title: Pan-cancer quantification of neoantigen-mediated immunoediting in cancer evolution

abstract: Immunoediting, which includes three temporally distinct stages, termed elimination, equilibrium, and escape, has been proposed to explain the interactions between cancer cells and the immune system during the evolution of cancer. However the status of immunoediting in cancer remains unclear, and the existence of neoantigen depletion signal in untreated cancer has been debated. Here we developed a distribution pattern based method for quantifying neoantigen mediated negative selection in cancer evolution. Our method provides a robust and reliable quantification for immunoediting signal in an individual cancer patient. The prevalence of immunoediting signal in immunotherapy untreated cancer genome has been demonstrated with this method. Importantly, the elimination and escape stages of immunoediting can be quantified separately, tumor types with strong immunoediting-elimination tend to have weak immunoediting-escape signal, and vice versa. Quantified immunoediting-elimination signal predicts cancer immunotherapy clinical response. Immunoediting quantification provides an evolutional perspective for evaluating the antigenicity of neoantigen, and reveals a potential biomarker for cancer precision immunotherapy.


title: Acquired resistance to anti-PD1 therapy in patients with NSCLC reveals changes in T cell phenotypes and MET amplification

abstract: The treatment of non-small cell lung cancer (NSCLC) patients with immune checkpoint inhibitors has prolonged their survival dramatically. However, some patients develop resistance after initial response. Here, we used imaging mass cytometry and whole exome and RNA sequencing to analyze matching tumor samples from a cohort of NSCLC patients who initially responded to immune checkpoint inhibitor therapy and later developed acquired resistance. We detected two patterns of resistance: One group of patients had reduced numbers of tumor-infiltrating CD8+ T cells and reduced expression of PD-L1 after development of resistance, whereas the other group showed high CD8+ T cell infiltration and high expression of PD-L1 and markedly elevated expression of other immune-inhibitory molecules. In two cases, we detected downregulation of type I and II IFN pathways after resistance developed, which could lead to an impaired anti-tumor immune response. This study adds to our knowledge of the mechanisms that cause resistance to immunotherapy in NSCLC patients.

category: cancer biology


title: Targeting N-Myc in Neuroblastoma with Selective Aurora Kinase A Degraders

abstract: Summary ParagraphMYCN amplification is the most frequent genetic driver in high-risk neuroblastoma (NB) and strongly associated with poor prognosis.1,2 The N-Myc transcription factor, which is encoded by MYCN, is a mechanistically validated, yet challenging target for NB therapy development.3,4 In normal neuronal progenitors, N-Myc undergoes rapid degradation, while in MYCN-amplified NB cells, Aurora kinase A (Aurora-A) binds to and stabilizes N-Myc, resulting in elevated protein levels.5,6 Allosteric Aurora-A inhibitors that displace N-Myc from binding can promote N-Myc degradation, but with limited efficacy.7-10 Here, we report a chemical approach to decrease N-Myc levels through the targeted protein degradation of Aurora-A. A first-in-class Aurora-A/N-Myc degrader, HLB-0532259 (compound 4), was developed from a novel Aurora-A-binding ligand that engages the Aurora-A/N-Myc complex. HLB-0532259 promotes the degradation of both Aurora-A and N-Myc with nanomolar potency and excellent selectivity and surpasses the cellular efficacy of established allosteric Aurora-A inhibitors. HLB-0532259 exhibits favorable pharmacokinetics properties and elicits tumor reduction in murine xenograft NB models. More broadly, this study delineates a novel strategy for targeting "undruggable" proteins that are reliant on accessory proteins for cellular stabilization.


title: A multi-omic dissection of super-enhancer driven oncogenic gene expression programs in ovarian cancer

abstract: The human genome contains regulatory elements, such as enhancers, that are often rewired by cancer cells for the activation of genes that promote tumorigenesis and resistance to therapy. This is especially true for cancers that have little or no known driver mutations within protein coding genes, such as ovarian cancer. Herein, we have utilized an integrated set of genomic and epigenomic datasets to identify clinically relevant super-enhancers that are preferentially amplified in ovarian cancer patients. We have systematically probed the top 86 super-enhancers, using CRISPR-interference and CRISPR-deletion assays coupled to RNA-sequencing, to nominate two salient super-enhancers that drive proliferation and migration of cancer cells. Utilizing Hi-C, we constructed chromatin interaction maps that enabled the annotation of direct target genes for these super-enhancers and later confirmed their activity specifically within the cancer cell compartment of human tumors using single-cell genomics data. Together, our multi-omic approach has examined a number of fundamental questions about how regulatory information encoded into super-enhancers drives gene expression networks that underlie the biology of ovarian cancer.


title: Protein kinase C alpha is a central node for tumorigenic transcriptional networks in human prostate cancer

abstract:
Aberrant expression of protein kinase C (PKC) isozymes is a hallmark of cancer. The different members of the PKC family control cellular events associated with cancer development and progression. Whereas the classical/conventional PKC isozyme has been linked to tumor suppression in most cancer types, here we demonstrate that this kinase is required for the mitogenic activity of aggressive human prostate cancer cells displaying aberrantly high PKC expression. Immunohistochemical analysis showed abnormal up-regulation of PKC in human primary prostate tumors. Interestingly, silencing PKC expression from aggressive prostate cancer cells impairs cell cycle progression, proliferation and invasion, as well as their tumorigenic activity in a mouse xenograft model. Mechanistic analysis revealed that PKC exerts a profound control of gene expression, particularly over genes and transcriptional networks associated with cell cycle progression and E2F transcription factors. PKC RNAi depletion from PC3 prostate cancer cells led to reduced expression of pro-inflammatory cytokine and epithelial-to-mesenchymal transition (EMT) genes, as well as a prominent down-regulation in the expression of the immune checkpoint ligand PD-L1. This PKC-dependent gene expression profile was corroborated in a human prostate cancer database. Our studies established PKC as a multifunctional kinase that plays pleiotropic roles in prostate cancer, particularly by controlling genetic networks associated with tumor growth and progression. The identification of PKC as a pro-tumorigenic kinase in human prostate cancer provides strong rationale for developing therapeutic approaches towards targeting PKC or its effectors.

IMPLICATIONSOur findings implicate PKC as a major node for transcriptional regulation of tumorigenic pathways in prostate cancer.


title: Comparative analysis of high- and low-level deep learning approaches in microsatellite instability prediction

abstract: Deep learning-based approaches in histopathology can be largely divided into two categories: a high-level approach using an end-to-end model and a low-level approach using feature extractors. Although the advantages and disadvantages of both approaches are well known, direct comparative analysis has rarely been conducted. Using the Cancer Genomic Atlas (TCGA) based dataset, we compared these two different approaches in microsatellite instability (MSI) prediction and analyzed morphological image features associated with MSI. Our high-level approach was based solely on EfficientNet while our low-level approach relied on LightGBM and multiple deep learning models trained on publicly available multi-class tissue, nuclei, and gland datasets. We compared their performance and important image features. Our high-level approach showed a superior performance compared to our low-level approach. In both approaches, debris, lymphocytes, and necrotic cells were revealed as important features of MSI, which is consistent with clinical knowledge. Then, during qualitative analysis, we discovered the weaknesses of our low-level approach and demonstrated that its performance can be improved by using different image features in a complementary way. We performed our study using open-access data, and we believe this study can serve as a useful basis for discovering image biomarkers for clinical application.

category: pathology


title: Nicotine measurement on Cambridge Filter PADs: an interlaboratory comparison to evaluate exposure by different electronic devices and traditional cigarette

abstract:
Inter-laboratory comparison is widely used to ensure quality control among laboratories. In in vitro toxicology studies for tobacco harm reduction (THR), exposure system performance and laboratory proficiency along with product smoke and aerosol stream are tested for variability to assess accuracy. Here we aim to test a novel inter-laboratory setup created in a new collaborative research group using identical and small footprint systems- in order to minimize variability factors and increase reproducibility.

Seven independent laboratories from different geographical areas tested the aerosol and smoke stream and exposure system performance (LM1 and LM4E) using Cambridge Filter Pad (CFP) trapping techniques. We tested 1R6F reference cigarettes, two electronic cigarettes (Vype e-Pen and Vype e-Stick Maxx), and two tobacco heating products (IQOS and Glo) under the appropriate ISO and/or HCI regimes. Nicotine quantification was performed by GC-FID at the laboratory of the leading center. The performance of participant laboratories was assessed by z-score values obtained from results either in relation to the mean and standard deviation of total participants or in relation to the reference leading center. Z-Scores were satisfactory when |z| [≤] 2, questionable when 2 < |z| < 3 and, unsatisfactory when |z| [≥] 3. In the first evaluation, for all the tested devices, Z- scores values generated by dosimetry data ranged from -2 to +2. However, high intra-laboratory variability (RSD> 10%) was observed for almost all laboratories. In the second, data showed borderline and unsatisfactory exposure performances versus LAB-A. Particularly, Z-scores [≥] 3 were observed once for LAB-B (e-Stick exposure) and LAB-G (e-Pen exposure), twice for LAB-C (1R6F-ISO and e-Stick exposures) and LAB-E (e-Pen and e-Stick exposures), and three times for LAB-F (1R6F-HCI, e-Pen, and Glo exposures).

