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Journal articles on the topic "Consensus sequence"
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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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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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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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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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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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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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Nelson, Adin, Ivelise Rijo, Zhigang Zhang, Andrew D. Zelenetz, and Ariela Noy. "Feasiblity and Implication of Bidirectional Sequencing Using a Multiplex Framework 2 Region Primer for Somatic Mutation Analysis of the Immunoglobulin (IgH) Heavy Chain in Chronic Lymphocytic Leukemia (CLL)." Blood 110, no. 11 (November 16, 2007): 4706. http://dx.doi.org/10.1182/blood.v110.11.4706.4706.
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Abstract Background: A somatic mutation rate of >2% of the immunoglobulin (IgH) heavy chain gene, in comparison to germline DNA, is a positive prognostic indicator in chronic lymphocytic leukemia (CLL). Genomic DNA is amplified using the Biomed-2 multiplex PCR primer set, sequenced in the reverse direction only using a 3′ JH primer, and compared to the germline sequence in VBase, a comprehensive directory of all human germline variable region sequences compiled from over a thousand published sequences. It is unknown whether forward sequencing using the multiplex 5′ Biomed-2 primers in a single reaction is feasible or whether doing so improves the accuracy of the mutational analysis. Methods: DNA was extracted from peripheral blood or bone marrow mononuclear cells from patients with CLL using the QIAGEN QIAspin DNA mini-kit. The FR2 region of the IgH gene was amplified using tube B of the Biomed-2 multiplex PCR primer set, separated in 2% agarose gel, excised, and prepared for sequencing using the QIAGEN QIAquick gel extraction kit. Bidirectional DNA sequencing was performed with the full set of multiplex 5′ FR2 primers combined in one reaction for the forward sequence and in a second reaction with the Biomed-2 3′ JH primer for the reverse sequence. A consensus sequence was obtained and mutation rates were calculated based on the consensus sequence and the reverse sequence separately. Results: The FR2 region was amplified from 30 CLL patients. 20 samples produced bidirectional consensus DNA sequences, 2 sequenced only with multiplex FR2 primers, 6 sequenced only with a JH primer, and 2 produced no sequences. Compared with unidirectional JH sequencing, bidirectional sequencing did not reassign any patient in the germline IgH group to the mutated category. In 15 patients, the uni- and bi-directional sequencing were identical. In 4 patients, a single basepair difference was noted. A random permutation test yields a two-sided p-value as 12.5%, indicating that no significant difference was detected between the uni- and bi-directional sequencing. Multiplex bidirectional sequencing did provide sequence information within the CDR3 region at the 3′ terminus of the amplimer which is partially truncated when using the JH primer alone. Conclusion: Bidirectional sequencing does not provide a somatic IgH mutation rate that differs significantly from that obtained from the reverse sequence alone and does not likely influence the IgH mutational prognostic assignment. Nonetheless, the bidirectional consensus sequence adds bases in the CDR3 region which can be used for research applications such as the generation of patient-specific primers for PCR. It is also noteworthy that multiplex PCR using the Biomed-2 primers is feasible.
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.<br>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.<br>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.<br>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.<br>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<br>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.<br>Thesis (PhD Doctorate)<br>Doctor of Philosophy (PhD)<br>School of Biomolecular and Biomedical Sciences<br>Science, Environment, Engineering and Technology<br>Full Text
Books on the topic "Consensus sequence"
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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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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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Kurt, Bayertz, ed. The Concept of moral consensus: The case of technological interventions in human reproduction. Dordrecht: Kluwer Academic Publishers, 1994.
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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.
Book chapters on the topic "Consensus sequence"
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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.
Full textConference papers on the topic "Consensus sequence"
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Jie, Penghai, and Jing Zhu. "Optimal Denial-of-Service Attack Sequence towards the Consensus of Multi-Agent Systems." In 2024 4th International Conference on Control Theory and Applications (ICoCTA), 286–90. IEEE, 2024. https://doi.org/10.1109/icocta64736.2024.00061.
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Bartos, Milan, SaadedineTebbal, Jorge Pacheco, Tracey Jackson, and Nathan Davis. "Surface Preparation of Test Specimens and Its Impact on Localized Corrosion." In CORROSION 2020, 1–14. NACE International, 2020. https://doi.org/10.5006/c2020-14844.
