. Johnson. "The molecular diversity of the 5S rRNA gene in barley (Hordeum vulgare)." Genome 37, no. 6 (December 1, 1994): 992–98. http://dx.doi.org/10.1139/g94-140.
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The 5S rDNA genes from several accessions of cultivated barley, Hordeum vulgare L., were amplified by the polymerase chain reaction, cloned, and sequenced. Analysis of the aligned sequences, followed by principal coordinate analysis, support the recognition of at least two distinct classes of 5S rDNA genes. The short repeat class corresponds to the 300-bp tandem repeat defined by E.V. Ananiev as containing several TAG repeating units. The long repeat class contains long tandem repeats and lacks the TAG repeating unit. Sequences in each class can be further subdivided, with the long repeat class containing two groups and the short repeat class containing two and possibly three groups. These results suggest that in cultivated barley the sequence diversity found within the 5S rDNA non-transcribed spacer region may be encoded by three or more loci and may be useful for phylogenetic analyses provided that orthology can be established.Key words: 5S rDNA, sequence diversity, barley, phylogenetic analysis.
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Puel, O., F. Galgani, C. Dalet, and P. Lassus. "Partial sequence of the 24S rRNA and polymerase chain reaction based assay for the toxic dinoflagellateDinophysis acuminata." Canadian Journal of Fisheries and Aquatic Sciences 55, no. 3 (March 1, 1998): 597–604. http://dx.doi.org/10.1139/f97-288.
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We describe the polymerase chain reaction (PCR) amplification of an 805 base pair fragment of 24S rRNA from the toxic dinoflagellate Dinophysis acuminata and the sequence of this fragment. We also describe a PCR-based assay for the specific detection of D. acuminata in seawater samples. Conserved primers, starting at positions 711 and 1489 of the 24S rRNA from the dinoflagellate Prorocentrum micans, were used for the PCR. The PCR product was cloned and sequenced. The fragment was aligned with rRNA sequences from other protists. Two oligonucleotides in variable domains of the sequence from D. acuminata were chosen and a protocol was defined for PCR-based detection of D. acuminata (30 cycles, 50°C). Experiments conducted with seawater samples led to the detection of D. acuminata in naturally contaminated samples. The PCR enabled us to detect down to 30 cells/L seawater. The problem of interference from large concentrations of other phytoplankton species may be solved using nested PCR.
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Bagasra, Omar. "Application on in situ PCR methods in histochemistry." Proceedings, annual meeting, Electron Microscopy Society of America 53 (August 13, 1995): 754–55. http://dx.doi.org/10.1017/s0424820100140142.
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Since the publication of the first report regarding the in situ amplification of HIV-1 gag gene in a HIV-l infected cell line in 1990, there has been an explosion of research in the area of in situ PCR. There are over 200 publications describing various forms of in situ gene, identifying various infectious agents, tumor marker genes and other genetic elements of interest, in peer reviewed journals (reviewed in 2-15). The polymerase chain reaction (PCR) method for amplification of defined gene sequences has proved a valuable tool not only for basic researchers but also for clinical scientists. Using even a minute amount of DNA or RNA and choosing a thermostable enzyme from a large variety of sources, one can enlarge the amount of the gene of interest, which can be analyzed and/or sequenced. Thus genes or portions of gene sequences present only in a small sample of cells or small fraction of mixed cellular populations can be examined.
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Grünberg, Sebastian, Michael S. Bartlett, Souad Naji, and Michael Thomm. "Transcription Factor E Is a Part of Transcription Elongation Complexes." Journal of Biological Chemistry 282, no. 49 (October 5, 2007): 35482–90. http://dx.doi.org/10.1074/jbc.m707371200.
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A homologue of the N-terminal domain of the α subunit of the general eukaryotic transcription factor TFE is encoded in the genomes of all sequenced archaea, but the position of archaeal TFE in transcription complexes has not yet been defined. We show here that TFE binds nonspecifically to single-stranded DNA, and photochemical cross-linking revealed TFE binding to a preformed open transcription bubble. In preinitiation complexes, the N-terminal part of TFE containing a winged helix-turn-helix motif is cross-linked specifically to DNA of the nontemplate DNA strand at positions –9 and –11. In complexes stalled at +20, TFE cross-linked specifically to positions +9, +11, and +16 of the non-template strand. Analyses of transcription complexes stalled at position +20 revealed a TFE-dependent increase of the resumption efficiency of stalled RNA polymerase and a TFE-induced enhanced permanganate sensitivity of thymine residues in the transcription bubble. These results demonstrate the presence of TFE in early elongation complexes and suggest a role of TFE in stabilization of the transcription bubble during elongation.
