Life Sciences Commons^™

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 …

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 …

High-Resolution Cryo-Electron Microscopy Structure Of Photosystem Ii From The Mesophilic Cyanobacterium, Synechocystis Sp. Pcc 6803, Christopher J. Gisriel, Jimin Wang, Jinchan Liu, David A. Flesher, Krystle M. Reiss, Hao-Li Huang, Ke R. Yang, William H. Armstrong, M. R. Gunner, Victor S. Batista, Richard J. Debus, Gary W. Brudvig

Publications and Research

Photosystem II (PSII) enables global-scale, light-driven water oxidation. Genetic manipulation of PSII from the mesophilic cyanobacterium Synechocystis sp. PCC 6803 has provided insights into the mechanism of water oxidation; however, the lack of a highresolution structure of oxygen-evolving PSII from this organism has limited the interpretation of biophysical data to models based on structures of thermophilic cyanobacterial PSII. Here, we report the cryo-electron microscopy structure of PSII from Synechocystis sp. PCC 6803 at 1.93-Å resolution. A number of differences are observed relative to thermophilic PSII structures, including the following: the extrinsic subunit PsbQ is maintained, the C terminus of the …

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."

Cryptococcus Neoformans Melanization Incorporates Multiple Catecholamines To Produce Polytypic Melanin, Rosanna P. Baker, Christine Chrissian, Ruth E. Stark, Arturo Casadevall

Publications and Research

Melanin is a major virulence factor in pathogenic fungi that enhances the ability of fungal cells to resist immune clearance. Cryptococcus neoformans is an important human pathogenic fungus that synthesizes melanin from exogenous tissue catecholamine precursors during infection, but the type of melanin made in cryptococcal meningoencephalitis is unknown. We analyzed the efficacy of various catecholamines found in brain tissue in supporting melanization using animal brain tissue and synthetic catecholamine mixtures reflecting brain tissue proportions. Solid-state NMR spectra of the melanin pigment produced from such mixtures yielded more melanin than expected if only the preferred constituent dopamine had been incorporated, …

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 …

Pushing It To The Limit: Determining Asian Elephant (Elephas Maximus) Olfactory Sensitivity And Discrimination Through A Behavioral Choice Task, Matthew S. Rudolph

Theses and Dissertations

Elephants have shown remarkable olfactory capabilities. Their sense of smell impacts their foraging choices, behavior, and ultimately, survival. Being able to detect a target odor can allow elephants to locate specific resources, identify threats, and find receptive conspecifics. Previous studies have shown that elephants can consistently detect target odors, but have not identified the limits of this detection. Thus, to investigate the extent of elephants’ odor detection capabilities, we tested Asian elephants in a two-step odor discrimination task. First, we investigated whether elephants could detect odors at varying levels of dilution after a training procedure, and then whether they could …

Dolphins In Ny? Researchers Turn To Boat Tours For Sightings, Aaron K. Tremper

Capstones

Before 2009, coastal bottlenose dolphins were a rare sight north of New Jersey. According to local researchers, large pods of bottlenose dolphins made their way that spring/summer along Long Island. While dolphin population data by state and federal wildlife regulators are spotty, studies by local scientists suggest more dolphins have been flocking to New York since 2009. Many researchers are turning to whale-watching ventures to learn more about what dolphins are up to in the Big Apple.

https://jkt711.github.io/capstone/

Lost At Sea, Anny Oberlink

Capstones

At the end of World War I and World War II, in a new era of peace, nations confronted an unprecedented logistical problem: millions of tons of unexploded ordnance—once a wartime boon—had become a peacetime burden. Faced with a mandate to dispose of excess munitions, militaries turned to dumping their stockpiles into the sea. But now a complex and urgent issue is emerging. Increasingly, as industry looks to build offshore—wind power turbines, internet cables, oil pipelines—they are facing a potential peril: millions of tons of unexploded bombs and ammunition that are lying on the ocean floor can explode or leak …

Elevated Growth And Biomass Along Temperate Forest Edges, Luca L. Morreale, Jonathan R. Thompson, Xiaojing Tang, Andrew B. Reinmann, Lucy R. Hutyra

