bluuebunny/crossref_metadata_2025 huggingface dataset:
Scheduled feeding improves behavioral outcomes and reduces inflammation in a mouse model of Fragile X syndrome
Authors: Wang Huei Bin , Smale Natalie E. , Brown Sarah H. , Villanueva Sophia Anne Marie , Zhou David , Mulji Aly , Nguyen-Ngo Kyle , Harvey John R. , Ghiani Cristina A. , Colwell Christopher S.
Published: September 2024

Fragile X syndrome (FXS) is a neurodevelopmental disorder caused by the abnormal expansion of CGG repeats in the fragile X mental retardation 1 (FMR1) gene. Many FXS patients experience sleep disruptions, and we sought to explore these symptoms along with the possible benefits of a scheduled feeding intervention using theFmr1knockout (KO) mouse model. These mutants displayed clear evidence for sleep and circadian disturbances including delay in the onset of sleep and fragmented activity rhythms with increases in cycle-to-cycle variability. Importantly, theFmr1KO mice exhibited deficits in their circadian behavioral response to light with reduced masking, longer time to resetting to shifts in the Light-Dark cycle, altered synchronization to a skeleton photoperiod and lower magnitude light-induced phase shifts of activity rhythms. Investigation of the retinal input to the surprachiasmatic nucleus (SCN) with the neurotracer cholera toxin (β subunit) and quantification of the light-evoked cFos expression in the SCN revealed an abnormal retinal innervation of the SCN in theFmr1KO, providing a possible mechanistic explanation for the observed behavioral deficits. Interestingly, disruptions in social and repetitive behaviors correlated with sleep duration and fragmentation. Understanding the nature of the deficits, we decided to apply a scheduled feeding regimen (6-hr/18-hr feed/fast cycle) as a circadian-based strategy to boast circadian rhythms independently of light. This intervention significantly improved the activity rhythms and sleep in the mutants. Strikingly, the scheduled feeding ameliorated social interactions and reduced repetitive behaviors as well as the levels of Interferon-gamma and Interleukin-12 in theFmr1KO mutants, suggesting that timed eating may be an effective way to lessen inflammation. Collectively, this work adds support to efforts to develop circadian based interventions to help with symptoms of neurodevelopmental disorders.
SaccharomycesGenome Database: Advances in Genome Annotation, Expanded Biochemical Pathways, and Other Key Enhancements
Authors: Engel Stacia R. , Aleksander Suzi , Nash Robert S. , Wong Edith D. , Weng Shuai , Miyasato Stuart R. , Sherlock Gavin , Cherry J. Michael
Published: September 2024

Budding yeast (Saccharomyces cerevisiae) is the most extensively characterized eukaryotic model organism and has long been used to gain insight into the fundamentals of genetics, cellular biology, and the functions of specific genes and proteins. TheSaccharomycesGenome Database (SGD) is a scientific resource that provides information about the genome and biology ofS. cerevisiae. For more than 30 years, SGD has maintained the genetic nomenclature, chromosome maps, and functional annotation for budding yeast along with search and analysis tools to explore these data. Here we describe recent updates at SGD, including the two most recent reference genome annotation updates, expanded biochemical pathways representation, changes to SGD search and data files, and other enhancements to the SGD website and user interface. These activities are part of our continuing effort to promote insights gained from yeast to enable the discovery of functional relationships between sequence and gene products in fungi and higher eukaryotes.
BayesAge 2.0: A Maximum Likelihood Algorithm to Predict Transcriptomic Age
Authors: Mboning Lajoyce , Costa Emma K. , Chen Jingxun , Bouchard Louis-S , Pellegrini Matteo
Published: September 2024

Aging is a complex biological process influenced by various factors, including genetic and environmental influences. In this study, we present BayesAge 2.0, an improved version of our maximum likelihood algorithm designed for predicting transcriptomic age (tAge) from RNA-seq data. Building on the original BayesAge framework, which was developed for epigenetic age prediction, BayesAge 2.0 integrates a Poisson distribution to model count-based gene expression data and employs LOWESS smoothing to capture non-linear gene-age relationships. BayesAge 2.0 provides significant improvements over traditional linear models, such as Elastic Net regression. Specifically, it addresses issues of age bias in predictions, with minimal age-associated bias observed in residuals. Its computational efficiency further distinguishes it from traditional models, as reference construction and cross-validation are completed more quickly compared to Elastic Net regression, which requires extensive hyperparameter tuning. Overall, BayesAge 2.0 represents a notable advance in transcriptomic age prediction, offering a robust, accurate, and efficient tool for aging research and biomarker development.
HDgraphiX: A web-based tool for visualization of hydrogen deuterium exchange mass spectrometry data
Authors: Vosper Kent R. , Velyvis Algirdas , Vahidi Siavash
Published: September 2024

Hydrogen deuterium exchange mass spectrometry (HDX-MS) investigates protein structural changes by measuring deuterium incorporation into the protein amide backbone. Due to richness of information provided on protein conformational dynamics, HDX-MS data can be challenging to visualize effectively. To address this, we have developed HDgraphiX, a web-based tool that visualizes HDX data by processing outputs from two popular analysis software packages, DynamX (Waters Corp.) and HDExaminer (Sierra Analytics Inc). HDgraphiX performs statistical analyses, filters data based on statistical significance and presents the results in several forms of user-friendly publication-quality heatmaps (Chiclet plots). Unique features of this tool include the generation of Woods plots, volcano plots, and PyMOL colouring scripts, which are used to map deuterium uptake differences onto protein structures. Additionally, HDgraphiX offers numerous advanced options for customizing data processing and plotting without the need for manual data editing.

