Life Sciences Commons^™

Organic Geochemical Evidence For Life In Archean Rocks Identified By Pyrolysis-Gc-Ms And Supervised Machine Learning, Michael L. Wong, Anirudh Prabhu, Conel O'D. Alexander, H. James Cleaves Ii, George D. Cody, Grethe Hystad, Marko Bermanec, Wouter Bleeker, C. Kevin Boyce, Andrea Corpolongo, Andrew D. Czaja, Souvik Das, Robert R. Gaines, Daniel D. Gregory, John A. Jaszczak, Emmanuelle J. Javaux, Jaganmoy Jodder, Andrew H. Knoll, Martin Van Kranendonk, Katie M. Maloney, Nora Noffke, Robert Rainbird, Emersyn Slaughter, Eva E. Stüeken, Roger E. Summons, Frances Westall, Jasmina Wiemann, Shuhai Xiao, Robert M. Hazen

OES Faculty Publications

Throughout Earth’s history, organic molecules from both abiogenic and biogenic sources have been buried in sedimentary rocks. Most of these organic molecules have been significantly altered by geologic processes through deep time. Nonetheless, the nature and distribution of those ancient fragmentary organic remains have the potential to reveal diagnostic biomolecular information after billions of years of burial. Here, we analyzed 406 fossil, modern biological, meteoritic, and synthetic samples using pyrolysis gas chromatography and mass spectrometry. We explored these analytical data via supervised machine-learning methods to discriminate samples of biogenic vs. abiogenic origin, plant vs. animal phylogenetic affinity, and photosynthetic vs. …

Association Of Prenatal Exposure To Phthalates And Phenols With Adverse Pregnancy Outcomes, Misa Hayasaka, Diana Aboukhater, George Saade, Tetsuya Kawakita

Department of Obstetrics & Gynecology Faculty Publications

OBJECTIVE:

To evaluate the association between prenatal exposures to phthalates and phenols and adverse pregnancy outcomes, including preterm birth (PTB), small-for-gestational-age (SGA) birth weight, and gestational diabetes mellitus (GDM).

METHODS:

This study analyzed data from the Environmental Influences on Child Health Outcomes consortium, which harmonized longitudinal data on more than 30,000 pregnancies and 57,000 children from 69 cohorts across the United States and Puerto Rico. Pregnancy outcomes included PTB, SGA, and GDM, identified from medical records or self-reports. Generalized estimating equations models with Poisson distribution and robust variance were used to estimate relative risks (RRs) and 95% CIs per interquartile …

Association Between The Intensity Of Exercise In The First Trimester And Early Second Trimester And The Risk Of Gestational Diabetes, Takaki Tanamoto, Misa Hayasaka, Tetsuya Kawakita

Department of Obstetrics & Gynecology Faculty Publications

Objective

Although some studies show that exercise decreases the incidence of gestational diabetes mellitus (GDM), the optimal exercise intensity during pregnancy remains unclear. We examined GDM risk according to exercise intensity in pregnant individuals.

Methods

We analyzed data from the Nulliparous Pregnancy Outcomes Study: Monitoring Mothers‐to‐Be (nuMoM2b), a prospective study enrolling nulliparous individuals in the first trimester. Participants with pregestational diabetes or delivery before 20 weeks were excluded. Exercise intensity during the first (6–13 weeks’ gestation) and early second (16–21 weeks’ gestation) trimesters was categorized by metabolic equivalent of task hours per week (MET‐hr/week) as none, low intensity (< 7.5), moderate intensity (7.5–14.9), or high intensity (≥ 15). The primary outcome was GDM; secondary outcomes included preeclampsia, gestational hypertension, preterm birth, small‐for‐gestational‐age birth, and stillbirth. Adjusted relative risks (aRRs) with 95% confidence intervals (CIs) were calculated using a generalized linear mixed‐effects model with a Poisson distribution and robust error variance, controlling for the random effects of individuals and potential confounders.

