bluuebunny/crossref_metadata_2025_split huggingface dataset:
Levels of Notch-regulated transcription are modulated by tissue movements at gastrulation
Authors: Falo-Sanjuan Julia , Bray Sarah J. 
Published: September 2021

AbstractCells sense and integrate external information from diverse sources that include mechanical cues. Shaping of tissues during development may thus require coordination between mechanical forces from morphogenesis and cell-cell signalling to confer appropriate changes in gene expression. By live-imaging Notch-induced transcription in real time we have discovered that morphogenetic movements duringDrosophilagastrulation bring about an increase in activity-levels of a Notch responsive enhancer. Mutations that disrupt the timing of gastrulation resulted in concomitant delays in transcription up-regulation that correlated with the start of mesoderm invagination. As a similar gastrulation-induced effect was detected when transcription was elicited by the intracellular domain NICD, it cannot be attributed to forces exerted on Notch receptor activation. A Notch independentvndenhancer also exhibited a modest gastrulation-induced activity increase in the same stripe of cells. Together, these observations argue that gastrulation-associated forces act on the nucleus to modulate transcription levels. This regulation was uncoupled when the complex linking the nucleoskeleton and cytoskeleton (LINC) was disrupted, indicating a likely conduit. We propose that the coupling between tissue level mechanics, arising from gastrulation, and enhancer activity represents a general mechanism for ensuring correct tissue specification during development and that Notch dependent enhancers are highly sensitive to this regulation.
CRAM 3.1: Advances in the CRAM File Format
Authors: Bonfield James K 
Published: September 2021

AbstractMotivationCRAM has established itself as a high compression alternative to the BAM file format for DNA sequencing data. We describe updates to further improve this on modern sequencing instruments.ResultsWith Illumina data CRAM 3.1 is 7 to 15% smaller than the equivalent CRAM 3.0 file, and 50 to 70% smaller than the corresponding BAM file. Long-read technology shows more modest compression due to the presence of high-entropy signals.AvailabilityThe CRAM 3.0 specification is freely available from https://samtools.github.io/hts-specs/CRAMv3.pdf. The CRAM 3.1 improvements are available from https://github.com/samtools/hts-specs/pull/433, with OpenSource implementations in HTSlib and HTScodecs.Contactjkb@sanger.ac.ukSupplementary informationSupplementary data are available online
Decoding the Mechanism of Specific RNA Targeting by Ribosomal Methytransferases
Authors: Singh Juhi , Raina Rahul , Vinothkumar Kutti R. , Anand Ruchi 
Published: September 2021

AbstractMethylation of specific nucleotides is integral for ribosomal biogenesis and serves as a common way to confer antibiotic resistance by pathogenic bacteria. Here, by determining the high-resolution structure of 30S-KsgA by cryo-EM, a state was captured, where KsgA juxtaposes between helices h44 and h45, separating them, thereby enabling remodeling of the surrounded rRNA and allowing the cognate site to enter the methylation pocket. With the structure as a guide, factors that direct the enzyme to its cognate site with high fidelity were unearthed by creating several mutant versions of the ribosomes, where interacting bases in the catalytic helix h45 and surrounding helices h44, h24, and h27 were mutated and evaluated for their methylation efficiency. The biochemical studies delineated specificity hotspots that enable KsgA to achieve an induced fit. This study enables the identification of distal exclusive allosteric pocket and other divergent structural elements in each rMTase, which can be exploited to develop strategies to reverse methylation, mediated drug resistance.
Fast and reliable sgRNA efficiency testing using HIReff
Authors: Marks David , Anstatt Jannis , Bachmann Lisa , Villarejo Lucia Gallego , Geidies Alexander , Müller Thorsten 
Published: September 2021

