bluuebunny/crossref_metadata_2025 huggingface dataset:
Contrasting patterns of differentiation among three taxa of the rapidly diversifying orchid genusOphryssect.Insectifera(Orchidaceae) where their range overlap
Authors: Salvado Pascaline , Gibert Anaïs , Schatz Bertrand , Vandenabeele Lucas , Buscail Roselyne , Vilasís David , Feldmann Philippe , Bertrand Joris A. M.
Published: April 2024

In rapidly diversifying groups, taxa defined on the basis of typological criteria can be difficult to support with genetic data. The diversity observed in the insect-mimicking orchid genusOphrysperfectly illustrates this situation; among 400 described species only 9-10 lineages are detectable by genetic markers such as nrITS. The three taxa described in theOphrys insectiferagroup:O. insectifera,O. subinsectiferaandO. aymoninii, can be clearly distinguished by their flowers, which have evolved different phenotypes as a result of adaptation to specific pollinator insect species from three different families. However, genetic differentiation between these three taxa has never been really supported by population genetic data and their taxonomic status is still debated. Using population genomic approaches, we found a clustering consistent with the existence of three genetic entities where the geographic distributions of the three taxa overlap. Two of these clusters correspond to France populations of the widespreadO. insectiferaand the micro-endemicO. aymoninii. However, the last cluster grouped together all the Iberian individuals, suggesting that individuals phenotypically identified as eitherO. insectiferaorO. subinsectiferaare genetically weakly differentiated there. Populations of the two pairs of taxa thus may have experienced different patterns of inter-specific gene flow.
Sperm derived H2AK119ub1 is required for embryonic development inXenopus laevis
Authors: Francois--Campion Valentin , Berger Florian , Oikawa Mami , Goumeidane Maissa , Mouniée Nolwenn , Chenouard Vanessa , Petrova Kseniya , Abreu Jose G , Fourgeux Cynthia , Poschmann Jeremie , Peshkin Leonid , Gibeaux Romain , Jullien Jérôme
Published: April 2024

Deposition of H2AK119ub1 by the polycomb repressive complexe-1 plays a key role in the initiation of facultative heterochromatin formation in somatic cells. Here we evaluate the contribution of sperm derived H2AK119ub1 to embryo development. InXenopus laeviswe found that H2AK119ub1 is present during spermiogenesis and into early embryonic development, highlighting its credential for a role in the transmission of epigenetic information from the sperm to the embryo.In vitrotreatment of sperm with USP21, a H2AK119ub1 deubiquitylase, just prior to injection to egg, results in developmental defects associated with gene upregulation. Sperm H2AK119ub1 editing disrupts egg factor mediated paternal chromatin remodelling processes. It leads to post-replication accumulation of H2AK119ub1 on repeat element of the genome instead of CpG islands. This shift in post-replication H2AK119ub1 distribution triggered by sperm epigenome editing entails a loss of H2AK119ub1 from genes misregulated in embryos derived from USP21 treated sperm. We conclude that sperm derived H2AK119ub1 instructs egg factor mediated epigenetic remodelling of paternal chromatin and is required for embryonic development.
Effect of seizures on the severity of myelin vacuolization in a mouse model of megalencephalic leukoencephalopathy with subcortical cysts
Authors: Brouwers Eelke , Breur Marjolein , Jorge Maria Susana , Mansvelder Huibert D. , van der Knaap Marjo S. , Bugiani Marianna , Min Rogier
Published: April 2024

Objective

Megalencephalic leukoencephalopathy with subcortical cysts (MLC) is a white matter disease characterized by myelin vacuolization and swollen perivascular astrocyte processes. Neuronal activity has been implicated as primary cause of myelin vacuolization and astrocyte swelling. Since acute and excessive increases in neuronal activity occur in MLC during seizures, we investigated whether seizure activity leads to the acute development of myelin vacuoles and swollen astrocyte processes.

Methods

Glialcam-null mice (an established MLC mouse model) and wild-type mice received repeated i.p. low dose (5 mg / kg) kainic acid (KA) injections until severe seizures developed. Following a 60-minute period of severe seizure activity, mice were terminated and brains were fixed and processed. Brain tissue was analyzed for myelin vacuolization and astrocyte process thickness using H&E and GFAP stains, respectively.

Results

Repeated low-dose injections of KA resulted in prolonged severe seizure activity in mice of both genotypes. Total amount of seizure activity was comparable betweenGlialcam-null and wild-type mice. KA-induced severe seizure activity did not significantly increase myelin vacuolization in eitherGlialcam-null or wild-type mice. The width of perivascular astrocyte processes was also not affected by severe seizure activity.

