bluuebunny/crossref_metadata_2025_split huggingface dataset:
Pseudophosphatase MK‐STYX regulates neurite outgrowth and alters the morphology of primary neurons
Authors: Hinton Shantá D. , Banks Dallas , Dahal Arya , McFarland Alexander , Flowers Brittany , Stephens Christina , Swack Benjamin , Gugssa Ayele , Anderson Winston 
Published: June 2021

Mitogen‐activated protein kinases (MAPKs) are essential players in important neuronal signaling pathways including neuronal development, plasticity, survival, learning, and memory. The inactivation of MAPKs is tightly controlled by MAPK phosphatases (MKPs), which also are important regulators of these neuronal processes. There is compelling evidence that a unique catalytically inactive member of the MKP family, MK‐STYX (mitogen activated kinase phosphoserine/threonine/tyrosine binding protein), is a regulator in neuronal processes such as neurite outgrowth. We previously reported that the MK‐STYX dramatically increases the number of primary neurites in rat pheochromocytoma (PC‐12) cells through the RhoA signaling pathway. MK‐STYX decreases RhoA activation, whereas knockdown of MK‐STYX increases RhoA activation. Furthermore, MK‐STYX increases phosphorylation of cofilin, a RhoA downstream effector, whereas phosphorylated cofilin decreases when MK‐STYX is knocked down with shRNA. Throughout the course of these experiments, we noticed that cells overexpressing MK‐STYX developed more neurites, which often branched. Here, we report that microtubules and microfilaments, components of the cytoskeleton that are involved in the formation of neurites, are present in MK‐STYX‐induced outgrowths. In addition, in response to nerve growth factor (NGF), MK‐STYX‐producing cells produced more actin growth cones than non‐MK‐STYX‐expressing cells. Transmission electron microscopy confirmed that MK‐STYX‐induced neurites form synapses. Furthermore, the expression of Tau‐1 and MAP2 (microtubule associated protein 2) in MK‐STYX‐induced neurites suggests that they have both axonal and dendritic properties. Further studies in hippocampal primary neurons demonstrated that MK‐STYX altered their morphology. A significant number of primary neurons expressing MK‐STYX had more than the normal number of primary neurites. Taken together these data provide evidence that MK‐STYX causes cytoskeletal rearrangement. It also highlights that this unique member of the MKP subfamily has the potential to have a major role in neuronal signaling.Support or Funding InformationThis work was supported by the National Science Foundation Grant MCB1113167 to S.D.H.; Coco Award to S.D.H.; Howard Hughes Medical Research Institute grant through the Undergraduate Science Education Program to the College of William and Mary; a DuPont Fund Student‐Faculty Research Team Stipend awarded to A.D. and S.D.H. through a grant by the Jessie Ball Grant Fund to the William and Mary Scholars for Undergraduate Research Experience program; Ferguson Awards to D.A.B., A.D., and C.S., and the Dintersmith Honors Fellowship to A.D.This abstract is from the Experimental Biology 2018 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
The First‐year Research Advancement Program (FRAP): Fostering Persistence of Underrepresented Students in Biology and Chemistry
Authors: Mills Kenneth Vincent , Paxson Julia 
Published: June 2021

We co founded the First Year Research Advancement Program (FRAP) in 2014, based on a workshop we attended by the Council on Undergraduate Research. Our goal is to increase persistence in STEM of academically promising students who belong to groups that traditionally do not persist at the same rate as majority students, including first‐generation students, PELL‐eligible students, and underrepresented minority students. Based on research that suggests that early exposure to research experiences increases discipline identity and persistence, we established FRAP. Two first‐year students per lab are paired with a senior student mentor, and each are paid for eight hours a week such that the experience replaces other work‐study. Students spend six hours a week in the lab, one hour in lab meeting, and one hour in a meeting with the cohort of 8–16 students in which faculty and students discuss college and STEM issues and form an academic professional network. Mentors are trained in coaching and mentorship. We have assessed the program in collaboration with the College's Office of Assessment and Research and found increases in self‐reported confidence and engagement. As our number of participants increases, we will study the effect on four‐year persistence versus matched sets of non‐participants. Over the last four years, 30 first year students have participated in FRAP. Our first cohort of FRAP students are now seniors; two current student mentors started as FRAP students themselves. Six of the eight FRAP students that started in the Mills lab are still part of the research groupSupport or Funding InformationThis work was supported by the National Science Foundation (MCB‐1517138 to KVM) and a Henry Dreyfus Teacher‐Scholar Award (KVM).This abstract is from the Experimental Biology 2018 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
A Competency‐Based Approach to Developing Biomolecular Visual Literacy
Authors: Dries Daniel R. , Dean Diane M. , Franzen Margaret A. , Jakubowski Henry V. , Novak Walter R. P. , Procko Kristen , Roca Alberto I. , Terrell Cassidy R. 
Published: June 2021

