bluuebunny/crossref_metadata_2025 huggingface dataset:
Neutrophils in the brain are sources of neuroprotective molecules and demonstrate functional heterogeneity during chronicToxoplasma gondiiinfection
Authors: Bergersen Kristina V. , Kavvathas Bill , David Clement , Ford Byron D. , Wilson Emma H.
Published: August 2022

Infection with the protozoan parasiteToxoplasma gondiileads to the formation of lifelong cysts in neurons of the brain that can have devastating consequences in the immunocompromised. However, despite the establishment of a chronic inflammatory state and infection-induced neurological changes, there are limited signs of clinical neuropathology resulting in an asymptomatic infection in the immunocompetent. This suggests the work of neuroprotective mechanisms to prevent clinical manifestations of disease. However, such sources of neuroprotection during infection remain largely unknown. This study identifies a population of neutrophils chronically present in the brain during Toxoplasma infection that express the neuroprotective molecules NRG-1, ErbB4, and MSR1. Further phenotyping of this population via flow cytometry and singe-cell RNA sequencing reveals two distinct subsets of neutrophils based on age that display functional heterogeneity. This includes cells transcriptionally prepared to function both as anti-parasitic effector cells and in a more alternative protective manner. Chronic depletion of neutrophils results in increased parasite burden and infection-induced vascular pathology. Lack of neutrophils during chronic infection also deleteriously affects neuronal regeneration and repair mechanisms. In conclusion, this work identifies and demonstrates a functionally diverse chronic neutrophil population that plays a dynamic role in controlling infection outcome in the CNS by balancing classical responses with neuroprotective functions.

Author Summary

The predominantly asymptomatic nature of chronicToxoplasma gondiiinfection despite the life-long infection of neurons suggests that there are neuroprotective mechanisms at work in the brain to maintain homeostasis and integrity. This study identifies neutrophils, normally considered a first-responding innate immune cell, as a prominent source of neuroprotective molecules duringToxoplasmainfection. Aged neutrophils in the brain exhibit an ability to be functionally flexible expressing signatures of classical proinflammatory responses; and neuroprotective, pro-angiogenic indicators. Lack of neutrophils during chronic infection leads to increased parasite burden, increased vascular damage, and decreased neuronal regeneration. We conclude that chronic brain neutrophils are a functionally dynamic population and a source of neuroprotection during infection and suggest that this is a potentially novel target to promote brain tissue repair without compromising anti-microbial activity.
Diversity of Ganglion Cell Responses to Saccade-like Image Shifts in the Primate Retina
Authors: Nitsche Steffen , Khani Mohammad H. , Karamanlis Dimokratis , Erol Yunus C. , Zapp Sören J. , Mietsch Matthias , Protti Dario A. , Rozenblit Fernando , Gollisch Tim
Published: August 2022

Saccades are a fundamental part of natural vision. They interrupt fixations of the visual gaze and rapidly shift the image that falls onto the retina. These stimulus dynamics can cause activation or suppression of different retinal ganglion cells, but how they affect the encoding of visual information in different types of ganglion cells is largely unknown. Here, we recorded spiking responses to saccade-like shifts of luminance gratings from ganglion cells in isolated marmoset retinas and investigated how the activity depended on the combination of pre- and post-saccadic images. All identified cell types, On and Off parasol and midget cells as well as a type of Large Off cells, displayed distinct response patterns, including particular sensitivity to either the pre- or the post-saccadic image or combinations thereof. In addition, Off parasol and Large Off cells, but not On cells, showed pronounced sensitivity to whether the image changed across the transition. Stimulus sensitivity of On cells could be explained based on their responses to step changes in light intensity, whereas Off cells, in particular, parasol and the Large Off cells, seem to be affected by additional interactions that are not triggered during simple light-intensity flashes. Together, our data show that ganglion cells in the primate retina are sensitive to different combinations of pre- and post-saccadic visual stimuli. This contributes to the functional diversity of the retina’s output signals and to asymmetries between On and Off pathways and provides evidence of signal processing beyond what is triggered by isolated steps in light intensity.
Climate change, biotic yield gaps and disease pressure in cereal crops
Authors: Raza Muhammad Mohsin , Bebber Daniel P.
Published: August 2022

Plant diseases are major causes of crop yield losses and exert a financial burden via expenditure on disease control. The magnitude of these burdens depends on biological, environmental and management factors, but this variation is poorly understood. Here we model the effects of weather on potential yield losses due to fungal plant pathogens (the biotic yield gap, Ygb) using experimental trials of fungicide-treated and untreated cereal crops in the UK, and project future Ygb under climate change. We find that Ygb varies between 10 and 20 % of fungicide-treated yields depending on crop, and increases under warmer winter and wetter spring conditions. Ygb will increase for winter wheat and winter barley under climate change, while declining for spring crops because drier summers offset the effects of warmer winters. Potential disease impacts are comparable in magnitude to the effects of suboptimal weather and crop varieties.
Top-down structuring of freshwater bacterial communities by mixotrophic and heterotrophic protists
Authors: Ivanković Marina , Ptacnik Robert , Bengtsson Mia Maria
Published: August 2022

