Life Sciences Commons^™

Investigating Social Preferences In A High Fission-Fusion Society Of Black And White Ruffed Lemur (Varecia Variegata), Patricia A. Adamo

Theses and Dissertations

Wild lemur primates were tested for social preferences across behaviors. Study found highly conservative social preferences that were very consistent across all behavioral states, despite high fission fusion traits common of lemur groups. This finding lays the foundation for using nearest-neighbor as a proxy of social preference for future endeavors.

The Tree Cover And Temperature Disparity In Us Urbanized Areas: Quantifying The Association With Income Across 5,723 Communities, Robert I. Mcdonald, Tanushree Biswas, Cedilla Sachar, Ian Housman, Timothy M. Boucher, Deborah Balk, David Nowak, Erica Spotswood, Charlotte K. Stanley, Stefan Leyk

Publications and Research

Urban tree cover provides benefits to human health and well-being, but previous studies suggest that tree cover is often inequitably distributed. Here, we use National Agriculture Imagery Program digital ortho photographs to survey the tree cover inequality for Census blocks in US large urbanized areas, home to 167 million people across 5,723 municipalities and other Census-designated places. We compared tree cover to summer land surface temperature, as measured using Landsat imagery. In 92% of the urbanized areas surveyed, low-income blocks have less tree cover than high-income blocks. On average, low-income blocks have 15.2% less tree cover and are 1.5˚C hotter …

Control Of Pre-Replicative Complex During The Division Cycle In Chlamydomonas Reinhardtii, Amy E. Ikui, Noriko Ueki, Kresti Pecani, Frederick R. Cross

Publications and Research

DNA replication is fundamental to all living organisms. In yeast and animals, it is triggered by an assembly of pre-replicative complex including ORC, CDC6 and MCMs. Cyclin Dependent Kinase (CDK) regulates both assembly and firing of the pre-replicative complex. We tested temperature-sensitive mutants blocking Chlamydomonas DNA replication. The mutants were partially or completely defective in DNA replication and did not produce mitotic spindles. After a long G1, wild type Chlamydomonas cells enter a division phase when it undergoes multiple rapid synchronous divisions (‘multiple fission’). Using tagged transgenic strains, we found that MCM4 and MCM6 were localized to the nucleus throughout …

A Systematic Review And Meta-Analysis On The Efficacy Of Repeated Transcranial Direct Current Stimulation For Migraine, Guoshuai Cai, Zhu Xia, Leigh Charvet, Feifei Xiao, Abhishek Datta, X Michelle Androulakis

Publications and Research

Purpose: Transcranial direct current stimulation (tDCS) may have therapeutic potential in the management of migraine. However, studies to date have yielded conflicting results. We reviewed studies using repeated tDCS for longer than 4 weeks in migraine treatment, and performed meta-analysis on the efficacy of tDCS in migraine.

Methods: In this meta-analysis, we included the common outcome measurements reported across randomized controlled trials (RCTs). Subgroup analysis was performed at different post-treatment endpoints, and with different stimulation intensities and polarities.

Results: Five RCTs were included in the quantitative meta-analysis with a total of 104 migraine patients. We found a significant reduction of …

Body States Of Asian Elephants Within And Around Protected Areas In The Salakpra Wildlife Sanctuary, Kanchanaburi, Thailand, Caitlyn Thai

Theses and Dissertations

Researchers are becoming increasingly aware that studying a species’ landscape of fear or, more broadly, their emotional states, can better inform cognitive questions about how animals navigate their environments. Vigilance behaviors are one way to determine how certain species perceive and respond to risky situations. Due to rapid environmental change, large animals such as elephants are experiencing risky encounters with humans more often than ever before. This study aims to investigate Asian elephants’ expressions of body states and how they might regulate their behavior based on perceived environmental risk or change. Specifically, we investigated the behavioral responses of Asian elephants …

