Digital Commons Network^™

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 …

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 …

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 …

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, …

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 …

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 …

Deep Machine Learning Techniques For The Detection And Classification Of Sperm Whale Bioacoustics, Peter C. Bermant, Michael M. Bronstein, Robert J. Wood, Shane Gero, David F. Gruber

Publications and Research

We implemented Machine Learning (ML) techniques to advance the study of sperm whale (Physeter macrocephalus) bioacoustics. This entailed employing Convolutional Neural Networks (CNNs) to construct an echolocation click detector designed to classify spectrograms generated from sperm whale acoustic data according to the presence or absence of a click. The click detector achieved 99.5% accuracy in classifying 650 spectrograms. The successful application of CNNs to clicks reveals the potential of future studies to train CNN-based architectures to extract finer-scale details from cetacean spectrograms. Long short-term memory and gated recurrent unit recurrent neural networks were trained to perform classification tasks, including (1) …

Activation Of Lxrβ Inhibits Tumor Respiration And Is Synthetically Lethal With Bcl-Xl Inhibition, Trang Thi Thu Nguyen, Chiaki Tsuge Ishida, Enyuan Shang, Chang Shu, Consuelo Torrini, Yiru Zhang, Elena Bianchetti, Maria J. Sanchez-Quintero, Giulio Kleiner, Catarina M. Quinzii, Mike-Andrew Westhoff, Georg Karpel-Massler, Peter Canoll, Markus D. Siegelin

Publications and Research

Liver-X-receptor (LXR) agonists are known to bear anti-tumor activity. However, their efficacy is limited and additional insights regarding the underlying mechanism are necessary. By performing transcriptome analysis coupled with global polar metabolite screening, we show that LXR agonists, LXR623 and GW3965, enhance synergistically the anti-proliferative effect of BH3 mimetics in solid tumor malignancies, which is predominantly mediated by cell death with features of apoptosis and is rescued by exogenous cholesterol. Extracellular flux analysis and carbon tracing experiments (U-¹³C-glucose and U-¹³C-glutamine) reveal that within 5 h, activation of LXRβ results in reprogramming of tumor cell metabolism, leading …

Inhibition Of Mitochondrial Permeability Transition By Deletion Of The Ant Family And Cypd, Jason Karch, Michael J. Bround, Hadi Khalil, Michelle A. Sargent, Nadina Latchman, Naohiro Terada, Pablo M. Peixoto, Jeffery D. Molkentin

Publications and Research

The mitochondrial permeability transition pore (MPTP) has resisted molecular identification. The original model of the MPTP that proposed the adenine nucleotide translocator (ANT) as the inner membrane pore-forming component was challenged when mitochondria from Ant1/2 double null mouse liver still had MPTP activity. Because mice express three Ant genes, we reinvestigated whether the ANTs comprise the MPTP. Liver mitochondria from Ant1, Ant2, and Ant4 deficient mice were highly refractory to Ca2+-induced MPTP formation, and when also given cyclosporine A (CsA), the MPTP was completely inhibited. Moreover, liver mitochondria from mice with quadruple deletion of Ant1, Ant2, Ant4, and Ppif (cyclophilin …

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

Open Educational Resources

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

In addition to the full text of the …

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

Open Educational Resources

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

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

Phylogenetic Trees And Networks Can Serve As Powerful And Complementary Approaches For Analysis Of Genomic Data, Christopher Blair, Cécile Ané

Publications and Research

Genomic data have had a profound impact on nearly every biological discipline. In systematics and phylogenetics, the thousands of loci that are now being sequenced can be analyzed under the multispecies coalescent model (MSC) to explicitly account for gene tree discordance due to incomplete lineage sorting (ILS). However, the MSC assumes no gene flow post divergence, calling for additional methods that can accommodate this limitation. Explicit phylogenetic network methods have emerged, which can simultaneously account for ILS and gene flow by representing evolutionary history as a directed acyclic graph. In this point-of-view we highlight some of the strengths and limitations …

Evaluation Of The Uncertainty In Satellite-Based Crop State Variable Retrievals Due To Site And Growth Stage Specific Factors And Their Potential In Coupling With Crop Growth Models, Nathaniel Levitan, Yanghui Kang, Mutlu Özdogan, Vincenzo Magliulo, Paulo Castillo, Fred Moshary, Barry Gross

