title: The impact of individual perceptual and cognitive factors on collective states in a data-driven fish school model

abstract:
In moving animal groups, social interactions play a key role in the ability of individuals to achieve coordinated motion. However, a large number of environmental and cognitive factors are able to modulate the expression of these interactions and the characteristics of the collective movements that result from these interactions. Here, we use a data-driven fish school model (Calovi et al., 2018; Lei et al., 2020) to quantitatively investigate the impact of perceptual and cognitive factors on coordination and collective swimming patterns. The model describes the interactions involved in the coordination of burst-and-coast swimming in groups of Hemigrammus rhodostomus. We perform a comprehensive investigation of the respective impacts of two interactions strategies between fish based on the selection of the most or the two most influential neighbors, of the range and intensity of social interactions, of the intensity of individual random behavioral fluctuations, and of the group size, on the ability of groups of fish to coordinate their movements. We find that fish are able to coordinate their movements when they interact with their most or two most influential neighbors, provided that a minimal level of attraction between fish exist to maintain group cohesion. A minimal level of alignment is also required to allow the formation of schooling and milling. However, increasing the strength of social interactions does not necessarily enhance group cohesion and coordination. When attraction and alignment strengths are too high, or when the heading random fluctuations are too large, schooling and milling can no longer be maintained and the school switches to a swarming phase. Increasing the interaction range between fish has a similar impact on collective dynamics as increasing the strengths of attraction and alignment. Finally, we find that coordination and schooling occurs for a wider range of attraction and alignment strength in small group sizes.

Author SummaryIn fish schools, social interactions allow individuals to coordinate their movements and their modulation shape the emergent patterns of collective behavior. Here, we use a data-driven fish school model to investigate the impact of perceptual and cognitive factors on collective swimming patterns in the rummy-nose tetra (H. rhodostomus). In this species, fish only pay attention to one or two neighbors that exert the largest influence on their behavior and the interactions consist for a fish to be attracted and aligned with these neighbors. We show that there must exist a minimum level of alignment and attraction between fish to maintain group cohesion and allow the emergence of schooling and milling. Moreover, increasing the interaction range has a similar impact on collective dynamics as increasing the strength of social interactions. However, when the intensity of these interactions becomes too strong, fish can no longer coordinate their swimming and the school adopts a swarming behavior. Our results also show that a moderate level of behavioral fluctuations in fish can induce spontaneous transitions between schooling and milling. Finally, in this species that performs burst-and-coast swimming, we find that coordination occurs for a wider range of interaction strengths only in small group sizes.


title: The Effects of Incline Level on Optimized Lower-Limb Exoskeleton Assistance

abstract: For exoskeletons to be successful in real-world settings, they will need to be effective across a variety of terrains, including on inclines. While some single-joint exoskeletons have assisted incline walking, recent successes in level-ground assistance suggest that greater improvements may be possible by optimizing assistance of the whole leg. To understand how exoskeleton assistance should change with incline, we used human-in-the-loop optimization to find whole-leg exoskeleton assistance torques that minimized metabolic cost on a range of grades. We optimized assistance for three expert, able-bodied participants on 5 degree, 10 degree and 15 degree inclines using a hip-knee-ankle exoskeleton emulator. For all assisted conditions, the cost of transport was reduced by at least 50% relative to walking in the device with no assistance, a large improvement to walking that is comparable to the benefits of whole-leg assistance on level-ground. This corresponds to large absolute reductions in metabolic cost, with the most strenuous conditions reduced by 4.9 W/kg, more than twice the entire energy cost of level walking. Optimized extension torque magnitudes and exoskeleton power increased with incline, with hip extension, knee extension and ankle plantarflexion often growing as large as allowed by comfort-based limits. Applied powers on steep inclines were double the powers applied during level-ground walking, indicating that larger exoskeleton power may be optimal in scenarios where biological powers and costs are higher. Future exoskeleton devices can be expected to deliver large improvements in walking performance across a range of inclines, if they have sufficient torque and power capabilities.

category: bioengineering


title: Development of an in-situ printing system with human platelet lysate based bioink to treat corneal perforation

abstract:
PurposeCorneal perforation is a clinical emergency. Tissue glue to seal the perforation, and supplementary topical medication represents existing standard treatment. Previously, our group developed a transparent human platelet lysate (hPL)-based biomaterial that showed good cell compatibility and accelerated corneal epithelial cells healing in-vitro. This study aims to develop a novel treatment method for corneal perforation using this biomaterial.

MethodsRheometry was used to measure the hPL-based biomaterial behaviour at room and corneal surface temperatures. Its adhesiveness to porcine skin and burst pressure limit were also measured. Based on rheological behaviour, a hand-held biopen was developed to extrude it onto the cornea. An animal trial (5 New Zealand white rabbits) to compare impact of the biomaterial and cyanoacrylate glue (control group) on a 2mm perforation was conducted to evaluate safety and efficacy.

ResultsThe hPL-based biomaterial showed higher adhesiveness compared to commercial fibrin glue and withstood burst pressure approximately 6.4x higher than routine intraocular pressure. Treatment rabbits had lower pain scores and faster recovery, despite generating similar scar-forming structure compared to controls. No secondary corneal ulcer was generated in rabbits treated with the bio-adhesive.

ConclusionsThis study reports a novel in-situ printing system capable of delivering a hPL-based, transparent bio-adhesive and successfully treating small corneal perforations. Bio-adhesive-treated rabbits recovered faster and required no additional analgesia. Both groups showed scarred corneal tissue after healing, however no infection and inflammation was observed by 3 weeks. The delivery system was easy to use and may represent an alternative treatment for corneal perforation.

HighlightsO_LIThis study presents a novel in situ printing system to treat corneal perforation
C_LIO_LIThe system is comprised of a human platelet lysate-based bio-adhesive and a pen-like hand held delivery system
C_LIO_LIMechanical tests showed our transparent bio-adhesive has a higher adhesiveness compared to existing treatments and burst pressure threshold approximately 6.4 times higher than normal intraocular pressure.
C_LIO_LIIn vivo rabbit trial showed that compared to cyanoacrylate glue, the bio-adhesive was safer, faster healing and led to less pain in rabbits.
C_LI


title: Development of an in-situ printing system with human platelet lysate-based bio-adhesive to treat corneal perforation


title: BioCAT: PSSM-based algorithm to search biosynthetic gene clusters producing nonribosomal peptides with known structure

abstract:
MotivationNonribosomal peptides are a class of secondary metabolites synthesized by multimodular enzymes named nonribosomal peptide synthetases and mainly produced by bacteria and fungi. It has been shown that non-ribosomal peptides have a huge structural and functional diversity including antimicrobial activity, therefore, they are of increasing interest for modern biotechnology. Methods such as NMR and LC-MS/MS allow to determine a peptide structure precisely, but it is often not a trivial task to find natural producers of them. Today, the search is usually performed manually, mostly with tools such as antiSMASH or Prism. However, there are cases when potential producers should be found among hundreds of strains, for instance, when analyzing metagenomes data. Thus, the development of automated approaches is a high-priority task for further nonribosomal peptides research.

ResultsWe developed BioCAT, a two-side approach to find biosynthetic gene clusters which may produce a given nonribosomal peptide when the structure of interesting nonribosomal peptide has already been found. Formally, BioCAT unites the antiSMASH software and the rBAN retrosynthesis tool but some improvements were added to both gene cluster and peptide chemical structure analyses. The main feature of the method is an implementation of position specific score matrix to store specificities of nonribosomal peptide synthetase modules, which has increased the alignment quality in comparison with more strict approaches developed earlier. An ensemble model was implemented to calculate the final alignment score. We tested the method on a manually curated nonribosomal peptides producers database and compared it with a competing tool called GARLIC. Finally, we showed the method applicability on several external examples.

AvailabilityBioCAT is available on the GitHub repository or via pip

Contactkonanovdmitriy@gmail.com

category: bioinformatics


title: BioCAT: a novel tool to search biosynthetic gene clusters producing nonribosomal peptides with a known structure


title: Mechanisms of loading and release of the 9-1-1 checkpoint clamp

abstract: 5 single-stranded/double-stranded DNA serve as loading sites for the checkpoint clamp, 9-1-1, which mediates activation of the apical checkpoint kinase, ATRMec1. However, the basis for 9-1-1s recruitment to 5 junctions is unclear. Here, we present structures of the yeast checkpoint clamp loader, Rad24-RFC, in complex with 9-1-1 and a 5 junction and in a post-ATP-hydrolysis state. Unexpectedly, 9-1-1 adopts both closed and planar open states in the presence of Rad24-RFC and DNA. Moreover, Rad24-RFC associates with the DNA junction in the opposite orientation of processivity clamp loaders with Rad24 exclusively coordinating the double-stranded region. ATP hydrolysis stimulates conformational changes in Rad24-RFC, leading to disengagement of DNA-loaded 9-1-1. Together, these structures explain 9-1-1s recruitment to 5 junctions and reveal new principles of sliding clamp loading.

category: biophysics


title: Orientation dependent transverse relaxation in human brain white matter: The magic angle effect on a cylindrical helix

abstract:
PurposeTo overcome some limitations of prior orientation-dependent proton transverse relaxation formalisms in white matter (WM) with a novel framework based on the generalized magic angle effect function.

MethodsA cylindrical helix model was developed embracing anisotropic rotational and translational diffusion of restricted molecules in human brain WM, with the former characterized by an axially symmetric system. Transverse relaxation rates R2 and [Formula] were divided into isotropic [Formula] and anisotropic parts, [Formula], with  denoting an open angle and{varepsilon} 0 an orientation ({Phi}) offset from DTI-derived primary diffusivity direction. The proposed framework (Fit A) was compared with prior models without{varepsilon} 0 on previously published water and methylene proton transverse relaxation rates from developing, healthy, and pathological WM at 3T. Goodness of fit was represented by root-mean-square error (RMSE). F-test and linear correlation were used with statistical significance set to P [≤] 0.05.

