title: Identifying Meta-QTLs for Stay-Green in Sorghum

abstract: To develop resilient crops it is necessary to understand the underlying genetics of climatic response. A strong association between stay-green and post-flowering drought tolerance in Sorghum has been established. Being a complex quantitative trait, Quantitative Trait Loci (QTL) mapping experiments of stay-green in Sorghum have been frequently performed. The objective of the current study was to find consensus genomic regions that control stay-green by integrating the QTLs mapped in previous studies. Meta-QTL analysis was performed to summarize 115 QTLs projected on the consensus map. The analysis generated 32 Meta-QTL regions within which candidate gene (CG) identification was undertaken. 7 candidate genes were identified using the markers tightly linked to the Meta-QTLs. The results from this study will facilitate future attempts aiming to improve and understand drought tolerance in Sorghum.


title: A LINCS microenvironment perturbation resource for integrative assessment of ligand-mediated molecular and phenotypic responses

abstract: The phenotype of a cell and its underlying molecular state is strongly influenced by extracellular signals, including growth factors, hormones, and extracellular matrix. While these signals are normally tightly controlled, their dysregulation leads to phenotypic and molecular states associated with diverse diseases. To develop a detailed understanding of the linkage between molecular and phenotypic changes, we generated a comprehensive dataset that catalogs the transcriptional, proteomic, epigenomic and phenotypic responses of MCF10A mammary epithelial cells after exposure to the ligands EGF, HGF, OSM, IFNG, TGFB and BMP2. Systematic assessment of the molecular and cellular phenotypes induced by these ligands comprise the LINCS Microenvironment (ME) perturbation dataset, which has been curated and made publicly available for community-wide analysis and development of novel computational methods (synapse.org/LINCS_MCF10A). In illustrative analyses, we demonstrate how this dataset can be used to discover functionally related molecular features linked to specific cellular phenotypes.

category: systems biology


title: Hippocampal-hypothalamic circuit controls context-dependent innate defensive responses

abstract: Preys use their memory - where they sensed a predatory threat and whether a safe shelter is nearby - to dynamically control their survival instinct to avoid harm and reach safety. However, it remains unknown which brain regions are involved, and how such top-down control of innate behaviour is implemented at the circuit level. Here, we show that the anterior hypothalamic nucleus (AHN) is best positioned to perform this task as an exclusive target of the hippocampus (HPC) within the medial hypothalamic defense system. Selective optogenetic stimulation and inhibition of hippocampal inputs to the AHN revealed that the HPC[->]AHN pathway not only mediates the contextual memory of predator threats but also controls the goal-directed escape by transmitting information about the surrounding environment. These results reveal a new mechanism for experience-dependent, top-down control of innate defensive behaviours.

category: neuroscience


title: Primary glia cells from bank vole propagate multiple rodent-adapted scrapie prions

abstract: Since the beginning prion research has been largely dependent on animal models for deciphering the disease, drug development or prion detection and quantification. Thereby, ethical as well as cost and labour-saving aspects call for alternatives in vitro. Cell models can replace or at least complement animal studies, but their number is still limited and the application usually restricted to certain strains and host species due to often strong transmission barriers. Bank voles promise to be an exception as they or materials prepared from them are uniquely susceptible to prions from various species in vivo, in vitro and in cell-free applications. Here we present a mainly astrocyte-based primary glia cell assay from bank vole, which is infectible with scrapie strains from bank vole, mouse and hamster. Stable propagation of bank vole-adapted RML, murine 22L and RML, and hamster 263K scrapie is detectable from 20 or 30 days post exposure onwards. Thereby, the infected bank vole glia cells show similar or even faster prion propagation than likewise infected glia cells of the corresponding murine or hamster hosts. We propose that our bank vole glia cell assay could be a versatile tool for studying and comparing multiple prion strains with different species backgrounds in a single cell assay.


title: Evaluation of a high-throughput deorphanization strategy to identify cytochrome p450s important for odor degradation in Drosophila

abstract: Members of the cytochrome p450 (CYP) enzyme family are abundantly expressed in insect olfactory tissues, where they are thought to act as Odorant Degrading Enzymes (ODEs). However, their contribution to olfactory signaling in vivo is poorly understood. This is due in part to the challenge of identifying which of the dozens of antennal-expressed CYPs might inactivate a given odorant. Here, we tested a high-throughput deorphanization strategy in Drosophila to identify CYPs that are transcriptionally induced by exposure to a plant volatile. We discovered three CYPs selectively upregulated by the odorant using transcriptional profiling. Although these CYPs are shown to be broadly expressed in the antenna in non-neuronal cells, electrophysiological recordings from CYP mutants did not reveal any changes in olfactory neuron responses to the odorant. Neurons were desensitized by pre-exposing flies to the odorant, but this effect was similar in CYP mutants. Together, our data suggest that this transcriptomic approach may not be useful for identifying CYPs that contribute to olfactory signaling. We go on to show that some CYPs have highly restricted expression patterns in the antenna, and suggest that such CYPs may be useful candidates for further studies on olfactory CYP function.


title: Hematopoietic-SLC37A2 deficiency impairs M2 macrophage polarization and accelerates atherosclerosis in LDL receptor-deficient mice

abstract: Macrophages play a central role in the pathogenesis of atherosclerosis. Our previous study demonstrated that solute carrier family 37 member 2 (SLC37A2), an endoplasmic reticulum-anchored phosphate-linked glucose-6-phosphate transporter, negatively regulates macrophage Toll-like receptor activation by fine-tuning glycolytic reprogramming in vitro. Whether macrophage SLC37A2 impacts in vivo macrophage inflammation and atherosclerosis under hyperlipidemic conditions is unknown. We generated hematopoietic cell-specific SLC37A2 knockout and control mice in C57Bl/6 Ldlr-/- mice by bone marrow transplantation. Hematopoietic-specific SLC37A2 deletion in Ldlr-/- mice increased plasma lipid concentrations 12-16 wks of Western diet induction, attenuated macrophage anti-inflammatory responses, and resulted in more atherosclerosis compared to Ldlr-/- mice transplanted with wild type bone marrow. Aortic root intimal area was inversely correlated with plasma IL-10 levels, but not total cholesterol concentrations, suggesting inflammation but not plasma cholesterol was responsible for increased atherosclerosis in bone marrow SLC37A2-deficient mice. Our in vitro study demonstrated that SLC37A2 deficiency impaired IL-4-induced macrophage activation, independently of glycolysis or mitochondrial respiration. Importantly, SLC37A2 deficiency impaired apoptotic cell-induced glycolysis, subsequently attenuating IL-10 production. Our study suggests that SLC37A2 expression is required to support alternative macrophage activation in vitro and in vivo. In vivo disruption of hematopoietic SLC37A2 accelerates atherosclerosis under hyperlipidemic pro-atherogenic conditions.

category: immunology


title: Hematopoietic-SLC37A2 deficiency accelerates atherosclerosis in LDL receptor-deficient mice


title: SIRPα sequesters SHP-2 to promote IL-4/13 signaling and alternative activation of macrophages

abstract: The Th2 cytokines IL-4 and IL-13 through activation of their shared receptor IL-4R direct macrophage alternative activation to promote immunosuppression and wound healing. However, the mechanisms that control macrophage responses to IL-4/13 are not fully understood. Apart from driving JAK-STAT and PI3K-Akt pathways to polarize macrophages toward the alternative phenotype, the activated IL-4/13 receptors recruit negative regulators SHP-1 and SHP-2, which dephosphorylate IL-4R and decrease its signaling. Here we report that SIRP spatially restricts SHP-2 and, by such, promotes IL-4/13 signaling and macrophage alternative activation. SIRP executes this regulation via its cytoplasmic ITIMs/ITSMs that undergo phosphorylation by IL-4/13-induced, Src kinase-activated Brutons tyrosine kinase (Btk), resulting in recruitment of SHP-2 and preclusion of SHP-2 from binding to and inhibiting IL-4/13 receptors. Despite that this regulation occurs independent of CD47, extracellular CD47 ligation of SIRP facilitates its cytoplasmic phosphorylation and SHP-2 sequestration, leading to stronger IL-4/13 signaling and enhanced macrophage expression of IL-10, TGF{beta}, CD206, arginase-1, etc. Conversely, deficiency of SIRP allows SHP-2 to freely bind to {gamma}C or IL-13R1 and through which dephosphorylate IL-4R, dampening its signaling. Consistent with these findings, impaired wound healing in Sirp-/- mice under experimental colitis correlated with a deficit of immunosuppressive macrophages in the colon, a condition that was corrected by transfusion of ex vivo-produced SIRPhigh alternatively activated macrophages.


title: Revealing how variations in antibody repertoires correlate with vaccine responses

abstract: An important challenge in vaccine development is to figure out why a vaccine succeeds in some individuals and fails in others. Although antibody repertoires hold a key to answering this question, there have been very few personalized immunogenomics studies so far aimed at revealing how variations in immunoglobulin genes affect a vaccine response. We conducted an immunosequencing study of 204 calves vaccinated against bovine respiratory disease (BRD) with the goal to reveal variations in immunoglobulin genes and somatic hypermutations that impact the efficacy of vaccine response. Our study represents the largest longitudinal personalized immunogenomics study reported to date across all species, including humans. To analyze the generated dataset, we developed an algorithm for identifying variations of the immunoglobulin genes (as well as frequent somatic hypermutations) that affect various features of the antibody repertoire and titers of neutralizing antibodies. In contrast to relatively short human antibodies, cattle have a large fraction of ultralong antibodies that have opened new therapeutic opportunities. Our study revealed that ultralong antibodies are a key component of the immune response against the costliest disease of beef cattle in North America. The detected variants of the cattle immunoglobulin genes, which are implicated in the success/failure of the BRD vaccine, have the potential to direct the selection of individual cattle for ongoing breeding programs.


