Relevant bibliographies by topics / Protein Sequence Analysis

Contents

  1. Journal articles
  2. Dissertations / Theses
  3. Books
  4. Book chapters
  5. Conference papers
  6. Reports

Academic literature on the topic 'Protein Sequence Analysis'

Author: Grafiati
Published: 4 June 2021
Last updated: 29 July 2024

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Journal articles on the topic "Protein Sequence Analysis"

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Plasterer, Thomas N. "PROTEAN: Protein Sequence Analysis and Prediction." Molecular Biotechnology 16, no. 2 (2000): 117–26. http://dx.doi.org/10.1385/mb:16:2:117.

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Johri, Parul, Mala Trivedi, and Sujeet Pratap Singh. "Atom based Profiling and Functional Enrichment analysis of Aquaporins." Research Journal of Biotechnology 16, no. 10 (September 25, 2021): 75–77. http://dx.doi.org/10.25303/1610rjbt7577.

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Sequence analysis is a computational biology method to study protein sequences by comparing amino acids of one protein sequence with the other (residual level comparison). This study reveals a new concept of comparing protein sequences at their basic atomic level. Aquaporins from various origin were compared at their atomic level and the study revealed that all the aquaporin proteins have a closed range of 31.0% to 34.2% of carbon atoms irrespective of their origin and amino acid sequence. Further the protein interaction and functional enrichment analysis of AQP7 showed significant interaction with glycerol kinase and ATP-sensitive inward rectifier potassium channel protein. Our insilico analysis on aquaporin proteins exposed that nature tends to maintain the overall carbon atom composition in the proteins regardless of their amino acid sequence composition which could be further used for their classification. Also, the most highly interacting partners for AQPs are the potassium buffering channel proteins.
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Kumari, Uma, Aastha Tanwar, Jositta George, and Daityari Nayak. "NGS Analysis to Detect Mutation in Brain Tumor Diagnostic." International Journal for Research in Applied Science and Engineering Technology 11, no. 7 (July 31, 2023): 1394–402. http://dx.doi.org/10.22214/ijraset.2023.54895.

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Abstract: This study presents an integrated computational approach for analyzing protein sequences and their 3D structures. By leveraging the MMDB Macromolecular database, homologs of a protein sequence of interest are identified, and interactive visualization of their structural properties is provided. The computational alignment method, using BLASTP, allows for efficient determination of sequence similarities and identification of conserved regions among multiple protein sequences. COBALT is employed to refine sequence alignments and facilitate graphical analysis of sequence relationships. RASMOL, a computational analysis program, generates 2-D representations of protein-ligand complexes, enabling visual exploration of their interactions. ORF finder is used to identify coding regions in mRNA sequences, aiding in the prediction of protein-coding regions. The approach is applied to brain tumor diagnostics using human biological samples, exploring the structural properties of brain tumor-related proteins with the help of the 2RHU protein structure and PYMOL visualization software. Overall, this integrated computational framework offers a comprehensive toolkit for protein sequence analysis, structure visualization, and homology modeling, with potential applications in drug discovery, molecular biology, and medical diagnostics
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Reguant, Roc, Yevgeniy Antipin, Rob Sheridan, Christian Dallago, Drew Diamantoukos, Augustin Luna, Chris Sander, and Nicholas Paul Gauthier. "AlignmentViewer: Sequence Analysis of Large Protein Families." F1000Research 9 (March 27, 2020): 213. http://dx.doi.org/10.12688/f1000research.22242.1.

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AlignmentViewer is a web-based tool to view and analyze multiple sequence alignments of protein families. The particular strengths of AlignmentViewer include flexible visualization at different scales as well as analysis of conservation patterns and of the distribution of proteins in sequence space. The tool is directly accessible in web browsers without the need for software installation. It can handle protein families with tens of thousands of sequences and is particularly suitable for evolutionary coupling analysis, e.g. via EVcouplings.org.
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Reguant, Roc, Yevgeniy Antipin, Rob Sheridan, Christian Dallago, Drew Diamantoukos, Augustin Luna, Chris Sander, and Nicholas Paul Gauthier. "AlignmentViewer: Sequence Analysis of Large Protein Families." F1000Research 9 (October 15, 2020): 213. http://dx.doi.org/10.12688/f1000research.22242.2.

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AlignmentViewer is a web-based tool to view and analyze multiple sequence alignments of protein families. The particular strengths of AlignmentViewer include flexible visualization at different scales as well as analysis of conservation patterns and of the distribution of proteins in sequence space. The tool is directly accessible in web browsers without the need for software installation. It can handle protein families with tens of thousands of sequences and is particularly suitable for evolutionary coupling analysis, e.g. via EVcouplings.org.
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Van Reenen, C. A., W. H. Van Zyl, and L. M. T. Dicks. "Expression of the Immunity Protein of Plantaricin 423, Produced by Lactobacillus plantarum 423, and Analysis of the Plasmid Encoding the Bacteriocin." Applied and Environmental Microbiology 72, no. 12 (October 20, 2006): 7644–51. http://dx.doi.org/10.1128/aem.01428-06.

