CT-derived body composition and differential association with age, TNM stage and systemic inflammation in patients with colon cancer.

Low skeletal muscle index/density (SMI/SMD) is prevalent in cancer, adversely prognostic and associated with tumour stage and the systemic inflammatory response (SIR). Age and SMI/SMD has not been widely studied. The present study analyses the association between age and SMI/SMD after adjustment for other clinicopathological factors. Patients undergoing resectional surgery for TNM Stage I-III disease within the West of Scotland between 2011 and 2014 were identified. A single CT slice was obtained from each patients staging CT scan. SMI and SMD were stratified normal/abnormal. The SIR was stratified using Systemic Inflammatory Grade (SIG). When stratified by age (< 50/50s/60s/70s/80+), 39%/38%/48%/62%/74% and 27%/48%/64%/82%/92% of patients had a low SMI and SMD respectively (both p < 0.001). Older age (OR 1.47, p < 0.001), female sex (OR 1.32, p = 0.032), lower socioeconomic deprivation (OR 1.15, p = 0.004), higher ASA (OR 1.30, p = 0.019), emergency presentation (OR 1.82, p = 0.003), lower BMI (OR 0.67, p < 0.002) and higher SIG (OR 1.23, p < 0.001) were independently associated with low SMI. Older age (OR 2.28, p < 0.001), female sex (OR 1.38, p = 0.038), higher ASA (OR 1.92, p < 0.001), emergency presentation (OR 1.71, p = 0.023), and higher SIG (OR 1.37, p < 0.001) were independently associated with lower SMD. Tumour factors were not independently associated with either SMI/SMD. Age was a major factor associated with low SMI/SMD in patients with colon cancer. Therefore, in these patients it is likely that this represents largely constitutional body composition as opposed to being a disease mediated effect. Adjustment for age is required when considering the cancer mediated effect on SMI/SMD in patients with colon cancer.

Temporally resolved proteomics identifies nidogen-2 as a cotarget in pancreatic cancer that modulates fibrosis and therapy response.

Pancreatic ductal adenocarcinoma (PDAC) is characterized by increasing fibrosis, which can enhance tumor progression and spread. Here, we undertook an unbiased temporal assessment of the matrisome of the highly metastatic KPC (Pdx1-Cre, LSL-KrasG12D/+, LSL-Trp53R172H/+) and poorly metastatic KPflC (Pdx1-Cre, LSL-KrasG12D/+, Trp53fl/+) genetically engineered mouse models of pancreatic cancer using mass spectrometry proteomics. Our assessment at early-, mid-, and late-stage disease reveals an increased abundance of nidogen-2 (NID2) in the KPC model compared to KPflC, with further validation showing that NID2 is primarily expressed by cancer-associated fibroblasts (CAFs). Using biomechanical assessments, second harmonic generation imaging, and birefringence analysis, we show that NID2 reduction by CRISPR interference (CRISPRi) in CAFs reduces stiffness and matrix remodeling in three-dimensional models, leading to impaired cancer cell invasion. Intravital imaging revealed improved vascular patency in live NID2-depleted tumors, with enhanced response to gemcitabine/Abraxane. In orthotopic models, NID2 CRISPRi tumors had less liver metastasis and increased survival, highlighting NID2 as a potential PDAC cotarget.

The local ordering of polar solvents around crystalline carbon nitride nanosheets in solution.

The crystalline graphitic carbon nitride, poly-triazine imide (PTI) is highly unusual among layered materials since it is spontaneously soluble in aprotic, polar solvents including dimethylformamide (DMF). The PTI material consists of layers of carbon nitride intercalated with LiBr. When dissolved, the resulting solutions consist of dissolved, luminescent single to multilayer nanosheets of around 60-125 nm in diameter and Li+ and Br- ions originating from the intercalating salt. To understand this unique solubility, the structure of these solutions has been investigated by high-energy X-ray and neutron diffraction. Although the diffraction patterns are dominated by inter-solvent correlations there are clear differences between the X-ray diffraction data of the PTI solution and the solvent in the 4-6 Å-1 range, with real space differences persisting to at least 10 Å. Structural modelling using both neutron and X-ray datasets as a constraint reveal the formation of distinct, dense solvation shells surrounding the nanoparticles with a layer of Br-close to the PTI-solvent interface. This solvent ordering provides a configuration that is energetically favourable underpinning thermodynamically driven PTI dissolution. This article is part of the theme issue 'Exploring the length scales, timescales and chemistry of challenging materials (Part 2)'.

