Life Sciences Commons^™

A Bifunctional Atpase Drives Tad Pilus Extension And Retraction, Courtney K. Ellison, Jingbo Kan, Jennifer L. Chlebek, Katherine R. Hummels, GaёL Panis, Patrick H. Viollier, Nicolas Biais, Ankur B. Dalia, Yves V. Brun

Publications and Research

A widespread class of prokaryotic motors powered by secretion motor adenosine triphosphatases (ATPases) drives the dynamic extension and retraction of extracellular fibers, such as type IV pili (T4P). Among these, the tight adherence (tad) pili are critical for surface sensing and biofilm formation. As for most other motors belonging to this class, how tad pili retract despite lacking a dedicated retraction motor ATPase has remained a mystery. Here, we find that a bifunctional pilus motor ATPase, CpaF, drives both activities through adenosine 5′-triphosphate (ATP) hydrolysis. We show that mutations within CpaF result in a correlated reduction in the rates of …

Feeding The Future Meat Doesn’T Come Cheap, Lukas C. Southard

Capstones

Cultured – or as it is referred to by companies innovating the technology clean – meat is expected to be the next innovation to change the way the world gets its animal protein. Meat from animal cells grown in a lab seems like science fiction but it is around the corner from hitting your supermarket shelves. The technology has been developed but how these companies intend on scaling up their production to meet retail demands remains a mystery. So far companies have relied on seed and early stage investment from venture capital companies and private sources to fund research. Predictions …

What If The Key To Climate Change Is Hiding Under The Sea?, Shira Feder

Capstones

“We know more about outer space than we do the ocean,” says Vicki Ferrini, a research scientist at Columbia University with over 20 ocean expeditions under her belt. And as the woman leading Seabed 2030, the charge to map the world’s oceans—which are 85% unexplored—she knows how vital this is to combat climate change and exactly how she’s going to do it. Read it here: https://medium.com/@shira.feder/what-if-the-key-to-climate-change-is-hiding-under-the-sea-4503565c33a2

Visual Modulation Of Resting State Α Oscillations, Kelly Webster, Tony Ro

Publications and Research

Once thought to simply reflect passive cortical idling, recent studies have demonstrated that α oscillations play a causal role in cognition and perception. However, whether and how cognitive or sensory processes modulate various components of the α rhythm is poorly understood. Sensory input and resting states were manipulated in human subjects while electroencephalography (EEG) activity was recorded in three conditions: eyes-open fixating on a visual stimulus, eyes-open without visual input (darkness), and eyes-closed without visual input (darkness). We show that α power and peak frequency increase when visual input is reduced compared to the eyes open, fixating condition. These results …

Green Roof System Integrated Soil Methods, Jude R. Vallon, Ivan L. Guzman

Publications and Research

Large metropolitan areas like NYC are seeking to integrate sustainability into retrofitting buildings for the development of green infrastructure. Among the many environmental issues of urbanization, the UHI (urban heat island) effect and storm water runoff are of particular interest when it comes building structures. Individual buildings can contribute towards mitigating these effects with implementation of vegetative rooftops, i.e. Green Roofs. Commercial buildings are currently receiving government incentives and new constructions are required to include green roof installations. However, if existing buildings are considering the addition of a green roof on an existing roof, they have to factor in the …

The Ethical Implications Of Bioengineering Advancements, Mainstream Media Coverage Of Those Developments, And The Future Of Motherhood, Aliff Abad, Katherine Gregory

Publications and Research

How do the media interpret reproductive interventions that involve genetic testing? When a scientist performed the first known genetic editing on twins, Lulu and Nana, he ignored ethical considerations of CRISPR use. This project provides a content analysis based on a review of popular science and newspaper articles. Our interpretation of these articles suggest that there is a lack of critical understanding of this unethical procedure and a similar attitude towards future genetic developments. While the public is curious about the repercussions of genetic editing, not enough focus is applied to the ethics of conducting such a procedure.

