bluuebunny/crossref_metadata_2025_split huggingface dataset:
Cryo-EM of native membranes reveals an intimate connection between the Krebs cycle and respiration in mycobacteria
Authors: Di Trani Justin M. , Yu Jiacheng , Courbon Gautier M. , Lobez Rodriguez Ana Paula , Cheung Chen-Yi , Liang Yingke , Coupland Claire E. , Bueler Stephanie A. , Cook Gregory M. , Brzezinski Peter , Rubinstein John L. 
Published: October 2024

AbstractImaging of endogenous protein complexes in their native membranes can reveal protein-protein interactions that are lost upon detergent solubilization. To investigate interactions in the mycobacterial oxidative phosphorylation machinery, we prepared inverted membrane vesicles fromMycobacterium smegmatisand enriched for vesicles containing complexes of interest by affinity chromatography. Electron cryomicroscopy (cryo-EM) of these vesicles revealed that malate-quinone oxidoreductase (Mqo), an enzyme from the Krebs cycle, physically associates with the electron transport chain Complex III2IV2(CIII2CIV2) supercomplex. Analysis of the Mqo:CIII2CIV2interaction shows that CIII2CIV2is necessary for malate-driven, but not NADH- driven, electron transport chain activity and oxygen consumption. Further, the association of Mqo with CIII2CIV2enables electron transfer from malate to CIII2CIV2with millisecond kinetics. Together, these findings indicate a connection between the Krebs cycle and respiration that directs electrons along a single branch of the mycobacterial electron transport chain.
Directed assembly of single-stranded DNA fragments for data storage via enzyme-free catalytic splint ligation
Authors: Mendonsa Gemma , Chari Sriram , Bao Mengdi , Herdendorf Brett , Reddy Anil 
Published: October 2024

ABSTRACTOligonucleotides or gene fragments can be ligated in a specified order to create longer DNA assemblies. We present a method where DNA symbols, or oligos designed to encode information for data storage, are joined to linker sequences at either end. These linkers dictate the assembly order of the symbols; the order of the symbols can be changed by changing the sequences of the linkers attached to them. Utilizing a ligating DNAzyme as a catalytic splint, we achieve room-temperature, enzyme-free assembly, offering a cost-effective alternative to traditional enzyme-based ligation methods. We demonstrate this technique by assembling three different five-symbol constructs, with the order of the symbols determined by their linking ends. This linker directed assembly technique allows data-encoding symbols to be assembled in any desired order. Furthermore, the DNAzyme-based assembly method is versatile and can be applied to various DNA assembly applications, particularly where cost-effectiveness and efficient room-temperature ligation are required.
Tunable, self-contained gene dosage control via proteolytic cleavage of CRISPR-Cas systems
Authors: Katz Noa , An Connie , Lee Yu-Ju , Tycko Josh , Zhang Meng , Kang Jeewoo , Bintu Lacramioara , Bassik Michael C , Huang Wei-Hsiang , Gao Xiaojing J 
Published: October 2024

SummaryGene therapy holds great therapeutic potential. Yet, controlling cargo expression in single cells is limited due to the variability of delivery methods. We implement an incoherent feedforward loop based on proteolytic cleavage of CRISPR-Cas activation or inhibition systems to reduce gene expression variability against the variability of vector delivery. We demonstrate dosage control for activation and inhibition, post-delivery tuning, and RNA-based delivery, for a genome-integrated marker. We then target theRAI1gene, the haploinsufficiency and triplosensitivity of which cause two autism-related syndromes, Smith-Magenis-Syndrome (SMS) and Potocki-Lupski-Syndrome, respectively. We demonstrate dosage control for RAI1 activation in HEK293s, Neuro-2As, and mouse cortical neurons via AAVs and lentiviruses. Finally, we activate the intactRAI1copy in SMS patient-derived cells to an estimated two-copy healthy range, avoiding the harmful three-copy regime. Our circuit paves the way for viable therapy in dosage-sensitive disorders, creating precise and tunable gene regulation systems for basic and translational research.
Activation and modulation of the host response to DNA damage by an integrative and conjugative element
Authors: McKeithen-Mead Saria , Anderson Mary E. , García-Heredia Alam , Grossman Alan D. 
Published: October 2024

