Biology Commons^™

Ancient Dna Of The Pygmy Marmoset Type Specimen Cebuella Pygmaea (Spix, 1823) Resolves A Taxonomic Conundrum, J. P. Boubli, M. C. Janiak, L. M. Porter, Stella De La Torre, L. Cortés-Ortiz, M. N. F. Da Silva, A. B. Rylands, Stephen Nash, F. Bertuol, H. Byrne, F. E. Silva, F. Rohe, D. De Vries, R. M. D. Beck, I. Ruiz-Gartzia, L. F. K. Kuderna, T. Marques-Bonet, Tomas Hrbek, I. P. Farias, A. H. Van Heteren, C. Roos

Biology Faculty Research

The pygmy marmoset, the smallest of the anthropoid primates, has a broad distribution in Western Amazonia. Recent studies using molecular and morphological data have identified two distinct species separated by the Napo and Solimões-Amazonas rivers. However, reconciling this new biological evidence with current taxonomy, i.e., two subspecies, Cebuella pygmaea pygmaea (Spix, 1823) and Cebuella pygmaea niveiventris (Lönnberg, 1940), was problematic given the uncertainty as to whether Spix’s pygmy marmoset (Cebuella pygmaea pygmaea) was collected north or south of the Napo and Solimões-Amazonas rivers, making it unclear to which of the two newly revealed species the name pygmaea would …

On The Relationship Between Pain Variability And Relief In Randomized Clinical Trials, Siddharth Tiwari '22

Student Publications & Research

Previous research suggests greater baseline variability is associated with greater pain relief in those who receive a placebo. However, studies that evidence this association do not control for confounding effects (natural history and regression-to-the-mean); for this reason, we analyzed data from two randomized clinical trials (Placebo I and Placebo II, N = 134) while adjusting for confounding effects via a no-treatment group. Results agree between the two placebo groups: both placebo groups showed a negligible correlation between baseline variability and adjusted response (r sp (CI 95% ) = 0.13 (−0.09, 0.37) and 0.01 (−0.15, 0.20) for Placebo I and II, …

The Enigma Of Clinical Next Generation Sequencing (Ngs) Based Genetic Testing Variant Annotation Tools: A Performance Evaluation Study, Sachleen Tuteja '23

Student Publications & Research

As the scientific community continues to discover novel genetic variants associated with human constitutional disorders, there is a growing need for a standardized approach for reporting of genetic variants, as accurate variant identification is crucial for effective diagnosis and treatment. Robust identification and annotation of genetic variants relevant for human germline disorders is foundational for clinical Next Generation Sequencing (NGS) assays. Using a manually curated set of 296 variants, generated by targeted gene panel sequencing using the ~4700 gene medical exome panel on 105 patients, we evaluated the performance of two variant annotation tools (Variant Effect Predictor and Alamut Batch) …

A Shift To Human Body Temperature (37°C) Rapidly Reprograms Multiple Adaptive Responses In Escherichia Coli That Would Facilitate Niche Survival And Colonization, Anastasia Gant Kanegusuku, Isidora N. Stankovic, Pamela A. Cote-Hammarlof, Priscilla H. Yong, Christine A. White-Ziegler

Biological Sciences: Faculty Publications

One of the first environmental cues sensed by a microbe as it enters a human host is an upshift in temperature to 37°C. In this dynamic time point analysis, we demonstrate that this environmental transition rapidly signals a multitude of gene expression changes in Escherichia coli. Bacteria grown at 23°C under aerobic conditions were shifted to 37°C, and mRNA expression was measured at time points after the shift to 37°C (t = 0.5, 1, and 4 h). The first hour is characterized by a transient shift to anaerobic respiration strategies and stress responses, particularly acid resistance, indicating that temperature serves …

Comparing Expression And Localization Of Syntaxin-1a And The Cystic Fibrosis Transmembrane Regulator In Adult Gallus Gallus Retinas, Rachel Lauren Butz

Honors Capstones

No abstract provided.

