bluuebunny/crossref_metadata_2025_split huggingface dataset:
Annotation and Comparison of Drosophila takahashii Genes on the Dot Chromosome
Authors: Spencer Danielle Lynette , Allen LaDaja , Brown Cierra , Buckner Erin , Davis Tyonna , Gleason Khayvion , Jackson Joshua , Lampkin Letha , Williams Jovan , Williams Nikita , Winfrey Tyrese , Woodland Cedric , Woods Arreonna , Van Stry Melanie 
Published: June 2021

The overall goal for this project is to understand how genes are expressed in a heterochromatic environment. Chromosome four (Dot chromosome; Muller F element) of Drosophila melanogaster is 1.3 Mb long with ~80 genes but is largely heterochromatic. In the Genomics Education Partnership (GEP) project, we are currently annotating a group of species that was diverged from D. melanogaster about 10 million years ago. Our project was to annotate genes on a 70,000 base pair region (contig40) of the D. takahashii Dot chromosome. In order to annotate the genes we used the BLASTX, gene predictors like Gene Scan, RNA‐sequence data, and the results from the Gene Model Checker. According to the gene predictor, Gene Scan, this contig contains five protein‐coding genes. It predicted the genes Slip1, Myo, CG11360, a gene of unknown function (GI25919), and another gene that appears to be a Mex3A‐Slip1 fusion. We annotated the genes Slip1, Myo, CG11360, and GI25919. We are currently annotating the gene Mex3A‐Slip1 fusion gene. The D. takahashii genes that are similar to D. melanogaster are Myo and Slip1. Myo has an identity of 73.1% and a similarity of 81.8%. Slip1 has an identity of 72.3% and a similarity of 82.2%. CG11360 is very different with an identity of 13.1% and a similarity of 26.8%. In contrast to the D. takahashii genes that are present in D. melanogaster, GI25919 is not present at all. It is predicted to be present in several other species including: D. mojavensis, Aedes albopictus, Stomoxys calcitrans, and Musca domestica. We compared GI25919 to D. mojavensis and it has an identity of 39% and a similarity of 55%. In conclusion, some D. takahashii Dot chromosome genes within this region are similar to D. melanogaster, but others are very divergent or missing in D. melanogaster. Our data will be combined with other gene annotations from students in the GEP for a comparative genomics study to identify conserved gene regulatory elements.Support or Funding InformationNSF HRD#1623340NSF IUSE #1431407This abstract is from the Experimental Biology 2019 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
Spatial Organization of a cAMP/Ca2+‐Regulated Signaling Complex: A Structural Study of an AKAP79‐Scaffolded Complex Containing Type IIβ PKA and Calcineurin
Authors: Hall James , Copps Jeff , Barry Rachael , Zhang Ping , Blumenthal Donald K. , Taylor Susan 
Published: June 2021

cAMP‐dependent protein kinase (PKA) regulates many cell processes including development, differentiation, and memory. In its resting state, PKA is a tetrameric holoenzyme consisting of a regulatory (R) subunit dimer and two catalytic (C) subunits. Four isoforms of the R‐subunit exist (RIα, RIβ, RIIα, and RIIβ). Although each isoform varies in sequence and quaternary structure, all share a common domain organization. The strength, duration, and specificity of PKA activity within the cell are mostly dependent upon isoform‐specific subcellular localization. The D/D domain interface of the R‐ subunits serves as a docking site for A Kinase Anchoring Proteins (AKAPs) that target PKA to specific cellular locations. In cardiac myocytes and neurons, PKA is localized to Cav1.2 L‐type calcium channels by AKAP79 and up‐regulates calcium influx by phosphorylating the channel's cytosolic C‐terminal tail. AKAP79 also binds the Ca2+/calmodulin‐dependent protein phosphatase type 2B (PP2B, or calcineurin) at a site very close to that of PKA binding. Given the close proximity of the calcineurin and PKA binding sites on AKAP79, calcineurin has been suggested to play roles in the regulation of calcium channels, along with regulation of PKA activity itself. Using a variety of biochemical and biophysical techniques, we have isolated and characterized a stable complex of the C‐terminal tail of AKAP79, RIIβ holoenzyme, and calciuneurin (“ARC” for short). We show a stoichiometry of 1:1:1 (AKAP79ct: RIIβ2‐C2 :CNt) using native mass spectroscopy, and SAXS/SANS techniques confirm that this is a compact complex, suggesting a close interaction between PKA and calcineurin when bound to AKAP79. Altogether, we suggest beyond its function of localizing PKA and CN in close spatial proximity to the Cav1.2 L‐type calcium channel, the ARC signalosome fosters extended protein‐protein interactions and regulations that suggest tight spatiotemporal control. Support for this work was provided through NIH GM034921.Support or Funding InformationJames Hall is an IRACDA fellow and was supported by NIGMS/NIH award K12GM068524. This work was also supported by a grant from the National Institutes of Health GM034921 to S.S. Taylor. This Research used resources at the High Flux Isotope Reactor and Spallation Neutron Source, which are DOE Office of Science User Facilities operated by Oak Ridge National Laboratory. This work utilized SasView software, originally developed by the DANSE project under NSF award DMR‐0520547.This abstract is from the Experimental Biology 2019 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
Dynamic Analysis of Discoidal Nascent HDL Structure by IPET
Authors: Li Jennifer Jinping , Lei Dongsheng , Liu Jianfang , Zhang Meng , Ren Gang 
Published: June 2021