title: Shotgun proteomic profiling of dormant, 'non-culturable' Mycobacterium tuberculosis

abstract: Dormant cells of Mycobacterium tuberculosis, in addition to low metabolic activity and a high level of drug resistance, are characterized by  non-culturability - a specific reversible state of the inability of the cells to grow on solid media. The biochemical characterization of this physiological state of the pathogen is only superficial, pending clarification of the metabolic processes that may exist in such cells. In this study, applying LC-MS proteomic profiling, we report the analysis of proteins accumulated in dormant,  non-culturable M. tuberculosis cells in an in vitro model of self-acidification of mycobacteria in the post-stationary phase, simulating the in vivo persistence conditions. This approach revealed the accumulation of a significant number of proteins (1379) in cells after 4 months of storage in dormancy; among them, 468 proteins were significantly different from those in the actively growing cells and bore a positive fold change (FC). Differential analysis revealed the proteins of the pH-dependent regulatory system phoP and allowed the reconstruction of the reactions of central carbon/glycerol metabolism, as well as revealing the salvaged pathways of mycothiol and UMP biosynthesis, establishing the cohort of survival enzymes of dormancy. The annotated pathways mirror the adaptation of the mycobacterial metabolic machinery to life within lipid-rich macrophages, especially the involvement of the methyl citrate and glyoxylate pathways. Thus, the current in vitro model of M. tuberculosis self-acidification reflects the biochemical adaptation of these bacteria to persistence in vivo. Comparative analysis with published proteins with antigenic properties makes it possible to distinguish immunoreactive proteins (40) among the proteins bearing a positive FC in dormancy, which may include specific antigens of latent tuberculosis. Additionally, the biotransformatory enzymes (oxidoreductases and hydrolases) capable of prodrug activation and stored up in the dormant state were annotated. These findings may potentially lead to the discovery of immunodiagnostic tests for early latent tuberculosis and trigger the discovery of efficient drugs/prodrugs with potency against non-replicating, dormant populations of mycobacteria.

category: microbiology


title: Elamipretide (SS-31) Treatment Attenuates Age-Associated Post-Translational Modifications of Heart Proteins

abstract: It has been demonstrated that elamipretide (SS-31) rescues age-related functional deficits in the heart but the full set of mechanisms behind this have yet to be determined. We investigated the hypothesis that elamipretide influences post-translational modifications to heart proteins. The S-glutathionylation and phosphorylation proteomes of mouse hearts were analyzed using shotgun proteomics to assess the effects of aging on these post-translational modifications and the ability of the mitochondria-targeted drug elamipretide to reverse age-related changes. Aging led to an increase in oxidation of protein thiols demonstrated by increased S-glutathionylation of cysteine residues on proteins from Old (24 months old at the start of the study) mouse hearts compared to Young (5-6 months old). This shift in the oxidation state of the proteome was almost completely reversed by 8-weeks of treatment with elamipretide. Many of the significant changes that occurred were in proteins involved in mitochondrial or cardiac function. We also found changes in the mouse heart phosphoproteome that were associated with age, some of which were partially restored with elamipretide treatment. Parallel reaction monitoring of a subset of phosphorylation sites revealed that the unmodified peptide reporting for Myot S231 increased with age, but not its phosphorylated form and that both phosphorylated and unphosphorylated forms of the peptide covering cMyBP-C S307 increased, but that elamipretide treatment did not affect these changes. These results suggest that changes to thiol redox state and phosphorylation status are two ways in which age may affect mouse heart function, which can be restored by treatment with elamipretide.

category: cell biology


title: Differences in personality / temperament in the endangered tortoise Testudo hermanni and their implications on dispersal and conservation

abstract: Behavioural studies are more an more implicated in species conservation. Determining individuals personality in the case of reintroduction operations may be very useful. Actually, indiviuals temperament may be associated to their dispersal capacities and their habilities to adapt to novel environments. Considered as asociable species, few studies have been conducted on reptiles and this is even worse in the case of endangered species. Hermann tortoise, Testudo hermanni, an endemic species from Mediterranean region is endangered because of the lost and modification of its habitats. Before conducting reintroduction actions it is important to have more information on individuals personality traits. We have tested the reaction of three groups of tortoises (domestic, wild and from the SOPTOM center) when confronted to a novel environment and to human presence. The aim was to discriminate individuals with << bold >> and << shy >> behaviours. Behavioural profiles are different between the three groups of tortoises, the domestic group appeared to be bolder than the wild one. Moreover, for the wild group, bold individuals travel longer distances in the field, sometimes outside the protected areas. Thus, it is important to take into account the personality of individuals choosen for translocation projects.

category: ecology


title: Data science competition for cross-site delineation and classification of individual trees from airborne remote sensing data

abstract: Delineating and classifying individual trees in remote sensing data is challenging. Many tree crown delineation methods have difficulty in closed-canopy forests and do not leverage multiple datasets. Methods to classify individual species are often accurate for common species, but perform poorly for less common species and when applied to new sites. We ran a data science competition to help identify effective methods for delineation of individual crowns and classification to determine species identity. This competition included data from multiple sites to assess the methods ability to generalize learning across multiple sites simultaneously, and transfer learning to novel sites where the methods were not trained. Six teams, representing 4 countries and 9 individual participants, submitted predictions. Methods from a previous competition were also applied and used as the baseline to understand whether the methods are changing and improving over time. The best delineation method was based on an instance segmentation pipeline, closely followed by a Faster R-CNN pipeline, both of which outperformed the baseline method. However, the baseline (based on a growing region algorithm) still performed well as did the Faster R-CNN. All delineation methods generalized well and transferred to novel forests effectively. The best species classification method was based on a two-stage fully connected neural network, which significantly outperformed the baseline (a random forest and Gradient boosting ensemble). The classification methods generalized well, with all teams training their models using multiple sites simultaneously, but the predictions from these trained models generally failed to transfer effectively to a novel site. Classification performance was strongly influenced by the number of field-based species IDs available for training the models, with most methods predicting common species well at the training sites. Classification errors (i.e., species misidentification) were most common between similar species in the same genus and different species that occur in the same habitat. The best methods handled class imbalance well and learned unique spectral features even with limited data. Most methods performed better than baseline in detecting new (untrained) species, especially in the site with no training data. Our experience further shows that data science competitions are useful for comparing different methods through the use of a standardized dataset and set of evaluation criteria, which highlights promising approaches and common challenges, and therefore advances the ecological and remote sensing field as a whole.


title: Morphological determinants of bite force capacity in insects: a biomechanical analysis of polymorphous leaf-cutter ants

abstract: The extraordinary success of social insects is partially based on  division of labour, i. e. individuals exclusively or preferentially perform specific tasks. Task-preference may correlate with morphological adaptations so implying task-specialisation, but the extent of such specialisation can be difficult to determine. Here, we demonstrate how the physical foundation of some tasks can be leveraged to quantitatively link morphology and performance. We study the allometry of bite force capacity in Atta vollenweideri leaf-cutter ants, polymorphic insects in which the mechanical processing of plant material is a key aspect of the behavioural portfolio. Through a morphometric analysis of tomographic scans, we show that the bite force capacity of the heaviest colony workers is twice as large as predicted by isometry. This disproportionate  boost is predominantly achieved through increased investment in muscle volume; geometrical parameters such as mechanical advantage, fibre length or pennation angle are likely constrained by the need to maintain a constant mandibular opening range. We analyse this preference for an increase in size-specific muscle volume and the adaptations in internal and external head anatomy required to accommodate it with simple geometric and physical models, so providing a quantitative understanding of the functional anatomy of the musculoskeletal bite apparatus in insects.

category: evolutionary biology


title: Evolutionary dynamics of DIRS-like and Ngaro-like retrotransposons in Xenopus laevis and Xenopus tropicalis genomes

abstract: Anuran genomes have a large number and diversity of transposable elements, but are little explored, mainly in relation to their molecular structure and evolutionary dynamics. Here, we investigated the retrotransposons containing tyrosine recombinase (YR) (order DIRS) in the genome of Xenopus tropicalis and Xenopus laevis. These anurans show 2n = 20 and the 2n = 36 karyotypes, respectively. They diverged about 48 million years ago (mya) and X. laevis had an allotetraploid origin (around 17-18 mya). Our investigation is based on the analysis of the molecular structure and the phylogenetic relationships of 95 DIRS families of Xenopus belonging to DIRS-like and Ngaro-like superfamilies. We were able to identify molecular signatures in the 5 and 3 non-coding terminal regions, preserved open reading frames (ORFs) and conserved domains that are specific to distinguish each superfamily. We recognize two ancient amplification waves of DIRS-like elements that occurred in the ancestor of both species and a higher density of the old/degenerate copies detected in the X. laevis. X. tropicalis showed more recent amplification waves estimated around 16 mya and 3.2 mya and corroborate with high diversity-level of families in this species and with transcriptional activity evidence. Ngaro-like elements presented less diversity and quantity in the genomes, although potentially active copies were also found. Our findings highlight a differential diversity-level and evolutionary dynamics of the YR retrotransposons in the diploid X. tropicalis and X. laevis species expanding our comprehension of the behavior of these elements in both genomes during the diversification process.

category: genetics


title: Comparative cytogenomics reveals genome reshuffling and centromere repositioning in the legume tribe Phaseoleae

abstract: The tribe Phaseoleae (Leguminosae; Papilionoideae) includes several legume crops with assembled genomes. Comparative genomic studies indicate the preservation of large genomic blocks among legumes, however, the chromosome dynamics during Phaseoleae evolution has not been investigated yet. We conducted a comparative genomic analysis to define an informative genomic block (GB) system and to reconstruct the ancestral Phaseoleae karyotype (APK). We defined the GBs based on the orthologous genes between Phaseolus vulgaris and Vigna unguiculata genomes. We searched for these GBs in different genome species belonging to the Phaseolinae (P. lunatus) and Glycininae subtribes (Amphicarpaea edgeworthii and Spatholobus suberectus), and in the Medicago truncaluta outgroup. To support our in silico analysis, we used oligo-FISH probes of P. vulgaris chromosomes 2 and 3 to paint the orthologous chromosomes of two non-sequenced Phaseolinae species (Macroptilium atropurpureum and Lablab purpureus). We inferred the APK with n = 11 and 19 GBs (A to S). We hypothesized five chromosome fusions that reduced the ancestral legume karyotype with n = 16 to n = 11 in APK. Furthermore, we identified the main rearrangements within Phaseolinae and observed an extensive centromere repositioning resulting from evolutionary new centromeres (ENC) in the Phaseolus lineage. Additionally, we demonstrated that the A. edgeworthii genome is more reshuffled than the dysploid S. suberectus genome, in which we could reconstruct the main events that lead the chromosome number reduction. The development of the GB system and the proposed APK provide useful approaches for future comparative genomic analyses of legume species.

