bluuebunny/crossref_metadata_2025 huggingface dataset:
Pesticidal Effects OfGmelina arborea(Roxb) Powders On Beans Weevil (Callosobruchus maculatus) At Vom
Authors: Olanrewaju Ojuolape Damilola , Edamaku Precious Josiah , Nwite Ofodile Peter , Usman Umoru , Murtala Aliyu Mohammed
Published: April 2023

Cowpea (Vigna unguiculata (L.) Walp. is one of the most nutritious grain legumes where it is valuable as a source of dietary protein yet most of the yields are lost as a result of infestation by pest especially Callosobruchus maculatus. cowpea weevil which is one of the most prevalent and a major destructive insect pest of stored legumes. Controlling of the pest by use of synthetic pesticides is raising serious concern on the environmental safety and consumer health hazards. This study was aimed at determining the pesticidal efficacy of Gmelina arborea stem bark and leaf powder on C. maculatus. The experiment was laid in a Completely Randomized Design (CRD) with three application rates (10g/200g grains, 10g/200g grains and 5+5g/200g cowpea grain) of the botanicals (leaf and stem bark powders and combination of leaf stem bark powders respectively) replicated three times was used in the assessment. The parameters and data collected in the experiment are; percentage of weevil mortality, Grain damaged, Number of Exit holes, newly emerged weevil, percentage of weight damaged. All data generated were statistically analyzed. The results of this study demonstrated the active potentials of these G. arborea plant parts as plant-derived pesticides against cowpea weevil. The effect of treated plant parts on percentage mortality rate showed significant difference (P < 0.05) over the untreated (control) as mixed leaf and stem bark powders recorded the highest mortality rate (85.00%). The leaf (51.70%) and stem bark (43.30%) powders also showed higher effect (51.70%) respectively while the lowest mortality rate was observed in the control (21.67%). The untreated (control) gave the highest number of newly emerged weevils (2.33) whereas the lowest (5.33) was found in Gmelina leaf + stem bark powders Gmelina leaf + stem bark powders attained the highest beans damage (11.00) while the lowest (9.67) was recorded in Gmelina leaf powders. The exit holes made by the weevils at the end of the experiment amongst G. arborea plant parts were highest (9.33) in Gmelina stem bark powders whereas lowest was recorded on Gmelina leaf + stem bark powders (5.33). Leaf + Stem bark powders was the most effective throughout the experiment followed by the leaf and stem bark powders respectively. In view of these findings G. arborea leaf and stem bark powders have a strong bioactivity and is effective against C. maculatus. Therefore, since these plant parts have no any adverse effects on the grains and safe to the environment, they are recommended for future usage in storage grains to control of C. maculatus.
Single Cell Resolution Spatial Mapping of Human Hematopoiesis Reveals Aging-Associated Topographic Remodeling
Authors: Sarachakov Aleksandr , Varlamova Arina , Svekolkin Viktor , Galkin Ilia , Valencia Itzel , Unkenholz Caitlin , Pannellini Tania , Akaeva Aida , Smirnova Sofia , Ovcharov Pavel , Polyakova Margarita , Tabakov Dmitrii , Postovalova Ekaterina , Sethi Isha , Shin Nara , Bagaev Alexander , Itkin Tomer , Crane Genevieve , Kluk Michael , Geyer Julia , Inghirami Giorgio , Patel Sanjay
Published: April 2023

The spatial anatomy of hematopoiesis in bone marrow has been extensively studied in mice and other preclinical models, but technical challenges have precluded a commensurate exploration in humans. Institutional pathology archives contain thousands of paraffinized bone marrow core biopsy tissue specimens, providing a rich resource for studying the intact human bone marrow topography in a variety of physiologic states. Thus, we developed an end-to-end pipeline involving multiparameter whole tissue staining, in situ imaging at single-cell resolution, and artificial intelligence (AI)-based digital image analysis, and then applied it to a cohort of disease-free samples to survey alterations in the hematopoietic topography associated with aging. Our data indicate heterogeneity in marrow adipose tissue (MAT) content within each age group, and an inverse correlation between MAT content and proportions of early myeloid and erythroid precursors, irrespective of age. We identify consistent endosteal and perivascular positioning of hematopoietic stem and progenitor cells (HSPCs) with medullary localization of more differentiated elements and, importantly, uncover new evidence of aging-associated changes in cellular and vascular morphologies, microarchitectural alterations suggestive of inflammaging, and diminution of a potentially active megakaryocytic niche. Overall, our findings suggest that there is topographic remodeling of human hematopoiesis associated with aging. More generally, we demonstrate the potential to deeply unravel the spatial biology of normal and pathologic human bone marrow states using intact archival tissue specimens.
Paracetamol/acetaminophen hepatotoxicity: new markers for monitoring the elimination of the reactive N-Acetyl-p-benzoquinone imine
Authors: Gorrochategui Eva , Vee Marc Le , Selmi Habiba , Gérard Anne , Chaker Jade , Krais Annette M , Lindh Christian , Fardel Olivier , Chevrier Cécile , Cann Pierre Le , Miller Gary W , Barouki Robert , Jégou Bernard , Gicquel Thomas , Kristensen David , David Arthur
Published: April 2023