This study demonstrates that nicotine dosimetry is a fundamental method for quality assurance of smoke/vapor run exposure in the early stage of an interlaboratory study, allowing the identification and possibly the resolution of gaps. Extended practice sessions on exposure runs and several rounds of nicotine dosimetry testing should be planned to keep in check overall equipment and operator performance.

category: pharmacology and toxicology


title: Integrated Systems-Level Proteomics and Metabolomics Reveals the Diel Molecular Landscape of Diverse Kale Cultivars

abstract: The diverse cultivars of Brassica oleracea and Brassica napus constitute an important global food source. Of those, the Brassica oleracea convar. acephala cultivar group containing var. sabellica and var. palmifolia and Brassica napus var. pabularia, collectively known as kale, are nutritious leafy greens consumed for their abundance of vitamins and micronutrients. Typified by their curly, serrated or wavy leaves, kale varieties have been primarily defined based on their leaf morphology and geographic origin, despite having complex genetic backgrounds. Kale is a very promising crop for vertical farming due to its high nutritional content. However, systematic analysis of kale growth and molecular composition under different light regimes suitable for vertical farming has been lacking. Hence, we selected nine diverse, publicly available and commercially grown kale cultivars for growth under light emitting diode (LED)-replicated sunlight-like conditions. We then analyzed their growth and nutrition using a combination of phenomics, proteomics and metabolomics. As plant growth and development are driven by the diel molecular activities of plants, we harvested kale leaf tissue at both end-of-day (ED) and end-of-night (EN) time-points for all molecular analyses. Our results reveal that diel metabolome and proteome signatures sub-divide the selected kale cultivars into two distinct groups, defined by their amino acid and sugar content, along with significant proteome differences involving carbon and nitrogen metabolism, mRNA splicing, protein translation and light harvesting. Together, our analysis has generated robust quantitative insights into the diel growth and development landscape of kale, significantly advancing our fundamental understanding of this nutritious leafy green for next-generation breeding and biotechnology.

category: plant biology


title: Type One Protein Phosphatase Regulates Fixed-Carbon Starvation-Induced Autophagy by Dephosphorylating ATG13a to Facilitate ATG1a-ATG13a Formation in Arabidopsis

abstract: Autophagy, a conserved pathway which carries out the bulk degradation of cytoplasmic material in eukaryotic cells, is critical in plant physiology and development. It is tightly regulated by ATG13, a core component of ATG1 kinase complex which initiates autophagy. Although it has been reported that ATG13 is dephosphorylated immediately after nutrient starvation, the phosphatase regulating this process is poorly understood. Here, we demonstrated that the septuple mutant (topp-7m) and octuple mutant (topp-8m) of type one protein phosphatase (TOPP) exhibited significantly reduced tolerance to fixed-carbon (C) starvation due to compromised autophagy activity. Genetic analysis placed TOPP upstream of autophagy. Interestingly, ATG13a was found to be an interactor of TOPP. And TOPP directly dephosphorylated ATG13a in vitro and in vivo. Meanwhile, eighteen phosphorylation sites of ATG13a were identified by LC-MS. Mimic dephosphorylation of ATG13a at these 18 sites significantly promoted autophagy and increased the atg13ab mutant tolerance to fixed-C starvation. Further study showed that the dephosphorylation of ATG13a facilitated ATG1a-ATG13a complex formation. Consistently, the recruitment of ATG13a for ATG1a was markedly inhibited in topp-7m-1. In addition, TOPP-controlled dephosphorylation of ATG13a boosted ATG1a phosphorylation. Taken together, our study reveals the crucial role of TOPP in regulating autophagy by stimulating the formation of ATG1a-ATG13a complex through dephosphorylating ATG13a in Arabidopsis.


title: Improvement of Gene Delivery and Mutation Efficiency in the CRISPR-Cas9 Wheat (Triticum aestivum L.) Genomics System via Biolistics

abstract: Discovery of the CRISPR-Cas9 gene editing system revolutionized the field of plant genomics. Despite advantages in ease of designing gRNA and the low cost of the CRISPR-Cas9 system, there are still hurdles to overcome in low mutation efficiencies, specifically in hexaploid wheat. In conjunction with gene delivery and transformation frequency, the mutation rate bottleneck has the potential to slow down advancements in genomic editing of wheat. In this study, nine bombardment parameter combinations using three gold particle sizes and three rupture disk pressures were tested to establish optimal stable transformation frequencies in wheat. Utilizing the best transformation protocol and a knockout cassette of the phytoene desaturase gene, we subjected transformed embryos to four temperature treatments and compared mutation efficiencies. The use of 0.6 m gold particles for bombardment increased transformation frequencies across all delivery pressures. A heat treatment of 34{degrees}C for 24 hours resulted in the highest mutation efficiency with no or minimal reduction in transformation frequency. The 34{degrees}C treatment produced two M0 mutant events with albino phenotypes, requiring biallelic mutations in all three genomes of hexaploid wheat. Utilizing optimal transformation and heat treatment parameters greatly increases mutation efficiency and can help advance research efforts in wheat genomics.


title: Additive and Dominant Loci Jointly Pyramiding the Grain Quality of Hybrid Rice

abstract: Hybrid rice has an advantage in its heterosis, resulting in high yield and resistance to biotic and abiotic stress. However, genetic improvement of grain quality is more challenging in hybrid rice than in inbred rice due to additional complexity, such as the dominant effect. It is critical to identify a path to efficiently develop inbreds and identify their superior crosses for hybrid production. Here, we developed a pipeline for joint analysis of phenotypes, effects, and generations (JPEG) and analysed 113 inbred varieties as male parents, five tester varieties as female parents, and their 565 (113x5) hybrid testcrosses for 12 grain quality traits, including grain length and width, chalkiness, and amylose content. A total of 1,619,588 single nucleotide polymorphisms were obtained for the parent varieties and inferred for the hybrids using whole-genome sequencing with an average sequencing depth of 11x. Genome-wide association studies with JPEG identified 128 loci associated with at least one of the 12 traits. There were 44 and 97 loci with additive and dominant effects, respectively, including 13 overlaps. Among the 128 associated loci, 42 loci are located in or near (<200 kb) 17 known genes. Pyramiding genetic loci with additive and/or dominant effects in genomic selection dramatically improves the accuracy of predicting hybrid performances. More than 45% of genetic variation was explained by the identified markers for all traits except one (30%). These results demonstrate that pyramiding genetically identified additive and dominant loci can afford substantial power for predicting hybrid performances, presenting opportunities to identify superior crosses from existing phenotypes and genotypes of inbreds and hybrids.


title: Manipulating the 3D organization of the largest synthetic yeast chromosome

abstract: Whether synthetic genomes can power life has attracted broad interest in the synthetic biology field, especially when the synthetic genomes are extensively modified with thousands of designer features. Here we report de novo synthesis of the largest eukaryotic chromosome thus far, synIV, a 1,454,621-bp Saccharomyces cerevisiae chromosome resulting from extensive genome streamlining and modification. During the construction of synIV, we developed a megachunk assembly method, combined with a hierarchical integration strategy. This strategy significantly increased the accuracy and flexibility of synthetic chromosome construction and facilitated chromosome debugging. In addition to the drastic sequence changes made to synIV by rewriting it, we further manipulated the three-dimensional structure of synIV in the yeast nucleus to explore spatial gene regulation within the nuclear space. Surprisingly, we found few gene expression changes, suggesting that positioning inside the yeast nucleoplasm plays a minor role in gene regulation. Therefore, our manipulation of the spatial structure of the largest synthetic yeast chromosome shed light on higher-order architectural design of the synthetic genomes.

category: synthetic biology


title: Learning inverse folding from millions of predicted structures

abstract: We consider the problem of predicting a protein sequence from its backbone atom coordinates. Machine learning approaches to this problem to date have been limited by the number of available experimentally determined protein structures. We augment training data by nearly three orders of magnitude by predicting structures for 12M protein sequences using AlphaFold2. Trained with this additional data, a sequence-to-sequence transformer with invariant geometric input processing layers achieves 51% native sequence recovery on structurally held-out backbones with 72% recovery for buried residues, an overall improvement of almost 10 percentage points over existing methods. The model generalizes to a variety of more complex tasks including design of protein complexes, partially masked structures, binding interfaces, and multiple states.

category: systems biology


title: Molecular signatures of proteostasis control in motor neurons with different sensitivity to Amyotrophic Lateral Sclerosis

abstract: Amyotrophic Lateral Sclerosis (ALS) is a fatal adult-onset neurodegenerative disease without cure or understanding of its molecular basis. It is characterized by progressive loss of spinal and upper motor neurons, but surprising resistance of cranial motor neurons until the late stages of the disease. There is no known single-gene cause of ALS, suggesting a failure of the entire cellular system to maintain proteostasis. To generate new hypotheses on the molecular differences between cranial and spinal motor neurons that underlie ALS-sensitivity, we exploited a unique platform that generates highly pure populations of induced cranial and spinal motor neurons (iCrMN and iSpMN). Exposing both iCrMNs and iSpMNs to proteotoxic stress, we monitored transcriptome and proteome changes over 36 hours and identified significant hundreds of statistically significant differences at either or both the RNA and protein level from a core set of 8,206 genes with complete data. While we observed a response to misfolding stress coordinated between transcript and protein changes, differences between the cell type were specific to RNA and protein expression. iCrMNs and iSpMNs differed in expression of many membrane proteins, including synaptic proteins, solute carriers, channels, and signaling molecules, as well as genes involved in ribosome biogenesis and subunits of the core proteasome. Differences exclusive to the transcriptome involved chaperones and the tricarboxylic acid cycle. Further, we found that the superior proteostasis capability of iCrMNs might, in part, be caused due to higher activity and abundance of the fully assembled 26S/30S proteasome in the nucleus, pointing to an increased role of ubiquitin-mediated, targeted protein degradation. The formation of the 26S/30S proteasome was highly dynamic under stress, likely mediated by a surplus of regulatory particles that attached and detached based on the action of proteasome regulators. Several lines of evidence supported this notion and described an intricate network of differentially expressed proteasome regulators and ubiquitination enzymes that defined the iCrMN- and iSpMN-specific ability to maintain proteostasis.


title: Dispersion and Plant Arrangement Condition the Timing and Magnitude of Coffee Rust Infection

abstract: One central issue in coffee-leaf rust (Hemileia vastatrix) epidemiology is to understand the role of rust dispersion on the intensity and the timing of yearly infections in coffee plantations. After reviewing the rust epidemic patterns of different sites, we present a spatially explicit and parameterized model where the host population is subdivided into discrete patches linked through spore dispersion. With this model, we study the role of the planting arrangement, the dispersion intensity and plant-level variables on the maximum average tree infection (MATI) and its timing. Our results suggest that the epidemic timeline can be divided into two phases: a time lag and a growth phase per se. The model shows that the combination of the dispersion intensity and the planting pattern modifies the MATI and the time to MATI, mainly by preventing some plants from reaching their maximum peak during the epidemic. It also affects the epidemic curves, which can have multiple peaks, or a rather smooth pattern in plots with otherwise similar conditions. The initial infection modulates the time lag and the leaf-fall rate drastically changes the MATI. These findings highlight the importance of explicitly considering the spatial aspects of coffee agroecosystems when measuring and managing rust infection.