Mixotrophic and heterotrophic protists hold a key position in aquatic microbial food webs. They account for the bulk of bacterivory in pelagic systems. However, the potential structuring effect of heterotrophic and especially mixotrophic protists on bacterial communities is far from clear. We conducted standardized short-term grazing experiments, to test for the overall impact on bacterial community structure and possible prey preferences of protist taxa with different phagotrophic nutritional modes. The used protist taxa covered a range from more phototrophic towards heterotrophic strategies, with obligate mixotrophic taxa employing phototrophy as the dominant strategy, towards facultative mixotrophic taxa relying more on phagotrophy, with the end of this gradient being covered by a phagoheterotroph lacking phototrophic capacity. Bacterioplankton from different lake systems was enriched and used to represent semi-natural bacterial assemblages that served as prey communities. Our study showed that similarities in protistan nutritional modes were reflected in similarities in their overall impact on bacterial communities. The impact intensity increased towards clear phagotrophic strategies, with mixotrophs in the phototrophic end of the gradient rather having a stabilizing impact on bacterial communities. Obligate mixotrophs grazed diverse prey in small amounts, while towards strict heterotrophic nutrition we observed an ingestion increase and selective depletion of bacteria with potential high growth rates. Future global change scenarios supporting the domination of obligate mixotrophic bacterivores might promote higher bacterial diversity in the illuminated zone of lakes.
Molecular characterization reveals subclasses of 1q gain in intermediate-risk Wilms tumors
Authors: van Belzen Ianthe A.E.M. , van Tuil Marc , Badloe Shashi , Strengman Eric , Janse Alex , Verwiel Eugène T.P. , van der Leest Douwe F.M. , de Vos Sam , Baker-Hernandez John , Groenendijk Alissa , de Krijger Ronald , Kerstens Hindrik H.D. , Drost Jarno , van den Heuvel-Eibrink Marry M. , Tops Bastiaan B.J. , Holstege Frank C.P. , Kemmeren Patrick , Hehir-Kwa Jayne Y.
Published: August 2022

Chromosomal alterations have recurrently been identified in Wilms tumors (WTs) and some are associated with poor prognosis. Gain of 1q (1q+) is of special interest given its high prevalence and is currently actively studied for its prognostic value. However, the underlying mutational mechanisms and functional effects remain unknown.

For 30 primary WTs, we integrated somatic SNVs, CNs and SVs with expression data and distinguished four clusters characterized by affected biological processes: muscle differentiation, immune system, kidney development and proliferation. We identified 1q+ in eight tumors that differ in mutational mechanisms, subsequent rearrangements and genomic contexts. 1q+ tumors were present in all four expression clusters and individual tumors overexpress different genes on 1q. Through integrating CNs, SVs and gene expression, we identified subgroups of 1q+ tumors reflecting differences in the functional effect of 1q gain, indicating that expression data is likely needed for further risk stratification of 1q+ WTs.
In-vitro Analysis of Hemostatic Cotton Khadi Dressing with Kaolin/Chitosan-based Composition and Its Application as Prospective Wound Dressing
Authors: Raval Aayushi A , Patel Vishwa N , Pancholi Utkarsh V
Published: August 2022

The current investigation illustrates the formulation of Kaolin/Chitosan-based composition by using a simple mechanochemical method that can produce a stabilized hemostatic composition. Chitosan is stabilized in sodium hydroxide solution with which kaolin solution is mixed under controlled conditions. When the formulated hemostatic composition was impregnated on cotton khadi dressing it showed drastically improved hemostatic efficiency as compared to standard cotton gauze. The tightly woven cotton khadi fabric has a larger surface area as compared to standard cotton gauze and so it retains more hemostatic composition. The hemostatic properties of the composition are characterized using various in-vitro testing techniques like bleeding time analysis, clotting time analysis, absorption strength study, and several other parameters. Investigation of the freshly drawn blood samples from humans was used for experimenting in order to obtain highly accurate results. The results demonstrate that Kaolin/Chitosan composite impregnated cotton khadi dressing can noticeably enhance the hemostasis other than being biocompatible as demonstrated through an animal model and fresh blood study.
Cytocipherdetermines significantly different populations of cells in single cell RNA-seq data
Authors: Balderson Brad , Piper Michael , Thor Stefan , Boden Mikael
Published: August 2022

Identification of cell types using single cell RNA-seq (scRNA-seq) is revolutionising the study of multicellular organisms. However, typical scRNA-seq analysis often involves post hoc manual curation to ensure clusters are transcriptionally distinct, which is time-consuming, error-prone, and irreproducible. To overcome these obstacles, we developedCytocipher, a bioinformatics method andscversecompatible software package that statistically determines significant clusters. Application ofCytocipherto normal tissue, development, disease, and large-scale atlas data reveals the broad applicability and power ofCytocipherto generate biological insights in numerous contexts. This included the identification of cell types not previously described in the datasets analyzed, such as CD8+ T cell subtypes in human peripheral blood mononuclear cells; cell lineage intermediate states during mouse pancreas development; and subpopulations of luminal epithelial cells over-represented in prostate cancer.Cytocipheralso scales to large datasets with high test performance, as shown by application to the Tabula Sapiens Atlas representing >480,000 cells.

