Miracle-dz/UniFAR-FTUs huggingface dataset:
The Contribution of Astrocyte and Neuronal Panx1 to Seizures Is Model and Brain Region Dependent

Pannexin1 (Panx1) is an ATP release channel expressed in neurons and astrocytes that plays important roles in CNS physiology and pathology. Evidence for the involvement of Panx1 in seizures includes the reduction of epileptiform activity and ictal discharges following Panx1 channel blockade or deletion. However, very little is known about the relative contribution of astrocyte and neuronal Panx1 channels to hyperexcitability. To this end, mice with global and cell type specific deletion of Panx1 were used in one in vivo and two in vitro seizure models. In the low-Mg2+ in vitro model, global deletion but not cell-type specific deletion of Panx1 reduced the frequency of epileptiform discharges. This reduced frequency of discharges did not impact the overall power spectra obtained from local field potentials. In the in vitro KA model, in contrast, global or cell type specific deletion of Panx1 did not affect the frequency of discharges, but reduced the overall power spectra. EEG recordings following KA-injection in vivo revealed that although global deletion of Panx1 did not affect the onset of status epilepticus (SE), SE onset was delayed in mice lacking neuronal Panx1 and accelerated in mice lacking astrocyte Panx1. EEG power spectral analysis disclosed a Panx1-dependent cortical region effect; while in the occipital region, overall spectral power was reduced in all three Panx1 genotypes; in the frontal cortex, the overall power was not affected by deletion of Panx1. Together, our results show that the contribution of Panx1 to ictal activity is model, cell-type and brain region dependent.
Molecular basis of ligand recognition and activation of human V2 vasopressin receptor

The V2 vasopressin receptor (V2R) is a class A G protein-coupled receptor (GPCR) and plays a vital role in controlling water homeostasis upon stimulation by the natural peptide arginine vasopressin (AVP). Thus, V2R has attracted intense interest as a drug target for diabetes insipidus, nocturia, and hyponatremia. However, how AVP recognizes and activates V2R remains elusive. Here, we report the 2.6 Å resolution structure of V2R bound to AVP and the stimulatory G protein Gs, determined by cryo-electron microscopy (cryo-EM). In this complex, AVP presents a unique cyclic conformation formed by an intramolecular disulfide bond and engages the orthosteric binding pocket of V2R in a ligand-specific mode. Comparison of the AVP–V2R–Gs complex to previously reported Gs-coupled class A GPCRs reveals distinct structural features, including a smaller outward movement of TM5 and TM6 and the concomitant shift of Gs protein. Our detailed structural analysis provides a framework for understanding AVP recognition and V2R activation, thereby offering a structural template for drug design targeting V2R.
Forebrain Shh overexpression improves cognitive function in a Down syndrome mouse model and euploid littermates

People with Down syndrome (DS) have intellectual disability, early-onset dementia, and cerebellar hypoplasia. Trisomic cerebellar granule cell precursors from Ts65Dn, a mouse model of DS, had a deficit in mitogenic response to Sonic hedgehog (Shh) in vitro, and newborn Ts65Dn mice received a single subcutaneous injection of the Shh signaling agonist SAG had normalized cerebellar morphology and improved spatial learning and hippocampal synaptic plasticity at adult. However, cognitive effects of Shh overexpression in vivo and where SAG acts to improve cognitive outcomes of trisomy are unknown. Here, we created an inducible human Shh (hShh) knock-in mouse, TRE-bi-hShh-Zsgreen1 (TRE-hShh), expressing dually-lipidated Shh-Np in the presence of transactivator (tTA). Double transgenic mice, Camk2a-tTA;TRE-hShh (Camk2a-hShh) and Pcp2-tTA;TRE-hShh (Pcp2-hShh), increased Shh signaling in forebrain and cerebellum, respectively. Forebrain Shh overexpression normalized hyperactivity, and spatial learning and memory deficits in 3-month-old Ts65Dn, while Shh overexpression in cerebellum had no effect. Further, Camk2a-hShh delayed early-onset severe cognitive impairment in 7-month-old Ts65Dn and enhanced spatial cognition in euploid (Eu) and showed no effect on the longevity of Eu or Ts65Dn, and MRI demonstrated that Pcp2-hShh mitigated disproportionately small cerebellum in Ts65Dn. Finally, Ts65Dn at postnatal day 6 had reduced Gli1 levels in hippocampus and cerebellum, which could be at least partially rescued by Camk2a-hShh and Pcp2-hShh, respectively. Our findings suggest restoration of impaired Shh signaling in forebrain from the perinatal and early postnatal period improves cognitive function.
Chitinase 3-like-1 Stimulates PD-L1 and Other Immune Checkpoint Inhibitors

