Epigenetic modifications that arise during plant and animal development, such as DNA and histone modification, are mostly reset during gamete formation, but some are inherited from the germline including those marking imprinted genes. Small RNAs guide these epigenetic modifications, and some are also inherited by the next generation. In C. elegans, inherited small RNA precursors have poly (UG) tails, but how inherited small RNAs are distinguished in other animals and plants is unknown. Pseudouridine ({Psi}) is the most abundant RNA modification but has not been explored in small RNAs. Here, we develop novel assays to detect {Psi} in short RNA sequences, demonstrating its presence in mouse and Arabidopsis microRNAs and their precursors. We also detect substantial enrichment in germline small RNAs, namely epigenetically activated siRNAs (easiRNAs) in Arabidopsis pollen, and piwi-interacting piRNAs in mouse testis. In pollen, pseudouridylated easiRNAs are localized to sperm cells, and we found that PAUSED/HEN5 (PSD), the plant homolog of Exportin-t, interacts genetically with {Psi} and is required for transport of easiRNAs into sperm cells from the vegetative nucleus. We further show that Exportin-t is required for the triploid block: chromosome dosage-dependent seed lethality that is epigenetically inherited from pollen. Thus, {Psi} has a conserved role in marking inherited small RNAs in the germline. | Make paid
Background: Single-cell immuno-heterogeneity has always been the forerunner of any change in homeostasis of cellular functions in the body. Mesenchymal stem cells represent a viable source for the development of cell-based therapies. Multiple conditions such as age, donor, and origin of source tissues, give rise to heterogeneity and multipotent differentiation ability of these cells of stromal origin. Cell surface markers which are important members of membrane proteins, ion channels, transporter, adhesion, and signaling molecules generally differentiate between stromal cells of different origin. However, existing analytical tools cannot always model a pattern of their surface distribution in successive generations of growth and proliferation. Results: In this study, we have developed a post-acquisition image analysis pipeline for human mesenchymal stromal cells obtained from exfoliated deciduous teeth (hSHEDs). Using the open-source image processing software CellProfiler, a pipeline has been developed to extract cellular features from 50,000- 100,000 single-cell images. We made use of the image flow cytometry technology to explore the morphometric properties of hSHEDs, along with their surface marker distribution. This unbiased pipeline can extract cellular, geometrical, and texture features such as shape, size, eccentricity, entropy, and intensities as a measure of cellular heterogeneity. Conclusion: For the first time, we have described an automated, unbiased image assessment protocol implemented in a validated open-source software, leveraging the suite of image-based measurements to develop the prototype nomenclatured as MSCProfiler. The hallmark of this screening workflow has been the identification and removal of image-based aberrations to identify the single-cell bright field and fluorescent images. | Make paid
Zika virus (ZIKV) is a Flavivirus responsible for recent epidemics in Pacific Islands and in the Americas. In humans, the consequences of ZIKV infection range from asymptomatic infection to severe neurological disease such as Guillain-Barre syndrome or fetal neurodevelopmental defects, suggesting the influence of host genetic factors. We previously reported similar diverse outcomes of ZIKV infection in mice of the Collaborative Cross, a collection of inbred strains with large genetic diversity. CC071 was the most susceptible strain with severe symptoms and lethality. Here, we investigated viral replication in mouse embryonic fibroblasts from CC071 and two resistant strains. CC071 showed enhanced viral replication associated with delayed induction of type-I interferons (IFN-I). Using a combination of genetic approaches, we identified a loss of function (LOF) mutation in the Irf3 gene, specific to CC071, and demonstrated that it fully explains the defective IFN-I response and uncontrolled viral replication in CC071 MEFs. However, this mutation was not sufficient to induce the high plasma viral load and clinical severity observed in CC071 mice, indicating the involvement of other susceptibility genes in vivo. Considering the susceptibility of the CC071 strain to multiple viruses, our results provide new insight into the role of Irf3 in innate antiviral response. | Make paid
Citrullination is the conversion of peptidyl-arginine into the non-coded amino acid citrulline. Despite its importance in physiology and disease, global identification of citrullinated proteins and precise modification sites has remained challenging. Here, we employed quantitative mass spectrometry-based proteomics to generate a comprehensive atlas of citrullination sites in a physiologically relevant cell type. Collectively, we identified 14.056 citrullination sites within 4.008 proteins and quantified their regulation upon inhibition of the citrullinating enzyme PADI4. Using this rich dataset, we uncover general mechanistic and cell biological principles of citrullination function, while providing site-specific and quantitative information on thousands of PAD4 substrates within cells. Our findings include signature histone marks and numerous modifications on transcriptional regulators and chromatin-related signaling effectors. Additionally, we identify precise citrullination sites on an extensive list of known autoantigens. Collectively, we describe systems attributes of the human citrullinome and provide a resource framework for understanding citrullinaiton at the mechanistic level. | Make paid
