Data Mining Techniques for Predicting Real Estate Trends

A wide variety of businesses and government agencies support the U.S. real estate market. Examples would include sales agents, national lenders, local credit unions, private mortgage and title insurers, and government sponsored entities (Freddie Mac and Fannie Mae), to name a few. The financial performance and overall success of these organizations depends in large part on the health of the overall real estate market. According to the National Association of Home Builders (NAHB), the construction of one single-family home of average size creates the equivalent of nearly 3 new jobs for a year (Greiner, 2015). The economic impact is significant, with residential construction and related activities contributing approximately 5 percent to overall gross domestic product. With these data points in mind, the ability to accurately predict housing trends has become an increasingly important function for organizations engaged in the real estate market. The government bailouts of Freddie Mac and Fannie Mae in July 2008, following the severe housing market collapse which began earlier that year, serve as an example of the risks associated with the housing market. The housing market collapse had left the two firms, which at the time owned or guaranteed about $5 trillion of home loans, in a dangerous and uncertain financial state (Olick, 2018). Countrywide Home Loans, Indy Mac, and Washington Mutual Bank are a few examples of mortgage banks that did not survive the housing market collapse and subsequent recession. In the wake of the financial crisis, businesses within the real estate market have recognized that predicting the direction of real estate is an essential business requirement. A business acquisition by Radian Group, the Philadelphia-based mortgage insurance company, illustrates the importance of predictive modeling for the mortgage industry. In January 2019, Radian Group acquired Five Bridges Advisors, a Maryland-based firm which develops data analytics and econometric predictive models leveraging artificial intelligence and machine learning techniques (Blumenthal, 2019)

The Extended and Eccentric E-DNA Structure Induced by Cytosine Methylation or Bromination

Cytosine methylation or bromination of the DNA sequence d(GGCGCC)2 is shown here to induce a novel extended and eccentric double helix, which we call E-DNA. Like B-DNA, E-DNA has a long helical rise and bases perpendicular to the helix axis. However, the 3′-endo sugar conformation gives the characteristic deep major groove and shallow minor groove of A-DNA. Also, if allowed to crystallize for a period of time longer than that yielding E-DNA, the methylated sequence forms standard A-DNA, suggesting that E-DNA is a kinetically trapped intermediate in the transition to A-DNA. Thus, the structures presented here chart a crystallographic pathway from B-DNA to A-DNA through the E-DNA intermediate in a single sequence. The E-DNA surface is highly accessible to solvent, with waters in the major groove sitting on exposed faces of the stacked nucleotides. We suggest that the geometry of the waters and the stacked base pairs would promote the spontaneous deamination of 5-methylcytosine in the transition mutation of dm5C-dG to dT-dA base pairs

A Crystallographic Map of the Transition from B-DNA to A-DNA

The transition between B- and A-DNA was first observed nearly 50 years ago. We have now mapped this transformation through a set of single-crystal structures of the sequence d(GGCGCC)(2), with various intermediates being trapped by methylating or brominating the cytosine bases. The resulting pathway progresses through 13 conformational steps, with a composite structure that pairs A-nucleotides with complementary B-nucleotides serving as a distinct transition intermediate. The details of each step in the conversion of B- to A-DNA are thus revealed at the atomic level, placing intermediates for this and other sequences in the context of a common pathway

Identification and RNA Binding Characterization of Plant Virus RNA Silencing Suppressor Proteins

Suppression is a common mechanism employed by viruses to evade the antiviral effects of the host’s RNA silencing pathway. The activity of suppression has commonly been localized to gene products in the virus, but the variety of mechanisms used in suppression by these viral proteins spans nearly the complete biochemical pathway of RNA silencing in the host. This review describes the agrofiltration assay and a slightly modified version of the agro-infiltration assay called co-infiltration, which are common methods used to observe RNA silencing and identify viral silencing suppressor proteins in plants, respectively. In addition, this review will provide an overview of two methods, electrophoretic mobility shift assay and fluorescence polarization, used to assess the binding of a suppressor protein to siRNA which has been shown to be a general mechanism to suppress RNA silencing by plant viruses

Effect of Sequence on the Conformation of DNA Holliday Junctions

Structures of the DNA sequences d(CCGGCGCCGG) and d(CCAGTACbr5UGG) are presented here as four-way Holliday junctions in their compact stacked-X forms, with antiparallel alignment of the DNA strands. Thus, the ACC-trinucleotide motif, previously identified as important for stabilizing the junction, is now extended to PuCPy, where Pu is either an adenine or guanine, and Py is either a cytosine, 5-methylcytosine, or 5-bromouracil but not thymine nucleotide. We see that both sequence and base substituents affect the geometry of the junction in terms of the interduplex angle as well as the previously defined conformational variables, Jroll (the rotation of the stacked duplexes about their respective helical axis) and Jslide (the translational displacement of the stacked duplexes along their respective helical axis). The structures of the GCC and parent ACC containing junctions fall into a distinct conformational class that is relatively undistorted in terms of Jslide and Jroll, with interduplex angles of 40-43°. The substituted ACbr5U structure, however, is more akin to that of the distorted methylated ACm5C containing junction, with Jslide (g2.3 Å) and a similar Jroll (164°) opening the major groove-side of the junction, but shows a reduced interduplex angle. In contrast, the analogous d(CCAGTACTGG) sequence has to date been crystallized only as resolved B-DNA duplexes. This suggests that there is an electronic effect of substituents at the pyrimidine Py position on the stability of four-stranded junctions. The single-crystal structures presented here, therefore, show how sequence affects the detailed geometry, and subsequently, the associated stability and conformational dynamics of the Holliday junction

