bluuebunny/crossref_metadata_2025_split huggingface dataset:
LIPIDIC AGENT AS VASCULAR CONSTRAST‐MEDIUM FOR MRI (3T) IN FETAL AND EMBRYONIC DEVELOPMENT: FEASABILITY‐STUDY ON EX‐VIVO RABBIT FETUS AT 3T
Authors: TONNELET Romain , PEREZ Manuela , GONDIM TEIXEIRA Pedro Augusto , SEWONU Anou , BEAUMONT Marine , HOSSU Gabriela , LABROUSSE Marc , BRAUN Marc 
Published: November 2023

IntroductionUnderstanding some dynamic processes such as the development of the cardiovascular system requires a global and precise anatomic vision of this dynamic and complex processA variety of imaging tools and reconstructions are available for the evaluation of embryonic development. Micro‐MRI was used as the “standard” technique in large study series1, 2 competing with micro‐CT and techniques requiring the preparation of the sample in serial sections (EFIC method3 / 3D reconstruction from serial histological sections : EmbryoForm Project4).Material & MethodEmbryonic imaging is also restricted by the use of vascular MRI contrast agents such as gadolinium coupled to albumin, which are particularly expensive.Lipidic agents have high viscosity at ambient temperatures and a T1 shortening effect for vascular rendering. Due to the non‐diffusion phenomenon related to its inherent hydrophobic properties, lipidic agents are restricted to the intra‐vascular compartment. These characteristics make lipidic agents a potentially available and cost effective option for embryonic vascular imaging.In this study we sought to evaluate the use of a lipidic contrast agent (Type‐B oil / Fisher Scientific) using dedicated coils with a 3Tclinical MR scanner. A qualitative analysis of the injected vascular anatomical structures and a quantitative analysis by the contrast‐to‐noise ratio (CNR) and signal‐to‐noise ratio (SNR) was performed on two rabbit fetuses.ResultsLarge and medium vessels structures including thoraco‐obdominal great vessels, intra‐hepatic vasculature and vascular brain structures were identified by two trained operators.CNR and SNR measures were in agreement with those of the literature.Such a technique have the potential to increase the availability of embryonic vascular imaging and facilitate research in the field of vasculogenesis.
The Interplay Between Taste and Chemesthesis
Authors: Huang Anthony Y , Wu Sandy Y 
Published: November 2023

Chemosensory afferent fibers, which contribute to chemesthesis, the general chemical sensitivity of the mucus membranes in the oronasal cavities and being perceived as pungency, irritation or heat, innervating taste buds store transmitters such as calcitonin gene‐related peptide (CGRP) but little is known about their function. The complex interplay between taste cells and chemosensory neurons, via transmitters, may play an important role during the processing of the complex stimuli involving both spicy and tasty components. In this study, we characterized CGRP receptors present on taste cells. These receptors appear to underlie the postulated efferent transmission. Specifically, we loaded mouse vallate taste cells with Fura 2, conducted functional imaging, and used cellular biosensors to monitor taste‐evoked transmitter (ATP) release. The findings are that a significant fraction of Presynaptic (Type III) taste bud cells (53%) respond to CGRP, but that only few Receptor (Type II) taste cells (4%) are activated by this transmitter. We demonstrated that this effect of CGRP was dependent on phospholipase C activation. Consistent with these results, applying CGRP elicited taste buds to secrete serotonin (5‐HT), a Presynaptic (Type III) taste cell transmitter. Furthermore, CGRP‐evoked 5‐HT release inhibited taste buds and reduced their ability to secrete transmitter (ATP) during gustatory stimulation. We conclude that the net effect of CGRP as an efferent transmitter in taste buds is inhibitory—i.e., CGRP acts via serotonergic mechanisms to shape peripheral taste signals during processing gustatory information in taste buds.Support or Funding InformationSupported by SIUSOM Research Seed Grant (AYH).
Middle and Inner Ear 3D Reconstructions using High Resolution X‐ray Micro‐Tomography
Authors: LABROUSSE Marc , DUBERNARD Xavier , SETTEMBRE Nicla , TONNELET Romain , AVISSE Claude , DEVY Jérôme , RENARD Yohann 
Published: November 2023

