bluuebunny/crossref_metadata_2025_split huggingface dataset:
Implementation of a place‐based, interdisciplinary, and research‐oriented teaching model to increase retention in STEM
Authors: Frederich Markus , Roese Ursula , Bymers Leah , Zeeman Stephan 
Published: June 2021

STEM education is becoming increasingly important for succeeding in a society that depends on science and technology. However, STEM persistence rates in undergraduate programs are low, nationally in the range of 40%. A pedagogical shift towards more experiential, project‐based education has shown to be successful in increasing STEM persistence rates, enhancing understanding of science, and increasing student's motivation to learn. Building on a strong track record in undergraduate research we are implementing a place‐ and theme‐based interdisciplinary project that spans all 4 years of undergraduate education in all STEM majors. We use our location at the mouth of the Saco River and the surrounding ecosystem as the overarching theme: TURBO: The Undergraduate Saco River Biodiversity Observatory. This project is modeled after an LTER‐research site. Multiple existing and newly developed lab activities and field trips in Biology, Marine Biology, Environmental Science, Chemistry and Physics, and Mathematics are focused on the Saco River Ecosystem and new activities are implemented to investigate in an LTER‐style the fresh and seawater systems surrounding the campus. Students collect data on water parameters, invasive species, invertebrates, DNA barcoding, fish, algae, plankton, marsh diversity, plants, invasive species, and more. All data are available to students and faculty in a central database, developed by students. Statistics courses will use student‐generated data instead of standard text book examples. Our annual assessment tools revealed actually a slight drop in confidence in STEM comparing the time points before starting college and after the first year. This drop potentially represents an initially idealized view of STEM, that becomes more realistic during the first college year. This highlights the importance of engaging and authentic STEM activities early in the college career to fully capture them. This place‐ and project‐based interdisciplinary approach can be used as a blueprint for other programs and schools.Support or Funding InformationFunded by NSF grant# DUE‐IUSE 1431955.This abstract is from the Experimental Biology 2018 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
3D Contrast Techniques for Visualizing Anatomy and Their Application for Human Education, Vertebrate Biomechanics and Paleobiology
Authors: Holliday Casey Monahan , McGetchie Faye , Johnson Laura , Hill Cheryl , Sellers Kaleb , Middleton Kevin , Sullivan Samuel , Schiffbauer James 
Published: June 2021

New contrast techniques for visualizing 3D anatomy of soft tissues using tomography are revealing outstanding new opportunities for understanding the internal anatomy of humans and other animals. Iodine‐contrast (DiceCT) combined with 3D modeling and computational approaches now enables new directions in anatomy education, body composition, muscle fiber architecture, biomechanics and evolutionary biology. Here we present several new applications of DiceCT‐derived soft‐tissue data used in education and research approaches. First we illustrate new methods using human material that reveal new data on complicated, high‐yield soft‐tissue centric regions including the infratemporal fossa and ear, throat, pelvic floor and wrist. Second we share new methods in applying 3D muscle fiber architecture estimates to biomechanical investigations of vertebrate function. Finally we show how soft‐tissue data help test taphonomic and paleobiological hypotheses of body composition in soft‐bodied fossils derived from conservat‐lagerstatten. These vignettes offer incredible utility for hypothesis testing, biomechanical modeling and anatomy education.Support or Funding InformationNSF IOS 1457319, NSF EAR 163753, Missouri Research Council, NSF CAREER 1652351, NSF IF 1636643This abstract is from the Experimental Biology 2018 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
Spatial and temporal processes involved in the naturally occurring sarcomere disassembly during electric organ regeneration in the teleost Sternopygus macrurus
Authors: Unguez Graciela Alexandra 
Published: June 2021

