Academic literature on the topic 'Unique molecular identifiers'
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Journal articles on the topic "Unique molecular identifiers"
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Schmierer, Bernhard, Sandeep K. Botla, Jilin Zhang, Mikko Turunen, Teemu Kivioja, and Jussi Taipale. "CRISPR/Cas9 screening using unique molecular identifiers." Molecular Systems Biology 13, no. 10 (October 2017): 945. http://dx.doi.org/10.15252/msb.20177834.
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Islam, Saiful, Amit Zeisel, Simon Joost, Gioele La Manno, Pawel Zajac, Maria Kasper, Peter Lönnerberg, and Sten Linnarsson. "Quantitative single-cell RNA-seq with unique molecular identifiers." Nature Methods 11, no. 2 (December 22, 2013): 163–66. http://dx.doi.org/10.1038/nmeth.2772.
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Liu, Daniel. "Algorithms for efficiently collapsing reads with Unique Molecular Identifiers." PeerJ 7 (December 16, 2019): e8275. http://dx.doi.org/10.7717/peerj.8275.
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Background Unique Molecular Identifiers (UMI) are used in many experiments to find and remove PCR duplicates. There are many tools for solving the problem of deduplicating reads based on their finding reads with the same alignment coordinates and UMIs. However, many tools either cannot handle substitution errors, or require expensive pairwise UMI comparisons that do not efficiently scale to larger datasets. Results We reformulate the problem of deduplicating UMIs in a manner that enables optimizations to be made, and more efficient data structures to be used. We implement our data structures and optimizations in a tool called UMICollapse, which is able to deduplicate over one million unique UMIs of length 9 at a single alignment position in around 26 s, using only a single thread and much less than 10 GB of memory. Conclusions We present a new formulation of the UMI deduplication problem, and show that it can be solved faster, with more sophisticated data structures.
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Kivioja, Teemu, Anna Vähärautio, Kasper Karlsson, Martin Bonke, Martin Enge, Sten Linnarsson, and Jussi Taipale. "Counting absolute numbers of molecules using unique molecular identifiers." Nature Methods 9, no. 1 (November 20, 2011): 72–74. http://dx.doi.org/10.1038/nmeth.1778.
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Johansson, Gustav, Melita Kaltak, Cristiana Rîmniceanu, Avadhesh K. Singh, Jan Lycke, Clas Malmeström, Michael Hühn, Outi Vaarala, Susanna Cardell, and Anders Ståhlberg. "Ultrasensitive DNA Immune Repertoire Sequencing Using Unique Molecular Identifiers." Clinical Chemistry 66, no. 9 (August 20, 2020): 1228–37. http://dx.doi.org/10.1093/clinchem/hvaa159.
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Abstract Background Immune repertoire sequencing of the T-cell receptor can identify clonotypes that have expanded as a result of antigen recognition or hematological malignancies. However, current sequencing protocols display limitations with nonuniform amplification and polymerase-induced errors during sequencing. Here, we developed a sequencing method that overcame these issues and applied it to γδ T cells, a cell type that plays a unique role in immunity, autoimmunity, homeostasis of intestine, skin, adipose tissue, and cancer biology. Methods The ultrasensitive immune repertoire sequencing method used PCR-introduced unique molecular identifiers. We constructed a 32-panel assay that captured the full diversity of the recombined T-cell receptor delta loci in γδ T cells. The protocol was validated on synthetic reference molecules and blood samples of healthy individuals. Results The 32-panel assay displayed wide dynamic range, high reproducibility, and analytical sensitivity with single-nucleotide resolution. The method corrected for sequencing-depended quantification bias and polymerase-induced errors and could be applied to both enriched and nonenriched cells. Healthy donors displayed oligoclonal expansion of γδ T cells and similar frequencies of clonotypes were detected in both enrichment and nonenriched samples. Conclusions Ultrasensitive immune repertoire sequencing strategy enables quantification of individual and specific clonotypes in a background that can be applied to clinical as well as basic application areas. Our approach is simple, flexible, and can easily be implemented in any molecular laboratory.
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Pflug, Florian G., and Arndt von Haeseler. "TRUmiCount: correctly counting absolute numbers of molecules using unique molecular identifiers." Bioinformatics 34, no. 18 (April 16, 2018): 3137–44. http://dx.doi.org/10.1093/bioinformatics/bty283.
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Clement, Kendell, Rick Farouni, Daniel E. Bauer, and Luca Pinello. "AmpUMI: design and analysis of unique molecular identifiers for deep amplicon sequencing." Bioinformatics 34, no. 13 (June 27, 2018): i202—i210. http://dx.doi.org/10.1093/bioinformatics/bty264.
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Babnigg, György, and Carol S. Giometti. "A database of unique protein sequence identifiers for proteome studies." PROTEOMICS 6, no. 16 (August 2006): 4514–22. http://dx.doi.org/10.1002/pmic.200600032.
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Jin, Huan, Joshua M. Mitchell, and Hunter N. B. Moseley. "Atom Identifiers Generated by a Neighborhood-Specific Graph Coloring Method Enable Compound Harmonization across Metabolic Databases." Metabolites 10, no. 9 (September 11, 2020): 368. http://dx.doi.org/10.3390/metabo10090368.
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Metabolic flux analysis requires both a reliable metabolic model and reliable metabolic profiles in characterizing metabolic reprogramming. Advances in analytic methodologies enable production of high-quality metabolomics datasets capturing isotopic flux. However, useful metabolic models can be difficult to derive due to the lack of relatively complete atom-resolved metabolic networks for a variety of organisms, including human. Here, we developed a neighborhood-specific graph coloring method that creates unique identifiers for each atom in a compound facilitating construction of an atom-resolved metabolic network. What is more, this method is guaranteed to generate the same identifier for symmetric atoms, enabling automatic identification of possible additional mappings caused by molecular symmetry. Furthermore, a compound coloring identifier derived from the corresponding atom coloring identifiers can be used for compound harmonization across various metabolic network databases, which is an essential first step in network integration. With the compound coloring identifiers, 8865 correspondences between KEGG (Kyoto Encyclopedia of Genes and Genomes) and MetaCyc compounds are detected, with 5451 of them confirmed by other identifiers provided by the two databases. In addition, we found that the Enzyme Commission numbers (EC) of reactions can be used to validate possible correspondence pairs, with 1848 unconfirmed pairs validated by commonality in reaction ECs. Moreover, we were able to detect various issues and errors with compound representation in KEGG and MetaCyc databases by compound coloring identifiers, demonstrating the usefulness of this methodology for database curation.
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Egorov, Evgeny S., Ekaterina M. Merzlyak, Andrew A. Shelenkov, Olga V. Britanova, George V. Sharonov, Dmitriy B. Staroverov, Dmitriy A. Bolotin, et al. "Quantitative Profiling of Immune Repertoires for Minor Lymphocyte Counts Using Unique Molecular Identifiers." Journal of Immunology 194, no. 12 (May 8, 2015): 6155–63. http://dx.doi.org/10.4049/jimmunol.1500215.
Full textDissertations / Theses on the topic "Unique molecular identifiers"
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Barilíková, Lujza. "Zpracování unikátních molekulárních indexů bez mapování k referenčnímu genomu." Master's thesis, Vysoké učení technické v Brně. Fakulta elektrotechniky a komunikačních technologií, 2020. http://www.nusl.cz/ntk/nusl-413015.
