VTechWorks Repository :: Browsing by Author "Sible, Jill C."

Browsing by Author "Sible, Jill C."

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Binding properties of adaptor proteins Tollip and Tom1
Brannon, Mary Katherine (Virginia Tech, 2015-07-02)
Adaptor proteins, like Tollip and Tom1, facilitate cellular cargo sorting through their ubiquitin-binding domains. Tollip and Tom1 bind to each other through their TBD and GAT domains, respectively, whereas Tollip interacts with phosphatidylinositol-3-phosphate (PtdIns(3)P)-containing endosomal membranes. Tom1 and Tollip interaction and association with endosomes is proposed to be involved in the lysosomal degradation of polyubiquitinated cargo. Through cellular, biochemical, and biophysical techniques, we have further characterized the association of Tom1 with Tollip. Mutations in the binding interface of the Tom1 GAT and Tollip TBD complex leads to a subcellular mis-localization of both proteins, indicating that Tom1 may serve to direct Tollip to specific cellular pathways. It was determined that Tom1 inhibits the binding of Tollip to PtdIns(3)P and inhibition was reversed when mutations in the binding interface of the Tom1 GAT and Tollip TBD were present. Furthermore, it was established that, upon the binding of Tollip TBD to Tom1 GAT, ubiquitin is inhibited from binding to Tom1 GAT. It was also demonstrated that Tom1 GAT, but not Tollip TBD, can weakly bind to PtdIns(3)P. Consequently, we propose that association of Tom1 may serve to direct Tollip for involvement in specific cell signaling pathways. Gaining insight into the function of Tom1 and Tollip may lead to their use as therapeutic targets for increasing the efficiency of cargo trafficking and also for patients recovering from various cardiac injuries.
Characterization of Gene Expression During Adenosine 3':5'-Cyclic Monophosphate Induced Neuroendocrine Differentiation in Human Prostatic Adenocarcinoma
Goodin, Jeremy Lee (Virginia Tech, 2002-04-03)
The LNCaP cell line is a versatile and useful model that is suitable for the study of human prostate cancer in vitro. The elevation of LNCaP intracellular cAMP levels through the addition of membrane permeable cAMP analogues, phosphodiesterase inhibitors, adenylate cyclase activators, or components of the cAMP signal transduction pathway can induce reversible neuroendocrine differentiation. Elucidation of those genes that are differentially expressed between undifferentiated prostate cancer cells and prostate cancer cells that have been induced to differentiate may present new insights for the molecular mechanisms governing neuroendocrine differentiation, early detection of prostate cancer, and/or potential targets for gene therapy. In this study, differential display PCR was used to identify 226 differentially expressed PCR products. Twelve of the differential display PCR products were confirmed by Northern blot analysis and cloned. DNA sequencing and database comparisons were performed. Among the differentially expressed genes, the human ribosomal S3a gene was identified as down regulated in response to LNCaP differentiation. In order to better ascertain the mechanism by which HRS3a gene expression is decreased during differentiation, the promoter region for this gene was analyzed. Electrophoretic mobility shift assay, antibody supershift assays, site-directed mutagenesis, and luciferase reporter gene analysis were employed to authenticate the roles of several transcription factors in the regulation of the HRS3a gene. Two cyclic AMP response elements, a Sp1 element and a GA-binding protein element, were involved in the regulation of HRS3a gene expression. In order to ascertain the effect of HRS3a down regulation in LNCaP cells, antisense phosphorothioate oligonucleotides were designed to inhibit HRS3a gene expression. Treatment of LNCaP cells with antisense HRS3a oligonucleotides did not influence cAMP induced neuroendocrine differentiation but antisense treatment did result in a decrease in LNCaP cell growth. In addition, it was determined that morphological changes associated with cAMP induced differentiation of LNCaP cells from the epithelial to the neuroendocrine state may not require alterations in gene expression nor the expression of novel proteins.
Characterizing the cargo binding and regulatory function of the tail domain in Ncd motor protein
Lonergan, Natalie Elaine (Virginia Tech, 2009-10-09)
Non-claret disjunctional (Ncd) is a kinesin-14 microtubule motor protein involved in the assembly and stability of meiotic and mitotic spindles in Drosophila oocytes and early embryos, respectively. Ncd functions by cross-linking microtubules through the tail and motor domains. It was originally believed that the role of the Ncd tail domain was to only statically bind microtubules. However, the Ncd tail domain has recently been shown to have properties that stabilize and bundle microtubules, and contribute to the overall motility of the Ncd protein. Continued characterization of the Ncd tail domain is essential to understanding the complete role of Ncd in cell division. This work explored the regulatory function and microtubule binding properties of the Ncd tail domain. Ncd activity is regulated during interphase by nuclear sequestration. GFP-Ncd fusion proteins, containing full length Ncd, individual Ncd domains, or combinations of Ncd domains, were used to identify the presence of a nuclear localization signal (NLS) in the Ncd polypeptide. The nuclear localization of only the GFP fusion proteins containing the Ncd tail sequence indicates that the NLS is contained within the tail domain. Subsequent, experiments performed with GFP fusion proteins containing segments of the tail domain indicate that essential NLS amino acid segments may span the length of the tail domain. Attempts to characterize the microtubule binding properties of the Ncd tail domain, using bacterially expressed MBP-Ncd tail-stalk, were unsuccessful. MBP-Ncd tail-stalk proteins aggregated under binding assay conditions, preventing an accurate determination of the stoichiometric binding relationship between Ncd and the tubulin dimer.
