Relevant bibliographies by topics / Analysis and molecular identification

Contents

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

Academic literature on the topic 'Analysis and molecular identification'

Author: Grafiati
Published: 4 May 2024

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Journal articles on the topic "Analysis and molecular identification"

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Alsanie, Walaa, Ebaa Felemban, Mona Farid, Mohamed Hassan, Ayman Sabry, and Ahmed Gaber. "Molecular Identification and Phylogenetic Analysis of Multidrug-resistant Bacteria using 16S rDNA Sequencing." Journal of Pure and Applied Microbiology 12, no. 2 (June 30, 2018): 489–96. http://dx.doi.org/10.22207/jpam.12.2.07.

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Birot, Anne-Marie, Laurent Duret, Laurent Bartholin, Bénédicte Santalucia, Isabelle Tigaud, Jean-Pierre Magaud, and Jean-Pierre Rouault. "Identification and molecular analysis of BANP." Gene 253, no. 2 (August 2000): 189–96. http://dx.doi.org/10.1016/s0378-1119(00)00244-4.

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Nováková, A., K. Šimáčková, J. Bárta, and V. Čurn. "Potato variety identification by molecular markers based on retrotransposon analyses." Czech Journal of Genetics and Plant Breeding 45, No. 1 (February 11, 2009): 1–10. http://dx.doi.org/10.17221/11/2008-cjgpb.

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We analyzed a set of twenty most grown potato (Solanum tuberosum L.) varieties listed in the Czech Variety List using the PCR-IRAP (Inter-Retrotransposon Amplified Polymorphism) method in order to distinguish fast and unambiguously the varieties. In total, 62 polymorphic alleles were amplified using the three primers P-Tst-1, P-Tst-3 and P-Tst-6. The recorded pattern of markers was stable and reproducible. The analyses were repeated three times and identical results were always obtained. The level of polymorphism varied from 11% to 79% depending on the respective primer. All analysed varieties could be reliably distinguished after multivariate statistics have been applied to the data obtained by the PCO and UPGMA analyses. The best resolution of individual varieties was obtained if all three primers were evaluated as a complex. The use of retrotransposon-based markers appears to be suitable for the differentiation of large sets of potato samples and should be an eligible complement to other molecular markers used in potato variety identification such as Simple Sequence Repeats (SSR) and Amplified Fragment Length Polymorphisms (AFLP).
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Duggal, S., and SR Rongpharpi. "Mucor -culture/molecular analysis necessary for identification." Indian Journal of Medical Microbiology 33, no. 5 (2015): 163. http://dx.doi.org/10.4103/0255-0857.150960.

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Araya-Kojima, Tomoko, Norio Ishibashi, Seiichi Shimamura, Kan Tanaka, and Hideo Takahashi. "Identification and Molecular Analysis ofLactococcus lactis rpoDOperon." Bioscience, Biotechnology, and Biochemistry 59, no. 1 (January 1995): 73–77. http://dx.doi.org/10.1271/bbb.59.73.

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Kaminskienė, Evelina, Jana Radzijevskaja, Loreta Griciuvienė, Michal Stanko, Justina Snegiriovaitė, Dalytė Mardosaitė-Busaitienė, and Algimantas Paulauskas. "Molecular Identification and Phylogenetic Analysis of Laelapidae Mites (Acari: Mesostigmata)." Animals 13, no. 13 (July 3, 2023): 2185. http://dx.doi.org/10.3390/ani13132185.

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The family Laelapidae (Dermanyssoidea) is morphologically and ecologically the most diverse group of Mesostigmata mites. Although molecular genetic data are widely used in taxonomic identification and phylogenetic analysis, most classifications in Mesostigmata mites are based solely on morphological characteristics. In the present study, eight species of mites from the Laelapidae (Dermanyssoidea) family collected from different species of small rodents in Lithuania, Norway, Slovakia, and the Czech Republic were molecularly characterized using the nuclear (28S ribosomal RNA) and mitochondrial (cytochrome oxidase subunit I gene) markers. Obtained molecular data from 113 specimens of mites were used to discriminate between species and investigate the phylogenetic relationships and genetic diversity among Laelapidae mites from six genera. This study provides new molecular data on Laelaps agilis, Laelaps hilaris, Laelaps jettmari, Haemogamasus nidi, Eulaelaps stabularis, Hyperlaelaps microti, Myonyssus gigas, and Hirstionyssus sp. mites collected from different rodent hosts and geographical regions in Europe.
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Chaudhary, Anshu. "Molecular Identification of Seven Myxobolus Species (Myxosporea: Myxobolidae) in Cyprinids from India." International Journal of Zoology and Animal Biology 7, no. 1 (2024): 1–18. http://dx.doi.org/10.23880/izab-16000550.

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This communication aims to detect the myxozoan infection in some cyprinid fishes that were mostly cultured and commonly used for food in the Meerut region, Uttar Pradesh, India. Myxozoan were identified morphologically and for molecular analysis we have used previously established PCR assays for genetic marker ssrDNA then phylogenetic analysis was performed. Total seven species of Myxobolus were identified i.e., Myxobolus bhadrensis, Myxobolus kalavatiae, Myxobolus haldari from Labeo rohita, Myxobolus calbasui, Myxobolus catlae, from Cirrihinus reba and Cirrihinus mrigala, Myxobolus hosadurgensis from Cirrihinus mrigala and Myxobolus saranae from Labeo bata. An integrated comparative analysis of the ssrDNA gene supported the identification of the collected species and represents the phylogenetic position of all species. This work addresses the problems in the taxonomy of myxozoans in India, where molecular studies are less focused. My species parasitized similar hosts for which genetic data is the only way to make a clear distinction between species and their validity.
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Makut, Makwin Danladi, Jibril Egwu Owuna, and Salmat Musah Salisu. "Molecular Identification of Lactic Acid Bacteria Isolated from Fermented Rice." AROC in Agriculture 2, no. 1 (December 11, 2022): 06–11. http://dx.doi.org/10.53858/arocagr02010611.

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Background: Fermented rice is known to possess probiotic capability. Probiotics are live microorganisms that confers consumer with enormous health benefits. This research was determined on isolation and molecularly identifies beneficial lactic acid bacteria from fermented rice water. Methods: Locally cultivated Osuemegbe Rice grains were steeped and fermented to isolate lactic acid bacteria strains. De Man Rogosa Sharpe (MRS) media was used for the isolation of lactic acid bacteria. The fermented rice water was serially diluted, plated and incubated at 37 °C for 48 hours under anaerobic conditions. Single colonies were subjected to biochemical analysis and gram-staining. Subsequently, 16s rRNA Identification of bacterial isolates was conducted. Results: The strains of LAB isolated were lactiplantibacillus plantarum CIP 103151and Limosilactobacillus fermentum CIP 102980 which are both beneficial and highly recommended as alternatives to antibiotics since their various mechanisms of growth inhibition against pathogenic bacteria have been extensively documented. Conclusion: The findings in this study confirmed rice to possess strains of probiotic Lactic acid bacteria (LAB) which can be exploited to achieving quality advancement in one health: integrated and unify approach aim at sustainably balance and optimize the health of people, animals, and ecosystem.
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Chacón-Monge, José Leonardo, Juan Ignacio Abarca-Odio, and Kaylen González-Sánchez. "Evaluating the reliability of DNA Barcoding for Central American Pacific shallow water echinoderms identification: a molecular taxonomy and database accuracy analysis." Revista de Biología Tropical 72, S1 (March 2, 2024): e58997. http://dx.doi.org/10.15517/rev.biol.trop..v72is1.58997.

