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The Utilization Of Eukaryotic Cell Types In Microbiomes For Semen, Vaginal Fluid, And Menstrual Blood Identification Using 18s Rdna, Ines Benaissa

Master of Science in Forensic Science Directed Research Projects

The accurate identification of body fluids is vital for crime scene investigation and forensic analysis. While many body fluids can be presumptively identified, there is a lack of confirmatory testing for verification. Therefore, the purpose of this study was to determine if body fluids (menstrual blood, vaginal fluid, and semen) could be differentiated based on their eukaryotic microbial communities. The target area of interest was the V9 hyper-variable region of 18S ribosomal DNA (18S rDNA). The samples were extracted, barcoded using a duel-index strategy, and PCR amplified before undergoing high throughput sequencing using the Illumina Miseq FGx instrument. The samples …

Biological Pathways Associated With Wild And Domestic Animals, Cayla Steemer, Laura Carson, Jim Hu, Gloria Regisford

Pursue: Undergraduate Research Journal

Background: Zoonotic diseases are problematic, in that, they impact both wild and domestic animals alike. Thus, there is a need to investigate the genomes of wild and domestic. Gene ontology (GO) is a major bioinformatics initiative, whereby descriptions of gene products across the database are developed and unified to describe all species. This process is performed by biocurators, who gather, annotate, and validate information on the databases, consequently affording easy access to accurate and updated data. In this study, we investigated the biocuration of two biological processes, DNA integration, which is used for DNA coding, and the tricarboxylic acid (TCA) …

Energy Content Of Seeds Of Common Sunflowers (Helianthus Annuus) In The Diet Of Scaled Quail (Callipepla Squamata) In Southeastern New Mexico, John L. Hunt, Matthew E. Grilliot, Troy L. Best, Dixie Lozano-Lopez, Emily R. Neilson, Isaac C. Castillo

Journal of the Arkansas Academy of Science

We analyzed the energy content of seeds of common sunflowers (Helianthus annuus) obtained from the crops of scaled quail (Callipepla squamata) collected from plains-mesa sand-scrub habitat in Eddy and Lea counties, New Mexico. Seeds were removed from crops and dried for 48 hours at 60°C to remove moisture and to standardize masses. Seeds were then analyzed for gross caloric value (i.e., energy content) in an oxygen bomb calorimeter. Energy content of seeds of common sunflowers from New Mexico was greater than that of many seeds previously reported from the diet of scaled quail and other granivorous …

The Effects Of Induced Polycystic Ovary Syndrome In Nag-1 Transgenic Mice, Nicholas Werner

All Master's Theses

Polycystic ovary syndrome (PCOS) is the leading cause of infertility among women in the US and the most common endocrine disorder among women. PCOS is characterized by cystic ovaries, hyperandrogenism (heightened levels of male sex hormones), altered menstrual cycles and various metabolic dysfunctions. The metabolic symptoms associated with PCOS are difficult to treat, as they are a result of hormonal imbalances, rather than diet. The human Non-Steroidal Anti-Inflammatory Drug Activated Gene (NAG-1) been shown to prevent diet-induced metabolic disorders and weight gain in mice. We hypothesized that the expression of NAG-1 may also prevent hormonal-induced metabolic disorders. To test this …

Group Differences In Mother-Infant Macaca Fascicularis Behavior, Parasite Load, And Body Condition Within An Anthropogenically Altered Forest, Elizabeth M.C. Coggeshall

All Master's Theses

This study aimed to establish preliminary health and behavioral data, as well as understand group variation for a large population of Macaca fascicularis individuals within an anthropogenically altered monkey forest. A parasitic analysis of 40 mother and infant individuals showed that M. fascicularis carried 13 different parasitic taxa, and that there was parasitic variation between groups. Body condition scores were determined using a newly created and adapted body condition scale from 146 sampled mother macaques. Body condition scores were significantly different between groups, specifically the pond group when compared to the three other groups. Mother-infant behavioral differences were seen between …

Effects Of Western Spruce Budworm Herbivory On Forest Soils And Litter Decomposition In Central Washington, Izak R. Neziri

All Master's Theses

Disturbances by herbivores can drive nutrient cycling in forest ecosystems by adding frass, carcasses, and molts to the forest floor which are broken down into nitrogen, phosphorous, and other elements to be recycled into biomass. Western spruce budworms are defoliators native to the central Cascades and their herbivory could increase the decomposition rate of forest materials by adding essential nutrients and/or by increasing light and rainfall penetration to the forest floor by thinning the forest canopy during outbreaks. Budworm defoliation events are expected to increase in severity as the climate warms, potentially altering forest ecosystem function. The purpose of this …

