bluuebunny/crossref_metadata_2025_split huggingface dataset:
Modeling Phage Survival in Limiting Bacterial Growth
Authors: Tomassi Nicole 
Published: June 2021

Phages are viruses that infect bacteria and play a key role in ecosystems, including the human body. The resources available in the environment affect bacterial growth, which controls the production of phage particles. The impact of this pipeline in the ecological coexistence of phage and bacteria, however, remains unclear. Here we address this problem introducing a new mathematical model for E. coli bacteria and T4 phage—two reference model systems found in humans. First, experimental data is analyzed using linear regressions to determine the dependency of the phage production parameters as a function of the bacterial growth rate, which led to high R‐squared values and statistically significant p‐values. Then, a Lotka‐Volterra predator‐prey model was extended to include the bacterial dependency on resources as well as the phage dependency on bacterial growth. Standard tools in dynamical systems were applied to study the equilibrium and stability of the system analytically and numerically. Our preliminary analysis suggests that the coexistence of phage and bacteria depends on the initial conditions of the system, contrary to the classical Lotka‐Volterra model. Additional analysis will be necessary to determine the biological implications of this result and its potential biomedical application, for example, in phage therapy.Support or Funding InformationFunded by a grant from the National Institute of General Medical Sciences of the National Institutes of Health: SDSU MARC U*STAR 5T34GM008303‐28This abstract is from the Experimental Biology 2018 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
HIV‐1 Infected NSG‐BLT Humanized Mice as a Model for HIV‐Associated Lung Complications
Authors: Geohring Jason L. , Cota‐Gomez Adela 
Published: June 2021

Human immunodeficiency virus (HIV) is an incurable and life‐threatening disease impacting over 36 million people world‐wide. Antiretroviral treatment (ART) suppresses the virus and allows many patients to live longer lives. However, even patients undergoing ART are susceptible to complications in many organ systems including the lung. HIV has been successfully linked to pulmonary complications including: tuberculosis, cytomegalovirus, Hodgkin's lymphoma, chronic obstructive pulmonary disease (COPD), and pulmonary arterial hypertension (PAH). Some of these diseases have a higher prevalence amongst patients infected with HIV. For example, in HIV patients, the incidence of PAH is 1:200, which is approximately 300‐fold higher than idiopathic PAH in the general population. Due to the limited host specificity of HIV, there are not many well‐developed animal models to study these complications. However, previous research in NOD‐Scid IL‐2 receptor γ chain knockout mice engrafted with human hematopoietic stem cells (hCD34+) and surgically implanted with human fetal thymic and liver tissue (NSG‐BLT mice) has shown disseminated HIV infection, making NSG‐BLT mice a promising in vivo model. In this study, we aimed to confirm HIV dissemination to the lungs in these mice and to examine pulmonary pathologies after an acute infection period. We infected NSG‐BLT mice with HIV for 5, 10, or 15 weeks and looked for viral RNA and pro‐viral DNA in the lungs using qPCR and nested PCR, respectively. To begin investigating possible lung pathology, we measured cytokines from lung tissue and cell‐free bronchoalveolar (BAL) fluid using an ELISA‐based protein array. Of the many proteins that were dysregulated in HIV infected mice, RAGE and IL‐25 (also known as IL‐17) are of particular interest because they have been implicated in endothelial dysfunction or vascular remodeling. This suggests a role of these proteins in HIV‐directed lung pathology in these mice. We are currently confirming the dysregulation of these genes by qPCR. In conclusion, NSG‐BLT mice constitute a useful model for studying pulmonary dissemination and pathologies during HIV infection.Support or Funding InformationNational Institutes of Health (NIH) 1R01HL125050‐01This abstract is from the Experimental Biology 2018 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
Selenium and Exendin‐4 Combination is a Promising Therapeutic Approach for Diabetes Mellitus
Authors: Moustafa Mohamed E. , Assi Layal Abou , Najem Sonia Abou , Merii Mohamed , Hasan Randa , Barakat Ghinwa , Dhaini Hassan R. , El‐Sabban Marwan 
Published: June 2021