Results …

Treatment Of Myocardial Infiltration Of Hodgkins Lymphoma: A Catch-22, Jennifer Priessnitz, Erin Biringen, Fadi Khoury, Christina Bergin

Department of Medicine Faculty Publications

Background: Cardiac sequelae in Hodgkin Lymphoma (HL) can manifest as involvement of the heart and pericardium. Direct cardiac involvement is rare, and myocardial infiltration is distinctly unusual.¹ When it does occur, it is often a late manifestation of lymphoma, with a median onset of 20 months after initial diagnosis, and it is usually associated with advanced-stage disease.²

Case: A 34-year-old male was diagnosed with classic HL by lymph node biopsy. During his hospitalization, the patient remained in sinus tachycardia with heart rate up to 150 with no dysrhythmias. Transthoracic echocardiogram (TTE) revealed a reduced ejection fraction (EF) of 36% concerning …

Drug-Induced Leukocytoclastic Vasculitis From An Unreported Source: Daptomycin, Jennifer K. Priessnitz, Timothy Kuzel, Lindsay Ackerman, Nelson Nicolasora

Department of Medicine Faculty Publications

Leukocytoclastic vasculitis (LCV) is a rare small-vessel vasculitis caused by immune-complex-mediated deposition on endothelial cells of dermal capillaries. Common triggers include medications, infections, autoimmune disorders, and malignancies. We present a case of a 58-year-old male who developed daptomycin-induced LCV after being treated for Methicillin-resistant Staphylococcus aureus (MRSA) endocarditis. The patient experienced painful palpable purpura on his lower extremities, which was diagnosed as LCV by skin biopsy. At the time of the biopsy, warfarin and daptomycin were discontinued, and the patient was transitioned to heparin and ceftaroline. MRSA-induced LCV was ruled out, due to negative blood cultures and adequate source control …

Late Diagnosis Of Klinefelter Syndrome: Overcoming Phenotypic Variability And Diagnostic Oversights, Amna Kamran, Chinelo Okigbo

Department of Medicine Faculty Publications

We report a case of Klinefelter syndrome (KS) diagnosed in adulthood, emphasizing the impact of phenotypic variability and the declining reliance on physical examination in delayed recognition. A 27-year-old male with obesity, low libido, and biochemical and clinical primary hypogonadism was found to have 47, XXY karyotype, consistent with KS. His hypogonadism was initially attributed to obesity and overlooked, despite classic signs of a micropenis and small testes. The case highlights the importance of physical examination, comprehensive history, and clinician awareness in diagnosing KS, particularly in atypical presentations. KS is associated with increased risks of osteoporosis, cardiovascular disease, and psychosocial …

Consumption Of The Food Groups With The Revised Benefits In The New Wic Food Package: A Scoping Review, Qi Zhang, Priyanka T. Patel, Bidusha Neupane, Caitlin M. Lowery, Futun Alkhalifah, Faezeh Mahdavi, Esther May Sarino

Epidemiology, Biostatistics, & Environmental Health Faculty Publications

Background: On 18 April 2024, the United States Department of Agriculture (USDA) published the first food package changes to the Special Supplemental Nutrition Program for Women, Infants, and Children (WIC) in over a decade, which reduced some food benefits (juice, milk, canned fish, and infant fruits and vegetables) and offered substitutes (cash-value vouchers (CVVs) or cash-value benefits (CVBs) to redeem for fruits and vegetables, cheese, soymilk, or other dairy products). Methods: To assess the impact of the changes on the consumption and redemption of these food groups, a systematic search was conducted, identifying 23 peer-reviewed publications between 2010 and 2024. …

Screening And Addressing Food Insecurity At Free Clinics: A Scoping Review, Gautam Ramanathan, William Zak, Daiwik Munjwani, Robert Fisher, Esther May Sarino, Mary J. Scourboutakos

Department of Medicine Faculty Publications

Food insecurity (FI) is highly prevalent amongst patients seeking care at free, student-run health clinics. This study sought to examine the existing literature of food insecurity screenings and interventions at free clinics across the U.S. In this review, we provide the rate of FI screenings, the prevalence of FI, demographic information of patients screened, and interventions and barriers faced by clinics while implementing interventions to improve FI. Studies included in this review needed to implement a FI screening and intervention program in a free clinic within the United States. Additionally, eligible studies could address additional social determinants of health or …

Copula-Based Bayesian Model For Detecting Differential Gene Expression, Prasansha Liyanaarachchi, N. Rao Chaganty

