title: Enhanced translation of leaderless mRNAs under oxidative stress in Escherichia coli

abstract:
The bacterial response to oxidative stress requires the adaptation of the proteome to the hostile environment. It has been reported that oxidative stress induces a strong and global inhibition of both, transcription and translation. Nevertheless, whereas it is well known that transcription of a small group of genes is induced thanks to transcription factors such as OxyR and SoxR, an equivalent mechanism has not been described for translation. Here we report that whereas canonical translation that depends on Shine Dalgarno recognition is inhibited by oxidative stress in Escherichia coli, the translation of leaderless mRNA (lmRNA) is enhanced under such conditions. Both, inhibition of canonical translation and enhancement of lmRNA translation, depend on the production of (p)ppGpp. We propose that such a mechanism would allow bacteria to rapidly adapt their proteome to hostile conditions and is, perhaps, a general strategy to confront strong stressful conditions.

Significance statementThe regulation of translation (the production of proteins based on genetic information) is central for the adaptation to environmental changes. In Escherichia coli translation may begin through two alternative pathways. 1.- A canonical initiation that is well understood and is regulated mostly by changes in the accessibility of ribosomes to specific sequences and 2.- Initiation of leaderless mRNAs (lmRNAs) that lack these sequences and for which we do not understand the regulation process. Our results indicate that under oxidative stress, the production of (p)ppGpp in E. coli inhibits canonical translation and simultaneously enhances translation of lmRNAs, showing for the first time a natural condition where lmRNA translation is regulated and a role for (p)ppGpp in this process.


title: RNAP II produces capped 18S and 25S ribosomal RNAs resistant to 5-monophosphate dependent processive 5-3 exonuclease in polymerase switched Saccharomyces cerevisiae

abstract: We have previously found in the pathogenic yeast Candida albicans, 18S and 25S ribosomal RNA components, containing more than one phosphate on their 5-end, resistant to 5-monophosphate requiring 5[->]3" exonuclease. Several lines of evidence pointed to RNAP II as the enzyme producing them. We now show in Saccharomyces cerevisiae, permanently switched to RNAP II, due to deletion part of RNAP I upstream activator alone or in combination with deletion of one component of RNAP I itself, the production of such 18S and 25S rRNAs. They contain multiple phosphates at their 5-end and an anti-cap specific antibody binds to them indicating capping of these molecules. These molecules are found in RNA isolated from nuclei, therefore are unlikely to be capped in the cytoplasm. This would be unlike recapping of decapped mRNAs which occurs in the cytoplasm. Our data confirm the existence of such molecules and firmly establish RNA II playing a role in their production. The fact that we see these molecules in wild type Saccharomyces cerevisiae indicates that they are not only a result of mutations but are part of the cells physiology. This adds another way RNAP II is involved in ribosome production in addition to their role in the production of ribosome associated proteins.

category: molecular biology


title: Cryo-EM structure of MukBEF reveals DNA loop entrapment at chromosomal unloading sites

abstract:
The ring-like structural maintenance of chromosomes (SMC) complex MukBEF folds the genome of Escherichia coli and related bacteria into large loops, presumably by active DNA loop extrusion. MukBEF activity within the replication terminus macrodomain is suppressed by the sequence specific unloader MatP. Here we present the complete atomic structure of MukBEF in complex with MatP and DNA as determined by electron cryomicroscopy (cryo-EM). The complex binds two distinct DNA double helices corresponding to the arms of a plectonemic loop. MatP-bound DNA threads through the MukBEF ring, while the second DNA is clamped by the kleisin MukF, MukE and the MukB ATPase heads. Combinatorial cysteine cross-linking confirms this topology of DNA loop entrapment in vivo. Our findings illuminate how a class of near-ubiquitous DNA organizers with important roles in genome maintenance interacts with the bacterial chromosome.

HighlightsO_LIComplete atomic structures of the bacterial SMC complex MukBEF on and off DNA.
C_LIO_LIMukBEF entraps two DNA double helices when bound to the unloader MatP.
C_LIO_LIIn vivo topology of DNA loop entrapment determined by cysteine cross-linking.
C_LIO_LIArms of the DNA loop thread through separate compartments of MukBEF.
C_LI

Graphical abstract

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title: The human RBM10 gene dually encodes a repressor of ribosome biogenesis that downregulates cell proliferation

abstract: Many unannotated microproteins and alternative proteins (alt-proteins) have recently been found to be co-encoded with canonical proteins, but few of their functions are known. Motivated by the hypothesis that alt-proteins undergoing active or stress-induced synthesis could play important cellular roles, here, we developed a chemoproteomic pipeline to identify nascent alt-proteins in human cells. We identified 22 actively translated unannotated alt-proteins, one of which is upregulated after DNA damage stress. We further defined MINAS-60 (MIcroprotein that Negatively regulates ASsembly of the pre-60S ribosomal subunit), a nucleolar localized alt-protein co-encoded with human RBM10.Depletion of MINAS-60 increases the amount of the mature 60S ribosomal subunit, consequently upregulating global protein synthesis and cell proliferation by repressing late-stage pre-60S assembly and export of the 60S ribosome subunit to the cytoplasm. Together, these results implicate MINAS-60 as a repressor of ribosome biogenesis, and demonstrate that chemoproteomics can enable generation of functional hypotheses for uncharacterized alt-proteins.


title: Nascent alt-protein chemoproteomics reveals a repressor of ribosome biogenesis


title: Chloride intracellular channel 4 (CLIC4) expression is transcriptionally regulated by crosstalk of the TGF-beta, Wnt and Hedgehog signalling pathways

abstract: Chloride intracellular channel 4 (CLIC4) is a recently discovered driver of fibroblast activation in Scleroderma (SSc) and cancer-associated fibroblasts. CLIC4 expression and activity are regulated by TGF-{beta} signalling through the SMAD3 transcription factor. In view of the aberrant activation of canonical Wnt and Hedgehog (Hh) signalling in fibrosis, we investigated their role in CLIC4 upregulation. Here, we show Wnt3a/{beta}-catenin and Smoothened/GLI signalling cooperate with SMAD3 to regulate CLIC4 expression in normal dermal fibroblasts, and that inhibition of SMAD3 expression or activity abolishes Wnt and Hh-dependent CLIC4 induction. We further show that expression of the profibrotic marker -smooth muscle actin strongly correlates with CLIC4 expression in dermal fibroblasts. Our data highlight novel mechanisms that regulate CLIC4 expression that present targetable pathways to prevent fibroblast activation in SSc and other fibrotic conditions.

category: cell biology


title: Control of division and microtubule dynamics in Chlamydomonas by cyclin B/CDKB1 and the anaphase-promoting complex

abstract: In yeast and animals, cyclin B binds and activates the cyclin-dependent kinase ( CDK) CDK1 to drive entry into mitosis. We show that CYCB1, the sole cyclin B in Chlamydomonas, activates the plant-specific CDKB1 rather than the CDK1 ortholog CDKA1. Time-lapse microscopy shows that CYCB1 is synthesized before each division in the multiple fission cycle, then is rapidly degraded 3-5 minutes before division occurs. CYCB1 degradation is dependent on the anaphase-promoting complex (APC). Like CYCB1, CDKB1 is not synthesized until late G1; however, CDKB1 is not degraded with each division within the multiple fission cycle. The microtubule plus-end-binding protein EB1 labeled with mNeonGreen (EB1-NG) allowed detection of mitotic events in live cells. The earliest detectable step in mitosis, splitting of polar EB1-NG signal into two foci, likely associated with future spindle poles, was dependent on CYCB1. CYCB1-GFP localized close to these foci immediately before spindle formation. Spindle breakdown, cleavage furrow formation and accumulation of EB1 in the furrow were dependent on the APC. In interphase, rapidly growing microtubules are marked by  comets of EB1; comets are absent in the absence of APC function. Thus CYCB1/CDKB1 and the APC mitosis modulate microtubule dynamics while regulating mitotic progression.


title: Analysis of expression Quantitative Trait Loci for NLGN4X in relation to language and neurodevelopmental function: an exploratory analysis using FUSION and GTEx workflows

abstract: Language disorders in children are highly heritable, but progress in identifying genetic variants that contribute to language phenotypes has been slow. Here we applied a novel approach by identifying SNPs that are associated with gene expression in the brain, taking as our focus a gene on the X chromosome, NLGN4X, which has been postulated to play a role in neurodevelopmental disorders affecting language and communication. We found no significant associations between expression quantitative trait loci (eQTLs) and phenotypes of nonword repetition, general language ability or neurodevelopmental disorder in two samples of twin children, who had been selected for a relatively high rate of language problems. We report here our experiences with two methods, FUSION and GTEx, for eQTL analysis. It is likely that our null result represents a true negative, but for the interest of others interested in using these methods, we note specific challenges encountered in applying this approach to our data: a) complications associated with studying a gene on the X chromosome; b) lack of agreement between expression estimates from FUSION and GTEx; c) software compatibility issues with different versions of the R programming language.

category: genetics


title: Systems Genetics of Single Nucleotide Polymorphisms at the Drosophila Obp56h Locus

abstract: Variation in quantitative traits arises from naturally segregating alleles with environmentally sensitive effects, but how individual variants in single genes affect the genotype-phenotype map and molecular phenotypes is not understood. We used CRISPR/Cas9 germline gene editing to generate naturally occurring variants with different site classes and allele frequencies in the Drosophila melanogaster Obp56h gene in a common genetic background. Single base pair changes caused large allele-specific and sexually dimorphic effects on the mean and micro-environmental variance for multiple fitness-related traits and in the Obp56h co-regulated transcriptome. However, these alleles were not associated with quantitative traits in the Drosophila Genetic Reference Panel, suggesting that the small allelic effects observed in genome wide association studies may be an artifact of averaging variable context-dependent allelic effects over multiple genetic backgrounds. Thus, the traditional infinitesimal additive model does not reflect the underlying biology of quantitative traits.


