bluuebunny/crossref_metadata_2025_split huggingface dataset:
How to measure bacterial genome plasticity? A novel time-integrated index helps gather insights on pathogens
Authors: Bellinzona Greta , Batisti Biffignandi Gherard , Baldanti Fausto , Brilli Matteo , Sassera Davide , Gaiarsa Stefano 
Published: January 2024

AbstractGenome plasticity can be defined as the capacity of a bacterial population to swiftly gain or lose genes. The time factor plays a fundamental role for the evolutionary success of microbes, particularly when considering pathogens and their tendency to gain antimicrobial resistance factors under the pressure of the extensive use of antibiotics. Multiple metrics have been proposed to provide insights into the gene content repertoire, yet they overlook the temporal component, which has a critical role in determining the adaptation and survival of a bacterial strain. In this study, we introduce a novel index that incorporates the time dimension to assess the rate at which bacteria exchange genes, thus fitting the definition of plasticity. Opposite to available indexes, our method also takes into account the possibility of contiguous genes being transferred together in one single event. We applied our novel index to measure plasticity in three widely studied bacterial species:Klebsiella pneumoniae,Staphylococcus aureus, andEscherichia coli. Our results highlight distinctive plasticity patterns in specific sequence types and clusters, suggesting a possible correlation between heightened genome plasticity and globally recognized high-risk clones. Our approach holds promise as an index for predicting the emergence of strains of potential clinical concern, possibly allowing for timely and more effective interventions.Impact statementHow quickly bacterial populations can acquire new functions is the key to their evolutionary success. This speed, called genome plasticity, is particularly relevant for human pathogens, especially when considering the acquisition of antimicrobial resistance. Today, the availability of large numbers of genomes from public databases makes it possible to develop a way to measure plasticity. However, none is currently available, besides indexes of gene content variability, which do not take into account the rate at which such gene content changes. In this work, we developed a plasticity index, called Flux Of Gene Segments (FOGS), and we tested it on large datasets of bacterial pathogen genomes. Interestingly, the subpopulations of the selected species that showed higher FOGS correspond to globally emerging high-risk clones. Therefore, we suggest that our index might be used not only to detect but also to predict emerging strains of human health concern.Data summaryThe authors confirm that all supporting data, code and protocols have been provided within the article or through supplementary data files.
Viral load dynamics in asymptomatic and symptomatic patients during Omicron BA.2 outbreak in Shanghai, China, 2022: a longitudinal cohort study
Authors: Ai Jingwen , Zhou Jiaxin , Li Yang , Sun Feng , Ge Shijia , Zhang Haocheng , Wu Yanpeng , Wang Yan , Zhang Yilin , Wang Hongyu , Cai Jianpeng , Zhou Xian , Wang Sen , Li Rong , Feng Zhen , Xu Xiangyanyu , Yan Xuemei , Zhao Yuchen , Zhang Juanjuan , Yu Hongjie , Zhang Wenhong 
Published: January 2024

AbstractBackgroundsThe SARS-CoV-2 virus has caused global outbreaks, including the recent Omicron BA.2 wave in Shanghai in spring 2022. While, the viral load dynamic of Omicron infections with different clinical severity was still unclear.MethodsA prospective cohort was conducted on 48,830 hospitalized COVID-19 patients in three hospitals in Shanghai, China, from 23 March and 15 May 2022. Regular nucleic acid testing was performed and the Cycle threshold (Ct) value tested by RT-PCR was used as a proxy of viral load. The viral load dynamic by different clinical severity since initial detection and the risk factors were analyzed.ResultsThe study included 31% asymptomatic cases, 68% mild-moderate cases, 1% severe cases, 1.29% critical and fatal cases. 57% of patients tested positive upon admission, average Ct value remained stable with peak viral concentrations occurring at 4 days (median Ct value of 27.5), followed by a decrease with a viral shedding time (VST) of 6.1 days (IQR, 4.0-8.8 days). Omicron viral load varied by age and clinical severity, but peak Ct values occurred at similar times. Unvaccinated status, age over 60, and comorbidities were associated with higher peak viral concentrations and longer shedding durations. Asymptomatic cases had a 40% contagious probability within 6 days of detection. Mild-moderate cases and severe cases had a 27%, >50% probability of infectiousness post-symptom resolution, respectively.ConclusionThe initial Ct value could forecast severe consequences. Unvaccinated older people with specific comorbidities are the high-risk groups associated with high viral load and long shedding duration.
Network Proteomics of the Lewy Body Dementia Brain Reveals Presynaptic Signatures Distinct from Alzheimer’s Disease
Authors: Shantaraman Anantharaman , Dammer Eric B. , Ugochukwu Obiadada , Duong Duc M. , Yin Luming , Carter E. Kathleen , Gearing Marla , Chen-Plotkin Alice , Lee Edward B. , Trojanowski John Q. , Bennett David A. , Lah James J. , Levey Allan I. , Seyfried Nicholas T. , Higginbotham Lenora 
Published: January 2024

