Life Sciences Commons^™

African Land Mammal Ages, John Van Couvering, Eric Delson

Publications and Research

We define 17 African land mammal ages, or AFLMAs, covering the Cenozoic record of the Afro-arabian continent, the planet’s second largest land mass. While fossiliferous deposits are absent on the eroded plateau of the continent’s interior, almost 800 fossil genera from over 350 locations have now been identified in coastal deposits, karst caves, and in the Neogene rift valleys. Given a well-developed geochronologic framework, together with continuing revision to the fossil record—both stimulated by the story of human evolution in Africa—and also to compensate for the variation in fossil ecosystems across such great distances, the AFLMAs are biochronological units defined …

Exploring Behavioral Flexibility, Problem-Solving, And Innovation In Captive Asian Elephants (Elephas Maximus), Amanda Puitiza

Theses and Dissertations

Asian elephants encounter and adapt to changing environments by problem-solving and innovating. In this study, we assessed behavioral measures, such as persistence and motivation, to determine potential predictors of problem-solving success. This is the first examination of problem-solving in elephants with a multi-solution puzzle box.

Variation In Personality Among Semi-Wild Myanmar Timber Elephants, Sateesh Venkatesh

Theses and Dissertations

This study examines two personality traits: exploration and neophobia, which could influence human-elephant conflicts. Thirty-one semi-wild elephants were tested over two trials using a custom novel puzzle tube containing three tasks and three rewards. Our studies show that elephants do vary significantly between individuals in both exploration and neophobia.

A Crisis Of Kelp, Rachel L. Sherman

Capstones

Along with insects and lab-grown meat, for years seaweed has been lauded as a sustainable “food of the future” by the U.N. Food and Agricultural Organization. As the world increasingly turns to alternative foods in pursuit of a healthier Earth, seaweed has all the makings of an ecological savior. It’s plentiful — seaweeds and ocean algae make up roughly nine tenths of all the plant life on Earth — it’s cheap to harvest and get to market, packed with nutrition, and keeps oceans clean, absorbing more carbon dioxide and releasing more oxygen than the world’s rainforests.

But outside of Japanese …

Bioscience: How One Industry Won The Pandemic And Will Change Us All, Sonya Swink

Capstones

A video and print capstone about the next great generation of biological sciences as a private industry since 2020. It encompasses the pandemic as the boost the industry needed, discussion of science’s bad reputation and the potential benefits, especially for new workspaces and real estate investors. Colorado is a focus as a burgeoning market. The news value of this story as a primer is how this will be both a beneficial industry and one that must be held to account if it becomes too monopolistic. Comparisons are from the viewpoint that bioscience is like the next Silicon Valley, but statements …

Enzymatic Analysis Of Yeast Cell Wall-Resident Gapdh And Its Secretion, Michael J. Cohen, Brianne Philippe, Peter N. Lipke

Publications and Research

In yeast, many proteins are found in both the cytoplasmic and extracellu- lar compartments, and consequently it can be difficult to distinguish nonconventional secretion from cellular leakage. Therefore, we monitored the extracellular glyceralde- hyde-3-phosphate dehydrogenase (GAPDH) activity of intact cells as a specific marker for nonconventional secretion. Extracellular GAPDH activity was proportional to the number of cells assayed, increased with incubation time, and was dependent on added substrates. Preincubation of intact cells with 100mM dithiothreitol increased the reac- tion rate, consistent with increased access of the enzyme after reduction of cell wall di- sulfide cross-links. Such treatment did not increase …

Extending Import Detection Algorithms For Concept Import From Two To Three Biomedical Terminologies, Vipina K. Keloth, James Geller, Yan Chen, Julia Xu

Publications and Research

Background: While enrichment of terminologies can be achieved in different ways, filling gaps in the IS-A hierarchy backbone of a terminology appears especially promising. To avoid difficult manual inspection, we started a research program in 2014, investigating terminology densities, where the comparison of terminologies leads to the algorithmic discovery of potentially missing concepts in a target terminology. While candidate concepts have to be approved for import by an expert, the human effort is greatly reduced by algorithmic generation of candidates. In previous studies, a single source terminology was used with one target terminology.

