Relevant bibliographies by topics / Target binding

Academic literature on the topic 'Target binding'

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Published: 11 March 2023

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Journal articles on the topic "Target binding"

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Cheung, S. H., G. E. Legge, S. T. L. Chung, and B. S. Tjan. "Target-flanker binding releases crowding." Journal of Vision 6, no. 6 (March 24, 2010): 807. http://dx.doi.org/10.1167/6.6.807.

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POOLSAP, UNYANEE, YUKI KATO, KENGO SATO, and TATSUYA AKUTSU. "USING BINDING PROFILES TO PREDICT BINDING SITES OF TARGET RNAs." Journal of Bioinformatics and Computational Biology 09, no. 06 (December 2011): 697–713. http://dx.doi.org/10.1142/s0219720011005628.

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Prediction of RNA–RNA interaction is a key to elucidating possible functions of small non-coding RNAs, and a number of computational methods have been proposed to analyze interacting RNA secondary structures. In this article, we focus on predicting binding sites of target RNAs that are expected to interact with regulatory antisense RNAs in a general form of interaction. For this purpose, we propose bistaRNA, a novel method for predicting multiple binding sites of target RNAs. bistaRNA employs binding profiles that represent scores for hybridized structures, leading to reducing the computational cost for interaction prediction. bistaRNA considers an ensemble of equilibrium interacting structures and seeks to maximize expected accuracy using dynamic programming. Experimental results on real interaction data validate good accuracy and fast computation time of bistaRNA as compared with several competitive methods. Moreover, we aim to find new targets given specific antisense RNAs, which provides interesting insights into antisense RNA regulation. bistaRNA is implemented in C++. The program and Supplementary Material are available at .
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JOHNSTON, Angus, and Eva VAN DER MAREL. "How Binding are the EU’s ‘Binding’ Renewables Targets?" Cambridge Yearbook of European Legal Studies 18 (August 9, 2016): 176–214. http://dx.doi.org/10.1017/cel.2016.7.

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AbstractThe EU’s current renewable energy legislation sets a binding EU target for renewables as a share of overall energy consumption, allied with binding national targets for renewables as well. Yet the precise implications of having imposed such ‘mandatory’ binding targets have received little attention to date. This contribution examines the history and evolution of such targets, the context within which they must be pursued and applied, and some of the problems in and prospects for their enforcement and effectiveness. Comparisons are drawn with other areas of EU law where appropriate and some tentative lessons learned, as well as challenges still to be faced, are offered by way of conclusion.
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Park, Keunwan, Young-Joon Ko, Prasannavenkatesh Durai, and Cheol-Ho Pan. "Machine learning-based chemical binding similarity using evolutionary relationships of target genes." Nucleic Acids Research 47, no. 20 (August 31, 2019): e128-e128. http://dx.doi.org/10.1093/nar/gkz743.

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Abstract Chemical similarity searching is a basic research tool that can be used to find small molecules which are similar in shape to known active molecules. Despite its popularity, the retrieval of local molecular features that are critical to functional activity related to target binding often fails. To overcome this limitation, we developed a novel machine learning-based chemical binding similarity score by using various evolutionary relationships of binding targets. The chemical similarity was defined by the probability of chemical compounds binding to identical targets. Comprehensive and heterogeneous multiple target-binding chemical data were integrated into a paired data format and processed using multiple classification similarity-learning models with various levels of target evolutionary information. Encoding evolutionary information to chemical compounds through their binding targets substantially expanded available chemical-target interaction data and significantly improved model performance. The output probability of our integrated model, referred to as ensemble evolutionary chemical binding similarity (ensECBS), was effective for finding hidden chemical relationships. The developed method can serve as a novel chemical similarity tool that uses evolutionarily conserved target binding information.
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Lipovsek, D. "Adnectins: engineered target-binding protein therapeutics." Protein Engineering Design and Selection 24, no. 1-2 (November 10, 2010): 3–9. http://dx.doi.org/10.1093/protein/gzq097.

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Chen, Zihao, Long Hu, Bao-Ting Zhang, Aiping Lu, Yaofeng Wang, Yuanyuan Yu, and Ge Zhang. "Artificial Intelligence in Aptamer–Target Binding Prediction." International Journal of Molecular Sciences 22, no. 7 (March 30, 2021): 3605. http://dx.doi.org/10.3390/ijms22073605.

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Aptamers are short single-stranded DNA, RNA, or synthetic Xeno nucleic acids (XNA) molecules that can interact with corresponding targets with high affinity. Owing to their unique features, including low cost of production, easy chemical modification, high thermal stability, reproducibility, as well as low levels of immunogenicity and toxicity, aptamers can be used as an alternative to antibodies in diagnostics and therapeutics. Systematic evolution of ligands by exponential enrichment (SELEX), an experimental approach for aptamer screening, allows the selection and identification of in vitro aptamers with high affinity and specificity. However, the SELEX process is time consuming and characterization of the representative aptamer candidates from SELEX is rather laborious. Artificial intelligence (AI) could help to rapidly identify the potential aptamer candidates from a vast number of sequences. This review discusses the advancements of AI pipelines/methods, including structure-based and machine/deep learning-based methods, for predicting the binding ability of aptamers to targets. Structure-based methods are the most used in computer-aided drug design. For this part, we review the secondary and tertiary structure prediction methods for aptamers, molecular docking, as well as molecular dynamic simulation methods for aptamer–target binding. We also performed analysis to compare the accuracy of different secondary and tertiary structure prediction methods for aptamers. On the other hand, advanced machine-/deep-learning models have witnessed successes in predicting the binding abilities between targets and ligands in drug discovery and thus potentially offer a robust and accurate approach to predict the binding between aptamers and targets. The research utilizing machine-/deep-learning techniques for prediction of aptamer–target binding is limited currently. Therefore, perspectives for models, algorithms, and implementation strategies of machine/deep learning-based methods are discussed. This review could facilitate the development and application of high-throughput and less laborious in silico methods in aptamer selection and characterization.
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Molina, Daniel Martinez, Rozbeh Jafari, Marina Ignatushchenko, Takahiro Seki, E. Andreas Larsson, Chen Dan, Lekshmy Sreekumar, Yihai Cao, and Pär Nordlund. "Monitoring Drug Target Engagement in Cells and Tissues Using the Cellular Thermal Shift Assay." Science 341, no. 6141 (July 4, 2013): 84–87. http://dx.doi.org/10.1126/science.1233606.

