bluuebunny/crossref_metadata_2025_split huggingface dataset:
Proteostasis function and disfunction: the delicate art of maintaining a healthy proteome
Authors: Frydman Judith 
Published: November 2023

Correct protein folding and quality control are essential for normal cellular function. The accumulation of misfolded proteins is emerging as central to a wide range of disease states, including many neurodegenerative disorders such as Huntington's and Prion Disease. A complex network of molecular chaperones facilitate protein folding and assembly and monitor all aspects of protein homeostasis. Chaperones assist the folding of newly translated and stress‐denatured proteins, as well as affects protein quality control.Our research investigates the mechanisms and pathways by which chaperones carry out these diverse functions. Systems approaches identified a chaperone network linked to the protein synthesis apparatus assists protein biogenesis. The emergence of this translation‐linked chaperone network likely underlies the elaborate co‐translational folding process necessary for the evolution of larger multidomain proteins characteristic of eukaryotic cells. A stress‐inducible chaperone network protects cells from environmental stress and assists quality control. These chaperones also communicate with the ubiquitin‐proteasome pathway to clear misfolded proteins from the cell. Protein quality control in the eukaryotic cytosol relies on the sequestration of misfolded cytosolic proteins in specific quality control compartments. Our studies of chaperone function provide a framework to understand the link between protein misfolding and human disease.
Structure‐based discovery of new chemotypes conferring new biology
Authors: Shoichet Brian 
Published: November 2023

Receptor binding sites are evolved to recognize a few endogenous ligands, but the degeneracy of molecular recognition ensures that multiple other ligands and chemotypes can bind to the same site. Sometimes these non‐biological molecules will confer activities that the native ligands do not.Structure‐based docking is a fruitful way to find such novel ligands, by screening large libraries of compounds for new chemotypes that physically complement a binding site, but do not resemble the endogenous ligands. If these searches are coupled to the right biological assays, they can find new molecules conferring unprecedented biology. This will be illustrated with a screen for novel agonists of the m‐opioid receptor. New opportunities arising from a great increase in the number of available, interesting molecules, now well‐over 108 of which are readily available and dockable, will be considered.Support or Funding InformationSupported by GM71896 and GM106990
Organelles without membranes: intrinsically‐disordered proteins bring order to the cytoplasm
Authors: Seydoux Geraldine , Smith Jarrett , Calidas Deepika , Schmidt Helen , Rasoloson Dominique 
Published: November 2023

RNA granules are non‐membrane bound cellular compartments that contain RNA and RNA binding proteins. The molecular mechanisms that regulate the spatial distribution of RNA granules in cells are poorly understood. During polarization of the C. elegans zygote, germline RNA granules, called P granules, assemble preferentially in the posterior cytoplasm. We have identified two intrinsically disordered proteins MEG‐3 and MEG‐4 that function redundantly to scaffold the assembly of P granules in the posterior cytoplasm. We will describe how MEG‐3 and MEG‐4's ability to phase separate with RNA, bind to other RNA‐binding proteins, and be phosphorylated by DYRK MBK‐2 contribute to localized P granule assembly.Support or Funding InformationWe gratefully acknowledge support from JHMI, HHMI and NIH
Novel Mechanisms of Regulation of Bioactive Sphingolipids in Cancer Biology
Authors: Obeid Lina M. , Senkal Can , Pulkoski‐Gross Michael 
Published: November 2023

Our laboratory focuses on studying the role and regulation of bioactive sphingolipids in cancer. Specifically, we are interested in metabolic pathways of ceramide ‐‐ the growth suppressor, proapoptotic, prosenescense lipid, and sphingosine‐1‐phosphate (S1P) ‐‐ the antiapoptotic, proangiogenic, promitotic lipid. Our recent studies have led us to uncover a novel metabolic pathway involving de novo ceramide acylation to lead to acylceramide generation by a protein complex of ceramide synthase (CerS), acyl‐CoA synthetase long‐chain family member 5 (ACSL5), and diglyceride acyltransferase 2 (DGAT2). This metabolic pathway leads to sequestration of acylceramide in lipid droplets thus making it unavailable for ceramide action in cell death pathways. The implications of this pathway to fatty liver and cancer will be discussed.In other recent studies, we have also uncovered a novel mechanism of regulation for the enzyme sphingosine kinase 1 by phosphatidic acid (PA) acid binding, activation and translocation to the cell membrane leading to several biologic consequences including ezrin phosphorylation and cell invasion. Moreover, this regulation of sphingosine kinase 1 appears to have implications to its role in endocytosis and other membrane structural changes.Taken all together these studies underscore the important role of bioactive sphingolipids and their metabolizing enzymes in cell regulation and cancer biology.Support or Funding Information5I01BX000156‐0 (Obeid ‐ PI) 1.2 cal. mos. 10/1/2010 – 9/30/2017Veteran's Administration Merit Award $258,300 “Bioactive Sphingolipid enzymes as targets in inflammation”The long‐term goal of this project is to define the role of ceramidases and sphingosine kinase in inflammation and to target these enzymes for novel anti‐inflammatory therapy.2P01CA097132‐11A1 (Hannun – PI, Obeid ‐ Project 3 Leader) 7/01/2002‐8/31/2019Agency: NIH/NCI 1.2 cal. mos. $133,257Sphingolipids in Cancer Biology and TherapyThe aims of this proposal are to study the role of sphingosine kinase in p53 null and mutant cancer development.9R01GM097741‐13A1(Obeid ‐ PI) 1.2 cal. mos. 8/1/2015‐6/31/2019Agency: NIGMS $250,000A novel ceramide metabolic pathway in cell regulationThe aim of this proposal is to study our newly discovered pathway of ceramide metabolism involving o‐acyl ceramide generation and its association with lipid droplets and regulation of cell death pathways.
Signaling through hydrogen sulfide
Authors: Banerjee Ruma 
Published: November 2023

