bluuebunny/crossref_metadata_2025_split huggingface dataset:
Human embryonic serial anatomy : 3D evolutionnary posterior fossa venous system
Authors: Braun Marc , Tonnelet Romain , Micard Emilien , Labrousse Marc 
Published: June 2021

IntroductionSince the mid 1950's, very little work has been done to contribute to a better understanding of venous vasculature developpement during embryogenesis. We present a new analysis method with multiplanar reformation process based on microscopic sections. This présentation focus on the brain stem arachnoïdo‐pial venous anastomoses evolutive morphology.Material and methodsHigh résolution numerised microscopic continuous sections (10 to 20 μ) from Carnegie stage XIX to XXIII human embryo were used. Specific image treatment was the following : binarisation‐thresholding‐labellisation, rigid shifting, median filtration (cubic matrix) (resolution 10μm/pixel) ; DICOM format images are exported for post‐treatment process. Angiographic rendering was obtained thanks to the Eosine/hematoxylin red cell fixation within the vessels.ResultsAt first step, we confirmed the embryonnic status relatively to the Carnegie classification in assessing the cochlear canal orientation. The evolutive morphology of the brain stem primitive network is presented ; at stage XIX, the initial longitudinal veins are separated from the caudal plexus. During the next stages, we demonstrate how they connected to transverse pial anastomoses. The next period (i.e the early and late post‐embryonic period) show these intrinsic pial veins lying between the arteries and the brain surface leading to a progressive simplication pattern. During the stages XX to XXIII, we present the changing morphology of the trijeminal ganglion venous plexus. These organisations are compared to the Padget and Streeter works.ConclusionWe present the preliminary work of the brain stem venous embryogenesis using 3D and angiographic rendering at the early post‐embryonic stages.
Raman spectroscopic signature of the cardiovascular commitment and cardiac phenotypes of mouse embryonic stem cells differentiated towards the cardiovascular lineage
Authors: Brauchle Eva , Linder Sandra , Knopf Anne , Schenke‐Layland Katja 
Published: June 2021

Raman spectroscopy is a powerful optical technology that can be used to generate biochemical profiles of living cells. In this study, Raman spectroscopy was employed as a non‐invasive approach for the characterization of murine embryonic stem cells (mESCs) and their cardiac derivatives, such as cardiac progenitor cells (CPCs) and cardiomyocytes (CMs). mESCs were differentiated towards the cardiovascular fate yielding CPCs as well as spontaneously beating CMs. Raman spectra of the in vitro‐differentiated cells were compared to spectra generated from isolated fetal and adult murine CMs. All Raman spectra displayed a unique pattern for all cardiovascular phenotypes. Interestingly, the Raman spectra of spontaneously beating mESC‐derived CMs and CMs isolated from murine fetal hearts showed similar spectral patterns; however, both were distinct when compared to the spectra of adult CMs. Raman spectra of CPCs also exhibited similarities to those of CMs, whereas non‐CPCs did not.To conclude, we identified the presence of a Raman spectral signature that helps predicting cardiovascular lineage commitment in early‐differentiated pluripotent stem cells.Grant Funding Source: : Fraunhofer‐Gesellschaft (Attract 692263), the BMBF (0316059), the DFG (SCHE 701/7–1), the Ministry of Science, Research and the Arts of Baden‐Württemberg (33–729.55–3/214) and the Landesstiftung Baden Württemberg (PLS‐SPII/18)
The Role of Nitric Oxide in Cardiopulmonary Endurance
Authors: Adar Tony , Baral Sumit , Márquez Samuel 
Published: June 2021

