title: Regulation of Nav1.6-mediated sodium currents underlie the homeostatic control of neuronal intrinsic excitability in the optic tectum of the developing Xenopus laevis tadpole

abstract: For individual neurons to function appropriately within a network that is undergoing synaptic reorganization and refinement due to developmental or experience-dependent changes in circuit activity, they must homeostatically adapt their intrinsic excitability to maintain a consistent output despite the changing levels of synaptic input. This homeostatic plasticity of excitability is particularly important for the development of sensory circuits, where subtle deficits in neuronal and circuit function cause developmental disorders including autism spectrum disorder and epilepsy. Despite the critical importance of this process for normal circuit development, the molecular mechanism by which this homeostatic control of intrinsic excitability is regulated is not fully understood. Here, we demonstrate that Xenopus optic tectal neurons express distinct fast, persistent and resurgent Na+ currents. Here, we demonstrate that Xenopus optic tectal neurons express distinct fast, persistent and resurgent Na+ currents. These are regulated with developmental changes in synaptic input, and homeostatically in response to changes in visual input. We show that expression of the voltage-gated Na+ channel subtype Nav1.6 is regulated with changes in intrinsic excitability, that blocking Nav1.6 channels is sufficient to decrease intrinsic excitability. Furthermore, that upregulation of Nav1.6 expression is necessary for experience-dependent increases in Na+ currents and intrinsic excitability. Finally, by examining behaviors that rely on visual and multisensory integration, we extend these findings to show that tight regulation of Na+ channel gene expression during a critical period of tectal circuit development is required for the normal functional development of the tectal circuitry.


title: Epigenetic Control of Temperature-Dependent Female Reproductive Life History Trade-Offs in Seed Beetles, Callosobruchus maculatus

abstract: Many species are threatened by climate change and must rapidly respond to survive changing environments. Epigenetic modifications, such as DNA methylation, can facilitate plastic responses by regulating gene expression in response to environmental cues. Understanding epigenetic responses is therefore essential for predicting species ability to rapidly adapt in the context of global environmental change. Here, we investigated the functional significance of DNA methylation on temperature-dependent life history in seed beetles, Callosobruchus maculatus. We assessed changes in DNA methyltransferase (Dnmt1 and Dnmt2) expression levels under ambient conditions and thermal stress, and reproductive performance following artificially-induced epimutation via 3-aminobenzamide (3AB) and Zebularine (Zeb), at a range of ambient and warmer temperatures over two generations. We found that Dnmt1 and Dnmt2 were greatly expressed in females, throughout the body, and exhibited temperature-dependence; in contrast, Dnmt expression was minimal in males. Epimutation led to shifts in female reproductive life history trade-off allocation, and differentially altered thermal optima of fecundity and offspring viability. This study revealed the optimal allocation strategy among these fitness components is temperature-dependent, and trade-offs become increasingly difficult to resolve epigenetically under more extreme warming. Results suggest that epigenetic mechanisms are strongly implicated in, and perhaps limiting of, invertebrate life history responses to temperature change. Further investigation will reveal targeted DNA methylation patterns and specific loci associated with temperature-dependent life history trade-offs in seed beetles and other invertebrates.

category: evolutionary biology


title: Transgenic Drosophila lines for LexA-dependent gene and growth regulation

abstract: Conditional expression of short hairpin RNAs (shRNAs) with binary genetic systems is an indispensable tool for studying gene function. Addressing mechanisms underlying cell-cell communication in vivo benefits from simultaneous use of two independent gene expression systems. To complement the abundance of existing Gal4/UAS-based resources in Drosophila, we and others have developed LexA/LexAop-based genetic tools. Here, we describe experimental and pedagogical advances that promote the efficient conversion of Drosophila Gal4 lines to LexA lines, and the generation of LexAop-shRNA lines to suppress gene function. We developed a CRISPR/Cas9-based knock-in system to replace Gal4 coding sequences with LexA, and a LexAop-based shRNA expression vector to achieve shRNA-mediated gene silencing. We demonstrate the use of these approaches to achieve targeted genetic loss-of-function in multiple tissues. We also detail our development of secondary school curricula that enable students to create transgenic flies, thereby magnifying the production of well-characterized LexA/LexAop lines for the scientific community. The genetic tools and teaching methods presented here provide LexA/LexAop resources that complement existing resources to study intercellular communication coordinating metazoan physiology and development.

category: genetics


title: Poly-glutamine-dependent self-association as a potential mechanism for regulation of androgen receptor activity

abstract: The androgen receptor (AR) plays a central role in prostate cancer. Development of castration resistant prostate cancer (CRPC) requires androgen-independent activation of AR, which involves its large N-terminal domain (NTD) and entails dramatic epigenetic changes depending in part on histone lysine demethylases (KDMs) that interact with AR. The AR-NTD is rich in low-complexity sequences, including a polyQ repeat. Longer polyQ sequences were reported to decrease transcriptional activity and to protect against prostate cancer. However, the molecular mechanisms underlying these observations are unclear. Using NMR spectroscopy, here we identify weak interactions between the AR-NTD and the KDM4A catalytic domain, and between the AR ligand-binding domain and a central KDM4A region that also contains low-complexity sequences. We also show that the AR-NTD can undergo liquid-liquid phase separation in vitro, with longer polyQ sequences phase separating more readily. Moreover, longer polyQ sequences hinder nuclear localization in the absence of hormone and increase the propensity for formation of AR-containing puncta in the nucleus of cells treated with dihydrotestosterone. These results lead us to hypothesize that polyQ-dependent liquid-liquid phase separation may provide a mechanism to decrease the transcriptional activity of AR, potentially opening new opportunities to design effective therapies against CRPC.

category: cancer biology


title: Computational modelling of trans-synaptic nanocolumns, a modulator of synaptic transmission

abstract:
Nanocolumns are trans-synaptic structures which align presynaptic vesicles release sites and postsynaptic receptors. However, how these nano structures shape synaptic signaling remains little understood. Given the difficulty to probe submicroscopic structures experimentally, computer modelling is a usefull approach to investigate the possible functional impacts of nanocolumns. In our in silico model, as has been experimentally observed, a nanocolumn is characterized by a tight distribution of postsynaptic receptors aligned with the presynaptic vesicle release site and by the presence of trans-synaptic molecules which can modulate neurotransmitter diffusion. We found that nanocolumns can play an important role in reinforcing synaptic current mostly when the presynaptic vesicle contains a small number of neurotransmitters. We also show that synapses with and without nanocolumns could have differentiated responses to spontaneous or evoked events. Our work provides a new methodology to investigate in silico the role of the submicroscopic organization of the synapse.

Author summaryNeurotransmitter release, diffusion, and binding to postsynaptic receptors are key steps in synaptic transmission. However, the submicroscopic arrangement of receptors and presynaptic sites of neurotransmitter release remains little investigated. Experimental observations revealed the presence of trans-synaptic nanocolumns which span both the pre and post synaptic sites and fine tune the position of the post synaptic receptors. The functional impact of these nanocolumns (i.e. their influence on synaptic current) is both little understood and difficult to investigate experimentally. Here we construct a novel in silico model to investigate the functional impact of nanocolumns and show that they could play a functional role in reinforcing weak synapses.

category: neuroscience


title: CircHIPK3 dysregulation of the miR-30c/DLL4 axis is essential for KSHV lytic replication

abstract: Non-coding RNA (ncRNA) regulatory networks are emerging as critical regulators of gene expression. These intricate networks of ncRNA:ncRNA interactions modulate multiple cellular pathways and impact the development and progression of multiple diseases. Herpesviruses, including Kaposis sarcoma-associated herpesvirus, are adept at utilising ncRNAs, encoding their own as well as dysregulating host ncRNAs to modulate virus gene expression and the host response to infection. Research has mainly focused on unidirectional ncRNA-mediated regulation of target protein-coding transcripts; however, we have identified a novel host ncRNA regulatory network essential for KSHV lytic replication in B cells. KSHV-mediated upregulation of the host cell circRNA, circHIPK3, is a key component of this network, functioning as a competing endogenous RNA of miR-30c, leading to increased levels of the miR-30c target, DLL4. Dysregulation of this network highlights a novel mechanism of cell cycle control during KSHV lytic replication in B cells. Importantly, disruption at any point within this novel ncRNA regulatory network has a detrimental effect on KSHV lytic replication, highlighting the essential nature of this network and potential for therapeutic intervention.

category: microbiology


title: A sensitive and specific genetically encodable biosensor for potassium ions

abstract: Potassium ions (K+) play a critical role as an essential electrolyte in all biological systems. Here we report the crystal structure-guided optimization and directed evolution of an improved genetically encoded fluorescent K+ biosensor, GINKO2. GINKO2 is highly sensitive and specific for K+ and enables in vivo detection of K+ dynamics in multiple species.

category: bioengineering


title: Kv1 channels regulate variations in spike patterning and temporal reliability in the avian cochlear nucleus angularis

abstract:
Diverse physiological phenotypes in a neuronal population can broaden the range of computational capabilities within a brain region. The avian cochlear nucleus angularis (NA) contains a heterogeneous population of neurons whose variation in intrinsic properties results in electrophysiological phenotypes with a range of sensitivities to temporally modulated input. The low-threshold potassium conductance (GKLT) is a key feature of neurons involved in fine temporal structure coding for sound localization but a role for these channels in intensity or spectrotemporal coding has not been established. To determine whether GKLT affects the phenotypical variation and temporal properties of NA neurons, we applied dendrotoxin (DTX), a potent antagonist of Kv1-type potassium channels, to chick brain stem slices in vitro during whole-cell patch clamp recordings. We found a cell-type specific subset of NA neurons were sensitive to DTX: single-spiking NA neurons were most profoundly affected, as well as a subset of tonic firing neurons. Both tonic I (phasic onset bursting) and tonic II (delayed firing) neurons showed DTX sensitivity in their firing rate and phenotypical firing pattern. Tonic III neurons were unaffected. Spike time reliability and fluctuation sensitivity measured in DTX-sensitive NA neurons was also reduced with DTX. Finally, DTX reduced spike threshold adaptation in these neurons, suggesting that GKLT contributes to the temporal properties that allow coding of rapid changes in the inputs to NA neurons. These results suggest that variation in Kv1 channel expression may be a key factor in functional diversity in the avian cochlear nucleus.

