title: Chloroplast protein import determines plant proteostasis and retrograde signaling

abstract: Proteins containing polyglutamine (polyQ) repeats are prone to aggregation and can lead to distinct human pathologies. For instance, Huntingtons disease is caused by an abnormal expansion of the polyQ stretch (> Q35) of Huntingtin (HTT) protein. However, plants express hundreds of proteins containing polyQ regions, but no pathologies arising from these factors have been reported to date. Here, we ask how plants maintain the proteostasis of polyQ-containing proteins, which are intrinsically enriched in the plant proteomes. To this end, we overexpressed an aggregation-prone fragment of human HTT (Q69) in plant cells. In contrast to invertebrate and mammalian transgenic models, we find that Arabidopsis thaliana plants suppress Q69 aggregation. This elevated proteostasis ability is mediated through the import and degradation of Q69 in chloroplasts. Conversely, inhibition of chloroplast protein import either genetically or pharmacologically reduces the capacity of plant cells to prevent Q69 aggregation. We find that Q69 interacts with the chloroplast stromal processing peptidase (SPP). Notably, expression of synthetic Arabidopsis SPP is sufficient to suppress aggregation of polyQ-expanded HTT in human cells. Beyond ectopically expressed Q69-HTT, endogenous polyQ-containing proteins also aggregate in Arabidopsis upon inhibition of chloroplast import. Among them, the plastid casein kinase 2 (pCK2), which contains a polyQ region next to the chloroplast targeting sequence motif, can also be localized into the nucleus. Upon inhibition of chloroplast import, pCK2 accumulates at higher levels in the nucleus and forms diamond-shaped amyloid-like fibrils surrounding the chloroplasts. These results indicate that the differential conformation and redistribution of pCK2 to the nucleus depends on chloroplast import efficiency, providing a role of polyQ repeats in chloroplast to nucleus communication (i.e. retrograde signaling). Together, our findings establish chloroplast protein import and proteases as determinants of polyQ proteostasis, with important implications for plant biology that can also lead to therapeutic approaches for human diseases that involve protein aggregation.


title: Informative and adaptive distances and summary statistics in sequential approximate Bayesian computation

abstract:
Calibrating model parameters on heterogeneous data can be challenging and inefficient. This holds especially for likelihood-free methods such as approximate Bayesian computation (ABC), which rely on the comparison of relevant features in simulated and observed data and are popular for otherwise intractable problems. To address this problem, methods have been developed to scale-normalize data, and to derive informative low-dimensional summary statistics using inverse regression models of parameters on data. However, while approaches only correcting for scale can be inefficient on partly uninformative data, the use of summary statistics can lead to information loss and relies on the accuracy of employed methods.

In this work, we first show that the combination of adaptive scale normalization with regression-based summary statistics is advantageous on heterogeneous parameter scales. Second, we present an approach employing regression models not to transform data, but to inform sensitivity weights quantifying data informativeness. Third, we discuss problems for regression models under non-identifiability, and present a solution using target augmentation. We demonstrate improved accuracy and efficiency of the presented approach on various problems, in particular robustness and wide applicability of the sensitivity weights. Our findings demonstrate the potential of the adaptive approach. The developed algorithms have been made available in the open-source Python toolbox pyABC.

category: systems biology


title: A deep learning classification task for accurate brain navigation during functional ultrasound imaging

abstract: Functional ultrasound imaging is a breakthrough technology for imaging brain activity at high spatiotemporal resolution. As it monitors hemodynamic activity, the resulting images are a non-standard representation of local anatomy. This leads to difficulties when determining the exact anatomical location of the recorded image, which is necessary for correctly interpreting the data. Here we propose a convolutional neural network-based framework for accurately navigating the brain during functional ultrasound imaging solely based on vascular landmarks. Our approach uses an image classification task to identify a suitable set of reference positions, from which the anatomical position of an image can be inferred with a precision of 102 {+/-} 98 {micro}m. Further analysis revealed that the predictions are driven by deep brain areas. The robustness of our approach was validated using an ischemic stroke model. It confirms that functional ultrasound imaging information is sufficient for positioning even when local blood flow is disrupted, as observed in many brain pathologies.

category: neuroscience


title: Drivers of nematode diversity in forest soils across climatic zones

abstract:
Nematodes are the most abundant multi-cellular animals in soil, influencing key processes and functions in terrestrial ecosystems. Yet, little is known about the drivers of nematode abundance and diversity in forest soils across climatic zones. This is despite forests cover approximately 30% of the earths land surface, provide many crucial ecosystem services but strongly vary in hydrothermal conditions and associated ecosystem properties across climatic zones.

Here, we collected nematode samples from 13 forests across a latitudinal gradient. We divided this gradient in temperate, warm-temperate, and tropical climatic zones. Using boosted regression trees, we showed that across the gradient, nematode abundance and diversity were mainly influenced by soil organic carbon. However, within climatic zones, other factors were more important in driving nematode alpha-diversity, nematode biomass and the abundance of different trophic groups: mean annual temperature and total soil phosphorus in temperate zones, soil pH in warm-temperate zones, and mean annual precipitation in tropical zones. Additionally, nematode beta-diversity was higher in temperate than in warm-temperate and tropical zones, and we did not find significant differences among climatic zones in nematode gamma diversity.

Together, our findings indicate a latitudinal shift in the main climatic variables controlling soil nematode communities and demonstrate that the drivers of soil nematode diversity in forested ecosystems are affected by the spatial scale and climatic conditions considered. This implies that high resolution studies are needed to accurately predict how soil functions respond if climate conditions move beyond the coping range of soil organisms. Our results also emphasize the importance of studying the area-diversity relationship of soil organisms under different climatic conditions.

category: ecology


title: High resolution species assignment of Anopheles mosquitoes using k-mer distances on targeted sequences

abstract: The ANOSPP amplicon panel is a genus-wide targeted sequencing panel to facilitate large-scale monitoring of Anopheles species diversity. Combining information from the 62 nuclear amplicons present in the ANOSPP panel allows for a more nuanced species assignment than single gene (e.g. COI) barcoding, which is desirable in the light of permeable species boundaries. Here, we present NNoVAE, a method using Nearest Neighbours (NN) and Variational Autoencoders (VAE), which we apply to k-mers resulting from the ANOSPP amplicon sequences in order to hierarchically assign species identity. The NN step assigns a sample to a species-group by comparing the k-mers arising from each haplotypes amplicon sequence to a reference database. The VAE step is required to distinguish between closely related species, and also has sufficient resolution to reveal population structure within species. In tests on independent samples with over 80% amplicon coverage, NNoVAE correctly classifies to species level 98% of samples within the An. gambiae complex and 89% of samples outside the complex. We apply NNoVAE to over two thousand new samples from Burkina Faso and Gabon, identifying unexpected species in Gabon. NNoVAE presents an approach that may be of value to other targeted sequencing panels, and is a method that will be used to survey Anopheles species diversity and Plasmodium transmission patterns through space and time on a large scale, with plans to analyse half a million mosquitoes in the next five years.

category: evolutionary biology


title: GBScleanR: Robust genotyping error correction using hidden Markov model with error pattern recognition.

abstract: The developments in sequencing technology have enabled researchers to acquire genotype data from large populations with dense markers. Recently developed methods that are based on reduced-representation sequencing (RRS), such as Genotyping By Sequencing (GBS), provide cost-effective and time-saving genotyping platforms; however, many drawbacks that are associated with these technologies, such as missing and false homozygous calls at heterozygous sites, significantly affect the accuracy. Several error correction methods that incorporate allele read counts in a hidden Markov model (HMM) have been developed to overcome these issues. Those methods assume that markers have a uniform error rate with no bias in the allele read ratio and infer a 50% chance of obtaining a read for either allele at a heterozygous site. However, bias does occur because of uneven amplification of genomic fragments and read mismapping. In this paper we introduce a novel error correction tool, GBScleanR, which enables robust and precise error correction for noisy RRS-based genotype data by incorporating marker-specific error rates into the HMM. The results indicate that GBScleanR improves the accuracy by 10-40 percentage points as compared to the existing tools in simulation datasets and achieves the most reliable genotype estimation in real data even with error prone markers.

category: bioinformatics


title: Sequence-structure-function relationships in the microbial protein universe

abstract: Abstract / SummaryFor the past half-century, structural biologists relied on the notion that similar protein sequences give rise to similar structures and functions. While this assumption has driven research to explore certain parts of the protein universe, it disregards spaces that dont rely on this assumption. Here we explore areas of the protein universe where similar protein functions can be achieved by different sequences and different structures. We predict ~200,000 structures for diverse protein sequences from 1,003 representative genomes1 across the microbial tree of life, and annotate them functionally on a per-residue basis. Structure prediction is accomplished using the World Community Grid, a large-scale citizen science initiative. The resulting database of structural models is complementary to the AlphaFold database, with regards to domains of life as well as sequence diversity and sequence length. We identify 148 novel folds and describe examples where we map specific functions to structural motifs. We also show that the structural space is continuous and largely saturated, highlighting the need for shifting the focus from obtaining structures to putting them into context, to transform all branches of biology, including a shift from sequence-based to sequence-structure-function based meta-omics analyses.


title: Mapping the Cell-Membrane Proteome to the Cancer Hallmarks

abstract: The hallmarks of biological processes that underlie the development of cancer have been long recognized, yet, existing therapeutic treatments cannot prevent cancer from continuing to be one of the leading causes of death worldwide. This work was aimed at exploring the extent to which the cell-membrane proteins are implicated in triggering cancer hallmark processes, and assessing the ability to pinpoint novel therapeutic targets through a combined membrane proteome/cancer hallmark perspective. By using GO annotations, a database of human proteins associated broadly with ten cancer hallmarks was created. Cell-membrane cellular subfractions of SKBR3/HER2+ breast cancer cells used as a model system were analyzed by high resolution mass spectrometry, and high-quality proteins (FDR<3 %) identified by at least two unique peptides were mapped to the cancer hallmark database. Over 1100 experimentally detected cell-membrane or cell-membrane associated proteins, representing ~8 % of the human cell-membrane proteome, were mapped to the hallmark database. Representative membrane constituents such as receptors, CDs, adhesion and transport proteins were distributed over the entire genome and present in every hallmark category. Sustained proliferative signaling/cell cycle, adhesion/tissue invasion, and evasion of immune destruction emerged as prevalent hallmarks represented by the membrane proteins. Construction of protein-protein interaction networks uncovered a high level of connectivity between the hallmark members, with some receptor (EGFR, ERBB2, FGFR, MTOR, CSF1R), antigen (CD44), and adhesion (MUC1) proteins being implicated in most hallmark categories. An illustrative subset of 116 hallmark proteins that included 44 oncogenes, 28 tumor suppressors, and 38 approved drug targets was subjected to a more in-depth analysis. The existing drug targets were implicated mainly in signaling processes. Network centrality analysis revealed that nodes with high degree, rather than betweenness, represent a good resource for informing the selection of putative novel drug targets. Through heavy involvement in supporting cancer hallmark processes, we show that the functionally diverse and networked landscape of cancer cell-membrane proteins fosters unique opportunities for guiding the development of novel therapeutic interventions, including multi-agent, immuno-oncology and precision medicine applications.

