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Relevant bibliographies by topics / DNA-protein complexes

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Academic literature on the topic 'DNA-protein complexes'

Author: Grafiati

Published: 7 September 2022

Last updated: 18 September 2022

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Journal articles on the topic "DNA-protein complexes"

1

Gololobov, G. V., S. V. Mikhalap, A. V. Starov, A. F. Kolesnikov, and A. G. Gabibov. "DNA-protein complexes." Applied Biochemistry and Biotechnology 47, no. 2-3 (May 1994): 305–15. http://dx.doi.org/10.1007/bf02787942.

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Běgusová, Marie, Nathalie Gillard, Denise Sy, Bertrand Castaing, Michel Charlier, and Melanie Spotheim-Maurizot. "Radiolysis of DNA–protein complexes." Radiation Physics and Chemistry 72, no. 2-3 (February 2005): 265–70. http://dx.doi.org/10.1016/j.radphyschem.2004.01.009.

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Sen, Taner Z., Andrzej Kloczkowski, and Robert L. Jernigan. "A DNA-Centric Look at Protein-DNA Complexes." Structure 14, no. 9 (September 2006): 1341–42. http://dx.doi.org/10.1016/j.str.2006.08.003.

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Spotheim-Maurizot, M., and M. Davídková. "Radiation damage to DNA in DNA–protein complexes." Mutation Research/Fundamental and Molecular Mechanisms of Mutagenesis 711, no. 1-2 (June 2011): 41–48. http://dx.doi.org/10.1016/j.mrfmmm.2011.02.003.

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Boryskina, O. P., M. Yu Tkachenko, and A. V. Shestopalova. "Protein-DNA complexes: specificity and DNA readout mechanisms." Biopolymers and Cell 27, no. 1 (January 20, 2011): 3–16. http://dx.doi.org/10.7124/bc.00007c.

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Travers, Andrew A. "DNA conformation and configuration in protein-DNA complexes." Current Opinion in Structural Biology 2, no. 1 (February 1992): 71–77. http://dx.doi.org/10.1016/0959-440x(92)90180-f.

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Sternberg, Michael JE, Henry A. Gabb, and Richard M. Jackson. "Predictive docking of protein—protein and protein—DNA complexes." Current Opinion in Structural Biology 8, no. 2 (April 1998): 250–56. http://dx.doi.org/10.1016/s0959-440x(98)80047-x.

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Sarai, A., Ponraj Prabakaran, Joerg Siebers, Shandar Ahmad, Michael Gromiha, and H. Kono. "QSAR analysis of protein-DNA complexes." Seibutsu Butsuri 43, supplement (2003): S30. http://dx.doi.org/10.2142/biophys.43.s30_4.

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Anashkina, A. A., N. G. Esipova, E. N. Kuznetsov, and V. G. Tumanyan. "Contact specificity in protein-DNA complexes." Computer Research and Modeling 1, no. 3 (September 2009): 281–86. http://dx.doi.org/10.20537/2076-7633-2009-1-3-281-286.

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Volodin, Alexander A., Helen A. Smirnova, and Tatjana N. Bocharova. "Periodicity in recA protein-DNA complexes." FEBS Letters 407, no. 3 (May 5, 1997): 325–28. http://dx.doi.org/10.1016/s0014-5793(97)00367-0.

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Dissertations / Theses on the topic "DNA-protein complexes"

1

DiCapua, Elisabeth. "Complexes of recA protein with DNA /." [S.l.] : [s.n.], 1986. http://e-collection.ethbib.ethz.ch/show?type=diss&nr=8212.

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Hammond, Maria. "DNA-Mediated Detection and Profiling of Protein Complexes." Doctoral thesis, Uppsala universitet, Molekylära verktyg, 2013. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-204861.

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Proteins are the effector molecules of life. They are encoded in DNA that is inherited from generation to generation, but most cellular functions are executed by proteins. Proteins rarely act on their own – most actions are carried out through an interplay of tens of proteins and other biomolecules. Here I describe how synthetic DNA can be used to study proteins and protein complexes. Variants of proximity ligation assays (PLA) are used to generate DNA reporter molecules upon proximal binding by pairs of DNA oligonucleotide-modified affinity reagents. In Paper I, a robust protocol was set up for PLA on paramagnetic microparticles, and we demonstrated that this solid phase PLA had superior performance for detecting nine candidate cancer biomarkers compared to other immunoassays. Based on the protocol described in Paper I I then developed further variants of PLA that allows detection of protein aggregates and protein interactions. I sensitively detected aggregated amyloid protofibrils of prion proteins in paper II, and in paper III I studied binary interactions between several proteins of the NFκB family. For all immunoassays the selection of high quality affinity binders represents a major challenge. I have therefore established a protocol where a large set of protein binders can be simultaneously validated to identify optimal pairs for dual recognition immunoassays (Paper IV).

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Berge, Torunn. "Structural analysis of DNA and DNA-protein complexes using atomic force microscopy." Thesis, University of Cambridge, 2001. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.621339.

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Preston, Nicola Susan. "Structure and DNA binding of HMG boxes." Thesis, University of Portsmouth, 1996. https://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.310386.

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Luo, Dan. "Novel crosslinking technologies to assess protein-DNA binding and DNA-DNA complexes for gene delivery and expression /." Connect to resource, 1998. http://rave.ohiolink.edu/etdc/view?acc%5Fnum=osu1114436532.

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Luo, Dan. "Novel crosslinking technologies to assess protein-DNA binding and DNA-DNA complexes for gene delivery and expression." The Ohio State University, 1997. http://rave.ohiolink.edu/etdc/view?acc_num=osu1114436532.

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Bielskienė, Kristina. "Analysis of the barley (Hordeum vulgare) tightly bound DNA-protein complexes." Doctoral thesis, Lithuanian Academic Libraries Network (LABT), 2009. http://vddb.library.lt/obj/LT-eLABa-0001:E.02~2009~D_20091202_111955-77123.

