bluuebunny/crossref_metadata_2025_split huggingface dataset:
An RNA‐Sequencing Approach to Understanding the Genetic Influences on Fetal Alcohol Syndrome
Authors: Bingham Stephanie , Gallagher Alayna , Flores Annalliam , Trinidad Jennyvette , Arboleda Vania , de Almeida Rego Julia , Villada Daniel 
Published: June 2021

Ethanol is a known teratogen, though the precise mechanisms by which it exerts this effect are not well understood. In the current study, we aimed to get a handle on the genetic pathways that are disrupted as a result of embryonic ethanol exposure. Using an RNA sequencing approach, we scanned the genome of embryonic zebrafish and performed a comparison of gene expression levels in treated and untreated embryos. The whole‐genome analysis revealed 86 gene sequences that were significantly up‐ or down‐regulated following embryonic exposure. Through prioritization, we narrowed this number down to 40. Using genome search engines, the genes were classified according to spatial expression and function and distinct gene categories were revealed. The most abundant gene category (21%) was that of metal‐binding proteins, followed by actin‐binding (14%) and oxidoreducatase and kinase functions (both 7%). Follow‐up studies are now being performed on the first two of the genes of interest: TyrP1 and CENPF. TyrP1 is an integral membrane protein with diverse roles including melanocyte differentiation. CENPF, on the other hand, is a nuclear matrix protein and regulator of the cell cycle. Further analysis of the latter and its function may reveal an answer to the age‐old question of whether the reduced brain size, a hallmark of fetal alcohol syndrome, is a result of reduced cell division, increased cell death, or a combination of the two.Support or Funding InformationThis research was funded by the Department of Biology and a Faculty Senate research minigrant, Barry 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.
PGF and VEGF‐C secreted by preosteoclasts induce migration and differentiation of Mesenchymal stem cells
Authors: Huh Jeong‐Eun , Yi Sol , Lee Soo Young 
Published: June 2021

Osteoblast‐mediated bone formation is coupled to osteoclast‐mediated bone resorption. Several studies suggested that the molecular mechanisms by which osteoblasts control osteoclastogenesis and bone degradation. But, the recruitment of mesenchymal stem cells (MSCs) and their differentiation to osteoblasts is poorly understood. Here we show that preosteoclasts secrete placental growth factor (PGF) and vascular endothelial growth factor C (VEGF‐C) to induce migration and osteogenesis of MSCs. Conditioned media from preosteoclasts increased migration ability of MSCs and alkaline phosphatase activity and mineralization in osteoblast cultures. Osteoclast precursors induced PGF and VEGF‐C expression in response to receptor activator of nuclear factor‐κB ligand (RANKL), an essential cytokine for osteoclast differentiation. In vitro experiments revealed that migration was stimulated by rhPGF and rhVEGF‐C in a dose‐dependent manner. Furthermore, these factors increased osteoblast differentiation. Vascular endothelial growth factor receptor (VEGFR) inhibitor treatment reduced these responses. Taken together, PGF and VEGF‐C secreted by preosteoclasts may enhance the recruitment of MSCs and further induce osteogenesis.Support or Funding InformationThis work was supported by Basic Science Research Program through the National Research Foundation of Korea (NRF) funded by the Ministry of Education (NRF‐ 2015R1D1A4A01020104).This abstract is from the Experimental Biology 2018 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
Arl4D modulates microtubule dynamics via its interaction with EB1
Authors: Lee Fang‐Jen Scott , Lin Shin‐Jin , Huang Chun‐fang , Wu Tsung‐Sheng , Li Chun‐Chun 
Published: June 2021

ADP‐ribosylation factor (Arf)‐like 4D (Arl4D), one of Arf small GTPases, functions in cell morphology, cell migration, and actin cytoskeleton remodelling. EB1 is a microtubule plus end– tracking proteins that preferentially localized at the tips of growing microtubule plus ends and centrosome. Depletion of EB1 is known to result in many centrosome‐related defect. Here, we report that Arl4D binding to EB1 modulates microtubule plus‐end dynamics at the centrosome. In vivo and in vitro binding assay showed that Arl4D interacts with EB1 in a GTP‐dependent manner and C‐terminal EBH region of EB1 is both required and sufficient for this interaction. We found that Arl4D co‐localizes with γ‐tubulin in centrosomes and depletion of Arl4D resulted in centrosomal microtubule regrowth defect in COS‐7 cell. Arl4D knockout mouse embryonic fibroblasts (MEF) cells were also observed microtubule regrowth defect, which can be rescued by expressing human Arl4D. We also show that Arl4D‐EB1 interaction is essential for microtubule regrowth at the centrosome. In addition, we demonstrate that Arl4D binding to EB1 increases the association of the p150Glued subunit of dynactin to EB1, which is important for microtubule stabilization. Together, our results indicate that Arl4D modulates microtubule dynamics through regulating EB1‐p150 association at the centrosome.Support or Funding InformationNational Health Research Institutes, Taiwan (NHRI‐EX106‐10601B1)This abstract is from the Experimental Biology 2018 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
NLRP12 binds to Hck potentially regulating the NF‐kB pathway
Authors: Zhang Yue , Okamoto Curtis 
Published: June 2021