category: cancer biology


title: Multifaceted Atlases of the Human Brain in its Infancy

abstract: Brain atlases agglomerate structural and functional features of a population of individuals in a standard coordinate space. Here, we introduce for the first time a collection of atlases that charts postnatal development of the human brain in a spatio-temporally dense manner from two weeks to two years of age. Atlases capturing month-to-month changes of the human brain are essentially nonexistent for the first two years of life -- the critical developmental period during which the brain is evolving in virtually all facets at an exponential pace. This unmet need is compounded by the lack of atlases that provide a unified and holistic picture of the brain from both the perspectives of cortical surface convolutions and tissue volumetric characteristics. Existing surface and volumetric atlases are typically constructed independently in different coordinate spaces, causing discrepancies and complications in multifaceted analyses. Our month-specific conjoint surface and volumetric atlases chart normative patterns and capture key traits of early brain development and are therefore critical for identifying aberrations from normal developmental trajectories. Our atlases represent a major advance toward providing the neuroscience community an invaluable resource to facilitate the understanding of early structural and functional development by mapping multiple measurements of infant brains in a common reference frame for precise spatio-temporal quantification of cortical and subcortical changes.


title: ASD modelling in organoids reveals imbalance of excitatory cortical neuron subtypes during early neurogenesis

abstract: There is no clear genetic etiology or convergent pathophysiology for autism spectrum disorders (ASD). Using induced pluripotent stem cell (iPSC)-derived brain organoids and single-cell transcriptomics, we modeled alterations in the formation of the forebrain between sons with ASD and their unaffected fathers in ten families. Relative to fathers, probands with macrocephaly presented an increase in dorsal cortical plate excitatory neurons (EN-DCP) to the detriment of preplate lineages, whereas normocephalic ASD probands presented an opposite decrease in EN-DCP-related gene expression. Both cohorts converged in a dysregulation of outer radial glia genes related to translation. In macrocephalic probands, an increase in progenitor self-renewal genes ID1/ID3 was coupled to a larger pool of cortical progenitors. Furthermore, changes in ID1/ID3 expression were best predictors of ASD clinical severity. We suggest that head circumference reveals a fundamental difference in etiological mechanisms of ASD rooted in alterations in progenitor fate and unbalanced excitatory cortical neuron diversity.


title: Species' ranges and the steepening-gradient hypothesis

abstract: One hypothesis invoked to explain limits to species ranges is a mismatch in environmental conditions between the central and marginal areas of species ranges. Low population size at the margins causes genetic drift to outplay selection locally, and limits the accumulation of genetic variance, so that adaptation is hindered locally. Earlier theoretical work shows that for a population expanding over a spatially heterogeneous environment without any geographical barriers, adaptation will fail abruptly, which establishes definite range margins only when the underlying environmental conditions change more and more severely across space, whereas an environment changing constantly results either in infinite expansion or rapid global extinction. Here, we extend the steepening-gradient hypothesis to encompass situations when environmental gradients are decomposed into selection acting on separate adaptive traits. We show that the two gradients steepen each other, particularly highlighting the importance of locally shallow gradients that could be overlooked in field studies. Finally, by decomposing the environmental gradient to selection on two adaptive traits, populations can withstand harsher environmental conditions than when selection acts on one adaptive traits alone.


title: A new method and tool for volumetric estimation of brain structures after serial sectioning.

abstract:
Volume estimations are crucial for many neuroscience studies, allowing the evaluation of changes in the size of brain areas that may have relevant functional consequences. Classical histological methods and modern human brain imaging techniques rely on obtaining physical or digital sections, with a known thickness, of the organ to be analyzed. This "slicing" strategy is associated with an ineludible loss of information about the three-dimensional organization of the analyzed structures, especially affecting the precision of volumetric measurements. To overcome this problem, several methods have been developed. One of the most commonly used approaches for volume estimation is the classical Cavalieris method.

Within this book chapter, we provide first an overview of Cavalieris method and propose a new one, named the Truncated Cone Shape method, for the estimation of volumes from tissue sections. Second, we compare the accuracy of both methods using computer-generated objects of different shapes and sizes. We conclude that, more frequently, the TCS method provides a better estimate of real volumes than Cavalieris method. And third, we describe a protocol to estimate volumes using a self-developed and freely available tool for ImageJ: VolumestJ. This new tool helps to implement both Cavalieris and TCS methods using digital images of tissue sections. We consider that VolumestJ will facilitate the labor of researchers interested in volume estimations.


title: Persistent postnatal migration of interneurons into the human entorhinal cortex

abstract: The entorhinal cortex (EC) is a highly-interconnected hub for multisensory integration and memory processing1-3, containing diverse neuronal subtypes4,5 including subpopulations that are uniquely spatially-tuned6,7. Although many spatial and memory functions develop in infancy, it is considered that neurogenesis and neuronal migration to the EC occurs prenatally. Here we show that the postnatal human temporal lobe contains a prominent stream with large chains of young migrating neurons and many individual neurons breaking away directed into the EC. The EC stream forms between the second and third trimesters of prenatal development when the lateral ventricle walls in the temporal lobe collapse, displacing the subventricular zone (SVZ) and dividing radial glia. At birth, the EC stream follows a path of radial glial [fi]bers in the site of the collapsed ventricle. Migratory chains persist up to 11 months postnatally; however, many individually migrating young neurons can still be detected in the EC at 2 years of age and a few isolated cells at 3 years of age. Within the EC at birth, immature neurons are a mixed population expressing markers of the medial ganglionic eminence (MGE) and caudal ganglionic eminence (CGE), but postnatally rapidly become primarily CGE-derived. Using single-nuclei RNAseq we identified these lineages and found that the MGE-derived neurons matured at earlier postnatal ages compared to those derived from the CGE. The CGE interneurons arriving and maturing the latest included subtypes expressing calretinin (CR), reelin (RELN), and vasoactive intestinal protein (VIP) many of which settle in layer II of the entorhinal cortex. This study reveals that the human EC is still being constructed during the first years of life revealing the largest known postnatal stream of migratory neurons in humans. The protracted postnatal arrival of a diverse population of interneurons could contribute to plasticity8,9 and proper excitation-inhibition balance10,11 within these highly connected brain circuits.


title: Genetic Analysis Suggests a Surface of PAT-4 (ILK) that Interacts with UNC-112 (kindlin)

abstract: The transmembrane protein integrin plays a crucial role in the attachment of cells to the extracellular matrix. Integrin recruits many proteins intracellularly, including a four protein complex (Kindlin, Integrin linked kinase (ILK), PINCH, and parvin). C. elegans muscle provides an excellent model to study integrin adhesion complexes. In C. elegans, UNC-112 (Kindlin) binds to the cytoplasmic tail of PAT-3 ({beta}-integrin) and to PAT-4 (ILK). We previously reported that PAT-4 binding to UNC-112 is essential for the binding of UNC-112 to PAT-3. Although there are crystal structures for ILK and a kindlin, there is no co-crystal structure available. To understand the molecular interaction between PAT-4 (ILK) and UNC-112 (Kindlin), we took a genetic approach. First, we isolated mutant PAT-4 proteins that cannot bind to UNC-112. Then, we isolated suppressor mutant UNC-112 proteins that restore interaction with mutant PAT-4 proteins. Second, these mutant PAT-4 proteins cannot localize to attachment structures in nematode muscle, but upon co-expression of an UNC-112 suppressor mutant protein, the mutant PAT-4 protein could localize to attachment structures. Third, overexpression of a mutant PAT-4 protein results in disorganization of the adhesion plaques at muscle cell boundaries, and co-expression of the UNC-112 supressor mutant protein alleviates this defect. Thus, we demonstrate that UNC-112 binding to PAT-4 is required for the localization and function of PAT-4 in integrin adhesion complexes in vivo. The missense mutations were mapped onto homology models of PAT-4 and UNC-112, and taking into account previously isolated mutations, we suggest a surface of PAT-4 that binds to UNC-112.

category: genetics


title: Evidence that conserved essential genes are enriched for pro-longevity factors

abstract: At the cellular level, many aspects of aging are conserved across species. This has been demonstrated by numerous studies in simple model organisms like Saccharomyces cerevisiae, Caenorhabdits elegans, and Drosophila melanogaster. Because most genetic screens examine loss of function mutations or decreased expression of genes through reverse genetics, essential genes have often been overlooked as potential modulators of the aging process. By taking the approach of increasing the expression level of a subset of conserved essential genes, we found that 25% of these genes resulted in increased replicative lifespan in S. cerevisiae. This is greater than the [~]3.5% of genes found to affect lifespan upon deletion, suggesting that activation of essential genes may have a relatively disproportionate effect on increasing lifespan. The results of our experiments demonstrate that essential gene overexpression is a rich, relatively unexplored means of increasing eukaryotic lifespan.