Computational Tools for Molecular Networks in Biological Systems
Zwolak, Jason W. (Virginia Tech, 2004-12-15)
Theoretical molecular biologists try to understand the workings of cells through mathematics. Some theoreticians use systems of ordinary differential equations (ODEs) as the basis for mathematical modelling of molecular networks. This thesis develops algorithms for estimating molecular reaction rate constants within those mathematical models by fitting the models to experimental data. An additional step is taken to fit non-timecourse experimental data (e.g., transformations must be performed on the ODE solutions before the experimental and simulation data are similar, and therefore, comparable). VTDIRECT is used to perform (a deterministic direct search) global estimation and ODRPACK is used to perform (a trust region Levenberg-Marquardt based) local estimation of rate constants. One such transformation performed on the ODE solutions determines the value of the steady state of the ODE solutions. A new algorithm was developed that finds all steady state solutions of the ODE system given that the system has a special structure (e.g., the right hand sides of the ODEs are rational functions). Also, since the rate constants in the models cannot be negative and may have other restrictions on the values, ODRPACK was modified to address this problem of bound constraints. The new Fortran 95 version of ODRPACK is named ODRPACK95.
Developmental Regulation of Prion Expression in Cattle and Mouse Embryonic Stem Cells
Peralta, Oscar A. (Virginia Tech, 2008-07-25)
The host encoded cellular prion protein (PrPC) is an N-linked glycoprotein tethered to the cell membrane by a glycophosphatidylinositol (GPI) anchor. Under certain conditions, PrPC can undergo conversion into a conformationally-altered isoform (PrPSc) widely believed to be the pathogenic agent of transmissible spongiform encephalopathies (TSEs). Thus, tissues expressing PrPC are potential sites for conversion of PrPSc during TSE pathogenesis. Although much is known about the role of PrPSc in prion diseases, the normal function of PrPC is poorly understood. Lines of mice and cattle in which PrPC has been ablated by gene knockout show no major phenotypical alterations other than resistance to TSE infection. However, recent reports using Prnp-null mouse models have suggested the participation of PrPC in neural stem/progenitor cell proliferation and differentiation. The first objective in our study was to map the expression of PrPC in twenty six somatic and reproductive tissues in ruminants. Our second objective was to characterize the ontogeny of PrPC expression during bovine embryonic and early fetal development. Finally, we used a mouse embryonic stem cell (mESC) model to study the potential role of PrPC during neurogenesis. In adult tissues, intense expression of PrPC was detected in the central nervous system (CNS), thymus and testes, whereas the liver, striated muscle and female reproductive tissues showed the lowest expression. We observed that PrPC was associated with tissues undergoing cellular differentiation including spermatogenesis, lymphocyte activation and hair follicle regeneration. Analyses in bovine embryos and fetuses indicated peaks in expression of PrPC at days 4 and 18 post-fertilization, stages associated with the maternal-zygote transition and the maternal recognition of pregnancy and initiation of placental attachment, respectively. Later in development, PrPC was expressed in the CNS where it was localized in mature neurons of the neuroepithelium and emerging neural trunks. Based on these observations, we hypothesized that PrPC was involved in neurogenesis. We tested this hypothesis in a murine embryonic stem cell model (mESC). mESC were induced to form embryoid bodies (EBs) by placing them in suspension culture under differentiating conditions and allowed to differentiate in vitro for 20 days. We detected increasing levels of PrPC starting on day 12 (8.21- fold higher vs. day 0; P < 0.05) and continuing until day 20 (20.77-fold higher vs. day 0; P < 0.05). PrPC expression was negatively correlated with pluripotency marker Oct-4 (r= -0.85) confirming that mESC had indeed differentiated. To provide a more robust system for assessing the role of PrPC in neural differentiation, mESC were cultured with or without retinoic acid (RA) to encourage differentiation into neural lineages. Induction of EBs with retinoic acid (RA) resulted in an earlier up-regulation of PrPC and nestin (day 12 vs. day 16; P < 0.05). In addition, immunofluorescence studies indicated co-expression of PrPC and nestin in the same cells. The results of these experiments suggested a temporal link between PrPC expression and expression of nestin, a marker of neural progenitor cells. We next tested whether PrPC was involved in RA-enhanced neural differentiation from mESC using a PrPC knockdown model. Plasmid vectors designed to express either a PrP-targeted shRNA or scrambled, control shRNA were transfected into mESC. Stable transfectants were selected under G418 and cloned. PrP-targeted and control shRNA clones, as well as wild-type mESC, were differentiated in presence of RA and sampled as above. PrPC expression was knocked down in PrP-targeted shRNA cultures between days 12 and 20 (62.2 % average reduction vs. scrambled shRNA controls). Nestin expression was reduced at days 16 and 20 in PrPC knockdown cells (61.3% and 70.7%, respectively vs. scrambled shRNA controls). These results provide evidence that PrPC plays a role in the neural differentiation at a point up-stream from the stages at which nestin is expressed. In conclusion, the widely distributed expression of PrPC in ruminant tissues suggests an important biological role for this protein. In the present work we have provided evidence for the participation of PrPC in the differentiation of mESC along the neurogenic pathway.