When you show a visual representation of a biomolecule, do your students “see” what you “see”? Are they able to interpret the model correctly and draw appropriate conclusions about the structure and atomic/molecular interactions? Do they grasp that cartoon and space‐filling models represent the same protein? Biochemistry instructors use visual representations of biomolecules to teach many concepts, yet there are few tools and frameworks to assess whether students can interpret these models. The BioMolViz.org group is a team of educators developing these tools. Over four years, we have identified a set of overarching themes that encompass biomolecular visualization skills with teachable objectives. We define proficiency levels for the objectives, describe student competency within the objective at the novice (first year) and amateur (junior/senior year) levels, and link these competencies with assessment questions. For example, the objective: “students will describe the significance of the monomer unit location within the three‐dimensional structure of a polymer” can be applied throughout the student's academic career. Novice students would be expected to identify the termini of a biological polymer, while more advanced students would catalog interactions of monomers that stabilize the macromolecule. Here, we present our current efforts on this Biomolecular Visualization Framework, including the results from four National Science Foundation‐funded 2018 workshops and our diversity SACNAS/ABRCMS outreach efforts. We propose targeted visual literacy development will enable students to understand the structure and associated function of biomolecules. The BioMolViz.org website makes resources widely available to help instructors facilitate this growth.Support or Funding InformationThis work was supported by the National Science Foundation under award numbers DUE‐1022793, ‐1323414, ‐1503811 and IUSE‐1712268. Any opinions, findings, and conclusions or recommendations expressed in this publication are those of the authors and do not necessarily reflect the views of the National Science Foundation.This abstract is from the Experimental Biology 2018 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
Pleiotropy and Flux Control in the Indolic Biochemical Pathways in Arabidopsis thaliana
Authors: Kack Jessa Joy , Leean Tori Kathryn 
Published: June 2021

Metabolic pathways are a series of highly interconnected networks. Predicting how changes in one pathway influence the rest of metabolism is a challenge. Small changes in the expression of one gene in a single pathway may have far reaching pleiotropic effects across the genome or, alternatively, large changes in expression of one gene may be buffered and have only local effects. However, taking into account pathway properties of an enzyme (including the connectedness to other parts of metabolism or the amount of control an enzyme has over pathway production) may lead to predictable impacts on gene expression across the genome (e.g. perturbations in highly connected enzymes to influence a wide range of pathways). To address this question, we are studying the indolic glucosinolate pathway in Arabidopsis thaliana. Glucosinolates are herbivore defense compounds produced by relatives of Arabidopsis and protect the plant against generalist herbivores. The indolic glucosinolate pathway is also connected to the incredibly important plant hormone pathway, auxin, in that the pathways share a product (indole‐3‐acetaldoxime). Auxin is a growth hormone involved in nearly every step of plant development, thus we predict that some changes to the indolic pathway will produce only local effects while some changes may produce wide‐ranging effects. To investigate the influence of pathway position and connectedness on global gene expression and glucosinolate production we created gene expression knockdown lines in every gene in the indolic glucosinolate pathway. By monitoring indole glucosinolate pathway output with High Performance Liquid Chromatography (HPLC) and measuring global gene expression with RNAseq, we can study how changing gene expression within a pathway influences the output of that pathway and gene expression across the genome.Support or Funding InformationSD BRIN P20GM103443SD EPSCOR IIA‐1355423This abstract is from the Experimental Biology 2018 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
mtDNMT1 and DNMT3b cooperate to methylate mitochondrial DNA and regulate mitochondrial transcription
Authors: Shock Lisa , Burton Elliot , Robinson Jason , Taylor Shirley 
Published: June 2021

