bluuebunny/crossref_metadata_2025 huggingface dataset:
Serum from patients with Idiopathic inflammatory myopathy induces skeletal muscle weakness
Authors: Leijding Cecilia , Andreasson Kristofer M. , Horuluoglu Begum , Galindo-Feria Angeles Shunashy , Van Gompel Eveline , Dastmalchi Maryam , Gastaldello Stefano , Alexanderson Helene , Lundberg Ingrid E. , Andersson Daniel C.
Published: April 2024

Idiopathic inflammatory myopathies (IIM) are a group of systemic autoimmune inflammatory disorders that primarily affect striated muscles leading to weakness and accelerated fatigue. The disseminated muscle phenotype points to systemic humoral factors as mediators of the disease. Autoantibodies are important biomarkers for disease classification; it is not known if they play a direct role in IIM disease development. This study aims to investigate if IIM patient serum or isolated IgG could directly impair contractile function in muscle.

Isolated flexor digitorum brevis (FDB) muscles from healthy mice were exposed to serum (10-50%) from healthy controls or patients with recent onset IIM. Some muscles were exposed to isolated total IgG (50 or 150μg/ml) from patients with IIM. Muscle force in whole muscles was measured before and after exposure to sera or IgG. Muscle force and intracellular [Ca2+] in single muscle fibers were measured after exposure to serum.

FDB muscles exposed to serum from patients with IIM displayed a marked reduction in force production in both 10% and 50% serum. Moreover, single myofibers dissected from FDB muscles exposed to IIM sera displayed lower force but unaffected Ca2+release during contractions, which indicates myofibrillar dysfunction, but not intracellular Ca2+release, as the cause to weakness. FDB muscles exposed to total IgG from IIM patients did not display any reduction in muscle force.

In conclusion IIM patient serum, but not total IgG, impairs force production in skeletal muscle fibers. As the experiments were performed in isolated muscle, our results cannot be explained by infiltrating immune cells, impaired neuronal or vascular functions. This suggests that humoral factors play a direct role in the pathogenesis of muscle weakness in recent onset IIM.
Fibroblast-like synoviocytes orchestrate daily rhythmic inflammation in arthritis
Authors: Downton Polly , Dickson Suzanna H. , Ray David W. , Bechtold David A. , Gibbs Julie E.
Published: April 2024

Rheumatoid arthritis is a chronic inflammatory disease that shows characteristic diurnal variation in symptom severity, where joint resident fibroblast-like synoviocytes (FLS) act as important mediators of arthritis pathology. We investigate the role of FLS circadian clock function in directing rhythmic joint inflammation in a murine model of inflammatory arthritis. We demonstrate FLS time of day-dependent gene expression is attenuated in arthritic joints, except for a subset of disease-modifying genes. Deletion of essential clock geneBmal1in FLS reduced susceptibility to collagen-induced arthritis (CIA), but did not impact symptomatic severity in affected mice. Notably, FLSBmal1deletion resulted in loss of diurnal expression of disease-modulating genes across the joint, and elevated production of MMP3, a prognostic marker of joint damage in inflammatory arthritis. This work identifies the FLS circadian clock as an influential driver of daily oscillations in joint inflammation, and a potential regulator of destructive pathology in chronic inflammatory arthritis.
The low abundance of antimicrobial resistance genes (ARGs) in bacteriophages and their transfer bottlenecks limit the ability of phages to contribute to the spread of ARGs
Authors: Kant Praveen , Petersen Bent , Sicheritz-Ponten Thomas , Kondabagil Kiran
Published: April 2024

The role of bacteriophages in the spread of antimicrobial resistance genes (ARGs) has been debated over the past decade. Several questions regarding the ARG dissemination potential of bacteriophages remain unanswered. For example, what is the frequency of acquisition of ARGs in phages? Are phages selective in acquiring the ARGs compared to other host genes? What is the predominant mechanism of transferring ARGs to phages? To address these questions, we thoroughly analyzed the available phage genomes, viromes, temperate phage, and prophage sequences for the presence of all known ARGs. Out of the 38,861 phage genome sequences we analyzed, only 182 phages contained a total of 314 ARGs. Interestingly, a few of the Streptococcus and Acinetobacter phages were found to carry an ARG cluster with four or more genes. One of the uncharacterized Myoviridae phages was found to carry the entire vancomycin operon. Furthermore, based on the presence of lysogenic marker sequences, the terminal location of ARGs on phage genomes, and complete ARG clusters transferred to phages, we suggest that ARGs are predominantly acquired from hosts by temperate phages via specialized transduction. The close association of most phage ARGs with lysogenic markers and mobile genetic elements (MGEs) also points towards specialized transduction as a potent mechanism of acquisition of ARGs by phages. Our study further suggests that the acquisition of ARGs by phages occurs by chance rather than through a selective process. Taken together, the limited presence of ARGs in phages, alongside various transfer bottlenecks, significantly restricts the role of phages in the dissemination of ARGs.
Airway injury induces alveolar epithelial and mesenchymal responses mediated by macrophages
Authors: Wong Irene G. , Stark Jillian , Ya VanNashlee , Moye Aaron L. , Vazquez Alan Baez , Dang Susanna M. , Shehaj Andrea , Rouhani Maral J. , Bronson Roderick , Janes Sam M. , Rowbotham Samuel P. , Paschini Margherita , Franklin Ruth A. , Kim Carla F.
Published: April 2024

