title: Spatial and temporal constraints on the composition of microbial communities in subsurface boreholes of the Edgar Experimental Mine

abstract:
The deep biosphere hosts uniquely adapted microorganisms overcoming geochemical extremes at significant depths within the crust of the Earth. While numerous novel microbial members with unique physiological modifications remain to be identified, even greater attention is required to understand the near-subsurface and its continuity with surface systems. This raises key questions about networking of surface hydrology, geochemistry affecting near-subsurface microbial composition, and resiliency of subsurface ecosystems. Here, we apply molecular and geochemical approaches to determine temporal microbial composition and environmental conditions of filtered borehole fluid from the Edgar Experimental Mine ([~]150 meters below the surface) in Idaho Springs, CO. Samples were collected over a 4-year collection period from expandable packers deployed to accumulate fluid in previously drilled boreholes located centimeters to meters apart, revealing temporal evolution of borehole microbiology. Meteoric water feeding boreholes demonstrated variable recharge rates likely due to a complex and undefined fracture system within the host rock. 16S rRNA gene analysis determined unique microbial communities occupy the four boreholes examined. Two boreholes yielded sequences revealing the presence of Proteobacteria, Firmicutes, and Nanoarcheota associated with endemic subsurface communities. Two other boreholes presented sequences related to soil-originating microbiota, which likely indicate a direct link to surface infiltration. High concentrations of sulfate suggest sulfur-related metabolic strategies dominate within these near-subsurface boreholes. Overall, results indicate microbial community composition in the near-subsurface is highly dynamic at very fine spatial scales (<20cm) within fluid-rock equilibrated boreholes, which additionally supports the role of a relationship for surface geochemical processes infiltrating and influencing subsurface environments.

ImportanceThe Edgar Experimental Mine, Idaho Springs, Colorado provides inexpensive and open access to borehole investigations for subsurface microbiology studies. Understanding how microbial processes in the near-subsurface are connected to surface hydrological influences like meteoric input is lacking. Investigating microbial communities of subsurface mine boreholes provides evidence of how geochemical processes are linked to biogeochemical processes within each borehole, and the geochemical connectedness and mobility of surface influences. This study details microbial community composition and fluid geochemistry over spatial and temporal scales from boreholes within the Edgar Mine. These findings are relevant to biogeochemistry of near-surface mines, caves and other voids across planetary terrestrial systems. In addition, this work can lead to understanding how microbial communities relating to both fluid-rock equilibration and geochemical influences may enhance our understanding of subsurface molecular biological tools that aid mining economic practices to reflect biological signals for lucrative veins in the near subsurface.


title: Fuzzy RNA-recognition by the Trypanosoma brucei editosome

abstract: The recognition of RNA-molecules by proteins and protein complexes is a critical step on all levels of gene expression. Typically, the generated ribonucleoprotein complexes rely on the binary interaction of defined RNA-sequences or precisely folded RNA-motifs with dedicated RNA-binding domains on the protein side. Here we describe a new molecular recognition principle of RNA-molecules by a high molecular mass protein complex. By chemically probing the solvent accessibility of mitochondrial pre-mRNAs when bound to the Trypanosoma brucei editosome we identified multiple similar but nonidentical RNA-motifs as editosome contact sites. However, by treating the different motifs as mathematical graph objects we demonstrate that they fit a consensus 2D-graph consisting of 4 vertices (V) and 3 edges (E) with a Laplacian eigenvalue of 0.523 ({lambda}2). We establish that a synthetic 4V(3E)-RNA is sufficient to compete for the editosomal pre-mRNA binding site and that it is able to inhibit RNA-editing in vitro. Our analysis corroborates that the editosome has adapted to the structural multiplicity of the mitochondrial mRNA-folding space by recognizing a fuzzy continuum of RNA-folds that fit a consensus graph-descriptor. This provides a mechanism on how the protein complex is able to bind the structurally pleomorphic pool of pre- and partially edited mRNAs. We speculate that other fuzzy RNA-recognition motifs exist especially for proteins that interact with multiple RNA-species.

category: molecular biology


title: Polypeptides IGF-1C and P24 synergistically promote osteogenic differentiation of bone marrow mesenchymal stem cells in vitro through the p38 and JNK signaling pathways

abstract:
ObjectivesInsulin-like growth factor-1 (IGF-1) and bone morphogenetic protein 2 (BMP-2) both promote osteogenesis of bone marrow mesenchymal stem cells (BMSCs). IGF-1C, the C domain peptide of IGF-1, and P24, a BMP-2-derived peptide, both have similar biological activities as their parent growth factors. This study aimed to investigate the effects and their mechanisms of polypeptides IGF-1C and P24 on the osteogenic differentiation of BMSCs.

MethodsThe optimum concentrations of IGF-IC and P24 were explored. The effects of the two polypeptides on the proliferation and osteogenic differentiation of BMSCs were examined using the Cell Counting Kit-8(CCK-8), Alkaline phosphatase (ALP) staining, ALP activity assay, alizarin red S staining, qPCR, and western blotting. In addition, specific pathway inhibitors were utilized to explore whether p38 and JNK pathways were involved in this process.

ResultsThe optimal concentrations of action were both 50 g/ml. IGF-1C and P24 synergistically promoted the proliferation of BMSCs, increased ALP activity and the formation of calcified nodules and upregulated the mRNA and protein levels of osterix (Osx), runt-related transcription factor 2 (Runx2), and osteocalcin (Ocn), phosphorylation level of p38 and JNK proteins also improved. Inhibition of the pathways significantly reduced the activation of p38 and JNK, blocked the expression of Runx2 while inhibiting ALP activity and the formation of calcified nodules.

ConclusionsThese findings suggest IGF-1C and P24 synergistically promote the osteogenesis of BMSCs through activation of p38 and JNK signal pathways.

category: cell biology


title: Megakaryocyte derived immune-stimulating cells regulate host-defense immunity against bacterial pathogens

abstract: Megakaryocytes (MKs) continuously produce platelets to support hemostasis and form a niche for hematopoietic stem cell maintenance in the bone marrow. MKs are also involved in inflammation responses; however, the mechanism remains poorly understood. Here, using single-cell sequencing we identified an MK-derived immune-stimulating cell (MDIC) population exhibiting both MK-specific and immune characteristics, which highly expresses CXCR4 and immune response genes to participate in host-protective response against bacteria. MDICs interact with myeloid cells to promote their migration and stimulate the bacterial phagocytosis of macrophages and neutrophils by producing TNF and IL-6. CXCR4high MDICs egress circulation and infiltrate into the spleen, liver, and lung upon bacterial infection. Ablation of MKs suppresses the innate immune response and T cell activation to impair the anti-bacterial effects in mice under the Listeria monocytogenes challenge. Using hematopoietic stem/progenitor cell lineage-tracing mouse line, we show that MDICs are generated from infection-induced emergency megakaryopoiesis in response to bacterial infection. Overall, we identify MDICs as an MK subpopulation, which regulates host-defense immune response against bacterial infection.


title: Interferon-gamma and TNF-alpha synergistically enhance the immunomodulatory capacity of Endometrial-Derived Mesenchymal Stromal Cell secretomes by differential microRNA and extracellular vesicle release

abstract:
Endometrial Mesenchymal Stromal Cells (endMSCs) can be easily isolated from menstrual blood by plastic adherence. These cells have a potent pro-angiogenic and immunomodulatory capacity, and their therapeutic effect is mediated by paracrine mechanisms where secretome have a key role. In this paper, we aimed to evaluate different priming conditions in endMSCs using pro-inflammatory cytokines and Toll-Like Receptor ligands. Our in vitro results revealed a synergistic and additive effect of IFN{gamma} and TNF on endMSCs. The combination of these pro-inflammatory cytokines significantly increased the release of Indoleamine 2,3-dioxygenase (IDO1) in endMSCs. Additionally, this study was focused on the phenotype of IFN{gamma}/TNF-primed endMSCs (endMSCs*). Here we found that immune system-related molecules such as CD49d, CD49e, CD54, CD56, CD58, CD63, CD126, CD152, or CD274 were significantly altered in endMSCs* when compared to control cells. Afterward, our study was completed with the characterization of released miRNAs by Next Generation Sequencing (NGS). Briefly, our system biology approaches demonstrated that endMSCs* showed an increased release of 25 miRNAs whose target genes were involved in immune response and inflammation. Finally, the cellular and molecular characterization was completed with in vitro functional assays.

In summary, the relevance of our results lies in the therapeutic potential of endMSCs*. The differences in cell surface molecules involved in migration, adhesion and immunogenicity, allowed us to hypothesize that endMSCs* may have an optimal homing and migration capacity towards inflammatory lesions. Secondly, the analysis of miRNAs, target genes and the subsequent lymphocyte activation assays demonstrated that IFN{gamma}/TNF-primed secretome may exert a potent effect on the regulation of adverse inflammatory reactions.


title: Parkin drives pS65-Ub turnover independently of canonical autophagy in Drosophila

abstract: Parkinsons disease-related proteins, PINK1 and Parkin, act in a common pathway to maintain mitochondrial quality control. While the PINK1-Parkin pathway can promote autophagic mitochondrial turnover (mitophagy) in cell culture, recent studies have questioned whether they contribute to mitophagy in vivo, and alternative PINK1- and Parkin-dependent mitochondrial quality control pathways have been proposed. To determine the mechanisms by which the Pink1-Parkin pathway operates in vivo, we developed methods to detect Ser65-phosphorylated ubiquitin (pS65-Ub) in Drosophila. Exposure to the oxidant paraquat led to robust, Pink1-dependent pS65-Ub production. Surprisingly, parkin-null flies displayed strikingly elevated basal levels of pS65-Ub, suggestive of disrupted flux through the Pink1-parkin pathway. Depletion of the core autophagy proteins Atg1, Atg5 and Atg8a did not cause pS65-Ub accumulation to the same extent as loss of parkin, and overexpression of parkin was able to reduce both basal and paraquat-induced pS65-Ub levels in an Atg5-null background. Taken together, these results suggest that the Pink1-parkin pathway is able to promote mitochondrial turnover independently of canonical autophagy in vivo.