Despite the excitement about the varied physiological effects mediated by H2S and the consequent profusion of literature on H2S biology, there are large gaps in our understanding of how cells maintain very low steady‐state levels of H2S and amplify the signal as needed (1). Three enzymes in the sulfur network are important for its biogenesis. Two catalyze well‐described non‐H2S producing reactions in the transsulfuration pathway and also synthesize cysteine persulfide from cystine (2), raising questions about how the decision between these competing reactions is made in the cell. The pathway for H2S oxidation resides in the mitochondrion where the enzymes successively oxidize sulfide to sulfate. While sulfate is innocuous, a number of the intermediates in the sulfide oxidation pathway are reactive and their role in sulfide‐based signaling remains to be assessed (3). We have recently discovered a noncanonical sulfide oxidation pathway (4, 5) and the challenging heme‐dependent oxidation chemistry will be discussed. We will also discuss how H2S signals via protein persulfidation in the context of cancer.Support or Funding InformationThis work was supported in part by the NIH (HL58984 and GM112455
Proliferation of Transplanted Hepatocytes Drives Efficient Repopulation in Juvenile Host Rat Livers
Authors: Stock Peggy , Hempel Madlen , Hsu Mei‐Ju , Christ Bruno 
Published: November 2023

To improve the engraftment of donor hepatocytes is a central goal to enhance the therapeutic efficacy of hepatocyte transplantation as an alternative to whole liver transplantation. We reported previously that efficient liver repopulation by transplanted hepatocytes was hampered in livers of old as compared to juvenile animals 6 weeks after transplantation. To investigate, whether this was due to a better initial entry into the host parenchyma of juvenile as compared to senescent donor cells, or to differences in proliferation, we determined repopulation rates in juvenile and senescent host livers 1 week after transplantation of juvenile and senescent hepatocytes by flow cytometry and quantification of DPPIV enzyme activity in liver sections. Proliferation was assessed in the liver parenchyma by the expression of Ki67 six weeks after cell transplantation.1 week after hepatocyte transplantation comparable numbers of scattered cell clusters appeared both in juvenile and senescent host livers, irrespective of the age of the donor hepatocytes. However, quantification by flow cytometry of isolated primary hepatocytes from these livers revealed significantly higher numbers of juvenile as compared to senescent transplanted hepatocytes in juvenile hosts and as compared to either cell type in senescent host livers. This indicates that no differences in the parenchymal entry were obvious but rather higher proliferation of juvenile hepatocytes for higher numbers of transplanted cells in the juvenile host livers. Indeed, 6 weeks after hepatocyte transplantation significantly higher proliferation rates of transplanted hepatocytes were observed in juvenile host livers (4.2%) as compared to senescent hosts (zero), respectively.Hence, irrespective of the age of donor hepatocytes the parenchymal entry is similar but the efficient repopulation by juvenile hepatocytes seemed to rely on higher proliferation rates during liver regeneration.
Rat Liver Repopulation by Transplanted Late Gestation Fetal Hepatocytes
Authors: Sanders Jennifer , Boylan Joan , Francois‐Vaughan Heather , Thomas Paul M , Sikora Jacek , Abshiru Nebiyu , Gruppuso Philip , Kelleher Neil 
Published: November 2023