Acute injury in the airways or the lung activates local progenitors and stimulates changes in cell-cell interactions to restore homeostasis, but it is not appreciated how more distant niches are impacted. We utilized mouse models of airway-specific epithelial injury to examine secondary tissue-wide alveolar, immune, and mesenchymal responses. Single-cell transcriptomics andin vivovalidation revealed transient, tissue-wide proliferation of alveolar type 2 (AT2) progenitor cells after club cell-specific ablation. The AT2 cell proliferative response was reliant on alveolar macrophages (AMs) via upregulation ofSpp1which encodes the secreted factor Osteopontin. A previously uncharacterized mesenchymal population we termed Mesenchymal Airway/Adventitial Niche Cell 2 (MANC2) also exhibited dynamic changes in abundance and a pro-fibrotic transcriptional signature after club cell ablation in an AM-dependent manner. Overall, these results demonstrate that acute airway damage can trigger distal lung responses including altered cell-cell interactions that may contribute to potential vulnerabilities for further dysregulation and disease.

Highlights

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Airway epithelial cell injury causes proliferation of AT2 cells, the alveolar epithelial progenitor cells

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Alveolar macrophages promote AT2 cell proliferation after airway injury via upregulation ofSpp1

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Alveolar macrophages have a pro-fibrotic effect on lung mesenchyme after airway injury

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Damage to one epithelial compartment can elicit altered epithelial- immune-mesenchymal cell crosstalk in another compartment of the same tissue
Multilayered interaction between CRISPR-Cas subtype I-A and adjacently encoded Acrs of virus SIRV2
Authors: Bhoobalan-Chitty Yuvaraj , Dwiputra Nicodemus , Mayo-Muñoz David , Baadsgaard Karen , Skafte Detlefsen Mette Rehtse Kvistrup , Peng Xu
Published: April 2024

Among the >100 anti-CRISPRs (Acrs) identified to date, the vast majority inhibit CRISPR-Cas immunity on its own. Here we report a multilayered interaction between CRISPR-Cas subtype I-A immunity and two Acrs encoded adjacently in the genome of Saccharolobus virus SIRV2, gp47 (AcrIA3) and gp48 (previously known as AcrIIIB1, hence termed AcrIIIB1/AcrIA4). The host subtype I-A CRISPR-Cas interference module was shown previously to be up-regulated upon SIRV2 infection, through the release of transcriptional repressor Csa3b from the promoter. We demonstrate that AcrIIIB1/AcrIA4 on its own increases viral infectivity 4-5 orders of magnitude in the presence of the host subtype I-A CRISPR-Cas immunity. This Acr is able to completely inhibit the subtype I-A CRISPR-Cas immunity when the transcriptional activation of the latter is artificially removed, suggesting that Acrs might be one of the driving forces for the evolution of CRISPR-Cas up-regulation. Interestingly, AcrIA3 cooperates with AcrIIIB1/AcrIA4 by inhibiting transcriptional activation of the host subtype I-A CRISPR-Cas interference module through interaction with the promoter of the latter. Taken together, our data shed light on how virus-host arms race shaped the evolution of CRISPR-Cas and Acrs.
A species difference in glycerol-3-phosphate metabolism reveals metabolic adaptations in hares
Authors: Gaertner Kateryna , Terzioglu Mügen , Michell Craig , Tapanainen Riikka , Pohjoismäki Jaakko L. O. , Dufour Eric , Saari Sina
Published: April 2024

The temperate climate adapted brown hare (Lepus europaeus) and the cold-adapted mountain hare (Lepus timidus) are evolutionarily closely related and interfertile. Still, their cultured skin fibroblasts show clear differences in the expression of genes related to basic cellular metabolism. To study this further, we utilized targeted metabolomics analysis, metabolite tracing, and high-resolution respirometry, and identified significant differences in metabolic pathways associated with adaptive thermogenesis, including a higher rate of glycerol 3-phosphate (G3P) production in the mountain hare. We therefore investigated mitochondrial heat production and its dependence on G3P in the two hare species. The mountain hare maintained lower mitochondrial temperature and had weaker thermal change following OXPHOS inhibition. Manipulating mitochondrial glycerol 3-phosphate dehydrogenase (GPD2) levels demonstrated its role in mitochondrial thermogenesis and revealed species-specific function in maintaining mitochondrial membrane potential. This study unveils previously undocumented and unexpected species differences in the mitochondrial properties of fibroblasts that could indicate differences in metabolic adaptability. These findings also demonstrate the utility of cell culture models in assessing trait differences between species and their evolutionary significance, contributing to a deeper understanding of metabolic adaptation in animals and underscoring the potential of in vitro approaches for eco-physiological studies.
Evolutionary insights into the emergence of virulentLeptospiraspirochetes
Authors: Giraud-Gatineau Alexandre , Nieves Cecilia , Harrison Luke B. , Benaroudj Nadia , Veyrier Frédéric J. , Picardeau Mathieu
Published: April 2024

PathogenicLeptospiraare spirochete bacteria which cause leptospirosis, a re-emerging zoonotic disease of global importance. Here, we use a recently described lineage of environmental-adapted leptospires, which are evolutionarily the closest relatives of the highly virulentLeptospiraspecies, to explore the key phenotypic traits and genetic determinants ofLeptospiravirulence. Through a comprehensive approach integrating phylogenomic comparisons within vitroandin vivophenotyping studies, we show that the evolution towards pathogenicity is associated with both a decrease of the ability to survive in the environment and the acquisition of strategies that enable successful host colonization. This includes the evasion of the human complement system and the adaptations to avoid activation of the innate immune cells. Moreover, our analysis reveals specific genetic determinants that have undergone positive selection during the course of evolution inLeptospira, contributing directly to virulence and host adaptation as demonstrated by gain-of-function and knock-down studies. Taken together, our findings define a new vision onLeptospirapathogenicity, identifying virulence attributes associated with clinically relevant species, and provide insights into the evolution and emergence of these life-threatening pathogens.

