bluuebunny/crossref_metadata_2025_split huggingface dataset:
Armed Macrophages as Hunters for Photodynamic Therapy of Systemic Bacterial Infections by Bathing in the Sunshine
Authors: Wang Zehui , Wang Lai , Zhou Lin , Zhang Xinfu , Xiao Yi 
Published: January 2024

AbstractThere has been a vision to conduct therapy using sunlight since ancient Greece, Egypt, and India. In modern medicine, photodynamic therapy is one popular form of therapy that uses light to excite photosensitizers to eliminate malignant and other diseased cells. It offers highly effective and broad-spectrum therapeutic efficacy. Yet, there are several hindrances to a real treatment of disease through photodynamic therapy, such as the limitation on the irradiation depth and areas, the regulation of side effects, etc. Usually, the patients should be kept in a dark environment during and after the therapeutic process for days to avoid side effects induced by light in daily life, not mention to conduct the phototherapy through sunbathing. Based on the above consideration, we propose an innovative idea to bring photodynamic therapy back to the origin of phototherapy-bathing in the sunshine. Namely, we designed a “live drug”, as a smart hunter, named A-RAWs, by loading an “off-on” type of photosensitizer in macrophages to solve two technical problems. Firstly, to find and capture bacteria accurately, and then transport these bacteria to the epidermis through the blood capillary, where sunlight is reachable. Secondly, to minimize the potential side effects and maximize the therapeutic time windows and efficacy by using bacteria as the trigger of the photodynamic effect. Specifically, we first designed and synthesized a lysosome-targeted and inflammation-activated NIR photosensitizer (Lyso710A), and loaded it in the lysosomes of macrophages. These “armed” macrophages were transferred into the infected host to capture deep-tissue bacteria through innate immunity and transport the captured bacteria through the bloodstream to superficial skin. Finally, the pathogenic bacteria are killed by the photodynamic effect when transported to the epidermis and receive sunbathing. In vivo experiment demonstrates a 100% therapeutic efficiency on systemic bacterial infection model. We also demonstrated the working mechanism of this “live drug” using a lung infection model. This hunter demonstrates high intelligence to break the limitations of current photodynamic therapy and executes photodynamic therapy of deep-tissue bacterial infection simply by bathing in the sunshine.Abstract Figure
Identifying the genetic and epigenetic basis for asymmetric bZIP expression in temperature-stressed bread wheat
Authors: Kaur Raminder , Singh Dalwinder , Kumar Pankaj , Kaur Gazaldeep , Shah Koushik , Pandey Harshita , Devi Shamjetsabam Gangarani , Pandey Ajay Kumar , Rishi Vikas 
Published: January 2024

AbstractAsymmetric expression in the bread wheat (Triticum aestivum) genome refers to the differential expression of genes from A, B, and D parental genomes. Bread wheat is a hexaploid crop with six copies of each chromosome. This complexity can result in unequal expression of genes from each parental genome, leading to asymmetry in gene expression. In other polyploid crops like cotton, transcription factors (TF) exhibit genome-biased expression; however, there are no comparable studies for bread wheat. One of the most prominent TFs families in plants is the basic Leucine Zippers (bZIP) which are eukaryote-specific proteins and regulate various biological processes, including stress-related responses. bZIP proteins are dimeric and several heptads long. They exhibit typical coiled-coil structures with strategically placed amino acids in each heptad, responsible for their stability and specificity. Here, we aim to decipher the structural basis of the asymmetric expression of the bZIP TFs in wheat under low and high-temperature conditions. Furthermore, 19 highly expressed stress-related TabZIP TFs were analysed for their asymmetric expression profiles as plants were exposed to temperature-stress conditions. Two benchmarks were used to analyse the asymmetric gene expression of bZIPs, i.e., a) the promoter’s occupancy by the epigenetic marker histones, namely, H3K4me3, H3k9ac (active) and H3K27me3 (repressive), b) density and diversity of cis-regulatory elements in the promoters. Notably, the genetic basis of the differences in protein sequences of bZIP triads was explored, which may impart structural stability to a specific homeolog enabling the plant to endure the stress conditions better.
The topography of DNA replication origins in Eukarya: GGN clusters, landmark nucleosomes, CDC6 and G4 structures
Authors: Bastolla Ugo , Gómez-Pinto Irene , Vergara Zaida , Gómez María , González Carlos , Gutiérrez Crisanto 
Published: January 2024

