Biology Commons^™

Depletion Of Hiv Reservoir By Activation Of Isr Signaling In Resting Cd4+T Cells, Dajiang Li, Lilly M. Wong, Yuyang Tang, Brigitte Allard, Katherine S. James, George R. Thompson, Satya Dandekar, Edward P. Browne, Qingsheng Li, Jeremy M. Simon, Nancie M. Archin, David M. Margolis, Guochun Jiang

School of Biological Sciences: Faculty Publications

HIV reservoirs are extremely stable and pose a tremendous challenge to clear HIV infection. Here, we demonstrate that activation of ISR/ATF4 signaling reverses HIV latency, which also selectively eliminates HIV+ cells in primary CD4⁺T cell model of latency without effect on HIV-negative CD⁴⁺T cells. The reduction of HIV+ cells is associated with apoptosis enhancement, but surprisingly is largely seen in HIV-infected cells in which gag-pol RNA transcripts are detected in HIV RNA-induced ATF4/IFIT signaling. In resting CD4⁺ (rCD4⁺) T cells isolated from people living with HIV on antiretroviral therapy, induction of ISR/ATF4 signaling …

Genomes Of Endangered Great Hammerhead And Shortfin Mako Sharks Reveal Historic Population Declines And High Levels Of Inbreeding In Great Hammerhead, Michael J. Stanhope, Kristina M. Ceres, Qi Sun, Minghui Wang, Jordan D. Zehr, Nicholas J. Marra, Aryn P. Wilder, Cheng Zou, Andrea M. Bernard, Paulina D. Pavinski Bitar, Mitchell G. Lokey, Mahmood Shivji

Biology Faculty Articles

Despite increasing threats of extinction to Elasmobranchii (sharks and rays), whole genome-based conservation insights are lacking. Here, we present chromosome-level genome assemblies for the Critically Endangered great hammerhead (Sphyrna mokarran) and the Endangered shortfin mako (Isurus oxyrinchus) sharks, with genetic diversity and historical demographic comparisons to other shark species. The great hammerhead exhibited low genetic variation, with 8.7% of the 2.77 Gbp genome in runs of homozygosity (ROH) > 1 Mbp and 74.4% in ROH >100 kbp. The 4.98 Gbp shortfin mako genome had considerably greater diversity and 1 Mbp. Both these sharks experienced precipitous declines in …

Rna Sequence To Structure Analysis From Comprehensive Pairwise Mutagenesis Of Multiple Self-Cleaving Ribozymes, Jessica M. Roberts, James D. Beck, Tanner B. Pollock, Devin P. Bendixsen, Eric J. Hayden

Biology Faculty Publications and Presentations

Self-cleaving ribozymes are RNA molecules that catalyze the cleavage of their own phosphodiester backbones. These ribozymes are found in all domains of life and are also a tool for biotechnical and synthetic biology applications. Self-cleaving ribozymes are also an important model of sequence-to-function relationships for RNA because their small size simplifies synthesis of genetic variants and self-cleaving activity is an accessible readout of the functional consequence of the mutation. Here, we used a high-throughput experimental approach to determine the relative activity for every possible single and double mutant of five self-cleaving ribozymes. From this data, we comprehensively identified non-additive effects …

The Inbio Barcoding Initiative Database: Dna Barcodes Of Iberian Trichoptera, Documenting Biodiversity For Freshwater Biomonitoring In A Mediterranean Hotspot, Joana Pauperio, Luis Martin Gonzalez, Jesus Martinez, Marcos A. González, Filipa Ms Martins, Joana Veríssimo, Pamela Puppo, Joana Pinto, Cátia Chaves, Catarina J. Pinho, José Manuel Grosso-Silva, Lorenzo Quaglietta, Teresa Luísa L. Silva, Pedro Sousa, Paulo Celio Alves, Nuno Fonseca, Pedro Beja, Sónia Ferreira

Biological Sciences Faculty Research

Background

The Trichoptera are an important component of freshwater ecosystems. In the Iberian Peninsula, 380 taxa of caddisflies are known, with nearly 1/3 of the total species being endemic in the region. A reference collection of morphologically identified Trichoptera specimens, representing 142 Iberian taxa, was constructed. The InBIO Barcoding Initiative (IBI) Trichoptera 01 dataset contains records of 438 sequenced specimens. The species of this dataset correspond to about 37% of Iberian Trichoptera species diversity. Specimens were collected between 1975 and 2018 and are deposited in the IBI collection at the CIBIO (Research Center in Biodiversity and Genetic Resources, Portugal) or …

