Beyond Equilibrium Phase Diagrams: Enzymatic Activity Shakes Up Bacterial Condensates.

Phase separation is a thermodynamic process, but cells are inherently out of equilibrium. Guilhas et al. (2020) identify an active process through which an ATP-dependent motor controls the number and position of biomolecular condensates in bacteria.

Let's phase it: viruses are master architects of biomolecular condensates.

Viruses compartmentalize their replication and assembly machinery to both evade detection and concentrate the viral proteins and nucleic acids necessary for genome replication and virion production. Accumulating evidence suggests that diverse RNA and DNA viruses form replication organelles and nucleocapsid assembly sites using phase separation. In general, the biogenesis of these compartments is regulated by two types of viral protein, collectively known as antiterminators and nucleocapsid proteins, respectively. Herein, we discuss how RNA viruses establish replication organelles and nucleocapsid assembly sites, and the evidence that these compartments form through phase separation. While this review focuses on RNA viruses, accumulating evidence suggests that all viruses rely on phase separation and form biomolecular condensates important for completing the infectious cycle.

Getting RNA and protein in phase.

Nonmembrane-bound organelles such as RNA granules behave like dynamic droplets, but the molecular details of their assembly are poorly understood. Several recent papers identify structural features that drive granule assembly, shedding light on how phase transitions functionally organize the cell and may lead to pathological protein aggregation.

Metabolic Diversity in Human Non-Small Cell Lung Cancer Cells.

Intermediary metabolism in cancer cells is regulated by diverse cell-autonomous processes, including signal transduction and gene expression patterns, arising from specific oncogenotypes and cell lineages. Although it is well established that metabolic reprogramming is a hallmark of cancer, we lack a full view of the diversity of metabolic programs in cancer cells and an unbiased assessment of the associations between metabolic pathway preferences and other cell-autonomous processes. Here, we quantified metabolic features, mostly from the 13C enrichment of molecules from central carbon metabolism, in over 80 non-small cell lung cancer (NSCLC) cell lines cultured under identical conditions. Because these cell lines were extensively annotated for oncogenotype, gene expression, protein expression, and therapeutic sensitivity, the resulting database enables the user to uncover new relationships between metabolism and these orthogonal processes.

Arabidopsis callus grafts: a system to study symplasmic intercellular macromolecular transport and gene silencing spread.

In the present study, we present callus grafting, comprising a method for reproducibly generating tissue chimeras from callus cultures of Arabidopsis thaliana. In this way, callus cultures of different genetic backgrounds may be co-cultivated such that cell-to-cell connectivity is achieved as a chimeric tissue is formed. To track intercellular connectivity and transport between non-clonal callus cells, we used transgenic lines expressing fluorescently tagged mobile and non-mobile fusion constructs. Using fluorescently-labelled reporter lines that label plasmodesmata, we show that secondary complex plasmodesmata are present at the cell walls of connected cells. We use this system to investigate cell-to-cell transport across the callus graft junction and show that different proteins and RNAs are mobile between non-clonal callus cells. Finally, we take advantage of the callus culture system to probe intercellular connectivity of grafted leaf and root calli and the effect of different light regimes of cell-to-cell transport. Taking advantage of the ability of callus to be cultivated in the complete absence of light, we show that the rate of silencing spread is significantly decreased in chimeric calli cultivated in total darkness. We propose that callus grafting is a fast and reliable method for analysing the capacity of a macromolecule to be exchanged between cells independent of the vasculature.

Clusters of bacterial RNA polymerase are biomolecular condensates that assemble through liquid-liquid phase separation.

Once described as mere "bags of enzymes," bacterial cells are in fact highly organized, with many macromolecules exhibiting nonuniform localization patterns. Yet the physical and biochemical mechanisms that govern this spatial heterogeneity remain largely unknown. Here, we identify liquid-liquid phase separation (LLPS) as a mechanism for organizing clusters of RNA polymerase (RNAP) in Escherichia coli Using fluorescence imaging, we show that RNAP quickly transitions from a dispersed to clustered localization pattern as cells enter log phase in nutrient-rich media. RNAP clusters are sensitive to hexanediol, a chemical that dissolves liquid-like compartments in eukaryotic cells. In addition, we find that the transcription antitermination factor NusA forms droplets in vitro and in vivo, suggesting that it may nucleate RNAP clusters. Finally, we use single-molecule tracking to characterize the dynamics of cluster components. Our results indicate that RNAP and NusA molecules move inside clusters, with mobilities faster than a DNA locus but slower than bulk diffusion through the nucleoid. We conclude that RNAP clusters are biomolecular condensates that assemble through LLPS. This work provides direct evidence for LLPS in bacteria and demonstrates that this process can serve as a mechanism for intracellular organization in prokaryotes and eukaryotes alike.

