bluuebunny/crossref_metadata_2025_split huggingface dataset:
Evolution of tunnels in α/β-hydrolase fold proteins – what can we learn from studying epoxide hydrolases?
Authors: Bzówka Maria , Mitusińska Karolina , Raczyńska Agata , Skalski Tomasz , Samol Aleksandra , Bagrowska Weronika , Magdziarz Tomasz , Góra Artur 
Published: December 2021

AbstractThe evolutionary variability of a protein’s residues is highly dependent on protein region and function. Solvent-exposed residues, excluding those at interaction interfaces, are more variable than buried residues whereas active site residues are considered to be conserved. The abovementioned rules apply also to α/β-hydrolase fold proteins - one of the oldest and the biggest superfamily of enzymes with buried active sites equipped with tunnels linking the reaction site with the exterior. We selected soluble epoxide hydrolases as representative of this family to conduct the first systematic study on the evolution of tunnels. We hypothesised that tunnels are lined by mostly conserved residues, and are equipped with a number of specific variable residues that are able to respond to evolutionary pressure. The hypothesis was confirmed, and we suggested a general and detailed way of the tunnels’ evolution analysis based on entropy values calculated for tunnels’ residues. We also found three different cases of entropy distribution among tunnel-lining residues. These observations can be applied for protein reengineering mimicking the natural evolution process. We propose a ‘perforation’ mechanism for new tunnels design via the merging of internal cavities or protein surface perforation. Based on the literature data, such a strategy of new tunnel design could significantly improve the enzyme’s performance and can be applied widely for enzymes with buried active sites.Author SummarySo far very little is known about proteins tunnels evolution. The goal of this study is to evaluate the evolution of tunnels in the family of soluble epoxide hydrolases - representatives of numerous α/β-hydrolase fold enzymes. As a result two types of tunnels evolution analysis were proposed (a general and a detailed approach), as well as a ‘perforation’ mechanism which can mimic native evolution in proteins and can be used as an additional strategy for enzymes redesign.
A mathematical model for cell-induced gel contraction incorporating osmotic effects
Authors: Reoch J. R. , Stokes Y. M. , Green J. E. F. 
Published: December 2021

AbstractBiological tissues are composed of cells surrounded by the extracellular matrix (ECM). The ECM can be thought of as a fibrous polymer network, acting as a natural scaffolding to provide mechanical support to the cells. Reciprocal mechanical and chemical interactions between the cells and the ECM are crucial in regulating the development of tissues and maintaining their functionality. Hence, to maintain in vivo-like behaviour when cells are cultured in vitro, they are often seeded in a gel, which aims to mimic the ECM. In this paper, we present a mathematical model that incorporate cell-gel interactions together with osmotic pressure to study the mechanical behaviour of biological gels. In particular, we consider an experiment where cells are seeded within a gel, which gradually compacts due to forces exerted on it by the cells. Adopting a one-dimensional Cartesian geometry for simplicity, we use a combination of analytical techniques and numerical simulations to investigate how cell traction forces interact with osmotic effects (which can lead to either gel swelling or contraction depending on the gel’s composition). Our results show that a number of qualitatively different behaviours are possible, depending on the composition of the gel (i.e. the chemical potentials) and the strength of the cell traction forces. We observe an unusual case where the gel oscillates between swelling and contraction. We also consider on how physical parameters like drag and viscosity affect the manner in which the gel evolves.
Exact breakpoints of In(1)wm4 rearrangement
Authors: Solodovnikov A. A. , Lavrov S. A. 
Published: December 2021

AbstractIn(1)wm4 was known for decades as a classic example of position effect variegation-causing rearrangement and was mentioned in hundreds of publications. Nevertheless, the euchromatin breakpoint position of the rearrangement was not precisely localized. We performed nanopore sequencing of DNA from In(1)wm4 homozygous flies and determined the exact position of euchromatic (chrX:2767875) and heterochromatic breakpoints of the rearrangement.
Isolation and characterization of fucosylated extracellular vesicles based on a novel high-throughput GlyExo-Capture technique
Authors: Li Boan , Hao Kun , Ma Cuidie , Li Zhengtai , Li Hongjiang , Du Wenqian , Sun Lijuan , Jia Tianye , Liu Aixia , Li Yanzhao , Xu Lida , Gao Qi , Yang Ruifu , Lin Changqing 
Published: December 2021

