bluuebunny/crossref_metadata_2025_split huggingface dataset:
Deep learning guided design of dynamic proteins
Authors: Guo Amy B. , Akpinaroglu Deniz , Kelly Mark J.S. , Kortemme Tanja 
Published: July 2024

AbstractDeep learning has greatly advanced design of highly stable static protein structures, but the controlled conformational dynamics that are hallmarks of natural switch-like signaling proteins have remained inaccessible tode novodesign. Here, we describe a general deep-learning-guided approach forde novodesign of dynamic changes between intra-domain geometries of proteins, similar to switch mechanisms prevalent in nature, with atom-level precision. We solve 4 structures validating the designed conformations, show microsecond transitions between them, and demonstrate that the conformational landscape can be modulated by orthosteric ligands and allosteric mutations. Physics-based simulations are in remarkable agreement with deep-learning predictions and experimental data, reveal distinct state-dependent residue interaction networks, and predict mutations that tune the designed conformational landscape. Our approach demonstrates that new modes of motion can now be realized throughde novodesign and provides a framework for constructing biology-inspired, tunable and controllable protein signaling behaviorde novo.
PINDER: The protein interaction dataset and evaluation resource
Authors: Kovtun Daniel , Akdel Mehmet , Goncearenco Alexander , Zhou Guoqing , Holt Graham , Baugher David , Lin Dejun , Adeshina Yusuf , Castiglione Thomas , Wang Xiaoyun , Marquet Céline , McPartlon Matt , Geffner Tomas , Rossi Emanuele , Corso Gabriele , Stärk Hannes , Carpenter Zachary , Kucukbenli Emine , Bronstein Michael , Naef Luca 
Published: July 2024

AbstractProtein-protein interactions (PPIs) are fundamental to understanding biological processes and play a key role in therapeutic advancements. As deep-learning docking methods for PPIs gain traction, benchmarking protocols and datasets tailored for effective training and evaluation of their generalization capabilities and performance across real-world scenarios become imperative. Aiming to overcome limitations of existing approaches, we introduce PINDER, a comprehensive annotated dataset that uses structural clustering to derive non-redundant interface-based data splits and includesholo(bound),apo(unbound), and computationally predicted structures. PINDER consists of 2,319,564 dimeric PPI systems (and up to 25 million augmented PPIs) and 1,955 high-quality test PPIs with interface data leakage removed. Additionally, PINDER provides a test subset with 180 dimers for comparison to AlphaFold-Multimer without any interface leakage with respect to its training set. Unsurprisingly, the PINDER benchmark reveals that the performance of existing docking models is highly overestimated when evaluated on leaky test sets. Most importantly, by retraining DiffDock-PP on PINDER interface-clustered splits, we show that interface cluster-based sampling of the training split, along with the diverse and less leaky validation split, leads to strong generalization improvements.
Oxygen is Toxic in the Cold inC. elegans
Authors: Suraci Cameron M. , Morrison Michael L. , Roth Mark B. 
Published: July 2024

AbstractTemperature and oxygen are two factors that profoundly affect survival limits of animals; too much or too little of either is lethal. However, both humans and animals can exhibit exceptional survival when oxygen and temperature are simultaneously low. To better understand this apparent synergistic interaction between oxygen and temperature, we assayed the survival ofCaenorhabditis elegansin experimental environments at different temperatures and oxygen concentrations. While nematodes cannot survive a day in room air at 2 °C (cold shock), we found that when oxygen is low, 200-fold less than room air, they can survive this temperature for 48 hours. Consistent with this, we found that worms exposed to high oxygen concentrations, 35 times greater than room air, are more sensitive to low temperature than worms in room air. These results show that normal atmospheric levels of oxygen are toxic in the cold. Using these survival assays, we found that cold acclimatization protects worms from lethal effects of high oxygen, mutations in the cold acclimatization pathway affect oxygen tolerance, and that the naturally occurring and physiologically relevant compounds glucose, manganese (II), and ascorbate improve survival limits in both low temperature and high oxygen when supplied early in life. These results show that the interdependence of temperature and oxygen on survival inC. elegansis based in part on shared physiological mechanisms involved in response to these two environmental stressors. The evolution and natural history of stress responses in animals suggest similar phenomena may function in humans.
Necrosis drives susceptibility toMycobacterium tuberculosisin PolgD257Amutator mice
Authors: Mabry CJ , Weindel CG , Stranahan LW , VanPortfliet JJ , Davis JR , Martinez EL , West AP , Patrick KL , Watson RO 
Published: July 2024

