The overexpression of the enzymes involved in the degradation of procollagen lysine is correlated with various tumor entities. Procollagen-lysine, 2-oxoglutarate 5-dioxygenase 3 (PLOD3) expression was found to be correlated to the progression and migration of cancer cells in gastric, lung and prostate cancer. Here, we analyzed the gene expression, protein expression, and the clinical parameters of survival across 33 cancers based on the Clinical Proteomic Tumor Analysis Consortium (CPTAC), function annotation of the mammalian genome 5 (FANTOM5), Gene Expression Omnibus (GEO), Genotype-Tissue Expression (GTEx), Human Protein Atlas (HPA) and The Cancer Genome Atlas (TCGA) databases. Genetic alteration, immune infiltration and relevant cellular pathways were analyzed in detail. PLOD3 expression negatively correlated with survival periods and the infiltration level of CD8+ T cells, but positively correlated to the infiltration of cancer associated fibroblasts in diverse cancers. Immunohistochemistry in colon carcinomas, glioblastomas, and soft tissue sarcomas further confirm PLOD 3 expression in human cancer tissue. Moreover, amplification and mutation accounted for the largest proportion in esophageal adenocarcinoma and uterine corpus endometrial carcinoma, respectively; the copy number alteration of PLOD3 appeared in all cancers from TCGA; and molecular mechanisms further proved the effect of PLOD3 on tumorigenesis. In particular, PLOD3 expression appears to have a tumor immunological effect, and is related to multiple immune cells. Furthermore, it is also associated with tumor mutation burden and microsatellite instability in various tumors. PLOD3 acts as an inducer of various cancers, and it could be a potential biomarker for prognosis and targeted treatment.

Colorectal cancer is the third most common cancer and the leading cause of cancer deaths in Western industrialised countries. Despite recent advances in the screening, diagnosis, and treatment of colorectal cancer, an estimated 608,000 people die every year due to colon cancer. Our current knowledge of colorectal carcinogenesis indicates a multifactorial and multi-step process that involves various genetic alterations and several biological pathways. The identification of molecular markers with early diagnostic and precise clinical outcome in colon cancer is a challenging task because of tumour heterogeneity. This Ph.D.-thesis presents the molecular and cellular mechanisms leading to colorectal cancer. A systematical review of the literature is conducted on Microarray Gene expression profiling, gene ontology enrichment analysis, microRNA and system Biology and various bioinformatics tools. We aimed this study to stratify a colon tumour into molecular distinct subtypes, identification of novel diagnostic targets and prediction of reliable prognostic signatures for clinical practice using microarray expression datasets. We performed an integrated analysis of gene expression data based on genetic, epigenetic and extensive clinical information using unsupervised learning, correlation and functional network analysis. As results, we identified 267-gene and 124-gene signatures that can distinguish normal, primary and metastatic tissues, and also involved in important regulatory functions such as immune-response, lipid metabolism and peroxisome proliferator-activated receptors (PPARs) signalling pathways. For the first time, we also identify miRNAs that can differentiate between primary colon from metastatic and a prognostic signature of grade and stage levels, which can be a major contributor to complex transcriptional phenotypes in a colon tumour.

No description available.

No description available.

<p>The brain serotonergic and dopaminergic systems broadly influence our internal experience and the ways in which we interact with the outside environment, with crucial regulatory roles in mood, sleep, appetite and the control of voluntary movement. Serotonin and dopamine neurons are themselves influenced by a wide variety of internal and external factors, many of which remain poorly understood. The central aim of this thesis was to better characterize several of these modulatory influences via exploratory investigations involving pharmaceutical agents or environmental modification. Specifically, I examined the modulatory effects of selective serotonin reuptake inhibitors (SSRIs), atypical neuroleptics and environmental enrichment with exercise on the regulation of brain serotonin and dopamine neurons.</p> <p>This thesis documents, for the first time, that (1) inhibition of the serotonin transporter (SERT) by SSRIs induces a rapid and region-selective reduction of tryptophan hydroxylase (TPH)-immunoreactive neurons in serotonergic brainstem nuclei that persists over a prolonged treatment course; that (2) selective blockade of SERT by SSRIs can rapidly induce a reduction of tyrosine hydroxylase (TH)-positive dopaminergic neurons in the substantia nigra (SN) and the ventral tegmental area (VTA) that, again, persists over a lengthy treatment course; that (3) environmental enrichment with exercise can potentiate the effect of SERT inhibition on SN dopaminergic neurons, but not the dorsal raphe nucleus (DRN) serotonergic neurons; that (4) that SSRI fluoxetine triggers a significant upregulation of microglia in the SN; that (5) environmental enrichment with exercise can reduce TPH immunoreactivity in the DRN and TH immunoreactivity in the SN and VTA, even in the absence of any pharmacological intervention, and finally, that (6) the atypical neuroleptic risperidone significantly reduces TPH in the DRN of both young and aged animals and reduces DRN Nissl counts in aged animals. Taken together, the body of work included in this thesis suggests that SSRIs, atypical neuroleptics and environmental enrichment with exercise can have profound effects on brain serotonergic and dopaminergic neurons, possibly accounting for some of the side effects and therapeutic benefits associated with these interventions.</p> / Doctor of Philosophy (PhD)