category: genomics


title: Lipid tracking at kilohertz sampling rates on live cell membranes through Interferometric Scattering microscopy

abstract: The lateral dynamics of lipids on the cellular membranes are one of the most challenging topics to study in membrane biophysics, needing simultaneously high spatial and temporal resolution. In this study, we have employed Interferometric scattering Microscopy (ISCAT) to explore the dynamics of a biotinylated lipid analogue labelled with streptavidin-coated gold nanoparticles (20 and 40nm in diameter) at 2kHz sampling rate. We developed a statistics-driven analysis pipeline to analyse both ensemble average and single trajectory Mean Squared Displacements from each dataset, and to discern the most likely diffusion mode. We found that the use of larger tags slows down the target motion without affecting the diffusion mode. Moreover, we determined from our statistical analysis that the prevalent diffusion mode of the tracked gold-labelled lipids is compartmentalized diffusion. This model describes the motion of particles diffusing on a corralled surface, with a certain probability of changing compartment. This is compatible with the picket-fence model of membrane structure, already observed by similar studies. Through our analysis, we could determine significant physical parameters, such as average compartment size, dynamic localization uncertainty, and the intra- and inter-compartmental diffusion rates. We then simulated diffusion in an environment compatible with the experimentally-derived parameters and model. The closeness of the results from the analysis of experimental and simulated trajectories validates our analysis and the proposed description of the cell membrane. Finally, we introduce the confinement strength metric to compare diffusivity measurements across techniques and experimental conditions, which we used to successfully compare the present results with other related studies.

category: biophysics


title: The role of fucose-containing glycan motifs across taxonomic kingdoms

abstract: The extraordinary diversity of glycans leads to large differences in the glycomes of different kingdoms of life. Yet, while most monosaccharides are solely found in certain taxonomic groups, there is a small set of monosaccharides with widespread distribution across nearly all domains of life. These general monosaccharides are particularly relevant for glycan motifs, as they can readily be used by commensals and pathogens to mimic host glycans or hijack existing glycan recognition systems. Among these, the monosaccharide fucose is especially interesting, as it frequently presents itself as a terminal monosaccharide, primed for interaction with proteins. Here, we analyze fucose-containing glycan motifs across all taxonomic kingdoms. Using a hereby presented large species-specific glycan dataset and a plethora of methods for glycan-focused bioinformatics and machine learning, we identify characteristic as well as shared fucose-containing glycan motifs for various taxonomic groups, demonstrating clear differences in fucose usage. Even within domains, fucose is used differentially based on an organisms physiology and habitat. We particularly highlight differences in fucose-containing motifs between vertebrates and invertebrates. With the example of pathogenic and non-pathogenic Escherichia coli strains, we also demonstrate the importance of fucose-containing motifs in molecular mimicry and thereby pathogenic potential. Finally, we also confirm and extend the role of fucosyltransferase-coding genes (FUT) in several important biological processes that include development, immunity, and diseases, especially cancer. We envision that this study will shed light on an important class of glycan motifs, with potential new insights into the role of fucosylated glycans in symbiosis, pathogenicity, and immunity.

category: bioinformatics


title: Kv4.3 channel downregulation mediates chronic post-lesional pacemaker acceleration in surviving dopamine substantia nigra neurons

abstract: Substantia nigra dopamine (SN DA) neurons are progressively lost in Parkinson disease (PD). While the molecular and cellular mechanisms of their differential vulnerability and degeneration have been extensively studied, we still know very little about potential functional adaptations of those SN DA neurons that - at least for some time - manage to survive during earlier stages of PD. We utilized a partial lesion 6-OHDA mouse model to characterize initial electrophysiological impairments and chronic adaptations of surviving identified SN DA neurons, both in vivo and in vitro. Early after lesion (3 weeks), we detected a selective loss of in vivo burst firing in surviving SN DA neurons, which was accompanied by in vitro pacemaker instability. In contrast, late after lesion (>2 months), in vivo firing properties of surviving SN DA neurons had recovered in the presence of 2-fold accelerated pacemaking in vitro. Finally, we show that this chronic cell-autonomous adaptation in surviving SN DA neurons was mediated by Kv4.3 channel downregulation. Our study demonstrates substantial homeostatic plasticity of surviving SN DA neurons after a single-hit non-progressive lesion, which might contribute to the phenotype of initially surviving SN DA neurons in PD.


title: Adrenergic Attenuation of Immune Activity is Associated with Anhedonia in Adolescents

abstract: While inflammation has been implicated in depression, little is known of immune-inhibitory agents for individuals with depression. This study sought to assess whether {beta}2-agonist clenbuterol (CBL) would attenuate increased cytokine secretion in adolescents with mood and anxiety symptoms following ex vivo exposure of whole blood to lipopolysaccharide (LPS). Our focus on adolescents aimed to target a critical developmental period when psychiatric conditions often emerge and prior to chronicity effects. Participants (15.25 {+/-} 2.16 years old, 59% female) were 97 psychotropic-medication free adolescents with mood and anxiety symptoms and 33 healthy controls. All had comprehensive evaluations and dimensional assessments of psychiatric symptoms. Fasting whole-blood samples were collected and stimulated with LPS in the presence and absence of CBL for 6 hours and analyzed for 41 cytokines. Comparison analyses used Bonferroni-corrected nonparametric tests. Exploratory factor analysis reduced 41 cytokines into 5 cytokine factors in each experimental condition, and their relationships with psychiatric symptoms were examined. Levels of nine cytokines were significantly reduced by CBL treatment compared to LPS alone. A cytokine factor in the LPS+CBL condition significantly correlated with anticipatory (rho = -0.39, p = 7.4 x 10-5) and consummatory anhedonia (rho = -0.36, p = 3.3 x 10-4), which remained significant when controlling for depression. This study supports the possible inhibitory effect of CBL on immune activation. Using a data-driven method, distinctive relationships between CBL-affected cytokines and dimensional anhedonia were reported, further elucidating the role of {beta}2-agonism in adolescent affective symptomatology.


title: Clenbuterol Attenuates Immune Reaction to Lipopolysaccharide and Its Relationship to Anhedonia in Adolescents


title: Single molecule fingerprinting reveals different amplification properties of α-synuclein oligomers and preformed fibrils in seeding assay.

abstract: The quantification of -synuclein (-syn) aggregates has emerged as a promising biomarker for synucleinopathies. Assays that amplify and detect such aggregates have revealed the presence of seeding-competent species in biosamples of patients diagnosed with Parkinsons disease. However, multiple species such as oligomers and amyloid fibrils, are formed during the aggregation of -synuclein and these species are likely to co-exist in biological samples and thus it remains unclear which species(s) are contributing to the signal detected in seeding assays. To identify which species can be detected in seeding assays, recombinant oligomers and preformed fibrils were produced and purified to characterise their individual biochemical and seeding potential. Here, we used single molecule spectroscopy to track the formation and purification of oligomers and fibrils at the single particle level and compare their respective seeding potential in an amplification assay. Single molecule detection validates that size-exclusion chromatography efficiently separates oligomers from fibrils. Oligomers were found to be seeding-competent but our results reveal that their seeding behaviour is very different compared to preformed fibrils in our amplification assay. Overall, our data suggest that even a low number of preformed fibrils present in biosamples are likely to dominate the response in seeding assays.


title: Comparison of Ferroptosis Related Genes expression in Human Oral Squamous Cell Carcinoma and Normal oral tissues

abstract:
IntroductionEvasion of programmed cell death (PCD) is a hall mark of oncogenesis. There are different types of PCD. Iron related PCD, ferroptosis is being increasingly associated with neoplastic process. There are very few reports that investigate the role of ferroptosis in Oral Squamous Cell Carcinoma (OSCC). An attempt is made to compare the ferroptosis related genes(FRGs) expression in human OSCC and normal oral tissues.

Materials and MethodsGene Expression Omnibus repository was scanned for OSCC mRNA datasets along with normal control tissues. Datasets fulfilling inclusion and exclusion criteria as well as that fulfilled the statistical correlation requirements were considered for this study. Differentially expressed mRNAs were identified. From the literature and ferroptosis database, FRGs were identified and those FRGs were differentially expressed were validated using The Human Cancer Genome dataset.

ResultsIn all 44 FRGs were identified to be differentially expressed between OSCC and control tissues. Of the 44, 21 were that promoted ferroptosis including 18 drivers of ferroptosis. Of the 21 FRGs that drives ferroptosis, 9 were found significantly elevated in controls while the remaining 12 were elevated in OSCC. The role of the differentially expressed FRGs were also studied. Of the 44 FRGs, 36 were validated using the human cancer genome dataset.

Discussion and ConclusionDrivers and suppressors of ferroptosis were differentially expressed in OSCC and controls. This reflects that ferroptosis has a dual role in oncogenesis - both as a promoter and a suppressor. The identified specific FRGs in this studied would help to understand the role of PCD in OSCC progression and help in designing better treatment.

category: cancer biology


title: Improving QSAR Modeling for Predictive Toxicology using Publicly Aggregated Semantic Graph Data and Graph Neural Networks

abstract: Quantitative Structure-Activity Relationship (QSAR) modeling is the most common computational technique for predicting chemical toxicity, but a lack of methodological innovations in QSAR have led to underwhelming performance. We show that contemporary QSAR modeling for predictive toxicology can be substantially improved by incorporating semantic graph data aggregated from open-access public databases, and analyzing those data in the context of graph neural networks (GNNs). Furthermore, we introspect the GNNs to demonstrate how they can lead to more interpretable applications of QSAR, and use ablation analysis to explore the contribution of different data elements to the final models performance.

category: pharmacology and toxicology


title: A new species of the genus Microhyla Tschudi, 1838 (Amphibia: Anura: Microhylidae) from eastern India with notes on Indian species

abstract:
A new species of the genus Microhyla, Microhyla bengalensis sp. nov., described from West Bengal state, India. The new species is distinguished from its congeners by a combination of the following morphological characters: 1) Small in size (SVL= 16.2 mm. in male); 2) truncated snout in dorsal view; 3) head wider than long (HW: HL= 1.36); 4) canthus rostralis and tympanum are indistinct; 5) nostril placed on the dorsal side of the snout; 6) tibiotarsal articulation not reaching the eye; 7) fingers and toes without disc; 8) toe webbing basal; 9) thigh and foot length are equal and smaller than shank; 10) skin tuberculated on dorsum; 11)  teddy bear dark brown mark on dorsum; 12) an inverted  V-shaped dark brown mark above the vent.