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Despite a great deal of research, the functional significance of tightly bound DNA-protein complexes is not yet clear, therefore these complexes are perfect object for pioneering research. Very little is known about plant TBP-DNA complexes. In this work we investigated barley TBP-DNA complexes from different organs (first leaves, roots and coleoptiles) at different developmental stages. We characterized individual components of tightly bound DNA-proteins complexes: polypeptides (TBP) and DNA. We isolated and characterized TBP proteins from barley first leaves, roots and coleoptiles of different age and differentiation stage. Also we isolated and characterized the DNA fragments from barley first leaves and water ripe and milky ripe grain TBP-DNA complexes. We demonstrated that in different developmental stages of coleoptiles, first leaves and roots TBP-DNA complexes were identified as a group of 15-160 kDa proteins, most of TBPs are acidic. Some of barley TBPs (10, 25, 38, 40 and 55 kDa) exhibit phosphatase, maybe Ser/Thr activity. We have identified also that some of TBPs tyrosines were phosphorylated, this modification depends on organ and developmental stage. Identified barley TBPs were involved in fundamental genetic processes, as well as in chromatin rearrangement and regulation processes. Nuclear matrix proteins, enzymes, transcription factors, serpins, immunophilins, and transposon polypeptides were identified among TBPs. We demonstrated that expression of TBPs depends... [to full text]
Žinoma, kad pastovi nehistoninių polipetidų frakcija yra išgryninama kartu su eukariotine DNR ir sudaro labai tvirtus (galbūt kovalentinius) kompleksus tarp branduolio baltymų ir DNR. Nustatyta, kad Erlicho ascito tvirtuose DNR-baltymų kompleksuose yra baltymas C1D, baltymai, pasižymintys fosfataziniu ir kinaziniu aktyvumais, kai kurie proteazių slopikliai ir kiti, dar neištirti baltymai. Nepaisant intensyvių tyrinėjimų, eukariotinių ląstelių tvirti DNR-baltymų kompleksai vis dar lieka menkai aprašyti ir yra objektas tolimesniems tyrimams. Augalų TBP-DNR kompleksai kol kas buvo tyrinėti labai mažai. Šiame darbe charakterizuojami miežių Hordeum vulgare tvirti DNR-baltymų kompleksai. Mes tyrėme TBP-DNR kompleksus iš miežių skirtingų ūglių organų ir skirtingų vystymosi stadijų ląstelių: lapų, šaknų, koleoptilės. Norint ištirti tokių nukleoproteidų funkcijas, svarbu charakterizuoti individualius komplekso komponentus: polipeptidus ir DNR. Taigi, išskyrėme tvirtai su DNR sąveikaujančius baltymus iš miežių skirtingos diferenciacijos bei skirtingo amžiaus ląstelių: pirminių lapelių, šaknų, koleoptilės ir juos charakterizavome. Taip pat išskyrėme ir charakterizavome DNR fragmentus iš miežių pirminių lapelių bei vandeninės brandos ir pieninės brandos grūdų TBP-DNR kompleksų. Parodėme, kad miežių TBP baltymai yra 15-160 kDa, dauguma baltymų yra rūgštiniai. Kai kurie iš miežių TBP baltymų (10, 25, 38, 40 ir 55 kDa) pasižymi fosfataziniu, galbūt, Ser/Thr aktyvumu. Nustatėme, kad tam... [toliau žr. visą tekstą]

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Luo, Dan. "Novel cross-linking technologies to assess protein-DNA binding and DNA-DNA complexes for gene delivery and expression /." The Ohio State University, 1997. http://rave.ohiolink.edu/etdc/view?acc_num=osu1487946776022443.

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Fischhaber, Paula L. "Investigations at the molecular interfaces of complexes formed by the proteins ADR1 and xUBF1 with DNA /." Thesis, Connect to this title online; UW restricted, 1998. http://hdl.handle.net/1773/8648.

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Yan, Junhong. "DNA-Assisted Immunoassays for High-Performance Protein Analyses." Doctoral thesis, Uppsala universitet, Institutionen för immunologi, genetik och patologi, 2014. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-236591.

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Proteins play important roles in most cellular functions, such as, replication, transcription regulation, signal transduction, for catalyzing chemical reaction, etc. Technologies developed to identify proteins rely either on observing their own properties such as charge, size, mass to charge ratio or sequence composition; or on using affinity reagents that recognize specific protein targets. Immunoassays utilizing functionalized affinity reagents are powerful for targeted proteomics. Among them, DNA-assisted immunoassays in which affinity reagents are labeled with DNA molecules, offer some unique advantages. In this thesis, I will present works to improve current DNA-assisted immunoassays such as proximity ligation assays (PLA), as well as to take advantage of DNA reactions to adress other problems. In paper I, a new solid support (MBC-Ts) was functionalized with antibodies and used in the solid-phase PLA for detection of VEGF. The assay using MBC-Ts was compared among the commercially available solid supports in different matrices and it was shown to exhibit enhanced limit of detection in complex matrices. In paper II, a two-step protocol was described to prepare high-quality probes used in homogeneous and in situ PLA by purifying DNA-labeled affinity reagents from unconjugated affinity reagents and excess oligonucleotides. In paper III, PLA was applied on a capillary western blotting instrument so that both the sensitivity and specificity of the original assay were improved. In paper IV, a new method was introduced to profile protein components in individual protein complexes by DNA-barcoded antibodies. This method has been used to profile protein complexes such as surface proteins on individual secreted vesicles.

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Books on the topic "DNA-protein complexes"

1

Flapan, Erica. Knots, molecules, and the universe: An introduction to topology. Providence, Rhode Island: American Mathematical Society, 2015.

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2

Arnold, Revzin, ed. Footprinting of nucleic acid-protein complexes. San Diego: Academic Press, 1993.

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3

Lilley, David M. J. 1948-, Heumann Hermann 1944-, and Suck D, eds. Structural tools for the analysis of protein-nucleic acid complexes. Basel: Birkhäuser, 1992.

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Maher, Christopher J., and Elaine R. Mardis. Genomic Landscape of Cancer. Oxford University Press, 2017. http://dx.doi.org/10.1093/oso/9780190238667.003.0004.

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The study of cancer genomics has advanced rapidly during the last decade due to the development of next generation or massively parallel technology for DNA sequencing. The resulting knowledge is transforming the understanding of both inherited (germline) genetic susceptibility and the somatic changes in tumor tissue that drive abnormal growth and progression. The somatic alterations in tumor tissue vary depending on the type of cancer and its characteristic “genomic landscape.” New technologies have increased the speed and lowered the cost of DNA sequencing and have enabled high-volume characterization of RNA, DNA methylation, DNA-protein complexes, DNA conformation, and a host of other factors that, when altered, can contribute to the development and/or progression of the cancer. Technologic advances have greatly expanded research on somatic changes in tumor tissue, revealing both the singularity of individual cancer genomes and the commonality of genetic alterations that drive cancer in different tissues.

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Ungermann, Christian. Protein-protein interactions in the bacteriophage T4-coded dCTPase-dUTPase. 1993.

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6

The Eukaryotic Replisome A Guide To Protein Structure And Function. Springer, 2012.

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Schadt, Eric E. Network Methods for Elucidating the Complexity of Common Human Diseases. Edited by Dennis S. Charney, Eric J. Nestler, Pamela Sklar, and Joseph D. Buxbaum. Oxford University Press, 2017. http://dx.doi.org/10.1093/med/9780190681425.003.0002.

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The life sciences are now a significant contributor to the ever expanding digital universe of data, and stand poised to lead in both the generation of big data and the realization of dramatic benefit from it. We can now score variations in DNA across whole genomes; RNA levels and alternative isoforms, metabolite levels, protein levels, and protein state information across the transcriptome, metabolome and proteome; methylation status across the methylome; and construct extensive protein–protein and protein–DNA interaction maps, all in a comprehensive fashion and at the scale of populations of individuals. This chapter describes a number of analytical approaches aimed at inferring causal relationships among variables in very large-scale datasets by leveraging DNA variation as a systematic perturbation source. The causal inference procedures are also demonstrated to enhance the ability to reconstruct truly predictive, probabilistic causal gene networks that reflect the biological processes underlying complex phenotypes like disease.

