Thesis(Master)--İzmir Institute of Technology, İzmir, 2005 / Keywords: Antioxidants, antioxidant activity, tomato, genetic mapping, genetic markers. Includes bibliographical references (p.47-51)

Thesis (Ph. D.)--University of Texas at Austin, 2002. / Vita. Includes bibliographical references. Available also from UMI Company.

Meeting future demands of food security will require enhanced rice production that is more environmentally sustainable. To achieve this it is important to know the genetic and molecular mechanism controlling the root traits. High throughput phenotyping which can keep pace with genotyping is needed, but for many researchers this needs to be cheap as well as meaningful. Here a very simple, low cost and reliable method of assessing root depth of seedling using a layer of diuron-soaked filter paper buried 25 cm deep in a soil-filled box has been developed which is suitable for screening of hundreds of accessions. The assumption is that deep-rooting plants die quicker. This method was then used to screen five established rice panels. Deep rooted cultivars were screened from a panel of an aus panel from IRRI and a panel of Brazilian and Japanese cultivars by using this method. Root QTLs were detected by using bi-parental mapping population and GWA study was performed in two panels, the rice diversity panel (RDP-1) and Bengal Assam Association Population. Assessing 139 RILs from Bala x Azucena bi-parental population revealed heritability of 55% for herbicide symptoms where eleven QTLs were detected, many of which were co-localised with previously reported root QTLs in this population. A GWA study was performed using RDP1) of 356 accessions with 44k SNP markers. Analysis revealed 17% of phenotypic variation of herbicide score was attributable to rice sub-population where the aus showed the deepest rooting systems. A number of QTLs have been identified and a number of positional candidate gene lists were produced. A further 298 cultivars from Bengal and Assam were screened and GWA was performed using 2 M SNP database available from sequencing. ANOVA revealed 37% variation for herbicide score explained by genotype. Soil-filled rhizotron were used to assess 12 of these cultivars, revealing strong xx correlations between deep root traits and herbicide score, confirming the reliability of this method. GWA revealed a number of significant SNPs associated with the traits in this population. Finally a set of mutant gene (LOC_Os09g31478, LOC_Os05g40330, LOC_Os11g34140) which are functional candidate gene for root growth QTLs were studied. Here hydroponic phenotypic screening approach were used to identify the T-DNA mutant lines. However, no convincing mutants were revealed. The herbicide screening method has been shown to be a quick and robust system for the assessment of deep rooting rice plants in soil. This method can now be used for screening large number of cultivars and the identification of QTLs and candidate genes.

In this thesis, we classified user comments posted on online forums related to “Newborn Genome Sequencing” (NGS). User comments were annotated as irrelevant, positive, negative, or mixed by two annotators. The objective was to create a classification model that could predict the sentiment of each user comment with a high accuracy. To compare classifiers, a baseline classifier (Accuracy 52%) was created. We created a single classifier (called flat comment-level classifier with accuracy of 65.14%) to classify comments into irrelevant, positive, negative, or mixed. A more sophisticated classifier, named two-level comment classifier, consisting of two classifiers, was created (Accuracy 69.81%): - The first classifier that classified each comment into relevant or irrelevant ones. - The second classifier that classified each relevant comment (predicted by the first classifier) as positive, negative, or mixed. 18 extra features were generated to improve the accuracy of the flat classification compared to baseline classifier (from 52% to 65.14% for flat comment classification, and 69.48% to 69.81% for two-level comment classification). Attempts were made to enhance the result of the two-level comment classifier by using the discourse structure of each sentence in a comment. The accuracy achieved by this enhanced two-level classifier was 64.24%. Therefore, removing irrelevant EDUs did not improve the accuracy. To achieve the above-mentioned enhancement, all comments were segmented into their consisting elementary discourse units (EDUs). We removed irrelevant EDUs from the relevant comments before running the second classifier. Furthermore, we performed EDU-level classification by creating two classifiers: - A flat classifier: classified all EDUs into irrelevant, positive, negative, or neutral - A two-level EDU: classified EDUs, first, into relevant or irrelevant and then classified the relevant EDUs (predicted by the first classifier) into positive, negative, or neutral ones. The accuracy achieved for the flat EDU-level classifier was 81.84%. However, due to the highly imbalanced nature of the EDU dataset, the F-measure for positive, negative, and neutral class was very low. Under-sampling was performed to improve the F-measure for positive, negative, and neutral class. Another topic investigated was to know why forum users supported or rejected NGS. To extract the arguments, the comments were segmented into EDUs. Following segmenting, each EDU was annotated as relevant or irrelevant to NGS. Each relevant EDU was annotated as for or against NGS. Topic related EDUs were selected as well as two EDUs before and after the topic-related EDUs. Bigrams, trigrams, four-grams and five-grams were created from extracted EDUs. Five-grams were more meaningful for human annotators, and were therefore favoured and ranked based on frequency in the dataset. Following ranking of the five grams, the top five were selected as the possible arguments.