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The efficacy of therapeutics is dependent on a drug binding to its cognate target. Optimization of target engagement by drugs in cells is often challenging, because drug binding cannot be monitored inside cells. We have developed a method for evaluating drug binding to target proteins in cells and tissue samples. This cellular thermal shift assay (CETSA) is based on the biophysical principle of ligand-induced thermal stabilization of target proteins. Using this assay, we validated drug binding for a set of important clinical targets and monitored processes of drug transport and activation, off-target effects and drug resistance in cancer cell lines, as well as drug distribution in tissues. CETSA is likely to become a valuable tool for the validation and optimization of drug target engagement.
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Yim, Hyung-Soon, and Jae-Hak Lee. "Prediction of Hypoxia-inducible Factor Binding Site in Whale Genome and Analysis of Target Genes Regulated by Predicted Sites." Journal of Marine Bioscience and Biotechnology 7, no. 2 (December 31, 2015): 35–41. http://dx.doi.org/10.15433/ksmb.2015.7.2.035.

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Ganotra, Gaurav K., and Rebecca C. Wade. "Prediction of Drug–Target Binding Kinetics by Comparative Binding Energy Analysis." ACS Medicinal Chemistry Letters 9, no. 11 (October 4, 2018): 1134–39. http://dx.doi.org/10.1021/acsmedchemlett.8b00397.

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Henrich, Stefan, Isabella Feierberg, Ting Wang, Niklas Blomberg, and Rebecca C. Wade. "Comparative binding energy analysis for binding affinity and target selectivity prediction." Proteins: Structure, Function, and Bioinformatics 78, no. 1 (August 17, 2009): 135–53. http://dx.doi.org/10.1002/prot.22579.

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Dissertations / Theses on the topic "Target binding"

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Collins, K. M. "Target recognition by multi-domain RNA-binding proteins." Thesis, University College London (University of London), 2015. http://discovery.ucl.ac.uk/1460867/.

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Multi-functional RNA binding proteins regulate and coordinate the many steps of RNA metabolism. Accurate functioning of these processes is vital in cells and misregulation has been linked to many human diseases. RNA binding proteins contain multiple RNA binding domains. The ability to perform multiple functions depends on the recognition of a diverse range of targets and domains are used combinatorially to achieve this. In this thesis I ask how the sequence specificity of low affinity RNA-binding domains and the interplay between said domains plays a role in RNA target selectivity. Within this question I focus on three proteins; TUT4, a uridyl transferase involved in the regulation of both non-coding RNAs and histone mRNA; FMRP, a translational repressor whose loss in cells is the cause of Fragile X Syndrome; and RBM10 a regulator of alternative splicing and miRNA biogenesis. I found that through the use of separate RNA binding domains both TUT4 and RBM10 are able to exert flexibility in target recognition; TUT4 by using two CCHC-type zinc fingers, working independently to recognise short RNA stretches; and RBM10 by using different subsets of domains to recognise either specific high affinity splice site sequences or pre-miRNAs. In FMRP the determination of the sequence specificity of KH1 allowed us to isolate its contribution to target selection. In a secondary objective, looking at methodologies used in RNA-protein interaction, SIA was improved to make it both less laborious and to reduce the sample requirements, and with FMRP a novel mutational strategy was used in combination with SIA to determine the sequence specificity of this low affinity domain. In summary these data extend our understanding of the RNA binding mechanisms of the three systems studied and introduces improved or novel methodologies to the future study of protein-RNA interactions.
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Bolotin, Eugene Leonidovich. "Investigation of transcription factor binding sequences and target genes using protein binding microarrays." Diss., [Riverside, Calif.] : University of California, Riverside, 2010. http://proquest.umi.com/pqdweb?index=0&did=2019822801&SrchMode=2&sid=3&Fmt=2&VInst=PROD&VType=PQD&RQT=309&VName=PQD&TS=1274203752&clientId=48051.

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Thesis (Ph. D.)--University of California, Riverside, 2010.
Includes abstract. Available via ProQuest Digital Dissertations. Title from first page of PDF file (viewed May 18, 2010). Includes bibliographical references. Also issued in print.
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Djurberg, Klara. "Applying Model Selection on Ligand-Target Binding Kinetic Analysis." Thesis, KTH, Proteinvetenskap, 2021. http://urn.kb.se/resolve?urn=urn:nbn:se:kth:diva-302137.

