bluuebunny/crossref_metadata_2025_split huggingface dataset:
RNA Modifications in Health and Disease
Authors: Suzuki Tsutomu 
Published: April 2020

RNA molecules are frequently modified post‐transcriptionally, and these modifications are required for proper RNA functions. To date, about 150 different types of chemical modifications have been identified in various RNA molecules across all domains of life. There are still a number of novel modifications to be discovered. RNA modifications appear to confer chemical diversities to simple RNA molecules basically composed of four letters, to acquire a greater variety of biological functions. These modifications play critical roles in stability and functions of RNA molecules. We’ve been carrying out a project to identify novel RNA modifications from various sources, and reported seven modifications so far. Taking advantage of mass spectrometric analysis of RNA modifications, we systematically screened a series of knockout strains for uncharacterized genes, and identified more than 40 genes responsible for tRNA modifications, rRNA modifications as well as mRNA modification. Recently, we identified a cap‐specific adenosine methyltransferase (CAPAM) responsible for N6‐methylation of m6Am at the transcription start site of eukaryotic mRNAs.It has been generally thought that tRNA modifications are stable and static, and their frequencies are rarely regulated. We previously reported that lack of tRNA modification causes major classes of mitochondrial diseases including MELAS and MERRF. Deficient tRNA modification results in defective protein synthesis, leading to mitochondrial dysfunction. These findings provided the first evidence of human disease caused by an RNA modification disorder. We call “RNA modopathy” as a new category of human diseases. I am going to show our recent studies on RNA modifications associated with human diseases and their dynamic regulation by sensing intracellular metabolites under physiological condition.
Structural Basis of Dystroglycan Function and the Pathogenesis of Muscular Dystrophy
Authors: Campbell Kevin P. 
Published: April 2020

(DG) is a widely expressed high‐affinity extracellular matrix receptor that requires extensive glycosylation and additional post‐translational processing. In skeletal muscle, DG is part of the dystrophin‐glycoprotein complex, which establishes a continuous link between laminin‐G‐like (LG) domains of extracellular matrix‐resident proteins (laminin, agrin, and perlecan) and the cytoskeleton. Extracellular matrix proteins that contain LG domains bind to α‐DG via a novel heteropolysaccharide [‐GlcA‐β1,3‐Xyl‐α1,3‐]n called matriglycan, which is synthesized by the bifunctional enzyme known as Like‐acetylglucosaminyltransferase (LARGE). We have used a multidisciplinary approach to provide the first atomic‐level insights into the structure of a unique protein‐carbohydrate interaction that is essential for the binding of α‐DG to the extracellular matrix. We first purified LARGE and synthesized matriglycan chains of defined lengths in sufficient quantities to perform both biochemical and structural studies. Using NMR spectroscopy, we found that matriglycan bound to laminin‐α2 LG4,5 with high affinity (Kd=0.23 μM) and that this binding was calcium dependent. Next, we initiated a collaboration with Erhard Hohenester, who had previously crystallized laminin‐α2 LG4,5. We provided Dr. Hohenester with enough matriglycan to soak into crystals of LG4,5 and to produce a high‐resolution crystal structure of LG4,5 bound to matriglycan. This analysis revealed that the LG4 domain is a Ca2+‐dependent lectin with specificity for GlcA‐β1,3‐Xyl disaccharides, and that a single glucuronic acid‐β1,3‐xylose disaccharide repeat straddles a Ca2+ ion in the LG4 domain, with oxygen atoms from both sugars replacing Ca2+‐bound water molecules. This chelating binding mode is unprecedented among animal lectins and accounts for the high affinity of this protein‐carbohydrate interaction as measured by NMR. Finally, we used two novel exoglycosidases to provide direct evidence that native α‐DG contains unmodified matriglycan and numerous GlcA‐Xyl repeats. The multiple tandem repeats in matriglycan are predicted to increase the apparent affinity of the protein for LG domains by favoring rapid rebinding after dissociation. Abnormalities in the post‐translational processing of DG lead to an absence or reduction of the matriglycan modification on α‐DG, and thereby lead to various forms of muscular dystrophy (secondary dystroglycanopathies). Our results represent a major conceptual advancement regarding a functional carbohydrate and shed light on the mechanism of protein‐carbohydrate interactions.Support or Funding InformationDr. Campbell is an investigator of the Howard Hughes Medical Institute. This work was supported in part by a Paul D. Wellstone Muscular Dystrophy Cooperative Research Center grant.
TGF‐beta Regulation by the Matricellular Protein Thrombospondin 1
Authors: Murphy-Ullrich Joanne E. , Lu Ailing , Lei Weiqi , Suto Mark J. 
Published: April 2020