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ABSTRACT Plantaricin 423 is a class IIa bacteriocin produced by Lactobacillus plantarum isolated from sorghum beer. It has been previously determined that plantaricin 423 is encoded by a plasmid designated pPLA4, which is now completely sequenced. The plantaricin 423 operon shares high sequence similarity with the operons of coagulin, pediocin PA-1, and pediocin AcH, with small differences in the DNA sequence encoding the mature bacteriocin peptide and the immunity protein. Apart from the bacteriocin operon, no significant sequence similarity could be detected between the DNA or translated sequence of pPLA4 and the available DNA or translated sequences of the plasmids encoding pediocin AcH, pediocin PA-1, and coagulin, possibly indicating a different origin. In addition to the bacteriocin operon, sequence analysis of pPLA4 revealed the presence of two open reading frames (ORFs). ORF1 encodes a putative mobilization (Mob) protein that is homologous to the pMV158 superfamily of mobilization proteins. Highest sequence similarity occurred between this protein and the Mob protein of L. plantarum NCDO 1088. ORF2 encodes a putative replication protein that revealed low sequence similarity to replication proteins of plasmids pLME300 from Lactobacillus fermentum and pYIT356 from Lactobacillus casei. The immunity protein of plantaricin 423 contains 109 amino acids. Although plantaricin 423 shares high sequence similarity with the pediocin PA-1 operon, no cross-reactivity was recorded between the immunity proteins of plantaricin 423 and pediocin PA-1.
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Nekrasov, Alexei N., Yuri P. Kozmin, Sergey V. Kozyrev, Rustam H. Ziganshin, Alexandre G. de Brevern, and Anastasia A. Anashkina. "Hierarchical Structure of Protein Sequence." International Journal of Molecular Sciences 22, no. 15 (August 3, 2021): 8339. http://dx.doi.org/10.3390/ijms22158339.

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Most non-communicable diseases are associated with dysfunction of proteins or protein complexes. The relationship between sequence and structure has been analyzed for a long time, and the analysis of the sequences organization in domains and motifs remains an actual research area. Here, we propose a mathematical method for revealing the hierarchical organization of protein sequences. The method is based on the pentapeptide as a unit of protein sequences. Employing the frequency of occurrence of pentapeptides in sequences of natural proteins and a special mathematical approach, this method revealed a hierarchical structure in the protein sequence. The method was applied to 24,647 non-homologous protein sequences with sizes ranging from 50 to 400 residues from the NRDB90 database. Statistical analysis of the branching points of the graphs revealed 11 characteristic values of y (the width of the inscribed function), showing the relationship of these multiple fragments of the sequences. Several examples illustrate how fragments of the protein spatial structure correspond to the elements of the hierarchical structure of the protein sequence. This methodology provides a promising basis for a mathematically-based classification of the elements of the spatial organization of proteins. Elements of the hierarchical structure of different levels of the hierarchy can be used to solve biotechnological and medical problems.
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Hansen, Scott G., Lisa I. Strelow, David C. Franchi, David G. Anders, and Scott W. Wong. "Complete Sequence and Genomic Analysis of Rhesus Cytomegalovirus." Journal of Virology 77, no. 12 (June 15, 2003): 6620–36. http://dx.doi.org/10.1128/jvi.77.12.6620-6636.2003.

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ABSTRACT The complete DNA sequence of rhesus cytomegalovirus (RhCMV) strain 68-1 was determined with the whole-genome shotgun approach on virion DNA. The RhCMV genome is 221,459 bp in length and possesses a 49% G+C base composition. The genome contains 230 potential open reading frames (ORFs) of 100 or more codons that are arranged colinearly with counterparts of previously sequenced betaherpesviruses such as human cytomegalovirus (HCMV). Of the 230 RhCMV ORFs, 138 (60%) are homologous to known HCMV proteins. The conserved ORFs include the structural, replicative, and transcriptional regulatory proteins, immune evasion elements, G protein-coupled receptors, and immunoglobulin homologues. Interestingly, the RhCMV genome also contains sequences with homology to cyclooxygenase-2, an enzyme associated with inflammatory processes. Closer examination identified a series of candidate exons with the capacity to encode a full-length cyclooxygenase-2 protein. Counterparts of cyclooxygenase-2 have not been found in other sequenced herpesviruses. The availability of the complete RhCMV sequence along with the ability to grow RhCMV in vitro will facilitate the construction of recombinant viral strains for identifying viral determinants of CMV pathogenicity in the experimentally infected rhesus macaque and to the development of CMV as a vaccine vector.
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Chang, P. C., M. L. Hsieh, J. H. Shien, D. A. Graham, M. S. Lee, and H. K. Shieh. "Complete nucleotide sequence of avian paramyxovirus type 6 isolated from ducks." Journal of General Virology 82, no. 9 (September 1, 2001): 2157–68. http://dx.doi.org/10.1099/0022-1317-82-9-2157.

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There are nine serotypes of avian paramyxovirus (APMV). Only the genome of APMV type 1 (APMV-1), also called Newcastle disease virus (NDV), has been completely sequenced. In this study, the complete nucleotide sequence of an APMV-6 serotype isolated from ducks is reported. The 16236 nt genome encodes eight proteins, nucleocapsid protein (NP), phosphoprotein (P), V protein, matrix protein (M), fusion protein (F), small hydrophobic (SH) protein, haemagglutinin–neuraminidase (HN) protein and large (L) protein, which are flanked by a 55 nt leader sequence and a 54 nt trailer sequence. Sequence comparison reveals that the protein sequences of APMV-6 are most closely related to those of APMV-1 (NDV) and -2, with sequence identities ranging from 22 to 44%. However, APMV-6 contains a gene that might encode the SH protein, which is absent in APMV-1, but present in the rubulaviruses simian virus type 5 and mumps virus. The presence of an SH gene in APMV-6 might provide a link between the evolution of APMV and rubulaviruses. Phylogenetic analysis demonstrates that APMV-6, -1, -2 (only the F and HN sequences were available for analysis) and -4 (only the HN sequences were available for analysis) all cluster into a single lineage that is distinct from other paramyxoviruses. This result suggests that APMV should constitute a new genus within the subfamily Paramyxovirinae.
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Kerim, Tursun, Nijat Imin, Jeremy J. Weinman, and Barry G. Rolfe. "Proteomic analysis reveals developmentally expressed rice homologues of grass group II pollen allergens." Functional Plant Biology 30, no. 8 (2003): 843. http://dx.doi.org/10.1071/fp03100.

