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Methods For Detecting Per2::Luciferase Bioluminescence Rhythms In Freely Moving Mice, B. Martin-Burgos, W. Wang, I. William, S. Tir, I. Mohammad, R. Javed, Smith College, Y. Cui, Ciearra B. Smith, V. van der Vinne, P.C. Molyneux, Stephen C. Miller, David R. Weaver, T.L. Leise, M.E. Harrington 2020 Smith College

Methods For Detecting Per2::Luciferase Bioluminescence Rhythms In Freely Moving Mice, B. Martin-Burgos, W. Wang, I. William, S. Tir, I. Mohammad, R. Javed, Smith College, Y. Cui, Ciearra B. Smith, V. Van Der Vinne, P.C. Molyneux, Stephen C. Miller, David R. Weaver, T.L. Leise, M.E. Harrington

University of Massachusetts Medical School Faculty Publications

Circadian rhythms are driven by daily oscillations of gene expression. An important tool for studying cellular and tissue rhythms is the use of a gene reporter, such as bioluminescence from the reporter gene luciferase controlled by a rhythmically expressed gene of interest. Here we describe methods that allow measurement of bioluminescence from a freely-moving mouse housed in a standard cage. Using a LumiCycle In Vivo81818app手机版下载 (Actimetrics), we determined conditions that allow detection of circadian rhythms of bioluminescence from the PER2 reporter, PER2::LUC, in freely behaving mice. We tested delivery of D-luciferin via a subcutaneous minipump and in the drinking ...


Inherent Regulatory Asymmetry Emanating From Network Architecture In A Prevalent Autoregulatory Motif, Zulfikar Ali, Vinuselvi Parisutham, Sandeep Choubey, Robert C. Brewster 2020 University of Massachusetts Medical School 81818app手机版下载

Inherent Regulatory Asymmetry Emanating From Network Architecture In A Prevalent Autoregulatory Motif, Zulfikar Ali, Vinuselvi Parisutham, Sandeep Choubey, Robert C. Brewster

Open Access Articles

81818app手机版下载Predicting gene expression from DNA sequence remains a major goal in the field of gene regulation. A challenge to this goal is the connectivity of the network, whose role in altering gene expression remains unclear. Here, we study a common autoregulatory network motif, the negative single-input module, to explore the regulatory properties inherited from the motif. Using stochastic simulations and a synthetic biology approach in E. coli, we find that the TF gene and its target genes have inherent asymmetry in regulation, even when their promoters are identical; the TF gene being more repressed than its targets. The magnitude of ...


Adapting Biotoxin Monitoring For The Future: An Opportunity For A Harmful Algae Bloom (Hab) Network In Casco Bay, Maine, Zachary B. Gordon 2020 University of New England 81818app手机版下载

Adapting Biotoxin Monitoring For The Future: An Opportunity For A Harmful Algae Bloom (Hab) Network In Casco Bay, Maine, Zachary B. Gordon

All Theses And Dissertations

81818app手机版下载Harmful Algae Blooms (HABs) related to marine biotoxins have considerable impacts on coastal communities and have been increasing in size and frequency globally. Maine is recognized as a leader in biotoxin management as it relates to bivalve shellfish, but it has been unclear how current management practices effect the growth of shellfish aquaculture and how they will adapt to future conditions. This research uses a collaborative approach to analyze the current state of biotoxin management in Maine. First, the current management practices in Maine were compared and contrasted with five other states dealing with similar issues. Then, the perspectives of ...


Building The Interphase Nucleus: A Study On The Kinetics Of 3d Chromosome Formation, Temporal Relation To Active Transcription, And The Role Of Nuclear Rnas, Kristin N. Abramo 2020 University of Massachusetts Medical School 81818app手机版下载

Building The Interphase Nucleus: A Study On The Kinetics Of 3d Chromosome Formation, Temporal Relation To Active Transcription, And The Role Of Nuclear Rnas, Kristin N. Abramo

GSBS Dissertations and Theses

81818app手机版下载Following the discovery of the one-dimensional sequence of human DNA, much focus has been directed on microscopy and molecular techniques to learn about the spatial organization of chromatin in a 3D cell. The development of these powerful tools has enabled high-resolution, genome-wide analysis of chromosome structure under many different conditions. In this thesis, I focus on how the organization of interphase chromatin is established and maintained following mitosis. Mitotic chromosomes are folded into helical loop arrays creating short and condensed chromosomes, while interphase chromosomes are decondensed and folded into a number of structures at different length scales ranging from loops ...


The Mayfly Newsletter, Donna Giberson 2020 Southwestern Oklahoma State University 81818app手机版下载

The Mayfly Newsletter, Donna Giberson

The Mayfly Newsletter

The Mayfly Newsletter is the official newsletter of the Permanent Committee of the International Conferences on Ephemeroptera.