Exploration Of Staphylococcus Aureus Immune Inhibitory Proteins’ Structures And Investigation Of Their Effects On Monocyte And T Cell Adhesion, Jena Elizabeth Bordelon

Honors Capstones

No abstract provided.

Juul 3% Menthol Aerosol Extracts Exhibit Toxicity And Alter Gene Expression Of Murine Macrophages, Samantha Jindia

Honors Capstones

No abstract provided.

Analysis Of Young, Lineage Specific Alu Elements In Cebus, Catherine Rockwell

Honors Capstones

No abstract provided.

Reduced Toxicity Of Centruroides Vittatus (Say, 1821) May Result From Lowered Sodium Β Toxin Gene Expression And Toxin Protein Production, Aimee Bowman, Chloe Fitzgerald, Jeff Pummill, Douglas D. Rhoads, Tsunemi Yamashita

Biological Sciences Faculty Publications and Presentations

Body tissue and venom glands from an eastern population of the scorpion Centruroides vittatus (Say, 1821) were homogenized and molecular constituents removed to characterize putative sodium beta toxin gene diversity, RT-qPCR, transcriptomic, and proteomic variation. We cloned sodium beta toxins from genomic DNA, conducted RT-qPCR experiments with seven sodium beta toxin variants, performed venom gland tissue RNA-seq, and isolated venom proteins for mass spectrophotometry. We identified >70 putative novel sodium beta toxin genes, 111 toxin gene transcripts, 24 different toxin proteins, and quantified sodium beta toxin gene expression variation among individuals and between sexes. Our analyses contribute to the growing …

Quantitative Super-Resolution Microscopy To Assess Adhesion Of Neuronal Cells On Single-Layer Graphene Substrates, Silvia Scalisi, Francesca Pennacchietti, Sandeep Keshavan, Nathan D. Derr, Alberto Diaspro, Dario Pisignano, Agnieszka Pierzynska-Mach, Silvia Dante, Francesca Cella Zanacchi

Biological Sciences: Faculty Publications

Single Layer Graphene (SLG) has emerged as a critically important nanomaterial due to its unique optical and electrical properties and has become a potential candidate for biomedical applications, biosensors, and tissue engineering. Due to its intrinsic 2D nature, SLG is an ideal surface for the development of large-area biosensors and, due to its biocompatibility, can be easily exploited as a substrate for cell growth. The cellular response to SLG has been addressed in different studies with high cellular affinity for graphene often detected. Still, little is known about the molecular mechanism that drives/regulates the cellular adhesion and migration on SLG …

College Of Natural Sciences Scholarship Brunch Program, November 6th 2021, College Of Natural Sciences

College of Natural Sciences Newsletters and Reports

This is the program for the first annual College of Natural Sciences Scholarship Brunch, held on November 6th, 2021 at McCrory Gardens.

College Of Natural Sciences Newsletter, November 2021, College Of Natural Sciences

College of Natural Sciences Newsletters and Reports

Volume 2, Issue 11

Page 1 Dean's Message
Page 2 Awards & Recognition
Page 3 Media Coverage of CNS
Page 4 2021 Day of Scholars
Page 5 Astronomy Outreach
Page 6 SDSU Faculty & Students Host American Society for Microbiology Annual Conference
Page 7 Scholarship Brunch
Page 8 Open PRAIRIE Data, SI Final Exam Review Sessions
Page 9 Aamlid Family Anatomy Lab Photos

Low Light Intensity Delays Vegetative Phase Change, Mingli Xu, Tieqiang Hu, R Scott Poethig

Faculty Publications

Plants that develop under low light (LL) intensity often display a phenotype known as the “shade tolerance syndrome (STS)”. This syndrome is similar to the phenotype of plants in the juvenile phase of shoot development, but the basis for this similarity is unknown. We tested the hypothesis that the STS is regulated by the same mechanism that regulates the juvenile vegetative phase by examining the effect of LL on rosette development in Arabidopsis (Arabidopsis thaliana). We found that LL prolonged the juvenile vegetative phase and that this was associated with an increase in the expression of the master …