title: Investigation of Thyroid Hormone Associated Gene-Regulatory Networks during Hepatogenesis using an Induced Pluripotent Stem Cell based Model

abstract: Currently, the only treatment of end-stage liver diseases is liver transplantation. The worldwide shortage of donor organs and the high number of patients suffering from end-stage liver diseases, require alternative treatment approaches. Therefore, the generation of hepatocyte-like cells (HLCs) derived from induced pluripotent stem cells (iPSCs) is a promising treatment option. HLCs are suitable for patient-specific drug screening, disease modeling and regenerative medicine. So far, they are immature and resemble the fetal state. In this study, we employed the combined thyroid hormones triiodo-L-thyronine (T3) and L-thyroxine (T4) to drive HLCs towards maturation. HLCs expressed the maturation markers ALBUMIN (ALB), ALPHA-1 ANTITRYPSIN (A1AT), CYTOCHROME P450 3A4 (CYP3A4) and TRANSTHYRETIN (TTR). Remarkably, stimulation with T3 and T4 slightly reduced the expression of the fetal marker CYTOCHROME P450 3A7 (CYP3A7) and had an even more pronounced effect on ALPHA-FETOPROTEIN (AFP) levels. Comparative transcriptome and associated pathways in unstimulated and T3 and T4 stimulated HLCs revealed regulated expression of numerous genes within for example the peroxisome proliferator-activated receptor (PPAR), transforming growth factor beta (TGF-{beta}), mitogen-activated protein kinase/extracellular-signal-regulated kinase (MAPK/ERK) signaling pathways and thyroid hormone synthesis. We propose the inclusion of combined T3 andT4 in HLC differentiation protocols to enhance maturation and therefore provide additional improvement in their applications in drug screening and disease modeling.

category: developmental biology


title: Land-use planning for health: Tradeoffs and nonlinearities govern how land-use change impacts vector-borne disease risk

abstract:
Patterns of land-use can affect the transmission of many infectious diseases with human health implications; yet, applied ecosystem service models have rarely accounted for disease transmission risk. A mechanistic understanding of how land-use changes alter infectious disease transmission would help to target public health interventions and to minimize human risk of disease with either ecosystem degradation or restoration. Here, we present a spatially explicit model of disease transmission on heterogeneous landscapes that is designed to serve as a road map for modeling the multifaceted impacts of land-use on disease transmission. We model the transmission of three vector-borne diseases with distinct transmission dynamics (parameterized using published literature to represent dengue, yellow fever, and malaria) on simulated landscapes of varying spatial heterogeneity in tree cover and urban area. Overall, we find that these three diseases depend on the biophysical landscape in different nonlinear ways, leading to tradeoffs in disease risk across the landscape; rarely do we predict disease risk to be high for all three diseases in a local setting. We predict that dengue risk peaks in areas of high urban intensity and human population density, yellow fever risk peaks in areas with low to moderate human population density and high tree cover, and malaria risk peaks where patchy tree cover abuts urban area. To examine how this approach can inform land use planning, we applied the model to a small landscape to the northwest of Bogota, Colombia under multiple restoration scenarios. We predict that in an area inhabited by both Aedes aegypti and Ae. albopictus, any increase in overall tree cover would increase dengue and yellow fever risk, but that risk can be minimized by pursuing a large contiguous reforestation project as opposed to many small, patchy projects. A large contiguous reforestation project is also able to both reduce overall malaria risk and the number of malaria hotspots. As sustainable development goals make ecosystem restoration and biodiversity conservation top priorities, it is imperative that land use planning account for potential impacts on both disease transmission and other ecosystem services.

Open Research statementAll data and code used in this study are available in the online supplemental material. Code and data are also hosted at: https://github.com/morgankain/Land-Use_Disease_Model.

category: ecology


title: Within-species trait diversity reorganizes consumer competitive hierarchy and prey community structure in an experimental microbial ecosystem

abstract: A popular idea in ecology is that trait variation among individuals from the same species may promote the coexistence of competing species. However, theoretical and empirical tests of this idea have yielded inconsistent findings. We manipulated intraspecific trait diversity in a ciliate competing with a nematode for bacterial prey in experimental microcosms. We found that intraspecific trait variation inverted the original competitive hierarchy to favor the consumer with variable traits, ultimately resulting in competitive exclusion. This competitive outcome was driven by foraging traits (size, speed, and directionality) that increased the ciliates fitness ratio and niche overlap with the nematode. The interplay between consumer trait variation and competition resulted in non-additive cascading effects - mediated through prey defense traits - on prey community assembly. Our results suggest that predicting consumer competitive population dynamics and the assembly of prey communities will require understanding the complexities of trait variation within consumer species.


title: Effects of phenotypic variation on consumer coexistence and prey community structure


title: Induce Pluripotency via Specific distal enhancer-promoter associations

abstract: Induced pluripotent stem cell (iPSC) technology promises to be an inexhaustible source of any type of cell needed for therapeutic and research purposes. It is unclear that how distal enhancer-promoter associations/ 3D chromatin conformation involving in the capacity of self-renewal and pluripotency maintenance. In this study, we have selected a few defined enhancer-promoter associations. After screening of enhancer specificity and activity individually, we design the different combinations and transfect these enhancers into the MEF cells. We simultaneously transfect 7 determined enhancers which represents various specific distal chromatin associations into a GFP tracing MEF cell line. We observe that the MEF cells start generating iPS-like clones at day 22. Importantly, our validations with three germ layer marker genes and in vitro experiments have further confirmed the pluripotency of these clones. Here, our study proposes a potential de novo method of a low-genetic risk iPS generation by introducing spatiotemporal distal chromatin associations. This result also paves out the way on utilizing 3D genomic information to alter cell identity and reprogramming for potential therapeutic strategy.

category: genomics


title: Mutational bias in spermatogonia impacts the anatomy of regulatory sites in the human genome

abstract: Mutation in the germline is the ultimate source of genetic variation, but little is known about the influence of germline chromatin structure on mutational processes. Using ATAC-seq, we profile the open chromatin landscape of human spermatogonia, the most proliferative cell-type of the germline, identifying transcription factor binding sites (TFBSs) and PRDM9-binding sites, a subset of which will initiate meiotic recombination. We observe an increase in rare structural variant (SV) breakpoints at PRDM9-bound sites, implicating meiotic recombination in the generation of structural variation. Many germline TFBSs, such as NRF, are also associated with increased rates of SV breakpoints, apparently independent of recombination. Singleton short insertions (>=5 bp) are highly enriched at TFBSs, particularly at sites bound by testis active TFs, and their rates correlate with those of structural variant breakpoints. Short insertions often duplicate the TFBS motif, leading to clustering of motif sites near regulatory regions in this male-driven evolutionary process. Increased mutation loads at germline TFBSs disproportionately affect neural enhancers with activity in spermatogonia, potentially altering neurodevelopmental regulatory architecture. Local chromatin structure in spermatogonia is thus pervasive in shaping both evolution and disease.


title: The Epiallelic Nature of Mouse rDNA

abstract:
BackgroundRibosomal DNA (rDNA) displays substantial inter-individual genetic variation in human and mouse. A systematic analysis of how this variation impacts epigenetic states and expression of the rDNA has thus far not been performed.

ResultsUsing a combination of long- and short-read sequencing, we establish that 45S rDNA units in the C57BL/6J mouse strain exist as distinct genetic haplotypes that influence the epigenetic state and transcriptional output of any given unit. DNA methylation dynamics at these haplotypes are dichotomous and life-stage specific: at one haplotype, the DNA methylation state is sensitive to the in utero environment, but refractory to post-weaning influences, whereas other haplotypes entropically gain DNA methylation during ageing only. On the other hand, individual rDNA units in human show limited evidence of genetic haplotypes, and hence little discernible correlation between genetic and epigenetic states. However, in both species, adjacent units show similar epigenetic profiles, and the overall epigenetic state at rDNA is strongly positively correlated with total rDNA copy number. Analysis of different mouse inbred strains reveals that in some strains, such as 129S1/SvImJ, rDNA copy number is only approximately 150 copies per diploid genome and DNA methylation levels are <5%.

ConclusionsOur work demonstrates that rDNA-associated genetic variation has a considerable influence on rDNA epigenetic state and consequently rRNA expression outcomes. In the future, it will be important to consider the impact of inter-individual rDNA (epi)genetic variation on mammalian phenotypes and diseases.


title: Genetic variation at mouse and human ribosomal DNA influences associated epigenetic states


title: Desmosomal connectomics of all somatic muscles in an annelid larva

abstract: Cells form networks in animal tissues through synaptic, chemical and adhesive links. In muscle tissue, cells often connect through desmosomes, adhesive structures anchored by intermediate filaments. To study desmosomal networks, we reconstructed 852 muscle cells and their desmosomal partners by serial electron microscopy in an entire larva of the annelid Platynereis. Muscle cells adhere to each other, to epithelial, glial, ciliated, and bristle-producing cells and to the basal lamina, forming a desmosomal connectome of over 2,000 cells. The aciculae - chitin rods that form an endoskeleton in the segmental parapodia - are highly connected hubs in this network. This agrees with the many degrees of freedom of their movement, as revealed by video microscopy. Mapping motoneuron synapses to the desmosomal connectome highlighted the extent of tissue influenced by individual motoneuron classes. Our work shows how cellular-level maps of synaptic and adherent force networks can elucidate body mechanics.

category: animal behavior and cognition


title: Most primary olfactory neurons have individually neutral effects on behavior

abstract: Animals use olfactory receptors to navigate mates, food, and danger. However, for complex olfactory systems, it is unknown what proportion of primary olfactory sensory neurons can individually drive avoidance or attraction. Similarly, the rules that govern behavioral responses to receptor combinations are unclear. We used optogenetic analysis in Drosophila to map the behavior elicited by olfactory-receptor neuron (ORN) classes: just one-fifth of ORN-types drove either avoidance or attraction. Although wind and hunger are closely linked to olfaction, neither had much effect on single-class responses. Several pooling rules have been invoked to explain how ORN types combine their behavioral influences; we activated two-way combinations and compared patterns of single- and double-ORN responses: these comparisons were inconsistent with simple pooling. We infer that the majority of primary olfactory sensory neurons have neutral behavioral effects individually, but participate in broad, odor-elicited ensembles with potent behavioral effects arising from complex interactions.