category: cell biology


title: Using a combination of CRISPR/Cas9, behavioural experiments and functional analysis to characterise taste receptors in honeybees

abstract: Honeybees (Apis mellifera) need their fine sense of taste to evaluate nectar and pollen sources. Gustatory receptors (Grs) translate taste signals into electrical responses. In vivo experiments primarily demonstrate collective responses of the whole Gr-set, but little is known about the individual impact of receptors. Here, we disentangle for the first time the contributions of three gustatory receptors (AmGr1-3) in sugar sensing of honeybees by combining CRISPR/Cas9 mediated genetic knock-out, electrophysiology and behaviour. AmGr1 responds to multiple sugars. Bees lacking this receptor have a reduced response to sucrose and glucose but not to fructose. AmGr2 acts as co-receptor of AmGr1 in a heterologous expression system, but honeybee knock-out mutants perform normally. Eliminating AmGr3 while preserving AmGr1 and AmGr2 abolishes the perception of fructose but not of sucrose. We thus dissociate the roles of AmGr1, AmGr2 and AmGr3 in honeybee taste perception.

category: physiology


title: Avatar error in your favor: Embodied avatars can fix users mistakes without them noticing

abstract: In immersive Virtual Reality (VR), users can experience the subjective feeling of embodiment for the avatar representing them in a virtual world. This is known to be strongly supported by a high Sense of Agency (SoA) for the movements of the avatar that follows the user. In general, users do not self-attribute actions of their avatar that are different from the one they actually performed. The situation is less clear when actions of the avatar satisfies the intention of the user despite distortions and noticeable differences between user and avatar movements. A within-subject experiment was here conducted to determine whether a finger swap helping users achieve a task would be more tolerated than one penalizing them. In particular, in a context of fast-paced finger movements and with clear correct or incorrect responses, we swapped the finger animation of the avatar (e.g. user moves the index finger, the avatar moves the middle one) to either automatically correct for spontaneous mistakes or to introduce incorrect responses. Subjects playing a VR game were asked to report when they noticed the introduction of a finger swap. Results based on 3256 trials (~24% of swaps noticed) show that swaps helping users have significantly fewer odds of being noticed (and with higher confidence) than the ones penalizing users. This demonstrates how the context and the intention for motor action are important factors for the SoA and for embodiment, opening new perspectives on how to design and study interactions in immersive VR.


title: The DC1 domain protein BINUCLEATE POLLEN is required for pollen development in Arabidopsis

abstract: Development of the male gametophyte is a tightly regulated process that requires precise control of cell division and gene expression. A relevant aspect to understand the events underlying pollen development regulation constitutes the identification and characterization of the genes required for this process. In this work we showed that the DC1 domain protein BINUCLEATE POLLEN (BNP) is essential for pollen development and germination. Pollen grains carrying the defective BNP allele failed to complete mitosis II and are impaired in pollen germination. By yeast two hybrid screening and bimolecular fluorescence complementation assays, we identified a set of BNP-interacting proteins. Among confirmed interactors we found NAC family transcriptional regulators Vascular plant One-Zinc finger 1 (VOZ1) and VOZ2. VOZ1 localization changes during pollen development, moving to the vegetative nucleus at the tricellular stage. We observed that this relocalization requires BNP, as in their absence in pollen from bnp/BNP plants, VOZ1 nuclear localization resulted impaired. As voz1voz2 double mutants showed the same developmental defect observed in bnp pollen grains, we propose that BNP requirement to complete microgametogenesis could be linked to its interaction with VOZ1/2 proteins. BNP could have a role of scaffold protein, recruiting VOZ1/2 to the endosomal system into assemblies that are required for their further translocation to the nucleus, where they act as transcriptional regulators.

category: plant biology


title: The DC1 domain protein BINUCLEATE POLLEN is required for pollen development in Arabidopsis thaliana


title: Frequency-specific neural signatures of perceptual content and perceptual stability

abstract: In the natural environment, we often form stable perceptual experiences from ambiguous and fleeting sensory inputs. Which neural activity underlies the content of perception and which neural activity supports perceptual stability remains an open question. We used a bistable perception paradigm involving ambiguous images to behaviorally dissociate perceptual content from perceptual stability, and magnetoencephalography (MEG) to measure whole-brain neural dynamics in humans. Combining multivariate decoding and neural state-space analyses, we found frequency band-specific neural signatures that underlie the content of perception and promote perceptual stability, respectively. Across different types of images, non-oscillatory neural activity in the slow cortical potential (SCP, <5 Hz) range supported the content of perception. By contrast, perceptual stability is influenced by the amplitude of alpha and beta oscillations. In addition, neural activity underlying perceptual memory, which supports perceptual stability when sensory input is temporally removed from view, also encodes elapsed time. Together, these results reveal distinct neural mechanisms that support the content vs. stability of visual perception.


title: Enteroendocrine cell lineages that differentially control feeding and gut motility

abstract: Enteroendocrine cells are specialized sensory cells of the gut-brain axis that are sparsely distributed along the intestinal epithelium. The functions of enteroendocrine cells have classically been inferred by the gut hormones they release. However, individual enteroendocrine cells typically produce multiple, sometimes apparently opposing, gut hormones in combination, and some gut hormones are also produced elsewhere in the body. Here, we developed approaches involving intersectional genetics to enable selective access to enteroendocrine cells in vivo. We constructed Villin1-p2a-FlpO knock-in mice to restrict reporter expression to intestinal epithelium and through combined use of Cre and Flp alleles, effectively targeted major transcriptome-defined enteroendocrine cell lineages that produce serotonin, glucagon-like peptide 1, cholecystokinin, somatostatin, or glucose insulinotropic peptide. Chemogenetic activation of different enteroendocrine cell types variably impacted feeding behavior, nausea-associated behaviors (conditioned flavor avoidance), and gut motility. Defining the physiological roles of different enteroendocrine cell types provides an essential framework for understanding sensory biology of the intestine.


title: Effects of habitual dart training on hemispheric lateralization in older adults: a cross-sectional study using functional near-infrared spectroscopy

abstract: Exercise training is one of the most effective ways of preventing dementia. In this study, we focus on exercise training using a dart game called Wellness Darts. Previous studies have shown that Wellness Darts is effective in preventing dementia through cognitive memory testing. However, the effects of continual Wellness Dart training on brain function are unclear. The purpose of this study was to elucidate the effects of sustained Wellness Darts practice on brain function in older adults. Here, we cross-sectionally compared the brain activity patterns between an expert older group who practiced darts continually against control groups of a non-expert older group and a younger group who had no experience with darts. Functional near-infrared spectroscopy (fNIRS) was used to measure brain activity, and their patterns were quantified by lateralization index (LI). The results showed that the younger group and the expert older group had significantly higher LI values than the non-expert older group and that these values did not differ between the expert older and younger groups. In addition, the accuracy of the dart-throwing test in the expert older group was positively correlated with the LI value. These results suggest that the Wellness Dart promotes hemispheric lateralization and has potential as exercise training in the prevention of dementia.


title: A Novel High-Throughput Single B-Cell Cloning Platform for Isolation and Characterization of High-Affinity and potent SARS-CoV-2 Neutralizing Antibodies

abstract:
Monoclonal antibodies (mAbs) that are specific to SARS-CoV-2 can be useful in diagnosing, preventing, and treating the coronavirus (COVID-19) illness. Strategies for the high-throughput and rapid isolation of these potent neutralizing antibodies are critical toward the development of therapeutically targeting COVID-19 as well as other infectious diseases. In the present study, a single B-cell cloning method was used to screen SARS-CoV-2 receptor-binding domain (RBD) specific, high affinity, and neutralizing mAbs from patients blood samples. An RBD-specific antibody, SAR03, was discovered that showed high binding (ELISA and SPR) and neutralizing activity (competitive ELISA and pseudovirus-based reporter assay) against Sars-CoV-2. Mechanistic studies on human cells revealed that SAR03 competes with the ACE-2 receptor for binding with the RBD domain (S1 subunit) present in the spike protein of Sars-CoV-2. This study highlights the potential of the single B cell cloning method for the rapid and efficient screening of high-affinity and effective neutralizing antibodies for Sars-CoV-2 and other emerging infectious diseases.

HighlightsO_LISingle B-cell cloning is a high-throughput and efficient method of generating high affinity neutralizing antibodies
C_LIO_LISingle B-cell cloning method was used to screen SARS-CoV-2 receptor-binding domain (RBD) specific, high affinity, and neutralizing monoclonal antibodies from patients blood samples.
C_LIO_LIAn RBD-specific antibody, SAR03, was discovered that showed high binding and neutralizing activity against SARS-CoV-2.
C_LI

category: immunology


title: Durable protection against SARS-CoV-2 Omicron induced by an adjuvanted subunit vaccine

abstract: Despite the remarkable efficacy of COVID-19 vaccines, waning immunity, and the emergence of SARS-CoV-2 variants such as Omicron represents a major global health challenge. Here we present data from a study in non-human primates demonstrating durable protection against the Omicron BA.1 variant induced by a subunit SARS-CoV-2 vaccine, consisting of RBD (receptor binding domain) on the I53-50 nanoparticle, adjuvanted with AS03, currently in Phase 3 clinical trial (NCT05007951). Vaccination induced robust neutralizing antibody (nAb) titers that were maintained at high levels for at least one year after two doses (Pseudovirus nAb GMT: 2207, Live-virus nAb GMT: 1964) against the ancestral strain, but not against Omicron. However, a booster dose at 6-12 months with RBD-Wu or RBD-{beta} (RBD from the Beta variant) displayed on I53-50 elicited equivalent and remarkably high neutralizing titers against the ancestral as well as the Omicron variant. Furthermore, there were substantial and persistent memory T and B cell responses reactive to Beta and Omicron variants. Importantly, vaccination resulted in protection against Omicron infection in the lung (no detectable virus in any animal) and profound suppression of viral burden in the nares (median peak viral load of 7567 as opposed to 1.3x107 copies in unvaccinated animals) at 6 weeks post final booster. Even at 6 months post vaccination, there was significant protection in the lung (with 7 out of 11 animals showing no viral load, 3 out of 11 animals showing ~20-fold lower viral load than unvaccinated controls) and rapid control of virus in the nares. These results highlight the durable cross-protective immunity elicited by the AS03-adjuvanted RBD-I53-50 nanoparticle vaccine platform.