title: Simultaneous Binding of the N- and C-terminal Cytoplasmic Domains of Aquaporin 4 to Calmodulin May Contribute to Vesicular Trafficking

abstract: Aquaporin 4 (AQP4) is a water transporting, transmembrane channel protein that has important regulatory roles in maintaining cellular water homeostasis. Several other AQP proteins exhibit calmodulin (CaM)-binding properties, and CaM has recently been implicated in the cell surface localization of AQP4 that occurs in response to osmotically-driven changes in cell swelling in the central nervous system. The objective of the present study was to assess the CaM-binding properties of AQP4 in detail. Inspection of AQP4 revealed two putative CaM-binding domains (CBDs) in the cytoplasmic N- and C-terminal regions, respectively. The Ca2+-dependent CaM-binding properties of synthetic and recombinant AQP4 CBD peptides were assessed using fluorescence spectroscopy, isothermal titration calorimetry, and two-dimensional 1H, 15N-HSQC NMR with 15N-labeled CaM. The N-terminal CBD peptide of AQP4 predominantly interacted with the N-lobe of CaM with a 1:1 binding ratio and a Kd of 3.4 M. CaM bound two C-terminal AQP4 peptides with interactions observed for both the C- and N-lobes of CaM (Kd1: 3.6 M, Kd2: 113.6 M, respectively). A recombinant AQP4 protein domain (rAQP4ct, containing the entire cytosolic C-terminal domain sequence) bound CaM in a 1:1 binding mode with a Kd of 6.1 M. A ternary bridging complex could be generated with the N- and C-lobes of CaM interacting simultaneously with the N- and C-terminal CBD peptides. These data suggest that this unique adapter protein binding mode of CaM and AQP4 may be an important regulatory mechanism for the vesicular trafficking of AQP4.

category: biochemistry


title: Substrate access mechanism in a novel membrane-bound phospholipase A of Pseudomonas aeruginosa concordant with specificity and regioselectivity

abstract: PlaF is a cytoplasmic membrane-bound phospholipase A1 from Pseudomonas aeruginosa that alters the membrane glycerophospholipid (GPL) composition and fosters the virulence of this human pathogen. PlaF activity is regulated by a dimer-to-monomer transition followed by tilting of the monomer in the membrane. However, how substrates reach the active site and how the characteristics of the active site tunnels determine the activity, specificity, and regioselectivity of PlaF for natural GPL substrates has remained elusive. Here, we combined unbiased and biased all-atom molecular dynamics (MD) simulations and configurational free energy computations to identify access pathways of GPL substrates to the catalytic center of PlaF. Our results map out a distinct tunnel through which substrates access the catalytic center. PlaF variants with bulky tryptophan residues in this tunnel revealed decreased catalysis rates due to tunnel blockage. The MD simulations suggest that GPLs preferably enter the active site with the sn-1 acyl chain first, which agrees with the experimentally demonstrated PLA1 activity of PlaF. We propose that the acyl chain-length specificity of PlaF is determined by the structural features of the access tunnel, which results in favorable free energy of binding of medium-chain GPLs. The suggested egress route conveys fatty acid products to the dimerization interface and, thus, contributes to understanding the product feedback regulation of PlaF by fatty acid-triggered dimerization. These findings open up opportunities for developing potential PlaF inhibitors, which may act as antibiotics against P. aeruginosa.


title: AUTS2 controls neuronal lineage choice through a novel PRC1-independent complex and BMP inhibition

abstract: Despite a prominent risk factor for Neurodevelopmental disorders (NDD), it remains unclear how Autism Susceptibility Candidate 2 (AUTS2) controls the neurodevelopmental program. Our studies investigated the role of AUTS2 in neuronal differentiation and discovered that AUTS2, together with WDR68 and SKI, forms a novel protein complex (AWS) specifically in neuronal progenitors and promotes neuronal differentiation through inhibiting BMP signaling. Genomic and biochemical analyses demonstrated that the AWS complex achieves this effect by recruiting the CUL4 E3 ubiquitin ligase complex to mediate poly-ubiquitination and subsequent proteasomal degradation of phosphorylated SMAD1/5/9. Furthermore, using primary cortical neurons, we observed aberrant BMP signaling and dysregulated expression of neuronal genes upon manipulating the AWS complex, indicating that the AWS-CUL4-BMP axis plays a role in regulating neuronal lineage specification in vivo. Thus, our findings uncover a sophisticated cellular signaling network mobilized by a prominent NDD risk factor, presenting multiple potential therapeutic targets for NDD.


title: Median based absolute quantification of proteins using Fully Unlabelled Generic Internal Standard

abstract: By reporting molar abundances of proteins, absolute quantification determines their stoichiometry in complexes, pathways or networks. Typically, absolute quantification relies either on protein-specific isotopically labelled peptide standards or on a semi-empirical calibration against the average abundance of peptides chosen from arbitrary selected proteins. In contrast, a generic protein standard FUGIS (for Fully Unlabelled Generic Internal Standard) requires no isotopic labelling, chemical synthesis or external calibration and is applicable to quantifying proteins of any organismal origin. The median intensity of peptide peaks produced by the digestion of FUGIS is used as a single point calibrant to determine the molar abundance of any co-digested protein. Powered by FUGIS, median based absolute quantification (MBAQ) outperformed other available methods of untargeted proteome-wide absolute quantification.


title: Metabolically Activated Proteostasis Regulators Protect Against Glutamate Toxicity by Activating NRF2

abstract: The extracellular accumulation of glutamate is a pathologic hallmark of numerous neurodegenerative diseases including ischemic stroke and Alzheimers disease. At high extracellular concentrations, glutamate causes neuronal damage by promoting oxidative stress which can lead to cellular death. This has led to significant interest in developing pharmacologic approaches to mitigate the oxidative toxicity caused by high levels of glutamate. Here, we show that the small molecule proteostasis regulator AA147 protects against glutamate-induced cell death in a neuronal-derived cell culture model by reducing intracellular levels of reactive oxygen species. While originally developed as an activator of the ATF6 arm of the unfolded protein response, we show AA147-dependent protection against glutamate toxicity is primarily mediated through activation of the NRF2-regulated oxidative stress response. We demonstrate that AA147 activates NRF2 through a mechanism involving metabolic activation to a reactive electrophile and covalent modification of KEAP1 - a mechanism analogous to that involved in AA147-dependent activation of ATF6. These results define the potential for AA147 to protect against glutamate induced oxidative toxicity and highlight the potential for metabolically-activated proteostasis regulators like AA147 to activate both protective ATF6 and NRF2 stress-responsive signaling pathways to mitigate oxidative damage associated with diverse neurologic diseases.


title: Tetrahymena thermophila Granule Lattice Protein 3 Improves Solubility of Sexual Stage Malaria Antigens Expressed in Escherichia coli

abstract: The requirement for low cost manufacturing makes bacterial cells a logical platform for the production of recombinant subunit vaccines for malaria. However, protein solubility has been a major stumbling block with prokaryotic expression systems. Notable examples include the transmission blocking vaccine candidates, Pfs25 and Pfs48/45, which are almost entirely insoluble when expressed as recombinant proteins in Escherichia coli. Various solubility tags have been used with limited success in improving solubility, although recent studies with granule lattice protein 1 (Grl1p) from the ciliated protozoan, Tetrahymena thermophila, have shown promise. Here, we examine a related solubility tag, granule lattice protein 3 (Grl3p) from T. thermophila, and compare it to both Grl1p and the well-studied maltose binding protein (MBP) used to improve the solubility of multiple protein targets. We find that Grl3p performs comparably to Grl1p when linked to Pfs25 but significantly improves solubility when paired with Pfs48/45.

category: bioengineering


title: GuideMaker: Software to design CRISPR-Cas guide RNA pools in non-model genomes

abstract:
BackgroundCRISPR-Cas systems have expanded the possibilities for gene editing in bacteria and eukaryotes. There are many excellent tools for designing the CRISPR-Cas guide RNAs for model organisms with standard Cas enzymes. GuideMaker is intended as a fast and easy-to-use design tool for atypical projects with 1) non-standard Cas enzymes, 2) non-model organisms, or 3) projects that need to design a panel of guide RNAs (gRNA) for genome-wide screens.

FindingsGuideMaker can rapidly design gRNAs for gene targets across the genome from a degenerate protospacer adjacent motif (PAM) and a GenBank file. The tool applies Hierarchical Navigable Small World (HNSW) graphs to speed up the comparison of guide RNAs. This allows the user to design gRNAs targeting all genes in a typical bacterial genome in about 1-2 minutes.

ConclusionsGuidemaker enables the rapid design of genome-wide gRNA for any CRISPR-Cas enzyme in non-model organisms. While GuideMaker is designed with prokaryotic genomes in mind, it can efficiently process smaller eukaryotic genomes as well. GuideMaker is available as command-line software, a stand-alone web application, and a tool in the CyCverse Discovery Environment. All versions are available under a Creative Commons CC0 1.0 Universal Public Domain Dedication.

category: bioinformatics


title: Biophysical Models of PAR Cluster Transport by Cortical Flow in C. elegans Early Embryogenesis

abstract: The clustering of membrane-bound proteins facilitates their transport by cortical actin flow in early Caenorhabditis elegans embryo cell polarity. PAR-3 clustering is critical for this process, yet the bio-physical processes that couple protein clusters to cortical flow remain unknown. We develop a discrete, stochastic agent-based model of protein clustering and test four hypothetical models for how clusters may interact with the flow. Results show that the canonical way to assess transport characteristics from single particle tracking data used thus far in this area, the Peclet number, is insufficient to distinguish these hypotheses and that all models can account for transport characteristics quantified by this measure. However, using this model, we demonstrate that these different cluster-cortex interactions may be distinguished using a different metric, namely, the scalar projection of cluster displacement on to the flow displacement vector. Our results thus provide a testable way to use existing single particle tracking data to test how endogenous protein clusters may interact with the cortical flow to localize during polarity establishment. To facilitate this investigation, we also develop both improved simulation and semi-analytic methodologies to quantify motion summary statistics (e.g., Peclet number and scalar projection) for these stochastic models as a function of biophysical parameters.

category: biophysics


title: The NUCKS1-SKP2-p21/p27 axis controls S phase entry

abstract: Efficient entry into S phase of the cell cycle is necessary for embryonic development and tissue homeostasis. However, unscheduled S phase entry triggers DNA damage and promotes oncogenesis, underlining the requirement for strict control. Here, we identify the NUCKS1-SKP2-p21/p27 axis as a checkpoint pathway for the G1/S transition. In response to mitogenic stimulation, NUCKS1, a transcription factor, is recruited to chromatin to activate expression of SKP2, the F-box component of the SCFSKP2 ubiquitin ligase, leading to degradation of p21 and p27 and promoting progression into S phase. In contrast, DNA damage induces p53-dependent transcriptional repression of NUCKS1, leading to SKP2 downregulation, p21/p27 upregulation, and cell cycle arrest. We propose that the NUCKS1-SKP2-p21/p27 axis integrates mitogenic and DNA damage signalling to control S phase entry. TCGA data reveal that this mechanism is hijacked in many cancers, potentially allowing cancer cells to sustain uncontrolled proliferation.

