Miracle-dz/UniFAR-FTUs huggingface dataset:
Critical role of deadenylation in regulating poly(A) rhythms and circadian gene expression

The mammalian circadian clock is deeply rooted in rhythmic regulation of gene expression. Rhythmic transcriptional control mediated by the circadian transcription factors is thought to be the main driver of mammalian circadian gene expression. However, mounting evidence has demonstrated the importance of rhythmic post-transcriptional controls, and it remains unclear how the transcriptional and post-transcriptional mechanisms collectively control rhythmic gene expression. In mouse liver, hundreds of genes were found to exhibit rhythmicity in poly(A) tail length, and the poly(A) rhythms are strongly correlated with the protein expression rhythms. To understand the role of rhythmic poly(A) regulation in circadian gene expression, we constructed a parsimonious model that depicts rhythmic control imposed upon basic mRNA expression and poly(A) regulation processes, including transcription, deadenylation, polyadenylation, and degradation. The model results reveal the rhythmicity in deadenylation as the strongest contributor to the rhythmicity in poly(A) tail length and the rhythmicity in the abundance of the mRNA subpopulation with long poly(A) tails (a rough proxy for mRNA translatability). In line with this finding, the model further shows that the experimentally observed distinct peak phases in the expression of deadenylases, regardless of other rhythmic controls, can robustly cluster the rhythmic mRNAs by their peak phases in poly(A) tail length and abundance of the long-tailed subpopulation. This provides a potential mechanism to synchronize the phases of target gene expression regulated by the same deadenylases. Our findings highlight the critical role of rhythmic deadenylation in regulating poly(A) rhythms and circadian gene expression.
Human dorsal anterior cingulate neurons signal conflict by amplifying task-relevant information

Hemodynamic activity in dorsal anterior cingulate cortex (dACC) correlates with conflict, suggesting it contributes to conflict processing. This correlation could be explained by multiple neural processes that can be disambiguated by population firing rates patterns. We used targeted dimensionality reduction to characterize activity of populations of single dACC neurons as humans performed a task that manipulates two forms of conflict. Although conflict enhanced firing rates, this enhancement did not come from a discrete population of domain-general conflict-encoding neurons, nor from a distinct conflict-encoding response axis. Nor was it the epiphenomenal consequence of simultaneous coactivation of action plans. Instead, conflict amplified the task-relevant information encoded across the neuronal population. Effects of conflict were weaker and more heterogeneous in the dorsolateral prefrontal cortex (dlPFC), suggesting that dACC’s role in conflict processing may be somewhat specialized. Overall, these results support the theory that conflict biases competition between sensorimotor transformation processes occurring in dACC.
Cantharidin alters GPI-anchored protein sorting by targeting Cdc1 mediated remodeling in Endoplasmic Reticulum

Cantharidin (CTD) is a potent anticancer small molecule produced by several species of blister beetle. It has been a traditional medicine for the treatment of warts and tumors for many decades. CTD suppresses the tumor growth by inducing apoptosis, cell cycle arrest, and DNA damage. It is a known inhibitor of PP2A and PP1. In this study, we identified new molecular targets of CTD using Saccharomyces cerevisiae as a model organism which expresses a Cantharidin Resistance Gene (CRG1). CRG1 encodes a SAM-dependent methyltransferase that inactivates CTD by methylation. CTD alters lipid homeostasis, cell wall integrity, endocytosis, adhesion, and invasion in yeast cells. We found that CTD specifically affects the phosphatidylethanolamine (PE) associated functions which can be rescued by supplementation of ethanolamine (ETA) in the growth media. CTD also perturbed ER homeostasis and cell wall integrity by altering the GPI-anchored protein sorting. The CTD dependent genetic interaction profile of CRG1 revealed that Cdc1 activity in GPI-anchor remodeling is the key target of CTD, which we found to be independent of PP2A and PP1. Furthermore, our experiments with human cells suggest that CTD functions through a conserved mechanism in higher eukaryotes as well. Altogether, we conclude that CTD induces cytotoxicity by targeting Cdc1 activity in GPI-anchor remodeling in the endoplasmic reticulum (ER).
Diffusion property and functional connectivity of superior longitudinal fasciculus underpin human metacognition

