Biology Commons^™

Implementing And Evaluating A Course-Based Undergraduate Research Experience (Cure) At A Hispanic-Serving Institution, Michele I. Shuster Phd, Jennifer Curtiss, Timothy F. Wright, Camilla Champion, Maryam Sharifi, Judith Bosland

Interdisciplinary Journal of Problem-Based Learning

We are examining the impact of a course-based undergraduate research experience (CURE) at a land-grant, Hispanic-serving institution in the southwestern United States. Students in our CURE completed one or two extended research projects over a single semester. Our CURE enrolled a high proportion of underrepresented minority students (70.3%), including 60.2% Hispanic students. One year after CURE completion, 31.5% of CURE students had graduated with a STEM degree, and 54.3% were enrolled in a STEM major. Pre- and postcourse surveys of indicators of persistence including scientific self-efficacy, scientific identity, valuing scientific community objectives, and intention to persist showed positive shifts. Impacts …

Analysis Of Post-Translational Modifications And Expression Of Stat3 Under Desferrioxamine Induced Hypoxia In Human Neuroblastoma Cells, Veronica Harrison

Seton Hall University Dissertations and Theses (ETDs)

ABSTRACT:

Oxygen homeostasis is critical for optimal energy production in eukaryotic organisms. The signal transduction pathways involved with detection and mitigation of hypoxia have been carefully scrutinized in an effort to elucidate how metabolism and survival is maintained. Characterization of these pathways and their involvement in physiological processes such as blood cell production in the bone marrow and microvessel formation in developing embryos provides a model of how these functions are executed. Less well-characterized mechanisms in disease states such as solid tumors still confound researchers whose efforts to find effective treatments are falling short. Cancer cells exploit the activities …

Phylogeny Of The Subfamilies Of Ichneumonidae (Hymenoptera), Andrew M.R. Bennett, Sophie Cardinal, Ian D. Gauld, David B. Wahl

Biology Faculty Publications

A combined morphological and molecular phylogenetic analysis was performed to evaluate the subfamily relationships of the parasitoid wasp family Ichneumonidae (Hymenoptera). Data were obtained by coding 135 morphological and 6 biological characters for 131 exemplar species of ichneumonids and 3 species of Braconidae (the latter as outgroups). The species of ichneumonids represent all of the 42 currently recognized subfamilies. In addition, molecular sequence data (cytochrome oxidase I “DNA barcoding” region, the D2 region of 28S rDNA and part of the F2 copy of elongation factor 1-alpha) were obtained from specimens of the same species that were coded for morphology (1309 …

Fipronil And Ivermectin Treatment Of Cattle Reduced The Survival And Ovarian Development Of Field-Collection Anopheles Albimanus In A Pilot Trial Conducted In Northern Belize, Staci M. Dreyer, Donovan Leiva, Marla Magana, Marie Pott, Jonathan Kay, Alvaro Cruz, Nicole L. Achee, John P. Grieco, Jefferson A. Vaughan

Biology Faculty Publications

Background: Most malaria vector control programmes rely on indoor residual spraying of insecticides and insecticide-treated bed nets. This is efective against vector species that feed indoors at night and rest inside the house afterwards. In Central America, malaria vectors have diferent behaviours and are typically exophagic (i.e., bite outdoors), exophilic (i.e., remain outdoors after feeding), and zoophagic (i.e., as likely to feed on non-humans as humans). Thus, malaria elimination in Central America may require additional tactics. This pilot study investigated whether commercially-available products used to treat livestock for ticks could also be used to kill and/or sterilize zoophagic malaria vectors …

“What Will I Experience In My College Stem Courses?” An Investigation Of Student Predictions About Instructional Practices In Introductory Courses, Clara L. Meaders, Emma S. Toth, A. K. Lane, J. Kenny Shuman, Brian A. Couch, Marilyne Stains, Mackenzie R. Stetzer, Erin Vinson, Michelle K. Smith

School of Biological Sciences: Faculty Publications

The instructional practices used in introductory college courses often differ dramatically from those used in high school courses, and dissatisfaction with these practices is cited by students as a prominent reason for leaving science, technology, engineering, and mathematics (STEM) majors. To better characterize the transition to college course work, we investigated the extent to which incoming expectations of course activities differ based on student demographic characteristics, as well as how these expectations align with what students will experience. We surveyed more than 1500 undergraduate students in large introductory STEM courses at three research-intensive institutions during the first week of classes …

Draft Genome Sequences Of Four Lactococcus Lactis Strains Isolated From Diverse Niches, Including Dairy Products, Grass, And Green Peas, Desirée Roman Naranjo, Michael Callanan, Et. Al.

