bluuebunny/crossref_metadata_2025 huggingface dataset:
T cells modulate the microglial response to brain ischemia
Authors: Benakis Corinne , Simats Alba , Tritschler Sophie , Heindl Steffanie , Besson-Girard Simon , Llovera Gemma , Pinkham Kelsey , Kolz Anna , Theis Fabian , Gökce Özgün , Peters Anneli , Liesz Arthur
Published: September 2021

Neuroinflammation after stroke is characterized by the activation of resident microglia and the invasion of circulating leukocytes into the brain. Although lymphocytes infiltrate the brain in small number, they have been consistently demonstrated to be the most potent leukocyte subpopulation contributing to secondary inflammatory brain injury. However, the exact mechanism how this minimal number of lymphocytes can profoundly affect stroke outcome is still largely elusive. Here, using a mouse model for ischemic stroke, we demonstrated that early activation of microglia in response to stroke is differentially regulated by distinct T cell subpopulations. Acute treatment with engineered T cells overexpressing IL-10 administered into the cisterna magna after stroke induces a switch of microglial gene expression to a profile associated with pro-regenerative functions. These findings substantiate the role of T cells in stroke with large impact on the cerebral inflammatory milieu by polarizing the microglial phenotype. Targeting T cell-microglia interactions can have direct translational relevance for further development of immune-targeted therapies for stroke and other neuroinflammatory conditions.

The crosstalk between brain infiltrating T cells and microglia in response to stroke remains elusive. Benakis et al. report that transcriptional signature of the stroke-associated microglia is reprogrammed by distinct T cell subpopulations. Engineered T cells overexpressing IL-10 administered four hours after stroke reinitiate microglial function inducing a pro-regenerative environment.
Normative and mechanistic model of an adaptive circuit for efficient encoding and feature extraction
Authors: Chapochnikov Nikolai M. , Pehlevan Cengiz , Chklovskii Dmitri B.
Published: September 2021

One major question in neuroscience is how to relate connectomes to neural activity, circuit function, and learning. We offer an answer in the peripheral olfactory circuit of the Drosophila larva, composed of olfactory receptor neurons (ORNs) connected through feedback loops with interconnected inhibitory local neurons (LNs). We combine structural and activity data and, using a holistic normative framework based on similarity-matching, we propose a biologically plausible mechanistic model of the circuit. Our model predicts the ORN → LN synaptic weights found in the connectome and demonstrate that they reflect correlations in ORN activity patterns. Additionally, our model explains the relation between ORN → LN and LN – LN synaptic weight and the arising of different LN types. This global synaptic organization can autonomously arise through Hebbian plasticity, and thus allows the circuit to adapt to different environments in an unsupervised manner. Functionally, we propose LNs extract redundant input correlations and dampen them in ORNs, thus partially whitening and normalizing the stimulus representations in ORNs. Our work proposes a comprehensive framework to combine structure, activity, function, and learning, and uncovers a general and potent circuit motif that can learn and extract significant input features and render stimulus representations more efficient.

Significance

The brain represents information with patterns of neural activity. At the periphery, due to the properties of the external world and of encoding neurons, these patterns contain correlations, which are detrimental for stimulus discrimination. We study the peripheral olfactory neural circuit of the Drosophila larva, that preprocesses neural representations before relaying them to higher brain areas. A comprehensive understanding of this preprocessing is, however, lacking. Here, we propose a mechanistic and normative framework describing the function of the circuit and predict the circuit’s synaptic organization based on the circuit’s input neural activity. We show how the circuit can autonomously adapt to different environments, extracts stimulus features, and decorrelate and normalize input representations, which facilitates odor discrimination downstream.
Express Arm Responses Appear Bilaterally on Upper-limb Muscles in an Arm Choice Reaching Task
Authors: Kearsley Sarah L. , Cecala Aaron L. , Kozak Rebecca A. , Corneil Brian D.
Published: September 2021

When required, humans can generate very short latency reaches towards visual targets, like catching a falling cellphone. During such rapid reaches, express arm responses are the first wave of upper limb muscle recruitment, occurring ~80-100 ms after target appearance. There is accumulating evidence that express arm responses arise from signaling along the tecto-reticulo-spinal tract, but the involvement of the reticulo-spinal tract has not been well-studied. Since the reticulospinal tract projects bilaterally, we studied whether express arm responses would be generated bilaterally. Human participants (n = 14; 7 female) performed visually guided reaches in a modified emerging target paradigm where either arm could intercept the target. We recorded electromyographic activity bilaterally from the pectoralis major muscle. Our analysis focused on target locations where participants reached with the right arm on some trials, and the left arm on others. In support of the involvement of the reticulospinal tract, express arm responses persisted bilaterally regardless of which arm reached to the target. The latency and magnitude of the express arm response did not depend on whether the arm was chosen to reach or not. However, on the reaching arm, the magnitude of the express arm response was correlated to the level of anticipatory activity. The bilateral generation of express arm responses supports the involvement of the reticulo-spinal tract. We surmise that the correlation between anticipatory activity and the magnitude of express arm responses on the reaching arm arises from convergence of cortically-derived signals with a parallel subcortical pathway mediating the express arm response.