ResultsFit A significantly (P<0.01) outperformed prior models as demonstrated by reduced RMSEs, e.g., 0.349 vs. 0.724 in myelin water. Fitted{varepsilon} 0 was in good agreement with calculated{varepsilon} 0 from directional diffusivities. Compared with those from healthy adult, the fitted [Formula], and  from neonates were substantially reduced but{varepsilon} 0 increased, consistent with incomplete myelination. Significant positive [Formula] and negative ( and [Formula]) correlations were found with aging (demyelination) in elderly.

ConclusionThe developed framework can better characterize orientation dependences from a wide range of proton transverse relaxation measurements in human brain WM, shedding new light on myelin microstructural alterations at the molecular level.


title: Orientation dependent proton transverse relaxation in the human brain white matter: The magic angle effect on a cylindrical helix


title: Single-Molecule Localization Microscopy of 3D Orientation and Anisotropic Wobble using a Polarized Vortex Point Spread Function

abstract: Within condensed matter, single fluorophores are sensitive probes of their chemical environments, but it is difficult to use their limited photon budget to image precisely their positions, 3D orientations, and rotational diffusion simultaneously. We demonstrate the polarized vortex point spread function (PSF) for measuring these parameters, including characterizing the anisotropy of a molecules wobble, simultaneously from a single image. Even when imaging dim emitters ([~]500 photons detected), the polarized vortex PSF is able to obtain 12 nm localization precision, 4-8{degrees} orientation precision, and 26{degrees} wobble precision. We use the vortex PSF to measure the emission anisotropy of fluorescent beads, the wobble dynamics of Nile red (NR) within supported lipid bilayers, and the distinct orientation signatures of NR in contact with amyloid-beta fibrils, oligomers, and tangles. The unparalleled sensitivity of the vortex PSF transforms single-molecule microscopes into nanoscale orientation imaging spectrometers, where the orientations and wobbles of individual probes reveal structures and organization of soft matter that are nearly impossible to perceive using molecular positions alone.


title: Morphometric Analysis of Lungfish Endocasts Elucidates Early Dipnoan Palaeoneurological Evolution

abstract: Lungfish (Dipnoi) are lobe-finned fish (Sarcopterygii) that have persisted for over 400 million years from the Devonian Period to present day. They are the extant sister group to tetrapods and thus have the ability to provide unique insight into the condition of the earliest tetrapods as well as their own evolutionary history. The evolution of their dermal skull and dentition is relatively well understood, but this is not the case for the central nervous system. While the brain itself has very poor preservation potential and is not currently known in any fossil lungfish, substantial indirect information about it and associated structures such as the inner ears can be obtained from the cranial endocast. However, before the recent development of X-ray tomography as a palaeontological tool, these endocasts could not be studied non-destructively, and few detailed studies were undertaken. Here we describe and illustrate the endocasts of six Palaeozoic lungfishes (Iowadipterus halli, Gogodipterus paddyensis, Pillararhynchus longi, Griphognathus whitei, Orlovichthys limnatis, and Rhinodipterus ulrichi) from tomographic scans. We combine these with six previously described lungfish endocasts (4 fossil and 2 recent taxa), also based on tomographic studies, into a 12-taxon data set for multivariate morphometric analysis using 17 variables. We find that the olfactory region appears to be more highly plastic than the hindbrain, and undergoes significant elongation in several taxa. Further, while the semicircular canals covary as an integrated module, the utriculus and sacculus of the inner ear instead vary independently of each other. The functional and phylogenetic implications of our findings are discussed.

category: paleontology


title: Model-Based Meta-Analysis of Relapsing Mouse Model Studies from the Critical Path to Tuberculosis Drug Regimens Initiative Database

abstract: Tuberculosis (TB), the disease caused by Mycobacterium tuberculosis (Mtb), remains a leading infectious disease-related cause of death worldwide, necessitating the development of new and improved treatment regimens. Non-clinical evaluation of candidate drug combinations via the relapsing mouse model (RMM) is an important step in regimen development, through which candidate regimens that provide the greatest decrease in probability of relapse following treatment in mice may be identified for further development. Although RMM studies are a critical tool to evaluate regimen efficacy, making comprehensive "apples to apples" comparisons of regimen performance in the RMM has been a challenge, in large part due to the need to evaluate and adjust for variability across studies arising from differences in design and execution. To address this knowledge gap, we performed a model-based meta-analysis on data for 17 unique regimens obtained from a total of 1592 mice across 28 RMM studies. Specifically, a mixed-effects logistic regression model was developed that described the treatment duration-dependent probability of relapse for each regimen and identified relevant covariates contributing to inter-study variability. Using the model, covariate-normalized metrics of interest, namely treatment duration required to reach 50% and 10% relapse probability, were derived and used to compare relative regimen performance. Overall, the model-based meta-analysis approach presented herein enables cross-study comparison of efficacy in the RMM, and provides a framework whereby data from emerging studies may be analyzed in the context of historical data to aid in selecting candidate drug combinations for clinical evaluation as TB drug regimens.

category: pharmacology and toxicology


title: Adenylate kinase 1 overexpression increases locomotor activity in medaka fish

abstract: Maintenance of the energy balance is indispensable for cell survival and function. Adenylate kinase (Ak) is a ubiquitous enzyme highly conserved among many organisms. Ak plays an essential role in energy regulation by maintaining adenine nucleotide homeostasis in cells. However, its role at the whole organism level, especially in animal behavior, remains unclear. Here, we established a model using medaka fish (Oryzias latipes) to examine the function of Ak in environmental adaptation. Medaka overexpressing the major Ak isoform Ak1 exhibited increased locomotor activity compared to that of the wild type. Interestingly, this increase was temperature dependent. Our findings suggest that cellular energy balance can modulate locomotor activity.

category: physiology


title: The role of superstition of cognitive control during neurofeedback training

abstract:
BackgroundReal-time fMRI neurofeedback is growing in reputation as a means to alter brain activity patterns and alleviate psychiatric symptoms. Activity in ventral striatum structures is considered an index of training efficacy. fMRI response in these brain regions indicates neurofeedback-driven associative learning. Here we investigated the impact of mere superstition of control as observed during neurofeedback training on patterns of fMRI activation.

MethodsWe examined the brain activations of a large sample of young participants (n = 97, 50 female, age range 18-54yrs) in a simple fMRI task. Participants saw a display similar to that typically used for real-time fMRI. They were instructed to watch the bars movements or to control them with their own brain activity. Bar movements were not connected with brain activity of participants in any way and perceptions of control were superstitious. After the pretended control condition, they rated how well they were able to control the bars movements.

ResultsStrong activation in the basal ganglia and ventral striatum as well as in large portions of the anterior insula, supplementary motor area, and the middle frontal gyrus due to the superstition of brain control.

ConclusionsThe superstition of control over ones own brain activity in a pretended neurofeedback training session activates the same neural networks as neurofeedback-driven learning. Therefore, activity in the basal ganglia and ventral striatum cannot be taken as evidence for neurofeedback-driven associative learning unless its effects are proven to supersede those elicited by appropriate sham conditions.

category: neuroscience


title: Synthetic amyloid beta does not induce a robust transcriptional response in innate immune cell culture systems

abstract: Alzheimers disease (AD) is a progressive neurodegenerative disease that impacts nearly 400 million people worldwide. The accumulation of amyloid beta (A{beta}) in the brain has historically been associated with AD, and recent evidence suggests that neuroinflammation plays a central role in its origin and progression. These observations have given rise to the theory that A{beta} is the primary trigger of AD, and induces proinflammatory activation of immune brain cells (i.e. microglia), which culminates in neuronal damage and cognitive decline. In order to test this hypothesis, many in vitro systems have been established to study A{beta}-mediated activation of innate immune cells. Nevertheless, the transcriptional resemblance of these models to the microglia in the AD brain has never been comprehensively studied on a genome-wide scale. To address this, we used bulk RNA-seq to assess the transcriptional differences between in vitro cell types used to model neuroinflammation in AD, including several established, primary and iPSC-derived immune cell lines (macrophages, microglia and astrocytes) and their similarities to primary cells in the AD brain. We then analyzed the transcriptional response of these innate immune cells to synthetic A{beta}. We found that human induced pluripotent stem cell (hIPSC)-derived microglia (IMGL) are the in vitro cell model that best resembles primary microglia. Surprisingly, synthetic A{beta} does not trigger a robust transcriptional response in any of the cellular models analyzed, despite testing a wide variety of A{beta} formulations, concentrations, and treatment conditions. Finally, we found that bacterial LPS and INF{gamma} activate microglia and induce transcriptional changes similar to those observed in disease associated microglia present in the AD brain, suggesting the potential suitability of this model to study AD-related neuroinflammation.


title: Visual Processing During the Interictal Period Between Migraines: A Meta-Analysis

abstract: Migraine is a poorly understood neurological disorder and a leading cause of disability in young adults. Migraines are characterized by severe pulsating unilateral headache and visual symptoms. Whether visual function is also impaired in the interictal period between migraines remains controversial. Thus, this meta-analysis investigated the evidence for altered visual function as measured electrophysiologically via pattern-reversal visual evoked potential (VEP) amplitudes and habituation in adult migraineurs with or without visual aura and control in the interictal period. Twenty-three studies were selected for random effects meta-analysis, demonstrating slightly diminished VEP amplitudes and substantially reduced habituation in the early P100 component in migraineurs without aura and with aura compared to controls. No differences were found between migraineurs with and without aura. Although heterogeneity between studies and insufficient published data for VEP latencies and the earlier N75 VEP component data was observed and require further testing, P100 anomalies may indicate abnormal functioning of the fast-conducting magnocellular visual pathway, in episodic migraineurs.