Effectiveness of Interdisciplinary Leadership Training for Early Career Professionals in the Field of Developmental Disabilities.

INTRODUCTION: The purpose of this paper is to describe the curriculum and self-reported outcomes on measures of interdisciplinary leadership skills for work within the field of developmental disabilities from trainees in one interprofessional training program. METHODS: The paper highlights one program's curriculum and strategy for capturing self-report survey measures from trainees in cohorts from 2014-2018 (n = 86) on two surveys (Interdisciplinary Attitudes and Skills and Leadership Self-Evaluation Form) and three time points across the training year: before training (T1), mid-year (T2), and after training (T3). RESULTS: Data from 86 trainees are reported including demographics (nearly 80% white, 92% female), non-descriptive statistics due to non-normative samples, and tertiles demonstrating changes between time points. Significant differences between medians are reported between T1-T3 specifically related to utilizing interdisciplinary skills and gains in leadership competencies. Specific utilization of skills was reported to be 'Greatly' attributable to the LEND program related to sharing ideas and asking for help across disciplines. DISCUSSION: Trainees' self-report from before training to after training indicates an increase in competence and utilization of interdisciplinary skills to be expected from participation in the curriculum. Self-report measures are.

Dissecting the complexity of biomolecular condensates.

Biomolecular condensates comprise a diverse and ubiquitous class of membraneless organelles. Condensate assembly is often described by liquid-liquid phase separation. While this process explains many key features, it cannot account for the compositional or architectural complexity that condensates display in cells. Recent work has begun to dissect the rich network of intermolecular interactions that give rise to biomolecular condensates. Here, we review the latest results from theory, simulations and experiments, and discuss what they reveal about the structure-function relationship of condensates.

Mu gets in the loop.

In this issue of Molecular Cell, Han and Mizuuchi present evidence for a possible Turing-like reaction-diffusion mechanism underlying target immunity by the bacteriophage Mu.

RNA transcription modulates phase transition-driven nuclear body assembly.

Nuclear bodies are RNA and protein-rich, membraneless organelles that play important roles in gene regulation. The largest and most well-known nuclear body is the nucleolus, an organelle whose primary function in ribosome biogenesis makes it key for cell growth and size homeostasis. The nucleolus and other nuclear bodies behave like liquid-phase droplets and appear to condense from the nucleoplasm by concentration-dependent phase separation. However, nucleoli actively consume chemical energy, and it is unclear how such nonequilibrium activity might impact classical liquid-liquid phase separation. Here, we combine in vivo and in vitro experiments with theory and simulation to characterize the assembly and disassembly dynamics of nucleoli in early Caenorhabditis elegans embryos. In addition to classical nucleoli that assemble at the transcriptionally active nucleolar organizing regions, we observe dozens of "extranucleolar droplets" (ENDs) that condense in the nucleoplasm in a transcription-independent manner. We show that growth of nucleoli and ENDs is consistent with a first-order phase transition in which late-stage coarsening dynamics are mediated by Brownian coalescence and, to a lesser degree, Ostwald ripening. By manipulating C. elegans cell size, we change nucleolar component concentration and confirm several key model predictions. Our results show that rRNA transcription and other nonequilibrium biological activity can modulate the effective thermodynamic parameters governing nucleolar and END assembly, but do not appear to fundamentally alter the passive phase separation mechanism.

Behind Closed Doors: The Stigma of Suicide Loss Survivors.

Many thousands of families lose a loved one to suicide each year. The stigma experienced by family survivors threatens to further burden families and impede the grieving process. This study used a community-based participatory research process to explore the family stigma of suicide from a social-cognitive perspective. We describe a secondary analysis of qualitative data focusing on stigma directed at bereaved families. Thematic analysis of focus group data ( n = 62) resulted in themes describing stereotypes, prejudice, and discrimination. Bereaved families were viewed as contributing to their loved ones death through abuse, neglect, denial, or failure to provide adequate help. Bereaved families were seen as emotionally strong, victims of the suicide, or as contaminated by their association. Families encounter pressure to keep the suicide a secret and experience withdrawal of support systems. Results suggest needs for evidence-based programs to address both public and internalized stigma experienced by bereaved families.

