• Biocatalytic Self-Assembly of Supramolecular Charge Transfer Nanostructures Based on n-Type Semiconductor-Appended Peptide

      Nalluri, S.K.M.; Berdugo, C.; Javid, Nadeem; Frederix, P.W.J.M.; Ulijn, R.V. (2014-05-30)
      The reversible in situ formation of a self-assembly building block (naphthalenediimide (NDI)–dipeptide conjugate) by enzymatic condensation of NDI-functionalized tyrosine (NDI-Y) and phenylalanine-amide (F-NH2) to form NDI-YF-NH2 is described. This coupled biocatalytic condensation/assembly approach is thermodynamically driven and gives rise to nanostructures with optimized supramolecular interactions as evidenced by substantial aggregation induced emission upon assembly. Furthermore, in the presence of di-hydroxy/alkoxy naphthalene donors, efficient charge-transfer complexes are produced. The dynamic formation of NDI-YF-NH2 and electronic and H-bonding interactions are analyzed and characterized by different methods. Microscopy (TEM and AFM) and rheology are used to characterize the formed nanostructures. Dynamic nanostructures, whose formation and function are driven by free-energy minimization, are inherently self-healing and provide opportunities for the development of aqueous adaptive nanotechnology.
    • Biocatalytically Triggered Co‐Assembly of Two‐Component Core/Shell Nanofibers

      Abul-Haija, Y.M.; Roy, S.; Frederix, P.W.J.M.; Javid, Nadeem; Jayawarna, V.; Ulijn, R.V. (2014-03-05)
      For the development of applications and novel uses for peptide nanostructures, robust routes for their surface functionalization, that ideally do not interfere with their self‐assembly properties, are required. Many existing methods rely on covalent functionalization, where building blocks are appended with functional groups, either pre‐ or post‐assembly. A facile supramolecular approach is demonstrated for the formation of functionalized nanofibers by combining the advantages of biocatalytic self‐assembly and surfactant/gelator co‐assembly. This is achieved by enzymatically triggered reconfiguration of free flowing micellar aggregates of pre‐gelators and functional surfactants to form nanofibers that incorporate and display the surfactants’ functionality at the surface. Furthermore, by varying enzyme concentration, the gel stiffness and supramolecular organization of building blocks can be varied.
    • Bioflavonoid coated materials

      Thomas, Howard; Dowling, D.P.; Katsikogianni, Maria G. (2014)
      Polymeric materials are described which have a bioflavonoid coating, the bioflavonoid content of the coating comprising at least naringin and neohesperidin. The use of such coated polymeric materials is also described as well as the process for making the coated polymeric materials.
    • Bioinformatic insights into the biosynthesis of the Group B carbohydrate in Streptococcus agalactiae

      Sutcliffe, I.C.; Black, G.W.; Harrington, Dean J. (2008-05-01)
      Streptococcus agalactiae is a major human and animal pathogen, most notable as a cause of life-threatening disease in neonates. S. agalactiae is also called the Group B Streptococcus in reference to the diagnostically significant Lancefield Group B typing antigen. Although the structure of this complex carbohydrate antigen has been solved, little is known of its biosynthesis beyond the identification of a relevant locus in sequenced S. agalactiae genomes. Analysis of the sugar linkages present in the Group B carbohydrate (GBC) structure has allowed us to deduce the minimum enzymology required to complete its biosynthesis. Most of the enzymes required to complete this biosynthesis can be identified within the putative biosynthetic locus. Surprisingly, however, three crucial N-acetylglucosamine transferases and enzymes required for activated precursor synthesis are not apparently located in this locus. A model for GBC biosynthesis wherein the complete polymer is assembled at the cytoplasmic face of the plasma membrane before translocation to the cell surface is proposed. These analyses also suggest that GBC is the major teichoic acid-like polymer in the cell wall of S. agalactiae, whereas lipoteichoic acid is the dominant poly(glycerophosphate) antigen. Genomic analysis has allowed us to predict the pathway leading to the biosynthesis of GBC of S. agalactiae.
    • Biological Imaging with a Near-Field Optical Setup.