IntroductionThe temporal bone is a complex 3D structure that is difficult to teach to ENT residents. Learning about this anatomy from classical textbooks requires considerable intellectual gymnastics to deal with this spatially complex structure. We present a new way for teaching this anatomy with high resolution 3D reconstructions using X‐ray micro‐tomography.Materials and Methods10 human petrous parts of temporal bones were fixed with Winckler's solution. CT images were acquired with a CT scanner (Skyscan 1076, Bruker, Kontich, Belgium). The camera was continuously rotated by 180° and the following parameters were used for acquisition: 50 kV, 0.5 mm Al filter, 200 A source current, 35 m isotropic resolution, 180 ms exposure time, and 0.7° rotation step. The projections were reconstructed with a filtered backprojection algorithm in Skyscan software (NRecon, Skyscan). Reconstructed images were analyzed with ORS Visual software.(v1.5, Montreal), which allowed multiple display and post‐processing possibilities (3D VR; orthogonal/curved multiplanar reformation).Results and DiscussionThree‐dimensional and multiplanar studies of the temporal bone morphology were possible with appropriate thresholding. The whole components of the middle ear (ossicles, tympanic cavity bony reliefs), the inner ear (cochlea, modiolus, cochlear canal, vestibule and semicircular canals) and their respective anatomic relationships are clearly visible. This method seems very effective in teaching this complex anatomy.Conclusion3D reconstructions using high resolution X‐ray micro‐tomography aid comprehension of temporal bone complex anatomy. This precise knowledge will help residents to better understand otological surgery.
From The Novice To The Experienced Ultrasound User: 7D Interactive Software Is Your Personal Tutor
Authors: Blandford Ian , Benninger Brion 
Published: November 2023

INTRODUCTIONUltrasound has become a very diverse tool in healthcare today. Ultrasound systems have improved significantly during the past decade. Unfortunately, the demand to learn is greater than available training. The objective of this study was to investigate if an ultrasound education software program could be successfully used by novice healthcare profession students.METHODSLiterature search was conducted regarding interactive ultrasound educational software applications. Infrastructure of 7D Imaging educational ultrasound software includes text, imaging (static and video), testing integration, and clinical applications. Twenty students (10 baccalaureate (BS), 10 medical (MS)) involved in an anatomy course were exposed to the 7D Imaging ultrasound education software. Each student was asked to navigate through the program to aid them in conducting an ultrasound exam on the supraspinatus tendon, Morrison's pouch, and the femoral triangle. Two weeks later, we examined the students conducting ultrasound imaging and identify structures using Fukuda Denshi UF‐760AG ultrasound machine and Sonivate Soniceye finger probes.SUMMARYLiterature search revealed no interactive ultrasound education software programs. However, a plethora of random, informative demonstration videos exist, but lack comprehensiveness and testing ability. Of the thirty structures to be identified, the BS students successfully demonstrated and identified 25 out of 30 structures, and the MS 27 out of 30. Ultrasound continues to be used in virtually all disciplines of medicine. The vast majority of experts practice their skills with patients and have virtually no time to train novices. Therefore, there is a need for efficient interactive training software which allows self‐assessment.CONCLUSIONThis study revealed that the 7D Imaging interactive educational software could be successfully integrated as part of an anatomy course.3
Markers of Hypoxia and Correlation with Disease Severity in Inflammatory Bowel Disease
Authors: Schwisow Kayla Danae , Colson Steven , Gerich Mark , Lovell Mark , Allshouse Amanda , Yeckes Alyson , Kessler Brittelle , Keely Simon , Hoffenberg Edward , de Zoeten Edwin , Colgan Sean 
Published: November 2023