Propagation Of A De Novo Gene Under Natural Selection: Antifreeze Glycoprotein Genes And Their Evolutionary History In Codfishes, Xuan Zhuang, C.-H. Christina Cheng

Biological Sciences Faculty Publications and Presentations

The de novo birth of functional genes from non-coding DNA as an important contributor to new gene formation is increasingly supported by evidence from diverse eukaryotic lineages. However, many uncertainties remain, including how the incipient de novo genes would continue to evolve and the molecular mechanisms underlying their evolutionary trajectory. Here we address these questions by investigating evolutionary history of the de novo antifreeze glycoprotein (AFGP) gene and gene family in gadid (codfish) lineages. We examined AFGP phenotype on a phylogenetic framework encompassing a broad sampling of gadids from freezing and non-freezing habitats. In three select species representing different AFGP-bearing …

Diagnostics To Support Elimination Of Lymphatic Filariasis-Development Of Two Target Product Profiles, Kimberly Y. Won, Katherine Gass, Marco Biamonte, Daniel Argaw Dagne, Camilla Ducker, Christopher Hanna, Achim Hoerauf, Patrick J. Lammie, Sammy M. Njenga, Rahmah Noordin, Kapa D. Ramaiah, Reda Ramzy, Ronaldo G.Carvalho Scholte, Anthony W. Solomon, Ashley A. Souza, Jordan Tappero, Emily Toubali, Gary J. Weil, Steven A. Williams, Jonathan D. King

Biological Sciences: Faculty Publications

As lymphatic filariasis (LF) programs move closer to established targets for validation elimination of LF as a public health problem, diagnostic tools capable of supporting the needs of the programs are critical for success. Known limitations of existing diagnostic tools make it challenging to have confidence that program endpoints have been achieved. In 2019, the World Health Organization (WHO) established a Diagnostic Technical Advisory Group (DTAG) for Neglected Tropical Diseases tasked with prioritizing diagnostic needs including defining use-cases and target product profiles (TPPs) for needed tools. Subsequently, disease-specific DTAG subgroups, including one focused on LF, were established to develop TPPs …

Nine-Banded Armadillo (Dasypus Novemcinctus) Activity Patterns Are Influenced By Human Activity, Brett A. Degregorio, Connor Gale, Ellery V. Lassiter, Andrhea Darleen Massey, Caleb P. Roberts, John T. Veon

Biological Sciences Faculty Publications and Presentations

As the human footprint upon the landscape expands, wildlife seeking to avoid human contact are losing the option of altering their spatial distribution and instead are shifting their daily activity patterns to be active at different times than humans. In this study, we used game cameras to evaluate how human development and activity were related to the daily activity patterns of the nine-banded armadillo (Dasypus novemcinctus) along an urban to rural gradient in Arkansas, USA during the winter of 2020–2021. We found that armadillos had substantial behavioral plasticity in regard to the timing of their activity patterns; >95% of …

Impact Of Date-Pit Activated Carbon In Different Applications: Biomedical And Environment, Betty Titus Mathew

Dissertations

Activated carbon (AC) or activated charcoal are black carbonaceous porous solid material with prominent physico-chemical properties such as low volume pore size distribution, high specific surface area, and high-degree of surface reactivity for adsorption and other chemicals reactions. AC as strong and reliable adsorbent have been reported to be employed in diverse applications stretching from water/air purification, medical, sewage treatment, energy storage devices, catalyst, supercapacitor electrodes fabrication, and as biosensors component. In this current work, AC was produced from date pits, which is a common biological waste product in UAE, and used for biomedical and environmental applications instead of using …

Neurotoxicological Effects Of Chlorpyrifos And Deltamethrin On Dopamine And Acetylcholine Systems In Drosophila Melanogaster, Hala Husam Abdul Baki

