title: Dietary habits of free-ranging banded langur (Presbytis femoralis) in a secondary-human modified forest in Johor, Malaysia

abstract: Banded langurs, Presbytis femoralis, are distributed in southern Peninsular Malaysia, i.e., Johor and its borders including Singapore. It has been estimated that there are only < 250 mature individuals of P. femoralis in Malaysia and Singapore, and it is currently assessed as Critically Endangered. The dietary information of P. femoralis and even other closely related species has rarely been reported. This study, therefore, aimed to describe their dietary habits and discuss interaction between their feeding behaviour and its surrounding. This study was conducted from February to November 2018, with 15 sampling days each month. We collected a total of 186 sighting hours, using a scan sampling method with 10-min intervals, on a five-langur focal group. We have identified 29 species with 47 items consumed by the banded langur, mostly young leaves (51 %) followed by fruits (45 %), and flowers (3.8 %). The study group spent slightly more time consuming non-cultivated plants but relied on cultivated plants for the fruits. Over 75% of fruit feeding involved consuming cultivar plants; in most cases (73%), they ate only the pulp, not the seeds. Since the cultivated plants was planted in human settlement, there is an urgent need to implement conservation measures to untangle the human-langur conflicts for instance, reforestation of a buffer region using non-cultivated plants. There is a potential for building upon our new findings with more detailed investigations, such as more extensive ecological factors influencing the dietary adaptation which would be necessary to support conservation efforts and management decisions of this species.

category: ecology


title: Microglia perform local protein synthesis at perisynaptic and phagocytic structures

abstract: Recent studies have illuminated the importance of several key signaling pathways in regulating the dynamic surveillance and phagocytic activity of microglia. Yet little is known about how these signals result in the assembly of phagolysosomal machinery near targets of phagocytosis, especially in processes distal from the microglial soma. Neurons, astrocytes, and oligodendrocytes locally regulate protein translation within distal processes. Therefore, we tested whether there is regulated local translation within peripheral microglia processes (PeMPs). We show that PeMPs contain ribosomes which engage in de novo protein synthesis, and these associate with a subpool of transcripts involved in pathogen defense, motility, and phagocytosis. Using a live slice preparation, we further show that acute translation blockade impairs the formation of PeMP phagocytic cups, the localization of lysosomal proteins within them, and phagocytosis. Collectively, these data argue for a regulated local translation in PeMPs and indicate a need for new translation to support dynamic microglial function.

category: neuroscience


title: RBCeq: An Integrated Bioinformatics Algorithm Designed to Improve Blood Type Compatibility Testing

abstract: While blood transfusion is an essential cornerstone of hematological care, patients that require repetitive transfusion remain at persistent risk of alloimmunization due to the diversity of human blood group polymorphisms. Next-generation sequencing (NGS) is an effective means of identifying genotypic and phenotypic variations among the blood groups, while the accurate interpretation of such NGS data is currently hampered by a lack of accessibility to bioinformatics support. To address this unmet need, we have developed the RBCeq (https://www.rbceq.org/) platform, which consists of a novel bioinformatics algorithm coupled with a user-friendly web server capable of comprehensively delineating different blood group variants from genomics data with advanced visualization of results. The software profiles genomic data for 36 blood group systems, including two transcription factors and can identify small genetic alterations, including small indels and copy number variants. The RBCeq algorithm was validated on 403 samples which include 58 complex serology cases from Australian Red Cross LifeBlood, 100 samples from The MedSeq Project (phs000958) and a further 245 from Indigenous Australian participants. The final blood typing data from RBCeq was 99.83% concordant for 403 samples (85 different antigens in 21 blood group systems) with that listed from the International Society for Blood Transfusion database.

category: bioinformatics


title: Learning interpretable cellular and gene signature embeddings from single-cell transcriptomic data

abstract: The advent of single-cell RNA sequencing (scRNA-seq) technologies has revolutionized transcriptomic studies. However, large-scale integrative analysis of scRNA-seq data remains a challenge largely due to unwanted batch effects and the limited transferabilty, interpretability, and scalability of the existing computational methods. We present single-cell Embedded Topic Model (scETM). Our key contribution is the utilization of a transferable neural-network-based encoder while having an interpretable linear decoder via a matrix tri-factorization. In particular, scETM simultaneously learns an encoder network to infer cell type mixture and a set of highly interpretable gene embeddings, topic embeddings, and batch effect linear intercepts from multiple scRNA-seq datasets. scETM is scalable to over 106 cells and confers remarkable cross-tissue and cross-species zero-shot transfer-learning performance. Using gene set enrichment analysis, we find that scETM-learned topics are enriched in biologically meaningful and disease-related pathways. Lastly, scETM enables the incorporation of known gene sets into the gene embeddings, thereby directly learning the associations between pathways and topics via the topic embeddings.


title: A touch of hierarchy. Population Receptive Fields reveal fingertip integration in Brodmann areas in human primary somatosensory cortex.

abstract: Several neuroimaging studies have shown the somatotopy of body part representations in primary somatosensory cortex (S1), but the functional hierarchy of distinct subregions in human S1 has not been adequately addressed. The current study investigates the functional hierarchy of cyto-architectonically distinct regions, Brodmann areas BA3, BA1, and BA2, in human S1. During functional MRI experiments, we presented participants with vibrotactile stimulation of the fingertips at 3 different vibration frequencies. Using population Receptive Field (pRF) modeling of the fMRI BOLD activity, we identified the hand region in S1 and the somatotopy of the fingertips. For each voxel, the pRF center indicates the finger that most effectively drives the BOLD signal, and the pRF size measures the spatial somatic pooling of fingertips. We find a systematic relationship of pRF sizes from lower-order areas to higher-order areas. Specifically, we found that pRF sizes are smallest in BA3, increase slightly towards BA1, and are largest in BA2, paralleling the increase in visual receptive field size as one ascends the visual hierarchy. Additionally, we find that the time-to-peak of the hemodynamic response in BA3 is roughly 0.5s earlier compared to BA1 and BA2, further supporting the notion of a functional hierarchy of subregions in S1. These results were obtained during stimulation of different mechanoreceptors, suggesting that different afferent fibers leading up to S1 feed into the same cortical hierarchy.


title: Lifecycle dominates the volatilome character of the dimorphic fungus Coccidioides spp.

abstract:
Valley fever (coccidioidomycosis) is an endemic fungal pneumonia of the North and South American deserts. The causative agents of Valley fever are the dimorphic fungi Coccidioides immitis and C. posadasii, which grow as mycelia in the environment and spherules within the lungs of vulnerable hosts. The current diagnostics for Valley fever are severely lacking due to poor sensitivity and invasiveness, contributing to a 23-day median time-to-diagnosis, and therefore new diagnostic tools are needed. We are working toward the development of a breath-based diagnostic for coccidioidomycosis, and in this initial study we characterized the volatile metabolomes (or volatilomes) of in vitro cultures of Coccidioides. Using solid-phase microextraction and comprehensive two-dimensional gas chromatography coupled to time-of-flight mass spectrometry (GCxGC-TOFMS), we characterized the VOCs produced by six strains of each species during mycelial or spherule growth. We detected a total of 353 VOCs that were at least two-fold more abundant in a Coccidioides culture versus medium controls and found the volatile metabolome of Coccidioides is more dependent on growth phase (spherule versus mycelia) than on the species. The volatile profiles of C. immitis and C. posadasii have strong similarities, indicating that a single suite of Valley fever breath biomarkers can be developed to detect both species.

IMPORTANCECoccidioidomycosis, or Valley fever, causes up to 30% of community-acquired pneumonias in endemic and highly populated areas of the US desert southwest. The infection is difficult to diagnose by standard serological and histopathological methods, which delays an appropriate treatment. Therefore, we are working toward the development of breath-based diagnostics for Valley fever. In this study, we characterized the volatile metabolomes of six strains each of Coccidioides immitis and C. posadasii, the dimorphic fungal species that cause Valley fever. By analyzing the volatilomes during the two modes of growth for the fungus--mycelia and spherules--we observed that the lifecycle plays a significant role in the volatiles produced by Coccidioides. In contrast, we observed no significant differences in the C. immitis versus C. posadasii volatilomes. These data suggest that lifecycle, rather than species, should guide the selection of putative biomarkers for a Valley fever breath test.

category: microbiology


title: Conditional deletion of HIF-1α provides new insight regarding the murine response to gastrointestinal infection with Salmonella Typhimurium

abstract: The hypoxia-inducible transcription factor 1 (HIF-1) has been shown to ameliorate different bacterial infections through enhancement of microbial killing. While the impact of HIF-1 on inflammatory diseases of the gut has been studied intensively, its function in bacterial infections of the intestine remains largely elusive. With the help of a publicly available gene expression data set, we could infer significant activation of the HIF-1 transcription factor after oral infection of mice with Salmonella Typhimurium. This prompted us to apply lineage-restricted deletion of the Hif1a locus in mice to examine cell type-specific functions of HIF-1 in this model. We show hypoxia-independent induction of HIF-1 activity upon Salmonella infection in the intestinal epithelium as well as in macrophages. Surprisingly, Hif1a deletion in intestinal epithelial cells impacted neither disease outcome nor inflammatory activity. The conditional knockout of Hif1a in myeloid cells enhanced the mRNA expression of the largely pro-inflammatory chemokine Cxcl2, revealing a potentially inflammatory effect of HIF-1 deficiency in myeloid cells in the gut in vivo. Again, the disease outcome was not affected. In vitro HIF-1-deficient macrophages showed an overall impaired transcription of pro-inflammatory factors, however, Salmonella bypassed direct intracellular, bactericidal HIF-1-dependent mechanisms in a Salmonella pathogenicity island (SPI)-2 independent manner. Taken together, our data suggest that HIF-1 in intestinal epithelial and myeloid cells is either dispensable or compensable in the immune defense against Salmonella Typhimurium.


