bluuebunny/crossref_metadata_2025_split huggingface dataset:
Induction andin silicostaging of human gastruloids with neural tube, segmented somites & advanced cell types
Authors: Hamazaki Nobuhiko , Yang Wei , Kubo Connor , Qiu Chengxiang , Martin Beth K. , Garge Riddhiman K. , Regalado Samuel G. , Nichols Eva , Lee Choli , Daza Riza M. , Srivatsan Sanjay , Shendure Jay 
Published: February 2024

ABSTRACTEmbryonic organoids are emerging as powerful models for studying early mammalian development. For example, stem cell-derived ‘gastruloids’ form elongating structures containing all three germ layers1–4. However, although elongated, human gastruloids do not morphologically resemble post-implantation embryos. Here we show that a specific, discontinuous regimen of retinoic acid (RA) robustly induces human gastruloids with embryo-like morphological structures, including a neural tube and segmented somites. Single cell RNA-seq (sc-RNA-seq) further reveals that these human ‘RA-gastruloids’ contain more advanced cell types than conventional gastruloids, including neural crest cells, renal progenitor cells, skeletal muscle cells, and, rarely, neural progenitor cells. We apply a new approach to computationally stage human RA-gastruloids relative to somite-resolved mouse embryos, early human embryos and other gastruloid models, and find that the developmental stage of human RA-gastruloids is comparable to that of E9.5 mouse embryos, although some cell types show greater or lesser progression. We chemically perturb WNT and BMP signaling in human RA-gastruloids and find that these signaling pathways regulate somite patterning and neural tube length, respectively, while genetic perturbation of the transcription factors PAX3 and TBX6 markedly compromises the formation of neural crest and somites/renal cells, respectively. Human RA-gastruloids complement other embryonic organoids in serving as a simple, robust and screenable model for decoding early human embryogenesis.
Structure-based design of a soluble human cytomegalovirus glycoprotein B antigen stabilized in a prefusion-like conformation
Authors: Sponholtz Madeline R. , Byrne Patrick O. , Lee Alison G. , Ramamohan Ajit R. , Goldsmith Jory A. , McCool Ryan S. , Zhou Ling , Johnson Nicole V. , Hsieh Ching-Lin , Connors Megan , Karthigeyan Krithika , Campbell John D. , Permar Sallie R. , Maynard Jennifer A. , Yu Dong , Bottomley Matthew J. , McLellan Jason S. 
Published: February 2024

AbstractHuman cytomegalovirus (HCMV) glycoprotein B (gB) is a class III membrane fusion protein required for viral entry. HCMV vaccine candidates containing gB have demonstrated moderate clinical efficacy, but no HCMV vaccine has been FDA-approved. Here, we used structure-based design to identify and characterize amino acid substitutions that stabilize gB in its metastable prefusion conformation. One variant containing two engineered interprotomer disulfide bonds and two cavity-filling substitutions (gB-C7), displayed increased expression and thermostability. A 2.8 Å resolution cryo-electron microscopy structure shows that gB-C7 adopts a prefusion-like conformation, revealing additional structural elements at the membrane-distal apex. Unlike previous observations for several class I viral fusion proteins, mice immunized with postfusion or prefusion-stabilized forms of soluble gB protein displayed similar neutralizing antibody titers, here specifically against an HCMV laboratory strain on fibroblasts. Collectively, these results identify initial strategies to stabilize class III viral fusion proteins and provide tools to probe gB-directed antibody responses.TeaserA structure-based design campaign leads to stabilization of the class III viral fusion protein from HCMV in a prefusion-like conformation.
Microtubule forces drive nuclear damage inLMNAcardiomyopathy
Authors: Amiad Pavlov Daria , Heffler Julie , Suay-Corredera Carmen , Dehghany Mohammad , Shen Kaitlyn M. , Zuela-Sopilniak Noam , Randell Rani , Uchida Keita , Jain Rajan , Shenoy Vivek , Lammerding Jan , Prosser Benjamin 
Published: February 2024