title: Mapping brain-wide excitatory projectome of primate prefrontal cortex at submicron resolution: relevance to diffusion tractography

abstract: Resolving trajectories of axonal pathways in the primate prefrontal cortex remains crucial to gain insights into higher-order processes of cognition and emotion, which requires a comprehensive map of axonal projections linking demarcated subdivisions of prefrontal cortex and the rest of brain. Here we report a mesoscale excitatory projectome issued from the ventrolateral prefrontal cortex (vlPFC) to the entire macaque brain by using viral-based genetic axonal tracing in tandem with high-throughput serial two-photon tomography, which demonstrated prominent monosynaptic projections to other prefrontal areas, temporal, limbic and subcortical areas, relatively weak projections to parietal and insular cortices but no projections directly to the occipital lobe. In a common 3D space, we quantitatively validated an atlas of diffusion tractography-derived vlPFC connections with correlative enhanced green fluorescent protein-labelled axonal tracing, and observed generally good agreement except a major difference in the posterior projections of inferior fronto-occipital fasciculus. These findings raise an intriguing question as to how neural information passes along long-range association fiber bundles in macaque brains, and call for the caution of using diffusion tractography to map the wiring diagram of brain circuits.


title: Individualized Assays of Temporal Coding in the Ascending Human Auditory System

abstract: Neural phase-locking to temporal fluctuations is a fundamental and unique mechanism by which acoustic information is encoded by the auditory system. The perceptual role of this metabolically expensive mechanism, the neural phase-locking to temporal fine structure (TFS) in particular, is debated. Although hypothesized, it is unclear if auditory perceptual deficits in certain clinical populations are attributable to deficits in TFS coding. Efforts to uncover the role of TFS have been impeded by the fact that there are no established assays for quantifying the fidelity of TFS coding at the individual level. While many candidates have been proposed, for an assay to be useful, it should not only intrinsically depend on TFS coding, but should also have the property that individual differences in the assay reflect TFS coding per se over and beyond other sources of variance. Here, we evaluate a range of behavioral and electroencephalogram (EEG)-based measures as candidate individualized measures of TFS sensitivity. Our comparisons of behavioral and EEG-based metrics suggest that extraneous variables dominate both behavioral scores and EEG amplitude metrics, rendering them ineffective. After adjusting behavioral scores using lapse rates, and extracting latency or percent-growth metrics from EEG, interaural timing sensitivity measures exhibit robust behavior-EEG correlations. Together with the fact that unambiguous theoretical links can be made relating binaural measures and phase-locking to TFS, our results suggest that these "adjusted" binaural assays may be well-suited for quantifying individual TFS processing.


title: c-Kit mediates cutaneous sensory axon innervation and multi-kinase inhibitor-induced neurotoxicity

abstract: Peripheral somatosensory neurons innervate the skin and sense the environment. Loss of skin innervation, often caused by the "dying back" of distal somatosensory axons, is a common side effect of drug-induced peripheral neuropathies (DIPNs) and results in pain and sensory dysfunction. Targeted cancer therapies frequently employ multi-kinase inhibitor (MKI) drugs that each block multiple receptor tyrosine kinases. Many MKIs produce DIPNs but the molecular targets and cellular mechanisms underlying these are unknown. We performed live-imaging of cutaneous somatosensory axons in larval zebrafish during treatment with several MKIs known to induce DIPNs, and observed axonal retraction consistent with a dying back pathology. These results were replicated in mouse somatosensory neurons. Genetic knockout of potential MKI targets identified c-Kit receptor as a regulator of sensory axon innervation and a major target of these MKIs mediating loss of axonal density. In both fish and mammals, Kit receptor is expressed in cutaneous somatosensory neurons and its ligand, Kitlg, is expressed in the skin. Mosaic misexpression of Kitlg in the skin induced dramatic increases in local sensory axon density, suggesting an important role for Kit signaling in cutaneous axon growth and maintenance. Immunostaining and structure-function analysis revealed Src, a downstream Kit target, mediates Kits role in cutaneous axon innervation and MKI neurotoxicity. Our data shows that the Kit-Src signaling pathway has a major role in cutaneous sensory axon innervation and is a potential therapeutic target to address DIPNs caused by MKIs and other compounds.


title: Social isolation is linked to classical risk factors of Alzheimer's disease-related dementias

abstract: Alzheimers disease and related dementias is a major public health burden - compounding over upcoming years due to longevity. Recently, clinical evidence hinted at the experience of social isolation in expediting dementia onset. In 502,506 UK Biobank participants and 30,097 participants from the Canadian Longitudinal Study of Aging, we revisited traditional risk factors for developing dementia in the context of loneliness and lacking social support. Across these measures of subjective and objective social deprivation, we have identified strong links between individuals social capital and various indicators of Alzheimers disease and related dementias risk, which replicated across both population cohorts. The quality and quantity of daily social encounters had deep connections with key aetiopathological factors, which represent 1) personal habits and lifestyle factors, 2) physical health, 3) mental health, and 4) societal and external factors. Our population-scale assessment suggest that social lifestyle determinants are linked to most neurodegeneration risk factors, highlighting them promising targets for preventive clinical action.


title: Methylphenidate as a causal test of translational and basic neural coding hypotheses

abstract: Most systems neuroscience studies fall into one of two categories: basic science work aimed at understanding the relationship between neurons and behavior, or translational work aimed at developing treatments for neuropsychiatric disorders. Here we use these two approaches to inform and enhance each other. Our study both tests hypotheses about basic science neural coding principles and elucidates the neuronal mechanisms underlying new, clinically relevant behavioral effects of systemically administered methylphenidate (Ritalin). We discovered that orally administered methylphenidate, used clinically to treat Attention Deficit Hyperactivity Disorder (ADHD) and generally to enhance cognition (Lakhan & Kirchgessner, 2012; Maher, 2008), increases spatially selective visual attention, enhancing visual performance at only the attended location. And as predicted by our previous work (Ni et al., 2018), we found that this causal manipulation enhances vision in rhesus macaques specifically when it decreases the mean correlated variability of neurons in visual area V4. Our findings demonstrate that the visual system is a platform for understanding the neural underpinnings of both complex cognitive processes (basic science) and neuropsychiatric disorders (translation). Addressing basic science hypotheses, our results are consistent with a scenario in which methylphenidate has cognitively specific effects by working through naturally selective cognitive mechanisms. Clinically, our findings suggest that the often staggeringly specific symptoms of neuropsychiatric disorders may be caused and treated by leveraging general mechanisms.


title: Impaired KDM2B-mediated PRC1 recruitment to chromatin causes neural stem cell senescence and ASD/ID-like behavioral deficits

abstract: Autism spectrum disorder (ASD) and intellectual disability (ID) are neurodevelopmental diseases associated with various genetic mutations. Recent clinical studies report that chromosomal 12q24.31 microdeletions are associated with human ASD/ID. However, the causality and underlying mechanisms linking 12q24.31 microdeletions to ASD/ID pathogenesis remain undetermined. Here we show Kdm2b, one of the genes located in chromosomal 12q24.31, plays a critical role in maintaining neural stem cells (NSCs) in the developing mouse brain. Loss of the CxxC-ZF domain of KDM2B impairs its function in recruiting Polycomb repressive complex 1 (PRC1) to chromatin, resulting in de-repression of genes involved in cell apoptosis, cell cycle arrest, NSC premature senescence, and leading to the loss of NSC populations in the brain. Importantly, the Kdm2b mutation is sufficient to induce ASD/ID-like social and memory deficits in adult mice. Thus, our study reveals a critical role of an epigenetic factor KDM2B in normal brain development, a causality between the Kdm2b mutation and genesis of ASD/ID-like phenotypes in mice, and potential molecular mechanisms linking the function of KDM2B-PRC1 in transcriptional regulation and NSC senescence to the12q24.31 microdeletion-associated ASD/ID.


title: Selective isolation of mouse glial nuclei optimized for reliable downstream omics analyses

abstract:
BackgroundIsolation of cell types of interest from the brain for molecular applications presents several challenges, including cellular damage during tissue dissociation or enrichment procedures, and low cell number in the tissue in some cases. Techniques have been developed to enrich distinct cell populations using immunopanning or fluorescence activated cell/nuclei sorting. However, these techniques often involve fixation, immunolabeling and DNA staining steps, which could potentially influence downstream omics applications.

New MethodTaking advantage of readily available genetically modified mice with fluorescent-tagged nuclei, we describe a technique for the purification of cell-type specific brain nuclei, optimized to decrease sample preparation time and to limit potential artefacts for downstream omics applications. We demonstrate the applicability of this approach for the purification of glial cell nuclei and show that the resulting cell-type specific nuclei obtained can be used effectively for omics applications, including ATAC-seq and RNA-seq.

ResultsWe demonstrate excellent enrichment of fluorescently-tagged glial nuclei, yielding high quality RNA and chromatin. We identify several critical steps during nuclei isolation that help limit nuclei rupture and clumping, including quick homogenization, dilution before filtration and loosening of the pellet before resuspension, thus improving yield. Sorting of fluorescent nuclei can be achieved without fixation, antibody labelling, or DAPI staining, reducing potential artifactual results in RNA-seq and ATAC-seq analyses. We show that reproducible glial cell type-specific profiles can be obtained in transcriptomic and chromatin accessibility assays using this rapid protocol.

Comparison with existing methodsOur method allows for rapid enrichment of glial nuclei populations from the mouse brain with minimal processing steps, while still providing high quality RNA and chromatin required for reliable omics analyses.

ConclusionsWe provide a reproducible method to obtain nucleic material from glial cells in the mouse brain with a quick and limited sample preparation.

Highlights- Fast and easy isolation and sorting of glial nuclei from the mouse brain
- Reproducible and versatile processing of enriched nuclei for omics applications

category: molecular biology


title: Pasture age impacts soil fungal composition while bacteria respond to soil chemistry

abstract:
Pasture is a globally important managed habitat providing both food and income. The way in which it is managed leads to a wide range of impacts on soil microbial communities and associated soil health. While there have been several studies comparing pasture farming to other forms of land use, we still have limited understanding of how the soil microbial communities vary between pasture farms and according to management practices. Here we present the results of a field survey across 56 UK livestock farms that are managed by members of the Pasture fed Livestock Association, using amplicon sequencing of the 16S and ITS regions to characterise the soil bacterial and fungal community within fields that have been under pasture for differing durations. We show that grazing management intensity has only limited effects upon microbial community structure, while the duration of pasture since ploughing (ranging from 1 year to over 100 years) impacted the fungal community structure. The impact of management duration was conditional upon soil physicochemical properties, particularly pH. Plant community effects on upon soil bacterial and fungal composition appear to also interact with the soil chemistry, highlighting the importance of plant-soil interactions in determining microbial community structure. Analyses of microbial indicators revealed proportionally more fungal taxa that responded to multiple ecosystem health associated properties than bacterial taxa. We also identified several fungal taxa that both acted as indicators of soil health related properties within our dataset and showed differentiation between grassland types in a national survey, indicating the generality of some fungal indicators to the national level. Members of the Agaricomycetes were associated with multiple indicators of soil health. Our results show the importance of maintaining grassland for the development of plant-soil interactions and microbial community structure with concomitant effects on soil and general ecosystem health.