Although circulating high density lipoproteins (HDL) are considered protective from cardiovascular disease, we have a remarkably limited understanding of their structure. In the recent decades, several models of HDL are built and debated each other, but the exact structure of HDL can't be confirmed even now. In our previous work, we used cross‐linking chemistry and mass spectrometry to generate detailed models of apoA‐I in reconstituted particles as well as “real” HDL from human plasma. Despite substantial differences in size and shape, these structures all shared the theme of an antiparallel belt‐like arrangement. Thus, direct visible observation of the conformation of discoidal HDL with the help of electron microscopy is a possible way to solve the debate. Here we report a study of structure of HDL by using negative‐staining electron microscopy and cryo‐electron microscopy as well as electron tomography. The 3D structures of dynamical individual HDL molecules are reconstructed by the individual‐particle electron tomography reconstruction (IPET). The reconstructed density maps at ~ 2 nm resolution display the size heterogeneity and conformation variety of HDL particles, and reveal a fusion/release mechanism of discoidal HDL in lipid transfer. These results revealed that apoA‐I makes highly specific contacts with itself to form a molecular scaffold that stabilizes HDL and facilitates, through specific protein: protein interactions, the association of HDL partner proteins to define particle function. The notion is crucial for us to further understand how the major HDL protein, apolipoprotein (apo)A‐I are involved in cholesterol transfer and lipid metabolism and cardiovascular disease.Support or Funding InformationThis work was supported by the National Heart, Lung, and Blood Institute of the National Institutes of Health (2R01 HL115153‐06, R01GM104427, and P01HL030086). Work conducted at the Molecular Foundry was supported by the Office of Basic Energy Sciences of the Office of Science at the U.S. Department of Energy under Contract No. DE‐AC02‐05CH11231.This abstract is from the Experimental Biology 2019 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
Comparison of Reinforcing and Antinociceptive Effects of Agonists with Mixed NOP and MOP Receptor Agonist Action in Nonhuman Primates
Authors: Ding Huiping , Kiguchi Norikazu , Trapella Claudio , Czoty Paul W , Calo’ Girolamo , Husbands Stephen M , Zaveri Nurulain T , Ko Mei‐Chuan 
Published: June 2021