Earth Law And The Rights Of Nature A New Generation Of Laws Built For Nature, Lindsey Kayman, Paul Bartlett, Milena Popov, Grant Wilson

Open Educational Resources

Earth Law and the Rights of Nature: A New Generation of Laws Built for Nature

Wilson, Grant, Kayman, Lindsey, Bartlett, Paul, and Milena Popov John Jay College of Criminal Justice, Earth Law Center, Environmental Education Fund

Forget doom and gloom. Let’s educate students about the Rights of Nature, an inspiring, evolving legal development which is gaining traction in the US and around the world, and which can promote the cultural shift needed to address our overlapping intersecting environmental crises — climate change, accelerating species extinction, and ecosystem collapse. The Rights of Nature is one aspect of Earth Law. Some of …

Nmr Solution Structures Of Runella Slithyformis Rna 2'-Phosphotransferase Tpt1 Provide Insights Into Nad+ Binding And Specificity, Sébastien Alphonse, Ankan Banerjee, Swathi Dantuluri, Stewart Shuman, Ranajeet Ghose

Publications and Research

Tpt1, an essential component of the fungal and plant tRNA splicing machinery, catalyzes transfer of an internal RNA 2′-PO₄ to NAD⁺ yielding RNA 2′-OH and ADP-ribose-1′,2′-cyclic phosphate products. Here, we report NMR structures of the Tpt1 ortholog from the bacterium Runella slithyformis (RslTpt1), as apoenzyme and bound to NAD⁺. RslTpt1 consists of N- and C-terminal lobes with substantial inter-lobe dynamics in the free and NAD⁺-bound states. ITC measurements of RslTpt1 binding to NAD⁺ (K_D ∼31 μM), ADP-ribose (∼96 μM) and ADP (∼123 μM) indicate that substrate affinity is determined primarily by …

Human Ace2‑Functionalized Gold “Virus‑Trap” Nanostructures For Accurate Capture Of Sars‑Cov‑2 And Single‑Virus Sers Detection, Yong Yang, Yusi Peng, Chenglong Lin, Li Long, Jingying Hu, Jun He, Hui Zeng, Zhengren Huang, Zhi-Yuan Li, Masaki Tanemura, Jianlin Shi, John R. Lombardi, Xiaoying Luo

Publications and Research

The current COVID-19 pandemic urges the extremely sensitive and prompt detection of SARS-CoV-2 virus. Here, we present a Human Angiotensin-converting-enzyme 2 (ACE2)-functionalized gold “virus traps” nanostructure as an extremely sensitive SERS biosensor, to selectively capture and rapidly detect S-protein expressed coronavirus, such as the current SARS-CoV-2 in the contaminated water, down to the single-virus level. Such a SERS sensor features extraordinary 106- fold virus enrichment originating from high-affinity of ACE2 with S protein as well as “virus-traps” composed of oblique gold nanoneedles, and 109- fold enhancement of Raman signals originating from multicomponent SERS effects. Furthermore, the identification standard of virus …

The Insular Herpetofauna Of Mexico: Composition, Conservation, And Biogeographic Patterns, Juan Valentín Pliego‐Sánchez, Christopher Blair, Aníbal H. Díaz De La Vega‐Pérez, Víctor H. Jiménez‐Arcos

Publications and Research

We compile a Mexican insular herpetofaunal checklist to estimate endemism, conservation status, island threats, net taxonomic turnover among six biogeographic provinces belonging to the Nearctic and Neotropical regions, and the relationships between island area and mainland distance versus species richness. We compile a checklist of insular herpetofaunal through performing a literature and collection review. We define the conservation status according to conservation Mexican law, the Red List of International Union for Conservation of Nature, and Environmental Vulnerability Scores. We determine threat percentages on islands according to the 11 major classes of threats to biodiversity. We estimate the net taxonomic turnover …

Semester Schedule For Cognitive And Behavioral Neuroscience, Megan V. Caldwell

Open Educational Resources

This course schedule has been created for an asynchronous 15-week, 4 credit Cognitive and Behavioral Neuroscience course. It is a comprehensive schedule including a week-by-week breakdown of lecture topics, reading material, assignments, and exam schedule. The course covers topics related to cognition and neuroscience including the action potential, neurotransmitters, cell gradients, sensation (vision, hearing, and pain/somatosensation), neuroplasticity, memory, and movement systems. The schedule is intended to be accompanied by a syllabus.

