bluuebunny/crossref_metadata_2025_split huggingface dataset:
Examining the Effects of Cardiovascular Effort on Blood Flow Velocity: A Duplex Doppler Ultrasonography Study
Authors: Kershaw Matthew , Ross David A , Stone Michael , Marquez Samuel 
Published: June 2021

Ultrasonography (US) is frequently used to investigate anatomical structures in a non‐invasive manner. Duplex US combines conventional US imaging of blood vessels with Doppler US analysis of blood flowing through them, providing an opportunity to acquire data on flow velocities in real‐time. This study compares the blood flow velocity in a resting individual with the velocity measured after cardiovascular activity. Velocity (cm/s) was measured through the abdominal aorta. A mixed‐sex sample of young, healthy volunteers (n=20) from the SUNY Downstate College of Medicine focused on physical activity on the lower limbs for four minutes, after which the post‐effort velocity was obtained. Results showed a mean increase in blood flow velocity of 61.5%, with a maximum increase of 166.5% and minimum positive increase of 21.6%. Standard deviation of the increase in blood flow velocity was 56.4%. An unexpected result was found in two cases, in which the post‐effort flow velocity showed a small decrease instead of the expected increase. These findings suggest that an increase in physical effort in the lower limbs requires a greater supply of blood; thus, the observed flow velocity increases. Duplex US allows for the capture and analysis of data in real‐time in various healthcare settings, without requiring invasive or expensive, radiation‐intense procedures such as MRI.Grant Funding Source: AAA
Protein Structure Initiative Material Repository (PSI‐MR): An open shared public resource for structural genomics plasmids
Authors: Cormier Catherine , LaBaer Joshua 
Published: June 2021

The PSI‐MR (http://psimr.asu.edu) provides centralized storage and distribution for the protein expression plasmids created by PSI researchers. These plasmids are a resource that allows the research community to dissect the biological function of proteins whose structures have been identified by the PSI. The plasmid annotation, which includes the full length sequence, vector information, and associated publications, is stored in a freely available, searchable database called DNASU (http://dnasu.asu.edu), and plasmid samples can be requested directly though the website. We have also developed a novel strategy to avoid the most common concern encountered when distributing plasmids, namely the complexity of material transfer agreement (MTA) processing and the resulting delays this causes. The Expedited Process MTA, in which we created a network of institutions that agree to the terms of transfer in advance of a material request, eliminates these delays. Our hope is that by creating a repository of expression‐ready plasmids and expediting the process for receiving these plasmids, we will help accelerate the accessibility and pace of scientific discovery.This work was supported by the National Institute of General Medical Sciences, the National Cancer Institute, the National Institute of Allergy and Infectious Disease, and the Virginia G. Piper Charitable Trust.
Functional and structural characterization of the glycine riboswitch
Authors: Ye Jingdong , Elsayed Galal , Elsayed Mohammed , Brinda Bryan , Zhang Wei , Stoner Breena 
Published: June 2021

Glycine riboswitch is unique in that the two glycine aptamers bind glycines cooperatively and control downstream gene expression in a more “digital” manner. The exact structural mechanism for this glycine binding cooperativity is not well understood. We hypothesize that the cooperativity is caused by the formation of “Aptamer Disruptor” in the absence of glycine, which involves an interaction between “b” region (on aptamer I) and “c” region (on aptamer II). In‐line probing data on a 5’ extended aptamer II shows reduced glycine binding activity compared to a previously reported aptamer II construct VCII122, consistent with this hypothesis. Sequence analysis identified the candidate regions of “b” and “c”. Breaker Lab reported that VC G17C completely abolished the aptamer I and reduced the aptamer II glycine binding by 1000 fold. According to our hypothesis, this is at least in part due to b/c interaction. Data on a double mutant, VCG17CM1, in which the b/c interaction was abolished by mutation in “b” region, shows that binding of VCG17CM1 with glycine is rescued compared to VCG17C, suggesting the direct involvement of “b” region in the formation of “Aptamer Disruptor”. Further experiment is being carried out to test the “c” region, the linker region and other important locations.We are also crystallizing the glycine riboswitch using a chaperone approach (CARC; Ye et al. PNAS 2008) for detailed structural elucidation.Source of research support: start‐up fund provided to JD Ye from University of Central Florida.
Changing the binding mode to peroxisome proliferator activated receptor (PPAR) alpha/gamma: a new ligand with improved antidiabetic and antiobesity properties
Authors: Mitro Nico , Gilardi Federica , Giudici Marco , Loiodice Fulvio , Fracchiolla Giuseppe , Laghezza Antonio , Pochetti Giorgio , Lavecchia Antonio , Guerrini Uliano , Tremoli Elena , Rando Gianpaolo , Maggi Adriana , Novellino Ettore , Crestani Maurizio 
Published: June 2021