Nitric Oxide (NO) has been intensely investigated in various physiological as well as pathophysiological processes in humans but has received its greatest attention for its vasodilator properties. Since the nose and paranasal sinuses have been implicated as the sole producers of NO in the upper respiratory system, NO may be regarded as an aerocrine hormone produced in the nasal complex and transported to a distal site of action with every inhalation by enhancing pulmonary oxygen uptake via local vasodilation, thus facilitating athletic endurance. Our study examines fractional NO concentration (FeNO) response in expired air during exercise (Ex). A strict three step Ex protocol was followed in which FeNO measurements were obtained in 18 healthy human volunteers prior to Ex (rest stage (RS)), during a strenuous 200 w ergometer cycle and 5 minutes into the recovery period. FeNO measurements were performed according to ERS/ATS recommendations with an electrochemical sensor (Niox Mino Aerocrine Stockholm, Sweden). Results showed an overall decrease in average FeNO levels from resting stage to endurance phase of Ex (16.4 to 12.6 ppb p< .005) with levels increasing towards the original RS value 5 minutes into the recovery phase (12.6 to 14.1 ppb p< .005). Further investigation may shed light as to the exact mechanism of NO recruitment by the lower respiratory tract in maximizing cardiopulmonary endurance.Grant Funding Source: SUNY Downstate Alumni Association
Functional Characterization Of Dbf4 Interactions With DNA Replication And Checkpoint Factors
Authors: Jones Darryl R , Matthews Lindsay A , McConkey Brendan J , Guarné Alba , Duncker Bernard P 
Published: June 2021

The Dbf4/Cdc7 kinase complex (DDK) is essential for the initiation of DNA replication, acting upon the MCM helicase complex to trigger the initiation of replication. DDK is also a target of the intra‐S phase checkpoint, important in preserving genomic stability. Dbf4, the regulatory subunit of this kinase complex, contains three regions that are highly conserved across eukaryotic species. Of these regions the amino terminal N motif adopts a modified BRCT fold that is crucial to maintain the interaction with the checkpoint kinase Rad53, while the M and C motifs are both involved with the interaction with Cdc7 and the Mcm2 component of the MCM helicase. Mutations to critical amino acids within either of the N or C motifs result in sensitivity to a variety of DNA damaging agents. Employing both bioinformatics and structural NMR based approaches we have identified a novel surface of the forkhead‐associated (FHA1) domain of Rad53 that mediates its interaction with Dbf4. Additionally, we have generated strains that combine Dbf4 motif C mutation with mutations in previously characterized checkpoint proteins in order to better define the checkpoint role of Dbf4. Together, these findings shed light on the mechanism by which Dbf4 aids in maintaining genome stability.This research was supported through grants from the Natural Sciences and Engineering Research Council of Canada (NSERC) and the Canadian Institutes of Health Research (CIHR)
Regulation of VEGF Expression in Hypoxic Pulmonary Artery Endothelial Cells (PAECs) by Base Excision DNA Repair (BER) Activity
Authors: Pastukh Viktor , Bardwell Gina , Pastukh Viktoriya , Gillespie Mark 
Published: June 2021

Reactive species generated by peri‐nuclear mitochondria cause formation of the common base oxidation product 8‐oxoguanine (8‐ oxoG) in hypoxic response elements (HRE) of inducible genes (Al‐Mehdi et al., Sci Signaling, 2012). Repair 8‐oxoG by the BER pathway is initiated by the lesion‐specific DNA glycosylase OGG1. The specific mechanism whereby DNA repair interacts with transcription is still unknown. We tested the idea that modulation of OGG1 alters transcription complex formation on the VEGF HRE and VEGF mRNA expression. In cultured PAECs, we confirmed that hypoxia increased 8‐oxoG in the VEGF HRE. siRNA‐mediated knockdown and transgenic over‐expression of OGG1 increased and decreased, respectively, the proportion of VEGF HREs harboring 8‐oxoG. The hypoxia‐induced increase in HRE sequences associating with Hif‐1 was inhibited by OGG1 knockdown and augmented by OGG1 over‐expression. Hypoxia‐induced Vegf mRNA expression tracked Hif‐1 binding in cells with modulated OGG1 activity. These findings indicate that the BER pathway may be important for transcription and point to new mechanisms linking hypoxia to mutagenesis, aging and other oxidant‐related disorders.Supported by NIH.
Mechanistic studies of transcription initiation by the yeast mitochondrial RNA polymerase
Authors: Deshpande Aishwarya P , Patel Smita S 
Published: June 2021