Publications and Research

Coupling crop growth models and remote sensing provides the potential to improve our understanding of the genotype x environment x management (G X E X M) variability of crop growth on a global scale. Unfortunately, the uncertainty in the relationship between the satellite measurements and the crop state variables across different sites and growth stages makes it diffcult to perform the coupling. In this study, we evaluate the effects of this uncertainty with MODIS data at the Mead, Nebraska Ameriflux sites (US-Ne1, US-Ne2, and US-Ne3) and accurate, collocated Hybrid-Maize (HM) simulations of leaf area index (LAI) and canopy light use …

A Comparison Of Individual Learning And Social Learning In Zebrafish Through An Ethorobotics Approach, Yanpeng Yang, Romain J. G. Clément, Stefano Ghirlanda, Maurizio Porfiri

Publications and Research

Social learning is ubiquitous across the animal kingdom, where animals learn from group members about predators, foraging strategies, and so on. Despite its prevalence and adaptive benefits, our understanding of social learning is far from complete. Here, we study observational learning in zebrafish, a popular animal model in neuroscience. Toward fine control of experimental variables and high consistency across trials, we developed a novel robotics-based experimental test paradigm, in which a robotic replica demonstrated to live subjects the correct door to join a group of conspecifics. We performed two experimental conditions. In the individual training condition, subjects learned the correct …

Bioluminescent Flashes Drive Nighttime Schooling Behavior And Synchronized Swimming Dynamics In Flashlight Fish, David F. Gruber, Brennan T. Phillips, Rory O'Brien, Vivek Boominathan, Ashok Veeraraghavan, Ganesh Vasan, Peter O'Brien, Vincent A. Pieribone, John S. Sparks

Publications and Research

Schooling fishes, like flocking birds and swarming insects, display remarkable behavioral coordination. While over 25% of fish species exhibit schooling behavior, nighttime schooling has rarely been observed or reported. This is due to vision being the primary modality for schooling, which is corroborated by the fact that most fish schools disperse at critically low light levels. Here we report on a large aggregation of the bioluminescent flashlight fish Anomalops katoptron that exhibited nighttime schooling behavior during multiple moon phases, including the new moon. Data were recorded with a suite of low-light imaging devices, including a high-speed, high-resolution scientific complementary metal-oxide-semiconductor …

Writing For Sciences, Michael Coppola

Open Educational Resources

No abstract provided.

Validity Evaluation Of The Genetics And Genomics In Nursing Practice Survey, Alexandra Plavskin, William E. Samuels, Kathleen A. Calzone

Publications and Research

Aim: To psychometrically test the Genetics and Genomics Nursing Practice Survey (GGNPS) for evidence of content, face and construct validity.

Design:This study was a secondary data analysis.

Method: Data collected from the Method for Introducing a New Competency into Nursing Practice (MINC) study were used to evaluate the GGNPS for evidence of construct validity via structural equation modelling and confirmatory factor analysis. Face validity was evaluated via feedback from practicing RNs without specific experience with or knowledge of genetics/genomics. Content validity was evaluated via content expert feedback and assessment of a content validity index.

Results: The thresholds …

Endothelial Iqgap1 Regulates Leukocyte Transmigration By Directing The Lbrc To The Site Of Diapedesis, David P. Sullivan, Prarthana J. Dalal, Fanny Jaulin, David B. Sacks, Geri Kreitzer, William A. Muller

Publications and Research

Transendothelial migration (TEM) of leukocytes across the endothelium is critical for inflammation. In the endothelium, TEM requires the coordination of membrane movements and cytoskeletal interactions, including, prominently, recruitment of the lateral border recycling compartment (LBRC). The scaffold protein IQGAP1 was recently identified in a screen for LBRC-interacting proteins. Knockdown of endothelial IQGAP1 disrupted the directed movement of the LBRC and substantially reduced leukocyte TEM. Expression of truncated IQGAP1 constructs demonstrated that the calponin homology domain is required for IQGAP1 localization to endothelial borders and that the IQ domain, on the same IQGAP1 polypeptide, is required for its function in TEM. …