Availability and Implementation

HDgraphiX is available free of charge for all users athttps://hdgraphix.net, the Python script and HTML template are deposited athttps://github.com/KentV-UofG/HDgraphiX.
Synergistic and antagonistic activities ofIRF8andFOSenhancer pairs during an immune cell fate switch
Authors: Klonizakis Antonios , Alcoverro-Bertran Marc , Massó Pere , Thomas Joanna , de Andrés-Aguayo Luisa , Wei Xiao , Varamogianni-Mamatsi Vassiliki , Nikolaou Christoforos , Graf Thomas
Published: September 2024

Cell-fate instructive genes tend to be regulated by large clusters of enhancers. Whether and how individual enhancers within such clusters cooperate in regulating gene expression is poorly understood. We have previously developed a computational method, SEGCOND, that identifies hubs consisting of enhancer clusters and their target genes, termed Putative Transcriptional Condensates (PTCs). Using SEGCOND, we identified PTCs in a CEBPA-induced B-cell to macrophage transdifferentiation system. We found them to be enriched for highly expressed, lineage-restricted genes and to associate with BRD4, a component of transcriptional condensates. Here we performed single and combinatorial deletions of enhancers within two active PTCs after transdifferentiation is induced, harboringIRF8andFOS. Two enhancers within theIRF8PTC were found to form a backup mechanism when combined, safeguardingIRF8expression and transdifferentiation kinetics. Unexpectedly, two individual enhancers within theFOSPTC antagonize each other at Day 1 of transdifferentiation, delaying the conversion of B-cells to macrophages and reducingFOSexpression, but cooperate to increaseFOSlevels in Day 7 induced cells. Our results reveal differentiation stage-specific, complex interactions, between individual enhancers within a cluster.
Molecular consequences of SCA5 mutations in the spectrin-repeat domains of β-III-spectrin
Authors: Denha Sarah A. , DeLaet Naomi R. , Abukamil Abeer W. , Alexopoulos Angelica N. , Keller Amanda R. , Atang Alexandra E. , Avery Adam W.
Published: September 2024

Spinocerebellar ataxia type 5 (SCA5) mutations in the protein β-III-spectrin cluster to the N-terminal actin-binding domain (ABD) and the central spectrin-repeat domains (SRDs). We previously reported that a common molecular consequence of ABD-localized SCA5 mutations is increased actin binding. However, little is known about the molecular consequences of the SRD-localized mutations. It is known that the SRDs of β-spectrin proteins interact with α-spectrin to form an α/β-spectrin dimer. In addition, it is known that SRDs neighbouring the β-spectrin ABD enhance actin binding. Here, we tested the impact of the SRD-localized R480W and the E532_M544del mutations on the binding of β-III-spectrin to α-II-spectrin and actin. Using multiple experimental approaches, we show that both the R480W and E532_M544del mutants can bind α-II-spectrin. However, E532_M544del causes partial uncoupling of complementary SRDs in the α/β-spectrin dimer. Further, the R480W mutant forms large intracellular inclusions when co-expressed with α-II-spectrin in cells, supporting that R480W mutation grossly disrupts the α-II/β-III-spectrin physical complex. Moreover, actin-binding assays show that E532_M544del, but not R480W, increases β-III-spectrin actin binding. Altogether, these data support that SRD-localized mutations alter key interactions of β-III-spectrin with α-II-spectrin and actin.
Variant scoring performance across selection regimes depends on variant-to-gene and gene-to-disease components
Authors: Finucane Hilary K. , Parsa Sophie , Guez Jeremy , Kanai Masahiro , Satterstrom F. Kyle , Nkambule Lethukuthula L. , Daly Mark J. , Seed Cotton , Karczewski Konrad J.
Published: September 2024

Variant scoring methods (VSMs) aid in the interpretation of coding mutations and their potential impact on health, but their evaluation in the context of human genetics applications remains inconsistent. Here, we describe GeneticsGym, a systematic approach to evaluating the real-world impact of VSMs on human genetic analysis. We show that the relative performance of VSMs varies across regimes of natural selection, and that both variant-to-gene and gene-to-disease components contribute.
Multiplexed lifetime imaging of single molecules with a gated single-photon camera
Authors: Ronceray Nathan , Bennani Salim , Mitsioni Marianna , Siegel Nicole , Marcaida Maria Josefina , Bruschini Claudio , Charbon Edoardo , Roy Rahul , Dal Peraro Matteo , Acuna Guillermo P. , Radenovic Aleksandra
Published: September 2024

Fluorescence lifetime imaging microscopy (FLIM) is a powerful tool to discriminate fluorescent molecules or probe their nanoscale environment. Traditionally, FLIM uses time-correlated single-photon counting (TCSPC), which is precise but intrinsically low-throughput due to its dependence on point detectors. Although time-gated cameras have demonstrated the potential for high-throughput FLIM in bright samples with dense labeling, their use in single-molecule microscopy has not been explored extensively. Here, we report fast and accurate single-molecule FLIM with a commercial time-gated single-photon camera. Our optimized acquisition scheme achieves single-molecule lifetime measurements with a precision only about three times less than TCSPC, while allowing for the simultaneous multiplexing of over 3000 molecules. With this approach, we demonstrate parallelized lifetime measurements of large numbers of labeled pore-forming proteins on supported lipid bilayers, and multiplexed temporal single-molecule Förster resonance energy transfer measurements at 5-25 Hz. This method holds considerable promise for advancing multi-target single-molecule localization microscopy and biopolymer sequencing.
Redefining the Limits of Functional Continuity in the Early Evolution of P-Loop NTPases
Authors: Demkiv Andrey O. , Toledo-Patiño Saacnicteh , Carmona Encarni Medina , Berg Andrej , Pinto Gaspar P. , Parracino Antonietta , Sanchez-Ruiz Jose M. , Hengge Alvan C. , Laurino Paola , Longo Liam M. , Kamerlin Shina Caroline Lynn
Published: September 2024

