bluuebunny/crossref_metadata_2025_split huggingface dataset:
Day One: What are the possibilities for the first day of gross anatomy courses?
Authors: Metzger Keith A , Elkowitz David E , Rennie William 
Published: June 2021

The first day of gross anatomy courses varies across curricula, potentially including cadaveric dissection, memorial services, or other introductory activities. We assert that the first day of an anatomy course is a crucial formative experience, and as such has great potential for the acquisition of knowledge, skills and attitudes related to a student's professional development.We present an overview of the day one activities at the Hofstra North Shore‐LIJ School of Medicine, focusing on how they address course and curricular objectives. Our first lab is a four‐hour session titled “Observation and Correlation.” In the first half of the session, students work in small groups, refining their clinical observation skills through external examination of a cadaver. Discussion with each other and a facilitator extends observations to inferences about the medical, psychological and social history of the cadaver. The second half involves pulse point dissection, allowing appreciation of relationships between external points and underlying structures. Faculty help to guide, but do not orchestrate the discussion. We believe these activities address several fundamental principles of clinical observation, including its dual sensory/cognitive nature, the distinction between observation and inference, the importance of description, and the goal‐oriented nature of clinical observation (Boudreau et al., 2008).
Refining the timeline of conjunctival papillae induction in the chick scleral ossicle system
Authors: Jourdeuil Karyn , Franz‐Odendaal Tamara 
Published: June 2021

The conjunctival papillae, epithelial thickenings on the surface of the eye, are required for the induction of the underlying neural crest‐derived, intramembranous bones (the scleral ossicles). However, very little research has been conducted in the past 50 years on the mechanisms underlying the induction and patterning of these papillae. In order to further investigate this question, single papillae were surgically removed using fine tungsten needles at various time points during their development and the embryos were cultured for 1 to 5 days post‐surgery. Our results show that papilla removal had no effect on the patterning of the adjacent conjunctival papillae, and surprisingly, a normal patterned scleral ossicle develops under the site of surgery. This research demonstrates that the developmental timeline of the conjunctival papillae is much more flexible than previously noted. Our results also suggest that there is some compensatory mechanism taking place at the epithelial level for the induction of a complete ring of scleral ossicles. Thus, this study provides new insights into the mechanisms patterning the epithelium involved in epithelial‐mesenchymal induction of intramembranous bones. This research was primarily funded by the Natural Sciences and Engineering Research Council of Canada.Grant Funding Source: Natural Sciences and Engineering Research Council of Canada
Multiscale modeling goes out on a limb: in silico simulations of developmental mechanisms shared between somitogenesis and the developing embryonic avian limb bud
Authors: Gens J. Scott , Srividhya Jeyaraman , Belmonte Julio M. , Hester Susan D. , Glazier James A. 
Published: June 2021

Avian limb buds form primarily from a mixture of ectodermal and mesenchymal cells. The mesenchymal cells derive from two sources, the lateral plate mesoderm and the somites. Somite‐derived structures in mature limbs include muscles, tendons, and vascular endothelium. Limb development potentially shares many regulatory pathways and developmental mechanisms with somitogenesis, such as WNT and FGF8 regulation of cell proliferation, MET transitions, and differentiation. Although some mechanisms are likely to be conserved, tissue‐specific contextual cues are likely to introduce differences both significant and subtle. We present three‐dimensional, multi‐scale, multicell models using the open‐source CompuCell3D modeling environment to simulate these experimentally‐observed developmental mechanisms. We combine sub‐cellular (genetic and signaling networks), cellular (cell growth, death, division, differentiation and motility) and tissue (extracellular matrix and morphogen production) level scales to explore if combining WNT, FGF8 and Delta/Notch signaling (active during somitogenesis) with contact inhibition of growth in the ectoderm and the formation and maintenance of the Dorsal‐Ventral boundary at the apical ecotodermal ridge suffices to generate the unique patterning and growth dynamics of the limb bud. Supported by NIH 2R01GM076692–07and EPA R‐10–0049A3.Grant Funding Source: N/A
Testing hypotheses of growth in the developing chicken limb bud
Authors: Fowler Donald Alexander , Searle Eric B , Button Christine , Chan Edna K , Larsson Hans C. E. 
Published: June 2021

