Tripartite assembly of RND multidrug efflux pumps

Tripartite multidrug efflux systems of Gram-negative bacteria are composed of an inner membrane transporter, an outer membrane channel and a periplasmic adaptor protein. They are assumed to form ducts inside the periplasm facilitating drug exit across the outer membrane. Here we present the reconstitution of native Pseudomonas aeruginosa MexAB–OprM and Escherichia coli AcrAB–TolC tripartite Resistance Nodulation and cell Division (RND) efflux systems in a lipid nanodisc system. Single-particle analysis by electron microscopy reveals the inner and outer membrane protein components linked together via the periplasmic adaptor protein. This intrinsic ability of the native components to self-assemble also leads to the formation of a stable interspecies AcrA–MexB–TolC complex suggesting a common mechanism of tripartite assembly. Projection structures of all three complexes emphasize the role of the periplasmic adaptor protein as part of the exit duct with no physical interaction between the inner and outer membrane components.

Tripartite efflux systems consist of inner membrane, outer membrane and periplasmic components. Here, Daury et al. reconstitute native versions of RND transporters in nanodiscs and present projection structures emphasizing the role of the periplasmic adaptor in linking the inner and outer membrane proteins.

Bottom-up solution synthesis of narrow nitrogen-doped graphene nanoribbons

Large quantities of nitrogen-doped graphene nanoribbons can be synthesized via Yamamoto coupling of molecular precursors followed by cyclodehydrogenation using Scholl reaction.

EFhd2 is a novel amyloid protein associated with pathological tau in Alzheimer's disease

EFhd2 is a conserved calcium-binding protein, abundant within the central nervous system. Previous studies identified EFhd2 associated with pathological forms of tau proteins in the tauopathy mouse model JNPL3, which expresses the human tau(P301L) mutant. This association was validated in human tauopathies, such as Alzheimer's disease (AD). However, the role that EFhd2 may play in tauopathies is still unknown. Here, we show that EFhd2 formed amyloid structures in vitro, a capability that is reduced by calcium ions. Electron microscopy (EM) analyses demonstrated that recombinant EFhd2 formed filamentous structures. EM analyses of sarkosyl-insoluble fractions derived from human AD brains also indicated that EFhd2 co-localizes with aggregated tau proteins and formed granular structures. Immunohistological analyses of brain slices demonstrated that EFhd2 co-localizes with pathological tau proteins in AD brains, confirming the co-aggregation of EFhd2 and pathological tau. Furthermore, EFhd2's coiled-coil domain mediated its self-oligomerization in vitro and its association with tau proteins in JNPL3 mouse brain extracts. The results demonstrate that EFhd2 is a novel amyloid protein associated with pathological tau proteins in AD brain and that calcium binding may regulate the formation of EFhd2's amyloid structures. Hence, EFhd2 may play an important role in the pathobiology of tau-mediated neurodegeneration.

Experimental silicification of the extremophilic Archaea Pyrococcus abyssi and Methanocaldococcus jannaschii: applications in the search for evidence of life in early Earth and extraterrestrial rocks

Hydrothermal activity was common on the early Earth and associated micro-organisms would most likely have included thermophilic to hyperthermophilic species. 3.5-3.3 billion-year-old, hydrothermally influenced rocks contain silicified microbial mats and colonies that must have been bathed in warm to hot hydrothermal emanations. Could they represent thermophilic or hyperthermophilic micro-organisms and if so, how were they preserved? We present the results of an experiment to silicify anaerobic, hyperthermophilic micro-organisms from the Archaea Domain Pyrococcus abyssi and Methanocaldococcus jannaschii, that could have lived on the early Earth. The micro-organisms were placed in a silica-saturated medium for periods up to 1 year. Pyrococcus abyssi cells were fossilized but the M. jannaschii cells lysed naturally after the exponential growth phase, apart from a few cells and cell remains, and were not silicified although their extracellular polymeric substances were. In this first simulated fossilization of archaeal strains, our results suggest that differences between species have a strong influence on the potential for different micro-organisms to be preserved by fossilization and that those found in the fossil record represent probably only a part of the original diversity. Our results have important consequences for biosignatures in hydrothermal or hydrothermally influenced deposits on Earth, as well as on early Mars, as environmental conditions were similar on the young terrestrial planets and traces of early Martian life may have been similarly preserved as silicified microfossils.

