title: Homothorax Controls a Binary Rhodopsin Switch in Drosophila Ocelli

abstract: Visual perception of the environment is mediated by specialized photoreceptor (PR) neurons of the eye. Each PR expresses photosensitive opsins, which are activated by a particular wavelength of light. In most insects, the visual system comprises a pair of compound eyes that are mainly associated with motion detection, color or polarized light perception and a triplet of ocelli that are thought to be critical during flight to detect horizon and movements. It is widely believed that evolutionary diversification of compound eye and ocelli in insects occurred from an ancestral visual organ around 500 million years ago. Concurrently, opsin genes were also duplicated to provide distinct spectral sensitivities to different PRs of compound eye and ocelli. In the fruit fly Drosophila melanogaster, Rhodopsin1 (Rh1) and Rh2 are closely related opsins that are originated from the duplication of a single ancestral gene. However, in the visual organs, Rh2 is uniquely expressed in ocelli whereas Rh1 is uniquely expressed in outer PRs of the compound eye. It is currently unknown how this differential expression of Rh1 and Rh2 in the two visual organs is controlled to provide unique spectral sensitivities to ocelli and compound eyes. Here, we show that Homothorax (Hth) is expressed in ocelli and confers proper rhodopsin expression. We find that Hth controls a binary Rhodopsin switch in ocelli to promote Rh2 expression and repress Rh1 expression. Genetic and molecular analysis of rh1 and rh2 supports that Hth acts through their promoters to regulate Rhodopsin expression in the ocelli. Finally, we also show that when ectopically expressed in the retina, hth is sufficient to induce Rh2 expression only at the outer PRs in a cell autonomous manner. We therefore propose that the diversification of rhodpsins in the ocelli and retinal outer PRs occurred by duplication of an ancestral gene, which is under the control of Homothorax.

category: genetics


title: Detection of ESKAPE pathogens and Clostridioides difficile in Simulated Skin Transmission Events with Metagenomic and Metatranscriptomic Sequencing

abstract:
1BackgroundAntimicrobial resistance is a significant global threat, posing major public health risks and economic costs to healthcare systems. Bacterial cultures are typically used to diagnose healthcare-acquired infections (HAI); however, culture-dependent methods provide limited presence/absence information and are not applicable to all pathogens. Next generation sequencing (NGS) has the capacity to detect a wide variety of pathogens, virulence elements, and antimicrobial resistance (AMR) signatures in healthcare settings without the need for culturing, but few research studies have explored how NGS could be used to detect viable human pathogen transmission events under different HAI-relevant scenarios.

MethodsThe objective of this project was to assess the capability of NGS-based methods to detect the direct and indirect transmission of high priority healthcare-related pathogens. DNA was extracted and sequenced from a previously published study exploring pathogen transfer with simulated skin containing background microorganisms, which allowed for complementary culture and metagenomic analysis comparisons. RNA was also isolated from an additional set of samples to evaluate metatranscriptomic analysis methods at different concentrations.

ResultsUsing various analysis methods and custom reference databases, both pathogenic and non-pathogenic members of the microbial community were taxonomically identified. Virulence and AMR genes known to reside within the community were also routinely detected. Ultimately, pathogen abundance within the overall microbial community played the largest role in successful taxonomic classification and gene identification.

ConclusionsThese results illustrate the utility of metagenomic analysis in clinical settings or for epidemiological studies, but also highlight the limits associated with the detection and characterization of pathogens at low abundance in a microbial community.

category: genomics


title: A dynamic occupancy model for interacting species with two spatial scales

abstract: 1Occupancy models have been developed independently to account for multiple spatial scales and species interactions in a dynamic setting. However, as interacting species (e.g., predators and prey) often operate at different spatial scales, including nested spatial structure might be especially relevant in models of interacting species. Here we bridge these two model frameworks by developing a multi-scale two-species occupancy model. The model is dynamic, i.e. it estimates initial occupancy, colonization and extinction probabilities - including probabilities conditional to the other species presence. With a simulation study, we demonstrate that the model is able to estimate parameters without bias under low, medium and high average occupancy probabilities, as well as low, medium and high detection probabilities. We further show the models ability to deal with sparse field data by applying it to a multi-scale camera trapping dataset on a mustelid-rodent predator-prey system. The field study illustrates that the model allows estimation of species interaction effects on colonization and extinction probabilities at two spatial scales. This creates opportunities to explicitly account for the spatial structure found in many spatially nested study designs, and to study interacting species that have contrasted movement ranges with camera traps.

category: ecology


title: Cellular abundance shapes function in piRNA-guided genome defense

abstract: Defense against genome invaders universally relies on RNA-guided immunity. Prokaryotic CRISPR/Cas and eukaryotic RNA interference pathways recognize targets by complementary base-pairing, which places the sequences of their guide RNAs at the center of self/nonself discrimination. Here, we explore the sequence space of PIWI-interacting RNAs (piRNAs), the genome defense of animals, and establish functional priority among individual sequences for the first time. Our results reveal that only the topmost abundant piRNAs are commonly present in every cell, while rare sequences generate cell-to-cell diversity in flies and mice. We identify a skewed distribution of sequence abundance as a hallmark of piRNA populations and show that quantitative differences of more than a thousand-fold are established by conserved mechanisms of biogenesis. Finally, our genomics analyses and direct reporter assays reveal that abundance determines function in piRNA-guided genome defense. Taken together, we identify an effective sequence space and untangle two classes of piRNAs that differ in complexity and function. The first class represents the topmost abundant sequences and drives silencing of genomic parasites. The second class sparsely covers an enormous sequence space. These rare piRNAs cannot function in every cell, every individual or every generation but create diversity with potential for adaptation in the ongoing arms race with genome invaders.

category: developmental biology


title: Focal Laser Stimulation of Fly Nociceptors Activates Distinct Axonal and Dendritic Ca2+ Signals

abstract:
Drosophila Class IV neurons are polymodal nociceptors that detect noxious mechanical, thermal, optical and chemical stimuli. Escape behaviors in response to attacks by parasitoid wasps are dependent on Class IV cells, whose highly branched dendritic arbors form a fine meshwork that is thought to enable detection of the wasps needle-like ovipositor barb. To understand how mechanical stimuli trigger cellular responses, we used a focused 405-nm laser to create highly local lesions to probe the precise position needed in evoke responses. By imaging calcium signals in dendrites, axons, and soma in response to stimuli of varying positions, intensities and spatial profiles, we discovered that there are two distinct nociceptive pathways. Direct stimulation to dendrites (the contact pathway) produces calcium responses in axons, dendrites and the cell body whereas stimulation adjacent to the dendrite (the non-contact pathway) produces calcium responses in the axons only. We interpret the non-contact pathway as damage to adjacent cells releasing diffusible molecules that act on the dendrites. Axonal responses have higher sensitivities and shorter latencies. In contrast, dendritic responses have lower sensitivities and longer latencies. Stimulation of finer, distal dendrites leads to smaller responses than stimulation of coarser, proximal dendrites, as expected if the contact response depends on the geometric overlap of the laser profile and the dendrite diameter. Because the axon signals to the CNS to trigger escape behaviors, we propose that the density of the dendritic meshwork is high not only to enable direct contact with the ovipositor, but also to enable neuronal activation via diffusing signals from damaged surrounding cells. Dendritic contact evokes responses throughout the dendritic arbor, even to regions distant and distal from the stimulus. These dendrite-wide calcium signals may facilitate hyperalgesia or cellular morphological changes following dendritic damage.

Statement of SignificanceAnimals encounter a wide range of noxious stimuli in the natural world. Nociceptive neurons are specialized cells that sense harmful stimuli and trigger avoidance responses. Class IV cells, located under the cuticle in Drosophila larvae, are polymodal nociceptors that respond to noxious mechanical, thermal, optical, and chemical stimuli. To investigate the spatial requirements of mechanoreception in Class IV neurons, we measured calcium signals evoked by a focused laser beam that creates highly localized tissue damage. We discovered that different cellular compartments - axons and dendrites - responded differentially depending on whether the stimulus makes direct contact with the neuron or not. This provides evidence that mechanical nociception in Class IV cells occurs via two distinct pathways.

category: neuroscience


title: Intestine-enriched apolipoprotein b orthologs regulate stem cell differentiation and regeneration in planarians

abstract: Lipid metabolism plays an instructive role in regulating stem cell state and differentiation. However, the roles of lipid mobilization and utilization in stem cell-driven regeneration are unclear. Planarian flatworms readily restore missing tissue due to injury-induced activation of pluripotent somatic stem cells called neoblasts. Here, we identify two intestine-enriched orthologs of apolipoprotein b, apob-1 and apob-2, which mediate transport of neutral lipid stores from the intestine to target tissues including neoblasts, and are required for tissue homeostasis and regeneration. Inhibition of apob function by RNAi causes head regression and lysis in uninjured animals, and delays body axis re-establishment and regeneration of multiple organs in amputated fragments. Furthermore, apob RNAi causes expansion of the population of differentiating neoblast progeny and dysregulates expression of genes enriched in differentiating and mature cells in eight major cell type lineages. We conclude that intestine-derived lipids serve as a source of metabolites required for neoblast differentiation.


title: Intestine-enriched apolipoprotein b orthologs are required for stem cell differentiation and regeneration in planarians


title: TRAIT2D: a Software for Quantitative Analysis of Single Particle Diffusion Data

abstract:
Single Particle Tracking (SPT) is one of the most widespread techniques to evaluate particle mobility in a variety of situations, such as in cellular and model membrane dynamics. The proposed TRAIT2D Python library is developed to provide object tracking, trajectory analysis and produce simulated datasets with graphical user interface. The tool allows advanced users to customise the analysis to their requirements.

Availability and implementation: the software has been coded in Python, and can be accessed from: https://github.com/Eggeling-Lab-Microscope-Software/TRAIT2D, or the pypi and condaforge repositories.

