bluuebunny/crossref_metadata_2025_split huggingface dataset:
Identification of nutrient metabolites capable of altering the epigenetic status at specific loci
Authors: Hayakawa Koji , Nishitani Kenta , Tanaka Satoshi 
Published: June 2021

Nutrients can influence cellular functions associated with physiological and pathological processes. Major energy sources in our body, such as glucose and amino acids, are decomposed, resynthesized via numerous synthetic pathways, and finally, metabolized into energy molecules (e.g., ATP) and metabolites involved in various molecular events such as gene expression. Our previous study demonstrates that a sugar metabolite, N‐acetyl mannosamine, when used as a supplement in the culture medium, can induce the differentiation of pluripotent stem cells into orexin neurons and activate the epigenetic status at the orexin‐coding gene locus. Thus, our observations suggest that some metabolites can change the fate of a cell by participating in epigenetic alterations at specific loci. However, there is insufficient information about the role of specific nutrients and their metabolites in altering the epigenetic status. In the present study, we aimed to screen for metabolites that function as epigenetic modulators. We supplemented the culture medium with 129 metabolites individually during the induction of neural differentiation from human iPS cells (hiPSCs). We investigated the epigenetic status at 40 loci of the neural peptide‐coding genes by ChIP‐qPCR, using a high‐throughput platform. Trimethylation of lysine 4 of histone H3 (H3K4me3) and histone O‐GlcNAcylation of serine 40 of H2A (H2AS40Gc) were used as active epigenetic markers. Metabolites 4 and 12 considerably altered the levels of H3K4me3 and H2AS40Gc, respectively, at the loci of most genes, except at those of genes encoding pan‐neural markers. Among them, metabolites produced via the kynurenine pathway (one of the tryptophan metabolic pathways) increased H3K4me3 and H2AS40Gc levels at multiple neural peptide‐encoding gene loci such as CART (cocaine‐and amphetamine‐regulated transcript) and OXT (oxytocin). The mRNA expression levels of these genes were also found to have increased following supplementation of the culture medium with metabolites of the kynurenine pathway. In other words, supplementation with these metabolites could effectively induce the differentiation of hiPSCs into CART‐ and OXT‐producing neurons. Collectively, we have identified metabolites that can alter the epigenetic status at specific loci. Our findings provide a better understanding of the use of nutrients or bioactive food components in modifying epigenetic mechanisms.Support or Funding InformationThis work was supported by Lotte Shigemitsu Prize.This abstract is from the Experimental Biology 2019 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
Analysis of Chromatin Accessibility Landscapes in Esophageal Squamous Cell Carcinoma
Authors: Choi Sangyong , Sathe Adwait , Mathe Ewy , Xing Chao , Pan Zui 
Published: June 2021

Esophageal cancer ranks sixth among all cancers in mortality and is associated with malfunction in gene regulation and expression. Assay for Transposase‐Accessible Chromatin with high‐throughput sequencing (ATAC‐seq) can reveal the locations of regulatory elements across the genome and discover the mechanisms of chromatin structure that govern gene expression programs. This study compared the chromatin accessibility landscapes between esophageal squamous cell carcinoma cell lines (ESCC), i.e. KYSE‐30 and KYSE‐150, and non‐cancerous esophageal epithelial cell lines (NC), i.e. HET‐1A and NES‐G4T. Opened and closed chromatin regions were associated to the nearest genes, and gene ontology analyses (GO) were performed. The results demonstrated that many regions were more accessible in ESCC cells than in NC cells. These regions belong to the GO terms including positive regulation of GTPase activity, metabolic process, and nucleosome assembly. Furthermore, the promoter‐proximal peaks at genome‐wide scale predicted that several genes in histone gene cluster 1 on chromosome 6p22 were transcriptionally active in ESCC cells. To confirm that the promoter region with enhanced accessibility indeed is indicative to gene expression, the mRNA level of a few representative genes were examined. For example, the expression of PLCB1 gene, which encodes phospholipase C beta 1, a key regulator for GTPase activity and MAPK signaling, was confirmed to be up‐regulated in both ESCC cells. There were also some regions more inaccessible in ESCC cells than in NC cells and they belonged to different GO terms, chiefly associated with cellular homeostasis. This study may aid to reveal the instrumental epigenetic changes responsible for differential gene expression and ESCC development.This abstract is from the Experimental Biology 2019 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
The Histone Acetyltransferase GCN5 and Transcriptional Coactivator ADA2b Affect Trichome Initiation in Arabidopsis thaliana
Authors: Hark Amy T. , Caiola Hanna , Sockler Patrick , Kotak Jenna , Kendig Ashley , Cann Kelly , McCain Elizabeth R. 
Published: June 2021