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Hlavným cieľom tejto práce je návrh nového algoritmu k spracovaniu unikátnych molekulárnych indexov bez mapovania na referenčný genóm. O tieto náhodné oligonukleotidové sekvencie neustále vzrastá záujem, pretože uľahčujú rozpoznávať PCR chyby a skresľovanie údajov. Keďže používanie technológií sekvenovania novej generácie neustále rastie, je vynaložené veľké úsilie vyvíjať nástroje pre analýzu produkovaných dát. V súčasnosti sú nástroje na riešenie týchto chýb relatívne časovo náročné a zložité z dôvodu výpočtovo náročného zarovnania. Najdôležitejšie obmedzenie týchto nástrojov spočíva v skutočnosti, že pri spracovávaní duplikátov sú povolené multi-mapované čítania. Tieto čítania sú zvyčajne ignorované, čo môže viesť k zníženiu kvantitatívnej presnosti a spôsobiť zavádzajúcu interpretáciu výsledkov daného sekvenovania. V snahe vyriešiť tento problém je v tejto práci uvedený nový prístup, ktorý umožňuje odhad absolútneho počtu jedinečných molekúl s relatívne rýchlym a spoľahlivým spôsobom.
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Marimuthu, Saranya. "Development of quantitative RNA sequencing methods to understand RNA variant diversity." Thesis, 2021. https://etd.iisc.ac.in/handle/2005/5548.
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The advent of next-generation sequencing (NGS) has accelerated biological research by providing the opportunity to connect genome level sequence information to function. One key application of NGS has been analysis of gene expression and variation by implementing ways to recapitulate RNA level differences accurately. However, for studies that require accurate estimates of closely related variants or isoforms, as in case of evolutionary dynamics of viral quasispecies, each of the available sequencing platforms have critical limitations.
In this thesis work, we have developed methods to eliminate three of the significant limitations of current NGS platforms. These new methods tackle (i) Inability to reconstruct individual whole viral genomes due to genome fragmentation during sequence library preparations in short-read platforms (ii) High sequencing errors associated with 1D Oxford Nanopore sequencing platform and (iii) High background levels of host RNA hampering the detection of pathogen or novel RNA species in metagenomics studies. Our three novel workflows, namely, Single RNA sequencing (sRNA-Seq), TelN proteolemerase based nanopore 2D sequencing (T2D-NanoSeq), and Direct RNA amplification (D-RAMP), are designed to resolve each of these three limitations respectively. We have demonstrated each of the workflows, benchmarked them using synthetic samples and measured their efficiency.
Our first method, sRNA-Seq, can report sequences distantly separated on a single RNA molecule with > 10% recovery and 87% specificity. On the other hand, T2D-NanoSeq, has 40% efficiency in covalently linking both forward and reverse sequences of a duplex DNA that enables tandem reads of both strands which can allow us to reduce sequencing errors. Finally, our third method can generate short DNA probes against target (host) RNA molecules from a physical sample of the RNA and has demonstrated a ~5 fold decrease in the target RNA compared to non-targeted RNA. Overall, these approaches provide improved sequencing alternatives for quantitative and accurate RNA sequencing.
Books on the topic "Unique molecular identifiers"
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Dunlop, Storm. 4. Water in the atmosphere. Oxford University Press, 2017. http://dx.doi.org/10.1093/actrade/9780199571314.003.0004.
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Among the planets in the Solar System, Earth is unique in possessing large quantities of water, and water’s properties are highly significant in determining weather. This is because water readily exists in three different phases (ice, liquid water, and water vapour) at temperatures frequently encountered on Earth. ‘Water in the atmosphere’ explains humidity and saturation: the number of molecules of water vapour in the air is determined solely by temperature. Unstable conditions lead to the formation of cumuliform clouds and precipitation is created by either glaciation or coalescence. There are three groups of clouds—cumuliform, stratiform, and cirriform—with ten types of cloud identified based on their altitude and structure.
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Weil, Andrew. Integrative Environmental Medicine. Edited by Aly Cohen and Frederick S. vom Saal. Oxford University Press, 2017. http://dx.doi.org/10.1093/med/9780190490911.001.0001.
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Integrative Environmental Medicine looks at the history and changing landscape of environmental issues in the United States, including water supply, air quality, extensive plastic pollution, harmful chemicals in cleaning and personal care products, radiofrequency radiation, food additives, pesticides, and medications. The unique properties of compounds such as endocrine-disrupting chemicals are explored along with their ability to disturb the body’s normal signaling pathways, genetic profile, and gut microbiome. Resulting molecular derangements promote thyroid and other autoimmune diseases, diabetes, cardiovascular disease, cancer, and influence developmental problems in children. Analysis of current research identifies ways to reduce exposures and health risks, improve regulations and appropriate testing for chemicals, remediate environmental pollution, and design healthier products for the future. Best practices are considered for clinicians to ascertain exposure history, test for toxins, and teach patients how to avoid harmful exposures. Patients will be prepared and empowered with information about healthier food choices and cooking practices, appropriate supplement use, water filtration, cleaning and personal care product selection, improved sleep, stress reduction, sauna, fasting, chelation, safe cell phone use, and other means of reducing harmful environmental exposures. Solutions at every level require interdisciplinary collaboration to advance assessment, design, stewardship, and regulation of chemicals to promote environmental and human health.
Book chapters on the topic "Unique molecular identifiers"
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Chochinov, Claire A., and Alex N. Nguyen Ba. "Bulk-Fitness Measurements Using Barcode Sequencing Analysis in Yeast." In Methods in Molecular Biology, 399–415. New York, NY: Springer US, 2022. http://dx.doi.org/10.1007/978-1-0716-2257-5_22.
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AbstractThe use of DNA barcodes for determining changes in genotype frequencies has been instrumental to increase the scale at which we can phenotype strain libraries by using next-generation sequencing technologies. Here, we describe the determination of strain fitness for thousands of yeast strains simultaneously in a single assay using recent innovations that increase the precision of these measurements, such as the inclusion of unique-molecular identifiers (UMIs) and purification by solid-phase reverse immobilization (SPRI) beads.
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Choo, Sung Yoon, Thomas St John, Harry T. Orr, and John A. Hansen. "Molecular Analysis of the Variant Alloantigen HLA-B27d Identifies a Unique Single Amino Acid Substitution." In Immunobiology of HLA, 113–14. Berlin, Heidelberg: Springer Berlin Heidelberg, 1989. http://dx.doi.org/10.1007/978-3-662-39946-0_22.
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Seki, Tomohiro, and Hajime Ito. "Luminescent Mechanochromism and the Photosalient Effect of Aryl Gold(I) Isocyanide Complexes." In The Materials Research Society Series, 53–85. Singapore: Springer Nature Singapore, 2023. http://dx.doi.org/10.1007/978-981-99-0260-6_5.
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AbstractA study of stimuli-responsive molecules that can change their physical properties or external shape owing to variations in the external environment has attracted much attention owing to potential application in sensors and actuators. Our group has intensively studied aryl gold(I) isocyanide complexes to develop stimuli-responsive molecular crystals that can show luminescent mechanochromism and crystal jumping through phase transitions induced by mechanical stimulation or photoirradiation. Interestingly, some of our gold(I) isocyanide complexes have crystalline or even single crystalline characteristic both before and after mechano-induced emission color changes or photoinduced crystal jump. Based on the detailed information on molecular arrangements of the aryl gold(I) isocyanide complexes, the underlying mechanism of the responses can be clearly identified. In the Sect. 5.2 of this chapter, we review luminescent mechanochromic aryl gold(I) isocyanide complexes that has unique characteristic such as multiple emission colors, infrared emission, and noncentrosymmetry/centrosymmetry switching. Section 5.3 describes the mechano-induced single-crystal-to-single-crystal phase transitions of aryl gold(I) isocyanide complexes with red- and blue-shifted emission color changes or reversibility. In Sect. 5.4, the photoinduced phase transition of a gold(I) complex which accompanied by mechanical motion, i.e., crystal jump is described.