[Leptomeningeal carcinomatosis as a rare metastatic spreading of BRAF-mutated microsatellite stable colon cancer]. / Meningeosis carcinomatosa als seltener Metastasierungsweg eines BRAF-mutierten Mikrosatelliten-stabilen Kolonkarzinoms.

Leptomeningeal carcinomatosis is a rare but serious complication of solid tumors such as melanoma, breast and lung cancer, as well as gastrointestinal carcinomas. Its clinical manifestation is highly variable, presenting as radicular pain with or without neurological deficits, as well as with headaches and hallucinatory irritation symptoms. Leptomeningeal carcinomatosis is often misdiagnosed, which delays treatment. Here we report a rare case of a patient with BRAF-mutated microsatellite stable colon carcinoma with lymphatic and skeletal metastases, who developed neurological symptoms one month after the initial diagnosis of malignancy. Based on the cytological detection of tumor cells in the cerebrospinal fluid, a leptomeningeal carcinomatosis was diagnosed, despite normal findings on MRI. Intrathecal chemotherapy with methotrexate, combined with intensive systemic immunochemotherapy, resulted in a good partial remission of the underlying malignant disease. However, approximately 8 months after the start of therapy, the patient developed progressive leptomeningeal carcinomatosis and died a few weeks later.

Assessing the impact of fine particulate matter (PM2.5) on respiratory-cardiovascular chronic diseases in the New York City Metropolitan area using Hierarchical Bayesian Model estimates.

An enhanced research paradigm is presented to address the spatial and temporal gaps in fine particulate matter (PM2.5) measurements and generate realistic and representative concentration fields for use in epidemiological studies of human exposure to ambient air particulate concentrations. The general approach for research designed to analyze health impacts of exposure to PM2.5 is to use concentration data from the nearest ground-based air quality monitor(s), which typically have missing data on the temporal and spatial scales due to filter sampling schedules and monitor placement, respectively. To circumvent these data gaps, this research project uses a Hierarchical Bayesian Model (HBM) to generate estimates of PM2.5 in areas with and without air quality monitors by combining PM2.5 concentrations measured by monitors, PM2.5 concentration estimates derived from satellite aerosol optical depth (AOD) data, and Community-Multiscale Air Quality (CMAQ) model predictions of PM2.5 concentrations. This methodology represents a substantial step forward in the approach for developing representative PM2.5 concentration datasets to correlate with inpatient hospitalizations and emergency room visits data for asthma and inpatient hospitalizations for myocardial infarction (MI) and heart failure (HF) using case-crossover analysis. There were two key objective of this current study. First was to show that the inputs to the HBM could be expanded to include AOD data in addition to data from PM2.5 monitors and predictions from CMAQ. The second objective was to determine if inclusion of AOD surfaces in HBM model algorithms results in PM2.5 air pollutant concentration surfaces which more accurately predict hospital admittance and emergency room visits for MI, asthma, and HF. This study focuses on the New York City, NY metropolitan and surrounding areas during the 2004-2006 time period, in order to compare the health outcome impacts with those from previous studies and focus on any benefits derived from the changes in the HBM model surfaces. Consistent with previous studies, the results show high PM2.5 exposure is associated with increased risk of asthma, myocardial infarction and heart failure. The estimates derived from concentration surfaces that incorporate AOD had a similar model fit and estimate of risk as compared to those derived from combining monitor and CMAQ data alone. Thus, this study demonstrates that estimates of PM2.5 concentrations from satellite data can be used to supplement PM2.5 monitor data in the estimates of risk associated with three common health outcomes. Results from this study were inconclusive regarding the potential benefits derived from adding AOD data to the HBM, as the addition of the satellite data did not significantly increase model performance. However, this study was limited to one metropolitan area over a short two-year time period. The use of next-generation, high temporal and spatial resolution satellite AOD data from geostationary and polar-orbiting satellites is expected to improve predictions in epidemiological studies in areas with fewer pollutant monitors or over wider geographic areas.

Exogenous α-synuclein induces toll-like receptor 4 dependent inflammatory responses in astrocytes.