New and Noteworthy

Express arm responses have been proposed to arise from the tecto-reticulo-spinal tract originating within the superior colliculus, but the involvement of the reticulo-spinal tract has not been well studied. Here, we show these responses appear bilaterally in a task where either arm can reach to a newly appearing stimulus. Our results suggest that the most rapid visuomotor transformations for reaching are performed by a subcortical pathway.
Emergent selectivity for scenes, object properties, and contour statistics in feedforward models of scene-preferring cortex
Authors: Li Donald Shi Pui , Bonner Michael F.
Published: September 2021

The scene-preferring portion of the human ventral visual stream, known as the parahippocampal place area (PPA), responds to scenes and landmark objects, which tend to be large in real-world size, fixed in location, and inanimate. However, the PPA also exhibits preferences for low-level contour statistics, including rectilinearity and cardinal orientations, that are not directly predicted by theories of scene- and landmark-selectivity. It is unknown whether these divergent findings of both low- and high-level selectivity in the PPA can be explained by a unified computational theory. To address this issue, we fit feedforward computational models of visual feature coding to the image-evoked fMRI responses of the PPA, and we performed a series of high-throughput experiments on these models. Our findings show that feedforward models of the PPA exhibit emergent selectivity across multiple levels of complexity, giving rise to seemingly high-level preferences for scenes and for objects that are large, spatially fixed, and inanimate/manmade while simultaneously yielding low-level preferences for rectilinear shapes and cardinal orientations. These results reconcile disparate theories of PPA function in a unified model of feedforward feature coding, and they demonstrate how multifaceted selectivity profiles naturally emerge from the feedforward computations of visual cortex and the natural statistics of images.

SIGNIFICANCE STATEMENT

Visual neuroscientists characterize cortical selectivity by identifying stimuli that drive regional responses. A perplexing finding is that many higher-order visual regions exhibit selectivity profiles spanning multiple levels of complexity: they respond to highly complex categories, such as scenes and landmarks, but also to surprisingly simplistic features, such as specific contour orientations. Using large-scale computational analyses and human brain imaging, we show how multifaceted selectivity in scene-preferring cortex can emerge from the feedforward, hierarchical coding of visual features. Our work reconciles seemingly divergent findings of selectivity in scene-preferring cortex and suggests that surprisingly simple feedforward feature representations may be central to the category-selective organization of the human visual system.
Transcriptome-wide association and prediction for carotenoids and tocochromanols in fresh sweet corn kernels
Authors: Hershberger Jenna , Tanaka Ryokei , Wood Joshua C. , Kaczmar Nicholas , Wu Di , Hamilton John P. , DellaPenna Dean , Buell C. Robin , Gore Michael A.
Published: September 2021

Sweet corn is consistently one of the most highly consumed vegetables in the U.S., providing a valuable opportunity to increase nutrient intake through biofortification. Significant variation for carotenoid (provitamin A, lutein, zeaxanthin) and tocochromanol (vitamin E, antioxidants) levels is present in temperate sweet corn germplasm, yet previous genome-wide association studies (GWAS) of these traits have been limited by low statistical power and mapping resolution. Here, we employed a high-quality transcriptomic dataset collected from fresh sweet corn kernels to conduct transcriptome-wide association studies (TWAS) and transcriptome prediction studies for 39 carotenoid and tocochromanol traits. In agreement with previous GWAS findings, TWAS detected significant associations for four causal genes,β-carotene hydroxylase (crtRB1),lycopene epsilon cyclase(lcyE),γ-tocopherol methyltransferase(vte4), andhomogentisate geranylgeranyltransferase(hggt1) on a transcriptome-wide level. Pathway-level analysis revealed additional associations fordeoxy-xylulose synthase2(dxs2),diphosphocytidyl methyl erythritol synthase2(dmes2),cytidine methyl kinase1(cmk1), andgeranylgeranyl hydrogenase1(ggh1), of which,dmes2, cmk1, andggh1have not previously been identified through maize association studies. Evaluation of prediction models incorporating genome-wide markers and transcriptome-wide abundances revealed a trait-dependent benefit to the inclusion of both genomic and transcriptomic data over solely genomic data, but both transcriptome- and genome-wide datasets outperformeda prioricandidate gene-targeted prediction models for most traits. Altogether, this study represents an important step towards understanding the role of regulatory variation in the accumulation of vitamins in fresh sweet corn kernels.

Core Ideas

Transcriptomic data aid the study of vitamin levels in fresh sweet corn kernels.

crtRB1, lcyE, dxs2, dmes2, andcmk1were associated with carotenoid traits.

vte4, hggt1, andggh1were associated with tocochromanol traits.

Transcriptomic data boosted predictive ability over genomic data alone for some traits.