Cytocipheris a novel and generalisable method that statistically determines transcriptionally distinct and programmatically reproducible clusters from single cell data.Cytocipheris available athttps://github.com/BradBalderson/Cytocipher.
A role for the centrosome in regulating the rate of neuronal efferocytosis by microglia in vivo
Authors: Möller Katrin , Brambach Max , Villani Ambra , Gallo Elisa , Gilmour Darren , Peri Francesca
Published: August 2022

During brain development, many newborn neurons undergo apoptosis and are engulfed by microglia, the tissue-resident phagocytes of the brain, in a process known as efferocytosis. A hallmark of microglia is their highly branched morphology characterised by the presence of numerous dynamic extensions that these cells use for scanning the brain parenchyma and engulfing unwanted material. The mechanisms driving branch formation and apoptotic cell engulfment in microglia are unclear. By taking a live imaging approach in zebrafish, we show that while microglia generate multiple microtubule-based branches, they only successfully engulf one apoptotic neuron at a time. Further investigation into the mechanism underlying this sequential engulfment revealed that targeted migration of the centrosome into one branch is predictive of phagosome formation and polarised vesicular trafficking. Moreover, experimentally doubling centrosomal numbers in microglia increases the rate of engulfment and even allows microglia to remove two neurons simultaneously, providing direct supporting evidence for a model where centrosomal migration is a rate-limiting step in branch-mediated efferocytosis. Conversely, light-mediated depolymerization of microtubules causes microglia to lose their typical branched morphology and switch to an alternative mode of engulfment, characterised by directed migration towards target neurons, revealing unexpected plasticity in their phagocytic ability. Finally, building on work focusing on the establishment of the immunological synapse, we identified a conserved signalling pathway underlying centrosomal movement in engulfing microglia.
Using computational simulations to quantify genetic load and predict extinction risk
Authors: Kyriazis Christopher C. , Robinson Jacqueline A. , Lohmueller Kirk E.
Published: August 2022

Small and isolated wildlife populations face numerous threats to extinction, among which is the deterioration of fitness due to an accumulation of deleterious genetic variation. Genomic tools are increasingly used to quantify the impacts of deleterious variation in small populations; however, these approaches remain limited by an inability to accurately predict the selective and dominance effects of individual mutations. Computational simulations of deleterious genetic variation offer an alternative and complementary tool that can help overcome these limitations, though such approaches have yet to be widely employed. In this Perspective, we aim to encourage conservation genomics researchers to adopt greater use of computational simulations to aid in quantifying and predicting the threat that deleterious genetic variation poses to extinction. We first provide an overview of the components of a simulation of deleterious genetic variation, describing the key parameters involved in such models. Next, we clarify several misconceptions about an essential simulation parameter, the distribution of fitness effects (DFE) of new mutations, and review recent debates over what the most appropriate DFE parameters are. We conclude by comparing modern simulation tools to those that have long been employed in population viability analysis, weighing the pros and cons of a ‘genomics-informed’ simulation approach, and discussing key areas for future research. Our aim is that this Perspective will facilitate broader use of computational simulations in conservation genomics, enabling a deeper understanding of the threat that deleterious genetic variation poses to biodiversity.
Identification, characterization of Apyrase (APY) gene family in rice (Oryza sativa) and analysis of the expression pattern under various stress conditions
Authors: Chowdhury Aniqua Tasnim , Hasan Md. Nazmul , Bhuiyan Fahmid H , Islam Md. Qamrul , Nayon Md. Rakib Wazed , Rahaman Md. Mashiur , Hoque Hammadul , Jewel Nurnabi Azad , Ashrafuzzaman Md , Prodhan Shamsul H.
Published: August 2022

Apyrase (APY) is a nucleoside triphosphate (NTP) diphosphohydrolase (NTPDase) which is a member of the superfamily of guanosine diphosphatase 1 (GDA1) - cluster of differentiation 39 (CD39) nucleoside phosphatase. Under various circumstances like stress, cell growth, the extracellular adenosine triphosphate (eATP) level increases, causing a detrimental influence on cells such as cell growth retardation, ROS production, NO burst, and apoptosis. Apyrase hydrolyses eATP accumulated in the extracellular membrane during stress, wounds, into adenosine diphosphate (ADP) and adenosine monophosphate (AMP) and regulates the stress- responsive pathway in plants. This study was designed for the identification, characterization, and for analysis ofAPYgene expression inOryza sativa. This investigation discovered nineAPYs in rice, including both endo- and ecto-apyrase. According to duplication event analysis, in the evolution ofOsAPYs, a significant role is performed by segmental duplication. Their role in stress control, hormonal responsiveness, and the development of cells is supported by the corresponding cis-elements present in their promoter regions. According to expression profiling by RNA-seq data, the genes were expressed in various tissues. Upon exposure to a variety of biotic as well as abiotic stimuli, including anoxia, drought, submergence, alkali, heat, dehydration, salt, and cold, they showed a differential expression pattern. The expression analysis from the RT-qPCR data also showed expression under various abiotic stress conditions, comprising cold, salinity, cadmium, drought, submergence, and especially heat stress. This finding will pave the way for futurein-vivoanalysis, unveil the molecular mechanisms ofAPYgenes in stress response, and contribute to the development of stress- tolerant rice varieties.
Genes encoding cytochrome P450 monooxygenases and glutathione S-transferases associated with herbicide resistance evolved before the origin of land plants
Authors: Casey Alexandra , Dolan Liam
Published: August 2022

