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Search indexed bioRxiv preprints in genomics, neuroscience, cell biology and bioinformatics. Read source abstracts and check manuscript versions; preprints are not peer reviewed.

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A comparison of visual features used by humans and machines to classify wildlife

In our quest to develop more intelligent machines, knowledge of the visual features used by machines to classify objects shall be helpful. The current state of the art in training machines to classify wildlife species from camera-trap data is to employ convolutional neural networks (CNN) encoded within deep learning algorithms. Here we report on results obtained in training a CNN to classify 20 African wildlife species with an overall accuracy of 87.5% from a dataset containing 111,467 images. We then used a gradient-weighted class-activation-mapping (Grad-CAM) procedure to extract the most salient pixels in the final convolution layer. We show that these pixels highlight features in particular images that are in most, but not all, cases similar to those used to train humans to identify these species. Further, we used mutual information methods to identify the neurons in the final convolution layer that consistently respond most strongly across a set of images of one particular species, and we then interpret the features in the image where the strongest responses occur. We also used hierarchical clustering of feature vectors (i.e., the state of the final fully-connected layer in the CNN) associated with each image to produce a visual similarity dendrogram of identified species. Finally, we evaluated how images that were not part of the training set fell within our dendrogram when these images were one of the 20 species \"known\" to our CNN in contrast to where they fell when these images were \"unknown\" to our CNN.

ecology

Meta-analysis of Drought-tolerant Genotypes in Oryza sativa: A Network-based Approach

BackgroundDrought is a severe environmental stress. It is estimated that about 50% of the world rice production is affected mainly by drought. Apart from conventional breeding strategies to develop drought-tolerant crops, innovative computational approaches may provide insights into the underlying molecular mechanisms of stress response and identify drought-responsive markers. Here we propose a network-based computational approach involving a meta-analytic study of seven drought-tolerant rice genotypes under drought stress.\n\nResultsCo-expression networks enable large-scale analysis of gene-pair associations and tightly coupled clusters that may represent coordinated biological processes. Considering differentially expressed genes in the co-expressed modules and supplementing external information such as, resistance/tolerance QTLs, transcription factors, network-based topological measures, we identify and prioritize drought-adaptive co-expressed gene modules and potential candidate genes. Using the candidate genes that are well-represented across the datasets as seed genes, two drought-specific protein-protein interaction networks (PPINs) are constructed with up-and down-regulated genes. Cluster analysis of the up-regulated PPIN revealed ABA signaling pathway as a central process in drought response with a probable crosstalk with energy metabolic processes. Tightly coupled gene clusters representing up-regulation of core cellular respiratory processes and enhanced degradation of branched chain amino acids and cell wall metabolism are identified. Cluster analysis of down-regulated PPIN provides a snapshot of major processes associated with photosynthesis, growth, development and protein synthesis, most of which are shut down during drought. Differential regulation of phytohormones, e.g., jasmonic acid, cell wall metabolism, signaling and posttranslational modifications associated with biotic stress are elucidated. Functional characterization of topologically important, drought-responsive uncharacterized genes that may play a role in important processes such as ABA signaling, calcium signaling, photosynthesis and cell wall metabolism is discussed. Further transgenic studies on these genes may help in elucidating their biological role under stress conditions.\n\nConclusionCurrently, a large number of resources for rice functional genomics exist which are mostly underutilized by the scientific community. In this study, a computational approach integrating information from various resources such as gene co-expression networks, protein-protein interactions and pathway-level information is proposed to provide a systems-level view of complex drought-responsive processes across the drought-tolerant genotypes.

bioinformatics

Cortisol Predicts Antidepressant Treatment Outcome, Memory Improvement, and Brain Response to Negative Emotions: The Importance of Aging

