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Relevant bibliographies by topics / Consensus sequence

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Academic literature on the topic 'Consensus sequence'

Author: Grafiati

Published: 4 June 2021

Last updated: 20 February 2023

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Journal articles on the topic "Consensus sequence"

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Holmes, S. G., and M. M. Smith. "Interaction of the H4 autonomously replicating sequence core consensus sequence and its 3'-flanking domain." Molecular and Cellular Biology 9, no. 12 (December 1989): 5464–72. http://dx.doi.org/10.1128/mcb.9.12.5464-5472.1989.

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Yeast autonomously replicating sequence (ARS) elements are composed of a conserved 11-base-pair (bp) core consensus sequence and a less well defined 3'-flanking region. We have investigated the relationship between the H4 ARS core consensus sequence and its 3'-flanking domain. The minimal sequences necessary and sufficient for function were determined by combining external 3' and 5' deletions to produce a nested set of ARS fragments. Sequences 5' of the core consensus were dispensable for function, but at least 66 bp of 3'-flanking domain DNA was required for full ARS function. The importance of the relative orientation of the core consensus element with respect to the 3'-flanking domain was tested by precisely inverting 14 bp of DNA including the core consensus sequence by oligonucleotide mutagenesis. This core inversion mutant was defective for all ARS function, showing that a fixed relative orientation of the core consensus and 3'-flanking domain is required for function. The 3'-flanking domain of the minimal functional H4 ARS fragment contains three sequences with a 9-of-11-bp match to the core consensus. The role of these near-match sequences was tested by directed mutagenesis. When all near-match sequences with an 8-of-11-bp match or better were simultaneously disrupted by point mutations, the resulting ARS construct retained full replication function. Therefore, multiple copies of a sequence closely related to the core consensus element are not required for H4 ARS function.

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Holmes, S. G., and M. M. Smith. "Interaction of the H4 autonomously replicating sequence core consensus sequence and its 3'-flanking domain." Molecular and Cellular Biology 9, no. 12 (December 1989): 5464–72. http://dx.doi.org/10.1128/mcb.9.12.5464.

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Yeast autonomously replicating sequence (ARS) elements are composed of a conserved 11-base-pair (bp) core consensus sequence and a less well defined 3'-flanking region. We have investigated the relationship between the H4 ARS core consensus sequence and its 3'-flanking domain. The minimal sequences necessary and sufficient for function were determined by combining external 3' and 5' deletions to produce a nested set of ARS fragments. Sequences 5' of the core consensus were dispensable for function, but at least 66 bp of 3'-flanking domain DNA was required for full ARS function. The importance of the relative orientation of the core consensus element with respect to the 3'-flanking domain was tested by precisely inverting 14 bp of DNA including the core consensus sequence by oligonucleotide mutagenesis. This core inversion mutant was defective for all ARS function, showing that a fixed relative orientation of the core consensus and 3'-flanking domain is required for function. The 3'-flanking domain of the minimal functional H4 ARS fragment contains three sequences with a 9-of-11-bp match to the core consensus. The role of these near-match sequences was tested by directed mutagenesis. When all near-match sequences with an 8-of-11-bp match or better were simultaneously disrupted by point mutations, the resulting ARS construct retained full replication function. Therefore, multiple copies of a sequence closely related to the core consensus element are not required for H4 ARS function.

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Burke, Kelly, Supriya Munshaw, William Osburn, Jordana Levine, Lin Liu, Stuart Ray, and Andrea Cox. "HCV genotype 1a representative sequence elicits broad CD8+ T cell responses (113.10)." Journal of Immunology 188, no. 1_Supplement (May 1, 2012): 113.10. http://dx.doi.org/10.4049/jimmunol.188.supp.113.10.

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Abstract Vaccines designed to prevent or to treat hepatitis C viral infection must achieve maximum cross-reactivity against widely divergent circulating strains. Computer-generated sequences minimize genetic distance between circulating strains, and can be generated as a consensus sequence (most common amino acid at each position) or a representative sequence (derived with Bayesian and maximal likelihood phylogenetic tools). Broad recognition of such sequences in HCV has not been demonstrated. Consensus and representative sequences were generated from 390 full-length HCV genotype 1a polypeptide sequences. Sequence mutations in known epitopes were identified by longitudinal sequencing of HCV-infected subjects. Peptides encoding consensus, representative, and variant epitope sequences were tested for the capacity to expand CD8 T cells from HCV-infected subjects and to elicit cross-reactive responses by IFNg ELISpot. The representative and consensus sequences were identical for 9/11 epitopes examined. T cell lines generated against representative sequence peptides were generally cross-reactive to consensus sequence and natural sequence variants. Furthermore, representative sequence peptides generated more robust T cell responses than did natural sequence variant peptides. The broadest recognition of highly diverse circulating HCV strains was achieved using CD8+ T cells expanded with representative sequence HCV. These data support the use of representative sequence in HCV vaccine design.

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Du Toit, Andrea. "A consensus pausing sequence." Nature Reviews Microbiology 12, no. 6 (May 16, 2014): 394. http://dx.doi.org/10.1038/nrmicro3286.

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Palca, Joseph. "No consensus on sequence." Nature 322, no. 6078 (July 1986): 397. http://dx.doi.org/10.1038/322397a0.

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Aitken, Alastair. "Protein Consensus Sequence Motifs." Molecular Biotechnology 12, no. 3 (1999): 241–54. http://dx.doi.org/10.1385/mb:12:3:241.

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TORSHIN, Ivan. "Direct and reversed amino acid sequence pattern analysis: structural reasons for activity of reversed sequence sites and results of kinase site mutagenesis." Biochemical Journal 345, no. 3 (January 25, 2000): 733–40. http://dx.doi.org/10.1042/bj3450733.

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During studies of kinase phosphorylation, not all functional kinase phosphorylation may be found using consensus sequence patterns. This type of phosphorylation is termed ‘non-consensus’ or ‘cryptic’ phosphorylation. Results presented here based on molecular dynamics of short peptides show that protein kinases may phosphorylate not only established consensus sequences (reading a sequence from N-terminus to C-terminus) but also reversed consensus sequences (reading from C- to N-terminus). Several protein sequences were analysed and corresponding biochemical data were presented. Similarity of molecular shapes of direct and reversed consensus peptides, and sequence conservation in the regions of reversed sites in the analysed proteins, indicate that at least part of the phosphorylation sites considered as ‘cryptic’ may be explained in terms of reversed consensus pattern occurrences.