The Dynamics of the Unreplicated DNA Checkpoint in Xenopus laevis Embryos and Extracts
Adjerid, Nassiba (Virginia Tech, 2008-03-25)
When unreplicated or damaged DNA is present, cell cycle checkpoint pathways cause cell cycle arrest by inhibiting cyclin-dependent kinases (Cdks). In Xenopus laevis, early embryonic development consists of twelve rapid cleavage cycles between DNA replication (S) and mitosis (M) without checkpoints or gap phases. However, checkpoints are engaged in Xenopus once the embryo reaches the midblastula transition (MBT). At this point, the embryo initiates transcription, acquires gap phases between S and M phases, and establishes a functional apoptotic program. During the cell cycle, there are two main checkpoints that regulate entrance into S and M phases. The focus of this study is the role of protein kinase Chk1 and the phosphatase Cdc25A in the DNA replication checkpoint. In the absence of active Chk1, Cdc25A activates cyclin dependent kinases (Cdks) allowing the cell to progress into S or M phase. Chk1 regulates cell cycle arrest in the presence of unreplicated DNA in somatic cells by phosphorylating Cdc25A and leading to its degradation. Chk1 is also transiently activated at the MBT in Xenopus laevis embryos, even when there is no block to DNA replication or damaged DNA. One goal of this work is to understand the developmental role and regulation of checkpoint signaling pathways due to its monitoring of DNA integrity within the cell. Chk1 plays a critical but not fully understood role in cell cycle remodeling and early embryonic development. In order to understand the function and regulation of Chk1 in checkpoints, the features of the MBT that activate Chk1 must be identified. The activation of Chk1 by two time-dependent events in the cell cycle, the critical nuclear to cytoplasmic (N/C) ratio and the cyclin E/Cdk2 maternal timer are explored in this study. Embryos treated with aphidicolin, resulting in a halted replication fork and therefore a reduced DNA concentration, were tested for Chk1 activation and Cdc25A degradation. Chk1 and Cdc25A were observed to undergo activation and degradation, respectively, in embryos with a reduced DNA concentration. In addition, embryos were injected with Δ34Xic cyclin E/Cdk2 inhibitor, in order to disturb the maternal timer and tested for Chk1 activation and Cdc25A degradation. Both Chk1 and Cdc25A were unaffected by the disruption of the cyclin E/Cdk2 maternal time in the embryo. Therefore, the N/C ratio and the cyclin E/Cdk2 maternal timer do not affect Chk1 activation and therefore Cdc25A degradation. Another means of characterizing the unreplicated DNA checkpoint is through the use of mathematical modeling of the checkpoint-signaling cascade of the cell cycle. Mathematical modeling is the translating of biological pathways into mathematical equations that can simulate interactions without performing laboratory experiments. The NovÃ¡k-Tyson checkpoint model made important predictions of hysteresis and bistability in the frog egg checkpoint model, predictions that were later confirmed experimentally. The model was updated with additional interactions, such as those including Myt1, a second inhibitor kinase, and lamin proteins, which become phosphorylated at the onset of nuclear envelope breakdown (NEB) at entry into mitosis. Also, experimental data was fit into the model while maintaining hysteresis and bistability. Therefore, the unreplicated DNA checkpoint model was updated with new interactions and experimental data while still preserving previously identified dynamic characteristics of the system. As described, Cdc25A regulation is dynamic in the embryo. The checkpoint original model represents the activity of Cdc25 phosphatase on the mitosis promoting factor (MPF) that leads the cell into mitosis. In the checkpoint model, Cdc25C is the phosphatase activating MPF. However, the model does not include Cdc25A, which is an integral part of the checkpoint-signaling pathway due to its role in activating the cyclin/Cdk complex allowing entry into S and possibly M phase. Experimental studies were performed in which Cdc25A levels were reduced in embryos and extracts using Cdc25A morpholinos. Embryos and extracts showed delayed cell cycle and mitotic entry, demonstrating the importance of Cdc25A plays in the cell cycle. Based upon experimental data, the mathematical model of the DNA replication checkpoint was expanded to include Cdc25A. The expanded model should more accurately demonstrate how checkpoints affect the core cell cycle machinery. Cdc25A was incorporated into the model by gathering experimental data and designing a signaling cascade, which was translated into differential equations. The updated model was then used to simulate the effect of synthesis and degradation rates of Cdc25A on the entry into mitosis dynamics. Therefore, using mathematical modeling and experimental design, we can further understand the role that Cdc25A plays in cell cycle progression during development. Understanding the regulation of Chk1 activity at the MBT and the role of Cdc25A in checkpoint signaling will help us further characterize the dynamics of early embryonic development. The use of mathematical modeling and experimental tools both contribute to further our understanding of controls of the checkpoint signaling pathway and therefore leading us one step closer to truly being able to model a pathway and make predictions as to the behavior of the cell during early embryonic development.
Dysregulated Apoptosis in Teratogen-Induced Neural Tube Defects in Mice
Mallela, Murali Krishna (Virginia Tech, 2011-01-27)
Dysregulation of apoptosis during development is a possible mechanism for teratogen-induced birth defects. Neural tube defects (NTDs) are the second most common fetal malformations. Non-specific stimulation of maternal immune system prevents birth defects. This study investigated the role of dysregulated apoptosis in formation of NTDs from two teratogens: valproic acid (VA) and an unknown teratogen found in tap water. Interferon- γ (IFN γ) was used to stimulate maternal immunity to evaluate the role of altered apoptosis in this protective mechanism. Apoptosis was evaluated using flow cytometry, Terminal Transferase dUTP Nick End Labeling (TUNEL) assay and gene expression changes by RT2 Profiler PCR arrays. Additionally, changes in the expression of key signal transduction pathway genes that play a role in development were determined. Increased apoptosis, suggesting involvement in VA teratogenicity, was observed along the neural tube in both normal and abnormal embryos from VA-exposed dams. Increased apoptosis in normal VA-exposed embryos suggests that VA may alter other cellular processes such as cell proliferation and differentiation in addition to apoptosis. Apoptotic percentages in embryos with NTDs from IFNγ+VA dams were similar to controls, which indicated resistance to teratogen-induced apoptosis. In IFNγ+VA-exposed embryos with NTDs, immune stimulation failed to prevent apoptosis. VA initiated both death and survival signaling in the embryos; however, upregulation of the apoptotic genes and down regulation of anti-apoptotic genes of p53 and Bcl2 family tended to shift the balance towards death signaling. This change in gene expression patterns could result in increased apoptosis and NTDs in VA-exposed embryos. Immune stimulation normalized changes in the expression of pro-apoptotic signaling molecules. These results suggest immune stimulation protects embryos from teratogenicity of VA by preventing VA-induced apoptosis. VA altered the hedgehog, Wnt, retinoic acid and fibronectin signaling pathways in embryos with NTDs. These results suggest that VA also disrupted signaling pathways required for various morphogenic events during organogenesis. Immune stimulation normalized the expression of Fn1 and Hspb1 and thus may mediate protection through these signaling pathways. In tap water exposed embryos, no change in apoptotic pattern was observed by flow cytometry, TUNEL assay and RT-PCR. Also, none of the signal transduction pathway genes tested were significantly altered in tap water-exposed embryos. This suggests that apoptosis is not a mechanism for teratogenicity resulting from exposure to the contaminant in tap water.