At the heart of many nucleoside triphosphatases is a conserved sequence motif that binds phosphate. A current model of early enzyme evolution proposes that this 6-8 residue motif could have sparked the emergence of the very first nucleoside triphosphatases – a striking example of evolutionary continuity from simple beginnings, if true. To test whether this provocative evolutionary model holds for the ancient and ubiquitous P-Loop NTPases, the properties of seven disembodied Walker A-derived peptides were extensively characterized by Hamiltonian replica exchange molecular dynamics simulations. Although dynamic flickers of nest-like conformations were observed, significant structural similarity between the situated peptide and its disembodied counterpart was not detected – even in the presence of orthophosphate or a nucleotide. Simulations suggest that phosphate binding is non-specific, with a slight preference for GTP over orthophosphate. Control peptides with the same amino acid composition but different sequences and situated conformations behaved similarly to the Walker A peptides with respect to conformational dynamics and phosphate binding, revealing no indication that the Walker A sequence is privileged as a disembodied peptide. We conclude that the evolutionary history of the P-Loop NTPase family is unlikely to have started with a disembodied Walker A peptide in an aqueous environment. The limits of evolutionary continuity for this protein family, and the environmental context within which it emerged, must be reconsidered. Finally, we argue that motifs such as the Walker A motif may represent incomplete or fragmentary molecular fossils – the true nature of which have been eroded by time.

Significance Statement

The first proteins were undoubtedly small, but when did those seeds emerge, and what did they look like? It is widely believed that the Walker A P-loop motif is a seed for the emergence of phosphate binding proteins, snugly binding phosphate in a structurally conserved nest. We probe this hypothesis through detailed computational characterization of disembodied Walker A and control peptides, showing that any nest formation is transient, and phosphate binding is weak and non-specific. Thus, we do not find structural continuity represented in the conserved Walker A motif, and current models of early P-loop evolution require revision. Further, care is required when interpreting highly conserved sequence fragments more broadly, as these may merely represent eroded molecular fossils.
Genomic Determinants of Biological Age Estimated By Deep Learning Applied to Retinal Images
Authors: Huang Yu , Syed Mohammad Ghouse , Chen Ruiye , Li Cong , Shang Xianwen , Wang Wei , Zhang Xueli , Zhang Xiayin , Tang Shulin , Liu Jing , Liu Shunming , Srinivasan Sundar , Hu Yijun , Mookiah Muthu Rama Krishnan , Wang Huan , Trucco Emanuele , Yu Honghua , Palmer Colin , Zhu Zhuoting , Doney Alexander S F , He Mingguang
Published: September 2024

With the development of deep learning (DL) techniques, there has been a successful application of this approach to determine biological age from latent information contained in retinal images. Retinal age gap (RAG) defined as the difference between chronological age and predicted retinal age has been established previously to predict the age-related disease. In this study, we performed discovery genome-wide association analysis (GWAS) on the RAG using the 31271 UK Biobank participants and replicated our findings in 8034 GoDARTs participants. The genetic correlation between RAGs predicted from the two cohorts was 0.67 (P=0.021). After meta-analysis, we found 13 RAG loci which might be related to retinal vessel density and other aging processes. The SNP-wide heritability (h2) of RAG was 0.15. Meanwhile, by performing Mendelian Randomization analysis, we found that glycated hemoglobin, inflammation hemocytes and anemia might be associated with accelerated retinal aging. Our study explored the biological implications and molecular level mechanism of RAG, which might enable causal inference of the aging process as well as provide potential pharmaceutical intervention targets for further treatment.
Digital Engagement of Neurocutaneous Syndrome Communities on Facebook: A Descriptive Study
Authors: Momen Donia , Patel Kushagra , Muzyka Logan , DeCuypere Michael , Lam Sandi K. , Raskin Jeffrey S.
Published: September 2024

Introduction

Social media has become a platform for healthcare providers and parents to communicate about common and rare pediatric disorders. Neurocutaneous syndromes including Tuberous Sclerosis Complex, Neurofibromatosis, and Sturge-Weber syndrome require lifelong monitoring and complex treatments. Clinician directed information is supplemented by online support groups, non-profit fundraising organizations, and educational programs through various Facebook features.

Objective

The objective of this study is to explore the socialization patterns of individuals affected by neurocutaneous syndromes as they interact and engage within various Facebook forums.

Methods

Public accounts on Facebook were analyzed throughout August 2022. The search terms used were “Sturge-Weber Syndrome”, “Sturge Weber”, “SWS”, “Tuberous Sclerosis”, “Tuberous Sclerosis Complex (TSC)”, and “Neurofibromatosis”, “Neurofibromatosis 1 (NF1)”, and “Neurofibromatosis 2 (NF2)”. Facebook accounts were analyzed on the basis of page ownership and video content.