Interpretation

We show that (i) repeatedly injecting a low dose of KA provides the opportunity to regulate seizure development and generate severe seizures in both wild-type and seizure-sensitiveGlialcam-null mice, and that (ii) the two major pathological features of MLC, myelin vacuolization and swollen astrocyte endfeet, are not acutely aggravated in response to KA-induced severe seizure activity.
Graph Contrastive Learning as a Versatile Foundation for Advanced scRNA-seq Data Analysis
Authors: Zhang Zhenhao , Liu Yuxi , Xiao Meichen , Wang Kun , Huang Yu , Bian Jiang , Yang Ruolin , Li Fuyi
Published: April 2024

Single-cell RNA sequencing (scRNA-seq) offers unprecedented insights into transcriptome-wide gene expression at the single-cell level. Cell clustering has been long established in the analysis of scRNA-seq data to identify the groups of cells with similar expression profiles. However, cell clustering is technically challenging, as raw scRNA-seq data have various analytical issues, including high dimensionality and dropout values. Existing research has developed deep learning models, such as graph machine learning models and contrastive learning-based models, for cell clustering using scRNA-seq data and has summarized the unsupervised learning of cell clustering into a human-interpretable format. While advances in cell clustering have been profound, we are no closer to finding a simple yet effective framework for learning high-quality representations necessary for robust clustering. In this study, we propose scSimGCL, a novel framework based on the graph contrastive learning paradigm for self-supervised pretraining of graph neural networks. This framework facilitates the generation of high-quality representations crucial for cell clustering. Our scSimGCL incorporates cell-cell graph structure and contrastive learning to enhance the performance of cell clustering. Extensive experimental results on simulated and real scRNA-seq datasets suggest the superiority of the proposed scSimGCL. Moreover, clustering assignment analysis confirms the general applicability of scSimGCL, including state-of-the-art clustering algorithms. Further, ablation study and hyperparameter analysis suggest the efficacy of our network architecture with the robustness of decisions in the self-supervised learning setting. The proposed scSimGCL can serve as a robust framework for practitioners developing tools for cell clustering. The source code of scSimGCL is publicly available athttps://github.com/zhangzh1328/scSimGCL.
Efficacy of foramen magnum decompression with and without cranioplasty in a rat model of Chiari-like malformation
Authors: Jung Jae-Hwan , Cho Chang-Hyeon , Kim Woo-Suk , Yoon Hun-Young
Published: April 2024

In veterinary medicine, canine Chiari-like malformation (CLM) disease is surgically managed through foramen magnum decompression (FMD) with cranioplasty. This study aimed to assess the efficacy of cranioplasty surgery by establishing a rat CLM model and then applying FMD with and without cranioplasty and comparing the outcomes. Twenty-four 8-week-old male Sprague‒Dawley rats underwent surgery to induce CLM by reducing the caudal cranial fossa volume, mimicking cerebellum herniation. The rats were randomly and equally assigned to three groups: a control group (induced CLM), an FO group (induced CLM rats undergoing FMD only), and a CR group (induced CLM rats undergoing FMD with cranioplasty). At 11 weeks of age, the FO and CR groups underwent FMD surgery. Four weeks later, magnetic resonance imaging (MRI) was used to measure the cisterna magna volume to assess surgical outcomes. Post-surgery MRI revealed that the mean cisterna magna volume was 23.82 ± 1.70, 34.88 ± 4.39, and 29.48 ± 2.20 mm3in the control, FO, and CR groups, respectively. There was a significant increase in the cisterna magna volume in the FO and CR groups compared to that in the control group (p < 0.05), with the FO group showing a significantly greater increase than the CR group (p < 0.05). These findings suggest that FMD surgery alone is more effective at restoring the cisterna magna volume than FMD surgery with cranioplasty. FMD surgery alone resulted in a greater increase in cisterna magna volume than FMD with cranioplasty in our rat CLM model, suggesting that FMD alone may be more effective to treat canine CLM. These findings challenge the typical approach of combining FMD with cranioplasty in treating canine CLM disease and underscore the need for further investigation into optimizing surgical techniques for CLM.
Hair follicles modulate skin barrier function
Authors: Ford Noah C. , Benedeck Rachel E. , Mattoon Matthew T. , Peterson Jamie K. , Mesler Arlee L. , Veniaminova Natalia A. , Gardon Danielle J. , Tsai Shih-Ying , Uchida Yoshikazu , Wong Sunny Y.
Published: April 2024

Our skin provides a protective barrier that shields us from our environment. Barrier function is typically associated with interfollicular epidermis; however, whether hair follicles influence this process remains unclear. Here, we utilize a potent genetic tool to probe barrier function by conditionally ablating a quintessential epidermal barrier gene,Abca12, which is mutated in the most severe skin barrier disease, harlequin ichthyosis. With this tool, we deduced 4 ways by which hair follicles modulate skin barrier function. First, the upper hair follicle (uHF) forms a functioning barrier. Second, barrier disruption in the uHF elicits non-cell autonomous responses in the epidermis. Third, deletingAbca12in the uHF impairs desquamation and blocks sebum release. Finally, barrier perturbation causes uHF cells to move into the epidermis. Neutralizing Il17a, whose expression is enriched in the uHF, partially alleviated some disease phenotypes. Altogether, our findings implicate hair follicles as multi-faceted regulators of skin barrier function.
A chance insight into the mechanism of phosgene toxicity
Authors: Daplan Ekin , Turin Luca
Published: April 2024

It has long been known that phosgene, a deadly war gas and industrial reagent, causes intense oxidative stress, but how it does so remains unclear. Here we report an accidental discovery: electron spin resonance spectroscopy (ESR) of live fruit flies reveals that phosgene exposure results in a distinctive manganese (II) hyperfine spectrum. The Mn(II) signal correlates with mitochondrial SOD2 expression. We suggest that phosgene acylates a highly conserved SOD2 active site tyrosine. This prevents the Mn redox cycling between ESR-silent Mn(III) and ESR-active Mn(II) that is required for superoxide dismutation. We propose that mitochondrial SOD2 inactivation is responsible for phosgene toxicity.
Mathematical modeling unveils the timeline of CAR-T cell therapy and macrophage-mediated cytokine release syndrome
Authors: Santurio Daniela S. , Barros Luciana R. C. , Glauche Ingmar , Fassoni Artur C.
Published: April 2024

