bluuebunny/crossref_metadata_2025_split huggingface dataset:
A crystallographic view of the reaction cycle in iron(II) and 2‐(oxo)‐glutarate‐dependent oxygenases
Authors: Boal Amie K. 
Published: June 2021

Iron(II)‐ and 2‐(oxo)‐glutarate‐ (Fe/2OG) dependent oxygenases are a large and functionally diverse family of oxidative tailoring enzymes, the majority of which are hydroxylases. Many other outcomes are possible, including halogenation, stereoinversion, cyclization, and desaturation reactions, but the structural adaptations that enable alternative transformations are not fully understood. All Fe/2OG enzymes, regardless of outcome, proceed through an Fe(IV)‐oxo intermediate that has been isolated in solution but has not been characterized crystallographically. We have determined high‐resolution x‐ray crystal structures of four distinct states in the reaction pathway of an Fe/2OG hydroxylase, including a previously unobserved intermediate. The study reveals key second‐sphere structural changes during the reaction cycle that explain known reactivity patterns in Fe/2OG enzymes and provide new opportunities for functional prediction and protein engineering in the super family.This abstract is from the Experimental Biology 2018 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
Tyrosine kinase in ulcerative colitis associated compromised microglial functions.
Authors: Kumar Narendra , Kumar Premranjan , Mishra Jayshree 
Published: June 2021

Microglia plays an essential role in the maintenance of brain homeostasis and compromise in microglia functions are well documented to trigger neurodegenerative disorders including Alzheimer's disease. However, the role of gut immunity and intestinal inflammation in microglia function and neurodegeneration remains unclear. Previously, we have established that the loss of Jak3 induces predisposition of compromised intestinal barrier function mediated colitis. In the present study, we demonstrate that loss of Jak3 induces chronic inflammation associated with increased circulating pro‐inflammatory cytokines that led to increased neuroinflammation and microglia dysfunction. Our data showed that DSS induced mucosal inflammation was more severe in Jak3 global knockout (KO) and intestinal epithelial‐specific knockout (Int‐KO) mouse compared to corresponding wild type mouse. Further, loss of Jak3 increased TLR signaling and associated pro‐inflammatory cytokines expression and together, exacerbated neuroinflammation in the brain. The increase in neuro‐inflammation triggered dysfunctional microglia (Iba1) and reduced TREM2 expression in brain further increased the β‐Amyloid and pTau accumulation in DSS treated KO and Int‐KO mice compared to corresponding control wild type group. Taken together these results demonstrate the essential role of intestinal‐Jak3 in mucosal homeostasis and microglial dysfunction associated Alzheimer's disease.This abstract is from the Experimental Biology 2018 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
Determining the effect of the WNT/b‐catenin pathway on the ischemic blood‐brain barrier using induced pluripotent stem cells
Authors: Page Shyanne , Al‐Ahmad Abraham 
Published: June 2021

The blood‐brain barrier (BBB) is a selectively permeable barrier made up of tight junctions formed by endothelial cells that separates the circulating blood from the brain extracellular fluid. The primary function of this barrier is to keep toxins, bacteria, viruses, and drugs from entering the brain. In the event of an ischemic stroke, the BBB becomes leaky due to the activation of hypoxia inducible factor 1‐alpha (HIF1‐a) and neurons become apoptotic. It is known that activation of the WNT pathway results in the production of B‐catenin, which has been shown to enhance HIF1‐a mediated transcription, which promotes the survival of cells and their adaptation to hypoxia. Currently, there are no drugs that have been formulated to restore the BBB function as well as neuron survival following ischemic stress. The purpose of our study was to determine the effect of small molecules on the BBB/WNT pathway during ischemia/re‐oxygenation. Brain microvascular endothelial cells (BMECs) derived from iPSCs and the immortalized human brain endothelial cell line, HCMEC/D3, were cultured and placed in ischemic stress for 6hrs, followed by a 24 hour period of re‐oxygenation. At the time of re‐oxygenation, cells were treated with small molecules CHIR99021, TWS (WNT activators), IWP‐4, IWR, and XAV (WNT inhibitors) in order to determine the effect of the WNT pathway on cell survival. Transendothelial Electrical Resistance (TEER) and permeability were performed to assess the effect that the WNT pathway has barrier integrity following re‐oxygenation. Further, MTT and ICC were performed to determine cell viability and tight junction expression, respectively. Preliminary results of this study have shown that inhibition of the WNT pathway during re‐oxygenation results in up‐regulation of tight junction proteins and an increase in cell viability as well as an increase in barrier function.Support or Funding InformationLaura W. Bush Institute for Women's HealthThis abstract is from the Experimental Biology 2018 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
Platelet Activating Factor Receptor (PAFR) Regulates Colitis‐induced Pulmonary Inflammation
Authors: Liu Gang , Mateer Sean , Mathe Andrea , Goggins Bridie , Hsu Alan , Minahan Kyra , Bruce Jessica , Fricker Michael , Wark Peter , Hansbro Philip , Keely Simon 
Published: June 2021