Mitochondria are dynamic modulators of cell physiology, rewiring their metabolic and signaling pathways to allow for rapid and flexible adaptions to environmental changes. Mitochondrial DNA (mtDNA) is packaged into DNA‐protein complexes called nucleoids, and the DNA is epigenetically modified (1,2). We, and others, have demonstrated that mtDNA methylation represents a powerful mechanism for regulating transcription of mtDNA‐encoded oxidative phosphorylation (OXPHOS) genes under conditions of cellular stress (1,3). We identified a mitochondrial (mt) isoform of DNA methyltransferase 1 (mtDNMT1) that translocates to the mt matrix, and binds to mtDNA in critical control regions (1). Our new data demonstrates that mtDNMT1 interacts with several proteins essential for proper functioning of mitochondria, including core components of the nucleoid. These findings place mtDNMT1 at the heart of mitochondrial nucleoid organization, and suggest that mtDNMT1 plays a critical role in regulating nucleoid structure and mitochondrial output, either as a consequence of, or independently from, its methylation activity. We now have evidence that mtDNMT1 is not working alone: DNMT3b works in concert with mtDNMT1 to methylate mtDNA and regulate mt transcription. CRISPR/Cas9‐mediated inactivation of mtDNMT1 and/or DNMT3b activity resulted in significant decrease in mitochondrial methylation across the heavy and light strand promoters of mtDNA, with a concomitant reduction in transcription of several mtDNA‐encoded OXPHOS genes. Cells lacking mtDNMT1 and/or DNMT3b exhibited a striking morphological change, undertaking an elongated, fibroblast‐like appearance with increased migration, reminiscent of cells undergoing epithelial‐to‐mesenchymal transition (EMT), a hallmark of cancer metastasis. These observations implicate mtDNA methylation in the phenotypic plasticity that occurs in response to changing cellular growth conditions, driving the initiation and progression of numerous pathologies. We propose that the mitochondrial DNA methylation machinery may constitute a novel target for therapeutic intervention.Support or Funding InformationMCB 1122018 (NSF) to Taylor, Start‐up funds (VCU Dept of Microbiology and Immunology) to Shock, IRG‐14‐192‐40 (ACS) to ShockThis abstract is from the Experimental Biology 2018 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
Accumulation of Gut Bacteria May Cause the Age‐Related Decline of Anoxia Tolerance in Adult Drosophila melanogaster
Authors: Sargent James , Campbell Jacob , Harrison Jon 
Published: June 2021

Cell death occurring from anoxia is the major pathology during heart attack, stroke and multiple other diseases. Humans vary substantially in their ability to survive anoxia, especially across ages, and the basis to this variation is not well‐understood. Drosophila melanogaster have similar metabolic pathways to humans but have much better capacities to tolerate anoxia, suggesting that understanding mechanisms of anoxia tolerance in flies may provide insight for the development of new medical treatments. We exposed adult Drosophila, ages 1, 3, 5, 7, 9, and 12 days old, to six hours of anoxia and assessed survival 24‐hours post‐treatment. Seventy‐nine percent of adults one day past eclosion survived; while only 10% of twelve‐day‐old adults survived; thus Drosophila show age‐related decline in anoxia tolerance like humans. In anoxia, ATP levels declined rapidly (< 30 min) to near‐zero levels in both 1 and 12 day old adults; thus the better anoxia‐tolerance of young adults is not due to a better capacity to maintain cellular energetic status. The concentration of bacteria in the gut is known to increase strongly with age in Drosophila. To test whether declining anoxia tolerance might be due to this increasing bacterial load, we replaced their food daily, every third day, or every sixth day, allowing us to vary gut bacterial load from low to high, respectively. At 12 days of age, each treatment group was exposed to six hours of anoxia and assayed for gut bacterial load. Anoxia tolerance was strongly and negatively affected by bacterial load. These data suggest that increasing bacterial load may play an important role in the age‐related decline of anoxia tolerance in Drosophila.Support or Funding InformationThis research was supported by NSF IOS 1256745 and the SOLUR program at ASU.This abstract is from the Experimental Biology 2018 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
Intestinal proteome response to salinity stress in three tilapiine spp
Authors: Root Larken , Kültz Dietmar , Cnaani Avner , Con Pazit 
Published: June 2021

