Relevant bibliographies by topics / Sequence-function

Academic literature on the topic 'Sequence-function'

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Published: 9 March 2023
Last updated: 10 March 2023

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Journal articles on the topic "Sequence-function"

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Holding, Cathy. "Can sequence predict function?" Genome Biology 4 (2004): spotlight—20040419–01. http://dx.doi.org/10.1186/gb-spotlight-20040419-01.

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K., Sahityabhilash. "Impact of Loss Function Using M-LSTM Classifier for Sequence Data." International Journal of Psychosocial Rehabilitation 24, no. 5 (April 20, 2020): 3487–94. http://dx.doi.org/10.37200/ijpr/v24i5/pr202059.

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Copp, Janine N., Eyal Akiva, Patricia C. Babbitt, and Nobuhiko Tokuriki. "Revealing Unexplored Sequence-Function Space Using Sequence Similarity Networks." Biochemistry 57, no. 31 (July 27, 2018): 4651–62. http://dx.doi.org/10.1021/acs.biochem.8b00473.

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Guzide. "The Conditional Sequence Information Function." Journal of Mathematics and Statistics 6, no. 2 (April 1, 2010): 89–91. http://dx.doi.org/10.3844/jmssp.2010.89.91.

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Licinio, J., and M.-L. Wong. "Sequence and function in pharmacogenomics." Pharmacogenomics Journal 3, no. 3 (January 2003): 123. http://dx.doi.org/10.1038/sj.tpj.6500185.

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Ameres, Stefan L., and Phillip D. Zamore. "Diversifying microRNA sequence and function." Nature Reviews Molecular Cell Biology 14, no. 8 (June 26, 2013): 475–88. http://dx.doi.org/10.1038/nrm3611.

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Starr, Tyler N., and Joseph W. Thornton. "Exploring protein sequence–function landscapes." Nature Biotechnology 35, no. 2 (February 2017): 125–26. http://dx.doi.org/10.1038/nbt.3786.

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Pauli-Magnus, Christiane, and Deanna L. Kroetz. "reference sequence and reference function." Clinical Pharmacology and Therapeutics 72, no. 1 (July 2002): 100–101. http://dx.doi.org/10.1067/mcp.2002.125561.

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Danchin, Antoine. "From protein sequence to function." Current Opinion in Structural Biology 9, no. 3 (June 1999): 363–67. http://dx.doi.org/10.1016/s0959-440x(99)80049-9.

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Whisstock, James C., and Arthur M. Lesk. "4. Predicting function from sequence." Reproduction, Fertility and Development 15, no. 9 (2003): 4. http://dx.doi.org/10.1071/srb03ab4.

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Dissertations / Theses on the topic "Sequence-function"

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McDougall, Rachel Clare. "Schizosaccharomyces pombe : from sequence to function." Thesis, University of Cambridge, 1997. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.627369.

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Spencer, Sarah Jean. "Linking sequence to function in microbial genomics." Thesis, Massachusetts Institute of Technology, 2017. http://hdl.handle.net/1721.1/113437.

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Thesis: Ph. D., Massachusetts Institute of Technology, Computational and Systems Biology Program, 2017.
This electronic version was submitted by the student author. The certified thesis is available in the Institute Archives and Special Collections.
Cataloged from student-submitted PDF version of thesis.
Includes bibliographical references (pages 129-140).
Microbial genomes show high plasticity due to horizontal transfer, large community sizes, and rapid growth paired with adaptive mutations. Despite this mutability of gene content, most studies of microbial communities still rely on bulk, single-gene amplicon sequencing. In this thesis, I present methods that interrogate the gene content of single cells derived from complex natural communities. In the first project, I present a novel molecular biology method to link a bacterial functional gene to its host species with single-cell resolution. This high-throughput protocol is applied to assess the distribution of anaerobic respiration genes in a lake ecosystem. In the second project, I demonstrate extensions of this methodology to link genes between spatially proximal microbial cells, and apply this approach to probe the spatial organization of human dental plaque using DNA sequencing. In the final project, I completed whole-genome sequencing of environmental isolates derived from single, cultivable cells and employ mutational and horizontal transfer analysis to demonstrate adaptation to harsh environmental conditions in contaminated groundwater. These projects demonstrate the rich information stored within each microbial genome and the impact of spatial distribution in the environment. Each effort also contributes or highlights new molecular biology techniques to generate genomic data from individual microbial cells.
by Sarah Jean Spencer.
Ph. D.
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Warnecke, Tobias. "Determinants of coding sequence evolution- beyong protein function." Thesis, University of Bath, 2010. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.531341.