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Introduction: Molecular divergence thresholds have been proposed to distinguish recently separated evolutive units, often displaying more accurate putative species assignments in taxonomic research compared to traditional morphological approaches. This makes DNA barcoding an attractive identification tool for a variety of marine invertebrates, especially for cryptic species complexes. Although GenBank and the Barcode of Life Data System (BOLD) are the major sequence repositories worldwide, very few have tested their performance in the identification of echinoderm sequences. Objective: We use COI echinoderm sequences from local samples and the molecular identification platforms from GenBank and BOLD, in order to test their accuracy and reliability in the DNA barcoding identification for Central American shallow water echinoderms, at genus and species level. Methods: We conducted sampling, tissue extraction, COI amplification, sequencing, and taxonomic identification for 475 specimens. The 348 obtained sequences were individually enquired with BLAST in GenBank as well as using the Identification System (IDS) in BOLD. Query sequences were classified depending on the best match result. McNemar’s chi-squared, Kruskal-Wallis’s and Mann-Whitney’s U tests were performed to prove differences between the results from both databases. Additionally, we recorded an updated list of species reported for the shallow waters of the Central American Pacific. Results: We found 324 echinoderm species reported for Central American Pacific shallow waters. Only 118 and 110 were present in GenBank and BOLD databases respectively. We proposed 325 solved morphology-based identities and 21 provisional identifications in 50 putative taxa. GenBank retrieved 348 molecular-based identifications in 58 species, including twelve provisional identifications in tree taxa. BOLD recovered 170 COI identifications in 23 species with one provisional identification. Nevertheless, 178 sequences retrieved unmatched terms (in 34 morphology-based taxa). Only 86 sequences (25 %) were retrieved as correct identifications and 128 (37 %) as identification errors in both platforms. We include 84 sequences for eleven species not represented in GenBank and 65 sequences for ten species in BOLD Echinoderm COI databases. The identification accuracy using BLAST (175 correct and 152 incorrect identifications) was greater than with IDS engine (110 correct and 218 identification errors), therefore GenBank outperforms BOLD (Kruskal-Wallis = 41.625, df = 1, p < 0.001). Conclusions: Additional echinoderm sample references are needed to improve the utility of the evaluated DNA barcoding identification tools. Identification discordances in both databases may obey specific parameters used in each search algorithm engine and the available sequences. We recommend the use of barcoding as a complementary identification source for Central American Pacific shallow water echinoderm species.
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Zhou, F., F. Kong, K. McPhie, M. Ratnamohan, G. L. Gilbert, and D. E. Dwyer. "Molecular Identification and Analysis of Nonserotypeable Human Enteroviruses." Journal of Clinical Microbiology 48, no. 4 (February 17, 2010): 1276–82. http://dx.doi.org/10.1128/jcm.02384-09.

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Dissertations / Theses on the topic "Analysis and molecular identification"

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Nielsen, Torsten. "Human origins of DNA replication : identification, analysis and application." Thesis, McGill University, 1996. http://digitool.Library.McGill.CA:80/R/?func=dbin-jump-full&object_id=40411.

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While replication origins, cis-acting sequences directing the initiation of DNA synthesis, have been well-characterized in many model organisms, the multiple sequence and protein components present at the chromosomal origins of higher eukaryotic organisms have not yet been fully defined. Genetic assays that identify origin function in cloned DNA fragments would provide a useful approach for the isolation and analysis of mammalian DNA replication origins.
In this thesis, (1) cloned fragments from a known mammalian origin, the ori$ beta$ of the hamster 3$ sp prime$ DHFR region, are demonstrated to replicate autonomously, both following transfection into human cells, and when used as templates in an in vitro replication system based on human cell extracts; (2) larger scale versions of these two assay methodologies are used to isolate over 40 novel putative origins of DNA replication from anticruciform purified human genomic DNA libraries; (3) transfection and in vitro autonomous replication assays are applied to demonstrate the potential origin function of a mitochondrial DNA sequence implicated in the insertional mutagenesis of a human genomic locus; (4) an origin mapping strategy based on the in vitro assay is used to provide evidence for the existence of a replication origin in a cloned and sequenced portion of the human 15q11q13 chromosomal subdomain, a region associated with allele-specific replication timing, genomic imprinting, and genetic disease; and (5) some of these autonomously replicating origins are cloned into a selectable YAC vector and are shown to permit the long term episomal maintenance, in human cells, of the transfected plasmid constructs.
These results consistently demonstrate that short mammalian genomic DNA fragments can replicate autonomously, supporting the applicability of the replicon model in humans, and could be extended to the search for an origin core consensus element, to the investigation of higher order organization and temporal control of human DNA replication origins, and to the construction of a complete human artificial chromosome.
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Esmaeil, Shalaby A. A. "Molecular analysis of chordomas and identification of therapeutic targets." Thesis, University College London (University of London), 2010. http://discovery.ucl.ac.uk/20213/.

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Chordoma is a rare malignant bone tumour, showing notochordal differentiation, which occurs in the axial skeleton. Brachyury, a molecule involved in notochordal development, is a highly specific and sensitive marker for chordoma. It is hypothesised that brachyury or genes involved in its activation are implicated in the pathogenesis of chordoma. As there is currently no effective drug therapy for chordoma the aim of this study was to identify genetic events involved in chordoma pathogenesis with a view to identifying potential therapeutic targets. One hundred chordomas (50 skull-based, 50 non-skull based) were studied. Immunohistochemistry showed that the PI3K/AKT/TSC/mTOR pathway was activated in 65% of chordomas, thereby providing a rationale for testing mTOR inhibitors for the treatment of selected cases. DNA sequencing revealed no mutations in PI3KCA or RAS homologue enriched in brain (Rheb) in 23 tumours. Immunohistochemistry and Western blotting showed activation of the fibroblastic growth factor receptor (FGFR)/RAS/RAF/MEK/ERK/ETS2/brachyury pathway in more than 90% of cases, but no mutations were found in the genes analysed (FGFRs, KRAS, BRAF and brachyury) in 23 tumours. Three percent of cases revealed brachyury amplification but nearly half of the cases showed chromosomal abnormalities involving the brachyury locus. Knockdown of brachyury was achieved in the U-CH1 chordoma cell line using shRNA and resulted in premature cell senescence. These findings demonstrate that brachyury plays an important role in chordoma pathology. FISH analysis showed EGFR copy number gain in 45% of chordomas, including 6% with amplification and 39% with high level polysomy. The EGFR inhibitor, tyrphostin (AG1478) significantly inhibited growth of the chordoma cell line, and Western blotting showed this was associated with reduced phosphorylation of EGFR in a dose dependent manner. This study provides evidence for the first time that selected chordomas may be susceptible to treatment with EGFR inhibitors.
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Pourahmad, Fazel. "Molecular detection and identification of aquatic mycobacteria." Thesis, University of Stirling, 2007. http://hdl.handle.net/1893/355.

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Mycobacteriosis (fish tuberculosis) is a progressive disease of a wide range of wild and captive marine and freshwater fish species. While Mycobacterium marinum, M. fortuitum and M. chelonae are the most frequently reported species to be involved in the disease, several new mycobacteria species have also recently been implicated. Conventional detection / identification of fish mycobacteria is based on histopathology, culture and biochemical characteristics. In this study complementary molecular approaches were developed to assist in Mycobacterium identification. First, a highly specific and sensitive multiplex PCR-based assay, targeting two genes (hsp65 and 16S RNA), was established to simultaneously detect the genus Mycobacterium and identify M. marinum, M. fortuitum or M. chelonae from culture or infected fish tissue, based on presence / absence of specific amplicons. In addition, PCR-restriction enzyme analysis (PRA) and DNA sequence analysis of the 16S-23S internal transcribed spacer (ITS) region and a 441 bp fragment of the hsp65 gene demonstrated the limitations of multiplex PCR (and commercial line probe assays) to differentiate among the species of the M. fortuitum complex. However DNA sequence analysis of the hsp65 gene fragment was found to reliably identify M. fortuitum from closely related species, M. conceptionense and M. senegalense. Reliable identification of novel species (or very similar species) of aquatic mycobacteria requires more extensive DNA sequence comparisons. Thus, multigene (polygenetic) analyses, as used here, provide rapid, accurate and reliable species identification of aquatic mycobacteria. Furthermore, a number of novel species of aquatic mycobacteria, M. stomatepiae, ‘M. angelicum’, ‘M. aemonae’ and M. salmoniphilum were discovered using the polygenetic analysis approach. Correct identification of Mycobacterium species by DNA sequence comparisons relies on accurate database information. Difficulties in this study in assigning M. marine and M. gordonae to their correct taxa suggest errors in the current public sequence repositories. The above methods were successfully applied to detect and identify mycobacteria in field samples including formalin-fixed, paraffin-embedded (FFPE) fish tissue, water and frozen fish tissue.
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Chandrashaker, Akhila. "Systems analysis of early endosome motility through identification of molecular motors." Doctoral thesis, Saechsische Landesbibliothek- Staats- und Universitaetsbibliothek Dresden, 2010. http://nbn-resolving.de/urn:nbn:de:bsz:14-qucosa-61594.