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Slack, Jonathan. Conclusion. Oxford University Press, 2014. http://dx.doi.org/10.1093/actrade/9780199676507.003.0007.

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There are many concepts of the gene. They range from defined sequences of DNA encoding proteins, to variant genes distinguishing individuals (markers), to unknown genes controlling quantitative traits, to hypothetical entities controlling behaviour as well as other complex characteristics. The science of genes is at its most precise and reliable when dealing with known protein coding genes. But all of the different concepts of the gene have been and continue to be important in numerous areas of human thought.

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Wang, Jason T. L., Bruce A. Shapiro, and Dennis Shasha, eds. Pattern Discovery in Biomolecular Data. Oxford University Press, 1999. http://dx.doi.org/10.1093/oso/9780195119404.001.0001.

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Finding patterns in biomolecular data, particularly in DNA and RNA, is at the center of modern biological research. These data are complex and growing rapidly, so the search for patterns requires increasingly sophisticated computer methods. Pattern Discovery in Biomolecular Data provides a clear, up-to-date summary of the principal techniques. Each chapter is self-contained, and the techniques are drawn from many fields, including graph theory, information theory, statistics, genetic algorithms, computer visualization, and vision. Since pattern searches often benefit from multiple approaches, the book presents methods in their purest form so that readers can best choose the method or combination that fits their needs. The chapters focus on finding patterns in DNA, RNA, and protein sequences, finding patterns in 2D and 3D structures, and choosing system components. This volume will be invaluable for all workers in genomics and genetic analysis, and others whose research requires biocomputing.

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Chess, Andrew, and Schahram Akbarian. The Human Brain and its Epigenomes. Edited by Dennis S. Charney, Eric J. Nestler, Pamela Sklar, and Joseph D. Buxbaum. Oxford University Press, 2017. http://dx.doi.org/10.1093/med/9780190681425.003.0003.

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Conventional psychopharmacology elicits an insufficient therapeutic response in more than one half of patients diagnosed with schizophrenia, bipolar disorder, depression, anxiety, or related disorders. This underscores the need to further explore the neurobiology and molecular pathology of mental disorders in order to develop novel treatment strategies of higher efficacy. One promising avenue of research is epigenetics.Deeper understanding of genome organization and function in normal and diseased human brain will require comprehensive charting of neuronal and glial epigenomes. This includes DNA cytosine and adenine methylation, hundred(s) of residue-specific post-translational histone modifications and histone variants, transcription factor occupancies, and chromosomal conformations and loopings. Epigenome mappings provide an important avenue to assign function to many risk-associated DNA variants and mutations that do not affect protein-coding sequences. Powerful novel single cell technologies offer the opportunity to understand genome function in context of the vastly complex cellular heterogeneity and neuroanatomical diversity of the human brain.

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Book chapters on the topic "DNA-protein complexes"

1

Schiessel, Helmut. "DNA–Protein Complexes." In Biophysics for Beginners, 299–420. 2nd ed. New York: Jenny Stanford Publishing, 2021. http://dx.doi.org/10.1201/9781003223108-8.

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Travers, Andrew. "DNA—protein interactions: The three-dimensional architecture of DNA—protein complexes." In DNA-Protein Interactions, 28–51. Dordrecht: Springer Netherlands, 1993. http://dx.doi.org/10.1007/978-94-011-1480-6_2.

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Hollis, Thomas. "Crystallization of Protein-DNA Complexes." In Methods in Molecular Biology, 225–37. Totowa, NJ: Humana Press, 2007. http://dx.doi.org/10.1007/978-1-59745-209-0_11.

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Kim, Soojeong, and Isabel K. Darcy. "Topological Analysis of DNA-Protein Complexes." In Mathematics of DNA Structure, Function and Interactions, 177–94. New York, NY: Springer New York, 2009. http://dx.doi.org/10.1007/978-1-4419-0670-0_9.

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Kyas, Andreas, Winfried Mäueler, and Joerg T. Epplen. "Polyacrylamide Gel Electrophoresis of DNA/Protein Complexes." In Nucleic Acid Electrophoresis, 292–310. Berlin, Heidelberg: Springer Berlin Heidelberg, 1998. http://dx.doi.org/10.1007/978-3-642-58924-9_12.

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ten Heggeler-Bordier, Béatrice, and Walter Wahli. "Electron Microscope Visualisation of Protein-DNA Complexes." In A Laboratory Guide to In Vitro Studies of Protein-DNA Interactions, 153–61. Basel: Birkhäuser Basel, 1991. http://dx.doi.org/10.1007/978-3-0348-7561-5_13.

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Jagannathan, Indu, and Jeffrey J. Hayes. "Hydroxyl Radical Footprinting of Protein-DNA Complexes." In Methods in Molecular Biology™, 57–71. Totowa, NJ: Humana Press, 2009. http://dx.doi.org/10.1007/978-1-60327-015-1_5.

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Manfield, Iain W., and Peter G. Stockley. "Ethylation Interference Footprinting of DNA-Protein Complexes." In Methods in Molecular Biology™, 105–20. Totowa, NJ: Humana Press, 2009. http://dx.doi.org/10.1007/978-1-60327-015-1_9.

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Harbers, Matthias. "Shift-Western Blotting: Separate Analysis of Protein and DNA from Protein–DNA Complexes." In Methods in Molecular Biology, 355–73. New York, NY: Springer New York, 2015. http://dx.doi.org/10.1007/978-1-4939-2694-7_36.

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Lyubchenko, Yuri L. "AFM Imaging in Liquid of DNA and Protein-DNA Complexes." In Atomic Force Microscopy in Liquid, 231–58. Weinheim, Germany: Wiley-VCH Verlag GmbH & Co. KGaA, 2012. http://dx.doi.org/10.1002/9783527649808.ch9.

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Conference papers on the topic "DNA-protein complexes"

1

Niu, Luming, Wenling Shaiu, James Vesenka, Drena D. Larson, and Eric Henderson. "Atomic force microscopy of DNA-colloidal gold and DNA-protein complexes." In OE/LASE'93: Optics, Electro-Optics, & Laser Applications in Science& Engineering, edited by Richard A. Keller. SPIE, 1993. http://dx.doi.org/10.1117/12.146706.

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"Classification of families of DNA-recognizing protein domains based on structural features of DNA-protein complexes." In Bioinformatics of Genome Regulation and Structure/Systems Biology (BGRS/SB-2022) :. Institute of Cytology and Genetics, the Siberian Branch of the Russian Academy of Sciences, 2022. http://dx.doi.org/10.18699/sbb-2022-176.

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Grokhlina, T. I., L. A. Panchenko, R. V. Polozov, V. S. Sivozhelezov, and V. V. Ivanov. "Classification of DNA complexes of homeodomain and zinc-finger protein families: statistical analysis of DNA structures in interfaces of homeodomain-DNA complexes." In Mathematical Biology and Bioinformatics. Pushchino: IMPB RAS - Branch of KIAM RAS, 2018. http://dx.doi.org/10.17537/icmbb18.98.