Neural anatomy of echinoid early juveniles and comparison of nervous system organization in echinoderms

The echinoderms are a phylum of marine deuterostomes characterized by the pentaradial (five fold) symmetry of their adult bodies. Due to this unusual body plan, adult echinoderms have long been excluded from comparative analyses aimed at understanding the origin and evolution of deuterostome nervous systems. Here, we investigated the neural anatomy of early juveniles of representatives of three of the five echinoderm classes: the echinoid Paracentrotus lividus, the asteroid Patiria miniata, and the holothuroid Parastichopus parvimensis. Using whole mount immunohistochemistry and confocal microscopy, we found that the nervous system of echinoid early juveniles is composed of three main structures: a basiepidermal nerve plexus, five radial nerve cords connected by a circumoral nerve ring, and peripheral nerves innervating the appendages. Our whole mount preparations further allowed us to obtain thorough descriptions of these structures and of several innervation patterns, in particular at the level of the appendages. Detailed comparisons of the echinoid juvenile nervous system with those of asteroid and holothuroid juveniles moreover supported a general conservation of the main neural structures in all three species, including at the level of the appendages. Our results support the previously proposed hypotheses for the existence of two neural units in echinoderms: one consisting of the basiepidermal nerve plexus to process sensory stimuli locally and one composed of the radial nerve cords and the peripheral nerves constituting a centralized control system. This study provides the basis for more in-depth comparisons of the echinoderm adult nervous system with those of other animals, in particular hemichordates and chordates, to address the long-standing controversies about deuterostome nervous system evolution.

PEGylated and Functionalized Aliphatic Polycarbonate Polyplex Nanoparticles for Intravenous Administration of HDAC5 siRNA in Cancer Therapy

Guanidine and morpholine functionalized aliphatic polycarbonate polymers are able to deliver efficiently histone deacetylase 5 (HDAC5) siRNA into the cytoplasm of cancer cells in vitro leading to a decrease of cell proliferation were previously developed. To allow these biodegradable and biocompatible polyplex nanoparticles to overcome the extracellular barriers and be effective in vivo after an intravenous injection, polyethylene glycol chains (PEG₇₅₀ or PEG₂₀₀₀) were grafted on the polymer structure. These nanoparticles showed an average size of about 150 nm and a slightly positive ζ-potential with complete siRNA complexation. Behavior of PEGylated and non-PEGylated polyplexes were investigated in the presence of serum, in terms of siRNA complexation (fluorescence correlation spectroscopy), size (dynamic light scattering and single-particle tracking), interaction with proteins (isothermal titration calorimetry) and cellular uptake. Surprisingly, both PEGylated and non-PEGylated formulations presented relatively good behavior in the presence of fetal bovine serum (FBS). Hemocompatibility tests showed no effect of these polyplexes on hemolysis and coagulation. In vivo biodistribution in mice was performed and showed a better siRNA accumulation at the tumor site for PEGylated polyplexes. However, cellular uptake in protein-rich conditions showed that PEGylated polyplex lost their ability to interact with biological membranes and enter into cells, showing the importance to perform in vitro investigations in physiological conditions closed to in vivo situation. In vitro, the efficiency of PEGylated nanoparticles decreases compared to non-PEGylated particles, leading to the loss of the antiproliferative effect on cancer cells.