New and noteworthyThe dendrotoxin-sensitive voltage-gated potassium conductance typically associated with neuronal coincidence detection the timing pathway for sound localization is demonstrated to affect spiking patterns and temporal input sensitivity in the intensity pathway in the avian auditory brain stem. The Kv1-family channels appear to be present in a subset of cochlear nucleus angularis neurons, regulate spike threshold dynamics underlying high-pass membrane filtering, and contribute to intrinsic firing diversity.


title: Comprehensive antibody profiling of mRNA vaccination in children

abstract:
While children have been largely spared from COVID-19 disease, the emergence of viral variants of concern (VOC) with increased transmissibility, combined with fluctuating mask mandates and school re-openings have led to increased infections and disease among children. Thus, there is an urgent need to roll out COVID-19 vaccines to children of all ages. However, whether children respond equivalently to adults to mRNA vaccines and whether dosing will elicit optimal immunity remains unclear. Given the recent announcement of incomplete immunity induced by the pediatric dose of the BNT162b2 vaccine in young children, here we aimed to deeply profile and compare the vaccine-induced humoral immune response in 6-11 year old children receiving the pediatric (50g) or adult (100g) dose of the mRNA-1273 vaccine compared to adults and naturally infected children or children that experienced multi inflammatory syndrome in children (MIS-C) for the first time. Children elicited an IgG dominant vaccine induced immune response, surpassing adults at a matched 100g dose, but more variable immunity at a 50g dose. Irrespective of titer, children generated antibodies with enhanced Fc-receptor binding capacity. Moreover, like adults, children generated cross-VOC humoral immunity, marked by a decline of omicron receptor binding domain-binding, but robustly preserved omicron Spike-receptor binding, with robustly preserved Fc-receptor binding capabilities, in a dose dependent manner. These data indicate that while both 50g and 100g of mRNA vaccination in children elicits robust cross-VOC antibody responses, 100ug of mRNA in children results in highly preserved omicron-specific functional humoral immunity.

One-Sentence SummarymRNA vaccination elicits robust humoral immune responses to SARS-CoV-2 in children 6-11 years of age.

category: immunology


title: SARS-CoV-2 infection induces inflammatory bone loss in golden Syrian hamsters

abstract:
Extrapulmonary complications of different organ systems have been increasingly recognized in patients with severe or chronic Coronavirus Disease 2019 (COVID-19). However, limited information on the skeletal complications of COVID-19 is known, even though inflammatory diseases of the respiratory tract have been known to perturb bone metabolism and cause pathological bone loss. In this study, we characterized the effects of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection on bone metabolism in an established golden Syrian hamster model for COVID-19. SARS-CoV-2 causes significant multifocal loss of bone trabeculae in the long bones and lumbar vertebrae of all infected hamsters. The bone loss progressively worsens from the acute phase to the post-recovery phase. Mechanistically, the bone loss was associated with SARS-CoV-2-induced cytokine dysregulation which upregulates osteoclastic differentiation of monocyte-macrophage lineage. The pro-inflammatory cytokines further trigger a second wave of cytokine storm in the skeletal tissues to augment their pro-osteoclastogenesis effect. Our findings in this established hamster model suggest that pathological bone loss may be a neglected complication which warrants more extensive investigations during the long-term follow-up of COVID-19 patients. The benefits of potential prophylactic and therapeutic interventions against pathological bone loss should be further evaluated.

O_FIG O_LINKSMALLFIG WIDTH=188 HEIGHT=200 SRC="FIGDIR/small/463665v1_ufig1.gif" ALT="Figure 1">
View larger version (81K):
org.highwire.dtl.DTLVardef@ada9b8org.highwire.dtl.DTLVardef@1617fcaorg.highwire.dtl.DTLVardef@cdcd3org.highwire.dtl.DTLVardef@75a0ab_HPS_FORMAT_FIGEXP  M_FIG C_FIG Graphical abstractSARS-CoV-2 infection causes pathological bone loss in golden Syrian hamsters through induction of cytokine storm and inflammation-induced osteoclastogenesis.


title: Gut Bacterial Dysbiosis and Instability is Associated with the Onset of Complications and Mortality in COVID-19

abstract:
ObjectiveThere is a growing debate about the involvement of the gut microbiome in COVID-19, although it is not conclusively understood whether the microbiome has an impact on COVID-19, or vice versa, especially as analysis of amplicon data in hospitalized patients requires sophisticated cohort recruitment and integration of clinical parameters. Here, we analyzed fecal and saliva samples from SARS-CoV-2 infected and post COVID-19 patients and controls considering multiple influencing factors during hospitalization.

Design16S rRNA gene sequencing was performed on fecal and saliva samples from 108 COVID-19 and 22 post COVID-19 patients, 20 pneumonia controls and 26 asymptomatic controls. Patients were recruited over the first and second corona wave in Germany and detailed clinical parameters were considered. Serial samples per individual allowed intra-individual analysis.

ResultsWe found the gut and oral microbiota to be altered depending on number and type of COVID-19-associated complications and disease severity. The occurrence of individual complications was correlated with low-risk (e.g., Faecalibacterium prausznitzii) and high-risk bacteria (e.g., Parabacteroides). We demonstrated that a stable gut bacterial composition was associated with a favorable disease progression. Based on gut microbial profiles, we identified a model to estimate mortality in COVID-19.

ConclusionGut microbiota are associated with the occurrence of complications in COVID-19 and may thereby influencing disease severity. A stable gut microbial composition may contribute to a favorable disease progression and using bacterial signatures to estimate mortality could contribute to diagnostic approaches. Importantly, we highlight challenges in the analysis of microbial data in the context of hospitalization.


title: Assessing the Live Decellularized Renal Microvasculature Post-Transplantation using Intravital Microscopy

abstract: Transplantation is the ideal solution for end-stage renal failure, but the growing mismatch between organ supply and demand accentuates the need for alternative solutions like the bioartificial kidney. Several approaches to developing this technology have been demonstrated, and whole organ decellularization appears to be a promising methodology. One major challenge to this strategy is maintaining vascular integrity and functionality post-transplantation. Most models to examine the microvasculature have primarily utilized in vitro or in vivo techniques that are incapable of providing adequate spatial and temporal resolution. Here, we show that decellularized scaffolds orthotopically transplanted into rats initially retain microvascular structure in vivo using intravital two-photon microscopy, as previously identified in vitro. Large molecular weight dextran molecules also provide real-time evidence of the onset of ischemia and increases in microvascular permeability, support substantial translocation of dextran macromolecules from glomerular and peritubular capillary tracks as early as 12 hours after transplantation. Macromolecular extravasation continued across a week, at which time the decellularized microarchitecture was significantly compromised. These results indicate that a in vivo method capable of tracking microvascular integrity represents a powerful interdisciplinary approach for studying scaffold viability and identifying ways to promote scaffold longevity and angiogenesis in bioartificial organs.


title: MetaScore: A novel machine-learning based approach to improve traditional scoring functions for scoring protein-protein docking conformations

abstract:
Protein-protein interactions play a ubiquitous role in biological function. Knowledge of the three-dimensional (3D) structures of the complexes they form is essential for understanding the structural basis of those interactions and how they orchestrate key cellular processes. Computational docking has become an indispensable alternative to the expensive and timeconsuming experimental approaches for determining 3D structures of protein complexes. Despite recent progress, identifying near-native models from a large set of conformations sampled by docking - the so-called scoring problem - still has considerable room for improvement.

We present here MetaScore, a new machine-learning based approach to improve the scoring of docked conformations. MetaScore utilizes a random forest (RF) classifier trained to distinguish near-native from non-native conformations using a rich set of features extracted from the respective protein-protein interfaces. These include physico-chemical properties, energy terms, interaction propensity-based features, geometric properties, interface topology features, evolutionary conservation and also scores produced by traditional scoring functions (SFs). MetaScore scores docked conformations by simply averaging of the score produced by the RF classifier with that produced by any traditional SF. We demonstrate that (i) MetaScore consistently outperforms each of nine traditional SFs included in this work in terms of success rate and hit rate evaluated over the top 10 predicted conformations; (ii) An ensemble method, MetaScore-Ensemble, that combines 10 variants of MetaScore obtained by combining the RF score with each of the traditional SFs outperforms each of the MetaScore variants. We conclude that the performance of traditional SFs can be improved upon by judiciously leveraging machine-learning.

category: bioinformatics


title: Auto-encoded Latent Representations of White Matter Streamlines for Quantitative Distance Analysis

abstract: Parcellation of whole brain tractograms is a critical step to study brain white matter structures and connectivity patterns. The existing methods based on supervised classification of streamlines into predefined streamline bundle types are not designed to explore sub-bundle structures, and methods with manually designed features are expensive to compute streamline-wise similarities. To resolve these issues, we propose a novel atlas-free method that learns a latent space using a deep recurrent auto-encoder. The method efficiently embeds any length of streamlines to fixed-size feature vectors, named streamline embedding, for tractogram parcellation using unsupervised clustering in the latent space. The method was evaluated on the ISMRM 2015 tractography challenge dataset with discrimination of major bundles using unsupervised clustering and streamline querying based on similarity. The learnt latent streamline and bundle representations open the possibility of quantitative studies of arbitrary granularity of sub-bundle structures using generic data mining techniques.


title: Identification of Key Ischemic Stroke Genes by Computational Systems Biology

abstract: Stroke is one of the leading causes of death in humans. Even if patients survive from stroke, they may suffer sequelae such as disability. Treatment for strokes remains unsatisfactory due to an incomplete understanding of its mechanisms. This study investigates Ischemic Stroke (IS), a primary subtype of stroke, through analyses based on microarray data. Limma (in R)derives differentially expressed genes, and the protein-protein interaction (PPI) network is mapped from the database. Gene co-expression patterns are obtained for clustering gene modules by the Weighted Correlation Network Analysis (WGCNA), and genes with high connectivity in the significantly co-expressed modules are selected as key regulators. Common hubs are identified as Cdkn1a, Nes and Anxa2. Based on our analyses, we hypothesize that these hubs might play a key role in the onset and progression of IS. Result suggests the potential of identifying unexplored key regulators by the systemic method used in this work. Further analyses aim at expanding candidate genes for screening biomarkers for IS, and experimental validation is required on identified potential hubs.