ABSTRACTThe genetic and molecular determinants that underlie the heterogeneity ofMycobacterium tuberculosis(Mtb) infection outcomes in humans are poorly understood. Multiple lines of evidence demonstrate that mitochondrial dysfunction can exacerbate mycobacterial disease severity and mutations in some mitochondrial genes confer susceptibility to mycobacterial infection in humans. Here, we report that mutations in mitochondria DNA (mtDNA) polymerase gamma (POLG) potentiate susceptibility to Mtb infection in mice. PolgD257Amutator mtDNA mice fail to mount a protective innate immune response at an early infection timepoint, evidenced by high bacterial burdens, reduced M1 macrophages, and excessive neutrophil infiltration in the lungs. Immunohistochemistry reveals signs of enhanced necrosis in the lungs of Mtb-infected PolgD257Amice and PolgD257Amutator macrophages are hyper-susceptible to extrinsic triggers of necroptosisex vivo. By assigning a role for mtDNA mutations in driving necrosis during Mtb infection, this work further highlights the requirement for mitochondrial homeostasis in mounting balanced immune responses to Mtb.
The Oral Bioavailability of Lurasidone is Impacted by Changes to the Gut Microbiome: Implications for Antipsychotic Therapy
Authors: Collins Kate , Kamath Srinivas , Meola Tahlia R. , Wignall Anthony , Joyce Paul 
Published: July 2024

AbstractAtypical antipsychotics are crucial for the management of schizophrenia and bipolar disorder, yet they exhibit significant pharmacokinetic variability which leads to inconsistent therapeutic responses. This study investigates the hypothesis that gut microbiome composition critically influences the oral bioavailability of lurasidone, a poorly soluble weak base antipsychotic with pH-dependent solubility. To investigate this, male Sprague-Dawley rats underwent systematic gut microbiome manipulation through pretreatment with antibiotics or prebiotics (inulin) for 14 days prior to a single oral dose of lurasidone. Pharmacokinetic analysis of collected plasma samples revealed a significant 4.3-fold increase in lurasidone bioavailability following prebiotic pretreatment, compared to a control (no pretreatment) group. Conversely, lurasidone bioavailability was highly variable in rats with a depleted microbiome (i.e., antibiotic treatment group), with 80% of animals demonstrating lower bioavailability than the control group. Characterisation of gut microbiome composition and short-chain fatty acid (SCFA) concentrations demonstrated positive correlations between lurasidone bioavailability, microbial diversity, and SCFA levels, mediated by modulation of luminal pH. Elevated SCFA levels created a favourable environment for lurasidone solubilisation by lowering intestinal pH. These findings highlight the potential for optimising antipsychotic pharmacokinetics through personalised microbiome interventions. Furthermore, the correlation between SCFAs and lurasidone bioavailability suggests their potential as biomarkers for predicting inter-patient pharmacokinetic variability, particularly for poorly soluble weak bases. Thus, new avenues are opened for developing novel co-therapies and screening tools to enhance antipsychotic pharmacokinetic performance, potentially improving treatment outcomes for patients with schizophrenia and bipolar disorder.Graphical Abstract
PAC-MAP: Proximity Adjusted Centroid Mapping for Accurate Detection of Nuclei in Dense 3D Cell Systems
Authors: Van De Looverbosch Tim , De Beuckeleer Sarah , De Smet Frederik , Sijbers Jan , De Vos Winnok H. 
Published: July 2024