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Bae, J., U. R. Desai, A. Pervin, E. E. O. Caldwell, J. M. Weiler, and R. J. Linhardt. "Interaction of heparin with synthetic antithrombin III peptide analogues." Biochemical Journal 301, no. 1 (July 1, 1994): 121–29. http://dx.doi.org/10.1042/bj3010121.

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Heparin-binding proteins may contain specific patterns of basic amino acids, called consensus sequences, that interact with heparin. Small peptides were synthesized that contained consensus sequences (i.e. FAKLNCRLYRKANKSSK) or disrupted consensus sequences (i.e. K136-->A) based on the known sequence of antithrombin III (amino acid residues 123-139). These peptides were then examined in both competitive and non-competitive binding experiments using bioassays, fluorescence spectroscopy, affinity chromatography and n.m.r. spectroscopy. Both the consensus and disrupted-consensus peptide bound to heparin. Peptides with consensus sequences bound specifically to the pentasaccharide antithrombin III-binding site within heparin. In contrast, peptides with disrupted consensus sequences showed no specificity, binding to any sequence within heparin. Proton nuclear Overhauser enhancement spectroscopy demonstrated the proximity of leucine and tyrosine (within the consensus sequence) to the N-acetyl moiety found primarily within the pentasaccharide antithrombin III-binding site of heparin. This experiment confirmed the findings of the other techniques and helped to localize the binding sites in both peptides and heparin. A model is proposed for both specific and non-specific heparin interaction with consensus and disrupted-consensus peptides.

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Yeh, Ren-Hwa, Tae Ryong Lee, and David S. Lawrence. "From Consensus Sequence Peptide to High Affinity Ligand, a “Library Scan” Strategy." Journal of Biological Chemistry 276, no. 15 (January 16, 2001): 12235–40. http://dx.doi.org/10.1074/jbc.m011232200.

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A wide variety of proteins have been shown to recognize and bind to specific amino acid sequences on other proteins. These sequences can be readily identified using combinatorial peptide libraries. However, peptides containing these preferred sequences (“consensus sequence peptides”) typically display only modest affinities for the consensus sequence-binding site on the intact protein. In this report, we describe a parallel synthesis strategy that transforms consensus sequence peptides into high affinity ligands. The work described herein has focused on the Lck SH2 domain, which binds the consensus peptide acetyl-Tyr(P)-Glu-Glu-Ile-amide with aKDof 1.3 μm. We employed a strategy that creates a series of spatially focused libraries that challenge specific subsites on the target protein with a diverse array of functionality. The final lead compound identified in this study displayed a 3300-fold higher affinity for the Lck SH2 domain than the starting consensus sequence peptide.

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Schneider, Thomas D., and R. Michael Stephens. "Sequence logos: a new way to display consensus sequences." Nucleic Acids Research 18, no. 20 (1990): 6097–100. http://dx.doi.org/10.1093/nar/18.20.6097.

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Dissertations / Theses on the topic "Consensus sequence"

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Wilson, Lindsay Anne. "The enterobacterial repeated intergenic consensus (ERIC) sequence." Thesis, University of Nottingham, 2000. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.342441.

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Mokin, Sergey. "Measuring deviation from a deeply conserved consensus in protein multiple sequence alignments." Thesis, McGill University, 2008. http://digitool.Library.McGill.CA:80/R/?func=dbin-jump-full&object_id=21956.

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Proteins across species show variable degrees of conservation. Different patterns of conservation in the columns of an alignment indicate different evolutionary pressures on sequences. Protein conservation analysis is useful for a wide variety of applications, including disease mutation assessment, pseudogene analysis and functional residue prediction. This study describes a novel measure of column conservation in protein multiple sequence alignments (‘MSA'), and the application of this measure to calculate statistical deviation from alignment consensus (‘SDAC'). We have assessed SDAC for two case studies of sequences: (a) putative pseudogenes in Mycobacteria, and (b) young lineage-specific retrotransposed sequences in the human and mouse genomes. In the procedure, we rank residue positions for deep conservation, and evaluate statistically significant violations from MSA consensus. Novel conservation measure clearly indicated a variable degree of physiochemical conservation for a given column entropy. That, in turn, enabled us to detect deviations from physiochemical consensus in a protein MSA, which are not found by entropy measures.
D'une espèce à l'autre, des variations peuvent survenir dans la composition des protéines. Les tendances suivies par les colonnes d'un alignement de séquences multiples reflètent les différentes pressions évolutionnaires imposes sur les séquences. Les analyses de conservation de protéines sont utiles à plusieurs fins, comme dans l'évaluation des mutations de maladies, l'analyse de pseudogenes ainsi que les prédictions fonctionnelles de résidus. Cette étude décrit une nouvelle mesure de conservation de colonnes pour les analyses d'alignement de séquences multiples. De plus, nous décrivons l'utilisation de cette nouvelle mesure pour calculer la déviation statistique avec un consensus d'alignement. Nous avons utilisé cette mesure pour deux études cas de séquence : (a) Celle de pseudogenes putatifs du Mycobactérie, et (b) Celle de jeunes séquences spécifiques a certains lignages rétrotransposés dans les génomes humains et souris. Ce faisant, nous avons classifié les positions de résidus hautement conservés et avons évalué les cas ou d'importantes variations existent avec les consensus des alignements de séquences multiples. Cette nouvelle échelle de conservation indique qu'il existe un degré variable de conservation physiochimique pour une entropie fixe des colonnes. En retour, ceci nous permet de détecter les variations physiochimiques des consensus d'une colonne qui ne serait autrement pas détecté par des mesures d'entropie.

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Kamura, Eri. "Exploring the Methylation Status of RAI1 and the RAI1 Consensus Binding Sequence." VCU Scholars Compass, 2009. http://scholarscompass.vcu.edu/etd/1891.

