bluuebunny/crossref_metadata_2025_split huggingface dataset:
ASBMB Student Chapter and Emory Science Advocacy Network (EScAN) Collaborations to Promote Diversity of Scientists in Advocacy and Policy
Authors: de Amorim Julia L , Zhang Sally , Enyenihi Liz , Corbett Anita H 
Published: June 2021

The newly organized ASBMB Student Chapter at Emory University aims to provide networking and career‐development opportunities coupled with access to research and science outreach. To broaden our impact, we have established a collaboration with the graduate student led organization, Emory Science Advocacy Network (EScAN). EScAN provides a forum to discuss current issues facing the biomedical field and determine how to support robust federal funding of biomedical research. The two organizations together are preparing for the annual EScAN‐sponsored Letter Writing Campaign. We aim to achieve record‐high participation this year of both undergraduate and graduate students from diverse educational and demographic backgrounds. Increases in political awareness and advocacy such as these will enhance the potential for productive legislative action. We will also participate in local (Atlanta) and national (Washington, D.C.) Hill Day in September 2019. In preparation for these events, we have organized focused workshops, including “Communicating Science to Non‐Scientists,” to ensure an effective interface between congress people and young scientists. Aligned with the ASBMB Student Chapter mission statement, our efforts will provide networking and career‐development opportunities for undergraduate students. This collaboration is supported and facilitated by a volunteer graduate student advisor, serving as a liaison between EScAN and the ASBMB Student Chapter. We will assess the outcomes of this collaboration by tracking the number of undergraduate students that participate in the Letter Writing Campaign as an initial metric of engagement. We also are working together with a sociologist to develop pre‐ and post‐surveys to assess the level of understanding of funding for biomedical science and commitment to advocacy for the ASBMB Student Chapter undergraduates. Ultimately, we seek to build a synergistic network of undergraduate and graduate students who are knowledgeable and engaged in scientific outreach and advocacy.Support or Funding InformationR01 GM130147 01, R25 GM125598 01, R01 MH107305 04This abstract is from the Experimental Biology 2019 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
Analysis of student attitudes on reflective minute paper responses in upper level biology classes
Authors: Chan Jason P 
Published: June 2021

Post class reflection is an important competent of learning. One exercise is to provide minute papers, which are short, post‐class responses to a question on immediate lecture material. As such, I gave minute paper prompts to biology students, asking them to reflect on lecture material and answer a thought questions centered on important learning goals. Reflective exercises such as minute papers are thought improve student learning by allowing students to review and summarize material, recall information prior to the next class, and assess their own understanding. My aim was for students to review material more often, as short ungraded writing exercises are known to improve conceptual learning. For my class, students are given a prompt based on the material covered in lecture, and they are allowed to answer the question at home prior the next class. Answers were submitted online. Also, using this system, I allow students to use this as a forum to raise questions about topics that were unclear, concerns about the class, or any comments they did not want to bring up in class. Here, I summarize response metrics for upper level courses in physiology and in cell and molecular biology. I also compare responses that were optional versus required. Using post‐course surveys, I will report on student depth of responses, attitudes toward minute papers, and possible impacts on their learning. Assessing the utility of minute papers may help inform instructors on a simple tool to reinforce important learning concepts.This abstract is from the Experimental Biology 2019 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
Increasing Research Opportunities for Deaf and Hard‐of‐Hearing Students
Authors: Craig Paul , Samar Vincent , Renner Stephanie , Womack Kathryn , Smith Scott R. 
Published: June 2021

The National Institutes of Health has recognized deaf and hard‐of‐hearing students as an underrepresented group in science research by supporting the RIT‐RISE (Research Initiative for Scientific Enhancement) Scholars program. Students join our program at the end of their first year and engage in research during the academic year, full‐time summer research at RIT after year two, and then full‐time summer research at an affiliated campus after year three. Students and their mentors are supported for travel to the ABRCMS (Annual Biomedical Research Conference for Minority Students), as well as a discipline‐specific conference before they apply for Ph.D. schools in their fourth year. The program includes mentored research experiences and supplemental research training that prepares students to apply for and enter biomedical, biobehavioral and clinical science Ph.D. programs. Several unique courses and a co‐curricular program have been created to better prepare the scholars for research careers. We will describe our curriculum and our recruiting process, as well as steps that we have taken to address communication challenges in the research lab setting, which are distinct from challenges that are typically encountered in classrooms and teaching labs.Support or Funding InformationThis project is supported by NIH 1R25GM122672.This abstract is from the Experimental Biology 2019 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
Reinventing Introductory Biology with an Emphasis on Skills, Thinking, and Research
Authors: Kruchten Anne , Freeman Pamela , Thoemke Kara 
Published: June 2021

