Life Sciences Commons^™

Enabling Precision Medicine Via Standard Communication Of Hts Provenance, Analysis, And Results, Gil Alterovitz, Dennis Dean, Carole Globe, Michael R. Crusoe, Stiam Soiland-Reyes, Amanda Bell, Anais Hayes, Anita Suresh, Anjan Purkkayastha, Charles H. King, Dan Taylor, Elaine Johanson, Elaine E. Thompson, Eric Donaldson, Hiroki Morizono, Hsinyi Tsang, Jeet K. Vora, Jeremy Goecks, Jianchao Yao, Jonas S. Almeida, Jonathon Keeney, Kanakadurga Addepalli, Konstantinos Krampis, Krista M. Smith, Lydia Guo, Mark Walderhaug, Marco Schito, Matthew Ezewudo, Nuria Guimera, Paul Walsh, Robel Kahsay, Srikanth Gottipati, Timothy C. Rodwell, Toby Bloom, Yuching Lai, Vahan Simonyan, Raja Mazumder

Publications and Research

A personalized approach based on a patient's or pathogen’s unique genomic sequence is the foundation of precision medicine. Genomic findings must be robust and reproducible, and experimental data capture should adhere to findable, accessible, interoperable, and reusable (FAIR) guiding principles. Moreover, effective precision medicine requires standardized reporting that extends beyond wet-lab procedures to computational methods. The BioCompute framework (https://w3id.org/biocompute/1.3.0) enables standardized reporting of genomic sequence data provenance, including provenance domain, usability domain, execution domain, verification kit, and error domain. This framework facilitates communication and promotes interoperability. Bioinformatics computation instances that employ the BioCompute framework are easily relayed, repeated …

Investigating The Impact Of Oxidative Stress On Tetrahymena Thermophila Sirtuin,Thd 18, Emmanuel Dubuisson

Publications and Research

Sirtuins are a family of enzymes that fulfill various important biological functions. Investigators have looked for the implication of Sirtuin genes in cell signaling mechanisms, in the formation and silencing of heterochromatin, in the regulation of ion channels, and in the modulation of the cellular redox reactions[2]. Different model organisms have been previously used to conduct these studies; among them, there are yeasts, nematodes, and fruit flies. Each one has made some valuable contribution into the vast body of knowledge related to this field.

However, gaps in the understanding of Sirtuins functions still remain to be filled. In this optic, …

Il-24 Promotes Apoptosis Through Camp-Dependent Pka Pathways In Human Breast Cancer Cells, Leah Persaud, Jason Mighty, Xuelin Zhong, Ashleigh Francis, Marifer Mendez, Hilal Muharam, Stephen M. Redenti, Dibash Das, Bertal Huseyin Aktas, Moira Sauane

Publications and Research

Interleukin 24 (IL-24) is a tumor-suppressing protein, which inhibits angiogenesis and induces cancer cell-specific apoptosis. We have shown that IL-24 regulates apoptosis through phosphorylated eukaryotic initiation factor 2 alpha (eIF2α) during endoplasmic reticulum (ER) stress in cancer. Although multiple stresses converge on eIF2α phosphorylation, the cellular outcome is not always the same. In particular, ER stress-induced apoptosis is primarily regulated through the extent of eIF2α phosphorylation and activating transcription factor 4 (ATF4) action. Our studies show for the first time that cyclic adenosine monophosphate (cAMP)-dependent protein kinase A (PKA) activation is required for IL-24-induced cell death in a variety of …

Maternal Choline And Betaine Supplementation Modifies The Placental Response To Hyperglycemia In Mice And Human Trophoblasts, Khatia Nanobashvili, Chauntelle Jack-Roberts, Rachel Bretter, Naudia Jones, Kathleen Axen, Anjana Saxena, Kali Blain, Xinyin Jiang

Publications and Research

Gestational diabetes mellitus (GDM) is characterized by excessive placental fat and glucose transport, resulting in fetal overgrowth. Earlier we demonstrated that maternal choline supplementation normalizes fetal growth in GDM mice at mid-gestation. In this study, we further assess how choline and its oxidation product betaine influence determinants of placental nutrient transport in GDM mice and human trophoblasts. C57BL/6J mice were fed a high-fat (HF) diet 4 weeks prior to and during pregnancy to induce GDM or fed a control normal fat (NF) diet. The HF mice also received 25 mM choline, 85 mM betaine, or control drinking water. We observed …

Biology Ii (Bio1201) Syllabus, Tatiana Voza

Open Educational Resources

No abstract provided.