Seasonal Plasticity In Morphology And Metabolism Differs Between Migratory North American And Resident Costa Rican Monarch Butterflies, Ayşe Tenger-Trolander, Cole R. Julick, Wei Lu, Delbert André Green, Kristi L. Montooth, Marcus R. Kronforst

School of Biological Sciences: Faculty Publications

Environmental heterogeneity in temperate latitudes is expected to maintain seasonally plastic life-history strategies that include the tuning of morphologies and metabolism that support overwintering. For species that have expanded their ranges into tropical latitudes, it is unclear the extent to which the capacity for plasticity will be maintained or will erode with disuse. The migratory generations of the North American (NA) monarch butterfly Danaus plexippus lead distinctly different lives from their summer generation NA parents and their tropical descendants living in Costa Rica (CR). NA migratory monarchs postpone reproduction, travel thousands of kilometers south to overwinter in Mexico, and subsist …

Seasonal Plasticity In Morphology And Metabolism Differs Between Migratory North American And Resident Costa Rican Monarch Butterflies, Ayşe Tenger-Trolander, Cole R. Julick, Wei Lu, Delbert André Green, Kristi L. Montooth, Marcus R. Kronforst

School of Biological Sciences: Faculty Publications

Environmental heterogeneity in temperate latitudes is expected to maintain seasonally plastic life-history strategies that include the tuning of morphologies and metabolism that support overwintering. For species that have expanded their ranges into tropical latitudes, it is unclear the extent to which the capacity for plasticity will be maintained or will erode with disuse. The migratory generations of the North American (NA) monarch butterfly Danaus plexippus lead distinctly different lives from their summer generation NA parents and their tropical descendants living in Costa Rica (CR). NA migratory monarchs postpone reproduction, travel thousands of kilometers south to overwinter in Mexico, and subsist …

Artificial Intelligence For Automated Detection Of Large Mammals Creates Path To Upscale Drone Surveys, Javier Lenzi, Andrew Barnas, Abdelrahman A. Elsaid, Travis Desell, Robert F. Rockwell, Susan N. Ellis-Felege

Biology Faculty Publications

Imagery from drones is becoming common in wildlife research and management, but processing data efficiently remains a challenge. We developed a methodology for training a convolutional neural network model on large-scale mosaic imagery to detect and count caribou (Rangifer tarandus), compare model performance with an experienced observer and a group of naïve observers, and discuss the use of aerial imagery and automated methods for large mammal surveys. Combining images taken at 75 m and 120 m above ground level, a faster region-based convolutional neural network (Faster-RCNN) model was trained in using annotated imagery with the labels: “adult …

Methylene Blue Inhibits Cromakalim-Activated K+ Currents In Follicle-Enclosed Oocytes, Dmytro Isaev, Keun-Hang Susan Yang, Georg Petroianu, Dietrich Ernst Lorke, Murat Oz

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

The effects of methylene blue (MB) on cromakalim-induced K⁺ currents were investigated in follicle-enclosed Xenopus oocytes. In concentrations ranging from 3–300 μM, MB inhibited K⁺ currents (IC₅₀: 22.4 μM) activated by cromakalim, which activates K_ATP channels. MB inhibited cromakalim-activated K⁺ currents in a noncompetitive and voltage-independent manner. The respective EC₅₀ and slope values for cromakalim-activation of K⁺ currents were 194 ± 21 µM and 0.91 for controls, and 206 ± 24 µM and 0.87 in the presence of 30 μM MB. The inhibition of cromakalim-induced K⁺ currents by MB was not …

The Effects Of Salinity And Acetaminophen On The Aquatic Snail Physa Acuta, Michelle Sackey-Ansah, Megan Mackey, Daniel Elias, Jason Doll, Alyssa Brookhart

Journal of the South Carolina Academy of Science

Pharmaceuticals are increasingly detected in water bodies, and their presence can negatively impact aquatic organisms. This effect can be amplified when combined with increasing salinity in freshwater ecosystems. Acetaminophen is a widely used analgesic that is commonly found in river, streams, and waters where it is discharged directly. Therefore, organisms present in these locations (e.g., insects, snails, amphibians, and fish) are likely to be affected by acetaminophen. In this study, we determined the effects of elevated salinity (0.68 g/L), acetaminophen (500 µg/L) and combined elevated salinity (0.68 g/L) and acetaminophen (500 µg/L), on the growth, reproduction, and movement of the …

Revisiting Plant Defense-Fitness Trade-Off Hypotheses Using Solanum As A Model Genus, Sakshi Watts, Satinderpal Kaur, Rupesh R. Kariyat

