title: DNA, Morphology, and Ecology Resurrect Previously Synonymized Species of North American Stereum and Suggest Extensive Undescribed Global Diversity

abstract: Stereum is an exceedingly common but taxonomically confounding genus of basidiomycete fungus with a cosmopolitan distribution. Lack of consensus about morphological and geographic boundaries of many Stereum species has resulted in a lack of consistency in identification of physical specimens, a problem that cascades to their associated published DNA sequences. A critical initial step towards addressing these issues is determining the scope of the problem. Here, we first use integrative taxonomy to delimit species in the North American Stereum ostrea complex. We use morphological and ecological characters, alongside ITS rDNA sequences of specimens from midwestern and eastern North America to show that "Stereum ostrea" in this region is a complex of at least three reproductively isolated sister species: S. lobatum, S. fasciatum, and S. subtomentosum. We then extend lessons from this case study to a set of publicly available Stereum ITS sequences to assess the accuracy of species names represented by existing sequence data. ASAP species delimitation successfully discriminates among the three newly revealed species in the S. ostrea species complex, but also reveals considerable cryptic diversity across global Stereum and widespread inconsistency in application of species names. Though ITS alone should not be used to delimit species or describe evolutionary relationships, its application here helps direct new hypotheses and suggests several areas of Stereum taxonomy that require revision. The critical future work of disentangling Stereum taxonomy and evolution should combine a multilocus genetic approach with morphology, ecology, and a global sampling strategy.


title: Lateralized functional responses in the cortex arise from the dynamic interactions in the structural connectome

abstract:
Structure-function relationships are fundamental to studies of neural systems, yet the mechanistic underpinnings of how structural networks shape hemispheric lateralization remain elusive. For instance, the asymmetric neuroanatomic embedding of primary auditory cortices was shown when connectivity with all other brain areas were considered. Concomitantly, functional lateralization e.g., left hemispheric dominance of speech processing and right hemispheric dominance of music perception, is widely acknowledged. The present article provides a parsimonious mechanistic explanation based on computational modelling and empirical recordings to demonstrate emergence of hemispheric lateralization of brain function. For validation of the model, empirical EEG recordings of auditory steady state responses (ASSR) were undertaken, and empirical findings suggest right hemispheric dominance at the level of cortical sources in binaural and monaural hearing conditions. Subsequently, we demonstrate the entrainment and phase of oscillations in connected brain regions based on a neurodynamic model constrained by empirically derived structural connectivity matrix from diffusion data. For relevance, we have taken into consideration time-delays in neural communication stemming from fibre distances and neuronal coupling arising from fibre densities. Based on relevant network parameters, we could demonstrate the emergence of right hemispheric dominance of ASSR in binaural and monaural hearing conditions when auditory cortical areas were chosen as triggers of entrained phase oscillators. Furthermore, we discovered emergence of left-lateralized functional response when bilateral Brocas area replaced auditory areas as triggers. Hence, a single unified mechanism based on entrainment of phase oscillators in a large-scale brain network could explain both emergence of right and left hemispheric laterality.

Significance statementThe origin of hemispheric specialization of sensory processing is a fundamental question in neuroscience. For instance, speech and language are predominantly processed in the left hemispheric regions, while the right hemisphere is specialized for processing rhythmic, tonal, and melodic stimuli. Identification of the network mechanisms that give rise to such functional lateralization from structural constraints remains elusive. In the present study, we simulate neural activity observed during human EEG recordings of auditory steady-state responses from a biophysically realistic large-scale model constrained by underlying structural connectivity. Subsequently, we demonstrate how hemispheric lateralization of brain responses to sensory stimuli emerge from the time-delayed interactions among whole-brain neuronal ensembles.

category: neuroscience


title: Mitochondrial phenotypes in purified human immune cell subtypes and cell mixtures

abstract: Using a high-throughput mitochondrial phenotyping platform to quantify multiple mitochondrial features among molecularly-defined immune cell subtypes, we quantify the natural variation in citrate synthase, mitochondrial DNA copy number (mtDNAcn), and respiratory chain enzymatic activities in human neutrophils, monocytes, B cells, and naive and memory T lymphocyte subtypes. In mixed peripheral blood mononuclear cells (PBMCs) from the same individuals, we show to what extent mitochondrial measures are confounded by both cell type distributions and contaminating platelets. Cell subtype-specific measures among women and men spanning 4 decades of life indicate potential age- and sex-related differences, including an age-related elevation in mtDNAcn, which are masked or blunted in mixed PBMCs. Finally, a proof-of-concept, repeated-measures study in a single individual validates cell type differences and also reveals week-to-week changes in mitochondrial activities. Larger studies are required to validate and mechanistically extend these findings. These mitochondrial phenotyping data build upon established immunometabolic differences among leukocyte sub-populations, and provide foundational quantitative knowledge to develop interpretable blood-based assays of mitochondrial health.

category: cell biology


title: Knockout of zebrafish desmin genes does not cause skeletal muscle degeneration but alters calcium flux

abstract: Desmin is a muscle-specific intermediate filament protein that has fundamental role in muscle structure and force transmission. Whereas human desmin protein is encoded by a single gene, two desmin paralogs (desma and desmb) exist in zebrafish. Desma and desmb show differential spatiotemporal expression during zebrafish embryonic and larval development, being similarly expressed in skeletal muscle until hatching, after which expression of desmb shifts to gut smooth muscle. We generated knockout (KO) mutant lines carrying loss-of-function mutations for each gene by using CRISPR/Cas9. Mutants are viable and fertile, and lack obvious skeletal muscle, heart or intestinal defects. In contrast to morphants, knockout of each gene did not cause any overt muscular phenotype, but did alter calcium flux in myofibres. These results point to a possible compensation mechanism in these mutant lines generated by targeting nonsense mutations to the first coding exon.

category: developmental biology


title: Predicting Brain Amyloid using Multivariate Morphometry Statistics, Sparse Coding, and Correntropy: Validation in 1,101 Individuals from the ADNI and OASIS Databases

abstract: Biomarker-assisted preclinical/early detection and intervention in Alzheimers disease (AD) may be the key to therapeutic breakthroughs. One of the presymptomatic hallmarks of AD is the accumulation of beta-amyloid (A{beta}) plaques in the human brain. However, current methods to detect A{beta} pathology are either invasive (lumbar puncture) or quite costly and not widely available (amyloid PET). Our prior studies show that MRI-based hippocampal multivariate morphometry statistics (MMS) are an effective neurodegenerative biomarker for preclinical AD. Here we attempt to use MRI-MMS to make inferences regarding brain A{beta} burden at the individual subject level. As MMS data has a larger dimension than the sample size, we propose a sparse coding algorithm, Patch Analysis-based Surface Correntropy-induced Sparse coding and max-pooling (PASCS-MP), to generate a low-dimensional representation of hippocampal morphometry for each subject. Then we apply these individual representations and a binary random forest classifier to predict brain A{beta} positivity for each person. We test our method in two independent cohorts, 841 subjects from the Alzheimers Disease Neuroimaging Initiative (ADNI) and 260 subjects from the Open Access Series of Imaging Studies (OASIS). Experimental results suggest that our proposed PASCS-MP method and MMS can discriminate A{beta} positivity in people with mild cognitive impairment (MCI) (Accuracy (ACC)=0.89 (ADNI)) and in cognitively unimpaired (CU) individuals (ACC=0.79 (ADNI) and ACC=0.81 (OASIS)). These results compare favorably relative to measures derived from traditional algorithms, including hippocampal volume and surface area, shape measures based on spherical harmonics (SPHARM), and our prior Patch Analysis-based Surface Sparse-coding and Max-Pooling (PASS-MP) methods.


title: Multiple neuronal networks coordinate Hydra mechanosensory behavior

abstract: Hydra vulgaris is an emerging model organism for neuroscience due to its small size, transparency, genetic tractability, and regenerative nervous system; however, fundamental properties of its sensorimotor behaviors remain unknown. Here, we use microfluidic devices combined with fluorescent calcium imaging and surgical resectioning to study how the diffuse nervous system coordinates Hydras mechanosensory response. Mechanical stimuli cause animals to contract, and we find this response relies on at least two distinct networks of neurons in the oral and aboral regions of the animal. Different activity patterns arise in these networks depending on whether the animal is contracting spontaneously or contracting in response to mechanical stimulation. Together, these findings improve our understanding of how Hydras diffuse nervous system coordinates sensorimotor behaviors. These insights help reveal how sensory information is processed in an animal with a diffuse, radially symmetric neural architecture unlike the dense, bilaterally symmetric nervous systems found in most model organisms.


title: Psychological Well-being, Age and Gender can Mediate Soundscapes Pleasantness and Eventfulness: A large sample study

abstract: Soundscape studies aim to consider the holistic human perception of a sound environment, including both the physical phenomena and how these are mediated by internal factors: the mechanisms underpinning the interactions between these two aspects are not well understood. This study aims to assess the influence of psychological well-being and demographic factors including age, gender, occupation status, and education levels on the dimensions of the soundscape circumplex, i.e., Pleasantness and Eventfulness. Data was collected in eleven urban locations in London through a large-scale (N=1134) soundscape survey according to the ISO 12913-2 technical specifications and incorporating the WHO-5 well-being index. Linear mixed-effects modelling applying backwards-step feature selection was used to model the interactions between internal factors including psychological well-being, age, gender, occupation status, education levels and the soundscape Pleasantness and Eventfulness, while accounting for the random effects of the survey location. The findings suggest that internal factors account for approximately 1.4% of the variance for Pleasantness and 3.9% for Eventfulness, while the influence of the locations accounted for approximately 34% and 14%, respectively. Psychological well-being is positively associated with perceived Pleasantness, while there is a negative association with Eventfulness only for males. Occupation status, in particular retirement as a proxy of age and gender, was identified as a significant factor for both dimensions. These findings offer empirical grounds for developing theories of the interaction between internal factors and soundscape formation whilst highlighting the importance of the location, namely: the context.