Able: Blockwise Site Frequency Spectrafor Inferring Complex Population Histories And Recombination, Champak R. Beeravolu, Michael J. Hickerson, Laurent A. F. Frantz, Konrad Lohse

Publications and Research

We introduce ABLE (Approximate Blockwise Likelihood Estimation), a novel simulation-based composite likelihood method that uses the blockwise site frequency spectrum to jointly infer past demography and recombination. ABLE is explicitly designed for a wide variety of data from unphased diploid genomes to genome-wide multi-locus data (for example, RADSeq) and can also accommodate arbitrarily large samples. We use simulations to demonstrate the accuracy of this method to infer complex histories of divergence and gene flow and reanalyze whole genome data from two species of orangutan. ABLE is available for download at https://github.com/champost/ABLE.

Digital Storytelling [Natural Sciences], Preethi Radhakrishnan

Open Educational Resources

A well-crafted and executed storytelling assignment can serve as an efficient and engaging learning activity which targets the three highest levels of Blooms’ taxonomy which are to Create, Evaluate and Analyze. This digital storytelling assignment is part of a signature assignment series (Stage 1) conducted in all courses of the First Year Seminar for Natural Sciences (NSF101). Students begin collecting pictures and videos for their assignment from the 3^rd week of the semester on a flash drive. During the fourth week of the semester, the instructor first describes the storytelling process and stages. This is followed by learning around …

Immobilization Nematodes For Live Imaging Using An Agarose Pad Produced With A Vinyl Record, Katherine A. Rivera Gomez, Mara Schvarzstein

Publications and Research

Numerous microfluidic systems have been developed and used for live imaging of Caenorhabditis nematodes (Allen et al., 2008; Zhang et al., 2008; Krajniak and Lu, 2010; Krajniak et al., 2013; Cornaglia et al., 2015). These systems can be costly, complex to set up, or require high-maintenance between uses. In addition, microfluidic rigs can be thick, preventing live imaging of worms from strains expressing low fluorescence fusion proteins. In the absence of elaborate microfluidic rigs, most live imaging protocols utilize flat agarose pads along with anesthetics and/or microbeads to immobilize the nematodes (Kim et al., 2013). Since this method does not …

The Transcriptome Of The Bermuda Fireworm Odontosyllis Enopla (Annelida: Syllidae): A Unique Luciferase Gene Family And Putative Epitoky-Related Genes, Mercer R. Brugler, M. Teresa Aguado, Michael Tessler, Mark Siddall

Publications and Research

The Bermuda fireworm Odontosyllis enopla exhibits an extremely tight circalunar circadian behavior that results in an impressive bioluminescent mating swarm, thought to be due to a conventional luciferase-mediated oxidation of a light-emitting luciferin. In addition, the four eyes become hypertrophied and heavily pigmented, and the nephridial system is modified to store and release gametes and associated secretions. In an effort to elucidate transcripts related to bioluminescence, circadian or circalunar periodicity, as well as epitoky-related changes of the eyes and nephridial system, we examined the transcriptomic profile of three female O. enopladuring a bioluminescent swarm in Ferry Reach, Bermuda. …

General Biology 1 Lab Manual (Bio1101l), Jeremy Seto

Open Educational Resources

No abstract provided.

Zero Textbook Cost Syllabus For Env 1004 (Fundamentals Of Ecology-Lecture And Lab), Brian Haggerty

Open Educational Resources

In this class you will learn basic concepts and tools used in ecological research through hands-on activities, complementing and expanding materials from ENV 1003. Field trips to local ecosystems and educational sites are required.

Zero Textbook Cost Syllabus For Env 1004 (Fundamentals Of Ecology-Lab), Rebecca Kulp

Open Educational Resources

This course introduces students to basic concepts and tools used in ecological research through hands-on activities, complementing and expanding materials from ENV 1003. Field trips to educational sites are required.

Zero Textbook Cost Syllabus For Env 1004 (Fundamentals Of Ecology-Lab), Jennifer Zhu

Open Educational Resources

Fundamentals of Ecological Research is a hands-on course designed to teach students the basic concepts and methodologies used in the field of ecology. The significance of ecological research to current environmental issues, both local and global, will be stressed throughout the course.

By the end of this course, you should be able discuss the complex linkages among biotic and abiotic factors that impact natural communities, explain how these factors may be measured, and predict impacts of change.

Zero Textbook Cost Syllabus For Env 1004 (Fundamentals Of Ecology-Lab), Sarah Bengston

Open Educational Resources

This course introduces students to basic concepts and tools used in ecological research through hands-on activities, complementing and expanding materials from ENV 1003. Field trips to local ecosystems and educational sites are required.