Thrombospondin 1 (TSP1) is a matricellular protein that plays multiple roles in disease. Activation of the TGF‐beta latent complex is a major regulatory node for controlling TGF‐beta in homeostasis and disease. TSP1 can regulate the conversion of latent transforming growth factor‐beta (TGF‐beta) to its biologically active form in certain fibrotic diseases and cancers. We have developed peptide and small molecule antagonists that block TSP1 binding to the latent complex and inhibit TSP1‐dependent activation of latent TGF‐beta. These antagonists reduce TGF‐beta activity and extracellular matrix production and fibrosis in multiple rodent models, particularly in fibrotic complications of diabetes. TGF‐beta also plays a role in the osteolytic bone destruction characteristic of the plasma cell cancer, multiple myeloma. In both immune competent syngeneic mouse and human xenograft models, we showed that treatment with the TSP1‐TGF‐beta antagonist reduced disease burden, TGF‐beta activity, and prevented bone destruction via a decrease in osteoclasts and an increase in osteoblasts. Current studies are examining the role of the TSP1‐TGF‐beta pathway in immune dysregulation in multiple myeloma.Support or Funding InformationThe most recent studies (myeloma, drug development) are supported by grants from the Alabama Drug Discovery Alliance and the UAB Comprehensive Cancer Center pilot grant program, the American Society for Hematology Bridge Grant with supporting funds from the UAB Department of Pathology, and NIH grant 1R01CA175012.
Mitochondrial NAD Transport
Authors: Baur Joseph A. , Luongo Timothy , Mukherjee Sarmistha , Eller Jared , Chellappa Karthikeyani , Lu Mu-Jie , Cambronne Lulu 
Published: April 2020

Tissue nicotinamide adenine dinucleotide (NAD) levels correlate with healthspan, falling with age or disease, and rising with exercise or caloric restriction. Moreover, the demonstration that supplemental NAD precursors drive beneficial effects in a variety of rodent models has led to a resurgence in interest in the basic biology of this molecule. Although it is widely recognized that NAD is present in the mitochondrial matrix and critical to the function of the organelle, the source of mitochondrial NAD has been debated. We recently used an isotopic labeling approach to demonstrate that direct uptake of intact NAD is one mechanism by which mitochondria are able to obtain this nucleotide. Here, we show that this activity is sufficient to restore respiratory capacity in NAD‐deficient isolated mitochondria, and identify SLC25A51 as a carrier that can mediate the transport of NAD across mitochondrial membranes. Compartment‐specific regulation of NAD concentration may be a crucial element in the adaptation of cells and tissues to changing metabolic environment that could be targeted therapeutically once the underlying mechanisms have been revealed.Support or Funding InformationDK098656 to J.A.B., GM126897 to L.A.C.
Nascent Protein Selection and Triage at the Ribosome Exit Site
Authors: Shan Shu-ou , Wang Shuai , Yang Chien-I , Hsieh Hao-Hsuan 
Published: April 2020

Proper protein biogenesis is a pre‐requisite for the generation and maintenance of a functional proteome. Accumulating data show that this process begins early, when nascent proteins begin to emerge from the ribosome. Indeed, the ribosome exit site is a crowded environment where a variety of ribosome‐associated protein biogenesis factors (RPBs) jostle for access to the nascent polypeptide. Within seconds, the nascent polypeptide must engage the correct set of factors and commit to the proper biogenesis pathway. These early decisions profoundly influence the folding, assembly, localization, maturation, and quality control of nascent proteins. This raises the question: How do these factors, which bind the ribosome at overlapping sites and prefers similar sequence features on the nascent polypeptide, compete or collaborate with one another to enable the efficient and accurate selection of nascent proteins into the proper biogenesis pathway? In this talk, I will describe recent works that begin to illustrate how the RPBs coordinate in space and time at the ribosome exit site and highlight the importance of this molecular crowding in enhancing the fidelity of individual protein biogenesis pathways.Support or Funding InformationR01 GM078024, R01 GM107368
Nuclear mechanics in migrating cells
Authors: Lele Tanmay 
Published: April 2020