While genome sequencing projects have helped us uncover what information is encoded in DNA of many species, one critical challenge that remains is to understand how gene function is controlled. We investigate the roles of chromatin‐modifying factors in regulating developmental processes in Arabidopsis thaliana. Our current work explores how the histone acetyltransferase GCN5 and the associated transcriptional adaptor ADA2b act to define which leaf cells are selected to become trichomes, single‐celled protrusions implicated in defense mechanisms. In a loss‐of‐function ada2b mutant background, trichome number on rosette leaves is decreased while in gcn5 mutant backgrounds the number of trichomes tends to increase. Using qRT‐PCR analysis, we have established a role for GCN5 in impacting the expression of key players in the trichome initiation pathway including the paralogs Repressor of GA (RGA) and GA Insensitive (GAI). Gibberellic acid (GA) signaling stimulates trichome initiation by blocking the DELLA repressors RGA and GAI, which in turn block a transcription factor cascade that controls trichome development. This approach has the potential to identify novel connections between GA, a critical plant hormone, and histone acetylation in plant growth. It also provides an example of how chromatin modifiers and transcription factors interact to drive developmental processes.This abstract is from the Experimental Biology 2019 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
Genome Wide Microarray Profiling Identified Differentially Expressed Circulating Biomarkers Associated with Early Development of Diabetic Cardiomyopathy
Authors: PANT TARUN , DHANASEKARAN ANURADHA , BAI XIAOWEN , BOSNJAK ZELJKO , GE ZHI‐DONG 
Published: June 2021

IntroductionCirculating long noncoding RNAs (lncRNAs) are emerging as valuable biomarkers in numerous diseases. However the expression signature of circulating lncRNAs is yet to be identified in diabetic cardiomyopathy (DCM). We used computational and system biology approach to predict circulating lncRNAs using plasma RNA before and after DCM.HypothesisWe hypothesized that lncRNAs could serve as blood‐based prognostic and diagnostic biomarkers in DCM detection.MethodsThe left ventricular function was measured with echocardiography in control and db/db mice. Expression profiling of lncRNAs was performed using LncRNA Array v3.0 (8 × 60K, Arraystar).ResultsA total of 17,124 lncRNAs and 13,333 mRNAs were profiled of which 814 lncRNAs and 2707 mRNAs were deregulated, and more than half were intergenic lncRNAs and antisense lncRNAs. Ten dysregulated plasma lncRNAs were validated by quantitative PCR assays. For the gene ontologies related to plasma, the enrichment was observed for those mRNAs which were found to be significantly co‐expressed with the neighboring lncRNAs during DCM. Bioinformatics analysis revealed that the altered lncRNAs regulated the differentially expressed mRNAs which were profoundly enriched for pathways such as insulin signaling, fatty acid metabolism, MAPK signaling, and hypertrophy cardiomyopathy which in the past has been associated with diabetic pathogenesis. To evaluate the translational efficiency of our mouse model, we experimentally validated the results using human induced pluripotent cell‐derived cardiomyocytes (hiPSCs‐CMs) for the in vitro DCM model. We found that most of the gene expression patterns were repeated in hiPSCs‐CMs and several of these lncRNAs genes have been associated with DCM in the past.ConclusionCirculating lncRNAs are dysregulated in DCM, and our results depict the changing transcriptome as a function of disease progression and functional role of lncRNAs. These lncRNAs may serve as promising targets for DCM prevention, early diagnosis, and therapy.Support or Funding InformationThis work was supported, in part, by a National Institutes of Health research grant P01GM 066730 (to Dr. Bosnjak) from the United States Public Health Services, Bethesda, Maryland, USA. The funding body had no role in the design of the study, collection, analysis, and interpretation of data, and in writing the abstract.This abstract is from the Experimental Biology 2019 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
Alcohol induces TGF‐beta through suppression of miR‐1946a
Authors: Sueblinvong Viranuj , Mills Stephen T , Fan Xian 
Published: June 2021