AbstractLewy body dementia (LBD), a class of disorders comprising Parkinson’s disease dementia (PDD) and dementia with Lewy bodies (DLB), features substantial clinical and pathological overlap with Alzheimer’s disease (AD). The identification of biomarkers unique to LBD pathophysiology could meaningfully advance its diagnosis, monitoring, and treatment. Using quantitative mass spectrometry (MS), we measured over 9,000 proteins across 138 dorsolateral prefrontal cortex (DLPFC) tissues from a University of Pennsylvania autopsy collection comprising control, Parkinson’s disease (PD), PDD, and DLB diagnoses. We then analyzed co-expression network protein alterations in those with LBD, validated these disease signatures in two independent LBD datasets, and compared these findings to those observed in network analyses of AD cases. The LBD network revealed numerous groups or “modules” of co-expressed proteins significantly altered in PDD and DLB, representing synaptic, metabolic, and inflammatory pathophysiology. A comparison of validated LBD signatures to those of AD identified distinct differences between the two diseases. Notably, synuclein-associated presynaptic modules were elevated in LBD but decreased in AD relative to controls. We also found that glial-associated matrisome signatures consistently elevated in AD were more variably altered in LBD, ultimately stratifying those LBD cases with low versus high burdens of concurrent beta-amyloid deposition. In conclusion, unbiased network proteomic analysis revealed diverse pathophysiological changes in the LBD frontal cortex distinct from alterations in AD. These results highlight the LBD brain network proteome as a promising source of biomarkers that could enhance clinical recognition and management.
ZNF827pleiotropic cardiovascular risk locus involves regulation by Nuclear factor-1
Authors: Liu Yingwei , Liu Lu , Esmael Asraa , Fustier Margaux-Alison , Georges Adrien , Bouatia-Naji Nabila 
Published: January 2024

AbstractIntroductionSCAD (spontaneous coronary artery dissection) is a form of myocardial infarction that disproportionately affects young women. SCAD is caused by the formation of a hematoma within coronary artery wall, resulting in its blockage. Sixteen SCAD susceptibility loci are currently known, includingZNF827gene locus on chromosome 4. Several common genetic variations withinZNF827are also linked to coronary artery disease (CAD), systolic blood pressure (SBP), and ascending aortic diameter. The molecular processes driving these genetic connections, however, are unknown.MethodsWe performed fine-mapping and genetic colocalization analysis atZNF827locus on multiple GWAS signals and quantitative expression traits. We explored the regulatory function of sequences of interest using a luciferase reporter system in rat smooth muscle cells. We used siRNA to knockdown the expression of gene and assessed transcriptomic changes through bulk RNA-Seq.ResultsThe genetic association signals for SCAD, CAD, blood pressure, and aorta dimensions could all be explained by a single causal variant. We identified rs13128814 as the most likely causative variant. This variant overlaps epigenetic regulatory markers specifically active in vascular SMCs and fibroblasts. A 1kb region containing the SCAD-risk allele (A) of rs13128814 variant had a transcriptional activation impact, while the protective allele (G) had no effect.In silicopredictions found nuclear factor 1 (NF1) transcription factors preferentially bind to the A allele of rs13128814. We found that overexpressing NFIA (Nuclear Factor 1 A-Type) activated transcription in this area. SCAD association andZNF827eQTL colocalization in various vascular tissues suggested the latter as a plausible target gene in this locus. Knockdown of ZNF827 in iPSC-derived SMCs and fibroblasts, followed by RNA-seq, identified a large number of dysregulated genes, including multiple genes involved in cardiovascular disease.ConclusionOur findings inZNF827locus support the hypothesis that the rs13128814 variant, which may affect the binding of NF1 family transcription factors and causeZNF827expression to be deregulated, is the molecular mechanism underpinning the relationship of theZNF827locus with numerous cardiovascular disorders.ZNF827acts as a regulator of gene expression in vascular SMCs and fibroblasts. Further investigation ofZNF827function in vascular tissue will be required to understand the implications of its dysregulation on cardiovascular physiopathology.
A high coverage Mesolithic aurochs genome and effective leveraging of ancient cattle genomes using whole genome imputation
Authors: Erven Jolijn A.M , Scheu Amelie , Verdugo Marta Pereira , Cassidy Lara , Chen Ningbo , Gehlen Birgit , Street Martin , Madsen Ole , Mullin Victoria E 
Published: January 2024