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Three isoallergens of Ory s 2, homologues of grass group II pollen allergens, were identified from rice and characterised by proteome and immunochemical analyses. The N-terminal amino acid sequence profiles of three proteins on a 2-dimensional electrophoresis (2-DE) gel of rice pollen proteins matched 100% to the protein sequences encoded by three rice expressed sequence tags (ESTs). The deduced protein sequences from these ESTs share sequence identities of 41–43% with the protein sequences of the group II pollen allergens of different grasses, and sequence identity of 39% with the C-terminal portion of rice group I pollen allergens. Signal peptide sequences, which are similar to the leader peptides of other major pollen allergens, are also present in the deduced amino acid sequences. Polyclonal antibodies, produced in rabbits using Ory s 2 proteins purified by 2-DE, were used to investigate the developmental-stage- and tissue-specific expression of Ory s 2 by immunochemical analysis. Results of immunochemical experiments show that Ory s 2 proteins are expressed only at the late stage of pollen development and they do not have cross-reactivity with group II pollen allergens from some other common grasses.
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Dissertations / Theses on the topic "Protein Sequence Analysis"

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Abhiman, Saraswathi. "Prediction of function shift in protein families /." Stockholm, 2006. http://diss.kib.ki.se/2006/91-7140-869-X/.

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Parsons, Jeremy David. "Computer analysis of molecular sequences." Thesis, University of Cambridge, 1993. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.282922.

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Boscott, Paul Edmond. "Sequence analysis in protein structure prediction." Thesis, University of Oxford, 1994. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.386870.

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Hollich, Volker. "Orthology and protein domain architecture evolution /." Stockholm, 2006. http://diss.kib.ki.se/2006/91-7140-783-9/.

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Lassmann, Timo. "Algorithms for building and evaluating multiple sequence alignments /." Stockholm, 2006. http://diss.kib.ki.se/2006/91-7140-887-8/.

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Tuason, Maria Clarita. "Functional analysis of Proteolipid Protein regulatory sequence." Thesis, McGill University, 2006. http://digitool.Library.McGill.CA:80/R/?func=dbin-jump-full&object_id=101805.

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Myelin is an evolutionarily late acquisition of the vertebrate nervous system which speeds electrochemical signaling in mature nerve fibers by providing insulation in the form of a lipid-rich multilammelar sheath. Proteolipid Protein (PLP) is the most abundant protein in mature mammalian central nervous system myelin where it serves as a structural component in addition to other yet undefined roles. It is coordinately regulated at the transcriptional level with other myelin genes such as Myelin Basic Protein (MBP). The major components of MBP transcriptional regulation have been defined using a strategy of targeted transgenesis at the hypoxanthine phosphoribosyl transferase (HPRT) locus allowing quantitative and qualitative in vivo analysis of the transcriptional control exerted by conserved non-protein-coding sequences in transgenic mice. This study describes the localization and functional characterization of PLP conserved non-protein-coding sequences. Conservation was surveyed using alignments of genome sequences for a number of vertebrates ranging in their evolutionary distance from mouse. Aligned sequences were also scanned for clusters of conserved consensus binding sites for sox 10, krox20, gtx and betaHLH transcription factors, which play key roles in nervous system development. Dissection of conserved non-protein-coding sequence resulted in the production of a series of 10 reporter constructs addressing the search for PLP regulatory elements. This series includes highly conserved regions, some of which contain clusters of transcription factor consensus sites, as well as lesser conserved regions which were suggested to have regulatory activity in previous investigations. Notably, in vivo evidence of the importance of intron 1 for expression in the nervous system led to subsequent deletion-transfection analyses revealing a seemingly potent enhancer, the antisilencer/enhancer (ASE) within the intron, which is functionally validated in this study. Of this series, 8 of the selected regions have been amplified successfully and cloned into HPRT targeting constructs with a minimal lisp promoter and LacZ reporter. All 8 constructs have been transfected into ES cells. Homologous recombinants with the transgene docked at HPRT were selected, and chimeras have been analyzed for 3 of these constructs. To our surprise, neither a construct containing 2kb of 5' flanking sequence, nor a construct containing the highly conserved intron 3, were able to drive expression at the peak of myelination. A construct containing the ASE was unexpectedly shown to drive expression in cells scattered within the central grey matter of the spinal cord in a pattern intriguingly similar to that seen embryonically from migrating oligodendrocyte progenitors. The lack of expression of the first 2 constructs suggests that PLP regulatory elements may be interdependent, but we anticipate that delivery into germline followed by developmental and analysis of the full series of constructs will bring light to the emerging picture of partnerships between regulatory elements, and will also reveal the identity of the cells driving expression from the ASE. Understanding PLP transcriptional control may lead to therapeutic interventions as associated diseases result predominantly from imbalances in gene dosage leading to abnormal levels of PLP protein.
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Russell, Robert Bruce. "Computer analysis of protein sequence and structure." Thesis, University of Oxford, 1993. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.358736.

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Hamby, Stephen Edward. "Data mining techniques for protein sequence analysis." Thesis, University of Nottingham, 2010. http://eprints.nottingham.ac.uk/11498/.

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This thesis concerns two areas of bioinformatics related by their role in protein structure and function: protein structure prediction and post translational modification of proteins. The dihedral angles Ψ and Φ are predicted using support vector regression. For the prediction of Ψ dihedral angles the addition of structural information is examined and the normalisation of Ψ and Φ dihedral angles is examined. An application of the dihedral angles is investigated. The relationship between dihedral angles and three bond J couplings determined from NMR experiments is described by the Karplus equation. We investigate the determination of the correct solution of the Karplus equation using predicted Φ dihedral angles. Glycosylation is an important post translational modification of proteins involved in many different facets of biology. The work here investigates the prediction of N-linked and O-linked glycosylation sites using the random forest machine learning algorithm and pairwise patterns in the data. This methodology produces more accurate results when compared to state of the art prediction methods. The black box nature of random forest is addressed by using the trepan algorithm to generate a decision tree with comprehensible rules that represents the decision making process of random forest. The prediction of our program GPP does not distinguish between glycans at a given glycosylation site. We use farthest first clustering, with the idea of classifying each glycosylation site by the sugar linking the glycan to protein. This thesis demonstrates the prediction of protein backbone torsion angles and improves the current state of the art for the prediction of glycosylation sites. It also investigates potential applications and the interpretation of these methods.
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Maccallum, Robert Matthew. "Computational analysis of protein sequence and structure." Thesis, University College London (University of London), 1997. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.285202.