The nod‐like receptor family pyrin domain containing 12 (Nlrp12) is a cytoplasmic protein that belongs to the Pattern Recognition Receptor family (PRR) of proteins, an important component of the innate immune system for identification of Pattern Associated Molecular Patterns (PAMPs) and Damage‐Associated Molecular Patterns (DAMPs). Nlrp12 is comprised of 1062 amino acids and has three functional domains: an N‐terminal pyrin domain, a Nucleotide‐ Binding Domain (NBD), and a C‐terminal leucine‐rich repeat region. Nlrp12 is mainly expressed in peripheral blood leukocytes, including granulocytes, eosinophils, monocytes, and dendritic cells. Nlrp12 has been shown to function as a negative regulator of inflammation through canonical and non‐canonical NF‐kB pathways. However, the detailed mechanism of how Nlrp12 inhibits NF‐kB is not clear.The Nlrp12 pyrin and NBD domain was used as bait in a yeast two‐hybrid screen for potential interacting partners in a human leukocyte cDNA library. The top hit was the C‐terminal fragment of Hck; it was shown to interact strongly with Nlrp12. Detailed mapping of the binding between Nlrp12 and Hck was performed. In subsequent yeast two‐hybrid assays, Nlrp12 was shown specifically to bind to Hck. The C‐terminal 30 amino acids of Hck was sufficient to bind with Nlrp12. This fragment carries the negative regulatory phosphotyrosine residue Y521. However, the binding did not require phosphorylation of Y521 residue of Hck. That is, Nlrp12 preferentially bound to unphosphorylated Hck (i.e., active Hck). Functional NF‐KB luciferase reporter assays were performed with 293T cells overexpressing either Nlrp12, or Hck, or Nlrp12 plus Hck. Overexpression of Nlrp12 alone decreased NF‐kB activity, while overexpression of Hck rescued the inhibition of NF‐kB activity by overexpressed Nlrp12. Overexpression of Hck alone had no effect on NF‐kB activity.We conclude that Hck may be a novel regulator of Nlrp12 activity in its inhibition of NF‐kB function.Support or Funding InformationUniversity of Southern California School of Pharmacy Intramural Research Funds 2017‐ 2021This abstract is from the Experimental Biology 2018 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
Yeast RNA polymerase I Core Factor binds to the ribosomal DNA promoter through the GC minor groove
Authors: Glover Danea M. , Jackobel Ashleigh J. , Knutson Bruce A. 
Published: June 2021

In Saccharomyces cerevisiae, Core Factor (CF) is a key evolutionary conserved transcription initiation factor that helps recruit RNA polymerase I (Pol I) to the ribosomal DNA (rDNA) promoter. Upregulated Pol I transcription has been linked to many cancers, and targeting Pol I is an attractive and emerging anti‐cancer strategy. Using the yeast model system, we characterized how CF binds to the Pol I promoter by electrophoretic mobility shift assays (EMSA). Synthetic DNA competitors along with anti‐tumor drugs and nucleic acid stains that act as DNA groove blockers were used to discover structural characteristics of CF binding. Our results show that CF employs a unique mechanism where it prefers the GC‐rich minor groove of the rDNA promoter, which may offer a new avenue to more specifically target upregulated Pol I activity in cancer.Support or Funding InformationThe work was supported by B.A.K. grants from the US National Institutes of Health (NIH) NCI (5K22CA184235), a Sinsheimer Scholar award from the Alexandrine and Alexander L. Sinsheimer Fund, Central New York Community Foundation, Joseph C. George Fund, and Virginia Simons & Dr. C. Adele Brown Fund.This abstract is from the Experimental Biology 2018 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
Pasteurella Multocida Toxin Mediated ECM Expression Is Independent of mTOR signaling pathway
Authors: Oubrahim Hammou , Leong Megan , Chock Boon P 
Published: June 2021