category: cancer biology


title: FoxA1 and FoxA2 regulate growth and cellular identity in NKX2-1-positive lung adenocarcinoma

abstract:
Changes in cellular identity (also known as histologic transformation or lineage plasticity) can drive malignant progression and resistance to therapy in multiple types of cancer, including lung adenocarcinoma (LUAD). The lineage specifying transcription factors FoxA1 and FoxA2 (FoxA1/2) regulate identity in NKX2-1/TTF1-negative LUAD. However, their role in NKX2-1-positive LUAD has not been systematically investigated. We find that Foxa1/2 knockout severely impairs tumorigenesis in KRAS-driven genetically engineered mouse models and human cell lines. Foxa1/2 deletion leads to the collapse of a dual identity state, marked by co-expression of pulmonary and gastrointestinal transcriptional programs, which has been implicated in LUAD progression. Mechanistically, loss of FoxA1/2 leads to aberrant NKX2-1 activity and genomic localization, which inhibits tumorigenesis and drives alternative cellular identity programs associated with non-proliferative states. This work demonstrates that FoxA1/2 expression is a novel lineage-specific vulnerability in NKX2-1-positive LUAD and identifies mechanisms of response and resistance to targeting FoxA1/2 in this disease.

SIGNIFICANCERecent advances in targeted protein degradation have the potential to make transcription factor inhibition a tractable therapeutic strategy in cancer. This study shows that targeting FoxA1/2 may have a major impact on NKX2-1-positive lung adenocarcinoma, including tumors driven by currently undruggable KRAS mutants.


title: The endoplasmic reticulum-resident protein TMEM-120/TMEM120A promotes fat storage in C. elegans and mammalian cells

abstract: The synthesis of triacylglycerol (TAG) is essential for the storage of excess fatty acids, which can subsequently be used for energy or cell growth. A series of enzymes act in the endoplasmic reticulum (ER) to synthesize TAG, prior to its transfer to lipid droplets (LDs), which are conserved organelles for fat storage. Here, we report that the deficiency of TMEM-120/TMEM120A, a protein with 6-transmembrane helices, retards TAG synthesis and LD expansion in C. elegans. A missense mutation near the predicted coenzyme A binding site of TMEM-120 confers strong loss of function phenotypes. GFP fusion proteins of TMEM-120, expressed at the endogenous level in live worms, were observed throughout the ER network. Using Stimulated Raman Scattering, we discovered a specific requirement of TMEM-120 in the storage of exogenous fatty acids in LDs. Knockdown of TMEM120A impedes adipogenesis of pre-adipocytes in vitro, while its over-expression is sufficient to promote LD expansion. Pharmacological studies indicate that TMEM120A most likely acts upstream of diacylglycerol O-acyltransferase 1 (DGAT1). Our results suggest that TMEM-120/TMEM120A plays a conserved role in increasing the efficiency of TAG synthesis.


title: Distinct epicardial gene regulatory programmes drive development and regeneration of the zebrafish heart

abstract: Unlike the adult mammalian heart, which has limited regenerative capacity, the zebrafish heart can fully regenerate following injury. Reactivation of cardiac developmental programmes is considered key to successfully regenerating the heart, yet the regulatory elements underlying the response triggered upon injury and during development remain elusive. Organ-wide activation of the epicardium is essential for zebrafish heart regeneration and is considered a potential regenerative source to target in the mammalian heart. Here we compared the transcriptome and epigenome of the developing and regenerating zebrafish epicardium by integrating gene expression profiles with open chromatin ATAC-seq data. By generating gene regulatory networks associated with epicardial development and regeneration, we inferred genetic programmes driving each of these processes, which were largely distinct. We identified wt1a, wt1b, and the AP-1 subunits junbb, fosab and fosb as central regulators of the developing network, whereas hif1ab, zbtb7a, tbx2b and nrf1 featured as putative central regulators of the regenerating epicardial network. By interrogating developmental gene regulatory networks that drive cell-specific transcriptional heterogeneity, we tested novel subpopulation-related epicardial enhancers in vivo. Taken together, our work revealed striking differences between the regulatory blueprint deployed during epicardial development and regeneration. These findings challenge the dogma that heart regeneration is essentially a reactivation of developmental programmes, and provide important insights into epicardial regulation that can assist in developing therapeutic approaches to enable tissue regeneration in the adult mammalian heart.

category: developmental biology


title: Lipid-mediated Association of the Slg1 Transmembrane Domains in Yeast Plasma Membranes

abstract: Clustering of transmembrane proteins underlies a multitude of fundamental biological processes at the plasma membrane (PM) such as receptor activation, lateral domain formation and mechanotransduction. The self-association of the respective transmembrane domains (TMD) has also been suggested to be responsible for the micron-scaled patterns seen for integral membrane proteins in the budding yeast plasma membrane. However, the underlying interplay between local lipid composition and TMD identity is still not mechanistically understood. In this work we combined coarse-grained molecular dynamics (MD) simulations of simplified bilayer systems with high resolution live-cell microscopy to analyze the distribution of a representative helical yeast TMD from the PM sensor Slg1 within different lipid environments. In our simulations we specifically evaluated the effects of acyl chain saturation and anionic lipids head groups on the association of two TMDs. We found that weak lipid-protein interactions significantly affect the configuration of TMD dimers and the free energy of association. Increased amounts of unsaturated phospholipids strongly reduced helix-helix interaction, while the presence of anionic phosphatidylserine (PS) hardly affected dimer formation. We could experimentally confirm this surprising lack of effect of PS using the network factor, a mesoscopic measure of PM pattern formation in yeast cells. Simulations also showed that formation of TMD dimers in turn increased the order parameter of the surrounding lipids and induced long-range perturbations in lipid organization. In summary, our results shed new light on the mechanisms for lipid-mediated dimerization of TMDs in complex lipid mixtures.


title: Task modulation of spatiotemporal dynamics in semantic brain networks: an EEG/MEG study

abstract:
How does brain activity in distributed semantic brain networks evolve over time, and how do these regions interact to retrieve the meaning of words? We compared spatiotemporal brain dynamics between visual lexical and semantic decision tasks (LD and SD), analysing whole-cortex evoked responses and spectral functional connectivity (coherence) in source-estimated electroencephalography and magnetoencephalography (EEG and MEG) recordings. Our evoked analysis revealed generally larger activation for SD compared to LD, starting in primary visual area (PVA) and angular gyrus (AG), followed by left posterior temporal cortex (PTC) and left anterior temporal lobe (ATL). The earliest activation effects in ATL were significantly left-lateralised. Our functional connectivity results showed significant connectivity between left and right ATLs and PTC and right ATL in an early time window, as well as between left ATL and IFG in a later time window. The connectivity of AG was comparatively sparse. We quantified the limited spatial resolution of our source estimates via a leakage index for careful interpretation of our results. Our findings suggest that semantic task demands modulate visual and attentional processes early-on, followed by modulation of multimodal semantic information retrieval in ATLs and then control regions (PTC and IFG) in order to extract task-relevant semantic features for response selection. Whilst our evoked analysis suggests a dominance of left ATL for semantic processing, our functional connectivity analysis also revealed significant involvement of right ATL in the more demanding semantic task. Our findings demonstrate the complementarity of evoked and functional connectivity analysis, as well as the importance of dynamic information for both types of analyses.

HighlightsO_LISemantic task demands affect activity and connectivity at different processing stages
C_LIO_LIEarliest task modulations occurred in posterior visual brain regions
C_LIO_LIATL, PTC and IFG effects reflect task-relevant retrieval of multimodal information
C_LIO_LIATL effects left-lateralised for activation but bilateral for functional connectivity
C_LIO_LIDynamic evoked and connectivity data are essential to study semantic networks
C_LI

category: neuroscience


title: NON-LINEAR SUSCEPTIBILITY TO INTERFERENCES IN DECLARATIVE MEMORY FORMATION

abstract: After encoding, memories go through a labile state followed by a stabilization process known as consolidation. Once consolidated they can enter a new labile state after the presentation of a reminder of the original memory, followed by a period of restabilization (reconsolidation). During these periods of lability the memory traces can be modified. Currently, there are studies that show a rapid stabilization after 30 min, while others show that stabilization occurs after longer periods (e.g. 6 h). Here we investigate the effect of an interference treatment on declarative memory consolidation, comparing distinct time intervals after acquisition. On day 1, participants learned a list of non-syllable pairs (List 1). Immediately after, 30 min, 3 h or 8 h later, they received an interference list (List 2) that acted as an amnesic agent. On day 2 (48 h after training) participants had to recall List 1 first, followed by List 2. We found that the List 1 memory was susceptible to interference when the List 2 was administered immediately or 3 h after learning; however, shortly after acquisition (e.g. 30 min) the List 1 memory becomes transiently protected against interference. We propose the possibility that this rapid memory protection could be induced by a fast and transient neocortical integration (where the memory is transiently protected) becoming partially independent from the hippocampus followed by a hippocampal re-engagement where the memory becomes susceptible to interferences again. Our results open a discussion about the contribution of molecular and systemic aspects to memory consolidation.


title: Heme-dependent siderophore utilization promotes iron-restricted growth of the Staphylococcus aureus hemB small colony variant

abstract:
The ability to acquire iron is essential for Staphylococcus aureus to cause infection. Respiration deficient S. aureus small colony variants (SCVs) frequently cause persistent infections, which necessitates they too acquire iron. How SCVs obtain iron remains unknown and so here we addressed this outstanding question by creating a stable hemB mutant in S. aureus USA300 strain LAC. The mutant, auxotrophic for hemin, was assessed for its ability to grow under iron- restriction and with various iron sources. The hemB SCV utilizes exogenously supplied heme but was attenuated for growth under conditions of iron starvation. RNA-seq analyses showed that both WT S. aureus and the hemB mutant sense and respond to iron starvation, however, growth assays show that the hemB mutant is defective for siderophore-mediated iron acquisition. Indeed, the hemB SCV demonstrates limited utilization of endogenous staphyloferrin B or exogenously provided staphyloferrin A, Desferal, and epinephrine, which enabled the SCV to sustain only minimal growth in iron deplete media. Direct measurement of intracellular ATP in hemB and WT S. aureus revealed that both strains can generate comparable levels of ATP during exponential growth suggesting defects in ATP production cannot account for the inability to efficiently utilize siderophores. Defective siderophore utilization by hemB bacteria was also evident in vivo. Indeed, the administration of Desferal failed to promote hemB bacterial growth in vivo, in contrast to WT, in every organ analyzed except for the murine kidney where growth was enhanced. In support of the hypothesis that S. aureus accesses heme in kidney abscesses, in vitro analyses revealed that increased heme availability enables hemB bacteria to utilize siderophores for growth when iron availability is restricted. Taken together, our data support the conclusion that heme is not only used as an iron source itself, but as a nutrient that promotes utilization of siderophore-iron complexes.