PD-1 and its ligand PD-L1 are major mediators of tumor-induced immunosuppression. Chitinase 3-like-1 (Chi3l1) is induced in many cancers where it portends a poor prognosis and contributes to tumor metastasis. Here we demonstrate that Chi3l1 regulates the expression of PD-L1, PD-L2, PD-1 and LAG3 in melanoma lung metastasis. Chi3l1 stimulates macrophage PD-L1 expression and mediates optimal IFN-γ-stimulated PD-L1 expression via IL-13Rα2. We also demonstrate that RIG-like helicase innate immune activation suppresses Chi3l1, PD-L1, LAG3 and pulmonary metastasis. At least additive antitumor responses were seen in metastasis models treated simultaneously with individual antibodies against PD-1 and Chi3l1. At least additive cytotoxic T cell-induced tumor cell death was also seen in co-cultures of T and tumor cells treated with antibodies that target Chi3l1 and PD-1. Thus, Chi3l1 contributes to pulmonary metastasis by stimulating the PD1-PD-L1 axis and other checkpoint molecules. The simultaneous targeting of Chi3l1 and the PD-1-PD-L1 axis, represents a promising therapeutic strategy for pulmonary metastasis.
Wnt target enhancer regulation by a CDX/TCF transcription factor collective and a novel DNA motif

Transcriptional regulation by Wnt signalling is primarily thought to be accomplished by a complex of β-catenin and TCF family transcription factors (TFs). Although numerous studies have suggested that additional TFs play roles in regulating Wnt target genes, their mechanisms of action have not been investigated in detail. We characterised a Wnt-responsive element (WRE) downstream of the Wnt target gene Axin2 and found that TCFs and Caudal-related homeodomain (CDX) proteins were required for its activation. Using a new separation-of-function TCF mutant, we found that WRE activity requires the formation of a TCF/CDX complex. Our systematic mutagenesis of this enhancer identified other sequences essential for activation by Wnt signalling, including several copies of a novel CAG DNA motif. Computational and experimental evidence indicates that the TCF/CDX/CAG mode of regulation is prevalent in multiple WREs. Put together, our results demonstrate the complex nature of cis- and trans- interactions required for signal-dependent enhancer activity.
Gene Expression Profiling of Lymph Node Sub-Capsular Sinus Macrophages in Cancer

Lymph nodes are key lymphoid organs collecting lymph fluid and migratory cells from the tissue area they survey. When cancerous cells arise within a tissue, the sentinel lymph node is the first immunological organ to mount an immune response. Sub-capsular sinus macrophages (SSMs) are specialized macrophages residing in the lymph nodes that play important roles as gatekeepers against particulate antigenic material. In the context of cancer, SSMs capture tumor-derived extracellular vesicles (tEVs), a form of particulate antigen released in high amounts by tumor cells. We have recently demonstrated that SSMs possess anti-tumor activity because in their absence tumors grow faster. A comprehensive profiling of SSMs represents an important first step to identify the cellular and molecular mechanisms responsible for SSM anti-tumor activity. Unfortunately, the isolation of SSMs for molecular analyses is very challenging. Here, we combined an optimized dissociation protocol, careful marker selection and stringent gating strategies to highly purify SSMs. We provide evidence of decreased T and B cell contamination, which allowed us to reveal the gene expression profile of this elusive macrophage subset. Squamous cell carcinomas induced an increase in the expression of Fc receptors, lysosomal and proteasomal enzymes in SSMs. These results suggest that SSMs may be able to capture immune complexes for antigen processing and presentation to B and T cells on both MHC class I and II.
Soil penetration by maize roots is negatively related to ethylene‐induced thickening