AbstractMotivationIn the past decade, deep learning algorithms have surpassed the performance of many conventional image segmentation pipelines. Powerful models are now available for segmenting cells and nuclei in diverse 2D image types, but segmentation in 3D cell systems remains challenging due to the high cell density, the heterogenous resolution and contrast across the image volume, and the difficulty in generating reliable and sufficient ground truth data for model training. Reasoning that most image processing applications rely on nuclear segmentation but do not necessarily require an accurate delineation of their shapes, we implemented PAC-MAP, a 3D U-net based method that predicts the position of nuclei centroids and their proximity to other nuclei.ResultsWe show that our model outperforms existing methods, predominantly by boosting recall, especially in conditions of high cell density. When trained from scratch PAC-MAP attained an average F1 score of 0.793 in dense spheroids. When pretraining using weakly supervised bulk data input and finetuning with few expert annotations the average F1 score could be significantly improved up to 0.817. We demonstrate the utility of our method for quantifying the cell content of spheroids and mapping the degree of glioblastoma multiforme infiltration in cerebral organoids.Availability and implementationThe code is available on GitHub, athttps://github.com/DeVosLab/PAC-MAP.ContactWinnok H. De Vos (winnok.devos@uantwerpen.be)
Spatial ciliary signaling regulates the dorsal/ventral regionalization of human brain organoids
Authors: Shimada Issei S. , Goto Akari , Hashimoto Yutaka , Takase Hiroshi , Itoh Masayuki , Kato Yoichi 
Published: July 2024

AbstractRegionalization of the brain is a fundamental question in human developmental biology. Primary cilia are known for a critical organelle for dorsal/ventral fate of brain formation in mice, but little is known about how signaling in the primary cilia regulate regionalization of the human brain. Here, we found that signaling in the primary cilia function in regionalization of the brain using brain organoids derived from human induced pluripotent stem (iPS) cells. Deletion of a ciliary GTPase,ARL13B, induced partially ventralized neural stem cells in the dorsal cortical organoids, despite using a guided dorsal cortical organoid differentiation protocol. Mechanistically,ARL13Bknockout (KO) neural stem cells decreased ciliary localization of GPR161, a negative regulator of SHH signaling in primary cilia and increased SONIC HEDGEHOG (SHH) signaling.GPR161deletion also induced ventralized neural stem cells in the dorsal cortical organoids, despite using the guided differentiation protocol.GPR161deletion increased SHH signaling mediated by decreased GLI3 repressor formation. Pharmacological treatment to increase cAMP levels rescued GLI3 repressor formation and the differentiation of dorsal neural stem cells inGPR161KO brain organoids. Importantly, elevating the amount of ciliary cAMP by optogenetics restored the generation of dorsal neural stem cells inGPR161KO brain organoids. These data indicate that spatial ciliary signaling, the ARL13B-GPR161-cAMP axis in primary cilia, is a fundamental regulator of the dorsal/ventral regionalization of the human brain.
SARS-CoV-2 B Epitope-Guided Neoantigen NanoVaccines Enhance Tumor-Specific CD4/CD8 T Cell Immunity Through B Cell Antigen Presentation
Authors: Li Chengyi , Mao Shuai , Montemayor Zera , Traore Mohamed Dit Mady , Duran Alejandra , Ke Fang , Djibo Mahamadou , Wen Hanning , Gao Wei , Sun Duxin 
Published: July 2024

ABSTRACTCurrent neoantigen cancer vaccines activate T cell immunity through dendritic cell /macrophage-mediated antigen presentation. It is unclear whether incorporating B cell-mediated antigen presentation into current neoantigen vaccines could enhance CD4/CD8 T cell immunity to improve their anticancer efficacy. We developed a SARS-CoV-2 B cell epitope-guided neoantigen peptide/mRNA cancer nanovaccines (BSARSTNeoAgVax) to improve anticancer efficacy by enhancing tumor-specific CD4/CD8 T cell antitumor immunity through B cell-mediated antigen presentation. BSARSTNeoAgVax crosslinked with B cell receptor, promoted SARS-CoV-2 B cell-mediated antigen presentation to tumor-specific CD4 T cells, increased tumor-specific follicular/non-follicular CD4 T cells, and enhanced B cell-dependent tumor-specific CD8 T cell immunity. BSARSTNeoAgVax achieved superior efficacy in melanoma, pancreatic, and breast cancer models compared to the current neoantigen vaccines. Our study provides a universal platform, SARS-CoV-2 B epitope-guided neoantigen nanovaccines, to improve anticancer efficacy against various cancer types by enhancing CD4/CD8 T cell antitumor immunity through viral-specific B cell-mediated antigen presentation.
The structure of a NEMO construct engineered for screening reveals novel determinants of inhibition
Authors: Kennedy Amy E. , Barczewski Adam H. , Arnoldy Christina R. , Pennington J. Pepper , Tiernan Kelly A. , Hidalgo Maria Beatriz , Reilly Caroline C. , Ragusa Michael J. , Grigoryan Gevorg , Mierke Dale F. , Pellegrini Maria M. 
Published: July 2024

