bluuebunny/crossref_metadata_2025_split huggingface dataset:
Uncovering the Dual Role of Mitochondrial and Nuclear DNA Variants in Pediatric Cardiomyopathies
Authors: Temena M. Arda , Erzurumluoglu Gokalp Ebru , Susam Ezgi , Cinar Duygu , Kiztanir Hikmet , Kosger Pelin , Durak Aras Beyhan , Artan Sevilhan , Cilingir Oguz 
Published: December 2023

ABSTRACTMyocardial defects, originating from disruptions in genes affecting mitochondrial proteins interacting with others, have received limited research attention. In our study involving 27 pediatric cardiomyopathy patients, we explored mitochondrial and nuclear genes for four main cardiomyopathy subtypes. Sequencing cardiomyopathy-associated genes in patients was followed by whole mtDNA sequencing in these individuals, with 31 healthy pediatric controls for the latter part. Our findings uncovered significant pathogenic variants: MYH7 variants in three hypertrophic cardiomyopathy cases, a notable TNNC1 variant inherited interestingly in an autosomal recessive manner in two related restrictive cardiomyopathy patients, and a pathogenic TRDN variant in a left-ventricular non-compaction patient. Both a variant in FOXRED1, functioning in mitochondrial complex I stability, and a MT-CO1 variant were detected in two siblings, influencing early onset together. Additionally, a novel MT-RNR1 variant (m.684T>C) in one case might explain the phenotype. Our study highlights how both mtDNA and nDNA variants could have interconnected roles in understanding cardiomyopathy genetics. This study emphasizes that the functional studies are needed to recognize this dual relationship within bioenergetic pathways in cardiac muscle.
Using Digital Tools in Clinical, Health and Social Care Research: A Mixed-Methods Study of UK Stakeholders
Authors: Clohessy Sophie , Arvanitis Theodoros N. , Rashid Umer , Craddock Carly , Evans Mark , Toro Carla , Elliott Mark T. 
Published: December 2023

AbstractObjectiveThe COVID-19 pandemic accelerated changes to clinical research methodology, with clinical studies being carried out via online/remote means. This mixed-methods study aimed to identify which digital tools are currently used across all stages of clinical research by stakeholders in clinical, health and social care research and investigate their experience using digital tools.DesignTwo online surveys followed by semi-structured interviews were conducted. Interviews were audio recorded, transcribed, and analysed thematically.Setting, ParticipantsTo explore the digital tools used since the pandemic, survey participants [Researchers and Related Staff (n=41), Research and Development staff (n=25)], needed to have worked on clinical, health or social care research studies over the past two years (2020-2022) in an employing organisation based in the West Midlands region of England (due to funding from a regional clinical research network). Survey participants had the opportunity to participate in an online qualitative interview to explore their experiences of digital tools in greater depth (n=8).ResultsSix themes were identified in the qualitative interviews: ‘Definition of a Digital Tool in Clinical Research’;‘Impact of the COVID-19 Pandemic’;‘Perceived Benefits/Drawbacks of Digital Tools’;‘Selection of a Digital Tool’; ‘Barriers and Overcoming Barriers’;and‘Future Digital Tool Use’.The context of each theme is discussed, based on the interview results.ConclusionsFindings demonstrate how digital tools are becoming embedded in clinical research, as well as the breadth of tools used across different research stages. The majority of participants viewed the tools positively, noting their ability to enhance research efficiency. Several considerations were highlighted; concerns about digital exclusion; need for collaboration with digital expertise/clinical staff, research on tool effectiveness and recommendations to aid future tool selection. There is a need for the development of resources to help optimise the selection and use of appropriate digital tools for clinical research staff and participants.Article SummaryStrengths and Limitations of the StudyMixed-method study to explore experiences of utilising digital tools in clinical research, utilising participants from a variety of roles; both Research and Research and Development staff.Survey and qualitative questions co-designed with an experienced stakeholder group.It is likely that participants were motivated to participate due to an underlying interest in digital tools, consequently some perspectives may not have been included in this study.The study was limited to exploring the views of stakeholders employed by organisations based in the West Midlands, United Kingdom.
PRDM3/16 Regulate Chromatin Accessibility Required for NKX2-1 Mediated Alveolar Epithelial Differentiation and Function
Authors: He Hua , Bell Sheila M. , Davis Ashley Kuenzi , Zhao Shuyang , Sridharan Anusha , Na Cheng-Lun , Guo Minzhe , Xu Yan , Snowball John , Swarr Daniel T. , Zacharias William J. , Whitsett Jeffrey A. 
Published: December 2023