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Katti, M. V. "Analysis of simple sequence repeats in genome and protein sequences and development of computational tools for comparative promoter sequence analysis." Thesis(Ph.D.), CSIR-National Chemical Laboratory, Pune, 2001. http://dspace.ncl.res.in:8080/xmlui/handle/20.500.12252/2323.

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Books on the topic "Protein Sequence Analysis"

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Imahori, Kazutomo, and Fumio Sakiyama, eds. Methods in Protein Sequence Analysis. Boston, MA: Springer US, 1993. http://dx.doi.org/10.1007/978-1-4899-1603-7.

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Wittmann-Liebold, Brigitte, ed. Methods in Protein Sequence Analysis. Berlin, Heidelberg: Springer Berlin Heidelberg, 1989. http://dx.doi.org/10.1007/978-3-642-73834-0.

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Jörnvall, Hans, Jan-Olov Höög, and Ann-Margreth Gustavsson, eds. Methods in Protein Sequence Analysis. Basel: Birkhäuser Basel, 1991. http://dx.doi.org/10.1007/978-3-0348-5678-2.

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Hans, Jörnvall, Höög J. -O, Gustavsson A. -M, and International Conference on Methods in Protein Sequence Analysis (8th : 1990 : Kiruna, Sweden), eds. Methods in protein sequence analysis. Basel: Birkhäuser Verlag, 1991.

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Kazutomo, Imahori, Sakiyama Fumio, and International Conference on Methods in Protein Sequence Analysis (9th : 1992 : Otsu, Japan), eds. Methods in protein sequence analysis. New York: Plenum Press, 1993.

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A, Walsh Kenneth, and International Conference on Methods in Protein Sequence Analysis (6th : 1986 : University of Washington, Seattle, Wash.), eds. Methods in protein sequence analysis, 1986. Clifton, N.J: Humana Press, 1987.

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John, Smith Bryan, ed. Protein sequencing protocols. 2nd ed. Totowa, N.J: Humana Press, 2002.

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Walsh, Kenneth A., ed. Methods in Protein Sequence Analysis · 1986. Totowa, NJ: Humana Press, 1987. http://dx.doi.org/10.1007/978-1-59259-480-1.

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1934-, Bhown Ajit S., ed. Protein/peptide sequence analysis: Current methodologies. Boca Raton, Fla: CRC Press, 1988.

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1927-, Jollès Pierre, and Jörnvall Hans, eds. Proteomics in functional genomics: Protein structure analysis. Basel: Birkhäuser Verlag, 2000.

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Book chapters on the topic "Protein Sequence Analysis"

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Lüthy, Roland, and David Eisenberg. "Protein." In Sequence Analysis Primer, 61–87. London: Palgrave Macmillan UK, 1991. http://dx.doi.org/10.1007/978-1-349-21355-9_2.

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Syed Ibrahim, Kalibulla, Guruswami Gurusubramanian, Zothansanga, Ravi Prakash Yadav, Nachimuthu Senthil Kumar, Shunmugiah Karutha Pandian, Probodh Borah, and Surender Mohan. "Protein Sequence Analysis." In Bioinformatics - A Student's Companion, 149–89. Singapore: Springer Singapore, 2017. http://dx.doi.org/10.1007/978-981-10-1857-2_4.

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Wong, Tuck Seng, and Kang Lan Tee. "Sequence Analysis." In A Practical Guide to Protein Engineering, 11–27. Cham: Springer International Publishing, 2020. http://dx.doi.org/10.1007/978-3-030-56898-6_2.

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Rehm, Bernd H. A., and Frank Reinecke. "Gene/Protein Sequence Analysis." In Springer Protocols Handbooks, 323–47. Totowa, NJ: Humana Press, 2008. http://dx.doi.org/10.1007/978-1-60327-375-6_22.

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Hermodson, Mark A. "Protein Chemistry Renascent." In Methods in Protein Sequence Analysis, 531–35. Berlin, Heidelberg: Springer Berlin Heidelberg, 1989. http://dx.doi.org/10.1007/978-3-642-73834-0_70.

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Inglis, Adam S., Robert L. Moritz, Geoffrey S. Begg, Gavin E. Reid, Richard J. Simpson, Horst Graffunder, Lothar Matschull, and Brigitte Wittmann-Liebold. "C-Terminal Sequence Analysis." In Methods in Protein Sequence Analysis, 23–34. Basel: Birkhäuser Basel, 1991. http://dx.doi.org/10.1007/978-3-0348-5678-2_2.

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Olson, Sue A. "Mac Vector: Protein Analysis." In Computer Analysis of Sequence Data, 237–46. Totowa, NJ: Humana Press, 1994. http://dx.doi.org/10.1385/0-89603-276-0:237.

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Findlay, John B. C. "A Protein Chemistry Approach to the Modelling of Integral Membrane Proteins." In Methods in Protein Sequence Analysis, 151–60. Basel: Birkhäuser Basel, 1991. http://dx.doi.org/10.1007/978-3-0348-5678-2_14.

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Rasmussen, H. H., J. Van Damme, G. Bauw, M. Puype, B. Gesser, J. E. Celis, and J. Vandekerckhove. "Protein-Electroblotting and Microsequencing in Establishing Integrated Human Protein Databases." In Methods in Protein Sequence Analysis, 103–14. Basel: Birkhäuser Basel, 1991. http://dx.doi.org/10.1007/978-3-0348-5678-2_9.

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Thiede, B. "Mass Spectrometry in Peptide and Protein Sequence Analysis." In Protein Structure Analysis, 279–93. Berlin, Heidelberg: Springer Berlin Heidelberg, 1997. http://dx.doi.org/10.1007/978-3-642-59219-5_19.