title: Non-phylogenetic identification of co-evolving genes for reconstructing the archaeal Tree of Life

abstract: Assessing the phylogenetic compatibility between individual gene families is a crucial and often computationally demanding step in many phylogenomics analyses. Here we describe the Evolutionary Similarity Index (IES) to assess shared evolution between gene families using a weighted Orthogonal Distance Regression applied to sequence distances. This approach allows for straightforward pairing of paralogs between co-evolving gene families without resorting to multiple tests, or a priori assumptions of molecular interactions between protein products from assessed genes. The utilization of pairwise distance matrices, while less informative than phylogenetic trees, circumvents error-prone comparisons between trees whose topologies are inherently uncertain. Analyses of simulated gene family evolution datasets showed that IES was more accurate and less susceptible to noise than popular tree-based methods (Robinson-Foulds and geodesic distance) for assessing evolutionary signal compatibility, since it bypasses phylogenetic reconstruction and its inherent uncertainty. Applying IES to a real dataset of 1,322 genes from 42 archaeal genomes identified eight major clusters of gene families with compatible evolutionary trends. Four of these clusters included genes with a taxonomic distribution across all archaeal phyla, while other clusters included a subset of taxa that do not map to generally accepted archaeal clades, indicating possible shared horizontal transfers by clustered gene families. We identify one strongly connected set of 62 genes from the same cluster, occurring as both single-copy and multiple homologs per genome, with compatible phylogenetic reconstructions closely matching previously published species trees for Archaea. An IES implementation is available at https://github.com/lthiberiol/evolSimIndex.

category: evolutionary biology


title: The Orbitofrontal Cortex in Temporal Cognition

abstract: One of the most important factors in decision making is estimating the value of available options. Subregions of the prefrontal cortex, including the orbitofrontal cortex (OFC), have been deemed essential for this process. Value computations require a complex integration across numerous dimensions, including, reward magnitude, effort, internal state, and time. The importance of the temporal dimension is well-illustrated by temporal discounting tasks, in which subjects select between smaller-sooner versus larger-later rewards. The specific role of OFC in telling time and integrating temporal information into decision making remains unclear. Based on the current literature, in this review we reevaluate current theories of OFC function, accounting for the influence of time. Incorporating temporal information into value estimation and decision making requires distinct, yet interrelated, forms of temporal information including the ability to tell time, represent time, create temporal expectations, and the ability to use this information for optimal decision making in a wide range of tasks, including temporal discounting and wagering. We use the term  temporal cognition to refer to the integrated use of these different aspects of temporal information. We suggest that the OFC may be a critical site for the integration of reward magnitude and delay, and thus important for temporal cognition.


title: Validation and comparison of three freely available methods for extracting white matter hyperintensities: FreeSurfer, UBO Detector and BIANCA

abstract:
White matter hyperintensities (WMH) of presumed vascular origin are frequently found in MRIs of healthy older adults. WMH are also associated with aging and cognitive decline. Here, we compared and validated three freely available algorithms for WMH extraction: FreeSurfer, UBO Detector, and BIANCA (Brain Intensity AbNormality Classification Algorithm) using a longitudinal dataset comprising MRI data of cognitively healthy older adults (baseline N = 231, age range 64-87 years). As reference we manually segmented WMH in T1w, 3D FLAIR, 2D FLAIR images. These manual segmentations were then used to assess the segmentation accuracy of the different automated algorithms. Further, we assessed the relationships of WMH volume estimates provided by the algorithms with Fazekas scores and age. FreeSurfer underestimated the WMH volumes and scored worst in Dice Similarity Coefficient (DSC = 0.434) but its WMH volumes strongly correlated with the Fazekas scores (rs = 0.73). BIANCA accomplished the highest DCS (0.602) with 3D FLAIR images. However, the relations with the Fazekas scores were only moderate, especially in the 2D FLAIR images (rs = 0.41), and many outlier WMH volumes were detected when exploring within-person trajectories (2D FLAIR: ~30%). UBO Detector performed similarly to BIANCA in DSC with both modalities and reached the best DSC in 2D FLAIR (0.531) without requiring a tailored training dataset. In addition, it achieved very high associations with the Fazekas scores (2D FLAIR: rs = 0.80).

In summary, our results emphasize the importance of carefully contemplating the choice of the WMH segmentation algorithm and MR-modality.


title: Performance of three freely available methods for extracting white matter hyperintensities: FreeSurfer, UBO Detector and BIANCA


title: Phosphate dysregulation via the XPR1:KIDINS220 protein complex is a therapeutic vulnerability in ovarian cancer

abstract: Clinical outcomes for patients with ovarian and uterine cancers have not improved greatly in the past twenty years. To identify ovarian and uterine cancer vulnerabilities, we analyzed genome-scale CRISPR/ Cas9 loss-of-function screens across 739 human cancer cell lines. We found that many ovarian cancer cell lines overexpress the phosphate importer SLC34A2, which renders them sensitive to loss of the phosphate exporter XPR1. We extensively validated the XPR1 vulnerability in cancer cell lines and found that the XPR1 dependency was retained in vivo. Overexpression of SLC34A2 is frequently observed in tumor samples and is regulated by PAX8 -a transcription factor required for ovarian cancer survival. XPR1 overexpression and copy number amplifications are also frequently observed. Mechanistically, SLC34A2 overexpression and impaired phosphate efflux leads to the accumulation of intracellular phosphate and cell death. We further show that proper localization and phosphate efflux by XPR1 requires a novel binding partner, KIDINS220. Loss of either XPR1 or KIDINS220 results in acidic vacuolar structures which precede cell death. These data point to the XPR1:KIDINS220 complex - and phosphate dysregulation more broadly -as a therapeutic vulnerability in ovarian cancer.

category: cancer biology


title: Multiple time-scales of decision making in the hippocampus and prefrontal cortex

abstract: The prefrontal cortex and hippocampus are crucial for memory-guided decision-making. Neural activity in the hippocampus exhibits place-cell sequences at multiple timescales, including slow behavioral sequences ([~]seconds) and fast theta sequences ([~]100-200 ms) within theta oscillation cycles. How prefrontal ensembles interact with hippocampal sequences to support decision-making is unclear. Here, we examined simultaneous hippocampal and prefrontal ensemble activity during learning of a spatial working-memory decision task. We found clear theta sequences in prefrontal cortex, nested within its behavioral sequences. In both regions, behavioral sequences maintained representations of current goals during navigation. In contrast, hippocampal theta sequences encoded alternatives for deliberation, and were coordinated with prefrontal theta sequences that predicted upcoming choices. During error trials, these representations were preserved to guide ongoing behavior, whereas replay sequences during inter-trial periods were impaired prior to navigation. These results establish cooperative interaction between hippocampal and prefrontal sequences at multiple timescales for memory-guided decision making.


title: Global distribution patterns of marine nitrogen-fixers by imaging and molecular methods

abstract: Biological nitrogen fixation plays a critical role in marine primary production, yet, our understanding of marine N2-fixers (diazotrophs) is hindered by limited observations. Here, we developed a quantitative image analysis pipeline in concert with mapping of molecular markers for mining >2,000,000 images and >1,300 metagenomes in surface, deep chlorophyll maximum and mesopelagic samples across 6 size fractions (<0.2-2000 m). Imaging and PCR-free molecular data were remarkably congruent. Sequences from diazotrophs were detected from the ultrasmall bacterioplankton (<0.2 m) to mesoplankton (180-2000 m), while images predicted symbiotic and colonial-forming diazotrophs (>20 {micro}m). Imaging and molecular data estimated that polyploidy can significantly impact gene abundances of symbiotic vs colonial-forming diazotrophs. In general our results support the canonical view that larger sized diazotrophs (>10 m) dominate the tropical belts, while sequences from unicellular cyanobacterial and non-cyanobacterial diazotrophs were globally distributed in surface and the mesopelagic. Co-occurring diazotrophic lineages of different lifestyles were frequently encountered, and several new high density regions of diazotrophs were identified in the global ocean. Overall, this work provides an update of marine diazotroph biogeographical diversity and contributes a new bio-imaging-informatic workflow.

category: microbiology


title: Relative time constraints improve molecular dating

abstract:
Dating the tree of life is central to understanding the evolution of life on Earth. Molecular clocks calibrated with fossils represent the state of the art for inferring the ages of major groups. Yet, other information on the timing of species diversification can be used to date the tree of life. For example, horizontal gene transfer events and ancient coevolutionary relationships such as (endo)symbioses can imply temporal relationships between two nodes in a phylogeny (Davin et al. 2018). These alternative sources of temporal constraints can be particularly helpful when the geological record is sparse, e.g. for microorganisms, which represent the vast majority of extant and extinct biodiversity.

Here, we present a new method to combine fossil calibrations and relative age constraints to estimate chronograms. We provide an implementation of relative age constraints in RevBayes (Hohna et al. 2016) that can be combined in a modular manner with the wide range of molecular dating methods available in the software.

