bluuebunny/crossref_metadata_2025_split huggingface dataset:
Brain natriuretic peptide improves heart regeneration after infarction by stimulating cardiomyocyte renewal
Authors: Bon-Mathier Anne-Charlotte , Déglise Tamara , Rignault-Clerc Stéphanie , Bielmann Christelle , Mazzolai Lucia , Rosenblatt-Velin Nathalie 
Published: July 2022

ABSTRACTAimBrain Natriuretic Peptide (BNP) supplementation after infarction increases heart function and decreases heart remodeling. BNP receptors, NPR-A and NPR-B, are expressed on adult cardiomyocytes (CMs). We thus investigated whether a part of the BNP cardioprotective effect in infarcted and unmanipulated hearts is due to modulation of the CM fate.Methods and ResultsBNP was injected in infarcted adult mice and in unmanipulated neonatal and adult mice. CMs were isolated, counted and characterized.Increased number of CMs was detected in the hypoxic area of infarcted hearts, and in unmanipulated neonatal and adult hearts after BNP treatment. Accordingly, Troponin T plasma concentration was significantly reduced 1 and 3 days after infarction in BNP-treated mice, demonstrating less CM death. Furthermore, higher number of small, dedifferentiated and mononucleated CMs were identified in adult BNP-treated hearts when compared to saline-treated hearts. BNP-treated CMs express higher levels of mRNAs coding forhif1 alphaand for the different cyclins than CMs isolated from saline-treated hearts. Higher percentages of CMs undergoing DNA synthesis, expressing Ki67, phospho histone3 and Aurora B were detected in all BNP-treated hearts, which suggests that BNP stimulates CMs to re-enter to the cell cycle. Resultsin vitroconfirmed that BNP stimulates the proliferation of the neonatal CMs and the dedifferentiation of the adult CMs.BNP effect on adult CMsin vivois mediated by NPR-A binding and activation of the ERK MAP kinase pathway. Interestingly, increased number of CMs was also detected in adult infarcted hearts treated with LCZ696, which inhibits all natriuretic peptide degradations.ConclusionsAltogether, our results identified BNP and all therapies aimed to increase BNP’s bioavailability (such as LCZ696 treatment) as new targets to increase heart regeneration. By protecting CMs from cell death, and by stimulating their proliferation, BNP treatment leads to increased number of CMs in neonatal, adult unmanipulated and infarcted hearts.
Establishment of a novel fetal ovine heart cell line by spontaneous cell fusion
Authors: Suleiman Khalid M. , Aljulidan Mutaib M. , Hussein Gamal eldin M. , Alkhalaf Habib N. 
Published: July 2022

AbstractWe established a unique immortal cell line designated, FOH-SA, by serial passage of fetal ovine heart cells. In a novel phenomenon in cell biology, we demonstrated that the immortalization of the line supervened as a result of spontaneous cellular and nuclear fusion of two morphologically distinct cardiocytes in passage 29. Fused cells gave progeny cells which grew into multicellular filaments. Trypsinization of the filamentous multicellular growth gave the immortal heart cell line.Comparative single nucleotide polymorphism (SNP) genotyping of the cell line before and after cell fusion revealed a large scale genetic conversion resulting in 96% homozygosity in SNPs genotypes in the progeny cells. Partial sequencing of the mitochondrial (mt) genome of the cell line revealed the occurrence of large mutational events in the control region, thetRNA-Pheand12S rRNAgenes of the mt genome of progeny cells. The cell line was found permissive to sheep pox, peste des petits ruminants (PPR), lumpy skin disease (LSD), rift valley fever (RVF), and camel pox viruses.This study would resolve the over half a century mystery of how the African Green Monkey cell line (VERO) had evolved. We authenticated the cell line at the European Collection of Authenticated Cell Cultures (ECACC) and deposited it at the American Type Culture Collection (ATCC) for the purpose of patenting under the Budapest Treaty.
Diagnostic tool to identify and treat DNA repair deficient gastroesophageal adenocarcinomas
Authors: Prosz Aurel , Sahgal Pranshu , Morris Clare X. , Sztupinszki Zsofia , Börcsök Judit , Diossy Miklos , Tisza Viktoria , Spisak Sandor , Rusz Orsolya , Csabai Istvan , Huffman Brandon M. , Singh Harshabad , Lazaro Jean-Bernard , Cecchini Michael , Cleary James M. , Szallasi Zoltan , Sethi Nilay S. 
Published: July 2022