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Conference papers on the topic "Protein Sequence Analysis"

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Yusen Zhang and Xiangtian Yu. "Analysis of protein sequence similarity." In 2010 IEEE Fifth International Conference on Bio-Inspired Computing: Theories and Applications (BIC-TA). IEEE, 2010. http://dx.doi.org/10.1109/bicta.2010.5645085.

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Sequeira, Ana Marta, Ivan Gomes, and Miguel Rocha. "Word embeddings for protein sequence analysis." In 2023 IEEE Conference on Computational Intelligence in Bioinformatics and Computational Biology (CIBCB). IEEE, 2023. http://dx.doi.org/10.1109/cibcb56990.2023.10264897.

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Jong Youl Choi, Youngik Yang, Sun Kim, and Dennis Gannon. "V-Lab-Protein: Virtual Collaborative Lab for protein sequence analysis." In 2007 IEEE International Conference on Bioinformatics and Biomedicine Workshops. IEEE, 2007. http://dx.doi.org/10.1109/bibmw.2007.4425417.

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Yang, Lina, Yuan Yan Tang, Yang Lu, Huiwu Luo, Yulong Wang, and Haoliang Yuan. "Protein sequence analysis based on fractal-wavelet scheme." In 2014 IEEE International Conference on Systems, Man and Cybernetics - SMC. IEEE, 2014. http://dx.doi.org/10.1109/smc.2014.6974569.

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Pellegrino, Donald, and Chaomei Chen. "Data repository mapping for influenza protein sequence analysis." In IS&T/SPIE Electronic Imaging. SPIE, 2011. http://dx.doi.org/10.1117/12.872266.

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Zhang, Ying, Changjiang Ding, and Jun Lu. "Recognition of protein phosphorylation site based on amino acids sequence features." In NUMERICAL ANALYSIS AND APPLIED MATHEMATICS ICNAAM 2012: International Conference of Numerical Analysis and Applied Mathematics. AIP, 2012. http://dx.doi.org/10.1063/1.4756458.

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Foster, D., B. Schach, M. Rudinsky, K. Berkner, A. Kumar, C. Sprecher, F. Hagen, and E. W. bavie. "The Effect of Changes in the Leader Sequence of Human Protein C on Biosynthetic Processing and Gamma-Carboxylation." In XIth International Congress on Thrombosis and Haemostasis. Schattauer GmbH, 1987. http://dx.doi.org/10.1055/s-0038-1643648.

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Protein C is the precursor to a serine protease in plasma which contains gamma-carboxy glutamic acid and functions as a potent anticoagulant. Protein C shows considerable structural homology with the other vitamin K-dependent coagulation factors including prothrombin, factor VII, factor IX and factor X. This homology includes the putative pro-peptide region of the prepro leader sequences for these proteins, as well as the leader sequences for gamma-carboxylated proteins from bone. Deletion mutants have been constructed in the cDNA for human protein C in order to test the possibility that the pro-peptide portion of the 42 amino acid leader sequence serves as a molecular signal for gamma-carboxylation. Accordingly, these mutants contain the pre-peptide (hydrophobic leader) plus portions of the pro-peptide at the amino terminus of the light chain. The mutant proteins were expressed in carboxylation-competent mammalian cells and analyzed by barium citrate precipitation and N-terminal amino acid sequencing. These studies have shown that deletions in the pro-peptide region interfere with gamma-carboxylation and removal of the pro-peptide. Deletion of residues −1 through −12 had little effect on the carboxylation or secretion. Deletion of −1 through −17 completely abolished gamma-carboxylation, but had no measurable effect on secretion. Amino terminal sequence analysis of the latter mutant showed that the light chain began with Thr-Pro-Ala-Pro... This corresponds to a sequence in the prepro leader starting at −24. This indicates that the signal peptidase cleavage site for human protein C is between residues −25 and −24 and removal of the pro-peptide had been blocked by the deletion.
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Bidargaddi, N. P., M. Chetty, and J. Kamruzzaman. "Fuzzy Profile Hidden Markov Models for Protein Sequence Analysis." In 2005 IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology. IEEE, 2005. http://dx.doi.org/10.1109/cibcb.2005.1594950.

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Selvitopi, Oguz, Saliya Ekanayake, Giulia Guidi, Georgios A. Pavlopoulos, Ariful Azad, and Aydin Buluc. "Distributed Many-to-Many Protein Sequence Alignment using Sparse Matrices." In SC20: International Conference for High Performance Computing, Networking, Storage and Analysis. IEEE, 2020. http://dx.doi.org/10.1109/sc41405.2020.00079.

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Yang, Lina, Yuan Yan Tang, Yulong Wang, Huiwu Luo, Jianjia Pan, Haoliang Yuan, Xianwei Zheng, Chunli Li, and Ting Shu. "Similarity analysis based on sparse representation for protein sequence comparison." In 2015 IEEE 2nd International Conference on Cybernetics (CYBCONF). IEEE, 2015. http://dx.doi.org/10.1109/cybconf.2015.7175964.

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Reports on the topic "Protein Sequence Analysis"

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Zemla, A. Protein Classification Based on Analysis of Local Sequence-Structure Correspondence. Office of Scientific and Technical Information (OSTI), February 2006. http://dx.doi.org/10.2172/893991.

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Zemla, A. Protein Classification Based on Analysis of Local Sequence-Structure Correspondence. Office of Scientific and Technical Information (OSTI), February 2006. http://dx.doi.org/10.2172/928169.

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Liao, Jianhua, Jingting Liu, Baoqing Liu, Chunyan Meng, and Peiwen Yuan. Effect of OIP5-AS1 on clinicopathological characteristics and prognosis of cancer patients: a meta-analysis. INPLASY - International Platform of Registered Systematic Review and Meta-analysis Protocols, October 2022. http://dx.doi.org/10.37766/inplasy2022.10.0118.