PPARs are ligand activated transcription factors playing a key role in lipid, glucose and energy metabolism. PPAR agonists are used as hypolipidemic and antidiabetic agents, however since these ligands have shown side effects, the hunt for selective PPAR modulators avoiding adverse reactions is still open.By a transfection based screening we identified LT175 that binds and activates both PPARα and γ subtypes. The 3D structures of PPARγ/LT175 complex reveals a new binding mode with a distinct coactivator recruitment profile. In transcription assays with PPRE‐Luc reporter mice, LT175 activates PPAR program in target tissues. In high fat fed mice, LT175 ameliorates the metabolic profile and reduces visceral adiposity. Circulating levels of adiponectin increases while plasma insulin decreases. LT175 enhances the expression of target genes in the liver and adipose tissue. We also observed increased brown fat mass that contributes to decrease body weight via fat burning an effect secondary to an increased FGF‐21 expression. Altogether, we demonstrate that LT175 is a lead compound with favorable effects on glucose and lipid metabolism that could be developed to treat diabetes and obesityFunded by FP6 LSHM‐CT‐2006‐037498 from the European Community to MC and The Giovanni Armenise‐Harvard Foundation career development grant to NM
Acetylcarnitine treatment increases mitochondrial protein‐lysine acetylation and protein expression
Authors: Kerner Janos , Yohannes Elizabeth , Virmani Ashraf , Koverech Aleardo , Chance Marc , Hoppel Charles 
Published: June 2021

Myocardial carnitine content of Fischer 344 rats decreases with age and proportionally affects total, free, acyl‐, and acetylcarnitine (ALC). In both adult and elderly hearts, ALC is the major acylcarnitine representing approximately 75% of the acylcarnitine fraction. The carnitine and ALC content of elderly hearts is restored by a single intraperitoneal (IP) injection of ALC (1.28mmol or 260mg/kg body weight) or by oral administration of ALC in drinking water (1.5%) over a two month period. In ALC‐treated rat hearts mitochondrial protein lysine acetylation is increased in both subsarcolemmal and interfibrillar mitochondria as assessed by immunoblotting. Moreover, there are qualitative differences in protein lysine acetylation between SSM and IFM. Furthermore, 2‐DIGE analysis showed that ALC induced changes in protein expression. Thirty one proteins showed a two‐fold or greater change, eight showed an increase and twenty three proteins a decrease. Identification of these proteins will direct our future studies into the mechanism of the physiological effects of acetylcarnitine.Supported in part by POI AG15885 and Sigma‐Tau SpA.
Development of a Real‐time PCR Assay to Quantify Mitochondrial DNA Deletions Relative to a Housekeeping Gene
Authors: Pitarresi Jason , Pogozelski Wendy 
Published: June 2021

Mitochondria contain DNA in the form of a double‐stranded circle. This DNA (mtDNA) is often found to contain large‐scale deletions of several hundred to several thousand base pairs. These deletions correlate with a variety of disorders in oxidative phosphorylation. Using a real‐time PCR assay based on an external cloned mtDNA quantification standard, we observed that a particular deletion increases in cells treated with gamma rays. However, the data have not always been consistent. We are examining the use of a parallel approach that involves real‐time PCR but measures the deletions and the total mtDNA relative to a nuclear DNA gene.This research was sponsored by the Camille and Henry Dreyfus Foundation, the Geneseo Foundation and the Geneseo Student Association.
Effect of LXR on the Renal NaPi transporters
Authors: Caldas Yupanqui A , Giral Hector , Sutherland Eileen , Sorribas Victor , Blaine Judith , Okamura Kayo , Levi Moshe 
Published: June 2021