Department of Biological Sciences Publications

Lactococcus lactis has been used for millennia as a starter organism in the production of many fermented dairy products. This announcement includes the draft genome sequences of four strains of Lactococcus lactis, two of dairy origin and two from nondairy sources.

A Comparison Of Cave Microbial Communities To Cave Roosting Bat Microbiota In El Malpais National Monument, Usa, Nicole A. Caimi

Biology ETDs

The arrival of white-nose syndrome (WNS), a devastating fungal disease, has highlighted the need to better understand bat microbiota and how bats acquire their microbiota. To address this need, we investigated how bat microbiota compare to microbiota from the cave walls in two El Malpais National Monument caves. The external surfaces of six roosting bats from each cave, representing four different bat species, and their associated microbial mats were sampled. One to three air samples were taken in each cave. Samples were sequenced using Illumina MiSeq sequencing of the 16S rRNA gene for bacterial diversity and the ITS region for …

Resolving The Genetic Paradox Of Invasions: Preadapted Genomes And Postintroduction Hybridization Of Bigheaded Carps In The Mississippi River Basin, Jun Wang, Sarah Gaughan, James T. Lamer, Cao Deng, Wanting Hu, Michael Wachholtz, Shishang Qin, Hu Nie, Xiaolin Liao, Qufei Ling, Weitao Li, Lifeng Zhu, Louis Bernatchez, Chenghui Wang, Guoqing Lu

Biology Faculty Publications

The genetic paradox of biological invasions is complex and multifaceted. In particular, the relative role of disparate propagule sources and genetic adaptation through postintroduction hybridization has remained largely unexplored. To add resolution to this paradox, we investigate the genetic architecture responsible for the invasion of two invasive Asian carp species, bighead carp (Hypophthalmichthys nobilis) and silver carp (H. molitrix) (bigheaded carps) that experience extensive hybridization in the Mississippi River Basin (MRB). We sequenced the genomes of bighead and silver carps (~1.08G bp and ~1.15G bp, respectively) and their hybrids collected from the MRB. We found moderate‐to‐high …

Extracellular Vesicles At The Fetal-Maternal Interface In Cattle, Heloisa M. Rutigliano

Funded Research Records

No abstract provided.

Total Rna Extraction From Transgenic Flies Misexpressing Foreign Genes To Perform Next Generation Rna Sequencing, Abijeet Singh Mehta, Agustin Luz-Madrigal, Jian-Liang Li, Panagiotis A. Tsonis, Amit Singh

Biology Faculty Publications

Due to absence of transgenic approaches in Notopthalmus Viridescens (newt), and conservation of genetic machinery across species, we generated transgenic Drosophila melanogaster to misexpress unique genes from newt. Novel newt genes cloned, and inserted at attP site in Drosophila were misexpressed ubiquitously using tubulin Gal-4. Sample (total RNA) for RNA sequencing was collected at 3rd instar larval stage during which major developmental events takes place in Drosophila. Total RNA was extracted, and purified using RNA clean and ConcentratorTM. RNA quality was quantitated by calculating absorbance at 260 nm (A260) and 280 nm (A280) wavelengths using Nanodrop 2000 spectrophotometer. Good quality …

Histology Atlas: Basic Mammalian Tissue Types (Biol 105), Joshua Barnes, Daniel J. Yakubov, Corinna Singleman, Nathalia G. Holtzman

Open Educational Resources

This book is a guide to the basic histology lab conducted as a part of the Queens College, CUNY Biology Department Bio105 General Biology: Physiology and Cell Biology course. This course is the first half our two-part series for biology majors. The actives are designed to be conducted over a single 3-hour lab periods which focus on the relationship of form and function of the cellular and organ level anatomy and physiology. Step by step instructions for each slide set are provided for all the key organs.

In addition to the full text of the book, we also provide a …

Fetal Pig Dissection Manual (Biol 105), Nathalia G. Holtzman, Daniel J. Yakubov

Open Educational Resources

This book is a guide to the basic fetal pig dissection conducted as a part of the Queens College, CUNY Biology Department Bio105 General Biology: Physiology and Cell Biology course. This course is the first half our two-part series for biology majors. The actives are designed to be conducted over a three- 3-hour lab periods which focus on the relationship of form and function of the pig anatomy and physiology. Step by step instructions for the dissection are provided along with some microscopy tasks to look at the histology of key organs.

