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Biomechanical Performances Of Networked Polyethylene Glycol Diacrylate: Effect Of Photoinitiator Concentration, Temperature, And Incubation Time, Morshed Khandaker, Albert Orock, Stefano Tarantini, Jeremiah White, Ozlem Yasar

Publications and Research

Nutrient conduit networks can be introduced within the Polyethylene Glycol Diacrylate (PEGDA) tissue construct to enable cells to survive in the scaffold. Nutrient conduit networks can be created on PEGDA by macrochannel to nanochannel fabrication techniques. Such networks can influence the mechanical and cell activities of PEGDA scaffold. There is no study conducted to evaluate the effect of nutrient conduit networks on the maximum tensile stress and cell activities of the tissue scaffold.The study aimed to explore the influence of the network architecture on the maximum tensile stress of PEGDA scaffold and compared with the nonnetworked PEGDA scaffold. Our study …

Two Distinct Modes Of Metal Ion Binding In The Nuclease Active Site Of A Viral Dna-Packaging Terminase: Insight Into The Two-Metal-Ion Catalytic Mechanism, Haiyan Zhao, Zihan Lin, Anna Y. Lynn, Brittany Varnado, John A. Beutler, Ryan P. Murelli, Stuart F.J. Le Grice, Liang Tang

Publications and Research

Many dsDNA viruses encode DNA-packaging terminases, each containing a nuclease domain that resolves concatemeric DNA into genome-length units. Terminase nucleases resemble the RNase H-superfamily nucleotidyltransferases in folds, and share a two-metal-ion catalytic mechanism. Here we show that residue K428 of a bacteriophage terminase gp2 nuclease domain mediates binding of the metal cofactor Mg2+. A K428A mutation allows visualization, at high resolution, of a metal ion binding mode with a coupled-octahedral configuration at the active site, exhibiting an unusually short metal-metal distance of 2.42 A° . Such proximity of the two metal ions may play an essential role in catalysis by …

Geospatial Resolution Of Human And Bacterial Diversity With City-Scale Metagenomics, Ebrahim Afshinnekoo, Cem Meydan, Shanin Chowdhury, Dyala Jaroudi, Collin Boyer, Nick Bernstein, Julia M. Maritz, Darryl Reeves, Jorge Gandara, Sagar Chhangawala, Sofia Ahsanuddin, Amber Simmons, Timothy Nessel, Bharathi Sundaresh, Elizabeth Pereira, Ellen Jorgensen, Sergios-Orestis Kolokotronis, Nell Kirchberger, Isaac Garcia, David Gandara, Sean Dhanraj, Tanzina Nawrin, Yogesh Saletore, Noah Alexander, Priyanka Vijay, Elizabeth M. Hénaff, Paul Zumbo, Michael Walsh, Gregory D. O'Mullan, Scott Tighe, Joel T. Dudley, Anya Dunaif, Sean Ennis, Eoghan O'Halloran, Tiago R. Magalhaes, Braden Boone, Angela L. Jones, Theodore R. Muth, Katie Schneider Paolantonio, Elizabeth Alter, Eric E. Schadt, Jeanne Garbarino, Robert J. Prill, Jane M. Carlton, Shawn Levy, Christopher E. Mason

Publications and Research

The panoply of microorganisms and other species present in our environment influence human health and disease, especially in cities, but have not been profiled with metagenomics at a city-wide scale. We sequenced DNA from surfaces across the entire New York City (NYC) subway system, the Gowanus Canal, and public parks. Nearly half of the DNA (48%) does not match any known organism; identified organisms spanned 1,688 bacterial, viral, archaeal, and eukaryotic taxa, which were enriched for harmless genera associated with skin (e.g., Acinetobacter). Predicted ancestry of human DNA left on subway surfaces can recapitulate U.S. Census demographic data, and bacterial …

Lesion-Specific Immune Response In Granulomas Of Patients With Pulmonary Tuberculosis: A Pilot Study, Selvakumar Subbian, Liana Tsenova, Mi-Jeong Kim, Helen C. Wainwright, Annalie Visser, Nirmalya Bandyopadhyay, Joel S. Bader, Petros C. Karakousis, Gabriele B. Murrmann, Linda-Gail Bekker, David G. Russell, Gilla Kaplan