We use both realistic simulations and empirical datasets of 40 Cyanobacteria and 62 Archaea to evaluate our method. We show that the combination of relative age constraints with fossil calibrations significantly improves the estimation of node ages.


title: The Design Principles of Discrete Turing Patterning Systems

abstract: The formation of spatial structures lies at the heart of developmental processes. However, many of the underlying gene regulatory and biochemical processes remain poorly understood. Turing patterns constitute a main candidate to explain such processes, but they appear sensitive to fluctuations and variations in kinetic parameters, raising the question of how they may be adopted and realised in naturally evolved systems. The vast majority of mathematical studies of Turing patterns have used continuous models specified in terms of partial differential equations. Here, we complement this work by studying Turing patterns using discrete cellular automata models. We perform a large-scale study on all possible two-species networks and find the same Turing pattern producing networks as in the continuous framework. In contrast to continuous models, however, we find these Turing pattern topologies to be substantially more robust to changes in the parameters of the model. We also find that diffusion-driven instabilities are substantially weaker predictors for Turing patterns in the discrete modelling framework in comparison to the continuous case, and show that a more refined criterion constitutes a stronger predictor. The similarity of the results for the two modelling frameworks suggests a deeper underlying principle of Turing mechanisms in nature. Together with the larger robustness in the discrete case this suggests that Turing patterns may be more robust than previously thought.

category: systems biology


title: Adult Stem Cell-derived Complete Lung Organoid Models Emulate Lung Disease in COVID-19

abstract:
SARS-CoV-2, the virus responsible for COVID-19, causes widespread damage in the lungs in the setting of an overzealous immune response whose origin remains unclear. We present a scalable, propagable, personalized, cost-effective adult stem cell-derived human lung organoid model that is complete with both proximal and distal airway epithelia. Monolayers derived from adult lung organoids (ALOs), primary airway cells, or hiPSC-derived alveolar type-II (AT2) pneumocytes were infected with SARS-CoV-2 to create in vitro lung models of COVID-19. Infected ALO-monolayers best recapitulated the transcriptomic signatures in diverse cohorts of COVID-19 patient-derived respiratory samples. The airway (proximal) cells were critical for sustained viral infection, whereas distal alveolar differentiation (AT2[->]AT1) was critical for mounting the overzealous host immune response in fatal disease; ALO monolayers with well-mixed proximodistal airway components recapitulated both. Findings validate a human lung model of COVID-19, which can be immediately utilized to investigate COVID-19 pathogenesis and vet new therapies and vaccines.

GRAPHIC ABSTRACT

O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=176 SRC="FIGDIR/small/344002v4_ufig1.gif" ALT="Figure 1">
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org.highwire.dtl.DTLVardef@1d1507aorg.highwire.dtl.DTLVardef@faa17forg.highwire.dtl.DTLVardef@80ceb1org.highwire.dtl.DTLVardef@81d61c_HPS_FORMAT_FIGEXP  M_FIG C_FIG HIGHLIGHTSO_LIHuman lung organoids with mixed proximodistal epithelia are created
C_LIO_LIProximal airway cells are critical for viral infectivity
C_LIO_LIDistal alveolar cells are important for emulating host response
C_LIO_LIBoth are required for the overzealous response in severe COVID-19
C_LI

IN BRIEFAn integrated stem cell-based disease modeling and computational approach demonstrate how both proximal airway epithelium is critical for SARS-CoV-2 infectivity, but distal differentiation of alveolar pneumocytes is critical for simulating the overzealous host response in fatal COVID-19.


title: CRISPR screening identifies novel PARP inhibitor classification based on distinct base excision repair pathway dependencies

abstract:
DNA repair deficiencies have become an increasingly promising target for novel therapeutics within the realm of clinical oncology. Recently, several inhibitors of Poly(ADP-ribose) Polymerases (PARPs) have received approval for the treatment of cancers primarily with deleterious mutations in the homologous recombination (HR) proteins, BRCA1 and BRCA2. Despite numerous clinical trials which have been completed or are currently ongoing, the mechanism of action by which PARP inhibitors selectively kill tumor cells is poorly understood. While many believe "trapping" of PARP proteins to DNA at sites of damage is the most important determinant driving cytotoxicity by these drugs, clinically effective inhibitors exist with a diverse range of PARP-trapping qualities. These findings suggest that characterization of inhibitors as strong versus weak trappers does not properly capture the intra-class characteristics of these drugs. Here, we use a novel, targeted DNA damage response (DDR) CRISPR/Cas9 screening library to reveal heterogenous genetic dependencies on the base excision repair (BER) pathway for PARP inhibitors, which is not correlated with PARP trapping ability or catalytic inhibition of PARP. These findings demonstrate that inhibition of PARylation and induction of PARP trapping are not the only factors contributing to distinct biological activity for different PARP inhibitors, and they provide insight into the optimal choice of PARP inhibitors for use in the setting of specific DDR defects.

AUTHOR SUMMARYTargeted cancer therapies rely on our general understanding of which genetic mutations are involved in both sensitivity and resistance to such anticancer agents. In this study, we describe the use of functional genetic screening to evaluate the role of various DNA repair proteins in response to inhibitors of PARP, a quintessential example of targeted therapy. While PARP inhibitors are best known for their utility in cancers with homologous recombination defects, we show that some inhibitors within this class may have additional functionality in cancers with deficient base excision repair. These findings highlight not only the importance of PARP inhibitor selection in the appropriate context, but also the mechanistic differences that exist within this class of inhibitors. It is our hope that our findings will inspire future work evaluating the use of specific PARP inhibitor selection in designing clinical trials to further expand the use of PARP inhibitors beyond tumors with homologous recombination deficiencies.


title: Respiratory tract explant infection dynamics of influenza A virus in California sea lions, northern elephant seals, and rhesus macaques

abstract:
To understand susceptibility of wild California sea lions and Northern elephant seals to influenza A virus (IAV), we developed an ex vivo respiratory explant model and used it to compare infection kinetics for multiple IAV subtypes. We first established the approach using explants from colonized rhesus macaques, a model for human IAV. Trachea, bronchi, and lungs from 11 California sea lions, 2 Northern elephant seals and 10 rhesus macaques were inoculated within 24 hours post-mortem with 6 strains representing 4 IAV subtypes. Explants from the 3 species showed similar IAV infection kinetics with peak viral titers 48-72 hours post-inoculation that increased by 2-4 log10 plaque forming units (PFU)/explant relative to the inoculum. Immunohistochemistry localized IAV infection to apical epithelial cells. These results demonstrate that respiratory tissue explants from wild marine mammals support IAV infection. In the absence of the ability to perform experimental infections of marine mammals, this ex vivo culture of respiratory tissues mirrors the in vivo environment and serves as a tool to study IAV susceptibility, host-range, and tissue tropism.

ImportanceAlthough influenza A virus can infect marine mammals, a dearth of marine mammal cell lines and ethical and logistical challenges prohibiting experimental infections of living marine mammals means that little is known about IAV infection kinetics in these species. We circumvented these limitations by adapting a respiratory tract explant model first to establish the approach with rhesus macaques and then for use with explants from wild marine mammals euthanized for non-respiratory medical conditions. We observed that multiple strains representing 4 IAV subtypes infected trachea, bronchi, and lungs of macaques and marine mammals with variable peak titers and kinetics. This ex vivo model can define infection dynamics for IAV in marine mammals. Further, use of explants from animals euthanized for other reasons reduces use of animals in research.


title: Differential effects of prediction error and adaptation along the auditory cortical hierarchy during deviance processing

abstract: Neural mismatch responses have been proposed to rely on different mechanisms, including prediction error-related activity and adaptation to frequent stimuli. However, the cortical hierarchical structure of these mechanisms is unknown. To investigate this question, we used functional magnetic resonance imaging (fMRI) and an auditory oddball design with a suited control condition that enabled us to delineate the contributions of prediction error- or adaptation-related brain activation during deviance processing. We found that while prediction-error related processes increased with the hierarchical position of the brain area, adaptation declined. This suggests that the relative contribution of different mechanisms in deviance processing varies across the cortical hierarchy.


title: Individual-based simulations of genome evolution with ancestry: the GENOMEADMIXR R package

abstract:
O_LIHybridization between populations or species results in a mosaic of the two parental genomes. This and other types of genome admixture have received increasing attention for their implications in speciation, human evolution, Evolve and Resequence (E&R) and genetic mapping. However, a thorough understanding of how local ancestry changes after admixture, and how selection affects patterns of local ancestry remains elusive. The complexity of these questions limits analytical treatment, but these scenarios are specifically suitable for simulation.
C_LIO_LIHere, we present the R package GO_SCPLOWENOMEC_SCPLOWAO_SCPLOWDMIXC_SCPLOWR, which uses an individual-based model to simulate genomic patterns following admixture forward in time. GO_SCPLOWENOMEC_SCPLOWAO_SCPLOWDMIXC_SCPLOWR provides user-friendly functions to set up and analyze simulations under evolutionary scenarios with selection, linkage and migration.
C_LIO_LIWe show the flexible functionality of the GO_SCPLOWENOMEC_SCPLOWAO_SCPLOWDMIXC_SCPLOWR workflow by demonstrating 1) how to design an E&R simulation using GO_SCPLOWENOMEC_SCPLOWAO_SCPLOWDMIXC_SCPLOWR and 2) how to use GO_SCPLOWENOMEC_SCPLOWAO_SCPLOWDMIXC_SCPLOWR to verify analytical expectations following from the theory of junctions.
C_LIO_LIGO_SCPLOWENOMEC_SCPLOWAO_SCPLOWDMIXC_SCPLOWR provides a mechanistic approach to explore expected genome responses to realistic admixture scenarios. With this package, we aim to aid researchers in testing specific hypotheses based on empirical findings involving admixing populations.
C_LI

category: bioinformatics


title: A laboratory module that explores RNA interference and codon optimization through fluorescence microscopy using Caenorhabditis elegans

abstract: Scientific research experiences are beneficial to students allowing them to gain laboratory and problem-solving skills, as well as foundational research skills in a team-based setting. We designed a laboratory module to provide a guided research experience to stimulate curiosity, introduce students to experimental techniques, and provide students with foundational skills needed for higher levels of guided inquiry. In this laboratory module, students learn about RNA interference (RNAi) and codon optimization using the research organism Caenorhabditis elegans (C. elegans). Students are given the opportunity to perform a commonly used method of gene downregulation in C. elegans where they visualize gene depletion using fluorescence microscopy and quantify the efficacy of depletion using quantitative image analysis. The module presented here educates students on how to report their results and findings by generating publication quality figures and figure legends. The activities outlined exemplify ways by which students can improve their critical thinking, data interpretation, and technical skills, all of which are beneficial for future laboratory classes, independent inquiry-based research projects, and careers in the life sciences and beyond.

category: scientific communication and education


title: 3D analysis of the synaptic organization in the Entorhinal cortex in Alzheimer's disease

abstract:
The entorhinal cortex (EC) is especially vulnerable in the early stages of Alzheimers disease (AD). In particular, cognitive deficits have been linked to alterations in the upper layers of EC. In the present report, we examined layers II and III from eight human brain autopsies (four subjects with no recorded neurological alterations and four AD cases). We used stereological methods to assess cortical atrophy of the EC, and possible changes in the volume occupied by different cortical elements (neuronal and glial cell bodies; blood vessels; and neuropil). We performed 3D ultrastructural analyses of synapses using Focused Ion Beam/Scanning Electron Microscopy (FIB/SEM) to examine possible alterations related to AD.