      Denyer, Morgan C.T.; Micheletto, R.; Nakajima, K.; Hara, M.; Okazaki, S. (2003)
      Noncontact scanning near-field optical microscope (SNOM) systems can be used to optically resolve samples in atmospheric conditions at theoretical resolutions comparable to those of transmission electron microscope and atomic force microscope systems. SNOM systems are also increasingly used to image biological samples. In this study we custom built a SNOM system with the aim of further demonstrating the potential applications of near-field optical examination of biological material. In this study we were able to image both fixed whole-cell samples in air and liquid environments and live whole-cell samples in liquids. The images acquired were of a relatively low resolution, but this work has shown that SNOM systems can be used to monitor the dynamics of living cells at subnanometric resolutions in the z axis and for fluorescent imaging of whole cells in a liquid medium.
    • The biology and genetics of curly hair

      Westgate, Gillian E.; Ginger, R.S.; Green, M.R. (2017-06-13)
      Hair fibres show wide diversity across and within all human populations, suggesting that hair fibre form and colour have been subject to much adaptive pressure over thousands of years. All human hair fibres typically have the same basic structure. However, the three-dimensional shape of the entire fibre varies considerably depending on ethnicity and geography, with examples from very straight hair with no rotational turn about the long axis, to the tightly sprung coils of African races. The creation of the highly complex biomaterials in hair follicle and how these confer mechanical functions on the fibre so formed is a topic that remains relatively unexplained thus far. We review the current understanding on how hair fibres are formed into a nonlinear coiled form and which genetic and biological factors are thought to be responsible for hair shape. We report on a new GWAS comparing low and high curl individuals in South Africa, revealing strong links to polymorphic variation in trichohyalin, a copper transporter protein CUTC and the inner root sheath component keratin 74. This builds onto the growing knowledge base describing the control of curly hair formation.
    • The biology of hair diversity.

      Westgate, Gillian E.; Botchkareva, Natalia V.; Tobin, Desmond J. (2013)
      Hair diversity, its style, colour, shape and growth pattern is one of our most defining characteristics. The natural versus temporary style is influenced by what happens to our hair during our lifetime, such as genetic hair loss, sudden hair shedding, greying and pathological hair loss in the various forms of alopecia because of genetics, illness or medication. Despite the size and global value of the hair care market, our knowledge of what controls the innate and within-lifetime characteristics of hair diversity remains poorly understood. In the last decade, drivers of knowledge have moved into the arena of genetics where hair traits are obvious and measurable and genetic polymorphisms are being found that raise valuable questions about the biology of hair growth. The recent discovery that the gene for trichohyalin contributes to hair shape comes as no surprise to the hair biologists who have believed for 100 years that hair shape is linked to the structure and function of the inner root sheath. Further conundrums awaiting elucidation include the polymorphisms in the androgen receptor (AR) described in male pattern alopecia whose location on the X chromosome places this genetic contributor into the female line. The genetics of female hair loss is less clear with polymorphisms in the AR not associated with female pattern hair loss. Lifestyle choices are also implicated in hair diversity. Greying, which also has a strong genetic component, is often suggested to have a lifestyle (stress) influence and hair follicle melanocytes show declining antioxidant protection with age and lowered resistance to stress. It is likely that hair research will undergo a renaissance on the back of the rising information from genetic studies as well as the latest contributions from the field of epigenetics.
    • Biomarkers and their Raman spectroscopic signatures: a spectral challenge for analytical astrobiology

      Edwards, Howell G.M.; Hutchinson, I.B.; Ingley, R.; Jehlička, J. (2014)
      The remote robotic exploration of extraterrestrial scenarios for evidence of biological colonization in 'search for life' missions using Raman spectroscopy is critically dependent on two major factors: firstly, the Raman spectral recognition of characteristic biochemical spectral signatures in the presence of mineral matrix features; and secondly, the positive unambiguous identification of molecular biomaterials which are indicative of extinct or extant life. Both of these factors are considered here: the most important criterion is the clear definition of which biochemicals truly represent biomarkers, whose presence in the planetary geological record from an analytical astrobiological standpoint will unambiguously be indicative of life as recognized from its remote instrumental interrogation. Also discussed in this paper are chemical compounds which are associated with living systems, including biominerals, which may not in themselves be definitive signatures of life processes and origins but whose presence provides an indicator of potential life-bearing matrices.
    • Biomaterial Functionalized Surfaces for Reducing Bacterial Adhesion and Infection

