Doctor of Philosophy

dissertationSpontaneous preterm birth (SPTB) is defined as birth before 37 completed weeks gestation that is not secondary to iatrogenic intervention. SPTB is both a pressing personal and public health issue that is not well understood. Previous studies have shown genetics as an important factor to SPTB. Here I present my PhD work on genetic analyses of SPTB. I dissected the problem with: (1) candidate gene, (2) quantitative genetics, and (3) genome-wide approaches. In Chapter 1, I explore why published candidate gene studies are inconsistent with each other. Allele frequency difference across populations provides one reason. I conducted a meta-analysis on the single nucleotide polymorphism (SNP) rs1800795, located in the promoter region of interleukin-6. With population stratification, I unmasked the signal showing that the CC genotype is protective against PTB in women of European descent. This also highlights how positive genetic signals can become obscured when the population structure is not controlled for. In Chapter 2, I use quantitative genetic approaches to decompose the etiologies of SPTB with massive data from the Utah Population Database. A generation effect, which confounds the heritability estimate, was discovered. I then utilized a sibling analysis and partitioned components contributing to the phenotypic variance of SPTB: iv heritability (13.33%), dominance genetic (11.12%), maternal effect (15.23%), and individual environment (60.33%). These findings shed light on the architecture of SPTB pathogenesis and quantify the maternal and fetal contribution to SPTB. In Chapter 3, I perform an unbiased genome-wide association study for SPTB on 22 autosomal chromosomes. The data, which contain cases and controls collected by the Danish National Birth Cohort, were acquired from the National Center for Biotechnology Information Genotypes and Phenotypes Database. No SNP reached genome-wide significance. Although negative, the result provides proof of principle regarding the relatively low heritability of SPTB. Finally, I address insights learned from these analyses that may help guide future SPTB research and may be applicable to other human genetic studies. With these lessons, progress can be made in understanding the genetics of SPTB

IT personnel sourcing decisions in IT projects.

The evolutionary growth of information technology, during the past few decades, has created the impetus for change in the organizational workplace from a focus on narrow and specific tasks, carried out by individuals, to a focus on collective efforts reflected through IT project teams (Nonaka 2001). With the increased abundance of IT project teams operating within and between organizations in the current business environment (Bolan 2001; Abdel-Hamid 1992 and 1989), a number of academic studies have focused on identifying the critical success factors for effective IT project success. Researchers in IT project management have pointed to the importance of IT personnel sourcing as a critical success factor (e.g. Nonaka 2001; Bolan 2001; Abdel-Hamid 1992).The issue of appropriate project IT personnel sourcing decisions has gained recognition as one of the core factors behind effective software project management (Agarwal & Feratt 2002, and Abdel-Hamid 1989). Some studies have in fact shown that the utilization of appropriate sourcing decisions does increase the likelihood of completing IT projects on time (Abdel-Hamid 1992) and within budget (Bolan 2001). While highlighting the importance of appropriate IT project sourcing as a key component for successful IT project management, these studies highlight a need for understanding how IT project personnel sourcing is determined. The purpose of this research study is to take an initial step towards understanding the "how" of project IT personnel sourcing decisions by developing and testing an IT personnel sourcing model for IT projects, based on theoretical and grounded perspectives

Maize tricin-oligolignol metabolites and their implications for monocot lignification

Lignin is an abundant aromatic plant cell wall polymer consisting of phenylpropanoid units in which the aromatic rings display various degrees of methoxylation. Tricin [5,7-dihydroxy-2-(4-hydroxy-3,5-dimethoxyphenyl)-4H-chromen-4-one], a flavone, was recently established as a true monomer in grass lignins. To elucidate the incorporation pathways of tricin into grass lignin, the metabolites of maize (Zea mays) were extracted from lignifying tissues and profiled using the recently developed 'candidate substrate product pair' algorithm applied to ultra-high-performance liquid chromatography and Fourier transform-ion cyclotron resonance-mass spectrometry. Twelve tricin-containing products (each with up to eight isomers), including those derived from the various monolignol acetate and p-coumarate conjugates, were observed and authenticated by comparisons with a set of synthetic tricin-oligolignol dimeric and trimeric compounds. The identification of such compounds helps establish that tricin is an important monomer in the lignification of monocots, acting as a nucleation site for starting lignin chains. The array of tricin-containing products provides further evidence for the combinatorial coupling model of general lignification and supports evolving paradigms for the unique nature of lignification in monocots

Mechanism of glycan receptor recognition and specificity switch for avian, swine, and human adapted influenza virus hemagglutinins: a molecular dynamics perspective.

Hemagglutinins (HA's) from duck, swine, and human influenza viruses have previously been shown to prefer avian and human glycan receptor analogues with distinct topological profiles, pentasaccharides LSTa (alpha-2,3 linkage) and LSTc (alpha-2,6 linkage), in comparative molecular dynamics studies. On the basis of detailed analyses of the dynamic motions of the receptor binding domains (RBDs) and interaction energy profiles with individual glycan residues, we have identified approximately 30 residue positions in the RBD that present distinct profiles with the receptor analogues. Glycan binding constrained the conformational space sampling by the HA. Electrostatic steering appeared to play a key role in glycan binding specificity. The complex dynamic behaviors of the major SSE and trimeric interfaces with or without bound glycans suggested that networks of interactions might account for species specificity in these low affinity and high avidity (multivalent) interactions between different HA and glycans. Contact frequency, energetic decomposition, and H-bond analyses revealed species-specific differences in HA-glycan interaction profiles, not readily discernible from crystal structures alone. Interaction energy profiles indicated that mutation events at the set of residues such as 145, 156, 158, and 222 would favor human or avian receptor analogues, often through interactions with distal asialo-residues. These results correlate well with existing experimental evidence, and suggest new opportunities for simulation-based vaccine and drug development