AUTHOR SUMMARY

Leptospirais a highly heterogeneous bacterial genus and leptospires are ubiquitous bacteria found as free-living saprophytes or as pathogens that can cause disseminated infections, from asymptomatic carriage in rats to lethal acute infection in both humans and animals. Leptospirosis is thus causing over one million cases and nearly 60,000 deaths annually. Despite leptospirosis being a re-emerging zoonosis, little is known about the ability of the etiologic agent to adapt to different hosts and cause disease. Here, combining genome analysis and phenotyping studies of representative species and mutant strains, we show that only a small group of species have the ability to evade the host immune system and cause disease. In addition, our findings provide key insight into the emergence of pathogens from a saprophytic ancestor through events of gene gain and genome reduction.
Agrochemical control of gene expression using evolved split RNA polymerase. II
Authors: Yuan Yuan , Miao Jin
Published: April 2024

Agrochemical inducible gene expression system provides cost-effective and orthogonal control of energy and information flow in bacterial cells. However, the previous version of Mandipropamid inducible gene expression system (Mandi-T7) became constitutively active at room temperature. We moved the split site of the eRNAP from position LYS179 to position ILE109. This new eRNAP showed proximity dependence at 23°C, but not at 37°C. We built Mandi-T7-v2 system based on the new eRNAP and it worked in bothEscherichia coli and Agrobacteria tumefaciens. The modified eRNAP when combined with the leucine zipper-based dimerization system, behaved as a cold inducible gene expression system. Our new system provides a means to broaden the application of agrochemicals for both research and agricultural application.
Functional activation of dorsal striatum astrocytes improves movement deficits in hemi-parkinsonian mice
Authors: Evans Wesley R. , Baskar Sindhuja S. , Ana Raquel Castro E Costa , Ravoori Sanya , Arigbe Abimbola , Huda Rafiq
Published: April 2024

Parkinson’s disease (PD) is characterized by the degeneration of dopaminergic nigrostriatal inputs, which causes striatal network dysfunction and leads to pronounced motor deficits. Recent evidence highlights astrocytes as a potential local source of striatal network modulation. However, it remains unknown how dopamine loss affects striatal astrocyte activity and whether astrocyte activity regulates behavioral deficits in PD. We addressed these questions by performing astrocyte-specific calcium recordings and manipulations usingin vivofiber photometry and chemogenetics. We find that locomotion elicits astrocyte calcium activity over a slower timescale than neurons. Unilateral dopamine depletion reduced locomotion-related astrocyte responses. Chemogenetic activation facilitated astrocyte activity, and improved asymmetrical motor deficits and open field exploratory behavior in dopamine lesioned mice. Together, our results establish a novel role for functional striatal astrocyte signaling in modulating motor function in PD and highlight non-neuronal targets for potential PD therapeutics.
Chromosome-level genome assembly of the primitive loach goby,Rhyacichthys aspro, reveals mechanisms underlying Gobioidei diversification
Authors: Wang Tzi-Yuan , Lu Hao-Jun , Wu Yu-Wei , Liao Te-Yu , Huang Shih-Pin , Wang Feng-Yu , Ting Chau-Ti , Chaw Shu-Miaw , Wang Hurng-Yi
Published: April 2024

The percomorph fish clade Gobioidei are a suborder that comprises over 2,200 species distributed in nearly all aquatic habitats. To understand the genetics underlying their diversification, we sequenced and annotated the genome of the loach goby,Rhyacichthys aspro, the basal most group, and compared it with nine additional Gobioidei species. Within Gobioidei, the loach goby possesses the smallest genome at 607 Mb, and a rise in species diversity from basal to derived lineages is mirrored by enlarged genomes and a higher presence of repeat elements (REs), particularly DNA transposons. These transposons are enriched in coding and regulatory regions and their copy number increase is strongly correlated with mutation rate, suggesting that DNA repair after transposon excision/insertion leads to nearby mutations. Consequently, the proliferation of DNA transposons might be the crucial driver of Gobioidei diversification and adaptability. The loach goby genome also points to mechanisms of ecological adaptation. It contains relatively few genes for lateral line development but an over representation of synaptic function genes, with genes putatively under selection linked to synapse organization and calcium signaling, suggesting a sensory system distinct from other Gobioidei species. We also see an overabundance of genes involved in neurocranium development and renal function, adaptations likely connected to its flat morphology suited for strong currents and an amphidromous life cycle. Comparative analyses with hill-stream loaches and the European eel reveal convergent adaptations in body shape and saltwater balance. These findings shed light on the loach goby’s survival mechanisms and the broader evolutionary trends within Gobioidei.
Estimating essential phenotypic and molecular traits from integrative biodiversity data
Authors: Peters Kristian , Ziegler Jörg , Neumann Steffen
Published: April 2024