Most species of freshwater cyclopoid copepods follow a conventional course of DNA replication during gametogenesis, but certain species regularly undergo chromatin diminution during early embryogenesis, a process that is accompanied by the exclusion of large amounts of heterochromatic DNA from progenitor somatic cells and selective retention of this DNA by primordial germ cells after their segregation from the soma. We have used scanning microdensitometry and image analysis cytometry of individual Feulgen-stained nuclei to determine the DNA levels of individual somatic cell nuclei, oocytes, spermatocytes, and sperm for seven species, including Acanthocyclops brevispinosus, Acanthocyclops vernalis, Ectocyclops phaleratus, Eucyclops agilis, Eucyclops ensifer, Macrocyclops albidus, and Thermocyclops decipiens. The oocyte nuclei of these species have twice the DNA content of their diploid somatic cell nuclei. In specimens of Cyclops strenuus, Mesocyclops edax, Mesocyclops longisetus, Mesocyclops longisetus curvatus, and Metacyclops mendocinus, marked increases in DNA levels were noted in both female and male germ cells before meiosis. The appearance of enlarged nuclei with densely stained chromocenters is a distinguishing feature of oocytes and spermatocytes of cyclopoid species that exhibit excessive accumulations of DNA during gametogenesis and subsequently undergo chromatin diminution. The net increase in DNA content of the prediminution nuclei is 6-10 times the DNA level of their somatic cell nuclei and is largely attributable to increases in the amount of DNA associated with their heterochromatic chromocenters. The identification of a morphologically distinctive type of germ cell and its dramatic accumulation of large amounts of DNA before meiosis are discussed in terms of the selective elimination of heterochromatin during early cleavage stages in these cyclopoid species.

Submitted to the faculty of the informatics Graduate Program in partial fulfillment of the requirements for the degree Master of Science in Bioinformatics in the School of Informatics, Indiana University, May 2006 / The publication of the draft human genome consisting of 30,000 genes is merely the beginning of genome biology. A new way to understand the complexity and richness of molecular and cellular function of proteins in biological processes is through understanding of biological networks. These networks include protein-protein interaction networks, gene regulatory networks, and metabolic networks. In this thesis, we focus on human protein-protein interaction networks using informatics techniques. First, we performed a thorough literature survey to document different experimental methods to detect and collect protein interactions, current public databases that store these interactions, computational software to predict, validate and interpret protein networks. Then, we developed the Human Annotated Protein-Protein Interaction (HAPPI) database to manage a wealth of integrated information related to protein functions, protein-protein functional links, and protein-protein interactions. Approximately 12900 proteins from Swissprot, 57900 proteins from Trembl, 52186 protein-domains from Swisspfam, 4084 gene-pathways from KEGG, 2403190 interactions from STRING and 51207 interactions from OPHID public databases were integrated into a single relational database platform using Oracle 10g on an IU Supercomputing grid. We further assigned a confidence score to each protein interaction pair to help assess the quality and reliability of protein-protein interaction. We hosted the database on the Discovery Informatics and Computing web site, which is now publicly accessible. HAPPI database differs from other protein interaction databases in these following aspects: 1) It focuses on human protein interactions and contains approximately 860000 high-confidence protein interaction records—one of the most complete and reliable sources of human protein interaction today; 2) It includes thorough protein domain, gene and pathway information of interacting proteins, therefore providing a whole view of protein functional information; 3) It contains a consistent ranking score that can be used to gauge the confidence of protein interactions. To show the benefits of HAPPI database, we performed a case study using Insulin Signaling pathway in collaboration with a biology team on campus. We began by taking two sets of proteins that were previously well studied as separate processes, set A and set B. We queried these proteins against the HAPPI database, and derived high-confidence protein interaction data sets annotated with known KEGG pathways. We then organized these protein interactions on a network diagram. The end result shows many novel hub proteins that connect set A or B proteins. Some hub proteins are even novel members outside of any annotated pathway, making them interesting targets to validate for subsequent biological studies.

京都大学 / 0048 / 新制・課程博士 / 博士(医学) / 甲第18897号 / 医博第4008号 / 新制||医||1009(附属図書館) / 31848 / 京都大学大学院医学研究科医学専攻 / (主査)教授 松岡 雅雄, 教授 朝長 啓造, 教授 竹内 理 / 学位規則第4条第1項該当 / Doctor of Medical Science / Kyoto University / DFAM