Paracetamol/acetaminophen (N-acetyl-p-aminophenol, APAP) overdose is one of the most important causes of drug-induced liver injury worldwide. Hepatotoxicity induced by APAP is mainly caused by the production of N-acetyl-p-benzoquinone imine (NAPQI), a highly reactive intermediate formed predominantly via the cytochrome P450 2E1. Here, we used human studies andin vitromodels to demonstrate that NAPQI-derived thiomethyl metabolites identified using high-resolution mass spectrometry could serve to monitor NAPQI detoxification and elimination in patients (after intake at recommended dose or after intoxication), and to study inter-individual variability in NAPQI production. Usingin vitrohuman models, we showed that these thiomethyl metabolites are directly linked to NAPQI detoxification since they are mainly formed after exposure to glutathione-derived conjugates via an overlooked pathway called the thiomethyl shunt. These long-term thiomethyl metabolites have great potential in future clinical studies in order to provide a more reliable history of APAP ingestion in case of acute intoxication or to study underlying causes involved in APAP-induced hepatotoxicity.

One Sentence Summary

Thiomethyl metabolites are new markers to monitor the elimination of the toxic N-acetyl-p-benzoquinone imine after therapeutic use or intoxication.
The double life of trichomes: understanding their dual role in herbivory and herbicide resistance
Authors: Johnson Nia M , Baucom Regina S
Published: April 2023

External features of organisms often serve as the first line of defense in their immediate environments. Trichomes are hair-like appendages on plant surfaces that can defend against damaging agents such as pathogens, herbivores, and UV radiation. It is currently unknown if the variation observed in trichome traits represents dual or conflicting roles against different types of stressors. Here, we assess whether trichomes serve as an herbicide resistance trait and how it coincides with the conventionally studied defensive strategy of herbivory resistance. In a series of experiments, we exposed the annual invasive velvetleaf (Abutilon theophrasti) to glyphosate (active ingredient in the herbicide ‘Roundup’) to investigate whether trichome traits (shape and density) are linked to herbicide resistance and to test whether herbicide alters selection on plant trichomes. We found that an increased proportion of branched trichomes positively impacted herbicide resistance as well as chewing herbivory resistance. We also found evidence that glyphosate imposes positive selection on branched trichomes in velvetleaf. Overall, our results indicate that branched trichomes can contribute to both herbicide and herbivory resistance, serving as a dual structural form of resistance reducing plant injury. If our results are to be applied more broadly, it would suggest that herbicide exposure can alter the composition of plant trichomes, potentially impacting trichome-mediated defenses against various external stressors.
The Influence of Brain MRI Defacing Algorithms on Brain-Age Predictions via 3D Convolutional Neural Networks
Authors: Cali Ryan J. , Bhatt Ravi R. , Thomopoulos Sophia I. , Gadewar Shruti , Gari Iyad Ba , Chattopadhyay Tamoghna , Jahanshad Neda , Thompson Paul M. ,   the Alzheimer’s Disease Neuroimaging Initiative
Published: April 2023

In brain imaging research, it is becoming standard practice to remove the face from the individual’s 3D structural MRI scan to ensure data privacy standards are met. Face removal - or ‘defacing’ - is being advocated for large, multi-site studies where data is transferred across geographically diverse sites. Several methods have been developed to limit the loss of important brain data by accurately and precisely removing non-brain facial tissue. At the same time, deep learning methods such as convolutional neural networks (CNNs) are increasingly being used in medical imaging research for diagnostic classification and prognosis in neurological diseases. These neural networks train predictive models based on patterns in large numbers of images. Because of this, defacing scans could remove informative data. Here, we evaluated 4 popular defacing methods to identify the effects of defacing on ‘brain age’ prediction – a common benchmarking task of predicting a subject’s chronological age from their 3D T1-weighted brain MRI. We compared brain-age calculations using defaced MRIs to those that were directly brain extracted, and those with both brain and face. Significant differences were present when comparing average per-subject error rates between algorithms in both the defaced brain data and the extracted facial tissue. Results also indicated brain age accuracy depends on defacing and the choice of algorithm. In a secondary analysis, we also examined how well comparable CNNs could predict chronological age from the facial region only (the extracted portion of the defaced image), as well as visualize areas of importance in facial tissue for predictive tasks using CNNs. We obtained better performance in age prediction when using the extracted face portion alone than images of the brain, suggesting the need for caution when defacing methods are used in medical image analysis.
Collecting-Gathering Biophysics of the BlackwormL. variegatus
Authors: Tuazon Harry , Nguyen Chantal , Kaufman Emily , Tiwari Ishant , Bermudez Jessica , Chudasama Darshan , Peleg Orit , Bhamla M. Saad
Published: April 2023

