bluuebunny/crossref_metadata_2025_split huggingface dataset:
Double and triple thermodynamic mutant cycles reveal the basis for specific MsbA-lipid interactions
Authors: Lyu Jixing , Zhang Tianqi , Marty Michael T. , Clemmer David , Russell David H. , Laganowsky Arthur 
Published: July 2023

AbstractStructural and functional studies of the ATP-binding cassette transporter MsbA have revealed two distinct lipopolysaccharide (LPS) binding sites: one located in the central cavity and the other at a membrane-facing, exterior site. Although these binding sites are known to be important for MsbA function, the thermodynamic basis for these specific MsbA-LPS interactions is not well understood. Here, we use native mass spectrometry to determine the thermodynamics of MsbA interacting with the LPS-precursor 3-deoxy-D-manno-oct-2-ulosonic acid (Kdo)2-lipid A (KDL). The binding of KDL is solely driven by entropy, despite the transporter adopting an inward-facing conformation or trapped in an outward-facing conformation with adenosine 5’-diphosphate and vanadate. An extension of the mutant cycle approach is employed to probe basic residues that interact with KDL. We find the molecular recognition of KDL is driven by a positive coupling entropy (as large as -100 kJ/mol at 298K) that outweighs unfavorable coupling enthalpy. These findings indicate that alterations in solvent reorganization and conformational entropy can contribute significantly to the free energy of protein-lipid association. The results presented herein showcase the advantage of native MS to obtain thermodynamic insight into protein-lipid interactions that would otherwise be intractable using traditional approaches, and this enabling technology will be instrumental in the life sciences and drug discovery.
Serotonergic Modulation of the BNST-CeA Circuit Promotes Sex Differences in Fear Learning
Authors: Ravenelle Rebecca , Fernandes-Henriques Carolina , Lee Jinah , Liu Jia , Likhtik Ekaterina , Burghardt Nesha S. 
Published: July 2023

AbstractPost-traumatic stress disorder (PTSD) is characterized by intense fear memory formation and is diagnosed more often in women than men. Here, we show that serotonin differentially affects fear learning and communication in the extended amygdala of male and female mice. Females showed higher sensitivity to the effects of pharmacologically increasing serotonin during auditory fear conditioning, which enhanced fear memory recall in both sexes. Optogenetic stimulation of dorsal raphe terminals in the anterior dorsal bed nucleus of the stria terminalis (adBNST) during fear conditioning increased c-Fos expression in the BNST and central nucleus of the amygdala (CeA), and enhanced fear memory recall via activation of adBNST 5-HT2C receptors in females only. Likewise, in females only, serotonin stimulation during learning enhanced adBNST-CeA high gamma (90-140Hz) synchrony and adBNST-to-CeA communication in high gamma during fear memory recall. We conclude that sex differences in the raphe-BNST-CeA circuit may increase risk of PTSD in women.
ent-Verticilide B1 inhibits type 2 ryanodine receptor channels and is antiarrhythmic in Casq2-/- mice
Authors: Gochman Aaron , Do Tri Q. , Kim Kyungsoo , Schwarz Jacob A. , Thorpe Madelaine P. , Blackwell Daniel J. , Smith Abigail N. , Akers Wendell S. , Cornea Razvan L. , Laver Derek R. , Johnston Jeffrey N. , Knollmann Bjorn C. 
Published: July 2023