Zero Textbook Cost Syllabus For Env 1003 (Fundamentals Of Ecology-Lecture), Mukesh Gautam

Open Educational Resources

Fundamentals of Ecology explores ecological characteristics and ecosystem processes through an evolutionary context. The course will demonstrate the interdisciplinary nature of the field of ecology by highlighting its significance to current environmental issues and the interconnectedness of the environment around us.

Zero Textbook Cost Syllabus For Env 1004 (Fundamentals Of Ecology-Lab), Kuhuk Sharma

Open Educational Resources

Fundamentals of Ecological Research is a hands-on course designed to teach students the basic concepts and methodologies used in the field of ecology. The significance of ecological research to current environmental issues, both local and global, will be stressed throughout the course.

Zero Textbook Cost Syllabus For Env 1004 (Fundamentals Of Ecology-Lab And Recitation), Naoko Kurata

Open Educational Resources

Fundamentals of Ecological Research is a hands-on course designed to teach students the basic concepts and methodologies used in the field of ecology. The significance of ecological research to current environmental issues, both local and global, will be stressed throughout the course. Field trips to local ecosystems and educational sites are required.

Zero Textbook Cost Syllabus For Env 1004 (Fundamentals Of Ecology-Lecture And Lab), Stephen Gosnell

Open Educational Resources

Fundamentals of Ecological Research is a hands-on course designed to teach students the basic concepts and methodologies used in the field of ecology. The significance of ecological research to current environmental issues, both local and global, will be stressed throughout the course.

Zero Textbook Cost Syllabus For Env 1004 (Fundamentals Of Ecology-Lab), Sara Rose Krivoshik

Open Educational Resources

Fundamentals of Ecological Research is a hands-on course designed to teach students the basic concepts and methodologies used in the field of ecology. The significance of ecological research to current environmental issues, both local and global, will be stressed throughout the course.

Zero Textbook Cost Syllabus For Env 1003 (Fundamentals Of Ecology-Lecture), Kuhuk Sharma

Open Educational Resources

Fundamentals of Ecology explores ecological characteristics and ecosystem processes through an evolutionary context. The course will demonstrate the interdisciplinary nature of the field of ecology by highlighting its significance to current environmental issues and the interconnectedness of the environment around us.

Zero Textbook Cost Syllabus For Env 1004 (Fundamentals Of Ecology-Lab), Mukesh Gautam

Open Educational Resources

Fundamentals of Ecological Research is a hands-on course designed to teach students the basic concepts and methodologies used in the field of ecology. The significance of ecological research to current environmental issues, both local and global, will be stressed throughout the course.

Biology Ii, Bio 1201, Course Outline, Tatiana Voza

Open Educational Resources

This course outline for Biology II includes resources for both students and instructors including the OpenStax Biology textbook, lecture schedule, lecture slides, labs, list of related resources and Interdisciplinary (ID) Biology II topics and assignments.

Directly Light-Regulated Binding Of Rgs-Lov Photoreceptors To Anionic Membrane Phospholipids, Spencer T. Glantz, Erin E. Berlew, Zaynab Jaber, Benjamin S. Schuster, Kevin H. Gardner, Brian Y. Chow

Publications and Research

We report natural light–oxygen–voltage (LOV) photoreceptors with a blue light-switched, high-affinity (KD ∼ 10−7 M), and direct electrostatic interaction with anionic phospholipids. Membrane localization of one such photoreceptor, BcLOV4 from Botrytis cinerea, is directly coupled to its flavin photocycle, and is mediated by a polybasic amphipathic helixinthelinker regionbetween the LOV sensor and its C-terminal domain of unknown function (DUF), as revealed through a combination of bioinformatics, computational protein modeling, structure–function studies, and optogenetic assays in yeast and mammalian cell line expression systems. In model systems, BcLOV4 rapidly translocates from the cytosol to plasma membrane (∼1 second). The reversible electrostatic interaction …

Zero Textbook Cost Syllabus For Env 1004 (Fundamentals Of Ecology-Lab And Recitation), Wendy Castillo

Open Educational Resources

Fundamentals of Ecological Research is a hands-on course designed to teach students the basic concepts and methodologies used in the field of ecology. The significance of ecological research to current environmental issues, both local and global, will be stressed throughout the course.

