Life Sciences Commons^™

Optimization Of In-Vitro Tissue Culture And Transformation System For Sweet Sorghum Cultivars Using Immature Inflorescence, Logayn Abushal

Theses and Dissertations

Background: Sweet sorghum is a multi-purpose crop that can be used for human food, animal feed, and bio-fuel production. This crop is drought-tolerant and can therefore be grown in arid and semi-arid regions especially in marginal areas in Egypt. Nevertheless, production of Sweet sorghum cannot coup with the increasing demand in consumption as a food, and fuel due to a lag in scientific research regarding its genetic improvement. Therefore, genetic improvement of Sweet sorghum is innately required so that new traits of economic importance could be introduced; however, this can only be achieved through the establishment of a robust in-vitro …

Soil Organic Carbon In Maine, Its Responses To Biochar Addition, And Climate Change, Xue Bai

Electronic Theses and Dissertations

Soil organic carbon (SOC), as one of the largest C pools in terrestrial ecosystems, plays a key role in governing soil ecosystem processes and climate regulation. Climate change concerns have resulted in a rapidly growing interest in understanding the potential for natural climate solutions (NCS) that include enhancing SOC sequestration and reduce net atmospheric greenhouse gas (GHG) emissions. This research focused on addressing information needs about SOC in Maine, specifically in evaluating available soil databases to accurately quantify SOC density and concentration, and study the response of selected representative Maine soils to biochar amendments under a changing climate.

Maine SOC …

Evaluating A Test For Shedding Propensity Using Tape Lifts From Different Skin Locations, Xiao M. Chen

Student Theses

The shedding propensity of a person can assist data interpretation in casework when assessing the possibility of passive transfer for DNA analysis. Past studies on shedding propensity evaluated palmar skin (washed and unwashed) deposits. This study compared different skin locations with respect to shedding propensity, and explored the potential of tape-lifts as a skin surface collection method. Eight different skin types and samples were collected with adhesive tape disks from 28 participants over three non-consecutive days; the washed and unwashed fingers from both hands, toe, and arm, neck below ear, and nape. Samples were extracted, quantified, amplified, genotyped, and evaluated …

Reproducibility Of Individual Dna Deposits Detected Through Cellular Fluorescence, Natalee Small-Davidson

Student Theses

Contact traces are an important part of DNA casework, but the probative value of any identified associations depends on the possibility of passive transfer. There is known individual variation in DNA left behind during contact, this DNA shedding propensity has an effect on whose DNA is detected. This study evaluated this variability using a cell staining approach. Volunteers were asked to deposit a fingerprint on a clean glass slide, then wash their hands and deposit a second fingerprint after a 30-minute wait without touching anything. Three sets of samples were collected over three consecutive weeks. Fingerprints were stained with a …

Linguistic Variation From Cognitive Variability: The Case Of English 'Have', Muye Zhang

Linguistics Graduate Dissertations

In this dissertation, I seek to construct a model of meaning variation built upon variability in linguistic structure, conceptual structure, and cognitive makeup, and in doing so, exemplify an approach to studying meaning that is both linguistically principled and neuropsychologically grounded. As my test case, I make use of the English lexical item ‘have' by proposing a novel analysis of its meaning based on its well-described variability in English and its embed- ding into crosslinguistically consistent patterns of variation and change.

I support this analysis by investigating its real-time comprehension patterns through behavioral, electropsychophysiological, and hemodynamic brain data, thereby incorporating …

Effects Of A Novel Dsrna-Based Insecticide On The Colorado Potato Beetle, Samuel J. Pallis

Electronic Theses and Dissertations

The Colorado potato beetle, Leptinotarsa decemlineata (Coleoptera: Chrysomelidae) is one of the most destructive pests of the cultivated potato, Solanum tuberosum. Colorado potato beetles have been devastating potato crops for the past 150 years and have expanded their range during that time, becoming a globally distributed agricultural pest. Potato beetles are well-suited to agricultural environments and have evolved some degree of resistance to virtually all chemical insecticides. As such, the development of novel control methods to both control potato beetle populations and manage the evolution of insecticide resistance are in constant demand

The knockdown of gene functioning through ribonucleic acid …

The Phase Behavior Of Ubqln Proteins And Implications For Protein Quality Control, Yiran Yang