The Liver X Receptor (LXR) agonists have shown to modulate the lipid composition of different tissues including the vascular tissue and kidney. Since dyslipidemia has been associated with chronic kidney disease (CKD) and hyperphosphatemia is a consequence of CKD, we used both an in vitro and in vivo system to study the effect of the LXR agonists on renal NaPi cotransport protein regulation given their important role in maintaining Pi homeostasis. C57BL/6 mice fed chronically with either of the LXR agonists TO901317 and DMHCA show a reduction in the abundance of renal brush border membrane (BBM) NaPi transport proteins: 57% for NaPi‐2a, 40% for NaPi‐2c, and 30% for PiT‐2. After incubation for 24 hours with TO901317 the same effect was also observed in opossum kidney cells (OK: a cell culture model of the renal proximal tubule) in which levels of NaPi4 protein (the main type II NaPi transporter in OK cells) were reduced by 55% and Pi transport by 49%. In this cell line we have demonstrated increased nuclear expression of the endogenous LXR receptor following treatment with the LXR agonists. In addition, LXR agonists cause changes in the lipid profile and lipid content of the OK cell membrane. Our studies therefore document a novel role for the LXR agonists in modulation of renal NaPi transporters.This research was supported by NIH (3R01 AG026529) supplemental minority grant.
Gene Profiles of Host Biological Processes Targeted by Yersinia pestis
Authors: Miller Stacy‐Ann , Muhie Seid , Juibitu Meskerem , Moyler Candace , Hammamieh Rasha , Jett Marti 
Published: June 2021

Yesrsinia pestis is a gram negative bacterium and is the causative agent of the bacterial disease plague. The bacterium is transmitted to humans via the bite of an infected flea or by inhalation of aerosolized infective droplets. Y.pestis causes deadly acute infection and has the ability to genetically manipulate the host and can potentially be used as a biological warfare weapon. Due to this it has been placed on the category A select agent list. One of the most important steps that will allow us to diagnosis plague early and quickly is understanding the early host responses at the molecular level. Our research focuses on defining the molecular events/network systems involved in the host‐pathogen interactions to identify biomarkers and therapeutic targets for pathogenic agents.We exposed non‐human primates by aerosol to CO92 Y. pestis/sham at different lengths of time. We have collected whole blood, plasma, Peripheral Blood Mononuclear Cells (PBMCs) and various tissues from infected and control NHPs. RNA is isolated using the TRIZOL method and overall RNA integrity was confirmed by spectrophotometery and the Agilent 2100 bioanalyzer. Using gene expression microarray, microRNA microarray and miRNA real time PCR, we have identified genes that were differentially expressed in reponse to the pathogen. Functional annotaion of these genes revelealed an enrichement in genes coding for the transcription HIF‐1 pathway, molecular transport and apoptosis in Y.pestis infected monkeys. These findings provide a better understanding of the systemic progression of illness and a more in‐depth characterization of the dynamics of regulatory networks that are vital in the host‐pathogen interactions. Our aim is to eventually identify markers that will predict the eventual course of impending illness.
Causation for inherited equine night blindness
Authors: Scott Michelle Lynn , Forsyth George W , Sandmeyer Lynne S , Bellone Rebecca R , Loewen Matthew E , Grahn Bruce H 
Published: June 2021

Mutations associated with equine night blindness (CSNB) have been mapped to the Transient Receptor Potential cation channel family Member 1 (TRPM1) gene on ECA1. Reduced TRPM1 mRNA expression has been reported in retina and melanocytes in CSNB horses. A single unique intronic snp has been found in all CSNB horses examined to date. We hypothesize that this unique snp creates a binding site for the Nova intronic splicing enhancer which promotes aberrant splicing of an 80 bp downstream acceptor, therefore targeting TRPM1 mRNA for degradation. Nova‐1 and TRPM1 mRNA levels were measured in retina and in primary melanocyte cell lines established from the choroid of normal and CSNB horses. TRPM1 mRNA level in retina from a CSNB horse was 0.2% of that in the control horse retina. Choroidal melanocyes from normal and CSNB horses both had low TRPM1 mRNA levels similar to those observed in CSNB retina. We are investigating whether similar levels of TRPM1 mRNA in CSNB and normal melanocytes are due to removal of the effect of some upstream enhancer element in tissue culture, or result from insufficient Nova‐1 expression to cause the destabilizing TRPM1 mRNA splice event in CSNB melanocytes.Supported by the WCVM Canadian Vitamins Class Action Settlement Research Grant.
Cleavage of Extracellular Matrix Molecules: a role for ADAM8 in tumour cell invasion
Authors: Ferdous Taheera , Golfi Panagiota , Schlomann Uwe , Zack Marc D , Bartsch Joerg W 
Published: June 2021