title: Genome-wide inference reveals that feedback regulations constrain promoter-dependent transcriptional burst kinetics

abstract: Gene expression in mammalian cells is highly variable and episodic, and results in a series of discontinuous bursts of mRNAs. A challenge is understanding how static promoter architecture and dynamic feedback regulations dictate bursting on a genome-wide scale. Although single-cell RNA sequencing (scRNA-seq) provides an opportunity to address this issue, effective analytical methods are scarce. We developed an interpretable and scalable inference framework, which combined experimental data with a mechanistic model to infer transcriptional burst kinetics (sizes and frequencies) and feedback regulations. Applying this framework to scRNA-seq data generated from embryonic mouse fibroblast cells, we found Simpsons paradoxes, i.e., genome-wide burst kinetics exhibited different characteristics in two cases without and with distinguishing feedback regulations. We show that feedbacks differently modulate burst frequencies and sizes and conceal the effects of transcription start site distributions on burst kinetics. Notably, only in the presence of positive feedback, TATA genes are expressed with high burst frequencies and enhancer-promoter interactions mainly modulate burst frequencies. The developed inference method provided a flexible and efficient way to investigate transcriptional burst kinetics and the obtained results would be helpful for understanding cell development and fate decision.


title: Dissecting brain grey and white matter microstructure: a novel clinical diffusion MRI protocol

abstract: Soma and Neurite Density Image (SANDI) is an advanced diffusion magnetic resonance imaging (dMRI) signal model devised to probe in vivo microstructural information from both grey and white matter. However, this model requires multi-shell acquisitions that include b-values that are at least 6 times higher than those used in clinical practice. Here we present a 10-minute acquisition protocol that enables to acquire the necessary images for SANDI modelling on a clinical 3T scanner. We demonstrate the feasibility and assess the repeatability and reproducibility of our approach by computing microstructural metrics of SANDI and other state-of-the-art models on five healthy subjects and we present its potential clinical impact on five subjects affected by multiple sclerosis with relapsing-remitting course. Our results suggest that SANDI is a repeatable, reproducible, feasible, and practical method to characterize both white and grey matter tissues in both the healthy brain and in neurological diseases.

category: neuroscience


title: Dynamic rewiring of electrophysiological brain networks during learning

abstract: Human learning is an active and complex process. However, the brain mechanisms underlying human skill learning and the effect of learning on the communication between brain regions, at different frequency bands, are still largely unknown. Here, we tracked changes in large-scale electrophysiological networks over a 6-week training period during which participants practiced a series of visuomotor sequences during 30 home training sessions. Our findings showed that brain networks become more flexible with learning in all the frequency bands from theta to gamma ranges. We found consistent increase of flexibility in the prefrontal and limbic regions in the theta and alpha band, and over sensorimotor and visual areas in the alpha band. Specific to the beta rhythm, we revealed that higher flexibility of prefrontal regions during the early stage of learning strongly correlated with better performance measured during home training sessions. Our findings provide novel evidence that prolonged visuomotor practice results in higher, frequency-specific, temporal variability in brain network structure.


title: Neuro-cognitive models of single-trial EEG measures describe latent effects of spatial attention during perceptual decision making

abstract: Visual perceptual decision-making involves multiple components including visual encoding, attention, accumulation of evidence, and motor execution. Recent research suggests that EEG oscillations can identify the time of encoding and the onset of evidence accumulation during perceptual decision-making. Although scientists show that spatial attention improves participant performance in decision making, little is know about how spatial attention influences the individual cognitive components that gives rise to that improvement in performance. We found evidence in this work that both visual encoding time (VET) before evidence accumulation and other non-decision time process after or during evidence accumulation are influenced by spatial top-down attention, but not evidence accumulation itself. Specifically we used an open-source data set in which participants were informed about the location of a target stimulus in the visual field on some trials during a face-car perceptual decision-making task. Fitting neural drift-diffusion models to response time, accuracy, and single-trial N200 latencies (~ 125 to 225 ms post-stimulus) of EEG allowed us to separate the processes of visual encoding and the decision process from other non-decision time processes such as motor execution. These models were fit in a single step in a hierarchical Bayesian framework. Model selection criteria and comparison to model simulations show that spatial attention manipulates both VET and other non-decision time process. We discuss why spatial attention may affect other non-evidence accumulation processes, such as motor execution time (MET), and why this may seem unexpected given the literature. We make recommendations for future work on this topic.


title: Cannabinoid 1/2 Receptor Activation Induces Strain-Dependent Behavioral and Neurochemical Changes in GAERS and NEC rats

abstract:
Childhood absence epilepsy (CAE) is characterized by absence seizures which are episodes of lack of consciousness accompanied by electrographic spike-wave discharges. About 60% of children and adolescents with ASs are affected by major neuropsychological comorbidities, including anxiety. Endocannabinoids and monoamines are likely involved in the pathophysiology of these CAE psychiatric comorbidities.

Here, we show that the synthetic cannabinoid receptor type 1/2 (CB1/2R) agonist WIN 55,212-2 (2 mg/kg, i.p.) has a strain-dependent effect on anxiety-like and motor behavior and cerebral monoaminergic levels in Genetic Absence Epilepsy Rats from Strasbourg (GAERS) and their non-epileptic control (NEC) rat strain. Using quantitative and Temporal-Pattern analysis, we found that WIN 55,212-2 did not affect the emotional status of GAERS but it was anxiolytic in NEC. Conversely, WIN 55,212-2 had a sedative effect in GAERS but was ineffective in NEC. Moreover, vehicle-treated GAERS are more motivated to explore by implementing more complex and articulated strategies. These behavioral changes correlate with the reduction of 5-HT in the hippocampus and substantia nigra (SN) and noradrenaline (NA) in the entopeduncular nucleus (EPN) in vehicle-treated GAERS compared to NEC rats which could contribute to their low anxiety status and hypermotility, respectively. On the other hand, the increased level of NA in the EPN and 5-HT in the SN is consistent with an activation of the basal ganglia output-mediated motor suppression observed in WIN 55,212-2-treated GAERS rats.

These data support the view of a strain-dependent alteration of the endocannabinoid system by adding evidence of lower emotional responsiveness and a basal ganglia hypersensitivity to cannabinoids in GAERS compared to NEC rats.


title: Functionally and structurally distinct fusiform face area(s) in over 1000 participants

abstract: The Fusiform Face Area (FFA) is a widely studied region causally involved in face perception. Even though cognitive neuroscientists have been studying the FFA for over two decades, answers to foundational questions regarding the structure, function, and connectivity of the FFA from a large (N>1000) group of participants are still lacking. To fill this gap, we quantified structural, functional, and connectivity features of fusiform face-selective regions in 1080 participants in the Human Connectome Project (HCP). After manually defining over 4,000 fusiform face-selective regions, we report five main findings. First, 68.94% of hemispheres have two cortically separate regions (pFus-faces/FFA-1 and mFus-faces/FFA-2). Second, in 26.48% of hemispheres, pFus-faces/FFA-1 and mFus-faces/FFA-2 are spatially contiguous, yet functionally and structurally distinct. Third, pFus-faces/FFA-1 is more face-selective than mFus-faces/FFA-2, and the two regions have distinct functional connectivity fingerprints. Fourth, pFus-faces/FFA-1 is cortically thinner and more heavily myelinated than mFus-faces/FFA-2. Fifth, face-selective patterns and functional connectivity fingerprints of each region were more similar in monozygotic than dizygotic twins and more so than structural gradients. As we share our areal definitions with the field, future studies can explore how structural and functional features of these regions will inform theories regarding how visual categories are represented in the brain.


title: ERPs responses to dominance features from human faces

abstract: Social dominance is an important feature of social life. Dominance has been proposed to be one of two trait dimensions underpinning social judgments of human faces. Yet, the neural bases of the ability to identify different dominance levels in others based on facial features remains poorly understood. Here, we used event-related potentials (ERPs) to determine the temporal dynamics of facial dominance evaluation based on facial features signaling physical strength/weakness in humans. Twenty-seven participants performed a dominance perception task where they passively viewed faces with different dominance levels. Dominance levels did not modulate an early component of face processing, known as the N170 component, but did modulate the Late Positive Potential (LPP) component. These findings indicate that participants inferred dominance levels at a late stage of face evaluation. Furthermore, the highest level of dominant faces and the lowest level of submissive faces both elicited higher LPP amplitudes than faces with a neutral dominance level. Taken together, the present study provides new insights regarding the dynamics of the neurocognitive processes underlying facial dominance evaluation.


title: T cell cholesterol efflux suppresses apoptosis and senescence and increases atherosclerosis in middle aged mice

abstract: Atherosclerosis is a chronic inflammatory disease driven by hypercholesterolemia. During aging, T-cells accumulate cholesterol, which could lead to a pro-inflammatory phenotype. However, the role of cholesterol efflux pathways mediated by ATP-binding cassette A1 and G1 (ABCA1/ABCG1) in T-cell-dependent age-related inflammation and atherosclerosis remains poorly understood. In this study, we generated mice with T-cell-specific Abca1/Abcg1-deficiency on the low-density-lipoprotein-receptor deficient (Ldlr-/-) background. T-cell Abca1/Abcg1-deficiency decreased blood, lymph node, and splenic T-cells, and increased T-cell activation and apoptosis. T-cell Abca1/Abcg1-deficiency induced a premature T-cell aging phenotype in middle-aged (12-13 months) Ldlr-/- mice, reflected by upregulation of senescence markers. Despite T-cell senescence and enhanced T-cell activation, T-cell Abca1/Abcg1-deficiency decreased atherosclerosis and aortic inflammation in middle-aged Ldlr-/- mice, accompanied by decreased T-cells in atherosclerotic plaques. We attribute these effects to T-cell apoptosis downstream of T-cell activation. Collectively, T-cell cholesterol efflux pathways are critical for maintaining T-cell numbers, suppress senescence, and induce atherosclerosis in middle-aged Ldlr-/- mice.