title: Minimal genetically encoded tags for fluorescent protein labeling in living neurons

abstract: Modern light microscopy, including super-resolution techniques, brought about a demand for small labeling tags that bring the fluorophore closer to the target. This challenge can be addressed by labeling unnatural amino acids (UAAs) with click chemistry. UAAs are site-specifically incorporated into a protein of interest by genetic code expansion. If the UAA carries a strained alkene or alkyne moiety it can be conjugated to a tetrazine-bearing fluorophore via a strain-promoted inverse-electron-demand Diels-Alder cycloaddition (SPIEDAC), a variant of bioorthogonal click chemistry. The minimal size of the incorporated tag and the possibility to couple the fluorophores directly to the protein of interest with single-residue precision make SPIEDAC live-cell labeling unique. However, until now, this type of labeling has not been used in complex, non-dividing cells, such as neurons. Using neurofilament light chain as a target protein, we established SPIEDAC labeling in living primary neurons and applied it for fixed-cell, live-cell, dual-color pulse--chase and super-resolution microscopy. We also show that SPIEDAC labeling can be combined with CRISPR/Cas9 genome engineering for tagging endogenous NFL. Due to its versatile nature and compatibility with advanced microscopy techniques, we anticipate that SPIEDAC labeling will contribute to novel discoveries in neurobiology.


title: Locally confined IFNγ production by CD4+ T cells provides niches for murine cytomegalovirus replication in the salivary gland

abstract: Cytomegalovirus (CMV) has evolved a unique virus-host relationship in the salivary glands (SGs) to sustain prolonged viral replication and hence chances for horizontal transmission. Previous reports have established a decisive role for IFN{gamma} producing CD4+ T cells to control murine CMV (MCMV) infection in the SGs; however, micro-anatomical information regarding their mode of action is largely missing. Here, we provide a spatiotemporal analysis of defined antiviral immune actions that eventually culminate in control of lytic MCMV replication in this preferred mucosal niche. CXCR3-mediated guidance of CD4+ T cells towards CXCL9 and CXCL10 expressing cells resulted in discrete clusters close to infection foci where they reported TCR engagement and produced IFN{gamma}. Of note, these clusters occasionally contained CD11c+ antigen-presenting cells with engulfed virus-associated remnants, most likely apoptotic bodies derived from previously infected cells, enabling antigen presentation to CD4+ T cells. The induced IFN{gamma} production within these CD4+ T cell accumulations triggered IFN{gamma}R signaling in a confined perimeter, thereby inducing local, but not organ-wide protection, and allowing MCMV replication to continue at not yet protected sites. Combining experimental data with a mathematical model of the spatiotemporal dynamics of infection and CD4+ T cell dynamics revealed a scenario, in which ultimate MCMV control is achieved through accumulating sites of regionally-confined tissue protection.

category: immunology


title: Cost efficiency of institutional incentives in finite populations

abstract:
Institutions can provide incentives to increase cooperation behaviour in a population where this behaviour is infrequent. This process is costly, and it is thus important to optimize the overall spending. This problem can be mathematically formulated as a multi-objective optimization problem where one wishes to minimize the cost of providing incentives while ensuring a desired level of cooperation within the population. In this paper, we provide a rigorous analysis for this problem. We study cooperation dilemmas in both the pairwise (the Donation game) and multi-player (the Public Goods game) settings. We prove the regularity of the (total incentive) cost function, characterize its asymptotic limits (infinite population, weak selection and large selection) and show exactly when reward or punishment is more efficient. We prove that the cost function exhibits a phase transition phenomena when the intensity of selection varies. We calculate the critical threshold in regards to the phase transition and study the optimization problem when the intensity of selection is under and above the critical value. It allows us to provide an exact calculation for the optimal cost of incentive, for a given intensity of selection. Finally, we provide numerical simulations to demonstrate the analytical results. Overall, our analysis provides for the first time a selection-dependent calculation of the optimal cost of institutional incentives (for both reward and punishment) that guarantees a minimum amount of cooperation. It is of crucial importance for real-world applications of institutional incentives since intensity of selection is specific to a given population and the underlying game payoff structure.

In this Supplementary Information, we provide detailed calculations and proofs as well as illustrative figures for the analytical results in the main text of the present paper.

category: evolutionary biology


title: Lower statistical support with larger datasets: insights from the Ochrophyta radiation

abstract: It is commonly assumed that increasing the number of characters has the potential to resolving radiations. We studied photosynthetic stramenopiles (Ochrophyta) using alignments of heterogeneous size and origin (6,762 sites for mitochondrion, 21,692 sites for plastid and 209,105 sites for nucleus). While statistical support for the relationships between the six major Ochrophyta lineages increases when comparing the mitochondrion and plastid trees, it decreases in the nuclear tree. Statistical support is not simply related to the dataset size but also to the quantity of phylogenetic signal available at each position and our ability to extract it. Here, we show that proper signal extraction is difficult to attain, as demonstrated by conflicting results obtained when varying taxon sampling. Even though the use of a better fitting model improved signal extraction and reduced the observed conflicts, the plastid dataset provided higher statistical support for the ochrophyte radiation than the larger nucleus dataset. We propose that the higher support observed in the plastid tree is due to an acceleration of the evolutionary rate in one short deep internal branch, implying that more phylogenetic signal per position is available to resolve the Ochrophyta radiation in the plastid than in the nuclear dataset. Our work therefore suggests that, in order to resolve radiations, beyond the obvious use of datasets with more positions, we need to continue developing models of sequence evolution that better extract the phylogenetic signal and design methods to search for genes/characters that contain more signal specifically for short internal branches.


title: De novo assembly, annotation, and comparative analysis of 26 diverse maize genomes

abstract:
We report de novo genome assemblies, transcriptomes, annotations, and methylomes for the 26 inbreds that serve as the founders for the maize nested association mapping population. The data indicate that the number of pan-genes exceeds 103,000 and that the ancient tetraploid character of maize continues to degrade by fractionation to the present day. Excellent contiguity over repeat arrays and complete annotation of centromeres further reveal the locations and internal structures of major cytological landmarks. We show that combining structural variation with SNPs can improve the power of quantitative mapping studies. Finally, we document variation at the level of DNA methylation, and demonstrate that unmethylated regions are enriched for cis-regulatory elements that overlap QTL and contribute to changes in gene expression.

One sentence summaryA multi-genome analysis of maize reveals previously unknown variation in gene content, genome structure, and methylation.

category: genomics


title: A sexual dimorphic role of the miR-465 cluster in placental development

abstract: A sexually dimorphic role of miRNAs in placental development has never been reported. Here, we show that ablation of the miR-465 cluster caused selective degeneration of female conceptuses as early as embryonic day (E)8.5, leading to a male-biased sex ratio (60% males) among miR-465 KO mice. Given that the miR-465 cluster miRNAs were predominantly expressed in the extraembryonic tissue and ablation of these miRNAs led to dysregulation of numerous critical placental genes, our data strongly suggest the miR-465 cluster is required for full developmental potential of the female, but not the male, extraembryonic tissue/placenta.

category: developmental biology


title: Using zebrafish to elucidate glial-vascular interactions during CNS development

abstract: An emerging area of interest in Neuroscience is the cellular relationship between glia and blood vessels, as many of the presumptive support roles of glia require an association with the vasculature. These interactions are best studied in vivo and great strides have been made using mice to longitudinally image glial-vascular interactions. However, these methods are cumbersome for developmental studies, which could benefit from a more accessible system. Zebrafish (Danio rerio) are genetically tractable vertebrates, and given their translucency, are readily amenable for daily live imaging studies. We set out to examine whether zebrafish glia have conserved traits with mammalian glia regarding their ability to interact with and maintain the developing brain vasculature. We utilized transgenic zebrafish strains in which oligodendrocyte transcription factor 2 (olig2) and glial fibrillary acidic protein (gfap) identify different glial populations in the zebrafish brain and document their corresponding relationship with brain blood vessels. Our results demonstrate that olig2 and gfap zebrafish glia have distinct lineages and each interact with brain vessels as previously observed in mouse brain. Additionally, we manipulated these relationships through pharmacological and genetic approaches to distinguish the roles of these cell types during blood vessel development. olig2 glia use blood vessels as a pathway during their migration and Wnt signaling inhibition decreases their single-cell vessel co-option. By contrast, the ablation of gfap glia at the beginning of CNS angiogenesis impairs vessel development through a reduction in Vascular endothelial growth factor (Vegf), supporting a role for gfap glia during new brain vessel formation in zebrafish. This data suggests that zebrafish glia, akin to mammalian glia, have different lineages that show diverse interactions with blood vessels, and are a suitable model for elucidating glial-vascular relationships during vertebrate brain development.


title: AlleleShift: An R package to predict and visualize population-level changes in allele frequencies in response to climate change

abstract:
BackgroundAt any particular location, frequencies of alleles in organisms that are associated with adaptive traits are expected to change in future climates through local adaption and migration, including assisted migration (human-implemented when climate change is more rapid than natural migration rates). Making the assumption that the baseline frequencies of alleles across environmental gradients can act as a predictor of patterns in changed climates (typically future but possibly paleo-climates), a methodology is provided by AlleleShift of predicting changes in allele frequencies at populations locations.

MethodsThe prediction procedure involves a first calibration and prediction step through redundancy analysis (RDA), and a second calibration and prediction step through a generalized additive model (GAM) with a binomial family. As such, the procedure is fundamentally different to an alternative approach recently proposed to predict changes in allele frequencies from canonical correspondence analysis (CCA). My methodology of AlleleShift is also different in modelling and predicting allele counts through constrained ordination (not frequencies as in the CCA approach) and modelling both alleles for a locus (not solely the minor allele as in the CCA method; both methods were developed for diploid organisms where individuals are homozygous (AA or BB) or heterozygous (AB)). Whereas the GAM step ensures that allele frequencies are in the range of 0 to 1 (negative values are sometimes predicted by the RDA and CCA approaches), the RDA step is based on the Euclidean distance that is also the typical distance used in Analysis of Molecular Variance (AMOVA). The AlleleShift::amova.rda enables users to verify that the same  mean-square values are calculated by AMOVA and RDA, and gives the same final statistics with balanced data.