A comprehensive user guide is provided at https://eggeling-lab-microscope-software.github.io/TRAIT2D/.

category: bioinformatics


title: Constrained standardization of count data from massive parallel sequencing

abstract: In high-throughput omics disciplines like transcriptomics, researchers face a need to assess the quality of an experiment prior to an in-depth statistical analysis. To efficiently analyze such voluminous collections of data, researchers need triage methods that are both quick and easy to use. Such a normalization method for relative quantitation, CONSTANd, was recently introduced for isobarically-labeled mass spectra in proteomics. It transforms the data matrix of abundances through an iterative, convergent process enforcing three constraints: (I) identical column sums; (II) each row sum is fixed (across matrices) and (III) identical to all other row sums. In this study, we investigate whether CONSTANd is suitable for count data from massively parallel sequencing, by qualitatively comparing its results to those of DESeq2. Further, we propose an adjustment of the method so that it may be applied to identically balanced but differently sized experiments for joint analysis. We find that CONSTANd can process large data sets with about 2 million count records in less than a second whilst removing unwanted systematic bias and thus quickly uncovering the underlying biological structure when combined with a PCA plot or hierarchical clustering. Moreover, it allows joint analysis of data sets obtained from different batches, with different protocols and from different labs but without exploiting information from the experimental setup other than the delineation of samples into identically processed sets (IPSs). CONSTANds simplicity and applicability to proteomics as well as transcriptomics data make it an interesting candidate for integration in multi-omics workflows.


title: TAFKAP: An improved method for probabilistic decoding of cortical activity

abstract: Cortical activity can be difficult to interpret. Neural responses to the same stimulus vary between presentations, due to random noise and other sources of variability. This unreliable relationship to external stimuli renders any pattern of activity open to a multitude of plausible interpretations. We have previously shown that this uncertainty in cortical stimulus representations can be characterized using a probabilistic decoding algorithm, which inverts a generative model of stimulus-evoked cortical responses. Here, we improve upon this method in two important ways, which both target the precision with which the generative model can be estimated from limited, noisy training data. We show that these improvements lead to considerably better estimation of the presented stimulus and its associated uncertainty. Estimates of the presented stimulus are recovered with an accuracy that exceeds that of standard decoding methods (SVMs), and in some cases even approaches the behavioral accuracy of human observers. Moreover, the uncertainty in the decoded probability distributions better characterizes the precision of cortical stimulus information from trial to trial.


title: Glucagon-like peptide 1 receptor-mediated stimulation of a GABAergic projection from the bed nucleus of the stria terminalis to the hypothalamic paraventricular nucleus

abstract: We previously reported that GABAergic neurons within the ventral anterior lateral bed nucleus of the stria terminalis (alBST) express glucagon-like peptide 1 receptor (GLP1R) in rats, and that virally-mediated "knock-down" of GLP1R expression in the alBST prolongs the hypothalamic-pituitary-adrenal axis response to acute stress. Given other evidence that a GABAergic projection pathway from ventral alBST serves to limit stress-induced activation of the HPA axis, we hypothesized that GLP1 signaling promotes activation of GABAergic ventral alBST neurons that project directly to the paraventricular nucleus of the hypothalamus (PVN). After PVN microinjection of fluorescent retrograde tracer followed by preparation of ex vivo rat brain slices, whole-cell patch clamp recordings were made in identified PVN-projecting neurons within the ventral alBST. Bath application of Exendin-4 (a specific GLP1R agonist) indirectly depolarized PVN-projecting neurons in the ventral alBST and adjacent hypothalamic parastrial nucleus (PS) via circuit-mediated effects that increased excitatory synaptic inputs and decreased inhibitory synaptic inputs to the PVN-projecting neurons; these effects were occluded by prior bath application of a GLP1R antagonist. Additional retrograde tracing experiments combined with in situ hybridization confirmed that PVN-projecting neurons within the ventral alBST/PS are GABAergic, and do not express GLP1R mRNA. Conversely, GLP1 mRNA is expressed by a subset of GABAergic neurons within the oval subnucleus of the dorsal alBST that project into the ventral alBST. Our novel findings reveal a potential GLP1R-mediated mechanism through which the alBST exerts inhibitory control over the endocrine HPA axis.


title: Modulation of tactile feedback for the execution of dexterous movement

abstract: While dexterity relies on the constant transmission of sensory information, unchecked feedback can be disruptive to behavior. Yet how somatosensory feedback from the hands is regulated as it first enters the brain, and whether this modulation exerts any influence on movement, remain unclear. Leveraging molecular-genetic access in mice, we find that tactile afferents from the hand recruit neurons in the brainstem cuneate nucleus whose activity is modulated by distinct classes of local inhibitory neurons. Selective manipulation of these inhibitory circuits can suppress or enhance the transmission of tactile information, affecting behaviors that rely on movement of the hands. Investigating whether these local circuits are subject to top-down control, we identify distinct descending cortical pathways that innervate cuneate in a complementary pattern. Somatosensory cortical neurons target the core tactile region of cuneate, while a large rostral cortical population drives feed-forward inhibition of tactile transmission through an inhibitory shell. These findings identify a circuit basis for tactile feedback modulation, enabling the effective execution of dexterous movement.


title: The spatial network structure of intertidal meiofaunal communities derived from environmental DNA metabarcoding surveys in Northwest Iberia

abstract: The identification of the patterns and mechanisms behind species distribution is one of the major challenges in ecology, having also important outcomes for the conservation and management of ecosystems. This is especially true for those components of biodiversity providing essential ecosystem functions and for which standard surveys may underestimate their real taxonomic diversity due to their high degree of cryptic diversity and inherent diagnosis difficulties, such as meiofaunal communities. Environmental DNA (eDNA) metabarcoding may provide a fast and reliable way to refine and scale-up the characterization of biological diversity in complex environmental samples, allowing to bypass such drawbacks and increase the resolution of biodiversity estimates. Moreover, the possibility of integrating eDNA metabarcoding-derived data with tools and methods rooted in network theory would deepen the knowledge of the structuring processes of ecological communities in ways that cannot be predicted from studying individual species/communities in isolation. Here, a sediment eDNA metabarcoding of mitochondrial cytochrome c oxidase I (COI) and the nuclear hypervariable V4 region of the 18S rDNA (18S) was used to reconstruct the spatial networks of intertidal meiofaunal OTUs from three estuaries of North-Western Iberian Peninsula. Null models were used to identify the role of environmental and spatial constraints on the structure of COI- and 18S-derived spatial networks and to characterize the macroecological features of surveyed phyla. Our results show the feasibility of eDNA metabarcoding, not only to capture a fair amount of diversity hard to detect with standard surveys procedures, but also to identify hierarchical spatial structures in intertidal meiofaunal assemblages. This suggests that exclusivity of occurrence rather than pervasiveness appears to be the norm in meiofaunal organisms and that niche-based processes predominantly drive the spatial aggregation and contemporary distribution of meiofaunal phyla within the system.


title: Robust optical autofocus system utilizing neural networks trained for extended range and time-course and automated multiwell plate imaging including single molecule localization microscopy

abstract: We present a robust, long-range optical autofocus system for microscopy utilizing machine learning. This can be useful for experiments with long image data acquisition times that may be impacted by defocusing resulting from drift of components, e.g. due to changes in temperature or mechanical drift. It is also useful for automated slide scanning or multiwell plate imaging where the sample(s) to be imaged may not be in the same horizontal plane throughout the image data acquisition. To address the impact of (thermal or mechanical) fluctuations over time in the optical autofocus system itself, we utilise a convolutional neural network (CNN) that is trained over multiple days to account for such fluctuations. To address the trade-off between axial precision and range of the autofocus, we implement orthogonal optical readouts with separate CNN training data, thereby achieving an accuracy well within the 600 nm depth of field of our 1.3 numerical aperture objective lens over a defocus range of up to approximately +/- 100 m. We characterise the performance of this autofocus system and demonstrate its application to automated multiwell plate single molecule localisation microscopy.

category: bioengineering


title: Zebrafish embryo screen identifies anti-metastasis drugs

abstract: Metastasis is responsible for approximately 90% of cancer-associated mortality but few models exist that allow for rapid and effective screening of anti-metastasis drugs. Current mouse models of metastasis are too expensive and time consuming to use for rapid and high-throughput screening. Therefore, we created a unique screening concept utilizing conserved mechanisms between zebrafish gastrulation and cancer metastasis for identification of potential anti-metastatic drugs. We hypothesized that small chemicals that interrupt zebrafish gastrulation might also suppress metastatic progression of cancer cells and developed a phenotype-based chemical screen to test the hypothesis. The screen used epiboly, the first morphogenetic movement in gastrulation, as a marker and enabled 100 chemicals to be tested in five hours. The screen tested 1280 FDA-approved drugs and identified Pizotifen, an antagonist for serotonin receptor 2C (HTR2C) as an epiboly-interrupting drug. Pharmacologic and genetic inhibition of HTR2C suppressed metastatic progression in a mouse model. Blocking HTR2C with Pizotifen restored epithelial properties to metastatic cells through inhibition of Wnt-signaling. In contrast, HTR2C induced epithelial to mesenchymal transition (EMT) through activation of Wnt-signaling and promoted metastatic dissemination of human cancer cells in a zebrafish xenotransplantation model. Taken together, our concept offers a novel platform for discovery of anti-metastasis drugs.

category: cancer biology


title: A chemical screen based on an interruption of zebrafish gastrulation identifies the HTR2C inhibitor Pizotifen as a suppressor of EMT-mediated metastasis


title: ChromeBat: A Bio-Inspired Approach to 3D Genome Reconstruction

abstract:
BackgroundWith the advent of Next Generation Sequencing and the Hi-C experiment, high quality genome-wide contact data is becoming increasingly available. This data represents an empirical measure of how a genome interacts inside the nucleus. Genome conformation is of particular interest as it has been experimentally shown to be a driving force for many genomic functions from regulation to transcription. Thus, the Three Dimensional Genome Reconstruction Problem seeks to take Hi-C data and produce the complete physical genome structure as it appears in the nucleus for genomic analysis.

ResultsWe propose and develop a novel method to solve the Chromosome and Genome Reconstruction problem based on the Bat Algorithm which we called ChromeBat. We demonstrate on real Hi-C data that ChromeBat is capable of state of the art performance. Additionally, the domain of Genome Reconstruction has been criticized for lacking algorithmic diversity, and the bio-inspired nature of ChromeBat contributes algorithmic diversity to the problem domain.