In the context of biodiversity, only few functional traits and mechanisms are known from underrepresented groups such as mosses (bryophytes). Here, we use 16 field samples of complex thallose liverworts (order Marchantiales) collected from biological soil crusts as reference data for the reusable computational framework iESTIMATE that integrates and extracts phenotypic and molecular traits; and estimates Essential Molecular Variables (EMV). Our reference data involves (1) bioimaging, (2) metabolomics, and (3) DNA marker sequencing. These data are used to demonstrate the systematic and standardized extraction of phenotypic and molecular traits. To demonstrate the reusability of our framework, we propose naming schemes, apply Random Forest to estimate EMVs, phylogenetic dendrograms and partitioning around medoids to connect evolutionary relationships with ecological hypotheses and to document knowledge gains across domains. With this work we want to encourage the combined assessment, reuse and integration of phenotypic and molecular traits into functional ecology, biodiversity and related disciplines.
Combination of oncolytic Maraba virus with immune checkpoint blockade overcomes therapy resistance in an immunologically cold model of advanced melanoma with dysfunctional T cell receptor signalling
Authors: Armstrong Edward , Chiu Matthew K.L. , Foo Shane , Appleton Lizzie , Nenclares Pablo , Patrikeev Anton , Mohan Nitya , Mclaughlin Martin , Bozhanova Galabina , Hoebart Julia , Roulstone Victoria , Patin Emmanuel C , Pedersen Malin , Kyula Joan , Errington-Mais Fiona , Bell John C. , Harrington Kevin J. , Melcher Alan A. , Jennings Victoria A.
Published: April 2024

Background

Over the past decade, cancer immunotherapies have revolutionised the treatment of melanoma; however, responses vary across patient populations. Recently, baseline tumour size has been identified as an independent prognostic factor for overall survival in melanoma patients receiving immune checkpoint inhibitors (ICIs). MG1 is a novel oncolytic agent with broad tumour tropism that has recently entered early phase clinical trials. The aim of this study was to characterise T cell responses in human and mouse melanoma models following MG1 treatment and to establish if features of the tumour immune microenvironment (TIME) at two distinct tumour burdens would impact the efficacy of oncolytic virotherapy.

Methods

Human 3Din vitropriming assays were performed to measure anti-tumour and anti-viral T cell responses following MG1 infection. TCR sequencing, T2 killing assay, and peptide recall assays were used to assess the evolution of the TCR repertoire, and measure specific T cell responses, respectively.In vivo, subcutaneous 4434 melanomas were characterised using RNAseq, immunohistochemistry (IHC), and flow cytometry. The effectiveness of intra-tumoural MG1 was assessed in advancing 4434 tumours and the generation of anti-tumour and anti-viral T cells measured by splenocyte recall assays. Finally, combination MG1 and α-PD-1 therapy was investigated in advanced 4434 tumours.

Results

MG1 effectively primed functional cytotoxic T cells (CTLs) against tumour associated antigens (TAA) as well as virus-derived peptides, as assessed using peptide recall and T2 killing assays, respectively. TCR sequencing revealed that MG1-primed CTL comprised larger clusters of similar CDR3 amino acid sequences compared to controls.In vivotesting of MG1 demonstrated that MG1 monotherapy was highly effective at treating early disease, resulting in 90% cures; however, the efficacy of MG1 reduced as the disease burden (local tumour size) increased, and the addition of α-PD-1 was required to overcome resistance in more advanced disease. Differential gene expression profiles revealed that increased tumour burden was associated with an immunologically colder TIME. Furthermore, analysis of TCR signalling in advancing tumours demonstrated a different dynamic of TCR engagement compared to smaller tumours, in particular a shift in antigen recognition by CD4+ cells, from conventional to regulatory subset.

Conclusion

Combination of MG1 with αPD-1 overcomes therapy resistance in an immunologically ‘cold’ model of advanced melanoma.
Transposable element products, functions, and regulatory networks in Arabidopsis
Authors: Borredá Carles , Leduque Basile , Colot Vincent , Quadrana Leandro
Published: April 2024

Transposable elements (TEs) are DNA sequences with the ability to propagate themselves within genomes. Their mobilization is catalyzed by self-encoded factors, yet these factors have been poorly investigated. Here, we leveraged extensive long-and short-read transcriptome data, structural predictions, and regulatory networks analyses, to construct a comprehensive atlas of TE transcripts and their encoded products in the model organismArabidopsis thaliana. We uncovered hundreds of transcriptionally competent TEs, each potentially encoding multiple proteins either through distinct genes, alternative splicing, or post-translational processing. Structural-based protein analyses revealed hitherto unidentified domains, uncovering proteins with multimerization and DNA binding domains forming macromolecular complexes. Furthermore, we demonstrate that TE expression is highly intertwined with the transcriptional network of cellular genes, and identified transcription factors and cis-regulatory elements associated with their coordinated expression during development or in response to environmental cues. This comprehensive functional atlas provides a valuable resource for studying the mechanisms involved in transposition and their consequences for genome and organismal function.
Cheap, Robust and Versatile Two-Dimensional Chromatography system for Proteomics of Nanogram Scale Samples
Authors: Kitano Eduardo S. , Nisbet Gareth , Demyanenko Yana , Kowalczyk Katarzyna M , Iselin Louisa , Cross Stephen , Castello Alfredo , Mohammed Shabaz
Published: April 2024