title: Global Plant Extinction Risk Assessment Informs Novel Biodiversity Hotspots

abstract: Curbing biodiversity loss and its impact on ecosystem services, resilience and Natures Contributions to People is one of the main challenges of our generation (IPBES, 2019b, 2019a; Secretariat of the United Nations Convention on Biological Diversity, 2020). A global baseline assessment of the threat status of all of biodiversity is crucial to monitor the progress of conservation policies worldwide (Mace & al., 2000; Secretariat of the United Nations Convention on Biological Diversity, 2021) and target priority areas for conservation (Walker & al., 2021). However, the magnitude of the task seems insurmountable, as even listing the organisms already known to science is a challenge (Nic Lughadha & al., 2016; Borsch & al., 2020; Govaerts & al., 2021). A new approach is needed to overcome this stumbling block and scale-up the assessment of extinction risk. Here we show that analyses of natural history mega-datasets using artificial intelligence allows us to predict a baseline conservation status for all vascular plants and identify target areas for conservation corresponding to hotspots optimally capturing different aspects of biodiversity. We illustrate the strong potential of AI-based methods to reliably predict extinction risk on a global scale. Our approach not only retrieved recognized biodiversity hotspots but identified new areas that may guide future global conservation action (Myers & al., 2000; Brooks & al., 2006). To further work in this area and guide the targets of the post-2020 biodiversity framework (Diaz & al., 2020a; Secretariat of the United Nations Convention on Biological Diversity, 2020; Mair & al., 2021), it will be necessary to accelerate the acquisition of fundamental data and allow inclusion of social and economic factors (Possingham & Wilson, 2005).

category: plant biology


title: Expression dynamics of ARGONAUTE proteins during meiosis in Arabidopsis

abstract: Meiosis is a specialized cell division that is key for reproduction and genetic diversity in sexually reproducing plants. Recently, different RNA silencing pathways have been proposed to carry a specific activity during meiosis, but the pathways involved during this process remain unclear. Here, we explored the subcellular localization of different ARGONAUTE (AGO) proteins, the main effectors of RNA silencing, during male meiosis in Arabidopsis thaliana using immunolocalizations with commercially available antibodies. We detected the presence of AGO proteins associated with posttranscriptional gene silencing (AGO1, 2 and 5) in the cytoplasm or the nucleus, while AGOs associated with transcriptional gene silencing (AGO4 and 9) localized exclusively in the nucleus. These results indicate that the localization of different AGOs correlates with their predicted roles at the transcriptional and posttranscriptional levels and provide an overview of their timing and potential role during meiosis.


title: Categorical encoding of speech sounds: beyond auditory cortices

abstract: Which processes in the human brain lead to the categorical perception of speech sounds? Investigation of this question is hampered by the fact that categorical speech perception is normally confounded by acoustic differences in the stimulus. By using ambiguous sounds, however, it is possible to dissociate acoustic from perceptual stimulus representations. Twenty-seven normally hearing individuals took part in an fMRI study in which they were presented with an ambiguous syllable (intermediate between /da/ and /ga/) in one ear and with disambiguating acoustic feature (third formant) in the other ear. Multi-voxel pattern searchlight analysis was used to identify brain areas that consistently differentiated between response patterns associated with different syllable reports. By comparing responses to different stimuli with identical syllable reports and identical stimuli with different syllable reports, we disambiguated whether these regions primarily differentiated the acoustics of the stimuli or the syllable report. We found that BOLD activity patterns in left perisylvian regions (STG, SMG), left inferior frontal regions (vMC, IFG, AI), left supplementary motor cortex (SMA/pre-SMA), and right motor and somatosensory regions (M1/S1) represent listeners syllable report irrespective of stimulus acoustics. Most of these regions are outside of what is traditionally regarded as auditory or phonological processing areas. Our results indicate that the process of speech sound categorization implicates decision-making mechanisms and auditory-motor transformations.


title: Speech sound categorization: beyond auditory cortices


title: Covert valuation for information sampling and choice

abstract: We use our eyes to assess the value of objects around us and carefully fixate options that we are about to choose. Neurons in the prefrontal cortex reliably encode the value of fixated options, which is essential for decision making. Yet as a decision unfolds, it remains unclear how prefrontal regions determine which option should be fixated next. Here we show that anterior cingulate cortex (ACC) encodes the value of options in the periphery to guide subsequent fixations during economic choice. In an economic decision-making task involving four simultaneously presented cues, we found rhesus macaques evaluated cues using their peripheral vision. This served two distinct purposes: subjects were more likely to fixate valuable peripheral cues, and more likely to choose valuable options whose cues were never even fixated. ACC, orbitofrontal cortex, dorsolateral prefrontal cortex, and ventromedial prefrontal cortex neurons all encoded cue value post-fixation. ACC was unique, however, in also encoding the value of cues before fixation and even cues that were never fixated. This pre-saccadic value encoding by ACC predicted which cue was next fixated during the decision process. ACC therefore conducts simultaneous processing of peripheral information to guide information sampling and choice during decision making.


title: Preserved motor representations after paralysis

abstract: AO_SCPLOWBSTRACTC_SCPLOWNeural plasticity allows us to learn skills and incorporate new experiences. What happens when our lived experiences fundamentally change, such as after a severe injury? To address this question, we analyzed intracortical population activity in a tetraplegic adult as she controlled a virtual hand through a brain-computer interface (BCI). By attempting to move her fingers, she could accurately drive the corresponding virtual fingers. Neural activity during finger movements exhibited robust representational structure and dynamics that matched the representational structure, previously identified in able-bodied individuals. The finger representational structure was consistent during extended use, even though the structure contributed to BCI decoding errors. Our results suggest that motor representations are remarkably stable, even after complete paralysis. BCIs re-engage these preserved representations to restore lost motor functions.


title: The value of corticospinal excitability and intracortical inhibition in predicting motor skill improvement driven by action observation

abstract:
BACKGROUND AND OBJECTIVEAction observation can sustain motor skill improvement. At the neurophysiological level, action observation affects the excitability of the motor cortices, as measured by transcranial magnetic stimulation. However, whether the cortical modulations induced by action observation may explain the amount of motor improvement driven by action observation training (AOT) remains to be addressed.

METHODSWe conducted a two-phase study involving 40 volunteers. First, we assessed the effect of action observation on corticospinal excitability (amplitude of motor evoked potentials), short-interval intracortical inhibition, and transcallosal inhibition (ipsilateral silent period). Subsequently, a randomized-controlled design was applied, with AOT participants asked to observe and then execute, as quickly as possible, a right-hand dexterity task six consecutive times, whereas controls had to observe a no-action video before performing the same task.

RESULTSAOT participants showed greater performance improvement relative to controls. The amount of improvement in the AOT group was predicted by the amplitude of corticospinal modulation during action observation and even more by the amount of intracortical inhibition induced by action observation. Importantly, these relations were found specifically for the AOT group and not for the controls.

CONCLUSIONSIn this study, we identified the neurophysiological signatures associated with, and potentially sustaining, the outcome of AOT. Intracortical inhibition driven by action observation plays a major role. These findings elucidate the cortical mechanisms underlying AOT efficacy and open to predictive assessments for the identification of potential responders to AOT, informing the rehabilitative treatment individualization.


title: Molecular rhythm alterations in prefrontal cortex and nucleus accumbens associated with opioid use disorder

abstract: Severe and persistent disruptions to sleep and circadian rhythms are common features of people with opioid use disorder (OUD). Preclinical findings suggest altered molecular rhythms in the brain are involved in opioid reward and dependence. However, whether molecular rhythms are disrupted in brains of people with OUD remained an open question, critical to understanding the role of circadian rhythms in opioid addiction. We previously used subjects times of death (TOD) as a marker of time of day to investigate transcriptional rhythm alterations in psychiatric disorders. Using TOD and RNA sequencing, we discovered rhythmic transcripts in both the dorsolateral prefrontal cortex (DLPFC) and nucleus accumbens (NAc), key brain areas involved in opioid addiction, were largely distinct between OUD and unaffected comparison subjects. Further, fewer rhythmic transcripts were identified in DLPFC of OUD subjects compared to unaffected subjects, but nearly double the number of rhythmic transcripts were found in the NAc of OUD subjects. In OUD, rhythmic transcripts in the NAc peaked either in the evening or near sunrise, and were associated with dopamine, opioid, and GABAergic neurotransmission. Co-expression network analysis identified several OUD-specific modules in the NAc, enriched for transcripts involved in the modulation of dopamine and GABA synapses, including glutamatergic signaling and extracellular matrices. Integrative analyses with human GWAS revealed that rhythmic transcripts in DLPFC and NAc were enriched for genomic loci associated with sleep duration and insomnia. Overall, our results connect transcriptional rhythm changes in dopamine, opioid, and GABAergic synaptic signaling in human brain to sleep-related phenotypes and OUD.


title: The Role of the Temporal Pole in Temporal Lobe Epilepsy: A Diffusion Kurtosis Imaging Study

abstract:
ObjectiveThis study aims to evaluate the use of diffusion kurtosis imaging (DKI) to detect microstructural abnormalities within the temporal pole (TP) in temporal lobe epilepsy (TLE) patients.

MethodsDKI quantitative maps were obtained from fourteen lesional (MRI+) and ten non-lesional (MRI-) TLE patients, along with twenty-one healthy controls. This included mean (MK); radial (RK) and axial kurtosis (AK); mean diffusivity (MD) and axonal water fraction (AWF). Automated fiber quantification (AFQ) was used to quantify DKI measurements along the inferior longitudinal (ILF) and uncinate fasciculus (Unc). ILF and Unc tract profiles were compared between groups and tested for correlation with seizure duration. To characterize temporopolar cortex (TC) microstructure, DKI maps were sampled at varying depths from superficial white matter (WM) towards the pial surface. Each patient group was separated according to side ipsilateral to the epileptogenic temporal lobe and their AFQ results were used as input for statistical analyses.