Abstract Radial expansion is a classic response of roots to a mechanical impedance that has generally been assumed to aid penetration. We analysed the response of maize nodal roots to impedance to test the hypothesis that radial expansion is not related to the ability of roots to cross a compacted soil layer. Genotypes varied in their ability to cross the compacted layer, and those with a steeper approach to the compacted layer or less radial expansion in the compacted layer were more likely to cross the layer and achieve greater depth. Root radial expansion was due to cortical cell size expansion, while cortical cell file number remained constant. Genotypes and nodal root classes that exhibited radial expansion in the compacted soil layer generally also thickened in response to exogenous ethylene in hydroponic culture, that is, radial expansion in response to ethylene was correlated with the thickening response to impedance in soil. We propose that ethylene insensitive roots, that is, those that do not thicken and can overcome impedance, have a competitive advantage under mechanically impeded conditions as they can maintain their elongation rates. We suggest that prolonged exposure to ethylene could function as a stop signal for axial root growth.
Ultrastructural features of presynaptic active zones and dense core vesicles of olfactory projection neuron boutons in Drosophila melanogaster

In Drosophila melanogaster, olfactory projection neurons (PNs) convey odor information from the peripheral olfactory center to higher brain regions. The anatomical and physiological properties of PNs have been well characterized at the cellular and circuit level. The ultrastructural features of PNs remain unknown however, particularly with respect to presynaptic active zones (PAZs) and dense core vesicles (DCVs). In the current study, membrane-labeled electron microscopy was used to volume-reconstruct 89 PN axonal boutons and identify the internal PAZs and DCVs. Based on ultrastructural parameters, these PN boutons could be classified into three morphological distinct subtypes. Interestingly, the distributions of PAZs and DCVs were distinct within these three subtypes. DCVs were enriched in membrane labeled GH146-positive boutons, suggesting that GH146-positive PNs release both neurotransmitters and neuromodulators. The study identified the detailed distributions of PAZs and DCVs in PN boutons and indicates that neuromodulators mediated by DCVs may play an important role in PNs for olfactory processing.
Correlation of Computerized Tomography (CT) Severity Score for COVID-19 pneumonia with Clinical Outcomes

Introduction Various CT severity scores have already been described in literature since the start of this pandemic. One pertinent issue with all of the previously described severity scores is their relative challenging calculation and variance in inter-observer agreement. The severity score proposed in our study is relatively simpler, easier to calculate and apart from a trained radiologist, can easily be calculated even by physicians with good inter-observer agreement. Therefore, a rapid CT severity score calculation can give a clue to physician about possible clinical outcome without being dependent on radiologist who may not be readily available especially in third world countries. Objective The objective of this study is to develop a simple CT severity score (CT-SS) with good inter-observer agreement and access its correlation with clinical outcome. Methods This retrospective study was conducted by the Department of Radiology and Internal Medicine, at the Aga Khan University Hospital Karachi, from April 2020 to August 2020. Non-probability consecutive sampling was used to include all patients who were positive for COVID-19 on PCR, and underwent CT chest examination at AKUH. Severity of disease was calculated in each lobe on the basis of following proposed CT severity scoring system (CT-SS). For each lobe the percentage of involvement by disease was scored – 0% involvement was scored 0, <50% involvement was scored 1 and >50% involvement was scored 2. Maximum score for one lobe was 2 and hence total maximum overall score for all lobes was 10. Continuous data was represented using mean and standard deviation, and compared using independent sample t-tests. Categorical data was represented using frequencies and percentages, and compared using Chi-squared tests. Inter-observer reliability between radiologist and COVID intensivist for the 10 point CT-SS rated on 0-10 was assessed using the Kappa statistic. A p-value < 0.05 was considered significant for all analyses. Results A total of 73 patients were included, the majority male (58.9%) with mean age 55.8 ± 13.93 years. The CT-SS rated on 0-10 showed substantial inter-observer reliability between radiologist and intensivist with a Kappa statistic of 0.78. Patients with CT-SS 8-10 had a significantly higher ICU admission & intubation rate (53.8% vs. 23.5%) and mortality rate (35.9% vs. 11.8%; p = 0.017), as compared to those with CT-SS 0-7. Conclusion We conclude that the described CT severity score (CT-SS) is a quick, effective and easily reproducible tool for prediction of adverse clinical outcome in patients with COVID 19 pneumonia. The tool shows good inter-observer agreement when calculated by radiologist and physician independently.
Local ecological knowledge, catch characteristics and evidence of elasmobranch depletions in Western Ghana