Morphogenesis is not only a story of genes and phenotypes, but also one of growth and movement. To explain the large‐scale changes in shape and size that the developing vertebrate limb undergoes, a more complete understanding of mechanisms acting between gene expression and the developed phenotype is needed. Recent evidence has indicated that there is an anterior to posterior direction in the relative movement of cells compared to the contour of the chick wing bud at an early stage, HH16 (Hamburger and Hamilton, 1951, Wyngaarden et al., 2010; doi: 10.1242/dev.046987). Although older evidence has indicated that at later stages (HH20–27) there is an opposite posterior to anterior movement of cells relative to the margin of the limb bud (Vargesson et al., 1997; Development 124). Dii injections into the developing chicken wing at various stages were performed to establish the timing and directionality of movements of cells relative to the margin of the developing limb. We found these anterior to posterior movements of cells relative to the movement of the wing margin occur only at a restricted early phase of limb development and posterior to anterior movements are present generally throughout the remainder of limb bud outgrowth.Grant Funding Source: by NSERC, McGill University, and a Canada Research Chair to HCEL
The chick embryo neural crest model system reveals a unique role for EphB6 in melanoma metastasis
Authors: Bailey Caleb Michael , Kulesa Paul M 
Published: June 2021

We hypothesize that melanoma metastasis mimics aspects of the emigration program of its ancestral cell type, the embryonic neural crest. To test our hypothesis, we performed a molecular comparison between melanoma and the neural crest. Our study revealed that melanoma cells exploit portions of the embryonic neural crest development program to facilitate invasion. In particular, the purported metastasis suppressor EphB6 was reduced in invasive melanoma cells compared to poorly invasive melanoma cells and primary human melanocytes. Thus, we utilized the chick embryo transplant model system to assay the effects of EphB6 re‐expression in melanoma cells. We report that EphB6 over‐expression alters cell directionality of migrating melanoma cells, while also reducing invasive ability. We confirmed the anti‐metastatic effect of EphB6 in melanoma cells using a chick CAM metastasis assay, while tumor formation appeared unaffected. These results suggest that EphB6 acts specifically as a metastasis suppressor, likely at the metastatic step of intravasation. Our studies also demonstrate the chick embryo as a powerful tool with which to compare and dissect the complex mechanisms of metastasis in vivo that are similar or distinct from normal developmental processes. This work was supported by NRSA 1F32CA144297 (cmb) from the NIH, and by the Stowers Institute for Medical Research.Grant Funding Source: NIH 1R01HD057922
Pch2 is a meiotic hexameric ATPase that binds to and alters Hop1 functions
Authors: Chen Cheng , Jomaa Ahmad , Ortega Joaquin , Alani Eric 
Published: June 2021

In most organisms, the segregation of chromosomes during the first meiotic division requires at least one crossover between pairs of homologous chromosomes. Crossovers come from programmed double‐strand breaks (DSBs) that are preferentially repaired using the homologous chromosome as a template (this preference is called interhomolog bias). In budding yeast, PCH2 is required to establish proper meiotic chromosome structure, regulate timing of recombination progression and promote interhomolog bias. How Pch2 functions at the molecular level is unknown despite its wide conservation. PCH2 open reading frame contains regions homologous to AAA ATPase proteins, and here we show that: 1. Pch2 is an ATPase that forms a hexamer in the presence of nucleotides. 2. Both ATP binding and hydrolysis by Pch2 are critical for its in vivo functions. 3. Pch2 binds to Hop1, an axial component of the synaptonemal complex, and alters its DNA binding activity. Based on these and previous cell biological observations, we propose that Pch2 acts as a stringency factor in meiosis to facilitate Hop1 binding to specific chromosomal regions, thus licensing steps that monitor recombination progression and lead to interhomolog bias.C.C. and E.A. are supported by NIH GM53085. J.O. is supported by Canadian Institutes of Health Research (MOP‐82930). A.J. is supported by a CIHR Doctoral Research Award.
Actin Bundling Mutants in Translation Elongation Factor 1A Induce Altered Protein Synthesis at both the Initiation and Elongation Steps
Authors: Perez Winder B , Kinzy Terri G. 
Published: June 2021