This mixed methods research investigated how young adult alumnae from a Catholic female high school perceive the impact of their high school service experience concerning their "beliefs" about the importance of service, current "engagement" in service, and their beliefs about and engagement with four Catholic Social Teaching principles (life and dignity, care for the poor, solidarity and common good, and rights and responsibilities) related to social justice. This research draws data from young adult alumnae from a Catholic female single-sex high school in a metropolitan city of the United States. The data collection included a web-based survey (N=131), individual interview (n=9), and school documents review. Catholic theology of the human person, and Catholic social teaching principles served as the conceptual framework for data analysis. This research draws data from young adult alumnae from a Catholic female single-sex high school in a metropolitan city of the United States. The data collection included a web-based survey (N=131), individual interview (n=9), and school documents review. Catholic theology of the human person, and Catholic social teaching principles served as the conceptual framework for data analysis. The quantitative data revealed that Catholic high school service program experience positively impacts participants' "beliefs" about the importance of service (65%), and the importance of four Catholic social teaching principles (73%). The qualitative data corroborates with the quantitative findings. However, participants lacked translating their beliefs in to action with only 42% reporting as "engaged" in service. Although a majority of participants (60%) reported as engaged in activities related to four CST principles, in reality only 25% are significantly engaged in service in the past 12 months. Catholic educators are invited to examine their service pedagogy and address factors that contribute to low level of service engagement. Further research is suggested to identify factors that would raise the level of service engagement in alumnae’s young adult life.

<p dir="ltr">Research on enhancing the plasma confinement characteristics in fusion reactors and tokamaks has focused heavily on Low-Z plasma facing components Be, BeO, and SiC in recent decades. Building reactors, reducing harmful effects, and creating materials resistant to radiation all depend on an understanding of the plasma material interactions. In nuclear reactors, material composition and properties are also influenced by an understanding of impurity interactions. This thesis aims to investigate the effects of varying sputtering rates and long-term plasma durability on structured materials sputtered by plasma under various situations. The majority of this research has been done on the sputtering of materials as it accelerates the degradation of materials. To understand the process of ion solid contacts, a thorough investigation of ions' interactions with target atoms is presented in this work. Monte Carlo (MC) simulation has been done in this entire research by using the transport of ions in matter (TRIM). The influence of ion energy (100–1000 eV) and ion incidence angle by deuterium ions has been simulated in this study. As expected, on one hand, sputtering yield, as a function of ion-energy peaks first and a sequential reduction afterword; on the other hand, as a function of ion-incidence angle shows sequential enhancement towards max value followed by sharp reduction afterwards. The simulated data have been compared with the relevant experimental data and very close agreements were observed. To investigate the behavior of ion energy loss in relation to ion range in the targets, distribution profiles associated with ion range, recoil, ionization, and phonons are developed. Deuterium accumulation and its impact on Be target also have been shown in this work. The sputtering yield of <a href="" target="_blank">BeD₂</a> is lowest when the D incident ion interacts with low percentage of D has been simulated as target. Gradually increasing the percentage of D as target results in higher yields.</p>