ConclusionsChromeBat is an effective approach at solving the Genome Reconstruction Problem. The source code and usage guide can be found here: https://github.com/OluwadareLab/ChromeBat.


title: Thermal biology of two sympatric Lacertids lizards (Lacerta diplochondrodes and Parvilacerta parva) from Western Anatolia

abstract: Sympatric lizard species differing in morphology present convenient models for studying the differentiation in thermal behavior and the role of morphological differences in thermal biology. Here we studied the thermal biology of two sympatric lizard species which occur together sympatrically in western Anatolia, Frig Valley. These two species differ in body size, with the larger Lacerta diplochondrodes and smaller Parvilacerta parva. Field body temperatures of the individuals belonging to both species were recorded in the activity period. Additionally, several environmental parameters including solar radiation, substrate temperature, air temperature and wind speed were also monitored to investigate the relative effect of these abiotic parameters on thermal biology of the two species. The field body temperature and temperature excess (difference between body and substrate temperature) of two species while being relatively close to each other, showed seasonal differences. Solar radiation, substrate temperature and air temperature were the main effective factors on thermal biology in the field. Additionally, although body size did not have a direct significant effect on body temperature or temperature excess, the interaction between body size and wind were effective on temperature excess. In conclusion, our study partially supports the conservation of thermal biology of related lizard species.


title: Oxaliplatin Resistance in Colorectal Cancer Enhances TRAIL Sensitivity Via Death Receptor 4 Upregulation and Lipid Raft Localization

abstract:
Colorectal cancer (CRC) remains a leading cause of cancer death, and its mortality is associated with metastasis and chemoresistance. We demonstrate that oxaliplatin-resistant CRC cells are sensitized to TRAIL-mediated apoptosis. Oxaliplatin-resistant cells exhibited transcriptional downregulation of caspase-10, but this had minimal effects on TRAIL sensitivity following CRISPR-Cas9 deletion of caspase-10 in parental cells. Sensitization effects in oxaliplatin-resistant cells were found to be a result of increased DR4, as well as significantly enhanced DR4 palmitoylation and translocation into lipid rafts. Raft perturbation via nystatin and resveratrol significantly altered DR4/raft colocalization and TRAIL sensitivity. Blood samples from metastatic CRC patients were treated with TRAIL liposomes, and a 57% reduction of viable CTCs was observed. Increased DR4/lipid raft colocalization in CTCs was found to correspond with increased oxaliplatin resistance and increased efficacy of TRAIL liposomes. To our knowledge, this is the first study to investigate the role of lipid rafts in primary CTCs.

Impact StatementOxaliplatin-resistant colorectal cancer cells exhibit unregulated death receptor 4 expression with increased receptor palmitoylation and translocation into lipid rafts, increasing their sensitivity to apoptosis via TRAIL.


title: Public science data suggest that fish is the most important factor in reducing small pond biodiversity in Czechia

abstract: AO_SCPLOWBSTRACTC_SCPLOWThis project tested a public-science approach to the assessment of freshwater habitat quality via simple invertebrate sampling. We combined a mobile phone application and simple instruction to children to sample 50 ponds in Central Czechia, and we analyzed the data using a standard ecological statistics approach. Despite the limitation in scope and taxonomic precision, our data revealed the same patterns as academic studies of the same topic. Specifically, we conclude that the main cause of invertebrate community decline is fish overstocking, while diverse invertebrate communities require aquatic macrophytes. Pollution detectable by children has an effect on invertebrate community structure, but a different effect than fish has, and not as statistically robust. Importantly, almost all large ponds were found overstocked with fish; therefore, they support not more diversity than small ponds, but less, and serve as ecological traps. Our findings suggest that pond conservation should focus primarily on the restoration of aquatic vegetation, and that the most effective approach will be the removal of excessive fish.


title: BORCS6 is involved in the enlargement of lung lamellar bodies in Lrrk2 knockout mice

abstract: Leucine-rich repeat kinase 2 (LRRK2) has been implicated in the pathogenesis of Parkinson disease. It has been shown that Lrrk2 knockout (KO) rodents have enlarged lamellar bodies (LBs) in their alveolar epithelial type II cells, although the underlying mechanisms remain unclear. Here we performed proteomic analyses on LBs isolated from Lrrk2 KO mice and found that the LB proteome is substantially different in Lrrk2 KO mice compared with wild-type mice. In Lrrk2 KO LBs, several Rab proteins were increased, and subunit proteins of BLOC-1-related complex (BORC) were decreased. The amount of surfactant protein C was significantly decreased in the bronchoalveolar lavage fluid obtained from Lrrk2 KO mice, suggesting that LB exocytosis is impaired in Lrrk2 KO mice. We also found that the enlargement of LBs is recapitulated in A549 cells upon KO of LRRK2 or by treating cells with LRRK2 inhibitors. Using this model, we show that KO of BORCS6, a BORC subunit gene, but not other BORC genes, causes LB enlargement. Our findings implicate the LRRK2-BORCS6 pathway in the maintenance of LB morphology.

category: cell biology


title: Semaphorin3F Drives Dendritic Spine Pruning through Rho-GTPase Signaling

abstract: Dendritic spines of cortical pyramidal neurons are initially overproduced then remodeled substantially in the adolescent brain to achieve appropriate excitatory balance in mature circuits. Here we investigated the molecular mechanism of developmental spine pruning by Semaphorin 3F (Sema3F) and its holoreceptor complex, which consists of immunoglobulin-class adhesion molecule NrCAM, Neuropilin-2 (Npn2), and PlexinA3 (PlexA3) signaling subunits. Structure-function studies of the NrCAM-Npn2 interface showed that NrCAM stabilizes binding between Npn2 and PlexA3 necessary for Sema3F-induced spine pruning. Using a mouse neuronal culture system, we identified a dual signaling pathway for Sema3F-induced pruning, which involves activation of Tiam1-Rac1-PAK1-3 -LIMK1/2-Cofilin1 and RhoA-ROCK1/2-Myosin II in dendritic spines. Inhibitors of actin remodeling impaired spine collapse in the cortical neurons. Elucidation of these pathways expands our understanding of critical events that sculpt neuronal networks and may provide insight into how interruptions to these pathways could lead to spine dysgenesis in diseases such as autism, bipolar disorder, and schizophrenia.


title: Evolution of VIM-1 producing Klebsiella pneumoniae isolates from a hospital outbreak reveals the genetic bases of the loss of the urease-positive identification character

abstract:
Outbreaks of carbapenemase producing Klebsiella pneumoniae (CPKp) represent a major threat for hospitals. We molecularly characterized the first outbreak of VIM-1 producing K. pneumoniae in Spain, that raised fears about the spread of this strain or of the plasmid carrying blaVIM-1. Through in-depth genomic analysis of 18 isolates recovered between October 2005 and September 2007, we show that 17 ST39 isolates were clonal, whereas the last isolate had acquired the VIM-1 plasmid from the epidemic clone. The index isolate carried 31 antibiotic resistance genes (ARGs) and was resistant to almost all antibiotics tested. Later isolates further gained mutations in efflux pumps regulators ramR and opxR, deletion of mgrB (colistin resistance) and frameshift mutations in ompK36 ({beta}-lactam resistance) likely selected by antibiotic usage. Comparison with publicly available genome sequences and literature review revealed no sign of dissemination of this CPKp strain. However, the VIM-1 plasmid was found in diverse Enterobacterales species, although restricted to Spain. One isolate became urease negative following IS5075 transposition into ureC. Analysis of 9755 K. pneumoniae genomes showed the same ureC::IS5075 insertion in 14.1% of the isolates and explained why urease activity is a variable identification trait for K pneumoniae. Transposition into ureC results from the similarity of its 3-end and the terminal inverted repeats of Tn21 like transposons, the targets of IS5075 and related ISs. As these transposons frequently carry ARGs, this might explain the frequent chromosomal invasion by these ISs and ureC inactivation in multidrug resistant isolates.

IMPORTANCEEvolution of multidrug resistant bacterial pathogens occurs at multiple scales, in the patient, locally in the hospital or more globally. Some mutations or gene acquisitions, for instance in response to antibiotic treatment, may be restricted to a single patient due to their high fitness cost. However, some events are more general. By analyzing the evolution of a hospital acquired multidrug resistant K. pneumoniae strain producing the carbapenemase VIM-1, we showed a likely environmental source in the hospital and identified mutations contributing to a further decrease in antibiotic susceptibility. By combining the genomic analysis of this outbreak with literature data and genome sequences available in databases, we showed that the VIM-1 plasmid has been acquired by different Enterobacterales but is only endemic in Spain. We also discovered that urease loss in K. pneumoniae results from the specific transposition of an IS element into the ureC gene and was more frequent in fluoroquinolone resistant isolates and carrying a carbapenemase gene.

category: evolutionary biology


title: Feedback ratiometric control of two microbial populations in a single chemostat

abstract: We address the problem of controlling the dilution rate in a chemostat to regulate the ratio between the concentrations of two microbial populations growing in continuous culture. After analyzing the open-loop dynamics of this multicellular system, we present two alternative feedback control strategies, one based on a gain-scheduled state feedback controller, the other on a switching control strategy. We show that both strategies are effective in solving the problem and illustrate the results by a set of representative numerical simulation.

category: synthetic biology


title: A non-coding RNA network involved in KSHV tumorigenesis

abstract: Regulatory pathways involving non-coding RNAs (ncRNAs) such as microRNAs (miRNAs) and long non-coding RNAs (lncRNA) have gained great relevance due to their role in the control of gene expression modulation. Using RNA sequencing of KSHV Bac36 transfected mouse endothelial cells (mECK36) and tumors, we have analyzed the host and viral transcriptome to uncover the role lncRNA-miRNA-mRNA driven networks in KSHV tumorigenesis. The integration of the differentially expressed ncRNAs, with an exhaustive computational analysis of their experimentally supported targets, led us to dissect complex networks integrated by the cancer-related lncRNAs Malat, Neat1, H19, Meg3 and their associated miRNA-target pairs. These networks would modulate pathways related to KSHV pathogenesis, such as viral carcinogenesis, p53 signaling, RNA surveillance, and Cell cycle control. Finally, the ncRNA-mRNA analysis allowed us to develop signatures that can be used to an appropriate identification of druggable gene or networks defining relevant AIDS-KS therapeutic targets.