Laboratory Techniques In Public Health: Bi-520 Introduction To Public Health Lab Manual, Anuradha Srivastava

Open Educational Resources

This laboratory manual for a foundations course Public Health is unique in the sense that very rarely, a foundations course in the field has a lab component offered with the lecture. This lab manual provides basic laboratory exercises that could be useful to introduce undergraduate students to the basics of public health laboratory practices.

Lighting The Way: Recent Insights Into The Structure And Regulation Of Phototropin Blue Light Receptors, Jaynee E. Hart, Kevin H. Gardner

Publications and Research

The phototropins (phots) are light-activated kinases that are critical for plant physiology and the many diverse optogenetic tools that they have inspired. Phototropins combine two bluelight- sensing Light–Oxygen–Voltage (LOV) domains (LOV1 and LOV2) and a C-terminal serine/threonine kinase domain, using the LOV domains to control the catalytic activity of the kinase. While much is known about the structure and photochemistry of the light-perceiving LOV domains, particularly in how activation of the LOV2 domain triggers the unfolding of alpha helices that communicate the light signal to the kinase domain, many questions about phot structure and mechanism remain. Recent studies have made …

Open-Source Computational Framework For Studying Drosophila Behavioral Phase, Boyan Kostadinov, Hannah Lee Pettibone, Evardra Valerie Bell, Xiaona Zhou, Ausra Pranevicius, Orie Thomas Shafer, Maria Paz Fernandez

Publications and Research

This protocol describes a standardized method for analyzing Drosophila behavioral rhythmicity under light dark cycles, temperature ramps, and free running conditions. The protocol constitutes a step-by-step guide from generation of appropriate Drosophila genetic crosses to behavioral experiments. We also provide an opensource computational framework using R for the analysis of the phase of behavior using circular statistics. An extended method for complete use is also provided. For complete details on the use and execution of this protocol, please refer to Fernandez et al. (2020).

Gap Junction-Mediated Glycinergic Inhibition Ensures Precise Temporal Patterning In Vocal Behavior, Boris P. Chagnaud, Jonathan T. Perelmuter, Paul M. Forlano, Andrew H. Bass

Publications and Research

Precise neuronal firing is especially important for behaviors highly dependent on the correct sequencing and timing of muscle activity patterns, such as acoustic signaling. Acoustic signaling is an important communication modality for vertebrates, including many teleost fishes. Toadfishes are well known to exhibit high temporal fidelity in synchronous motoneuron firing within a hindbrain network directly determining the temporal structure of natural calls. Here, we investigated how these motoneurons maintain synchronous activation. We show that pronounced temporal precision in population-level motoneuronal firing depends on gap junction-mediated, glycinergic inhibition that generates a period of reduced probability of motoneuron activation. Super-resolution microscopy confirms …

Predicting Vasovagal Responses: A Model-Based And Machine Learning Approach, Theodore Raphan, Sergei B. Yakushi

Publications and Research

Vasovagal syncope (VVS) or neurogenically induced fainting has resulted in falls, fractures, and death. Methods to deal with VVS are to use implanted pacemakers or beta blockers. These are often ineffective because the underlying changes in the cardiovascular system that lead to the syncope are incompletely understood and diagnosis of frequent occurrences of VVS is still based on history and a tilt test, in which subjects are passively tilted from a supine position to 20◦ from the spatial vertical (to a 70◦ position) on the tilt table and maintained in that orientation for 10–15 min. Recently, is has been shown …