<p dir="ltr">To meet the growing demands for pork products, lactating sows are often housed in farrowing crates to reduce piglet crushing. However, the public has raised welfare concerns about farrowing crate systems due to the confinement and barren environment, which can impair social interactions between sow and piglets, change their activity levels, and alter how sows and piglets satisfy their motivated behaviors to chew and explore by oral manipulation of pen and pen mates. Barren and confined environments can result in skin abrasions caused by oral manipulations and fighting, physiological stress, inactivity, and abnormal behaviors, which can have an impact on sows’ and piglets’ welfare, productivity, and behavior. Previous work on environmental enrichments has shown promise to improve average daily gain, activity levels, stress, and behavioral repertoire. However, the majority of studies on pig environmental enrichments take place after weaning and research investigating the impact enrichments have during lactation is limited. In addition, research on maximizing the use of environmental enrichments based on the location inside the farrowing crate systems has not been conducted. To address the knowledge gaps concerning the impact of the location of environmental enrichments on the welfare, behavior, and productivity of sows and piglets in farrowing crate systems and to provide educational material on pig enrichment, this dissertation consists of two parts: Chapters 2 and 3 examine the effects of the location of environmental enrichments in farrowing crate systems on sows’ and piglet’s welfare, productivity, and behavior. Chapter 5 is an extension article on the different types of environmental enrichments and the best strategies for implementing enrichment in swine operations.</p><p dir="ltr">In Chapter 2, sows (n = 37) and focal piglets (n = 148) were assigned to three treatment groups: SPE (both sows and piglets had access to enrichment objects), PE (only piglets had access to enrichment objects), and CON (control group with no enrichment) blocked by sow parity and genetics. Sow posture and piglet behavior during the lactation and nursery phases were observed at various times after birth and weaning. Environmental enrichments significantly influenced the behaviors of suckling piglets, reducing pig-directed and agonistic behaviors. Piglets with enrichments tended to explore the pen less and engage in more social behaviors. The location of enrichments also impacted behaviors, with higher nursing behavior observed during mid-lactation for piglets with access to enrichments (PE) and increased interaction with enrichments when they were accessible to both sows and piglets (SPE). Treatment did not affect sow postural changes or most nursery behaviors, except for walking, which increased in SPE nursery piglets compared to CON piglets. Overall, the study demonstrated positive effects of environmental enrichments on suckling piglets in farrowing crate systems, highlighting the importance of enrichment placement on nursing behaviors and enrichment interaction.</p><p dir="ltr">In Chapter 3, the same sows and piglets were used to investigate the effects of enrichment location on the welfare (skin lesions, pressure sores, salivary cortisol, and tear stains) and performance (average daily gain and piglet crushing) of the sows and piglets. This study used the same animals that were assigned the treatment group, housing, and management practices from Chapter 2. Salivary cortisol samples were collected from sows at four time points: 24 hours after moving into farrowing crates, 24 hours after treatment group assignment, midway between moving into crates and weaning, and on the day of weaning. Pressure sores of sows were scored on days 1, 4, 7, 10, 14, and 17 after farrowing. For suckling piglets, tear stains and skin lesions were assessed on the same days, and their average daily gain (ADG) was analyzed weekly during lactation. In the nursery phase, salivary cortisol was collected from piglets on the day of weaning and days 1, 7, and 14 post-weaning, with tear stains and skin lesions measured on those days as well. Nursery ADG was analyzed from weaning to day 14 post-weaning. Results indicated that control (CON) sows were less likely to have no pressure sores compared to sows with shared (SPE) enrichments, while piglets in the enriched treatment groups (PE and SPE) had smaller tear stain areas than those in the CON group. Treatment influenced skin lesions in suckling piglets, with enriched piglets having fewer lesions in the ear and front body regions. There was no treatment effect on salivary cortisol for both sows and nursery piglets, nor did treatment affect ADG, piglet crushing, or nursery skin lesions. The provision of environmental enrichments in farrowing crates reduced pressure sores of sows, skin lesions of suckling piglets and tear stains of suckling and nursery piglets.</p><p dir="ltr">Overall, providing environmental enrichments to suckling piglets reduced aggression, as evidenced by fewer agonistic and pig-directed behaviors, and resulted in fewer skin lesions compared to piglets without enrichments. This suggests potentially reduced stress levels in enriched piglets, indicated by smaller tear stain areas. While most behaviors and skin lesion scores showed no significant differences during the nursery phase, enriched piglets continued to have smaller tear stains. Enrichment location influenced the following: sows had fewer pressure sores, and suckling piglets interacted more with enrichments and exhibited fewer pig-directed behaviors when enrichments were accessible to both sows and piglets compared to the only piglet enriched treatment group. Piglets with access only to enrichments also performed more nursing behaviors during mid-lactation compared to the control group. Overall, the study highlights the benefits of environmental enrichments in farrowing crate systems, particularly the positive impact of enrichment location on the welfare and behavior of sows and piglets.</p><p dir="ltr">Lastly, in Chapter 5, the extension article discusses the definition of environmental enrichment and its impact on pigs’ welfare. The article also delves into the five types of environmental enrichments (nutritional, occupational, physical, sensory, and social), providing examples of each. Additionally, the article offers five practical tips for efficiently and successfully implementing environmental enrichments in swine herds.</p>

