Relevant bibliographies by topics / Sequence motif

Contents

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

Academic literature on the topic 'Sequence motif'

Author: Grafiati
Published: 4 June 2021
Last updated: 20 February 2023

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Journal articles on the topic "Sequence motif"

1

Roebuck, K. A., D. P. Szeto, K. P. Green, Q. N. Fan, and W. E. Stumph. "Octamer and SPH motifs in the U1 enhancer cooperate to activate U1 RNA gene expression." Molecular and Cellular Biology 10, no. 1 (January 1990): 341–52. http://dx.doi.org/10.1128/mcb.10.1.341-352.1990.

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The transcriptional enhancer of a chicken U1 small nuclear RNA gene has been shown to extend over approximately 50 base pairs of DNA sequence located 180 to 230 base pairs upstream of the U1 transcription initiation site. It is composed of multiple functional motifs, including a GC box, an octamer motif, and a novel SPH motif. The contributions of these three distinct sequence motifs to enhancer function were studied with an oocyte expression assay. Under noncompetitive conditions in oocytes, the SPH motif is capable of stimulating U1 RNA transcription in the absence of the other functional motifs, whereas the octamer motif by itself lacks this ability. However, to form a transcription complex that is stable to challenge by a second competing small nuclear RNA transcription unit, both the octamer and SPH motifs are required. The GC box, although required for full enhancer activity, is not essential for stable complex formation in oocytes. Site-directed mutagenesis was used to study the DNA sequence requirements of the SPH motif. Functional activity of the SPH motif is spread throughout a 24-base-pair region 3' of the octamer but is particularly dependent upon sequences near an SphI restriction site located at the center of the SPH motif. Using embryonic chicken tissue as a source material, we identified and partially purified a factor, termed SBF, that binds sequence specifically to the SPH motif of the U1 enhancer. The ability of this factor to recognize and bind to mutant enhancer DNA fragments in vitro correlates with the functional activity of the corresponding enhancer sequences in vivo.
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Roebuck, K. A., D. P. Szeto, K. P. Green, Q. N. Fan, and W. E. Stumph. "Octamer and SPH motifs in the U1 enhancer cooperate to activate U1 RNA gene expression." Molecular and Cellular Biology 10, no. 1 (January 1990): 341–52. http://dx.doi.org/10.1128/mcb.10.1.341.

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The transcriptional enhancer of a chicken U1 small nuclear RNA gene has been shown to extend over approximately 50 base pairs of DNA sequence located 180 to 230 base pairs upstream of the U1 transcription initiation site. It is composed of multiple functional motifs, including a GC box, an octamer motif, and a novel SPH motif. The contributions of these three distinct sequence motifs to enhancer function were studied with an oocyte expression assay. Under noncompetitive conditions in oocytes, the SPH motif is capable of stimulating U1 RNA transcription in the absence of the other functional motifs, whereas the octamer motif by itself lacks this ability. However, to form a transcription complex that is stable to challenge by a second competing small nuclear RNA transcription unit, both the octamer and SPH motifs are required. The GC box, although required for full enhancer activity, is not essential for stable complex formation in oocytes. Site-directed mutagenesis was used to study the DNA sequence requirements of the SPH motif. Functional activity of the SPH motif is spread throughout a 24-base-pair region 3' of the octamer but is particularly dependent upon sequences near an SphI restriction site located at the center of the SPH motif. Using embryonic chicken tissue as a source material, we identified and partially purified a factor, termed SBF, that binds sequence specifically to the SPH motif of the U1 enhancer. The ability of this factor to recognize and bind to mutant enhancer DNA fragments in vitro correlates with the functional activity of the corresponding enhancer sequences in vivo.
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XING, ERIC P., WEI WU, MICHAEL I. JORDAN, and RICHARD M. KARP. "LOGOS: A MODULAR BAYESIAN MODEL FOR DE NOVO MOTIF DETECTION." Journal of Bioinformatics and Computational Biology 02, no. 01 (March 2004): 127–54. http://dx.doi.org/10.1142/s0219720004000508.

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The complexity of the global organization and internal structure of motifs in higher eukaryotic organisms raises significant challenges for motif detection techniques. To achieve successful de novo motif detection, it is necessary to model the complex dependencies within and among motifs and to incorporate biological prior knowledge. In this paper, we present LOGOS, an integrated LOcal and GlObal motif Sequence model for biopolymer sequences, which provides a principled framework for developing, modularizing, extending and computing expressive motif models for complex biopolymer sequence analysis. LOGOS consists of two interacting submodels: HMDM, a local alignment model capturing biological prior knowledge and positional dependency within the motif local structure; and HMM, a global motif distribution model modeling frequencies and dependencies of motif occurrences. Model parameters can be fit using training motifs within an empirical Bayesian framework. A variational EM algorithm is developed for de novo motif detection. LOGOS improves over existing models that ignore biological priors and dependencies in motif structures and motif occurrences, and demonstrates superior performance on both semi-realistic test data and cis-regulatory sequences from yeast and Drosophila genomes with regard to sensitivity, specificity, flexibility and extensibility.
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Zhai, Xiandun, and Adilai Tuerxun. "DNA Sequence Specificity Prediction Algorithm Based on Artificial Intelligence." Mathematical Problems in Engineering 2022 (October 3, 2022): 1–8. http://dx.doi.org/10.1155/2022/4150106.