AbstractBackgroundWe recently identified tandem repeats of GGN triplets as a sequence motif strongly enriched in the DNA replication origins (ORIs) of theArabidopsis thalianagenome, where it correlates with the ORI strength quantified through short nascent strands sequencing.ResultsHere we show that clusters of four or more GGN repeats separated by short tracts (<7 nucleotides) are present in more than 65% ORIs of six model eukaryotic organisms:Leishmania major,Arabidopsis thaliana,Caenorhabditis elegans,Drosophila melanogaster,Mus musculusandHomo sapiens. The measured percentages vary with the experimental technique adopted for ORI determination. For all studied techniques and organisms, ORIs are significantly prone to be located within or near strong GGN clusters, although these are neither necessary nor sufficient for ORI activation. Interestingly, for same experimental technique, the association between ORIs and GGN clusters was stronger al later developmental stages for all organisms for which we could perform this comparison.In accordance with a biophysical model of nucleosome positioning, the GGN clusters strongly favor nucleosome occupancy. At the same time, both GGN clusters and ORIs occur frequently within 1kb from nucleosome-depleted regions (NDR). We propose a structural model based on chromatin secondary structure in which the NDR and the well-positioned nucleosome at the GGN are close in space, which may favor functional interactions. We hypothesize that the presence of GGN at ORIs arose in part for promoting the above nucleosome organization Moreover, at least inArabidopsis, the replication protein CDC6 is very strongly associated with GGN clusters.NMR experiments showed that clusters of at least four GGN can form G-quadruplex (G4)in vitro.Our data support the view that GGN clusters are formed through the interplay of mutational processes (GC skew at ORIs plus triplet expansion), and that similar mutational processes, i.e. AT skew at transcription start sites (TSS) and ORIs, might facilitate the formation of the NDR, thus favoring the evolvability of chromatin.ConclusionsGGN clusters are easily evolvable sequence motifs enriched at ORIs of eukaryotic genomes. They favor G4 secondary structure and a nucleosome organization that may unify the apparent discrepancy between ORIs of higher eukaryotes and yeast.
AMAPEC: accurate antimicrobial activity prediction for fungal effector proteins
Authors: Mesny Fantin , Thomma Bart PHJ 
Published: January 2024

AbstractFungi typically occur in environments where numerous and diverse other microbes occur as well, often resulting in fierce competition for nutrients and habitat. To support fungal fitness in these environments, they evolved various mechanisms that mediate direct antagonism towards niche competitors. Among these, the secretion of proteins with antimicrobial activities has been reported in fungi with diverse lifestyles. Recently, several plant-associated fungi were shown to rely on the secretion of antimicrobial effector proteins to antagonize certain members of plant hosts’ microbiota and to successfully colonize plant tissues. Some of these effectors do not share homology with known antimicrobials and represent novel antibiotics. Accordingly, the occurrence and conservation of proteinaceous antimicrobials throughout the fungal tree of life remains enigmatic. Here we present a computational approach to annotate candidate antimicrobial effectors in fungal secretomes based on protein physicochemical properties. After curating a set of proteins that were experimentally verified to display antimicrobial activity and a set of proteins that lack such activity, we trained a machine learning classifier on properties of protein sequences and predicted structures. This predictor performs particularly well on fungal proteins (R2=0.89) according to our validations and is delivered as a software package named AMAPEC, dedicated toantimicrobialactivityprediction foreffectorcandidates. We subsequently used this novel software to predict antimicrobial effector catalogs in three phylogenetically distant fungi with distinct lifestyles, revealing relatively large catalogs of candidate antimicrobials for each of the three fungi, and suggesting a broad occurrence of such proteins throughout the fungal kingdom. Thus, AMAPEC is a unique method to uncover antimicrobials in fungal secretomes that are often sparsely functionally annotated, and may assist biological interpretations during omic analyses. It is freely available athttps://github.com/fantin-mesny/amapec.
Single-cell RNA sequencing of peripheral blood mononuclear cells reveals complex cellular signalling signatures of metformin treatment type 2 diabetes mellitus
Authors: Zhao Jin-Dong , Fang Zhao-Hui 
Published: January 2024

