Biology Commons^™

Identification Of The Functional Domain Of The Dense Core Vesicle Biogenesis Factor Hid-1, Blake H. Hummer, Theodore Carter, Breanna L. Sellers, Jenna D. Triplett, Cedric S. Asensio

Biological Sciences: Faculty Scholarship

Large dense core vesicles (LDCVs) mediate the regulated release of neuropeptides and peptide hormones. HID-1 is a trans-Golgi network (TGN) localized peripheral membrane protein contributing to LDCV formation. There is no information about HID-1 structure or domain architecture, and thus it remains unknown how HID-1 binds to the TGN and performs its function. We report that the N-terminus of HID-1 mediates membrane binding through a myristoyl group with a polybasic amino acid patch but lacks specificity for the TGN. In addition, we show that the C-terminus serves as the functional domain. Indeed, this isolated domain, when tethered to the TGN, …

Rna World And The Development Of Rna Protocells, Benjamin C. Mayfield

PANDION: The Osprey Journal of Research and Ideas

Origins of life research, also known as pre-biotic chemistry or astrobiology, aims to unravel the mystery of the first cell’s origin on Earth. This interdisciplinary field encompasses biology, chemistry, and physics, with the primary goal of understanding the conditions necessary for life to emerge from abiotic environments. The RNA world hypothesis suggests that early life initially used RNA instead of DNA to store genomic information and for enzymatic functions. Protocells, membrane-bound entities with metabolic processes and self-replication capabilities, likely preceded the emergence of true cells. The challenges associated with RNA world is currently an active field of research. Advancements in …

Alligator Skull, Katherine Weaver

PANDION: The Osprey Journal of Research and Ideas

Artist Statement

Alligator Skull was created through mimicking the shadows on the bones of a giant creature with the dots of my pen. Living in Florida, I have known these animals my entire life, and I have been mesmerized by them the whole time. To see one humbled into a skeleton form is so intriguing. They are apex predators that encompass fear in many, but they are just as mortal as the rest of us. They only kill to survive, but the power they possess over the waters has humans either petrified or entranced. This individual from the Alligator mississippiensis …

Leafy Sea Dragon, Phycodurus Sp., Kennedi X. Light

PANDION: The Osprey Journal of Research and Ideas

Artist Statement

Leafy sea dragons, Phycodurus sp. are part of the Syngnathidae family. Syngnathidae is a genus made up of seahorses, pipefishes, and sea dragons. All three of the species are known to have beautiful patterning. However, leafy sea dragons got their name from their leafy appendages like their fins and limbs. The reason I chose to draw a leafy sea dragon is due to my own interest in astrobiology. Astrobiology is the study of life in the universe and astrobiologists look for signs of life within the universe. I would like to be an astrobiologist one day and focus …

The Florida Scrub-Jay, Emily Hill

PANDION: The Osprey Journal of Research and Ideas

Artist Statement

The Florida Scrub-Jay is a digital scientific illustration of Aphelocoma coerulescens, the only native bird species endemic to Florida. This piece celebrates the natural beauty of the Florida scrub-jay and its key features that allow it to thrive in scrub habitats. These habitats are threatened by anthropogenic activity and climate change, leading to the fragmentation, degradation, or eventual loss of these areas. Through this artwork, I hope to emphasize the importance of conservation and inspire viewers to appreciate and protect this bird species.

Every stroke and color choice were carefully considered to accurately depict the bird’s physical attributes. …

Peer Leader Perspectives From A Pltl Implementation In A Hispanic-Serving Institution, Madhavan Narayanan, Kasey Powers, Dhananjaya Premawardena, Davida S. Smyth, Et Al.