ResultsBesides data sets with predicted frequencies, AlleleShift provides several visualization methods to depict the predicted shifts in allele frequencies from baseline to changed climates. These include  dot plot graphics (function shift.dot.ggplot), pie diagrams (shift.pie.ggplot), moon diagrams (shift.moon.ggplot),  waffle diagrams (shift.waffle.ggplot) and smoothed surface diagrams of allele frequencies of baseline or future patterns in geographical space (shift.surf.ggplot). As these were generated through the ggplot2 package, methods of generating animations for a climate change time series are straightforward, as shown in the documentation of AlleleShift and in the supplementary materials. In addition, graphical methods are provided of showing shifts of populations in environmental space (population.shift) and to assess how well the predicted frequencies reflect the original frequencies for the baseline climate (freq.ggplot).

AvailabilityAlleleShift is available as an open-source R package from https://github.com/RoelandKindt/AlleleShift. Genetic input data is expected to be in the adegenet::genpop format, which can be generated from the adegenet::genind format. Climate data is available from various resources such as WorldClim and Envirem.


title: Discovery of 10,828 new putative human immunoglobulin heavy chain IGHV variants

abstract:
The correct identification of immunoglobulin alleles in genome sequences is a challenge. Nevertheless, it can assist in the study of several human diseases associated with the antibody repertoire and in the development of new therapies using antibody engineering techniques. The advent of next-generation sequencing of human genomes and antibody repertoires enabled the development of several tools for the mapping and identification of new immunoglobulin (Ig) alleles. Some of these tools use 1,000 Genomes (G1K) data for new Ig alleles discovery. However, genome data from G1K present low coverage and variant call problems. Here, a computational screen of immunoglobulin alleles was carried out in the Genome Aggregation Database (gnomAD), the largest high-quality catalogue of variation from 125,748 exomes and 15,708 human genomes.

A total of 10,909 putative IGHV alleles were identified, in which 10,828 of them are new and 2,024 appear at least in 6 different alleles from genomes/exomes. The IGHV2-70 was the IGHV gene segment with the largest number of variants described. The majority of the variants were found in the framework 3 and most of them are missense. Interestingly, a large number of variants were found to be population exclusive. A database integrated with a web platform was created (YGL-DB) to store and make accessible the likely new variants found.

This available data can help the scientific community to validate new IGHV variants as well as it can shed light on the importance of variants in disease development and immunization protocols.


title: EmptyNN: A neural network based on positive-unlabeled learning to remove cell-free droplets and recover lost cells in single-cell RNA sequencing data

abstract: Droplet-based single-cell RNA sequencing (scRNA-seq) has significantly increased the number of cells profiled per experiment and revolutionized the study of individual transcriptomes. However, to maximize the biological signal robust computational methods are needed to distinguish cell-free from cell-containing droplets. Here, we introduce a novel cell-calling algorithm called EmptyNN, which trains a neural network based on positive-unlabeled learning for improved filtering of barcodes. We leveraged cell hashing and genetic variation to provide ground-truth. EmptyNN accurately removed cell-free droplets while recovering lost cell clusters, and achieved an Area Under the Receiver Operating Characteristics (AUROC) of 94.73% and 96.30%, respectively. The comparisons to current state-of-the-art cell-calling algorithms demonstrated the superior performance of EmptyNN, as measured by the number of recovered cell-containing droplets and cell types. EmptyNN was further applied to two additional datasets and showed good performance. Therefore, EmptyNN represents a powerful tool to enhance scRNA-seq quality control analyses.


title: The impact of artifact removal approaches on TMS-EEG signal

abstract: Transcranial magnetic stimulation (TMS)-evoked potentials (TEPs) allow one to assess cortical excitability and effective connectivity in clinical and basic research. However, obtaining clean TEPs is challenging due to the various TMS-related artifacts that contaminate the electroencephalographic (EEG) signal when the TMS pulse is delivered. Different preprocessing approaches have been employed to remove the artifacts, but the degree of artifact reduction or signal distortion introduced in this phase of analysis is still unknown. Knowing and controlling this potential source of uncertainty will increase the inter-rater reliability of TEPs and improve the comparability between TMS-EEG studies. The goal of this study was to assess the variability in TEP waveforms due to of the use of different preprocessing pipelines. To accomplish this aim, we preprocessed the same TMS-EEG data with four different pipelines and compared the results. The dataset was obtained from 16 subjects in two identical recording sessions, each session consisting of both left dorsolateral prefrontal cortex and left inferior parietal lobule stimulation at 100% of the resting motor threshold. Considerable differences in TEP amplitudes were found between the preprocessing pipelines. Topographies of TEPs from the different pipelines were all highly correlated ({rho}>0.8) at latencies over 100 ms. By contrast, waveforms at latencies under 100 ms showed a variable level of correlation, with {rho} ranging between 0.2 and 0.9. Moreover, the test-retest reliability of TEPs depended on the preprocessing pipeline. Taken together, these results take us to suggest that the choice of the preprocessing approach has a marked impact on the final TEP, and that caution should be taken when comparing TMS-EEG studies that used different approaches. Finally, we propose strategies to control this source of variability.


title: HIV-1 uncoating occurs via a series of rapid biomechanical changes in the core related to individual stages of reverse transcription

abstract: The HIV core consists of the viral genome and associated proteins encased by a cone-shaped protein shell termed the capsid. Successful infection requires reverse transcription of the viral genome and disassembly of the capsid shell within a cell in a process known as uncoating. The integrity of the viral capsid is critical for reverse transcription, yet the viral capsid must be breached to release the nascent viral DNA prior to integration. We employed atomic force microscopy to study the stiffness changes in HIV-1 cores during reverse transcription in vitro in reactions containing the capsid-stabilizing host metabolite IP6. Cores exhibited a series of stiffness spikes, with up to three spikes typically occurring between 10-30, 40-80, and 120-160 minutes after initiation of reverse transcription. Addition of the reverse transcriptase (RT) inhibitor efavirenz eliminated the appearance of these spikes and the subsequent disassembly of the capsid, thus establishing that both result from reverse transcription. Using timed addition of efavirenz, and analysis of an RNAseH-defective RT mutant, we established that the first stiffness spike requires minus-strand strong stop DNA synthesis, with subsequent spikes requiring later stages of reverse transcription. Additional rapid AFM imaging experiments revealed repeated morphological changes in cores that were temporally correlated with the observed stiffness spikes. Our study reveals discrete mechanical changes in the viral core that are likely related to specific stages of reverse transcription. Our results suggest that reverse-transcription-induced changes in the capsid progressively remodel the viral core to prime it for temporally accurate uncoating in target cells.

category: biophysics


title: DProj: A toolbox for local 2D projection and accurate morphometrics of large 3D microscopy images.

abstract:
BO_SCPLOWACKGROUNDC_SCPLOWQuantitative imaging of epithelial tissues prompts for bioimage analysis tools that are widely applicable and accurate. In the case of imaging 3D tissues, a common pre-processing step consists in projecting the acquired 3D volume on a 2D plane mapping the tissue surface. Indeed, while segmenting the tissue cells is amenable on 2D projections, it is still very difficult and cumbersome in 3D. However, for many specimen and models used in Developmental and Cell Biology, the complex content of the image volume surrounding the epithelium in a tissue often reduces the visibility of the biological object in the projection, compromising its subsequent analysis. In addition, the projection may distort the geometry of the tissue and can lead to strong artifacts in the morphology measurement.

RO_SCPLOWESULTSC_SCPLOWHere we introduce a user-friendly toolbox built to robustly project epithelia on their 2D surface from 3D volumes, and to produce accurate morphology measurement corrected for the projection distortion, even for very curved tissues. Our toolbox is built upon two components. LocalZProjector is a user-friendly and configurable Fiji plugin that generates 2D projections and height-maps from potentially large 3D stacks (larger than 40 GB per time-point) by only incorporating signal of the planes with local highest variance/mean intensity, despite a possibly complex image content. DeProj is a MATLAB tool that generates correct morphology measurements by combining the height-map output (such as the one offered by LocalZProjector) and the results of a cell segmentation on the 2D projection, hence effectively deprojecting the 2D segmentation in 3D. In this paper we demonstrate their effectiveness over a wide range of different biological samples. We then compare its performance and accuracy against similar existing tools.

CO_SCPLOWONCLUSIONSC_SCPLOWWe find that LocalZProjector performs well even in situations where the volume to project also contains un-wanted signal in other layers. We show that it can process large images without a pre-processing step. We study the impact of geometrical distortions on morphological measurements induced by the projection. We measured very large distortions which are then corrected by DeProj, providing accurate outputs.


title: LocalZProjector and DeProj: A toolbox for local 2D projection and accurate morphometrics of large 3D microscopy images.


title: Integrated single-cell transcriptomics and epigenomics reveals strong germinal center-associated etiology of autoimmune risk loci

abstract:
The germinal center (GC) response is critical for both effective adaptive immunity and establishing peripheral tolerance by limiting auto-reactive B cells. Dysfunction in these processes can lead to defects in immune response to pathogens or contribute to autoimmune disease. To understand the gene regulatory principles underlying the GC response, we generated a single-cell transcriptomic and epigenomic atlas of the human tonsil, a widely studied and representative lymphoid tissue. We characterize diverse immune cell subsets and build a trajectory of dynamic gene expression and transcription factor activity during B cell activation, GC formation, and plasma cell differentiation. We subsequently leverage cell type-specific transcriptomic and epigenomic maps to interpret potential regulatory impact of genetic variants implicated in autoimmunity, revealing that many exhibit their greatest regulatory potential in GC cell populations. Together, these analyses provide a powerful new cell type-resolved resource for the interpretation of cellular and genetic causes underpinning autoimmune disease.