Apart from its canonical function in translation elongation, eukaryotic translation elongation factor 1A (eEF1A) has been shown to interact with the actin cytoskeleton. Amino acid substitutions in eEF1A that reduce its ability to bind and bundle actin in vitro, cause improper actin organization in vivo, as well as reduce total translation. Although initial analysis indicated the reduced translation was through initiation, in vitro analysis of the mutant proteins shows changes at the level of elongation. These strains exhibit increased levels of phosphorylated initiation factor 2α (eIF2α), suggesting the involvement of the Gcn2p protein kinase. Gcn2p is a key regulator of the general amino acid control (GAAC) pathway by responding to increases in uncharged tRNA levels in the cell and causing downregulation of total protein synthesis at the level of initiation. However, these eEF1A mutant strains do not exhibit increased levels of uncharged tRNAs, suggesting an alternate mechanism of Gcn2p activation. Thus, we hypothesize there is interplay between the translation initiation and elongation defects in eEF1A actin bundling mutant strains. The recent finding that Gcn2p and eEF1A directly interact sheds light on this new function. The interactions between Gcn2p and eEF1A actin bundling mutants as well as the specific functions of eEF1A within elongation are being assessed.Support: NIH 5T32AI007403–18
Cloning and Characterization of Leucyl‐tRNA Synthetase from Pseudomonas aeruginosa
Authors: Medellin Eduardo , Salazar Humberto , Quach Nathalie , Chavero Pamela , Bullard James 
Published: June 2021

IntroductionPseudomonas aeruginosa is an opportunistic pathogen and a common cause of nosocomial infections. Aminoacyl‐tRNA synthetases (aaRSs) are a class of enzymes that catalyze the covalent attachment of amino acids to their cognate tRNAs during protein biosynthesis. We describe here the cloning and enzymatic characterization of the class I leucyl tRNA synthetase (LeuRS) from P. aeruginosa.ResultsLeuRS from P. aeruginosa was cloned and expressed in E. coli and purified to greater than 98% homogeneity. Sequence analysis shows that this protein contains the characteristic motifs of class I aminoacyl‐tRNA synthetases. The ability of LeuRS to function in aminoacylation of its cognate tRNA was determined in tRNA aminoacylation assays. The kinetic parameters for the interaction of P. aeruginosa LeuRS with its three substrates (tRNA, ATP, leucine) were determined. Initial velocities were determined for charging of tRNA using tRNA concentrations between 6.5 and 10 μM tRNALeu. The KM and Vmax for the interaction of LeuRS with the substrate tRNALeu was determined to be 7.14 μM and 0.36 μM min−1, respectively. The ATP:PPi exchange reaction was used to monitor interaction with ATP and leucine.ConclusionLeuRS identified in P. aeruginosa was cloned, expressed and purified and shown to be functional in assays suggesting that it is functional in protein synthesis. Research was partially supported by NIH grant 1SC3GM098173–01A1.
Cloning and characterization of EF‐Tu and EF‐Ts from Bacillus subtilis
Authors: Rivera Carlos , Garcia Velia , Bullard James 
Published: June 2021

IntroductionElongation factors (EF) facilitate many steps in the process of the biosynthesis of proteins. EF‐Tu in particular plays a central role in the GTP‐dependent placement of aminoacylated tRNA at the A site of the ribosome. EF‐Ts acts by catalyzing the change of EF‐Tu from a GDP‐bound inactive state to a GTP‐bound active state. Much work has been done with elongation factors from Gram − bacteria but little work has been carried out to analyze the activity of these proteins from Gram + organisms. We describe here analysis of EF‐Tu and EF‐Ts from B. subtilis.ResultsAnalysis of both B. subtilis EF‐Tu and EF‐Ts showed they are 77% and 47% identical to their E. coli counterparts, respectively. Both B. subtilis EF‐Tu and EF‐Ts were cloned and over‐expressed in E. coli and purified to greater than 95% homogeneity. B. subtilis EF‐Tu was shown to be active when assayed for activity using the GDP binding assay. Kinetic parameters for the interaction of EF‐Tu with its substrate GDP were determined in the absence and presence of EF‐Ts. The dissociation constant (KGDP) for EF‐Tu•GDP was determined by forming the complex at 4 °C and diluting the complex 100 fold and measuring the amount of complex remaining at different times at various temperatures. EF‐Ts was shown to stimulated the exchange of GDP by EF‐Tu. EF‐Tu was also shown to be active in ternary complex formation as well as delivery of aminoacylated tRNA to the A site on B. subtilis ribosomes.ConclusionEF‐Tu and EF‐Ts identified in B. subtilis were cloned, expressed and purified and shown to be functional in assays suggesting that each is functional in protein synthesis.
Evolution of ribosomal RNA: universal and domain‐specific conserved sequences
Authors: Gerbi Susan A , Doris Stephen M , Smith Deborah , Raphael Benjamin , Beamesderfer Julia , Nathanson Judith 
Published: June 2021