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Bhalla, Parinishtha, Anukriti Verma, Bhawna Rathi, Shivani Sharda, and Pallavi Somvanshi. "Exploring Molecular Signatures in Spondyloarthritis: A Step Towards Early Diagnosis." In Proceedings of the Conference BioSangam 2022: Emerging Trends in Biotechnology (BIOSANGAM 2022), 142–55. Dordrecht: Atlantis Press International BV, 2022. http://dx.doi.org/10.2991/978-94-6463-020-6_15.
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AbstractSpondyloarthritis is an acute inflammatory disorder of the musculoskeletal system often accompanied by pain, stiffness, bone and tissue damage. It majorly consists of ankylosing spondylitis, psoriatic arthritis and reactive arthritis. It follows a differential diagnosis pattern for demarcation between the spondyloarthritis subtypes and other arthritic subtypes such as rheumatoid arthritis, juvenile arthritis and osteoarthritis due to the heterogeneity causing gradual chronicity and complications. Presence of definite molecular markers can not only improve diagnosis efficiency but also aid in their prognosis and therapy. This study is an attempt to compose a refined list of such unique and common molecular signatures of the considered subtypes, by employing a reductionist approach amalgamating gene retrieval, protein-protein interaction network, functional, pathway, micro-RNA-gene and transcription factor-gene regulatory network analysis. Gene retrieval and protein-protein interaction network analysis resulted in unique and common interacting genes of arthritis subtypes. Functional annotation and pathway analysis found vital functions and pathways unique and common in arthritis subtypes. Furthermore, miRNA-gene and transcription factor-gene interaction networks retrieved unique and common miRNA’s and transcription factors in arthritis subtypes. Furthermore, the study identified important signatures of arthritis subtypes that can serve as markers assisting in prognosis, early diagnosis and personalized treatment of arthritis patients requiring validation via prospective experimental studies.
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Cruz, Cristina, and Jonathan Houseley. "Protocols for Northern Analysis of Exosome Substrates and Other Noncoding RNAs." In Methods in Molecular Biology, 83–103. New York, NY: Springer New York, 2019. http://dx.doi.org/10.1007/978-1-4939-9822-7_5.
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AbstractOver the past decade a plethora of noncoding RNAs (ncRNAs) have been identified, initiating an explosion in RNA research. Although RNA sequencing methods provide unsurpassed insights into ncRNA distribution and expression, detailed information on structure and processing are harder to extract from sequence data. In contrast, northern blotting methods provide uniquely detailed insights into complex RNA populations but are rarely employed outside specialist RNA research groups. Such techniques are generally considered difficult for nonspecialists, which is unfortunate as substantial technical advances in the past few decades have solved the major challenges. Here we present simple, reproducible and highly robust protocols for separating glyoxylated RNA on agarose gels and heat denatured RNA on polyacrylamide–urea gels using standard laboratory electrophoresis equipment. We also provide reliable transfer and hybridization protocols that do not require optimization for most applications. Together, these should allow any molecular biology lab to elucidate the structure and processing of ncRNAs of interest.
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Hawthorne, Christopher, Donal Harrison, Eva McEvoy, and Guillermo Lopez Campos. "Electromagnetic Fields Literature Analysis for Precision Medicine." In Caring is Sharing – Exploiting the Value in Data for Health and Innovation. IOS Press, 2023. http://dx.doi.org/10.3233/shti230349.
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During the last century technological advances have increased the number of anthropogenic electromagnetic fields (EMFs) and therefore human exposures. In this work we have mined from more than 30,000 EMF-related publications the genes, diseases and molecular mechanisms associated with the exposure to six different subsets of EMFs. Results show 3653 unique disease MeSH terms and 9966 unique genes identified of which only 4340 genes are human. Overall, our approach highlights the molecular aspects of the increasing exposure to EMFs.
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Shepherd, Gordon M. "Pleasure." In Neuroenology, 162–67. Columbia University Press, 2016. http://dx.doi.org/10.7312/columbia/9780231177009.003.0020.
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Like everything else involved in the taste of wine, the pleasure that a good wine gives is created by the brain. A half century of research has identified centers in the brain whose stimulation creates the feeling of pleasure. These are especially related to the hypothalamus, the cingulate cortex, and the deep regions of the forebrain. Current studies of these areas are distinguishing between the behavior of “liking” something, and “wanting” it. The higher sensory centers we have discussed merge into this pleasure network to constitute the “human brain flavor system”. Research has even gone so far that the pleasantness of the aroma of given molecule can be predicted from its molecular structure. The future will hold many opportunities like this to unite brain science with enology to advance our understanding of wine flavor.
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Faris, Mo'ez Al-Islam Ezzat, and Hadeel Ghazzawi. "Health-Improving and Disease-Preventing Potential of Camel Milk Against Chronic Diseases and Autism." In Handbook of Research on Health and Environmental Benefits of Camel Products, 155–84. IGI Global, 2020. http://dx.doi.org/10.4018/978-1-7998-1604-1.ch008.
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Camel milk has been used as part of the human diet since ancient times. This chapter tries to elaborate the different aspects of nutraceutical functional properties of camel milk, focusing on the nutritional composition, presence of bioactive zoochemicals and peptides, antioxidant nutrients (vitamin C), and health rendering properties of this unique milk. Recent research has identified camel milk as a prophylactic and therapeutic functional food due to its noticeable content of essential macronutrients, namely bioactive functional proteins and peptides, along with its considerable content of essential micronutrients. Indeed, the presence of this unique mixture has shown to be promising contributors to the management and prevention of chronic diseases, such as cancer, diabetes, liver and kidney, metabolic syndrome, inflammatory bowel diseases in adults, and autism. In vivo, in vitro, and epidemiological and experimental studies were reviewed, and molecular mechanisms were highlighted for better understanding of the health-promoting, disease-preventing potential of camel milk.
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Sanyal, Saptarshi, and Priyanka Banerjee. "Implementation of In-Silico Drug Design to Find Natural Product-Based SARS-CoV 2 Spike Protein Inhibitor." In New Avenues in Drug Discovery and Bioactive Natural Products, 168–87. BENTHAM SCIENCE PUBLISHERS, 2023. http://dx.doi.org/10.2174/9789815136326123020010.
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COVID-19 has been a threat to the whole world due to its massive amount of infectivity. The causative SARS- CoV virus has an extremely small biological footprint. However, it has the ability to bind with the host cell, which, in this case, the human upper respiratory tract, with the intervention of a minimal amount of enzymes and energy. For this anchoring, this virus uses a specially designed protein known as the spike protein or S-protein which also gives the virus its unique shape. Unfortunately, even after the discovery of the vaccine, the number of people getting it is still significant. This is due to the ability of the virus to prevaricate immunity through constant mutation. Therefore, the search for an antiviral drug is still necessary. While there are only a few identified targets of anti-SARS-CoV drug designing, the S-protein can be unique for two reasons; first, it can be both virostatic and can be used as a post.exposure prophylaxis measure. Here, in this book chapter, we look into several drug.designing techniques that can be utilized for designing a molecule that can prevent the first stage of infection, and that is to attach with the ACE receptor of the host cell using the S-protein. Both ligand-based and structure-based designs have been taken into consideration, with a special focus on lead molecules obtained from natural products.
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Wittig, Curt, and Ahmed H. Zewail. "Dynamics of Ground State Bimolecular Reactions." In Chemical Reactions in Clusters. Oxford University Press, 1996. http://dx.doi.org/10.1093/oso/9780195090048.003.0006.