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The time-course of interaction formation or breaking can be studied using LigandTracer, and the data obtained from an experiment can be analyzed using a model of ligand-target binding kinetics. There are different kinetic models, and the choice of model is currently motivated by knowledge about the interaction, which is problematic when the knowledge about the interaction is unsatisfactory. In this project, a Bayesian model selection procedure was implemented to motivate the model choice using the data obtained from studying a biological system. The model selection procedure was implemented for four kinetic models, the 1:1 model, the 1:2 model, the bivalent model and a new version of the bivalent model.Bayesian inference was performed on the data using each of the models to obtain the posterior distributions of the parameters. Afterwards, the Bayes factor was approximated from numerical calculations of the marginal likelihood. Four numerical methods were implemented to approximate the marginal likelihood, the Naïve Monte Carlo estimator, the method of Harmonic Means of the likelihood, Importance Sampling and Sequential Monte Carlo. When tested on simulated data, the method of Importance Sampling seemed to yield the most reliable prediction of the most likely model. The model selection procedure was then tested on experimental data which was expected to be from a 1:1 interaction and the result of the model selection procedure did not agree with the expectation on the experimental test dataset. Therefore no reliable conclusion could be made when the model selection procedure was used to analyze the interaction between the anti-CD20 antibody Rituximab and Daudi cells.
Interaktioner kan analyseras med hjälp av LigandTracer. Data från ett LigandTracer experiment kan sedan analyseras med avseende på en kinetisk modell. Det finns olika kinetiska modeller, och modellvalet motiveras vanligen utifrån tidigare kunskap om interaktionen, vilket är problematiskt när den tillgängliga informationen om en interaktion är otillräcklig. I det här projektet implementerades en Bayesiansk metod för att motivera valet av modell utifrån data från ett LigandTracer experiment. Modellvalsmetoden implementerades för fyra kinetiska modeller, 1:1 modellen, 1:2 modellen, den bivalenta modellen och en ny version av den bivalenta modellen. Bayesiansk inferens användes för att få fram aposteriorifördelningarna för de olika modellernas parametrar utifrån den givna datan. Sedan beräknades Bayes faktor utifrån numeriska approximationer av marginalsannolikeheten. Fyra numeriska metoder implementerades för att approximera marginalsannolikheten; Naïve Monte Carlo estimator, det harmoniska medelvärdet av likelihood-funktionen, Importance Sampling och Sekventiell Monte Carlo. När modellvalsmetoden testades på simulerad data gav metoden Importance Sampling den mest tillförlitliga förutsägelsen om vilken modell som generade datan. Metoden testades också på experimentell data som förväntades följa en 1:1 interaktion och resultatet avvek från det förväntade resultatet. Följaktligen kunde ingen slutsas dras av resultet från modelvalsmetoden när den sedan används för att analysera interaktionen mellan anti-CD antikroppen Rituximab och Daudi-celler.
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Zhao, Qian, and 赵倩. "Identification of a binding target of triptolide and related studies." Thesis, The University of Hong Kong (Pokfulam, Hong Kong), 2012. http://hub.hku.hk/bib/B48199163.

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Triptolide, a diterpene triepoxide extracted from traditional Chinese medicinal herb Tripterygium wilfordii Hook. F has been shown to have profound inhibitory effects against tumor progression, pathological angiogenesis and inflammation. However, the mechanisms by which triptolide exerts these effects remain unclear. To understand its cellular mode of action, biotinylated/desthiobiotinylated and fluorophore-labeled triptolide derivatives were used as probes to identify cellular proteins that bind to triptolide. By using two different approaches for screening drug-protein interactions, the most prominent cellular protein bound to triptolide was confirmed to be peroxiredoxin 1 (PRDX1). This result was validated by demonstrating the ability of triptolide or its conjugated probes to bind recombinant human PRDX1. Specificity of the drug-protein interaction was established by competitive inhibition of binding of fluorophore-labeled triptolide to PRDX1 by triptolide itself. Two binding sites of triptolide to PRDX1 were found, one of which being Cys173 as confirmed by orbitrap LC-MS/MS analysis. Further study by size exclusive chromatography revealed that triptolide altered the oligomeric state of PRDX1. The decameric form of PRDX1 was dissociated into lower molecular weight species in the presence of triptolide. This observation was responsible for attenuation of PRDX1’s chaperone activity upon triptolide treatment, which was supported by evidence from both light scattering and native mass spectrometry studies. Functionally, triptolide’s synergistic effect on stress-induced cell apoptosis may be mediated, at least in part, by the interaction of triptolide with PRDX1 and the consequent inhibition of its chaperone activity. Several natural products, Celastrol, Withaferin A and Radiciol were discovered as new PRDX1 inhibitors and confirmed to physically interact with PRDX1 and exert similar functional effects as triptolide. The interaction between PRDX1 and those natural products may shed light on the detailed mechanism of their biological actions and render PRDX1 a potential target for cancer therapy.
published_or_final_version
Chemistry
Doctoral
Doctor of Philosophy
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Kasturi, Rama. "Kinetics of calmodulin binding to its smooth muscle target proteins /." The Ohio State University, 1991. http://rave.ohiolink.edu/etdc/view?acc_num=osu1487694702782747.

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Xie, He Fang. "Understanding the interaction between xylan-binding domains and their target ligands." Thesis, University of Newcastle Upon Tyne, 2000. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.324858.

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Chapman, Edwin R. "Functional domains of neuromodulin and the interaction of calmodulin with target peptides /." Thesis, Connect to this title online; UW restricted, 1992. http://hdl.handle.net/1773/6288.

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Farnie, Gillian. "MDM2-p53 binding interaction as a potential therapeutic target for cancer." Thesis, University of Newcastle Upon Tyne, 2003. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.437553.

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Ma, Jun. "Mass Spectrometry Method Development to Identify Binding Ligands Against A2AR Nanodisc Complex." Thesis, Griffith University, 2017. http://hdl.handle.net/10072/380580.

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Protein is essential for human physiological processes and signalling pathways. Mass spectrometry (MS) is an important tool for ligand identification against protein target. This project aims to establish an MS-based ligand identification method towards neurodegenerative disease-related protein targets, including cytosolic LRRK2 protein, adenosine A2A receptor (A2AR), and α2-adrenergic receptor (α2AR). The LRRK2 subdomains (Roc/GTPase, COR, and MAPKKK/kinase) and GPCRs (A2AR, A2AR-GFP, and α2AR) were cloned, sequenced, expressed and purified for MS assay. The proteins were solubilised in different types of detergents (such as Triton X-100 and n-dodecyl-β- D-maltoside). Moreover, the A2AR, A2AR-GFP, and α2AR were reconstituted into selfassembled phospholipid bilayers (or nanodisc) to improve the solubility and stability. Because LRRK2 subdomains and α2AR had solubility and yield problems that would limit the MS analysis, the A2AR nanodisc was consequently demonstrated as a suitable protein target for MS method development. Two MS methods, native ESI MS and ultrafiltrationbased affinity LC/MS, were attempted for ligand identification against A2AR nanodisc. The ultrafiltration-based affinity LC/MS was successfully developed to assay the interactions (binding affinities) between A2AR nanodiscs and 15-ligand mixture (eight known ligands with seven unrelated negative ligands). The ultrafiltration-based affinity LC/MS allowed identification of ligands to a relatively stable unliganded/apo GPCR in nanodisc environment.
Thesis (PhD Doctorate)
Doctor of Philosophy (PhD)
School of Environment and Sc
Science, Environment, Engineering and Technology
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Zhou, Yiqing, and 周怡青. "Identification of a cellular target of triptonide and its functional study." Thesis, The University of Hong Kong (Pokfulam, Hong Kong), 2011. http://hub.hku.hk/bib/B46923561.

