bluuebunny/crossref_metadata_2025_split huggingface dataset:
Disease‐causing mutations of Lamin A lead to loss of calcium homeostasis in the endo/sarcoplasmic reticulum
Authors: Chi Ya‐Hui , Lin Wen‐Hsin , Wang Wan‐Ping , Kao Cheng‐Heng , Wang Jing‐Ya , Teng Yuan‐Chi , Tsai Ting‐Fen 
Published: June 2021

Mutations in nuclear lamin A are responsible for several rare human diseases, including the Emery‐Dreifuss muscular dystrophy (AD‐EDMD) and the Hutchinson‐Gilford progeria syndrome (HGPS). Here we show that structure of the endo/sarcoplasmic reticulum (ER/SR) is disrupted in HGPS cells and skeletal muscle of Lmna mutant mice. However, only a slight increase in ER stress‐associated genes was observed. Microarray analysis revealed that expression of several calcium signaling‐associated genes were disturbed in the skeletal muscle of Lmna mutant mice compare to the wild type cohorts. Sacrolipin (Sln), a SERCA activity modulator, is highly expressed and serves as a protective factor for the lifespan of Lmna−/− mice. In a myoblast cellular system inducibly expressing progerin to model HGPS, we found increased store operated Ca2+ entry (SOCE) and colocalization of Stim1 and Orai1. These findings suggest that the nuclear lamin A is structurally and functionally connected to the robustness of ER/SR for calcium homeostasis.Support or Funding InformationThis work was supported by grants from the Ministry of Science and Technology, Taiwan (MOST 105‐2633‐B‐400‐001 and MOST 105‐2320‐B‐400‐020).This abstract is from the Experimental Biology 2018 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
Protein‐Protein Interaction Prediction Yields WNK‐SPAK/OSR1 Pathway as Regulator of Kir2.1 and Kir2.3 K+ Channels
Authors: Taylor Clinton Albert , An Sung‐Wan , Kankanamalage Sachith Gallolu , Huang Chou‐Long , Cobb Melanie Houston 
Published: June 2021

The WNK‐SPAK/OSR1 pathway is a key regulator of cellular ion transport and homeostasis, and has a role in physiological processes such as neurotransmission and blood pressure regulation. WNK kinases respond to changes in intracellular Cl−, osmolarity, and cell volume by activating the closely related kinases, SPAK and OSR1. The pathway mediates ion flux through Na+, K+, and Cl‐− cotransporters and ion channels via SPAK and OSR1‐dependent and independent mechanisms. SPAK and OSR1 use a protein interaction domain to bind linear R‐F‐x‐V/I sequence motifs in WNKs, cotransporters, and other proteins. Our goal was to identify novel SPAK and OSR1 interacting proteins by further defining the specificity determinants of the interaction, and predicting new interactions using the refined specificity profile. We used peptide arrays and biophysical measurements to define specificity, and used this information to search and rank motifs in the Uniprot database. All motifs not conserved in mice, not solvent exposed, and not present in the cytosol or nucleus were excluded. Nearly all of the previously validated interactions clustered within the top ten percent of our rankings and none were excluded, thus providing strong evidence that our ranking methodology was successful. Members of the inward rectifier K+ channel family were predicted to have a high probability of interacting with SPAK and OSR1 based on our rankings. We determined that OSR1 kinase activity activates two of the channels, Kir2.1 and Kir2.3, and activation is dependent on the presence of the binding motif. SiRNA knockdown of OSR1 and chemical inhibition of WNK kinases disrupted NaCl‐induced plasma membrane localization of Kir2.3. Our results suggest that activation of the WNK‐SPAK/OSR1 pathway enhances Kir2.1 and Kir2.3 channel activity by increasing plasma membrane localization of the channels. Our interaction predictions imply that additional inward rectifier K+ channel family members may be regulated in a similar manner. On a broader scale, our interaction predictions may help identify additional novel regulatory functions of the WNK‐SPAK/OSR1 pathway.Support or Funding InformationThis work was supported by National Institutes of Health GM53032 and Welch Foundation I‐1243 for M.H.C. Additional funding support to C.L.H.This abstract is from the Experimental Biology 2018 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
PGC‐1α, a Novel Substrate for Protein Arginine Methyltransferase 7?
Authors: Cuala Janielle , Osuji Immaculeta , Zurita‐Lopez Cecilia 
Published: June 2021

