Thesis (Ph. D.) -- California Institute of Technology, 2010. / Title from home page (viewed 03/05/2010). Advisor and committee chair names found in the thesis' metadata record in the digital repository. Includes bibliographical references.

Thesis (M.S. in Biomedical Informatics)--Vanderbilt University, Aug. 2007. / Title from title screen. Includes bibliographical references.

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Lens culinaris, the common lentil, contains a lectin which has been shown to be specific for a glycoprotein saliva antigen and a glycolipoprotein serum antigen. Both the saliva and serum precipitin reactions with the lectin are directly inhibited with saccharides, especially those related to D-mannose. Electrophoresis of the serum antigen showed that it migrates as three bands, while appearing as a single band in double diffusion precipitin patterns. Quantitative studies of the saliva antigen levels by hemagglutination inhibition titration indicated a polygenic, quantitative mode of inheritance with a minimum heritability of O. 34. Blood group ABH secretor individuals were found to have a significantly lower mean saliva antigen level than nonsecretor individuals. The lectins from Pisum sativum and Canavaliafiensiformis formed precipitin bands of identity with L.culinaris lectin against saliva. C. ensiformis and L. culinaris lectins exhibited precipitin bands of partial identity against serum; and P. sativum and L. culinaris lectins exhibited a pattern of identity against serum. In addition, precipitin patterns of partial identity with the non-H lectin from Lotus tetragonolobus has been demonstrated. Using Ulex europaeus lectin in hemagglutination inhibition experiments with saliva from blood group O secretor individuals, a minimum heritability of approximately 0.40 for H antigen levels was found. A higher frequency of nonsecretor individuals was observed in the Black population compared with the White population.

Thesis advisor: Gabor T. Marth / Rapid advances in genome sequencing enable a wide range of biological experiments on a scale that was until recently restricted to large genome centers. However, the analysis of the resulting vast genomic datasets is time-consuming, unintuitive and requires considerable computational expertise and costly infrastructure. Collectively, these factors effectively exclude many bench biologists from genome-scale analyses. Web-based visualization and analysis libraries, frameworks, and applications were developed to empower all biological researchers to easily, interactively, and in a visually driven manner, analyze large biomedical datasets that are essential for their research, without bioinformatics expertise and costly hardware. / Thesis (PhD) — Boston College, 2014. / Submitted to: Boston College. Graduate School of Arts and Sciences. / Discipline: Biology.

Thesis (Ph.D.)--Boston University / PLEASE NOTE: Boston University Libraries did not receive an Authorization To Manage form for this thesis or dissertation. It is therefore not openly accessible, though it may be available by request. If you are the author or principal advisor of this work and would like to request open access for it, please contact us at open-help@bu.edu. Thank you. / MspJI is a novel modification-dependent restriction endonuclease that specifically recognizes cytosine C5 modification (methylation or hydroxymethylation) in DNA and cleaves at a constant distance (N12/N16) away from the modified cytosine site. The biochemical characterization of MspJI and several homologs, including FspEI, LpnPI, AspBHI, RiaI, and SgrTI is presented in this thesis. Each displays its own sequence context preference, favoring different nucleotides flanking the modified cytosine. Despite the difference in the recognition sequence, the MspJI family enzymes display similarities in their other properties, such as the distance from the modified cytosine to the cleavage site, stimulation of cleavage by a short DNA oligonucleotide containing the recognition site and the ability to produce a double strand break in molecules with a single recognition site. Here, the possibility of multimerization as part of the mechanism by which these enzymes are able to display those properties is discussed. In addition, by cleaving on both sides of fully modified CpG sites, these enzymes allow the extraction of 32-base long fragments around the modified sites from the genomic DNA, providing powerful tools for direct interrogation of the epigenome. For example, Rial , an enzyme that prefers mcwG but not mCpG sites, generates digestion patterns that differ between plant and mammalian genomic DNA, highlighting the difference between their epigenomic patterns. Furthermore, deep sequencing of the digested DNA fragments generated from these enzymes provides a feasible method to map the modified sites in the genome. / 2031-01-01