title: Salvage of Ribose from Uridine or RNA Supports Glycolysis when Glucose is Limiting

abstract: Summary paragraphGlucose is vital for life, serving both as a source of energy and as a carbon building block for growth. When glucose availability is limiting, alternative nutrients must be harnessed. To identify mechanisms by which cells can tolerate complete loss of glucose, we performed nutrient-sensitized, genome-wide genetic screening and growth assays of 482 pooled PRISM cancer cell lines. We report that catabolism of uridine enables the growth of cells in the complete absence of glucose. While previous studies have shown that the uracil base of uridine can be salvaged to support growth in the setting of mitochondrial electron transport chain deficiency (1), our work shows that the ribose moiety of uridine can be salvaged via a pathway we call "uridinolysis" defined as: [1] the phosphorylytic cleavage of uridine by UPP1/2 into uracil and ribose-1-phosphate (R1P), [2] the conversion of R1P into fructose-6-P and glyceraldehyde-3-P by PGM2 and the non-oxidative branch of the pentose phosphate pathway (non-oxPPP), and [3] their glycolytic utilization to fuel ATP production, biosynthesis and gluconeogenesis. Intriguingly, we report that uridine nucleosides derived from RNA are also a substrate for uridinolysis and that RNA can support growth in glucose-limited conditions. Our results underscore the malleability of central carbon metabolism and raise the provocative hypothesis that RNA can also serve as a potential storage for energy.

category: biochemistry


title: High-throughput screening and selection of PCB-bioelectrocholeaching, electrogenic microbial communities using single chamber microbial fuel cells based on 96-well plate array.

abstract: We demonstrate a single chamber, 96-well plate based Microbial Fuel Cell (MFC). This invention is aimed at robust selection of electrogenic microbial community under specific conditions, (pH, external resistance, inoculum) that can be altered within the 96 well plate array. Using this device, we selected and multiplicated electrogenic microbial communities fed with acetate and lactate that can operate under different pH and produce current densities up to 19.4 A/m3 (0.6 A/m2) within 5 days past inoculation. Moreover, studies shown that Cu mobilization through PCB bioleaching occurred, thus each community was able to withstand presence of Cu2+ ions up to 600 mg/L. Metagenome analysis reveals high abundance of Dietzia spp., previously characterized in MFCs, but not reported to grow at pH 4, as well as novel species, closely related to Actinotalea ferrariae, not yet associated with electrogenicity. Microscopic observations (combined SEM and EDS) reveal that some of the species present in the anodic biofilm were adsorbing copper on their surface, probably due to the presence of metalloprotein complexes on their outer membranes. Taxonomy analysis indicated that similar consortia populate anodes, cathodes and OCP controls, although total abundances of aforementioned species are different among those groups. Annotated metagenomes showed high presence of multicopper oxidases and Cu-resistance genes, as well as genes encoding aliphatic and aromatic hydrocarbon-degrading enzymes. Comparison between annotated and binned metagenomes from pH 4 and 7 anodes, as well as their OCP controls revealed unique genes present in all of them, with majority of unique genes present in pH 7 anode, where novel Actinotalea spp. was present.

category: bioengineering


title: Inferring relevant tissues and cell types for complex traits in genome-wide association studies

abstract: More than a decade of genome-wide association studies (GWASs) have identified genetic risk variants that are significantly associated with complex traits. Emerging evidence suggests that the function of trait-associated variants likely acts in a tissue- or cell-type-specific fashion. Yet, it remains challenging to prioritize trait-relevant tissues or cell types to elucidate disease etiology. Here, we present EPIC (cEll tyPe enrIChment), a statistical framework that relates large-scale GWAS summary statistics to cell-type-specific gene expression measurements from single-cell RNA sequencing (scRNA-seq). We derive powerful gene-level test statistics for common and rare variants, separately and jointly, and adopt generalized least squares to prioritize trait-relevant cell types while accounting for the correlation structures both within and between genes. Using enrichment of loci associated with four lipid traits in the liver and enrichment of loci associated with three neurological disorders in the brain as ground truths, we show that EPIC outperforms existing methods. We apply our framework to multiple scRNA-seq datasets from different platforms and identify cell types underlying type 2 diabetes and schizophrenia. The enrichment is replicated using independent GWAS and scRNA-seq datasets and further validated using PubMed search and existing bulk case-control testing results.

category: bioinformatics


title: EPIC: inferring relevant cell types for complex traits by integrating genome-wide association studies and single-cell RNA sequencing


title: Functional annotation-driven unsupervised clustering of single-cell transcriptomes

abstract:
MotivationSingle-cell RNA sequencing (scRNA-seq) analysis reveals heterogeneity and dynamic cell transitions. However, conventional gene-based analyses require intensive manual curation to interpret the biological implications of computational results. Hence, a theory for efficiently annotating individual cells is necessary.

ResultsWe present ASURAT, a computational pipeline for simultaneously performing unsupervised clustering and functional annotation of disease, cell type, biological process, and signaling pathway activity for single-cell transcriptomic data, using correlation graph-based decomposition of genes based on database-derived functional terms. We validated the usability and clustering performance of ASURAT using scRNA-seq datasets for human peripheral blood mononuclear cells, which required fewer manual curations than existing methods. Moreover, we applied ASURAT to scRNA-seq and spatial transcriptome datasets for small cell lung cancer and pancreatic ductal adenocarcinoma, identifying previously overlooked subpopulations and differentially expressed genes. ASURAT is a powerful tool for dissecting cell subpopulations and improving biological interpretability of complex and noisy transcriptomic data.

AvailabilityA GPLv3-licensed implementation of ASURAT is on GitHub (https://github.com/keita-iida/ASURAT).


title: ASURAT: functional annotation-driven unsupervised clustering of single-cell transcriptomes


title: Gotree/Goalign : Toolkit and Go API to facilitate the development of phylogenetic workflows

abstract: Besides computer intensive steps, phylogenetic analysis workflows are usually composed of many small, reccuring, but important data manipulations steps. Among these, we can find file reformatting, sequence renaming, tree re-rooting, tree comparison, bootstrap support computation, etc. These are often performed by custom scripts or by several heterogeneous tools, which may be error prone, uneasy to maintain and produce results that are challenging to reproduce. For all these reasons, the development and reuse of phylogenetic workflows is often a complex task. We identified many operations that are part of most phylogenetic analyses, and implemented them in a toolkit called Gotree/Goalign. The Gotree/Goalign toolkit implements more than 120 user-friendly commands and an API dedicated to multiple sequence alignment and phylogenetic tree manipulations. It is developed in Go, which makes executables efficient, easily installable, integrable in workflow environments, and parallelizable when possible. This toolkit is freely available on most platforms (Linux, MacOS and Windows) and most architectures (amd64, i386). Sources and binaries are available on GitHub at https://github.com/evolbioinfo/gotree, Bioconda, and DockerHub.


title: VSTseed: periodic spaced seeds for reads with substitutions

abstract:
MotivationTechnical progress in computer hardware made it possible to access and process large amounts of data even on budget workstations. Therefore new or existing alignment algorithms may use large index files to increase performance. Spaced seeds with large weights reduce the number of possible locations of a read within a reference sequence. Optimal patterns for spaced seeds may guarantee to align reads even with several substitutions.

ResultsFor reads of 64-200 bp periodic spaced seeds of 32, 40, 48, 56, 64 weights are found that guarantee to locate all positions within a reference sequence for a specified number of point mutations. SIMD instructions to convert masked reads into 64, 80, 96, 112, 128-bit numbers are provided.

AvailabilityC codes to generate spaced seeds and find optimal SIMD instructions for them are freely available under MIT license at https://github.com/vtman/VSTseed


title: Thermodynamic genome-scale metabolic modeling of metallodrug resistance in colorectal cancer

abstract:
BackgroundMass spectrometry-based metabolomics approaches provide an immense opportunity to enhance our understanding of the mechanisms that underpin the cellular reprogramming of cancers. Accurate comparative metabolic profiling of heterogeneous conditions, however, is still a challenge.

MethodsMeasuring both intracellular and extracellular metabolite concentrations, we constrain four instances of a thermodynamic genome-scale metabolic model of the HCT116 colorectal carcinoma cell line to compare the metabolic flux profiles of cells that are either sensitive or resistant to ruthenium- or platinum-based treatments with BOLD-100/KP1339 and oxaliplatin, respectively.

ResultsNormalizing according to growth rate and normalizing resistant cells according to their respective sensitive controls, we are able to dissect metabolic responses specific to the drug and to the resistance states. We find the normalization steps to be crucial in the interpretation of the metabolomics data and show that the metabolic reprogramming in resistant cells is limited to a select number of pathways.

ConclusionsHere we elucidate the key importance of normalization steps in the interpretation of metabolomics data, allowing us to uncover drug-specific metabolic reprogramming during acquired metal-drug resistance.

category: cancer biology


title: Biological, Molecular And Phiysiological Characterization Of Four Soybean mosaic virus Isolates Present In Argentine Soybean Crops

abstract: Soybean mosaic virus (SMV) causes systemic infections in soybean plants, leading to chlorotic mosaic and producing significant yield losses. The virus is widely distributed in all soybean production areas in the world. In Argentina, three geographical isolates were identified: Marcos Juarez (MJ), Manfredi (M), and North Western Argentina (NOA), and another isolate named "Planta Vinosa" (PV), which causes severe necrosis symptoms in some cultivars. Here, the biological, molecular and physiological characterization of these isolates was performed for the first time. Three of the four isolates showed a low genetic divergence in the evaluated genes (P1, CI and CP). Although SMV-NOA and SMV-PV had high homology at the sequence level, they showed wide differences in pathogenicity, seed mottling and the ability of transmission by seeds or aphids, as well as in physiological effects. SMV-NOA caused early alterations (before symptom appearance, BS) in {Phi}PSII and MDA content in leaves with respect to the other isolates. After the appearance of macroscopic symptoms (late symptoms, LS), SMV-M caused a significant increase in the content of MDA, total soluble sugars, and starch with respect to the other isolates. Thus, early alterations of {Phi}PSII and soluble sugars might have an impact on late viral symptoms. Likewise, SMV-MJ developed more severe symptoms in the susceptible Davis cultivar than in DM 4800. Therefore, our results show differences in genome, biological properties and physiological effects among SMV isolates as well as different interactions of SMV-MJ with two soybean cultivars.

category: plant biology


title: Multiscale computer model of the spinal dorsal horn reveals changes in network processing associated with chronic pain

abstract:
Pain-related sensory input is processed in the spinal dorsal horn (SDH) before being relayed to the brain. That processing profoundly influences whether stimuli are correctly or incorrectly perceived as painful. Significant advances have been made in identifying the types of excitatory and inhibitory neurons that comprise the SDH, and there is some information about how neuron types are connected, but it remains unclear how the overall circuit processes sensory input or how that processing is disrupted under chronic pain conditions. To explore SDH function, we developed a computational model of the circuit that is tightly constrained by experimental data. Our model comprises conductance-based neuron models that reproduce the characteristic firing patterns of spinal neurons. Excitatory and inhibitory neuron populations, defined by their expression of genetic markers, spiking pattern, or morphology, were synaptically connected according to available qualitative data. Using a genetic algorithm, synaptic weights were tuned to reproduce projection neuron firing rates (model output) based on primary afferent firing rates (model input) across a range of mechanical stimulus intensities. Disparate synaptic weight combinations could produce equivalent circuit function, revealing degeneracy that may underlie heterogeneous responses of different circuits to perturbations or pathological insults. To validate our model, we verified that it responded to reduction of inhibition (i.e. disinhibition) and ablation of specific neuron types in a manner consistent with experiments. Thus validated, our model offers a valuable resource for interpreting experimental results and testing hypotheses in silico to plan experiments for examining normal and pathological SDH circuit function.