Chimeric antigen receptor (CAR)-T cell therapy holds significant potential for cancer treatment, although disease relapse and cytokine release syndrome (CRS) remain as frequent clinical challenges. To better understand the mechanisms underlying the temporal dynamics of CAR-T cell therapy response and CRS, we developed a novel multi-layer mathematical model incorporating antigen-mediated CAR-T cell expansion, antigen-negative resistance, and macrophage-associated cytokine release. Three key mechanisms of macrophage activation are considered: release of damage-associated molecular patterns, antigen-binding mediated activation, and CD40-CD40L contact. The model accurately describes 25 patient time courses with different responses and IL-6 cytokine kinetics. We successfully link the dynamic shape of the response to interpretable model parameters and investigate the influence of CAR-T cell dose and initial tumor burden on the occurrence of CRS and treatment outcome. By disentangling the timeline of macrophage activation, the model identified distinct contributions of each activation mechanism, suggesting the CD40-CD40L axis as a major driver of CRS and a clinically feasible target to control the activation process and modulate cytokine peak height. Our multi-layer model provides a comprehensive framework for understanding the complex interactions between CAR-T cells, tumor cells, and macrophages during therapy.
Chemical Coverage of the Human Reactome
Authors: Kwak Haejin Angela , Liu Lihua , Tredup Claudia , Röhm Sandra , Prinos Panagiotis , Böttcher Jark , Schapira Matthieu
Published: April 2024

Chemical probes and chemogenomic compounds are valuable tools to link gene to phenotype, explore human biology and uncover novel targets for precision medicine. A growing federation of scientists is contributing to the mission of Target 2035 – discovering chemical tools for all druggable human proteins by the year 2035. It is expected that these compounds will enable the understanding of the regulation of cellular machineries and biological processes across the compendium of signaling pathways that animate cellular life. Here, we draw a landscape of the current chemical coverage of the human Reactome. We find that even though available chemical probes and chemogenomic compounds are targeting only 3% of the human proteome, they cover 53% of the human Reactome, due to the fact that 46% of human proteins are involved in more than one cellular pathway. As such, existing chemical probes and chemogenomic compounds already represent a versatile toolkit to manipulate a vast portion of human biology. Pathways targeted by existing drugs may be enriched in unknown but valid drug targets and could be prioritized in future Target 2035 efforts.
Fish CDK2 recruits Dtx4 to degrade TBK1 through ubiquitination in the antiviral response
Authors: Lu Long-Feng , Zhang Can , Li Zhuo-Cong , Cui Bao-Jie , Wang Yang-Yang , Han Ke-Jia , Xu Xiao , Zhou Chu-Jing , Zhou Xiao-Yu , Wu Yue , Xu Na , Yang Xiao-Li , Chen Dan-Dan , Li Xi-Yin , Zhou Li , Li Shun
Published: April 2024

Although the classical biological protein cell cycle protein kinase CDK2 has been extensively studied in higher vertebrates, its function in lower vertebrates beyond the regulation of mitosis remains unknown. In this study, we report a distinct mechanism whereby IFN expression is negatively regulated in fish by CDK2. After infection with the spring viremia of carp virus (SVCV), fish CDK2 expression significantly increased in tissues and cells. Moreover, antiviral resistance was improved incdk2−/−homozygotes, and the antiviral cytokine interferon (IFN) expression was significantly higher. At the cellular level, CDK2 overexpression reduced IFN expression, whilecdk2knockdown increased the ability of cells to produce IFN. Subsequently, it was discovered that fish CDK2 binds and degrades TBK1, resulting in reduced IFN. CDK2 increases the K48-linked ubiquitination of TBK1, causing its degradation, while E3 ubiquitin ligase Dtx4 was found to be involved in this process following the significant enhancement of TBK1 K48-linked ubiquitination. Protein mass spectrometry and immunoblot analysis confirmed that the K567 site on TBK1 is essential for CDK2 to engage with Dtx4 and degrade TBK1; thus, after mutating the K567 site, K48-linked ubiquitination of TBK1 was not enhanced by Dtx4, and TBK1 was not degraded by CDK2. Our data demonstrate that fish CDK2 recruits the E3 ubiquitin ligase Dtx4 to target the K567 site of TBK1 and promote its degradation. These results suggest that CDK2 in lower vertebrates is implicated in a specialized role for antiviral innate immunity.
Optimizing biomedical information retrieval with a keyword frequency-driven Prompt Enhancement Strategy
Authors: Aftab Wasim , Apostolou Zivkos , Bouazoune Karim , Straub Tobias
Published: April 2024

Background

Mining the enormous pool of biomedical literature to extract accurate responses and relevant references is a daunting challenge, made more difficult by the domain’s interdisciplinary nature, specialized jargon, and continuous evolution. Early natural language processing (NLP) approaches faced considerable hurdles in comprehending the nuances of natural language which frequently led to false answers. However, the discovery of transformer models has immensely boosted the cause by enabling researchers to create larger and more potent language models known as large language models (LLMs). These LLMs have opened up new possibilities for enhancing question-answering (QA) tasks. Even with these technological advances, the current LLM-based solutions for querying specialized domains like biology and biomedicine still have issues in generating up to date responses while preventing “hallucination” or the generation of plausible but factually incorrect responses.

