Life Sciences Commons^™

From Free-Energy Profiles To Activation Free Energies, Johannes C. Dietschreit, Dennis J. Diestler, Andreas Hulm, Christian Ochsenfeld, Rafael Gómez-Bombarelli

Department of Agronomy and Horticulture: Faculty Publications

Given a chemical reaction going from reactant (R) to the product (P) on a potential energy surface (PES) and a collective variable (CV) discriminating between R and P, we define the free-energy profile (FEP) as the logarithm of the marginal Boltzmann distribution of the CV. This FEP is not a true free energy. Nevertheless, it is common to treat the FEP as the “free-energy” analog of the minimum potential energy path and to take the activation free energy, ΔF‡ _RP, as the difference between the maximum at the transition state and the minimum at R. We show that this …

Igg Antibodies To Sars-Cov-2 In Asymptomatic Blood Donors At Two Time Points In Karachi, Muhammad Hasan, Bushra Moiz, Shama Qaiser, Kiran I. Masood, Zara Ghous, Areeba Hussain, Natasha Bahadur Ali, Syed Hani Abidi, Kulsoom Ghias, Erum Khan, Zahra Hasan

Department of Pathology and Laboratory Medicine

Introduction: An estimated 1.5 million cases were reported in Pakistan until 23 March, 2022. However, SARS-CoV-2 PCR testing capacity has been limited and the incidence of COVID-19 infections is unknown. Volunteer healthy blood donors can be a control population for assessment of SARS-CoV-2 exposure in the population. We determined COVID-19 seroprevalence during the second pandemic wave in Karachi in donors without known infections or symptoms in 4 weeks prior to enrollment.
Materials and methods: We enrolled 558 healthy blood donors at the Aga Khan University Hospital between December 2020 and February 2021. ABO blood groups were determined. Serum IgG reactivity …

Cellular Bioenergetics: Experimental Evidence For Alcohol-Induced Adaptations, Liz Simon, Patricia E. Molina

School of Medicine Faculty Publications

At-risk alcohol use is associated with multisystemic effects and end-organ injury, and significantly contributes to global health burden. Several alcohol-mediated mechanisms have been identified, with bioenergetic maladaptation gaining credence as an underlying pathophysiological mechanism contributing to cellular injury. This evidence-based review focuses on the current knowledge of alcohol-induced bioenergetic adaptations in metabolically active tissues: liver, cardiac and skeletal muscle, pancreas, and brain. Alcohol metabolism itself significantly interferes with bioenergetic pathways in tissues, particularly the liver. Alcohol decreases states of respiration in the electron transport chain, and activity and expression of respiratory complexes, with a net effect to decrease ATP content. …

Identification Of Secondary Structural Elements Contained Within The Intrinsically Disordered N-Terminal Tail Of The Bloom’S Syndrome Helicase., Vivek Somasundaram

USF Tampa Graduate Theses and Dissertations

The Bloom’s Syndrome Helicase (BLM) is one of five human RecQ helicases and is necessary for maintenance of genome stability. Whilst a crystal structure exists for the C-terminal domain of BLM, very limited structural knowledge is known about the intrinsically disordered N-terminal tail. This lack of insight exists, despite the fact that the N-terminus of BLM is essential for the overall biological activity of BLM. Here we provide an Nuclear Magnetic Resonance spectroscopy based approach that we used to identify two distinct ⍺-helices contained within the first 100 residues of BLM. In addition, we propose a mutagenesis-based approach involving rationally …

Mechanisms And Roles Of Dynamic Actin Assembly Around Dysfunctional Mitochondria, Tak Shun Fung

Dartmouth College Ph.D Dissertations

Possessing the ability to efficiently generate ATP required to sustain cellular functions, mitochondria are often considered the ‘powerhouses of the cell’. However, our understanding of mitochondria in cell biology was further expanded when we recognized that communication between this unique organelle and the rest of the cell regulates cellular bioenergetics, metabolism and signaling processes such as mitophagy and apoptosis. Here, I investigate signaling between mitochondria and the actin cytoskeleton, and how this signaling regulates mitochondrial dynamics and cellular function. Specifically, I find that, upon mitochondrial dysfunction, actin polymerizes rapidly around the dysfunctional organelle, which we term ‘acute damage-induced actin’ (ADA). …

Smokejumper Obituary: Gregerson, Ralph Rudolph (Mccall 1950), National Smokejumper Association

Smokejumper Obituaries

No abstract provided.