In this work we describe a low loss fractionation system comprised of a reconfigured Evosep One LC system for the first dimension and a repurposed 3D-printer as a fraction collector. The setup operates as a high-pH fractionation system capable of effectively working with nanogram scales of lysate digests. The 2D RP-RP system demonstrated superior proteome coverage over single-shot data-dependent acquisition (DDA) analysis using only 5 ng of human cell lysate digest with performance increasing with increasing amounts of material. We found that the fractionation system allowed over 70% signal recovery at the peptide level and, more importantly, we observed over 30% increase on protein level intensity which indicates the complexity reduction afforded by the system outweighs the sample losses endured. The application of data-independent acquisition (DIA) and wide window acquisition (WWA) to fractionated samples allowed more than 8,000 proteins to be identified from 50 ng of material. The utility of the 2D system was further investigated for phosphoproteomics (>21,000 phosphosites from 50 μg starting material) and pull-down type experiments and showed substantial improvements over single-shot experiments. We show that the 2D RP-RP system is highly versatile and powerful tool for many proteomics workflows.
Age-associated growth control modifies leaf proximodistal symmetry and enables leaf shape diversification
Authors: Li Xin-Min , Jenke Hannah , Strauss Sören , Wang Yi , Bhatia Neha , Kierzkowski Daniel , Lymbouridou Rena , Huijser Peter , Smith Richard S. , Runions Adam , Tsiantis Miltos
Published: April 2024

Biological shape diversity is often manifested in modulation of organ symmetry and modification of the patterned elaboration of repeated shape elements.1–5Whether and how these two aspects of shape determination are coordinately regulated is unclear.5–7Plant leaves provide an attractive system to investigate this problem, because they usually show asymmetries along their proximodistal axis, along which they can also produce repeated marginal outgrowths such as serrations or leaflets.1One case of leaf shape diversity is heteroblasty, where the leaf form in a single genotype is modified with progressive plant age.8–11InArabidopsis thaliana,a plant with simple leaves, SQUAMOSA PROMOTER BINDING PROTEIN-LIKE9 (SPL9) controls heteroblasty by activatingCyclinD3expression, thereby sustaining proliferative growth and retarding differentiation in adult leaves.12However, the precise significance of SPL9 action for leaf symmetry and marginal patterning is unknown. By combining genetics, quantitative shape analyses, and time-lapse imaging, we show that, inA. thaliana, proximodistal symmetry of the leaf blade decreases in response to an age-dependentSPL9expression gradient, and that SPL9 action coordinately regulates the distribution and shape of marginal serrations and overall leaf form. Using comparative analyses, we demonstrate that heteroblastic growth reprogramming inCardamine hirsuta,a complex-leafed relative ofA. thaliana,also involves prolonging the duration of cell proliferation and delaying differentiation. We further provide evidence that SPL9 enables species-specific action of homeobox genes that promote leaf complexity. In conclusion, we identify an age-dependent layer of organ proximodistal growth regulation that modulates leaf symmetry and has enabled leaf shape diversification.

In Brief

Age-dependent regulation of proliferative growth and differentiation along the proximodistal axis of leaves modulates organ symmetry and marginal patterning in heteroblasty, and enabled the action of homeobox genes in complex leaf shape evolution.

Highlights

An age-dependent growth gradient underpins regulation ofA. thalianaleaf symmetry

SPL9-mediated heteroblastic growth control potentiates leaf histogenic capacity

A common growth framework underlies heteroblasty in complex and simple leaves

SPL9 enables the action of homeobox genes that promote leaf complexity
Targeting the Atypical Chemokine Receptor 2 (ACKR2) improves the benefit of anti-PD-1 immunotherapy in melanoma
Authors: Noman Muhammad Zaeem , Szpakowska Martyna , Xiao Malina , Van Moer Kris , Ollert Markus , Berchem Guy , Chevigné Andy , Janji Bassam
Published: April 2024

Immune checkpoint blockade (ICB) therapies, targeting PD-1 or PD-L1, have transformed cancer treatment, particularly for aggressive cancers. However, many patients fail to benefit from ICBs due to tumor characteristics, including a non-inflammatory tumor microenvironment (TME) that impedes immune cell infiltration. This study investigated the potential of targeting the Atypical Chemokine Receptor 2 (ACKR2), known for scavenging CXCR3-related chemokines crucial for lymphocyte recruitment to tumors. Genetic targeting of ACKR2 in melanoma cells increased the release of essential chemokines associated with the inflamed TME. In mouse models, ACKR2 inhibition suppressed tumor growth, improved survival, and enhanced activated immune cell infiltration into the TME. Moreover, ACKR2 targeting synergized with anti-PD-1 therapy, overcoming resistance to anti-PD-1 and improving its efficacy. Analysis of melanoma patient data from The Cancer Genome Atlas (TCGA) revealed that patients with high levels of chemokines scavenged by ACKR2 had significantly better survival rates, with increased expression of NK cell and CD8 T cell markers indicating their presence in the TME. Notably, even in patients with high CD8 expression, those expressing low ACKR2 survived better than those expressing high ACKR2. This study emphasizes the clinical importance of targeting ACKR2 as an attractive strategy for the development of combination immunotherapies to treat cold tumors, which are clinically stratified to not be eligible for ICB-based therapy.
Text-related functionality and dynamics of visual human pre-frontal activations revealed through neural network convergence
Authors: Shoham Adva , Broday-Dvir Rotem , Yaron Itay , Yovel Galit , Malach Rafael
Published: April 2024