Results

Searching Sturge-Weber syndrome (SWS) yielded 99 Facebook pages and 37 Facebook videos. Tuberous sclerosis resulted in 100 Facebook pages and 139 Facebook videos. Neurofibromatosis yielded 102 Facebook pages and 129 Facebook Videos. Patient released stories comprised 51% of the Facebook videos (157/305), educational videos comprised 37% (112/305), and 12% (36/305) related to the syndromes’ awareness day. Facebook Pages were managed by nonprofit organizations 37% (111/301), community support groups 36% (108/301), and patients creating a “private blog” 23% (70/301), and physicians 4% (12/301). Figure 1 shows a breakdown of the Facebook page ownership and video content of neurocutaneous syndromes.

Conclusion

This study describes the online discussion of neurocutaneous syndromes through social media. The benefits of anonymized discussion for patients and families are many. Physicians manage only 4% of the Facebook pages and this may represent an opportunity to further disseminate medical advice in the future.
Rare Variant Association Analysis Uncovers Involvement ofVNN2in Stroke Outcome
Authors: Alcaide-Consuegra Estefanía , Mola-Caminal Marina , Escaramís Georgia , Lazcano Uxue , Pérez Isabel Fernández , Jimenez-Balado Joan , Giralt-Steinhauer Eva , Cuadrado-Godia Elisa , Ois Angel , Rodríguez-Campello Ana , Vallverdú Marta , Medina-Dols Aina , Jiménez Carmen , Tur Silvia , Díaz Rosa M , Bruque Carlos David , Andreu-Somavilla Nuria , González-Navarrete Irene , Vives-Bauzà Cristòfol , Fernández-Cadenas Israel , Jiménez-Conde Jordi , Balcells Susanna , Rabionet Raquel
Published: September 2024

BACKGROUND

A stroke’s functional outcome presents vast variability among patients, which is influenced by age, sex, characteristics of the lesion, and genetic factors. However, there is very little knowledge about stroke recovery genetics. Recently, some GWAS (Genome-Wide Association Studies) have highlighted the involvement of common or low-frequency variants near or withinPATJ,PPP1R21, PTCH1, NTN4andTEK genes, whereas the role of rare variants is still unclear. This study aims to identify the genetic contributions to differences in stroke outcome analyzing the effect of rare variants.

METHODS

We performed a pilot study analyzing 90 exomes of extreme good or bad recovery (modified Rankin Scale (mRS) at 3 months 0-1 vs 4-5) to select target genes involved in stroke recovery. To expand this study, 702 additional samples were sequenced by Targeted Next-Generation Sequencing capturing loci selected from the pilot study, GWAS studies and literature input. Here, we performed continuous (mRS 0-6) and dichotomous (mRS 0-1 vs 3-6) analyses, yielding one candidate gene. Protein structure and stability analysis were performed on selected variants.

RESULTS

Our work identified rare coding variants inVNN2associated with patients with a better stroke recovery (ΔDIC > 10, equivalent to p-value < 0.001). Six rare variants were predicted to significantly affect protein stability (ΔΔG > 1.6 kcal/mol), meanwhile, another variant, located in the active site, could affect the electrostatic surface.

CONCLUSIONS

VNN2could play a role in post-stroke inflammation altering the cell adhesion and migration of neutrophils during recovery.
Pangenome-Informed Language Models for Privacy-Preserving Synthetic Genome Sequence Generation
Authors: Huang Pengzhi , Charton François , Schmelzle Jan-Niklas M. , Darnell Shelby S. , Prins Pjotr , Garrison Erik , Suh G. Edward
Published: September 2024

The public availability of genome datasets, such as The Human Genome Project (HGP), The 1000 Genomes Project, The Cancer Genome Atlas, and the International HapMap Project, has significantly advanced scientific research and medical understanding. Here our goal is to share such genomic information for downstream analysis while protecting the privacy of individuals through Differential Privacy (DP). We introduce synthetic DNA data generation based on pangenomes in combination with Pretrained-Language Models (PTLMs).

We introduce two novel tokenization schemes based on pangenome graphs to enhance the modeling of DNA. We evaluated these tokenization methods, and compared them with classical single nucleotide andk-mer tokenizations. We findk-mer tokenization schemes, indicating that our tokenization schemes boost the model’s performance consistency with long effective context length (covering longer sequences with the same number of tokens). Additionally, we propose a method to utilize the pangenome graph and make it comply with DP privacy standards. We assess the performance of DP training on the quality of generated sequences with discussion of the trade-offs between privacy and model accuracy. The source code for our work will be published under a free and open source license soon.
Rendering Proteins Fluorescent Inconspicuously: Genetically Encoded 4-Cyanotryptophan Conserves Their Structure and Enables the Detection of Ligand Binding Sites
Authors: Qianzhu Haocheng , Abdelkader Elwy H. , Welegedara Adarshi P. , Habel Edan , Paul Nathan , Frkic Rebecca L. , Jackson Colin J. , Huber Thomas , Otting Gottfried
Published: September 2024

