bluuebunny/crossref_metadata_2025_split huggingface dataset:
Coiling of cellular protrusions around extracellular fibers
Authors: Sadhu Raj Kumar , Hernandez-Padilla Christian , Eisenbach Yael Eshed , Zhang Lixia , Vishwasrao Harshad D , Behkam Bahareh , Shroff Hari , Iglič Aleš , Peles Elior , Nain Amrinder S. , Gov Nir S 
Published: May 2022

Protrusions at the leading-edge of a cell play an important role in sensing the extracellular cues, during cellular spreading and motility. Recent studies provided indications that these protrusions wrap (coil) around the extra-cellular fibers. The details of this coiling process, and the mechanisms that drive it, are not well understood. We present a combined theoretical and experimental study of the coiling of cellular protrusions on fibers of different geometry. Our theoretical model describes membrane protrusions that are produced by curved membrane proteins that recruit the protrusive forces of actin polymerization, and identifies the role of bending and adhesion energies in orienting the leading-edges of the protrusions along the azimuthal (coiling) direction. Our model predicts that the cell’s leading-edge coils on round fibers, but the coiling ceases for a fiber of elliptical (flat) cross-section. These predictions are verified by 3D visualization and quantitation of coiling on suspended fibers using Dual-View light-sheet microscopy (diSPIM). Overall, we provide a theoretical framework supported by high spatiotemporal resolution experiments capable of resolving coiling of cellular protrusions around extracellular fibers of varying diameters.Significance StatementCells adhere and migrate in environments that are composed of fibrous structures, such as the thin filaments of the extracellular matrix, or the wider axons and dendrites of neurons. In recent experiments, cells have been observed to form leading edge protrusions on such surfaces, that seem to coil around the extracellular fibers. However, the mechanism responsible for the formation of such coiling protrusions is not understood. Here, we provide a combined experimental and theoretical approach to explain the emergence of coiling protrusions. Our model is based on the self-organization of curved proteins that recruit actin polymerization at the leading edge of the cell, when spreading over an adhesive fiber.
Decreased miRNA-148a-3p expression in skeletal muscle of patients with chronic kidney disease
Authors: Robinson KA , Baker LA , Graham-Brown MPM , Ashford RU , Pawlyckz Izabella , Major RW , Burton JO , Sylvius N. , Cooper A , Philp A , Watson EL 
Published: May 2022

AbstractIntroductionSkeletal muscle wasting is a common complication of chronic kidney disease which leads to a loss of muscle function. The pathogenesis of skeletal muscle wasting is incompletely understood, which is preventing the development of targeted therapeutics. Recent evidence implicates miRNAs in the of skeletal muscle wasting. Our aim was to firstly examine miRNA profiles of CKD human skeletal muscle for the identification of aberrant expression patterns compared to a healthy control (HC) cohort, and secondly, investigate the role these miRNAs may play in inducing or promoting skeletal muscle atrophy using a novel human primary skeletal muscle cell model of CKD skeletal muscle.MethodsFor the comparison between CKD and HC populations, skeletal muscle biopsies were collected from the vastus lateralis of n=15 non-dialysis dependent CKD patient’s stage 3b-5 CKD patients, and n=15 healthy controls matched for age, gender and physical activity. n=5 biopsies from each group underwent next generation sequencing to obtain complete microRNA profiles in CKD vs HC cohorts, which were then validated in a separate cohort by PCR (N=10 in each group). A causative role in muscle wasting was determined by transfection of key microRNAs into a primary culture model of CKD skeletal muscle and changes in protein degradation determined by L-[3H]- phenylalanine release into the media.ResultsNext Generation Sequencing identified differential expression of 16 miRNAs in skeletal muscle of CKD patients versus controls, and PCR validation confirmed miRNA-148a-3p expression was significantly decreased in CKD patients. The reduced miRNA-148a-3p expression was also maintained in the primary culture model. Upon overexpression of miRNA-148a-3p in CKD myotubes, protein degradation rates were decreased non-significantly (p=0.28) by 16.3% compared to un-transfected CKD cells.ConclusionCKD was associated with a significant reduction in miRNA-148a-3p expression in skeletal muscle compared to non-CKD controls which was retained in our in vitro model. Overexpression of miRNA-148a-3p in primary skeletal myotubes non-significantly decreased muscle protein degradation by 16.3%. In order to determine the importance of miRNA-148a-regulation of protein degradation, a deeper understanding of miRNA-148a-3p targets and their associated pathways with respect to those dysregulated in skeletal muscle wasting is required.
“A CRISPR-dCas13 RNA-editing tool to study alternative splicing”
Authors: Núñez-Álvarez Yaiza , Espie--Caullet Tristan , Buhagiar Géraldine , Rubio-Zulaika Ane , Alonso-Marañón Josune , Perez-Luna Elvira , Blazquez Lorea , Luco Reini F. 
Published: May 2022