Theses

Emerging evidence suggests a positive association between pesticide exposure and sporadic Parkinson's disease (PD) development. The molecular mechanisms of PD and other neurodegenerative diseases are not fully understood, which hinders the development of therapeutic agents to cure or prevent the development of such diseases. Drosophila has been widely used as a model organism to study various neurodegenerative diseases and to screen for promising therapeutic agents. The aims of this study were: (i) investigating the toxic effect of 24 hours exposure to chlorpyrifos (CPF) and deltamethrin (DLM) on the dopaminergic system and AChE activity in Drosophila melanogaster; (ii) comparing different methodologies …

Studying Neurotoxic Effects Of Three Synthetic Insecticides And Two Herbal Infusions On The Nervous System Of The Fruit Fly Drosophila Melanogaster, Sara Khamis Obaid Hamarain Al Dhaheri

Theses

Pesticides applied on plants and animals can reach the human diet once they enter food chains. Insecticides are neurotoxic agents; they have the potential of causing damage to the nervous system in people. The damage could induce or promote neurodegenerative diseases such as the Parkinson’s and Alzheimer's. It is well-documented that the exposure to the insecticide chlorpyrifos (CPF) stimulate the Parkinson disease in humans and experimental animals. Thus, this research project will study effect of three synthetic insecticides pirimicarb, tefluthrin, and CPF on the nervous system of Drosophila melanogaster as a model organism. In addition, the project will evaluate the …

Adsorption Of Perfluorooctanoic Acid (Pfoa) And Perfluorooctanesulfonic Acid (Pfos) By Aluminum-Based Drinking Water Treatment Residuals, Zhiming Zhang, Dibyendu Sarkar, Rupali Datta, Yang Deng

Michigan Tech Publications, Part 1

Per- and polyfluoroalkyl substances (PFAS) represent a family of emerging persistent organic pollutants. Cost-effective remediation of PFAS contamination via chemical or biochemical degradation is challenging due to their extremely high stability. This study reports the removal of two representative PFAS species, perfluorooctanoic acid (PFOA) and perfluorooctanesulfonic acid (PFOS), from water by adsorption using aluminum-based water treatment residuals (Al-WTR), a non-hazardous waste generated during the process of drinking water treatment by alum salts. Rapid adsorption of PFOA and PFOS onto Al-WTR followed a pseudo 2nd order kinetic pattern. Lower pH facilitated the adsorption process with a faster adsorption rate and greater …

Overfishing Drives Over One-Third Of All Sharks And Rays Toward A Global Extinction Crisis, Nicholas K. Dulvy, Nathan Pacoureau, Cassandra L. Rigby, Riley A. Pollom, Rima W. Jabado, David A. Ebert, Brittany Finucci, Caroline M. Pollock, Jessica Cheok, Danielle H. Derrick, Katelyn B. Herman, C. Samantha Sherman, Wade J. Vanderwright, Julia M. Lawson, Rachel H.L. Walls, John K. Carlson, Patricia Charvet, Kinattumkara K. Bineesh, Daniel Fernando, Gina M. Ralph, Jay H. Matsushiba, Craig Hilton-Taylor, Sonja V. Fordham, Colin A. Simpfendorfer

Biological Sciences Faculty Publications

The scale and drivers of marine biodiversity loss are being revealed by the International Union for Conservation of Nature (IUCN) Red List assessment process. We present the first global reassessment of 1,199 species in Class Chondrichthyes-sharks, rays, and chimeras. The first global assessment (in 2014) concluded that one-quarter (24%) of species were threatened. Now, 391 (32.6%) species are threatened with extinction. When this percentage of threat is applied to Data Deficient species, more than one-third (37.5%) of chondrichthyans are estimated to be threatened, with much of this change resulting from new information. Three species are Critically Endangered (Possibly Extinct), representing …

