Short-chain fatty acid level and field cancerization show opposing associations with enteroendocrine cell number and neuropilin expression in patients with colorectal adenoma

BACKGROUND: Previous reports have suggested that the VEGF receptor neuropilin-1 (NRP-1) is expressed in a singly dispersed subpopulation of cells in the normal colonic epithelium, but that expression becomes dysregulated during colorectal carcinogenesis, with higher levels in tumour suggestive of a poor prognosis. We noted that the spatial distribution and morphology if NRP-1 expressing cells resembles that of enteroendocrine cells (EEC) which are altered in response to disease state including cancer and irritable bowel syndrome (IBS). We have shown that NRP-1 is down-regulated by butyrate in colon cancer cell lines in vitro and we hypothesized that butyrate produced in the lumen would have an analogous effect on the colon mucosa in vivo. Therefore we sought to investigate whether NRP-1 is expressed in EEC and how NRP-1 and EEC respond to butyrate and other short-chain fatty acids (SCFA - principally acetate and propionate). Additionally we sought to assess whether there is a field effect around adenomas. METHODOLOGY: Biopsies were collected at the mid-sigmoid, at the adenoma and at the contralateral wall (field) of 28 subjects during endoscopy. Samples were fixed for IHC and stained for either NRP-1 or for chromogranin A (CgA), a marker of EEC. Stool sampling was undertaken to assess individuals' butyrate, acetate and propionate levels. RESULT: NRP-1 expression was inversely related to SCFA concentration at the colon landmark (mid-sigmoid), but expression was lower and not related to SCFA concentration at the field. Likewise CgA+ cell number was also inversely related to SCFA at the landmark, but was lower and unresponsive at the field. Crypt cellularity was unaltered by field effect. A colocalisation analysis showed only a small subset of NRP-1 localised with CgA. Adenomas showed extensive, weaker staining for NRP-1 which contrastingly correlated positively with butyrate level. Field effects cause this relationship to be lost. Adenoma tissue shows dissociation of the co-regulation of NRP-1 and EEC. CONCLUSION: NRP-1 is inversely associated with levels of butyrate and other SCFA in vivo and is expressed in a subset of CgA expressing cells. EEC number is related to butyrate level in the same way

Development of tools to automate quantitative analysis of radiation damage in SAXS experiments

Biological small-angle X-ray scattering (SAXS) is an increasingly popular technique used to obtain nanoscale structural information on macromolecules in solution. However, radiation damage to the samples limits the amount of useful data that can be collected from a single sample. In contrast to the extensive analytical resources available for macromolecular crystallography (MX), there are relatively few tools to quantitate radiation damage for SAXS, some of which require a significant level of manual characterization, with the potential of leading to conflicting results from different studies. Here, computational tools have been developed to automate and standardize radiation damage analysis for SAXS data. RADDOSE-3D, a dose calculation software utility originally written for MX experiments, has been extended to account for the cylindrical geometry of the capillary tube, the liquid composition of the sample and the attenuation of the beam by the capillary material to allow doses to be calculated for many SAXS experiments. Furthermore, a library has been written to visualize and explore the pairwise similarity of frames. The calculated dose for the frame at which three subsequent frames are determined to be dissimilar is defined as the radiation damage onset threshold (RDOT). Analysis of RDOTs has been used to compare the efficacy of radioprotectant compounds to extend the useful lifetime of SAXS samples. Comparison of the RDOTs shows that, for radioprotectant compounds at 5 and 10 mM concentration, glycerol is the most effective compound. However, at 1 and 2 mM concentrations, di­thio­threitol (DTT) appears to be most effective. Our newly developed visualization library contains methods that highlight the unusual radiation damage results given by SAXS data collected using higher concentrations of DTT: these observations should pave the way to the development of more sophisticated frame merging strategies

Green Propellant Infusion Mission Program Development and Technology Maturation

The NASA Space Technology Mission Directorate's (STMD) Green Propellant Infusion Mission (GPIM) Technology Demonstration Mission (TDM) is comprised of a cross-cutting team of domestic spacecraft propulsion and storable green propellant technology experts. This TDM is led by Ball Aerospace & Technologies Corp. (BATC), who will use their BCP- 100 spacecraft to carry a propulsion system payload consisting of one 22 N thruster for primary divert (DeltaV) maneuvers and four 1 N thrusters for attitude control, in a flight demonstration of the AF-M315E technology. The GPIM project has technology infusion team members from all three major market sectors: Industry, NASA, and the Department of Defense (DoD). The GPIM project team includes BATC, includes Aerojet Rocketdyne (AR), Air Force Research Laboratory, Aerospace Systems Directorate, Edwards AFB (AFRL), NASA Glenn Research Center (GRC), NASA Kennedy Space Center (KSC), and NASA Goddard Space Flight Center (GSFC). STMD programmatic and technology oversight is provided by NASA Marshall Space Flight Center. The GPIM project shall fly an operational AF-M315E green propulsion subsystem on a Ball-built BCP-100 spacecraft