ABSTRACTAlternative splicing allows multiple transcripts to be generated from the same gene to diversify the protein repertoire and gain new functions despite a limited coding genome. It can impact a wide spectrum of biological processes, including disease. However, its significance has long been underestimated due to limitations in dissecting the precise role of each splicing isoform in a physiological context. Furthermore, identifying key regulatory elements to correct deleterious splicing isoforms has proven equally challenging, increasing the difficulty to tackle the role of alternative splicing in cell biology. In this work, we take advantage of dCasRx, a catalytically inactive RNA targeting CRISPR-dCas13 ortholog, to efficiently switch alternative splicing patterns of endogenous transcripts without affecting overall gene expression levels in a cost-effective manner. Additionally, we demonstrate a new application for the dCasRx splice-editing system to identify key regulatory RNA elements of specific splicing events. With this approach, we are expanding the RNA toolkit to better understand the regulatory mechanisms underlying alternative splicing and its physiological impact in various biological processes, including pathological conditions.
Discovery of a new class of reversible TEA-domain transcription factor inhibitors with a novel binding mode
Authors: Hu Lu , Sun Yang , Liu Shun , Erb Hannah , Singh Alka , Mao Junhao , Luo Xuelian , Wu Xu 
Published: May 2022

ABSTRACTThe TEA domain (TEAD) transcription factor forms a transcription co-activation complex with the key downstream effector of the Hippo pathway, YAP/TAZ. TEAD-YAP controls the expression of Hippo-responsive genes involved in cell proliferation, development, and tumorigenesis. Hyperactivation of TEAD-YAP activities is observed in many human cancers, and is associated with cancer cell proliferation, survival and immune evasion. Therefore, targeting the TEAD-YAP complex has emerged as an attractive therapeutic approach. We previously reported that the mammalian TEAD transcription factors (TEAD1-4) possess auto-palmitoylation activities and contain an evolutionarily conserved palmitate-binding pocket (PBP), which allows small molecule modulation. Since then, several reversible and irreversible inhibitors have been reported by binding to PBP. Here, we report a new class of TEAD inhibitors with a novel binding mode. Representative analog TM2 shows potent inhibition of TEAD auto-palmitoylation both in vitro and in cells. Surprisingly, the co-crystal structure of the human TEAD2 YAP-binding domain (YBD) in complex with TM2 reveals that TM2 adopts an unexpected binding mode by occupying not only the hydrophobic PBP, but also a new side binding pocket formed by hydrophilic residues. RNA-seq analysis shows that TM2 potently and specifically suppresses TEAD-YAP transcriptional activities. Consistently, TM2 exhibits strong anti-proliferation effects as a single agent or in combination with a MEK inhibitor in YAP-dependent cancer cells. These findings establish TM2 as a promising small molecule inhibitor against TEAD-YAP activities and provide new insights for designing novel TEAD inhibitors with enhanced selectivity and potency.
Anterior insular cortex firing links initial and sustained encoding during aversion-resistant alcohol consumption
Authors: Starski Phillip , Morningstar Mitch , Katner Simon , Frasier Raizel , De Oliveira Sergio Thatiane , Wean Sarah , Lapish Christopher , Hopf F Woodward 
Published: May 2022