A comparative morphological data of all the 14 Indian species of Microhyla is also provided.

category: zoology


title: Development of Functional Connectome Gradients during Childhood and Adolescence

abstract:
Connectome mapping studies have documented a principal primary-to-transmodal gradient in the adult brain network, capturing a functional spectrum which ranges from perception and action to abstract cognition. However, how this gradient pattern develops and whether its development is linked to cognitive growth, topological reorganization, and gene expression profiles remain largely unknown. Using longitudinal resting-state functional magnetic resonance imaging data from 305 children (ages 6-14), we describe substantial changes in the primary-to-transmodal gradient between childhood and adolescence, including emergence as the principal gradient, expansion of global topography, and focal tuning in primary and default-mode regions. These gradient changes are mediated by developmental changes in network integration and segregation, and are associated with abstract processing functions such as working memory and expression levels of calcium ion regulated exocytosis, synaptic transmission, and axon and synapse part related genes. Our findings have implications for understanding connectome maturation principles in normal development and developmental disorders.

TeaserOur study reported the maturation of the core connectome gradient and its association with cognitions and genes expression.


title: IGF-1 Differentially Modulates Glutamate-Induced Toxicity and Stress in Cells of the Neurogliovascular Unit

abstract: The age-related reduction in circulating levels of insulin-like growth factor-1 (IGF-1) is associated with increased risk of stroke and neurodegenerative diseases in advanced age. Numerous reports highlight behavioral and physiological deficits in blood-brain barrier function and neurovascular communication when IGF-1 levels are low. Administration of exogenous IGF-1 reduces the extent of tissue damage and sensorimotor deficits in animal models of ischemic stroke, highlighting the critical role of IGF-1 as a regulator of neurovascular health. The beneficial effects of IGF-1 in the nervous system are often attributed to direct actions on neurons; however, glial cells and the cerebrovasculature are also modulated by IGF-1, and systemic reductions in circulating IGF-1 likely influence the viability and function of the entire neuro-glio-vascular unit. We recently observed that reduced IGF-1 led to impaired glutamate handling in astrocytes. Considering glutamate excitotoxicity is one of the main drivers of neurodegeneration following ischemic stroke, the age-related loss of IGF-1 may also compromise neural function indirectly by altering the function of supporting glia and vasculature. In this study, we assess and compare the effects of IGF-1 signaling on glutamate-induced toxicity and reactive oxygen species (ROS)-produced oxidative stress in primary neuron, astrocyte, and brain microvascular endothelial cell cultures. Our findings verify that neurons are highly susceptible to excitotoxicity, in comparison to astrocytes or endothelial cells, and that a prolonged reduction in IGFR activation increases the extent of toxicity. Moreover, prolonged IGFR inhibition increased the susceptibility of astrocytes to glutamate-induced toxicity and lessened their ability to protect neurons from excitotoxicity. Thus, IGF-1 promotes neuronal survival by acting directly on neurons and indirectly on astrocytes. Despite increased resistance to excitotoxic death, both astrocytes and cerebrovascular endothelial cells exhibit acute increases in glutamate-induced ROS production and mitochondrial dysfunction when IGFR is inhibited at the time of glutamate stimulation. Together these data highlight that each cell type within the neuro-glio-vascular unit differentially responds to stress when IGF-1 signaling was impaired. Therefore, the reductions in circulating IGF-1 observed in advanced age are likely detrimental to the health and function of the entire neuro-glio-vascular unit.


title: Testing the perilesional neuroplastic recruitment hypothesis in aphasia

abstract:
ObjectiveA prominent theory proposes that neuroplastic recruitment of perilesional tissue supports aphasia recovery, especially when language-capable cortex is spared by smaller lesions. This theory has rarely been tested directly, and findings have been inconclusive. Here, we test the perilesional plasticity hypothesis using two fMRI tasks in two groups of stroke survivors.

MethodsTwo cohorts totaling 84 chronic left-hemisphere stroke survivors with prior aphasia diagnosis, and 80 control participants underwent fMRI using either a naming task or a reliable semantic decision task. Individualized perilesional tissue was defined by dilating anatomical lesions, and language regions were defined using meta-analyses. Mixed modeling examined differences in activity between groups. Relationships with lesion size and aphasia severity were examined.

ResultsStroke survivors exhibited reduced activity in perilesional language tissue relative to controls in both tasks. Although a few cortical regions exhibited greater activity irrespective of distance from the lesion, or only when distant from the lesion, no regions exhibited increased activity only when near the lesion. Larger lesions were associated with reduced language activity irrespective of distance from the lesion. Using the reliable fMRI task, reduced language activity related to aphasia severity independent of lesion size.

InterpretationWe find no evidence for neuroplastic recruitment of perilesional tissue in aphasia beyond its typical role in language. Rather, our findings are consistent with alternative hypotheses that left-hemisphere activation changes during recovery relate to normalization of language network dysfunction and possibly recruitment of alternate cortical processors. These findings clarify left-hemisphere neuroplastic mechanisms supporting language recovery after stroke.

Summary for Social Media If AcceptedO_ST_ABSTwitter handleC_ST_ABS@crlgeorgetown

What is the current knowledge on the topic?After left-hemisphere stroke, many individuals experience long-term language impairment (aphasia) while others recover their communication abilities. Although there are several hypotheses concerning the kind of brain neuroplasticity that allows some individuals to recover, these mechanisms are not understood in aphasia.

What question did this study address?This study tested the perilesional plasticity hypothesis as it relates to aphasia recovery. This predominant theory posits that tissue around the stroke lesion boundary becomes recruited to support recovered language function in post-stroke aphasia.

What does this study add to our knowledge?This study clarifies the mechanisms of neuroplasticity in stroke aphasia recovery. The results are not consistent with the conventional perilesional plasticity hypothesis, but rather favor an interpretation that recovery is supported by normalization of language network dysfunction and possibly recruitment of alternate brain regions

How might this potentially impact on the practice of neurology?These conclusions will give practicing neurologists a better understanding of how the brain recovers from aphasia after stroke.


title: Enterococcus spp. have higher fitness for survival, in a pH-dependent manner, in pancreatic juice among duodenal bacterial flora

abstract:
ObjectivesBacterial infection is involved in the progression of many gastrointestinal diseases, including cancer; however, how and which bacteria colonize in pancreatic juice and tissue have yet to be elucidated. Recently, we reported that Enterococcus faecalis exists in the pancreatic juice and tissues of patients with chronic pancreatic disease. Here, we investigated the survival of E. faecalis in duodenal juice with different pH conditions.

MethodsPancreatic juice samples from 62 patients with cancers of the duodeno-pancreato-biliary region were evaluated for the presence of E. faecalis. 16S ribosomal RNA PCR and 16S-based metagenome analyses were performed to determine the bacterial composition. The survival of E. faecalis in various pancreatic juice conditions was evaluated.

ResultsOf 62 samples, 27% (17/62) were positive for Enterococcus spp., among which 71% (12/17) contained E. faecalis. Enterococcus spp. showed the highest fitness for survival in alkaline pancreatic juice among various bacterial species. The microbiome of pancreatic juice from patients with pancreatic and bile duct cancer showed diversity, but Enterococcus spp. were enriched among duodenal tumors and intraductal papillary mucinous neoplasms.

ConclusionsAlkalinity is important for the selective survival of E. faecalis among microbiota. E. faecalis may induce pancreatic inflammation with changes in pancreatic juice conditions.


title: Mesoderm-Derived PDGFRA+ Cells Regulate the Emergence of Hematopoietic Stem Cells in the Dorsal Aorta

abstract: Mouse hematopoietic stem cells (HSCs) first emerge at embryonic day 10.5 (E10.5) on the ventral surface of the dorsal aorta, by endothelial-to-hematopoietic transition (EHT). We investigated whether cells with mesenchymal stem cell-like activity, which provide an essential niche for long-term HSCs (LT-HSCs) in the bone marrow, reside in the aorta- gonad-mesonephros (AGM) and contribute to the structural development of the dorsal aorta and EHT. Using transgenic mice, we demonstrate a lineage hierarchy for AGM stromal cells and traced the E10.5/E11.5 aortic endothelium and HSCs to mesoderm derived (Mesp1) PDGFRA+ stromal cells (Mesp1der PSCs). Mesp1der PSCs dominate the sub-endothelial and ventral stroma in the E10.5-E11.5 AGM but by E13.5 were replaced by neural crest (Wnt1) derived PDGFRA+ stromal cells (Wnt1der PSCs). Co-aggregating non-hemogenic embryonic and adult endothelial cells with Mesp1der PSCs but not with Wnt1der PSCs resulted in activation of a hematopoietic transcriptional program in endothelial cells accompanied by EHT and generation of LT-HSCs. Dose-dependent inhibition of PDGFRA signalling or BMP, WNT, NOTCH signalling interrupted this reprogramming event. This partnership between endothelial cells and AGM Mesp1der PSCs could potentially be harnessed to manufacture LT-HSCs from endothelium.

category: developmental biology


title: Diauxic lags explain unexpected coexistence in multi-resource environments

abstract: How the coexistence of species is affected by the presence of multiple resources is a major question in microbial ecology. We experimentally demonstrate that differences in diauxic lags, which occur as species deplete their own environments and adapt their metabolisms, allow slow-growing microbes to stably coexist with faster-growing species in multi-resource environments despite being excluded in single-resource environments. In our focal example, an Acinetobacter species (Aci2) competitively excludes Pseudomonas aurantiaca (Pa) on alanine and on glutamate. However, they coexist on the combination of both resources. Experiments reveal that Aci2 grows faster but Pa has shorter diauxic lags. We establish a tradeoff between Aci2s fast growth and Pas short lags as their mechanism for coexistence. We model this tradeoff to accurately predict how environmental changes affect community composition. We extend our work by surveying a large set of competitions and observe coexistence nearly three times as frequently when the slow-grower is the fast-switcher. Our work illustrates a potentially common mechanism for the emergence of multi-resource coexistence despite single-resource competitive exclusions.