ABSTRACTOwing to their diagnostic and therapeutic potential, extracellular vesicles (EVs) derived from tumour cells have recently garnered great interest. The presence of different glycosylation sites at the EV surface supports the need for efficient glycosylated EV isolation. Here, we developed a GlyExo-Capture technique for robustly capturing fucosylated EVs from sera and cell supernatants. Lens culinaris lectin (LCA)-immobilized magnetic complexes were found to capture approximately 60% of the total EVs from HepG2 cells. The capture efficiency was reduced to less than 40% in nontumorigenic MIHA cells. Notably, the cellular uptake pattern of highly fucosylated EVs was markedly different from that of EVs with low fucosylation. The unearthing of enriched fucosylated EV miRNA cargos by next-generation deep sequencing (NGS) revealed 75 differentially expressed miRNAs (DEMs) in hepatocellular carcinoma (HCC). Among them, a 4-miRNA panel was chosen and yielded an area under the ROC curve (AUC) of 0.86 and 0.84 for the detection of HCC from non-HCC controls in testing samples and independent validation samples, respectively. The 4-miRNA signature was independent of alpha-fetoprotein (AFP), and a combined model with AFP yielded an increased AUC of 0.92. In conclusion, we developed a high-throughput method for capturing fucosylated EVs efficiently and shed light on the use of fucosylated EVs as potential sources of miRNAs for cancer biomarker detection.
Preliminary Characterization of Phage-like Particles from the Male-Killing MollicuteSpiroplasma poulsonii(an Endosymbiont ofDrosophila)
Authors: Ramirez Paulino , Leavitt Justin C. , Gill Jason J. , Mateos Mariana 
Published: December 2021

AbstractBacteriophages are vastly abundant, diverse, and influential, but with few exceptions (e.g. the Proteobacteria generaWolbachiaandHamiltonella), the role of phages in heritable bacteria-arthropod interactions, which are ubiquitous and diverse, remains largely unexplored. Despite prior studies documenting phage-like particles in the mollicuteSpiroplasmaassociated withDrosophilaflies, genomic sequences of such phage are lacking, and their effects on theSpiroplasma-Drosophilainteraction have not been comprehensively characterized. We used a density step gradient to isolate phage-like particles from the male-killing bacteriumSpiroplasma poulsonii(strains NSRO and MSRO-Br) harbored byDrosophila melanogaster. Isolated particles were subjected to DNA sequencing, assembly, and annotation. Several lines of evidence suggest that we recovered phage-like particles of similar features (shape, size, DNA content) to those previously reported inDrosophila-associatedSpiroplasmastrains. We recovered three ∼19 kb phage-like contigs (two in NSRO and one in MSRO-Br) containing 21–24 open reading frames, a read-alignment pattern consistent with circular permutation, and terminal redundancy (at least in NSRO). Although our results do not allow us to distinguish whether these phage-like contigs represent infective phage-like particles capable of transmitting their DNA to new hosts, their encoding of several typical phage genes suggests that they are at least remnants of functional phage. We also recovered two smaller non-phage-like contigs encoding a knownSpiroplasmatoxin (Ribosome Inactivating Protein; RIP), and an insertion element, suggesting that they are packaged into particles. Substantial homology of our particle-derived contigs was found in the genome assemblies of members of theSpiroplasma poulsoniiclade.
InterPepScore: A Deep Learning Score for Improving the FlexPepDock Refinement Protocol
Authors: Johansson-Åkhe Isak , Wallner Björn 
Published: December 2021

AbstractMotivationInteractions between peptide fragments and protein receptors are vital to cell function yet difficult to experimentally determine the structural details of. As such, many computational methods have been developed to aid in peptide-protein docking or structure prediction. One such method is Rosetta FlexPepDock which consistently refines coarse peptide-protein models into sub-Ångström precision using Monte-Carlo simulations and statistical potentials. Deep learning has recently seen increased use in protein structure prediction, with graph neural network seeing use in protein model quality assessment.ResultsHere, we introduce a graph neural network, InterPepScore, as an additional scoring term to complement and improve the Rosetta FlexPepDock refinement protocol. InterPepScore is trained on simulation trajectories from FlexPepDock refinement starting from thousands of peptide-protein complexes generated by a wide variety of docking schemes. The addition of InterPepScore into the refinement protocol consistently improves the quality of models created, and on an independent benchmark on 109 peptide-protein complexes its inclusion results in an increase in the number of complexes for which the top-scoring model had a DockQ-score of 0.49 (Medium quality) or better from 14.8% to 26.1%.AvailabilityInterPepScore is available online at http://wallnerlab.org/InterPepScore.
The role of surface adhesion on the macroscopic wrinkling of biofilms
Authors: Geisel Steffen , Secchi Eleonora , Vermant Jan 
Published: December 2021