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DNA sequence specificity refers to the ability of DNA sequences to bind specific proteins. These proteins play a central role in gene regulation such as transcription and alternative splicing. Obtaining DNA sequence specificity is very important for establishing the regulatory model of the biological system and identifying pathogenic variants. Motifs are sequence patterns shared by fragments of DNA sequences that bind to specific proteins. At present, some motif mining algorithms have been proposed, which perform well under the condition of given motif length. This research is based on deep learning. As for the description of motif level, this paper constructs an AI based method to predict the length of the motif. The experimental results show that the prediction accuracy on the test set is more than 90%.
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Wang, Mengchi, David Wang, Kai Zhang, Vu Ngo, Shicai Fan, and Wei Wang. "Motto: Representing Motifs in Consensus Sequences with Minimum Information Loss." Genetics 216, no. 2 (August 19, 2020): 353–58. http://dx.doi.org/10.1534/genetics.120.303597.

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Sequence analysis frequently requires intuitive understanding and convenient representation of motifs. Typically, motifs are represented as position weight matrices (PWMs) and visualized using sequence logos. However, in many scenarios, in order to interpret the motif information or search for motif matches, it is compact and sufficient to represent motifs by wildcard-style consensus sequences (such as [GC][AT]GATAAG[GAC]). Based on mutual information theory and Jensen-Shannon divergence, we propose a mathematical framework to minimize the information loss in converting PWMs to consensus sequences. We name this representation as sequence Motto and have implemented an efficient algorithm with flexible options for converting motif PWMs into Motto from nucleotides, amino acids, and customized characters. We show that this representation provides a simple and efficient way to identify the binding sites of 1156 common transcription factors (TFs) in the human genome. The effectiveness of the method was benchmarked by comparing sequence matches found by Motto with PWM scanning results found by FIMO. On average, our method achieves a 0.81 area under the precision-recall curve, significantly (P-value < 0.01) outperforming all existing methods, including maximal positional weight, Cavener’s method, and minimal mean square error. We believe this representation provides a distilled summary of a motif, as well as the statistical justification.
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Wright, Elisé P., Mahmoud A. S. Abdelhamid, Michelle O. Ehiabor, Melanie C. Grigg, Kelly Irving, Nicole M. Smith, and Zoë A. E. Waller. "Epigenetic modification of cytosines fine tunes the stability of i-motif DNA." Nucleic Acids Research 48, no. 1 (November 28, 2019): 55–62. http://dx.doi.org/10.1093/nar/gkz1082.

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Abstract i-Motifs are widely used in nanotechnology, play a part in gene regulation and have been detected in human nuclei. As these structures are composed of cytosine, they are potential sites for epigenetic modification. In addition to 5-methyl- and 5-hydroxymethylcytosine modifications, recent evidence has suggested biological roles for 5-formylcytosine and 5-carboxylcytosine. Herein the human telomeric i-motif sequence was used to examine how these four epigenetic modifications alter the thermal and pH stability of i-motifs. Changes in melting temperature and transitional pH depended on both the type of modification and its position within the i-motif forming sequence. The cytosines most sensitive to modification were next to the first and third loops within the structure. Using previously described i-motif forming sequences, we screened the MCF-7 and MCF-10A methylomes to map 5-methylcytosine and found the majority of sequences were differentially methylated in MCF7 (cancerous) and MCF10A (non-cancerous) cell lines. Furthermore, i-motif forming sequences stable at neutral pH were significantly more likely to be epigenetically modified than traditional acidic i-motif forming sequences. This work has implications not only in the epigenetic regulation of DNA, but also allows discreet tunability of i-motif stability for nanotechnological applications.
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MAURER-STROH, SEBASTIAN, HE GAO, HAO HAN, LIES BAETEN, JOOST SCHYMKOWITZ, FREDERIC ROUSSEAU, LOUXIN ZHANG, and FRANK EISENHABER. "MOTIF DISCOVERY WITH DATA MINING IN 3D PROTEIN STRUCTURE DATABASES: DISCOVERY, VALIDATION AND PREDICTION OF THE U-SHAPE ZINC BINDING ("HUF-ZINC") MOTIF." Journal of Bioinformatics and Computational Biology 11, no. 01 (February 2013): 1340008. http://dx.doi.org/10.1142/s0219720013400088.

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Data mining in protein databases, derivatives from more fundamental protein 3D structure and sequence databases, has considerable unearthed potential for the discovery of sequence motif—structural motif—function relationships as the finding of the U-shape (Huf-Zinc) motif, originally a small student's project, exemplifies. The metal ion zinc is critically involved in universal biological processes, ranging from protein-DNA complexes and transcription regulation to enzymatic catalysis and metabolic pathways. Proteins have evolved a series of motifs to specifically recognize and bind zinc ions. Many of these, so called zinc fingers, are structurally independent globular domains with discontinuous binding motifs made up of residues mostly far apart in sequence. Through a systematic approach starting from the BRIX structure fragment database, we discovered that there exists another predictable subset of zinc-binding motifs that not only have a conserved continuous sequence pattern but also share a characteristic local conformation, despite being included in totally different overall folds. While this does not allow general prediction of all Zn binding motifs, a HMM-based web server, Huf-Zinc, is available for prediction of these novel, as well as conventional, zinc finger motifs in protein sequences. The Huf-Zinc webserver can be freely accessed through this URL ( http://mendel.bii.a-star.edu.sg/METHODS/hufzinc/ ).
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Liu, Xiang-Qin, and Jing Yang. "Bacterial Thymidylate Synthase with Intein, Group II Intron, and Distinctive ThyX Motifs." Journal of Bacteriology 186, no. 18 (September 15, 2004): 6316–19. http://dx.doi.org/10.1128/jb.186.18.6316-6319.2004.