The functional role of visual activations of human pre-frontal cortex remains a deeply debated question. Its significance extends to fundamental issues of functional localization and global theories of consciousness. Here we addressed this question by comparing, dynamically, the potential parallels between the relational structure of prefrontal visual activations and visual and textual-trained deep neural networks (DNNs). The frontal visual relational structures were revealed in intra-cranial recordings of human patients, conducted for clinical purposes, while the patients viewed familiar images of faces and places. Our results reveal that visual relational structures in frontal cortex were, surprisingly, predicted by text and not visual DNNs. Importantly, the temporal dynamics of these correlations showed striking differences, with a rapid decline over time for the visual component, but persistent dynamics including a significant image offset response for the text component. The results point to a dynamic text-related function of visual prefrontal responses in the human brain.
MPRAVarDB: an online database and web server for exploring regulatory effects of genetic variants
Authors: Nizomov Javlon , Jin Weijia , Xia Yi , Liu Yunlong , Li Zhigang , Chen Li
Published: April 2024

Massively parallel reporter assay (MPRA) is an important technology to evaluate the impact of genetic variants on gene regulation. Here, we present MPRAVarDB, an online database and web server, for exploring regulatory effects of genetic variants. MPRAVarDB harbors 18 MPRA experiments designed to assess the regulatory effects of genetic variants associated with GWAS loci, eQTLs and various genomic features, resulting in a total of 242,818 variants tested across more than 30 cell lines and 30 human diseases or traits. MPRAVarDB empowers the query of MPRA variants by genomic region, disease and cell line or by any combination of these query terms. Notably, MPRAVarDB offers a suite of pretrained machine learning models tailored to the specific disease and cell line, facilitating the genome-wide prediction of regulatory variants. MPRAVarDB is friendly to use, and users only need a few clicks to receive query and prediction results.

Availability

https://mpravardb.rc.ufl.edu

Supplementary information

Supplementary data are available atBioinformaticsonline.
High-resolutionIn-situStructures of Mammalian Mitochondrial Respiratory Supercomplexes in Reaction within Native Mitochondria
Authors: Zheng Wan , Chai Pengxin , Zhu Jiapeng , Zhang Kai
Published: April 2024

Mitochondria play a pivotal role in ATP energy production through oxidative phosphorylation, which occurs within the inner membrane via a series of respiratory complexes. Despite extensivein-vitrostructural studies, revealing the atomic details of their molecular mechanisms in physiological states remains a major challenge, primarily because of the loss of the native environment during purification. Here, we directly image porcine mitochondria using anin-situcryo-electron microscopy approach. This enables us to determine the structures of various high-order assemblies of respiratory supercomplexes in their native states, achieving up to 1.8-Å local resolution. We identify four major supercomplex organizations: I1III2IV1, I1III2IV2, I2III2IV2, and I2III4IV2, which can potentially expand into higher-order arrays on the inner membranes. The formation of these diverse supercomplexes is largely contributed by ‘protein-lipids-protein’ interactions, which in turn dramatically impact the local geometry of the surrounding membranes. Ourin-situstructures also capture numerous reactive intermediates within these respiratory supercomplexes, shedding light on the dynamic processes of the ubiquinone/ubiquinol exchange mechanism in complex I and the Q-cycle in complex III. By comparing supercomplex structures from mitochondria treated under distinct conditions, we elucidate how conformational changes and ligand binding states interplay between complexes I and III in response to environmental redox alterations. Our approach, by preserving the native membrane environment, enables structural studies of mitochondrial respiratory supercomplexes in reaction at high resolution across multiple scales, spanning from atomic-level details to the broader subcellular context.
Deciphering Bacterial and Archaeal Transcriptional Dark Matter and Its Architectural Complexity
Authors: Mattick John S. A. , Bromley Robin E. , Watson Kaylee J. , Adkins Ricky S. , Holt Christopher I. , Lebov Jarrett F. , Sparklin Benjamin C. , Tyson Tyonna S. , Rasko David A. , Hotopp Julie C. Dunning
Published: April 2024

Transcripts are potential therapeutic targets, yet bacterial transcripts remain biological dark matter with uncharacterized biodiversity. We developed and applied an algorithm to predict transcripts for Escherichia coli K12 and E2348/69 strains (Bacteria:gamma-Proteobacteria) with newly generated ONT direct RNA sequencing data while predicting transcripts for Listeria monocytogenes strains Scott A and RO15 (Bacteria:Firmicute), Pseudomonas aeruginosa strains SG17M and NN2 strains (Bacteria:gamma-Proteobacteria), and Haloferax volcanii (Archaea:Halobacteria) using publicly available data. From >5 million E. coli K12 ONT direct RNA sequencing reads, 2,484 mRNAs are predicted and contain more than half of the predicted E. coli proteins. While the number of predicted transcripts varied by strain based on the amount of sequence data used for the predictions, across all strains examined, the average size of the predicted mRNAs is 1.6-1.7 kbp while the median size of the predicted bacterial 5'- and 3'- UTRs are 30-90 bp. Given the lack of bacterial and archaeal transcript annotation, most predictions are of novel transcripts, but we also predicted many previously characterized mRNAs and ncRNAs, including post-transcriptionally generated transcripts and small RNAs associated with pathogenesis in the E. coli E2348/69 LEE pathogenicity islands. We predicted small transcripts in the 100-200 bp range as well as >10 kbp transcripts for all strains, with the longest transcript for two of the seven strains being the nuo operon transcript, and for another two strains it was a phage/prophage transcript. This quick, easy, inexpensive, and reproducible method will facilitate the presentation of operons, transcripts, and UTR predictions alongside CDS and protein predictions in bacterial genome annotation as important resources for the research community.
Plant Growth analysis using computer. An auxiliary computational program. II
Authors: Portes Tomás de Aquino
Published: April 2024