Processing of extracellular matrix (ECM) components is attributed mainly to zinc‐dependent proteases such as MMPs, as they are associated with invasive behavior of tumor cells. Interestingly, ADAM8, a member of the membrane‐bound zinc‐dependent family of ADAM proteases, seems to adapt an invasive phenotype when overexpressed and has been described in highly invasive cancer pathologies. It is also involved in conditions such as allergy, asthma and neurodegeneration. We postulate that cellular processing of ADAM8 eventually leads to ‘MMP‐like’ activity which could modulate the tumor microenvironment.We investigate the mechanism by which ADAM8 contributes to cancer cell invasion. We identified a soluble form of murine ADAM8 released from transfected cells by proteolytic processing, which cleaves CD23 fluorescence peptide suggesting proteolytic activity. In vitro assay shows that recombinant soluble human ADAM8 cleave fibronectin, collagen IV and collagen type I. Furthermore, in both matrigel invasion and FITC‐labeled fibronectin assays, we have seen migration and cleavage of COS‐7 cells transfected with wildtype ADAM8 compared to an inactive mutant. Cancer cell lines with upregulated ADAM8 expression, such as human osteosarcoma (HOS), degrade collagen type I.We conclude that ADAM8 degrades ECM molecules, both in vitro and in vivo, enabling cancer cell invasion. Thus, ADAM8 may be a potential target for therapeutic intervention in metastatic cancer.
4.0 Å Resolution Cryo‐EM Structure of the Mammalian Chaperonin TRiC/CCT Reveals its Unique Subunit Arrangement
Authors: Cong Yao , Baker Matthew L. , Jakana Joanita , Woolford David , Miller Erik J. , Reissmann Stefanie , Kumar Ramya N. , Redding‐Johanson Alyssa M. , Batth Tanveer S. , Mukhopadhyay Aindrila , Ludtke Steven J. , Frydman Judith , Chiu Wah 
Published: June 2021

TRiC is a eukaryotic chaperonin essential for de novo folding of ~10% newly synthesized cytosolic proteins, many of which cannot be folded by other chaperones. This is likely linked to TRiC's unique subunit organization, whereby each ring consists of eight different subunits in an arrangement that remains uncertain. Using single particle cryo‐EM without imposing symmetry, we determined the mammalian TRiC structure at 4.7 Å resolution, which is the highest resolution asymmetric cryo‐EM structure to date. This revealed the existence of a two‐fold axis between its two rings. A subsequent two‐fold symmetrized map yielded a 4.0 Å resolution structure that evinces the densities of a large fraction of side‐chains, loops and insertions, which permitted unambiguous identification of all eight individual subunits. Independent biochemical near‐neighbor analysis supports our TRiC subunit arrangement. This allowed the optimization of a Cα backbone model of the entire TRiC complex from the homology models against the cryo‐EM density. A refined atomic model for one subunit showed ~95% of the dihedral angles in the allowable regions of the Ramachandran plot. Our model reveals an unevenly distributed positively charged wall lining the closed folding chamber of TRiC is strikingly different from those of prokaryotic and archaeal chaperonins. These interior surface chemical properties likely play an important role in TRiC's cellular substrate specificity.Supported by Nanomedicine Development Center (PN1EY016525) and NCRR (P41RR02250).
Elucidation of the mechanism for TAO import in T.brucei mitochondria
Authors: Hamilton VaNae Nierra , Singha Ujjal , Sharma Shvetank , Chaudhuri Minu 
Published: June 2021

TAO is the only terminal oxidase in the mitochondria of the bloodstream form of T.brucei. It is a nuclear encoded protein that needs to be imported in mitochondria to be functional. TAO possesses a predicted N‐terminal mitochondrial targeting sequence (MTS). Unlike other MTS containing proteins TAO does not need mitochondrial membrane potential (ψ) for its import in mitochondria of the bloodstream (BS) form but depends on ψ in the procyclic (PS) form of the parasite. To understand the import mechanisms of TAO in the two developmental forms, N‐terminal deletion mutants of this protein were generated. In vitro import of radiolabelled wild type and mutant TAO proteins into mitochondria from BS and PS forms has shown that deletion of the first ten amino acids did not affect the import of TAO in mitochondria from either form, whereas deletion of the first twenty amino acids inhibited import in mitochondria of the PS form only. Unlike the full‐length protein, the first ten amino acid deletion mutant of TAO depends on membrane potential for import in mitochondria of the BS form. These results suggest that length of and basic residues within the MTS of TAO play important roles in requirement of ψ during import.This project is supported by NIH Grants 1SC1GM081146 and 1F31 AI083011‐01.
Hepatic long‐chain acyl‐CoA synthetase 5 (ACSL5) partitions fatty acids between anabolic and catabolic pathways
Authors: Bu So Young , Mashek Douglas G 
Published: June 2021