AbstractCRISPR/Cas9 is the method of choice for gene editing like the endogenous knock-in of sequences in order to investigate protein function, abundance or intracellular localization. One of the crucial steps in the preparation of CRISPR/Cas9-mediated knock-ins is the design of sgRNAs, which need to be tested carefully in order to minimize off-target binding and reach highest cleavage efficiency. Usually, sgRNA is evaluated via mismatch cleavage assays, like Surveyor or T7 endonuclease 1 assay. We demonstrate that these methods are often highly cost- and time-intensive with a low sensitivity and high fail rate. As an alternative, we present a new HITI-based sgRNA efficiency (HIReff) test to precisely evaluate sgRNA efficiency. HIReff is based on a sophisticated integration vector with on-site generation of a linear donor fragment that allows a comparably easy read-out via fluorescence signal and integrates several internal controls. Next to a quantifiable sgRNA assessment, HIReff provides additional information on the ‘gene/protein to be studied’ abundance, subcellular localization and promoter activity and allows derivation of fluorescence protein labeled clonal lines. We highlight benefits of HIReff in comparison to commonly used enzyme-based assays and demonstrate improved practicability and high sensitivity, while being less time-, labor- and costintensive at the same time. Our results suggest HIReff as a fast and easy-to-use alternative for sgRNA efficiency testing.
Source-to-Target Automatic Rotating Estimation (STARE) – a publicly-available, blood-free quantification approach for PET tracers with irreversible kinetics: Theoretical framework and validation for [18F]FDG
Authors: Bartlett Elizabeth A , Ogden R Todd , Mann J John , Zanderigo Francesca 
Published: September 2021

ABSTRACTIntroductionFull quantification of positron emission tomography (PET) data requires an input function. This generally means arterial blood sampling, which is invasive, labor-intensive and burdensome. There is no current, standardized method to fully quantify PET radiotracers with irreversible kinetics in the absence of blood data. Here, we present Source-to-Target Automatic Rotating Estimation (STARE), a novel, data-driven approach to quantify the net influx rate (Ki) of irreversible PET radiotracers, that requires only individual-level PET data and no blood data. We validate STARE with [18F]FDG PET and assess its performance using simulations.MethodsSTARE builds upon a source-to-target tissue model, where the tracer time activity curves (TACs) in multiple “target” regions are expressed at once as a function of a “source” region, based on the two-tissue irreversible compartment model, and separates target region Ki from source Ki by fitting the source-to-target model across all target regions simultaneously. To ensure identifiability, data-driven, subject-specific anchoring is used in the STARE minimization, which takes advantage of the PET signal in a vasculature cluster in the FOV that is automatically extracted and partial volume-corrected. To avoid the need for any a priori determination of a single source region, each of the considered regions acts in turn as the source, and a final Ki is estimated in each region by averaging the estimates obtained in each source rotation.ResultsIn a large dataset of [18F]FDG human scans (N=69), STARE Ki estimates were in good agreement with corresponding arterial blood-based estimates (regression slope=0.88, r=0.80), and were precisely estimated, as assessed by comparing STARE Ki estimates across several runs of the algorithm (coefficient of variation across runs=6.74 ± 2.48%). In simulations, STARE Ki estimates were largely robust to factors that influence the individualized anchoring used within its algorithm.ConclusionThrough simulations and application to [18F]FDG PET data, feasibility is demonstrated for STARE blood-free, data-driven quantification of Ki. Future work will include applying STARE to PET data obtained with a portable PET camera and to other irreversible radiotracers.
Synaptotagmin-1-dependent phasic axonal dopamine release is dispensable for basic motor behaviors in mice
Authors: Delignat-Lavaud Benoît , Kano Jana , Ducrot Charles , Massé Ian , Mukherjee Sriparna , Giguère Nicolas , Moquin Luc , Lévesque Catherine , Burke Samuel , Denis Raphaëlle , Bourque Marie-Josée , Tchung Alex , Neto Pedro Rosa- , Lévesque Daniel , Beaumont Louis De , Trudeau Louis-Éric 
Published: September 2021