Cells shape and position the nucleus by transmitting forces from the cytoskeleton onto the nuclear surface. In response to these forces, the nucleus can deform and/or it can move. Nuclear movement will occur when there is a net differential in mechanical force across the nucleus, while nuclear deformation will occur when mechanical forces overcome the mechanical resistance of the various structures that comprise the nucleus. In this talk, I will describe our efforts to 1) identify the sources of mechanical forces and quantify the magnitude of mechanical force generation on the nucleus, 2) understand the mechanical response of the nucleus to these forces, and 3) uncover the relevance of nuclear force transfer in cell and tissue function.Support or Funding InformationNIHNSF
Clocks, Hourglasses, and History‐dependent Clocks
Authors: Murugan Arvind , Husain Kabir , Pittayakanchit Weerapat , Chew Justin , Leypunskiy Eugene , Lin Jenny , Pattanayak Gopal , Rust Michael 
Published: April 2020

Many organisms have free‐running circadian clocks to anticipate the time of the day, including the Kai protein‐based clock in the cyanobacterium Synechococcus elongatus. However, other species have an ‘hourglass’ timer, such as the cyanobacterium Prochlorococcus marinus. What conditions favor an hourglass timer or a free running clock over the other? We argue that this evolutionary choice is influenced by the noise levels in the external environment (e.g., light fluctuations due to weather) relative to noise levels in the internal environment of the cell (e.g., molecular fluctuations). Besides different clock dynamics in different species, we find that the clock of a single species, S. elongatus, exploits a clock‐metabolic coupling to tune its clock dynamics towards an hourglass timer to deal with changing noise levels.Support or Funding InformationK.H. thanks the James S. McDonnell Foundation for support via a Postdoctoral Fellowship. A.M. thanks the Simons Foundation for support.
Preventing and Overcoming Sexual Harassment
Authors: Helman Alex 
Published: April 2020

The 2018 National Academy of Science report on Sexual Harassment of Women: Climate, Culture, and Consequences in the Academic Sciences, Engineering and Medicine revealed just how prevalent the sexual harassment of women is in STEM. The report demonstrated that 50% of women faculty and staff and 20–50% women students encounter or experience sexually harassing conduct in academia. It also detailed the effects of this harassment to the STEM community, concludes that system‐wide changes to the culture and climate in higher education are needed to prevent and address sexual harassment, and provides a roadmap for institutions of higher education to make these changes.Since the release of the report, the National Academies have joined with over 40 colleges, universities, and research institutions to launch an Action Collaborative on Preventing Sexual Harassment in Higher Education. The purpose of the Action Collaborative is to bring together leaders from academic institutions and key stakeholders to work toward targeted, collective action on addressing and preventing sexual harassment across all disciplines and among all people in higher education. This session will focus on the report’s key findings and recommendations for implementing changes that can prevent sexual harassment and promote equity within scientific organizations and institutions and will provide an overview of the ongoing work of the Action Collaborative on Preventing Sexual Harassment in Higher Education.Support or Funding InformationNSF, NIH, NASA, NOAA, NIST, Luce Foundation, Burroughs Wellcome Fund, Alfred P. Sloan Foundation
Lipids and Hedgehogs
Authors: Salic Adrian , Wierbowski Bradley , Petrov Kostadin 
Published: April 2020

The Hedgehog cell‐cell signaling pathway governs critical processes in the embryonic development of most animals, in adult stem cell maintenance, and in cancer. The pathway is activated by the secreted Hedgehog morphogen, such as the prototypical vertebrate homologue, Sonic hedgehog (SHH). SHH is generated in the endoplasmic reticulum of signal‐producing cells, as a hydrophobic protein uniquely modified with palmitate at the N‐terminus and with cholesterol at the C‐terminus. These lipid modifications, which are critical for SHH function, render SHH strongly attached to the plasma membrane; yet the SHH morphogen must travel through the extracellular space, to reach responding cells located far away. I will present our recent work aimed at elucidating the biochemical mechanisms that allow the lipidated SHH morphogen to be released in diffusible form from producing cells, and then be delivered to its receptor, the tumor suppressor membrane protein Patched1, on the surface of responding cells.Support or Funding InformationNIH/NIGMS R01 GM122920
Getting There: Thyroid Hormone Receptor Intracellular Trafficking
Authors: Allison Lizabeth A. 
Published: April 2020

