bluuebunny/crossref_metadata_2025_split huggingface dataset:
An optimized somatic embryo transformation system assisted homozygous edited rubber tree generation method mediated by CRISPR/Cas9
Authors: Yang Xianfeng , Lin Qiufei , Udayabhanu Jinu , Hua Yuwei , Dai Xuemei , Xin Shichao , Wang Xiaoyi , Huang Huasun , Huang Tiandai 
Published: March 2024

AbstractPreviously, we have realized the CRISPR/Cas9-RNP and plasmid mediated protoplast transient transformation genome editing in the rubber tree (Hevea brasiliensis), but no gene editing plants were acquired due to the bottleneck of genetic transformation. In present study, antibiotic sensitivity tests against kanamycin, hygromycin and basta were analyzed for embryo screening, the results demonstrated that 10 mg/L hygromycin is the best for transformation. ThenAgrobacteriummediated transformation ofH. brasiliensisembryos was carried out using a pCAMBIA1300-based CRISPR/Cas9 vector targeting Phytoene desaturase gene (HbPDS). High-throughput sequencing of T0 generation positive embryos which were used as regeneration materials in typical transformation procedure showed that more than 90% T0 edited embryos are chimeric with a 3.2% editing efficiency. A T0 embryo with 9.8% edited cells was sliced into small pieces for one more cycle embryogenesis to produce T1 generation embryos in order to improve the ratio of homozygous embryos. Subsequently, next-generation sequencing (NGS) demonstrated that 29 out of 33 T1 embryos were edited, nearly 50% of which were found homozygous. At last, besides four chimeric plantlets with partial albino leaves, four plantlets with complete albino phenotype were regenerated from the 29 T1 generation edited embryos, among which one is a homozygous mono-allelic mutant and the other three are homozygous bi-allelic mutants. NGS demonstrated that the threshold for the proportion of edited cells with expected albino phenotype is between 70-85%. Additionally, Tail-PCR indicate that the T-DNA was inserted into different genome positions in the four homozygous edited plantlets, combined with the different genotypes are considered, the four homozygous plantlets can be confirmed as independently derived from single transformed cells. Overall, this is the first edited rubber trees with expected phenotype reported publicly, which shows the potential in genetic improvement ofH. brasiliensisby CRISPR/Cas9 gene editing, and subculture of T0 positive transformed somatic embryos into T1 generation is proved to be an effective and necessary procedure to produce homozygous transgenic plantlets. This study presents a significant advancement in transgenic and gene editing for rubber tree.
Lack of dominant-negative activity for tumor-associated ZNRF3 missense mutations at endogenous expression levels
Authors: Li Shanshan , Niu Jiahui , Zhang Ruyi , Massaar Sanne , Merode Jenna van , Schipper Nicky de , Kamp Lisa van de , Peppelenbosch Maikel P. , Smits Ron 
Published: March 2024

AbstractZNRF3, a negative regulator of β-catenin signaling, removes Wnt receptors from the membrane. Currently, it is unknown which tumor-associated variants can be considered driver mutations and through which mechanisms they contribute to cancer. Here we show that all truncating mutations analyzed at endogenous levels exhibit loss-of-function, with longer variants retaining partial activity. Regarding missense mutations, we show that 27/82 ZNRF3 variants in the RING and R-Spondin domain structures, lead to (partial) loss-of-function/hyperactivation. Mechanistically, defective R-spondin domain variants appear to undergo endoplasmic-reticulum-associated degradation due to protein misfolding. They show reduced stability and fail to reach the membrane correctly, which can be partially restored for several variants by culturing cells at 27°C. Although RING and R-spondin domain mutations in RNF43/ZNRF3 are often considered to possess dominant-negative oncogene-like activity in cancers, our findings challenge this notion. When representative variants are heterozygously introduced into endogenous ZNRF3, their impact on β-catenin signaling mirrors that of heterozygous knockout, suggesting that the supposed dominant-negative effect is non-existent. In other words, so-called “hyperactivating” ZNRF3/RNF43 mutations behave as classical loss-of-function mutations at endogenous levels. Taken together, our findings provide valuable information on ZNRF3 mutation impact in tumorigenesis and clarify their mechanism of action.
Integration of molecular coarse-grained model into geometric representation learning framework for protein-protein complex property prediction
Authors: Yue Yang , Li Shu , Cheng Yihua , Zhu Zexuan , Wang Lie , Hou Tingjun , He Shan 
Published: March 2024