Results

This paper focuses on prompt enhancement using retrieval-augmented architecture as a strategy to guide LLMs towards generating more meaningful responses for biomedical question-answering tasks. We evaluated two prompt enhancement approaches using GPT-3 and GPT-4, examining their effectiveness in retrieving relevant information from complex landscape of biomedical literature. Our proposed approach leverages explicit signals in user queries to extract meaningful contexts from a vast pool of information, addressing the shortcomings of traditional text embedding-based prompt enhancement methods. We developed a QA bot ‘WeiseEule’ (https://github.com/wasimaftab/WeiseEule-LocalHost) utilizing these prompt enhancement methods and allowing for comparative analysis of their performances.

Conclusions

Our findings highlight the importance of prompt enhancement methods that utilize explicit signals in user’s query over traditional text embedding based counterparts to improve LLM-generated responses in specialized domains such as biology and biomedicine. By providing users complete control over the information that goes into the LLM, our approach tackles some of the major drawbacks of existing web-based chatbots and LLM-based QA systems including hallucinations and the generation of irrelevant or outdated responses.
Two modes in the velocity statistics in cautious walks of laboratory rodents
Authors: Midzyanovskaya I. S. , Rebik A. A. , Idzhilova O. S. , Strelkov V. V. , Komarova N. L. , Chichigina O. A.
Published: April 2024

We have analyzed a large number of rodent tracks in open-field tests, in order to elucidate the statistics of their velocities. We found that the probability distribution of the absolute velocity of rodents can be approximated by a superposition of two Rayleigh distributions, with distinct characteristic velocitiesv1andv2withv1< v2; this is in contrast to the single Rayleigh distribution for the velocity of a Brownian particle executing 2D random motion. We propose that the part of the distribution near the larger velocity,v2, characterizes rodents’ progressions in space, while the part nearv1describes other types of motion, such as lingering and body micromovements. We observed that the animals switched randomly between these two modes. While both velocities,v1andv2, increase with age, their ratio,v2/v1, also grows with age, implying an increased efficacy of switches between the two modes in older animals. Since the existence of the modes is observed both in preweaned, blind pups and in older animals, it cannot be ascribed to foraging, but instead reflects risk assessment and proactive inhibition. We called such motion “cautious walks”. Statistical analysis of the data further revealed a biphasic decline in the velocity auto-correlation function, with two characteristic times,τs< τl, whereτscharacterizes the width of velocity peaks, andτlis associated with the timing of the switches between progression and lingering. To describe the motion, we propose a stochastic model, which assumes the existence of two interfering processes: impulses to move that arrive at random times, and continuous deceleration. Its 2D Langevin-like equation has a damping coefficient that switches between two values, representing mode switching in rodents. Techniques developed here may be applicable for locomotion studies in a wide variety of contexts, as long as tracking data of sufficient resolution are available.
Effects of fire and fire-induced changes in soil properties on post-burn soil respiration
Authors: Johnson Dana B. , Yedinak Kara M. , Sulman Benjamin N. , Berry Timothy D. , Kruger Kelsey , Whitman Thea
Published: April 2024

Background

Boreal forests cover vast areas of land in the northern hemisphere and store large amounts of carbon (C) both aboveground and belowground. Wildfires, which are a primary ecosystem disturbance of boreal forests, affect soil C via combustion and transformation of organic matter during the fire itself, and via changes in plant growth and microbial activity post-fire. Wildfire regimes in many areas of the boreal forests of North America are shifting towards more frequent and severe fires driven by changing climate. As wildfire regimes shift and the effects of fire on belowground microbial community composition are becoming clearer, there is a need to link fire-induced changes in soil properties to changes in microbial functions such as respiration in order to better predict the impact of future fires on C cycling.

Results

We used laboratory burns to simulate boreal crown fires on both organic-rich and sandy soil cores collected from Wood Buffalo National Park, Alberta, Canada, to measure the effects of burning on soil properties including pH, total C, and total nitrogen (N). We used 70-day soil incubations and two-pool exponential decay models to characterize the impacts of burning and its resulting changes in soil properties on soil respiration. Laboratory burns successfully captured a range of soil temperatures that were realistic for natural wildfire events. We found that burning increased pH and caused small decreases in C:N in organic soil. Overall, respiration per gram total (post-burn) C in burned soil cores was 16% lower than in corresponding unburned control cores, indicating that soil C lost during a burn may be partially offset by burn-induced decreases in respiration rates. Simultaneously, burning altered how remaining C cycled, causing an increase in the proportion of C represented in the modelled slow-cycling vs. fast-cycling C pool as well as an increase in fast-cycling C decomposition rates.