Delivery Strategies for Live Therapeutic Microbes

Humans are hosts for trillions of microbes that comprise distinct microbiomes across the human body and are implicated in a wide range of disease states. Live bacteria can be used as therapeutics to mediate these microbiome-related diseases, acting as self-sustaining drug factories in the body. These living biological products (LBPs) have shown potential in clinical trials for chronic inflammatory conditions, pathogen infections, autoimmune disorders and beyond, but their delivery remains a challenge. Many LBPs suffer from high interpatient variability, low viability after delivery, and poor persistence at target sites, contributing to translational failures. In this dissertation, I present two methods for improving the attachment of LBPs to target sites on the human body, providing strategies to improve the persistence and delivery of LBPs after topical or oral administration. Inspired by bacterial adhesins that facilitate bacterial attachment and colonization, NHS ester chemistry was used to conjugate targeting ligands to LBP surfaces to act as “synthetic adhesins” (SAs). In the first method, SAs with affinity for endogenous biological targets were conjugated to the LBP surface, significantly improving LBP attachment to abiotic surfaces, live mammalian cells, and in vivo intestinal targets. During in vivo studies, SAs targeted to the intestinal mucosa enabled rapid LBP colonization and a 20% improvement in total LBP exposure compared to the unmodified control. In the second method, non-native targets that undergo a highly selective reaction with modified LBPs were introduced to topical sites, enabling specificity of LBP attachment on the skin even in the absence of a defined biological target. Unlike previous strategies to improve LBP attachment, the platform described in this dissertation does not rely on genetic engineering, providing greater flexibility over the SA selection and complete compatibility across the wide range of LBP species. Collectively, this dissertation represents the first non-genetic platform for controlling the adhesion, colonization, and efficacy of LBPs.Doctor of Philosoph

Intrinsically Bent DNA in the Promoter Regions of the Yeast GAL1–10 and GAL80 Genes

Circular permutation analysis has detected fairly strong sites of intrinsic DNA bending on the promoter regions of the yeast GAL1–10 and GAL80 genes. These bends lie in functionally suggestive locations. On the promoter of the GAL1–10 structural genes, strong bends bracket nucleosome B, which lies between the UASG and the GAL1 TATA. These intrinsic bends could help position nucleosome B. Nucleosome B plus two other promoter nucleosomes protect the TATA and start site elements in the inactive state of expression but are completely disrupted (removed) when GAL1–10 expression is induced. The strongest intrinsic bend (;70°) lies at the downstream edge of nucleosome B; this places it approximately 30 base pairs upstream of the GAL1 TATA, a position that could allow it to be involved in GAL1 activation in several ways, including the recruitment of a yeast HMG protein that is required for the normally robust level of GAL1 expression in the induced state (Paull, T., Carey, M., and Johnson, R. (1996) Genes Dev. 10, 2769–2781). On the regulatory gene GAL80, the single bend lies in the non-nucleosomal hypersensitive region, between a GAL80-specific far upstream promoter element and the more gene-proximal promoter elements. GAL80 promoter region nucleosomes contain no intrinsically bent DNA

Size Selective Recognition of siRNA by an RNA Silencing Suppressor

RNA silencing in plants likely exists as a defense mechanism against molecular parasites such as RNA viruses, retrotransposons, and transgenes. As a result, many plant viruses have adapted mechanisms to evade and suppress gene silencing. Tombusviruses express a 19 kDa protein (p19), which has been shown to suppress RNA silencing in vivo and bind silencing-generated and synthetic small interferingRNAs (siRNAs) in vitro. Here we report the 2.5 A° crystal structure of p19 from the Carnation Italian ringspot virus (CIRV) bound to a 21 nt siRNA and demonstrate in biochemical and in vivo assays that CIRV p19 protein acts as molecular caliper to specifically select siRNAs based on the length of the duplex region of the RNA

The Holliday Junction in an Inverted Repeat DNA Sequence: Sequence Effects on the Structure of Four-way Junctions

Holliday junctions are important structural intermediates in recombination, viral integration, and DNA repair. We present here the single-crystal structure of the inverted repeat sequence d(CCGGTACCGG) as a Holliday junction at the nominal resolution of 2.1 Å. Unlike the previous crystal structures, this DNA junction has B-DNA arms with all standard Watson–Crick base pairs; it therefore represents the intermediate proposed by Holliday as being involved in homologous recombination. The junction is in the stacked-X conformation, with two interconnected duplexes formed by coaxially stacked arms, and is crossed at an angle of 41.4° as a right-handed X. A sequence comparison with previous B-DNA and junction crystal structures shows that an ACC trinucleotide forms the core of a stable junction in this system. The 3*-CzG base pair of this ACC core forms direct and water-mediated hydrogen bonds to the phosphates at the crossover strands. Interactions within this core define the conformation of the Holliday junction, including the angle relating the stacked duplexes and how the base pairs are stacked in the stable form of the junction