Cyano-tryptophans (CN-Trp) are privileged multimodal reporters on protein structure. They are similar in size to the canonical amino acid tryptophan and some of them exhibit bright fluorescence which responds sensitively to changes in the environment. We selected aminoacyl-tRNA synthetases specific for 4-, 5-, 6-, and 7-CN-Trp for high-yield in vivo production of proteins with a single, site-specifically introduced nitrile label. The absorption maximum of 4-CN-Trp is distinct from Trp, allowing the selective excitation of its intense fluorescence. 4-CN-Trp features bright fluorescence in the visible range. Crystal structures of maltose binding protein demonstrate near-complete structural conservation when a native buried Trp residue is replaced by 4-CN-Trp. Besides presenting an inconspicuous tag for live cell microscopy, the high fluorescence of 4-CN-Trp enables measurements of subnanomolar ligand binding affinities in isotropic solution, as demonstrated by the complex between rapamycin and the peptidyl–prolyl isomerase FKBP12 furnished with a 4-CN-Trp residue in the substrate binding pocket. Furthermore, 4-CN-Trp residues positioned at different locations of a protein containing multiple tryptophan residues permits using fluorescence quenching experiments to detect the proximity of individual Trp residues to the binding site of aromatic ligands.
One Health in Eastern Africa: No barriers for ESBL producingE. colitransmission or independent antimicrobial resistance gene flow across ecological compartments
Authors: Musicha Patrick , Beale Mathew A , Cocker Derek , Oruru Fiona A , Zuza Allan , Salifu Chifundo , Katende George , Nanono Sylvia , Isaasi Fred , Chidziwisano Kondwani , Mugisha Lawrence , Kajumbula Henry , Musoke David , Morse Tracy , Jacob Shevin , Feasey Nicholas A , Thomson Nicholas R
Published: September 2024

The One Health paradigm considers the interdependence of human, animal and environmental health. In high-income countries, limited evidence has been found from recent studies to support the importance of a One Health approach to addressing spread of antimicrobial resistance (AMR). Given AMR is a global threat, and we are all interconnected it would be important to know if closer interaction of humans with animals and the environment in low-income present a contrasting picture. We used whole genome sequencing to investigate the genomic diversity and to infer transmission of extended spectrum beta-lactamase producingEscherichia coli(ESBL-Ec) between different ecological niches (humans, animals and the environment). We found high diversity of ESBL-Ec with 172 genomic clusters and 167 sequence types identified from 2,344 genomes. Common ESBL genes,blaCTX-M-15(67.6%) andblaCTX-M-27(14.2%) were carried on a complex network of different plasmids, presenting multiple pathways for dissemination and revealing the high force of selection. Using fine-scale genomic clustering across multiple thresholds ranging from 0 to 20 single nucleotide polymorphisms, we found that genomes isolated from humans, animals and the environment formed overlapping clusters, indicating recent ESBL-Ec transmission and co-circulation both within and between ecological compartments. These findings demonstrate that the One Health approach is highly relevant to tackling AMR in low-income settings, and therefore critical to consider if we are to address the rise of AMR globally.
MicroED Structures of Fluticasone Furoate and Fluticasone Propionate Provide New Insights to Their Function
Authors: Lin Jieye , Unge Johan , Gonen Tamir
Published: September 2024

The detailed understanding of fluticasone, a widely prescribed medicine for allergic rhinitis, asthma, and chronic obstructive pulmonary disease (COPD), has not been complete due to challenges in structural elucidation. The three-dimensional (3D) structure of fluticasone furoate1remained undetermined for decades, while the existing structures of fluticasone propionate2required refinement against improved data. In this study, we applied microcrystal electron diffraction (MicroED) to determine the 3D structures of1and2in their drug formulation state. Density functional theory (DFT) calculations were utilized to model solvent effects to determine the preferred geometries in solution. A comparative analysis of structures of1and2across three states (drug formulation state, in solution, and biologically active state) revealed major conformational changes during the entire transition. Potential energy plots were calculated for the most dynamic bonds, uncovering their rotational barriers. This study underscores the combined use of MicroED and DFT calculations to provide a comprehensive understanding of conformational and energy changes during drug functioning in humans. The quantitative comparison highlights the subtle structural differences that can lead to significant functional changes in pharmaceutical properties.
Molecular insights into substrate translocation in an elevator-type metal transporter
Authors: Zhang Yao , Jafari Majid , Zhang Tuo , Sui Dexin , Sagresti Luca , Merz Kenneth M. , Hu Jian
Published: September 2024

The Zrt/Irt-like protein (ZIP) metal transporters are key players in maintaining the homeostasis of a panel of essential microelements. The prototypical ZIP fromBordetella bronchiseptica(BbZIP) is an elevator transporter, but how the metal substrate moves along the transport pathway and how the transporter changes conformation to allow alternating access remain to be elucidated. Here, we combined structural, biochemical, and computational approaches to investigate the process of metal substrate translocation along with the global structural rearrangement. Our study revealed an upward hinge motion of the transport domain in a high-resolution crystal structure of a cross-linked variant, elucidated the mechanisms of metal release from the transport site into the cytoplasm and activity regulation by a cytoplasmic metal-binding loop, and unraveled an unusual elevator mode in enhanced sampling simulations that distinguishes BbZIP from other elevator transporters. This work provides important insights into the metal transport mechanism of the ZIP family.
scaLR: a low-resource deep neural network-based platform for single cell analysis and biomarker discovery
Authors: Jogani Saiyam , Pol Anand Santosh , Prajapati Mayur , Samal Amit , Bhatia Kriti , Parmar Jayendra , Patel Urvik , Shah Falak , Vyas Nisarg , Gupta Saurabh
Published: September 2024

Purpose

Single-cell RNA sequencing (scRNA-seq) is producing vast amounts of individual cell profiling data. Analysis of such datasets presents a significant challenge in accurately annotating cell types and their associated biomarkers. scRNA-seq datasets analysis will help us understand diseases such as Alzheimer’s, Cancer, Diabetes, Coronavirus disease 2019 (COVID-19), Systemic Lupus Ery-thematosus (SLE), etc. Recently different pipelines based on machine learning (ML) and Deep Neural Network (DNN) methods have been employed to tackle these issues utilizing scRNA-seq datasets. These pipelines have arisen as a promising resource and are capable of extracting meaningful and concise features from noisy, diverse, and high-dimensional data to enhance annotations and subsequent analysis. Existing tools require high computational resources to execute large sample datasets.