Peroxisome proliferator‐activated receptor γ coactivator 1α (PGC‐1α) is a protein that plays an important role in the regulation of energy metabolism. It participates in the regulation of both carbohydrate and lipid metabolism and is activated by insulin. For these reasons, it has been implicated in obesity, aging, diabetes and cardiomyopathy. Despite many studies on the role of this master regulator, the precise way it becomes regulated remains unknown. A recent study found that PGC‐1α becomes phosphorylated at Ser570 by kinase B (Akt/PKB) and this stops it from promoting gluconeogenesis and fatty acid oxidation. PGC‐1α is also modified by protein arginine methyltransferase 1 (PRMT1) at several arginine residues, which enhance its regulation. In this study, we set out to determine whether PGC‐1α is modified by PRMT7, another member of the PRMT family. We hypothesize that PRMT7 methylates PGC‐1α because it contains many RXR motifs, a known PRMT7 motif. In addition, they both are active at similar temperatures. To test this hypothesis, truncated constructs corresponding to PGC‐1α and full‐length PRMT7 were expressed and purified in bacterial cells. In vitro methylation reactions using tritiated AdoMet were carried out. Through fluorography of the methylation reactions, it was determined that PRMT7 methylates PGC‐1α within amino acid residues 532–640. Upon confirmation of the methylated arginine residue(s) through immunoblotting and mass spectrometry, further studies will be carried out to investigate the function of arginine methylation by PRMT7. These results will enhance our understanding of PGC‐1α with the broader goal of understanding its regulation in the context of obesity and diabetes.Support or Funding InformationCSULA Minority Access to Research Careers‐Undergraduate Student Training for Academic Research (MARC‐U*STAR), Grant: T34 GM008228 and Louis Stokes Alliance for Minority Participation (LSAMP), Grant: HRD‐1302873This abstract is from the Experimental Biology 2018 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
Investigating the Contribution of Sinorhizobium meliloti Flagella on Biofilm Formation and Symbiosis During Host Colonization
Authors: Amir Zhainib Adel , Chen Joseph C. 
Published: June 2021

Many bacteria transition from a motile to a sessile, aggregate state, known as a biofilm, ensuring bacterial survival in harsh environments. Biofilms pose serious threats to public health due to their association with bacterial resistance to antimicrobial treatments against infections. Sinorhizobium meliloti, a nitrogen‐fixing bacterium, forms biofilms on abiotic surfaces and on roots of leguminous plants. Our laboratory is currently investigating the contribution of biofilm to symbiosis between Sinorhizobium meliloti and the model host legume Medicago truncatula. Recently our laboratory detected a nonsense mutation in the podJ gene of the commonly used S. meliloti laboratory strain, Rm1021. By correcting this mutation, the new strain, podJ+, showed an ability to produce a polar adhesive called holdfast, and to build more robust biofilms. PodJ regulates flagellar motility and chemotaxis in S. meliloti, and the full‐length protein appears to be required for holdfast production, which in turn contributes to surface adhesion and biofilm formation. However, previous studies showed that holdfast alone is insufficient for biofilm formation; for example, holdfast and flagella together facilitate the surface attachment of cells in the related bacterium Caulobacter crescentus. The goal of this project is to investigate whether the flagella of S. meliloti contribute to holdfast‐dependent biofilm formation in S. meliloti. Additionally, I would like to determine whether the presence of flagella improves symbiosis of S. meliloti with the legume host. To achieve this goal, the presence of flagella was examined in strains with mutations in flagellar genes, in both the podJ+ background (JOE3759) and the original, uncorrected background (Rm1021). First, soft‐agar plates were used to assess the flagellar motility of the strains: this test indicates which strains synthesize or lack flagella. To confirm the presence and absence of flagella and to assess the formation of adhesive clusters in these strains, scanning electron microscopy and scanning transmission electron microscopy were utilized to examine the cells. Next, competitive infection assays were performed to assess the effect of flagella on symbiosis efficiency. This was performed by inoculating the Medicago host simultaneously with podJ+ strains that lack or produce flagella, thereby, determining which strain colonizes more root nodules. These results will help uncover the molecular pathways by which rhizobia form biofilms, thereby providing the basis for understanding and controlling biofilm formation in related pathogens.Support or Funding InformationNIH RISE programThis abstract is from the Experimental Biology 2018 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
The Genomics Education Partnership: Course‐based Research Experiences for Undergraduates
Authors: Van Stry Melanie , Saville Ken , Leung Wilson , Lopatto David , Elgin Sarah C.R. 
Published: June 2021