At the light microscope level, we found a significantly lower volume fraction occupied by neuronal bodies in layer III and a higher volume fraction occupied by glial cell bodies in layer II in AD cases. At the ultrastructural level we observed that (i) there was a significantly lower synaptic density in both layers in AD cases; (ii) synapses were larger and more complex in layer II in AD cases; and (iii) there was a greater proportion of small and simple synapses in layer III in AD cases than in control individuals. These structural differences may play a role in the anatomical basis for the impairment of cognitive functions in AD.

Significant StatementAnalysis of the synaptic characteristics provides critical data on synaptic organization. Using 3D electron microscopy, the present study shows the synaptic organization of the neuropil of the human entorhinal cortex (EC) at the ultrastructural level. The EC is especially vulnerable in the early stages of Alzheimers disease (AD). Our present results show structural differences that may contribute as anatomical basis for the impairment of cognitive functions in AD. Thus, these results may help to understand the relationship between alterations of the synaptic circuits and the cognitive deterioration in AD.


title: DROL1 subunit of U5 snRNP in the spliceosome is specifically required to splice AT--AC-type introns in Arabidopsis

abstract:
An Arabidopsis mutant named defective repression of OLE3::LUC 1 (drol1) was originally isolated as a mutant with defects in the repression of OLEOSIN3 (OLE3) after seed germination. In this study, we show that DROL1 is an Arabidopsis homolog of yeast DIB1, a subunit of U5 snRNP in the spliceosome. It is also part of a new subfamily that is specific to a certain class of eukaryotes. Comprehensive analysis of the intron splicing using RNA-Seq analysis of the drol1 mutants revealed that most of the minor introns with AT-AC dinucleotide termini had reduced levels of splicing. Only two nucleotide substitutions from AT-AC to GT-AG enabled AT-AC-type introns to be spliced in drol1 mutants. Forty-eight genes, including those having important roles in abiotic stress responses and cell proliferation, exhibited reduced splicing of AT-AC-type introns in the drol1 mutants. Additionally, drol1 mutant seedlings showed retarded growth, similar to that caused by the activation of abscisic acid signaling, possibly as a result of reduced AT-AC-type intron splicing in the endosomal Na+/H+ antiporters and plant-specific histone deacetylases. These results indicate that DROL1 is specifically involved in the splicing of minor introns with AT-AC termini, and that this plays an important role in plant growth and development.

Significance statementDefective Repression of OLE3::LUC 1 (DROL1) is a homolog of yeast DIB1, which is a subunit of the U5 snRNP in the spliceosome, but is also part of a new subfamily that is specific to a certain class of eukaryotes. Using RNA-Seq we show that introns with AT-AC dinucleotide termini were specifically retained in the transcriptome of drol1 mutants and that their splicing plays an important role in plant growth and development.

category: molecular biology


title: Consensus clustering applied to multi-omic disease subtyping

abstract:
BackgroundFacing the diversity of omic data and the difficulty of selecting one result over all those produced by several methods, consensus strategies have the potential to reconcile multiple inputs and to produce robust results.

ResultsHere, we introduce ClustOmics, a generic consensus clustering tool that we use in the context of cancer subtyping. ClustOmics relies on a non-relational graph database, which allows for the simultaneous integration of both multiple omic data and results from various clustering methods. This new tool conciliates input clusterings, regardless of their origin, their number, their size or their shape. ClustOmics implements an intuitive and flexible strategy, based upon the idea of evidence accumulation clustering. It computes co-occurrences of pairs of samples in input clusters and uses this score as a similarity measure to reorganise data into consensus clusters.

ConclusionWe applied ClustOmics to multi-omic disease subtyping on real TCGA cancer data from ten different cancer types. We showed that ClustOmics is robust to heterogeneous qualities of input partitions, smoothing and reconciling preliminary predictions into high quality consensus clusters, both from a computational and a biological point of view. The comparison to a state-of-the-art consensus based integration tool, COCA, further corroborated this statement. However, the main interest of ClustOmics is not to compete with other tools, but rather to make profit from their various predictions when no gold-standard metric is available to assess their significance.

AvailabilityClustOmics source code, released under MIT licence, as well as the results obtained on TCGA cancer data are available on Github: https://github.com/galadrielbriere/ClustOmics.


title: Child abuse associates with increased recruitment of perineuronal nets in the ventromedial prefrontal cortex: a possible implication of oligodendrocyte progenitor cells

abstract: Child abuse (CA) is a strong predictor of psychopathologies and suicide, altering normal trajectories of brain development in areas closely linked to emotional responses such as the prefrontal cortex (PFC). Yet, the cellular underpinnings of these enduring effects are unclear. Childhood and adolescence are marked by the protracted formation of perineuronal nets (PNNs), which orchestrate the closure of developmental windows of cortical plasticity by regulating the functional integration of parvalbumin interneurons (PV) into neuronal circuits. Using well-characterized post-mortem brain samples, we show that a history of CA is specifically associated with increased densities and morphological complexity of WFL-labeled PNNs in the ventromedial PFC (BA11/12), possibly suggesting increased recruitment and maturation of PNNs. Through single-nucleus sequencing and fluorescent in-situ hybridization, we found that the expression of canonical components of PNNs is enriched in oligodendrocyte progenitor cells (OPCs), and that they are upregulated in CA victims. These correlational findings suggest that early-life adversity may lead to persistent patterns of maladaptive behaviors by reducing the neuroplasticity of cortical circuits through the enhancement of developmental OPC-mediated PNN formation.


title: Multimodal Analysis for Human ex vivo Studies Shows Extensive Molecular Changes from Delays in Blood Processing

abstract: Multi-omic profiling of human peripheral blood is increasingly utilized to identify biomarkers and pathophysiologic mechanisms of disease. The importance of these platforms in clinical and translational studies led us to investigate the impact of delayed blood processing on the numbers and state of peripheral blood mononuclear cells (PBMC) and on the plasma proteome. Similar to previous studies, we show minimal effects of delayed processing on the numbers and general phenotype of PBMCs up to 18 hours. In contrast, profound changes in the single-cell transcriptome and composition of the plasma proteome become evident as early as 6 hours after blood draw. These reflect patterns of cellular activation across diverse cell types that lead to progressive distancing of the gene expression state and plasma proteome from native in vivo biology. Differences accumulating during an overnight rest (18 hours) could confound relevant biologic variance related to many underlying disease states.

category: immunology


title: Allele-specific collateral and fitness effects determine the dynamics of fluoroquinolone-resistance evolution

abstract:
Collateral sensitivity (CS), which arises when resistance to one antibiotic increases sensitivity towards other antibiotics, offers novel treatment opportunities to constrain or reverse the evolution of antibiotic-resistance. The applicability of CS-informed treatments remains uncertain, in part because we lack an understanding of the generality of CS effects for different resistance mutations, singly or in combination. Here we address this issue in the Gram-positive pathogen Streptococcus pneumoniae by measuring collateral and fitness effects of clinically relevant gyrA and parC alleles, and their combinations, that confer resistance to fluoroquinolones. We integrated these results in a mathematical model which allowed us to evaluate how different in silico combination treatments impact the dynamics of resistance evolution. We identified common and conserved CS effects of different gyrA and parC alleles; however, the spectrum of collateral effects was unique for each allele or allelic pair. This indicated that allelic identity can impact the evolutionary dynamics of resistance evolution during monotreatment and combination treatment. Our model simulations, which included the experimentally derived antibiotic susceptibilities and fitness effects, and antibiotic specific pharmacodynamics, revealed that both collateral and fitness effects impact the population dynamics of resistance evolution. Overall, we provide evidence that allelic identity and interactions can have a pronounced impact on collateral effects to different antibiotics and suggest that these need to be considered in models examining CS-based therapies.

SignificanceA promising strategy to overcome the evolution of antibiotic resistant bacteria is to use collateral sensitivity-informed antibiotic treatments that rely on cycling or mixing of antibiotics, such that that resistance towards one antibiotic confers increased sensitivity to the other. Here, focusing on multi-step fluoroquinolone resistance in Streptococcus pneumoniae, we show that antibiotic-resistance induces diverse collateral responses whose magnitude and direction are determined by allelic identity. Using mathematical simulations, we show that these effects can be exploited via combination treatment regimens to suppress the de novo emergence of resistance during treatment.


title: Septate junction proteins are required for egg elongation and border cell migration during oogenesis in Drosophila

abstract:
Protein components of the invertebrate occluding junction - known as the septate junction (SJ) - are required for morphogenetic developmental events during embryogenesis in Drosophila melanogaster. In order to determine whether SJ proteins are similarly required for morphogenesis during other developmental stages, we investigated the localization and requirement of four representative SJ proteins during oogenesis: Contactin, Macroglobulin complement-related, Neurexin IV, and Coracle. A number of morphogenetic processes occur during oogenesis, including egg elongation, formation of dorsal appendages, and border cell migration. We found that all four SJ proteins are expressed in egg chambers throughout oogenesis, with the highest and most sustained levels in the follicular epithelium (FE). In the FE, SJ proteins localize along the lateral membrane during early and mid-oogenesis, but become enriched in an apical-lateral domain (the presumptive SJ) by stage 10b. SJ protein relocalization requires the expression of other SJ proteins, as well as rab5 and rab11 in a manner similar to SJ biogenesis in the embryo. Knocking down the expression of these SJ proteins in follicle cells throughout oogenesis results in egg elongation defects and abnormal dorsal appendages. Similarly, reducing the expression of SJ genes in the border cell cluster results in border cell migration defects. Together, these results demonstrate an essential requirement for SJ genes in morphogenesis during oogenesis, and suggests that SJ proteins may have conserved functions in epithelial morphogenesis across developmental stages.