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

Plants possess physical and chemical defenses which have been found to deter herbivores that feed and oviposit on them. Despite having wide variety of defenses which can be constitutive or induced, plants are attacked and damaged by insects associated with different mouthparts and feeding habits. Since these defenses are costly, trade-offs for growth and defense traits play an important role in warding off the herbivores, with consequences for plant and herbivore growth, development and fitness. Solanum is a diverse and rich genus comprising of over 1,500 species with economic and ecological importance. Although a large number of studies on Solanum …

Localization Of Arabidopsis Glucan Synthase-Like 5, 8, And 12 To Plasmodesmata Andthe Gsl8-Dependent Role Of Pdlp5 In Regulating Plasmodesmal Permeability, Behnaz Saatian, Susanne Kohalmi, Yuhai Cui

Biology Publications

Cell-to-cell communication via membranous channels called plasmodesmata (PD) plays critical rolesduring plant development and in response to biotic and abiotic stresses. Several enzymes and receptor-like proteins (RLPs), including Arabidopsis thaliana glucan synthase-likes (GSLs), also known as callosesynthases (CALSs), and PD-located proteins (PDLPs), have been implicated in plasmodesmal permeabilityregulation and intercellular communication. Localization of PDLPs to punctate structures at the cellperiphery and their receptor-like identity have raised the hypothesis that PDLPs are involved in theregulation of symplastic trafficking during plant development and in response to endogenous andexogenous signals. Indeed, it was shown that PDLP5 could limit plasmodesmal permeability throughinducing an increase …

Change And Stasis Of Distinct Sediment Microbiomes Across Port Everglades Inlet (Pei) And The Adjacent Coral Reefs, Lauren E. Krausfeldt, Jose V. Lopez, Catherine Bilodeau, Hyo Won Lee, Shelby L. Casali

Biology Faculty Articles

Deep water ports are human built coastal structures that by definition welcome ship traffic and disturbance. Evidence is accumulating that enhanced port activities such as dredging or deepening have negatively affected nearby natural habitats. Port Everglades Inlet (PEI) is a large active South Florida cargo port for over two million people and lies adjacent to coral reefs, dwindling mangroves, and recreational beaches. In this study, the microbial communities of PEI and adjacent reef sediments were characterized to serve as indicators for change due to dredging and assess anthropogenic influence on these sensitive ecosystems by sequencing the V4 region of 16S …

Environmental Enrichment Factors Associated With The Activity Level Of Bottlenose Dolphins Under Professional Care, Lisa K. Lauderdale, K. Alex Shorter, Joaquin Gabaldon, Jill D. Mellen, Multiple Additional Authors

Biology Faculty Publications and Presentations

Environmental enrichment can be used to improve the welfare of dolphins in zoos and aquariums. Bottlenose dolphins under professional care are typically provided with a range of enrichment that has a variety of features and levels of complexity at various frequencies. In the present study, a subset of data from a larger study entitled “Towards understanding the welfare of cetaceans in zoos and aquariums” (colloquially called the Cetacean Welfare Study) was used to examine the relationship between activity level and enrichment buoyancy as well as enrichment provisioning schedules. Survey data were collected from accredited zoos and aquariums related to the …

Insight From Biology Program Learning Outcomes: Implications For Teaching, Learning, And Assessment, Noelle Clark, Jeremy L. Hsu

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

Learning goals and objectives are a key part of instruction, informing curricular design, assessment, and learning. These goals and objectives are also applied at the programmatic level, with program learning outcomes (PLOs) providing insight into the skills that undergraduate biology programs intend for their students to master. PLOs are mandated by all major higher education accreditation agencies and play integral roles in programmatic assessment. Despite their importance, however, there have not been any prior attempts to characterize PLOs across undergraduate biology programs in the United States. Our study reveals that many programs may not be using PLOs to communicate learning …

Investigating The Absence Of A Dietary Response At The Neuromuscular Junction In Larval Drosophila Melanogaster, Suzanna Louise Marbach

Honors Program Theses and Research Projects

Research in Drosophila melanogaster (D. melanogaster) has been growing in order to identify the fundamental processes of human disorders of the central nervous system such as Alzheimer’s disease, diabetes, and other neurological disorders at a molecular level. Altered insulin signaling itself has been linked to widespread nervous system dysfunction including cognitive dysfunction, neuropathies, and susceptibility to neurodegenerative disease. However, knowledge of the cellular mechanisms underlying the effects of insulin on nervous system function is still incomplete. The focus behind investigating the insulin signaling pathway is derived from our observations in the adult D. melanogaster neuromuscular junction (NMJ) to changes in …