Hepatocyte transplantation has the potential to be an effective therapy for liver failure. However, the application of this therapy has been hampered by identification of an appropriate cell population and limited understanding of the factors accounting for the ability of cells to repopulate injured liver. Late gestation (E19) fetal hepatocyte proliferation in the rat is mitogen‐independent in vivo and in vitro. Fetal hepatocytes also differ from adult hepatocytes with regard to ribosome biogenesis, translation control, gene expression and cell cycle regulation. Our current studies are based on the hypothesis that histone posttranslational modifications (PTMs) acting through effects on chromatin structure account for the fetal hepatocyte signaling phenotype and that this phenotype will result in a selective growth advantage for fetal cells in the injured adult liver microenvironment. Late gestation fetal hepatocytes were isolated using antibodies against hepatic and ductal cell surface markers. The engraftment and repopulating ability of these cells was assessed using the mitomycin C dipeptidyl peptidase IV (DPPIV) transplant model. Liver harvested at 4 and 42 weeks posttransplantation contained well defined donor hepatocyte and endothelial colonies. Morphologic and phenotypic analysis using antibodies against well characterized markers revealed the formation of ductal colonies by 10 months. The average size of the donor colonies increased so that by 10 months up to 30% of the liver was repopulated by donor‐derived cells. Characterization of the donor cells pretransplant revealed that a large subpopulation of the hepatocytes also expressed ductal markers. Transcriptomic analysis revealed that these cells represent a distinct subpopulation of less well differentiated hepatocytes. Mass spectrometry‐based profiling of 77 modifications across 26 lysines on Histones H1, H2A, H3 & H4 revealed 23 significant changes including differential methylation of H3K27, H3K36 and H4K20 as well as acetylation of H3K4 comparing fetal to adult hepatocytes. In contrast, only 5 sites were significant comparing the two subpopulations of fetal hepatocytes. In conclusion, late gestation fetal hepatocytes are capable of extensive long‐term liver repopulation. These cells possess a histone PTM profile that is distinct from that of adult hepatocytes and may contribute to the maintenance of a fetal hepatocyte phenotype upon transplantation.Support or Funding InformationThe studies were supported by NIH grants R01DK100301 and P41GM108569. Support was also provided by the Rhode Island Hospital Department of Pediatrics.
Serotonin Receptor Regulation of Eosinophil Transendothelial Migration
Authors: Walker Matthew , Green Jeremy , Ferrie Ryan , Cook‐Mills Joan 
Published: November 2023

The tryptophan amino acid metabolite, 5‐hydroxytryptophan (5HTP), is a metabolic precursor of serotonin. 5HTP reduces allergic inflammation in the lungs of mice and blocks eosinophil migration across endothelial monolayers in vitro. Blocking the metabolic conversion of 5HTP to serotonin decreases inhibition of eosinophil transendothelial migration, indicating that its metabolism is required for inhibition. Currently it is not known if serotonin receptors are involved in mediating this regulation by 5HTP. We determined which serotonin receptors are expressed by endothelial cells and eosinophils by western blot and qPCR. There was expression of the serotonin receptors 1A, 1B, 3A, and 6. The function of the receptors in eosinophil transendothelial migration was analyzed in vitro using serotonin receptor inhibitors. Selective receptor inhibitors for serotonin receptors 1A and 1B blocked 5HTP inhibition of migration. This suggests that these serotonin receptors are involved in 5HTP inhibition of transendothelial migration and thus may serve as a target for intervention during allergic inflammation. These results will help design clinical studies addressing whether 5HTP supplementation reduces allergic asthmatic responses.Support or Funding InformationNIH R01HL111624
Force‐Induced α4 Integrin‐Dependent Monocyte Adhesion Strengthening and F‐Actin Remodeling Requires Actomyosin Contractility and Talin‐1
Authors: Ibrahim Hisham M , Hyduk Sharon J , Cybulsky Myron I 
Published: November 2023

During inflammation, monocytes roll and arrest on inflamed endothelium, at which point they are subjected to increased hydrodynamic forces imparted by the flowing blood. We showed previously that stabilization of α4 integrin‐mediated monocyte adhesion and resistance to detachment involves rapid actin polymerization and accumulation of filamentous actin (F‐actin) at upstream adhesion sites and in the adjacent cortical actin cytoskeleton (J Cell Biol 2012; 197:115–129). Using parallel plate flow chamber assays with a VCAM‐1‐coated adhesion surface, U937 monocyte‐like cell line and confocal imaging we further investigated mechanisms of adhesion strengthening and actin cytoskeleton dynamics in cells undergoing α4 integrin‐mediated adhesion. Myosin ATPase, calcium/calmodulin, myosin light chain kinase and Rho kinase signaling were required for α4 integrin‐mediated adhesion strengthening in the presence of hydrodynamic force. Upon introduction of fluid flow (2 dynes/cm2), adherent U937 cells flattened and the cell contact area with the adhesion surface increased both parallel and perpendicular to the direction of fluid flow. In addition, F‐actin at the adhesion surface redistributed towards the periphery of the adhesion surface contact area. Increased cell adhesion surface contact area and F‐actin redistribution were highly reproducible responses observed in >90% of adherent cells. Unlike F‐actin, α4 integrins remained localized throughout the adhesion contact area, and formed clusters in response to flow. Inhibition of myosin ATPase prevented force‐induced lateral spreading of U937 cells and F‐actin redistribution at the adhesion surface. siRNA knockdown of talin‐1, an adaptor molecule that binds to the integrin β‐chain cytoplasmic tail and mediates outside‐in‐signaling as well as interaction with the actin cytoskeleton, also inhibited α4 integrin‐dependent adhesion stabilization, lateral spreading and redistribution of F‐actin. These data suggest that integrin‐dependent adhesion stabilization and cytoskeletal remodeling induced by hydrodynamic force require both actomyosin contraction and talin‐1. When U937 cells were adhered to poly‐L‐lysine, we observed that hydrodynamic force induced a similar increase in the cell adhesion surface contact area and F‐actin redistribution; however, in this setting neither myosin ATPase nor talin‐1 were required. This suggests that adherent cells can respond to hydrodynamic force in an integrin‐independent manner, but adhesion mediated by α4 integrins inhibits the force‐induced, integrin‐independent response.Support or Funding InformationFunded by CIHR
Annual PhUN Week Service Learning Events improve student content mastery and civic engagement
Authors: Rhinehart Erin M 
Published: November 2023