title: Glue genes are subjected to diverse selective forces during Drosophila development

abstract:
Molecular evolutionary studies usually focus on genes with clear roles in adult fitness or on developmental genes expressed at multiple time points during the life of the organism. Here, we examine the evolutionary dynamics of Drosophila glue genes, a set of eight genes tasked with a singular primary function during a specific developmental stage: the production of glue that allows animal pupa to attach to a substrate for several days during metamorphosis. Using phenotypic assays and available data from transcriptomics, PacBio genomes, and genetic variation from global populations, we explore the selective forces acting on the glue genes within the cosmopolitan D. melanogaster species and its five closely related species, D. simulans, D. sechellia, D. mauritiana, D. yakuba, and D. teissieri. We observe a three-fold difference in glue adhesion between the least and the most adhesive D. melanogaster strain, indicating a strong genetic component to phenotypic variation. These eight glue genes are among the most highly expressed genes in salivary glands yet they display no notable codon bias. New copies of Sgs3 and Sgs7 are found in D. yakuba and D. teissieri with the Sgs3 coding sequence evolving rapidly after duplication in the D. yakuba branch. Multiple sites along the various glue genes appear to be constrained. Our population genetics analysis in D. melanogaster suggests signs of local adaptive evolution for Sgs3, Sgs5 and Sgs5bis and traces of selective sweeps for Sgs1, Sgs3, Sgs7 and Sgs8. Our work shows that stage-specific genes can be subjected to various dynamic evolutionary forces. (249 words)

Significance statementDrosophila larvae produce a glue to stick themselves to a substrate for several days during metamorphosis. Here we observe wide variation in stickiness among Drosophila melanogaster strains and we analyze the molecular evolution of eight glue genes. We find several recent gene duplications and heterogenous rates of evolution among these genes.


title: Patient Informed Domain Adaptation Improves Clinical Drug Response Prediction

abstract: In-silico modeling of patient clinical drug response (CDR) promises to revolutionize personalized cancer treatment. State-of-the-art CDR predictions are usually based on cancer cell line drug perturbation profiles. However, prediction performance is limited due to the inherent differences between cancer cell lines and primary tumors. In addition, current computational models generally do not leverage both chemical information of a drug and a gene expression profile of a patient during training, which could boost prediction performance. Here we develop a Patient Adapted with Chemical Embedding (PACE) dual convergence deep learning framework that a) integrates gene expression along with drug chemical structures, and b) is adapted in an unsupervised fashion by primary tumor gene expression. We show that PACE achieves better discrimination between sensitive and resistant patients compared to the state-of-the-art linear regularized method (9/12 VS 3/12 drugs with available clinical outcomes) and alternative methods.


title: Prediction of therapy outcomes of CLL using gene expression intensity, clustering, and ANN classification of single cell transcriptomes

abstract:
BackgroundSingle cell transcriptomics is a new technology that enables us to measure the expression levels of genes from an individual cell. The expression information reflects the activity of that individual cell which could be used to indicate the cell types. Chronic lymphocytic leukemia (CLL) is a malignancy of B cells, one of the peripheral blood mononuclear cells subtypes. We applied five analytical tools for the study of single cell gene expression in CLL course of therapy. These tools included the analysis of gene expression distributions - median, interquartile ranges, and percentage above quality control (QC) threshold; hierarchical clustering applied to all cells within individual single cell data sets; and artificial neural network (ANN) for classification of healthy peripheral blood mononuclear cell (PBMC) subtypes. These tools were applied to the analysis of CLL data representing states before and during the therapy.

ResultsWe identified patterns in gene expression that distinguished two patients that had complete remission (complete response), a patient that had a relapse, and a patient that had partial remission within three years of Ibrutinib therapy. Patients with complete remission showed a rapid decline of median gene expression counts, and the total number of gene counts below the QC threshold for healthy cells (670 counts) in 80% of more of the cells. These patients also showed the emergence of healthy-like PBMC cluster maps within 120 days of therapy and distinct changes in predicted proportions of PBMC cell types.

ConclusionsThe combination of basic statistical analysis, hierarchical clustering, and supervised machine learning identified patterns from gene expression that distinguish four CLL patients treated with Ibrutinib that experienced complete remission, partial remission, or relapse. These preliminary results suggest that new bioinformatics tools for single cell transcriptomics, including ANN comparison to healthy PBMC, offer promise in prognostics of CLL.


title: A DNA-structured mathematical model of cell-cycle progression in cyclic hypoxia

abstract: New experimental data have shown how the periodic exposure of cells to low oxygen levels (i.e., cyclic hypoxia) impacts their progress through the cell-cycle. Cyclic hypoxia has been detected in tumours and linked to poor prognosis and treatment failure. While fluctuating oxygen environments can be reproduced in vitro, the range of oxygen cycles that can be tested is limited. By contrast, mathematical models can be used to predict the response to a wide range of cyclic dynamics. Accordingly, in this paper we develop a mechanistic model of the cell-cycle that can be combined with in vitro experiments, to better understand the link between cyclic hypoxia and cell-cycle dysregulation. A distinguishing feature of our model is the inclusion of impaired DNA synthesis and cell-cycle arrest due to periodic exposure to severely low oxygen levels. Our model decomposes the cell population into four compartments and a time-dependent delay accounts for the variability in the duration of the S phase which increases in severe hypoxia due to reduced rates of DNA synthesis. We calibrate our model against experimental data and show that it recapitulates the observed cell-cycle dynamics. We use the calibrated model to investigate the response of cells to oxygen cycles not yet tested experimentally. When the re-oxygenation phase is sufficiently long, our model predicts that cyclic hypoxia simply slows cell proliferation since cells spend more time in the S phase. On the contrary, cycles with short periods of re-oxygenation are predicted to lead to inhibition of proliferation, with cells arresting from the cell-cycle when they exit the S phase. While model predictions on short time scales (about a day) are fairly accurate (i.e, confidence intervals are small), the predictions become more uncertain over longer periods. Hence, we use our model to inform experimental design that can lead to improved model parameter estimates and validate model predictions.


title: Sex-specific tuning of modular muscle activation patterns for locomotion in young and older adults

abstract: There is increasing evidence that including sex as a biological variable is of crucial importance to promote rigorous, repeatable and reproducible science. In spite of this, the body of literature that accounts for the sex of participants in human locomotion studies is small and often produces controversial results. Here, we investigated the modular organization of muscle activation patterns for human locomotion using the concept of muscle synergies with a double purpose: i) uncover possible sex-specific characteristics of motor control and ii) assess whether these are maintained in older age. We recorded electromyographic activities from 13 ipsilateral muscles of the lower limb in young and older adults of both sexes walking (young and old) and running (young) on a treadmill. The data set obtained from the 215 participants was elaborated through non-negative matrix factorization to extract the time-independent (i.e., motor modules) and time-dependent (i.e., motor primitives) coefficients of muscle synergies. We found sparse sex-specific modulations of motor control. Motor modules showed a different contribution of hip extensors, knee extensors and foot dorsiflexors in various synergies. Motor primitives were wider (i.e., lasted longer) in males in the propulsion synergy for walking (but only in young and not in older adults) and in the weight acceptance synergy for running. Moreover, the complexity of motor primitives was similar in younger adults of both sexes, but lower in older females as compared to older males. In essence, our results revealed the existence of small but defined sex-specific differences in the way humans control locomotion and that these strategies are not entirely maintained in older age.


title: Adulthood Deficiency of the Insulin-like Growth Factor-1 Receptor in Hippocampal Neurons Impairs Cell Structure and Spatial Learning and Memory in Male and Not Female Mice

abstract: Reductions in insulin-like growth factor-1 (IGF-1) are associated with cognitive impairment and increased risk of neurodegenerative disease in advanced age. In mouse models, reduced IGF-1 early-in-life leads to memory impairments and synaptic dysfunction; however, these models are limited by systemic reductions in IGF-1. We hypothesized that IGF-1 continues to promote hippocampal neuron structure and function after development, and as such, the loss of IGF-1 signaling in adult neurons would lead to impaired spatial learning and memory. To test this, the IGF-1 receptor (IGF-1R) was genetically targeted in hippocampal neurons of adult male and female mice. Male mice deficient in neuronal IGF-1R exhibited spatial learning impairments as evidenced by increased pathlength and errors in the radial arm water maze. No differences in learning and memory were observed in female mice. Golgi-Cox staining revealed a reduced number of dendritic boutons of neurons the CA1 region of the hippocampus in male mice. Decreased MAPK and increased ROCK activity were also observed in these tissues. In vitro studies revealed that impaired neurite outgrowth due to inhibited IGF-1R signaling could be rescued by pharmacological inhibitors of ROCK. However, ROCK inhibition in neuronal IGF-1R-deficient mice did not fully rescue learning impairments or bouton numbers. Together, our study highlights that IGF-1 continues to support spatial learning and memory and neuronal structure in adulthood.


title: Arabidopsis spliceosome factor SmD3 modulates immunity to Pseudomonas syringae infection

abstract: SmD3 is a core component of the small nuclear ribonucleoprotein (snRNP) that is essential for pre-mRNA splicing. The role of Arabidopsis SmD3 in plant immunity was assessed by testing sensitivity of smd3a and smd3b mutants to Pseudomonas syringae pv. tomato (Pst) DC3000 infection and its pathogenesis effectors flagellin (flg22), EF-Tu (elf18) and coronatine (COR). Both smd3 mutants exhibited enhanced susceptibility to Pst accompanied by marked changes in the expression of key pathogenesis markers. mRNA levels of these factors were also altered upon treatment with Pseudomonas effectors. We showed that SmD3-b dysfunction impairs mainly stomatal immunity as a result of defects in stomatal development. Our genome-wide transcriptome analysis of the smd3b-1 mutant infected with Pst revealed that lack of SmD3-b deregulates defense against Pst infection at the transcriptional and posttranscriptional levels including defects in splicing and an altered pattern of alternative splicing. Other changes in the smd3b-1 mutant involved enhanced elf18- and flg22-induced callose deposition, reduction of flg22-triggered production of early ROS and boost of secondary ROS caused by Pst infection. Together, our data indicate that SmD3 contributes to the plant immune response possibly via regulation of mRNA splicing of key pathogenesis factors.

category: molecular biology


title: The role of viscoelasticity in long-time cell rearrangement

abstract: Although collective cell migration (CCM) is a highly coordinated and ordered migratory mode, perturbations in the form of mechanical waves appear even in 2D. These perturbations caused by the viscoelastic nature of cell rearrangement are involved in various biological processes, such as embryogenesis, wound healing and cancer invasion. The mechanical waves, as a product of the active turbulence occurred at low Reynolds number, represent an oscillatory change in cell velocity and the relevant rheological parameters. The velocity oscillations, in the form of forward and backward flows, are driven by: viscoelastic force, surface tension force, and traction force. The viscoelastic force represents a consequence of inhomogeneous distribution of cell residual stress accumulated during CCM. This cause-consequence relation is considered on a model system such as the cell monolayer free expansion. The collision of forward and backward flows causes an increase in cell packing density which has a feedback impact on the tissue viscoelasticity and on that base influences the tissue stiffness. The evidence of how the tissue stiffness is changed near the cell jamming is conflicting. To fill this gap, we discussed the density driven change in the tissue viscoelasticity by accounting for the cell pseudo-phase transition from active (contractile) to passive (non-contractile) state appeared near cell jamming in the rheological modeling consideration.