Accurate and complete DNA replication is essential for maintaining the integrity of the genome. In eukaryotes, this process requires the coordinated action of numerous molecular machines. Based on yeast and animal model systems, we defined a set of fifty-one ?core DNA replication proteins? that are integral to the initiation, DNA synthesis, and Okazaki fragment maturation functions of DNA replication. We used computational analyses to identify putative homologs in the genomes of two plants, Arabidopsis thaliana (Arabidopsis) and Oryza sativa (rice), providing the first comprehensive view of the core DNA replication machinery in plants. Our results indicated that the overall composition of this apparatus is conserved, but plants are unique in that multiple DNA replication genes exist as small gene families. Fourteen of the genes we annotated in this study have not been previously reported in the literature, and we have provided revised gene models for seventeen plant proteins. To better understand how the DNA replication machinery functions in plants, we cloned multiple subunits of the pre-replication complex (pre-RC) from Arabidopsis and generated antibodies against four key components of this complex ? AtORC1, AtORC2, AtMCM5, and AtMCM7. We demonstrated that the pre-RC is developmentally regulated in Arabidopsis and, consistent with a role in DNA replication, is abundant in proliferating tissues. We used immunocytochemical and biochemical methods to characterize MCM7 in plants. We observed two distinct localization patterns for plant MCM7 proteins. In most cells, MCM7 was nuclear and colocalized with DNA. In a small fraction of cells, MCM7 was dispersed throughout the cytoplasmic compartment. Biochemical analysis confirmed that MCM7 binds to chromatin and that it is present in the nucleus at least during the G1, S and G2 cell cycle stages. Together, these analyses support a model where the MCM complex is loaded onto DNA in late M and early G1, released into the nucleoplasm during S phase followed by a brief dispersion into the cytoplasmic compartment concurrent with nuclear envelope breakdown in mitosis.

Bacteria are remarkable in their ability to adapt to environmental conditions that are continually in flux between growth-promoting and growth-limiting. Responses to a host of environmental situations are equally varied, ranging from the secretion of antimicrobial compounds and polymer degrading enzymes, to the up-regulation of alternative cellular developmental pathways leading to complete physiological transformation. In endospore forming bacteria this results in a metabolically inert, yet highly resistant endospore. The first study presented here deals with the NMR structural and dynamic characterization of a class of proteins in Bacillus subtilis known as transition-state regulators, responsible for global gene regulation during the transition from the vegetative mode of growth to the semi-quiescent stationary phase. The utilization of protein-DNA docking protocols further allows for the first description of a structural model for the interaction between these DNA-binding proteins and a cognate DNA promoter sequence. The later portions of this dissertation deal with the characterization of proteins involved in the ubiquitous bacterial signal transduction system known as the two-component signal transduction pathway. In the basic two-component signal transduction paradigm, an environmental signal is detected by a multi-domain sensor kinase that, via phosphorylation, activates a response regulator protein for its cellular role (be it DNA-binding, RNA-binding, enzymatic, etc). In the second study, a comparative modeling analysis of the predicted receiver domains the response regulators from Vibrio vulnificus YJ016 was performed, using the hydrophobic characteristics of the response regulator surface known to interact with the four-helix bundle of the cognate sensor kinase as the basis for sub-classification. In the final study, a new mass spectrometric technique to detail the structural changes in proteins resulting from oxidative damage was applied to the single domain response regulator Spo0F from B. subtilis.

Protein disulfide isomerases (PDIs) contain thioredoxin domains and aid in the formation of proper disulfide bonds during protein folding. Iterative BLAST searches of sequence databases were used to identify 22 PDI-like (PDIL) genes in Arabidopsis thaliana and maize (Zea mays) and 19 in rice (Oryza sativa). The PDIL genes were resolved into 10 phylogenetic groups. Genes in groups I-V had two active thioredoxin domains while members of groups VI-X had one active thioredoxin domain. One single domain PDIL, maize PDIL5-1, showed increased accumulation in the endosperm mutants that produced defective storage proteins, but PDIL5-1 was not localized to endomembrane fractions. Expression analysis was done in eighteen PDIL genes in maize endosperm, a storage tissue, and two vegetative organs, embryo and leaves. Eight PDIL genes were expressed mainly in endosperm, and two of these genes (PDIL1-2 and 2-3) had increased expression levels only in the endosperm that produced defective storage proteins. There were three PDIL genes (1-3, 1-4, 1-5) that showed the highest expression levels in the embryo, while two other genes, adenosine 5?-phosphosulfate reductase-like (APRL) 2 and APRL8, had elevated expression levels in leaves. To further characterize members of the gene family, isomerase and reductase assays were conducted to test for recombinant maize PDIL1-1, 1-3, 2-3 and 5-1 enzymatic activity in vitro. Recombinant and endogenous maize PDIL1-1 showed both isomerase and reductase activity while recombinant PDIL1-3 showed anti-chaperone activity. Recombinant PDIL2-3 and PDIL5-1 showed no activity under the assay conditions tested.