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Smith Magenis Syndrome (SMS) is a multiple congenital anomalies/ mental retardation disorder caused by deletion or mutation of the RAI1 gene on chromosome 17p11.2. The majority of patients with SMS phenotypes have a deletion or mutation of RAI1. However, some patients have been observed with SMS-like phenotypes and yet have no deletions or mutations in the RAI1 gene. One possible explanation could be aberrant methylation of RAI1 since RAI1 is present and yet may be silenced. In order to study this possibility, patient cell lines were treated with 5-Aza-2’-deoxycytidine. RNA was extracted and real-time PCR was used to check the RAI1 expression status on the cells. RAI1 is thought to be a transcription factor, but the DNA binding sequence is still unknown. Sequences from ChIP-chip data were compared to identify a consensus sequence. One gene which contained this consensus sequence was the chemokine-like receptor-1 gene (CMKLR1), which was investigated by luciferase assay. CMKLR1 showed upregulation when co-transfected with RAI1.

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Babst, Scheán. "Mitochondrial DNA consensus sequence for the Tswana population of South Africa / Scheán Babst." Thesis, North-West University, 2012. http://hdl.handle.net/10394/9110.

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Evolutionary studies are critical in eliciting the fundamental phylogeny within and among populations of living organisms. Genetic diversity is displayed in human mitochondrial DNA (mtDNA) as haplogroups that consist of shared mutations, which are carried to the following generation through the maternal lineage. The current haplogroup hierarchies commonly used to describe and compare the genetic diversity of global human populations are based on the available mtDNA sequence variation datasets of numerous continent-specific populations. The description of mtDNA variation in human populations is furthermore of importance, as it allows the identification of population-specific genetic variation that has an effect on gene function, as well as on adaptation and susceptibility to disease. Owing to the limited amount of available mtDNA variation data from the numerous African populations currently residing in Africa, a lack of genetic diversity data exists for the determination of a sufficient baseline standard sequence representing the genetic variation present in African populations and thus also for a representative African haplogroup hierarchy. In this study, the mtDNA variation of 50 Tswana-speaking individuals from South Africa was determined and a novel Tswana consensus sequence was constructed to contribute to the urgent need for information of the mtDNA variation present in African populations. The consensus mtDNA sequence variation data obtained through this analysis should be regarded as a baseline for the observed sequence variance and genetic diversity of the maternal ancestral genetic pool of a Bantu-speaking population of South Africa. This study therefore contributes novel information regarding the mitochondrial genetic diversity of a South African Tswana-speaking population to the current body of literature. The results of this study provide strong evidence to support the ancient nature of African haplogroups and also provide evidence in support of the presence of Khoi-San maternal ancestry in the origins of the current Bantu-speaking populations of southern Africa. In addition, the observed sequence variation contributes to the current haplogroup hierarchy of African lineages and provides information in support of the previously reported distinct phylogenetic relationship between individuals of African and non-African origin, thereby explaining the high level of genetic diversity among and between African populations.
Thesis (PhD (Biochemistry))--North-West University, Potchefstroom Campus, 2013

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Mouton, Christa. "Mitochondrial genome consensus sequence for the South African Khoi-San population / Christa Mouton." Thesis, North-West University, 2003. http://hdl.handle.net/10394/9618.

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Maternal inheritance and the absence of recombination have contributed to mitochondrial deoxyribonucleic acid (mtDNA) being utilised to study human evolution. This, together with an increased mutation rate in mtDNA, provides information about the most recent common ancestor of modern humans. Previous studies suggested that Africa harbours the highest mtDNA diversity, supporting an out-of-Africa hypothesis for modern human evolution. From subsequent studies it was suggested that the Khoi-San population, in particularly the !Kung, cluster at the deepest root of the global phylogenetic tree. The Cambridge reference sequence is used worldwide in mitochondrial studies as a reference. However, recent studies have observed discrepancies from this sequence, which were confirmed by reanalysis. During this investigation the complete mitochondrial sequences of 13 !Kung individuals were determined. From phylogenetic analyses their clustering in the African LO-Iineage was revealed. The evolutionary rate of the derived sequences was investigated through statistical analysis and the hypothesis of neutral evolution was rejected. Pairwise nucleotide distribution suggested that sequences representing haplogroups LO, L 1 and L2 are examples of populations that were of stable population size for a long time. However, L3 was suggested to have been subjected to population expansion, in support of the out-of-Africa theory of evolution. From the comparative analysis of the 13 !Kung sequences with an LO-specific haplogroup tree it was observed that the 13 individuals clustered in two main groups. Ten individuals were added to one branch of the phylogenetic tree, revealing further branching, while three individuals were added to the terminal branches of another tree topology. A consensus sequence was derived from the 13 Khoi-San sequences, which was 99.25% similar to each of the sequences. This sequence could be utilised to investigate evolution of the mitochondrial genome over time as well as to evaluate the pathogenicity of mutations in patients.
MSc (Biochemistry) North-West University, Potchefstroom Campus, 2004

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Wynn, Anna. "Four differentially expressed cDNAs containing the Rebers-Riddiford consensus sequence in Callinectes sapidus /." Electronic version (PDF), 2004. http://dl.uncw.edu/etd/2004/wynna/annawynn.pdf.

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Ng, Harald. "Distributed Consensus: Performance Comparison of Paxos and Raft." Thesis, KTH, Skolan för elektroteknik och datavetenskap (EECS), 2020. http://urn.kb.se/resolve?urn=urn:nbn:se:kth:diva-281973.