In our work at the College of Saint Scholastica, we used a backwards design model to develop a new sequence of introductory biology courses to better prepare students for upper division work in the biology major. We present here our alternative model to the traditional year‐long introductory biology survey sequence for biology and biochemistry majors. Our three course introductory sequence for Biology majors now includes a science‐process, skills‐based course BIO 1115 Global Challenges: Scientific Solutions, a one semester survey course BIO 1125 Foundations in Biology, and a course based undergraduate research experience (CURE) BIO 1116 Novel Antimicrobial Discoveries in partnership with the Small World Initiative.A key aspect of our introductory curriculum is a focus on student skills, thinking, and research, both in the CURE Novel Antimicrobial Discoveries and in Global Challenges. Global Challenges uses the topic of climate change to help students develop skills needed for success in the biology major. In this course, the learning outcomes include:

Collaborate effectively on a team and also develop skills in independent learning,
Find informative sources, assess their relevance, and evaluate their claims,
Produce clear, effective, evidence‐based writing,
Prepare and deliver engaging and effective presentations,
Be able to identify answerable questions, and select and evaluate suitable solutions, when confronted ‐with complex, open‐ended problems,
Use awareness of different climate change experiences for peoples of different regions/cultures/economic status in problem solving.
The learning outcomes for these courses connect closely with the competencies outlined in the 2011 Vision and Change: A Call to Action report1. These competencies include: ability to apply the process of science; ability to use quantitative reasoning; ability to use modeling and simulation; ability to tap into the interdisciplinary nature of science; ability to communicate and collaborate with other disciplines; and ability to understand the relationship between science and society. Here we describe the activities and assessments used to assist students in achieving these learning outcomes and present data describing the successes of students in both improving their process of science skills and developing an identity as a scientist.This abstract is from the Experimental Biology 2019 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
Building Bridges: The Biochemistry Major at Albion College
Authors: Rohlman Christopher E , Streu Craig N 
Published: June 2021

We present here our planning, implementation, outcomes, and future directions for the biochemistry major, with a focus on lessons learned and what works. The Albion College Biochemistry Major has been developed over the past eighteen years in the context of significant changes in the institution's vision and curriculum. The original initiative was founded on establishing vital student‐faculty collaborative research in biochemistry and molecular biology as part of a campus wide undergraduate research and scholarship program. Undergraduate biochemistry research at Albion was supported by a college commitment to new laboratory facilities and equipment that would house both the summer undergraduate research program as well as laboratory courses for all students that emphasized active learning, experimental design, and research methodology. The framework for the course curriculum was initially based upon guidelines developed by Boyer and Zimmerman in 1992, which they later updated and disseminated in 2003. Our biochemistry curriculum emphasizes core concept driven modules, which can evolve to reflect the ever‐changing landscape of biochemistry and molecular biology (Vision and Change, 2009.) The biochemistry major is designed and implemented by two faculty FTE's within the chemistry department with expertise in biological chemistry and chemical biology. Albion faculty have worked to adapt this model by utilizing the strengths and talents of chemistry and biology faculty, and serving the needs and interests of our students. Our formal laboratory experiences engage students with current methods, instrumentation and research problems in preparation for professional, graduate and clinical careers (Caldwell et al., 2004.) Critical to the success of the program is the collaboration with faculty in the biology department. This includes colleagues that provide molecular biology, bioinformatics, physiology, microbiology, immunology and cell biology coursework and research opportunities to biochemistry students. The biochemistry and molecular biology curriculum has adapted to and evolved with curricular reforms in the chemistry and biology departments along with institutional efforts for pre‐clinical students. The chemistry department is currently planning and revising the core curriculum, which we will begin to implement in the fall of 2019. This new curriculum is designed to improve student success for both biochemistry majors along with all Albion College STEM students.This abstract is from the Experimental Biology 2019 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
DNA Damage Response Activates Respiration to Elevate dNTP Levels and Promote Cell Survival in Budding Yeast
Authors: Nagar Shreya , Bhagwat Madhura , Kaur Pritpal , Bu Pengli , Vancura Ales 
Published: June 2021