BackgroundStudies testing the relationship between cortisol levels, depression, and antidepressant treatment response have yielded divergent results suggesting the possibility of moderators of a cortisol effect. Several studies indicate that age may moderate the relationship between cortisol and psychopathology. In patients with Major Depressive Disorder (MDD), we studied the interactive effects of age and cortisol on predicting diagnostic status, improvement in mood and memory function with antidepressant treatment, and brain response to negative emotional stimuli.\n\nMethods66 unmedicated patients with MDD and 75 matched healthy controls had serum assayed at pre-treatment baseline for cortisol. Logistic regression was used to determine an association of age, cortisol and their interaction with MDD diagnosis. Thirty-four of the MDD participants (age range: 19-65 years; median: 36) underwent treatment with a selective serotonin reuptake inhibitor (SSRl) for 8 weeks. Clinician and self-ratings of depression symptoms, as well as tests of verbal and visual delayed recall were obtained at baseline and post treatment. Moderation analyses determined the effect of age on the relationship between baseline cortisol and treatment outcome. A separate sample of 8 MDD participants prospectively underwent fMRI neuroimaging and cortisol collection while viewing negative emotional faces.\n\nResultsAge moderated the effects of cortisol on predicting MDD diagnosis (p<.05), treatment-associated reduction of depression symptoms (p<.001), improvement of delayed recall (p<.001), and baseline brain response to negative emotions (p<.05, whole brain corrected). Modeling the Age X Cortisol interaction suggested that for the participants below the median age of our sample, lower cortisol levels predicted a lower rate of MDD diagnosis, higher antidepressant effects and decreased brain reactivity in emotion regulation regions such as the anterior cingulate gyrus. On the contrary, in those above the median sample age, lower cortisol predicted a higher rate of MDD, less improvement in depression symptoms and memory performance, and more brain reactivity in the anterior cingulate.\n\nConclusionsOur results indicate that age moderates the relationship between peripheral cortisol levels and (1) MDD diagnosis, (2) brain reactivity to emotional stimuli, and (3) antidepressant-associated improvement in depression and memory symptoms. These results indicate that previous disparities in the literature linking peripheral cortisol levels with depression characteristics and treatment response may critically relate, at least in part, to the age of the patients studied.

physiology

Genomic variants concurrently listed in a somatic and a germline mutation database have implications for disease-variant discovery and genomic privacy

BackgroundMutations arise in the human genome in two major settings: the germline and soma. These settings involve different inheritance patterns, chromatin structures, and environmental exposures, all of which might be predicted to differentially affect the distribution of substitutions found in these settings. Nonetheless, recent studies have found that somatic and germline mutation rates are similarly affected by endogenous mutational processes and epigenetic factors.\n\nResultsHere, we quantified the number of single nucleotide variants that co-occur between somatic and germline call-sets (cSNVs), compared this quantity with expectations, and explained noted departures. We found that three times as many variants are shared between the soma and germline than is expected by independence. We developed a new, general-purpose statistical framework to explain the observed excess of cSNVs in terms of the varying mutation rates of different kinds substitution types and of genomic regions. Using this metric, we find that more than 90% of this excess can be explained by our observation that the basic substitution types (such as N[C->T]G, C->A, etc.) have correlated mutation rates in the germline and soma. Matched-normal read depth analysis suggests that an appreciable fraction of this excess may also derive from germline contamination of somatic samples.\n\nConclusionOverall, our results highlight the commonalities in substitution patterns between the germline and soma. The universality of some aspects of human mutation rates offers insight into the potential molecular mechanisms of human mutation. The highlighted similarities between somatic and germline mutation rates also lay the groundwork for future studies that distinguish disease-causing variants from a genomic background informed by both somatic and germline variant data. Moreover, our results also indicate that the depth of matched normal sequencing necessary to ensure genomic privacy of donors of somatic samples may be higher than previously appreciated. Furthermore, the fact that we were able to explain such a high portion of recurrent variants using known determinants of mutation rates is evidence that the genomics community has already discovered the most important predictors of mutation rates for single nucleotide variants.

genomics

Massively parallel fitness profiling reveals multiple novel enzymes in Pseudomonas putida lysine metabolism