AbstractDifferential chromatin accessibility accompanies and mediates transcriptional control of diverse cell fates and their differentiation during embryogenesis. While the critical role of NKX2-1 and its transcriptional targets in lung morphogenesis and pulmonary epithelial cell differentiation is increasingly known, mechanisms by which chromatin accessibility alters the epigenetic landscape and how NKX2-1 interacts with other co-activators required for alveolar epithelial cell differentiation and function are not well understood. Here, we demonstrate that the paired domain zinc finger transcriptional regulators PRDM3 and PRDM16 regulate chromatin accessibility to mediate cell differentiation decisions during lung morphogenesis. Combined deletion ofPrdm3andPrdm16in early lung endoderm caused perinatal lethality due to respiratory failure from loss of AT2 cell function.Prdm3/16deletion led to the accumulation of partially differentiated AT1 cells and loss of AT2 cells. Combination of single cell RNA-seq, bulk ATAC-seq, and CUT&RUN demonstrated that PRDM3 and PRDM16 enhanced chromatin accessibility at NKX2-1 transcriptional targets in peripheral epithelial cells, all three factors binding together at a multitude of cell-type specific cis-active DNA elements. Network analysis demonstrated that PRDM3/16 regulated genes critical for perinatal AT2 cell differentiation, surfactant homeostasis, and innate host defense. Lineage specific deletion of PRDM3/16 in AT2 cells led to lineage infidelity, with PRDM3/16 null cells acquiring partial AT1 fate. Together, these data demonstrate that NKX2-1-dependent regulation of alveolar epithelial cell differentiation is mediated by epigenomic modulation via PRDM3/16.Graphical AbstractModel of the role of PRMD3/16 in alveolar developmentPRMD3/16 participate in cell fate specification in the lung by modulating chromatin accessibility (top row) and by partnering with NKX2-1 and partner transcription factors to drive gene expression (second row) via a gene regulatory network required for terminal cell differentiation and surfactant expression in AT2 cells (third row). Loss of PRDM3/16 activity in lung endoderm leads to reduced AT2 quorum, failure of AT2 surfactant function, and transition to an immature AT1 phenotype (bottom panel).
Temperature impacts SARS-CoV-2 spike fusogenicity and evolution
Authors: Dufloo Jérémy , Sanjuán Rafael 
Published: December 2023

AbstractSARS-CoV-2 infects both the upper and lower respiratory tracts, which are characterized by different temperatures (33°C and 37°C, respectively). In addition, fever is a common COVID-19 symptom. SARS-CoV-2 has been shown to replicate more efficiently at low temperatures but the effect of temperature on different viral proteins remains poorly understood. Here, we investigate how temperature affects the SARS-CoV-2 spike function and evolution. We first observed that rising temperature from 33°C to 37°C or 39°C increased spike-mediated cell-cell fusion. We then experimentally evolved a recombinant vesicular stomatitis virus expressing the SARS-CoV-2 spike at these different temperatures. We found that spike-mediated cell-cell fusion was maintained during evolution at 39°C, but was lost in a high proportion of viruses evolved at 33°C or 37°C. Consistently, sequencing of the spikes evolved at 33°C or 37°C revealed the accumulation of mutations around the furin cleavage site, a region that determines cell-cell fusion, whereas this did not occur in spikes evolved at 39°C. Finally, using site-directed mutagenesis, we found that disruption of the furin cleavage site had a temperature-dependent effect on spike-induced cell-cell fusion and viral fitness. Our results suggest that variations in body temperature may affect the activity and diversification of the SARS-CoV-2 spike.ImportanceWhen it infects humans, SARS-CoV-2 is exposed to different temperaures (e.g. replication site, fever…). Temperature has been shown to strongly impact SARS-CoV-2 replication but how it affects the activity and evolution of the spike protein remains poorly understood. Here, we first show that high temperatures increase the SARS-CoV-2 spike fusogenicity. Then, we demonstrate that the evolution of the spike activity and variants depends on temperature. Finally, we show that the functional effect of specific spike mutations is temperature-dependent. Overall, our results suggest that temperature may be a factor influencing the activity and adapatation of the SARS-CoV-2 spike in vivo, which will help understanding viral tropism, pathogenesis, and evolution.
Uncertainty Quantification in Acoustic Impedance of Atlantic Salmon Fish Scale using Scanning Acoustic Microscopy
Authors: Agarwal Komal , Ojha Shivam , Dalmo Roy Ambil , Seternes Tore , Shelke Amit , Melandsø Frank , Habib Anowarul 
Published: December 2023