AbstractBiofilms, bacterial communities of cells encased by a self-produced matrix, exhibit a variety of three-dimensional structures. Specifically, channel networks formed within the bulk of the biofilm have been identified to play an important role in the colonies viability by promoting the transport of nutrients and chemicals. Here, we study channel formation and focus on the role of the adhesion of the biofilm matrix to the substrate in Pseudomonas aeruginosa biofilms grown under constant flow in microfluidic channels. We perform phase contrast and confocal laser scanning microscopy to examine the development of the biofilm structure as a function of the substrates surface energy. The formation of the wrinkles and folds is triggered by a mechanical buckling instability, controlled by biofilm growth rate and the film’s adhesion to the substrate. The three-dimensional folding gives rise to hollow channels that rapidly increase the overall volume occupied by the biofilm and facilitate bacterial movement inside them. The experiments and analysis on mechanical instabilities for the relevant case of a bacterial biofilm grown during flow enable us to predict and control the biofilm morphology.
Comparing Brain Asymmetries Independently of Brain Size
Authors: Williams Camille Michèle , Peyre Hugo , Toro Roberto , Ramus Franck 
Published: December 2021

AbstractStudies examining cerebral asymmetries typically divide the L-R Measure (e.g., Left– Right Volume) by the L+R Measure to obtain an Asymmetry Index (AI). However, contrary to widespread belief, such a division fails to render the AI independent from the L+R Measure and/or from total brain size. As a result, variations in brain size may bias correlation estimates with the AI or group differences in AI. We investigated how to analyze brain asymmetries in to distinguish global from regional effects, and report unbiased group differences in cerebral asymmetries.We analyzed the extent to which the L+R Measure, Total Cerebral Measure (TCM, e.g., Total Brain Volume), and L-R TCM predict regional asymmetries. As a case study, we assessed the consequences of omitting each of these predictors on the magnitude and significance of sex differences in asymmetries.We found that the L+R Measure, the TCM, and the L-R TCM predicted the AI of more than 89% of regions and that their relationships were generally linear. Removing any of these predictors changed the significance of sex differences in 33% of regions and the magnitude of sex differences across 13-42% of regions. Although we generally report similar sex and age effects on cerebral asymmetries to those of previous large-scale studies, properly adjusting for regional and global brain size revealed additional sex and age effects on brain asymmetry.Highlights-The typical Asymmetry Index (AI) scales with the size of a region and brain size.-Omitting the Left+Right Measure influences reported sex differences in asymmetries.-Omitting brain size or asymmetry influences reported sex differences in asymmetries.-We report sex and age effects on AIs independent of regional and global brain size.
A novel Alex3/Gαqprotein complex regulating mitochondrial dynamics, dendritic complexity, and neuronal survival
Authors: Izquierdo-Villalba Ismael , Mirra Serena , Manso Yasmina , Parcerisas Antoni , Rubio Javier , Del Valle Jaume , Gil-Bea Francisco J. , Ulloa Fausto , Herrero-Lorenzo Marina , Verdaguer Ester , Benincá Cristiane , Castro-Torres Rubén D. , Rebollo Elena , Marfany Gemma , Auladell Carme , Navarro Xavier , Enríquez José A. , de Munain Adolfo López , Aragay Anna M. , Soriano Eduardo 
Published: December 2021