A study protocol to investigate the relationship between dietary fibre intake and fermentation, colon cell turnover, global protein acetylation and early carcinogenesis: the FACT study

Background: A number of studies, notably EPIC, have shown a descrease in colorectal cancer risk associated with increased fibre consumption. Whilst the underlying mechanisms are likely to be multifactorial, production of the short-chain fatty-acid butyrate fro butyratye is frequently cited as a major potential contributor to the effect. Butyrate inhibits histone deacetylases, which work on a wide range of proteins over and above histones. We therefore hypothesized that alterations in the acetylated proteome may be associated with a cancer risk phenotype in the colorectal mucosa, and that such alterations are candidate biomarkers for effectiveness of fibre interventions in cancer prevention. Methods an design: There are two principal arms to this study: (i) a cross-sectional study (FACT OBS) of 90 subjects recruited from gastroenterology clinics and; (ii) an intervention trial in 40 subjects with an 8 week high fibre intervention. In both studies the principal goal is to investigate a link between fibre intake, SCFA production and global protein acetylation. The primary measure is level of faecal butyrate, which it is hoped will be elevated by moving subjects to a high fibre diet. Fibre intakes will be estimated in the cross-sectional group using the EPIC Food Frequency Questionnaire. Subsidiary measures of the effect of butyrate on colon mucosal function and precancerous phenotype will include measures of apoptosis, apoptotic regulators cell cycle and cell division. Discussion: This study will provide a new level of mechanistic data on alterations in the functional proteome in response to the colon microenvironment which may underwrite the observed cancer preventive effect of fibre. The study may yield novel candidate biomarkers of fibre fermentation and colon mucosal function

Wiggle-match radiocarbon dating of the Taupo eruption

The Taupo eruption deposit is an isochronous marker bed that spans much of New Zealand’s North Island and pre-dates human arrival. Holdaway et al. (2018, Nature Comms 9, 4110) propose that the current Taupo eruption date is inaccurate and that the eruption occurred “…decades to two centuries…” after the published wiggle-match estimate of 232 ± 10 CE (2 s.d.) derived from a tanekaha (Phyllocladus trichomanoides) tree at the Pureora buried forest site (Hogg et al. 2012, The Holocene 22, 439-449). Holdaway et al. (2018) propose that trees growing at Pureora (and other near-source areas) that were killed and buried by the climactic ignimbrite event were affected by ¹⁴C-depleted (magmatic) CO₂. Holdaway et al.'s (2018) proposal utilises a wide range of published ¹⁴C data, but their work results in assertions that are implausible. Four parts to their hypothesis are considered here

Experimental Wind Characterization with the SuperCam Microphone under a Simulated martian Atmosphere

Located on top of the mast of the Mars 2020 Perseverance rover, the SuperCam instrument suite includes a microphone to record audible sounds from 100 Hz to 10 kHz on the surface of Mars. It will support SuperCam’s Laser-Induced Breakdown Spectroscopy investigation by recording laser-induced shock-waves but it will also record aeroacoustic noise generated by wind flowing past the microphone. This experimental study was conducted in the Aarhus planetary wind-tunnel under low CO2 pressure with wind generated at several velocities. It focused on understanding the wind-induced acoustic signal measured by microphones instrumented in a real scale model of the rover mast as a function of the wind speed and wind orientation. Acoustic spectra recorded under a wind flow show that the low-frequency range of the microphone signal is mainly influenced by the wind velocity. In contrast, the higher frequency range is seen to depend on the wind direction relative to the microphone. On the one hand, for the wind conditions tested inside the tunnel, it is shown that the Root Mean Square of the pressure, computed over the 100 Hz to 500 Hz frequency range, is proportional to the dynamic pressure. Therefore, the SuperCam microphone will be able to estimate the wind speed, considering an in situ cross-calibration with the Mars Environmental Dynamic Analyzer. On the other hand, for a given wind speed, it is observed that the root mean square of the pressure, computed over the 500 Hz to 2000 Hz frequency range, is at its minimum when the microphone is facing the wind whereas it is at its maximum when the microphone is pointing downwind. Hence, a full 360° rotation of the mast in azimuth in parallel with sound recording can be used to retrieve the wind direction. We demonstrate that the SuperCam Microphone has a priori the potential to determine both the speed and the direction of the wind on Mars, thus contributing to atmospheric science investigations