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During the past decade, the study of photoinitiated reactive and inelastic processes within weakly bound gaseous complexes has evolved into an active area of research in the field of chemical physics. Such specialized microscopic environments offer a number of unique opportunities which enable scientists to examine regiospecific interactions at a level of detail and precision that invites rigorous comparisons between experiment and theory. Specifically, many issues that lie at the heart of physical chemistry, such as reaction probabilities, chemical branching ratios, rates and dynamics of elementary chemical processes, curve crossings, caging, recombination, vibrational redistribution and predissociation, etc., can be studied at the state-to-state level and in real time. Inevitably, understanding the photophysics and photochemistry of weakly bound complexes lends insight into corresponding processes in less rarefied surroundings, for example, molecules physisorbed on crystalline insulator and metal surfaces, molecules residing on the surfaces of various ices, and molecules weakly solvated in liquids. However, such ties to the real world are not the main driving force behind studies of photoinitiated reactions in complexed gaseous media. Rather, it is the lure of going a step beyond the more common molecular environments. Theoretical modeling, which in many areas purports to challenge experiment, must rise to the occasion here if it is to offer predictive capability for even the simplest of such microcosms. Subtleties abound. Roughly speaking, two disparate regimes can be identified which are accessible experimentally and which correspond to qualitatively different kinds of chemical transformations. These are distinguished by their reactants: electronically excited versus ground state. For example, it is possible to study the chemical selectivity that derives from the alignment and orientation of excited electronic orbitals, albeit at restricted sets of nuclear coordinates. This is achieved by electronically exciting a complexed moiety, such as a metal atom, which then undergoes chemical transformations that depend on the geometric properties of the electronic orbitals such as their alignments and orientations relative to the other moiety (or moieties) in the complex.
Conference papers on the topic "Unique molecular identifiers"
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Liu, Pingfang, Keerthana Krishnan, Camille X. Devoe, Bradley W. Langhorst, Eileen Dimalanta, and Theodore B. Davis. "Abstract 3526: Incorporation of unique molecular identifiers (UMIs) into unique dual sample indexing (UDI) improves the accuracy of quantitative next generation sequencing." In Proceedings: AACR Annual Meeting 2019; March 29-April 3, 2019; Atlanta, GA. American Association for Cancer Research, 2019. http://dx.doi.org/10.1158/1538-7445.am2019-3526.
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Liu, Pingfang, Keerthana Krishnan, Camille X. Devoe, Bradley W. Langhorst, Eileen Dimalanta, and Theodore B. Davis. "Abstract 3526: Incorporation of unique molecular identifiers (UMIs) into unique dual sample indexing (UDI) improves the accuracy of quantitative next generation sequencing." In Proceedings: AACR Annual Meeting 2019; March 29-April 3, 2019; Atlanta, GA. American Association for Cancer Research, 2019. http://dx.doi.org/10.1158/1538-7445.sabcs18-3526.
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Robinson, Jacob E., and Christine E. Cutucache. "Abstract LB-345: Unique molecular identifiers of indolent versus aggressive phenotyping in non-Hodgkin lymphoma: Spotlight on SMZL." In Proceedings: AACR Annual Meeting 2018; April 14-18, 2018; Chicago, IL. American Association for Cancer Research, 2018. http://dx.doi.org/10.1158/1538-7445.am2018-lb-345.
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Kraushaar, Daniel C., Sarah K. Bowman, Theodore B. Davis, Amy B. Emerman, Noa Henig, Kruti M. Patel, Salvatore Russello, and Cynthia L. Hendrickson. "Abstract 1387: Application of target enrichment combined with unique molecular identifiers to determine allelic frequencies of human cancers." In Proceedings: AACR 107th Annual Meeting 2016; April 16-20, 2016; New Orleans, LA. American Association for Cancer Research, 2016. http://dx.doi.org/10.1158/1538-7445.am2016-1387.
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Lee, Lucie S., Yang Lily Liu, Kathryn Pendleton, Jeffrey Liu, Lifeng Phil Lin, Guoying Liu, and Zhitong Liu. "Abstract 3533: Low-frequency variant detection in cell-free DNA by integrating double-stranded unique molecular identifiers with ultrafast amplicon-based library preparations." In Proceedings: AACR Annual Meeting 2019; March 29-April 3, 2019; Atlanta, GA. American Association for Cancer Research, 2019. http://dx.doi.org/10.1158/1538-7445.am2019-3533.
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Lee, Lucie S., Yang Lily Liu, Kathryn Pendleton, Jeffrey Liu, Lifeng Phil Lin, Guoying Liu, and Zhitong Liu. "Abstract 3533: Low-frequency variant detection in cell-free DNA by integrating double-stranded unique molecular identifiers with ultrafast amplicon-based library preparations." In Proceedings: AACR Annual Meeting 2019; March 29-April 3, 2019; Atlanta, GA. American Association for Cancer Research, 2019. http://dx.doi.org/10.1158/1538-7445.sabcs18-3533.
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Keup, Corinna, Karim Benyaa, Peter Hahn, Siegfried Hauch, Pawel Mach, Mitra Tewes, Hans-Christian Kolberg, and Sabine Kasimir-Bauer. "Abstract 3650: Use of unique molecular identifiers to gain insight about the true positive mutations in cfDNA of breast cancer patients for implementation of personalized treatment." In Proceedings: AACR Annual Meeting 2018; April 14-18, 2018; Chicago, IL. American Association for Cancer Research, 2018. http://dx.doi.org/10.1158/1538-7445.am2018-3650.
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Macoritto, Michael P., Daphna Laifenfeld, Natalie Catlett, Milena Jorge, Andrea Matthews, Kurt R. Auger, and Rakesh Kumar. "Abstract C58: Causal Network™ Modeling identifies common and unique mechanisms for sensitivity to the PI3K inhibitor GSK1059615 and the AKT inhibitor GSK690693." In Abstracts: AACR-NCI-EORTC International Conference: Molecular Targets and Cancer Therapeutics--Nov 15-19, 2009; Boston, MA. American Association for Cancer Research, 2009. http://dx.doi.org/10.1158/1535-7163.targ-09-c58.
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Guarnieri, Anna, Mark Chicarelli, LouAnn Cable, Francis Sullivan, Howard Ball, Shannon Winski, and John Robinson. "Abstract P257: Preclinical data identifies bezuclastinib as a differentiated KIT inhibitor with unique selectivity to KIT D816V and minimal evidence of brain penetration." In Abstracts: AACR-NCI-EORTC Virtual International Conference on Molecular Targets and Cancer Therapeutics; October 7-10, 2021. American Association for Cancer Research, 2021. http://dx.doi.org/10.1158/1535-7163.targ-21-p257.
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Halima, Ahmed, Jiaren Zhang, Giuseppe Galletti, Allyson J. Ocean, and Paraskevi Giannakakou. "Abstract 454: Transferrin receptor identifies a novel circulating tumor cell population in patients with pancreatic cancer with a unique metastasis-associated molecular signature." In Proceedings: AACR Annual Meeting 2019; March 29-April 3, 2019; Atlanta, GA. American Association for Cancer Research, 2019. http://dx.doi.org/10.1158/1538-7445.sabcs18-454.
Full textReports on the topic "Unique molecular identifiers"
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Paran, Ilan, and Molly Jahn. Analysis of Quantitative Traits in Pepper Using Molecular Markers. United States Department of Agriculture, January 2000. http://dx.doi.org/10.32747/2000.7570562.bard.
