• The RAC1 target NCKAP1 plays a crucial role in progression of BRAF/PTEN -driven melanoma in mice

      Swaminathan, Karthic; Campbell, A.; Papalazarou, V.; Jaber-Hijazi, F.; Nixon, C.; McGhee, E.; Strathdee, D.; Sansom, O.J.; Machesky, L.M. (2020)
      BRAF V600E is the most common driver mutation in human cutaneous melanoma and is frequently accompanied by loss of the tumor suppressing phosphatase PTEN. Recent evidence suggests a co-operative role for RAC1 activity in BRAF V600E -driven melanoma progression and drug resistance. However, the underlying molecular mechanisms and the role of RAC1 downstream targets are not well explored. Here, we examine the role of the NCKAP1 subunit of the pentameric cytoskeletal SCAR/WAVE complex, a major downstream target of RAC1, in a mouse model of melanoma driven by BRAF V600E; PTEN loss. The SCAR/WAVE complex is the major driver of lamellipodia formation and cell migration downstream of RAC1 and depends on NCKAP1 for its integrity. Targeted deletion of Nckap1 in the melanocyte lineage delayed tumor onset and progression of a mutant Braf ; Pten loss driven melanoma mouse model. Nckap1 depleted tumors displayed fibrotic stroma with increased collagen deposition concomitant with enhanced immune infiltration. Nckap1 loss slowed proliferation and tumor growth, highlighting a role in cell cycle progression. Altogether, we propose that NCKAP1-orchestrated actin polymerization is essential for tumor progression and maintenance of tumor tissue integrity in a mutant Braf ; Pten loss driven mouse model for melanoma.
    • Racemic compound versus conglomerate: concerning the crystal chemistry of the triazoylketone, 1-(4-chlorophenyl)-4,4- dimethyl-2-(1H-1,2,4-triazol-1-yl)pentan-3-one

      Davey, R.J.; Sadiq, G.; Seaton, Colin C.; Pritchard, R.G.; Coquerel, G.; Rougeot, C. (2014-06-07)
      The triazoylketone discussed in this paper crystallises from racemic solutions as a conglomerate. Here, we report the ternary phase diagram confirming the conglomerate behaviour of this molecule. Through computation we also explore the underlying reasons for the absence of a racemic compound in this system and the evident epitaxial crystallisation leading to crystals of almost racemic compositions but which retain the crystal structure of the pure enantiomer.
    • Radiographically recognizable? An investigation into the appearance of osteomalacic pseudofractures

      Jennings, E.; Buckberry, Jo; Brickley, M.B. (2018-12)
      Pseudofractures, lucent bands that occur due to a build-up of osteoid, are a key feature of osteomalacia. In paleopathology, pseudofractures are often marked by small, linear cracks in the cortex of the bone surrounded by irregular, bony spicule formation. Radiography can be used to help diagnose pseudofractures, both clinically and in paleopathology. A detailed understanding of the radiographic appearance of pseudofractures and their development is, therefore, necessary to aid a diagnosis of vitamin D deficiency. The present study examined the clinical literature to determine current ideas on the appearance of pseudofractures with the aim of applying this knowledge to paleopathology. A radiographic study of the characteristics of pseudofractures was performed on five individuals with clear skeletal features of osteomalacia from archaeological sites in Canada and the United Kingdom dating to the medieval period (5th to 15th centuries) and the 18th to 19th century. Results show that the radiographic appearance of pseudofractures could potentially reveal information about the cause of the deficiency and the chronicity of pseudofractures. This type of information has the potential to further our understanding of the lived experiences of archaeological individuals with osteomalacia.
    • Radiography in Palaeopathology: Where Next?