BACKGROUND: The pathological hallmarks of Parkinson's disease are intracellular inclusions composed mainly of misfolded α-synuclein (αSYN). Under physiological conditions αSYN is mostly localized in synapses. In addition, a portion of αSYN is secreted to the extracellular space, where it may be sequestered by neighboring cells and could induce inflammatory responses. The mechanisms of αSYN internalization and signal transduction are not unequivocally clarified. In this work we investigated in primary mouse astrocytes the involvement of toll-like receptor 4 (TLR4) in the induction of inflammatory responses upon exposure to purified human αSYN produced in bacteria. RESULTS: The mRNA induction of pro-inflammatory cytokines, inducible nitric oxide synthase and cyclooxygenase-2 was significantly reduced in TLR4 knockout astrocytes. The αSYN-mediated activation of c-Jun N-terminal kinases and p38 mitogen-activated protein kinase tended to be diminished, and nuclear translocation of the p65 subunit of nuclear factor κB was abolished in TLR4 knockout astrocytes. In contrast, the uptake of exogenous αSYN was unaffected by TLR4 knockout. CONCLUSIONS: Extracellular αSYN can activate pro-inflammatory TLR4 pathways in astrocytes, whereas αSYN uptake is independent of TLR4.

Nonthermal ATP-dependent fluctuations contribute to the in vivo motion of chromosomal loci.

Chromosomal loci jiggle in place between segregation events in prokaryotic cells and during interphase in eukaryotic nuclei. This motion seems random and is often attributed to brownian motion. However, we show here that locus dynamics in live bacteria and yeast are sensitive to metabolic activity. When ATP synthesis is inhibited, the apparent diffusion coefficient decreases, whereas the subdiffusive scaling exponent remains constant. Furthermore, the magnitude of locus motion increases more steeply with temperature in untreated cells than in ATP-depleted cells. This "superthermal" response suggests that untreated cells have an additional source of molecular agitation, beyond thermal motion, that increases sharply with temperature. Such ATP-dependent fluctuations are likely mechanical, because the heat dissipated from metabolic processes is insufficient to account for the difference in locus motion between untreated and ATP-depleted cells. Our data indicate that ATP-dependent enzymatic activity, in addition to thermal fluctuations, contributes to the molecular agitation driving random (sub)diffusive motion in the living cell.

Knockdown of transactive response DNA-binding protein (TDP-43) downregulates histone deacetylase 6.

TDP-43 is an RNA/DNA-binding protein implicated in transcriptional repression and mRNA processing. Inclusions of TDP-43 are hallmarks of frontotemporal dementia and amyotrophic lateral sclerosis. Besides aggregation of TDP-43, loss of nuclear localization is observed in disease. To identify relevant targets of TDP-43, we performed expression profiling. Thereby, histone deacetylase 6 (HDAC6) downregulation was discovered on TDP-43 silencing and confirmed at the mRNA and protein level in human embryonic kidney HEK293E and neuronal SH-SY5Y cells. This was accompanied by accumulation of the major HDAC6 substrate, acetyl-tubulin. HDAC6 levels were restored by re-expression of TDP-43, dependent on RNA binding and the C-terminal protein interaction domains. Moreover, TDP-43 bound specifically to HDAC6 mRNA arguing for a direct functional interaction. Importantly, in vivo validation in TDP-43 knockout Drosophila melanogaster confirmed the specific downregulation of HDAC6. HDAC6 is necessary for protein aggregate formation and degradation. Indeed, HDAC6-dependent reduction of cellular aggregate formation and increased cytotoxicity of polyQ-expanded ataxin-3 were found in TDP-43 silenced cells. In conclusion, loss of functional TDP-43 causes HDAC6 downregulation and might thereby contribute to pathogenesis.

TDP-43 regulates global translational yield by splicing of exon junction complex component SKAR.

TDP-43 is linked to neurodegenerative diseases including frontotemporal dementia and amyotrophic lateral sclerosis. Mostly localized in the nucleus, TDP-43 acts in conjunction with other ribonucleoproteins as a splicing co-factor. Several RNA targets of TDP-43 have been identified so far, but its role(s) in pathogenesis remains unclear. Using Affymetrix exon arrays, we have screened for the first time for splicing events upon TDP-43 knockdown. We found alternative splicing of the ribosomal S6 kinase 1 (S6K1) Aly/REF-like target (SKAR) upon TDP-43 knockdown in non-neuronal and neuronal cell lines. Alternative SKAR splicing depended on the first RNA recognition motif (RRM1) of TDP-43 and on 5'-GA-3' and 5'-UG-3' repeats within the SKAR pre-mRNA. SKAR is a component of the exon junction complex, which recruits S6K1, thereby facilitating the pioneer round of translation and promoting cell growth. Indeed, we found that expression of the alternatively spliced SKAR enhanced S6K1-dependent signaling pathways and the translational yield of a splice-dependent reporter. Consistent with this, TDP-43 knockdown also increased translational yield and significantly increased cell size. This indicates a novel mechanism of deregulated translational control upon TDP-43 deficiency, which might contribute to pathogenesis of the protein aggregation diseases frontotemporal dementia and amyotrophic lateral sclerosis.