RationaleWe previously showed that chronic alcohol ingestion promotes fibroproliferative disrepair following bleomycin‐induced acute lung injury in a mouse model and that is associated with exaggerated constitutive and injury‐provoked expression of TGFβ. Importantly, the aberrant expression of TGFβ has been identified as a proximal event that mediates the ‘alcoholic lung’ phenotype. However, the mechanisms by which alcohol induces TGFβ1 has not been identified. Several microRNAs (miR) have been shown to directly target TGFβ. Using an in silico analysis, we identified that miR‐1946a is predicted to directly bind to the 3′ untranslated region (UTR) of the TGFβ mRNA and thereby inhibit its transcription. We hypothesize that alcohol‐mediated miR‐1946a leading to an induction of TGFβ expression.MethodsMouse primary lungfibroblasts (PLFs) were cultured ± alcohol (60 mM) for 24–48 hrs, miR‐1946aexpression was quantified. In parallel, PLFs were cultured with miR‐1946amimic, miR‐1946a inhibitor, or appropriate controls in the presence of absent of alcohol, then assessed for TGFβ gene and protein expression. Lastly, to further comfirm the miR‐1946abinding site on TGFβ 3′UTR, PLFs were transfected with vector containing TGFβ3′UTR (or control clone) tagged with luciferase reporter and miR‐1946a mimic(or negative mimic), then analyzed for luciferase activity.ResultsAlcohol suppressed PLFs expression of miR‐1946a. Treatment of PLFs with miR‐1946a mimic suppressed alcohol‐induced TGFβ expression while miR‐1946a inhibitor induced TGFβ expression. Lastly, miR‐1946a mimic suppressed TGFβ 3′UTR luciferase activity.ConclusionThese data suggest that miR‐1946a modulates TGFβ expression likely through direct interaction with TGFβ 3′UTR. These findings identify a novel mechanism by which alcohol induces TGFβ in the lung which would help us design therapeutic or preventative tools for alcoholic patients with or at risk of acute lung injury.Support or Funding InformationNIH K08 AA021404‐01This abstract is from the Experimental Biology 2019 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
Measuring the Stability of RNA5.0 in Human Cytomegalovirus (HCMV)
Authors: Tsingine Hannah P , Kulesza Caroline 
Published: June 2021

Human Cytomegalovirus (HCMV) is a member of the beta herpesvirus family. HCMV establishes a lifelong latent infection in its host, and although it infects a variety of cell types and replicates persistently, it has an asymptomatic effect in healthy humans. Primary or reactivated HCMV infections have the ability to be transferred via bodily secretions such as saliva, urine, or breast milk, and through organ transplants. Unfortunate organ recipients who contract the virus may suffer from pneumonia and/or acute organ rejection. HCMV is the largest of the human herpesviruses containing a DNA genome of approximately 240 kilobases encoding 225 open reading frames (ORFs). It's large and complex genome also encodes long noncoding RNAs (lncRNA) which are known for not being translated, but rather function as RNA. In HCMV, one of the lncRNA, known as RNA5.0, is a stable intron that is believed to play an important role in viral pathogenesis. Recent studies have shown that RNA5.0 is a nuclear localized stable intron that is transcribed by RNA polymerase II, and that it also consists of high adenine and thymine sequences. The true role of RNA5.0 is still unknown, so it could activate transcription, regulate gene silencing, or play a role in HCMV latency. To begin to understand why an intron that should be degraded within minutes is stable for hours, we will measure the half‐lives of viral noncoding RNAs using transfected cultured 293T cells.Support or Funding InformationNIH MARC T34GM092711This abstract is from the Experimental Biology 2019 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
Micro‐RNA isolated from liquid biopsies serve as novel molecular biomarkers for congestive heart failure in dogs
Authors: Shands Kristal , Ewing Carl , Ewing Coralis , Bohan Amy 
Published: June 2021