ABSTRACTScanning Acoustic Microscopy (SAM) emerges as a versatile label-free imaging technology with broad applications in biomedical imaging, non-destructive testing, and material research. This article presents a framework for the estimation of stochastic impedance through SAM, with a particular focus on its application to the salmon fish scale. The framework leverages uncertain reflectance, marking its pioneering application to uncertainty quantification in the acoustic impedance of fish scales through acoustic responses. The study uses maximal overlap discrete wavelet transform, to decompose acoustic responses effectively and is further processed to predict the acoustic impedance. To establish the effectiveness of the proposed framework, well-known materials like a pair of target medium (polyvinylidene fluoride) and reference medium (polyimide) are employed for impedance characterization. Results demonstrate over 90%accuracy in PVDF impedance estimation, validating the framework. A stochastic impedance map, using Kriging with a Gaussian variogram, offers insights into the complex biomechanics of a fish’s scale.
RCPedia: A global resource for studying and exploring retrocopies in diverse species
Authors: Conceição Helena B. , Mercuri Rafael L. V. , de Castro Matheus P. M. , Ohara Daniel T. , Guardia Gabriela D. A. , Galante Pedro A F 
Published: December 2023

MotivationGene retrocopies, or processed pseudogenes, arise from the reverse transcription and genomic insertion of processed mRNA transcripts. These elements have significantly contributed to genetic diversity and novelties throughout the evolution of many species. However, the study of retrocopies has been challenging, owing to the absence of comprehensive, complete, and user-friendly databases for diverse species.ResultsHere, we introduce an improved version of RCPedia, an integrative database meticulously designed for the study of retrocopies. RCPedia offers an extensive catalog of retrocopies identified across 44 species, which includes 13 primates, 4 rodents, 6 chiropterans, 12 other mammals, 4 birds, turtle, lizard, frog, zebrafish, and drosophila. The database offers the most complete compilation of retrocopies per species, accompanied by detailed genomic annotations, expression data, and links to other data portals. Furthermore, RCPedia features a streamlined representation of data and an efficient querying system, establishing it as an invaluable tool for researchers in the fields of genomics, evolutionary biology and transposable elements. In summary, RCPedia aims to enhance the investigation of retrocopies and their pivotal roles in shaping the genomic landscapes of diverse species.AvailabilityRCPedia is available athttps://www.rcpediadb.org
Minimal vertex model explains how the amnioserosa avoids fluidization duringDrosophiladorsal closure
Authors: Tah Indrajit , Haertter Daniel , Crawford Janice M. , Kiehart Daniel P. , Schmidt Christoph F. , Liu Andrea J. 
Published: December 2023

Dorsal closure is a process that occurs during embryogenesis ofDrosophila melanogaster. During dorsal closure, the amnioserosa (AS), a one-cell thick epithelial tissue that fills the dorsal opening, shrinks as the lateral epidermis sheets converge and eventually merge. During this process, both shape index and aspect ratio of amnioserosa cells increase markedly. The standard 2-dimensional vertex model, which successfully describes tissue sheet mechanics in multiple contexts, would in this case predict that the tissue should fluidize via cell neighbor changes. Surprisingly, however, the amnioserosa remains an elastic solid with no such events. We here present a minimal extension to the vertex model that explains how the amnioserosa can achieve this unexpected behavior. We show that continuous shrinkage of the preferred cell perimeter and cell perimeter polydispersity lead to the retention of the solid state of the amnioserosa. Our model accurately captures measured cell shape and orientation changes and predicts non-monotonic junction tension that we confirm with laser ablation experiments.Significance StatementDuring embryogenesis, cells in tissues can undergo significant shape changes. Many epithelial tissues fluidize, i.e. cells exchange neighbors, when the average cell shape index increases above a threshold value, consistent with the standard vertex model. During dorsal closure inDrosophila melanogaster, however, the amnioserosa tissue remains solid even as the average cell shape index increases well above threshold. We introduce perimeter polydispersity and allow the preferred cell perimeters, usually held fixed in vertex models, to decrease linearly with time as seen experimentally. With these extensions to the standard vertex model, we capture experimental observations quantitatively. Our results demonstrate that vertex models can describe the behavior of the amnioserosa in dorsal closure by allowing normally fixed parameters to vary with time.
Inhibition of the Rho/MRTF pathway improves the response of BRAF-resistant melanoma to PD1/PDL1 blockade
Authors: Foda Bardees M. , Misek Sean A. , Gallo Kathleen A. , Neubig Richard R. 
Published: December 2023