Long‐chain acyl‐CoA synthetases (ACSL) and fatty acid transport proteins (FATP) catalyze the initial step of fatty acid metabolism. Of numerous ACSL and FATP isoforms, ACSL5 is expressed predominantly in tissues with high rates of TAG synthesis suggesting it may have an anabolic role in lipid metabolism. To characterize the role of ACSL5 in hepatic energy metabolism, we knocked down ACSL5 by using siRNA in rat primary hepatocytes. Compared to cells transfected with control siRNA, knockdown of ACSL5 significantly decreased fatty acid or glucose induced lipid droplet formation observed by Oil‐red O staining. These findings were further extended with metabolic labeling studies showing that ACSL5 knockdown resulted in decreased [1‐14C] oleic acid or acetic acid incorporation into intracellular glycerolipids (30–50%) without altering fatty acid uptake. ACSL5 knockdown increased acid soluble metabolites (ASM), a measure of fatty acid β‐oxidation, without changing PPAR‐α activity and target gene expression indicating that the effect was not mediated by transcriptional regulation. These changes in fatty acid metabolism were similar during pulse and chase periods, which indicate that ACSL5 may not affect intracellular lipid turnover. These results suggest that ACSL5 has a unique role in channeling both exogenous and endogenous fatty acid towards glycerolipid synthesis rather than catabolic pathways.This study was supported by American Diabetes Association.
A novel microdissection model for probing cellular interactions. I. alpha methyl mannose blocks the cellular interaction
Authors: Coyle‐Thompson Catherine , Askari Tina , Mkrtchian Mary , Portillo Georgina , Manukyan Mariam , Abramian Sarineh , Qubrosi Mirey , Makhoul Elias , Frederick Robert , Allen Jenieke , Dreyfuss Justin , Oppenheimer Steven B. 
Published: June 2021

Adhesion between the archenteron tip and blastocoel roof in the NIH designated sea urchin embryo model is a cellular interaction that has interested investigators for over a century, but its molecular basis is not understood. Here we microdissect the two components of this cellular interaction and use alpha methyl mannose to map molecular groups that may be involved in mediating the cellular interaction. Whole 48–54 hour fixed Lytechinus pictus embryos were washed three times and then dissected in pH 8.0 artificial sea water (ASW), 15°C. The roofs of the blastocoel and the tips of the archenteron were put together and observed to stick together. In over 50 separate trials using bound sets of roof and archenterons attached together, either 0.2 M or 1.0 M alpha methyl mannose was added to the pieces. The pieces remained together. However in 100% of the cases, manually separating the pieces in alpha methyl mannose at either molarity resulted in blocking the rebinding of the blastocoel roofs and archenteron tips.Re‐binding occurred in the absence of the sugar. The results suggest that alpha methyl mannose binding receptors are involved in mediating the cellular interaction. These studies offer a novel approach to map glycans and glycan binding partners that may be functionally important. By microdissecting the components of cellular interactions out of the embryo proper, these components can be probed in pristine media away from factors in intact embryos that could confuse results (Supported by NIH NIGMS SCORE S0648680, MARC, RISE, the Joseph Drown Foundation, the Sidney Stern Memorial Trust, and CSU Northridge Biology Full Immersion Research Experience (FIRE) course funding).
Design of a Three Dimensional Physical Model of P‐glycoprotein
Authors:   Lincoln SMART Team, Colton Shannon , Herman Tim , Giles Kurt , Koo Ben , Jeske Sabine , Grover Anita , Gin Richard 
Published: June 2021

Expressed in a large variety of tissues, the transporter P‐glycoprotein (P‐gp) facilitates small molecule efflux from cells as a detoxification mechanism for a remarkable range of drug substrates. Of interest to clinicians and drug development scientists is the number of drug‐drug interactions mediated by competitive inhibition of the protein. Similarly, as it is highly expressed in enterocytes, P‐gp can be a significant barrier to drug absorption, and, therefore, considerable effort has been spent on the discovery of a non‐absorbed P‐gp inhibitor. Traditional methods for visualizing protein structures and interactions with small molecules are limited in the amount of information that can be conveyed in two dimensions. Using rapid prototyping technology, we have built tangible 3D models of P‐gp using the recently resolved structure (PDB: 3g5u), allowing students and scientists alike to more fully explore the transporter protein and its small molecule substrates and inhibitors.The SMART (Students Modeling A Research Topic) program was established by theCenter of BioMolecular Modeling at the Milwaukee School of Engineering and involves partnerships between university researchers and local high schools. This work is funded by NIH‐NCRR‐SEPA and HHMI.