ResultsSignificant differences were observed between MRI+ and controls (p < 0.005), towards the most anterior of ILF and Unc proximal to the TP of the left (not right) ipsilateral temporal lobe for MK, RK, AWK and MD. Noticeable differences were also observed mostly towards the TP for MK, RK and AWK in the MRI-group. DKI measurements correlated with seizure duration, mostly towards the anterior segments of the WM bundles. Stronger differences in MK, RK and AWF within the TC were observed in the MRI+ and noticeable differences (except for MD) in MRI-groups compared to controls.

SignificanceThe study demonstrates that DKI has potential to detect subtle microstructural alterations within the anterior segments of the ILF and Unc and the connected TC in TLE patients including MRI-subjects. This could aid our understanding of the extrahippocampal areas involved in seizure generation in TLE and might inform surgical planning, leading to better seizure outcomes.


title: Self-regulation of the brain's Beta rhythm using a brain-computer interface improves inhibitory control

abstract: Neural oscillations, or brain rhythms, fluctuate in a manner reflecting ongoing behavior. Whether these fluctuations are instrumental or epiphenomenal to the behavior remains elusive. Attempts to experimentally manipulate neural oscillations exogenously using non-invasive brain stimulation have shown some promise, but difficulty with tailoring stimulation parameters to individuals has hindered progress in this field. We demonstrate here using electroencephalography (EEG) neurofeedback in a brain-computer interface that human participants (n=44) learned over multiple sessions across a 6-day period to self-regulate their Beta rhythm (13-20 Hz) over the right inferior frontal cortex (rIFC). The modulation was evident only during neurofeedback task performance but did not lead to offline alteration of Beta rhythm characteristics at rest, nor to changes in subsequent cognitive behavior. Likewise, a control group (n=38) who underwent training of the Alpha rhythm (8-12 Hz) did not exhibit behavioral changes. Although the right frontal Beta rhythm has been repeatedly implicated as a key component of the brains inhibitory control system, the present data suggest that its manipulation offline prior to cognitive task performance does not result in behavioral change. Thus, this form of neurofeedback training of the tonic Beta rhythm would not serve as a useful therapeutic target for disorders with dysfunctional inhibitory control as their basis.


title: Self-regulation of the brain's right frontal Beta rhythm using a brain-computer interface


title: A robust receptive field code for optic flow detection and decomposition during self-motion

abstract: The perception of optic flow is essential for any visually guided behaviour of a moving animal. To mechanistically predict behaviour and understand the emergence of self-motion perception in vertebrate brains, it is essential to systematically characterize the motion receptive fields (RFs) of optic flow processing neurons. Here, we present the fine-scale RFs of thousands of motion-sensitive neurons studied in the diencephalon and the midbrain of zebrafish. We found neurons that serve as linear filters and robustly encode directional and speed information of translation-induced optic flow. These neurons are topographically arranged in pretectum according to translation direction. The unambiguous encoding of translation enables the decomposition of translational and rotational self-motion information from mixed optic flow. In behavioural experiments, we successfully demonstrated the predicted decomposition in the optokinetic and optomotor responses. Together, our study reveals the algorithm and the neural implementation for self-motion estimation in a vertebrate visual system.


title: Patient-Derived Organoids Recapitulate Intrinsic Immune Landscapes and Progenitor Populations of Glioblastoma.

abstract: Glioblastoma stem cells (GSCs) are highly self-renewing, resistant to therapy, and are able to form lethal tumors1, 2. Tumor organoids have been developed to study tumor evolution1-4, and while GSCs can form organoids for glioblastoma multiforme, our understanding of their intrinsic immune, metabolic, genetic, and molecular programs is limited. To address this, we deeply characterized GSC-derived GBM organoids using a modified protocol (GBMOsm) from several patient-derived GSCs and found they develop into complex 3D tissues with unique self-organization, cancerous metabolic states, and burdensome genetic landscapes. We discovered that GBMOsc recapitulate the presence of two important cell populations thought to drive GBM progression, SATB2+ and HOPX+ progenitors. Despite being devoid of immune cells, transcriptomic analysis across GBMOsc revealed an immune-like molecular program, enriched in cytokine, antigen presentation and processing, T-cell receptor inhibitors, and interferon genes. We determined that SATB2+ and HOPX+ populations contribute to this immune and interferon landscape in GBM in vivo and GBMOsm. Our work deepens our understanding of the intrinsic molecular and cellular architecture of GSC-derived GBMO and defines a novel GBMOsc intrinsic immune-like program.


title: Txn1 mutation causes epilepsy associated with vacuolar degeneration in the midbrain

abstract: Thioredoxin (TXN), encoded by Txn1, acts as a critical antioxidant in the defense against oxidative stress by regulating the dithiol/disulfide balance of interacting proteins. The role of TXN in the central nervous system (CNS) is largely unknown. A phenotype-driven study of N-ethyl-N-nitrosourea-mutated rats with running seizures at around five-week of age revealed the relevance of Txn1 mutations to CNS disorders. Genetic mapping identified Txn1-F54L in epileptic rats. The insulin-reducing activity of Txn1-F54L rats was approximately one-third that of the wild-type. Vacuolar degeneration in the midbrain, mainly in the thalamus and the inferior colliculus, was observed in the Txn1-F54L rats. The lesions displayed neuronal and oligodendrocyte cell death. Neurons in Txn1-F54L rats showed morphological changes in the mitochondria. Vacuolar degeneration began at three weeks of age, and spontaneous repair began at seven weeks; a dramatic change from cell death to repair occurred in the midbrain during a restricted period. In conclusion, Txn1 is essential for the development of the midbrain in juvenile rats.


title: Targeting a central feature of asthma using a cell type-selective IL-13-responsive enhancer

abstract: IL-13 is a central mediator of asthma1-3. Here, we used genome-wide approaches to characterize genes and regulatory elements modulated by IL-13 and other asthma-associated cytokines in airway epithelial cells and showed how they can be used for therapeutic purposes. Using bulk and single cell RNA-seq, we found distinctive responses to IL-13, IL-17, and interferons in human bronchial epithelial basal, ciliated, and secretory cells. H3K27ac ChIP-seq revealed that IL-13 had widespread effects on regulatory elements. Detailed characterization of an enhancer of SPDEF, a transcription factor required for pathologic mucin production, revealed that STAT6 and KLF5 binding sites cooperate to drive IL-13-dependent transcription selectively in secretory cells. Using this enhancer to drive CRISPRi and knockdown either SPDEF or the mucin MUC5AC showed the potential use of this approach for asthma therapeutics. This work identifies numerous genes and regulatory elements involved in cell type-selective cytokine responses and showcases their use for therapeutic purposes.


title: Nanchangmycin regulates FYN, FAK and ERK to control the fibrotic activity of hepatic stellate cells

abstract: Chronic liver injury causes fibrosis, characterized by the formation of scar tissue resulting from excessive accumulation of extracellular matrix (ECM) proteins. Hepatic stellate cell (HSC) myofibroblasts are the primary cell type responsible for liver fibrosis, yet there are currently no therapies directed at inhibiting the activity of HSC myofibroblasts. To search for potential anti-fibrotic drugs, we performed a high-throughput compound screen in primary human HSC myofibroblasts and identified 19 small molecules that induce HSC inactivation, including the polyether ionophore nanchangmycin (NCMC). NCMC induces lipid re-accumulation while reducing collagen expression, deposition of collagen in the extracellular matrix, cell proliferation, and migration. We find that NCMC increases cytosolic Ca2+ and reduces the phosphorylated protein levels of FYN, FAK, ERK1/2, HSP27 and STAT5B. Further, depletion of each of these kinases suppress COL1A1 expression. These studies reveal a signaling network triggered by NCMC to inactivate HSC myofibroblasts and reduce expression of proteins that compose the fibrotic scar. The identification of the antifibrotic effects of NCMC and the pathways by which NCMC inhibits fibrosis provides new tools and therapeutic targets to combat the development and progression of liver fibrosis.

category: cell biology


title: Peroxisome-derived hydrogen peroxide can modulate the sulfenylation profiles of key redox signaling proteins

abstract:
Ever since the first characterization of peroxisomes, a central theme has been their involvement in cellular hydrogen peroxide (H2O2) metabolism. While the reputation of H2O2 drastically changed from an exclusively toxic molecule to a signaling messenger, the regulatory role of peroxisomes in these signaling events is still largely underappreciated. This is mainly because the number of known protein targets of peroxisome-derived H2O2 is rather limited and testing of specific targets is predominantly based on knowledge previously gathered in related fields of research. To gain a broader and more systematic insight into the role of peroxisomes in redox signaling, an unbiased approach is urgently needed. To accomplish this goal, we have combined a previously developed cell system in which peroxisomal H2O2 production can be modulated with a yeast AP-1-like-based sulfenome mining strategy to inventory protein thiol targets of peroxisome-derived H2O2 in different subcellular compartments. Using this unbiased approach, we were able to identify specific and common targets of peroxisome-derived and exogenous H2O2 in peroxisomes, the cytosol, and mitochondria. We also observed that the sulfenylation kinetics profiles of key targets belonging to different protein families can vary considerably. In addition, we obtained compelling but indirect evidence that peroxisome-derived H2O2 may oxidize at least some of its targets through a redox relay mechanism. In conclusion, given that sulfenic acids function as key intermediates in H2O2 signaling, the findings presented in this study provide initial but critical insight into how peroxisomes may be integrated in the cellular H2O2 signaling network.

HighlightsO_LIYAP1C-trapping is a robust tool to assess the peroxisomal H2O2-dependent sulfenome
C_LIO_LIExogenous and peroxisome-derived H2O2 have both common and distinct targets
C_LIO_LIANXA2, PRDX1, and SKP1 are major targets of peroxisome-derived H2O2
C_LIO_LIThe sulfenylation kinetics profiles of key redox-active proteins vary considerably
C_LIO_LIProduction of H2O2 inside peroxisomes directly impacts the mitochondrial sulfenome
C_LI


title: A Proposed Unified Interphase Nucleus Chromosome Structure: Preliminary Preponderance of Evidence

abstract:
Cellular cryo-electron tomography (CET) of the cell nucleus using Scanning Transmission Electron Microscopy (STEM) and the use of deconvolution (DC) processing technology has highlighted a large-scale, 100-300 nm interphase chromosome structure (LSS), that is present throughout the nucleus. This chromosome structure appears to coil the nucleosome 11-nm fiber into a defined hollow structure, analogous to a Slinky (S) (1, motif used in 2) helical spring. This S architecture can be used to build chromosome territories, extended to polytene chromosome structure, as well as to the structure of Lampbrush chromosomes.