The yeast mitochondrial DNA contains multiple promoters that direct the synthesis of rRNAs, tRNAs, and the mRNAs of the ATP synthesis complex. These RNAs are transcribed by a distinct two‐component complex consisting of the core RNA polymerase, Rpo41, which is the catalytic subunit and an accessory factor, Mtf1, which is necessary for promoter opening and start site selection. Although, currently we have a basic understanding of the mechanism of open complex formation and the respective roles of Rpo41 and Mtf1, we lack a similar understanding of the initial transcription mechanism involving +1 and +2 NTP binding and promoter strength. Using synthetic promoters, we observed a range of transcriptional efficiency from various promoters. Using promoter mutants and fluorescence‐based assays, we show that these differences in transcriptional efficiencies stem from differences in downstream promoter melting, which go hand in hand with differential NTP binding affinities. We propose a model, where either Rpo41 or Mtf1 or both through an orchestration of interactions with the promoter region as well as the incoming nucleotides regulate the transcriptional efficiency of various promoters.This work was supported by the NIH grant RM51966 to S.S.P
The JmjC Domain‐containing Regulator Gis1 Is Regulated by Heme and Oxygen
Authors: Cao Thai , Shah Ajit , Lal Sneha , Zhang Li 
Published: June 2021

JmjC domain‐containing proteins have demethylase activity and can remove specific methyl groups on histones or other proteins. There are over 100 proteins in diverse organisms known to contain the JmjC domain. These proteins act by oxidizing the methyl group to yield formaldehyde and the unmodified lysine or arginine. Due to the requirement for oxygen for demethylase activity, these proteins can serve as oxygen sensors. The yeast Gis1 is a unique transcriptional regulator belonging to the JHDM3/JMJD2 subfamily of demethylases. Further, Gis1 is highly homologous to the mammalian JmjC domain‐containing JMJD2B protein that is likely to play important roles in histone demethylation, oxygen regulation and hormonal signaling. Recently, our studies showed that Gis1 activity is regulated by both heme and oxygen. Analysis of PDS‐LEU2‐lacZ reporter gene showed a significant increase in PDS reporter gene under high heme concentration. However, a decrease in the Gis1 activity was observed under hypoxia as compared to normoxia. Confocal fluorescent live cell imaging of Gis1 showed that over 95% of the Gis1 protein were nuclear in normoxic cells, while over 90% of Gis1 protein were retained in the cytosol in hypoxic cells. Time course characterization of relocalization of Gis1 showed that Gis1 relocalized in a significantly shorter time period in response to both hypoxia and reoxygenation.Grants: Cecil H. and Ida Green Funds
Binding of Eukaryotic Initiation Factor (eIF) 4F to Barley Yellow Dwarf Virus (BYDV) 3′ UTR Correlates Well With Protein Synthesis Efficiency
Authors: Banerjee Bidisha , Goss Dixie J. 
Published: June 2021