Publications and Research

The formation and maintenance of granulomas is central to the host response to Mycobacterium tuberculosis (Mtb) infection. It is widely accepted that the lungs of patients with tuberculosis (TB) usually contain multiple infection foci, and that the granulomas evolve and differentiate independently, resulting in considerable heterogeneity. Although gene expression profiles of human blood cells have been proposed as biomarkers of Mtb infection and/or active disease, the immune profiles of discrete lesion types has not been studied extensively. Using histology, immunopathology and genome-wide transcriptome analysis, we explored the immunological profile of human lung TB granulomas. We show that although the different …

Inhibition Of Cell Differentiation In Bacillus Subtilis By Pseudomonas Protegens, Matthew J. Powers, Edgardo Sanabria-Valentín, Albert A. Bowers, Elizabeth A. Shanka

Publications and Research

Interspecies interactions have been described for numerous bacterial systems, leading to the identification of chemical compounds that impact bacterial physiology and differentiation for processes such as biofilm formation. Here, we identified soil microbes that inhibit biofilm formation and sporulation in the common soil bacterium Bacillus subtilis. We did so by creating a reporter strain that fluoresces when the transcription of a biofilm-specific gene is repressed. Using this reporter in a coculture screen, we identified Pseudomonas putida and Pseudomonas protegens as bacteria that secrete compounds that inhibit biofilm gene expression in B. subtilis. The active compound produced by P. protegens was …

Use Of Rna Sequencing To Evaluate Rheumatic Disease Patients, Eugenia Giannopoulou, Olivier Elemento, Lionel B. Ivashkiv

Publications and Research

Studying the factors that control gene expression is of substantial importance for rheumatic diseases with poorly understood etiopathogenesis. In the past, gene expression microarrays have been used to measure transcript abundance on a genome-wide scale in a particular cell, tissue or organ. Microarray analysis has led to gene signatures that differentiate rheumatic diseases, and stages of a disease, as well as response to treatments. Nowadays, however, with the advent of next-generation sequencing methods, massive parallel sequencing of RNA tends to be the technology of choice for gene expression profiling, due to several advantages over microarrays, as well as for the …

Molecular Diversity And Gene Evolution Of The Venom Arsenal Of Terebridae Predatory Marine Snails, Juliette Gorson, Girish Ramrattan, Aida Verdes, Elizabeth M. Wright, Yuri Kantor, Ramakrishnan Rajaram Srinivasan, Raj Musunuri, Daniel Packer, Gabriel Albano, Wei-Gang Qiu, Mandë Holford

Publications and Research

Venom peptides from predatory organisms are a resource for investigating evolutionary processes such as adaptive radiation or diversification, and exemplify promising targets for biomedical drug development. Terebridae are an understudied lineage of conoidean snails,which also includes cone snails and turrids. Characterization of cone snail venompeptides, conotoxins, has revealed a cocktail of bioactive compounds used to investigate physiological cellular function, predator-prey interactions, and to develop novel therapeutics. However, venom diversity of other conoidean snails remains poorly understood. The present research applies a venomics approach to characterize novel terebrid venom peptides, teretoxins, from the venom gland transcriptomes of Triplostephanus anilis and Terebra …

Phylogenomic Identification Of Regulatory Sequences In Bacteria: An Analysis Of Statistical Power And An Application To Borrelia Burgdorferi Sensu Lato, Che I. Martin, Tika Y. Sukarna, Saymon Akther, Girish Ramrattan, Pedro Pagan, Lia Di, Emmanuel F. Mongodin, Claire M. Fraser, Steven E. Schutzer, Benjamin J. Luft, Sherwood R. Casjens, Wei-Gang Qiu

Publications and Research

Phylogenomic footprinting is an approach for ab initio identification of genome-wide regulatory elements in bacterial species based on sequence conservation. The statistical power of the phylogenomic approach depends on the degree of sequence conservation, the length of regulatory elements, and the level of phylogenetic divergence among genomes. Building on an earlier model, we propose a binomial model that uses synonymous tree lengths as neutral expectations for determining the statistical significance of conserved intergenic spacer (IGS) sequences. Simulations show that the binomial model is robust to variations in the value of evolutionary parameters, including base frequencies and the transition-to-transversion ratio. We …

Improved Evidence-Based Genome-Scale Metabolic Models For Maize Leaf, Embryo, And Endosperm, Samuel M. D. Seaver, Louis M. T. Bradbury, Océane Frelin, Raphy Zarecki, Eytan Ruppin, Andrew D. Hanson, Christopher S. Henry