The result of photosynthetic activity by plants is mass gain. Essential mineral elements are immobilized in the plant mass, the main element being carbon. In photosynthesis, this element is linked to one another forming carbon chains and to link one carbon to another the plant uses solar energy, making the mass rich in energy. Therefore, quantifying plant mass is interesting to estimate the efficiency of plants in accumulating mass and energy. Mass quantification is done using the growth analysis technique. The objective of this work was to develop a computer program to assist in the plant growth analysis. It consisted of adjusting mathematical equations to data on leaf area, total and leaf dry mass. Once the best equations were found, the instantaneous growth indicators, CGR, RGR, NAR, SLA, LAR, LAD and carbon flux (pn) were estimated from them. The adjusted equations were linear, logistic, quadratic, cubic, quadratic exponential and cubic exponential. The equations that best fit to the data were the quadratic exponential and cubic exponential. The program was developed in the C* language. For comparison purposes, the average physiological indicators of growth were estimated using the classic equations found in the literature.

Highlight

Plant growth analysis is a very useful technique for evaluating plant mass gain. To facilitate the analysis, a computer program presented in this article was developed. The software is important because there is nothing similar available and will facilitate the work of researchers working on the subject
GLP1R agonists activate human POMC neurons
Authors: Mazzaferro Simone , Chen Hsiao-Jou Cortina , Cahn Oliver , Yang Andrian , Shepilov Dmytro , Chen Jiahui , Alcaino Contanza , Macarelli Viviana , Mali Iman , Gribble Fiona , Reimann Frank , Marioni John , Merkle Florian T.
Published: April 2024

Drugs like Semaglutide (a.k.a. Ozempic/Wegovy) that activate the glucagon-like peptide-1 receptor (GLP1R) are a promising therapy for obesity and type 2 diabetes (T2D). Animal studies suggest that appetite-suppressing proopiomelanocortin (POMC) neurons in the arcuate nucleus of the hypothalamus are a likely target of these drugs, but the mechanisms by which they reduce food intake in humans are still unclear. We therefore generated POMC neurons from human pluripotent stem cells (hPSCs) to study their acute responses to GLP1R agonists by calcium imaging and electrophysiology. We found that hPSC-derived POMC neurons expressedGLP1Rand many of them robustly responded to GLP1R agonists by membrane depolarization, increased action potential firing rate, and extracellular calcium influx that persisted long after agonist withdrawal and was likely mediated by L-type calcium channels. Prolonged administration of Semaglutide upregulated transcriptional pathways associated with cell survival in POMC neurons, and downregulated pathways associated with oxidative stress and neurodegeneration. These findings suggest that POMC neurons contribute to the long-term appetite-suppressive effects of GLP1R agonists in humans.
Leading researchers in the leadership of leading research universities: meta-research analysis
Authors: Ioannidis John
Published: April 2024

It is unknown to what extent leading researchers are currently involved in the leadership of leading research universities as presidents or as executive board members. The academic administrative leader (president or equivalent role) of each of the 146 Carnegie tier 1 USA universities and of any of the top-100 universities per Times Higher Education (THE) 2024 ranking and the members of the executive governing bodies (Board of Trustees, Council, Corporation or similar) for the each of the top-20 universities per THE 2024 ranking were examined for high citation impact in their scientific subfield. Highly-cited was defined as the top-2% of a composite citation indicator (that considers citations, h-index, co-authorship adjusted hm-index and citations to papers as single, first, last authors) in their main scientific subfield based on career-long impact until end-2022 among all scholars focusing in the same subfield and having published ≥5 full papers. Very highly-cited was similarly defined as the top-0.2%. Science was divided into 174 fields per Science-Metrix classification. 38/146 (26%) tier 1 USA university leaders as of end-2023 were highly-cited and 5/146 (3%) were very highly-cited. The respective figures for the top-100 THE 2024 universities globally were 43/100 and 12/100. For the 13 US universities among the top-20 of THE 2024, the probability of their leader being highly-cited was lower (6/13, 46%) than the probability of a randomly chosen active full tenured professor from their faculty being highly-cited (52-77%). Across 444 board members of 14 top-10 THE 2024 universities with data, only 65 (15%) were academics, and 19 (4%) were highly-cited; academics were rare in USA university boards. Board members had predominantly careers in for-profit companies. In conclusion, leading research universities have a dearth of leaders who are high-impact researchers.
Cell-specific polymerization-driven biomolecular condensate formation fine-tunes root tissue morphogenesis
Authors: Su Jianbin , Xu Xianjin , Cseke Leland J. , Whittier Sean , Zhou Ruimei , Zhang Zhengzhi , Dietz Zackary , Singh Kamal , Yang Bing , Chen Shi-You , Picking William , Zou Xiaoqin , Gassmann Walter
Published: April 2024