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With the growth of the internet, distributed systems have become increasingly important in order to provide more available and scalable applications. Con- sensus is a fundamental problem in distributed systems where multiple pro- cesses have to agree on the same proposed value in the presence of partial failures. Distributed consensus allows for building various applications such as lock services, configuration manager services or distributed databases.Two well-known consensus algorithms for building distributed logs are Multi-Paxos and Raft. Multi-Paxos was published almost three decades before Raft and gained a lot of popularity. However, critics of Multi-Paxos consider it difficult to understand. Raft was therefore published with the motivation of being an easily understood consensus algorithm. The Raft algorithm shares similar characteristics with a practical version of Multi-Paxos called Leader- based Sequence Paxos. However, the algorithms differ in important aspects such as leader election and reconfiguration.Existing work mainly compares Multi-Paxos and Raft in theory, but there is a lack of performance comparisons in practice. Hence, prototypes of Leader- based Sequence Paxos and Raft have been designed and implemented in this thesis. The prototypes were implemented using the Rust programming lan- guage and the message-passing framework Kompact and then benchmarked in real-world scenarios to compare the performance of Leader-based Sequence Paxos and Raft.The results show that Leader-based Sequence Paxos and Raft have simi- lar performance in geographically distributed deployments. However, the un- predictable leader election in Raft could greatly affect the performance if the elected leader is in an undesired location. In our experiments, the location of the Raft leader affected the average throughput by up to 35%. Furthermore, the results indicate that implementation details could have a significant impact on performance even in the parts where the algorithms are similar. By batch- ing messages more efficiently, Leader-based Sequence Paxos achieved up to 17% higher average throughput than Raft.
Med tillväxten av internet har distribuerade system blivit allt mer viktiga för att bygga mer tillgängliga och skalbara applikationer. Konsensus är ett funda- mentalt problem i distribuerade system där flera processer ska komma överens om samma föreslagna värde, samtidigt som partiella fel kan ske. Distribuerad konsensus kan appliceras till olika användningsomården som låstjänster, kon- figurationshanterare och distribuerade databaser.Två välkända konsensusalgoritmer för att bygga distribuerade loggar är Multi-Paxos och Raft. Multi-Paxos publicerades nästintill tre årtionden före Raft och blev populär. Men kritiker av Multi-Paxos anser att algoritmen är svår att förstå. Av denna anledning publicerades Raft med motivationen att vara en konsensusalgoritm som är enkel att förstå. Raft delar likheter med Leader- based Sequence Paxos, en praktisk version av Multi-Paxos. Dock skiljer sig algoritmerna i viktiga aspekter som leaderval och rekonfigurering.Befintliga arbeten jämför i huvudsak Multi-Paxos och Raft i teorin, men det saknas jämförelse av prestandan i praktiken. Av denna anledning har pro- totyper av Leader-based Sequence Paxos och Raft blivit designade och imple- menterade i denna avhandling. Dessa prototyper implementerades i program- meringsspråket Rust och message-passing ramverket Kompact, som sedan tes- tades i verkliga situationer för att jämföra Leader-based Sequence Paxos och Raft.Resultaten visar att Leader-based Sequence Paxos och Raft har liknande prestanda i geografiskt distribuerade sammanhang. Dock kan det oförutsäga- bara ledarvalet i Raft påverka prestandan avsevärt ifall den valde ledaren befin- ner sig på en oönskad plats. I våra experiment påverkade Raft ledarens plats den genomsnittliga kapaciteten med upp till 35%. Resultaten visar även att implementationsdetaljer kan ha en signifikant effekt på prestandan även i de delar där algoritmerna är liknande. Genom att sammanfoga meddelanden mer effektivt uppnådde Leader-based Sequence Paxos 17% högre genomsnittlig kapacitet än Raft.

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Wen, Meimei. "Structural studies of a consensus sequence peptide (CSP) ABAB of apolipoproteins through NMR spectroscopy." Thesis, Boston University, 2013. https://hdl.handle.net/2144/11084.

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Thesis (Ph.D.)--Boston University
The apolipoproteins play critical roles in lipid transport, lipid metabolism and the pathophysiology of dyslipoproteinemias, most importantly atherosclerosis. ApoA-1 is a representative member of the family of exchangeable apolipoproteins and the major apolipoprotein of high density lipoprotein (HDL). HDL is responsible for the pathway of reverse cholesterol transport and the only particle capable of removing cholesterol from peripheral cells for transport to the liver. The sequences ofthe exchangeable apolipoproteins contain 11/22 residue tandem sequence repeats forming amphipathic α-helices that are believed to be responsible for lipid binding. The consensus sequence peptide (CSP) for this repeat was derived based on the characteristic residue distribution of the exchangeable apolipoproteins. The derived consensus sequence containing motifs A, (PLAEELRARLR), and B, (AQLEELRERLG), represent an idealized lipid binding model and fundamental structural motif of the exchangeable apolipoproteins. The recombinant CSP-ABAB peptide was successfully expressed in E. coli and purified. Circular dichroism showed that CSP-ABAB is ~62% α-helical, i.e.~27 residues of 44 residues are in helical conformation. The CSP-ABAB peptide was successfully 15N, 13C labeled and the detailed tertiary structure was explored by NMR spectroscopy. The peptide's backbone and side-chain resonances were successfully assigned and ten water refined structural conformers of CSP-ABAB were generated. The ten structural conformers all employ anti-parallel helical conformation in solution. Hydrophobic inter-helical interactions play a major role to stabilize the antiparallel helical hairpin conformation. There are also intra-/inter-helical salt bridges present on the surface of the CSP-ABAB molecule providing additional stabilization. The structural features of the NMR structures suggest a lipid binding model of CSP-ABAB. When lipids are introduced, the exposed hydrophobic ridge contributed by the twelve leucine residues firstly bind to the lipids. At the same time, a hydrophobic concave surface created by the four alanine residues at the center of the interface is accessed by the introduced lipids. These two steps open the anti-parallel helical hairpin conformation to form a fully extended α-helix. Similar hydrophobic inter-helical stabilization interactions and new intra-/inter-helical salt bridges between two different CSP-ABAB molecules are reformed to stabilize the 'double-belt' arrangement. This lipid binding model of CSP-ABAB sheds light on the lipid binding of apoA-I and the mechanism of HDL formation.

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McMillen, Lyle, and l. mcmillen@sct gu edu au. "Isolation and Characterisation of the 5'-Nucleotidase from Escherichia coli." Griffith University. School of Biomolecular and Biomedical Science, 2001. http://www4.gu.edu.au:8080/adt-root/public/adt-QGU20030226.153545.