Significance StatementCryo-preservation of the nuclear interior allows a large scale interphase chromosome structure--present throughout the nucleus--to be seen for the first time. This structure can be proposed to be a defined coiled entity, a Slinky. This structure can be further used to explain polytene chromosome structure, an unknown chromosome architecture as well as for lampbrush chromosomes. In addition, this new structure can be further organized as chromosome territories, using all 46 human interphase chromosomes as an example, easily into a 10 micron diameter nucleus. Thus, interphase chromosomes can be unified into a flexible defined structure.


title: Precise control of microtubule disassembly in living cells

abstract: Microtubules (MTs) are components of the evolutionarily conserved cytoskeleton, which tightly regulates various cellular activities. Our understanding of MTs is largely based on MT-targeting agents, which, however, are insufficient to dissect the dynamic mechanisms of specific MT populations due to their slow effects on the entire pool of MTs in cells. To address this limitation, we have used chemogenetics and optogenetics to disassemble specific MT subtypes by rapid recruitment of engineered MT-cleaving enzymes. Acute MT disassembly swiftly halted vesicular trafficking and lysosome dynamics. We also used this approach to disassemble MTs specifically modified by tyrosination and several MT-based structures including primary cilia, mitotic spindles, and intercellular bridges. These effects were rapidly reversed by inhibiting the activity or MT association of the cleaving enzymes. The disassembly of targeted MTs with spatial and temporal accuracy enables to uncover new insights of how MTs precisely regulate cellular architectures and functions.


title: Extracellular signalling modulates Scar/WAVE complex activity through Abi phosphorylation

abstract: The lamellipodia and pseudopodia of migrating cells are produced and maintained by the Scar/WAVE complex. Thus, actin-based cell migration is largely controlled through regulation of Scar/WAVE. Here we report that the Abi subunit - not Scar/WAVE - is phosphorylated in response to extracellular signalling. Like Scar, Abi is phosphorylated after the complex has been activated, implying that Abi phosphorylation modulates pseudopodia, rather than causing new ones to be made. Consistent with this, Scar/WAVE complex mutants that cannot bind Rac are also not phosphorylated. Several environmental cues also affect Abi phosphorylation - cell-substrate adhesion promotes it and increased extracellular osmolarity diminishes it. Both unphosphorylatable and phosphomimetic Abi efficiently rescue the chemotaxis of Abi KO cells and pseudopodia formation, confirming that Abi phosphorylation is not required for activation or inactivation of the Scar/WAVE complex. However, pseudopodia and Scar/WAVE patches in the cells with unphosphorylatable Abi protrude for longer, altering pseudopod dynamics and cell speed. Cells in which Scar and Abi are both unphosphorylatable can still form pseudopods, but migrate substantially faster. We conclude that extracellular signals and environmental responses modulate cell migration by tuning the behaviour of the Scar/WAVE complex after it has been activated.


title: Omitting age-dependent mosquito mortality in malaria models underestimates the effectiveness of insecticide-treated nets

abstract:
Mathematical models of vector-borne infections, including malaria, often assume age-independent mortality rates of vectors, despite evidence that many insects senesce. In this study we present survival data on insecticide-resistant Anopheles gambiae s.l. from field experiments in Cote dIvoire. We fit a constant mortality function and two age-dependent functions (logistic and Gompertz) to the data from mosquitoes exposed (treated) and not exposed (control) to insecticidetreated nets (ITNs), to establish biologically realistic survival functions. This enables us to explore the effects of insecticide exposure on mosquito mortality rates, and the extent to which insecticide resistance might impact the effectiveness of ITNs. We investigate this by calculating the expected number of infectious bites a mosquito will take in its lifetime, and by extension the vectorial capacity. Our results show that the predicted vectorial capacity is substantially lower in mosquitoes exposed to ITNs, despite the mosquitoes in the experiment being highly insecticide-resistant. The more realistic age-dependent functions provide a better fit to the experimental data compared to a constant mortality function and, hence, influence the predicted impact of ITNs on malaria transmission potential. In models with age-independent mortality, there is a reduction of 56.52% ({+/-}14.66) for the vectorial capacity under exposure compared to no exposure. However, the two age-dependent functions predicted a larger reduction due to exposure: for the logistic function the reduction is 74.38% ({+/-}9.93) and for the Gompertz 74.35% ({+/-}7.11), highlighting the impact of incorporating age in the mortality rates. These results further show that multiple exposures to ITNs had a considerable effect on the vectorial capacity. Overall, the study highlights the importance of including age dependency in mathematical models of vector-borne disease transmission and in fully understanding the impact of interventions.

Author summaryInterventions against malaria are most commonly targeted on the adult mosquitoes, which transmit the infection from person to person. One of the most important interventions are bed-nets, treated with insecticides. Unfortunately, extensive exposure of mosquitoes to insecticide has led to widespread evolution of insecticide resistance, which might threaten control strategies. Piecing together the overall impact of resistance on the efficacy of insecticide-treated nets is complex, but can be informed by the use of mathematical models. However, there are some assumptions that the models frequently use which are not realistic in terms of the mosquito biology. In this paper, we formulate a model that includes age-dependent mortality rates, an important parameter in vector control since control strategies most commonly aim to reduce the lifespan of the mosquitoes. By using novel data collected using field-derived insecticide-resistant mosquitoes, we explore the effects that the presence of insecticides on nets have on the mortality rates, as well as the difference incorporating age dependency in the model has on the results. We find that including age-dependent mortality greatly alters the anticipated effects of insecticide-treated nets on mosquito transmission potential, and that ignoring this realism potentially overestimates the negative impact of insecticide resistance.

category: ecology


title: Low heritability and high phenotypic plasticity of salivary cortisol in response to environmental heterogeneity in fur seals

abstract: Individuals are unique in how they interact with and respond to their environment. Correspondingly, unpredictable challenges or environmental stressors often produce an individualized response of the hypothalamic-pituitary-adrenal axis and its downstream effector cortisol. We used a fully crossed, repeated measures design to investigate the factors shaping individual variation in baseline cortisol in Antarctic fur seal pups and their mothers. Saliva samples were collected from focal individuals at two breeding colonies, one with low and the other with high density, during two consecutive years of contrasting food availability. Mothers and pups were sampled concurrently at birth and shortly before weaning, while pups were additionally sampled every 20 days. We found that heritability was low for baseline cortisol, while within-individual repeatability and among-individual variability were high. A substantial proportion of the variation in baseline cortisol could be explained in pups and mothers by a combination of intrinsic and extrinsic factors including sex, weight, day, season, and colony of birth. Our findings provide detailed insights into the individualization of endocrine phenotypes and their genetic and environmental drivers in a wild pinniped. Furthermore, the strong associations between cortisol and life history traits that we report in fur seals could have important implications for understanding the population dynamics of species impacted by environmental change.


title: Low heritability and high phenotypic plasticity of salivary cortisol in response to environmental heterogeneity in a wild pinniped


title: Genetic patterns in Montipora capitata across an environmental mosaic in Kaneohe Bay

abstract: Spatial genetic structure (SGS) is important to a populations ability to adapt to environmental change. For species that reproduce both sexually and asexually, the relative contribution of each reproductive mode has important ecological and evolutionary implications because asexual reproduction can have a strong effect on SGS. Reef building corals reproduce sexually, but many species also propagate asexually under certain conditions. In order to understand SGS and the relative importance of reproductive mode across environmental gradients, we evaluated genetic relatedness in almost 600 colonies of Montipora capitata across 30 environmentally characterized sites in K[a]neohe Bay, Oahu, Hawaii using low-depth restriction digest associated sequencing. Clonal colonies were relatively rare overall but influenced SGS. Clones were located significantly closer to one another spatially than average colonies and were more frequent on sites where wave energy was relatively high, suggesting a strong role of mechanical breakage in their formation. Excluding clones, we found no evidence of isolation by distance within sites or across the bay. Several environmental characteristics were significant predictors of the underlying genetic variation (including degree heating weeks, time spent above 30{degrees}C, depth, sedimentation rate and wave height); however, they only explained 5% of this genetic variation. Our results show that colony fragmentation contributes to the ecology of M. capitata at local scales and that genetic diversity is maintained despite strong environmental gradients in a highly impacted ecosystem, suggesting potential for broad adaptation or acclimatization in this population.


title: Prioritizing Management for Cumulative Impacts

abstract: Determining where environmental management is best applied, either through regulating single sectors of human activities or across sectors, is complicated by interactions between human impacts and the environment. In this article, we show how an explicit representation of human-environment interactions can help, via "impact networks" including activities (e.g. shipping), stressors (e.g. ship strikes), species (e.g. humpback whales) or ecosystem services (e.g. marine recreation). Impact networks can enable the identification of "leverage nodes", which, if present, can direct managers to the activities and stressors crucial for reducing risk to important ecosystem components. Exploring an impact network for a coastal ecosystem in British Columbia, Canada, we seek to identify these leverage nodes using a new approach employing Bayesian Belief Networks of risks to ecosystems. In so doing, we address three key questions: (1) Do leverage nodes exist? (2) Do management plans for species correctly identify leverage nodes? (3) Does the management of leverage nodes for certain species realize benefits for other species and ecosystem services? We show that there are several leverage nodes across all species investigated, and show that preconceptions about the regulation of risk to species can misidentify leverage nodes, potentially leading to ineffective management. Notably, we show that managing fisheries does not reduce overall risk to herring whereas managing diverse cumulative impacts including nutrient runoff, oil spills, and marine debris can reduce risk to herring, additional species, and related ecosystem services. Thus, by targeting leverage nodes, managers can efficiently mitigate risks for whole communities, ecosystems, and ecosystem services.


title: Tracing the invasion of a leaf-mining moth in the Palearctic through DNA barcoding of historical herbaria

abstract:
Historical herbaria are valuable sources of data in invasion biology. Here we study the invasion history of the lime leaf-miner, Phyllonorycter issikii, by surveying over 15 thousand herbarium specimens of limes (Tilia spp.) collected in the Palearctic during last 253 years (1764-2016). The majority of herbarium specimens with the pests mines (89%) originated from East Asia (1859-2015), whereas remaining 11% of specimens with the mines came from Europe, European Russia and Western Siberia (1987-2015). These results support the hypothesis of a recent Ph. issikii invasion from Eastern to Western Palearctic.