ABSTRACTObjectiveType 2 diabetes mellitus (T2DM) is a complex polygenic disease. The onset of the disease is related to autoimmunity. However, how immune cells function in the peripheral blood remains to be elucidated. Metformin is the first-line treatment. Exploring biomarkers of T2DM based on single-cell sequencing technology can provide new insights for the discovery of metformin treatment T2DM in molecular mechanisms.MethodsWe profiled 43,971 cells and 20,228 genes from peripheral blood mononuclear cells (PBMCs) of T2DM patients and healthy controls by single-nucleotide RNA sequencing.ResultsB cells, T cells, monocytes/macrophages, platelets, neutrophils, NK cells and cDC2s were grouped into 7 subclusters. Furthermore, T cells and monocytes/macrophages might be significantly correlated with the clinical characteristics of T2DM patients. RPL27 and AC018755.4 expression were strongly negative correlated with HbA1c. CD4+ T cells are mainly in the memory activation stage, and CD8+ T cells are effectors. The 50 genes whose expression varied with developmental time were associated with cytoplasmic translation, cell‒cell adhesion mediated by integrin, and the regulation of the inflammatory response. Monocytes/macrophages include classic monocytes and nonclassical monocytes. The GSEA results showed that the marker genes were enriched in the HALLMARK_INTERFERON_GAMMA_RESPONSE and HALLMARK_TNFA_SIGNALING_VIA_NFKB. The WGCNA results showed 14 modules. Meanwhile, TNFRSF1A is the most core genes in network interaction. Further analysis revealed ligand‒receptor pairs, including MIF-(CD74 + CD44), MIF-(CD74 + CXCR4), ANXA1-FPR1 and LGALS9-CD45.ConclusionsOur study revealed that the transcriptional map of immune cells from PBMCs provided a framework for understanding the immune status of T2DM patients with metformin treatment via scRNA-seq analysis.
The Interpretable Multimodal Machine Learning (IMML) framework reveals pathological signatures of distal sensorimotor polyneuropathy
Authors: Nguyen Phong BH , Garger Daniel , Maalmi Haifa , Prokisch Holger , Thorand Barbara , Adamski Jerzy , Kastenmüller Gabi , Waldenberger Melanie , Gieger Christian , Peters Annette , Suhre Karsten , Bönhof Gidon J , Rathmann Wolfgang , Roden Michael , Grallert Harald , Ziegler Dan , Herder Christian , Menden Michael P 
Published: January 2024

AbstractDistal sensorimotor polyneuropathy (DSPN) is a common neurological disorder in elderly adults and people with obesity, prediabetes and diabetes and is associated with high morbidity and premature mortality. DSPN is a multifactorial disease and not fully understood yet. Here, we developed the Interpretable Multimodal Machine Learning (IMML) framework for predicting DSPN prevalence and incidence based on sparse multimodal data. Exploiting IMMLs interpretability further empowered biomarker identification. We leveraged the population-based KORA F4/FF4 cohort including 1,091 participants and their deep multimodal characterisation, i.e. clinical data, genomics, methylomics, transcriptomics, proteomics, inflammatory proteins and metabolomics. Clinical data alone is sufficient to stratify individuals with and without DSPN (AUROC = 0.752), whilst predicting DSPN incidence 6.5±0.2 years later strongly benefits from clinical data complemented with two or more molecular modalities (improved ΔAUROC >0.1, achieved AUROC of 0.714). Important and interpretable features of incident DSPN prediction include up-regulation of proinflammatory cytokines, down-regulation of SUMOylation pathway and essential fatty acids, thus yielding novel insights in the disease pathophysiology. These may become biomarkers for incident DSPN, guide prevention strategies and serve as proof of concept for the utility of IMML in studying complex diseases.
A split crRNA with CRISPR-Cas12a enables highly sensitive, selective, and multiplexed detection of RNA and DNA
Authors: Qiao Jie , Chen Yichuan , Wang Xinping , He Baoxia , Yin Wenhao , Liu Yi 
Published: January 2024