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Escherichia coli 5'-nucleotidase is a periplasmically localised enzyme capable of hydrolysing a broad range of substrates, including all 5'-ribo- and 5'-deoxyribonucleotides, uridine diphosphate sugars, and a number of synthetic substrates such as bis (r-nitrophenyl) phosphate. The enzyme has been shown to contain at least one zinc ion following purification, and to have two metal binding sites in the catalytic cleft. 5'-Nucleotidase activity is significantly stimulated by the addition of particular divalent metal ions, most notably cobalt which results in a 30-50 fold increase in activity. Significant sequence homology between the E. coli 5'-nucleotidase and members of the Ser/Thr protein phosphatase family in the catalytic site has lead to 5'-nucleotidase being included in this protein family. This thesis describes the development of a rapid purification methodology for milligram quantities of 5'-nucleotidase, and the investigation of a number of physical and biochemical properties of the enzyme with the aim of comparing these properties to those of certain catalytic site mutants. The molecular weight of the mature protein was estimated as 58219 daltons, with a specific activity for 5'-AMP, in the presence of 4 mM Co2+ and 13 mM Ca2+ at pH 6.0, of 730 mmol/min/mg. The presence of up to two zinc ions associated with the purified enzyme was observed using ICP-ES analysis, suggesting both metal ion binding sites are occupied by zinc in vivo, and some degree of displacement of zinc by cobalt could be observed. Mass spectrometry data, gathered at 60 and 70 mS orifice potential, suggested the presence of a small proportion of material with a mass 118 to 130 daltons greater than the main 5'-nucleotidase mass estimation. This study suggests that this mass difference, only evident at the lower orificepotential, is due to the presence of two zinc ions closely associated with 5'-nucleotidase. To account for the observed high level of activation of 5'-nucleotidase activity by particular divalent metal ions, this thesis describes a proposed model in which these divalent ions may displace the zinc ion at one of the metal ion binding sites. This displacement only occurs at one of the two metal ion binding sites, with the other metal binding site retaining the zinc ion already present. Studies with purified enzyme, each with a single amino acid substitution, lend support to this hypothesis and suggest the identity of the metal ion binding site at which displacement occurs. Seven key catalytic site residues (Asp-41, His-43, Asp-84, His-117, Glu-118, His-217 and His-252) were selected on the basis of sequence conservation within the Ser/Thr protein phosphatases and 5'-nucleotidases. X-ray crystallographic data published by others during this study implicated five of the selected residues (Asp-41, His-43, Asp-84, His-217 and His-252) directly in metal ion binding, including two residues from each metal ion binding site and one directly involved in both sites (Asp-84). The remaining two residues (His-117 and Glu-118) are highly conserved but were not thought to play direct roles in metal ion binding. The seven selected residues were modified by site-directed mutagenesis, and the effect of the amino acid substitutions upon the kinetic properties of 5'-nucleotidase activity was determined. Residues hypothesised to be involved in metal ion displacement, and subsequent activation of 5'-nucleotidase activity, were identified by reductions in metal ion affinity and increased levels of activation by cobalt compared to the wild type 5'-nucleotidase. This study suggests that the metal binding site, M2, that includes residues Asp-84, His-217 and His-252, is involved in metal ion displacement, while the other metal binding site, M1, is not. This, in turn, suggests the metal binding sites are functionally non-equivalent and kinetically distinct. No residues were identified in this study as playing significant roles in substrate binding, as there was no significant reduction observed in affinity for 5'-AMP observed in any of the catalytic site mutants.

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McMillen, Lyle. "Isolation and Characterisation of the 5'-Nucleotidase from Escherichia coli." Thesis, Griffith University, 2001. http://hdl.handle.net/10072/366487.

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Escherichia coli 5'-nucleotidase is a periplasmically localised enzyme capable of hydrolysing a broad range of substrates, including all 5'-ribo- and 5'-deoxyribonucleotides, uridine diphosphate sugars, and a number of synthetic substrates such as bis (r-nitrophenyl) phosphate. The enzyme has been shown to contain at least one zinc ion following purification, and to have two metal binding sites in the catalytic cleft. 5'-Nucleotidase activity is significantly stimulated by the addition of particular divalent metal ions, most notably cobalt which results in a 30-50 fold increase in activity. Significant sequence homology between the E. coli 5'-nucleotidase and members of the Ser/Thr protein phosphatase family in the catalytic site has lead to 5'-nucleotidase being included in this protein family. This thesis describes the development of a rapid purification methodology for milligram quantities of 5'-nucleotidase, and the investigation of a number of physical and biochemical properties of the enzyme with the aim of comparing these properties to those of certain catalytic site mutants. The molecular weight of the mature protein was estimated as 58219 daltons, with a specific activity for 5'-AMP, in the presence of 4 mM Co2+ and 13 mM Ca2+ at pH 6.0, of 730 mmol/min/mg. The presence of up to two zinc ions associated with the purified enzyme was observed using ICP-ES analysis, suggesting both metal ion binding sites are occupied by zinc in vivo, and some degree of displacement of zinc by cobalt could be observed. Mass spectrometry data, gathered at 60 and 70 mS orifice potential, suggested the presence of a small proportion of material with a mass 118 to 130 daltons greater than the main 5'-nucleotidase mass estimation. This study suggests that this mass difference, only evident at the lower orificepotential, is due to the presence of two zinc ions closely associated with 5'-nucleotidase. To account for the observed high level of activation of 5'-nucleotidase activity by particular divalent metal ions, this thesis describes a proposed model in which these divalent ions may displace the zinc ion at one of the metal ion binding sites. This displacement only occurs at one of the two metal ion binding sites, with the other metal binding site retaining the zinc ion already present. Studies with purified enzyme, each with a single amino acid substitution, lend support to this hypothesis and suggest the identity of the metal ion binding site at which displacement occurs. Seven key catalytic site residues (Asp-41, His-43, Asp-84, His-117, Glu-118, His-217 and His-252) were selected on the basis of sequence conservation within the Ser/Thr protein phosphatases and 5'-nucleotidases. X-ray crystallographic data published by others during this study implicated five of the selected residues (Asp-41, His-43, Asp-84, His-217 and His-252) directly in metal ion binding, including two residues from each metal ion binding site and one directly involved in both sites (Asp-84). The remaining two residues (His-117 and Glu-118) are highly conserved but were not thought to play direct roles in metal ion binding. The seven selected residues were modified by site-directed mutagenesis, and the effect of the amino acid substitutions upon the kinetic properties of 5'-nucleotidase activity was determined. Residues hypothesised to be involved in metal ion displacement, and subsequent activation of 5'-nucleotidase activity, were identified by reductions in metal ion affinity and increased levels of activation by cobalt compared to the wild type 5'-nucleotidase. This study suggests that the metal binding site, M2, that includes residues Asp-84, His-217 and His-252, is involved in metal ion displacement, while the other metal binding site, M1, is not. This, in turn, suggests the metal binding sites are functionally non-equivalent and kinetically distinct. No residues were identified in this study as playing significant roles in substrate binding, as there was no significant reduction observed in affinity for 5'-AMP observed in any of the catalytic site mutants.
Thesis (PhD Doctorate)
Doctor of Philosophy (PhD)
School of Biomolecular and Biomedical Sciences
Science, Environment, Engineering and Technology
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Books on the topic "Consensus sequence"

1

Aitken, Alastair. Identification of protein consensus sequences: Active site motifs, phosphorylation, and other post-translational modifications. New York: Ellis Horwood, 1990.