Methods: In this paper, we are extending …

Missing Lateral Relationships In Top‑Level Concepts Of An Ontology, Ling Zheng, Yan Chen, Hua Min, P. Lloyd Hildebrand, Hao Liu, Michael Halper, James Geller, Sherri De Coronado, Yehoshua Perl

Publications and Research

Background: Ontologies house various kinds of domain knowledge in formal structures, primarily in the form of concepts and the associative relationships between them. Ontologies have become integral components of many health information processing environments. Hence, quality assurance of the conceptual content of any ontology is critical. Relationships are foundational to the definition of concepts. Missing relationship errors (i.e., unintended omissions of important definitional relationships) can have a deleterious effect on the quality of an ontology. An abstraction network is a structure that overlays an ontology and provides an alternate, summarization view of its contents. One kind of abstraction network is …

Outlier Concepts Auditing Methodology For A Large Family Of Biomedical Ontologies, Ling Zheng, Hua Min, Yan Chen, Vipina Keloth, James Geller, Yehoshua Perl, George Hripcsak

Publications and Research

Background: Summarization networks are compact summaries of ontologies. The “Big Picture” view offered by summarization networks enables to identify sets of concepts that are more likely to have errors than control concepts. For ontologies that have outgoing lateral relationships, we have developed the "partial-area taxonomy" summarization network. Prior research has identified one kind of outlier concepts, concepts of small partials-areas within partial-area taxonomies. Previously we have shown that the small partial-area technique works successfully for four ontologies (or their hierarchies).

Methods: To improve the Quality Assurance (QA) scalability, a family-based QA framework, where one QA technique is potentially applicable to …

Pandemic Vibrio Cholerae Shuts Down Site-Specific Recombination To Retain An Interbacterial Defence Mechanism, Francis J. Santoriello, Lina Michel, Daniel Unterweger, Stefan Pukatzki

Publications and Research

Vibrio cholerae is an aquatic microbe that can be divided into three subtypes: harmless environmental strains, localised pathogenic strains, and pandemic strains causing global cholera outbreaks. Each type has a contact-dependent type VI secretion system (T6SS) that kills neighbouring competitors by translocating unique toxic effector proteins. Pandemic isolates possess identical effectors, indicating that T6SS effectors may affect pandemicity. Here, we show that one of the T6SS gene clusters (Aux3) exists in two states: a mobile, prophage-like element in a small subset of environmental strains, and a truncated Aux3 unique to and conserved in pandemic isolates. Environmental Aux3 can be readily …

Data Analysis And Visualizations Of Drosophila Behavioral Phases, Xiaona Zhou

Publications and Research

We analyze drosophila behavioral data from the neuroscience labs of Professor Maria de la Paz Fernandez, Barnard College of Columbia University, and Professor Orie Shafer, the Neuroscience Initiative of the CUNY Advanced Science Research Center. The main goal of this project is to create algorithms for analyzing and visualizing the average activity of drosophila across a specified number of days and across all live flies and use this analysis to calibrate a smoothing filter to be applied to the raw fly activity so that the drosophila behavioral phases can be computed and visualized. We also investigate how to compute and …

Unconventional Constituents And Shared Molecular Architecture Of The Melanized Cell Wall Of C. Neoformans And Spore Wall Of S. Cerevisiae, Christine Chrissian, Coney Pei-Chin Lin, Emma Camacho, Arturo Casadevall, Aaron M. Neiman, Ruth E. Stark

Publications and Research

The fungal cell wall serves as the interface between the cell and the environment. Fungal cell walls are composed largely of polysaccharides, primarily glucans and chitin, though in many fungi stress-resistant cell types elaborate additional cell wall structures. Here, we use solid-state nuclear magnetic resonance spectroscopy to compare the architecture of cell wall fractions isolated from Saccharomyces cerevisiae spores and Cryptococcus neoformans melanized cells. The specialized cell walls of these two divergent fungi are highly similar in composition. Both use chitosan, the deacetylated derivative of chitin, as a scaffold on which a polyaromatic polymer, dityrosine and melanin, respectively, is assembled. …

Network-Level Mechanisms Underlying Effects Of Transcranial Direct Current Stimulation (Tdcs) On Visuomotor Learning, Pejman Sehatpour, Clément Dondé, Matthew J. Hoptman, Johanna Kreither, Devin Adair, Elisa Dias, Blair Vail, Stephanie Rohrig, Gail Silipo, Javier Lopez-Calderon, Antigona Martinez, Daniel C. Javitt