Chronic salinity stress is likely to have significant impacts on organismal performance, especially near the upper bounds of the Critical Salinity maximum (CSmax), the “zone of resistance”. Some euryhaline fish species maintain stable internal osmolality over great salinity ranges, while close relatives tolerate much narrower ranges. Greater tolerance ranges have also been linked to reduced growth under optimum conditions. For example, breeding for improved growth rates in the tilapia species Oreochromis niloticus has inadvertently resulted in decreased tolerance to hypersaline water conditions. To examine changes in growth and stress tolerance at the cellular and tissue levels, high salinity acclimation challenges were conducted for three cichlid species, including the previously mentioned O. niloticus with reduced salinity tolerance, wild‐type (WT) O. mossambicus which exhibit tolerance to salt concentrations greater than seawater, and WT Astatotilapia burtoni which exhibit low salinity tolerance similar in range to the O. niloticus strain. Three intestinal sections were sampled from salinity‐challenged fish at 90% CSmax, and from control fish maintained in freshwater, and used to establish a standardized data‐independent acquisition (DIA) assay for label‐free quantitative proteomics for a large number of proteins in each species. Spectral libraries created by data‐dependent acquisition (DDA) and annotated using multiple search engines were used for DIA assay construction. Skyline and a sample training set were used for automated and manual assay curation to select and validate reproducible transitions and proteotypic peptides for protein quantitation. Salinity effects on intestinal protein expression patterns in each species were statistically evaluated and corresponding protein sets analyzed for gene ontology enrichment. The resulting data on salinity‐dependent intestinal proteome dynamics provide insight into biochemical processes controlling growth and stress tolerance.Support or Funding InformationFunded by BARD and NSF Grant IOS‐1355098This abstract is from the Experimental Biology 2018 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
Prematurity and postnatal development regulate the expression of the FXR‐FGF19 axis in neonatal pigs
Authors: Smith Victoria Alice , Jiang Yanjun , Thymann Thomas , Sangild Per , Manjarin Rodrigo , Burrin Douglas 
Published: June 2021

The farnesoid X receptor (FXR) is a nuclear bile acid receptor that regulates bile acid homeostasis. A key FXR target is fibroblast growth factor 19 (FGF19), which functions as an endocrine hormone. FGF19 is produced in both the intestine and liver in humans and pigs, whereas mice and rats express the human ortholog FGF15 only in the intestine, thus making pigs a more relevant model of human FGF19 biology. Gut bile acids activate small intestinal FXR triggering FGF19 secretion which circulates via the portal blood to inhibit hepatic bile acid synthesis by suppressing the rate limiting enzyme in bile acid synthesis, CYP7A1, via activation of extracellular‐signal‐regulated kinases (ERK) and c‐Jun N‐terminal kinase (JNK‐1) MAP kinase pathways and the orphan nuclear receptor, small heterodimer partner (SHP). Thus, enterohepatic FXR‐FGF19 signaling functions as a negative feedback signal to regulate bile acid homeostasis. Bile acid secretion has been shown to increase with gestational age. We hypothesized that expression and activation of the intestinal FXR‐FGF19 axis would be diminished in premature vs. term pigs and increased with postnatal age. We studied piglets delivered by cesarean‐section at 10 days preterm and full term. All pigs were fitted with orogastric and umbilical arterial catheters and fed minimal enteral nutrition with bovine colostrum for 5 d and then bovine mature milk until 26 d‐of‐age. Plasma and tissue samples were collected at days 0, 5, 11, and 26 d. We developed a porcine FGF19 specific sandwich ELISA assay by cloning the porcine FGF19 gene, overexpressing the protein using a baculovirus expression system, and developing monoclonal antibodies. We quantified the plasma FGF19 concentration using the ELISA and assayed distal intestinal gene expression of FGF19 and FXR by RT qPCR. We found that plasma FGF19 levels are strikingly lower (P<0.05) in premature vs. term newborn pigs. In addition, postnatal age markedly altered activity of the FXR‐FGF19 axis, where plasma FGF19 levels increased significantly 5 d after birth in preterm, but not term pigs. Plasma FGF19 levels then decreased (P<0.05) significantly between 5 and 26 d‐of‐age in both preterm and term pigs. Intestinal FXR and FGF19 expression were lower (P<0.05) in premature vs term newborn pigs and decreased (P<0.05) between day 5 and 26 d‐of‐age. We conclude that both prematurity and postnatal age regulate the FXR‐FGF19 axis in neonatal pigs. These findings have implications for the bile acid homeostasis, FGF19 function and growth of preterm and term infants during early postnatal life.Support or Funding InformationAgricultural Research Institute, USDA‐ARS, NIH, CalPoly Summer Undergraduate Research Program (SURP), NEOMUNEThis abstract is from the Experimental Biology 2018 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
PABP and eIF4B Effects Binding Affinity and Kinetic Rates of Genome Linked Viral Protein (VPg) with Eukaryotic Initiation Factor 4F
Authors: Khan Mateen A. , Goss Dixie J. 
Published: June 2021