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ABSTRACT The ThyX class of thymidylate synthases was previously characterized by a common ThyX motif, RHRX7S. We report bacterial ThyX sequences having distinctive ThyX motifs, suggesting a more general ThyX motif, R/THRX7-8S. One ThyX sequence has an intein in its ThyX motif that was shown to do protein splicing and a group II intron in its gene, suggesting a hot spot for these self-splicing mobile elements.
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Pal, Soumitra, Jan Hoinka, and Teresa M. Przytycka. "Co-SELECT reveals sequence non-specific contribution of DNA shape to transcription factor binding in vitro." Nucleic Acids Research 47, no. 13 (June 21, 2019): 6632–41. http://dx.doi.org/10.1093/nar/gkz540.

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Abstract Understanding the principles of DNA binding by transcription factors (TFs) is of primary importance for studying gene regulation. Recently, several lines of evidence suggested that both DNA sequence and shape contribute to TF binding. However, the following compelling question is yet to be considered: in the absence of any sequence similarity to the binding motif, can DNA shape still increase binding probability? To address this challenge, we developed Co-SELECT, a computational approach to analyze the results of in vitro HT-SELEX experiments for TF–DNA binding. Specifically, Co-SELECT leverages the presence of motif-free sequences in late HT-SELEX rounds and their enrichment in weak binders allows Co-SELECT to detect an evidence for the role of DNA shape features in TF binding. Our approach revealed that, even in the absence of the sequence motif, TFs have propensity to bind to DNA molecules of the shape consistent with the motif specific binding. This provides the first direct evidence that shape features that accompany the preferred sequence motifs also bestow an advantage for weak, sequence non-specific binding.
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Gunawardana, D., V. A. Likic, and K. R. Gayler. "A Comprehensive Bioinformatics Analysis of the Nudix Superfamily inArabidopsis thaliana." Comparative and Functional Genomics 2009 (2009): 1–13. http://dx.doi.org/10.1155/2009/820381.

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Nudix enzymes are a superfamily with a conserved common reaction mechanism that provides the capacity for the hydrolysis of a broad spectrum of metabolites. We used hidden Markov models based on Nudix sequences from the PFAM and PROSITE databases to identify Nudix hydrolases encoded by theArabidopsisgenome. 25 Nudix hydrolases were identified and classified into 11 individual families by pairwise sequence alignments. Intron phases were strikingly conserved in each family. Phylogenetic analysis showed that all multimember families formed monophyletic clusters. Conserved familial sequence motifs were identified with the MEME motif analysis algorithm. One motif (motif 4) was found in three diverse families. All proteins containing motif 4 demonstrated a degree of preference for substrates containing an ADP moiety. We conclude that HMM model-based genome scanning and MEME motif analysis, respectively, can significantly improve the identification and assignment of function of new members of this mechanistically-diverse protein superfamily.
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Dissertations / Theses on the topic "Sequence motif"

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Leung, Chi-ming. "Motif discovery for DNA sequences." Click to view the E-thesis via HKUTO, 2006. http://sunzi.lib.hku.hk/hkuto/record/B3859755X.

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Leung, Chi-ming, and 梁志銘. "Motif discovery for DNA sequences." Thesis, The University of Hong Kong (Pokfulam, Hong Kong), 2006. http://hub.hku.hk/bib/B3859755X.

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Liu, Agatha H. "Motif-based mining of protein sequences /." Thesis, Connect to this title online; UW restricted, 2002. http://hdl.handle.net/1773/6894.

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Dinh, Hieu Trung. "Algorithms for DNA Sequence Assembly and Motif Search." University of Connecticut, 2013.

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Siu, Man-hung. "Finding motif pairs from protein interaction networks." Click to view the E-thesis via HKUTO, 2008. http://sunzi.lib.hku.hk/hkuto/record/B40987760.

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Siu, Man-hung, and 蕭文鴻. "Finding motif pairs from protein interaction networks." Thesis, The University of Hong Kong (Pokfulam, Hong Kong), 2008. http://hub.hku.hk/bib/B40987760.

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Al-Ouran, Rami. "Motif Selection: Identification of Gene Regulatory Elements using Sequence CoverageBased Models and Evolutionary Algorithms." Ohio University / OhioLINK, 2015. http://rave.ohiolink.edu/etdc/view?acc_num=ohiou1449003717.

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Lin, Jasper Chua. "Application of the Trp-cage motif to polypeptide folding questions /." Thesis, Connect to this title online; UW restricted, 2007. http://hdl.handle.net/1773/8684.

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Chen, Bernard. "Discovery and Extraction of Protein Sequence Motif Information that Transcends Protein Family Boundaries." Digital Archive @ GSU, 2009. http://digitalarchive.gsu.edu/cs_diss/42.

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Protein sequence motifs are gathering more and more attention in the field of sequence analysis. The recurring patterns have the potential to determine the conformation, function and activities of the proteins. In our work, we obtained protein sequence motifs which are universally conserved across protein family boundaries. Therefore, unlike most popular motif discovering algorithms, our input dataset is extremely large. As a result, an efficient technique is essential. We use two granular computing models, Fuzzy Improved K-means (FIK) and Fuzzy Greedy K-means (FGK), in order to efficiently generate protein motif information. After that, we develop an efficient Super Granular SVM Feature Elimination model to further extract the motif information. During the motifs searching process, setting up a fixed window size in advance may simplify the computational complexity and increase the efficiency. However, due to the fixed size, our model may deliver a number of similar motifs simply shifted by some bases or including mismatches. We develop a new strategy named Positional Association Super-Rule to confront the problem of motifs generated from a fixed window size. It is a combination approach of the super-rule analysis and a novel Positional Association Rule algorithm. We use the super-rule concept to construct a Super-Rule-Tree (SRT) by a modified HHK clustering, which requires no parameter setup to identify the similarities and dissimilarities between the motifs. The positional association rule is created and applied to search similar motifs that are shifted some residues. By analyzing the motifs results generated by our approaches, we realize that these motifs are not only significant in sequence area, but also in secondary structure similarity and biochemical properties.
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Pei, Shermin. "Identification of functional RNA structures in sequence data." Thesis, Boston College, 2016. http://hdl.handle.net/2345/bc-ir:107275.