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Books on the topic "Target binding"

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Symposium on RNA Biology (2nd 1997 North Carolina Biotechnology Center). Symposium on RNA Biology: RNA tool and target : held at North Carolina Biotechnology Center, Research Triangle Park, North Carolina, USA, October 17-19, 1997. [Oxford]: Oxford University Press, 1997.

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Snoeck, Eric. Mechanism-based pharmacokinetic-pharmacodynamic modelling of specific target site binding to red blood cells: Application to the development of draflazine. [Leiden: University of Leiden, 1998.

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Podjarny, Alberto, Annick P. Dejaegere, and Bruno Kieffer, eds. Biophysical Approaches Determining Ligand Binding to Biomolecular Targets. Cambridge: Royal Society of Chemistry, 2011. http://dx.doi.org/10.1039/9781849732666.

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Ponte-Sucre, Alicia. ABC transporters in microorganisms: Research, innovation and value as targets against drug resistance. Norfolk, UK: Caister Academic, 2009.

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Chandrudu, M. V. Rama. Bench marking of APRLP processes: Binding the programs with processes : redefining targets. Secunderabad: WASSAN, 2006.

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Dufau, Maria. Hormone Binding and Target Cell Activation in the Testis. Springer, 2013.

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Dufau, Maria. Hormone Binding and Target Cell Activation in the Testis. Springer, 2012.

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Matulis, Daumantas. Carbonic Anhydrase as Drug Target: Thermodynamics and Structure of Inhibitor Binding. Springer, 2019.

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Ming, Liang. Identification of DNA-binding domains and target genes of the Hindsight zinc-finger protein. 2006.

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Baauw, Sergio. The Acquisition of Binding and Coreference. Edited by Jeffrey L. Lidz, William Snyder, and Joe Pater. Oxford University Press, 2016. http://dx.doi.org/10.1093/oxfordhb/9780199601264.013.22.

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In this chapter the acquisition of pronouns and reflexives is discussed. It reviews several accounts of the so-called Delay of Principle B Effect, the absence of this effect in some languages, and the structural factors that influence its appearance in child language. It also discusses children’s alledged target-like performance on reflexives in several languages with different type of reflexives. The chapter concludes that provided a balanced experimental design is used, the experimental results point at early mastery of Principle A and B, and that children’s difficulties with the interpretation of pronouns and reflexives are to be found at the interfaces between syntax and discourse or semantics, and may be due to limited (syntactic) processing resources.
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Book chapters on the topic "Target binding"

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Copeland, Robert A. "Drug-Target Residence Time." In Thermodynamics and Kinetics of Drug Binding, 155–67. Weinheim, Germany: Wiley-VCH Verlag GmbH & Co. KGaA, 2015. http://dx.doi.org/10.1002/9783527673025.ch8.

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Norden, Diana M., and Benjamin J. Doranz. "Testing for Off-target Binding." In Translational Medicine, 117–30. Boca Raton: CRC Press, 2021. http://dx.doi.org/10.1201/9781003124542-13.

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Rodríguez, Santiago, Juan I. Alice, Carolina L. Bellera, and Alan Talevi. "Structure-Based Binding Pocket Detection and Druggability Assessment." In Drug Target Selection and Validation, 83–97. Cham: Springer International Publishing, 2022. http://dx.doi.org/10.1007/978-3-030-95895-4_5.

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Kairys, Visvaldas, Kliment Olechnovič, Vytautas Raškevičius, and Daumantas Matulis. "In Silico Modeling of Inhibitor Binding to Carbonic Anhydrases." In Carbonic Anhydrase as Drug Target, 215–32. Cham: Springer International Publishing, 2019. http://dx.doi.org/10.1007/978-3-030-12780-0_15.

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Paketurytė, Vaida, Asta Zubrienė, Wen-Yih Chen, Sandro Keller, Margarida Bastos, Matthew J. Todd, John E. Ladbury, and Daumantas Matulis. "Inhibitor Binding to Carbonic Anhydrases by Isothermal Titration Calorimetry." In Carbonic Anhydrase as Drug Target, 79–95. Cham: Springer International Publishing, 2019. http://dx.doi.org/10.1007/978-3-030-12780-0_6.

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Petrauskas, Vytautas, Asta Zubrienė, Matthew J. Todd, and Daumantas Matulis. "Inhibitor Binding to Carbonic Anhydrases by Fluorescent Thermal Shift Assay." In Carbonic Anhydrase as Drug Target, 63–78. Cham: Springer International Publishing, 2019. http://dx.doi.org/10.1007/978-3-030-12780-0_5.

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Zubrienė, Asta, and Daumantas Matulis. "Observed Versus Intrinsic Thermodynamics of Inhibitor Binding to Carbonic Anhydrases." In Carbonic Anhydrase as Drug Target, 107–23. Cham: Springer International Publishing, 2019. http://dx.doi.org/10.1007/978-3-030-12780-0_8.

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Demchenko, Alexander P. "Basic Theoretical Description of Sensor-Target Binding." In Introduction to Fluorescence Sensing, 37–72. Cham: Springer International Publishing, 2023. http://dx.doi.org/10.1007/978-3-031-19089-6_2.

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Smirnov, Alexey, Elena Manakova, and Daumantas Matulis. "Correlations Between Inhibitor Binding Thermodynamics and Co-crystal Structures with Carbonic Anhydrases." In Carbonic Anhydrase as Drug Target, 249–61. Cham: Springer International Publishing, 2019. http://dx.doi.org/10.1007/978-3-030-12780-0_17.