Keratin 8 expression in colon cancer associates with low faecal butyrate levels

<p>Abstract</p> <p>Background</p> <p>Butyrate has been implicated in the mechanistic basis of the prevention of colorectal cancer by dietary fibre. Numerous in vitro studies have shown that butyrate regulates cell cycle and cell death. More recently we have shown that butyrate also regulates the integrity of the intermediate filament (IF) cytoskeleton <it>in vitro</it>. These and other data suggest a link between the role of diet and the implication of a central role for the keratin 8 (K8) as guardian of the colorectal epithelium.</p> <p>Methods</p> <p>In this cross-sectional study possible links between butyrate levels, field effects and keratin expression in cancer were addressed directly by analysing how levels of expression of the IF protein K8 in tumours, in adjacent fields and at a distant landmark site may be affected by the level of butyrate in the colon microenvironment. An immunohistochemical scoring protocol for K8 was developed and applied to samples, findings were further tested by immunoblotting.</p> <p>Results</p> <p>Levels of K8 in colorectal tumours are lower in subjects with higher levels of faecal butyrate. Immunoblotting supported this finding.Although there were no significant relationships with butyrate on the non-tumour tissues, there was a consistent trend in all measures of extent or intensity of staining towards a reduction in expression with elevated butyrate, consistent with the inverse association in tumours.</p> <p>Conclusions</p> <p>The data suggest that butyrate may associate with down-regulation of the expression of K8 in the cancerized colon. If further validated these findings may suggest the chemopreventive value of butyrate is limited to early stage carcinogenesis as low K8 expression is associated with a poor prognosis.</p

Natural history of SLC11 genes in vertebrates: tales from the fish world

<p>Abstract</p> <p>Background</p> <p>The <it>SLC11A1/Nramp1 </it>and <it>SLC11A2/Nramp2 </it>genes belong to the <it>SLC11/Nramp </it>family of transmembrane divalent metal transporters, with <it>SLC11A1 </it>being associated with resistance to pathogens and <it>SLC11A2 </it>involved in intestinal iron uptake and transferrin-bound iron transport. Both members of the <it>SLC11 </it>gene family have been clearly identified in tetrapods; however <it>SLC11A1 </it>has never been documented in teleost fish and is believed to have been lost in this lineage during early vertebrate evolution. In the present work we characterized the <it>SLC11 </it>genes in teleosts and evaluated if the roles attributed to mammalian <it>SLC11 </it>genes are assured by other fish specific <it>SLC11 </it>gene members.</p> <p>Results</p> <p>Two different <it>SLC11 </it>genes were isolated in the European sea bass (<it>Dicentrarchus. labrax</it>), and named <it>slc11a2-α </it>and <it>slc11a2-β</it>, since both were found to be evolutionary closer to tetrapods <it>SLC11A2</it>, through phylogenetic analysis and comparative genomics. Induction of <it>slc11a2-α </it>and <it>slc11a2-β </it>in sea bass, upon iron modulation or exposure to <it>Photobacterium damselae </it>spp. <it>piscicida</it>, was evaluated in <it>in vivo </it>or <it>in vitro </it>experimental models. Overall, <it>slc11a2-α </it>was found to respond only to iron deficiency in the intestine, whereas <it>slc11a2-β </it>was found to respond to iron overload and bacterial infection in several tissues and also in the leukocytes.</p> <p>Conclusions</p> <p>Our data suggests that despite the absence of <it>slc11a1</it>, its functions have been undertaken by one of the <it>slc11a2 </it>duplicated paralogs in teleost fish in a case of synfunctionalization, being involved in both iron metabolism and response to bacterial infection. This study provides, to our knowledge, the first example of this type of sub-functionalization in iron metabolism genes, illustrating how conserving the various functions of the SLC11 gene family is of crucial evolutionary importance.</p

Allele-Specific HLA Loss and Immune Escape in Lung Cancer Evolution

Immune evasion is a hallmark of cancer. Losing the ability to present neoantigens through human leukocyte antigen (HLA) loss may facilitate immune evasion. However, the polymorphic nature of the locus has precluded accurate HLA copy-number analysis. Here, we present loss of heterozygosity in human leukocyte antigen (LOHHLA), a computational tool to determine HLA allele-specific copy number from sequencing data. Using LOHHLA, we find that HLA LOH occurs in 40% of non-small-cell lung cancers (NSCLCs) and is associated with a high subclonal neoantigen burden, APOBEC-mediated mutagenesis, upregulation of cytolytic activity, and PD-L1 positivity. The focal nature of HLA LOH alterations, their subclonal frequencies, enrichment in metastatic sites, and occurrence as parallel events suggests that HLA LOH is an immune escape mechanism that is subject to strong microenvironmental selection pressures later in tumor evolution. Characterizing HLA LOH with LOHHLA refines neoantigen prediction and may have implications for our understanding of resistance mechanisms and immunotherapeutic approaches targeting neoantigens. Video Abstract [Figure presented] Development of the bioinformatics tool LOHHLA allows precise measurement of allele-specific HLA copy number, improves the accuracy in neoantigen prediction, and uncovers insights into how immune escape contributes to tumor evolution in non-small-cell lung cancer