Perinatal Pb2+ Exposure Alters The Expression Of Genes Related To The Neurodevelopmental Gaba-Shift In Postnatal Rats, Lorenz Simon Neuwirth, Greg R. Phillips, Abdeslem El Idrissi

Publications and Research

Background: Lead (Pb2+) is an environmental neurotoxicant that disrupts neurodevelopment, communication, and organization through competition with Ca2+ signaling. How perinatal Pb2+ exposure affects Ca2+-related gene regulation remains unclear. However, Ca2+ activates the L-Type voltage sensitive calcium channel β-3 subunit (Ca-β3), which autoregulates neuronal excitability and plays a role in the GABA-shift from excitatory-toinhibitory neurotransmission.

Method: A total of eight females (n = 4 Control and n = 4 Perinatal) and four males (n = 2 Control and n = 2 Perinatal) rats were used as breeders to serve as Dams and Sires. The Dam’s litters each ranged from N = …

Zero Textbook Cost Syllabus For Env 1004 (Fundamentals Of Ecology-Lab), Aleksandra Kravtsova

Open Educational Resources

Fundamentals of Ecological Research is a hands-on course designed to teach students the basic concepts and methodologies used in the field of ecology. The significance of ecological research to current environmental issues, both local and global, will be stressed throughout the course.

Dextran Hydrogels By Crosslinking With Amino Acid Diamines And Their Viscoelastic Properties, Naphtali O'Connor, Andrei Jitianu, G Nunez, Quentin Picard, Madeline Wong, D Akpatsu, Adam Negrin, Rajendra Ghardbaran, D Lugo, S Shaker, Mihaela Jitianu, Stephen Redenti

Publications and Research

Amine functionalized polysaccharide hydrogels such as those based on chitosan are widely examined as biomaterials. Here we set out to develop a facile procedure for developing such hydrogels by crosslinking dextran with amino acid diamines. The dextran-amino acid gels were formed by the addition of the amino acid diamines to a dextran and epichlorohydrin solution once it became homogeneous. This was demonstrated with three amino acid diamines, lysine, lysine methyl ester, and cystine dimethyl ester. Hydrogel networks with albumin entrapped were also demonstrated. These hydrogels were characterized by FTIR, SEM, rotational rheometry, swelling studies and cell biocompatibility analysis. These hydrogels …

Phase Diagram Of Water Confined By Graphene, Zhenghan Gao, Nicolas Giovambattista, Ozgur Sahin

Publications and Research

The behavior of water confined at the nanoscale plays a fundamental role in biological processes and technological applications, including protein folding, translocation of water across membranes, and filtration and desalination. Remarkably, nanoscale confinement drastically alters the properties of water. Using molecular dynamics simulations, we determine the phase diagram of water confined by graphene sheets in slab geometry, at T = 300 K and for a wide range of pressures. We find that, depending on the confining dimension D and density σ, water can exist in liquid and vapor phases, or crystallize into monolayer and bilayer square ices, as observed in …

Maternal Choline Supplementation During Normal Murine Pregnancy Alters The Placental Epigenome: Results Of An Exploratory Study, Sze Ting (Cecilia) Kwan, Julia H. King, Jennifer K. Grenier, Jian Yan, Xinyin Jiang, Mark S. Roberson, Marie A. Caudill

Publications and Research

The placental epigenome regulates processes that affect placental and fetal development, and could be mediating some of the reported effects of maternal choline supplementation (MCS) on placental vascular development and nutrient delivery. As an extension of work previously conducted in pregnant mice, the current study sought to explore the effects of MCS on various epigenetic markers in the placenta. RNA and DNA were extracted from placentas collected on embryonic day 15.5 from pregnant mice fed a 1X or 4X choline diet, and were subjected to genome-wide sequencing procedures or mass-spectrometry-based assays to examine placental imprinted gene expression, DNA methylation patterns, …

Market Integration Predicts Human Gut Microbiome Attributes Across A Gradient Of Economic Development, Keaton Stagaman, Tara J. Cepon-Robins, Melissa A. Liebert, Theresa E. Gildner, Samuel S. Urlacher, Felicia C. Madimenos, Karen Guillemin, J. Josh Snodgrass, Lawrence S. Sugiyama, Brendan J. M. Bohannan

Publications and Research

Economic development is marked by dramatic increases in the incidence of microbiome-associated diseases, such as autoimmune diseases and metabolic syndromes, but the lifestyle changes that drive alterations in the human microbiome are not known. We measured market integration as a proxy for economically related lifestyle attributes, such as ownership of specific market goods that index degree of market integration and components of traditional and nontraditional (more modern) house structure and infrastructure, and profiled the fecal microbiomes of 213 participants from a contiguous, indigenous Ecuadorian population. Despite relatively modest differences in lifestyle across the population, greater economic development correlated with significantly …