Digital Commons Network^™

Light-Driven Dynamics Between Calcification And Production In Functionally Diverse Coral Reef Calcifiers, Jennifer Mallon, Tyler Cyronak, Emily R. Hall, Anastazia T. Banaszak, Dan A. Exton, Adrian M. Bass

Marine & Environmental Sciences Faculty Articles

Coral reef metabolism underpins ecosystem function and is defined by the processes of photosynthesis, respiration, calcification, and calcium carbonate dissolution. However, the relationships between these physiological processes at the organismal level and their interactions with light remain unclear. We examined metabolic rates across a range of photosynthesising calcifiers in the Caribbean: the scleractinian corals Acropora cervicornis, Orbicella faveolata, Porites astreoides, and Siderastrea siderea, and crustose coralline algae (CCA) under varying natural light conditions. Net photosynthesis and calcification showed a parabolic response to light across all species, with differences among massive corals, branching corals, and CCA that …

Iron Dysregulation In Covid-19 And Reciprocal Evolution Of Sars-Cov-2: Natura Nihil Frustra Facit, Yash Gupta, Dawid Maciorowski, Brian Medernach, Daniel P. Becker Ph.D., Ravi Durvasula, Claudia R. Libertin, Prakasha Kempaiah

Chemistry: Faculty Publications and Other Works

After more than a year of the COVID-19 pandemic, SARS-CoV-2 infection rates with newer variants continue to devastate much of the world. Global healthcare systems are overwhelmed with high positive patient numbers. Silent hypoxia accompanied by rapid deterioration and some cases with septic shock is responsible for COVID-19 mortality in many hospitalized patients. There is an urgent need to further understand the relationships and interplay with human host components during pathogenesis and immune evasion strategies. Currently, acquired immunity through vaccination or prior infection usually provides sufficient protection against the emerging variants of SARS-CoV-2 except Omicron variant requiring recent booster. New …

Role Of Inflammatory Niche And Adult Cardiomyocyte Coculture On Differentiation, Matrix Synthesis, And Secretome Release By Human Bone Marrow Mesenchymal Stem Cells, Jyotsna Joshi, Chandrasekhar R. Kothapalli

Chemical & Biomedical Engineering Faculty Publications

Myocardial infarction (MI) causes cardiomyocyte death, provokes innate immune response, and initiates tissue remodeling. The intrinsic healing process is insufficient to replace the lost cells, or regenerate and restore the functional features of the native myocardium. Autologous bone marrow-derived mesenchymal stem cell (BM-MSC) transplantation is being explored to offer therapeutic potential after MI. Here, we cultured human BM-MSC spheroids in three-dimensional collagenous gels for 28 days under exposure to tumor necrosis factor-alpha (+ TNFα), and coculture with adult human cardiomyocytes, or with conditioned media (CM) pooled from TNFα-stimulated adult cardiomyocytes. MSC differentiation marker (CD90, GATA4, cTnI, cTnT, Cx43, MHC, α-actin) …

Channelopathy-Causing Mutations In The S45A/S45B And Ha/Hb Helices Of KCa2.3 And KCa3.1 Channels Alter Their Apparent Ca2+ Sensitivity, Razan Orfali, Young-Woo Nam, Hai Minh Nguyen, Mohammad Asikur Rahman, Grace Yang, Meng Cui, Heike Wulff, Miao Zhang

Pharmacy Faculty Articles and Research

Small- and intermediate-conductance Ca²⁺-activated potassium (K_Ca2.x and K_Ca3.1, also called SK and IK) channels are activated exclusively by a Ca²⁺-calmodulin gating mechanism. Wild-type K_Ca2.3 channels have a Ca²⁺ EC₅₀ value of ∼0.3 μM, while the apparent Ca²⁺ sensitivity of wild-type K_Ca3.1 channels is ∼0.27 μM. Heterozygous genetic mutations of K_Ca2.3 channels have been associated with Zimmermann-Laband syndrome and idiopathic noncirrhotic portal hypertension, while K_Ca3.1 channel mutations were reported in hereditary xerocytosis patients. K_Ca2.3_S436C and K_Ca2.3_V450L channels with …

Analysis Of A Generalized Discrete Periodic Model For The Spread Of Wolbachia In A Mosquito Population, Alexandra Nicole Osgood Fedrigo

Honors Capstone Projects and Theses

No abstract provided.

