bluuebunny/crossref_metadata_2025_split huggingface dataset:
Topographic organization of bidirectional connections between the cingulate region (infralimbic area and anterior cingulate area, dorsal part) and the interbrain (diencephalon) of the adult male rat
Authors: Negishi Kenichiro , Montes Laura P. , Navarro Vanessa I. , Soto Arzate Lidice , Oliveros Cindy , Khan Arshad M. 
Published: October 2024

AbstractThe medial prefrontal cortex [cingulate region (Brodmann, 1909)(CNG)] in the rat is a connectionally and functionally diverse structure. It harbors cerebral nuclei that use long-range connections to promote adaptive changes to ongoing behaviors. The CNG is often described across functional and anatomical gradients, a dorsal-ventral gradient being the most prominent. Topographic organization is a general feature of the nervous system, and it is becoming clear that such spatial arrangements can reflect connectional, functional, and cellular differences. Portions of the CNG are known to form reciprocal connections with cortical areas and thalamus; however, these connectional features have not been described in detail or mapped to standardized rat brain atlases. Here, we used co-injected anterograde (Phaseolus vulgarisleucoagglutinin) and retrograde (cholera toxin B subunit) tracers throughout the CNG to identify zones of reciprocal connectivity in the diencephalon [orinterbrain (Baer, 1837)(IB)]. Tracer distributions were observed using a Nissl-based atlas-mapping approach that facilitates description of topographic organization. This draft report describes CNG connections of theinfralimbic area (Rose & Woolsey, 1948)(ILA) andthe anterior cingulate area, dorsal part (Krettek & Price, 1977)(ACAd) throughout the IB. We found that corticothalamic connections are predominantly reciprocal, and that ILA and ACAd connections tended to be spatially segregated with minimal overlap. In thehypothalamus (Kuhlenbeck, 1927), we found dense and specific ILA-originating terminals in the followingBrain Maps 4.0 atlas territories:dorsal region (Swanson, 2004)(LHAd) andsuprafornical region (Swanson, 2004)(LHAs) of thelateral hypothalamic area (Nissl, 1913),parasubthalamic nucleus (Wang & Zhang, 1995)(PSTN),tuberal nucleus, terete part (Petrovich et al., 2001)(TUte), and an ill-defined dorsal cap of themedial mammillary nucleus (Gudden, 1881)(MM). We discuss these findings in the context of feeding behaviors.
Electrical Impedance Spectroscopy as a Tool to Detect the Epithelial to Mesenchymal Transition in Prostate Cancer Cells
Authors: Crowell Lexi L. , Henriquez Luis A. , Tran Mary , Adams Tayloria N.G. 
Published: October 2024

AbstractProstate cancer (PCa) remains a significant health threat, with chemoresistance and recurrence posing major challenges despite advances in treatment. The epithelial to mesenchymal transition (EMT), a biochemical process where cells lose epithelial features and gain mesenchymal traits, is linked to chemoresistance and metastasis. Electrical impedance spectroscopy (EIS), a novel label-free electrokinetic technique, offers promise in detecting cell phenotype changes. In this study, we employed EIS to detect EMT in prostate cancer cells (PCCs). PC3, DU145, and LNCaP cells were treated with an EMT induction media for five days. EIS characterization revealed unique impedance spectra correlating with metastatic potential, distinguishing DU145 EMT+ and EMT-cells, and LNCaP EMT+ and EMT-cells (in combination with dielectrophoresis), with comparisons made to epithelial and mesenchymal controls. These changes were supported by shifts in electrical signatures, morphological, and protein expression, including downregulation of E-cadherin and upregulation of vimentin. No phenotype change was observed in PC3 cells, which maintained a mesenchymal phenotype. EMT+ cells were also distinguishable from mixtures of EMT+ and EMT-cells. This study demonstrates key advancements: application of EIS and dielectrophoresis for label-free EMT detection in PCCs, characterization of cell electrical signature after EMT, and EIS sensitivity to EMT transitions. Detecting EMT in PCa is important to the development of more effective treatments and overcoming the challenges of chemoresistance.
A Large Scale Multi-dataset Investigation of Brain Metastases Distribution Based on Primary Cancer Type
Authors: Lyu Qing , Yuan Hongyu , Lin Zhen , Barcus Richard , Hudson Jeremy , Jiang Yuming , Kim Jeongchul , Whitlow Christopher T 
Published: October 2024