All Faculty Scholarship (Archived)

Peer-Led Team Learning (PLTL) is a pedagogical approach that has been shown to benefit all students, especially underrepresented minority students and peer leaders in Science, Technology, Engineering, and Mathematics (STEM) disciplines. In this work, we present results from our study of the impact of PLTL on our peer leaders from a controlled implementation in general biology, general chemistry, and statistics courses at a Hispanic-serving, minority-serving institution. More specifically, we have measured our PLTL program’s impact on our peer leaders' skill development, engagement with the subject material, and sense of belonging as peer leaders. Weekly peer leader reflections analyzed using the …

A High-Efficiency Gene Silencing In Plants Using Two-Hit Asymmetrical Artificial Micrornas, Sachin Teotia, Xiaoran Wang, Na Zhou, Mengmeng Wang, Haiping Liu, Jun Qin, Dianwei Han, Chingwen Li, Christine E. Li, Shangjin Pan, Haifeng Tang, Wenjun Kang, Zhanhui Zhang, Xiaoqing Tang, Ting Peng, Guiliang Tang

Michigan Tech Publications, Part 1

MicroRNAs (miRNAs) are small non-coding RNA molecules that play a crucial role in gene regulation. They are produced through an enzyme-guided process called dicing and have an asymmetrical structure with two nucleotide overhangs at the 3' ends. Artificial microRNAs (amiRNAs or amiRs) are designed to mimic the structure of miRNAs and can be used to silence specific genes of interest. Traditionally, amiRNAs are designed based on an endogenous miRNA precursor with certain mismatches at specific positions to increase their efficiency. In this study, the authors modified the highly expressed miR168a in Arabidopsis thaliana by replacing the single miR168 stem-loop / …

Site Familiarity Makes An Enduring Impact On Breeding Success, Walter H. Piper, Katy Dahl, Martha Kebeh, Allison J. Piper

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

Most studies of vertebrate breeding success have been unable to pinpoint the cause for a simple and almost universal pattern: its steady increase during an animal's lifetime. Yet potential causes of increased breeding success have profound implications for the evolution of reproductive behaviour. An age-related increase might come about through (1) higher breeding investment by older animals, (2) breeding improvement through learning, (3) better reproductive coordination between familiar mates or (4) accumulated benefits of site familiarity. We used mixed models to investigate age-related predictors of hatching and fledging success in a population of common loons, Gavia immer, that contained …

The Emerging Oral Pathogen, Filifactor Alocis, Modulates Antimicrobial Responses Of Primed Human Neutrophils., Ian J. Snider, Aruna Vashishta, Richard J. Lamont, Silvia M. Uriarte

The Cardinal Edge

Almost 50% of the adult population older than 30 years of age suffers from some form of periodontitis, a chronic inflammatory disease of the periodontal tissue caused by microbial subversion of the host immune response. Neutrophils are the most abundant leukocyte present in the oral mucosa. In periodontitis, periodontal pathogens have developed strategies to evade neutrophil antimicrobial responses and promote bacterial growth. Among these oral pathogens is Filifactor alocis which can modulate neutrophils’ antimicrobial responses by preventing phagosome maturation. During inflammation, neutrophils that reach the gingival tissue are primed by cytokines and chemokines. However, the response of primed human neutrophils …

Effects Of Osmotic Stress On Dna And Cell Viability In A Desiccation-Sensitive Cell Line, Brady D. Russell, Rajib Hassan, Michael A. Menze

The Cardinal Edge

Kc167 is a widely used Drosophila cell line, known to be sensitive to the extreme water loss caused by desiccation. In order to characterize the effects of this desiccation-sensitivity on DNA and cell viability, a series of osmotic stressors of differing concentrations were introduced to the cell line. These cells were then imaged via the Cytation1 cell imaging machine using fluorescence microscopy. Specifically, cells were stained using the DAPI staining solution, a blue fluorescent DNA stain that binds strongly to A-T rich regions within the DNA, forming a fluorescent complex. As DAPI more readily enters the membrane and thereby stains …

Resolving Commingling, Restoring Identity: An Interdisciplinary Collaboration And Ethical Study Of Individuals From A Human Skeletal Teaching Collection, Morgann L. Lucas, Morgan J. Elmore, Christine Chen, Carolann Cockerill, Mekenzie Davis, Vivian N. Pham, Matthew Kolmann, Linda Fuselier, Kathryn E. Marklein

The Cardinal Edge

In Fall 2022, human skeletal remains were discovered in the Department of Biology’s Comparative Vertebrate Anatomy Laboratory. No documentation about the acquisition or curation history was found. With no current protocols for repatriating individuals in university skeletal teaching collections, an interdisciplinary research team analyzed the skeletal remains to resolve to commingle and identify the people. Using standardized methods in forensic anthropology, we estimated the minimum number of individuals represented through taphonomic, demographic, paleopathological, and morphological variables and variation. Results indicated, minimally, 36 to 56 individuals represented by 250 bones. Of these individuals, 12 were estimated as probable female, 16 as …

