bluuebunny/crossref_metadata_2025_split huggingface dataset:
Validating a computational framework for ionic electrodiffusion with cortical spreading depression as a case study
Authors: Ellingsrud Ada Johanne , Enger Rune , Dukefoss Didrik Bakke , Halnes Geir , Pettersen Klas Henning , Rognes Marie E 
Published: November 2021

ABSTRACTCortical spreading depression (CSD) is a wave of pronounced depolarization of brain tissue accompanied by substantial shifts in ionic concentrations and cellular swelling. Here, we validate a computational framework for modelling electrical potentials, ionic movement, and cellular swelling in brain tissue during CSD. We consider different model variations representing wild type or knock-out/knock-down mice and systematically compare the numerical results with reports from a selection of experimental studies. We find that the data for several CSD hallmarks obtained computationally, including wave propagation speed, direct current shift duration, peak in extracellular K+ concentration as well as a pronounced shrinkage of extracellular space, are well in line with what has previously been observed experimentally. Further, we assess how key model parameters including cellular diffusivity, structural ratios, membrane water and/or K+ permeabilities affect the set of CSD characteristics.Significance StatementMovement of ions and molecules in and between cellular compartments is fundamental for brain function. Cortical spreading depression (CSD) is associated with dramatic failure of brain ion homeostasis. Better understanding the sequence of events in CSD could thus provide new insight into physiological processes in the brain. Despite extensive experimental research over the last decades, even basic questions related to mechanisms underlying CSD remain unanswered. Computational modelling can play an important role going forward, since simulation studies can address hypotheses that are difficult to target experimentally. Here, we assess the physiological validity of a novel mathematical framework for detailed modelling of brain electrodiffusion and osmosis – and provide a platform for in silico studies of CSD and other cerebral electro-mechanical phenomena.
Consistent predictors of microbial community composition across scales in grasslands reveal low context-dependency
Authors: Radujković Dajana , Vicca Sara , van Rooyen Margaretha , Wilfahrt Peter , Brown Leslie , Jentsch Anke , Reinhart Kurt O. , Brown Charlotte , De Gruyter Johan , Jurasinski Gerald , Askarizadeh Diana , Bartha Sandor , Beck Ryan , Blenkinsopp Theodore , Cahill James , Campetella Giandiego , Canullo Roberto , Chelli Stefano , Enrico Lucas , Fraser Lauchlan , Hao Xiying , Henry Hugh A. L. , Hohn Maria , Jouri Mohammad Hassan , Koch Marian , Lawrence Lodge Rachael , Li Frank Yonghong , Lord Janice M. , Milligan Patrick , Minggagud Hugjiltu , Palmer Todd , Schröder Birgit , Szabó Gábor , Zhang Tongrui , Zimmermann Zita , Verbruggen Erik 
Published: November 2021

AbstractEnvironmental circumstances shaping soil microbial communities have been studied extensively, but due to disparate study designs it has been difficult to resolve whether a globally consistent set of predictors exists, or context-dependency prevails. Here, we used a network of 18 grassland sites (11 sampled across regional plant productivity gradients) to examine i) if the same abiotic or biotic factors predict both large- and regional-scale patterns in bacterial and fungal community composition, and ii) if microbial community composition differs consistently with regional plant productivity (low vs high) across different sites. We found that there is high congruence between predictors of microbial community composition across spatial scales; bacteria were predominantly associated with soil properties and fungi with plant community composition. Moreover, there was a microbial community signal that clearly distinguished high and low productivity soils that was shared across worldwide distributed grasslands suggesting that microbial assemblages vary predictably depending on grassland productivity.
Distinctive nuclear zone for RAD51-mediated homologous recombinational DNA repair
Authors: Horikoshi Yasunori , Shima Hiroki , Sun Jiying , Kobayashi Wataru , Schmid Volker J. , Ochiai Hiroshi , Shi Lin , Fukuto Atsuhiko , Kinugasa Yasuha , Kurumizaka Hitoshi , Ikura Tsuyoshi , Markaki Yolanda , Tate Shin-ichi , Igarashi Kazuhiko , Cremer Thomas , Tashiro Satoshi 
Published: November 2021