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Skvarnavičius, Gediminas, Daumantas Matulis, and Vytautas Petrauskas. "Change in Volume Upon Inhibitor Binding to Carbonic Anhydrases by Fluorescent Pressure Shift Assay." In Carbonic Anhydrase as Drug Target, 97–106. Cham: Springer International Publishing, 2019. http://dx.doi.org/10.1007/978-3-030-12780-0_7.

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Conference papers on the topic "Target binding"

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Li, Mei, Sihan Xu, Xiangrui Cai, Zhong Zhang, and Hua Ji. "Contrastive Meta-Learning for Drug-Target Binding Affinity Prediction." In 2022 IEEE International Conference on Bioinformatics and Biomedicine (BIBM). IEEE, 2022. http://dx.doi.org/10.1109/bibm55620.2022.9995372.

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Zhao, Qichang, Fen Xiao, Mengyun Yang, Yaohang Li, and Jianxin Wang. "AttentionDTA: prediction of drug–target binding affinity using attention model." In 2019 IEEE International Conference on Bioinformatics and Biomedicine (BIBM). IEEE, 2019. http://dx.doi.org/10.1109/bibm47256.2019.8983125.

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Reyes-Herrera, Paula Helena, Andrea Acquaviva, Elisa Ficarra, and Enrico Macii. "MicroRNA Target Prediction and Exploration through Candidate Binding Sites Generation." In 2010 International Conference on Complex, Intelligent and Software Intensive Systems (CISIS). IEEE, 2010. http://dx.doi.org/10.1109/cisis.2010.129.

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Barroso, Margarida, Alena Rudkouskaya, Jason Smith, John Williams, and Xavier Intes. "Antibody-target binding in living tumors using macroscopy fluorescence lifetime imaging." In Multiphoton Microscopy in the Biomedical Sciences XXII, edited by Ammasi Periasamy, Peter T. So, and Karsten König. SPIE, 2022. http://dx.doi.org/10.1117/12.2609024.

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Zhijian, Lyu, Jiang Shaohua, Liang Yigao, and Gao Min. "GDGRU-DTA: Predicting Drug-Target Binding Affinity based on GNN and Double GRU." In 3rd International Conference on Data Mining and Machine Learning (DMML 2022). Academy and Industry Research Collaboration Center (AIRCC), 2022. http://dx.doi.org/10.5121/csit.2022.120703.

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The work for predicting drug and target affinity(DTA) is crucial for drug development and repurposing. In this work, we propose a novel method called GDGRU-DTA to predict the binding affinity between drugs and targets, which is based on GraphDTA, but we consider that protein sequences are long sequences, so simple CNN cannot capture the context dependencies in protein sequences well. Therefore, we improve it by interpreting the protein sequences as time series and extracting their features using Gate Recurrent Unit(GRU) and Bidirectional Gate Recurrent Unit(BiGRU). For the drug, our processing method is similar to that of GraphDTA, but uses two different graph convolution methods. Subsequently, the representation of drugs and proteins are concatenated for final prediction. We evaluate the proposed model on two benchmark datasets. Our model outperforms some state-of-the-art deep learning methods, and the results demonstrate the feasibility and excellent feature capture ability of our model.
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Ullal, Adeeti V., Thomas Reiner, Katherine S. Yang, Rostic Gorbatov, Changwook Min, David Issadore, Hakho Lee, and Ralph Weissleder. "Abstract 1968: Nanoparticle mediated measurement of target-drug binding in cancer cells." In Proceedings: AACR 103rd Annual Meeting 2012‐‐ Mar 31‐Apr 4, 2012; Chicago, IL. American Association for Cancer Research, 2012. http://dx.doi.org/10.1158/1538-7445.am2012-1968.

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Ghazaly, Essam A., John Le Quesne, Dahai Jiang, Selanere L. Mangala, James Chettle, Cristian Rodriguez-Aguayo, Gabriel Lopez-Berestein, et al. "Abstract B30: The RNA-binding protein LARP1 is a cancer therapeutic target." In Abstracts: AACR Special Conference on Translational Control of Cancer: A New Frontier in Cancer Biology and Therapy; October 27-30, 2016; San Francisco, CA. American Association for Cancer Research, 2017. http://dx.doi.org/10.1158/1538-7445.transcontrol16-b30.

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Lennox, Mark, Neil Robertson, and Barry Devereux. "Modelling Drug-Target Binding Affinity using a BERT based Graph Neural network." In 2021 43rd Annual International Conference of the IEEE Engineering in Medicine & Biology Society (EMBC). IEEE, 2021. http://dx.doi.org/10.1109/embc46164.2021.9629695.

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Nguyen, Thai Huu, and Qiao Lin. "An Aptamer-Functionalized Microfluidic Platform for Biomolecular Purification and Sensing." In ASME 2009 7th International Conference on Nanochannels, Microchannels, and Minichannels. ASMEDC, 2009. http://dx.doi.org/10.1115/icnmm2009-82142.

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Aptamers are oligonucleotides (DNA or RNA) that bind to chemical and biological analyte targets via affinity interactions. Through an in vitro synthetic process, aptamers can be developed for an extremely broad spectrum of analytes, such as small molecules, proteins, cells, viruses, and bacteria. Target recognition by aptamers is highly selective, as affinity interactions result in secondary aptamer conformational structures that specifically fit the target. The aptamer-target binding is also reversible and depends strongly on external stimuli such as pH and temperature. The specificity and stimuli-responsiveness of aptamers are highly attractive to biological purification and sensing, which generally involve isolating minute quantities of targets from complex samples with non-specific molecules and impurities present at orders-of-magnitude higher concentrations. We present an aptamer-functionalized microfluidic platform that by design exploits the specificity and temperature-dependent reversibility of aptamers to enable biomolecular purification and sensing. Using the specificity of aptamers, we demonstrate highly selective capture and enrichment of biomolecules. Employing thermally induced, reversible disruption of aptamer-target binding, we accomplish isocratic elution of the captured analytes and regeneration of the aptamer surfaces, thereby eliminating the use of potentially harsh reagents. Using integrated microfluidic control, the eluted analytes are detected in a label-free fashion by mass spectrometric methods.
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Vishwakarma, Ajaykumar, Yi Sun, Amina Fu, Emily Robitschek, Arvin Iracheta-Vellve, Susanna Stinson, Aliasger Salem, Robert Manguso, and Russell Jenkins. "Abstract B065: TANK-Binding Kinase 1 (TBK1) as a novel cancer immunotherapy target." In Abstracts: AACR-NCI-EORTC International Conference on Molecular Targets and Cancer Therapeutics; October 26-30, 2019; Boston, MA. American Association for Cancer Research, 2019. http://dx.doi.org/10.1158/1535-7163.targ-19-b065.