Significance StatementWe developed a multiscale computer model of the posterior part of spinal cord gray matter (spinal dorsal horn), involved in perception of touch and pain. The model reproduces several experimental observations and makes predictions about how specific types of spinal neurons and synapses influence projection neurons that send information to the brain. Misfiring of these projection neurons can produce anomalous sensations associated with chronic pain. Our computer model will not only assist in planning future experiments, but will also be useful for developing new pharmacotherapy for chronic pain disorders, connecting the effect of drugs acting at the molecular scale with emergent properties of neurons and circuits that shape the pain experience.

category: neuroscience


title: The hedgehog signaling pathway is expressed in the adult mouse hypothalamus and modulated by fasting

abstract:
The importance of the primary cilium was initially highlighted by the class of human genetic disorders known as ciliopathies. Patients with ciliopathies such as Bardet-Biedl and Alstrom syndrome exhibit hyperphagia-associated obesity as a core clinical phenotype. How primary cilia contribute to energy homeostasis and feeding behavior is complex and unclear, but cilia appear important in both developmental and homeostatic processes. Primary cilia are important signaling centers, required for hedgehog signaling and localization of specific G protein-coupled receptors (GPCRs) with known roles in feeding behavior in mammals. The hedgehog pathway is best known for its role in developmental patterning, but now has recognized roles in adult tissues as well. In the postnatal brain, cilia and hedgehog signaling are important for growth and maintenance of neural progenitors, however, the role of hedgehog signaling in the differentiated adult brain is less clear. Here, we provide a detailed analysis of the expression of core components of the hedgehog signaling pathway in the adult mouse hypothalamus with an emphasis on feeding centers. We show that hedgehog pathway genes continue to be expressed in differentiated neurons important for regulation of feeding behavior. Furthermore, we demonstrate for the first time that pathway activity is regulated at the transcriptional level by fasting. These data suggest that hedgehog signaling is involved in the proper functioning of brain regions which regulate feeding behavior and that hedgehog pathway dysfunction may play a role in the obesity observed in certain ciliopathies.

Significance StatementHere we investigate the expression of hedgehog pathway components in the adult mouse hypothalamus. Using dual labeling in situ hybridization we show that core components of the signaling pathway are expressed in multiple neuronal cell types within the hypothalamic feeding centers. Our findings also support previous findings that astrocytes are responsive to hedgehog signaling, as determined by Gli1 and Ptch1 expression. Using qPCR analysis, we show that hypothalamic hedgehog pathway activity is upregulated in response to fasting and this response is nuclei specific. These data not only provide a more detailed understanding of hedgehog pathway expression in the adult mouse hypothalamus but also provide direct evidence of a novel role for hedgehog signaling in the physiological response to fasting.


title: Remote cortical perturbation dynamically changes the network solutions 1 to given tactile inputs in neocortical neurons

abstract: The neocortex is a widely interconnected neuronal network. All such networks have a connectivity structure, which limits the possible combinations of neuronal activations across it. In this sense, the network can be said to contain solutions, i.e., for each given external input the cortex may yield a specific combination of neuronal activations/output. If the cortex has a variety of states, a given input could result in a range of possible outputs. There will also be a vast range of outputs that are not possible due to the network structure. Here we use intracellular recordings in SI neurons to show that remote intracortical electrical perturbation can impact such constraints on the responses to given tactile input patterns. Whereas each given tactile input pattern induced a wide set of preferred response states, when combined with cortical perturbation they induced response states that did not otherwise occur. The findings indicate that the physiological network structure can dynamically change as the state of any given cortical region changes, thereby enabling a very rich, multifactorial, perceptual capability.


title: Computational inference, validation, and analysis of 5'UTR-leader sequences of alleles of immunoglobulin heavy chain variable genes

abstract: Upstream and downstream sequences of immunoglobulin genes may affect the expression of such genes. However, these sequences are rarely studied or characterized in most studies of immunoglobulin repertoires. Inference from large, rearranged immunoglobulin transcriptome data sets offers an opportunity to define the upstream regions (5-untranslated regions and leader sequences). We have now established a new data pre-processing procedure to eliminate artifacts caused by a 5-RACE library generation process, reanalyzed a previously studied data set defining human immunoglobulin heavy chain genes, and identified novel upstream regions, as well as previously identified upstream regions that may have been identified in error. Upstream sequences were also identified for a set of previously uncharacterized germline gene alleles. Several novel upstream region variants were validated, for instance by their segregation to a single haplotype in heterozygotic subjects. SNPs representing several sequence variants were identified from population data. Finally, based on the outcomes of the analysis, we define a set of testable hypotheses with respect to the placement of particular alleles in complex IGHV locus haplotypes, and discuss the evolutionary relatedness of particular heavy chain variable genes based on sequences of their upstream regions.

category: immunology


title: Molecular dissection of pro-fibrotic signaling identifies the mechanism underlying IL11-driven fibrosis gene translation, reveals non-specific effects of STAT3 and suggests a new mechanism of action for nintedanib

abstract: In fibroblasts, TGF{beta}1 stimulates IL11 upregulation that leads to an autocrine loop of IL11-dependent pro-fibrotic protein translation. The signalling pathways downstream of IL11 are contentious and both STAT3 and ERK have been implicated. Here we show that TGF{beta}1- or IL11-induced ERK activation is consistently associated with fibrogenesis whereas STAT3 phosphorylation (pSTAT3) is unrelated to fibroblast activation. Surprisingly, recombinant human IL11, which has been used extensively in mouse experiments to infer STAT3 activity downstream of IL11, non-specifically increases pSTAT3 in Il11ra1 null mouse fibroblasts. Pharmacologic inhibition of STAT3 prevents TGF{beta}1-induced fibrogenesis but this effect was found to reflect fibroblast dysfunction due to severe proteotoxic ER stress. In contrast, inhibition of MEK/ERK prevented fibrosis in the absence of ER stress. TGF{beta}1-stimulated ERK/mTOR/P70RSK-driven protein translation was IL11-dependent and selectivity for pro-fibrotic protein synthesis was ascribed to an EPRS-related mechanism. In TGF{beta}1-stimulated fibroblasts, the anti-fibrotic drug nintedanib caused dose-dependent ER stress, reduced pSTAT/pERK and inhibited pro-fibrotic protein translation, similarly to generic STAT3 inhibitors or ER stressors. Pirfenidone, while anti-fibrotic, had no effect on ER stress whereas anti-IL11 inhibited the ERK/mTOR axis while reducing ER stress. These studies discount a specific role for STAT3 in pro-fibrotic signaling, suggest a novel mechanism of action for nintedanib and prioritise further the IL11 pathway as a therapeutic target for fibrosis.


title: Enhanced Immunoprecipitation Techniques for the Identification of RNA Binding Protein Partners: CRD-BP interactions in mammary epithelial cells

abstract: RNA binding proteins (RBPs) regulate expression of large cohorts of RNA species to affect programmatic changes in cellular phenotypes. In order to describe the function of RBPs within a cell, it is key to identify their mRNA binding partners. This is often done by cross-linking nucleic acids to RBPs, followed by chemical release of the nucleic acid fragments for analysis. However, this methodology is lengthy, involves complex processing leading to extraordinary losses, requires large amounts of starting materials, and is prone to artifacts due to the labile nature of mRNA. To evaluate potential alternative technologies, we tested "exclusion-based" purification of immunoprecipitates (oil-based IFAST or air-based SLIDE), and report here that these methods can efficiently, rapidly and specifically isolate RBP-RNA complexes with minimal handling. The analysis starts with >100x less material than for techniques that include cross-linking. Depending on the specific antibody used, 50-100% of starting protein is retrieved, allowing the assay of endogenous levels of RBP instead of tagged and over-expressed ectopic proteins. Isolated protein and nucleic acid components are purified and analyzed using standard techniques to provide a comprehensive portrait of RBP complexes. Using exclusion-based techniques, we show that the mRNA binding partners for CRD-BP/IMP1/IGF2BP1/ZBP1 in cultured mammary epithelial cells are enriched in mRNAs important for de-toxifying superoxides (glutathione metabolic enzymes) and other mRNAs encoding mitochondrial proteins.


title: Dimensional reduction of phenotypes from 53,000 mouse models reveals a diverse landscape of gene function

abstract: Animal models have long been used to study gene function and the impact of genetic mutations on phenotype. Through the research efforts of thousands of research groups, systematic curation of published literature, and high-throughput phenotyping screens, the collective body of knowledge for the mouse now covers the majority of protein-coding genes. We here collected data for over 53,000 mouse models with mutations in over 15,000 genomic markers and characterized by more than 254,000 annotations using more than 9,000 distinct ontology terms. We investigated dimensional reduction and embedding techniques as means to facilitate access to this diverse and high-dimensional information. Our analyses provide the first visual maps of the landscape of mouse phenotypic diversity. We also summarize some of the difficulties in producing and interpreting embeddings of sparse phenotypic data. In particular, we show that data preprocessing, filtering, and encoding have as much impact on the final embeddings as the process of dimensional reduction. Nonetheless, techniques developed in the context of dimensional reduction create opportunities for explorative analysis of this large pool of public data, including for searching for mouse models suited to study human diseases.