Dissertations - ALL

The ubiquitin-proteasome system (UPS) and autophagy are essential pathways for maintaining protein quality control (PQC) in cells. Misfolded proteins and large aggregates are cleared by UPS and autophagy signaled by ubiquitin (Ub) or polyubiquitin (polyUb) chains. Shuttle proteins facilitate cargo transporting by interacting with both ubiquitin and degradation machineries. Previously, our lab discovered that the shuttle protein Ubiquilin-2 (UBQLN2) is recruited to stress granules in cells and undergoes liquid-liquid phase separation (LLPS) in vitro. LLPS is a biophysical process by which proteins separate themselves from the surrounding aqueous solution by forming protein-rich droplets. The overarching goals of this work are …

Direct Single Molecule Imaging Of Enhanced Diffusion For Enzymes And Enzyme-Conjugated Dna Origami, Mengqi Xu

Dissertations - ALL

Enzymes have been shown to diffuse faster in the presence of their substrates. Recently, we revealed new insights into this process of enhanced diffusion using single-particle tracking (SPT) with total internal reflection fluorescence (TIRF) microscopy. We found that the mobility of individual enzymes was enhanced three-fold in the presence of the substrate, and the motion remained Brownian. We showed that the relative increase in diffusion is independent of the total enzyme concentrations; and the oligomerization state of enzymes did not change during the catalytic turnover. These experiments ruled out the possibility that the enhanced enzyme diffusion was caused by the …

Fine Scales, Broad Consequences: Drivers And Effects Of Microclimatic Variation In Great Smoky Mountains National Park, Jordan Rebecca Stark

Theses - ALL

Climate is highly variable at scales that are not captured by most weather and climate models due to local effects of topography and living systems. This variation in microclimate has been noted for many decades but has been difficult to incorporate into quantitative understanding of ecological systems and processes due to the large amount of data and complex models required to adequately describe fine-scale patterns across complex landscapes. In recent years, models of thermal microclimate variation have been developed using low-cost temperature sensors, but few of these models have been used to predict the effects of microclimatic variation on ecological …

Investigating The Behavioral And Social Context Of Sound In The Surface Foraging Strategies Of Humpback Whales (Megaptera Novaeangliae), Sarah Weiss

Theses - ALL

Humpback whales are known for the plastic and variable nature of their acoustic communication, social interactions, and foraging behaviors. Distinct foraging strategies are used to capture different prey types at the surface and on the seafloor. Sounds produced during foraging are thought to facilitate intraspecific social communication. Previous studies have identified specific sound types produced by humpbacks associated exclusively with benthic foraging strategies, suggesting functions related to foraging behavior. In this study, we use suction cup acoustic tags (DTAGs) deployed on humpbacks in the western North Atlantic from 2006-2009 to investigate the social sound production associated with surface foraging ecology, …

Evaluating Apoptosis, Autophagy, And Hormonal Effects On Oocyte Regulation And Cyst Breakdown, Jessica M. O'Connell

Theses - ALL

Infertility in women is caused by a depletion of eggs below the threshold for functional ovulation. Unlike men where sperm production is maintained throughout their reproductive lifespan, a women's proliferation of eggs ceases prior to birth. Interestingly during development, a fetus has up to 7 million eggs and two-thirds of these eggs die via apoptosis before they are born, further signifying the importance of the quantity control of eggs to maintain fertility. The remaining eggs break apart from each other and become enclosed individually by pre-granulosa cells together forming primordial follicles. Over time, the number of oocytes will continue to …

Cardiorespiratory Function In Young Adults With A History Of Covid-19 Infection, Danielle Arcidiacono

Theses - ALL

Objective. Respiratory complications may persist several months into the recovery period following COVID-19 infection. This study evaluated respiratory function and oxygen saturation variability between young adults with a history of COVID-19 infection and controls. Associations between cardiorespiratory function with potential biobehavioral correlates of COVID-19 infection were also explored.Methods. 57 adults ages 18 to 65 participated in this study (24 COVID+, 33 Control). Spirometry was used to assess pulmonary function volumes of forced vital capacity (FVC), forced expiratory volume in 1 second (FEV1), FEV1/FVC and peak expiratory flow (PEF). Exhaled nitric oxide (FeNO) was measured using the NiOX VERO, a handheld …

A Comparison Of The Effects Of Heat Therapy And Exercise Training On Vascular Function During Passive And Active Exercise, Taysom Erica Wallace

