bluuebunny/crossref_metadata_2025_split huggingface dataset:
Exploring the Physiological Roles of Unsaturated Fatty Acids Using C. elegans
Authors: Kessler Benjamin , Alan Jamie , Lee Kin Sing Stephen 
Published: April 2020

Monounsaturated fatty acids (MUFAs) and polyunsaturated fatty acids (PUFAs), classified broadly as unsaturated fatty acids, are macronutrients that have a wide range of physiological effects. It is known that unsaturated fatty acids play a crucial role in a diet, but it is unclear which specific MUFAs and PUFAs are required and what the physiological consequences of having different amounts of these fatty acids and their metabolites in the body are. Specific omega‐3 and omega‐6 PUFAs have been shown to be beneficial to human diseases, such as cardiovascular disease, inflammatory conditions, and certain cognitive impairments. This study aims to investigate the physiological roles of individual MUFAs and PUFAs. From this study, we will gain the preliminary knowledge for making dietary and treatment suggestions for patients with various disease states and in normal aging. To do this, we will use the model organism C. elegans because of its short lifespan and abundance of genetic tools available (including single and multiple genetic knockouts of fatty acid desaturase enzymes). Additionally, findings from studies in C. elegans reliably translate to human disease. Preliminary data suggests that specific MUFAs and PUFAs are essential for normal lifespan, physiological functions, and neurodevelopment. This study will expand on this by examining every available genetic knockout of fatty acid desaturase enzyme in the worm. We will conduct lifespan assays in order to observe changes in the median and maximum lifespans of different genetic knockouts compared to the wild type as well as thrashing assays, a measure of physical fitness. We hypothesize that certain unsaturated fatty acids play more important physiologic roles than others and the corresponding downstream metabolites are important lipid signaling molecules. Preliminary results from the lab confirm these hypotheses, as the genetic strains tested thus far show variations in lifespan and fitness.Support or Funding InformationThis project was funded by the MSU Startup Fund, NIEHS ‐ R00 ES024806, and NSF ‐DMS‐1761320.
Investigation of the role of GABARAP family proteins in cargo recruitment to the autophagosome
Authors: Amos Shandon , Jensen Liv , Hurley James 
Published: April 2020

Autophagy is a conserved cellular process critical for removing cellular waste and recycling nutrients. During autophagy cargo is engulfed by a crescent shaped membrane called the phagophore and subsequently degraded into reusable material. There are two types of autophagy: selective and bulk. Bulk autophagy is a non‐specific process, whereas in selective autophagy, only cargo tagged for degradation is enveloped by the phagophore. A defining characteristic of selective autophagy is the relationship between Atg8‐like membrane proteins and cargo adaptor proteins. A classically studied example of this relationship in mammalian systems is the interaction between cargo adaptor, p62 and Atg8‐like protein, LC3B. It has been shown that LC3B binds to the LC3‐Interacting Region (LIR) in p62. This interaction has been studied extensively, but mammals have two subfamilies of Atg8‐like proteins: LC3 and GABARAP. GABARAP family proteins have significant homology with LC3B and therefore should have binding affinity for proteins with LIR motifs. However, the interaction between GABARAP family proteins and cargo adaptors is not well characterized. The aim of this work is to investigate the ability of GABARAP family proteins to bind to synthetic lipid membranes, and recruit cargo adaptor proteins to these membranes. We used biochemical assays and fluorescence imaging to characterize the activity of GABARAP family proteins in vitro. Our preliminary results show via pulldown that GABARAPL2 has less affinity for cargo adaptor proteins, p62 and NDP52, than LC3B. We also demonstrated using fluorescence microscopy that GABARAPL2 is readily conjugated to lipid vesicles by Atg7, Atg3, and the Atg 5/12/16 complex. Taken together, these results show GABARAPL2 has a different role than LC3B in cargo recruitment to the autophagosome, although the specific role has yet to be elucidated.Support or Funding InformationThis investigation was sponsored by NIH/NIGMS MARC U*STAR T34 HHS 00026 National Research Service Award to UMBC.
Tissue‐specific roles of cardiolipin in the control of systemic energy homeostasis
Authors: Gerhart-Hines Zachary 
Published: April 2020