Translation initiation is a critical early step in the viral replication cycle. Interaction of eukaryotic translational initiation factors with VPg of Turnip mosaic virus (TuMV) plays an important role in the cap‐independent initiation of protein synthesis. To understand this process in potyviruses, we investigated the equilibrium binding, thermodynamic parameters and rate constants for the interaction of VPg with eIF4F in the presence of PABP and eIF4B using fluorescence and stopped‐flow spectroscopy. Equilibrium studies showed that PABP increased VPg binding to eIF4F about 3‐fold; however, both PABP and eIF4B together enhanced VPg binding to eIF4F about 4‐fold, showing an additive effect rather than the large increase in affinity shown for cap binding. Temperature dependent studies showed the increase in VPg binding to eIF4F in the presence of PABP and eIF4B was enthalpy‐driven and entropy‐favorable. PABP and eIF4B decreased the entropic contribution for VPg binding to eIF4F. The decrease in entropy for the formation of eIF4F·4Bmiddot;PABP‐VPg complex suggested weakened hydrophobic interactions for complex formation and an overall conformational change. Rate constant for eIF4F interaction with VPg in the presence of PABP and eIF4B was 4‐fold faster; and dissociation rate was 3‐fold slower as compared to eIF4F alone. The temperature dependence of the VPg binding to eIF4F was significantly reduced in activation energy in the presence of PABP and eIF4B. When both PABP and eIF4B were present, not only was the energy barrier reduced but the binding rate was faster and dissociation rate was slower for the formation of eIF4F‐4B‐PABP‐VPg complex suggests more stable platform for further initiation complex formation. These results further support the importance of PABP and eIF4B interaction to eIF4F with VPg for efficient viral translation.Support or Funding InformationNational Science Foundation MCB‐1513737 (to D.J.G.) and Alfaisal University Research Support IRG‐16414 (to M.A.K.)This abstract is from the Experimental Biology 2018 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
Differential protein splicing of salt‐dependent inteins from Haloquadratum walsbyi
Authors: Lynch Abigeal Kathleen , Amunya Shirley , Gomez Alvin , Reitter Julie , Mills Kenneth 
Published: June 2021

Protein splicing is a self‐catalyzed, post‐translational process in which an intervening polypeptide sequence, or an intein, catalyzes its removal from two flanking polypeptide sequences, or exteins, as well as the ligation of the exteins. We are interested in the splicing capabilities of two inteins that interrupt the cdc21 protein from Haloquadratum walsbyi (Hwa). Hwa is a halophilic archaeon found in high salt environments such as the Red Sea. For this reason, we hypothesize that protein splicing may be salt dependent. We are interested in studying the splicing capabilities of both inteins separately and when expressed as part of the same protein. One intein, Cdc21a, does not splice on overexpression in E. coli, but can be induced to splice in vitro on incubation with 2.5 M sodium chloride at 28°. The other intein, Cdc21d, splices in vivo, and can be induced to splice further with higher concentrations of salt. When expressed in the same precursor fusion protein, the inteins continue to show differential activity conditional on salt concentration, leading to alternative spliced products.Support or Funding InformationThis work was supported by the National Science Foundation (grants MCB‐1244089 and MCB‐1517138 to KVM), the Dreyfus Foundation (KVM), and Diane D. Brink P12 to the Alumni/Parent Summer Research Scholarship Fund. ALThis abstract is from the Experimental Biology 2018 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.