The lysine metabolism of Pseudomonas putida can produce multiple important commodity chemicals and is implicated in rhizosphere colonization. However, despite intensive study, the biochemical and genetic links between lysine metabolism and central metabolism remain unresolved in P. putida. Here, we leverage Random Barcode Transposon Sequencing (RB-TnSeq), a genome-wide assay measuring the fitness of thousands of genes in parallel, to identify multiple novel enzymes in both L- and D-lysine metabolism. We first describe three pathway enzymes that catabolize 2-aminoadipate (2AA) to 2-ketoglutarate (2KG) connecting D-lysine to the TCA cycle. One of these enzymes, PP_5260, contains a DUF1338 domain, a family without a previously described biological function. We demonstrate PP_5260 converts 2-oxoadipate (2OA) to 2-hydroxyglutarate (2HG), a novel biochemical reaction. We expand on recent work showing that the glutarate hydroxylase, CsiD, can co-utilize both 2OA and 2KG as a co-substrate in the hydroxylation of glutarate. Finally we demonstrate that the cellular abundance of D- and L-lysine pathway proteins are highly sensitive to pathway specific substrates. This work demonstrates the utility of RB-TnSeq for discovering novel metabolic pathways in even well-studied bacteria.\n\nImportanceO_LIP. putida is an attractive host for metabolic engineering as its lysine metabolism can be utilized for the production of multiple important commodity chemicals.\nC_LIO_LIWe demonstrate the first biochemical evidence of a bacterial 2OA catabolic pathway to central metabolites.\nC_LIO_LIDUF1338 proteins are widely dispersed across many kingdoms of life. Here we demonstrate the first biochemical evidence of function for a member of this protein family.\nC_LI

microbiology

Bayesian reassessment of the epigenetic architecture of complex traits

1Epigenetic DNA modification is partly under genetic control, and occurs in response to a wide range of environmental exposures. Linking epigenetic marks to clinical outcomes may provide greater insight into underlying molecular processes of disease, assist in the identification of therapeutic targets, and improve risk prediction. Here, we present a statistical approach, based on Bayesian inference, that estimates associations between disease risk and all measured epigenetic probes jointly, automatically controlling for both data structure (including cell-count effects, relatedness, and experimental batch effects) and correlations among probes. We benchmark our approach in simulation study, finding improved estimation of probe associations across a wide range of scenarios over existing approaches. Our method estimates the total proportion of disease risk captured by epigenetic probe variation, and when we applied it to measures of body mass index (BMI) and cigarette consumption behaviour in 5,101 individuals, we find that 66.7% (95% CI 60.0-72.8) of the variation in BMI and 67.7% (95% CI 58.4-76.9) of the variation in cigarette consumption can be captured by methylation array data from whole blood, independent of the variation explained by single nucleotide polymorphism markers. We find novel associations, with smoking behaviour associated with a methylation probe at the MNDA gene with >95% posterior inclusion probability, which is a myeloid cell nuclear differentiation antigen gene previously implicated as a biomarker for inflammation and non-Hodgkin lymphoma risk. We conduct unique genome-wide enrichment analyses, identifying blood cholesterol, lipid transport and sterol metabolism pathways for BMI, and response to xenobiotic stimulus and negative regulation of RNA polymerase II promoter transcription for smoking, all with >95% posterior inclusion probability of having methylation probes with associations >1.5 times larger than the average. Finally, we improve phenotypic prediction in two independent cohorts by 28.7% and 10.2% for BMI and smoking respectively over a LASSO model. These results imply that probe measures may capture large amounts of variance because they are likely a consequence of the phenotype rather than a cause. As a result, 'omics' data may enable accurate characterization of disease progression and identification of individuals who are on a path to disease. Our approach facilitates better understanding of the underlying epigenetic architecture of complex common disease and is applicable to any kind of genomics data.