AbstractCa2+leak from cardiac ryanodine receptor (RyR2) is an established mechanism of sudden cardiac death (SCD), whereby dysregulated Ca2+handling causes ventricular arrhythmias. We previously discovered the RyR2-selective inhibitorent-(+)-verticilide (ent-1), a 24-membered cyclooligomeric depsipeptide that is the enantiomeric form of a natural product (nat-(-)-verticilide). Here, we examined its 18-membered ring-size oligomer (ent-verticilide B1; “ent-B1”) in single RyR2 channel assays, [3H]ryanodine binding assays, and inCasq2-/-cardiomyocytes and mice, a gene-targeted model of SCD.ent-B1 inhibited RyR2 single-channels and [3H]ryanodine binding with low micromolar potency, and RyR2-mediated spontaneous Ca2+release in Casq2-/- cardiomyocytes with sub-micromolar potency.ent-B1 was a partial RyR2 inhibitor, with maximal inhibitory efficacy of less than 50%.ent-B1 was stable in plasma, with a peak plasma concentration of 1460 ng/ml at 10 min and half-life of 45 min after intraperitoneal administration of 3 mg/kg in mice. Both 3 mg/kg and 30 mg/kgent-B1 significantly reduced catecholamine-induced ventricular arrhythmia in Casq2-/- mice. Hence, we have identified a novel chemical entity –ent-B1 – that preserves the mechanism of action of a hit compound and shows therapeutic efficacy. These findings strengthen RyR2 as an antiarrhythmic drug target and highlight the potential of investigating the mirror-image isomers of natural products to discover new therapeutics.Significance statementThe cardiac ryanodine receptor (RyR2) is an untapped target in the stagnant field of antiarrhythmic drug development. We have confirmed RyR2 as an antiarrhythmic target in a mouse model of sudden cardiac death and shown the therapeutic efficacy of a second enantiomeric natural product.
ColabDock: inverting AlphaFold structure prediction model for protein-protein docking with experimental restraints
Authors: Feng Shihao , Chen Zhenyu , Zhang Chengwei , Xie Yuhao , Ovchinnikov Sergey , Gao Yiqin , Liu Sirui 
Published: July 2023

AbstractPrediction of protein complex structures and interfaces potentially has wide applications and can benefit the study of biological mechanisms involving protein-protein interactions. However, the surface prediction accuracy of traditional docking methods and AlphaFold-Multimer is limited. Here we present ColabDock, a framework that makes use of ColabDesign, but reimplements it for the purpose of restrained complex conformation prediction. With a generation-prediction architecture and trained ranking model, ColabDock outperforms HADDOCK and ClusPro not only in complex structure predictions with simulated residue and surface restraints, but also in those assisted by NMR chemical shift perturbation as well as covalent labeling. It further assists antibody-antigen interface prediction with emulated interface scan restraints, which could be obtained by experiments such as Deep Mutation Scan. ColabDock provides a general approach to integrate sparse interface restraints of different experimental forms and sources into one optimization framework.
Transcriptional clusters follow a conserved condensation-dispersal sequence during stem cell differentiation
Authors: Klingberg Tim , Wachter Irina , Pancholi Agnieszka , Gohar Yomna , Kumar Priya , Sobucki Marcel , Kämmer Elisa , Eroğlu-Kayıkçı Süheyla , Erhardt Sylvia , Ferrai Carmelo , Zaburdaev Vasily , Hilbert Lennart 
Published: July 2023

AbstractSpatiotemporal organization of transcription is essential for organism development. Most eukaryotic genes are transcribed by RNA polymerase II (Pol II). In stem cells, Pol II forms prominent clusters, which gradually disappear during differentiation, such that only smaller clusters remain. Here, we ask whether the formation and loss of large Pol II clusters is a stereotypical process explicable by changes in the Pol II transcriptional state during differentiation. We assess clusters by super-resolution microscopy in differentiating mouse embryonic stem cells, sperm precursor formation in fruit flies, and germ layer induction in zebrafish. In all cases, Pol II clusters first become larger and rounder, then unfold, and finally disperse into small clusters. These shape changes are accompanied by initial increase in recruited Pol II, subsequent transition into transcript elongation, and finally reduction of active enhancers. We reproduce these observations using a biophysical surface condensation model, where enhancers support Pol II cluster formation, and transcriptional activity unfolds clusters. Our work indicates that changes in enhancer marks and transcriptional activity during differentiation define a stereotyped trajectory through a generally applicable space of cluster shapes.Graphical Abstract
Identifying conceptual neural responses to symbolic numerals
Authors: Retter Talia L. , Eraßmy Lucas , Schiltz Christine 
Published: July 2023