Allometric Relationships Of Ecologically Important Antarctic And Arctic Zooplankton And Fish Species, Fokje L. Schaafsma, Carmen L. David, Doreen Kohlbach, Julia Ehrlich, Giulia Castellani, Benjamin A. Lange, Martina Vortkamp, André Meijboom, Anna Fortuna-Wünsch, Antonia Immerz, Hannelore Cantzler, Apasiri Klasmeier, Nadezhda Zakharova, Katrin Schmidt, Anton P. Van De Putte, Jan Andries Van Franeker, Hauke Flores

School of Geography, Earth and Environmental Sciences

Allometric relationships between body properties of animals are useful for a wide variety of purposes, such as estimation of biomass, growth, population structure, bioenergetic modelling and carbon flux studies. This study summarizes allometric relationships of zooplankton and nekton species that play major roles in polar marine food webs. Measurements were performed on 639 individuals of 15 species sampled during three expeditions in the Southern Ocean (winter and summer) and 2374 individuals of 14 species sampled during three expeditions in the Arctic Ocean (spring and summer). The information provided by this study fills current knowledge gaps on relationships between length and …

Transforming Science Into Practice, Janice Jiggins

IGC Proceedings (1977-2023)

The space for action that might move agricultural systems toward sustainability is narrowing. In so far as increasing dis-order in agroecosystems and food systems is caused by human agency, then remedial action must take account of cognition. This article argues that an understanding of cognitive processes is essential, as the foundation for participatory R, D & E that builds platforms of cooperation, binding actors into communities of learning that are trasnforming both science and practice.

Technology Transfer And Education Training And Extension In Grassland Farming, K. G. Rickert

IGC Proceedings (1977-2023)

Stakeholders in grassland farming, including farmers, rural communities, urban consumers, politicians, educators, and service agencies, widely agree that the goal for grassland farming is the triple bottom line: farming systems that are ecologically sustainable, profitable and socially acceptable. This paper considers how extension and training might contribute to that worthy goal by encouraging practitioners to better manage their management environment. The notion of a management environment refers to a holistic consideration of those factors that impact on farmers, farm advisors or educators, that subset of grassland farming ‘practitioners’ within the wider range of stakeholders.

The difficulty faced by these practitioners …

Gis-Based Forage Species Adaptation Mapping, David B. Hannaway, C. Daly, W. Gibson, G. Taylor, J. P. Bolte, I. Sriprisan, T. Griggs

IGC Proceedings (1977-2023)

Selecting forage crops adapted to the climatic and edaphic conditions of specific locations is essential for economic sustainability and environmental protection. Yet, currently, proper selection is difficult due to the absence of advanced selection tools. Significant improvements are being made in the process through Geographic Information System (GIS)-based mapping. Climate and soil GIS layers are being matched with forage characteristics through rules describing species tolerances. Better matching will reduce economic risks and environmental hazards associated with sub-optimal crop selection and subsequent performance. Once developed, these forage crop selection strategies and tools can be adapted for use with other crops. A …

On Farm Riparian Grazing Demonstration, J. T. Green Jr., M. H. Poore, S. P. Morgan

IGC Proceedings (1977-2023)

Two farm demonstrations were designed to show effects of periodic grazing of riparian areas. Sites were monitored for vegetative cover, degree of treading or hoof prints and dung deposition within three m of stream edge following grazing by beef cattle. A fenced enclosure was established along a 350 m stream reach on Farm-1, and eleven permanent stations were monitored following six graze periods over 12-months. Farm-2 involved grazing of two 0.13 ha paddocks, each of which contained a 22 m stream reach. On Farm-1 the cover improved following riparian exclusion, and evidence of treading in the 11 stations declined following …

Obituaries

Colby Magazine

No abstract provided.

Class Notes

Colby Magazine

No abstract provided.