genomics

Widespread alteration of protein autoinhibition in human cancers

Autoinhibition is a prevalent allosteric regulatory mechanism in signaling proteins as it prevents spurious pathway activation and primes for signal propagation only under appropriate inputs. Altered functioning of inhibitory allosteric switches underlies the tumorigenic potential of numerous cancer drivers. However, whether protein autoinhibition is altered generically in cancer cells remains elusive. Here, we reveal that cancer-associated missense mutations and fusion breakpoints are found with significant enrichment within inhibitory allosteric switches across all cancer types, which in the case of the fusion breakpoints is specific to cancer and not present in other diseases. Recurrently disrupted or mutated allosteric switches identify established and new cancer drivers. Cancer-specific mutations in allosteric switches are associated with distinct changes in signaling, and suggest molecular mechanisms for altered protein regulation, which in the case of ASK1, DAPK2 and EIF4G1 were supported by biophysical simulations. Our results demonstrate that autoinhibition-modulating genetic alterations are positively selected for by cancer cells, and that their study provides valuable insights into molecular mechanisms of cancer misregulation.

cancer biology

Metabolome-scale genome-wide association studies reveal chemical diversity and genetic control of maize specialized metabolites

One Sentence SummaryHPLC-MS metabolite profiling of maize seedlings, in combination with genome-wide association studies, identifies numerous quantitative trait loci that influence the accumulation of foliar metabolites.\n\nAbstractCultivated maize (Zea mays) retains much of the genetic and metabolic diversity of its wild ancestors. Non-targeted HPLC-MS metabolomics using a diverse panel of 264 maize inbred lines identified a bimodal distribution in the prevalence of foliar metabolites. Although 15% of the detected mass features were present in >90% of the inbred lines, the majority were found in <50% of the samples. Whereas leaf bases and tips were differentiated primarily by flavonoid abundance, maize varieties (stiff-stalk, non-stiff-stalk, tropical, sweet corn, and popcorn) were differentiated predominantly by benzoxazinoid metabolites. Genome-wide association studies (GWAS), performed for 3,991 mass features from the leaf tips and leaf bases, showed that 90% have multiple significantly associated loci scattered across the genome. Several quantitative trait locus hotspots in the maize genome regulate the abundance of multiple, often metabolically related mass features. The utility of maize metabolite GWAS was demonstrated by confirming known benzoxazinoid biosynthesis genes, as well as by mapping isomeric variation in the accumulation of phenylpropanoid hydroxycitric acid esters to a single linkage block in a citrate synthase-like gene. Similar to gene expression databases, this metabolomic GWAS dataset constitutes an important public resource for linking maize metabolites with biosynthetic and regulatory genes.

genetics

I know that I don’t know: Structural and functional connectivity underlying meta-ignorance in pre-schoolers

Research Highlights[1] Children develop the ability to report that they do not know something at around five years of age.\n\n[2] Children who could correctly report their own ignorance in a partial-knowledge task showed thicker cortices within medial orbitofrontal cortex.\n\n[3] This region was functionally connected to parts of the default-mode network.\n\n[4] The default-mode network might support the development of correct metacognitive monitoring.\n\nAbstractMetacognition plays a pivotal role in human development. The ability to realize that we do not know something, or meta-ignorance, emerges after approximately five years of age. We aimed at identifying the brain systems that underlie the developmental emergence of this ability in a preschool sample.\n\nTwenty-four children aged between five and six years answered questions under three conditions of a meta-ignorance task twice. In the critical partial knowledge condition, an experimenter first showed two toys to a child, then announced that she would place one of them in a box behind a screen, out of sight from the child. The experimenter then asked the child whether or not she knew which toy was in the box.\n\nChildren who answered correctly both times to the metacognitive question in the partial knowledge condition (n=9) showed greater cortical thickness in a cluster within left medial orbitofrontal cortex than children who did not (n=15). Further, seed-based functional connectivity analyses of the brain during resting state revealed that this region is functionally connected to the medial orbitofrontal gyrus, posterior cingulate gyrus and precuneus, and mid- and inferior temporal gyri.\n\nThis finding suggests that the default mode network, critically through its prefrontal regions, supports introspective processing. It leads to the emergence of metacognitive monitoring allowing children to explicitly report their own ignorance.