Mathematics & Statistics Faculty Publications

Deoxyribonucleic acid, more commonly known as DNA, is a fundamental genetic material in all living organisms, containing thousands of genes, but only a subset exhibit differential expression and play a crucial role in diseases. Microarray technology has revolutionized the study of gene expression, with two primary types available for expression analysis: spotted cDNA arrays and oligonucleotide arrays. This research focuses on the statistical analysis of data from spotted cDNA microarrays. Numerous models have been developed to identify differentially expressed genes based on the red and green fluorescence intensities measured using these arrays. We propose a novel approach using a Gaussian …

Heterogeneous Clustering Of Multiomics Data For Breast Cancer Subgroup Classification And Detection, Joseph Pateras, Musaddiq Lodi, Pratip Rana, Preetam Ghosh

Computer Science Faculty Publications

The rapid growth of diverse -omics datasets has made multiomics data integration crucial in cancer research. This study adapts the expectation–maximization routine for the joint latent variable modeling of multiomics patient profiles. By combining this approach with traditional biological feature selection methods, this study optimizes latent distribution, enabling efficient patient clustering from well-studied cancer types with reduced computational expense. The proposed optimization subroutines enhance survival analysis and improve runtime performance. This article presents a framework for distinguishing cancer subtypes and identifying potential biomarkers for breast cancer. Key insights into individual subtype expression and function were obtained through differentially expressed gene …

A Data-Driven Sliding-Window Pairwise Comparative Approach For The Estimation Of Transmission Fitness Of Sars-Cov-2 Variants And The Construction Of The Evolution Fitness Landscape, Md Jubair Pantho, Richard Annan, Landen Alexander Bauder, Sophia Huang, Letu Qingge, Hong Qin

Computer Science Faculty Publications

Estimating the transmission fitness of SARS-CoV-2 variants and understanding their evolutionary fitness trends are important for epidemiological forecasting. Existing methods are often constrained by their parametric natures and do not satisfactorily align with the observations during COVID-19. Here, we introduce a sliding-window data-driven pairwise comparison method, the differential population growth rate (DPGR) that uses viral strains as internal controls to mitigate sampling biases. DPGR is applicable in time windows in which the logarithmic ratio of two variant subpopulations is approximately linear. We apply DPGR to genomic surveillance data and focus on variants of concern (VOCs) in multiple countries and regions. …

Cath-Ddg: Towards Robust Mutation Effect Prediction On Protein-Protein Interactions Out Of Cath Homologous Superfamily, Guanglei Yu, Xuehua Bi, Teng Ma, Yaohang Li, Jianxin Wang

Computer Science Faculty Publications

Motivation: Protein-protein interactions (PPIs) are fundamental aspects in understanding biological processes. Accurately predicting the effects of mutations on PPIs remains a critical requirement for drug design and disease mechanistic studies. Recently, deep learning models using protein 3D structures have become predominant for predicting mutation effects. However, significant challenges remain in practical applications, in part due to the considerable disparity in generalization capabilities between easy and hard mutations. Specifically, a hard mutation is defined as one with its maximum TM-score < 0.6 when compared to the training set. Additionally, compared to physics-based approaches, deep learning models may overestimate performance due to potential data leakage.

Results: We propose new training/test splits that mitigate data leakage according to the CATH homologous superfamily. Under the constraints of physical …

Foundation Models In Bioinformatics, Fei Guo, Renchu Guan, Yaohang Li, Qi Liu, Xiaowo Wang, Can Yang, Jianxin Wang

Computer Science Faculty Publications

With the adoption of foundation models (FMs), artificial intelligence (AI) has become increasingly significant in bioinformatics and has successfully addressed many historical challenges, such as pre-training frameworks, model evaluation and interpretability. FMs demonstrate notable proficiency in managing large-scale, unlabeled datasets, because experimental procedures are costly and labor intensive. In various downstream tasks, FMs have consistently achieved noteworthy results, demonstrating high levels of accuracy in representing biological entities. A new era in computational biology has been ushered in by the application of FMs, focusing on both general and specific biological issues. In this review, we introduce recent advancements in bioinformatics FMs …

Benchmarking Batch-Effect Correction Methods Towards The Construction Of A Triple-Negative Breast Cancer Cell Atlas, Peter Scheible, Amy H. Tang, Jing He, Jiangwen Sun