AbstractNuclear homeostasis requires a balance of forces between the cytoskeleton and nucleus. Mutations in theLMNAgene, which encodes the nuclear envelope proteins lamin A/C, disrupt this balance by weakening the nuclear lamina. This results in nuclear damage in contractile tissues and ultimately muscle disease. Intriguingly, disrupting the LINC complex that connects the cytoskeleton to the nucleus has emerged as a promising strategy to ameliorateLMNA-associated cardiomyopathy. Yet how LINC complex disruption protects the cardiomyocyte nucleus remains unclear. To address this, we developed an assay to quantify the coupling of cardiomyocyte contraction to nuclear deformation and interrogated its dependence on the nuclear lamina and LINC complex. We found that, surprisingly, the LINC complex was mostly dispensable for transferring contractile strain to the nucleus, and that increased nuclear strain in lamin A/C-deficient cardiomyocytes was not rescued by LINC complex disruption. Instead, LINC complex disruption eliminated the cage of microtubules encircling the nucleus. Disrupting microtubules was sufficient to prevent nuclear damage and rescue cardiac function induced by lamin A/C deficiency. We computationally simulated the stress fields surrounding cardiomyocyte nuclei and show how microtubule forces generate local vulnerabilities that damage lamin A/C-deficient nuclei. Our work pinpoints localized, microtubule-dependent force transmission through the LINC complex as a pathological driver and therapeutic target forLMNA-cardiomyopathy.Graphical abstract
Characterisation of RNA editing and gene therapy with a compact CRISPR-Cas13 in the retina
Authors: Kumar Satheesh , Hsiao Yi-Wen , Wong Vickie H Y , Aubin Deborah , Wang Jiang-Hui , Lisowski Leszek , Rakoczy Elizabeth P , Li Fan , Alarcon-Martinez Luis , Gonzalez-Cordero Anai , Bui Bang V , Liu Guei-Sheung 
Published: February 2024

AbstractCRISPR-Cas13 nucleases are programmable RNA-targeting effectors that can silence gene expression in a reversible manner. Recent iterations of Cas13 nucleases are compact for adeno-associated virus (AAV) delivery to achieve strong and persistent expression in various organs in a safe manner. Here, we report significant transcriptomic signatures of Cas13bt3 expression in retinal cells and show all-in-one AAV gene therapy with Cas13bt3 can effectively silenceVEGFAmRNA in human retinal organoids and humanisedVEGFtransgenic mouse (trVEGF029, Kimba) models. Specifically, human embryonic stem cells (hESC)-derived retinal pigment epithelium cells show high expression of Cas13bt3 from virus delivery corresponding to a significant reduction ofVEGFAmRNA. We further show that intravitreal delivery of Cas13bt3 can transduce mouse retinal cells efficiently, reaching the photoreceptors for specific knockdown of humanVEGFAin the Kimba mouse. Our results reveal important considerations for assessing Cas13 activity and establish Cas13bt3 as a potential anti-VEGF agent that can achieve long-term control of VEGFA for the treatment of retinal neovascularization.
A Predictive Model: The Key to Success for Badminton Servers and Receivers
Authors: Liu Cheng 
Published: February 2024

ABSTRACTTo explore the influence of technical actions on badminton competition outcomes, this study analyzes the frequency and impact of specific movements made by players, distinguishing between the server and receiver roles. Focusing on international competitions from 2019 to 2023, we collected data on 23 distinct technical actions (e.g., Net Front, Slice/Drop, Push) to construct a predictive model. The study distinguishes itself by employing a Random Forest algorithm to ascertain the significance of each technical action, utilizing forward stepwise selection and 5-fold cross-validation for feature refinement. SHAP value analysis further validated the pivotal roles of ‘Net Front’, ‘Slice/Drop’, and ‘Push’ across both sexes, linking higher frequencies of ‘Net Front’ with increased match-winning probabilities. Model validation on a test set demonstrated effective performance in both sexes, with the model based on male data exhibiting higher accuracy and predictive values, surpassing the performance of the female data model. This comprehensive examination, grounded in quantitative analysis, not only enhances our understanding of badminton gameplay dynamics but also offers valuable insights for coaching strategies and training methodologies.
Identification Drug Targets for Oxaliplatin-Induced Cardiotoxicity without Affecting Cancer Treatment through Inter Variability Cross-Correlation Analysis (IVCCA)
Authors: Du Junwei , Sudlow Leland C. , Biswas Hridoy , Mitchell Joshua D. , Mollah Shamim , Berezin Mikhail Y. 
Published: February 2024