One sentence summarySingle-cell chromatin accessibility landscapes of immune cell subsets reveal regulatory potential of autoimmune-associated genetic variants during the germinal center response.


title: Genetic analysis of the contribution of the proprotein convertases to the in vivo regulation of FGF23

abstract: Fibroblast growth factor 23 (FGF23) is a hormone secreted from fully differentiated osteoblasts and osteocytes that inhibits phosphate reabsorption by kidney proximal tubules. The full-length (i.e., intact) protein mediates FGF23 endocrine functions, while endoproteolytic cleavage at a consensus cleavage sequence for the proprotein convertases (PCs) inactivates FGF23. Two PCs, furin and PC5, were shown to cleave FGF23 in vitro at RHTR179{downarrow}, but whether they are fulfilling this function in vivo is currently unknown. To address this question we used here mice lacking either or both furin and PC5 in cell-specific manners and mice lacking the paired basic amino acid-cleaving enzyme 4 (PACE4) in all cells. Our analysis shows that furin inactivation in osteoblasts and osteocytes results in a 25% increase in circulating intact FGF23, without any significant impact on serum phosphate levels, whether mice are maintained on a normal or a low phosphate diet. Under conditions of iron deficiency, FGF23 is normally processed in control mice, but its processing is impaired in mice lacking furin in osteoblasts and osteocytes. In contrast, FGF23 is normally cleaved following erythropoietin or IL-1{beta} injections in mice lacking furin or both furin and PC5, and in PACE4-deficient mice. Altogether, these studies suggest that furin is only partially responsible for FGF23 cleavage under certain conditions in vivo. The processing of FGF23 may therefore involve the redundant action of multiple PCs or of other peptidases in osteoblasts, osteocytes and hematopoietic cells.

category: physiology


title: In vivo analysis of the contribution of proprotein convertases to the processing of FGF23


title: High-resolution model of Arabidopsis Photosystem II reveals the structural consequences of digitonin-extraction

abstract: In higher plants, the photosynthetic process is performed and regulated by Photosystem II (PSII). Arabidopsis thaliana was the first higher plant with a fully sequenced genome, conferring it the status of a model organism; nonetheless, a high-resolution structure of its Photosystem II is missing. We present the first Cryo-EM high-resolution structure of Arabidopsis PSII supercomplex with average resolution of 2.79 [A], an important model for future PSII studies. The digitonin extracted PSII complexes demonstrate the importance of: the LHG2630-lipid-headgroup in the trimerization of the light-harvesting complex II; the stabilization of the PsbJ subunit and the CP43-loop E by DGD520-lipid; the choice of detergent for the integrity of membrane protein complexes. Furthermore, our data shows at the anticipated Mn4CaO5-site a single metal ion density as a reminiscent early stage of Photosystem II photoactivation.

category: plant biology


title: Targeting primary and metastatic uveal melanoma with a G protein inhibitor

abstract: Uveal melanoma (UM) is the most common intraocular tumor in adults. Nearly half of UM patients develop metastatic disease and often succumb within months because effective therapy is lacking. A novel therapeutic approach has been suggested by the discovery that UM cell lines driven by mutant constitutively active Gq or G11 can be targeted by FR900359 (FR) or YM-254890, which are bioavailable, selective inhibitors of the Gq/11/14 subfamily of heterotrimeric G proteins. Here, we have addressed the therapeutic potential of FR for UM. We found that FR inhibited all oncogenic Gq/11 mutants reported in UM. FR arrested growth of all Gq/11-driven UM cell lines tested, but induced apoptosis only in a few. Similarly, FR inhibited growth of, but did not efficiently kill, UM tumor cells from biopsies of primary or metastatic tumors. FR evoked melanocytic redifferentiation of UM tumor cells with low (class 1), but not high (class 2), metastatic potential. FR administered systemically below its LD50 strongly inhibited growth of PDX-derived class 1 and class 2 UM tumors in mouse xenograft models, and reduced blood pressure transiently. FR did not regress xenografted UM tumors, or significantly affect heart rate, liver function, hematopoiesis, or behavior. These results indicated the existence of a therapeutic window in which FR can be explored for treating UM, and potentially other diseases caused by constitutively active Gq/11.

category: cancer biology


title: Fluorescent Glycan Fingerprinting of SARS2 Spike Proteins

abstract: Glycosylation is the most common post-translational modification and has myriad biological functions. However, glycan analysis and research has always been a challenge. Here, we would like to present new techniques of glycan fingerprinting based on enzymatic fluorescent labeling and gel electrophoresis. The method is illustrated on SARS-2 spike (S) glycoproteins. SARS-2, a novel coronavirus and the causative agent of COVID-19 pandemic, has devastated the world since the end of 2019. To obtain the N-glycan fingerprint of a S protein, glycans released from the protein are first labeled through enzymatic incorporation of fluorophore-conjugated sialic acid or fucose, and then separated on acrylamide gel through electrophoresis, and finally visualized with a fluorescent imager. To identify the labeled glycans of a fingerprint, glycan standards and glycan ladders that are enzymatically generated are run alongside the samples as references. By comparing the mobility of a labeled glycan to that of a glycan standard, the identity of glycans maybe determined. Due to lack of enzyme for broad O-glycans releasing, O-glycans on the RBD protein are labeled with fluorescent sialic acid and digested with trypsin to obtain labeled glycan peptides that are then separated on gel. Glycan fingerprinting could serve as a quick way for global assessment of the glycosylation of a glycoprotein.

category: biochemistry


title: Intact synapse structure and function after combined knockout of PTPδ, PTPσ and LAR

abstract: It has long been proposed that Leukocyte common Antigen-Related Receptor Protein Tyrosine Phosphatases (LAR-RPTPs) are cell-adhesion proteins for the control of synapse assembly. Their synaptic nanoscale localization, however, has not been established, and the fine structure of synapses after knockout of the three vertebrate genes for LAR-RPTPs (PTP{delta}, PTP{sigma} and LAR) has not been tested. Here, we find that PTP{delta} is precisely apposed to postsynaptic scaffolds at excitatory and inhibitory synapses using superresolution microscopy. We generated triple-conditional knockout mice for PTP{delta}, PTP{sigma} and LAR to test whether they are essential for synapse structure. While mild effects on synaptic vesicle clustering and active zone architecture were detected, synapse numbers and their overall structure were unaffected, membrane anchoring of the active zone persisted, and vesicle docking and release were normal. We conclude that LAR-RPTPs, despite their localization at synaptic appositions, are dispensable for the organization and function of presynaptic nerve terminals.


title: The viral oncoproteins Tax and HBZ reprogram the cellular mRNA splicing landscape

abstract:
While viral infections are known to hijack the transcription and translation of the host cell, the extent to which encoded viral proteins coordinate these perturbations remains unclear. Here we demonstrate that the oncoviral proteins Tax and HBZ interact with specific components of the spliceosome machinery, including the U2 auxiliary factor large subunit (U2AF2), and the complementary factor for APOBEC-1 (A1CF), respectively. Tax and HBZ perturb the splicing landscape in T-cells by altering cassette exons in opposing manners, with Tax inducing exon inclusion while HBZ induces exon exclusion. Among Tax- and HBZ-dependent splicing changes, we identify events that are also altered in Adult T cell leukemia (ATL) patients, and in well-known cancer census genes. Our interactome mapping approach, applicable to other viral oncogenes, has identified spliceosome perturbation as a novel mechanism coordinately used by Tax and HBZ to reprogram the transcriptome.

HighlightsO_LITax and HBZ interact with RNA-binding proteins as well as transcription factors
C_LIO_LIHTLV-1 encoded proteins Tax and HBZ alter the splicing landscape in T-cells
C_LIO_LITax and HBZ expression affect alternative splicing of 33 and 63 cancer genes, respectively
C_LIO_LIOpposing roles for Tax and HBZ in deregulation of gene expression
C_LI

Graphical abstract

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category: systems biology


title: Effect of luminal surface structure of decellularized aorta on thrombus formation and cell behavior

abstract: As the number of cardiovascular diseases increases, artificial heart valves and blood vessels have been developed. Although cardiovascular application using decellularized tissue have been studied, the mechanism of their functionality is still unknown. To find the important factor for preparing decellularized cardiovascular prothesis which shows good in vivo performance, the effect of luminal surface structure of decellularized aorta on thrombus formation and cell behavior was investigated. Various luminal surface structures of decellularized aorta were prepared by heating, drying and peeling. The luminal surface structure and collagen denaturation was evaluated by immunohistological staining, collagen hybridizing peptide (CHP) staining and scanning electron microscopy (SEM) analysis. To evaluate the effect of luminal surface structure of decellularized aorta on thrombus formation and cell behavior, blood clotting test and recellularization of endothelial cells and smooth muscular cells were performed. The results of blood clotting test showed that the closer the luminal surface structure is to native aorta, the higher the anti-coagulant property. From the result of cell seeding-test, it was suggested that vascular cells recognize the luminal surface structure and regulate adhesion, proliferation and functional expression. These results will provide important factor for preparing decellularized cardiovascular prothesis and lead to future development on decellularized cardiovascular applications.

category: bioengineering


title: Prosodic categories in speech are acoustically multidimensional: evidence from dimension-based statistical learning

abstract: Segmental speech units such as phonemes are cued by multiple acoustic dimensions (e.g. F0 and duration), but dimensions do not carry equal perceptual weight. The relative perceptual weights of acoustic speech dimensions are not fixed but vary with context. For example, when speech is altered to create an  accent in which two acoustic dimensions are correlated in a manner opposite that of long-term experience, the dimension that carries less perceptual weight is down-weighted to contribute less in category decisions. It remains unclear, however, whether this short-term reweighting is limited to segmental categorization, or if it extends to categorization of suprasegmental features which span multiple phonemes, syllables, or words, which would suggest that such "dimension-based statistical learning" is a widespread phenomenon in speech perception. Here we investigated the relative contribution of two acoustic dimensions to word emphasis. Participants categorized instances of a two-word phrase pronounced with typical covariation of fundamental frequency (F0) and duration, and in the context of an artificial  accent in which F0 and duration (established in prior research on English speech as  primary and  secondary dimensions, respectively) covaried atypically. When categorizing  accented speech, listeners rapidly down-weighted the secondary dimension (duration) while continuing to rely on the primary dimension (F0). This result indicates that listeners continually track short-term regularities across speech input and dynamically adjust the weight of acoustic evidence for suprasegmental categories. Thus, dimension-based statistical learning appears to be a widespread phenomenon in speech perception extending to both segmental and suprasegmental categorization.