Theses and Dissertations

Recent evidence suggests that heat, a major byproduct of exercise, may be the mediator for many vascular adaptations that come from exercise. Thus, heat therapy that increases muscle temperature in a comparable way to exercise may be an advantageous alternative for enhancing cardiovascular health in individuals where treatment with exercise is either not possible or undesired. PURPOSE: Compare the effects of exercise and heat training on resistance artery function at rest and during exercise. METHODS: Thirty-five (18 female) healthy, untrained subjects completed a 6-week training program utilizing either high intensity knee extension (KE) exercise (40 min), localized heat therapy (pulsed …

Assessment Of Virus-Induced Myocarditis In Human Heart Tissue Samples, Gabriel Galeotos

Honors Theses

The heart is a major organ whose function is to transport nutrients and waste throughout the body. This organ can become infected by pathogens, such as viruses, bacteria, or parasites. Infection of the middle heart layer, or myocardium, is often caused by a viral agent. This disease has three stages: viral infiltration, adaptive immune system activation, and finally either viral clearance or cardiac cell remodeling. During this process the immune system will begin to secrete cytokines, which are signaling molecules that alert other members of the immune pathways, and also participate in cardiac remodeling. Evaluating the correlation between the cytokine …

Studying The Behavioral Role Of The Kcnn2 Gene In Zebrafish Embryos, Gina Dragonette

Honors Theses

Introduction: Mutations in the KCNN2 gene have been linked to phenotypes of movement disorders and autism. The goal of this experiment was to use the CIUSPR-Cas9 system to create a deletion within the KCNN2 gene and to observe the effect on the expression of movement in zebra fish embryos.

Methods: Linearized Cas9 DNA and guide DNA underwent in vitm transcription (IVT) reactions to produce RNA to be injected into zebrafish embryos at the one cell stage. KCNN guide RNAs were produced for the KCNN2 and KCNN3 genes (to prevent KCNN3 protein function from compensating for loss ofKCNN2's protein function), and …

Behavioral Patterns Of Goldfish (Carassius Auratus) Exploring A “Fish Tower”, Sasha Prasad-Shreckengast

Theses and Dissertations

Fish are held in captivity at some of the highest numbers of any taxa, but their curiosity is rarely studied. With this study, we set the groundwork to investigate the presence and nature of curiosity in goldfish (Carassius auratus) via novel free-choice exploration opportunities by creating a “fish tower."

Identifying Micrornas Panel Associated With Hepatocellular Carcinoma In Serum Of Chronic Hepatitis C Patients, Areeg Dabbish

Theses and Dissertations

Introduction: early detection of hepatocellular carcinoma (HCC) will reduce morbidity and mortality rates of this poorly diagnosed widely-spread disease. Dysregulation in microRNA (miRNAs) expression is associated with HCC progression. Objective: Is to identify a panel of differentially expressed miRNAs (DE-miRNAs) to enhance HCC early prediction in hepatitis C virus (HCV) infected patients. Methodology: Candidate miRNAs were selected using bioinformatic analysis of microarray and RNA-sequencing datasets, resulting in nine DE- miRNAs (miR-142, miR-150, miR-183, miR-199a, miR-215, miR-217, miR-224, miR-424 and miR-3607). Their expressions were validated in the serum of 44 healthy individuals, 62 non-cirrhotic HCV patients, 67 cirrhotic-HCV and 72 HCV-associated …

Deep Learning For Human Microrna Precursor Prediction: A Systematic Literature Review, Martina Ojonah

Master of Science in Information Technology Theses

The discovery of MicroRNA (miRNA) sparked medical breakthroughs, leading to the development of drugs/vaccines and biomarkers for some terminal diseases such as cancer. Due to the relatively short length of microRNAs, research has shown that discovering them on their own is a difficult task; thus, the focus has shifted to predicting precursor miRNAs, which are longer than miRNAs. Computational techniques evolve because of flaws discovered in existing designs, discoveries, and the desire to make the process as seamless as possible. Most researchers in recent studies indicated that the use of few input features and a lack of domain understanding of …

The Effects Of Temperature And Phasins On Polyhydroxyalkanoic Acid (Pha) Accumulation In Heterologous Hosts Containing A Pha Synthase From Vibrio Species B-18, Edward R. Lyons

