bluuebunny/crossref_metadata_2025_split huggingface dataset:
Mentorship for developing course‐based undergraduate research experiences (CUREs): The Council on Undergraduate Research Mentorship for Integrating Research into the Classroom (MIRIC) program
Authors: Wolyniak Michael J , Resendes Karen K 
Published: June 2021

The life science education community has responded to the recommendations of the American Association for the Advancement of Science (AAAS) Vision and Change document with several initiatives designed to improve the way in which undergraduates learn science. These initiatives have often taken the form of one‐time workshops that generate awareness of and interest in developing authentic research experiences for undergraduate STEM classrooms. However, they have been less successful with respect to generating the sustainable change necessary to bring real reform to undergraduate science education. To create sustainable change, long‐term faculty development initiatives focused on mentorship are needed so that instructors seasoned in developing and implementing course‐based undergraduate research experiences (CUREs) can convey their experiences to mentees interested in using these pedagogical techniques as the centerpiece of their own teaching. The Council on Undergraduate Research (CUR) Biology Division has created the Mentorship for Integrating Research Into the Classroom (MIRIC) program to provide a means for members with an interest in developing improved and sustainable active learning techniques to gain experience in this style of teaching through close, long‐term interaction with a veteran teaching mentor.Developed from the former ASCB Mentorship in Active Learning and Teaching (MALT) program, MIRIC focuses on the development of instructors who wish to develop a dynamic CURE. Current and future life science instructors pair themselves up with seasoned veterans of CURE development and work with them and their students over the course of a semester or longer to develop a CURE that will allow the mentee to bring authentic research into his or her classes.In our pilot studies, we collected qualitative and quantitative data based on participant interviews and coding videos of student and instructor actions during classroom activity (Smith et al., 2013), respectively, that suggest that MIRIC mentorships have made positive gains in promoting sustainable active learning techniques among participants. Going forward, we wish to use instruments like the Laboratory Course Assessment Survey (Corwin et al., 2015) and Experimental Design Ability Test (Sirum and Humburg 2011) to assess the effectiveness of the MIRIC laboratory intervention.Support or Funding InformationCouncil on Undergraduate Research (CUR)This abstract is from the Experimental Biology 2019 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
UR in Curriculum: DNA Barcoding Research Tool can be Scaled from Traditional to Course‐based Research Project with Ease
Authors: Gadura Nidhi 
Published: June 2021

Most of our students at Queensborough Community College, CUNY are first generation, non‐traditional students with a vast majority working full‐time or part‐time to meet family obligations and sustain themselves outside the classroom. As an educator, one has to constantly be mindful of this reality. While a few of our students can follow a traditional one‐on‐one research model, majority cannot. Therefore, the option to bring research to them in their classrooms was considered as part of the CUR (Council on Undergraduate Research) initiative. This pedagogy was reluctantly implemented in honors courses in the Biotechnology degree program.UR (undergraduate research) has since been institutionalized and used cross curriculum in multiple disciplines. A formal approach has been implemented for faculty development. Authentic research experiences are embedded in the curriculum. I partnered with Cold Spring Harbor DNA Barcoding Lab that runs an Urban Barcoding project. This was originally done to help local high school students with authentic research experience. Later, I requested the Urban Barcoding Project team to allow my Queens borough students to participate in the project. I incorporated a DNA Barcoding experiment in my Genetics course as an honors component. Biotechnology students served as mentors to Genetics students while being closely supervised. This served as a capstone experience for sophomores at a community college. A detailed curriculum and assessment strategy was developed for the DNA Barcoding to be incorporated in the curriculum. The Queens borough honors committee then approved this project and its timeline. Students developed a hypothesis driven project while working in teams of three. They met during free club hours all semester long to complete their lab work and analyze their results. This experience also became part of their resume and helped them tremendously as they applied for senior colleges or competitive summer research programs after graduation. After seeing the significant success of this project, my belief that students learn more when they get to do hands on science was reaffirmed. Students not only retained skills that are transferrable but also gainedvconfidence in their skills and work as a team toward completion of their project.This experience also made me realize that the DNA Barcoding project can be scaled from two to twenty students with great ease! I have offered DNA Barcoding project in three settings: Traditional mentor mentee experience; Course‐based authentic research experience and Peer‐Led authentic research experience. Pros and cons for all three will be discussed.Support or Funding InformationNIH‐BioPREP QCC ‐ Stony Brook CollaborationThis abstract is from the Experimental Biology 2019 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
Elucidating the role of Mre11 gene variants in cancer
Authors: Mateos Cristina , Headrick Ashley , Romero Itzel , Kuehn Sydney , Ray Sreerupa 
Published: June 2021

