Biology Commons^™

Employing High Probability Gene Choice Elements To Understand Singular Odorant Receptor Expression, Raena Mina

Dissertations, Theses, and Capstone Projects

The ability to detect odorous chemicals in the environment is the oldest of the senses necessary for survival, from escaping danger, finding mates, to locating food. It is said that humans can identify and discriminate up to a trillion different odor mixtures. For chemoreception to have such a high discriminatory power, would require a diverse population of cells dedicated for odor detection. These detector cells are the olfactory sensory neurons (OSNs), which express odorant receptors (ORs) that bind to chemical odors in the environment. In order to increase specificity and sensitivity, an essential property in olfaction is for each OSN …

Defining The Relationship Between Maternal Care Behavior And Sensory Development In Wistar Rats: Auditory Periphery Development, Eye Opening And Brain Gene Expression, Jingyun Qiu, Preethi Singh, Geng Pan, Annalisa De Paolis, Frances A. Champagne, Jia Liu, Luis Cardoso, Adrián Rodríguez-Contreras

Advanced Science Research Center

Defining the relationship between maternal care, sensory development and brain gene expression in neonates is important to understand the impact of environmental challenges during sensitive periods in early life. In this study, we used a selection approach to test the hypothesis that variation in maternal licking and grooming (LG) during the first week of life influences sensory development in Wistar rat pups. We tracked the onset of the auditory brainstem response (ABR), the timing of eye opening (EO), middle ear development with micro-CT X-ray tomography, and used qRT-PCR to monitor changes in gene expression of the hypoxia-sensitive pathway and neurotrophin …

Further Evaluation Of A Dry Vacuuming Technique For Recovery Of Dna From Handwritten Documents, Christian Hopkins

Student Theses

A previously developed, non-destructive, homemade vacuum method for collecting biological material from handwritten documents had promising DNA results for white copy paper, preserved indented writing, and latent prints. Prior to casework implementation, additional validation experiments are warranted and here the method was tested for different paper substrates. This work describes testing of notebook paper, bank deposit slips, magazine pages, and manila envelopes. The quantity of recovered DNA varied from donor to donor, but the mean quantities showed a trend that can be explained by the different sizes and surface properties of the tested paper types. The rougher paper type, like …

Identification Of Tandem Repeat Families From Long-Read Sequences Of Humulus Lupulus, Katherine A. Easterling, Nicholi J. Pitra, Taylan B. Morcol, Jenna R. Aquino, Lauren G. Lopes, Kristin C. Bussey, Paul D. Matthews, Hank W. Bass

Publications and Research

Hop (Humulus lupulus L.) is known for its use as a bittering agent in beer and has a rich history of cultivation, beginning in Europe and now spanning the globe. There are five wild varieties worldwide, which may have been introgressed with cultivated varieties. As a dioecious species, its obligate outcrossing, non-Mendelian inheritance, and genomic structural variability have confounded directed breeding efforts. Consequently, understanding the hop genome represents a considerable challenge, requiring additional resources. In order to facilitate investigations into the transmission genetics of hop, we report here a tandem repeat discovery pipeline developed using k-mer filtering and dot plot …

Elucidating The Role Of Apl-1, The C. Elegans Ortholog Of The Human Amyloid Precursor Protein, Adanna G. Alexander

Dissertations, Theses, and Capstone Projects

Alzheimer’s disease (AD) is a progressive neurodegenerative disorder, impacting approximately 6 million Americans. AD is the leading cause of dementia amongst the aged population. Post mortem analysis of the brains of AD patients shows high quantities of extracellular Aβ peptide deposits, which are derived from cleavage of the amyloid precursor protein (APP). Mutations in APP and proteins responsible for APP cleavage, PSENs, greatly increase the incidence of developing AD at an early age. Despite its strong correlation to the progression of AD, the role of APP remains unclear.

Here we investigate the role of the Caenorhabditis elegans ortholog, APL-1. We …

Molecular Roles Of Small Inner Membrane Proteins In Escherichia Coli Cell Envelope Integrity, Aaron Mychack

Dissertations, Theses, and Capstone Projects

The biological membrane is an essential, defining feature of all cells. Biological membranes comprise phospholipid bilayers as well as a complement of proteins which are unique to a given organism. These proteins play a central role in dictating the biochemical state of the cell’s internal cytoplasm by controlling selective passage of solutes in and out of the cell, transducing signals in response to extracellular stimuli, and controlling the biogenesis of the bilayer itself which is critical towards barrier function. For most bacteria, the periphery of the cell is multi-layered, including both a biological membrane as well as a peptidoglycan cell …