Versatile microbial surface-display for environmental remediation and biofuels production

Surface display is a powerful technique that utilizes natural microbial functional components to express proteins or peptides on the cell exterior. Since the reporting of the first surface-display system in the mid-1980s, a variety of new systems have been reported for yeast, Gram-positive and Gram-negative bacteria. Non-conventional display methods are emerging, eliminating the generation of genetically modified microorganisms. Cells with surface display are used as biocatalysts, biosorbents and biostimulants. Microbial cell-surface display has proven to be extremely important for numerous applications ranging from combinatorial library screening and protein engineering to bioremediation and biofuels production

Investigation into the mechanism of action of the antimicrobial peptide epilancin 15X

Addressing the current antibiotic-resistance challenge would be aided by the identification of compounds with novel mechanisms of action. Epilancin 15X, a lantibiotic produced by Staphylococcus epidermidis 15 × 154, displays antimicrobial activity in the submicromolar range against a subset of pathogenic Gram-positive bacteria. S. epidermidis is a common member of the human skin or mucosal microbiota. We here investigated the mechanism of action of epilancin 15X. The compound is bactericidal against Staphylococcus carnosus as well as Bacillus subtilis and appears to kill these bacteria by membrane disruption. Structure–activity relationship studies using engineered analogs show that its conserved positively charged residues and dehydroamino acids are important for bioactivity, but the N-terminal lactyl group is tolerant of changes. Epilancin 15X treatment negatively affects fatty acid synthesis, RNA translation, and DNA replication and transcription without affecting cell wall biosynthesis. The compound appears localized to the surface of bacteria and is most potent in disrupting the membranes of liposomes composed of negatively charged membrane lipids in a lipid II independent manner. Epilancin 15X does not elicit a LiaRS response in B. subtilis but did upregulate VraRS in S. carnosus. Treatment of S. carnosus or B. subtilis with epilancin 15X resulted in an aggregation phenotype in microscopy experiments. Collectively these studies provide new information on epilancin 15X activity

Germline Mutations in NFKB2 Implicate the Noncanonical NF-κB Pathway in the Pathogenesis of Common Variable Immunodeficiency

Common variable immunodeficiency (CVID) is a heterogeneous disorder characterized by antibody deficiency, poor humoral response to antigens, and recurrent infections. To investigate the molecular cause of CVID, we carried out exome sequence analysis of a family diagnosed with CVID and identified a heterozygous frameshift mutation, c.2564delA (p.Lys855Serfs∗7), in NFKB2 affecting the C terminus of NF-κB2 (also known as p100/p52 or p100/p49). Subsequent screening of NFKB2 in 33 unrelated CVID-affected individuals uncovered a second heterozygous nonsense mutation, c.2557C>T (p.Arg853∗), in one simplex case. Affected individuals in both families presented with an unusual combination of childhood-onset hypogammaglobulinemia with recurrent infections, autoimmune features, and adrenal insufficiency. NF-κB2 is the principal protein involved in the noncanonical NF-κB pathway, is evolutionarily conserved, and functions in peripheral lymphoid organ development, B cell development, and antibody production. In addition, Nfkb2 mouse models demonstrate a CVID-like phenotype with hypogammaglobulinemia and poor humoral response to antigens. Immunoblot analysis and immunofluorescence microscopy of transformed B cells from affected individuals show that the NFKB2 mutations affect phosphorylation and proteasomal processing of p100 and, ultimately, p52 nuclear translocation. These findings describe germline mutations in NFKB2 and establish the noncanonical NF-κB signaling pathway as a genetic etiology for this primary immunodeficiency syndrome

Differential Regulation of the PGC Family of Genes in a Mouse Model of Staphylococcus aureus Sepsis

The PGC family of transcriptional co-activators (PGC-1α [Ppargc1a], PGC-1β [Ppargc1b], and PRC [Pprc]) coordinates the upregulation of mitochondrial biogenesis, and Ppargc1a is known to be activated in response to mitochondrial damage in sepsis. Therefore, we postulated that the PGC family is regulated by the innate immune system. We investigated whether mitochondrial biogenesis and PGC gene expression are disrupted in an established model of Staphylococcus aureus sepsis both in mice with impaired innate immune function (TLR2−/− and TLR4−/−) and in wild-type controls. We found an early up-regulation of Ppargc1a and Ppargc1b post-infection (at 6 h) in WT mice, but the expression of both genes was concordantly dysregulated in TLR2−/− mice (no increase at 6 h) and in TLR4−/− mice (amplified at 6 h). However, the third family member, PRC, was regulated differently, and its expression increased significantly at 24 h in all three mouse strains (WT, TLR2−/−, and TLR4−/−). In silico analyses showed that Ppargc1a and Ppargc1b share binding sites for microRNA mmu-mir-202-3p. Thus, miRNA-mediated post-transcriptional mRNA degradation could account for the failure to increase the expression of both genes in TLR2−/− mice. The expression of mmu-mir-202-3p was measured by real-time PCR and found to be significantly increased in TLR2−/− but not in WT or TLR4−/− mice. In addition, it was found that mir-202-3p functionally decreases Ppargc1a mRNA in vitro. Thus, both innate immune signaling through the TLRs and mir-202-3p-mediated mRNA degradation are implicated in the co-regulation of Ppargc1a and Ppargc1b during inflammation. Moreover, the identification of mir-202-3p as a potential factor for Ppargc1a and Ppargc1b repression in acute inflammation may open new avenues for mitochondrial research and, potentially, therapy