AbstractStructure-based machine learning algorithms have been utilized to predict the properties of protein-protein interaction (PPI) complexes, such as binding affinity, which is critical for understanding biological mechanisms and disease treatments. While most existing algorithms represent PPI complex graph structures at the atom-scale or residue-scale, these representations can be computationally expensive or may not sufficiently integrate finer chemical-plausible interaction details for improving predictions. Here, we introduce MCGLPPI, a novel geometric representation learning framework that combines graph neural networks (GNNs) with the MARTINI molecular coarse-grained (CG) model to predict overall PPI properties accurately and efficiently. This framework maps proteins onto a concise CG-scale complex graph, where nodes represent CG beads and edges encode chemically plausible interactions. The GNN-based encoder is tailored to extract high-quality representations from this graph, efficiently capturing the overall properties of the protein complex structure. Extensive experiments on three different downstream PPI property prediction tasks demonstrate that MCGLPPI achieves competitive performance compared with the counterparts at the atom- and residue-scale, but with only a third of the computational resource consumption. Furthermore, the CG-scale pre-training on protein domain-domain interaction structures enhances its predictive capabilities for PPI tasks. MCGLPPI offers an effective and efficient solution for PPI overall property predictions, serving as a promising tool for the large-scale analysis of biomolecular interactions.
The molecular impact of cigarette smoking resembles aging across tissues
Authors: Ramirez Jose Miguel , Ribeiro Rogério , Soldatkina Oleksandra , Moraes Athos , García-Pérez Raquel , Ferreira Pedro G. , Melé Marta 
Published: March 2024

AbstractTobacco smoke is the main cause of preventable mortality worldwide. Smoking increases the risk of developing many diseases and has been proposed as an aging accelerator. Yet, the molecular mechanisms driving smoking-related health decline and aging acceleration in most tissues remain unexplored. Here, we characterize gene expression, alternative splicing, DNA methylation and histological alterations induced by cigarette smoking across human tissues. We show that smoking impacts tissue architecture and triggers systemic inflammation. We find that in many tissues, the effects of smoking significantly overlap those of aging in the same direction. Specifically, both age and smoking upregulate inflammatory genes and drive hypomethylation at enhancers. In addition, we observe widespread smoking-driven hypermethylation at target regions of the Polycomb repressive complex, which is a well-known aging effect. Smoking-induced epigenetic changes overlap causal aging CpGs, suggesting that these methylation changes may directly mediate aging acceleration observed in smokers. Finally, we find that smoking effects that are shared with aging are more persistent over time. Overall, our multi-tissue and multi-omic analysis of the effects of cigarette smoking provides an extensive characterization of the impact of tobacco smoke across tissues and unravels the molecular mechanisms driving smoking-induced tissue homeostasis decline and aging acceleration.
Extreme temperatures impede the release success of captive-bred avian scavengers
Authors: Anglister Nili , Acácio Marta , Vaadia Gideon , Arnon Eitam , Bruer Michael , Hatzofe Ohad , Miller Ygal , King Roni , Pinter-Wollman Noa , Spiegel Orr 
Published: March 2024