Many organisms exhibit collecting and gathering behaviors as a foraging and survival method. Certain benthic macroinvertebrates are classified as collector-gatherers due to their collection of particulate matter as a food source, such as the aquatic oligochaeteLumbriculus variegatus(California blackworms). Blackworms demonstrate the ability to ingest organic and inorganic materials, including microplastics, but previous work has only qualitatively described their possible collecting behaviors for such materials. The mechanism through which blackworms consolidate discrete particles into a larger clumps remains unexplored quantitatively. By analyzing a group of blackworms in a large arena with an aqueous algae solution, we discover that their relative collecting efficiency is proportional to population size. Examining individual blackworms under a microscope reveals that both algae and microplastics physically adhere to the worm’s body due to external mucus secretions, which cause the materials to clump around the worm. We observe that this clumping reduces the worm’s exploration of its environment, potentially due to thigmotaxis. To validate the observed biophysical mechanisms, we create an active polymer model of a worm moving in a field of particulate debris with a short-range attractive force on its body to simulate its adhesive nature. We find that the attractive force increases gathering efficiency. This study offers insights into the mechanisms of collecting-gathering behavior, informing the design of robotic systems, as well as advancing our understanding the ecological impacts of microplastics on benthic invertebrates.
Ribozyme synthesis of both L- and D- amino acid oligos
Authors: Wang Yuhong
Published: April 2023

The ribosome is responsible for assembling proteins using 20 naturally occurring L-handed amino acids. However, incorporating non-natural amino acids into a protein is a challenging process needs improvement. In this study, we report a new possible approach to creating nonnatural peptides using ribozymes inspired by the peptidyl transfer center. These RNA scaffolds, which are approximately 100 nucleotides in length, bind to RNase T1 truncated tRNA-like chimeras and bring them into close proximity to facilitate peptide ligation. We used single-molecule fluorescence resonance energy transfer (smFRET) to show close distances between RNA-RNA, tRNALys-tRNALys, and RNA-tRNALyspairs, which strongly suggests that the mechanism of peptide ligation is due to the proximity of the substrate through dimerization of the enzymes. Mass spectrometry analysis confirmed the detection of oligopeptides from four amino acids, including L-Lysine, D-Lysine, L-Phenylalanine, and D-Phenylalanine. These results indicate that ribozymes have greater flexibility in accommodating nonnatural amino acids. Our findings pave the way for potentially new avenues in the synthesis of nonnatural peptides, beyond the limitations of ribosomal peptide synthesis and other existing methods.

GRAPHICAL ABSTRACT
Combining LIANA and Tensor-cell2cell to decipher cell-cell communication across multiple samples
Authors: Baghdassarian Hratch , Dimitrov Daniel , Armingol Erick , Saez-Rodriguez Julio , Lewis Nathan E.
Published: April 2023

In recent years, data-driven inference of cell-cell communication has helped reveal coordinated biological processes across cell types. While multiple cell-cell communication tools exist, results are specific to the tool of choice, due to the diverse assumptions made across computational frameworks. Moreover, tools are often limited to analyzing single samples or to performing pairwise comparisons. As experimental design complexity and sample numbers continue to increase in single-cell datasets, so does the need for generalizable methods to decipher cell-cell communication in such scenarios. Here, we integrate two tools, LIANA and Tensor-cell2cell, which combined can deploy multiple existing methods and resources, to enable the robust and flexible identification of cell-cell communication programs across multiple samples. In this protocol, we show how the integration of our tools facilitates the choice of method to infer cell-cell communication and subsequently perform an unsupervised deconvolution to obtain and summarize biological insights. We explain how to perform the analysis step-by-step in both Python and R, and we provide online tutorials with detailed instructions available athttps://ccc-protocols.readthedocs.io/. This protocol typically takes ∼1.5h to complete from installation to downstream visualizations on a GPU-enabled computer, for a dataset of ∼63k cells, 10 cell types, and 12 samples.
A small epitope shared by p53 and an unrelated protein upregulated after adenovirus infection
Authors: Miciak Jessica J. , Bunz Fred
Published: April 2023

Cancers commonly harbor point mutations inTP53that cause overexpression of functionally inactive p53 proteins. These mutant forms of p53 are immunogenic, and therefore present tantalizing targets for new forms of immunotherapy. Understanding how the immune system recognizes p53 is an important prerequisite for the development of targeted therapeutic strategies designed to exploit this common neoantigen. Monoclonal antibodies have been extensively used to probe the structural conformation of the varied isoforms of p53 and their respective mutants, and are still indispensable tools for studying the complex biological functions of these proteins. In this report, we describe the mapping of a novel epitope on p53 that appears to be shared by heat shock proteins (HSPs), which are typically upregulated in response to a variety of viral infections.
Serial Lift-Out – Sampling the Molecular Anatomy of Whole Organisms
Authors: Schiøtz Oda Helene , Kaiser Christoph J.O. , Klumpe Sven , Morado Dustin R. , Poege Matthias , Schneider Jonathan , Beck Florian , Thompson Christopher , Plitzko M. Jürgen
Published: April 2023