Author summaryS. aureus small colony variants (SCVs) represent a difficult to treat subpopulation of bacteria that are associated with chronic recurrent infection and worsened clinical outcome. Indeed, SCVs persist within the host despite appropriate administration of antibiotics. This study yields insight into the mechanisms by which S. aureus SCVs acquire iron which, during infection of a host, is a difficult-to-acquire metal nutrient. Under heme limited conditions, hemB S. aureus is severely impaired for siderophore-dependent growth and, in agreement, murine infection indicates that hemin-deficient SCVs meet their nutritional requirement for iron through utilization of heme in vivo. Importantly, we demonstrate that hemB SCVs rely upon heme as a nutrient to promote siderophore utilization. Therefore, perturbation of heme biosynthesis and/or utilization represents a viable to strategy to mitigate the ability of SCV bacteria to acquire siderophore- bound iron during infection.

category: microbiology


title: GLI transcriptional repression is inert prior to Hedgehog pathway activation

abstract: In the absence of Hedgehog (HH) signaling, GLI proteins are post-translationally modified within cilia into transcriptional repressors that subsequently prevent sub-threshold activation of HH target genes. GLI repression is presumably important for preventing precocious expression of target genes before the onset of HH pathway activation, a presumption that underlies the pre-patterning model of anterior-posterior limb polarity. Here, we report that GLI3 repressor is abundant and binds to target genes in early limb development. However, contrary to expectations, GLI3 repression neither regulates the activity of GLI enhancers nor expression of HH target genes as it does after HH signaling has been established. Within the cilia, the transition to active GLI repression is accompanied by increases in axonemal GLI3 localization, possibly signifying altered GLI3 processing. Together, our results demonstrate that GLI3 repression does not prevent precocious activation of HH target genes, or have a pre-patterning role in regulating anterior-posterior limb polarity.


title: HPLC Method to Resolve, Identify and Quantify Guanine Nucleotides Bound to the GTPase Ras

abstract: The Ras superfamily of small G proteins play central roles in diverse signaling pathways. Superfamily members act as molecular on-off switches defined by their occupancy with GTP or GDP, respectively. In vitro functional studies require loading with a hydrolysis-resistant GTP analogue to increase the on-state lifetime, as well as knowledge of fractional loading with activating and inactivating nucleotides. The present study describes a method combining elements of previous approaches with new, optimized features to analyze the bound nucleotide composition of a G protein loaded with activating (GMPPNP) or inactivating (GDP) nucleotide. After nucleotide loading, the complex is washed to remove unbound nucleotides then bound nucleotides are heat-extracted and subjected to ion-paired, reverse-phase HPLC-UV to resolve, identify and quantify the individual nucleotide components. These data enable back-calculation to the nucleotide composition and fractional activation of the original, washed G protein population prior to heat extraction. The method is highly reproducible. Application to multiple HRas preparations and mutants confirms its ability to fully extract and analyze bound nucleotides, and to resolve the fractional on- and off-state populations. Furthermore, the findings yield a novel hypothesis for the molecular disease mechanism of Ras mutations at the E63 and Y64 positions.


title: Early lock-in of structured and specialised information flows during neural development

abstract:
The brains of many organisms are capable of complicated distributed computation underpinned by a highly advanced information processing capacity. Although substantial progress has been made towards characterising the information flow component of this capacity in mature brains, there is a distinct lack of work characterising its emergence during neural development. This lack of progress has been largely driven by the lack of effective estimators of information processing operations for the spiking data available for developing neural networks. Here, we leverage recent advances in this estimation task in order to quantify the changes in information flow during development. We do so by studying the changes in the intrinsic dynamics of the spontaneous activity of developing dissociated neural cell cultures. We find that the quantity of information flowing across these networks undergoes a dramatic increase across development. Moreover, the spatial structure of these flows is locked-in during early development, after which there is a substantial temporal correlation in the information flows across recording days. We analyse the flow of information during the crucial periods of population bursts. We find that, during these bursts, nodes undertake specialised computational roles as either transmitters, mediators or receivers of information, with these roles tending to align with their spike ordering -- either early, mid or late in the bursts. Further, we find that the specialised computational roles occupied by nodes during bursts tend to be locked-in early. Finally, we briefly compare these results to information flows in a model network developing according to an STDP learning rule from a state of independent firing to synchronous bursting. The phenomena of large increases in information flow, early lock-in of information flow spatial structure and computational roles based on burst position were also observed in this model, hinting at the broader generality of these phenomena.

AUTHOR SUMMARYThis paper studies the development of computation in biological systems by analysing changes in the flow of information in developing neural cell cultures. Although there have been a number of previous studies of information flows in neural cell cultures, this work represents the first study which compares information flows in the intrinsic dynamics across development time. Moreover, we make use of a recently proposed continuous-time transfer entropy estimator for spike trains, which, in comparison to the discrete-time estimator used previously, is able to capture important effects occurring on both small and large timescales simultaneously. We find that information flows begin to emerge after 5-10 days of activity, and crucially, the spatial structure of information flows remains significantly temporally correlated over the first month of recording. Furthermore, the magnitude of information flows across the culture are strongly related to burst position, and the roles of regions as information flow sources, sinks and mediators are found to remain consistent across development. Finally, we confirm that these early lock-ins also occur in a simple model network developing under an STDP update rule, suggesting a plausible mechanism undergirding this phenomenon.


title: Persistence of Hippocampal and Striatal Multivoxel Patterns during Awake Rest after Motor Sequence Learning

abstract: Memory consolidation, the process by which newly encoded and fragile memories become more robust, is thought to be supported by the reactivation of brain regions - including the hippocampus - during post-learning rest. While hippocampal reactivations have been demonstrated in humans in the declarative memory domain, it remains unknown whether such a process takes place after motor learning. Using multivariate analyses of task-related and resting state fMRI data, here we show that patterns of brain activity within both the hippocampus and striatum elicited during motor learning persist into post-learning rest, indicative of reactivation of learning-related neural activity patterns. Moreover, results indicate that hippocampal reactivation reflects the spatial representation of the learned motor sequence. These results thus provide insights into the functional significance of neural reactivation after motor sequence learning.


title: A centronuclear myopathy-causing mutation in dynamin-2 perturbs the actin-dependent structure of dendritic spines leading to excitatory synaptic defects in a murine model of the disease

abstract: Dynamin-2 is a large GTP-ase, member of the dynamin superfamily, that regulates membrane remodeling and cytoskeleton dynamics. In the mammalian nervous system dynamin-2 modulates synaptic vesicle (SV)-recycling at the nerve terminals and receptor-trafficking to and from postsynaptic densities (PSDs). Mutations in dynamin-2 cause autosomal dominant centronuclear myopathy (CNM), a congenital neuromuscular disorder characterized by progressive weakness and atrophy of distal skeletal muscles. Cognitive defects have also been reported in dynamin-2-linked CNM patients suggesting a concomitant impairment of the central nervous system. Here we addressed the mechanisms that lead to cognitive defects in dynamin-2-linked CNM using a knock-in mouse model that harbors the p.R465W mutation in dynamin-2, the most common causing CNM. Our results show that these mice exhibit reduced capability to learn and acquire spatial and recognition memory, impaired long-term potentiation of the excitatory synaptic strength and perturbed dendritic spine morphology, which seem to be associated with actin defects. Together, these data reveal for the first time that structural and functional synaptic defects underlie cognitive defects in the CNM context. In addition our results contribute to the still scarce knowledge about the importance of dynamin-2 at central synapses.


title: A gradient of force in the endocytic coat is revealed by new coiled-coil force sensors

abstract:
Forces are central to countless cellular processes, yet in vivo force measurement at the molecular scale remains difficult if not impossible. During clathrin-mediated endocytosis, forces produced by the actin cytoskeleton are transmitted to the plasma membrane by a multi-protein coat for membrane deformation. However, the magnitudes of these forces remain unknown. Here, we present new in vivo force sensors that phase separate under force. We measured the forces on the fission yeast HIP1R homologue End4p, a protein that links the membrane to the actin cytoskeleton. End4p is under [~]15 pN force near the actin cytoskeleton, [~] 11 pN near the clathrin lattice, and [~]9 pN near the plasma membrane. Our results demonstrate that forces are collected and redistributed across the endocytic machinery.