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Thesis advisor: Michelle M. Meyer
Thesis advisor: Peter Clote
Structured RNAs have many biological functions ranging from catalysis of chemical reactions to gene regulation. Many of these homologous structured RNAs display most of their conservation at the secondary or tertiary structure level. As a result, strategies for natural structured RNA discovery rely heavily on identification of sequences sharing a common stable secondary structure. However, correctly identifying the functional elements of the structure continues to be challenging. In addition to studying natural RNAs, we improve our ability to distinguish functional elements by studying sequences derived from in vitro selection experiments to select structured RNAs that bind specific proteins. In this thesis, we seek to improve methods for distinguishing functional RNA structures from arbitrarily predicted structures in sequencing data. To do so, we developed novel algorithms that prioritize the structural properties of the RNA that are under selection. In order to identify natural structured ncRNAs, we bring concepts from evolutionary biology to bear on the de novo RNA discovery process. Since there is selective pressure to maintain the structure, we apply molecular evolution concepts such as neutrality to identify functional RNA structures. We hypothesize that alignments corresponding to structured RNAs should consist of neutral sequences. During the course of this work, we developed a novel measure of neutrality, the structure ensemble neutrality (SEN), which calculates neutrality by averaging the magnitude of structure retained over all single point mutations to a given sequence. In order to analyze in vitro selection data for RNA-protein binding motifs, we developed a novel framework that identifies enriched substructures in the sequence pool. Our method accounts for both sequence and structure components by abstracting the overall secondary structure into smaller substructures composed of a single base-pair stack. Unlike many current tools, our algorithm is designed to deal with the large data sets coming from high-throughput sequencing. In conclusion, our algorithms have similar performance to existing programs. However, unlike previous methods, our algorithms are designed to leverage the evolutionary selective pressures in order to emphasize functional structure conservation
Thesis (PhD) — Boston College, 2016
Submitted to: Boston College. Graduate School of Arts and Sciences
Discipline: Biology
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Books on the topic "Sequence motif"

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A motif of mathematics: [history and application of the mediant and the Farey sequence]. Boston: Docent Press, 2011.

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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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Comics and the city: Urban space in print, picture, and sequence. New York: Continuum, 2010.

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Taylor, Catherine Yvonne. Analysis of protein binding motifs in the nucleotide sequence of the human [gamma]-actin gene promoter. Ottawa: National Library of Canada = Bibliothèque nationale du Canada, 1993.

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Sun, Qing. Generation and characterization of antibodies with defined specificity towards fibronectin-binding sequences within the D-motifs of staphylococcus. Ottawa: National Library of Canada, 1998.

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Rowett, Catherine. Introduction and Summary for Part IV: Plato’s Theaetetus. Oxford University Press, 2018. http://dx.doi.org/10.1093/oso/9780199693658.003.0009.

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The chapter summarizes the results of Part IV and explains and introduces the work on the Theaetetus in Chapters 10, 11, and 12. It explains what misguided assumptions undermine all Theaetetus’s attempts to define knowledge (focusing especially on the reductionist assumptions throughout the dialogue). Second, it examines the significance of the motif of the midwife, whose task is twofold: first to provide life-saving aids for each failing infant, and then to judge its viability once those aids are in place. The dialogue therefore manifests an alternating sequence of constructive work, to prop up failing theories, and destructive work to prove their non-viability. Third, it explains the importance of the search for ousia (being) and its relation to the quest for ‘what it is’ about a concept.
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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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Hicks, Matthew Raymond. Coiled-coil assembly by proteins and peptides with unusual sequence motifs. 2000.

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(Contributor), P. Bengert, T. Dandekar (Contributor), D. Ostareck (Contributor), A. Ostareck-Lederer (Contributor), and Thomas Dandekar (Editor), eds. RNA Motifs and Regulatory Elements. 2nd ed. Springer, 2002.

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Book chapters on the topic "Sequence motif"

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Han, Shin-Kap. "Motif of Sequence, Motif in Sequence." In Life Course Research and Social Policies, 21–38. Cham: Springer International Publishing, 2014. http://dx.doi.org/10.1007/978-3-319-04969-4_2.

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Kim, Ju Han. "Motif and Regulatory Sequence Analysis." In Genome Data Analysis, 189–211. Singapore: Springer Singapore, 2019. http://dx.doi.org/10.1007/978-981-13-1942-6_11.

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Chen, Bernard. "Protein Sequence Motif Information Discovery." In Algorithmic and Artificial Intelligence Methods for Protein Bioinformatics, 41–55. Hoboken, NJ, USA: John Wiley & Sons, Inc., 2013. http://dx.doi.org/10.1002/9781118567869.ch2.

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Liang, Jie, and Ronald Jackups. "Sequence and Spatial Motif Discovery in Short Sequence Fragments." In Encyclopedia of Algorithms, 1945–52. New York, NY: Springer New York, 2016. http://dx.doi.org/10.1007/978-1-4939-2864-4_601.

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Liang, Jie, and Ronald Jackups. "Sequence and Spatial Motif Discovery in Short Sequence Fragments." In Encyclopedia of Algorithms, 1–10. Boston, MA: Springer US, 2014. http://dx.doi.org/10.1007/978-3-642-27848-8_601-1.

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Liu, Jin S., Mayetri Gupta, Xiaole Liu, Linda Mayerhofere, and Charles E. Lawrence. "Statistical Models for Biological Sequence Motif Discovery." In Case Studies in Bayesian Statistics, 3–32. New York, NY: Springer New York, 2002. http://dx.doi.org/10.1007/978-1-4612-2078-7_1.