Chromosome-Scale Assembly Of The Coral Endosymbiont Symbiodinium Microadriaticum Genome Provides Insight Into The Unique Biology Of Dinoflagellate Chromosomes, Ankita Nand, Ye Zhan, Octavio R. Salazar, Manuel Aranda, Christian R. Voolstra, Job Dekker 2020 University of Massachusetts Medical School

Chromosome-Scale Assembly Of The Coral Endosymbiont Symbiodinium Microadriaticum Genome Provides Insight Into The Unique Biology Of Dinoflagellate Chromosomes, Ankita Nand, Ye Zhan, Octavio R. Salazar, Manuel Aranda, Christian R. Voolstra, Job Dekker

University of Massachusetts Medical School Faculty Publications

Dinoflagellates are major primary producers in the world’s oceans, the cause of harmful algal blooms, and endosymbionts of marine invertebrates. Much remains to be understood about their biology including their peculiar crystalline chromosomes. Here we used Hi-C to order short read-based sub-scaffolds into 94 chromosome-scale scaffolds of the genome of the coral endosymbiont Symbiodinium microadriaticum. Hi-C data show that chromosomes are folded as linear rods within which loci separated by up to several Mb are highly packed. Each chromosome is composed of a series of structural domains separated by boundaries. Genes are enriched towards the ends of chromosomes and ...


Advancing Human Health In The Decade Ahead: Pregnancy As A Key Window For Discovery: A Burroughs Wellcome Fund Pregnancy Think Tank., Yoel Sadovsky, Sam Mesiano, Graham J Burton, Michelle Lampl, Jeffrey C Murray, Rachel M Freathy, Anita Mahadevan-Jansen, Ashley Moffett, Nathan D Price, Paul H Wise, Derek E Wildman, Ralph Snyderman, Nigel Paneth, John Anthony Capra, Marcelo A Nobrega, Yaacov Barak, Louis J Muglia 2020 Institute for Systems Biology, Seattle, WA 81818app手机版下载

Advancing Human Health In The Decade Ahead: Pregnancy As A Key Window For Discovery: A Burroughs Wellcome Fund Pregnancy Think Tank., Yoel Sadovsky, Sam Mesiano, Graham J Burton, Michelle Lampl, Jeffrey C Murray, Rachel M Freathy, Anita Mahadevan-Jansen, Ashley Moffett, Nathan D Price, Paul H Wise, Derek E Wildman, Ralph Snyderman, Nigel Paneth, John Anthony Capra, Marcelo A Nobrega, Yaacov Barak, Louis J Muglia

Articles, Abstracts, and Reports

81818app手机版下载Recent revolutionary advances at the intersection of medicine, omics, data sciences, computing, epidemiology, and related technologies inspire us to ponder their impact on health. Their potential impact is particularly germane to the biology of pregnancy and perinatal medicine, where limited improvement in health outcomes for women and children has remained a global challenge. We assembled a group of experts to establish a Pregnancy Think Tank to discuss a broad spectrum of major gestational disorders and adverse pregnancy outcomes that affect maternal-infant lifelong health and should serve as targets for leveraging the many recent advances. This report reflects avenues for future ...


Coping With Stress: The Caulobacter Approach, Bronson R. Weston, Yang Cao, John J. Tyson 2020 Virginia Polytechnic Institute and State University

Coping With Stress: The Caulobacter Approach, Bronson R. Weston, Yang Cao, John J. Tyson

Biology and Medicine Through Mathematics Conference

No abstract provided.


A Phosphoinositide-Based Model Of Actin Waves In Frustrated Phagocytosis, Marco A. Avila Ponce de Leon 2020 University of Minnesota - Twin Cities 81818app手机版下载

A Phosphoinositide-Based Model Of Actin Waves In Frustrated Phagocytosis, Marco A. Avila Ponce De Leon

Biology and Medicine Through Mathematics Conference

No abstract provided.


Modeling Hybrid Novel Traits: A Case Study In Complex Petal Pigment Patterning In Hybrid Mimulus, Xingyu Zheng 2020 William & Mary

Modeling Hybrid Novel Traits: A Case Study In Complex Petal Pigment Patterning In Hybrid Mimulus, Xingyu Zheng

Undergraduate Honors Theses

Hybridization between species, by introducing dramatic trait variation into the population and creating viable, transgressive offsprings with novel phenotypes, can have huge evolutionary implications. Some hybrid traits have been studied in the classical genetics or population genetics context, but most complex traits are determined by multiple causes, e.g. the number of loci involved, the rewiring of the genetic circuitries, and the changes in gene expression pattern. Using the hybrid monkeyflower petal pigment patterning as an example, we present a case study to investigate complex hybrid traits in a systematic manner that includes empirical data analysis and quantitative mathematical modeling ...