In addition to the full text of the …

Comparative Brain Anatomy Of Lamniform Sharks (Elasmobranchii: Lamniformes) And Its Implications To Function, Behavioral Ecology, And Evolution, Francesco Guzzo

College of Science and Health Theses and Dissertations

Understanding the diversity of brain morphology is important to understand the evolution of cognitive ability and how ecology and phylogeny have influenced the variation in brain complexity. I examined the morphological variation of the brain in the shark order Lamniformes based on museum specimens and literature. Where I illustrate a wide range of morphological diversity in lamniform brains, my study shows that there is a strong positive correlation between brain size and body size that sharks with a larger brain tend to have a more foliated cerebellum, but that the body weight over brain weight did not correlate with cerebellar …

A New Pachyrhizodontid Fish (Actinopterygii: Teleostei) From The Tarrant Formation (Cenomanian) Of The Upper Cretaceous Eagle Ford Group Of Texas, U.S.A., Maxwell G. London

College of Science and Health Theses and Dissertations

SMU 76938 is a fossil skeleton of a large, nearly complete actinopterygian bony fish housed in Southern Methodist University in Dallas, Texas, USA. It was collected from the Upper Cretaceous Tarrant Formation (middle Cenomanian; ~96 Ma) of the Eagle Ford Group in Tarrant County, Texas, an area where it was near the western margin of the East Texas Embayment during the Late Cretaceous. Although parts of the skull and dorsal fin are damaged, SMU 76938 is relatively complete, especially in the preservation of the caudal fin with its soft tissue outline. The fish has a fusiform body and measures about …

Integument-Based Inferences On The Swimming Ability And Prey Hunting Strategy Of The Bigeye Thresher Shark, Alopias Superciliosus (Lamniformes: Alopiidae), Joseph Aaron Frumkin

College of Science and Health Theses and Dissertations

Alopias is a group of lamniform sharks characterized by a highly elongate caudal fin with three known extant species: A. pelagicus (pelagic thresher shark), A. superciliosus (bigeye thresher shark), and A. vulpinus (common thresher shark). Alopias pelagicus and A. vulpinus are considered fast swimmers and use their caudal fin to hunt for small schooling fish by stunning them, but the feeding behavior has never been directly observed for A. superciliosus. Under the ecomorphological framework, I examined the following four integumentary variables of selected fast swimming (e.g., A. pelagicus, A. vulpinus, and Lamna) and slow swimming (e.g., Mitsukurina and Megachasma) lamniform …

Zygote Gene Expression And Plasmodial Development In Didymium Iridis, Sean Schaefer

College of Science and Health Theses and Dissertations

Didymium iridis is a cosmopolitan species of plasmodial slime mold consisting of two distinct life stages. Haploid amoebae and diploid plasmodia feed on microscopic organisms such as bacteria and fungi through phagocytosis. Sexually compatible haploid amoebae act as gametes which when fused embark on an irreversible developmental change resulting in a diploid zygote. The zygote can undergo closed mitosis resulting in a multinucleated plasmodium. Little is known about changes in gene expression during this developmental transition. Our principal goal in this study was to provide a comprehensive list of genes likely to be involved in plasmodial development. We performed suppressive …

Histone H4 H75e Mutation Attenuates Global Genomic And Rad26-Independent Transcription-Coupled Nucleotide Excision Repair, Shisheng Li, Kathiresan Selvam, Sheikh Arafatur Rahman

Faculty Publications

Nucleotide excision repair (NER) consists of global genomic NER (GG-NER) and transcription coupled NER (TC-NER) subpathways. In eukaryotic cells, genomic DNA is wrapped around histone octamers (an H3-H4 tetramer and two H2A-H2B dimers) to form nucleosomes, which are well known to profoundly inhibit the access of NER proteins. Through unbiased screening of histone H4 residues in the nucleosomal LRS (loss of ribosomal DNA-silencing) domain, we identified 24 mutations that enhance or decrease UV sensitivity of Saccharomyces cerevisiae cells. The histone H4 H75E mutation, which is largely embedded in the nucleosome and interacts with histone H2B, significantly attenuates GG-NER and Rad26-independent …

Precision Nomenclature For The New Genomics, Harris A. Lewin, Jennifer A. Marshall Graves, Oliver A. Ryder, Alexander S. Graphodatsky, Stephen James O'Brien