AbstractBrain metastases (BM) present a significant clinical challenge, characterized by poor prognosis and high morbidity. Previous research has demonstrated heterogeneous distribution patterns of BMs depending on the primary tumor type. This study aims to further investigate the distribution patterns of BMs. Utilizing three public datasets and one private dataset, we analyzed 1,344 patients with a total of 9,431 identified BMs, categorizing them into lung, breast, melanoma, kidney cancer, and other groups. Our findings indicate that lung cancer BMs predominantly localize in the cerebellum, as well as the frontal, temporal, occipital, and parietal lobes. Breast cancer BMs are commonly found in the cerebellum, frontal, occipital, and temporal lobes, while melanoma BMs are most frequently located in the occipital, temporal, and frontal lobes. Kidney cancer BMs, less studied in existing literature, primarily affect the frontal and temporal lobes. Additionally, we explored the relationship between BM volume and tumor type, revealing that lung and breast cancer BMs are more likely to have smaller tumor volumes compared to melanoma and kidney cancer BMs. These findings confirm and expand upon previous research, offering new insights into the distribution and characteristics of kidney cancer BMs.
Long-Read Sequencing Increases Diagnostic Yield for Pediatric Sensorineural Hearing Loss
Authors: Redfield Shelby E. , Shao Wanqing , Sun Tieqi , Pastolero Adrian , Rowell William J. , French Courtney E. , Nolan Cillian , Holt J. Matthew , Saunders Christopher T. , Fanslow Cairbre , Lampraki Eirini Maria , Lambert Christine , Kenna Margaret , Eberle Michael , Rockowitz Shira , Shearer Aiden Eliot 
Published: October 2024

AbstractThe diagnostic yield of genetic testing for pediatric sensorineural hearing loss (SNHL) has remained at around 40% for over a decade despite newly discovered causative genes and the expanded use of exome sequencing (ES). This stagnation may be due to (1) a focus on coding regions of the genome and (2) an inability to resolve variants in complex genomic regions due to reliance on short-read sequencing technologies. Short-read genome sequencing (srGS) and long-read genome sequencing (lrGS) both provide exonic single nucleotide variant (SNV) and small indel detection at the same sensitivity as ES, but also evaluate intronic regions. lrGS provides improved resolution for structural variants (SV) and repetitive genomic regions. We sought to investigate the potential utility of lrGS in the diagnostic evaluation of a small cohort of patients with SNHL of unknown etiology after ES and srGS. 19 pediatric patients with SNHL underwent lrGS via PacBio SMRT sequencing. Sequencing data were processed using the PacBio WGS variant pipeline. The diagnostic yield for this lrGS cohort was 4/19 (21%). Relevant variants detected only with lrGS included a hemizygous deletionin transwith a missense variant in an area of high genomic homology (OTOA) and two single nucleotide loss-of-function variantsin transto a known copy-number-loss for a gene with a highly homologous pseudogene (STRC). A complex inversion was identified in theMITFgene which was also identified on post-hoc analysis by srGS. LrGS provides improved resolution for complex genomic structural variation which may increase diagnostic yield for genetic pediatric SNHL, and, potentially, rare disease more broadly.
Chlorobaculum tepidumOuter Membrane Vesicles Are Likely a Significant Route for Biogenic Sulfur Transport
Authors: Noundou Vadesse L. , Levy Amalie , Modla Shannon , Yu Yanbao , Qu Jing , Hanson Thomas E. 
Published: October 2024