Ongoing inflammation results in a significant shift in tissue metabolism. Previous studies indicate that inflammation and hypoxia occur concomitantly. Here, we sought to determine whether circulating and tissue indicators of hypoxia could serve as surrogate indicators of disease severity in patients with inflammatory bowel disease (IBD). Serum and colon biopsies were obtained at a tertiary care center from 24 pediatric subjects with active IBD colitis and 26 non‐colitis controls. Serum was also collected from adult subjects: 10 with active IBD, 10 IBD patients with inactive disease, and 19 non‐colitis controls. Disease severity for the pediatric samples was graded by histopathology and inflammatory cytokine profile. Erythropoietin (EPO), vascular endothelial growth factor (VEGF), and macrophage inflammatory protein 3α (MIP3α) were measured in serum and tissue biopsies and correlated with disease severity. An initial screen of serum hypoxia markers revealed that children with colitis had higher circulating levels of EPO, VEGF and MIP3α than non‐colitis controls (all p<0.05). In parallel, analysis of colon tissue MIP3α RNA and protein revealed increased expression in children with IBD colitis compared to controls (p<0.05 and p<0.01 for RNA and protein, respectively). All three serum markers significantly differed across histology grade (VEGF p<0.01, EPO p<0.001, MIP3α p<0.001) and disease severity correlated with tissue IL‐6, IL‐8, and TNFα protein levels. In adult subjects, the same trends were seen in the circulating levels of EPO, VEGF, and MIP3α, with significant increases in EPO and MIP3α in active IBD patients compared to non‐colitis controls (p>0.0005 and p>0.05 for EPO and MIP3α, respectively). These results reveal that markers of hypoxia strongly correlate with histologically‐graded colitis as well as tissue inflammatory cytokine levels. Peripheral blood hypoxia markers may be useful surrogates to assess colon inflammation and could be utilized as potential indicators of disease activity for IBD.Support or Funding InformationThis work was supported by National Institutes of Health grants RO1‐HL60569, T32 DK067009, and UL1 RR025780 and by support from the Crohn's and Colitis Foundation of America.
Characterization of the E. coli SOS response protein YbfE
Authors: Kramer Caitlin , Muenter Mark , Leifer Becky , Travers Meghan , Judge Richard , Beuning Penny 
Published: November 2023

The transcription of DNA damage response genes in prokaryotes is largely regulated by LexA and controlled through the SOS mechanism. Over 50 genes have been identified as part of the LexA regulon by their upstream LexA binding sequences. Prior work by our lab has shown that loss of the uncharacterized LexA‐regulated gene ybfE is associated with poor survival in E. coli exposed to alkylating agents. In order to elucidate a mechanism, the structure and function of the ybfE gene product were examined. A homology model was built that indicates that YbfE is a DNA‐binding protein that contains a C‐terminal ribbon‐helix‐helix motif and a domain of unknown function at its N‐terminus. The in vivo transcription start site of YbfE is not known, therefore two open reading frames downstream of the SOS operator were examined in vitro for sequence‐specific DNA binding. The first open reading frame contains an additional 23 amino acids at the N‐terminus. Both open reading frames were cloned, expressed, and purified. Electrophoretic mobility shift assays (EMSAs) were performed using the YbfE protein and DNA sequences selected to test binding specificity. Our observations support that YbfE binds DNA nonspecifically in vitro at concentrations above 500 nM. Characterization of sequence specific DNA binding at lower concentrations and protein‐protein interactions is ongoing.Support or Funding InformationSupported by American Cancer Society Research Scholar Grant RSG‐12‐161‐01‐DMC.
Investigating the Metabolism of a Major Peroxidation DNA adduct, M1dG, in the Genome
Authors: Wauchope Orrette R , Beavers William N , Galligan James J , Mitchener Michelle M , Kingsley Philip J , Marnett Lawrence J 
Published: November 2023

Chronic inflammation results in increased production of reactive oxygen species (ROS), which can oxidize cellular molecules including lipids and DNA. Our laboratory has shown that 3‐(2‐deoxy‐b‐D‐erythro‐pentofuranosyl)pyrimido[1,2‐a]purin‐10(3H)‐one (M1dG) is the most abundant DNA adduct formed from the lipid peroxidation product, malondialdehyde, or the DNA peroxidation product, base propenal. M1dG is mutagenic in bacterial and mammalian cells and is repaired via the nucleotide excision repair system. Here, we report that M1dG levels in intact nuclear DNA were increased from basal levels of 1 adduct per 108 nucleotides to 2 adducts per 106 nucleotides following adenine propenal treatment of RKO, HEK293 or HepG2 cells. We also found that M1dG in genomic DNA was oxidized in a time‐dependent fashion to a single product, 6‐oxo‐M1dG, (to ~ 5 adducts per 107 nucleotides) and that this oxidation correlated with a decline in M1dG levels. Investigations in RAW264.7 macrophages indicate the presence of high basal levels of M1dG (1 adduct per 106 nucleotides) and the endogenous formation of 6‐oxo‐M1dG. Interestingly, in all cell lines investigated, 6‐oxo‐M1dG was not observed in mitochondrial DNA. Basal levels of M1dG in the mitochondria were found to be approximately two orders of magnitude higher (~ 1 adduct per 106 nucleotides) than those observed in nuclear DNA and were increased with electrophilic stimulation. Further studies, in all the investigated cell lines, indicated a correlation between M1dG levels and oxidative stress in the mitochondrion. This is the first report of M1dG in mitochondrial DNA in intact cells and it has significant implications for understanding the role of inflammation in DNA damage, mutagenesis and repair.Support or Funding InformationThis work was supported by a research grant from the National Institutes of Health, R37 CA0878819 (L.J.M.)
Mutations in The RQC Domain of Human WRN Helicase Compromise It's Ability To Unwind G‐Quadruplex DNA
Authors: Ketkar Amit , Voehler Markus , Mukiza Tresor , Eoff Robert Lawton 
Published: November 2023

