Miracle-dz/UniFAR-FTUs huggingface dataset:
JCB: REPORT

A. Van Keymeulen and G. Mascre contributed equally to this paper. Correspondence to Cédric Blanpain: Cedric.Blanpain@ulb.ac. be Abbreviations used in this paper: cKO, conditional knockout; CREER, estrogen receptor–inducible CRE; CREPR, Cre progesterone receptor fusion protein; HF, hair follicle; MC, Merkel cell; NCC, neural crest cell; P-cadherin, placental cadherin; SC, stem cell; TAM, tamoxifen. Introduction
Myosin VI moves on nuclear actin filaments and supports long-range chromatin rearrangements

Nuclear myosin VI (MVI) enhances RNA polymerase II – dependent transcription, but the molecular mechanism is unclear. We used live cell single molecule tracking to follow individual MVI molecules inside the nucleus and observed micrometer-long motion of the motor. Besides static chromatin interactions lasting for tens of seconds, ATPase-dependent directed motion occurred with a velocity of 2 µm/s. The movement was frequently interrupted by short periods of slow restricted diffusion and increased in frequency upon stimulation of transcription. Mutagenesis and perturbation experiments demonstrated that nuclear MVI motion is independent of dimerization and occurs on nuclear actin filaments, which we also observed by two-color imaging. Using chromosome paint to quantify distances between chromosomes, we found that MVI is required for transcription-dependent long-range chromatin rearrangements. Our measurements reveal a transcription-coupled function of MVI in the nucleus, where it actively undergoes directed movement along nuclear actin filaments. Motion is potentially mediated by cooperating monomeric motors and might assist in enhancing transcription by supporting long-range chromatin rearrangements.
Fatal toxicity of chloroquine or hydroxychloroquine with metformin in mice

Guided by the principle of primum non nocere (first do no harm), we report a cautionary note on the potential fatal toxicity of chloroquine (CQ) or hydroxychloroquine (HCQ) in combination with anti-diabetic drug metformin. We observed that the combination of CQ or HCQ and metformin, which were used in our studies as potential anti-cancer drugs, killed 30-40% of mice. While our observations in mice may not translate to toxicity in humans, the reports that CQ or HCQ has anti-COVID-19 activity, the use of CQ resulting in toxicity and at least one death, and the recent Emergency Use Authorization (EUA) for CQ and HCQ by the US Food and Drug Administration (FDA) prompted our report. Here we report the lethality of CQ or HCQ in combination with metformin as a warning of its potential serious clinical toxicity. We hope that our report will be helpful to stimulate pharmacovigilance and monitoring of adverse drug reactions with the use of CQ or HCQ, particularly in combination with metformin.
Pangaea: A modular and extensible collection of tools for mining context dependent gene relationships from the biomedical literature

Motivation Pangaea is a scalable and extensible command line interface (CLI) software that integrates gene-relationship detection features to extract context-dependent structured gene-gene and gene-term relationships from the biomedical literature. It provides computational methods to identify biological relationships between a collection of genes and can be used to search and extract different types of contextual relationships amongst genes. Results We implemented a CLI-based software for downloading PubMed articles and extracting gene relationships from abstracts using natural language processing methods. In terms of scalability, the software was designed to support the retrieval and processing of millions of articles whilst minimising memory requirements and optimising for parallel processing on multiple CPU cores. To allow extensibility, the tool permits the use of contextual custom-made models for the text processing parts, and the output is serialised as JSON objects to allow flexible post-processing workflows. Availability The software is available online at: https://github.com/ss-lab-cancerunit/pangaea
Layer-specific Loss and Compensation of Parvocellular Response in Subcortical Pathways of Adult Human Amblyopia