title: Peptidome Surveillance Across Evolving SARS-CoV-2 Lineages Reveals HLA Binding Conservation in Nucleocapsid Among Variants With Most Potential for T-Cell Epitope Loss In Spike

abstract: To provide a unique global view of the relative potential for evasion of CD8+ and CD4+ T cells by SARS-CoV-2 lineages as they evolve over time, we performed a comprehensive analysis of predicted HLA-I and HLA-II binding peptides in spike (S) and nucleocapsid (N) protein sequences of all available SARS-CoV-2 genomes as provided by NIH NCBI at a bi-monthly interval between March and December of 2021. A data supplement of all B.1.1.529 (Omicron) genomes from GISAID in early December was also used to capture the rapidly spreading variant. A key finding is that throughout continued viral evolution and increasing rates of mutations occurring at T-cell epitope hotspots, protein instances with worst case binding loss did not become the most frequent for any Variant of Concern (VOC) or Variant of Interest (VOI) lineage; suggesting T-cell evasion is not likely to be a dominant evolutionary pressure on SARS-CoV-2. We also determined that throughout the course of the pandemic in 2021, there remained a relatively steady ratio of viral variants that exhibit conservation of epitopes in the N protein, despite significant potential for epitope loss in S relative to other lineages. We further localized conserved regions in N with high epitope yield potential, and illustrated HLA-I binding heterogeneity across the S protein consistent with empirical observations. Although Omicrons high volume of mutations caused it to exhibit more epitope loss potential than most frequently observed versions of proteins in almost all other VOCs, epitope candidates across its most frequent N proteins were still largely conserved. This analysis adds to the body of evidence suggesting that N may have merit as an additional antigen to elicit immune responses to vaccination with increased potential to provide sustained protection against COVID-19 disease in the face of emerging variants.


title: Human Galectin-9 Potently Enhances SARS-CoV-2 Replication and Inflammation in Airway Epithelial Cells

abstract: The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic has caused a global economic and health crisis. Recently, plasma levels of galectin-9 (Gal-9), a {beta}-galactoside-binding lectin involved in immune regulation and viral immunopathogenesis, were reported to be elevated in the setting of severe COVID-19 disease. However, the impact of Gal-9 on SARS-CoV-2 infection and immunopathology remained to be elucidated. Here, we demonstrate that Gal-9 treatment potently enhances SARS-CoV-2 replication in human airway epithelial cells (AECs), including primary AECs in air-liquid interface (ALI) culture. Gal-9 promotes SARS-CoV-2 attachment and entry into AECs in an ACE2-dependent manner, enhancing the binding affinity of the viral spike protein to ACE2. Transcriptomic analysis revealed that Gal-9 and SARS-CoV-2 infection synergistically induced the expression of key pro-inflammatory programs in AECs including the IL-6, IL-8, IL-17, EIF2, and TNF signaling pathways. Our findings suggest that manipulation of Gal-9 should be explored as a therapeutic strategy for SARS-CoV-2 infection.

category: microbiology


title: Numb-associated kinases are required for SARS-CoV-2 infection and are cellular targets for therapy

abstract: The coronavirus disease 2019 (COVID-19) pandemic caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) continues to pose serious threats to global health. We previously reported that AAK1, BIKE and GAK, members of the Numb-associated kinase family, control intracellular trafficking of multiple RNA viruses during viral entry and assembly/egress. Here, using both genetic and pharmacological approaches, we probe the functional relevance of NAKs for SARS-CoV-2 infection. siRNA-mediated depletion of AAK1, BIKE, GAK, and STK16, the fourth member of the NAK family, suppressed SARS-CoV-2 infection in human lung epithelial cells. Both known and novel small molecules with potent AAK1/BIKE, GAK or STK16 activity suppressed SARS-CoV-2 infection. Moreover, combination treatment with the approved anti-cancer drugs, sunitinib and erlotinib, with potent anti-AAK1/BIKE and GAK activity, respectively, demonstrated synergistic effect against SARS-CoV-2 infection in vitro. Time-of-addition experiments revealed that pharmacological inhibition of AAK1 and BIKE suppressed viral entry as well as late stages of the SARS-CoV-2 life cycle. Lastly, suppression of NAKs expression by siRNAs inhibited entry of both wild type and SARS-CoV-2 pseudovirus. These findings provide insight into the roles of NAKs in SARS-CoV-2 infection and establish a proof-of-principle that pharmacological inhibition of NAKs can be potentially used as a host-targeted approach to treat SARS-CoV-2 with potential implications to other coronaviruses.


title: A dataset of 5 million city trees: species clustering and climate effects in urban forests

abstract: Sustainable cities depend on urban forests. City trees improve our health, clean the air, store CO2, and cool local temperatures. Comparatively less is known about urban forests as ecosystems, particularly their spatial composition, nativity statuses, biodiversity, and tree health. Here, we assembled and standardized a new dataset of N=5,132,890 trees from 63 of the largest US cities with detailed information on location, health, nativity status, and species. We further designed new tools to analyze the ecosystem structure of urban forests, including spatial clustering and abundance of native trees, and validate these tools in comparison to past methods. We show that city trees are significantly clustered by species in 93% of cities, potentially increasing pest vulnerability (even in cities with biodiverse urban forests). Further, non-native species significantly homogenize urban forests across cities, while native trees comprise 0.44%-85.6% (median=45.6%) of city tree populations. Native trees are less frequent in drier cities, and indeed climate significantly shapes both nativity and biodiversity in urban forests. Parks are more biodiverse than urban settings. Compared to past work which focused primarily on canopy cover and species richness, we show the importance of analyzing spatial composition and nativity statuses in urban forests (and we created new datasets and tools to do so). This dataset could be analyzed in combination with citizen-science datasets on bird, insect, or plant biodiversity; social and demographic data; or data on the physical environment. Urban forests offer a rare opportunity to intentionally design biodiverse, heterogenous, rich ecosystems.


title: Cannabinoids regulate an insula circuit controlling water intake

abstract: The insular cortex, or insula, is a large brain region involved in the detection of thirst and the control of water intake. However our understanding of the topographical, circuit and molecular mechanisms the controlling water intake within the insula remains parcellated. We found that type-1 cannabinoid receptors (CB1) within the insular cortex participate to the regulation of water intake, and deconstructed circuit mechanisms of this control. Topographically, we revealed that the activity of excitatory neurons in both anterior (aIC) and posterior (pIC) insula increases in response to water intake, yet removal of CB1 receptors only in the pIC decreases water intake. Interestingly, we found that CB1 receptors are highly expressed in insula projections to the basolateral amygdala (BLA), while undetectable in the neighboring central part of the amygdala. Thus, we imaged the neurons of the anterior or posterior insula targeting the BLA (aIC-BLA and pIC-BLA), and found they oppositely respond to water intake, respectively decreasing and increasing their activity upon water drinking. Consistently, chemogenetic activation of pIC-BLA neurons decreased water intake. Finally, we uncovered CB1-dependent short term synaptic plasticity (depolarization-induced suppression of excitation, DSE) selectively in pIC-BLA, compared to aIC-BLA synapses. Altogether, our results support a model where CB1 signaling in the pIC-BLA pathway exerts a positive control on water intake.


title: STING controls T cell memory fitness during infection through T cell intrinsic and IDO dependent mechanisms

abstract:
Stimulator of interferon genes (STING) signaling has been extensively studied in inflammatory diseases and cancer while its role in T cell responses to infection is unclear. Using Listeria monocytogenes strains engineered to induce different levels of c-di-AMP, we found that strong STING signals impaired T cell memory upon infection via increased Bim levels and apoptosis. Unexpectedly, reduction of TCR signal strength or T cell-STING expression decreased Bim expression, T cell apoptosis and recovered T cell memory. We found that TCR signal intensity coupled STING signal strength to the Unfolded Protein Response (UPR) and T cell survival. Under strong STING signaling, IDO inhibition also reduced apoptosis and led to a recovery of T cell memory in STING sufficient CD8 T cells. Thus, STING signaling regulates CD8 T cell memory fitness through both cell-intrinsic and extrinsic mechanisms. These studies provide insight into how IDO and STING therapies could improve long-term T cell protective immunity.

Significance StatementSTING signaling is an innate pathway that triggers host immunity against pathogens and cancer in response to cytosolic DNA. Additionally, STING signaling overactivation has been linked to autoimmunity. Yet, the interaction between antigenic and STING signaling and its impact in the development of protective immunity has remained unexplored. We found that strong levels of STING signaling impair CD8 T cell memory but only in response to high affinity TCR-pMHC interactions. Here, we provide evidence of how TCR signal strength controls STING signaling and IDO metabolism to regulate T cells survival as they mature to memory. These data have important implications for the design of STING and IDO combination immunotherapies


title: Lysosomal vesiculophagy terminates STING signalling

abstract: Stimulator of interferon genes (STING) is essential for the type I interferon response against a variety of DNA pathogens1,2. Upon emergence of cytosolic DNA, STING translocates from the endoplasmic reticulum (ER) to the Golgi where STING activates the downstream kinase TBK1, then to lysosome through recycling endosomes (REs) for its degradation3-6. Although the molecular machinery of STING activation is extensively studied and defined7, the one underlying STING degradation has not yet been fully elucidated. Here we show an unanticipated mechanism termed "lysosomal vesiculophagy" dictates STING degradation. Airyscan super-resolution microscopy and correlative light/electron microscopy show that a cluster of STING-positive vesicles of an RE origin are directly encapsulated into lysosome. Screening of mammalian Vps genes, the yeast homologues of which regulate Golgi-to-vacuole transport8, shows that the endosomal sorting complexes required for transport (ESCRT) is essential for the STING encapsulation into lysosome. Knockdown of Tsg101 and Vps4, components of ESCRT9, results in the accumulation of STING vesicles in the cytosol, leading to the sustained type I interferon response. STING undergoes ubiquitination at REs and degradation of STING requires the ubiquitin-binding domain of Tsg101, ensuring the selective degradation of activated STING. Our results reveal a novel mode of autophagy that prevents hyperactivation of innate immune signalling and provide insights into the ER-Golgi-REs-lysosomes pathway for degradation of transmembrane proteins.