title: Molecular basis for redox control by the human cystine/glutamate antiporter System xc-.

abstract: Cysteine plays an essential role in cellular redox homeostasis as a key constituent of the tripeptide glutathione (GSH). A rate limiting step in cellular GSH synthesis is the availability of cysteine. However, circulating cysteine exists in the blood as the oxidised di-peptide cystine, requiring specialised transport systems for its import into the cell. System xc- is a dedicated cystine transporter, importing cystine in exchange for intracellular glutamate. To counteract elevated levels of reactive oxygen species in cancerous cells system xc- is frequently upregulated, making it an attractive target for anticancer therapies. However, the molecular basis for ligand recognition remains elusive, hampering efforts to specifically target this transport system. Here we present the cryo-EM structure of system xc- in both the apo and glutamate bound states. Structural comparisons reveal an allosteric mechanism for ligand discrimination, supported by molecular dynamics and cell-based assays, establishing a mechanism for cystine transport in human cells.

category: biochemistry


title: 3D single molecule localization microscopy reveals the topography of the immunological synapse at isotropic precision below 15 nm

abstract: T-cells engage with antigen-presenting cells in search for antigenic peptides and form transient interfaces termed immunological synapses. A variety of protein-protein interactions in trans-configuration defines the topography of the synapse and orchestrates the antigen-recognition process. In turn, the synapse topography affects receptor binding rates and the mutual segregation of proteins due to size exclusion effects. For better understanding it is hence critical to map the 3D topography of the immunological synapse at high precision. Current methods, however, provide only rather coarse images of the protein distribution within the synapse, which do not reach the dimension of the protein ectodomains. Here, we applied supercritical angle fluorescence microscopy combined with defocused imaging, which allows 3-dimensional single molecule localization microscopy (3D-SMLM) at an isotropic localization precision below 15 nm. Experiments were performed on hybrid synapses between primary T-cells and functionalized glass-supported lipid bilayers. We used 3D-SMLM to quantify the cleft size within the synapse by mapping the position of the T-cell receptor (TCR) with respect to the supported lipid bilayer, yielding average distances of 18 nm up to 31 nm for activating and non-activating bilayers, respectively.


title: A photo-switchable assay system for dendrite degeneration and repair in Drosophila melanogaster

abstract: Neurodegeneration arising from aging, injury or disease has devastating health consequences. Whereas neuronal survival and axon degeneration have been studied extensively, much less is known about how neurodegeneration impacts dendrites. To develop an assay for dendrite degeneration and repair in the Drosophila peripheral nervous system, we used photo-switchable caspase-3 (caspase-LOV) to induce neuronal damage with tunable severity by adjusting illumination duration, thereby revealing cell type-specific responses to caspase-3 induced dendrite degeneration in dendrite arborization (da) neurons. To ask whether mechanisms underlying axon degeneration also govern dendrite degeneration, we tested the involvement of the Wallerian degeneration pathway by examining the effects of expressing the mouse Wallerian degeneration slow (WldS) protein and knockdown of the Drosophila sterile alpha/Armadillo/Toll-Interleukin receptor homology domain protein (dSarm1) and Axundead (Axed) in class 4 da neurons. Here we report WldS expression or knockdown of dSarm1 improved dendrite repair following caspase- 3 induced dendrite degeneration. Whereas both dSarm1 and Axed were required for thermal nocifensive behavior in uninjured animals, WldS expression improved the recovery of thermal nocifensive behavior that was impaired by chronic low-level of caspase-LOV activity. By establishing ways to induce graded dendrite degeneration, we uncover a protective role of WldS in caspase-3 induced dendrite degeneration and repair.


title: ACE2 is the critical in vivo receptor for SARS-CoV-2 in a novel COVID-19 mouse model with TNF- and IFNγ-driven immunopathology

abstract:
Despite tremendous progress in the understanding of COVID-19, mechanistic insight into immunological, disease-driving factors remains limited. We generated maVie16, a mouse-adapted SARS-CoV-2, by serial passaging of a human isolate. In silico modelling revealed how Spike mutations of maVie16 enhanced interaction with murine ACE2. MaVie16 induced profound pathology in BALB/c and C57BL/6 mice and the resulting mouse COVID-19 (mCOVID-19) replicated critical aspects of human disease, including early lymphopenia, pulmonary immune cell infiltration, pneumonia and specific adaptive immunity. Inhibition of the proinflammatory cytokines IFN{gamma} and TNF substantially reduced immunopathology. Importantly, genetic ACE2-deficiency completely prevented mCOVID-19 development. Finally, inhalation therapy with recombinant ACE2 fully protected mice from mCOVID-19, revealing a novel and efficient treatment. Thus, we here present maVie16 as a new tool to model COVID-19 for the discovery of new therapies and show that disease severity is determined by cytokine-driven immunopathology and critically dependent on ACE2 in vivo.

Key pointsO_LIThe mouse-adapted SARS-CoV-2 strain maVie16 causes fatal disease in BALB/c mice and substantial inflammation, pneumonia and immunity in C57BL/6 mice
C_LIO_LITNF/IFN{gamma} blockade ameliorates maVie16-induced immunopathology
C_LIO_LIMaVie16 infection depends on ACE2 and soluble ACE2 inhalation can prevent disease
C_LI


title: SIGNR1 promotes immune dysfunction in systemic candidiasis by modulating neutrophil lifespan via T cell-derived histones and G-CSF

abstract: The mechanisms regulating immune dysfunction during sepsis are poorly understood. Here, we show that neutrophil-derived myeloperoxidase delays the onset of immune dysfunction during systemic candidiasis by controlling microbes captured by splenic marginal zone (MZ) macrophages. In contrast, SIGNR1-mediated microbe capture accelerates MZ colonization and immune dysfunction by triggering T cell death, T cell-dependent chromatin release and the synergistic induction of G-CSF by histones and fungi. Histones and G-CSF promote the prevalence of immature Ly6Glow neutrophils with defective oxidative burst, by selectively shortening the lifespan of mature Ly6Ghigh neutrophils. Consistently, T cell deficiency, or blocking SIGNR1, G-CSF or histones delayed neutrophil dysfunction. Furthermore, histones and G-CSF in the plasma of sepsis patients, shortened neutrophil lifespan and correlated with neutrophil mortality markers associated with a poor prognosis. Hence, the compromise of internal antimicrobial barrier sites drives neutrophil dysfunction by selectively modulating neutrophil lifespan via pathogenic T cell death, extracellular histones, and G-CSF.


title: Fully Human Antibody Immunoglobulin from Transchromosomic Bovines is Potent Against SARS-CoV-2 Variant Pseudoviruses

abstract: SAB-185 is a fully human polyclonal anti-SARS-CoV-2 immunoglobulin produced from the plasma of transchromosomic bovines that are hyperimmunized with recombinant SARS-CoV-2 Wuhan-Hu-1 Spike protein. SAB-185 is being evaluated for efficacy in aphase 3 clinical trial. The World Health Organization (WHO) has identified multiple Variants-of-Concern and Variants-of-Interest (VOC/VOI) that have mutations in their Spike protein that appear to increase transmissibility and/or reduce the effectiveness of therapeutics and vaccines, among other parameters of concern. SAB-185 was evaluated using lentiviral-based pseudovirus assays performed in a BSL2 environment that incorporates stable or transient cell lines that express human angiotensin converting enzyme 2 (ACE2) and transmembrane serine protease 2 (TMPRSS2). The results indicate that SAB-185 retained neutralization potency against multiple SARS-CoV-2 pseudovirus variants, including the Delta, Kappa, Lambda and Omicron variants, that have or are supplanting other VOC/VOI in many countries and regions around the world.


title: Intrinsically disordered pathogen effector alters the STAT1 dimer to prevent recruitment of co-transcriptional activators CBP/p300

abstract: Signal transducer and activator of transcription (STATs) proteins signal from cell-surface receptors to drive transcription of immune response genes. The parasite Toxoplasma gondii blocks STAT1-mediated gene expression by secreting the intrinsically disordered protein TgIST that traffics to the host nucleus, binds phosphorylated STAT1 dimers, and occupies nascent transcription sites that unexpectantly remain silenced. Here we define a core repeat region within internal repeats of TgIST that is necessary and sufficient to block STAT1-mediated gene expression. Cellular, biochemical, mutational, and structural studies demonstrate that the repeat region of TgIST adopts a helical conformation upon binding to STAT1 dimers. The binding interface is defined by a groove formed from two loops in the STAT1 SH2 domains that reorient during dimerization. TgIST binding to this newly exposed site at the STAT1 dimer interface altered its conformation and prevented recruitment of co-transcriptional activators, thus defining the mechanism of blocked transcription.


title: Broad neutralizing nanobody against SARS-CoV-2 engineered from pre-designed synthetic library

abstract: SARS-CoV-2 infection is initiated with Spike glycoprotein binding to the receptor of human angiotensin converting enzyme 2 via its receptor binding domain. Blocking this interaction is considered as an effective approach to inhibit virus infection. Here we report the discovery of a neutralizing nanobody, VHH60, directly produced from a humanized synthetic nanobody library. VHH60 competes with human ACE2 to bind the receptor binding domain of the Spike protein with a KD of 2.56 nM, inhibits infections of both live SARS-CoV-2 and pseudotyped viruses harboring wildtype, escape mutations and prevailing variants at nanomolar level. VHH60 also suppresses SARS-CoV-2 infection and propagation 50-fold better and protects mice from death two times longer than that of control group after live virus inoculation on mice. VHH60 therefore is a powerful synthetic nanobody with a promising profile for disease control against COVID19.