Computer Science Faculty Publications

Triple-negative breast cancer (TNBC) requires detailed cellular mapping given its aggressive nature, immense tumor heterogeneity and genetic diversity. We integrated 156,794 cells from six scRNA-seq datasets—including tumors, metastases, and cell lines—to build a TNBC scRNA cell atlas, focusing on batch effect mitigation while maintaining biological and molecular details. Preprocessing f ilters noise, normalizes data, and leverages PCA for integration readiness. We utilized scANVI, a semi-supervised tool, to align datasets, preserving TNBC’s complex tumor heterogeneity via marker annotations [1]. UMAPs demonstrate biological clustering in integrated data, contrasted with datasetdriven unintegrated patterns. Assessments verifying effective batch correction. This method aligns with NASA’s …

A Survey On Deep Learning For Drug-Target Binding Prediction: Models, Benchmarks, Evaluation, And Case Studies, Kusal Debnath, Pratip Rana, Preetam Ghosh

Computer Science Faculty Publications

Conventional drug discovery is expensive, time-consuming, and prone to failure. Artificial intelligence has become a potent substitute over the last decade, providing strong answers to challenging biological issues in this field. Among these difficulties, drug-target binding (DTB) is a key component of drug discovery techniques. In this context, drug-target affinity and drug–target interaction are complementary and essential frameworks that work together to improve our comprehension of DTB dynamics. In this work, we thoroughly analyze the most recent deep learning models, popular benchmark datasets, and assessment metrics for DTB prediction. We look at the paradigm shift in the development of drug …

Deepssetracer 2.0: Improved Deep Learning Model Performance For Protein Secondary Structure Segmentation From Cryo-Em Maps, Bryan Hawickhorst, Thu Nguyen, Willy Wriggers, Jiangwen Sun, Jing He

Computer Science Faculty Publications

DeepSSETracer is a method for segmenting protein secondary structure from medium-resolution (5-10Å) cryogenic electron microscopy (cryo-EM) density maps. We conducted experiments and ablation studies to examine the effects of normalization methods, max-pooling, activation functions, and loss calculation region on DeepSSETracer. By combining multiple technical improvements, the performance of the new version, DeepSSETracer 2.0, was significantly enhanced compared to DeepSSETracer 1.1. On a set of 77 test cases, the weighted average per-voxel F1 score increased from 62.1% to 70.3% for helix detection, and from 47.8% to 62.5% for β-sheet detection. While each of the five modifications in the network enhanced the …

Benchmarking And Improving Foundation Model Dietary Estimates From Meal Images, Yongcheng Mu, Jiangwen Sun, Jing He

Computer Science Faculty Publications

Accurate quantifying dietary contents, such as calories, proteins, carbohydrates, and fats, from an image of a meal plate is vital for managing diabetes. Recently, Large Multimodal Models (LMMs) have excelled in complex vision-language tasks due to their use of very large, highly diverse data. This study benchmarked the use of seven LMMs that include full and lightweight models of GPT, Gemini, and Llama for nutrition estimation based on Google's Nutrition5k dataset and our own phone-collected DonateAndLearn dataset. We analyzed the performance of LMMs and the RGB-D fusion model, in which the RGB-D model was specifically trained using Nutrition5k data. On …

Mxene-Based Materials For Enhanced Water Quality: Advances In Remediation Strategies, Ali Mohammad Amani, Milad Abbasi, Atena Najdian, Farzaneh Mohamadpour, Seyed Reza Kasaee, Hesam Kamyab, Shreeshivadasan Chelliapan, Mostafa Shafiee, Lobat Tayebi, Ahmad Vaez, Atefeh Najafian, Ehsan Vafa, Sareh Mosleh-Shirazi

Electrical & Computer Engineering Faculty Publications

Two-dimensional MXenes are promising candidates for water treatment because of their large surface area (e.g., exceeding 1000 m²/g for certain structures), high electrical conductivity (e.g., >1000 S/m), hydrophilicity, and chemical stability. Their strong sorption selectivity and effective reduction capacity, exemplified by heavy metal adsorption efficiencies exceeding 95 % in several studies, coupled with facile surface modification, make them suitable for removing diverse contaminants. Applications include the removal of heavy metals (e.g., achieving >90 % removal of Pb(II)), dye removal (e.g., demonstrating >80 % removal of methylene blue), and radioactive waste elimination. Furthermore, 3D MXene architecture exhibit enhanced performance in antibacterial …