neuroscience

A fast and general method to empirically estimate the complexity of distributed causal interactions in the brain

BackgroundThe Perturbational Complexity Index (PCI) was recently introduced to assess the capacity of thalamocortical circuits to engage in complex patterns of causal interactions. While showing high accuracy in detecting consciousness in brain injured patients, PCI depends on elaborate experimental setups and offline processing and has restricted applicability to other types of brain signals beyond transcranial magnetic stimulation and high-density EEG (TMS/hd-EEG) recordings. ObjectiveWe aim to address these limitations by introducing PCIST, a fast method for estimating perturbational complexity of any given brain response signal. MethodsPCIST is based on dimensionality reduction and state transitions (ST) quantification of evoked potentials. The index was validated on a large dataset of TMS/hd-EEG recordings obtained from 108 healthy subjects and 108 brain injured patients, and tested on sparse intracranial recordings (SEEG) of 9 patients undergoing intra-cerebral single-pulse electrical stimulation (SPES). ResultsWhen calculated on TMS/hd-EEG potentials, PCIST performed with the same accuracy as the original PCI, while improving on the previous method by being computed in less than a second and requiring a simpler set-up. In SPES/SEEG signals, the index was able to quantify a systematic reduction of intracerebral complexity during sleep, confirming the occurrence of state-dependent changes in the effective connectivity of thalamocortical circuits, as originally assessed through TMS/hd-EEG. ConclusionsPCIST represents a fundamental advancement towards the implementation of a reliable and fast clinical tool for the bedside assessment of consciousness as well as a general measure to explore the neuronal mechanisms of loss/recovery of brain complexity across scales and models.

neuroscience

Rapid high throughput SYBR green assay for identifying the malaria vectors Anopheles arabiensis, Anopheles coluzzii and Anopheles gambiae s.s. Giles

The Anopheles gambiae sensu lato species complex consists of a number of cryptic species with different habitats and behaviours. These morphologically indistinct species are identified by chromosome banding and molecular diagnostic techniques which are still under improvement even though the current SINE method for identification between An. coluzzii and An. gambiae works reliably. This study describes a refinement of the SINE method to increase sensitivity and high throughput method for the identification of both species and An. arabiensis using amplicon dissociation characteristics.\n\nField collected samples, laboratory reared colonies and crossed specimens of the two species were used for the design of the protocol. An. gambiae, An. coluzzii, and hybrids of the two species were provided by the insectary of Vestergaard-NMIMR Vector Labs at the Noguchi Memorial Institute for Medical Research (Ghana) and An. arabiensis from Kenya. Samples were first characterised using conventional SINE PCR method, and further assayed using SYBR green, an intercalating fluorescent dye.\n\nThe three species and hybrids were clearly differentiated using the melting temperature of the dissociation curves, with derivative peaks at 72 Celsius for An. arabiensis, 75{degrees}C for An. gambiae and 86{degrees}C for An. coluzzii. The hybrids (An. gambiae / An. coluzzii) showed both peaks. This work is the first to describe a SYBR green real time PCR method for the characterization of An. arabiensis, An. gambiae and An. coluzzii and was purposely designed for basic melt-curve analysis (rather than high-resolution melt-curve) to allow it to be used on a wide range of real-time PCR machines.

molecular biology

The Caspase-3 homolog DrICE regulates endocytic trafficking during Drosophila tracheal morphogenesis

Although well known for its role in apoptosis, the executioner caspase DrICE has a non-apoptotic function that is required for elongation of the epithelial tubes of the Drosophila tracheal system. Here, we show that DrICE acts downstream of the Hippo Network to regulate endocytic trafficking of at least four cell polarity, cell junction and apical extracellular matrix proteins involved in tracheal tube size control: Crumbs, Uninflatable, Kune-Kune and Serpentine. We further show that tracheal cells are competent to undergo apoptosis, even though developmentally-regulated DrICE function rarely kills tracheal cells. Our results reveal a novel developmental role for caspases, a previously unidentified pool of DrICE that colocalizes with Clathrin, and a mechanism by which the Hippo Network controls endocytic trafficking. Given published reports of in vitro regulation of endocytosis by mammalian caspases during apoptosis, we propose that caspase-mediated regulation of endocytic trafficking is an evolutionarily conserved function of caspases that can be deployed during morphogenesis.