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Review question / Objective: According to recent studies, long non-coding RNA (lncRNAs) i.e., OPA-interacting protein 5 antisense RNA 1 (OIP5-AS1) has an important role in various carcinomas. However, its role in the cancer is contradictory. Therefore, we aimed to evaluate the link between OIP5-AS1 and cancer patients' clinicopathological characteristics and prognosis to better understand OIP5-AS1's role in cancer. Condition being studied: Reported studies have revealed that long non-coding RNA (lncRNAs) are considerably involved in crucial physiological events in several carcinomas, it can inhibit or promote the occurrence and development of tumors by changing the sequence and spatial structure, modulating epigenetic, regulating the expression level and interacting with binding proteins. However, the mechanism of cancer regulation via lncRNAs was incompletely understood. Hence, clarifying the application value of lncRNAs in preclinical and clinical disease diagnosis and treatment was therefore the prime objective in the field of cancer research at the time.
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Vakharia, Vikram, Shoshana Arad, Yonathan Zohar, Yacob Weinstein, Shamila Yusuff, and Arun Ammayappan. Development of Fish Edible Vaccines on the Yeast and Redmicroalgae Platforms. United States Department of Agriculture, February 2013. http://dx.doi.org/10.32747/2013.7699839.bard.

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Betanodaviruses are causative agents of viral nervous necrosis (VNN), a devastating disease of cultured marine fish worldwide. Betanodavirus (BTN) genome is composed of two single-stranded, positive-sense RNA molecules. The larger genomic segment, RNA1 (3.1 kb), encodes the RNA-dependent RNA polymerase, while the smaller genomic segment, RNA 2 (1.4kb), encodes the coat protein. This structural protein is the host-protective antigen of VNN which assembles to form virus-like particles (VLPs). BTNs are classified into four genotypes, designated red-spotted grouper nervous necrosis virus (RGNNV), barfin flounder nervous necrosis virus (BFNNV), tiger puffer nervous necrosis virus (TPNNV), and striped jack nervous necrosis virus (SJNNV), based on phylogenetic analysis of the coat protein sequences. RGNNV type is quite important as it has a broad host-range, infecting warm-water fish species. At present, there is no commercial vaccine available to prevent VNN in fish. The general goal of this research was to develop oral fish vaccines in yeast and red microalgae (Porphyridium sp.) against the RGNNV genotype. To achieve this, we planned to clone and sequence the coat protein gene of RGNNV, express the coat protein gene of RGNNV in yeast and red microalgae and evaluate the immune response in fish fed with recombinantVLPs antigens produced in yeast and algae. The collaboration between the Israeli group and the US group, having wide experience in red microalgae biochemistry, molecular genetics and large-scale cultivation, and the development of viral vaccines and eukaryotic protein expression systems, respectively, was synergistic to produce a vaccine for fish that would be cost-effective and efficacious against the betanodavirus infection.
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Yalovsky, Shaul, and Julian Schroeder. The function of protein farnesylation in early events of ABA signal transduction in stomatal guard cells of Arabidopsis. United States Department of Agriculture, January 2002. http://dx.doi.org/10.32747/2002.7695873.bard.

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Loss of function mutations in the farnesyltransferase β subunit gene ERA1 (enhanced response to abscisic acid), cause abscisic acid hypersensitivity in seedlings and in guard cells. This results in slowed water loss of plants in response to drought. Farnesyltransferase (PFT) catalyses the attachment of the 15-carbon isoprenoid farnesyl to conserved cysteine residues located in a conserved C-terminal domain designated CaaX box. PFT is a heterodimeric protein comprised of an a and b sununits. The a subunit is shared between PFT and geranylgeranyltransferase-I (PGGTI) which catalyses the attachemt of the 20-carbon isoprenoid geranylgeranyl to CaaX box proteins in which the last amino acid is almost always leucine and in addition have a polybasic domain proximal to the CaaL box. Preliminary data presented in the proposal showed that increased cytoplasmic Ca2+ concentration in stomal guard cells in response to non-inductive ABA treatements. The goals set in the proposal were to characterize better how PFT (ERA1) affects ABA induced Ca2+ concentrations in guard cells and to identify putative CaaX box proteins which function as negative regulators of ABA signaling and which function is compromised in era1 mutant plants. To achieve these goals we proposed to use camelion Ca2+ sensor protein, high throughput genomic to identify the guard cell transcriptome and test prenylation of candidate proteins. We also proposed to focus our efforts of RAC small GTPases which are prenylated proteins which function in signaling. Our results show that farnesyltransferaseprenylates protein/s that act between the points of ABA perception and the activation of plasma membrane calcium influx channels. A RAC protein designated AtRAC8/AtRop10 also acts in negative regulation of ABA signaling. However, we discovered that this protein is palmitoylated and not prenylated although it contains a C-terminal CXXX motif. We further discovered a unique C-terminal sequence motif required for membrane targeting of palmitoylatedRACs and showed that their function is prenylation independent. A GC/MS based method for expression in plants, purification and analysis of prenyl group was developed. This method would allow highly reliable identification of prenylated protein. Mutants in the shared α subunit of PFT and PGGT-I was identified and characterized and was shown to be ABA hypersensitive but less than era1. This suggested that PFT and PGGT-I have opposing functions in ABA signaling. Our results enhanced the understanding of the role of protein prenylation in ABA signaling and drought resistance in plants with the implications of developing drought resistant plants. The results of our studies were published 4 papers which acknowledge support from BARD.
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Barefoot, Susan F., Bonita A. Glatz, Nathan Gollop, and Thomas A. Hughes. Bacteriocin Markers for Propionibacteria Gene Transfer Systems. United States Department of Agriculture, June 2000. http://dx.doi.org/10.32747/2000.7573993.bard.