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Endocytosis is an evolutionary conserved process of internalization of cargo from the extracellular environment, be they ligands, nutritional and signaling or pathogens into cells. Following their entry, cargo is received into vesiculo-tubular network of early endosomal compartments from where they are sorted and routed to appropriate cellular destinations through transport along the endocytic network. Recycling cargo is sorted away from other cargo resident in early endosomes through tubulation resulting in fission of recycling vesicles, while those to be degraded are progressively concentrated in early endosomes to be degraded in lysosomes. Early endosomes are dynamic organelles that have been shown to move centripetally following the internalization of cargo into at the cell periphery. Their motility from the cell periphery to the juxtanuclear location of the cell involves convoluted trajectories that include directed motility, bi-directional switches, saltatory behavior and stalls. This complex motility presumably contributes toward the cargo sorting, duration of cargo residence and spatio-temporal signaling by early endosomes. How the different regimes of motility, and nature and number of molecular motors involved in early endosome motility contribute toward endosome function is not understood. The aim of this study was to probe into the regulation of endosome motility and understand how transport organizes early endosome network. Towards this end, live cell time-lapse movies of Rab5 endosomes were analyzed to derive motility properties contributing to organization of early endosomes. Consistent and significant bias toward the cell centre (minus end motility) in kinetic parameters such as speed, displacement and duration of motility contribute to centripetal flux of Rab5 early endosomes. A phenomenological property of early endosome motility is its saltatory behavior that produces saturation curves in Mean Square Displacement (MSD) plots. This phase of motility is descriptive, with no understanding of its mechanism or function. Live cell candidate RNAi screen and cytoskeletal perturbation analysis were performed to identify molecules regulating saltatory motility. To this end, cellular microtubule perturbation and RNAi knock down of several Kinesin motor candidates showed a loss in saturation behavior. Potential candidates identified have to be tested for their effect on endosome function through cargo sorting and kinetic assays to gain insights into the role of saltatory motility in endosome function. Molecular motors mediate Rab5 motility. Therefore, understanding regulation of motility requires identifying number and nature of molecular motors involved in their transport. Towards this end, a functional cargo (LDL) degradation RNAi screen targeting molecular motors was performed. The Ambion Select technology was used with 3 siRNAs targeting every gene in the library. Analysis of screen produced by lack of phenotype consistency between the multiple siRNAs targeting the same gene. Hence, a search for technology with better target specificity was initiated. Technologies tested were Ambion Select, Ambion Silencer Select, Dharmacon ON-TARGET Plus, esiRNA and Invitrogen Stealth. Invitrogen Stealth technology was found to produce the least off-targets and was most specific in terms of consistency of phenotypes produced by multiple siRNAs silencing the same target gene. Assay conditions were also found to influence the silencing specificities to a significant extent. Hence, a systematic assay optimization exercise was performed in terms of the concentration of siRNA used for transfection and time window of assay to maximize specificity of siRNA silencing. Insights obtained from methodologies developed herein not only provide invaluable guidelines in choosing RNAi commercial libraries for screens, but also underscore the importance of establishing optimal assay conditions to minimize off-targets and improve specificity of silencing target genes. The motor screen was repeated with RNAi library from Invitrogen Stealth. Several potentially interesting candidates have been identified. Also, correlation analyses of phenotypes produced in the screen have indicated toward potential regulatory motor complexes, all of which await biochemical validation.
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Neels, Jacobus Gerardus. "LDL receptor-related protein molecular analysis and identification of new ligands /." [S.l. : Amsterdam : s.n.] ; Universiteit van Amsterdam [Host], 2001. http://dare.uva.nl/document/60201.

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de, Sousa Ines Girao Meireles. "Molecular genetics of autism : Identification and analysis of autism susceptibility genes." Thesis, University of Oxford, 2010. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.526435.

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Hoang, Tiffany Truc. "Speciation and identification of low molecular weight organoselenium metabolites in human urine." Diss., Georgia Institute of Technology, 2003. http://hdl.handle.net/1853/30671.

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Amagase, Yoko. "Identification and molecular analysis of novel splice variants of the SUR1 gene." Thesis, University of Cambridge, 2003. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.619509.

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Yu, Xuejie. "Molecular identification of rickettsial bacteria by using monoclonal antibodies and genetic analysis." Aix-Marseille 2, 1993. http://www.theses.fr/1993AIX22058.

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Nous avons mis au point une methode d'analyse par restriction enzymatique (rflp) de fragments d'adn rickettsien amplifies (pcr) pour differencier les rickettsies du groupe boutonneux. Nous avons isole et identifie deux souches de rickettsies du groupe boutonneux, dont l'une est nouvelle. Nous avons produit des anticorps monoclonaux specifiques d'espece reagissant contre des bacteries rickettsiennes recemment caracterisees, telles qu'afipia felis ehrlichia chaffeensis et rochalimaea henselae, pour le diagnostic d'infections provoquees par ces organismes. Nous avons demontre qu'il n'y a pas de correlation entre souches de coxiella burnetii et les deux formes de fievre q, c'est-a-dire la forme aigue et les endocardites, en utilisant des anticorps monoclonaux diriges specifiquement contre la souche priscilla, consideree comme etant le representant des isolats obtenus de patients souffrant d'endocardite
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Pyz, Elwira. "Identification of rat NKT cells and molecular analysis of their surface receptor mediated activation." Doctoral thesis, [S.l.] : [s.n.], 2004. http://deposit.ddb.de/cgi-bin/dokserv?idn=972705112.

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Books on the topic "Analysis and molecular identification"

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Anna, Panchenko, and Przytycka Teresa, eds. Protein-protein interactions and networks: Identification, computer analysis, and prediction. London: Springer, 2008.

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Anna, Panchenko, and Przytycka Teresa, eds. Protein-protein interactions and networks: Identification, computer analysis, and prediction. London: Springer, 2008.

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Przytycka, Teresa, and Anna Panchenko. Protein-protein interactions and networks: Identification, computer analysis, and prediction. [New York]: Springer, 2010.

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Dostal, Stefan. Concise guide to mycobacteria and their molecular differentiation. Würzburg, Germany: Ridom Press, 2003.

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Jayprakasha, Guddadarangavvanahally K., Bhimanagouda S. Patil, and Federica Pellati, eds. Instrumental Methods for the Analysis and Identification of Bioactive Molecules. Washington, DC: American Chemical Society, 2014. http://dx.doi.org/10.1021/bk-2014-1185.

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Louis, Edward E. Molecular and morphological analyses of the sportive lemurs (Family Megaladapidae: Genus Lepilemur) reveals 11 previously unrecognized species. Lubbock, TX: Museum of Texas Tech University, 2006.

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State University College at Buffalo. Dept. of Art Conservation., ed. Molecular studies of asphalt, mummy and Kassel earth pigments: Their characterisation, identification and effect on the drying of traditional oil paint. [S.l: s.n.], 2004.

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P, Schlunegger Urs, and Schweizerischer Chemiker-Verband, eds. Biologically active molecules: Identification, characterization, and synthesis : proceedings of a Seminar on Chemistry on Biologically Active Compounds and Modern Analytical Methods, Interlaken, September 5-7, 1988. Berlin: Springer-Verlag, 1989.