Abnormal visual experience in critical period causes amblyopia or lazy eye, reducing visual abilities even with corrected optics. A long-standing question is where in the human visual system does the amblyopic deficit arise. In particular, whether amblyopia induces selective deficits of the magnocellular (M) or the parvocellular (P) geniculostriate pathways, and whether the more ancient retinotectal pathway is also affected. Technical limitations to non-invasively measure layer-specific activity in human lateral geniculate nucleus (LGN) and superior colliculus (SC) hampered efforts in addressing these questions. In the current study, using lamina-resolved 3T and 7T fMRI and visual stimuli selectively activating the M and P pathways, we investigated layer-specific response properties of the LGN and the SC of amblyopia patients and normal controls. With stimuli presented to the amblyopic eye, there was a stronger response loss in the P layers than in the M layers of the LGN. Compared to normal controls, amblyopic eye’s response to the P stimulus was selectively reduced in the superficial SC, while the fellow eye’s response was robustly increased in the deep SC. Selective P response deficits of amblyopia were also observed in the visual pulvinar, early visual cortex, and ventral but not dorsal visual streams. These results provide strong in vivo evidence in adult amblyopic patients for selective deficits of parvocellular functions in the visual thalamus, and additionally reveal response deficits to the amblyopic eye and neural compensation to the fellow eye in the retinotectal pathway. Highlights Parvocellular response loss in the LGN P layers, visual pulvinar and ventral visual stream Selective amblyopic deficits of the parvocellular pathway Amblyopic eye’s response decreased in the superficial SC Fellow eye’s response increased in the deep SC Amblyopic deficits and neural compensation in the retinotectal pathway
Focused Ultrasound Stimulates ER Localized Mechanosensitive PANNEXIN-1 to Mediate Intracellular Calcium Release in Invasive Cancer Cells

Focused ultrasound (FUS) is a rapidly developing stimulus technology with the potential to uncover novel mechanosensory dependent cellular processes. Since it is noninvasive, it holds great promise for future therapeutic applications in patients used either alone or as a complement to boost existing treatments. For example, FUS stimulation causes invasive but not noninvasive cancer cell lines to exhibit marked activation of calcium signaling pathways. Here, we identify the membrane channel PANNEXIN1 (PANX1) as a mediator for activation of calcium signaling in invasive cancer cells. Knockdown of PANX1 decreases calcium signaling in invasive cells, while PANX1 overexpression enhances calcium elevations in non-invasive cancer cells. We demonstrate that FUS may directly stimulate mechanosensory PANX1 localized in endoplasmic reticulum to evoke calcium release from internal stores. This process does not depend on mechanosensory stimulus transduction through an intact cytoskeleton and does not depend on plasma membrane localized PANX1. Plasma membrane localized PANX1 however plays a different role in mediating the spread of intercellular calcium waves via ATP release. Additionally, we show that FUS stimulation evokes cytokine/chemokine release from invasive cancer cells, suggesting that FUS could be an important new adjuvant treatment to improve cancer immunotherapy.
LCM-seq identifies robust markers of vulnerable and resistant human midbrain dopamine neurons

Defining transcriptional profiles of substantia nigra pars compacta (SNc) and ventral tegmental area (VTA) dopamine neurons in human is critical to understanding their differential vulnerability in Parkinson Disease. However, reported marker profiles for these neuron populations are derived predominantly from rodents, utilize small sample sizes and display extensive variability between studies. Here, we map selective expression profiles of dopamine neurons in an extensive collection of human SNc and VTA using laser capture microdissection coupled with Smart-seq2 RNA sequencing (LCM-seq). By applying a bootstrapping strategy as sample input to DESeq2, we identify 33 differentially expressed SNc- or VTA-specific markers and we also compute the minimal cohort size required to identify differentially expressed genes (DEGs) that are concordant regardless of cohort size. Among the identified DEGs, ZCCHC12, CDH13 and SERPINE2, are minimally required to distinguish SNc or VTA dopamine neurons in both human and mouse. In summary, our study identifies novel markers, besides previously identified ones, which will be instrumentsal for future studies aiming to modulate dopamine neuron resilience as well as validate cell identity of stem cell-derived dopamine neurons.
Local and global dichotomic dysfunction in resting and evoked functional connectivity precedes tauopathy