Cytochrome P450 (CYP) monooxygenases and glutathione S-transferases (GST) are enzymes that catalyse chemical modifications of a range of organic compounds. Herbicide tolerance is associated with higher levels of CYP and GST gene expression in some herbicide-resistant weed populations compared to sensitive populations of the same species. By comparing the protein sequences of 9 representative species of the Archaeplastida – the lineage which includes red algae, glaucophyte algae, chlorophyte algae, and streptophytes – and generating phylogenetic trees, we identified the CYP and GST proteins that existed in the common ancestor of the Archaeplastida. All CYP clans and all but one land plant GST classes present in land plants evolved before the divergence of streptophyte algae and land plants from their last common ancestor. We also demonstrate that there are more genes encoding CYP and GST proteins in land plants than in algae. The larger numbers of genes among land plants largely results from gene duplications in CYP clans 71, 72, and 85 and in the GST Phi and Tau classes. Enzymes that either chemically alter herbicides or confer herbicide resistance belong to CYP clans 71 and 72 and the GST Phi and Tau classes. These results demonstrate that the clan and class diversity in extant plant CYP and GST proteins evolved in the Proterozoic before the divergence of land plants and streptophyte algae from a last common ancestor. Then, early in embryophyte evolution during the Palaeozoic, gene duplication in four of the twelve CYP clans, and in two of the fourteen GST classes, led to the large numbers of CYP and GST proteins found in extant land plants. It is among the genes of CYP clans 71 and 72 and GST classes Phi and Tau that alleles conferring herbicide resistance evolved in the last fifty years.
The Spike protein of SARS-coV2 19B (S) clade mirrors critical features of viral adaptation and coevolution
Authors: Hussein Bidour K. , Ibrahium Omnia M. , Alamin Marwa F. , Ahmed Lamees A.M , Abuswar Safa A.E , Abdelraheem Mohammed H. , Ibrahim Muntaser E.
Published: August 2022

Pathogens including viruses evolve in tandem with diversity in their animal and human hosts. For SARS-coV2, the focus is generally for understanding such coevolution on the virus spike protein since it demonstrates high mutation rates compared to other genome regions, particularly in the receptor-binding domain (RBD).

Viral sequences of the SARS-coV2 19B (S) clade and variants of concern from different continents, were investigated, with a focus on the A.29 lineage which presented with different mutational patterns within the 19B (S) lineages in order to learn more about how SARS-coV2 may have evolved and adapted to widely diverse populations globally.

Results indicated that SARS-coV2 went through evolutionary constrains and intense selective pressure, particularly in Africa. This was manifested in a departure from neutrality with excess nonsynonymous mutations and a negative Tajima D consistent with rapid expansion and directional selection as well as deletion and deletion-frameshifts in the N-terminal domain (NTD region) of the spike protein.

In conclusion, viral transmission during epidemics through population of diverse genomic structure and marked complexity may be a significant factor for the virus to acquire distinct patterns of mutations within these populations in order to ensure its survival and fitness, hence in the emergence of novel variants and strains.

Importance

In this study, we justify the fact that the virus’s evolution varies across continents, with each continent showing different amounts and patterns of mutations and deletions, which was manifested in the 19B (S) clade of SARS-coV2, particularly in areas with high population complexity, such as Africa, despite the low rate of sampling and data sharing. The findings show that SARS-coV2 was subject to evolutionary constraints and intense selective pressure. This study will contribute to the scanty amount of research on the SARS-coV2 coevolution and adaptation, in which the host variation is of great significance in understanding the intricacies of viral host coevolution.
Worldwide late-Quaternary population declines in extant megafauna are due to Homo sapiens rather than climate
Authors: Bergman Juraj , Pedersen Rasmus Ø. , Lundgren Erick J. , Lemoine Rhys T. , Monsarrat Sophie , Schierup Mikkel H. , Svenning Jens-Christian
Published: August 2022

The worldwide loss of large animal species over the past 100,000 years is evident from the fossil record, with climate and human impact as the most likely causes of megafauna extinctions. To help distinguish between these two scenarios, we analysed whole-genome sequence data of 142 species to infer their population size histories during the Quaternary. We modelled differences in population dynamics among species using ecological factors, paleoclimate and human presence as covariates. We report a significant population decline towards the present time in more than 90% of species, with larger megafauna experiencing the strongest decline. We find that population decline became ubiquitous approximately 100,000 years ago, with the majority of species experiencing their lowest population sizes during this period. We assessed the relative impact of climate fluctuations and human presence on megafauna dynamics and found that climate has limited explanatory power for late-Quaternary shifts in megafauna population sizes, which are largely explained by Homo sapiens arrival times. As a consequence of megafauna decline, total biomass and metabolic input provided by these species has drastically reduced to less than 25% compared to 100,000 years ago. These observations imply that the worldwide expansion of H. sapiens caused a major restructuring of ecosystems at global scale.
Spectral Representation of EEG Data using Learned Graphs with Application to Motor Imagery Decoding
Authors: Miri Maliheh , Abootalebi Vahid , Saeedi-Sourck Hamid , Van De Ville Dimitri , Behjat Hamid
Published: August 2022