Cryo-focused ion beam milling of frozen-hydrated cells and subsequent cryo-electron tomography (cryo-ET) has enabled the structural elucidation of macromolecular complexes directly inside cells. Application of the technique to multicellular organisms and tissues, however, is still limited by sample preparation. While high-pressure freezing enables the vitrification of thicker samples, it prolongs subsequent preparation due to increased thinning times and the need for extraction procedures. Additionally, thinning removes large portions of the specimen, restricting the imageable volume to the thickness of the final lamella, typically < 300 nm. Here, we introduce Serial Lift-Out, an enhanced lift-out technique that increases throughput and obtainable contextual information by preparing multiple sections from single transfers. We apply Serial Lift-Out toC. elegansL1 larvae yielding a cryo-ET dataset sampling the worm’s anterior-posterior axis and resolve its ribosome structure to 7 Å, illustrating how Serial Lift-Out enables the study of multicellular molecular anatomy.
Computational design of intrinsically disordered protein regions by matching bulk molecular properties
Authors: Strome Bob , Elemam Khaled , Pritisanac Iva , Forman-Kay Julie D. , Moses Alan M.
Published: April 2023

Algorithms for computational protein design usually begin with a 3D structure and design an amino acid sequence that will fold into that structure. Since intrinsically disordered protein regions lack stable 3D structures, strategies for their design have been limited. Here we describe and validate a general computational strategy for design of intrinsically disordered regions (IDRs). Our algorithm designs synthetic IDRs by minimizing the distance of an initially random amino acid sequence to a known IDR in a high-dimensional space of molecular properties, such as repeat content, charge and hydrophobicity. We tested a handful of IDRs designed to target proteins to mitochondria and heat-induced condensates, and several showed the expected patterns in cells.

One sentence summary

We design synthetic mitochondrial targeting signals and condensate forming intrinsically disordered regions
The bacterial community of the European spruce bark beetle in space and time
Authors: Moussa Abdelhameed , Nones Stefano , Vannucchi Patrizia Elena , Shahzad Gul-i-Rayna , Dittmer Jessica , Corretto Erika , Schebeck Martin , Faccoli Massimo , Battisti Andrea , Stauffer Christian , Schuler Hannes
Published: April 2023

The European spruce bark beetleIps typographusis a pest causing severe damages in forests dominated by the Norway spruce in Europe. Microorganisms play an essential role in the host species performance, including nutrition, fitness as well as in overcoming host defenses. Here, we performed high-throughput 16S rRNA metabarcoding ofI. typographusacross different populations in Europe, to assess its bacterial community. We investigated four postglacial refugial areas in Europe and focused specifically on a current bark beetle hot spot in the Dolomites where we compared populations with different epidemiological phases (outbreaking vs. non-outbreaking) and across different seasons (pre-overwintering vs. overwintering). Our results show that the bacterial community structure varied among populations from the refugial areas and between different regions within the Dolomites. We found a significant difference in the bacterial community between pre-overwintering and overwintering individuals, but we did not find differences between epidemic and endemic populations. The prevalence of the genusErwiniawhich was present in every individual andPseudoxanthomonasin almost every individual across all populations, suggests that these taxa form the core bacterial community ofI. typographus. Furthermore, several additional bacterial taxa occurred in all populations, but with variable frequencies. This study highlights a complex interaction ofI. typographusand various bacterial taxa across different regions and ecological phases ofI. typographuspopulations and provides new insights into the role of microorganisms in the biology of this important pest species.
A novel biomechanical indicator for impaired ankle dorsiflexion function during walking in individuals with chronic stroke
Authors: Srivastava Shraddha , Kindred John H , Seamon Bryant A. , Charalambous Charalambos C. , Boan Andrea D. , Kautz Steven A. , Bowden Mark G
Published: April 2023

Ankle dorsiflexion function during swing phase of the gait cycle contributes to foot clearance and plays an important role in walking ability post-stroke. Commonly used biomechanical measures such as foot clearance and ankle joint excursion have limited ability to accurately evaluate dorsiflexor function in stroke gait. We retrospectively evaluated ankle angular velocity and ankle angular acceleration as direct measures for swing phase dorsiflexor function in post-stroke gait of 61 chronic stroke survivors. Our linear regression models revealed that peak ankle angular velocity (AAVP), peak ankle angular acceleration (AAAP), peak dorsiflexion angle (DFAP) and peak foot clearance (FCLP) during swing had a significant relationship (p < 0.05) with impaired dorsiflexion function. AAAPand DFAPaccounted for the most variance of dorsiflexion function. Additionally, AAVP, AAAP, FCLPduring swing, correlated significantly with all clinical outcome measures of walking ability. DFAPduring swing had a positive correlation only with FMA-LE. Post-hoc William’st-tests, used to compare the magnitude of difference between two non-independent correlations, revealed that the correlation between all clinical measures and DFAPwere significantly weaker than with AAVPand AAAP. We also found that correlation between FMA-LE and FCLPwas weaker than with AAVPand AAAP. We found an excellent test-retest reliability for both AAVP(ICC = 0.968) and AAAP(ICC = 0.947). These results suggest that DFAPmay only be associated with non-task specific isolated dorsiflexion movement, but not during walking. FCLPis associated with dorsiflexion function and walking ability measures but not as strongly as AAVPand AAAPpossibly because FCLPis influenced by contribution from hip and knee joint movements during walking. Therefore, we believe that AAVPand AAAPboth can be used as reliable measures of impaired dorsiflexion function in post-stroke gait.
Semantic Representation of Neural Circuit Knowledge inCaenorhabditis elegans
Authors: Prakash Sharan J. , Van Auken Kimberly M. , Hill David P. , Sternberg Paul W.
Published: April 2023