Metacognition as the capacity of monitoring one’s own cognition operates across domains. Here, we addressed whether metacognition in different cognitive domains rely on common or distinct neural substrates with combined diffusion tensor imaging (DTI) and functional magnetic resonance imaging (fMRI) techniques. After acquiring DTI and resting-state fMRI data, we asked participants to perform a temporal-order memory task and a perceptual discrimination task, followed by trial-specific confidence judgments. DTI analysis revealed that the structural integrity (indexed by fractional anisotropy) in the anterior portion of right superior longitudinal fasciculus (SLF) was associated with both perceptual and mnemonic metacognitive abilities. Using perturbed mnemonic metacognitive scores produced by inhibiting the precuneus using TMS, the mnemonic metacognition scores did not correlate with individuals’ SLF structural integrity anymore, revealing the relevance of this tract in memory metacognition. In order to further verify the involvement of several cortical regions connected by SLF, we took the TMS-targeted precuneus region as a seed in a functional connectivity analysis and found the functional connectivity between precuneus and two SLF-connected regions (inferior parietal cortex and precentral gyrus) differentially mediated mnemonic but not perceptual metacognition performance. These results illustrate the importance of SLF and a putative white-matter grey-matter circuitry that supports human metacognition.
Excessive Polyamine Generation in Keratinocytes Promotes Self-RNA Endosomal Sensing by Dendritic Cells in Psoriasis

The mechanisms underlying tissue-specific chronic inflammation are elusive. Here we report that mice lacking Protein Phosphatase 6 in keratinocytes are predisposed to psoriasis-like skin inflammation, with an inordinate urea cycle and enhanced oxidative phosphorylation that supports hyperproliferation. This phenotype is mediated by increased Arginase-1 production resulting from CCAAT/enhancer-binding protein beta activation. Single-cell RNA-seq of the psoriatic epidermis revealed that the rate-limiting enzyme for Arginine biosynthesis, Argininosuccinate synthetase 1, maintains the Arginine pool, which is indispensable for immune responses. Accumulated polyamines branched from the urea cycle promote endosomal Tlr7-dependent self-RNA sensing by myeloid dendritic cells. This process is achieved with the assistance of an RNA-binding peptide that originates from the heterogeneous nuclear ribonucleoprotein A1, a probable autoantigen in psoriasis. Finally, targeting urea cycle wiring with an arginase inhibitor markedly improved skin inflammation in murine and non-human primate models of psoriasis. Our findings suggest that urea cycle alteration and excessive polyamine production by psoriatic keratinocytes promote self-RNA sensing by dendritic cells, which links the hyperproliferation of stationary cells with innate-immune activation in an auto-inflammatory condition.
The immune vulnerability landscape of the 2019 Novel Coronavirus, SARS-CoV-2

The outbreak of the 2019 Novel Coronavirus (SARS-CoV-2) rapidly spread from Wuhan, China to more than 150 countries, areas, or territories, causing staggering numbers of infections and deaths. In this study, bioinformatics analyses were performed on 5,568 complete genomes of SARS-CoV-2 virus to predict the T cell and B cell immunogenic epitopes of all viral proteins, which formed a systematic immune vulnerability landscape of SARS-CoV-2. The immune vulnerability and genetic variation profiles of SARS-CoV were compared with those of SARS-CoV and MERS-CoV. In addition, a web portal was developed to broadly share the data and results as a resource for the research community. Using this resource, we showed that genetic variations in SARS-CoV-2 are associated with loss of B cell immunogenicity, an increase in CD4+ T cell immunogenicity, and a minimum loss in CD8+ T cell immunogenicity, indicating the existence of a curious correlation between SARS-CoV-2 genetic evolutions and the immunity pressure from the host. Overall, we present an immunological resource for SARS-CoV-2 that could promote both therapeutic/vaccine development and mechanistic research.
γ-H2AX is present at mouse meiotic kinetochores