title: Short-term perceptual re-weighting in suprasegmental categorization


title: Less is more: a dose-response mechanistic account of intranasal oxytocin pharmacodynamics in the human brain

abstract: Intranasal oxytocin is receiving increasing research attention as a potential treatment for several brain disorders due to promising preclinical results. However, translating these findings to humans has been hampered by remaining uncertainties about its pharmacodynamics and the methods used to probe its effects in the human brain. Using a dose-response design (9, 18 and 36 IU) and a novel administration device, we demonstrate that oxytocin-induced physiological changes in the amygdala at rest, a key-hub of the brain oxytocin system, follow a dose-response curve with maximal effects for lower doses. Yet, the effects of oxytocin vary by amygdala subdivision, highlighting the need to qualify dose-response curves within subregion. We further link physiological changes with the density of the oxytocin receptor gene mRNA across brain regions, strengthening our confidence in intranasal oxytocin as a valid approach to engage central targets. Finally, we demonstrate that intranasal oxytocin does not disrupt cerebrovascular reactivity; the absence of major vascular confounds corroborates the validity of haemodynamic neuroimaging to probe the effects of intranasal oxytocin in the human brain.


title: Less is more: a dose-response account of intranasal oxytocin pharmacodynamics in the human brain


title: Local Shape Descriptors for Neuron Segmentation

abstract: We present a simple, yet effective, auxiliary learning task for the problem of neuron segmentation in electron microscopy volumes. The auxiliary task consists of the prediction of Local Shape Descriptors (LSDs), which we combine with conventional voxel-wise direct neighbor affinities for neuron boundary detection. The shape descriptors are designed to capture local statistics about the neuron to be segmented, such as diameter, elongation, and direction. On a large study comparing several existing methods across various specimen, imaging techniques, and resolutions, we find that auxiliary learning of LSDs consistently increases segmentation accuracy of affinity-based methods over a range of metrics. Furthermore, the addition of LSDs promotes affinitybased segmentation methods to be on par with the current state of the art for neuron segmentation (Flood-Filling Networks, FFN), while being two orders of magnitudes more efficient--a critical requirement for the processing of future petabyte-sized datasets. Implementations of the new auxiliary learning task, network architectures, training, prediction, and evaluation code, as well as the datasets used in this study are publicly available as a benchmark for future method contributions.


title: Low cost and sustainable hyaluronic acid production in a manufacturing platform based on Bacillus subtilis 3NA strain

abstract:
Hyaluronic acid (HA) is a high value glycosaminoglycan mostly used in health and cosmetic applications. Commercial HA is produced from animal tissues or in toxigenic bacteria of the genus Streptococcus grown in complex media, which are expensive and raise environmental concerns due to the disposal of large amounts of broth with high organic loads. Other microorganisms were proposed as hosts for the heterologous production of HA, but the methods are still costly. The extraordinary capacity of this biopolymer to bind and retain water attracts interest for large scale applications where biodegradable materials are needed, but its high cost and safety concerns are barriers for its adoption.

Bacillus subtilis 3NA strain is prototrophic, amenable for genetic manipulation, GRAS, and can rapidly reach high cell densities in salt-based media. These phenotypic traits were exploited to create a platform for biomolecule production using HA as a proof of concept. First, the 3NA strain was engineered to produce HA; second, a chemically defined medium was formulated using commodity-priced inorganic salts combined at the stoichiometric ratios needed to build the necessary quantities of biomass and HA; and third, a scalable fermentation process, where HA can be produced at the maximum volumetric productivity (VP), was designed.

A comparative economic analysis against other methods indicates that the new process may increase the operating profit of a manufacturing plant by more than 100 %. The host, the culture medium, and the rationale employed to develop the fermentation process described here, introduce an IP free platform that could be adaptable for production of other biomolecules.

Key PointsO_LIA platform for the production of biomolecules was designed based on B. subtilis 3NA, a chemically defined medium and a fermentation process.
C_LIO_LIAs proof of concept, high quality hyaluronic acid was produced with an environmentally friendly process.
C_LIO_LIA techno-economic analysis indicates that the process is more that 100% profitable than current methods.
C_LI


title: Computational and experimental approaches to controlling bacterial microcompartment assembly

abstract: Bacterial microcompartments compartmentalize the enzymes that aid chemical and energy production in many bacterial species. These protein organelles are found in various bacterial phyla and are postulated to help many of these organisms survive in hostile environments such as the gut of their hosts. Metabolic engineers are interested in repurposing these organelles for non-native functions. Here, we use computational, theoretical and experimental approaches to determine mechanisms that effectively control microcompartment self-assembly. As a model system, we find via multiscale modeling and mutagenesis studies, the interactions responsible for the binding of hexamer-forming proteins propanediol utilization bacterial microcompartments from Salmonella and establish conditions that form various morphologies. We determine how the changes in the microcompartment hexamer protein preferred angles and interaction strengths can modify the assembled morphologies including the naturally occurring polyhedral microcompartment shape, as well as other extended shapes or quasi-closed shapes. We demonstrate experimentally that such altered strengths and angles are achieved via amino acid mutations. A thermodynamic model that agrees with the coarse-grained simulations provides guidelines to design microcompartments. These findings yield insight in controlled protein assembly and provide principles for assembling microcompartments for biochemical or energy applications as nanoreactors.


title: Dermatan Sulfate Is a Potential Master Regulator of IgH via Interactions with Pre-BCR, GTF2I, and BiP ER Complex in Pre-B Lymphoblasts

abstract: Dermatan sulfate (DS) and autoantigen (autoAg) complexes are capable of stimulating autoreactive CD5+ B-1 cells. We examined the activity of DS on CD5+ pre-B lymphoblast NFS-25 cells. CD19, CD5, CD72, PI3K, and Fas possess varying degrees of DS affinity. The three pre-BCR components, Ig heavy chain mu (IgH), VpreB, and lambda 5, display differential DS affinities, with IgH having the strongest affinity. DS attaches to NFS-25 cells, gradually accumulates in the ER, and eventually localizes to the nucleus. DS and IgH co-localize on the cell surface and in the ER. DS associates strongly with 17 ER proteins (e.g., BiP/Grp78, Grp94, Hsp90ab1, Ganab, Vcp, Canx, Kpnb1, Prkcsh, Pdia3), which points to an IgH-associated multiprotein complex in the ER. In addition, DS interacts with nuclear proteins (Ncl, Xrcc6, Prmt5, Eftud2, Supt16h) and Lck. We also discovered that DS binds GTF2I, a required gene transcription factor at the IgH locus. These findings support DS as a potential master regulator of IgH in pre-B cells at protein and gene levels. We propose a (DS*autoAg)-autoBCR dual signal model in which an autoBCR is engaged by both autoAg and DS, and, once internalized, DS recruits a cascade of molecules that may help avert apoptosis and steer autoreactive B cell fate. Through its affinity with autoAgs and its control of IgH, DS emerges as a potential key player in the development of autoreactive B cells and autoimmunity.


title: Structural and functional characterization of a putative de novo gene in Drosophila

abstract:
Comparative genomic studies have repeatedly shown that new protein-coding genes can emerge de novo from non-coding DNA. Still unknown is how and when the structures of encoded de novo proteins emerge and evolve. Combining biochemical, genetic and evolutionary analyses, we elucidate the function and structure of goddard, a gene which appears to have evolved de novo at least 50 million years ago within the Drosophila genus.

Previous studies found that goddard is required for male fertility. Here, we show that Goddard protein localizes to elongating sperm axonemes and that in its absence, elongated spermatids fail to undergo individualization. Combining modelling, NMR and CD data, we show that Goddard protein contains a large central -helix, but is otherwise partially disordered. We find similar results for Goddards orthologs from divergent fly species and their reconstructed ancestral sequences. Accordingly, Goddards structure appears to have been maintained with only minor changes over millions of years.


title: In-Pero: Exploiting deep learning embeddings of protein sequences to predict the localisation of peroxisomal proteins

abstract: Peroxisomes are ubiquitous membrane-bound organelles, and aberrant localisation of peroxisomal proteins contributes to the pathogenesis of several disorders. Many computational methods focus on assigning protein sequences to subcellular compartments, but there are no specific tools tailored for the sub-localisation (matrix vs membrane) of peroxisome proteins. We present here In-Pero, a new method for predicting protein sub-peroxisomal cellular localisation. In-Pero combines standard machine learning approaches with recently proposed multi-dimensional deep-learning representations of the protein amino-acid sequence. It showed a classification accuracy above 0.9 in predicting peroxisomal matrix and membrane proteins. The method is trained and tested using a double cross-validation approach on a curated data set comprising 160 peroxisomal proteins with experimental evidence for sub-peroxisomal localisation. We further show that the proposed approach can be easily adapted (In-Mito) to the prediction of mitochondrial protein localisation obtaining performances for certain classes of proteins (matrix and inner-membrane) superior to existing tools. All data sets and codes are available at https://github.com/MarcoAnteghini and at www.systemsbiology.nl


title: Molecular programs of fibrotic change in aging human lung

abstract: Aging is associated with both overt and subclinical lung fibrosis, which increases risk for mortality from viruses and other respiratory pathogens. The molecular programs that induce fibrosis in the aging lung are not well understood. To overcome this knowledge gap, we undertook multimodal profiling of distal lung samples from healthy human donors across the lifespan. Telomere shortening, a cause of cell senescence and fibrosis, was progressive with age in a sample of 86 lungs and was associated with foci of DNA damage. Bulk RNA sequencing confirmed activation of cellular senescence and pro-fibrotic pathways as well as genes necessary for collagen processing with increasing age. These findings were validated in independent datasets for lung and sun-exposed skin, but not other organs including heart, liver and kidney. Cell type deconvolution analysis revealed a progressive loss of lung epithelial cells and an increasing proportion of fibroblasts. Consistent with the observed pro-fibrotic transcriptional profile, second harmonic imaging demonstrated increased density of interstitial collagen in aged human lungs. Furthermore, regions of parenchymal fibrosis were associated with decreased alveolar expansion and surfactant secretion. These findings reveal the transcriptional and structural features of fibrosis and associated physiologic impairments in normal lung aging.