ABSTRACTBackground and aimsDNA repair deficiency is a common feature of cancer. Homologous recombination (HR) and nucleotide excision repair (NER) are the two most frequently disabled DNA repair pathways in solid tumors. HR deficient breast, ovarian, pancreatic and prostate cancers respond well to platinum chemotherapy and PARP inhibitors. However, the frequency of DNA repair pathway deficiency in gastric and esophageal adenocarcinoma (GEA) still lacks diagnostic and functional validation. Furthermore, whether DNA repair deficient GEA have enhanced responsiveness to platinum chemotherapy and sensitivity to PARP inhibitors is not well characterized.MethodsUsing whole exome and genome sequencing data, we measured various HR deficiency-associated mutational signatures in patient specimen of gastric, esophageal and colorectal cancer specimens and gastric cancer cell lines. Gold-standard immunofluorescence assays were used to confirm HR and NER deficiency in cancer cell lines. The relationship between PARP inhibitor treatment and tumor response was evaluated in patients with gastric cancer. Drug sensitivity was determined using standard in vitro cell culture assays. Single-cell RNA-sequencing was performed to evaluate gastric cancer response to commonly used chemotherapeutics.ResultsWe found that a significant subset of GEA, but very few colorectal tumors, show evidence of HR deficiency by mutational signature analysis (HRD score). Gastric cancer cell lines with high HRD mutational signature scores demonstrated functional HR deficiency by RAD51 assay and increased sensitivity to platinum and PARP inhibitors. There was a positive association between HRD scores and tumor response in patients with gastric cancer treated with a PARP inhibitor on a clinical trial. A gastric cancer cell line with strong sensitivity to cisplatin showed HR proficiency but exhibited NER deficiency by DDB2 proteo-probe assay. Single-cell RNA-sequencing revealed that, in addition to inducing general apoptosis, cisplatin treatment triggered ferroptosis in a NER-deficient gastric cancer, which may explain the outlier sensitivity.ConclusionA subset of upper gastrointestinal tumors have genomic features of HR and NER deficiency and therefore may be more likely to benefit from platinum chemotherapy and PARP inhibition.
Expanding the scope of bacterial CRISPR activation with PAM-flexible dCas9 variants
Authors: Kiattisewee Cholpisit , Karanjia Ava V. , Legut Mateusz , Daniloski Zharko , Koplik Samantha E. , Nelson Joely , Kleinstiver Benjamin P. , Sanjana Neville E. , Carothers James M. , Zalatan Jesse G. 
Published: July 2022

AbstractCRISPR-Cas transcriptional tools have been widely applied for programmable regulation of complex biological networks. In comparison to eukaryotic systems, bacterial CRISPR activation (CRISPRa) has stringent target site requirements for effective gene activation. While genes may not always have an NGG PAM at the appropriate position, PAM-flexible dCas9 variants can expand the range of targetable sites. Here we systematically evaluate a panel of PAM-flexible dCas9 variants for their ability to activate bacterial genes. We observe that dxCas9-NG provides a high dynamic range of gene activation for sites with NGN PAMs while dSpRY permits modest activity across almost any PAM. Similar trends were observed for heterologous and endogenous promoters. For all variants tested, improved PAM-flexibility comes with the tradeoff that CRISPRi-mediated gene repression becomes less effective. Weaker CRISPRi gene repression can be partially rescued by expressing multiple sgRNAs to target many sites in the gene of interest. Our work provides a framework to choose the most effective dCas9 variant for a given set of gene targets, which will further expand the utility of CRISPRa/i gene regulation in bacterial systems.
Aberrant extracellular matrix and cardiac development in models lacking the PR-DUB component ASXL3
Authors: McGrath BT , Tsan YC , Salvi S , Ghali N , Martin DM , Hannibal M , Keegan CE , Helms A , Srivastava A , Bielas SL 
Published: July 2022