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Otto, Gary Edward. "Sequence comparison and the prediction of protein function." Thesis, Massachusetts Institute of Technology, 1986. http://hdl.handle.net/1721.1/14888.

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Hamilton, Russell S. "DAROGAN : enzyme function prediction from multiple sequence alignments." Thesis, University of Edinburgh, 2006. http://hdl.handle.net/1842/14972.

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The function of an enzyme is often dependent on a few key functional residues and the principal objective of this project was to develop a novel function prediction system which takes advantage of this by comparing the conserved amino acids in known enzyme families to those in a putative enzyme. Multiple sequence alignments of well characterised enzyme families (with an E.C. number assigned) are used to create unordered sets of conserved functional residues, termed Treads.  Comparison of a query proteins Tread  to the reference Treads is undertaken by projecting them in multidimensional space and measuring distance between them. A major advantage of this prediction strategy implemented in DAROGAN is that it should be able to recognise similarities in the functions of enzymes that are not similar in structure or sequence. The method has been tested with regard to its ability to predict cofactor-dependencies toward pyridoxal-5’-phosphate, thiamine, glutathione and folic acid utilising enzymes. An area of application for DAROGAN is the prediction of previously described enzyme functions in organisms with completed genomes to which no gene and protein sequence could be assigned though the standard annotation processes. Investigations were made into the potential of utilising the DAROGAN method to propose candidates for the missing pyridoxal-5’-phosphate utilising enzymes in the E. coli genome according to EcoCyc. Candidates are proposed by assessing the 511 sequences from the GeneQuiz project, to which there are homologues in other species, but with uncertain functions. The assessment takes the form of using the DAROGAN method to determine the similarities of each of the sequences to the reference Treads.
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Colafranceschi, Mauro. "Distribution of Hydrophobicity patterns in proteins primary structures: a statistical study." Doctoral thesis, La Sapienza, 2005. http://hdl.handle.net/11573/916823.

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Rünger, Dennis. "On the generation and function of conscious sequence knowledge." Doctoral thesis, Humboldt-Universität zu Berlin, Mathematisch-Naturwissenschaftliche Fakultät II, 2008. http://dx.doi.org/10.18452/15845.