AbstractThe complete 40-nt CRISPR RNA (crRNA) of Cas12a can be artificially divided into two parts, including the 20-nt scaffold RNA with fixed sequences and the 20-nt spacer RNA with variable sequences, respectively. Herein, we found that Cas12a protein, scaffold RNA, and spacer RNA can be reassembled into an active ribonucleoprotein (RNP) which has atrans-cleavage activity comparable to that of wild-type Cas12a RNP. By leveraging such split CRISPR-Cas12a system (SCas12a), we devised fast fluorescence and lateral flow assays for highly sensitive, selective, and multiplexed detection of miRNAs without the need for reverse transcription and pre-amplification, achieving a limit of detection (LoD) of 10 fM. Additionally, our SCas12a assay enables detecting long-stranded RNA without secondary structure, as well as distinguishing mature miRNA from its precursor (pre-miRNA) that comprises the same sequence of miRNA. Beyond RNA detection, SCas12a outperforms wild-type Cas12a in specificity towards DNA point mutations. In combination with recombinase polymerase amplification (RPA), we set up a one-pot assay to detect attomolar concentrations of human papillomavirus (HPV) in patient samples. In conclusion, this work provides a simple, cost-effective, yet powerful SCas12a-based rapid nucleic acid detection platform in various diagnostic settings.Significance StatementConventional Cas12a-based diagnostic methods cannot directly detect RNA targets. Here, we develop rapid fluorescence and lateral flow assays based on a split Cas12a system (called SCas12a), achieving amplification-free detection of RNA with high sensitivity and specificity. By supplying pooled activators, our method enables multiplexed detection of miRNA and DNA targets. In addition, SCas12a can discriminate mature miRNA from its pre-miRNA, which was achieved for the first time with CRISPR detection technology. Moreover, SCas12a outperforms wild-type Cas12a in specificity towards point mutation and can be combined with RPA to detect attomolar concentration of HPV in patient samples. Overall, this work offers a generic “split crRNA-activator” strategy for developing new CRISPR diagnostic tools.
Plural molecular and cellular mechanisms of pore domainKCNQ2encephalopathy
Authors: Abreo Timothy J. , Thompson Emma C. , Madabushi Anuraag , Soh Heun , Varghese Nissi , Vanoye Carlos G. , Springer Kristen , Park Kristen L. , Johnson Jim , Sims Scotty , Ji Zhigang , Chavez Ana G. , Jankovic Miranda J. , Habte Bereket , Zuberi Aamir R. , Lutz Cathleen , Wang Zhao , Krishnan Vaishnav , Dudler Lisa , Einsele-Scholz Stephanie , Noebels Jeffrey L. , George Alfred L. , Maheshwari Atul , Tzingounis Anastasios V. , Cooper Edward C. 
Published: January 2024

AbstractKCNQ2variants in children with neurodevelopmental impairment are difficult to assess due to their heterogeneity and unclear pathogenic mechanisms. We describe a child with neonatal-onset epilepsy, developmental impairment of intermediate severity, andKCNQ2G256W heterozygosity. Analyzing prior KCNQ2 channel cryoelectron microscopy models revealed G256 as a node of an arch-shaped non-covalent bond network linking S5, the pore turret, and the ion path. Co-expression with G256W dominantly suppressed conduction by wild-type subunits in heterologous cells. Ezogabine partly reversed this suppression. G256W/+ mice have epilepsy leading to premature deaths. Hippocampal CA1 pyramidal cells from G256W/+ brain slices showed hyperexcitability. G256W/+ pyramidal cell KCNQ2 and KCNQ3 immunolabeling was significantly shifted from axon initial segments to neuronal somata. Despite normal mRNA levels, G256W/+ mouse KCNQ2 protein levels were reduced by about 50%. Our findings indicate that G256W pathogenicity results from multiplicative effects, including reductions in intrinsic conduction, subcellular targeting, and protein stability. These studies provide evidence for an unexpected and novel role for the KCNQ2 pore turret and introduce a valid animal model ofKCNQ2encephalopathy. Our results, spanning structure to behavior, may be broadly applicable because the majority ofKCNQ2encephalopathy patients share variants near the selectivity filter.
Understanding the Energy Landscape of Intrinsically Disordered Protein Ensembles
Authors: Viegas Rafael G. , Martins Ingrid B. S. , Leite Vitor B.P. 
Published: January 2024

AbstractA substantial portion of various organisms’ proteomes comprises intrinsically dis-ordered proteins (IDPs) that lack a defined three-dimensional structure. These IDPs exhibit a diverse array of conformations, displaying remarkable spatio-temporal het-erogeneity and exceptional conformational flexibility. Characterizing the structure or structural ensemble of IDPs presents significant conceptual and methodological challenges owing to the absence of a well-defined native structure. While databases such as the Protein Ensemble Database (PED) provide IDP ensembles obtained through a combination of experimental data and molecular modeling, the absence of reaction coordinates poses challenges in comprehensively understanding pertinent aspects of the system. In this study, we leverage the Energy Landscape Visualization Method (JCTC, 6482, 2019) to scrutinize four IDP ensembles sourced from PED. ELViM, a methodology that circumvents the need fora priorireaction coordinates, aids in analyzing the ensembles. The specific IDP ensembles investigated are as follows: two fragments of Nucleoporin (NUL: 884-993 and NUS: 1313-1390), Yeast Sic 1 N-terminal (1-90), and the N-terminal SH3 domain of Drk (1-59). Utilizing ELViM enables comprehensive validation of ensembles, facilitating the detection of potential inconsistencies in the sampling process. Additionally, it allows for identifying and characterizing the most prevalent conformations within an ensemble. Moreover, ELViM facilitates the comparative analysis of ensembles obtained under diverse conditions, thereby providing a powerful tool for investigating the functional mechanisms of IDPs.
Unveiling the Impact of Vernalization on Seed Oil Content and Fatty Acid Composition in Rapeseed Through Simulated Shorter Winters
Authors: Çağlı İrem , Kıvrak Büşra Elif , Altunbaş Osman , Sönmez Çağla 
Published: January 2024