The histone variant H2AX phosphorylated on serine 139, named γ-H2AX, is a canonical DNA double-strand breaks marker. During mammalian meiotic prophase I, γ-H2AX participates in meiotic recombination, meiotic sex chromosome inactivation and meiotic silencing of unsynapsed chromatin. In this study, we have analyzed the distribution of γ-H2AX during male mouse meiosis by immunofluorescence on spread and squashed spermatocytes. We have found that γ-H2AX locates at the inner kinetochore plate of meiotic kinetochores in both meiotic divisions. Therefore our results, for the first time, uncover a novel role for γ-H2AX at mammalian meiotic kinetochores.
microRNA-184 and Its lncRNA Sponge UCA1 are Induced in Wounded Keratinocytes in a Store-Operated Calcium Entry-Dependent Manner

Emerging evidence implicates microRNAs (miRNA) in the regulation of keratinocyte migration. However, the putative roles of microRNA-184 (miR-184) in keratinocyte migration have not been examined. Here, we show that miR-184 expression was elevated following wounding of human keratinocyte monolayers. The induction of miR-184 was dependent on store-operated calcium entry (SOCE) as it was abolished by pharmacologic SOCE blockers. The long non-coding RNA urothelial cancer associated 1 (UCA1), which is thought to acts as a sponge or competing endogenous RNA (ceRNA) against miR-184 was also induced in scratched monolayers. Induction of UCA1 was impaired, but not abolished, by SOCE inhibition. Transfection of keratinocytes with a miR-184 mimic stimulated migration in scratch assays, whereas inhibition of miR-184 dampened the ability of keratinocytes to migrate. Together, our data suggest, for the first time, that SOCE promotes miR-184 induction in wounded monolayers to support keratinocyte migration while also increasing lncRNA UCA1 expression, which may in turn regulate miR-184 activity in keratinocytes.
Calcium-induced calcium release and type 3 ryanodine receptors modulate the slow afterhyperpolarising current, sIAHP, and its potentiation in hippocampal pyramidal neurons

The slow afterhyperpolarising current, sIAHP, is a Ca2+-dependent current that plays an important role in the late phase of spike frequency adaptation. sIAHP is activated by voltage-gated Ca2+ channels, while the contribution of calcium from ryanodine-sensitive intracellular stores, released by calcium-induced calcium release (CICR), is controversial in hippocampal pyramidal neurons. Three types of ryanodine receptors (RyR1-3) are expressed in the hippocampus, with RyR3 showing a predominant expression in CA1 neurons. We investigated the specific role of CICR, and particularly of its RyR3-mediated component, in the regulation of the sIAHP amplitude and time course, and the activity-dependent potentiation of the sIAHP in rat and mouse CA1 pyramidal neurons. Here we report that enhancement of CICR by caffeine led to an increase in sIAHP amplitude, while inhibition of CICR by ryanodine caused a small, but significant reduction of sIAHP. Inhibition of ryanodine-sensitive Ca2+ stores by ryanodine or depletion by the SERCA pump inhibitor cyclopiazonic acid caused a substantial attenuation in the sIAHP activity-dependent potentiation in both rat and mouse CA1 pyramidal neurons. Neurons from mice lacking RyR3 receptors exhibited a sIAHP with features undistinguishable from wild-type neurons, which was similarly reduced by ryanodine. However, the lack of RyR3 receptors led to a faster and reduced activity-dependent potentiation of sIAHP. We conclude that ryanodine receptor-mediated CICR contributes both to the amplitude of the sIAHP at steady state and its activity-dependent potentiation in rat and mouse hippocampal pyramidal neurons. In particular, we show that RyR3 receptors play an essential and specific role in shaping the activity-dependent potentiation of the sIAHP. The modulation of activity-dependent potentiation of sIAHP by RyR3-mediated CICR contributes to plasticity of intrinsic neuronal excitability and is likely to play a critical role in higher cognitive functions, such as learning and memory.
Dynamics of Gut Microbiome, IgA Response and Plasma Metabolome in Development of Pediatric Celiac Disease

