bluuebunny/crossref_metadata_2025_split huggingface dataset:
Undergraduate Student (Mis)understandings of Mutations
Authors: Seipelt‐Thiemann Rebecca , Reid Joshua , Grimes Zachary , Wasendorf Chloe , Couch Brock , James Olena , Peters Nick , Boury Nancy 
Published: June 2021

Genetics is known to have difficult concepts to learn and understand due to its use of complex, nuanced, and technical vocabulary, as well as the abstract nature of many concepts, the requirement to think across multiple scales, particularly the symbolic scale, and the pace of change to the field. The concept of mutation and its effects are particularly important due to the foundational level they play in many critical areas of modern biology including evolution, central dogma, genotype‐phenotype connections, genomic identity, and personalized medicine. This project aimed to gain a thorough perspective of student understanding and alternative concepts they hold regarding mutations. Student response data were gathered using open‐ended questions focused on three distinct learning objectives. The student should be able to: 1) define mutation, 2) categorize changes to DNA and predict the outcome of these changes on a protein produced from the altered DNA using the genetic code, 3) differentiate between somatic and germline mutations and predict the inheritance patterns of each type of mutation, 4) predict the nature of changes to DNA exposed to intercalating agents, base analogs, and radiation (ionizing and non‐ionizing). More than 400 student responses to seventeen questions were analyzed qualitatively. Student responses showed that students have major issues understanding: 1) the difference between a mutation and any change in RNA, protein, or function, 2) central dogma terminology and how genetic information “flows” within it, 3) the relationships of somatic and germline mutations to heritability, and 4) how mutagens cause mutations. It is hoped that knowing which alternative conceptions students commonly hold will aid faculty in designing instruction that enables students to form a more accurate conceptual framework regarding mutation.Support or Funding InformationNational Science Foundation Grant 1710262 to RLST and NMBThis abstract is from the Experimental Biology 2019 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
Project 80: A system that produces students who use need finding, targeted marketing strategies, and primary literature to address scientific misunderstandings that fuel hate and social ill
Authors: Frank Toby Hwang , Paczuski Anna , McGraw Kyle J , Das Briana , Lipka Ethan , Garber Julianna , Savaterre Gabby , Wang Dana , Leef Max , Sweeney Robert , De Luke 
Published: June 2021

Misunderstandings in genetics and human behavior fuel some of society's most destructive attitudes such as racism and homophobia. These misunderstandings are often prevalent in students. However, current mediums often fail to reach youth populations. Here we describe a system that educates a given target audience about contemporary scientific topics, increasing the number of people who use scientific data to inform their everyday decisions. The group uses marketing, social media, websites, podcasts, and any medium necessary to instill change in 80% of that target population. Named Project 80, this system also produces lifelong science learners. It allows students to identify the problems most relevant to their lives and allows students to immediately see the impact of education.As a proof of concept, Project 80 produced three podcasts, commercials, a website, graphic design, and paper media that address broad topics in a target population: marijuana use, video games, and anxiety disorders in teens. Data indicates that Project 80 generates more student engagement than almost all other extra‐curricular science projects. In addition to this level of engagement, our data shows that the Project 80 infrastructure can be run with minimal faculty involvement and a low budget, making it a preferred method of student engagement and scientific analysis.This abstract is from the Experimental Biology 2019 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
Novel Research Projects in the Bioinformatics Classroom
Authors: Bennett Jennifer Ann , Wei Derek , Clinton Tim D , Bowman Bridget A 
Published: June 2021

Bioinformatics research has become increasingly important for fields in Biochemistry and Molecular Biology. An important question considers how to best engage undergraduate students with bioinformatics topics in the classroom. Students in my upper‐level bioinformatics classroom each chose an unknown gene from the RNA Sequencing data generated from my undergraduate research group. This exposed the students in the class to this commonly used Next Gen Sequencing technique that is not typically accessible to undergraduates. It then allowed the students to each have a unique gene/protein to generate novel bioinformatics data with the techniques that they were learning in the classroom. Each student created an annotated portfolio with figures for the various bioinformatics techniques that they applied to their gene of interest. By employing a workshop approach instead of a largely lecture format for the bioinformatics course, the course remained highly interactive. Students were highly invested in the individual gene that they chose, knowing that the techniques they employed would uncover novel information. All twelve students presented their data in class and three of the students presented their projects at a regional scientific conference. The benefits that the students gained from this approach is coupled to the impact on the professor/principal investigator's research program.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 effects of mCI inhibition on RecA activity
Authors: Mbele Neema A , Ghodke Harshad , Cox Michael , van Oijen Antoine 
Published: June 2021