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Klimenko, Irina, Nikolay Kozlov, Sergey Kostenko, Anastasia Shamustakimova, and Yulian Mavlyutov. Identification and certification of forage grasses (meadow clover, alfalfa, sowing and hop) based on DNA markers. ru: Federal Williams Research Center of Forage Production and Agroecology, 2020. http://dx.doi.org/10.33814/978-5-6043194-9-9.

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A technology has been developed for DNA identification and certification of varieties of meadow clover (Trifolium pratense L.), alfalfa (Medicago varia Mart.), Sowing (M. sativa L.) and hop (M. lupuli-na L.) based on molecular analysis with using SSR and SRAP markers. The recommendations contain a description of the sequence of experiments and protocols for DNA typing procedures. The presented methods were developed by the authors on the basis of their own experimental research and using the data available in the literature. A characteristic of informative primers for each marking system is given, a set of DNA identification markers is proposed, and unique molecular genetic formulas of varieties are drawn up as the basis for a reference genetic passport. Methodological recommendations were prepared with the aim of mastering the technology of DNA certification of forage grasses in practice. Designed for managers and specialists of research and control laboratories, can serve as a textbook for students and postgraduates in specialized specialties.
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Gherbawy, Youssuf, and Kerstin Voigt, eds. Molecular Identification of Fungi. Berlin, Heidelberg: Springer Berlin Heidelberg, 2010. http://dx.doi.org/10.1007/978-3-642-05042-8.

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Book chapters on the topic "Analysis and molecular identification"

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Tsongalis, Gregory J., and Andrew Ricci. "Specimen Identification Through DNA Analysis." In Molecular Pathology in Clinical Practice, 533–37. New York, NY: Springer New York, 2007. http://dx.doi.org/10.1007/978-0-387-33227-7_47.

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Bocsi, Gregary, Andrew Ricci, Gregory J. Tsongalis, and Vivianna M. Van Deerlin. "Specimen Identification Through DNA Analysis." In Molecular Pathology in Clinical Practice, 849–64. Cham: Springer International Publishing, 2016. http://dx.doi.org/10.1007/978-3-319-19674-9_57.

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Bandeira, Nuno. "Protein Identification by Spectral Networks Analysis." In Methods in Molecular Biology, 151–68. Totowa, NJ: Humana Press, 2010. http://dx.doi.org/10.1007/978-1-60761-977-2_11.

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Tsongalis, Gregory J., and Andrew Ricci. "Specimen Identification Through DNA Analysis." In Molecular Pathology in Clinical Practice: Oncology, 243–48. Boston, MA: Springer US, 2009. http://dx.doi.org/10.1007/978-0-387-87366-4_23.

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Joseph, Loren. "Specimen Identification and Bone Marrow Engraftment Analysis." In Molecular Genetic Pathology, 1049–64. New York, NY: Springer New York, 2012. http://dx.doi.org/10.1007/978-1-4614-4800-6_41.

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Yang, Yongliang, S. James Adelstein, and Amin I. Kassis. "Integrated Bioinformatics Analysis for Cancer Target Identification." In Methods in Molecular Biology, 527–45. Totowa, NJ: Humana Press, 2011. http://dx.doi.org/10.1007/978-1-61779-027-0_25.

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Fu, Yan. "Data Analysis Strategies for Protein Modification Identification." In Methods in Molecular Biology, 265–75. New York, NY: Springer New York, 2016. http://dx.doi.org/10.1007/978-1-4939-3106-4_17.

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Dowling, Paul. "DIGE Analysis Software and Protein Identification Approaches." In Methods in Molecular Biology, 39–50. New York, NY: Springer US, 2022. http://dx.doi.org/10.1007/978-1-0716-2831-7_3.

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Hmmier, Abduladim, and Paul Dowling. "DIGE Analysis Software and Protein Identification Approaches." In Methods in Molecular Biology, 41–50. New York, NY: Springer New York, 2017. http://dx.doi.org/10.1007/978-1-4939-7268-5_4.

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Mandal, Chandan, and Chitra Mandal. "Identification and Analysis of O-Acetylated Sialoglycoproteins." In Methods in Molecular Biology, 57–93. Totowa, NJ: Humana Press, 2012. http://dx.doi.org/10.1007/978-1-62703-305-3_6.

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Conference papers on the topic "Analysis and molecular identification"

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Long, S. Randolph. "Application of UV Lasers to Detection and Identification." In Laser Applications to Chemical Analysis. Washington, D.C.: Optica Publishing Group, 1990. http://dx.doi.org/10.1364/laca.1990.tua3.

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Principal processes occurring in molecules under the influence of focused UV laser radiation include fragmentation and ionization. These processes can facilitate substantially the detection and identification of molecular species.
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Castro, Alonso, and Brooks Shera. "Electrophoresis of Single Fluorescent Molecules." In Laser Applications to Chemical Analysis. Washington, D.C.: Optica Publishing Group, 1994. http://dx.doi.org/10.1364/laca.1994.thd.3.

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The fast, efficient detection and separation of minute quantities of biologically important molecules plays a central role in a variety of fields, such as molecular biology, biotechnology, immunology, medical diagnostics, and forensic analysis. It has proven difficult to identify and separate biomolecules at such low concentrations by existing means. Thus, it is of importance to develop methods that are able to probe such low concentrations with adequate sensitivity, resolution and ease. Here, we describe a new method for detecting and identifying individual fluorescent molecules in solution. The technique involves the measurement of electrophoretic velocities of individual molecules in a mixture, and identification by comparison with the electrophoretic velocity known to be characteristic of a particular molecular species. The application of the method to the detection and size identification of DNA restriction fragments in solution at the single molecule level has been demonstrated. In a similar experiment, the electrophoretic velocities of single molecules of the protein phycoerythrin was determined. Although we have focused on the detection and identification of biologically important molecules, the technique has the potential to find applications in organic and inorganic chemical analysis.
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Lykke, Keith R., Peter Wurz, Deborah H. Parker, Jerry E. Hunt, Michael J. Pellin, and Dieter M. Gruen. "Molecular Surface Analysis Utilizing Laser Desorption/Laser Ionization." In Laser Applications to Chemical Analysis. Washington, D.C.: Optica Publishing Group, 1992. http://dx.doi.org/10.1364/laca.1992.thb4.

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The ability to analyze surface elemental composition has existed for some time. The various methods include Auger Electron Spectroscopy (AES), Secondary Ion Mass Spectrometry (SIMS), and many more.1 However, molecular surface analysis is only now achieving the same sensitivity and selectivity. Molecular surface analysis often utilizes various optical probes: IR Reflection Absorption Spectroscopy, Sum-Frequency (or Second Harmonic) Generation Spectroscopy on Surfaces, etc. These techniques are generally lacking species-specific information. Another approach is to remove the molecule from the surface and probe it in the gas phase, e.g., with state- of-the-art mass spectrometry. Since mass spectrometry offers high resolution and high sensitivity, the remaining problems are removal of the molecule from the surface and ionization without alteration of the molecule (e.g., fragmentation). These pose serious complications for large molecules, in particular. Furthermore, if the molecule of interest is only a minor constituent of a sample, mass resolution and sensitivity are not sufficient for species identification, and a pre- selection in the ionization is often necessary. Our solution is to employ lasers for both desorption from the sample and ionization (post-ionization) of the gas-phase species. The ability to choose the wavelength and intensity of the desorption laser and the post-ionization laser allows for proper tailoring to the needs of the investigation. This will be demonstrated with two examples. First, a vulcanizate (rubber) will be analyzed with a time-of-flight mass spectrometer for the organic additives present in minor concentrations in the near-surface region. Second, a new class of carbon molecules (fullerenes) will be examined with a Fourier transform mass spectrometer.
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Lee, Kelvin, and Michael McCarthy. "BENZENE'S INFERNO, PART II: AUTOMATED ANALYSIS AND IDENTIFICATION." In 74th International Symposium on Molecular Spectroscopy. Urbana, Illinois: University of Illinois at Urbana-Champaign, 2019. http://dx.doi.org/10.15278/isms.2019.ri02.