ABSTRACTThe successful treatment of side effects of chemotherapy faces two major limitations: the need to avoid interfering with pathways essential for the cancer-destroying effects of the chemotherapy drug, and the need to avoid helping tumor progression through cancer promoting cellular pathways. To address these questions and identify new pathways and targets that satisfy these limitations, we have developed the bioinformatics tool Inter Variability Cross-Correlation Analysis (IVCCA). This tool calculates the cross-correlation of differentially expressed genes, analyzes their clusters, and compares them across a vast number of known pathways to identify the most relevant target(s). To demonstrate the utility of IVCCA, we applied this platform to RNA-seq data obtained from the hearts of the animal models with oxaliplatin-induced CTX. RNA-seq of the heart tissue from oxaliplatin treated mice identified 1744 differentially expressed genes with False Discovery Rate (FDR) less than 0.05 and fold change above 1.5 across nine samples. We compared the results against traditional gene enrichment analysis methods, revealing that IVCCA identified additional pathways potentially involved in CTX beyond those detected by conventional approaches. The newly identified pathways such as energy metabolism and several others represent promising target for therapeutic intervention against CTX, while preserving the efficacy of the chemotherapy treatment and avoiding tumor proliferation. Targeting these pathways is expected to mitigate the damaging effects of chemotherapy on cardiac tissues and improve patient outcomes by reducing the incidence of heart failure and other cardiovascular complications, ultimately enabling patients to complete their full course of chemotherapy with improved quality of life and survival rates.
An Organism-Level Quantitative Flux Model of Energy Metabolism in Mice
Authors: Yuan Bo , Doxsey Will , Tok Özlem , Kwon Young Yon , Inouye Karen E. , Hotamışlıgil Gökhan S. , Hui Sheng 
Published: February 2024

SummaryMammalian tissues feed on nutrients in the blood circulation. At the organism-level, mammalian energy metabolism comprises of oxidation, storage, interconverting, and releasing of circulating nutrients. Though much is known about the individual processes and nutrients, a holistic and quantitative model describing these processes for all major circulating nutrients is lacking. Here, by integrating isotope tracer infusion, mass spectrometry, and isotope gas analyzer measurement, we developed a framework to systematically quantify fluxes through these metabolic processes for 10 major circulating energy nutrients in mice, resulting in an organism-level quantitative flux model of energy metabolism. This model revealed in wildtype mice that circulating nutrients have more dominant metabolic cycling fluxes than their oxidation fluxes, with distinct partition between cycling and oxidation flux for individual circulating nutrients. Applications of this framework in obese mouse models showed on a per animal basis extensive elevation of metabolic cycling fluxes in ob/ob mice, but not in diet-induced obese mice. Thus, our framework describes quantitatively the functioning of energy metabolism at the organism-level, valuable for revealing new features of energy metabolism in physiological and disease conditions.HighlightsA flux model of energy metabolism integrating13C labeling of metabolites and CO2Circulating nutrients have characteristic partition between oxidation and storageCirculating nutrients’ total cycling flux outweighs their total oxidation fluxCycling fluxes are extensively elevated in ob/ob but not in diet-induced obese miceGraphical Abstract
Whole-Plant Physiological Identification and Quantification of Disease Progression
Authors: Friedman Shani , Dalal Ahan , Batat Dor , Burdman Saul , Sela Yheonatan , Hipsch Matanel , Rosenwaser Shilo , Hadad Evgeniya Marcos , Covo Shay , Moshelion Menachem 
Published: February 2024

SummaryVisual estimates of plant symptoms are traditionally used to quantify disease severity. Yet, the methodologies used to assess these phenotypes are often subjective and do not allow for tracking the disease’s progression from very early stages. Here, we hypothesized that quantitative analysis of whole-plant physiological vital functions can be used to objectively determine plant health, providing a more sensitive way to detect disease.We studied the tomato wilt that is caused byFusarium oxysporumf. sp.lycopersici(Fol). Physiological performance of infected and non-infected tomato plants was compared using a whole-plant lysimeter functional-phenotyping system. Water-balance traits of the plants were measured continuously and simultaneously in a quantitative manner.Infected plants exhibited early reductions in transpiration and biomass gain, which preceded visual disease symptoms. These changes in transpiration proved to be effective quantitative indicators for assessing both the plant’s susceptibility to infection and the virulence of the fungus. Physiological changes linked to fungal outgrowth and toxin release contributed to reduced hydraulic conductance during initial infection stages.The functional-phenotyping method objectively captures early-stage disease progression, advancing plant disease research and management. This approach emphasizes the potential of quantitative whole-plant physiological analysis over traditional visual estimates for understanding and detecting plant diseases.
Functional dynamics and selectivity of two parallel corticocortical pathways from motor cortex to layer 5 circuits in somatosensory cortex
Authors: Kim Hye-Hyun , Bonekamp Kelly E. , Gillie Grant R. , Autio Dawn M. , Keller Tryton , Crandall Shane R. 
Published: February 2024