Previous studies suggested that selenium (Se) or exendin‐4 (Ex4) exerts antidiabetic effects. The mechanisms of the effects of Se, Ex4 and their combination on diabetes require further investigation. This study examined the effects of Se, Ex4, insulin or their combinations on hyperglycemia and on the expression of insulin‐signaling transducers: insulin receptor substrate 1 (IRS‐1), phosphoinositide‐3‐kinase (PI3K), and serine/threonine‐specific protein kinase (AKT) and glucose transporter‐2 (GLUT2) in diabetic rats. Diabetic rats were injected intraperitoneally twice daily with 4 U insulin/Kg body weight or 0.03 μg exendin‐4/Kg body weight, and/or treated with 5 ppm Se as sodium selenite in drinking water. All treatment modalities were continued for 6 days. Se/Ex4 combination lowered blood glucose level to 142 ± 7.0 mg/dL, increased mRNA levels of IRS‐1, PI3K, AKT and GLUT2 in the liver, and GLUT2 mRNA level in the kidneys. Se treatment of diabetic rats alone resulted in a significant increase in IRS‐1, AKT and GLUT2 mRNA expression levels in the kidneys. The hepatic protein levels of AKT were increased by all treatment modalities, whereas a significant increase in GLUT2 was found in rats treated with Se alone and Se/Ex4 combination as compared to untreated diabetic rats. Se/Ex4 combination was effective in controlling hyperglycemia and increased the levels of AKT and GLUT2 in the liver, and thus is a promising therapeutic approach for diabetes.Support or Funding InformationNational Council for Scientific Research (CNRS), Lebanon, research fund to M.E.M. (Grant No. 01‐11‐08)This abstract is from the Experimental Biology 2018 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
Crystallographic and enzyme kinetic analyses of the human Inositol Polyphosphate Multikinase (IPMK)
Authors: Blind Ray 
Published: June 2021

Inositol polyphosphate multikinase (IPMK, IPK2) is a nuclear, non‐canonical PI3‐kinase and a member of the IPK‐superfamily of inositol kinases. IPMK also has important non‐catalytic roles in p53, mTOR, AMPK and TRAF6 signaling, mediated largely by two disordered domains that decorate the well‐ordered ATP‐grasp kinase domain of IPMK. Ablation of IPMK disordered domains alters non‐catalytic IPMK functions, however it is unknown if these domains intrinsically alter the PI3‐kinase activity of IPMK. We present enzyme kinetic analyses of a highly engineered human IPMK devoid of all disordered domains (ΔIPMK) that has a 10‐fold increase in the apparent KM/kcat for PI(4,5)P2 (PIP2) compared to wild‐type, suggesting that the disordered domains inhibit IPMK activity in vitro. Further, the apparent KM for ATP is 17‐fold worse for ΔIPMK compared to wild type, indicating that sequences in the disordered domains affect ATP binding. We present the 2.9Å crystal structure of this human IPMK construct, showing that the conserved ATP‐grasp fold is maintained in ΔIPMK and providing structural rationales for the observed kinetic behavior. Taken together, these studies suggest that in addition to mediating protein‐protein interactions, the disordered domains of human IPMK impart intrinsic regulatory capacity to the PI3‐kinase activity of human IPMK.Support or Funding InformationJournal of Biological Chemistry Herb Tabor Award, American Cancer Society Research Scholar Award, Vanderbilt Ingram Cancer Center Ambassador Discovery Award, Jimmy V Foundation for Cancer Research V‐Scholar Award, Vanderbilt Diabetes Center Discovery Award, Vanderbilt Diabetes Research and Training Center Pilot and Feasibility Grant, and an American Cancer Society Institutional Research Grant.This abstract is from the Experimental Biology 2018 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
The Glycerophosphocholine Acyltransferase, Gpc1, Impacts PC Remodeling and Stationary Phase Cell Viability in Saccharomyces cerevisiae
Authors: Anaokar Sanket Pramod , Kodali Ravindra , Jonik Benjamin , Nikiforov Alexiy , Lager Ida , Stymne Sten , de Kroon A.I.P.M. (toon) , Patton‐Vogt Jana 
Published: June 2021