In modern biology, new knowledge is generated quickly, making it challenging for researchers to efficiently acquire and synthesise new information from the large volume of primary publications. To address this problem, computational approaches that generate machine-readable representations of scientific findings in the form of knowledge graphs have been developed. These representations can integrate different types of experimental data from multiple papers and biological knowledge bases in a unifying data model, providing a complementary method to manual review for interacting with published knowledge. The Gene Ontology Consortium (GOC) has created a semantic modelling framework that extends individual functional gene annotations to structured descriptions of causal networks representing biological processes (Gene Ontology Causal Activity Modelling, or GO-CAM). In this study, we explored whether the GO-CAM framework could represent knowledge of the causal relationships between environmental inputs, neural circuits and behavior in the model nematodeC. elegans(C. elegansNeural Circuit Causal Activity Modelling (CeN- CAM)). We found that, given extensions to several relevant ontologies, a wide variety of author statements from the literature about the neural circuit basis of egg-laying and carbon dioxide (CO2) avoidance behaviors could be faithfully represented withCeN-CAM. Through this process, we were able to generate generic data models for several categories of experimental results. We also discuss how semantic modelling may be used to functionally annotate theC. elegansconnectome. Thus, Gene Ontology-based semantic modelling has the potential to support various machine-readable representations of neurobiological knowledge.

Graphical Abstract
Anin vitroassay to investigate venom neurotoxin activity on muscle-type nicotinic acetylcholine receptor activation and for the discovery of toxin-inhibitory molecules
Authors: Patel Rohit N , Clare Rachel H , Ledsgaard Line , Nys Mieke , Kool Jeroen , Laustsen Andreas H , Ulens Chris , Casewell Nicholas R
Published: April 2023

Snakebite envenoming is a neglected tropical disease that causes over 100,000 deaths annually. Envenomings result in variable pathologies, but systemic neurotoxicity is among the most serious and is currently only treated with difficult to access and variably efficacious commercial antivenoms. Venom-induced neurotoxicity is often caused by α-neurotoxins antagonising the muscle-type nicotinic acetylcholine receptor (nAChR), a ligand-gated ion channel. Discovery of therapeutics targeting α-neurotoxins is hampered by relying on binding assays that do not reveal restoration of receptor activity or more costly and/or lower throughput electrophysiology-based approaches. Here, we report the validation of a screening assay for nAChR activation using immortalised TE671 cells expressing the γ-subunit containing muscle-type nAChR and a fluorescent dye that reports changes in cell membrane potential. Assay validation using traditional nAChR agonists and antagonists, which either activate or block ion fluxes, was consistent with previous studies. We then characterised antagonism of the nAChR by a variety of elapid snake venoms that cause muscle paralysis in snakebite victims, before defining the toxin-inhibiting activities of commercial antivenoms, and new types of snakebite therapeutic candidates, namely monoclonal antibodies, decoy receptors, and small molecules. Our findings show robust evidence of assay uniformity across 96-well plates and highlight the amenability of this approach for the future discovery of new snakebite therapeutics via screening campaigns. The described assay therefore represents a useful first-step approach for identifying α-neurotoxins and their inhibitors in the context of snakebite envenoming, and it should provide wider value for studying modulators of nAChR activity from other sources.
Radio-Immune Response Modelling for Spatially Fractionated Radiotherapy
Authors: Cho Young-Bin , Yoon Nara , Suh John H. , Jacob Scott G.
Published: April 2023

Radiation-induced cell death is a complex process influenced by physical, chemical and biological phenomena. Strong dose gradient may intensify the complexity and reportedly creates significantly more cell death known as bystander effect. Although consensus on the nature and the mechanism of the bystander effect were not yet made, the immune process presumably plays an important role in many aspects of the radiotherapy including the bystander effect. Immune response of host body and immune suppression of tumor cells are modelled with four compartments in this study; viable tumor cells, T cell lymphocytes, immune triggering cells, and doomed cells. The growth of tumor was analyzed in two distinctive modes of tumor status (immune limited and immune escape) and its bifurcation condition. Tumors in the immune limited mode can grow only up to a finite size, named as terminal tumor volume analytically calculated from the model. The dynamics of the tumor growth in the immune escape mode is much more complex than the tumors in the immune limited mode especially when the status of tumor is close to the bifurcation condition. Radiation can kill tumor cells not only by radiation damage but also by boosting immune reaction. The model demonstrated that the highly heterogeneous dose distribution in spatially fractionated radiotherapy (SFRT) can make a drastic difference in tumor cell killing compared to the homogeneous dose distribution. SFRT can not only enhance but also moderate the cell killing depending on the immune response triggered by many factors such as dose prescription parameters, tumor volume at the time of treatment and tumor characteristics. The model was applied to the lifted data of 67NR tumors on mice and a sarcoma patient treated multiple times over 1200 days for the treatment of tumor recurrence as a demonstration.
PersonalizedClostridioides difficileengraftment risk prediction and probiotic therapy assessment in the human gut
Authors: Carr Alex , Baliga Nitin S. , Diener Christian , Gibbons Sean M.
Published: April 2023