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Original objectives: The overall goal of the proposal was to determine the genetic and molecular control of pathways leading to the production of secondary metabolites determining major fruit quality traits in pepper. The specific objectives were to: (1) Generate a molecular map of pepper based on simple sequence repeat (SSR) markers. (2) Map QTL for capsaicinoids content (3) Determine possible association between capsaicinoids and carotenoid content and structural genes for capsaicinoid and carotenoid biosynthesis. (4) Map QTL for quantitative traits controlling additional fruit traits. (5) Map fruit-specific ESTs and determine possible association with fruit QTL (6) Map the C locus that determines the presence and absence of capsaicinoids in pepper fruit and identify candidate genes for C. Background: Pungency, color, fruit shape and fruit size are among the most important fruit quality characteristics of pepper. Despite the importance of the pepper crop both in the USA and Israel, the genetic basis of these traits was only little known prior to the studies conducted in the present proposal. In addition, molecular tools for use in pepper improvement were lacking. Major conclusions and achievements: Our studies enabled the development of a saturated genetic map of pepper that includes numerous simple sequence repeat (SSR) markers and the integration of several independent maps into a single resource map that consists of over 2000 markers. Unlike previous maps that consisted mostly of tomato-originated RFLP markers, the SSR-based map consists of largely pepper markers. Therefore, the SSR and integrated maps provide ample of tools for use in marker-assisted selection for diverse targets throughout the Capsicum genome. We determined the genetic and molecular bases of qualitative and quantitative variation of pungency, the most unique characteristics of pepper fruit. We mapped and subsequently cloned the Pun1 gene that serves as a master key for capsaicinoids accumulation and showed that it is an acyltransferase. By sequencing the Pun1 gene in pungent and non-pungent cultivars we identified a deletion that abolishes the expression of the gene in the latter cultivars. We also identified QTLs that control capsaicinoids content and therefore pungency level. These genes will allow pepper breeders to manipulate the level of pungency for specific agricultural and industrial purposes. In addition to pungency we identified genes and QTLs that control other key developmental processes of fruit development such as color, texture and fruit shape. The A gene controlling anthocyanin accumulation in the immature fruit was found as the ortholog of the petunia transcription factor Anthocyanin2. The S gene required for the soft flesh and deciduous fruit nature typical of wild peppers was identified as the ortholog of tomato polygalacturonase. We identified two major QTLs controlling fruit shape, fs3.1 and fs10.1, that differentiate between elongated and blocky and round fruit shapes, respectively. Scientific and agricultural implications: Our studies allowed significant advancement of our understanding at the genetic and molecular levels of important processes of pepper fruit development. Concomitantly to gaining biological knowledge, we were able to develop molecular tools that can be implemented for pepper improvement.
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Paran, Ilan, and Molly Jahn. Genetics and comparative molecular mapping of biochemical and morphological fruit characters in Capsicum. United States Department of Agriculture, March 2005. http://dx.doi.org/10.32747/2005.7586545.bard.
Full textAbstract:
Original objectives: The overall goal of our work was to gain information regarding the genetic and molecular control of pathways leading to the production of secondary metabolites determining major fruit quality traits in pepper and to develop tools based on this information to assist in crop improvement. The specific objectives were to: (1) Generate a molecular map of pepper based on simple sequence repeat (SSR) markers. (2) Map QTL for capsaicinoid (pungency) content (3) Determine possible association between capsaicinoid and carotenoid content and structural genes for capsaicinoid and carotenoid biosynthesis. (4) Map QTL for quantitative traits controlling additional fruit traits. (5) Map fruit-specific ESTs and determine possible association with fruit QTL (6) Map the C locus that determines the presence and absence of capsaicinoid in pepper fruit and identify candidate genes for C.locus. Background: Pungency, color, fruit shape and fruit size are among the most important fruit quality characteristics of pepper. Despite the importance of the pepper crop both in the USA and Israel, the genetic basis of these traits was poorly understood prior to the studies conducted in the present proposal. In addition, molecular tools for use in pepper improvement were lacking. Major conclusions and achievements: Our studies enabled the development of a saturated genetic map of pepper that includes numerous SSR markers. This map has been integrated with a number of other independent maps resulting in the publication of a single resource map consisting of more than 2000 markers. Unlike previous maps based primarily on tomato-originated RFLP markers, the new maps are based on PCR markers that originate in Capsicum providing a comprehensive and versatile resource for marker-assisted selection in pepper. We determined the genetic and molecular bases of qualitative and quantitative variation of pungency, a character unique to pepper fruit. We mapped and subsequently cloned the Pun1 gene that serves as a master regulatoar for capsaicinoid accumulation and showed that it is an acyltransferase. By sequencing the Pun1 gene in pungent and non-pungent cultivars we identified a deletion that abolishes the expression of the gene in the latter cultivars. We also identified QTL that control capsaicinoid content and therefore pungency level. These genes will allow pepper breeders to manipulate the level of pungency for specific agricultural and industrial purposes. In addition to pungency we identified genes and QTL that control other key developmental processes of fruit development such as color, texture and fruit shape. The A gene controlling anthocyanin accumulation in the immature fruit was found as the ortholog of the petunia transcription factor Anthocyanin2. The S gene required for the soft flesh and deciduous fruit nature typical of wild peppers was identified as the ortholog of tomato polygalacturonase. We identified two major QTL controlling fruit shape, fs3.1 and fs10.1, that differentiate elongated and blocky and round fruit shapes, respectively. Scientific and agricultural implications: Our studies allowed significant advances in our understanding of important processes of pepper fruit development including the isolation and characterization of several well known genes. These results also provided the basis for the development of molecular tools that can be implemented for pepper improvement. A total of eleven refereed publications have resulted from this work, and several more are in preparation.
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Cahaner, Avigdor, Susan J. Lamont, E. Dan Heller, and Jossi Hillel. Molecular Genetic Dissection of Complex Immunocompetence Traits in Broilers. United States Department of Agriculture, August 2003. http://dx.doi.org/10.32747/2003.7586461.bard.
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Objectives: (1) Evaluate Immunocompetence-OTL-containing Chromosomal Regions (ICRs), marked by microsatellites or candidate genes, for magnitude of direct effect and for contribution to relationships among multiple immunocompetence, disease-resistance, and growth traits, in order to estimate epistatic and pleiotropic effects and to predict the potential breeding applications of such markers. (2) Evaluate the interaction of the ICRs with genetic backgrounds from multiple sources and of multiple levels of genetic variation, in order to predict the general applicability of molecular genetic markers across widely varied populations. Background: Diseases cause substantial economic losses to animal producers. Emerging pathogens, vaccine failures and intense management systems increase the impact of diseases on animal production. Moreover, zoonotic pathogens are a threat to human food safety when microbiological contamination of animal products occurs. Consumers are increasingly concerned about drug residues and antibiotic- resistant pathogens derived from animal products. The project used contemporary scientific technologies to investigate the genetics of chicken resistance to infectious disease. Genetic enhancement of the innate resistance of chicken populations provides a sustainable and ecologically sound approach to reduce microbial loads in agricultural populations. In turn, animals will be produced more efficiently with less need for drug treatment and will pose less of a potential food-safety hazard. Major achievements, conclusions and implications:. The PI and co-PIs had developed a refined research plan, aiming at the original but more focused objectives, that could be well-accomplished with the reduced awarded support. The successful conduct of that research over the past four years has yielded substantial new information about the genes and genetic markers that are associated with response to two important poultry pathogens, Salmonella enteritidis (SE) and Escherichia coli (EC), about variation of immunocompetence genes in poultry, about relationships of traits of immune response and production, and about interaction of genes with environment and with other genes and genetic background. The current BARD work has generated a base of knowledge and expertise regarding the genetic variation underlying the traits of immunocompetence and disease resistance. In addition, unique genetic resource populations of chickens have been established in the course of the current project, and they are essential for continued projects. The US laboratory has made considerable progress in studies of the genetics of resistance to SE. Microsatellite-marked chromosomal regions and several specific genes were linked to SE vaccine response or bacterial burden and the important phenomenon of gene interaction was identified in this system. In total, these studies demonstrate the role of genetics in SE response, the utility of the existing resource population, and the expertise of the research group in conducting such experiments. The Israeli laboratories had showed that the lines developed by selection for high or low level of antibody (Ab) response to EC differ similarly in Ab response to several other viral and bacterial pathogens, indicating the existence of a genetic control of general capacity of Ab response in young broilers. It was also found that the 10w-Ab line has developed, possibly via compensatory "natural" selection, higher cellular immune response. At the DNA levels, markers supposedly linked to immune response were identified, as well as SNP in the MHC, a candidate gene responsible for genetic differences in immunocompetence of chickens.