title: Stability-instability transition in tripartite merged ecological networks

abstract: Although ecological networks are typically constructed based on a single type of interaction, e.g. trophic interactions in a food web, a more complete picture of ecosystem composition and functioning arises from merging networks of multiple interaction types. In this work, we consider tripartite networks constructed by merging two bipartite networks, one mutualistic and one antagonistic. Taking the interactions within each sub-network to be distributed randomly, we consider the stability of the dynamics of the network based on the spectrum of its community matrix. In the asymptotic limit of a large number of species, we show that the spectrum undergoes an eigenvalue phase transition, which leads to an abrupt destabilisation of the network as the ratio of mutualists to antagonists is increased. We also derive results that show how this transition is manifest in networks of finite size, as well as when disorder is introduced in the segregation of the two interaction types. Our random-matrix results will serve as a baseline for understanding the behaviour of merged networks with more realistic structures and/or more detailed dynamics.


title: A comprehensive meta-analysis of human assortative mating in 22 complex traits

abstract: Assortative mating (AM) occurs when the correlation for a trait between mates is larger than would be expected by chance. AM can increase the genetic and environmental variation of traits, can increase the prevalence of disorders in a population, and can bias estimates in genetically informed designs. In this study, we conducted the largest set of meta-analyses on human AM published to date. Across 22 traits, meta-analyzed correlations ranged from r = .08 to r = .58, with social attitude, substance use, and cognitive traits showing the highest correlations and personality, disorder, and biometrical traits generally yielding smaller but still positive and nominally significant (p < .05) correlations. We observed high between-study heterogeneity for most traits, which could have been the result of phenotypic measurement differences between samples and/or differences in the degree of AM across time or cultures.


title: LINE-1 retrotransposon activation intrinsic to interneuron development

abstract: Transposable elements (TEs) are a reservoir of new transcription factor binding sites for protein-coding genes1-3. Developmental programs that activate TE-derived regulatory elements could, in principle, manifest in lineage-specific TE mobility. While somatic LINE-1 (L1) retrotransposon insertions have been detected in human neurons4-6, the impact of L1 insertions on neurodevelopmental gene regulation, and whether L1 mobility is restricted to certain neuronal lineages, is unknown. Here, we reveal programmed L1 activation by SOX6, a transcription factor critical for parvalbumin (PV+) interneuron development7-9. PV+ neurons harbor unmethylated and euchromatic L1 promoters, express L1 mRNA, and permit L1 transgene mobilization in vivo. Elevated L1 expression in adult dentate gyrus PV+ neurons is however attenuated by environmental enrichment. Nanopore sequencing of PV+ neurons identifies unmethylated L1 loci providing alternative promoters to core PV+ neuron genes, such as CAPS2. These data depict SOX6-mediated L1 activation as an ingrained component of the mammalian PV+ neuron developmental program.

category: genomics


title: A Tailored Approach To Study Legionella Infection Using Lattice Light Sheet Microscope (LLSM)

abstract: Legionella is a genus of ubiquitous environmental pathogens found in freshwater systems, moist soil, and composted materials. More than four decades of Legionella research has provided important insights into Legionella pathogenesis [1]. Although standard commercial microscopes have led to significant advances in understanding Legionella pathogenesis [2,3], great potential exists in the deployment of more advanced imaging techniques to provide additional insights. The Lattice Light Sheet Microscope (LLSM) is a recently developed microscope for 4D live cell imaging with high resolution and minimum photo-damage [4]. We built and commissioned a LLSM to study Legionella pneumophila infection with a tailored workflow designed over instrumentation, experiments, and data processing methods. Our results indicate that Legionella pneumophila infection is correlated with a series of morphological signatures such as smoothness, migration pattern and polarity both statistically and dynamically. Our work demonstrates the benefits of using LLSM for studying long-term questions in bacterial infection. Our free-for-use modifications and workflow designs on the use of LLSM system contributes to the adoption and promotion of the state-of-the-art LLSM technology for both academic and commercial applications.

category: bioengineering


title: TATTOO-seq delineates spatial and cell type-specific regulatory programs during limb patterning

abstract: The coordinated differentiation of progenitor cells into specialized cell types and their spatial organization into distinct domains is central to embryogenesis. Here, we applied a new unbiased spatially resolved single-cell transcriptomics method to identify the genetic programs that underlie the emergence of specialized cell types during limb development and their integration in space. We uncovered combinations of transcription factors whose expression patterns are predominantly associated with cell type specification or spatial position, enabling the deconvolution of cell fate and position identity. We demonstrate that the embryonic limb undergoes a complex multi-scale re-organization upon perturbation of one of its spatial organizing centers, including the loss of specific cell populations, specific alterations in the molecular identities of other pre-existing cell states and changes in their relative spatial distribution. Altogether, our study shows how multi-dimensional single-cell and spatially resolved molecular atlases could reveal the interconnected genetic networks that regulate the intricacies of organogenesis and its reorganization upon genetic alterations.


title: Lack of a key stage of hyper-connectivity between deep and superficial layers during barrel cortex development in a rat model of Absence Epilepsy

abstract:
The development of cortical neuronal wiring is precisely orchestrated and goes through several stages, some of which coincide with critical periods when sensory experience is most influential. In particular, although ascending excitatory and inhibitory projections from the deep layer 5 to upper layers are first strong, they recede by the end of the critical period of their targets cells located in upper layers. Alterations in these transient innervations impair the construction of the later circuits that remain at adulthood, but it is unknown whether they could lead to pathologies. Here, we address this question in a genetic model of Absence Epilepsy, a neuro-developmental disease, where epileptogenesis occurs during the postnatal maturation of barrel cortex, the seizure initiation site. Using functional mapping by laser scanning photostimulation with glutamate uncaging in slices, we investigated the pattern of projections onto layers 2/3 pyramidal cells from 2-week old rats. We found that its maturation skipped the key stage during which pyramidal cells received strong projections from both excitatory and inhibitory neurons located in deep layers. At the same age, neuronal activity recorded in vivo with two-photon functional imaging was organized in fewer clusters than in control rat pups during this transient hyper-innervation. Later, around the onset of typical absence seizures ([~]1 month old), over-excitability of cells was observed across layers. Using this genetic model of childhood epilepsy, we provide first evidence that failure to develop this transient hyper-innervation from deep cortical layers plays a role in pathological neural dysfunctions.

Significance StatementDuring development of cortex, innervation from deep to upper layers is thought to provide a temporary scaffold for the construction of the circuits that remain at adulthood. Whether an alteration in this sequence causes brain malfunctions in neuro-developmental diseases is unknown. Using functional approaches, we investigated in a genetic model of Absence Epilepsy and control rats the maturation of innervation onto layer 2/3 pyramidal cells of barrel cortex and the cell organization into neuronal assemblies. We found that development in this model lacks this early surge of connectivity with deep layers and the concomitant structuring into multiple assemblies. Later on, at seizure onset, neurons in all layers are hyper-excitable, suggesting this feature of epilepsy develops from prior connectivity defects.


title: Barrel cortex development lacks a key stage of hyperconnectivity from deep to superficial layers in a rat model of Absence Epilepsy


title: Young adults who improve performance during dual-task walking show more flexible reallocation of cognitive resources: A Mobile Brain-Body Imaging (MoBI) study.

abstract: In young adults, pairing a taxing cognitive task with walking can have different effects on gait and cognitive task performance. In some cases, performance clearly declines whereas in others compensatory mechanisms maintain performance even under dual-task conditions. This study set out to investigate the preliminary finding of behavioral improvement in Go-NoGo response inhibition task performance during walking compared to sitting, which was observed at the piloting stage. Mobile Brain/Body Imaging (MoBI) was used to record electroencephalographic (EEG) activity, three-dimensional (3D) gait kinematics and behavioral responses in the cognitive task, during sitting or walking on a treadmill. In a cohort of twenty-six (26) young adults, fourteen (14) participants improved in measures of cognitive task performance while walking compared to sitting. These participants exhibited walking-related EEG amplitude reductions over frontal brain scalp regions during key stages of inhibitory control (conflict monitoring, control implementation and pre-motor stages), accompanied by reduced stride-to-stride variability and faster responses to stimuli compared to those who did not improve. In contrast, the twelve (12) participants who did not improve exhibited no EEG amplitude differences across physical condition. The neural activity changes associated with performance improvement during dual tasking hold promise as cognitive flexibility markers that can potentially help assess cognitive decline in aging and neurodegeneration.


title: Ultrasound Neuromodulation and Correlation Change in the Rat Somatosensory Cortex

abstract: Transcranial focused ultrasound (tFUS) is a neuromodulation technique which has been the focus of increasing interest for noninvasive brain stimulation with high spatial specificity. Its ability to excite and inhibit neural circuits as well as to modulate perception and behavior has been demonstrated, however, we currently lack understanding of how tFUS modulates the ways neurons interact with each other. This understanding would help explain tFUSs mechanism of high-level neuromodulation and allow future development of therapies for neurological disorders. In this study we investigate how tFUS modulates neural interaction and response to peripheral electrical limb stimulation through intracranial multi-electrode recordings in the rat somatosensory cortex. We deliver ultrasound in a pulsed pattern to attempt to induce frequency dependent plasticity in a manner similar to that found following electrical stimulation. We show that neural firing in response to peripheral electrical stimulation is increased after ultrasound stimulation at all frequencies, showing tFUS induced excitation in individual neurons in vivo. We demonstrate tFUS frequency dependent pairwise correlation changes between neurons, with both potentiation and depression observed at different frequencies. These results extend previous research showing tFUS to be capable of inducing synaptic depression and demonstrate its ability to modulate network dynamics as a whole.


title: In vivo low-intensity magnetic pulses durably alter neocortical neuron excitability and spontaneous activity.

abstract: Magnetic brain stimulation is a promising treatment for neurological and psychiatric disorders. However, a better understanding of its effects at the individual neuron level is essential to improve its clinical application. We combined focal low-intensity repetitive transcranial magnetic stimulation (LI-rTMS) to the rat somatosensory cortex with intracellular recordings of subjacent pyramidal neurons in vivo. Continuous 10 Hz LI-rTMS reliably evoked firing at [~]4-5 Hz during the stimulation period and induced durable attenuation of synaptic activity and spontaneous firing in cortical neurons, through membrane hyperpolarization and a reduced intrinsic excitability. However, inducing firing in individual neurons by repeated intracellular current injection did not reproduce LI-rTMS effects on neuronal properties. These data provide novel understanding of mechanisms underlying magnetic brain stimulation showing that, in addition to inducing biochemical plasticity, even weak magnetic fields can activate neurons and enduringly modulate their excitability.