Clostridioides difficilecolonizes up to 30-40% of community-dwelling adults without causing disease.C. difficileinfections (CDIs) are the leading cause of antibiotic-associated diarrhea in the U.S. and typically develop in individuals following disruption of the gut microbiota due to antibiotic or chemotherapy treatments. Further treatment of CDI with antibiotics is not always effective and can lead to antibiotic resistance and recurrent infections (rCDI). The most effective treatment for rCDI is the reestablishment of an intact microbiota via fecal microbiota transplants (FMTs). However, the success of FMTs has been difficult to generalize because the microbial interactions that prevent engraftment and facilitate the successful clearance ofC. difficileare still only partially understood. Here we show how microbial community-scale metabolic models (MCMMs) accurately predicted known instances ofC. difficilecolonization susceptibility or resistancein vitroandin vivo. MCMMs provide detailed mechanistic insights into the ecological interactions that governC. difficileengraftment, like cross-feeding or competition involving metabolites like succinate, trehalose, and ornithine, which differ from person to person. Indeed, three distinctC. difficilemetabolic niches emerge from our MCMMs, two associated with positive growth rates and one that represents non-growth, which are consistently observed across 15,204 individuals from five independent cohorts. Finally, we show how MCMMs can predict personalized engraftment andC. difficilegrowth suppression for a probiotic cocktail (VE303) designed to replace FMTs for the treatment rCDI. Overall, this powerful modeling approach predicts personalizedC. difficileengraftment risk and can be leveraged to assess probiotic treatment efficacy. MCMMs could be extended to understand the mechanistic underpinnings of personalized engraftment of other opportunistic bacterial pathogens, beneficial probiotic organisms, or more complex microbial consortia.
BCAT1 regulates glioblastoma cell plasticity and contributes to immunosuppression
Authors: Boskovic Pavle , Wilke Nathalie , Lichter Peter , Francois Liliana , Radlwimmer Bernhard
Published: April 2023

Glioblastoma is the most common malignant brain tumor in adults. Cellular plasticity and the poorly differentiated features result in a fast relapse of the tumors following treatment. Moreover, the immunosuppressive microenvironment proved to be a major obstacle to immunotherapeutic approaches. Branched-chain amino acid transaminase 1 (BCAT1) is a metabolic enzyme that converts branched-chain amino acids into branched-chain keto acids, depleting cellular α-ketoglutarate and producing glutamate. BCAT1 is expressed in and drives the growth of glioblastoma and other cancers. Here we show that low-BCAT1 expression correlates with differentiated glioblastoma subtypes and its knockout (KO) results in a differentiated phenotype in human and mouse glioblastoma cells. Consistent with these observations, Bcat1-KO mouse glioblastoma cells were highly susceptible to serum-induced differentiationin vitro. The transition to a differentiated cell state was linked to the increased activity of TET demethylases and the hypomethylation and activation of neuronal differentiation genes. Orthotopic tumor injection into immunocompetent mice demonstrated that the brain microenvironment is sufficient to induce differentiation of Bcat1-KO tumorsin vivo. In addition, the knockout of Bcat1 attenuated immunosuppression, allowing for an extensive infiltration of CD8+cytotoxic T-cells and complete abrogation of tumor growth. Additional analysis in immunodeficient hosts revealed that both Bcat1-KO-induced differentiation and immunomodulation contribute to the long-term suppression of tumor growth. In summary, our study demonstrates that BCAT1 promotes glioblastoma growth by blocking tumor cell differentiation and sustaining an immunosuppressive microenvironment. These findings suggest novel modes limiting glioblastoma phenotypic plasticity and therapeutic failure through targeting BCAT1.

Importance of the study

High expression of BCAT1 occurs in many tumor entities and is related to aggressiveness, proliferation and invasion of tumor cells. In this study, we show that its expression is crucial for the continuous growth of glioblastoma cells by preventing their differentiation. Furthermore, we show that the expression of BCAT1 modulates the tumor immune microenvironment, suppressing the CD8 T-cell response. BCAT1 knockout causes glioblastoma cell differentiation and a persistent CD8 T-cell response, which is sufficient to abrogate tumor growth and prolong survival inin vivoimmunocompetent and immunodeficient models, respectively. Our findings consolidate BCAT1 as a major player in glioblastoma and highlight its importance as a potential future target of research in this and other tumor entities.

Key Points

BCAT1 expression maintains poorly differentiated features of glioblastoma cells and provides resistance to differentiation.

Expression of BCAT1 in glioblastoma cells contributes to the immunosuppressive features of the tumor.
The Genome-wide Signature of Short-term Temporal Selection
Authors: Lynch Michael , Wei Wen , Ye Zhiqiang , Pfrender Michael
Published: April 2023

Despite evolutionary biology’s obsession with natural selection, few studies have evaluated multi-generational series of patterns of selection on a genome-wide scale in natural populations. Here, we report on a nine-year population-genomic survey of the microcrustaceanDaphnia pulex.The genome-sequences of > 800 isolates provide insights into patterns of selection that cannot be obtained from long-term molecular-evolution studies, including the pervasiveness of near quasi-neutrality across the genome (mean net selection coefficients near zero, but with significant temporal variance about the mean, and little evidence of positive covariance of selection across time intervals), the preponderance of weak negative selection operating on minor alleles, and a genome-wide distribution of numerous small linkage islands of observable selection influencing levels of nucleotide diversity. These results suggest that fluctuating selection is a major determinant of standing levels of variation in natural populations, challenge the conventional paradigm for interpreting patterns of nucleotide diversity and divergence, and motivate the need for the development of new theoretical expressions for the interpretation of population-genomic data.