In E. coli, Recombinase A (RecA) is involved in the SOS response of DNA repair. RecA serves as the activator for the SOS response by cleaving the repressor LexA. The protein mCI is an inhibitor based on the bacteriophage □ repressor CI. mCI has been shown to bind to the helical groove of active RecA filaments which are formed after the cleavage of LexA. It is predicted that this binding results in the inhibition of RecA activity. Two types of in vitro experiments were carried out to test the effects of mCI on the overall catalytic activity of RecA. In the strand exchange assays, it was observed that mCI's inhibition on RecA was dependent on concentration and timing. The mCI protein blocked the initiation of strand exchange, but had relatively small effects once strand exchange was underway. In addition, mCI affected RecA‐mediated ATP hydrolysis. The implications of these results will be discussed.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 Effect of Calcitriol in the DNA Damage by Molecular Subtypes of Breast Cancer Cell Lines
Authors: Padilla Luis , Vergne Ralphdy , Ortiz Carmen , Encarnación Jarline , Matta Jaime 
Published: June 2021

Calcitriol is the physiologically‐active form of vitamin D which can regulate different cellular mechanisms, such as cell cycle arrest, differentiation, migration, invasion, and proliferation of some tumor cell types. Fluorouracil (5‐FU) is one of the most commonly used drugs to treat several types of cancer, including breast cancer. Its main mechanism of action is based on interfering with DNA or RNA synthesis. Breast cancer is a heterogenous disease in which the behavior and biological characteristic of tumors can vary widely, affecting the prognosis and the treatment of the patient. Breast tumors are classified into four principal molecular subtypes: Luminal A, Luminal B, HER2+ and triple‐negative. Our main objective is to assess the DNA damaging effects of calcitriol pre‐ and post‐treatment in cells treated with 5‐FU in breast cancer cells with different molecular subtypes. We hypothesize that calcitriol will induce DNA damage alone and in combination with 5‐FU in Luminal A cells when compared with Luminal B cells. Breast cancer cell lines resembling Luminal A (MCF‐7) and Luminal B (BT474) were grown with their respective media. To select the appropriate doses of 5‐FU and calcitriol, the MTT assay was used to calculate the inhibitory concentration 50 (IC50). Protein was extracted to assess changes in expression of key proteins involved in DNA damage checkpoint and repair. DNA damage for each treatment was assessed using the comet assay. For 5‐FU, the IC50 was calculated to be 40 μM while for calcitriol it was 1 μM in cells treated for 24 hours. Our preliminary results show that when MCF‐7 cells were treated with calcitriol, a higher DNA damage index was observed when compared to untreated cells (p=0.0351). Moreover, when MCF‐7 were treated with calcitriol before 5‐FU treatment a higher DNA damage index was observed when compared with calcitriol only (p=0.0172). However, when comparing the extent of DNA damage in cells treated with calcitriol after 5‐FU treatment no significant differences were found (p=0.999) when compared calcitriol only. In BT474 cells, no statistically significant differences were observed when comparing calcitriol treated with untreated cells. Currently, we are performing additional experiments to confirm these preliminary results. Also, we are assessing expression changes in protein related to DNA damage and cell cycle checkpoints.Support or Funding InformationThis study was supported by UPR‐Ponce RISE NIH‐NIGMS R25GM096955. This study was supported by NIH‐NIGMS #2R25GM096955, #S06GM008239‐20, 9SC1CA182846‐04, #U54CA163068, and G12‐MD007579. We appreciate the technical support of the Molecular and Genomics Core Laboratory at Ponce Health Sciences University‐Ponce Research Institute (Grant R003050/MD007579).This abstract is from the Experimental Biology 2019 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
Cancer‐associated variants of POLQ induce genomic instability
Authors: Headrick Ashley , Wanchu Sahaj , Avalos Lisbeth , Victorino Jorge , Towle‐Weicksel Jamie , Ray Sreerupa 
Published: June 2021