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Aitken, Alastair. Identification of protein consensus sequences: Active site motifs, phosphorylation, and other post-translational modifications. New York: Ellis Horwood, 1990.

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Identification of Protein Consensus Sequences: Active Site Motifs, Phosphorylation, and Other Posttranslational Modifications (Ellis Horwood Books in the Biological Sciences). Ellis Horwood Ltd, 1990.

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Lilja, Sven. Climate, History, and Social Change in Sweden and the Baltic Sea Area From About 1700. Oxford University Press, 2017. http://dx.doi.org/10.1093/acrefore/9780190228620.013.633.

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The growing concern about global warming has turned focus in Sweden and other Baltic countries toward the connection between history and climate. Important steps have been taken in the scientific reconstruction of climatic parables. Historic climate data have been published and analyzed, and various proxy data have been used to reconstruct historic climate curves. The results have revealed an ongoing regional warming from the late 17th to the early 21st century. The development was not continuous, however, but went on in a sequence of warmer and colder phases.Within the fields of history and socially oriented climate research, the industrial revolution has often been seen as a watershed between an older and a younger climate regime. The breakthrough of the industrial society was a major social change with the power to influence climate. Before this turning point, man and society were climate dependent. Weather and short-term climate fluctuations had major impacts on agrarian culture. When the crops failed several years in sequence, starvation and excess mortality followed. As late as 1867–1869, northern Sweden and Finland were struck by starvation due to massive crop failures.Although economic activities in the agricultural sector had climatic effects before the industrial society, when industrialization took off in Sweden in the 1880s it brought an end to the large-scale starvations, but also the start of an economic development that began to affect the atmosphere in a new and broader way. The industrial society, with its population growth and urbanization, created climate effects. Originally, however, the industrial outlets were not seen as problems. In the 18th century, it was thought that agricultural cultivation could improve the climate, and several decades after the industrial take-off there still was no environmental discourse in the Swedish debate. On the contrary, many leading debaters and politicians saw the tall chimneys, cars, and airplanes as hopeful signs in the sky. It was not until the late 1960s that the international environmental discourse reached Sweden. The modern climate debate started to make its imprints as late as the 1990s.During the last two decades, the Swedish temperature curve has unambiguously turned upwards. Thus, parallel to the international debate, the climate issue has entered the political agenda in Sweden and the other Nordic countries. The latest development has created a broad political consensus in favor of ambitious climate goals, and the people have gradually started to adapt their consumption and lifestyles to the new prerequisites.Although historic climate research in Sweden has had a remarkable expansion in the last decades, it still leans too much on its climate change leg. The clear connection between the climate fluctuations during the last 300 years and the major social changes that took place in these centuries needs to be further studied.

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Henzi, Bettina, and Maja Steinlin. Stroke in children. Oxford University Press, 2018. http://dx.doi.org/10.1093/med/9780198722366.003.0013.

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Stroke in children is a rare, but terrifying disease and its lifelong sequelae weigh heavy on patients and families. It is also increasingly recognized as a socioeconomic burden, ongoing for many years after the acute manifestation. There is a significant delay in diagnosis of childhood stroke. This is caused by several factors: lack of awareness among the public and professionals, childhood-specific manifestations, numerous stroke mimics, and last but not least, limited access to emergency neuroimaging for children. Fast stroke recognition tools need adaption to the special needs in children. Childhood arterial ischaemic stroke differs in aetiology from adult stroke with cerebral vasculopathies being the leading cause and cardioembolic aetiology ranking second. However, treatment guidelines are largely based on adult guidelines and expert consensus. Future research has to put emphasis on understanding pathophysiology, defining specific treatment options, and providing evidence for treatment guidelines in paediatric stroke.

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Book chapters on the topic "Consensus sequence"

1

Ruan, Jianhua. "Consensus Sequence." In Encyclopedia of Systems Biology, 487. New York, NY: Springer New York, 2013. http://dx.doi.org/10.1007/978-1-4419-9863-7_333.

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Gooch, Jan W. "Consensus Sequence." In Encyclopedic Dictionary of Polymers, 884. New York, NY: Springer New York, 2011. http://dx.doi.org/10.1007/978-1-4419-6247-8_13457.

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Valášek, Leoš Shivaya. "Kozak Consensus Sequence." In Encyclopedia of Systems Biology, 1087. New York, NY: Springer New York, 2013. http://dx.doi.org/10.1007/978-1-4419-9863-7_1265.

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Aitken, Alastair. "Protein Consensus Sequence Motifs." In Protein Sequencing Protocols, 465–85. Totowa, NJ: Humana Press, 2003. http://dx.doi.org/10.1385/1-59259-342-9:465.

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Piech, Henryk. "Sequence Automata for Researching Consensus Levels." In Lecture Notes in Computer Science, 82–101. Berlin, Heidelberg: Springer Berlin Heidelberg, 2012. http://dx.doi.org/10.1007/978-3-642-34645-3_4.

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Piech, Henryk. "Sequence Automata for Researching Consensus Levels." In Agent and Multi-Agent Systems: Technologies and Applications, 251–60. Berlin, Heidelberg: Springer Berlin Heidelberg, 2011. http://dx.doi.org/10.1007/978-3-642-22000-5_27.

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Kociumaka, Tomasz, Jakub W. Pachocki, Jakub Radoszewski, Wojciech Rytter, and Tomasz Waleń. "On the String Consensus Problem and the Manhattan Sequence Consensus Problem." In String Processing and Information Retrieval, 244–55. Cham: Springer International Publishing, 2014. http://dx.doi.org/10.1007/978-3-319-11918-2_24.