ABSTRACTIn the rodent whisker system, active sensing and sensorimotor integration are mediated in part by the dynamic interactions between the motor cortex (M1) and somatosensory cortex (S1). However, understanding these dynamic interactions requires knowledge about the synapses and how specific neurons respond to their input. Here, we combined optogenetics, retrograde labeling, and electrophysiology to characterize the synaptic connections between M1 and layer 5 (L5) intratelencephalic (IT) and pyramidal tract (PT) neurons in S1 of mice (both sexes). We found that M1 synapses onto IT cells displayed modest short-term depression, whereas synapses onto PT neurons showed robust short-term facilitation. Despite M1 inputs to IT cells depressing, their slower kinetics resulted in summation and a response that increased during short trains. In contrast, summation was minimal in PT neurons due to the fast time course of their M1 responses. The functional consequences of this reduced summation, however, were outweighed by the strong facilitation at these M1 synapses, resulting in larger response amplitudes in PT neurons than IT cells during repetitive stimulation. To understand the impact of facilitating M1 inputs on PT output, we paired trains of inputs with single backpropagating action potentials, finding that repetitive M1 activation increased the probability of bursts in PT cells without impacting the time-dependence of this coupling. Thus, there are two parallel but dynamically distinct systems of M1 synaptic excitation in L5 of S1, each defined by the short-term dynamics of its synapses, the class of postsynaptic neurons, and how the neurons respond to those inputs.SIGNIFICANCE STATEMENTNormal sensorimotor integration depends in part on the dynamic interactions between the primary motor cortex and the somatosensory cortex, but the functional properties of the excitatory synapses interconnecting the motor cortex with the somatosensory cortex are poorly understood. Our results show that the short-term dynamics of excitatory motor cortex synapses and the nature of the postsynaptic response they generate onto layer 5 pyramidal neurons in the somatosensory cortex depend on the postsynaptic cell type and if their axons project to other cortical areas or subcortical regions. These two parallel but dynamically distinct channels of synaptic excitation constitute previously unknown synaptic circuits by which different temporal patterns of motor cortex activity can shape how signals propagate out of the somatosensory cortex.
Whole-Genome Sequencing of aJanthinobacterium sp. Isolated from the Patagonian Desert
Authors: Cavanaugh Nicole T , Kumar Girish , Reverdy Pearson Alicyn , Colbert Julia , Riquelme Carlos , Hudson André O , Chai Yunrong , Godoy-Carter Veronica 
Published: February 2024

AbstractJanthinobacteriumis a genus of Gram-negative environmental bacteria that survive extreme conditions by forming biofilms and producing pigments.Janthinobacteriumsp. LS2A, an extremophile isolated from soil in the Chilean Patagonia, contains seven known biosynthetic gene clusters, including the purple pigment violacein, which may aid in its survival in harsh environments.
HiCrayon reveals distinct layers of multi-state 3D chromatin organization
Authors: Nolan Ben , Harris Hannah L. , Kalluchi Achyuth , Reznicek Timothy E. , Cummings Christopher T. , Rowley M. Jordan 
Published: February 2024