Understanding The Effects Of Phthalate Exposure, Karen Orenshteyn

Graduate Student Dissertations, Theses, Capstones, and Portfolios

Phthalates are found in nearly all everyday products; therefore, human exposure is inevitable. Phthalates are groups of chemicals classified as plasticizers that help increase the durability and shelf life of whatever product they are put into. The effects of phthalates can occur prenatally and throughout adulthood. Despite phthalates being understood to be endocrine disruptors, chemicals that block hormones and certain receptors, phthalate use within plastics is increasing every year- raising concern to find different alternatives. This research analysis will aim to define and explain what phthalates are and where they are found along with the harmful effects that occur due …

Analysis Of Sanitizer Rotation On The Susceptibility, Biofilm Forming Ability And Caco-2 Cell Adhesion And Invasion Of Listeria, Md Asfakur Rahman, Nirakar Sahoo, Veerachandra K. Yemmireddy

School of Integrative Biological & Chemical Sciences (Formerly Dept. of Biology)

The purpose of this study was to determine the effect of sanitizer use conditions on the susceptibility, biofilm forming ability and pathogenicity of Listeria monocytogenes. Two different strains of L. monocytogenes and a non-pathogenic L. innocua were exposed to sodium hypochlorite, benzalkonium chloride and peroxyacetic acid at different concentrations (4 to 512 ppm) and treatment times (30 s to 5 min), respectively. Under the tested conditions, no significant difference (p > 0.05) in reduction was observed among the three tested sanitizers. A reduction of 1 to 8 log CFU/mL was observed depending upon the sanitizer concentration and treatment times. The survived …

Explicit And Implicit Emotion Processing In The Cerebellum: A Meta‑Analysis And Systematic Review, Jordan E. Pierce, Marine Thomasson, Philippe Voruz, Garance Selosse, Julie Péron

Center for Brain, Biology, and Behavior: Faculty Publications

The cerebellum’s role in affective processing is increasingly recognized in the literature, but remains poorly understood, despite abundant clinical evidence for affective disruptions following cerebellar damage. To improve the characterization of emotion processing and investigate how attention allocation impacts this processing, we conducted a meta-analysis on task activation foci using GingerALE software. Eighty human neuroimaging studies of emotion including 2761 participants identified through Web of Science and ProQuest databases were analyzed collectively and then divided into two categories based on the focus of attention during the task: explicit or implicit emotion processing. The results examining the explicit emotion tasks identified …

Roundup And Glyphosate’S Impact On Gaba To Elicit Extended Proconvulsant Behavior In Caenorhabditis Elegans, Akshay Naraine, Rebecca Aker, Isis Sweeney, Meghan Kalvey, Alexis Surtel, Venkatesh Shanbhag, Ken Dawson-Scully

Chemistry and Physics Faculty Articles

As 3 billion pounds of herbicides are sprayed over farmlands every year, it is essential to advance our understanding how pesticides may influence neurological health and physiology of both humans and other animals. Studies are often one-dimensional as the majority examine glyphosate by itself. Farmers and the public use commercial products, like Roundup, containing a myriad of chemicals in addition to glyphosate. Currently, there are no neurological targets proposed for glyphosate and little comparison to Roundup. To investigate this, we compared how glyphosate and Roundup affect convulsant behavior in C. elegans and found that glyphosate and Roundup increased seizure-like behavior. …

Niche Partitioning Of Food Resources By Freshwater Mussels In A Multispecies Mussel Bed In The Sabine River, Marissa Netti

Biology Theses

Freshwater mussels (Unionids) are a very diverse group of bivalves, with about 300 species in the United States. Although freshwater mussels are very diverse, they are also critically endangered and are declining at extremely high rates. In fact, the U.S. Fish and Wildlife Service proposed excluding eight freshwater mussel species from the Endangered Species Act (ESA) in 2021 because they went extinct. Mussels play a key role in keeping our water systems healthy because of their filter feeding method. Filter feeding influences the rest of the ecosystem through the transfer of energy, cycling of nutrients, and purification of the surrounding …