Single molecule real-time sequencing of the COI barcode region of 93 archival larvae and pupae (7-162 years old) dissected from the mines on historical herbaria allowed to distinguish between Ph. issikii and Ph. messaniella, a polyphagous species rarely feeding on Tilia, which mines were found in herbarium from Europe dated by 1915-1942. We discovered 25 haplotypes of Ph. issikii, of which 16 haplotypes were present solely in East Asia, and revealed wide distribution of the species in China. Six haplotypes shared between Eastern and Western Palearctic suggest the contribution of Ph. issikii populations from the Russian Far East, China and Japan to the westward invasion.


title: Punch in the gut: Parasite tolerance of phytochemicals reflects host diet

abstract:
Gut parasites of plant-eating insects are exposed to antimicrobial phytochemicals that can reduce infection. Trypanosomatid gut parasites infect insects of diverse nutritional ecologies as well as mammals and plants, raising the question of how host diet-associated phytochemicals shape parasite evolution and host specificity. To test the hypothesis that phytochemical tolerance of trypanosomatids reflects the chemical ecology of their hosts, we compared related parasites from honey bees and mosquitoes--hosts that differ in phytochemical consumption--and contrasted our results with previous studies on phylogenetically related, human-parasitic Leishmania.

We identified one bacterial and ten plant-derived substances with known antileishmanial activity that also inhibited honey bee parasites associated with colony collapse. Bee parasites exhibited greater tolerance of chrysin--a flavonoid found in nectar, pollen, and plant resin-derived propolis. In contrast, mosquito parasites were more tolerant of cinnamic acid--a product of lignin decomposition present in woody debris-rich larval habitats. Parasites from both hosts tolerated many compounds that inhibit Leishmania, hinting at possible trade-offs between phytochemical tolerance and mammalian infection. Our results implicate the phytochemistry of host diets as a potential driver of insect-trypanosomatid associations, and identify compounds that could be incorporated into colony diets or floral landscapes to ameliorate infection in bees.

ORIGINALITY AND SIGNIFICANCETrypanosomatid parasites of insects pose threats to beneficial insects, crop plants, and human health. Elucidation of the environmental factors that determine host-parasite specificity and transmission of trypanosomatids is essential to predict the spread and spillover potential of trypanosomatids in wild and agricultural ecosystems. Our comparisons between trypanosomatids of bees and mosquitoes implicate the phytochemical composition of host diets as a potential determinant of insect-trypanosomatid associations. To our knowledge, this is the first comparative study of phytochemical tolerance in insect trypanosomatids. As the first characterization of phytochemical tolerance among honey bee-associated trypanosomatids, our results also identify compounds that could ameliorate infection of managed bees with parasites of concern to wild pollinators and associated with colony collapse.


title: Population-scale long-read sequencing uncovers transposable elements contributing to gene expression variation and associated with adaptive signatures in Drosophila melanogaster

abstract: High quality reference genomes are crucial to understanding genome function, structure and evolution. The availability of reference genomes has allowed us to start inferring the role of genetic variation in biology, disease, and biodiversity conservation. However, analyses across organisms demonstrate that a single reference genome is not enough to capture the global genetic diversity present in populations. In this work, we generated 32 high-quality reference genomes for the well-known model species D. melanogaster and focused on the identification and analysis of transposable element variation as they are the most common type of structural variant. We showed that integrating the genetic variation across natural populations from five climatic regions increases the number of detected insertions by 58%. Moreover, 26% to 57% of the insertions identified using long-reads were missed by short-reads methods. We also identified hundreds of transposable elements associated with gene expression variation and new TE variants likely to contribute to adaptive evolution in this species. Our results highlight the importance of incorporating the genetic variation present in natural populations to genomic studies, which is essential if we are to understand how genomes function and evolve.


title: StarBeast3: Adaptive Parallelised Bayesian Inference of the Multispecies Coalescent

abstract: As genomic sequence data becomes increasingly available, inferring the phylogeny of the species as that of concatenated genomic data can be enticing. However, this approach makes for a biased estimator of branch lengths and substitution rates and an inconsistent estimator of tree topology. Bayesian multispecies coalescent methods address these issues. This is achieved by embedding a set of gene trees within a species tree and jointly inferring both under a Bayesian framework. However, this approach comes at the cost of increased computational demand. Here, we introduce StarBeast3 - a software package for efficient Bayesian inference of the multispecies coalescent model via Markov chain Monte Carlo. We gain efficiency by introducing cutting-edge proposal kernels and adaptive operators, and StarBeast3 is particularly efficient when a relaxed clock model is applied. Furthermore, gene tree inference is parallelised, allowing the software to scale with the size of the problem. We validated our software and benchmarked its performance using three real and two synthetic datasets. Our results indicate that StarBeast3 is up to one-and-a-half orders of magnitude faster than StarBeast2, and therefore more than two orders faster than *BEAST, depending on the dataset and on the parameter, and is suitable for multispecies coalescent inference on large datasets (100+ genes). StarBeast3 is open-source and is easy to set up with a friendly graphical user interface.


title: Genomic architecture of three newly isolated unclassified Butyrivibrio species elucidate their potential role in the rumen ecosystem

abstract: One cellulose-degrading strain CB08 and two xylan-degrading strains XB500-5 and X503 were isolated from buffalo rumen. All the strains were designated as putative novel species of Butyrivibrio based on phylogeny, phylogenomy, digital DNA-DNA hybridization, and average nucleotide identity with their closest type strains. The draft genome length of CB08 was [~]3.54 Mb, while X503 and XB500-5 genome sizes were [~]3.24 Mb and [~]3.27 Mb, respectively. Only 68.28% of total orthologous clusters were shared among three genomes, and 40-44% of genes were identified as hypothetical proteins. The presence of genes encoding diverse carbohydrate-active enzymes (CAZymes) exhibited the lignocellulolytic potential of these strains. Further, the genome annotations revealed the metabolic pathways for monosaccharide fermentation to acetate, butyrate, lactate, ethanol, and hydrogen. The presence of genes for chemotaxis, antibiotic resistance, antimicrobial activity, synthesis of vitamins, and essential fatty acid suggested the versatile metabolic nature of these Butyrivibrio strains in the rumen environment.

category: genomics


title: "XR Mark Test" Reveals Sensorimotor Body Representation in Toddlers

abstract: The mark test is a popular test for self-recognition. Although the extent to which self-recognition can be assessed remains controversial, the test elicits visually guided, self-oriented, and spontaneous reaching movements. In this study, we demonstrated that this self-oriented reaching is suitable for estimating sensorimotor body representation in toddlers. We developed a non-verbal task (Bodytoypo) to assess the localization of body parts by gamifying the mark test and conducted it with thirty 2- and 3-year old children. Specifically, we detected the childrens skeletal data in real-time, displayed virtual marks on various parts of their body, and estimated their reaction time and accuracy of body part localization. Subsequently, a statistical-based automated analysis using 2-D image processing and conventional frame-by-frame coding were performed. The results revealed developmental changes in the childrens reaching strategies. A few errors were observed around the face. A reduction in the error rate for joint and movable areas was observed in children between the ages of 2 and 3 years. An analysis of movement trajectories using a combination of image processing and machine learning algorithms showed that 2-year-olds acquired visually guided reaching (feedback control) from ballistic exploratory reaching and 3-year-olds acquired rapid and predictive reaching (feedforward control) from visually guided cautious reaching. It was also found that the accuracy of localization could be predicted by examining the coordination of body parts. Evaluation of the developmental changes in self-oriented reaching reveals new possibilities for the mark test and development of body representation.

category: animal behavior and cognition


title: An Anatomically and Hemodynamically Realistic Simulation Framework for 3D Ultrasound Localization Microscopy

abstract: The resolution of 3D Ultrasound Localization Microscopy (ULM) is determined by acquisition parameters such as frequency and transducer geometry but also by microbubble (MB) concentration, which is also linked to the total acquisition time needed to sample the vascular tree at different scales. In this study, we introduce a novel 3D anatomically- and physiologically-realistic ULM simulation framework based on two-photon microscopy (2PM) and in-vivo MB perfusion dynamics. As a proof of concept, using metrics such as MB localization error, MB count and network filling, we could quantify the effect of MB concentration and PSF volume by varying probe transmit frequency (3-15 MHz). We find that while low frequencies can achieve sub-wavelength resolution as predicted by theory, they are also associated with prolonged acquisition times to map smaller vessels, thus limiting effective resolution. A linear relationship was found between maximal MB concentration and inverse point spread function (PSF) volume. Since inverse PSF volume roughly scales cubically with frequency, the reconstruction of the equivalent of 10 minutes at 15 MHz would require hours at 3 MHz. We expect that these findings can be leveraged to achieve effective reconstruction and serve as a guide for choosing optimal MB concentrations in ULM.


title: Shiitake mycelium fermentation improves digestibility, nutritional value, flavor and functionality of plant proteins

abstract: Plant proteins can serve as inexpensive and environmentally friendly meat-replacements. However, poor taste characteristics and relatively low nutritional value prevent their full acceptance as meat substitutes. Fermentation of food has been historically used to improve the quality of foods. In this work we describe the improvement in digestibility, nutritional value, physical properties, and organoleptic characteristics, of a pea and rice protein concentrate blend through fermentation with shiitake mushroom mycelium. Ileal digestibility pig studies show increases in the DIAAS for the shiitake fermented pea and rice protein blend turning the blend into an "excellent source" of protein for humans. The fermentation also increases the solubility of the protein blend and reduces the content of the antinutrient compounds phytates and protease inhibitor. Mass spectrometry and sensory analyses of fermented protein blend indicates that fermentation leads to a reduction in off-note compounds substantially improving its organoleptic performance.


title: Controlling astrocyte-mediated synaptic pruning signals for schizophrenia drug repurposing with Deep Graph Networks

abstract:
Schizophrenia is a debilitating psychiatric disorder, leading to both physical and social morbidity. Worldwide 1% of the population is struggling with the disease, with 100,000 new cases annually only in the United States. Despite its importance, the goal of finding effective treatments for schizophrenia remains a challenging task, and previous work conducted expensive large-scale phenotypic screens. This work investigates the benefits of Machine Learning for graphs to optimize drug phenotypic screens and predict compounds that mitigate abnormal brain reduction induced by excessive glial phagocytic activity in schizophrenia subjects. Given a compound and its concentration as input, we propose a method that predicts a score associated with three possible compound effects, i.e., reduce, increase, or not influence phagocytosis. We leverage a high-throughput screening to prove experimentally that our method achieves good generalization capabilities. The screening involves 2218 compounds at five different concentrations. Then, we analyze the usability of our approach in a practical setting, i.e., prioritizing the selection of compounds in the SWEETLEAD library. We provide a list of 64 compounds from the library that have the most potential clinical utility for glial phagocytosis mitigation. Lastly, we propose a novel approach to computationally validate their utility as possible therapies for schizophrenia.