AbstractIn Parkinson’s disease (PD), motor dysfunctions only become apparent after extensive loss of DA innervation. This resilience has been hypothesized to be due to the ability of many motor behaviors to be sustained through a diffuse basal tone of DA; but experimental evidence for this is limited. Here we show that conditional deletion of the calcium sensor synaptotagmin-1 (Syt1) in DA neurons (Syt1 cKODAmice) abrogates most activity-dependent axonal DA release in the striatum and mesencephalon, leaving somatodendritic (STD) DA release intact. Strikingly, Syt1 cKODAmice showed intact performance in multiple unconditioned DA-dependent motor tasks and even in a task evaluating conditioned motivation for food. Considering that basal extracellular DA levels in the striatum were unchanged, our findings suggest that activity-dependent DA release is dispensable for such tasks and that they can be sustained by a basal tone of extracellular DA. Taken together, our findings reveal the striking resilience of DA-dependent motor functions in the context of a near-abolition of phasic DA release, shedding new light on why extensive loss of DA innervation is required to reveal motor dysfunctions in PD.
Poly (acetyl, arginyl) glucosamine disrupts Pseudomonas aeruginosa biofilms and enhances bacterial clearance in a rat lung infection model
Authors: Garcia Bryan A. , McDaniel Melissa S. , Loughran Allister J. , Johns J. Dixon , Narayanaswamy Vidya , Petty Courtney Fernandez , Birket Susan E. , Baker Shenda M. , Barnaby Roxana , Stanton Bruce A. , Foote Jeremy B. , Rowe Steven M. , Swords W. Edward 
Published: September 2021

AbstractPseudomonas aeruginosa is a common opportunistic pathogen that can cause chronic infections in multiple disease states, including respiratory infections in patients with cystic fibrosis (CF) and non-CF bronchiectasis. Like many opportunists, P. aeruginosa forms multicellular biofilm communities that are widely thought to be an important determinant of bacterial persistence and resistance to antimicrobials and host immune effectors during chronic/recurrent infections. Poly (acetyl, arginyl) glucosamine (PAAG) is a glycopolymer which has antimicrobial activity against a broad range of bacterial species, and also has mucolytic activity which can normalize rheologic properties of cystic fibrosis mucus. In this study, we sought to evaluate the effect of PAAG on P. aeruginosa bacteria within biofilms in vitro, and in the context of experimental pulmonary infection in a rodent infection model. PAAG treatment caused significant bactericidal activity against P. aeruginosa biofilms, and a reduction in the total biomass of preformed P. aeruginosa biofilms on abiotic surfaces, as well as on the surface of immortalized cystic fibrosis human bronchial epithelial cells. Studies of membrane integrity indicated that PAAG causes changes to P. aeruginosa cell morphology and dysregulates membrane polarity. PAAG treatment reduced infection and consequent tissue inflammation in experimental P. aeruginosa rat infections. Based on these findings we conclude that PAAG represents a novel means to combat P. aeruginosa infection, which may warrant further evaluation as a therapeutic.
Human - murine concordance of molecular signatures in nerve-sparing murine partial bladder outlet obstruction (NeMO)
Authors: Sidler Martin , Ahmed Abdalla , Jiang Jia-Xin , Koshkebaghi Dursa , Yadav Priyank , Davani Dariush , Huang Ryan , Weksberg Rosanna , Delgado-Olguin Paul , Aitken KJ , Bägli Darius 
Published: September 2021

ABSTRACTRecently we demonstrated the utility of a nerve-sparing mid-urethra model of partial outlet obstruction (NeMO) that has high consistency and minimal mortalities, unlike the traditional model proximal to the bladder neck. Our goal was to uncover potential therapeutic targets by investigating the genome wide transcriptional changes and pathways altered in NeMO to compare with published human bladder obstruction data. We performed RNAseq and analysed the differentially upregulated and downregulated genes for associated pathways, transcription factor binding site analysis (TFBS), upstream regulators and Gene Set Enrichment Analysis (GSEA). NeMO increased bladder mass, relative bladder mass and hyperactivity, and decreased voiding efficiency. In NeMO vs. sham, 831 genes were differentially expressed (adjusted p<0.05) and correlated significantly with at least one physiologic parameter. Gene ontology revealed an enrichment for matrix pathways in the upregulated genes, and for cardiac contraction, oxidative phosphorylation and pyruvate metabolism in downregulated genes. TFBS analysis revealed a differential regulation of up vs downregulated genes, with KLF4 strongly associated with the downregulated genes. Downregulated genes of Human bladder obstruction were also associated with the TFBS of KLF4. GSEA of the NeMO gene set confirmed the DAVID results, but also showed a cluster of cytokine activation genes. In human bladder underactive obstruction, cytokines were also highly upregulated. The common cytokine pathway upregulation provided an example of the use of RNAseq for uncovering potential new therapeutic targets. As TNF and the innate immune pathways were strongly implicated in both human and mouse, and TNF is produced by macrophages, we depletion macrophages with clodronate (CL) during NeMO. Although CL did not block hypertrophy, it significantly decreased NeMO-induced hyperactive voiding (p<0.01) and increased voiding efficiency (p<0.05). The expression of several cytokines/chemokines correlated significantly with bladder functional parameters such as residual volumes, and hyperactivity. Conclusions: Gene expression signatures of NeMO were consistent with human bladder obstruction, supporting the use of the nerve-sparing mouse obstruction model for therapeutic exploration.
Adenylate kinase 1 overexpression increases locomotor activity in medaka fish
Authors: Maruyama Michiyo , Furukawa Yuko , Kinoshita Masato , Mukaiyama Atsushi , Akiyama Shuji , Yoshimura Takashi 
Published: September 2021