AbstractIn neurons, mitochondrial dynamics and trafficking are essential to provide the energy required for neurotransmission and neuronal activity. Recent studies point to GPCR and G proteins as important regulators of mitochondrial dynamics and energy metabolism. Here we show that activation of Gαqnegatively regulates mitochondrial dynamics and trafficking in neurons. Gαqinteracts with the mitochondrial trafficking protein Alex3. By generating a CNS-specificarmcx3knock-out mouse line, we demonstrate that Alex3 is required for Gαqeffects on mitochondrial dynamics and trafficking, and dendritic growth.Armcx3-deficient mice present decreased OXPHOS complex and ER stress response protein levels, which correlate with increased neuronal death, motor neuron and neuromuscular synaptic loss, and severe motor alterations. Finally, we show that Alex3 disassembles from the Miro1/Gαqcomplex upon calcium rise. These data uncover a novel Alex3/Gαqcomplex that regulates neuronal mitochondrial dynamics and neuronal death and allows the control of mitochondrial functions by GPCRs.
Variable oxygen environments and DNMT2 determine the DNA cytosine epigenetic landscape of Plasmodium falciparum
Authors: Hammam Elie , Miled Samia , Bonhomme Frédéric , Arcangioli Benoit , Arimondo Paola B. , Scherf Artur 
Published: December 2021

AbstractDNA cytosine methylation and its oxidized products are important epigenetic modifications in mammalian cells. Although 5-methylcytosine (5mC) was detected in the human malaria parasite Plasmodium falciparum, the presence of oxidized 5mC forms remain to be characterized. Here we establish a protocol to optimize nuclease-based DNA digestion for the extremely AT-rich genome of P. falciparum (>80% A+T) for quantitative LC-MS/MS analysis of 5-hydroxymethylcytosine (5hmC), 5-formylcytosine (5fC) and 5-carboxylcytosine (5caC). We demonstrate the presence of 5hmC, 5fC and 5caC cytosine modifications in a DNMT2-only organism and observe striking ratio changes between 5mC and 5hmC during the 48-hour blood stage parasite development. Parasite-infected red blood cells cultured in different physiological oxygen concentrations revealed a shift in the cytosine modifications distribution towards the oxidized 5hmC and 5caC forms. In the absence of the canonical C5-DNA methyltransferase (DNMT1 and DNMT3A/B) in P. falciparum, we show that all cytosine modifications depend on the presence of DNMT2. We conclude that DNMT2 and oxygen levels are critical determinants that shape the dynamic cytosine epigenetic landscape in this human pathogen.
NITROGEN LIMITATION ADAPTATIONfunctions as a negative regulator of Arabidopsis immunity
Authors: Val-Torregrosa Beatriz , Bundó Mireia , Chiou Tzyy-Jen , Flors Victor , Segundo Blanca San 
Published: December 2021

AbstractBackgroundPhosphorus is an important macronutrient required for plant growth and development. It is absorbed through the roots in the form of inorganic phosphate (Pi). To cope with Pi limitation, plants have evolved an array of adaptive mechanisms to facilitate Pi acquisition and protect them from stress caused by Pi starvation. The NITROGEN LIMITATION ADAPTION (NLA) gene plays a key role in the regulation of phosphate starvation responses (PSR), its expression being regulated by the microRNA miR827. Stress caused by Pi limiting conditions might also affect the plant’s response to pathogen infection. However, cross-talk between phosphate signaling pathways and immune responses remains unclear.ResultsIn this study, we investigated whetherNLAplays a role in Arabidopsis immunity. We show that loss-of-function ofNLAandMIR827overexpression causes an increase in phosphate (Pi) content which results in resistance to infection by the fungal pathogenPlectosphaerella cucumerina. Thenlamutant plants accumulated callose in their leaves, a response that is also observed in wild-type plants that have been treated with high Pi. We also show that pathogen infection and treatment with fungal elicitors is accompanied by transcriptional activation ofMIR827and down-regulation ofNLA. Upon pathogen challenge,nlaplants exhibited higher levels of the phytoalexin camalexin compared to wild type plants. Camalexin level also increases in wild type plants treated with high Pi. Furthermore, thenlamutant plants accumulated salicylic acid (SA) and jasmonic acid (JA) in the absence of pathogen infection whose levels further increased upon pathogen.ConclusionsThis study shows thatNLAacts as a negative regulator of Arabidopsis immunity. Overaccumulation of Pi innlaplants positively affects resistance to infection by fungal pathogens. This piece of information reinforces the idea of signaling convergence between Pi and immune responses for the regulation of disease resistance in Arabidopsis.
Divalent metal ions boost effect of nucleic acids delivered by cell-penetrating peptides
Authors: Maloverjan Maria , Padari Kärt , Abroi Aare , Rebane Ana , Pooga Margus 
Published: December 2021