The mitochondrial inner membrane is a dynamic interface that supports bioenergetic processes, intracellular communication, and transport of metabolites, lipids, and ions. The phospholipid, cardiolipin, is one of the most enriched components of this membrane and is classically ascribed an indispensable role in mitochondrial structure and function. Disruption of cardiolipin biology is causally linked to numerous pathophysiologies, including diabetes, nonalcoholic fatty liver disease, Parkinson’s disease, and Barth syndrome. Yet how cardiolipin controls metabolic function of individual mammalian tissues remains largely unknown. Therefore, we generated conditional genetic models with cardiolipin synthesis deficiency in tissues with predominantly uncoupled (i.e. brown adipose) or coupled (i.e. skeletal muscle) mitochondria. We found that tissue‐specific loss of cardiolipin had dramatically different outcomes on respiration and systemic energy homeostasis. Cardiolipin deficiency in brown adipose significantly reduced organismal insulin sensitivity and glucose tolerance, whereas loss of cardiolipin in skeletal muscle unexpectedly improved glycemic control. Moreover, in contrast to the dogmatic belief that cardiolipin is ubiquitously required, we found that certain skeletal muscle fiber types retained respiratory capacity in the face of cardiolipin depletion through mitochondrial biogenesis and fiber‐type switching. Our collective findings on tissue‐specific roles of cardiolipin reshape the fundamental understanding of mitochondrial structure and function with potential therapeutic implications for phospholipid disorders.Support or Funding InformationNovo Nordisk Foundation and the European Research Council (aCROBAT 639382)
Rhomboid Proteins in Cell Signaling
Authors: Freeman Matthew 
Published: April 2020

Cellular membranes are important biological interfaces. Not only do they compartmentalise cells from the environment and organelles from each other, but they also act as signalling platforms. Membrane proteases mediate many of their functions and are primary triggers of signalling. Rhomboids, which are intramembrane serine proteases, are a relatively recently discovered family of membrane proteases that control both signalling and membrane quality control. Rhomboid proteases are members of a much wider rhomboid‐like superfamily, most of which are pseudoproteases, having lost their proteolytic activity.The bottleneck in understanding the biological role of rhomboid proteases is identifying their substrates. This has proved to be a difficult problem with all proteases and there is no single definitive approach. We have now successfully developed a combined bioinformatic and experimental pipeline to reveal the substrates if mammalian rhomboids. This has led us to uncover a role for rhomboids in controlling calcium signalling and I shall discuss this novel mechanism of signalling homeostasis, as well as its physiological consequences in human cells.
The role of Organelle Contact During Chlamydia Developmental Cycle
Authors: Derré Isabelle 
Published: April 2020

Elucidating the molecular mechanisms supporting host‐pathogen interactions is a crucial step towards the eradication of infectious diseases. We study the obligate intracellular bacterium Chlamydia trachomatis, which is the leading cause of sexually transmitted infection of bacterial origin in the United States. Upon invading the epithelium of the genital tract, Chlamydia completes its life cycle in a membrane‐bound vacuole, called the inclusion. To convert the inclusion into an intracellular niche favorable for survival and replication, Chlamydia has evolved sophisticated mechanisms to manipulate the eukaryotic cell. Many studies have focused on understanding how Chlamydia, intercept the vesicular trafficking of the host cell. However, our laboratory has shed light on sites of intimate contact, with no fusion occurring, between the Chlamydia inclusion membrane and the endoplasmic reticulum (ER). Based on similarities to inter‐organelles membrane contact sites (MCS) observed in naïve cells, we refer to these structures as ER‐Inclusion MCS. Over the past several years, our lab has identified several molecular components of ER‐Inclusion MCS. More specifically, we have uncovered a role for Inc proteins (a subset of Chlamydia specific proteins that are embedded into the inclusion membrane) in the subversion of the endoplasmic reticulum. The recurrent theme is that, at ER‐Inclusion MCS, distinct Inc proteins mediate the recruitment of and associate with specific host factors that usually associate to distinct MCS in naïve cells. Here, we will discuss our current understanding of how these Inc protein‐host factor complexes contribute to the formation and function of ER‐Inclusion MCS and the establishment of Chlamydia replicative niche.Support or Funding InformationThis work is supported by NIH‐NIAID grants R01 AI101441, R21 AI141841 and R03 AI146649.
Structure of the Alternative Complex III from Flavobacterium johnsoniae in a Supercomplex with Cytochrome c Oxidase
Authors: Gennis Robert , Sun Chang , Benlekbir Samir , Venkatakrishnan Padmaja , Wang Yuhang , Hong Sangjin , Hosler Jonathan , Tajkhorshid Emad , Rubinstein John L. 
Published: April 2020