Role Of Microorganisms In Horticulture To Improve Plant Quality, Domenico Prisa

Karbala International Journal of Modern Science

One of the most anticipated challenges in the field of agriculture is to ensure high production levels while limiting the use of environmentally harmful synthetic chemicals. One of the most interesting strategies to overcome this challenge is the exploitation of the interactions between soil microorganisms and plants which result in stimulating plants’ natural activity. The interactions among mycorrhiza, growth-promoting microorganisms and plants play a crucial role in soil fertility, biocontrol and protection. The use of mixed microbial products can simulate interactions between fungi and bacteria, realising all the benefits that can be obtained from these associations in terms of quantity …

Do Regional Dna Barcode Databases Lead To More Efficient Specimen Identification?, Michael Kerr, Steven D. Leavitt

Library/Life Sciences Undergraduate Poster Competition 2023

DNA barcoding is a method for identifying specimens from specific regions of DNA. 1 Metabarcoding focuses on large, multi specimen scales. 2 These approaches rely on DNA databases for sequence identification, 2 but these databases often lack data from many species, 3 especially from poorly studied groups such as fungi 4 and lichens, which can lead to failure in specimen identification.

Evolution And Molecular Basis Of A Novel Allosteric Property Of Crocodilian Hemoglobin, Chandrasekhar Natarajan, Anthony V. Signore, Naim M. Bautista, Federico G. Hoffmann, Jeremy R.H. Tame, Angela Fago, Jay F. Storz

School of Biological Sciences: Faculty Publications

The extraordinary breath-hold diving capacity of crocodilians has been ascribed to a unique mode of allosterically regulating hemoglobin (Hb)-oxygenation in circulating red blood cells. We investigated the origin and mechanistic basis of this novel biochemical phenomenon by performing directed mutagenesis experiments on resurrected ancestral Hbs. Comparisons of Hb function between the common ancestor of archosaurs (the group that includes crocodilians and birds) and the last common ancestor of modern crocodilians revealed that regulation of Hb-O₂ affinity via allosteric binding of bicarbonate ions represents a croc-specific innovation that evolved in combination with the loss of allosteric regulation by ATP binding. …

Traditional Plants That Are Utilized To Treat Urinary Tract Infections: A Review, Rasha Hadi Saleh, Aseel Mohammad Omran, Rafah S. Almuttairi Alhilla

Maaen Journal for Medical Sciences

Among the most serious problems affecting public health is urinary tract infection (UTI). There are several parts of the urinary tract affected by this type of inflammation and affects women more frequently than men. As the antibacterial resistance problem is growing in urological medicine, there is a increasing and a continuing requirement to add antimicrobial medication which could be from medicinal herbs in regulatory UTIs. Since the beginning of civilization, medicinal plants have been an integral element of human society in the fight against diseases. For the aim of reducing costs, increasing the effectiveness of treatment and eliminating the side …

Temperature Fluctuation Alters Optimal Predator Community Composition For Anticipated Biological Control, Amanda N. Laubmeier, Nusrat Tabassum, Brigitte Tenhumberg

School of Biological Sciences: Faculty Publications

Alongside pesticides and specialist predators, natural communities of generalist beetle and spider predators play an important role in suppressing agricultural pests. However, the predation pressure of natural communities can be unpredictable. Overall predation pressure is influenced by a dense network of potential intraguild interactions, which are further shaped by species traits and environmental factors. Understanding how these different influences combine to impact pest control is especially important in the context of changing global temperatures. Recent empirical studies have demonstrated that the foraging behavior of arthropod predators is influenced by an interaction between temperature and predator body size. To explore the …

Selective And Differential Feeding On Marine Prokaryotes By Mucous Mesh Feeders, Carey P. Sweeney, Kelly R. Sutherland, Anne Thompson

Biology Faculty Publications and Presentations

Microbial mortality impacts the structure of food webs, carbon flow, and the interactions that create dynamic patterns of abundance across gradients in space and time in diverse ecosystems. In the oceans, estimates of microbial mortality by viruses, protists, and small zooplankton do not account fully for observations of loss, suggesting the existence of underappreciated mortality sources. We examined how ubiquitous mucous mesh feeders (i.e. gelatinous zooplankton) could contribute to microbial mortality in the open ocean. We coupled capture of live animals by blue-water diving to sequence-based approaches to measure the enrichment and selectivity of feeding by two coexisting mucous grazer …