AbstractMobile genetic elements help drive horizontal gene transfer and bacterial evolution. Conjugative elements and temperate bacteriophages can be stably maintained in host cells. They can alter host physiology and regulatory responses and typically carry genes that are beneficial to their hosts. We found that ICEBs1, an integrative and conjugative element ofBacillus subtilis, inhibits the host response to DNA damage (the SOS response). Activation of ICEBs1before DNA damage reduced host cell lysis that was caused by SOS-mediated activation of two resident prophages. Further, activation of ICEBs1itself activated the SOS response in a subpopulation of cells, and this activation was attenuated by the functions of the ICEBs1genesydcTandyddA(nowramTandramA, for RecA modulator). Double mutant analyses indicated that RamA functions to inhibit and RamT functions to both inhibit and activate the SOS response. Both RamT and RamA caused a reduction in RecA filaments, one of the early steps in activation of the SOS response. We suspect that there are several different mechanisms by which mobile genetic elements that generate ssDNA during their lifecycle inhibit the host SOS response and RecA function, as RamT and RamA differ from the known SOS inhibitors encoded by conjugative elements.
Infectivity and persistence of influenza viruses in raw milk
Authors: Zulli Alessandro , Zhang Mengyang , Jong Sehee , Blish Catherine , Boehm Alexandria B. 
Published: October 2024

AbstractInfluenza A viruses present a significant public health risk, with recent outbreaks of highly pathogenic avian influenza (HPAI) H5N1 in dairy cattle raising concerns about potential transmission through raw milk consumption. This study investigated the persistence of influenza A virus PR8 (IAV PR8) in raw cow milk at 4 °C. We found that IAV PR8 remained infectious in raw milk for up to 5 days, with a decay rate constant of −2.05 day−1. In contrast, viral RNA remained detectable and stable for at least 57 days, with no significant degradation. Pasteurization (63°C for 30 minutes) significantly reduced detectable viral RNA concentrations, but reduction was less than 1 log. These findings highlight the potential risk of zoonotic virus transmission through raw milk consumption and underscore the importance of milk pasteurization. The prolonged persistence of viral RNA in both raw and pasteurized milk has implications for food safety assessments and environmental monitoring, particularly in the context of environmental surveillance for influenza viruses.SynopsisInfluenza A RNA is persistent in milk, even after pasteurization, and it remains infectious for 5 days in refrigerated milk.
A novelex vivomodel of muscle contraction to measure muscle endocrine and paracrine signalling
Authors: Dabadie Carole , Belaidi Élise , Moretta Antonio , Lemarié Lucas , Allard Bruno , Kneppers Anita , Mounier Rémi 
Published: October 2024

ABSTRACTSkeletal muscle is a highly organized tissue that possesses the ability to contract and that exerts metabolic, endocrine and paracrine functions. Previous studies explored these functions throughin vitromodels, computational analyses, and endpoint measurements. To include the cellular complexity that modulates muscle endocrine and paracrine functions, and to allow us to study the kinetics of released and/or depleted factors, we developed a novel setup forex vivocontraction of whole skeletal muscle.Ex vivocontraction of theExtensor Digitorum Longus(EDL) induced by either electrical field stimulation or direct nerve stimulation resulted in a reduction of relative maximal force and a depletion of muscle glycogen content. Differential proteomics confirmed that proteins upregulated upon electrical pulse stimulation (EPS) were enriched for biological processes and molecular functions associated to cytoskeletal organization and muscle contraction. Finally, EPS induced the release of lactate, and IL6 secretion was induced after cessation of EPS. Taken together, we have developed and validated a new model ofex vivocontraction that includes the full cellular complexity of the muscle and mimics thein vivophysiological response to contraction. Importantly, this model supports for the first time to study the kinetics of the endocrine and paracrine response of the muscle to contraction, and to investigate its effects on various cell-typesin vitro.
Chai-1: Decoding the molecular interactions of life
Authors:   Chai Discovery, Boitreaud Jacques , Dent Jack , McPartlon Matthew , Meier Joshua , Reis Vinicius , Rogozhnikov Alex , Wu Kevin 
Published: October 2024