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Abstract Laboratory qualification of corrosion inhibitors for oilfield applications is a multistage process consisting of a suite of performance and compatibility tests mimicking the field conditions as closely as possible. The final and often decisive step in this sequence is typically a longer-term test focusing on the performance of corrosion inhibitor candidates against localized corrosion. Despite its fundamental importance in the decision-making process, there is currently no consensus in the industry about the definition of localized corrosion and the pass/fail criteria for tested inhibitors. This paper provides a brief summary of the different views and opinions about this subject currently adopted by various producers, chemical vendors and independent third- party labs with an emphasis on the potential relationship between surface characteristics of corrosion samples and initiation and propagation of localized corrosion.
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Sousa, Maria J. P., Armando J. Pinho, and Diogo Pratas. "Improving the Generation of Viral Consensus Sequences Using Adaptive Models." In 2024 32nd European Signal Processing Conference (EUSIPCO), 1691–95. IEEE, 2024. http://dx.doi.org/10.23919/eusipco63174.2024.10715352.
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Guha, Soumee, Lisa S. Berlizova, Zongli Lin, and Scott T. Acton. "Dynamic Average Consensus for Improving Classifier Accuracy for Multi-Camera Video Sequences." In 2024 58th Asilomar Conference on Signals, Systems, and Computers, 475–79. IEEE, 2024. https://doi.org/10.1109/ieeeconf60004.2024.10942702.
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Senkowski, E. Bud. "Corrosion: the Destructive Stowaway on Marine Vessels Determining the Cost-Benefit of Protective Marine Coating Systems." In SSPC 2015 Greencoat, 1–26. SSPC, 2015. https://doi.org/10.5006/s2015-00056.
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Abstract Marine coating systems installed aboard commercial and military vessels are exposed to extremely aggressive environmental conditions during maritime operation. A key element in prolonging the useful life of any ship, both commercial and military, lies in the selection and installation of cost-effective corrosion control methods and materials at newbuild, followed by an effective painting and preservation program to minimize the corrosive effects of operating in a marine environment, extend the service life and maintenance requirements of the installed systems, and thereby reduce the total operating cost (TOC) for the vessel. This paper provides guidelines for calculating approximate installed costs of coating systems, expected coating service lives for each system identified, and methods for determining the most cost-effective systems to use, the effect of maintenance sequences on long-term costs and system performance is also reviewed. The analysis utilizes trade studies from coating manufacturers, scholarly papers, technical reports, engineering studies and specifications from maritime and naval sources, and technical and consensus organizations that focus on the design, implementation, and testing of marine coating systems. New coating technologies that show promise of providing enhanced corrosion protection are identified and their relative contribution to lowering the operational costs of shipboard systems are demonstrated through the use of software programs that predict coating service life and maintenance requirements following initial installation. Corrosion is the silent stowaway that travels on every ship, regardless of their design or nature of maritime service. A key element in prolonging the useful life of any ship, both military and commercial, lies in the selection and installation of cost-effective corrosion control methods and materials during initial construction, followed by an effective painting and preservation program to minimize the corrosive effects of operating in a marine environment. Marine coating systems installed aboard commercial and military vessels are exposed to extremely aggressive environmental conditions during maritime operation. They include exposures to: seawater, freeze/thaw cycling, the ultraviolet component of sunlight, mechanical damage, stack exhaust, temperature extremes, erosion, and more. Marine vessels, whether they are in commercial or military service, contain common elements in their construction. These areas include: topsides and superstructure, deck, interior crew spaces, cargo hold, cargo tanks, ballast tanks, and underwater hull. Coating manufacturers, commercial shipping consensus organizations, and the international military community have identified paints and specialized coating systems with superior performance, durability, and economic effectiveness for maritime service.i,ii Important factors like ship mission, operating schedules, areas of operation, and drydocking intervals for maintenance will also influence the selection and type of coating system to be applied. With the development of high strength steels, scantling dimensions have been reduced to lower the weight of vessels to reduce fuel consumption. However reduced plate thicknesses have increased the potential of structural failure through corrosion. Coating selection will also impact the cleaning and painting requirements for the shipboard maintenance of painted surfaces. Additionally, the corrosion the protective coating systems over various substrates have also been evaluated. These factors have been considered during the course of this study. Coating repairs at sea are regarded as temporary and when detected, only made to avoid component failure before laying up the vessel for depot repairs. For instance, ballast tanks cannot be inspected unless they are drained and cleaned. These operations are typically performed when the vessel is in for shipyard or depot repairs. Over the past 40 years, new technologies in protective coatings and preservation systems for marine applications have been developed that show promise of providing greater corrosion protection and reduced maintenance. A plethora of data exists in such information sources as: trade studies from coating manufacturers, scholarly papers, technical reports, engineering studies and specifications from such organizations and agencies as: Naval Sea System Command (NAVSEA), Office of Naval Research (ONR), department of Department of Defense (DoD), US Bureau of Ships, National Association of Corrosion Engineers (NACE) Symposia, Marine industry Symposia, Military Sealift Command (MSC), International Maritime Organization) IMO, National Institute for Standards and Technology (NIST), American Bureau of Shipping (ABS), U.S. Corps of Engineers, American Society for Testing and Materials (ASTM), International Standards Organization (ISO), and the Society for Protective Coatings (SSPC). Existing statistical methodology was used to develop information relative to the prediction of coating service life and maintenance requirements following initial installation. A principal source in this area was data published by the SSPC and NACE.