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The antibotulinal baceriocins, propionicin PLG-1 and jenseniin G., were the first to be identified, purified and characterized for the dairy propionibaceria and are produced by Propionibacterium thoenii P127 and P. thoenii/jensenii P126, respectively. Objectives of this project were to (a) produce polyclonal antibodies for detection, comparison and monitoring of propionicin PLG-1; (b) identify, clone and characterize the propionicin PLG-1 (plg-1) and jenseniin G (jnG) genes; and (3) develop gene transfer systems for dairy propionibacteria using them as models. Polyclonal antibodies for detection, comparison and monitoring of propionicin PLG-1 were produced in rabbits. Anti-PLG-1 antiserum had high titers (256,000 to 512,000), neutralized PLG-1 activity, and detected purified PLG-1 at 0.10 mg/ml (indirect ELISA) and 0.033 mg/ml (competitive indirect ELISA). Thirty-nine of 158 strains (most P. thoenii or P. jensenii) yielded cross-reacting material; four strains of P. thoenii, including two previously unidentified bacteriocin producers, showed biological activity. Eight propionicin-negative P127 mutants produced neither ELISA response nor biological activity. Western blot analyses of supernates detected a PLG-1 band at 9.1 kDa and two additional protein bands with apparent molecular weights of 16.2 and 27.5 kDa. PLG-1 polyclonal antibodies were used for detection of jenseniin G. PLG-1 antibodies neutralized jenseniin G activity and detected a jenseniin G-sized, 3.5 kDa peptide. Preliminary immunoprecipitation of crude preparations with PLG-1 antibodies yielded three proteins including an active 3-4 kDa band. Propionicin PLG-1 antibodies were used to screen a P. jensenii/thoenii P126 genomic expression library. Complete sequencing of a cloned insert identified by PLG-1 antibodies revealed a putative response regulator, transport protein, transmembrane protein and an open reading frame (ORF) potentially encoding jenseniin G. PCR cloning of the putative plg-1 gene yielded a 1,100 bp fragment with a 355 bp ORF encoding 118 amino acids; the deduced N-terminus was similar to the known PLG-1 N-terminus. The 118 amino acid sequence deduced from the putative plg-1 gene was larger than PLG-1 possibly due to post-translational processing. The product of the putative plg-1 gene had a calculated molecular weight of 12.8 kDa, a pI of 11.7, 14 negatively charged residues (Asp+Glu) and 24 positively charged residues (Arg+Lys). The putative plg-1 gene was expressed as an inducible fusion protein with a six-histidine residue tag. Metal affinity chromatography of the fused protein yielded a homogeneous product. The fused purified protein sequence matched the deduced putative plg-1 gene sequence. The data preliminarily suggest that both the plg-1 and jnG genes have been identified and cloned. Demonstrating that antibodies can be produced for propionicin PLG-1 and that those antibodies can be used to detect, monitor and compare activity throughout growth and purification was an important step towards monitoring PLG-1 concentrations in food systems. The unexpected but fortunate cross-reactivity of PLG-1 antibodies with jenseniin G led to selective recovery of jenseniin G by immunoprecipitation. Further refinement of this separation technique could lead to powerful affinity methods for rapid, specific separation of the two bacteriocins and thus facilitate their availability for industrial or pharmaceutical uses. Preliminary identification of genes encoding the two dairy propionibacteria bacteriocins must be confirmed; further analysis will provide means for understanding how they work, for increasing their production and for manipulating the peptides to increase their target species. Further development of these systems would contribute to basic knowledge about dairy propionibacteria and has potential for improving other industrially significant characteristics.
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Gelb, Jr., Jack, Yoram Weisman, Brian Ladman, and Rosie Meir. Identification of Avian Infectious Brochitis Virus Variant Serotypes and Subtypes by PCR Product Cycle Sequencing for the Rational Selection of Effective Vaccines. United States Department of Agriculture, December 2003. http://dx.doi.org/10.32747/2003.7586470.bard.

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Objectives 1. Determine the serotypic identities of 40 recent IBV isolates from commercial chickens raised in the USA and Israel. 2. Sequence all IBV field isolates using PCR product cycle sequencing and analyze their S 1 sequence to detennine their homology to other strains in the Genbank and EMBL databases. 3. Select vaccinal strains with the highest S 1 sequence homology to the field isolates and perform challenge of immunity studies in chickens in laboratory trials to detennine level of protection afforded by the vaccines. Background Infectious bronchitis (IB) is a common, economically important disease of the chicken. IB occurs as a respiratory form, associated with airsacculitis, condemnation, and mortality of meat-type broilers, a reproductive form responsible for egg production losses in layers and breeders, and a renal form causing high mortality in broilers and pullets. The causative agent is avian coronavirus infectious bronchitis virus (IBV). Replication of the virus' RNA genome is error-prone and mutations commonly result. A major target for mutation is the gene encoding the spike (S) envelope protein used by the virus to attach and infect the host cell. Mutations in the S gene result in antigenic changes that can lead to the emergence of variant serotypes. The S gene is able to tolerate numerous mutations without compromising the virus' ability to replicate and cause disease. An end result of the virus' "flexibility" is that many strains of IBV are capable of existing in nature. Once formed, new mutant strains, often referred to as variants, are soon subjected to immunological selection so that only the most antigenically novel variants survive in poultry populations. Many novel antigenic variant serotypes and genotypes have been isolated from commercial poultry flocks. Identification of the field isolates of IBV responsible for outbreaks is critical for selecting the appropriate strain(s) for vaccination. Reverse transcriptase polymerase chain reaction (RT-PCR) of the Sl subunit of the envelope spike glycoprotein gene has been a common method used to identify field strains, replacing other time-consuming or less precise tests. Two PCR approaches have been used for identification, restriction fragment length polymorphism (RFLP) and direct automated cycle sequence analysis of a diagnostically relevant hypervariab1e region were compared in our BARD research. Vaccination for IB, although practiced routinely in commercial flocks, is often not protective. Field isolates responsible for outbreaks may be unrelated to the strain(s) used in the vaccination program. However, vaccines may provide varying degrees of cross- protection vs. unrelated field strains so vaccination studies should be performed. Conclusions RFLP and S1 sequence analysis methods were successfully performed using the field isolates from the USA and Israel. Importantly, the S1 sequence analysis method enabled a direct comparison of the genotypes of the field strains by aligning them to sequences in public databases e.g. GenBank. Novel S1 gene sequences were identified in both USA and Israel IBVs but greater diversity was observed in the field isolates from the USA. One novel genotype, characterized in this project, Israel/720/99, is currently being considered for development as an inactivated vaccine. Vaccination with IBV strains in the US (Massachusetts, Arkansas, Delaware 072) or in Israel (Massachusetts, Holland strain) provided higher degrees of cross-protection vs. homologous than heterologous strain challenge. In many cases however, vaccination with two strains (only studies with US strains) produced reasonable cross-protection against heterologous field isolate challenge. Implications S1 sequence analysis provides numerical similarity values and phylogenetic information that can be useful, although by no means conclusive, in developing vaccine control strategies. Identification of many novel S1 genotypes of IBV in the USA is evidence that commercial flocks will be challenged today and in the future with strains unrelated to vaccines. In Israel, monitoring flocks for novel IBV field isolates should continue given the identification of Israel/720/99, and perhaps others in the future. Strains selected for vaccination of commercial flocks should induce cross- protection against unrelated genotypes. Using diverse genotypes for vaccination may result in immunity against unrelated field strains.
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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.