G‐quadruplex (G4) DNA is a specialized DNA structure that is now well established to occur in vivo. G4‐DNA structures present a significant block for replication, and must be overcome to complete the process efficiently. G4 motifs have been shown to occur at functional regions of prokaryotic and eukaryotic genomes, like promoters of oncogenes, replication origins and telomeres. G4 sequences are also enriched at chromosomal breakpoints in multiple types of cancer. The Werner's syndrome protein (WRN) is a RecQ‐family helicase that has been implicated in efficiently unwinding G4‐DNA structures during replication in humans. The aim of our study was to identify the residues of WRN that were involved in this role. Using a c‐Myc G4‐DNA model sequence and recombinant WRN, we determined that the RecQ‐C‐terminal (RQC) domain of WRN imparted a 2‐fold preference for binding to G4‐DNA relative to non‐G4 DNA substrates. NMR spectroscopic studies were performed using 15N‐labeled RQC‐domain in DNA titration experiments where both non‐structured and G4‐DNA substrates were used to identify residues that are involved specifically in interacting with G4‐DNA. Residues that showed the largest G4‐specific changes in NMR signal were chosen for further validation. Point mutations were made in these RQC‐domain residues in the WRN construct 500–1092, to generate single‐mutant proteins WRNT1024G, WRNL1063G, WRNT1086G, and a double‐mutant WRNT1024G/T1086G. The mutant proteins were studied in detail for their ATPase activity, ability to unwind G4‐DNA and their relative affinities towards non‐structured or G4‐DNA substrates. ATPase activity of all mutant proteins was reduced compared to wild‐type. The effect was moderate when nonG4‐DNA was used, and most pronounced for the double mutant when G4‐ssDNA was used to stimulate ATPase activity (activity was only 40% of wild‐type). The helicase/DNA‐unwinding activity of all mutant proteins was relatively unaffected on a non‐G4‐DNA substrate. However, for the WRNT1024G mutant, this activity was reduced by ~50% on a G4‐DNA substrate, while for the double mutant, it was drastically reduced (by 90%) on G4‐DNA as compared to wild‐type. DNA‐binding affinity of all mutant proteins except WRNT1024G/T1086G was relatively unaffected for both control and G4‐DNA substrates. Binding preference towards G4‐DNA was reduced only moderately for the single mutants. In the case of the double mutant, the preference for G4‐DNA was reduced from ~2‐fold (in wild‐type) to ~1.1‐fold. Our work has, thus, for the first time, helped identify the residues of WRN that are involved specifically in its interaction with G4‐DNA, and has laid the groundwork for future studies on properties of RecQ‐helicases, which enable several of them to unwind G‐quadruplex DNA.Support or Funding InformationGrants GM084460, CA183895
IDENTIFICATION AND CHARACTERIZATION OF HISTONE VARIANT H2A.Z IN THE LONG TERMINAL REPEAT RETROTRANSPOSON INTEGRATION
Authors: Rai Sudhir K. , Guo Yabin , Levin Henry L. 
Published: November 2023