Coculture Model Of Blood-Brain Barrier On Electrospun Nanofibers, Mustafa Görkem Özyurt, Ece Bayir, Şule Doğan, Şükrü Öztürk, Ayli̇n Şendemi̇r

Turkish Journal of Biology

The blood-brain barrier (BBB) is a control mechanism that limits the diffusion of many substances to the central nervous system (CNS). In this study, we designed an in-vitro 3-dimensional BBB system to obtain a fast and reliable model to mimic drug delivery characteristics of the CNS. A support membrane of polycaprolactone nanofiber surfaces was prepared using electrospinning. After confirming the fiber morphology and size, endothelial cells (HUVEC) and glial cells were cultured on either side of this membrane. The model's similarity to in vivo physiology was tested with a home-designed transmembrane resistance (TR) device, with positive and negative control molecules. …

Akt-Mediated Phosphorylation Of Twist1 Is Essential For Breast Cancer Cell Metastasis, Mustafa Gökhan Ertosun, Suray Pehli̇vanoğlu, Sayra Di̇lmaç, Gamze Tanriöver, Osman Ni̇dai̇ Özeş

Turkish Journal of Biology

Previously, it was shown that human TWIST1 (basic helix-loop-helix (b-HLH) is phosphorylated by Akt kinase at S42, T121, and S123. To show in vivo effect of these phosphorylations, we created mouse TWIST1 expression vector and converted the codons of S42, T125, and S127 to unphosphorylatable alanine and phosphorylation mimicking Glutamic acid. We hypothesized that alanine mutants would inhibit the metastatic ability of 4T1 cells while glutamic acid mutants would convert nonmetastatic 67NR cells into metastatic phenotype. To confirm this hypothesis, we created metastatic 4T1 and nonmetastatic 67NR cells expressing alanine mutants and glutamic acid mutants mouse TWIST1, respectively. Then, we …

Simultaneous Production Of Alpha And Beta Amylase Enzymes Using Separate Gene Bearing Recombinant Vectors In The Same Escherichia Coli Cells, Di̇lek Özcan Yardim, Hi̇kmet Murat Si̇pahi̇oğlu

Turkish Journal of Biology

The present study describes the simultaneous expression of thermostable industrial alpha (α) and beta (ß) amylase enzymes that have been used widely in starch industry. Genomic DNA of Bacillus stearothermophilus DSM 22 strain for α amylase and, Thermoanaerobacterium (Clostridium) thermosulfurogenes DSM 2229 strain for ß amylase were used as gene sources. Both genes were ligated into pETDuet-1 expression vector separately and resulting recombinant vectors were transformed into Escherichia coli BL21 competent cells by electroporation. The cells were first transformed by pETDuet-1/ αAmy recombinant plasmid, then the competent cells carrying this plasmid were prepared for the transformation of pETDuet-1/ ßAmy plasmid. …

Walleye Sander Vitreus Visceral Fat Accumulation, Cole Daleiden, Seth Renner

Journal of Earth and Life Science

For ectothermic species, proper lipid retention is critical to surviving in regions with limited growing seasons. Visceral fat is the dominant form of this energy storage in fish. Build up and depletion of these lipids occur seasonally as activity levels change throughout winter and spring. Due to this annual pattern, the purpose of this study is to determine a trend in the amount of visceral fat Walleye Sander vitreus accumulate in a time of year when metabolic rates are low and transition into the spawning process has yet to occur. Angling was the method of capture conducted during the months …

Effects Of Gap Junction Blockage On Regenerating Body Segments Of Lumbriculus Variegatus, Monica K. Richmond

Cal Poly Humboldt theses and projects

Lumbriculus variegatus is a freshwater annelid that is well known for its regenerative capacity. There are many different factors that affect regeneration in animals. Cell-to-cell communication is a key component of regeneration. Gap junctions are made up of proteins that create a channel that connects the cytoplasm of two cells. Many molecules and ions pass through the gap junctions that can affect regeneration. The purpose of this study was to determine if blocking gap junctions would have an impact on regenerating body segments of L. variegatus and what effects it would produce. L. variegatus was exposed to a known gap …

Full Issue: Volume 14, Number 1, Fall 2020

The Science Journal of the Lander College of Arts and Sciences

Complete .pdf file of Volume 14, number 1 of The Science Journal of the Lander College of Arts and Sciences. Published Fall 2020.