Exciting new findings are increasing our understanding of the protein composition of sarcomeres – the highly ordered contractile units of striated muscle – and the common pathways of sarcomere assembly in both heart and skeletal muscle. Although disruption s in these pathways are implicated in muscle diseases, events involved in the disassembly of sarcomeres remain largely unknown. The electric fish S. macrurus has the unique ability to regenerate all tail tissues after amputation including skeletal muscle and the muscle ‐ derived cells of the electric organ, i.e., electrocytes. During regeneration, some muscle fibers fuse and disassemble their sarcomeres to convert into electrocytes. To study changes in the spatial and temporal expression of protein components of distinct sarcomeric regions during the muscle ‐ to ‐ electrocyte conversion, we have begun to use immunofluorescence and ultrastructural approaches. Specifically, we are using markers of the Z ‐ disk (EA53 antibody), inter ‐ Z ‐ disk region (E398P antibody), A ‐ b ands (MF20 antibody), and I ‐ bands (phalloidin stain) to describe this naturally occurring process of sarcomere disassembly during electrocyte differentiation. Our preliminary data suggest a pattern of sarcomere breakdown characterized by dissociation of the I ‐ band followed by loss of A ‐ band then Z ‐ disks structures while the inter ‐ Z ‐ disk components are conserved. This pattern of sarcomere disassembly differs from a dedifferentiation process predicted by a current model of sarcomere formation during muscle differentiation (Ehler and Gautel, Adv. Exp. Med. Biol., 2008).Support or Funding InformationThe following grants funded this work: NIH SCORE Grant 1SC1GM092297‐01A1 (GAU), NSF Grant CNS‐1248109 (GAU), and Howard Hughes Medical Institute Science Education Grant 5200693.This abstract is from the Experimental Biology 2018 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
Effects of the Organophosphate Pesticide Chlorpyrifos on Muscle Architecture in 72 hour Zebrafish Embryos
Authors: Willrich Robert C. , Watanabe Taylor H. , Fradinger Erica A. 
Published: June 2021

Chlorpyrifos (CPF) and other organophosphate pesticides (OP) are commonly used in the agricultural industries of the United States and developing countries. High concentrations of OP's in rivers and lakes have led to concerns for its negative effects on the wildlife and humans. These substances have been documented to act as neurotoxins that lead to the buildup of acetylcholinesterase in cholinergic neurons. This study was performed to determine the effects of CPF on the development of muscles for zebrafish embryos 72 hours post‐fertilization (hpf) in a calcium‐depleted medium. Using confocal microscopy of wholemount MF20 immuno‐labeled embryos, several morphological changes were observed. There was an increase in the length of muscle myomeres and width of individual muscle fibers in CPF exposed embryos. Additionally, some embryos showed strong muscle fiber disorganization. These observations show that CPF has a clear effect to muscle development and architecture possibly due to increased cholinergic stimulation during development.Support or Funding InformationDepartment of Defense, ARO 66367‐RT‐REP; Keck Foundation Undergraduate Fellowship to R.C.W.; James Irvine Chair in Biological Sciences to E.A.F.This abstract is from the Experimental Biology 2018 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
High Fat Diet Blunts the Activation of Canonical Wnt Signaling Pathway Induced by Radiation Therapy in Mouse Colon Epithelia
Authors: Xu Guanying , Emmons Russel , De Lisio Michael , Pan Yuan‐Xiang , Chen Hong 
Published: June 2021