AbstractAncient genomic analyses are often restricted to utilising pseudo-haploid data due to low genome coverage. Leveraging low coverage data by imputation to calculate phased diploid genotypes that enable haplotype-based interrogation and SNP calling at unsequenced positions is highly desirable. This has not been investigated for ancient cattle genomes despite these being compelling subjects for archaeological, evolutionary and economic reasons. Here we test this approach by sequencing a Mesolithic European aurochs (18.49x; 9852-9376 calBC), an Early Medieval European cow (18.69x; 427-580 calAD), and combine these with published individuals; two ancient and three modern. We downsample these genomes (0.25x, 0.5x, 1.0x, 2.0x) and impute diploid genotypes, utilising a reference panel of 171 published modern cattle genomes that we curated for 21.7 million (Mn) phased single-nucleotide polymorphisms (SNPs). We recover high densities of correct calls with an accuracy of >99.1% at variant sites for the lowest downsample depth of 0.25x, increasing to >99.5% for 2.0x (transversions only, minor allele frequency (MAF) ≥2.5%). The recovery of SNPs correlates with coverage, on average 58% of sites are recovered for 0.25x increasing to 87% for 2.0x, utilising an average of 3.5 million (Mn) transversions (MAF ≥2.5%), even in the aurochs which is temporally and morphologically distinct from the reference panel. Our imputed genomes behave similarly to directly called data in allele-frequency-based analyses; for example consistently identifying runs of homozygosity >2mb, including a long homozygous region in the Mesolithic European aurochs.
Wnt/β-catenin signaling improves oxidative metabolism in skeletal muscle of obese ob/ob mice
Authors: Christodoulou-Vafeiadou Eleni , Lepeigneux Céline , Naviere Aurore , Pujol Julien , Benhamed Fadila , Maire Pascal , Guillet-Deniau Isabelle 
Published: January 2024

ABSTRACTBackgroundCanonical Wnt signaling is involved in many physiological and pathological states. As it regulates lipid metabolism and glucose homeostasis, its misregulation may lead to the development of diabetes and obesity. We have already reported that activation of the Wnt/β-catenin canonical signaling pathway increased insulin sensitivity and prevented lipid deposits in rat skeletal muscle through a reciprocal regulation of Wnt10b and the lipogenic factor SREBP-1c.ResultsHere we have studied the role of Wnt/β-catenin canonical signaling in skeletal muscle of genetically obese and diabetic (ob/ob)mice and their control ob/+ mice. We showed thatWnt10bandSREBP-1cexpressions were conversely regulated in cultured mouse myoblasts isolated from lean ob/+ or obese ob/ob mice. Activation of the Wnt/β-catenin pathway using Wnt10b overexpression or the selective GSK3 inhibitor 6-Bromo-indirubin-3’oxime (BIO) was sufficient to decrease lipogenic genes expression in cultured myoblasts isolated from control and obese mice. In vivo, we performed direct electrotransfection of Wnt10b cDNA or BIO injections inTibialis Anterior(TA) muscles of ob/ob and ob/+ mice. Both up-regulatedWnt10bgene expression and down-regulatedSREBP-1cexpression. Canonical Wnt signaling increased slow Myosin Heavy Chain-I (MHC-I) oxidative fiber number as well as fast Myosin Heavy Chain-IIA (MHC-IIA) oxidative fiber number, while decreasing fast glycolytic fiber number in TA muscle. In addition, Wnt signaling increased mitochondrial oxidative metabolism and respiratory reserve capacity by 2- and 3-fold in myotubes cultured from ob/ob and ob/+ mice muscles respectively. Surprisingly, the activation of the Wnt pathway was sufficient to reduce hyperglycemia by 30% within 3 weeks in ob/ob mice.ConclusionsOur results show that activation of Wnt/β-catenin signaling in skeletal muscle induced a shift towards a more oxidative metabolism in myofibers, thus mimicking the effects of exercise training. Wnt10b could be a valuable candidate to develop therapeutic drugs for the treatment of obesity and/or type 2 diabetes.
Two paralogous PHD finger proteins participate inParamecium tetraurelia’s natural genome editing
Authors: Häußermann Lilia , Singh Aditi , Swart Estienne C. 
Published: January 2024