Service‐Learning (SL) integrates meaningful community service with instruction and reflection to enrich the learning experience, teach civic responsibility, and strengthen communities. In language, arts and social science courses, it enhances learning and facilitates classroom inclusivity, providing opportunities to apply learned content to real‐world situations with guided reflection. While Physiology and Biology courses use SL less frequently, it is likely to enhance learning outcomes in these courses as well, while providing resources for K‐12 science education and public science literacy. Therefore, we tested the hypothesis that SL in introductory biological/physiological sciences courses would enhance student engagement, civic responsibility and course content mastery. To test this hypothesis, we conducted and assessed annual K‐2 educational outreach events in connection with the American Physiological Society program PhUN (Physiology Understanding) week over a period of 3 years. The SL project assignment required students to use backward design strategies to create stand‐alone learning module lesson plans with learning goals aligned with K‐2 state and federal standards of science education. The annual 3 hour, Friday night events were open to the public and structured as “reverse science fairs”. Over the three years, more than 200 children and their families were participated in hands‐on learning activities designed to teach a variety of concepts such as the connection between exercise and metabolism, sensation and perception and brain structure and function. Pre‐ and post‐service reflections and surveys show that SL, in this context, facilitates students' confidence in content mastery and enhances student engagement, especially in 1st year and 1st generation undergraduates. The experience especially enhanced “commitment to civic engagement” in male students, and had the greatest impact on the “confidence to talk to the public about science” for female students. The SL attitude pre‐ and post‐assessments also revealed that underrepresented minority students in the sciences (URM) had greater gains than non‐URM students in commitment to “future SL activities” and the notion that it is essential for “universities to perform community service”. In addition, the multi‐year project produced a book of state‐standard‐aligned K‐2 lessons for the local elementary school and much needed support for local public science literacy. Therefore, SL, as a pedagogy in introductory biological/physiological sciences courses, functions as a student‐centered, high‐impact practice, giving students new views on the applications of classroom course content and enhancing civic responsibility, while also inspiring the next generation of physiologists.Support or Funding InformationNSF CAREER IOS‐1350448 and APS PhUN week
A Comparison of High Fidelity Patient Simulations and Computerized Clinical Cases on Undergraduate Student Learning of Physiology
Authors: Harris David M , Li Wei 
Published: November 2023

High fidelity patient simulations (HFPS) have been shown to improve learning of science knowledge and skills in nursing and medical students. A few studies have shown improved learning in undergraduate students. Because HFPS are expensive and resource intensive, it is important to determine whether the increase in learning is worth the high cost. The purpose of this study was to determine if computerized clinical cases (CC), a low cost alternative, could produce similar learning as HFPS.MethodsThirty‐two undergraduate biomedical students were randomly assigned to two groups. Group A participated in a HFPS about asthma and then a CC on hemorrhage. Group B participated in a CC on asthma and then a HFPS on hemorrhage. The HFPS and CC were identical cases. A pretest with 10 questions was given before their activities and a post‐test was given after their activities. Students also took a survey regarding their confidence levels after the simulation activities. The 10 questions consisted of 4 related to asthma, 4 to hemorrhage and 2 unrelated to the cases as controls.ResultsBoth groups achieved higher scores on the posttest for the asthma questions with no difference between groups. There was no significant increase in scores on either the hemorrhage or control questions. There was a significant increase in 2 of the 7 statements about confidence. One involved confidence in understanding pathophysiology of a patient and the other was the relevance of physiology to medicine.DiscussionThese data suggest that CC and HFPS are similar in short term learning for some material. Future studies are needed to determine if there are other benefits of HFPS in undergraduate students and whether these justify the cost of this pedagogy in undergraduate students.