HighlightsO_LISoil bacteria and fungi from >50 pastures were analysed using DNA metabarcoding
C_LIO_LIDuration of pasture since ploughing impacted fungal community composition
C_LIO_LIBacteria were more associated with soil physicochemical properties than fungi
C_LIO_LIPlant effects on soil microbes were through interactions with soil chemistry
C_LIO_LIMicrobial indicators of soil health were disproportionately fungal taxa
C_LI

category: ecology


title: Mapping vegetation types in Antarctic Peninsula and South Shetlands islands using Sentinel-2 images and Google Earth Engine cloud computing

abstract: The Antarctic vegetation maps are usually made using very high-resolution images collected by orbital sensors or unmanned aerial vehicles, generating isolated maps with information valid only for the time of image acquisition. In the context of global environmental change, mapping the current Antarctic vegetation distribution on a regular basis is necessary for a better understanding of the changes in this fragile environment. This work aimed to generate validated vegetation maps for the North Antarctic Peninsula and South Shetlands Islands based on Sentinel-2 images using cloud processing. Sentinel-2 imagery level 1C, acquired between 2016 and 2021 (January-April), were used. Land pixels were masked with the minimum value composite image for the "water vapor" band. The NDVI maximum value composite image was sliced, and its classes were associated with the occurrence of algae (0.15 - 0.20), lichens (0.20 - 0.50), and mosses (0.50 - 0.80). The vegetation map was validated by comparing it with those from the literature. The present study showed that Sentinel-2 images allow building a vegetation type distribution map for Antarctica Peninsula and South Shetlands Islands.


title: Performance of the sea turtle Lepidochelys olivacea hatchlings from a hatchery on the Pacific coast of Guatemala

abstract:
Sea turtles are marine species that are generally in danger of extinction. The conservation strategies in the different countries are attempting to preserve these species and should be constantly updating their policies according to research results taking place on site. The most abundant and frequent species of sea turtle that nest in the Pacific Coast of Guatemala is Lepidochelys olivacea (Eschscholtz, 1829), therefore human predation has been historically high. The solution to this predation, since the 1970s, as a conservation strategy was to place eggs in enclosed protected spaces called hatcheries, where collectors must give 20% of the nest as a conservation quota. Since this program leads to no natural nests (in situ) remaining on the beaches, the good functioning of the hatcheries plays a fundamental role in the conservation process to work. To understand and predict the fitness of the hatchlings being produced in Guatemalan hatcheries, crawling performance and self-righting performance were measured in 210 hatchlings of the Multiple Uses Area of Hawaii, in the Pacific Coast of Guatemala. The results of the performance were contrasted with incubation conditions to provide an insight into how the management may influence it. We found that self-righting may be a more meaningful measure of variable behavior than crawling performance, showing that there was little variation due to the homogeneous environment of the hatcheries. We can conclude that a greater number of eggs result in faster self-righting, while deeper nests produce hatchlings with slower rates of self-righting.

Summary statementWhen hatcheries are the only sea turtle conservation strategy, and their well-functioning is vital to achieve this purpose, performance can provide information of hatchlings fitness in response to management conditions.


title: Functional group-dependent responses of forest bird communities to invasive predator control and habitat fragmentation

abstract:
AimMounting global pressure on bird populations from invasive predators and habitat loss has driven a rapid growth in restorative and protective conservation action around the world, yet the efficacy of such actions is still not well understood. We investigated the relative effects of invasive predator control and habitat fragmentation on the abundance of native birds and invasive mammalian predators in native forest fragments.

LocationWaikato region, New Zealand

MethodsWe sampled invasive mammalian predator and native bird abundances using camera traps and bird counts at 26 sites in 15 forest fragments across New Zealands Waikato region. Fragment area, shape complexity, and surrounding land cover of exotic and native forest were determined in ArcMap. We further created two composite gradients reflecting predator control intensity and temporal distribution of control based on seven quantitative variables recorded in each of the five years preceding native bird data collection. Finally, we estimated the relative influence of these drivers on invasive mammals and functional groups of native birds using model averaging.

ResultsOf the two invasive predator control variables, only control intensity significantly affected invasive predator abundance and was also a more important driver than landscape or fragment structure, but responses varied among invasive mammal species. In contrast, both invasive predator control intensity and fragment structure were similarly important drivers of native bird abundance, though bird community responses varied markedly between functional groups.

Main conclusionsOur findings suggest that spatial extent of invasive mammal control is important for controlling mammal numbers and enhancing bird abundance, especially for small insectivorous species, and that habitat fragmentation is less important for invasive mammals but at least as important for native bird communities. Consequently, both drivers should be given strong consideration when undertaking landscape-scale conservation and restoration of bird communities in human-altered landscapes threatened by invasive predators.


title: Embracing imperfection: machine-assisted invertebrate classification in real-world datasets

abstract:
O_LIDespite growing concerns over the health of global invertebrate diversity, terrestrial invertebrate monitoring efforts remain poorly geographically distributed. Machine-assisted classification has been proposed as a potential solution to quickly gather large amounts of data; however, previous studies have often used unrealistic or idealized datasets to train their models.
C_LIO_LIIn this study, we describe a practical methodology for including machine learning in ecological data acquisition pipelines. Here we train and test machine learning algorithms to classify over 56,000 bulk terrestrial invertebrate specimens from morphometric data and contextual metadata. All vouchered specimens were collected in pitfall traps by the National Ecological Observatory Network (NEON) at 27 locations across the United States in 2016. Specimens were photographed, and morphometric data was extracted as feature vectors using ImageJ. Issues stemming from inconsistent taxonomic label specificity were resolved by making classifications at the lowest identified taxonomic level (LITL). Taxa with too few specimens to be included in the training dataset were classified by the model using zero-shot classification.
C_LIO_LIWhen classifying specimens that were known and seen by our models, we reached an accuracy of 72.7% using extreme gradient boosting (XGBoost) at the LITL. Models that were trained without contextual metadata underperformed models with contextual metadata by an average of 7.2%. We also classified invertebrate taxa that were unknown to the model using zero-shot classification, with an accuracy of 39.4%, resulting in an overall accuracy of 71.5% across the entire NEON dataset.
C_LIO_LIThe general methodology outlined here represents a realistic application of machine learning as a tool for ecological studies. Hierarchical and LITL classifications allow for flexible taxonomic specificity at the input and output layers. These methods also help address the  long tail problem of underrepresented taxa missed by machine learning models. Finally, we encourage researchers to consider more than just morphometric data when training their models, as we have shown that the inclusion of contextual metadata can provide significant improvements to accuracy.
C_LI


title: Embracing imperfection: machine-assisted invertebrate classification in difficult datasets


title: Evolution of reproductive strategies in incipient multicellularity

abstract: Multicellular organisms can potentially show a large degree of diversity in reproductive strategies, as they could reproduce offspring with varying sizes and compositions compared to their unicellular ancestors. In reality, only a few of these reproductive strategies are prevalent. To understand why this could be the case, we develop a stage-structured population model to probe the evolutionary growth advantages of reproductive strategies in incipient multicellular organisms. The performance of reproductive strategies is evaluated by the growth rates of corresponding populations. We identify the optimal reproductive strategy, which leads to the largest growth rate for a population. Considering the effects of organism size and cellular interaction, we found that distinct reproductive strategies could perform uniquely or equally well under different conditions. Only binary-splitting reproductive strategies can be uniquely optimal. Our results show that organism size and cellular interaction can play crucial roles in shaping reproductive strategies in nascent multicellularity. Our model sheds light on understanding the mechanism driving the evolution of reproductive strategies in incipient multicellularity. Meanwhile, beyond multicellularity, our results imply a crucial factor in the evolution of reproductive strategies of unicellular species - organism size.

category: evolutionary biology


title: Novel genotyping algorithms for rare variants significantly improve the accuracy of Applied Biosystems™ Axiom™ array genotyping calls

abstract:
ObjectiveTo significantly improve the positive predictive value (PPV) and sensitivity of Applied Biosystems Axiom array variant calling, by means of novel improvement to genotyping algorithms and careful quality control of array probesets. The improvement makes array genotyping more suitable for very rare variants.

DesignRetrospective evaluation of UK Biobank array data re-genotyped with improved algorithms for rare variants.

Participants488,359 people recruited to the UK Biobank with Axiom array genotyping data including 200,630 with exome sequencing data.

Main Outcome MeasuresA comparison of genotyping calls from array data to genotyping calls on a subset of variants with exome sequencing data.

ResultsAxiom genotyping [18] performed well, based on comparison to sequencing data, for over 100,000 common variants directly genotyped on the Axiom UK Biobank array and also exome sequenced by the UK Biobank Exome Sequencing Consortium. However, in a comparison to the initial exome sequencing results of the first 50K individuals, Weedon et al. [1] observed that when grouping these variants by the minor allele frequency (MAF) observed in UK Biobank, the concordance with sequencing and resulting positive predictive value (PPV) decreased with the number of heterozygous (Het) array calls per variant. An improved genotyping algorithm, Rare Heterozygous Adjustment (RHA) [16], released mid-2020 for genotyping on Axiom arrays, significantly improves PPV in all MAF ranges for the 50K data as well as when compared to the exome sequencing of 200K individuals, released after Weedon et al. [1] performed their comparison. The RHA algorithm improved PPVs in the 200K data in the lowest three frequency groups [0, 0.001%), [0.001%, 0.005%) and [0.005%, 0.01%) to 83%, 82% and 88%; respectively. PPV was above 95% for higher MAF ranges without algorithm improvement. PPVs are somewhat higher in the 200K dataset, due to a different "truth set" from exome sequencing and because monomorphic exome loci are not included in the joint genotyping calls for the 200K data set, as explained in the methods section.