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Preppernau, B. L., and P. J. Hargis. "Trace Organic Chemical Detection Using an Ultraviolet Excitation Molecular Beam Fluorometer." In Laser Applications to Chemical Analysis. Washington, D.C.: Optica Publishing Group, 1994. http://dx.doi.org/10.1364/laca.1994.tub.5.

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Detection of air-borne environmental contaminants, such as organic solvents, requires unambiguous compound identification and sensitivity to concentrations below those permitted by regulating agencies. One promising detection approach uses a pulsed supersonic molecular beam vacuum expansion in combination with fluorescence signal spectral analysis to identify species in a chemical mixture. Expanding a contaminated atmospheric sample through a supersonic molecular beam expansion acts to cool the sample and greatly reduce the spectral density in a fluorescence or photoionization spectrum. Most organic contaminants of interest have electronic transitions in the ultraviolet with near-featureless broad band fluorescence spectra when recorded at atmospheric pressure and room temperature. By using a supersonic vacuum expansion, cooling to within a few degrees of absolute zero can reduce the effective rotational and translational temperatures of the sample molecules and provide a sharply defined spectra which can be used to unambiguously identify specific molecules and their concentrations.
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Chen, Yao, Cheng Wang, Samuel Streeter, Sassan Hodge, Brian W. Pogue, and Kimberley S. Samkoe. "Fluorescence-based radiomics analysis improves the identification of head and neck cancer in preclinical studies." In Molecular-Guided Surgery: Molecules, Devices, and Applications VIII, edited by Summer L. Gibbs, Brian W. Pogue, and Sylvain Gioux. SPIE, 2022. http://dx.doi.org/10.1117/12.2608791.

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Olsen, Rachel. "Molecular identification ofTrogoderma granariumand phylogenetic analysis of USTrogoderma." In 2016 International Congress of Entomology. Entomological Society of America, 2016. http://dx.doi.org/10.1603/ice.2016.95470.

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Pester, Paul D., and Andrew R. Hopkins. "Surface Plasmon Enhanced Raman Spectroscopy As A Generic Sensing Technology." In Laser Applications to Chemical Analysis. Washington, D.C.: Optica Publishing Group, 1990. http://dx.doi.org/10.1364/laca.1990.tuc12.

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Raman Spectroscopy is one of the most versatile methods of molecular analysis. The Raman effect is seen when light interacts with an atomic or molecular species, in the solid, liquid or gas phase, to produce scattered light, the frequency of which is shifted from that of the incident light. The shift in frequency corresponds to electronic, vibrational or rotational energy transitions in the sample and, since these energies are species specific, the scattered Raman light can provide identification of the molecules irradiated.
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Wehry, E. L. "Low-Temperature and Fragmentation Methods in Analytical Molecular Fluorescence Spectrometry." In Laser Applications to Chemical Analysis. Washington, D.C.: Optica Publishing Group, 1987. http://dx.doi.org/10.1364/laca.1987.ma8.

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Molecular fluorescence spectrometry is widely used in chemical analysis for several reasons, including (a) the ability to achieve very low limits of detection for intensely fluorescent analytes; (b) its capabilities for remote detection (e.g., by laser and/or fiber optic probe techniques), and (c) acquisition of information useful for molecular identification (excitation and emission spectra; decay times; polarization).
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Kulakova, N. V., and I. N. Egorova. "Comparative analysis of molecular markers for identification of green microalgae (Chlorophyta)." In The international field workshop «Cryptogams of North Asia». SIPPB SB RAS, 2018. http://dx.doi.org/10.31255/cna.irk-18-19.

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Reports on the topic "Analysis and molecular identification"

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Wagner, D. Ry, Eliezer Lifschitz, and Steve A. Kay. Molecular Genetic Analysis of Flowering in Arabidopsis and Tomato. United States Department of Agriculture, May 2002. http://dx.doi.org/10.32747/2002.7585198.bard.

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The primary objectives for the US lab included: the characterization of ELF3 transcription and translation; the creation and characterization of various transgenic lines that misexpress ELF3; defining genetic pathways related to ELF3 function regulating floral initiation in Arabidopsis; and the identification of genes that either interact with or are regulated by ELF3. Light quality, photoperiod, and temperature often act as important and, for some species, essential environmental cues for the initiation of flowering. However, there is relatively little information on the molecular mechanisms that directly regulate the developmental pathway from the reception of the inductive light signals to the onset of flowering and the initiation of floral meristems. The ELF3 gene was identified as possibly having a role in light-mediated floral regulation since elj3 mutants not only flower early, but exhibit light-dependent circadian defects. We began investigating ELF3's role in light signalling and flowering by cloning the ELF3 gene. ELF3 is a novel gene only present in plant species; however, there is an ELF3 homolog within Arabidopsis. The Arabidopsis elj3 mutation causes arrhythmic circadian output in continuous light; however, we show conclusively normal circadian function with no alteration of period length in elj3 mutants in dark conditions and that the light-dependent arrhythmia observed in elj3 mutants is pleiotropic on multiple outputs regardless of phase. Plants overexpressing ELF3 have an increased period length in constant light and flower late in long-days; furthermore, etiolated ELF3-overexpressing seedlings exhibit a decreased acute CAB2 response after a red light pulse, whereas the null mutant is hypersensitive to acute induction. This finding suggests that ELF3 negatively regulates light input to both the clock and its outputs. To determine whether ELF3's action is phase dependent, we examined clock resetting by light pulses and constructed phase response curves. Absence of ELF3 activity causes a significant alteration of the phase response curve during the subjective night, and overexpression of ELF3 results in decreased sensitivity to the resetting stimulus, suggesting that ELF3 antagonizes light input to the clock during the night. Indeed, the ELF3 protein interacts with the photoreceptor PHYB in the yeast two-hybrid assay and in vitro. The phase ofELF3 function correlates with its peak expression levels of transcript and protein in the subjective night. ELF3 action, therefore, represents a mechanism by which the oscillator modulates light resetting. Furthermore, flowering time is dependent upon proper expression ofELF3. Scientifically, we've made a big leap in the understanding of the circadian system and how it is coupled so tightly with light reception in terms of period length and clock resetting. Agriculturally, understanding more about the way in which the clock perceives and relays temporal information to pathways such as those involved in the floral transition can lead to increased crop yields by enabling plants to be grown in suboptimal conditions.
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Porat, Ron, Doron Holland, and Linda Walling. Identification of Citrus Fruit-Specific and Pathogen-Induced Promoters and Their Use in Molecular Engineering. United States Department of Agriculture, January 2001. http://dx.doi.org/10.32747/2001.7585202.bard.

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This one year BARD project was funded to develop methods to monitor promoter activity a gene expression patterns in citrus fruit. To fulfill this goal, we divided the research tasks between both labs so that the Israeli side evaluated the use of microprojectile bombardment ; a tool to evaluate transient gene expression in various citrus fruit tissues, and the US side optimized technical parameters required for Agrobacterium-mediated transformation of various citrus cultivars. Microprojectile bombardment appeared to be a very efficient method for transient gene expression analysis in citrus leaf tissues but was somewhat less applicable in fruit tissues. Nevertheless, we did succeeded to achieve significant levels of 35S-GUS gene expression in young green flavedo tissue. However, only single random spots of 35S-GUS gene expression were detected mature flavedo and in juice sacs and albedo tissue. Overall, we assume that following some more technical improvements particle bombardment could provide a useful technique to rapidly analyze promoter activity at least in the flavedo tissue. For Agrobacterium-mediated transformation, we found that shoot cultures of 'Washington' navel oranges,'Fairchild' mandarins,'Eureca' lemons,'Troyer' citrange and various grapefruits provided a more reliable and consistent source of tissue for transformation than germinated seedlings. Moreover, various growth media's (McCown, Quoirin & Lepoivre, DCR) further improved shoot and root growth relative to MS mineral media, which is commonly used. Also pure white light (using bulbs which do not emit UV or blue light) improved shoot growth in various citrus varieties, and paromomycin appeared to be a more efficient antibiotic for the selection of transgenic plants than Kanamycin. Overall, these optimizations improve transformation efficacy and shoot growth and rooting capacity. In addition to the development of transformation methods, both Israeli and US labs achieved progress in the identification of citrus fruit-specific promoters. In Israel, we isolated a 3.6 kb promoter fragment of the thiamine biosynthesis c-thi gene, which is highly expressed in fruit peel tissue, whereas in the US we isolated a 1.5 kb promoter fragment of the citrus seed-specific cDNA CssH. The identification of more fruit-specific cDNAs and their corresponding promoter regions is currently in progress.
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Levisohn, Sharon, Maricarmen Garcia, David Yogev, and Stanley Kleven. Targeted Molecular Typing of Pathogenic Avian Mycoplasmas. United States Department of Agriculture, January 2006. http://dx.doi.org/10.32747/2006.7695853.bard.