AbstractMetastatic cutaneous melanoma is a fatal skin cancer. Resistance to targeted and immune therapies limits the benefits of current treatments. Identifying and adding anti-resistance agents to current treatment protocols can potentially improve clinical responses. Myocardin-related transcription factor (MRTF) is a transcriptional coactivator whose activity is indirectly regulated by actin and the Rho family of GTPases. We previously demonstrated that development of BRAF inhibitor (BRAFi) resistance frequently activates the Rho/MRTF pathway in human and mouse BRAFV600Emelanomas. In clinical trials, pre-treatment with BRAFi reduces the benefit of immune therapies. We aimed to test the efficacy of concurrent treatment with our MRTF pathway inhibitor CCG-257081 and anti-PD1in vivoand to examine its effects on the melanoma immune microenvironment. Because MRTF pathway activation upregulates the expression of immune checkpoint inhibitor genes/proteins, we asked whether CCG-257081 can improve the response to immune checkpoint blockade. CCG-257081 reduced the expression of PDL1 in BRAFi-resistant melanoma cells and decreased surface PDL1 levels on both BRAFi- sensitive and -resistant melanoma cells. Using our recently described murine vemurafenib-resistant melanoma model, we found that CCG-257081, in combination with anti-PD1 immune therapy, reduced tumor growth and increased survival. Moreover, anti-PD1/CCG-257081 co-treatment increased infiltration of CD8+T cells and B cells into the tumor microenvironment and reduced tumor-associated macrophages. Here, we propose CCG-257081 as an anti-resistance and immune therapy-enhancing anti-melanoma agent.Novelty and ImpactWe present a study that provides evidence for a new combined approach for targeting BRAF inhibitor-resistant melanoma. Pharmacological inhibition of the resistance-inducing Rho/MRTF pathway using CCG-257081 enhanced the response to PD1/PDL-1 blockadein vivo. These results indicate a role of the Rho/MRTF pathway in regulating tumor-immune interactions. Thus, CCG-257081 emerges as a potential new anti-resistance agent that can improve the response to immune checkpoint inhibitors in advanced melanoma and, possibly, other cancers.
Unexpected roles for AMPK in the suppression of autophagy and the reactivation of mTORC1 signaling during prolonged amino acid deprivation
Authors: Kazyken Dubek , Dame Sydney G. , Wang Claudia , Wadley Maxwell , Fingar Diane C. 
Published: December 2023

AbstractAMPK promotes catabolic and suppresses anabolic cell metabolism to promote cell survival during energetic stress, in part by inhibiting mTORC1, an anabolic kinase requiring sufficient levels of amino acids. We found that cells lacking AMPK displayed increased apoptotic cell death during nutrient stress caused by prolonged amino acid deprivation. We presumed that impaired autophagy explained this phenotype, as a prevailing view posits that AMPK initiates autophagy (often a pro-survival response) through phosphorylation of ULK1. Unexpectedly, however, autophagy remained unimpaired in cells lacking AMPK, as monitored by several autophagic readouts in several cell lines. More surprisingly, the absence of AMPK increased ULK1 signaling and LC3b lipidation during amino acid deprivation while AMPK-mediated phosphorylation of ULK1 S555 (a site proposed to initiate autophagy) decreased upon amino acid withdrawal or pharmacological mTORC1 inhibition. In addition, activation of AMPK with compound 991, glucose deprivation, or AICAR blunted autophagy induced by amino acid withdrawal. These results demonstrate that AMPK activation and glucose deprivation suppress autophagy. As AMPK controlled autophagy in an unexpected direction, we examined how AMPK controls mTORC1 signaling. Paradoxically, we observed impaired reactivation of mTORC1 in cells lacking AMPK upon prolonged amino acid deprivation. Together these results oppose established views that AMPK promotes autophagy and inhibits mTORC1 universally. Moreover, they reveal unexpected roles for AMPK in the suppression of autophagy and the support of mTORC1 signaling in the context of prolonged amino acid deprivation. These findings prompt a reevaluation of how AMPK and its control of autophagy and mTORC1 impact health and disease.
The radiation of nodulatedChamaecristaspecies from the rainforest into more diverse habitats has been accompanied by a reduction in growth form and a shift from fixation threads to symbiosomes
Authors: Casaes Patricia Alves , Ferreira dos Santos José Miguel , Silva Verônica Cordeiro , Rhem Mariana Ferreira Kruschewsky , Teixeira Cota Matheus Martins , de Faria Sergio Miana , Rando Juliana Gastaldello , James Euan K. , Gross Eduardo 
Published: December 2023