ObjectiveTo characterize expression profiles of circulating microRNAs via miRNA isolation from plasma (Qiagen) for dogs with congestive heart failure (CHF) secondary to myxomatous mitral valve degeneration (MMVD).Materials and Methods9 healthy small breed client‐owned dogs and 9 small breed client‐owned dogs (ages 9 and up) with CHF secondary to MMVD. Blood samples were collected from both healthy and affected dogs. Isolated microRNAs from plasma were subjected to quantitative reverse transcription PCR (qRT‐PCR) used to examine expression profiles of differentially expressed circulating microRNAs of dogs with CHF.ResultsResults of qRT‐PCR assays confirmed up‐regulation of several microRNAs as well as downregulation of multiple microRNAs. Results of qRT‐PCR assays were highly correlated with NGS data from a prior study done and supported our results.ConclusionThese results suggested that miRNAs serve as novel biomarkers for congestive heart failure (CHF) in small breed canines.This abstract is from the Experimental Biology 2019 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
miRNAs regulate the expression of sterol‐O acyltransferase 1 through inhibiting the 3′UTR of TGFβ receptor type 1 during embryonic development
Authors: LIN HAN‐JEN , DING SHIH‐TORNG 
Published: June 2021

Nutrients are utilized and re‐constructed by endodermal epithelial cells (EECs) of yolk sac membrane (YSM) in avian species during embryonic development. Sterol‐O acyltransferase 1 (SOAT1) is the key enzyme to convert cholesterol to cholesteryl ester, and for packaging into very‐low‐density lipoproteins for further delivering to growing embryos. During embryonic development, the quick absorption of yolk is matched with the significant changes of SOAT1 mRNA and enzymatic activity. MicroRNAs (miRNAs), groups of highly conserved small non‐coding RNA molecules, are usually ~23 nucleotides across species, serving classical biofunctions as mRNA‐targeting cleavage, translation repression and mRNA deadenylation. miRNAs have been identified to regulate angiogenesis, invasion and metabolism during mammalian development. However, the involvement and importance of miRNAs in lipid utilization during avian embryogenesis remains unclear.Using a RNA sequencing technique, we found many miRNAs expressed during quail embryonic development. We confirmed the expression pattern with real time PCR and several miRNAs (gga‐miR‐181a‐5p, gga‐miR‐133a‐5p, and gga‐miR‐429‐3p) were selected because they are candidates targeting to the receptor (TGFβ receptor type 1, TGFBR1) that regulates the expression of SOAT1. Similar to SOAT1 mRNA concentration, the gga‐miR‐181a‐5p expressions were gradually elevated during development, but gga‐miR‐429‐3p were presented in the opposite direction. Moreover, transfection with gga‐miR‐181a‐5p, gga‐133a‐5p, or gga‐429‐3p inhibited TGFBR1 and SOAT1 mRNA expressions in EECs. The 3′ untranslated region (3′UTR) of TGFBR1 is speculated to be one of the targets of miRNAs (gga‐miR‐181a‐5p, gga‐miR‐133a‐5p, and gga‐miR‐429‐3p).Taken together, miRNAs expression during embryonic development can regulate SOAT1 expression through inhibiting the 3′UTR of TGFBR1. This is indicative of possible regulation of avian yolk lipid utilization and modification of hatchability by modifying miRNA expression.Support or Funding InformationMinistry of Science and Technology, Taiwan (ROC)This abstract is from the Experimental Biology 2019 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
Rapid RNA‐Protein Interaction Detection with RNA5.0 of HCMV
Authors: Mickens Kassandra , Mickens Kaylee , Kulesza Caroline 
Published: June 2021