One-Sentence SummaryPhase-separating coiled-coil force sensors reveal an unexpected mode of force transduction during endocytosis in vivo.


title: Force redistribution during clathrin-mediated endocytosis revealed by new phase-separating force sensors


title: Force redistribution in clathrin-mediated endocytosis revealed by phase-separating force sensors


title: An RNAi screen for genes that affect nuclear morphology in Caenorhabditis elegans reveals the involvement of unexpected processes

abstract: Aberration in nuclear morphology is one of the hallmarks of cellular transformation. However, the processes that, when mis-regulated, result aberrant nuclear morphology are poorly understood. In this study we carried out a systematic, high-throughput RNAi screen for genes that affect nuclear morphology in Caenorhabditis elegans embryos. The screen employed over 1700 RNAi constructs against genes required for embryonic viability. Nuclei of early embryos are typically spherical and their NPCs are evenly distributed. The screen was performed on early embryos expressing a fluorescently tagged component of the nuclear pore complex (NPC), allowing visualization of nuclear shape as well as the distribution of NPCs around the nuclear envelope. Our screen uncovered 182 genes whose down-regulation resulted in one or more abnormal nuclear phenotypes, including multiple nuclei, micronuclei, abnormal nuclear shape, anaphase bridges and abnormal NPC distribution. Many of these genes fall into common functional groups, including some that were not previously known to affect nuclear morphology, such as genes involved in mitochondrial function, the vacuolar ATPase and the CCT chaperonin complex. The results of this screen add to our growing knowledge of processes that affect nuclear morphology and that may be altered in cancer cells that exhibit abnormal nuclear shape.


title: Oncofetal protein CRIPTO regulates wound healing and fibrogenesis in regenerating liver and is associated with the initial stages of cardiac fibrosis

abstract:
BackgroundOncofetal protein, Cripto, is silenced during postnatal life and often re-expressed in different neoplastic processes. In the present study we investigated the potential role of Cripto in hepatic and cardiac fibrosis. In this study, the aim was to explore whether Cripto is expressed during liver fibrogenesis and whether this is related to the disease severity and pathogenesis of fibrogenesis. Furthermore, we aimed to identify the impact of Cripto expression on fibrogenesis in organs with high versus low regenerative capacity, represented by murine liver fibrogenesis and adult murine heart fibrogenesis

MethodsCirculating CRIPTO levels were measured in plasma samples of patients with cirrhosis registered at the waitlist for liver transplantation (LT) and one year after LT. The expression of Cripto and fibrotic markers (aSMA, collagen I) were determined in human liver tissues of patients with cirrhosis (on a basis of viral hepatitis or alcoholic disease), in cardiac tissue samples of patients with end-stage heart failure and of mice with experimental liver and heart fibrosis using immuno-histochemical stainings and qPCR. Mouse models with experimental chronic liver fibrosis, induced with multiple shots of carbon tetrachloride (CCl4) and acute liver fibrosis (one shot of CCl4) were evaluated for Cripto expression and fibrotic markers. Cripto was overexpressed in vivo (Adenoviral delivery) or functionally sequestered by ALK4Fc ligand trap in the acute liver fibrosis mouse model. Murine heart tissues were evaluated for Cripto and fibrotic markers, in three models of heart injury; following myocardial infarction, pressure overload and ex vivo induced fibrosis.

ResultsPatients with end-stage liver cirrhosis showed elevated Cripto levels in plasma, which had decreased one year after LT. Cripto expression was observed in fibrotic tissues of patients with end-stage liver cirrhosis and in patients with heart failure. The expression of Cripto in the liver was found specifically in the hepatocytes and was positively correlated with the Model for End-stage Liver Disease (MELD) score for end-stage liver disease. Cripto expression in the samples of cardiac fibrosis was limited and mostly observed in the interstitial cells. In the chronic and acute mouse models of liver fibrosis, Cripto-positve cells were observed in damaged liver areas around the central vein, which preceded the expression of aSMA-positive stellate cells, i.e. mediators of fibrosis. Whereas in the chronic mouse models the fibrosis and Cripto expression was still present after 11 weeks, in the acute model the liver regenerated and the fibrosis and Cripto expression resolved. In vivo overexpression of Cripto in this model, led to an increase in fibrotic markers while blockage of Cripto secreted function inhibited the extend of fibrotic areas and marker expression (SMA, Collagen type I and III) and induced higher proliferation of residual healthy hepatocytes. Cripto expression was also upregulated in several mouse models of cardiac fibrosis. During myocardial infarction Cripto is upregulated initially in cardiac interstitial cells, followed by expression in SMA-positive myofibroblasts throughout the infarct area. After the scar formation, Cripto expression decreased concomitantly with the aSMA expression. Temporal expression of Cripto in SMA-positive myofibroblasts was also observed surrounding the coronary arteries in the pressure overload model of cardiac fibrosis. Furthermore, Cripto expression was upregulated in interstitial myofibroblasts in hearts cultured in an ex vivo model for cardiac fibrosis.

ConclusionOur results are indicative for a functional role of Cripto in induction of fibrogenesis and potential applications in antifibrotic treatments and stimulation of tissue regeneration.


title: Actin force generation in vesicle formation: mechanistic insights from cryo-electron tomography

abstract:
Actin assembly provides force for a multitude of cellular processes. Compared to actin assembly- based force production during cell migration, relatively little is understood about how actin assembly generates pulling forces for vesicle formation. Here, cryo-electron tomography revealed actin filament number, organization, and orientation during clathrin-mediated endocytosis in human cells, showing that force generation is robust despite variance in network organization. Actin dynamics simulations incorporating a measured branch angle indicate that sufficient force to drive membrane internalization is generated through polymerization, and that assembly is triggered from [~]4 founding "mother" filaments, consistent with tomography data. Hip1R actin filament anchoring points are present along the entire endocytic invagination, where simulations show that it is key to pulling force generation, and along the neck, where it targets filament growth and makes internalization more robust. Actin cytoskeleton organization described here allowed direct translation of structure to mechanism with broad implications for other actin-driven processes.

Highlights- Filament anchorage points are key to pulling force generation and efficiency.
- Native state description of CME-associated actin force-producing networks.
- Branched actin filament assembly is triggered from multiple mother filaments.
- Actin force production is robust despite considerable network variability.


title: Conserved Transcription Factors Control Chromatin Accessibility and Gene Expression to Maintain Cell Fate Stability and Restrict Reprogramming of Differentiated Cells

abstract:
The comprehensive characterization of mechanisms safeguarding cell fate identity in differentiated cells is crucial for 1) our understanding of how differentiation is maintained in healthy tissues or misregulated in disease states and 2) to improve our ability to use direct reprogramming for regenerative purposes. To uncover novel fate-stabilizing regulators, we employed a genome-wide TF siRNA screen followed by a high-complexity combinatorial evaluation of top performing hits, in a cardiac reprogramming assay in mouse embryonic fibroblasts, and subsequently validated our findings in cardiac, neuronal and iPSCs reprogramming assays in primary human fibroblasts and adult endothelial cells. This approach identified a conserved set of 4 TFs (ATF7IP, JUNB, SP7, and ZNF207 [AJSZ]) that robustly opposes cell fate reprogramming, as demonstrated by up to 6-fold increases in efficiency upon AJSZ knockdown in both lineage- and cell type-independent manners. Mechanistically, ChIP-seq and single-cell ATAC-seq analyses, revealed that AJSZ bind to both open and closed chromatin in a genome-wide and regionalized fashion, thereby limiting reprogramming TFs access to target DNA and ability to remodel the chromatin. In parallel, integration of ChIP-seq and RNA-seq data followed by systematic functional gene testing, identified that AJSZ also promote cell fate stability by proximally down-regulating a conserved set of genes involved in the regulation of cell fate specification (MEF2C), proteome remodeling (TPP1, PPIC), ATP homeostasis (EFHD1), and inflammation signaling (IL7R), thereby limiting cells ability to undergo large-scale phenotypic changes. Finally, simultaneous knock-down of AJSZ in combination with cardiac reprogramming TFs overexpression improved heart function by 250% as compared to no treatment and 50% as compared to MGT, 1 month after myocardial infarction. In sum, this study uncovers a novel evolutionarily conserved mechanism mediating cell fate stability in differentiated cells and also identifies AJSZ as promising therapeutic targets for regenerative purposes in adult organs.

Significance StatementDifferentiated cells can be converted from one cell type into another by overexpressing lineage-determining transcription factors. Direct lineage reprogramming represents a promising strategy for regenerative medicine, but current clinical applications remain limited by the low yield of the reprogramming process. Here, we present the identification and detailed mechanistic study of a novel mechanisms opposing reprogramming process and promoting cell fate stability. Using a highthroughput screening technique, we identified four transcription factors that act as blockades to cell type change. By tracking chromatin and gene expression changes, we reconstructed a conserved pathway mediating cell fate stability in differentiated cells.


title: Unbiased in vivo exploration of nuclear bodies-enhanced sumoylation reveals that PML orchestrates embryonic stem cell fate

abstract: Membrane-less organelles are condensates formed by phase separation whose functions often remain enigmatic. Upon oxidative stress, PML scaffolds Nuclear Bodies (NBs) to regulate senescence or metabolic adaptation, but their role in pluripotency remains elusive. Here we establish that PML is required for basal SUMO2/3 conjugation in mESCs and oxidative stress-driven sumoylation in mESCs or in vivo. PML NBs create an oxidation-protective environment for UBC9-driven SUMO2/3 conjugation of PML partners, often followed by their poly-ubiquitination and degradation. Differential in vivo proteomics identified several members of the KAP1 complex as PML NB-dependent SUMO2-targets. The latter drives functional activation of this key epigenetic repressor. Accordingly, Pml-/- mESCs re-express transposable elements and display features of totipotent-like cells, a process further enforced by PML-controlled SUMO2-conjugation of DPPA2. Finally, PML is required for adaptive stress responses in mESCs. Collectively, PML orchestrates mESC fate through SUMO2-conjugation of key transcriptional or epigenetic regulators, raising new mechanistic hypotheses about PML roles in normal or cancer stem cells.


title: Laminin-binding Integrins Regulate Angiogenesis by Distinct and Overlapping Mechanisms in Organotypic Cell Culture Models

abstract:
Endothelial cells engage extracellular matrix and basement membrane components through integrin-mediated adhesion to promote angiogenesis. Our previous studies demonstrated that endothelial expression of laminin-411 and laminin-511 as well as 6 integrins is required for endothelial sprouting and tube formation in organotypic angiogenesis assays. These studies demonstrated that 6 integrins promote migration and regulate the expression of ANGPT2 and CXCR4 and that 6-dependent regulation of CXCR4 contributes to endothelial morphogenesis in our assays. However, these studies did not identify specific roles for the 6{beta}1, 6{beta}4, or 3{beta}1 laminin-binding integrins. Here, we employ RNAi technology to parse the contributions of these integrins. We demonstrate that 6{beta}4 promotes migration, sprouting, and tube formation, and also positively regulates the expression of ANGPT2, but does not promote CXCR4 expression, suggesting that 6{beta}1 functions in this regulation. Additionally, we show that 3{beta}1 regulates endothelial sprouting and tube formation, but is not required for migration in our assays or for the expression of ANGPT2 or CXCR4. Integrin 3{beta}1 promotes the expression of NRP1 and ID1 RNAs, both of which are known to promote angiogenesis. Taken together, our results indicate that laminin-binding integrins play distinct roles during endothelial morphogenesis and do not compensate for one another in organotypic culture.