Phosphatidylcholine (PC) is the most abundant glycerophospholipid found in most eukaryotic membranes. Changes in its synthesis, turnover and remodeling play a crucial role in maintaining membrane homeostasis. PC species vary depending upon the acyl chains attached at the sn‐1 and sn‐2 position of the glycerol backbone. The fatty acid components of yeast PC are relatively simple, consisting of mostly C16:0, C16:1, C18:0 and C18:1 combined to produce PC species in which either one or both acyl chains is monounsaturated. Thus, the four major PC species found in yeast consist predominantly of the following chain combinations: two C16:1 to produce 32:2 PC, C16:0 and C16:1 to produce 32:1PC, C16:1 and C18:1 to produce 34:2PC, C16:0 and C18:1 or 18:0 and C16;1 to produce 34:1PC. Acyl chain composition is important as it affects the physical properties of membranes such as thickness, curvature and fluidity. We have recently reported on the characterization of glycerophosphocholine acyltransferase, Gpc1. Gpc1 acylates glycerophosphocholine (GPC), the product of the complete deacylation of PC, to produce lysophosphatidylcholine (LysoPC). LysoPC can then be converted to PC by the lysophospholipd acyltransferase, Ale1. In order to investigate the role of Gpc1 in PC remodeling, we performed PC species analyses on strains lacking or overexpressing GPC1. Our data indicates that the loss of GPC1 results in a decrease in PC species with a single unsaturation (32:1 and 34:1) and an increase in PC species with two unsaturations (32:2 and 34:2). Conversely, the overexpression of GPC1 results in an increase in singly unsaturated PC species (32:1 and 34:1). Expression analyses indicate that the GPC1 is upregulated upon attenuation of PC and sphingolipid biosynthetic pathways. Finally, preliminary phenotypic studies indicate that while loss of GPC1 does not affect log phase doubling time, it does result in a decrease in long‐term cell survival. Overall, we provide evidence that the remodeling of PC to more saturated species by Gpc1 is regulated in coordination with other lipid biosynthetic pathways and impacts stationary phase cell viability.Support or Funding InformationWe acknowledge support from National Institute of Health Grant NIH R15 GM104876 and Duquesne University.This abstract is from the Experimental Biology 2018 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
Structure and Function of Lipins: Key Enzymes in Triglyceride Metabolism
Authors: Airola Michael 
Published: June 2021

Triglycerides serve as a major reservoir for energy and elevated levels of triglycerides strongly correlate with increased risk for cardiovascular disease and diabetes. Triglyceride biosynthesis is carried out by a series of enzymes, with lipins catalyzing the penultimate step. Lipins are a family of evolutionarily conserved lipid phosphatases that convert phosphatidic acid to diacylglycerol. In mammals, lipins also function in the nucleus as transcriptional co‐activators to upregulate fatty acid oxidation genes. Accordingly, expression levels and mutations in lipins can affect whole‐body energy metabolism, obesity, adipocyte differentiation, and myopathy.Lipins are structurally uncharacterized and contain several unique but highly conserved protein domains. The lack of homology and structural information has hampered our understanding of how lipins can participate as both enzymes in lipid metabolism and in the nucleus to regulate gene expression.We will present new structural information that identifies a novel protein fold/domain in mammalian lipins whose molecular function was not previously determined. This domain forms a tightly associated dimer. The dimer interface is conserved among lipin paralogs that suggests a role in homo and hetero‐dimerization. A large surface patch of this domain is also highly conserved that suggests a potential binding interface for DNA, membranes, or proteins. Functional assays testing these hypotheses will be discussed.Support or Funding InformationAmerican Heart Association Scientist Development Award #17SDG33410860This abstract is from the Experimental Biology 2018 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
Polymorphic Pseudogenization of SIGLEC12 in Humans: Relationship to Late Stage Cancer Progression
Authors: Siddiqui Shoib Sarwar , Do Raymond , Zhang Wu , Lenz Heinz‐Josef , Johnson‐Pais Teresa , Leach Robin , Fraser Gary , Wang Charles , Varki Nissi , Varki Ajit 
Published: June 2021