Drift Macroalgal Distribution In Northern Gulf Of Mexico Seagrass Meadows, Kelly M. Correia, Scott B. Alford, Benjamin A. Belgrad, Kelly M. Darnell, M. Zachary Darnell, Bradley T. Furman, Margaret O. Hall, Christian T. Hayes, Charles W. Martin, Ashley M. Mcdonald, Delbert L. Smee

Faculty Publications

Drift macroalgae, often found in clumps or mats adjacent to or within seagrass beds, can increase the value of seagrass beds as habitat for nekton via added food resources and structural complexity. But, as algal biomass increases, it can also decrease light availability, inhibit faunal movements, smother benthic communities, and contribute to hypoxia, all of which can reduce nekton abundance. We quantified the abundance and distribution of drift macroalgae within seagrass meadows dominated by turtle grass Thalassia testudinum across the northern Gulf of Mexico and compared seagrass characteristics to macroalgal biomass and distribution. Drift macroalgae were most abundant in areas …

A Yield Comparison Between Small-Plot And On-Farm Foliar Fungicide Trials In Soybean And Maize, Anabelle Laurent, Emily Heaton, Peter Kyveryga, David Makowski, Laila A. Puntel, Alison E. Robertson, Laura J. Thompson, Fernando Miguez

Department of Agronomy and Horticulture: Faculty Publications

Agronomic research provides management recommendations based on small-plot trials (SPTs) and on-farm trials (OFTs) with very different characteristics. SPTs are traditionally conducted at agricultural experiment stations by research institutes or universities, while OFTs are conducted under commercial-scale conditions and managed by farmers using their own equipment. Several researchers claimed that discrepancies could occur between these two types of trials, which can make the extrapolation of results from SPTs to the farm level difficult. In our study, we conducted an extensive comparison of small-plot and on-farm trials to analyze the effect of foliar fungicide application on maize and soybean yields. We …

Metabolic Model Of Necrotizing Enterocolitis In The Premature Newborn Gut Resulting From Enteric Dysbiosis, Giorgio Casaburi, Jingjing Wei, Sufyan Kazi, Junlin Liu, Kewei Wang, Guo-Zhong Tao, Po-Yu Lin, James C. Y. Dunn, Bethany M. Henrick, Steven A. Frese, Karl G. Sylvester

Department of Nutrition and Health Sciences: Faculty Publications

Necrotizing enterocolitis (NEC) is a leading cause of premature newborn morbidity and mortality. The clinical features of NEC consistently include prematurity, gut dysbiosis and enteral inflammation, yet the pathogenesis remains obscure. Herein we combine metagenomics and targeted metabolomics, with functional in vivo and in vitro assessment, to define a novel molecular mechanism of NEC. One thousand six hundred and forty seven publicly available metagenomics datasets were analyzed (NEC = 245; healthy = 1,402) using artificial intelligence methodologies. Targeted metabolomic profiling was used to quantify the concentration of specified fecal metabolites at NEC onset (n = 8), during recovery ( …

Energy Drink Usage By Students Attending An Online University, Jodi Lynn Hutak, Ali Boolani, Lauri O. Byerley

School of Medicine Faculty Publications

Objective: This study determined the frequency, reasons for, and side effects of energy drinks (ED) consumption among online students. Participants: Students attending an online university. Methods: Participants were recruited by email and completed a 59-question survey about their prior months ED practices using a combination of validated surveys previously published examining similar constructs in on-campus students. Results: 307 students (age = 32.4 ± 6.5yrs) completed the survey, and 88% reported consuming EDs. Students’ reasons for consuming ED included school (p < .001), work (p < .001), an event/competition (p < .001), pick me up (p < .001), lack of rest (p < .001), more energy (p < .001), and staying awake while driving (p < .001). Only individuals who consumed > 10 ED/month reported side effects of headaches (p = .01) and speeding (p=.01). Conclusions: In our sample, a majority of …

Great-Tailed Grackles (Quiscalus Mexicanus) As A Tolerant Host Of Avian Malaria Parasites, M. Andreína Pacheco, Francisco C. Ferreira, Corina J. Logan, Kelsey B. Mccune, Maggie P. Macpherson, Sergio Albino Miranda, Diego Santiago-Alarcon, Ananias A. Escalante