ABSTRACTCell-penetrating peptides (CPPs) are promising tools for transfection of various substances, including nucleic acids, into cells. The aim of current work was to search for novel safe and effective approaches for enhancing transfection efficiency of nanoparticles formed of CPP and splice-correcting oligonucleotide (SCO) without increasing the concentration of peptide. We analyzed an effect of inclusion of calcium and magnesium ions into nanoparticles on CPP-mediated transfection in cell culture. We also studied the mechanism of such transfection as well as its efficiency, applicability in case of different cell lines, nucleic acid types and peptides, and possible limitations. We discovered a strong positive effect of these ions on transfection efficiency of SCO, that translated to enhanced synthesis of functional reporter protein. We observed significant changes in intracellular distribution and trafficking of nanoparticles formed with addition of the ions, without increasing cytotoxicity. We propose a novel strategy of preparing CPP-oligonucleotide nanoparticles with enhanced efficiency and, thus, higher therapeutic potential. Our discovery may be translated to primary cell cultures and, possibly, in vivo studies, in the aim to increase CPP-mediated transfection efficiency and likelihood of using CPPs in clinics.
BioImageIT: Open-source framework for integration of image data-management with analysis
Authors: Prigent Sylvain , Valades-Cruz Cesar Augusto , Leconte Ludovic , Maury Leo , Salamero Jean , Kervrann Charles 
Published: December 2021

AbstractOpen science and FAIR principles have become major topics in the field of bioimaging. This is due to both new data acquisition technologies that generate large datasets, and new analysis approaches that automate data mining with high accuracy. Nevertheless, data are rarely shared and rigorously annotated because it requires a lot of manual and tedious management tasks and software packaging. We present BioImageIT, an open-source framework for integrating data management according to FAIR principles with data processing.
Novel piece of the puzzle: ALI1 is required for oxo-C14-HSL priming in Arabidopsis
Authors: Shrestha Abhishek , Hernández-Reyes Casandra , Grimm Maja , Krumwiede Johannes , Stein Elke , Schenk Sebastian T. , Schikora Adam 
Published: December 2021

AbstractQuorum sensing (QS) molecules mediate communication between bacterial cells. N-acyl homoserine lactones (AHL) are one of the best-studied groups of QS molecules. In addition to bacterial communication, AHL are involved in interactions with eukaryotes. Short side-chain AHL are readily taken up by plants. They induce root elongation and growth promotion. Hydrophobic long side-chain AHL are usually not transported over long distances although, they may prime plants for enhanced resistance. Unfortunately, studies elucidating the plant factors required for response to AHL are sparse. Here, we provide evidence of a plant protein, namely the AHL-priming protein 1 (ALI1), indispensable for enhanced resistance response induced by the N-3-oxotetradecanoyl-homoserine lactone (oxo-C14-HSL). Comparing Col-0 and the ali1 mutant, we revealed loss of AHL-priming in ali1. This phenomenon is reverted with the reintroduction of ALI1 into ali1. Additional transcriptome analysis revealed that ali1 is less sensitive to oxo-C14-HSL treatment compared to the wild-type. Our results suggest, therefore, that ALI1 is required for oxo-C14-HSL-dependent priming for enhanced resistance in Arabidopsis.
Clonal transcriptomics identifies mechanisms of chemoresistance and empowers rational design of combination therapies
Authors: Wild Sophia A , Cannell Ian G , Kania Katarzyna , Nicholls Ashley , Bressan Dario ,   CRUK IMAXT Grand Challenge Team, Hannon Gregory J , Sawicka Kirsty 
Published: December 2021

AbstractTumor heterogeneity is thought to be a major barrier to successful cancer treatment due to the presence of drug resistant clonal lineages. However, identifying the characteristics of such lineages that underpin resistance to therapy has remained challenging. Here we utilize clonal transcriptomics with WILD-seq; Wholistic Interrogation of Lineage Dynamics by sequencing, in mouse models of triple-negative breast cancer (TNBC) to understand response and resistance to therapy, including BET bromodomain inhibition and taxane-based chemotherapy. This analysis revealed oxidative stress protection by NRF2 as a major mechanism of taxane resistance and led to the discovery that our tumor models are collaterally sensitive to asparagine deprivation therapy using the clinical stage drug L-asparaginase after frontline treatment with docetaxel. In summary, clonal transcriptomics with WILD-seq identifies mechanisms of resistance to chemotherapy that are also operative in patients and pin points asparagine bioavailability as a druggable vulnerability of taxane resistant lineages.