Master's Theses, Dissertations, Graduate Research and Major Papers Overview

Polyhydroxyalkanoic acids (PHA) are bacterial carbon reserves with application as biodegradable biocompatible plastics. PHA synthase, encoded by phaC, creates the PHA polymer. Evidence presented by many researchers has emphasized the role of phasin proteins in PHA accumulation. Phasins have been implicated in PHA granule localization, PHA synthase activation, and possibly chaperone and nucleoid binding functions. The phaC gene from Vibrio species B-18 with and without an upstream gene showing homology to phasin genes (orf2) were placed into runaway replication vectors, which use temperature to control gene expression. The aim of this thesis is to explore earlier observations that lower temperatures …

Using Spatial Methods To Analyse Anthropogenic Predation Risk And Movement Ecology Of White-Tailed Deer (Odocoileus Virginianus), Rhiannon D. Kirton

Electronic Thesis and Dissertation Repository

Hunting has been used as a central tool by wildlife managers to maintain populations of game species, however, we still lack a good understanding of exactly how hunting influences deer biology. Technological advances in GPS data over the last two decades now enable us to perform more detailed analysis on the effects of human hunters on wildlife populations. This research explores the spatial ecology of hunters and White-tailed deer in the Cross Timbers ecoregion of Oklahoma. Using new statistical methodologies to analyse simultaneous GPS tracking data on deer and hunters to study their spatial interactions. The results show how new …

Determining Effects Of Management Practices On Potato Early Dying And Soil Microbiome And Assessing Risk Of Fungicide Resistance In Verticillium Dahliae, Kedi Li

Electronic Theses and Dissertations

Potato early dying (PED) is a yield-constraining soilborne disease of potato, caused by Verticillium spp. with V. dahliae being the predominant causal agent. Since the pathogen inhabits soil for long periods, PED management aims to reduce the population of V. dahliae in soil. Benzovindiflupyr and azoxystrobin are effective chemicals and frequently used in the control of V. dahliae. In this study, field trials were conducted at Aroostook Farm, Presque Isle, ME in 2019 and 2020. Chemical and biological products have been studied for PED control, and fungicide resistance was also examined. To evaluate fungicide resistance, benzovindiflupyr was characterized on …

Economics And Operational Decision Constraints Of Small-Diameter Tree Harvesting, Libin Thaikkattil Louis

Electronic Theses and Dissertations

Sustainably managed forests are crucial in balancing trade-off between various ecosystem functions and optimum product utilization. Improving the utilization of these renewable resources through diversified forest wood products faces various socio-economic, ecological, and cultural challenges. A major challenge faced by forest managers in the Northeastern United States is overstocked stands dominated by small-diameter trees (SDT). Major woody portion of the harvested residues is constituted by SDT and are typically of low value. Data from the national inventory indicates a high number of SDT in Northeastern forests such that the average size of all trees in the region is less than …

Identifying And Knocking Out Non-Visual Opsins In The Optic Tectum Of Zebrafish Larvae, Sarah Jarrett

Undergraduate Honors Theses

Deep brain photoreceptors (DBPs) are non-visual photoreceptors found in the brains of non-mammalian vertebrates like zebrafish. While using optogenetic techniques in our lab to photo-activate the ear (by expressing the light-gated channel: channelrhodopsin) in efforts of identifying optic tectum (OT) neurons that respond to and integrate auditory and visual stimuli, we found that violet light was able to elicit OT neuronal activity. OT activity was also detected in cases when visual and auditory stimulation was not possible due to removal of the eyes and absence of the exogenously expressed channelrhodopsin, respectively. Analyzing OT single-cell sequencing data of 7day post fertilization …

Real-Time Monitoring Of Cell Death Progress Using Capacitance Spectroscopy, Suyang Wu

Electronic Theses and Dissertations

Biologics, including the monoclonal antibody (mAb), has experienced rapid development in the last decade. However, the price of biologics is often prohibitively high because of the low process efficiency. Delaying the inevitable cell death improves the productivity of upstream bioprocessing, whose success relies on monitoring the cell death onset that indicates the timing for preventive actions.

