bluuebunny/crossref_metadata_2025_split huggingface dataset:
Metabolic and age-associated epigenetic barriers during direct reprogramming of mouse fibroblasts into induced cardiomyocytes
Authors: Santos Francisco , Correia Magda , Dias Rafaela , Bola Bárbara , Noberini Roberta , Ferreira Rita S. , Domingues Pedro , Teixeira José , Bonaldi Tiziana , Oliveira Paulo J. , Bär Christian , Bernardes de Jesus Bruno , Nóbrega-Pereira Sandrina 
Published: March 2024

ABSTRACTHeart disease is the leading cause of mortality in developed countries novel regenerative procedures are warranted for improving patients well fare. Direct cardiac conversion (DCC) can create induced cardiomyocytes (iCMs) and besides holding great promise, lacks clinical effectiveness for cardiac regeneration as metabolic and age-associated barriers remains elusive. Here, we identify by histone post-translational analysis that DCC triggers major age-dependent alterations in the epigenetic landscape. Metabolomics revealed decrease abundance of anabolic metabolites related to TCA cycle and glutaminolysis and profound mitochondrial network remodeling, with increased elongation and interconnectivity and reliance in mitochondrial respiration in iCMs.Importantly, adult-derived iCMs present increase accumulation of oxidative stress in the mitochondria and pharmacological activation of mitophagy increase DCC of adult fibroblastsin vitro. Metabolic modulationin vitroand dietary manipulationsin vivoimproves DCC efficiency and are accompanied by significant alterations in the histone acetylation and methylation landscape and mitochondria homeostasis. Our study provides evidence that metaboloepigenetics as a direct role in cell fate transitions driving direct cardiac conversion into iCMs, highlighting the potential use of metabolic modulation in increasing cardiac regenerative strategies.
Architecture and flexibility of native kinetochores revealed by structural studies utilizing a thermophilic yeast
Authors: Barrero Daniel J. , Wijeratne Sithara S. , Zhao Xiaowei , Cunningham Grace F. , Yan Rui , Nelson Christian R. , Arimura Yasuhiro , Funabiki Hironori , Asbury Charles L. , Yu Zhiheng , Subramanian Radhika , Biggins Sue 
Published: March 2024

AbstractEukaryotic chromosome segregation requires kinetochores, multi-megadalton protein machines that assemble on the centromeres of chromosomes and mediate attachments to dynamic spindle microtubules. Kinetochores are built from numerous complexes, and understanding how they are arranged is key to understanding how kinetochores perform their multiple functions. However, an integrated understanding of kinetochore architecture has not yet been established. To address this, we purified functional, native kinetochores fromKluyveromyces marxianusand examined them by electron microscopy, cryo-electron tomography and atomic force microscopy. The kinetochores are extremely large, flexible assemblies that exhibit features consistent with prior models. We assigned kinetochore polarity by visualizing their interactions with microtubules and locating the microtubule binder Ndc80c. This work shows that isolated kinetochores are more dynamic and complex than what might be anticipated based on the known structures of recombinant subassemblies, and provides the foundation to study the global architecture and functions of kinetochores at a structural level.
Analysis of protein levels and solubility in distinct brain regions reveals several elements of the protein homeostasis network that are impacted by aging
Authors: Molzahn Cristen , Kuechler Erich , Nierves Lorenz , Cole Gary , Wang Jing , Cashman Neil , Karsan Aly , Lange Philipp F. , Gsponer Jörg , Mayor Thibault 
Published: March 2024

AbstractThe onset of protein conformation diseases is inextricably linked to aging. During aging, cellular protein quality control declines which results in diminished protein homeostasis (proteostasis). In model organisms, such asC. elegansand killifish, proteostatic decline with age has been linked to the onset of aggregation of proteins in wild-type animals, observed through detergent-insoluble fractionation. Analysis of studies applying detergent-insoluble fractionation in mice revealed that the composition of detergent-insoluble proteins changes with age. However, these individual fractionation studies have generally been limited to small numbers of mice. Herein, we expand on our previous analysis by extending the experiments to a larger cohort of mice and to two brain regions implicated in neurodegenerative diseases, the cortex and hippocampus. These experiments unveil insights into alterations in the abundance and solubility of proteins involved in protein quality control and in inflammation. For example, ribosomal proteins and many chaperone proteins are downregulated with age. Consistent enrichment of subunits of the extracellular C1q complex was also observed in both brain regions alongside an increase in immunoglobulin signal indicating that markers of increased inflammation may also become insoluble during aging. More generally, insoluble proteins share features observed in datasets of impaired protein degradation indicating that the loss of activity of cellular protein degradation machinery may contribute to the specific aggregation of these proteins.
Protective effect and molecular mechanisms of human non-neutralizing cross-reactive spike antibodies elicited by SARS-CoV-2 mRNA vaccination
Authors: Clark Jordan , Hoxie Irene , Adelsberg Daniel C. , Sapse Iden A. , Andreata-Santos Robert , Yong Jeremy S. , Amanat Fatima , Tcheou Johnstone , Raskin Ariel , Singh Gagandeep , González-Domínguez Irene , Edgar Julia E. , Bournazos Stylianos , Sun Weina , Carreño Juan Manuel , Simon Viviana , Ellebedy Ali H. , Bajic Goran , Krammer Florian 
Published: March 2024