AbstractMaintenance of the energy balance is indispensable for cell survival and function. Adenylate kinase (Ak) is a ubiquitous enzyme highly conserved among many organisms. Ak plays an essential role in energy regulation by maintaining adenine nucleotide homeostasis in cells. However, its role at the whole organism level, especially in animal behavior, remains unclear. Here, we established a model using medaka fish (Oryzias latipes) to examine the function of Ak in environmental adaptation. Medaka overexpressing the major Ak isoform Ak1 exhibited increased locomotor activity compared to that of the wild type. Interestingly, this increase was temperature dependent. Our findings suggest that cellular energy balance can modulate locomotor activity.
Dual domain recognition determines SARS-CoV-2 PLpro selectivity for human ISG15 and K48-linked di-ubiquitin
Authors: Wydorski Pawel M. , Osipiuk Jerzy , Lanham Benjamin T. , Tesar Christine , Endres Michael , Engle Elizabeth , Jedrzejczak Robert , Mullapudi Vishruth , Michalska Karolina , Fidelis Krzysztof , Fushman David , Joachimiak Andrzej , Joachimiak Lukasz A. 
Published: September 2021

ABSTRACTThe Papain-like protease (PLpro) is a domain of a multi-functional, non-structural protein 3 of coronaviruses. PLpro cleaves viral polyproteins and posttranslational conjugates with poly-ubiquitin and protective ISG15, composed of two ubiquitin-like (UBL) domains. Across coronaviruses, PLpro showed divergent selectivity for recognition and cleavage of posttranslational conjugates despite sequence conservation. We show that SARS-CoV-2 PLpro binds human ISG15 and K48-linked di-ubiquitin (K48-Ub2) with nanomolar affinity and detect alternate weaker-binding modes. Crystal structures of untethered PLpro complexes with ISG15 and K48-Ub2combined with solution NMR and cross-linking mass spectrometry revealed how the two domains of ISG15 or K48-Ub2are differently utilized in interactions with PLpro. Analysis of protein interface energetics predicted differential binding stabilities of the two UBL/Ub domains that were validated experimentally. We emphasize how substrate recognition can be tuned to cleave specifically ISG15 or K48-Ub2modifications while retaining capacity to cleave mono-Ub conjugates. These results highlight alternative druggable surfaces that would inhibit PLpro function.
E3 ligase TRIM47 positively regulates endothelial activation and pulmonary inflammation through potentiating the K63-linked ubiquitination
Authors: Qian Yisong , Wang Ziwei , Lin Hongru , Lei Tianhua , Zhou Zhou , Huang Weilu , Wu Xuehan , Zuo Li , Wu Jie , Liu Yu , Wang Ling-Fang , Guan Xiao-Hui , Deng Ke-Yu , Fu Mingui , Xin Hong-Bo 
Published: September 2021