category: immunology


title: Alleviation of salt stress in winter wheat by Pantoea spp. endophytes isolated from spontaneous desert plants of the Sahara

abstract: To develop bio-fertilizers for salt stress mitigation in winter wheat, 5 Pantoea spp. strains isolated from spontaneous plants of the Algerian Sahara were selected and identified based on the 16S rRNA gene, and distinguished at "strain" level by the IGS sequences. A plant test (greenhouse condition, non-sterile substrate) showed their effectiveness in promoting the growth of winter wheat cv. Gold Korn, under normal and saline conditions. An improvement of shoot length (no stress: up to +37.34% for Pantoea sp. BS27; salt stress at 200 mM: up to +32.95% for Pantoea sp. BS27) and dry weight (no stress: up to +23.89% for Pantoea sp. OT18; salt stress at 100 mM: up to +56.42 % for Pantoea sp. ME3; salt stress at 200 mM: up to 39.18% for Pantoea sp. OT18) was recorded. We suggest the Pantoea spp. strains ME3, OT37, and OT18 as promising inocula for yield improvement in salt-impacted soils.

category: microbiology


title: Photodynamic inactivation of pathogenic bacteria on human skin by applying a potent photosensitizer in a hydrogel

abstract: The antibiotic crisis increasingly threatens the health systems world-wide. Especially as there is an innovation gap in the development of novel antibiotics, treatment options for bacterial infections become fewer. The photodynamic inactivation (PDI) of bacteria appears to be a potent, new technology that may support the treatment of colonized or infected skin. In photodynamic inactivation, a dye - called photosensitizer - absorbs light and generates reactive singlet oxygen. This singlet oxygen is then capable of killing bacteria independent of species or strain and their antibiotic resistance profile. In order to provide a practical application for the skin surface, the photosensitizer was included in an aqueous hydrogel (photodynamically active hydrogel). The efficacy of this gel was initially tested on an inanimate surface and then on the human skin ex vivo. NBTC staining and TUNEL assays were carried out on skin biopsies to investigate potential harmful effects of the surface PDI to the underlying skin cells. The photosensitizer in the gel sufficiently produced singlet oxygen while showing only little photobleaching. On inanimate surfaces as well as on the human skin, the number of viable bacteria was reduced by over or nearly up to 4 log10 steps, equal to 99.99% reduction or even more. Furthermore, histological staining showed no harmful effects of the gel towards the tissue. The application of this hydrogel represents a valuable method in decolonizing human skin including the potential to act against superficial skin infections. The presented results are promising and should lead to further investigation in a clinical study to check the effectivity of the photodynamically active hydrogel on patients.


title: Bile acid-CoA:amino acid N-acyltransferase gene knockout alters early life development, the gut microbiome and reveals unusual bile acid conjugates in mice

abstract: Bile acids are steroid detergents in bile that contribute to fat absorption, cell signaling and microbiome interactions in mammals. The final step in their synthesis is amino acid conjugation with either glycine or taurine to a cholic acid or chenodeoxycholic acid backbone in the liver by the enzyme bile acid-CoA:amino acid N-acyltransferase (BAAT). Here, we describe the microbial, chemical, and physiological consequences of BAAT gene deletion in mice. BAAT-/- mice were underweight after weaning but quickly exhibited catch-up growth. At 3-weeks-of-age, KO animals had increased phospholipid excretion and decreased subcutaneous fat pad mass, glycogen staining in hepatocytes and vitamin A stores in the liver, but these phenotypes were less marked in adulthood. Their bile acid (BA) pool was highly altered throughout the 8-weeks of life but was not completely devoid of conjugated BAs. These animals had 27-fold lower amounts of taurine-conjugated BAs than wildtype in their liver, but similar concentrations of glycine-conjugated BAs and higher microbially-conjugated BAs. The BA pool in BAAT-/- was enriched in a variety of unusual bile acids that were putatively sourced from cysteamine conjugation with subsequent oxidation and methylation of the sulfur group to mimic taurine. KO mice also had an altered microbiome, but most strongly in the first 3-weeks, indicating bile acid conjugation is important for proper microbiome development during the postnatal period. Finally, antibiotic treatment increased taurine, glycine, and the unusually conjugated BAs in BAAT-/- animals, indicating the microbiome was not the likely source of the conjugation. Instead, BA conjugation in KO animals was likely derived from the peroxisomal acyltransferases ACNAT1 and ACNAT2, which are duplications of BAAT in the mouse genome, but inactivated in humans. This study demonstrates that BA conjugation is important for early life development in mice and is facilitated by other host or microbial enzymes besides BAAT in a manner that results in molecular mimics of taurine that may rescue pathological phenotypes.


title: Multishot Tomography for High-Resolution In Situ Subtomogram Averaging.

abstract: Cryo-electron tomography (cryo-ET) and subtomogram averaging (STA) can resolve protein complexes at near atomic resolution, and when combined with focused ion beam (FIB) milling, macromolecules can be observed within their native context. Unlike single particle acquisition (SPA), cryo-ET can be slow, which may reduce overall project throughput. We here propose a fast, multi-position tomographic acquisition scheme based on beam-tilt corrected beam-shift imaging along the tilt axis, which yields sub-nanometer in situ STA averages.

category: molecular biology


title: Autophagic state prospectively identifies facultative stem cells in the intestinal epithelium

abstract: The intestinal epithelium exhibits a rapid and efficient regenerative response to injury. Emerging evidence supports a model where plasticity of differentiated cells, particularly those in the secretory lineages, contributes to epithelial regeneration upon ablation of injury-sensitive stem cells. However, such facultative stem cell activity is rare within secretory populations. Here we ask whether specific functional properties predict facultative stem cell activity. We utilize in vivo labeling combined with ex vivo organoid formation assays to evaluate how cell age and autophagic state contribute to facultative stem cell activity within secretory lineages. Strikingly, we find that cell age (time elapsed since cell cycle exit) does not correlate with secretory cell plasticity. Instead, high autophagic activity predicts plasticity and resistance to DNA damaging injury independently of cell lineage. Our findings indicate that autophagic status prior to injury serves as a lineageagnostic marker for the prospective identification of facultative stem cells.

category: cell biology


title: CCDC66 regulates primary cilium length and signaling competence via multi-site interactions with transition zone and axonemal proteins

abstract: The primary cilium is a conserved microtubule-based organelle that serves as a hub for many signaling pathways. It functions as part of the centrosome/cilium complex, which also contains the basal body and the centriolar satellites. Little is known about the mechanisms by which the microtubule-based axoneme of the cilium is assembled with proper length and structure, particularly in terms of the activity of microtubule- associated proteins (MAPs) and the crosstalk between the different compartments of the centrosome/cilium complex. Here, we analyzed CCDC66, a MAP implicated in cilium biogenesis and ciliopathies affecting eye and brain. Live-cell imaging revealed that CCDC66 compartmentalizes between centrosomes, centriolar satellites, and the ciliary axoneme and tip during cilium assembly and disassembly. CCDC66 loss-of- function in human cells causes defects in cilium assembly, length and morphology. Notably, CCDC66 interacts with the MAPs and ciliopathy proteins CEP104 and CSPP1 at the cilia and cooperates with them during axonemal microtubule polymerization. Moreover, CCDC66 interacts with the transition zone protein CEP290 selectively at the centriolar satellites. Its loss disrupts basal body recruitment of transition zone proteins and IFT-B machinery and causes defective Hedgehog signaling. Overall, our results establish CCDC66 as a multifaceted regulator of the primary cilium, and propose a mechanistic insight into how the cooperation of ciliary MAPs as well as subcompartments ensures assembly of a functional cilium.


title: WDR47 facilitates cell-specific ciliogenesis by modulating intraflagellar transport

abstract: Cilia are conserved organelles found in many cell types in eukaryotes, and their dysfunction causes defects in environmental sensing and signaling transduction; such defects are termed ciliopathies. Distinct cilia have cell-specific morphologies and exert distinct functions. However, the underlying mechanisms of cell-specific ciliogenesis and regulation are unclear. Here we identified a WD40-repeat (WDR) protein, WDR47/NMTN-1, and show that it is specifically required for ciliogenesis of AWB chemosensory neurons in C. elegans. WDR47/NMTN-1 is expressed in the AWB chemosensory neuron pair, and is localized at the basal body (BB) of the AWB cilia. Knockout of wdr47/nmtn-1 specifically causes abnormal AWB neuron cilia morphology, structural integrity, and induces aberrant AWB-mediated aversive behaviors. We further demonstrate that wdr47/nmtn-1 deletion results in ciliary ultrastructure defects, and affects movement of intraflagellar transport (IFT) particles and their cargo delivery in AWB neurons. Our results indicate that WDR47/NMTN-1 is essential for AWB neuron ciliary morphology and function, which reveal a novel mechanism for cell-specific ciliogenesis. Since WDR47/NMTN-1 is conserved in mammals, our findings may help understand the process of cell-specific ciliogenesis and provide insights for treating ciliopathies.

category: developmental biology


title: Heterogeneity in the size of the apical surface of cortical progenitors

abstract: The apical surface of epithelial cells is highly specialized, it is important for morphogenetic processes that are essential to shape organs and tissues and it plays a role in morphogen and growth factor signaling. Apical progenitors in the mammalian neocortex are pseudoepithelial cells whose apical surface lines the ventricle. Whether changes in their apical surface sizes are important for cortical morphogenesis and/or other aspects of neocortex development after neurulation has not been thoroughly addressed. Here we show that apical progenitors are heterogeneous with respect to their apical surface area. In Efnb1 mutants, the size of the apical surface is modified and this correlates with discrete alterations of tissue organization without impacting proliferation or differentiation. Altogether, our data reveal heterogeneity in apical progenitors AS area in the developing neocortex and shows a role for Ephrin B1 in controlling AS size. Our study also indicates that changes in AS size does not have strong repercussion on apical progenitor behavior.


title: Pelagic seabirds reduce risk by flying into the eye of the storm

abstract:
Cyclones can cause mass mortality of seabirds, sometimes wrecking thousands of individuals. The few studies to track pelagic seabirds during cyclones show they tend to circumnavigate the strongest winds. We tracked adult shearwaters in the Sea of Japan over 11 years and find that the response to cyclones varied according to the wind speed and direction. In strong winds, birds that were sandwiched between the storm and mainland Japan flew away from land and towards the eye of the storm, flying within [≤] 30 km of the eye and tracking it for up to 8 hours. This exposed shearwaters to some of the highest wind speeds near the eye wall ([≤] 21 m s-1), but enabled them to avoid strong onshore winds in the storms wake. Extreme winds may therefore become a threat when an inability to compensate for drift could lead to forced landings and collisions. Birds may need to know where land is in order to avoid it. This provides additional selective pressure for a map sense and could explain why juvenile shearwaters, which lack a map sense, instead navigating using a compass heading, are susceptible to being wrecked. We suggest that the ability to respond to storms is influenced by both flight and navigational capacities. This may become increasingly pertinent due to changes in extreme weather patterns.