title: Protein-bound sialic acid in saliva contributes directly to salivary anti-influenza virus activity

abstract: The oral cavity is an entrance for respiratory viruses, such as influenza. Recently, saliva has been shown to exert both antimicrobial and antiviral activities. Thus, saliva may be a biological factor that contributes to the prevention of influenza infection. However, the actual salivary anti-influenza A virus (IAV) activity in individuals and its determinant factors are unknown. By assessing individual variations in salivary anti-IAV activity in 92 people using an established new high-throughput system in this study, we found that the anti-IAV activity varied widely between individuals and showed a significant positive correlation with protein-bound sialic acid (BSA) level ({rho}=0.473; p < 0.001). Furthermore, the anti-IAV activity of saliva with enzymatically reduced BSA content was significantly lower. These results indicate that BSA is a direct regulator of salivary anti-IAV activity and is a determinant of individual differences. Additionally, after comparing the anti-IAV activity across the groups by age, anti-IAV activity in young people (aged 5-19 years) were lower than in adults aged 20-59 years and elderly people aged 60-79 years. Our study suggests that BSA levels in saliva may be important in preventing influenza infection.

category: immunology


title: Diversification of B. subtilis during experimental evolution on A. thaliana leads to synergism in root colonization of evolved subpopulations

abstract:
The soil bacterium Bacillus subtilis is known to suppress pathogens as well as promote plant growth. However, in order to fully exploit the potential as natural fertilizer, we need a better understanding of the interactions between B. subtilis and plants. Here, B. subtilis was examined for root colonization through experimental evolution on Arabidopsis thaliana. The populations evolved rapidly, improved in root colonization and diversified into three distinct morphotypes. In order to better understand the adaptation that had taken place, single evolved isolates from the final transfer were randomly selected for further characterization, revealing changes in growth and pellicle formation in medium supplemented with plant polysaccharides. Intriguingly, certain evolved isolates showed improved root colonization only on the plant species they evolved on, but not on another plant species, namely tomato, suggesting A. thaliana specific adaption paths. Finally, the mix performed better than the sum of its constituents in monoculture, which was demonstrated to be caused by complementarity effects. Our results suggest, that genetic diversification occurs in an ecological relevant setting on plant roots and proves to be a stable strategy for root colonization.

Significance StatementUnderstanding how plant-growth-promoting rhizobacteria (PGPR) colonize plant roots is crucial to fully utilize their potential for agricultural applications. Here, we employ experimental evolution of the PGPR Bacillus subtilis on Arabidopsis thaliana to study root colonization. We revealed that evolving populations rapidly improve in root colonization and diversify into distinct morphotypes. Notably, improved root colonization by evolved isolates was observed on A. thaliana, not on tomato. Moreover, isolates of distinct morphotypes interacted during root colonization and the mixture of morphotypes showed higher productivity than predicted. These findings suggest that genetic diversification might be a stable strategy to maximize root colonization.

category: microbiology


title: Diversification of B. subtilis during experimental evolution on A. thaliana and the complementarity in root colonization of evolved subpopulations


title: Eliminating Mosquitoes with Precision Guided Sterile Males

abstract: The mosquito Aedes aegypti is the principal vector for arboviruses including dengue/yellow fever, chikungunya, and zika, infecting hundreds of millions of people annually. Unfortunately, traditional control methodologies are insufficient, so innovative control methods are needed. To complement existing measures, here we develop a molecular genetic control system termed precision guided sterile insect technique (pgSIT) in Aedes aegypti. PgSIT uses a simple CRISPR-based approach to generate sterile males that are deployable at any life stage. Supported by mathematical models, we empirically demonstrate that released pgSIT males can compete, suppress, and eliminate mosquitoes in multigenerational population cages. This platform technology could be used in the field, and adapted to many vectors, for controlling wild populations to curtail disease in a safe, confinable, and reversible manner.


title: H3 acetylation selectively promotes basal progenitor proliferation and neocortex expansion by activating TRNP1 expression

abstract:
Increase in the size of human neocortex, acquired in evolution, accounts for the unique cognitive capacity of humans. This expansion appears to reflect the evolutionarily-enhanced proliferative ability of basal progenitors (BPs) in mammalian cortex, which may have been acquired through epigenetic alterations in BPs. However, whether or how the epigenome in BPs differs across species is not known. Here, we report that histone H3 acetylation is a key epigenetic regulation in BP amplification and cortical expansion. Through epigenetic profiling of sorted BPs, we show that H3K9 acetylation is low in murine BPs and high in human BPs. Elevated H3K9ac preferentially increases BP proliferation, increasing the size and folding of the normally smooth mouse neocortex. Mechanistically, H3K9ac drives BP amplification by increasing expression of the evolutionarily regulated gene, TRNP1, in the developing cortex. Our findings demonstrate a previously unknown mechanism that controls cortical architecture.

One Sentence SummaryH3K9ac promotes basal progenitor amplification, neocortex expansion and gyrification by activating TRNP1 expression in evolution.


title: Multi-modal imaging reveals dynamic interactions of Staphylococcus aureus within human neutrophils

abstract: Staphylococcus aureus is an important human pathogen that causes a wide range of infections. Neutrophils are an essential component of our innate immune system and understanding S. aureus-neutrophil interactions on a sub-cellular level is crucial to developing new therapeutic strategies to promote immunity during S. aureus infections. To this end we have developed a multi-modal imaging platform capable of following host-pathogen processes in biological systems, this is achieved by switching imaging modalities between a low photo-toxicity and low resolution imaging modality through an increasing illumination intensity to achieve live super-resolution imaging. This novel imaging platform was applied to the study of human neutrophils infected by S. aureus. We show that we can image different infection stages of S. aureus in live neutrophils with super resolution microscopy. We see evidence of binary fission occurring in intracellular S. aureus within a neutrophil.

category: biophysics


title: A Simple Fluorescence Assay for Cystine Uptake via the xCT in Cells using Selenocystine and a Fluorescent Probe

abstract: The cystine/glutamate antiporter (xCT) is a crucial transporter that maintains cellular redox balance by regulating intracellular glutathione synthesis via cystine uptake. However, no robust and simple method to determine the cystine uptake activity of xCT is currently available. We have developed a method to measure the xCT activity via the reaction of selenocysteine and fluorescein O,O'-diacrylate (FOdA). Selenocystine, a cystine analog, is transported into cells through xCT on the cell membrane. The amount of the transported selenocystine was then determined by a reaction using tris(2-carboxyethyl)phosphine (TCEP) and FOdA in a weak acidic buffer at pH 6. Using this method, the cystine uptake activity of xCT in various cells, and the inhibitory efficiency of xCT inhibitors, were evaluated.


title: Sacsin cotranslational degradation causes autosomal recessive spastic ataxia of Charlevoix-Saguenay

abstract:
Autosomal recessive spastic ataxia of Charlevoix-Saguenay is caused by more than 200 different mutations in the SACS gene encoding sacsin, a huge multimodular protein of unknown function. ARSACS phenotypic spectrum is highly variable. Previous studies correlated the nature and position of SACS mutations with age of onset or disease severity, though the effects on protein stability were not considered.

In this study, we explain mechanistically the lack of genotype-phenotype correlation in ARSACS, with important consequences for disease diagnosis and treatment.

We found that sacsin is almost absent in ARSACS fibroblasts, regardless of the nature of the mutation. We did not detect sacsin in patients with truncating mutations, while we found it strikingly reduced or absent also in compound heterozygotes carrying diverse missense mutations. We excluded SACS mRNA decay, defective translation, or faster post-translational degradation as causes of protein reduction. Conversely, we demonstrated that nascent mutant sacsin protein undergoes preemptive cotranslational degradation, emerging as a novel cause of a human disease. Based on these findings, sacsin levels should be included in the diagnostic algorithm for ARSACS.


title: Reduction of genotyping marker density for genomic selection is not an affordable approach to long-term breeding in cross-pollinated crops

abstract: The selection of informative markers has been studied massively as an alternative to reduce genotyping costs for the genomic selection (GS) application. Low-density marker panels are attractive for GS because they decrease computational time-consuming and multicollinearity beyond more individuals can be genotyped with the same cost. Nevertheless, these inferences are usually made empirically using "static" training sets and populations, which are adequate only to predict a breeding programs initial cycles but might not for long-term cycles. Moreover, to the best of our knowledge, none of these inferences considered the inclusion of dominance into the GS models, which is particularly important to predict cross-pollinated crops. Therefore, that reveals an important and unexplored topic for allogamous long-term breeding. To achieve this goal, we employed two approaches: the former used empirical maize datasets, and the latter simulations of long-term breeding cycles of phenotypic and genomic recurrent selection (intrapopulation and reciprocal). Then, we observed the reducing marker density effect on populations (mean, the best genotypes performance, accuracy, additive variance) over cycles and models (additive, additive-dominance, specific combining ability (SCA)). Our results indicate that the markers reduction based on different linkage disequili brium (LD) levels is viable only within a cycle and brings a significant decrease in predictive ability over generations. Furthermore, in the long-term, regardless of the selection scheme adopted, the more makers, the better because they buffer LD losses caused by recombination over breeding cycles. Finally, regarding the accuracy, the additive-dominant models tend to outperform the additive ones and perform similar to the SCA.


title: Transcriptional census of epithelial-mesenchymal plasticity in cancer

abstract: Epithelial-mesenchymal plasticity (EMP) contributes to tumour progression, promoting therapy resistance and immune cell evasion. Definitive molecular features of this plasticity have largely remained elusive due to the limited scale of most studies. Leveraging scRNA-seq data from 160 tumours spanning 8 different cancer types, we identify expression patterns associated with intratumoural EMP. Integrative analysis of these programs confirmed a high degree of diversity among tumours. These diverse programs are associated with combinations of various common regulatory mechanisms initiated from cues within the tumour microenvironment. We highlight that inferring regulatory features can inform effective therapeutics to restrict EMP.