Article SummarySeptate junction (SJ) proteins are essential for forming an occluding junction in epithelial tissues of Drosophila melanogaster, and also for morphogenetic events that occur prior to the formation of the junction during embryogenesis. Here we show that SJ proteins are expressed in the follicular epithelium of egg chambers during oogenesis and are required for morphogenetic events including egg elongation, dorsal appendages formation, and border cell migration. Additionally, the formation of SJs during oogenesis is similar to that in embryonic epithelia.


title: Activation by Cleavage of the Epithelial Na+ Channel α and γ Subunits Independently Coevolved with the Vertebrate Terrestrial Migration

abstract: Vertebrates evolved mechanisms for sodium conservation and gas exchange in conjunction with migration from aquatic to terrestrial habitats. Epithelial Na+ channel (ENaC) function is critical to systems responsible for extracellular fluid homeostasis and gas exchange. ENaC is activated by cleavage at multiple specific extracellular polybasic sites, releasing inhibitory tracts from the channels  and {gamma} subunits. We found that proximal and distal polybasic tracts in ENaC subunits coevolved, consistent with the dual cleavage requirement for activation observed in mammals. Polybasic tract pairs evolved with the terrestrial migration and the appearance of lungs, coincident with the ENaC activator aldosterone, and appeared independently in the  and {gamma} subunits. In summary, sites within ENaC for protease activation developed in vertebrates when renal Na+ conservation and alveolar gas exchange was required for terrestrial survival.


title: Evaluation of CRISPR gene-editing tools in zebrafish

abstract:
BackgroundZebrafish have practical features that make them a useful model for higher-throughput tests of gene function using CRISPR/Cas9 editing to create  knockout models. In particular, the use of G0 mosaic mutants has potential to increase throughput of functional studies significantly but may suffer from transient effects of introducing Cas9 via microinjection. Further, a large number of computational and empirical tools exist to design CRISPR assays but often produce varied predictions across methods leaving uncertainty in choosing an optimal approach for zebrafish studies.

MethodsTo systematically assess accuracy of tool predictions of on- and off-target gene editing, we subjected zebrafish embryos to CRISPR/Cas9 with 50 different guide RNAs (gRNAs) targeting 14 genes. We also investigate potential confounders of G0-based CRISPR screens by screening control embryos for spurious mutations and altered gene expression.

ResultsWe compared our experimental in vivo editing efficiencies in mosaic G0 embryos with those predicted by eight commonly used gRNA design tools and found large discrepancies between methods. Assessing off-target mutations (predicted in silico and in vitro) found that the majority of tested loci had low in vivo frequencies (<1%). To characterize if commonly used  mock CRISPR controls (larvae injected with Cas9 enzyme or mRNA with no gRNA) exhibited spurious molecular features that might exacerbate studies of G0 mosaic CRISPR knockout fish, we generated an RNA-seq dataset of various control larvae at 5 days post fertilization. While we found no evidence of spontaneous somatic mutations of injected larvae, we did identify several hundred differentially-expressed genes with high variability between injection types. Network analyses of shared differentially-expressed genes in the  mock injected larvae implicated a number of key regulators of common metabolic pathways, and gene-ontology analysis revealed connections with response to wounding and cytoskeleton organization, highlighting a potentially lasting effect from the microinjection process that requires further investigation.

ConclusionOverall, our results provide a valuable resource for the zebrafish community for the design and execution of CRISPR/Cas9 experiments.

category: genetics


title: Effect of high proportion concentrate dietary on Yak jejunal structure, physiological function and protein composition during cold season

abstract: The current study aimed to investigate the damage of long-term high concentrate diet feeding pattern on Yak jejunal structure, physiological function and protein composition during cold season. Twelve Datong male Yak (Bos grunniens) with the same age from cold season were randomly selected and slaughtered to determine Yak jejunal digestive enzyme activity, morphology and protein composition on different feeding patterns in Tibetan Plateau. The results showed that Yak jejunum digestive enzyme activity and morphology of grazing reared group were better than those in the intensively reared group. A total of 96 differentially expressed proteins were identified by label-free Mass Spectrometry (MS), which could be concluded to two predominant themes: protein structure and inflammatory response. Nine differentially expressed proteins were correlated in Yak jejunum damage in different feeding patterns. According to our study, feeding patterns resulted in the differences in Yak jejunum physiological function, morphology and protein composition. Our results confirmed that feeding of long-term high concentrate diet could damage the jejunum epithelial morphology and function.


title: Dendritic spines are lost in clusters in Alzheimers disease

abstract: Alzheimers disease (AD) is a progressive neurodegenerative disorder characterized by a deterioration of neuronal connectivity. The pathological accumulation of tau in neurons is one of the hallmarks of AD and has been connected to the loss of dendritic spines of pyramidal cells, which are the major targets of cortical excitatory synapses and key elements in memory storage. However, the detailed mechanisms underlying the loss of dendritic spines in individuals with AD are still unclear. Here, we used graph-theory approaches to compare the distribution of dendritic spines from neurons with and without tau pathology of AD individuals. We found that the presence of tau pathology determines the loss of dendritic spines in clusters, ruling out alternative models where spine loss occurs at random locations. Since memory storage has been associated with synaptic clusters, the present results provide a new insight into the mechanisms by which tau drives synaptic damage in AD, paving the way to memory deficits through alterations of spine organization.


title: Neural oscillations track natural but not artificial fast speech: Novel insights from speech-brain coupling using MEG

abstract: Speech processing is supported by the synchronization of cortical oscillations to its rhythmic components, including syllable rate. This has been shown to be the case for normal rate speech as well as artificially accelerated speech. However, the case of natural speech rate variations, which are among the most ubiquitous sources of variability in speech, has been largely overlooked. Here, we directly compared changes in the properties of cortico-acoustic coupling when speech naturally shifts from normal to fast rate and when it is artificially accelerated. Neuromagnetic brain signals of 24 normal-hearing adults were recorded with magnetoencephalography (MEG) while they listened to natural normal ([~]6 syllables/s), natural fast ([~]9 syllables/s) and time-compressed ([~]9 syllables/s) sentences, as well as to envelope-matched amplitude-modulated noise. We estimated coherence between the envelope of the acoustic input and MEG source time-series at frequencies corresponding to the mean syllable rates of the normal and fast speech stimuli. We found that listening to natural speech at normal and fast rates was associated with coupling between speech signal envelope and neural oscillations in right auditory and (pre)motor cortices. This oscillatory alignment occurred at [~]6.25 Hz for normal rate sentences and shifted up to [~]8.75 Hz for naturally-produced fast speech, mirroring the increase in syllable rate between the two conditions. Unexpectedly, despite being generated at the same rate as naturally-produced fast speech, the time-compressed sentences did not lead to significant cortico-acoustic coupling at [~]8.75 Hz. Interestingly, neural activity in putative right articulatory cortex exhibited stronger tuning to natural fast rather than to artificially accelerated speech, as well as stronger phase-coupling with left temporo-parietal and motor regions. This may reflect enhanced tracking of articulatory features of naturally-produced speech. Altogether, our findings provide new insights into the oscillatory brain signature underlying the perception of natural speech at different rates and highlight the importance of using naturally-produced speech when probing the dynamics of brain-to-speech coupling.


title: Chronic lung diseases are associated with gene expression programs favoring SARS-CoV-2 entry and severity

abstract: Patients with chronic lung disease (CLD) have an increased risk for severe coronavirus disease-19 (COVID-19) and poor outcomes. Here, we analyzed the transcriptomes of 605,904 single cells isolated from healthy and CLD lungs to identify molecular characteristics of lung cells that may account for worse COVID-19 outcomes in patients with chronic lung diseases. We observed a similar cellular distribution and relative expression of SARS-CoV-2 entry factors in control and CLD lungs. CLD epithelial cells expressed higher levels of genes linked directly to the efficiency of viral replication and innate immune response. Additionally, we identified basal differences in inflammatory gene expression programs that highlight how CLD alters the inflammatory microenvironment encountered upon viral exposure to the peripheral lung. Our study indicates that CLD is accompanied by changes in cell-type-specific gene expression programs that prime the lung epithelium for and influence the innate and adaptive immune responses to SARS-CoV-2 infection.


title: Hierarchical Bayesian Models of Reinforcement Learning: Introduction and comparison to alternative methods

abstract: Reinforcement learning models have been used extensively to capture learning and decision-making processes in humans and other organisms. One essential goal of these computational models is the generalization to new sets of observations. Extracting parameters that can reliably predict out-of-sample data can be difficult, however. The use of prior distributions to regularize parameter estimates has been shown to help remedy this issue. While previous research has suggested that empirical priors estimated from a separate dataset improve predictive accuracy, this paper outlines an alternate method for the derivation of empirical priors: hierarchical Bayesian modeling. We provide a detailed introduction to this method, and show that using hierarchical models to simultaneously extract and impose empirical priors leads to better out-of-sample prediction while being more data efficient.


title: Brain organization, not size alone, as key to high-level vision: Evidence from marmoset monkeys

abstract: Bigger brains are thought to support richer abilities, including perceptual abilities. But bigger brains are typically organized differently (e.g., with more cortical areas). Thus, the extent to which a neural systems size versus organization underlies complex abilities remains unclear. The marmoset monkey is evolutionarily peculiar: it has a small brain, yet many cortical areas. We used this natural experiment to test organization as source of high-level visual abilities independent of size, via large-scale psychophysics comparing marmosets to different species on identical tasks. Marmosets far out--performed rats--a marmoset-sized rodent--on a simple visual recognition task. On another visual task, which is difficult for both humans and machines, marmosets achieved high performance. Strikingly, their image-by-image behavior revealed that they did so in a manner highly similar to humans--marmosets were nearly as human-like as were macaques. These results suggest a key role for brain organization--not simply size--in the evolution of sophisticated abilities.