Electroencephalography (EEG) data entail a complex spatiotemporal structure that reflects ongoing organization of brain activity. Characterization of the spatial patterns is an indispensable step in numerous EEG processing pipelines within the setting of brain-computer interface systems as well as cognitive neuroscience. We present an approach for transforming EEG data into a spectral representation by using the harmonic basis of a graph structure that is learned from the data. The harmonic basis is obtained by integrating principles from graph learning and graph signal processing (GSP). First, we learn subject-specific graphs from each subject’s EEG data. Second, by eigendecomposition of the normalized Laplacian matrix of each subject’s graph, an orthonormal basis is obtained onto which each EEG map can be decomposed, providing a spectral representation of the data. We show that energy of the EEG maps is strongly associated with low frequency components of the learned basis, reflecting the smooth topography of EEG maps as expected. As a proof-of-concept for this alternative view of EEG data, we consider the task of decoding two-class motor imagery (MI) data. To this aim, the spectral representations are first mapped into a discriminative subspace for differentiating two-class data using a projection matrix obtained by the Fukunaga-Koontz transform (FKT), providing a minimal subspace from which features are extracted. An SVM classifier is then trained and tested on the resulting features to differentiate MI classes. The proposed method is evaluated on Dataset IVa of the BCI Competition III and its performance is compared to using features extracted from a subject-specific functional connectivity matrix and four state-of-the-art alternative methods. Experimental results indicate the superiority of the proposed method over alternative approaches, reflecting the added benefit of i) decomposing EEG data using data-driven, subject-specific harmonic bases, and ii) accounting for class-specific temporal variations in spectral profiles via the FKT. The proposed method and results underline the importance of integrating spatial and temporal characteristics of EEG signals in extracting features that can more powerfully differentiate MI classes.
rde-3 reduces piRNA-mediated silencing and abolishes inherited silencing in C. elegans
Authors: Priyadarshini Monika , AlHarbi Sarah , Frøkjær-Jensen Christian
Published: August 2022

Small RNA-mediated silencing of target genes can persist across generations and C. elegans is a well-established model for studying the molecular basis for epigenetic inheritance. We recently developed a piRNA-based inherited silencing assay that causes a high incidence of males by targeting him-5 and him-8. Acute gene silencing is determined in the presence of the piRNAi extra-chromosomal array and inherited silencing after loss of the piRNA trigger. This assay has the advantage of targeting endogenous genes that are easily scored in mutant backgrounds and obviates the need for mutant validation and genetic crosses, which can influence inherited silencing. Here we show an example of the assay by testing acute and inherited piRNA-mediated him-5 silencing in ribonucleotidyltransferase rde-3 (ne3370) mutant animals. In the absence of rde-3, acute silencing was reduced but still detectable, whereas inherited silencing was abolished.
High throughput analysis of vacuolar acidification
Authors: Zhang Chi , Balutowski Adam , Feng Yilin , Calderin Jorge D. , Fratti Rutilio A.
Published: August 2022

Eukaryotic cells are compartmentalized into membrane-bound organelles, allowing each organelle to maintain the specialized conditions needed for their specific functions. One of the features that change between organelles is luminal pH. In the endocytic and secretory pathways, luminal pH is controlled by isoforms and concentration of the vacuolar-type H+-ATPase (V-ATPase). In the endolysosomal pathway, copies of complete V-ATPase complexes accumulate as membranes mature from early endosomes to late endosomes and lysosomes. Thus, each compartment becomes more acidic as maturation proceeds. Lysosome acidification is essential for the breakdown of macromolecules delivered from endosomes as well as cargo from different autophagic pathways, and dysregulation of this process is linked to various diseases. Thus, it is important to understand the regulation of the V-ATPase. Here we describe a high-throughput method for screening inhibitors/activators of V-ATPase activity using Acridine Orange (AO) as a fluorescent reporter for acidified yeast vacuolar lysosomes. Through this method, the acidification of purified vacuoles can be measured in real-time in half-volume 96-well plates or a larger 384-well format. This not only reduces the cost of expensive low abundance reagents, but it drastically reduces the time needed to measure individual conditions in large volume cuvettes.
Quantitative reconstitution of yeast RNA processing bodies
Authors: Currie Simon L , Xing Wenmin , Muhlrad Denise , Decker Carolyn J , Parker Roy , Rosen Michael K
Published: August 2022

Many biomolecular condensates appear to form through liquid-liquid phase separation (LLPS). Individual condensate components can often undergo LLPS in vitro, capturing some features of the native structures. However, natural condensates contain dozens of components with different concentrations, dynamics, and contributions to compartment formation. Most biochemical reconstitutions of condensates have not benefitted from quantitative knowledge of these cellular features nor attempted to capture natural complexity. Here, we build on prior quantitative cellular studies to reconstitute yeast RNA processing bodies (P bodies) from purified components. Individually, five of the seven highly-concentrated P-body proteins form homotypic condensates at cellular protein and salt concentrations, using both structured domains and intrinsically disordered regions. Combining the seven proteins together at their cellular concentrations with RNA, yields phase separated droplets with partition coefficients and dynamics of most proteins in reasonable agreement with cellular values. The dynamics of most proteins in the reconstitution are also comparable to cellular values. RNA delays the maturation of proteins within, and promotes reversibility of, P bodies. Our ability to quantitatively recapitulate the composition and dynamics of a condensate from its most concentrated components suggests that simple interactions between these components carry much of the information that defines the physical properties of the cellular structure.
Structural principles of B-cell antigen receptor assembly
Authors: Dong Ying , Pi Xiong , Bartels-Burgahn Frauke , Saltukoglu Deniz , Liang Zhuoyi , Yang Jianying , Zheng Yumei , Alt Frederick W. , Reth Michael , Wu Hao
Published: August 2022