title: Towards improved resistance of Corynebacterium glutamicum against nisin

abstract: The bacteriocin nisin is one of the best studied antimicrobial peptides. It is widely used as a food preservative due to its antimicrobial activity against various Gram-positive bacteria including human pathogens such as Listeria monocytogenes and others. The receptor of nisin is the universal cell wall precursor lipid II, which is present in all bacteria. Thus, nisin has a broad spectrum of target organisms. Consequently, heterologous production of nisin with biotechnological relevant organisms including Corynebacterium glutamicum is difficult. Nevertheless, bacteria have evolved several mechanisms of resistance against nisin and other cationic antimicrobial peptides (CAMPs). Here, we transferred resistance mechanisms described in other organisms to C. glutamicum with the aim to improve nisin resistance. The presented approaches included: expression of (i) nisin immunity genes nisI and/or nisFEG or (ii) nisin ABC-transporter genes of Staphylococcus aureus and its homologues of C. glutamicum, (iii) genes coding for enzymes for alanylation or lysinylation of the cell envelope to introduce positive charges, and/or (iv) deletion of genes for porins of the outer membrane. None of the attempts alone increased resistance of C. glutamicum more than two-fold. To increase resistance of C. glutamicum to levels that will allow heterologous production of active nisin at relevant titers, further studies are needed.


title: Interactions of the Trypanosoma brucei brucei zinc-finger-domain protein ZC3H28

abstract: In Trypanosoma brucei and related Kinetoplastids, regulation of gene expression occurs mostly post-transcriptionally, and RNA-binding proteins play a critical role in the regulation of mRNA and protein abundance. Trypanosoma brucei ZC3H28 is a 114 KDa cytoplasmic mRNA-binding protein with a single C(x)7C(x)5C(x)sH zinc finger at the C-terminus and numerous proline-, histine- or glutamine-rich regions. We here show that N-terminally tagged ZC3H28 copurifies ribosomes, various RNA-binding proteins, and the translation initiation complex EIF4E4/EIF4G3. ZC3H28 is preferentially associated with long RNAs that have low complexity sequences in their 3-untranslated regions. When tethered to a reporter mRNA, ZC3H28 increased the mRNA level without a corresponding increase in protein expression; this suggests that it stabilized the reporter but at the same time suppressed its translation. Indeed, there was a clear negative correlation between ZC3H28 mRNA binding and ribosome density. After ZC3H28 depletion, the relative levels of ribosomal protein mRNAs increased while levels of some long mRNAs decreased, but there is no overall correlation between binding and RNAi effects on mRNA abundance. We speculate that ZC3H28 might be implicated in stabilizing poorly-translated mRNAs.


title: NAD kinase controls antibiotic susceptibility and pathogenic potential in Staphylococcus aureus

abstract: Nicotinamide adenine dinucleotide phosphate (NADPH) is the primary electron donor for reductive reactions that are essential for the biosynthesis of major cell components in all organisms. Nicotinamide adenine dinucleotide kinase (NADK) is the only enzyme that catalyzes synthesis of NADP(H) from NAD(H). While the enzymatic properties and physiological functions of NADK have been thoroughly studied, the role of NADK in bacterial pathogenesis remains unknown. Here, we used CRISPR interference to knockdown NADK gene expression to address the role of this enzyme in Staphylococcus aureus pathogenic potential. We find that NADK inhibition drastically decreases mortality of zebrafish infected with S. aureus. Further, we show that NADK promotes S. aureus survival in infected macrophages by protecting bacteria from antimicrobial defense mechanisms. Proteome-wide data analysis revealed that production of major virulence associated factors is sustained by NADK. We demonstrate that NADK is required for expression of the quorum-sensing response regulator AgrA, which controls critical S. aureus virulence determinants. These findings support a key role for NADK in bacteria survival within innate immune cells and the host during infection.


title: NAD kinase promotes Staphylococcus aureus pathogenesis by supporting production of virulence factors and protective enzymes


title: Acetylation regulates the oligomerization state and activity of RNase J, the major ribonuclease of Helicobacter pylori

abstract: In Helicobacter pylori, post-transcriptional regulation strongly relies on the activity of an RNA degradosome, composed of the essential ribonuclease RNase J and the DEAD-box RNA helicase RhpA. Here, we describe post-translational modifications of this protein complex that affect its activity. Cell-extracted RNase J is acetylated on multiple residues, one of which, K649, strongly impacts RNase J oligomerization, which in turn influences ribonuclease activity. Corroborating the link between oligomerization and activity, mutations targeting K649 and other residues affect the dimerization and in vitro activity of RNase J. Our crystal structure of RNase J reveals three loops that gate access to the active site and rationalizes how oligomerization state influences activity. The acetylated residues of RNase J are important for H. pylori morphology, highlighting that the modifications affect the RNase J cellular function. We propose acetylation as a regulatory level controlling the activity of RNase J and the H. pylori RNA degradosome.


title: The obesity-linked human lncRNA AATBC regulates adipocyte plasticity by stimulating mitochondrial dynamics and respiration

abstract: Adipocytes are critical regulators of metabolism and energy balance. While white adipocyte dysfunction is a hallmark of obesity-associated disorders, the activation of thermogenic brown and beige adipocytes is linked to improved cardiometabolic health. As adipocytes dynamically adapt to environmental cues by functionally switching between white and thermogenic phenotypes, a molecular understanding of this adipocyte plasticity could help improving energy balance and weight loss. Here, we show that the long non-coding RNA (lncRNA) Apoptosis associated transcript in bladder cancer (AATBC) is a human-specific regulator of adipocyte plasticity. Searching for new human lncRNAs implicated in adipocyte biology we compared transcriptional profiles of human adipose tissues and cultured adipocytes and discovered that AATBC was enriched in thermogenic conditions. Using primary human adipocytes and immortalized human adipocytes we found that gain-of-function of AATBC enhanced the thermogenic phenotype whereas loss-of-function diminished this effect. The AATBC-mediated increase in mitochondrial respiration was linked to a more fragmented mitochondrial network and vice versa. While we found that AATBC is predominantly located in the nucleus, its effect on global transcription was only marginal. As AATBC is specific to humans, we expressed AATBC in adipose tissue of mice to study its systemic impact, which led to lower plasma leptin levels. Interestingly, this association was also present in human subjects, as AATBC in adipose tissue was inversely correlated with plasma leptin levels, body mass index and other measures of metabolic health. In conclusion, AATBC is a novel obesity-linked regulator of adipocyte plasticity and mitochondrial function in humans.


title: Surveying the global landscape of post-transcriptional regulators

abstract: Numerous proteins regulate gene expression by modulating mRNA translation and decay. In order to uncover the full scope of these post-transcriptional regulators, we conducted an unbiased survey that quantifies regulatory activity across the budding yeast proteome and delineates the protein domains responsible for these effects. Our approach couples a tethered function assay with quantitative single-cell fluorescence measurements to analyze [~]50,000 protein fragments and determine their effects on a tethered mRNA. We characterize hundreds of strong regulators, which are enriched for canonical and unconventional mRNA-binding proteins. Regulatory activity typically maps outside the RNA-binding domains themselves, highlighting a modular architecture that separates mRNA targeting from post-transcriptional regulation. Activity often aligns with intrinsically disordered regions that can interact with other proteins, even in core mRNA translation and degradation factors. Our results thus reveal networks of interacting proteins that control mRNA fate and illuminate the molecular basis for post-transcriptional gene regulation.


title: Individual cells traffic the Vasopressin 2 Receptor to their cell surface with different success

abstract:
G protein coupled receptors (GPCRs) translate the actions of hormones into intracellular signalling events. Mutations in GPCRs can prevent their correct expression and trafficking to the cell surface and cause disease. We use single cell measurements in HEK293 cells to show that the balance between endoplasmic reticulum (ER) and cell surface localisation of the Vasopressin 2 receptor (V2R) varies significantly from cell to cell. We find that mutations in the V2R affect the proportion of cells able to send this GPCR to the cell surface but do not prevent all cells in the population from correctly trafficking the mutant receptors. These findings reveal that the ability of cells to correctly traffic V2R to the cell surface depends not only on the expressed V2R mutant but also on the individual cell environment.

Significance statementMissense mutations in the Vasopressin 2 Receptor (V2R) cause Nephrogenic Diabetes Insipidus. Some of these mutations prevent correct expression and trafficking of V2R to the cell surface resulting in a loss-of-function. We show -using single cell measurements-that the balance between endoplasmic reticulum and cell surface localisation of the V2R varies significantly from cell to cell, independent from its expression level. Mutations affect the proportion of cells able to send V2R to the cell surface but do not prevent all cells in the population from correctly trafficking the mutant receptors. Hence, the ability of cells to correctly traffic V2R to the cell surface depends not only on expressed V2R mutant but also on the cell environment.


title: Cell-to-cell variations in subcellular localisation of V2R are independent of its expression level


title: NFIC regulates ribosomal biology and ER stress in pancreatic acinar cells and suppresses PDAC initiation

abstract: Tissue-specific differentiation is driven by specialized transcriptional networks. Pancreatic acinar cells crucially rely on the PTF1 complex, and on additional transcription factors, to deploy their transcriptional program. Here, we identify NFIC as a novel regulator of acinar differentiation using a variety of methodological strategies. NFIC binding sites are found at very short distances from NR5A2-bound genomic regions and both proteins co-occur in the same complex. Nfic knockout mice show reduced expression of acinar genes and, in ChIP-seq experiments, NFIC binds the promoters of acinar genes. In addition, NFIC binds to the promoter of, and regulates, genes involved in RNA and protein metabolism; in Nfic knockout mice, p-RS6K1 and p-IEF4E are down-regulated indicating reduced activity of the mTOR pathway. In 266-6 acinar cells, NFIC dampens the ER stress program through its binding to ER stress gene promoters and is required for complete resolution of Tunicamycin-mediated ER stress. Normal human pancreata from subjects with low NFIC mRNA levels display reduced epxression of genes down-regulated in Nfic knockout mice. Consistently, NFIC displays reduced expression upon induced acute pancreatitis and is required for proper recovery after damage. Finally, expression of NFIC is lower in samples of mouse and human pancreatic ductal adenocarcinoma and Nfic knockout mice develop an increased number of mutant Kras-driven pre-neoplastic lesions.


title: Synergistic Phase Separation of Two Pathways Promotes Integrin Clustering and Integrin Adhesion Complex Formation

abstract: Integrin adhesion complexes (IACs) are integrin-based plasma membrane-associated compartments where cells sense environmental cues. The physical mechanisms and molecular interactions that mediate nascent IAC formation are unclear. We found that both p130Cas ("Cas") and Focal adhesion kinase ("FAK") undergo liquid-liquid phase separation in vitro under physiologic conditions. Cas- and FAK- driven phase separation is sufficient to reconstitute kindlin-dependent integrin clustering in vitro. In vitro condensates and cellular IACs exhibit similar sensitivities to environmental perturbations including changes in temperature and pH. Furthermore, mutations that inhibit or enhance phase separation in vitro reduce or increase the number of IACs in cells, respectively. Finally, we find that the Cas and FAK pathways act synergistically to promote phase separation, integrin clustering and IAC formation in vitro and in cells. We propose that Cas- and FAK- driven phase separation provides an intracellular trigger for integrin clustering and nascent IAC formation.