Alternative Complex III (ACIII), like Complex III, catalyzes the oxidation of membrane‐bound quinol and reduction of cytochrome c, but is structurally unrelated to Complex III. We solubilized the ACIII directly from membranes of Flavobacterium johnsoniae using styrene maleic acid (SMA) copolymer in the absence of traditional detergents. The ACIII was isolated as a functional 1:1 supercomplex with an aa3‐type cytochrome c oxidase (cyt aa3) within SMA copolymer nanodiscs. We determined the structure of the ACIII component of the supercomplex to 3.4 Å resolution by cryo‐EM and constructed an atomic model for its six subunits, two of which are anchored to the lipid bilayer with N‐terminal triacylated cysteine residues, resolved here for the first time. The structure also contains a [3Fe‐4S] cluster, a [4Fe‐4S] cluster, and six hemes c along with 11 phospholipid molecules. The ACIII is in direct contact with subunit III of the cyt aa3 component of the supercomplex. The structure revealed that this subunit is structurally modified from the canonical form of subunit III to facilitate association with ACIII, suggesting a specific role of the supercomplex in the respiratory system of this bacterium.Support or Funding InformationThis work was supported by funds from the National Institutes of Health (R01‐HL16101 to R.B.G., P41‐GM104601, U54‐GM087519, and R01‐GM123455 to E.T.) and Canadian Institutes of Health Research (MOP‐81294 to J.L.R.); J.L.R. was supported by the Canada Research Chairs program. Some of this work was performed at the Simons Electron Microscopy Center and National Resource for Automated Molecular Microscopy, supported by grants from the Simons Foundation (349247), and the National Institute of General Medical Sciences (GM103310, OD019994). Molecular dynamics simulations were performed at Blue Waters (ACI‐1713784 to E.T.) and XSEDE (MCA06N060 to E.T.). Blue Waters is supported by the National Science Foundation (OCI‐0725070 and ACI‐1238993) and the state of Illinois. XSEDE is supported by the National Science Foundation (ACI‐1548562). We thank Mark Mcbride for kindly providing us with the Flavobacterium johnsoniae UW101 strain. We thank Bridget Carragher and Clint Potter for facilitating access to the Titan Krios and Zhening Zhang for collecting data. We also thank Mohammad Mazhab‐Jafari for advice on building atomic models.
The Role of tRNA Derived Small RNAs in Gene Regulation in Normal Tissues and Cancer
Authors: Kay Mark A. 
Published: April 2020

The function of tRNAs is not merely to provide the specific amino acids for a growing peptide chain during protein synthesis. Precursor and mature tRNAs can be enzymatically cleaved into various tRNA derived small RNAs. While there are thousands of different RNA species that can be generated, the function of most are not known. I will provide a brief introduction into this field and describe the mechanism of how at least one specific tsRNA derived from the 3′end of a mature tRNA is involved in regulating ribosome biogenesis (Kim et al. Nature 2017). This 3′tsRNA is upregulated in many tumors. Reducing the tsRNA in patient derived hepatocellular carcinomas using antisense oligonucleotides induced apoptosis and tumor shrinkage in mice. This as well as other 3′tsRNAs are being studied as potential targets for cancer therapeutics. I will provide an update on current approaches we are developing to help us identify, quantify, and define the targets of the myriad of various tsRNAs present in various cell types. This will further allow investigation as to their role in maintaining health and disease states.Support or Funding InformationNational Institutes of Health ‐ National Institute of Diabetes and Digestive and Kidney Diseases R01‐DK114483
The Piwi‐piRNA Pathway: a New Paradigm in Gene Regulation
Authors: Lin Haifan 
Published: April 2020