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Raghothama, Kashchandra G., Avner Silber, and Avraham Levy. Biotechnology approaches to enhance phosphorus acquisition of tomato plants. United States Department of Agriculture, January 2006. http://dx.doi.org/10.32747/2006.7586546.bard.
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Abstract: Phosphorus is one of the least available macronutrient in the soil. The high affinity phosphate transporters are known to be associated with phosphate acquisition under natural conditions. Due to unique interactions of phosphate with soil particles, up to 80% of the applied phosphates may be fixed forcing the farmers to apply 4 to 5 times the fertilizers necessary for crop production. Efficient uptake and utilization of this essential nutrient is essential for sustainability and profitability of agriculture. Many predictions point to utilization/exhaustion of high quality phosphate rocks within this century. This calls for efforts to improve the ability of plants to acquire and utilize limiting sources of phosphate in the rhizosphere. Two important molecular and biochemical components associated with phosphate efficiency are phosphate transporters and phosphatases. This research project is aimed at defining molecular determinants of phosphate acquisition and utilization in addition to generating phosphate uptake efficient plants. The main objectives of the project were; Creation and analysis of transgenic tomato plants over-expressing phosphatases and transporters Characterization of the recently identified members (LePT3 and LePT4) of the Pi transporter family Generate molecular tools to study genetic responses of plants to Pi deficiency During the project period we have successfully identified and characterized a novel phosphate transporter associated with mycorrhizal symbiosis. The expression of this transporter increases with mycorrhizal symbiosis. A thorough characterization of mutant tomato lacking the expression of this gene revealed the biological significance of LePT3 and another novel gene LePT4. In addition we have isolated and characterized several phosphate starvation induced genes from tomato using a combination of differential and subtractive mRNA hybridization techniques. One of the genes, LePS2 belongs to the family of phospho-protein phosphatase. The functionality of the recombinant protein was determined using synthetic phosphor-peptides. Over expression of this gene in tomato resulted in significant changes in growth, delay in flowering and senescence. It is anticipated that phospho-protein phosphatase may have regulatory role in phosphate deficiency responses of plants. In addition a novel phosphate starvation induced glycerol 3-phosphate permease gene family was also characterized. Two doctoral research students are continuing the characterization and functional analysis of these genes. Over expression of high affinity phosphate transporters in tobacco showed increased phosphate content under hydroponic conditions. There is growing evidence suggesting that high affinity phosphate transporters are crucial for phosphate acquisition even under phosphate sufficiency conditions. This project has helped train several postdoctoral fellows and graduate students. Further analysis of transgenic plants expressing phosphatases and transporters will not only reveal the biological function of the targeted genes but also result in phosphate uptake and utilization efficient plants.
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Elizur, Abigail, Amir Sagi, Gideon Hulata, Clive Jones, and Wayne Knibb. Improving Crustacean Aquaculture Production Efficiencies through Development of Monosex Populations Using Endocrine and Molecular Manipulations. United States Department of Agriculture, June 2010. http://dx.doi.org/10.32747/2010.7613890.bard.
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Background Most of Australian prawn aquaculture production is based on P. monodon. However, the Australian industry is under intense competition from lower priced overseas imports. The availability of all-female monosex populations, by virtue of their large size and associated premium prize, will offer competitive advantage to the industry which desperately needs to counteract competitors within this market. As for the redclaw production in Israel, although it is at its infancy, the growers realized that the production of males is extremely advantageous and that such management strategy will change the economic assumptions and performances of this aquaculture to attract many more growers. Original objectives (as in original proposal) Investigating the sex inheritance mechanism in the tiger prawn. Identification of genes expressed uniquely in the androgenic gland (AG) of prawns and crayfish. The above genes and/or their products will be used to localize the AG in the prawn and manipulate the AG activity in both species. Production of monosex populations through AG manipulation. In the prawn, production of all-female populations and in the crayfish, all-male populations. Achievements In the crayfish, the AG cDNA library was further screened and a third AG specific transcript, designated Cq-AG3, had been identified. Simultaneously the two AG specific genes, which were previously identified, were further characterized. Tissue specificity of one of those genes, termed Cq-AG2, was demonstrated by northern blot hybridization and RNA in-situ hybridization. Bioinformatics prediction, which suggested a 42 amino acid long signal anchor at the N-terminus of the deduced Cq-AG2, was confirmed by immunolocalization of a recombinant protein. Cq-IAG's functionality was demonstrated by dsRNA in-vivo injections to intersex crayfish. Cq-IAGsilencing induced dramatic sex-related alterations, including male feature feminization, reduced sperm production, extensive testicular apoptosis, induction of the vitellogeningene expression and accumulation of yolk proteins in the ovaries. In the prawn, the AG was identified and a cDNA library was created. The putative P. monodonAG hormone encoding gene (Pm-IAG) was identified, isolated and characterized for time of expression and histological localization. Implantation of the AG into prawn post larvae (PL) and juveniles resulted in phenotypic transformation which included the appearance of appendix masculina and enlarged petasma. The transformation however did not result in sex change or the creation of neo males thus the population genetics stage to be executed with Prof. Hulata did not materialized. Repeated AG implantation is currently being trialed. Major conclusions and Implications, both scientific and agricultural Cq-IAG's involvement in male sexual differentiation had been demonstrated and it is strongly suggested that this gene encodes an AG hormone in this crayfish. A thorough screening of the AG cDNA library shows Cq-IAG is the prominent transcript within the library. However, the identification of two additional transcripts hints that Cq-IAG is not the only gene mediating the AG effects. The successful gene silencing of Cq-IAG, if performed at earlier developmental stages, might accomplish full and functional sex reversal which will enable the production of all-male crayfish populations. Pm-IAG is likely to play a similar role in prawns. It is possible that repeated administration of the AG into prawn will lead to the desired full sex reversal, so that WZ neo males, crossed with WZ females can result in WW females, which will form the basis for monosex all-female population.
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Sordillo, Lorraine, Don Wojchowski, Gary Perdew, Arthur Saran, and Gabriel Leitner. Identification of Staphylococcus aureaus Virulence Factors Associated with Bovine Mastitis. United States Department of Agriculture, February 2001. http://dx.doi.org/10.32747/2001.7574340.bard.