title: Structural variants are a major source of gene expression differences in humans and often affect multiple nearby genes

abstract: Structural variants (SVs) are an important source of human genome diversity but their functional effects are not well understood. We mapped 61,668 SVs in 613 individuals with deep genome sequencing data from the GTEx project and measured their effects on gene expression. We estimate that common SVs are causal at 2.66% of eQTLs, which is a 10.5-fold enrichment relative to their abundance in the genome and consistent with prior work using smaller sample sizes. Duplications and deletions were the most impactful variant types, whereas the contribution of mobile element insertions was surprisingly small (0.12% of eQTLs, 1.9-fold enriched). Multi-tissue analysis of expression effects revealed that gene-altering SVs show significantly more constitutive effects than other variant types, with 62.09% of coding SV-eQTLs active in all tissues with known eQTL activity compared to 23.08% of coding SNV- and indel-eQTLs, whereas noncoding SVs, SNVs and indels show broadly similar patterns. We also identified 539 rare SVs associated with nearby gene expression outliers. Of these, 62.34% are noncoding SVs that show strong effects on gene expression yet modest enrichment at known regulatory elements, demonstrating that rare noncoding SVs are a major source of gene expression differences but remain difficult to predict from current annotations. Remarkably, both common and rare noncoding SVs often show strong regional effects on the expression of multiple genes: SV-eQTLs affect an average of 1.82 nearby genes compared to 1.09 genes affected by SNV- and indel-eQTLs, and 21.34% of rare expression-altering SVs show strong effects on 2-9 different genes. We also observe significant effects on gene expression extending 1 Mb from the SV. This provides a mechanism by which individual noncoding SVs may have strong and/or pleiotropic effects on phenotypic variation and disease.


title: Longer study length, standardized sampling techniques, and broader geographic scope leads to higher likelihood of detecting stable abundance patterns in long term deer tick (Ixodes scapularis) studies

abstract: Ixodes scapularis (deer ticks) are a taxon of ecological and human health concern due to their status as primary vectors of Borrelia burgdorferi, the bacteria that transmits Lyme disease. Deer ticks are thought to be expanding in geographic range and population size across the eastern United States (US), leading to concern that tick-vectored illness will correspondingly rise. However, because of wide variability in deer tick monitoring strategies, synthesis efforts may be limited by the sensitivity and reliability of data produced by existing long term studies, especially to inform forecasting and proactive deer tick management. To address this, we explicitly examined the role of how study design parameters affect the likelihood of observing temporal trends in deer tick studies. We used a moving window approach to investigate the temporal stability of deer tick population trajectories across the US. We found several study factors can have an impact on the likelihood of a study reaching stability and the likelihood of tick abundance data leading to misleading results if the study does not reach stability. Our results underscore the need for longer studies of deer ticks when trying to assess long term or broad spatial patterns. Moreover, our results showcase the importance of study length, sampling technique, life stage, and geographic scope in shaping the inferences from deer tick studies. This is especially important for synthesizing across the variety of existing surveys and for potential ecological forecasting.


title: Evotuning protocols for Transformer-based variant effect prediction on multi-domain proteins

abstract:
Accurate variant effect prediction has broad impacts on protein engineering. Recent machine learning approaches toward this end are based on representation learning, by which feature vectors are learned and generated from unlabeled sequences. However, it is unclear how to effectively learn evolutionary properties of an engineering target protein from homologous sequences, taking into account the proteins sequence-level structure called domain architecture (DA). Additionally, no optimal protocols are established for incorporating such properties into Transformer, the neural network well-known to perform the best in natural language processing research. This article proposes DA-aware evolutionary fine-tuning, or "evotuning", protocols for Transformer-based variant effect prediction, considering various combinations of homology search, fine-tuning, and sequence vectorization strategies. We exhaustively evaluated our protocols on diverse proteins with different functions and DAs. The results indicated that our protocols achieved significantly better performances than previous DA-unaware ones. The visualizations of attention maps suggested that the structural information was incorporated by evotuning without direct supervision, possibly leading to better prediction accuracy.

Availabilityhttps://github.com/dlnp2/evotuning_protocols_for_transformers

Supplementary informationSupplementary data are available at Briefings in Bioinformatics online.


title: Single cell analysis of the aging hypothalamus

abstract: Alterations in metabolism, sleep patterns, body composition, and hormone status are all key features of aging. The hypothalamus is a well-conserved brain region that controls these homeostatic and survival-related behaviors. Despite the importance of this brain region in healthy aging, little is known about the intrinsic features of hypothalamic aging. Here, we utilize single nuclei RNA-sequencing to assess the transcriptomes of 40,064 hypothalamic nuclei from young and aged female mice. We identify cell type-specific signatures of aging in neurons, astrocytes, and microglia, as well as among the diverse collection of neuronal subtypes in this region. We uncover key changes in cell types critical for metabolic regulation and body composition, as well as in an area of the hypothalamus linked to cognition. In addition, our analysis reveals an unexpected female-specific feature of hypothalamic aging. Specifically, we discover that the master regulator of X-inactivation, Xist, is elevated with age, particularly in hypothalamic neurons. Moreover, using machine learning, we show that levels of X-chromosome genes, and Xist itself, are the best predictors of cellular age. Together, this study identifies critical cell-specific changes of the aging hypothalamus in mammals, and uncovers a novel marker of neuronal aging in females.


title: Single cell analysis of the aging female hypothalamus


title: The developing brain structural and functional connectome fingerprint

abstract: In the mature brain, structural and functional connectivity  fingerprints can be used to identify the uniqueness of an individual. However, whether the characteristics that make a brain distinguishable from others already exist at birth remains unknown. Here, we used neuroimaging data of preterm born neonates who were scanned twice during the perinatal period to assess the developing brain fingerprint. We found that 62% of the participants could be identified based on the congruence of the later structural connectome to the initial connectivity matrix derived from the earlier timepoint. In contrast, similarity between functional connectomes only allowed to identify 12% of the participants. These suggests that structural connectivity is more stable in early life and can represent a potential connectome fingerprint. Thus, a relatively stable structural connectome appears to support a changing functional connectome at a time when neonates must rapidly acquire new skills to adapt to their new environment.


title: Mito-nuclear variation in transgenerational and reproductive effects of amino acid and lipid nutrition

abstract: Animals vary genetically in responses to dietary change. Both mitochondrial and nuclear genomes contribute to this variation, but the role of combinatorial "mito-nuclear" genetic variation is understudied. We do not know whether specific nutrients modify patterns of mito-nuclear variation, nor whether putative epigenetic mechanisms play a role. Here, we show that enriching dietary essential amino acids or lipids modifies patterns of mito-nuclear variation in Drosophila life-history, including transgenerational effects of lipids. Systematically evaluating alternative statistical models revealed that diet-mito-nuclear interactions were a leading driver of phenotypic variation. Mito-nuclear genotype repeatably predicted phenotypic impacts of nutritional changes, but genotypes bearing naturally co-occurring pairs of mitochondria and nuclei did not necessarily outperform novel pairings, suggesting that nutrition-dependent phenotypes cannot easily be optimised by matching mitochondria to coincident nuclear genotypes. These results enhance understanding of how nutrition and genetics sculpt phenotype, with potential implications for human mitochondrial transfer therapies.


title: Cyclodextrins increase membrane tension and are universal activators of mechanosensitive channels

abstract: The bacterial mechanosensitive channel of small conductance, MscS, has been extensively studied to understand how mechanical forces are converted into the conformational changes that underlie mechanosensitive (MS) channel gating. We showed that lipid removal by {beta}-cyclodextrin can mimic membrane tension. Here, we show that all cyclodextrins (CDs) can activate reconstituted E. coli MscS, that MscS activation by CDs depends on CD-mediated lipid removal, and that the CD amount required to gate MscS scales with the channels sensitivity to membrane tension. CD-mediated lipid removal ultimately causes MscS desensitization, which we show is affected by the lipid environment. CDs can also activate the structurally unrelated MscL. While many MS channels respond to membrane forces, generalized by the  force-from-lipids principle, their different molecular architectures suggest that they use unique ways to convert mechanical forces into conformational changes. CDs emerge as a universal tool for the structural and functional characterization of unrelated MS channels.


title: Atrx deletion impairs cGAS-STING signaling and increases response to radiation and oncolytic herpesvirus in sarcoma

abstract: ATRX is one of the most frequently altered genes in solid tumors, and mutation is especially frequent in soft tissue sarcomas. However, the role of ATRX in tumor development and response to cancer therapies remains poorly understood. Here, we developed a primary mouse model of soft tissue sarcoma and showed that Atrx deleted tumors are more sensitive to radiation therapy. In the absence of Atrx, irradiated sarcomas have increased persistent DNA damage, telomere dysfunction, and mitotic catastrophe. We find that Atrx deleted sarcomas have a reduced adaptive immune response, impaired cGAS-STING signaling, and increased sensitivity to an oncolytic herpesvirus therapy. Translation of these results to patients with ATRX mutant cancers could enable genomically-guided cancer therapeutic approaches that improve patient outcomes.


title: Discrete dynamic model of the mammalian sperm acrosome reaction: the influence of acrosomal pH and biochemical heterogeneity

abstract: The acrosome reaction (AR) is an exocytotic process essential for mammalian fertilization. It involves diverse biochemical and physiological changes that culminate in the release of the acrosomal content to the extracellular medium as well as a reorganization of the plasma membrane (PM) that allows sperm to interact and fuse with the egg. In spite of many efforts, there are still important pending questions regarding the molecular mechanism regulating the AR. Particularly, the contribution of acrosomal alkalinization to AR triggering in physiological conditions is not well understood. Also, the dependence of the proportion of sperm capable of undergoing AR on the biochemical heterogeneity within a sperm population has not been studied. Here we present a discrete mathematical model for the human sperm AR, based on the biophysical and biochemical interactions among some of the main components of this complex exocytotic process. We show that this model can qualitatively reproduce diverse experimental results, and that it can be used to analyze how acrosomal pH (pHa) and cell heterogeneity regulate AR. Our results confirm that pHa increase can on its own trigger AR in a subpopulation of sperm, and furthermore, it indicates that this is a necessary step to trigger acrosomal exocytosis through progesterone, a known physiological inducer of AR. Most importantly, we show that the proportion of sperm undergoing AR is directly related to the detailed structure of the population biochemical heterogeneity.

