Methods of Making Modified Polypeptides

Novel polypeptides and the corresponding nucleic acids encoding such polypeptides are disclosed herein. The invention provides methods of making modified polypeptides by altering one or more amino acid residues involved in the active site of a preselected polypeptide

Synthases

Novel synthases and the corresponding nucleic acids encoding such synthases are disclosed herein. Such synthases possess an active site pocket that includes key amino acid residues that are modified to generate desired terpenoid reaction intermediates and products. Synthase modifications are designed based on, e.g., the three-dimensional coordinates of tobacco 5-epi-aristolochene synthase with or without a substrate bound in the active site

Automated protein NMR data analysis and its application to a-synuclein fibrils

In principle, nuclear magnetic resonance (NMR) spectroscopy provides structural and conformational information with sub-Angstrom precision and the ability to measure dynamics with timescales ranging from femtoseconds to years, all with atomic specificity. However, due to the relatively low sensitivity of NMR, fundamental limits on spectral resolution, and the complexity of the quantum mechanical phenomena NMR exploits, that wealth of information often remains out of reach. The highly varied presentation of molecular information in NMR spectra and the difficulty of numerical simulation of non-trivial systems has lead the majority of data analysis to be performed by trained experts, and because of its time-intensive nature, that analysis is rarely replicated by a third party or validated in an objective manner. In this dissertation I report my efforts to automate NMR data analysis in an objective and replicable manner and to provide tools for validation of resulting three-dimensional structures by direct comparison to raw spectral data. The first method, COMPASS, attempts to extract as much information as possible from a single 13C-13C two-dimensional spectrum for the determination of protein structure and successfully identified the true structure of 15 test proteins. The second method, GPS, predicts features of data that would be expected given a set of chemical shift assignments and possibly a three-dimensional structure and uses the presence or absence of those features in experimental spectra to refine or validate a given structure. I then report my application of these computational methods to the problems of refining an a-synuclein fibril structure with proton-detected NMR data, the analysis and characterization of a pair of interrelated a-synuclein fibril strains with distinct pathological properties, and to the general question of fibril polymorphism, a phenomenon that presents a substantial challenge to forming consistent conclusions about fibril properties and interactions across samples and research groups

Synthases

Novel synthases and the corresponding nucleic acids encoding such synthases are disclosed herein. Such synthases possess an active site pocket that includes key amino acid residues that are modified to generate desired terpenoid reaction intermediates and products. Synthase modifications are designed based on, e.g., the three-dimensional coordinates of tobacco 5-epi-aristolochene synthase. with or without a substrate bound in the active site

Genomic profiling of malignant peritoneal mesothelioma reveals recurrent alterations in epigenetic regulatory genes BAP1, SETD2, and DDX3X.

Malignant mesothelioma is a rare cancer that arises from the mesothelial cells that line the pleural cavity and less commonly from the peritoneal lining of the abdomen and pelvis. Most pleural mesotheliomas arise in patients with a history of asbestos exposure, whereas the association of peritoneal mesotheliomas with exposure to asbestos and other potential carcinogens is less clear, suggesting that the genetic alterations that drive malignant peritoneal mesothelioma may be unique from those in pleural mesothelioma. Treatment options for all malignant mesotheliomas are currently limited, with no known targeted therapies available. To better understand the molecular pathogenesis of malignant peritoneal mesothelioma, we sequenced 510 cancer-related genes in 13 patients with malignant mesothelioma arising in the peritoneal cavity. The most frequent genetic alteration was biallelic inactivation of the BAP1 gene, which occurred in 9/13 cases, with an additional two cases demonstrating monoallelic loss of BAP1. All 11 of these cases demonstrated loss of BAP1 nuclear staining by immunohistochemistry, whereas two tumors without BAP1 alteration and all 42 cases of histologic mimics in peritoneum (8 multilocular peritoneal inclusion cyst, 6 well-differentiated papillary mesothelioma of the peritoneum, 16 adenomatoid tumor, and 12 low-grade serous carcinoma of the ovary) demonstrated intact BAP1 nuclear staining. Additional recurrently mutated genes in this cohort of malignant peritoneal mesotheliomas included NF2 (3/13), SETD2 (2/13), and DDX3X (2/13). While these genes are known to be recurrently mutated in pleural mesotheliomas, the frequencies are distinct in peritoneal mesotheliomas, with nearly 85% of peritoneal tumors harboring BAP1 alterations versus only 20-30% of pleural tumors. Together, these findings demonstrate the importance of epigenetic modifiers including BAP1, SETD2, and DDX3X in mesothelial tumorigenesis and suggest opportunities for targeted therapies

Synthases

Novel synthases and the corresponding nucleic acids encoding such synthases are disclosed herein. Such synthases possess an active site pocket that includes key amino acid residues that are modified to generate desired terpenoid reaction intermediates and products. Synthase modifications are designed based on, e.g., the three-dimensional coordinates of tobacco 5-epi-aristolochene synthase, with or without a substrate bound in the active site