Dolphinnext: A Distributed Data Processing Platform For High Throughput Genomics, Onur Yukselen, Osman Turkyilmaz, Ahmet R. Ozturk, Manuel Garber, Alper Kucukural 2020 University of Massachusetts Medical School

Dolphinnext: A Distributed Data Processing Platform For High Throughput Genomics, Onur Yukselen, Osman Turkyilmaz, Ahmet R. Ozturk, Manuel Garber, Alper Kucukural

Open Access Articles

BACKGROUND: The emergence of high throughput technologies that produce vast amounts of genomic data, such as next-generation sequencing (NGS) is transforming biological research. The dramatic increase in the volume of data, the variety and continuous change of data processing tools, algorithms and databases make analysis the main bottleneck for scientific discovery. The processing of high throughput datasets typically involves many different computational programs, each of which performs a specific step in a pipeline. Given the wide range of applications and organizational infrastructures, there is a great need for highly parallel, flexible, portable, and reproducible data processing frameworks. Several platforms currently ...


Dugesia Japonica Is The Best Suited Of Three Planarian Species For High-Throughput Toxicology Screening, D. Ireland, Veronica Bochenek , '22, Daniel Chaiken , '20, C. Rabeler, Sumi Onoe , '21, Ameet Soni, Eva-Maria S. Collins 2020 Swarthmore College 81818app手机版下载

Dugesia Japonica Is The Best Suited Of Three Planarian Species For High-Throughput Toxicology Screening, D. Ireland, Veronica Bochenek , '22, Daniel Chaiken , '20, C. Rabeler, Sumi Onoe , '21, Ameet Soni, Eva-Maria S. Collins

Biology Faculty Works

High-throughput screening (HTS) using new approach methods is revolutionizing toxicology. Asexual freshwater planarians are a promising invertebrate model for neurotoxicity HTS because their diverse behaviors can be used as quantitative readouts of neuronal function. Currently, three planarian species are commonly used in toxicology research: Dugesia japonica, Schmidtea mediterranea, and Girardia tigrina. However, only D. japonica has been demonstrated to be suitable for HTS. Here, we assess the two other species for HTS suitability by direct comparison with D. japonica. Through quantitative assessments of morphology and multiple behaviors, we assayed the effects of 4 common solvents (DMSO, ethanol, methanol, ethyl acetate ...


Detecting Chromatin Interactions Along And Between Sister Chromatids With Sisterc, Marlies E. Oomen, Adam K. Hedger, Jonathan K. Watts, Job Dekker 2020 University of Massachusetts Medical School

Detecting Chromatin Interactions Along And Between Sister Chromatids With Sisterc, Marlies E. Oomen, Adam K. Hedger, Jonathan K. Watts, Job Dekker

University of Massachusetts Medical School Faculty Publications

Accurate chromosome segregation requires chromosome compaction with concordant disentanglement of the two sister chromatids. This process has been studied extensively by microscopy but has remained a challenge for genomic methods, such as Hi-C, because sister chromatids have identical DNA sequences. Here we describe SisterC, a chromosome conformation capture assay that can distinguish interactions between and within sister chromatids. The assay is based on BrdU incorporation during S-phase, which labels the newly replicated strands of the sister chromatids. This is followed by Hi-C, e.g. during different stages of mitosis, and the selective destruction of BrdU containing strands by UV/Hoechst ...


The Cancer Microbiome: Distinguishing Direct And Indirect Effects Requires A Systemic View, Joao B. Xavier, Amir Mitchell 2020 Memorial Sloan-Kettering Cancer Center

The Cancer Microbiome: Distinguishing Direct And Indirect Effects Requires A Systemic View, Joao B. Xavier, Amir Mitchell

Open Access Articles

81818app手机版下载The collection of microbes that live in and on the human body - the human microbiome - can impact on cancer initiation, progression, and response to therapy, including cancer immunotherapy. The mechanisms by which microbiomes impact on cancers can yield new diagnostics and treatments, but much remains unknown. The interactions between microbes, diet, host factors, drugs, and cell-cell interactions within the cancer itself likely involve intricate feedbacks, and no single component can explain all the behavior of the system. Understanding the role of host-associated microbial communities in cancer systems will require a multidisciplinary approach combining microbial ecology, immunology, cancer cell biology, and ...