BackgroundRadiation stimulates multiple metabolic pathways in colon epithelial cells in mice, including the Wnt signaling pathway. Activation of Wnt/β‐catenin pathway was indicated to increase resistance to radiation therapy. On the other hand, we have shown that long‐term consumption of high fat diet inhibits Wnt signaling through the down‐regulation of β‐catenin expression in colon.ObjectivesThe main goal of this present study is to examine the impact from high fat diet on the expression of genes involved in the Wnt/β‐catenin pathway on colon epithelial in mice exposed to radiation.MethodsIn this study, 5‐week‐old male mice were fed either a control diet (n=22, 10% kcal fat) or a high‐fat diet (n=24, 45% kcal fat) for 11 weeks. Half of the mice were sampled as pre‐irradiation (Pre‐CON and Pre‐HF). The rest of the mice were treated with a single dose of radiation at 3 Gy (IR‐CON and IR‐HF) and tissue collection was conducted after 4 more weeks of respective dietary treatments. mRNA expression of Wnt pathway genes were analyzed in the colon tissue.ResultsRadiation significantly increased mRNA expression of canonical Wnt signaling related genes including APC, AXIN1, CTNNB1 (β‐catenin) and cMyc in IR‐CON comparing to Pre‐CON (p<0.05). On the other hand, APC, AXIN1 and cMyc remain unchanged in IR‐HF comparing to Pre‐HF, only CTNNB1 increased. Sfrp2, a Wnt signaling antagonist, was significantly increased in IR‐HF comparing to Pre‐HF (p<0.05), while remained unchanged in IR‐CON comparing to Pre‐CON. Furthermore, mRNA expression of a cell cycle control gene, p21, was significantly increased in IR‐HF. This is accompanied with a significant decrease of CyclinD1 expression (p<0.05, when comparing to Pre‐HF).ConclusionOverall, analysis of mRNA expression suggests that high fat diet blunts the effects of radiation on inducing the Wnt signaling pathway, which is associated with cell cycle pathway in mouse colon epithelia. Our study shows that high fat diet may interfere with radiation treatment in colon.Support or Funding InformationThis project was supported in part by the Campus Research Board of University of Illinois at Urbana‐Champaign and the USDA Cooperative State Research, Education and Extension Service, Hatch project numbers # ILLU‐698‐923 and ILLU‐698‐379 to H.C.This abstract is from the Experimental Biology 2018 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
Role of eukaryotic initiation factor 3 in the non‐canonical mechanism of Barley Yellow Dwarf Virus translation initiation
Authors: Powell Paul , Bhardwaj Usha , Mitra Sondeb , Gonzalez Ruben , Goss Dixie 
Published: June 2021

Plant viruses are a world‐wide threat both economically and to the food supply. Many of these are positive‐strand RNA viruses that have developed a myriad of non‐canonical translation initiation mechanisms. These unique mechanisms circumvent cap‐dependent translational controls and enable the viruses to outcompete host cell mRNA for the translation machinery. Many RNA viruses lack the canonical 5′ 7‐methylguanosine cap in their mRNAs, thereby allowing them to bypass canonical translation initiation. Instead, these mRNAs utilize structures in the 3′ untranslated region (UTR) of their mRNA known as a 3′ CITE (cap‐independent translation element) to drive non‐canonical translation initiation. Recently, we have shown that a 3′ CITE in Barley Yellow Dwarf Virus (BYDV), termed the 3′ BTE (BYDV 3′ CITE), can bind eukaryotic translation initiation factor (eIF) 4G, eIF4A, and ATP‐bound eIF4B in order to recruit the 40S ribosomal subunit and form a pre‐initiation complex (PIC) at the 3′ BTE. These eIFs cannot directly recruit the 40S subunit to the 5′ UTR of BYDV, but must instead transfer the 40S subunits to the 5′ end of the mRNA scanning, AUG detection, and translation elongation to proceed. This transfer process is aided by a long‐distance, ‘kissing‐loop’, base pairing interaction between stem‐loops in the 5′ and 3′ ends of BYDV. This kissing loop interaction is relatively weak, leading to the hypothesis that additional factors are required to create a stable 5′–3′ interaction capable of efficiently transferring the PIC. Data from pulldown experiments have shown that, in addition to eIF4G, almost every subunit of eIF3 is bound to the BTE. Single‐molecule fluorescence co‐localization experiments have shown that eIF3 specifically and significantly enhanced binding of 40S subunits to the BTE. Moreover, fluorescence anisotropy‐based binding studies have shown that eIF3 binds directly to both the BTE and the 5′ UTR of BYDV, that the BTE and 5′ UTR do not compete for binding to eIF3, and that the presence of the 40S subunit increases the affinity with which eIF3 binds to the BTE and 5′ UTR. Collectively, these data suggest that eIF3, the 40S subunit, the 3′ BTE, and the 5′ UTR are components of a single macromolecular complex. Based on this interpretation of our data, we propose that eIF3 bridges the 3′ and 5′ ends of BYDV and aids the kissing loop interaction in transferring the PIC from the 3′ to the 5′ end of BYDV.Support or Funding InformationGrant Support: NSF MCB‐1513737 (to DJG), NSF‐IGERT Fellowship 0965983 (to PP), and NIH GM 084288 (to RLG).This abstract is from the Experimental Biology 2018 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
Pervasive, coordinated protein level changes driven by transcript isoform switching
Authors: Brar Gloria , Otto George , Cheng Ze , Powers Emily , Keskin Abdurrahman , Jovanovic Marko 
Published: June 2021