Author summaryPhagocytosis is a fundamental biological process to protect biological organisms from exogenous infectious particles as well as to preserve equilibrium and efficiency of the host by removing its unwanted cells. A dysregulation of the phagocytic activity can lead to severe consequences for the host. In this study, we focus on a recent theory that relates an excessive phagocytic activity in brain cells, and a consequent abnormal reduction in brain volume, to the development of schizophrenia. Our working hypothesis is that pharmaceutical compounds that can reduce excessive of phagocytic activity might prove effective as a schizophrenia treatment. Rather than attempting to develop ex-novo such a chemical compound, we rely on a more cost-effective and efficient approach that seeks candidate therapies in a set of approved chemical compounds. To achieve this, we train a machine learning model capable of predicting, with good accuracy, the ability of a molecular compound to increase or decrease phagocytosis in the target brain cells. Our approach leverages learning models capable of directly processing the molecular graph of the compound, leading to the identification of 64 candidate drugs of potential clinical utility.


title: Lpnet: Reconstructing Phylogenetic Networks from Distances Using Integer Linear Programming

abstract: We present Lpnet, a variant of the widely used Neighbor-net method that approximates pairwise distances between taxa by a circular phylogenetic network. We first apply standard methods to construct a binary phylogenetic tree and then use integer linear programming to compute an optimal circular orderings that agrees with all tree splits. This approach achieves an improved approximation of the input distance for the clear majority of experiments that we have run for simulated and real data. We release an implementation in R that can handle up to 94 taxa and usually needs about one minute on a standard computer for 80 taxa. For larger taxa sets, we include a top-down heuristic which also tends to perform better than Neighbor-net.


title: Prediction and Expression Analysis of Deleterious Nonsynonymous SNPs of Arabidopsis ACD11 Gene by Combining Computational Algorithms and Molecular Docking Approach

abstract: Accelerated cell death 11 (ACD11) is an autoimmune gene that suppresses pathogen infection in plants by preventing plant cells from becoming infected by any pathogen. This gene is widely known for growth inhibition, premature leaf chlorosis, and defense-related programmed cell death (PCD) in seedlings before flowering in Arabidopsis plant. Specific amino acid changes in the ACD11 proteins highly conserved domains are linked to autoimmune symptoms including constitutive defensive responses and necrosis without pathogen awareness. The molecular aspect of the aberrant activity of the ACD11 protein is difficult to ascertain. The purpose of our study was to find the most deleterious mutation position in the ACD11 protein and correlate them with their abnormal expression pattern. Using several computational methods, we discovered PCD vulnerable single nucleotide polymorphisms (SNPs) in ACD11. We analysed the RNA-Seq data, identified the detrimental nonsynonymous SNPs (nsSNP), built genetically mutated protein structures and used molecular docking to assess the impact of mutation. Our results demonstrated that the A15T and A39D variations in the GLTP domain were likely to be extremely detrimental mutations that inhibit the expression of the ACD11 protein domain by destabilizing its composition, as well as disrupt its catalytic effectiveness. When compared to the A15T mutant, the A39D mutant was more likely to destabilize the protein structure. In conclusion, these mutants can aid in the better understanding of the vast pool of PCD susceptibilities connected to ACD11 gene GLTP domain activation.


title: Mining hidden knowledge: Embedding models of cause-effect relationships curated from the biomedical literature

abstract:
We explore the use of literature-curated signed causal gene expression and gene-function relationships to construct un-supervised embeddings of genes, biological functions, and diseases. Our goal is to prioritize and predict activating and inhibiting functional associations of genes, and to discover hidden relationships between functions. As an application, we are particularly interested in the automatic construction of networks that capture relevant biology in a given disease context.

We evaluated several unsupervised gene embedding models leveraging literature-curated signed causal gene expression findings. Using linear regression, it is shown that, based on these gene embeddings, gene-function relationships can be predicted with about 95% precision for the highest scoring genes. Function embedding vectors, derived from parameters of the linear regression model, allow to infer relationships between different functions or diseases. We show for several diseases that gene and function embeddings can be used to recover key drivers of pathogenesis, as well as underlying cellular and physiological processes. These results are presented as disease-centric networks of genes and functions. To illustrate the applicability of the computed gene and function embeddings to other machine learning tasks we expanded the embedding approach to drug molecules, and used a simple neural network to predict drug-disease associations.


title: Detecting expressed cancer somatic mutations from single-cell RNA sequencing data

abstract: Identifying expressed somatic mutations directly from single-cell RNA sequencing (scRNA-seq) data is challenging but highly valuable. Computational methods have been attempted but no reliable methods have been reported to identify somatic mutations with high fidelity. We present RESA -- Recurrently Expressed SNV Analysis, a computational framework that identifies expressed somatic mutations from scRNA-seq data with high precision. We test RESA in multiple cancer cell line datasets, where RESA demonstrates average area under the curve (AUC) of 0.9 on independently held out test sets, and achieves average precision of 0.71 when evaluated by bulk whole exome, which is substantially higher than previous approaches. In addition, RESA detects a median of 201 mutations per cell, 50 times more than what was reported in experimental technologies with simultaneous expression and mutation profiling. Furthermore, applying RESA to scRNA-seq from a melanoma patient, we demonstrate that RESA recovers the known BRAF driver mutation of the sample and melanoma dominating mutational signatures, identifies mutation associated expression signatures, reveals nondriver perturbed and stage specific cancer hallmarks, and unveils the complex relationship between genomic and transcriptomic intratumor heterogeneity. Therefore, RESA could provide novel views in the study of intratumor heterogeneity and relate genetic alterations to transcriptional changes at single cell level.


title: In silico discovery of small molecules for efficient stem cell differentiation into definitive endoderm

abstract: Improving methods for human embryonic stem cell differentiation represents a challenge in modern regenerative medicine research. Using drug repurposing approaches, we discover small molecules that regulate the formation of definitive endoderm. Among them are inhibitors of known processes involved in endoderm differentiation (mTOR, PI3K, and JNK pathways) and a new compound, with an unknown mechanism of action, capable of inducing endoderm formation in the absence of growth factors in the media. Optimization of the classical protocol by including this compound achieves the same differentiation efficiency with a 90% cost reduction. The gene expression profile induced by the compound suggests that it is an inhibitor of the MYC pathway. The proposed in silico procedure for candidate molecule selection has broad potential for improving stem cell differentiation protocols.


title: Live cell imaging of metabolic heterogeneity by quantitative fluorescent ATP indicator protein, QUEEN-37C.

abstract: Adenosine triphosphate (ATP) is often referred as the energy currency of the cell. Yet, non-invasive, real-time, and quantitative measurement of its concentration in living mammalian cells has been difficult. Here we report an improved fluorescent ATP indicator protein, QUEEN-37C, which is optimized for measuring ATP concentration in living mammalian cells. Absolute value of the ATP concentration can be estimated from the ratiometric fluorescence imaging, and its accuracy was verified by the luciferase assay. Since QUEEN-37C enables the single-cell measurement of ATP concentration, we can not only measure its mean but its distribution in the cell population, which revealed that the ATP concentration is tightly regulated in most cells. We also noted the positive correlations in the ATP concentration among adjacent cells in epithelial cell sheet and mouse embryonic stem cell colonies. Thus, QUEEN-37C would serve as a new tool for the investigation of the single cell heterogeneity of metabolic states.

category: biophysics


title: Novel Real-Time Library Search driven data acquisition strategy for identification and characterization of metabolites.

abstract:
Identification and structural characterization of novel metabolites in drug discovery or metabolomics experiments is one of the most challenging tasks. Multi-level fragmentation (MSn) based approaches combined with various dissociation modes are frequently utilized for facilitating structure assignment of the unknown compounds. As each of the MS precursors undergoes MSn, the instrument cycle time can limit the total number of precursors analyzed in a single run for complex samples. This necessitates splitting data acquisition into several LC/MS analyses where the results obtained in one acquisition inform the experimental design for the successive experiment.