Harold W. Manter Laboratory of Parasitology: Library Materials

Great-tailed Grackles (Quiscalus mexicanus) are a social, polygamous bird species whose populations have rapidly expanded their geographic range across North America over the past century. Before 1865, Great-tailed Grackles were only documented in Central America, Mexico, and southern Texas in the USA. Given the rapid northern expansion of this species, it is relevant to study its role in the dynamics of avian blood parasites. Here, 87 Great-tailed grackles in Arizona (a population in the new center of the range) were screened for haemosporidian parasites using microscopy and PCR targeting the parasite mitochondrial cytochrome b gene. Individuals were caught …

Climate Warming Amplifies The Frequency Of Fish Mass Mortality Events Across North Temperate Lakes, Simon P. Tye, Adam M. Siepielski, Andrew Bray, Andrew L. Rypel, Nicholas B.D. Phelps, Samuel B. Fey

Biological Sciences Faculty Publications and Presentations

Recent increases of animal mass mortality events have coincided with substantial changes in global climate. Yet, tractable approaches that predict how climate change will accentuate occurrences of these ecological catastrophes remain nascent. We compiled one of the most comprehensive datasets of lentic fish mortality events, thermal tolerances of affected families, and 1.2 million air and water temperature profiles across 8891 north temperate lakes in North America. Temperature extremes within and across lakes were strongly associated with the three most frequent cause types (infectious agents, summerkills, winterkills). Thermal tolerances mediated the lethality of direct thermal stress, but mortalities of warm- and …

Whole Genome Association Study Of The Plasma Metabolome Identifies Metabolites Linked To Cardiometabolic Disease In Black Individuals, Usman A. Tahir, Daniel H. Katz, Julian Avila-Pachecho, Alexander G. Bick, Akhil Pampana, John Blangero, Joanne Curran, Juan M. Peralta, Harald H. H. Goring, Michael Mahaney

School of Medicine Publications

Integrating genetic information with metabolomics has provided new insights into genes affecting human metabolism. However, gene-metabolite integration has been primarily studied in individuals of European Ancestry, limiting the opportunity to leverage genomic diversity for discovery. In addition, these analyses have principally involved known metabolites, with the majority of the profiled peaks left unannotated. Here, we perform a whole genome association study of 2,291 metabolite peaks (known and unknown features) in 2,466 Black individuals from the Jackson Heart Study. We identify 519 locus-metabolite associations for 427 metabolite peaks and validate our findings in two multi-ethnic cohorts. A significant proportion of these …

Grk3 Is A Poor Prognosticator And Serves As A Therapeutic Target In Advanced Gastric Adenocarcinoma, Yuan Li, Yibo Fan, Jinbang Xu, Longfei Huo, Ailing W Scott, Boxuan Yang, Lang Ma, Ying Wang, Xiaodan Yao, Melissa Pool Pizzi, Matheus Sewastjanow Da Silva, Guoliang Zhang, Lijuan Zhuo, Eun Jeong Cho, Kevin N Dalby, Namita D Shanbhag, Zhenning Wang, Wenliang Li, Shumei Song, Jaffer A Ajani

Faculty, Staff and Student Publications

Background: G protein-coupled receptor (GPCR) is the most targeted protein family by the FDA-approved drugs. GPCR-kinase 3 (GRK3) is critical for GPCR signaling. Our genomic analysis showed that GRK3 expression correlated with poor prognosis of gastric adenocarcinoma (GAC) patients. However, GRK3's functions and clinical utility in GAC progression and metastases are unknown.

Methods: We studied GRK3 expression in normal, primary, and metastatic GAC tissues. We identified a novel GRK3 inhibitor, LD2, through a chemical-library screen. Through genetic and pharmacologic modulations of GRK3, a series of functional and molecular studies were performed in vitro and in vivo. Impact of GRK3 on …

Two Interaction Surfaces Between Xpa And Rpa Organize The Preincision Complex In Nucleotide Excision Repair, Mihyun Kim, Hyun-Suk Kim, Areetha D'Souza, Kaitlyn Gallagher, Eunwoo Jeong, Kateryna Ogorodnik Le Meur, Miaw-Sheue Tsai, Minyong Kee, John A Tainer, Jung-Eun Yeo, Walter J Chazin, Orlando D Schärer

