bluuebunny/crossref_metadata_2025_split huggingface dataset:
Building predictive Markov State Models of ion channel permeation from Molecular Dynamics
Authors: Catacuzzeno Luigi , Leonardi Maria Vittoria , Franciolini Fabio , Domene Carmen , Michelucci Antonio , Furini Simone 
Published: February 2024

AbstractMolecular dynamics (MD) simulation of biological processes has always been a very challenging task due to the long timescales of the processes involved and the challenges associated with handling the large amount of output data. Markov State Models (MSMs) have been recently introduced as a powerful tool in this area of research, as they provide a mechanistically comprehensible synthesis of the large amount of MD data and, at the same time, can be used to estimate experimental properties of biological processes. Of the many studies on protein simulation and the MSM-assisted approach, only a few have addressed ion channel permeation and, more importantly, none of these have tried to build a model capable to predict the currents passing through the channels, which are ultimately crucial for comparing simulations with experimental results. Herein, we propose a method for building an MSM of ion channel permeation that correctly evaluates the current flowing through the channel. This was done by including in the model the definition of a flux matrix carrying information on the charge moving across the channel, suitably built to be used in conjunction with the transition matrix to predict the ion current. The proposed method is also able to drastically reduce the number of states so to obtain an MSM simple enough to be easily understood. Finally, we applied the method to the KcsA channel, obtaining a four-state MSM capable of accurately reproducing the single channel ion current from microseconds MD trajectories.
NINJ1 regulates ferroptosis via xCT antiporter interaction and CoA modulation
Authors: Chen Ssu-Yu , Lin Chao-Chieh , Wu Jianli , Chen Yubin , Wang Ya-En , Setayeshpour Yasaman , Mestre Alexander , Chi Jen-Tsan 
Published: February 2024

AbstractNinjurin-1 (NINJ1), initially identified as a stress-induced protein in neurons, recently emerged as a key mediator of plasma membrane rupture during apoptosis, necrosis, and pyroptosis. However, its involvement in ferroptosis remains unknown. Here, we demonstrate that NINJ1 also plays a crucial role in ferroptosis, but through a distinct mechanism. NINJ1 knockdown significantly protected cancer cells against ferroptosis induced by xCT inhibitors but no other classes of ferroptosis-inducing compounds (FINs). Glycine, known to inhibit canonical NINJ1-mediated membrane rupture in other cell deaths, had no impact on ferroptosis. A compound screen revealed that NINJ1-mediated ferroptosis protection can be abolished by pantothenate kinase inhibitor (PANKi), buthionine sulfoximine (BSO), and diethylmaleate (DEM). These results suggest that this ferroptosis protection is mediated via Coenzyme A (CoA) and glutathione (GSH), both of which were found to be elevated upon NINJ1 knockdown. Furthermore, we discovered that NINJ1 interacts with the xCT antiporter, which is responsible for cystine uptake for the biosynthesis of CoA and GSH. The removal of NINJ1 increased xCT levels and stability, enhanced cystine uptake, and contributed to elevated CoA and GSH levels, collectively contributing to ferroptosis protection. These findings reveal that NINJ1 regulates ferroptosis via a non-canonical mechanism, distinct from other regulated cell deaths.Graphical abstract
Ubiquitinated histone H2B as gatekeeper of the nucleosome acidic patch
Authors: Hicks Chad W. , Rahman Sanim , Gloor Susan L. , Fields James K. , Husby Natalia Ledo , Vaidya Anup , Maier Keith E. , Morgan Michael , Keogh Michael-Christopher , Wolberger Cynthia 
Published: February 2024