Small non‐coding RNAs have been recognized as key players in gene regulation. In 2006, we and others discovered a novel class of small RNAs that interact with Piwi proteins in the germline of diverse organisms. These Piwi‐interacting RNAs (piRNAs), mostly 26–32 nucleotide in length and correspond to all types of genomic sequences, represent a distinct small‐RNA pathway. In my talk, I will report our recent progress that reveal the crucial roles of the Piwi‐piRNA pathway in mediating the regulation of mRNA and lncRNA stability by transposons and pseudogenes, which represent a new paradigm of regulation among the major constituents of the genome.Support or Funding InformationThis work was supported by the NIH grant R37HD42012 and a Mathers Foundation award.
RNA Modification in Cancer
Authors: Chen Jianjun 
Published: April 2020

N6‐methyladenosine (m6A), the most abundant internal modification in eukaryotic mRNAs, has been shown to play essential roles in various normal bioprocesses. We show recently that histone H3 trimethylation at Lys36 (H3K36me3) guided m6A deposition co‐transcriptionally. Evidence is emerging that m6A modification and the associated regulatory proteins also play critical roles in cancers. We have revealed the important functions of m6A regulatory proteins (e.g., FTO, METTL14 and IGF2BP1/2/3) in the development and drug response of cancer, especially acute myeloid leukemia (AML), and in the self‐renewal of leukemia stem cells (LSCs). We found that FTO is highly expressed in certain subtypes of AMLs including AMLs carrying t(11q23), t(15;17), NPM1 mutation, and/or FLT3‐ITD, in which FTO plays an essential oncogenic role in promoting leukemogenesis and in affecting drug response through post‐transcriptionally regulating expression of its critical target RNAs (such as ASB2 and RARA) in an m6A‐dependent manner. Subsequently, we found that FTO is also a direct target of R‐2‐hydroxyglutarate (R‐2HG), which is produced at high levels by mutant isocitrate dehydrogenase 1/2 (IDH1/2) enzymes and has been reported as an oncometabolite. We show that by targeting the FTO/m6A/MYC‐CEBPA axis, R‐2HG exhibits a broad and intrinsic anti‐tumor effect in vitro and in vivo. We also show that METTL14 is overexpressed in AML and plays a critical role in the development and drug response of AML, and is also required for the self‐renewal of leukemia stem cells, by post‐transcriptionally regulating of expression of a set of essential oncogenes such as MYC and MYB. Very recently, we have developed highly selective and effective FTO inhibitor compounds that shows potent therapeutic effects in treating human AML and solid tumors in preclinical animal models, demonstrating that as an mRNA demethylase, FTO is a druggable target for cancer treatment. Collectively, our studies highlight the critical roles and therapeutic implication of m6A modification and its regulatory proteins in cancers.Support or Funding InformationThis work is supported in part by the National Institutes of Health (NIH) Grants R01 CA214965 (J.C.), R01 CA236399 (J.C.), R01 CA211614 (J.C.). J.C. is a Leukemia & Lymphoma Society (LLS) Scholar.
Control of Macrophage Activation by Coenzyme A
Authors: Divakaruni Ajit S. 
Published: April 2020

Macrophages are innate immune cells responsible for processes as varied as killing pathogens, initiating wound‐healing programs, and presenting antigens to T cells. To achieve this broad range of functions, they acquire pro‐ or anti‐inflammatory programs (or ‘polarize’) by integrating intrinsic, extrinsic, and environmental signals. It is now well established that metabolic changes are critical for this process, though it remains unclear precisely which metabolic alterations are indispensable for (rather than merely being associated with) activation.Pro‐inflammatory macrophage polarization with lipopolysaccharide (LPS) collapses mitochondrial ATP production. This profound decrease in oxidative phosphorylation is associated with increases in glycolysis, signaling metabolites from the TCA cycle, and mitochondrially derived redox signals. Conversely, anti‐inflammatory activation with interleukin‐4 (IL‐4) is associated with substantial increases in oxidative phosphorylation and fatty acid oxidation (FAO). Previous work in our laboratory has shown that although FAO and mitochondrial ATP production are strongly associated with the IL‐4 response, these are surprisingly dispensable, whereas coenzyme A homeostasis is obligatory [Divakaruni et al. (2018)
Cell Metabolism]. This presentation will cover our current understanding of the essential metabolic requirements of macrophage activation, with a focus on the potential mechanisms by which coenzyme A may control the IL‐4 response.
Tuning receptor signaling through ligand engineering
Authors: Garcia Chris 
Published: April 2020