AbstractNeural processing of numerical concepts may be measured in humans automatically, without a related numerical task. However, the extent to which neural responses to symbolic numbers are due to physical stimulus confounds independently of conceptual representations remains unknown. Here, we targeted conceptual responses to parity (evenvs.odd), using an electroencephalographic (EEG) frequency-tagging approach with a symmetry/asymmetry paradigm. Fifty second sequences of Arabic numerals (2–9) were presented at 7.5 Hz; odd and even numbers were alternated, so that differential responses to parity would be captured at 3.75 Hz (7.5 Hz/2). Parity responses were probed with four different stimulus sets, increasing in intra-numeral stimulus variability. Moreover, two control conditions were tested for each stimulus set, comprised of non-conceptual numeral alternations (strong control, for small inter-group physical differences: 2,3,6,7vs.4,5,8 and 9; weak control, for large physical differences: 2,4,5,7vs. 3,6,8,9). Significant asymmetrical responses at 3.75 Hz were found over the occipitotemporal cortex to all conditions, thus even for arbitrary numeral groups. The weak control condition elicited the largest response in the stimulus set with the lowest level of variability (1 font). Only in the stimulus set with the highest level of variability (20 hand-drawn, colored exemplars per numeral) did the response to parity surpass both control conditions. These findings show that physical differences across small sets of Arabic numerals can strongly influence, and even account for, automatic brain responses. However, carefully designed control conditions and highly variable stimulus sets may be used towards identifying truly conceptual neural responses.
Gcn5 – mTORC1 – TFEB signalling axis mediated control of autophagy regulatesDrosophilablood cell homeostasis
Authors: Arjun AR , Math Suraj , Kata Laxmi , Khadilkar Rohan Jayant 
Published: July 2023

AbstractBlood progenitors are regulated by a variety of signals from their environment. In theDrosophilalymph gland (LG), the Posterior Signalling Center (PSC) acts as a stem cell niche striking a balance between progenitors and differentiated blood cells. While the response of blood progenitors to extrinsic signals is well characterized, their ability to respond to cell intrinsic cues is unexplored. Autophagy is one such intrinsic cellular process that maintains cellular homeostasis by removing unnecessary or dysfunctional cell components through autophagic degradation and recycling. Here, we show that autophagy plays a critical role in regulating blood cell homeostasis in the lymph gland. General control non-derepressible 5 (Gcn5), a histone acetyltransferase is expressed in all the cellular subsets of the LG and modulation of Gcn5 levels in various cellular subsets of the LG perturbs LG homeostasis. Gcn5 through its known non-histone acetylation target, TFEB controls autophagic flux thereby regulating hematopoiesis. Additionally, we demonstrate that modulation of mTORC1 activity can perturb hematopoiesis. We show that Gcn5 acts as a nutrient sensor and mTORC1 activity regulates Gcn5. mTORC1 over-rides the effect exerted by Gcn5 in regulating LG hematopoiesis. Together, our findings indicate that Gcn5 – mTORC1 – TFEB signaling axis mediated control of autophagy is required for maintaining blood cell homeostasis inDrosophila.
Comparison of robotic automated and manual injection methods in zebrafish embryos for high throughput RNA silencing using CRISPR-CasRx
Authors: Abugattas-Nuñez Del Prado Joaquin , Ding Yi , de Sonneville Jan , van der Kolk Kees-Jan , Moreno-Mateos Miguel A. , Málaga-Trillo Edward , Spaink Herman P. 
Published: July 2023

ABSTRACTRecently, the CRISPR-RfxCas13d (CasRx) system was proven to induce efficient mRNA knockdown in animal embryos. Here we compared the efficiency of CasRx-based RNA depletion with that of Cas9-mediated DNA targeting under the same conditions, using automated robotic and manual injection methods. As a proof-of-principle target, we used the no tail (tbxta) gene in zebrafish embryos, for which knockdown and knockout embryonic phenotypes were easy to be scored. Both Cas9 and CasRx systems induced loss of function phenotypes oftbxtagene. Higher percentage of severe phenotype was observed using Cas9 protein compared to the mRNA while the efficiency was similar in terms of Cas13d protein and mRNA. In addition, both the robotic and manual injection approaches yielded similar percentages of phenotypes and mortality rates. Therefore, our study not only showcases the potential of RNA-targeting CRISPR effectors for precise and potent gene knockdown, but also emphasizes automated microinjection in zebrafish embryos as an excellent alternative to manual methods for achieving gene knockdown at a high throughput level.
Activating the NFE2L1-ubiquitin-proteasome system by DDI2 protects from ferroptosis
Authors: Ofoghi Anahita , Kotschi Stefan , Lemmer Imke L. , Haas Daniel T. , Willemsen Nienke , Bayer Batoul , Möller Sophie , Haberecht-Müller Stefanie , Krüger Elke , Krahmer Natalie , Bartelt Alexander 
Published: July 2023