Unique integration patterns of Long Terminal Repeat (LTR)‐retrotransposons and the use of retroviruses in gene therapy have generated great interest in target‐site selection. Initially, the RNA transcripts of retroviruses and retrovirus‐like elements are reverse transcribed into full‐length cDNA copies that are subsequently inserted into the host cell genome. Although integrase (IN), encoded by retroviruses and LTR‐retrotransposons, is responsible for catalyzing the insertion of cDNA into the host genome, it is now clear that a variety of host factors are required for targeting and selection of the integration sites. To understand how retroviruses and LTR‐retrotransposons position their sites of integration in the host genome, we study the LTR‐retrotransposon Tf1 of Schizosaccharomyces pombe. Tf1 integrates with a strong preference for the promoters of RNA pol II transcribed genes. A genetic assay that measures cDNA present in the nucleus allows us to determine whether mutations that reduce transposition frequencies have a direct impact on the process of integration. We utilized these assays to screen a collection of 3,004 S. pombe deletion strains to identify genes that contribute to integration. We found that 181 deletion strains had reduced transposition and 98 of these likely have specific defects in integration. All 98 deletion strains were tested for Tf1 IN and Gag expression using immunoblots. A total of 73 strains had normal levels of IN and GAG proteins, suggesting the deleted genes played a direct role in various steps of Tf1 integration. Candidates that may contribute to integration include factors responsible for DNA repair, transcription activation, signal transduction, and nucleosome structure. We characterized the role of candidate protein H2A.Z (pht1) because this histone variant assembles into the nucleosomes at the promoters of RNA pol II transcribed genes. We found that the reduced transposition of the strain lacking pht1 could be complemented with a plasmid encoding a wild type copy of pht1. In addition, bioinformatics analysis of 73,125 unique Tf1 integration sites demonstrated that the nucleosome‐free regions (NFRs) of promoters were the preferred targets of integration. Nucleosomes with H2A.Z are adjacent the NFR suggesting the possibility that H2A.Z may contribute directly to targeting integration.Support or Funding InformationNICHD/NIH Intramural Research Funding
Transcriptional Activity of TEAD4 Ensures Self‐Renewal of Trophoblast Progenitors during Post‐Implantation Placental Development
Authors: Saha Biswarup , Home Pratik , Gunewardena Sumedha , Paul Soumen 
Published: November 2023

In placental mammals, trophoblast cells are essential for embryo implantation leading to successful progression of pregnancy. During placental development, distinct trophoblast cell types are specified from trophoblast stem cells (TSCs) or TSC‐like progenitors. However, the molecular mechanisms that regulate self‐renewal or differentiation of trophoblast stem/progenitor cells are poorly understood. In this study, we show that transcriptional activity of TEAD4, a TEA domain containing transcription factor, plays a crucial role in promoting cell growth and proliferation of the trophoblast progenitors in post‐implantation developing placenta. TEAD4 is expressed in trophoblast progenitors throughout the placental development and conditional depletion of TEAD4 in post‐implantation mouse embryos result in impaired placental development causing embryonic lethality by embryonic day (E) 9.5. Our global gene expression (RNA‐Seq) analysis with TEAD4‐depleted murine trophoblast stem cells (mTSCs) along with ChIP‐Seq data revealed that TEAD4 directly regulates different cell cycle regulators including multiple Cyclins/CDKs. Our ex‐vivo analysis with mouse ectoplacental cone (EPC) explant cultures confirmed direct TEAD4‐mediated regulation of Cyclins/CDKs in primary trophoblast progenitors and found to be essential for their self‐renewal and expansion. Collectively, our data indicate that TEAD4 plays an essential role in trophoblast cells homeostasis during placental development to prevent placental insufficiency leading to successful pregnancy in mammals.Support or Funding InformationThis project was supported by grants from National Institute of Child Health and Human Development to S.P., HD079363, HD062546 and HD075233.
Investigating the Structural Dynamics of Oncogenic Histone Methyltransferases
Authors: Teichert Kristian Eric , Iacob Roxana E. , Wales Thomas , Paulk Joshiawa , St. Pierre Roodolph , Engen John , Bradner James 
Published: November 2023

Aberrant expression or activity of histone‐modifying enzymes has been linked to a number of cancers, such as multiple myeloma, diffuse‐intrinsic pontine glioma (DIPG), B‐cell lymphomas and others. Drug discovery for inhibitors of histone‐modifying enzymes, such as histone methyltransferases (HMTs) is critical for the well‐being of patients with malignancies involving these enzymes. The structures of several of the histone‐modifying enzymes have been reported, however information regarding their structural dynamics is lacking. We have previously reported that binding of a peptide substrate accelerates the conformational dynamics of a small region of histone methyltransferase NSD2. This insight directed us to investigate the flexibility of several other histone methyltransferases, such as G9A, SUV39H2 and SETD2 with and without their peptide substrates. These data help us to further understand the conformational dynamics of histone methyltransferases and their mechanisms of substrate engagement. Through this understanding, critical regions and movements required for substrate binding can be identified and compared across several HMTs. This insight can be utilized in drug discovery efforts to develop a substrate‐competitive inhibitor to specific histone methyltransferases such as NSD2.Support or Funding InformationNIH R21 CA179159‐01A1