Publications and Research

Fragmentation transforms the environment along forest edges. The prevailing narrative, driven by research in tropical systems, suggests that edge environments increase tree mortality and structural degradation resulting in net decreases in ecosystem productivity. We show that, in contrast to tropical systems, temperate forest edges exhibit increased forest growth and biomass with no change in total mortality relative to the forest interior. We analyze > 48,000 forest inventory plots across the north-eastern US using a quasi- experimental matching design. At forest edges adjacent to anthropogenic land covers, we report increases of 36.3% and 24.1% in forest growth and biomass, respectively. Inclusion of …

Inter-Subject Correlation While Listening To Minimalist Music: A Study Of Electrophysiological And Behavioral Responses To Steve Reich’S Piano Phase, Tysen Dauer, Duc T. Nguyen, Nick Gang, Jacek P. Dmochowski, Jonathan Berger, Blair Kaneshiro

Publications and Research

Musical minimalism utilizes the temporal manipulation of restricted collections of rhythmic, melodic, and/or harmonic materials. One example, Steve Reich’s Piano Phase, offers listeners readily audible formal structure with unpredictable events at the local level. For example, pattern recurrences may generate strong expectations which are violated by small temporal and pitch deviations. A hyper-detailed listening strategy prompted by these minute deviations stands in contrast to the type of listening engagement typically cultivated around functional tonal Western music. Recent research has suggested that the inter-subject correlation (ISC) of electroencephalographic (EEG) responses to natural audio-visual stimuli objectively indexes a state of “engagement,” demonstrating …

Genomic Epidemiology Of Clostridium Difficile Colonization And Transmission In An Intensive Care Unit Cohort, Brianne Ciferri

Dissertations and Theses

Abstract

Genomic epidemiology of Clostridium difficile colonization and transmission in an intensive care unit cohort

by Brianne Ciferri, MPH

Advisor: C. Mary Schooling, PhD

Introduction: Clostridiodes difficile (C. difficile) is a leading cause of healthcare associated infections (HAI) in the United States and responsible for an estimated incidence of 223,900 cases and 12,800 deaths per year^1,2. C. difficile can cause gastrointestinal illness with symptoms ranging from mild diarrheal illness to a life-threatening condition. C. difficile is an opportunistic pathogen in which spores can live in an undisturbed dormant state within the intestinal tract and become …

Exploration Of Dark Chemical Genomics Space Via Portal Learning: Applied To Targeting The Undruggable Genome And Covid-19 Anti-Infective Polypharmacology, Tian Cai, Li Xie, Muge Chen, Yang Liu, Di He, Shuo Zhang, Cameron Mura, Philip Boume, Lei Xie

Publications and Research

Advances in biomedicine are largely fueled by exploring uncharted territories of human biology. Machine learning can both enable and accelerate discovery, but faces a fundamental hurdle when applied to unseen data with distributions that differ from previously observed ones—a common dilemma in scientific inquiry. We have developed a new deep learning framework, called Portal Learning , to explore dark chemical and biological space. Three key, novel components of our approach include: (i) end-to-end, step-wise transfer learning, in recognition of biology’s sequence-structure-function paradigm, (ii) out-of-cluster meta-learning, and (iii) stress model selection. Portal Learning provides a practical solution to the out-of-distribution (OOD) …

A Preliminary Investigation Into The Effects Of Lucilia Sericata (Meigen) Blow Fly Larval Feeding On Sharp Force Trauma (Sft) Wound Patterns In Decomposing Bones Of Sus Scrofa Domesticus, Erica L. Klafehn

Student Theses

An important aspect of forensic investigations involves the characterization and analysis of bone related trauma as this can provide valuable information regarding the manner and circumstances of death. Bone trauma can be classified into three main categories, which include Sharp Force Trauma (SFT), Blunt Force Trauma (BFT), and Gunshot Trauma. Previous experiments have explored SFT on flesh and bones, specifically made with knives or saws, coupled with various microscopic analytical methods. Minimal research has been done integrating both a forensic entomology and forensic anthropology approach, so it is imperative to understand previous literature detailing the behaviors of insects (blow flies), …

Impact Of Blood Collection Tubes In Cannabinoid Quantitative Analysis, Tega E. Obruche-Akponah

Student Theses

In forensic toxicological cases, sample stability and storage are pivotal for obtaining adequate analytical results. Currently, limited information is available about the impact of different preservatives and anticoagulants present in the blood tubes used in the collection of blood samples containing cannabinoids. This study investigated the impact of sodium fluoride (gray top) and sodium citrate (blue top) blood collection tubes on the concentrations of tetrahydrocannabinol (THC), cannabidiol (CBD), cannabinol (CBN) and 5 THC metabolites (THC-OH, THC-COOH, THC-diOH, THC-glucuronide, THCCOOH-glucuronide) in whole blood samples, stored at room temperature, 4ºC and -20ºC for up to 3.5 months. The samples were extracted using …