Formation of biomolecular condensates can be driven by weak multivalent interactions and emergent polymerization. However, the mechanism of polymerization-mediated condensate formation is less studied. We found lateral root cap cell (LRC)-specific SUPPRESSOR OF RPS4-RLD1 (SRFR1) condensates fine-tune primary root development. Polymerization of the SRFR1 N-terminal domain is required for both LRC condensate formation and optimal root growth. Surprisingly, the first intrinsically disordered region (IDR1) of SRFR1 can be functionally substituted by a specific group of intrinsically disordered proteins known as dehydrins. This finding facilitated the identification of functional segments in the IDR1 of SRFR1, a generalizable strategy to decode unknown IDRs. With this functional information we further improved root growth by modifying the SRFR1 condensation module, providing a strategy to improve plant growth and resilience.
Genetic editing of primary human dorsal root ganglion neurons using CRISPR-Cas9 with functional confirmation
Authors: Palomino Seph , Gabriel Katherin , Mwirigi Juliet , Cervantes Anna , Horton Peter , Funk Geoffrey , Moutal Aubin , Martin Laurent , Khanna Rajesh , Price Theodore , Patwardhan Amol
Published: April 2024

CRISPR-Cas9 editing is now the leading method for genome editing and is being advanced for the treatment of human disease. CRIPSR editing could have many applications for treatment of neurological diseases, including pain but traditional viral vector delivery approaches have neurotoxicity limiting their use. Overcoming these issues could open the door for genome editing treatments for diseases like intractable pain where the dorsal root ganglia (DRG) would be the desired target. To this end, we describe a simple method for viral-vector-independent transfection of primary human DRG (hDRG) neurons for CRISPR-Cas9 editing. As proof of principle, we editedTRPV1, NTSR2, andCACNA1Eusing a lipofection method with CRISPR-Cas9 plasmids containing reporter tags (GFP or mCherry). Transfection was successful as demonstrated by the expression of the reporters as early as two daysin vitro. CRISPR-Cas9 editing was confirmed at the genome level with insertion and deletion detection system T7-endonuclease-I assay; protein level with immunocytochemistry and Western blot; and functional level through capsaicin-induced Ca2+accumulation in a high-throughput compatible fluorescent imaging plate reader (FLIPR) system. This work establishes a reliable, target specific, non-viral CRISPR-Cas9-mediated genetic editing in primary human neurons with potential for future clinical application for intractable pain.

Teaser

We describe a non-viral transfection method for CRISPR-Cas9 gene editing in human dorsal root ganglion neurons.
Native molecular architectures of centrosomes inC. elegansembryos
Authors: Tollervey Fergus , Rios Manolo U. , Zagoriy Evgenia , Woodruff Jeffrey B. , Mahamid Julia
Published: April 2024

Centrosomes organize microtubules that are essential for mitotic divisions in animal cells. They consist of centrioles surrounded by Pericentriolar Material (PCM). Questions related to mechanisms of centriole assembly, PCM organization, and microtubule formation remain unanswered, in part due to limited availability of molecular-resolution structural analysesin situ. Here, we use cryo-electron tomography to visualize centrosomes across the cell cycle in cells isolated fromC. elegansembryos. We describe a pseudo-timeline of centriole assembly and identify distinct structural features including a cartwheel in daughter centrioles, and incomplete microtubule doublets surrounded by a star-shaped density in mother centrioles. We find that centriole and PCM microtubules differ in protofilament number (13 versus 11) indicating distinct nucleation mechanisms. This difference could be explained by atypical γ-tubulin ring complexes with 11-fold symmetry identified at the minus ends of short PCM microtubules. We further characterize a porous and disordered network that forms the interconnected PCM. Thus, our work builds a three-dimensional structural atlas that helps explain how centrosomes assemble, grow, and achieve function.
The kinesin motor Kif9 regulates centriolar satellite positioning and mitotic progression
Authors: Vicente Juan Jesus , Wagenbach Michael , Decarreau Justin , Zelter Alex , MacCoss Michael J. , Davis Trisha N. , Wordeman Linda
Published: April 2024

Centrosomes are the principal microtubule-organizing centers of the cell and play an essential role in mitotic spindle function. Centrosome biogenesis is achieved by strict control of protein acquisition and phosphorylation prior to mitosis. Defects in this process promote fragmentation of pericentriolar material culminating in multipolar spindles and chromosome missegregation. Centriolar satellites, membrane-less aggrupations of proteins involved in the trafficking of proteins toward and away from the centrosome, are thought to contribute to centrosome biogenesis. Here we show that the microtubule plus-end directed kinesin motor Kif9 localizes to centriolar satellites and regulates their pericentrosomal localization during interphase. Lack of Kif9 leads to aggregation of satellites closer to the centrosome and increased centrosomal protein degradation that disrupts centrosome maturation and results in chromosome congression and segregation defects during mitosis. Our data reveal roles for Kif9 and centriolar satellites in the regulation of cellular proteostasis and mitosis.
Towards self-regeneration: exploring the limits of protein synthesis in the PURE cell-free transcription-translation system
Authors: Ganesh Ragunathan Bava , Maerkl Sebastian J.
Published: April 2024

Self-regeneration is a key function of living systems that needs to be recapitulatedin vitroto create a living synthetic cell. A major limiting factor for protein self-regeneration in the PURE cell-free transcription-translation system is its high protein concentration, which far exceed the system’s protein synthesis rate. Here we were able to drastically reduce the non-ribosomal PURE protein concentration up to 97.3% while increasing protein synthesis efficiency. Although crowding agents were not effective in the original PURE formulation, we found that in highly dilute PURE formulations addition of 6% dextran considerably increased protein synthesis rate and total protein yield. These new PURE formulations will be useful for many cell-free synthetic biology applications and we estimate that PURE can now support the complete self-regeneration of all 36 non-ribosomal proteins, which is a critical step towards the development of a universal biochemical constructor and living synthetic cell.