ABSTRACTConservation translocations (reinforcements and reintroductions) are central for managing various endangered species, yet, their implementation is logistically and financially challenging. Because many translocations fail due to the mortality of released individuals, identifying and preventing these factors is crucial. Here we examine risk factors affecting the post-release survival of the Griffon vulture (Gyps fulvus). The Israeli population is facing extinction, and the recovery efforts by the local Nature and Parks Authority include supplemental releases of individuals from captive-breeding or rehabilitated birds (mostly imported from Spain). We use GPS tracking and thermometers to compare movement, behavior, and weather conditions experienced by released and wild-born individuals active in the same area and time. Our results show that the Judean Desert release site had a significantly lower survival rate than other release sites included in the program. After excluding several possible factors (e.g. known pathogens) with pathological examinations, we found that released individuals at this area were exposed to higher temperatures preceding their death (compared to wild-born griffons nearby), suggesting heat stress as the cause of death. Arguably, they failed to avoid the harsh environmental conditions, resulting in overheating due to their inexperience and undeveloped flight ability, as reflected by their lower probabilities of flying and shorter travel distances per day compared to wild-born vultures. These findings have led to adjustments of the local release protocol, (namely winter releases) resulting in a significant improvement in the early survival of translocated Griffons in the Judean Desert. Accounting for the harmful effects of extreme weather conditions is particularly important in a world facing climate change. More broadly, this sequence of scientific investigation with data integration from ecological, clinical, and biotelemetry sources, leading to improvement in translocation success demonstrates how conservation practices can be optimized by supporting studies to ensure the survival of endangered species in the wild.
First concrete documentation for presence ofAedes (Stegomyia) albopictusin Bolivia: Dispelling previous anecdotes
Authors: Lardeux Frédéric , Boussès Philippe , Tejerina-Lardeux Rosenka , Berger Audric , Barnabé Christian , Garcia Lineth 
Published: March 2024

AbstractBackgroundThe presence ofAedes albopictusin Bolivia has been a subject of controversy, lacking concrete documentation until now.ObjectivesThis study aimed to furnish evidence ofAe. albopictuspresence in Bolivia.MethodsLarval breeding sites were sampled in two northern Bolivian localities, Rosario del Yata and San Agustin, both situated in the Beni department within the Vaca Diez province and Guayaramerin Municipio, approximately 10 km apart. Mosquito larvae collected underwent rearing to L4 and adult stages for morphological identification, with some specimens sequenced for confirmation.FindingsAe. albopictuswas identified in multiple breeding sites in both localities, confirming its establishment in the area. This marks the first concrete documentation of the species in Bolivia. The collections (larvae and adults) have been deposited in the Medical Entomology Laboratory of the Universidad Mayor de San Simón in Cochabamba, Bolivia, and the Laboratory of Entomology of the Instituto Nacional de Laboratorios de Salud of the Ministry of Health in La Paz, Bolivia.Main conclusionAcknowledging its role as a vector for arboviruses like dengue and Chikungunya,Ae. albopictusshould be incorporated into the Bolivian National Program of Vector Control for monitoring.
Graphical pangenomics-enabled characterisation of structural variant impact on gene expression in Brassica napus
Authors: Golicz Agnieszka A. , Yildiz Gözde , Weber Sven , Kox Tobias , Abbadi Amine , Snowdon Rod J. , Zanini Silvia F. 
Published: March 2024

AbstractStructural variants (SVs, eg. insertions and deletions) are genomic variations > 50 bp that are known to be associated with a range of crop traits, from yield to flowering behaviour and stress responses. Recently, pangenome graphs have emerged as a powerful framework for analysing genomic data by encoding population- or species-level diversity in one data structure. Pangenome graphs have the potential to serve as unbiased references for downstream applications, including SV genotyping and pan-transcriptomic analyses.In this work, we hypothesized that extensive variation affects transcript quantification and expression quantitative trait locus (eQTL) analysis when relying on a single reference, and that using pangenome graphs can mitigate reference sequence bias.We combined long and short read whole genome sequencing data with expression profiling ofBrassica napus(oilseed rape) to assess the impact of SVs on gene expression regulation and explored the utility of pangenome graphs for eQTL analysis. We demonstrate that pangenome graphs provides a superior framework for eQTL analysis by eliminating single reference bias in gene expression quantification. Combined with the graph-based genotyping of SVs, we identified 240 eQTL-SVs found in close proximity of target loci. These SVs affect expression of genes related to important traits, are often not in linkage with SNPs and represent diversity unaccounted for in classical SNP-based analyses.This study highlights the multiple advantages of graph-based approaches in population-scale studies and provides novel insight into gene expression regulation in an important crop.
The Hitchhiker’s Guide to Sequencing Data Types and Volumes for Population-Scale Pangenome Construction
Authors: Sarashetti Prasad , Lipovac Josipa , Tomas Filip , Šikic Mile , Liu Jianjun 
Published: March 2024