Biology Faculty Articles

The confluence of two scientific disciplines may lead to nomenclature conflicts that require new terms while respecting historical definitions. This is the situation with the current state of cytology and genomics, which offer examples of distinct nomenclature and vocabularies that require reconciliation. In this article, we propose the new terms C-scaffold (for chromosome-scale assemblies of sequenced DNA fragments, commonly named scaffolds) and scaffotype (the resulting collection of C-scaffolds that represent an organism's genome). This nomenclature avoids conflict with the historical definitions of the terms chromosome (a microscopic body made of DNA and protein) and karyotype (the collection of images …

Avian Binocularity And Adaptation To Nocturnal Environments: Genomic Insights Froma Highly Derived Visual Phenotype, Rui Borges, Joao Fonseca, Cidalia Gomes, Warren E. Johnson, Stephen James O'Brien, Guojie Zhang, M. Thomas P. Gilbert, Erich D. Jarvis, Agostinho Antunes

Biology Faculty Articles

Typical avian eyes are phenotypically engineered for photopic vision (daylight). In contrast, the highly derived eyes of the barn owl (Tyto alba) are adapted for scotopic vision (dim light). The dramatic modifications distinguishing barn owl eyes from other birds include: 1) shifts in frontal orientation to improve binocularity, 2) rod-dominated retina, and 3) enlarged corneas and lenses. Some of these features parallel mammalian eye patterns, which are hypothesized to have initially evolved in nocturnal environments. Here, we used an integrative approach combining phylogenomics and functional phenotypes of 211 eye-development genes across 48 avian genomes representing most avian orders, …

Inevitable Future: Space Colonization Beyond Earth With Microbes First, Jose Lopez, Raquel S. Peixoto, Alexandre S. Rosado

Biology Faculty Articles

Based on modern microbiology, we propose a major revision in current space exploration philosophy and planetary protection policy, especially regarding microorganisms in space. Mainly, microbial introduction should not be considered accidental but inevitable. We hypothesize the near impossibility of exploring new planets without carrying and/or delivering any microbial travelers. In addition, although we highlight the importance of controlling and tracking such contaminations—to explore the existence of extraterrestrial microorganisms—we also believe that we must discuss the role of microbes as primary colonists and assets, rather than serendipitous accidents, for future plans of extraterrestrial colonization. This paradigm shift stems partly from the …

Nature And Nurture: How Our Genes And Environments Shape Our Lives Bio 440g, Michael Cerbo

Library Impact Statements

No abstract provided.

Impacts Of Hiv Cure Interventions On Viral Reservoirs In Tissues, Paul W. Denton, Ole S. Søgaard, Martin Tolstrup

Biology Faculty Publications

HIV reservoirs persist in infected individuals despite combination antiretroviral therapy and can be identified in secondary lymphoid tissues, in intestinal tissues, in the central nervous system as well as in blood. Clinical trials have begun to explore effects of small molecule interventions to perturb the latent viral infection, but only limited information is available regarding the impacts of HIV cure-related clinical interventions on viral reservoirs found in tissues. Of the 14 HIV cure-related clinical trials since 2012 that have evaluated the effects of small molecule interventions in vivo, four trials have examined the impacts of the interventions in peripheral …

Conservation Genomic Analysis Reveals Ancient Introgression And Declining Levels Of Genetic Diversity In Madagascar’S Hibernating Dwarf Lemurs, Rachel C. Williams, Marina B. Blanco, Jelmer W. Poelstra, Kelsie E. Hunnicutt, Aaron A. Comeault, Anne D. Yoder

Biological Sciences: Faculty Scholarship

Madagascar’s biodiversity is notoriously threatened by deforestation and climate change. Many of these organisms are rare, cryptic, and severely threatened, making population-level sampling unrealistic. Such is the case with Madagascar’s dwarf lemurs (genus Cheirogaleus), the only obligate hibernating primate. We here apply comparative genomic approaches to generate the first genome-wide estimates of genetic diversity within dwarf lemurs. We generate a reference genome for the fat-tailed dwarf lemur, Cheirogaleus medius, and use this resource to facilitate analyses of high-coverage (~30×) genome sequences for wild-caught individuals representing species: C. sp. cf. medius, C. major, C. crossleyi, and C. sibreei. This study represents …

Avian Dispersal Networks, Metacommunity Structure, And Bryophyte Community Assemblages, Matthew Wojciech Chmielewski

Dissertations and Theses

Spatial processes have a profound influence on the structure and function of community assemblages. The dispersal of organisms from their place of origin to the location in which they live out their reproductive life is particularly important for plant communities, which generally cannot adjust their location post-germination. Connection between communities at a landscape scale can also influence species persistence, local and regional diversity, and functional turnover at the metacommunity scale. Animals have been shown to disproportionately deposit propagules in particular microsites in many plant species, facilitating the arrival of plants to appropriate niche-space. Birds are particularly notable seed dispersers, given …