Sensitivity was higher in the 200K data set than in the original 50K data as well, especially for low MAF ranges. This increase is in part due to the larger data set over which sensitivity could be computed and in part due to the different WES algorithms used for the 200K data [7]. Filtering of a relatively small number of non-performing probesets (determined without reference to the exome sequencing data) significantly improved sensitivities for all MAF ranges, resulting in 70%, 88% and 94% respectively in the three lowest MAF ranges and greater than 98% and 99.9% for the two higher MAF ranges ([0.01%, 1%), [1%, 50%]).

ConclusionsImproved algorithms for genotyping along with enhanced quality control of array probesets, significantly improve the positive predictive value and the sensitivity of array data, making it suitable for the detection of very rare variants. The probeset filtering methods developed have resulted in better probe designs for arrays and the new genotyping algorithm is part of the standard algorithm for all Axiom arrays since early 2020.

category: genetics


title: Active sensing in bees through antennal movements is independent of odor molecule

abstract:
When sampling odors, many insects are moving their antennae in a complex but repeatable fashion. Previous works with bees have tracked antennal movements in only two dimensions, with a low sampling rate and with relatively few odorants. A detailed characterization of the multimodal antennal movement patterns as function of olfactory stimuli is thus wanting. The aim of this study is to test for a relationship between the scanning movements and the properties of the odor molecule.

We tracked several key locations on the antennae of 21 bumblebees at high frequency (up to 1200 fps) and in three dimensions while submitting them to puffs of 11 common odorants released in a low-speed continuous flow. To cover the range of diffusivity and molecule size of most odors sampled by bees, compounds as different as butanol and farnesene were chosen, with variations of 200% in molar masses. Water and paraffin were used as negative controls. Movement analysis was done on the tip, the scape and the base of the antennae tracked with the neural network Deeplabcut.

Bees use a stereotypical motion of their antennae when smelling odors, similar across all bees, independently of the identity of the odors and hence their diffusivity. The variability in the movement amplitude among odors is as large as between individuals. The first oscillation mode at low frequencies and large amplitude (ca. 1-3 Hz, ca. 100{degrees}) is triggered by the presence of an odor and is in line with previous work, as is the speed of movement. The second oscillation mode at higher frequencies and smaller amplitude (40 Hz, ca. 0.1{degrees}) is constantly present. Antennae are quickly deployed when a stimulus is perceived, decorrelate their movement trajectories rapidly and oscillate vertically with a large amplitude and laterally with a smaller one. The cone of air space thus sampled was identified through the 3D understanding of the motion patterns.

The amplitude and speed of antennal scanning movements seem to be function of the internal state of the animal, rather than determined by the odorant. Still, bees display an active olfaction strategy. First, they deploy their antennae when perceiving an odor rather than let them passively encounter it. Second, fast vertical scanning movements further increase the flow speed experienced by an antenna and hence the odorant capture rate. Finally, lateral movements might enhance the likelihood to locate the source of odor, similarly to the lateral scanning movement of insects at odor plume boundaries. Definitive proofs of this function will require the simultaneous 3D recordings of antennal movements with both the air flow and odor fields.

category: animal behavior and cognition


title: Control Cell Migration by Engineering Integrin Ligand Assembly

abstract:
Advances in mechanistic understanding of integrin-mediated adhesion highlight the importance of precise control of ligand presentation in directing cell migration. Top-down nanopatterning limited the spatial presentation to sub-micron. To enhance it to molecular level, we propose a bottom-up nanofabrication strategy. Via self-assembly and co-assembly, precise control of ligand presentation is succeeded by varying the proportions of assembling ligand and nonfunctional peptide. Assembled nanofilaments fulfill multi-functions exerting enhancement to suppression effect on cell migration with tunable amplitudes. Self-assembled nanofilaments possessing super high ligand density selectively suppress cancer cell migration by preventing integrin/actin disassembly at cell rear, which provides new insights to ligand-density-dependent-modulation, revealing valuable inputs to therapeutic innovations in tumor metastasis.

One-Sentence SummaryEngineering integrin ligand assembly from bottom-up offers a generalized tool to selectively control cell migration with tunable amplitudes.


title: Convex-PLR - Revisiting affinity predictions and virtual screening using physics-informed machine learning

abstract:
Virtual screening is an essential part of the modern drug design pipeline, which significantly accelerates the discovery of new drug candidates. Structure-based virtual screening involves ligand conformational sampling, which is often followed by re-scoring of docking poses. A great variety of scoring functions have been designed for this purpose. The advent of structural and affinity databases and the progress in machine-learning methods have recently boosted scoring function performance. Nonetheless, the most successful scoring functions are typically designed for specific tasks or systems. All-purpose scoring functions still perform poorly on the virtual screening tests, compared to precision with which they are able to predict co-crystal binding poses. Another limitation is the low interpretability of the heuristics being used.

We analyzed scoring functions performance in the CASF benchmarks and discovered that the vast majority of them have a strong bias towards predicting larger binding interfaces. This motivated us to develop a physical model with additional entropic terms with the aim of penalizing such a preference. We parameterized the new model using affinity and structural data, solving a classification problem followed by regression. The new model, called Convex-PLR, demonstrated high-quality results on multiple tests and a substantial improvement over its predecessor Convex-PL. Convex-PLR can be used for molecular docking together with VinaCPL, our version of AutoDock Vina, with Convex-PL integrated as a scoring function. Convex-PLR, Convex-PL, and VinaCPL are available at https://team.inria.fr/nano-d/convex-pl/.


title: RUNIMC: An R-based package for imaging mass cytometry data analysis and pipeline validation

abstract: We propose a novel pipeline for the analysis of imaging mass cytometry data, comparing an unbiased approach, representing the actual gold standard, with a novel biased method. We made use of both synthetic/ controlled datasets as well as two datasets obtained from FFPE sections of follicular lymphoma, and head and neck patients, stained with a 14 and 29-markers panels respectively. The novel pipeline, denominated RUNIMC, has been completely developed in R and contained in a single package. The novelty resides in the ease with which multi-class random forest classifier can be used to classify image features, making the pathologists and expert classification pivotal, and the use of a random forest regression approach that permits a better detection of cell boundaries, and alleviates the necessity of relying on a perfect nuclear staining.

category: cancer biology


title: XePhIR: The zebrafish Xenograft Phenotype Interactive Repository

abstract: Zebrafish xenografts are an established model in cancer biology, with a steadily rising number of models and users. However, as of yet, there is no platform dedicated to standardizing protocols and sharing data regarding zebrafish xenograft phenotypes. Here, we present the Xenograft Phenotype Interactive Repository (XePhIR, www.xephir.org) as an independent data sharing platform to deposit, share and repurpose zebrafish xenograft data. Deposition of data and publication with XePhIR will be done after the acceptation of the original publication. This will enhance the reach of the original research article, enhance visibility, and does not interfere with publication or copyrights of the original article. With XePhIR, we strive to fulfill these objectives and reason that this resource will enhance reproducibility and showcase the appeal and applicability of the zebrafish xenograft model.


title: Environmental and molecular modulation of motor individuality in larval zebrafish

abstract: Innate behavioral biases such as human handedness are a ubiquitous form of inter-individual variation that are not strictly hardwired into the genome and are influenced by diverse internal and external cues. Yet, genetic and environmental factors modulating behavioral variation remain poorly understood, especially in vertebrates. To identify genetic and environmental factors that influence behavioral variation, we take advantage of larval zebrafish light-search behavior. During light-search, individuals preferentially turn in leftward or rightward loops, in which directional bias is sustained and non-heritable, and maintained by a habenula-rostral PT circuit. Here we use a medium-throughput recording strategy and unbiased analysis to show that significant individual to individual variation exists in wildtype larval zebrafish turning preference. We classify stable left, right, and unbiased turning types, with most individuals exhibiting a directional preference. Raising larvae at elevated temperature selectively reduces the leftward turning type and impacts rostral PT neurons, specifically. Exposure to conspecifics, variable salinity, environmental enrichment, and physical disturbance does not significantly impact inter-individual turning bias. Pharmacological manipulation of Notch signaling and carrying a mutant allele of a known Notch pathway affecter gene, gsx2, disrupted turn bias individuality in a dose-dependent manner. These results establish that larval zebrafish is a powerful vertebrate model for inter-individual variation with sensitivity to specific environmental perturbations and gene dosage.


title: A Role for Visual Areas in Physics Simulations

abstract: To engage with the world, we must regularly make predictions about the outcomes of physical scenes. How do we make these predictions? Recent evidence points to simulation - the idea that we can introspectively manipulate rich, mental models of the world - as one possible explanation for how such predictions are accomplished. While theories based on simulation are supported by computational models, neuroscientific evidence for simulation is lacking and many important questions remain. For instance, do simulations simply entail a series of abstract computations? Or are they supported by sensory representations of the objects that comprise the scene being simulated? We posit the latter and suggest that the process of simulating a sequence of physical interactions is likely to evoke an imagery-like envisioning of those interactions. Using functional magnetic resonance imaging, we demonstrate that when participants predict how a ball will fall through an obstacle-filled display, motion-sensitive brain regions are activated. We further demonstrate that this activity, which occurs even though no motion is being sensed, resembles activity patterns that arise while participants perceive the balls motion. This finding suggests that the process of simulating the balls movement is accompanied by a sensory representation of this movement. These data thus demonstrate that mental simulations recreate sensory depictions of how a physical scene is likely to unfold.