The Effect Of Seasonality On Yellow Perch Ecology And Ecotoxicology Within Lake Manganese, Bailey Duxbury

Dissertations, Master's Theses and Master's Reports

Seasonality is a consistent component of aquatic ecosystems yet most fish biological and ecotoxicological studies commonly employ field sampling protocols focused during the warm open water season with minimal emphasis placed on winter sampling, especially for north-temperate latitude ecosystems. Such strategies limit our understanding of poikilotherm biology and ecology during the overwintering seasons. Here, I investigated seasonal changes in yellow perch (Perca flavescens) biology, ecology and ecotoxicology over a one-year period in Lake Manganese. Significant seasonality was observed for metrics including fish energy densities (kJ/g), gonadosomatic indices, whole-body lipid contents, and carbon stable isotope values (δ¹³C). …

Detection And Classification Of Eurasian Watermilfoil With Multispectral Drone-Enabled Sensing, Colin Brooks

Dissertations, Master's Theses and Master's Reports

Littoral zones support growth of submerged aquatic vegetation, creating productive areas that provide food and habitat for fish, amphibians, macroinvertebrates, and other parts of the food web. Understanding macrophyte dynamics requires the identification of submerged aquatic vegetation (SAV) taxa, which can be possible if taxa of interest are spectrally distinct with data collected at appropriate scales. Eurasian watermilfoil, Myriophyllum spicatum or EWM, is a non-native SAV species that forms thick, often monotypic beds that reduce benthic species richness, restrict recreation, reduce property values, clog water intakes, and lower dissolved oxygen concentrations. Remote sensing of SAV species has to address the …

Evaluation Of Recombinant Human Vascular Endothelial Growth Factor Vegf121-Loaded Poly-L-Lactide Microparticles As A Controlled Release Delivery System, Sunil Abraham, Srinivasa Prasad Rangaswamy, Amutha Chinnaiah

Turkish Journal of Biology

Vascular endothelial growth factor A (VEGF-A) is an important growth factor that plays a major role in angiogenesis. With different isoforms distributed in various tissues, the shortest isoform of VEGF-A is VEGF121, one of the physiologically functional variants next to VEGF165. It is well known that VEGF has a shorter half-life, and the stability of the protein must be considered in therapeutic aspects. Poly-l-lactide (PLA) microparticles can release the encapsulated protein in a sustained release mode. In this study, the VEGF121 gene was cloned and expressed in a prokaryotic expression system (Escherichia coli). The recombinant VEGF121 was encapsulated with PLA …

The Methanolic Extract Of Garcinia Atroviridis (Mega) Reduces Body Weight And Food Intake, And Improves Lipid Profiles By Altering The Lipid Metabolism: A Rat Model, Wai Feng Lim, Suriati Mohd Nasir, Lay Kek Teh, Richard Johari James, Mohd Hafidz Mohd Izhar, Mohd Zaki Salleh

Turkish Journal of Biology

Garcinia species are widely used for their slimming effects via increased fat burning and suppression of satiety. However, scientific evidence for the biological effects of Garcinia atroviridis (GA) is lacking. We investigated the phytochemical composition, safety profiles, and antioxidant and antiobesity effects of methanolic extracts of Garcinia atroviridis (MeGa) in obese female rats. Repeated dose toxicity studies were conducted according to the OECD guidelines. Upon sacrifice, haematological, biochemical, lipid profile, and serum-based metabolomics analyses were performed to evaluate metabolic expression changes and their related pathways. MeGa contains several phytochemical groups and GA fruit acids. MeGa was found to be nontoxic …

A Planarian Kinesin Associated Protein 3 Homolog Is Required For Spermatogenesis And Ciliogenesis, Donovan Christman

Browse all Theses and Dissertations

Microtubule-based structures are an essential part of eukaryotic cells as they are involved in a number of processes such as phagocytosis, chromosome separation, intracellular transport, and cell motility. Transport along microtubules is accomplished by kinesin superfamily proteins (KIFs), which are motor proteins that bind cargo and use ATPase activity to move along microtubules in an anterograde fashion. One of the most common kinesin complexes is the heterotrimeric Kinesin 2 complex which is composed of KIF3 subunit dimers and the Kinesin Associated Protein 3 (KAP3). This complex is known as the KIF3 complex and functions along microtubules in cilia and flagella. …

Claw Morphology Impacts Clinging Performance On Rough Substrates, Alexandra Pamfilie

Williams Honors College, Honors Research Projects

The digits of anoles and geckos have been extensively investigated for their adhesive pads, which allow them to adhere effectively to smooth surfaces. Many pad-bearing lizards also possess claws, which have been posited as the principal contributor to clinging on rough surfaces. Previous studies have found correlations between habitat use and claw morphology, but whether variation in claw morphology impacts function or not has remained relatively understudied. In addition, it is reasonable to suggest that abrasive wear of the claws may impact clinging ability. I examined both natural and induced variation in the claw morphology of Cuban knight anoles ( …

A Mechanism For Sex Determination In Dioecious Cultivated Spinach, Nicholas West

Wayne State University Dissertations

While unisexual flowers have evolved repeatedly throughout angiosperm families, the actual identity of sex determining genes has been elusive, and their regulation within populations remains largely undefined. Additionally, sex liability is often observed in unisexual plants and has been correlated to external and internal cues, suggesting that the genes responsible for unisexual morphology are not necessarily segregating but rather differentially regulated. Understanding these processes will be of significant theoretical and agronomical importance.