title: Development of larvae of the Australian blowfly, Calliphora augur (Diptera: Calliphoridae), at constant temperatures

abstract: Calliphora augur (Diptera: Calliphoridae) is a common carrion-breeding blowfly of forensic, medical and agricultural importance in eastern Australia. Despite this, detailed information on the developmental biology of C. augur is lacking. Here, we present the first comprehensive study on the development of all three larval instars of C. augur, fed on sheeps liver, at constant temperatures of 15, 20, 25, 30 and 35{degrees}C. We provide thermal summation models describing instar duration, as well as 95% prediction intervals for larval length at each constant temperature, enabling the age of larvae of C. augur to be estimated from their developmental stage and their average length. These data provide a basis for the application of this species to forensic investigations.


title: Interferon-regulated genetic programs and JAK/STAT pathway activate the intronic promoter of the short ACE2 isoform in renal proximal tubules

abstract: Recently, a short, interferon-inducible isoform of Angiotensin-Converting Enzyme 2 (ACE2), dACE2 was identified. ACE2 is a SARS-Cov-2 receptor and changes in its renal expression have been linked to several human nephropathies. These changes were never analyzed in context of dACE2, as its expression was not investigated in the kidney. We used Human Primary Proximal Tubule (HPPT) cells to show genome-wide gene expression patterns after cytokine stimulation, with emphasis on the ACE2/dACE2 locus. Putative regulatory elements controlling dACE2 expression were identified using ChIP-seq and RNA-seq. qRT-PCR differentiating between ACE2 and dACE2 revealed 300- and 600-fold upregulation of dACE2 by IFN and IFN{beta}, respectively, while full length ACE2 expression was almost unchanged. JAK inhibitor ruxolitinib ablated STAT1 and dACE2 expression after interferon treatment. Finally, with RNA-seq, we identified a set of genes, largely immune-related, induced by cytokine treatment. These gene expression profiles provide new insights into cytokine response of proximal tubule cells.


title: Context and Phase Dependent Effects of Delta transcranial Alternating Current Stimulation on Dynamic Attending

abstract: Attention requires the allocation of limited resources to properly interpret our environment, making it ultimately unsustainable. Dynamic Attending Theory suggests that, in order to realistically maintain vigilance to our surroundings, attention likely fluctuates between high and low energetic states, such that information can be processed more quickly and accurately during attentional peaks and vice versa. Additionally, prior studies have suggested that the phase of delta oscillations (1-4 Hz) are critically involved in the entrainment of attention. We investigated the physiological and behavioral entrainment of attention and the role that delta phase plays to moderate the benefits of this attending. Participants (N=28) passively listened to a background auditory rhythm and were required to complete a visual discrimination task while undergoing 2 Hz transcranial alternating current stimulation (tACS). The task involved identifying an image, either upright or inverted, presented either on or before the final beat, while receiving delta stimulation that was either aligned or unaligned with image presentation. As expected, reaction times (RTs) were faster for on-beat than off-beat stimuli, and for upright images than inverted. Crucially, tACS phase-aligned with the beat led to faster RTs over out-of-phase stimulation, but only for upright images; remarkably, this pattern was reversed for inverted images presented on-beat, with slower RTs for inverted stimuli during in-phase tACS. These results suggest that the effects of delta tACS are both phase and context dependent, and mediate a potential form of speed-accuracy tradeoff in the allocation of attentional resources during rhythmic entrainment.


title: Brain networks are decoupled from external stimuli during internal cognition

abstract: Our cognition can be directed to external stimuli or to internal information. While there are many different forms of internal cognition (mind-wandering, recall, imagery etc.), their essential feature is independence from the immediate sensory input. This is thought to be reflected in the decoupling of brain networks from the external stimuli, but a quantitative investigation of this remains outstanding. Here we present a conceptual and analysis framework that links stimulus responses to connectivity between brain networks. This allows us to quantify the coupling of brain networks to the external stimuli. We tested this framework by presenting subjects with an audiovisual stimulus and instructing them to either attend to the stimulus (external task) or engage in mental imagery, recall or arithmetic (internal tasks) while measuring the evoked brain activity using functional MRI. We found that stimulus responses were generally attenuated for the internal tasks, though they increased in a subset of tasks and brain networks. However, using our new measure of coupling, we showed that brain networks became increasingly decoupled from the stimulus, even in the subset of tasks and brain networks in which stimulus responses increased. These results quantitatively demonstrate that during internal cognition brain networks are decoupled from external stimuli, opening the door for a fundamental and quantitative understanding of internal cognition.


title: Large lakes harbor streamlined free-living nitrifiers

abstract:
Microbial nitrification is a critical process governing nitrogen availability in aquatic systems. Freshwater nitrifiers have received little attention, leaving many unanswered questions about their taxonomic distribution, functional potential, and ecological interactions. Here, we reconstructed genomes to infer the metabolism and ecology of free-living picoplanktonic nitrifiers across the Laurentian Great Lakes, a connected series of five of Earths largest lakes. Surprisingly, ammonia oxidizing Bacteria (AOB) related to Nitrosospira dominated over ammonia oxidizing Archaea (AOA) at nearly all stations, with distinct ecotypes prevailing in the transparent, oligotrophic upper lakes compared to Lakes Erie and Ontario. Unexpectedly, one ecotype of Nitrosospira encodes proteorhodopsin, which could enhance survival in conditions where ammonia oxidation is inhibited or substrate limited. Nitrite oxidizing Bacteria (NOB) Ca. Nitrotoga and Nitrospira fluctuated in dominance, with the latter prevailing in deeper, less productive basins. Genome reconstructions reveal highly reduced genomes and features consistent with genome streamlining, along with diverse adaptations to sunlight and oxidative stress and widespread capacity for organic nitrogen use. Our findings expand the known functional diversity of nitrifiers and establish their ecological genomics in large lake ecosystems. By elucidating links between microbial biodiversity and biogeochemical cycling, our work also informs ecosystem models of the Laurentian Great Lakes, a critical freshwater resource experiencing rapid environmental change.

ImportanceMicroorganisms play critical roles in Earths nitrogen cycle. In lakes, microorganisms called nitrifiers derive energy from reduced nitrogen compounds. In doing so, they transform nitrogen into a form that can ultimately be lost to the atmosphere by a process called denitrification, which helps mitigate nitrogen pollution from fertilizer runoff and sewage. Despite their importance, freshwater nitrifiers are virtually unexplored. To understand their diversity and function, we reconstructed genomes of freshwater nitrifiers across some of Earths largest freshwater lakes, the Laurentian Great Lakes. We discovered several new species of nitrifiers specialized for clear low nutrient waters, and distinct species in comparatively turbid Lake Erie. Surprisingly, one species may be able to harness light energy using a protein called proteorhodopsin, despite the fact that nitrifiers typically live in deep dark water. Our work reveals unique biodiversity of the Great Lakes and fills key gaps in our knowledge of an important microbial group, the nitrifiers.


title: Genome streamlining, proteorhodopsin, and organic nitrogen metabolism in freshwater nitrifiers


title: Evolution of phenotypic variance provides insights into the genetic basis of adaption

abstract: Most traits are polygenic and the contributing loci can be identified by GWAS. Their adaptive architecture is, however, difficult to characterize. Here, we propose to study the adaptive architecture of traits by monitoring the evolution of their phenotypic variance during adaptation to a new environment in well-defined laboratory conditions. Extensive computer simulations show that the evolution of phenotypic variance in a replicated experimental evolution setting provides power to distinguish between oligogenic and polygenic adaptive architectures. We compared gene expression variance in male Drosophila simulans before and after 100 generations of adaptation to a novel hot environment. The variance change in gene expression was indistinguishable for genes with and without a significant change in mean expression after 100 generations of evolution. We suggest that a majority of adaptive gene expression evolution can be explained by a polygenic architecture. We propose that tracking the evolution of phenotypic variance across generations can provide an approach to characterize the adaptive architecture.


title: Evolution of phenotypic variance provides insights into the genetic basis of adaptation


title: Deep Learning Achieves Neuroradiologist-Level Performance in Detecting Hydrocephalus

abstract:
PurposeIn large clinical centers a small subset of patients present with hydrocephalus that requires surgical treatment. We aimed to develop a screening tool to detect such cases from the head MRI with performance comparable to neuroradiologists.

MethodsWe leveraged 496 clinical MRI exams collected retrospectively at a single clinical site from patients referred for any reason. This diagnostic dataset was enriched to have 259 hydrocephalus cases. A 3D convolutional neural network was trained on 16 manually segmented exams (ten hydrocephalus) and subsequently used to automatically segment the remaining 480 exams and extract volumetric anatomical features. A linear classifier of these features was trained on 240 exams to detect cases of hydrocephalus that required treatment with surgical intervention. Performance was compared to four neuroradiologists on the remaining 240 exams. Performance was also evaluated on a separate screening dataset of 451 exams collected from a routine clinical population to predict the consensus reading from four neuroradiologists using images alone. The pipeline was also tested on an external dataset of 31 exams from a 2nd clinical site.

ResultsThe most discriminant features were the Magnetic Resonance Hydrocephalic Index (MRHI), ventricle volume, and the ratio between ventricle and brain volume. At matching sensitivity, the specificity of the machine and the neuroradiologists did not show significant differences for detection of hydrocephalus on either dataset (proportions test, p > 0.05). ROC performance compared favorably with the state-of-the-art (AUC 0.90-0.96), and replicated in the external validation.