This study proposes to develop a real-time monitoring model that quantifies the dying cell percentage in lab-scale bioreactors using capacitance spectroscopy. The capacitance spectroscopy contains cell death-related information due to various physical properties changes during the cell death process, e.g., cytoplasmic conductivity change. The …

Probing The Role Of Astrocytes In The Pathology Of Fragile X Syndrome With Human Stem Cells, Baiyan Ren

Theses & Dissertations

Fragile X syndrome (FXS) is an X-linked neurodevelopmental disorder related to intellectual disability and the most common monogenic cause of autism spectrum disorder. FXS is mainly caused by an expansion of CGG repeats in the 5’-untranslated region of fragile X mental retardation 1 (FMR1) gene, leading to the loss of expression of fragile X mental retardation protein (FMRP). Astrocytes are the most abundant glial cells in the central nervous system (CNS). Loss of FMRP in astrocytes has been found to contribute to structural and functional synaptic deficits in the Fmr1-KO mouse model. The contribution of human astrocytes, however, to the …

Understanding Snow Leopard (Panthera Uncia) Population Structure, Diet, And Human-Wildlife Dimensions Using Noninvasive Genetic Approaches, Charlotte Hacker

Electronic Theses and Dissertations

Snow leopards (Panthera uncia) are a large cat endemic to the mountains of Central Asia. Despite their status as a flagship species, there are numerous knowledge gaps surrounding their population status, dietary ecology, and relationship with humans. Such knowledge gaps are prohibitive for effective conservation action for the species. Snow leopards are threatened by habitat loss, decreased prey availability, retaliatory killings, and large-scale negative impacts associated with climate change. In order to help bridge these gaps, noninvasive genetic methodologies were deployed in this work across several disciplines. Population genetic metrics were garnered at local, regional, and range-wide scales, …

Analysis Of Spore Shape Determination In Streptomyces, Ning Sun

Electronic Theses and Dissertations

Streptomycetes are Gram-positive, soil-dwelling bacteria that possess a complex life cycle with the alternation of vegetative mycelium, aerial mycelium, and spores. Streptomyces. coelicolor spore maturation is a complex process that involves spore shape metamorphosis from cylindrical pre-spores into ellipsoid spores, but the details of this process have remained enigmatic. Previously, our lab identified a novel gene ssdA that might play a role in spore shape determination using a transposon-based insertion mutagenesis in S. coelicolor. In this study, I isolated a S. coelicolor ssdA-null mutant that showed increased colony hydrophobicity and misshapen spores in sizes and shapes, confirming the …

Cgrp-Driven Lateralization Of Pain Modulation By The Central Amygdala, Heather Allen

Electronic Theses and Dissertations

The central amygdala (CeA) is a bilateral, mid limbic brain region involved in the processing of pain and emotion. Interestingly, the left and right CeA are functionally lateralized in the context of bladder pain, with the left and right CeA having opposing effects on bladder pain-like behavior. However, the specific mechanisms driving these divergent functions are unknown. Nociceptive signals from the bladder are relayed to the CeA via projection neurons in the parabrachial nucleus (PBN) that express high levels of calcitonin gene-related peptide (CGRP). In these studies, we investigated the influence of PBN CGRP signaling in the left and right …

Who Pays To Clean Up What A Dying Industry Leaves Behind?, Audrey Carleton

Capstones

As the birthplace of oil and gas, Pennsylvania is home to the highest number of orphaned abandoned oil and gas wells in the country — an estimated 300,000 to 500,000 dot the Keystone State, all remnants of a dying industry. These wells emit methane, a potent greenhouse gas, and have, for decades, caused alarm to hundreds of residents, documents obtained in a months-long capstone investigation show. The state is currently plugging 10 to 12 abandoned wells per year, on average, out of hundreds of thousands, in part because it has not collected enough in cleanup funds from producers to fund …

Spaceflight And Differential Gene Expression Analysis Of Mice Quadriceps Exposed To Microgravity, Tommy Nguyen

Master's Projects

he trip to Mars and back is planned for the next 20 years. Improvement in technology and research has allowed data analysis, at a larger scale, on spaceflight specimen. However, research involving spaceflight is decentralized, as research is spread across laboratories with different methodologies. NASA’S GeneLab is a public repository for spaceflight-related omics data and promotes centralizing spaceflight RNA-Seq studies using NASA’s RNA-Seq pipeline. Jonathan Oribello, a SJSU’s Bioinformatics graduate and now an employee at GeneLab, has implemented Nextflow to NASA’s RNA-Seq pipeline. The Nextflow RNA-Seq pipeline was ran on San Jose State University’s College of Science High Performance Computing …