Development And Validation Of A Method For The Determination Of Designer Benzodiazepines In Hair By Liquid Chromatography Tandem Mass Spectrometry (Lc-Ms/Ms), Laura C. Defreitas

Student Theses

In recent years, new designer benzodiazepines have become a challenge in forensic toxicology. These substances are analogues of the classic benzodiazepines, but their pharmacology is not well known, and many of them have been associated with overdoses and deaths. As a result, there has been a surge in efforts to develop ways to accurately test for these compounds in different biological matrices. This study focused to develop and validate a method for determining 17 new designer benzodiazepines in hair by liquid chromatography tandem mass spectrometry (LC-MS/MS). Hair samples were decontaminated, pulverized, and 20 mg of the sample was incubated in …

Genome-Scale Data Reveal Deep Lineage Divergence And A Complex Demographic History In The Texas Horned Lizard (Phrynosoma Cornutum) Throughout The Southwestern And Central Us, Nicholas Finger, Keaka Farleigh, Jason T. Bracken, Adam D. Leaché, Olivier François, Ziheng Yang, Tomas Flouri, Tristan Charran, Tereza Jezkova, Dean A. Williams, Christopher Blair

Publications and Research

The southwestern and central US serve as an ideal region to test alternative hypotheses regarding biotic diversification. Genomic data can now be combined with sophisticated computational models to quantify the impacts of paleoclimate change, geographic features, and habitat heterogeneity on spatial patterns of genetic diversity. In this study we combine thousands of genotyping-by-sequencing (GBS) loci with mtDNA sequences (ND1) from the Texas Horned Lizard (Phrynosoma cornutum) to quantify relative support for different catalysts of diversification. Phylogenetic and clustering analyses of the GBS data indicate support for at least three primary populations. The spatial distribution of populations appears concordant …

Phylogenomics Of Alligator Lizards Elucidate Diversification Patterns Across The Mexican Transition Zone And Support The Recognition Of A New Genus, Christopher Blair, Robert W. Bryson Jr, Uri O. García-Vázquez, Adrián Nieto-Montes De Oca, David Lazcano, John E. Mccormack, John Klicka

Publications and Research

Genomic data continue to advance our understanding of species limits and biogeographic patterns. However, there is still no consensus regarding appropriate methods of phylogenomic analysis that make the best use of these heterogeneous data sets. In this study, we used thousands of ultraconserved element (UCE) loci from alligator lizards in the genus Gerrhonotus to compare and contrast species trees inferred using multiple contemporary methods and provide a time frame for biological diversification across the Mexican Transition Zone (MTZ). Concatenated maximum likelihood (ML) and Bayesian analyses provided highly congruent results, with differences limited to poorly supported nodes. Similar topologies were inferred …

Competition And Geography Underlie Speciation And Morphological Evolution In Indo-Australasian Monitor Lizards, Carlos J. Pavón-Vázquez, Ian G. Brennan, Alexander Skeels, J. Scott Keogh

Publications and Research

How biotic and abiotic factors act together to shape biological diversity is a major question in evolutionary biology. The recent availability of large datasets and development of new methodological approaches provide new tools to evaluate the predicted effects of ecological interactions and geography on lineage diversification and phenotypic evolution. Here, we use a near complete phylogenomic-scale phylogeny and a comprehensive morphological dataset comprising more than a thousand specimens to assess the role of biotic and abiotic processes in the diversification of monitor lizards (Varanidae). This charismatic group of lizards shows striking variation in species richness among its clades and multiple …

Oligomerization Of Mutant P53 R273h Is Not Required For Gain-Of-Function Chromatin Associated Activities, George K. Annor, Nour Elshabassy, Devon Lundine, Don-Gerard Conde, Gu Xiao, Viola Ellison, Jill Bargonetti

Publications and Research

The TP53 gene is often mutated in cancer, with missense mutations found in the central DNA binding domain, and less often in the C-terminal oligomerization domain (OD). These types of mutations are found in patients with the rare inherited cancer predisposition disorder called Li-Fraumeni syndrome. We previously found that mutant p53 (mtp53) R273H associates with replicating DNA and promotes the chromatin association of replication-associated proteins mini-chromosome maintenance 2 (MCM2), and poly ADP-ribose polymerase 1(PARP1). Herein, we created dual mutants in order to test if the oligomerization state of mtp53 R273H played a role in chromatin binding oncogenic gain-of-function (GOF) activities. …