Significance

Except for mono/oligogenic traits known in advance to be under strong selection, there is little information on genome-wide patterns of temporal dynamics of allele-frequency changes in well-defined and unmanipulated natural populations. A multi-year survey of a population of the microcrustaceanDaphnia pulexprovides insight into these matters. Genome-wide analysis of > 800 genetic isolates demonstrates that temporal variation in selection intensity is a major determinant of levels of nucleotide polymorphism and divergence. Most nucleotide sites experience fluctuating selection with mean selection coefficients near zero, with little covariance in the strength of selection across time intervals, and with selection distributed across large numbers of genomic islands of linked sites. These results raise challenges for the conventional interpretation of measures of nucleotide diversity and divergence as indicators of effective population sizes and intensities of positive/negative selection.
Cortical parvalbumin neurons are responsible for homeostatic sleep rebound through CaMKII activation
Authors: Kon Kazuhiro , Ode Koji L. , Mano Tomoyuki , Fujishima Hiroshi , Tone Daisuke , Shimizu Chika , Shiono Shinnosuke , Yada Saori , Garçon Junko Yoshida , Kaneko Mari , Shinohara Yuta , Takahashi Riina R. , Yamada Rikuhiro G. , Shi Shoi , Sumiyama Kenta , Kiyonari Hiroshi , Susaki Etsuo A. , Ueda Hiroki R.
Published: April 2023

The homeostatic regulation of sleep is characterized by rebound sleep after prolonged wakefulness, but the molecular and cellular mechanisms underlying this regulation are still unknown. We show here that CaMKII-dependent activity control of parvalbumin (PV)-expressing cortical neurons is involved in sleep homeostasis regulation. Prolonged wakefulness enhances cortical PV-neuron activity. Chemogenetic suppression or activation of cortical PV neurons inhibits or induces rebound sleep, implying that rebound sleep is dependent on increased activity of cortical PV neurons. Furthermore, we discovered that CaMKII kinase activity boosts the activity of cortical PV neurons, and that kinase activity is important for homeostatic sleep rebound. We propose that CaMKII-dependent PV-neuron activity represents negative feedback inhibition of cortical neural excitability, which serves as the distributive cortical circuits for sleep homeostatic regulation.
Differentiation of Large Extracellular Vesicles in Oral Fluid: Combined Protocol of Small Force Centrifugation and Pattern Analysis
Authors: Kawano Takamasa , Okamura Kohji , Shinchi Hiroki , Ueda Koji , Takeshi Nomura , Shiba Kiyotaka
Published: April 2023

Extracellular vesicles (EVs) in biofluids are highly heterogeneous entities in terms of their origins and physicochemical properties. Considering the application of EVs in diagnostic and therapeutic fields, it is of extreme importance to establish differentiating methods by which focused EV subclasses are operationally defined. Several differentiation protocols have been proposed; however, they have mainly focused on smaller types of EVs, and the heterogeneous nature of large EVs has not yet been fully explored. In this report, to classify large EVs into subgroups based on their physicochemical properties, we have developed a protocol, named EV differentiation by sedimentation patterns (ESP), in which entities in the crude large EV fraction are first moved through a density gradient of iodixanol with small centrifugation forces, and then the migration patterns of molecules through the gradients are analyzed using a non-hierarchical data clustering algorithm. Based on this method, proteins in the large EV fractions of oral fluids clustered into three groups: proteins shared with small EV cargos and enriched in immuno-related proteins (Group 1), proteins involved in energy metabolism and protein synthesis (Group 2), and proteins required for vesicle trafficking (Group 3). These observations indicate that the physiochemical properties of EVs, which are defined through low-speed gradient centrifugation, are well associated with their functions within cells. This protocol enables the detailed subclassification of EV populations that are difficult to differentiate using conventional separation methods.
The outer membrane and peptidoglycan layer form a single mechanical device balancing turgor
Authors: Deghelt Michaël , Cho Seung-Hyun , Govers Sander K. , Janssens Arne , Dachsbeck Alix , Remaut Han K. , Collet Jean-François
Published: April 2023

Bacteria are subject to a substantial concentration differential of osmolytes between the interior and exterior of the cell, which results in cytoplasmic turgor pressure. Failure to mechanically balance turgor pressure causes cells to burst. Here, we show that in Gram-negative bacteria, the outer membrane and peptidoglycan layer function together to resist turgor: when attached to each other, these two layers form a robust mechanical unit that allows pressure build-up in the periplasmic compartment, which in turn balances cytoplasmic turgor across the inner membrane, preventing cell death. Thus, the peptidoglycan layer is necessary but not sufficient to maintain turgor, which challenges the general view that protecting cells from bursting is the specific task of the peptidoglycan cell wall.