Variability Of Hybridization In Topminnows, David D. Duvernell

Biological Sciences Faculty Research & Creative Works

Pairs of species that exhibit broadly overlapping distributions, and multiple geographically isolated contact zones, provide opportunities to investigate the mechanisms of reproductive isolation. Such naturally replicated systems have demonstrated that hybridization rates can vary substantially among populations, raising important questions about the genetic basis of reproductive isolation. The topminnows, Fundulus notatus and F. olivaceus, are reciprocally monophyletic, and co-occur in drainages throughout much of the central and southern United States. Hybridization rates vary substantially among populations in isolated drainage systems. We employed genome-wide sampling to investigate geographic variation in hybridization, and to assess the possible importance of chromosome fusions …

Assessing The Unionid Assemblage Of The Robert C. Byrd Pool, Ohio River, Ethan Hunter Bellamy

Theses, Dissertations and Capstones

Unionid mussels are the most imperiled taxa in the United States and are vastly understudied. The entire Robert C. Byrd (RCB) pool of the Ohio River is the study area. I selected sites from the 2019 and 2013 ORSANCO RCB pool assessments that utilize random site selection across the pool. I used SCUBA to survey and collect data on unionid diversity, reproduction, and habitat. I collected 1,083 individuals over 19 species in RCB pool. I compared results from RCB pool survey to two similar surveys conducted in Greenup Pool. Both richness and abundance in the Upper Section of Greenup Pool …

Nonconsumptive Effects Of Crustaceans And An Echinoderm On Spat Of The Eastern Oyster Crassostrea Virginica (Gmelin, 1791), Maria Rosa, Mike Gilman, Sarah Anderson, Adrian Beckford, Ben Gilfond, Nicole Wright, David M. Hudson

Biology Faculty Publications

Predation by crustaceans and echinoderms is a significant driver of mortality for sessile invertebrates in near-shore marine ecosystems. As a response, shellfish growers use predator exclusion cages to grow their product. Oysters grown in these cages and clams in and under nets have been observed to exhibit thinner, brittle shells, which is not optimal for market, nor for those being grown for restoration purposes. Here, the nonconsumptive predator effects of several native and nonnative predators on shell morphology of Crassostrea virginica oyster spat. Juvenile (1–3 mm) seed oysters were exposed separately to chemical cues of five different predators and one …

Genetically Encoded Iron Sensor Cell Line: A Model For Studying Ferroptosis And Cellular Iron Metabolism, Daoud F. Rahman

Theses and Dissertations

Cell death is a biological process that is essential in proper cellular homeostasis, development, and function. Malfunction of this system can lead to different diseases and cancers. Ferroptosis is a form of cell death that occurs as a result of the accumulation of lipid peroxides, that are dependent on intracellular levels of iron. Iron is essential to multiple metabolic processes in the cell, including the catalyzation of lipid peroxides. Thus, intracellular iron levels must be tightly regulated. Our goal is to create a cellular model to study and detect changes in intracellular iron levels. Through the use of a genetically …

Figure 1, Marquette University, Lisa N. Petrella

Mikeworth 2023

No abstract provided.

Figure 2, Marquette University, Lisa N. Petrella

Mikeworth 2023

No abstract provided.

Figure 5, Marquette University, Lisa Petrella

Mikeworth 2023

No abstract provided.

What Is The Optimal Timing Of Embryo Biopsy For Diagnosing Genetic Abnormalities?, Nekhama Riznyk

The Science Journal of the Lander College of Arts and Sciences

Introduction and Purpose: This paper examines current trends in assisted reproductive technology, specifically the use of preimplantation genetic diagnosis (PGD to help in the preimplantation detection of genetic abnormalities such as monogenetic diseases and aneuploidy. PGD can be carried out in different stages, and the timing of the procedure has become one of the major issues in implementation. Three major stages of biopsy have been applied when carrying out PGD: Polar body biopsy (pre-conception), cleavage stage biopsy (3 days after conception), and blastocyst stage biopsy (6 days after conception). The purpose of the paper was to explore these stages and …

Improving The Prediction And Management Of Intrauterine Growth Restriction, Shulamis Sadowsky

The Science Journal of the Lander College of Arts and Sciences

Intrauterine growth restriction (IUGR) is a potentially fatal and often missed obstetric complication. The fetus is deprived of vital blood, oxygen, and nutrients due to faulty maternofetal circulation, leading to a severe lack of fetal growth. Since current prenatal testing is highly ineffective at diagnosing the condition, many babies with IUGR are negatively impacted before, during, and after birth. This paper assesses alternative and innovative detection and management methods of IUGR. Current routine prenatal care includes simple fundal height measurements to screen for IUGR. This analysis finds that other testing may increase the rate of detection of the disease. Maternal …