AbstractEndothelial activation plays an essential role in the pathology of sepsis-induced acute lung injury, but the detailed regulatory mechanisms remain largely unknown. Here, we demonstrated that TRIM47, an ubiquitin E3 ligase of tripartite protein family, is highly expressed in vascular endothelial cells and is up-regulated during TNFα-induced endothelial activation. Knockdown of TRIM47 in endothelial cells prevents the transcription of multiple pro-inflammatory cytokines, reduces monocyte adhesion and the expression of adhesion molecules, and inhibits the secretion of IL-1β and IL-6 into the supernatant. By contrast, overexpression of TRIM47 promotes inflammatory response and monocyte adhesion upon TNFα stimulation. TRIM47 modulates the activation of NF-κB and MAPK signaling pathways during endothelial activation. Further experiment confirmed that TRIM47 interacts with TRAF2 and mediates K63-linked ubiquitination. In addition, TRIM47-deficient mice are more resistant to lipopolysaccharide-induced acute lung injury and death, due to attenuated pulmonary inflammation. Taken together, our studies suggest that TRIM47 promotes pulmonary inflammation and injury at least partly through potentiating the K63-linked ubiquitination of TRAF2, which in turn activates NF-κB and MAPK signaling pathways to trigger inflammatory response in endothelial cells.
PL1 Peptide Engages Acidic Surfaces on Tumor-Associated Fibronectin and Tenascin Isoforms to Trigger Cellular Uptake
Authors: Lingasamy Prakash , Põšnograjeva Kristina , Kopanchuk Sergei , Tobi Allan , Rinken Ago , General Ignacio J. , Asciutto Eliana K. , Teesalu Tambet 
Published: September 2021

AbstractTumor extracellular matrix (ECM) is a high-capacity and genetically stable target for the precision delivery of affinity ligand-guided drugs and imaging agents. Recently, we developed a PL1 peptide (sequence: PPRRGLIKLKTS) for systemic targeting of malignant ECM. Here we map the dynamics of PL1 binding to its receptors Fibronectin Extra Domain B (FN-EDB) and Tenascin C C-isoform (TNC-C) by computational modeling and cell-free binding studies on mutated receptor proteins, and study cellular binding and internalization of PL1 nanoparticles in cultured cells. Molecular dynamics simulation and docking analysis suggested that the engagement of PL1 peptide with both receptors is primarily driven by electrostatic interactions. Substituting acidic amino acid residues with neutral amino acids at predicted PL1 binding sites in FN-EDB (D52N-D49N-D12N) and TNC-C (D39N-D45N) resulted in the loss of binding of PL1 nanoparticles. Remarkably, PL1-functionalized nanoparticles (NPs) were not only deposited on the target ECM but bound the cells and initiated a robust cellular uptake via a pathway resembling macropinocytosis. Our studies establish the mode of engagement of the PL1 peptide with its receptors and suggest applications for intracellular delivery of nanoscale payloads. The outcomes of this work can be used for the development of PL1-derived peptides with improved stability, affinity and specificity for precision targeting of the tumor ECM and malignant cells.One Sentence SummaryPL1 peptide is recruited to the acidic surfaces on oncofetal fibronectin EDB and tenascin C-C isoform, triggering cellular uptake of PL1-functionalized nanoparticles.
Ownership structure, board characteristics and dividend policy: evidence from Turkey
Authors: Khan Ajab 
Published: September 2021

PurposeThis study aims to investigate the impact of ownership structure and board characteristics on dividend policy in the listed Turkish firms between 2013 and 2019.Design/methodology/approachThis study uses the probability of paying dividends, dividend payout ratio and dividend yield measures. The suitable regression procedures (logit, probit and Tobit models) are used to examine the research hypotheses by focusing on a panel data set drawn from the Borsa Istanbul (BIST) 100 index, excluding financial and utility firms.FindingsThe empirical findings indicate that institutional and concentrated ownerships are significant and positively associated with dividend payouts, whereas family ownership does not influence dividend policy. On the other end, board size is positive, while chief executive officer duality is negatively related to dividend policy. Additionally, the female directors and board independence are insignificant in influencing firms to pay high dividends.Research limitations/implicationsFuture researchers can validate this paper’s findings by considering the stock dividends as well. Additionally, future researchers may investigate the relationship between these constructs by extending the sample size of firms listed on BIST or in other emerging markets.Practical implicationsThis study’s findings may serve policymakers, regulators, investors and academic researchers to get valuable guidance from relevant literature. The Turkish firms may improve dividend policy by implementing the regulatory framework introduced by the Capital Markets Law in 2012 for effective monitoring and protecting the minority shareholders’ rights. The controlling shareholders may alleviate principal-principal conflicts by ensuring the independence of directors and increasing the number of female directors according to the critical mass of at least 30% of board members.Originality/valueThis study contributes to agency theory and signaling theory by considering ownership structure and board attributes among Turkish firms related to dividend payments.