AbstractGenome-based functions are inseparable from the dynamic higher-order architecture of the cell nucleus. In this context, the repair of DNA damage is coordinated by precise spatiotemporal controls that target and regulate the repair machinery required to maintain genome integrity. However, the mechanisms that pair damaged DNA with intact template for repair by homologous recombination (HR) without illegitimate recombination remain unclear. This report highlights the intimate relationship between nuclear architecture and HR in mammalian cells. RAD51, the key recombinase of HR, forms spherical foci in S/G2 phases spontaneously. Using super-resolution microscopy, we show that following induction of DNA double-strand breaks RAD51 foci at damaged sites elongate to bridge between intact and damaged sister chromatids; this assembly occurs within bundle-shaped distinctive nuclear zones, requires interactions of RAD51 with various factors, and precedes ATP-dependent events involved the recombination of intact and damaged DNA. We observed a time-dependent transfer of single-stranded DNA overhangs, generated during HR, into such zones. Our observations suggest that RAD51-mediated homologous pairing during HR takes place within the distinctive nuclear zones to execute appropriate recombination.
Public T-Cell Receptors (TCRs) Revisited by Analysis of the Magnitude of Identical and Highly-Similar TCRs in Virus-Specific T-Cell Repertoires of Healthy Individuals
Authors: Huisman Wesley , Hageman Lois , Leboux Didier A.T. , Khmelevskaya Alexandra , Efimov Grigory A. , Roex Marthe C.J. , Amsen Derk , Falkenburg J.H.F. , Jedema Inge 
Published: November 2021

AbstractSince multiple different T-cell receptor (TCR) sequences can bind to the same peptide-MHC combination and the number of TCR-sequences that can theoretically be generated even exceeds the number of T cells in a human body, the likelihood that many public identical (PUB-I) TCR-sequences frequently contribute to immune responses has been estimated to be low. Here, we quantitatively analyzed the TCR-repertoires of 190 purified virus-specific memory T-cell populations, directed against 21 antigens of Cytomegalovirus, Epstein-Barr virus and Adenovirus isolated from 29 healthy individuals, and determined the magnitude, defined as prevalence within the population and frequencies within individuals, of PUB-I TCR and of TCR-sequences that are highly-similar (PUB-HS) to these PUB-I TCR-sequences. We found that almost one third of all TCR nucleotide-sequences represented PUB-I TCR amino-acid (AA) sequences and found an additional 12% of PUB-HS TCRs differing by maximally 3 AAs. We illustrate that these PUB-I and PUB-HS TCRs were structurally related and contained shared core-sequences in their TCR-sequences. We found a prevalence of PUB-I and PUB-HS TCRs of up to 50% among individuals and showed frequencies of virus-specific PUB-I and PUB-HS TCRs making up more than 10% of each virus-specific T-cell population. These findings were confirmed by using an independent TCR-database of virus-specific TCRs. We therefore conclude that the magnitude of the contribution of PUB-I and PUB-HS TCRs to these virus-specific T-cell responses is high. Because the T cells from these virus-specific memory TCR-repertoires were the result of successful control of the virus in these healthy individuals, these PUB-HS TCRs and PUB-I TCRs may be attractive candidates for immunotherapy in immunocompromised patients that lack virus-specific T cells to control viral reactivation.Significance statementPublic T-cell responses, in which T cells expressing the same T-cell receptor (TCR) are found in different individuals, have been described. However, the magnitude of the contribution of these TCRs to immune responses, defined as prevalence within the population and frequencies within individuals, is not known. In this study we characterized and quantified public T-cell responses within virus-specific memory T cells of healthy individuals by determining identical and highly-similar TCRs recognizing the same antigen and sharing conserved CDR3 motifs. The magnitude of public T-cell responses was surprisingly high and we argue that these dominant TCRs with shared core-sequences could be utilized for diagnostic purposes and may provide attractive TCRs to be used for immunotherapy in immunocompromised patients.
Constraints on the evolution of toxin-resistant Na,K-ATPases have limited dependence on sequence divergence
Authors: Mohammadi Shabnam , Herrera-Álvarez Santiago , Yang Lu , Pilar Rodríguez-Ordoñez María del , Zhang Karen , Storz Jay F. , Dobler Susanne , Crawford Andrew J. , Andolfatto Peter 
Published: November 2021