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Wyatt, Jacqueline R., and C. A. Stein. "Oligonucleotides Containing the G-Quartet Sequence Motif." In Applications of Antisense Therapies to Restenosis, 133–40. Boston, MA: Springer US, 1999. http://dx.doi.org/10.1007/978-1-4615-5183-6_8.

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Zheleva, Elena, and Abdullah N. Arslan. "Fast Motif Search in Protein Sequence Databases." In Computer Science – Theory and Applications, 670–81. Berlin, Heidelberg: Springer Berlin Heidelberg, 2006. http://dx.doi.org/10.1007/11753728_67.

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Ceci, Michelangelo, Corrado Loglisci, Eliana Salvemini, Domenica D’Elia, and Donato Malerba. "Mining Spatial Association Rules for Composite Motif Discovery." In Mathematical Approaches to Polymer Sequence Analysis and Related Problems, 87–109. New York, NY: Springer New York, 2010. http://dx.doi.org/10.1007/978-1-4419-6800-5_5.

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Kitakami, Hajime, Tomoki Kanbara, Yasuma Mori, Susumu Kuroki, and Yukiko Yamazaki. "Modified PrefixSpan Method for Motif Discovery in Sequence Databases." In Lecture Notes in Computer Science, 482–91. Berlin, Heidelberg: Springer Berlin Heidelberg, 2002. http://dx.doi.org/10.1007/3-540-45683-x_52.

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Conference papers on the topic "Sequence motif"

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Chandar, V. Ravindra Krishna, and V. Sathiya Moorthi. "Sequence clustering using motif algorithm." In 2012 International Conference on Computer Communication and Informatics (ICCCI). IEEE, 2012. http://dx.doi.org/10.1109/iccci.2012.6158838.

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Yu, Qiang, Hongwei Huo, Ruixing Zhao, Dazheng Feng, Jeffrey Scott Vitter, and Jun Huan. "Reference sequence selection for motif searches." In 2015 IEEE International Conference on Bioinformatics and Biomedicine (BIBM). IEEE, 2015. http://dx.doi.org/10.1109/bibm.2015.7359745.

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PRAKASH, A., M. BLANCHETTE, S. SINHA, and M. TOMPA. "MOTIF DISCOVERY IN HETEROGENEOUS SEQUENCE DATA." In Proceedings of the Pacific Symposium. WORLD SCIENTIFIC, 2003. http://dx.doi.org/10.1142/9789812704856_0033.

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Ramanujam, E., and S. Padmavathi. "Constraint Frequent Motif Detection in sequence datasets." In 2012 Fourth International Conference on Advanced Computing (ICoAC). IEEE, 2012. http://dx.doi.org/10.1109/icoac.2012.6416844.

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Karaçalı, Bilge. "Hierarchical Motif Vectors for Amino Acid Sequence Alignment." In Biomedical Engineering. Calgary,AB,Canada: ACTAPRESS, 2012. http://dx.doi.org/10.2316/p.2012.764-055.

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Ng, Patrick, and Uri Keich. "Factoring local sequence composition in motif significance analysis." In Proceedings of the 19th International Conference. IMPERIAL COLLEGE PRESS, 2008. http://dx.doi.org/10.1142/9781848163324_0002.

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Sayed, Khaled, Nahed Solouma, and Yasser Kadah. "Yeast protein function motif extraction based on sequence alignment." In 2011 28th National Radio Science Conference (NRSC). IEEE, 2011. http://dx.doi.org/10.1109/nrsc.2011.5873650.

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Birch-Hirschfeld, Eckhard, Axel Walter, Anna Gabrielyan, Axel Stelzner, Hartmut Fritzsche, and Holger Schütz. "A new parallel triplex motif: sequence dependence of thermal stability." In XIth Symposium on Chemistry of Nucleic Acid Components. Prague: Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, 1999. http://dx.doi.org/10.1135/css199902313.

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Gokalp, Osman. "DNA Sequence Motif Discovery Using Greedy Construction Algorithm Based Techniques." In 2020 5th International Conference on Computer Science and Engineering (UBMK). IEEE, 2020. http://dx.doi.org/10.1109/ubmk50275.2020.9219366.

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Li, Jiwei, Xianghua Zhang, Chun Yuan, Zhaohui Jiang, and Huanqing Feng. "Motif Extraction with Indicative Events for System Call Sequence Classification." In Fourth International Conference on Fuzzy Systems and Knowledge Discovery (FSKD 2007). IEEE, 2007. http://dx.doi.org/10.1109/fskd.2007.411.

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Reports on the topic "Sequence motif"

1

Millan, Jose L. Sequence Motifs Specifying Homing and Metastasis to Bone. Fort Belvoir, VA: Defense Technical Information Center, July 2002. http://dx.doi.org/10.21236/ada407485.

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2

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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Yaron, Zvi, Abigail Elizur, Martin Schreibman, and Yonathan Zohar. Advancing Puberty in the Black Carp (Mylopharyngodon piceus) and the Striped Bass (Morone saxatilis). United States Department of Agriculture, January 2000. http://dx.doi.org/10.32747/2000.7695841.bard.