title: In silico study predicts a key role of RNA-binding domains 3 and 4 in nucleolin-miRNA interactions.

abstract:
RNA binding proteins (RBPs) regulate many important cellular processes through their interactions with RNA molecules. RBPs are critical for post-transcriptional mechanisms keeping gene regulation in a fine equilibrium. Conversely, dysregulation of RBPs and RNA metabolism pathways is an established hallmark of tumorigenesis. Human nucleolin (NCL) is a multifunctional RBP that interacts with different types of RNA molecules, in part through its four RNA binding domains (RBDs). Particularly, NCL interacts directly with microRNAs (miRNAs) and is involved in their aberrant processing linked with many cancers, including breast cancer. Nonetheless, molecular details of the NCL-miRNA interaction remain obscure. In this study, we used an in silico approach to characterize how NCL targets miRNAs and whether this specificity is imposed by a definite RBD-interface. Here, we present structural models of NCL-RBDs and miRNAs, as well as predict scenarios of NCL- miRNA interactions generated using docking algorithms. Our study suggests a predominant role of NCL RBDs 3 and 4 (RBD3-4) in miRNA binding. We provide detailed analyses of specific motifs/residues at the NCL- substrate interface in both these RBDs and miRNAs. Finally, we propose that the evolutionary emergence of more than two RBDs in NCL in higher organisms coincides with its additional role/s in miRNA processing. Our study shows that RBD3-4 display sequence/structural determinants to specifically recognize miRNA precursor molecules. Moreover, the insights from this study can ultimately support the design of novel antineoplastic drugs aimed at regulating NCL-dependent biological pathways with a causal role in tumorigenesis.

Importance/impact of the studyNucleolin is a multifunctional RNA binding protein that is often linked with many cancers. Similarly, microRNAs are often dysregulated in many cancers and linked to tumorigenesis. This study focuses on the interaction of nucleolin with microRNAs to identify previously unknown mechanistic details/specificity of these interactions. The insights from this study can ultimately support the design of novel drugs aimed at regulating NCL- dependent pathways implicated in tumorigenesis.


title: HAUSP Stabilizes SOX2 through Deubiquitination to Maintain Self-renewal and Tumorigenic Potential of Glioma Stem Cells

abstract:
Glioblastoma (GBM) is the most lethal brain tumor containing glioma stem cells (GSCs) that promote malignant growth and therapeutic resistance. The self-renewal and tumorigenic potential of GSCs are maintained by core stem cell transcription factors including SOX2. Defining the posttranslational regulation of SOX2 may offer new insights into GSC biology and potential therapeutic opportunity. Here, we discover that HAUSP stabilizes SOX2 through deubiquitination to maintain GSC self-renewal and tumorigenic potential. HAUSP is preferentially expressed in GSCs in perivascular niches in GBMs. Disrupting HAUSP by shRNA or its inhibitor P22077 promoted SOX2 degradation, induced GSC differentiation, impaired GSC tumorigenic potential, and suppressed GBM tumor growth. Importantly, pharmacological inhibition of HAUSP synergized with radiation to inhibit GBM growth and extended animal survival, indicating that targeting HAUSP may overcome GSC-mediated radioresistance. Our findings reveal an unappreciated crucial role of HAUSP in the GSC maintenance and provide a promising target for developing effective anti-GSC therapeutics to improve GBM treatment.

HighlightsO_LIHAUSP deubiquitinates and stabilizes SOX2 in glioma stem cells (GSCs).
C_LIO_LIHAUSP is preferentially expressed by GSCs in perivascular niches in GBMs.
C_LIO_LIHAUSP is required for maintaining GSC self-renewal and tumorigenic potential.
C_LIO_LITargeting HAUSP inhibited malignant growth in GSC-derived GBM xenografts.
C_LIO_LIInhibition of HAUSP synergized with radiation to suppress GBM tumor growth.
C_LI


title: Comprehensive profiling of liver x receptor splicing in triple negative breast cancer reveals existence of novel splice variants that are prognostic for survival

abstract:
The liver x receptors (LXR) alpha and beta are ligand-responsive transcription factors that link homeostatic control of lipid metabolism with cancer pathophysiology and prognosis. LXR activity is elevated in triple negative breast cancer relative to other breast cancer subtypes, driving gene signatures associated with drug resistance and metastasis. The loci encoding LXR and LXR{beta} produce multiple alternatively spliced proteins, but the true range of variants and their relevance to cancer remain poorly defined. Seven splice variants of LXR or LXR{beta} were detected. Three have not been recorded previously and five were prognostic. High expression of full length LXR was associated with shorter disease-free survival but splice variants harbouring truncations of the ligand binding domain were prognostic for improved survival. All LXR{beta} variants were associated with longer disease-free survival. Mechanistically, while full length LXR positively correlated with target gene expression in primary samples, LXR{beta} was inversely correlated. We conclude that canonical LXR function is an oncogenic driver of triple negative tumour pathophysiology that can be countered by high expression of truncated splice variants and/or full length LXR{beta}.

HighlightsO_LIExpression of full length LXR is associated with shorter disease-free survival of triple negative breast cancer patients
C_LIO_LIA systematic evaluation of cell lines and primary tumour samples indicates LXR splicing is extensive in breast cancer
C_LIO_LIConfirmation of three new LXR splice variants at transcript and protein level
C_LIO_LIExpression of full length LXR{beta} or LXR splice variants that harbour truncated ligand binding domains are associated with better prognosis
C_LIO_LIExpression of LXR target genes is positively correlated with LXR in relapsed patients and inversely correlated with LXR{beta} in survivors.
C_LI


title: Changes In Ploidy Affect Vascular Allometry And Hydraulic Function In Trees

abstract:
O_LIThe enucleated vascular elements of the xylem and the phloem offer an excellent system to test the effect of ploidy on plant function because variation in vascular geometry has a direct influence on transport efficiency. However, evaluations of conduit sizes in polyploid plants have remained elusive, most remarkably in woody species.
C_LIO_LIWe used a combination of molecular, physiological, and microscopy techniques to model the hydraulic resistance between source and sinks in tetraploid and diploid mango trees.
C_LIO_LITetraploids exhibited larger chloroplasts, mesophyll cells, and stomatal guard cells, resulting in higher leaf elastic modulus and lower dehydration rates despite the high water potentials of both ploidies in the field. Both the xylem and the phloem displayed a scaling of conduits with ploidy, revealing attenuated hydraulic resistance in tetraploids.
C_LIO_LIConspicuous wall hygroscopic moieties in the cells involved in processes of transpiration and transport advocates a role in volumetric adjustments due to turgor change in polyploids, which, together with the enlargement of organelles, cells, and tissues that are critical for water and photo assimilate transport at long distances, imply major physiological novelties of polyploidy.
C_LI


title: Readiness Potential Prevalence During A Deliberate Decision-making Task

abstract: This study investigated the hypothesis that neural markers associated with arbitrary decision-making are present in higher order, deliberate decisions. Furthermore, the study aimed to investigate the effect of higher order decision content on neurophysiological markers such as the readiness potential and the P300 potential. An experiment was designed to measure, evaluate, and compare these electroencephalographic potentials under both arbitrary and deliberate choice conditions. Participants were presented with legal cases and had to convict and acquit criminal offenders. Distinct readiness potentials and P300 potentials were observed for both arbitrary and deliberate decisions across all participants. These findings support the hypothesis that the readiness potential and the P300 potential are present in the neurophysiological data for higher order deliberate decisions. The study also showed initial findings of how the readiness potential may inherently relate to decision content. Increased readiness potential amplitudes were observed for participants with previous exposure to violent crime when they had to acquit or convict criminals accused of violent crimes.


title: Distributed and diverse hindbrain neuronal activity contributes to sensory processing and motor control in the Xenopus laevis tadpole

abstract: An animals survival depends heavily on the selection and execution of timely and well-coordinated motor responses. The brainstem controls the activity of spinal neural circuits to produce and modify movements. However, important questions remain unanswered about the origin of this descending control and how brainstem neuronal activity integrates sensory inputs and determines motor functions. Here, we record hindbrain extracellular activity in response to trunk skin stimulation, which in turn leads to fictive swimming in the hatchling Xenopus laevis tadpole. We identify four distinct classes of single unit activity, distributed along the hindbrain rostro-caudal axis, whose firing patterns correlate to distinct motor states. We observe different firing patterns in response to stimulation that leads to fictive swimming versus the application of a weak stimulus which does not evoke movement. We identify differences in the temporal activation of the four classes of hindbrain activity in relation to the initiation of fictive swimming. We propose a simple network encompassing the novel neuronal populations embedded within the currently known sensory pathway and central pattern generators of the tadpole brainstem. By identifying the contribution of the individual supraspinal neuronal populations we build a better understanding of how the brain controls and modulates movement.


title: Novel and highly distributed classes of hindbrain neuronal activity contribute to sensory processing and motor control in the Xenopus laevis tadpole.


title: Mapping RNA-binding proteins in human B cells and Tcells upon differentiation

abstract: B cells and T cells are key players in the defence against infections and malignancies. To exert their function, B cells and T cells differentiate into effector and memory cells. Tight regulation of these differentiation processes is key to prevent their malfunction, which can result in life-threatening disease. Lymphocyte differentiation relies on the appropriate timing and dosage of regulatory molecules, and post-transcriptional gene regulation (PTR) is a key player herein. PTR includes the regulation through RNA-binding proteins (RBPs), which control the fate of RNA and its translation into proteins. To date, a comprehensive RBP expression map throughout lymphocyte differentiation is lacking. Using transcriptome and proteome analyses, we here provide an RBP expression map for human B cells and T cells. We observed that even though the overall RBP expression is conserved, the relative RBP expression is distinct between B cells and T cells. Differentiation into effector and memory cells alters the RBP expression, resulting into preferential expression of different classes of RBPs. For instance, whereas naive T cells express high levels of translation-regulating RBPs, effector T cells preferentially express RBPs that modulate mRNA stability. Lastly, we found that cytotoxic CD8+ and CD4+ T cells express a common RBP repertoire. Combined, our study reveals a cell type-specific and differentiation-dependent RBP expression landscape in human lymphocytes, which will help unravel the role of RBPs in lymphocyte function.


title: Equine intestinal O-seroconverting temperate coliphage Hf4s: genomic and biological characterization

abstract:
Tailed bacteriophages constitute the bulk of the intestinal viromes of the vertebrate animals. However, the relationships between lytic and lysogenic lifestyles of the phages in these ecosystems are not always clear and may vary between the species or even between the individuals. The human intestinal (fecal) viromes are believed to be dominated by temperate phages, while in the horse feces the virulent phages are more prevalent. Almost all the isolates of horse fecal coliphages are virulent. Phage Hf4s is the first temperate equine intestinal coliphage characterized. It was isolated from the horse feces on the indigenous equine E. coli 4s strain. It is a podovirus, related to Lederbergvirus genus (including the well-characterized Salmonella phage P22). Hf4s recognizes the host O antigen as its primary receptor and possesses a functional O-antigen seroconversion cluster that renders the lysogens protected from the superinfection by the same phage and also abolishes the adsorption of some indigenous equine virulent coliphages, such as DT57C, while the other phages, such as G7C or phiKT retain the ability to infect E. coli 4s (Hf4s) lysogens.