AbstractWe introduce Chai-1, a multi-modal foundation model for molecular structure prediction that performs at the state-of-the-art across a variety of tasks relevant to drug discovery. Chai-1 can optionally be prompted with experimental restraints (e.g. derived from wet-lab data) which boosts performance by double-digit percentage points. Chai-1 can also be run in single-sequence mode with-out MSAs while preserving most of its performance. We release Chai-1 model weights and inference code as a Python package for non-commercial use and via a web interface where it can be used for free including for commercial drug discovery purposes.
Polyserine peptides are toxic and exacerbate tau pathology in mice
Authors: Van Alstyne Meaghan , Nguyen Vanessa L. , Hoeffer Charles A. , Parker Roy 
Published: October 2024

AbstractPolyserine domains mediate the association of nuclear RNA binding proteins with cytoplasmic tau aggregates that occurs across tauopathy models and patient samples. In cell lines, polyserine peptides co-localize with and promote formation of tau aggregates suggesting the cytoplasmic mislocalization of polyserine-containing proteins might contribute to human disease. Moreover, polyserine can be produced by repeat associated non-AUG translation in CAG repeat expansion diseases. However, whether polyserine expressed in a mammalian brain is toxic and/or can exacerbate tau pathology is unknown. Here, we used AAV9-mediated delivery to express a 42-repeat polyserine protein in wild-type and tau transgenic mouse models. We observe that polyserine expression has toxic effects in wild-type animals indicated by reduced weight, behavioral abnormalities and a striking loss of Purkinje cells. Moreover, in the presence of a pathogenic variant of human tau, polyserine exacerbates disease markers such as phosphorylated and insoluble tau levels and the seeding capacity of brain extracts. These findings demonstrate that polyserine domains can promote tau-mediated pathology in a mouse model and are consistent with the hypothesis that cytoplasmic mislocalization of polyserine containing proteins might contribute to the progression of human tauopathies.
SMYD5 is a ribosomal methyltransferase which trimethylates RPL40 lysine 22 through recognition of a KXY motif
Authors: Hamey Joshua J. , Shah Manan , Wade John D. , Bartolec Tara K. , Wettenhall Richard E. H. , Quinlan Kate G.R. , Williamson Nicholas A. , Wilkins Marc R. 
Published: October 2024

SummaryThe eukaryotic ribosome is highly modified by protein methylation, yet many of the responsible methyltransferases remain unknown. Here we have identified SMYD5 as a ribosomal protein methyltransferase that catalyses trimethylation of RPL40/eL40 at lysine 22. Through a systematic mass spectrometry-based approach, we show that the human ribosome has 12 primary sites of protein methylation, including at RPL40 K22. Throughin vitromethylation of synthetic RPL40 using fractionated lysate, we then identify SMYD5 as a candidate RPL40 K22 methyltransferase. We show that recombinant SMYD5 has robust activity towards RPL40 K22in vitro, and that active site mutations ablate this activity. Knockouts ofSMYD5in K562 cells show a complete loss of RPL40 K22 methylation and decrease polysome levels. By systematic analysis of its recognition motif, we show that SMYD5 requires a tyrosine in the +2 position, and thereby is incapable of methylating its previously reported histone substrates.
PROPERMAB: an integrative framework forin silicoprediction of antibody developability using machine learning
Authors: Li Bian , Luo Shukun , Wang Wenhua , Xu Jiahui , Liu Dingjiang , Shameem Mohammed , Mattila John , Franklin Matthew , Hawkins Peter G. , Atwal Gurinder S. 
Published: October 2024