SummaryNEMO is an essential component in the activation of the canonical NF-κB pathway and exerts its function by recruiting the IκB kinases (IKK) to the IKK complex. Inhibition of the NEMO/IKKs interaction is an attractive therapeutic paradigm for diseases related to NF-κB mis-regulation, but a difficult endeavor because of the extensive protein-protein interface. Here we report the design and characterization of novel engineered constructs of the IKK-binding domain of NEMO, programmed to render this difficult protein domain amenable to NMR and X-ray characterization, while preserving the biological function. ZipNEMO binds IKKβ with nanomolar affinity, is amenable to heteronuclear NMR techniques and structure determination by X-ray crystallography. We show that NMR spectra of zipNEMO allow to detect inhibitor binding in solution and resonance assignment. The X-ray structure of zipNEMO highlights a novel ligand binding motif and the adaptability of the binding pocket and inspired the design of new peptide inhibitors.
Engineering the novel extremophile algaChlamydomonas pacificafor high lipid and high starch production as a path to developing commercially relevant strains
Authors: Gupta Abhishek , Dutra Molino João Vitor , Wnuk-Fink Kathryn MJ , Bruckbauer Aaron , Tessman Marissa , Kang Kalisa , Diaz Crisandra J. , Saucedo Barbara , Malik Ashleyn , Mayfield Stephen P 
Published: July 2024

AbstractMicroalgae offer a compelling platform for the production of commodity products, due to their superior photosynthetic efficiency, adaptability to non-arable lands and non-potable water, and their capacity to produce a versatile array of bioproducts, including biofuels and biomaterials. However, the scalability of microalgae as a bioresource has been hindered by challenges such as costly biomass production related to vulnerability to pond crashes during large-scale cultivation. This study presents a pipeline for the genetic engineering and pilot-scale production of biodiesel and thermoplastic polyurethane precursors in the extremophile speciesChlamydomonas pacifica. This extremophile microalga exhibits exceptional resilience to high pH, high salinity, and elevated temperatures. Initially, we evolved this strain to also have a high tolerance to high light intensity through mutagenesis, breeding, and selection. Subsequently, we genetically engineeredC. pacificato produce high levels of lipids and starch without compromising growth. We demonstrated the scalability of these engineered strains by cultivating them in pilot-scale raceway ponds and converting the resulting biomass into biodiesel and thermoplastic polyurethanes. This study showcases the complete cycle of transforming a newly discovered species into a commercially relevant commodity production strain. This research underscores the potential of extremophile algae, includingC. pacifica, as a key species for the burgeoning sustainable bioeconomy, offering a viable path forward in mitigating environmental challenges and supporting global bioproduct demands.Graphical Abstract
DEVELOPMENT AND CONTENT VALIDITY OF THE HANDWASHING INDEX (HWI)
Authors: Lamptey Emmanuel , Senkyire Ephraim Kumi , Agoha Doris Selorm 
Published: July 2024

AbstractHandwashing is the simplest way to stop the spread of infections and maintain health. To the best of our knowledge, there is no validated scale to measure this habit. Given the need to raise awareness and its importance, a study was undertaken to develop, test, and validate the HWI. The Physical Activity Questionnaire for Adolescents (PAQ-A) was adapted and substantially modified to draft the first version of the index (HWQ). The COnsensus-based Standards for the Selection of Health Measurement Instrument (COSMIN) guided our approach. The HWQ The questionnaire consisted of six questions with a five-point scale response for each item, ranging from the lowest [1] to the highest activity [5] as scoring criteria. We followed a four-stage procedure in validating the instrument: Stage I: items were created from the review of the relevant literature (PAQ-A, COSMIN); Stage II: the study targeted and recruited 57 health professionals from different backgrounds and vetted them as decliners, non-regulars, and regular hand washers through a scoring process.This crucial phase ensured that the respondents had hands-on experience in handwashing in addition to their expertise. In Stage III, 10 respondents from the regular hand washers were randomly selected as expert judges. They were divided into two (2) groups (Group one and Group two) of four and six members, respectively. Further comprehensibility and comprehensiveness of the HWQ were established through a review by the four members of Group 1, and revisions were made to create HWQ-I. At stage IV, the HWQ-I was administered to the six members of the second group for ratings and content validity index calculations. The final draft of the HWI includes 4 items. Item CVI ranges between 0.8 and 1.The average scale CVI was 0.9.The HWI demonstrated excellent content validity, showing its relevance for monitoring handwashing, and individuals can track their compliance, promoting a healthy life. We propose further studies to test the psychometric properties of the scale.
The deletion of aldehyde:ferredoxin oxidoreductase-encoding genes inClostridium ljungdahliiresults in changes in the product spectrum with various carbon sources
Authors: Baur Saskia T. , Schulz Sarah , Cluskey Joshua B. M , Velázquez Gómez José Antonio , Angenent Largus T. , Molitor Bastian 
Published: July 2024