Inflammatory bowel disease (IBD) is a progressive disease that includes Crohn's diseases and ulcerative colitis. Over one third of IBD patients have secondary organ pathologies and pulmonary manifestations are common. The platelet activating factor receptor (PAFR) plays a critical role in regulating inflammation and it is expressed on epithelial cells and neutrophils in both colon and lung. Having identified increased expression of PAFR in both the gastrointestinal (GI) tract and lungs of mice with dextran sulfate sodium (DSS) colitis, we hypothesised that PAFR was a mediator of the pulmonary inflammation associated with colitis. We aimed to elucidate the role of PAFR in gut‐lung inflammatory cross‐talk using of the DSS‐induced experimental model of colitis (7 days). DSS mice were treated with PAFR antagonist CV6209 both intranasally and intravenously and lung, colon and blood were assessed for inflammatory cells and mediators by qPCR, immunoblot, immunohistochemistry and flow cytometry. We demonstrated that DSS‐induced colitis resulted in inflammation in mouse bronchoalveolar lavage fluid (BALF) and lungs, as well as increased PAFR protein levels in lungs and colons. Pulmonary neutrophils in DSS animals showed increased PAFR staining. Bacterial 16S mRNA expression were also increased in mouse lungs after 7 days DSS challenge. Both intravenous and intranasal inhibition of PAFR by CV6209 reduced colitis‐induced numbers of neutrophils, but not macrophages, in mouse lungs. Inhibition of PAFR also reduced levels of TNF and IL‐1b proteins and bacterial 16S expression in mouse lungs. Importantly, intravenous administration of CV6209 reduced colitis pathology, TNF and IL‐1b protein levels in mouse colons after 7 days DSS challenge. In the DSS model, increased PAFR protein expression was associated with inflammasome activation, characterized by increased NLRP3 and mature caspase‐1 proteins, however inhibition of PAFR by CV6209 reduced NLRP3 and caspase‐1 levels after DSS challenge in mouse lungs. In vitro, NLRP3, activated caspase‐1 and secreted IL‐1b protein levels were increased in human alveolar epithelial cell culture (A549) after 24h LPS stimulation, and this was inhibited by treatment with CV6209. These data suggest that PAFR regulates colitis‐induced lung inflammation by IL‐1b protein activation via the NLRP3 inflammasome signalling pathway. PAFR may act as an inflammasome‐activating pattern recognition receptor during mucosal inflammation thus is a potential therapeutic target for lung inflammation associated with colitis and bacteraemia.Support or Funding InformationThis study was supported by a grant from National Health Medical Research Council (NHMRC) AustraliaThis abstract is from the Experimental Biology 2018 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
Glucose limited enhance the cancer stem cell population through PKM2/AMPK‐dependent signaling
Authors: Yang Yi‐Chieh , Chien Ming‐Hsien , Hsiao Michael 
Published: June 2021