title: Investigating the temporal pattern of neuroimaging-based brain age estimation as a biomarker for Alzheimer's Disease related neurodegeneration

abstract: Neuroimaging-based brain-age estimation via machine learning has emerged as an important new approach for studying brain aging. The difference between ones estimated brain age and chronological age, the brain age gap (BAG), has been proposed as an Alzheimers Disease (AD) biomarker. However, most past studies on the BAG have been cross-sectional. Identifying how an individuals BAG temporal pattern changes over time would enable improved prediction of clinical outcome based on neurophysiological changes and better understanding of AD progression. To fill this gap, our study conducted predictive modeling using large neuroimaging data with up to 8 years of follow-up to examine the temporal patterns of the BAGs trajectory and how it varies by subject-level characteristics and disease status. To the best of our knowledge, this is the first effort to take a longitudinal approach to investigate the pattern and rate of change in BAG over time in individuals who progress from mild cognitive impairment (MCI) to clinical AD. Combining multimodal imaging data in a support vector regression model to estimate brain age yielded improved performance than single modality. Multilevel modeling results showed the BAG followed a linear increasing trajectory with a significantly faster rate in individuals with MCI who progressed to AD compared to cognitively normal or MCI individuals who did not progress. The dynamic changes in the BAG during AD progression were further moderated by gender and APO{varepsilon}4 carriership. Findings demonstrate the BAG as a potential biomarker for understanding individual specific temporal patterns related to AD progression.


title: Shared and distinct brain regions targeted for immediate early gene expression by ketamine and psilocybin

abstract:
BackgroundPsilocybin is a psychedelic with therapeutic potential. While there is growing evidence that psilocybin exerts its beneficial effects through enhancing neural plasticity, the exact brain regions involved are not completely understood. Determining the impact of psilocybin on plasticity-related gene expression throughout the brain can broaden our understanding of the neural circuits involved in psychedelic-evoked neural plasticity.

MethodsWhole-brain serial two-photon microscopy and light sheet microscopy were employed to map the expression of the immediate early gene, c-Fos, in male and female mice. The drug-induced c-Fos expression following psilocybin administration was compared to that of subanesthetic ketamine and saline control. To gain insights into the contributions of receptors and cell types, the c-Fos expression maps were related to brainwide in situ hybridization data.

ResultsPsilocybin and ketamine produced acutely comparable elevations in c-Fos expression in numerous brain regions, including anterior cingulate cortex, locus coeruleus, primary visual cortex, central and basolateral amygdala, and claustrum. Select regions exhibited drug-preferential differences, such as dorsal raphe, lateral habenula, and insular cortex for psilocybin and retrosplenial cortex for ketamine. Correlation of psilocybins effects with gene expression highlighted potential roles of 5-HT2A and GluN2B subunit of NMDA receptors.

ConclusionsThe systematic mapping approach produced an unbiased list of brain regions impacted by psilocybin and ketamine. The data are a valuable resource that highlights previously underappreciated regions for future investigations. By identifying regions with similar and disparate effects, the results provide insights into how psilocybin and ketamine may produce their rapid-acting and long-lasting therapeutic effects.


title: Interleukin-27 skews TNF-alpha-induced inflammatory microenvironment in keratinocytes

abstract: Inflammaging has received considerable attention because aging is characterized by low-grade, chronic and asymptomatic inflammation, concomitant with increased blood levels of senescence-associated secretory phenotype (SASP) factors, including IL-1, IL-6, IL-8, IL-18 and tumor necrosis factor-alpha (TNF-alpha). On the other hand, IL-27 is not categorized as SASP factors though it is known that IL-27 has pleiotropic roles in inflammation. Here, we evaluated the interaction between TNF-alpha and IL-27 in the context of low-grade inflammation by using in HaCaT cells. TNF-alpha induced significant upregulation of IL-6 and IL-8 through the experimental concentrations (~10 ng/ml) of TNF-alpha, while the mRNA expression levels of IL-1RA, IL-10 and IL-18BP were unchanged. After confirming the expression of IL-27 receptor in HaCaT cells, we examined the effects of IL-27 alone on the cytokine expression. IL-27 alone significantly enhanced mRNA expression levels of IL-10 and IL-18BP by 1.61-fold and 1.46-fold, respectively, and also enhanced mRNA expression levels of IL-6 by 2.32-fold. In the presence of 100 ng/ml IL-27, the expression levels of anti-inflammatory cytokines, IL-1RA, IL-10 and IL-18BP, were significantly upregulated with the treatment of a physiological concentration (1 ng/ml) TNF-alpha. Taken together, a high concentration of IL-27 exhibits anti-inflammatory effects in the presence of a low concentration of TNF-alpha when keratinocytes are the recipient of IL-27 signaling, suggesting the anti-inflammatory roles of IL-27 in inflammaging may be regulated by TNF-alpha concentration.


title: Environmental and genetic disease modifiers of haploinsuffciency of A20

abstract: Monogenic diseases can often manifest diverse clinical phenotypes and cause diagnostic dilemmas. While monoallelic loss-of-function variants in TNFAIP3 (Haploinsufficiency of A20; HA20) cause a highly penetrant autoinflammatory disease, the variable expressivity suggest a role for additional genetic and environmental disease modifiers. Here, we identify critically ill children who inherited a family-specific TNFAIP3 deletion from one of their otherwise healthy parents. Each of the probands also inherited in trans a subtle loss-of-function I207L TNFAIP3 variant that is common in Oceania, originally introgressed from Denisovans. Modelling this compound heterozgous state in mice under specific pathogen free conditions demonstrated a reduced threshold to break immune tolerance. Exaggerated immune responses were precipitated by inheriting the two genetic hits on the TNFAIP3 checkpoint coupled with increasing the microbial challenge to immune tolerance, either by co-housing with pet store mice carrying a wild microbial burden or by transient dietary exposure to a chemical that diminishes the intestinal mucin barrier separating gut microbes from immune sensing systems. These data illuminate second-hit genetic and environmental modifiers contributing to complex inflammatory and autoimmune disease. Increased mechanistic understanding of the presence and contribution of disease modifiers will aid diagnostic and prognostic patient stratification and potentially reveal novel therapeutic opportunities.


title: Environmental and genetic disease modifiers of haploinsufficiency of A20


title: PrrA modulates Mycobacterium tuberculosis response to multiple environmental cues and is critically regulated by serine/threonine protein kinases

abstract: The ability of Mycobacterium tuberculosis (Mtb) to adapt to its surrounding environment is critical for the bacterium to successfully colonize its host. Transcriptional changes are a vital mechanism by which Mtb responds to key environmental signals experienced, such as pH, chloride (Cl-), nitric oxide (NO), and hypoxia. However, much remains unknown regarding how Mtb coordinates its response to the disparate signals seen during infection. Utilizing a transcription factor (TF) overexpression plasmid library in combination with a pH/Cl--responsive luciferase reporter, we identified the essential TF, PrrA, part of the PrrAB two-component system, as a TF involved in modulation of Mtb response to pH and Cl-. Further studies revealed that PrrA also affected Mtb response to NO and hypoxia, with prrA overexpression dampening induction of NO and hypoxia- responsive genes. PrrA is phosphorylated not just by its cognate sensor histidine kinase PrrB, but also by serine/threonine protein kinases (STPKs) at a second distinct site. Strikingly, a STPK phosphoablative PrrA variant was significantly dampened in its response to NO versus wild type Mtb, disrupted in its ability to adaptively enter a non-replicative state upon extended NO exposure, and attenuated for in vivo colonization. Together, our results reveal PrrA as an important regulator of Mtb response to multiple environmental signals, and uncover a critical role of STPK regulation of PrrA in its function.


title: Eusocial insect queens show costs of reproduction and transcriptomic signatures of reduced longevity

abstract: Eusocial insect queens have been suggested to be counter-examples to the standard evolutionary theory of ageing through lacking costs of reproduction. Using the bumblebee (Bombus terrestris), we tested this hypothesis experimentally against the alternative that costs of reproduction exist in eusocial insect queens, but are latent, resulting in the positive fecundity-longevity relationship typically found in unmanipulated queens. We experimentally increased queens costs of reproduction by removing their eggs, which causes queens to increase their egg-laying rate. Treatment queens had significantly reduced longevity relative to control queens whose egg-laying rate was not increased. In addition, treatment and control queens differed in age-related gene expression based on mRNA-seq in both their overall expression profiles and the expression of ageing-related genes. Remarkably, this occurred principally with respect to relative age, not chronological age. These results provide the first simultaneously phenotypic and transcriptomic experimental evidence of costs of reproduction in queens of eusocial insects and suggest how the genetic pathways underpinning ageing might become remodelled during eusocial evolution.


title: Cloning of Nine Glucocorticoid Receptor Isoforms from the Slender African lungfish (Protopterus dolloi)

abstract: We wanted to clone the glucocorticoid receptor (GR) from slender African lungfish (Protopterus dolloi) for comparison to P. dolloi MR, which we had cloned and were characterizing, as well as for comparison to the GRs from humans, elephant shark and zebrafish. However, although sequencing of the genome of the Australian lungfish (Neoceratodus forsteri), as well as, that of the West African lungfish (Protopterus annectens) were reported in the first three months of 2021, we could not retrieve a GR sequence with a BLAST search of GenBank, when we submitted our research for publication in July 2021. Moreover, we were unsuccessful in cloning the GR from slender African lungfish using a cDNA from the ovary of P. dolloi and PCR primers that had successfully cloned a GR from elephant shark, Xenopus and gar GRs. On October 21, 2021 the nucleotide sequence of West African lungfish (P. annectens) GR was deposited in GenBank. We used this GR sequence to construct PCR primers that successfully cloned the GR from the slender spotted lungfish. Here, we report the sequences of nine P. dolloi GR isoforms and explain the basis for the previous failure to clone a GR from slender African lungfish using PCR primers that cloned the GR from elephant shark, Xenopus and gar. Studies are underway to determine corticosteroid activation of these slender African lungfish GRs.


title: No evidence for asymmetric sperm deposition in a species with asymmetric male genitalia

abstract:
BackgroundAsymmetric genitalia have repeatedly evolved in animals, yet the underlying causes for their evolution are mostly unknown. The fruitfly Drosophila pachea has asymmetric external genitalia and an asymmetric phallus with a right-sided gonopore. The complex of female and male genitalia is asymmetrically twisted during copulation and males adopt a right-sided copulation posture on top of the female. We wished to investigate if asymmetric male genital morphology and a twisted gentitalia complex may be associated with differential allocation of sperm into female sperm storage organs.

