title: Neuromuscular connectomes across development reveal synaptic ordering rules

abstract: The connections between motor neurons and muscle fibers are dramatically reorganized in early postnatal life. This work attempts to better understand this synaptic rewiring by using a connectomic approach, i.e., tracing out all the connections between motor neurons and muscle fibers, at successive ages in a small mouse muscle. We reconstructed 31 partial-complete neuromuscular connectomes, using serial section scanning electron microscopy in a neonatal mouse and Brainbow-based and XFP-based fluorescent reconstructions in older animals. Our data included a total of more than 6000 neuromuscular junctions (NMJs), including complete connectomes from one newborn, seven developmental ages (P6-P9), and two adults. Analysis confirmed the massive rewiring that takes place as axons prune their motor units but add more synaptic areas at the NMJs with which they remain in contact. Interestingly, we found synaptic ordering rules that likely underlie this circuit maturation and yield the resulting adult neuromuscular pattern, as manifest in Hennemans size principle. In particular, by analyzing both the identities of axons sharing NMJs at developing ages and muscle fibers with multiple endplates, we found evidence suggesting an activity-based linear ranking of motor neurons such that neurons co-innervated the same endplates and same muscle fibers (if there were more than one endplate) when the axons were similar in activity and hence rank. In addition, this ranking provided a means for understanding action at a distance in which the activity at one neuromuscular junction can impact the fate of the axons at another junction at a different site on the same muscle fiber. These activity-dependent mechanisms provide insight into the means by which timing of activity among different axons innervating the same population of cells, that start out with nearly all-to-all connectivity, can produce a well-organized system of axons, a system that is necessary for the recruitment order of neurons during a graded behavior like muscle contraction.


title: Marker-free genome engineering in Amycolatopsis using the pSAM2 site-specific recombination system

abstract:
Actinobacteria belonging to the genus Amycolatopsis are important for antibiotic production and other valuable biotechnological applications such as biodegradation or bioconversion. Despite their industrial importance, tools and methods for the genetic manipulation of Amycolatopsis are less developed than in other actinobacteria such as Streptomyces. Moreover, most of the existing methods do not support convenient marker-free genome engineering. Here, we report the use of the pSAM2 site-specific recombination system for the efficient deletion of marker genes or large DNA regions in Amycolatopsis. For this purpose, we constructed a shuttle vector, replicating in Escherichia coli and Amycolatopsis, expressing the Xis and Int proteins from the Streptomyces integrative and conjugative element pSAM2. These proteins are sufficient for site-specific recombination between the attachment sites attL and attR. We also constructed two plasmids, replicative in E. coli but not in Amycolatopsis, for the integration of the recombination sites attL and attR on each side of a region targeted for deletion. We exemplified the use of these tools in Amycolatopsis mediterranei DSM 40773 by obtaining with high efficiency (>95%) a marker-free deletion of one single gene in the rifamycin biosynthetic gene cluster or of the entire 90-kb cluster.

IMPORTANCEThe genus Amycolatopsis is regarded as an important source of diverse specialized metabolites. Members of this genus are used in industry for the production of valuable antibiotics such as rifamycins or vancomycin. Amycolatopsis spp. also present a great interest for biotechnological applications such as biodegradation or bioconversion. Despite their importance, their genetic manipulation was somehow hampered by the lack of efficient tools. Here we report the successful use of the pSAM2 site-specific recombination system to construct unmarked deletion mutants, allowing marker recycling, or to create large deletions in A. mediterranei DSM 40773. The high efficiency of this site-specific recombination system and it possible application to other Amycolatopsis species open new opportunities for marker-free genome engineering in this genus.

category: molecular biology


title: OGT controls mammalian cell viability by regulating the proteasome/mTOR/ mitochondrial axis

abstract: O-GlcNAc transferase (OGT) is an essential X-chromosome-encoded enzyme that catalyzes the addition of N-acetylglucosamine (GlcNAc) to the hydroxyl groups of serine and threonine residues on many nuclear and cytosolic proteins. This posttranslational modification is reversible and is actively removed by the O-GlcNAcase OGA. It was shown more than two decades ago that OGT is essential for mammalian cell viability, but the underlying mechanisms are still enigmatic. Given the close association between OGT and human diseases, such as cancer, diabetes and cardiovascular disease, identification of the mechanisms by which OGT controls cell viability will facilitate the development of therapeutic strategies to manipulate OGT activity. Here, we employ a genome-wide CRISPR-Cas9 viability screen in mouse embryonic stem cells (mESCs) with inducible Ogt deletion to show that the block in cell viability induced by Ogt-deficiency stems from a deleterious increase in mitochondrial oxidative phosphorylation (OXPHOS). Mechanistically, we demonstrate that OGT safeguards mTOR (mechanistic target of rapamycin) activity to maintain mitochondrial fitness through modulation of proteasome activity and intracellular amino acid homeostasis. In the absence of OGT, increased proteasome activity results in increased steady-state amino acid levels, which in turn promote mTOR translocation and activation and increased oxidative phosphorylation. This mechanism also operates in CD8+ T cells, indicating its generality across mammalian cell types. Genome-wide proteomic and phosphoproteomic analyses show extensive changes in global signaling and confirm our finding of mTOR hyperactivation in OGT-deficient cells. In sum, our study highlights a novel function for OGT in regulating the proteasome/ mTOR/ mitochondrial axis in a manner that maintains homeostasis of intracellular amino acid levels, mitochondrial fitness and cell viability. Since many of the proteins involved in proteasome, mTOR and mitochondrial activity are aberrantly expressed in cancer, and since inhibitors for proteasome and mTOR have been used in cancer therapy, manipulating OGT activity may have therapeutic potential in diseases in which this signaling axis is impaired.

category: cell biology


title: Volumetric ultrasound localization microscopy of the whole brain microvasculature

abstract: Technologies to visualize whole organs across scales in vivo are essential for our understanding of biology in health and disease. To date, only post-mortem techniques such as perfused computed tomography scanning or optical microscopy of cleared tissues achieve cellular resolution across entire organs and imaging methods with equal performance in living mammalian organs have yet to be developed. Recently, 2D ultrasound localization microscopy has successfully mapped the fine-scale vasculature of various organs down to a 10 m precision. However, reprojection issues and out-of-plane motion prevent complex blood flow quantification and fast volumetric imaging of whole organs. Here, we demonstrate for the first time in vivo volumetric ultrasound localization microscopy mapping of the rodent brain vasculature. We developed a complete methodological pipeline that includes specific surgery, a dedicated 3D ultrasound acquisition sequence, localization and tracking algorithms, motion correction and realignment, as well as the post-processing quantification of cerebral blood flow. We illustrate the power of this approach, by mapping the whole rat brain vasculature at a resolution of 12 m, revealing mesoscopic to macroscopic vascular architectures and cerebral blood flows ranging from 1 to 100 mm/s. Our results pave the way to the investigation of in vivo vascular processes across the mammalian brain in health and disease, in a wide range of contexts and models.

category: bioengineering


title: PREDICTING SPEECH INTELLIGIBILITY FROM A SELECTIVE ATTENTION DECODING PARADIGM IN COCHLEAR IMPLANT USERS

abstract:
1.ObjectivesElectroencephalography (EEG) can be used to decode selective attention in cochlear implant (CI) users. This work investigates if selective attention to an attended speech source in the presence of a concurrent speech source can predict speech understanding in CI users.

ApproachCI users were instructed to attend to one out of two speech streams while EEG was recorded. Both speech streams were presented to the same ear and at different signal to interference ratios (SIRs). Speech envelope reconstruction of the to-be-attended speech from EEG was obtained by training decoders using regularized least squares. The correlation coefficient between the reconstructed and the attended ({rho}ASIR) and between the reconstructed and the unattended ({rho}USIR) speech stream at each SIR was computed.

Main ResultsSelective attention decoding in CI users is possible even if both speech streams are presented monaurally. A significant effect of SIR on the correlation coefficient to the attended signal{rho} ASIR, as well as on the difference correlation coefficients{rho} ASIR -{rho} USIR and{rho} ASIR -{rho} USIR was observed, but not on the unattended correlation coefficient{rho} USIR. Finally, the results show a significant correlation between speech understanding performance and the correlation coefficients{rho} ASIR-{rho}USIR or -{rho}USIR across subjects. Moreover, the difference correlation coefficient{rho} ASIR -{rho} U-SIR, which is less affected by the CI electrical artifact, presented a correlation trend with speech understanding performance.

SignificanceSelective attention decoding in CI users is possible, however care needs to be taken with the CI artifact and the speech material used to train the decoders. Even if only a small correlation trend between selective attention decoding and speech understanding was observed, these results are important for future development of objective speech understanding measures for CI users.


title: Genome-wide mapping implicates R-loops in lineage-specific processes and formation of DNA break hotspots in neural stem/progenitor cells

abstract: Recent work has revealed classes of recurrent DNA double-strand breaks (DSBs) in neural stem/progenitor cells, including transcription-associated, promoter-proximal breaks and recurrent DSB clusters in late-replicating, long neural genes. However, the mechanistic factors promoting these different classes of DSBs in neural stem/progenitor cells are not understood. Here, we elucidated the genome-wide landscape of DNA:RNA hybrid structures called "R-loops" in primary neural stem/progenitor cells in order to assess their contribution to the different classes of DNA break "hotspots". We report that R-loops in neural stem/progenitor cells are associated primarily with transcribed regions that replicate early and genes that show GC skew in their promoter region. Surprisingly, the majority of genes with recurrent DSB clusters in long, neural genes does not show substantial R-loop accumulation. We implicate R-loops in promoter-proximal DNA break formation in highly transcribed, early replicating regions and conclude that R-loops are not a driver of recurrent double-strand break cluster formation in most long, neural genes. Together, our study provides an understanding of how R-loops may contribute to DNA break hotspots and affect lineage-specific processes in neural stem/progenitor cells.