Agonists with mixed nociceptin/orphanin FQ peptide (NOP) and mu opioid peptide (MOP) receptor agonist activities have been demonstrated as effective analgesics with fewer side effects. However, these newly developed compounds with different efficacies at the NOP and MOP receptors have not been compared in terms of their reinforcing and antinociceptive effects. The aim of this study was to determine and compare effects of AT‐121 and BU08028 (NOP/MOP partial agonists), AT‐175 (NOP full/MOP partial agonist), and cebranopadol (mixed NOP and opioid full agonist) in a series of behavioral assays established in rhesus monkeys (Macaca mutatta). Following systemic administration, AT‐121 (3–30 ug/kg), BU08028 (1–10 ug/kg), AT‐175 (1–10 ug/kg), and cebranopadol (1–5.6 ug/kg) all dose‐dependently produced antinociceptive effects against an acute noxious stimulus and attenuated capsaicin‐induced hypersensitivity. In the intravenous drug self‐administration assay, the relative reinforcing strengths (i.e., abuse potential) of these compounds were compared in monkeys under a progressive‐ratio schedule of reinforcement over a wide dose range. Unlike oxycodone and heroin producing robust reinforcing effects, AT‐121, BU08028, and AT‐175 did not significantly produce reinforcing effects. However, cebranopadol produced moderate reinforcing effects as compared to oxycodone and heroin. Taken together, these pharmacological studies in primates indicate that agonists with mixed NOP and MOP receptor agonist activities exert opioid‐like analgesic effects. Although the NOP receptor activation could attenuate the reinforcing effects mediated MOP partial agonist action, the NOP full agonist activity may not be able to completely attenuate the reinforcing effects mediated by MOP full agonist activity in primates.Support or Funding InformationThe US. NIH/NIDA grants (DA023281, DA027811, DA032568, and DA035359) and US. Department of Defense (W81XWH‐13‐2‐0045).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 Pleiotropic GPCR Ligand Rotigotine Acts as a β‐arrestin Biased Ligand on Orphan Receptor GPR52
Authors: Filipeanu Catalin , Ogunlade Blessing , Ghita Ioana , Wood Michael W , Fang Yayin 
Published: June 2021

Despite large progress made on understanding G protein‐coupled receptors (GPCRs) roles, there is still a large group in this family which has no identified endogenous ligand and thus are defined as ‘orphan’ GPCRs. One such orphan GPCR is GPR52, which has little homology to other members of this family, the highest identity being with another orphan GPCR, GPR21 (71%). GPR52 is a Gs‐coupled receptor which constitutively increases cellular cAMP levels and it has been proposed to play a role in locomotor activity through modulation of dopamine receptors. On the other hand, rotigotine, a non‐ergoline dopamine agonist, is a FDA approved drug for treatment of Parkinson's disease (PD) and restless leg syndrome. However, rotigotine binds to high affinity to other GPCRs, including α2‐adrenergic and HTR1A receptors, but the clinical relevance of these effects remains unknown. To find new ligands for GPCRs we examined the effects of multiple pleiotropic ligands, like rotigotine, against 45 orphan GPCRs. We found that rotigotine induced β‐arrestin mobilization by GPR52 (232 ± 28 %, n=8) but not by any other tested orphan GPR. Surprisingly, rotigotine did not change cAMP levels in GPR52‐transfected HEK293 cells (98.5 ± 23.38%, n=4). In contrast, FTBMT, a previously reported GPR52 agonist, strongly increased cAMP levels (290.85 ± 25.65%, n=4), but it failed to change β‐arrestin mobilization (86.88 ± 16%, n=4). Our data indicate that rotigotine and FTBMT act as biased ligands on GPR52 preferentially activating specific signaling pathways. This conclusion is supported by the effects on other signaling pathways: both rotigotine and FTBMT stimulated GPR52 mediated MAPK phosphorylation, but only FTBMT enhanced AKT phosphorylation. Although the overall sequence similarity between GPR52 and DRD2 dopamine receptor is less than 15%, the alignment of these two receptors in the transmembrane domains resembles 28% homology. Based on the crystal structure of risperidone binding to its receptor DRD2, the binding of rotigotine to DRD2 was modelled and the computational model was extended to rotigotine interaction with GPR52. Using this method, two key amino acids in the 3rd transmembrane domain of GPR52, I121 and K125, were identified as crucial sites for binding for both rotigotine and FTBMT. In conclusion, rotigotine and FTBMT are biased agonists of orphan GPR52, which can be used for further exploring its patho‐physiological functions.Support or Funding InformationSupported by HUMAA Endowed Founder's Chair in Basic Science Award and Office of Naval Research (N00014‐17‐1‐2105 and N00014‐18‐1‐2145) to YF.This abstract is from the Experimental Biology 2019 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
No significant change of extracranial conduit vessel diameter during cerebral vasomotor reactivity test with moderately‐altered end‐tidal CO2
Authors: Liu Jie , Le Thuy Tien Cao , Knox Allan , Serrador Jorge M 
Published: June 2021