Joint transcriptome- and genome-wide models achieved the highest predictive abilities.
Single-cell RNA Sequencing Reveals Immunosuppressive Myeloid Cell Diversity and Restricted Cytotoxic Effector Cell Trafficking and Activation During Malignant Progression in Glioma
Authors: Rajendran Sakthi , Peterson Clayton , Canella Alessandro , Hu Yang , Gross Amy , Cam Maren , Serin-Harmanci Akdes , Distefano Rosario , Nigita Giovanni , Wang Wesley , Miller Katherine E. , Elemento Olivier , Roberts Ryan , Holland Eric C. , Rao Ganesh , Mardis Elaine R. , Rajappa Prajwal
Published: September 2021

Low grade gliomas (LGG) account for about two-thirds of all glioma diagnoses in adolescents and young adults (AYA) and malignant progression of these patients leads to dismal outcomes. Recent studies have shown the importance of the dynamic tumor microenvironment in high-grade gliomas (HGG), yet its role is still poorly understood in low-grade glioma malignant progression. Here, we investigated the heterogeneity of the immune microenvironment using a platelet-derived growth factor (PDGF)-driven RCAS (replication-competent ASLV long terminal repeat with a splice acceptor) glioma model that recapitulates the malignant progression of low to high-grade glioma in humans and also provides a model system to characterize immune cell trafficking and evolution. To illuminate changes in the immune cell landscape during tumor progression, we performed single-cell RNA sequencing on immune cells isolated from animals bearing no tumor (NT), LGG and HGG, with a particular focus on the myeloid cell compartment, which is known to mediate glioma immunosuppression. LGGs demonstrated significantly increased infiltrating T cells, CD4 T cells, CD8 T cells, B cells, and natural killer cells in the tumor microenvironment, whereas HGGs significantly abrogated this infiltration. Our study identified two distinct macrophage clusters in the tumor microenvironment; one cluster appeared to be bone marrow-derived while another was defined by overexpression of Trem2, a marker of tumor associated macrophages. Our data demonstrates that these two distinct macrophage clusters show an immune-activated phenotype (Stat1, Tnf, Cxcl9 and Cxcl10) in LGG which evolves to an immunosuppressive state (Lgals3, Apoc1 and Id2) in HGG that restricts T cell recruitment and activation. We identified CD74 and macrophage migration inhibition factor (MIF) as potential targets for these distinct macrophage populations. Interestingly, these results were mirrored by our analysis of the TCGA dataset, which demonstrated a statistically significant association between CD74 overexpression and decreased overall survival in AYA patients with grade II gliomas. Targeting immunosuppressive myeloid cells and intra-tumoral macrophages within this therapeutic window may ameliorate mechanisms associated with immunosuppression before and during malignant progression.
Dynamic coupling of residues within proteins as a mechanistic foundation of many enigmatic pathogenic missense variants
Authors: Ose Nicholas J. , Butler Brandon M. , Kumar Avishek , Sanderford Maxwell , Kumar Sudhir , Ozkan S. Banu
Published: September 2021

Many pathogenic missense mutations are found in protein positions that are neither well-conserved nor belong to any known functional domains. Consequently, we lack any mechanistic underpinning of dysfunction caused by such mutations. We explored the disruption of allosteric dynamic coupling between these positions and the known functional sites as a possible mechanism for such mutations. In this study, we present an analysis of 144 human enzymes containing 591 pathogenic missense variants, in which allosteric dynamic coupling of mutated positions with known active sites provides insights into a primary biophysical mechanism and evidence of their functional importance. We illustrate this mechanism in a case study of β-Glucocerebrosidase (GCase), which contains 94 Gaucher disease-associated missense variants located some distance away from the active site. An analysis of the conformational dynamics of GCase suggests that mutations on these distal sites cause changes in the flexibility of active site residues despite their distance, indicating a dynamic communication network throughout the protein. The disruption of the long-distance dynamic coupling due to the presence of missense mutations may provide a plausible general mechanistic explanation for biological dysfunction and disease.

Author Summary

Genetic diseases occur when mutations to a particular gene cause a gain/loss in function of the related protein. Although several methods based on conservation and protein biochemistry exist to predict which genetic mutations may impact function, many disease causing changes remain unexplained by these metrics. In this study, we propose an explanation for these genetic changes may cause disease. In order to function, important regions of a protein must be able to exhibit collective motion. Through computer simulations, we observed that changing even a single amino acid within a protein can change the protein motion. Notably, disease causing genetic changes tend to alter the motion of regions which are critically important to protein function, even the mutations are far from these critical regions. In addition, we examined the degree that two amino acids within a protein may “couple” to one another, meaning the degree to which motion in one amino acid will affect the other. We found that amino acids which are highly coupled to the active site of a protein are more likely to result in disease if mutated, thereby offering a new tool for predicting genetic disease which incorporates internal protein dynamics.
FSTruct: anFST-based tool for measuring ancestry variation in inference of population structure
Authors: Morrison Maike L. , Alcala Nicolas , Rosenberg Noah A.
Published: September 2021

In model-based inference of population structure from individual-level genetic data, individuals are assigned membership coefficients in a series of statistical clusters generated by clustering algorithms. Distinct patterns of variability in membership coefficients can be produced for different groups of individuals, for example, representing different predefined populations, sampling sites, or time periods. Such variability can be difficult to capture in a single numerical value; membership coefficient vectors are multivariate and potentially incommensurable across groups, as the number of clusters over which individuals are distributed can vary among groups of interest. Further, two groups might share few clusters in common, so that membership coefficient vectors are concentrated on different clusters. We introduce a method for measuring the variability of membership coefficients of individuals in a predefined group, making use of an analogy between variability across individuals in membership coefficient vectors and variation across populations in allele frequency vectors. We show that in a model in which membership coefficient vectors in a population follow a Dirichlet distribution, the measure increases linearly with a parameter describing the variance of a specified component of the membership vector. We apply the approach, which makes use of a normalizedFSTstatistic, to data on inferred population structure in three example scenarios. We also introduce a bootstrap test for equivalence of two or more groups in their level of membership coefficient variability. Our methods are implemented in the R package FSTruct.
Bakdrive: Identifying the Minimum Set of Bacterial Driver Species across Multiple Microbial Communities
Authors: Wang Qi , Nute Michael , Treangen Todd
Published: September 2021