Among the different damages that a cell can undergo, DNA double‐strand break (DSB) is the most detrimental one. DNA contains all the necessary information for a cell's proper functioning and replication, therefore a break that damages both of its strands completely destabilizes the DNA molecules. If not properly repaired this could lead to genomic instability and tumorigenesis. Cells repair DSBs by two repair pathways‐ homology‐directed repair (HDR) and non‐homologous end‐joining (NHEJ). Recently, a back‐up NHEJ pathway has been reported and is referred to as alternate‐NHEJ (Alt‐NHEJ). Although Alt‐NHEJ is advantageous for damaged cells, it can mutate the DNA sequences at the junctions, which may lead to an altered genome that can have severe biological consequences like cancer. Mre11 plays a role in DSB repair pathways as HDR, NHEJ and Alt‐NHEJ. Mre11 possesses single‐strand endonuclease activity and 3′–5′ exonuclease activity which are essential for DNA end‐processing. Recently Mre11 is shown to be overexpressed in breast cancer and high Mre11 expression was associated with a more malignant behavior in breast cancer. Furthermore, germline mutations of the Mre11 gene was identified in a recent screening of hereditary susceptibility to breast and/or ovarian cancer. Mutations in DNA repair genes can have a significant impact on cancer prognosis and treatment. Here we show that cells expressing variants of Mre11 are sensitive to DNA damaging agent bleomycin. Work is ongoing to characterize how the Mre11 variants influence response to various DNA damaging agents and induce genomic instability. This will provide mechanistic insights into the role of the Mre11 variants inducing genomic instability and cancer and has potential to impact the treatment of cancer.Support or Funding InformationThis research was supported by Linfield College Start‐Up Funds and Linfield College Faculty Student Research Collaborative Grant (FSRCG) to SR.This abstract is from the Experimental Biology 2019 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
Kub5‐Hera deficiency compromises homologous recombination and enhances vulnerability to PARP inhibition in BRCA‐proficient breast cancers
Authors: Motea Edward 
Published: June 2021

PurposeIdentification of novel factors that compromise homologous recombination (HR) is key toward innovative strategies to expand the use of poly(ADP‐ribose) polymerase (PARP) inhibitors beyond BRCA deficiency. Our lab discovered that partial loss of Kub5‐Hera (K‐H), a transcription termination factor, stimulates the formation of various BRCA‐related cancers in female mice that was accelerated by single exposure to ionizing radiation (IR, 1 Gy). Here, we investigated how K‐H functionally impacts homologous recombination (HR) and cellular response to PARP inhibition in a subset of BRCA‐proficient breast cancer cell linesExperimental MethodsThe functional impact of K‐H alterations in a subset of breast cancer cell lines were assessed by targeted gene silencing, bioinformatics, mutagenesis techniques, plasmid reporter assays, immunofluorescence, microarray/qPCR analyses, chromatin immunoprecipitation, colony formation assays, rescue experiments and Western blots.ResultsKub5‐Hera promotes the expression of a critical DNA damage response and repair effector, cyclin dependent kinase 1 (CDK1), which phosphorylates BRCA1 for efficient repair of double‐strand breaks (DSBs). Mechanistically, we demonstrate that K‐H binds RNA Polymerase II (RNAPII) at the CDK1 promoter to efficiently enhance CDK1 transcription. K‐H depletion compromises HR, but upregulates poly(ADP‐ribose) polymerase 1 (PARP1) activity for cancer cell survival. Genetic and pharmacological ablation of PARP1 activity in a subset of BRCA‐proficient cell lines with aberrant K‐H reduction leads to synthetic lethality, which is reversed by re‐expression of wild‐type K‐H but not the mutant with reduced RNAPII binding.ConclusionsK‐H deficiency promotes genomic instability and a state of “BRCAness” in a subset of breast cancers. These cells may have an exploitable addiction to PARP‐mediated DNA repair for survival that could greatly expand the use of PARP inhibitors beyond BRCA mutations. Collectively, these results suggest that aberrant K‐H alterations may impact overall cellular response and survival to DNA damage and have clinical implications in cancer.Support or Funding InformationNIH R01 CA210489 (PI: David A. Boothman); Minority Supplement CURE Award CA139217‐05S1 and T32CA124334 to E.A. MoteaThis abstract is from the Experimental Biology 2019 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
Epichlorohydrin‐Induced DNA‐Protein Cross‐Links in Human Leukemia Cells
Authors: Passang Tenzin , Millard Julie T 
Published: June 2021