Publications and Research

Transcranial direct current stimulation (tDCS) is a non-invasive brain stimulation approach in which low level currents are administered over the scalp to influence underlying brain function. Prevailing theories of tDCS focus on modulation of excitation-inhibition balance at the local stimulation location. However, network level effects are reported as well, and appear to depend upon differential underlying mechanisms. Here, we evaluated potential network-level effects of tDCS during the Serial Reaction Time Task (SRTT) using convergent EEG- and fMRI-based connectivity approaches. Motor learning manifested as a significant (p <.0001) shift from slow to fast responses and corresponded to a significant increase in beta-coherence (p <.0001) and fMRI connectivity (p <.01) particularly within the visual-motor pathway. Differential patterns of tDCS effect were observed within different parametric task versions, consistent with network models. Overall, these findings demonstrate objective physiological effects of tDCS at the network level that result in effective behavioral modulation when tDCS parameters are matched to network-level requirements of the underlying task.

Immunohistochemical Localization Of Prolactin Receptor (Prlr) To Hodgkin's And Reed-Sternberg Cells Of Hodgkin's Lymphoma, Rajendra Gharbaran, Onyekwere Onwumere, Naomi Codrington, Latchman Somenarian, Stephen Redenti

Publications and Research

Prolactin receptor (PRLR), a type-1 cytokine receptor, is overexpressed in a number of cancer types. It has attracted much attention for putative pro-oncogenic roles, which however, remains controversial in some malignancies. In this study, we reported the localization of PRLR to the Hodgkin's and Reed-Sternberg (HRS) cells of Hodgkin's lymphoma (HL), a neoplasm of predominantly B cell origin. Immunohistochemistry performed on 5-μm thick FFPE sections revealed expression of PRLR in HRS cells. Cellular immunofluorescence experiments showed that the HL-derived cell lines, Hs445, KMH2 and L428 overexpressed PRLR. The PRLR immunofluorescent signal was depleted after treating the cell lines with 10 …

Applications Of Non-Invasive Neuromodulation For The Management Of Disorders Related To Covid-19, Abrahão Fontes Baptista, Adriana Baltar, Alexandre Hideki Okano, Alexandre Moreira, Ana Carolina Pinheiro Campos, Ana Mércia Fernandes, André Russowsky Brunoni, Bashar W. Badran, Clarice Tanaka, Daniel Ciampi De Andrade, Daniel Gomes Da Silva Machado, Edgard Morya, Eduardo Trujillo, Jaiti K. Swami, Joan A. Camprodon, Katia Monte-Silva, Katia Nunes Sá, Isadora Nunes, Juliana Barbosa Goulardins, Marom Bikson, Pedro Sudbrack-Oliveira, Priscila De Carvalho, Rafael Jardim Duarte-Moreira, Rosana Lima Pagano, Samuel Katsuyuki Shinjo, Yossi Zana

Publications and Research

Background: Novel coronavirus disease (COVID-19) morbidity is not restricted to the respiratory system, but also affects the nervous system. Non-invasive neuromodulation may be useful in the treatment of the disorders associated with COVID-19.

Objective: To describe the rationale and empirical basis of the use of non-invasive neuromodulation in the management of patients with COVID-10 and related disorders.

Methods: We summarize COVID-19 pathophysiology with emphasis of direct neuroinvasiveness, neuroimmune response and inflammation, autonomic balance and neurological, musculoskeletal and neuropsychiatric sequela. This supports the development of a framework for advancing applications of non-invasive neuromodulation in the management COVID-19 and related disorders.

Results: …

Multimodal Computational Modeling Of Visual Object Recognition Deficits But Intact Repetition Priming In Schizophrenia, Pejman Sehatpour, Anahita Bassir Nia, Devin Adair, Zhishun Wang, Heloise M. Debaun, Gail Silipo, Antigona Martinez, Daniel C. Javitt

Publications and Research

The term perceptual closure refers to the neural processes responsible for “filling-in” missing information in the visual image under highly adverse viewing conditions such as fog or camouflage. Here we used a closure task that required the participants to identify barely recognizable fragmented line-drawings of common objects. Patients with schizophrenia have been shown to perform poorly on this task. Following priming, controls and importantly patients can complete the line-drawings at greater levels of fragmentation behaviorally, suggesting an improvement in their ability to performthe task. Closure phenomena have been shown to involve a distributed network of cortical regions, notably the lateral …