The DNA damage response (DDR), a highly conserved process, senses and repairs damaged DNA. It is widely believed that DDR downregulates respiration to protect DNA from endogenous reactive oxygen species (ROS). Our data go against this dogma and show that DDR activates respiration to increase ATP production and to elevate dNTP levels, which are required for efficient DNA repair and cell survival upon DNA damage. The underlying mechanism involves DNA damage‐induced downregulation of histone expression and altered chromatin structure, leading to increased transcription of genes encoding enzymes of tricarboxylic acid cycle, electron transport chain, and oxidative phosphorylation. This study reveals an unexpected connection between respiration and DDR, and indicates that the benefit of increased dNTP synthesis for cell survival offsets the deleterious effect of respiratory metabolism on DNA repair.Support or Funding InformationSupported by NIH GM120710This abstract is from the Experimental Biology 2019 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
Studying the Human Mobile Element LINE‐1
Authors: Stenson Jazmin Marie 
Published: June 2021

Long interspersed element‐1 (LINE‐1) is a 6kb long transposable element making up 17% of the human genome. LINE1 is the only currently active autonomous retro element within the human genome. LINE‐1 uses a copy and paste method to retrotranspose itself in the genome. Within the LINE‐1 mobile element are two open reading frames (ORF). ORF1 codes for a protein that acts as a chaperone and ORF2 codes for a protein that has both endonuclease and a reverse transcriptase function. Studies characterizing LINE1 endonuclease function demonstrated that LINE1 endonuclease activity induces formation of double‐stranded breaks (DSBs). Only a small fraction of LINE1‐induced DSBs results in a retrotransposition event, suggesting that the damage from the LINE1 endonuclease activity may be greater than previously considered. While LINE1 mutagenic insertion events have been associated with diseases such as breast and colon cancer as well as muscular dystrophy, the full effect of LINE1 endonuclease upon stability of the genome is undetermined. Our lab has identified inhibitors of the LINE‐1 endonuclease to elucidate the contribution of the LINE‐1 endonuclease associated DNA damage to the onset or progression of diseases such as cancer. Our lab has cell lines containing an inducible LINE‐1 at a single locus. By inserting an inducible LINE1 element integrated at a single locus we will investigate the effectiveness of our inhibitor in cells with various levels of LINE‐1 expression.Support or Funding InformationThe Louisiana Cancer Research Consortium, the NIH‐RCMI grant #8G12MD007595‐04, and NIH‐NIGMS BUILD Grant TL4GM118968, 5RL5GM118966This abstract is from the Experimental Biology 2019 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
Roles of the Initial Transcribed Sequence on Productive and Non‐Productive Initiation
Authors: Dyke Sarah , Tang Rebecca , Felth Lindsey C. , Henderson Kate L. , Record M. Thomas 
Published: June 2021

Transcription initiation by E. coli RNA polymerase (RNAP) begins with specific binding of RNAP to promoter DNA, the ~100 bp region from the UP‐element (−40 to −60) and farther‐upstream DNA to the initial transcribed region (ITR), extending ~20 bp downstream from the transcription start site (+1). The sequence and length of upstream promoter DNA elements (including −10, −35 and UP elements) are major determinants of the rate of formation of the open promoter complex [1], while the sequence and length of the discriminator element (between the −10 element and the transcription start site (+1) and the length of the ITR are major determinants of the lifetime of the open complex [2,3].Recently, we investigated the effects of the discriminator on initiation of productive and abortive transcription, as well as on escape of RNAP from promoter contacts in the open complex during productive initiation [2]. For the four T7A1 and λPR promoter/discriminator combinations, we found that the discriminator determined the lifetime and stability of the open complex and the escape point of RNAP in initiation. Here we compare initiation kinetics and RNA product distributions for the previously‐characterized ITR of the λPR promoter with two variant ITR: a repeating trinucleotide sequence (AUG), and a scrambled (“random”) sequence of A, U, and G. Initiation experiments are performed by adding mixtures of ribonucleotides (NTP, one 32P‐labeled) to preformed RNAP‐promoter open complexes, either by conventional mixing (10 seconds), or with a rapid quench flow (RQF) methods (1 millisecond). RNA products are separated by gel electrophoresis and visualized with a phosphorimager. Preliminary experiments comparing these ITR show similar kinetics of escape from the promoter and productive initiation of long RNA, but very different patterns of synthesis of short (abortive) RNAs by nonproductive complexes which cannot efficiently escape. In addition, a post‐escape transient pause at a RNA length of 13 nucleotides, at which length the nascent RNA has entered the RNA exit channel of RNAP, shows very different kinetics for the random ITR as compared to the repeating and original λPR ITR. Measurements of lifetimes and stabilities of these open complexes are planned to determine if they are affected by the ITR.This abstract is from the Experimental Biology 2019 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
Cellular Genes Involved in Redox Regulation Are Altered by Inhibitors of Epstein‐Barr Virus Lytic Gene Expression
Authors: Gorres Kelly , Miller George 
Published: June 2021