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Gusev, Yu S., I. V. Volokhina, V. V. Fadeev, and M. I. Chumakov. "Study of the agrobacterial protein VirE2 - ssDNA interaction under various conditions for delivery technology development." In 2nd International Scientific Conference "Plants and Microbes: the Future of Biotechnology". PLAMIC2020 Organizing committee, 2020. http://dx.doi.org/10.28983/plamic2020.100.

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The effects of DNA length and conditions on the formation of VirE2-ssDNA complexes were studied by dynamic light scattering and electron microscopy. The disordered regions of the VirE2 protein are predicted.

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Cheng, Wen, and Changhui Yan. "A method for discriminating native protein-DNA complexes from decoys using spatial specific scoring matrices." In 2013 7th International Conference on Systems Biology (ISB). IEEE, 2013. http://dx.doi.org/10.1109/isb.2013.6623804.

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Chen, Kok Hao, and Jong Hyun Choi. "DNA Oligonucleotide-Templated Nanocrystals: Synthesis and Novel Label-Free Protein Detection." In ASME 2009 International Mechanical Engineering Congress and Exposition. ASMEDC, 2009. http://dx.doi.org/10.1115/imece2009-11958.

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Semiconductor and magnetic nanoparticles hold unique optical and magnetic properties, and great promise for bio-imaging and therapeutic applications. As part of their stable synthesis, the nanocrystal surfaces are usually capped by long chain organic moieties such as trioctylphosphine oxide. This capping serves two purposes: it saturates dangling bonds at the exposed crystalline lattice, and it prevents irreversible aggregation by stabilizing the colloid through entropic repulsion. These nanocrystals can be rendered water-soluble by either ligand exchange or overcoating, which hampers their widespread use in biological imaging and biomedical therapeutics. Here, we report a novel scheme of synthesizing fluorescent PbS and magnetic Fe3O4 nanoparticles using DNA oligonucleotides. Our method of PbS synthesis includes addition of Na2S to the mixture solution of DNA sequence and Pb acetate (at a fixed molar ratio of DNA/S2−/Pb2+ of 1:2:4) in a standard TAE buffer at room temperature in the open air. In the case of Fe3O4 particle synthesis, ferric and ferrous chloride were mixed with DNA in DI water at a molar ratio of DNA/Fe2+/Fe3+ = 1:4:8 and the particles were formed via reductive precipitation, induced by increasing pH to ∼11 with addition of ammonium hydroxide. These nanocrystals are highly stable and water-soluble immediately after the synthesis, due to DNA termination. We examined the surface chemistry between oligonucleotides and nanocrystals using FTIR spectroscopy, and found that the different chemical moieties of nucleobases passivate the particle surface. Strong coordination of primary amine and carbonyl groups provides the chemical and colloidal stabilities, leading to high particle yields (Figure 1). The resulting PbS nanocrystals have a distribution of 3–6 nm in diameter, while a broader size distribution is observed with Fe3O4 nanoparticles as shown in Figure 1b and c, respectively. A similar observation was reported with the pH change-induced Fe3O4 particles of a bimodal size distribution where superparamagnetic and ferrimagnetic magnetites co-exist. In spite of the differences, FTIR measurements suggest that the chemical nature of the oligonucleotide stabilization in this case is identical to the PbS system. As a particular application, we demonstrate that aptamer-capped PbS QD can detect a target protein based on selective charge transfer, since the oligonucleotide-templated synthesis can also serve the additional purpose of providing selective binding to a molecular target. Here, we use thrombin and a thrombin-binding aptamer as a model system. These QD have diameters of 3∼6 nm and fluoresce around 1050 nm. We find that a DNA aptamer can passivate near IR fluorescent PbS nanocrystals, rendering them water-soluble and stable against aggregation, and retain the secondary conformation needed to selectively bind to its target, thrombin, as shown in Figure 2. Importantly, we find that when the aptamer-functionalized nanoparticles binds to its target (only the target), there is a highly systematic and selective quenching of the PL, even in high concentrations of interfering proteins as shown in Figure 3a and b. Thrombin is detected within one minute with a detection limit of ∼1 nM. This PL quenching is attributed to charge transfer from functional groups on the protein to the nanocrystals. A charge transfer can suppress optical transition mechanisms as we observe a significant decrease in QD absorption with target addition (Figure 3c). Here, we rule out other possibilities including Forster resonance energy transfer (FRET) and particle aggregation, because thrombin absorb only in the UV, and we did not observe any significant change in the diffusion coefficient of the particles with the target analyte, respectively. The charge transfer-induced photobleaching of QD and carbon nanotubes was observed with amine groups, Ru-based complexes, and azobenzene compounds. This selective detection of an unlabeled protein is distinct from previously reported schemes utilizing electrochemistry, absorption, and FRET. In this scheme, the target detection by a unique, direct PL transduction is observed even in the presence of high background concentrations of interfering negatively or positively charged proteins. This mechanism is the first to selectively modulate the QD PL directly, enabling new types of label free assays and detection schemes. This direct optical transduction is possible due to oligonucleotidetemplated surface passivation and molecular recognition. This chemistry may lead to more nanoparticle-based optical and magnetic probes that can be activated in a highly chemoselective manner.

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Hendrix, P., J. Witsch, V. Spalart, K. Martinod, H. Schneider, J. Oertel, J. Geisel, and S. Hemmer. "E-192 Association of myeloperoxidase-DNA complexes and high mobility group box 1 protein with delayed cerebral ischemia following aneurysmal subarachnoid hemorrhage." In SNIS 19th Annual Meeting Abstracts. BMA House, Tavistock Square, London, WC1H 9JR: BMJ Publishing Group Ltd., 2022. http://dx.doi.org/10.1136/neurintsurg-2022-snis.303.

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8

MATSSON, L. "LONG RANGE INTERACTION BETWEEN PROTEIN COMPLEXES IN DNA CONTROLS REPLICATION AND CELL CYCLE PROGRESSION: THE DOUBLE HELIX AND MICROTUBULES BEHAVE LIKE ELASTICALLY BRACED STRINGS." In Proceedings of the First Workshop. WORLD SCIENTIFIC, 2001. http://dx.doi.org/10.1142/9789812811301_0008.

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9

Krasnoshtanova, Alla, and Elisaveta Borovkova. "OBTAINING NUCLEIC ACID PREPARATIONS AND THEIR HYDROLYSATES FROM BIOMASS OF METHANE-OXIDIZING BACTERIA." In GEOLINKS Conference Proceedings. Saima Consult Ltd, 2021. http://dx.doi.org/10.32008/geolinks2021/b1/v3/14.