Faculty, Staff and Student Publications

The xeroderma pigmentosum protein A (XPA) and replication protein A (RPA) proteins fulfill essential roles in the assembly of the preincision complex in the nucleotide excision repair (NER) pathway. We have previously characterized the two interaction sites, one between the XPA N-terminal (XPA-N) disordered domain and the RPA32 C-terminal domain (RPA32C), and the other with the XPA DNA binding domain (DBD) and the RPA70AB DBDs. Here, we show that XPA mutations that inhibit the physical interaction in either site reduce NER activity in biochemical and cellular systems. Combining mutations in the two sites leads to an additive inhibition of NER, …

Clavibacter Nebraskensis Causing Goss's Wilt Of Maize: Five Decades Of Detaining The Enemy In The New World, Ebrahim Osdaghi, Alison E. Robertson, Tamra Jackson-Ziems, Hamid Abachi, Xiang Li, Robert M. Harveson

Department of Plant Pathology: Faculty Publications

Goss's bacterial wilt and leaf blight of maize (Zea mays) caused by the gram-positive coryneform bacterium Clavibacter nebraskensis is an economically important disease in North America. C. nebraskensis is included within the high-risk list of quarantine pathogens by several plant protection organizations (EPPO code: CORBMI), hence it is under strict quarantine control around the world. The causal agent was reported for the first time on maize in Nebraska (USA) in 1969. After an outbreak during the 1970s, prevalence of the disease decreased in the 1980s to the early 2000s, before the disease resurged causing a serious threat to …

Novel Designer Benzodiazepines: Comprehensive Review Of Evolving Clinical And Adverse Effects., Amber N. Edinoff, Catherine A. Nix, Amira S. Odisho, Caroline P. Babin, Alyssa G. Derouen, Salim C. Lutfallah, Elyse M. Cornett, Kevin S. Murnane, Adam M. Kaye, Alan David Kaye

School of Pharmacy Faculty Articles

As tranquilizers, benzodiazepines have a wide range of clinical uses. Recently, there has been a significant rise in the number of novel psychoactive substances, including designer benzodiazepines. Flubromazolam(8-bromo-6-(2-fluorophenyl)-1-methyl-4

Microplastics: Water And Oyster Data For The Indian River Lagoon, Linda Walters, Casey Craig

CEELAB Research Data

Microplastic (MP) abundances in surface waters and tissues of the oyster Crassostrea virginica were examined for one year in the Indian River Lagoon (IRL), a 251-km long estuary on the east coast of central FL, USA to better understand spatial and temporal variability. A total of 3755 MP were found in 44% of lagoon-wide water samples. Mean density (± CI) was 1.47 ± 0.09 MP/L. Central IRL sites had the lowest MP abundance, while the south had the most, likely associated with proximity to urbanization, inlets (MP sinks) and tributaries (MP sources). More MP were found in water …

Western Australia's Bulk And Containerised Grain Exports In A National Context, Ross Kingwell, Dipesh Maharjan

Research Reports

This report describes containerised and bulk grain exports from Western Australia and all other main grain-producing Australian states. The types of grain, their export volumes and destinations, since 2011-12 until 2021-22 are described.

Clavibacter Nebraskensis Causing Goss's Wilt Of Maize: Five Decades Of Detaining The Enemy In The New World, Ebrahim Osdaghi, Alison E. Robertson, Tamra Jackson-Ziems, Hamid Abachi, Xiang Li, Robert M. Harveson

Department of Plant Pathology: Faculty Publications

Goss's bacterial wilt and leaf blight of maize (Zea mays) caused by the gram-positive coryneform bacterium Clavibacter nebraskensis is an economically important disease in North America. C. nebraskensis is included within the high-risk list of quarantine pathogens by several plant protection organizations (EPPO code: CORBMI), hence it is under strict quarantine control around the world. The causal agent was reported for the first time on maize in Nebraska (USA) in 1969. After an outbreak during the 1970s, prevalence of the disease decreased in the 1980s to the early 2000s, before the disease resurged causing a serious threat to …

Clavibacter Nebraskensis Causing Goss's Wilt Of Maize: Five Decades Of Detaining The Enemy In The New World, Ebrahim Osdaghi, Alison E. Robertson, Tamra A. Jackson-Ziems, Hamid Abachi, Xiang Li, Robert M. Harveson