ABSTRACTCompulsive-like alcohol drinking (CLAD), where intake persists despite adverse consequences, is often a core facet of alcohol use disorder. Recent work sheds light on underlying mechanisms, but much remains unknown about CLAD etiology. Previously, we showed that projections from anterior insula (aINS), a central mediator of emotion, motivation, and interoception, promote CLAD in rodents, and heavy human drinkers exhibit similar insula-circuit recruitment under compulsion-like conditions. However, global aINS inhibition also reduces alcohol-only drinking (AOD), and one major obstacle is the lack of information on aINS firing patterns that could promote different aspects of intake. Here, we recorded single-unit activity in right aINS from 15 rats during AOD or CLAD (10mg/L or 60mg/L quinine in alcohol). Neurons with a sustained-increase or sustained-decrease phenotype (SIP, SDP) showed no firing differences across drinking conditions. In contrast, aINS neurons with a phenotype of strong firing increase at initiation of responding (IRP) showed significantly greater activity across the rest of licking during CLAD versus AOD, concurring with our previous behavioral findings suggesting quick evaluation and response strategy adjustment under CLAD. There were also no condition-related differences in firing-phenotype abundance. Further, total responding only correlated with abundance of SDP cells, but SDP firing returned to baseline during pauses in licking, while IRP and SIP sustained responding through pauses in licking. Thus, only aINS cells with a particular strong firing at licking onset showd greater sustained responding under compulsion-like conditions, while other cells likely promoted drinking more generally, providing critical new information about how aINS activity could promote alcohol consumption under different drinking conditions.
The structure of yeast Npl3 bound to RNA reveals a cooperative sequence-specific recognition and an RNA chaperone role in splicing
Authors: Moursy Ahmed , Cléry Antoine , Gerhardy Stefan , Betz Katharina M. , Rao Sanjana , Campagne Sébastien , Beusch Irene , Duszczyk Malgorzata M. , Robinson Mark D. , Panse Vikram Govind , Allain Frédéric H.-T. 
Published: May 2022

ABSTRACTThe conserved SR-like protein Npl3 promotes splicing of diverse pre-mRNAs. However, the RNA sequence(s) recognized by the RNA Recognition Motifs (RRM1 & RRM2) of Npl3 during the splicing reaction remain elusive. Here, we developed a split-iCRAC approach in yeast to uncover the consensus sequence bound to each RRM. High-resolution NMR structures show that RRM2 recognizes a 5’-GNGG-3’ motif leading to an unusual mille-feuille topology. These structures also reveal how RRM1 preferentially interacts with a CC-dinucleotide upstream of this motif, and how the inter-RRM linker and the region C-terminal to RRM2 contributes to cooperative RNA-binding. Structure-guided functional studies show that Npl3 genetically interacts with U2 snRNP specific factors and we provide evidence that Npl3 melts U2 snRNA stem-loop I, a prerequisite for U2/U6 duplex formation within the catalytic center of the Bactspliceosomal complex. Thus, our findings provide insights into an unanticipated RNA chaperoning role for Npl3 during spliceosome active site formation.
Functional analysis in a model sea anemone reveals phylogenetic complexity and a role in cnidocyte discharge of DEG/ENaC ion channels
Authors: Aguilar-Camacho Jose Maria , Foreman Katharina , Aharoni Reuven , Gründer Stefan , Moran Yehu 
Published: May 2022

AbstractIon channels of the DEG/ENaC family share a similar structure but serve strikingly diverse biological functions, such as Na+ reabsorption, mechanosensing, proton-sensing, chemosensing and cell-cell communication via neuropeptides. This functional diversity raises the question of the ancient function of DEG/ENaCs. Using an extensive phylogenetic analysis across many different animal groups, we found a surprising diversity of DEG/ENaCs already in Cnidaria (corals, sea anemones, hyrdoids and jellyfish). Using a combination of gene expression analysis, electrophysiological and functional studies combined with pharmacological inhibition as well as genetic knockout in the model cnidarian Nematostella vectensis, we reveal an unanticipated role for a proton-sensitive DEG/ENaC in discharge of N. vectensis cnidocytes, the stinging cells typifying all cnidarians. Our study supports the view that DEG/ENaCs are versatile channels that have been co-opted for diverse functions since their early occurrence in animals and that respond to simple and ancient stimuli, such as omnipresent protons.TeaserThe analysis of an ion channel class in a sea anemone reveals its role in acidity-induced discharge of stinging cells.
“Replication stalling activates SSB for recruitment of DNA damage tolerance factors”
Authors: Thrall Elizabeth S. , Piatt Sadie C. , Chang Seungwoo , Loparo Joseph J. 
Published: May 2022

AbstractTranslesion synthesis (TLS) polymerases bypass DNA lesions that block replicative polymerases, allowing cells to tolerate DNA damage encountered during replication. It is well known that most bacterial TLS polymerases must interact with the sliding clamp processivity factor to carry out TLS, but recent work in Escherichia coli has revealed that single-stranded DNA-binding protein (SSB) plays a key role in enriching the TLS polymerase Pol IV at stalled replication forks in the presence of DNA damage. It remains unclear how this interaction with SSB enriches Pol IV in a stalling-dependent manner given that SSB is always present at the replication fork. In this study we use single-molecule imaging in live E. coli cells to investigate this SSB-dependent enrichment of Pol IV. We find that Pol IV is enriched through its interaction with SSB in response to a range of different replication stresses, and that changes in SSB dynamics at stalled forks may explain this conditional Pol IV enrichment. Finally, we show that other SSB-interacting proteins (SIPs) are likewise selectively enriched in response to replication perturbations, suggesting that this mechanism is likely a general one for enrichment of repair factors near stalled replication forks.
Disruption of integrin alpha-5/beta-1-dependent transforming growth factor beta-1 signaling pathway attenuates vessel co-option in colorectal cancer liver metastases
Authors: Rada Miran , Kapelanski-Lamoureux Audrey , Zlotnik Oran , Petrillo Stephanie , Lazaris Anthoula , Metrakos Peter 
Published: May 2022