Conclusions

Together, our findings imply that C storage in boreal forests following wildfires will be driven by the combination of C losses during the fire itself as well as fire-induced changes to the soil C pool that modulate post-fire respiration rates. Moving forward, we will pair these results with soil microbial community data to understand how fire-induced changes in microbial community composition may influence respiration.
RAG suppresses group 2 innate lymphoid cells
Authors: Ver Heul Aaron M. , Mack Madison , Zamidar Lydia , Tamari Masato , Yang Ting-Lin , Trier Anna M. , Kim Do-Hyun , Janzen-Meza Hannah , Van Dyken Steven J. , Hsieh Chyi-Song , Karo Jenny M. , Sun Joseph C. , Kim Brian S.
Published: April 2024

Antigen specificity is the central trait distinguishing adaptive from innate immune function. Assembly of antigen-specific T cell and B cell receptors occurs through V(D)J recombination mediated by the Recombinase Activating Gene endonucleases RAG1 and RAG2 (collectively called RAG). In the absence of RAG, mature T and B cells do not develop and thus RAG is critically associated with adaptive immune function. In addition to adaptive T helper 2 (Th2) cells, group 2 innate lymphoid cells (ILC2s) contribute to type 2 immune responses by producing cytokines like Interleukin-5 (IL-5) and IL-13. Although it has been reported that RAG expression modulates the function of innate natural killer (NK) cells, whether other innate immune cells such as ILC2s are affected by RAG remains unclear. We find that in RAG-deficient mice, ILC2 populations expand and produce increased IL-5 and IL-13 at steady state and contribute to increased inflammation in atopic dermatitis (AD)-like disease. Further, we show that RAG modulates ILC2 function in a cell-intrinsic manner independent of the absence or presence of adaptive T and B lymphocytes. Lastly, employing multiomic single cell analyses of RAG1 lineage-traced cells, we identify key transcriptional and epigenomic ILC2 functional programs that are suppressed by a history of RAG expression. Collectively, our data reveal a novel role for RAG in modulating innate type 2 immunity through suppression of ILC2s.
Evaluation of Inducible Gene Expression Systems for Beet Cyst Nematode Infection Assays inArabidopsis thaliana
Authors: Liu Xunliang , Mitchum Melissa G
Published: April 2024

Cyst nematodes co-opt plant developmental programs for the establishment of a permanent feeding site called a syncytium in plant roots. In recent years, the role of plant developmental genes in syncytium formation has gained much attention. One main obstacle in studying the function of development-related genes in syncytium formation is that mutation or ectopic expression of such genes can cause pleiotropic phenotypes making it difficult to interpret nematode-related phenotypes, or in some cases, impossible to carry out infection assays due to aberrant root development. Here, we tested three commonly used inducible gene expression systems for their application in beet cyst nematode infection assays of the model plantArabidopsis thaliana. We found that even a low amount of ethanol diminished nematode development, deeming the ethanol-based system unsuitable for use in cyst nematode infection assays; whereas treatment with estradiol or dexamethasone did not negatively affect cyst nematode viability. Dose and time course responses showed that in both systems, a relatively low dose of inducer (1 μM) is sufficient to induce high transgene expression within 24 hours of treatment. Transgene expression peaked at 3-5 days post induction and began to decline thereafter, providing a perfect window for inducible transgenes to interfere with syncytium establishment while minimizing any adverse effects on root development. These results indicate that both estradiol- and dexamethasone-based inducible gene expression systems are suitable for cyst nematode infection assays. The employment of such systems provides a powerful tool to investigate the function of development essential plant genes in syncytium formation.
Tree Surface Area Allometry
Authors: Shenkin Alexander , Wilkes Phil , Enquist Brian , Sarmiento Alvaro , Burt Andy , Calders Kim , Raumonen Pasi , Patrick Bentley Lisa , Disney Mat , Malhi Yadvinder
Published: April 2024

Utilizing terrestrial laser scanning (TLS) and three-dimensional modeling, this study quantitatively assessed the woody surface areas of 2161 trees across ecosystems encompassing both tropical and temperate forests. TLS enables precise measurement of tree structures at unprecedented scales. This research builds on theoretical scaling relationships with empirical data, significantly refining our understanding of tree woody surface area. Key findings indicate that direct measurements diverge from theoretical predictions, particularly in the finer branch structures, suggesting modifications to existing allometric models might be necessary. This integration of direct measurements with TLS not only challenges established theories but also enhances our capability to accurately model tree surface area, which is key for understanding forest carbon dynamics and metabolic scaling in ecological systems.
Generation of a zebrafish neurofibromatosis model via inducible knockout ofnf2
Authors: Desingu Rajan Ayyappa Raja , Huang Yuanyun , Stundl Jan , Chu Katelyn , Irodi Anushka , Yang Zihan , Applegate Brian E. , Bronner Marianne E.
Published: April 2024

Neurofibromatosis Type 2 (NF-2) is a dominantly inherited genetic disorder that results from mutations in the tumor suppressor gene, neurofibromin 2 (NF2) gene. Here, we report the generation of a conditional zebrafish model of neurofibromatosis established by an inducible genetic knockout ofnf2a/b, the zebrafish homolog of human NF2. Analysis ofnf2aandnf2bexpression reveals ubiquitous expression ofnf2bin the early embryo, with overlapping expression in the neural crest and its derivatives and in the cranial mesenchyme. In contrast,nf2adisplays lower expression levels. Induction ofnf2a/bknockout at early stages increases the proliferation of larval Schwann cells and meningeal fibroblasts. Subsequently, in adult zebrafish,nf2a/bknockout triggers the development of a spectrum of tumors, including vestibular schwannomas, spinal schwannomas, meningiomas, and retinal hamartomas, mirroring the tumor manifestations observed in patients with NF-2. Collectively, these findings highlight the generation of a novel zebrafish model that mimics the complexities of the human NF-2 disorder. Consequently, this model holds significant potential for facilitating therapeutic screening and elucidating key driver genes implicated in NF-2 onset.
Engineering Memory T Cells as a platform for Long-Term Enzyme Replacement Therapy in Lysosomal Storage Disorders
Authors: Laoharawee Kanut , Kleinboehl Evan W , Jensen Jacob D , Peterson Joseph J , Slipek Nicholas J , Wick Bryce J , Johnson Matthew J , Webber Beau R , Moriarity Branden S
Published: April 2024