SummaryNeutralizing antibodies correlate with protection against SARS-CoV-2. Recent studies, however, show that binding antibody titers, in the absence of robust neutralizing activity, also correlate with protection from disease progression. Non-neutralizing antibodies cannot directly protect from infection but may recruit effector cells thus contribute to the clearance of infected cells. Also, they often bind conserved epitopes across multiple variants. We characterized 42 human mAbs from COVID-19 vaccinated individuals. Most of these antibodies exhibited no neutralizing activityin vitrobut several non-neutralizing antibodies protected against lethal challenge with SARS-CoV-2 in different animal models. A subset of those mAbs showed a clear dependence on Fc-mediated effector functions. We determined the structures of three non-neutralizing antibodies with two targeting the RBD, and one that targeting the SD1 region. Our data confirms the real-world observation in humans that non-neutralizing antibodies to SARS-CoV-2 can be protective.
Sec23IP recruits the Cohen syndrome factor VPS13B/COH1 to ER exit site-Golgi interface for tubular ERGIC formation
Authors: Du Yuanjiao , Fan Xinyu , Song Chunyu , Xiong Juan , Ji Wei-Ke 
Published: March 2024

AbstractVPS13B/COH1 is the only known causative factor for Cohen syndrome, an early-onset autosomal recessive developmental disorder with intellectual inability, developmental delay, joint hypermobility, myopia and facial dysmorphism as common features, but the molecular basis of VPS13B/COH1 in pathogenesis is unknown. Here, we identify Sec23 interacting protein (Sec23IP) at ER exit site (ERES) as a VPS13B adaptor that recruits VPS13B to ERES-Golgi interfaces. VPS13B interacts directly with Sec23IP via the VPS13 adaptor binding domain (VAB), and the interaction promotes the association between ERES and the Golgi. Disease-associated missense mutations of VPS13B-VAB impair the interaction with Sec23IP. Knockout of VPS13B or Sec23IP blocks the formation of tubular ERGIC, an unconventional cargo carrier that expedites ER-to-Golgi transport. In addition, depletion of VPS13B or Sec23IP delays ER export of procollagen, suggesting a link between procollagen secretion and joint laxity in patients with Cohen disease. Together, our study reveals a crucial role of VPS13B-Sec23IP interaction at ERES-Golgi interface in the pathogenesis of Cohen syndrome.
Peptide Mold: A Novel Strategy for Mapping Potential Binding Sites in Protein Targets
Authors: Bagwe Pritam V. , Jagtap Yogesh , Ghegade Vaibhav , Machhar Janvhi , Martis Elvis , Joshi Shreerang V. , Kharkar Prashant S. 
Published: March 2024