Functional activity alterations are one of the earliest hallmarks of Alzheimer9s disease (AD), already detected prior to beta-amyloid plaque and tau-tangle accumulation. To reveal the physiological basis underpinning these changes at the onset of the pathology, we leveraged fMRI in the 3xTgAD mouse model for AD. Resting-state fMRI revealed functional connectivity loss within areas homologous to the human temporal lobe, particularly the entorhinal cortex. Optogenetic activation of the entorhinal cortex results, instead, in enhanced fMRI signal, thus denoting an increase in metabolic demand under load. This is corroborated by synaptic hyperexcitability in the highlighted projection targets, reported with electrophysiological recordings. Thus, 3xTgAD mice reveal a dichotomic behavior between resting and evoked states, resulting in a functional brain-wide reorganization with local underpinnings, which reconciles evidence from the human literature. The 3xTgAD tauopathy profile resembles that in AD patients closely, suggesting that similar pathophysiological mechanisms might underlie network dysfunction in clinical cases.
Adverse Effect of Nighttime Blood Pressure on the Outcome of Lacunar Infarct Patients

Background and Purpose—Antihypertensive therapy has dramatically reduced the incidence of stroke recurrence; however, recent studies have suggested that the excessive lowering of blood pressure (BP) could cause ischemic cerebral lesions. We conducted a prospective study using MRI and ambulatory blood pressure monitoring to elucidate the appropriate BP control level for the prevention of silent and symptomatic cerebral infarction. Methods—We studied 105 patients with symptomatic lacunar infarcts who underwent repeated MRI and 24-hour BP monitoring in the period between the two MRI examinations. The patients were divided into five groups according to their outcome as follows: group 1, those who showed neither symptomatic episodes nor the development of new silent lesions detected by repeated MRI; group 2, those who only showed the development of silent lacunae; group 3, those who showed development of diffuse white matter lesions only; group 4, those who showed the development of both silent lacunae and dif.
Activation of SnRK2 by the Raf-like kinase ARK represents a common mechanism of ABA response in embryophytes

The Raf-like protein kinase ARK previously identified in the moss Physcomitrella patens acts as an upstream regulator of subgroup III SnRK2, the key regulator of abscisic acid (ABA) and abiotic stress responses. However, the mechanisms underlying activation of ARK by ABA and abiotic stress for the regulation of SnRK2 including the role of ABA receptor-associated group A PP2C (PP2C-A) are not understood. We identified Ser1029 as the phosphorylation site in the activation loop of ARK, which provided a possible mechanism for regulation of its activity. Analysis of transgenic ark lines expressing ARK-GFP with Ser1029-to-Ala mutation indicated that this replacement causes reductions in ABA-induced gene expression, stress tolerance and SnRK2 activity. Immunoblot analysis using an anti-phosphopeptide antibody indicated that ABA treatments rapidly stimulate Ser1029 phosphorylation in wild type. The phosphorylation profile of Ser1029 in ABA-hypersensitive ppabi1 lacking PP2C-A was similar to that in wild type, whereas little Ser1029 phosphorylation was observed in ABA-insensitive ark missense lines. Furthermore, newly isolated ppabi1 ark lines showed ABA-insensitive phenotypes similar to those of ark lines. These results indicate that ARK is a primary activator of SnRK2, preceding negative regulation by PP2C-A in bryophytes, which provides a prototypal mechanism for ABA and abiotic stress-responses in embryophytes. One sentence summary Physiological characterization of various moss mutants revealed a common mechanism for phytohormone responses under water deficit in all land plants.
Development of an in vitro senescent hepatic cell model for metabolic studies in aging