AbstractA growing body of theoretical and experimental evidence suggests that intramolecular epistasis is a major determinant of rates and patterns of protein evolution and imposes a substantial constraint on the evolution of novel protein functions. Here, we examine the role of intramolecular epistasis in the recurrent evolution of resistance to cardiotonic steroids (CTS) across tetrapods, which occurs via specific amino acid substitutions to the α-subunit family of Na,K-ATPases (ATP1A). After identifying a series of recurrent substitutions at two key sites of ATP1A that are predicted to confer CTS resistance in diverse tetrapods, we then performed protein engineering experiments to test the functional consequences of introducing these substitutions onto divergent species backgrounds. In line with previous results, we find that substitutions at these sites can have substantial background-dependent effects on CTS resistance. Globally, however, these substitutions also have pleiotropic effects that are consistent with additive rather than background-dependent effects. Moreover, the magnitude of a substitution’s effect on activity does not depend on the overall extent of ATP1A sequence divergence between species. Our results suggest that epistatic constraints on the evolution of CTS-resistant forms of Na,K-ATPase likely depend on a small number of sites, with little dependence on overall levels of protein divergence. We propose that dependence on a limited number sites may account for the observation of convergent CTS resistance substitutions observed among taxa with highly divergent Na,K-ATPases.Significance StatementIndividual amino acid residues within a protein work in concert to produce a functionally coherent structure that must be maintained even as orthologous proteins in different species diverge over time. Given this dependence, we expect identical mutations to have more similar effects on protein function in more closely related species. We tested this hypothesis by performing protein-engineering experiments on ATP1A, an enzyme mediating target-site insensitivity to cardiotonic steroids (CTS) in diverse animals. These experiments reveal that the phenotypic effects of substitutions can sometimes be background-dependent, but also that the magnitude of these phenotypic effects does not correlate with overall levels of ATP1A sequence divergence. Our results suggest that epistatic constraints are determined by states at a small number of sites, potentially explaining the frequent convergent CTS resistance substitutions among Na,K-ATPases of highly divergent taxa.
A mechanical G2 checkpoint controls epithelial cell division through E-cadherin-mediated regulation of Wee1-Cdk1
Authors: Donker Lisa , Vliem Marjolein J. , Canever Helena , Gómez-González Manuel , Bosch-Padrós Miquel , Pannekoek Willem-Jan , Trepat Xavier , Borghi Nicolas , Gloerich Martijn 
Published: November 2021

AbstractEpithelial cell divisions must be tightly coordinated with cell loss to preserve epithelial integrity. However, it is not well understood how the rate of epithelial cell division adapts to changes in cell number, for instance during homeostatic turnover or upon wounding of epithelia. Here, we show epithelial cells sense local cell density through mechanosensitive E-cadherin adhesions to control G2/M cell cycle progression. We demonstrate that tensile forces on E-cadherin adhesions are reduced as local cell density increases, which prompts the accumulation of the G2 checkpoint kinase Wee1. This elevated abundance of Wee1 results in inhibitory phoshorylation of Cdk1, and thereby establishes a pool of cells that is temporarily halted in G2-phase. Importantly, these cells are readily triggered to divide upon epithelial wounding, due to the consequent increase in intercellular forces and resulting degradation of Wee1. Our data thus demonstrate that epithelial cell division is controlled by a mechanical G2 checkpoint, which is regulated by cell density-dependent intercellular forces sensed and transduced by E-cadherin adhesions.
Hydrothermal Synthesis of Clove Bud-Derived Multifunctional Carbon Dots Passivated with PVP- Antioxidant, Catalysis, and Cellular Imaging Applications
Authors: Pandey Anurag Kumar , Bankoti Kamakshi , Nath Tapan Kumar , Dhara Santanu 
Published: November 2021