category: neuroscience


title: The dissociable effects of reward on sequential motor behaviour

abstract: Reward has consistently been shown to enhance motor performance however its beneficial effects appear to be largely unspecific. While reward has been shown to invigorate performance, it also enhances learning and/or retention. Therefore, a mechanistic account of the effects of reward on motor behaviour is lacking. Here we tested the hypothesis that these distinct reward-based improvements are driven by dissociable reward types: explicit reward (i.e. money) and performance feedback (i.e. points). Experiment 1 showed that explicit reward instantaneously improved movement times (MT) using a novel sequential reaching task. In contrast, performance-based feedback led to learning-related improvements. Importantly, pairing both maximised MT performance gains and accelerated movement fusion. Fusion describes an optimisation process during which neighbouring sequential movements blend together to form singular actions. Results from experiment 2 served as a replication and showed that fusion led to enhanced performance speed whilst also improving movement efficiency through increased smoothness. Finally, experiment 3 showed that these improvements in performance persist for 24 hours even without reward availability. This highlights the dissociable impact of explicit reward and performance feedback, with their combination maximising performance gains and leading to stable improvements in the speed and efficiency of sequential actions.


title: Circumscribing laser cuts attenuate seizure propagation in a mouse model of focal epilepsy

abstract:
In partial onset epilepsy, seizures arise focally in the brain and often propagate, causing acute behavior changes, chronic cognitive decline, and increased mortality. Patients frequently become refractory to medical management, leaving neurosurgical resection of the seizure focus as a primary treatment, which can cause neurologic deficits. In the cortex, focal seizures are thought to spread through horizontal connections in layers II/III, suggesting that selectively severing these connections could block seizure propagation while preserving normal columnar circuitry and function. We induced focal neocortical epilepsy in mice and used tightly-focused femtosecond-duration laser pulses to create a sub-surface, opencylinder cut surrounding the seizure focus and severing cortical layers II-IV. We monitored seizure propagation using electrophysiological recordings at the seizure focus and at distant electrodes for 3-8 months. With laser cuts, only 5% of seizures propagated to the distant electrodes, compared to 85% in control animals. Laser cuts also decreased the number of seizures that were initiated, so that the average number of propagated seizures per day decreased from 42 in control mice to 1.5 with laser cuts. Physiologically, these cuts produced a modest decrease in cortical blood flow that recovered within days and, at one month, left a ~20-m wide scar with increased gliosis and localized inflammatory cell infiltration but minimal collateral damage. When placed over motor cortex, cuts did not cause notable deficits in a skilled reaching task. Femtosecond laser produced sub-surface cuts hold promise as a novel neurosurgical approach for intractable focal cortical epilepsy, as might develop following traumatic brain injury.

Once sentence summaryIn a mouse model of focal epilepsy, sub-surface laser-produced cuts encircling the seizure focus attenuate propagation without behavioral impairment.


title: Sensorimotor feedback loops are selectively sensitive to reward

abstract: While it is well established that motivational factors such as earning more money for performing well improve motor performance, how the motor system implements this improvement remains unclear. For instance, feedback-based control, which uses sensory feedback from the body to correct for errors in movement, improves with greater reward. But feedback control encompasses many feedback loops with diverse characteristics such as the brain regions involved and their response time. Which specific loops drive these performance improvements with reward is unknown, even though their diversity makes it unlikely that they are contributing uniformly. This lack of mechanistic insight leads to practical limitations in applications using reward, such as clinical rehabilitation, athletic coaching, and brain-inspired robotics. We systematically tested the effect of reward on the latency (how long for a corrective response to arise?) and gain (how large is the corrective response?) of eight distinct sensorimotor feedback loops in humans. Only the feedback responses known to rely on prefrontal associative cortices showed sensitivity to reward, while feedback responses that relied mainly on premotor and sensorimotor cortex did not show sensitivity to reward. Our results may have implications regarding feedback control performance in pathologies showing a cognitive decline, or on athletic coaching. For instance, coaching methodologies that rely on reinforcement or "reward shaping" may need to specifically target aspects of movement that rely on reward-sensitive feedback responses.


title: Similar cognitive processing synchronizes brains, hearts, and eyes

abstract: Neural, physiological and behavioral signals synchronize between human subjects in a variety of settings. Multiple hypotheses have been proposed to explain this interpersonal synchrony, but there is no clarity under which conditions it arises, for which signals, or whether there is a common underlying mechanism. We hypothesized that similar cognitive processing of a shared stimulus is the source of synchrony between subjects, measured here as inter-subject correlation. To test this we presented informative videos to participants in an attentive and distracted condition and subsequently measured information recall. Inter-subject correlation was observed for electro-encephalography, gaze position, pupil size and heart rate, but not respiration and head movements. The strength of correlation was co-modulated in the different signals, changed with attentional state, and predicted subsequent recall of information presented in the videos. There was robust within-subject coupling between brain, heart and eyes, but not respiration or head movements. The results suggest that inter-subject correlation is the result of similar cognitive processing and thus emerges only for those signals that exhibit a robust brain-body connection. While physiological and behavioral fluctuations may be driven by multiple features of the stimulus, correlation with other individuals is co-modulated by the level of attentional engagement with the stimulus.


title: Cognitive processing of a common stimulus synchronizes brains, hearts, and eyes


title: Experience-dependent changes in hippocampal spatial activity and hippocampal circuit function are disrupted in a rat model of Fragile X Syndrome

abstract: Fragile X syndrome (FXS) is a common single gene cause of intellectual disability and Autism Spectrum Disorder. Cognitive inflexibility is one of the hallmarks of FXS with affected individuals showing extreme difficulty adapting to novel or complex situations. To explore the neural correlates of this cognitive inflexibility, we used a rat model of FXS (Fmr1-/y), and recorded from the CA1 region of the hippocampus while animals habituated in a novel environment for two consecutive days. On the first day of exploration, the firing rate and spatial tuning of CA1 pyramidal neurons was similar between wild-type (WT) and Fmr1-/y rats. However, while CA1 pyramidal neurons from WT rats showed experience-dependent changes in firing and spatial tuning between the first and second day of exposure to the environment, these changes were decreased or absent in CA1 neurons of Fmr1-/y rats. These findings were consistent with increased excitability of Fmr1-/y CA1 neurons in ex-vivo hippocampal slices, which correlated with reduced synaptic inputs from the medial entorhinal cortex. Lastly, activity patterns of CA1 pyramidal neurons were discoordinated with respect to hippocampal oscillatory activity in Fmr1-/y rats. These findings suggest a network-level origin of cognitive deficits in FXS.


title: Sexually dimorphic interplay between anxiety-related phenotype and fear memory extinction

abstract: The authors have withdrawn this manuscript because they want to validate their conclusions further using additional analytic strategies. Therefore, the authors do not wish this work to be cited as reference for the project. If you have any questions, please contact the corresponding author


title: Mitochondrial UPR negatively regulates wounding-induced innate immune response in C. elegans epidermis

abstract:
Tissue damage elicits a rapid innate immune response that is essential for efficient wound healing and survival of metazoans. It is well known that p38 MAPK kinase, TGF-{beta}, and hemidesmosome signaling pathways have been involved in wounding-induced innate immunity in C. elegans. Here, we find that loss of function of ATFS-1 increased innate immune response while an elevated level of mitochondrial unfolded protein response (mitoUPR) inhibits the innate immune response upon epidermal wounding. Epidermal wounding triggers the nucleus export of ATFS-1 and inhibits themitoUPR in C. elegans epidermis. Moreover, genetic analysis suggests that ATFS-1 functions upstream of the p38 MAP kinase, TGF-{beta} and DAF-16 signaling pathways in regulating AMPs induction. Thus, our results suggest that the mitoUPR function as an intracellular signal required to fine-tune innate immune response after tissue damage.

Highlights-- ATFS-1 inhibits the wounding-induced innate immune response in C. elegans
-- mitoUPR inhibits wounding-induced innate immune response
-- Epidermal wounding induces downregulation of ATFS-1 in the epidermis
-- mitoUPR acts upstream of p38MAPK and TGF-{beta} pathways to regulate innate immunity


title: Core cysteine residues in the PAN domain are critical for HGF/c-MET signaling

abstract:
The Plasminogen-Apple-Nematode (PAN) domain, with a core of four to six cysteine residues, is found in > 28,000 proteins across 959 genera but its role in protein function is not fully understood. The PAN domain was initially characterized to be present in numerous proteins including hepatocyte growth factor (HGF). Dysregulation of HGF-mediated signaling results in numerous deadly cancers. All biological impacts of HGF in cell proliferation are triggered by binding of HGF to its cell surface receptor, cellular mesenchymal-epidermal transition (c-MET). Here, we show that four PAN domain cysteine residues are essential for HGF/c-MET signaling. Mutating these residues resulted in retardation of perinuclear localization, cellular internalization of HGF and its receptor, c-MET, and c-MET ubiquitination. Our observations indicate that the PAN domain of HGF is required for the c-MET binding and subsequent c-MET autophosphorylation and phosphorylation of its downstream targets, protein kinase B (AKT), extracellular signal-regulated kinase (ERK), and signal transducer and activator of transcription 3 (STAT3). Furthermore, transcriptional activation of HGF/c-MET signaling-related genes including matrix metalloproteinase-9 (MMP9), ETS translocation variant 1, 4, and 5 (ETV1, ETV4, ETV5), and early growth response 1 (EGR1) was impaired and cell proliferation was attenuated. These results suggest that core cysteine residues in the PAN domain are critical for HGF/c-MET interaction, c-MET mediated signal transduction, and cell survival. Thus, targeting the PAN domain of HGF may represent a mechanism for selectively regulating the binding and activation of the c-MET pathway.