title: Interpreting sensory and cognitive signals in the cortical reading network

abstract: Voxels in the visual cortex contain neurons that are responsive to small regions of the visual field; these regions can be quantified using population receptive field (pRF) analysis. We measured pRFs using several types of patterns: words, visually matched false-fonts, and visually dissimilar checker patterns. In visual field maps pRF estimates using words and false-fonts are similar, but pRF estimates using checkers differ substantially. The pattern of results in the contiguous ventral occipito-temporal reading circuitry is different: word pRF estimates differ from false-fonts and checkers. These findings were replicated at two research sites. We explain these results with a qualitative model, where the response differences in the visual field maps arise from sensory signals, and the differences in the reading circuitry arise from the integration of sensory and cognitive signals.


title: Optimization of long-term human iPSC-derived spinal motor neuron culture using a dendritic polyglycerol amine-based substrate

abstract: Human induced pluripotent stem cells (h-iPSCs) derived from healthy and diseased individuals can give rise to many cell types, facilitating the study of mechanisms of development, human disease modeling, and early drug target validation. In this context, experimental model systems based on h-iPSC-derived motor neurons (MNs) have been used to study MN diseases such as spinal muscular atrophy and amyotrophic lateral sclerosis. Modeling MN disease using h-iPSC-based approaches requires culture conditions that can recapitulate in a dish the events underlying differentiation, maturation, aging, and death of MNs. Current h-iPSC-derived MN-based applications are often hampered by limitations in our ability to monitor MN morphology, survival, and other functional properties over a prolonged timeframe, underscoring the need for improved long-term culture conditions. Here we describe a cytocompatible dendritic polyglycerol amine (dPGA) substrate-based method for prolonged culture of h-iPSC-derived MNs. We provide evidence that MNs cultured on dPGA-coated dishes are more amenable to long-term study of cell viability, molecular identity, and spontaneous network electrophysiological activity. The present study has the potential to improve iPSC-based studies of human MN biology and disease.


title: Model-based characterization of the selectivity of neurons in primary visual cortex

abstract:
To understand the complexity of stimulus selectivity in primary visual cortex (V1), models constructed to match observed responses to complex time-varying stimuli, instead of to explain responses to simple parametric stimuli, are increasingly used. While such models often can more accurately reflect the computations performed by V1 neurons in more natural visual environments, they do not by themselves provide insight into established measures of V1 neural selectivity such as receptive field size, spatial frequency tuning and phase invariance. Here, we suggest a series of analyses that can be directly applied to encoding models to link complex encoding models to more interpretable aspects of stimulus selectivity, applied to nonlinear models of V1 neurons recorded in awake macaque in response to random bar stimuli. In linking model properties to more classical measurements, we demonstrate several novel aspects of V1 selectivity not available to simpler experimental measurements. For example, we find that individual spatiotemporal elements of the V1 models often have a smaller spatial scale than the overall neuron sensitivity, and that this results in non-trivial tuning to spatial frequencies. Additionally, our proposed measures of nonlinear integration suggest that more classical classifications of V1 neurons into simple versus complex cells are spatial-frequency dependent. In total, rather than obfuscate classical characterizations of V1 neurons, model-based characterizations offer a means to more fully understand their selectivity, and provide a means to link their classical tuning properties to their roles in more complex, natural, visual processing.

Significance statementVisual neurons are increasingly being studied with more complex, natural visual stimuli, with increasingly complex models necessary to characterize their response properties. Here, we describe a battery of analyses that relate these more complex models to classical characterizations. Using such model-based characterizations of V1 neurons furthermore yields several new insights into V1 processing not possible to capture in more classical means to measure their visual selectivity.


title: RTICBM-74 is a Brain-Penetrant CB1 Receptor Allosteric Modulator that Reduces Alcohol Intake in Rats

abstract:
The endocannabinoid system is implicated in the neuronal mechanisms of alcohol use disorder (AUD), with the cannabinoid receptor subtype 1 (CB1) representing a promising target for AUD therapeutic interventions. We have previously shown negative allosteric modulators (NAMs) of the CB1 receptor attenuated the reinstatement of other drugs of abuse including cocaine and methamphetamine in rats; however, their effects on alcohol-related behaviors have not been investigated. Here, we tested the pharmacokinetic properties of one such CB1 NAM, RTICBM-74, and its effects on alcohol self-administration in rats. RTICBM-74 showed low aqueous solubility and high protein binding but had excellent half-life and low clearance against rat liver microsomes and hepatocytes, and excellent brain penetrance in rats. RTICBM-74 pretreatment specifically reduced alcohol intake across a range of doses in male or female Wistar or Long-Evans rats that were trained to self-administer alcohol. These effects were similar to the CB1 antagonist/inverse agonist rimonabant which was tested as a positive control. Importantly, RTICBM-74 was effective at reducing alcohol intake at doses that did not affect locomotion or sucrose self-administration. Our findings suggest that CB1 NAMs such as RTICBM-74 have promising therapeutic potential in treatment of AUD.

SIGNIFICANCE STATEMENTThe present work shows that a metabolically stable and brain penetrant CB1 receptor negative allosteric modulator (NAM) reduces alcohol self-administration in rats without affecting locomotion or sucrose self-administration, suggesting potential therapeutic relevance for the treatment of AUD.


title: The individuality of shape asymmetries of the human cerebral cortex

abstract: Asymmetries of the cerebral cortex are found across diverse phyla and are particularly pronounced in humans, with important implications for brain function and disease. Here, we introduce a novel approach to characterize asymmetries of the whole cortical shape across different spatial frequencies using magnetic resonance imaging data in three independent datasets. We find that cortical shape asymmetry is highly individualized and robust, akin to a cortical fingerprint, and identifies individuals more accurately than size-based descriptors, such as cortical thickness and surface area, or measures of inter-regional functional coupling of brain activity. Individual identifiability is optimal at coarse spatial scales ([~]37 mm wavelength), and shape asymmetries show scale-specific associations with sex and cognition, but not handedness. While unihemispheric cortical shape shows significant heritability at coarse scales ([~]65 mm wavelength), shape asymmetries are determined primarily by subject-specific environmental effects. Thus, coarse-scale shape asymmetries are highly personalized, sexually dimorphic, linked to individual differences in cognition, and are primarily driven by stochastic environmental influences.


title: Naturalistic stimuli reveal a critical period in visual cortex development: Evidence from adult-onset blindness

abstract: How do life experiences impact cortical function? In people who are born blind, the "visual" cortices are recruited for nonvisual tasks such as Braille reading and sound localization (e.g., Collignon et al., 2011; Sadato et al., 1996). The mechanisms of this recruitment are not known. Do visual cortices have a latent capacity to respond to nonvisual information that is equal throughout the lifespan? Alternatively, is there a sensitive period of heightened plasticity that makes visual cortex repurposing possible during childhood? To gain insight into these questions, we leveraged naturalistic auditory stimuli to quantify and compare cross-modal responses congenitally blind (CB, n=22), adult-onset blind (vision loss >18 years-of-age, AB, n=14) and sighted (n=22) individuals. Participants listened to auditory excerpts from movies; a spoken narrative; and matched meaningless auditory stimuli (i.e., shuffled sentences, backwards speech) during fMRI scanning. These rich naturalistic stimuli made it possible to simultaneous engage a broad range of cognitive domains. We correlated the voxel-wise timecourses of different participants within each group. For all groups, all stimulus conditions induced synchrony in auditory cortex and for all groups only the narrative stimuli synchronized responses in higher-cognitive fronto-parietal and temporal regions. Inter-subject synchrony in visual cortices was high in the CB group for the movie and narrative stimuli but not for meaningless auditory controls. In contrast, visual cortex synchrony was equally low among AB and sighted blindfolded participants. Even many years of blindness in adulthood fail to enable responses to naturalistic auditory information in visual cortices of people who had sight as children. These findings suggest that cross-modal responses in visual cortex of people born blind reflect the plasticity of developing visual cortex during a sensitive period.


title: AAV-PHP.S-mediated delivery of reporters to cranial ganglion sensory neurons

abstract:
Because of their ease of use and low risk containment, Adeno-Associated Virus vectors are indispensable tools for much of neuroscience. Yet AAVs have been used relatively little to study the identities and connectivity of peripheral sensory neurons because methods to selectively target particular receptive fields or neuron types have been limited. The introduction of the AAV-PHP.S capsid with selective tropism for peripheral neurons (Chan et al., 2017) offered a solution, which we further elaborate here. We demonstrate using AAV-PHP.S with GFP or mScarlet reporters, that all cranial sensory ganglia, i.e. for cranial nerves V, VII, IX and X, are targeted. Pseudounipolar neurons of both somatic and visceral origin, but not satellite glia, are efficiently transduced rapidly and express the gene of interest within 1 week of injection. Fluorescent reporter proteins are transported into the central and peripheral axons of these sensory neurons, permitting visualization of terminals at high resolution, and/or in intact, cleared brain using light sheet microscopy. By combining a Cre-dependent reporter with the AAV-PHP.S capsid, we confirmed expression in a cell-type dependent manner for both anatomical and targeted functional analyses. The AAV-PHP.S capsid will be a powerful tool for mapping the receptive fields and circuits of molecular subtypes of many somatosensory, gustatory and visceral sensory neurons.