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Es besteht weitgehend Einigkeit darüber, dass inzidentelles Lernen bewusstes Wissen über eine sequenziell strukturierte Regelhaftigkeit erzeugen kann, auch wenn die zu Grunde liegenden Lernprozesse nur ungenügend verstanden sind. Ob jedoch Sequenzlernen auch „implizit“ oder unbewusst erfolgen kann, ist umstritten. Fortschritte in diese Frage sind von Untersuchungen zu bewusstem und unbewusstem Lernen zu erwarten, die vor dem Hintergrund übergreifender Bewusstseinstheorien erfolgen. Rünger und Frensch (2008a) zeigen, wie „bewusstes Sequenzwissen“ in Rückgriff auf die „global workspace“-Theorie des Bewusstseins definiert und operationalisiert werden kann. Im Rahmen dieser Theorie wird „inferenzielle Promiskuität“ als zentrales funktionales Merkmal bewusster mentaler Repräsentationen betrachtet. Rünger und Frensch (2008b) überprüfen eine zentrale Vorhersage der „unexpected event“-Hypothese, einer Theorie zur Entstehung bewussten Wissens in inzidentellen Lernsituationen. In einer Serie von Experimenten wurden unerwartete Ereignisse durch Unterbrechungen des inzidentellen Lernprozesses experimentell induziert. In Übereinstimmung mit der „unexpected event“-Hypothese fanden die Autoren, dass sich die Verfügbarkeit bewussten Sequenzwissens erhöhte. Rünger, Nagy und Frensch (in Druck) untersuchen schließlich die Funktion bewussten Sequenzwissens im Kontext eines Rekognitionstests. Die empirischen Befunde deuten darauf hin, dass bewusstes Sequenzwissen die epistemische Grundlage für rationale Urteile im Gegensatz zu intuitiven oder heuristischen Urteilen darstellt.
There is a general consensus that incidental learning can produce conscious knowledge about a hidden sequential regularity, even though the underlying learning mechanisms are still poorly understood. By contrast, whether sequence learning can also be “implicit” or nonconscious is a matter of intense debate. Progress can be achieved by grounding research on conscious and nonconscious learning in larger theoretical frameworks of consciousness. Rünger and Frensch (2008a) show how “conscious sequence knowledge” can be defined and operationalized in reference to global workspace theory of consciousness that depicts “inferential promiscuity” as the functional hallmark of conscious mental representations. Rünger and Frensch (2008b) test a central prediction of the unexpected-event hypothesis — a theoretical account of the generation of conscious knowledge in incidental learning situations. In a series of experiments, unexpected events were induced experimentally by disrupting the incidental learning process. In line with the unexpected-event hypothesis, the authors observed an increased availability of conscious sequence knowledge. Finally, Rünger, Nagy, and Frensch (in press) explore the function of conscious sequence knowledge in the context of a sequence recognition test. The empirical results suggest that conscious sequence knowledge provides the epistemic basis for reasoned — as opposed to intuitive or heuristic — judgments.
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Kandaswamy, Krishna Kumar [Verfasser]. "Sequence function classification by machine learning methods / Krishna Kumar Kandaswamy." Lübeck : Zentrale Hochschulbibliothek Lübeck, 2012. http://d-nb.info/1023624257/34.

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Pryde, Fiona E. "Function of subtelomeric repeat sequence in the yeast Saccharomyces cerevisiae." Thesis, University of Oxford, 1999. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.302603.

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Wang, Pam Shou-Ping. "Exploring the sequence-structure-function relationship in beta-peptide foldamers." Thesis, Yale University, 2014. http://pqdtopen.proquest.com/#viewpdf?dispub=3580893.

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The interplay between sequence, structure and function is an underlying theme in biological systems. Proteins, in particular, have evolved the ability to access a virtually infinite set of three-dimensional architectures from a small collection of building blocks; it is precisely this complexity of form that finely tunes their functional specificity. β-Peptides are a class of unnatural polyamides known to adopt structural motifs that are in many ways reminiscent of protein folds in nature. This dissertation first investigates the relationship between sequence and structure in self-assembling β-peptides, then demonstrates how the latter translates into function.

Chapter 1 provides an overview of the fundamental principles guiding β-peptide helix formation and self-assembly, and describes their applications both within and outside of the biological context. The ability of β-peptides to mimic natural α-helices while maintaining proteolytic resistance allows them to serve as therapeutic agents by targeting, for example, protein-protein interactions. Their unique stability in both aqueous and organic environments further enables the development of β-peptide-based nanomaterials and organocatalysts.

Chapter 2 elucidates the relationship between β-peptide primary sequence and quaternary structure based on the biophysical characterization of the Acid-3Y bundle. Acid-3Y was designed by substituting isoleucine for leucine side-chains in the sequence of the previously characterized octamer, Acid-1Y. The finding that Acid-3Y assembles into a tetrameric bundle suggests that branching at the γ-carbon of hydrophobic residues plays a critical role in determining β-peptide bundle stoichiometry.