ABSTRACTOuter membrane-derived vesicles (OMVs) have been studied in different phyla of Gram-negative bacteria, most extensively in the Pseudomonadota, where they have been shown to participate in diverse biological and environmental processes. To date, the production of OMVs has not been reported in the Chlorobiaceae within the phylum Chlorobiota.Chlorobaculum. tepidumis the model organism for the Chlorobiaceae that synthesizes and consumes insoluble extracellular sulfur (S(0)) globules by an unknown mechanism. Here, we report evidence implicating outer membrane vesicles in biogenic S(0) globule synthesis. First we demonstrate thatCba. tepidumsecretes OMVs in the extracellular milieu, and that OMV yield and size vary with growth conditions, particularly sulfide concentration. A core of 28 proteins involved in diverse biological processes such as cell wall biogenesis, inorganic ion transport and metabolism were found to be shared between OMVs, extracellular S(0) globules andCba. tepidumintact cells. Multiple analytical methods indicated that OMVs contain S(0) and that OMVs and biogenic S(0) globules share protein and polysaccharide signatures, including lipooligosaccharides. Together these lines of evidence indicate thatCba. tepidum’s OMVs are one component of sulfur transport between cells and extracellular sulfur globules.IMPORTANCEAll living cells must exchange material with their environment while maintaining cellular integrity. This is a particular challenge for materials that are not water soluble, yet many bacteria utilize insoluble materials for energy conservation and as nutrients for growth. Here we show thatCba. tepidummakes outer membrane vesicles and that these vesicles are likely involved in the exchange of material with extracellular elemental sulfur globules formed and consumed byCba. tepidumas part of its energy metabolism based on oxidizing reduced sulfur compounds like hydrogen sulfide. These data expand our basic understanding ofCba. tepidum’s metabolism. As elemental sulfur is an industrial by-product with a limited number of uses, the information here may help enable the use of additional sulfur compounds byCba. tepidumto drive the synthesis of biomass and/or specialty biochemicals from waste elemental sulfur by this autotrophic bacterium.
An all-in-one AAV vector for cardiac-specific gene silencing by an adenine base editor
Authors: Liu Zhanzhao , Yang Luzi , Yang Yuhan , Li Jiting , Chen Zhan , Guo Congting , Guo Qianhao , Li Qiuxuan , Sun Yueshen , Zhao Dongyu , Hu Xiaomin , Gao Fei , Guo Yuxuan 
Published: October 2024

AbstractABE editing outcomes are highly variable and unpredictable, depending on various factors. Therefore, the success rate of creating targeted A•T-to-G•C conversions using ABE is not high. But utilizing ABE to target RNA splicing sites for gene silencing has a higher success rate. Another challenge for base editing in the heart is that traditional ABE is too large in size, necessitating dual AAV delivery. Whether single AAV delivery can be achieved remains to be explored. In this study, we demonstrated how the diversity of Cas9 homologs and screening of sgRNAs can facilitate cardiac base editing. Single-AAV base editing outperformed dual-AAV systems in the heart, potentially benefiting from chromatin accessibility-guided sgRNA selection. These findings have important implications for the development of more effective and predictable base editing tools for cardiac gene therapy.
Unlocking the Potential of Low Quality Total RNA-seq Data: A Stepwise Mapping Approach for Improved Quantitative Analyses
Authors: Lee Jiwoon , Gim JungSoo 
Published: October 2024

ABSTRACTHigh-throughput sequencing assays face persistent challenges when analyzing low-quality RNAs, often assessed by the RNA integrity number (RIN). Current preprocessing methods and pipelines designed for mRNA-seq presume high-quality RNAs, overlooking the nuanced complexities arising from degraded transcripts in low-quality samples. This study questions the applicability of standard analysis pipelines, especially when sequencing low-quality total RNAs, which are sometimes the sole recourse for specific inquiries. To address this, we conducted a comprehensive investigation using large sequencing reads obtained from blood biospecimens with varying RINs. Introducing a novel mapping approach, termed ’stepwise mapping’, our systematic comparative analyses propose an optimal practice for total RNA-seq data analysis. Contrary to conventional mapping procedures, the ’stepwise mapping’ approach unveils additional transcriptome information, crucial for stable differential expression analysis, even with total RNA-seq data from specimens with relatively low RINs. Our method proves particularly valuable when analyzing limited specimens with low RNA quality.
Probabilistic modelling improves relative dating from gene phylogenies
Authors: Bernabeu Moisès , Armero Carmen , Gabaldón Toni 
Published: October 2024

AbstractEstablishing the timing of past evolutionary events is a fundamental task in the reconstruction of the history of life. State-of-the-art molecular dating methods generally involve the reconstruction of a species tree from conserved, vertically evolving genes, and the assumption of a molecular clock calibrated with the fossil record. Although this approach is extremely useful, its use is limited to speciation events and does not account for genes following different evolutionary paths. Recently, an alternative methodology for the relative dating of evolutionary events has been proposed that considers the distribution of branch lengths across sets of gene trees. Here, we validate this methodology using a fossil-calibrated phylogeny and propose a model-based formalisation using a Bayesian framework. Our analyses revealed that the normalisation of the compared branch lengths with branch lengths of a shared reference clade results in narrower distributions, allowing the correct inference of the relative ordering of evolutionary events. Moreover, we show that distributions of normalised lengths can be modelled using gamma or lognormal distributions. Finally, we demonstrate that inference of the posterior distribution of the mode allows accurate relative age estimation, as assessed by a strong correlation with the molecular clock-dated tree. Overall, we provide a novel, model-based approach to infer relative ages from sets of gene phylogenies.
Megakaryocytes assemble a three-dimensional cage of extracellular matrix that controls their maturation and anchoring to the vascular niche
Authors: Masson Claire , Scandola Cyril , Rinckel Jean-Yves , Proamer Fabienne , Janus-Bell Emily , Batool Fareeha , Osmani Naël , Goetz Jacky G. , Mallo Léa , Léon Catherine , Bornert Alicia , Poincloux Renaud , Destaing Olivier , Mansson Alma , Qian Hong , Lehmann Maxime , Eckly Anita 
Published: October 2024