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Intraspecies identification (DNA "fingerprinting") of pathogenic avian mycoplasmas is a powerful tool for epidemiological studies and monitoring strain identity. However the only widely method available for Mycoplasma gallisepticum (MG) and M. synoviae (MS)wasrandom amplified polymorphic DNA (RAPD). This project aimed to develop alternative and supplementary typing methods that will overcome the major constraints of RAPD, such as the need for isolation of the organism in pure culture and the lack of reproducibility intrinsic in the method. Our strategy focussed on recognition of molecular markers enabling identification of MG and MS vaccine strains and, by extension, pathogenic potential of field isolates. Our first aim was to develop PCR-based systems which will allow amplification of specific targeted genes directly from clinical material. For this purpose we evaluated the degree of intraspecies heterogeneity in genes encoding variable surface antigens uniquely found in MG all of which are putative pathogenicity factors. Phylogenic analysis of targeted sequences of selected genes (pvpA, gapA, mgc2, and lp) was employed to determine the relationship among MG strains.. This method, designated gene targeted sequencing (GTS), was successfully employed to identify strains and to establish epidemiologically-linked strain clusters. Diagnostic PCR tests were designed and validated for each of the target genes, allowing amplification of specific nucleotide sequences from clinical samples. An mgc2-PCR-RFLP test was designed for rapid differential diagnosis of MG vaccine strains in Israel. Addressing other project goals, we used transposon mutagenesis and in vivo and in vitro models for pathogenicity to correlated specific changes in target genes with biological properties that may impact the course of infection. An innovative method for specific detection and typing of MS strains was based on the hemagglutinin-encoding gene vlhA, uniquely found in this species. In parallel, we evaluated the application of amplified fragment length polymorphism (AFLP) in avian mycoplasmas. AFLP is a highly discriminatory method that scans the entire genome using infrequent restriction site PCR. As a first step the method was found to be highly correlated with other DNA typing methods for MG species and strain differentiation. The method is highly reproducible and relatively rapid, although it is necessary to isolate the strain to be tested. Both AFLP and GTS are readily to amenable to computer-assisted analysis of similarity and construction of a data-base resource. The availability of improved and diverse tools will help realize the full potential of molecular typing of avian mycoplasmas as an integral and essential part of mycoplasma control programs.
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Firon, Nurit, Prem Chourey, Etan Pressman, Allen Hartwell, and Kenneth J. Boote. Molecular Identification and Characterization of Heat-Stress-Responsive Microgametogenesis Genes in Tomato and Sorghum - A Feasibility Study. United States Department of Agriculture, October 2007. http://dx.doi.org/10.32747/2007.7591741.bard.

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Exposure to higher than optimal temperatures - heat-stress (HS) - is becoming increasingly common to all crop plants worldwide. Heat stress coinciding with microgametogenesis, especially during the post-meiotic phase that is marked by starch biosynthesis, is often associated with starch-deficient pollen and male sterility and ultimately, greatly reduced crop yields. The molecular basis for the high sensitivity of developing pollen grains, on one hand, and factors involved in pollen heat-tolerance, on the other, is poorly understood. The long-term goal of this project is to provide a better understanding of the genes that control pollen quality under heat-stress conditions. The specific objectives of this project were: (1) Determination of the threshold heat stress temperature(s) that affects tomato and sorghum pollen quality whether: a) Chronic mild heat stress conditions (CMHS), or b) Acute heat stress (AHS). (2) Isolation of heat-responsive, microgametogenesis-specific sequences. During our one-year feasibility project, we have accomplished the proposed objectives as follows: Objectrive 1: We have determined the threshold HS conditions in tomato and sorghum. This was essential for achieving the 2nd objective, since our accumulated experience (both Israeli and US labs) indicate that when temperature is raised too high above "threshold HS levels" it may cause massive death of the developing pollen grains. Above-threshold conditions have additional major disadvantages including the "noise" caused by induced expression of genes involved in cell death and masking of the differences between heatsensitive and heat-tolerant pollen grains. Two different types of HS conditions were determined: a) Season-long CMHS conditions: 32/26°C day/night temperatures confirmed in tomato and 36/26°C day maximum/night minimum temperatures in sorghum. b) Short-term AHS: In tomato, 2 hour exposure to 42-45°C (at 7 to 3 days before anthesis) followed by transfer to 28/22±2oC day/night temperatures until flower opening and pollen maturation, caused 50% reduced germinating pollen in the heat-sensitive 3017 cv.. In sorghum, 36/26°C day/night temperatures 10 to 5 days prior to panicle emergence, occurring at 35 days after sowing (DAS) in cv. DeKalb28E, produced starch-deficient and sterile pollen. Objective 2: We have established protocols for the high throughput transcriptomic approach, cDNA-AFLP, for identifying and isolating genes exhibiting differential expression in developing microspores exposed to either ambient or HS conditions and created a databank of HS-responsivemicrogametogenesis-expressed genes. A subset of differentially displayed Transcript-Derived Fragments (TDFs) that were cloned and sequenced (35 & 23 TDFs in tomato and sorghum, respectively) show close sequence similarities with metabolic genes, genes involved in regulation of carbohydrate metabolism, genes implicated in thermotolerance (heat shock proteins), genes involved in long chain fatty acids elongation, genes involved in proteolysis, in oxidation-reduction, vesicle-mediated transport, cell division and transcription factors. T-DNA-tagged Arabidopsis mutants for part of these genes were obtained to be used for their functional analysis. These studies are planned for a continuation project. Following functional analyses of these genes under HS – a valuable resource of genes, engaged in the HS-response of developing pollen grains, that could be modulated for the improvement of pollen quality under HS in both dicots and monocots and/or used to look for natural variability of such genes for selecting heat-tolerant germplasm - is expected.
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Morrison, Mark, Joshuah Miron, Edward A. Bayer, and Raphael Lamed. Molecular Analysis of Cellulosome Organization in Ruminococcus Albus and Fibrobacter Intestinalis for Optimization of Fiber Digestibility in Ruminants. United States Department of Agriculture, March 2004. http://dx.doi.org/10.32747/2004.7586475.bard.