Histological Evaluation Of Offspring Kidneys Following Prenatal Vaping, Lucas Georges, Katelyn Chism, Selma Podbicanin, Isaiah Burciaga, Cynthia Corbitt, Rachel Neal

The Cardinal Edge

Pregnant women are advised to switch from cigarettes to electronic cigarettes to reduce the toxic effects on the fetus, however little research has been done on the impact of vaping on child development. In this study investigating the impact of inhalation exposure to a commercial product on reproductive and developmental functions, C57BL/6 dams were exposed to vapor from Vuse^TM e-cigarette golden tobacco pod for 3 hours/day at two puffs per minute throughout gestation (Vape) or to filtered air (Sham). This resulted in smaller litter sizes, along with greater weights for Vape offspring at birth that returned to average by …

The Impact Of Prenatal Vape Exposure On Weanling Liver Gene Expression, Isabella R. Fieger, Cristina Isabel Pauig, Mindy Yin, Anna Lipinski, Barrett Blevins, Tyler Plake, Lucas Georges, Katelyn Chism, Isaiah Burciaga, Selma Podbicanin, Cynthia Corbitt, Rachel Neal

The Cardinal Edge

The use of E-cigarettes is a fairly recent phenomenon. Vaping is seen as the “healthier” alternative to smoking cigarettes, yet we know little about the developmental toxicity of commercially available vaping products. In the current study, C57Bl/6 mice were exposed to Vuse Alto Golden Tobacco pods (5% nicotine) 4 days before mating and throughout gestation (GD19) for 1 hour/day every day. Offspring birth outcomes were measured with liver tissue collected at weaning. Gross histology and gene expression in the SIRT1-FXR pathway were examined via qPCR analysis with male and female offspring analyzed separately. No differences in gross morphology or cell …

Characterization Of Oral Pathogen, Filifactor Alocis, And Its Virulence Factors That Contribute To The Progression Of Periodontitis., Ian J. Snider

The Cardinal Edge

No abstract provided.

Eggshell-Alginate Composites (Eacs) As Eco-Friendly Adsorbents For Rhodamine B Uptake From Aqueous Solutions, Rusnadi Rusnadi, Mar’Atus Sholihah, Nurrahmi Handayani, Muhammad Ali Zulfikar

Karbala International Journal of Modern Science

The contamination of wastewater by Rhodamine B (RhB) poses a significant environmental concern due to its negative impacts on aesthetics, ecosystems, and human well-being. This study successfully synthesized eco-friendly egg-shell-alginate composites (EACs) as adsorbents by combining alginate solution, eggshell powder, and a 2% CaCl2 solu-tion. Characterization techniques including FTIR, SEM, TGA, and SAA were employed to analyze the EACs. FTIR analysis revealed characteristic absorption peaks corresponding to -OH groups, C=O groups, C-O groups, and the pres-ence of CO32-. The structural analysis confirmed the physical mixture of functional groups from eggshells and alginate, resulting in a homogeneous EACs mixture. TGA analysis …

Synthesizing Of Alginate Coated-Silver Nanoparticles Core-Shell For Detecting Of S-Naproxen Enantiomer In Pharmaceutical Formulation, Abdolrasol Barazandeh, Ghasem Najafpour-Darz, Afshar Alihossein, Sohrab Kazemi

Karbala International Journal of Modern Science

Core-shell nanoparticles were used in a unique direct UV-Vis spectrophotometric technique to detect the S-naproxen enantiomer. Silver nanoparticles (Ag NPs) covered with sodium alginate (Alg) shell, a naturally occurring biopolymer, made the core of the nanostructure. To name a few, TEM, FESEM, UV-Visible, DLS, ZP, AFM, XRD, EDX and FT-IR are among the analytical methods used to analyze the creation of the core-shell structure. Based on obtained results, spherical Ag@ Alg NPs with an average size of 27.4 nm (DTEM), hydrolytic size of 46 nm (DDLS) and surface charge of -60.9 mV were successfully synthesized. The effect of various reaction …