Effects Of Mercury On The Dopamine Transporter Cell Surface Expression In Pc12 Cells, Christina Hui

Student Theses

Environmental factors, such as heavy metal exposures, have been suggested to have an impact not only on neurodegenerative disease, such as Parkinson’s disease, but also on psychostimulants abuse and their toxicity. In this study, two questions were addressed: 1) effects of mercuric chloride on parkinsonian toxicant 1-methyl-4-phenylpyridinium (MPP⁺) induced cytotoxicity and 2) effects of mercuric chloride on cell surface dopamine transporter. Pheochromocytorma cells (PC12) were treated with various concentrations of mercuric chloride (0.02~2.0 ppm) for 4 hours with and without 0.1 mM MPP⁺. Significant potentiation of toxicity was observed when there was co-treatment with 0.5 ppm …

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 …

Rasp 4: Ancestral State Reconstruction Tool For Multiple Genes And Characters, Yan Yu, Christopher Blair, Xingjin He

Publications and Research

With the continual progress of sequencing techniques, genome-scale data are increasingly used in phylogenetic studies. With more data from throughout the genome, the relationship between genes and different kinds of characters is receiving more attention. Here, we present version 4 of RASP, a software to reconstruct ancestral states through phylogenetic trees. RASP can apply generalized statistical ancestral reconstruction methods to phylogenies, explore the phylogenetic signal of characters to particular trees, calculate distances between trees, and cluster trees into groups. RASP 4 has an improved graphic user interface and is freely available from http://mnh.scu.edu.cn/soft/blog/RASP (program) and https://github.com/sculab/RASP (source code).

Venom Diversity And Evolution In The Most Divergent Cone Snail Genus Profundiconus, Guilia Fassio, Maria Vittoria Modica, Lou Mary, Paul Zaharias, Alexander E. Fedosov, Juliette Gorson, Yuri I. Kantor, Mandë E. Holford, Nicolas Puillandre

Publications and Research

Profundiconus is the most divergent cone snail genus and its unique phylogenetic position, sister to the rest of the family Conidae, makes it a key taxon for examining venom evolution and diversity. Venom gland and foot transcriptomes of Profundiconus cf. vaubani and Profundiconus neocaledonicus were de novo assembled, annotated, and analyzed for differential expression. One hundred and thirty-seven venom components were identified from P. cf. vaubani and 82 from P. neocaledonicus, with only four shared by both species. The majority of the transcript diversity was composed of putative peptides, including conotoxins, profunditoxins, turripeptides, insulin, and prohormone-4. However, there were also …

From The Human To The Planetary: Speculative Futures Of Care, Miriam Ticktin

Publications and Research

This is largely a theoretical, speculative essay that takes on the question of what ‘care’ looks like at a moment when climate change is increasingly taking center stage in public and political discussions. Starting with two new practices, namely, humanitarian care for nonhumans and One Health collaborations, I seek to determine what forms of political care can incorporate the well-being of future generations and future iterations of the earth. After an exploration of One Health as an approach to planetary care, I ask what its parts enable us to think, despite its limitations; I focus on the new human-nonhuman assemblages …

Invertebrate Retinal Progenitors As Regenerative Models In A Microfluidic System, Caroline D. Pena, Stephanie Zhang, Robert Majeska, Tadmiri Venkatesh, Maribel Vazquez

Publications and Research

Regenerative retinal therapies have introduced progenitor cells to replace dysfunctional or injured neurons and regain visual function. While contemporary cell replacement therapies have delivered retinal progenitor cells (RPCs) within customized biomaterials to promote viability and enable transplantation, outcomes have been severely limited by the misdirected and/or insuffcient migration of transplanted cells. RPCs must achieve appropriate spatial and functional positioning in host retina, collectively, to restore vision, whereas movement of clustered cells differs substantially from the single cell migration studied in classical chemotaxis models. Defining how RPCs interact with each other, neighboring cell types and surrounding extracellular matrixes are critical to …

Nuclear Tau, P53 And Pin1 Regulate Parn-Mediated Deadenylation And Gene Expression, Jorge Baquero, Sophia Varriano, Martha Ordonez, Pawel Kuczaj, Michael R. Murphy, Gamage Aruggoda, Devon Lundine, Viktoriya Morozova, Ali Elhadi Makki, Alejandra Del C. Alonso, Frida E. Kleiman

Publications and Research

While nuclear tau plays a role in DNA damage response (DDR) and chromosome relaxation, the mechanisms behind these functions are not fully understood. Here, we show that tau forms complex(es) with factors involved in nuclear mRNA processing such as tumor suppressor p53 and poly(A)-specific ribonuclease (PARN) deadenylase. Tau induces PARN activity in different cellular models during DDR, and this activation is further increased by p53 and inhibited by tau phosphorylation at residues implicated in neurological disorders. Tau’s binding factor Pin1, a mitotic regulator overexpressed in cancer and depleted in Alzheimer’s disease (AD), also plays a role in the activation of …