Preservation and evolution of organic matter during experimental fossilisation of the hyperthermophilic archaea Methanocaldococcus jannaschii

Identification of the earliest traces of life is made difficult by the scarcity of the preserved microbial remains and by the alteration and potential contamination of the organic matter (OM) content of rocks. These factors can confuse interpretations of the biogenicity and syngenicity of fossilised structures and organic molecules found in ancient rocks. In order to improve our knowledge of the fossilisation processes and their effects at the molecular level, we made a preliminary study of the fate of OM during experimental fossilisation. Changes in the composition and quantity of amino acids, monosaccharides and fatty acids were followed with HPLC, GC and GC-MS analyses during 1 year of silicification of the hyperthermophilic Archaea Methanocaldococcus jannaschii. Although the cells themselves did not fossilise and the accompanying extracellular polymeric substances (EPS) did, our analyses showed that the OM initially present in both cells and EPS was uniformly preserved in the precipitated silica, with amino acids and fatty acids being the best preserved compounds. This study thus completes previous data obtained by electron microscopy investigations of simulated microbial fossilisation and can help better identification and interpretation of microbial biosignatures in both ancient rocks and in recent hydrothermal formations and sediments.

Fire and grass-bedding construction 200 thousand years ago at Border Cave, South Africa

Early plant use is seldom described in the archaeological record because of poor preservation. We report the discovery of grass bedding used to create comfortable areas for sleeping and working by people who lived in Border Cave at least 200,000 years ago. Sheaves of grass belonging to the broad-leafed Panicoideae subfamily were placed near the back of the cave on ash layers that were often remnants of bedding burned for site maintenance. This strategy is one forerunner of more-complex behavior that is archaeologically discernible from ~100,000 years ago.

Variation of Goliathus orientalis (Moser, 1909) Elytra Nanostructurations and Their Impact on Wettability

Among the different species of flower beetles, there is one of particular notoriety: the Goliath beetle. This large insect can grow up to 11 cm long and is well-known for its distinctive black and white shield. In this paper, we focus on a particular Goliathus species: G. orientalis (Moser, 1909). We investigated the variations in properties of both the black and white parts of the upper face of G. orientalis; more precisely, the variation in surface properties with respect to the wettability of these two parts. This work reveals that the white parts of the shield have a higher hydrophobic character when compared to the black regions. While the black parts are slightly hydrophobic (θ = 91 ± 5°) and relatively smooth, the white parts are highly hydrophobic (θ = 130 ± 3°) with strong water adhesion (parahydrophobic); similar to the behavior observed for rose petals. Roughness and morphology analyses revealed significant differences between the two parts, and, hence, may explain the change in wettability. The white surfaces are covered with horizontally aligned nanohairs. Interestingly, vertically aligned microhairs are also present on the white surface. Furthermore, the surfaces of the microhairs are not smooth, they contain nanogrooves that are qualitatively similar to those observed in cactus spines. The nanogrooves may have an extremely important function regarding water harvesting, as they preferentially direct the migration of water droplets; this process could be mimicked in the future to capture and guide a large volume of water.

Curing of a bisphenol E based cyanate ester using magnetic nanoparticles as an internal heat source through induction heating

We report on the control of cyclotrimerization forming a polycyanurate polymer using magnetic iron oxide nanoparticles in an alternating-current (ac) field as an internal heat source, starting from a commercially available monomer. Magnetic nanoparticles were dispersed in the monomer and catalytic system using sonication, and the mixture was subjected to an alternating magnetic field, causing the magnetic nanoparticles to dissipate the energy of the magnetic field in the form of heat. Internal heating of the particle/monomer/catalyst system was sufficient to start and sustain the polymerization reaction, producing a cyanate ester network with conversion that compared favorably to polymerization through heating in a conventional laboratory oven. The two heating methods gave similar differential scanning calorimetry temperature profiles, conversion rates, and glass transition temperatures when using the same temperature profile. The ability of magnetic nanoparticles in an ac field to drive the curing reaction should allow for other reactions forming high-temperature thermosetting polymers and for innovative ways to process such polymers.