General Biology 2 Laboratory Manual, Dmitry Y. Brogun, Azure N. Faucette, Kristin Polizzotto, Farshad Tamari

Open Educational Resources

Currently, many academic institutions are using one or more variations of online modalities due to the Covid-19 pandemic, and science educators face a unique challenge with distance-learning laboratories. Many resources to engage students in virtual, interactive laboratory activities exist, but we found that high costs and/or overlooked content left gaps for several topics typically taught in a general, introductory biology course for undergraduate biology majors (e.g., organismal biology). Additionally, resources for an online lab must be identified and curated from multiple sources, requiring intense demands on the instructors’ time. To meet this need and to overcome the financial burden of …

Pirnas As Modulators Of Disease Pathogenesis, Kayla J. Rayford, Ayorinde Cooley, Jelonia T. Rumph, Ashutosh Arun, Girish Rachakonda, Fernando Villalta, Maria F. Lima, Siddharth Pratap, Smita Misra, Pius N. Nde

Publications and Research

Advances in understanding disease pathogenesis correlates to modifications in gene expression within different tissues and organ systems. In depth knowledge about the dysregulation of gene expression profiles is fundamental to fully uncover mechanisms in disease development and changes in host homeostasis. The body of knowledge surrounding mammalian regulatory elements, specifically regulators of chromatin structure, transcriptional and translational activation, has considerably surged within the past decade. A set of key regulators whose function still needs to be fully elucidated are small non-coding RNAs (sncRNAs). Due to their broad range of unfolding functions in the regulation of gene expression during transcription and …

Effects Of Structural Isomers Of Spermine On The Higher-Order Structure Of Dna And Gene Expression, Tomoki Kitagawa, Takashi Nishio, Yuko Yoshikawa, Naoki Umezawa, Tsunehiko Higuchi, Chwen-Yang Shew, Takahiro Kenmotsu, Kenichi Yoshikawa

Publications and Research

Polyamines are involved in various biological functions, including cell proliferation, differentiation, gene regulation, etc. Recently, it was found that polyamines exhibit biphasic effects on gene expression: promotion and inhibition at low and high concentrations, respectively. Here, we compared the effects of three naturally occurring tetravalent polyamines, spermine (SPM), thermospermine (TSPM), and N4-aminopropylspermidine (BSPD). Based on the single DNA observation with fluorescence microscopy together with measurements by atomic force microscopy revealed that these polyamines induce shrinkage and then compaction of DNA molecules, at low and high concentrations, respectively. We also performed the observation to evaluate the effects of these polyamine isomers …

Mutational And Biophysical Robustness In A Prestabilized Monobody, Peter G. Chandler, Li Lynn Tan, Benjamin T. Porebski, James S. Green, Blake T. Riley, Sebastian S. Broendum, David E. Hoke, Robert J. Falconer, Trent P. Munro, Malcolm Buckle, Colin J. Jackson, Ashley M. Buckle

Advanced Science Research Center

The fibronectin type III (FN3) monobody domain is a promising non-antibody scaffold, which features a less complex architecture than an antibody while maintaining analogous binding loops. We previously developed FN3Con, a hyperstable monobody derivative with diagnostic and therapeutic potential. Prestabilization of the scaffold mitigates the stability–function trade-off commonly associated with evolving a protein domain toward biological activity. Here, we aimed to examine if the FN3Con monobody could take on antibody-like binding to therapeutic targets, while retaining its extreme stability. We targeted the first of the Adnectin derivative of monobodies to reach clinical trials, which was engineered by directed evolution for …

When The Pandemic Opts For The Lockdown: Secretion System Evolution In The Cholera Bacterium, Francis J. Santoriello, Stefan Pukatzki