Effects of ammonium perchlorate exposure on the thyroid function and the expression of thyroid-responsive genes in Japanese quail embryos and post hatch chicks
Chen, Yu (Virginia Tech, 2008-04-28)
Perchlorate ion interferes with thyroid function by competitively inhibiting the sodium-iodide symporter, thus blocking iodide uptake into the thyroid gland. In this study, the effect of perchlorate exposure on thyroid function and thyroid-responsive gene expression were examined in (1) embryos from eggs laid by perchlorate-treated Japanese quail hens and (2) perchlorate-treated young Japanese quail. I hypothesized that perchlorate exposure would decrease thyroid function and that the consequent hypothyroidism would alter the expression of thyroid sensitive genes. Laying Japanese quail hens were treated with 2000 mg/l and 4000 mg/l ammonium perchlorate in drinking water. Eggs from these hens were incubated. Embryos, exposed to perchlorate in the egg, were sacrificed at day 14 of the 16.5 day incubation period. Japanese quail chicks, 4-5 days old, were treated with 2000 mg/l ammonium perchlorate in drinking water for 2 and 7.5 weeks. Thyroid status was evaluated by measuring plasma thyroid hormone concentrations, thyroid gland weight and thyroidal thyroid hormone storage. Expression of thyroid-responsive genes was evaluated by measuring the mRNA levels of Type 2 deiodinase (D2) in the brain and liver, RC3/neurogranin mRNA level in the brain and Spot 14 mRNA level in the liver. Maternal perchlorate exposure led to embryonic hypothyroidism, demonstrated by thyroid hypertrophy and very low embryonic thyroidal TH storage. Embryonic hypothyroidism decreased body growth and increased D2 mRNA level in the liver (a presumed compensatory response to hypothyroidism) but did not affect the mRNA levels of D2 and RC3 in the brain. Spot 14 mRNA was not detected in embryonic liver. In the second part of the study, quail chicks showed early signs of hypothyroidism after two weeks of 2000 mg/l ammonium perchlorate exposure; plasma concentration and thyroid gland stores of both T4 and T3 were significantly decreased. After 7.5 weeks of perchlorate exposure, all thyroid variables measured indicated that the chicks had become overtly hypothyroid. D2 mRNA level was increased, a compensatory response to hypothyroidism, and spot 14 mRNA level was decreased, a substrate-driven response in the liver of quail chicks after two weeks of perchlorate exposure. However, no difference was observed in the mRNA levels of D2 and spot 14 in the liver after 7.5 weeks of perchlorate exposure, suggesting there was some adaptation to the hypothyroid condition. The mRNA level of D2 and RC3 in the brain was not affected by perchlorate-induced hypothyroidism in quail chicks after either 2 or 7.5 weeks of perchlorate exposure. As in the embryos, this suggests the brain of chicks was "protected" from the hypothyroid body conditions.
The Effects of Cell Culture Oxygen Levels on the Replicative Senescence Processes of Primary Human Fibroblasts
Stab II, Bernd Robert (Virginia Tech, 2009-07-17)
Serial passaging of primary human fibroblasts leads to the formation of non-dividing senescent cells by a process termed replicative senescence. This tissue culture-based methodology is currently used as a model system to determine the underlying mechanisms of in vivo cellular aging and tumor suppression. Senescence is regarded as an alternative pathway to apoptosis, where cells undergo multiple changes in metabolic and cellular signaling pathways in order to prevent proliferation but still maintain a metabolically-active cell. Whether or not this model accurately reflects in vivo processes is presently controversial; however, replicative senescence is currently the most applicable model through which one can investigate the underlying causes of human cellular aging in the context of controlled environmental stress over time. This work was directed at understanding the molecular processes involved in replicative senescence with specific emphasis on the role of the mitochondria. A series of experiments were performed to assess changes during the induction of replicative senescence under conditions of low (3%) and high (20%) oxygen levels. Measurements were made at the transcriptional, protein, and metabolite levels. Microscopy wasalso utilized to monitor changes in mitochondrial morphology and volume. While previous studies have evaluated specific pathways and/or products; this work combines a more complete metabolomic, genomic, proteomic, and morphological picture of cells undergoing senescence and oxidative stress. Considering the low cell population densities of primary adherent fibroblasts and the subsequent low concentrations of small polar metabolites involved in glycolysis and the TCA cycle, methodologies needed to be developed in order to optimize metabolite extraction and liquid chromatography-mass spectrometric analysis. Protein kinase and transcriptional microarrays were also performed in order to quantify the changes in activated/deactivated signaling cascades as well as gene expression and relate these findings to metabolomic data. Mitochondrial dynamics of cells at different age time points and under different oxygen conditions were also assessed including mitochondrial size, shape, membrane potential, and percent volume per cell volume using confocal microscopy. The results obtained not only confirm the major pathways involved in senescence (p53/p21, PTEN/p27, and RTK/Raf/MAPK) but also provide evidence at both the transcriptional and protein levels for additional senescence-associated pathways. The majority of the changes observed were related to pathways involved in cellular stress, cell cycle control, and the survival response. Metabolic data suggested a –pooling effect– of glycolysis and TCA precursor molecules due to attenuation in enzyme function; this theory was also supported by an observed up regulation of gene expression as a compensatory mechanism. Mitochondria exhibited changes in membrane potential as well as volume and percent volume per cell which suggested compensatory hypertrophy and/or attenuation of mitochondrial fission processes. When the aforementioned analyses are tied together, a “theoretical model of senescence” can be formulated and is characterized by increased metabolic protein and associated metabolite levels due to attenuation in their respective enzyme function, resulting in increases in expression of their associated genes as a compensatory mechanism.