Cannabinoid-2 Receptor Activation Attenuates Sulfur Mustard Analog 2-Chloroethyl-Ethyl-Sulfide-Induced Acute Lung Injury In Mice, Gregory Nicholson, Nicholas Richards, Janette Lockett, My Boi Ly, Raj V. Nair, Woong-Ki Kim, K. Yaragudri Vinod, Nagaraja Nagre

Department of Biomedical and Translational Sciences Faculty Publications

Background: Exposure to sulfur mustard (SM; 2,2′-dichlorodiethyl sulfide) causes toxicity in the human body, particularly the lungs. The molecular mechanisms of SM-induced lung damage are elusive, and no effective treatments exist. This study explores the anti-inflammatory potential of cannabinoid receptor 2 (CB2R) activation in mitigating acute lung injury (ALI) and inflammation induced by 2-chloroethyl ethyl sulfide (CEES), a structural analog of SM. Methods: C57BL/6J mice were exposed to CEES via intratracheal administration to model ALI. CB2R activation was achieved through the intraperitoneal administration of HU308, a selective synthetic agonist. ALI and inflammation were evaluated at 48 h post-exposure to CEES. …

Eeg Spectral Analysis Of Nighttime Sleep And Daytime Mslts And Neurocognitive Evaluations In Subjects With Co-Morbid Insomnia And Osa, Yuan Shi, Yuru Nie, Fengyi Hao, Xujun Feng, Ye Zhang, Larry D. Sanford, Rong Ren, Xiangdong Tang

Department of Biomedical and Translational Sciences Faculty Publications

Background

Chronic insomnia and obstructive sleep apnea commonly co-occur. Few studies have explored the neurophysiological and neurocognitive characteristics of COMISA, which could help guide improving treatment diagnostic tools and determining novel therapeutic targets. This study aims to explore the neurophysiological and neurocognitive characteristics of COMISA using electroencephalographic (EEG) spectral analysis and subjective and objective neurocognitive measurements.

Methods

Participants were from our community recruited OSA-insomnia-COMISA cohort with 206 included for our current analysis including 74 chronic insomniacs (CIs), 55 OSA patients and 77 COMISA patients. Standard polysomnography (PSG) and multiple sleep latency tests (MSLTs) were recorded and used to obtain relative …

Phenotype Specific Nuclear Lamina Remodeling In Hipsc Derived Cardiomyocytes Bearing Tnnt2 Sarcomeric Variants, Isabella Leite Coscarella, Olalekan H. Usman, Lili Wang, Maicon Landim-Vieira, Lillian Wirstiuk, Amber N. Brown, Diego A. R. Zorio, Brian K. Washburn, Cynthia Vied, Bjorn C. Knollmann, Christopher Solís, Vitold E. Galkin, P. Bryant Chase, J. Travis Hinson, Jerome Irianto, Jose Renato Pinto

Department of Biomedical and Translational Sciences Faculty Publications

[Summary] Cardiomyocytes endure physical stress from the myocardium environment while generating their own mechanical strains. The force generated by sarcomeres is transmitted both longitudinally to adjacent sarcomeres and laterally to the cytoskeleton via intermediate filaments. This mechanical stimulus impacts other organelles, including the nucleus, thus playing a vital role in sensing and signaling nuclear adaptations. However, there is limited understanding of how changes in cardiac contractility affect nuclear mechanics. Here, we sought to investigate the effects of hyper- and hypo-contractility in nuclei of human induced pluripotent stem cell-derived cardiomyocytes (hiPSC-CMs) bearing TNNT2 pathogenic variants associated with hypertrophic (HCM) or dilated …

Monitoring Plastic Pollution Using Bioindicators: A Global Review And Recommendations For Marine Environments, Matthew S. Savoca, Neil Angelo Abreo, Andres H. Arias, Laura Baes, Matteo Baini, Elisa Bergami, Susanne Brander, C. Anela Choy, Illaria Corsi, Bavo De Witte, Camila Domit, Sarah Dudas, Emily M. Duncan, Claudia E. Fernández, Maria Cristina Fossi, Ostin Garcés-Ordóñez, Brendan J. Godley, Daniel Gonzalez-Parades, Victoria González Carman, Bonnie M. Hamilton, Britta Denise Hardesty, Sang Hee Hong, Shirel Kahane-Rapport, Lauren M. Kashiwabara, Mariana Baptista Lacerda, Guillermo Luna-Jorquera, Clara Manno, Sarah E. Nelms, Cristina Panti, Diego J. Pérez-Venegas, Christopher K. Pham, Jennifer F. Provencher, Sara Purca, Harunur Rashid, Yasmina Rodríguez, Conrad Sparks, Chengjun Sun, Martin Thiel, Catherine Tsangaris, Robson G. Santos