Epstein‐Barr virus (EBV), a member of the herpesvirus family, causes infectious mononucleosis and is associated with human cancers, such as Burkitt and Hodgkin lymphomas, gastric carcinoma, and nasopharyngeal carcinoma. EBV establishes a latent infection in B cells, but must be reactivated into the viral lytic cycle to produce more virions and spread the infection among cells and hosts. The viral lytic cascade is initiated by the expression of two viral genes BZLF1 and BRLF1. The transcription of these viral immediate‐early genes is highly regulated. Reactivation of the viral lytic cycle is triggered by a variety of chemical and environmental stimuli. Chemical lytic inducing agents must alter cellular signaling pathways and transcription factors that control viral lytic gene expression. To discover cellular genes involved in viral reactivation, EBV‐positive cells were treated with activators or inhibitors of the viral lytic cycle. Changes in cellular gene expression were measured by next‐generation RNA sequencing (RNA‐seq). Transcriptome analysis identified large changes in expression of cellular genes involved in the redox status of the cell. Future work will connect these cellular pathways to the control of viral lytic gene expression.This abstract is from the Experimental Biology 2019 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
SOX18 mutations associated with human HLTRS syndrome reveal modification of protein‐protein interactions
Authors: Moustaqil Mehdi Denis 
Published: June 2021

Key transcription factors (TFs) including SRY‐related HMG box‐containing protein 18 (SOX18), COUP‐TFII, and prospero‐related homeobox 1 (PROX1) are responsible for the molecular control of the lymphatic endothelial cell fate. Mutations or truncations in the coding sequence of these TFs can cause a variety of human diseases. In particular, mutations in the transcription factor SOX18 cause the Hypotricosis‐Lymphedema‐Telangiectasia syndrome (HTLS), a congenital condition characterized for presenting swelling of tissue due to malformation or malfunction of lymphatics (Lymphedema), furthermore the people who present the disease also present alopecia (Hypotricosis) and the presence of small dilated vessels near the surface of the skin (Telangiectasia). Some patients also present with renal defect and hypertension, in a new variant of the disease called HLTRS (Hypotricosis‐Lymphedema‐Telangiectasia renal defect syndrome). So far two types of SOX18 variants have been described to be associated with HTLS: missense mutations that lack the transactivation domain and nonsense mutations, in the DNA binding domain. We aimed at identifying how the protein‐protein interactions (PPI) network is affected by these mutations and correlate interactions losses with phenotypic outcomes.We first established a SOX18 interactome, validating interaction with 31 SOX18 potential co‐factors. Then we characterized the stability of the mutated proteins by single‐molecule fluorescence and measured physical interactions using different in vitro techniques. Our data show that the SOX18 mutants are thermally stable and still able to bind DNA. However they are losing a significant number of protein partners, the extent and profile of these interaction losses was found to depend on the mutations. This preliminary data set is slowly providing a molecular view of the disease and is opening the door for potential pharmaceutical treatment.This abstract is from the Experimental Biology 2019 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
Identification of a TetR‐like repressor involved in the regulation of error‐prone DNA polymerases in Acinetobacter baumannii
Authors: Nguyen Brian H , Macguire Ashley E , Ching Carly , Godoy Veronica H 
Published: June 2021

Current knowledge about bacterial DDRs is based off of Escherichia coli, where the global SOS repressor, LexA, controls genes involved in the response to DNA damage. Acinetobacter baumannii is an emerging opportunistic pathogen able to quickly acquire antibiotic resistances and survive desiccation better than other bacteria. Remarkably, A. baumannii does not have a LexA homologue and as a result, there is much to learn about the A. baumannii gene network in response to DNA damage and environmental stress. Clearly, A. baumannii is adept at surviving harsh environments, and we have previously shown that A. baumannii acquires antibiotic resistances due to activities controlled by the DNA damage response (DDR).Moreover, we have evidence suggesting that there are multiple regulators involved in the induction of the A. baumannii DDR and that there are multiple layers involved in its regulation. In this work, we have identified a DDR regulator of error prone DNA polymerases, the DDR‐regulated activities responsible for cellular mutagenesis. Through a forward genetic screen, we have found that when a TetR‐like protein is inactivated, there is deregulation of the expression of several genes that encode error‐prone DNA polymerases and of another previously identified transcription factor, UmuDAb. Here, we refer to the TetR‐like regulator as EppR (Error Prone DNA Polymerase Regulator), and we show that it binds to the promoter region of several genes encoding error‐prone polymerases and that it represses their expression. Our data is consistent with EppR playing a role in the A. baumannii DDR as a repressor of expression of error‐prone DNA polymerases.This abstract is from the Experimental Biology 2019 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.