Enzymopathy disorders are the result of missing or defective enzymes. Amongst these enzymopathies, mucopolysaccharidosis type I, is a rare genetic lysosomal storage disorder caused by mutations in the gene encoding alpha-L-iduronidase (IDUA), ultimately causes toxic build-up of glycosaminoglycans (GAGs). There is currently no cure and standard treatments provide insufficient relief to the skeletal structure and central nervous system (CNS). Human memory T cells (Tm) migrate throughout the body’s tissues and can persist for years, making them an attractive approach for cellular-based, systemic enzyme replacement therapy. Here, we tested genetically engineered, IDUA-expressing Tm as a cellular therapy in an immunodeficient mouse model of MPS I. Our results demonstrate that a single dose of engineered Tm leads to detectable IDUA enzyme levels in the blood for up to 22 weeks and reduced urinary GAG excretion. Furthermore, engineered Tm take up residence in nearly all tested tissues, producing IDUA and leading to metabolic correction of GAG levels in the heart, lung, liver, spleen, kidney, bone marrow, and the CNS. Our study indicates that genetically engineered Tm holds great promise as a platform for cellular-based enzyme replacement therapy for the treatment of mucopolysaccharidosis type I and potentially many other enzymopathies and protein deficiencies.
Exploration of the genetic landscape of bacterial dsDNA viruses reveals an ANI gap amidst extensive mosaicism
Authors: Ndovie Wanangwa , Havránek Jan , Leconte Jade , Koszucki Janusz , Chindelevitch Leonid , Adriaenssens Evelien M. , Mostowy Rafal J.
Published: April 2024

Average Nucleotide Identity (ANI) is a widely used metric to estimate genetic relatedness, especially in microbial species delineation. While ANI calculation has been well optimised for bacteria and closely related viral genomes, accurate estimation of ANI below 80%, particularly in large reference datasets, has been challenging due to a lack of accurate and scalable methods. To bridge this gap, here we introduce MANIAC, an efficient computational pipeline optimised for estimating ANI and alignment fraction (AF) in viral genomes with divergence around ANI of 70%. Using a rigorous simulation framework, we demonstrate MANIAC’s accuracy and scalability compared to existing approaches, even to datasets of hundreds-of-thousands of viral genomes. Applying MANIAC to a curated dataset of complete bacterial dsDNA viruses revealed a multimodal ANI distribution, with a distinct gap around 80%, akin to the bacterial ANI gap (∼90%) but shifted, likely due to viral-specific evolutionary processes such as recombination dynamics and mosaicism. We then evaluated ANI and AF as predictors of genus-level taxonomy using a logistic regression model. We found that this model has strong predictive power (PR-AUC=0.981), but that it works much better for virulent (PR-AUC=0.997) than temperate (PR-AUC=0.847) bacterial viruses. This highlights the complexity of taxonomic classification in temperate phages, known for their extensive mosaicism, and cautions against over-reliance on ANI in such cases. MANIAC can be accessed underhttps://github.com/bioinf-mcb/MANIAC.

Importance

We introduce a novel computational pipeline called MANIAC, designed to accurately assess Average Nucleotide Identity (ANI) and alignment fraction (AF) between diverse viral genomes, scalable to datasets of over 100k genomes. Through the use of computer simulations and real data analyses, we show that MANIAC could ac- curately estimate genetic relatedness between pairs of viral genomes around 60-70% ANI. We applied MANIAC to investigate the question of ANI discontinuity in bacterial dsDNA viruses, finding evidence for an ANI gap, akin to the one seen in bacteria but around ANI of 80%. We then assessed the ability of ANI and AF to predict taxonomic genus boundaries, finding its strong predictive power in virulent, but not in temperate phages. Our results suggest that bacterial dsDNA viruses may exhibit an ANI threshold (on average around 80%) above which recombination helps maintain population cohesiveness, as previously argued in bacteria.
Immune perturbations in human pancreas lymphatic tissues prior to and after type 1 diabetes onset
Authors: Golden Gregory J. , Wu Vincent H. , Hamilton Jacob T. , Amses Kevin R. , Shapiro Melanie R. , Japp Alberto Sada , Liu Chengyang , Pampena Maria Betina , Kuri-Cervantes Leticia , Knox James J. , Gardner Jay S. ,   HPAP Consortium, Atkinson Mark A. , Brusko Todd M. , Prak Eline T. Luning , Kaestner Klaus H. , Naji Ali , Betts Michael R.
Published: April 2024