BackgroundSolid tumor cells encounter stress from oxygen and glucose limitation as tumors continue to grow. This kind of metabolic stress in the solid tumor interiors affects cancer stem cell (CSC) formation. However, the mechanisms of how cancer stem cells are affected by glucose, a key nutrient in the microenvironment, exist many controversial reports and it still remain largely elusive.DesignThe enhancement of cancer stem cell population were detecting by the ability of sphere formation, percentage of CD133+ positive cells, and expression of cancer stem cell markers under glucose limitation condition. We investigated the detailed mechanism of nuclear translocation of PKM2 and AMP2 under glucose limited condition by Western blot and immunoprecipitation. We also assessed the effects of nuclear PKM2 in vitro and in vivo.Results and ConclusionIn response to glucose limited, we found that nuclear translocation of the glycolic key enzyme, pyruvate kinase M2 (PKM2), helps cancer cells survive under metabolic stress. We demonstrate here that limited of glucose concentration stimulates AMPK activation, resulting in co‐translocation of AMPK and PKM2 through Ran‐mediated nuclear transport. Translocated PKM2 subsequently binds with OCT4 to promote expression of cancer stemness‐related genes. In this way, nuclear PKM2 is able to enrich a cancer stem cell population under metabolic stress. Nuclear PKM2 is also shown to promote cancer metastasis in an orthotopic xenograft model. In conclusion, our work not only reveals the critical role of nuclear PKM2 in CSC formation, but also identifies a detailed mechanism of PKM2 nuclear translocation, which cooperates with the cytosolic nutrient sensor AMPK, under a glucose limited environment. These details suggest the possibility of finding new targets for therapeutic intervention.Support or Funding InformationMinistry of Science and Technology (ROC): MOST 105‐2320‐B‐038‐058‐MY3, MOST 106‐0210‐01‐15‐02This abstract is from the Experimental Biology 2018 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
Galectin‐9 is a Novel Modulator of Epithelial Restitution
Authors: Robinson Brian Scott , Saeedi Bejan , Naudin Crystal , Arthur Connie , Darby Trevor , Jones Rheinallt , Stowell Sean , Neish Andrew 
Published: June 2021

Galectins represent a diverse class of secreted lectins with high‐affinity for □‐galactoside residues present on glycoprotein and glycolipid glycans. Through regulation of protein stabilization at the cell surface, membrane localization, receptor activation, and interactions with the ECM, galectins can affect a diverse set of cellular activities required for epithelial tissue homeostasis and response to injury. To date, five mucosal‐associated galectins (Galectin‐1, 3, 4, 6, and 9) have been identified, each with different glycan binding properties and expression patterns, yet the roles of these galectins in epithelial restitution remains poorly understood. In order to investigate the role of individual galectins in these processes, we have begun to characterize the phenotypes of individual galectin‐deficient animals. We demonstrate that Galectin‐9 (Gal‐9) deficient mice show increased susceptibility to multiple models of epithelial damage and restitution, including radiation‐induced gastrointestinal syndrome and DSS‐induced colitis. Given its localization to intestinal crypts, we next tested the ability of Gal‐9 deficient crypts to grow in ex vivo cultures. We observe that organoid cultures obtained from Gal‐9 deficient animals have marked growth defects and reduced complexity compared to their wild‐type counterparts. Finally, on a molecular level, we see alterations in several signaling pathways required for epithelial restitution and cellular differentiation. In summary, these studies highlight the requirement of galectins in regulating epithelial function, and demonstrate a specific role for Gal‐9 in mediating these effects.Support or Funding InformationThis work was supported by NIH R01 AI064462. BR was supported by the Research Training in Translational Gastroenterology and Hepatology Training grant (NIH T32 DK108735).This abstract is from the Experimental Biology 2018 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
Chemical‐proteomic strategies to investigate reactive cysteines
Authors: Weerapana Eranthie 
Published: June 2021