SignificanceHGF/c-MET signaling induces multifunctional cellular responses. Dysregulation of HGF/c-MET signaling cascade can lead to tumorigenesis by transforming normal cells to tumor cells. This work defines the importance of core cysteine residues in the PAN domain of HGF in downstream activation of HGF/c-MET signaling. To understand the role of cysteines in the PAN domain, PAN mutants of HGF were used to stimulate c-MET signaling in cells and the impact was delineated by determining phosphorylation and transcription of downstream targets. Mutations in core cysteines in the HGF-PAN domain completely blocked downstream phosphorylation and perinuclear accumulation of c-MET. These results suggest an indispensable role for the cysteine-rich PAN domain in HGF/c-MET interaction and could set the stage for future therapies that selectively disrupt the MET signaling cascade with limited off-target effects in tumors overexpressing HGF/c-MET.


title: Optineurin links Hace1-dependent Rac ubiquitylation to integrin-mediated mechanotransduction to control bacterial invasion and cell division

abstract: Extracellular matrix (ECM) elasticity is perceived by cells via focal adhesion structures, which transduce mechanical cues into chemical signalling to conform cell behaviour. Although the contribution of ECM compliance to the control of cell migration or division has been extensively studied, little has been reported regarding infectious processes. We have studied how mechanical properties of the ECM impact invasion of cells by the extraintestinal Escherichia coli pathogen UTI89. We show that UTI89 takes advantage, via its CNF1 toxin, of integrin mechanoactivation to trigger its invasion into cells. We identified OPTN as a protein regulated by ECM stiffness whose function is required for bacterial invasion and integrin mechanical coupling and for stimulation of HACE1 E3 ligase activity towards the Rac1 GTPase. We showed that OPTN knockdown cells display enhanced Rac1 activation, strong mechanochemical adhesion signalling and increased cyclin D1 translation, together with enhanced cell proliferation independent of ECM stiffness. Despite such features, OPTN knockdown cells displayed defective traction force buildup associated with limited cellular invasion by UTI89. Together, our data indicate that OPTN, through a new role in mechanobiology, supports CNF1-producing uropathogenic E. coli invasion and links HACE1-mediated ubiquitylation of Rac1 to ECM mechanical properties and integrin mechanotransduction.


title: The Transcription Factor Xrp1 is Required for PERK-Mediated Antioxidant Gene Induction in Drosophila

abstract: PERK is an endoplasmic reticulum (ER) transmembrane sensor that phosphorylates eIF2 to initiate the Unfolded Protein Response (UPR). eIF2 phosphorylation promotes stress-responsive gene expression most notably through the transcription factor ATF4 that contains a regulatory 5 leader. Possible PERK effectors other than ATF4 remain poorly understood. Here, we report that the bZIP transcription factor Xrp1 is required for ATF4-independent PERK signaling. Cell type-specific gene expression profiling in Drosophila indicated that delta-family glutathione-S-transferases (gstD) are prominently induced by the UPR-activating transgene Rh1G69D. Perk was necessary and sufficient for such gstD induction, but ATF4 was not required. Instead, Perk and other regulators of eIF2 phosphorylation regulated Xrp1 protein levels to induce gstDs. The Xrp1 5 leader has a conserved upstream Open Reading Frame (uORF) analogous to those that regulate ATF4 translation. The gstD-GFP reporter induction required putative Xrp1 binding sites. These results indicate that antioxidant genes are highly induced by a previously unrecognized UPR signaling axis consisting of PERK and Xrp1.


title: Crotamiton derivative JM03 extends lifespan and improves oxidative and hypertonic stress resistance in Caenorhabditis elegans via inhibiting OSM-9

abstract: While screening our in-house 1,072 marketed drugs for their ability to extend the lifespan using Caenorhabditis elegans (C. elegans) as an animal model, crotamiton (N-ethyl-o-crotonotoluidide) showed anti-aging activity and was selected for further structural optimization. After replacing the ortho-methyl of crotamiton with ortho-fluoro, crotamiton derivative JM03 was obtained and showed better activity in terms of lifespan-extension and stress resistance than crotamiton. It was further explored that JM03 extended the lifespan of C. elegans through osmotic avoidance abnormal-9 (OSM-9). Besides, JM03 improves the ability of nematode to resist oxidative stress and hypertonic stress through OSM-9, but not osm-9/capsaicin receptor related-2 (OCR-2). Then the inhibition of OSM-9 by JM03 reduces the aggregation of Q35 in C. elegans via upregulating the genes associated with proteostasis. SKN-1 signaling was also found to be activated after JM03 treatment, which might contribute to proteostasis, stress resistance and lifespan extension. In summary, this study explored a new small molecule derived from crotamiton, which has efficient anti-oxidative, anti-hypertonic and anti-aging effects, and could further lead to promising application prospects.


title: Transcriptomics based prediction of metastasis in TNBC patients: Challenges in cross-platforms validation

abstract: Triple-negative breast cancer (TNBC) is more prone to metastasis and recurrence than other breast cancer subtypes. This study aimed to identify genes that can act as diagnostic biomarkers for predicting lymph node metastasis in TNBC patients. The transcriptomic data of TNBC with or without lymph node metastasis was acquired from TCGA, and the differentially expressed genes were identified. Further, logistic-regression method has been used to identify the top 15 genes (or 15 gene signatures) based on their ability to predict metastasis (AUC>0.65). These 15 gene signatures were used to develop machine learning techniques based prediction models; Gaussian Naive Bayes classifier outperformed other with AUC>0.80 on both training and validation datasets. The best model failed drastically on nine independent microarray datasets obtained from GEO. We investigated the reason for the failure of our best model, and it was observed that the certain genes in 15 gene signatures were showing opposite regulating trends, i.e., genes are upregulated in TCGA-TNBC patients while it is downregulated on other microarray datasets or vice-versa. In conclusion, the 15 gene signatures may act as diagnostic markers for the detection of lymph node metastatic status in TCGA dataset, but quite challenging across multiple platforms. We also identified the prognostic potential of the 15 selected genes and found that overexpression of ZNRF2, FRZB, and TCEAL4 was associated with poor survival with HR>2.3 and p-value[≤]0.05. In order to provide services to the scientific community, we developed a webserver named "MTNBCPred" for the prediction of metastatic and non-metastatic lymph node status of TNBC patients (http://webs.iiitd.edu.in/raghava/mtnbcpred/).

category: bioinformatics


title: Integrative Analysis of Spatial Transcriptome with Single-cell Transcriptome and Single-cell Epigenome in Mouse Lungs after Immunization

abstract: Immunological memory is key to productive adaptive immunity. An unbiased, high throughput gene expression profiling of tissue-resident memory T cells at their precise anatomical locations within the lung is fundamental to understanding lung immunity, but such spatial information has yet to be characterized. In this study, using a well-established Klebsiella pneumoniae infection model, we performed an integrative analysis of spatial transcriptome with single-cell RNA-seq and single-cell ATAC-seq on lung cells from mice after immunization using the 10x Genomics Chromium and Visium platform. We employed several deconvolution algorithms and established an optimized deconvolution pipeline to accurately decipher specific cell-type composition by anatomic location. We identified and located 12 major cell types by scRNA-seq and spatial transcriptomic analysis. Integrating scATAC-seq data from the same cells processed in parallel with scRNA-seq, we found epigenomic profiles provide more robust cell type identification, especially for lineage-specific T helper cells. When combining all three data modalities, we observed a dynamic change in the location of T helper cells as well as their corresponding chemokines for chemotaxis. Furthermore, cell-cell communication analysis of spatial transcriptome provided evidence of lineage-specific T helper cells receiving designated cytokine signaling. In summary, our first-in-class study demonstrated the power of multi-omics analysis to uncover intrinsic spatial- and cell-type-dependent molecular mechanisms of lung immunity. Our data provides a rich research resource of single cell multi-omics data as a reference for understanding spatial dynamics of lung immunization.


title: Arabidopsis iron superoxide dismutase 1 protects against methyl viologen-induced oxidative stress in a copper-dependent manner

abstract: Iron superoxide dismutase 1 (FSD1) was recently characterized as a plastidial, cytoplasmic, and nuclear superoxide dismutase with osmoprotective and antioxidative functions. However, its role in oxidative stress tolerance is not well understood. Here, we characterized the role of FSD1 in response to methyl viologen (MV)-induced oxidative stress in Arabidopsis thaliana. The findings demonstrated that the antioxidative function of FSD1 depends on the availability of Cu2+ in growth media. Prolonged MV exposure led to a decreased accumulation rate of superoxide, higher levels of hydrogen peroxide production, and higher protein carbonylation in the fsd1 mutants and transgenic plants lacking a plastidial pool of FSD1, compared to the wild type. MV led to a rapid increase in FSD1 activity, followed by a decrease. Chloroplastic localization of FSD1 is necessary for these changes. Proteomic analysis showed that the sensitivity of the fsd1 mutants coincided with decreased abundance of ferredoxin and light PSII harvesting complex proteins, with altered levels of signaling proteins. Collectively, the study provides evidence for the conditional antioxidative function of FSD1 and its possible role in signaling.

category: plant biology


title: small RNA can move long distances through plant vasculature to influence gene expression in shoot apical meristems

abstract: In plants, small RNA (sRNA) can regulate gene expression via post transcriptional gene silencing (PTGS) or through RNA-directed DNA methylation (RdDM) leading to transcriptional gene silencing (TGS). sRNA is mobile throughout the plant, with movement occurring short distances from cell-to-cell as well as long distances through the vasculature via phloem trafficking. The range of long-distance sRNA mediated signaling from the vasculature to the shoot apical meristem (SAM) is not clear. To investigate this, two independent transgenic approaches were used to examine trafficking of phloem-expressed sRNA to the SAM in Arabidopsis thaliana. First, the phloem companion-cell specific promoter SUC2 was used to drive expression of an inverted repeat complementary to FLOWERING LOCUS D (FD), a flowering time regulator expressed exclusively in the SAM. In a separate experiment, the SUC2 promoter was used to express an artificial microRNA (aMiR) designed to target a synthetic CLAVATA3 (CLV3) target in the SAM stem cells. Both systems provide evidence of a phloem-to-SAM sRNA communication axis connecting distal regions of the plant to the stem cells of the SAM, which ultimately gives rise to all shoot tissues, including gametes. Thus, phloem-to-SAM sRNA movement defines an important link between sRNA expressed in distal regions of the plant and the growing shoot. Importantly, phloem-to-SAM sRNA trafficking may allow somatic sRNA to direct SAM RdDM, fixing transient sRNA expression events into stable epigenetic changes.


title: Examining the effects of free gaze and dynamic video stimuli on engagement, eye movements, and EEG signal quality in a visual aesthetic rating task

abstract:
AO_SCPLOWBSTRACTC_SCPLOWFree gaze and moving images are typically avoided in EEG experiments due to the expected generation of artifacts and noise. Yet for a growing number of research questions, loosening these rigorous restrictions would be beneficial. Among these is research on visual aesthetic experiences, which often involve open-ended exploration of highly variable stimuli. Here we systematically compare the effect of conservative vs. more liberal experimental settings on various measures of behavior, brain activity and physiology in an aesthetic rating task. Our primary aim was to assess EEG signal quality. 43 participants either maintained fixation or were allowed to gaze freely, and viewed either static images or dynamic (video) stimuli consisting of dance performances or nature scenes. A passive auditory background task (auditory steady-state response; ASSR) was added as a proxy measure for overall EEG recording quality. We recorded EEG, ECG and eyetracking data, and participants rated their aesthetic preference and state of boredom on each trial. Whereas both behavioral ratings and gaze behavior were affected by task and stimulus manipulations, EEG SNR was barely affected and generally robust across all conditions, despite only minimal preprocessing and no trial rejection. In particular, we show that using video stimuli does not necessarily result in lower EEG quality and can, on the contrary, significantly reduce eye movements while increasing both the participants aesthetic response and general task engagement. We see these as encouraging results indicating that - at least in the lab - more liberal experimental conditions can be adopted without significant loss of signal quality.