ConclusionHydrocephalus cases requiring treatment can be detected automatically from MRI in a heterogeneous patient population based on quantitative characterization of brain anatomy with performance comparable to that of neuroradiologists.


title: Deep Learning Achieves Neuroradiologist-Level Performance in Detecting Hydrocephalus Requiring Treatment


title: Conserved Architecture of Brain Transcriptome Changes between Alzheimer's Disease and Progressive Supranuclear Palsy in Pathologically Affected and Unaffected Regions

abstract: We identify a striking correlation in the directionality and magnitude of gene expression changes in brain transcriptomes between Alzheimers disease (AD) and Progressive Supranuclear Palsy (PSP). Further, the transcriptome architecture in AD and PSP is highly conserved between the temporal and cerebellar cortices, indicating highly similar transcriptional changes occur in pathologically affected and "unaffected" areas of the brain. These data have broad implications for interpreting transcriptomic data in neurodegenerative disorders.


title: CometChip Enables Parallel Analysis of Multiple DNA Repair Activities

abstract: DNA damage can be cytotoxic and mutagenic and is directly linked to aging, cancer, and heritable diseases. To counteract the deleterious effects of DNA damage, cells have evolved highly conserved DNA repair pathways. Many commonly used DNA repair assays are relatively low throughput and are limited to analysis of one protein or one pathway. Here, we have explored the capacity of the CometChip platform for parallel analysis of multiple DNA repair activities. Taking advantage of the versatility of the traditional comet assay and leveraging micropatterning techniques, the CometChip platform offers increased throughput and sensitivity compared to the traditional comet assay. By exposing cells to DNA damaging agents that create substrates of Base Excision Repair, Nucleotide Excision Repair, and Non-Homologous End Joining, we show that the CometChip is an effective method for assessing repair deficiencies in all three pathways. With these advanced applications of the CometChip platform, we expand the efficacy of the comet assay for precise, high-throughput, parallel analysis of multiple DNA repair activities.

category: molecular biology


title: A Universal Bacteriophage T4 Nanoparticle Platform to Design Multiplex SARS-CoV-2 Vaccine Candidates by CRISPR Engineering

abstract: A "universal" vaccine design platform that can rapidly generate multiplex vaccine candidates is critically needed to control future pandemics. Here, using SARS-CoV-2 pandemic virus as a model, we have developed such a platform by CRISPR engineering of bacteriophage T4. A pipeline of vaccine candidates were engineered by incorporating various viral components into appropriate compartments of phage nanoparticle structure. These include: expressible spike genes in genome, spike and envelope epitopes as surface decorations, and nucleocapsid proteins in packaged core. Phage decorated with spike trimers is found to be the most potent vaccine candidate in mouse and rabbit models. Without any adjuvant, this vaccine stimulated robust immune responses, both TH1 and TH2 IgG subclasses, blocked virus-receptor interactions, neutralized viral infection, and conferred complete protection against viral challenge. This new type of nanovaccine design framework might allow rapid deployment of effective phage-based vaccines against any emerging pathogen in the future.


title: Topological analysis of single-cell data reveals shared glial landscape of macular degeneration and neurodegenerative diseases

abstract:
1One Sentence SummaryA novel topological machine learning approach applied to single-nucleus RNA sequencing from human retinas with age-related macular degeneration identifies interacting disease phase-specific glial activation states shared with Alzheimers disease and multiple sclerosis.

2 AbstractNeurodegeneration occurs in a wide range of diseases, including age-related macular degeneration (AMD), Alzheimers disease (AD), and multiple sclerosis (MS), each with distinct inciting events. To determine whether glial transcriptional states are shared across phases of degeneration, we sequenced 50,498 nuclei from the retinas of seven AMD patients and six healthy controls, generating the first single-cell transcriptomic atlas of AMD. We identified groupings of cells implicated in disease pathogenesis by applying a novel topologically-inspired machine learning approach called  diffusion condensation. By calculating diffusion homology features and performing persistence analysis, diffusion condensation identified activated glial states enriched in the early phases of AMD, AD, and MS as well as an AMD-specific proangiogenic astrocyte state promoting pathogenic neovascularization in advanced AMD. Finally, by mapping the expression of disease-associated genes to glial states, we identified key signaling interactions creating hypotheses for therapeutic intervention. Our topological analysis identified an integrated disease-phase specific glial landscape that is shared across neurodegenerative conditions affecting the central nervous system.


title: Tianeptine, but not fluoxetine, decreases avoidant behavior in a mouse model of early developmental exposure to fluoxetine

abstract:
Depression and anxiety are two of the most common mental health disorders, often sharing symptoms and administrations. Most pharmacological agents available to treat these disorders target monoamine systems. Currently, finding the most effective treatment for an individual is a process of trial and error. Therefore, to better understand how disease etiology may predict treatment response, we studied mice exposed developmentally to the selective serotonin reuptake inhibitor (SSRI) fluoxetine (FLX). These mice show the murine equivalent of anxiety- and depression-like symptoms in adulthood and here we report that these mice are also behaviorally resistant to the antidepressant-like effects of adult SSRI administration. We investigated whether tianeptine (TIA), which exerts its therapeutic effects through the mu-opioid receptor (MOR) instead of directly targeting monoaminergic systems, would be more effective in this model.

We injected C57BL/6J (C57) pups with either FLX (10 mg/kg, i.p) or vehicle from postnatal (PN) day 2 to 11, a period in which mouse brain development parallels that of the third trimester of a human pregnancy. Prior work established that adult 129SvEv (129) mice exposed to FLX in this time period (PN-FLX) showed increased avoidant and decreased hedonic behaviors, which correspond to anxiety- and depressive-like symptoms in humans, respectively. We performed baseline testing in adulthood in C57 PN-FLX animals and confirmed a similar avoidant phenotype to that reported in 129 PN-FLX mice. We then treated these animals with chronic FLX (18 mg/kg in the drinking water) and evaluated effects on two tasks that measure avoidant behavior - the open field and novelty suppressed feeding (NSF) tasks. This administration failed to improve, and even exacerbated, avoidance symptoms in PN-FLX mice. The same animals then underwent chronic administration with TIA (30 mg/kg, 2x/day, i.p.) as an alternative treatment strategy. TIA administration decreased avoidance behavior as measured in the open field and NSF. Overall, this demonstrates that TIA may be a promising alternative treatment to typical antidepressants, especially in patients whose serotonergic system has been altered.


title: Shape analysis of gamma rhythm supports a superlinear inhibitory regime in an inhibition-stabilized network

abstract: Visual inspection of stimulus-induced gamma oscillations (30-70 Hz) often reveals a non-sinusoidal shape. Such distortions are a hallmark of non-linear systems and are also observed in mean-field models of gamma oscillations. A thorough characterization of the shape of the gamma cycle can therefore provide additional constraints on the operating regime of such models. However, the gamma waveform has not been quantitatively characterized, partially because the first harmonic of gamma, which arises because of the non-sinusoidal nature of the signal, is typically weak and gets masked due to a broadband increase in power related to spiking. To address this, we recorded local field potential (LFP) from the primary visual cortex (V1) of two awake female macaques while presenting full-field gratings or iso-luminant chromatic hues that produced huge gamma oscillations with prominent peaks at harmonic frequencies in the power spectra. We found that gamma and its first harmonic always maintained a specific phase relationship, resulting in a distinctive shape with a sharp trough and a shallow peak. Interestingly, a Wilson-Cowan (WC) model operating in an inhibition stabilized mode could replicate this shape, but only when the inhibitory population operated in the super-linear regime, as predicted recently. However, another recently developed model of gamma that operates in a linear regime driven by stochastic noise failed to produce salient harmonics or the observed shape. Our results impose additional constraints on models that generate gamma oscillations and their operating regimes.


title: Computational analysis of GAL pathway pinpoints mechanisms underlying natural variation

abstract:
Quantitative traits such as human height are measurable phenotypes that show continuous variation over a wide phenotypic range. Enormous effort has recently been put into determining the genetic influences on a variety of quantitative traits, including human genetic diseases, with mixed success. We identified a quantitative trait in a tractable model system, the GAL pathway in yeast, which controls the uptake and metabolism of the sugar galactose. GAL pathway activation depends both on galactose concentration and on the concentrations of competing, preferred sugars such as glucose. Natural yeast isolates show substantial variation in the behavior of the pathway. All studied yeast strains exhibit bimodal responses relative to external galactose concentration, i.e. a set of galactose concentrations existed at which both GAL-induced and GAL-repressed subpopulations were observed. However, these concentrations differed in different strains. We built a mechanistic model of the GAL pathway and identified parameters that are plausible candidates for capturing the phenotypic features of a set of strains including standard lab strains, natural variants, and mutants. In silico perturbation of these parameters identified variation in the intracellular galactose sensor, Gal3p, the negative feedback node within the GAL regulatory network, Gal80p, and the hexose transporters, HXT, as the main sources of the bimodal range variation. We were able to switch the phenotype of individual yeast strains in silico by tuning parameters related to these three elements. Determining the basis for these behavioral differences may give insight into how the GAL pathway processes information, and into the evolution of nutrient metabolism preferences in different strains. More generally, our method of identifying the key parameters that explain phenotypic variation in this system should be generally applicable to other quantitative traits.