Spatial Upscaling Of Forest Response To Drought, Wei Fang, Peipei Xu, Tao Zhao, Xiang Zhao, Hui Luo, George Hendrey, Chuixiang Yi

Publications and Research

We have integrated the observational capability of satellite remote sensing with plot-scale tree ring data to up-scale the evaluation of forest responses to drought. Satellite data, such as Normalized Difference Vegetation Index (NDVI), can provide a spatially continuous measure with limited temporal coverage, while tree Ring Width Index (RWI) provides accurate assessment with much longer time series local scales. Here, we explored the relationship between RWI and NDVI of three dominant species in the Southwestern United States (SWUS), and predicted RWI spatial distribution from 2001 to 2017 based on MODIS 1-km resolution NDVI data with stringent quality control. We detected …

An Amyloid Core Sequence In The Major Candida Albicans Adhesin Als1p Mediates Cell-Cell Adhesion, Vida Ho, Philippe Herman-Bausier, Christopher Shaw, Karen A. Conrad, Melissa C. Garcia-Sherman, Jeremy Draghi, Yves F. Dufrene, Peter N. Lipke, Jason M. Rauceo

Publications and Research

ABSTRACT The human fungal commensal Candida albicans can become a serious opportunistic pathogen in immunocompromised hosts. The C. albicans cell adhesion protein Als1p is a highly expressed member of a large family of paralogous adhesins. Als1p can mediate binding to epithelial and endothelial cells, is upregulated in infections, and is important for biofilm formation. Als1p includes an amyloidforming sequence at amino acids 325 to 331, identical to the sequence in the paralogs Als5p and Als3p. Therefore, we mutated Val326 to test whether this sequence is important for activity. Wild-type Als1p (Als1pWT) and Als1p with the V326N mutation (Als1pV326N) were expressed …

Microwave Solventless Synthesis Of Meso-Tetrakis (Pentafluorophenyl)Poprphyrin (Tppf20) And Tris(Pentafluorophenyl))Corrole [Chemistry], Sunaina Singh

Open Educational Resources

Organic chemistry is a two-semester course (Organic Chemistry I, SCC 251 and Organic Chemistry II, SCC 252) required for majors in Biology. The SCC 251 course has been designated for the Integrative Learning Core Competency as well the Digital Communication Ability. This course emphasizes the synthesis, structure, reactivity, and mechanisms of reaction of organic compounds. Laboratory stresses various organic synthetic and analytic techniques (distillation, extraction, chromatography and spectroscopy).

This lab provided an opportunity for students to go deeper with the chemistry content by correlating to the concepts they learned in General Chemistry courses such as Valence shell electron pair repulsion …

Titration Of A Newtown Creek Environmental Water Sample To Determine The Amount Of Chloride Ions [Chemistry], Kevin Mark

Open Educational Resources

Main Course Learning Objectives:

The General Chemistry 1 (SCC 201) course has multiple course learning objectives, which articulate key introductory chemistry concepts that all STEM students should possess. In particular, the Newtown Creek titration experiment aligns with SCC 201 learning objectives of:

1. Demonstrate an appreciation of the role of chemistry in various aspects of life
2. Perform basic laboratory skills such as the proper execution of titration techniques
3. Describe and explain the fundamental chemistry concept of solution concentration
4. Analyze and represent experimental data in tables and graphs, interpret experimental results and write laboratory reports

In the SCC 201 laboratory, students are …

Human Biology Oer, Bio 1100, Course Outline, Tatiana Voza

Open Educational Resources

This course will include selected biological concepts, including the chemical basis of life, cell structure and division, a broad survey of the major systems of the human body with a special emphasis on human health disease, human evolution and ecology. This course should provide students who do not plan to continue in the sciences or pre-health programs with a working knowledge of life science that will be useful in making informed decisions on health and the environment

Inclusion Of Enclosed Hydration Effects In The Binding Free Energy Estimation Of Dopamine D3 Receptor Complexes, Rajat Kumar Pal, Satishkumar Gadhiya, Steven Ramsey, Pierpaolo Cordone, Lauren Wickstrom, Wayne W. Harding, Tom Kurtzman, Emilio Gallicchio