Department of Plant Pathology: Faculty Publications

Goss's bacterial wilt and leaf blight of maize (Zea mays) caused by the gram-positive coryneform bacterium Clavibacter nebraskensis is an economically important disease in North America. C. nebraskensis is included within the high-risk list of quarantine pathogens by several plant protection organizations (EPPO code: CORBMI), hence it is under strict quarantine control around the world. The causal agent was reported for the first time on maize in Nebraska (USA) in 1969. After an outbreak during the 1970s, prevalence of the disease decreased in the 1980s to the early 2000s, before the disease resurged causing a serious threat to maize production …

Assessing Changes In Freshwater And Marine Food Web Connections Following Restoration On The Penobscot River, Maine, Using Stable Isotope Analysis, Matthew Brewer Ms

Student Scholarship

Oiadromous fish provide ecological subsidies to freshwater and marine food

webs, connecting both ecosystems. A main goal of the Penobscot River Restoration

Project was to increase connectivity between food webs by removing two mainstem

dams, improving fish passage, and reintroducing river herring through stocking.

Oiadromous fish now reach historic spawning habitat that was not accessible for

centuries. As a result, river herring runs in the Penobscot River increased from

2,336 fish in 2009 to over 3 million fish by 2018. To assess food web connectivity in

the Penobscot watershed, I analyzed stable isotopes from samples collected before

(2009-2010) and after …

Nup211 Plays An Important Role In Regulating Mrna Export And Stress Response, Ayana Ikenouchi

Theses and Dissertations

Nup211 is a nuclear pore basket component in Schizosaccharomyces pombe and roles in the gating functions of NPCs. Using RT-qPCR, I found that in nup211-shutoff cells, the transcript levels of genes in mRNA export and stress-response pathways were significantly changed, suggesting nup211 is involved in regulating stress response pathways.

Associations Of Rare Caddisflies With The Western Dwarf Salamander Eurycea Paludicola, Lillie Hawkins

Biology Theses

There is limited information on the three species of caddisflies Philopotamidae Chimarra holzenthali, Hydropsychidae Cheumatopsyche morsei, Hydroptilidae Hydroptila ouachita and the western dwarf salamander Eurycea paludicola. In particular, there is a lack of any habitat associations between these caddisflies and the western dwarf salamander. Museum specimens of the caddisflies are scarce; however, the literature suggests they are spring dwelling like the western dwarf salamander. The goal of this project was to sample previously known and new habitats where these organisms might be found and report overall quality of the habitats and whether the caddisflies were associated with …

The Global Spread Of Misinformation On Spiders, Stefano Mammola, Jagoba Malumbres-Olarte, Valeria Arabesky, Diego Alejandro Barrales-Alcalá, Aimee Lynn Barrion-Dupo, Marco Antonio Benamú, Tharina L. Bird, Maria Bogomolova, Pedro Cardoso, Maria Chatzaki, Ren Chung Cheng, Tien Ai Chu, Leticia M. Classen-Rodríguez, Iva Čupić, Naufal Urfi Dhiya'ulhaq, André Philippe Drapeau Picard, Hisham K. El-Hennawy, Mert Elverici, Caroline S. Fukushima, Zeana Ganem, Efrat Gavish-Regev, Naledi T. Gonnye, Axel Hacala, Charles R. Haddad, Thomas Hesselberg, Tammy Ai Tian Ho, Thanakorn Into, Marco Isaia, Dharmaraj Jayaraman, Nanguei Karuaera, Rajashree Khalap, Kiran Khalap, Dongyoung Kim, Tuuli Korhonen, Laura Segura-Hernández, Et Al.

School of Biological Sciences: Faculty Publications

In the internet era, the digital architecture that keeps us connected and informed may also amplify the spread of misinformation. This problem is gaining global attention, as evidence accumulates that misinformation may interfere with democratic processes and undermine collective responses to environmental and health crises1,2. In an increasingly polluted information ecosystem, understanding the factors underlying the generation and spread of misinformation is becoming a pressing scientific and societal challenge3. Here, we studied the global spread of (mis-)information on spiders using a high-resolution global database of online newspaper articles on spider–human interactions, covering stories of spider–human encounters and biting events published …