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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.
Full textReports on the topic "Consensus sequence"
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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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MR MSK Cartilage for Joint Disease, Consensus Profile. Chair Thomas Link and Xiaojuan Li. Radiological Society of North America (RSNA) / Quantitative Imaging Biomarkers Alliance (QIBA), September 2021. http://dx.doi.org/10.1148/qiba/20210925.
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The goal of a QIBA Profile is to help achieve a useful level of performance for a given biomarker. The Claim (Section 2) describes the biomarker performance. The Activities (Section 3) contribute to generating the biomarker. Requirements are placed on the Actors that participate in those activities as necessary to achieve the Claim. Assessment Procedures (Section 4) for evaluating specific requirements are defined as needed. This QIBA Profile (MR-based cartilage compositional biomarkers (T1ρ, T2) ) addresses the application of T1ρ and T2 for the quantification of cartilage composition, which can be used as an imaging biomarker to diagnose, predict and monitor early osteoarthritis. It places requirements on Acquisition Devices, Technologists, MRI Physicists, Radiologists, Reconstruction Software and Image Analysis Tools involved in Subject Handling, Image Data Acquisition, Image Data Reconstruction, Image Quality Assurance (QA) and Image Analysis. The requirements are focused on achieving sufficient reproducibility and accuracy for measuring cartilage composition. The clinical performance target is to achieve a reproducibility of 4-5% for measurements of global cartilage composition with T2 and T1ρ relaxation time measurements and a 95% confidence level for a true/critical change in cartilage composition (least significant change) with a precision of 11-14% and 9-12% if only an increase is expected (claim is one-sided). The target applies to 3T MR scanners of one manufacturer with identical scan parameters across different sites. It does not apply to scanners from different manufacturers. This document is intended to help clinicians basing decisions on this biomarker, imaging staff generating this biomarker, vendor staff developing related products, purchasers of such products and investigators designing trials with imaging endpoints. Note that this document only states requirements to achieve the claim, not “requirements on standard of care.” Conformance to this Profile is secondary to properly caring for the patient. Summary for Clinical Trial Use The MR-based cartilage compositional biomarkers profile defines the behavioral performance levels and quality control specifications for T1ρ, T2 scans used in single- and multi-center clinical trials of osteoarthritis and other trials assessing cartilage composition longitudinally with a focus on therapies to treat degenerative joint disease. While the emphasis is on clinical trials, this process is also intended to be applied for clinical practice. The specific claims for accuracy are detailed below in the Claims. The specifications that must be met to achieve conformance with this Profile correspond to acceptable levels specified in the T1ρ, T2 Protocols. The aim of the QIBA Profile specifications is to minimize intra- and inter-subject, intra- and inter-platform, and interinstitutional variability of quantitative scan data due to factors other than the intervention under investigation. T1ρ and T2 studies performed according to the technical specifications of this QIBA Profile in clinical trials can provide quantitative data for single timepoint assessments (e.g. disease burden, investigation of predictive and/or prognostic biomarker(s)) and/or for multi-time-point comparative assessments (e.g., response assessment, investigation of predictive and/or prognostic biomarkers of treatment efficacy). A motivation for the development of this Profile is that while a typical MR T1ρ and T2 measurement may be stable over days or weeks, this stability cannot be expected over the time that it takes to complete a clinical trial. In addition, there are well known differences between scanners and the operation of the same type of scanner at different imaging sites. The intended audiences of this document include: Biopharmaceutical companies, rheumatologists and orthopedic surgeons, and clinical trial scientists designing trials with imaging endpoints. Clinical research professionals. Radiologists, technologists, physicists and administrators at healthcare institutions considering specifications for procuring new MRI equipment for cartilage measurements. Radiologists, technologists, and physicists designing T1ρ and T2 acquisition protocols. Radiologists, and other physicians making quantitative measurements from T1ρ and T2 sequence protocols. Regulators, rheumatologists, orthopedic surgeons, and others making decisions based on quantitative image measurements. Technical staff of software and device manufacturers who create products for this purpose. Note that specifications stated as 'requirements' in this document are only requirements to achieve the claim, not 'requirements on standard of care.' Specifically, meeting the goals of this Profile is secondary to properly caring for the patient.