Structure Of A Monomeric Photosystem Ii Core Complex From A Cyanobacterium Acclimated To Far-Red Light Reveals The Functions Of Chlorophylls D And F, Christopher J. Gisriel, Gaozhong Shen, Ming-Yang Ho, Vasily Kurashov, David A. Flesher, Jimin Wang, William H. Armstrong, John H. Golbeck, Marilyn R. Gunner, David J. Vinyard, Richard J. Debus, Gary W. Brudvig, Donald A. Bryant

Publications and Research

Far-red light (FRL) photoacclimation in cyanobacteria provides a selective growth advantage for some terrestrial cyanobacteria by expanding the range of photosynthetically active radiation to include far-red/near-infrared light (700–800 nm). During this photoacclimation process, photosystem II (PSII), the water:plastoquinone photooxidoreductase involved in oxygenic photosynthesis, is modified. The resulting FRL-PSII is comprised of FRL-specific core subunits and binds chlorophyll (Chl) d and Chl f molecules in place of several of the Chl a molecules found when cells are grown in visible light. These new Chls effectively lower the energy canonically thought to define the “red limit” for light required to drive photochemical …

Insights Into Using Plants In Management Of Viral Diseases., Vyacheslav Dushenkov, Anna Dushenkov

Publications and Research

Botanical therapeutics possess a unique potential in the treatment of viral diseases. The pharmacological base and clinical use of botanical therapeutics have been extensively reviewed. The mode of action(s) may be built either on the direct interference with the virus's ability to enter human cells, virus replication, or exerting immune-modulatory and anti-inflammatory effects. The adjuvant treatment with botanical therapeutics has the potential to result in advances in symptom resolution, decrease in disease burden and shortening its duration.

Type Vi Secretion System Mutations Reduced Competitive Fitness Of Classical Vibrio Cholerae Biotype, Benjamin Kostiuk, Francis J. Santoriello, Laura Diaz-Satizabal, Fabiana Bisaro, Kyung-Jo Lee, Anna N. Dhody, Daniele Provenzano, Daniel Unterweger, Stefan Pukatzki

Publications and Research

The gram-negative bacterium Vibrio cholerae is the causative agent of the diarrhoeal disease cholera and is responsible for seven recorded pandemics. Several factors are postulated to have led to the decline of 6th pandemic classical strains and the rise of El Tor biotype V. cholerae, establishing the current 7th pandemic. We investigated the ability of classical V. cholerae of the 2nd and 6th pandemics to engage their type six secretion system (T6SS) in microbial competition against non-pandemic and 7th pandemic strains. We report that classical V. cholerae underwent sequential mutations in T6SS genetic determinants that initially exposed 2nd pandemic strains …

The Temperature-Dependent Conformational Ensemble Of Sars-Cov-2 Main Protease (Mpro), Ali Ebrahim, Blake T. Riley, Desigan Kumaran, Babak Andi, Martin R. Fuchs, Sean Mcsweeney, Daniel A. Keedy

Publications and Research

The COVID-19 pandemic, instigated by the SARS-CoV-2 coronavirus, continues to plague the globe. The SARS-CoV-2 main protease, or M^pro, is a promising target for development of novel antiviral therapeutics. Previous X-ray crystal structures of M^pro were obtained at cryogenic temperature or room temperature only. Here we report a series of high-resolution crystal structures of unliganded M^pro across multiple temperatures from cryogenic to physiological, and another at high humidity. We interrogate these datasets with parsimonious multiconformer models, multi-copy ensemble models, and isomorphous difference density maps. Our analysis reveals a temperature-dependent conformational landscape for M^pro, including …

Cryo-Em Structure Of Mechanosensitive Channel Ynai Using Sma2000: Challenges And Opportunities, Claudio Catalano, Danya Ben-Hail, Weihua Qiu, Paul Blount, Amedee Des Georges, Youzhong Guo