AbstractLong-read (LR) technologies from Pacific Biosciences (PacBio) and Oxford Nanopore Technologies (ONT) have transformed genomics research by providing diverse data types like HiFi, Duplex, and ultra-long ONT (ULONT). Despite recent strides in achieving haplotype-phased gapless genome assemblies using long-read technologies, concerns persist regarding the representation of genetic diversity, prompting the development of pangenome references. However, pangenome studies face challenges related to data types, volumes, and cost considerations for each assembled genome, while striving to maintain sensitivity. The absence of comprehensive guidance on optimal data selection exacerbates these challenges. To fill this gap, our study evaluates available data types, their significance, and the required volumes for robust de novo assembly in population-level pangenome projects. The results show that achieving chromosome-level haplotype-resolved assembly requires 20x high-quality long reads (HQLR) such as PacBio HiFi or ONT duplex, combined with 15-20x of ULONT per haplotype and 30x of long-range data such as Omni-C. High-quality long reads from both platforms yield assemblies with comparable contiguity, with HiFi excelling in NG50 and phasing accuracies, while usage of duplex generates more T2T contigs. As Long-Read Technologies advance, our study reevaluates recommended data types and volumes, providing practical guidelines for selecting sequencing platforms and coverage. These insights aim to be vital to the pangenome research community, contributing to their efforts and pushing genomic studies with broader impacts.
In Situ-Crosslinked Zippersomes Enhance Cardiac Repair by Increasing Accumulation and Retention
Authors: Jasiewicz Natalie E. , Mei Kuo-Ching , Oh Hannah M. , Bonacquisti Emily E. , Chaudhari Ameya , Byrum Camryn , Jensen Brian C. , Nguyen Juliane 
Published: March 2024

AbstractMesenchymal stem cell (MSC)-derived extracellular vesicles (EVs) are a promising treatment for myocardial infarction, but their therapeutic efficacy is limited by inefficient accumulation at the target site. A non-invasive MSC EV therapy that enhances EV accumulation at the disease site and extends EV retention could significantly improve post-infarct cardiac regeneration. Here we show that EVs decorated with the next-generation of high-affinity heterodimerizing leucine zippers, termed high-affinity (HiA) Zippersomes, amplify targetable surface areas through in situ crosslinking and exhibited ∼7-fold enhanced accumulation within the infarcted myocardium in mice after three days and continued to be retained up to day 21, surpassing the performance of unmodified EVs. After myocardial infarction in mice, high-affinity Zippersomes increase the ejection fraction by 53% and 100% compared with unmodified EVs and PBS, respectively. This notable improvement in cardiac function played a crucial role in restoring healthy heart performance. High-affinity Zippersomes also robustly decrease infarct size by 52% and 60% compared with unmodified EVs and PBS, respectively, thus representing a promising platform for non-invasive vesicle delivery to the infarcted heart.Translational Impact StatementTherapeutic delivery to the heart remains inefficient and poses a bottleneck in modern drug delivery. Surgical application and intramyocardial injection of therapeutics carry high risks for most heart attack patients. To address these limitations, we have developed a non-invasive strategy for efficient cardiac accumulation of therapeutics using in situ crosslinking. Our approach achieves high cardiac deposition of therapeutics without invasive intramyocardial injections. Patients admitted with myocardial infarction typically receive intravenous access, which would allow painless administration of Zippersomes alongside standard of care.
Modeling interpretable correspondence between cell state and perturbation response with CellCap
Authors: Xu Yang , Fleming Stephen , Tegtmeyer Matthew , McCarroll Steven A. , Babadi Mehrtash 
Published: March 2024