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Kashkoush, Mohamed, and Hoda A. ElMaraghy. "Generating Master Assembly Sequence Using Consensus Trees." In Enabling Manufacturing Competitiveness and Economic Sustainability, 261–66. Cham: Springer International Publishing, 2014. http://dx.doi.org/10.1007/978-3-319-02054-9_44.

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Shyu, Conrad, and James A. Foster. "Evolving Consensus Sequence for Multiple Sequence Alignment with a Genetic Algorithm." In Genetic and Evolutionary Computation — GECCO 2003, 2313–24. Berlin, Heidelberg: Springer Berlin Heidelberg, 2003. http://dx.doi.org/10.1007/3-540-45110-2_124.

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Bodlaender, Hans, Rodney G. Downey, Michael R. Fellows, and Harold T. Wareham. "The parameterized complexity of sequence alignment and consensus." In Combinatorial Pattern Matching, 15–30. Berlin, Heidelberg: Springer Berlin Heidelberg, 1994. http://dx.doi.org/10.1007/3-540-58094-8_2.

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Conference papers on the topic "Consensus sequence"

1

Sahu, Anit Kumar, and Soummya Kar. "Distributed sequence prediction: A consensus+innovations approach." In 2016 IEEE Global Conference on Signal and Information Processing (GlobalSIP). IEEE, 2016. http://dx.doi.org/10.1109/globalsip.2016.7905854.

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Danckaert, A., S. Hazout, and A. J. Valleron. "Automated DNA sequencing and construction of consensus sequence." In Proceedings of the Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE, 1988. http://dx.doi.org/10.1109/iembs.1988.94560.

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Al Khatib, Hebah A., Fatiha M. Benslimane, Israa El Bashir, Asmaa A. Al Thani, and Hadi M. Yassine. "Within-Host Diversity of SARS-Cov-2 in COVID-19 Patients with Variable Disease Severities." In Qatar University Annual Research Forum & Exhibition. Qatar University Press, 2020. http://dx.doi.org/10.29117/quarfe.2020.0280.

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Background: The ongoing pandemic of SARS-COV-2 has already infected more than eight million people worldwide. The majority of COVID-19 patients are either asymptomatic or have mild symptoms. Yet, about 15% of the cases experience severe complications and require intensive care. Factors determining disease severity are not yet fully characterized. Aim: Here, we investigated the within-host virus diversity in COVID-19 patients with different clinical manifestations. Methods: We compared SARS-COV-2 genetic diversity in 19 mild and 27 severe cases. Viral RNA was extracted from nasopharyngeal samples and sequenced using Illumina MiSeq platform. This was followed by deep-sequencing analyses of SARS-CoV-2 genomes at both consensus and sub-consensus sequence levels. Results: Consensus sequences of all viruses were very similar, showing more than 99·8% sequence identity regardless of the disease severity. However, the sub-consensus analysis revealed significant differences in within-host diversity between mild and severe cases. Patients with severe symptoms exhibited a significantly (p-value 0.001) higher number of variants in coding and non-coding regions compared to mild cases. Analysis also revealed higher prevalence of some variants among severe cases. Most importantly, severe cases exhibited significantly higher within-host diversity (mean= 13) compared to mild cases (mean=6). Further, higher within-host diversity was observed in patients above the age of 60 compared to the younger age group. Conclusion: These observations provided evidence that within-host diversity might play a role in the development of severe disease outcomes in COVID19 patients; however, further investigations is required to elucidate this association.

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Cull, P., and J. L. Holloway. "Optimistically building a consensus sequence using F-inexact matches (DNA)." In Proceedings of the Twenty-Fifth Hawaii International Conference on System Sciences. IEEE, 1992. http://dx.doi.org/10.1109/hicss.1992.183217.

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Haghpanahi, Masoumeh, Reza Sameni, and David A. Borkholder. "Scoring consensus of multiple ECG annotators by optimal sequence alignment." In 2014 36th Annual International Conference of the IEEE Engineering in Medicine and Biology Society (EMBC). IEEE, 2014. http://dx.doi.org/10.1109/embc.2014.6943971.

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Mirali, Furugh, and Herbert Werner. "A Novel Sequence Weighting Method for First-Order Consensus Problems." In 2018 IEEE Conference on Decision and Control (CDC). IEEE, 2018. http://dx.doi.org/10.1109/cdc.2018.8619131.

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Dongardive, Jyotshna, and Siby Abraham. "Finding consensus by sequence evolution: An application of Differential evolution." In 2012 World Congress on Information and Communication Technologies (WICT). IEEE, 2012. http://dx.doi.org/10.1109/wict.2012.6409083.

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Yuan, Ye, Yiwen Zhao, Ming Su, Gang Wang, and Xiaoguang Liu. "A New PoW Consensus of Blockchain Based on Legendre Sequence." In 2022 IEEE International Conference on Blockchain (Blockchain). IEEE, 2022. http://dx.doi.org/10.1109/blockchain55522.2022.00033.

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Yao, Dengfeng, Minghu Jiang, Xu You, Abudoukelimu Abulizi, and Renkui Hou. "An algorithm of multiple sequence alignment based on consensus sequence searched by simulated annealing and star alignment." In 2015 International Symposium on Bioelectronics and Bioinformatics (ISBB). IEEE, 2015. http://dx.doi.org/10.1109/isbb.2015.7344909.

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Shen, Xiaohu, Manohar Shamaiah, and Haris Vikalo. "Message passing algorithm for inferring consensus sequence from next-generation sequencing data." In 2013 IEEE International Symposium on Information Theory (ISIT). IEEE, 2013. http://dx.doi.org/10.1109/isit.2013.6620503.

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Reports on the topic "Consensus sequence"

1

Montville, Thomas J., and Roni Shapira. Molecular Engineering of Pediocin A to Establish Structure/Function Relationships for Mechanistic Control of Foodborne Pathogens. United States Department of Agriculture, August 1993. http://dx.doi.org/10.32747/1993.7568088.bard.