Significance StatementCyclones can cause billions of dollars of damage and loss of human life. They can also cause mass mortality and strandings in seabirds. We used GPS tracking data from streaked shearwaters breeding in the worlds most active cyclone basin to understand how seabirds respond to these systems. Birds varied their response according to the wind speed and direction, generally flying towards the eye of the cyclone in strong winds. This surprising strategy enables dynamic soaring birds to control their exposure to risky wind vectors that could drift them onshore. Nonetheless, birds may need to know where land is in order to avoid it. Juveniles lack this "map sense", making them susceptible to wrecking in some scenarios.

category: ecology


title: Drought selection on Arabidopsis populations and their microbiomes

abstract: Microbes affect plant health, stress tolerance1 and life history2. In different regions of the globe, plants are colonized by distinct pathogenic and commensal microbiomes, but the factors driving their geographic variation are largely unknown3. We identified and measured the core leaf microbiome of Arabidopsis thaliana in its native range, from almost 300 populations across Europe. Comparing the distribution of the approximately 500 major bacterial phylotypes, we discovered marked, geography-dependent differences in microbiome composition within A. thaliana and between A. thaliana and other Brassicaceae, with two distinct microbiome types segregating along a latitudinal gradient. The differences in microbiome composition mirror the spatial genetics of A. thaliana, with 52-68% of variance in the first two principal coordinates of microbiome type explained by host genotype. Microbiome composition is best predicted by drought-associated metrics that are well known to be a major selective agent on A. thaliana populations. The reproducible and predictable associations between specific microbes and water availability raise the possibility that drought not only directly shapes genetic variation in A. thaliana, but does so also indirectly through its effects on the leaf microbiome.


title: Growth limitation via chemically complex carbohydrates reduces sensitivity of synthetic human gut communities to perturbations

abstract: Dietary fiber affects the composition and functions of microbial communities that reside in the human gut. However, we lack a detailed and quantitative understanding of how these nutrients shape microbial community dynamics, interaction networks and systems-level properties. Using synthetic human gut communities coupled to computational modeling, we dissect the effects of varied fiber types or their constituent sugars on community assembly and sensitivity to perturbations. By quantifying carbohydrate chemical complexity, we demonstrate that microbial growth decreases as a function of complexity. We further demonstrate that the balance of species occupying distinct metabolic niches is altered by the presence of chemically complex carbohydrates. The frequency of negative inter-species interactions is reduced in the presence of complex carbohydrates. Communities grown in complex carbohydrates reproducibly assemble from a wide range of initial species abundances and display reduced sensitivity to invasion. Resource competition is identified as a key mechanism influencing the response of communities to perturbations. The strength of resource competition can promote sensitivity of community assembly to variations in initial species proportions and impact community resistance to invasion. By limiting microbial growth, complex carbohydrates promote the expansion of species occupying niches beyond carbohydrate utilization, shape the distribution of inter-species interactions, which in turn determines the communitys response to perturbations.


title: Molecular mechanisms of microbiome modulation by the diatom secondary metabolite azelaic acid

abstract: Photosynthetic eukaryotes, such as plants and microalgae, modulate their microbiome using the dicarboxylate metabolite azelaic acid (Aze), a molecule that is used as a carbon source for some heterotrophs but is toxic to others. Uptake and assimilation mechanisms of Aze into bacterial cells are mostly unknown, nor its ability to promote or inhibit growth. Here, we use transcriptomics, isotope labeling, and coexpression networks of master transcriptional factors in two marine bacteria to identify the first putative Aze transporter in bacteria, map Aze catabolism through fatty acid degradation and downstream pathways, infer Aze toxicity to the ribosome, and show that Aze catabolism is restricted to 13 bacterial families across terrestrial and marine ecosystems dominated by algal and plant symbionts. Seawater mesocosms amended with Aze enrich for bacterial families that are able to catabolise Aze. These findings shed light on the role of infochemicals in modulating eukaryote-microbiome interactions across diverse ecosystems.


title: On the evolutionary trade-off between growth anddispersal during a range expansion

abstract: Eco-evolutionary processes play a key role shaping the invasion dynamics of populations expanding in new habitats. The expansion process is driven by co-evolving species traits, in particular, those traits related to body dimensions, competitive skills, movement abilities controlling also their responses to landscape heterogeneity gradients. Typically, individuals who invest more in the development of their traits related to the dispersal strategy reduce investment in reproduction. Thus, there are two possible trading-off eco-evolutionary strategies: growing faster or dispersing faster (R - D trade-off). We explore the spreading dynamics of a consumer species exploiting a resource in a heterogeneous environment through a reaction-diffusion model. We focus on the co-evolution of growth rate and dispersal traits for assessing the phenotype having the highest spreading speed and leading the expansion front. We evaluate spreading properties numerically and analytically, when theoretical formulas are available. We found that the perfect symmetry of the effects of growth and dispersal on the speed of propagation is broken in the presence of competition between phenotypic traits. While the latter tends to favor R-strategies in spatially homogeneous environments, D-strategies become more effective in certain heterogeneous configurations, especially when heterogeneities affect dispersion.

category: evolutionary biology


title: Diversity and evolution of telomere and subtelomere DNA sequences in insects

abstract:
In insects, two types of telomere length maintenance are known: telomerase-dependent, resulting in chromosome ends consisting of short nucleotide repeats (typically TTAGG), and telomerase-independent, resulting in chromosome ends consisting of long nucleotide repeats or transposon-like elements. However, only a few species have been previously studied with regard to their telomere DNA sequences. Here, based on analysis of chromosome-level genome assemblies, I present the data on telomere and subtelomere organization for 180 species from 148 genera, 53 families and 8 orders of insects.

Analysis of these taxa reveals that in fact chromosome ends of most insect species have an intermediate structure and consist of numerous arrays of short telomeric repeats interspersed with telomere-specific non-LTR retrotransposons. An unexpectedly high level of diversity of short telomeric motifs (22 variants ranging in length from 1 to 17 nucleotides) is documented. Telomeres consisting of long repeats (from 173 to 374 bp) are confirmed for flies (the order Diptera) and also found in the orders Odonata and Hymenoptera. The most unusual telomere structure is found in the bee Lasioglossum lativentre, in which the chromosomes possess the short telomeric repeat TTAGGTCTGGG at only one end, whereas opposing ends terminate with medium and long repeats.

I conclude that different types of telomere organization and numerous variants of long and short T-containing motifs, including the (T)n mononucleotide sequence, are compatible with the performance of telomere functions. I argue that both telomerase-dependent and telomerase-independent mechanisms for maintaining telomere length operate simultaneously in many insects. The balance between them and the exchange of sequences between telomeres and subtelomeres are most likely the key factors that determine the structure and evolution of telomeres.

SignificanceMultilayer telomeres, resulted from numerous, site-specific insertions of retrotransposons into the region of short telomeric repeats, are not an aberrant type of organization, as previously thought. They are widely distributed among insects and can represent up to 30-40 % of eukaryotic species diversity. Accordingly, the telomere maintenance mechanism based on the joint work of telomerase-dependent and telomerase-independent mechanisms can also be extremely widespread in nature.


title: Multiple mating rescues offspring sex ratio but not productivity in a haplodiploid exposed to developmental heat stress

abstract:
O_LIReproduction is generally more sensitive to high temperatures than survival and arguably a better predictor of the response of populations to climate change than survival estimates. Still, how temperature simultaneously impacts male and female reproductive success, the mating system and the operational sex ratio remains an open question.
C_LIO_LIHere, we addressed how a sublethal high temperature affects the reproductive system of the spider mite Tetranychus urticae. Males and females maintained at 25{degrees}C or 36{degrees}C during development were paired and the fertility of both sexes, their mating and remating eagerness, and the paternity of the offspring of females with different mating histories were measured.
C_LIO_LIThere was a decrease in female and male fertility at 36{degrees}C compared to 25{degrees}C that resulted in lower offspring production and a more male-biased sex ratio, respectively, because spider mites are haplodiploids. However, when females remated, the pattern of first male sperm precedence typically seen in this species was disrupted, with more than one male contributing to the offspring. This was accompanied by reduced mating eagerness in pairs with partially sterile males and increased remating eagerness in pairs in which at least one sex was partially sterile in the first mating.
C_LIO_LIThe observed temperature-induced changes in pre- and post-copulatory traits allowed restoring the offspring sex ratio but did not lead to the recovery of offspring number.
C_LIO_LIOur results show that temperature induces changes in the spider mite mating behaviour and mating system, with potential impact on sexual selection and sexual conflict. However, such changes may not be sufficient to buffer the impact of extreme temperatures on their populations.
C_LI


title: Evolutionary history mediates population response to rapid environmental change through within-generational and transgenerational plasticity

abstract: Rapid environmental change is affecting many organisms; some are coping well but many species are in decline. A key mechanism for facilitating success following environmental change is phenotypic plasticity. Organisms use cues to respond phenotypically to environmental conditions; many incorporate recent information (within-generation plasticity) and information from previous generations (transgenerational plasticity). We extend an existing evolutionary model where organisms utilize within-generational plasticity, transgenerational plasticity, rapid evolution, and bet-hedging. We show how, when rapid evolution of plasticity is not possible, the effect of environmental change (altering the environment mean, variance, or autocorrelation, or cue reliability) on population growth rate depends on selection for within-generation plasticity and transgenerational plasticity under historical environmental conditions. We then evaluate the predictions that populations adapted to highly variable environments, or with greater within-generational plasticity, are more likely to successfully respond to environmental change. We identify when these predictions fail, and show environmental change is most detrimental when previously reliable cues become unreliable. When multiple cues become unreliable, environmental change can cause deleterious effects regardless of the populations evolutionary history. Overall, this work provides a general framework for understanding the role of plasticity in population responses to rapid environmental change.


title: Evolution of selfish multicellularity: collective organisation of individual spatio-temporal regulatory strategies

abstract:
Recent studies have shown that many major signalling pathways involved in embryonic development are ancient, and likely evolved before or at the onset of multicellularity. In the unicellular ancestors, these pathways may have been involved in regulating their ecological interactions. To understand the early evolution of development, we therefore need to study how the ancestral genetic toolkit was co-opted to coordinate nascent multicellularity in this ecology-to-development transition.