Bacterial virulence factors that interfere with cell signaling and result in disruption of normal cell division and apoptosis could facilitate cancer metastasis via unknown mechanisms. Pasteurella multocida toxin (PMT) is an intracellular acting bacterial protein known for its potent mitogenic properties in vitro and in vivo and its ability to induce strong anchorage‐independent growth for certain type of cells. These properties suggest that PMT might have the potential to act as a tumor promoter especially in the case of chronic infections. We have shown that rPMT induces cell proliferation in serum‐starved Swiss 3T3 cells by hijacking cellular signal transduction pathways via deamidation of heterotrimeric G‐proteins and leads to a sustained activation of mTOR, MAPK, and membrane associated tyrosine kinase signaling. In addition, further experiments revealed that PMT induced a prolonged upregulation of chromosomal passenger complex (CPC) proteins including survivin and aurora kinase B both at mRNA and protein levels in serum starved Swiss 3T3 cells treated with PMT in a manner dependent on both mTOR and MAPK signaling pathways.An increasing body of evidence supports the idea that extracellular matrix (ECM) proteins are major players in the global control of intercellular communication and integration of environmental signals. It was not known whether rPMT‐treated cells are able to express and secrete into the medium a substrate(s) capable of activating autocrine and/or paracrine signaling. Microarray analysis identified connective tissue growth factor (CTGF) mRNA as the most upregulated gene in 3T3 cells, along with other genes involved in cell proliferation and cancer biology. The elevation of CTGF, along with other extracellular matrix proteins, were confirmed by RT‐PCR and Western blot analysis. In accord with rPMT‐induced mTOR activation, upregulation of CTGF was mediated by deamidation of Gαq/11, and was independent of TGFβ, a well‐known inducer of CTGF. However, PMT‐induced ECM expression is independent of both mTOR, MAPK and membrane associated tyrosine kinase activation. Taken together, our results show that PMT activates mTOR and membrane associated tyrosine kinase, and MAPK leading to the upregulation of proteins involved in cell proliferation but do not have any effect on the expression of ECM proteins.This abstract is from the Experimental Biology 2018 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
Liraglutide improves insulin sensitivity in diabetic mice through reduction of inflammation and induction of thermogenesis.
Authors: Zhou Joseph , Poudel Anil , Li Lixin 
Published: June 2021

Glucagon like peptide ‐1 (GLP‐1) is released from the ileal mucosa L cells after food digestion to promote glucose stimulated insulin secretion. Liraglutide, a full agonist of the GLP‐1 receptor, has been known to reduce body weight in obese subjects and patients with type 2 diabetes. However, the underlying mechanisms of this effect remains unclear. Mice were fed with high fat high sucrose diet for 3 months to induce diabetes. Two groups of diabetic mice were injected with liraglutide or vehicle daily for 14 days. Improved glycemic control and intra‐peritoneal glucose tolerance test were observed in liraglutide treated group after 14 days. In addition, liraglutide treatment group showed significant reduction of liver weight in association with reduced expression of the phosphorylated Acetyl‐CoA carboxylase‐2 (ACC2) and upregulation of LCAD, cAMP‐activated protein kinase (AMPK)‐α as well as Sirt‐1 in liver and perigonadal fat. The elevation of fatty acid oxidation induced by liraglutide might be mediated through AMPKα‐SIRT‐1 cell signaling pathway.Brown adipose tissue (BAT) plays a key role in regulating energy balance via uncoupling of mitochondria ATP synthesis in rodents. Liraglutide induced BAT differentiation in skeletal muscle, including induction of the uncoupling protein‐1 (UCP‐1), a brown fat specific marker, PR domain‐containing 16 (PRDM16) protein expression, a transcription factor that regulates the thermogenic gene program in brown and beige adipocytes. Mitochondrial biogenesis and functional gene such as PPAR‐γ, PGC‐1αand SIRT‐1 were also upregulated by liraglutide in insulin sensitive tissues.Lastly, liraglutide displayed anti‐inflammatory effect. Liraglutide treatment leads to a significantly reduction of circulating IL‐6 as well as IL‐6 content in liver. Expression of iNOS‐1 and COX2 in insulin sensitive tissues were also reduced followed liraglutide treatment.Taken together, our study indicates liraglutide improves insulin sensitivity through multiple pathways which includes suppression of food intake, reduction of inflammation, elevation of fatty acid oxidation and induction of thermogenesis.Support or Funding InformationStart Up Fund ( Central Michigan 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.
Subnormothermic Regulated Hepatic Reperfusion Preserves Mitochondrial Function in Swine Liver Procured after Cardiac Death
Authors: Stowe David F , Yang Meiying , Mishra Jyotsna , Kim Joohyun , Heisner James S , Zimmerman Michael , Camara Amadou KS , Hong Jonny 
Published: June 2021