Melanoma is the most severe form of skin cancer and it develops when unrepaired DNA damage in skin cells causes mutations which further leads to genomic instability. The widely accepted environmental cause of melanoma is ultra‐violet (UV) radiation, which leads to DNA damage in skin cells. Failure to repair DNA, or its error‐prone repair, can lead to mutagenesis which can propagate further through rounds of replication, eventually resulting in uncontrolled cell growth leading to cancer. However, the cell has a mechanism for repair using a variety of highly specialized enzymes known as DNA polymerases. DNA Polymerase theta (Pol θ or POLQ) is hypothesized to be an important DNA polymerase involved in double‐strand break (DSB) repair through microhomology‐mediated end‐joining (MMEJ), an alternative non‐homologous end‐joining (alt‐NHEJ) pathway, however it is a low fidelity enzyme that often leads to numerous errors during repair. There is evidence that breast cancer patients that overexpress POLQ tend to have poorer survival rate suggesting a potential role for POLQ in cancer. In collaboration with the Yale SPORE in Skin Cancer and Rhode Island College, we have identified several variants of POLQ in melanoma patients. Here we demonstrate that the cancer‐associated variants of POLQ induce genomic instability and have accumulation of DNA DSBs. In addition, biochemical studies indicate that these variants display an inherently slower polymerization rate compared to wild‐type (WT) suggesting a different mechanism for nucleotide incorporation. Together, this suggests that the cancer‐associated variants lead to genomic instability and may play a role in cancer. Our studies suggest that variants of POLQ alter the DNA repair 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.
Post‐Translational Modifications of Mitochondrial Proteins MRPL12 and POLRMT as a Potential Regulatory Mechanism for Mitochondrial DNA Transcription
Authors: Bostwick Alicia M , Senti Mackenna L , Dittenhafer‐Reed Kristin E. 
Published: June 2021

Mitochondrial DNA (mtDNA) encodes 13 of the protein subunits of the oxidative phosphorylation pathway, the pathway that produces the majority of ATP in eukaryotic cells. Mitochondrial dysfunction is associated with neurodegenerative disorders, cancer, inherited mitochondrial diseases, and other pathologies, making mitochondrial biochemistry an important area of investigation. However, there lacks an understanding of key elements of this biochemistry, including the mechanisms that regulate mtDNA transcription. mtDNA is known to be complexed to various proteins in structures known as nucleoids. Some nucleoid proteins are key members of the mtDNA transcription machinery; these include the mitochondrial RNA polymerase (POLRMT) and mitochondrial ribosomal protein L12 (MRPL12), which maintains POLRMT stability and promotes mtDNA transcription. We hypothesize that reversible post‐translational modifications (PTMs), such as phosphorylation of threonine, serine, or tyrosine residues or acetylation of lysine residues within these and other nucleoid proteins, may play a role in regulating mtDNA transcription. The objective of our study is to determine the effects of MRPL12 and POLRMT post‐translational modifications on the activities of these proteins in the context of mtDNA transcription in order to assess the roles of such modifications in regulating this process. To test this, we performed mutagenesis PCR on MRPL12 and POLRMT genes within bacterial expression vectors to replace the sequence encoding an amino acid at a PTM site with a sequence encoding a modified or unmodified amino acid mimic (T, S, Y → E/A, phosphorylated/dephosphorylated mimic; K → Q/R, acetylated/deacetylated mimic). We optimized bacterial expression and protein purification conditions and purified wild‐type and mutant MRPL12 proteins, as well as wild‐type POLRMT. We performed preliminary in vitro transcription assays to assess POLRMT functionality and found that our protein successfully transcribed short mtDNA templates. Going forward, we will perform protein‐protein binding assays to determine the effects of MRPL12 modifications on MRPL12's ability to bind POLRMT, as well as POLRMT mutagenesis and more in vitro transcription assays to measure the effects of MRPL12 and POLRMT modifications 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, with additional funding from the Arnold and Mabel Beckman Foundation Beckman Scholars Award and the ASBMB Undergraduate Research award.This abstract is from the Experimental Biology 2019 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
Probing the Effects of Androgen and Glucocorticoid Receptor Sequences on DNA Binding Preferences
Authors: Boulanger Kyle R. , Miller Austin M , Pufall Miles A , Hall Bonnie L. 
Published: June 2021

Prostate cancer is the second leading cause of cancer among men and although survival rates are high for regional tumors, it is estimated that almost 30,000 men will succumb to their diagnosis in 2018. Androgen hormones fuel prostate tumor growth by signaling through the androgen receptor (AR), a member of the nuclear receptor superfamily of transcription factors. Blocking androgen signaling through administration of antagonists (e.g bicalutamide, enzalutamide) or halting production of androgens through chemical or surgical castration arrests progression of the disease. Patients often relapse with castration resistant prostate cancer (CRPC) that continues to grow despite the lack of androgens. One mechanism of resistance is due to upregulation of a related nuclear receptor, the glucocorticoid receptor (GR). Because AR and GR have overlapping DNA binding specificities, GR is able to functionally substitute for AR at key disease genes. We have shown previously, using SELEX (Selective Evolution of Ligands by Exponential Enrichment) coupled with a novel computational algorithm (SelexGLM), that although AR and GR bind similar sequences, they recognize DNA differently. GR is less specific than AR, allowing it to accommodate predominantly AR sequences. To better understand the selectivity of AR and GR, and to identify the determinants of their specificity, we are measuring the sequence preference of AR and GR mutants using the No Read Left Behind (NRLB) method. As opposed to traditional SELEX, NRLB yields high resolution models of specificity with a single round of selection, which allows rapid screening of our mutants. We have over‐expressed and purified both the AR and GR DNA binding domains, and have designed hybrid mutants. Comparison of the DNA binding preferences of AR, GR and the hybrid molecules by NRLB should help uncover how GR might be playing a role in CRPC.Support or Funding InformationThis work was supported in part by the FUTURE program of the University of Iowa Carver College of Medicine.This abstract is from the Experimental Biology 2019 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
Evaluating the Role of Piccolo Splice Variants in Regulated Secretion of Insulin from Rat Pancreatic Cells
Authors: Quintana Victoria G , Fenster Steven D. 
Published: June 2021