Publications and Research

Vibrio cholerae, the causative agent of the diarrheal disease cholera, is a microbe capable of inhabiting two different ecosystems: chitinous surfaces in brackish, estuarine waters and the epithelial lining of the human gastrointestinal tract. V. cholerae defends against competitive microorganisms with a contact-dependent, contractile killing machine called the type VI secretion system (T6SS) in each of these niches. The T6SS resembles an inverted T4 bacteriophage tail and is used to deliver toxic effector proteins into neighboring cells. Pandemic strains of V. cholerae encode a unique set of T6SS effector proteins, which may play a role in pathogenesis or pandemic …

The Neural Correlates Of Cued Reward Omission, Jessica A. Mollick, Luke J. Change, Anjali Krishnan, Thomas E. Hazy, Kai A. Krueger, Guido K. W. Frank, Tor D. Wager, Randall C. O'Reilly

Publications and Research

Compared to our understanding of positive prediction error signals occurring due to unexpected reward outcomes, less is known about the neural circuitry in humans that drives negative prediction errors during omission of expected rewards. While classical learning theories such as Rescorla–Wagner or temporal difference learning suggest that both types of prediction errors result from a simple subtraction, there has been recent evidence suggesting that different brain regions provide input to dopamine neurons which contributes to specific components of this prediction error computation. Here, we focus on the brain regions responding to negative prediction error signals, which has been well-established in …

Beauty That Moves: Dance For Parkinson’S Effects On Affect, Self-Efficacy, Gait Symmetry, And Dual Task Performance, Cecilia Fontanesi, Joseph F. X. Desouza

Publications and Research

Background: Previous studies have investigated the effects of dance interventions on Parkinson’s motor and non-motor symptoms in an effort to develop an integrated view of dance as a therapeutic intervention. This within-subject study questions whether dance can be simply considered a form of exercise by comparing a Dance for Parkinson’s class with a matched-intensity exercise session lacking dance elements like music, metaphorical language, and social reality of art-partaking.

Methods: In this repeated-measure design, 7 adults with Parkinson’s were tested four times; (i) before and (ii) after a Dance for Parkinson’s class, as well as (iii) before and (iv) after a …

Anti-Cancer Effects By Interleukin 24, Xuelin Zhong

Dissertations, Theses, and Capstone Projects

Cancers develop as some cells acquire the ability, either by exogenous stimulation or by spontaneous mutation, to keep growing despite normal restraints. Up-regulating translation of oncogenes involved in cell proliferation and tumor development and down-regulating translation of tumor-suppressors that normally suppress tumor development are two most common mechanisms by which cancers develop. Therefore, it is crucial to study how these proteins get either up-regulated or down-regulated at translational level.

The eukaryotic translation initiation factor, which is composed of subunits such as eIF4A, eIF4G and eIF4E, is one of the key factors that contribute to efficient translation initiation. Interleukin 24 (IL-24), …

Cell Cycle Progression Effects Of Albumin, Sharmeen Uddin

Dissertations, Theses, and Capstone Projects

Progression through G₁ phase of the cell cycle is controlled largely by growth factors in early G₁ and by nutrients in late G₁ indicating sufficient raw material for cell division. We previously mapped a late G₁ cell cycle checkpoint for lipids upstream from a mammalian target of rapamycin complex 1 (mTORC1)-mediated checkpoint and downstream from a mid-G₁ checkpoint known as the Restriction point. We therefore investigated a role for lipids in progression through late G₁ into S-phase. Quiescent BJ-hTERT human fibroblasts primed back into G1 with FBS treatment, were treated with a mixture of …

The C. Neoformans Cell Wall: A Scaffold For Virulence, Christine Chrissian

Dissertations, Theses, and Capstone Projects

Cryptococcus neoformans is a globally distributed opportunistic fungal pathogen and the causative agent of life threatening cryptococcal meningoencephalitis in immunocompromised individuals, resulting in ~180,000 deaths each year worldwide. A primary virulence-associated trait of this organism is the production of melanin. Melanins are a class of diverse pigments produced via the oxidation and polymerization of aromatic ring compounds that have a characteristically complex, heterogenous, and amorphous structure. They are synthesized by representatives of all biological kingdoms and share a multitude of remarkable properties such as the ability to absorb ultraviolet (UV) light and protect against ionizing radiation. Melanin production in fungi …