Protein Phosphatase 2a Suppresses Spindle Elongation In Saccharomyces Cerevisiae, Shoily P. Khondker

Dissertations, Theses, and Capstone Projects

Eukaryotic cell division is an essential process that is carried out by the cell cycle, a tightly controlled process that has been extensively studied in the budding yeast Saccharomyces cerevisiae. The cell cycle is driven by Cyclin Dependent Kinase (Cdk1) activity. Protein phosphatase 2A-Cdc55 (PP2A^Cdc55) reverses Cdk1 phosphorylation events during late stages of the cell cycle to ensure the correct order of events. This thesis presents evidence that the anaphase inhibitor Pds1 is a PP2A^Cdc55 target. Pds1 binds to and inhibits separase (Esp1). Esp1 triggers sister chromatid segregation by cleaving the cohesin complex that holds the …

Evaluating Satellite-Based Sea Surface Temperatures, In Situ Observations, And Coral Symbioses In Southwestern Puerto Rico, Andrea Michelle Gomez

Dissertations, Theses, and Capstone Projects

I examined the effects of in situ and satellite-based sea surface temperatures (SST) on the seasonal coral-algae symbiotic relationship in La Parguera, Puerto Rico. Climate change-driven rising sea temperatures are endangering most of the world’s reefs, which are currently in decline. Satellite remote sensing datasets support global-scale characterization and monitoring of risks to reefs associated with increasing temperatures. Corals’ unique symbiotic relationship with unicellular algae in the family Symbiodiniaceae is largely responsible for helping corals cope with increasing ocean temperatures, and some corals are able to adjust their symbiont species in response to temperature disturbances. My research had two components …

Pvt1 Exon 9 A Regulator Of Claudin Expression In Triple Negative Breast Cancer, Fayola Levine

Theses and Dissertations

Claudin low triple negative breast cancer (TNBC) has the worst clinical outcomes in comparison to other breast cancer subtypes. The underlying molecular mechanisms associated with the aberrant expression of claudins are not well understood. The transcript from PVT1 exon 9 is a regulator of claudin expression, and migration, in TNBC.

Cytotoxic Analysis Of Old Drugs: New Drugs For Alzheimer’S Disease, Sebastian Yumiseba

Theses and Dissertations

Microglia are the resident immune cells of the CNS and constitute about 10% of all cells in the CNS. They have a vital role in Alzheimer’s pathogenesis as either cytotoxic or neuroprotective. Recent efforts are being put into repurposing drugs to target the microglia to treat Alzheimer’s disease.

Taking A Closer Look On The Coronavirus, Alisha Barday, Janina Duran, Lisa Agranov

Publications and Research

No abstract provided.

Cov Genome Tracker: Tracing Genomic Footprints Of Covid-19 Pandemic, Saymon Akther, Edgaras Bezrucenkovas, Brian Sulkow, Christopher Panlasigui, Li Li, Wei-Gang Qiu, Lia Di

Publications and Research

Genome sequences constitute the primary evidence on the origin and spread of the 2019-2020 Covid-19 pandemic. Rapid comparative analysis of coronavirus SARS-CoV-2 genomes is critical for disease control, outbreak forecasting, and developing clinical interventions. CoV Genome Tracker is a web portal dedicated to trace Covid-19 outbreaks in real time using a haplotype network, an accurate and scalable representation of genomic changes in a rapidly evolving population. We resolve the direction of mutations by using a bat-associated genome as outgroup. At a broader evolutionary time scale, a companion browser provides gene-by-gene and codon-by-codon evolutionary rates to facilitate the search for molecular …

C-Di-Gmp Modulates Type Iv Msha Pilus Retraction And Surface Attachment In Vibrio Cholerae, Kyle A. Floyd, Calvin K. Lee, Wujing Xian, Mahmoud Nametalla, Aneesa Valentine, Benjamin Crair, Shiwei Zhu, Hannah Q. Hughes, Jennifer L. Chlebek, Daniel C. Wu, Jin Hwan Park, Ali M. Farhat, Charles J. Lomba, Courtney K. Ellison, Yves V. Brun, Javier Campos-Gomez, Ankur B. Dalia, Jun Liu, Nicolas Biais, Gerard C. L. Wong, Fitnat H. Yildiz