Secretion of insulin from pancreatic beta‐cells is required for proper glucose homeostasis; however, the molecular mechanism of insulin granule exocytosis has not been fully elucidated. In pancreatic beta‐cells, glucose‐induced insulin secretion is synergistically potentiated through an Epac2‐Rim2‐Piccolo signaling response mechanism. Both Piccolo and Rim2 were originally identified as active zone proteins in neurons and have been shown to regulate synaptic vesicle cycling and neurotransmitter signaling. A recent study showed that a number of active zone proteins, including Rim2 and Piccolo, are downregulated in human pancreatic islet cells isolated from patients with type 2 diabetes (T2D). Understanding the role of Piccolo in regulated secretion of insulin may provide valuable insights into the causes of T2D. The C‐terminal region of Piccolo contains a Ca2+‐binding C2A domain. It is likely that Piccolo may regulate secretion from insulin granule vesicles by serving as a Ca2+‐sensor. Alternative splicing of exons within the coding region of the C2A domain results in an exon‐skipping event generating either a splice variant that lacks the 27‐nucleotide exon 16 (short C2A) or a variant that retains this exon (long C2A). Exclusion of the 9 amino acid residue sequence in the short C2A domain results in enhanced Ca2+‐binding affinity. In this study, we sought to examine the differential roles of the short C2A and long C2A variants in Ca2+‐mediated insulin secretion from rat INS‐832/13 pancreatic beta‐cells. We demonstrate that INS‐832/13 cells express both long and short variants of the C2A domain and real‐time qPCR demonstrated differential expression of the variants. In addition, we examined the effects of overexpression of the short and long C2A domains on glucose‐stimulated insulin secretion from INS‐832/13 cells.Support or Funding InformationMaximizing Access to Research Careers Program at Fort Lewis College (NIH‐T34GM092711)This abstract is from the Experimental Biology 2019 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
Investigating the Role of Histone H4 Acetylation in RNA Splicing in Saccharomyces cerevisiae
Authors: Kopew Jessica S , Mendizabal Adriana G , Lin Mengjia M , Kress Tracy L 
Published: June 2021

The ability of RNA splicing and transcription to take place simultaneously allows for efficient coordination and regulation within cells. Few known connections exist between chromatin modifications, which regulate transcription, and RNA splicing in the yeast Sacchraomyces cerevisiae, as well as in metazoa1,2, leaving much to explore. Our previous research has shown that genetic interactions exist between splicing protein genes and the NuA4 complex genes in S. cerevisiae. In addition, we found that deletion or mutation of these NuA4 complex genes impact RNA splicing. Nua4 plays a key role in regulating transcription by acetylating histone H4; following this, the Swr1 chromatin remodeling complex is recruited to the acetylated histone and ultimately deposits H2A.Z in place of H2A, allowing for transcriptional activity3–5. Given these findings, our current research is focused on elucidating whether specific acetylation of histone H4 is required for coordinating splicing with transcription. We constructed an array of double mutant yeast strains comprising a deletion of an essential splicing factor gene and a point mutation in either H4K5, H4K8, H4K12, or H4K16 thus preventing a chemical modification. We conducted genetic interaction studies to identify synthetic sick/lethal, or suppressive genetic interactions between the two genes. The majority of the double mutant growth phenotypes reveal synthetic sick/lethal interactions when compared to single mutant strains, suggesting a functional link between H4 acetylation and RNA splicing. Using RT‐qPCR we determined that mutation of H4 resulted in a reduction in pre‐mRNA splicing. In addition, mutation of H4 exacerbates the splicing defects observed in splicing factor deletion strains, which is consistent with the genetic interactions. Our future research will focus on identifying the specific mechanism by which the histone H4 acetylation is functioning to regulate RNA splicing. To this end we are currently using chromatin immunoprecipitation to examine the impact of these H4 mutations on the recruitment of splicing factors.Support or Funding InformationResearch Corporation for the Advancement of Science (Cottrell College Science award no. 20186) National Institutes of Health (R15GM122026).This abstract is from the Experimental Biology 2019 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.