Livers procured after cardiac death can have an extreme degree of ischemia‐reperfusion injury (IRI) and are at increased risk of graft failure after liver transplantation. Reductions in respiratory control index (RCI) and Ca2+ retention capacity (CRC) are markers of mitochondrial dysfunction and cell apoptosis. Regulated hepatic reperfusion (RHR) is a novel organ resuscitation therapy that may facilitate hepatic mitochondrial recovery from IRI using an energy substrate‐enriched, leukocyte‐depleted, oxygen‐saturated perfusate delivered in a pressure, and temperature‐controlled milieu. We used a swine donation after cardiac death (DCD) model, in which all livers were subjected to 60 min of in situ warm ischemia and 120 min of cold static (CS) preservation. All livers were subsequently reperfused and monitored for 2 h in the ex vivo perfusion machine. Four methods of reperfusion were compared with 5 animals in each treatment group. Group I: Sanguineous‐Subnormothermic (SS); Group II: RHR‐Subnormothermic (s‐RHR); Group III: Sanguineous‐Normothermic (NS); Group IV: RHR‐Normothermic (n‐RHR). Liver biopsies were collected at baseline (pre‐ischemia), at 2 h of CS following 1 h of in situ warm ischemia, and after 30 min of ex vivo reperfusion. We isolated mitochondria via differential centrifugation and measured mitochondrial bioenergetics, i.e. the ability to utilize nutrients and O2 (respiration) to generate energy (state 3 (added ADP)/state 4 (depleted ADP) respiration = RCI) and CRC, i.e. the capability of mitochondria to tolerate a challenge of 20 μM CaCl2 boluses every 90 s until mitochondrial bioenergetic failure. We found that with substrate glutamate/malate (GM), RCI with s‐RHR was 60% higher than its baseline and 2.3‐fold higher than after NS reperfusion. With substrate succinate (SC), RCI with s‐RHR reperfusion was 99% of its baseline and 2‐fold higher than NS. These changes were due mostly to the lower state 4 respiration rate in the s‐RHR group, indicating less proton leaking compared to other groups. Reperfusion lowered CRC by about 33% across all groups; however, with substrate GM, CRC after s‐RHR was 2‐fold larger than in the SS group; with substrate SC, CRC after s‐RHR was 3‐fold larger compared to other groups. Mitochondria likely play a critical role in control of hepatocyte function and viability during liver transplantation; thus preservation of mitochondrial function is critically important. Ex vivo subnormothermic‐regulated hepatic reperfusion best preserved mitochondrial function and viability. This novel strategy has potential applicability to human liver transplantation.Support or Funding InformationMCW Institutional FundingThis abstract is from the Experimental Biology 2018 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
Differential Expression of PPARγ and CHOP‐10 During Adipogenic Differentiation of Human Bone Marrow Derived Mesenchymal Stem Cells
Authors: Rony R M Imtiaz Karim , Hull Barbara E. , Excoffon Katherine , Ramirez‐Vick Jaime E 
Published: June 2021

Mesenchymal stem cells (MSCs) hold great promise for cell‐based therapy and regenerative medicine owing to their multilineage differentiation potential that ranges from osteogenic to cardiac lineages. Osteogenic and adipogenic differentiation of MSCs in particular is of great interest since any imbalance that perturbs the regulation of osteogenesis and adipogenesis is typically associated with diseases such as obesity, osteoporosis, and other age‐related diseases. In our project, we sought to profile the gene expression pattern of key osteogenic and adipogenic transcription factors during differentiation using time course experiments. Adipogenesis was induced in passage 4 human bone marrow derived mesenchymal stem cells (BM‐MSCs) seeded with a density of 6579 cells/cm2 and RNA was collected at Day 0 (control), Day 3, Day 7, and Day 14 after differentiation to analyze the expression level of master adipogenic transcription factor peroxisome proliferator activated receptor‐γ (PPARγ) and negative adipogenic factor CHOP‐10. Our preliminary data suggests that compared to control (Day 0, undifferentiated) samples, PPARγ expression increases about 20‐fold, 22‐fold, and 168‐fold at Day 3, 7, 14 respectively. In contrast, expression of CHOP‐10, which is a negative regulator of adipogenesis, is upregulated approximately 2.4‐fold at Day 3, then downregulated 1.13‐fold at Day 7, and again increased 1.1‐fold at Day 14 respectively. Future work will compare these results and expression pattern of other adipogenic transcription factors to MSC differentiation in a 3D culture system.Support or Funding InformationFunding for these projects are supported by Wright State 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.
Analysis of experimental feed impacts on fatty acid profiles of captive and wild Arctic Ground Squirrels
Authors: Mikes Monica L , Rice Sarah A , Bibus Doug , Drew Kelly 
Published: June 2021