Empowerment in the Transition to Adulthood: Supporting Career Exploration in College Using Participatory Design
Mouchrek, Najla (Virginia Tech, 2019-07-02)
Developmental challenges in the transition to adulthood call for a process of empowerment that supports young people in guiding themselves and building capacities toward adult commitments and roles. The purpose of this study is to investigate empowerment in emerging adulthood, aiming to develop interventions to promote college student developmental outcomes, particularly in career exploration processes. A process of theory construction generated an innovative model of developmental empowerment in the transition to adulthood. Empowerment is conceptualized as a systemic process that emerges through the ongoing interaction between individual and relational environment. Empowerment constructs include personal agency and sense of purpose (as internal experiences), and mentoring and engagement in community (as external experiences). In the first study, a survey investigated empowering experiences in college among Virginia Tech students (N= 255). The findings support the theoretical model, confirming the salience and interdependence of the four main empowerment constructs. Preliminary evidence suggests relevant connections among the empowerment constructs and outcomes such as definition of life goals and career identity. Additionally, qualitative findings offered insights about the role of mentors and community in relation to empowerment. In its second phase, the research project narrowed the focus to study how the empowerment framework may be used to support the process of career exploration in college. The final study integrates the conceptual model and findings from the first study in a participatory design-based intervention for Virginia Tech first-year students exploring career options (N=126). A series of workshops generated an extensive data collection, yielding further investigation about empowerment, definition of life goals and career identity. Qualitative and quantitative data analysis demonstrate that the intervention improved scores for agency and purpose, besides improving student career adapting responses, major decidedness, and progress in career choice. Participants also advanced self-knowledge and purpose-driven orientation, and developed personal criteria for choice of major and career.
Evaluating Immunotoxicity of Quaternary Ammonium Compounds
McDonald, Valerie Alexandra (Virginia Tech, 2017-10-19)
Alkyl dimethyl benzyl ammonium chloride (ADBAC) and didecyl dimethyl ammonium chloride (DDAC) are common quaternary ammonium compounds used as disinfectants in households, medical, and restaurant settings. They cause occupational skin and respiratory hazards in humans, and developmental and reproductive toxicity in mice. They also cause increased secretions of proinflammatory cytokines in cell lines and vaginal inflammation in porcine models; but have not been evaluated for developmental immunotoxicity. We assessed immunotoxicity in-vitro with J774A.1 murine macrophage cell line by analyzing cytokine production and phagocytosis; and evaluated developmental immunotoxicity in CD-1 mice by analyzing antibody production. Additionally, because of the associations between gut microbiome dysbiosis and immune disease, we monitored changes in the microbiome as a result of ADBAC+DDAC exposure. Production of cytokines TNF-alpha and IL-6 increased at low ADBAC+DDAC concentrations, and IL-10 decreased in the murine macrophages with ADBAC+DDAC exposure. The phagocytic function of macrophages was also severely decreased. ADBAC+DDAC altered the mouse microbiome by decreasing the relative abundance of Bacteroides and increases in Clostridia in F0 and F1 generations. IgG primary and secondary responses were altered in F1 male mice; and IgA and IgM production were decreased in secondary response in F2 male mice. Since ADBAC+DDAC show signs of immunotoxicity in mice, further studies are needed to reassess risk for human exposure as ADBAC+DDAC may be contributing to immune disease.
Examination of 2-Oxoglutarate Dependant Dioxygenases Leading to the Production of Flavonols in Arabidopsis thaliana
Owens, Daniel Kenneth (Virginia Tech, 2005-09-22)
The flavonols are a varied and abundant sub-class of flavonoids that are associated with a number of essential physiological functions in plants and pharmacological activities in animals. The 2-oxoglutarate-dependant dioxygenases(2-ODDs), flavonol synthase (FLS) and flavanone 3-hydroxylase (F3H), are essential for flavonol synthesis. The primary goal of this study has been to gain a deeper understanding of the biochemistry of these enzymes in Arabidopsis. To accomplish this goal, an activity assay employing recombinant protein expression and HPLC as a detection system was developed for F3H and adapted for use with FLS. The assay was employed to establish the biochemical parameters of F3H from Arabidopsis, and to further characterize the F3H mutant allele, tt6(87). Enzymatic activity was demonstrated for F3H enzymes from Ipomoea alba (moonflower), Ipomoea purpurea (common morning glory), Citrus sinensis (sweet orange), and Malus X domestica (newton apple), each of which had previously been identified solely based on sequence homology. Arabidopsis contains six genes with high similarity to FLS from other plant species; however, all other central flavonoid pathway enzymes in Arabidopsis are encoded by single genes. The hypothesis that differential expression of FLS isozymes with varying substrate specificities is responsible for observed tissue-specific differences in flavonol accumulation was tested. Sequence analysis revealed that AtFLS2, 4 and 6 contain premature stop codons that eliminate residues essential for enzyme activity. AtFLS1 was found to have a strong preference for dihydrokaempferol as a substrate. However, no enzyme activity was observed for AtFLS3 or AtFLS5 with a number of different substrates under a variety of reaction conditions. To identify structural elements that may contribute to the observed differences in biochemical activity, homology models for each of the isoforms were generated utilizing Arabidopsis anthocyanin synthase (ANS) as a template. A domain at the N-terminus of AtFLS1 that is missing in the other isozymes was insufficient to convey activity to an AtFLS1/5 chimera. These findings suggest a single catalytically-active form of FLS exists in Arabidopsis. The possibility that the apparently expressed but non-catalytic proteins, AtFLS2, 3, and 5, serve noncatalytic roles in flavonol production were explored by yeast 2-hybrid analysis.