Cerebral vasomotor reactivity (CVMR) is often assessed using transcranial Doppler (TCD) to measure the cerebral blood flow velocity (CBFV) in the middle cerebral artery (MCA). Recently the validity of this technique has been questioned because of the assumption that MCA diameter does not change. The goal of this work was to test if the extracranial cerebral arteries, i.e. internal carotid and vertebral arteries (ICA and VA), have a significant diameter change during moderate alteration of end‐tidal carbon dioxide (ETCO2). Fifteen healthy subjects (6 males; age: 32±10 yrs) were enrolled. The CBFV at the MCA was continuously recorded with TCD during an 8‐min CVMR test, i.e. 2‐min resting ventilation, 2‐min inspiration of 5% CO2, 21% O2, balance nitrogen, 2‐min recovery, and 2‐min mild hyperventilation. 8 min protocol was repeated on the same subjects, to allow measurement of ICA diameter during one run and VA during the other using high‐frequency ultrasound. CVMR is expressed as the percent change in MCA's CBFV per mmHg change in ETCO2, as quantified by the slope of this relationship. The time‐averaged diameter during each static stage was measured offline with echo‐tracking software. All results presented as Mean ± SD. The experimental protocol resulted in a moderated change of ETCO2 (mmHg) during 5% CO2 inspiration (+6.9±2.0) and mild hyperventilation (−14.8±5.8) relative to the baseline values (34.6±2.7). Both hypercapnic and hypocapnic stages showed no significant changes (relative to the baseline) in blood pressure, heart rate, diameters of ICA (5.23±0.83 and 5.21±0.71, vs. baseline 5.22 ±0.83 mm; P = 0.88 and 0.86) and VA (3.91±0.69 and 3.91±0.72, vs. baseline 3.87±0.65 mm; P = 0.40 and 0.55), except for a slight increase (+7±8 bpm, P < 0.001) of HR during hypocapnia. The individual variation of the diameter response showed no correlation with the concurrent blood pressure, heart rate, and CBFV responses. Based on these results, we concluded that the TCD appears to still be a reliable method to assess the CBF response during CVMR test with a moderate change of ETCO2, as no significant change of the conduit vessel diameter is likely to occur. However, future work is necessary to confirm that flow changes in the extracranial arteries are reflective of relative changes in TCD values.Support or Funding InformationSupported by the Funding from Rutgers University and U.S. Department of Defense.This abstract is from the Experimental Biology 2019 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
Analgesics in the Pre‐Hospital Setting: Simulated Hemorrhagic Tolerance in Humans is not Impaired by Ketamine Administration
Authors: Huang Mu , Moralez Gilbert , Cramer Matthew N. , Hendrix Joseph M. , Hinojosa‐Laborde Carmen , Ryan Kathy L. , Crandall Craig G. 
Published: June 2021

Hemorrhage is the leading cause of battlefield and civilian trauma deaths. Given that a hemorrhagic injury on the battlefield is virtually always associated with pain, it is paramount that the administered pain medication does not disrupt the physiological mechanisms that are beneficial towards the maintenance of blood pressure and vital organ blood flow during that hemorrhagic insult. Current guidelines from the US Army's Committee on Tactical Combat Casualty Care (CoTCCC) for the selection of pain medications administered to a hemorrhaging soldier are based upon limited scientific evidence, with the clear majority of supporting studies being conducted on anesthetized animals. Specifically, the influence of ketamine, one of three analgesics employed in the pre‐hospital setting by the US Army, on hemorrhagic tolerance in humans is entirely unknown. Thus, the purpose of this study is to test the hypothesis that ketamine will impair the capacity for a conscious human to tolerate a simulated hemorrhagic insult. Twelve subjects (4 females, 29±7 years old, 181±6 cm, 84±10 kg) participated in this double‐blinded, randomized, placebo‐controlled investigation. Tolerance to a simulated hemorrhage was performed using a progressive lower body negative pressure (LBNP) protocol to pre‐syncope following intravenous administration of Ketamine (20 mg—consistent with the US Army's CoTCCC guidelines) or placebo (saline). Tolerance was quantified as a cumulative stress index (CSI, mmHg•min). Tolerance to the LBNP challenge was not different between the ketamine and placebo trials (CSI: 746±368 mmHg•min and 795±316 mmHg•min respectively, P=0.61). These data, the first to be obtained in conscious humans, demonstrate that administration of ketamine does not compromise tolerance to a simulated hemorrhagic insult. These findings may be insightful in choosing the most suitable analgesic medication in the pre‐hospital setting during a hemorrhagic insult.Support or Funding InformationFunding: Department of Defense – US Army, W81XWH1820012This abstract is from the Experimental Biology 2019 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
Long Term Hypoxia Negatively Influences Ca2+ Signaling in Basilar Arterial Myocytes of Fetal and Adult Sheep
Authors: Reid Casey , Romero Monica , Dobyns Abigail , Hessinger David A , Puglisi Jose L , Wilson Christopher G , Zhang Lubo , Wilson Sean M 
Published: June 2021