Arctic Ground Squirrels (AGS) are widely studied in laboratories for their capability to hibernate for months without any bodily repercussions while dormant. Hibernation is the ability to decrease metabolism, core body temperature and activity to conserve energy. Despite being heavily studied, information on the impact of the laboratory diet, a basic component of their husbandry protocol, lacks in scientific research. Polyunsaturated fatty acids are renowned for their effect on hibernation. The increase of omega 6 PUFAs has been shown to improve captive hibernation (Geiser 1993, Frank 2008). In contrast, when omega 3s were given in abundance compared to omega 6s hibernation was inhibited (Florant 1999). No literature, to our knowledge, has tested feeding natural omega 3:6 ratios to captive AGS. Our preliminary data spotlights a significant difference in the ratio of omega 3 and omega 6 PUFA levels between wild and captive AGS. The captive diet does not represent the natural ratio of omega 3 to omega 6. We hypothesize that substituting captive AGS with a Test Diet comparable to the natural diet will mirror wild AGS fatty acid profiles. To test this hypothesis we fed a pilot study Test Diet comprised of a 1:1 ratio of omega 3 to omega 6s. The Test Diet significantly reduced some divergent fatty acid profiles between wild and captive AGS. Further work, however, needs to continue to adjust specific fatty acids in the Test Diet and measure the impact of the diet on hibernation.This abstract is from the Experimental Biology 2018 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
High Throughput Validation of Orphan Riboswitch Candidates
Authors: Arachchilage Gayan Mirihana , Sherlock Madeline E , White Neil , Panchapakesan Shanker SS , Breaker Ronald R 
Published: June 2021

Riboswitches are cis‐acting gene controlling RNA elements often found in 5′ UTRs of bacterial mRNAs. The discovery of riboswitches and identification of their cognate ligands have led to the revelation of several important biological pathways and processes. At least 40 different riboswitch classes have been experimentally validated, but many more are waiting to be validated (orphan riboswitches). Computational approaches including comparative genomics have proven to be very successful in identifying riboswitch candidates with a high level of confidence. However, these riboswitch candidates need to be experimentally validated by identifying their cognate ligands which can be challenging and may take much more time. Our recent bioinformatics approach to discover rare riboswitch classes by focusing on GC‐rich, long intergenic regions (IGRs) in bacteria continues to add new riboswitch candidates to the growing collection of orphan riboswitches. Therefore, a high throughput and systematic method for the validation of orphan riboswitches is crucial to keep up with the pace of new riboswitch discovery by computational approaches. We are developing a higher throughput strategy to experimentally validate orphan riboswitches. This systematic process of validation includes using bioinformatics to update consensus structure models, biochemical investigation by in‐line probing, and genetic validation using reporter assays. For the initial investigation, we subjected five different orphan riboswitch candidates, SLH, chrB‐a, algC, aceE, and Bifido‐metK to this systemic validation process. We identified Bifido‐metK as the sixth class of riboswitches (SAM‐VI) that sense either S‐adenosylmethionine (SAM) or S‐adenosylhomocysteine (SAH), and the results from the other riboswitch candidates have provided valuable information about their structures and functions. Thus, our improved validation methods should help to expedite the experimental validation of riboswitch candidates and make the riboswitch discovery more productive.Support or Funding InformationM.E.S. was supported by an NIH Cellular and Molecular Biology Training 13 Grant (T32GM007223). This work was also supported by NIH grants to R.B. (GM022778 and DE022340). R.R.B. is also supported by the Howard Hughes Medical Institute.This abstract is from the Experimental Biology 2018 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.