Chapter 3 explores the potential of β-peptide bundles to mimic enzyme structure and function. The demonstration of β-peptide mutarotase activity in benzene highlights the importance of macromolecular preorganization in catalysis, while the ability of rationally designed β-peptide bundles to catalyze ester hydrolysis in water represents a crucial step towards the functionalization of these unnatural macromolecules. The dependence of catalytic activity on both active site geometry and bundle assembly, together with their substrate selectivity, underscores the unique biomimetic capacity of β-peptides.

Chapter 4 describes the rational design of a β-peptide ligand for the parathyroid hormone 1 receptor (PTH1R). Using previous strategies that led to the identification of p53 and GLP-1 mimics, a 12-member β-peptide library was constructed and tested in vitro for binding to the receptor protein. Although no hits were found from this initial screen, subsequently designed α/β-peptide chimeras showed promise as synthetic antagonists of PTH1R with improved pharmacokinetic properties.

Chapter 5 summarizes the key results of this dissertation and offers a perspective on possible future research directions. A breakthrough in the field of β-peptides would rely on the development of a method to synthesize genuine "β-proteins" with more sophisticated structure and function.

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Books on the topic "Sequence-function"

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Koonin, Eugene V., and Michael Y. Galperin. Sequence — Evolution — Function. Boston, MA: Springer US, 2003. http://dx.doi.org/10.1007/978-1-4757-3783-7.

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R, Pennington S., and Dunn M. J, eds. Proteomics: From protein sequence to function. Oxford: BIOS, 2001.

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Gromiha, M. Michael. Protein bioinformatics: From sequence to function. Amsterdam: Academic Press/Elsevier, 2010.

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Koonin, Eugene V. Sequence - evolution - function: Computational approaches in comparative genomics. Boston: Kluwer Academic, 2003.

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Koonin, Eugene V. Sequence - evolution - function: Computational approaches in comparative genomics. Boston: Kluwer Academic, 2003.

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Y, Galperin Michael, ed. Sequence - evolution - function: Computational approaches in comparative genomics. Boston: Kluwer Academic, 2003.

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Gorodkin, Jan, and Walter L. Ruzzo, eds. RNA Sequence, Structure, and Function: Computational and Bioinformatic Methods. Totowa, NJ: Humana Press, 2014. http://dx.doi.org/10.1007/978-1-62703-709-9.

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RNA sequence, structure, and function: Computational and bioinformatic methods. New York: Humana Press, 2014.

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Human Genome Organisation. European Meeting. Genome analysis: From sequence to function : 1st European meeting 1990, Human Genome Organisation (HUGO). Edited by Collins J, Driesel Albert J, and Human Genome Organisation. Heidelberg: Hüthig, 1991.

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The pots and potters of Assyria: Technology and organisation of production, ceramic sequence and vessel function at late Bronze Age, Tell Sabi Abyad, Syria. Turnhout: Brepols, 2008.

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Book chapters on the topic "Sequence-function"

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Koonin, Eugene V., and Michael Y. Galperin. "Introduction: Personal Interludes." In Sequence — Evolution — Function, 1. Boston, MA: Springer US, 2003. http://dx.doi.org/10.1007/978-1-4757-3783-7_1.

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Koonin, Eugene V., and Michael Y. Galperin. "Epilogue: Peering through the crystal ball." In Sequence — Evolution — Function, 371–80. Boston, MA: Springer US, 2003. http://dx.doi.org/10.1007/978-1-4757-3783-7_10.

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Koonin, Eugene V., and Michael Y. Galperin. "Genomics: From Phage to Human." In Sequence — Evolution — Function, 3–24. Boston, MA: Springer US, 2003. http://dx.doi.org/10.1007/978-1-4757-3783-7_2.