Over 1.5 million tons of epichlorohydrin (ECH) are used annually in the manufacturing of epoxy resins and polymers. A probable human carcinogen, ECH shares structural homology to nitrogen mustards, the oldest class of anti‐tumor drugs. Such bifunctional alkylating agents can react with DNA and proteins, leading to genotoxic effects. Previous work in our lab has shown that treating human leukemia (HL‐60) cells with toxic doses of ECH leads to the formation of cross‐links and triggers apoptosis. In these studies, cross‐linking was quantified via single cell gel electrophoresis (the comet assay), which does not distinguish between DNA‐DNA cross‐links and DNA‐protein cross‐links (DPCs). The goal of this work is to further characterize ECH‐induced DPCs. Nuclear proteins that bind to biotinylated DNA after treating HL‐60 cells with ECH under different conditions are captured via streptavidin beads. Cross‐linked proteins are then characterized through gel electrophoresis. Preliminary data suggest that ECH does induce DPC formation, with greater cross‐linking efficiency at higher concentrations of ECH. Our findings could have significance for understanding the occupational risks of ECH exposure among industrial workers.Support or Funding InformationSupported by an Institutional Development Award (IDeA) from the National Institute of General Medical Sciences of the National Institutes of Health under grant number P20GM0103423.This abstract is from the Experimental Biology 2019 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
Effects of Transcriptional Dysregulation on the DNA Damage Response in Ewing's Sarcoma
Authors: Rollins Matthew , Schwartz Jacob 
Published: June 2021

Ewing's sarcoma is a soft‐tissue bone malignancy characterized by a translocation event wherein the N‐terminal low complexity domain of EWSR1 is fused with the DNA binding domain of the ETS transcription factor Fli1. The resulting EWS‐Fli1 fusion protein drives expression of oncogenes and knockdown of tumor suppressor proteins. More specifically, EWS‐Fli1 acts as transcriptional regulator by helping recruit RNA Pol II to promoter regions, which is subsequently phosphorylated by CDK9 to escape initiation into elongation. Interestingly, Ewing's sarcoma is particularly susceptible to chemotherapy compared to other cancers; however, the underlying reason for this sensitivity to DNA damage has not been elucidated. Given EWS‐Fli1's role in disrupting transcription, it was hypothesized EWS‐Fli1 is concurrently disrupting the DNA damage response. Here, a combination of CDK9 inhibition with DNA damage was found to drastically diminish cell viability in Ewing's cell lines but not in non‐Ewing's osteosarcoma or HEK293 cells. Ordinarily, after DNA damage γH2A.X phosphorylation occurs on histones near sites of damaged DNA early during the DNA damage response to signal DNA damage repair initiation. Further work has shown Ewing's cells undergoing the combination treatment above have a marked decrease in this DNA damage marker γH2A.X as compared to non‐Ewing's cells. Together, these results suggest Ewing's sarcoma cells are sensitized to DNA damage due in part to transcriptional dysregulation.Support or Funding InformationNIH Grant #214660This abstract is from the Experimental Biology 2019 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
MRE11 Regulation by SIRT2 in DNA Double‐Strand Break Repair
Authors: Zhang Hui , Head Pamela Sara , Bastien Amanda , Li Chunyang , Duong Duc , Seyfried Nicholas , Yu David 
Published: June 2021