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Staphylococcus aureus is a major cause of mastitis in dairy cattle. The organism is able to adhere to and penetrate mammary epithelium, forming deep seated abscesses that result in chronic infections. This study was based on the observation that certain genotypes of S. aureus are isolated more frequently from field cases of bovine mastitis than others and the most prevalent genotypes of S. aureus have an increased ability to resist neutrophil phagocytosis and killing compared to the rare variants. It was hypothesized that these predominating genotypes differentially express virulence factors that allow them to overcome or suppress essential host defense mechanisms and successfully colonize mammary parenchyma. The overall objective of this study was to determine the mechanisms by which predominating S. aureus genotypes were able to resist mammary gland defense mechanisms. The following specific aims were accomplished to address the overall objectives of this project: 1. Analyze and compare cell surface and secreted protein profiles of common and rare S. aureus genotypes isolated from field cases of bovine mastitis. 2. Purify and sequence selectively synthesized proteins unique to the most prevalent genotypes of S. aureus . 3. Determine the in vitro effects of isolated proteins on essential host defense mechanisms. Results from each specific aim showed that these redominating genotypes differentially express factors that may allow them to overcome or suppress essential host defense mechanisms and successfully colonize mammary parenchyma. Using complementary approaches, both the US and Israeli teams identified differentially expressed S. aureus factors that were positively correlated with virulence as determined by the ability to modify host immune cell responses and increase disease pathogenesis. Several candidate virulence factors have ben identified at both the molecular (US team) and protein (Israeli team) levels. Components of the phosphotransferase system were shown to be differentially expressed in prevalent strains of S. aureus and to modify the growth potential of these strains in a milk microenvironment. Evidence provided by both the Israeli and US teams also demonstrated a potential role of Staphylococcal enterotoxins in the pathogenesis of mastitis. Certain enterotoxins were shown to directly affect neutrophil bactericidal activities which can profoundly affect the establishment of new intramammary infections. Other evidence suggests that S. aureus superantigens can suppress mammary defenses by enhancing lymphoid suppressor cell activity. Collectively, these data suggest that unique factors are associated with predominating S. aureus genotypes that can affect in vitro and in vivo virulence as related to the pathogenesis of bovine mastitis. The potential development of a subunit mastitis vaccine which incorporates only relevant antigenic determinants has not been investigated in depth. Experiments outlined in this proposal has identified putative virulence factors which contribute to the pathogenesis of S. aureus mastitis and which may be used to formulate an efficacious subunit mastitis vaccine. Results from these studies may lead to the development of new methods to prevent this costly disease, providing a viable alternative to less effective mastitis control procedures based on chemotherapy.
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Shomer, Ilan, Ruth E. Stark, Victor Gaba, and James D. Batteas. Understanding the hardening syndrome of potato (Solanum tuberosum L.) tuber tissue to eliminate textural defects in fresh and fresh-peeled/cut products. United States Department of Agriculture, November 2002. http://dx.doi.org/10.32747/2002.7587238.bard.
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The project sought to understand factors and mechanisms involved in the hardening of potato tubers. This syndrome inhibits heat softening due to intercellular adhesion (ICA) strengthening, compromising the marketing of industrially processed potatoes, particularly fresh peeled-cut or frozen tubers. However, ICA strengthening occurs under conditions which are inconsistent with the current ideas that relate it to Ca-pectate following pectin methyl esterase (PME) activity or to formation of rhamnogalacturonan (RG)-II-borate. First, it was necessary to induce strengthening of the middle lamellar complex (MLX) and the ICA as a stress response in some plant parenchyma. As normally this syndrome does not occur uniformly enough to study it, we devised an efficient model in which ICA-strengthening is induced consistently under simulated stress by short-chain, linear, mono-carboxylic acid molecules (OAM), at 65 oC [appendix 1 (Shomer&Kaaber, 2006)]. This rapid strengthening was insufficient for allowing the involved agents assembly to be identifiable; but it enabled us to develop an efficient in vitro system on potato tuber parenchyma slices at 25 ºC for 7 days, whereas unified stress was reliably simulated by OAMs in all the tissue cells. Such consistent ICA-strengthening in vitro was found to be induced according to the unique physicochemical features of each OAM as related to its lipophilicity (Ko/w), pKa, protonated proportion, and carbon chain length by the following parameters: OAM dissociation constant (Kdiss), adsorption affinity constant (KA), number of adsorbed OAMs required for ICA response (cooperativity factor) and the water-induced ICA (ICAwater). Notably, ICA-strengthening is accompanied by cell sap leakage, reflecting cell membrane rupture. In vitro, stress simulation by OAMs at pH<pKa facilitated the consistent assembly of ICAstrengthening agents, which we were able to characterize for the first time at the molecular level within purified insoluble cell wall of ICA-strengthened tissue. (a) With solid-state NMR, we established the chemical structure and covalent binding to cell walls of suberin-like agents associated exclusively with ICA strengthening [appendix 3 (Yu et al., 2006)]; (b) Using proteomics, 8 isoforms of cell wall-bound patatin (a soluble vacuolar 42-kDa protein) were identified exclusively in ICA-strengthened tissue; (c) With light/electron microscopy, ultrastructural characterization, histochemistry and immunolabeling, we co-localized patatin and pectin in the primary cell wall and prominently in the MLX; (d) determination of cell wall composition (pectin, neutral sugars, Ca-pectate) yielded similar results in both controls and ICA-strengthened tissue, implicating factors other than PME activity, Ca2+ or borate ions; (e) X-ray powder diffraction experiments revealed that the cellulose crystallinity in the cell wall is masked by pectin and neutral sugars (mainly galactan), whereas heat or enzymatic pectin degradation exposed the crystalline cellulose structure. Thus, we found that exclusively in ICA-strengthened tissue, heat-resistant pectin is evident in the presence of patatin and suberinlike agents, where the cellulose crystallinity was more hidden than in fresh control tissue. Conclusions: Stress response ICA-strengthening is simulated consistently by OAMs at pH< pKa, although PME and formation of Ca-pectate and RG-II-borate are inhibited. By contrast, at pH>pKa and particularly at pH 7, ICA-strengthening is mostly inhibited, although PME activity and formation of Ca-pectate or RG-II-borate are known to be facilitated. We found that upon stress, vacuolar patatin is released with cell sap leakage, allowing the patatin to associate with the pectin in both the primary cell wall and the MLX. The stress response also includes formation of covalently bound suberin-like polyesters within the insoluble cell wall. The experiments validated the hypotheses, thus led to a novel picture of the structural and molecular alterations responsible for the textural behavior of potato tuber. These findings represent a breakthrough towards understanding of the hardening syndrome, laying the groundwork for potato-handling strategies that assure textural quality of industrially processed particularly in fresh peeled cut tubers, ready-to-prepare and frozen preserved products.
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Michelmore, Richard, Eviatar Nevo, Abraham Korol, and Tzion Fahima. Genetic Diversity at Resistance Gene Clusters in Wild Populations of Lactuca. United States Department of Agriculture, February 2000. http://dx.doi.org/10.32747/2000.7573075.bard.
Full textAbstract:
Genetic resistance is often the least expensive, most effective, and ecologically-sound method of disease control. It is becoming apparent that plant genomes contain large numbers of disease resistance genes. However, the numbers of different resistance specificities within a genepool and the genetic mechanisms generating diversity are poorly understood. Our objectives were to characterize diversity in clusters of resistance genes in wild progenitors of cultivated lettuce in Israel and California in comparison to diversity within cultivated lettuce, and to determine the extent of gene flow, recombination, and genetic instability in generating variation within clusters of resistance genes. Genetic diversity of resistance genes was analyzed in wild and cultivated germplasm using molecular markers derived from lettuce resistance gene sequences of the NBS-LRR type that mapped to the major cluster if resistance genes in lettuce (Sicard et al. 1999). Three molecular markers, one microsatellite marker and two SCAR markers that amplified LRR- encoding regions, were developed from sequences of resistance gene homologs at the Dm3 cluster (RGC2s) in lettuce. Variation for these markers was assessed in germplasm including 74 genotypes of cultivated lettuce, L. saliva and 71 accessions of the three wild Lactuca spp., L. serriola, L. saligna and L. virosa that represent the major species in the sexually accessible genepool for lettuce. Diversity was also studied within and between natural populations of L. serriola from Israel and California. Large numbers of haplotypes were detected indicating the presence of numerous resistance genes in wild species. We documented a variety of genetic events occurring at clusters of resistance genes for the second objective (Sicard et al., 1999; Woo el al., in prep; Kuang et al., in prepb). The diversity of resistance genes in haplotypes provided evidence for gene duplication and unequal crossing over during the evolution of this cluster of resistance genes. Comparison of nine resistance genes in cv. Diana identified 22 gene conversion and five intergenic recombinations. We cloned and sequenced a 700 bp region from the middle of RGC2 genes from six genotypes, two each from L. saliva, L. serriola, and L. saligna . We have identified over 60 unique RGC2 sequences. Phylogenetic analysis surprisingly demonstrated much greater similarity between than within genotypes. This led to the realization that resistance genes are evolving much slower than had previously been assumed and to a new model as to how resistance genes are evolving (Michelmore and Meyers, 1998). The genetic structure of L. serriola was studied using 319 AFLP markers (Kuang et al., in prepa). Forty-one populations from Turkey, Armenia, Israel, and California as well as seven European countries were examined. AFLP marker data showed that the Turkish and Armenian populations were the most polymorphic populations and the European populations were the least. The Davis, CA population, a recent post-Columbian colonization, showed medium genetic diversity and was genetically close to the Turkish populations. Our results suggest that Turkey - Armenia may be the center of origin and diversity of L. serriola and may therefore have the greatest diversity of resistance genes. Our characterization of the diversity of resistance genes and the genetic mechanisms generating it will allow informed exploration, in situ and ex situ conservation, and utilization of germplasm resources for disease control. The results of this project provide the basis for our future research work, which will lead to a detailed understanding of the evolution of resistance genes in plants.