AbstractThe present study reports a one-step synthesis of PVP-passivated clove buds derived carbon dots (PPCCDs) using clove buds and polyvinylpyrrolidone (PVP) as the starting precursors via the hydrothermal route. The adopted technique is facile and environmentally friendly for the production of carbon dots (CDs) with in situ PVP passivation. The study evidenced the significant modulation in optical properties of passivated CDs as compared to non-passivated ones. Structural and morphological studies evidenced the spherical PPCCDs with a diameter of ∼ 2 nm and crystalline in nature with an interlayer spacing of 0.33 nm. The PPCCDs showed excellent antioxidant activity against DPPH and superoxide anion radicals and also showed good catalytic activity for the degradation of Rhodamine-B (Rh-B) dye under the studied conditions. Their bioimaging potential was evidenced through live-cell fluorescent imaging with 3T3 and L929 cell lines.
Fracture healing is delayed in the absence of gasdermin signaling
Authors: Sun Kai , Wang Chun , Xiao Jianqiu , Brodt Michael D. , Yuan Luorongxin , Yang Tong , Alippe Yael , Hu Huimin , Hao Dingjun , Abu-Amer Yousef , Silva Matthew J. , Shen Jie , Mbalaviele Gabriel 
Published: November 2021

AbstractAmino-terminal fragments from proteolytically cleaved gasdermins (GSDMs) form plasma membrane pores that enable the secretion of interleukin-1β (IL-1β) and IL-18. Excessive GSDM- mediated pore formation can compromise the integrity of the plasma membrane thereby causing the lytic inflammatory cell death, pyroptosis. We found that GSDMD and GSDME were the only GSDMs that were readily expressed in bone microenvironment. Therefore, we tested the hypothesis that GSDMD and GSDME are implicated in fracture healing owing to their role in the obligatory inflammatory response following injury. We found that bone callus volume and biomechanical properties of injured bones were significantly reduced in mice lacking either GSDM compared with wild-type (WT) mice, indicating that fracture healing was compromised in mutant mice. However, compound loss of GSDMD and GSDME did not exacerbate the outcomes, suggesting shared actions of both GSDMs in fracture healing. Mechanistically, bone injury induced IL-1β and IL-18 secretion in vivo, a response that was mimicked in vitro by bone debris and ATP, which function as inflammatory danger signals. Importantly, the secretion of these cytokines was attenuated in conditions of GSDMD deficiency. Finally, deletion of IL-1 receptor reproduced the phenotype of Gsdmd or Gsdme deficient mice, implying that inflammatory responses induced by the GSDM-IL-1 axis promote bone healing after fracture.
The VINE complex is a VPS9-domain GEF-containing SNX-BAR coat involved in endosomal sorting
Authors: Shortill Shawn P. , Frier Mia S. , Davey Michael , Conibear Elizabeth 
Published: November 2021

AbstractMembrane trafficking pathways perform important roles in establishing and maintaining the endolysosomal network. Retrograde protein sorting from the endosome is promoted by conserved SNX-BAR-containing coat complexes including retromer which enrich cargo at tubular microdomains and generate transport carriers. In metazoans, retromer cooperates with VARP, a conserved VPS9-domain GEF, to direct an endosomal recycling pathway. The function of the yeast VARP homolog Vrl1 has been overlooked due an inactivating mutation in commonly studied strains. Here, we demonstrate that Vrl1 has features of a SNX-BAR coat protein and forms an obligate complex with Vin1, the paralog of the retromer SNX-BAR protein Vps5. Unique features in the Vin1 N-terminus allow Vrl1 to distinguish it from Vps5, thereby forming what we have named the VINE complex. VINE occupies endosomal tubules and promotes the delivery of a conserved mannose 6-phosphate receptor-like protein to the vacuolar membrane. In addition to sorting functions, membrane recruitment by Vin1 is essential for Vrl1 GEF activity, suggesting that VINE is a multifunctional coat complex that regulates trafficking and signaling events at the endosome.
Distinct roles of the Na+ binding sites in the allosteric coupling mechanism of the glutamate transporter homolog, GltPh
Authors: Riederer Erika , Moenne-Loccoz Pierre , Valiyaveetil Francis I. 
Published: November 2021