Publications and Research

Confined hydration and conformational flexibility are some of the challenges encountered for the rational design of selective antagonists of G-protein coupled receptors.We present a set of C3-substituted (-) -stepholidine derivatives as potent binders of the dopamine D3 receptor.The compounds are characterized biochemically, as well as by computer modeling using a novel molecular dynamics-based alchemical binding free energy approach which incorporates the effect of the displacement of enclosed water molecules from the binding site.The free energy of displacement of specific hydration sites is obtained using the Hydration Site Analysis method with explicit solvation. This work underscores the critical role of confined …

Bright Green Biofluorescence In Sharks Derives From Bromo-Kynurenine Metabolism, Hyun Bong Park, Yick Chong Lam, Jean P. Gaffney, James C. Weaver, Sara Rose Krivoshik, Randy Hamchand, Vincent Pieribone, David F. Gruber, Jason M. Crawford

Publications and Research

Although in recent years there has been an increased awareness of the widespread nature of biofluorescence in the marine environment, the diversity of the molecules responsible for this luminescent phenotype has been mostly limited to green fluorescent proteins (GFPs), GFP-like proteins, and fluorescent fatty acid-binding proteins (FABPs). In the present study, we describe a previously undescribed group of brominated tryptophan-kynurenine small molecule metabolites responsible for the green biofluorescence in two species of sharks and provide their structural, antimicrobial, and spectral characterization. Multi-scale fluorescence microscopy studies guided the discovery of metabolites that were differentially produced in fluorescent versus non-fluorescent skin, as …

Neural Correlates Of Decision Making Related To Information Security: Self-Control And Moral Potency, Robert West, Emily Budde, Qing Hu

Publications and Research

Security breaches of digital information represent a significant threat to the wellbeing of individuals, corporations, and governments in the digital era. Roughly 50% of breaches of information security result from the actions of individuals inside organizations (i.e., insider threat), and some evidence indicates that common deterrence programs may not lessen the insiders’ intention to violate information security. This had led researchers to investigate contextual and individual difference variables that influence the intention to violate information security policies. The current research builds upon previous studies and explores the relationship between individual differences in self-control and moral potency and the neural correlates …

Multi-Scale Predictors Of Parasite Risk In Wild Male Savanna Baboons (Papio Cynocephalus), Bobby Habig, David A.W.A.M. Jansen, Mercy Y. Akinyi, Laurence R. Gesquiere, Susan C. Alberts, Elizabeth A. Archie

Publications and Research

Several factors are thought to shape male parasite risk in polygynous and polygynandrous mammals, including male-male competition, investment in potentially immunosuppressive hormones, and dispersal. Parasitism is also driven by processes occurring at larger scales, including host social groups and populations. To date, studies that test parasite-related costs of male behavior at all three scales—individual hosts, social groups, and the host population—remain rare. To fill this gap, we investigated multi-scale predictors of helminth parasitism in 97 male savanna baboons (Papio cynocephalus) living in the Amboseli ecosystem in Kenya over a 5-year span. Controlling for multi-scale processes, we found that many of …

Development And Sensory Experience Dependent Regulation Of Microglia In Barrel Cortex, Joshua C. Brumberg, John Kalambogias, Chia-Chien Chen, Safraz Khan, Titus Son, Carolyn Headlam, Cindy Lin

Publications and Research

The barrel cortex is within the primary somatosensory cortex of the rodent, and processes signals from the vibrissae. Much focus has been devoted to the function of neurons, more recently, the role of glial cells in the processing of sensory input has gained increasing interest. Microglia are the principal immune cells of the nervous system that survey and regulate the cellular constituents of the dynamic nervous system. We investigated the normal and disrupted development of microglia in barrel cortex by chronically depriving sensory signals via whisker trimming for the animals’ first postnatal month. Using immunohistochemistry to label microglia, we performed …

Association Of Fish Oil And Physical Activity On Mobility Disability In Older Adults, Anoop T. Balachandran

Publications and Research

Purpose: This study aimed to examine whether long-term fish oil (FO) supplementation is associated with a lower risk of mobility disability and enhances benefits of physical activity (PA). Methods: A total of 1635 sedentary adults age 70 to 89 yr from the Lifestyle Interventions and Independence for Elders single-blinded randomized,multicenter clinical trial, which compared a structured PA program to a health education program. Primary outcome was incident major mobility disability (MMD), defined by loss of ability to walk 400 m, measured every 6 months for an average of 2.6 yr. Secondary outcomes included persistent mobility disability, Short Physical Performance Battery, …