Amphoteric dissolution of two-dimensional polytriazine imide carbon nitrides in water.

Crystalline two-dimensional carbon nitrides with polytriazine imide (PTI) structure are shown to act amphoterically, buffering both HCl and NaOH aqueous solutions, resulting in charged PTI layers that dissolve spontaneously in their aqueous media, particularly for the alkaline solutions. This provides a low energy, green route to their scalable solution processing. Protonation in acid is shown to occur at pyridinic nitrogens, stabilized by adjacent triazines, whereas deprotonation in base occurs primarily at basal plane NH bridges, although NH2 edge deprotonation is competitive. We conclude that mildly acidic or basic pHs are necessary to provide sufficient net charge on the nanosheets to promote dissolution, while avoiding high ion concentrations which screen the repulsion of like-charged PTI sheets in solution. This article is part of the theme issue 'Exploring the length scales, timescales and chemistry of challenging materials (Part 2)'.

Nanomechanical properties of SSTSAA microcrystals are dominated by the inter-sheet packing.

Amyloid fibrils have been associated with human disease for many decades, but it has also become apparent that they play a functional, non-disease-related role in e.g. bacteria and mammals. Moreover, they have been shown to possess interesting mechanical properties that can be harnessed for future man-made applications. Here, the mechanical behaviour of SSTSAA microcrystals has been investigated. The SSTSAA peptide organization in these microcrystals has been related to that in the corresponding amyloid fibrils. Using high-pressure X-ray diffraction experiments, the bulk modulus K, which is the reciprocal of the compressibility ß, has been calculated to be 2.48 GPa. This indicates that the fibrils are tightly packed, although the packing of most native globular proteins is even better. It is shown that the value of the bulk modulus is mainly determined by the compression along the c-axis, that relates to the inter-sheet distance in the fibrils. These findings corroborate earlier data obtained by AFM and molecular dynamics simulations that showed that mechanical resistance varies according to the direction of the applied strain, which can be related to packing and hydrogen bond contributions. Pressure experiments provide complementary information to these techniques and help to acquire a full mechanical characterization of biomolecular assemblies. This article is part of the theme issue 'Exploring the length scales, timescales and chemistry of challenging materials (Part 2)'.

Plasmodium falciparum formins are essential for invasion and sexual stage development.

The malaria parasite uses actin-based mechanisms throughout its lifecycle to control a range of biological processes including intracellular trafficking, gene regulation, parasite motility and invasion. In this work we assign functions to the Plasmodium falciparum formins 1 and 2 (FRM1 and FRM2) proteins in asexual and sexual blood stage development. We show that FRM1 is essential for merozoite invasion and FRM2 is required for efficient cell division. We also observed divergent functions for FRM1 and FRM2 in gametocyte development. Conditional deletion of FRM1 leads to a delay in gametocyte stage progression. We show that FRM2 controls the actin and microtubule cytoskeletons in developing gametocytes, with premature removal of the protein resulting in a loss of transmissible stage V gametocytes. Lastly, we show that targeting formin proteins with the small molecule inhibitor of formin homology domain 2 (SMIFH2) leads to a multistage block in asexual and sexual stage parasite development.

Understanding the emergence of the boson peak in molecular glasses.

A common feature of glasses is the "boson peak", observed as an excess in the heat capacity over the crystal or as an additional peak in the terahertz vibrational spectrum. The microscopic origins of this peak are not well understood; the emergence of locally ordered structures has been put forward as a possible candidate. Here, we show that depolarised Raman scattering in liquids consisting of highly symmetric molecules can be used to isolate the boson peak, allowing its detailed observation from the liquid into the glass. The boson peak in the vibrational spectrum matches the excess heat capacity. As the boson peak intensifies on cooling, wide-angle x-ray scattering shows the simultaneous appearance of a pre-peak due to molecular clusters consisting of circa 20 molecules. Atomistic molecular dynamics simulations indicate that these are caused by over-coordinated molecules. These findings represent an essential step toward our understanding of the physics of vitrification.

Platinum deposition on functionalised graphene for corrosion resistant oxygen reduction electrodes.