Summary StatementThe laminin-binding integrins 3{beta}1, 6{beta}1, and 6{beta}4 contribute to endothelial sprouting and tube formation in organotypic angiogenesis assays.


title: Insulin-dependent and -independent dynamics of insulin receptor trafficking in muscle cells

abstract: Insulin resistance contributes to type 2 diabetes and can be driven by hyperinsulinemia. Insulin receptor (INSR) internalization and cell-surface dynamics at rest and during insulin exposure are incompletely understood in muscle cells. Using surfacing labeling and live-cell imaging, we observed robust basal internalization of INSR in C2C12 myoblasts, without a robust effect of added insulin. Mass-spectrometry analysis of INSR-binding proteins identified potential molecular mechanisms associated with internalization. We confirmed known interactors, including IGF1R, but also identified underappreciated INSR-binding factors such as ANXA2. Protein-protein interaction network mapping suggested links between INSR and caveolin-mediated endocytosis. INSR interacted with both caveolin and clathrin heavy chain (CLTC) in mouse skeletal muscle and C2C12 myoblasts. Whole cell 2D super-resolution imaging revealed that high levels of insulin (20 nM) increased INSR colocalization with CAV1 but decreased its colocalization with CLTC. Single particle tracking confirmed the colocalization of cell-surface INSR with both over-expressed CAV1-mRFP and CLTC-mRFP. INSR tracks that colocalized with CAV1 exhibited longer radii and lifetimes, regardless of insulin exposure, compared to non-colocalized tracks, whereas insulin further increased the lifetime of INSR/CLTC colocalized tracks. Overall, these data suggest that muscle cells utilize both CAV1 and CLTC-dependent pathways for INSR dynamics and internalization.


title: Mechanical Stimulation via Muscle Activity is Necessary for the Maturation of Tendon Multiscale Mechanics during Embryonic Development

abstract: During embryonic development, tendons transform into a hypocellular tissue with robust tensile load-bearing capabilities. Previous work suggests that this mechanical transformation is due to increases in collagen fibril length and is dependent on mechanical stimulation via muscle activity. However, the relationship between changes in the microscale tissue structure and changes in macroscale tendon mechanics is still unclear. Additionally, the specific effect of mechanical stimulation on the multiscale structure-function relationships of developing tendons is also unknown. Therefore, the objective of this study was to measure the changes in tendon mechanics and structure at multiple length scales during embryonic development with and without skeletal muscle paralysis. Tensile testing of tendons from chicken embryos was performed to determine the macroscale tensile modulus as well as the magnitude of the fibril strains and interfibrillar sliding with applied tissue strain. Embryos were also treated with either decamethonium bromide or pancuronium bromide to produce rigid or flaccid paralysis. Histology was performed to assess changes in tendon size, spacing between tendon subunits, and collagen fiber diameter. We found that the increase in the macroscale modulus observed with development is accompanied by an increase in the fibril:tissue strain ratio, which is consistent with an increase in collagen fibril length. Additionally, we found that flaccid paralysis reduced the macroscale tendon modulus and the fibril:tissue strain ratio, whereas less pronounced effects that were not statistically significant were observed with rigid paralysis. Finally, skeletal paralysis also reduced the size of collagen fibril bundles (i.e., fibers). Together, these data suggest that more of the applied tissue strain is transmitted to the collagen fibrils at later embryonic ages, which leads in an increase the tendon macroscale tensile mechanics. Furthermore, our data suggest that mechanical stimulation during development is necessary to induce structural and mechanical changes at multiple physical length scales. This information provides valuable insight into the multiscale structure-function relationships of developing tendons and the importance of mechanical stimulation in producing a robust tensile load-bearing soft tissue.


title: Ketamine decreases HPA axis reactivity to a novel stressor in male but not female mice

abstract: Ketamine is an antidepressant drug that interacts with the hypothalamic-pituitary-adrenal (HPA) axis, but whether this interaction is important for its behavioral effect is unknown. The goal of this experiment was to determine whether the behavioral response to ketamine depends on intact HPA axis function. Male and female C57BL/6J mice underwent chronic unpredictable stress prior to ketamine (30 mg/kg, i.p.) or vehicle treatment, with or without the glucocorticoid synthesis inhibitor metyrapone (20 mg/kg, i.p.) to block adrenal corticosterone production. Mice were tested in the forced swim test (FST) and open field test one and two days after injection, respectively. Fecal corticosterone was measured at select time points. No significant drug effects on behavior were observed. Males consistently had higher fecal corticosterone levels and stress-induced increases than females. Ketamine lowered the fecal corticosterone response to the FST only in males. These data show that ketamine after chronic stress decreases the corticosterone response to a novel stressor (the FST) in males, but not females. Corticosterone levels in all mice correlated with immobility in the FST, suggesting that shared neural circuitry could mediate both endocrine and behavioral responses. This circuitry may be ketamine-responsive only in males.

category: animal behavior and cognition


title: Prefrontal cortical connectivity mediates locus coeruleus noradrenergic regulation of inhibitory control in older adults

abstract: Response inhibition is a core executive function enabling adaptive behaviour in dynamic environments. Human and animal models indicate that inhibitory control and control networks are modulated by noradrenaline, arising from the locus coeruleus. The integrity (i.e., cellular density) of the locus coeruleus noradrenergic system can be estimated from magnetization transfer sensitive magnetic resonance imaging, in view of neuromelanin present in noradrenergic neurons of older adults. Noradrenergic psychopharmacological studies indicate noradrenergic modulation of prefrontal and frontostriatal stopping-circuits in association with behavioural change. Here we test the noradrenergic hypothesis of inhibitory control, in healthy adults. We predicted that locus coeruleus integrity is associated with age-adjusted variance in response inhibition, mediated by changes in connectivity between frontal inhibitory control regions. In a preregistered analysis, we used magnetization transfer MRI images from N=63 healthy adults aged above 50 years who performed a stop-signal task, with atlas-based measurement of locus coeruleus contrast. We confirm that better response inhibition is correlated with locus coeruleus integrity and stronger connectivity between pre-supplementary motor area and right inferior frontal gyrus, but not volumes of the cortical regions. We confirmed a significant role of prefrontal connectivity in mediating the effect of individual differences in the locus coeruleus on behaviour, whereby this effect was moderated by age, over and above adjustment for the mean effects of age. Our results support the hypothesis that in normal populations, as in clinical settings, the locus coeruleus noradrenergic system regulates inhibitory control.


title: Generation of liver organoids from human induced pluripotent stem cells as liver fibrosis and steatosis models

abstract:
Background & AimsLiver cirrhosis is a major cause of death worldwide, and its prevalence is growing rapidly due to the growth of obesity and diabetes population with non-alcoholic fatty liver disease (NAFLD). Yet, no effective therapeutics have been developed to treat NAFLD or its more advanced stage, non-alcoholic steatohepatitis (NASH). This has raised great concern for a representative liver model to be developed so that novel drugs could be screened, identified and developed. Presently, we aim to develop a liver organoid entirely from human induced pluripotent stem cells (hiPSC) to model liver fibrogenesis and NAFLD.

MethodsHepatoblasts (HBs), mesenchymal stem cells (MSCs), hepatic stellate cell (HSCs) and endothelial cells (ECs) were derived from hiPSCs, allowed to self-organized and differentiated into liver organoids. Liver functions, transcriptomic and protein expression of liver organoids were characterized and validated. Liver organoids were exposed to thioacetamide (TAA) and free fatty acids (FFA) to be induced into liver disease model.

ResultsThe liver organoids we fabricated were highly vascularized, exhibited liver-specific functions and hepatic cellular spatial organization. The presence of liver specific ECs, macrophages and cholangiocytes were found within our organoids. TAA induced fibrosis in our liver organoids that exhibited diminished liver functions, elevated pro-inflammatory cytokines and fibrosis-related gene expression, as well as extensive collagen deposit. Organoids treated with FFA developed steatosis, inflammation and fibrosis.

ConclusionsWe generated a novel method, that is Matrigel-independent and size-controllable, for making human liver organoids. These organoids can potentially be utilized as tissue-mimetic in vitro model for high throughput screening to identify drugs that can be used to treat liver fibrosis and NAFLD.


title: Heat stress reveals the existence of a specialized variant of the pachytene checkpoint in meiosis of Arabidopsis thaliana

abstract: Plant growth and fertility strongly depend on environmental conditions such as temperature. Remarkably, temperature also influences meiotic recombination and thus, the current climate change will affect the genetic make-up of plants. To further understand temperature effects on meiosis, we have followed male meiocytes of Arabidopsis thaliana by live cell imaging under three different temperature regimes, at 21{degrees}C and at heat shock conditions of 30{degrees}C and 34{degrees}C as well as after an acclimatization phase of one week at 30{degrees}C. This work led to a cytological framework of meiotic progression at elevated temperature. We found that an increase to 30{degrees}C, sped up meiotic progression with specific phases being more amenable to heat than others. An acclimatization phase often moderated this effect. A sudden increase to 34{degrees}C promoted a faster progression of meiosis in early prophase compared to 21{degrees}C. However, the phase in which cross-overs maturate was found to be prolonged at 34{degrees}C. Interestingly, mutants involved in the recombination pathway did not show the extension of this phase at 34{degrees}C demonstrating that the delay is recombination dependent. Further analysis revealed the involvement of the ATM kinase in this prolongation indicating the existence of a specialized variant of the pachytene checkpoint in plants.