Experimental simulation of evaporation-driven silica sinter formation and microbial silicification in hot spring systems

Evaporation of silica-rich geothermal waters is one of the main abiotic drivers of the formation of silica sinters around hot springs. An important role in sinter structural development is also played by the indigenous microbial communities, which are fossilized and eventually encased in the silica matrix. The combination of these two factors results in a wide variety of sinter structures and fabrics. Despite this, no previous experimental fossilization studies have focused on evaporative-driven silica precipitation. We present here the results of several experiments aimed at simulating the formation of sinters through evaporation. Silica solutions at different concentrations were repeatedly allowed to evaporate in both the presence and absence of the cyanobacterium Synechococcus elongatus. Without microorganisms, consecutive silica additions led to the formation of well-laminated deposits. By contrast, when microorganisms were present, they acted as reactive surfaces for heterogeneous silica particle nucleation; depending on the initial silica concentration, the deposits were then either porous with a mixture of silicified and unmineralized cells, or they formed a denser structure with a complete entombment of the cells by a thick silica crust. The deposits obtained experimentally showed numerous similarities in terms of their fabric to those previously reported for natural hot springs, demonstrating the complex interplay between abiotic and biotic processes during silica sinter growth.

Oxidative peeling of carbon black nanoparticles

We demonstrate that layered carbon black nanoparticles can be oxidatively peeledviathe reaction with potassium permanganate in sulfuric acid.

Micro- and nanoscopic observations of sexual dimorphisms in Mecynorhina polyphemus confluens (Kraatz, 1890) (Coleoptera, Cetoniidae, Goliathini) and consequences for surface wettability

In the animal kingdom, macroscopic variations in size, color, and even hairiness are frequently observed between male and female, making the sex of various species easy to discern. In the case of insects, similar variances also exist. While direct observation is a quick and efficient way to differentiate between sexes, there are also variations which are unseen to the naked eye and occur on a micro- or nanoscopic scale. Sometimes, these micro/nanoscopic variations can lead to significant variations in surface properties as a function of sex. Such is the case for the Mecynorhina polyphemus confluens (Kraatz, 1890). In this work, we characterize these micro- and nanoscale differences, and describe their impact on the surface properties (e.g. wettability). It is found that water interacts quite differently with the surface of the cuticle of Mecynorhina polyphenus confluens, depending on the specimen sex. On a female, water spreads readily across the elytra indicating hydrophilic behavior. However, on the surface of the male elytra, strong hydrophobicity is observed. Microscopic observations reveal differences in microscale surface morphology across the male and female cuticle. These observations contribute to a better, global understanding of the wettability behavior observed on M. polyphemus confluens.

Variations in surface structures and wettability in the genus Pachnoda Burmeister

In order to grow and live, all species need access to water and often the ability to control their intake thereof. Among species throughout the world, several animals and plants are known for unique surface patterns and features that influence their wettability in such a way that water is always readily accessible, even in arid and hot climates. In this work, the authors report a journey into the genus Pachnoda, studying 12 species or subspecies to compare their surface properties and wettabilities. This work reveals exceptional natural surface morphologies based on a honeycomb structure with significant variations depending on the Pachnoda genus. Even if the materials present on their surface are intrinsically hydrophilic, some of the species have parahydrophobic properties with apparent contact angles of up to 145° and extremely strong water adhesion. Only the Cassie–Baxter equation can explain these results indicating the presence of trapped air within these surface structures when a liquid, such as water, makes contact. Among the species explored here, water hydrophobicity and adhesion are controlled by the dimensions of the honeycombs, the presence of lamellar structures on the border of these features and the presence of roughness in their internal structures.

The stereomicroscope and scanning electron microscope comparison of false starts bones produced by an oscillating autopsy saw

In forensic anthropology, saw mark analysis plays an important role in cases of criminal dismemberment. Autopsy saw is not used by the perpetrator in cases of dismemberment, but the forensic pathologist may accidentally create false starts with this saw during an autopsy, especially while sampling bones for further analysis, and these autopsy false starts can be confused with false starts produced by the offender. In this study, the characteristics of 20 false starts were compared using stereomicroscopy (SM) and scanning electron microscopy (SEM). These bone false starts were selected at random from a previous study of 100 false starts created by an electrical oscillating autopsy saw on human femoral bones. That study had enabled the categorization of the lesions into two groups ("superficial group" and "deep group") with a 0.52 mm depth cut off, based on the dramatic differences in lesion characteristics between these two groups. In the current study, SEM confirmed the characteristics of the false starts (walls and profile shapes, striae, bone islands and bone debris were studied), and above all explained the mechanism whereby oval bone islands in deep lesions are formed. Bone islands are due to the horizontal and vertical movement of the oscillating autopsy blade.