AbstractThe unicellular eukaryoteParamecium tetraureliacontains functionally distinct nuclei: germline micronuclei (MICs) and a somatic macronucleus (MAC). During sexual reproduction, the MIC genome is reorganized into a new MAC genome and the old MAC is lost. Almost 45,000 unique Internal Eliminated Sequences (IESs) distributed throughout the genome require precise excision to guarantee a functional new MAC genome. Here, we characterize a pair of paralogous PHD finger proteins involved in DNA elimination. DevPF1, the early-expressed paralog, is present in only some of the gametic and post-zygotic nuclei during meiosis. Both DevPF1 and DevPF2 localize in the new developing MACs, where IESs excision occurs. InDevPF2knockdown (KD) long IESs are preferentially retained and late-expressed small RNAs decrease; no length preference for retained IESs was observed inDevPF1-KD and development-specific small RNAs were abolished. The expression of at least two genes from the new MAC with roles in genome reorganization seems to be influenced byDevPF1-andDevPF2-KD. Thus, both PHD fingers are crucial for new MAC genome development, with distinct functions, potentially via regulation of non-coding and coding transcription in the MICs and new MACs.
F420reduction as a cellular driver for anaerobic ethanotrophy
Authors: Lemaire Olivier N , Wegener Gunter , Wagner Tristan 
Published: January 2024

AbstractThe anaerobic ethane oxidation performed by seafloor archaea and sulfate-reducing partner bacteria involves largely uncharted biochemistry. This study deciphers the molecular basis of the CO2-generating steps by characterizing the native archaeal enzymes isolated from a thermophilic enrichment culture. While other microorganisms couple these steps to ferredoxin reduction, we found that the CO-dehydrogenase and the formylmethanofuran-dehydrogenase are bound to an F420-reductase module. The crystal structures of these multi-metalloenzyme complexes revealed a [4Fe-4S]-cluster networks electronic bridges coupling C1-oxidation to F420-reduction. Accordingly, both systems exhibit robust F420-reductase activities, which are not detected in methanogenic or methanotrophic relative organisms. We speculate that the whole catabolism of these archaea is reoriented towards F420-reduction, which facilitates the electron transfer to the sulfate-reducing partner, therefore representing the driving force of ethanotrophy.
FLUAV RAM-IGIP: A modified live influenza virus vaccine that enhances humoral and mucosal responses against influenza
Authors: Joaquín Cáceres C. , Claire Gay L. , Jain Aarti , Mejías Teresa D. , Cardenas Matias , Seibert Brittany , Faccin Flavio Cargnin , Cowan Brianna , Geiger Ginger , Baker Amy Vincent , Carnaccini Silvia , Huw Davies D. , Rajao Daniela S. , Perez Daniel R. 
Published: January 2024

ABSTRACTCurrent influenza A vaccines fall short, leaving both humans and animals vulnerable. To address this issue, we have developed attenuated modified live virus (MLV) vaccines against influenza using genome rearrangement techniques targeting the internal gene segments of FLUAV. The rearranged M2 (RAM) strategy involves cloning the M2 ORF downstream of the PB1 ORF in segment 2 and incorporating multiple early stop codons within the M2 ORF in segment 7. Additionally, the IgA-inducing protein (IGIP) coding region was inserted into the HA segment to further attenuate the virus and enhance protective mucosal responses. RAM-IGIP viruses exhibit similar growth rates to wild type (WT) viruses in vitro and remain stable during multiple passages in cells and embryonated eggs. The safety, immunogenicity, and protective efficacy of the RAM-IGIP MLV vaccine against the prototypical 2009 pandemic H1N1 strain A/California/04/2009 (H1N1) (Ca/04) were evaluated in Balb/c mice and compared to a prototypic cold-adapted live attenuated virus vaccine. The results demonstrate that the RAM-IGIP virus exhibits attenuated virulence in vivo. Mice vaccinated with RAM-IGIP and subsequently challenged with an aggressive lethal dose of the Ca/04 strain exhibited complete protection. Analysis of the humoral immune response revealed that the inclusion of IGIP enhanced the production of neutralizing antibodies and augmented the antibody-dependent cellular cytotoxicity response. Similarly, the RAM-IGIP potentiated the mucosal immune response against various FLUAV subtypes. Moreover, increased antibodies against NP and NA responses were observed. These findings support the development of MLVs utilizing genome rearrangement strategies in conjunction with the incorporation of immunomodulators.IMPORTANCECurrent influenza vaccines offer suboptimal protection, leaving both humans and animals vulnerable. Our novel attenuated MLV vaccine, built by rearranging FLUAV genome segments and incorporating the IgA-inducing protein, shows promising results. This RAM-IGIP vaccine exhibits safe attenuation, robust immune responses, and complete protection against lethal viral challenge in mice. Its ability to stimulate broad-spectrum humoral and mucosal immunity against diverse FLUAV subtypes makes it a highly promising candidate for improved influenza vaccines.
Overloading And unpacKing (OAK) - droplet-based combinatorial indexing for ultra-high throughput single-cell multiomic profiling
Authors: Wu Bing , Bennett Hayley M. , Ye Xin , Sridhar Akshayalakshmi , Eidenschenk Celine , Everett Christine , Nazarova Evgeniya V. , Chen Hsu-Hsin , Kim Ivana K. , Deangelis Margaret , Owen Leah A. , Chen Cynthia , Lau Julia , Shi Minyi , Lund Jessica M. , Xavier-Magalhaes Ana , Patel Neha , Liang Yuxin , Modrusan Zora , Darmanis Spyros 
Published: January 2024