AbstractFerroptosis is an iron-dependent, non-apoptotic form of cell death initiated by oxidative stress and lipid peroxidation. Recent evidence has linked ferroptosis to the action of the transcription factor Nuclear factor erythroid-2 derived,-like-1 (NFE2L1). NFE2L1 regulates proteasome abundance in an adaptive fashion, maintaining protein quality control to secure cellular homeostasis, but the regulation of NFE2L1 during ferroptosis and the role of the ubiquitin-proteasome system (UPS) herein are still unclear. In the present study, using an unbiased proteomic approach charting the specific ubiquitylation sites, we show that induction of ferroptosis leads to recalibration of the UPS. RSL3-induced ferroptosis inhibits proteasome activity and leads to global hyperubiquitylation, which is linked to NFE2L1 activation. As NFE2L1 resides in the endoplasmic reticulum tethered to the membrane, it undergoes complex posttranslational modification steps to become active and induce the expression of proteasome subunit genes. We show that proteolytic cleavage of NFE2L1 by the aspartyl protease DNA-damage inducible 1 homolog 2 (DDI2) is a critical step for the ferroptosis-induced feed-back loop of proteasome function. Cells lacking DDI2 cannot activate NFE2L1 in response to RSL3 and show global hyperubiquitylation. Genetic or chemical induction of ferroptosis in cells with a disrupted DDI2-NFE2L1 pathway diminishes proteasomal activity and promotes cell death. Also, treating cells with the clinical drug nelfinavir, which inhibits DDI2, sensitized cells to ferroptosis. In conclusion, our results provide new insight into the importance of the UPS in ferroptosis and highlight the role of the DDI2-NFE2L1 as a potential therapeutic target. Manipulating DDI2-NFE2L1 activity through chemical inhibition might help sensitizing cells to ferroptosis, thus enhancing existing cancer therapies.Graphical abstract
Widespread analytical pitfalls in empirical coexistence studies and a checklist for improving their statistical robustness
Authors: Terry J. Christopher D. , Armitage David W. 
Published: July 2023

AbstractModern Coexistence Theory (MCT) offers a conceptually straightforward approach for connecting empirical observations with an elegant theoretical framework, gaining popularity rapidly over the past decade. However, beneath this surface-level simplicity lie various assumptions and subjective choices made during data analysis. These can lead researchers to draw qualitatively different conclusions from the same set of experiments. As the predictions of MCT studies are often treated as outcomes, and many readers and reviewers may not be familiar with the framework’s assumptions, there is a particular risk of “researcher degrees of freedom” inflating the confidence in results, thereby affecting reproducibility and predictive power.To tackle these concerns, we introduce a checklist consisting of statistical best-practices to promote more robust empirical applications of MCT. Our recommendations are organised into four categories: presentation and sharing of raw data, testing model assumptions and fits, managing uncertainty associated with model coefficients, and incorporating this uncertainty into coexistence predictions.We surveyed empirical MCT studies published over the past 15 years and discovered a high degree of variation in the level of statistical rigour and adherence to best practices. We present case studies to illustrate the dependence of results on seemingly innocuous choices among competition model structure and error distributions, which in some cases reversed the predicted coexistence outcomes. These results demonstrate how different analytical approaches can profoundly alter the interpretation of experimental results, underscoring the importance of carefully considering and thoroughly justifying each step taken in the analysis pathway.Our checklist serves as a resource for authors and reviewers alike, providing guidance to strengthen the empirical foundation of empirical coexistence analyses. As the field of empirical MCT shifts from a descriptive, trailblazing phase to a stage of consolidation, we emphasise the need for caution when building upon the findings of earlier studies. To ensure that progress made in the field of ecological coexistence is based on robust and reliable evidence, it is crucial to subject our predictions, conclusions, and generalizability to a more rigorous assessment than is currently the trend.
The structure of a novel ferredoxin – FhuF, a ferric-siderophore reductase from E. coli K-12 with a novel 2Fe-2S cluster coordination
Authors: Trindade I.B. , Rollo F. , Todorovic S. , Catarino T. , Moe E. , Matias P.M. , Piccioli M. , Louro R.O. 
Published: July 2023