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Reports on the topic "Target binding"

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Beerman, Terry A. Discovery of DNA Binding Anticancer Drugs That Target Oncogenic Transcription Factors Associated With Human Breast Cancer. Fort Belvoir, VA: Defense Technical Information Center, October 2001. http://dx.doi.org/10.21236/ada403322.

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DeSombre, E. R. Receptor-DNA binding to target auger electrons for cancer therapy. Final report, August 1, 1993--January 31, 1997. Office of Scientific and Technical Information (OSTI), May 1997. http://dx.doi.org/10.2172/477720.

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Kolodny, Gerald M., and Joel Yisraeli. Riboswitch-Mediated Aptamer Binding for Imaging and Therapy (RABIT): A Novel Technique to Selectively Target an Intracellular Ligand Specific for Ovarian Cancer. Fort Belvoir, VA: Defense Technical Information Center, October 2014. http://dx.doi.org/10.21236/ada613755.

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Kolodny, Gerald M., and Joel Yisraeli. Riboswitch-Mediated Aptamer Binding for Imaging and Therapy (RABIT): A Novel Technique to Selectively Target an Intracellular Ligand Specific for Ovarian Cancer. Fort Belvoir, VA: Defense Technical Information Center, October 2013. http://dx.doi.org/10.21236/ada594525.

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Rahimipour, Shai, and David Donovan. Renewable, long-term, antimicrobial surface treatments through dopamine-mediated binding of peptidoglycan hydrolases. United States Department of Agriculture, January 2012. http://dx.doi.org/10.32747/2012.7597930.bard.

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There is a need for renewable antimicrobial surface treatments that are semi- permanent, can eradicate both biofilms and planktonic pathogens over long periods of time and that do not select for resistant strains. This proposal describes a dopamine binding technology that is inexpensive, bio-friendly, non-toxic, and uses straight-forward commercially available products. The antimicrobial agents are peptidoglycanhydrolase enzymes that are non-toxic and highly refractory to resistance development. The goal of this project is to create a treatment that will be applicable to a wide variety of surfaces and will convey long-lasting antimicrobial activity. Although the immediate goal is to create staphylolytic surfaces, the technology should be applicable to any pathogen and will thus contribute to no less than 3 BARD priorities: 1) increased animal production by protecting animals from invasive and emerging diseases, 2) Antimicrobial food packaging will improve food safety and security and 3) sustainable bio- energy systems will be supported by coating fermentation vats with antimicrobials that could protect ethanolic fermentations from Lactobacillus contamination that reduces ethanol yields. The dopamine-based modification of surfaces is inspired by the strong adhesion of mussel adhesion proteins to virtually all types of surfaces, including metals, polymers, and inorganic materials. Peptidoglycanhydrolases (PGHs) meet the criteria of a surface bound antimicrobial with their site of action being extracellular peptidoglycan (the structural basis of the bacterial cell wall) that when breached causes osmotic lysis. As a proof of principle, we will develop technology using peptidoglycanhydrolase enzymes that target Staphylococcus aureus, a notoriously contagious and antimicrobial-resistant pathogen. We will test for susceptibility of the coating to a variety of environmental stresses including UV light, abrasive cleaning and dessication. In order to avoid resistance development, we intend to use three unique, synergistic, simultaneous staphylococcal enzyme activities. The hydrolases are modular such that we have created fusion proteins with three lytic activities that are highly refractory to resistance development. It is essential to use multiple simultaneous activities to avoid selecting for antimicrobial resistant strains. This strategy is applicable to both Gram positive and negative pathogens. We anticipate that upon completion of this award the technology will be available for commercialization within the time required to achieve a suitable high volume production scheme for the required enzymes (~1-2 years). We expect the modified surface will remain antimicrobial for several days, and when necessary, the protocol for renewal of the surface will be easily applied in a diverse array of environments, from food processing plants to barnyards.
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Whitham, Steven A., Amit Gal-On, and Victor Gaba. Post-transcriptional Regulation of Host Genes Involved with Symptom Expression in Potyviral Infections. United States Department of Agriculture, June 2012. http://dx.doi.org/10.32747/2012.7593391.bard.