Interactions among microbes within microbial communities have been shown to play crucial roles in human health. In spite of recent progress, low-level knowledge of bacteria driving microbial interactions within microbiomes remains unknown, limiting our ability to fully understand and control microbial communities. In this study, we present a novel approach for identifying driver species within microbiomes. Bakdrive infers ecological networks of given metagenomic sequencing samples and identifies minimum sets of driver species using control theory. Bakdrive has three key innovations in this space: (i) it leverages inherent information from metagenomic sequencing samples to identify driver species, (ii) it explicitly takes host-specific variation into consideration, and (iii) it does not require a known ecological network. In extensive simulated data, we demonstrate identifying driver species identified from healthy donor samples and introducing them to the disease samples, we can restore the gut microbiome in recurrent Clostridioides difficile infection patients to a healthy state. We also applied Bakdrive to two real datasets, rCDI and Crohn’s disease patients, uncovering driver species consistent with previous work. In summary, Bakdrive provides a novel approach for teasing apart microbial interactions. Bakdrive is open-source and available at https://gitlab.com/treangenlab/bakdrive
BRCA2 BRC missense variants disrupt RAD51-dependent DNA repair
Authors: Jimenez-Sainz Judit , Mathew Joshua , Moore Gemma , Lahiri Sudipta , Garbarino Jennifer , Eder Joseph P. , Rothenberg Eli , Jensen Ryan B.
Published: September 2021

Pathogenic mutations in the BRCA2 tumor suppressor gene predispose to breast, ovarian, pancreatic, prostate, and other cancers. BRCA2 maintains genome stability through homology-directed repair (HDR) of DNA double-strand breaks (DSBs) and replication fork protection. Nonsense or frameshift mutations leading to truncation of the BRCA2 protein are typically considered pathogenic, however, missense mutations resulting in single amino acid substitutions can be challenging to functionally interpret. The majority of missense mutations in BRCA2 have been classified as Variants of Uncertain Significance (VUS) with unknown functional consequences. In this study, we identified three BRCA2 VUS located within the BRC repeat region to determine their impact on canonical HDR and fork protection functions. We provide evidence that S1221P and T1980I, which map to conserved residues in the BRC2 and BRC7 repeats, compromise the cellular response to chemotherapeutics and ionizing radiation, and display deficits in fork protection. We further demonstrate biochemically that S1221P and T1980I disrupt RAD51 binding and diminish the ability of BRCA2 to stabilize RAD51-ssDNA complexes. The third variant, T1346I, located within the spacer region between BRC2 and BRC3 repeats, is fully functional. We conclude that T1346I is a benign allele whereas S1221P and T1980I are hypomorphic disrupting the ability of BRCA2 to fully engage and stabilize RAD51 nucleoprotein filaments. Our results underscore the importance of correctly classifying BRCA2 VUS as pathogenic variants can impact both future cancer risk and guide therapy selection during cancer treatment.

Graphical Abstract
Social behavioral profiling by unsupervised deep learning reveals a stimulative effect of dopamine D3 agonists on zebrafish sociality
Authors: Geng Yijie , Peterson Randall T.
Published: September 2021

It has been a major challenge to systematically evaluate and compare how pharmacological perturbations influence social behavioral outcomes. Although some pharmacological agents are known to alter social behavior, precise description and quantification of such effects have proven difficult. The complexity of brain functions regulating sociality makes it challenging to predict drug effects on social behavior without testing in live animals, and most existing behavioral assays are low-throughput and provide only unidimensional readouts of social function. To achieve richer characterization of drug effects on sociality, we developed a scalable social behavioral assay for zebrafish named ZeChat based on unsupervised deep learning. High-dimensional and dynamic social behavioral phenotypes are automatically classified using this method. By screening a neuroactive compound library, we found that different classes of chemicals evoke distinct patterns of social behavioral fingerprints. By examining these patterns, we discovered that dopamine D3 agonists possess a social stimulative effect on zebrafish. The D3 agonists pramipexole, piribedil, and 7-hydroxy-DPAT-HBr rescued social deficits in a valproic acid-induced zebrafish autism model. The ZeChat platform provides a promising approach for dissecting the pharmacology of social behavior and discovering novel social-modulatory compounds.
The germline-specific region of the sea lamprey genome plays a key role in spermatogenesis
Authors: Yasmin Tamanna , Grayson Phil , Docker Margaret F. , Good Sara V.
Published: September 2021