category: systems biology


title: Rapid Identification of Methylase Specificity (RIMS-seq) jointly identifies methylated motifs and generates shotgun sequencing of bacterial genomes

abstract: DNA methylation is widespread amongst eukaryotes and prokaryotes to modulate gene expression and confer viral resistance. 5-methylcytosine (m5C) methylation has been described in genomes of a large fraction of bacterial species as part of restriction-modification systems, each composed of a methyltransferase and cognate restriction enzyme. Methylases are site-specific and target sequences vary across organisms. High-throughput methods, such as bisulfite-sequencing can identify m5C at base resolution but require specialized library preparations and Single Molecule, Real-Time (SMRT) Sequencing usually misses m5C. Here, we present a new method called RIMS-seq (Rapid Identification of Methylase Specificity) to simultaneously sequence bacterial genomes and determine m5C methylase specificities using a simple experimental protocol that closely resembles the DNA-seq protocol for Illumina. Importantly, the resulting sequencing quality is identical to DNA-seq, enabling RIMS-seq to substitute standard sequencing of bacterial genomes. Applied to bacteria and synthetic mixed communities, RIMS-seq reveals new methylase specificities, supporting routine study of m5C methylation while sequencing new genomes.


title: Activation of a signaling pathway by the physical translocation of a chromosome

abstract: In every organism, the cell cycle requires the execution of multiple cellular processes in a strictly defined order. However, the mechanisms used to ensure such order remain poorly understood, particularly in bacteria. Here, we show that the activation of the essential CtrA signaling pathway that triggers cell division in Caulobacter crescentus is intrinsically coupled to the successful initiation of DNA replication via the physical translocation of a newly-replicated chromosome, powered by the ParABS system. We demonstrate that ParA accumulation at the new cell pole during chromosome segregation recruits ChpT, an intermediate component of the CtrA signaling pathway. ChpT is normally restricted from accessing the selective PopZ polar microdomain until the new chromosome and ParA arrive. Consequently, any disruption to DNA replication initiation prevents the recruitment of ChpT and, in turn, cell division. Collectively, our findings reveal how major cell-cycle events are coordinated in Caulobacter and, importantly, how the physical translocation of a chromosome triggers an essential signaling pathway.


title: Molecular and Structural Basis of Olfactory Sensory Neuron Coalescence by Kirrel Receptors

abstract: Projections from sensory neurons of olfactory systems coalesce into glomeruli in the brain. The Kirrel receptors are believed to homodimerize via their ectodomains and help separate sensory neuron axons into Kirrel2- or Kirrel3-expressing glomeruli. Here we present the crystal structures of homodimeric Kirrel receptors and show that the closely related Kirrel2 and Kirrel3 have evolved specific sets of polar and hydrophobic interactions, respectively, disallowing heterodimerization while preserving homodimerization, likely resulting in proper segregation and coalescence of Kirrel-expressing axons into glomeruli. We show that the dimerization interface at the N-terminal IG domains is necessary and sufficient to create homodimers, and fail to find evidence for a secondary interaction site in Kirrel ectodomains. Furthermore, we show that abolishing dimerization of Kirrel3 in vivo leads to improper formation of glomeruli in the mouse accessory olfactory bulb as observed in Kirrel3-/- animals. Our results provide strong evidence for Kirrel3 homodimerization controlling axonal coalescence.


title: State anxiety alters the neural oscillatory correlates of predictions and prediction errors during reward learning

abstract: Anxiety influences how the brain estimates and responds to uncertainty. These behavioural effects have been described within predictive coding and Bayesian inference frameworks, yet the associated neural correlates remain unclear. Recent work suggests that predictions in generative models of perception are represented in alpha (8-12 Hz) and beta oscillations (13-30 Hz). Updates to predictions are driven by prediction errors weighted by precision (inverse variance; pwPE), and are encoded in gamma oscillations (>30 Hz) and associated with suppression of beta activity. We tested whether state anxiety alters the neural oscillatory activity associated with predictions and pwPE during learning. Healthy human participants performed a probabilistic reward-learning task in a volatile environment. In our previous work, we described learning behaviour in this task using a hierarchical Bayesian model, revealing more precise (biased) beliefs about the reward tendency in state anxiety, consistent with reduced learning in this group. The model provided trajectories of predictions and pwPEs for the current study, allowing us to assess their parametric effects on the time-frequency representations of EEG data. Using convolution modelling for oscillatory responses, we found that, relative to a control group, state anxiety increased beta activity in frontal and sensorimotor regions during processing of pwPE, and in fronto-parietal regions during encoding of predictions. No effects of state anxiety on gamma modulation were found. Our findings expand prior evidence on the oscillatory representations of predictions and pwPEs into the reward-learning domain. The results suggest that state anxiety modulates beta-band oscillatory correlates of pwPE and predictions in generative models, providing insights into the neural processes associated with biased belief updating and poorer reward learning.


title: Relative effects of edaphic conditions and climate on palm communities in the Central Andes

abstract:
Palms (family Arecaceae) are conspicuous and structural elements in forests ecosystems of tropical regions and mountain forests in South America. Additionally, many species of palms are culturally and economically important to human populations. Because of their ecological and ethnobotanical significance, understanding the drivers of palm distribution and diversity is critical. However, most past research has focused in tropical lowland palm communities, while our understanding of montane tropical palm ecology and biogeography is comparatively lacking. We investigate the environmental factors that influence patterns of richness, composition, and abundance of palms in the Central Andes. In particular, we are interested in the relative effects that soil edaphic conditions and climate have on palm community structure. For these analyses, we used a network of 88 forest plots distributed along a broad elevational gradient (1,000 - 3,200 meters), which are part of the Madidi Project in north-western Bolivia. We carried out palm community-level analysis, as well as species-specific analyses for each of the 16 most common species. We found that soils and climate contribute differentially to shaping Andean palm diversity and distributions. We found that soils explain more variation in species composition (14.4%) than climate (3.45%), but that climate explains more variation in species richness (13%) than soils (6.1%). Moreover, species-specific analyses reveal that there is great variation in how different common species respond to their abiotic environment. Our results contribute to understanding the drivers of biodiversity for a highly important group of plants in one of the most important hotspots for biodiversity.

RESUMENEn el neotropico, las palmeras (Arecaceae) son un grupo diverso y abundante de plantas que constituyen elementos estructurales en bosques tropicales tanto de tierras bajas como de montana. Ademas, muchas especies de palmeras son culturalmente y economicamente importantes para muchas poblaciones humanas. Debido a su importancia ecologica y etnobotanica, entender los mecanismos que controlan la diversidad y la distribucion de las palmeras es extremadamente importante. Sin embargo, la mayoria de la investigacion hasta el momento se ha enfocado en comunidades de palmeras de tierras bajas, mientras que la ecologia y biogeografia de las palmeras de montanas es relativamente poco entendida. En este estudio, nosotros investigamos los factores ambientales que influencian la riqueza, composicion y abundancia de palmeras en los Andes Centrales. En particular, estamos interesados en entender los efectos relativos de las condiciones edaficas del suelo y el clima en la estructura de comunidades de palmeras. Para nuestros analisis, usamos una red de 88 parcelas de arboles distribuidas a lo largo de un gradiente elevacional (1,000 - 3,200 metros), la misma que es parte del Proyecto Madidi en Bolivia. Encontramos que el suelo y el clima tienen efectos diferentes. El suelo explica mas variacion en la composicion de especies (14.4%) que el clima (3.45%), pero el clima explica mas variacion en la riqueza de especies (13%) que los suelos (6.1%). Ademas, analisis independientes para las 16 especies mas comunes demuestran gran variacion en como cada especie responde a las condiciones ambientales. Nuestros resultados contribuyen a entender los factores que controlan la diversidad de un grupo importante de plantas en una de las regiones mas diversas del planeta.


title: Temporally and Spatially Regulated Collagen XVIII Isoforms Impact Ureteric Patterning Through Their TSP1-like Domain

abstract: Collagen XVIII (ColXVIII) is a component of the extracellular matrix implicated in embryogenesis and control of homeostasis. We provide evidence that ColXVIII has a specific role in kidney ontogenesis by regulating the interaction between mesenchymal and epithelial tissues as observed in analyses of total and isoform-specific knockout embryos, mice, and ex vivo organ primordia. ColXVIII deficiency, both temporally and spatially, impacts the 3D pattern of ureteric tree branching morphogenesis via its specific isoforms. Proper development of ureteric tree depends on a tight control of the nephron progenitor cells (NPCs). ColXVIII-deficient NPCs are leaving the NPC pool faster than in controls. Moreover, the data suggests that ColXVIII mediates the kidney epithelial tree patterning via its N-terminal domains, and especially the Thrombospondin-1-like domain, and that this morphogenetic effect involves ureteric epithelial integrins. Altogether, the results propose a significant role for ColXVIII in a complex signalling network regulating renal progenitors and kidney development.


title: A common polymorphism that protects from cardiovascular disease increases fibronectin processing and secretion

abstract:
BackgroundFibronectin (FN1) is an essential regulator of homodynamic processes and tissue remodeling which has been proposed to contribute to atherosclerosis. Moreover, recent large scale genome wide association studies have linked common genetic variants within the FN1 gene to coronary artery disease (CAD) risk.

MethodsPublic databases were analyzed by two-Sample Mendelian Randomization. Expression constructs encoding short FN1 reporter constructs and full-length plasma FN1, differing in the polymorphism, were designed and introduced in various cell models. Secreted and cellular levels were then analyzed and quantified by SDS-PAGE and fluorescence approaches. Mass spectrometry and glycosylation analyses were performed to probe possible post-transcriptional differences.

ResultsHigher FN1 protein levels in plasma associates with a reduced risk of cardiovascular disease. Moreover, common CAD risk SNPs in the FN1 locus associate with circulating levels of FN1. This region is shown to encompass a L15Q polymorphism within the FN1 signal peptide. The presence of the minor allele that predisposes to CAD, corresponding to the Q15 variant, alters glycosylation and reduces FN1 secretion in a direction consistent with the bioinformatic analyses.