Goodworks: In Houston, A Covid-19 Storm, Gabe Souza

Colby Magazine

Marlen Guerrero ’18, a Posse Scholar from Houston, Texas, began helping families long distance from Mayflower Hill after Hurricane Harvey hit her hometown. She continues that work, but recently saw her nonprofit pivot to address needs during the pandemic. She spoke with Colby Multimedia Producer Gabe Souza.

Media

Colby Magazine

No abstract provided.

Rapid Response: Cat-Scan Machine And 3d Printers Vital In Covid-19, Laura Meader

Colby Magazine

Colby’s Assistant Professor of Biology Josh Martin is using his expertise and sophisticated scientific equipment to create face shields, respirator masks, and air filter cartridges for local first responders and hospitals in need of equipment that is crucial to treating patients with COVID-19.

Soblu At 50, Kardelen Koldas

Colby Magazine

I think it’s extraordinary that the organization has not only endured but has thrived. It has changed with the times over these last 50 years.

Full Issue, Colby College

Colby Magazine

Colby Magazine vol. 107, no. 3 (2019-2020): full issue

Medical School Watercooler Newsletter - January 7, 2022, Lindsey Lyle

Watercooler Newsletter

This is the January 7, 2022 edition of the Frederick P. Whiddon College of Medicine's newsletter - Watercooler.

Contents include:

• Taylor to present on signal patterning at pathology research seminar
• USA Center for Lung Biology faculty uncover mechanism behind neurocognitive dysfunction after pneumonia
• Calling all alumni couples: Send us your stories
• Meet a Med Student: Zach Aggen
• Last call for bands to register for Doc Rock
• USA researcher receives grant to study racial disparities in cervical cancer prevention
• USA College of Medicine alumna recognized as Tampa Bay Community Hero

Red Blood Cell Distribution Width In Hospitalized Covid-19 Patients., Preethi Ramachandran, Mahesh Gajendran, Abhilash Perisetti Md, Karim Osama Elkholy, Abhishek Chakraborti, Giuseppe Lippi, Hemant Goyal

Other Specialties

Introduction: Coronavirus disease-2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), is causing dramatic morbidity and mortality worldwide. The Red Blood Cell Distribution Width (RDW) has been strongly associated with increased morbidity and mortality in multiple diseases.

Objective: To assess if elevated RDW is associated with unfavorable outcomes in hospitalized COVID-19.

Methods: We retrospectively studied clinical outcomes of hospitalized COVID-19 patients for their RDW values. In-hospital mortality was defined as primary outcome, while septic shock, need for mechanical ventilation, and length of stay (LOS) were secondary outcomes.

Results: A total of 294 COVID-19 patients were finally studied. Overall prevalence …

Falling Through The Cracks: Deaf New Americans And Their Unsupported Educational Needs, Michael A. Schwarz, Brent Elder, Monu Chhetri

College of Education Departmental Research

Members of the Deaf New American community reported they arrived in the United States with no formal education, unable to read or write in their native language, and had zero fluency in English. Efforts to educate them have floundered, and the study aims to find out why and how to fix the problem. Interviews of eight Deaf New Americans yielded rich data that demonstrates how education policy in the form of the Individuals with Disabilities Education Act (IDEA) and other laws fail to address their needs, because these laws do not include them in their coverage. The study’s main findings …

Impact Of Impaired Glucose Metabolism On Periodontitis Progression Over Three Years, Oelisoa M. Andriankaja, Kaumudi Joshipura, Francisco Muñoz, Bruce A. Dye, Frank B. Hu, Cynthia M. Pérez

Center for Oral Health Research Faculty Publications

We evaluated the relationship between glucose abnormalities and periodontitis in overweight/obese individuals. Eight hundred and seventy (870) diabetes-free participants aged 40–65 years completed the three-year follow-up in the San Juan Overweight Adults Longitudinal Study. The ADA thresholds for fasting and 2-h post-load glucose and HbA1c were used to define prediabetes. The NHANES methods were used to assess periodontitis. Multivariable linear regression was used to evaluate the relationship between baseline glucose metabolism measures and periodontitis at follow-up, adjusting for potential confounders. There was no association between impaired glucose measures and mean pocket depth (PD), mean clinical attachment loss (CAL), or mean …