The sea lamprey genome undergoes programmed genome rearrangement (PGR) in which ∼20% is jettisoned from somatic cells soon after fertilization. Although the role of PGR in embryonic development has been studied, the role of the germline-specific region (GSR) in gonad development is unknown. We analysed RNA-sequence data from 28 sea lamprey gonads sampled across life-history stages, generated a genome-guided de novo superTransciptome with annotations, and identified genes in the GSR. We found that the 638 genes in the GSR are enriched for reproductive processes, exhibit 36x greater odds of being expressed in testes than ovaries, show little evidence of conserved synteny with other chordates, and most have putative paralogues in the GSR and/or somatic genomes. Further, several of these genes play known roles in sex determination and differentiation in other vertebrates. We conclude that the GSR of sea lamprey plays an important role in testicular differentiation and potentially sex determination.
Leafy and Weedy Seadragon Genomes Connect Genic and Repetitive DNA Features to the Extravagant Biology of Syngnathid Fishes
Authors: Small Clayton M. , Healey Hope M. , Currey Mark C. , Beck Emily A. , Catchen Julian , Lin Angela S. P. , Cresko William A. , Bassham Susan
Published: September 2021

Seadragons are a remarkable lineage of teleost fishes, and they are members of the family Syngnathidae renowned for having evolved male pregnancy. Comprising three known species, seadragons are widely recognized and admired for their fantastical body forms and coloration, and their specific habitat requirements have made them flagship representatives for marine conservation and natural history interests. Until recently, a gap has been the lack of significant genomic resources for seadragons. We have produced gene-annotated, chromosome-scale genome models for the leafy and weedy seadragon to advance investigations into evolutionary innovation and elaboration of morphological traits in seadragons as well as their pipefish and seahorse relatives. We identified several interesting features specific to seadragon genomes, including divergent non-coding regions near a developmental gene important for integumentary outgrowth, a high genome-wide density of repetitive DNA, and recent expansions of transposable elements and a vesicular trafficking gene family. Surprisingly, comparative analyses leveraging the seadragon genomes and additional syngnathid and outgroup genomes revealed striking, syngnathid-specific losses in the family of fibroblast growth factors (FGFs), which likely involve re-organization of highly conserved gene regulatory networks in ways that have not previously been documented in natural populations. The resources presented here serve as important tools for future evolutionary studies of developmental processes in syngnathids and will be a key resource for conservation studies of the extravagant seadragons and their relatives.
‘Wanting’ versus ‘Needing’ related value: an fMRI meta-analysis
Authors: Bosulu J , Allaire M.-A. , Tremblay-Grénier L. , Luo Y. , Eickhoff S. , Hétu S.
Published: September 2021

Consumption and its excesses are sometimes explained by imbalance of need or lack of control over ‘wanting’. ‘Wanting’ assigns value to cues that predict rewards, whereas ‘needing’ assigns value to biologically significant stimuli that one is deprived of. Here we aimed at studying how the brain activation patterns related to value of ‘wanted’ stimuli differs from that of ‘needed’ stimuli using ALE neuroimaging meta-analysis approaches. We used the perception of a cue predicting a reward for ‘wanting’ related value and the perception of food stimuli in a hungry state as a model for ‘needing’ related value. We carried out separate, contrasts, and conjunction meta-analyses to identify differences and similarities between ‘wanting’ and ‘needing’ values. Our overall results for ‘wanting’ related value show consistent activation of the ventral tegmental area, striatum and pallidum, regions that both activate behaviour and direct choice; while for ‘needing’ related value we found an overall consistent activation of the middle insula and to some extent the caudal-ventral putamen, regions that only direct choice. Our study suggests that wanting has more control on consumption, and a needed stimuli must become wanted in order to be pursued.
Rapid in vivo development of resistance to daptomycin in vancomycin-resistant Enterococcus faecium due to genomic rearrangements
Authors: Mollerup Sarah , Elmeskov Christine , Gumpert Heidi , Pinholt Mette , Sejersen Tobias Steen , Pedersen Martin Schou , Worning Peder , Frees Dorte , Westh Henrik
Published: September 2021

Background

Daptomycin is a cyclic lipopeptide used in the treatment of vancomycin-resistant Enterococcus faecium (VREfm). However, the development of daptomycin-resistant VREfm challenges the treatment of nosocomial VREfm infections. Resistance mechanisms of daptomycin are not fully understood. Here we analysed the genomic changes leading to a daptomycin-susceptible VREfm isolate becoming resistant after 40 days of daptomycin and linezolid combination therapy.

Methods

The two isogenic VREfm isolates (daptomycin-susceptible and daptomycin-resistant) were analysed using whole genome sequencing with Illumina and Nanopore.

Results

Whole genome comparative analysis identified the loss of a 46.5 kb fragment and duplication of a 29.7 kb fragment in the daptomycin-resistant isolate, with many implicated genes involved in cell wall synthesis. Two plasmids of the daptomycin-susceptible isolate were also found integrated in the chromosome of the resistant isolate. One nonsynonymous SNP in the rpoC gene was identified in the daptomycin-resistant isolate.