Zebrafish Paralogs Brd2a And Brd2b Are Needed For Proper Circulatory, Excretory And Central Nervous System Formation And Act As Genetic Antagonists During Development, Gregory L Branigan, Kelly S Olsen, Isabella Burda, Matthew W Haemmerle, Jason Ho, Alexandra Venuto, Nicholas D D'Antonio, Ian E Briggs, Angela J Dibenedetto

Department of Biochemistry and Molecular Biology Faculty Papers

Brd2 belongs to the BET family of epigenetic transcriptional co-regulators that act as adaptor-scaffolds for the assembly of chromatin-modifying complexes and other factors at target gene promoters. Brd2 is a protooncogene and candidate gene for juvenile myoclonic epilepsy in humans, a homeobox gene regulator in Drosophila, and a maternal-zygotic factor and cell death modulator that is necessary for normal development of the vertebrate central nervous system (CNS). As two copies of Brd2 exist in zebrafish, we use antisense morpholino knockdown to probe the role of paralog Brd2b, as a comparative study to Brd2a, the ortholog of human Brd2. A deficiency …

The Mentored Mentoring Approach To Lecturer- And Peer-Led Inter-Institutional Instruction Among Undergraduate Biomedical Science Students: A Case Study, Brigid Lucey, Róisín Spriggs, Katie O'Brien, Craig P. Murphy, Angela Wright

Department of Biological Sciences Publications

Biomedical science undergraduate students of accredited biomedical science programmes in Ireland are training to become professional medical scientists who diagnose disease. Hence, there is a strong emphasis at undergraduate level on practical laboratory skills, scientific writing and continuing professional development. In October 2020, a student-led webinar was held whereby one fourth-year and one third-year undergraduate student, having engaged their lecturer-mentor, conducted a webinar for first- and second-year undergraduate students with the intention of demystifying the art of writing a high quality laboratory report. The webinar consisted of four elements, namely a presentation by each of the three organisers; the fourth …

Comparing An Exponential Respiration Model To Alternative Models For Soil Respiration Components In A Canadian Wildfire Chronosequence (Fireresp V1.0), John Zobitz, Heidi Aaltonen, Xuan Zhou, Frank Berninger, Jukka Pumpanen, Kajar Köster

Faculty Authored Articles

Forest fires modify soil organic carbon and suppress soil respiration for many decades after the initial disturbance. The associated changes in soil autotrophic and heterotrophic respiration from the time of the forest fire, however, are less well characterized. The FireResp model predicts soil autotrophic and heterotrophic respiration parameterized with a novel dataset across a fire chronosequence in the Yukon and Northwest Territories of Canada. The dataset consisted of soil incubation experiments and field measurements of soil respiration and soil carbon stocks. The FireResp model contains submodels that consider a Q10 (exponential) model of respiration compared to models of heterotrophic respiration …

Biological Characterization Of Plasmodium Falciparum Mitochondrial Heat Shock Protein Pfhsp70-3: Possible Involvement In Malaria Pathogenesis, David O. Nyakundi, Aileen Boshoff

Tanzania Journal of Science

Malaria remains a global health burden accounting for many deaths and illnesses in sub-Saharan Africa notwithstanding many decades of research on the disease. P. falciparum, the causative agent of the most fatal form of malaria, expresses a repertoire of heat shock proteins (Hsp) that cushion the parasite against heat shocks as it shuttles between extreme temperatures in human and mosquito vector hosts. By so doing, such proteins promote parasite’s cytoprotection, survival and pathogenesis. Heat shock proteins are named according to their molecular weights and there are six P. falciparum Hsp70 (PfHsp70) found in various cell compartments with mitochondrial putative PfHsp70-3. …

The Multifaceted Role Of Ccar-1 In The Alternative Splicing And Germline Regulation In Caenorhabditis Elegans, Doreen Ikhuva Lugano