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"Due to the unfavourable environmental, social and economic situation, the need for the treatment of oncological diseases and diseases associated with impaired activity of the immune system is increasing. A lot of these drugs are made on the basis of nucleic acid components, the industrial production of which is practically non-existent in Russia. Therefore, a task of current interest is to develop the basis of the technology for obtaining components of nucleic acids, which can be widely used in medicine as immunomodulatory, wound-healing, antiviral, and diagnostic medicine, as well as for cancer treatment. Most of the described in literature methods of isolating nucleic acid components from plant, animal and microbial raw materials are based on the use of toxic and expensive organic solvents, that’s why it is impossible to apply these methods outside of laboratory conditions. The most promising source of raw materials for nucleic acids is the biomass of microorganisms (yeast and bacteria) from biomass, since the use of such source makes it possible to quickly obtain a large enough amount of biomass, and, consequently, a larger amount of nucleic acids. This allows obtaining DNA in addition to RNA. RNA and DNA substances can be used to obtain nucleosides and nitrogenous bases, which are also widely used in medicine. The purpose of these studies was to select the conditions for the extraction of RNA and DNA from the biomass of methane-oxidizing bacteria in one technological cycle, as well as to compare the efficiency of alkaline and acid hydrolysis of microbial RNA and DNA. The need for a two-stage extraction of nucleic acids from the biomass of methane-oxidizing bacteria in order to separately extract RNA and DNA was Substantiated. It was ascertained that at the first stage of extraction at a temperature of 90 ° C, pH 9.0 for 90 min, at least 85% of RNA is extracted. After the separation of the extract by centrifugation, the partially denuclearized biomass must be re-processed under the same conditions in order to extract DNA by at least 83%. The modes of concentration of RNA and DNA solutions by ultrafiltration were selected. It was found that in order to achieve effective deposition of nucleic acids at the isoelectric point, the concentration of the RNA solution must be carried out on the UPM-10 membrane at the concentration degree of 7, and the DNA solution on the UPM-100 membrane at the concentration degree 6. The dynamics of decomposition of nucleic-protein complexes in the medium of monoammonium phosphate was investigated. It was shown that the transition of NA into solution by at least 80% is achieved at a monoammonium phosphate concentration of 1.7 M, a temperature of 55 ° C for 90 min. The use of 5-fold washing of oligonucleotide substances with acidified water (pH 2.0) to remove excess mineral impurities was substantiated. А comparative assessment of acid and alkaline hydrolysis of RNA and DNA was carried out in order to obtain derivatives of nucleic acids."

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Vermeer, C., BA M. Soute, and MM W. Ulrich. "IN VITRO CARBOXYLATION OF EXOGENOUS PROTEIN SUBSTRATES BY VITAMIN K-DEPENDENT CARBOXYLASE." In XIth International Congress on Thrombosis and Haemostasis. Schattauer GmbH, 1987. http://dx.doi.org/10.1055/s-0038-1643994.

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In vivo treatment of experimental animals with vitamin K-antagonists induces the accumulation of non-carboxylated coagulation factor precursors in the liver, where they are tightly bound to vitamin K-dependent carboxylase. If hepatic carboxylase is isolated from warfarin-treated animals, it is obtained therefore almost exclusively in the form of an enzyme/substrate complex. If carboxylase is prepared from non-treated animals, on the other hand, the resulting enzyme is predominantly substrate-free. Small substrates like F L E E L or decarboxylated osteocalcinare carboxylated equally well by both types of carboxylase, but protein substrates(Mr > 30 000) are recognized exclusively by substrate-free carboxylase.Initial attempts to purify carboxylasewere performed with livers from warfarin-treated cows as a starting material. Antibodies against the normal blood coagulation factors crossreact with the hepatic precursor proteins so that the enzyme/substrate complexes could be specifically extracted from detergent-solubilized microsomes by the substrate/antibody interaction. This procedure resulted ina substantial purification of carboxylase, but because its endogenous substrate remained firmly bound, even after it had been carboxylated in vitro, the enzyme system was not suitable for the carboxylation of protein substrates.Therefore a second strategy was developed by which substrate-free carboxylase (from normal livers) was partly purified by sequential extraction of the microsomal membranes with detergents, followed by ammonium sulfate precipitation and size exclusion chromatography.This procedure resulted in a soluble carboxylase complex, still consisting of 7 proteins and phosphatidylcholine. Although further dissociation of the complex resulted in a complete loss of activity, it is not sure if all components play a role in the carboxylation reaction. Exogenous substrates which could be carboxylated by substrate-free carboxylase were: the penta-peptide F L E E L, descarboxyprothrombin from bovine plasma, thermally decarboxylated osteocalcin from bovine bone and non-car-boxy lated coagulaton factor precursors which had been produced by recombinant-DNA techniques in various laboratories. The . efficiency of CO^ incorporation was: 1 mole per 100 moles of F L E E L, 1 mole per 240 moles of descarboxy-prothrombin, 1 mole per mole of decarboxylated osteocalcin and 8 moles per mole of a recombinant factor IX precursor. We assume that the high efficiency with which the recombinant coagulation factor precursors were carboxylated is due to the presence of at least part of their leader sequence. The importance of the aminoacid chain preceding the first carboxylatable Glu residue is demonstrated by the fact that descarboxylated osteocalcin of bovine origin is carboxylated with a relatively high efficiency, whereas descarboxylated osteocalcin from monkey bone is not recognized atal.. Yet the only difference between the two substrates is found in their aminoacids 3 and 4, whereas the first carboxylatable Glu occurs at position 17. It seems, therefore, that the aminoacids 1-16 in bovine osteocalcin mimic to some extent part of the leader sequence in the coagulation factor precursors. Chemical or biochemical modification of decarboxylated osteocalcin might reveal which structural features contribute to its recognition by hepatic carboxylase.The optimal conditions for carboxylation include a high concentration of dithiols (e.g. DTT) and under these conditions disulfide bridges are reduced. Obviously this will lead to a complete destruction of the biological activity of various carboxylated products. Therefore we have searched for a more natural reducing system and it was found that the bacterial thioredoxin/thiore-doxin-reductase system in the presence of 40 uM NADFH was able to replace DTT in the reaction mixtures. Since a comparable system also occurs in calf liver it seems not unlikely that this is the physiological counterpart of the dithiols used in vitro.

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Reports on the topic "DNA-protein complexes"

1

Gupta, G., S. V. Santhana Mariappan, X. Chen, P. Catasti, L. A. III Silks, R. K. Moyzis, E. M. Bradbury, and A. E. Garcia. Structural biology of disease-associated repetitive DNA sequences and protein-DNA complexes involved in DNA damage and repair. Office of Scientific and Technical Information (OSTI), July 1997. http://dx.doi.org/10.2172/505319.

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Bradbury, E. M., P. Catasti, X. Chen, G. Gupta, B. Imai, R. Moyzis, R. Ratliff, and S. Velupillai. Neutron scattering and nuclear magnetic resonance spectroscopy structural studies of protein-DNA complexes. Office of Scientific and Technical Information (OSTI), March 1996. http://dx.doi.org/10.2172/206538.

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Ohad, Nir, and Robert Fischer. Regulation of plant development by polycomb group proteins. United States Department of Agriculture, January 2008. http://dx.doi.org/10.32747/2008.7695858.bard.