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Sherman, A., D. N. Kuhn, Y. Cohen, R. Ophir, and R. Goenaga. Exploring the polyembryonic seed trait in mango as a basis for a biotechnology platform for fruit tree crops. Israel: United States-Israel Binational Agricultural Research and Development Fund, 2021. http://dx.doi.org/10.32747/2021.8134176.bard.
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Mango is one of the most important fruit crops. However, the biology of this fruit tree is under studied. The lack of genetic and genomic resources has limited progress in mango research and breeding. Several research groups have recently started developing genomic tools for mango by creating transcriptome and genomic data. Sexual reproduction in plants is the main pathway for the creation of new genetic combinations. In modern agriculture, breeders exploit the genetic diversity generated through sexual reproduction to develop elite cultivars; however, these cultivars require genetic stabilization before they are suitable for mass propagation for uniform crop production. In heterozygous plants such as fruit trees, vegetative propagation (cloning) is the primary path for the propagation of genetically uniform plants. Another natural plant mechanism that can create genetically uniform plants (clones) is apomixes. Apomixis is defined as asexual reproduction through seeds that lead to the production of clonal progeny whose genotype is identical to that of the mother plant. In fruit crops like citrus and mango, sporophytic apomixes result in polyembryony, where seeds contain multiple embryos, one of which is sexually originated, and the others are clones of the mother tree. As part of this research, the reference genome of mango was established as a basic platform for mango breeding and research. It was used to map two important mango traits fruit size and polyembryony. The draft genome 'Tommy Atkins' sequence was generated using NRGene de-novo Magic on high molecular weight DNA of 'Tommy Atkins,' supplemented by 10X Genomics long read sequencing to improve the initial assembly. The final 'Tommy Atkins' genome assembly was a consensus sequence that included 20 pseudomolecules representing the 20 chromosomes of mango. The availability of a genome enables the genetic dissection of important traits. We demonstrated the utility of the genome assembly and the 'Tommy Atkins' x 'Kensington Pride' map by analyzing fruit weight phenotypic data and identifying two QTLs for this trait.
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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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Walker, Michael, Gill Holcombe, Clare Mills, Chiara Nitride, and Adrian Rogers. Development of Reference Materials for food allergen analysis. Food Standards Agency, June 2023. http://dx.doi.org/10.46756/sci.fsa.hwt621.