We present a new bioinformatics approach to identify Conserved Nucleotide Elements (CNEs) in the three domains of life (Eukarya, Bacteria, Archaea), that play important functional roles. Using ARB/SILVA, we developed a Full Length Organismal rRNA Alignment database (FLORA) that was filtered to include only complete rRNA sequences, each entered only once in the database. Our analysis identified 63, 49 and 48 CNEs that are ≥6 nt in 23S–28S rRNA of Eukarya, Bacteria and Archaea. Nine of these CNEs are universally conserved (uCNE) in all domains of life. They map to area of known function, but also to areas of undiscovered function in rRNA. In addition, structure‐based quantification of motifs across all domains of life identified domain‐specific CNEs: 12 uniquely conserved in all Eukarya, 3 only in Bacteria and 1 only in Archaea. Thus, domain specific CNEs are largely a eukaryotic phenomenon, and represent new structural features in eukaryotic ribosomes. We are completing a similar analysis to identify CNEs in the small ribosomal subunit, where we have identified 26, 24 and 24 CNEs in 16S–18S rRNA of Eukarya, Bacteria and Archaea.(NSF grants MCB‐0718714, MCB‐1120971)
Nuclear MMP‐2: presence and activity in cardiac myocytes
Authors: Kondo Marcia Yuri , Castro Michele Mazzaron , Fan Frank (Xiaohu) , Schulz Richard 
Published: June 2021

MMP‐2 is expressed in almost all heart cells and is found in subcellular compartments including the nucleus. MMP‐2 can be directly activated by oxidative stress (as peroxynitrite). Its activity is further regulated by its phosphorylation. To better study nuclear MMP‐2 in the heart, we extracted the nuclear, cytosolic and membrane fractions from isolated rat hearts (briefly perfused to clear them of blood). Western Blots for lamin A/C (nucleus), GAPDH (cytosol) and VDAC/Porin (membrane) were used as specific markers to confirm fraction purity. Gelatin zymography of these fractions revealed MMP‐2 but not MMP‐9 activities and MMP‐2 activity was about 15 times higher in the cytoplasm than in the nucleus. Interestingly, Western blot analysis showed that MMP‐2 is present in similar amounts both in the nucleus and in the cytoplasm. In order to characterize possible regulators of MMP‐2 activity, we analyzed for the presence of tissue inhibitors of metalloproteases (TIMPs). Western blots revealed that all forms of TIMPs (1–4) are found in the cytoplasm, TIMP‐4 is also present in the membrane fraction, and no TIMP was detected in the nucleus. Our data suggest that myocardial MMP‐2 activity in the nucleus is regulated by a mechanism different from inhibition by TIMPs, possibly by its phosphorylation.Funding: Canadian Institutes of Health Research.
Mass Spectrometric Immunoassay for Insulin‐Like Growth Factor 1
Authors: Nedelkov Dobrin , Niederkofler Eric , Phillips David , Krastins Bryan , Kiernan Urban , Tubbs Kemmons , Lopez Mary 
Published: June 2021

Mass Spectrometric Immunoassays (MSIA) are protein quantification methods that utilize mass spectrometric detection for quantification of targeted protein analytes affinity retrieved by surface‐immobilized antibodies. This rather straightforward concept is realized through affinity pipette devices (MSIA‐Tips) that enable high‐throughput assaying of hundreds of samples per day. Described here is the development and validation of mass spectrometric immunoassay for insulin‐like growth factor 1 (IGF1).MSIA‐Tips derivatized with anti‐IGF‐1 antibody were used for affinity isolation of IGF1 from human samples. Long R3 (LR3) IGF1, spiked into samples prior to the affinity isolation, served as internal reference standard for signal normalization and IGF1 quantification. Following capture and elution, both the intact proteins and their surrogate tryptic peptides were analyzed via LC/MS. Linear standard curves were built that spanned the range of 1–1,500 ng/mL. The assay exhibited intra‐ and inter‐assay precisions of <10%, and linearity and spiking‐recovery in the 90–110% range. Data was compared to that obtained with a commercially available ELISA, yielding good correlation. The data correlation between intact IGF1 and peptide‐based IGF1 MS analyses was good, demonstrating the applicability of the IGF1 MSIA across MS platforms.
Carbon monoxide induces chromatin remodeling to facilitate endothelial cell migration
Authors: Li Mailin , Gallo David , Csizmadia Eva , Otterbein Leo , Wegiel Barbara 
Published: June 2021