Microbial Mercury Methylation At Caddo Lake: A Molecular Ecology Approach, Nevada King

Biology Theses

Caddo Lake in northeastern Texas is a cypress-Spanish moss dominated lake ecosystem. Contamination of mercury (Hg), especially methylmercury (MeHg), was reported in this lake a decade ago. MeHg is a neurotoxicant accumulated in major fish species and reptiles. Due to the biomagnification feature of MeHg transfer, Hg contamination in the fishes of Caddo Lake has caused health concerns for the wildlife and local people. However, the source and synthesis of MeHg in this lake, primarily the microbial Hg methylation mechanisms, have not been investigated. We investigated the lake for the past three years (2016-2018), by taking sediment and plant samples …

Comparative Transcriptomic Analysis And Structure Prediction Of Novel Newt Proteins, Abijeet Singh Mehta, Agustin Luz-Madrigal, Jian-Liang Li, Panagiotis A. Tsonis, Amit Singh

Biology Faculty Publications

Notophthalmus viridescens (Red-spotted Newt) possess amazing capabilities to regenerate their organs and other tissues. Previously, using a de novo assembly of the newt transcriptome combined with proteomic validation, our group identified a novel family of five protein members expressed in adult tissues during regeneration in Notophthalmus viridescens. The presence of a putative signal peptide suggests that all these proteins are secretory in nature. Here we employed iterative threading assembly refinement (I-TASSER) server to generate three-dimensional structure of these novel Newt proteins and predicted their function. Our data suggests that these proteins could act as ion transporters, and be involved …

From Single Cells To Human Disease: High-Resolution Phenotyping Of Male Infertility Models Using Single-Cell Rna Sequencing, Min Jung

Arts & Sciences Graduate Student Theses and Dissertations

Male infertility is a complex disease that can result in significant emotional distress and treatment costs. Globally, male infertility affects 7% of males, and while its incidence is rising, its etiology remains elusive. In order to improve patient care, it is critical to identify the nature of spermatogenic failure in as many men as possible. The extensive cellular heterogeneity of testis has limited the application of bulk expression measurements to capture crucial information to dissect molecular mechanisms of defects in the infertile patients. Thus, the application of single-cell RNA-sequencing on male germ cells provides an amazing new set of scientific …

The Impact Of Mrna Structure On Trna Selection And Ribosome Rescue, Erica Nicole Thomas

Arts & Sciences Graduate Student Theses and Dissertations

The faithful and rapid translation of proteins from genetic information is an essential feature of the ribosome. The general process of tRNA selection is governed by the ability of the ribosome to select for the aminoacylated tRNA (aa-tRNA) that matches the codon in its A-site. The efficiency and accuracy of this selection depends on the ability of nucleotides to form proper hydrogen bonds. While much is known about how chemical alterations of tRNA and rRNA can impact the fidelity of translation, less is known about how similar changes to mRNA affect decoding. In this work, we describe several studies aimed …

Mesothelium-Derived Factors Shape Tissue Resident Macrophage, Chin-Wen Lai

Arts & Sciences Graduate Student Theses and Dissertations

The studies outlined in this thesis provide several new insights into Msln-related pathways necessary for peritoneal immune responses and mucosal repair. We found that Msln and its binding partner mucin 16 from mesothelium influenced peritoneal and pleural macrophage differentiation. We found that Msln was required for proper tissue repair after colonic biopsy injury and was required for maximal polyp growth in APCMin/+ mice. Overall, this work describes mesothelial and epithelial-derived factors that are important for tissue resident macrophage differentiation and wound repair after colonic mucosal injury. Understanding the complex interactions between stromal cells and immune cells will lead to better …

Fast-Forward Protein Folding And Design: Development, Analysis, And Applications Of The Fast Sampling Algorithm, Maxwell Isaac Zimmerman

Arts & Sciences Graduate Student Theses and Dissertations

Molecular dynamics simulations are a powerful tool to explore conformational landscapes, though limitations in computational hardware commonly thwart observation of biologically relevant events. Since highly specialized or massively parallelized distributed supercomputers are not available to most scientists, there is a strong need for methods that can access long timescale phenomena using commodity hardware. In this thesis, I present the goal-oriented sampling method, Fluctuation Amplification of Specific Traits (FAST), that takes advantage of Markov state models (MSMs) to adaptively explore conformational space using equilibrium-based simulations. This method follows gradients in conformational space to quickly explore relevant conformational transitions with orders of …