AbstractMegakaryocytes, the progenitor cells of blood platelets, play a crucial role in hemostasis by residing in the bone marrow and ensuring continuous platelet production. Unlike other hematopoietic cells, megakaryocytes do not enter the blood circulation intact. They remain anchored within the bone marrow while extending cytoplasmic protrusions called proplatelets through the sinusoidal endothelial barrier. These proplatelets subsequently fragment into functional platelets. This unique process of intravasation facilitates efficient platelet production while maintaining the megakaryocyte cell body within the bone marrow niche, thus preventing potential thrombotic complications. How the extracellular matrix (ECM) influences the delicate balance between megakaryocyte retention and proplatelet extension remains largely unknown. Here, we investigate the spatial organization and functional role of ECM components in the megakaryocyte vascular niche. Our findings reveal that laminin and collagen IV form three-dimensional (3D) ECM cages encompassing megakaryocytes and anchor them to the sinusoidal basement membrane. Gene deletion shows the existence of laminin α4 in the ECM cage that is necessary to maintain megakaryocyte-sinusoid interactions. Notably, megakaryocytes actively contribute to the ECM cage assembly; β1/β3 integrin knockout weakens these structures, increasing intravasation and entire megakaryocyte entry into circulation. The retention of megakaryocytes by these 3D ECM cages depends on dynamic remodeling processes. Inhibition of ECM proteolysis results in denser cage formation, increasing the frequence of immature megakaryocytes with impaired demarcation membrane system (DMS) development. Thus, the ECM cage represents a novel concept of an active and dynamic 3D microenvironment that is continuously remodeled and essential for maintaining megakaryocyte perivascular positioning. This specific microarchitecture guides megakaryocyte maturation and intravasation, underscoring the critical role of ECM microarchitecture and dynamics in megakaryocyte function.Key PointsMegakaryocytes form a three-dimensional (3D) cage composed of laminin and collagen IV connected to the basement membrane surrounding them. This microarchitecture stabilizes megakaryocytes within their vascular niche.β1/β3 integrins and MMP are key ECM cage regulators that assist megakaryocyte maturation and intravasation at the bone marrow-blood interface.
Irregular light schedules induce alterations on daily rhythms and gene expression in mice
Authors: Berbegal-Sáez Paula , Gallego-Landin Ines , Macía Javier , Valverde Olga 
Published: October 2024

ABSTRACTSynchronization of internal biological rhythms with external light-dark cycles is crucial for proper function and survival of the organisms, however modern life often imposes irregular light exposure, disrupting these internal clocks. This study investigated the effects of short-term shifted light-dark cycles on mice rhythmicity, and whether these alterations trigger molecular or behavioral changes. We evaluated locomotor activity, different behavioral domains and gene expression in the hypothalamus and medial prefrontal cortex. Despite non prominent behavioral impairments, such as anxiety or cognitive deficits, we observed a notable simplification in the locomotor activity patterns of the mice subjected to disrupted light-dark cycles. Molecular alterations included dysregulations in oscillations of core clock genes (Cry2,Per2) and disruptions in expression of genes involved in neuroplasticity, motivation, and stress responses, includingGluA1,Crhr2, andVipin both studied brain areas. Our study reveals that even brief light cycle shifts can disrupt circadian regulation at the molecular level, despite minimal behavioral changes. This molecular-behavioral discrepancy may suggest a complex adaptive response to drastic short-term light perturbations. Understanding the complex interplay between external light cues and internal biological rhythms regulation is crucial for mitigating the negative consequences of irregular light exposure on physiological processes and overall well-being.
Hypomorphic NOTCH1 Expression Alters Cardiomyocyte Cellular Architecture in Hypoplastic Left Heart Syndrome
Authors: Lewis Jordann , Lear Travis B. , Schlegel Brent , Woods Dominic , Rao Krithika , Sentis Amy , Tan Jay , Jagannathan Rajaganapathi , Javed Zaineb , Boudreau Aine N. , Nelson Timothy , Moulik Mousumi , Hempel Nadine , Chen Bill B. , Shiva Sruti , Rajasundaram Dhivyaa , Finkel Toren , Saraf Anita 
Published: October 2024