Publications and Research

There is a growing demand for genome-scale metabolic reconstructions for plants, fueled by the need to understand the metabolic basis of crop yield and by progress in genome and transcriptome sequencing. Methods are also required to enable the interpretation of plant transcriptome data to study how cellular metabolic activity varies under different growth conditions or even within different organs, tissues, and developmental stages. Such methods depend extensively on the accuracy with which genes have been mapped to the biochemical reactions in the plant metabolic pathways. Errors in these mappings lead to metabolic reconstructions with an inflated number of reactions and …

Protein Sectors: Statistical Coupling Analysis Versus Conservation, Tiberiu Teşileanu, Lucy J. Colwell, Stanislas Leibler

Publications and Research

Statistical coupling analysis (SCA) is a method for analyzing multiple sequence alignments that was used to identify groups of coevolving residues termed “sectors”. The method applies spectral analysis to a matrix obtained by combining correlation information with sequence conservation. It has been asserted that the protein sectors identified by SCA are functionally significant, with different sectors controlling different biochemical properties of the protein. Here we reconsider the available experimental data and note that it involves almost exclusively proteins with a single sector. We show that in this case sequence conservation is the dominating factor in SCA, and can alone be …

The Regulatory Function Of Sphingosine-1-Phosphate Signaling Axis On Regulatory T Cells In Colorectal Cancer, Andrew V. Nguyen, Yuan-Yuan Wu, Elaine Y. Lin

Publications and Research

In tumors associated with inflammation such as inflammatory bowel disease (IBD) and colorectal cancer (CRC), high numbers of regulatory T cells (Tregs) are associated with both favorable and poor prognoses. The functions of Tregs in CRC remain elusive and have yet to be clearly defined. With new evidence supporting many subsets of Tregs, the research on the development and functions of these cells has begun to come to fruition. The sphingosine 1 phosphate (S1P) pathway was recently reported to regulate the development and function of regulatory T cells. This pathway may shine new light into the pleiotropic nature of these …

Human Anatomy And Physiology I (Laboratory), Cecilia Ortiz

Open Educational Resources

Students will be able to understand and do the following: describe the mechanism by which osmosis and different types of diffusion occur and compare and contrast the effects of hypertonic, isotonic and hypotonic conditions on cells.

Biology: Inquiry-Based Learning Assignment, Richa Gupta

Open Educational Resources

Students perform a literature review on a biology topic, choose 2-3 papers published in scientific journals to discuss in their assignment, provide a final opinion on the topic, and some voluntarily present on their selected topic.

Human Anatomy And Physiology Ii, Jhonny Ordonez

Open Educational Resources

Students will learn and understand the importance of reflexes in human body, understand how the nerve impulse travels through the nerves and how to test a reflex.

High-Throughput Comparison, Functional Annotation, And Metabolic Modeling Of Plant Genomes Using The Plantseed Resource, Samuel M. D. Seaver, Svetlana Gerdes, Océane Frelin, Claudia Lerma-Ortiz, Louis M. T. Bradbury, Rémi Zallot, Ghulam Hasnain, Thomas D. Niehaus, Basma El Yacoubi, Shiran Pasternak, Robert Olson, Gordon Pusch, Ross Overbeek, Valérie De Crécy-Lagarde, Doreen Ware, Andrew D. Hanson, Christopher S. Henry

Publications and Research

There is a growing demand for genome-scale metabolic reconstructions for plants, fueled by the need to understand the metabolic basis of crop yield and by progress in genome and transcriptome sequencing. Methods are also required to enable the interpretation of plant transcriptome data to study how cellular metabolic activity varies under different growth conditions or even within different organs, tissues, and developmental stages. Such methods depend extensively on the accuracy with which genes have been mapped to the biochemical reactions in the plant metabolic pathways. Errors in these mappings lead to metabolic reconstructions with an inflated number of reactions and …

Human Anatomy And Physiology Preparatory Course (1st Edition), Carlos Liachovitzky

Open Educational Resources

The overall purpose of this preparatory course textbook is to help students familiarize with some terms and some basic concepts they will find later in the Human Anatomy and Physiology I course.

The organization and functioning of the human organism generally is discussed in terms of different levels of increasing complexity, from the smallest building blocks to the entire body. This Anatomy and Physiology preparatory course covers the foundations on the chemical level, and a basic introduction to cellular level, organ level, and organ system levels. There is also an introduction to homeostasis at the beginning.

Introduction To Neuroscience, Charles Keller

Open Educational Resources

Working with a partner from the class, students will choose a topic of interest relevant to the field of neuroscience, explore the relevant literature, write a 5-7 page paper on the topic, and present the results of their research to the class in the form of a 5-10 minute oral presentation.