I will present the results of studies in our laboratory investigating the role of extracellular ligand‐receptor complex structure on the nature of signaling outputs in a range of systems. Most cell surface receptors are activated by some degree of ligand‐mediated clustering or oligomerization, but it is less clear to what degree the nature of the downstream signal induced by ligand can be ‘tuned’ or manipulated by natural or engineered ligands that engage the receptors with alternative geometries or binding parameters. Typically, ligands that elicit distinct pharmacologies through a single receptor have been observed GPCRs, but we have engineered ligands for T cell and cytokine receptors that exhibit partial agonism and inverse agonism. As one example, we have modulated cytokine receptor signaling by altering the orientation and proximity of a cytokine receptor dimer using diabodies and other synthetic designed scaffolds as surrogate ligands. We directly correlated the intact receptor dimer structures, determined crystallographically, with functional outcome and we find that indeed such systems are ‘tunable’ by remodeling dimer topology and distance. Thus, induced alterations in receptor dimer geometry can ‘tune’ signaling and extracellular ligands that enforce large receptor inter‐subunit distances can counteract intracellular oncogenic ligand‐independent receptor activation. The approach of modulating signaling output through receptors is important to overcoming the therapeutic limitations of cytokine pleiotropy. In my talk I will discuss recent results bearing on this topic.Support or Funding Information1Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, California, USA. 2Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, California, USA.
Sugary Coats: Synthesis and Secretion of Extracellular Polysaccharides
Authors: Zimmer Jochen 
Published: April 2020

Complex carbohydrates are frequently deposited on the cell surface to form cell walls, capsules, or 3‐dimensional matrices called biofilms. Often, the high molecular weight polymers are synthesized intracellularly and transported across at least one biological membrane by dedicated translocation machineries. We are interested in how polysaccharides are assembled and deposited on the cell surface. In particular, bacterial cellulose is a major biofilm component of many enterobacteria and secreted during its synthesis by the membrane‐embedded cellulose synthase, a processive glycosyltransferase. Using the tools of structural and molecular biology, we delineated the mechanism by which the enzyme elongates a cellulose polymer and translocates it across the membrane through a pore formed by its own transmembrane region.We have also examined O antigens, which constitute the variable region of lipopolysaccharides in the outer membrane of Gram‐negative bacteria. The polymers are synthesized inside the cell on a lipid anchor and transported to the periplasm by the WzmWzt ABC transporter. Crystal structures of the transporter in nucleotide‐free and ATP‐bound states suggest a processive translocation mechanism through a channel formed by the transporter. Molecular dynamics simulations suggest that membrane lipids are a fundamental part of the transporter’s function by sealing its channel in a resting state.
Malva pseudolavatera leaf extract promotes ROS induction leading to apoptosis in Acute Myeloid Leukemia cells in vitro
Authors: Rizk Sandra , El Khoury Marianne , Haykal Tony , Hodroj Mohammad Hassan , Najem Sonia Abou , Taleb Robin I. 
Published: April 2020

Malva pseudolavatera Webb & Berthel is a plant from the Malvaceae family that has long been included in the human diet due to its various curative effects. Many plant leaf extracts from the various species of Malva genus have been reported to possess anti‐cancer properties, however, studies on M. pseudolavatera Webb & Berthel leaves have documented anti‐inflammatory and anti‐oxidant effects with no emphasis on their possible anti‐cancer potential. The present study explores the anti‐cancer properties of Malva pseudolavatera Webb & Berthel leaf extract on Acute Myeloid Leukemia (AML) cell lines in vitro and deciphers the underlying molecular mechanism. Treatment of AML cell lines with M. pseudolavatera methanolic leaf extract showed a dose and time dependent inhibition of proliferation and a dose‐dependent increase in apoptotic hallmarks such as an increase in phosphatidylserine on the outer membrane leaflet, membrane leakage in addition to DNA fragmentation. The pro‐apoptotic effect was induced by ROS induction as well as an upregulation of cleaved PARP, an increase in Bax/Bcl‐2 ratio, and the release of cytochrome‐c from the mitochondria. Major compounds of the extract included methyl linolenate, phytol, γ‐sitosterol and stigmasterol as revealed by Gas Chromatography coupled to Mass Spectrometry.Support or Funding InformationSchool Research and Development Council, Lebanese American University