cell biology

GFP-Forked, a genetic reporter for studying Drosophila oocyte polarity

The polarized organization of the Drosophila oocyte can be visualized by examining the asymmetric localization of mRNAs, which is supported by networks of polarized microtubules (MTs). In this study, we used the gene forked, the putative Drosophila homologue of espin, to develop a unique genetic reporter for asymmetric oocyte organization. We generated a null allele of the forked gene using the CRISPRCas9 system and found that forked is not required for determining the axes of the Drosophila embryo. However, ectopic expression of a truncated form of GFP-Forked generated a distinct network of asymmetric Forked, which first accumulated at the oocyte posterior and was then restricted to the anterolateral region of the oocyte cortex in mid-oogenesis. This localization pattern resembled that reported for the polarized MTs network. Indeed, pharmacological and genetic manipulation of the polarized organization of the oocyte showed that the filamentous Forked network diffused throughout the entire cortical surface of the oocyte, as would be expected upon perturbation of oocyte polarization. Finally, we demonstrated that Forked associated with Short-stop and Patronin foci, which assemble non-centrosomal microtubule-organizing centers. Our results thus show that clear visualization of asymmetric GFP-Forked network localization can be used as a novel tool for studying oocyte polarity.\n\nSummary statementThe novel asymmetric Forked network could be used as a genetic reporter for visualizing and studying oocyte polarity.

developmental biology

Temporal correlation of elevated PRMT1 gene expression with mushroom body neurogenesis during bumblebee brain development

Proper neural development in insects depends on the controlled proliferation and differentiation of neural precursors. In holometabolous insects, these processes must be coordinated during larval and pupal development. Recently, protein arginine methylation has come into focus as an important mechanism of controlling neural stem cell proliferation and differentiation in mammals. Whether a similar mechanism is at work in insects is unknown. We investigated this possibility by determining the expression pattern of three protein arginine methyltransferase mRNAs (PRMT1, 4 and 5) in the developing brain of bumblebees by in situ hybridisation. We detected expression in neural precursors and neurons in functionally important brain areas throughout development. We found markedly higher expression of PRMT1, but not PRMT4 and PRMT5, in regions of mushroom bodies containing dividing cells during pupal stages at the time of active neurogenesis within this brain area. At later stages of development, PRMT1 expression levels were found to be uniform and did not correlate with actively dividing cells. Our study suggests a role for PRMT1 in regulating neural precursor divisions in the mushroom bodies of bumblebees during the period of neurogenesis.

developmental biology

SpermQ - a simple analysis software to comprehensively study flagellar beating and sperm steering

Motile cilia, also called flagella, drive cell motility across a broad range of species; some cilia propel prokaryotes and eukaryotic cells like sperm, while cilia on epithelial surfaces create complex fluid patterns e.g. in the brain or lung. For sperm, the picture has emerged that the motile cilium, also called flagellum, is not only a motor, but also a sensor that detects stimuli from the environment, computing the beat pattern according to the sensory input. Thereby, the flagellum of the sperm cell navigates the sperm through a complex environment like the female genital tract. However, we know very little about how environmental signals change the flagellar beat and, thereby, the swimming behaviour of sperm. It has been proposed that distinct signalling domains in the flagellum control the flagellar beat. A detailed analysis has been mainly hampered by the fact that current comprehensive analysis approaches rely on complex microscopy and analysis systems. Thus, knowledge on sperm signalling regulating the flagellar beat is based on custom quantification approaches that are limited to only a few aspects of the flagellar beat, do not resolve the kinetics of the entire flagellum, rely on manual, qualitative descriptions, and are little comparable among each other. Here, we present SpermQ, a ready-to-use and comprehensive analysis software to quantify sperm motility. SpermQ provides a detailed quantification of the flagellar beat based on common time-lapse images acquired by dark-field or epi-fluorescence microscopy, making SpermQ widely applicable. We envision SpermQ becoming a standard tool in flagellar and motile cilia research that allows to readily link studies on individual signalling components in sperm and distinct flagellar beat patterns.