Although aging in the liver contributes to the development of chronic liver diseases such as NAFLD and insulin resistance, little known about the molecular and metabolic details of aging in hepatic cells. To examine these issues, we used sequential oxidative stress with hydrogen peroxide to induce premature senescence in AML12 hepatic cells. The senescent cells exhibited molecular and metabolic signatures, increased SA-βGal and γH2A. X staining, and elevated senescence and pro-inflammatory gene expression that resembled livers from aged mice. Metabolic phenotyping showed fuel switching towards glycolysis and mitochondrial glutamine oxidation as well as impaired energy production. The senescent AML12 cells also had increased mTOR signaling and decreased autophagy which likely contributed to the fuel switching from β-oxidation that occurred in normal AML12 cells. Additionally, senescence activated secretory proteins from conditioned media of senescent cells sensitized normal AML12 cells to palmitate-induced toxicity, a known pathological effect of hepatic aging. In summary, we have generated senescent AML12 cells which displayed the molecular hallmarks of aging, and also exhibited the aberrant metabolic phenotype, mitochondrial function, and cell signaling that occur in the aged liver.
Molecular development of muscle spindle and Golgi tendon organ sensory afferents revealed by single proprioceptor transcriptome analysis

Anatomical and physiological analyses have long revealed differences between proprioceptive groups Ia, II, and Ib sensory neurons, yet the molecular correlates of these three muscle afferent subtypes remain unknown. We performed single cell RNA sequencing of genetically identified adult proprioceptors and, using unbiased bioinformatics approaches, detected five molecularly distinct neuronal clusters. Validation of cluster-specific transcripts in dorsal root ganglia (DRG) and skeletal muscle provides evidence these clusters correspond to functionally distinct muscle spindle (MS) or Golgi tendon organ (GTO) afferent proprioceptors. Remarkably, while we uncovered just one type of GTO afferents, four of the five clusters represent MS afferents, thus demonstrating a previously unappreciated diversity among these muscle proprioceptors. In vitro electrophysiological recordings reveal just two broadly distinct proprioceptor types, and suggest that the refinement of functional subtype diversity may occur along multiple axes of maturation. Lineage analysis between proprioceptor transcriptomes at different developmental stages show little or no correlation for transcripts that define adult MS or GTO afferents, supporting the idea that proprioceptor subtype identity emerges late in development. Together, our data provide the first comprehensive molecular signature for groups Ia and II MS afferents and group Ib GTO afferents, and offer new strategies for genetic interrogation of the role of these individual proprioceptor subtypes in regulating voluntary motor behavior.
KnetMiner: a comprehensive approach for supporting evidence-based gene discovery and complex trait analysis across species

Generating new ideas and scientific hypotheses is often the result of extensive literature and database reviews, overlaid with scientists’ own novel data and a creative process of making connections that were not made before. We have developed a comprehensive approach to guide this technically challenging data integration task and to make knowledge discovery and hypotheses generation easier for plant and crop researchers. KnetMiner can digest large volumes of scientific literature and biological research to find and visualise links between the genetic and biological properties of complex traits and diseases. Here we report the main design principles behind KnetMiner and provide use cases for mining public datasets to identify unknown links between traits such grain colour and pre-harvest sprouting in Triticum aestivum, as well as, an evidence-based approach to identify candidate genes under an Arabidopsis thaliana petal size QTL. We have developed KnetMiner knowledge graphs and applications for a range of species including plants, crops and pathogens. KnetMiner is the first open-source gene discovery platform that can leverage genome-scale knowledge graphs, generate evidence-based biological networks and be deployed for any species with a sequenced genome. KnetMiner is available at http://knetminer.org.
PresRAT: A server for identification of bacterial small-RNA sequences and their targets with probable binding region