HighlightsO_LIWe assess trade-offs between EEG quality and behavior for common task constraints
C_LIO_LIInvestigated constraints: fixation task vs. free gaze, and video vs. static stimuli
C_LIO_LIMeasures: EEG quality, aesthetic preference, task engagement, gaze and heart rate
C_LIO_LIVideo stimuli reduce eye movements, increase engagement and do not affect EEG SNR
C_LIO_LIFixation task only slightly increases SNR and does not influence ratings
C_LI


title: Naturalistic viewing conditions increase task engagement and aesthetic preference but have only minimal impact on EEG quality


title: Naturalistic viewing conditions can increase task engagement and aesthetic preference but have only minimal impact on EEG quality


title: A shared brain system forming confidence judgment across cognitive domains

abstract: Confidence is typically defined as a subjective judgment about whether a decision is right. Decisions are based on sources of information that come from various cognitive domains and are processed in different brain systems. An unsettled question is whether the brain computes confidence in a similar manner whatever the domain or in a manner that would be idiosyncratic to each domain. To address this issue, human participants of both sexes performed two tasks probing confidence in decisions made about the same material (history and geography statements), but based on different cognitive processes: semantic memory for deciding whether the statement was true or false, and duration perception for deciding whether the statement display was long or short. At the behavioral level, we found that the same factors (difficulty, accuracy, response time and confidence in the preceding decision) predicted confidence judgments in both tasks. At the neural level, we observed using fMRI that confidence judgments in both tasks were associated to activity in the same brain regions: positively in the ventromedial prefrontal cortex and negatively in a prefronto-parietal network. Together, these findings suggest the existence of a shared brain system that generates confidence judgments in a similar manner across cognitive domains.


title: Myelin Imaging Using 3D Dual-echo Ultra-short Echo Time MRI with Rosette k-Space Pattern

abstract:
PurposeThis study aimed to develop a new 3D dual-echo rosette k-space trajectory, specifically for ultra-short echo time (UTE) magnetic resonance imaging (MRI) applications. The direct imaging of the myelin bilayer, which has ultra-short transverse relaxation time (uT2), was acquired to test the performance of the proposed UTE sequence.

Theory and MethodsThe rosette trajectory was developed based on rotations of a  petal-like pattern in the kx-ky plane, with oscillated extensions in kz-direction for 3D coverage. Five healthy volunteers were recruited and underwent ten dual-echo 3D rosette UTE scans with various echo times (TEs). Dual-exponential complex model fitting was performed on the magnitude data to separate uT2 signals, with the output of uT2 fraction, uT2 value, and long T2 value.

ResultsThe reconstructed images signal contrast between whiate matter (WM) and grey matter (GM) increased with longer TEs. The WM regions had higher uT2 fraction values than GM (10.9%{+/-}1.9% vs. 5.7%{+/-}2.4%). The uT2 value was approximately 0.15 milliseconds in WM.

ConclusionThe higher uT2 fraction value in WM compared to GM demonstrated the ability of the proposed sequence to capture rapidly decaying signals.


title: Regulation of the cognitive aging process by the transcriptional repressor RP58

abstract: Aging involves a decline in physiology which is a natural event in all living organisms. An accumulation of DNA damage contributes to the progression of aging. DNA is continually damaged by exogenous sources and endogenous sources. If the DNA repair pathway operates normally, DNA damage is not life threatening. However, impairments of the DNA repair pathway may result in an accumulation of DNA damage, which has a harmful effect on health and causes an onset of pathology. RP58, a zinc-finger transcriptional repressor, plays a critical role in cerebral cortex formation. Recently, it has been reported that the expression level of RP58 decreases in the aged human cortex. Furthermore, the role of RP58 in DNA damage is inferred by the involvement of DNMT3, which acts as a co-repressor for RP58, in DNA damage. Therefore, RP58 may play a crucial role in the DNA damage associated with aging. In the present study, we investigated the role of RP58 in aging. We used RP58 hetero-knockout and wild-type mice in adolescence, adulthood, or old age. We performed immunohistochemistry to determine whether microglia and DNA damage markers responded to the decline in RP58 levels. Furthermore, we performed an object location test to measure cognitive function, which decline with age. We found that the wild-type mice showed an increase in single-stranded DNA and gamma-H2AX foci. These results indicate an increase in DNA damage or dysfunction of DNA repair mechanisms in the hippocampus as age-related changes. Furthermore, we found that, with advancing age, both the wild-type and hetero-knockout mice showed an impairment of spatial memory for the object and increase in reactive microglia in the hippocampus. However, the RP58 hetero-knockout mice showed these symptoms earlier than the wild-type mice did. These results suggest that a decline in RP58 level may lead to the progression of aging.


title: Limitations of a proposed correction for slow drifts in decision criterion

abstract: Trial history biases in decision-making tasks are thought to reflect systematic updates of decision variables, therefore their precise nature informs conclusions about underlying heuristic strategies and learning processes. However, random drifts in decision variables can corrupt this inference by mimicking the signatures of systematic updates. Hence, identifying the trial-by-trial evolution of decision variables requires methods that can robustly account for such drifts. Recent studies (Lak20, Mendonca 20) have made important advances in this direction, by proposing a convenient method to correct for the influence of slow drifts in decision criterion, a key decision variable. Here we apply this correction to a variety of updating scenarios, and evaluate its performance. We show that the correction fails for a wide range of commonly assumed systematic updating strategies, distorting ones inference away from the veridical strategies towards a narrow subset. To address these limitations, we propose a model-based approach for disambiguating systematic updates from random drifts, and demonstrate its success on real and synthetic datasets. We show that this approach accurately recovers the latent trajectory of drifts in decision criterion as well as the generative systematic updates from simulated data. Our results offer recommendations for methods to account for the interactions between history biases and slow drifts, and highlight the advantages of incorporating assumptions about the generative process directly into models of decision-making.


title: Reactivating Hippocampal-Mediated Memories to Disrupt the Reconsolidation of Fear

abstract: Memories are stored in the brain as cellular ensembles activated during learning and reactivated during retrieval. Using the Tet-tag system, we labeled dorsal dentate gyrus (dDG) neurons activated by positive, neutral or negative experiences with channelrhodopsin-2. Following fear-conditioning, these cells were artificially reactivated during fear memory recall. Optical stimulation of a competing positive memory was sufficient to disrupt reconsolidation, thereby reducing conditioned fear acutely and enduringly. Moreover, mice demonstrated operant responding for reactivation of a positive memory, confirming its rewarding properties. These results show that interference from a rewarding experience can counteract negative affective states. While interference induced by memory reactivation involved a relatively small set of neurons, we also found that activating a large population of randomly labeled dDG neurons was effective at disrupting reconsolidation. Importantly, reconsolidation-interference was specific to the fear memory. These findings implicate the dDG as a potential therapeutic node for modulating memories to suppress fear.


title: Full bandwidth electrophysiology of seizures and epileptiform activity enabled by flexible graphene micro-transistor depth neural probes

abstract: Mapping the entire frequency bandwidth of neuronal oscillations in the brain is of paramount importance for understanding physiological and pathological states. The ability to record simultaneously infraslow activity (<0.1 Hz) and higher frequencies (0.1-600 Hz) using the same recording electrode would particularly benefit epilepsy research. However, commonly used metal microelectrode technology is not well suited for recording infraslow activity. Here we use flexible graphene depth neural probes (gDNP), consisting of a linear array of graphene microtransistors, to concurrently record infraslow and high frequency neuronal activity in awake rodents. We show that gDNPs can reliably record and map with high spatial resolution seizures, post-ictal spreading depolarisation, and high frequency epileptic activity through cortical laminae to the CA1 layer of the hippocampus in a mouse model of chemically-induced seizures. We demonstrate functionality of chronically implanted devices over 10 weeks by recording with high fidelity spontaneous spike-wave discharges and associated infraslow activity in a rat model of absence epilepsy. Altogether, our work highlights the suitability of this technology for in vivo electrophysiology research, in particular, to examine the contributions of infraslow activity to seizure initiation and termination.


title: Inhibitory hippocampo-septal projection controls locomotion and exploratory behavior

abstract: Although the hippocampus is generally considered a cognitive center for spatial representation, learning and memory, increasing evidence supports its roles in regulation of locomotion. However, the neuronal mechanisms of hippocampal regulation of locomotion and exploratory behavior remain unclear. Here we found that the inhibitory hippocampo-septal projection bi-directionally controls locomotion speed of mice. Pharmacogenetic activation of these septum-projecting interneurons decreased locomotion and exploratory behavior. Similarly, activation of the hippocampus-originated inhibitory terminal in the medial septum reduced locomotion. On the other hand, inhibition of the hippocampus-originated inhibitory terminal increased locomotion. The locomotion-regulative roles were specific to the septal projecting interneurons as activation of hippocampal interneurons projecting to the retrosplenial cortex did not change animal locomotion. Therefore, this study reveals a specific long-range inhibitory output from the hippocampus in the regulation of animal locomotion.