Trafficking of regulatory proteins into and out of the nucleus is fundamental to the function of all living cells. A long‐standing interest in my lab is exploring the diversity of signals regulating traffic control of the thyroid hormone receptors, TRα1 and TRβ1, transcription factors that either activate or repress the expression of target genes in response to thyroid hormone. Although primarily residing in the nucleus, TRα1 and TRβ1 shuttle rapidly between the nucleus and cytoplasm. Set against a backdrop of my path as a woman in STEM, milestones in our understanding of TR’s pathway to the nucleus will be reviewed, while at the same time the innovative contributions of the diverse community of talented scientists in my lab will be showcased. Along the way, we have identified multiple nuclear localization signals (NLSs) and nuclear export signals (NESs) within TRα1 and TRβ1 that interact with importins and exportins, respectively, to mediate translocation across the nuclear envelope. To begin to understand the molecular mechanisms underlying TR’s journey, we have focused on the role of post‐translational modifications and interactions with transcriptional coregulators in modulating intracellular localization. Using a combined approach in transfected human cells of fluorescence‐based nucleocytoplasmic scoring, fluorescence recovery after photobleaching (FRAP), overexpression, and knockdown studies, we have revealed that acetylation promotes cytoplasmic localization of TR, while Mediator subunit MED1 and nuclear receptor corepressor 1 (NCoR1) are key regulators of its nuclear retention. Given the pivotal role of TRα1 in human health, development, and metabolism, we hypothesized that in some types of cancer and endocrine disorders, TRα1’s highly regulated traffic control may be disrupted. To analyze key structural components of TRα1 and to further explore the correlation between TRα1 trafficking, misfolding, and disease, recently we have examined the impact of cancer‐associated and Resistance to Thyroid Hormone (RTH) syndrome mutations on TRα1 localization patterns. Results show striking shifts towards a more cytoplasmic localization for many of the mutants and an increased tendency to form cytoplasmic and nuclear aggregates. Although the journey is far from over, what has emerged so far is that the fine balance between nuclear import, nuclear retention, and nuclear export of TR is a critical control point for modulating the cellular response to thyroid hormone.Support or Funding InformationNIH 2R15DK058028
Shedding Light on Phosphatidic Acid Signaling with Chemical Tools
Authors: Baskin Jeremy M. 
Published: April 2020

The fidelity of intracellular signaling pathways requires that cells control the production of signaling agents in space and in time. Phosphatidic acid (PA) is both a central phospholipid biosynthetic intermediate and a multifunctional lipid second messenger produced at several discrete subcellular locations. The modes of action of PA can differ based on upstream stimulus, biosynthetic source, and site of production. How cells regulate the local production of PA to direct diverse signaling outcomes remains elusive. To begin to unravel these questions, we have focused our efforts on improving and expanding the toolkit for both visualizing and perturbing cellular PA production, with spatiotemporal precision. Toward the first goal, we have harnessed the exquisite selectivity of chemoenzymatic labeling and click chemistry tagging to develop a method for directly visualizing PA production by phospholipase D (PLD) enzymes. This method, termed IMPACT for Imaging PLD Activity with Clickable Alcohols via Transphosphatidylation, has revealed sites of PLD‐mediated PA signaling elicited by diverse physiological stimuli and features subcellular, organelle‐level resolution. To complement these tools for visualizing PA production, we have also generated a suite of light‐controllable, optogenetic PLDs to precisely generate tunable amounts of PA, on demand, at specific organelle membranes. Collectively, these new approaches represent powerful and precise approaches for revealing spatiotemporally defined functions of PA in response to physiological and pathological stimuli.Support or Funding InformationNIH R00GM110121, NIH R01GM131101, NSF CAREER CHE‐1749919, Beckman Young Investigator, Sloan Research Fellowship
Cellular Communication via Adhesion
Authors: Arac Demet 
Published: April 2020