AbstractSelection of lead therapeutic molecules is often driven predominantly by pharmacological efficacy and safety. Candidate developability, such as biophysical properties that affect the formulation of the molecule into a product, is usually evaluated only toward the end of the drug development pipeline. The ability to evaluate developability properties early in the process of antibody therapeutic development could accelerate the timeline from discovery to clinic and save considerable resources.In silicopredictive approaches, such as machine learning models, which map molecules to predictions of developability properties could offer a cost-effective and high-throughput alternative to experiments for antibody developability assessment. We developed a computational framework, PROPERMAB, for large-scale and efficientin silicoprediction of developability properties for monoclonal antibodies, using custom molecular features and machine learning modeling. We demonstrate the power of PROPERMABby using it to develop models to predict antibody hydrophobic interaction chromatography retention time and high-concentration viscosity. We further show that structure-derived features can be rapidly and accurately predicted directly from sequences by pre-training simple models for molecular features, thus providing the ability to scale these approaches to repertoire-scale sequence datasets.
Mapping synaptic ensembles throughin vitrofunctional cell assemblies
Authors: Zaccaria Clara , Malkoç Asiye , Auslender Ilya , Heydari Yasaman , Canossa Marco , Vignoli Beatrice , Pavesi Lorenzo 
Published: October 2024

SummaryIn memory circuits, synaptic engrams consist of ensembles of strengthened synapses that form between engram neurons encoding distinct memory traces. As proposed in Hebb’s seminal postulate, these potentiated synapses enable the functional cell assembly essential for neuronal wiring. While existing technologies can track potentiated synapses in behaving animals, understanding thein vivospatial-temporal organization of synaptic engrams remains challenging. We developed anin vitrohybrid system that integrates digital light processing with optogenetics and used optical stimulation to synchronize the firing patterns of two-neuron modules within a network, supporting Hebb’s postulate experimentally. After illumination, we observed that synapses predominantly strengthen on dendrites between the two illuminated neurons, reflecting neuron responses to the wiring activity. This observation provides a strong conceptual foundation for our methodology. Our setup also allows for direct illumination and strengthening of synaptic ensembles, granting spatial-temporal control over the synaptic networks. Building on Hebb’s theoretical framework, our system offers a solid experimental approach to test the fundamental principles underlying synaptic engrams.
Step-by-step methodology for building a capsule to sample small intestine content
Authors: Ollagnier Catherine , Tretola Marco , García Viñado Inés , Morel Benoit 
Published: October 2024

AbstractBackgroundResearch on the intestinal microbiome has been hindered by limited access to intestinal content. Recently, a few capsule prototypes have demonstrated their potential for sampling intestinal material while using the natural pathway. However, access to these capsules is restricted because most of them are not yet commercially available. Pigs offer significant potential to inform human research due to the many physiological similarities between the two species. The unique features of pig anatomy have made it difficult to conduct research using swallowable devices. This article provides a detailed account of the manufacturing process and composition of a capsule, along with all the necessary steps for successfully sampling small intestine content in pigs.ResultsThe capsule moves passively through the digestive tract, relying solely on intestinal peristalsis for propulsion. Engineered to open when it encounters a pH level greater than 6, the upper part dissolves, allowing intestinal fluids to enter the inner chamber. This triggers a plunger to expand, drawing luminal content into the storage chamber. Once the plunger mechanism is fully extended the capsule is automatically sealed. The capsule has a size of a 0 hard capsule and consists of two main components: a dissolvable exterior with an enteric coating and a 3D-printed bottom part. The printing files of the 3D-printed bottom part are provided for replication. In vitro testing shows that the capsule can withstand two hours in an acidic medium and successfully samples within an hour of being transferred to a neutral medium. When tested in vivo in pigs, the capsule successfully collected intestinal content from the upper and middle sections of the small intestine.ConclusionsThis article provides essential details for the rapid development of a cost-effective tool that has been already validated for non-invasive sampling of small intestine content in pigs. By providing access to the exact production steps and printing files, this article empowers others to innovate and expand upon this foundational work. This open-source approach opens up new avenues for intestinal research, making it more accessible and adaptable for a wide range of studies in both animal and human models.
Systematic Mining of gut microbiota biomarkers for IBD
Authors: Zhang Yuchen , Lai Wenkai , Wang Meiling , Lai Shirong , Liu Qing , Luo Qi , Dou Lijun , Yang Fenglong 
Published: October 2024