title: Demographic changes of a tropical understory bird in naturally patchy montane habitats in southern India

abstract: The occurrence, density and survival of a species often depend on various aspects of the habitat that it occupies including patch size and disturbance. The demography of most threatened tropical species largely remain unstudied but could provide valuable information about their biology and insights for their conservation. Our study examined the effect of patch size and disturbance on different demographic parameters of an understory, threatened, endemic bird, the white-bellied shortwing in the tropical biodiversity hotspot of the Western Ghats in India. We sampled eight plots on a sky-island using mist-nets for four years in a  Robust design mark-recapture framework. Based on model selection using AIC values, the model with survival as a function of disturbance fits the data better than models with abundance or with these parameters modeled as functions of forest patch size. Shortwing density and sex ratio were not different across forest patch sizes or differing disturbance regimes. However, the survival rate of the species significantly decreased with increasing disturbance but was not related to forest patch size. Our study is possibly the first to provide critical baseline information on the demography of a tropical understory species from this region.

category: ecology


title: Why do fungicide mixtures delay the evolution of resistance? An experimental evolutionary approach

abstract: Pesticide resistance poses a critical threat to agriculture, human health and biodiversity. Mixtures of fungicides are recommended and widely used in resistance management strategies. However, the components of the efficiency of such mixtures remain unclear. We performed an experimental evolution study on the fungal pathogen Z. tritici, to determine how mixtures managed resistance. We compared the effect of the continuous use of single active ingredients to that of mixtures, at the minimal dose providing full control of the disease, which we refer to as the "efficient" dose. We found that the performance of efficient-dose mixtures against an initially susceptible population depended strongly on the components of the mixture. Such mixtures were either as durable as the best mixture component used alone, or worse than all components used alone. Moreover, efficient-dose mixture regimes probably select for generalist resistance profiles as a result of the combination of selection pressures exerted by the various components and their lower doses. Our results indicate that mixtures should not be considered a universal strategy. Experimental evaluations of specificities for the pathogens targeted, their interactions with fungicides and the interactions between fungicides are crucial for the design of sustainable resistance management strategies.

category: evolutionary biology


title: Endogenous virus sRNA regulates gene expression following genome shock in tomato hybrids

abstract: Hybridization and environmental stress trigger genome shock that perturbs patterns of gene expression leading to phenotypic changes. In extreme examples it is associated to transposon mobilization and genome rearrangement. Here we discover a novel alternative mechanism in interspecific Solanum hybrids in which changes to gene expression were associated with DCL2-mediated small (s)RNAs derived from endogenous (para)retroviruses (EPRVs). Correspondingly, the altered patterns of gene expression overlapped with the effects of dcl2 mutation and the changes to sRNA profiles involved 22nt species produced in the DCL2 biogenesis pathway. These findings implicate hybridization-induced genome shock leading to EPRV activation and sRNA silencing as causing changes in gene expression. Such hybridization-induced variation in gene expression could increase the range of traits available for selection in natural evolution or in breeding for agriculture.

category: genetics


title: Effects of short-term salinity exposure on haemolymph osmolality, gill morphology and Na+/K+ - ATPase activity in Solenaia oleivora

abstract: In order to explore the physiological reaction to hyperosmotic environment, Solenaia oleivora were exposed to 2.23{per thousand} salinity. In 48h, the hemolymph osmolality kept increasing, and the hemolymph protein concentration increased in the first 6h and then decreased significantly, while the free amino acid content increased in the first 24h and then kept stable (P < 0.05). The activity of Na+/K+-ATPase at 0h was significantly higher than other times in most organs except intestine, which was highest at 3h (P < 0.05). The ions concentration were also influenced. The concentration of Na+ rose in haemolymph, axe foot and intestine, but decreased in gill and hepatopancreas. In hemolymph, gill, hepatopancreases and adductor muscle, the K+ concentration was the highest at 0h, while in axe foot and intestine, it showed a positive tendency. The concentration of Cl- in haemolymph, adductor muscle, intestine and axe foot were positively correlated with treatment time, while hepatopancreas showed opposite tendency. High salinity stress caused a difference in the gill histological structure, the gill structure shrunk, the gill lamellas space and shrinking degree showed an enlarging trend with salinity treatment time.

category: animal behavior and cognition


title: pcnaDeep: A Fast and Robust Single-Cell Tracking Method Using Deep-Learning Mediated Cell Cycle Profiling

abstract:
MotivationComputational methods that track single-cells and quantify fluorescent biosensors in time-lapse microscopy images have revolutionised our approach in studying the molecular control of cellular decisions. One barrier that limits the adoption of single-cell analysis in biomedical research is the lack of efficient methods to robustly track single-cells over cell division events.

ResultsHere, we developed an application that automatically tracks and assigns mother-daughter relationships of single-cells. By incorporating cell cycle information from a well-established fluorescent cell cycle reporter, we associate mitosis relationships enabling high fidelity long-term single-cell tracking. This was achieved by integrating a deep-learning based fluorescent PCNA signal instance segmentation module with a cell tracking and cell cycle resolving pipeline. The application offers a user-friendly interface and extensible APIs for customized cell cycle analysis and manual correction for various imaging configurations.

Availability and ImplementationpcnaDeep is an open-source Python application under the Apache 2.0 licence. The source code, documentation and tutorials are available at https://github.com/chan-labsite/PCNAdeep.

Supplementary InformationSupplementary data are available online.


title: iCOMIC: a graphical interface-driven bioinformatics pipeline for analyzing cancer omics data

abstract:
Despite the tremendous increase in omics data generated by modern sequencing technologies, their analysis can be tricky and often requires substantial expertise in bioinformatics. To address this concern, we have developed a user-friendly pipeline to analyze (cancer) genomic data that takes in raw sequencing data (FASTQ format) as input and outputs insightful statistics on the nature of the data. Our iCOMIC toolkit pipeline can analyze whole-genome and transcriptome data and is embedded in the popular Snakemake workflow management system. iCOMIC is characterized by a user-friendly GUI that offers several advantages, including executing analyses with minimal steps, eliminating the need for complex command-line arguments. The toolkit features many independent core workflows for both whole genomic and transcriptomic data analysis. Even though all the necessary, well-established tools are integrated into the pipeline to enable  out-of-the-box analysis, we provide the user with the means to replace modules or alter the pipeline as needed. Notably, we have integrated algorithms developed in-house for predicting driver and passenger mutations based on mutational context and tumor suppressor genes and oncogenes from somatic mutation data. We benchmarked our tool against Genome In A Bottle (GIAB) benchmark dataset (NA12878) and got the highest F1 score of 0.971 and 0.988 for indels and SNPs, respectively, using the BWA MEM - GATK HC DNA-Seq pipeline. Similarly, we achieved a correlation coefficient of r=0.85 using the HISAT2-StringTie-ballgown and STAR-StringTie-ballgown RNA-Seq pipelines on the human monocyte dataset (SRP082682). Overall, our tool enables easy analyses of omics datasets, with minimal steps, significantly ameliorating complex data analysis pipelines.

Availability: https://github.com/RamanLab/iCOMIC


title: Development of novel potent ligands for GPR85, an orphan G protein-coupled receptor expressed in the brain

abstract: GPR85 is a member of the G protein-coupled receptor and is a super-conserved receptor expressed in the brain sub-family (SREB) with GPR27 and GPR173. These three receptors are "orphan receptors"; however, their endogenous ligands have not been identified. SREB has garnered the interest of many scientists because it is expressed in the central nervous system and is evolutionarily conserved. In particular, brain mass is reported to be increased and learning and memory are improved in GPR85 knockout mice (Matsumoto et al., 2008). In this study, we characterized newly synthesized compounds using a GPR85-Gs fusion protein and the [35S]GTP{gamma}S binding assay and identified novel GPR85 inverse-agonists with IC50 values of approximately 1 {micro}M. To analyze the neurochemical character of the compounds and investigate the physiological significance of GPR85, we used cerebellar Purkinje cells expressing GPR85 and an electrophysiological technique. Based on the results, the inverse-agonist compound for GPR85 modulated potassium channel opening. Together with the results of previous gene analysis of GPR85, we expect that the development of the GPR85 ligand will provide new insights into a few types of neurological disorders.

category: pharmacology and toxicology


title: Age-related differences in performance and fatigability during an isometric quadriceps intermittent fatigue test

abstract: The aim of the present study was to investigate age-related differences in fatigability induced by an isometric quadriceps intermittent fatiguing test in young (<35 years old), old (>60 years old) and very old (>80 years old) men and women. Maximal force loss, contractile function and voluntary activation of the knee extensors were evaluated throughout an isometric fatiguing test using femoral nerve magnetic stimulations. Older adults performed more contractions (index of relative performance) than young (P = 0.046) and very old adults (P = 0.007), without differences between young and very old adults. Total work (absolute performance) was greater for young and old adults compared to very old adults (P < 0.001), without differences between young and old adults. At exhaustion, force loss was greater for young (-28 {+/-} 9%) compared to old adults (-19 {+/-} 8%), but not very old adults (-23 {+/-} 8%). The response to femoral nerve stimulation decreased similarly at exhaustion for the three age groups, indicating similar alteration in contractile function with age. No impairment in voluntary activation was observed. Impairments in neuromuscular parameters were similar for men and women. This study showed that older adults were less fatigable than young adults during an isometric intermittent fatiguing task of the knee extensors. This greater fatigue resistance was not maintained in very old adults independent of sex. Fatigability at exhaustion was likely due to impairments in contractile function for the three age groups.

category: physiology


title: Individualised computational modelling of immune mediated disease onset, flare and clearance in psoriasis

abstract:
Despite increased understanding about psoriasis pathophysiology, currently there is a lack of predictive computational models. We developed a personalisable ordinary differential equations model of human epidermis and psoriasis that incorporates immune cells and cytokine stimuli to regulate the transition between healthy and disease skin. In line with experimental data, an immune stimulus initiated transition from healthy skin to psoriasis and apoptosis induced by UVB phototherapy returned the epidermis back to the healthy state. The flexibility of our model permitted the development of a patient-specific "UVB sensitivity" parameter that enabled simulation of individual patients clinical response trajectory. In a prospective clinical study of 94 patients, serial individual UVB doses and clinical response (Psoriasis Area Severity Index) values collected over the first three weeks of UVB therapy informed estimation of the "UVB sensitivity" parameter and the prediction of individual patient outcome at the end of phototherapy. Notably, our model was able to distinguish disease flares and offers the potential for clinical application in early assessment of response to UVB therapy, and for individualised optimisation of phototherapy regimes to improve clinical outcome.