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Koonin, Eugene V., and Michael Y. Galperin. "Evolutionary Concept in Genetics and Genomics." In Sequence — Evolution — Function, 25–49. Boston, MA: Springer US, 2003. http://dx.doi.org/10.1007/978-1-4757-3783-7_3.

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Koonin, Eugene V., and Michael Y. Galperin. "Information Sources for Genomics." In Sequence — Evolution — Function, 51–110. Boston, MA: Springer US, 2003. http://dx.doi.org/10.1007/978-1-4757-3783-7_4.

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Koonin, Eugene V., and Michael Y. Galperin. "Principles and Methods of Sequence Analysis." In Sequence — Evolution — Function, 111–92. Boston, MA: Springer US, 2003. http://dx.doi.org/10.1007/978-1-4757-3783-7_5.

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Koonin, Eugene V., and Michael Y. Galperin. "Genome Annotation and Analysis." In Sequence — Evolution — Function, 193–226. Boston, MA: Springer US, 2003. http://dx.doi.org/10.1007/978-1-4757-3783-7_6.

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Koonin, Eugene V., and Michael Y. Galperin. "Comparative Genomics and New Evolutionary Biology." In Sequence — Evolution — Function, 227–94. Boston, MA: Springer US, 2003. http://dx.doi.org/10.1007/978-1-4757-3783-7_7.

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Koonin, Eugene V., and Michael Y. Galperin. "Evolution of Central Metabolic Pathways: The Playground of Non-orthologous Gene Displacement." In Sequence — Evolution — Function, 295–355. Boston, MA: Springer US, 2003. http://dx.doi.org/10.1007/978-1-4757-3783-7_8.

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Koonin, Eugene V., and Michael Y. Galperin. "Genomes and the Protein Universe." In Sequence — Evolution — Function, 357–69. Boston, MA: Springer US, 2003. http://dx.doi.org/10.1007/978-1-4757-3783-7_9.

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Conference papers on the topic "Sequence-function"

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Rocha, Rodrigo C. O., Pavlos Petoumenos, Zheng Wang, Murray Cole, and Hugh Leather. "Function Merging by Sequence Alignment." In 2019 IEEE/ACM International Symposium on Code Generation and Optimization (CGO). IEEE, 2019. http://dx.doi.org/10.1109/cgo.2019.8661174.

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Sheng Hong, Kefei Liu, Ying Li, Hang Zou, Yunping Qi, and Kan Hong. "A new direct-sequence UWB transceiver based on Bridge function sequence." In 2010 Second International Conference on Computational Intelligence and Natural Computing (CINC). IEEE, 2010. http://dx.doi.org/10.1109/cinc.2010.5643750.

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PAWŁOWSKI, K., Ł. JAROSZEWSKI, L. RYCHLEWSKI, and A. GODZIK. "SENSITIVE SEQUENCE COMPARISON AS PROTEIN FUNCTION PREDICTOR." In Proceedings of the Pacific Symposium. WORLD SCIENTIFIC, 1999. http://dx.doi.org/10.1142/9789814447331_0005.

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Yuta Tsuboi and Hisashi Kashima. "A new objective function for sequence labeling." In 2008 19th International Conference on Pattern Recognition (ICPR). IEEE, 2008. http://dx.doi.org/10.1109/icpr.2008.4761442.

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Wang, Shixian, Qingjie Zhao, Yuehui Chen, and Peng Wu. "Function Sequence Genetic Programming for pattern classification." In 2011 Seventh International Conference on Natural Computation (ICNC). IEEE, 2011. http://dx.doi.org/10.1109/icnc.2011.6022170.

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Modi, Rohan, Kush Naik, Tarjni Vyas, Shivani Desai, and Sheshang Degadwala. "E-mail autocomplete function using RNN Encoder-decoder sequence-to-sequence model." In 2021 5th International Conference on Electronics, Communication and Aerospace Technology (ICECA). IEEE, 2021. http://dx.doi.org/10.1109/iceca52323.2021.9675961.