Anti-Cancer Effects Of Oleocanthal And Extra Virgin Olive Oil, Limor Goren

Dissertations, Theses, and Capstone Projects

Oleocanthal is a phenolic compound found in varying concentrations in extra virgin olive oil. Oleocanthal has been shown to be active physiologically, benefiting several diseased states by conferring anti-inflammatory and neuroprotective benefits. Recently, we and other groups have demonstrated its specific and selective toxicity toward cancer cells; however, the mechanism leading to cancer cell death is still disputed. The current study demonstrates that oleocanthal induced damage to cancer cells’ lysosomes leading to cellular toxicity in vitro. Non-cancer cells were significantly less affected. Lysosomal membrane permeabilization following oleocanthal treatment in various cell lines was assayed via three complementary methods. Additionally, …

Systematics And Ecology Of The Andean Neotropical Schefflera (Araliaceae) With Globose Capitate Inflorescences And Use Of Niche Modeling For Iucn Red List Threat Assessment Of Plerandra Elegantissima (Araliaceae), Carlos V. Rodrigues

Dissertations, Theses, and Capstone Projects

Since the end of the 19^thcentury, ScheffleraJ.R. Forst. & G. Forst.has been recognized as the largest and most wide-ranging genus of Araliaceae. It can be found throughout the humid tropics and subtropics, is not particularly diverse at low elevations in the warmest regions, and a few taxa extend into warm-temperate areas. As currently circumscribed, the genus contains 605 described species and many hundreds more awaiting formal description. However, a succession of phylogenetic studies have confirmed that Schefflera, as currently circumscribed,is polyphyletic, comprising five geographically centered lineages scattered across the phylogenetic tree of Araliaceae, and …

Eugenics In The 21st Century, Jessica Linn Chin

Dissertations, Theses, and Capstone Projects

Eugenics is the science of enhancing the human population through the management of breeding and hereditary traits. This thesis explores the history of eugenics and shows how eugenic practices continue in the 21^st century with advancements in technology and positive eugenic goals that can result in adverse effects on the human body and society. When Sir Francis Galton coined the term eugenics in 1883, he intended to improve British society with the use of positive eugenics. Galton used positive eugenics to encourage people with good mental and physical qualities to produce more children. He avoided negative eugenics, which involved …

Emotion Processing Deficits In Psychopathy: Does Cueing To Relevant Facial Features Increase Cognitive And Emotional Empathy?, Shawn E. Fagan

Dissertations, Theses, and Capstone Projects

Psychopathy is a multifaceted disorder characterized by a lack of cognitive and emotional empathy. The traditional model of psychopathy divides the disorder into two factors: Factor 1 consists of the interpersonal and affective traits of psychopathy while Factor 2 measures antisocial behaviors and lifestyle choices. The attention-to-the-eyes hypothesis argues that psychopathic individuals have impaired emotion recognition (specifically for fear) due to deficits in orienting attention to salient facial features like the eyes. Psychopathic individuals also display blunted autonomic responding to emotional stimuli, though whether this is due to attention-orienting deficits remains to be clarified. The present project investigated whether empathy-related …

Structure And Function Of Dopamine In The Inner Ear And Auditory Efferent System Of A Vocal Fish, Jonathan T. Perelmuter

Dissertations, Theses, and Capstone Projects

The neuromodulator dopamine is considered essential for coordinating the internal motivational state of an organism with appropriate behavioral responses to stimuli in the external environment. This could be accomplished by modifying the function of neural circuits involved in sensory processing such that they are “tuned in” and optimally sensitive to important stimuli during critical time windows. While dopamine modulation of auditory processing has been studied in the central nervous system, neuromodulation can also occur outside the brain, in the inner ear. The majority of investigations of dopamine in the ear are conducted using rodents and focus on its role in …

Hyaluronan At The Brain-Environment Interface, Donald M. Thevalingam

Dissertations, Theses, and Capstone Projects

Hyaluronan (HA; Hyaluronic Acid), a primary scaffolding component of the brain extracellular matrix, serves as an integral structural component to the brain extracellular space (ECS). The fossorial African naked mole-rat (Heterocephalus glaber; NM-R), a mammal which lives in a low-oxygen environment and is capable of tolerating hypoxia and hypercapnia, has been shown to synthesize and sustain a unique high-molecular-mass variant of hyaluronan macromolecule (HMM-HA). This body of work highlights HA’s role in mediating the interplay between brain ECM composition, ECS structure, and cell viability.

Here we employ the NM-R as a unique animal model to observe the role of the …