At the core of MRN (MRE11‐RAD50‐NBS1) complex, MRE11 is an essential player in DNA end resection and homologous recombination (HR) repair in DNA double‐strand breaks (DSBs). However, the mechanisms by which MRE11 is regulated in DSB repair are not completely understood. We have previously shown that SIRT2, an NAD+ dependent protein deacetylase, implicated in aging, metabolism, genome maintenance, and tumor suppression, plays a critical role in directing the DNA damage response (DDR). In this regard, SIRT2 depletion in cells results in hypersensitivity to ionizing radiation (IR) and impaired HR. To identify the global landscape of DDR proteins regulated by SIRT2, we performed proteomic analysis to identify acetylated peptides regulated by SIRT2 in response to DNA damage in cells. Our analysis revealed a network of proteins regulated by SIRT2, including MRE11. We validated that SIRT2 interacts with MRE11. In addition, SIRT2 deacetylates MRE11 in vitro and in cells. SIRT2 depletion impairs the accumulation of MRE11 to DNA damage sites in response to micro‐irradiation. Our results identify MRE11 as a novel SIRT2 deacetylation target, critical for the repair of DNA DSBs by DNA end resection and provide insight into how dysregulation of SIRT2 and MRE11 results in genomic instability and cancer development. Moreover, MRE11 deacetylation by SIRT2 may be targeted as an adjunct to improve the efficacy of ionizing radiation for cancer therapy.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 recognition by bZIP transcription factors
Authors: Rodriguez‐Martinez Jose Arcadio 
Published: June 2021

Eukaryotic transcription factors rarely function by binding DNA as monomers. However, how transcription factor dimerization impacts DNA recognition is poorly understood. bZIP transcription factors are obligate dimers that regulate gene expression in multiple cellular process. Guided by bZIP dimerization properties, we examined DNA binding specificities of 270 human bZIP pairs. DNA interactomes of for 102 bZIP dimers revealed that 72% of heterodimer motifs correspond to conjoined half‐sites preferred by partnering monomers. Remarkably, the remaining motifs are composed of variably‐spaced half‐sites or “emergent” sites that cannot be readily inferred from half‐site preferences of partnering monomers. Identified cognate sites were validated by in vitro binding assays. Furthermore, bZIP heterodimer‐preferred sites were overrepresented in genomic regions co‐occupied by two bZIP proteins as determined by ChIP‐seq peaks. Focusing on ATF3, we observed distinct cognate site preferences conferred by different bZIP partners, and demonstrated that genome‐wide binding of ATF3 is best explained by considering many dimers in which it participates. Notably, our compendium of bZIP‐DNA interactomes were applied to predict the impact of non‐coding mutations on bZIP‐DNA binding.Support or Funding InformationT32HG002760This abstract is from the Experimental Biology 2019 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
Regulation of Mitochondrial DNA Transcription by Post‐Translational Modifications of Mitochondrial Transcription Factor B2
Authors: Senti Mackenna L , Bostwick Alicia M , Dittenhafer‐Reed Kristin E 
Published: June 2021