title: Restructuring of genomic provinces of surface ocean plankton under climate change

abstract: The impact of climate change on diversity, functioning and biogeography of marine plankton remains a major unresolved issue. Here, niche theory is applied to plankton metagenomes of 6 size fractions, from viruses to meso-zooplankton, sampled during the Tara Oceans expedition. Niches are used to derive plankton size-dependent structuring of the oceans south of 60{degrees}N in climato-genomic provinces characterized by signature genomes. By 2090, assuming the RCP8.5 high warming scenario, provinces would be reorganized over half of the considered ocean area and quasi-systematically displaced poleward. Particularly, tropical provinces would expand at the expense of temperate ones. Sea surface temperature is identified as the main driver of changes (50%) followed by phosphate (11%) and salinity (10%). Compositional shifts among key planktonic groups suggest impacts on the nitrogen and carbon cycles. Provinces are linked to estimates of carbon export fluxes which are projected to decrease on average by 4% in response to biogeographical restructuring.

category: ecology


title: Temporal prediction elicits rhythmic pre-activation of relevant sensory cortices

abstract:
Being able to anticipate events before they happen facilitates stimulus processing. The anticipation of the contents of events is thought to be implemented by the elicitation of prestimulus templates in sensory cortex. In contrast, the anticipation of the timing of events is typically associated with entrainment of neural oscillations. It is so far unknown whether and in which conditions temporal expectations interact with feature-based expectations, and, consequently, whether entrainment modulates the generation of content-specific sensory templates. In this study, we investigated the role of temporal expectations in a sensory discrimination task. We presented participants with rhythmically interleaved visual and auditory streams of relevant and irrelevant stimuli while measuring neural activity using magnetoencephalography. We found no evidence that rhythmic stimulation induced prestimulus feature templates. However, we did observe clear anticipatory rhythmic pre-activation of the relevant sensory cortices. This oscillatory activity peaked at behaviourally relevant, in-phase, intervals. Our results suggest that temporal expectations about stimulus features do not behave similarly to explicitly cued, non-rhythmic, expectations; yet elicit a distinct form of modality-specific pre-activation.

Graphical abstract

O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=165 SRC="FIGDIR/small/347005v3_ufig1.gif" ALT="Figure 1">
View larger version (35K):
org.highwire.dtl.DTLVardef@fce8corg.highwire.dtl.DTLVardef@1c16c3corg.highwire.dtl.DTLVardef@1a90d62org.highwire.dtl.DTLVardef@1adaa17_HPS_FORMAT_FIGEXP  M_FIG C_FIG The brain extracts temporal regularities from the environment to anticipate upcoming events. Furthermore, with prior knowledge about their contents, the brain is thought to leverage this by instantiating anticipatory sensory templates. We investigated if sensory templates occur in response to a rhythmic stimulus stream with predictable temporal structure. We found that temporal rhythmic predictions did not induce sensory templates, but rather modulated the excitability in early sensory cortices.


title: Helping Behavior in Prairie Voles: A Model of Empathy and the Importance of Oxytocin

abstract: Several studies suggest that rodents show empathic responses and helping behavior toward others. We examined whether prairie voles (Microtus ochrogaster) would help conspecifics who were soaked in water by opening a door to a safe area. Door-opening latency decreased as task sessions progressed. When the conspecific was not soaked in water, the latency of the door-opening did not decrease, indicating that the distress of the conspecific is necessary for the learning of the door-opening. These suggest that prairie voles learn helping behavior. We found no sex difference in the door-opening latency or the interest in other voles soaked in water. Additionally, we also examined the helping behavior in prairie voles in which oxytocin receptors were genetically knocked out. Oxytocin receptor knockout voles demonstrated less learning of the door-opening and less interest in other voles soaked in water. This suggests that oxytocin is important for the emergence of helping behavior.

category: animal behavior and cognition


title: Rit2 reduces LRRK2 kinase activity and protects against alpha-synuclein neuropathology

abstract: In Parkinsons disease (PD) misfolded alpha-synuclein (aSyn) accumulates in the substantia nigra, where dopaminergic neurons are progressively lost. The mechanisms underlying aSyn pathology are still unclear but hypothesized to involve the autophagy-lysosome pathway (ALP). LRRK2 mutations are a major cause of familial and sporadic PD, hyperactivate kinase activity and its pharmacological inhibition reduces pS129-aSyn inclusions. We observed selective downregulation of the novel PD risk factor RIT2 in G2019S-LRRK2 expressing cells. Here we studied whether RIT2 could modulate LRRK2 kinase activity. RIT2 overexpression in G2019S-LRRK2 cells rescued ALP abnormalities and diminished aSyn inclusions. In vivo, viral mediated overexpression of RIT2 conferred neuroprotection against AAV-A53T-aSyn. Furthermore, RIT2 overexpression prevented the A53T-aSyn-dependent increase of LRRK2 kinase activity in vivo. Our data indicate that RIT2 inhibits overactive LRRK2 to ameliorate ALP impairment and counteract aSyn aggregation and related deficits. Targeting RIT2 could represent a novel strategy to combat neuropathology in familial and idiopathic PD.


title: General auditory and speech-specific contributions to cortical envelope tracking revealed using auditory chimeras

abstract:
1.In recent years research on natural speech processing has benefited from recognizing that low frequency cortical activity tracks the amplitude envelope of natural speech. However, it remains unclear to what extent this tracking reflects speech-specific processing beyond the analysis of the stimulus acoustics. In the present study, we aimed to disentangle contributions to cortical envelope tracking that reflect general acoustic processing from those that are functionally related to processing speech. To do so, we recorded EEG from subjects as they listened to "auditory chimeras" - stimuli comprised of the temporal fine structure (TFS) of one speech stimulus modulated by the amplitude envelope (ENV) of another speech stimulus. By varying the number of frequency bands used in making the chimeras, we obtained some control over which speech stimulus was recognized by the listener. No matter which stimulus was recognized, envelope tracking was always strongest for the ENV stimulus, indicating a dominant contribution from acoustic processing. However, there was also a positive relationship between intelligibility and the tracking of the perceived speech, indicating a contribution from speech specific processing. These findings were supported by a follow-up analysis that assessed envelope tracking as a function of the (estimated) output of the cochlea rather than the original stimuli used in creating the chimeras. Finally, we sought to isolate the speech-specific contribution to envelope tracking using forward encoding models and found that indices of phonetic feature processing tracked reliably with intelligibility. Together these results show that cortical speech tracking is dominated by acoustic processing, but also reflects speech-specific processing.

This work was supported by a Career Development Award from Science Foundation Ireland (CDA/15/3316) and a grant from the National Institute on Deafness and Other Communication Disorders (DC016297). The authors thank Dr. Aaron Nidiffer, Dr. Aisling OSullivan, Thomas Stoll and Lauren Szymula for assistance with data collection, and Dr. Nathaniel Zuk, Dr. Aaron Nidiffer, Dr. Aisling OSullivan for helpful comments on this manuscript.

2. Significance StatementActivity in auditory cortex is known to dynamically track the energy fluctuations, or amplitude envelope, of speech. Measures of this tracking are now widely used in research on hearing and language and have had a substantial influence on theories of how auditory cortex parses and processes speech. But, how much of this speech tracking is actually driven by speech-specific processing rather than general acoustic processing is unclear, limiting its interpretability and its usefulness. Here, by merging two speech stimuli together to form so-called auditory chimeras, we show that EEG tracking of the speech envelope is dominated by acoustic processing, but also reflects linguistic analysis. This has important implications for theories of cortical speech tracking and for using measures of that tracking in applied research.


title: The collapse of the spindle following ablation in S. pombe is mediated by microtubules and the motor protein dynein

abstract:
A microtubule-based machine called the mitotic spindle segregates chromosomes when eukaryotic cells divide. In the fission yeast S. pombe, which undergoes closed mitosis, the spindle forms a single bundle of microtubules inside the nucleus. During elongation, the spindle extends via antiparallel microtubule sliding by molecular motors. These extensile forces from the spindle are thought to resist compressive forces from the nucleus. We probe the mechanism and maintenance of this force balance via laser ablation of spindles at various stages of mitosis. We find that spindle pole bodies collapse toward each other following ablation, but spindle geometry is often rescued, allowing spindles to resume elongation. While this basic behavior has been previously observed, many questions remain about this phenomenons dynamics, mechanics, and molecular requirements. In this work, we find that previously hypothesized viscoelastic relaxation of the nucleus cannot fully explain spindle shortening in response to laser ablation. Instead, spindle collapse requires microtubule dynamics and is powered at least partly by the minus-end directed motor protein dynein. These results suggest a role for dynein in redundantly supporting force balance and bipolarity in the S. pombe spindle.

STATEMENT OF SIGNIFICANCES. pombe serves as an important model organism for understanding cell division. Its structurally simple mitotic spindle is especially suited for mechanical perturbation. Since S. pombe undergoes a process of closed cell division, without breakdown of the nuclear envelope, force may be exerted between its nuclear envelope and spindle. Here, we mechanically sever spindles via laser ablation to probe this force balance. Following ablation, S. pombe spindle fragments collapse toward each other. We find that, contrary to prior expectations, forces from the chromosomes and nuclear envelope are not responsible for this collapse. Instead, it is microtubule-dependent, and is powered at least in part by the minus-end directed microtubule motor protein dynein.

category: biophysics


title: Direct observation of the mechanical role of bacterial chaperones in protein folding

abstract:
Protein folding under force is an integral source of generating mechanical energy in various cellular processes, ranging from protein translation to degradation. Although chaperones are well known to interact with proteins under mechanical force, how they respond to force and control cellular energetics remains unknown.