AbstractBiofuels, such as ethanol, can be produced by the microbial fermentation of waste gases that contain carbon dioxide (CO2) and carbon monoxide (CO). The acetogenic model microbeClostridium ljungdahliiconverts those substrates into acetyl-CoA with the Wood-Ljungdahl pathway. During autotrophic conditions, acetyl-CoA can be reduced further to ethanolviaacetic acid by the enzymes aldehyde:ferredoxin oxidoreductase (AOR) and alcohol dehydrogenase. Here, the genes encoding both tungsten-dependent AORs (aor1, CLJU_c20110 andaor2, CLJU_c20210) were deleted from the genome ofC. ljungdahlii. Ethanol formation was enhanced forC. ljungdahliiΔaor1with different carbon sources, that is, fructose, a mixture of hydrogen (H2) and CO2, and CO. The highest and lowest ethanol:acetic acid ratio was detected during growth with H2/CO2and CO, respectively. Oscillating patterns were observed during growth with CO, underpinning the importance of a balanced redox metabolism.
Deep Profiling of Plasma Proteoforms with Engineered Nanoparticles for Top-down Proteomics
Authors: Huang Che-Fan , Hollas Michael A. , Sanchez Aniel , Bhattacharya Mrittika , Ho Giang , Sundaresan Ambika , Caldwell Michael A. , Zhao Xiaoyan , Benz Ryan , Siddiqui Asim , Kelleher Neil L. 
Published: July 2024

ABSTRACTThe dynamic range challenge for detection of proteins and their proteoforms in human plasma has been well documented. Here, we use the nanoparticle protein corona approach to enrich low-abundant proteins selectively and reproducibly from human plasma and use top-down proteomics to quantify differential enrichment for the 2841 detected proteoforms from 114 proteins. Furthermore, nanoparticle enrichment allowed top-down detection of proteoforms between ∼1 µg/mL and ∼10 pg/mL in absolute abundance, providing up to 105-fold increase in proteome depth over neat plasma in which only proteoforms from abundant proteins (>1 µg/mL) were detected. The ability to monitor medium and some low abundant proteoforms through reproducible enrichment significantly extends the applicability of proteoform research by adding depth beyond albumin, immunoglobins and apolipoproteins to uncover many involved in immunity and cell signaling. As proteoforms carry unique information content relative to peptides, this report opens the door to deeper proteoform sequencing in clinical proteomics of disease or aging cohorts.
Mutational landscape and molecular bases of echinocandin resistance
Authors: Durand Romain , Torbey Alexandre G. , Giguere Mathieu , Pageau Alicia , Dubé Alexandre K. , Lagüe Patrick , Landry Christian R. 
Published: July 2024

AbstractOne of the front-line drug classes used to treat invasive fungal infections is echinocandins, which target the fungal-specific beta-glucan synthase (Fks). Treatment failure due to resistance often coincides with mutations in two protein regions known as hotspots. The biophysical bases by which such mutations confer resistance and cross-resistance among echinocandins are largely unknown. Here, we use deep-mutational scanning to quantify the resistance level of 660 mutations in the hotspots of two homologous Fks. We detail the constraints acting on drug binding and explain the resistance specificity for some mutations using the drug-protein interactions from our molecular models. Our findings will enable DNA sequence-based predictions of resistance to this important drug family and the improvement of future molecules that could overcome current resistance mutations.One sentence summaryDisruption of specific interactions between echinocandins and key residues from their target lead to drug-specific resistance.