Yeast Copper Proteins And Reactive Oxygen Species In Effecting Lifespan, Megan Bestwick 2020 Linfield College

Yeast Copper Proteins And Reactive Oxygen Species In Effecting Lifespan, Megan Bestwick

Post-Grant Reports

Mitochondria are essential organelles in most eukaryotic cells because of their role in metabolism and the production of ATP by the oxidative phosphorylation (OXPHOS) pathway, as well as other key cellular processes. Metal cofactors, such as copper (Cu) and iron (Fe), are incorporated into OXPHOS protein complexes of yeast located within the inner membrane of the mitochondria. Misincorporation or modulation of these available metals in mitochondrial enzymes leads to the production of reactive oxygen species (ROS). ROS are reactive molecules containing oxygen such as peroxides, superoxide, and hydroxyl radicals. Yeast are a good model for studying aging and the effect ...


Micom: Metagenome-Scale Modeling To Infer Metabolic Interactions In The Gut Microbiota., Christian Diener, Sean M Gibbons, Osbaldo Resendis-Antonio 2020 Institute for Systems Biology, Seattle, Washington, USA.

Micom: Metagenome-Scale Modeling To Infer Metabolic Interactions In The Gut Microbiota., Christian Diener, Sean M Gibbons, Osbaldo Resendis-Antonio

Articles, Abstracts, and Reports

Compositional changes in the gut microbiota have been associated with a variety of medical conditions such as obesity, Crohn's disease, and diabetes. However, connecting microbial community composition to ecosystem function remains a challenge. Here, we introduce MICOM, a customizable metabolic model of the human gut microbiome. By using a heuristic optimization approach based on L2 regularization, we were able to obtain a unique set of realistic growth rates that corresponded well with observed replication rates. We integrated adjustable dietary and taxon abundance constraints to generate personalized metabolic models for individual metagenomic samples. We applied MICOM to a balanced cohort ...


The Bioethical Significance Of “The Origin Of Man’S Ethical Behavior” (October 1941, Unpublished) By Ernest Everett Just And Hedwig Anna Schnetzler Just, Theodore Walker Jr. 2020 Southern Methodist University 81818app手机版下载

The Bioethical Significance Of “The Origin Of Man’S Ethical Behavior” (October 1941, Unpublished) By Ernest Everett Just And Hedwig Anna Schnetzler Just, Theodore Walker Jr.

Journal of the South Carolina Academy of Science

Abstract –

E. E. Just (1883-1941) is an acknowledged “pioneer” in cell biology, and he is perhaps the pioneer in study of egg cell fertilization. Here we discover that Just also made pioneering contributions to general biology and evolutionary bioethics.

Within Just’s published contributions to observational cell biology, there are substantial fragments of his theory of ethical behavior, a theory with roots in cell biology. In addition to such previously available fragments, Just’s fully developed theory is now available. This recently discovered unpublished book-length manuscript argues for the biological origins of ethical behavior81818app手机版下载 (evolving from cells to humans, within ...


Non-Invasive Method For Leptin Supplementation In Zebrafish (Danio Rerio), Regan McNamara 2020 The University of Akron

Non-Invasive Method For Leptin Supplementation In Zebrafish (Danio Rerio), Regan Mcnamara

Williams Honors College, Honors Research Projects

I tested the hypothesis that recombinant leptin protein can be introduced to zebrafish in vivo through non-invasive soaking in a solution containing the protein. One way to study various molecules’ effects in vivo is through intraperitoneal or intracerebroventricular injections during the embryonic or larval stage, which is invasive, difficult to administer, and can have a high mortality rate. 48 hours post fertilization (hpf) zebrafish were soaked in a His-tagged recombinant leptin protein solution at 10 nM and 100 nM concentrations (produced by Genscript). After soaking, zebrafish larvae were washed extensively to remove all recombinant protein on their exterior before homogenization ...


Covers, 2020 Occidental College

Covers

Bulletin of the Southern California Academy of Sciences

81818app手机版下载No abstract provided.


Protecting The Wui In California: Greenbelts Vs Thinning For Wildfire Threats To Homes, Jon E. Keeley 2020 U.S. Geological Survey 81818app手机版下载

Protecting The Wui In California: Greenbelts Vs Thinning For Wildfire Threats To Homes, Jon E. Keeley

Bulletin of the Southern California Academy of Sciences

81818app手机版下载This study utilized native chaparral and sage scrub shrubs to evaluate the impact of light summer irrigation on live fuel moisture content (LFMC) and predicted fire behavior. As to be expected LFMC varied markedly throughout the year being over 100% in winter in all species and treatments but differed markedly by treatment in the summer and fall. For most species lightly irrigated plants had the highest LFMC in the summer and fall, followed by thinned treatments and controls. These differences in moisture content coupled with structural differences in the vegetation contributed to expected differences in flame length and rate of ...