Cultivated spinach is a dioecious species in which an individual will bear alternative sexual organs. Previous work has identified spinach B class floral organ identity genes, SpAP3 and …

Inaccurate And Biased Global Media Coverage Underlies Public Misunderstanding Of Shark Conservation Threats And Solutions, Sarah Joy Bittick

Biology Faculty Works

Sharks are a taxon of significant conservation concern and associated public interest. The scientific community largely supports management policies focusing on sustainable fisheries exploitation of sharks, but many concerned members of the public and some environmental advocates believe that sustainable shark fisheries cannot and do not exist and therefore support total bans on all shark fisheries and/or trade in shark products. The belief that sustainable shark fisheries cannot and do not exist persists despite scientific evidence showing that they can and do, and are important to livelihoods. Additionally, many concerned members of the public are only aware of one threat …

The Impact Of Key Processing Stages And Flock Variables On The Prevalence And Levels Of Campylobacter On Broiler Carcasses, Malgorzata Emanowicz, Joseph Meade, Declan Bolton, Olwen Golden, Montserrat Gutierrez, William Byrne, John Egan, Helen Lynch, Lisa O'Connor, Aidan Coffey, Brigid Lucey, Paul Whyte

Department of Biological Sciences Publications

This study examined the impact of key processing stages and flock variables on the prevalence of Campylobacter on broiler carcasses. Overall, the prevalence of Campylobacter was 62% in caeca, and 68%, 65% and 62% in neck skin samples collected after evisceration, final wash and carcass chilling, respectively. Campylobacter were found in 32% of caeca, and 52%, 40% and 32% of neck skin samples collected after evisceration, final wash and carcass chilling, respectively from first thin broiler batches. Final thin broiler batches were more frequently contaminated with prevalences of 83% found in caeca, 80% in neck skin samples collected after evisceration …

Investigating The Nightime Departures Of Glaucous-Winged Gulls (Larus Glaucescens) And The Role Of Social Facilitation, Devon Leigh Mcclain

Master's Theses

Daytime behaviors and occupancy patterns of Glaucous-winged Gulls (Larus glaucescens) have been described and can be mathematically predicted based on environmental factors. However, little is known about the nighttime behaviors of Glaucous-winged Gulls. I used trail cameras to study the daytime and nighttime colony occupancy patterns of Glaucous-winged Gulls on a breeding colony on Protection Island, Washington, USA. Early in the breeding season gulls desert the colony en masse during nighttime even after some gulls have initiated clutches. Using acoustic recording units to identify an acoustic cue that signals the onset of the coordinated nightly departures from the colony, I …

Paleoenvironmental Implications Of Small-Animal Fossils From The Black Mountain Turtle Layer And Associated Layers, Eocene Of Wyoming, Jeremy Mclarty

Master's Theses

The Bridger Formation is an Early Middle Eocene deposit in southwestern Wyoming that preserves a rich record of life from North America. Some horizons within the Bridger Formation contain abundant fossil turtle shells, but turtle skulls are rarely found. Previous research focused on one of these fossil-rich horizons, the Black Mountain turtle layer, to develop a model for the abundance and taphonomic condition of the fossil turtles. The proposed model begins with a limestone layer deposited in a lake. Then, an influx of fine-grained volcanic ash (forming the Black Mountain turtle layer) was rapidly deposited into this lake likely causing …

The Use Of Multiple Sensory Modalities By The Antillean Manatee (Trichechus Manatus Manatus) To Locate Food In Their Natural Environments, Amanda Marie Moore

Master's Theses

Manatees are herbivorous aquatic mammals found in the coastal and inland waters of the Atlantic Ocean. All three manatee species are currently listed as vulnerable on the IUCN red list and there still remains much unknown about their ecology. It is currently unknown what sensory modalities manatees use to locate their food in the wild. A literature review of the Paenungulata clade (sirenians, proboscideans, and hyracoideans) was conducted in order to compare and contrast what is known about the sensory modalities of the clade, to better understand the sensory modalities of manatees, particularly the ones they use to locate their …