      Buckberry, Jo; O'Connor, Sonia A. (2007)
      Radiography has frequently been used during palaeopathological research, and plays an important role in the differential diagnosis of many diseases, including Paget¿s disease and carcinomas. Traditionally, radiographs were taken in hospitals with clinical equipment. However industrial radiography techniques have gradually become more commonly used, as their superior image quality and improved potential for diagnoses become recognised. The introduction of radiographic scanners has facilitated the digitisation of these images for dissemination and publication. However this is not all that radiographic digitisation can offer the researcher. Digital image processing (DIP) allows the researcher to focus on an area of interest and to adjust the brightness and contrast of the captured image. This allows the investigation of areas of high radio-opacity and radio-lucency, providing detailed images of the internal structures of bone and pathological lesions undetectable by the naked eye. In addition 3D effects, edge enhancement and sharpening algorithms, available through commonly used image processing software, can be very effective in enhancing the visibility of specific features. This paper will reveal how radiographic digitisation and manipulation can enhance radiographic images of palaeopathological lesions and potentially further our understanding of the bony manifestations of disease.
    • RAFT dispersion polymerization : a method to tune the morphology of thymine-containing self-assemblies

      Kang, Y.; Pitto-Barry, Anaïs; Maitland, A.; O'Reilly, R.K. (2015-07-21)
      The synthesis and self-assembly of thymine-containing polymers were performed using RAFT dispersion polymerization. A combination of microscopy and scattering techniques was used to analyze the resultant complex morphologies. The primary observation from this study is that the obtained aggregates induced during the polymerization were well-defined despite the constituent copolymers possessing broad dispersities. Moreover, a variety of parameters, including the choice of polymerization solvent, the degree of polymerization of both blocks and the presence of an adenine-containing mediator, were observed to affect the resultant size and shape of the assembly.
    • Raman and SEM analysis of a biocolonised hot spring travertine terrace in Svalbard, Norway

      Jorge Villar, Susana E.; Benning, L.G.; Edwards, Howell G.M.; AMASE team (2007)
      A profile across 8 layers from a fossil travertine terrace from a low temperature geothermal spring located in Svalbard, Norway has been studied using both Raman spectroscopy and SEM (Scanning Electron Microscopy) techniques to identify minerals and organic life signals. Calcite, anatase, quartz, haematite, magnetite and graphite as well as scytonemin, three different carotenoids, chlorophyll and a chlorophyll-like compound were identified as geo- and biosignatures respectively, using 785 and/or 514 nm Raman laser excitation wavelengths. No morphological biosignatures representing remnant microbial signals were detected by high-resolution imaging, although spectral analyses indicated the presence of organics. In contrast, in all layers, Raman spectra identified a series of different organic pigments indicating little to no degradation or change of the organic signatures and thus indicating the preservation of fossil biomarker compounds throughout the life time of the springs despite the lack of remnant morphological indicators. With a view towards planetary exploration we discuss the implications of the differences in Raman band intensities observed when spectra were collected with the different laser excitations. We show that these differences, as well as the different detection capability of the 785 and 514 nm laser, could lead to ambiguous compound identification. We show that the identification of bio and geosignatures, as well as fossil organic pigments, using Raman spectroscopy is possible. These results are relevant since both lasers have been considered for miniaturized Raman spectrometers for planetary exploration.
    • Raman spectroscopic analyses of preserved historical specimens of human hair attributed to Robert Stephenson and Sir Isaac Newton

      Edwards, Howell G.M.; Hassan, N.F.; Wilson, Andrew S. (2004)
      The Raman spectra of two historical specimens of human hair attributed to the engineer Robert Stephenson and scientist Sir Isaac Newton, preserved in private collections are reported. Comparisons are made with the Raman spectra of modern hair specimens and with hair from archaeological excavations. The hair spectra collected with a laser excitation of 785 nm are of a better quality than those collected using 1064 nm. The historical hair specimens are remarkably well-defined spectroscopically in terms of the amide I vibrational mode and the ν(SS), ascribed to a predominantly gauche–gauche–gauche CSSC conformation. The contrast with degraded hair specimens recovered from archaeological excavations is striking. The presence of a weak feature near 2590 cm−1 in the hair samples attributed to a ν(SH) vibration could be indicative of a reduction process operative on the CSSC cystine keratotic linkages and a possible origin of this is bacterial biodegradation identified histologically. This study demonstrates the molecular information available from non-destructive Raman spectroscopic analysis from single hair shafts or small bundles of fibres which complements information available from histological and destructive analytical techniques for rare biological specimens subjected to conservation or curation procedures in museums or private collections.
    • Raman spectroscopic analysis of human remains from a seventh century cist burial on Anglesey, UK