Here we present a new LC/MS data acquisition strategy, termed Met-IQ, where the decision to perform an MSn acquisition is automatically made in real time based on the similarity between an acquired experimental MS2 spectrum and a spectrum in a reference spectral library. Each MS2 spectrum is searched in real time against the spectra for the known compounds of interest. If a similarity to a spectrum in the library is found, the instrument performs a decision-dependent event, such as an MS3 scan. Compared to an intensity-based, data-dependent MSn experiment, only a selective number of MS3 are triggered using Met-IQ, increasing the overall MS2 instrument sampling rate. We applied this strategy to an Amprenavir sample incubated with human liver microsomes. The number of MS2 scan events increased nearly 3.5-fold compared to the standard data dependent experiment where MS3 was triggered for each precursor ion, resulting in identification and structural characterization of 55% more unique metabolites. Furthermore, the MS3 precursor fragments were selected intelligently, focusing on higher mass fragments of sufficient intensity to maximize acquisition of MS3 data relevant for structure assignment. The described Met-IQ strategy is not limited to metabolism experiments, and can be applied to analytical samples where the detection of unknown compounds structurally related to a known compound(s) is sought.

category: pharmacology and toxicology


title: The mechanical and morphological properties of systemic and pulmonary arteries differ in the earth boa, a snake without ventricular pressure separation

abstract: The walls of the mammalian aorta and pulmonary artery are characterized by diverging morphologies and mechanical properties, which has been correlated with high systemic and low pulmonary blood pressures, as a result of intraventricular pressure separation in the mammalian ventricle. However, the relation between intraventricular pressure separation and diverging aortic and pulmonary artery wall morphologies and mechanical characteristics is not understood. The snake cardiovascular system poses a unique model for the study of this question, since representatives both with and without intraventricular pressure separation exist. In this study we perform uniaxial tensile testing on vessel samples taken from the aortas and pulmonary arteries of the earth boa, Acrantophis madagascariensis, a species without intraventricular pressure separation. We then compare these morphological and mechanical characteristics with samples from the ball python, Python regius, and the yellow anaconda, Eunectes notaeus, species with and without intraventricular pressure separation, respectively. Strikingly, we find that although the aortas and pulmonary arteries of A. madagascariensis respond similarly to the same intramural blood pressures, they diverge strongly in morphology, and that this is a common attribute among species without intraventricular pressure separation in this study. In contrast, P. regius aortas and pulmonary arteries diverge both morphologically and in terms of their mechanical properties. Altogether our data indicate that intraventricular pressure separation does not explain diverging aortic and pulmonary artery morphologies. Following the Law of Laplace, we propose that thin pulmonary arteries represent a mechanism to protect the fragile pulmonary vascular bed by reducing the blood volume that passes through, to which genetic factors may contribute more strongly than physiological parameters.

category: physiology


title: EXTRA LARGE G-PROTEIN 2 (XLG2) mediates cell death and hyperimmunity via a novel, apoplastic ROS-independent pathway in Arabidopsis thaliana

abstract:
O_LIHeterotrimeric G-Proteins are signal transduction complexes comprised of three subunits, G, G{beta} and G{gamma}, and are involved in many aspects of plant life. The non-canonical G subunit XLG2 mediates PAMP-induced ROS generation and immunity downstream of PRRs. A mutant of the chitin receptor component CERK1, cerk1-4, maintains normal chitin signalling capacity, but shows excessive cell death upon infection with powdery mildews. We identified XLG2 mutants as suppressors of the cerk1-4 phenotype.
C_LIO_LIWe generated stably transformed Arabidopsis lines expressing Venus-XLG2 and numerous mutated variants. These were analysed by confocal microscopy, Western blotting and pathogen infection. We also crossed cerk1-4 with several mutants involved in immunity and analysed their phenotype. Phosphorylation of XLG2 was investigated by quantitative proteomics.
C_LIO_LIMutations in XLG2 complex partners AGB1 and AGG1 have a partial cerk1-4 suppressor effect. The cerk1-4 phenotype is independent of NADPH oxidase-generated ROS, BAK1 and SOBIR1, but requires PUB2. XLG2 mediates cerk1-4 cell death at the cell periphery. Integrity of the XLG2 N-terminal domain, but not its phosphorylation, is essential for correct XLG2 localisation and cerk1-4 signalling.
C_LIO_LIOur results suggest that XLG2 transduces signals from an unknown cell surface receptor that activates an apoplastic ROS-independent cell death pathway in Arabidopsis.
C_LI


title: Development and verification of SSR markers from drought stress-responsive miRNAs in common wild rice

abstract:
PREMISEDongxiang wild rice (Oryza rufipogon Griff., DXWR) is the northernmost common wild rice found in the world, which possesses abundant elite genetic resources. We developed a set of drought stress-responsive microRNA (miRNA)-based single sequence repeat (SSR) markers for DXWR, which will help breed drought stress-resistant rice varieties.

METHODS AND RESULTSNinety-nine SSR markers were developed from the drought stress-responsive miRNAs of DXWR. The SSR loci were distributed in all 12 rice chromosomes and most were in chromosomes 2 and 6, with di- and trinucleotides being the most abundant repeat motifs. Nine out of ten synthesized SSR markers were displayed high levels of genetic diversity in the genomes of DXWR and 41 modern rice varieties worldwide. The number of alleles per locus ranged from 2 to 6, and the observed and expected heterozygosity ranged from 0.000 to 0.024 and 0.461 to 0.738, respectively.

CONCLUSIONSThese SSR markers developed from drought stress-responsive miRNAs in DXWR could be additional tools for elite genes mapping and useful for drought stress-resistant rice breeding.


title: The effector FEP3/IRON MAN1 modulates interaction between BRUTUS-LIKE1 and bHLH subgroup IVb and IVc proteins

abstract:
Plants use the micronutrient iron (Fe) efficiently to balance the requirements for Fe during growth with its potential cytotoxic effects. A cascade of basic helix-loop-helix (bHLH) transcription factors is initiated by bHLH proteins of the subgroups IVb and IVc. This induces more than 50 genes in higher plants that can be grouped in co-expression clusters. Gene co-expression networks contain information on functional protein interactomes. We conducted a targeted yeast two-hybrid screen with pairwise combinations of 23 proteins stemming from previously characterized Fe-deficiency-induced gene co-expression clusters and regulators. We identified novel and described interactions, as well as interaction hubs with multiple interactions within the network. We found that BRUTUS-LIKE E3 ligases (BTSL1, BTSL2) interacted with basic helix-loop-helix (bHLH) transcription factors of the subgroups IVb and IVc including PYE, bHLH104 and ILR3, and with small FE UPTAKE-INDUCING PEPTIDE3/IRON MAN1 (FEP3/IMA1). Through deletion studies and with support of molecular docking, we mapped the interaction sites to three-amino-acid regions in BTSL1 and FEP3/IMA1. The FEP3/IMA1 active residues are present in interacting sites of the bHLH IVc factors. FEP3/IMA1 attenuated interaction of BTSL1 with bHLH proteins in a quantitative yeast three-hybrid assay suggesting that it is an inhibitor. Co-expression of BTSL1 and bHLH IVb and IVc factors uncovered unexpected patterns of subcellular localization. Combining deletion mapping, protein interaction and physiological analysis, we discuss the model that FEP3/IMA1 is a small effector protein inhibiting BTSL1/BTSL2-mediated degradation of bHLH subgroup IVb and IVc proteins.

HighlightsO_LIA targeted yeast two-hybrid screen of Fe deficiency-regulated proteins reveals a regulatory protein interactome consisting of E3 ligases BTS/BTSL, bHLH transcription factors of subgroups IVb and IVc and small protein FEP3/IMA1.
C_LIO_LIInteraction sites between BTSL1, FEP3/IMA1, and bHLH IVc transcription factors were fine-mapped.
C_LIO_LIFEP3/IMA1 is as a small effector protein that selectively attenuates the bHLH interaction with BTSL1 to regulate Fe deficiency responses.
C_LI

One sentence summaryA targeted protein interaction screen uncovered a interactions of E3 ligase BTSL1, bHLH proteins of subgroup IVb and IVc and effector protein FEP3/IMA1 to regulate Fe deficiency responses.


title: Effects of culture medium and temperature on fungal growth of Mycena and marasmioid isolates and in vitro symbiotic culture in mycoheterotrophic orchid, Gastrodia pubilabiata

abstract: In vitro symbiotic culture of Gastrodia pubilabiata seeds were conducted with the fungal isolates from G. pubilabiata roots. We obtained five fungal isolates, which belonged to Mycena, Marasmiaceae and Omphalotaceae. Firstly, optimal temperature and culture medium for subculture of these fungal isolates were examined. All five isolates grew the fastest on malt extract agar medium. Mycelial growth rate was highest at 25 {degrees}C between 10 {degrees}C and 40 {degrees}C. Secondly, we evaluated suitable culture vessels and organic materials for symbiotic culture. Seeds germinated well in petri dishes with Quercus leaf disc on water agar medium, and the seed germination process was well observed without dense mycelium. The most developed seedlings were found in glass bottles filled with Japanese cedar leaves, but densely grew mycelium prevent accurate seedling counts. Leaves of Quercus, Japanese cedar and bamboo were used as organic materials for symbiotic culture. All three leaves induced seed germination with Mycena and Marasmiaceae fungi, but material types affected subsequent seedling growth. Our method will contribute to understanding the mycorrhizal association of Gastrodia species and also other mycoheterotrophic plants.


title: Vernalization-triggered expression of the antisense transcript COOLAIR is mediated by CBF genes

abstract: Many plants undergo vernalization, a long-term winter-triggered acceleration of flowering, to align their flowering time with spring. In Arabidopsis thaliana, this is achieved by silencing a floral repressor, FLOWERING LOCUS C (FLC). COOLAIR, an antisense noncoding RNA expressed at the FLC locus, is induced during the early phase of vernalization, preceding FLC suppression. However, the mechanism by which long-term cold induces COOLAIR is not well understood. Here, we showed that C-repeat (CRT)/dehydration-responsive elements (DREs) at the 3-end of FLC and CRT/DRE-binding factors (CBFs) are required for vernalization-induced COOLAIR activation. The CBFs bind to CRT/DREs at the 3-end of FLC, both in vitro and in vivo, and the CBFs levels increased gradually during vernalization. Additionally, vernalization-induced COOLAIR expression was highly suppressed in the cbfs mutant, in which all CBFs were knocked-out. Contrastingly, CBF-overexpressing plants showed COOLAIR upregulation, even at warm temperatures. We propose that COOLAIR is induced by CBFs in the early phase of vernalization but is downregulated as CBFs are evicted from closed FLC chromatin during the late vernalization phase. We also demonstrated that cbfs and FLC{Delta}COOLAIR mutants have a normal vernalization response, although they show defects in vernalization-induced COOLAIR activation, indicating that COOLAIR is not necessary for this process.