Graphene-related materials are promising supports for electrocatalysts due to their stability and high surface area. Their innate surface chemistries can be controlled and tuned via functionalisation to improve the stability of both the carbon support and the metal catalyst. Functionalised graphenes were prepared using either aryl diazonium functionalisation or non-destructive chemical reduction, to provide groups adapted for platinum deposition. XPS and TGA-MS measurements confirmed the presence of polyethyleneglycol and sulfur-containing functional groups, and provided consistent values for the extent of the reactions. The deposited platinum nanoparticles obtained were consistently around 2 nm via reductive chemistry and around 4 nm via the diazonium route. Although these graphene-supported electrocatalysts provided a lower electrochemical surface area (ECSA), functionalised samples showed enhanced specific activity compared to a commercial platinum/carbon black system. Accelerated stress testing (AST) showed improved durability for the functionalised graphenes compared to the non-functionalised materials, attributed to edge passivation and catalyst particle anchoring.

Paraspeckle subnuclear bodies depend on dynamic heterodimerisation of DBHS RNA-binding proteins via their structured domains.

RNA-binding proteins of the DBHS (Drosophila Behavior Human Splicing) family, NONO, SFPQ, and PSPC1 have numerous roles in genome stability and transcriptional and posttranscriptional regulation. Critical to DBHS activity is their recruitment to distinct subnuclear locations, for example, paraspeckle condensates, where DBHS proteins bind to the long noncoding RNA NEAT1 in the first essential step in paraspeckle formation. To carry out their diverse roles, DBHS proteins form homodimers and heterodimers, but how this dimerization influences DBHS localization and function is unknown. Here, we present an inducible GFP-NONO stable cell line and use it for live-cell 3D-structured illumination microscopy, revealing paraspeckles with dynamic, twisted elongated structures. Using siRNA knockdowns, we show these labeled paraspeckles consist of GFP-NONO/endogenous SFPQ dimers and that GFP-NONO localization to paraspeckles depends on endogenous SFPQ. Using purified proteins, we confirm that partner swapping between NONO and SFPQ occurs readily in vitro. Crystallographic analysis of the NONO-SFPQ heterodimer reveals conformational differences to the other DBHS dimer structures, which may contribute to partner preference, RNA specificity, and subnuclear localization. Thus overall, our study suggests heterodimer partner availability is crucial for NONO subnuclear distribution and helps explain the complexity of both DBHS protein and paraspeckle dynamics through imaging and structural approaches.

Targeting of microvillus protein Eps8 by the NleH effector kinases from enteropathogenic E. coli.

Attaching and effacing (AE) lesion formation on enterocytes by enteropathogenic Escherichia coli (EPEC) requires the EPEC type III secretion system (T3SS). Two T3SS effectors injected into the host cell during infection are the atypical kinases, NleH1 and NleH2. However, the host targets of NleH1 and NleH2 kinase activity during infection have not been reported. Here phosphoproteomics identified Ser775 in the microvillus protein Eps8 as a bona fide target of NleH1 and NleH2 phosphorylation. Both kinases interacted with Eps8 through previously unrecognized, noncanonical "proline-rich" motifs, PxxDY, that bound the Src Homology 3 (SH3) domain of Eps8. Structural analysis of the Eps8 SH3 domain bound to a peptide containing one of the proline-rich motifs from NleH showed that the N-terminal part of the peptide adopts a type II polyproline helix, and its C-terminal "DY" segment makes multiple contacts with the SH3 domain. Ser775 phosphorylation by NleH1 or NleH2 hindered Eps8 bundling activity and drove dispersal of Eps8 from the AE lesion during EPEC infection. This finding suggested that NleH1 and NleH2 altered the cellular localization of Eps8 and the cytoskeletal composition of AE lesions during EPEC infection.

Shock-formed carbon materials with intergrown sp3- and sp2-bonded nanostructured units.

Studies of dense carbon materials formed by bolide impacts or produced by laboratory compression provide key information on the high-pressure behavior of carbon and for identifying and designing unique structures for technological applications. However, a major obstacle to studying and designing these materials is an incomplete understanding of their fundamental structures. Here, we report the remarkable structural diversity of cubic/hexagonally (c/h) stacked diamond and their association with diamond-graphite nanocomposites containing sp3-/sp2-bonding patterns, i.e., diaphites, from hard carbon materials formed by shock impact of graphite in the Canyon Diablo iron meteorite. We show evidence for a range of intergrowth types and nanostructures containing unusually short (0.31 nm) graphene spacings and demonstrate that previously neglected or misinterpreted Raman bands can be associated with diaphite structures. Our study provides a structural understanding of the material known as lonsdaleite, previously described as hexagonal diamond, and extends this understanding to other natural and synthetic ultrahard carbon phases. The unique three-dimensional carbon architectures encountered in shock-formed samples can place constraints on the pressure-temperature conditions experienced during an impact and provide exceptional opportunities to engineer the properties of carbon nanocomposite materials and phase assemblages.