Efficient flotation separation approach of apatite from calcite for phosphate up-grading using phosphorylated starch macromolecules as a selective depressant

Physico-chemical similarities of surface proprieties of calcite and apatite make their separation challenging. Effective flotation separation requires sustainable depressants to mitigate environmental consequences associated with traditional chemical reagents. Here, for the first time we explore the potential of phosphorylated starch (PS) derived from potato waste as a green and effective depressant. Starch was modified using a straightforward phosphorylation process, resulting in PS with a remarkable charge density exceeding 6000 mmol kg-1. The PS was then evaluated for its ability to depress apatite, enhancing the separation efficiency of apatite from calcite in phosphate rock beneficiation via reverse flotation. Micro-flotation experiments revealed PS's distinct depression effect on apatite while minimally impacting calcite. Floatability rates of apatite and calcite were 90.45 % and 92.68 %, respectively. Introducing 10 mg/g PS drastically reduced apatite recovery to <19 %, while calcite recovery remained at 78.80 %. The bench-scale flotation tests demonstrated an upgrading of the phosphate rock to 70,64 % Bone Phosphate of Lime (BPL) with a yield of 89,41 %. Mechanistic studies employing zeta potential (ZP), and wettability analysis elucidated the depression mechanism. Apatite retained hydrophilicity post-PS addition and conditioning with ester, while calcite-acquired hydrophobicity even in the presence of PS. Furthermore, PS exhibited substantial adsorption onto the apatite surface through chemical reactions involving the phosphate groups and the activated calcium sites on the apatite. Overall, PS stands out as a promising, eco-friendly, and remarkably efficient depressant for separating apatite from calcite through flotation.

Non-canonical role for the BAF complex subunit DPF3 in mitosis and ciliogenesis

DPF3, along with other subunits, is a well-known component of the BAF chromatin remodeling complex, which plays a key role in regulating chromatin remodeling activity and gene expression. Here, we elucidated a non-canonical localization and role for DPF3. We showed that DPF3 dynamically localizes to the centriolar satellites in interphase and to the centrosome, spindle midzone and bridging fiber area, and midbodies during mitosis. Loss of DPF3 causes kinetochore fiber instability, unstable kinetochore-microtubule attachment and defects in chromosome alignment, resulting in altered mitotic progression, cell death and genomic instability. In addition, we also demonstrated that DPF3 localizes to centriolar satellites at the base of primary cilia and is required for ciliogenesis by regulating axoneme extension. Taken together, these findings uncover a moonlighting dual function for DPF3 during mitosis and ciliogenesis.

Application of array tomography to elucidate nuclear clustering architecture in giant-feeding cells induced by root-knot nematodes

Plant-parasitic nematodes like root-knot nematodes (RKN; Meloidogyne spp.) cause great losses in agriculture by inducing root swellings, named galls, in host roots disturbing plant growth and development. Previous two-dimensional studies using different microscopy techniques revealed the presence of numerous nuclear clusters in nematode-induced giant cells within galls. Here, we show in three dimensions (3D) that nuclear clustering occurring in giant cells is revealed to be much more complex, illustrating subclusters built of multiple nuclear lobes. These nuclear subclusters are unveiled to be interconnected and likely communicate via nucleotubes, highlighting the potential relevance of this nuclear transfer for disease. In addition, microtubules and microtubule organizing centers are profusely present between the densely packed nuclear lobes, suggesting that the cytoskeleton might be involved in anchoring nuclear clusters in giant cells. This study illustrates that it is possible to apply volume electron microscopy (EM) approaches such as array tomography (AT) to roots infected by nematodes using basic equipment found in most EM facilities. The application of AT was valuable to observe the cellular ultrastructure in 3D, revealing the remarkable nuclear architecture of giant cells in the model host Arabidopsis thaliana. The discovery of nucleotubes, as a unique component of nuclear clusters present in giant cells, can be potentially exploited as a novel strategy to develop alternative approaches for RKN control in crop species.