The Regulation Of Irs1 Via S6k-1 And P300 Activity, Vhuthuhawe Tintswalo Madzinge

Doctoral Dissertations and Projects

The study of IRS-1 has increased over the years due to the prevalence of cardiometabolic diseases. An increase in IRS-1 serine phosphorylation is often associated with the development of insulin resistance due to the downregulation bestowed upon it by different kinases such as p70 S6K-1. Recently, p300 has been shown to acetylate IRS-1 thus leading to its downregulation. However, studies have not looked into the relationship that exists between serine phosphorylation and lysine acetylation of IRS-1. In this study, insulin stimulated HepG2 cells were treated with either PF4708671, a selective p70 S6K-1 inhibitor, or C646, a selective p300 inhibitor. PF4708671 …

The Effect Of Slow-Release Milk Replacer Feeding On Health And Behaviour Parameters In Dairy Breed Calves, Lea Krump, Ríona G. Sayers, Katie Sugrue, Emer Kennedy, Jim O'Mahony, Gearoid Sayers

Department of Biological Sciences Publications

The aim of this research paper was to evaluate the effect of a slow-release milk replacer on health and behaviour of neonatal dairy calves. This was done with the potential benefits to welfare during transport in mind. A total of 15 calves were randomly divided into three groups of 5, namely, a control group fed twice in 24 h with 3 l of a conventional milk replacer, a slow-release group fed once in 24 h with 2 l of conventional milk replacer and 1 litre of a specialised micro-encapsulated feed and an enriched-replacer group fed once in 24h with 3L …

Homeostatic Synaptic Plasticity Of Miniature Excitatory Postsynaptic Currents In Mouse Cortical Cultures Requires Neuronal Rab3a, Andrew G. Koesters, Mark M. Rich, Kathrin L. Engisch

Biological Sciences Faculty Publications

Following prolonged activity blockade, amplitudes of miniature excitatory postsynaptic currents (mEPSCs) increase, a form of homeostatic plasticity termed “synaptic scaling.” We previously showed that a presynaptic protein, the small GTPase Rab3A, is required for full expression of the increase in miniature endplate current amplitudes following prolonged blockade of action potential activity at the mouse neuromuscular junction in vivo (Wang et al., 2011), but it is unknown whether this form of Rab3A-dependent homeostatic plasticity shares any characteristics with central synapses. We show here that synaptic scaling of mEPSCs is impaired in mouse cortical neuron cultures prepared from Rab3A-/- and Rab3A Earlybird …

Resistance To Dna Interstrand Crosslinks In Escherichia Coli Arises Through Prevention Rather Than Repair, Travis Kim Worley

Dissertations and Theses

DNA interstrand crosslinks are particularly lethal lesions that form in DNA when certain molecules intercalate between complementary strands of DNA and form covalent bonds with both strands. Once formed, these lesions present an absolute block to replication and transcription, ultimately resulting in cell death. Because of this lethality, chemicals that form DNA interstrand crosslinks are found in nature as defensive chemicals produced by plants and microbes. Moreover, crosslinking agents have proven effective the treatment of dysplastic conditions and are often first line chemotherapeutics.

However, cancer cells can become resistant to DNA interstrand crosslinks. Unlike other DNA lesions, the double-stranded nature …

Charting The Landscape Of Ventral Stream Neural Code On Generative Image Manifolds, Binxu Wang

Arts & Sciences Graduate Student Theses and Dissertations

The natural world features high-dimensional retinal inputs to the visual system. In contrast, to study vision in the lab, only sparsely sampled image sets are used. Given this immense natural image manifold, what is a principled way to sample and understand the neural representations on it? In this thesis, we frame the neural coding question in a geometric way. Neural tuning can be conceptualized as a landscape on the natural image manifold, and generative models such as GANs provide a concrete instantiation of the manifolds. We hypothesized that the maximally activating images or peaks on these landscapes are critical for …

A Role Of Glutathione-Encoding Gene (Gsha) In Oxidative Stress And Antibiotic Susceptibility In Multidrug Resistant Pseudomonas Aeruginosa: A Possible Drug Target, Mital Vasoya, Sarah Alsaleh, Dong H. Kwon