Disentangling water, ion and polymer dynamics in an anion exchange membrane.

Semipermeable polymeric anion exchange membranes are essential for separation, filtration and energy conversion technologies including reverse electrodialysis systems that produce energy from salinity gradients, fuel cells to generate electrical power from the electrochemical reaction between hydrogen and oxygen, and water electrolyser systems that provide H2 fuel. Anion exchange membrane fuel cells and anion exchange membrane water electrolysers rely on the membrane to transport OH- ions between the cathode and anode in a process that involves cooperative interactions with H2O molecules and polymer dynamics. Understanding and controlling the interactions between the relaxation and diffusional processes pose a main scientific and critical membrane design challenge. Here quasi-elastic neutron scattering is applied over a wide range of timescales (100-103 ps) to disentangle the water, polymer relaxation and OH- diffusional dynamics in commercially available anion exchange membranes (Fumatech FAD-55) designed for selective anion transport across different technology platforms, using the concept of serial decoupling of relaxation and diffusional processes to analyse the data. Preliminary data are also reported for a laboratory-prepared anion exchange membrane especially designed for fuel cell applications.

Monodisperse Carbon Nitride Nanosheets as Multifunctional Additives for Efficient and Durable Perovskite Solar Cells.

Two-dimensional (2D) materials are promising components for defect passivation of metal halide perovskites. Unfortunately, commonly used polydisperse liquid-exfoliated 2D materials generally suffer from heterogeneous structures and properties while incorporated into perovskite films. We introduce monodisperse multifunctional 2D crystalline carbon nitride, poly(triazine imide) (PTI), as an effective defect passivation agent in perovskite films via typical solution processing. Incorporation of PTI into perovskite film can be readily attained by simple solution mixing of PTI dispersions with perovskite precursor solutions, resulting in the highly selective distribution of PTI localized at the defective crystal grain boundaries and layer interfaces in the functional perovskite layer. Several chemical, optical, and electronic characterizations, in conjunction with density functional theory calculations, reveal multiple beneficial roles from PTI: passivation of undercoordinated organic cations at the surface of perovskite crystal, suppression of ion migration by blocking diffusion channels, and prevention of hole quenching at perovskite/SnO2 interfaces. Consequently, a noticeably improved power conversion efficiency is achieved in perovskite solar cells, accompanied with promoted stability under humid air and thermal stress. Our strategy highlights the potential of judiciously designed 2D materials as a simple-to-implement material for various optoelectronic devices, including solar cells, based on hybrid perovskites.

Scalable Sacrificial Templating to Increase Porosity and Platinum Utilisation in Graphene-Based Polymer Electrolyte Fuel Cell Electrodes.

Polymer electrolyte fuel cells hold great promise for a range of applications but require advances in durability for widespread commercial uptake. Corrosion of the carbon support is one of the main degradation pathways; hence, corrosion-resilient graphene has been widely suggested as an alternative to traditional carbon black. However, the performance of bulk graphene-based electrodes is typically lower than that of commercial carbon black due to their stacking effects. This article reports a simple, scalable and non-destructive method through which the pore structure and platinum utilisation of graphene-based membrane electrode assemblies can be significantly improved. Urea is incorporated into the catalyst ink before deposition, and is then simply removed from the catalyst layer after spraying by submerging the electrode in water. This additive hinders graphene restacking and increases porosity, resulting in a significant increase in Pt utilisation and current density. This technique does not require harsh template etching and it represents a pathway to significantly improve graphene-based electrodes by introducing hierarchical porosity using scalable liquid processes.

Progress in neutron techniques: towards improved polymer electrolyte membranes for energy devices.

Design and implementation of advanced membrane formulations for selective transport of ions and molecular species are critical for creating the next generations of fuel cells and separation devices. It is necessary to understand the detailed transport mechanisms over time- and length-scales relevant to the device operation, both in laboratory models and in working systems under realistic operational conditions. Neutron scattering techniques including quasi-elastic neutron scattering, reflectivity and imaging are implemented at beamline stations at reactor and spallation source facilities worldwide. With the advent of new and improved instrument design, detector methodology, source characteristics and data analysis protocols, these neutron scattering techniques are emerging as a primary tool for research to design, evaluate and implement advanced membrane technologies for fuel cell and separation devices. Here we describe these techniques and their development and implementation at the ILL reactor source (Institut Laue-Langevin, Grenoble, France) and ISIS Neutron and Muon Spallation source (Harwell Science and Technology Campus, UK) as examples. We also mention similar developments under way at other facilities worldwide, and describe approaches such as combining optical with neutron Raman scattering and x-ray absorption with neutron imaging and tomography, and carrying out such experiments in specialised fuel cells designed to mimic as closely possible actualoperandoconditions. These experiments and research projects will play a key role in enabling and testing new membrane formulations for efficient and sustainable energy production/conversion and separations technologies.