      Edwards, Howell G.M.; Wilson, Andrew S.; Nik Hassan, N.F.; Davidson, A.; Burnett, A. (2006-02)
      Specimens from human remains exhibiting unusual preservation excavated from a seventh century stone cist burial at Towyn y Capel in Anglesey, UK, have been analysed using Raman spectroscopy with near-infrared laser excitation at 1,064 and 785 nm. Specimens of hair and bone provided evidence for severe degradation and microbial colonisation. The deposits within the stone cist showed that some microbially mediated compounds had been formed. Analysis of crystals found at the interface between the hair and the skeletal neck vertebrae revealed a mixture of newberyite and haematite, associated with decomposition products of the hair and bone. An interesting differential degradation was noted in the specimens analysed which could be related to the air-void and the presence of plant root inclusions into the stone cist. This is the first time that Raman spectroscopy has been used in the forensic archaeological evaluation of burial remains in complex and dynamic environments.
    • Raman spectroscopic analysis of the effect of the lichenicolous fungus Xanthoriicola physciae on its lichen host

      Edwards, Howell G.M.; Seaward, Mark R.D.; Preece, T.F.; Jorge Villar, Susana E.; Hawksworth, D.L. (2016)
      Lichenicolous (lichen-dwelling) fungi have been extensively researched taxonomically over many years, and phylogenetically in recent years, but the biology of the relationship between the invading fungus and the lichen host has received limited attention, as has the effects on the chemistry of the host, being difficult to examine in situ. Raman spectroscopy is an established method for the characterization of chemicals in situ, and this technique is applied to a lichenicolous fungus here for the first time. Xanthoriicola physciae occurs in the apothecia of Xanthoria parietina, producing conidia at the hymenium surface. Raman spectroscopy of apothecial sections revealed that parietin and carotenoids were destroyed in infected apothecia. Those compounds protect healthy tissues of the lichen from extreme insolation and their removal may contribute to the deterioration of the apothecia. Scytonemin was also detected, but was most probably derived from associated cyanobacteria. This work shows that Raman spectroscopy has potential for investigating changes in the chemistry of a lichen by an invading lichenicolous fungus.
    • Raman spectroscopic and structural investigation of 1,4-diphenylbuta-1,3-diene and selected monomethyl and dimethyl substituted homologues

      Bowen, Richard D.; Edwards, Howell G.M.; Waller, Zoe A.E. (2006)
      The Raman and mass spectra of 1,4-diphenylbuta-1,3-diene and several of its monomethyl and dimethyl homologues are reported and discussed, with a view to developing a spectroscopic protocol for detecting the presence and position of a methyl group in these compounds. Raman spectroscopy and mass spectrometry are shown to provide complementary information, by which the four available monomethyl homologues may be readily distinguished from each other and 1,4-diphenylbuta-1,3-diene itself. The utility of these 1,4-diarylbutadienes as model compounds for carotenoids and related materials, which may serve as indicators of extinct or extant extraterrestrial life, is considered.
    • Raman Spectroscopic and structural studies of indigo and its four 6,6'-Dihalogeno analogues

      Bowen, Richard D.; Edwards, Howell G.M.; Jorge Villar, Susana E.; Karapanayiotis, Thanassis (2004)
      The Raman and electron impact mass spectra of synthetic indigo and its four 6,6'-dihalogeno analogues are reported and discussed. The influence of varying the halogen on these Raman spectra is considered. Particular emphasis is laid on distinguishing indigo from 6,6'-dibromoindigo and differentiating between the dihalogenocompounds, so as to develop protocols for determining whether artefacts are coloured with dyes of marine or terrestrial origin and whether such artefacts are dyed with genuine Tyrian Purple or with dihalogenoindigo substitutes that do not contain bromine. The value of even low resolution electron impact mass spectrometry in a forensic context as a means of identifying authentic 6,6'-dibromoindigo and distinguishing it from its dihalogenoanalogues is emphasised.
    • Raman spectroscopic characterisations and analytical discrimination between caffeine and demethylated analogues of pharmaceutical relevance