Local Ecological Knowledge has the potential to improve fishery management by providing new data on the fishing efforts, behavior, and abundance trends of fish and other aquatic animals. Here, we relied on local knowledge of fishers to investigate ecological factors that affect elasmobranch fishers‟ operations and the changes in stock status of sharks and rays from 1980 to 2020 in five coastal communities in Ghana. Data were gathered from fishers using participant observation, interviews, focus group discussions, and participatory rural appraisal techniques. The results revealed fisher‟s understanding of six main ecological variables, which are mostly applied to enhance their fishing operations: season and weather conditions, lunar phase, bait type, presence of seabirds and fish movement, color of seawater, and sea current. These ecological features have been applied over the years to enhance fishing operations as well as maximize fisher catch. Fishers reported a profound decline in shark and ray catch from 1980 to 2020 and attributed the decline in size, number, and composition of their catch to overfishing and Illegal, Unreported and Unregulated (IUU) fishing operations. In general, most shark and ray species were abundant in 1980 but have been severely depleted as of 2020, with the exception of Blue Shark (Prionace glauca) and Devil rays (Mobula spp), which were reported to be common by the interviewed fishers. The first species depleted were the Thresher sharks (Alopiidae), Tiger Shark (Galeocerdo cuvier), Blackchin Guitarfish (Glaucostegus cemiculus), and Lemon Shark (Negaprion brevirostris), which were depleted early in the 2000s. The next depletions of Hammerhead sharks (Sphyrnidae), Bull Shark (Carcharhinus leucas), Sand Tiger Shark (Carcharias taurus), Stingrays (Fontitrygon spp), and Spineback Guitarfish (Rhinobatos irvinei) occurred in the 2010s. We found Local Ecological Knowledge of fishers to be surprisingly consistent with scholarly knowledge and call for their inclusion in research, decision-making and management interventions by biologists and policy makers.
Assessing biomass and primary production of microphytobenthos in depositional coastal systems using spectral information

In depositional intertidal coastal systems, primary production is dominated by benthic microalgae (microphytobenthos) inhabiting the mudflats. This benthic productivity is supporting secondary production and supplying important services to humans including food provisioning. Increased frequencies of extreme events in weather (such as heatwaves, storm surges and cloudbursts) are expected to strongly impact the spatiotemporal dynamics of the microphytobenthos and subsequently their contribution to coastal food webs. Within north-western Europe, the years 2018 and 2019 were characterized by record-breaking summer temperatures and accompanying droughts. Field-calibrated satellite data (Sentinel 2) were used to quantify the seasonal dynamics of microphytobenthos biomass and production at an unprecedented spatial and temporal resolution during these years. We demonstrate that the Normalized Difference Vegetation Index (NDVI) should be used with caution in depositional coastal intertidal systems, because it may reflect import of remains of allochthonous pelagic productivity rather than local benthic biomass. We show that the reduction in summer biomass of the benthic microalgae cannot be explained by grazing but was most probably due to the high temperatures. The fivefold increase in salinity from January to September 2018, resulting from reduced river run-off during this exceptionally dry year, cannot have been without consequences for the vitality of the microphytobenthos community and its resistance to wind stress and cloud bursts. Comparison to historical information revealed that primary productivity of microphytobenthos may vary at least fivefold due to variations in environmental conditions. Therefore, ongoing changes in environmental conditions and especially extreme events because of climate change will not only lead to changes in spatiotemporal patterns of benthic primary production but also to changes in biodiversity of life under water and ecosystem services including food supply. Satellite MPB data allows for adequate choices in selecting coastal biodiversity conservation and coastal food supply. HIGHLIGHTS Expected seasonality changes require large-scale and high-resolution coastal data NDVI of tidal flats reflects local benthic biomass and allochthonous phytoplankton High summer temperatures reduced biomass and productivity of benthic microalgae Long-term data revealed a five-fold variation in MPB biomass and production Satellite MPB data allow for adequate conservation of coastal biodiversity
Induced systemic resistance impacts the phyllosphere microbiome through plant-microbe-microbe interactions