Human Siglec‐XII (a receptor encoded by the SIGLEC12 gene) is expressed in tissue macrophages and some epithelial cell surfaces. Humans (but not the closely related “great apes”) harbor a universally fixed missense mutation that eliminated the sialic acid binding property of this protein, a canonical functional feature of all other human Siglecs. Population analysis of the SIGLEC12 locus identified a polymorphic frameshift mutation, which leads to truncation of the Siglec‐XII polypeptide, and loss of expression. The homozygous null state of this mutation is present in all human populations with an average frequency of ~40%, and the locus was independently identified as undergoing an unexplained “negative selective sweep”, apparently favoring the null state. In the current study, immunohistochemistry using a monoclonal antibody to Siglec‐XII showed that while some epithelia in ~35% of normal human tissue samples from human autopsies express Siglec‐XII on epithelial cells (approximately the expected rate based on the frequency of the null state), high expression was observed in about 80% of samples from advanced carcinomas. Genomic studies on population cohorts with a low frequency of carcinomas (Seventh‐day Adventists) and in early stage prostate cancers diagnosed clinically by PSA expression did not show any correlation of disease risk or early‐stage progression with the SIGLEC12 frameshift mutation. In contrast, analysis of two advanced colorectal cancer cohorts (TRIBE and FIRE3) demonstrated that more than 80% of the patients had wild‐type SIGLEC12. Moreover, in one of the colorectal cancer cohorts (FIRE3), the presence of wild‐type SIGLEC12 was correlated with significantly decreased survival. Meanwhile, gene expression data comparing a tumor cell line transfected with a human SIGLEC12 cDNA with sham‐transfected cells shows upregulation of pathways associated with cancer progression. Taken together, all of these evolutionary clues and experimental findings suggest that while SIGLEC12 likely lost its function in the immune system of humans prior to the origin of our species, its persistence in some humans could be associated with the pathobiology of late stage carcinomas. In this regard, we have taken advantage of the expression of wild type Siglec‐XII on urinary epithelial cells, to develop a simple urine test to check for the expression status of SIGLEC12. This approach can be combined with future genomic analyses and signaling studies, to explore this unusual human specific evolution of an apparent evolutionary liability.Support or Funding InformationThe G. Harold & Leila Y. Mathers Charitable Foundation grantThis abstract is from the Experimental Biology 2018 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
Rapid Evolution of Bacterial Exotoxin B Subunits Independent of A subunits: Sialic Acid Binding Preferences Correlate with Host Range and Intrinsic Toxicity
Authors: KHAN NAAZNEEN , Verhagen Andrea , Khedri Zahra , Diaz Sandra , Varki Nissi , Paton Adrienne , Beddoe Travis , Paton James , Varki Ajit 
Published: June 2021