SIGNIFICANCE STATEMENTAAV vectors have become an essential tool for visualizing, manipulating, and recoding from neurons of the central nervous system. However, the technology is not widely used for peripheral neurons because of several technical limitations. The AAV-PHP.S synthetic capsid, which targets peripheral neurons, was recently introduced (Chan et al., 2017). Here, we establish key parameters for using this virus, including which cells are transduced, the timing of expression in central and peripheral terminals, distant from neuronal somata, and the effectiveness of Cre-dependent constructs for cell type selective expression. This permits the use of AAV for constructing detailed anatomic and functional maps of the projections of molecular subtypes of peripheral sensory neurons.


title: Naive and in vitro-activated primary mouse CD8+ T cells retain in vivo immune responsiveness after electroporation-based CRISPR/Cas9 genetic engineering

abstract: CRISPR/Cas9 technology has revolutionized genetic engineering of primary cells. Although its use is gaining momentum in studies on CD8+ T cell biology, it remains elusive to what extent CRISPR/Cas9 affects in vivo function of CD8+ T cells. Here, we optimized nucleofection-based CRISPR/Cas9 genetic engineering of naive and in vitro-activated primary mouse CD8+ T cells and tested their in vivo immune responses. Nucleofection of naive CD8+ T cells preserved their in vivo antiviral immune responsiveness to an extent that is indistinguishable from non-nucleofected cells, whereas in vitro activation of CD8+ T cells prior to nucleofection led to slightly impaired expansion/survival. Of note, different target proteins displayed distinct decay rates after gene editing. This is in stark contrast to a comparable period of time required to complete gene inactivation. Thus, for optimal experimental design, it is crucial to determine the kinetics of the loss of target gene product to adapt incubation period after gene editing. In sum, nucleofection-based CRISPR/Cas9 genome editing achieves efficient and rapid generation of mutant CD8+ T cells without imposing detrimental constraints on their in vivo functions.

category: immunology


title: The role of antigen recognition in the γδ T cell response at the controlled stage of M. tuberculosis infection.

abstract: {gamma}{delta} T cells contribute to host immune defense uniquely; but how they function in different stages (e.g., acute versus chronic) of a specific infection remains unclear. As the role of{gamma}{delta} T cells in early, active Mycobacterium tuberculosis (Mtb) infection is well documented, we focused on elucidating the{gamma}{delta} T cell response in persistent or controlled Mtb infection. Systems analysis of circulating{gamma}{delta} T cells from a South African adolescent cohort identified a distinct population of CD8+{gamma}{delta} T cells that expanded in this state. These cells had features indicative of persistent antigenic exposure but were robust cytolytic effectors and cytokine/chemokine producers. While these{gamma}{delta} T cells displayed an attenuated response to TCR-mediated stimulation, they expressed Natural Killer (NK) cell receptors and had robust CD16 (Fc{gamma}RIIIA)-mediated cytotoxic response, suggesting alternative ways for{gamma}{delta} T cells to control this stage of the infection. Despite this NK- like functionality, the CD8+{gamma}{delta} T cells consisted of highly expanded clones, which utilized TCRs with different V{gamma}/{delta} pairs. Theses TCRs could respond to an Mtb-lysate, but not to phosphoantigens, which are components of Mtb-lysate that activate{gamma}{delta} T cells in acute Mtb infection, indicating that the CD8+{gamma}{delta} T cells were induced in a stage-specific, antigen-driven manner. Indeed, trajectory analysis showed that these{gamma}{delta} T cells arose from naive cells that had traversed distinct differentiation paths in this infection stage. Importantly, increased levels of CD8+{gamma}{delta} T cells were also found in other chronic inflammatory conditions, including cardiovascular disease and cancer, suggesting that persistent antigenic exposure may lead to similar{gamma}{delta} T cell responses.


title: An improved culture protocol for the differentiation and survival of human promyelocytic leukaemia PLB-985 cell-line into mature neutrophil-like granulocytes

abstract: Circulating blood neutrophils are short-lived, lack proliferation capacity and cannot be transfected in vitro to express exogenous genes or proteins. These properties have made the ex vivo genetic manipulation of neutrophils challenging and hindered biochemical and molecular studies investigating the function of specific genes and proteins. Improved methodology for differentiating cell lines into mature neutrophil-like phenotypes, with similar morphological and functional properties to blood neutrophils would, therefore, be an important tool to probe the molecular properties of mature cells. The PLB-985 cell line was cultured in RPMI-1640 medium supplemented foetal calf serum (FCS) and penicillin/streptomycin. For induction of differentiation into neutrophil-like cells, the medium was supplemented with sodium pyruvate, N, N-dimethylformamide (DMF) and all-trans retinoic acid (ATRA), FCS and penicillin/streptomycin. The cytokines G-CSF and GM-CSF were used to enhance differentiation, prolong viability and delay the progression of the differentiated cells into apoptosis. The modified culture protocol and conditions induced PLB-985 cells to differentiate into mature, neutrophil-like granulocytes that resembled the morphology of mature blood neutrophils as evident by acquisition of a multi-lobed nucleus and granulated cytoplasm. These modified culture conditions resulted in enhanced differentiation into neutrophil-like cells and the apoptosis of these differentiated cells was delayed by supplementation with cytokines. This experimental system should be useful for studies probing the function of specific genes and proteins in human neutrophils.


title: The secrets to domestic bliss - Partner fidelity and environmental filtering preserve stage-specific turtle ant gut symbioses for over 40 million years

abstract:
BackgroundGut microbiomes can vary across development, a pattern often found for insects with complete metamorphosis. With varying nutritional need and distinct opportunities for microbial acquisition, questions arise as to how such  holometabolous insects retain helpful microbes at larval and adult stages. Ants are an intriguing system for such study. In a number of lineages adults digest only liquid food sources, while larvae digest solid foods. Like some other social insects, workers and soldiers of some ant species engage in oral-anal trophallaxes, enabling microbial transfer among siblings. But do queens, the typical colony founding caste, obtain symbionts through such transfer? Does this enable transgenerational symbiont passage? And does the resulting partner fidelity promote the evolution of beneficial symbionts? Furthermore, how might such adult-centric biology shape larval microbiomes? To address these questions, we characterized symbiotic gut bacteria across 13 species of Cephalotes turtle ants, with up to 40-million years of divergence. Adding to the prior focus on workers we, here, study underexplored castes and stages including queens, soldiers, and larvae, by performing 16S rRNA qPCR, amplicon sequencing, and phylogenetic classification.

ResultsWe show that adult microbiomes are conserved across species and largely across castes. Nearly 95% of the bacteria in adults have, thus far, been found only in Cephalotes ants. Furthermore, the microbiomes from most adults exhibit phylosymbiosis, a trend in which microbiome community similarity recapitulates patterns of host relatedness. Additionally, an abundant, adult-enriched symbiont cospeciates with some Cephalotes. Evidence here suggests that these partner fidelity patterns extend from transgenerational symbiont transfer through alate gyne dispersal and subsequent colony-founding by queens. Like adults, larvae of Cephalotes species exhibit strong microbiome conservation. Phylosymbiosis patterns are weaker, however, with further evidence elevating environmental filtering as a primary mechanism behind such conservation. Specifically, while adult-enriched symbionts are found in most larvae, symbionts of older larvae are highly related to free-living bacteria from the Enterobacteriaceae, Lactobacillales, and Actinobacteria.

ConclusionsOur findings suggest that both partner fidelity and conserved environmental filtering drive stable, stage-specific, social insect symbioses. We discuss the implications for our broader understanding of insect microbiomes, and the means of sustaining a beneficial microbiome.


title: Life-history genotype explains variation in migration activity in Atlantic salmon (Salmo salar).

abstract: One of the most important life-history continuums is the fast-slow axis, where "fast" individuals mature earlier than "slow" individuals. "Fast" individuals are predicted to be more active than "slow" individuals; high activity is required to maintain a fast life-history strategy. Recent meta-analyses revealed mixed evidence for such integration. Here, we test whether known life-history genotypes differ in activity expression by using Atlantic salmon (Salmo salar) as a model. In salmon, variation in Vgll3, a transcription co-factor, explains [~]40% of variation in maturation timing. We predicted that the allele related to early maturation (vgll3*E) would be associated with increased activity. We used an automated surveillance system to follow [~]1900 juveniles including both migrants and non-migrants (i.e. smolt and parr fish, respectively) in semi-natural conditions over 31 days ([~]580 000 activity measurements). Against our prediction, vgll3 did not explain variation in activity in pooled migrant and non-migrant data. However, in migrants, vgll3 explained variation in activity according to our prediction in a sex-dependent manner. Specifically, in females the vgll3*E allele was related to increasing activity, whereas in males the vgll3*L allele (later maturation allele) was related to increasing activity. These sex-dependent effects might be a mechanism maintaining within-population genetic life-history variation.


title: Integrated gene analyses of de novo mutations from 46,612 trios with autism and developmental disorders

abstract: Most genetic studies consider autism spectrum disorder (ASD) and developmental disorder (DD) separately despite overwhelming comorbidity and shared genetic etiology. Here we analyzed de novo mutations (DNMs) from 15,560 ASD (6,557 are new) and 31,052 DD trios independently and combined as broader neurodevelopmental disorders (NDD) using three models. We identify 615 candidate genes (FDR 5%, 189 potentially novel) by one or more models, including 138 reaching exome-wide significance (p < 3.64e-07) in all models. We find no evidence for ASD-specific genes in contrast to 18 genes significantly enriched for DD. There are 53 genes show particular mutational-bias including enrichments for missense (n=41) or truncating DNM (n=12). We find 22 genes with evidence of sex-bias including five X chromosome genes also with significant female burden (DDX3X, MECP2, SMC1A, WDR45, and HDAC8). NDD risk genes group into five functional networks associating with different brain developmental lineages based on single-cell nuclei transcriptomic data, which provides important insights into disease subtypes and future functional studies.


title: The 3D spatial constraint on 6.1 million amino acid sites in the human proteome

abstract: Quantification of the tolerance of protein-coding sites to genetic variation within human populations has become a cornerstone of the prediction of the function of genomic variants. We hypothesize that the constraint on missense variation at individual amino acid sites is largely shaped by direct 3D interactions with neighboring sites. To quantify the constraint on protein-coding genetic variation in 3D spatial neighborhoods, we introduce a new framework called COntact Set MISsense tolerance (or COSMIS) for estimating constraint. Leveraging recent advances in computational structure prediction, large-scale sequencing data from gnomAD, and a mutation-spectrum-aware statistical model, we comprehensively map the landscape of 3D spatial constraint on 6.1 amino acid sites covering >80% (16,533) of human proteins. We show that the human proteome is broadly under 3D spatial constraint and that the level of spatial constraint is strongly associated with disease relevance both at the individual site level and the protein level. We demonstrate that COSMIS performs significantly better at a range of variant interpretation tasks than other population-based constraint metrics while also providing biophysical insight into the potential functional roles of constrained sites. We make our constraint maps freely available and anticipate that the structural landscape of constrained sites identified by COSMIS will facilitate interpretation of protein-coding variation in human evolution and prioritization of sites for mechanistic or functional investigation.