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Both the genes and cDNA sequences encoding the b-subunits of black carp LH and FSH were isolated, cloned and sequenced. Sequence analysis of the bcFSHb and LHb5'flanking regions revealed that the promoter region of both genes contains canonical TATA sequences, 30 bp and 17 bp upstream of the transcription start site of FSHb and LHb genes, respectively. In addition, they include several sequences of cis-acting motifs, required for inducible and tissue-specific transcriptional regulation: the gonadotropin-specific element (GSE), GnRH responsive element (GRE), half sites of estrogen and androgen response elements, cAMP response element, and AP1. Several methods have been employed by the Israeli team to purify the recombinant b subunits (EtOH precipitation, gel filtration and lentil lectin). While the final objective to produce pure recombinantGtH subunits has not yet been achieved, we have covered much ground towards this goal. The black carp ovary showed a gradual increase in both mass and oocyte diameter. First postvitellogenic oocytes were found in 5 yr old fish. At this age, the testes already contained spermatozoa. The circulating LH levels increased from 0.5 ng/ml in 4 yr old fish to >5ng/ml in 5 yr old fish. In vivo challenge experiments in black carp showed the initial LH response of the pituitary to GnRH in 4 yr old fish. The response was further augmented in 5 yr old fish. The increase in estradiol level in response to gonadotropic stimulation was first noted in 4 yr old fish but this response was much stronger in the following year. In vivo experiments on the FSHb and LHb mRNA levels in response to GnRH were carried out on common carp as a model for synchronom spawning cyprinids. These experiments showed the prevalence of FSHP in maturing fish while LHP mRNA was prevalent in mature fish, especially in females. The gonadal fat-pad was found to originate from the retroperitoneal mesoderm and not from the genital ridge, thus differing from that reported in certain amphibians This tissue possibly serves as the major source of sex steroids in the immature black carp. However, such a function is taken over by the developing gonads in 4 yr old fish. In the striped bass, we described the ontogeny of the neuro-endocrine parameters along the brain-pituitary-gonadal axis during the first four years of life, throughout gonadal development and the onset of puberty. We also described the responsiveness of the reproductive axis to long-term hormonal manipulations at various stages of gonadal development. Most males reached complete sexual maturity during the first year of life. Puberty was initiated during the third year of life in most females, but this first reproductive cycle did not lead to the acquisition of full sexual maturity. This finding indicates that more than one reproductive cycle may be required before adulthood is reached. Out of the three native GnRHs present in striped bass, only sbGnRH and cGnRH II increased concomitantly with the progress of gonadal development and the onset of puberty. This finding, together with data on GtH synthesis and release, suggests that while sbGnRH and cGnRH II may be involved in the regulation of puberty in striped bass, these neuropeptides are not limiting factors to the onset of puberty. Plasma LH levels remained low in all fish, suggesting that LH plays only a minor role in early gonadal development. This hypothesis was further supported by the finding that experimentally elevated plasma LH levels did not result in the induction of complete ovarian and testicular development. The acquisition of complete puberty in 4 yr old females was associated with a rise in the mRNA levels of all GtH subunit genes, including a 218-fold increase in the mRNA levels of bFSH. mRNA levels of the a and PLH subunits increased only 11- and 8-fold, respectively. Although data on plasma FSH levels are unavailable, the dramatic increase in bFSH mRNA suggests a pivotal role for this hormone in regulating the onset and completion of puberty in striped bass. The hormonal regulation of the onset of puberty and of GtH synthesis and release was studied by chronic administration of testosterone (T) and/or an analog of gonadotropin-releasing hormone (G). Sustained administration of T+G increased the mRNA levels of the PLH subunit to the values characteristic of sexually mature fish, and also increased the plasma levels of LH. However, these changes did not result in the acceleration of sexual maturation. The mRNA levels of the bFSH subunit were slightly stimulated, but remained about 1/10 of the values characteristic of sexually mature fish. It is concluded that the stimulation of FSH gene expression and release does not lead to the acceleration of sexual maturity, and that the failure to sufficiently stimulate the bFSH subunit gene expression may underlie the inability of the treatments to advance sexual maturity. Consequently, FSH is suggested to be the key hormone to the initiation and completion of puberty in striped bass. Future efforts to induce precocious puberty in striped bass should focus on understanding the regulation of FSH synthesis and release and on developing technologies to induce these processes. Definite formulation of hormonal manipulation to advance puberty in the striped bass and the black carp seems to be premature at this stage. However, the project has already yielded a great number of experimental tools of DNA technology, slow-release systems and endocrine information on the process of puberty. These systems and certain protocols have been already utilized successfully to advance maturation in other fish (e.g. grey mullet) and will form a base for further study on fish puberty.
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Pawlowski, Wojtek P., and Avraham A. Levy. What shapes the crossover landscape in maize and wheat and how can we modify it. United States Department of Agriculture, January 2015. http://dx.doi.org/10.32747/2015.7600025.bard.

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Meiotic recombination is a process in which homologous chromosomes engage in the exchange of DNA segments, creating gametes with new genetic makeup and progeny with new traits. The genetic diversity generated in this way is the main engine of crop improvement in sexually reproducing plants. Understanding regulation of this process, particularly the regulation of the rate and location of recombination events, and devising ways of modifying them, was the major motivation of this project. The project was carried out in maize and wheat, two leading crops, in which any advance in the breeder’s toolbox can have a huge impact on food production. Preliminary work done in the USA and Israeli labs had established a strong basis to address these questions. The USA lab pioneered the ability to map sites where recombination is initiated via the induction of double-strand breaks in chromosomal DNA. It has a long experience in cytological analysis of meiosis. The Israeli lab has expertise in high resolution mapping of crossover sites and has done pioneering work on the importance of epigenetic modifications for crossover distribution. It has identified genes that limit the rates of recombination. Our working hypothesis was that an integrative analysis of double-strand breaks, crossovers, and epigenetic data will increase our understanding of how meiotic recombination is regulated and will enhance our ability to manipulate it. The specific objectives of the project were: To analyze the connection between double-strand breaks, crossover, and epigenetic marks in maize and wheat. Protocols developed for double-strand breaks mapping in maize were applied to wheat. A detailed analysis of existing and new data in maize was conducted to map crossovers at high resolution and search for DNA sequence motifs underlying crossover hotspots. Epigenetic modifications along maize chromosomes were analyzed as well. Finally, a computational analysis tested various hypotheses on the importance of chromatin structure and specific epigenetic modifications in determining the locations of double-strand breaks and crossovers along chromosomes. Transient knockdowns of meiotic genes that suppress homologous recombination were carried out in wheat using Virus-Induced Gene Silencing. The target genes were orthologs of FANCM, DDM1, MET1, RECQ4, and XRCC2.
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Altstein, Miriam, and Ronald Nachman. Rationally designed insect neuropeptide agonists and antagonists: application for the characterization of the pyrokinin/Pban mechanisms of action in insects. United States Department of Agriculture, October 2006. http://dx.doi.org/10.32747/2006.7587235.bard.