Author summaryMicrobes adopt elaborate strategies for the preferred uptake and use of nutrients to cope with complex and fluctuating environments. As a result, yeast strains originating from different ecological niches show significant variation in the way they induce genes in the galactose metabolism (GAL) pathway in response to nutrient signals. To identify the mechanistic sources of this variation, we built a mathematical model to simulate the dynamics of the galactose metabolic regulation network, and studied how parameters with different biological implications contributed to the natural variation. We found that variations in the behavior of the galactose sensor Gal3p, the negative feedback node Gal80p, and the hexose transporters HXT were critical elements in the GAL pathway response. Tuning single parameters in silico was sufficient to achieve phenotype switching between different yeast strains. Our computational approach should be generally useful to help pinpoint the genetic and molecular bases of natural variation in other systems.


title: Two contrasting mediodorsal thalamic circuits target the medial prefrontal cortex

abstract: At the heart of the prefrontal executive and limbic networks is the mediodorsal thalamus (MD). Despite the importance of MD in a broad range of behaviors and neuropsychiatric disorders, virtually nothing is known about the physiology of neurons in MD. Here, we injected the retrograde tracer cholera toxin subunit B (CTB) into the medial prefrontal cortex (mPFC) of adult (8 - 12 week old) male and female wildtype mice. We prepared acute brain slices and used current clamp electrophysiology to measure and compare the intrinsic properties of the neurons in MD that project to mPFC (MD[->]mPFC neurons). MD[->]mPFC neurons are located predominantly in the medial (MD-M) and lateral (MD-L) subnuclei of MD. We found that that MD-M[->]mPFC neurons have longer membrane time constants, higher membrane resistance, less Hyperpolarization and Cyclic Nucleotide gated (HCN) channel activity, and more readily generate action potentials compared to MD-L[->]mPFC neurons. Additionally, MD-M[->]mPFC neurons have larger and more complex dendritic arbors compared to MD-L[->]mPFC neurons. These data demonstrating that the two populations of MD[->]mPFC neurons have distinct physiologies and morphologies suggests a differential role in thalamocortical information processing and potentially behavior.


title: Modulations of local synchrony over time lead to resting-state functional connectivity in a parsimonious large-scale brain model

abstract:
Biophysical models of large-scale brain activity are a fundamental tool for understanding the mechanisms underlying the patterns observed with neuroimaging. These models combine a macroscopic description of the within- and between-ensemble dynamics of neurons within a single architecture. A challenge for these models is accounting for modulations of within-ensemble synchrony over time. Such modulations in local synchrony are fundamental for modeling behavioral tasks and resting-state activity. Another challenge comes from the difficulty in parametrizing large scale brain models which hinders researching principles related with between-ensembles differences. Here we derive a parsimonious large scale brain model that can describe fluctuations of local synchrony. Crucially, we do not reduce within-ensemble dynamics to macroscopic variables first, instead we consider within and between-ensemble interactions similarly while preserving their physiological differences. The dynamics of within-ensemble synchrony can be tuned with a parameter which manipulates local connectivity strength. We simulated resting-state static and time-resolved functional connectivity of alpha band envelopes in models with identical and dissimilar local connectivities. We show that functional connectivity emerges when there are high fluctuations of local and global synchrony simultaneously (i.e. metastable dynamics). We also show that for most ensembles, leaning towards local asynchrony or synchrony correlates with the functional connectivity with other ensembles, with the exception of some regions belonging to the default-mode network.

Author summaryHere we present and evaluate a parsimonious model of large-scale brain activity. The model represents the brain as a network-of-networks structure. The sub-networks describe the neural activity within a brain region, and the global network encodes interactions between brain regions. Unlike other models, it capture progressive changes of local synchrony and local dynamics can be tuned with one parameter. Therefore the model could be used not only to model resting-state, but also behavioural tasks. Furthermore, we describe a simple framework that can deal with the arduous task of identifying global and local parameters.


title: In-silico studies of Neurocognitive and Neuropharmacological effect of Bacopa monnieri (L.)

abstract: Different Indian therapeutic plants have picked up consideration for their restorative properties against neurodevelopmental disorders lately. Bacopa monnieri (B. monnieri), being one of them, finds its utilization significantly in the treatment of cognition and learning. Despite the fact that it possesses such great capacity to treat neurological issues, how precisely it confers its influence is muddled. This study makes a stride towards knowing which phytochemical is significantly associated with granting B. monnieri with therapeutic properties. The docking investigation and the molecular simulation studies proposes that there is no single phytochemical included that imparts B. monnieri a significant medicinal effect. It is really the blend of dominant part of natural phytochemicals present in B. monnieri that bestows the anti-neurological activity to B. monnieri. The ADME studies shows the convergence of properties of phytochemicals of B. monnieri with that of commercially available drugs which suggests that phytochemicals of B. monnieri can used as a potential drug source to treat neurodegenerative and neurodevelopmental disorders.

category: pharmacology and toxicology


title: Low photorespiratory capacity is sufficient to block photosynthetic capacity acclimation in high light

abstract: The induction of high photosynthetic capacity in high light (HL) is a common response among many herbaceous dicot plants, however, the signals that control this response remain largely unknown. Here, multiple independent lines of evidence are presented in support of the conclusion that low photorespiratory capacity acts a negative signal to limit photosynthetic capacity acclimation in HL in Arabidopsis thaliana. Using a panel of natural accessions, primary nitrogen (N) assimilation and photorespiration rates early after a shift to growth in HL, as well as activities for key enzymes in these pathways, were shown to positively correlate with the magnitude of the subsequent induction of photosynthetic capacity, which occurred several days later. Time-resolved metabolomic data during acclimation to HL were collected using a strongly acclimating ecotype and a weakly acclimating ecotype, revealing in greater detail the differences in N assimilation, photorespiration, and triose-phosphate utilization pathways underlying efficient photosynthetic capacity acclimation. When shifted into HL growth conditions under non-photorespiratory conditions, weakly acclimating ecotypes and even photorespiratory mutants gained the ability to strongly induce high photosynthetic capacity in HL. Thus, a negative, photorespiration-dependent signal early in the HL shift appears to block photosynthetic capacity acclimation in accessions with low photorespiratory capacity, whereas accessions with high photorespiratory capacity are licensed to increase photosynthetic capacity.


title: Low photorespiratory capacity is sufficient to block the induction of photosynthetic capacity in high light


title: The DYRK1A protein kinase regulates ribosome mass and translation rates through transcriptional control of ribosomal protein genes expression

abstract: Ribosomal proteins (RPs) are evolutionary conserved proteins that are essential for protein translation. RP expression must be tightly regulated to ensure the appropriate assembly of ribosomes and to respond to the growth demands of cells. The elements regulating the transcription of RP genes (RPGs) have been characterized in yeast and Drosophila, yet how cells regulate the production of RPs in mammals is less well understood. Here, we show that a subset of RPG promoters is characterized by the presence of the palindromic TCTCGCGAGA motif and marked by the recruitment of the protein kinase DYRK1A. The presence of DYRK1A at these promoters is associated with enhanced binding of the TATA-binding protein, TBP, and it is negatively correlated with the binding of the GABP transcription factor, establishing at least two clusters of RPGs that could be coordinately regulated. However, DYRK1A silencing leads to a global reduction of RPGs, mRNA pointing at DYRK1A activities beyond those dependent on its chromatin association. Significantly, cells in which DYRK1A is depleted have reduced RP levels, fewer ribosomes, reduced global protein synthesis and smaller size. We therefore propose a novel role for DYRK1A in coordinating the expression of genes encoding RPs, thereby controlling cell growth in mammals.


title: Loss of the DYRK1A protein kinase results in reduction of ribosomal protein genes expression, ribosome mass and translation defects


title: Association between land cover, plant genera and pollinator dynamics in mixed-use landscapes

abstract: Pollinators are globally threatened by land-use change, but its effect varies depending on the taxa and the intensity of habitat degradation. However, pollinator-landscape studies typically focus on regions of intensive human activities and on a few focal species. Evaluating pollinator responses in landscapes with moderate land-use changes and on multiple pollinator groups would therefore fill an important knowledge gap. This study aims to determine the predictive capacity and effect of habitat characteristics on the relative abundance of multiple pollinator groups in mixed-use landscapes. To do this, we collected field data on the relative abundance of nectivorous birds, bees, beetles, and butterflies across the Tasman Peninsula (Tasmania, Australia). We then applied Random Forests to resolve the effects of land use (protected areas, plantation, and pasture), land cover at different radii (100 m and 2000 m), and plant genera on pollinator abundance. Overall, land cover and plant genera were more important predictors of pollinator abundance than land use. And the effect of land use, land cover, and plant genera varied depending on the pollinating group. Pollinator groups were associated with a range of plant genera, with the native genera Acacia, Leptospermum, Leucopogon, Melaleuca, Pomaderris, and Pultenaea being among the most important predictors. Our results highlight that one size does not fit all--that is pollinator response to different landscape characteristics vary, emphasise the importance of considering multiple habitat factors to manage and support a dynamic pollinator community, and demonstrates how land management can be informed using predictive modelling.

category: ecology


title: Association between land use, land cover, plant genera, and pollinator abundance in mixed-use landscapes


title: The human olfactory bulb process odor valence representation and initiate motor avoidance behavior

abstract: Determining the valence of an odor to provide information to guide rapid approach-avoidance behavior is thought to be one of the core tasks of the olfactory system, yet little is known of its initial neural mechanisms or subsequent behavioral manifestation in humans. In two experiments, we measured the functional processing of odor valence perception in the human olfactory bulb (OB)--the first processing stage of the olfactory system--using a non-invasive method as well as assessed subsequent motor avoidance response. We demonstrate that odor valence perception is associated with both gamma and beta activity in the human OB. Moreover, we show that negative, but not positive, odors initiate an early beta response in the OB, a response that is linked to a preparatory neural motor response in motor cortex. Finally, in a separate experiment we show that negative odors trigger a full-body motor avoidance response, manifested as a rapid leaning away from the odor, in the time period predicted by the OB results. Taken together, these results demonstrate that the human OB processes odor valence in a sequential manner in both the gamma and beta frequency bands and suggest that early processing of unpleasant odors in the OB might underlie rapid approach-avoidance decisions.

category: neuroscience


title: Simulating lesion-dependent functional recovery mechanisms

abstract: Functional recovery after brain damage varies widely and depends on many factors, including lesion site and extent. When a neuronal system is damaged, recovery may occur by engaging residual (e.g., perilesional) components. When damage is extensive, recovery depends on the availability of other intact neural structures that can reproduce the same functional output (i.e., degeneracy). A systems response to damage may occur rapidly, require learning or both. Here, we simulate functional recovery from four different types of lesions, using a generative model of word repetition that comprised a default premorbid system and a less used alternative system. The synthetic lesions (i) completely disengaged the premorbid system, leaving the alternative system intact, (ii) partially damaged both premorbid and alternative systems, and (iii) limited the experience-dependent plasticity of both. The results, across 1000 trials, demonstrate that (i) a complete disconnection of the premorbid system naturally invoked the engagement of the other, (ii) incomplete damage to both systems had a much more devastating long-term effect on model performance and (iii) the effect of reducing learning capacity within each system. These findings contribute to formal frameworks for interpreting the effect of different types of lesions.