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Our genetic and molecular studies have indicated that FIE a WD-repeat Polycomb group (PcG) protein takes part in multi-component protein complexes. We have shown that FIE PcG protein represses inappropriate programs of development during the reproductive and vegetative phases of the Arabidopsis life cycle. Moreover, we have shown that FIE represses the expression of key regulatory genes that promote flowering (AG and LFY), embryogenesis (LEC1), and shoot formation (KNAT1). These results suggest that the FIE PcG protein participates in the formation of distinct PcG complexes that repress inappropriate gene expression at different stages of plant development. PcG complexes modulate chromatin compactness by modifying histones and thereby regulate gene expression and imprinting. The main goals of our original project were to elucidate the biological functions of PcG proteins, and to understand the molecular mechanisms used by FIE PcG complexes to repress the expression of its gene targets. Our results show that the PcG complex acts within the central cell of the female gametophyte to maintain silencing of MEA paternal allele. Further more we uncovered a novel example of self-imprinting mechanism by the PgG complex. Based on results obtained in the cures of our research program we extended our proposed goals and elucidated the role of DME in regulating plant gene imprinting. We discovered that in addition to MEA,DME also imprints two other genes, FWA and FIS2. Activation of FWA and FIS2 coincides with a reduction in 5-methylcytosine in their respective promoters. Since endosperm is a terminally differentiated tissue, the methylation status in the FWA and FIS2 promoters does not need to be reestablished in the following generation. We proposed a “One-Way Control” model to highlight differences between plant and animal genomic imprinting. Thus we conclude that DEMETER is a master regulator of plant gene imprinting. Future studies of DME function will elucidate its role in processes and disease where DNA methylation has a key regulatory role both in plants and animals. Such information will provide valuable insight into developing novel strategies to control and improve agricultural traits and overcome particular human diseases.

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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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Elbaum, Michael, and Peter J. Christie. Type IV Secretion System of Agrobacterium tumefaciens: Components and Structures. United States Department of Agriculture, March 2013. http://dx.doi.org/10.32747/2013.7699848.bard.

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Objectives: The overall goal of the project was to build an ultrastructural model of the Agrobacterium tumefaciens type IV secretion system (T4SS) based on electron microscopy, genetics, and immunolocalization of its components. There were four original aims: Aim 1: Define the contributions of contact-dependent and -independent plant signals to formation of novel morphological changes at the A. tumefaciens polar membrane. Aim 2: Genetic basis for morphological changes at the A. tumefaciens polar membrane. Aim 3: Immuno-localization of VirB proteins Aim 4: Structural definition of the substrate translocation route. There were no major revisions to the aims, and the work focused on the above questions. Background: Agrobacterium presents a unique example of inter-kingdom gene transfer. The process involves cell to cell transfer of both protein and DNA substrates via a contact-dependent mechanism akin to bacterial conjugation. Transfer is mediated by a T4SS. Intensive study of the Agrobacterium T4SS has made it an archetypal model for the genetics and biochemistry. The channel is assembled from eleven protein components encoded on the B operon in the virulence region of the tumor-inducing plasmid, plus an additional coupling protein, VirD4. During the course of our project two structural studies were published presenting X-ray crystallography and three-dimensional reconstruction from electron microscopy of a core complex of the channel assembled in vitro from homologous proteins of E. coli, representing VirB7, VirB9, and VirB10. Another study was published claiming that the secretion channels in Agrobacterium appear on helical arrays around the membrane perimeter and along the entire length of the bacterium. Helical arrangements in bacterial membranes have since fallen from favor however, and that finding was partially retracted in a second publication. Overall, the localization of the T4SS within the bacterial membranes remains enigmatic in the literature, and we believe that our results from this project make a significant advance. Summary of achievements : We found that polar inflations and other membrane disturbances relate to the activation conditions rather than to virulence protein expression. Activation requires low pH and nutrient-poor medium. These stress conditions are also reflected in DNA condensation to varying degrees. Nonetheless, they must be considered in modeling the T4SS as they represent the relevant conditions for its expression and activity. We identified the T4SS core component VirB7 at native expression levels using state of the art super-resolution light microscopy. This marker of the secretion system was found almost exclusively at the cell poles, and typically one pole. Immuno-electron microscopy identified the protein at the inner membrane, rather than at bridges across the inner and outer membranes. This suggests a rare or transient assembly of the secretion-competent channel, or alternatively a two-step secretion involving an intermediate step in the periplasmic space. We followed the expression of the major secreted effector, VirE2. This is a single-stranded DNA binding protein that forms a capsid around the transferred oligonucleotide, adapting the bacterial conjugation to the eukaryotic host. We found that over-expressed VirE2 forms filamentous complexes in the bacterial cytoplasm that could be observed both by conventional fluorescence microscopy and by correlative electron cryo-tomography. Using a non-retentive mutant we observed secretion of VirE2 from bacterial poles. We labeled the secreted substrates in vivo in order detect their secretion and appearance in the plant cells. However the low transfer efficiency and significant background signal have so far hampered this approach.

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Christopher, David A., and Avihai Danon. Plant Adaptation to Light Stress: Genetic Regulatory Mechanisms. United States Department of Agriculture, May 2004. http://dx.doi.org/10.32747/2004.7586534.bard.

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Original Objectives: 1. Purify and biochemically characterize RB60 orthologs in higher plant chloroplasts; 2. Clone the gene(s) encoding plant RB60 orthologs and determine their structure and expression; 3. Manipulate the expression of RB60; 4. Assay the effects of altered RB60 expression on thylakoid biogenesis and photosynthetic function in plants exposed to different light conditions. In addition, we also examined the gene structure and expression of RB60 orthologs in the non-vascular plant, Physcomitrella patens and cloned the poly(A)-binding protein orthologue (43 kDa RB47-like protein). This protein is believed to a partner that interacts with RB60 to bind to the psbA5' UTR. Thus, to obtain a comprehensive view of RB60 function requires analysis of its biochemical partners such as RB43. Background & Achievements: High levels of sunlight reduce photosynthesis in plants by damaging the photo system II reaction center (PSII) subunits, such as D1 (encoded by the chloroplast tpsbAgene). When the rate of D1 synthesis is less than the rate of photo damage, photo inhibition occurs and plant growth is decreased. Plants use light-activated translation and enhanced psbAmRNA stability to maintain D1 synthesis and replace the photo damaged 01. Despite the importance to photosynthetic capacity, these mechanisms are poorly understood in plants. One intriguing model derived from the algal chloroplast system, Chlamydomonas, implicates the role of three proteins (RB60, RB47, RB38) that bind to the psbAmRNA 5' untranslated leader (5' UTR) in the light to activate translation or enhance mRNA stability. RB60 is the key enzyme, protein D1sulfide isomerase (Pill), that regulates the psbA-RN :Binding proteins (RB's) by way of light-mediated redox potentials generated by the photosystems. However, proteins with these functions have not been described from higher plants. We provided compelling evidence for the existence of RB60, RB47 and RB38 orthologs in the vascular plant, Arabidopsis. Using gel mobility shift, Rnase protection and UV-crosslinking assays, we have shown that a dithiol redox mechanism which resembles a Pill (RB60) activity regulates the interaction of 43- and 30-kDa proteins with a thermolabile stem-loop in the 5' UTR of the psbAmRNA from Arabidopsis. We discovered, in Arabidopsis, the PD1 gene family consists of II members that differ in polypeptide length from 361 to 566 amino acids, presence of signal peptides, KDEL motifs, and the number and positions of thioredoxin domains. PD1's catalyze the reversible formation an disomerization of disulfide bonds necessary for the proper folding, assembly, activity, and secretion of numerous enzymes and structural proteins. PD1's have also evolved novel cellular redox functions, as single enzymes and as subunits of protein complexes in organelles. We provide evidence that at least one Pill is localized to the chloroplast. We have used PDI-specific polyclonal and monoclonal antisera to characterize the PD1 (55 kDa) in the chloroplast that is unevenly distributed between the stroma and pellet (containing membranes, DNA, polysomes, starch), being three-fold more abundant in the pellet phase. PD1-55 levels increase with light intensity and it assembles into a high molecular weight complex of ~230 kDa as determined on native blue gels. In vitro translation of all 11 different Pill's followed by microsomal membrane processing reactions were used to differentiate among PD1's localized in the endoplasmic reticulum or other organelles. These results will provide.1e insights into redox regulatory mechanisms involved in adaptation of the photosynthetic apparatus to light stress. Elucidating the genetic mechanisms and factors regulating chloroplast photosynthetic genes is important for developing strategies to improve photosynthetic efficiency, crop productivity and adaptation to high light environments.