Methods

We have developed a cutting-edge platform known as scaLR (Single Cell Analysis using Low Resource) that efficiently processes data in batches, and reduces the required resources for processing large datasets and running NN models. scaLR is equipped with data processing, feature extraction, training, evaluation, and downstream analysis. The data processing module consists of sample-wise & standard scaler normalization and splitting of data. Its novel feature extraction algorithm, first trains the model on a feature subset and stores feature importance for all the features in that subset. At the end of this process, top K features are selected based on their importance. The model is trained on top K features, its performance evaluation and associated downstream analysis provide significant biomarkers for different cell types and diseases/traits.

Results

To showcase the capabilities of scaLR, we utilized several scRNA-seq datasets of Peripheral Blood Mononuclear Cells (PBMCs), Alzheimer’s patients, and large datasets from human and mouse embryonic development. Our findings indicate that scaLR offers comparable prediction accuracy and requires less model training time and compute resources than existing Python-based pipelines and frameworks. Moreover, scaLR efficiently handles large sample datasets (>11.4 million cells) with minimal resource usage (29GB RAM, 12GB GPU, and 8 CPUs) while maintaining high prediction accuracy and being capable of ranking the biomarker association with specific cell types and diseases.

Conclusion

We present scaLR a Python-basedplatform, engineered to utilize minimal computational resources while maintaining comparable execution times to existing frameworks. It is highly scalable and capable of efficiently handling datasets containing millions of cell samples and providing their classification and important biomarkers.
Glucomannan engineering highlights the role of galactosyl modification in fine-tuning cellulose-glucomannan interaction in Arabidopsis cell walls
Authors: Yoshimi Yoshihisa , Yu Li , Cresswell Rosalie , Guo Xinyu , Echevarría-Poza Alberto , Lyczakowski Jan J. , Dupree Ray , Kotake Toshihisa , Dupree Paul
Published: September 2024

Widely found in most plant lineages, β-mannans are structurally diverse polysaccharides that can bind to cellulose fibrils to form the complex polysaccharide architecture of the cell wall. Glucomannan backbones acquire variable patterns of galactosyl substitutions, depending on plant developmental stage and species. How the changes in polysaccharide structure influence its cell wall solubility or promote appropriate interaction with cellulose fibrils is poorly understood. Here, we show that fine-tuning of galactosyl modification on glucomannans is achieved by the differing acceptor recognition of mannan α-galactosyltransferases (MAGTs). Biochemical analysis and13C solid-state nuclear magnetic resonance spectroscopy of Arabidopsis with cell wall glucomannan engineered by MAGTs revealed that the degree of galactosylation strongly affects the interaction with cellulose. The findings indicate that plants tailor galactosyl modification on glucomannans for constructing an appropriate cell wall architecture, paving the way to convert properties of lignocellulosic biomass for better use.
Impact ofO-GlcNAcylation elevation on mitophagy and glia in the dentate gyrus
Authors: Kramer Joshua , Chatham John C , Young Martin E , Darley-Usmar Victor , Zhang Jianhua
Published: September 2024

O-GlcNAcylation is a dynamic and reversible protein post-translational modification of serine or threonine residues which modulates the activity of transcriptional and signaling pathways and controls cellular responses to metabolic and inflammatory stressors. We and others have shown thatO-GlcNAcylation has the potential to regulate autophagy and mitophagy to play a critical role in mitochondrial quality control, but this has not been assessedin vivoin the brain. This is important since mitochondrial dysfunction contributes to the development of neurodegenerative disease. We used mito-QC reporter mice to assess mitophagy in diverse cells in the dentate gyrus in response to pharmacological inhibition of OGA with thiamet G which leads to elevation of proteinO-GlcNAcylation. We demonstrate that mitophagy occurs predominantly in the GFAP positive astrocytes and is significantly decreased in response to elevatedO-GlcNAcylation. Furthermore, with increasedO-GlcNAcylation, the levels of astrocyte makers GFAP and S100B, and microglial cell marker IBA1 were decreased in the dentate gyrus, while the levels of microglial cell marker TMEM119 were increased, indicating significant changes in glia homeostasis. These results provide strong evidence of the regulation of mitophagy and glia signatures by theO-GlcNAc pathway.
Local optogenetic NMYII activation within the zebrafish neural rod results in long-range, asymmetric force propagation
Authors: Crellin Helena A , Zhu Chengxi , Serrano-Nájera Guillermo , Race Amelia , O’Holleran Kevin , Lenz Martin O , Buckley Clare E
Published: September 2024