Publications and Research

Biofilm formation by Vibrio cholerae facilitates environmental persistence, and hyperinfectivity within the host. Biofilm formation is regulated by 3’,5’-cyclic diguanylate (c-di-GMP) and requires production of the type IV mannose-sensitive hemagglutinin (MSHA) pilus. Here, we show that the MSHA pilus is a dynamic extendable and retractable system, and its activity is directly controlled by c-di-GMP. The interaction between c-di-GMP and the ATPase MshE promotes pilus extension, whereas low levels of c-di-GMP correlate with enhanced retrac- tion. Loss of retraction facilitated by the ATPase PilT increases near-surface roaming motility, and impairs initial surface attachment. However, prolonged retraction upon surface attach- ment results …

Predictor Species: Improving Assessments Of Rare Species Occurrence By Modeling Environmental Co-Responses, Peter R. Thompson, William F. Fagan, Phillip P. A. Staniczenko

Publications and Research

Designing an effective conservation strategy requires understanding where rare species are located. Because rare species can be difficult to find, ecologists often identify other species called conservation surrogates that can help inform the distribution of rare species. Species distribution models typically rely on environmental data when predicting the occurrence of species, neglecting the effect of species' co-occurrences and biotic interactions. Here, we present a new approach that uses Bayesian networks to improve predictions by modeling environmental co-responses among species. For species from a European peat bog community, our approach consistently performs better than single-species models and better than conventional multi-species …

Hydrophilic Porphyrins Based Chemosensors For First Transition Series Metal Ions [Chemistry], Sunaina Singh

Open Educational Resources

General Chemistry is a two-semester course (General Chemistry I, SCC 201 and General Chemistry II, SCC 202) required for majors in Biology and Environmental Sciences.

This lab experiment, aligned to LaGuardia Community College’s Inquiry and Problem Solving Core Competency and Written Communication Ability was designed for General Chemistry I (SCC 201 Honors) course. Honors courses in LaGuardia emphasize critical thinking, analytical writing, and introduce students to research. This lab experiment provides an opportunity for students to engage in hands-on laboratory work, to develop laboratory skills, and to conduct research in the classroom by using two water soluble porphyrins to detect …

Transposon Mutagenesis In Mycobacterium Kansasii Links A Small Rna Gene To Colony Morphology And Biofilm Formation And Identifies 9,885 Intragenic Insertions That Do Not Compromise Colony Outgrowth, William C. Budell, Gabrielle A. Germain, Niklas Janisch, Zaid Mckie-Krisberg, Anitha D. Jayaprakash, Andrew E. Resnick, Luis E. N. Quadri

Publications and Research

Mycobacterium kansasii (Mk) is a resilient opportunistic human pathogen that causes tuberculosis-like chronic pulmonary disease and mortality stemming from comorbidities and treatment failure. The standard treatment of Mk infections requires costly, long-term, multidrug courses with adverse side effects. The emergence of drug-resistant isolates further complicates the already challenging drug therapy regimens and threatens to compromise the future control of Mk infections. Despite the increasingly recognized global burden of Mk infections, the biology of this opportunistic pathogen remains essentially unexplored. In particular, studies reporting gene function or generation of defined mutants are scarce. Moreover, no transposon (Tn) mutagenesis tool has been …

Intrinsic Disorder Controls Two Functionally Distinct Dimers Of The Master Transcription Factor Pu.1, Suela Xhani, Sangchoon Lee, Hye Mi Kim, Siming Wang, Shingo Esaki, Van L. T. Ha, Mahtab Khanezarrin, Giselle L. Fernandez, Amanda V. Albrecht, James Aramini, Markus W. Germann, Gregory M. K. Poon

Advanced Science Research Center

Transcription factors comprise a major reservoir of conformational disorder in the eukaryotic proteome. The hematopoietic master regulator PU.1 presents a well-defined model of the most common configuration of intrinsically disordered regions (IDRs) in transcription factors. We report that the structured DNA binding domain (DBD) of PU.1 regulates gene expression via antagonistic dimeric states that are reciprocally controlled by cognate DNA on the one hand and by its proximal anionic IDR on the other. The two conformers are mediated by distinct regions of the DBD without structured contributions from the tethered IDRs. Unlike DNA-bound complexes, the unbound dimer is markedly destabilized. …

Hur Ubiquitination By Brca1/Bard1 And Its Role In Controlling Gene Expression During Dna Damage Response, Gamage M. Aruggoda

Dissertations, Theses, and Capstone Projects

Despite our understanding of the biochemistry of the BRCA1/BARD1 E3 ligase, we know very little of the mechanism by which its cellular substrates, how they are chosen, how its E3 Ub ligase activity is regulated, which are the cofactors involved in this regulation, and how the substrates are modified during DDR. In this dissertation, I further evaluate BRCA1/BARD1-mediated E3 ligase activity and how CstF-50 and p97 regulate this reaction working as cofactors. My data show that BRCA1/BARD1 is an E3 ligase that ubiquitinates the RNA binding protein Human antigen R(HuR).