The B-cell antigen receptor (BCR) is composed of a membrane-bound immunoglobulin (mIg) of class M, D, G, A or E for antigen recognition and a disulfide-linked heterodimer between Igα and Igβ (Igα/β, also known as CD79A and CD79B) that functions as the signalling entity. The organizing principle of BCR assembly remains elusive. Here we report the cryo-electron microscopy structures of the intact IgM class BCR at 8.2 Å resolution and its Fab-deleted form (IgM BCRΔFab) at 3.6 Å resolution. At the ectodomain (ECD), Igα and Igβ position their respective Ig folds roughly in parallel with an approximate 2-fold symmetry, which is distinct from structures of Igβ/β homodimers. Unlike previous predictions, the BCR structure displays an asymmetric arrangement, in which the Igα/β ECD heterodimer mainly uses Igα to associate with Cµ3-Cµ4 domains of one heavy chain (µHC) while leaving the other heavy chain (µHC’) empty. The transmembrane domain (TMD) helices of the two µHCs also deviate from the 2-fold symmetry of the Cµ3-Cµ4 domain dimer and form together with the TMD helices of the Igα/β heterodimer a tight 4-helix bundle. The asymmetry at the TMD helices prevents the recruitment of two Igα/β heterodimers. Surprisingly, the connecting peptides (CPs) between the ECD and TMD are braided together through striking charge complementarity, resulting in intervening of the CP of µHC in between those of Igα and Igβ and crossover of the TMD relative to ECD for the Igα/β heterodimer, to guide the TMD assembly. Interfacial analyses suggest that the IgM BCR structure we present here may represent a general organizational architecture of all BCR classes. Our studies thus provide a structural platform for understanding B-cell signalling and for designing rational therapies against BCR-mediated diseases.
Integrated single-cell functional and molecular profiling of extracellular vesicle secretion in metastatic breast cancer
Authors: Fathi Mohsen , Martinez-Paniagua Melisa , Rezvan Ali , Montalvo Melisa J. , Mohanty Vakul , Chen Ken , Mani Sendurai A , Varadarajan Navin
Published: August 2022

Extracellular vesicles (EVs) regulate the tumor microenvironment by facilitating transport of biomolecular cargo including RNA, protein, and metabolites. The biological effects of EV-mediated transport have been studied using supra-physiological concentrations of EVs, but the cells that are responsible for EV secretion and the mechanisms that support EV secretion are not well characterized. We developed an integrated method based on arrays of nanowells to identify individual cells with differences in EV secretion and used an automated robot to perform linked single-cell RNA-sequencing on cloned single cells from the metastatic breast cancer cell line, MDAMB231. Gene expression profiles of clonal cells with differences in EV secretion were analyzed, and a four-gene signature of breast cancer EV secretion was identified: HSP90AA1, HSPH1, EIF5, and DIAPH3. We functionally validated this gene signature by testing it across different cell lines with different metastatic potential demonstrating that the signature correlated with levels of EV secretion. Analysis of the TCGA and METABRIC datasets showed that this signature is associated with poor survival, more invasive breast cancer types, and reduced CD8+ T cell infiltration in human tumors. We anticipate that our method for directly identifying the molecular determinants of EV secretion will have broad applications across cell types and diseases.
Dynamics, signals and influencing factors of CD4 T cell activation revealed by single cell RNA-seq
Authors: Liu Hongyi , Li Hui , Liu Yifei , Wang Xuefei , Yu Shiya , Shen Xiangru , Zhang Qi , Hong Ni , Jin Wenfei
Published: August 2022

T cell activation is a key event in adaptive immunity. However, factors affecting T cell activation have not been systematically analyzed. Here, we analyzed stimulated CD4 T cells with anti-CD3/CD28 under several conditions to explore the factors affecting T cell activation. We defined stimulated T overlapped with resting T on UMAP as inert T. Inert T expressed activated T specific genes and cytokines, indicating it is a special functional state. Stimulated T derived from peripheral CD4 T has higher fraction of effector T (TEFF) while stimulated T derived from CD4 TNhas higher fraction of proliferation T and interferon highly expressed T (IFNhiT). CD4 T was more likely to differentiate into TEFFand less likely to differentiate into heat shock protein specific T (HSPhiT) and IFNhiT in the presence of CD8 T. Interestingly,CXCR4lowT responded to stimulation more efficiently thanCXCR4hiT. These information facilitates we design stimulation to obtain ideal activated T.
Pleiotropic roles for mycobacterial DinB2 in frameshift and substitution mutagenesis
Authors: Dupuy Pierre , Ghosh Shreya , Adefisayo Oyindamola , Bean James , Gupta Richa , Shuman Stewart , Glickman Michael
Published: August 2022