Biological Sciences Faculty Publications

Monitoring the movement of plastic into marine food webs is central to understanding and mitigating the plastic pollution crisis. Bioindicators have been a component of the environmental monitoring toolkit for decades, but how, where, and which bioindicators are used in long-term monitoring programs has not yet been assessed. Moreover, these programs have yet to be synthesized and evaluated globally. Doing so is imperative if we are to learn from these pioneering programs and expand on their efforts. We reviewed global monitoring programs using bioindicators that focus on plastic pollution and found 11 worldwide that met our definition of long-term monitoring. …

Edge Effects Impact Blue Carbon Dynamics Across Coastal Ecotones In A Tropical Seascape, Erik S. Yando, Jahson B. Alemu I, Kiah Eng Lim, Taylor M. Sloey, Michiel Van Breugel, Natasha Bhatia, Daniel A. Friess

Biological Sciences Faculty Publications

Coastal wetlands are important for their ability to regulate global climate through the sequestration and long-term storage of carbon. Accurate quantification of ecosystem-specific carbon dynamics (including sequestration, storage, and fluxes) is needed to develop accurate carbon budgets that inform climate change mitigation. Most work to quantify carbon dynamics either use subsampling in core habitats or benefit transfers to upscale values. While these approaches are valuable, our understanding of carbon dynamics across ecosystem transitions and overall heterogeneity remains a critical gap in coastal ecosystems as boundaries are not always clear. In this study, we established transects across both mangrove and seagrass …

Caveolin-Mediated Endocytosis: Bacterial Pathogen Exploitation And Host-Pathogen Interaction, Dibyasri Barman, Rishi Drolia

Biological Sciences Faculty Publications

Within mammalian cells, diverse endocytic mechanisms, including phagocytosis, pinocytosis, and receptor-mediated endocytosis, serve as gateways exploited by many bacterial pathogens and toxins. Among these, caveolae-mediated endocytosis is characterized by lipid-rich caveolae and dimeric caveolin proteins. Caveolae are specialized microdomains on cell surfaces that impact cell signaling. Caveolin proteins facilitate the creation of caveolae and have three members in vertebrates: caveolin-1, caveolin-2, and caveolin-3. Many bacterial pathogens hijack caveolin machinery to invade host cells. For example, the Gram-positive facultative model intracellular bacterial pathogen Listeria monocytogenes exploits caveolin-mediated endocytosis for efficient cellular entry, translocation across the intestinal barrier, and cell–cell spread. Caveolin …

Cellular Responses Of Astrangia Poculata (Ellis And Solander, 1786) And Its Symbiont To Experimental Heat Stress, Tyler E. Harman, Daniel Barshis, Briana Hauff Salas, Kevin B. Strychar

Biological Sciences Faculty Publications

Climate change has had devastating effects on tropical coral reefs; however, much less is known regarding how heat stress affects temperate coral. This research focuses on Astrangia poculata (Ellis and Solander, 1786) collected from Narragansett Bay, RI, during the summer and winter seasons and understanding the effect of experimental thermal extremes (i.e., 26 °C) on seasonally different populations. Photosynthetic efficiency (Fv/Fm), symbiont density (via an inverse relationship with pixel intensity), and oxidative stress via reactive oxygen species (ROS) concentrations were measured on symbiotic and aposymbiotic A. poculata. Higher Fv/Fm rates were observed in summer- vs. winter-collected corals (p ≤ …

Impacts Of Tick Parasitism On The Rodent Gut Microbiome, Robert J. Brinkerhoff, Joshua Pandian, Meghan Leber, Isabella D. Hauser, Holly D. Gaff