HuR is abundant in the nucleus and is transported to …

Through The Back Door: Proteins Escape Cells Without Conventional Permission, Michael J. Cohen

Dissertations, Theses, and Capstone Projects

Proteins secreted to the extracellular environment play a fundamental role as signals, in metabolism, and a variety of other processes. The process of secretion through the endoplasmic reticulum and Golgi to the plasma membrane is well documented, and all cargo in this pathway contains a signal peptide. However, a variety of proteins secreted from eukaryotes lack a signal peptide and are called unconventionally secreted proteins. Here we discuss known mechanisms of unconventional protein secretion, as well as model proteins which follow characterized pathways. Additionally, we summarize the roles various unconventionally secreted proteins play outside of cells and suggest criteria for …

A Neural Mechanism For Capnotaxis In The Naked Mole-Rat, Michael Zions

Dissertations, Theses, and Capstone Projects

A Neural Mechanism for Capnotaxis in the Naked Mole-Rat

The Naked Mole-Rat (NM-R) is a small hairless rodent that has thrived underground in the Horn of Africa for the past 40 million years. It was first discovered in 1847, but has only been maintained in captivity and studied as a laboratory animal over the past 40 years. To date, more than 400 scientific papers have been published on this species. This is relatively few compared to established lab animals like rats and mice, but those papers contain a trove of information that has changed our understanding of the constraints of …

Structure Of The Cell-Binding Component Of The Clostridium Difficile Binary Toxin Reveals A Di-Heptamer Macromolecular Assembly, Xingjian Xu, Raquel Godoy-Ruiz, Kaylin A. Adipietro, Christopher Peralta, Danya Ben-Hail, Kristeny M. Varney, Mary E. Cook, Braden M. Roth, Paul T. Wilder, Thomas Cleveland, Alexander Grishaev, Heather M. Neu, Sarah L. J. Michel, Wenbo Yu, Dorothy Beckett, Richard R. Rustand, Catherine Lancaster, John W. Loughney, Adam Kristopeit, Sianny Christantii, Jessica W. Olson, Alexander D. Mackerell, Amedee Des Georges, Edwin Pozharski, David J. Weber

Advanced Science Research Center

Targeting Clostridium difficile infection is challenging because treatment options are limited, and high recurrence rates are common. One reason for this is that hypervirulent C. difficile strains often have a binary toxin termed the C. difficile toxin, in addition to the enterotoxins TsdA and TsdB. The C. difficile toxin has an enzymatic component, termed CDTa, and a pore-forming or delivery subunit termed CDTb. CDTb was characterized here using a combination of singleparticle cryoelectron microscopy, X-ray crystallography, NMR, and other biophysical methods. In the absence of CDTa, 2 di-heptamer structures for activated CDTb (1.0 MDa) were solved at atomic resolution, including …

Exploring The Potential Of Nitric Oxide And Hydrogen Sulfide (Nosh)-Releasing Synthetic Compounds As Novel Priming Agents Against Drought Stress In Medicago Sativa Plants, Chrystalla Antoniou, Rafaella Xenofontos, Giannis Chatzimichail, Anastasis Christou, Khosrow Kashfi, Vasileios Fotopoulos

Publications and Research

Land plants are continuously exposed to multiple abiotic stress factors like drought, heat, and salinity. Nitric oxide (NO) and hydrogen sulfide (H2S) are two well-examined signaling molecules that act as priming agents, regulating the response of plants to stressful conditions. Several chemical donors exist that provide plants with NO and H2S separately. NOSH is a remarkable novel donor as it can donate NO and H2S simultaneously to plants, while NOSH-aspirin additionally provides the pharmaceutical molecule acetylsalicylic acid. The current study aimed to investigate the potential synergistic effect of these molecules in drought-stressed Medicago sativa L. plants by following a pharmacological …

Water In Your Neighbourhood: A Model For Implementing A Semester-Long Course-Based Undergraduate Research Project In Introductory Biology, Ana Lucia Fuentes, Maria Entezari

Publications and Research

Undergraduate biology education has changed over the past decade, incorporating an iterative and evidence-based approach. Many educational assessments have confirmed the effectiveness of integrating authentic research and open-ended inquiry into introductory biology courses, demonstrating a significant positive impact on students’ learning and attitude towards STEM majors. Despite these findings, only a handful of Biology instructors in 2-year colleges adopt this approach, and when adopted, most activities constitute a small fraction of these courses. Finding a feasible, sustainable, semester-long, and cost-effective strategy to incorporate authentic research in the curriculum which promotes integrated understanding of science and addresses socio-scientific issues, is a …

Biological Foundations I, Fardad Firooznia

Open Educational Resources

This is a syllabus for a first-semester introductory biology class, including reading links for current news articles related to the course topics as well as an OpenStax textbook.