cell biology

Gating modules of the AMPA receptor pore domain revealed by unnatural amino acid mutagenesis

Ionotropic glutamate receptors (iGluRs) are responsible for fast synaptic transmission throughout the nervous system. Conformational changes of the transmembrane domain (TMD) underlying ion channel activation and desensitization remain poorly understood. Here, we explored the dynamics of the TMD of AMPA-type iGluRs using genetically-encoded unnatural amino acid (UAA) photo-crosslinkers, p-benzoyl-L-phenylalanine (BzF) and p-azido-L-phenylalanine (AzF). We introduced UAAs at sites throughout the TMD of the GluA2 receptor and characterized these mutants in patch-clamp recordings, exposing them to glutamate and UV light. This approach revealed a range of optical effects on the activity of mutant receptors. We found evidence that an interaction between the Pre-M1 and the M4 TMD helix was essential for normal activation and desensitization. Photoactivation at F579AzF, a residue behind the selectivity filter, had extraordinarily broad effects on gating and desensitization. This observation suggests coupling to other parts of the receptor and like in other tetrameric channels, selectivity filter gating.

neuroscience

Epiblast formation by Tead-Yap-dependent expression of pluripotency factors and competitive elimination of unspecified cells

The epiblast is a pluripotent cell population first formed in preimplantation embryos and its quality is important for proper development. Here, we examined the mechanisms of epiblast formation and found that the Hippo pathway transcription factor Tead and its coactivator Yap regulate expression of pluripotency factors. After specification of the inner cell mass, Yap accumulates in the nuclei and activates Tead. Tead activity is required for strong expression of pluripotency factors and is variable in the forming epiblast. Cells showing low Tead activity are eliminated from the epiblast through cell competition. Pluripotency factor expression and Myc control cell competition downstream of Tead activity. Cell competition eliminates unspecified cells and is required for proper organization of the epiblast. These results suggest that induction of pluripotency factors by Tead activity and elimination of unspecified cells via cell competition ensure the production of an epiblast with naive pluripotency.

developmental biology

JNK-IN-8, a c-Jun N-terminal kinase inhibitor, improves functional recovery through suppressing neuroinflammation in ischemic stroke

c-Jun N-terminal kinase (JNK), a mitogen activated protein kinase, is activated in ischemia brain injury and plays an important role in cerebral ischemic injury. Emerging studies demonstrated that JNK-IN-8 (a specific JNK inhibitor) regulates traumatic brain injury through controlling neuronal apoptosis and inflammation. However, the role of JNK-IN-8 in ischemic stroke and the underlying mechanisms of JNK-IN-8 involving neuroprotection remain poorly understood. In the present study, male rats were subjected to tMCAO (transient middle cerebral artery occlusion) followed by treatment with JNK-IN-8, and then the modified improved neurological function score (mNSS), the Foot-fault test and the level of inflammatory cytokines (IL-1{beta}, IL-6 and TNF-) were assessed. We found that JNK-IN-8-treated rats with MCAO exerted a significant improvement in spatial learning as measured by the improved mNSS, and showed sensorimotor functional recovery as measured by the Foot-fault test. JNK-IN-8 also exerted anti-inflammatory effects as indicated by decreased activation of microglia and the decreased expresson of IL-6, IL-1{beta} and TNF-. Furthermore, JNK-IN-8 suppressed the activation of JNK and subsequent activation of NF-{kappa}B signaling as indicated by the decreased level of phosphorylated JNK (p-JNK) and p65. These data suggest that JNK-IN-8 suppressed neuroinflammation and improved neurological function by inhibiting JNK/NF-{kappa}B pathway after ischemic brain injury, thus offering a new target for prevention of ischemic brain injury.

cancer biology