AbstractColorectal cancer liver metastases (CRCLM) have two major histopathological growth patterns (HGPs) including angiogenic desmoplastic HGP (DHGP) and non-angiogenic replacement HGP (RHGP). The RHGP lesions obtain their blood supply through vessel co-option, where the cancer cells hijack the pre-existing blood vessels of the surrounding liver tissue. Consequently, anti-angiogenic therapies are less efficacious in CRCLM patients with RHGP lesions. Recently, we identified a positive correlation between the expression of Angiopoietin1 (Ang1) and the development of vessel co-opted CRCLM lesions in vivo. However, the mechanisms underlying Ang1 upregulation in vessel co-opting CRCLM lesions are unclear. Herein, we demonstrated that transforming growth factor β1 (TGFβ1) modulates the expression of Ang1 in hepatocytes in vitro. Significantly, pharmaceutical inhibition of integrin alpha-5/beta-1 (ITGα5β1) through ATN-161 impaired TGFβ1-dependent Ang1 expression in vitro and in vivo. Moreover, blocking ITGα5β1 attenuated the formation of vessel co-opting lesions. Furthermore, treatment with ATN-161 significantly improved survival in tumour-bearing mice. Taken together, our results suggest the molecular mechanism of Ang1 upregulation in vessel co-opting CRCLM and targeting this pathway may serve as promising therapeutic strategy to overcome the development of vessel co-option in CRCLM.
Cell walls are dynamically O-acetylated in the green seaweed, Ulva compressa
Authors: Bothwell John H. , Goodridge Alexander J. , Rapin Marie , Brennan Patrick J. , López Alexandra Traslaviña , Agrawal Akanksha , Fry Stephen C. , Campbell Georgia , Blomme Jonas 
Published: May 2022

AbstractWe report that cell wall polymers in the chlorophyte algae may be modified by O-acetylation. The importance of cell wall modifications in the green algae is not well understood, although similar modifications play key roles in land plants by modulating the properties of cell wall carbohydrate polymers. Using a combination of biophysical (Fourier-transform infrared and cross-polarisation heteronuclear correlation nuclear magnetic resonance spectroscopy), biochemical (thin-layer chromatography) and molecular approaches (yellow fluorescent protein-tagged transgene localisation), we show that the extractable ulvan fractions of Ulva compressa cell walls contain O-acetyl sidechains, we demonstrate that acetylation is dynamic and decreases reversibly in response to metal-induced stress, we note interactions between acetyl and borate sidechains and we locate two candidate genes that, together, may encode an acetyltransferase. We therefore propose that O-acetylation of ulvan residues is involved in the normal cell wall physiology of at least some chlorophyte algae. To the best of our knowledge, this is the first demonstration of O-acetyl sidechains in green algal cell wall polymers, and of reversible changes in algal cell wall polymer modification in response to stress.
Par3/Bazooka binds NICD and promotes Notch signalling duringDrosophiladevelopment
Authors: Wu Jun , Tannan Neeta Bala , Vuong Linh T. , Koca Yildiz , Collu Giovanna M. , Mlodzik Marek 
Published: May 2022