ImportanceThe relationships between virulent and temperate bacteriophages and their impact on high-density symbiotic microbial ecosystems of the animal are not always clear and may vary between the species or even between the individuals. The horse intestinal virome is dominated by the virulent phages, and Hf4s is the first temperate equine intestinal coliphage characterized. It recognizes the host O antigen as its primary receptor and possesses a functional O-antigen seroconversion cluster that renders the lysogens protected from the superinfection by some indigenous equine virulent coliphages, such as DT57C, while the other phages, such as G7C or phiKT retain the ability to infect E. coli 4s (Hf4s) lysogens. microbial viruses in the mammal intestinal ecosystems.

category: microbiology


title: Notch pathway is required for protection against heat-stress in spermatogonial stem cells

abstract: Environmentally favorable conditions the sustainability of spermatogenesis is brought about by a balance between two types of division, the self-renewal division for the maintenance of the stem cell pool and the differentiation division for continuous production of spermatozoa. The production of gametes under unfavorable, stressful conditions can decrease or even be interrupted, compromising fertility parameters. Thus, the survival of spermatogonial stem cells (SSCs) is crucial for the recovery of spermatogenesis after stressful situations (e.g. high temperature). Here, we show that the Notch pathway protects the spermatogonial stem cells against thermal stress, ensuring reproductive success after normal conditions are restored. First, presenilin enhancer-2 (pen-2), the catalytic subunit of {gamma}-secretase complex, was localized in SSCs of the medaka testis. The exposure of adult males to thermal stress condition induced apoptosis in all spermatogenics cells, with the exception of SSCs. Concomitantly, the Notch pathways was up-regulated, including the pen-2, its ligands (dll4, jag1-2) and its receptors (notch1a-3); pen-2 expression was restricted to the SSCs during thermal stress. The importance of this pathway was further supported by an ex vivo approach, in which the inhibition of Notch activity induced a loss of SSCs. Overall, this study demonstrates that the Notch pathways activity is necessary for the protection of SSCs under chronic thermal stress.


title: AP-2α and AP-2β cooperatively function in the craniofacial surface ectoderm to regulate chromatin and gene expression dynamics during facial development.

abstract: The facial surface ectoderm is essential for normal development of the underlying cranial neural crest cell populations, providing signals that direct appropriate growth, patterning, and morphogenesis. Despite the importance of the ectoderm as a signaling center, the molecular cues and genetic programs implemented within this tissue are understudied. Here we show that removal of two members of the AP-2 transcription factor family, AP-2 and AP-2{beta}, within the early embryonic ectoderm leads to major alterations in the mouse craniofacial complex. Significantly, there are clefts in both the upper face and mandible, accompanied by fusion of the upper and lower jaws in the hinge region. Comparison of ATAC-seq and RNA-seq analyses between controls and mutants revealed significant changes in chromatin accessibility and gene expression centered on multiple AP-2 binding motifs associated with enhancer elements within these ectodermal lineages. In particular, loss of these AP-2 proteins affects both skin differentiation as well as multiple signaling pathways, most notably the WNT pathway. The role of reduced Wnt signaling throughput in the mutant phenotype was further confirmed using reporter assays and rescue experiments involving Wnt1 ligand overexpression. Collectively, these findings highlight a conserved ancestral function for AP-2 transcription factors in ectodermal development and signaling, and provide a framework from which to understand the gene regulatory network operating within this tissue that directs vertebrate craniofacial development.


title: A community-driven roadmap to advance research on translated open reading frames detected by Ribo-seq

abstract: Ribosome profiling (Ribo-seq) has catalyzed a paradigm shift in our understanding of the translational  vocabulary of the human genome, discovering thousands of translated open reading frames (ORFs) within long non-coding RNAs and presumed untranslated regions of protein-coding genes. However, reference gene annotation projects have been circumspect in their incorporation of these ORFs due to uncertainties about their experimental reproducibility and physiological roles. Yet, it is indisputable that certain Ribo-seq ORFs make stable proteins, others mediate gene regulation, and many have medical implications. Ultimately, the absence of standardized ORF annotation has created a circular problem: while Ribo-seq ORFs remain unannotated by reference biological databases, this lack of characterisation will thwart research efforts examining their roles. Here, we outline the initial stages of a community-led effort supported by GENCODE / Ensembl, HGNC and UniProt to produce a consolidated catalog of human Ribo-seq ORFs.


title: Dynamic urine proteome changes in a rat model of simvastatin-induced skeletal muscle injury.

abstract:
BackgroundStatin-associated muscle symptoms (SAMS) are the main side effects of statins. Currently, there are no effective biomarkers for accurate clinical diagnosis. Urine is not subject to homeostatic control and therefore accumulates early changes, making it an ideal biomarker source. We therefore examined urine proteome changes associated with SAMS in an animal model.

MethodsHere, we established a SAMS rat model by intragastric intubation with simvastatin (80 mg/kg). Biochemical analyses and hematoxylin and eosin (H&E) staining were used to evaluate the degree of muscle injury. The urine proteome on days 3, 6, 9 and 14 was profiled using liquid chromatography coupled with tandem mass spectrometry (LC-MS/MS) with the data-independent acquisition (DIA) method.

ResultsDifferential proteins on day 14 of SAMS were mainly associated with glycolysis/gluconeogenesis, pyruvate metabolism, metabolism of reactive oxygen species and apoptosis, all of which were reported to be associated with the pathological mechanism of SAMS. Among the 14 differentially expressed proteins on day 3, FIBG, OSTP and CRP were associated with muscle damage, while EHD1, CUBN and FINC were associated with the pathogenic mechanisms of SAMS. MYG and PRVA increased dramatically compared with CK elevation in serum on day 14 of SAMS.

ConclusionsOur preliminary results indicated that the urine proteome can reflect early changes in the SAMS rat model, providing the potential for monitoring drug side effects in future clinical research.


title: Discovering single-cell eQTLs from scRNA-seq data only

abstract: eQTL studies are essential for understanding genomic regulation. Effects of genetic variations on gene regulation are cell-type-specific and cellular-context-related, so studying eQTLs at a single-cell level is crucial. The ideal solution is to use both mutation and expression data from the same cells. However, current technology of such paired data in single cells is still immature. We present a new method, eQTLsingle, to discover eQTLs only with single cell RNA-seq (scRNA-seq) data, without genomic data. It detects mutations from scRNA-seq data and models gene expression of different genotypes with the zero-inflated negative binomial (ZINB) model to find associations between genotypes and phenotypes at single-cell level. On a glioblastoma and gliomasphere scRNA-seq dataset, eQTLsingle discovered hundreds of cell-type-specific tumor-related eQTLs, most of which cannot be found in bulk eQTL studies. Detailed analyses on examples of the discovered eQTLs revealed important underlying regulatory mechanisms. eQTLsingle is a unique powerful tool for utilizing the huge scRNA-seq resources for single-cell eQTL studies, and it is available for free academic use at https://github.com/horsedayday/eQTLsingle.


title: The dynamic properties of a nuclear coactivator binding domain are evolutionarily conserved

abstract: Evolution of proteins is constrained by their structure and function. While there is a consensus that the plasticity of intrinsically disordered proteins relaxes the structural constraints on evolution there is a paucity of data on the molecular details of these processes. The Nuclear co-activator binding domain (NCBD) from CREB-binding protein is a protein-protein interaction domain, which contains a hydrophobic core but is not behaving as a typical globular domain, and has been desribed as  molten-globule like. The highly dynamic properties of NCBD makes it an interesting model system for evolutionary structure-function investigation of intrinsically disordered proteins. We have here compared the structure and biophysical properties of an ancient version of NCBD present in a bilaterian animal ancestor living around 600 million years ago with extant human NCBD. Using a combination of NMR spectroscopy, circular dichroism and kinetic methods we show that although NCBD has increased its thermodynamic stability, it has retained its dynamic biophysical properties in the ligand-free state in the evolutionary lineage leading from the last common bilaterian ancestor to humans. Our findings suggest that the dynamic properties of NCBD have been maintained by purifying selection and thus are important for its function, which includes mediating several distinct protein-protein interactions.

category: biophysics


title: A chemical strategy toward novel brain-penetrant EZH2 inhibitors

abstract: Aberrant gene-silencing through dysregulation of polycomb protein activity has emerged as an important oncogenic mechanism in cancer, implicating polycomb proteins as important therapeutic targets. Recently, an inhibitor targeting EZH2, the methyltransferase component of PRC2, received FDA approval following promising clinical responses in cancer patients. However, the current array of EZH2 inhibitors have poor brain-penetrance limiting their use in patients with CNS malignancies, a number of which have been shown to be sensitive to EZH2 inhibition. To address this need, we have identified a chemical strategy, based on computational modeling of pyridone-containing EZH2 inhibitor scaffolds, to minimize P-glycoprotein activity and here we report the first brain-penetrant EZH2 inhibitor, TDI-6118 (compound 5). Additionally, in the course of our attempts to optimize this compound we discovered TDI-11904 (compound 21); a novel, highly-potent, and peripherally active EZH2 inhibitor based on a 7 member ring structure.