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Improving plant cell wall (fiber) degradation remains one of the highest priority research goals for all ruminant enterprises dependent on forages, hay, silage, or other fibrous byproducts as energy sources, because it governs the provision of energy-yielding nutrients to the host animal. Although the predominant species of microbes responsible for ruminal fiber degradation are culturable, the enzymology and genetics underpinning the process are poorly defined. In that context, there were two broad objectives for this proposal. The first objective was to identify the key cellulosomal components in Ruminococcus albus and to characterize their structural features as well as regulation of their expression, in response to polysaccharides and (or) P AA/PPA. The second objective was to evaluate the similarities in the structure and architecture of cellulosomal components between R. albus and other ruminal and non-ruminal cellulolytic bacteria. The cooperation among the investigators resulted in the identification of two glycoside hydrolases rate-limiting to cellulose degradation by Ruminococcus albus (Cel48A and CeI9B) and our demonstration that these enzymes possess a novel modular architecture specific to this bacterium (Devillard et al. 2004). We have now shown that the novel X-domains in Cel48A and Cel9B represent a new type of carbohydrate binding module, and the enzymes are not part of a ceiluiosome-like complex (CBM37, Xu et al. 2004). Both Cel48A and Cel9B are conditionally expressed in response to P AA/PPA, explaining why cellulose degradation in this bacterium is affected by the availability of these compounds, but additional studies have shown for the first time that neither PAA nor PPA influence xylan degradation by R. albus (Reveneau et al. 2003). Additionally, the R. albus genome sequencing project, led by the PI. Morrison, has supported our identification of many dockerin containing proteins. However, the identification of gene(s) encoding a scaffoldin has been more elusive, and recombinant proteins encoding candidate cohesin modules are now being used in Israel to verify the existence of dockerin-cohesin interactions and cellulosome production by R. albus. The Israeli partners have also conducted virtually all of the studies specific to the second Objective of the proposal. Comparative blotting studies have been conducted using specific antibodies prepare against purified recombinant cohesins and X-domains, derived from cellulosomal scaffoldins of R. flavefaciens 17, a Clostridium thermocellum mutant-preabsorbed antibody preparation, or against CbpC (fimbrial protein) of R. albus 8. The data also suggest that additional cellulolytic bacteria including Fibrobacter succinogenes S85, F. intestinalis DR7 and Butyrivibrio fibrisolvens Dl may also employ cellulosomal modules similar to those of R. flavefaciens 17. Collectively, our work during the grant period has shown that R. albus and other ruminal bacteria employ several novel mechanisms for their adhesion to plant surfaces, and produce both cellulosomal and non-cellulosomal forms of glycoside hydrolases underpinning plant fiber degradation. These improvements in our mechanistic understanding of bacterial adhesion and enzyme regulation now offers the potential to: i) optimize ruminal and hindgut conditions by dietary additives to maximize fiber degradation (e.g. by the addition of select enzymes or PAA/PPA); ii) identify plant-borne influences on adhesion and fiber-degradation, which might be overcome (or improved) by conventional breeding or transgenic plant technologies and; iii) engineer or select microbes with improved adhesion capabilities, cellulosome assembly and fiber degradation. The potential benefits associated with this research proposal are likely to be realized in the medium term (5-10 years).
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Cohen, Yuval, Christopher A. Cullis, and Uri Lavi. Molecular Analyses of Soma-clonal Variation in Date Palm and Banana for Early Identification and Control of Off-types Generation. United States Department of Agriculture, October 2010. http://dx.doi.org/10.32747/2010.7592124.bard.

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Date palm (Phoenix dactylifera L.) is the major fruit tree grown in arid areas in the Middle East and North Africa. In the last century, dates were introduced to new regions including the USA. Date palms are traditionally propagated through offshoots. Expansion of modern date palm groves led to the development of Tissue Culture propagation methods that generate a large number of homogenous plants, have no seasonal effect on plant source and provide tools to fight the expansion of date pests and diseases. The disadvantage of this procedure is the occurrence of off-type trees which differ from the original cultivar. In the present project we focused on two of the most common date palm off-types: (1) trees with reduced fruit setting, in which most of the flowers turn into three-carpel parthenocarpic fruits. In a severe form, multi-carpel flowers and fruitlets (with up to six or eight carpels instead of the normal three-carpel flowers) are also formed. (2) dwarf trees, having fewer and shorter leaves, very short trunk and are not bearing fruits at their expected age, compared to the normal trees. Similar off-types occur in other crop species propagated by tissue culture, like banana (mainly dwarf plants) or oil palm (with a common 'Mantled' phenotype with reduced fruit setting and occurrence of supernumerary carpels). Some off-types can only be detected several years after planting in the fields. Therefore, efficient methods for prevention of the generation of off-types, as well as methods for their detection and early removal, are required for date palms, as well as for other tissue culture propagated crops. This research is aimed at the understanding of the mechanisms by which off-types are generated, and developing markers for their early identification. Several molecular and genomic approaches were applied. Using Methylation Sensitive AFLP and bisulfite sequencing, we detected changes in DNA methylation patterns occurring in off-types. We isolated and compared the sequence and expression of candidate genes, genes related to vegetative growth and dwarfism and genes related to flower development. While no sequence variation were detected, changes in gene expression, associated with the severity of the "fruit set" phenotype were detected in two genes - PdDEF (Ortholog of rice SPW1, and AP3 B type MADS box gene), and PdDIF (a defensin gene, highly homologous to the oil palm gene EGAD). We applied transcriptomic analyses, using high throughput sequencing, to identify genes differentially expressed in the "palm heart" (the apical meristem and the region of embryonic leaves) of dwarf vs. normal trees. Among the differentially expressed genes we identified genes related to hormonal biosynthesis, perception and regulation, genes related to cell expansion, and genes related to DNA methylation. Using Representation Difference Analyses, we detected changes in the genomes of off-type trees, mainly chloroplast-derived sequences that were incorporated in the nuclear genome and sequences of transposable elements. Sequences previously identified as differing between normal and off-type trees of oil palms or banana, successfully identified variation among date palm off-types, suggesting that these represent highly labile regions of monocot genomes. The data indicate that the date palm genome, similarly to genomes of other monocot crops as oil palm and banana, is quite unstable when cells pass through a cycle of tissue culture and regeneration. Changes in DNA sequences, translocation of DNA fragments and alteration of methylation patterns occur. Consequently, patterns of gene expression are changed, resulting in abnormal phenotypes. The data can be useful for future development of tools for early identification of off-type as well as for better understanding the phenomenon of somaclonal variation during propagation in vitro.
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Azem, Abdussalam, George Lorimer, and Adina Breiman. Molecular and in vivo Functions of the Chloroplast Chaperonins. United States Department of Agriculture, June 2011. http://dx.doi.org/10.32747/2011.7697111.bard.

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We present here the final report for our research project entitled "The molecular and in vivo functions of the chloroplast chaperonins”. Over the past few decades, intensive investigation of the bacterial GroELS system has led to a basic understanding of how chaperonins refold denatured proteins. However, the parallel is limited in its relevance to plant chaperonins, since the plant system differs from GroEL in genetic complexity, physiological roles of the chaperonins and precise molecular structure. Due to the importance of plant chaperonins for chloroplast biogenesis and Rubisco assembly, research on this topic will have implications for many vital applicative fields such as crop hardiness and efficiency of plant growth as well as the production of alternative energy sources. In this study, we set out to investigate the structure and function of chloroplast chaperonins from A. thaliana. Most plants harbor multiple genes for chaperonin proteins, making analysis of plant chaperonin systems more complicated than the GroEL-GroES system. We decided to focus on the chaperonins from A. thaliana since the genome of this plant has been well defined and many materials are available which can help facilitate studies using this system. Our proposal put forward a number of goals including cloning, purification, and characterization of the chloroplast cpn60 subunits, antibody preparation, gene expression patterns, in vivo analysis of oligomer composition, preparation and characterization of plant deletion mutants, identification of substrate proteins and biophysical studies. In this report, we describe the progress we have made in understanding the structure and function of chloroplast chaperonins in each of these categories.
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Hulata, Gideon, Thomas D. Kocher, Micha Ron, and Eyal Seroussi. Molecular Mechanisms of Sex Determination in Cultured Tilapias. United States Department of Agriculture, October 2010. http://dx.doi.org/10.32747/2010.7697106.bard.