      Edwards, Howell G.M.; Munshi, Tasnim; Anstis, M. (2005)
      The FT Raman spectrum of caffeine was analysed along with that of its demethylated analogues, theobromine and theophylline. The similar but not identical structures of these three compounds allowed a more detailed assignment of the Raman bands. Noticeable differences in the Raman spectra of these compounds were apparent and key marker bands have been identified for the spectroscopic identification of these three compounds.
    • Raman spectroscopic fingerprints of scytonemin-imine: density functional theory calculations of a novel potential biomarker

      Varnali, T.; Edwards, Howell G.M. (2014-12-13)
      Scytonemin-imine, a novel derivative of scytonemin, has been isolated and identified very recently and proposed to serve as a photoprotective biomarker for certain bacteria growing under intense photon flux density. This study predicts theoretically the Raman spectrum of scytonemin-imine by density functional theory calculations and provides comparison of major bands to those of scytonemin, the parent compound for which both the experimentally characterized and theoretically predicted spectra exist in the literature. It is proposed to be an addendum to the collection of our previous work on scytonamin and its derivatives to facilitate recognition of the diagnostic Raman spectral signatures for scytonemin-imine.
    • Raman spectroscopic identification of scytonemin and its derivatives as key biomarkers in stressed environments

      Varnali, T.; Edwards, Howell G.M. (2014-12-13)
      Raman spectroscopy has been identified as an important first-pass analytical technique for deployment on planetary surfaces as part of a suite of instrumentation in projected remote space exploration missions to detect extant or extinct extraterrestrial life signatures. Aside from the demonstrable advantages of a non-destructive sampling procedure and an ability to record simultaneously the molecular signatures of biological, geobiological and geological components in admixture in the geological record, the interrogation and subsequent interpretation of spectroscopic data from these experiments will be critically dependent upon the recognition of key biomolecular markers indicative of life existing or having once existed in extreme habitats. A comparison made with the characteristic Raman spectral wavenumbers obtained from standards is not acceptable because of shifts that can occur in the presence of other biomolecules and their host mineral matrices. In this paper, we identify the major sources of difficulty experienced in the interpretation of spectroscopic data centring on a key family of biomarker molecules, namely scytonemin and its derivatives; the parent scytonemin has been characterized spectroscopically in cyanobacterial colonies inhabiting some of the most extreme terrestrial environments and, with the support of theoretical calculations, spectra have been predicted for the characterization of several of its derivatives which could occur in novel extraterrestrial environments. This work will form the foundation for the identification of novel biomarkers and for their Raman spectroscopic discrimination, an essential step in the interpretation of potentially complex and hitherto unknown biological radiation protectants based on the scytoneman and scytonin molecular skeletons which may exist in niche geological scenarios in the surface and subsurface of planets and their satellites in our Solar System.
    • Raman spectroscopic study of "The Malatesta": a Renaissance painting?

      Edwards, Howell G.M.; Vandenabeele, P.; Benoy, T.J. (2015-02-25)
      Raman spectroscopic analysis of the pigments on an Italian painting described as a “Full Length Portrait of a Gentleman”, known also as the “Malatesta”, and attributed to the Renaissance period has established that these are consistent with the historical research provenance undertaken earlier. Evidence is found for the early 19th Century addition of chrome yellow to highlighted yellow ochre areas in comparison with a similar painting executed in 1801 by Sir Thomas Lawrence of John Kemble in the role of Hamlet, Prince of Denmark. The Raman data are novel in that no analytical studies have previously been made on this painting and reinforces the procedure whereby scientific analyses are accompanied by parallel historical research.
    • Raman spectroscopic study of antioxidant pigments from cup corals Tubastraea spp