The Genomics Education Partnership (GEP) is a collaboration between faculty from over 100 diverse institutions with the goal of providing authentic course‐based undergraduate research experiences (CUREs) in bioinformatics and genomics for undergraduate students. The GEP faculty have developed curricula for undergraduates at all levels that allow faculty to implement bioinformatics instruction and research within their courses. The research projects have primarily focused on the comparative genomics of the Muller F element (dot chromosome) in several Drosophila species. This chromosome is unusual in that it is largely heterochromatic, but contains ca. 80 genes that are expressed at levels similar to those found in euchromatin. Our students have focused on sequence improvement (finishing), and the annotation of protein‐coding genes and transcription start sites. Through these evolutionary comparisons, we are gaining insights into the regulation of gene expression within this heterochromatic environment. Our most recent paper on the expansion of the Drosophila ananassae F element includes 239 undergraduate students and 31 faculty co‐authors. Our faculty and student surveys, pre/post‐quiz results, and focus groups suggest that students gain the most from CUREs when faculty treat them like members of a research team. They also learn through formative failures — when challenges arise that must be resolved. In addition to research projects, we are developing new curricula, such as the “Understanding Eukaryotic Genes” modules, designed to familiarize beginning students with genome browsers while teaching eukaryotic gene structure, and units on Hidden Markov Models and Dynamic Programming for more advanced students. The GEP is collaborating with Galaxy to create G‐OnRamp (http://gonramp.org), a workflow that constructs UCSC Assembly Hubs and JBrowse genome browsers for newly sequenced eukaryotic genomes. G‐OnRamp enables faculty to engage students in novel annotation projects from a variety of organisms (e.g., Puerto Rican parrot, parasitoid wasps). If interested in participating in a grant‐supported workshop either June 12–15 or July 16–19, 2018 to learn to use G‐OnRamp, contact Sarah Elgin (selgin@wustl.edu).Support or Funding InformationSupported by NSF IUSE #1431407 and NIH R25GM119157 to SCRE.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 role of the ESCRT pathway in prion disease
Authors: Lawrence Jessica 
Published: June 2021

Prion diseases are infectious neurodegenerative disorders caused by PrPSc, a misfolded and aggregated isoform of the cellular prion protein, PrPC. During late disease stages, PrPSc spreads through the CNS, causing neurodegeneration, gliosis, and ultimately death, however the mechanisms of prion cell to cell transport remain poorly defined. Here we investigated the role of exosomes in the intercellular spread of prions. Exosomes are extracellular nanovesicles that originate from the endosomal pathway and are important for intercellular communication, transporting proteins and mRNA to nearby cells. Exosomes harbor infectious prions isolated immortalized cell lines and mice, and these exosomes efficiently cause prion disease in mice. Exosomes are produced by the ESCRT pathway, an endosomal pathway consisting of four protein complexes functioning sequentially. Previous research has shown that knocking down components of this pathway reduce prion conversion and release in vitro. We hypothesize that prions exploit the exosome pathway as the primary mechanism of prion spread within the CNS. We have manipulated the ESCRT pathway in neuronal cells to understand its role in both prion conversion and spread in vitro. We have discovered that inhibiting the initial stages of prion entry into endosomes severely impacts both prion generation as well as autophagic degradation pathways.Support or Funding InformationNIH F31 NS103588This abstract is from the Experimental Biology 2018 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
Characterizing Native American mitochondrial DNA Haplogroups in Puerto Ricans by Next‐Generation Sequencing (NGS)
Authors: Matos Paola M. , Martínez‐Cruzado Juan C. 
Published: June 2021