Update On The Use Of Transcranial Electrical Brain Stimulation To Manage Acute And Chronic Covid-19 Symptoms, Giuseppina Pilloni, Marom Bikson, Bashar W. Badran, Mark S. George, Steven A. Kautz, Alexandre Hideki Okano, Abrahão Fontes Baptista, Leigh E. Charvet

Publications and Research

The coronavirus disease 19 (COVID-19) pandemic has resulted in the urgent need to develop and deploy treatment approaches that can minimize mortality and morbidity. As infection, resulting illness, and the often prolonged recovery period continue to be characterized, therapeutic roles for transcranial electrical stimulation (tES) have emerged as promising non-pharmacological interventions. tES techniques have established therapeutic potential for managing a range of conditions relevant to COVID-19 illness and recovery, and may further be relevant for the general management of increased mental health problems during this time. Furthermore, these tES techniques can be inexpensive, portable, and allow for trained self-administration. Here, …

A Multi‑Disciplinary Comparison Of Great Ape Gut Microbiota In A Central African Forest And European Zoo, Victor Narat, Katherine R. Amato, Noémie Ranger, Maud Salmona, Séverine Mercier‑Delarue, Stephanie Rupp, Philippe Ambata, Richard Njouom, François Simon, Tamara Giles‑Vernick, Jérôme Legoff

Publications and Research

Comparisons of mammalian gut microbiota across different environmental conditions shed light on the diversity and composition of gut bacteriome and suggest consequences for human and animal health. Gut bacteriome comparisons across different environments diverge in their results, showing no generalizable patterns linking habitat and dietary degradation with bacterial diversity. The challenge in drawing general conclusions from such studies lies in the broad terms describing diverse habitats (“wild”, “captive”, “pristine”). We conducted 16S ribosomal RNA gene sequencing to characterize intestinal microbiota of free-ranging sympatric chimpanzees and gorillas in southeastern Cameroon and sympatric chimpanzees and gorillas in a European zoo. We conducted …

Hypogean Communities As Cybernetic Systems: Implications For The Evolution Of Cave Biotas, Aldemaro Romero Jr.

Publications and Research

Ramón Margalef proposed in 1968 that ecosystems could be better understood if they were viewed as cybernetic systems. I tested this hypothesis in the case of hypogean ecosystems using available pieces of evidence. I looked on how information on feedbacks, stability, succession, organization, diversity, and energy flows in the hypogean environment fit the cybernetics hypothesis. The results were that there are convincing arguments that the application of the concept of cybernetics in biospeleology can be beneficial to broadening our understanding of cave biota in terms of their structure. I also make the case that this approach can provide more clarity …

A Putative Chordate Luciferase From A Cosmopolitan Tunicate Indicates Convergent Bioluminescence Evolution Across Phyla, Michael Tessler, Jean P. Gaffney, Anderson G. Oliveira, Andrew Guarnaccia, Krista C. Dobi, Nehaben A. Gujarati, Moira Galbraith, Jeremy D. Mirza, John S. Sparks, Vincent A. Pieribone, Robert J. Wood, David F. Gruber

Publications and Research

Pyrosomes are tunicates in the phylum Chordata, which also contains vertebrates. Their gigantic blooms play important ecological and biogeochemical roles in oceans. Pyrosoma, meaning “firebody”, derives from their brilliant bioluminescence. The biochemistry of this light production is unknown, but has been hypothesized to be bacterial in origin. We found that mixing coelenterazine—a eukaryote-specific luciferin—with Pyrosoma atlanticum homogenate produced light. To identify the bioluminescent machinery, we sequenced P. atlanticum transcriptomes and found a sequence match to a cnidarian luciferase (RLuc). We expressed this novel luciferase (PyroLuc) and, combined with coelenterazine, it produced light. A similar gene was recently predicted from a …

Genomic Adaptations To Salinity Resist Gene Flow In The Evolution Of Floridian Watersnakes, Rhett M. Rautsaw, Tristan D. Schramer, Rachel Acuña, Lindsay N. Arick, Mark Dimeo, Kathryn P. Mercier, Michael Schrum, Andrew J. Mason, Mark J. Margres, Jason L. Strickland, Christopher L. Parkinson