ONE-SENTENCE SUMMARY

The peptidoglycan and outer membrane are interconnected layers that cooperate to balance cytoplasmic turgor.
To deliberate, remember; to anticipate, forget: Cognitive deliberation profiles underpinning active forgetting-dependent everyday-like memory performance in young and aged mice
Authors: Stevens Christopher , Al Abed Shaam , Sellami Azza , Ducourneau Eva , Lacroix Cathy , Bouchet Mathilde , Roudier Faustine , Marsicano Giovanni , Marighetto Aline
Published: April 2023

Recalling a specific past episode that will enable us to decide which action is suited to a given present situation is a core element of everyday life. A wealth of research has demonstrated that such selective remembering is dependent upon a capacity to inhibit or provisionally ‘forget’ related yet inappropriate memory episodes which could orient behavior in unwilled directions. Everyday-like memory (EdM) refers to this type of common organizational mnemonic capacity, known to deteriorate significantly with age, putatively as a result of decline in the cognitive capacity for selective inhibition or ‘active forgetting’. Moreover, this memory retrieval-concomitant active forgetting comes at the cost of genuine amnesic weakening of the inhibited episodes, a phenomenon referred to as retrieval-induced forgetting (RIF). In the present study, we introduce a novel characterization of our previously validated mouse model of EdM in terms of the existing active forgetting and RIF literature. We also introduce novel behavioral analyses of the deliberation processes elicited by EdM challenge and use detailed multi-factorial explorations to reveal how these processes are impacted by age, temporal retention demand, difficulty of EdM challenge, and anticipation of trial outcome. Our observations indicate that deliberation requires remembering while accurate anticipation—in which a critical age-related deficit is also observed—requires active forgetting. Our results represent a significant advance towards unifying our understanding of the neurocognitive processes underpinning everyday-like memory, RIF, mnemonic deliberation, anticipatory function, and how they all are impacted by the physiological ageing process. In parallel, we present preliminary results using a transgenic mouse model which point to a fundamental role for the endocannabinoid system (eCS) in active forgetting and EdM, thereby demonstrating that deeper investigation of previously characterized age-related decline of the eCS should be a pre-clinical priority with a view to developing treatments for age-related decline of EdM function.
Per-pixel unmixing of spectrally overlapping fluorophores using intra-exposure excitation modulation
Authors: Valenta Hana , Bierbuesse Franziska , Vitale Raffaele , Ruckebusch Cyril , Vandenberg Wim , Dedecker Peter
Published: April 2023

Multilabel fluorescence imaging is essential for the visualization of complex systems, though a major challenge is the limited width of the usable spectral window. Here, we present a new method, exNEEMO, that enables per-pixel quantification of spectrally-overlapping fluorophores based on their light-induced dynamics, in a way that is compatible with a very broad range of timescales over which these dynamics may occur. Our approach makes use of intra-exposure modulation of the excitation light to distinguish the different emitters given their reference responses to this modulation. We use approach to simultaneously image four green photochromic fluorescent proteins at the full spatial resolution of the imaging.

Graphical abstract
An integrative trait-based framework to infer resource budgets and life-histories of long-lived plants
Authors: Cooksley Huw , Schleuning Matthias , Neu Alexander , Esler Karen J. , Schurr Frank M.
Published: April 2023

A fundamental assumption of functional ecology is that functional traits determine life-histories. Yet correlations between traits and life-history components are often weak, especially for long lived plants. This is because trade-offs, constraints, dynamic resource budgets and the scaling from single organs to entire plants cause complex relationships between traits and life-history. To elucidate these relationships, we present an integrated Trait-Resource-Life-History (TRL) framework that infers how functional traits affect organ-level costs and benefits of different life history components, how these costs and benefits shape the dynamics of whole-plant resource acquisition and allocation, and how these dynamics translate into life history. We illustrate this framework by developing a TRL model for a functionally diverse group of woody plants (22 species of the genusProteafrom the South African Greater Cape Floristic Region). Using hierarchical Bayesian latent state-space modelling, we statistically parameterise this model from data on year-to-year variation in growth, reproduction and maternal care (serotiny) for 600 individuals. The parameterised model reveals that higher resource acquisition translates into both larger absolute resource pools and greater proportional resource allocation to reproduction. Accordingly, specific leaf area, a key trait increasing resource acquisition, is associated with larger resource pools, an earlier age of maturity as well as increased vegetative and reproductive performance at young to intermediate ages. In contrast, seed nitrogen content has opposing effects on the benefits of different organs and thus only shows weak correlations with life-history components. Importantly, the TRL model identifies trait and resource-mediated trade-offs at the level of organs, whole-plant resource budgets and life-histories. It can thus quantify key components of life-history theory that are so far largely inaccessible for long-lived plants. This permits novel insights into ecological and evolutionary mechanisms shaping life-histories. Application of the proposed framework to a broad range of plant systems should be facilitated by the increasing availability of trait and demographic data, whole-plant phenotyping and high resolution remote sensing. The integration of the TRL framework with models of biotic interactions further holds promise for a resource-based understanding of community dynamics across trophic levels and a closer integration of functional ecology, evolutionary ecology, community ecology and ecosystem science.