<p>This thesis details a study of saprophytic competence in the Gram-negative bacterium Sinorhizobium meliloti, and comprises three main areas of research. The B-ketoadipate pathway is required for the catabolism of a wide range of aromatic compounds that are released into soil through the degradation of lignin. We demonstrate that S. meliloti encodes enzymes associated with the protocatechuate branch of the B-ketoadipate pathway within two operons (pcaDCHGB and pcaIJF) whose expression is regulated by the LysR-protein PcaQ and the IclR-type regulator PcaR, respectively. We show that purified PcaQ recognizes a motif with partial dyad symmetry (5' ATAACCN4-GGTTAA 3') positioned upstream of the pcaD promoter, and that this site is required for the regulated expression of pcaD in vivo. We report that PcaQ also regulates the expression of a protocatechuate-inducible ABC-type transport system that we infer is involved in the uptake of this aromatic acid, and we extend this analysis to identify PcaQbinding motifs in the genomes of a-,B-, and y-proteobacteria. </p> <p>In addition to protocatechuate, S. meliloti may utilize hydroxyproline as an energy source, as this amino acid is released into soil during the natural decay of plant tissue. We demonstrate that S. meliloti encodes a hydroxyproline-inducible ABC-type transport system that mediates the uptake of trans-4-hydrox-L-proline, as determined via growth and transport assays. </p> <p>As a more comprehensive method of examining saprophytic competence, we assayed the growth of S. meliloti upon inoculation into sterile bulk soil. We screened 40 S. meliloti strains carrying deletions within the pSymA or pSymB megaplasmids for growth in soil, and report that the majority of strains establish a stable population (greater than or equal to 10^8 cells g^(-1) soil) that persists for several weeks. In contrast, two S. meliloti strains exhibited a decreased ability to colonize soil, indicating that loci within the deleted regions play a role in saprophytic competence. </p> / Thesis / Doctor of Philosophy (PhD)

<p> In the past two decades or so. microsatellites have become a very widely used genetic tool in many disciplines of biology. Their major downfalL however. is that they often need to be isolated de novo before they can be applied to molecular studies. Traditional shotgun cloning can be successfuL but it is often overly costly and time consuming. Compounding this downfall, isolating microsatellites from some taxa has been shown to be difficult. For example. on average only 0.46% of all clones screened using avian genomes will yield positive clones. This is thought to be a result of a smaller avian genome, a requirement for flight. Several alternative methods have been developed for isolating microsatellites, but the choice as to which isolation method to use is often arbitrary. To address this. four species of birds. the smooth-billed ani (Crotophaga ani). herring gull (Larus argentatus), yellow-bellied elaenia (Elaenia flavogaster), and pukeko (Porphyria porphyria), representing four different orders were used to compare two alternative isolation methods. Enrichment via selective hybridization versus cloning with Lambda Zap phage vector were compared in terms of monetary requirements (total startup cost as well as per isolation attempt cost). and time requirements (total time from start to finish and hands-on experimentation time). No significant difference was detected in terms of number of polymorphic microsatellite loci isolated by each method (p = 0.57), with enrichment yielding more for the anis and elaenias, Lambda Zap yielding more for herring gulls. and both methods isolating equal numbers for pukekos. Nor was any difference found between the methods for dollars spent per sequence with repeat (SWR) using the startup cost (p = 0.30). Enrichment. however. proved to be significantly more effective in terms of dollars per SWR isolated using the per use cost (p = 0.004) as well as hands-on minutes per SWR (p = 0.01) and total minutes per SWR (p < 0.01 ). Based on these tindings. selective hybridization is the better choice for microsatellite isolation. </p> / Thesis / Master of Science (MSc)

The adenovirus genome is a linear double stranded DNA molecule and the current widely accepted model of viral DNA replication proposes linear viral DNA intermediates at all stages of replication. Although the experimental evidence for this mechanism of replication is very strong, circular forms of adenovirus serotype 5 (Ad5) DNA molecules have also been detected in both permissive and non-permissive cell lines. In some experiments the circular structures were detected before the onset of viral DNA replication and thus suggested a possible role for circular forms of Ad5 DNA in the life cycle of the virus after infection. This study was undertaken to better understand the role of circular forms of the adenovirus genome in virus replication. The approach was to subclone the viral junction internally into the linear genome thus creating mutant viruses with embedded terminal sequences and to study the effect of such inserts on DNA structure. A total of five mutant viruses were constructed containing a variety of inserts and viral DNA from infected cells and banded viruses was analyzed by Southern Blot hybridization. The data clearly showed that embedded viral junctions have biological activity in that they generated novel, rear ranged viral DNA molecules, and that embedded single ITR sequences were also biologically active, but to a lesser extent. It was also observed that the copy numbers of the rearranged molecules were variable. It appeared that the embedded viral junction was active in recombination and replication of the viral genome, creating the rearrangements through these two processes. However, the results suggested that circular forms are not obligatory intermediates in DNA replication. The analysis of banded viral DNA in this study suggested that the encapsidation signal from the left end of the linear genome was required in cis for packaging of the viral genome, confirming previous results which identified an encapsidation signal for viral DNA packaging. The banding experiments also showed that truncated viral DNA molecules containing 75% of the viral genome were packaged. / Thesis / Master of Science (MS)