AbstractAll non-mimosoid nodulated genera in the legume subfamily Caesalpinioideae confine their rhizobial symbionts within cell wall-bound “fixation threads” (FTs). The exception is the large genusChamaecristain which shrubs and subshrubs house their rhizobial bacteroids more intimately within symbiosomes, whereas large trees have FTs. This study aimed to unravel the evolutionary relationships betweenChamaecristagrowth habit, habitat, nodule bacteroid type, and rhizobial genotype. The growth habit, bacteroid anatomy, and rhizobial symbionts of 30 nodulatedChamaecristaspecies native to different biomes in the Brazilian state of Bahia, a major centre of diversity for the genus, was plotted onto an ITS-TrnL-F-derived phylogeny ofChamaecrista. The bacteroids from most of theChamaecristaspecies examined were enclosed in symbiosomes (SYM-type nodules), but those in arborescent species in the sectionApoucouita, at the base of the genus, were enclosed in cell wall material containing homogalacturonan (HG) and cellulose (FT-type nodules). Most symbionts wereBradyrhizobiumgenotypes grouped according to the growth habits of their hosts, but the tree,C. eitenorum,was nodulated byParaburkholderia.Chamaecristahas a range of growth habits that allow it to occupy several different biomes and to co-evolve with a wide range of (mainly) bradyrhizobial symbionts. FTs represent a less intimate symbiosis linked with nodulation losses, so the evolution of SYM-type nodules by mostChamaecristaspecies may have (a) aided the genus-wide retention of nodulation, and (b) assisted in its rapid speciation and radiation out of the rainforest into more diverse and challenging habitats.
Metabolite Fingerprinting for Phenotypic Screening by Infrared Matrix-Assisted Laser Desorption Electrospray Ionization Mass Spectrometry
Authors: Joignant Alena N. , Pu Fan , McLoughlin Shaun M. , Sawicki James W. , Radosevich Andrew J. , Ma Renze , Williams Jon D. , Gopalakrishnan Sujatha M. , Elsen Nathaniel L. 
Published: December 2023

ABSTRACTThe adoption of mass spectrometry for high-throughput screening in drug discovery has become increasingly prevalent and has enabled label-free screening against diverse targets. Cellular assays for phenotypic screening, however, are primarily conducted by microscopy as there remain many challenges associated with conducting phenotypic screens via ultra-high throughput mass spectrometry.Following a simple on-plate extraction, infrared matrix assisted laser desorption electrospray ionization (IR-MALDESI) was employed to directly sample the cell lysate at a speed of one second per sample. A549 cells were treated with compounds identified as hits in literature including a recently reported glutaminase cellular screen. Among the test compounds, there were confirmed glutaminase inhibitors, proposed nuisance compounds, and cell-active but enzyme-inactive compounds. Filtered data were further processed in R for dimensionality reduction and unsupervised clustering.Though it was observed that all compounds affected the intracellular conversion of glutamine to glutamate, there were clear metabolic differences between the biochemically active compounds and the off-target hits. Moreover, two nuisance compounds were observed to cluster separately from the confirmed glutaminase inhibitors in the observed metabolite fingerprints.This proof-of-concept work establishes a complete workflow that enables highthroughput mass spectrometry-based phenotypic screening. The methods proposed herein, at the throughput enabled by IR-MALDESI, could offer a new avenue for discovery of novel drugs.