AbstractThe conservedbazooka (baz/par3) gene acts as a key regulator of asymmetrical cell divisions across the animal kingdom. Associated Par3/Baz-Par6-aPKC protein complexes are also well known for their role in the establishment of apical/basal cell polarity in epithelial cells. Here we define a novel, positive function of Baz/Par3 in the Notch pathway. UsingDrosophilawing and eye development, we demonstrate that Baz is required for Notch signaling activity and optimal transcriptional activation of Notch target genes. Baz appears to act independently of aPKC in these contexts, as knockdown ofaPKCdoes not causeNotchloss-of-function phenotypes. Using transgenic Notch constructs, our data positions Baz activity downstream of activating Notch cleavage steps and upstream of Su(H)/CSL transcription factor complex activity on Notch target genes. We demonstrate a biochemical interaction between NICD and Baz, suggesting that Baz is required for NICD activity before NICD binds to Su(H). Taken together, our data define a novel role of the polarity protein Baz/Par3, as a positive and direct regulator of Notch signaling through its interaction with NICD.
Loss-of-function mutation in humanOxidation Resistance gene 1disrupts the spatial-temporal regulation of histone arginine methylation in early brain development
Authors: Lin Xiaolin , Wang Wei , Yang Mingyi , Damseh Nadirah , de Sousa Mirta Mittelstedt Leal , Jacob Fadi , Lång Anna , Kristiansen Elise , Pannone Marco , Kissova Miroslava , Almaas Runar , Kuśnierczyk Anna , Siller Richard , Shahrour Maher , Al-Ashhab Motee , Abu-Libdeh Bassam , Tang Wannan , Slupphaug Geir , Elpeleg Orly , Bøe Stig Ove , Eide Lars , Sullivan Gareth J , Rinholm Johanne Egge , Song Hongjun , Ming Guo-li , van Loon Barbara , Edvardson Simon , Ye Jing , Bjørås Magnar 
Published: May 2022

AbstractWe report a loss-of-function mutation in the TLDc domain of humanOxidation Resistance 1(OXR1) gene, resulting in early-onset epilepsy, developmental delay, cognitive disabilities, and cerebellar atrophy. Patient lymphoblasts show impaired cell survival, proliferation, and hypersensitivity to oxidative stress. These phenotypes are rescued by TLDc domain replacement. We generated patient derived induced pluripotent stem cells (iPSCs) revealing impaired neural differentiation along with dysregulation of genes essential for neurodevelopment. We identified that OXR1 influences histone arginine methylation by activating protein arginine methyltransferases (PRMTs), suggesting OXR1 dependent mechanisms regulating gene expression during neurodevelopment. We modeled the function of OXR1 in early human brain development using patient derived brain organoids revealing that OXR1 contributes to the spatial-temporal regulation of histone arginine methylation in specific brain regions. Our work provides new insights into pathological features and molecular underpinnings associated with OXR1 deficiency, highlighting the therapeutic potential of OXR1 in numerous neurodegenerative and neurodevelopmental disorders.
Open science resources from the Tara Pacific expedition across coral reef and surface ocean ecosystems
Authors: Lombard Fabien , Bourdin Guillaume , Pesant Stéphane , Agostini Sylvain , Baudena Alberto , Boissin Emilie , Cassar Nicolas , Clampitt Megan , Conan Pascal , Silva Ophélie Da , Dimier Céline , Douville Eric , Elineau Amanda , Fin Jonathan , Flores J. Michel , Ghiglione Jean François , Hume Benjamin C.C. , Jalabert Laetitia , John Seth G. , Kelly Rachel L. , Koren Ilan , Lin Yajuan , Marie Dominique , McMinds Ryan , Mériguet Zoé , Metzl Nicolas , Paz-García David A. , Pedrotti Maria Luiza , Poulain Julie , Pujo-Pay Mireille , Ras Joséphine , Reverdin Gilles , Romac Sarah , Rouan Alice , Röttinger Eric , Vardi Assaf , Voolstra Christian R. , Moulin Clémentine , Iwankow Guillaume , Banaigs Bernard , Bowler Chris , de Vargas Colomban , Forcioli Didier , Furla Paola , Galand Pierre E. , Gilson Eric , Reynaud Stéphanie , Sunagawa Shinichi , Sullivan Matthew B. , Thomas Olivier , Troublé Romain , Thurber Rebecca Vega , Wincker Patrick , Zoccola Didier , Allemand Denis , Planes Serge , Boss Emmanuel , Gorsky Gaby 
Published: May 2022

AbstractThe Tara Pacific expedition (2016-2018) sampled coral ecosystems around 32 islands in the Pacific Ocean and the ocean surface waters at 249 locations, resulting in the collection of nearly 58,000 samples. The expedition was designed to systematically study warm coral reefs and included the collection of corals, fish, plankton, and seawater samples for advanced biogeochemical, molecular, and imaging analysis. Here we provide a complete description of the sampling methodology, and we explain how to explore and access the different datasets generated by the expedition. Environmental context data were obtained from taxonomic registries, gazetteers, almanacs, climatologies, operational biogeochemical models, and satellite observations. The quality of the different environmental measures has been validated not only by various quality control steps but also through a global analysis allowing the comparison with known environmental large-scale structures. Such a wide released datasets opens the perspective to address a wide range of scientific questions.