ABSTRACTMonoubiquitination of histones H2B-K120 (H2BK120ub) and H2A-K119 (H2AK119ub) play opposing roles in regulating transcription and chromatin compaction. H2BK120ub is a hallmark of actively transcribed euchromatin, while H2AK119ub is highly enriched in transcriptionally repressed heterochromatin. Whereas H2BK120ub is known to stimulate the binding or activity of various chromatin-modifying enzymes, this post-translational modification (PTM) also interferes with the binding of several proteins to the nucleosome H2A/H2B acidic patch via an unknown mechanism. Here we report cryoEM structures of an H2BK120ub nucleosome showing that ubiquitin adopts discrete positions that occlude the acidic patch. Molecular dynamics simulations show that ubiquitin remains stably positioned over this nucleosome region. By contrast, our cryoEM structures of H2AK119ub nucleosomes show ubiquitin adopting discrete positions that minimally occlude the acidic patch. Consistent with these observations, H2BK120ub, but not H2AK119ub, abrogates nucleosome interactions with acidic patch-binding proteins RCC1 and LANA, and single-domain antibodies specific to this region. Our results suggest a mechanism by which H2BK120ub serves as a gatekeeper to the acidic patch and point to distinct roles for histone H2AK119 and H2BK120 ubiquitination in regulating protein binding to nucleosomes.
Identification of Alpha-Gal conjugated Lipids in Saliva of Lone-Star Tick (Amblyomma americanum)
Authors: Sharma Surendra Raj , Hussain Sabir , Choudhary Shailesh K. , Commins Scott P. , Karim Shahid 
Published: February 2024

AbstractAlpha-Gal Syndrome (AGS) is a delayed allergic reaction triggered by IgE antibodies targeting galactose-α-1,3-galactose (α-gal), prevalent in red meat. Its global significance has increased, with over 450,000 estimated cases in the United States alone. AGS is linked to tick bites, causing sensitization and elevated α-gal specific IgE levels. However, the precise mechanisms and tick intrinsic factors contributing to AGS development post-tick bites remain unclear. This study aims to characterize the alphagal conjugated lipid antigens inAmblyomma americanum(Am. americanum) salivary glands and saliva. Nanospray ionization mass spectrometry (NSI-MS) analysis revealed the identification of α-gal bound lipid antigens inAm. americanumsaliva. Additionally, activation of basophils by isolated alpha-gal bound lipids and proteins provides evidence of their antigenic capabilities.
Modern Insights into Muscle Glycogen Phosphorylase Activity
Authors: Kiriaev Leonit , Oakhill Jonathan S. , Tiong Chrystal F. , Seto Jane T. , Crossman Vanessa G. , Quinlan Kate G.R. , North Kathryn N. , Houweling Peter J. , Ling Naomi X.Y. 
Published: February 2024

ABSTRACTRecent identification of new human muscle glycogen phosphorylation sites has renewed interest in understanding human variations in the regulation of glycogen metabolism and glucose homeostasis. This paper presents a detailed method for the measurement of glycogen phosphorylase (GPh) activity in skeletal muscle. Our approach incorporates modifications to existing radiolabelling assays, optimizing specificity and sensitivity while enabling the assessment of both active and total enzyme activity levels. The utilization of radioisotope tracers and scintillation counting ensures accurate quantification of GPh activity, which we use to validate a previously published reduction in GPh activity in anActn3deficient mouse model. Moreover, we introduce a step-by-step guide for data acquisition, highlight the use of appropriate homogenization, discuss the need for allosteric activators/inhibitors and the importance of assay optimization to record a GPh activity assay for skeletal muscle. In conclusion, our refined method not only contributes to a deeper understanding of glycogen metabolism in muscle tissue but also provides a framework for future investigations, underscoring its role in advancing research on glycogen utilization and glucose homeostasis.NEW & NOTEWORTHYThe study optimizes the glycogen phosphorylase radiolabelled activity assay, unveiling nuances in muscle homogenization, sample dilution, and caffeine inclusion. The research introduces standardized conditions, enhancing assay reliability and reproducibility across mouse strains to reveal sex specific variations in GPh activity and underscore novel distinctions in an Actn3 deficient mouse model. These findings advance our understanding of muscle glycogen metabolism, offering a crucial tool for researchers and facilitating meaningful inter-laboratory comparisons.
Another fly diuretic hormone: tachykinins increase fluid and ion transport by adultDrosophila melanogasterMalpighian ‘renal’ tubules
Authors: Agard Marishia A. , Zandawala Meet , Paluzzi Jean-Paul V. 
Published: February 2024