Conclusions

Daptomycin resistance developed through chromosomal rearrangements leading to altered cell wall structure. Such novel types of resistance mechanisms can only be identified by comparing closed genomes of isogenic isolates.
Kin discrimination modifies fitness, spatial segregation and matrix sharing between strains with low relatedness inBacillus subtilisbiofilms
Authors: Bolješić Maja , Kraigher Barbara , Dogša Iztok , Kokelj Barbara Jerič , Mulec Ines Mandić
Published: September 2021

Microorganisms in nature form multicellular groups called biofilms. In biofilms bacteria embedded in a matrix of extracellular polymeric substances (EPS) interact intensely, due to their proximity to each other. Most studies have investigated genetically homogeneous biofilms, leaving a gap in knowledge on genetically heterogeneous biofilms. Recent insights show that a Gram-positive model bacterium,Bacillus subtilis, discriminates between strains of high (kin) and low (non-kin) phylogenetic relatedness, reflected in merging (kin) and boundaries (non-kin) between swarms. However, it is not clear how kinship between interacting strains affects their fitness, the genotype distribution, and the EPS sharing in floating biofilms (pellicles). To address this gap in knowledge we cultivateB. subtilisstrains as mixtures of kin and non-kin strains in static cultures, allowing them to form pellicles. We show here that in non-kin pellicles only one strain’s fitness was reduced; at the same time, strains segregated into larger patches and exhibited decreased matrix sharing, as compared to kin and isogenic pellicles, in which both strains had comparable colony forming units (CFU) counts and more homogenous cell mixing. Overall, our results emphasize kin discrimination (KD) as a social behavior that shapes fitness, spatial segregation and sharing of the extracellular matrix in genetically heterogenous biofilms ofB. subtilis.

IMPORTANCE

Biofilm communities have both beneficial and harmful effects on human societies in natural, medical and industrial environments.Bacillus subtilis, a Gram-positive and biotechnologically important bacterium, serves as a model for studying biofilms. Recent studies have shown that this species engages in kin discriminatory behavior during swarming, which may have implications for community assembly, thus being of fundamental importance. Effects of KD on fitness, genotype segregation and matrix sharing in biofilms is not well understood. By using environmental strains with determined kin types and integrated fluorescent reporters we provide evidence that KD involves antagonism of the dominant strain against non-kin, which has important implications for genotype segregation and sharing of matrix polysaccharides between producers and non-producers. Our results reveal novel consequences of KD and are important for advancing our fundamental understanding of microbial sociality, and its role in the assembly of multicellular groups and in the shaping of microbial diversity.
Human metapneumovirus P protein independently drives phase separation and recruits N protein to liquid-like inclusion bodies
Authors: Boggs Kerri Beth , Cifuentes-Munoz Nicolas , Edmonds Kearstin , Najjar Farah El , Ossandón Conny , Roe McKenna , Moncman Carole L. , Creamer Trevor , Dutch Rebecca Ellis
Published: September 2021

Human metapneumovirus (HMPV) inclusion bodies (IBs) are dynamic structures required for efficient viral replication and transcription. The minimum components needed to form IB-like structures in cells are the nucleoprotein (N) and the tetrameric phosphoprotein (P). HMPV P binds to two versions of N protein in infected cells: C-terminal P residues interact with oligomeric, RNA-bound N (N-RNA), and N-terminal P residues interact with monomeric N (N0) to maintain a pool of protein to encapsidate new RNA. Recent work on other negative-strand viruses has suggested that IBs are liquid-like organelles formed via liquid-liquid phase separation (LLPS). Here, HMPV IBs in infected or transfected cells were shown to possess liquid organelle properties, such as fusion and fission. Recombinant versions of HMPV N and P proteins were purified to analyze the interactions required to drive LLPS in vitro. Purified HMPV P was shown to form liquid droplets in the absence of other protein binding partners, a novel finding compared to other viral systems. Removal of nucleic acid from purified P altered phase separation dynamics, suggesting that nucleic acid interactions also play a role in IB formation. HMPV P also recruits monomeric N (N0-P) and N-RNA to IBs in vitro. These findings suggest that, in contrast to what has been reported for other viral systems, HMPV P acts as a scaffold protein to mediate multivalent interactions with monomeric and oligomeric HMPV N to promote phase separation of IBs.

IMPORTANCE

Human metapneumovirus (HMPV) is a leading cause of respiratory disease among children, immunocompromised individuals, and the elderly. Currently, no vaccines or antivirals are available for treatment of HMPV infections. Cytoplasmic inclusion bodies (IBs), where HMPV replication and transcription occur, represent a promising target for the development of novel antivirals. The HMPV nucleoprotein (N) and phosphoprotein (P) are the minimal components needed for IB formation in eukaryotic cells. However, interactions that regulate the formation of these dynamic structures are poorly understood. Here, we showed that HMPV IBs possess the properties of liquid organelles and that purified HMPV P phase separates independently in vitro. Our work suggests that HMPV P phase separation dynamics are altered by nucleic acid. We provide strong evidence that, unlike results reported from other viral systems, HMPV P alone serves as a scaffold for multivalent interactions with monomeric (N0) and oligomeric (N-RNA) HMPV N for IB formation.
Means, motive, and opportunity for biological invasions: genetic introgression in a fungal pathogen
Authors: Rogério Flávia , Van Oosterhout Cock , Ciampi-Guillardi Maisa , Correr Fernando Henrique , Hosaka Guilherme Kenichi , Cros-Arteil Sandrine , Margarido Gabriel Rodrigues Alves , Massola Nelson S. , Gladieux Pierre
Published: September 2021