Influence Of Demographic, Clinical, And Neuroimaging Variables On Neuropsychological Recovery Trajectories After Moderate-To-Severe Traumatic Brain Injury, Elizabeth J. Leif

Dissertations, Theses, and Capstone Projects

Traumatic brain injury (TBI) is prevalent in people of all ages and all walks of life. Cognitive deficits are common after TBI and the recovery patterns are known to be variable across individuals. The current study investigates diffuse axonal injury (DAI), cerebral blood flow (CBF), and focal lesions, in addition to post-traumatic amnesia (PTA), as possible predictors of cognitive trajectory in moderate-to-severe TBI patients. Cognitive trajectory was evaluated with a battery of neuropsychological tests that were combined into three domains: processing speed, verbal learning, and executive function. Patients (N=44) were tested three times at 3, 6, and 12 months post-injury. …

Third Harmonic Generation: A Method For Visualizing Myelin In The Murine Cerebral Cortex, Michael Redlich

Dissertations, Theses, and Capstone Projects

Here we present the use of Third Harmonic Generation (THG) for the label-free imaging of myelinated axons in the murine cerebral cortex. Myelin plays an important role in the processes of learning and disease. However, much of the myelin biology research thus far has focused on white matter tracts where myelin is more visible. Much is still unknown, particularly with regard to myelin in gray matter. First, we engage in THG microscopy using an optical parametric oscillator pumped by a titanium-sapphire laser to demonstrate the utility of the technique for imaging myelin in vivo. Second, we investigate the use of …

Insights Into Leptopilina Spp. Immune-Suppressive Strategies Using Mixed-Omics And Molecular Approaches, Brian Wey

Dissertations, Theses, and Capstone Projects

Host-parasite interactions influence the biology of each over the course of evolution. Parasite success allows for the passage of potent virulence strategies from generation to generation. Host success passes stronger immunity and resistance strategies to the following generations as well. Only by studying both partners within their natural contexts can we begin to understand the relationship between the two and how immune mechanisms and virulence strategies interact as a molecular arms race.

In this work, we focus on a natural host-parasite pair, the Drosophila-Leptopilina model. Leptopilina species are parasites of several fruit fly species, including Drosophila melanogaster. This model …

Using The Marcus Inverted Region And Artificial Cofactors To Create A Charge Separated State In De Novo Designed Proteins, Eskil Me Andersen

Dissertations, Theses, and Capstone Projects

To create an efficient de novo photosynthetic protein it is important to create long lived charge separated states. Achieving stable charge separation leads to an increase in the efficiency of the photosynthetic reaction which in turn leads to higher yields of end products, such as biofuels, electrical charge, or synthetic chemicals. In an attempt to create charge separated states in de novo proteins we hypothesized that we could engineer the free energy gaps in the proteins from excited primary donor (PD) to acceptor (A), and A back to ground state PD such that the forward electron transfer (ET) would be …

Consumer Likings Of Different Miracle Fruit Products On Different Sour Foods, Sung-Eun Choi, Jeff Garza

Publications and Research

Miracle fruit has a high potential as a healthy sweetening enhancer, due to its powerful antioxidant capacity and its unique ability to transform sour taste into sweet taste. The aim of this study was to analyze the effect of different miracle fruit products on the likings of different sour foods.In total, 200 healthy adults (women 55%, 18–65 years old) evaluated five sour foods (apple, goat cheese, lemonade, yogurt, pickle) before and after miracle fruit application. Four commercial miracle fruit products (pills-Y; G; M, powder-P) were randomly assigned to each panelist. The pre- and post-test likings for overall, flavor, texture, and …