Both above- and below-ground parts of plants are constantly confronted with microbes, which are main drivers for the development of plant-microbe interactions. Plant growth-promoting rhizobacteria enhance the immunity of above-ground tissues, which is known as induced systemic resistance (ISR). We show here that ISR also influences the leaf microbiome. We compared ISR triggered by the model strain Pseudomonas simiae WCS417r (WCS417) to that triggered by Bacillus thuringiensis israelensis (Bti) in Arabidopsis thaliana. In contrast to earlier findings, immunity elicited by both strains depended on salicylic acid. Both strains further relied on MYC2 for signal transduction in the plant, while WCS417-elicited ISR additionally depended on SAR-associated metabolites, including pipecolic acid. A metabarcoding approach applied to the leaf microbiome revealed a significant ISR-associated enrichment of amplicon sequence variants with predicted plant growth-promoting properties. WCS417 caused a particularly dramatic shift in the leaf microbiota with more than 50% of amplicon reads representing two bacterial species: WCS417 and Flavobacterium sp. Co-inoculation experiments using WCS417 and At-LSPHERE Flavobacterium sp. Leaf82, suggest that the proliferation of these bacteria is influenced by both microbial and plant-derived factors. Together, our data connect systemic immunity with leaf microbiome dynamics and highlight the importance of plant- microbe-microbe interactions for plant health.
Small Molecule Analysis of Extracellular Vesicles Produced by Cryptococcus gattii: Identification of a Tripeptide Controlling Cryptococcal Infection in an Invertebrate Host Model

The small molecule (molecular mass < 900 Daltons) composition of extracellular vesicles (EVs) produced by the pathogenic fungus Cryptococcus gattii is unknown, which limits the understanding of the functions of cryptococcal EVs. In this study, we analyzed the composition of small molecules in samples obtained from solid cultures of C. gattii by a combination of chromatographic and spectrometric approaches, and untargeted metabolomics. This analysis revealed previously unknown components of EVs, including small peptides with known biological functions in other models. The peptides found in C. gattii EVs had their chemical structure validated by chemical approaches and comparison with authentic standards, and their functions tested in a Galleria mellonella model of cryptococcal infection. One of the vesicular peptides (isoleucine-proline-isoleucine, Ile-Pro-Ile) improved the survival of G. mellonella lethally infected with C. gattii or C. neoformans. These results indicate that small molecules exported in EVs are biologically active in Cryptococcus. Our study is the first to characterize a fungal EV molecule inducing protection, pointing to an immunological potential of extracellular peptides produced by C. gattii.
A Novel in vitro Model for Mature Toxoplasma gondii Bradyzoites Reveals their Metabolome and a Diminished Role of the Mitochondrial Tricarboxylic Acid Cycle

The apicomplexan parasite Toxoplasma gondii causes chronic and drug-tolerant infections, yet current models do not permit metabolomic characterization of these persisting tissue cysts. Here, we developed a human myotube-based in vitro culture model of functionally mature tissue cysts that enabled direct measurements of their metabolome. The cysts are functionally mature and tolerate exposure to a range of antibiotics and to extended temperature stresses and are orally infectious to mice. Metabolomic characterization of purified cysts reveals global changes that comprise systematically increased levels of amino acids and decrease abundance of nucleobase- and tricarboxylic acid cycle-associated metabolites. Consequently, pharmacological modulation of the TCA cycle in T. gondii bradyzoites reveals that this pathway is rendered dispensable during parasite stage conversion. Direct access to persisting parasite stages will be essential for the dissection of functionally important host-parasite interactions and drug evasion mechanisms and also help to identify new strategies for therapeutic intervention. –Toxoplasma gondii forms mature tissue cysts in immortalized human myotubes–In vitro cysts of T. gondii develop drug tolerance and temperature stress resistance–Untargeted metabolomic characterization of tissue cysts reveals a distinct metabolome–The mitochondrial tricarboxylic acid cycle is dispensable in T. gondii bradyzoites