Synthases

Novel synthases and the corresponding nucleic acids encoding such synthases are disclosed herein. Such synthases possess an active site pocket that includes key amino acid residues that are modified to generate desired terpenoid reaction intermediates and products. Synthase modifications are designed based on, e.g., the three-dimensional coordinates of tobacco 5-epi-aristolochene synthase, with or without a substrate bound in the active site

Shifts in Species Interactions Due to the Evolution of Functional Differences between Endemics and Non-Endemics: An Endemic Syndrome Hypothesis

Species ranges have been shifting since the Pleistocene, whereby fragmentation, isolation, and the subsequent reduction in gene flow have resulted in local adaptation of novel genotypes and the repeated evolution of endemic species. While there is a wide body of literature focused on understanding endemic species, very few studies empirically test whether or not the evolution of endemics results in unique function or ecological differences relative to their widespread congeners; in particular while controlling for environmental variation. Using a common garden composed of 15 Eucalyptus species within the subgenus Symphyomyrtus (9 endemic to Tasmania, 6 non-endemic), here we hypothesize and show that endemic species are functionally and ecologically different from non-endemics. Compared to non-endemics, endemic Eucalyptus species have a unique suite of functional plant traits that have extended effects on herbivores. We found that while endemics occupy many diverse habitats, they share similar functional traits potentially resulting in an endemic syndrome of traits. This study provides one of the first empirical datasets analyzing the functional differences between endemics and non-endemics in a common garden setting, and establishes a foundation for additional studies of endemic/non-endemic dynamics that will be essential for understanding global biodiversity in the midst of rapid species extinctions and range shifts as a consequence of global change

Adenomatoid tumors of the male and female genital tract are defined by TRAF7 mutations that drive aberrant NF-kB pathway activation.

Adenomatoid tumors are the most common neoplasm of the epididymis, and histologically similar adenomatoid tumors also commonly arise in the uterus and fallopian tube. To investigate the molecular pathogenesis of these tumors, we performed genomic profiling on a cohort of 31 adenomatoid tumors of the male and female genital tracts. We identified that all tumors harbored somatic missense mutations in the TRAF7 gene, which encodes an E3 ubiquitin ligase belonging to the family of tumor necrosis factor receptor-associated factors (TRAFs). These mutations all clustered into one of five recurrent hotspots within the WD40 repeat domains at the C-terminus of the protein. Functional studies in vitro revealed that expression of mutant but not wild-type TRAF7 led to increased phosphorylation of nuclear factor-kappa B (NF-kB) and increased expression of L1 cell adhesion molecule (L1CAM), a marker of NF-kB pathway activation. Immunohistochemistry demonstrated robust L1CAM expression in adenomatoid tumors that was absent in normal mesothelial cells, malignant peritoneal mesotheliomas and multilocular peritoneal inclusion cysts. Together, these studies demonstrate that adenomatoid tumors of the male and female genital tract are genetically defined by TRAF7 mutation that drives aberrant NF-kB pathway activation

Physical and social environmental characteristics of physical activity for Mexican-origin children: examining differences between school year and summer perceptions

BACKGROUND: Colonias are substandard residential areas along the U.S.-Mexico border. Families of Mexican-origin living in colonias face health burdens characterized by environmental and socioeconomic hardships. Mexican Americans and low-income families, including colonias children, do not frequently participate in physical activity despite the known link to disease risk reduction. For colonias children, schools are the most commonly reported location for physical activity. School closures and extreme temperatures during summer months create a need to explore seasonal differences in environmental supports and barriers in this population. The purpose of this study was to examine the effect of seasonality on perceived environmental barriers, opportunities, and social support for physical activity among colonias children. As a secondary aim, mother-child discordance for each factor was analyzed. METHODS: Promotora-researchers recruited mother-child dyads (n=101 dyads, n=202 participants) from colonias in Hidalgo County, Texas. Mothers and children were separately administered surveys at two time points to capture perceived barriers, opportunities, and social support for physical activity (school-year: February-May; summertime: July-August). Summative scores for each outcome were calculated and three multilevel longitudinal models for continuous outcomes were examined; children were nested within households. Mother-child discordance was measured using Cohen’s Kappa statistic. RESULTS: Physical activity barriers and environmental opportunities (household and neighborhood) increased from school-year to summer by 1.16 and 2.83 points respectively (p≤0.01), after adjusting for covariates. Significant predictors of increased barriers included household income of >$900/month and having more household members. Children of mothers with significant others who were employed part-time or full-time saw significant decreases in barriers. Mother-child agreement of barriers, environmental opportunities, and social support across seasons was slight to fair (range: median κ=0.047 to κ=0.262). CONCLUSIONS: These results suggest a complex relationship between dimensions of economic hardship (employment status, household income, etc…) and perceived opportunities and barriers of children’s physical activity engagement during the school-year and summer. In this study, both barriers and opportunities increased from school-year to summer, further demonstrating that interactions among these characteristics need to be better understood and addressed when considering physical activity initiatives for colonias and other Mexican-American children, specifically during summer when school-based physical activity resources are unavailable