BYDV belonging to the luteoviridae family is an economically important plant virus lacking a 5′ cap and 3′poly (A) tail and is translated by cap‐independent translation (CIT) mechanism. The BYDV 3′ Untranslated Region (UTR) translation enhancer element (BTE) stimulates CIT initiation at the 5′upstream AUG via base‐pairing (kissing stem loop interaction) to a complementary loop, 5′UTR SL‐D. 3′ BTE recruits eIFs and transfers them to the 5′ end of the viral RNA where translation initiates.Wild type BTE and BTE mutants with in‐vitro translation efficiencies from 5–164 % were studied. eIF4F binding is the first committed step in cap‐dependent protein synthesis. The role of eIF4F in viral protein synthesis is not fully understood.eIF4F binding to BTE and BTE mutants gave equilibrium binding constant values (Kds) which are a measure of relative complex stability. We show: 1) translation efficiencies correlated well with eIF4F binding with one exception; 2) Kinetics, higher activation energy and interaction of other eIFs contribute; 3) BTE and BTE mutants‐eIF4F interaction is both enthalpically (52–90%) and entropically favorable with more enthalpic contribution to ΔG° at 25°C. The stability measurements and kinetics determine the nature of interactions and provides unique information on the sequential assembly of the initiation complex and it's binding to viral mRNA.Grant Support: NSF MCB 1157632
Mechanism of Activator (eIF4F) and Suppressor (IRP) Binding to Iron Responsive Element mRNA
Authors: Ma Jia , Khan Mateen , Merrick William C , Theil Elizabeth C. , Goss Dixie J. 
Published: June 2021

Cellular iron metabolism is regulated by expression of iron responsive element (IRE) containing‐mRNAs to control iron related protein levels (e.g. ferritin). The cytoplasmic iron regulatory proteins, IRPs, repress IRE‐mRNA translation by binding to the iron response element (IRE). Our previous study (Ma et al. (2012) PNAS 109: 8417–8422) showed that Fe2+ decreased IRP (suppressor)/IRE binding affinity and increased eIF4F (activator)/IRE binding affinity. Fluorescence studies showed that Fe2+can bind to the IRE‐RNA structure and induce conformational changes. These conformational changes affect IRP/IRE interacting bases and consequently affect protein binding. Mn2+(O2resistant Fe2+surrogate) both decrease the association rate (kon) for IRP and increases the dissociation rate (koff), lowering the binding affinity of IRP for IRE‐RNA. In contrast to IRP/IRE binding, Fe2+increases eIF4F/IRE binding and eIF4F:IRP competitively bind to the IRE. Kinetic and thermodynamic data suggest a model for IRE‐RNA riboregulator function, illustrating the potential of specific metal ion interactions with folded untranslated mRNA structures for gene regulation.Grant support: NSF MCB 1157632 NIH DK20251
Rab1a regulates endocytic vesicle processing through interaction with Kifc1
Authors: Quiroz Jose , Mukhopadhyay Aparna , Wolkoff Allan W. 
Published: June 2021

Rab1a regulates endocytic vesicle processing by recruiting the microtubule‐based motor Kifc1. The mechanism by which this occurs is unknown and therefore we examined whether Kifc1 and Rab1a interact with each other either directly or through a protein complex.Human embryonic kidney‐derived HEK293 cell lines expressing super folder green fluorescent protein (SFGFP) or Rab1a‐SFGFP fusion protein were prepared. To test whether Kifc1 interacts with Rab1a, a plasmid encoding Kifc1‐flag was transfected into Rab1a‐SFGFP expressing HEK293 cells. Cell lysates were subjected to immunoprecipitation with GFP antibody. Following SDS‐PAGE, analysis revealed the presence of Kifc1 in immunoprecipitates from Rab1a‐SFGFP expressing cells.In summary, immunofluorescence microscopy verified stable cell lines expressing Rab1a‐SFGFP in HEK293. Immunoprecipitation of Rab1a‐SFGFP cells transiently transfected with Kifc1‐Flag showed that Rab1a and Kifc1 were in the immunoprecipitate. We conclude that Rab1a and Kifc1 are associated with each other in a protein complex and do not just independently bind to endocytic vesicles. Whether other proteins are in this complex remains to be discovered.
The role of modulator residues in PDZ domain binding interactions
Authors: Amacher Jeanine , Cushing Patrick R , Brooks Lionel , Boisguerin Prisca , Madden Dean R 
Published: June 2021