      Maia, L.F.; Ferreira, G.R.; Costa, R.C.; Lucas, N.C.; Teixeira, R.I.; Fleury, B.G.; Edwards, Howell G.M.; de Oliveira, L.F.C. (2014)
      Chemical investigation of nonindigenous Tubastraea coccinea and T. tagusensis by Raman spectroscopy resulted in the identification of carotenoids and indolic alkaloids. Comparison of Raman data obtained for the in situ and crude extracts has shown the potential of the technique for characterizing samples which are metabolic fingerprints, by means of band analysis. Raman bands at ca. 1520, 1160, and 1005 cm–1 assigned to ν1(C═C), ν2(C—C), and ρ3(C—CH3) modes were attributed to astaxanthin, and the band at 1665 cm–1 could be assigned to the ν(C—N), ν(C—O), and ν(C—C) coupled mode of the iminoimidazolinone from aplysinopsin. The antioxidant activity of the crude extracts has also been demonstrated, suggesting a possible role of these classes of compounds in the studied corals.
    • Raman spectroscopic study of the Chromobacterium violaceum pigment violacein using multiwavelength excitation and DFT calculations

      Jehlička, J.; Edwards, Howell G.M.; Nemec, I.; Oren, A. (2015)
      Violacein is a bisindole pigment occurring as a biosynthetic product of Chromobacterium violaceum and Janthinobacterium lividum. It has some structural similarities to the cyanobacterial UV-protective pigment scytonemin, which has been the subject of comprehensive spectroscopic and structural studies. A detailed experimental Raman spectroscopic study with visible and near-infrared excitation of violacein produced by C. violaceum has been undertaken and supported using theoretical DFT calculations. Raman spectra with 514 and 785 nm excitation of cultivated cells as well as extracts and Gaussian (B3LYP/6-311++G(d,p)) calculations with proposed molecular vibrational assignments are reported here.
    • Raman spectroscopy as a non-destructive screening technique for studying white substances from archaeological and forensic burial contexts

      Schotsmans, Eline M.J.; Wilson, Andrew S.; Brettell, Rhea C.; Munshi, Tasnim; Edwards, Howell G.M. (2014)
      Raman spectroscopy was evaluated as a non-destructive analytical tool for the characterisation of white substances in burials. In addition, Fourier transform Raman spectroscopy was used to assess the conversion of hydrated lime into calcium carbonate. Fourteen samples of white substances from archaeological and forensic sites were analysed and characterised. The results show that not all white residues in burials are lime. Lime can easily be mistaken for other building materials (gypsum), for minerals (brushite) or degraded metal (cerussite). This study highlights the need for chemical analysis of white residues when encountered in burials. Analytical information derived from Raman spectra of white substances can further assist in the interpretation of the taphonomic processes of burials and their funerary context. Copyright (c) 2014 John Wiley & Sons, Ltd.
    • Raman spectroscopy meets extremophiles on Earth and Mars: studies for successful search of life

      Jehlička, J.; Edwards, Howell G.M. (2014)
      Recent studies relating to the analytical chemical characterization of terrestrial extremophiles reveal the presence of biomolecules that have been synthesized for the survival of the colonies in response to the extreme environmental conditions, where otherwise life could not exist. This is a vital part of the planned space missions now being undertaken to planets and their satellites in the search for extinct or extant life signatures in our Solar System. Extremophiles have existed on the Earth for some 3.8 Gyr and their interrogation indicates their strategic survival methods which can be associated and compared with extraterrestrial scenarios on Mars, Titan, Enceladus and Europa.
    • Raman spectroscopy of microbial pigments

      Jehlička, J.; Edwards, Howell G.M.; Oren, A. (2014)
      Raman spectroscopy is a rapid nondestructive technique providing spectroscopic and structural information on both organic and inorganic molecular compounds. Extensive applications for the method in the characterization of pigments have been found. Due to the high sensitivity of Raman spectroscopy for the detection of chlorophylls, carotenoids, scytonemin, and a range of other pigments found in the microbial world, it is an excellent technique to monitor the presence of such pigments, both in pure cultures and in environmental samples. Miniaturized portable handheld instruments are available; these instruments can be used to detect pigments in microbiological samples of different types and origins under field conditions.