Publications and Research

The migration-selection balance often governs the evolution of lineages, and speciation with gene flow is now considered common across the tree of life. Ecological speciation is a process that can facilitate divergence despite gene flow due to strong selective pressures caused by ecological differences; however, the exact traits under selection are often unknown. The transition from freshwater to saltwater habitats provides strong selection targeting traits with osmoregulatory function. Several lineages of North American watersnakes (Nerodia spp.) are known to occur in saltwater habitat and represent a useful system for studying speciation by providing an opportunity to investigate gene flow …

Not Withering On The Evolutionary Vine: Systematic Revision Of The Brown Vine Snake (Reptilia: Squamata: Oxybelis) From Its Northern Distribution, Robert C. Jadin, Christopher Blair, Sarah A. Orlofske, Michael J. Jowers, Gilson A. Rivas, Laurie J. Vitt, Julie M. Ray, Eric N. Smith, John C. Murphy

Publications and Research

The genus Oxybelis currently is composed of four taxa despite numerous studies suggesting and describing multiple taxa within the O. aeneus complex. Here, we utilize a multilocus molecular dataset (i.e. cyt b, ND4, 12S, 16S, cmos, PRLR, 3663 bp) to conduct phylogenetic analyses to assess the evolutionary history of Oxybelis. Our molecular analyses find three major lineages of Oxybelis (i.e. O. aeneus complex, O. brevirostris, O. fulgidus complex) with a sister relationship between O. brevirostris and the O. aeneus complex to the exclusion of the O. fulgidus complex. More specifically, O. aeneus appears to harbor at least …

Visual Corticocortical Inputs To Ferret Area 18, Reem Khalil, Moody Roberne Jensy Saint Louis, Shaima Alsuwaidi, Jonathan B. Levitt

Publications and Research

Visual cortical areas in the adult mammalian brain are linked by a network of interareal feedforward and feedback circuits. We investigated the topography of feedback projections to ferret (Mustela putorius furo) area 18 from extrastriate areas 19, 21, and Ssy. Our objective was to characterize the anatomical organization of the extrastriate feedback pool to area 18. We also wished to determine if feedback projections to area 18 share similar features as feedback projections to area 17. We injected the tracer cholera toxin B subunit (CTb) into area 18 of adult ferrets to visualize the distribution and pattern of retrogradely labeled …

Cryo‑Electron Microscopy Structure Of The 70s Ribosome From Enterococcus Faecalis, Eileen L. Murphy, Kavindra V. Singh, Bryant Avila, Torsten Kleffmann, Steven T. Gregory, Barbara E. Murray, Kurt L. Krause, Reza Khayat, Gerwald Jogl

Publications and Research

Enterococcus faecalis is a gram-positive organism responsible for serious infections in humans, but as with many bacterial pathogens, resistance has rendered a number of commonly used antibiotics ineffective. Here, we report the cryo-EM structure of the E. faecalis 70S ribosome to a global resolution of 2.8 Å. Structural differences are clustered in peripheral and solvent exposed regions when compared with Escherichia coli, whereas functional centres, including antibiotic binding sites, are similar to other bacterial ribosomes. Comparison of intersubunit conformations among five classes obtained after three-dimensional classification identifies several rotated states. Large ribosomal subunit protein bL31, which forms intersubunit bridges to …

3,7-Dihydroxytropolones Inhibit Initiation Of Hepatitis B Virus Minus-Strand Dna Synthesis, Ellen Bak, Jennifer T. Miller, Andrea Noronha, John Tavis, Emilio Gallicchio, Ryan P. Murelli, Stuart F. J. Le Grice

Publications and Research

Initiation of protein-primed (-) strand DNA synthesis in hepatitis B virus (HBV) requires interaction of the viral reverse transcriptase with epsilon (ε), a cis-acting regulatory signal located at the 5’ terminus of pre-genomic RNA (pgRNA), and several host-encoded chaperone proteins. Binding of the viral polymerase (P protein) to ε is necessary for pgRNA encapsidation and synthesis of a short primer covalently attached to its terminal domain. Although we identified small molecules that recognize HBV ε RNA, these failed to inhibit protein-primed DNA synthesis. However, since initiation of HBV (-) strand DNA synthesis occurs within a complex of viral and host …