Cysteine residues regulate the activity of diverse proteins via post translational modification by endogenous electrophiles and reactive oxygen species. These modified cysteine residues do not conform to a conserved sequence or structural motif, rendering the global identification of regulatory cysteines a considerable challenge. To identify regulatory cysteines in human proteomes, we have developed chemical‐proteomic tools to monitor cysteine reactivity both in vitro as well as directly in living cells. These global profiling methods have been applied to monitor the susceptibility of cysteines to S‐nitrosation and to identify redox‐active disulfides induced by epidermal‐growth factor (EGF) stimulation. In order to identify cysteine residues hypersensitive to S‐nitrosation, we developed a chemical‐proteomic platform that ranks cysteines in the human proteome by sensitivity to a variety of transnitrosating agents. Our proteomic studies identified several previously unannotated cysteines, which we proceeded to demonstrate were important regulators of protein activity. To identify cysteine oxidation events triggered by EGF stimulation, we developed a caged cysteine‐reactive probe to enable profiling of cysteine reactivity directly in living cells. We identified several redox‐active disulfides that were formed upon EGF stimulation for future functional characterization. Overall, our studies aim to unearth novel functional cysteine residues in the proteome, with the long‐term goal of identifying new modes of protein regulation through reactive cysteines.This abstract is from the Experimental Biology 2018 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
Shrinking the Metabolome for Systems Biology Reveals a New Metabolic Function of an Old Protein
Authors: Patti Gary 
Published: June 2021

When using liquid chromatography/mass spectrometry to perform metabolomics, it is common to detect thousands of signals from biological samples. A substantial number of these signals, however, cannot be biochemically identified. This has complicated the use of metabolomics for discovery profiling and created uncertainty about the number of “unknown metabolites” in a data set. Here we describe a suite of informatic and experimental approaches that were applied to completely annotate one metabolomic data set. The analysis revealed that >90% of our signals corresponded to artifacts, contaminants, and redundancies. A workflow will be presented for removing such signals to simplify discovery analysis by metabolomics. As an example, a study will be described in which we applied metabolomics to discover a new function of the protein carnitine palmitoyltransferase I (CPT1) that is unrelated to fatty acid oxidation.Support or Funding InformationThis work was supported by the National Institutes of Health Grant R35 ES028365, the Alfred P. Sloan Foundation, the Pew Scholars Program in the Biomedical sciences, and the Edward Mallinckrodt, Jr. Foundation.This abstract is from the Experimental Biology 2018 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
Subclavius Posticus Muscle: Accessory Muscle with Clinical Relevance to Thoracic Outlet Syndrome
Authors: Arrick Denise Mary , Stevens Kelsey , Inglis Stuart , Das Manas 
Published: June 2021

During a routine anatomical dissection, an aberrant muscle was discovered in the left neck region in a cadaver of an 80‐yr‐old male. The accessory muscle originated from the superior angle of the scapula and inserted to the superior margin of the first rib cartilage. The muscle ran anterior to the trunks of the brachial plexus and subclavian vessels. Due to its origin and insertion, the aberrant muscle was considered to be the subclavius posticus muscle. The subclavius posticus muscle has been reported to play a role in thoracic outlet syndrome, which occurs by neurovascular structures being compressed in the thoracic outlet region. The variants of subclavius posticus muscle, its development and its clinical significance to thoracic outlet syndrome will be discussed.This abstract is from the Experimental Biology 2018 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
Sexual Dimorphism of the Fetal, Neonatal, and Infantile Supraorbital Rim between Races
Authors: Koons Aaron W. , Zdilla Matthew J. 
Published: June 2021

The adult orbital rim is known to exhibit sexual dimorphism. However, the development of the orbital sexual dimorphism is poorly understood. Moreover, there has been little study of sexual dimorphism in the supraorbital rim in the early development of fontal bones. Therefore, this study assessed 188 supraorbital rims among black and white females and males of fetal, neonatal, and infantile age. The population consisted of 47 black female, 36 white female, 54 black male, and 51 white male supraorbital rims. Canonical variate analysis revealed statistically significant contour differences among all groups (p<0.0001). Further, all groups separated by Mahalanobis distances greater than 11 except for black females and white males (Mahalanobis distance = 6.84). The results of this study suggest that sexual dimorphism of the supraorbital rim exists within and between races, even among fetuses.Support or Funding InformationWV Research Challenge Fund [HEPC.dsr.17.06] and [HEPC.dsr.14.13]This abstract is from the Experimental Biology 2018 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
Tyr1 phosphorylation of RNA polymerase II CTD directs and expands the CTD code.
Authors: Mayfield Joshua E. , Mehaffey M. Rachel , Irani Seema , Walker Levi , Robinson Michelle , Burkholder Nathaniel Tate , Prescott Nicholas , Kathuria Karan , Brodbelt Jennifer S. , Zhang Yan Jessie 
Published: June 2021