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Tzfira, Tzvi, Michael Elbaum, and Sharon Wolf. DNA transfer by Agrobacterium: a cooperative interaction of ssDNA, virulence proteins, and plant host factors. United States Department of Agriculture, December 2005. http://dx.doi.org/10.32747/2005.7695881.bard.

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Agrobacteriumtumefaciensmediates genetic transformation of plants. The possibility of exchanging the natural genes for other DNA has led to Agrobacterium’s emergence as the primary vector for genetic modification of plants. The similarity among eukaryotic mechanisms of nuclear import also suggests use of its active elements as media for non-viral genetic therapy in animals. These considerations motivate the present study of the process that carries DNA of bacterial origin into the host nucleus. The infective pathway of Agrobacterium involves excision of a single-stranded DNA molecule (T-strand) from the bacterial tumor-inducing plasmid. This transferred DNA (T-DNA) travels to the host cell cytoplasm along with two virulence proteins, VirD2 and VirE2, through a specific bacteriumplant channel(s). Little is known about the precise structure and composition of the resulting complex within the host cell and even less is known about the mechanism of its nuclear import and integration into the host cell genome. In the present proposal we combined the expertise of the US and Israeli labs and revealed many of the biophysical and biological properties of the genetic transformation process, thus enhancing our understanding of the processes leading to nuclear import and integration of the Agrobacterium T-DNA. Specifically, we sought to: I. Elucidate the interaction of the T-strand with its chaperones. II. Analyzing the three-dimensional structure of the T-complex and its chaperones in vitro. III. Analyze kinetics of T-complex formation and T-complex nuclear import. During the past three years we accomplished our goals and made the following major discoveries: (1) Resolved the VirE2-ssDNA three-dimensional structure. (2) Characterized VirE2-ssDNA assembly and aggregation, along with regulation by VirE1. (3) Studied VirE2-ssDNA nuclear import by electron tomography. (4) Showed that T-DNA integrates via double-stranded (ds) intermediates. (5) Identified that Arabidopsis Ku80 interacts with dsT-DNA intermediates and is essential for T-DNA integration. (6) Found a role of targeted proteolysis in T-DNA uncoating. Our research provide significant physical, molecular, and structural insights into the Tcomplex structure and composition, the effect of host receptors on its nuclear import, the mechanism of T-DNA nuclear import, proteolysis and integration in host cells. Understanding the mechanical and molecular basis for T-DNA nuclear import and integration is an essential key for the development of new strategies for genetic transformation of recalcitrant plant species. Thus, the knowledge gained in this study can potentially be applied to enhance the transformation process by interfering with key steps of the transformation process (i.e. nuclear import, proteolysis and integration). Finally, in addition to the study of Agrobacterium-host interaction, our research also revealed some fundamental insights into basic cellular mechanisms of nuclear import, targeted proteolysis, protein-DNA interactions and DNA repair.

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Weller, Joel I., Derek M. Bickhart, Micha Ron, Eyal Seroussi, George Liu, and George R. Wiggans. Determination of actual polymorphisms responsible for economic trait variation in dairy cattle. United States Department of Agriculture, January 2015. http://dx.doi.org/10.32747/2015.7600017.bard.

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The project’s general objectives were to determine specific polymorphisms at the DNA level responsible for observed quantitative trait loci (QTLs) and to estimate their effects, frequencies, and selection potential in the Holstein dairy cattle breed. The specific objectives were to (1) localize the causative polymorphisms to small chromosomal segments based on analysis of 52 U.S. Holstein bulls each with at least 100 sons with high-reliability genetic evaluations using the a posteriori granddaughter design; (2) sequence the complete genomes of at least 40 of those bulls to 20 coverage; (3) determine causative polymorphisms based on concordance between the bulls’ genotypes for specific polymorphisms and their status for a QTL; (4) validate putative quantitative trait variants by genotyping a sample of Israeli Holstein cows; and (5) perform gene expression analysis using statistical methodologies, including determination of signatures of selection, based on somatic cells of cows that are homozygous for contrasting quantitative trait variants; and (6) analyze genes with putative quantitative trait variants using data mining techniques. Current methods for genomic evaluation are based on population-wide linkage disequilibrium between markers and actual alleles that affect traits of interest. Those methods have approximately doubled the rate of genetic gain for most traits in the U.S. Holstein population. With determination of causative polymorphisms, increasing the accuracy of genomic evaluations should be possible by including those genotypes as fixed effects in the analysis models. Determination of causative polymorphisms should also yield useful information on gene function and genetic architecture of complex traits. Concordance between QTL genotype as determined by the a posteriori granddaughter design and marker genotype was determined for 30 trait-by-chromosomal segment effects that are segregating in the U.S. Holstein population; a probability of <10²⁰ was used to accept the null hypothesis that no segregating gene within the chromosomal segment was affecting the trait. Genotypes for 83 grandsires and 17,217 sons were determined by either complete sequence or imputation for 3,148,506 polymorphisms across the entire genome. Variant sites were identified from previous studies (such as the 1000 Bull Genomes Project) and from DNA sequencing of bulls unique to this project, which is one of the largest marker variant surveys conducted for the Holstein breed of cattle. Effects for stature on chromosome 11, daughter pregnancy rate on chromosome 18, and protein percentage on chromosome 20 met 3 criteria: (1) complete or nearly complete concordance, (2) nominal significance of the polymorphism effect after correction for all other polymorphisms, and (3) marker coefficient of determination >40% of total multiple-regression coefficient of determination for the 30 polymorphisms with highest concordance. The missense polymorphism Phe279Tyr in GHR at 31,909,478 base pairs on chromosome 20 was confirmed as the causative mutation for fat and protein concentration. For effect on fat percentage, 12 additional missensepolymorphisms on chromosome 14 were found that had nearly complete concordance with the suggested causative polymorphism (missense mutation Ala232Glu in DGAT1). The markers used in routine U.S. genomic evaluations were increased from 60,000 to 80,000 by adding markers for known QTLs and markers detected in BARD and other research projects. Objectives 1 and 2 were completely accomplished, and objective 3 was partially accomplished. Because no new clear-cut causative polymorphisms were discovered, objectives 4 through 6 were not completed.