Translesion synthesis mediated by translesion polymerases is a conserved mechanism of DNA damage tolerance. In bacteria, DinB enzymes are widely distributed promutagenic translesion polymerases. The role of DinBs in mycobacterial mutagenesis was unclear until recent studies revealed a role for mycobacterial DinB1 in substitution and frameshift mutagenesis, overlapping with that of translesion polymerase DnaE2. M. smegmatis encodes two additional DinBs (DinB2 and DinB3) and M. tuberculosis encodes DinB2, but the roles of these polymerases in mycobacterial damage tolerance and mutagenesis is unknown. The biochemical properties of DinB2, including facile utilization of ribonucleotides and 8-oxo-guanine, suggest that DinB2 could be a promutagenic polymerase. Here we examine the effects of DinB2 and DinB3 overexpression in mycobacterial cells. We demonstrate that DinB2 can drive diverse substitution mutations conferring antibiotic resistance. DinB2 induces frameshift mutations in homopolymeric sequences, both in vitro and in vivo. DinB2 switches from less to more mutagenic in the presence of manganese in vitro. This study indicates that DinB2 may contribute to mycobacterial mutagenesis and antibiotic resistance acquisition in combination with DinB1 and DnaE2.
Comparative assessment of morphology, anatomy and phylogeny of two exceptionally rare narrow endemic Tephrosia spp. (Leguminosae) from the Indian subcontinent
Authors: Vanzara Akash , Bhambra Gagandeep Kaur , Nagar Padamnabhi S.
Published: August 2022

Leguminosae is the third most abundant family of angiosperm in the world, and have a distinct difference that serves to identify and differentiate closely related species. Among 650 genera and 18,000 species of legumes in India, Tephrosia is the most emerged genus, of which two endangered and narrow endemic species Tephrosia jamnagarensis Sant and T. colina var. lanuginocarpa Sharma, possess a greater challenges for biological, ecological, and competitive improvement than other plants. Both the species are very unique and only found in a few isolated pockets of Gujarat around the globe. Therefore, in light of this, the present research aims to understand how morphological, anatomical, and genetically both species vary based on their variability nature are contextualized in an Indian context. Studies carried out on Morpho-anatomical observations and classical taxonomic approaches, such as the axillary cyme vs terminal raceme in T. jamnagarensis vs T. colina var. lanuginocarpa Sharma, the corolla being 4.5 cm long vs 1.5 cm long, the wings being 5.5 cm long vs 1.40 cm long, the keel being 3.4 cm long vs 1.5 cm long. First, ever genetic identity of the plants was assessed by using matK gene of the rbcl chloroplast region, and phylogenetic trees were constructed using sister clade separation. Sequences of both the plant species and others species that are found in India were submitted to NCBI and the embryonic stage of seeds were then used to examine seed morphology and propagation.
Huntingtin-KIF1A-mediated axonal transport of synaptic vesicle precursors influences synaptic transmission and motor skill learning in mice
Authors: Vitet Hélène , Bruyère Julie , Xu Hao , Brocard Jacques , Abada Yah Sé , Delatour Benoît , Scaramuzzino Chiara , Venance Laurent , Saudou Frédéric
Published: August 2022

Neurotransmitters are released at synapses by synaptic vesicles (SVs), which originate from SV precursors (SVPs) that have traveled along the axon. Because each synapse maintains a pool of SVs, only a small fraction of which are released, it is unclear whether axonal transport of SVPs modifies synaptic function. Here, studying the corticostriatal network both in microfluidic devices and in mice, we find that phosphorylation of the Huntingtin protein (HTT) causes it to recruit the kinesin motor KIF1A, which in turn increases axonal transport of SVPs and synaptic glutamate release. In mice, constitutive HTT phosphorylation leads to SV over-accumulation at synapses, increases the probability of SV release, and impairs motor skill learning on the rotating rod. Silencing KIF1A in these mice restored SV transport and motor skill learning to wild-type levels. Axonal SVP transport within the corticostriatal network thus influences synaptic plasticity and motor skill learning.
Single session of rTMS enhances brain metastability and intrinsic ignition
Authors: Bhardwaj Sujas , Panda Rajanikant , Bharath Rose Dawn , Stezin Albert , Khokhar Sunil Kumar , Prasad Shweta , Tyagi Vidhi , Kamble Nitish , Kumar Keshav , M Netravathi , Yadav Ravi , Kashyap Rajan , Udupa Kaviraja , Annen Jitka , Laureys Steven , Deco Gustavo , Pal Pramod Kumar
Published: August 2022

Background

Emerging evidence support the view that brain stimulation might improve essential tremor (ET) by altering brain networks and facilitating plasticity. Yet, we are still missing a mechanistic explanation of the whole brain dynamics underlying these plasticity defining changes.

Method

In this study, we explored the effect of low-frequency repetitive transcranial magnetic stimulation (rTMS) over left primary motor cortex (L-M1) on functional connectivity dynamics (FCD) in patients with ET. Resting-state fMRI (RsfMRI) was acquired before and after a single session of rTMS in 30 patients with ET and compared with RsfMRI of 20 age and gender matched healthy controls (HCs). We have measured the effect of brain stimulation using network topological re-organization through whole brain integration and segregation, brain stability and capacity of neural propagation through metastability and intrinsic ignition.