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This project relates the structure of the bacteriocin molecule (which is genetically determined) to its antimicrobial function. We have sequenced the 19,542 bp pediocin plasmid pMD136 and developed a genetic transfer system for pediococci. The pediocin A operon is complex, containing putative structural, immunity, processing, and transport genes. The deduced sequence of the pediocin A molecule contains 44 amino acids and has a predicted PI of 9.45. Mechanistic studies compared the interaction of pediocin PA-1 and nisin with Listeria monocytgenes cells and model lipid systems. While significant nisin-induced intracellular ATP depletion is caused by efflux, pediocin-induced depletion is caused exclusively by hydrolysis. Liposomes derived from L. monocytogenes phospholipids were used to study the physical chemistry of pediocin and nisin interactions with lipids. Their different pH optima are the results of different specific ionizable amino acids. We generated a predicted 3-D structural model for pediocin PA-1 and used a variety of mutant pediocins to demonstrate that the "positive patch" at residues 11 and 12 (and not the YGNGV consensus sequence) is responsible for the binding step of pediocin action. This structure/function understanding gained here provides necessary prerequisites to the more efficacious use of bacteriocins to control foodborne pathogens.

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Shapira, Roni, Judith Grizzle, Nachman Paster, Mark Pines, and Chamindrani Mendis-Handagama. Novel Approach to Mycotoxin Detoxification in Farm Animals Using Probiotics Added to Feed Stuffs. United States Department of Agriculture, May 2010. http://dx.doi.org/10.32747/2010.7592115.bard.

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T-2 toxin, a toxic product belongs to the trichothecene mycotoxins, attracts major interest because of its severe detrimental effects on the health of human and farm animals. The occurrence of trichothecenes contamination is global and they are very resistant to physical or chemical detoxification techniques. Trichothecenes are absorbed in the small intestine into the blood stream. The hypothesis of this project was to develop a protecting system using probiotic bacteria that will express trichothecene 3-O-acetyltransferase (Tri101) that convert T-2 to a less toxic intermediate to reduce ingested levels in-situ. The major obstacle that we had faced during the project is the absence of stable and efficient expression vectors in probiotics. Most of the project period was invested to screen and isolate strong promoter to express high amounts of the detoxify enzyme on one hand and to stabilize the expression vector on the other hand. In order to estimate the detoxification capacity of the isolated promoters we had developed two very sensitive bioassays.The first system was based on Saccharomyces cerevisiae cells expressing the green fluorescent protein (GFP). Human liver cells proliferation was used as the second bioassay system.Using both systems we were able to prove actual detoxification on living cells by probiotic bacteria expressing Tri101. The first step was the isolation of already discovered strong promoters from lactic acid bacteria, cloning them downstream the Tri101 gene and transformed vectors to E. coli, a lactic acid bacteria strain Lactococcuslactis MG1363, and a probiotic strain of Lactobacillus casei. All plasmid constructs transformed to L. casei were unstable. The promoter designated lacA found to be the most efficient in reducing T-2 from the growth media of E. coli and L. lactis. A prompter library was generated from L. casei in order to isolate authentic probiotic promoters. Seven promoters were isolated, cloned downstream Tri101, transformed to bacteria and their detoxification capability was compared. One of those prompters, designated P201 showed a relatively high efficiency in detoxification. Sequence analysis of the promoter region of P201 and another promoter, P41, revealed the consensus region recognized by the sigma factor. We further attempted to isolate an inducible, strong promoter by comparing the protein profiles of L. casei grown in the presence of 0.3% bile salt (mimicking intestine conditions). Six spots that were consistently overexpressed in the presence of bile salts were isolated and identified. Their promoter reigns are now under investigation and characterization.

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Zhou, Ting, Roni Shapira, Peter Pauls, Nachman Paster, and Mark Pines. Biological Detoxification of the Mycotoxin Deoxynivalenol (DON) to Improve Safety of Animal Feed and Food. United States Department of Agriculture, July 2010. http://dx.doi.org/10.32747/2010.7613885.bard.

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The trichothecene deoxynivalenol (DON, vomitoxin), one of the most common mycotoxin contaminants of grains, is produced by members of the Fusarium genus. DON poses a health risk to consumers and impairs livestock performance because it causes feed refusal, nausea, vomiting, diarrhea, hemolytic effects and cellular injury. The occurrence of trichothecenes contamination is global and they are very resistant to physical or chemical detoxification techniques. Trichothecenes are absorbed in the small intestine into the blood stream. The overall objective of this project was to develop a protecting system using probiotic bacteria that will express trichothecene 3-O-acetyltransferase (Tri101) that convert T-2 to a less toxic intermediate to reduce ingested levels in-situ. The major obstacle that we had faced during the project is the absence of stable and efficient expression vectors in probiotics. Most of the project period was invested to screen and isolate strong promoter to express high amounts of the detoxify enzyme on one hand and to stabilize the expression vector on the other hand. In order to estimate the detoxification capacity of the isolated promoters we had developed two very sensitive bioassays.The first system was based on Saccharomyces cerevisiae cells expressing the green fluorescent protein (GFP). Human liver cells proliferation was used as the second bioassay system.Using both systems we were able to prove actual detoxification on living cells by probiotic bacteria expressing Tri101. The first step was the isolation of already discovered strong promoters from lactic acid bacteria, cloning them downstream the Tri101 gene and transformed vectors to E. coli, a lactic acid bacteria strain Lactococcuslactis MG1363, and a probiotic strain of Lactobacillus casei. All plasmid constructs transformed to L. casei were unstable. The promoter designated lacA found to be the most efficient in reducing T-2 from the growth media of E. coli and L. lactis. A prompter library was generated from L. casei in order to isolate authentic probiotic promoters. Seven promoters were isolated, cloned downstream Tri101, transformed to bacteria and their detoxification capability was compared. One of those prompters, designated P201 showed a relatively high efficiency in detoxification. Sequence analysis of the promoter region of P201 and another promoter, P41, revealed the consensus region recognized by the sigma factor. We further attempted to isolate an inducible, strong promoter by comparing the protein profiles of L. casei grown in the presence of 0.3% bile salt (mimicking intestine conditions). Six spots that were consistently overexpressed in the presence of bile salts were isolated and identified. Their promoter reigns are now under investigation and characterization.

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