AbstractInsects like the model organismDrosophila melanogastermust modulate their internal physiology to withstand changes in temperature and availability of water and food. Regulation of the excretory system by peptidergic hormones is one mechanism by which insects maintain their internal homeostasis. Tachykinins are a family of neuropeptides that have been shown to stimulate fluid secretion from the Malpighian ‘renal’ tubules (MTs) in some insect species, but it is unclear if that is the case in the fruit fly,D. melanogaster. A central objective of the current study was to examine the physiological role of tachykinin signaling in the MTs of adultD. melanogaster. Using the genetic toolbox available in this model organism along within vitroand whole animal bioassays, our results indicate thatDrosophilatachykinins (DTKs) function as diuretic hormones by binding to the DTK receptor (DTKR) expressed in stellate cells of the MTs. Specifically, DTK activates cation and anion transport across the stimulated MTs, which impairs their survival in response to desiccation due to their inability to conserve water. Thus, besides their previously described roles in neuromodulation of pathways controlling locomotion and food search, olfactory processing, aggression, lipid metabolism and metabolic stress, processing of noxious stimuli and hormone release, DTKs also appear to function asbona fideendocrine factors regulating the excretory system and appear essential for the maintenance of hydromineral balance.Summary statementDrosophilatachykinins are diuretic hormones in the fly that regulate activity of the MTs and, consequently, contribute towards the maintenance of ionic and osmotic homeostasis.
Generation of diversity in the blue cheese moldPenicillium roquefortiand identification of pleiotropic QTL for key cheese-making phenotypes
Authors: Caron Thibault , Crequer Ewen , Le Piver Mélanie , Le Prieur Stéphanie , Brunel Sammy , Snirc Alodie , Cueff Gwennina , Roueyre Daniel , Place Michel , Chassard Christophe , Simon Adeline , Rodriguez de la Vega Ricardo , Coton Monika , Coton Emmanuel , Foulongne-Oriol Marie , Branca Antoine , Giraud Tatiana 
Published: February 2024

AbstractElucidating the genomic architecture of quantitative traits is essential for our understanding of adaptation and for breeding in domesticated organisms.Penicillium roquefortiis the mold used worldwide for the blue cheese maturation, contributing to flavors through proteolytic and lipolytic activities. The two domesticated cheese populations display very little genetic diversity, but are differentiated and carry opposite mating types. We produced haploid F1 progenies from five crosses, using parents belonging to cheese and non-cheese populations. Analyses of high-quality genome assemblies of the parental strains revealed five large translocations, two having occurred via a circular intermediate. Offspring genotyping with genotype-by-sequencing (GBS) revealed several genomic regions with segregation distortion, possibly linked to degeneration in cheese lineages. We found transgressions for several traits relevant for cheese making, with offspring having more extreme trait values than parental strains. We identified quantitative trait loci (QTLs) for colony color, lipolysis, proteolysis, extrolite production, including mycotoxins, but not for growth rates. Some genomic regions appeared rich in QTLs for both lipid and protein metabolism, and other regions for the production of multiple extrolites, indicating that QTLs have pleiotropic impacts. Some QTLs corresponded to known biosynthetic gene clusters, e.g., for the production of melanin or extrolites. F1 hybrids constitute valuable strains for cheese producers, with new traits and genetic diversity, and allowed identifying target genomic regions for traits important in cheese making, paving the way for strain improvement. The findings further contribute to our understanding of the genetic mechanisms underlying rapid adaptation, revealing convergent adaptation targeting major regulators.
Enhancement of colorectal cancer therapy through interruption of the HSF1-HSP90 axis by p53 activation or cell cycle inhibition
Authors: Isermann Tamara , Schneider Kim Lucia , Wegwitz Florian , De Oliveira Tiago , Conradi Lena-Christin , Volk Valery , Feuerhake Friedrich , Papke Björn , Stintzing Sebastian , Mundt Bettina , Kühnel Florian , Moll Ute M. , Schulz-Heddergott Ramona 
Published: February 2024