PDZ domains are the most common interaction domain in the human proteome. PDZ interactions are classified by motif residues, or, preferences distinguished by high throughput techniques. However, these motifs are degenerate, and fail to predict the affinities of each peptide‐binding domain for its unique set of interacting partners, making design of specific therapeutic inhibitors a challenge. Through biochemical, structural, and computational studies, we reveal that targeted inhibitor design requires an understanding of modulatory, or non‐motif affinity determinant, residues in PDZ domains. Our work investigates modulatory preferences in the CFTR Associated Ligand (CAL) protein.Despite a motif dependent on two residues, we previously reported the engineering of a selective inhibitor of CAL PDZ via a peptide array pipeline. Our approach allowed us to identify multiple residues along the binding cleft that influenced affinity and/or selectivity. We now investigate the stereochemistry and binding affinities of over a dozen co‐complex structures of CAL PDZ bound to high, intermediate, and low affinity peptides, revealing distinct modulator preferences that are hidden from high throughput motif analysis. We extend our analysis to additional PDZ domains, which share cellular targets. Our data suggests that modulator preferences dictate endogenous PDZ networks.
A role for endomucin‐1 in maintaining a non‐inflammatory endothelial surface and in the regulation of leukocyte‐endothelial cell interactions
Authors: Yang Jinling , Zahr Alisar , Alcaide Pilar , Jones Alexander , Gregory‐Ksander Meredith , Luscinskas Francis W. , Ksander Bruce , Argueso Pablo , D'Amore Patricia A 
Published: June 2021

Leukocyte‐endothelial cell (EC) interactions, including leukocyte rolling, adhesion and transmigration, are central to vascular inflammation. Endomucin‐1 (EMCN‐1) is a transmembrane glycoprotein specifically expressed by venous and capillary endothelium. This study was aimed at determining the role of EMCN‐1 in regulating leukocyte‐EC interaction in inflammation. Whereas leukocytes do not adhere to the surface of cultured human umbilical vein endothelial cells (HUVECs), transfection with siRNA against EMCN‐1 led to dramatic increase in leukocyte‐EC interaction compared to scramble siRNA control by flow adhesion assay. HUVECs were also treated with TNF‐alpha (0.1 – 25 ng/ml), a prominent inflammatory cytokine. TNF‐alpha led to a dramatic reduction of in EMCN‐1 in cell surface protein, total protein and mRNA levels assayed by biotinylation, Western blot and quantitative real‐time PCR. Overexpression of EMCN‐1 by adenovirus (Ad‐EMCN‐1) in HUVECs led to a significant reduction in TNF‐alpha‐induced leukocyte‐EC interaction compared to control cells transduced with GFP‐expressing adenovirus (Ad‐GFP) determined by flow adhesion assay. For analysis of the role of EMCN‐1 in vivo, C57/B6 mice were injected intravitreally with Ad‐EMCN‐1 or Ad‐GFP seven days prior to invtravitreal injection of 10 ng TNF‐alpha or saline. Ciliary bodies, a primary site of leukocyte infiltration, were harvested 48 hr later. Administration of TNF‐alpha led to a reduction in EMCN‐1 protein and to an increase in CD45+ infiltrating inflammatory cells measured by flow cytometry, which was blocked by Ad‐EMCN‐1. These results suggest a critical role for EMCN‐1 in maintaining non‐inflammatory state of ECs at quiescent conditions and regulating leukocyte‐EC interaction during inflammation.This research was supported by the Department of Defense (PAD), a grant for new collaborative research projects from Schepens Eye Research Institute (PaA and PAD), HL‐097406 (PA) and HL‐36028 (FWL).
Identification of tomosyn as a new downstream target of Akt
Authors: Nagano Koki , Takeuchi Hiroshi , Sugiyama Goro , Gao Jing , Otani Takahito , Hirata Masato 
Published: June 2021