ABSTRACTBackgroundClinical and research based genetic testing has uncovered genes that encode chromatin modifying complex components required for organogenesis. Covalent histone modifications play a key role in establishing transcriptional plasticity during development, required for cell fate specification, and have been implicated as a developmental mechanism that accounts for autism spectrum disorder (ASD) and CHD co-occurrence. ASXL3 has been identified as a high confidence ASD gene. ASXL3 is a component of the Polycomb Repressive Deubiquitination (PR-DUB) complex, which deubiquitinates histone H2A. However, the role of ASXL3 in cardiac development remains unknown.MethodsWe used CRISPR/Cas9 gene editing to generate clinically relevant Asxl3 frameshift alleles in a mouse model and human embryonic stem cells (hESCs). To evaluate ASXL3 function in developing hearts, we performed structural, molecular, immunostaining and histological analyses. Transcriptomic and cellular compositional changes were assessed with bulk RNA sequencing of mouse hearts and single-cell RNA sequencing (scRNA-seq) of human cardiac tissue differentiated from isogenic hESC lines.ResultsBiallelic genetic inactivation of Asxl3 leads to perinatal lethality and increased levels of histone H2A mono-ubiquitination, which are regulated by PR-DUB. Asxl3+/fs and Asxl3fs/fs mice display cardiac abnormalities including ventricular hypoplasia, septal defects, and bifid cardiac apex with variable penetrance. The presence of underdeveloped ventricles is preceded by increased progenitor proliferation in the ventricles, as determined by EdU incorporation. Differential gene expression, assessed by bulk RNA sequencing implicates extracellular matrix dysfunction as a pathogenic mechanism. This correlates with a reduction in vimentin-positive cardiac fibroblasts. scRNA-seq of cardiac cultures differentiated from human ASXL3fs/fs ESC lines exhibit altered ratios of cardiac fibroblasts and cardiomyocytes. Similar to the mouse data, genes essential for extracellular matrix composition and signaling are differentially expressed between ASXL3+/+ and ASXL3fs/fs human in vitro differentiated cardiac tissue. The observed transcriptomic changes predict diminished cell-cell signaling interactions between cardiac fibroblasts and cardiomyocyte progenitors in ASXL3 cultures.ConclusionsCollectively, our data implicates species-specific roles for ASXL3 in both human and mouse cardiac development. These results highlight the role of extracellular matrix gene programs by cardiac fibroblast during cardiomyocyte development and provide insight into mechanisms of altered cardiogenesis by autism risk genes.
Crossmodal reorganization in deaf auditory cortices compensates for the impaired body-centered visuomotor transformation after early deafness
Authors: Song Li , Wang Pengfei , Li Hui , Weiss Peter H. , Fink Gereon R. , Zhou Xiaolin , Chen Qi 
Published: July 2022

AbstractEarly deafness leads to the reorganization of large-scale brain networks, involving and extending beyond the auditory system. Body-centered visuomotor transformation is impaired after early auditory deprivation, associated with a hyper-crosstalk between the task-critical frontoparietal network (FPN) and the default-mode network (DMN). It remains to be elucidated, how the reorganized functional connectivity between the auditory system, the FPN, and the DMN contributes to the impaired visuomotor transformation after early deafness. In this fMRI study, we asked early deaf participants and hearing controls to judge the spatial location of a visual target, either about the middle-sagittal line of their own body (the egocentric task) or another background object (the allocentric task). The bilateral superior temporal gyrus (STG) in the deaf group exhibited cross-modal reorganization, with generally enhanced neural activity during the visual tasks, compared to hearing controls. Moreover, the STG showed significantly increased functional connectivity with both the FPN and the DMN in the deaf group compared to hearing controls, specifically during the egocentric task. The increased STG-FPN and STG-DMN coupling, however, showed antagonistic effects on the egocentric performance of the deaf participants. The increased STG-FPN connectivity was associated with improved (i.e., a beneficial role) while the increased STG-DMN with deteriorated (i.e., a detrimental role) egocentric performance in the deaf participants. No such effect was observed in hearing controls. Therefore, the auditory cortex is reorganized to functionally resemble the FPN in the deaf brain, representing compensatory neuroplasticity to mitigate the impaired visuomotor transformation after early deafness.Significance StatementOur brain constantly plans vision-guided actions, transforming visuospatial representations of external visual targets into visuomotor representations. The frontoparietal network (FPN) critically supports this visuomotor transformation process, which is impaired after early deafness. To mitigate the impaired visuomotor transformation, the ‘deaf’ auditory cortex in the bilateral superior temporal gyrus (STG) shows compensatory cross-modal reorganization that functionally resembles the FPN regions. Specifically, the deaf auditory cortex becomes functionally coupled with the dorsal FPN regions. The stronger the STG-FPN coupling, the more improved the deaf adults’ visuomotor transformation performance, indicating the reorganized STG as a critical node of the task-critical network. Correspondingly, increased coupling between the task-critical deaf STG and the default-mode network impairs the visuomotor transformation.
A case of mycobacteriosis associated with Mycobacterium pseudoshottsii in aquarium-reared fish in Japan
Authors: Komine Takeshi , Hyogo Ihara , Kentaro Ono , Yoshida Mitsumi , Sugimoto Yuma , Inohana Mari , Fukano Hanako , Kurata Osamu , Wada Shinpei 
Published: July 2022