To better understand the gene regulatory mechanisms that program developmental processes, we carried out simultaneous, genome‐wide measurements of mRNA, translation and protein through meiotic differentiation in budding yeast. Surprisingly, we observed that the levels of several hundred mRNAs are anti‐correlated with their corresponding protein products. We show that rather than arising from canonical forms of gene regulatory control, the regulation of at least 380 such cases—or over 8% of all measured genes—involves temporally regulated switching between production of a canonical, translatable transcript and a 5′ extended isoform that is not efficiently translated into protein. By this pervasive mechanism for the modulation of protein levels through a natural developmental program, a single transcription factor can coordinately activate and repress protein synthesis for distinct sets of genes. The distinction is not based on whether an mRNA is induced or not, but rather based on the type of transcript produced.Support or Funding InformationThis work was supported by NIH funding to G.A.B. (DP2‐GM‐119138), investigator awards from the Alfred P. Sloan Foundation and Pew Charitable Trusts to G.A.B., UC‐Berkeley start‐up funding to G.A.B. G.M.O. is supported by an NIH training grant (GM0007232) to UCB MCB. E.P. is supported by an NSF predoctoral fellowship. M.J. was supported by the Marie Sklodowska‐Curie IOF and he and A.K. are supported by Columbia start‐up funding.This abstract is from the Experimental Biology 2018 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
Kinetics and Binding Studies of the (NRPS)‐Independent Siderophore (NIS) Synthetase DesD
Authors: Lathan Kiera , Hoffmann Katherine 
Published: June 2021

Pathogenic bacteria have always been a problem in human health. They do not discriminate when it comes to finding a human host for them to survive in, so it effects all people regardless of ethnicity and socioeconomic background. Pathogenic bacteria use their host to supply them with something that they lack. In the case of iron, bacteria synthesize, secrete, and reacquire small molecule chelators called siderophores. Our lab is specifically focusing on siderophores made with the non‐ribosomal peptide synthetase independent siderophore (NIS) pathways, which always contain at least one NIS synthetase family protein. These proteins are excellent drug targets because of their association with virulence, their unique chemistry, and their unique fold. A drug that successfully targeted and inhibited this family of proteins might represent a new class of antibiotics.The best studied NIS synthetase is Desferrioxamine synthetase D (DesD) from Streptomyces coelicolor, which makes the group of siderophores called desferrioxamines. Desferrioxamine E is the biggest siderophore made of 3 N‐hydoxysuccinylcadaverine units repeatedly added by DesD and then cyclized. This broad substrate specificity (the variation in size recognized by the same protein), is the reason why we are interested in mapping the thermodynamics of binding to different substrates to see if there is a variation in association constants. We are using Isothermal Titration Calorimetry (ITC) because it is label‐free and have successfully piloted the conditions for the assay. If we are able to delineate the priority requirements for binding, we will progress to designing an inhibitor to maximize the binding affinity. ITC methods will also be used to characterize the kinetics DesD so that a better overall picture of the proteins' biochemistry may be understood.Support or Funding InformationThis work was supported by the National Science Foundation grant to K.M.H. (MSP ‐ 1716986) and by California Lutheran University.This abstract is from the Experimental Biology 2018 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
Characterization of the 3rd and 4th EF‐hand Motifs of NADPH Oxidase 5 by Spectroscopy and Calorimetry
Authors: Wei Chin‐Chuan , Fabry Emily 
Published: June 2021