AbstractThe co-visualization of chromatin conformation with 1D ‘omics data is key to the multi-omics driven data analysis of 3D genome organization. Chromatin contact maps are often shown as 2D heatmaps and visually compared to 1D genomic data by simple juxtaposition. While common, this strategy is imprecise, placing the onus on the reader to align features with each other. To remedy this, we developed HiCrayon, an interactive tool that facilitates the integration of 3D chromatin organization maps and 1D datasets. This visualization method integrates data from genomic assays directly into the chromatin contact map by coloring interactions according to 1D signal. HiCrayon is implemented using R shiny and python to create a graphical user interface (GUI) application, available in both web or containerized format to promote accessibility. HiCrayon is implemented in R, and includes a graphical user interface (GUI), as well as a slimmed-down web-based version that lets users quickly produce publication-ready images. We demonstrate the utility of HiCrayon in visualizing the effectiveness of compartment calling and the relationship between ChIP-seq and various features of chromatin organization. We also demonstrate the improved visualization of other 3D genomic phenomena, such as differences between loops associated with CTCF/cohesin vs. those associated with H3K27ac. We then demonstrate HiCrayon’s visualization of organizational changes that occur during differentiation and use HiCrayon to detect compartment patterns that cannot be assigned to either A or B compartments, revealing a distinct 3rd chromatin compartment. Overall, we demonstrate the utility of co-visualizing 2D chromatin conformation with 1D genomic signals within the same matrix to reveal fundamental aspects of genome organization.Local version:https://github.com/JRowleyLab/HiCrayonWeb version:https://jrowleylab.com/HiCrayon
Prevalence and Associated Risk Factors of Bovine Trypanosomosis in Diga District, Western Ethiopia
Authors: Gessese Abebe Tesfaye , Yadesa Gemechis 
Published: February 2024

ABSTRACTTrypanosomosis is a protozoal disease caused by different species of unicellular parasites found in the blood and other tissues of vertebrates including livestock, wildlife, and people. It is the most serious animal production problem in sub-Saharan Africa including Ethiopia. The present study was conducted to assess the prevalence of bovine trypanosomosis and prevailing species of Tyrpanosomes in Diga district and to identify host related risk factors for trypanosomosis prevalence in Western Ethiopia. Blood samples were collected from 384 randomly selected indigenous cattle (Bos indicus) and analyzed using parasitological and hematological techniques. Out of the 384 animals examined 22 (5.73%) were found trypanosomosis positive. Of which 11 (2.87%) were infected withT. vivax, 9 (2.34%) withT. congolenseand 2 (0.52%) with mixed infection ofT. vivaxandT. congolense. This difference in trypanosomes species prevalence was not statistically significant (P>0.05). The association of prevalence with the various risk factors including kebele, age, sex, body condition and coat color were measured. There was a significant variation in the prevalence of trypanosomosis (P<0.05) among cattles with different body conditions, poor body conditioned animals with the highest prevalence followed by medium and good body condition animals, respectively. There was no any statistically significant difference in other variables considered. The overall Packed Cell Volume (PCV) mean PCV value of 25.67 was recorded during the study period. The mean PCV value of infected animals was lower (20.18) than that of non-infected animals (26.0). The difference was statistically significant (P<0.05). The result of the present study indicated the prevailing occurrence of trypanosomosis in the study area necessitating integrated control measures.
Cytotoxicity and resistance evolution of a novel antifungal carbon nanoparticle
Authors: Poudel Sharma Sijan , Paudyal Suraj , Domena Justin , Zhou Yiqun , Cleven Elliot , Agatemor Christian , Van Dyken J. David , Leblanc Roger 
Published: February 2024

AbstractAntifungal drug resistance is a major problem in healthcare and agriculture. Synthesizing new drugs is one of the major mitigating strategies for overcoming this problem. In this context, carbon-dots (CDs) are a newer category of nanoparticles that have wide applications, potentially including use as antibiotics. However, there is a lack of understanding of the effect of long-term use of CDs as antimicrobials, particularly the ability of microbes to evolve resistance to antibiotic CDs. In this study, we synthesized novel florescent the bottom-up method using two antifungal drugs fluconazole and nourseothricin sulphate (ClonNAT). We first extensively characterized the physical properties of the newly synthesized carbon dots, Flu-Clo CDs. We measured the cytotoxicity of Flu-Clo CDs on budding yeastSaccharomyces cerevisiaeand determined that it had comparable antifungal inhibition with extensively used drug fluconazole. Furthermore, we demonstrate that Flu-CLO CDs are not cytotoxic to human fibroblasts cell lines. Then, we quantified the ability of yeast to evolve resistance to Flu-Clo CDs. We evolved replicate laboratory yeast populations for 250 generations in the presence of Flu-Clo CDs or aqueous fluconazole. We found that yeast evolved resistance to Flu-Clo CDs and aqueous fluconazole at similar rates. Further, we found that resistance to Flu-Clo CDs conferred cross-resistance to aqueous fluconazole. Overall, the results demonstrate the efficacy of CDs as potential antifungal drugs. We can conclude that yeast populations can adapt quickly to novel antibiotics including CD based antibiotics, including CD-based antibiotics indicating the importance of proper use of antimicrobials in combating infections.