title: Slow expanders invade by forming dented fronts in microbial colonies

abstract:
Most organisms grow in space, whether they are viruses spreading within a host tissue or invasive species colonizing a new continent. Evolution typically selects for higher expansion rates during spatial growth, but it has been suggested that slower expanders can take over under certain conditions. Here, we report an experimental observation of such population dynamics. We demonstrate that the slower mutants win not only when the two types are intermixed at the front but also when they are spatially segregated into sectors. The latter was thought to be impossible because previous studies focused exclusively on the global competitions mediated by expansion velocities but overlooked the local competitions at sector boundaries. We developed a theory of sector geometry that accounts for both local and global competitions and describes all possible sector shapes. In particular, the theory predicted that a slower, but more competitive, mutant forms a dented V-shaped sector as it takes over the expansion front. Such sectors were indeed observed experimentally and their shapes matched up quantitatively with the theory. In simulations, we further explored several mechanism that could provide slow expanders with a local competitive advantage and showed that they are all well-described by our theory. Taken together, our results shed light on previously unexplored outcomes of spatial competition and establish a universal framework to understand evolutionary and ecological dynamics in expanding populations.

SignificanceLiving organisms never cease to evolve, so there is a significant interest in predicting and controlling evolution in all branches of life sciences from medicine to agriculture. The most basic question is whether a trait should increase or decrease in a given environment. The answer seems to be trivial for traits such as the growth rate in a bioreactor or the expansion rate of a tumor. Yet, it has been suggested that such traits can decrease rather than increase during evolution. Here, we report a mutant that outcompeted the ancestor despite having a slower expansion velocity. To explain this observation, we developed and validated a theory that describes spatial competition between organisms with different expansion rates and arbitrary competitive interactions.


title: Differential effects of two catalytic mutations on full-length PRDM9 and its isolated PR/SET domain reveal a case of pseudo-modularity

abstract: PRDM9 is a DNA-binding histone methyltransferase that designates and activates recombination hotspots in mammals by locally trimethylating lysines 4 and 36 of histone H3. In mice, we recently reported two independently produced point mutations at the same residue, glu360pro (Prdm9EP) and glu360lys (Prdm9EK), which severely reduce its H3K4 and H3K36 methyltransferase activities in vivo. Prdm9EP is slightly less hypomorphic than Prdm9EK, but both mutations reduce both the number and amplitude of PRDM9-dependent H3K4me3 and H3K36me3 peaks in spermatocytes. While both mutations cause infertility with complete meiotic arrest in males, Prdm9EP, but not Prdm9EK, is compatible with some female fertility. When we tested the effects of these mutations in vitro, both Prdm9EP and Prdm9EK abolished H3K4 and H3K36 methyltransferase activity in full-length PRDM9. However, in the isolated PRDM9 PR/SET domain, these mutations selectively compromised H3K36 methyltransferase activity, while leaving H3K4 methyltransferase activity intact. The difference in these effects on the PR/SET domain versus the full-length protein show that PRDM9 is not an intrinsically modular enzyme; its catalytic domain is influenced by its tertiary structure and possibly by its interactions with DNA and other proteins in vivo. These two informative mutations illuminate the enzymatic chemistry of PRDM9, and potentially of PR/SET domains in general, reveal the minimal threshold of PRDM9-dependent catalytic activity for female fertility, and potentially have some practical utility for genetic mapping and genomics.


title: Marine gregarine genomes illuminate current understanding of apicomplexan glideosome

abstract: Our current view of the evolutionary history, coding and adaptive capacities of Apicomplexa, protozoan parasites of a wide range of metazoan, is currently strongly biased toward species infecting humans, as data on early diverging apicomplexan lineages infecting invertebrates is extremely limited. Here, we characterized the genome of the marine eugregarine Porospora gigantea, intestinal parasite of Lobsters, remarkable for the macroscopic size of its vegetative feeding forms (trophozoites) and its gliding speed, the fastest so far recorded for Apicomplexa. Two highly syntenic genomes named A and B were assembled. Similar in size (~9 Mb) and coding capacity (~5300 genes), A and B genomes are 10.8% divergent at the nucleotide level, corresponding to 16-38 My in divergent time. Orthogroup analysis across 25 (proto)Apicomplexa species, including Gregarina niphandrodes, showed that A and B are highly divergent from all other known apicomplexan species, revealing an unexpected breadth of diversity. Phylogenetically these two species branch sister to Cephaloidophoroidea, and thus expand the known crustacean gregarine superfamily. The genomes were mined for genes encoding proteins necessary for gliding, a key feature of apicomplexans parasites, currently studied through the molecular model called glideosome. Sequence analysis shows that actin-related proteins and regulatory factors are strongly conserved within apicomplexans. In contrast, the predicted protein sequences of core glideosome proteins and adhesion proteins are highly variable among apicomplexan lineages, especially in gregarines. These results confirm the importance of studying gregarines to widen our biological and evolutionary view of apicomplexan species diversity, and to deepen our understanding of the molecular bases of key functions enabling parasitism, such as the glideosome.


title: Marine gregarine genomes reveal the breadth of apicomplexan diversity and provide new insights on gliding motility


title: A Capped Tudor Domain within a Core Subunit of the Sin3L/Rpd3L Histone Deacetylase Complex Binds Nucleic Acids

abstract: Chromatin-modifying complexes containing histone deacetylase (HDAC) activities play critical roles in the regulation of gene transcription in eukaryotes. These complexes are thought to lack intrinsic DNA-binding activity, but according to a well-established paradigm, they are recruited via protein-protein interactions by gene-specific transcription factors and post-translational histone modifications to their sites of action on the genome. The mammalian Sin3L/Rpd3L complex, comprising more than a dozen different polypeptides, is an ancient HDAC complex found in diverse eukaryotes. The subunits of this complex harbor conserved domains and motifs of unknown structure and function. Here we show that Sds3, a constitutively associated subunit critical for the proper functioning of the complex, harbors a type of Tudor domain that we designate the capped Tudor domain (CTD). Unlike canonical Tudor domains that bind modified histones, the Sds3 CTD binds to nucleic acids that can form higher-order structures such as G-quadruplexes, and shares similarities with the knotted Tudor domain of the Esa1 histone acetyltransferase (HAT) that was previously shown to bind single-stranded RNA. Our findings expand the range of macromolecules capable of recruiting the Sin3L/Rpd3L complex and draws attention to potentially new roles for this HDAC complex in transcription biology.


title: Discovery of aryl aminothiazole γ-secretase modulators with novel effects on amyloid β-peptide production

abstract:
A series of analogs based on a prototype aryl aminothiazole {gamma}-secretase modulator (GSM) were synthesized and tested for their effects on the profile of 37-to-42-residue amyloid {beta}-peptides (A{beta}), generated through processive proteolysis of precursor protein substrate by {gamma}-secretase. Certain substitutions on the terminal aryl D ring resulted in an altered profile of A{beta} production compared to that seen with the parent molecule. Small structural changes led to concentration-dependent increases in A{beta}37 and A{beta}38 production without parallel decreases in their precursors A{beta}40 and A{beta}42, respectively. The new compounds therefore apparently also stimulate carboxypeptidase trimming of A{beta} peptides [≥]43 residues, providing novel chemical tools for mechanistic studies of processive proteolysis by {gamma}-secretase.

Graphical Abstract O_FIG_DISPLAY_L [Figure 1] M_FIG_DISPLAY C_FIG_DISPLAY


title: Reprogramming of the intestinal epithelial-immune cell interactome during SARS-CoV-2 infection

abstract: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) represents an unprecedented worldwide health problem. Although the primary site of infection is the lung, growing evidence points towards a crucial role of the intestinal epithelium. Yet, the exact effects of viral infection and the role of intestinal epithelial-immune cell interactions in mediating the inflammatory response are not known. In this work, we apply network biology approaches to single-cell RNA-seq data from SARS-CoV-2 infected human ileal and colonic organoids to investigate how altered intracellular pathways upon infection in intestinal enterocytes leads to modified epithelial-immune crosstalk. We point out specific epithelial-immune interactions which could help SARS-CoV-2 evade the immune response. By integrating our data with existing experimental data, we provide a set of epithelial ligands likely to drive the inflammatory response upon infection. Our integrated analysis of intra- and inter-cellular molecular networks contribute to finding potential drug targets, and suggest using existing anti-inflammatory therapies in the gut as promising drug repurposing strategies against COVID-19.


title: A Tethered Ligand Assay to Probe SARS-CoV-2:ACE2 Interactions

abstract: SARS-CoV-2 infections are initiated by attachment of the receptor-binding domain (RBD) on the viral Spike protein to angiotensin-converting enzyme-2 (ACE2) on human host cells. This critical first step occurs in dynamic environments, where external forces act on the binding partners and multivalent interactions play critical roles, creating an urgent need for assays that can quantitate SARS-CoV-2 interactions with ACE2 under mechanical load and in defined geometries. Here, we introduce a tethered ligand assay that comprises the RBD and the ACE2 ectodomain joined by a flexible peptide linker. Using magnetic tweezers and atomic force spectroscopy as highly complementary single-molecule force spectroscopy techniques, we investigate the RBD:ACE2 interaction over the whole physiologically relevant force range. We combine the experimental results with steered molecular dynamics simulations and observe and assign fully consistent unbinding and unfolding events across the three techniques, enabling us to establish ACE2 unfolding as a molecular fingerprint. Measuring at forces of 2-5 pN, we quantify the force dependence and kinetics of the RBD:ACE2 bond in equilibrium. We show that the SARS-CoV-2 RBD:ACE2 interaction has higher mechanical stability, larger binding free energy, and a lower dissociation rate in comparison to SARS-CoV-1, which helps to rationalize the different infection patterns of the two viruses. By studying how free ACE2 outcompetes tethered ACE2, we show that our assay is sensitive to prevention of bond formation by external binders. We expect our results to provide a novel way to investigate the roles of mutations and blocking agents for targeted pharmaceutical intervention.