Full textAbstract:
Food hypersensitivity is an increasing problem for many stakeholders with much effort focused on assessment and management of the risks including risk assessment toolkits (for example, the Allergen Bureau (Opens in a new window) Voluntary Incidental Trace Allergen Labelling VITAL®, the iFAAM consortium (Opens in a new window) and the ILSI-Europe Allergen Quantitative Risk Assessment guidance (Opens in a new window)). These toolkits describe the use of action levels and reference doses to assess the risks. A combination of the estimated eliciting dose of allergenic food, (in milligrams as protein) and the amount of food consumed in a single eating occasion can give a threshold or action level as milligrams (as protein) per kilogram (kg) of food) (mg kg-1 as protein) that would provoke an reaction in a given proportion of the allergic population. The eliciting dose is extrapolated from oral food clinical dose-distribution relationships. The results of analysis can be compared to the thresholds or action levels in risk assessment and risk management. Precautionary allergen labelling, well recognized as sub-optimal, could also be improved via an action level approach. Implementation and regulation depend on the ability to measure allergens properly; yet all current analytical approaches exhibit deficiencies, many of which can be addressed by the proper use of appropriate allergen reference materials (RMs). This report describes a pilot project to: 1) Systematically review allergen analytical targets used in ELISA, PCR and MS to allow the creation of a repository of reliable markers and open access verified allergen sequence sets for the studied allergens; 2) Facilitate a guided stakeholder workshop to achieve consensus on priority allergens, physical format of RMs, incurred concentrations and impact of processing; 3) Prepare a RM kit containing (a) a food matrix shown to be devoid of the target allergens, (b) the food matrix incurred with 5 allergens and (c) the raw materials (the allergenic foods); 4) Disseminate to encourage RM use to achieve tangible improvements in allergen analysis, establish a template of best practice for the future and make recommendations for follow up work to complete a set of RMs for the legislated and priority allergens. The RM matrix is based on that used for clinical dose-distribution studies and the raw allergen materials have been characterised by proteomics. The matrix and incurred allergens are industrially relevant to processed foods and the allergen concentrations are clinically relevant in the light of eliciting dose studies. The RM kit has been prepared following a well-established process that includes prescribed homogeneity and stability studies and a formal sign-off procedure of the statements of measurement, in accordance with ISO 17034:2016 ‘General requirements for the competence of reference material producers’ (an updated standard originally ISO GUIDE 34:2009). In October 2020 following detailed external assessment the RM kit was confirmed within the NML scope of ISO 17034 accreditation. ISO 17034:2016 covers the production of all reference materials, including certified reference materials. It is intended as part of the general quality assurance procedures of the reference material producer. LGC formed a consortium which was awarded this project by the FSA following an open competitive tender. The consortium consisted of LGC, the University of Manchester and Romer Laboratories Ltd. The consortium is world leading in (a) the preparation, curation and distribution of RMs in an accredited environment and (b) the characterisation of allergen proteins. Synergy with other concurrent work (for example, by iFAAM, EFSA, ILSI, MoniQA, JRC, and AOAC) has ensured value for money. This report has been compiled from a review of a broad range of data sources including: the scientific literature the tender documents progress reports and minutes of project meetings LGC internal documents and in particular the Material Report[1] UoM reports Romer Lab reports.
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Severe Cutaneous Adverse Reactions. A consensus by a CIOMS Working Group. CIOMS, April 2025. https://doi.org/10.56759/lrty1600.
Full textAbstract:
In clinical practice, there is mounting concern about the burden of SCAR in relation to novel biologics as well as the increasing cost of diagnosis and management. This consensus report provides unique insights and the latest thinking from renowned experts on this important topic. The skin is among the parts of the body most commonly affected by adverse drug reactions (ADRs). Cutaneous ADRs affect 2% to 3% of all hospitalized patients and have a wide spectrum of clinical manifestations, are caused by various medicinal products, and result from different pathophysiologic mechanisms. Hence, their diagnosis and management are challenging. However, approximately 0.1% to 1% of patients with medicinal product eruptions have serious ADRs which can lead to disabling sequelae and in some cases, fatalities. Although Severe Cutaneous Adverse Reactions (SCAR) are rare, they are a significant health challenge and hinder the safe and effective use of medicines. In short, they pose substantial hurdles to drug developers, medicines regulators and health professionals. SCAR include Stevens-Johnson syndrome (SJS), toxic epidermal necrolysis (TEN), drug reaction with eosinophilia and systemic symptoms (DRESS), acute generalized exanthematous pustulosis (AGEP), and generalized bullous fixed drug eruptions (GBFDE). Premarketing randomized clinical trials have limited power to detect SCAR. There is also a lack of specific diagnostic tests for SCAR, which today, depend on subjective causality assessment methods. These factors highlight the urgent need for guidelines, including how to predict, prevent, detect and diagnose SCAR either during drug development or in the post-marketing phase.