Retrieving Functional Pathways Of Biomolecules From Single-Particle Snapshots, Ali Dashti, Ghoncheh Mashayekhi, Mrinal Shekhar, Danya Ben Hail, Salah Salah, Peter Schwander, Amedee Des Georges, Abhishek Singharoy, Joachim Frank, Abbas Ourmazd

Publications and Research

A primary reason for the intense interest in structural biology is the fact that knowledge of structure can elucidate macromolecular functions in living organisms. Sustained effort has resulted in an impressive arsenal of tools for determining the static structures. But under physiological conditions, macromolecules undergo continuous conformational changes, a subset of which are functionally important. Techniques for capturing the continuous conformational changes underlying function are essential for further progress. Here, we present chemically-detailed conformational movies of biological function, extracted data-analytically from experimental single-particle cryo-electron microscopy (cryo-EM) snapshots of ryanodine receptor type 1 (RyR1), a calcium-activated calcium channel engaged in the …

A Paradigm For Peptide Hormone-Gpcr Analyses, Fred Naider, Jeffrey M. Becker

Publications and Research

Work from our laboratories over the last 35 years that has focused on Ste2p, a G protein-coupled receptor (GPCR), and its tridecapeptide ligand α-factor is reviewed. Our work utilized the yeast Saccharomyces cerevisiae as a model system for understanding peptide-GPCR interactions. It explored the structure and function of synthetic α-factor analogs and biosynthetic receptor domains, as well as designed mutations of Ste2p. The results and conclusions are described using the nuclear magnetic resonance interrogation of synthetic Ste2p transmembrane domains (TMs), the fluorescence interrogation of agonist and antagonist binding, the biochemical crosslinking of peptide analogs to Ste2p, and the phenotypes of …

The Cognitive Thalamus: Source Analysis Of Scene Working Memory Delay Activity, Bernard A. Gomes

Dissertations, Theses, and Capstone Projects

Working Memory represents a limited-capacity store for maintaining information and manipulating the store's contents over a short period for the guidance of goal-directed behavior. Working Memory is an essential component of executive functions that are intricately associated with the prefrontal cortex (PFC). The PFC has been implicated in maintaining task-related information online for brief periods in the absence of relevant information. This active maintenance phase is called the delay period that occurs between encoding and retrieval of the stimulus. Previous studies have attempted to understand the relationship between working memory and the PFC, especially during the delay or maintenance phase …

Luteolin Induces Cytotoxicity In Mix Cellularity Classical Hodgkin's Lymphoma Via Caspase Activated-Cell Death, Rajendra Gharbaran, Enyuan Shang, Onyekwere Onwumere, Naomi Codrington, Evangelina Dankwa Sarpong, Stephen M. Redenti

Publications and Research

Background/aim: We investigated the effects of luteolin (LUT) on classical Hodgkin's lymphoma (cHL), since such studies in malignant lymphomas are lacking.

Materials and methods: Effect of LUT on cell growth was assessed with water-soluble tetrazolium 1 (WST-1) cell proliferation assay and automated hemocytometry on trypan blue-exclusion assay. Cell death was investigated with acridine orange/ethidium bromide live-dead assay, propidium iodide (PI) flow cytometry, and Annexin-V-PI microscopy. Caspase activation was studied using CellEvent Caspase-3/7 Green detection reagent. High resolution immunofluorescence microscopy was used to detect cleaved-PARP-1.

Results: LUT induced a dose-dependent decrease in the growth of KMH2 and L428 cells, cellular models …

Dietary Development And Nutritional Ontogeny In Gorilla Beringei : A Multi-Layered, -Omics Approach, Emma C. Cancelliere

Dissertations, Theses, and Capstone Projects

In species who consume folivorous diets, immature individuals must contend with the challenges of extracting nutrients from fibrous foods before dietary adaptations and strategies are fully developed. Additionally, immatures have distinct nutritional needs to support their stage-specific metabolic and biophysiological requirements. To meet these stage-specific needs, while constrained by underdeveloped feeding strategies and digestive capacities, immatures may adopt distinct diets better suited to their specific developmental context. However, where dietary modification is constrained by low dietary diversity or landscape homogeneity, it is unclear how immature individuals compensate through alternative strategies. In turn, little is known about the nutritional and life …