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Clark, M. R., S. B. Clarkson, P. A. Ory, N. Stollman, and I. M. Goldstein. "Molecular basis for a polymorphism involving Fc receptor II on human monocytes." Journal of Immunology 143, no. 5 (September 1, 1989): 1731–34. http://dx.doi.org/10.4049/jimmunol.143.5.1731.
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Abstract IgG Fc receptor II (Fc gamma RII) on human monocytes is polymorphic with respect to its appearance on gels after isoelectric focusing and with respect to its ability to mediate T lymphocyte proliferation induced by murine anti-CD3 mAb of the IgG1 isotype (i.e., its ability to bind murine IgG1). To determine the molecular basis for this polymorphism, we isolated total cellular RNA from PBMC of responders and nonresponders (defined by Leu-4-induced [3H] thymidine incorporation) and synthesized corresponding cDNA. Sequences encoding the extracellular domain of Fc gamma RII were then amplified using the Taq polymerase chain reaction. Amplified DNA fragments were cloned into pUC vectors, and sequenced. Analysis of clones from two nonresponders revealed a single base change (G for A) at position 519, which would result in the substitution of a histidine for an arginine at residue 133 in the mature Fc gamma RII protein. These findings suggest that the polymorphism involving human monocyte Fc gamma RII results from allelic variation of a single gene.
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Hong, Soo Jong, Do Hyun Kim, Da Jin Sol Jung, Md Najmul Haque, and Myunggi Baik. "PSII-7 Complete genome analysis of a novel mucolytic bacterium, Prevotella mucinisolvens sp. nov., isolated from bovine rumen epithelium." Journal of Animal Science 98, Supplement_4 (November 3, 2020): 406. http://dx.doi.org/10.1093/jas/skaa278.711.
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Abstract We report the complete genome sequence of a novel mucolytic bacterium, Prevotella mucinisolvens sp. nov. Mucolytic bacteria were isolated from rumen epithelium of the dorsal sac of Korean cattle steer using a targeted cultivation on a mucin defined medium as a sole carbon source in anaerobic conditions. The genome of P. mucinisolvens was sequenced by means of both the Illumina HiSeq™ X and PacBio RSII platforms. The genome (2,730,135 bp) was found to contain 2,445 genes, 2,374 coding sequences, 61 transfer RNA, 1 transfer-messenger RNA, and 9 ribosomal RNA. The P. mucinisolvens had a total 51 glycoside hydrolases (GHs), of which 14 GHs, including β-galactosidases (GH2, GH20), α-N-acetylgalactosaminidases (GH101), α-N-acetylglucosaminidase (GH89), sialidase (GH33), and fucosidases (GH29, GH95), were identified as enzymes involved in mucin degradation. Following the KEGG pathways, the putative mucolytic pathway was constructed, including the metabolism of carbon sources such as galactose, N-acetylglucosamine, sialic acid (N-acetylneuraminic acid), and mannose. The presence of putative extracellular polysaccharide biosynthesis pathways, including Wzx/Wzy-dependent pathway (4 putative glycosyltransferases, 3 acetyltransferases, 1 flippase, 1 polymerase, 1 polysaccharide co-polymerase, and 1 outer membrane transport protein) and synthase-dependent pathway (1 putative synthase, 3 precursors of synthesis), was confirmed in P. mucinisolvens. Twelve putative virulence factors associated with adherence (hasB, KpsF, and htpB), stress reactions (clpP and clpC), antiphagocytosis (hasB and bcs1), O-antigen (gmd, fcl, and galE), and metabolic adaption (panD) were identified. This study contributes to a better understanding of epimural bacteria in putative mucin-degrading ability.
Dissertations / Theses on the topic "Sequenced-Defined polymers"
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Launay, Kévin. "Synthèse de nouveaux espaceurs alcoxyamine pour la préparation de polymères encodés." Electronic Thesis or Diss., Aix-Marseille, 2020. http://www.theses.fr/2020AIXM0487.