Gestational long term hypoxia (LTH) is a common prenatal stress caused by maternal anemia, high altitude living, smoking, and other disorders. Such gestational LTH can lead to a variety of cerebrovascular disorders in the neonate that compromise brain blood flow. Local and whole‐cell Ca2+ signals are important to the regulation of cerebrovascular tone. Rapid and localized Ca2+ transients, often referred to as sparks, activate large‐conductance K+ channels (BK), which dilate vessels. Whole‐cell Ca2+ oscillations, in comparison, are important to arterial contraction. Previous work shows that LTH and post‐natal maturity influence BK channel function in basilar arteries, arterial wall Ca2+ signals, cerebrovascular tone, as well as brain blood flow. We hypothesize that LTH‐dependent changes in spontaneous and depolarization mediated Ca2+ sparks and whole‐cell oscillations are important to BK channel activity, arterial wall Ca2+ signals, and vascular reactivity changes our group has previously observed. To begin evaluating the role of individual myocyte Ca2+ signals to the observed changes in cerebrovascular function, we isolated basilar arteries from adult and near term fetal (~141 gestational days) normoxic and hypoxic sheep that were raised at 3,800 m. for 110+ days. Cytosolic Ca2+ signals were examined in individual myocytes of intact arterial preparations loaded with fluo‐4 using laser scanning confocal microscopy techniques. Ca2+ spark activity as well as whole‐cell oscillations were enhanced by depolarizing myocytes with 30 mM K+. Maturation increased Ca2+ spark activity and depolarization‐dependent oscillations. LTH decreased oscillatory activity in fetal and adult animals but only spark frequency in adult myocytes. LTH decreased the area under the curve for Ca2+ oscillations independent of age as well as suppressed the ability of adult myocytes to respond to membrane depolarization. Depolarization, maturation, and LTH also influenced the spatial and temporal relationships of the Ca2+ oscillations. Overall, these observations illustrate that maturation and gestation at high‐altitude modify local and whole‐cell Ca2+ signaling, which likely contribute to adjustments in BK channel function, arterial wall Ca2+ signals, vasoreactivity, and cerebral blood flow that our group has examined in the past.Support or Funding InformationThis material is based upon work supported by NIH grants P01HD083132 (LZ). Imaging was performed in the LLUSM Advanced Imaging and Microscopy Core with support of NSF Grant MRI‐DBI 0923559 and the Loma Linda University School of Medicine.This abstract is from the Experimental Biology 2019 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
Molecular CaseNet: Developing case studies using molecular representations for use in introductory chemistry, biology and biochemistry classes
Authors: Jakubowski Henry , Cortes Kimberly Linenberger , Lenahan Melanie , Marcey David , Marsteller Pat , Terrell Cassidy R. , Dutta Shuchusmita 
Published: June 2021

Understanding “Structure and Function” relationships is foundational to learning biology, chemistry, and biochemistry. However, exploring and using biochemical data resources, especially the Protein Data Bank, to develop a deeper understanding of the relationship between structure and function are not common practices, especially in introductory courses. This project brings together biology and chemistry educators to develop case studies centered around molecular representations of biomolecules. We hope these studies, at the interface between both disciplines, will facilitate deeper understanding of structure/function in biology and chemistry and reduce conceptual barriers that hinder a common understanding. This presentation will focus on a hemoglobin case study that was developed and used in introductory chemistry and a one‐semester biochemistry course. Discussion will focus on implementation of using the same case at different levels of instruction, ideas for other content that could be used to bridge the disciplines of biology and chemistry using molecular representations and how you can get involved in the Molecular CaseNet.Support or Funding InformationThis work was supported by the National Science Foundation under award #1827011. Any opinions, findings, and conclusions or recommendations expressed in this publication are those of the authors and do not necessarily reflect the views of the National Science Foundation.This abstract is from the Experimental Biology 2019 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.