The development of automatic methods for image and video quality assessment that correlate well with the perception of human observers is a very challenging open problem in vision science, with numerous practical applications in disciplines such as image processing and computer vision, as well as in the media industry. In the past two decades, the goal of image quality research has been to improve upon classical metrics by developing models that emulate some aspects of the visual system, and while the progress has been considerable, state-of-the-art quality assessment methods still share a number of shortcomings, like their performance dropping considerably when they are tested on a database that is quite different from the one used to train them, or their significant limitations in predicting observer scores for high framerate videos. In this work we propose a novel objective method for image and video quality assessment that is based on the recently introduced Intrinsically Non-linear Receptive Field (INRF) formulation, a neural summation model that has been shown to be better at predicting neural activity and visual perception phenomena than the classical linear receptive field. Here we start by optimizing, on a classic image quality database, the four parameters of a very simple INRF-based metric, and proceed to test this metric on three other databases, showing that its performance equals or surpasses that of the state-of-the-art methods, some of them having millions of parameters. Next, we extend to the temporal domain this INRF image quality metric, and test it on several popular video quality datasets; again, the results of our proposed INRF-based video quality metric are shown to be very competitive. | Make paid
To identify causation, model-free inference methods, such as Granger Causality, have been widely used due to their flexibility. However, they have difficulty distinguishing synchrony and indirect effects from direct causation, leading to false predictions. To overcome this, model-based inference methods that test the reproducibility of data with a specific mechanistic model to infer causality were developed. However, they can only be applied to systems described by a specific model, greatly limiting their applicability. Here, we address this limitation by deriving an easily testable condition for a general monotonic ODE model to reproduce time-series data. We built a user-friendly computational package, GOBI (General ODE-Based Inference), which is applicable to nearly any monotonic system with positive and negative regulations described by ODE. GOBI successfully inferred positive and negative regulations in various networks at both the molecular and population levels, unlike existing model-free methods. Thus, this accurate and broadly applicable inference method is a powerful tool for understanding complex dynamical systems. | Make paid
Crossover interference (COI) is a widespread feature of homologous meiotic recombination. It can be quantified by the classical coefficient of coincidence (CoC) `but this characteristic is highly variable and specific to the pair of chromosomal intervals considered. Several models were proposed to characterize COI on a chromosome-wise level. In the gamma model, the strength of interference is characterized by a shape parameter {nu}, while the gamma-sprinkled two-pathway model (GS) accounts for both interference-dependent and independent crossover (CO) events by fitting a mixture of gamma distributions with v>1 and v=1, correspondingly, and mixture proportions 1-p and p. In reality, COI can vary along chromosomes resulting in low compliance of the fitted model to real data. Additional inconsistency can be caused by common neglecting of possible negative COI in the model, earlier reported for several organisms. In this work, we propose an extension of the GS-model to take possible negative COI into account. We propose a way for data simulation and parameter estimation for such situations. | Make paid
Recurrent neural networks (RNNs) based on model neurons that communicate via continuous signals have been widely used to study how cortical neurons perform cognitive tasks. Training such networks to perform tasks that require information maintenance over a brief period (i.e., working memory tasks) remains a challenge. Critically, the training process becomes difficult when the synaptic decay time constant is not fixed to a large constant number for all the model neurons. We hypothesize that the brain utilizes intrinsic cortical noise to generate a reservoir of heterogeneous synaptic decay time constants optimal for maintaining information. Here, we show that introducing random, internal noise to the RNNs not only speeds up the training but also produces stable models that can maintain information longer than the RNNs trained without internal noise. Importantly, this robust working memory performance induced by incorporation of internal noise during training is attributed to an increase in synaptic decay time constants of a distinct subset of inhibitory units. This increase leads to slower decay of stimulus-specific activity, which plays a critical role in memory maintenance. | Make paid