The shared decision-making tool for caregivers of children with prenatal opioid exposure: A pilot and acceptability study.

This pilot and acceptability study sought to report provider acceptability and developmental concerns expressed by caregivers of children with prenatal opioid exposure using the Shared Decision-Making Tool (SDMT), an instrument created by study authors. Data were collected from five health care and early intervention providers and 83 caregivers from a medical clinic and early intervention service center. Descriptive statistics were used to identify frequency, mean level, and prioritization of developmental concerns using the SDMT, and to summarize provider acceptability about integrating the SDMT into their workflow. Communication was the most frequently cited concern in four consecutive age categories, followed by Inattention/impulsivity and Problem behavior. All providers "strongly agreed" or "agreed" with all statements on the provider feedback survey, except two instances. Results of this study support the SDMT as a potential tool to help engage caregivers and providers of children with prenatal opioid exposure in the shared decision-making process by standardizing communication related to areas of developmental concern and caregivers' priority needs. Findings from this pilot study will inform modifications to the SDMT and administration instructions before our next study, which will examine psychometric properties and caregiver acceptability of the scale.

Transcription templated assembly of the nucleolus in the C. elegans embryo.

The nucleolus is a multicomponent structure made of RNA and proteins that serves as the site of ribosome biogenesis within the nucleus. It has been extensively studied as a prototype of a biomolecular condensate whose assembly is driven by phase separation. While the steady-state size of the nucleolus is quantitatively accounted for by the thermodynamics of phase separation, we show that experimental measurements of the assembly dynamics are inconsistent with a simple model of a phase-separating system relaxing to its equilibrium state. Instead, we show that the dynamics are well described by a model in which the transcription of ribosomal RNA actively drives nucleolar assembly. We find that our model of active transcription-templated assembly quantitatively accounts for the rapid kinetics observed in early embryos at different developmental stages, and for different RNAi perturbations of embryo size. Our model predicts a scaling of the time to assembly with the volume of the nucleus to the one-third power, which is confirmed by experimental data. Our study highlights the role of active processes such as transcription in controlling the placement and timing of assembly of membraneless organelles.

Loss of DJ-1 protein stability and cytoprotective function by Parkinson's disease-associated proline-158 deletion.

DJ-1 is a ubiquitous protein regulating cellular viability. Recessive mutations in the PARK7/DJ-1 gene are linked to Parkinson's disease (PD). Although the most dramatic L166P point mutation practically eliminates DJ-1 protein and function, the effects of other PD-linked mutations are subtler. Here, we investigated two recently described PD-associated DJ-1 point mutations, the A179T substitution and the P158Δ in-frame deletion. [A179T]DJ-1 protein was as stable as wild-type [wt]DJ-1, but the P158Δ mutant protein was less stable. In accord with the notion that dimer formation is essential for DJ-1 protein stability, [P158Δ]DJ-1 was impaired in dimer formation. Similar to our previous findings for [M26I]DJ-1, [P158Δ]DJ-1 bound aberrantly to apoptosis signal-regulating kinase 1. Thus, the PD-associated P158Δ mutation destabilizes DJ-1 protein and function. As there is also evidence for an involvement of DJ-1 in multiple system atrophy, a PD-related α-synucleinopathy characterized by oligodendroglial cytoplasmic inclusions, we studied an oligodendroglial cell line stably expressing α-synuclein. α-Synuclein aggregate dependent microtubule retraction upon co-transfection with tubulin polymerization-promoting protein p25α was ameliorated by [wt]DJ-1. In contrast, DJ-1 mutants including P158Δ failed to protect in this system, where we found evidence of apoptosis signal-regulating kinase 1 (ASK1) involvement. In conclusion, the P158Δ point mutation may contribute to neurodegeneration by protein destabilization and hence loss of DJ-1 function.