AbstractGlutamate transporters carry out the concentrative uptake of glutamate by harnessing the ionic gradients present across cellular membranes. A central step in the transport mechanism is the coupled binding of Na+ and substrate. The sodium coupled Asp transporter, GltPh is an archaeal homolog of glutamate transporters that has been extensively used to probe the transport mechanism. Previous studies have shown that hairpin-2 (HP2) functions as the extracellular gate for the aspartate binding site and plays a key role in the coupled binding of sodium and aspartate to GltPh. The binding sites for three Na+ ions (Na1-3) have been identified in GltPh but the specific roles of the individual Na+ sites in the binding process has not been elucidated. In this study, we developed assays to probe Na+ binding to the Na1 and Na3 sites and to monitor the conformational switch in the NMDGT motif. We used these assays along with a fluorescence assay to monitor HP2 movement and EPR spectroscopy to show that Na+ binding to the Na3 site is required for the NMDGT conformational switch while Na+ binding to the Na1 site is responsible for the partial opening of HP2. Complete opening of HP2 requires the conformational switch of the NMDGT motif and therefore Na+ binding to both the Na1 and the Na3 sites. Based on our studies we also propose an alternate pathway for the coupled binding of Na+ and Asp.
Pontin/Reptin-associated complexes differentially impact plant development and viral pathology
Authors: Chatterjee Snigdha , Xu Min , Shemyakina Elena A. , Brunkard Jacob O. 
Published: November 2021

AbstractPontin and Reptin are essential eukaryotic AAA+ ATPases that work together in several multiprotein complexes, contributing to chromatin remodeling and TARGET OF RAPAMCYIN (TOR) kinase complex assembly, among other functions. Null alleles of pontin or reptin are gametophyte lethal in plants, which has hindered studies of their crucial roles in plant biology. Here, we used virus-induced gene silencing (VIGS) to interrogate the functions of Pontin and Reptin in plant growth and physiology, focusing on Nicotiana benthamiana, a model species for the agriculturally significant Solanaceae family. Silencing either Pontin or Reptin caused pleiotropic developmental and physiological reprogramming, including aberrant leaf shape, reduced apical growth, delayed flowering, increased branching, chlorosis, and decreased spread of the RNA viruses Tobacco mosaic virus (TMV) and Potato virus X (PVX). To dissect these pleiotropic phenotypes, we took a comparative approach and silenced expression of key genes that encode subunits of each of the major Pontin/Reptin-associated chromatin remodeling or TOR complexes (INO80, SWR-C/PIE1, TIP60, TOR, and TELO2). We found that many of the pontin/reptin phenotypes could be attributed specifically to disruption of one of these complexes, with tip60 and tor knockdown plants each phenocopying a large subset of pontin/reptin phenotypes. We conclude that Pontin/Reptin complexes are crucial for proper plant development, physiology, and stress responses, highlighting the multifaceted roles these conserved enzymes have evolved in eukaryotic cells.
Origins and breadth of pairwise epistasis in an α-helix of β-lactamase TEM-1
Authors: Birgy André , Roussel Clément , Kemble Harry , Mullaert Jimmy , Panigoni Karine , Chapron Audrey , Chatel Jérémie , Magnan Mélanie , Jacquier Hervé , Cocco Simona , Monasson Rémi , Tenaillon Olivier 
Published: November 2021

AbstractEpistasis affects genome evolution together with our ability to predict individual mutation effects. The mechanistic basis of epistasis remains, however, largely unknown. To quantify and better understand interactions between fitness-affecting mutations, we focus on a 11 amino-acid α-helix of the protein β-lactamase TEM-1, and build a comprehensive library of more than 15,000 double mutants. Analysis of the growth rates of these mutants shows pervasive epistasis, which can be largely explained by a non-linear two-state model, where inactivating, destabilizing, neutral, or stabilizing mutations additively contribute to the phenotype. Hence, most epistatic interactions can be predicted by a non-linear model informed by single-point mutational measurements only. Deviations from the two-state model are consistently found for few pairs of residues, in particular when they are in contact. This result, as well as single-point mutation parameters, can be quantitatively found back through direct-coupling-analysis-based statistical models inferred from homologous sequence data. Our results thus shed light on the existence and the origins of the multiple determinants of the epistatic landscape, even at the level of small structural components of a protein, and suggest that the corresponding constraints shape the entire β-lactamase family.