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Thalapathiraj, S., B. Baskaran, J. Ravikumar, and R. Venkatraman. "Some difference sequence spaces defined by Orlicz function." In 4TH INTERNATIONAL CONFERENCE ON THE SCIENCE AND ENGINEERING OF MATERIALS: ICoSEM2019. AIP Publishing, 2020. http://dx.doi.org/10.1063/5.0029028.

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Wu, Yi, and Edward Y. Chang. "Distance-function design and fusion for sequence data." In the Thirteenth ACM conference. New York, New York, USA: ACM Press, 2004. http://dx.doi.org/10.1145/1031171.1031238.

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Ofie, M., and E. Herawati. "Matrix Operator of Musielak-j Function Sequence Space." In International Conference of Science, Technology, Engineering, Environmental and Ramification Researches. SCITEPRESS - Science and Technology Publications, 2018. http://dx.doi.org/10.5220/0010080309790981.

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Eretnova, O., and A. Dudorov. "The mass function of pre-main sequence stars." In ASTRONOMY AT THE EPOCH OF MULTIMESSENGER STUDIES. Proceedings of the VAK-2021 conference, Aug 23–28, 2021. Crossref, 2022. http://dx.doi.org/10.51194/vak2021.2022.1.1.040.

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The information about 26 pre-man sequence (PMS) binary stars and 34 stars with protoplanetary disks with well determinedmasses from the observations is collected. We constructed the mass distribution of PMS stars and approximated it with apower law dN ∼M −γ dM . The slope is γ = 2.16±0.17 for stars in a mass range of 0.6M ⊙ < M < 6.3M ⊙ , which is close tothe Salpeter mass function. Over the entire mass range, the mass distribution of young stars may be approximated with alognormal law, which the most probable mass M prob = (0.78 ± 0.12)M ⊙ .
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Reports on the topic "Sequence-function"

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Haussler, D., R. Hughey, K. Karplus, M. Cline, L. Grate, D. Kulp, K. Sjolander, and A. S. Lapedes. Covariation of mutations: A computational approach for determination of function and structure from sequence. Office of Scientific and Technical Information (OSTI), November 1998. http://dx.doi.org/10.2172/674904.

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Mockler, Todd C. The Brachypodium ENCODE Project – from sequence to function: Predicting physiological responses in grasses to facilitate engineering of biofuel crops. Office of Scientific and Technical Information (OSTI), January 2020. http://dx.doi.org/10.2172/1593294.

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Wallace, Susan S. Structure/Function Analysis of DNA-glycosylases That Repair Oxidized Purines and Pyrimidines and the Influence of Surrounding DNA Sequence on Their Interactions. Office of Scientific and Technical Information (OSTI), August 2005. http://dx.doi.org/10.2172/900301.

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

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This project relates the structure of the bacteriocin molecule (which is genetically determined) to its antimicrobial function. We have sequenced the 19,542 bp pediocin plasmid pMD136 and developed a genetic transfer system for pediococci. The pediocin A operon is complex, containing putative structural, immunity, processing, and transport genes. The deduced sequence of the pediocin A molecule contains 44 amino acids and has a predicted PI of 9.45. Mechanistic studies compared the interaction of pediocin PA-1 and nisin with Listeria monocytgenes cells and model lipid systems. While significant nisin-induced intracellular ATP depletion is caused by efflux, pediocin-induced depletion is caused exclusively by hydrolysis. Liposomes derived from L. monocytogenes phospholipids were used to study the physical chemistry of pediocin and nisin interactions with lipids. Their different pH optima are the results of different specific ionizable amino acids. We generated a predicted 3-D structural model for pediocin PA-1 and used a variety of mutant pediocins to demonstrate that the "positive patch" at residues 11 and 12 (and not the YGNGV consensus sequence) is responsible for the binding step of pediocin action. This structure/function understanding gained here provides necessary prerequisites to the more efficacious use of bacteriocins to control foodborne pathogens.
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Rafaeli, Ada, Russell Jurenka, and Daniel Segal. Isolation, Purification and Sequence Determination of Pheromonotropic-Receptors. United States Department of Agriculture, July 2003. http://dx.doi.org/10.32747/2003.7695850.bard.