We construct an evolutionary cell-based model in which cells use their genetic toolkit to compete for resources in a spatially structured environment. First, we let unicellular ancestors evolve a genetic toolkit that enables them to survive by regulating their behaviour in response to the environment. Then, when adhesion can evolve, we find that adhering groups of cells interpret environmental cues more effectively than their unicellular ancestors, which enables them to locate resources more quickly - this selects for multicellularity. Once cells have evolved multicellularity, their genetic toolkit evolves to a drastically different strategy from the unicellular ancestor, resulting in striking patterns of spatio-temporal cell state changes that visually resemble animal development. Surprisingly, these coordinated patterns are not a consequence of cells cooperating with each other. Rather, they result from cells using their genetic toolkit to compete with other cells in the cluster, selfishly maximising their own reproductive success.

Our model demonstrates how emergent selection pressures at the onset of multicellularity can drive the evolution of the ecological interactions between cells to give rise to developmental pattern formation.


title: An oligogenic inheritance test detects risk genes and their interactions in congenital heart defects and developmental comorbidities

abstract: Exome sequencing of thousands of families has revealed many individual risk genes for congenital heart defects (CHD), yet most cases cannot be explained by a single causal mutation. Further, those who carry de novo and inherited mutations in known risk genes often demonstrate variable phenotypes even within the same family, indicating the presence of genetic modifiers. To explore oligogenic causes of CHD without assessing billions of variant combinations, we developed an efficient, simulation-based method to detect gene sets that carry damaging variants in probands at a higher rate than expected given parental genotypes. We implemented this approach in software called Gene Combinations in Oligogenic Disease (GCOD) and applied it to a cohort of 3382 trios with exome sequencing. This analysis detected 353 high-confidence risk genes in 202 pairs that appear together in multiple probands but rarely or never appear in combination in their unaffected parents. Stratifying analyses by specific CHD diagnosis and considering gene combinations of higher orders yielded an additional 244 gene sets. The oligogenic genes we discovered cluster in pathways specific to heart development and suggest new molecular disease mechanisms, such as arylsulfatase activity and de novo nucleotide biosynthesis. Finally, by combining CHD families with an autism spectrum disorder cohort, we were able to detect 925 oligogenic sets transmitted in renal disease, a known co-morbidity of both conditions. As genome sequencing is applied to more families and other disorders, GCOD will enable detection of increasingly large, novel gene combinations, shedding light on combinatorial causes of genetic diseases.

category: genetics


title: Droplet array-based platform for parallel optical analysis of dynamic extracellular vesicle secretion from single cells

abstract: Extracellular vesicles (EVs) are essential intercellular communication tools, but the regulatory mechanisms governing heterogeneous EV secretion are still unclear due to the lack of methods for precise analysis. Monitoring the dynamics of secretion from individually isolated cells is crucial because, in bulk analysis, secretion activity can be perturbed by cell-cell interactions, and a cell population rarely performs secretion in a magnitude- or duration-synchronized manner. Although various microfluidic techniques have been adopted to evaluate the abundance of single-cell-derived EVs, none can track their secretion dynamics continually for extended periods. Here, we have developed a droplet array-based method that allowed us to optically quantify the EV secretion dynamics of >300 single cells every 2 hours for 36 hours, which covers the cell doubling time of many cell types. The experimental results clearly show the highly heterogeneous nature of single-cell EV secretion and suggest that cell division facilitates EV secretion, showing the usefulness of this platform for discovering EV regulation machinery.

category: bioengineering


title: TIGER: A Web Portal of Tumor Immunotherapy Gene Expression Resource

abstract: Immunotherapy is a promising cancer treatment method, but only a few patients benefit from it. Developing new immunotherapy strategies and effective biomarkers of response and resistance is urgent. Recent high-throughput bulk and single-cell gene expression profiling technologies have generated valuable resources in these regards. However, these resources are not well organized and systematic analysis is difficult. Here, we present TIGER, a tumor immunotherapy gene expression resource, which contains bulk transcriptome data of 1508 tumor samples with immunotherapy clinical outcome and 11,057 tumor/normal samples without immunotherapy clinical outcome, as well as single-cell transcriptome data of 2,116,945 immune cells of 655 samples. TIGER provides many useful modules to analyze the collected data and user-provided data. Using the resource in TIGER, we identified a tumor enriched subset of CD4+ T cells. Melanoma patients with higher signature score of this subset have significantly better response and survival under immunotherapy. We believe that TIGER will be helpful for understanding anti-tumor immunity mechanisms and discovering effective biomarkers. TIGER is freely accessible at http://tiger.canceromics.org/.

category: bioinformatics


title: Sequence Analysis of WRKY Transcription Factor Family in Dendrobium officinale

abstract: WRKY transcription factors are a key class of plant regulators that regulate Dendrobium growth, development, and stress tolerance. In this work, 74 Dendrobium WRKY genes were found in the Dendrobium whole genome file using tbtools software, hmmer3.0 software, pfam website, mega6.0 software, genedoc software, meme online analysis website, and other tools, and tbtools software was utilized after amino acid alignment. A phylogenetic tree of the Dendrobium and Arabidopsis WRKY transcription factors sequence alignment was built, as well as the chromosomal location, gene structure analysis, conserved domain analysis, and cis-acting element analysis of the Dendrobium WRKY gene. The phylogenetic tree comparison analysis revealed that Dendrobium WRKY transcription factors were classified into three groups: I, II, and III, with Group II subdivided into five subgroups: II-a, II-b, II-c, II-d, and II-e. According to amino acid alignment research, the Dendrobium WRKY transcription factor contains a highly conserved WRKYGQK sequence. According to gene chromosomal mapping, the Dendrobium WRKY gene was found to be irregularly distributed across many chromosomes of Dendrobium officinale. Introns vary greatly in terms of quantity and starting place. According to conserved domain analysis, the Dendrobium WRKY gene comprised diverse patterns in number and species, but all had the conserved domain WRKYGQK, and there were certain distinguishing motifs amongst subfamilies. Elements with a cis-action It was found that the Dendrobium WRKY gene has a lot of cis-acting elements, like light response, low temperature stress response, drought response, hormone response, growth differentiation responses.


title: DeepTMHMM predicts alpha and beta transmembrane proteins using deep neural networks

abstract: Transmembrane proteins span the lipid bilayer and are divided into two major structural classes, namely alpha helical and beta barrels. We introduce DeepTMHMM, a deep learning protein language model-based algorithm that can detect and predict the topology of both alpha helical and beta barrels proteins with unprecedented accuracy. DeepTMHMM (https://dtu.biolib.com/DeepTMHMM) scales to proteomes and covers all domains of life, which makes it ideal for metagenomics analyses.


title: Weighted Kernels Improve Multi-Environment Genomic Prediction

abstract: Crucial to variety improvement programs is the reliable and accurate prediction of genotypes performance across environments. However, due to the impactful presence of genotype by environment (GxE) interaction that dictates how changes in expression and function of genes influence target traits, prediction performance of genomic selection (GS) using single-environment models often falls short. Furthermore, despite the successes of genome-wide association studies (GWAS), the genetic insights derived from genome-to-phenome mapping have not yet been incorporated in predictive analytics, making GS models that use Gaussian kernel primarily an estimator of genomic similarity, instead of the underlying genetics characteristics of the populations. Here, we developed a GS framework that, in addition to capturing the overall genomic relationship, can capitalize on the signal of genetic associations of the phenotypic variation as well as the genetic characteristics of the populations. The capacity of predicting the performance of populations across environments was demonstrated by an overall gain in predictability up to 31% for the winter wheat DH population. Compared to Gaussian kernels, we showed that our multienvironment weighted kernels could better leverage the significance of genetic associations and yielded a marked improvement of 4-33% in prediction accuracy for half-sib families. Furthermore, the flexibility incorporated in our Bayesian implementation provides the generalizable capacity required for predicting multiple highly genetic heterogeneous populations across environments, allowing reliable GS for genetic improvement programs that have no access to genetically uniform material.


title: NS1 from Two Zika Virus Strains Differently Interact with a Membrane: A Plausible Explanation for their Differential Virulence

abstract:
Zika virus (ZIKV) from Uganda (UG) expresses a phenotype related to fetal loss whereas the variant from Brazil (BR) induces microcephaly in neonates. The differential virulence has a direct relation to biomolecular mechanisms that make one strain more aggressive than the other. The non-structural protein 1 (NS1) is a key viral toxin to comprehend these viral discrepancies because of its versatility in many processes of the virus life cycle. Here, we aim to examine through coarse-grained models and molecular dynamics simulations the protein-membrane interactions for both NS1ZIKV-UG and NS1ZIKV-BR dimers. A first evaluation allowed us to establish that the NS1 proteins, in the membrane presence, explore new conformational spaces when compared to systems simulated without a lipid bilayer. These events derive from both differential coupling patterns and discrepant binding affinities to the membrane. The N-terminal domain, intertwined loop, and greasy finger proposed previously as binding membrane regions were also computationally confirmed by us. The anchoring sites have aromatic and ionizable residues that manage the assembly of NS1 toward the membrane, especially for the Ugandan variant. Furthermore, the protein-membrane interaction induces perturbation in the distal part related to putative epitopes. These results open up new strategies for the treatment of flaviviruses.