How do cellular forces propagate through tissue to allow large-scale morphogenetic events? To investigate this question, we used anin vivooptogenetic approach to reversibly manipulate actomyosin contractility at depth within the developing zebrafish neural rod. Contractility was induced along the lateral cortices of a small patch of developing neural epithelial progenitor cells, resulting in a shortening of these cells along their mediolateral axis. Imaging the immediate response of surrounding tissue uncovered a long-range, tangential, and elastic tissue deformation along the anterior-posterior axis. Unexpectedly, this was highly asymmetric, propagating in either the anterior or the posterior direction in response to local gradients in optogenetic activation. The degree of epithelialisation did not have a significant impact on the extent of force propagation via lateral cortices. We also uncovered a dynamic oscillatory expansion and contraction of the tissue along the anterior-posterior axis, with wavelength within the range of rhombomere length. Together, this study shows dynamic and wave-like propagation of force along the anterior-posterior axis. It also suggests that cell generated forces are actively propagated over long distances within the tissue, and that local anisotropies in tissue organisation and contractility are sufficient to drive directional force propagation.
InTraSeq: A Multimodal Assay that Uncovers New Single-Cell Biology and Regulatory Mechanisms
Authors: Ariss Majd M. , Huang Linglin , Ding Xiaokai , Sheth Shivani , Levy Tyler , Fisher Jeremy , Loebelenz Jean , Arlotta Keith , Dixon Karen , Polakiewicz Roberto , Kuchroo Vijay K. , Beausoleil Sean A.
Published: September 2024

Single-cell RNA sequencing (scRNA-seq) has revolutionized cell biology by enabling the profiling of transcriptomes at a single-cell resolution, leading to important discoveries that have advanced our understanding of cellular and tissue heterogeneity, developmental trajectories, and disease progression. Despite these important advances, scRNA-seq is limited to measuring the transcriptome providing a partial view of cellular function. To address this limitation, multimodal scRNA-seq assays have emerged, allowing for the simultaneous measurement of RNA expression and protein. Intracellular Transcriptomic and Protein Sequencing (InTraSeq), a novel multimodal scRNA-seq technology described here, enables the concurrent measurement of mRNA, surface markers, cytoplasmic proteins, and nuclear proteins within individual cells through oligo-barcoded antibodies. This method offers a comprehensive approach to studying cellular function by combining RNA and protein profiling from the same sample and utilizing a relatively simple protocol. The InTraSeq method enables researchers to expand their view of critical intracellular protein expression including post-translational modifications (PTMs) and transcription factors, allowing for the identification of novel cellular subtypes and states that may be obscured by RNA-based analyses alone. This is particularly valuable in understanding the heterogeneity of cell populations and identifying distinct functional states. In this report, we used InTraSeq to characterize the complex cellular states and regulatory mechanisms during Th17 cell differentiation. We simultaneously profiled RNA and protein expression in over 85,000 cells, capturing transcriptional changes, changes in protein expression and the dynamics of signaling pathways at a high resolution. Our results revealed novel insights into Th17 cell differentiation, including the identification of key regulatory factors and their target genes. By simultaneously measuring mRNA, extra and intra-cellular proteins, signaling proteins, and PTMs, InTraSeq offers a comprehensive understanding of cellular processes and enables the identification of novel regulatory mechanisms.
Elicitor specific mechanisms of defence priming in oak seedlings against powdery mildew
Authors: Sanchez-Lucas Rosa , Bosanquet Jack L. , Henderson James , Catoni Marco , Pastor Victoria , Luna Estrella
Published: September 2024

Defence priming sensitises plant defences to enable a faster and/or stronger response to subsequent stress. Various chemicals can trigger priming; however, the response remains unexplored in oak. Here, we characterise salicylic acid (SA)-, jasmonic acid (JA)-, and β-aminobutyric acid (BABA)-induced priming of oak seedlings against the causal agent of powdery mildew (Erysiphe alphitoides,PM). Whilst JA had no effects, BABA and SA enhanced resistance by priming callose deposition and SA-dependent gene expression, respectively. Untargeted transcriptome and metabolome analyses revealed genes and metabolites uniquely primed by BABA, SA, and JA. Enrichment analyses demonstrated a limited number of pathways differentiating the three treatments or the resistance-inducing elicitors BABA and SA. However, a similar mode of action between BABA and JA was identified. Moreover, our analyses revealed a lack of crosstalk between SA and JA. Interestingly, priming by BABA was linked to alkaloid, lignan, phenylpropanoid, and indolitic compounds biosynthesis. Moreover, integration of the omics analyses revealed the role of ubiquitination and protein degradation in priming by BABA. Our results confirm the existence of chemical-induced priming in oak and has identified specific molecular markers associated with well-characterised elicitor.
Investigation of plant virus-like particle formation in bacterial and yeast expression systems
Authors: Balke Ina , Resevica Gunta , Zeltina Vilija , Silamikelis Ivars , Liepa Elva , Liepa Reinis , Kalnciema Ieva , Radovica-Spalvina Ilze , Gudra Dita , Pjalkovskis Janis , Freivalds Janis , Kazaks Andris , Zeltins Andris
Published: September 2024