Celiac disease (CD) is an autoimmune disorder triggered by gluten consumption. To identify the role of gut microbes in CD onset, we performed a longitudinal study focusing on two important phases of gut microbiota development at ages 2.5 and 5 (n=16). We obtained samples from children who developed CD during or after the study (CD progressors) and age, sex, and HLA-matched healthy controls. CD progressors had a distinct gut microbiota composition and IgA-sequencing identified unique IgA targets in the gut. Three cytokines, one chemokine, and 19 plasma metabolites were significantly altered in CD progressors at age 5. Feeding C57BL/6J mice with taurodeoxycholic acid (TDCA), a 2-fold increased microbiota-derived metabolite in CD progressors, caused villous atrophy, increased intraepithelial lymphocytes (IELs), CD4+ T-cells, Natural Killer cells, and Qa-1 expression on T-cells while decreasing T-regulatory cells in IELs. Thus, TDCA drives inflammation in the small intestines that potentially contribute to the CD onset. Highlights CD progressors have a distinct gut microbiome composition compared to healthy controls in two important phases of gut microbiota development (age 2.5 and 5 years) CD progressors have more IgA-coated bacteria in their gut at age 5 compared to healthy controls. Further, IgA-sequencing identified unique bacterial targets in CD progressors. Three plasma proinflammatory cytokines and a chemokine were increased in CD progressors years before diagnosis, indicating an early inflammatory response. We identified 19 metabolites that are significantly altered in CD progress at age 5 and microbiota-derived TDCA increased two-fold. TDCA treatment in B6 mice increased CD4+ cells and NK cells while decreasing CD8+ T-regulatory (Treg) cells. It also increased Qa-1 expression on immune cells.
Rab27b regulates the release, autophagic clearance, and toxicity of alpha-synuclein

Alpha synuclein (αsyn) is the primary component of proteinaceous aggregates termed Lewy Bodies that pathologically define synucleinopathies including Parkinson’s disease (PD) and Dementia with Lewy Bodies (DLB). αSyn is hypothesized to spread through the brain in a prion-like fashion by misfolded protein forming a template for aggregation of endogenous αsyn. The release and uptake of αsyn from cell to cell are considered important processes for this prion-like spread. Rab27b is one of several GTPases essential to the endosomal-lysosomal pathway and is implicated in protein secretion and clearance but has yet to be characterized in its role in αsyn spread. In this study, we used a paracrine αsyn in vitro model to test the impact of Rab27b on αsyn release, clearance, and toxicity. shRNA-mediated knockdown (KD) of Rab27b increased αsyn-mediated paracrine toxicity. While Rab27b reduced αsyn release primarily through non-exosomal pathways, the αsyn released under KD conditions was of higher molecular weight species by size exclusion chromatography. Rab27b KD increased intracellular insoluble αsyn levels and led to an accumulation of endogenous LC3 positive puncta. Rab27b KD also decreased LC3 turnover with chloroquine treatment, indicating a defect in autophagic flux. Rab27b protein levels were increased in postmortem human brain lysates from PD and DLB subjects compared to healthy controls. These data indicate a role for Rab27b in the release, clearance, and toxicity of αsyn and ultimately in the pathogenesis of synucleinopathies.
Expanding the Coverage of Metabolic Landscape in Cultivated Rice with Integrated Computational Approaches

Genome-scale metabolomics analysis is increasingly used for pathway and function discovery in post-genomics era. The great potential offered by developed mass spectrometry (MS)-based technology has been hindered by the obstacle that only a small portion of detected metabolites were identifiable so far. To address the critical issue of low identification coverage in metabolomics, we adopted a deep metabolomics analysis strategy by integrating advanced algorithms and expanded reference databases. The experimental reference spectra, and in silico reference spectra were adopted to facilitate the structural annotation. To further characterize the structure of metabolites, two approaches, structural motif search combined with neutral loss scanning, and metabolite association network were incorporated into our strategy. An untargeted metabolomics analysis was performed on 150 rice cultivars using Ultra Performance Liquid Chromatography (UPLC)-Quadrupole (Q)-Orbitrap mass spectrometer. 1939 of 4491 metabolite features in MS/MS spectral tag (MS2T) library were annotated, representing an extension of annotation coverage by an order of magnitude on rice. The differential accumulation patterns of flavonoids between indica and japonica cultivars were revealed, especially O-sulfated flavonoids. A series of closely-related flavonolignans were characterized, adding further evidence for the crucial role of tricin-oligolignols in lignification. Our study provides a great template in the exploration of phytochemical diversity for more plant species.
proABC-2: PRediction of AntiBody contacts v2 and its application to information-driven docking