Experimental evidnece for hysteresis in the cell cycles of Xenopus Laevis egg extracts
Sha, Wei (Virginia Tech, 2002-08-05)
In 1993, Novak and Tyson published a comprehensive mathematical model of the regulation of M-phase promoting factor (MPF) activity in Xenopus laevis eggs and egg extracts. Although this model was in agreement with existing and subsequent experimental data, fundamental predictions that the cell cycle is driven by a hysteresis loop have never been validated experimentally. The model's predictions of bifurcations that create and destroy MPF activity, indicative of hysteresis, were tested in this study. Prediction 1: The threshold concentration of cyclin B required to activate MPF is measurably higher than the threshold concentration required to inactivate MPF. The difference in thresholds implies that the MPF control system is hysteretic and bistable. To measure these thresholds, extracts in interphase or M-phase were supplemented with varying concentrations of non-degradable human cyclin B1 protein. MPF activity was determined by the morphology of sperm nuclei and by assays of histone H1 kinase activity. Consistent with the model, the activation threshold was determined to be 40 nM, which is two-fold higher than the inactivation threshold, 20 nM. Prediction 2: For cyclin levels marginally above the activation threshold concentration of cyclin B, there is a dramatic "slowing-down" in the rate of MPF activation. Supra-threshold concentrations of nondegradable cyclin B1 were added to cycloheximide-treated CSF-released extracts, and samples taken at various time-points were analyzed for MPF activity. At 40 nM cyclin B1, just above the activation threshold, the lag time for MPF activation was 45 - 60 minutes; at 50 nM cyclin B1, the lag time was between 30 - 45 minutes; and at 60 nM or higher concentrations of cyclin B1, the lag time was 20 - 30 minutes, thus confirming the prediction of the Novak-Tyson model. Prediction 3: DNA replication checkpoint increases the activation threshold concentration of cyclin B by increasing the hysteresis loop. Cycloheximide-treated, CSF-released extracts containing 1200 sperm nuclei/μl were treated with aphidicolin, then supplemented with varying concentrations of nondegradable cyclin B1. The activation threshold was 100 nM, 2.5 fold higher than in extracts lacking aphidicolin. Conclusions: These studies confirm three predictions of the Novak-Tyson model and indicate that hysteresis underlies cell cycle control in Xenopus egg extracts. These experiments validate use of mathematical models to study complex biological control systems such as the eukayotic cell cycle.
Expression and Function of the Chloroplast-encoded Gene matK
Barthet, Michelle Marie (Virginia Tech, 2006-02-09)
The chloroplast matK gene has been identified as a rapidly evolving gene at nucleotide and corresponding amino acid levels. The high number of nucleotide substitutions and length mutations in matK has provided a strong phylogenetic signal for resolving plant phylogenies at various taxonomic levels. However, these same features have raised questions as to whether matK produces a functional protein product. matK is the only proposed chloroplast-encoded group II intron maturase. There are 15 genes in the chloroplast that would require a maturase for RNA splicing. Six of these genes have introns that are not excised by a nuclear imported maturase, leaving MatK as the only candidate for processing introns in these genes. Very little research has been conducted concerning the expression and function of this important gene and its protein product. It has become crucial to understand matK expression in light of its significance in RNA processing and plant systematics. In this study, we examined the expression, function and evolution of MatK using a combination of molecular and genetic methods. Our findings indicate that matK RNA and protein is expressed in a variety of plant species, and expression of MatK protein is regulated by development. In addition, matK RNA levels are affected by light. Furthermore, genetic analysis has revealed that although MatK has a high rate of amino acid substitution, these substitutions are not random but are constrained to maintain overall chemical structure and stability in this protein. We have also identified an alternate start codon for matK in some plant species that buffers indels (insertions and deletions) in the open reading frame (ORF) that are not in multiples of three in the gene sequence. Usually, indels not in multiples of three result in frame shifts that destroy the reading frame. Our results indicate that an out-of-frame matK start codon in some orchids compensates for these otherwise deleterious indels. This research represents the first in-depth analysis of matK gene expression and contributes to several fields of biology including plant systematics, genetics and gene expression.
Fostering Communities of Transformation in STEM Higher Education: A Multi-institutional Collection of DEI Initiatives
Briganti, Jonathan S.; Sible, Jill C.; Brown, Anne M. (Virginia Tech Publishing, 2024-02-01)

Dive into the multifaceted landscape of inclusive excellence in STEM education with Fostering Communities of Transformation in STEM Higher Education. This scholarly work examines transformative initiatives from Virginia Tech, Radford University, Trinity Washington University, and Towson University, showcasing their role as catalysts in cultivating inclusive excellence across diverse STEM disciplines. Take inspiration from their projects and guidance from their lessons learned with this collection. Are you reviewing or adopting this book for a course?
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The main landing page for this book is https://doi.org/10.21061/fosteringcommunities.