The Human Disease Ontology 2022 Update., Lynn M Schriml, James B Munro, Mike Schor, Dustin Olley, Carrie Mccracken, Victor Felix, J Allen Baron, Rebecca Jackson, Susan M. Bello, Cynthia Bearer, Richard Lichenstein, Katharine Bisordi, Nicole Campion Dialo, Michelle Giglio, Carol Greene

Faculty Research 2022

The Human Disease Ontology (DO) (www.disease-ontology.org) database, has significantly expanded the disease content and enhanced our userbase and website since the DO's 2018 Nucleic Acids Research DATABASE issue paper. Conservatively, based on available resource statistics, terms from the DO have been annotated to over 1.5 million biomedical data elements and citations, a 10× increase in the past 5 years. The DO, funded as a NHGRI Genomic Resource, plays a key role in disease knowledge organization, representation, and standardization, serving as a reference framework for multiscale biomedical data integration and analysis across thousands of clinical, biomedical and computational research projects and …

How Does Lc/Ms Compare To Uv In Coffee Authentication And Determination Of Antioxidant Effects? Brazilian And Middle Eastern Coffee As Case Studies, Enas A. El-Hawary, Ahmed Zayed, Annegret Laub, Luzia V. Modolo

Faculty Journal Articles

Coffee is a popular beverage owing to its unique flavor and diverse health benefits. The current study aimed at investigating the antioxidant activity, in relation to the phytochemical composition, of authenticated Brazilian green and roasted Coffea arabica and C. robusta, along with 15 commercial specimens collected from the Middle East. Ultra-high-performance liquid chromatography coupled to high-resolution mass spectrometry (UHPLC-ESI–HRMS) and UV spectrometry were employed for profiling and fingerprinting, respectively. With the aid of global natural product social molecular networking (GNPS), a total of 88 peaks were annotated as belonging to different chemical classes, of which 11 metabolites are reported for …

Plant Canopy May Promote Seed Dispersal By Wind, Xuanping Qin, Wei Liang, Zhimin Liu, Minghu Liu, Carol C. Baskin, Jerry M. Baskin, Zhiming Xin, Zhigang Wang, Quanlai Zhou

Biology Faculty Publications

Seed dispersal has received much research attention. The plant canopy can intercept diaspores, but the effect of the plant canopy (the aboveground portion of a plant consisting of branches and leaves) on dispersal distance has not been explored empirically. To determine the effect of plant canopy on seed dispersal distance, a comparison of diaspores falling through open air and through plant canopy was made in a wind tunnel using three wind speeds and diaspores with various traits. Compared with diaspores falling through open air, the dispersal distance of diaspores falling through plant canopy was decreased or increased, depending on wind …

Plga/Peg Nanoparticles Loaded With Cyclodextrin-Peganum Harmala Alkaloid Complex And Ascorbic Acid With Promising Antimicrobial Activities, Sherif Ashraf Fahmy, Noha Khalil Mahdy, Hadeer Al Mulla, Hassan Mohamed El Said Azzazy

Faculty Journal Articles

Antimicrobial drugs face numerous challenges, including drug resistance, systemic toxic effects, and poor bioavailability. To date, treatment choices are limited, which warrants the search for novel potent antivirals, including those extracted from natural products. The seeds of Peganum harmala L. (Zygophyllaceae family) have been reported to have antimicrobial, antifungal, and anticancer activities. In the present study, a 2-hydroxy propyl-β-cyclodextrin (HPβCD)/harmala alkaloid-rich fraction (HARF) host–guest complex was prepared using a thin-film hydration method to improve the water solubility and bioavailability of HARF. The designed complex was then co-encapsulated with ascorbic acid into PLGA nanoparticles coated with polyethylene glycol (HARF–HPßCD/AA@PLGA-PEG NPs) using …

Vimentin Intermediate Filaments Mediate Cell Morphology On Viscoelastic Substrates, Maxx Swoger, Sarthak Gupta, Elisabeth E. Charrier, Michael Bates, Heidi Hehnly, Alison E. Patteson