Autoimmune destruction of pancreatic β cells results in type 1 diabetes (T1D), with pancreatic immune infiltrate representing a key feature in this process. Studies of human T1D immunobiology have predominantly focused on circulating immune cells in the blood, while mouse models suggest diabetogenic lymphocytes primarily reside in pancreas-draining lymph nodes (pLN). A comprehensive study of immune cells in human T1D was conducted using pancreas draining lymphatic tissues, including pLN and mesenteric lymph nodes, and the spleen from non-diabetic control, β cell autoantibody positive non-diabetic (AAb+), and T1D organ donors using complementary approaches of high parameter flow cytometry and CITEseq. Immune perturbations suggestive of a proinflammatory environment were specific for T1D pLN and AAb+ pLN. In addition, certain immune populations correlated with high T1D genetic risk independent of disease state. These datasets form an extensive resource for profiling human lymphatic tissue immune cells in the context of autoimmunity and T1D.
Genotype Representation Graphs: Enabling Efficient Analysis of Biobank-Scale Data
Authors: DeHaas Drew , Pan Ziqing , Wei Xinzhu
Published: April 2024

Computational analysis of a large number of genomes requires a data structure that can represent the dataset compactly while also enabling efficient operations on variants and samples. Current practice is to store large-scale genetic polymorphism data using tabular data structures and file formats, where rows and columns represent samples and genetic variants. However, encoding genetic data in such formats has become unsustainable. For example, the UK Biobank polymorphism data of 200,000 phased whole genomes has exceeded 350 terabytes (TB) in Variant Call Format (VCF), cumbersome and inefficient to work with. To mitigate the computational burden, we introduce the Genotype Representation Graph (GRG), an extremely compact data structure to losslessly present phased whole-genome polymorphisms. A GRG is a fully connected hierarchical graph that exploits variant-sharing across samples, leveraging ideas inspired by Ancestral Recombination Graphs. Capturing variant-sharing in a multitree structure compresses biobank-scale human data to the point where it can fit in a typical server’s RAM (5-26 gigabytes (GB) per chromosome), and enables graph-traversal algorithms to trivially reuse computed values, both of which can significantly reduce computation time. We have developed a command-line tool and a library usable via both C++ and Python for constructing and processing GRG files which scales to a million whole genomes. It takes 160GB disk space to encode the information in 200,000 UK Biobank phased whole genomes as a GRG, more than 13 times smaller than the size of compressed VCF. We show that summaries of genetic variants such as allele frequency and association effect can be computed on GRG via graph traversal that runs significantly faster than all tested alternatives, includingvcf.gz, PLINK BED, tree sequence, XSI, and Savvy. Furthermore, GRG is particularly suitable for doing repeated calculations and interactive data analysis. We anticipate that GRG-based algorithms will improve the scalability of various types of computation and generally lower the cost of analyzing large genomic datasets.
A Dynamic Entropy Approach Reveals Reduced Functional Network Connectivity Trajectory Complexity in Schizophrenia
Authors: Blair David Sutherland , Miller Robyn L. , Calhoun Vincent D.
Published: April 2024

Over the past decade and a half, dynamic functional imaging has revolutionized the neuroimaging field. Since 2009, it has revealed low dimensional brain connectivity measures, has identified potential common human spatial connectivity states, has tracked the transition patterns of these states, and has demonstrated meaningful alterations in these transition and spatial patterns in neurological disorders, psychiatric disorders, and over the course of development. More recently, researchers have begun to analyze this data from the perspective of dynamic system and information theory in the hopes of understanding the constraints within which these dynamics occur and how they may support less easily quantified processes, such as information processing, cortical hierarchy, and consciousness. Progress has begun to accelerate in this area, particularly around consciousness, which appears to be strongly linked to entropy production in the brain. Outside of disorders of consciousness, however, little attention has been paid to the effects of psychiatric disease on entropy production in the human brain. Even disorders characterized by substantial changes in conscious experience have not been widely analyzed from this perspective.

Here, we begin to rectify this gap by examining the complexity of subject trajectories in this state space through the lens of information theory. Specifically, we identify a basis for the dynamic functional connectivity state space and track subject trajectories through this state space over the course of the scan. The dynamic complexity of these trajectories is estimated using a Kozachenko-Leonenko entropy estimator, which assesses the rate of Shannon entropy production along each dimension of the proposed basis space. Using these estimates, we demonstrate that schizophrenia patients display substantially simpler trajectories than demographically matched healthy controls, and that this drop in complexity concentrates along specific dimensions of projected basis space. We also demonstrate that entropy generation in at least one of these dimensions is linked to cognitive performance. Overall, results suggest great value in applying dynamic systems theory to problems of neuroimaging and reveal a substantial drop in the complexity of schizophrenia patients’ brain function.
Fairy: fast approximate coverage for multi-sample metagenomic binning
Authors: Shaw Jim , Yu Yun William
Published: April 2024

Background

Metagenomic binning, the clustering of assembled contigs that belong to the same genome, is a crucial step for recovering metagenomeassembled genomes (MAGs). Contigs are linked by exploiting consistent read coverage patterns across a genome. Using coverage from multiple samples leads to higher-quality MAGs; however, standard pipelines require all-to-all read alignments for multiple samples to compute coverage, becoming a key computational bottleneck.