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title: Probing the Drug Dynamics and Mode-of-Action of Chemotherapeutics Using Metasurface-Enhanced Infrared Reflection Spectroscopy of Live Cells

abstract: Infrared spectroscopy has drawn considerable interests in biological applications, but the measurement of live cells is impeded by the attenuation of infrared light in water. Metasurfaceenhanced infrared reflection spectroscopy (MEIRS) had been shown to mitigate the problem, enhance the cellular infrared signal through surface-enhanced infrared absorption, and encode the cellular vibrational signatures in the reflectance spectrum at the same time. In this study, we used MEIRS to study the dynamic response of live cancer cells to a newly developed chemotherapeutic metal complex with distinct modes of action (MoAs): tricarbonyl rhenium isonitrile polypyridyl (TRIP). MEIRS measurements demonstrated that administering TRIP resulted in long-term (several hours) reduction in protein, lipid, and overall refractive index signals, and in short-term (tens of minutes) increase in these signals that was consistent with the induction of endoplasmic reticulum stress. The unique tricarbonyl IR signature of TRIP in the bio-orthogonal spectral window was monitored in real time, and was used as an infrared tag to detect the precise drug delivery time that was shown to be closely correlated with the onset of the phenotypic response. These results demonstrate that MEIRS is an effective label-free real-time cellular assay capable of detecting and interpreting the early phenotypic responses of cells to IR-tagged chemotherapeutics.

category: biophysics


title: Saccades are locked to the phase of alpha oscillations during natural reading

abstract:
We saccade three to five times per second when reading. However, little is known about the neuronal mechanisms coordinating the oculomotor and visual system during such rapid processing. Here we ask if brain oscillations play a role in the temporal coordination of the visuomotor integration. We simultaneously acquired MEG and eye-tracking data while participants read sentences silently. Every sentence was embedded with target words of either high or low lexical frequency. Our key finding demonstrated that saccade onsets were locked to the phase of alpha oscillations (8 - 13 Hz); in particular, for saccades towards low-frequency words. Source modelling demonstrated that the alpha oscillations to which the saccades were locked, were generated in the right-associative visual cortex (BA 19). Our findings suggest that the alpha oscillations serve to time the processing between the oculomotor and visual systems during natural reading, and that this coordination becomes more pronounced for demanding words.

Significance StatementReading is an essential skill in modern society that allows us to acquire information from written language. While we effortlessly can acquire the meaning of a text, the task of reading requires precisely timed saccades as our eyes jump from word to word. By using a natural reading task, we demonstrate that the coordination between saccades and visual processing is clocked by ongoing ~10 Hz alpha oscillations in the visual cortex. The clocking of the saccades by brain oscillations became particularly pronounced when the participants made saccades to demanding words.

category: physiology


title: Polerovirus N-terminal readthrough domain structures reveal novel molecular strategies for mitigating virus transmission by aphids

abstract: Poleroviruses, enamoviruses, and lutoeviruses are icosahedral, positive sense RNA viruses that cause economically important diseases in food and fiber crops. They are transmitted by phloem-feeding aphids in a circulative manner that involves the movement across and within insect tissues. The N-terminal portion of the viral readthrough domain (NRTD) has been implicated as a key determinant of aphid transmission in each of these genera. Here, we report crystal structures of the NRTDs from the poleroviruses turnip yellow virus (TuYV) and potato leafroll virus (PLRV) at 1.53-[A] and 2.22-[A] resolution, respectively. These adopt a two-domain arrangement with a unique interdigitated topology and form highly conserved dimers that are stabilized by a C-terminal peptide that is critical for proper folding. We demonstrate that the PLRV NRTD can act as an inhibitor of virus transmission and identify NRTD mutant variants that are lethal to aphids. Sequence conservation argues that enamovirus and luteovirus NRTDs will follow the same structural blueprint, which affords a novel approach to block the spread of these agricultural pathogens in a generalizable manner.


title: Learning-related congruent and incongruent changes of excitation and inhibition in distinct cortical areas

abstract: Excitatory and inhibitory neurons in diverse cortical regions are likely to contribute differentially to the transformation of sensory information into goal-directed motor plans. Here, we investigate the relative changes across mouse sensorimotor cortex in the activity of putative excitatory and inhibitory neurons - categorized as regular or fast spiking according to their action potential waveform - comparing before and after learning of a whisker detection task with delayed licking as perceptual report. Surprisingly, we found that the whisker-evoked activity of regular versus fast spiking neurons changed in opposite directions after learning in primary and secondary whisker motor cortices, while it changed similarly in primary and secondary orofacial motor cortices. Our results suggest that changes in the balance of excitation and inhibition in local circuits concurrent with changes in the long-range synaptic inputs in distinct cortical regions might contribute to performance of delayed sensory-to-motor transformation.


title: Hypothalamic gene network dysfunction is associated with cognitive decline and body weight loss in Alzheimer's disease mice

abstract: Recent studies, both clinical and experimental, indicate that many neurodegenerative disorders including Alzheimers disease (AD) often display coexisting metabolic dysfunctions, which may exacerbate neurological symptoms. The hypothalamus is a brain region highly involved in maintaining metabolic and other homeostatic processes and is known to be involved in the etiology of AD, although the role of hypothalamic dysfunction in the onset, progression, and severity of AD is poorly understood. In this study, we demonstrate that our new model of genetic diversity in AD, the AD-BXDs, exhibits non-cognitive symptoms consistent with hypothalamic dysfunction and examined hypothalamic bulk RNA sequencing data in the AD-BXD panel to investigate how the AD transgene impacts gene expression profiles in the hypothalamus. Mostly notably, we identified strong neuroinflammatory signatures from the hypothalamus in the AD-BXDs as early as six months of age. A functionally unknown WGCNA module showed correlation to female body weight and contextual fear acquisition. Eigengene expression of microglial/macrophagic modules and their hub gene expressions were correlated to cognitive phenotypes. From these analyses, we nominated Plek and Laptm5 as new targets to attenuate neuroinflammation in AD.


title: Polymer physics-based classification of neurons

abstract: Recognizing that diverse morphologies of neurons are reminiscent of structures of branched polymers, we put forward a principled and systematic way of classifying neurons that employs the ideas of polymer physics. In particular, we use 3D coordinates of individual neurons to calculate the form factor, F(q), a Fourier transform of density-density correlation of particles comprising an object of interest. For a polymer-like object consisting of n monomers, F(q) scales with the wavenumber q as [Formula] at an intermediate range of q, where [Formula] is the fractal dimension or the inverse scaling exponent [Formula] characterizing the geometrical feature (r ~ n{nu}) of the object over a length scale r(= 2{pi}/q). F(q) can be used to describe a neuron morphology in terms of its size (Rn) and the extent of branching quantified by [Formula]. By assessing the similarity between F(q)s calculated for a set of neurons, we tackle the neuron classification problem. Our F(q)-based classification, applied to publicly available neuron datasets from three different organisms, not only complements other classification methods but also offers a physical picture of how the dendritic and axonal branches of an individual neuron fill the space of dense neural networks inside the brain.


title: Intrinsically photosensitive retinal ganglion cells evade temporal filtering to encode environmental light intensity

abstract: The retina encodes environmental light intensity to drive innate physiological responses. The synaptic basis of such coding remains obscure. Intrinsically photosensitive retinal ganglion cells (ipRGCs) are the only retinal output neurons stably encoding intensity. They do so even without their melanopsin photopigment, so specializations in their synaptic drive from bipolar cells (BCs) must also contribute. Here, we shed new light on mechanisms responsible for this unique intensity-coding drive. By ultrastructural reconstruction, we show that specific BC types and unusual ribbon synapses carry photoreceptor signals to ipRGCs. By glutamate imaging and electrophysiology, we show that their light responses are unusually persistent. Still, we find that virtually all BCs encode intensity. Intensity coding becomes restricted to ipRGCs primarily because other RGCs filter out steady-state intensity signals postsynaptically. Thus, neural "pinholes" in global, persistent neural "masking" allow intensity signals to be encoded by ipRGCs and sent to specific centers of the visual brain.


title: Mechanistic Neural Mass Modeling: from physiology to pathophysiological brain activity

abstract: Brain rhythms emerge from the mean-field activity of networks of neurons. There have been many efforts to build mathematical and computational embodiments in the form of discrete cell-group activities - termed neural masses - to understand particular the origins of evoked potentials, intrinsic patterns of activities such as theta, regulation of sleep, Parkinsons disease related dynamics, and instabilities such as seizure dynamics. As originally utilized, standard neural masses convert input through a sigmoidal function to a firing rate, and firing rate through a synaptic alpha function to other masses. Here we define a process to build almost from first principles (i.e. Hodgkin Huxley type models) mean field models of different neuron types that duplicate the stability, firing rate, and associated bifurcations as function of relevant slow variables - such as extracellular potassium - and synaptic current; and whose output is both firing rate and impact on the slow variables - such as transmembrane potassium flux. Small networks composed of just excitatory and inhibitory masses demonstrate expected dynamical states including stable firing, runaway excitation and depolarization block, and these transitions change in biologically observed ways with changes in extracellular potassium and excitatory-inhibitory balance.


title: Phosphorylation of the novel mTOR substrate Unkempt regulates cellular morphogenesis

abstract:
Mechanistic target of rapamycin (mTOR) is a protein kinase that integrates multiple inputs to regulate anabolic cellular processes. mTOR has key functions in nervous system development and mis-regulation of mTOR signalling causes aberrant neurodevelopment and results in neurological disease. Very little is understood about the signalling components that act downstream of mTOR to regulate neuronal development and morphogenesis. Here we show that the RNA-binding protein Unkempt, which is primarily expressed in the nervous system, is a novel substrate of mTOR complex I (mTORC1). Unkempt phosphorylation is regulated by nutrient levels and growth factors via mTORC1. Unkempt physically interacts with and is directly phosphorylated by mTORC1 through binding to the regulatory-associated protein of mTOR, Raptor. Phosphorylation of Unkempt during nervous system development is mTORC1-dependent, suggesting that Unkempt is a key mTORC1 substrate in the developing brain. Unkempt phosphorylation by mTORC1 occurs largely within a highly serine-rich intrinsically disordered region. Mutation analysis of key serine/threonine residues in the serine-rich region indicates that phosphorylation inhibits the ability of Unkempt to induce early bipolar neuronal-like morphology. Phosphorylation within this serine-rich region thus profoundly affects the ability of Unkempt to regulate cellular morphogenesis. Our findings reveal a molecular link between mTOR signalling and cellular morphogenesis and shed new light on this critical aspect of nervous system development.