Invasions by fungal plant pathogens pose a significant threat to the health of agriculture ecosystems. Despite limited standing genetic variation, many invasive fungal species can adapt and spread rapidly, resulting in significant losses in crop yields. Here, we report on the population genomics of Colletotrichum truncatum, a polyphagous pathogen that can infect more than 460 plant species, and an invasive pathogen on soybean in Brazil. We study the whole-genome sequences of 18 isolates representing 10 fields from two major regions of soybean production. We show that Brazilian C. truncatum is subdivided into three phylogenetically distinct lineages that exchange genetic variation through hybridization. Introgression affects 2 to 30% of the nucleotides of genomes and varies widely between the lineages. We find that introgressed regions comprise secreted protein-encoding genes, suggesting possible co-evolutionary targets for selection in those regions. We highlight the inherent vulnerability of genetically uniform crops in the agro-ecological environment, particularly when faced with pathogens that can take full advantage of the opportunities offered by an increasingly globalized world. Finally, we discuss “The Means, Motive, and Opportunity” of fungal pathogens and how they can become invasive species of crops. We call for more population genomic studies because such analyses can help identify geographic areas and pathogens that pose a risk, thereby helping to inform control strategies to better protect crops in the future.
Auditory Hypersensitivity and Processing Deficits in a Rat Model of Fragile X Syndrome
Authors: Auerbach Benjamin D. , Manohar Senthilvelan , Radziwon Kelly , Salvi Richard
Published: September 2021

Fragile X (FX) syndrome is one of the leading inherited causes of autism spectrum disorder (ASD). A majority of FX and ASD patients exhibit sensory hypersensitivity, including auditory hypersensitivity or hyperacusis, a condition in which everyday sounds are perceived as much louder than normal. Auditory processing deficits in FX and ASD also afford the opportunity to develop objective and quantifiable outcome measures that are likely to translate between humans and animal models due to the well-conserved nature of the auditory system and well-developed behavioral read-outs of sound perception. Therefore, in this study we characterized auditory hypersensitivity in aFmr1knockout (KO) transgenic rat model of FX using an operant conditioning task to assess sound detection thresholds and suprathreshold auditory reaction time-intensity (RT-I) functions, a reliable psychoacoustic measure of loudness growth, at a variety of stimulus frequencies, bandwidths and durations. MaleFmr1KO and littermate WT rats both learned the task at the same rate and exhibited normal hearing thresholds. However,Fmr1KO rats had faster auditory RTs over a broad range of intensities and steeper RT-I slopes than WT controls, perceptual evidence of excessive loudness growth inFmr1KO rats. Furthermore, we found thatFmr1KO animals exhibited abnormal perceptual integration of sound duration and bandwidth, with diminished temporal but enhanced spectral integration of sound intensity. Because temporal and spectral integration of sound stimuli were altered in opposite directions inFmr1KO rats, this suggests that abnormal RTs in these animals are evidence of aberrant auditory processing rather than generalized hyperactivity or altered motor responses. Together, these results are indicative of fundamental changes to low-level auditory processing inFmr1KO animals. Finally, we demonstrated that antagonism of metabotropic glutamate receptor 5 (mGlu5) selectively and dose-dependently restored normal loudness growth inFmr1KO rats, suggesting a pharmacologic approach for alleviating sensory hypersensitivity associated with FX. This study leverages the tractable nature of the auditory system and the unique behavioral advantages of rats to provide important insights into the nature of a centrally important yet understudied aspect of FX and ASD.
Elucidation of sub-cellular H2S metabolism inSolanum lycopersicumL. and its assessment under development and biotic stress
Authors: Chowdhary Aksar Ali , Mishra Sonal , Singh Vikram , Srivastava Vikas
Published: September 2021

The signalling molecules serve as a fundamental requirement in plants and respond to various internal and external cues. Among several signalling molecules, the significance of gasotransmitters has been realized in several plant developmental and environmental constraints. The hydrogen sulfide (H2S) is a novel signalling molecule in higher plants and is involved in several physiological processes right from seed germination to flowering and fruit ripening. Moreover, H2S also assist plants in managing biotic and abiotic stresses, therefore serves as one of the imperative choice of chemical priming. Yet, the metabolism of H2S is not much explored and only appraisal study is made till date fromArabidopsis thaliana. Therefore, the present investigation explored the elucidation of H2S metabolism in crop plantSolanum lycopersicumL. Through in silico investigations the study demonstrated the participation of 29 proteins involved in H2S metabolism, which are mainly localized in cytosol, chloroplast, and mitochondria. Additionally, the relevant protein-protein interactomes were also inferred for sub-cellular compartments and expression data were explored under development and biotic stresses namely PAMPs treatment and bacterial infection. The information generated here will be of high relevance to better target the H2S metabolism to enhance the tomato prospects and also serve a preliminary investigation to be adopted in other agronomic important crops.
The wheat dioxygenase BX6 is involved in the formation of benzoxazinoids in planta and contributes to plant defense against insect herbivores
Authors: Shavit Reut , Batyrshina Zhaniya S. , Yaakov Beery , Florean Matilde , Köllner Tobias G. , Tzin Vered
Published: September 2021