Discovery Day

Background: Pseudomonas aeruginosa is a major causative agent of hospital- and community-acquired infections. Antibacterial treatment of the infections is often difficult due to presence of antibiotic resistant P. aeruginosa. A number of intrinsic and acquired antibiotic resistance mechanisms reported in P. aeruginosa. Recently, scavenging intracellular reactive oxygen species (ROS) has suggested as an intrinsic antibiotic resistance mechanism to all bacterial species since antibiotics induce oxidative stress in the bacterial species. However, this intrinsic resistance mechanism is currently controversial and further clarification requires. Glutathione is a sulfuhydryl (-SH)-containing tri-peptide intracellular antioxidant and serves as a scavenger of the intracellular ROS. Aim: …

The Phylogeny Predicts Potential New Sources Of Antibiotics From Plants, Malini Anna Prasad, Jeanmaire Molina

Discovery Day

The evolution and spread of antibiotic resistance has been the greatest threat to successful antibiotic treatment, and hence the driving force behind the search for new therapies. None of our modern pharmaceutical antibiotics have been developed from plants, albeit plants have been used since antiquity in traditional medicine to fight bacterial infections. We phylogenetically analyzed 138 plant species with antibacterial activity and found 5 plant families that are disproportionately important, with confamilials exerting similar antibacterial mechanisms, as expected due to common ancestry. Myrtaceae (guava family) was shown to inhibit quorum sensing, disrupting bacterial communication implicated in pathogenicity, due to its …

Asymmetric Response Of Amazon Forest Water And Energy Fluxes To Wet And Dry Hydrological Extremes Reveals Onset Of A Local Drought-Induced Tipping Point, Natalia Restrepo-Coupe, Bradley O. Christoffersen, Marcos Longo, Luciana F. Alves, Kleber Silva Campos, Alessandro C. Da Araujo, Raimundo C. De Oliveira Jr., Neill Prohaska, Rodrigo Da Silva, Raphael Tapajos

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

Understanding the effects of intensification of Amazon basin hydrological cycling—manifest as increasingly frequent floods and droughts—on water and energy cycles of tropical forests is essential to meeting the challenge of predicting ecosystem responses to climate change, including forest “tipping points”. Here, we investigated the impacts of hydrological extremes on forest function using 12+ years of observations (between 2001–2020) of water and energy fluxes from eddy covariance, along with associated ecological dynamics from biometry, at the Tapajós National Forest. Measurements encompass the strong 2015–2016 El Niño drought and La Niña 2008–2009 wet events. We found that the forest responded strongly to …

Role Of Copyback Viral Genomes In Activating Cellular Stress Responses During Pneumovirus And Paramyxovirus Infection, Lavinia Jose Gonzalez Aparicio

Arts & Sciences Graduate Student Theses and Dissertations

The interactions that occur between a virus and the infected cell determine the success of an infection. During negative-sense single-stranded RNA virus infections, copyback viral genomes (cbVGs) drive key virus-host interactions by activating the Mitochondrial Antiviral Signaling (MAVS) pathway that induces antiviral immunity and leads to reduced levels of virus replication. Whether cbVGs induce other cellular pathways and how these relate to their immunostimulatory activity is unknown. Here we show that cbVGs also induce a cellular stress response during pneumovirus and paramyxovirus infections. cbVGs activate the cellular stress response through Protein Kinase R (PKR) signaling, triggering translation inhibition and stress …

Combining Simulations And Single Molecule Spectroscopy To Understand Sars-Cov-2 Nucleocapsid Protein-Rna Interactions, Jhullian Jamille Alston

Arts & Sciences Graduate Student Theses and Dissertations

Disordered protein regions play crucial roles in various cellular functions, exhibiting high heterogeneity and sampling an ensemble of conformations distinct from folded domains. However, our understanding of their behavior and contributions to protein-protein and protein-nucleic acid interactions remains limited. This dissertation focuses on investigating the interactions between disordered regions and RNA, as well as folded regions of proteins, utilizing computational modeling and single-molecule fluorescence spectroscopy. The SARS-CoV-2 Nucleocapsid (N) protein serves as a model system to address broader questions concerning disordered protein behavior and N protein-mediated RNA genome packaging. I employed coarse-grained molecular dynamic simulations to characterize the cooperative binding …