Several well‐known AB bacterial toxins have cytotoxic A subunits that are delivered to the cytosol following B subunit binding to terminal sialic acid‐presenting glycans on host cell surfaces. Phylogenetic analysis of known and predicted B subunits in available genomes showed a poor correlation with that of associated A subunits, or even with that of the bacterial species phylogeny. In some cases, such as an exported protein of Yersinia pestis (YpB) there also appears to be no associated A subunit encoded in the genome. Y. pestis is the etiologic agent of Plague, responsible for major devastating epidemics in human history and is of global importance to public health and biodefense. Plague can never be eradicated because of the adaptability of the organism to infect more than 200 known host species. We noted that YpB shares 58% identity/79% similarity with the homopentameric B subunit of Subtilase cytotoxin, an AB5 toxin of E. coli, which also has 48% identity/68% similarity with that of the A2B5 S. Typhi typhoid toxin. We previously studied binding of such toxin B5 pentamers to a sialoglycan microarray and shown selective binding to different kinds of sialic acids that happen to be enriched in corresponding host cells, such as N‐acetylneuraminic acid (Neu5Ac; prominent in humans) or N‐glycolylneuraminic acid (Neu5Gc; prominent in ruminant mammals and rodents). Consistent with the much broader host range of Y. pestis, we have now found that YpB binds to essentially all types of sialic acids studied including Neu5Ac, Neu5Gc and their modified versions, and even to Kdn (2‐keto‐3‐deoxy‐D‐glycero‐D‐galacto‐nononic acid) a sialic acid prominent in reptiles and amphibians. Notably, YpB toxin alone can cause cytotoxicity that is abolished by mutations eliminating sialic acid recognition, suggesting that both uncontrolled cell proliferation and cell death might be mediated via lectin‐like cross‐linking of cell surface glycoproteins. These findings may help explain the wide host range of Y. pestis and could be important for understanding pathogenic mechanisms. Taken together, the data suggest Red Queen effects that are driving ongoing rapid evolution of both host sialic acids and pathogen toxin binding properties. Further studies of this clade of B5 toxins are revealing additional correlations of sialic acid binding preferences with host range and intrinsic toxicity, and molecular modeling studies are underway to define amino acid residues that determine binding differences.Support or Funding InformationNIH U01 CA199792This abstract is from the Experimental Biology 2018 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
Autoimmune Nature of Type I Diabetes Mellitus
Authors: Janvier Darlyne L. , Tulp Orien L. , Einstein George P. 
Published: June 2021

Type 1 diabetes Mellitus (T1DM) is a chronic autoimmune disease in which pancreatic β‐cell destruction results in loss of endogenous insulin production. Already one of the most prevalent chronic childhood diseases, the incidence of T1DM in children and young adults is projected to continue to increase over the next several decades. Although advances in technology have allowed for improved glucose monitoring and insulin delivery, no curative therapy is currently available for this growing patient population. Moreover, patients continue to experience long‐term complications such as blindness and kidney failure, even with the most intensive insulin regimens currently available.T1DM predominantly originates when insulin‐producing beta (β)‐cells in the pancreas are destroyed or suppressed due to an autoimmune response caused by the auto‐reactive T‐helper 1 (Th1) cells. Interestingly, the antigens responsible for this immune response, glutamic acid decarboxylase, are normally present in β‐cells; however, their destructive capabilities are restrained by the regulatory mechanisms of the body. When a person has certain genetic factors (e.g. the absence of certain protective histocompatibility locus antigen) and exposure to certain environmental factors, they are predisposed to immunologic injury of β‐cells. Furthermore, the odds of presenting with T1DM diminish with treatment with immune‐suppressive regimens that specifically target T‐cells. As a result, Th1 cells dominate the protective regulatory T‐cells. In turn, Th1 cells secrete cytokines, interleukin 2, and interferon gamma, which initiate inflammation of the islet cells that appears to result in the development of T1DM.In 2001 it was found that diabetes might be the first disease for which stem cell therapy is an option, when insulin‐producing embryonic stem cells of R1‐mice were transplanted into streptozotocin‐induced diabetic animals and normal blood glucose levels were achieved, and in other studies implantation of embryonic Sertoli cells into diabetic db mice also resulted in amelioration of the diabetic state. In contrast, infusion of cord blood derived stem cells in the absence of immunomodulation was without lasting effect on the diabetic state. Minor complications in R1‐mice aside, this event once again renewed the quest to find more practical and functional means to create human islets to treat diabetes.Can pancreatic stem cell transplant be used as a cure for T1DM, an autoimmune disease, and how does it stand against other cell transplants and other treatment modalities in the US? The bulk of preliminary evidence to date suggests encouraging potential for such approaches in the treatment of T1DM.Support or Funding InformationSupported by Institutional Resources of USAT, the Einstein Institute, and the University of Massassachusetts.This abstract is from the Experimental Biology 2018 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.