Adhesion G Protein‐Coupled Receptors (GPCRs) are cell adhesion proteins that mediate cellular communication and play critical roles in embryonic and neural development. Their mechanisms of action remain poorly understood. In the past several years, three‐dimensional structures of adhesion GPCRs and their ligands have been reported at atomic resolutions and revealed distinct protein folds and unique structural features. In this talk, we will discuss these structures which, together with structure‐guided biochemical and functional analyses, provide hints for the mechanisms of trans‐cellular communication at the synapse and other cell‐cell contact sites.Support or Funding InformationNIGMS, NIMH, Chicago Biomedical Consortium
Glutamine Transporter as a Target of mTOR Signaling Modulating Longevity
Authors: Sedivy John M. 
Published: April 2020

Mice that express reduced levels of the c‐Myc gene (Myc+/− heterozygotes) are long‐lived. Myc hypomorphic mice display reduced rates of protein translation and decreased activity of the mammalian target of rapamycin (mTOR) complex 1 (mTORC1). Given the prominent effect of mTOR on aging, lower mTORC1 activity could contribute to the exceptional longevity and enhanced healthspan of Myc+/− animals. However, given the downstream position of MYC in these signaling cascades, the mechanism through which mTORC1 activity is downregulated in Myc+/− mice is not understood. We have found that the high‐affinity glutamine transporter SLC1A5, which is critical for activation of mTORC1 activity by amino acids, is a transcriptional target of MYC. Myc+/− cells display decreased Slc1a5 gene expression that leads to lower glutamine uptake and consequently reduced mTORC1 activity. Decreased mTORC1 activity in turn mediates an elevation of fatty acid oxidation (FAO) by indirectly upregulating the expression of carnitine palmitoyltransferase 1a (Cpt1a) that mediates the rate‐limiting step of β‐oxidation. Increased FAO has been noted in a number of long‐lived mouse models. Taken together, our results show that transcriptional feedback loops regulated by MYC modulate upstream signaling pathways such as mTOR and impact FAO on an organismal level.Support or Funding InformationSupported by NIH grant R37 AG016694 to J.M.S.
Beneficial Effects of Inhibition of the Mitochondrial Pyruvate Carrier and the Mechanism of Action of Thiazolidinediones
Authors: Murphy Anne N. 
Published: April 2020

We demonstrated a number of years ago that thiazolidinediones including pioglitazone (insulin sensitizers used in the treatment of type 2 diabetes) have a direct inhibitory effect on the mitochondrial pyruvate carrier (MPC). This metabolite transporter of the inner mitochondrial membrane is responsible for carrying pyruvate from the cytoplasm into mitochondrial matrix for further oxidation, and is key to determining the pattern of cellular substrate oxidation. Since then, multiple studies have described somewhat counter‐intuitive findings of potential benefit of loss of MPC activity through genetic or pharmacologic means in normal cells both in vitro and in vivo. For instance, we have provided evidence that loss of MPC activity in myocytes induces changes consistent with insulin sensitization, including enhanced fatty acid oxidation, elevation of glucose uptake, and phosphorylation of AMPK, similar to what is observed in the skeletal muscle of diabetic patients treated with pioglitazone. Perhaps the more surprising finding was in primary cultures of cortical neurons. Mapping the pattern of neuronal metabolism upon MPC inhibition using stable isotope tracing and metabolomics allowed us to determine the extent of metabolic flexibility in neurons, and determine whether adjustments in neuronal substrate oxidation could affect susceptibility to injury by excessive exposure to the neurotransmitter glutamate. We found that metabolism of cortical neurons in culture and hippocampal slices is characterized by metabolic plasticity, and oxidative metabolism can be maintained in spite of large reductions in mitochondrial pyruvate uptake because of a selective increase in glutamate oxidation as an energy substrate, even in the presence of ketone bodies. Increased glutamate oxidation decreased the glutamate available for packaging into synaptic vesicles and synaptic release and, in turn, minimized the positive feedback cascade of excitotoxic injury. Thus, reductions in mitochondrial pyruvate metabolism can be neuroprotective. These findings will be placed in the context of other studies designed to enhance healthy energy metabolism in neurological disease, as well as a re‐evaluation of the mechanism of action of thiazolidinediones.Support or Funding InformationNIH R01NS087611