CMV is the most common cause of both congenital infection and post‐transplant infection worldwide. CMV infection can cause severe symptoms: pneumonia, encephalitis, and inflammation of vital organs. There is currently no vaccine for CMV. An understanding of how CMV progresses from its acute phase to persistence would illuminate features of the pathogen that could lead to novel treatments for the disease which block the virus from reaching latency.RNA5.0 is a lncRNA produced during CMV infection. Studies using the homologous RNA7.2 a mouse model has shown when the RNA is not expressed in vivo, CMV infection cannot reach its persistent phase. However, how it performs this function remains unclear. Our study hopes to help the field to move forward by expanding the limited knowledge about RNA5.0's function in viral persistence at a molecular level by purifying and identifying the proteins. We propose identifying proteins that bind to RNA5.0 with known cellular functions will allow us to narrow the speculation surrounding RNA5.0's function, as their functions are likely related.To purify these proteins, we will utilize the RaPID (RNA–protein interaction detection) method outlined in Ramanathan et al. 2018. In this novel approach, RNA stem loops flank RNA sequence of interest and recruits the RaPID fusion protein that biotinylates proteins proximal to inserted RNA. A streptavidin pulldown is used to capture biotinylated proteins for analysis by mass spectrometry (MS). Because the RaPID method has limited reach, in order to characterize all the proteins that bind to the 5kb lncRNA of CMV we will use 50 overlapping 150bp segments with 50bp overlaps.Support or Funding InformationFort Lewis College Undergraduate Research, Scholarship, and Creative Activity GrantThis abstract is from the Experimental Biology 2019 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
Structural Basis for NLRP6 Inflammasome Assembly and Activation
Authors: Shen Chen , Lu Alvin , Fu Tian‐Min , Wu Hao 
Published: June 2021

Inflammasomes are multi‐protein complexes that detect infectious microbes and cellular stressors, and that activate inflammatory caspases for cytokine maturation and pyroptosis. NLRP6, a sensor protein in the nucleotide‐binding domain (NBD) and leucine‐rich repeat (LRR)containing (NLR) family, is shown to play multiple roles in regulation of inflammation and other innate immune signaling pathways. However, little is known about the molecular mechanism of NLRP6 inflammasome assembly and activation. Using cryo‐Electron Microscopy (Cryo‐EM) and X‐ray crystallography, we found that NLRP6 PYD domain is able to self‐assemble into filamentous structures accompanied by large conformational changes, and can recruit the adaptor protein ASC through homotypic PYD/PYD interactions. We further observed that full‐length NLRP6 assembles into wider filaments in a concentration dependent manner with a PYD core surrounded by the NBD and LRR domain. In conclusion, our results indicate a unified filamentous assembly mode of NLRP family proteins for downstream signal transduction. These findings will be of value for researchers to conceive the structural study of full‐length NLRP inflammasomes.Support or Funding InformationThis work was supported by US National Institutes of Health grants Al124491 and HD087988 (to H.W.) and the Harvard Digestive and Disease Center Grant HDDC P30 DK034854 (to T.M.F.).This abstract is from the Experimental Biology 2019 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
Increasing Versatility of Small Angle X‐ray Scattering in Studying Biological Macromolecules
Authors: Chakravarthy Srinivas , Hopkins Jesse , Bilsel Osman , Irving Thomas 
Published: June 2021

The Biophysics Collaborative Access Team (BioCAT), which operates the high‐brilliance undulator Beamline 18ID at the Advanced Photon Source, Argonne National Laboratory, is dedicated to studying biological macromolecules in solution using Small‐Angle X‐ray Scattering (SAXS). The combination of a highly brilliant X‐ray source and advanced micro‐focusing optics at BioCAT enables significant insights into the structure and dynamics of bio‐macromolecules from both equilibrium and time‐resolved SAXS experiments. The quality and interpretability of SAXS data is largely contingent on sample homogeneity. Size‐exclusion chromatography (SEC)‐SAXS, which was pioneered at BioCAT has therefore emerged as a powerful mode of data acquisition as it ensures optimal sample quality by purification immediately before exposure to x‐rays. In addition, we have also incorporated multi‐angle light scattering (MALS), dynamic light scattering (DLS), and differential refractive index (dRI) detectors in line with the SAXS camera thus enabling acquisition of a full complement of biophysical data typically required to structurally characterize biological macromolecules simultaneously with SAXS data. Demonstrably increased efficiency in terms of sample consumption and overall logistical ease have made SAXS much more accessible to non‐expert users.The new frontier in the field is to study real‐time structural changes in biological systems as a response to very specific environmental stimuli such as a change in denaturant concentration, ionic strength, pH or ligand binding. Forefront time resolved SAXS techniques using chaotic mixing continuous flow, continuous laminar flow and stopped flow mixing are now available to a wide variety of bio‐medical projects at BioCAT primarily on account of being optimized over the past few years both for sample consumption and mixing efficiency.Support or Funding InformationThis project was supported by grant 9 P41 GM103622 from the National Institute of General Medical Sciences of the National Institutes of Health.This abstract is from the Experimental Biology 2019 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.