Benzoxazinoids are plant specialized metabolites with defense properties, highly abundant in wheat (Triticum), one of the world’s most important crops. The goal of our study was to characterize dioxygenase BX6 genes in tetraploid and hexaploid wheat genotypes and to elucidate their effects on defense against herbivores. Phylogenetic analysis revealed four BX6 genes in the hexaploid wheat T. aestivum, but only one ortholog was found in tetraploid (T. turgidum) wild emmer wheat and the cultivated durum wheat. Transcriptome sequencing of durum wheat plants damaged either by aphids or caterpillars revealed that several BX genes including TtBX6 were upregulated upon caterpillar feeding relative to undamaged control plants. A virus-induced gene silencing approach was used to reduce the expression of BX6 in T. aestivum plants and exhibited both reduced transcript levels and reduced accumulation of different benzoxazinoids. To elucidate the effect of BX6 on plant defense, bioassays with different herbivores feeding on BX6-silenced leaves were conducted. The results showed that plants with silenced BX6 were more susceptible to aphids and the two-spotted spider mite compared to controls. Overall, our study indicates that wheat BX6 is involved in the formation of benzoxazinoids in planta and contributes to plant resistance against insect herbivores.
Post-trauma behavioral phenotype predicts vulnerability to fear relapse after extinction
Authors: Demars Fanny , Todorova Ralitsa , Makdah Gabriel , Forestier Antonin , Krebs Marie-Odile , Godsil Bill P. , Jay Thérèse M. , Wiener Sidney I. , Pompili Marco N.
Published: September 2021

Current treatments for trauma-related disorders remain ineffective for many patients. Here, we modeled interindividual differences in post-therapy fear relapse with a novel ethologically relevant trauma recovery paradigm. After traumatic fear conditioning, male rats underwent fear extinction while foraging in a large enriched arena, permitting the expression of a wide spectrum of behaviors, assessed by an automated pipeline. This multidimensional behavioral assessment revealed that post-conditioning fear response profiles clustered into two groups, respectively characterized by active vs. passive fear responses. After trauma, some animals expressed fear by freezing, while others darted, as if fleeing from danger. Remarkably, belonging to the darters or freezers group predicted differential levels of vulnerability to fear relapse after extinction. Moreover, genome-wide transcriptional profiling revealed that these groups differentially regulated specific sets of genes, some of which have previously been implicated in anxiety and trauma-related disorders. Our results suggest that post-trauma behavioral phenotypes and the associated epigenetic landscapes can serve as markers of fear relapse susceptibility, and thus may be instrumental for future development of more effective treatments for psychiatric patients.
Instant Taq: Rapid Autoinducible Expression and Chromatography-free Purification of Taq polymerase
Authors: Menacho-Melgar Romel , Yang Tian , Lynch Michael D.
Published: September 2021

DNA modifying enzymes are ubiquitous reagents in synthetic biology. Producing these enzymes often requires large culture volumes, purified nucleases and chromatographic separations to make enzymes of necessary quality. We sought to leverage synthetic biology tools to develop engineered strains allowing for not only the production but rapid purification of these reagents. Toward this goal, we report an E. coli strain enabling the rapid production and purification of Taq polymerase. The method relies on 1) autoinducible expression achieving high protein titers, 2) autolysis and auto DNA/RNA hydrolysis via lysozyme and a mutant benzonase™, and 3) heat denaturation under reducing conditions to precipitate contaminating proteins including the mutant benzonase™. Taq polymerase is obtained at high purities (>95% pure by SDS-PAGE) and is readily usable in standard reactions. The method takes less than 1 hour of hands-on time, does not require special equipment, expensive reagents or affinity purification. We expect this simple methodology and approach will improve access not only to Taq polymerase but to numerous additional commonly utilized reagent proteins.

Highlights

Protein titers ~ 1g/L achieved in 20 mL shakeflasks.

4 mg of purified Taq (corresponding to 5,000 Units, or 4,000 PCR reactions) per 20 mL shake flask.

Instant Taq is equivalent to commercial preparations in routine PCR
Direct reprogramming of the intestinal epithelium by parasitic helminths subverts type 2 immunity
Authors: Karo-Atar Danielle , Ouladan Shaida , Javkar Tanvi , Joumier Loick , Matheson Macy K. , Merritt Sydney , Westfall Susan , Rochette Annie , Gentile Maria E. , Fontes Ghislaine , Fonseca Gregory J. , Parisien Marc , Diatchenko Luda , von Moltke Jakob , Malleshaiah Mohan , Gregorieff Alex , King Irah L.
Published: September 2021

Enteric helminths form intimate physical connections with the intestinal epithelium, yet their ability to directly alter epithelial stem cell fate has not been resolved. Here we demonstrate that infection of mice with the symbiotic parasite Heligmosomoides polygyrus bakeri (Hbp), reprograms the intestinal epithelium into a fetal-like state marked by the emergence of Clusterin-expressing revival stem cells (revSCs). Organoid-based studies using parasite-derived excretory/secretory products reveal that Hpb-mediated revSC generation occurs independent of host-derived immune signals and inhibits type 2 cytokine-driven differentiation of secretory epithelial lineages that promote their expulsion. Reciprocally, type 2 cytokine signals limit revSC differentiation and, consequently, Hpb fitness indicating that helminths compete with their host for control of the intestinal stem cell niche to promote continuation of their life cycle.