Puerto Ricans are an admixed people with three different parental populations: European, African, and Native Americans. When Puerto Rico became a United States colony in 1898, the results of the census reported no trace of Native Americans (e.g. Taínos) on the island. Therefore, the percentage of Native American ancestry in Puerto Ricans has been questioned. Using mtDNA and restriction length polymorphism analysis (RFLP), my lab identified and quantified the frequency of four different Native American haplogroups (e.g A, B, C, and D). However, the genetic diversity within these haplogroups across the entire island needs further characterization. The experimental design consists of three phases: 1) genotype individuals using Real Time‐PCR, 2) library preparation for next‐generation sequencing, 3) mapping and sequencing of the mtDNA genome. Over 320 human saliva DNA samples have been screened. So far, 102 individuals have been identified for haplogroup A and 26 for haplogroup C. Further work will include the continuation of genotyping of individuals, and preparation of samples for sequencing and mapping of the mtDNA genome for the four haplogroups. This project will help discover the continental origins of the different lineages within each haplogroup and their time of arrival to the island.Support or Funding InformationResearch reported in this publication was supported by the National Institute of General Medical Sciences of the National Institute of Health under Award Number: T34GM008419This abstract is from the Experimental Biology 2018 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
Ultrasensitive Immunoassay for Ex‐Vivo Human Soluble Epoxide Hydrolase Detection
Authors: Li Dongyang , Cui Yongliang , Morisseau Christophe , Bellien Jérémy , Hammock Bruce 
Published: June 2021

Soluble epoxide hydrolase (sEH) is a potential pharmacological target for the treatment of hypertension, inflammation, cancer, pain and multiple cardiovascular related diseases and a marker of inflammation. Detecting and quantifying sEH appears an important diagnostic tool for numerous pathologies. However, current methods rely on expensive technologies such as radioactive markers or mass spectrometry that are available by the bench side. Here, we report the development of an ultrasensitive nanobody based immunoassay for human sEH ex vivo. Nanobodies are the variable domain of the heavy chain antibody, which permit high stability, ease of genetic manipulation, bacterial expression, and ability for continuous manufacture, thus providing a constant high quality biochemical reagent. Llama nanobodies against non‐denatured human sEH were used as the detection antibody in a sandwich ELISA format with polyclonal anti‐sEH as the capture antibody. To enhance the reporting signal, the conventional HRP labeled anti‐HA tag tracer was replaced with polymeric horseradish peroxidase (PolyHRP) reporter system. This yields a 141‐fold increase in the sensitivity and 57‐fold decrease in limit of detection. Systematic comparison of three different tracers in four ELISA formats demonstrated the overwhelming advantage of PolyHRP as a label for nanobody based immunoassay. The enhanced sEH immunoassay was further evaluated in terms of selectivity against other epoxide hydrolases and detection of the target protein in human tissue homogenate samples. Comparison with a radioactive enzyme activity based assay and a Western‐blot for sEH detection reveals good correlation with the immunoassay. Moreover, the enhanced ELISA was used successfully to detect the sEH level in peripheral blood mononuclear cells isolated from 90 patients with different disease status, which have in general very low abundance of sEH hard to detect by classic methods. The work demonstrates the promise of nanobody based ELISA as a diagnostic tool for detection of and other pharmacologically and toxicologically important proteins.Support or Funding InformationNational Institute of Health (Superfund P42ES04699 and R01 ES002710) and National Natural Science Foundation of China (81402722)This abstract is from the Experimental Biology 2018 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
Pharmacological inhibition or genetic ablation of soluble epoxide hydrolase attenuates obesity‐induced nonalcoholic fatty liver disease
Authors: Zhang Jianan , Yang Jun , Wang Weicang , Yang Haixia , Sanidad Katherine z. , Yang Szu‐Hao , Sukamtoh Elvira , Zhang Guodong 
Published: June 2021