Functional Analysis Of Fam83d And Dupd1 – Two Novel Neruogenic Skeletal Muscle Atrophy-Induced Genes, Lisa Michelle Cooper

UNF Graduate Theses and Dissertations

Fam83d and Dupd1 have been identified as novel genes in skeletal muscle that are upregulated in response to neurogenic atrophy in a mouse model. qPCR analysis reveaed both genes are expressed in skeletal muscle with Fam83d expression being highest during myoblast proliferation, while Dupd1 expression is highest during myotube differentiation. Overexpression of either protein results in inhibition of proper muscle cell differentiation as evidenced by repression of both myosin heavy chain and myogenin expression. Characterization of transcriptional activity revealed both genes are modulated by myogenic regulatory factors and additionally, Dupd1 expression is enhanced by dexamethasone treatment. Assessment of subcellular localization …

An Insight Into The Epitope-Based Peptide Vaccine Design Strategy And Studies Against Covid-19, Murat Topuzoğullari, Tayfun Acar, Peli̇n Peli̇t Arayici, Burcu Uçar, Erennur Uğurel, Emrah Şefi̇k Abamor, Tüli̇n Arasoğlu, Di̇lek Balik, Serap Derman

Turkish Journal of Biology

SARS-CoV-2 is a new member of the coronavirus family and caused the pandemic of coronavirus disease 2019 (COVID-19) in 2020. It is crucial to design and produce an effective vaccine for the prevention of rapid transmission and possible deaths wcaused by the disease. Although intensive work and research are being carried out all over the world to develop a vaccine, an effective and approved formulation that can prevent the infection and limit the outbreak has not been announced yet. Among all types of vaccines, epitope-based peptide vaccines outshine with their low-cost production, easy modification in the structure, and safety. In …

Gut Microbiota Composition Is Correlated To Host Hummingbird Protein Requirements, Ryan C. Stanton , '20

Senior Theses, Projects, and Awards

The gut microbiome shapes and is shaped by a host animal’s physiology. Avian taxa hold physiological characteristics unique from mammals and might inform novel pressures experienced by microbial communities. Further, the symbionts’ relative abundance and their abilities to adapt to available resources are of critical importance to a holobiont’s fitness in rapidly changing climates. Therefore, wild populations of hummingbirds Selasphorus rufus and Calypte anna were studied. The two systems differ in S. rufus’s annual migrations from wintering grounds to their breeding grounds in the Pacific Northwest, whereas C. anna are resident in the latter region. Previous findings have indicated …

The Evolution Of Dragons, Laura J. Mayfield

Undergraduate Theses, Professional Papers, and Capstone Artifacts

Dragons have been depicted in human art as early as 4500 BCE. For centuries, these fantasy creatures have inspired countless folk and fantasy tales, as well as appearing in the art of different cultures around the world. Now there are thousands of different depictions of these huge, flying, fire-breathing lizards, but are any of them possible? In this study, I reference peer-reviewed scientific articles, phylogenetic analysis, and paleoart studies to create biologically-sound dragons. Basing the dragon lineage on a real branch of webbed-winged scansoriopterygids—an extinct family of climbing and gliding maniraptoran dinosaurs—I explored the possible wing-structure, fire-breathing abilities, and effects …

Examining Traumatic Bone Fracture Healing Versus Surgical Osteotomies In Canines And Resulting Rates Of Infection, Grace Gsellman

Williams Honors College, Honors Research Projects

The development of osteomyelitis after surgical osteotomies and fracture repair in canines can propose serious health risks, ultimately leading to additional intervention from veterinarians that can become costly for pet owners and effect prognosis for the patient. Preventive measures are currently implemented during surgery and postoperatively. However, infection rates still range from 3.0% to 7.9% (Clark et al., 2018). By examining traumatic bone fracture healing versus surgical osteotomies in canines through the collection of both clinical and radiographic medical records, our primary objective was to further understand the physiological mechanism by which osteomyelitis develops. Limitations related to the collection of …

Brown Booby Family Units: Comparing Mothers, Fathers, And Chicks Through Stable Isotopes, Erin Taylor

Williams Honors College, Honors Research Projects

Seabird behavior and diet is important to study in order to determine where to focus conservation efforts in a rapidly changing climate. A primary aim of my project is to understand how brown booby family members from a breeding colony on Islas Marietas, Mexico relate to each other isotopically and in terms of their diet. Comparing the family units (mother, father, and chick from the same nest) of these seabirds and sex trends overall will help develop the big picture to determine the best conservation efforts for this species. I also aim to improve our ability to compare seabird plasma …