AbstractClimate change is leading to warmer winters world-wide with an increasing number of extreme events every year. Plants are majorly impacted by the escalating effects of global warming. In this study, we set up an experimental model to simulate warmer and shorter winters under laboratory conditions. Winter and spring varieties of rapeseed (Brassica napusL.) were subjected to diverse vernalization scenarios including three and four weeks-long vernalization as well as vernalization interruptions by one week-long devernalization at warm temperatures. The aim of the study was to assess the effects of the ‘vernalization models’ onBnaFLC(BnaFLCA02,BnaFLCA10andBnaFLCC02) expression, some yield related traits, a set of genes involved in fatty acid synthesis and seed oil content and fatty acid composition. A notable difference in vernalization responsiveness was observed inBnaFLCA02,BnaFLCA10, andBnaFLCC02between the late-flowering winter variety, Darmor, the early-flowering winter variety Bristol and the spring variety, Helios, after a three-week vernalization period. Our findings unveil a robust correlation between vernalization and seed oil content, as well as fatty acid composition in rapeseed. While the expression levels of fatty acid synthesis-related genes, includingBnaFAD2,BnaFAD5,BnaFATB,BnaMCOA(AAE13), andBnaWD40, exhibited significant changes under cold conditions in leaves, the expression levels of the same genes in developing seeds did not exhibit a strong correlation with vernalization, flowering time, or oil and fatty acid contents in seeds. Our results suggest that vernalization plays a role in seed oil biosynthesis beyond its impact on flowering time.
Genomic and transcriptomic characteristics of type VI secretion system inKlebsiella pneumoniae
Authors: Li Wanzhen , Huang Xiaolan , Li Dan , Liu Xiaofen , Jiang Xiaoying , Bian Xingchen , Li Xin , Zhang Jing 
Published: January 2024

AbstractThe Type VI secretion system (T6SS) serves as a crucial molecular weapon in interbacterial competition and significantly influences cell-cell interactions. Various bacterial species utilize their T6SSs to execute a multitude of functions, dictated by their ecological niche. However, the characteristics of T6SS in clinicalKlebsiella pneumoniae, a common opportunistic nosocomial pathogen, have not been fully elucidated. Here, we conducted a genomic analysis of 65 clinicalK. pneumoniaeisolates obtained from patients with varying infections. Genes encoding a T6SS cluster were present in all analyzed strains ofK. pneumoniae. Strains of identical sequence type (ST) carried structurally and numerically identical T6SS. Our study also highlights the importance of selecting conserved regions in key T6SS genes for effective primer design in PCR identification. We then utilized the predominant ST11K. pneumoniaeHS11286 to investigate the effect of knocking out T6SS marker geneshcporvgrG. Transcriptome analysis identified a total of 1,298 co-upregulated and 1,752 co-downregulated differentially expressed genes. Additionally, the absence ofhcporvgrGgene suppressed the expression of other T6SS-related genes within the locus I cluster. Pathway analysis showed that the Δhcpmutant exhibited alterations in transport, establishment of localization, localization and cell processes. Furthermore, interbacterial competition experiments showed thathcpandvgrGare essential for competitive ability of ST11K. pneumoniaeHS11286. This study furthers our understanding of the genomic characteristics of T6SS inK. pneumoniaeand suggested that the involvement of multiple genes in T6SS of strain HS11286.ImportanceGram-negative bacteria use T6SS to deliver effectors that interact with neighboring cells for niche advantage.K. pneumoniaeis an opportunistic nosocomial pathogen that often carriers multiple T6SS loci, the function of which has not yet been elucidated. We performed a genomic analysis of 65 clinicalK. pneumoniaestrains isolated from various sources, confirming that all strains contained T6SS. We then used transcriptomics to further study changes in gene expression and effect upon interbacterial competition following knockout of key T6SS genes in ST11K. pneumoniaeHS11286. Our findings revealed the distribution and genomic characteristics of T6SS in clinicalK. pneumoniae. This study also described the overall transcriptional changes in the predominant Chinese ST11 strain HS11286 upon deletion of crucial T6SS genes. Additionally, this work provides a reference for future research on the identification of T6SS in bacteria.