Author SummaryWe present a new computer model for psoriasis, an immune-mediated disabling skin disease which presents with red, raised scaly plaques that can appear over the whole body. Psoriasis affects millions of people in the UK alone and causes significant impairment to quality of life, and currently has no cure. Only a few treatments (including UVB phototherapy) can induce temporary remission. Despite our increased understanding about psoriasis, treatments are still given on a  trial and error basis and there are no reliable computer models that can a) elucidate the mechanisms behind psoriasis onset or flare and b) predict a patients response to a course of treatment (e.g., phototherapy) and the likelihood of inducing a period of remission. Our computer model addresses both these needs. First, it explicitly describes the interaction between the immune system and skin cells. Second, our model captures response to therapy at the individual patient level and enables personalised prediction of clinical outcomes. Notably, our model also supports prediction of amending individual UVB phototherapy regimes based on the patients initial response that include for example personalised delivery schedules (i.e., 3x weekly vs. 5x weekly phototherapy). Therefore, our work is a crucial step towards precision medicine for psoriasis treatment.

category: systems biology


title: Intrinsic neural activity predisposes susceptibility to a body illusion

abstract:
Susceptibility to the rubber hand illusion (RHI) varies. Thus far, however, there is no consensus as regards how to explain this variation. Previous studies, focused on the role of multisensory integration, have searched for neural correlates of the illusion. Those studies, however, have failed to identify a sufficient set of functionally specific neural correlates. An alternative explanation of the illusion is that it results from demand characteristics, chiefly variability in the disposition to respond to imaginative suggestion: the degree to which intrinsic neural activity allows for a blurring of boundaries between self and external objects. Some evidence suggests that frontal  power is one means of tracking neural instantiations of self; therefore, we hypothesized that the higher the frontal  power during eyes-closed resting state, the more stable the self. As a corollary, we infer that the more stable the self, the less susceptible are participants to a blurring of boundaries--to feeling that the rubber hand belongs to them. Indeed, we found that frontal  amplitude oscillations negatively correlate with susceptibility. Moreover, since  and {delta} oscillations seem to be associated in pathological states that allow for a blurring of boundaries between self and external objects, we conjectured that the high frontal  power observed in low-RHI participants is modulated by {delta} frequency oscillations. Indeed, we found this to be the case. Based on our findings we propose that the two explanatory frameworks might be complementary: that is, the neural correlates of multisensory integration might be necessary for the RHI, but a sufficient explanation requires investigation of variable intrinsic neural activity that acts to modulate how the brain responds to incompatible sensory stimuli.

Highlights~Intrinsic frontal  power negatively correlates with susceptibility to the RHI.
~Intrinsic  power modulated by {delta} oscillations varies with susceptibility to the RHI.
~Sufficient explanation of RHI requires understanding of intrinsic neural dispositions that regulate the boundary between self and the external world.


title: The synaptic basis of activity-dependent eye-specific competition

abstract:
Binocular vision requires proper developmental wiring of eye-specific inputs to the brain. Axons from the two eyes initially overlap in the dorsal lateral geniculate nucleus and undergo activity-dependent competition to segregate into target domains. The synaptic basis of such refinement is unknown. Here we used volumetric super-resolution imaging to measure the nanoscale molecular reorganization of developing retinogeniculate eye-specific synapses in the mouse brain. The outcome of binocular synaptic competition was determined by the relative eye-specific maturation of presynaptic vesicle content. Genetic disruption of spontaneous retinal activity prevented subsynaptic vesicle pool maturation, recruitment of vesicles to the active zone, synaptic development and eye-specific competition. These results reveal an activity-dependent presynaptic basis for axonal refinement in the mammalian visual system.

One-Sentence SummarySpontaneous activity regulates the nanoscale remodeling of presynaptic terminals underlying eye-specific synaptogenesis and competition.


title: Analysis of the upper respiratory tract microbiota in mild and severe COVID-19 patients

abstract: The microbiota of the respiratory tract remains a relatively poorly studied subject. At the same time, like the intestinal microbiota, it is involved in modulating the immune response to infectious agents in the host organism. A causal relationship between the composition of the respiratory microbiota and the likelihood of development and the severity of COVID-19 may be hypothesized. We analyze biomaterial from nasopharyngeal smears from 336 patients with a confirmed diagnosis of COVID-19, selected during the first and second waves of the epidemic in Russia. Sequences from a similar study conducted in Spain were also included in the analysis. We investigated associations between disease severity and microbiota at the level of microbial community (community types) and individual microbes (differentially represented species). To search for associations, we performed multivariate analysis, taking into account comorbidities, type of community and lineage of the virus. We found that two out of six community types are associated with a more severe course of the disease, and one of the community types is characterized by high stability (very similar microbiota profiles in different patients) and low level of lung damage. Differential abundance analysis with respect to comorbidities and community type suggested association of Rothia and Streptococcus genera representatives with more severe lung damage, and Leptotrichia, unclassified Lachnospiraceae and Prevotella with milder forms of the disease.


title: Global and regional ecological boundaries drive abrupt changes in avian frugivory interactions

abstract:
Species interactions can propagate disturbances across space, though ecological and biogeographic boundaries may limit this spread. We tested whether large-scale ecological boundaries (ecoregions and biomes) and human disturbance gradients increase dissimilarity among ecological networks, while accounting for background spatial and elevational effects and differences in network sampling. We assessed network dissimilarity patterns over a broad spatial scale, using 196 quantitative avian frugivory networks (encompassing 1,496 plant and 1,003 bird species) distributed across 67 ecoregions and 11 biomes. Dissimilarity in species and interactions, but not in network structure, increased significantly across ecoregion and biome boundaries and along human disturbance gradients. Our findings suggest that ecological boundaries contribute to maintaining the worlds biodiversity of interactions and mitigating the propagation of disturbances at large spatial scales.

One-Sentence SummaryEcoregions and biomes delineate the large-scale distribution of plant-frugivore interactions.


title: A novel method for an unbiased estimate of cross-ancestry genetic correlation using individual-level data

abstract: Cross-ancestry genetic correlation is an important parameter to understand the genetic relationship between two ancestry groups for a complex trait. However, existing methods cannot properly account for ancestry-specific genetic architecture, which is diverse across ancestries, producing biased estimates of cross-ancestry genetic correlation. Here, we present a method to construct a genomic relationship matrix (GRM) that can correctly account for the relationship between ancestry-specific allele frequencies and ancestry-specific causal effects. Through comprehensive simulations, we show that the proposed method outperforms existing methods in the estimations of SNP-based heritability and cross-ancestry genetic correlation. The proposed method is further applied to six anthropometric traits from the UK Biobank data across 5 ancestry groups. One of our findings is that for obesity, the estimated genetic correlation between African and European ancestry cohorts is significantly different from unity, suggesting that obesity is genetically heterogenous between these two ancestry groups.


title: Characterizing the human methylome across the life course: findings from eight UK-based studies

abstract:
Variation in DNA methylation (DNAm) is associated with multiple biological processes that track growth and development, ageing and age-related diseases. However, there is little understanding of what constitutes typical patterns of DNAm variation and how these patterns change across the life course. In this study, we synthesised a map of the human methylome across the life course, focussing on changes in variability and mean DNAm.

Harmonizing DNAm datasets across eight longitudinal and cross-sectional UK-based studies, we meta-analysed n=13,215 blood samples from n=7,037 unique individuals from birth to 98 years of age. Changes in CpG-specific variability and means were described across the life course using a meta-regression framework. CpG-specific associations of variability or mean DNAm in relation to the likelihood of association with 100 traits linked to environmental exposures, health and disease were tested within and across ten developmental age bins across the life course.

Age was linked to DNAm variability at 29,212 CpG sites. On average, we observed a 1.26 fold increase in DNAm variability per year across the life course. 33,730 CpGs displayed changes in mean DNAm, with 64% of these loci showing decreases in DNAm over time. CpG sites linked to traits were in general more variable across the life course.

Our study provides, for the first time, a map of the human methylome across the life course, which is publicly accessible through a searchable online database. This resource allows researchers to query CpG-specific trajectories from birth to old age and link these to health and disease.


title: Microbial induced calcite precipitation can consolidate martian and lunar regolith simulants

abstract: We demonstrate that Microbial Induced Calcite Precipitation (MICP) can be utilized for creation of consolidates of Martian Simulant Soil (MSS) and Lunar Simulant Soil (LSS) in the form of a  brick. A urease producer bacteria, Sporosarcina pasteurii, was used to induce the MICP process for the both simulant soils. An admixture of guar gum as an organic polymer and NiCl2, as bio-catalyst to enhance urease activity, was introduced to increase the compressive strength of the biologically grown bricks. A casting method was utilized for a slurry consisting of the appropriate simulant soil and microbe; the slurry over a few days consolidated in the form of a  brick of the desired shape. In case of MSS, maximum strength of 3.3 MPa was obtained with 10mM NiCl2 and 1% guar gum supplementation whereas in case of LSS maximum strength of 5.65 MPa was obtained with 1% guar gum supplementation and 10mM NiCl2. MICP mediated consolidation of the simulant soil was confirmed with field emission scanning electron microscopy (FESEM) and X-ray diffraction (XRD). Our work demonstrates a biological approach with an explicit casting method towards manufacturing of consolidated structures using extra-terrestrial regolith simulant; this is a promising route for in situ development of structural elements on the extra-terrestrial habitats.


