Arsenic trioxide stimulates SUMO-2/3 modification leading to RNF4-dependent proteolytic targeting of PML

We have recently reported that poly-SUMO-2/3 conjugates are subject to a ubiquitin-dependent proteolytic control in human cells. Here we show that arsenic trioxide (ATO) increases SUMO-2/3 modification of promyelocytic leukemia (PML) leading to its subsequent ubiquitylation in vivo. The SUMO-binding ubiquitin ligase RNF4 mediates this modification and causes disruption of PML nuclear bodies upon treatment with ATO. Reconstitution of SUMO-dependent ubiquitylation of PML by RNF4 in vitro and in a yeast trans vivo system revealed a preference of RNF4 for chain forming SUMOs. Polysumoylation of PML in response to ATO thus leads to its recognition and ubiquitylation by RNF4.     

Induction of TNF in human alveolar macrophages as a potential evasion mechanism of virulent Mycobacterium tuberculosis.

The ability of macrophages to release cytokines is crucial to the host response to intracellular infection. In particular, macrophage-derived TNF plays an important role in the host response to infection with the intracellular pathogen Mycobacterium tuberculosis. In mice, TNF is indispensable for the formation of tuberculous granulomas, which serve to demarcate the virulent bacterium. TNF is also implicated in many of the immunopathological features of tuberculosis. To investigate the role of TNF in the local immune response, we infected human alveolar macrophages with virulent and attenuated mycobacteria. Infection with virulent strains induced the secretion of significantly higher levels of bioactive TNF than attenuated strains correlating with their ability to multiply intracellularly. Treatment of infected macrophages with neutralizing anti-TNF Abs reduced the growth rate of intracellular bacteria, whereas bacterial replication was augmented by addition of exogenous TNF. Infected and uninfected macrophages contributed to cytokine production as determined by double-staining of M. tuberculosis and intracellular TNF. The induction of TNF by human alveolar macrophages at the site of infection permits the multiplication of intracellular bacteria and may therefore present an evasion mechanism of human pathogens.     

Quantification of nematic cell polarity in three-dimensional tissues

How epithelial cells coordinate their polarity to form functional tissues is an open question in cell biology. Here, we characterize a unique type of polarity found in liver tissue, nematic cell polarity, which is different from vectorial cell polarity in simple, sheet-like epithelia. We propose a conceptual and algorithmic framework to characterize complex patterns of polarity proteins on the surface of a cell in terms of a multipole expansion. To rigorously quantify previously observed tissue-level patterns of nematic cell polarity (Morales-Navarrete et al., eLife 2019), we introduce the concept of co-orientational order parameters, which generalize the known biaxial order parameters of the theory of liquid crystals. Applying these concepts to three-dimensional reconstructions of single cells from high-resolution imaging data of mouse liver tissue, we show that the axes of nematic cell polarity of hepatocytes exhibit local coordination and are aligned with the biaxially anisotropic sinusoidal network for blood transport. Our study characterizes liver tissue as a biological example of a biaxial liquid crystal. The general methodology developed here could be applied to other tissues and in-vitro organoids.     

Virulence of parasites in hosts under environmental stress: experiments with anoxia and starvation

Most environments periodically impose severe stress that may cause high mortality and alter population structure, for example, by removing sick and old individuals. We examined how anoxic conditions and starvation of the host affect virulence of two closely related trematode parasites, Rhipidocotyle campanula and R. fennica . These parasites differ by prevalence of infection and by exploitation rate of individual hosts (freshwater clam, Anodonta piscinalis ). Infection by R. campanula is rare (<5% prevalence of infection) and destroys on average 90% of the gonad tissue of the individual host. Infection by R. fennica is more common (20–60% prevalence of infection) and leads to on average 30% gonad destruction. In the end, both infections lead to host infertility. We predicted that R. campanula induces higher host mortality than R. fennica under host stress. In two laboratory experiments, we exposed naturally-infected and uninfected clams to anoxia and to starvation. Anoxia occasionally takes place during winter in eutrophic lakes, while some degree of starvation should occur seasonally. We found that mortality rate of clams was much higher under anoxia than under starvation, and that infection increased mortality rate under both types of host stress. As predicted, R. campanula induced higher host mortality than R. fennica . Host survival was population-specific, suggesting that clams of different origins carried different amount of energy reserves. Severe environmental perturbation may remove R. campanula infected individuals from the host population, but recolonization from the fish host is likely to prevent extinction of the parasite suprapopulation. The observed high host mortality induced by R. campanula may be one ecological explanation for the consistently lower prevalence of infection of R. campanula when compared to R. fennica .     