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The general objective of this BARD project focused on rationally designed insect neuropeptide (NP) agonists and antagonists, their application for the characterization of the mechanisms of action of the pyrokinin/PBAN (PK-PBAN) family and the development of biostable, bioavailable versions that can provide the basis for development of novel, environmentally-friendly pest insect control agents. The specific objectives of the study, as originally proposed, were to: (i) Test stimulatory potencies of rationally designed backbone cyclic (BBC) peptides on pheromonotropic, melanotropic, myotropic and pupariation activities; (ii) Test the inhibitory potencies of the BBC compounds on the above activities evoked either by synthetic peptides (PBAN, LPK, myotropin and pheromonotropin) or by the natural endogenous mechanism; (iii) Determine the bioavailability of the most potent BBC compounds that will be found in (ii); (iv) Design, synthesize and examine novel PK/PBAN analogs with enhanced bioavailability and receptor binding; (v) Design and synthesize ‘magic bullet’ analogs and examine their ability to selectively kill cells expressing the PK/PBAN receptor. To achieve these goals the agonistic and antagonistic activities/properties of rationally designed linear and BBC neuropeptide (NP) were thoroughly studied and the information obtained was further used for the design and synthesis of improved compounds toward the design of an insecticide prototype. The study revealed important information on the structure activity relationship (SAR) of agonistic/antagonistic peptides, including definitive identification of the orientation of the Pro residue as trans for agonist activity in 4 PK/PBANbioassays (pheromonotropic, pupariation, melanotropic, & hindgut contractile) and a PK-related CAP₂b bioassay (diuretic); indications that led to the identification of a novel scaffold to develop biostbiostable, bioavailable peptidomimetic PK/PBANagonists/antagonists. The work led to the development of an arsenal of PK/PBAN antagonists with a variety of selectivity profiles; whether between different PKbioassays, or within the same bioassay between different natural elicitors. Examples include selective and non-selective BBC and novel amphiphilic PK pheromonotropic and melanotropic antagonists some of which are capable of penetrating the moth cuticle in efficacious quantities. One of the latter analog group demonstrated unprecedented versatility in its ability to antagonize a broad spectrum of pheromonotropic elicitors. A novel, transPro mimetic motif was proposed & used to develop a strong, selective PK agonist of the melanotropic bioassay in moths. The first antagonist (pure) of PK-related CAP₂b diuresis in flies was developed using a cisPro mimetic motif; an indication that while a transPro orientation is associated with receptor agonism, a cisPro orientation is linked with an antagonist interaction. A novel, biostablePK analog, incorporating β-amino acids at key peptidase-susceptible sites, exhibited in vivo pheromonotropic activity that by far exceeded that of PBAN when applied topically. Direct analysis of neural tissue by state-of-the-art MALDI-TOF/TOF mass spectrometry was used to identify specific PK/PK-related peptides native to eight arthropod pest species [house (M. domestica), stable (S. calcitrans), horn (H. irritans) & flesh (N. bullata) flies; Southern cattle fever tick (B. microplus), European tick (I. ricinus), yellow fever mosquito (A. aegypti), & Southern Green Stink Bug (N. viridula)]; including the unprecedented identification of mass-identical Leu/Ile residues and the first identification of NPs from a tick or the CNS of Hemiptera. Evidence was obtained for the selection of Neb-PK-2 as the primary pupariation factor of the flesh fly (N. bullata) among native PK/PK-related candidates. The peptidomic techniques were also used to map the location of PK/PK-related NP in the nervous system of the model fly D. melanogaster. Knowledge of specific PK sequences can aid in the future design of species specific (or non-specific) NP agonists/antagonists. In addition, the study led to the first cloning of a PK/PBAN receptor from insect larvae (S. littoralis), providing the basis for SAR analysis for the future design of 2ⁿᵈgeneration selective and/or nonselective agonists/antagonists. Development of a microplate ligand binding assay using the PK/PBAN pheromone gland receptor was also carried out. The assay will enable screening, including high throughput, of various libraries (chemical, molecular & natural product) for the discovery of receptor specific agonists/antagonists. In summary, the body of work achieves several key milestones and brings us significantly closer to the development of novel, environmentally friendly pest insect management agents based on insect PK/PBANNPs capable of disrupting critical NP-regulated functions.
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McElwain, Terry F., Eugene Pipano, Guy H. Palmer, Varda Shkap, Stephn A. Hines, and Wendy C. Brown. Protection of Cattle against Babesiosis: Immunization against Babesia bovis with an Optimized RAP-1/Apical Complex Construct. United States Department of Agriculture, September 1999. http://dx.doi.org/10.32747/1999.7573063.bard.