AbstractIn 2019, several aquarium-reared fish died at a sea life park in Japan. Necropsy revealed micronodules on the spleen in the dotted gizzard shad (Konosirus punctatus). Seven of 16 fish exhibited microscopic multifocal granulomas associated with acid-fast bacilli in the spleen, kidney, liver, alimentary tract, mesentery, gills, and/or heart. Bacterial cultures yielded isolates from the dotted gizzard shad and a Japanese sardine (Sardinops melanostictus). Microbiological examination, multilocus sequence typing analysis, and variable number of tandem repeats analysis with a newly proposed 6-loci set revealed the isolates as Mycobacterium pseudoshottsii. To our knowledge, this is the first isolation of M. pseudoshottsii from aquarium-reared fish.
Bridging the gap between in vitro and in silico single-molecule force spectroscopy
Authors: Gomes Diego E. B. , Melo Marcelo C. R. , Gomes Priscila S. F. C. , Bernardi Rafael C. 
Published: July 2022

AbstractStaphylococci bacteria use an arsenal of virulence factors, mainly composed of proteins such as adhesins, to target and adhere to their host. Adhesins play critical roles during infection, mainly during the early steps of adhesion when cells are exposed to high mechanical stress. S. epidermidis SdrG:Fgβ force resilience has been investigated using AFM-based single molecule force spectroscopy experiments paired with steered molecular dynamics (SMD) simulations. However, there is still a gap between both kinds of experiments at high force-loading rates. Here, we leveraged the high-speed of coarse-grained (CG) SMD simulations to bridge the gap between the data obtained in vitro and in silico with all-atom SMD. We used the DHS theory to connect the two types of SMD simulations and the predictions are consistent with theory and experimentation. We believe that, when associated with all-atom SMD, course-grained SMD can be a powerful ally to help explain and complement the results of single-molecule force spectroscopy experiments.
WNT4 regulates cellular metabolism via intracellular activity at the mitochondria in breast and gynecologic cancers
Authors: Sottnik Joseph L. , Shackleford Madeleine T. , Villagomez Fabian R. , Bahnassy Shaymaa , Oesterreich Steffi , Hu Junxiao , Madak-Erdogan Zeynep , Riggins Rebecca B. , Corr Bradley R. , Cook Linda S. , Treviño Lindsey S. , Bitler Benjamin G. , Sikora Matthew J. 
Published: July 2022

ABSTRACTWnt ligand WNT4 is critical in female reproductive tissue development, with WNT4 dysregulation linked to related pathologies including breast cancer (invasive lobular carcinoma, ILC) and gynecologic cancers. WNT4 signaling in these contexts is distinct from canonical Wnt signaling yet inadequately understood. We previously identified atypical intracellular activity of WNT4 (independent of Wnt secretion) regulating mitochondrial function, and herein examine intracellular functions of WNT4. We further examine how convergent mechanisms ofWNT4dysregulation impact cancer metabolism. In ILC,WNT4is co-opted by estrogen receptor α (ER) via genomic binding inWNT4intron 1, while in gynecologic cancers, a common genetic polymorphism (rs3820282) at this ER binding site altersWNT4regulation. Using proximity biotinylation (BioID), we show canonical Wnt ligand WNT3A is trafficked for secretion, but WNT4 is localized to the cytosol and mitochondria. We identified DHRS2, mTOR, and STAT1 as putative WNT4 cytosolic/mitochondrial signaling partners. Whole metabolite profiling, and integrated transcriptomic data, support that WNT4 mediates metabolic reprogramming via fatty acid and amino acid metabolism. Further, ovarian cancer cell lines with rs3820282 variant genotype are WNT4-dependent and have active WNT4 metabolic signaling. In protein array analyses of a cohort of 103 human gynecologic tumors enriched for patient diversity, germline rs3820282 genotype is associated with metabolic remodeling. Variant genotype tumors show increased AMPK activation and downstream signaling, with the highest AMPK signaling activity in variant genotype tumors from non-White patients. Taken together, atypical intracellular WNT4 signaling, in part via genetic dysregulation, regulate the distinct metabolic phenotypes of ILC and gynecologic cancers.SignificanceWNT4 regulates breast and gynecologic cancer metabolism via a previously unappreciated intracellular signaling mechanism at the mitochondria, with WNT4 mediating metabolic remodeling. Understanding WNT4 dysregulation by estrogen and genetic polymorphism offers new opportunities for defining tumor biology, precision therapeutics, and personalized cancer risk assessment.
mdciao: Accessible Analysis and Visualization of Molecular Dynamics Simulation Data
Authors: Pérez-Hernández Guillermo , Hildebrand Peter. W. 
Published: July 2022