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Understanding how RNA viruses cause disease symptoms in their hosts is expected to provide information that can be exploited to enhance modern agriculture. The helper component-proteinase (HC-Pro) protein of potyviruses has been implicated in symptom development. Previously, we demonstrated that symptom expression is associated with binding of duplex small-interfering-RNA (duplex-siRNA) to a highly conserved FRNK amino acid motif in the HC-Pro of Zucchini yellow mosaic virus (ZYMV). This binding activity also alters host microRNA (miRNA) profiles. In Turnip mosaic virus (TuMV), which infects the model plant Arabidopsis, mutation of the FRNK motif to FINK was lethal providing further indication of the importance of this motif to HC-Pro function. In this continuation project, our goal was to further investigate how ZYMV and TuMV cause the mis-expression of genes in cucurbits and Arabidopsis, respectively, and to correlate altered gene expression with disease symptoms. Objective 1 was to examine the roles of aromatic and positively charged residues F164RNH and K215RLF adjacent to FR180NK in small RNA binding. Objective 2 was to determine the target genes of the miRNAs which change during HC-Pro expression in infected tissues and transgenic cucumber. Objective 3 was to characterize RNA silencing mechanisms underlying differential expression of host genes. Objective 4 was to analyze the function of miRNA target genes and differentially expressed genes in potyvirus-infected tissues. We found that the charged K/R amino acid residues in the FKNH and KRLF motifs are essential for virus viability. Replacement of K to I in FKNH disrupted duplex-siRNA binding and virus infectivity, while in KRLF mutants duplex-siRNA binding was maintained and virus infectivity was limited: symptomless following a recovery phenomenon. These findings expanded the duplex-siRNA binding activity of HC-Pro to include the adjacent FRNK and FRNH sites. ZYMV causes many squash miRNAs to hyper-accumulate such as miR166, miR390, mir168, and many others. Screening of mir target genes showed that only INCURVATA-4 and PHAVOLUTA were significantly upregulated following ZYMVFRNK infection. Supporting this finding, we found similar developmental symptoms in transgenic Arabidopsis overexpressing P1-HC-Pro of a range of potyviruses to those observed in miR166 mutants. We characterized increased transcription of AGO1 in response to infection with both ZYMV strains. Differences in viral siRNA profiles and accumulation between mild and severe virus infections were characterized by Illumina sequencing, probably due to the differences in HC-Pro binding activity. We determined that the TuMV FINK mutant could accumulate and cause symptoms in dcl2 dcl4 or dcl2 dcl3 dcl4 mutants similar to TuMV FRNK in wild type Arabidopsis plants. These dcl mutant plants are defective in antiviral defenses, and the results show that factors other than HC-ProFRNK motif can induce symptoms in virus-infected plants. As a result of this work, we have a better understanding of the FRNK and FKNH amino acid motifs of HC-Pro and their contributions to the duplex-siRNA binding functions. We have identified plant genes that potentially contribute to infectivity and symptoms of virus infected plants when they are mis-expressed during potyviral infections. The results establish that there are multiple underlying molecular mechanisms that lead viral pathogenicity, some dependent on HC-Pro. The potential benefits include the development of novel strategies for controlling diseases caused by viruses, methods to ensure stable expression of transgenes in genetically improved crops, and improved potyvirus vectors for expression of proteins or peptides in plants.
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Fromm, Hillel, and Joe Poovaiah. Calcium- and Calmodulin-Mediated Regulation of Plant Responses to Stress. United States Department of Agriculture, September 1993. http://dx.doi.org/10.32747/1993.7568096.bard.

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We have taken a molecular approach to clone cellular targets of calcium/calmodulin (Ca2+/CaM). A 35S-labeled recombinant CaM was used as a probe to screen various cDNA expression libraries. One of the isolated clones from petunia codes for the enzyme glutamate decarboxylase (GAD) which catalyzes the conversion of glutamate to g-aminobutyric acid (GABA). The activity of plant GAD has been shown to be dramatically enhanced in response to cold and heat shock, anoxia, drought, mechanical manipulations and by exogenous application of the stress phytohormone ABA in wheat roots. We have purified the recombinant GAD by CaM-affinity chromatography and studied its regulation by Ca2+/CaM. At a physiological pH range (7.0-7.5), the purified enzyme was inactive in the absence of Ca2+ and CaM but could be stimulated to high levels of activity by the addition of exogenous CaM (K0.5 = 15 nM) in the presence of Ca2+ (K 0.5 = 0.8 mM). Neither Ca2+ nor CaM alone had any effect on GAD activity. Transgenic tobacco plants expressing a mutant petunia GAD lacking the CaM-binding domain, or transgenic plants expressing the intact GAD were prepared and studied in detail. We have shown that the CaM-binding domain is necessary for the regulation of glutamate and GABA metabolism and for normal plant development. Moreover, we found that CaM is tightly associated with a 500 kDa GAD complex. The tight association of CaM with its target may be important for the rapid modulation of GAD activity by Ca2+ signaling in response to stresses.
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Gurevitz, Michael, Michael E. Adams, Boaz Shaanan, Oren Froy, Dalia Gordon, Daewoo Lee, and Yong Zhao. Interacting Domains of Anti-Insect Scorpion Toxins and their Sodium Channel Binding Sites: Structure, Cooperative Interactions with Agrochemicals, and Application. United States Department of Agriculture, December 2001. http://dx.doi.org/10.32747/2001.7585190.bard.

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Integrated pest management in modern crop protection may combine chemical and biological insecticides, particularly due to the risks to the environment and livestock arising from the massive use of non-selective chemicals. Thus, there is a need for safer alternatives, which target insects more specifically. Scorpions produce anti-insect selective polypeptide toxins that are biodegradable and non-toxic to warm-blooded animals. Therefore, integration of these substances into insect pest control strategies is of major importance. Moreover, clarification of the molecular basis of this selectivity may provide valuable information pertinent to their receptor sites and to the future design of peptidomimetic anti-insect specific substances. These toxins may also be important for reducing the current overuse of chemical insecticides if they produce a synergistic effect with conventional pesticides. Based on these considerations, our major objectives were: 1) To elucidate the three-dimensional structure and toxic-site of scorpion excitatory, "depressant, and anti-insect alpha toxins. 2) To obtain an initial view to the sodium channel recognition sites of the above toxins by generating peptide decoys through a phage display system. 3) To investigate the synergism between toxins and chemical insecticides. Our approach was to develop a suitable expression system for toxin production in a recombinant form and for elucidation of toxin bioactive sites via mutagenesis. In parallel, the mode of action and synergistic effects of scorpion insecticidal toxins with pyrethroids were studied at the sodium channel level using electrophysiological methods. Objective 1 was achieved for the alpha toxin, LqhaIT Zilberberg et al., 1996, 1997; Tugarinov et al., 1997; Froy et al., 2002), and the excitatory toxin, Bj-xtrIT (Oren et al., 1998; Froy et al., 1999; unpublished data). The bioactive surface of the depressant toxin, LqhIT2, has been clarified and a crystal of the toxin is now being analyzed (unpublished). Objective 2 was not successful thus far as no phages that recognize the toxins were obtained. We therefore initiated recently an alternative approach, which is introduction of mutations into recombinant channels and creation of channel chimeras. Objective 3 was undertaken at Riverside and the results demonstrated synergism between LqhaIT or AaIT and pyrethroids (Lee et al., 2002). Furthermore, negative cross-resistance between pyrethroids and scorpion toxins (LqhaIT and AaIT) was demonstrated at the molecular level. Although our study did not yield a product, it paves the way for future design of selective pesticides by capitalizing on the natural competence of scorpion toxins to distinguish between sodium channels of insects and vertebrates. We also show that future application of anti-insect toxins may enable to decrease the amounts of chemical pesticides due to their synergism.
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Fromm, A., Avihai Danon, and Jian-Kang Zhu. Genes Controlling Calcium-Enhanced Tolerance to Salinity in Plants. United States Department of Agriculture, March 2003. http://dx.doi.org/10.32747/2003.7585201.bard.