title: Rpi-amr3 confers resistance to multiple Phytophthora species by recognizing a conserved RXLR effector

abstract: Diverse pathogens from the genus Phytophthora cause disease and reduce yields in many crop plants. Although many Resistance to Phytophthora infestans (Rpi) genes effective against potato late blight have been cloned, few have been cloned against other Phytophthora species. Most Rpi genes encode nucleotide-binding domain, leucine-rich repeat-containing (NLR) proteins, that recognize RXLR effectors. However, whether NLR proteins can recognize RXLR effectors from multiple different Phytophthora pathogens has rarely been investigated. Here, we report the effector AVRamr3 from P. infestans that is recognized by Rpi-amr3 from S. americanum. We show here that AVRamr3 is broadly conserved in many different Phytophthora species, and that recognition of AVRamr3 homologs enables resistance against multiple Phytophthora pathogens, including P. parasitica and P. palmivora. Our findings suggest a novel path to identifying R genes against important plant pathogens.


title: Adaptive diversification in the cellular circadian behavior of Arabidopsis leaf- and root-derived cells

abstract: The plant circadian system is based on self-sustained cellular oscillations and is utilized to adapt to daily and seasonal environmental changes. The cellular circadian clocks in the above- and belowground plant organs are subjected to diverse local environments. Individual cellular clocks are affected by other cells/tissues in plants, and the intrinsic properties of cellular clocks remain to be elucidated. In this study, we showed the circadian properties of leaf- and root-derived cells of a CCA1::LUC Arabidopsis transgenic plant and demonstrated that the cells in total isolation from other cells harbor a genuine circadian clock. Quantitative and statistical analyses for individual cellular bioluminescence rhythms revealed a difference in amplitude and precision of light/dark entrainment between the two cell-types, suggesting that leaf-derived cells have a clock with a stronger persistence against fluctuating environments. Circadian systems in the leaves and roots are diversified to adapt to their local environments at the cellular level.


title: Variability in white matter structure relates to hallucination proneness

abstract: Hallucinations are a prominent transdiagnostic psychiatric symptom but are also prevalent in individuals who do not require clinical care. Moreover, persistent psychosis-like experience in otherwise healthy individuals may be related to increased risk to transition to a psychotic disorder. This suggests a common etiology across clinical and non-clinical individuals along a multidimensional psychosis continuum that may be detectable in structural variations of the brain. The current diffusion tensor imaging study assessed healthy individuals to identify possible differences in white matter associated with hallucination proneness (HP). This approach circumvents potential confounds related to medication, hospitalization, and disease progression common in clinical individuals. We determined how HP relates to white matter integrity in selected association, commissural, and projection fiber pathways putatively linked to psychosis. Increased HP was associated with enhanced fractional anisotropy (FA) in the right uncinate fasciculus, the right anterior and posterior arcuate fasciculus, and the corpus callosum. Although FA in cortico-cerebellar pathways revealed no relationship, streamline quantity between the left cerebellum and the right motor cortex positively correlated with HP. These findings support the notion of a psychosis continuum, providing first evidence of structural white matter variability associated with HP in healthy individuals. Furthermore, alterations in the targeted pathways likely indicate an association between HP-related structural variations and the putative salience and attention mechanisms that these pathways subserve.


title: Psychophysical evidence and perceptual observations show that object recognition is not hierarchical but is a parallel, simultaneous, egalitarian, non-computational system.

abstract: Object recognition models have at their core similar essential characteristics: feature extraction and hierarchical convergence leading to a code that is unique to each object and immune to variations in the object appearance. To compare computational, biologically-feasible models to human performance, subjects viewed objects displayed at a wide range of orientations and sizes, and were able to recognize them almost perfectly. These empirical results, together with consideration of thought experiments and analysis of everyday perceptual performance, lead to a conclusion that biologically-plausible object perception models do not even come close to matching our perceptual abilities. We can categorize many thousands of objects, discriminate between enormous numbers of different exemplars within each category, and recognize an object as unique although it may appear in countless variations[-]most of which have never been seen. This seemingly technical, quantitative failure stems from a fundamental property of our perception: the ability to perceive spatial information instantaneously and in parallel, retain details including their relative properties, and yet be able to integrate details into a meaningful percept such as an object. I present an alternative view of object perception whereby objects are represented by responses in primary visual cortex (V1) which is the only cortical area responding to small spatial elements. The rest of the visual cortex is dedicated to scene understanding and interpretation such as constructing 3D percepts from 2D inputs, coding motion, categorization and memories. Since our perception abilities cannot be explained by convergence to "object cells" or by interactions implemented by axonal transmissions, a parallel-to-parallel field-like process is suggested. In this view, spatial information is not modified by multiple neural interactions but is retained by affecting changes in a "neural field" which preserves the identity of individual elements while enabling a new holistic percept when these elements change.


title: The Consciousness Theories Studies (ConTraSt) database: analyzing and comparing empirical studies of consciousness theories

abstract: Understanding how consciousness arises from neural activity remains one of the biggest challenges for neuroscience. Numerous theories have been proposed in recent years, each gaining independent empirical support. Currently, there is no comprehensive, quantitative and theory-neutral overview of the field that enables an evaluation of how theoretical frameworks interact with empirical research. We provide a birds eye view on studies that interpreted their findings in light of at least one of four leading neuroscientific theories of consciousness (N=412 experiments), asking how methodological choices of the researchers might affect the final conclusions. We found that supporting a specific theory can be predicted solely from methodological choices, irrespective of findings. Furthermore, most studies interpret their findings post-hoc, rather than a-priori testing critical predictions of the theories. Our results highlight challenges for the field and provide researchers with a unique, open-access website to further analyze trends in the neuroscience of consciousness.


title: Detection of Xanthomonas translucens pv. undulosa from wheat by quantitative PCR

abstract: A probe-based quantitative PCR (qPCR) protocol was developed for detection and evaluation of the wheat bacterial leaf streak pathogen Xanthomonas translucens pv. undulosa (Xtu). The protocol can also detect X. translucens pv. translucens (Xtt), but cant differentiate the two pathovars. When tested on DNA from plant, non-target bacteria and culture of microorganisms from wheat seeds, the qPCR showed a high specificity. On purified Xtu DNA, the qPCR was more sensitive than a loop-mediated isothermal amplification (LAMP) assay. When DNA samples from a set of serial dilutions of Xtu cells were tested, the qPCR method could repeatedly generate quantification cycle (Cq) values from the dilutions containing [≥]1,000 cells. Since 2 {micro}L of the total of 50 {micro}L DNA was used in one reaction, one qPCR reaction could detect the presence of the bacteria in samples containing as few as 40 bacterial cells. The qPCR could detect the bacteria from both infected seed and leaf tissues. For seed testing, a protocol for template preparation was standardized, which allowed one qPCR reaction to test DNA from the surface of one seed. Thus, the qPCR system could theoretically detect Xtu and/or Xtt in samples where the bacteria had an average concentration [≥]40 cells per seed.


title: Fresh insights into Mediterranean biodiversity: Environmental DNA reveals spatio-temporal patterns of stream invertebrate communities on Sicily

abstract: The Mediterranean region with its islands is among top biodiversity hotspots. It houses numerous freshwater taxa with a high rate of endemism, but is heavily impacted by anthropogenic pressures and global climate change. To conserve biodiversity, reliable data on species and genetic diversity are needed especially for the scarcely known insular freshwater ecosystems. Environmental DNA metabarcoding provide a straight-forward opportunity to assess aquatic biodiversity. Therefore, we conducted the first eDNA metabarcoding study in one stream catchment on Sicily. Specifically, we aimed to i) investigate spatial diversity patterns of macroinvertebrate communities, ii) assess seasonal changes, and iii) check if dispersal barriers can be identified. Water samples were taken at 27 different sites in two seasons and eDNA metabarcoding performed using the COI gene. In total, we detected 98 macroinvertebrate species, including 28 taxa potentially new to Sicily. Exact sequence variant (ESV) and species composition data showed that diversity differed between seasons with less taxa detected in winter. We also detected a dispersal barrier, which had a stronger effect in autumn. Our findings show that eDNA metabarcoding provides valuable information on Sicilian freshwater biodiversity. We therefore encourage its application for understudied regions to better understand the state and dynamics of freshwater biodiversity.


title: Time-resolved secretome analysis of three Colletotrichum species identifies copper radical alcohol oxidases for the production of fatty aldehydes

abstract:
Copper Radical Alcohol Oxidases (CRO-AlcOx), which have been recently discovered among fungal phytopathogens are attractive for the production of fragrant fatty aldehydes. To investigate the secretion of CRO-AlcOx by natural fungal strains, we undertook time-course analyses of the secretomes of three Colletotrichum species (C. graminicola, C. tabacum and C. destructivum) using proteomics. The addition of a copper-manganese-ethanol mixture to Colletotrichum cultures unexpectedly induced the secretion of up to 400 proteins, 29-52% of which were carbohydrate-active enzymes (CAZymes), including a wide diversity of copper-containing oxidoreductases from the auxiliary activities (AA) class (AA1, AA3, AA5, AA7, AA9, AA11-AA13, AA16). Under these specific conditions, while a CRO-glyoxal oxidase from the AA5_1 subfamily was among the most abundantly secreted proteins, the targeted AA5_2 CRO-AlcOx were secreted at lower levels, suggesting heterologous expression as a more promising strategy for CRO-AlcOx production and utilization. C. tabacum and C. destructivum CRO-AlcOx were expressed in Pichia pastoris and their preference toward both aromatic and aliphatic primary alcohols was assessed. The CRO-AlcOx from C. destructivum was further investigated in applied settings, revealing a full conversion of C6 and C8 alcohols into their corresponding fragrant aldehydes.