ConclusionIn addition to providing novel functional evidence implicating FN1 as a protective force in cardiovascular disease, these findings demonstrate that a common variant within a secretion signal peptide regulates protein function.

category: biochemistry


title: Phage Display Broadly Identifies Inhibitor-reactive Regions in von Willebrand Factor

abstract:
BackgroundCorrection of von Willebrand factor (VWF) deficiency with replacement products containing VWF can lead to the development of anti-VWF alloantibodies (i.e., VWF inhibitors) in patients with severe von Willebrand disease (VWD).

ObjectiveLocate inhibitor-reactive regions within VWF using phage display.

MethodsWe screened a phage library displaying random, overlapping fragments covering the full length VWF protein sequence for binding to a commercial anti-VWF antibody or to immunoglobulins from three type 3 VWD patients who developed VWF inhibitors in response to treatment with plasma-derived VWF. Immunoreactive phage clones were identified and quantified by next generation DNA sequencing (NGS).

ResultsNGS markedly increased the number of phage analyzed for locating immunoreactive regions within VWF following a single round of selection and identified regions not recognized in previous reports using standard phage display methods. Extending this approach to characterize VWF inhibitors from three type 3 VWD patients (including two siblings homozygous for the same VWF gene deletion) revealed patterns of immunoreactivity distinct from the commercial antibody and between unrelated patients, though with notable areas of overlap. Alloantibody reactivity against the VWF propeptide is consistent with incomplete removal of the propeptide from plasma-derived VWF replacement products.

ConclusionThese results demonstrate the utility of phage display and NGS to characterize diverse anti-VWF antibody reactivities.

category: pathology


title: Legionella pneumophila CRISPR-Cas suggests recurrent encounters with Gokushovirinae

abstract:
Legionella pneumophila is a ubiquitous freshwater pathogen and the causative agent of Legionnaires disease. This pathogen and its ability to cause disease is closely tied to its environmental encounters. From phagocytic protists, L. pneumophila has "learned" how to avoid predation and exploit conserved eukaryotic processes to establish an intracellular replicative niche. Legionnaires disease is a product of these evolutionary pressures as L. pneumophila uses the same molecular mechanisms to replicate in grazing protists and in macrophages of the human lung. L. pneumophila growth within protists also provides a refuge from desiccation, disinfection, and other remediation strategies. One outstanding question has been whether this protection extends to phages. L. pneumophila isolates are remarkably devoid of prophages and to date no Legionella phages have been identified. Nevertheless, many L. pneumophila isolates maintain active CRISPR-Cas defenses. So far, the only known target of these systems has been an episomal element that we previously named Legionella Mobile Element-1 (LME-1). In this study, we have identified over 150 CRISPR-Cas systems across 600 isolates, to establish the clearest picture yet of L. pneumophilas adaptive defenses. By leveraging the sequence of 1,500 unique spacers, we can make two main conclusions: current data argue against CRISPR-Cas targeted integrative elements beyond LME-1 and the heretofore "missing" L. pneumophila phages are most likely lytic gokushoviruses.

IMPORTANCEThe causative agent of Legionnaires disease, an often-fatal pneumonia, is an intracellular bacterium, Legionella pneumophila, that normally grows inside amoebae and other freshwater protists. Unfortunately for us, this has two major consequences: the bacterium can take what it has learned in amoebae and use similar strategies to grow inside our lungs; and these amoebae can protect Legionella from various forms of chemical and physical disinfection regimes. Legionella are ubiquitous in the environment and frequently found in man-made water systems. Understanding the challenges to Legionella survival before it reaches the human lung is critical to preventing disease.

We have leveraged our earlier discovery that L. pneumophila CRISPR-Cas systems are active and adaptive - meaning that they respond to contemporary threats encountered in the environment. In this way, CRISPR arrays can be considered genomic diaries of past encounters, with spacer sequences used to identify elements that may impinge on the pathogens survival. One outstanding question in the field is whether L. pneumophila is susceptible to phage, given the presumptive protection provided by intracellular replication within its eukaryotic hosts. In this work, we use CRISPR spacer sequences to suggest that the heretofore "missing" L. pneumophila phage are most likely lytic gokushoviruses. Such information is critical to the long-term goal of developing of new strategies for preventing colonization of our water systems by Legionella and subsequent human exposure to the pathogen.


title: A low-cost, long-term underwater camera trap network coupled with deep residual learning image analysis

abstract:
AO_SCPLOWBSTRACTC_SCPLOWO_LIUnderstanding long-term trends in marine ecosystems requires accurate and repeatable counts of fishes and other aquatic organisms on spatial and temporal scales that are difficult or impossible to achieve with diver-based surveys. Long-term, spatially distributed cameras, like those used in terrestrial camera trapping, have not been successfully applied in marine systems due to limitations of the aquatic environment.
C_LIO_LIHere, we develop methodology for a system of low-cost, long-term camera traps (Dispersed Environment Aquatic Cameras), deployable over large spatial scales in remote marine environments. We use machine learning to classify the large volume of images collected by the cameras. We present a case study of these combined techniques use by addressing fish movement and feeding behavior related to grazing halos, a well-documented benthic pattern in shallow tropical reefscapes.
C_LIO_LICameras proved able to function continuously underwater at deployed depths (up to 7 m, with later versions deployed to 40 m) with no maintenance or monitoring for over five months, and collected time-lapse images during daylight hours for a total of over 100,000 images. Our ResNet-50-based deep learning model achieved 92.5% overall accuracy in sorting images with and without fish, and diver surveys revealed that the camera images accurately represented local fish communities.
C_LIO_LIThe cameras and machine learning classification represent the first successful method for broad-scale underwater camera trap deployment, and our case study demonstrates the cameras potential for addressing questions of marine animal behavior, distributions, and large-scale spatial patterns.
C_LI


title: Infraslow locus coeruleus activity coordinates spindle rhythms and heart rate to gate fluctuating non-REM sleep substates

abstract: One promising approach towards understanding what makes sleep vulnerable in disease is to look at how wake-promoting mechanisms affect healthy sleep. Wake-promoting neuronal activity is inhibited during non-REM sleep (NREMS). However, many mammalian species, including humans, show recurrent moments of sleep fragility during which sensory reactivity is elevated. Wake-related neuronal activity could thus remain active in NREMS, but its roles in dynamic variations of sensory reactivity remain unknown. Here, we demonstrate that mouse NREMS is a brain state with recurrent fluctuations of the wake-promoting neurotransmitter noradrenaline on the [~]50-seconds time-scale. These fluctuations occurred around mean noradrenaline levels greater than the ones of quiet wakefulness, while they declined steeply in REMS. They coincided with a clustering of sleep spindle rhythms in the forebrain and with heart rate variations. We addressed the origins of these fluctuations by using closed-loop optogenetic locus coeruleus (LC) activation or inhibition timed to moments of low and high spindle activity during NREMS. We could suppress, lock or entrain sleep spindle clustering or heart rate variations, demonstrating that both fore- and hindbrain-projecting LC neurons show synchronized infraslow activity variations in natural NREMS. Noradrenergic modulation of thalamic but not cortical circuits was required for sleep spindle clustering and involved noradrenaline release into primary sensory and reticular thalamic nuclei that activated both 1- and {beta}-adrenergic receptors to cause slowly decaying membrane depolarizations. Noradrenergic signaling by LC, primarily known for attention promotion in wakefulness, renders mammalian NREMS more  wake-like on the close-to-minute-time scale through sustaining thalamocortical and autonomic sensory arousability.


title: Noradrenergic control of non-REM sleep substates


title: Recurrent chromosome reshuffling and the evolution of neo-sex chromosomes in parrots

abstract: The karyotype of most birds has remained considerably stable during more than 100 million years evolution, except for some groups, such as parrots. The evolutionary processes and underlying genetic mechanism of chromosomal rearrangements in parrots, however, are poorly understood. Here, using chromosome-level assemblies of three parrot genomes (monk parakeet, blue-fronted amazon, budgerigar), we uncovered frequent chromosome fusions and fissions among parrots, with most of them being lineage-specific. In particular, at least 12 chromosomes recurrently experienced inter-chromosomal fusions in different parrot lineages. Two conserved vertebrate genes, ALC1 and PARP3, with known functions in the repair of double-strand breaks and maintenance of genome stability, were specifically lost in parrots. The loss of ALC1 was associated with multiple deletions and an accumulation of CR1-psi, a novel subfamily of transposable elements (TEs) that recently amplified in parrots, while the loss of PARP3 was associated with an inversion. Additionally, the fusion of the ZW sex chromosomes and chromosome 11 has created a pair of neo-sex chromosomes in the ancestor of parrots, and the chromosome 25 has been further added to the sex chromosomes in monk parakeet. The newly formed neo-sex chromosomes were validated by our chromosomal painting, genomic and phylogenetic analyses. Transcriptome profiling for multiple tissues of males and females did not reveal signals of female-specific selection driving the formation of neo-sex chromosomes. Finally, we identified one W-specific satellite repeat that contributed to the unusual enlargement of the W chromosome in monk parakeet. Together, the combination of our genomic and cytogenetic analyses highlight the role of TEs and genetic drift in promoting chromosome rearrangements, gene loss and the evolution of neo-sex chromosome in parrots.


title: Using summary statistics to evaluate the genetic architecture of multiplicative combinations of initially analyzed phenotypes with a flexible choice of covariates

abstract: While the promise of electronic medical record and biobank data is large, major questions remain about patient privacy, computational hurdles, and data access. One promising area of recent development is pre-computing non-individually identifiable summary statistics to be made publicly available for exploration and downstream analysis. In this manuscript we demonstrate how to utilize pre-computed linear association statistics between individual genetic variants and phenotypes to infer genetic relationships between products of phenotypes (e.g., ratios; logical combinations of binary phenotypes using  and and  or) with customized covariate choices. We propose a method to approximate covariate adjusted linear models for products and logical combinations of phenotypes using only pre-computed summary statistics. We evaluate our methods accuracy through several simulation studies and an application modeling various fatty acid ratios using data from the Framingham Heart Study. These studies show consistent ability to recapitulate analysis results performed on individual level data including maintenance of the Type I error rate, power, and effect size estimates. An implementation of this proposed method is available in the publicly available R package pcsstools.

category: genetics


title: Regulation of oogenesis in the queen honey bee (Apis mellifera)

abstract:
In the honey bee (Apis mellifera), queen and worker castes originate from identical genetic templates but develop into different phenotypes. Queens lay up to 2,000 eggs daily whereas workers are sterile in the queens presence. Periodically queens stop laying; during swarming, when resources are scarce in winter and when they are confined to a cage by beekeepers. We used confocal microscopy and gene expression assays to investigate the control of oogenesis in honey bee queen ovaries. We show that queens use different combination of  checkpoints to regulate oogenesis compared to honey bee workers and other insect species. However, both queen and worker castes use the same programmed cell death pathways to terminate oocyte development at their caste-specific checkpoints. Our results also suggest that the termination of oogenesis in queens is driven by nutritional stress. Thus, queens may regulate oogenesis via the same regulatory pathways that were utilised by ancestral solitary species but have adjusted physiological checkpoints to suit their highly-derived life history.