title: A Genotype-to-Phenotype Modeling Framework to Predict Human Pathogenicity of Novel Coronaviruses

abstract: Leveraging prior viral genome sequencing data to make predictions on whether an unknown, emergent virus harbors a  phenotype-of-concern has been a long-sought goal of genomic epidemiology. A predictive phenotype model built from nucleotide-level information alone has previously been considered un-tenable with respect to RNA viruses due to the ultra-high intra-sequence variance of their genomes, even within closely related clades. Building from our prior work developing a degenerate k-mer method to accommodate this high intra-sequence variation of RNA virus genomes for modeling frameworks, and leveraging a taxonomic  group-shuffle-split paradigm on complete coronavirus assemblies from prior to October 2018, we trained multiple regularized logistic regression classifiers at the nucleotide k-mer level capable of accurately predicting withheld SARS-CoV-2 genome sequences as human pathogens and accurately predicting withheld Swine Acute Diarrhea Syndrome coronavirus (SADS-CoV) genome sequences as non-human pathogens. LASSO feature selection identified several degenerate nucleotide predictor motifs with high model coefficients for the human pathogen class that were present across widely disparate classes of coronaviruses. However, these motifs differed in which genes they were present in, what specific codons were used to encode them, and what the translated amino acid motif was. This emphasizes the importance of a phenetic view of emerging pathogenic RNA viruses, as opposed to the canonical phylogenetic interpretations most-commonly used to track and manage viral zoonoses. Applying our model to more recent Orthocoronavirinae genomes deposited since October 2018 yields a novel contextual view of pathogen-potential across bat-related, canine-related, porcine-related, and rodent-related coronaviruses and critical adaptations which may have contributed to the emergence of the pandemic SARS-CoV-2 virus. Finally, we discuss the utility of these predictive models (and their associated predictor motifs) to novel biosurveillance protocols that substantially increase the  pound-for-pound information content of field-collected sequencing data and make a strong argument for the necessity of routine collection and sequencing of zoonotic viruses.


title: The supramolecular organization of SARS-CoV and SARS-CoV-2 virions revealed by coarse-grained models of intact virus envelopes

abstract: The coronavirus disease 19 (COVID-19) pandemic is causing a global health crisis and has already caused a devastating societal and economic burden. The pathogen, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has a high sequence and architecture identity with SARS-CoV, but far more people have been infected by SARS-CoV-2. Here, combining structural data from cryo-EM and structure prediction, we constructed bottom-up Martini coarse-grained models of intact SARS-CoV and SARS-CoV-2 envelopes. Microsecond molecular dynamics simulations were performed, allowing us to explore their dynamics and supramolecular organization. Both SARS-CoV and SARS-CoV-2 envelopes present a spherical morphology with structural proteins forming multiple string-like islands in the membrane and clusters between heads of spike proteins. Critical differences between the SARS-CoV and SARS-CoV-2 envelopes are the interaction pattern between spike proteins and the flexibility of spike proteins. Our models provide structural and dynamic insights in the SARS virus envelopes, and could be used for further investigation, such as drug design, and fusion and fission processes.

category: biophysics


title: Phenotypic Heterogeneity Facilitates Survival While Hindering the Evolution of Drug Resistance

abstract:
Rising rates of resistance to antimicrobial drugs threatens the effective treatment of infections across the globe. Drug resistance has been established to emerge from non-genetic mechanisms, such as "persistence" in quiescent microbes and fluctuations in gene expression in actively replicating cells, as well as from genetic mutations. However, it is still unclear how non-genetic drug resistance affects the evolution of genetic drug resistance. We develop deterministic and stochastic population models that incorporate resource competition to quantitatively investigate the transition from non-genetic to genetic resistance during the exposure to static and cidal drugs. We find that non-genetic resistance facilitates the survival of cell populations during drug treatment, but that it hinders the development of genetic resistance due to the competition between the non-genetically and genetically resistant subpopulations. Non-genetic drug resistance in the presence of subpopulation competition is found to increase the first-appearance and fixation times of drug resistance mutations, while increasing the probability of mutation before population extinction during cidal drug treatment. Intense intraspecific competition during drug treatment leads to extinction of the susceptible and non-genetically resistant subpopulations. These findings advance our fundamental understanding of the evolution of drug resistance and may guide novel treatment strategies for patients with drug-resistant infections.

SIGNIFICANCEDrug resistance is predicted to kill as many as 10 million people per year and cost over 100 trillion USD in cumulative lost production globally by 2050. To mitigate these socio-economic costs, we need to fundamentally understand the drug resistance process. We investigate the effect that different forms of resistance have on the evolution of drug resistance using mathematical modeling and computer simulations. We find that the presence of non-genetically drug-resistant cells (whose resistance is temporary and not encoded in a genetic mutation) allows the population to survive drug treatment, while competition between these subpopoulations simultaneously slows down the evolution of permanent genetic drug resistance and in some cases drives them extinct. These findings have important implications for advancing evolutionary theory and for developing effective "resistance-proof" treatments.


title: Phenotypic Heterogeneity Facilitates Survival While Hindering the Evolution of Drug Resistance Due to Intraspecific Competition


title: Planning and Conducting an Online Conference at the time of COVID-19: Lessons Learned from EGREPA 2021

abstract:
BackgroundThis paper describes the realisation and evaluation of the EGREPA 2021 conference, in online format. As an example, and support for future conferences, the decision process to switch during the COVID-19 pandemic from onsite to online, the conception and tools, the experiences of the organisers and the feedback of the participants are described.

MethodsThe CERN tool "Indico" served as the central conference management system including public homepage, submission and payment system, abstract review and decision platform, and conference material repository. Zoom, YouTube Live and Open Broadcaster Software (OBS) were utilised for keynotes and other presentation sessions, including livestreaming of pre-recorded presentations. Gather was implemented for poster sessions and individual meetings. An anonymous survey included Likert-type questions on acceptance and quality of the tools and instructions, open questions related to positive and negative issues, and ideas for the next online-conference.

ResultsThe event was evaluated well, with mostly fluently working technical solutions. A few participants indicated problems switching from YouTube to Zoom between presentations and discussions. Opinions on pre-recordings of talks were divided. Participants required more time for socialising. Guidelines and materials were mostly rated helpful.

Lessons LearnedSimplifying the livestreaming, presenters choice between pre-recording or presenting live, more time for socialising and breaks are discussed. Tools for conducting an online conference should be introduced to the participants in advance. Indico is rated as a very helpful tool for planning and conducting an online-conference.

category: scientific communication and education


title: Influenza A (N1-N9) and Influenza B (B/Vic and B/Yam) Neuraminidase Pseudotypes as Tools for Pandemic Preparedness and Improved Influenza Vaccine design

abstract: To better understand how inhibition of the influenza neuraminidase (NA) protein contributes to protection against influenza, and to investigate its breadth and cross-neutralizing activity, we have produced lentiviral vectors pseudotyped with an avian H11 hemagglutinin (HA) and the NA (N1-N9) of all influenza A and (B/Victoria and B/Yamagata) influenza B subtypes. These NA viral pseudotypes (PV) possess stable NA activity and can be utilized as target antigens in in vitro assays to assess vaccine immunogenicity. Employing these NA PV, we have developed an enzyme-linked lectin assay (pELLA) for routine serology to measure neuraminidase inhibition (NI) titers of reference antisera, monoclonal antibodies, and post-vaccination sera with various influenza antigens. We have also shown that pELLA is more sensitive than the commercially available NA-Fluor in detecting NA inhibition in these samples. Our studies may lead to establishing the protective NA titer that contributes to NA-based immunity. This will aid in the design of superior, longer lasting, and more broadly protective vaccines that can be employed together with HA-targeted vaccines in a pre-pandemic approach.

category: immunology


title: Oxidized thioredoxin-1 restrains the NLRP1 inflammasome

abstract: At least six human proteins detect danger-associated signals, assemble into complexes called inflammasomes, and trigger pyroptotic cell death. NLRP1 was the first protein discovered to form an inflammasome, but the danger signals and molecular mechanisms that control its activation have not yet been fully established. Here, we report that the NACHT-LRR region of NLRP1 directly binds to oxidized form of thioredoxin-1 (TRX1). We found that NLRP1 requires the ATPase activity of its NACHT domain to associate with TRX1, and that this interaction represses inflammasome activation. Moreover, we discovered that several patient-derived missense mutations in the NACHT-LRR region of NLRP1 weaken TRX1 binding, leading to inflammasome hyperactivation and autoinflammatory disease. Overall, our results establish that oxidized TRX1 binds to and restrains the NLRP1 inflammasome, thereby revealing a link between the cellular redox environment and innate immunity.


title: Dormant phages communicate to control exit from lysogeny

abstract: Temperate bacterial viruses (phages) can transition between lysis - replicating and killing the host, and lysogeny - existing as dormant prophages while keeping the host viable. It was recently shown that upon invading a naive cell, some phages communicate using a peptide signal, termed arbitrium, to control the decision of entering lysogeny. Whether communication can also serve to regulate exit from lysogeny (known as phage induction) remains unclear. Here we show that arbitrium-coding prophages continue to communicate from the lysogenic state by secreting and sensing the arbitrium signal. Signaling represses DNA-damage dependent phage induction, enabling prophages to reduce induction rate when surrounded by other lysogens. We show that the mechanism by which DNA damage and communication are integrated differs between distantly related arbitrium-coding phages. Additionally, signaling by prophages tilts the decision of nearby infecting phages towards lysogeny. Altogether, we find that phages use small molecule communication throughout their entire life-cycle to measure the abundance of lysogens in the population, thus avoiding wasteful attempts at secondary infections when they are unlikely to succeed.

category: microbiology


title: The E34 Phage Tailspike Protein: An in vitro characterization, Structure Prediction, Potential Interaction with S. newington LPS and Cytotoxicity Assessment to Animal Cell Line.