category: genomics


title: Genome-wide association studies of global Mycobacterium tuberculosis resistance to thirteen antimicrobials in 10,228 genomes

abstract: The emergence of drug resistant tuberculosis is a major global public health concern that threatens the ability to control the disease. Whole genome sequencing as a tool to rapidly diagnose resistant infections can transform patient treatment and clinical practice. While resistance mechanisms are well understood for some drugs, there are likely many mechanisms yet to be uncovered, particularly for new and repurposed drugs. We sequenced 10,228 Mycobacterium tuberculosis (MTB) isolates worldwide and determined the minimum inhibitory concentration (MIC) on a grid of twofold concentration dilutions for 13 antimicrobials using quantitative microtiter plate assays. We performed oligopeptide- and oligonucleotide-based genome-wide association studies using linear mixed models to discover resistance-conferring mechanisms not currently catalogued. Use of MIC over binary resistance phenotypes increased heritability for the new and repurposed drugs by 26-37%, increasing our ability to detect novel associations. For all drugs, we discovered uncatalogued variants associated with MIC, including in the Rv1218c promoter binding site of the transcriptional repressor Rv1219c (isoniazid), upstream of the vapBC20 operon that cleaves 23S rRNA (linezolid) and in the region encoding an -helix lining the active site of Cyp142 (clofazimine, all p<10-7.7). We observed that artefactual signals of cross resistance could be unravelled based on the relative effect size on MIC. Our study demonstrates the ability of very large-scale studies to substantially improve our knowledge of genetic variants associated with antimicrobial resistance in M. tuberculosis.


title: Proximal CA3 is the primary locus of age-related pattern separation deficits in rats

abstract: Age-related deficits in pattern separation have been postulated to bias the output of hippocampal memory processing toward pattern completion, which can cause deficits in accurate memory retrieval. While the CA3 region of the hippocampus is often conceptualized as a homogeneous network involved in pattern completion, growing evidence demonstrates a functional gradient in CA3 along the transverse axis, as pattern-separated outputs (dominant in the more proximal CA3) transition to pattern-completed outputs (dominant in the more distal CA3). We examined the neural representations along the CA3 transverse axis in young (Y), aged memory-unimpaired (AU), and aged memory-impaired (AI) rats when different changes were made to the environment. Functional heterogeneity in CA3 was observed in Y and AU rats when the environmental similarity was high (altered cues or altered environment shapes in the same room), with more orthogonalized representations in proximal CA3 than in distal CA3. In contrast, AI rats showed reduced orthogonalization in proximal CA3 but showed normal (i.e., generalized) representations in distal CA3, with little evidence of a functional gradient. Under experimental conditions when the environmental similarity was low (different rooms), representations in proximal and distal CA3 remapped in all rats, showing that CA3 of AI rats is able to encode distinctive representations for inputs with greater dissimilarity. These experiments support the hypotheses that the aged-related bias towards hippocampal pattern completion is due to the loss in AI rats of the normal transition from pattern separation to pattern completion along the CA3 transverse axis.


title: Loss of functional heterogeneity along the CA3 transverse axis in aging


title: Sensitivity of discrete symmetry metrics: implications for metric choice

abstract:
Gait asymmetry is present in several pathological populations, including those with Parkinsons disease, Huntingtons disease, and stroke survivors. Previous studies suggest that commonly used discrete symmetry metrics, which compare single bilateral variables, may not be equally sensitive to underlying effects of asymmetry, and the use of a metric with low sensitivity could result in unnecessarily low statistical power. The purpose of this study was to provide a comprehensive assessment of the sensitivity of commonly used discrete symmetry metrics to better inform design of future studies. Monte Carlo simulations were used to estimate the statistical power of each symmetry metric at a range of asymmetry magnitudes, group/condition variabilities, and sample sizes. Power was estimated by repeated comparison of simulated symmetric and asymmetric data with a paired t-test, where the proportion of significant results is equivalent to the power. Simulation results confirmed that not all common discrete symmetry metrics are equally sensitive to reference effects of asymmetry. Multiple symmetry metrics exhibit equivalent sensitivities, but the most sensitive discrete symmetry metric in all cases is a bilateral difference (e.g. left - right). A ratio (e.g. left/right) has poor sensitivity when group/condition variability is not small, but a log-transformation produces increased sensitivity. Additionally, two metrics which included an absolute value in their definitions showed increased sensitivity when the absolute value was removed. Future studies should consider metric sensitivity when designing analyses to reduce the possibility of underpowered research.

Summary statementStatistical power is an important factor in study design. Our results show that not all discrete symmetry metrics have similar or sufficient sensitivity to detect effects of asymmetry.


title: MAGI-MS: Multiple seed-centric module discovery

abstract:
Complex disorders manifest by the interaction of multiple genetic and environmental factors. Through the construction of genetic modules that consist of highly co-expressed genes, it is possible to identify genes that participate in common biological pathways relevant to specific phenotypes. We have previously developed tools MAGI and MAGI-S for genetic module discovery by incorporating co-expression and protein-interaction networks. Here we introduce an extension to MAGI-S, denoted as Merging Affected Genes into Integrated Networks - Multiple Seeds (MAGI-MS), that permits the user to further specify a disease pathway of interest by selecting multiple seed genes likely to function in the same molecular mechanism. By providing MAGI-MS with pairs of seed genes involved in processes underlying certain classes of neurodevelopmental disorders, such as epilepsy, we demonstrate that MAGI-MS can reveal modules enriched in genes relevant to chemical synaptic transmission, glutamatergic synapse, and other functions associated with the provided seed genes.

Availability and implementationMAGI-MS is free and is available at: https://github.com/jchow32/MAGI-MS


title: Multiphase Organization Is a Second Phase Transition Within Multi-Component Biomolecular Condensates

abstract:
We present a mean-field theory for the multiphase organization of multi-component biomolecular condensates and validate the theory by molecular dynamics simulations of model mixtures. A first phase transition results in the separation of the dense phase from the bulk phase. In a second phase transition, the components in the dense phase demix to localize in separate regions that attach to each other. The second phase transition occurs when the strength of cross-species attraction goes below the mean strength of the self-attraction of the individual species and reaches a critical value. At a given strength of cross-species attraction, both of the phase transitions can be observed by decreasing temperature, leading first to phase separation and then to demixing of the dense phase. The theory and simulations establish the disparity in strength between self and cross-species attraction as a main driver for the multiphase organization of multi-component biomolecular condensates.

TOC GRAPHICS

O_FIG O_LINKSMALLFIG WIDTH=196 HEIGHT=200 SRC="FIGDIR/small/460104v1_ufig1.gif" ALT="Figure 1">
View larger version (55K):
org.highwire.dtl.DTLVardef@e17fdcorg.highwire.dtl.DTLVardef@9168deorg.highwire.dtl.DTLVardef@7c07bcorg.highwire.dtl.DTLVardef@e0077d_HPS_FORMAT_FIGEXP  M_FIG C_FIG


title: Molecular Drivers of Tumor Progression in Microsatellite Stable APC Mutation-Negative Colorectal Cancers

abstract:
BackgroundThe tumor suppressor gene adenomatous polyposis coli (APC) is the initiating mutation in approximately 80% of all colorectal cancers (CRC), underscoring the importance of aberrant regulation of intracellular WNT signaling in CRC development. Recent studies have found that early-onset CRC exhibits an increased proportion of tumors lacking an APC mutation. We set out to identify mechanisms underlying APC mutation-negative (APCmut-) CRCs.

MethodsWe analyzed data from The Cancer Genome Atlas to compare clinical phenotypes, somatic mutations, copy number variations, gene fusions, RNA expression, and DNA methylation profiles between APCmut- and APC mutation-positive (APCmut+) microsatellite stable CRCs.

ResultsTranscriptionally, APCmut- CRCs clustered into two approximately equal groups. Cluster One was associated with enhanced mitochondrial activation. Cluster Two was strikingly associated with genetic inactivation or decreased RNA expression of the WNT antagonist RNF43, increased expression of the WNT agonist RSPO3, activating mutation of BRAF, or increased methylation and decreased expression of AXIN2. APCmut- CRCs exhibited evidence of increased immune cell infiltration, with significant correlation between M2 macrophages and RSPO3.

ConclusionsAPCmut- CRCs comprise two groups of tumors characterized by enhanced mitochondrial activation or increased sensitivity to extracellular WNT, suggesting that they could be respectively susceptible to inhibition of these pathways.


title: Aberrant epigenetic and transcriptional events associated with breast cancer risk

abstract:
BackgroundGenome-wide association studies have identified several breast cancer susceptibility loci. However, biomarkers for risk assessment are still missing. Here, we investigated cancer-related molecular changes detected in tissues from women at high risk for breast cancer prior to disease manifestation. Disease-free breast tissue cores donated by healthy women (N=146, median age=39 years) were processed for both methylome (MethylCap) and transcriptome (Illuminas HiSeq4000) sequencing. Analysis of tissue microarray and primary breast epithelial cells was used to confirm gene expression dysregulation.

ResultsTranscriptomic analysis identified 69 differentially expressed genes between women at either high and those at average risk of breast cancer (Tyrer-Cuzick model) at FDR<0.05 and fold change[≥]2. The majority of the identified genes were involved in DNA damage checkpoint, cell cycle, and cell adhesion. Two genes, FAM83A and NEK2, were overexpressed in tissue sections (FDR<0.01) and primary epithelial cells (p<0.05) from high-risk breasts. Moreover, 1698 DNA methylation aberrations were identified in high-risk breast tissues (FDR<0.05), partially overlapped with cancer-related signatures and correlated with transcriptional changes (p<0.05, r[≤]0.5). Finally, among the participants, 35 women donated breast biopsies at two time points, and age-related molecular alterations enhanced in high-risk subjects were identified.

ConclusionsNormal breast tissue from women at high risk of breast cancer bears molecular aberrations that may contribute to breast cancer susceptibility. This study is the first molecular characterization of the true normal breast tissues and provides an opportunity to investigate molecular markers of breast cancer risk, which may lead to new preventive approaches.