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ISBN (EPUB): 978-1-957213-83-5
ISBN (print): 978-1-957213-82-8
Table of contents 1. Preparing STEM Teachers to Be Change Makers 2. Resequencing the Chemistry Curriculum to Retain Chemistry Majors 3. Delayed Enrollment in General Chemistry Recitation 4. Assessing Changes in Student Engagement Using a Mixed-Methods Approach 5. Development and Assessment of a Four-Week Summer Research Experience for Undergraduates 6. Creating Impactful Moments 7. Community, Curriculum, and CUREs 8. We’re All in This Together
VIGNETTE: Reflecting on the Impact of Engelpalooza 9. Teaching to Make Math Resonate 10. Strategies for Creating and Sustaining Inclusive Makerspaces 11. Creating a Space in the Curriculum for Effective Mentoring to Foster Student Connections and Agency 12. Gunpowder Code Club 13. Using Departmental Book Clubs to Bridge the Faculty-Staff-Student Gap 14. Institutionally Advancing Inclusive Excellence 15. From the Soul
About the editors
Jonathan S. Briganti
Jonathan S. Briganti works in the Virginia Tech University Libraries as the manager of the DataBridge program, which trains undergraduate students from across all disciplines in applied data science and consults with partners across and beyond campus to improve the quality of their data and its outputs. He received both his BS and MS from Virginia Tech and has since found passion in creating open-source educational resources and accessible research environments to bring a more engaged and diverse pool of researchers to the table. Jill C. Sible
Jill C. Sible serves as Associate Vice Provost for Undergraduate Education and Professor of Biological Sciences at Virginia Tech where she has worked since 1998. She is the Program Director of Virginia Tech’s Inclusive Excellence project, which has empowered science faculty and departments to apply a learning mindset and data-informed approach to changing classes, curricula, and culture to be inclusive of all students, especially those historically marginalized in science and higher education. Anne M. Brown
Anne M. Brown is an Associate Professor and Associate Director in Research and Informatics under University Libraries, Virginia Tech and is an Affiliate Professor in the Biochemistry Department. As a computational biochemist, her research focuses on computer-aided drug discovery and the aggregation process of amyloids. She is committed to undergraduate research and outreach. Today, she continues in her lifelong mission to create and expand opportunities for students of all backgrounds and provide them with mentorship to facilitate their success. Suggested citation
Jonathan S. Briganti, Jill C. Sible, and Anne M. Brown, eds. (2024). Fostering Communities of Transformation in STEM Higher Education: A Multi-institutional Collection of DEI Initiatives. Blacksburg: Virginia Tech Publishing. https://doi.org/10.21061/fosteringcommunities. Licensed with CC BY 4.0. View errata | Report an error Accessibility
Virginia Tech is committed to making its publications accessible in accordance with the Americans with Disabilities Act of 1990. Please contact publishing@vt.edu if you are a person with a disability and have suggestions to make this book more accessible. Cover design: Catherine Freed
Identification of Regulatory Binding Sites and Corresponding Transcription Factors Involved in the Developmental Control of 5'-nucleotidase Expression in Dictyostelium discoideum
Wiles, Natasha Shawn (Virginia Tech, 2005-05-06)
Gene regulation is a critical aspect of normal development, energy conservation, metabolic control, and responses to environmental cues, diseases and pathogens in eukaryotic organisms. In order to appropriately respond to environmental changes and advance through the life cycle, an organism must manage the expression levels of a large number of genes by utilizing available gene regulation mechanisms. The developmental control of 5â -nucleotidase (5nt) expression in the model system Dictyostelium discoideum has provided a focal point for studies of gene regulation at the level of transcription. In order to identify temporally-regulated control elements within the promoter of the 5nt gene, 5â and internal promoter deletions were designed and fused to the luciferase and lacZ reporter genes, and reporter enzyme activity was measured in cells from the slug stage of development. The results from these experiments enabled the identification of a 250 bp region of the promoter, which was used as a template for subsequent site-directed mutagenesis experiments. These experiments involved altering 6-12 bp regions of the promoter by substitution. Twelve mutagenized promoters were fused to the luciferase and lacZ reporter genes, and activity was measured at the slug stage of development to more precisely locate cis-acting temporally-regulated control elements. In addition, cAMP induction experiments were performed on amoebae transformed with the mutagenized promoters to identify control elements within the promoter influenced by the presence of cAMP. The regions between -530 and -560 bp and -440 and -460 bp from the ATG translation start site. In order to evaluate the functions of the cis-acting promoter control elements, electromobility gel shift assays were performed to identify specific DNA-protein interactions on the 5nt promoter. These assays enabled the detection of a 0.13 Rf and 0.33 Rf binding activity to specific sites of the promoter. After characterization of these binding activities, both proteins were purified by a series of column chromatography techniques and characterized after mass spectrometry. The proteins purified were identified as formyltetrahydrofolate synthase and hydroxymethylpterin pyrophosphokinase. These enzymes function in the biosynthetic pathway of tetrahydrofolate and the production of folate coenzymes. The specific interactions of these enzymes with the 5nt promoter suggest these proteins may also function in regulating 5nt expression.
Individual and Interactive Effects of Maternally- and Trophically-Derived Mercury on Early Amphibian Development
Bergeron, Christine Marie (Virginia Tech, 2011-11-04)
Mercury (Hg) is an important environmental contaminant due to its global distribution, tendency to bioaccumulate, and toxicity to wildlife. However, Hg has received little attention in amphibians compared to other vertebrates, despite the fact that amphibian population declines have been documented worldwide and environmental contaminants are believed to contribute to some declines. During my dissertation research, I used a pluralistic approach which combined field studies and manipulative laboratory and mesocosm experiments to examine the bioaccumulation and ecological effects of environmentally relevant Hg exposure routes acting at various early life stages in amphibians. By collecting amphibians in the field at the Hg-contaminated South River, VA, I confirmed that amphibians exhibiting different life histories and occupying different ecological niches (Plethodon cinereus, Eurycea bislineata, and Bufo americanus) can bioaccumulate sufficient levels of Hg to warrant concern (Chapter 2) and female Bufo americanus transfer accumulated Hg to their eggs (Chapter 3). Maternal transfer of contaminants is a parental effect which typically has negative consequences for offspring because early development is a critical organizational period in the ontogeny of vertebrates. Through laboratory observations and mesocosm experiments, I examined the short and long-term effects of maternal contaminant exposure on offspring, and found the negative effects of maternal Hg exposure manifested either immediately at the embryonic stage or later during the larval stage, depending on the year in which the study was conducted (Chapters 4 and 5). Lastly, using a factorial laboratory experiment, I examined whether the latent effects of maternal transfer of contaminants manifests differently depending on the environment in which offspring develop, and found both maternal and dietary Hg exposure independently produced negative, but different, sublethal effects on larval development. Most importantly, maternal exposure to Hg combined with high dietary Hg exposure later in ontogeny had a lethal effect in larvae (Chapter 6). This study is one of the first to demonstrate that the latent effects of maternally transferred contaminants may be exacerbated by further exposure later in ontogeny, findings that may have important implications for both wildlife and human health.