AbstractMultiomic profiling of single cells by sequencing is a powerful technique for investigating cellular diversity in complex biological systems. Although the existing droplet-based microfluidic methods have advanced single-cell sequencing, they produce a plethora of cell-free droplets and underutilize barcoding capacities due to their low cell concentration prerequisites. Meanwhile, combinatorial indexing on microplates can index cells in a more effective way; however, it requires time-consuming and laborious protocols involving multiple splitting and pooling steps. Addressing these constraints, we have developed “Overloading And unpacKing” (OAK). With reduced labor intensity, OAK can provide cost-effective multiomic profiling for hundreds of thousands of cells, offering detection sensitivity on par with commercial droplet-based methods. To demonstrate OAK’s versatility, we conducted single-cell RNA sequencing (scRNA-Seq) as well as joint single-nucleus RNA sequencing (snRNA-Seq) and single-nucleus Assay for Transposase Accessible Chromatin with sequencing (snATAC-Seq) using cell lines. We further showcased OAK’s performance on more complex samples, includingin vitrodifferentiated bronchial epithelial cells and primary retinal tissues. Finally, we examined transcriptomic responses of 408,000 melanoma cells across around 1,000 starting lineages over a 90-day treatment with a RAF inhibitor, belvarafenib. We discovered a rare cell population (0.12%) that underwent a sequence of transcriptomic changes, resulting in belvarafenib resistance. Ultra-high throughput, broad compatibility with diverse molecular modalities, high detection sensitivity, and simplified experimental procedures distinguish OAK from previous methods, and render OAK a powerful tool for large-scale analysis of molecular signatures, even for rare cells.
MSK1 absence hinders BDNF-dependent striatal neurodevelopment and leads to schizophrenia symptoms
Authors: Varela-Andrés Natalia , Cebrián-León Alejandro , Hernández-del Caño Carlos , Fernández del Campo Inés S. , García-Losada Sandra , Martín-Ávila Noelia , Arévalo Juan Carlos , Merchán Miguel A. , Sánchez-Martín Manuel , Deogracias Rubén 
Published: January 2024

AbstractBrain-derived neurotrophic factor (BDNF) plays a critical role in postnatal development by modulating the architecture of specific neuronal populations and brain areas. However, the precise molecular program controlling this differential responsiveness to BDNF is still unclear. In the present study, we describe that this program is governed by the restricted expression of the mitogen- and stress-activated protein kinase-1 (MSK1) in GABAergic neurons. Also, we show that whileMsk1expression declines in cortical interneurons along early postnatal development, its expression in striatal neurons increases until adulthood. Utilizing a novel MSK1 loss-of-function mouse model, we reveal its essential role in postnatal growth of the striatum, as it interacts with and modulates the BDNF-dependent phosphorylation of the methyl-CpG binding protein-2 (MeCP2). Furthermore, these mutant mice exhibit an altered transcription pattern of genes involved in the control of the dopamine and GABAergic signalling pathways. Consequently, MSK1 knockout mice behaviour is markedly altered, showing social dysfunction, altered anxiety- and depressive-like responses unequally manifested in males and females. These results elucidate how disruptions in the BDNF/MSK1 pathway impact GABAergic neurite outgrowth and contribute to behaviours reminiscent of schizophrenia in humans.