IMPORTANCEIn the context of the industrial shift toward greener processes, the biocatalytic production of aldehydes is of utmost interest owing to their importance as intermediates in preparative chemistry and for their use as flavors and fragrances ingredients. In the search for new biocatalysts, CRO-AlcOx have the potential to become platform enzymes for the oxidation of alcohols to aldehydes. The use of crude fungal secretomes is often seen has an appealing approach by industries since alleviating various costs pertaining to biocatalysts production. However, the secretion of CRO-AlcOx by natural fungal strains has never been explored. This study showed that Colletotrichum species can secrete a broad diversity of copper-containing enzymes, but only little amount of CRO-AlcOx. Thus, recombinant expression remains the most promising approach. The potential of CRO-AlcOx as biocatalyst for flavor and fragrance applications was confirmed through the production of two new enzymes with activity on fatty alcohols.


title: Alzheimer's disease BIN1 coding variants increase intracellular Aβ by interfering with BACE1 recycling

abstract: Genetics identified BIN1 as the second most important risk locus associated with late-onset Alzheimers disease, after APOE4. Here we show the consequences of two coding variants in BIN1 (rs754834233 and rs138047593), both in terms of intracellular beta-amyloid accumulation (iAbeta) and early endosome enlargement, two interrelated early cytopathological Alzheimers disease phenotypes, supporting their association with LOAD risk. We previously found that Bin1 deficiency potentiates beta-amyloid production by decreasing BACE1 recycling and enlarging early endosomes. Here, we demonstrate that the expression of the two LOAD mutant forms of Bin1 did not rescue the iAbeta accumulation and early endosome enlargement induced by Bin1 knockdown and recovered by wild-type Bin1. The LOAD coding variants reduced Bin1 interaction with BACE1 likely causing a dominant-negative effect since Bin1 mutants, but not wild-type Bin1, overexpression increased iAbeta42 due to defective BACE1 recycling and accumulation in early endosomes. Endocytic recycling of transferrin was similarly affected by Bin1 wild-type and mutants, indicating that Bin1 is a general regulator of endocytic recycling. These data show that the LOAD mutations in Bin1 lead to a loss of function, suggesting that endocytic recycling defects are an early causal mechanism of Alzheimers disease.


title: Associative learning drives longitudinally-graded presynaptic plasticity of neurotransmitter release along axonal compartments

abstract: Anatomical and physiological compartmentalization of neurons is a mechanism to increase the computational capacity of a circuit, and a major question is what role axonal compartmentalization plays. Axonal compartmentalization may enable localized, presynaptic plasticity to alter neuronal output in a flexible, experience-dependent manner. Here we show that olfactory learning generates compartmentalized, bidirectional plasticity of acetylcholine release that varies across the longitudinal compartments of Drosophila mushroom body (MB) axons. The directionality of the learning-induced plasticity depends on the valence of the learning event (aversive vs. appetitive), varies linearly across proximal to distal compartments following appetitive conditioning, and correlates with learning-induced changes in downstream mushroom body output neurons (MBONs) that modulate behavioral action selection. Potentiation of acetylcholine release was dependent on the CaV2.1 calcium channel subunit cacophony. In addition, contrast between the positive conditioned stimulus and other odors required the inositol triphosphate receptor (IP3R), which was required to maintain responsivity to odors in untrained conditions. Downstream from the mushroom body, a set of MBONs that receive their input from the {gamma}3 MB compartment were required for normal appetitive learning, suggesting that they represent a key node through which discriminative effects influence appetitive memory and decision-making. These data demonstrate that learning drives valence-correlated, compartmentalized, bidirectional potentiation and depression of synaptic neurotransmitter release, which rely on distinct mechanisms and are distributed across axonal compartments in a learning circuit.


title: Meditation-induced effects on whole-brain structural and effective connectivity

abstract: In the past decades, there has been a growing scientific interest in characterizing neural correlates of meditation training. Nonetheless, the mechanisms underlying meditation remain elusive. In the present work, we investigated meditation-related changes in structural and functional connectivities (SC and FC, respectively). For this purpose, we scanned experienced meditators and control (naive) subjects using magnetic resonance imaging (MRI) to acquire structural and functional data during two conditions, resting-state and meditation (focused attention on breathing). In this way, we aimed to characterize and distinguish both short-term and long-term modifications in the brains structure and function. First, we performed a network-based analysis of anatomical connectivity. Then, to analyze the fMRI data, we calculated whole-brain effective connectivity (EC) estimates, relying on a dynamical network model to replicate BOLD signals spatio-temporal structure, akin to FC with lagged correlations. We compared the estimated EC, FC, and SC links as features to train classifiers to predict behavioral conditions and group identity. The whole-brain SC analysis revealed strengthened anatomical connectivity across large-scale networks for meditators compared to controls. We found that differences in SC were reflected in the functional domain as well. We demonstrated through a machine-learning approach that EC features were more informative than FC and SC solely. Using EC features we reached high performance for the condition-based classification within each group and moderately high accuracies when comparing the two groups in each condition. Moreover, we showed that the most informative EC links that discriminated between meditators and controls involved the same large-scale networks previously found to have increased anatomical connectivity. Overall, the results of our whole-brain model-based approach revealed a mechanism underlying meditation by providing causal relationships at the structure-function level.


title: Identification of novel human derived influenza viruses in pigs with zoonotic potential.

abstract: In 2009, a novel swine influenza A virus (IAV) emerged causing a global pandemic that highlighted the role of swine as a reservoir. To date, there is limited information about swine IAV circulating in Latin America. We identified two swine H1N2 and one divergent swine H3N2 viruses that co-circulated in Chilean swine together with the 2009 H1N1 pandemic strain (A(H1N1)pdm09). Phylogenetic analysis revealed several human-to-swine IAV introductions occurring as early as the mid-1980s, and since 2009, several introductions of the A(H1N1)pdm09 strain. Antigenic cartography confirmed that these viruses were antigenically unique and identified drifted variants within the clusters. Human sera from the Chilean general population showed an age dependent mid to low-level antibody mediated protection against swine H1N2 and A(H1N1)pdm09-like viruses and a poor protection against the swine H3N2 virus, highlighting the zoonotic potential of this strain. Our results underscore the epidemiological importance of studying swine IAV in Latin America for epidemic and pandemic preparedness.


title: Aspergillus fumigatus acetate utilisation impacts virulence traits and pathogenicity

abstract:
Aspergillus fumigatus is a major opportunistic fungal pathogen of immunocompromised and immunocompetent hosts. To successfully establish an infection, A. fumigatus needs to use host carbon sources, such as acetate, present in the body fluids and peripheral tissues. However, utilisation of acetate as a carbon source by fungi in the context of infection has not been investigated. This work shows that acetate is metabolised via different pathways in A. fumigatus and that acetate utilisation is under the regulatory control of a transcription factor (TF), FacB. A. fumigatus acetate utilisation is subject to carbon catabolite repression (CCR), although this is only partially dependent on the TF and main regulator of CCR CreA. The available extracellular carbon source, in this case glucose and acetate, significantly affected A. fumigatus virulence traits such as secondary metabolite secretion and cell wall composition, with the latter having consequences for resistance to oxidative stress, to anti-fungal drugs and to human neutrophil-mediated killing. Furthermore, deletion of facB significantly impaired the in vivo virulence of A. fumigatus in both insect and mammalian models of invasive aspergillosis. This is the first report on acetate utilisation in A. fumigatus and this work further highlights the importance of available host-specific carbon sources in shaping fungal virulence traits and subsequent disease outcome, and a potential target for the development of anti-fungal strategies.

ImportanceAspergillus fumigatus is an opportunistic fungal pathogen in humans. During infection, A. fumigatus is predicted to use host carbon sources, such as acetate, present in body fluids and peripheral tissues, to sustain growth and promote colonisation and invasion. This work shows that A. fumigatus metabolises acetate via different pathways, a process that is dependent on the transcription factor FacB. Furthermore, the type and concentration of the extracellular available carbon source were determined to shape A. fumigatus virulence determinants such as secondary metabolite secretion and cell wall composition. Subsequently, interactions with immune cells are altered in a carbon source-specific manner. FacB is required for A. fumigatus in vivo virulence in both insect and mammalian models of invasive aspergillosis. This is the first report that characterises acetate utilisation in A. fumigatus and highlights the importance of available host-specific carbon sources in shaping virulence traits and potentially subsequent disease outcome.


title: ZFC3H1 and U1-70K promote the nuclear retention of mRNAs with 5' splice site motif within nuclear speckles

abstract: Quality control of mRNA represents an important regulatory mechanism for gene expression in eukaryotes. One component of this quality control is the nuclear retention and decay of misprocessed RNAs. Previously, we demonstrated that mature mRNAs containing a 5 splice site (5SS) motif, which is typically found in misprocessed RNAs such as intronic polyadenylated (IPA) transcripts, are nuclear retained and degraded. Here we demonstrate that these transcripts require the zinc finger protein ZFC3H1 for their decay and nuclear retention into nuclear speckles. Furthermore, we find that U1-70K, a component of the U1 snRNP spliceosomal complex, is also required for their nuclear retention and likely functions in the same pathway as ZFC3H1. Finally, we show that the disassembly of nuclear speckles impairs the nuclear retention of mRNAs with 5SS motifs. Together, our results suggest a model where mRNAs with 5SS motifs are recognized by U1 snRNP, which then acts with ZFC3H1 to both promote their decay and prevent nuclear export of these mRNAs by sequestering them in nuclear speckles. Our results highlight a splicing independent role of U1 snRNP and indicate that it works in conjunction with ZFC3H1 in preventing the nuclear export of misprocessed mRNAs.


title: Role of distinct fibroblast lineages and immune cells in dermal repair following UV radiation induced tissue damage

abstract:
Solar ultraviolet radiation (UVR) is a major source of skin damage, resulting in inflammation, premature ageing and cancer. While several UVR-induced changes, including extracellular matrix reorganisation and epidermal DNA damage, have been documented, the role of different fibroblast lineages and their communication with immune cells has not been explored. We show that acute and chronic UVR exposure led to selective loss of fibroblasts from the upper dermis in human and mouse skin. Lineage tracing and in vivo live imaging revealed that repair following acute UVR is predominantly mediated by papillary fibroblast proliferation and migration. In contrast, chronic UVR exposure led to a permanent loss of papillary fibroblasts, with expansion of fibroblast membrane protrusions partially compensating for the reduction in cell number. Although UVR strongly activated Wnt-signalling in skin, stimulation of fibroblast proliferation by epidermal {beta}-catenin stabilisation did not support papillary dermis repair. Acute UVR triggered an infiltrate of neutrophils and T cell subpopulations and increased pro-inflammatory prostaglandin signalling in skin. Depletion of CD4 and CD8 positive cells resulted in increased papillary fibroblast depletion, which correlated with an increase in DNA damage and reduction in fibroblast proliferation. Conversely, topical COX-2 inhibition prevented fibroblast depletion and neutrophil infiltration after UVR. We conclude that loss of papillary fibroblasts is primarily induced by a deregulated inflammatory response, with infiltrating T cells supporting fibroblast survival upon UVR-induced environmental stress.

Graphical abstract

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