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Le monde numérique est en croissance permanente, ce qui nécessite de plus en plus d’espace de stockage. Cependant, les données numériques sont stockées sur des supports dont la durée de vie n’excède généralement pas quelques dizaines d’années. Ainsi, certaines entreprises leaders du monde numérique comme Microsoft, ont engagé des efforts dans la production de systèmes de stockage basés sur de l’ADN. Ce polymère souffre cependant d’un désavantage majeur : sa structure est fixée par la biologie. A l’inverse, la structure de polymères synthétiques peut être choisie et ajustée en fonction des besoins de l’utilisateur en termes d’écriture et de lecture. Cette thèse s’inscrit dans un projet de stockage d’informations digitales sur des poly(phosphodiester)s qui ont démontré leur capacité à produire des chaînes de taille comparable à celle de brins d’ADN synthétiques. Ces polymères sont séquencés en spectrométrie de masse par la dissociation des liaisons phosphodiester entre les bits dans des expériences de MS/MS. Afin de faciliter le séquençage des plus longues chaînes, elles ont été segmentées par l’ajout d’espaceurs de faible énergie de dissociation : les alcoxyamines. Les sous-segments sont séparés en MS/MS puis séquencés en pseudo-MS puissance 3. La lecture ne pouvait cependant être automatisée à cause de pics parasites provenant de réactions induites par le radical carboné issu de la rupture de la liaison alcoxyamine. Deux stratégies ont été suivies pour empêcher ces réactions : diminuer la réactivité du radical et rigidifier l’espaceur. La première s’est avérée insuffisante, mais la seconde a permis une couverture complète et automatisée de la séquence en quelques millisecondesThe constant growth of the digital world requires more and more storage space. Data is however stored on devices whose life-times are counted in decades at best. Therefore, leading companies of the digital world like Microsoft have engaged efforts to produce DNA-based storage systems. This polymer however suffers from a major disadvantage: its structure is fixed by biology. Conversely, the structure of synthetic polymers can be chosen and adjusted to fit the user’s requirements in terms of writing and reading. This thesis is included in a project involving digital storage of information on poly(phosphodiester)s which proved able to produce polymer chains of size comparable to man-made DNA strands. These polymers are sequenced in mass spectrometry by dissociation of the phosphodiester bonds between the bits in MS/MS experiments. In order to facilitate their sequencing, the longest chains were separated into sub-segments through the inclusion of spacers with a low bond dissociation energy: alkoxyamines. Sub-segments were separated in MS/MS and sequenced in pseudo-MSpower3 experiments. However, the reading could not be automatized because of several undesired peaks. Indeed, the flexibility of the chain was so that the highly reactive carbon-radical issued from alkoxyamine fragmentation induced several undesired dissociation pathways leading to their emergence. Two strategies were pursued in this thesis to prevent these side reactions: reducing the radical reactivity and increasing the stiffness of the backbone structure. The first one proved insufficient but the second one allowed complete, automated millisecond sequencing
Book chapters on the topic "Sequenced-Defined polymers"
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Bagasra, Omar, Thikkavarapu Seshamma, and Roger J. Pomerantz. "In Situ Polymerase Chain Reaction: A Powerful New Methodology." In In Situ Hybridization in Neurobiology, 143–56. Oxford University PressNew York, NY, 1994. http://dx.doi.org/10.1093/oso/9780195075076.003.0011.
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Abstract The polymerase chain reaction (PCR) (Bell, 1989) has proven a valuable tool for amplifying defined DNA sequences, even if they are available in only minute amounts, to obtain quantities that can be analyzed and/or sequenced. Using a variety of thermostable DNA polymerase enzymes (e.g., Tag), the PCR can quickly and efficiently amplify a genetic sequence utilizing an automated thermocycler (Bell, 1989). Thus genes or virus sequences (Chehab et al., 1989; Krone et al., 1990; Meltzer et al., 1990; Saito et al., 1989) present only in a small sample of cells, or in a small fraction of cells in a heterogeneous population can be traced. A specific area of study especially important for PCR has been in the area of human immunodeficiency virus type I/acquired immune deficiency (HIV-1/AIDS) research, as the actual percentage of HIV-I-infected cells in the peripheral blood has been subject of controversy (Ho et al., 1989; Harper et al., 1986).
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Bagasra, Omar, Lisa E. Bobroski, Muhammed Amjad, Roger J. Pomerantz,, and John Hansen. "Application of in situ PCR techniques to human tissues." In PCR3, 117–38. Oxford University PressOxford, 1997. http://dx.doi.org/10.1093/oso/9780199636327.003.0007.
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Abstract Since we first reported our findings regarding in situ amplification of the HIV-1 gag gene in an HIV-1-infected cell line in March 1990 (1), there has been an explosion of research in the area of in situ polymerase chain reaction (in situ PCR). There are over 300 publications describing various forms of in situ gene amplifications (reviewed in 2,3,13) , identifying various infectious agents, tumour marker genes, cytokines, growth factors and their receptors, and other genetic elements of interest, in peer-reviewed journals (1–25). The solution-based PCR method for amplifying defined gene sequences has proved a valuable tool not only for basic researchers but also for clinical scientists. Using even a minute amount of DNA or RNA and choosing a thermostable enzyme from a large variety of sources, the gene of interest can be amplified and then analysed and/or sequenced. Thus genes or segments of gene sequences present only in a small sample of cells or a small fraction of mixed cellular populations can be examined. However, one of the major drawbacks of solution-based PCR is that it does not allow the association of amplified signals of a specific gene segment with the histological cell type(s) (13,14). For example, it would be advantageous to determine what types of cells in the peripheral blood carry aberrant genes in a leukaemia patient and what percentage of leukaemia cells is present after various forms of anti tumour therapy.