Summary statementHoney bee queens regulate oogenesis using a different combination of  checkpoints to workers, but both castes use the same molecular pathways.


title: Cost-effective long-read assembly of a hybrid Formica aquilonia x Formica polyctena wood ant genome from a single haploid individual

abstract: Formica red wood ants are a keystone species of boreal forest ecosystems and an emerging model system in the study of speciation and hybridization. Here we performed a standard DNA extraction from a single, field-collected Formica aquilonia x Formica polyctena haploid male and assembled its genome using [~]60x of PacBio long reads. After polishing and contaminant removal, the final assembly was 272 Mb (4,687 contigs, N50 = 1.16 Mb). Our reference genome contains 98.5% of the core Hymenoptera BUSCOs and was scaffolded using the pseudo-chromosomal assembly of a related species, F. selysi (28 scaffolds, N50 = 8.49 Mb). Around one third of the genome consists of repeats, and 17,426 gene models were annotated using both protein and RNAseq data (97.4% BUSCO completeness). This resource is of comparable quality to the few other single individual insect genomes assembled to date and paves the way to genomic studies of admixture in natural populations and comparative genomic approaches in Formica wood ants.

category: genomics


title: Remote teaching versus blended learning: exploring discourse richness and learning effectiveness

abstract: The Internet has changed the way teachers and students access information and build knowledge. The recent COVID-19 pandemic has created challenges for both teachers and students and a demand for new methodologies of remote learning. In the life sciences, mixing online content with practical activities represents an even greater challenge. In microbiology, the implementation of an active teaching methodology, the #Adopt project, based on the social network Facebook(R), represents an excellent option for connecting remote education with classroom activities. In 2020, the version applied in high school, "Adopt a Microorganism", was adapted to meet the demands of emergency remote education owing to the suppression of face-to-face activities caused by the pandemic. In the present study, we assessed how the change in methodology impacted the discourse richness of students from high school integrated with technical education in the Business Administration program of the Federal Institute of Sao Paulo, Sorocaba Campus. Three questionnaires related to the groups of microorganisms (Archaea, Bacteria, Virus, Fungi, and Protozoan) were applied. The students responses in the 2019 and 2020 classes were compared concerning content richness and multiplicity of concepts through the application of the Shannon diversity index, an approach that is generally used to assess biodiversity in different environments. The observed results suggest that remote learning provided students with a conceptual basis and richness of content equivalent to that achieved by students subjected to the hybrid teaching model. In conclusion, this study suggests that the #Adopt project methodology increases students discourse richness in microbiology even without face-to-face traditional classes.

category: scientific communication and education


title: "Adopt a Microorganism" methodology enhances the discourse richness of high school students in both hybrid learning and remote education


title: Comparison of hybrid learning and remote education in the implementation of the 'Adopt a Microorganism' methodology


title: Dorsal skull meningeal lymphatic vessels drain blood-solutes after intracerebral hemorrhage

abstract:
Drainage of intraparenchymal hematoma is crucial for the treatment of intracerebral hemorrhage (ICH). We investigated here the possible function of the meningeal lymphatic vessels (mLVs) in ICH resolution. Meningeal lymphatics have been reported to be involved in cerebrospinal fluid drainage, but their role in the drainage and clearance of brain parenchyma has not been characterized in details. Using two preclinical models of ICH, mimicking focal cortical ischemic hemorrhage and subcortical extended hemorrhage, we characterized the dynamics of blood drainage through the dorsal mLVs by two-photon real time imaging in awake mice. After ICH induction, we observe the flow of blood-derived components within the mLVs, suggesting that meningeal lymphatics can play a role in facilitating the drainage of the hemorrhage. We also found that local formation of new mLVs is directly correlated with ICH-related neuroinflammation levels. These findings suggest that meningeal lymphatics could provide a valuable therapeutic target for ICH resolution.

SummaryIn vivo awake imaging reveals the direct drainage of extravasated blood-solutes from brain parenchyma into dorsal meningeal lymphatic vessels, following focal or diffuse intracranial hemorrhage


title: Social learning about rewards: how information from others helps to adapt to changing environment

abstract: Being a part of a social structure is key for survival and reproduction. Living with conspecifics boosts evolutionary fitness, by providing essential information about the environment. Nonetheless, studying neural mechanisms of social learning has not yet been established under laboratory conditions. To examine how socially passed information about the reward affects the behavior of individuals we used Eco-HAB, an automated system for tracing voluntary behavior of group-housed mice living under semi-naturalistic conditions. We show that a scent of a rewarded individual has profound effects on the conspecifics ability to find the reward in both familiar and novel environments. Importantly, the animals display clear and stable individual differences in social behavior. As a result, socially conveyed information has different effects on individual mice. Further, we show that disrupting neuronal plasticity in the prelimbic cortex with nanoparticles gradually releasing TIMP metallopeptidase inhibitor 1, disrupts animals social behavior and results in decreased ability to adapt to environmental changes. The experimental paradigm we developed can be further used to study neuronal mechanisms of social learning.


title: rdacca.hp: an R package for generalizing hierarchical and variation partitioning in multiple regression and canonical analysis

abstract:
O_LICanonical analysis, a generalization of multiple regression to multiple response variables, is widely used in ecology. Because these models often involve large amounts of parameters (one slope per response per predictor), they pose challenges to model interpretation. Currently, multi-response canonical analysis is constrained by two major challenges. Firstly, we lack quantitative frameworks for estimating the overall importance of single predictors. Secondly, although the commonly used variation partitioning framework to estimate the importance of groups of multiple predictors can be used to estimate the importance of single predictors, it is currently computationally constrained to a maximum of four predictor matrices.
C_LIO_LIWe established that commonality analysis and hierarchical partitioning, widely used for both estimating predictor importance and improving the interpretation of single-response regression models, are related and complementary frameworks that can be expanded for the analysis of multiple-response models.
C_LIO_LIIn this application, we aim at: a) demonstrating the mathematical links between commonality analysis, variation and hierarchical partitioning; b) generalizing these frameworks to allow the analysis of any number of responses, predictor variables or groups of predictor variables in the case of variation partitioning; and c) introducing and demonstrating the usage of the R package rdacca.hp that implements these generalized frameworks.
C_LI

category: ecology


title: Detection of the germline specific NAC protein paralog enriched by intrinsically disordered regions in Drosophila melanogaster

abstract: Nascent polypeptide associated complex (NAC) consisting of - and {beta}-subunits is an essential conserved ubiquitously expressed ribosome-associated protein in eukaryotes. NAC is considered as a chaperone and co-translational regulator of nascent protein sorting providing homeostasis of cellular proteins. Here we discovered the germinal cell specific NAC (gNAC) homologue, which differs from the ubiquitously expressed NAC by the presence of expanded intrinsically disordered regions (IDRs) at the N- and C-ends of the - and {beta}-subunits, respectively. We propose these evolutionary acquisition of long IDRs drive gNAC to endow both the specific conformational plasticity for binding client proteins and novel functions regulated by post-transcriptional modifications (PTM). At the same time, we demonstrated that the well-known lethal effect of the loss of ubiquitous NAC-{beta} is suppressed by ectopic expression of its germinal paralog indicating the absence of strict functional differences between the ubiquitous and germline NAC-{beta} subunit paralogs for protein homeostasis.

category: molecular biology


title: Molecular mechanism underlying substrate recognition of the peptide macrocyclase PsnB

abstract: Graspetides, also known as omega-ester-containing peptides (OEPs), are a family of ribosomally synthesized and post-translationally modified peptides (RiPPs) bearing side-to-side macrolactone or macrolactam linkages. Here we present molecular details of the precursor recognition of the macrocyclase enzyme PsnB in the biosynthesis of plesiocin, a Group 2 graspetide. Biochemical analysis revealed that, in contrast to other RiPPs, the core region of the plesiocin precursor peptide noticeably enhanced the enzyme-precursor interaction via the conserved glutamates. We obtained four crystal structures of symmetric or asymmetric PsnB dimers including those with a bound core peptide and a nucleotide, and suggest that the highly conserved Arg213 at the enzyme active site specifically recognizes a ring-forming acidic residue and escorts it to ATP for phosphorylation. Collectively, this study provides insights into the mechanism underlying substrate recognition in the graspetide biosynthesis, and lays a foundation for engineering new variants.


title: High frequency rTMS modulates functional connectivity nodes and boundaries differently in the human brain

abstract: Repetitive transcranial magnetic stimulation (rTMS) has gained considerable importance in the treatment of disorders, e.g. depression. However, it is not yet understood how rTMS alters brains functional connectivity. Here we report the changes captured by resting state functional magnetic resonance imaging (rsfMRI) within the first hour after 10Hz rTMS in (1) nodes, where the strongest functional connectivity of regions is seen, and (2) boundaries, where functional transitions between regions occur. We use support vector machines (SVM), a widely used machine learning algorithm that has been proven to be robust and effective, for the classification and characterization of time intervals of major changes in node and boundary maps, while respecting the variability between subjects. Particularly in the posterior cingulate cortex and precuneus, our results reveal that the changes in connectivity at the boundaries are slower and more complex than in those observed in the nodes, but of similar magnitude according to accuracy confidence intervals. As the network boundaries are under studied in comparison to nodes in connectomics research, our results highlight their contribution for functional adjustments to rTMS.

category: neuroscience