Results

Patients with ET had altered FCD measures compared to controls. After a single session rTMS, the brain connectivity measures approached normality and patients with ET revealed significantly higher integration, lower segregation with higher metastability and increased intrinsic ignition.

Conclusion

Brain metastability and intrinsic ignition measures could be valuable tools in appreciating mechanisms of brain stimulation in ET and other neurological diseases.
Localized network hyperconnectivity leads to hyperexcitability after injury
Authors: Ghiasvand Shabnam , Ferdous Zubayer Ibne , Buczak Monika , Hasan Md Fayad , Berdichevsky Yevgeny
Published: August 2022

Brain injury increases the risk of the development of epilepsy. Axonal sprouting and synaptogenesis are homeostatically mediated responses by neurons to injury-induced de-afferentation and de-efferentation. Rewiring which occurs due to axonal sprouting and synaptogenesis may alter network excitability and lead to epilepsy. Excitatory and inhibitory connectivity are both subject to homeostatic rewiring. Thus, post-sprouting hyperexcitability cannot be simply explained as result of altered inhibitory/excitatory balance. In this work, we show computationally and experimentally that hyperconnected local networks are created by homeostatic rewiring near the injury site. These local networks are characterized by altered system dynamics despite preservation of excitatory/inhibitory balance. Hyperconnected local networks have a lower threshold for burst initiation, and generate spontaneous bursts, which in turn ignite seizure-like activity in the larger network. Our findings demonstrate a novel network mechanism of hyperexcitability and seizure generation due to maladaptive recovery after injury.
A 4-bp natural deletion of maize Na+/H+ exchanger gene alters maize salt stress tolerance
Authors: Luo Meijie , Zhao Yanxin , Zhang Yunxia , Zhang Ruyang , Cai Manjun , Zhang Panpan , Du Dengxiang , Li Jingna , Xing Jinfeng , Sun Xuan , Duan Minxiao , Lu Xiaoduo , Xue Yadong , Liu Ya , Wang Fengge , Lu Baishan , Wang Yuandong , Wang Ronghuan , Song Wei , Zhao Jiuran
Published: August 2022

Soil salinity is a major environmental constraint severely reducing plant growth and crop productivity worldwide. Knowledge of salt tolerance-related genes can facilitate improving crop salt tolerance and alleviating the threat of increasing saline area to world food security. Here, we identified a major locus SALT TOLERANCE 1 (qST1) conferring maize salt tolerance via bulked segregant RNA-Seq (BSR-Seq). qST1 encodes a plasma membrane Na+/H+ exchanger ZmSOS1 which is the ortholog of Arabidopsis thaliana SOS1 gene. In salt-sensitive variety D9H, the natural variation of 4-bp deletion in the coding sequence of ZmSOS1 gene was the causal allele for salt sensitivity. We identified two ethyl methanesulfonate-induced mutants, zmsos1-1 and zmsos1-2, which were sensitive to salt stress and can’t complement salt-sensitive variety under salt stress within an allelism test. Overexpression of ZmSOS1 enhanced maize seedling salt tolerance. ZmSOS1 can increase the salt tolerance of Arabidopsis sos1-1 mutant and can be activated by AtSOS2 and AtSOS3 in yeast cells, suggesting that ZmSOS1 confers salt tolerance through the conserved SOS signaling pathway in maize. The detrimental allele harboring the 4-bp deletion was rarely found in the natural population but appeared in an important heterotic group composed of x1132x-derived inbred lines which have been used widely for breeding dozens of hybrid varieties in China. The 4-bp deletion-based molecular marker has been successfully used to improve salt-sensitive varieties in a backcross and marker-assisted breeding program by screening and purging this deleterious allele.
Combining DNA scaffolds and acoustic force spectroscopy to characterize individual protein bonds
Authors: Wang Yong Jian , Valotteau Claire , Aimard Adrien , Villanueva Lorenzo , Kostrz Dorota , Follenfant Maryne , Strick Terence , Chames Patrick , Rico Felix , Gosse Charlie , Limozin Laurent
Published: August 2022

Single-molecule data are of great significance in biology, chemistry, and medicine. However, experimental tools to characterize, in a multiplexed manner, protein bond rupture under force are needed. Acoustic force spectroscopy (AFS) is an emerging manipulation technique which generates acoustic waves to apply force in parallel on a large population of microbeads tethered to a surface. We have exploited this configuration on a recently developed modular Junctured-DNA (J-DNA) scaffold designed to study protein-protein interactions at the single-molecule level. By applying repetitive constant force steps on the FKBP12-rapamycin-FRB complex, we measured its unbinding kinetics under force at the single-bond level. Special effort was made in analyzing the data in order to identify potential pitfalls. We established a calibration method allowing in situ force determination during the course of the unbinding measurement. We compare our results with well established techniques, such as magnetic tweezers, to ensure their accuracy. We also apply our strategy for measuring the force dependent rupture of a single domain antibody with its antigen. We get a good agreement with standard measurement at zero force. Our technique offers single molecule precision for multiplexed measurements of interactions of biotechnological and medical interest.