Reactive Oxygen Species generated by NADPH oxidases (Nox's) are implicated in intracellular signaling leading to altered gene expression, protein biosynthesis, apoptosis, kinase activation, and oxygen sensing. Among the Nox family, Nox5 contains an additional EF‐hand domain (EFD) along with transmembrane domain and dehydrogenase domain. It is believed that Ca2+ binding to EFD triggers a conformational change, leading to interaction with its dehydrogenase domain and triggers ROS‐production. However, the Ca2+ binding to Nox5‐EFD and its domain‐domain interaction is not completely understood. Previously, we have characterized the Ca2+ binding to EF1 and EF2 located in the N‐terminus of Nox5 (N‐EFD) using isothermal titration calorimetry (ITC). Here we extended to our study to EF3 and EF4 of C‐EFD. Our preliminary data indicates that EF3 is specific to the Ca2+/Mg2+ ions with an unusually high Ca2+ binding affinity (Ka = ~108 M−1) while EF4 is specific to Ca2+ only. The results were supported by mutation studies, in which Glu at the 12th position of each EF loop were replaced with Gln. The mutants lose their Ca2+ binding ability significantly, which allows us to determine microscopic Ca2+ binding affinity for each EF‐hand. Currently we are measuring the Ca2+ binding using different buffers and at different temperatures, which will reveal the heat capacity change upon Ca2+ binding. The heat capacity along with melting measured with differential scanning calorimetry will provide valuable information about the conformational change of EFD.Support or Funding InformationNational Science Foundation CHE‐1608484This abstract is from the Experimental Biology 2018 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
A Biochemical and Structural Look into the Functional Role of Transferrin in D. melanogaster
Authors: Weber Jacob , Brummett Lisa , Geisbrecht Brian , Kanost Michael , Gorman Maureen 
Published: June 2021

Transferrins (TFs) are a family of vertebrate and invertebrate proteins that have high affinity for ferric iron. The extensively studied mammalian TFs are typically bilobal in structure and have iron binding sites in both their lobes—critical to their essential role in proper iron sequestration and transport in blood. These sites coordinate iron binding through four conserved residues—aspartate, tyrosine, tyrosine and histidine—and a carbonate ion cofactor. Aside from their function of transporting iron to cells, their ability to sequester and tightly bind iron is a crucial defense against invading pathogens. Many insect TFs show less sequence conservation and have only one iron binding site. They have not been adequately studied for their roles in iron metabolism and immunity. Our research aims to determine the function(s) of insect TF via biochemical and structural analysis using Drosophila melanogaster transferrin (DmTsf1) as a model. We purified DmTsf1 from a baculovirus expression system using ammonium sulfate precipitation, and ion exchange and gel filtration chromatography, and generated apo‐ and holo‐forms. Apo‐DmTsf1 but not holo‐DmTsf1 inhibited Escherichia coli growth, suggesting an immune function that relies on iron sequestration. A homology model of DmTsf1 showed a similar bilobal structure but iron binding in only one lobe. The putative binding residues are glutamate, tyrosine, and tyrosine. If the model is correct, a loss of the histidine residue in DmTsf1 should result in a lower binding affinity for iron. We are using crystallography to identify the actual iron binding residues. Initial protein‐ligand binding kinetics using equilibrium dialysis have shown Apo‐DmTsf1 to indeed having one binding site for ferric iron and a lower Kd of 10−18. Further biochemical pursuits into the role of insect TFs will include examining DmTsf1's ability to bind other metals.Support or Funding InformationNIH NGMS R37 GM041247, NSF IOS 1656388This abstract is from the Experimental Biology 2018 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.