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Previous research and current efforts at control of babesiosis fall short of meeting the needs of countries where the disease is endemic, such as Israel, as well as the needs of exporting countries and countries bordering on endemic areas, such as the U.S. Our long-term goal is to develop improved methods of immunization against bovine babesiosis based on an understanding of the molecular mechanisms of immune protection and parasite targets of a protective immune response. In our previous BARD project, we established the basis for focusing on rhoptry antigens as components of a subunit vaccine against bovine babesiosis, and for additional research to better characterize rhoptry associated protein-1 (RAP-1) as a target of protective immunity. In this continuation BARD project, our objectives were to [1] optimize the immune response against RAP-1, and [2] identify additional rhoptry candidate vaccine antigens. The entire locus encoding B. bovis RAP-1 was sequenced, and the rap-1 open reading frame compared among several strains. Unlike B. bigemina, in which multiple gene copies with variant domains encode RAP-1, the B. bovis RAP-1 locus contains only two identical genes which are conserved among strains. Through testing of multiple truncated constructs of rRAP-1, one or more immunodominant T cell epitopes were mapped to the amino terminal half of RAP-1. At least one linear and one conformational B cell epitope have been demonstrated in the same amino terminal construct, which in B. bigemina RAP-1 also contains an epitope recognized by neutralizing antibody. The amine terminal half of the molecule represents the most highly conserved part of the gene family and contains motifs conserved broadly among the apicomplexa. In contrast, the carboxy terminal half of B. bovis RAP-1 is less well conserved and contains multiple repeats encoding a linear B cell epitope potentially capable of inducing an ineffective, T cell independent, type 2 immune response. Therefore, we are testing an amino terminal fragment of RAP-1 (RAP-1N) in an immunization trial in cattle. Cattle have beer immunized with RAP-1N or control antigen, and IL-12 with Ribi adjuvant. Evaluation of the immune response is ongoing, and challenge with virulent B. bovis will occur in the near future. While no new rhoptry antigens were identified, our studies did identify and characterize a new spherical body antigen (SBP3), and several heat shock proteins (HSP's). The SBP3 and HSP21 antigens stimulate T cells from immune cattle and are considered new vaccine candidates worthy of further testing. Overall, we conclude that a single RAP-1 vaccine construct representing the conserved amino terminal region of the molecule should be sufficient for immunization against all strains of B. bovis. While results of the ongoing immunization trial will direct our next research steps, results at this time are consistent with our long term goal of designing a subunit vaccine which contains only the epitopes relevant to induction of protective immunity. Parallel studies are defining the mechanisms of protective immunity. Apicomplexan protozoa, including babesiosis and malaria, cause persistent diseases for which control is inadequate. The apical organelles are defining features of these complex protozoa, and have been conserved through the evolutionary process, Past and current BARD projects on babesiosis have established the validity and potential of exploiting these conserved organelles in developing improved control methods applicable to all apicomplexan diseases.
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Palmer, Guy, Varda Shkap, Wendy Brown, and Thea Molad. Control of bovine anaplasmosis: cytokine enhancement of vaccine efficacy. United States Department of Agriculture, March 2007. http://dx.doi.org/10.32747/2007.7695879.bard.

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Anaplasmosis an arthropod-born disease of cattle caused by the rickettsia Anaplasma marginale and is an impediment to efficient production of healthy livestock in both Israel and the United States. Currently the only effective vaccines are derived from the blood of infected cattle. The risk of widespread transmission of both known and newly emergent pathogens has prevented licensure of live blood-based vaccines in the U.S. and is a major concern for their continued use in Israel. Consequently development of a safe, effective vaccine is a high priority. In this collaborative project we focused on two approaches to vaccine development. The first focused o n improving antigen delivery to livestock and specifically examined how DNA vaccines could be improved to enhance priming and expansion of the immune response. This research resulted in development and testing of two novel vaccine delivery systems--one that targeted antigen spread among dendritic cells (the key cell in priming immune responses and a follow-on construct that also specifically targeted antigen to the endosomal-lysosomal compartment the processing organelle within the dendritic cell that directs vaccine antigen to the MHC class ll-CD4* T cell priming pathway). The optimized construct targeting vaccine antigen to the dendritic cell MHC class II pathway was tested for ability to prime A. marginale specific immune responses in outbred cattle. The results demonstrated both statistically significant effects of priming with a single immunization, continued expansion of the primary immune response including development of high affinity lgG antibodies and rapid recall of the memory response following antigen challenge. This portion of the study represented a significant advance in vaccine delivery for livestock. Importantly the impact of these studies is not limited to A. marginale a s the targeting motifs are optimized for cattle and can be adapted to other cattle vaccinations by inserting a relevant pathogen-specific antigen. The second approach (which represented an addition to the project for which approval was requested as part of the first annual report) was a comparative approach between A . marginale and the Israel A . centrale vaccines train. This addition was requested as studies on Major Surface Protein( MSP)- 2 have shown that this antigen is highly antigenically variable and presented solely as a "static vaccine" antigen does not give cross-strain immunity. In contrast A. . centrale is an effective vaccine which Kimron Veterinary institute has used in the field in Israel for over 50 years. Taking advantage of this expertise, a broad comparison of wild type A. marginale and vaccine strain was initiated. These studies revealed three primary findings: i) use of the vaccine is associated with superinfection, but absence of clinical disease upon superinfection with A. marginale; ii) the A. centrale vaccine strain is not only less virulent but transmission in competent in Dermacentor spp. ticks; and iii) some but not all MSPs are conserved in basic orthologous structure but there are significant polymorphisms among the strains. These studies clearly indicated that there are statistically significant differences in biology (virulence and transmission) and provide a clear path for mapping of biology with the genomes. Based on these findings, we initiated complete genome sequencing of the Israel vaccine strain (although not currently funded by BARD) and plant to proceed with a comparative genomics approach using already sequenced wild-type A. marginale. These findings and ongoing collaborative research tie together filed vaccine experience with new genomic data, providing a new approach to vaccine development against a complex pathogen.
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