Investigating The Role Of Dcia During The Cell Cycle In Mycobacterium, Helen Catherine Blaine

Arts & Sciences Graduate Student Theses and Dissertations

The mycobacterial family contains many human pathogens, including Mycobacterium tuberculosis, Mycobacterium abcessus, and Mycobacterium leprae. Mycobacterium tuberculosis, the causative agent of the disease tuberculosis (TB), is a major public health problem. The emergence of increasing numbers of antibiotic resistant cases of TB has led to a push for novel drug development. A popular target for antibiotic development is DNA replication, as this is an essential process in bacterial cell development. Further understanding of the DNA replication process in mycobacteria will be key to drug development efforts. The process of DNA replication has been well studied in Escherichia coli and Bacillus …

Lichens Of Iller Creek: A Checklist For The Iller Creek Unit, A Division Of Dishman Hills Conservation Area, Spokane Valley, Wa, Devin M. Mumey, Giovanna Bishop, Jessica L. Allen

2023 Symposium

The field of biodiversity documentation encompasses a broad range of research including new species discovery and description, compilation of species present in a given area, and investigation of interspecies interaction. In an era of increasingly devastating and rapid environmental change, documenting biodiversity has become increasingly important. Anthropogenic effects on urban-adjacent natural areas are especially significant, as they can cause numerous, often drastic, responses in ecosystems. Our objective here was to document the lichen biodiversity in a large urban-adjacent protected area: the Iller Creek Unit of the Dishman Hills Conservation Area in Spokane Valley, Washington. This unit encompasses a diversity of …

Impact Of A Tlr9 Agonist And Broadly Neutralizing Antibodies On Hiv-1 Persistence: The Randomized Phase 2a Titan Trial, Jesper D. Gunst, Jesper Falkesgaard Højen, Marie H. Pahus, Miriam Rosás-Umbert, Birgitte Stiksrud, James Mcmahon, Paul Denton, Henrik Nielsen, Isik S. Johansen, Thomas Benfield, Steffen Leth, Jan Gerstoft, Lars Østergaard, Mariane H. Schleimann, Rikke Olesen, Henrik Støvring, Line K. Vibholm, Nia Weis, Anne M. Dyrhol-Riise, Karen B.H. Pedersen, Jillian S.Y. Lau, Dennis C. Copertino, Noemi Linden, Tan T. Huynh, Victor Ramos, Rl Brad Jones, Sharon R. Lewin, Martin Tolstrup, Thomas A. Rasmussen, Michel C. Nussenzweig, Marina Caskey, Dag Henrik Reikvam, Ole Schmeltz Søgaard

Biology Faculty Publications

Inducing antiretroviral therapy (ART)-free virological control is a critical step toward a human immunodeficiency virus type 1 (HIV-1) cure. In this phase 2a, placebo-controlled, double-blinded trial, 43 people (85% males) with HIV-1 on ART were randomized to (1) placebo/placebo, (2) lefitolimod (TLR9 agonist)/placebo, (3) placebo/broadly neutralizing anti-HIV-1 antibodies (bNAbs) or (4) lefitolimod/bNAb. ART interruption (ATI) started at week 3. Lefitolimod was administered once weekly for the first 8 weeks, and bNAbs were administered twice, 1 d before and 3 weeks after ATI. The primary endpoint was time to loss of virologic control after ATI. The median delay in time to …

Dfcp1 Regulates Lipid Droplet Catabolism In An Ntpase-Dependent Manner, Victoria Anne Ismail

Arts & Sciences Graduate Student Theses and Dissertations

Lipid Droplets (LDs) are lipid storage organelles that can be readily tapped to resupply cells with energy or lipid building blocks, and, therefore, play a central role in cellular metabolism. It has emerged that Double FYVE Domain Containing Protein 1 (DFCP1), which has routinely been used as a marker for early autophagy, is an LD-associated protein and is implicated in establishing contacts between the endoplasmic reticulum (ER) and LDs, but little is known about DFCP1’s function or how it influences either autophagy or LD metabolism. Here, we show that DFCP1 contains a novel NTPase domain that regulates its assembly onto …