Long noncoding RNAs (lncRNAs) are believed to regulate expression of neighbouring target genes. However, such 'cis-lncRNAs' are presently defined using ad hoc criteria that, we show, are prone to false-positive predictions. The resulting lack of confident cis-lncRNA catalogues hinders our understanding of their extent, characteristics and mechanisms. Here, we introduce TransCistor, a framework for defining and identifying cis-lncRNAs based on enrichment of targets amongst proximal genes. TransCistor's simple and conservative statistical models are compatible with functionally-defined target gene maps generated by existing and future technologies, and generate predictions at controlled false discovery rates. Using transcriptome-wide perturbation experiments for 268 human and 134 mouse lncRNAs, we provide the first large-scale survey of cis-lncRNAs. Our results suggest that cis-activity is confined to a minority of lncRNAs, with a prevalence of activators over repressors. Cis-lncRNAs are detected by both RNA interference (RNAi) and antisense oligonucleotide (ASO) perturbations. Mechanistically, we find weak associations of cis-lncRNAs with enhancer elements. Moreover, they are not distinguished from other lncRNAs by evolutionary conservation nor nuclear enrichment, nor are they frequently linked to target genes by chromatin looping. In summary, our study will enable researchers to evaluate the regulatory mode of their lncRNA of interest at controlled false discovery rates and places cis-lncRNAs on a quantitative foundation for the first time. | Make paid
While inhomogeneous viscosity has been identified as a ubiquitous feature of the cellular interior, its implications for particle mobility and concentration at different length scales remain largely unexplored. In this work, we use agent-based simulations of diffusion to investigate how heterogenous viscosity affects movement and concentration of diffusing particles. We propose that a nonequilibrium mode of membraneless compartmentalization arising from the convergence of diffusive trajectories into viscous sinks, which we call "diffusive lensing," can occur in a wide parameter space and is thus likely to be ubiquitous in living systems. Our work highlights the phenomenon of diffusive lensing as a potentially key driver of mesoscale dynamics in the cytoplasm, with possible far-reaching implications for biochemical processes. | Make paid
The utilization of RNA interference (RNAi) for pest management has garnered global interest. The bioassay results suggested the knockout of PxRdl2 significantly increased the insecticidal activities of the {gamma}-aminobutyric acid receptor (GABAR) targeting compounds (Fipronil, two pyrazoloquinazolines and two isoxazolines), thereby presenting a viable target gene for RNAi-mediated pest control. Consequently, we suggest enhancing the insecticidal activities of GABAR-targeting compounds by knockdown the transcript level of PxRdl2. Furthermore, PxRdl2 dsRNA was expressed in HT115 Escherichia coli to reduce costs and protect dsRNA against degradation. In comparison to in vitro synthesized dsRNA, the recombinant bacteria (ds-B) exhibited superior interference efficiencies and greater stability when exposed to UV irradiation. Collectively, our results provide a new strategy of insecticide spray which combined synergistically with insecticidal activities by suppressing PxRdl2 using ds-B, and may be beneficial for reducing the usage of insecticide and slowing pest resistance. | Make paid
Prediction errors have a prominent role in many forms of learning. For example, in reinforcement learning, agents learn by updating the association between states and outcomes as a function of the prediction error elicited by the event. One paradigm often used to study error-driven learning is blocking. In forward blocking, participants are first presented with stimulus A, followed by outcome X (A[->]X). In the second phase, A and B are presented together, followed by X (AB[->]X). Here, A[->]X blocks the formation of B[->]X, given that X is already fully predicted by A. In backward blocking, the order of phases is reversed. Here, the association between B and X that is formed during the first learning phase of AB[->]X is weakened when participants learn exclusively A[->]X in the second phase. The present study asked the question whether forward and backward blocking occur during visual statistical learning, the largely automatic and incidental learning of the statistical structure of the environment. In a series of studies, using both forward and backward blocking, we observed robust statistical learning of temporal associations among pairs of images. While we found no compelling evidence for forward blocking, we observed reliable backward blocking in visual statistical learning. | Make paid
The objective was to explore the effects of H1 receptor signaling on NMDA and GABA responses. By making patch-clamp whole-cell recordings of neurons from primary rat hippocampal cultures, we observe the effects of several histaminergic agonists and antagonists on the rundown of NMDA and GABA currents. Mepyramine, an H1 antagonist, at nanomolar concentrations increases significantly the NMDA responses by about 35 %, this effect is mimicked by another H1 antagonist, Triprolidine. Histamine alone has no effect on NMDA rundown but 100 micro M Histamine can reduce partially the effect of Mepyramine. An H1 receptor agonist 2,3 bromophenyl histamine suppresses the effect of Mepyramine similar to Histamine. Our results suggest that the H1 receptor of Histamine is constitutively active, and its blockade by Mepyramine significantly increases the NMDA responses. Neither Mepyramine nor Histamine altered the rundown of GABA responses. Inhibition of H1 receptors with Mepyramine at nanomolar concentrations reveals an interaction between constitutive Histamine H1 receptor activity and the NMDAR responses. Curiously, Histamine alone does not alter NMDAR responses, but partially suppresses the effect of Mepyramine, suggesting Mepyramine acts as an inverse agonist to block the constitutive activity of the H1 receptor. The constitutive activity of the H1 receptor seems to be crucial in the regulation of NMDA receptor activity. | Make paid