USF Tampa Graduate Theses and Dissertations

The Cell Division Cycle and Apoptosis Regulator (CCAR) family members are an enigmatic family of proteins regulating metabolism, cancer, apoptosis, DNA damage, and stress. Mammals have CCAR family members, CCAR1 and CCAR2/DBC1, which evolved from the founding family member CCAR-1/LST-3 expressed in Caenorhabditis elegans. Several studies have shown the importance of understanding these proteins' function in standard and altered physiological processes. Our studies aim to understand the genome-wide alternative splicing and germline regulation of Caenorhabditis elegans CCAR-1 in normal and heat shock conditions. Recently, mammalian CCAR family member CCAR2/DBC1 regulates the alternative splicing by forming a complex with ZNF326. This …

Collections Education: The Extended Specimen And Data Acumen, Anna K. Monfils, Erica R. Krimmel, Debra L. Linton, Travis D. Marsico, Ashley B. Morris, Brad R. Ruhfel

Open Access Fund Publications

Biodiversity scientists must be fluent across disciplines; they must possess the quantitative, computational, and data skills necessary for working with large, complex data sets, and they must have foundational skills and content knowledge from ecology, evolution, taxonomy, and systematics. To effectively train the emerging workforce, we must teach science as we conduct science and embrace emerging concepts of data acumen alongside the knowledge, tools, and techniques foundational to organismal biology. We present an open education resource that updates the traditional plant collection exercise to incorporate best practices in twenty-first century collecting and to contextualize the activities that build data acumen. …

Developing Inside A Layer Of Germs—A Potential Role For Multiciliated Surface Cells In Vertebrate Embryos, Ryan R. Kerney

Biology Faculty Publications

This paper reviews current research on the microbial life that surrounds vertebrate embryos. Several clades are believed to develop inside sterile—or near-sterile—embryonic microhabitats, while others thrive within a veritable zoo of microbial life. The occurrence of embryo-associated microbes in some groups, but not others, is an under-appreciated transition (possibly transitions) in vertebrate evolution. A lack of comparable studies makes it currently impossible to correlate embryo-associated microbiomes with other aspects of vertebrate evolution. However, there are embryonic features that should instruct a more targeted survey. This paper concludes with a hypothesis for the role of multiciliated surface cells in amphibian and …

The Effect Of Calcium Ions On Mechanosensation And Neuronal Activity In Proprioceptive Neurons, Devan E. Atkins, Kimberly L. Bosh, Grace W. Breakfield, Sydney E. Daniels, Makayla J. Devore, Hailey E. Fite, Landys Z. Guo, Danielle K. J. Henry, Alana K. Kaffenberger, Katherine S. Manning, Tatum E. Mowery, Cecilia L. Pankau, Nyla Parker, Malina E. Serrano, Yamaan Shakhashiro, Hannah N. Tanner, Ruth. A. Ward, Aubrey H. Wehry, Robin L. Cooper

Biology Faculty Publications

Proprioception of all animals is important in being able to have coordinated locomotion. Stretch activated ion channels (SACs) transduce the mechanical force into electrical signals in the proprioceptive sensory endings. The types of SACs vary among sensory neurons in animals as defined by pharmacological, physiological and molecular identification. The chordotonal organs within insects and crustaceans offer a unique ability to investigate proprioceptive function. The effects of the extracellular environment on neuronal activity, as well as the function of associated SACs are easily accessible and viable in minimal saline for ease in experimentation. The effect of extracellular [Ca²⁺] on …

The Effect Of Optogenetically Activating Glia On Neuronal Function, Cecilia Pankau, Shelby Mccubbin, Robin L. Cooper

Biology Faculty Publications

Glia, or glial cells, are considered a vital component of the nervous system, serving as an electrical insulator and a protective barrier from the interstitial (extracellular) media. Certain glial cells (i.e., astrocytes, microglia, and oligodendrocytes) within the CNS have been shown to directly affect neural functions, but these properties are challenging to study due to the difficulty involved with selectively-activating specific glia. To overcome this hurdle, we selectively expressed light-sensitive ion channels (i.e., channel rhodopsin, ChR2-XXL) in glia of larvae and adult Drosophila melanogaster. Upon activation of ChR2, both adults and larvae showed a rapid contracture of body wall …