Physics - All Scholarship

The ability of cells to take and change shape is a fundamental feature underlying development, wound repair, and tissue maintenance. Central to this process is physical and signaling interactions between the three cytoskeletal polymeric networks: F-actin, microtubules, and intermediate filaments (IFs). Vimentin is an IF protein that is essential to the mechanical resilience of cells and regulates cross-talk among the cytoskeleton, but its role in how cells sense and respond to the surrounding extracellular matrix is largely unclear. To investigate vimentin’s role in substrate sensing, we designed polyacrylamide hydrogels that mimic the elastic and viscoelastic nature of in vivo tissues. …

Targeting Dnmts To Overcome Enzalutamide Resistance In Prostate Cancer, Elia Farah, Zhuangzhuang Zhang, Sagar M. Utturkar, Jinpeng Liu, Timothy L. Ratliff, Xiaoqi Liu

Toxicology and Cancer Biology Faculty Publications

Prostate cancer is the second leading cause of cancer death among men in the United States. The androgen receptor (AR) antagonist enzalutamide is an FDA-approved drug for treatment of patients with late-stage prostate cancer and is currently under clinical study for early-stage prostate cancer treatment. After a short positive response period to enzalutamide, tumors will develop drug resistance. In this study, we uncovered that DNA methylation was deregulated in enzalutamide-resistant cells. DNMT activity and DNMT3B expression were upregulated in resistant cell lines. Enzalutamide induced the expression of DNMT3A and DNMT3B in prostate cancer cells with a potential role of p53 …

Exploratory Content Analysis Of Direct-To-Consumer Pet Genomics: What Is Being Marketed And What Are Consumers Saying?, Nikki E. Bennett, Silvio Ernesto Mirabal Torres, Peter B. Gray

Anthropology Faculty Research

Mars Petcare introduced the first direct-to-consumer domestic dog genetic test in 2009 and Basepaws introduced the first direct-to-consumer cat genetic test in 2016. Social science research has evaluated numerous aspects of the human direct-to-consumer market, yet no such exploration has evaluated the occurrence of pet owners pursuing pet genetic tests. Using a mixed methods approach, we conducted an exploratory content analysis of direct-to-consumer pet genetic company webpages and consumer reviews shared on Amazon. Initial data reviews indicated some companies may be key industry players, relative to others. Our results present content frequency for each group (key industry players, all other …

Lncrnafunc: A Knowledgebase Of Lncrna Function In Human Cancer, Mengyuan Yang, Huifen Lu, Jiajia Liu, Sijia Wu, Pora Kim, Xiaobo Zhou

Faculty, Staff and Student Publications

The long non-coding RNAs associating with other molecules can coordinate several physiological processes and their dysfunction can impact diverse human diseases. To date, systematic and intensive annotations on diverse interaction regulations of lncRNAs in human cancer were not available. Here, we built lncRNAfunc, a knowledgebase of lncRNA function in human cancer at https://ccsm.uth.edu/lncRNAfunc, aiming to provide a resource and reference for providing therapeutically targetable lncRNAs and intensive interaction regulations. To do this, we collected 15 900 lncRNAs across 33 cancer types from TCGA. For individual lncRNAs, we performed multiple interaction analyses of different biomolecules including DNA, RNA, and protein levels. …

Fusiongdb 20: Fusion Gene Annotation Updates Aided By Deep Learning, Pora Kim, Hua Tan, Jiajia Liu, Haeseung Lee, Hyesoo Jung, Himanshu Kumar, Xiaobo Zhou

Faculty, Staff and Student Publications

A knowledgebase of the systematic functional annotation of fusion genes is critical for understanding genomic breakage context and developing therapeutic strategies. FusionGDB is a unique functional annotation database of human fusion genes and has been widely used for studies with diverse aims. In this study, we report fusion gene annotation updates aided by deep learning (FusionGDB 2.0) available at https://compbio.uth.edu/FusionGDB2/. FusionGDB 2.0 has substantial updates of contents such as up-to-date human fusion genes, fusion gene breakage tendency score with FusionAI deep learning model based on 20 kb DNA sequence around BP, investigation of overlapping between fusion breakpoints with 44 human …