Bacterial small-RNA (sRNA) sequences are functional RNAs, which play an important role in regulating the expression of a diverse class of genes. It is thus critical to identify such sRNA sequences and their probable mRNA targets. Here, we discuss new procedures to identify and characterize sRNA and their targets via the introduction of an integrated online platform named PresRAT (Prediction of sRNA and their Targets). PresRAT uses the primary and secondary structural attributes of sRNA sequences to predict sRNA from a given sequence or bacterial genome. PresRAT also finds probable target mRNAs of sRNA sequences from a given bacterial chromosome and further concentrates on identification of the probable sRNA-mRNA binding regions. Using PresRAT we have identified a total of 60,518 potential sRNA sequences from 54 bacterial genomes and 2447 potential targets from 13 bacterial genomes. We have also implemented a protocol to build and refine 3D models of sRNA and sRNA-mRNA duplex regions and generated 3D models of 50 known sRNAs and 81 sRNA-mRNA duplexes using this platform. Along with the server part, PresRAT also contains a database section, which enlists the predicted sRNA sequences, sRNA targets and their corresponding 3D models with structural dynamics information.
Computational prediction of Drug-Disease association based on Graph-regularized one bit Matrix completion

Motivation Investigation of existing drugs is an effective alternative to discovery of new drugs for treating diseases. This task of drug re-positioning can be assisted by various kinds of computational methods to predict the best indication for a drug given the open-source biological datasets. Owing to the fact that similar drugs tend to have common pathways and disease indications, the association matrix is assumed to be of low-rank structure. Hence, the problem of drug-disease association prediction can been modelled as a low-rank matrix-completion problem. Results In this work, we propose a novel matrix completion framework which makes use of the sideinformation associated with drugs/diseases for the prediction of drug-disease indications modelled as neighborhood graph: Graph regularized 1-bit matrix compeltion (GR1BMC). The algorithm is specially designed for binary data and uses parallel proximal algorithm to solve the aforesaid minimization problem taking into account all the constraints including the neighborhood graph incorporation and restricting predicted scores within the specified range. The results of the proposed algorithm have been validated on two standard drug-disease association databases (Fdataset and Cdataset) by evaluating the AUC across the 10-fold cross validation splits. The usage of the method is also evaluated through a case study where top 5 indications are predicted for novel drugs and diseases, which then are verified with the CTD database. The results of these experiments demonstrate the practical usage and superiority of the proposed approach over the benchmark methods. Contact aanchalm@iiitd.ac. in
Substrate sensing institutes sequential and asymmetric electron transfer in the nitrogenase-like DPOR complex

Dark-operative protochlorophyllide oxidoreductase (DPOR) catalyzes the reduction of protochlorophyllide (Pchlide) to chlorophyllide (Chlide), a key penultimate step in the biosynthesis of bacteriochlorophyll. DPOR shares structural homology with nitrogenase and is made of electron donor (BchL) and electron acceptor (BchNB) component proteins. ATP driven assembly of the BchL and BchNB proteins drives electron transfer and Pchlide reduction. BchNB is composed of two subunits each of BchN and BchB arranged as an α2ß2 heterotetramer. Here, we describe extensive allosteric communication between the two identical active sites in BchNB that drives sequential and asymmetric electron transfer. Pchlide binding and electron transfer activities in one half of the BchNB tetramer allosterically regulates activities in the other half. Pchlide binding is sensed and recognized in trans by an Asp274 from the opposing half and is positioned in the active site to likely serve as the initial proton donor. An Asp274 to Ala substituted DPOR binds to two Pchlide molecules in the BchNB complex but is unable to conformationally poise one Pchlide molecule. Thus, stalling Pchlide reduction in both active sites. The [4Fe-4S] cluster of the BchNB protein is pre-reduced and donates the first electron to Pchlide, a mechanism similar to the deficit-spending model observed in nitrogenase. In half-reactive DPOR complexes, incapacitating proton donation in one half generates a stalled intermediate and Pchlide reduction in both halves is abolished. The results showcase long-range allosteric communication and sequential ET in the two symmetric halves. The findings shed light on the functional advantages imparted by the oligomeric architecture found in many electron transfer enzymes.