ABSTRACTWe present mdciao, an open-source command line tool and Python Application-Programmers-Interface (API) for easy, one-shot analysis and representation of molecular dynamics (MD) simulation data. Building upon the widely used concept of residue-residue contact-frequencies, mdciao offers a wide spectrum of further analysis and representations, enriched with domain specific annotations when possible. It tries offer a user-friendly interface, which simplifies most decisions for non-expert users, while keeping customizability for expert ones. Emphasis has been put into automatically producing annotated, paper-ready figures and tables. Furthermore, seamless on-the-fly query and inclusion of consensus nomenclatures for GPCR, G-proteins, and kinases is made possible through the respective online databases, which allows for bulk selection and comparison across different systems. Finally, the fully documented Python API allows users to include the basic or advanced mdciao functions in their analysis workflows, and provides numerous examples and Jupyter Notebook Tutorials. The source code is published under the GNU Lesser General Public License v3.0 or later and hosted on https://github.com/gph82/mdciao.
A fluorescently labelled quaternary ammonium compound (NBD-DDA) to study mode-of-action and resistance mechanisms in bacteria
Authors: Nordholt Niclas , O’Hara Kate , Resch-Genger Ute , Blaskovich Mark A. T. , Rühle Bastian , Schreiber Frank 
Published: July 2022

AbstractQuaternary ammonium compounds (QACs) are widely used as active agents in disinfectants, antiseptics, and preservatives. Despite being in use since the 1940s, there remain multiple open questions regarding their detailed mode-of-action and the mechanisms, including phenotypic heterogeneity, that can make bacteria less susceptible to QACs. To facilitate mode-of-action studies, we synthesized a fluorescent analogue of the quaternary ammonium compound benzalkonium chloride, namely N-dodecyl-N,N-dimethyl-[2-[(4-nitro-2,1,3-benzoxadiazol-7-yl)amino]ethyl]azanium-iodide (NBD-DDA). NBD-DDA is readily detected by flow cytometry and fluorescence microscopy with standard GFP/FITC-settings, making it suitable for molecular and single-cell studies. NBD-DDA was then used to investigate resistance mechanisms which can be heterogeneous among individual bacterial cells. Our results reveal that the antimicrobial activity of NBD-DDA against E. coli, S. aureus and P. aeruginosa is comparable to that of benzalkonium chloride (BAC), a widely used QAC. Characteristic time-kill kinetics and increased tolerance of a BAC tolerant E. coli strain against NBD-DDA suggest that the mode of action of NBD-DDA is similar to that of BAC. Leveraging these findings and NBD-DDA’s fluorescent properties, we show that reduced cellular adsorption is responsible for the evolved BAC tolerance in the BAC tolerant E. coli strain. As revealed by confocal laser scanning microscopy (CLSM), NBD-DDA is preferentially localized in the cell envelope of E. coli, which is a primary target of BAC and other QACs. Overall, NBD-DDA’s antimicrobial activity, its fluorescent properties, and its ease of detection render it a powerful tool to study the mode-of-action and the resistance mechanisms of QACs in bacteria.
HMGN5, an RNA or Nucleosome binding protein - potentially switching between the substrates to regulate gene expression
Authors: Araya Ingrid , Nardocci Gino , Schwartz Uwe , Babl Sabrina , Barros Miriam , Carrasco-Wong Ivo , Imhof Axel , Montecino Martín , Längst Gernot 
Published: July 2022

AbstractThe packaging of DNA into chromatin and its compaction within cells renders the underlying DNA template un-accessible for processes like transcription, replication and repair. Active mechanisms as chromatin modifying activities or the association with non-coding RNAs can de-condense chromatin, rendering it accessible for the DNA dependent processes. High mobility group proteins (HMG) are small architectural chromatin proteins that were shown to contribute to the regulation of chromatin accessibility and condensation. Here we show that HMGN5, a member of the HMGN family that is capable to de-compact chromatin exhibits a novel RNA binding domain that overlaps with its nucleosome binding domain (NBD). HMGN5 binds exclusively to nucleosomes or RNA, suggesting that molecular function relies on switching between these two substrates. We show the specific binding of HMGN5 to regulatory regions and at the same time to bind the RNA of the genes it tends to activate. Furthermore, HMGN5 co-localizes and directly interacts with CTCF, suggesting a cooperative role of both proteins in organizing higher order structures of chromatin and active chromatin domains.