Insulin stimulates glucose uptake into skeletal muscle and adipose tissues by increasing the available number of glucose transporter (GLUT) 4 on the cell surface. GLUT4‐loaded vesicles are targeted to plasma membrane from the intracellular reservoir through multiple trafficking steps that are regulated by protein kinase Akt. Although many clues that regulate targeting and docking of GLUT4‐vesicles to the plasma membrane had been identified, it is still largely unknown how the membrane fusion is promoted by insulin. Thus, we tried to identify a new target of Akt which is responsible for up‐regulation of SNARE‐mediated membrane fusion in insulin‐stimulated cell.We first searched for proteins bearing the recognized motif to be phosphorylated by Akt on databases. Among them, an Akt‐site was highly conserved at Ser‐783 in rat tomosyn, a SNARE binding protein, which might be involved in GLUT4 trafficking. Both Akt1 and Akt2 phosphorylated recombinant tomosyn in vitro, and the phosphorylation was diminished by replacing Ser‐783 with Ala (S783A). Protein kinase A (PKA) also phosphorylated tomosyn, but S783 is not the residue phosphorylated by PKA. The interaction of tomosyn and syntaxin 4 was modulated by the phosphorylation. The results suggest that tomosyn would be involved in insulin‐triggered membrane fusion between docked GLUT4 vesicle and the target plasma membrane.
Aerobic exercise during pregnancy increases antioxidant status in nulliparous women
Authors: Ramírez‐Vélez Robinson 
Published: June 2021

AimTo determine the effects of exercise in the second half of pregnancy on antioxidant status in pregnant women.MethodsThis was clinical trial of 20 primigravid women between 16 and 20 weeks’ gestation. Antioxidant status was measured using the antioxidant assay kit in samples of the maternal peripheral blood serum at baseline, at the end of the three‐month intervention period and cord blood at 15 min of delivery.ResultsAt 3 months, the supervised aerobic exercise program, showed slightly higher values for antioxidant status in maternal peripheral blood serum in the experimental group compared to the control group, (0.58±0.24mM) vs. (0.28±0.06mM), respectively(p=0.25). Two‐way ANOVA analysis revealed that umbilical cord blood antioxidant status was significantly higher in the exercise group at the end of the intervention (p<0.001, F=8.09).ConclusionsThis study showed that 12 weeks of aerobic exercise increased antioxidant status in nulliparous women. It has been suggested that regular exercise is associated with beneficial effects on the incidence of preeclampsia because of its antioxidant effects
Effect of tree nuts on features of the metabolic syndrome: A systematic review and meta‐analysis of randomized controlled dietary trials
Authors: Mejia Sonia Blanco , Sievenpiper John L. , de Souza Russell J , Augustin Livia S , Viguiliouk Effie , Ha Vanessa , Mirrahimi Arash , Chiavaroli Laura , Cozma Adrian I , Jenkins David J A , Kendall Cyril W C 
Published: June 2021

ObjectiveTo assess the effect of tree nuts on features of the metabolic syndrome (MetS), we conducted a systematic review and meta‐analysis of randomized dietary trials.MethodsWe searched MEDLINE, EMBASE, CINAHL, and the Cochrane Library (through May 25, 2012). We included relevant randomized dietary trials of ≥ 3 weeks reporting all 5 features of MetS (waist circumference, fasting glucose, triglycerides, HDL‐cholesterol [HDL‐C], blood pressure [BP]). Two independent reviewers extracted all relevant data. Data were pooled using the generic inverse variance method and expressed as mean differences (MD) with 95% CI. Heterogeneity was assessed by Cochran's Q and quantified by I2. Study quality was assessed by the Heyland score.Results7 trials (n=1018) met the eligibility criteria. Diets high in tree nuts lowered triglycerides compared with control diets low in tree nuts (MD = −0.09 mmol/L [95% CI, −0.17, −0.01]). There was no effect on waist circumference, HDL‐C, BP, and fasting glucose, with evidence of heterogeneity in all analyses.LimitationsMost of the trials were of short duration (<12 months) and of poor quality.ConclusionPooled analyses show that diets high in tree nuts lower triglycerides. Longer and higher quality trials are warranted. Clinicaltrials.gov identifier: NCT01630980Funding source: International Nut Council