SummaryNOTCH1 is a protein involved in cardiac development and mutations in NOTCH1 are implicated in left sided congenital heart disease, including hypoplastic left heart syndrome (HLHS). Therapeutic advances for HLHS patients have been hampered by the absence of suitable experimental models. Here, using human induced pluripotent stem cells (hiPSCs), we have generated a series of CRISPR-edited complex heterozygous hypomorphic mutations in NOTCH1 that recapitulate mutations seen in HLHS patients. These cells demonstrate the downregulation of genes associated with mitochondria, the actin cytoskeleton, and cardiomyocyte development. In addition, these hypomorphic NOTCH1 hiPSCs cells showed an increased propensity to differentiate towards non-cardiomyocyte lineages such as fibroblasts and smooth muscle cells, a finding confirmed in HLHS patient-derived myocardial tissue. Abnormalities in sarcomeric and mitochondrial architecture contributed to decreased ATP production, abnormal calcium transients, and reduced contractility. Using a split nano-luciferase system as a NOTCH1 intracellular reporter, we screened a library of FDA-approved compounds. Auranofin, an agent currently employed for rheumatoid arthritis, was identified as a candidate drug that could rescue impaired differentiation and contractility seen in the hypomorphic NOTCH1 model. These findings point to cell-autonomous abnormalities in hypomorphic NOTCH1 pre-cardiomyocyte cells that can be leveraged to identify potential therapeutic strategies for patients with severe congenital cardiac abnormalities.Highlights:CRISPR edited and patient-derived iPSCs with hypomorphic NOTCH1 expression were used to characterize a cell-based model of hypoplastic left heart syndrome.Hypomorphic NOTCH1 iPSCs have abnormalities in pathways associated with mitochondrial function, actin cytoskeleton, and cardiomyocyte development.Hypomorphic NOTCH1 iPSCs have less pluripotency and tend to skew differentiation away from cardiomyocytes and towards fibroblasts and smooth muscle cells.NOTCH1 is required for cardiac cytoskeletal and mitochondrial architecture, and to preserve contractility and ATP production.A high-throughput drug screen identified auranofin as an agent that may benefit patients with hypoplastic left heart syndrome.
The Plasmodium falciparum NCR1 membrane protein is a novel antimalarial target that exports cholesterol to maintain membrane homeostasis
Authors: Zhang Zhemin , Lyu Meinan , Han Xu , Bandara Sepalika , Cui Meng , Istvan Eva S. , Geng Xinran , Tringides Marios L. , Gregor William D. , Miyagi Masaru , Oberstaller Jenna , Adams John H. , Zhang Youwei , Nieman Marvin T. , von Lintig Johannes , Goldberg Daniel E. , Yu Edward W. 
Published: October 2024

AbstractMalaria is an extremely devastating parasitic infection that kills over half a million people each year. It is the leading cause of death in many developing countries, in part, due to a lack of resources and readily available therapeutics. Unfortunately, the most prevalent and deadliest causative agent of malaria,Plasmodium falciparum, has developed resistance to nearly all currently available antimalarial drugs. TheP. falciparumNiemann-Pick Type C1-related (PfNCR1) transporter has been identified as a druggable target, as it is required for membrane homeostasis of the parasite. However, the structure and detailed molecular mechanism of this membrane protein are not yet available. Here we present three structures of PfNCR1 both in the absence and presence of the functional inhibitor MMV009108 at resolutions between 2.98 Å and 3.81 Å using single-particle cryo-electron microscopy (cryo-EM). The data suggest that PfNCR1 binds cholesterol and forms a cholesterol transport tunnel to modulate the composition of the parasite plasma membrane. Cholesterol efflux assays substantiate this as they show that PfNCR1 is an exporter capable of extruding cholesterol from the membrane. Additionally, the inhibition mechanism of MMV009108 appears to be due to a direct blockage of PfNCR1, preventing this transporter from shuttling cholesterol.