title: Age-related declines in neural distinctiveness correlate across brain areas and result from both decreased reliability and increased confusability

abstract: According to the neural dedifferentiation hypothesis, age-related reductions in the distinctiveness of neural representations contribute to sensory, cognitive, and motor declines associated with aging: neural activity associated with different stimulus categories becomes more confusable with age and behavioural performance suffers as a result. Initial studies investigated age-related dedifferentiation in the visual cortex, but subsequent research has revealed declines in other brain regions, suggesting that dedifferentiation may be a general feature of the aging brain. In the present study, we used functional magnetic resonance imaging to investigate age-related dedifferentiation in the visual, auditory, and motor cortices. Participants were 58 young adults and 79 older adults. The similarity of activation patterns across different blocks of the same condition was calculated (within-condition correlation, a measure of reliability) as was the similarity of activation patterns elicited by different conditions (between-category correlations, a measure of confusability). Neural distinctiveness was defined as the difference between the mean within- and between-condition similarity. We found age-related reductions in neural distinctiveness in the visual, auditory, and motor cortices, which were driven by both decreases in within-category similarity and increases in between-category similarity. There were significant positive cross-region correlations between neural distinctiveness in different regions. These correlations were driven by within-category similarities, a finding that indicates that declines in the reliability of neural activity appear to occur in tandem across the brain. These findings suggest that the changes in neural distinctiveness that occur in healthy aging result from changes in both the reliability and confusability of patterns of neural activity


title: Information redundancy across spatial scales modulates early visual cortical processing

abstract: Visual images contain redundant information across spatial scales where low spatial frequency contrast is informative towards the location and likely content of high spatial frequency detail. Previous research suggests that the visual system makes use of those redundancies to facilitate efficient processing. In this framework, a fast, initial analysis of low-spatial frequency (LSF) information guides the slower and later processing of high spatial frequency (HSF) detail. Here, we used multivariate classification as well as time-frequency analysis of MEG responses to the viewing of intact and phase scrambled images of human faces to demonstrate that the availability of redundant LSF information, as found in broadband intact images, correlates with a reduction in HSF representational dominance in both early and higher-level visual areas as well as a reduction of gamma-band power in early visual cortex. Our results indicate that the cross spatial frequency information redundancy that can be found in all natural images might be a driving factor in the efficient integration of fine image details.


title: Diverse soil RNA viral communities have the potential to influence grassland ecosystems across multiple trophic levels

abstract: Grassland ecosystems form 30-40%1 of total land cover and provide essential ecosystem services, including food production, flood mitigation and carbon storage2. Their productivity is closely related to soil microbial communities3, yet the role of viruses within these critical ecosystems is currently undercharacterised4 and in particular, our knowledge of soil RNA viruses is significantly limited5. Here, we applied viromics6 to characterise soil RNA viral communities along an altitudinal productivity gradient of peat, managed grassland and coastal soils. We identified 3,462 viral operational taxonomic units (vOTUs) and assessed their spatial distribution, phylogenetic diversity and potential host ranges. Soil types exhibited showed minimal similarity in viral community composition, but with >10-fold more vOTUs shared between managed grassland soils when compared with peat or coastal soils. Phylogenetic analyses of viral sequences predicted broad host ranges including bacteria, plants, fungi, vertebrates and invertebrates, contrasting with soil DNA viromes which are typically dominated by bacteriophages7. RNA viral communities therefore likely have the ability to influence soil ecosystems across multiple trophic levels. Our study represents an important step towards the characterisation of terrestrial RNA viral communities and the intricate interactions with their hosts, which will provide a more holistic view of the biology of economically and ecologically important terrestrial ecosystems.

category: ecology


title: High-throughput screening of aqueous two-phase systems for polyphenol extraction from A. nodosum: a green chemistry approach

abstract:
Brown macroalgae are an attractive third-generation feedstock of natural products, in order to design green chemistry-compliant processes and reduce the use of organic solvents in bioactive product extraction, aqueous two-phase systems (ATPS) was applied. This research aimed to develop a high-throughput screening (HTS) to recover polyphenols from Ascophyllum nodosum using ATPS. In total, 384 different 2-phase systems were assessed using an automated liquid-handling system to evaluate polyphenol recovery using a model system of phloroglucinol to establish an optimal 2-phase system for polyphenol partitioning. Various ratios of PEG:potassium phosphate solutions were explored to evaluate partitioning of polyphenols via a scale-down approach. Scale-down selected system showed a recovery of phloroglucinol of 62.9{+/-}12.0%, this system was used for scale-up trials. Scale-up studies confirmed that the HTS method was able to recover polyphenols with a 54.8{+/-}14.2% in the phloroglucinol model system. When the optimised ATPS system was tested with a polyphenol extract, 93.62{+/-}8.24% recovery was observed. When ATPS was applied to a fucoidan and alginate biorefinery residue, 88.40{+/-}4.59% polyphenol was recovered. These findings confirm that ATPS is a valuable addition to the bioprocess toolkit for sustainable extraction of natural products from macroalgae in a multiproduct biorefinery approach.

Practical applicationSelection of the best concentrations of phase-forming components and recovery conditions for the application of aqueous two-phase systems in an industrial setup has been proved to be laborious and cumbersome. This paper presents an automated platform to rapidly assess several ATPS to recover polyphenols from brown macroalgae and a subsequent confirmation with the scale-up of the potential candidates and contrasted with two case studies. This methodology allows a quick screening for the best aqueous two-phase system and can be expanded to recover high-value products from other types of macroalgae or microalgae.


title: Voxelated Bioprinting of Mechanically Robust Multiscale Porous Scaffolds for Pancreatic Islets

abstract:
Three-dimensional (3D) bioprinting additively assembles bio-inks to manufacture tissue-mimicking biological constructs, but with the typical building blocks limited to one-dimensional filaments. Here, we develop a technique for the digital assembly of spherical particles (DASP), which are effectively zero-dimensional voxels - the basic unit of 3D structures. We show that DASP enables on-demand generation, deposition, and assembly of viscoelastic bio-ink droplets. We establish a phase diagram that outlines the viscoelasticity of bio-inks required for printing spherical particles of good fidelity. Moreover, we develop a strategy for engineering bio-inks with independently controllable viscoelasticity and mesh size. Using DASP, we create mechanically robust, multiscale porous scaffolds composed of interconnected yet distinguishable hydrogel particles. Finally, we demonstrate the application of the scaffolds in encapsulating human pancreatic islets for responsive insulin release. Together with the knowledge of bio-ink design, DASP might be used to engineer highly heterogeneous yet tightly organized tissue constructs for therapeutic applications.

Table of ContentsA three-dimensional bioprinting technology is developed to enable on-demand generation, deposition, and assembly of viscoelastic bio-ink droplets in a biofriendly environment. A strategy is developed to independently control elasticity, viscosity, and mesh size of bio-inks. The technique allows for easy manufacturing mechanically robust multiscale porous scaffolds, which can be used to encapsulate human pancreatic islets for sustained responsive insulin release.

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title: Raloxifene reduces sex- and age-related intervertebral disc degeneration in mice by estrogen signaling

abstract:
Estrogen agonist raloxifene is an FDA-approved treatment for osteoporosis in postmenopausal women that may also be a promising prophylactic for painful intervertebral disc (IVD) degeneration. Here, we hypothesized that raloxifene would augment IVD structure and reduce neurokinin-1 (substance P) in young and old mice by stimulating estrogen signaling. 2.5 month (male and female) and 22.5 month (female) C57Bl/6J mice were subcutaneously injected with raloxifene hydrochloride (5x/week, 6week, n=7-9/grp). Next, to determine the impact of estrogen-deficiency to IVD structure and substance P, female mice were ovariectomized (OVX) at 4mo and tissues from OVX and sham-operated mice were harvested at 6mo (n=5-6/grp). First, compared to male IVD, female IVD expressed less col2 and osterix transcription, early markers of IVD degeneration. Irrespective of sex, raloxifene increased the transcriptional expression for extracellular matrix anabolism, proliferation, notochordal cells (vs chondrocyte-like cells) and estrogen signaling in young IVD. Next, we determined that biological sex and aging each induced structural features of lumbar IVD degeneration. Therapeutically, injection of raloxifene countered these features by increasing IVD height in young mice, preventing mild sex-related IVD degeneration in young female mice and partially reversing age-related IVD degeneration in old female mice. Further, estrogen agonist raloxifene upregulated er- protein and downregulated substance P protein in young and old IVD. By contrast, estrogen-deficiency by OVX increased IVD degeneration and substance P protein in IVD cells. Similarly, substance P protein in vertebral osteocytes was upregulated in females relative to males and by estrogen-deficiency and downregulated by raloxifene. Overall, raloxifene augmented IVD structure and reduced substance P expression in young and old female murine IVD, whereas estrogen-deficiency increased substance P in the spine. These data suggest that raloxifene may potentially relieve painful IVD degeneration in postmenopausal women induced by biological sex, estrogen-deficiency and advanced age.

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Injection of raloxifene promotes IVD health by engaging estrogen and Wnt signaling to promote cell proliferation and IVD structure. Differential estrogen signaling by raloxifene and ovariectomy regulated nerve signaling protein substance P in the spine. Raloxifene may also bind water to collagen to promote hydration. Acan: aggrecan, AF: annulus fibrosus, NC: notochordal cell, NP: nucleus pulposus

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title: SenseNet, a tool for analysis of protein structure networks obtained from molecular dynamics simulations

abstract:
Computational methods play a key role for investigating allosteric mechanisms in proteins, with the potential of generating valuable insights for innovative drug design. Here we present the SenseNet ("Structure ENSEmble NETworks") framework for analysis of protein structure networks, which differs from established network models by focusing on interaction timelines obtained by molecular dynamics simulations. This approach is evaluated by predicting allosteric residues reported by NMR experiments in the PDZ2 domain of hPTP1e, a reference system for which previous computational predictions have shown considerable variance. We applied two models based on the mutual information between interaction timelines to estimate the conformational influence of each residue on its local environment. In terms of accuracy our prediction model is comparable to the top performing model published for this system, but by contrast benefits from its independence from NMR structures. Our results are complementary to experimental data and the consensus of previous predictions, demonstrating the potential of our new analysis tool SenseNet. Biochemical interpretation of our model suggests that allosteric residues in the PDZ2 domain form two distinct clusters of contiguous sidechain surfaces. SenseNet is provided as a plugin for the network analysis software Cytoscape, allowing for ease of future application and contributing to a system of compatible tools bridging the fields of system and structural biology.