Mitochondrial DNA (mtDNA) encodes for 13 protein components required for oxidative phosphorylation (OXPHOS), the primary cellular energy production pathway. While the critical roles of mitochondria in metabolism and cellular function are well established, the mechanisms regulating expression of mtDNA‐encoded genes are poorly understood. Defects in the regulation of mtDNA transcription are implicated in numerous pathologies such as neurodegenerative disorders and cancers. mtDNA is complexed to proteins in structures known as nucleoids, of which some proteins play critical roles in transcriptional regulation. Our objective is to determine whether reversible post‐translational modifications (PTMs) of nucleoid proteins, including lysine acetylation and serine/threonine/tyrosine phosphorylation, regulate mtDNA transcription. Our central hypothesis is that PTMs alter the function of these proteins and provide a means of regulating mitochondrial gene expression. We highlight our work on the characterization of mitochondrial transcription factor B2 (TFB2M), focusing on the mutagenesis, bacterial expression, purification, and analysis. Site‐directed mutagenesis was used to alter the amino acids known to be post‐translationally modified to amino acids mimicking either the modified or unmodified state. Purified mutants and wild type TFB2M were analyzed in a mtDNA binding assay to determine the effects of PTMs on TFB2M function. Initial data suggest that TFB2M relies on modified or unmodified states of key PTM sites to regulate its ability to bind to mtDNA. Characterization of these sites is critical for determining TFB2M's role in mtDNA transcriptional regulation. Future work involves additional screening of TFB2M mutants, optimization of the mtDNA binding assay for analysis of other nucleoid proteins, and in vitro transcription assays to assess mutant protein functionality on mtDNA transcription.Support or Funding InformationThis research is based upon work supported by the National Science Foundation Division of Molecular and Cellular Biosciences under Grant No. 1814845.This abstract is from the Experimental Biology 2019 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
The Cataract‐associated RNA‐Binding Protein Celf1 Post‐transcriptionally Regulates the Key Eye Transcription Factor Pax6
Authors: Weatherbee Bailey , Sandeep Aryal , Siddam Archana , Gautier‐Courteille Carole , Viet Justine , Paillard Luc , Lachke Salil 
Published: June 2021

The lens is a transparent tissue that focuses light on the retina allowing high‐resolution vision. Loss of lens transparency is defined as cataract, the leading cause of blindness worldwide. An estimated 25–50% of congenital cataract cases arise from underlying genetic alterations, making it important to characterize cataract‐linked genes and their pathological mechanisms.Recently, our lab demonstrated that deficiency of the gene Celf1 causes cataract in fish and mouse, indicating its conserved function in vertebrate lens development. Celf1 encodes an RNA‐binding protein (RBP) that directly binds to specific mRNAs and control them on multiple “post‐transcriptional” levels, impacting their alternative splicing, decay or translation into protein. An important unresolved question is whether a post‐transcriptional regulator like Celf1 controls key transcription factors (TFs) in lens development. To address this fundamental question, I generated and characterized lens‐specific Celf1 conditional knockout mice (Celf1cKO/lacZKI). Using immunofluorescence assays, I demonstrate that Celf1cKO/lacZKI lenses exhibit abnormally high protein levels of the homeodomain‐TF Pax6. Further, by performing Celf1‐antibody coupled RNA‐immunoprecipitation (RIP) followed by RT‐qPCR, I demonstrate that Celf1 protein directly associates with Pax6 mRNA.Next, I investigated if Celf1 coordinately functions with other RBPs to exert combinatorial control over gene expression. I performed co‐immunoprecipitation to demonstrate that Celf1 is associated with another RBP, specifically HuR/Elavl1 in lens cells. Finally, by performing HuR/Elval1‐antibody coupled RIP‐RT‐qPCR assay I show that HuR/Elavl1 binds to Pax6 mRNA.These data indicate that the RBPs Celf1 and HuR/Elavl1 directly interact and bind to Pax6 mRNA to mediate combinatorial control of Pax6 protein expression in mouse lens development. Alterations of Pax6 levels are known to cause severe eye defects in human and animal models. Thus, my research uncovers a novel RBP‐based molecular mechanism for regulation of Pax6 expression in the lens, in turn, informing on a new pathway for the pathology of eye defects, including cataract.Support or Funding InformationNEI/NIH RO1 EY021505, Milton H. Stetson Memorial Undergraduate Research FellowshipThis abstract is from the Experimental Biology 2019 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.