ABSTRACTThe stress-associated molecular chaperone system is an actionable target in cancer therapies. It is ubiquitously upregulated in cancer tissues and enables tumorigenicity by stabilizing hundreds of oncoproteins and disturbing the stoichiometry of protein complexes. Most inhibitors target the key component heat-shock protein 90 (HSP90). However, although classical HSP90 inhibitors are highly tumor-selective, they fail in phase 3 clinical oncology trials. These failures are at least partly due to an interference with a negative feedback loop by HSP90 inhibition, known as heat-shock response (HSR): in response to HSP90 inhibition there is compensatory synthesis of stress-inducible chaperones, mediated by the transcription factor heat-shock factor 1 (HSF1). We recently identified that wildtype p53 (p53) actively reduces the HSR by repressing HSF1 via a p21-CDK4/6-MAPK-HSF1 axis. Here we test the hypothesis that in HSP90-based therapies simultaneous p53 activation or direct cell cycle inhibition interrupts the deleterious HSF1-HSR axis and improves the efficiency of HSP90 inhibitors.Indeed, we find that the clinically relevant p53 activator Idasanutlin suppresses the HSF1-HSR activity in HSP90 inhibitor-based therapies. This combination synergistically reduces cell viability and accelerates cell death in p53-proficient colorectal cancer (CRC) cells, murine tumor-derived organoids and patient-derived organoids (PDOs). Mechanistically, upon combination therapy human CRC cells strongly upregulate p53-associated pathways, apoptosis, and inflammatory immune pathways. Likewise, in the chemical AOM/DSS CRC model in mice, dual HSF1-HSP90 inhibition strongly represses tumor growth and remodels immune cell composition, yet displays only minor toxicities in mice and normal mucosa-derived organoids. Importantly, inhibition of the cyclin dependent kinases 4 and 6 (CDK4/6) under HSP90 inhibition phenocopies synergistic repression of the HSR in p53-proficient CRC cells. Even more important, in p53-deficient (mutp53-harboring) CRC cells, an HSP90 inhibition in combination with CDK4/6 inhibitors similarly suppresses the HSF1-HSR system and reduces cancer growth. Likewise, p53-mutated PDOs strongly respond to dual HSF1-HSP90 pathway inhibition and thus, providing a strategy to target CRC independent of the p53 status.In sum, activating p53 (in p53-proficient cancer cells) or inhibiting CDK4/6 (independent of the p53 status) provide new options to improve the clinical outcome of HSP90-based therapies and to enhance colorectal cancer therapy.
PL-PatchSurfer3: Improved Structure-Based Virtual Screening for Structure Variation Using 3D Zernike Descriptors
Authors: Shin Woong-Hee , Kihara Daisuke 
Published: February 2024

ABSTRACTStructure-based virtual screening (SBVS) is a widely used method in silico drug discovery. It necessitates a receptor structure or binding site to predict the binding pose and fitness of a ligand. Therefore, the performance of the SBVS is affected by the protein conformation. The most frequently used method in SBVS is the protein-ligand docking program, which utilizes atomic distance-based scoring functions. Hence, they are highly prone to sensitivity towards variation in receptor structure, and it is reported that the conformational change significantly drops the performance of the docking program.To address the problem, we have introduced a novel program of SBVS, named PL-PatchSurfer. This program makes use of molecular surface patches and the Zernike descriptor. The surfaces of the pocket and ligand are segmented into several patches by the program. These patches are then mapped with physico-chemical properties such as shape and electrostatic potential before being converted into the Zernike descriptor, which is rotationally invariant. A complementarity between the protein and the ligand is assessed by comparing the descriptors and geometric distribution of the patches in the molecules. A benchmarking study showed that PL-PatchSurfer2 was able to screen active molecules regardless of the receptor structure change with fast speed. However, the program could not achieve high performance for the targets that the hydrogen bonding feature is important such as nuclear hormone receptors.In this paper, we present the newer version of PL-PatchSurfer, PL-PatchSurfer3, which incorporates two new features: a change in the definition of hydrogen bond complementarity and consideration of visibility that contains curvature information of a patch. Our evaluation demonstrates that the new program outperforms its predecessor and other SBVS methods while retaining its characteristic tolerance to receptor structure changes. Interested individuals can access the program atkiharalab.org/plps3.
Optimising the production of dsRNA biocontrols in microbial systems using multiple transcriptional terminators
Authors: Ross Sebastian J. , Owen Gareth R. , Hough James , Philips Annelies , Maddelein Wendy , Ray John , Kilby Peter M. , Dickman Mark J. 
Published: February 2024