Investigating the Roles of the Stk Locus in Development, Motility and Exopolysaccharide Production in Myxococcus Xanthus
Lauer, Pamela L. M. (Virginia Tech, 2007-03-19)
Myxococcus xanthus, a Gram-negative bacterium with a developmental cycle, displays a type IV pili (TFP) mediated surface motility known as social (S) gliding. Beside the polarly localized TFP, the fibril or extracellular polysaccharide (EPS) is also required for S-motility to function. It is proposed that S-motility, along with the related bacterial twitching motility in other species, is powered by TFP retraction. EPS is proposed to anchor and trigger such retractions in M. xanthus. EPS production is known to be regulated by TFP and the Dif signal transduction pathway. Two genetic screens were performed previously to identify additional genes important for EPS production. The first was for the isolation of pilA suppressors, the second for the identification of mutants underproducing EPS in a difA suppressor background. Both screens identified transposon insertions at the stk locus. In particular, StkA, a DnaK homolog, was identified as a possible negative regulator of EPS production by a stkA transposon insertion that suppressed a pilA mutation. A stkB transposon insertion was found to have diminished EPS production in a difA suppressor background. In this study, in-frame deletion mutants of the five genes at the stk locus, stkY, stkZ, stkA, stkB and stkC, were constructed and examined. In addition, mutations of rbp and bskL, two genes downstream of the stk locus, were constructed. Like transposon insertions, the stkA in-frame deletion resulted in overproduction of EPS. The stkB and to a less extent the stkC mutants underproduced EPS. Mutations in the other genes had no obvious effects on EPS production. Genetic epistasis suggests that StkA functions downstream of TFP and upstream of the Dif sensory proteins in EPS regulation in M. xanthus. Epistasis analysis involving stkB was inconclusive. It is unresolved whether StkB plays a role in the biosynthesis or the regulation of EPS production in M. xanthus.
Investigation of the role of the toxins perfringolysin O (PFO) and sialidase in Clostridium perfringens gas gangrene infections
Therit, Blair H. (Virginia Tech, 2006-09-08)
Clostridium perfringens is the causative agent of gas gangrene. A lethal infection in mice requires a large inoculum suggesting that the immune system is involved in inhibiting disease. Human monocytic cells and neutrophils killed C. perfringens in vitro when complement was present. Macrophages and neutrophils co-localized with C. perfringens in vivo when bacterial numbers were low. Depletion of neutrophils and monocytes in mice revealed that monocytic cells play a role in inhibiting C. perfringens gas gangrene in mice infected with an intermediate dose. C. perfringens can persist in the tissues and this could be mediated by persistence within macrophages. To examine if the toxin perfringolysin O (PFO) could mediate this, less active variants of PFO were used to examine what occurs between phagosomal escape and cell lysis. The mutant forms of PFO did mediate phagosomal escape in macrophages and were found within macrophages at higher numbers than wild-type C. perfringens. Our data were preliminary but may indicate that less active PFO mediates intracellular persistence. To investigate the role of sialidase in C. perfringens gas gangrene we made nanI-, nanJ-, and nanI-/nanJ- mutants. We observed that NanI is responsible for the majority of sialidase activity of C. perfringens strain 13, that NanJ is an extracellular sialidase, and that these genes are transcriptionally regulated by sialic acid. Murine infection trials revealed that these sialidases may be protective for mice during infection. In conclusion, murine monocytes inhibit disease onset and C. perfringens sialidase enhances mouse survival. However, the toxin PFO if less active promotes the survival of C. perfringens with macrophages.
An investigation of the stickinness mechanism and the role of nodes in cribellar spider capture thread
Campbell-Hawthorn, Anya (Virginia Tech, 2002-10-04)
Sticky prey capture threads are produced by many members of the spider Infraorder Araneomorphae. Cribellar threads are plesiomorphic for this clade, and adhesive threads are apomorphic. The surface of cribellar thread is formed of thousands of fine fibrils. Basal araneomorphs produce cylindrical fibrils, whereas more derived members produce fibrils with nodes. Cribellar fibrils snag and hold rough surfaces, but other forces are required to explain their adherence to smooth surfaces. Threads of Hypochilus pococki (Hypochilidae) that are formed of non-noded fibrils hold to a smooth acetate surface with the same force under low and high humidities. In contrast, threads of Hyptiotes cavatus and Uloborus glomosus (Uloboridae) that are formed of noded fibrils hold with greater forces to the same surface at intermediate and high humidities. Threads spun by eight species representing seven genera and four families with noded fibrils absorb water, while that of two families, represented by one species each with smooth fibrils, repel water, indicating increase hygroscopisity associated with the presence of nodes. Additionally, equations describing van der Waals and hygroscopic forces can predict the observed stickiness of these threads. This model supports the hypothesis that van der Waals forces allow non-noded cribellar fibrils to adhere to smooth surfaces, whereas noded fibrils employ van der Waals forces at low humidities and add hygroscopic forces at higher humidities. Thus, there appear to have been two major events in the evolution of spider prey capture thread: the addition of hydrophilic nodes to the fibrils of cribellar threads and the replacement of cribellar fibrils by glycoprotein glue.

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