ABSTRACTA novel concept titled ‘Peptide Mold’ for mapping potential binding sites in protein targets is presented. A large multiconformer tetrapeptide library comprising of 32 million conformations of all possible combinations of naturally-occurring amino acids was constructed and used for molecular docking analysis in the substrate-binding site of SARS-CoV-2 PLpro enzyme. The top-ranking, structurally-diverse tetrapeptide docked conformations (symbolizing peptide mold, analogous to a clay mold) were used then for elucidating a five-point pharmacophore. Ligand-based virtual screening of a large, multiconformer library of phytoconstituents using the derived five-point pharmacophore led to identification of potential binders for SARS-CoV-2 PLpro at its substrate-binding site. The approach is based on generating the imprint of a macromolecular binding site (cavity) using tetrapeptides (clay), thereby generating a reverse mold (with definitive shape and size), which can further be used for identifying small-molecule ligands matching the captured features of the target binding site. The approach is based on the fact that the individual amino acids in the tetrapeptide represent all possible drug-receptor interaction features (electrostatic, H-bonding, van der Waals, dispersion and hydrophobic among others). The ‘peptide mold’ approach can be extended to any protein target for mapping the binding site(s), and further use of the generated pharmacophore model for virtual screening of potential binders. The peptide mold approach is a robust, hybrid computational screening strategy, overcoming the present limitations of structure-based methods, e.g., molecular docking and the ligand-based methods such as pharmacophore search. Exploration of the peptide mold strategy is expected to yield high-quality, reliable and interesting virtual hits in the computational screening campaigns during the hit and lead identification stages.
Validation of the performance of a point of care molecular test for leprosy: from a simplified DNA extraction protocol to a portable qPCR
Authors: Bertão-Santos Amanda , Dias Larisse da Silva , Ribeiro-Alves Marcelo , Pinheiro Roberta Olmo , Moraes Milton Ozório , Manta Fernanda Saloum de Neves , Costa Alexandre Dias Tavares 
Published: March 2024

AbstractThe study aimed to optimize qPCR reactions using oligonucleotides from the first Brazilian molecular diagnostic kit for leprosy on a portable platform (Q3-Plus). In addition, we sought to develop a simplified protocol for DNA extraction that met point-of-care criteria. During optimization on the Q3-Plus, optical parameters, thresholds, and cutoffs for the16S rRNAand RLEP targets ofM. lepraewere established using synthetic DNA, purified DNA fromM. leprae, and pre-characterized clinical samples. In the simplified extraction step, different lysis solutions were evaluated using chaotropic agents, and purification was carried out by depositing the lysed material on FTA cards. The complete protocol (simplified extraction + qPCR on the portable platform) was evaluated with pre-characterized clinical skin biopsy samples and compared with standard equipment (QuantStudio-5). LOD95%for the optimized reactions was 113.31 genome-equivalents/μL for16S rRNAand 17.70 genome-equivalents/μL for RLEP. Among the lysis solutions, the best-performing was composed of urea (2 M), which provided good dissolution of the skin fragment and a lower Ct value, indicating higher concentrations of DNA. The complete technological solution showed a sensitivity of 52% in reactions. Our results highlight the need for additional optimization to deal with paucibacillary samples, but also demonstrate the applicability of the portable platform in the detection ofM.leprae in low infrastructure settings.
Oro-faecal transmission of SARS-CoV-2: A systematic review of studies employing viral culture from gastrointestinal and other potential sources
Authors: Gandini Sara , Conly John , Spencer Elizabeth A. , Evans David , Rosca Elena C , Brassey Jon , Maltoni Susanna , Onakpoya Igho , Plüddemann Annette , Jefferson Tom , Heneghan Carl 
Published: March 2024

AbstractBackgroundThe extent to which the oro-faecal route contributes to the transmission of SARS-CoV-2 is not established.MethodsWe systematically reviewed the evidence on the presence of infectious SARS-CoV-2 in faeces and other gastrointestinal sources by examining studies that used viral culture to investigate the presence of replication-competent virus in these samples. We conducted searches in the WHO Covid-19 Database, LitCovid, medRxiv, and Google Scholar for SARS-CoV-2 using keywords and associated synonyms, with a search date up to 28th of November 2023.ResultsWe included 13 studies involving 328 COVID-19 subjects - providing 314 faecal or rectal swab SARS-CoV2 positive samples tested also with viral culture. The methods used for viral culture across the studies were heterogeneous. Three studies (2 cohorts and 1 case-series) reported observing replication-competent SARS-CoV-2 confirmed by quantitative RT-PCR (qPCR) and whole genome sequencing, and qPCR including appropriate cycle threshold changes. Overall, six (1.9%) of 314 faecal samples subjected to cell culture showed replication-competent virus. One study found replication competent samples from one immunocompromised patient. No studies were identified demonstrating direct evidence of oro-faecal transmission to humans.ConclusionsOur review found a relatively low frequency of replication-competent SARS-CoV-2 in faecal and other gastrointestinal sources. Although it is biologically plausible, more research is needed, using standardized cell culture methods, control groups, adequate follow-up and robust epidemiologic methods, including whether secondary infections occurred, to determine the role of the oro-faecal route in the transmission of SARS-CoV-2.
How many labels do I need? Self-supervised learning strategies for multiple blood parasites classification in microscopy images
Authors: Mancebo-Martín Roberto , Lin Lin , Dacal Elena , Luengo-Oroz Miguel , Bermejo-Peláez David 
Published: March 2024