The breast cancer susceptibility protein, BRCA1, is a tumor suppressor that helps maintain genomic integrity. Changes in BRCA1 that effect DNA repair processes can fuel cancer induction. The Kelly lab, at the Virginia Tech Carilion Research Institute, has recently developed a new methodology that employs silicon nitride (SiN) microchips to isolate BRCA1 assemblies from the nuclear material of breast cancer cells. These microchips are coated with adaptor proteins that include antibodies against target proteins of interest. The adaptor proteins are added in sequential steps to the coated microchips, followed by an aliquot of sample containing the protein of interest, such as BRCA1. The Kelly lab, partnered with Protochips Inc., developed these devices as a robust, tunable platform to monitor molecular processes, and refer to them as 'Cryo-SiN' in cryo-Electron Microscopy (EM) imaging. We are currently using Cryo-SiN to recruit BRCA1 protein assemblies to the microchip surface under mild conditions, while simultaneously preparing them for cryogenic preservation and EM imaging. This strategy presents a viable alternative to antibody affinity columns that require stringent elution steps to obtain protein complexes from the column. Another advantage of the microchip strategy is that it requires only a 30-minute nuclear extraction, a 60-minute enrichment procedure, and a 5-minute microchip capture step--a total of 95 minutes from initially lysing the cells to plunge-freezing the EM specimens. Therefore, these novel approaches represent a major departure from classical separation procedures that often require days to complete, during which time active protein assemblies can readily dissociate or become inactive. Overall, our use of BRCA1-specific microchips may reveal changes in the BRCA1 architecture during various stages of cancer progression--a major gap in knowledge that persists in cancer research. / M. S. / Modern advances in the imaging technology used for cryogenic electron microscopy (cryo-EM) have offered researchers an extraordinary view into the world of biology at the nanoscale. Supplemental to these technical innovations is the development of tunable substrates based on functional new materials that revolutionize the sequestering of biological components from human cells, such as protein complexes formed in breast cancer cells. New developments of novel viewing substrates, given traditional electron microscopy viewing grids have remained unchanged for decades, is the logical next step into the future of enhanced cryo-EM imaging. Tunable microchip substrates, made using recently enhanced micro-engineering techniques, are currently under development for use in cryo-EM imaging. In this work I have examined these microchip substrates for their capacity to streamline the isolation of biomolecules such as the protein most prominently cited in breast cancer, known as the breast cancer susceptibility protein (BRCA1). Utilizing these novel microchip substrates in the Kelly Lab, I have collected and analyzed data containing BRCA1 proteins, formed in human breast cancer cells, toward the development of 3-dimensional protein structures that allow us to peer into the structure-function relationships of these proteins. New and exciting Cryo-EM data, collected using these newly developed microchips, has the potential to reveal obscure disease mechanisms being propagated at the molecular level in modern clinical practice, such as breast cancer.

Doctor of Philosophy / Department of Psychology / Stephen W. Kiefer / Exposing rats to differential rearing conditions, during early post-weaning development, has been shown to produce changes in a number of behaviors displayed during adulthood. The purpose of the current study was to investigate whether rearing alcohol-preferring (P) and non-preferring (NP) rats in an environmental enrichment condition (EC), a social condition (SC), or an impoverished condition (IC) would differentially affect the consumption of and operant responding for 10% ethanol. In Experiment 1 rats were tested for both limited access and free access (two bottle choice between water and ethanol) consumption of 10% ethanol. For, Experiment 2 rats were trained to respond in an operant chamber for ethanol and then provided concurrent access to 10% ethanol (right lever) and water (left lever). After concurrent access, rats were required to respond over a gradually increasing fixed-ratio schedule for 10% ethanol and finally a progressive ratio schedule for 10% ethanol, 15% ethanol, and 10% sucrose. For Experiment 3 rats were trained to respond for 10% sucrose and then assessed for the maintenance of operant responding for 10% sucrose. The data from this series of experiments shows that EC P rats consumed, responded for, and preferred 10% ethanol significantly less than their IC P counterparts. Also, EC P rats did not significantly differ from NP rats during any aspect of testing for all experiments. Experiment 3 failed to reveal a significant effect of rearing although there was a line effect that has been previously observed in the literature. Thus, it would appear from these results that rearing in an EC condition acts to protect alcohol-preferring rats from increased levels of consumption of, preference for, and responding for ethanol compared to rearing in an impoverished environment.