AbstractSingle-cell transcriptomics, in conjunction with genetic and compound perturbations, offers a robust approach for exploring cellular behaviors in diverse contexts. Such experiments allow un-covering cell-state-specific responses to perturbations, a crucial aspect in unraveling the intricate molecular mechanisms governing cellular behavior and potentially discovering novel regulatory pathways and therapeutic targets. However, prevailing computational methods predominantly focus on predicting average cellular responses, disregarding the inherent response heterogeneity associated with cell state diversity. In this study, we present CellCap, a deep generative model designed for the end-to-end analysis of single-cell perturbation experiments. CellCap employs sparse dictionary learning in a latent space to deconstruct cell-state-specific perturbation responses into a set of transcriptional response programs. These programs are then utilized by each perturbation condition and each cell at varying degrees. The incorporation of specific model design choices, such as dot-product cross-attention between cell states and response programs, along with a linearly-decoded latent space, underlay the interpretation power of CellCap. We evaluate CellCap’s model interpretability through multiple simulated scenarios and apply it to two real single-cell perturbation datasets. These datasets feature either heterogeneous cellular populations or a complex experimental setup. Our results demonstrate that CellCap successfully uncovers the relationship between cell state and perturbation response, unveiling novel insights overlooked in previous analyses. The model’s interpretability, coupled with its effectiveness in capturing heterogeneous responses, positions CellCap as a valuable tool for advancing our understanding of cellular behaviors in the context of perturbation experiments.
Mapping the Cellular Biogeography of Human Bone Marrow Niches Using Single-Cell Transcriptomics and Proteomic Imaging
Authors: Bandyopadhyay Shovik , Duffy Michael , Ahn Kyung Jin , Pang Minxing , Smith David , Duncan Gwendolyn , Sussman Jonathan , Zhang Iris , Huang Jeffrey , Lin Yulieh , Xiong Barbara , Imtiaz Tamjid , Chen Chia-Hui , Thadi Anusha , Chen Changya , Xu Jason , Reichart Melissa , Pillai Vinodh , Snaith Oraine , Oldridge Derek , Bhattacharyya Siddharth , Maillard Ivan , Carroll Martin , Nelson Charles , Qin Ling , Tan Kai 
Published: March 2024

AbstractThe bone marrow is the organ responsible for blood production. Diverse non-hematopoietic cells contribute essentially to hematopoiesis. However, these cells and their spatial organization remain largely uncharacterized as they have been technically challenging to study in humans. Here, we used fresh femoral head samples and performed single-cell RNA sequencing (scRNA-Seq) to profile 29,325 enriched non-hematopoietic bone marrow cells and discover nine transcriptionally distinct subtypes. We next employed CO-detection by inDEXing (CODEX) multiplexed imaging of 18 individuals, including both healthy and acute myeloid leukemia (AML) samples, to spatially profile over one million single cells with a novel 53-antibody panel. We discovered a relatively hyperoxygenated arterio-endosteal niche for early myelopoiesis, and an adipocytic, but not endosteal or perivascular, niche for early hematopoietic stem and progenitor cells. We used our atlas to predict cell type labels in new bone marrow images and used these predictions to uncover mesenchymal stromal cell (MSC) expansion and leukemic blast/MSC-enriched spatial neighborhoods in AML patient samples. Our work represents the first comprehensive, spatially-resolved multiomic atlas of human bone marrow and will serve as a reference for future investigation of cellular interactions that drive hematopoiesis.
Neural correlates in the time course of inferences: costs and benefits for less-skilled readers at the university level
Authors: Urrutia Mabel , Pino Esteban J. , Troncoso-Seguel María , Bustos Claudio , Guevara Pamela , Torres-Ocampo Karina , Mariángel Sandra , Fu Yang , Marrero Hipólito 
Published: March 2024

AbstractInferences are an indicator of a greater reading comprehension, as they imply a combination of implicit and explicit information that usually combines a textual representation with background knowledge of the reader. The aim of this study is to explore the costs and benefits of the time course of inferences in university students with reading comprehension difficulties at 3 stages during a narration. The method used was the event-related potential (ERP) technique in order to register the brain activity of 63 teaching program students while they read familiar, less-familiar and neutral stories. Results show a slow negativity potential component with greater negativity in words coming from familiar contexts when compared to less familiar and neutral ones in the first locus; an N400 component and a Post-N400 component in the second locus, reflecting greater negativity in familiar contexts when compared to less-familiar ones; and, lastly, through the use of a lexical decision task, FN400 and N400 components were found in the third locus, especially for pseudowords. These results are interpreted as a preferably bottom-up processing, which is characterized by lexical access difficulties in less-skilled readers.