Virus-like particles (VLPs) have garnered significant attention due to their potential applications in various fields, particularly in biomedicine, where they are used for drug delivery, vaccine development, and as diagnostic tools. Plant virus-derived VLPs have been especially successful, leading to a surge in research aimed at developing new VLPs. Despite this growing interest, not all attempts at VLP formation are successful. Understanding the factors that contribute to successful VLP assembly is crucial for advancing this field. In this study, we focus on the coat proteins (CPs) of three plant viruses belonging to the Sobemovirus genus as a model to investigate the process of VLP formation. Our findings demonstrated that the strong binding of CPs to ssDNA can be a major reason for unsuccessful VLP production. This issue can potentially be overcome by transitioning from an episomal to a chromosome-integrated expression system. By doing so, we aim to elucidate the mechanisms that facilitate successful VLP assembly. Our findings provide valuable insights into the properties of sobemovirus CPs and highlight their potential for encapsulating foreign nucleic acids, thereby providing additional applications as nanocontainers or vaccine platforms with interior modification capabilities for enhanced immune response. Moreover, our RNA-Seq data indicates that sobemovirus-derived VLPs predominantly package their CP mRNA, irrespective of the expression system used. This characteristic can be utilized for the functional encapsulation of nucleic acids, enhancing the versatility and utility of these VLPs in various biotechnological applications.
Weak-coupling theory of magic-angle twisted bilayer graphene
Authors: Zhu Jihang , Torre Iacopo , Polini Marco , MacDonald A. H.
Published: September 2024

Strong correlations occur in magic-angle twisted bilayer graphene (MATBG) when the octet of flat moiré minibands centered on charge neutrality (CN) is partially occupied. The octet consists of a single valence band and a single conduction band for each of four degenerate spin-valley flavors. Motivated by the importance of Hartree electrostatic interactions in determining the filling-factor-dependent band structure, we use a time-dependent Hartree approximation to gain insight into electronic correlations. We find that the electronic compressibility is dominated by Hartree interactions, that paramagnetic states are stable over a range of density near CN, and that the dependence of energy on flavor polarization is strongly overestimated by mean-field theory.

Published by the American Physical Society
2024
Gauged Gaussian projected entangled pair states: A high dimensional tensor network formulation for lattice gauge theories
Authors: Kelman Ariel , Borla Umberto , Gomelski Itay , Elyovich Jonathan , Roose Gertian , Emonts Patrick , Zohar Erez
Published: September 2024

Gauge theories form the basis of our understanding of modern physics—ranging from the description of quarks and gluons to effective models in condensed matter physics. In the nonperturbative regime, gauge theories are conventionally treated discretely as lattice gauge theories. The resulting systems are evaluated with path-integral based Monte Carlo methods. These methods, however, can suffer from the sign problem and do not allow for a direct evaluation of real-time dynamics. In this work, we present a unified and comprehensive framework for gauged Gaussian projected entangled pair states (PEPS), a variational ansatz based on tensor networks. We review the construction of Hamiltonian lattice gauge theories, explain their similarities to PEPS, and detail the construction of the ansatz state. The estimation of ground states is based on a variational Monte Carlo procedure with the PEPS as an ansatz state. This sign-problem-free ansatz can be efficiently evaluated in any dimension with arbitrary gauge groups, and can include dynamical fermionic matter, suggesting new options for the simulation of nonperturbative regimes of gauge theories, including quantum chromodynamics.

Published by the American Physical Society
2024
Dynamics of Active Defects on the Anisotropic Surface of an Ellipsoidal Droplet
Authors: Clairand Martina , Mozaffari Ali , Hardoüin Jerôme , Zhang Rui , Doré Claire , Ignés-Mullol Jordi , Sagués Francesc , de Pablo Juan J. , Lopez-Leon Teresa
Published: September 2024

We investigate the steady state of an ellipsoidal active nematic shell using experiments and numerical simulations. We create the shells by coating microsized ellipsoidal droplets with a protein-based active cytoskeletal gel, thus obtaining ellipsoidal core-shell structures. This system provides the appropriate conditions of confinement and geometry to investigate the impact of nonuniform curvature on an orderly active nematic fluid that features the minimum number of defects required by topology. We identify new time-dependent states where topological defects periodically oscillate between translational and rotational regimes, resulting in the spontaneous emergence of chirality. Our simulations of active nematohydrodynamics demonstrate that, beyond topology and activity, the dynamics of the active material are profoundly influenced by the local curvature and viscous anisotropy of the underlying droplet, as well as by external hydrodynamic forces stemming from the self-sustained rotational motion of defects. These results illustrate how the incorporation of curvature gradients into active nematic shells orchestrates remarkable spatiotemporal patterns, offering new insights into biological processes and providing compelling prospects for designing bioinspired micromachines.

Published by the American Physical Society
2024
Synthesis and crystal structure of poly[ethanol(μ-4-methylpyridine N-oxide)di-μ-thiocyanato-cobalt(II)]
Authors: Näther Christian , Jess Inke
Published: September 2024

Reaction of 4-methylpyridine N-oxide and Co(NCS)2 in ethanol as solvent accidentally leads to the formation of single crystals of Co(NCS)2(4-methylpyridine N-oxide)(ethanol) or [Co(NCS)2(C6H7NO)(C2H6O)]
n
. The asymmetric unit of the title compound consists of one CoII cation, two crystallographically independent thiocyanate anions, one 4-methylpyridine N-oxide coligand and one ethanol molecule on general positions. The cobalt cations are sixfold coordinated by one terminal and two bridging thiocyanate anions, two bridging 4-methylpyridine N-oxide coligands and one ethanol molecule, with a slightly distorted octahedral geometry. The cobalt cations are linked by single μ-1,3(N,S)-bridging thiocyanate anions into corrugated chains, that are further connected into layers by pairs of μ-1,1(O,O)-bridging 4-methylpyridine N-oxide coligands. The layers are parallel to the bc plane and are separated by the methyl groups of the 4-methylpyridine N-oxide coligands. Within the layers, intralayer hydrogen bonding is observed.