MethodsWe examined the internal complex of female and male reproductive organs by micro-computed tomography using Synchrotron X-rays before, during and after copulation. In additon, we monitored sperm aggregation states and timing of sperm transfer during copulation by premature interruption of copulation at different time-points.

ResultsThe asymmetric phallus is located at the most caudal end of the female abdomen during copulation. The female reproductive tract, in particular the oviduct, re-arranges during copulation. It is narrow in virgin females and forms a broad vesicle at 20 min after the start of copulation. Sperm transfer into female sperm storage organs (spermathecae) was only in a minority of examined copulation trials (13 / 64). Also, we found that sperm was mainly transferred early, at 2 - 4 min after the start of copulation. We did not detect a particular pattern of sperm allocation in the left or right spermathecae. Sperm adopted a granular or filamentous aggregation state in the female uterus and spermathecae, respectively.

DiscussionNo evidence for asymmetric sperm deposition was identified that could be associated with asymmetric genital morphology or twisted complexing of genitalia. Male genital asymmetry may potentially have evolved as a consequence of a complex internal alignment of reproductive organs during copulation in order to optimize low sperm transfer rates.


title: Near telomere-to-telomere nuclear phased chromosomes of the dikaryotic wheat fungus Rhizoctonia cerealis

abstract:
Rhizoctonia cerealis (Rce), which causes sharp eyespot, is one of the most destructive wheat pathogens. However, the genetic and molecular virulence mechanisms of Rce have not been elucidated. As a dikaryotic organism, the haplotype phasing of this fungus has not been completed so far. We applied a haplotype phasing algorithm to generate a high-quality near telomere-to-telomere nuclear-phased genome sequence of Rce strain R0301. Sixteen pairs of chromosomes were assigned to the A and B genomes with a total size of 83 Mb. Based on a dual-time course RNA-seq, 25308 genes were predicted. Genes for steroid biosynthesis and starch and sucrose metabolism were significantly enriched, together with many genes encoding carbohydrate-active enzymes (CAZymes) and secreted effector proteins, which should be involved in infection of wheat plants. Population genomic analysis of 31 isolates collected in China during the last forty years suggests that this population has not undergone substantial differentiation over time.

ImportanceThe finished genome reference is the basis of revealing pathogens biology base. Many efforts have been made to produce the chromosome-scale assembly of fungi. However, the reference of many pathogenic fungi is highly fragmented, which prevents the analysis of genome structure variation, evolution and import pathogenicity genes. Here, we assembly the only chromosome-scale haplotype-phased reference of dikaryotic fungus so far. This assembly achieves the gold standard based on many evaluation software, which indicates that the pipeline developed in this study can be applied to assemble references for other dikaryotic organisms. This work can also promote the research on the globes destructive wheat pathogens, sharp eyespot, caused by R. cerealis.


title: Engineering Antioxidant and Oxygen-Releasing Lignin Composites to Accelerate Wound Healing

abstract: The application of engineered biomaterials for wound healing has been pursued since the beginning of tissue engineering. Here, we attempt to apply functionalized lignin to confer antioxidation to wound extracellular microenvironments and to deliver oxygen via calcium peroxide for enhanced vascularization and healing responses without eliciting inflammatory responses. We demonstrated in vitro that thiolated lignosulfonate in alkene-incorporated gelatin effectively promoted the expression of angiogenesis and extracellular matrix production genes and attenuated the expression of oxidative stress genes of human dermal fibroblasts. Elemental analysis of oxygen releasing nanoparticles showed the positive incorporation of calcium peroxide. Lignin composites including nanoparticles of sodium lignosulfonate and calcium peroxide released around 0.05% oxygen per day at least for 7 days. By modulating the concentration the alkene-incorporated gelatin, we were able to maintain the injectability of lignin composite precursors and the stiffness of lignin composites after photo-crosslinking. In situ formation of lignin composites with oxygen generation nanoparticles enhanced the formation of blood vessels and promoted infiltration of a-smooth muscle actin+ fibroblasts into the wounds over 7 days. At 30 days after surgery, the lignin composite with oxygen generating nanoparticles remodeled the collagen architecture resembling to the reticular pattern of normal collagen with minimal scar formation. Thus, our study shows the potential of functionalized lignosulfonate for wound healing applications requiring balanced antioxidation and controlled release of oxygen for enhanced vascularization and maturation of collagens.


title: CNETML: Maximum likelihood inference of phylogeny from copy number profiles of spatio-temporal samples

abstract: Phylogenetic trees based on copy number alterations (CNAs) for multi-region samples of a single cancer patient are helpful to understand the spatio-temporal evolution of cancers, especially in tumours driven by chromosomal instability. Due to the high cost of deep sequencing data, low-coverage data are more accessible in practice, which only allow the calling of (relative) total copy numbers due to the lower resolution. However, methods to reconstruct sample phylogenies from CNAs often use allele-specific copy numbers and those using total copy number are mostly distance matrix or maximum parsimony methods which do not handle temporal data or estimate mutation rates. In this work, we developed a new maximum likelihood method based on a novel evolutionary model of CNAs, CNETML, to infer phylogenies from spatio-temporal samples taken within a single patient. CNETML is the first program to jointly infer the tree topology, node ages, and mutation rates from total copy numbers when samples were taken at different time points. Our extensive simulations suggest CNETML performed well even on relative copy numbers with subclonal whole genome doubling events and under slight violation of model assumptions. The application of CNETML to real data from Barretts esophagus patients also generated consistent results with previous discoveries and novel early CNAs for further investigations.


title: A Cambrian soft-bodied conical animal illustrates the origins of lophophorate phyla

abstract: The origin and early evolution of lophotrochozoans remain a difficult but crucial issue in reconstructing metazoan phylogeny. Exceptionally preserved fossils have provided hopeful information for resolving this lophotrochozoan problem. Here we identify that Conicula striata, a soft-bodied conical animal from the early Cambrian Chengjiang Lagerstatte, has mosaic characteristics of different lophophorate phyla. C. striata possesses a phoronid-like vermiform trunk housing a U-shaped gut and a coiled lophophore comprising [≥]12 arms with numerous tentacles, but it also bears brachiopod-like features including an undivided mantle enclosing lophophore and a pedicle-like protrusion on annulated trunk. Phylogenetic analysis retrieves C. striata as a total-group lophophorate and as an intermediate taxon between Phoronida and Brachiopoda. This suggests that the bivalved architecture of brachiopods originated from an undivided mantle in a phoronid-like ancestor, and that the ancestral vermiform trunk became reduced during the origin of Brachiopoda, illuminating the origins of body plans in the lophophorate phyla.

category: paleontology


title: Structural connectivity gradient associated with a dichotomy reveals the topographic organization of the macaque insular cortex

abstract: Histology studies revealed that the macaque insular cortex was characterized by the gradual organizations containing agranular, dysgranular and granular insula. However, no consensus has been reached on the elaborate subdivisions of macaque insula. Until now, no neuroimaging study to our knowledge combining connectivity-based gradients and parcellation has been performed to investigate the topographic organization of the macaque insular cortex. In this study, we used high-resolution ex vivo diffusion-weighted imaging data to explore the macaque insular cortexs global gradient organization and subdivisions. We found a rostrocaudal organization of the dominant gradient in the macaque insula using a diffusion map embedding. Meanwhile, extracting the 25% top and bottom components from the dominant and second gradient, which explained variance over 60% in total within ten gradients, the connectivity-based parcellation method was performed to subdivide each component into two subregions confirmed by the cross-validation analysis. Furthermore, permutations tests identified that two subregions from each component showed significant differences between their connectivity fingerprints. Finally, we found that the dominant and second gradients were significantly correlated with the T1w/T2w and cortical thickness maps in the macaque insula. Taken together, the global gradients combining the subdivisions examined the topographic organization of the macaque insular cortex based on the structural connectivity, which may contribute to a better understanding of the intricate insular cortex anatomy.


title: Identification of Microbial Flora and Isolation of Functional Strains Related to the Degradation of Domestic Waste

abstract: A large amount of food waste is currently generated due to rapid global population growth, which results in environmental pollution and economical burdens for waste disposal. Composting is one of the most environmentally friendly and cost-effective methods for food waste treatment. This study aims to give insight into microbial community structure and functional strains of household food waste compost, which might optimize the composting process and help increase food waste treatment efficiency. The microbial community is characterized via 16S rRNA sequencing. The dominant microbes are assigned to the three phyla of Firmicutes, Proteobacteria and Bacteroidetes, and the main fungi are assigned to the phylum of Ascomycota. We isolated some functional microbes from the compost microbiota, including Alcaligenes faecalis, Paenochrobactrum glaciei, Lysinibacillus fusiformis, and Proteus terrae. Moreover, we detected lipase and cellulase activities in the compost liquid. However, the measured lipase and cellulase activity is low, and further enhancement of the lipase activity in the food waste compost might increase waste treatment ability. Therefore, we isolated a cellulase and lipase harboring Bacillus cereus strain from municipal a wastewater treatment plant. The B. cereus strain have high-level lipase activity, which could be used for food waste treatment in the future.


title: RAD52 underlies the synthetic-lethal relationship between BRCA1/2 and 53BP1 deficiencies and DNA polymerase theta loss.

abstract: Introductory paragraphCells lacking several DNA repair proteins, including those promoting homologous recombination (HR), are sensitive to polymerase theta (Pol{theta}) repression1-4. Pol{theta} drives theta-mediated end joining (TMEJ) and suppresses HR but what mediates its synthetic lethal relationships is unclear. Here we examine murine Brca1C61G/C61G 53bp1-/-cells and find they are largely HR proficient by using RNF168 and RAD52. They exhibit no more TMEJ than 53bp1-/- cells yet are more sensitive to targeting of Pol{theta}. We find that RAD52 recruitment to damaged chromatin is increased following Pol{theta} depletion. RAD52 accumulation and cellular sensitivity to Pol{theta} repression can be curbed by the RAD51-binding regions of BARD1 and BRCA2, and sensitivity of BRCA1/2 depleted cells to Pol{theta} repression is suppressed by RAD52 inhibition. 53bp1-/- cells exhibit a smaller increase in RAD52 recruitment following Pol{theta} repression and also become resistant to Pol{theta} repression following RAD52 inhibition. Thus, RAD52 mediates sensitivity to targeting Pol{theta} in these contexts.