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Feldman, Moshe, Eitan Millet, Calvin O. Qualset, and Patrick E. McGuire. Mapping and Tagging by DNA Markers of Wild Emmer Alleles that Improve Quantitative Traits in Common Wheat. United States Department of Agriculture, February 2001. http://dx.doi.org/10.32747/2001.7573081.bard.

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The general goal was to identify, map, and tag, with DNA markers, segments of chromosomes of a wild species (wild emmer wheat, the progenitor of cultivated wheat) determining the number, chromosomal locations, interactions, and effects of genes that control quantitative traits when transferred to a cultivated plant (bread wheat). Slight modifications were introduced and not all objectives could be completed within the human and financial resources available, as noted with the specific objectives listed below: 1. To identify the genetic contribution of each of the available wild emmer chromosome-arm substitution lines (CASLs) in the bread wheat cultivar Bethlehem for quantitative traits, including grain yield and its components and grain protein concentration and yield, and the effect of major loci affecting the quality of end-use products. [The quality of end-use products was not analyzed.] 2. To determine the extent and nature of genetic interactions (epistatic effects) between and within homoeologous groups 1 and 7 for the chromosome arms carrying "wild" and "cultivated" alleles as expressed in grain and protein yields and other quantitative traits. [Two experiments were successful, grain protein concentration could not be measured; data are partially analyzed.] 3. To derive recombinant substitution lines (RSLs) for the chromosome arms of homoeologous groups 1 and 7 that were found previously to promote grain and protein yields of cultivated wheat. [The selection of groups 1 and 7 tons based on grain yield in pot experiments. After project began, it was decided also to derive RSLs for the available arms of homoeologous group 4 (4AS and 4BL), based on the apparent importance of chromosome group 4, based on early field trials of the CASLs.] 4. To characterize the RSLs for quantitative traits as in objective 1 and map and tag chromosome segments producing significant effects (quantitative trait loci, QTLs by RFLP markers. [Producing a large population of RSLs for each chromosome arm and mapping them proved more difficult than anticipated, low numbers of RSLs were obtained for two of the chromosome arms.] 5. To construct recombination genetic maps of chromosomes of homoeologous groups 1 and 7 and to compare them to existing maps of wheat and other cereals [Genetic maps are not complete for homoeologous groups 4 and 7.] The rationale for this project is that wild species have characteristics that would be valuable if transferred to a crop plant. We demonstrated the sequence of chromosome manipulations and genetic tests needed to confirm this potential value and enhance transfer. This research has shown that a wild tetraploid species harbors genetic variability for quantitative traits that is interactive and not simply additive when introduced into a common genetic background. Chromosomal segments from several chromosome arms improve yield and protein in wheat but their effect is presumably enhanced when combination of genes from several segments are integrated into a single genotype in order to achieve the benefits of genes from the wild species. The interaction between these genes and those in the recipient species must be accounted for. The results of this study provide a scientific basis for some of the disappointing results that have historically obtained when using wild species as donors for crop improvement and provide a strategy for further successes.

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10

Bercovier, Herve, and Ronald P. Hedrick. Diagnostic, eco-epidemiology and control of KHV, a new viral pathogen of koi and common carp. United States Department of Agriculture, December 2007. http://dx.doi.org/10.32747/2007.7695593.bard.

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Original objectives and revisions-The proposed research included these original objectives: field validation of diagnostic tests (PCR), the development and evaluation of new sensitive tools (LC-PCR/TaqManPCR, antibody detection by ELISA) including their use to study the ecology and the epidemiology of KHV (virus distribution in the environment and native cyprinids) and the carrier status of fish exposed experimentally or naturally to KHV (sites of virus replication and potential persistence or latency). In the course of the study we completed the genome sequence of KHV and developed a DNA array to study the expression of KHV genes in different conditions. Background to the topics-Mass mortality of koi or common carp has been observed in Israel, USA, Europe and Asia. These outbreaks have reduced exports of koi from Israel and have created fear about production, import, and movements of koi and have raised concerns about potential impacts on native cyprinid populations in the U.S.A. Major conclusions-A suite of new diagnostic tools was developed that included 3 PCR assays for detection of KHV DNA in cell culture and fish tissues and an ELISA assay capable of detecting anti-KHV antibodies in the serum of koi and common carp. The TKPCR assay developed during the grant has become an internationally accepted gold standard for detection of viral DNA. Additionally, the ELISA developed for detecting serum anti-KHV antibodies is now in wide use as a major nonlethal screening tool for evaluating virus status of koi and common carp populations. Real time PCR assays have been able to detect viral DNA in the internal organs of survivors of natural and wild type vaccine exposures at 1 and 10³ genome equivalents at 7 months after exposure. In addition, vaccinated fish were able to transmit the virus to naive fish. Potential control utilizing hybrids of goldfish and common carp for production demonstrated they were considerably more resistant than pure common carp or koi to both KHV (CyHV-3). There was no evidence that goldfish or other tested endemic cyprinids species were susceptible to KHV. The complete genomic sequencing of 3 strains from Japan, the USA, and Israel revealed a 295 kbp genome containing a 22 kbp terminal direct repeat encoding clear gene homologs to other fish herpesviruses in the family Herpesviridae. The genome encodes156 unique protein-coding genes, eight of which are duplicated in the terminal repeat. Four to seven genes are fragmented and the loss of these genes may be associated with the high virulence of the virus. Viral gene expression was studies by a newly developed chip which has allowed verification of transcription of most all hypothetical genes (ORFs) as well as their kinetics. Implications, both scientific and agricultural- The results from this study have immediate application for the control and management of KHV. The proposal provides elements key to disease management with improved diagnostic tools. Studies on the ecology of the virus also provide insights into management of the virus at the farms that farmers will be able to apply immediately to reduce risks of infections. Lastly, critical issues that surround present procedures used to create “resistant fish” must be be resolved (e.g. carriers, risks, etc.). Currently stamping out may be effective in eradicating the disease. The emerging disease caused by KHV continues to spread. With the economic importance of koi and carp and the vast international movements of koi for the hobby, this disease has the potential for even further spread. The results from our studies form a critical component of a comprehensive program to curtail this emerging pathogen at the local, regional and international levels.

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