AbstractBloodborne parasitic diseases such as malaria, filariasis or chagas pose significant challenges in clinical diagnosis, with microscopy as the primary tool for diagnosis. However, limitations such as time-consuming processes and the dependence on trained microscopists is critical, particularly in resource-constrained settings. Deep learning techniques have shown value to interpret microscopy images using large annotated databases for training. In this work, we propose a methodology leveraging self-supervised learning as a foundational model for blood parasite classification. Using a large unannotated database of blood microscopy images, the model is able to learn important image representations that are subsequently transferred to perform parasite classification of 11 different species of parasites requiring a smaller amount of labeled data. Our results show enhanced performance over fully supervised approaches, with ∼100 labels per class sufficient to attain an F1 score of ∼0.8. This approach is promising for advancing in-vitro diagnostic systems in primary healthcare settings.
Systematic mutagenesis assay promotes comprehension of the strand-bias laws for mutations induced by oxidative DNA damage
Authors: Kawai Hidehiko , Ebi Shungo , Sugihara Ryusei , Fujiwara Chiho , Fujikawa Yoshihiro , Kimura Shingo , Kamiya Hiroyuki 
Published: March 2024

ABSTRACTWe have recently developed an efficient and sensitive method for analyzing mutations caused by various environmental and endogenous factors which utilizes nucleotide-barcodedsupFshuttle vector libraries with a multiplexed NGS assay, referred to hereafter assupFNGS assay. Ionizing-radiation-induced cancer is known to be difficult to distinguish from spontaneous cancer, especially in the case of low-dose and low-dose-rate exposure, and discerning the underlying mechanisms of ionizing-radiation-induced cancer, especially the relationship between mutagenesis and carcinogenesis, is likely to be an arduous task. In the present study, we have attempted to address the mutations characteristic for exposure to low levels of ionizing radiation by using thesupFNGS assay. As a result, a significant increase in mutations was detected at cytosines and guanines within 5’-TC-3’:5’-GA-3’ sites following chronic gamma-irradiation at a dose-rate of 1 Gy per day for the duration of 2 days. Since the number of detected mutations exceeded the expectations based on the quantity of DNA-damage induced by irradiation, we proceeded to explore the possibilities that a single DNA-lesion induced by irradiation may cause amplification of mutations. For this purpose, we utilized shuttle vector libraries with a single 8-oxo-7,8-dihydroguanine (8-oxo-G)-damaged residue introduced at different sites via anin vitroenzymatic method. Through a set of experiments, we revealed that a single 8-oxo-G-damaged residue can become a trigger for peripheral mutagenesis; intense generation of strand-biased mutations occured at 5’-TC-3’:5’-GA-3’ sites with specific localization in the secondary structures of single-stranded DNA, more frequently than not at sites different from the 8-oxo-G-damaged sites. Thus, this study provides a novel prospect for the role of DNA-lesions induced by environmentally or endogenously generated ROS in additional mutations. The high-performance mutagenesis assay presented in this study will advance research aimed at uncovering the mechanisms of mutagenesis and the intricacies relevant to carcinogenesis.
Study of Impacts of Two Types of Cellular Aging on the Yeast Bud Morphogenesis
Authors: Tsai Kevin , Zhou Zhen , Yang Jiadong , Xu Zhiliang , Xu Shixin , Zandi Roya , Hao Nan , Chen Weitao , Alber Mark 
Published: March 2024