AbstractBackgroundInflammatory bowel disease (IBD), encompassing ulcerative colitis (UC) and Crohn’s disease (CD), represents a chronic inflammatory condition with an incompletely understood etiology. Emerging evidence suggests that alterations in gut microbiota composition play a pivotal role in disease development. Here, we leveraged gut fecal metagenomic data (3044 samples: 2248 IBD and 796 healthy) from publicly available sources to explore microbiome biomarkers related to IBD to provide new ideas for clinical treatment.ResultsOur analyses revealed marked disparities in microbial species abundance and composition between IBD and healthy samples in both male and female subjects from the United States, whereas such distinctions were absent in subjects from Spain. Hierarchical and systematic investigations uncovered microbial phyla, such as Verrucomicrobia and Firmicutes, associated with IBD in US cohorts. Furthermore, we identified 127 highly correlated pathways with these differential microbes, covering functions such as peptidoglycan biosynthesis III, dTDP-L-rhamnose biosynthesis I, starch degradation, and glucose-1-phosphate degradation. Gut microbial metabolites were predicted based on metagenomic data using the MelonnPan workflow and 16 metabolites with significant differences were identified that collectively contribute to energy metabolism, digestion, skin integrity and general bodily function.ConclusionsThis study identified differences in microbial species and metabolic pathways related to Inflammatory Bowel Disease (IBD) through hierarchical and systematic analysis, which can aid in the clinical diagnosis of IBD. Pathways such as Peptidoglycan Biosynthesis III and dTDP-L-Rhamnose Biosynthesis I are associated with the generation of bacterial cell walls, and disruptions in these pathways affect bacterial activity, leading to an imbalance in the host’s gut microbiota. Based on the hypotheses regarding the pathogenesis of IBD derived from the above mining results, it provides a theoretical basis for selecting precise treatment options.
Predicting treatment-free remission outcomes in Chronic Myeloid Leukemia patients using an integrated model of tumor-immune dynamics
Authors: Fassoni Artur C. , Yong Agnes , Clark Richard E. , Roeder Ingo , Glauche Ingmar 
Published: October 2024

AbstractThe interactions between tumor and the immune system are main factors in determining cancer treatment outcomes. In Chronic Myeloid Leukemia (CML), considerable evidence shows that the dynamics between residual leukemia and the patient’s immune system can result in either sustained disease control, leading to treatment-free remission (TFR), or disease recurrence. The question remains how to integrate mechanistic and data-driven models to support prediction of treatment outcomes. Starting from classical ecological modeling concepts, which allow to explicitly account for immune interactions at the cellular level, we incorporate time-course data on natural killer (NK) cell number, function, and their tumor-induced suppression into our general model of CML treatment. We identify relevant time scales governing treatment and immune response, enabling refined model calibration using tumor and NK cell time courses from different datasets. While the model successfully describes patient-specific response dynamics, critical parameters for predicting treatment outcome remain uncertain. However, by explicitly incorporating tumor load changes in response to TKI dose alterations, these parameters can be estimated and used to derive model predictions for treatment cessation. Further exploring dynamic changes in the number of functional immune cells, we suggest specific measurement strategies of immune effector cell populations to enhance prediction accuracy for CML recurrence following treatment cessation. The generalizability and flexibility of our approach represent a significant step towards quantitative, personalized medicine that integrates tumor-immune dynamics to guide clinical decisions and optimize dynamic cancer therapies.