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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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Gershoni, Jonathan M., David E. Swayne, Tal Pupko, Shimon Perk, Alexander Panshin, Avishai Lublin, and Natalia Golander. Discovery and reconstitution of cross-reactive vaccine targets for H5 and H9 avian influenza. United States Department of Agriculture, January 2015. http://dx.doi.org/10.32747/2015.7699854.bard.

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Research objectives: Identification of highly conserved B-cell epitopes common to either H5 or H9 subtypes of AI Reconstruction of conserved epitopes from (1) as recombinantimmunogens, and testing their suitability to be used as universal vaccine components by measuring their binding to Influenza vaccinated sera of birds Vaccination of chickens with reconstituted epitopes and evaluation of successful vaccination, clinical protection and viral replication Development of a platform to investigate the dynamics of immune response towards infection or an epitope based vaccine Estimate our ability to focus the immune response towards an epitope-based vaccine using the tool we have developed in (D) Summary: This study is a multi-disciplinary study of four-way collaboration; The SERPL, USDA, Kimron-Israel, and two groups at TAU with the purpose of evaluating the production and implementation of epitope based vaccines against avian influenza (AI). Systematic analysis of the influenza viral spike led to the production of a highly conserved epitope situated at the hinge of the HA antigen designated “cluster 300” (c300). This epitope consists of a total of 31 residues and was initially expressed as a fusion protein of the Protein 8 major protein of the bacteriophagefd. Two versions of the c300 were produced to correspond to the H5 and H9 antigens respectively as well as scrambled versions that were identical with regard to amino acid composition yet with varied linear sequence (these served as negative controls). The recombinantimmunogens were produced first as phage fusions and then subsequently as fusions with maltose binding protein (MBP) or glutathioneS-transferase (GST). The latter were used to immunize and boost chickens at SERPL and Kimron. Furthermore, vaccinated and control chickens were challenged with concordant influenza strains at Kimron and SEPRL. Polyclonal sera were obtained for further analyses at TAU and computational bioinformatics analyses in collaboration with Prof. Pupko. Moreover, the degree of protection afforded by the vaccination was determined. Unfortunately, no protection could be demonstrated. In parallel to the main theme of the study, the TAU team (Gershoni and Pupko) designed and developed a novel methodology for the systematic analysis of the antibody composition of polyclonal sera (Deep Panning) which is essential for the analyses of the humoral response towards vaccination and challenge. Deep Panning is currently being used to monitor the polyclonal sera derived from the vaccination studies conducted at the SEPRL and Kimron.
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Mevarech, Moshe, Jeremy Bruenn, and Yigal Koltin. Virus Encoded Toxin of the Corn Smut Ustilago Maydis - Isolation of Receptors and Mapping Functional Domains. United States Department of Agriculture, September 1995. http://dx.doi.org/10.32747/1995.7613022.bard.

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Ustilago maydis is a fungal pathogen of maize. Some strains of U. maydis encode secreted polypeptide toxins capable of killing other susceptible strains of U. maydis. Resistance to the toxins is conferred by recessive nuclear genes. The toxins are encoded by genomic segments of resident double-strande RNA viruses. The best characterized toxin, KP6, is composed of two polypeptides, a and b, which are not covalently linked. It is encoded by P6M2 dsRNA, which has been cloned, sequenced and expressed in a variety of systems. In this study we have shown that the toxin acts on the membranes of sensitive cells and that both polypeptides are required for toxin activity. The toxin has been shown to function by creating new pores in the cell membrane and disrupting ion fluxes. The experiments performed on artificial phospholipid bilayers indicated that KP6 forms large voltage-independent, cation-selective channels. Experiments leading to the resolution of structure-function relationship of the toxin by in vitro analysis have been initiated. During the course of this research the collaboration also yielded X-ray diffracion data of the crystallized a polypeptide. The effect of the toxin on the pathogen has been shown to be receptor-mediated. A potential receptor protein, identified in membrane fractions of sensitive cells, was subjected to tryptic hydrolysis followed by amino-acid analysis. The peptides obtained were used to isolate a cDNA fragment by reverse PCR, which showed 30% sequence homology to the human HLA protein. Analysis of other toxins secreted by U. maydis, KP1 and KP4, have demonstrated that, unlike KP6, they are composed of a single polypeptide. Finally, KP6 has been expressed in transgenic tobacco plants, indicating that accurate processing by Kex2p-like activity occurs in plants as well. Using tobacco as a model system, we determined that active antifungal toxins can be synthesized and targeted to the outside of transgenic plant cells. If this methodology can be applied to other agronomically crop species, then U. maydis toxins may provide a novel means for biological control of pathogenic fungi.
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