AbstractIron is a vital element for life. However, after the Great Oxidation Event, the bioavailability of this element became limited. To overcome iron shortage and to scavenge this essential nutrient, microorganisms use siderophores, secondary metabolites that have some of the highest affinities for ferric iron. The crucial step of iron release from these compounds to be subsequently integrated into cellular components is mediated by Siderophore-Interacting Proteins (SIPs) or Ferric-siderophore reductases (FSRs).In this work, we report the structure of an FSR for the first time. FhuF from laboratory strain Escherichia coli K-12 is the archetypical FSR, known for its atypical 2Fe-2S cluster with the binding motif C-C-X10-C-X2-C. The 1.9 Å resolution crystallographic structure of FhuF shows it to be the only 2Fe-2S protein known to date with two consecutive cysteines binding different Fe atoms. This novel coordination provides a rationale for the unusual spectroscopic properties of FhuF. Furthermore, FhuF shows an impressive ability to reduce hydroxamate-type siderophores at very high rates when compared to flavin-based SIPs, but like SIPs it appears to use the redox-Bohr effect to achieve catalytic efficiency.Overall, this work closes the knowledge gap regarding the structural properties of ferric-siderophore reductases and simultaneously opens the door for further understanding of the diverse mechanistic abilities of these proteins in the siderophore recycling pathway.
Adaptative Laboratory Evolution reveals biofilm regulating genes as key players inB. subtilisroot colonization
Authors: Pomerleau Maude , Charron-Lamoureux Vincent , Léonard Lucille , Grenier Frédéric , Rodrigue Sébastien , Beauregard Pascale B. 
Published: July 2023

AbstractRoot-associated microorganisms play an important role in plant health, such as plant growth-promoting rhizobacteria from theBacillusandPseudomonasgenera. Although bacterial consortia including these two genera would represent a promising avenue to efficient biofertilizer formulation, we observed thatB. subtilisroot colonization is decreased by the presence ofP. fluorescensandP. protegens. To determine ifB. subtiliscan adapt to the inhibitory effect ofPseudomonason roots, we conducted adaptative laboratory evolution experiments withB. subtilisin mono-association or co-cultured withP. fluorescenson tomato plant roots. Evolved isolates with various colony morphology and stronger colonization capacity of both tomato plant andA. thalianaroots emerged rapidly from the two evolution experiments. Certain evolved isolates had also a better fitness on root in presence of other Pseudomonas species. Whole genome sequencing revealed that single nucleotide polymorphism (SNPs) in negative biofilm regulator genesywcCorsinRwere found in all independent lineages, suggesting their involvement in enhanced root colonization. These findings provide insights into the molecular mechanisms underlyingB. subtilisadaptation to root colonization and highlight the potential of directed evolution to enhance beneficial traits of PGPRs.
STCGCN: a spatio-temporal complete graph convolutional network for remaining useful life prediction of power transformer
Authors: Xing Mengda , Ding Weilong , Zhang Tianpu , Li Han 
Published: July 2023

Purpose
Remaining useful life (RUL) prediction for power transformer maintenance is a challenging task on heterogeneous data. Monitoring data of power transformers are not always compatible or in an identical format; therefore, RUL predictions traditionally work separately on different data. Moreover, chemical molecules used in RUL prediction can be transformed into each other under different conditions, thus forming a complete graph with uncertain adjacency matrix (UAM). This study aims to find and evaluate a new model to achieve better results of RUL prediction than the other baselines.

Design/methodology/approach
In this work, the authors propose a spatiotemporal complete graph convolutional network (STCGCN) for RUL prediction in two branches, in which daily and hourly features are extracted from correlated heterogeneous data separately. This study provides a thorough evaluation of the proposed model on real-world data and compare the proposed model with state-of-the-art RUL prediction models.

Findings
By using the multibranch structure and EucCos similarity aggregation, STCGCN was able to capture the dynamic spatiotemporal patterns on a variety of heterogeneous data and obtain more accurate prediction results, compared to other time series prediction methods.

Originality/value
In this work, the authors propose a novel multibranch structure to compute feature maps from two heterogeneous data sources efficiently and a novel similarity aggregation method to compute the spatial UAM within the complete graph. Compared with traditional time series prediction models, the model pays attention to the spatial relationships in time series data.