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Tilapias are among the most important aquaculture commodities worldwide. Commercial production of tilapia is based on monosex culture of males. Current methods for producing all-male fingerlings, including hormone treatments and genetic manipulations, are not entirely reliable, in part because of the genetic complexity of sex determination and sexual differentiation in tilapias. The goals of this project are to map QTL and identify genes regulating sex determination in commonly cultured tilapia species, in order to provide a rational basis for designing reliable genetic approaches for producing all-male fingerlings. The original objectives for this research were: 1) to identify the gene underlying the QTL on LG1 through positional cloning and gene expression analysis; 2) to fine map the QTL on LG 3 and 23; and 3) to characterize the patterns of dominance and epistasis among QTL alleles influencing sex determination. The brain aromatase gene Cyp19b, a possible candidate for the genetic or environmental SD, was mapped to LG7 using our F2 mapping population. This region has not been identified before as affecting SD in tilapias. The QTL affecting SD on LG 1 and 23 have been fine-mapped down to 1 and 4 cM, respectively, but the key regulators for SD have not been found yet. Nevertheless, a very strong association with gender was found on LG23 for marker UNH898. Allele 276 was found almost exclusively in males, and we hypothesized that this allele is a male-associated allele (MAA). Mating of males homozygous for MAA with normal females is underway for production of all-male populations. The first progeny reaching size allowing accurate sexing had 43 males and no females. During the course of the project it became apparent that in order to achieve those objectives there is a need to develop genomic infrastructures that were lacking. Efforts have been devoted to the development of genomic resources: a database consisting of nearly 117k ESTs representing 16 tissues from tilapia were obtained; a web tool based on the RepeatMasker software was designed to assist tilapia genomics; collaboration has been established with a sequencing company to sequence the tilapia genome; steps have been taken toward constructing a microarray to enable comparative analysis of the entire transcriptome that is required in order to detect genes that are differentially expressed between genders in early developmental stages. Genomic resources developed will be invaluable for studies of cichlid physiology, evolution and development, and will hopefully lead to identification of the key regulators of SD. Thus, they will have both scientific and agricultural implications in the coming years.
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Wisniewski, Michael E., Samir Droby, John L. Norelli, Noa Sela, and Elena Levin. Genetic and transcriptomic analysis of postharvest decay resistance in Malus sieversii and the characterization of pathogenicity effectors in Penicillium expansum. United States Department of Agriculture, January 2014. http://dx.doi.org/10.32747/2014.7600013.bard.

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Blue mold of apple caused by Penicilliumexpansumis a major postharvest disease. Selection for postharvest disease resistance in breeding programs has been ignored in favor of fruit quality traits such as size, color, taste, etc. The identification of postharvest disease resistance as a heritable trait would represent a significant accomplishment and has not been attempted in apple. Furthermore, insight into the biology of the pathogenicity of P. expansumin apple could provide new approaches to postharvest decay management. Hypothesis: Postharvest resistance of apple to P. expansumcan be mapped to specific genetic loci and significant quantitative-trait-loci (QTLs) can be identified that account for a major portion of the population variance. Susceptibility of apple fruit to P. expansumis dependent on the ability of the pathogen to produce LysM effectors that actively suppress primary and/or secondary resistance mechanisms in the fruit. Objectives: 1) Identify QTL(s) and molecular markers for blue mold resistance in GMAL4593 mapping population (‘Royal Gala’ X MalussieversiiPI613981), 2) Characterize the transcriptome of the host and pathogen (P. expansum) during the infection process 3) Determine the function of LysM genes in pathogenicity of P. expansum. Methods: A phenotypic evaluation of blue mold resistance in the GMAL4593 mapping population, conducted in several different years, will be used for QTL analysis (using MapQTL 6.0) to identify loci associated with blue mold resistance. Molecular markers will be developed for the resistance loci. Transcriptomic analysis by RNA-seq will be used to conduct a time course study of gene expression in resistant and susceptible apple GMAL4593 genotypes in response to P. expansum, as well as fungal responses to both genotypes. Candidate resistance genes identified in the transcriptomic study and or bioinformatic analysis will be positioned in the ‘Golden Delicious’ genome to identify markers that co-locate with the identified QTL(s). A functional analysis of LysM genes on pathogenicity will be conducted by eliminating or reducing the expression of individual effectors by heterologous recombination and silencing technologies. LysMeffector genes will also be expressed in a yeast expression system to study protein function. Expected Results: Identification of postharvest disease resistance QTLs and tightly-linked genetic markers. Increased knowledge of the role of effectors in blue mold pathogenic
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10

Manulis, Shulamit, Christine D. Smart, Isaac Barash, Guido Sessa, and Harvey C. Hoch. Molecular Interactions of Clavibacter michiganensis subsp. michiganensis with Tomato. United States Department of Agriculture, January 2011. http://dx.doi.org/10.32747/2011.7697113.bard.

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Clavibacter michiganensis subsp. michiganensis (Cmm), the causal agent of bacterial wilt and canker of tomato, is the most destructive bacterial disease of tomato causing substantial economic losses in Israel, the U.S.A. and worldwide. The molecular strategies that allow Cmm, a Gram-positive bacterium, to develop a successful infection in tomato plants are largely unknown. The goal of the project was to elucidate the molecular interactions between Cmmand tomato. The first objective was to analyze gene expression profiles of susceptible tomato plants infected with pathogenic and endophytic Cmmstrains. Microarray analysis identified 122 genes that were differentially expressed during early stages of infection. Cmm activated typical basal defense responses in the host including induction of defense-related genes, production of scavenging of free oxygen radicals, enhanced protein turnover and hormone synthesis. Proteomic investigation of the Cmm-tomato interaction was performed with Multi-Dimensional Protein Identification Technology (MudPIT) and mass spectroscopy. A wide range of enzymes secreted by Cmm382, including cell-wall degrading enzymes and a large group of serine proteases from different families were identified in the xylem sap of infected tomato. Based on proteomic results, the expression pattern of selected bacterial virulence genes and plant defense genes were examined by qRT-PCR. Expression of the plasmid-borne cellulase (celA), serine protease (pat-1) and serine proteases residing on the chp/tomA pathogenicity island (chpCandppaA), were significantly induced within 96 hr after inoculation. Transcription of chromosomal genes involved in cell wall degradation (i.e., pelA1, celB, xysA and xysB) was also induced in early infection stages. The second objective was to identify by VIGS technology host genes affecting Cmm multiplication and appearance of disease symptoms in plant. VIGS screening showed that out of 160 tomato genes, which could be involved in defense-related signaling, suppression of 14 genes led to increase host susceptibility. Noteworthy are the genes Snakin-2 (inhibitor of Cmm growth) and extensin-like protein (ELP) involved in cell wall fortification. To further test the significance of Snakin -2 and ELP in resistance towards Cmm, transgenic tomato plants over-expressing the two genes were generated. These plants showed partial resistance to Cmm resulting in a significant delay of the wilt symptoms and reduction in size of canker lesion compared to control. Furthermore, colonization of the transgenic plants was significantly lower. The third objective was to assess the involvement of ethylene (ET), jasmonate (JA) and salicylic acid (SA) in Cmm infection. Microarray and proteomic studies showed the induction of enzymes involved in ET and JA biosynthesis. Cmm promoted ET production 8 days after inoculation and SIACO, a key enzyme of ET biosynthesis, was upregulated. Inoculation of the tomato mutants Never ripe (Nr) impaired in ET perception and transgenic plants with reduced ET synthesis significantly delayed wilt symptoms as compared to the wild-type plants. The retarded wilting in Nr plants was shown to be a specific effect of ET insensitivity and was not due to altered expression of defense related genes, reduced bacterial population or decrease in ethylene biosynthesis . In contrast, infection of various tomato mutants impaired in JA biosynthesis (e.g., def1, acx1) and JA insensitive mutant (jai1) yielded unequivocal results. The fourth objective was to determine the role of cell wall degrading enzymes produced by Cmm in xylem colonization and symptoms development. A significance increase (2 to 7 fold) in expression of cellulases (CelA, CelB), pectate lyases (PelA1, PelA2), polygalacturonase and xylanases (XylA, XylB) was detected by qRT-PCR and by proteomic analysis of the xylem sap. However, with the exception of CelA, whose inactivation led to reduced wilt symptoms, inactivation of any of the other cell wall degrading enzymes did not lead to reduced virulence. Results achieved emphasized the complexity involved in Cmm-tomato interactions. Nevertheless they provide the basis for additional research which will unravel the mechanism of Cmm pathogenicity and formulating disease control measures.
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