Sediment Microbiomes Associated With Critical Habitat Of The Juvenile American Horseshoe Crab; Limulus Polyphemus, J. Petersen, Christina P. Colon, J. L. Joyner

Publications and Research

Plumb Beach, Brooklyn, New York in USA is an important horseshoe crab breeding and nursery ground that has experienced substantial anthropogenic influence, including pollution, erosion and subsequent restoration. Since little is known about the relationship between sediment microbial communities and juvenile horseshoe crab survival, next generation sequencing was used to characterize and compare the sediment microbiome of three distinct areas of Plumb Beach:- a tidal creek with abundant juveniles, East Beach with moderate number of juveniles, and West Beach- a highly disturbed area where juvenile crabs are rarely seen. The microbiome of juvenile crab intestinal content (both dissected gut content …

Bioenergetic Modulation Of Retinal Progenitor Cell Glycolysis To Drive Invasion For Photoreceptor Replacement, Jei Espinal

Theses and Dissertations

Given the limited regenerative capacity of the mammalian retina, cell-replacement strategies are necessary. To replace photoreceptors lost to disease or trauma and restore visual function, laboratories throughout the world are researching photoreceptors replacement strategies using subretinal transplantation of retinal progenitor cells (RPCs). A major obstacle to the advancement of photoreceptor cell-replacement strategies includes low rates of invasion and integration of transplanted cells into the host retina. Currently, there is a limited understanding of how RPC glycolysis may facilitate invasion. To further understand RPC glycolysis-driven invasion, the current investigation involved the bioenergetic modulation RPCs for glycolysis analysis and invasion modeling. The …

Sinorhizobium Meliloti Changes Motility Phenotypes In The Presence Of Serum, Eris K. Bisal

Theses and Dissertations

Sinorhizobium meliloti is a nitrogen-fixing flagellated soil bacterium that engages in a mutual symbiotic relationship with the legume Medicago sativa. Using its flagella, S. meliloti is chemotactic in response to varying environmental cues thereby directed to a target, which is typically the root hairs of M. sativa. Lu et al, 2012 suggested that a signal from the plant can switch S. meliloti from a free-living flagellated microbe to a host-invading non-flagellated microbe, although this signal has not been identified. This switch is thought to occur inside curled root hairs of the plant, and after becoming non-flagellated, S. …

Diffusion And Osmosis: Passive Movement Of Molecules In Biological Systems, Ana Lucia Fuentes, Maria Entezari

Open Educational Resources

During this lab, students determine the salinity of collected water samples. They also compare the effect of the solute concentration of their samples with that of solutions of known solute concentrations on plant cells.

Analysis Of Adult Neural Retina Extracellular Vesicle Release, Rna Transport And Proteomic Cargo, Jason Mighty, Jing Zhou, Alberto Benito-Martin, Sami Sauma, Samer Hanna, Onyekwere Onwumere, Cui Shi, Martin Muntzel, Moira Sauane, Michael Young, Henrik Molina, Dianne Cox, Stephen Redenti

Publications and Research

PURPOSE. Extracellular vesicles (EVs) contain RNA and protein cargo reflective of the genotype and phenotype of the releasing cell of origin. Adult neural retina EV release, RNA transfer, and proteomic cargo are the focus of this study.

METHODS. Adult wild-type mouse retinae were cultured and released EV diameters and concentrations quantified using Nanosight. Immunogold transmission electron microscopy (TEM) was used to image EV ultrastructure and marker protein localization. Quantitative real-time polymerase chain reaction (qRT-PCR) was used to analyze retinal cell transcripts present in EVs. Super-resolution microscopy was used to image fluorescent (green) RNA and (red) lipid membrane labeled EVs, released …

Development Of Multiplex Pcr Assay As A Basis For Predicting Pigment Related Features, Stephanie A. Rodriguez

Student Theses

Currently, short tandem repeats are used in forensic DNA typing to identify the DNA profiles recovered from evidence samples and deceased individuals. Recently, SNPs that are related to pigmentation have been researched for their use in the identification of phenotypic traits. The development of a SNP panel that could successful identify the eye and skin color of an individual, would be immensely useful in missing person cases or mass disaster victim identification. Eight SNPs were selected into a SNaPshot assay that could accurately predict eye and skin color, five for eye color and six for skin color. Development of the …