AbstractCrop pests and pathogens annually cause over $100 billion in global crop damage, with insects consuming 5-20% of major grain crops. Current crop pest and disease control strategies rely on insecticidal and fungicidal sprays, plant genetic resistance, transgenes and agricultural practices. dsRNA is emerging as a novel sustainable method of plant protection as an alternative to traditional chemical pesticides. Successful commercialisation of dsRNA based biocontrols requires the economical production of large quantities of dsRNA combined with suitable delivery methods to ensure RNAi efficacy against the target pest. In this study, we have optimised the design of plasmid DNA constructs to produce dsRNA biocontrols inE. coli, by employing a wide range of alternative synthetic transcriptional terminators prior to measurement of dsRNA yield. We demonstrate that a 7.8-fold increase of dsRNA was achieved using triple synthetic transcriptional terminators within a dual T7 dsRNA production system compared to the absence of transcriptional terminators. Moreover, our data demonstrates that batch fermentation production dsRNA using multiple transcriptional terminators is scalable and generates significantly higher yields of dsRNA generated in the absence of transcriptional terminators at both small-scale batch culture and large-scale fermentation. In addition, we show that application of these dsRNA biocontrols expressed inE. colicells results in increased insect mortality. Finally, novel mass spectrometry analysis was performed to determine the precise sites of transcriptional termination at the different transcriptional terminators providing important further mechanistic insight.
An efficientin vivo-inducible CRISPR interference system for group AStreptococcusgenetic analysis and pathogenesis studies
Authors: Bjånes Elisabet , Stream Alexandra , Janssen Axel B. , Gibson Paddy S. , Bravo Afonso M. , Dahesh Samira , Baker Jonathon L. , Varble Andrew , Nizet Victor , Veening Jan-Willem 
Published: February 2024

AbstractWhile genome-wide transposon mutagenesis screens have identified numerous essential genes in the significant human pathogenStreptococcus pyogenes(group AStreptococcusor GAS), many of their functions remain elusive. This knowledge gap is attributed in part to the limited molecular toolbox for controlling GAS gene expression and the bacterium’s poor genetic transformability. CRISPR interference (CRISPRi), using catalytically inactive GAS Cas9 (dCas9), is a powerful approach to specifically repress gene expression in both bacteria and eukaryotes, but ironically has never been harnessed for controlled gene expression in GAS. In this study, we present a highly transformable and fully virulent serotype M1T1 GAS strain and introduce a doxycycline-inducible CRISPRi system for efficient repression of bacterial gene expression. We demonstrate highly efficient, oligo-based sgRNA cloning directly to GAS, enabling the construction of a gene knockdown strain in just two days, in contrast to the several weeks typically required. The system is shown to be titratable and functional bothin vitroandin vivousing a murine model of GAS infection. Furthermore, we provide directin vivoevidence that the expression of the conserved cell division geneftsZis essential for GAS virulence, highlighting its promise as a target for emerging FtsZ-inhibitors. Finally, we introduce SpyBrowse (https://veeninglab.com/SpyBrowse), a comprehensive and user-friendly online resource for visually inspecting and exploring GAS genetic features. The tools and methodologies described in this work are poised to facilitate fundamental research in GAS, contribute to vaccine development, and aid in the discovery of antibiotic targets.Significance statementWhile GAS remains a predominant cause of bacterial infections worldwide, there are limited genetic tools available to study its basic cell biology. Here, we bridge this gap by creating a highly transformable, fully virulent M1T1 GAS strain. In addition, we established a tight and titratable doxycycline-inducible system and developed CRISPR interference for controlled gene expression in GAS. We show that CRISPRi is functionalin vivoin a mouse infection model. Additionally, we present SpyBrowse, an intuitive and accessible genome browser (https://veeninglab.com/SpyBrowse). Overall, this work overcomes significant technical challenges of working with GAS, and together with SpyBrowse, represents a valuable resource for researchers in the GAS field.
Chromosome-level genome assembly and annotation of the social amoebaDictyostelium firmibasis
Authors: Edelbroek Bart , Kjellin Jonas , Jerlström-Hultqvist Jon , Koskiniemi Sanna , Söderbom Fredrik 
Published: February 2024

AbstractDicytostelium firmibasisis a member of Dictyostelia, a group of social amoebae that upon starvation display aggregative multicellularity where the amoebae transition from uni-to multicellular life. TheD. firmibasisgenome assembly that is currently available is of limited use due to its low contiguity, large number of undetermined bases, and lack of annotations. Here we used Nanopore long read sequencing, complemented with Illumina sequencing, and developmental transcriptomics as well as small RNA-sequencing, to present a new, fully annotated, chromosome-levelD. firmibasisgenome assembly. The new assembly contains no undetermined bases, and consists mainly of six large contigs representing the chromosomes, as well as a complete mitochondrial genome. This new genome assembly will be a valuable tool, allowing comprehensive comparison toDictyostelium discoideum, the dictyostelid genetically tractable model. Further, the new genome will be important for studies of evolutionary processes governing the transition from unicellular to multicellular organisms and will aid in the sequencing and annotation of other dictyostelids genomes, many of which are currently of poor quality.