Results

We present fairy (https://github.com/bluenote-1577/fairy), anapproximatecoverage calculation method for metagenomic binning. Fairy is a fast k-mer-based alignment-free method. For multi-sample binning, fairy can be>250×faster than read alignment and accurate enough for binning. Fairy is compatible with several existing binners on host and non-host-associated datasets. Using MetaBAT2, fairy recovers98.5%of MAGs with>50%completeness and<5%incompleteness relative to alignment with BWA. Notably, multi-sample binning with fairy isalwaysbetter than single-sample binning using BWA (>1.5×more>50%complete MAGs on average) while still being faster. For a public sediment metagenome project, we demonstrate that multisample binning recovers higher quality Asgard archaea MAGs than single-sample binning and that fairy’s results are indistinguishable from read alignment.

Conclusions

Fairy is a new tool for approximately and quickly calculating multi-sample coverage for binning, resolving a longstanding computational bottleneck for metagenomics.
Multi-spectral photoacoustic imaging combined with acoustic radiation force impulse imaging for applications in tissue engineering
Authors: Nguyen Christopher D. , Chen Ying , Kaplan David L. , Mallidi Srivalleesha
Published: April 2024

Tissue engineering is a dynamic field focusing on the creation of advanced scaffolds for tissue and organ regeneration. These scaffolds are customized to their specific applications and are often designed to be complex, large structures to mimic tissues and organs. This study addresses the critical challenge of effectively characterizing these thick, optically opaque scaffolds that traditional imaging methods fail to fully image due to their optical limitations. We introduce a novel multi-modal imaging approach combining ultrasound, photoacoustic, and acoustic radiation force impulse imaging. This combination leverages its acoustic-based detection to overcome the limitations posed by optical imaging techniques. Ultrasound imaging is employed to monitor the scaffold structure, photoacoustic imaging is employed to monitor cell proliferation, and acoustic radiation force impulse imaging is employed to evaluate the homogeneity of scaffold stiffness. We applied this integrated imaging system to analyze melanoma cell growth within silk fibroin protein scaffolds with varying pore sizes and therefore stiffness over different cell incubation periods. Among various materials, silk fibroin was chosen for its unique combination of features including biocompatibility, tunable mechanical properties, and structural porosity which supports extensive cell proliferation. The results provide a detailed mesoscale view of the scaffolds’ internal structure, including cell penetration depth and biomechanical properties. Our findings demonstrate that the developed multimodal imaging technique offers comprehensive insights into the physical and biological dynamics of tissue-engineered scaffolds. As the field of tissue engineering continues to advance, the importance of non-ionizing and non-invasive imaging systems becomes increasingly evident, and by facilitating a deeper understanding and better characterization of scaffold architectures, such imaging systems are pivotal in driving the success of future tissue-engineering solutions.
Divergent neural circuits for proprioceptive and exteroceptive sensing of theDrosophilaleg
Authors: Lee Su-Yee J. , Dallmann Chris J. , Cook Andrew , Tuthill John C. , Agrawal Sweta
Published: April 2024

Somatosensory neurons provide the nervous system with information about mechanical forces originating inside and outside the body. Here, we use connectomics from electron microscopy to reconstruct and analyze neural circuits downstream of the largest somatosensory organ in theDrosophilaleg, the femoral chordotonal organ (FeCO). The FeCO has been proposed to support both proprioceptive sensing of the fly’s femur-tibia joint and exteroceptive sensing of substrate vibrations, but it was unknown which sensory neurons and central circuits contribute to each of these functions. We found that different subtypes of FeCO sensory neurons feed into distinct proprioceptive and exteroceptive pathways. Position- and movement-encoding FeCO neurons connect to local leg motor control circuits in the ventral nerve cord (VNC), indicating a proprioceptive function. In contrast, signals from the vibration-encoding FeCO neurons are integrated across legs and transmitted to mechanosensory regions in the brain, indicating an exteroceptive function. Overall, our analyses reveal the structure of specialized circuits for processing proprioceptive and exteroceptive signals from the fly leg. These findings are consistent with a growing body of work in invertebrate and vertebrate species demonstrating the existence of specialized limb mechanosensory pathways for sensing external vibrations.
Transcriptome analysis reveals role for WRKY70 in earlyN-hydroxy-pipecolic acid signaling
Authors: Foret Jessica , Kim Jung-Gun , Sattely Elizabeth S. , Mudgett Mary Beth
Published: April 2024

N-hydroxy-pipecolic acid (NHP) is a mobile metabolite essential for inducing and amplifying systemic acquired resistance (SAR) following pathogen attack. Early phases of NHP signaling leading to immunity have remained elusive. Here we report the early transcriptional changes mediated by NHP and the role salicylic acid (SA) plays during this response. We show that distinct waves of expression within minutes to hours of NHP treatment include increased expression of WRKY transcription factors as the primary transcriptional response, followed by the induction of WRKY-regulated defense genes as the secondary response. The majority of genes induced by NHP within minutes were SA-dependent, whereas those induced within hours were SA-independent. These data suggest that NHP induces the primary transcriptional response in a low SA environment and new SA biosynthesis is dispensable for induction of the secondary transcriptional response. We demonstrate that WRKY70 is required for the induced expression of a set of genes defining some of the secondary transcriptional response, SAR protection, and NHP-dependent enhancement of ROS production in response to flagellin treatment. Taken together, our study highlights the key genes and pathways defining early NHP responses and a role for WRKY70 in the regulation of NHP-dependent transcription.