The prevalence of nonalcoholic fatty liver disease (NAFLD) in western countries is 20–30%; it is of critical importance to identify new therapeutic target, in order to reduce the risks of NAFLD and associated diseases. Here, we report that the expression of soluble epoxide hydrolase (sEH) is increased in liver tissues of a high‐fat diet‐induced NAFLD model; in addition, pharmacological inhibition or genetic ablation of sEH attenuates high‐fat diet‐induced NAFLD, suggesting that sEH could be a novel therapeutic target of NAFLD. We find that after 8‐week dietary feeding of high‐fat diet (60%cal), the expression of sEH is dramatically increased in liver. To explore the roles of sEH in obesity‐induced NAFLD, we test whether pharmacological inhibition or genetic ablation of sEH affects the development of NAFLD. We find that oral administration of TPPU and t‐TUCB, which are two different sEH inhibitors, attenuates high‐fat diet‐induced fat accumulation in liver (assess by liver triglyceride analysis, oil red o staining and H&E histology staining), and reduces expressions of pro‐inflammatory genes in liver (Mcp‐1 and Tnf‐α). Similar results are observed in sEH knockout mice. Regarding the mechanisms, we find that pharmacological inhibition or genetic ablation of sEH suppresses the expression of Srebf1, Ppar‐γ, Cd36 and Dgat2, which play critical roles in lipid synthesis; and increases the expression of Ppar‐α, regulating fatty acid β‐oxidation. Together, these results support that sEH could be a promising therapeutic target for NAFLD, suppressing fat accumulation and inflammation in liver. This could lead to rapid human translations, because the pharmacological inhibitors of sEH are being evaluated in human clinical trials targeting multiple disorders.This abstract is from the Experimental Biology 2018 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
Characterization of the In Vivo Catalytic Efficiency of CYP2C9 M1L, a Novel and Common Variant in the Yup'ik Alaska Native Population
Authors: Henderson Lindsay M. , Hopkins Scarlett , Boyer Bert B. , Thummel Kenneth E. 
Published: June 2021

The Yup'ik Alaska Native people are under‐represented in genetic research, but have unique pharmacogene variation that may critically impact their response to drug therapy. Full gene resequencing of CYP2C9 in the Yup'ik population identified novel, relatively common CYP2C9 variants, including CYP2C9M1L (M1L), a coding region single nucleotide polymorphism hypothesized to confer a poor metabolism activity phenotype by disrupting the start codon. M1L is present at a minor allele frequency of 7.1% in the Yup'ik, placing the population at risk for adverse drug interactions with narrow therapeutic index CYP2C9 substrates such as (S)‐warfarin, phenytoin, and tolbutamide. This study's objective was to characterize the catalytic efficiency of MIL in vivo by evaluating the pharmacokinetic behavior of naproxen, a probe for CYP2C9 activity, in genotyped Yup'ik participants. Targeted genotyping was conducted to identify heterozygous and homozygous M1L individuals from 906 representative members of the Yup'ik population. CYP2C9 mediates the O‐demethylation of naproxen to its 6‐O‐desmethyl metabolite, which is glucuronidated or sulfonated to secondary metabolites, all of which are excreted into the urine. Thus, a change in the urinary metabolite to parent ratio is indicative of a change in CYP2C9 intrinsic formation clearance to 6‐O‐desmethyl naproxen. We developed and validated a novel LC/MS method for simultaneous quantification of (S)‐naproxen, (S)‐6‐O‐desmethyl naproxen, and (S)‐naproxen acyl glucuronide in human urine. Preliminary analysis of one‐half of the final study population revealed an average ratio of 6‐O‐desmethyl naproxen to unchanged naproxen of 18.0 ± 7.7 (n = 7), 10.1 ± 4.5 (n = 7), and 15.6 (n = 2) for the M1L reference, heterozygote, and homozygote variant groups, respectively. ANOVA analysis was borderline significant (p = 0.06) and pairwise comparison of the homozygous reference and heterozygous groups (p = 0.06) suggested reduced activity for the M1L variant. The effect of the novel M1L variant and its potential to alter the pharmacokinetics of drugs metabolized by CYP2C9 have clinical implications, including phenotypic misclassification from currently available pharmacogenetic tests, in the Alaska Native population.Support or Funding InformationP01 GM116691, T32 GM 007750This abstract is from the Experimental Biology 2018 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.