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Moths constitute a major group of pest insects in agriculture. Pheromone blends are utilised by a variety of moth species to attract conspecific mates, which is under circadian control by the neurohormone, PBAN (pheromone-biosynthesis-activating neuropeptide). Our working hypothesis was that, since the emission of sex-pheromone is necessary to attract a mate, then failure to produce and emit pheromone is a potential strategy for manipulating adult moth behavior. The project aimed at identifying, characterising and determining the sequence of specific receptors responsible for the interaction with pheromonotropic neuropeptide/s using two related moth species: Helicoverpa armigera and H. lea as model insects. We established specific binding to a membrane protein estimated at 50 kDa in mature adult females using a photoaffinity-biotin probe for PBAN. We showed that JH is required for the up-regulation of this putative receptor protein. In vitro studies established that the binding initiates a cascade of second messengers including channel opening for calcium ions and intracellular cAMP production. Pharmacological studies (using sodium fluoride) established that the receptor is coupled to a G-protein, that is, the pheromone-biosynthesis-activating neuropeptide receptor (PBAN-R) belongs to the family of G protein-coupled receptor (GPCR)'s. We showed that PBAN-like peptides are present in Drosophila melanogaster based on bioassay and immunocytochemical data. Using the annotated genome of D. melanogaster to search for a GPCR, we found that some were similar to neuromedin U- receptors of vertebrates, which contain a similar C-terminal ending as PBAN. We established that neuromedin U does indeed induce pheromone biosynthesis and cAMP production. Using a PCR based cloning strategy and mRNA isolated from pheromone glands of H. zea, we successfully identified a gene encoding a GPCR from pheromone glands. The full-length PBAN-R was subsequently cloned and expressed in Sf9 insect cells and was shown to mobilize calcium in response to PBAN in a dose-dependent manner. The successful progress in the identification of a gene, encoding a GPCR for the neurohormone, PBAN, provides a basis for the design of a novel battery of compounds that will specifically antagonize pheromone production. Furthermore, since PBAN belongs to a family of insect neuropeptides with more than one function in different life stages, this rationale may be extended to other physiological key-regulatory processes in different insects.
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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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Nechushtai, Rachel, and Parag Chitnis. Role of the HSP70 Homologue from Chloroplasts in the Assembly of the Photosynthetic Apparatus. United States Department of Agriculture, July 1993. http://dx.doi.org/10.32747/1993.7568743.bard.

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The major goal of the proposed research was to study the role of a 70-kDa heat shock cognate protein from chloroplasts (ct-HSP70) in the assembly of chlorophyll-protein complexes. The latters are mostly important in allowing photosynthesis to occur. Photosynthesis is at the heart of crop productivity and the knowledge of the biogenesis of the photosynthetic apparatus is essential to manipulate the efficiency of photosynthesis. The characterization of the function of the ct-HSP70 was planned to be studied in vitro by assaying its capability to physically interact with the thylakoid proteins and to assist their assembly into thylakoid membranes. We planned to identify regions in the light-harvesting complex protein (LHCP) that interact with the ct-HSP70 and characterize the interaction between them. We also intended to isolate cDNA clones encoding ct-HSP70, sequence them, express one of them in E. coli and use the purified protein for functional assays. The research in this BARD proposal aimed at providing insights and aid in understanding the mechanism by which plants may respond to the heat stress. Since plants often experience increased temperatures.
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Galili, Gad, and Alan Bennett. Role of Molecular Chaperone in Wheat Storage Protein Assembly. United States Department of Agriculture, April 1995. http://dx.doi.org/10.32747/1995.7604926.bard.