Author SummaryRegulation and signal transduction processes in proteins are often correlated to structural changes induced by ligand binding, which can lead to suppression or enhancement of protein function. A common method to investigate such changes are numerical simulations of protein dynamics. We developed the analysis software SenseNet for predicting how protein dynamics and function is affected by e.g. ligand binding events based on molecular dynamics simulations. Our model estimates which structural elements of the protein confer the most information about their local environment, reasoning that these elements are essential for signal propagation. Applying this method on the PDZ2 domain of the hPTP1e protein, we were able to accurately predict structure elements with known signaling roles as determined by previous experiments. Integrating these experimental data with the consensus of other computational models and our predictions, we find two separate pathways which may transmit information through the PDZ2 protein structure. In addition to deepening our insight into the behavior of this particular protein, these results demonstrate the usefulness of our methods for other systems, such as potential drug targets. To make this analysis available to a broad audience, we implemented it as a plugin for the popular network analysis software Cytoscape.


title: MICRA-Net: MICRoscopy Analysis Neural Network to solve detection, classification, and segmentation from a single simple auxiliary task

abstract: High throughput quantitative analysis of microscopy images presents a challenge due to the complexity of the image content and the difficulty to retrieve precisely annotated datasets. In this paper we introduce a weakly-supervised MICRoscopy Analysis neural network (MICRA-Net) that can be trained on a simple main classification task using image-level annotations to solve multiple the more complex auxiliary semantic segmentation task and other associated tasks such as detection or enumeration. MICRA-Net relies on the latent information embedded within a trained model to achieve performances similar to state-of-the-art architectures when no precisely annotated dataset is available. This learnt information is extracted from the network using gradient class activation maps, which are combined to generate detailed feature maps of the biological structures of interest. We demonstrate how MICRA-Net significantly alleviates the Expert annotation process on various microscopy datasets and can be used for high-throughput quantitative analysis of microscopy images.


title: Genomic characterization of metastatic patterns from prospective clinical sequencing of 25,000 patients

abstract: Progression to metastatic disease remains the main cause of cancer death. Yet, the underlying genomic mechanisms driving metastasis remain largely unknown. Here, we present MSK-MET, an integrated pan-cancer cohort of tumor genomic and clinical outcome data from more than 25,000 patients. We analyzed this dataset to identify associations between tumor genomic alterations and patterns of metastatic dissemination across 50 tumor types. We found that chromosomal instability is strongly correlated with metastatic burden in some tumor types, including prostate adenocarcinoma, lung adenocarcinoma and HR-positive breast ductal carcinoma, but not in others, such as colorectal adenocarcinoma, pancreatic adenocarcinoma and high-grade serous ovarian cancer. We also identified specific somatic alterations associated with increased metastatic burden and specific routes of metastatic spread. Our data offer a unique resource for the investigation of the biological basis for metastatic spread and highlight the crucial role of chromosomal instability in cancer progression.


title: Spatial epitope barcoding reveals subclonaltumor patch behaviors

abstract: Intratumoral variability is a seminal feature of human tumors contributing to tumor progression and response to treatment. Current technologies are unsuitable to accurately track phenotypes and subclonal evolution within tumors, especially in response to genetic manipulations. Here, we developed epitope combinatorial tags (EpicTags), which we coupled to multiplexed ion beam imaging (EpicMIBI) for in situ tracking of barcodes within tissue microenvironments. Using this platform, we dissected the spatial component of cell lineages and phenotypes in a xenograft model of small-cell lung cancer. We observed emergent properties from mixed clones leading to the preferential expansion of subclonal patches for both neuroendocrine and non-neuroendocrine cancer cell states in this model. In tumors harboring a fraction of PTEN-deficient cancer cells, we uncovered a non-autonomous increase of subclonal patch size in PTEN wildtype cancer cells. EpicMIBI can facilitate in situ interrogation of cell-intrinsic and cell-extrinsic processes involved in intratumoral heterogeneity.


title: Plant lipid metabolism in susceptible and tolerant soybean (Glycine max) cultivars in response to Phytophthora sojae colonization and infection

abstract: Soybean is one of the most cultivated crops globally and a staple food for much of the worlds population. The annual global crop losses due to infection by the Phytophthora sojae are currently estimated at approximately $2B USD, yet we have limited understanding of the role of lipid metabolism in the adaptative strategies used to limit infection and crop loss. We employed a multi-modal lipidomics approach to investigate how soybean cultivars remodel their lipid metabolism to successfully limit infection by Phytophthora sojae. Both the tolerant and susceptible soybean cultivars showed alterations in lipid metabolism in response to Phytophthora sojae infection. Relative to non-inoculated controls, induced accumulation of stigmasterol was observed in the susceptible cultivar whereas, induced accumulation of phospholipids and glycerolipids occurred in tolerant soybean cultivar. We have generated a comprehensive metabolic map of susceptible and tolerant soybean root and stem lipid metabolism to identify lipid modulators of host immune or tolerance response to Phytophthora sojae infection and identified potential pathways and unique lipid biomarkers like TG(15:0/22:0/22:5), TG(10:0/10:0/10:0), TG(10:0/10:0/14:0), DG(18:3/18:3), DG(16:0/18:3) and DG(24:0/18:2) as possible targets for the development of future plant protection solutions.

category: pathology


title: Human engineered heart tissue transplantation in a guinea pig chronic injury model

abstract: AO_SCPLOWBSTRACTC_SCPLOWMyocardial injury leads to an irreversible loss of cardiomyocytes (CM). The implantation of human engineered heart tissue (EHT) has become a promising regenerative approach. Previous studies exhibited beneficial, dose-dependent effects of human induced pluripotent stem cell (hiPSC)-derived EHT patch transplantation in a guinea pig model in the subacute phase of myocardial injury. Yet, advanced heart failure often results from a chronic remodeling process. Therefore, from a clinical standpoint it is worthwhile to explore the ability to repair the chronically injured heart. In this study human EHT patches were generated from hiPSC-derived CMs (15x106 cells) and implanted epicardially four weeks after injury in a guinea-pig cryo-injury model. Cardiac function was evaluated by echocardiography after a follow-up period of four weeks. Hearts revealed large transmural myocardial injuries amounting to 27% of the left ventricle. EHT recipient hearts demonstrated compact muscle islands of human origin in the scar region, as indicated by a positive staining for human Ku80 and dystrophin, remuscularizing 5% of the scar area. Echocardiographic analysis demonstrated no significant difference between animals that received EHT patches and animals in the control group (fractional area change 36% vs. 34%). Thus, EHT patches engrafted in the chronically injured heart but in contrast to the subacute model, grafts were smaller and EHT patch transplantation did not improve left ventricular function, highlighting the difficulties for a regenerative approach.

category: pharmacology and toxicology


title: Interrogation of genome-wide, experimentally dissected gene regulatory networks reveals mechanisms underlying dynamic cellular state control

abstract: Pooled CRISPRi-mediated silencing of >1,000 transcriptional regulators expressed in single colorectal adenocarcinoma cells, followed by single-cell RNA-seq profiling at two timepoints, 1 day and 4 days, allowed reverse engineering the underlying tumor context-specific, causal regulatory network. Furthermore, the availability of experimentally derived, highly multiplexed gene reporter assays for each regulator, as identified by this analysis, allowed accurate assessment of differential protein activity following silencing of each regulator, thus providing proof-of-concept for generating comprehensive, tissue-specific networks of transcriptional and post-translational interactions. Analysis of this causal network allowed elucidation of complex autoregulatory mechanisms that have eluded previous computational approaches and supported systematic elucidation of cooperative mechanisms, where one regulatory protein can modulate the activity of another regulatory protein, as well as transcriptional mimicry, where one regulatory protein can phenocopy others.

category: systems biology


title: Brain signaling dynamics after vagus nerve stimulation

abstract: The vagus nerve projects to a well-defined neural circuit via the nucleus tractus solitarii (NTS) and its stimulation elicits a wide range of metabolic, neuromodulatory, and behavioral effects. Transcutaneous vagus nerve stimulation (tVNS) has been established as a promising technique to non-invasively alter brain function. However, the precise dynamics elicited by tVNS in humans are still largely unknown. Here, we performed fMRI with concurrent right-sided tVNS (vs. sham) following a randomized cross-over design (N=40). First, to unravel the temporal profile of tVNS-induced changes in the NTS, we compared fMRI time series to canonical profiles for stimulation ON and OFF cycles. Model comparisons indicated that NTS time series were best fit by block-wise shifts in signal amplitude with stimulation ON and OFF estimates being highly correlated. Therefore, we compared stimulation (ON + OFF) versus baseline phases and found that tVNS increased fMRI BOLD activation in the NTS, but this effect was dependent on sufficient temporal signal-to-noise ratio (tSNR) in the mask. Second, to identify the spatiotemporal evolution of tVNS-induced changes in the brain, we examined lagged co-activation patterns and phase coherence. In contrast to our hypothesis, tVNS did not alter dynamic functional connectivity after correction for multiple comparisons. Third, to establish a positive control for future research, we measured changes in gastric myoelectrical frequency via an electrogastrogram. Again, in contrast to our hypothesis, tVNS induced no changes in gastric frequency. Collectively, our study provides evidence that tVNS can perturb brain signaling in the NTS, but these effects are dependent on tSNR and require precise localization. In light of an absence of acute tVNS-induced effects on dynamic functional connectivity and gastric motility, we discuss which steps are necessary to advance future research on afferent and efferent effects of tVNS.


title: Brain histone beta-hydroxy-butyrylation couples metabolism with gene expression

abstract:
Metabolic status has a well-documented influence on peripheral organs physiology and pathology, however mounting evidence suggests that it can also affect brain function. For example, brain resilience to aging is enhanced by caloric restriction, and ketogenic diets have been used to treat neurological diseases. Unfortunately, little is known about the impact of metabolic stimuli on brain tissue at a molecular level. Recent data obtained in liver tissue suggest that beta-hydroxybutyrate (BHB) can also be a key signaling molecule regulating gene transcription. Thus, we adopted a ketogenic metabolic challenge, based on 48 hrs of fasting, and then assessed lysine beta-hydroxybutyrylation (K-bhb) levels in proteins extracted from the cerebral cortex. We found that fasting enhanced K-bhb in a variety of proteins and on histone H3. ChIP-seq experiments showed that K9 beta-hydroxybutyrylation of H3 (H3K9-bhb) was significantly enriched by fasting on more than 8000 DNA loci. Transcriptomic analysis showed that H3K9-bhb on enhancers and promoters correlated with active gene expression. Since one of the most enriched functional annotations both at the epigenetic and transcriptional level was "circadian rhythms", we studied the expression of core-clock genes in the cortex during fasting.

We found that the diurnal oscillation of specific transcripts was modulated at distinct times of the day along the circadian cycle. Thus, our results suggest that fasting dramatically impinges on the cerebral cortex transcriptional and epigenetic landscape, and BHB acts as a powerful epigenetic molecule in the brain through direct and specific histone marks remodelling in neural tissue cells.