category: molecular biology


title: Pore-forming protein 	βγ-CAT promptly responses to fasting with capacity to deliver macromolecular nutrients

abstract: During animal fasting, the nutrient supply and metabolism switch from carbohydrates to a new reliance on the catabolism of energy-dense lipid stores. Assembled under tight regulation, {beta}{gamma}-CAT is a pore-forming protein and trefoil factor complex identified in toad Bombina maxima. Here, we determined that this protein complex is a constitutive component in toad blood, that actively responds to the animal fasting. The protein complex was able to promote cellular albumin and albumin-bound fatty acid uptake in a variety of epithelial and endothelial cells, and the effects were attenuated by a macropinocytosis inhibitor. Endothelial cell-derived exosomes containing largely enriched albumin and fatty acids, called nutrisomes, were released in the presence of {beta}{gamma}-CAT. These specific nutrient vesicles were readily taken by starved muscle cells to support their survival. The results uncovered that pore-forming protein {beta}{gamma}-CAT is a fasting responsive element able to drive cell vesicular import and export of macromolecular nutrients.


title: Combination of the Systemin peptide with the beneficial fungus Trichoderma afroharzianum T22 improves plant defense responses against pests and diseases

abstract: Trichoderma spp. are among the most widely used plant beneficial fungi in agriculture. A novel approach to enhance their effectiveness in plant defense is to use the fungi in combination with bioactive molecules including plant-derived compounds. Here, we show that plant treatment with Trichoderma afroharzianum (strain T22) and Systemin (Sys), a tomato plant peptide active in triggering plant defense, confers protection against the fungal pathogens Fusarium oxysporum, Botrytis cinerea and the insect pest Tuta absoluta. The observed defensive response was associated with increased accumulation of metabolites and transcripts involved in the Jasmonic acid (JA) pathway. Our findings suggest that the innovative combination of T. afroharzianum T22 and Sys can result in a more effective and robust control of different biotic stress agents.


title: The miR-15a/16-1 and miR-15b/16-2 clusters regulate early B cell development by limiting IL-7 receptor expression

abstract:
Pleiotropic functions of miRNAs as transcriptional repressors have been reported for multiple biological processes. One prominent miRNA family is the miR-15 family, which is a well-established tumor-suppressor in B-cell chronic lymphocytic leukemia (CLL). The miR-15 family consists of three bicistronic clusters, miR-15a/16-1, miR-15b/16-2 and miR-497/195, all sharing the same seed sequence suggesting that loss one cluster can be functionally compensated by the remaining miR-15 family members. Thus, a combined deletion may be necessary to reveal its physiological function in vivo.

A combined knockout of the most prominent miR-15 clusters, miR-15a/16-1 and miR-15b/16-2 in the hematopoietic system reveals a novel role of the miR-15 family in early B cell development highlighted by an increase of the pro-B cell compartment. Mechanistically, this effect is mediated by enhanced IL-7 receptor expression, which we identified as direct miR-15 target gene. Notably, elevated IL-7 receptor levels were sufficient to trigger increased activation of the STAT5 and PI3K/AKT pathways. Moreover, derepression of directly targeted cell cycle regulators such as Ccne1, Chek1 and Wee1 further facilitates G-to-S transition.

Thus, by deregulating a target gene network of cell cycle and signaling mediators, loss of the miR-15 family establishes a pro-proliferative milieu manifesting in an enlarged pro-B cell pool.


title: Complete chloroplast genomes and phylogeny in three Euterpe palms (E. edulis, E. oleraceae and E. precatoria) from different Brazilian biomes

abstract: The Brazilian palm fruits and hearts-of-palm of Euterpe edulis, E. oleracea and E. precatoria are an important source for agro-industrial production, but overexploitation requires conservation strategies to maintain genetic diversity. Chloroplast genomes have conserved sequences, which are useful to explore evolutionary questions. Besides the plastid DNA, genome skimming allows the identification of other genomic resources, such as single nucleotide polymorphisms (SNPs), providing information about the genetic diversity of species. We sequenced the chloroplast genome and identified gene content in the three Euterpe species. We performed comparative analyses, described the polymorphisms among the chloroplast genome sequences (repeats, indels and SNPs) and performed a phylogenomic inference based on 55 palm species chloroplast genomes. Finally, using the remaining data from genome skimming, the nuclear and mitochondrial reads, we identified SNPs and estimated the genetic diversity among these Euterpe species. The Euterpe chloroplast genomes varied from 159,232 to 159,275 bp and presented a conserved quadripartite structure with high synteny with other palms. In a pairwise comparison, we found a greater number of insertions/deletions (indels = 93 and 103) and SNPs (284 and 254) between E. edulis/E. oleracea and E. edulis/E. precatoria when compared to E. oleracea/E. precatoria (58 indels and 114 SNPs). Also, the phylogeny indicated a closer relationship between E. oleracea/E. precatoria. The nuclear and mitochondrial genome analyses identified 1,077 SNPs and high divergence among species (FST = 0.77), especially between E. edulis and E. precatoria (FST = 0.86). These results showed that, despite the few structural differences among the chloroplast genomes of these Euterpe palms, a differentiation between E. edulis and the other Euterpe species can be identified by point mutations. This study not only brings new knowledge about the evolution of Euterpe chloroplast genomes, but also these new resources open the way for future phylogenomic inferences and comparative analyses within Arecaceae.


title: Mapping the Neural Dynamics of Locomotion across the Drosophila Brain

abstract: Walking is a fundamental mode of locomotion, yet its neural correlates are unknown at brain-wide scale in any animal. We use volumetric two-photon imaging to map neural activity associated with walking across the entire brain of Drosophila. We detect locomotor signals in approximately 40% of the brain, identify a global signal associated with the transition from rest to walking, and define clustered neural signals selectively associated with changes in forward or angular velocity. These networks span functionally diverse brain regions, and include regions that have not been previously linked to locomotion. We also identify time-varying trajectories of neural activity that anticipate future movements, and that represent sequential engagement of clusters of neurons with different behavioral selectivity. These motor maps suggest a dynamical systems framework for constructing walking maneuvers reminiscent of models of forelimb reaching in primates and set a foundation for understanding how local circuits interact across large-scale networks.


title: A reinforcement learning algorithm shapes maternal care in mice

abstract:
The neural substrates for processing classical rewards such as food or drugs of abuse are well-understood. In contrast, the mechanisms by which organisms perceive social contact as rewarding and subsequently modify their interactions are unclear. Here we tracked the gradual emergence of a repetitive and highly-stereotyped parental behavior and show that trial-by-trial performance correlates with the history of midbrain dopamine (DA) neuron activity. We used a novel behavior paradigm to manipulate the subjects expectation of imminent pup contact and show that DA signals conform to reward prediction error, a fundamental component of reinforcement learning (RL). Finally, closed-loop optogenetic inactivation of DA neurons at the onset of pup contact dramatically slowed emergence of parental care. We conclude that this prosocial behavior is shaped by an RL mechanism in which social contact itself is the primary reward.

One-Sentence SummaryMaternal interactions with offspring are shaped by a dopaminergic reinforcement learning mechanism.


title: PiSpy: An Affordable, Accessible, and Flexible Imaging Platform for the Automated Observation of Organismal Biology and Behavior.

abstract: A great deal of understanding can be gleaned from direct observation of organismal growth, development, and behavior. However, direct observation can be time consuming and influence the organism through unintentional stimuli. Additionally, video capturing equipment can often be prohibitively expensive, difficult to modify to ones specific needs, and may come with unnecessary features. Here, we describe the PiSpy, a low-cost, automated video acquisition platform that uses a Raspberry Pi computer and camera to record video or images at specified time intervals or when externally triggered. All settings and controls, such as programmable light cycling, are accessible to users with no programming experience through an easy-to-use graphical user interface. Importantly, the entire PiSpy system can be assembled for less than $100 using laser-cut and 3D-printed components. We demonstrate the broad applications and flexibility of the PiSpy across a range of model and non-model organisms. Designs, instructions, and code can be accessed through an online repository, where a global community of PiSpy users can also contribute their own unique customizations and help grow the community of open-source research solutions.

category: animal behavior and cognition


title: Screening of hydrocarbon-stapled peptides for inhibition of calcium-triggered exocytosis

abstract: The so-called primary interface between the SNARE complex and synaptotagmin-1 (Syt1) is essential for Ca2+-triggered neurotransmitter release in neuronal synapses. The interacting residues of the primary interface are conserved across different species for synaptotagmins (Syt1, Syt2, Syt9), SNAP-25, and syntaxin-1A homologs involved in fast synchronous release. This Ca2+-independent interface forms prior to Ca2+-triggering and plays a role in synaptic vesicle priming. This primary interface is also conserved in the fusion machinery that is responsible for mucin granule membrane fusion. Ca2+ stimulated mucin secretion is mediated by the SNAREs syntaxin-3, SNAP-23, VAMP8, synaptotagmin-2, and other proteins. Here, we designed and screened a series of hydrocarbon-stapled peptides consisting of SNAP-25 fragments that included some of the key residues involved in the primary interface as observed in high-resolution crystal structures. We selected a subset of four stapled peptides that were highly -helical as assessed by circular dichroism and that inhibited both Ca2+-independent and Ca2+- triggered ensemble lipid-mixing with neuronal SNAREs and Syt1. In a single-vesicle content-mixing assay with reconstituted neuronal SNAREs and synaptotagmin-1 or with reconstituted airway SNAREs and synaptotagmin-2, the selected peptides also suppressed Ca2+-triggered fusion. Taken together, hydrocarbon-stapled peptides that interfere with the primary interface consequently inhibit Ca2+-triggered exocytosis. Our inhibitor screen suggests that these compounds may be useful to combat mucus hypersecretion that is a major cause of airway obstruction in the pathophysiology of COPD, asthma and cystic fibrosis.

category: pharmacology and toxicology