AbstractUnderstanding the mechanisms of cellular aging processes is crucial for attempting to extend organismal lifespan and for studying age-related degenerative diseases. Yeast cells divide through budding, providing a classical biological model for studying cellular aging. With their powerful genetics, relatively short lifespan and well-established signaling pathways also found in animals, yeast cells offer valuable insights into the aging process. Recent experiments suggested the existence of two aging modes in yeast characterized by nucleolar and mitochondrial declines, respectively. In this study, by analyzing experimental data it was shown that cells evolving into those two aging modes behave differently when they are young. While buds grow linearly in both modes, cells that consistently generate spherical buds throughout their lifespan demonstrate greater efficacy in controlling bud size and growth rate at young ages. A three-dimensional chemical-mechanical model was developed and used to suggest and test hypothesized mechanisms of bud morphogenesis during aging. Experimentally calibrated simulations showed that tubular bud shape in one aging mode could be generated by locally inserting new materials at the bud tip guided by the polarized Cdc42 signal during the early stage of budding. Furthermore, the aspect ratio of the tubular bud could be stabilized during the late stage, as observed in experiments, through a reduction on the new cell surface material insertion or an expansion of the polarization site. Thus model simulations suggest the maintenance of new cell surface material insertion or chemical signal polarization could be weakened due to cellular aging in yeast and other cell types.Significance StatementAging yeast exhibits two modes with different bud shapes. Experimental data analysis reveals that control of growth rate and bud size is more robust in cells aging in a spherical budding mode than in cells aging in a tubular budding mode. A computational model was developed and used in combination with experiments to test the hypothesized mechanisms underlying different types of budding in aging cells. Model simulations suggest that localized growth is sufficient to generate tubular budding and its aspect ratio can be stabilized through the regulation of chemical signals with an expanding polarization site or a decline on the new cell surface material insertion. Proposed mechanisms of morphological changes in aging yeast can be present in other cell types.
DELE1 promotes translation-associated homeostasis, growth, and survival in mitochondrial myopathy
Authors: Lin Hsin-Pin , Petersen Jennifer D. , Gilsrud Alexandra J. , Madruga Angelo , D’Silva Theresa M. , Huang Xiaoping , Shammas Mario K. , Randolph Nicholas P. , Li Yan , Jones Drew R. , Pacold Michael E. , Narendra Derek P. 
Published: March 2024

AbstractMitochondrial dysfunction causes devastating disorders, including mitochondrial myopathy. Here, we identified that diverse mitochondrial myopathy models elicit a protective mitochondrial integrated stress response (mt-ISR), mediated by OMA1-DELE1 signaling. The response was similar following disruptions in mtDNA maintenance, from knockout ofTfam, and mitochondrial protein unfolding, from disease-causing mutations in CHCHD10 (G58R and S59L). The preponderance of the response was directed at upregulating pathways for aminoacyl-tRNA biosynthesis, the intermediates for protein synthesis, and was similar in heart and skeletal muscle but more limited in brown adipose challenged with cold stress. Strikingly, models with early DELE1 mt-ISR activation failed to grow and survive to adulthood in the absence ofDele1, accounting for some but not all of OMA1’s protection. Notably, the DELE1 mt-ISR did not slow net protein synthesis in stressed striated muscle, but instead prevented loss of translation-associated proteostasis in muscle fibers. Together our findings identify that the DELE1 mt-ISR mediates a stereotyped response to diverse forms of mitochondrial stress and is particularly critical for maintaining growth and survival in early-onset mitochondrial myopathy.
Pulses of Class I PI3kinase activity identify the release and recapture of prey from neutrophil phagosomes
Authors: Muir Clare F , Reyes-Aldasoro Constantino Carlos , Ellett Felix E , Prajsnar Tomasz K , Ho Yin X , Bernut Audrey , Loynes Catherine A , Elworthy Stone , Bowden Kieran A , Cadbury Ashley J , Prince Lynne R , King Jason S , Condliffe Alison M , Renshaw Steven A 
Published: March 2024

SummaryClass I PI3kinases coordinate the delivery of microbicidal effectors to the phagosome by forming the phosphoinositide lipid second messenger, phosphatidylinositol (3, 4, 5)-trisphosphate (PIP3). However, the dynamics of PIP3 in neutrophils during a bacterial infection are unknown. We have therefore developed anin vivo,live zebrafish infection model that enables visualisation of dynamic changes in Class 1 PI3kinases (PI3K) signalling on neutrophil phagosomes in real-time. We have identified that on approximately 12% of neutrophil phagosomes PHAkt-eGFP, a reporter for Class 1 PI3K signalling, re-recruits in pulsatile bursts. This phenomenon occurred on phagosomes containing structurally and morphologically distinct prey, includingStaphylococcus aureusandMycobacterium abscessus, and was dependent on the activity of the Class 1 PI3K isoform, PI3kinase γ. Detailed imaging suggested that ‘pulsing phagosomes’ represent neutrophils transiently reopening and reclosing phagosomes. This finding challenges the concept that phagosomes remain closed after prey engulfment and we propose that neutrophils occasionally use this alternative pathway of phagosome maturation to release phagosome contents and/or to restart phagosome maturation if digestion has stalled.