Biological Sciences Faculty Publications

Host microbiota may impact disease vector behavior and pathogen transmission, but little is known about associations between ectoparasites and microbial communities in wildlife reservoir species. We used Illumina metagenomic sequencing to explore the impacts of tick parasitism on the rodent fecal microbiome in both a field and laboratory setting. We found that tick parasitism on wild hosts was associated with variation in the fecal microbiota of both the white-footed deermouse, Peromyscus leucopus, and the southern cotton rat, Sigmodon hispidus. In a lab experiment, we detected significant changes to the fecal microbiome after experimental exposure to immature ticks in …

The First Iucn Red List Of Cold-Water Corals Highlights Global Declines, Julia D. Sigwart, A. Louise Allcock, Renata Carolina Mikosz Arantes, Kelsey Archer Barnhill, Narissa Bax, Julia S. Beneti, Saskia Brix, Gudmundur Gudmundsson, Catherine S. Mcfadden, Severin A. Korfhage, Christi Linardich, Declan Morrissey, Pedro De Oliveira Nascimento, Bárbara De Moura Neves, Steinunn H. Ólafsdóttir, Stefán Ragnarsson, Kaveh Samimi-Namin, Íris Sampaio, Mark E. De Wilt

Biological Sciences Faculty Publications

The most well-known species-based conservation tool is the International Union for the Conservation of Nature (IUCN) Red List of Threatened Species. The current coverage of species in the Red List is known to under-represent benthic marine species. Cold-water corals (CWCs) are increasingly recognised as key to deep-water biodiversity and integral to protected vulnerable marine ecosystems (VMEs), but no deep-sea coral species were previously included in the Red List. We selected 22 cold-water coral species in the Northeast Atlantic, including 4 reef-forming stony corals and 18 octocorals including sea pens and gorgonians, and completed the first IUCN Red List global assessments …

Dengue Virus Modulates Critical Cell Cycle Regulatory Proteins In Human Megakaryocyte Cells, Swarnendu Basak, Shovan Dutta, Supreet Khanal, Girish Neelakanta, Hameeda Sultana

Biological Sciences Faculty Publications

Suppression of human megakaryocytes by dengue virus (DENV) infection significantly reduces the platelet count that eventually leads to thrombocytopenia, severe dengue and death. To understand DENV interactions with megakaryocytes, we investigated the cell cycle in leukemic human megakaryocytic in vitro cell line (MEG-01 cells). Megakaryocytes are known for complex endomitotic cell cycle leading to their polyploidy state. Our study shows that DENV uses these polyploid cells for its replication. Understanding the modulation of DENV-mediated cell cycle regulation in megakaryocytes is therefore highly important. We show that DENV2 (serotype 2) infection significantly modulates cell cycle signaling. Our protein profile microarray data …

Addressing The Productivity-Susceptibility Analysis In Data-Limited Fisheries For Understudied Fish In The Marine Aquarium Trade, Alice Wynn, Jemelyn Baldisimo, Gabrielle Baillargeon, Michael Tlusty, Andrew Rhyne

Biological Sciences Faculty Publications

The marine aquarium trade (MAT) harvests millions of coral reef fishes from the wild yearly. While the MAT supports fishers, hobbyists and marine education, harvested fishes are crucial in maintaining coral reef health and balanced marine cycles within their native habitats. Understanding the impact of the MAT on fish populations is critical for sustaining the trade in the long-term. Productivity-susceptibility analyses (PSAs) offer semiquantitative methods of analyzing the productive capacity of each fish stock, as well as its susceptibility to overfishing. The present study revises and expands upon a PSA conducted by Baillargeon et al. (2020) that focused on 32 …

Divergent Floral And Vegetative Trait Responses To Abiotic Factors Drive Phenotypic Diversity In Platanthera Dilatata (Orchidaceae) Across Alaska, Marlin L. Bowles, Lisa E. Wallace

Biological Sciences Faculty Publications

Multiple traits make up an integrated phenotype, but traits may be shaped by differing drivers. It is often assumed that selection by biotic agents drives floral variation, but abiotic factors are also known to influence floral traits. Understanding trait covariations and their association with diverse environmental factors is a central question in evolution and ecology. Here, we studied covariation in floral and vegetative traits in relation to climate and topo-edaphic variation in the orchid Platanthera dilatata. In Platanthera, nectar spur length is associated with pollinator tongue length, but much variation exists in other traits too, likely to be …