To address this question, we introduce novel real-time magnetic-tweezers technology to mimic physiological force environment on client proteins, keeping the chaperones unperturbed. We studied two structurally distinct client proteins with seven different chaperones, independently and in combination, and proposed novel mechanical activity of chaperones. We found chaperones behave differently, while these client proteins are under force than its previously known functions. For instance, tunnel associated chaperones (DsbA and trigger factor), otherwise working as holdase without force, assist folding under force. This process generates an additional mechanical energy up to [~]147 zJ to facilitate translation or translocation. However, well-known cytoplasmic foldase chaperones (PDI, thioredoxin, or DnaKJE), does not possess the mechanical folding ability under force. Notably, the transferring chaperones (DnaK, DnaJ, SecB), act as unfoldase and slow down folding process, both in the presence and absence of force, to prevent misfolding of the client proteins. This provides an emerging insight of mechanical roles of chaperones: they can generate or consume energy by shifting energy landscape of the client proteins towards folded or unfolded state; suggesting an evolutionary mechanism to minimize the energy consumption in various biological processes.


title: Daily running enhances molecular and physiological circadian rhythms in skeletal muscle

abstract:
Structured AbstractO_ST_ABSObjectiveC_ST_ABSExercise is a critical component of a healthy lifestyle and a key strategy for the prevention and management of metabolic disease. Identifying molecular mechanisms underlying adaptation in response to chronic physical activity is of critical interest in metabolic physiology. Circadian rhythms broadly modulate metabolism, including muscle substrate utilization and exercise capacity. Here, we define the molecular and physiological changes induced across the daily cycle by voluntary low intensity daily exercise.

MethodsWildtype c57BL6/J male and female mice were housed with or without access to a running wheel for six weeks. Maximum running speed was measured at four different zeitgeber times (ZTs, hours after lights on) using either electrical or manual stimulation to motivate continued running on a motorized treadmill. RNA isolated from plantaris muscles at six ZTs was sequenced to establish the impact of daily activity on genome-wide transcription. Patterns of gene expression were analyzed using Gene Set Enrichment Analysis (GSEA) and Detection of Differential Rhythmicity (DODR). Blood glucose, lactate, and ketones, and muscle and liver glycogen were measured before and after exercise.

ResultsWe demonstrate that the use of mild electrical shocks to motivate running negatively impacts maximum running speed and describe a manual method to motivate running in rodent exercise studies. Using this method, we show that time of day influences the increase in exercise capacity afforded by six weeks of voluntary wheel running: when maximum running speed is measured at the beginning of the nighttime active period in mice, there is no measurable benefit from a history of daily voluntary running, while maximum increase in performance occurs at the end of the night. We show that daily voluntary exercise dramatically remodels the muscle circadian transcriptome. Finally, we describe daily rhythms in carbohydrate metabolism associated with the timedependent response to moderate daily exercise.

ConclusionsCollectively, these data indicate that chronic nighttime physical activity dramatically remodels daily rhythms of muscle gene expression, which in turn support daily fluctuations in exercise performance.

category: physiology


title: Hippocampal replay of experience at real-world speeds

abstract: Representations related to past experiences play a critical role in memory and decision-making processes. The rat hippocampus expresses these types of representations during sharp-wave ripple (SWR) events, and previous work identified a minority of SWRs that contain "replay" of spatial trajectories at ~20x the movement speed of the animal. Efforts to understand replay typically make multiple assumptions about which events to examine and what sorts of representations constitute replay. We therefore lack a clear understanding of both the prevalence and the range of representational dynamics associated with replay. Here we develop a state space model that uses a combination of movement dynamics of different speeds to capture the spatial content and time evolution of replay during SWRs. Using this model, we find that the large majority of replay events contain spatially coherent, interpretable content. Furthermore, many events progress at real-world, rather than accelerated, movement speeds, consistent with actual experiences.


title: Asymmetries around the visual field: From retina to cortex to behavior

abstract: Visual performance varies around the visual field. It is best near the fovea compared to the periphery, and at iso-eccentric locations it is best on the horizontal, intermediate on the lower, and poorest on the upper meridian. The fovea-to-periphery performance decline is linked to the decreases in cone density, retinal ganglion cell (RGC) density, and V1 cortical magnification factor (CMF) as eccentricity increases. The origins of polar angle asymmetries are not well understood. Optical quality and cone density vary across the retina, but recent computational modeling has shown that these factors can only account for a small percentage of behavior. Here, we investigate how visual processing beyond the cone photon absorptions contributes to polar angle asymmetries in performance. First, we quantify the extent of asymmetries in cone density, midget RGC density, and V1 CMF. We find that both polar angle asymmetries and eccentricity gradients increase from cones to mRGCs, and from mRGCs to cortex. Second, we extend our previously published computational observer model to quantify the contribution of phototransduction by the cones and spatial filtering by mRGCs to behavioral asymmetries. Starting with photons emitted by a visual display, the model simulates the effect of human optics, cone isomerizations, phototransduction, and mRGC spatial filtering. The model performs a forced choice orientation discrimination task on mRGC responses using a linear support vector machine classifier. The model shows that asymmetries in a decision-makers performance across polar angle are greater when assessing the photocurrents than when assessing isomerizations and are greater still when assessing mRGC signals. Nonetheless, the polar angle asymmetries of the mRGC outputs are still considerably smaller than those observed from human performance. We conclude that cone isomerizations, phototransduction and the spatial filtering properties of mRGCs contribute to polar angle performance differences, but that a full account of these differences will entail additional contribution from cortical representations.


title: Uncovering the mechanisms of real-world attentional control over the course of primary education

abstract:
Schooling may shape childrens abilities to control their attention, but it is unclear if this impact extends from control over visual objects to encompass multisensory objects, which are more typical of everyday environments. We compared children across three primary school grades ([country] 1st, 3rd, and 5th grade) on their performance on a game-like audio-visual attentional control task, while recording their EEG. Behavioral markers of visual attentional control were present from 3rd grade (after 2 years of schooling), whereas multisensory attentional control was not detected in any group. However, multivariate whole-brain EEG analyses ( electrical neuroimaging) revealed stable patterns of brain activity that indexed both types of attentional control - visual control in all groups, and multisensory attentional control from 3rd grade onwards. Multivariate EEG approaches can uncover otherwise undetectable mechanisms of attentional control over visual and multisensory objects and characterize how they differ at different educational stages.

Lay AbstractWe measured how visual and audiovisual distractors differ in capturing the attention of 1st- to 5th-graders while recording the childrens brain activity. Brain activity results showed that all children were sensitive to visual distraction, and from 3rd grade onwards, children were also sensitive to audiovisual distraction. These results deepen our understanding of how school children control their attention in everyday environments, which are made up of information that stimulates multiple senses at a time.


title: Functional Connectome Fingerprinting Using Shallow Feedforward Neural Networks

abstract: Although individual subjects can be identified with high accuracy using correlation matrices computed from resting-state functional magnetic resonance imaging (rsfMRI) data, the performance significantly degrades as the scan duration is decreased. Recurrent neural networks can achieve high accuracy with short duration (72s) data segments but are designed to use temporal features not present in the correlation matrices. Here we show that shallow feedforward neural networks that rely solely on the information in rsfMRI correlation matrices can achieve state-of-the-art identification accuracies ([≥] 99.5%) with data segments as short as 20s and across a range of input data-size combinations when the total number of data points (# regions x # time points) is on the order of 10,000.


title: The magnitude of airway remodelling is not altered by distinct allergic inflammatory responses in BALB/c vs C57BL/6 mice but matrix composition differs

abstract: Allergic airway inflammation is heterogenous with variability in immune phenotypes observed across asthmatic patients. Inflammation has been thought to directly contribute to airway remodelling in asthma, but clinical data suggests that neutralising type 2 cytokines does not necessarily alter disease pathogenesis. Here, we utilised C57BL/6 and BALB/c mice to investigate the development of allergic airway inflammation and remodelling. Exposure to an allergen cocktail for up to 8 weeks led to type 2 and type 17 inflammation, characterized by airway eosinophilia and neutrophilia and increased expression of chitinase-like proteins in both C75BL/6 and BALB/c mice. However, BALB/c mice developed much greater inflammatory responses than C57BL/6 mice, effects possibly explained by a failure to induce pathways that regulate and maintain T cell activation in C57BL/6 mice, as shown by whole lung RNA transcript analysis. Allergen administration resulted in a similar degree of airway remodelling between mouse strains but with differences in collagen subtype composition. Increased collagen III was observed around the airways of C57BL/6 but not BALB/c mice while allergen-induced loss of basement membrane collagen IV was only observed in BALB/c mice. This study highlights a model of type 2/type 17 airway inflammation in mice whereby development of airway remodelling can occur in both BALB/c and C57BL/6 mice despite differences in immune response dynamics between strains. Importantly, compositional changes in the ECM between genetic strains of mice may help us better understand the relationships between lung function, remodelling and airway inflammation.


title: Diet unmasks genetic variants that regulate lifespan in outbred Drosophila

abstract: Evolutionary theory suggests that lifespan-associated alleles should be purged from the gene pool, and yet decades of GWAS and model organism studies have shown they persist. Here, we address one potential explanation, the idea that the alleles that regulate lifespan do so only in certain contexts. We exposed thousands of outbred Drosophila to a standard and a high sugar diet. We then sequenced over 10,000 individuals and track genome-wide allele frequency changes over time, as these populations aged. We mapped thousands of lifespan-altering alleles, some associated with early vs late life tradeoffs, late-onset effects, and genotype-by-environment interactions. We find that lifespan-reducing alleles are most likely to be recently derived, have stronger effects on a high-sugar diet, consistent with the hypothesis that historically neutral or beneficial alleles can become detrimental in novel conditions. We also show that the gene midway, a regulator of lipid storage and ortholog of the lifespan-associated gene DGAT1 in mice, also regulates lifespan in Drosophila. Our results provide insight into the highly polygenic and context-dependent genetic architecture of lifespan, as well as the evolutionary processes that shape this key trait.