Publications and Research

Mechanosensitive channels respond to mechanical forces exerted on the cell membrane and play vital roles in regulating the chemical equilibrium within cells and their environment. Highresolution structural information is required to understand the gating mechanisms of mechanosensitive channels. Protein-lipid interactions are essential for the structural and functional integrity of mechanosensitive channels, but detergents cannot maintain the crucial native lipid environment for purified mechanosensitive channels. Recently, detergent-free systems have emerged as alternatives for membrane protein structural biology. This report shows that while membrane-active polymer, SMA2000, could retain some native cell membrane lipids on the transmembrane domain of the mechanosensitive-like YnaI channel, …

Dietary Diversity And Nutrient Intake Of Han And Dongxiang Smallholder Farmers In Poverty Areas Of Northwest China, Zhuo Wang, Youhai Chen, Shihua Tang, Siqi Chen, Shaoqing Gong, Xinyin Jiang, Liang Wang, Ying Zhang

Publications and Research

This study aimed to evaluate the status of dietary diversity and nutrient intake among Han and Dongxiang smallholder farmers in poor rural areas of northwest China. In this cross-sectional study, dietary intake was assessed in 499 smallholder farmers aged 18–75 years from two nationally designated impoverished counties in Gansu Province, China, using three consecutive 24 h dietary recalls. The dietary diversity score (DDS) and nutrient adequacy ratio (NAR) were adopted to assess dietary diversity and micronutrient adequacy, respectively. The mean DDS (range from 1 to 9) in participants was relatively low (3.81 ± 1.01). Consumption of grains was excessive, while …

Clock Time Of First Eating Episode And Prospective Risk Of All-Cause Mortality In Us Adults, Ashima K. Kant, Barry I. Graubard

Publications and Research

Background: There is increasing recognition that morning or evening preference is associated with time of eating, metabolic health, and morbidity. However, few studies have examined the association of time of eating with mortality.

Objective: To examine the association of time of first recalled ingestive episode with prospective risk of all-cause mortality.

Design: We used mortality-linked data from the National Health and Nutrition Examination Surveys (NHANES) conducted in 1988-1994 and 1999-2014 (n=34609; age >40 y). Quartiles (Q1-Q4) of clock time of first eating episode self-reported in the baseline 24-h dietary recall was the exposure. Follow-up time from date of NHANES examination …

Regulatory Non-Coding Rnas Modulate Transcriptional Activation During B Cell Development, Mary Attaway, Tzippora Chwat-Edelstein, Bao Q. Vuong

Publications and Research

B cells play a significant role in the adaptive immune response by secreting immunoglobulins that can recognize and neutralize foreign antigens. They develop from hematopoietic stem cells, which also give rise to other types of blood cells, such as monocytes, neutrophils, and T cells, wherein specific transcriptional programs define the commitment and subsequent development of these different cell lineages. A number of transcription factors, such as PU.1, E2A, Pax5, and FOXO1, drive B cell development. Mounting evidence demonstrates that non-coding RNAs, such as microRNAs (miRNAs) and long non-coding RNAs (lncRNAs), modulate the expression of these transcription factors directly by binding …

Expression, Purification And Refolding Of A Human Na V 1.7 Voltage Sensing Domain With Native-Like Toxin Binding Properties, Ryan V. Schroder, Leah S. Cohen, Ping Wang, Joekeem D. Arizala, Sébastien F. Poget

Publications and Research

The voltage-gated sodium channel NaV1.7 is an important target for drug development due to its role in pain perception. Recombinant expression of full-length channels and their use for biophysical characterization of interactions with potential drug candidates is challenging due to the protein size and complexity. To overcome this issue, we developed a protocol for the recombinant expression in E. coli and refolding into lipids of the isolated voltage sensing domain (VSD) of repeat II of NaV1.7, obtaining yields of about 2 mg of refolded VSD from 1 L bacterial cell culture. This VSD is known to be involved in the …

Globe Mosquito Habitat Mapper Citizen Science Data 2017–2020, Russanne Low, Rebecca Boger, Peder Nelson, Matteo Kimura

Publications and Research

The GLOBE Program's GLOBE Observer application is a free citizen science mobile data collection and visualization tool compatible with iOS and Android operating systems. Citizen scientists armed with the app can report the mosquito larval habitats they identify using the GLOBE Mosquito Habitat Mapper tool. This data can complement the climate, weather, and land cover data obtained from satellite measurements by scientists who develop risk models for mosquito-borne diseases. Public participation in mosquito surveillance research provides the opportunity to obtain the volume, velocity and variety of data needed to fight the threat of vector-borne diseases, especially in under-resourced communities with …