Significance StatementMechanistic target of rapamycin (mTOR) signalling regulates a variety of key cellular processes, but we understand little about the cell and tissue specificity of this pathway at the molecular level. mTOR signalling is particularly important in nerve cells, regulating their development. We have identified a novel substrate of mTOR complex I (mTORC1) in nerve cells, called Unkempt. Unkempt physically interacts with and is directly phosphorylated by mTORC1 in cultured nerve cells and during nervous system development. We show that phosphorylation dramatically alters the ability of Unkempt to regulate cell shape. Unkempt provides a new entry point to understand mTOR signalling in the nervous system at the molecular level.


title: A distributed and efficient population code of mixed selectivity neurons for flexible navigation decisions

abstract: Decision-making requires flexibility to rapidly switch sensorimotor associations depending on behavioral goals stored in memory. We identified cortical areas and neural activity patterns that mediate this flexibility during virtual-navigation, where mice switched navigation toward or away from a visual cue depending on its match to a remembered cue. An optogenetics screen identified V1, posterior parietal cortex (PPC), and retrosplenial cortex (RSC) as necessary for accurate decisions. Calcium imaging revealed neurons that can mediate rapid sensorimotor switching by encoding a conjunction of a current and remembered visual cue that predicted the mouses navigational choice from trial-to-trial. Their activity formed efficient population codes before correct, but not incorrect, choices. These neurons were distributed across posterior cortex, even V1, but were densest in RSC and sparsest in PPC. We propose the flexibility of navigation decisions arises from neurons that mix visual and memory information within a visual-parietal-retrosplenial network, centered in RSC.


title: Assessing TMS-evoked cognitive network responses depending on neurocognitive and oscillatory brain state: A simultaneous TMS-EEG-fMRI project

abstract: Human cognition arises from information exchange within and between functionally connected brain networks. Alterations in such signal propagation across networks are linked to numerous disorders. Brain-wide signal propagation can be experimentally studied with simultaneous transcranial magnetic stimulation (TMS) and functional magnetic resonance imaging (fMRI), where TMS pulses introduce a signal at a certain network node and fMRI charts its propagation through the network. Yet, this approach ignores the fact that the (network) impact of a TMS pulse depends on brain state, where brain state fluctuates spontaneously from moment to moment (e.g. oscillatory state) as well as depending on what a participant does (neurocognitive state). Here, we assessed TMS-evoked fMRI activations as a function of neurocognitive state (eyes open versus eyes closed in complete darkness) and oscillatory state (low versus high pre-TMS alpha power, as measured with simultaneous electroencephalography (EEG)). We applied supra-versus sub-threshold triple-pulse TMS to the right posterior parietal cortex in eight participants, while simultaneously recording EEG and fMRI during two different ocular states. In this first application of the multimodal TMS-EEG-fMRI paradigm to a cognitive network hub, we did not find evidence for a brain state modulation of TMS-induced signal propagation. Instead, we found state-independent TMS-evoked fMRI responses mostly in sensory areas such as the insula, superior temporal gyrus, anterior cingulate cortex, and thalamus, but also in the frontal eye fields. Interestingly, neurocognitive state did seem to modulate the fMRI response to indirect TMS effects such as sensory stimulation. These results lead to several important insights for future cognitive multimodal TMS experiments.


title: A Spiking Neural Network Model for the Control of Oscillatory Phase Differences Between Multiple Brain Areas

abstract: The causal mechanisms which underlie rapid, transient, and dynamic coordination of large-scale functional brain networks remain unknown. Neuronal oscillations have been hypothesized to play a critical role influencing long-range communication between brain areas, with oscillatory phase differences influencing the effective connectivity between areas (Fries, 2005). However, it remains unclear how networks of spiking neurons could causally and mechanistically control the relative phase difference between cortical regions. Here we describe a simple model of spiking neurons that can dynamically control the relative phase differences between multiple brain areas. The model applies to any inhibition-based rhythm, and has four essential elements: a) tonic excitation of local recurrent networks of excitatory and inhibitory cells produces oscillations (Borgers et al., 2012); b) winner-take-all (WTA) dynamics permit only a small fraction of cells to fire on any given cycle (de Almeida et al., 2009); c) di-synaptic feed-forward inhibition leads to oscillatory phase resetting in a target area (Traub et al., 1996); and d) the range of conduction delays for inter-regional axonal projections span the duration of one oscillatory cycle (Swadlow, 1998). The key assumption of our model is to link WTA dynamics to conduction delays, such that only axons with a narrow range of delays are active at one time and are selected via local activity. Phase resetting in the target area converts this conduction delay into a specific phase difference. Thus, the model converts local differences in cellular excitation into inter-areal phase differences via WTA dynamics and feed-forward inhibition, where excitatory cells act as phase difference effectors or detectors. Including several WTA modules within a given area allows it to serve as a coordinating hub, controlling the relative phase differences of multiple distributed brain regions. Finally, we show how this model can help explains recent empirical results showing that individual neurons are sensitive to the relative phase difference between areas (Canolty et al., 2010).


title: K2P channel TWK-40 Regulates a Rhythmic Behavior in C. elegans

abstract: Background potassium (K+) currents, conducted by two-pore domain K+ (K2P) channels, are critical for the stabilization of the membrane potential. The effect of K2P channels on motor rhythm remains enigmatic. We show here that the K2P TWK-40 regulates the rhythmic defecation motor program (DMP) in Caenorhabditis elegans. Disrupting TWK-40 suppresses the expulsion defects of nlp-40 and aex-2 mutants. By contrast, a gain-of-function (gf) mutant of twk-40 significantly reduces the expulsion frequency per DMP cycle. In situ whole-cell patch clamping demonstrates that TWK-40 forms an outward current that hyperpolarize the resting membrane potential of DVB neuron. In addition, TWK-40 substantially contributes to the rhythmic activity of DVB. Specifically, DVB Ca2+ oscillations exhibit obvious defects in twk-40 mutants. Expression of TWK-40(gf) in DVB recapitulates the expulsion deficiency of the twk-40(gf) mutant, and inhibits DVB Ca2+ oscillations in both wild-type and twk-40(lf) animals. Moreover, DVB innervated enteric muscles also exhibit rhythmic Ca2+ defects. Taken together, these results demonstrate that TWK-40 is an essential inhibitor of DMP, thus revealing a cellular mechanism linking K2P channels with rhythmic motor activity.


title: Growth form matters: crustose lichens are sensitive to forest management on dead wood

abstract: Lichens have a vital role in forest ecosystems and they are a threatened group in boreal forests. However, the conservation ecology of the total lichen community has very rarely been studied. Here we studied lichen species and communities, including macrolichens (= foliose and fruticose growth forms) and rarely studied crustose lichens, on decaying wood in boreal spruce-dominated forests in Finland. We also studied obligate lignicoles that grow only on dead wood and are mostly crustose in growth form. Species richness and community composition were examined on decaying logs and natural or cut stumps of Picea abies at different decay stages (2-5) in 14 stands, half of which were natural or seminatural and half recently managed. We used thorough search to yield a species list as close to complete as possible. Our study questions were: 1) Are species richness and lichen communities different in natural and managed forests, and if so, are there differences between macrolichens, crustose lichens and obligate lignicoles in how they respond to forest management? 2) How does the decay stage and dead wood type affect the lichens, i.e. are there differences between stumps and logs? We found a total of 127 lichen species. Most (75%) of the recorded lichen species were crustose. With a generalized linear model we found that crustose lichens and obligate lignicoles had a higher species richness in natural than managed forests, but macrolichen richness was not significantly affected by forest management. Utilizing non-metric multidimensional scaling we discovered that site level community composition of macrolichens, crustose lichens and obligate lignicoles was also significantly different between natural and managed forests. We found that on dead wood unit level the decay stage had a significant effect on species richness and community composition, so that the species richness of all studied groups declined during the decay process. The dead wood type (stump vs. log) had a significant effect on species richness of macrolichens and obligate lignicoles, as well as on the communities of crustose lichens.


title: Ecological and evolutionary drivers of phenotypic and genetic variation in the European crabapple (Malus sylvestris (L.) Mill.), a wild relative of the cultivated apple

abstract:
O_LICharacterizing the phenotypic and genetic variation among populations of crop wild relatives help understanding the ecological and evolutionary processes involved in population divergence, and better harness their diversity to mitigate the impact of climate change on crops. We assessed genetic and phenotypic diversity of the European crabapple, Malus sylvestris, a main contributor to the cultivated apple genome (Malus domestica), and investigated for ecological divergence.
C_LIO_LIWe assessed variation in growth rate and traits related to carbon uptake between seedlings measured in a common garden, and related it to the genetic ancestry of the seedlings, assessed using 13 microsatellite loci and Bayesian clustering method. The occurrence of patterns of isolation-by-distance, -by-climate and -by-adaptation that might have caused genetic and phenotypic differentiation among M. sylvestris populations was also tested.
C_LIO_LISeedlings belonged to seven M. sylvestris populations in Europe, with 11.6% of seedlings introgressed by M. domestica. Significant trait variation among M. sylvestris populations was observed, which for some was of moderate to high heritability. Lack of association between trait and genetic divergence suggests that this significant phenotypic variation is not adaptive, but strong association between genetic variation and the climate during the last glacial maximum suggests local adaptation of M. sylvestris to past climates.
C_LIO_LIThis study provides an insight into the ecological and evolutionary drivers of phenotypic and genetic differentiation among populations of a wild apple species and relative of cultivated apples, which is a starting point for future breeding programs.
C_LI

Societal impact StatementApple is a major fruit crop worldwide and a model species for understanding the evolutionary processes underlying perennial crop domestication. Several wild species have contributed to the genetic make-up of the cultivated apple, yet phenotypic and genetic diversity data across their natural distribution is lacking. This study revealed phenotypic variation between populations of the European crabapple, and showed that both geography, and surprisingly, past but not current climate, shaped its genetic structure. We provide a starting point for harnessing wild apple diversity for apple breeding programs to mitigate the impact of climate change on this perennial crop.