Complementation in trans of Porphyromonas gingivalis Lipopolysaccharide Biosynthetic Mutants Demonstrates Lipopolysaccharide Exchange.

Porphyromonas gingivalis, a bacterial pathogen contributing to human periodontitis, exports and anchors cargo proteins to its surface, enabling the production of black pigmentation using a type IX secretion system (T9SS) and conjugation to anionic lipopolysaccharide (A-LPS). To determine whether T9SS components need to be assembled in situ for correct secretion and A-LPS modification of cargo proteins, combinations of nonpigmented mutants lacking A-LPS or a T9SS component were mixed to investigate in trans complementation. Reacquisition of pigmentation occurred only between an A-LPS mutant and a T9SS mutant, which coincided with A-LPS modification of cargo proteins detected by Western blotting and coimmunoprecipitation/quantitative mass spectrometry. Complementation also occurred using an A-LPS mutant mixed with outer membrane vesicles (OMVs) or purified A-LPS. Fluorescence experiments demonstrated that OMVs can fuse with and transfer lipid to P. gingivalis, leading to the conclusion that complementation of T9SS function occurred through A-LPS transfer between cells. None of the two-strain crosses involving only the five T9SS OM component mutants produced black pigmentation, implying that the OM proteins cannot be transferred in a manner that restores function and surface pigmentation, and hence, a more ordered temporal in situ assembly of T9SS components may be required. Our results show that LPS can be transferred between cells or between cells and OMVs to complement deficiencies in LPS biosynthesis and hemin-related pigmentation to reveal a potentially new mechanism by which the oral microbial community is modulated to produce clinical consequences in the human host.IMPORTANCEPorphyromonas gingivalis is a keystone pathogen contributing to periodontitis in humans, leading to tooth loss. The oral microbiota is essential in this pathogenic process and changes from predominantly Gram-positive (health) to predominantly Gram-negative (disease) species. P. gingivalis uses its type IX secretion system (T9SS) to secrete and conjugate virulence proteins to anionic lipopolysaccharide (A-LPS). This study investigated whether components of this secretion system could be complemented and found that it was possible for A-LPS biosynthetic mutants to be complemented in trans both by strains that had the A-LPS on the cell surface and by exogenous sources of A-LPS. This is the first known example of LPS exchange in a human bacterial pathogen which causes disease through complex microbiota-host interactions.

Interactions between Cellulose and (1,3;1,4)-ß-glucans and Arabinoxylans in the Regenerating Wall of Suspension Culture Cells of the Ryegrass Lolium multiflorum.

Plant cell walls (PCWs) form the outer barrier of cells that give the plant strength and directly interact with the environment and other cells in the plant. PCWs are composed of several polysaccharides, of which cellulose forms the main fibrillar network. Enmeshed between these fibrils of cellulose are non-cellulosic polysaccharides (NCPs), pectins, and proteins. This study investigates the sequence, timing, patterning, and architecture of cell wall polysaccharide regeneration in suspension culture cells (SCC) of the grass species Lolium multiflorum (Lolium). Confocal, superresolution, and electron microscopies were used in combination with cytochemical labeling to investigate polysaccharide deposition in SCC after protoplasting. Cellulose was the first polysaccharide observed, followed shortly thereafter by (1,3;1,4)-ß-glucan, which is also known as mixed-linkage glucan (MLG), arabinoxylan (AX), and callose. Cellulose formed fibrils with AX and produced a filamentous-like network, whereas MLG formed punctate patches. Using colocalization analysis, cellulose and AX were shown to interact during early stages of wall generation, but this interaction reduced over time as the wall matured. AX and MLG interactions increased slightly over time, but cellulose and MLG were not seen to interact. Callose initially formed patches that were randomly positioned on the protoplast surface. There was no consistency in size or location over time. The architecture observed via superresolution microscopy showed similarities to the biophysical maps produced using atomic force microscopy and can give insight into the role of polysaccharides in PCWs.