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Following sequestration into the ER, wheat gliadins assemble into complexes that initiate the formation of protein bodies. In the present work we have characterized the DNA sequence and regulation of expression of a plant BiP and also studied its interaction with wheat storage proteins as well as its role in the maturation of these storage proteins. In the Israeli lab, immunoprecipitation studies were made using anti BiP and anti storage proteins sera, both in wheat and in transgenic tobacco plants expressing a wheat gliadin storage proteins. In both cases, we could show that BiP interacts with the gliadin storage proteins. In addition, we could show that BiP also played an important role in the initial assembly of the gliadins. In the American lab, the complexity, structure and properties of tomato BiP was characterized at the molecular and biochemical levels. In addition, tomato BiP was also overexpressed in bacteria and the overexpressed protein was found to be active. The cooperative findings of the Israeli and American labs clearly improves our understanding of the structure and expression of a plant BiP as well as its role in the maturation of storage proteins in plants seeds. In addition, it will serve as a foundation for future studies of the mechanisms of BiP function in in vitro studies using purified storage proteins and purified recombinant active BiP.
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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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Elroy-Stein, Orna, and Dmitry Belostotsky. Mechanism of Internal Initiation of Translation in Plants. United States Department of Agriculture, December 2010. http://dx.doi.org/10.32747/2010.7696518.bard.

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Original objectives Elucidation of PABP's role in crTMV148 IRES function in-vitro using wheat germ extract and krebs-2 cells extract. Fully achieved. Elucidation of PABP's role in crTMV148 IRES function in-vivo in Arabidopsis. Characterization of the physical interactions of PABP and other potential ITAFs with crTMV148 IRES. Partly achieved. To conduct search for additional ITAFs using different approaches and evaluate the candidates. Partly achieved. Background of the topic The power of internal translation via the activity of internal ribosomal entry site (IRES) elements allow coordinated synthesis of multiple gene products from a single transcription unit, and thereby enables to bypass the need for sequential transformation with multiple independent transgenes. The key goal of this project was to identify and analyze the IRES-trans-acting factors (ITAFs) that mediate the activity of a crucifer-infecting tobamovirus (crTMV148) IRES. The remarkable conservation of the IRES activity across the phylogenetic spectrum (yeast, plants and animals) strongly suggests that key ITAFs that mediate its activity are themselves highly conserved. Thus, crTMV148 IRES offers opportunity for elucidation of the fundamental mechanisms underlying internal translation in higher plants in order to enable its rational manipulation for the purpose of agricultural biotechnology. Major conclusions and achievements. - CrTMV IRES requires PABP for maximal activity. This conclusion was achieved by PABP depletion and reconstitution of wheat germ- and Krebs2-derived in-vitro translation assays using Arabidopsis-derived PABP2, 3, 5, 8 and yeast Pab1p. - Mutations in the internal polypurine tract of the IRES decrease the high-affinity binding of all phylogenetically divergent PABPs derived from Arabidopsis and yeast in electro mobility gel shift assays. - Mutations in the internal polypurine tract decrease IRES activity in-vivo. - The 3'-poly(A) tail enhances crTMV148 IRES activity more efficiently in the absence of 5'-methylated cap. - In-vivo assembled RNPs containing proteins specifically associated with the IRES were purified from HEK293 cells using the RNA Affinity in Tandem (RAT) approach followed by their identification by mass spectroscopy. - This study yielded a list of potential protein candidates that may serve as ITAFs of crTMV148 IRES activity, among them are a/b tubulin, a/g actin, GAPDH, enolase 1, ribonuclease/angiogenin inhibitor 1, 26S proteasome subunit p45, rpSA, eEF1Bδ, and proteasome b5 subunit. Implications, both scientific and agriculture. The fact that the 3'-poly(A) tail enhances crTMV148 IRES activity more efficiently in the absence of 5'-methylated cap suggests a potential joint interaction between PABP, the IRES sequence and the 3'-poly(A). This has an important scientific implication related to IRES function in general.
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