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The specific objectives of the proposed research were to identify, clone and characterize downstream cellular target(s) of SOS3 in Arabidopsis thaliana, to analyze the Ca2+-binding characteristics of SOS3 and the sos3-1 mutant and their interactions with SOS3 cellular targets to analyze the SOS3 cell-specific expression patterns, and its subcellular localization, and to assess the in vivo role of SOS3 target protein(s) in plant tolerance to salinity stress. In the course of the study, in view of recent opportunities in identifying Ca2+ - responsive genes using microarrays, the group at Weizmann has moved into identifying Ca2+-responsive stress genes by using a combination of aqeuorin-based measurements of cytosolic Ca and analysis by DNA microarrays of early Ca-responsive genes at the whole genome level. Analysis of SOS3 (University of Arizona) revealed its expression in both roots and shoots. However, the expression of this gene is not induced by stress. This is reminiscent of other stress proteins that are regulated by post-transcriptional mechanisms such as the activation by second messengers like Ca. Further analysis of the expression of the gene using promoter - GUS fusions revealed expression in lateral root primordial. Studies at the Weizmann Institute identified a large number of genes whose expression is up-regulated by a specific cytosolic Ca burst evoked by CaM antagonists. Fewer genes were found to be down-regulated by the Ca burst. Among the up-regulated genes many are associated with early stress responses. Moreover, this study revealed a large number of newly identified Ca-responsive genes. These genes could be useful to investigate yet unknown Ca-responsive gene networks involved in plant response to stress.
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Landau, Sergei Yan, John W. Walker, Avi Perevolotsky, Eugene D. Ungar, Butch Taylor, and Daniel Waldron. Goats for maximal efficacy of brush control. United States Department of Agriculture, March 2008. http://dx.doi.org/10.32747/2008.7587731.bard.

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Background. Brush encroachment constitutes a serious problem in both Texas and Israel. We addressed the issue of efficacy of livestock herbivory - in the form of goat browsing - to change the ecological balance to the detriment of the shrub vegetation. Shrub consumption by goats is kept low by plant chemical defenses such as tannins and terpenes. Scientists at TAES and ARO have developed an innovative, cost-effective methodology using fecal Near Infrared Spectrometry to elucidate the dietary percentage of targeted, browse species (terpene-richredberry and blueberry juniper in the US, and tannin-rich Pistacialentiscus in Israel) for a large number of animals. The original research objectives of this project were: 1. to clarify the relative preference of goat breeds and the individual variation of goats within breeds, when consuming targeted brush species; 2. to assess the heritability of browse intake and validate the concept of breeding goat lines that exhibit high preference for chemically defended brush, using juniper as a model; 3. to clarify the relative contributions of genetics and learning on the preference for target species; 4. to identify mechanisms that are associated with greater intake of brush from the two target species; 5. to establish when the target species are the most vulnerable to grazing. (Issue no.5 was addressed only partly.) Major conclusions, solutions, achievements: Both the Israel and US scientists put significant efforts into improving and validating the technique of Fecal NIRS for predicting the botanical composition of goat diets. Israeli scientists validated the use of observational data for calibrating fecal NIRS, while US scientists established that calibrations could be used across animals differing in breed and age but that caution should be used in making comparisons between different sexes. These findings are important because the ability to select goat breeds or individuals within a breed for maximal efficiency of brush control is dependent upon accurate measurement of the botanical composition of the diet. In Israel it was found that Damascus goats consume diets more than twice richer in P. lentiscus than Mamber or Boer goats. In the US no differences were found between Angora and Boer cross goats but significant differences were found between individuals within breeds in juniper dietary percentage. In both countries, intervention strategies were found that further increased the consumption of the chemically defended plant. In Israel feeding polyethylene glycol (PEG, MW 4,000) that forms high-affinity complexes with tannins increased P. lentiscus dietary percentage an average of 7 percentage units. In the US feeding a protein supplement, which enhances rates of P450-catalyzed oxidations and therefore the rate of oxidation of monoterpenes, increased juniper consumption 5 percentage units. However, the effects of these interventions were not as large as breed or individual animal effects. Also, in a wide array of competitive tannin-binding assays in Israel with trypsin, salivary proteins did not bind more tannic acid or quebracho tannin than non-specific bovine serum albumin, parotid saliva did not bind more tannins than mixed saliva, no response of tannin-binding was found to levels of dietary tannins, and the breed effect was of minor importance, if any. These fundings strongly suggest that salivary proteins are not the first line of defense from tannin astringency in goats. In the US relatively low values for heritability and repeatability for juniper consumption were found (13% and 30%, respectively), possibly resulting from sampling error or non-genetic transfer of foraging behavior, i.e., social learning. Both alternatives seem to be true as significant variation between sequential observations were noted on the same animal and cross fostering studies conducted in Israel demonstrated that kids raised by Mamber goats showed lower propensity to consume P. lentiscus than counterparts raised by Damascus goats.
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