ObjectivesVascular injury to the endothelial monolayer (EC), either by mechanical removal or by chronic inflammation, is still awaiting effective therapies. The homeostatic enzyme, heme oxgenase‐1 (HO‐1) is induced by various stimuli such as oxidizing agents and its substrate, heme. HO‐1 degradation of heme generates the vasomodulatory gas carbon monoxide (CO), in addition to biliverdin and iron.ResultsIn this study, we show that administration of exogenous CO enhanced acetylation of Histone H3 (Lysine 9) via the GSK3β‐dependent stabilization of Rev‐ERBα protein to increase migration of EC in response to mechanical injury. We found that CO acting via chromatin remodeling pathways inhibits PAI‐1 and thrombospondin genes, while concomitantly upregulating transcription of proangiogenic molecules such as VCAM‐1.ConclusionsIn summary, CO modifies chromatin structure through enhanced acetylation of histone H3 through the GSK3β‐Rev‐erbα pathway to increase migration and proliferation in EC. This mechanism is demonstrated to be important for vascular homeostasis as well as treatment of vascular complications associated with dysregulated thrombosis, wound healing, and angiogenesis. This work was supported by AHA 10SDG2640091 grant (BW) as well as Department of Surgery BIDMC internal funds (BW) and NIH grant HL‐071797 & HL‐076167 (LEO).
The predictive validity of formative anatomy assessments
Authors: Finn Gabrielle Maria , Hanson Elizabeth 
Published: June 2021

This retrospective study aimed to establish whether formative practical laboratory exams, taken after minimal anatomy teaching, were predictive of performance on end of year summative anatomy exams.Exam (1 × formative, 2 × summative) results were collected for 8 cohorts of medical students (2004–12). Parametric tests were used as all data were normally distributed. Correlations were determined using a Pearson's rank test.Consistently highly significant positive correlation (P<0.0010) between short, formative examinations taken and final summative examinations were demonstrated within all 8 cohorts. Students’ formative performance also correlated with their mid‐year summative examination performance (P<0.0010). There was also a significant correlation between mid‐year and final examination performance for the same 6 cohorts (P<0.0010).Formative exams introduce students to practical anatomy exams. This is the first time that students have completed a timed exam where they can't look ahead review questions. We have demonstrated that students who do well in the formative exam do well in the subsequent exam, and conversely, students who perform poorly continue to do so. This raises debate as to whether anatomy practical exams test knowledge or instead are tapping into other unknown constructs as other formative written exams are not predictive of eventual performance.
The role and mechanisms of microRNA let‐7g in regulating lipid metabolism in macrophages
Authors: Juo Suh‐Hang H , Wang Yung‐Song , Liao Yi‐Chu , Cheng Hsin‐Yun , Lin Ruey‐Tay 
Published: June 2021

The transformation of foam cells from macrophages can lead to atherosclerosis. A micorRNA can bind to one or multiple mRNAs to inhibit protein synthesis, and/or degrade mRNA. We previously reported that microRNA let‐7g can bind to LOX‐1 mRNA, an oxLDL scavenger receptor, to knock down LOX‐1 expression. The present study aims to investigate let‐7g function macrophages.Let‐7g regulates macrophage functions:During foam cell transformation, macrophage's let‐7g level was significantly down‐regulated. Transfecting let‐7g mimic to macrophages led to a significant decrease of intracellular lipid. In addition, transfection of let‐7g mimic to macrophages could increase cell survival and reduce the levels of proinflammatory substances including IL‐1β, IL‐6 and MCP‐1.Let‐7g contributes to cholesterol homeostasis:We investigated whether let‐7g regulates cholesterol by influencing ABCA1 and SERBP2 expression. ABCA1 could be decreased by oxLDL but let‐7g could restore ABCA1 expression. Furthermore, SREBP2 expression was simultaneously down‐regulated by let‐7g mimic.Let‐7g inhibits NF‐kB pathway:Bioinformatic databases predicted that IKKα in the NF‐kB pathway is one potential target of let‐7g. Using the luciferase reporter assay, we proved that let‐7g can bind to IKKα to inactivate the NF‐kB cascade pathway. Our data suggest that let‐7g may play an important role in cholesterol metabolism in macrophages.This research is supportedby National Health Research Institutes, Taiwan (NHRI‐Ex101–10107PI), National Science Council, Taiwan (NSC 101–2628‐B‐037–003‐MY2 and NSC 99–2628‐B‐037–037 ‐MY3)