Monoclonal antibodies (mAbs) are essential tools in the contemporary therapeutic armoury. Understanding how these recognize their antigen is a fundamental step in their rational design and engineering. The rising amount of publicly available data is catalysing the development of computational approaches able to offer valuable, faster and cheaper alternatives to classical experimental methodologies used for the study of antibody-antigen complexes. Here we present proABC-2, an update of the original random-forest antibody paratope predictor, based on a convolutional neural network algorithm. We also demonstrate how the predictions can be fruitfully used to drive the docking in HADDOCK. The proABC-2 server is freely available at: https://bianca.science. uu.nl/proabc2/.
Excessive visual crowding effects in developmental dyscalculia

Visual crowding refers to the inability to identify objects when surrounded by other similar items. Crowding-like mechanisms are thought to play a key role in numerical perception by determining the sensory mechanisms through which ensembles are perceived. Enhanced visual crowding might hence prevent the normal development of a system involved in segregating and perceiving discrete numbers of items and ultimately the acquisition of more abstract numerical skills. Here, we investigated whether excessive crowding occurs in developmental dyscalculia (DD), a neurodevelopmental disorder characterized by difficulty in learning the most basic numerical and arithmetical concepts, and whether it is found independently of associated major reading and attentional difficulties. We measured spatial crowding in two groups of adult individuals with DD and control subjects. In separate experiments, participants were asked to discriminate the orientation of a Gabor patch either in isolation or under spatial crowding. Orientation discrimination thresholds were comparable across groups when stimuli were shown in isolation, yet they were much higher for the DD group with respect to the control group when the target was crowded by closely neighbouring flanking gratings. The difficulty in discriminating orientation (as reflected by the combination of accuracy and reaction times) in the DD compared to the control group persisted over several larger target flanker distances. Finally, we found that the degree of such spatial crowding correlated with impairments in mathematical abilities even when controlling for visual attention and reading skills. These results suggest that excessive crowding effects might be a characteristic of DD, independent of other associated neurodevelopmental disorders. Bullet points People with DD have difficulty learning about numbers and arithmetics. Perception of non-symbolic number seems to be modulated by visual crowding. Can stronger than normal crowding effects contribute to the origin of DD? We measured crowding with orientation discrimination tasks using Gabor gratings. Abnormal crowding characterizes DD independently of other developmental deficits.
GABAergic neurons and NaV1.1 channel hyperactivity: a novel neocortex-specific mechanism of Cortical Spreading Depression

Cortical spreading depression (CSD) is a pathologic mechanism of migraine. We have identified a novel neocortex-specific mechanism of CSD initiation and a novel pathological role of GABAergic neurons. Mutations of the NaV1.1 sodium channel (the SCN1A gene), which is particularly important for GABAergic neurons’ excitability, cause Familial Hemiplegic Migraine type-3 (FHM3), a subtype of migraine with aura. They induce gain-of-function of NaV1.1 and hyperexcitability of GABAergic interneurons in culture. However, the mechanism linking these dysfunctions to CSD and FHM3 has not been elucidated. Here, we show that NaV1.1 gain-of-function, induced by the specific activator Hm1a, or mimicked by optogenetic-induced hyperactivity of cortical GABAergic neurons, is sufficient to ignite CSD by spiking-generated extracellular K+ build-up. This mechanism is neocortex specific because, with these approaches, CSD was not generated in other brain areas. GABAergic and glutamatergic synaptic transmission is not required for optogenetic CSD initiation, but glutamatergic transmission is implicated in CSD propagation. Thus, our results reveal the key role of hyper-activation of Nav1.1 and GABAergic neurons in a novel mechanism of CSD initiation, which is relevant for FHM3 and possibly also for other types of migraine.