abstract: The E34 phage is a member of the podoviridae family of phages, (short non-contractile tailed bacteriophages) that uses Salmonella newington as its host. This phage initiates the infection of its host via a specific interaction between its tailspike protein (TSP) and the lipopolysaccharides (LPS) of the bacterial. The E34 TSP is structurally similar and functionally equivalent to the P22 phage whose TSP has been well characterized and electron micrographs of both phages appear indistinguishable. The crystal structure of P22 phage TSP in complex with the O-antigen of S. typhimurium has been determined; and the active site of the TSP demonstrated to be the residues Asp392, Asp395 and Glu359 of the receptor binding domain. In another phage called E15, a phylogenetic relative of E34 phage, a short polysaccharide consisting of  repeating units is responsible for the interaction between the E15 phage and Salmonella anatums LPS leading to the adsorption of the phage to the bacteria. Studies on E34 phage shows that it interacts with Salmonella newingtons O antigen polysaccharide component of the LPS, this polysaccharide consists of mannosyl-rhamnosyl-galactose repeating units joined together by {beta}-galactosyl linkages. However, no data exist regarding the specific residues of E34 TSP that are responsible for LPS binding and hydrolysis. In this study, the tailspike gene was cloned onto vector pET30a-LIC and expressed as a fusion protein termed the extended E34 TSP (EE34 TSP). We characterized the protein based on resistance to heat, SDS, and proteases; showing that the protein is heat resistant, shows aberrant electrophoretic mobility in the presence of SDS gradient, and actively binds to P22 phage heads to form hybrid phages that cannot infect P22 host. We also demonstrate via in silico study that the E34 TSP binds to and hydrolyses the O-antigen of its host via the ALA250, SER279 and ASP280 residues. Finally, testing E34 phage ability to protect Vero cells from Salmonella infection shows highly encouraging results, implying that E34 phage can be used in therapeutic/preventive medicine.


title: A contribution to the larval amphibian microbiome: characterization of bacterial microbiome of Ichthyophis bannanicus (Order: Gymnophiona) and comparison with the other two amphibian orders

abstract: It is known that animal-associated microbiomes form indispensable relationships with hosts and are responsible for many functions important for host-survival. Next-gen driven approaches documenting the remarkable diversity of microbiomes have burgeoned, with amphibians too, benefiting from such treatments. The microbiome of Gymnophiona (caecilians), one of the three amphibian orders, constituting of 3% of amphibians, however, remains almost unknown. The present study aims to address this knowledge gap through analysis of the microbiome of Ichthyophis bannanicus. As these caecilian larvae are aquatic and hence exposed to a greater propensity for bacterial microbiomic interchange, we hypothesize that bacterial phyla would overlap between gut and skin. Further, from the host-specificity patterns observed in other vertebrate taxa, we hypothesize that Gymnophiona have different dominant gut bacterial microbiomes at a higher taxonomic level when compared to the larvae of the other two amphibian orders (Anura and Caudata). We used 16S rRNA gene amplicon sequencing based on Illumina Nova sequencing platform to characterize and compare the gut (represented by faecal samples) and skin microbiome of I. bannanicus larvae (N = 13), a species distributed across South-East-Asia and the only caecilian species occurring in China. We compared our gut microbiome results with published anuran and caudate larval microbiomes. For I. bannanicus, a total of 4,053 operational taxonomic units (OTU) across 13 samples were detected. Alpha-diversity indices were significant between gut and skin samples. Non-metric multidimensional scaling analysis suggest that gut and skin samples each contained a distinct microbiome at OTU level. We record significant differences between the bacterial phyla of gut and skin samples in larvae of I. bannanicus. The study provides an overview of gut and skin bacterial microbiomes of a caecilian, while highlighting the major differences between larval microbiomes of the three amphibian orders. We find a partial overlap of gut bacterial microbiomes at phylum level for the three orders; however, the relative abundance of the dominant phyla is distinct. The skin and gut microbiomes are distinct with little overlap of species, highlighting that gut-skin axis is weak. This in turn suggests that many of the microbial species on skin and gut are functionally specialized to those locations. We also show that the skin microbiome is more diverse than the gut microbiome at species level; however, a reason for this could be a portion of the gut microbiome not being represented in faecal samples. These first microbiome information from a caecilian lay the foundation for comparative studies of the three amphibian orders.


title: A novel R3H protein, OsDIP1, confers ABA-mediated adaptation to drought and salinity stress in rice

abstract: Abscisic acid (ABA) is a key component of many signaling networks mediating plant adaptation to various stresses. In this context, ABA-induced antioxidant defence is considered to be a main mechanism to that enhances water stress tolerance in plants. The specific details of this activation remain, however, elusive. In this work, we show that DIP1, a protein from novel R3H family, played a central role in modulating water stress tolerance in rice. OsDIP1 transcripts were induced by hydrogen peroxide (H2O2), ABA, drought (polyethylene glycol treatment), and salt stress. Overexpression of OsDIP1 in rice enhanced drought and salinity tolerance while knocking out OsDIP1 by CRISPR-Cas9 editing resulted in drought and salt sensitive phenotype. The activity and gene expression of antioxidant defence enzymes, superoxide dismutase (SOD), catalase (CAT), increased in OsDIP1-overexpressed transgenic rice plants, while the content of malondialdehyde (MDA) decreased. In contrast, the content and gene expression of SOD and CAT, decreased, and the content of MDA increased in knockout of OsDIP1 rice plants, suggesting that overexpression of OsDIP1 enhances the antioxidant capacity of rice plants. The yeast two hybrid screening test revealed that OsDIP1 interacted with ZFP36, a key zinc finger transcription factor involved in ABA-induced antioxidant defence. Moreover, OsDIP1 could modulate some key ABA-responsive genes via interacting with ZFP36. Overall, our findings indicate an important role of OsDIP1 in ABA-induced antioxidant defence signaling and adaptation to salinity and drought in rice.

category: molecular biology


title: RNA polymerase II dynamics and mRNA stability feedback determine mRNA scaling with cell size

abstract: A defining feature of cellular growth is that protein and mRNA amounts scale with cell size so that concentrations remain approximately constant, thereby ensuring similar reaction rates and efficient biosynthesis. A key component of this biosynthetic scaling is the scaling of mRNA amounts with cell size, which occurs even among cells with the same DNA template copy number. Here, we identify RNA polymerase II as a major limiting factor increasing transcription with cell size. Other components of the transcriptional machinery are only minimally limiting and the chromatin environment is largely invariant with size. However, RNA polymerase II activity does not increase in direct proportion to cell size, inconsistent with previously proposed DNA-titration models. Instead, our data support a dynamic equilibrium model where the rate of polymerase loading is proportional to the unengaged nucleoplasmic polymerase concentration. This sublinear transcriptional increase is then balanced by a compensatory increase in mRNA stability as cells get larger. Taken together, our results show how limiting RNA polymerase II and feedback on mRNA stability work in concert to ensure the precise scaling of mRNA amounts across the physiological cell size range.


title: RNA-dependent RNA polymerases in the black-legged tick produce Argonaute-dependent small RNAs and regulate genes

abstract:
Small regulatory RNAs (sRNAs) are involved in anti-viral defense and gene regulation. Although RNA-dependent RNA Polymerases (RdRPs) are known to produce sRNA in nematodes, plants and fungi, whether they play roles in sRNA biogenesis in other animals remains controversial. In this study, we study sRNAs in the ISE6 cell line, which is derived from the black-legged tick, an important vector of human and animal pathogens. We identify abundant classes of ~22nt sRNAs that require specific combinations of RdRPs and sRNA effector proteins (Argonautes or AGOs). RdRP-dependent sRNAs are mainly derived from sense and antisense strands of RNA polymerase III-transcribed genes and repetitive elements. Unlike C. elegans sRNA pathways, 5-tri-phosphorylated sRNAs are not detected, suggesting that the tick pathways are distinct from the pathways known in worms. Knockdown of one of the RdRPs unexpectedly results in downregulation of a subset of viral transcripts, in contrast to their upregulation by AGO knockdown. Furthermore, we show that knockdown of AGO/RdRP causes misregulation of protein-coding genes including RNAi-related genes, suggesting feedback regulation. Luciferase assays demonstrate that one of the RdRP-regulated genes, the MEK1 ortholog IscDsor1 is regulated through its 3UTR, where a putative sRNA target site resides. These results provide evidence that arachnid RdRPs are important sRNA biogenesis factors, and the discovery of novel pathways underscores the importance of characterizing sRNA biogenesis in various organisms to understand virus-vector interactions and to exploit RNAi for pest control.

Significance statementRNA-dependent RNA Polymerases (RdRPs) are essential for biogenesis of small regulatory RNAs (sRNAs) in many organisms such as plants and fungi, but its general importance in animals besides nematodes remains controversial because experimental evidence is lacking. By using a tick cell line, we demonstrate that RdRP-dependent sRNAs are abundantly expressed and tick RdRPs regulate gene expression. These results indicate that ticks have unexpectedly complex sRNA biogenesis pathways that are essential for proper gene regulation. Because ticks are important vectors of human and animal pathogens, and their sRNA pathways control tick-borne viruses, studying the novel tick sRNA pathways may provide important information for a better understanding of vector-virus interactions and for developing RNA-based pesticides by utilizing ticks RNA silencing mechanisms.


title: TGS1: a novel regulator of β-cell mass and function

abstract: Type 2 diabetes (T2D) is a metabolic disorder associated with abnormal glucose homeostasis and is characterized by intrinsic defects in {beta}-cell function and mass. Trimethylguanosine synthase 1 (TGS1) is an evolutionarily conserved enzyme that methylates small nuclear and nucleolar RNAs (snRNAs and snoRNAs) and is involved in pre-mRNA splicing, transcription, and ribosome production. However, the role of TGS1 in {beta}-cells and glucose homeostasis had not been explored. Here we show that TGS1 is upregulated by insulin and upregulated in islets from mice exposed to a high-fat diet and in human {beta}-cells from T2D donors. Using mice with conditional ({beta}TGS1KO and {beta}TGS1Het) and inducible (MIP-CreERT-TGS1KO) TGS1 deletion, we determine that TGS1 regulates {beta}-cell mass and function. Unbiased approaches allowed us to identify a link between TGS1 and ER stress and cell cycle arrest and how TGS1 regulates {beta}-cell apoptosis. Deletion of TGS1 results in an increase in the unfolded protein response by increasing XBP-1, ATF-4, and the phosphorylation of eIF2, and several changes in cell cycle inhibitors and activators such as p27 and Cyclin D2. This study establishes TGS1 as a key player regulating {beta}-cell mass and function as well as playing a role in the adaptive {beta}-cell function to a high-fat diet. These observations can be used as a stepping-stone for the design of novel strategies using TGS1 as a therapeutic target for the treatment of diabetes.

category: cell biology