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Porat, Ron, Gregory T. McCollum, Amnon Lers, and Charles L. Guy. Identification and characterization of genes involved in the acquisition of chilling tolerance in citrus fruit. United States Department of Agriculture, December 2007. http://dx.doi.org/10.32747/2007.7587727.bard.
Full textAbstract:
Citrus, like many other tropical and subtropical fruit are sensitive to chilling temperatures. However, application of a pre-storage temperature conditioning (CD) treatment at 16°C for 7 d or of a hot water brushing (HWB) treatment at 60°C for 20 sec remarkably enhances chilling tolerance and reduces the development of chilling injuries (CI) upon storage at 5°C. In the current research, we proposed to identify and characterize grapefruit genes that are induced by CD, and may contribute to the acquisition of fruit chilling tolerance, by two different molecular approaches: cDNA array analysis and PCR cDNA subtraction. In addition, following the recent development and commercialization of the new Affymetrix Citrus Genome Array, we further performed genome-wide transcript profiling analysis following exposure to CD and chilling treatments. To conduct the cDNA array analysis, we constructed cDNA libraries from the peel tissue of CD- and HWB-treated grapefruit, and performed an EST sequencing project including sequencing of 3,456 cDNAs from each library. Based on the obtained sequence information, we chose 70 stress-responsive and chilling-related genes and spotted them on nylon membranes. Following hybridization the constructed cDNA arrays with RNA probes from control and CD-treated fruit and detailed confirmations by RT-PCR analysis, we found that six genes: lipid-transfer protein, metallothionein-like protein, catalase, GTP-binding protein, Lea5, and stress-responsive zinc finger protein, showed higher transcript levels in flavedo of conditioned than in non-conditioned fruit stored at 5 ᵒC. The transcript levels of another four genes: galactinol synthase, ACC oxidase, temperature-induced lipocalin, and chilling-inducible oxygenase, increased only in control untreated fruit but not in chilling-tolerant CD-treated fruit. By PCR cDNA subtraction analysis we identified 17 new chilling-responsive and HWB- and CD-induced genes. Overall, characterization of the expression patterns of these genes as well as of 11 more stress-related genes by RNA gel blot hybridizations revealed that the HWB treatment activated mainly the expression of stress-related genes(HSP19-I, HSP19-II, dehydrin, universal stress protein, EIN2, 1,3;4-β-D-glucanase, and SOD), whereas the CD treatment activated mainly the expression of lipid modification enzymes, including fatty acid disaturase2 (FAD2) and lipid transfer protein (LTP). Genome wide transcriptional profiling analysis using the newly developed Affymetrix Citrus GeneChip® microarray (including 30,171 citrus probe sets) revealed the identification of three different chilling-related regulons: 1,345 probe sets were significantly affected by chilling in both control and CD-treated fruits (chilling-response regulon), 509 probe sets were unique to the CD-treated fruits (chilling tolerance regulon), and 417 probe sets were unique to the chilling-sensitive control fruits (chilling stress regulon). Overall, exposure to chilling led to expression governed arrest of general cellular metabolic activity, including concretive down-regulation of cell wall, pathogen defense, photosynthesis, respiration, and protein, nucleic acid and secondary metabolism. On the other hand, chilling enhanced various adaptation processes, such as changes in the expression levels of transcripts related to membranes, lipid, sterol and carbohydrate metabolism, stress stimuli, hormone biosynthesis, and modifications in DNA binding and transcription factors.
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Ostersetzer-Biran, Oren, and Jeffrey Mower. Novel strategies to induce male sterility and restore fertility in Brassicaceae crops. United States Department of Agriculture, January 2016. http://dx.doi.org/10.32747/2016.7604267.bard.
Full textAbstract:
Abstract Mitochondria are the site of respiration and numerous other metabolic processes required for plant growth and development. Increased demands for metabolic energy are observed during different stages in the plants life cycle, but are particularly ample during germination and reproductive organ development. These activities are dependent upon the tight regulation of the expression and accumulation of various organellar proteins. Plant mitochondria contain their own genomes (mtDNA), which encode for rRNAs, tRNAs and some mitochondrial proteins. Although all mitochondria have probably evolved from a common alpha-proteobacterial ancestor, notable genomic reorganizations have occurred in the mtDNAs of different eukaryotic lineages. Plant mtDNAs are notably larger and more variable in size (ranging from 70~11,000 kbp in size) than the mrDNAs in higher animals (16~19 kbp). Another unique feature of plant mitochondria includes the presence of both circular and linear DNA fragments, which undergo intra- and intermolecular recombination. DNA-seq data indicate that such recombination events result with diverged mitochondrial genome configurations, even within a single plant species. One common plant phenotype that emerges as a consequence of altered mtDNA configuration is cytoplasmic male sterility CMS (i.e. reduced production of functional pollen). The maternally-inherited male sterility phenotype is highly valuable agriculturally. CMS forces the production of F1 hybrids, particularly in predominantly self-pollinating crops, resulting in enhanced crop growth and productivity through heterosis (i.e. hybrid vigor or outbreeding enhancement). CMS lines have been implemented in some cereal and vegetables, but most crops still lack a CMS system. This work focuses on the analysis of the molecular basis of CMS. We also aim to induce nuclear or organellar induced male-sterility in plants, and to develop a novel approach for fertility restoration. Our work focuses on Brassicaceae, a large family of flowering plants that includes Arabidopsis thaliana, a key model organism in plant sciences, as well as many crops of major economic importance (e.g., broccoli, cauliflower, cabbage, and various seeds for oil production). In spite of the genomic rearrangements in the mtDNAs of plants, the number of genes and the coding sequences are conserved among different mtDNAs in angiosperms (i.e. ~60 genes encoding different tRNAs, rRNAs, ribosomal proteins and subunits of the respiratory system). Yet, in addition to the known genes, plant mtDNAs also harbor numerous ORFs, most of which are not conserved among species and are currently of unknown function. Remarkably, and relevant to our study, CMS in plants is primarily associated with the expression of novel chimericORFs, which likely derive from recombination events within the mtDNAs. Whereas the CMS loci are localized to the mtDNAs, the factors that restore fertility (Rfs) are identified as nuclear-encoded RNA-binding proteins. Interestingly, nearly all of the Rf’s are identified as pentatricopeptide repeat (PPR) proteins, a large family of modular RNA-binding proteins that mediate several aspects of gene expression primarily in plant organelles. In this project we proposed to develop a system to test the ability of mtORFs in plants, which are closely related to known CMS factors. We will induce male fertility in various species of Brassicaceae, and test whether a down-relation in the expression of the recombinantCMS-genes restores fertility, using synthetically designed PPR proteins.