The C‐terminal domain of RNA polymerase II (CTD) acts as a platform to recruit factors that facilitate gene expression, RNA processing, and integrate transcription with the essential cellular processes of DNA repair and histone modification. This domain is composed of a species‐specific number of repeats of the consensus amino acid heptad YSPTSPS, classically numbered as Tyr1‐Ser2‐Pro3‐Thr4‐Ser5‐Pro6‐Ser7. The targeted recruitment of these myriad factors is accomplished by post‐translational modification (PTM) of these heptads, specifically phosphorylation of Tyr1, Ser2, Ser5, and Ser7. Although the contribution of these marks in isolation is extensively studied, the ability of these marks to co‐exist or influence one another has not been rigorously investigated.We take the first steps to characterize “cross‐talk” between phosphorylation marks and reveal a previously unknown role for Tyr1 phosphorylation in diversifying and directing CTD modification events. Tyr1 phosphorylation has been previously implicated in RNA polymerase II stability, antisense and enhancer transcription, anti‐termination, and as an indicator of DNA damage. However, the mechanism through which Tyr1 influences this diverse array of functions is unknown. Using a combination of mass spectrometry, molecular biology, and targeted cellular assays we find that Tyr1 phosphorylation generates a chemically diverse CTD landscape and can influence the specificity of downstream modification enzymes, resulting in novel and uncharacterized marks in the CTD code. We provide direct evidence for combinatorial CTD phosphorylation events, expand the lexicon of CTD coding marks, and demonstrate unexplored mechanisms to precisely control eukaryotic transcription and transcription coupled‐processes.Support or Funding InformationThis work is supported by grants from the National Institutes of Health (R01 GM104896 to Y.J.Z. and R21EB018391 to J.S.B.) and Welch Foundation (F‐1778 to Y.J.Z. and F‐1155 to J.S.B.). Voyager DE‐PROT MALDI MS data was collected in the University of Texas at Austin Proteomics Facility. Funding from the UT System for support of the UT System Proteomics Core Facility Network is gratefully acknowledged.This abstract is from the Experimental Biology 2018 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
FIH is an oxygen sensor for G9a/GLP‐driven epigenetic regulation of metastasis‐related genes in ovarian cancer
Authors: KANG JENGMIN , Park Jong‐Wan 
Published: June 2021

The dioxygenases PHD1‐3 and FIH are the oxygen sensors for hypoxia‐inducible factor (HIF)‐driven transcription of hypoxia‐induced genes. However, little is known about the oxygen sensors responsible for oxygen‐dependent epigenetic regulation. We here show that FIH plays additional roles as an oxygen sensor in G9a‐ and GLP‐driven epigenetic regulation. FIH hydroxylates and inhibits G9a and GLP under normoxia. When the FIH reaction is limited under hypoxia, G9a and GLP are activated and repress the metastasis suppressor genes, thereby triggering cancer cell migration and peritoneal dissemination of ovarian cancer xenografts. FIH and G9a expressions are reciprocally associated with clinical outcomes of ovarian cancer. Mutations of FIH‐target motifs in G9a and GLP were identified in human cancers, and they exhibit excessive H3K9 methylation and facilitate cell invasion. This study provides insight into a new function of FIH as an upstream regulator of oxygen‐dependent chromatin remodeling. It also implies that the FIH‐G9a/GLP pathway could be a potential target for inhibiting hypoxia‐induced cancer metastasis.Support or Funding InformationThis work was supported by a grant from the National Research Foundation of Korea (2017R1A4A1015015 and 2016R1A2A1A05005082 to J.W.P). Kang J received a scholarship from the BK21‐plus education program provided by the National Research Foundation of Korea.This abstract is from the Experimental Biology 2018 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.