title: The Thermosynechococcus genus: wide environmental distribution, but a highly conserved genomic core

abstract: Cyanobacteria thrive in very diverse environments. However, questions remain about possible growth limitations in ancient environmental conditions. As a single genus, the Thermosynechococcus are cosmopolitan and live in chemically diverse habitats. To understand the genetic basis for this, we compared the protein coding component of Thermosynechococcus genomes. Supplementing the known genetic diversity of Thermosynechococcus, we report draft metagenome-assembled genomes of two Thermosynechococcus recovered from ferrous carbonate hot springs in Japan. We find that as a genus, Thermosynechococcus is genomically conserved, having a small pan-genome with few accessory genes per individual strain and only 14 putative orthologous protein groups appearing in all Thermosynechococcus but not in any other cyanobacteria in our analysis. Furthermore, by comparing orthologous protein groups, including an analysis of genes encoding proteins with an iron related function (uptake, storage or utilization), no clear differences in genetic content, or adaptive mechanisms could be detected between genus members, despite the range of environments they inhabit. Overall, our results highlight a seemingly innate ability for Thermosynechococcus to inhabit diverse habitats without having undergone substantial genomic adaptation to accommodate this. The finding of Thermosynechococcus in both hot and high iron environments without adaptation recognizable from the perspective of the proteome has implications for understanding the basis of thermophily within this clade, and also for understanding the possible genetic basis for high iron tolerance in cyanobacteria on early Earth. The conserved core genome may be indicative of an allopatric lifestyle - or reduced genetic complexity of hot spring habitats relative to other environments.

category: genomics


title: Efficient plasmid transfer via natural competence in a synthetic microbial community

abstract: The molecular and ecological factors shaping horizontal gene transfer (HGT) via natural transformation in microbial communities are largely unknown, which is critical for understanding the emergence of antibiotic-resistant pathogens. We investigate key factors shaping HGT in a microbial community by quantifying extracellular DNA release, species growth and HGT efficiency over time. In the community, plasmid release and HGT efficiency are significantly enhanced than the respective monocultures. The donor is a key determinant of HGT efficiency as plasmids induce the SOS response, enter a multimerized state, and are released at high concentrations, yielding efficient HGT. HGT is independent of the donor viability state as live and dead donor cells transfer the plasmid with high efficiency and is only reduced in response to high donor lysis rates. In sum, plasmid HGT via natural competence depends on an interplay of plasmid properties, donor stress responses and lysis rates and inter-species interactions.


title: SpecSeg: cross spectral power-based segmentation of neurons and neurites in chronic calcium imaging datasets

abstract: Imaging calcium signals in neurons of awake, behaving animals using single- or multi-photon microscopy facilitates the study of coding in large neural populations. Such experiments produce massive datasets requiring powerful methods to extract responses from hundreds of neurons. We present SpecSeg, a new open-source toolbox for 1) segmentation of regions of interest (ROIs) representing neuronal structures, 2) inspection and manual editing of ROIs, 3) neuropil correction and signal extraction and 4) matching of ROIs in sequential recordings. SpecSeg uses a novel method for ROI registration, based on temporal cross-correlations of low-frequency components derived by Fourier analysis, of each pixel with its neighbors. The approach is insightful and enables ROI detection around neurons or neurites. It works for single- (miniscope) and multi-photon microscopy data, eliminating the need for separate toolboxes. SpecSeg thus provides an efficient and user-friendly approach for analyzing calcium responses in neuronal structures imaged over prolonged periods of time.

category: neuroscience


title: Mice alternate between discrete strategies during perceptual decision-making

abstract: Classical models of perceptual decision-making assume that subjects use a single, consistent strategy to form decisions, or that strategies evolve slowly over time. Here we present new analyses suggesting that this common view is incorrect. We analyzed data from mouse and human decision-making experiments and found that choice behavior relies on an interplay between multiple interleaved strategies. These strategies, characterized by states in a hidden Markov model, persist for tens to hundreds of trials before switching, and may alternate multiple times within a session. The identified mouse decision-making strategies were highly consistent across individuals and comprised a single "engaged" state, in which decisions relied heavily on the sensory stimulus, and several biased states in which errors frequently occurred. These results provide a powerful alternate explanation for "lapses" often observed in rodent psychophysical experiments, and suggest that standard measures of performance mask the presence of dramatic changes in strategy across trials.


title: Cell-Type-Specific Decrease of the Intrinsic Excitability of Motor Cortical Pyramidal Neurons in Parkinsonism

abstract:
The hypokinetic motor symptoms of Parkinsons disease (PD) are closely linked with a decreased motor cortical output as a consequence of elevated basal ganglia inhibition. However, whether and how the loss of dopamine alters the cellular properties of motor cortical neurons in PD remains undefined. We induced parkinsonism in adult C57BL6 mice of both sexes by injecting neurotoxin, 6-hydroxydopamine, into the medial forebrain bundle. By using ex vivo patch-clamp recording and retrograde tracing approach, we found that the intrinsic excitability of pyramidal tract neurons (PTNs) in the motor cortical layer 5b was greatly decreased in parkinsonism; but the intratelencephalic neurons (ITNs) were not affected. The cell-type-specific intrinsic adaptations were associated with a depolarized threshold and broadened width of action potentials in PTNs. Moreover, the loss of midbrain dopaminergic neurons impaired the capability of M1 PTNs to sustain high-frequency firing, which could underlie their abnormal pattern of activity in the parkinsonian state. We also showed that the decreased excitability in parkinsonism was caused by an impaired function of both persistent sodium channels and the large conductance, Ca2+-activated K+ channels. Acute activation of dopaminergic receptors failed to rescue the impaired intrinsic excitability of M1 PTNs in parkinsonian mice. Altogether, our data demonstrated a cell-type-specific decrease of the excitability of M1 pyramidal neurons in parkinsonism. Thus, intrinsic adaptations in the motor cortex, together with pathological basal ganglia inhibition, underlie the decreased motor cortical output in parkinsonian state and exacerbate parkinsonian motor deficits.

Significance statementThe degeneration of midbrain dopaminergic neurons in Parkinsons disease remodels the connectivity and function of cortico-basal ganglia-thalamocortical network. However, whether and how dopaminergic degeneration and the associated basal ganglia dysfunction alter motor cortical circuitry remain undefined. We found that pyramidal neurons in the layer 5b of the primary motor cortex (M1) exhibit distinct adaptations in response to the loss of midbrain dopaminergic neurons, depending on their long-range projections. Besides the decreased thalamocortical synaptic excitation as proposed by the classical model of Parkinsons pathophysiology, these results, for the first time, show novel cellular and molecular mechanisms underlying the abnormal motor cortical output in parkinsonism.


title: The E3 ligase TRIM1 ubiquitinates LRRK2 and controls its localization, degradation, and toxicity

abstract: Missense mutations in leucine-rich repeat kinase 2 (LRRK2) are the most common cause of familial Parkinsons Disease (PD); however, pathways regulating LRRK2 subcellular localization, function, and turnover are not fully defined. We performed quantitative mass spectrometry-based interactome studies to identify 48 novel LRRK2 interactors, including the microtubule-associated E3 ubiquitin ligase TRIM1 (Tripartite Motif Family 1). TRIM1 recruits LRRK2 to the microtubule cytoskeleton for ubiquitination and proteasomal degradation by binding LRRK2911-920, a nine amino acid segment within a flexible interdomain region (LRRK2853-981), which we designate the "Regulatory Loop" (RL). Phosphorylation of LRRK2 Ser910/Ser935 within LRRK2 RL serves as a molecular switch controlling LRRK2s association with cytoplasmic 14-3-3 versus microtubule-bound TRIM1. Association with TRIM1 modulates LRRK2s interaction with Rab29 and prevents upregulation of LRRK2 kinase activity by Rab29 in an E3-ligase-dependent manner. Finally, TRIM1 rescues neurite outgrowth deficits caused by PD-driving mutant LRRK2 G2019S. Our data suggest that TRIM1 is a critical regulator of LRRK2, controlling its degradation, localization, binding partners, kinase activity, and cytotoxicity.


title: Evolution of diversity in metabolic strategies

abstract: Understanding the origin and maintenance of biodiversity is a fundamental problem. Many theoretical approaches have been investigating ecological interactions, such as competition, as potential drivers of diversification. Classical consumer-resource models predict that the number of coexisting species should not exceed the number of distinct resources, a phenomenon known as the competitive exclusion principle. It has recently been argued that including physiological tradeoffs in consumer-resource models can lead to violations of this principle and to ecological coexistence of very high numbers of species. Here we show that these results crucially depend on the functional form of the tradeoff. We investigate the evolutionary dynamics of resource use constrained by tradeoffs and show that if the tradeoffs are non-linear, the system either does not diversify, or diversifies into a number of coexisting species that does not exceed the number of resources. In particular, very high diversity can only be observed for linear tradeoffs.


title: Mutational meltdown of microbial altruists in Streptomyces coelicolor colonies

abstract: In colonies of the filamentous multicellular bacterium Streptomyces coelicolor, a sub-population of cells arise that hyper-produce metabolically costly antibiotics, resulting in division of labor that maximizes colony fitness. Because these cells contain large genomic deletions that cause massive reductions to individual fitness, their behavior is altruistic, much like worker castes in social insects or somatic cells in multicellular organisms. To understand the reproductive and genomic fate of these mutant cells after their emergence, we use experimental evolution by serially transferring populations via spore-to-spore transfer for 25 cycles, reflective of the natural mode of bottlenecked transmission for these spore-forming bacteria. We show that, in contrast to wild-type cells, altruistic mutant cells continue to significantly decline in fitness during transfer while they delete larger and larger fragments from their chromosome ends. In addition, altruistic mutants acquire a roughly 10-fold increase in their base-substitution rates possibly due to mutations in genes for DNA replication and repair. Ecological damage, caused by reduced sporulation, coupled with irreversible DNA damage due to point mutations and deletions, leads to an inevitable and irreversible type of mutational meltdown in these cells. Taken together, these results suggest that the altruistic cells arising in this division of labor are analogous to reproductively sterile castes of social insects.