Making the connection: expanding the role of restoration genetics in restoring and evaluating connectivity

The success of restoration activities is affected by connectivity with the surrounding landscape. From a genetic perspective, landscape connectivity can influence gene flow, effective size, and genetic diversity of populations, which in turn have impacts on the fitness and adaptive potential of species in restored areas. Researchers and practitioners are increasingly using genetic data to incorporate elements of connectivity into restoration planning and evaluation. We show that genetic studies of connectivity can improve restoration planning in three main ways. First, by comparing genetic estimates of contemporary and historical gene flow and population size, practitioners can establish historical baselines that may provide targets for restoration of connectivity. Second, empirical estimates of dispersal, landscape resistance to movement, and adaptive genetic variance can be derived from genetic data and used to parameterize existing restoration planning tools. Finally, restoration actions can also be targeted to remove barriers to gene flow or mitigate pinch‐points in corridors. We also discuss appropriate methods for evaluating the restoration of gene flow over timescales required by practitioners. Collaboration between restoration geneticists, ecologists, and practitioners is needed to develop practical and innovative ways to further incorporate connectivity into restoration practice.     

LuTHy: a double‐readout bioluminescence‐based two‐hybrid technology for quantitative mapping of protein–protein interactions in mammalian cells

Information on protein–protein interactions (PPIs) is of critical importance for studying complex biological systems and developing therapeutic strategies. Here, we present a double‐readout bioluminescence‐based two‐hybrid technology, termed LuTHy, which provides two quantitative scores in one experimental procedure when testing binary interactions. PPIs are first monitored in cells by quantification of bioluminescence resonance energy transfer (BRET) and, following cell lysis, are again quantitatively assessed by luminescence‐based co‐precipitation (LuC). The double‐readout procedure detects interactions with higher sensitivity than traditional single‐readout methods and is broadly applicable, for example, for detecting the effects of small molecules or disease‐causing mutations on PPIs. Applying LuTHy in a focused screen, we identified 42 interactions for the presynaptic chaperone CSPα, causative to adult‐onset neuronal ceroid lipofuscinosis (ANCL), a progressive neurodegenerative disease. Nearly 50% of PPIs were found to be affected when studying the effect of the disease‐causing missense mutations L115R and ?L116 in CSPα with LuTHy. Our study presents a robust, sensitive research tool with high utility for investigating the molecular mechanisms by which disease‐associated mutations impair protein activity in biological systems.     

Detection of mitochondrial defects by laser fluorimetry

The mitochondrial function in skeletal muscle biopsies of three patients with chronic progressive external ophthalmoplegia, having deletions of the mitochondrial DNA, was studied by laser-excited fluorescence measurements of NAD(P)H and flavoproteins in saponin-skinned fibers. We detected substantially elevated steady state redox states of the mitochondrial NAD-system in the muscle fibers of these patients. Moreover, the respiratory chain-linked autofluorescence changes in the muscle fibers of these patients were larger in comparison to controls indicating substantial alterations of the mitochondrial content. These results are in line with the presence of elevated numbers of partially respiratory chain inhibited mitochondria in the skeletal muscle of chronic progressive external ophthalmoplegia patients. (Mol Cell Biochem 174: 97–100, 1997)     

Native faunal communities depend on habitat from non-native plants in novel but not in natural ecosystems

Invasive non-native plants are a major driver of native biodiversity loss, yet native biodiversity can sometimes benefit from non-native species. Depending on habitat context, even the same non-native species can have positive and negative effects on biodiversity. Blackberry (Rubus fruticosus aggregate) is a useful model organism to better understand a non-native plant with conflicting impacts on biodiversity. We used a replicated capture-mark-recapture study across 11 consecutive seasons to examine the response of small mammal diversity and abundance to vegetation structure and density associated with non-native blackberry (R. anglocandicans) in native, hybrid and blackberry-dominated novel ecosystems in Australia. Across the three habitat types, increasing blackberry dominance had a positive influence on mammal diversity, while the strength and direction of this influence varied for abundance. At a microhabitat scale within hybrid and native habitat there were no significant differences in diversity, or the abundance of most species, between microhabitats where blackberry was absent versus dominant. In contrast, in novel ecosystems diversity and abundances were very low without blackberry, yet high (comparable to native ecosystems) within blackberry as it provided functionally-analogous vegetation structure and density to the lost native understory. Our results indicate the ecological functions of non-native plant species vary depending on habitat and need to be considered for management. Comparative studies such as ours that apply a standardized approach across a broad range of conditions at the landscape and habitat scale are crucial for guiding land managers on control options for non-native species (remove, reduce or retain and contain) that are context-sensitive and scale-dependent.     

Hyalinoecia artifex: Field notes on a charismatic and abundant epifaunal polychaete on the US Atlantic continental margin

Hyalinoecia artifex is an abundant species on the US Atlantic margin, although little is known about its behavior, ecology, or reproduction. We provide field notes and high‐resolution in situ imagery of this species observed and collected in 2013 and 2015. Hyalinoecia artifex occurred primarily on soft sediment at a density of 10.9±0.95 individuals m^?2 (mean±standard error). Although they were found adjacent to mussel beds associated with methane seeps, worms were negatively associated with authigenic carbonate and other epibenthic megafauna in the study area. Quill worms moved across the sediment by extending their heads from the tubes and dragging the tubes forward. Stable isotope analysis indicated that H. artifex is a secondary consumer. Most individuals collected in 2015 were ripe, with mature oocytes up to 400 μm. Oocytes were yolky, yellow in color and positively buoyant; no brooding was observed.