      Katsikogianni, Maria G.; Wood, David J.; Missirlis, Y.F. (2016)
      This chapter describes the current approaches to reduce bacterial adhesion to various biomaterial surfaces, focusing on nonfouling surfaces through patterning and hydrophobicity plasma-assisted surface treatment and deposition; incorporation of antimicrobials, antibiotics, antibiofilms, and natural extracts that are either immobilized or released; dual function antimicrobial surfaces; incorporation of nonpathogenic bacteria, bacteriophages, and biofilm dispersal agents but also reduced bacterial adhesion through tissue integration. To facilitate the design of new materials, the role of physical, chemical, and biological surface properties on bacterial adhesion is reviewed in each case, as an insight into the chemical and physical cues that affect bacterial adhesion and biofilm formation can provide ideas for creating successful antifouling or antimicrobial surfaces. The application of these surfaces is explored based on the clinical needs and the market gaps. How multidisciplinary research on surface design and engineering may have an impact on both fundamental understanding of bacterial adhesion to biomaterials and applied biomaterial science and technology is finally discussed.
    • Biometry of eyes in type 1 diabetes

      Adnan, X.; Suheimat, M.; Efron, N.; Edwards, K.; Pritchard, N.; Mathur, A.; Mallen, Edward A.H.; Atchison, D.A. (2015)
      This is a comprehensive study of a large range of biometric and optical parameters in people with type 1 diabetes. The parameters of 74 people with type 1 diabetes and an age matched control group were assessed. Most of the people with diabetes had low levels of neuropathy, retinopathy and nephropathy. Marginal or no significant differences were found between groups for corneal shape, corneal thickness, pupil size, and pupil decentrations. Relative to the control group, the diabetes group demonstrated smaller anterior chamber depths, more curved lenses, greater lens thickness and lower lens equivalent refractive index. While the optics of diabetic eyes make them appear as older eyes than those of people of the same age without diabetes, the differences did not increase significantly with age. Age-related changes in the optics of the eyes of people with diabetes need not be accelerated if the diabetes is well controlled.
    • Biophysical characteristics of cells cultured on cholesteryl ester liquid crystals

      Soon, Chin Fhong; Omar, W.I.W.; Berends, Rebecca F.; Nayan, N.; Basri, H.; Tee, K.S.; Youseffi, Mansour; Blagden, Nicholas; Denyer, Morgan C.T. (2014-01)
      This study aimed at examining the biophysical characteristics of human derived keratinocytes (HaCaT) cultured on cholesteryl ester liquid crystals (CELC). CELC was previously shown to improve sensitivity in sensing cell contractions. Characteristics of the cell integrin expressions and presence of extracellular matrix (ECM) proteins on the liquid crystals were interrogated using various immunocytochemical techniques. The investigation was followed by characterization of the chemical properties of the liquid crystals (LC) after immersion in cell culture media using Fourier transform infrared spectroscopy (FTIR). The surface morphology of cells adhered to the LC was studied using atomic force microscopy (AFM). Consistent with the expressions of the integrins α2, α3 and β1, extracellular matrix proteins (laminin, collagen type IV and fibronectin) were found secreted by the HaCaT onto CELC and these proteins were also secreted by cells cultured on the glass substrates. FTIR analysis of the LC revealed the existence of spectrum assigned to cholesterol and ester moieties that are essential compounds for the metabolizing activities of keratinocytes. The immunostainings indicated that cell adhesion on the LC is mediated by self-secreted ECM proteins. As revealed by the AFM imaging, the constraint in cell membrane spread on the LC leads to the increase in cell surface roughness and thickness of cell membrane. The biophysical expressions of cells on biocompatible CELC suggested that CELC could be a new class of biological relevant material.
    • Bis-Picolinamide ruthenium (III) dihalide complexes: dichloride to diiodide exchange generates single trans isomers with high potency and cancer cell selectivity

      Basri, A.M.; Lord, Rianne M.; Allison, Simon J.; Rodríguez-Bárzano, A.; Lucas, S.J.; Janeway, F.X.; Shepherd, H.J.; Pask, C.M.; Phillips, Roger M.; McGowan, P.C. (2017-05-05)
      A library of new bis-picolinamide ruthenium(III) dihalide complexes of the type RuX2L2 (X = Cl or I and L = picolinamide) have been synthesised and characterised. They exhibit different picolinamide ligand binding modes, whereby one ligand is bound (N,N) and the other bound (N,O). Structural studies reveal a mixture of cis and trans isomers for the RuCl2L2 complexes but upon a halide exchange reaction to RuI2L2, only single trans isomers are present. High cytotoxic activity against human cancer cell lines was observed, with potencies for some complexes similar to or better than cisplatin. Conversion to RuI2L2 substantially increased activity towards cancer cell lines by >12-fold. The RuI2L2 complexes displayed potent activity against the A2780cis (cisplatin-resistant human ovarian cancer) cell line, with >4-fold higher potency than cisplatin. Equitoxic activity was observed against normoxic and hypoxic cancer cells, indicating the potential to eradicate both the hypoxic and aerobic fractions of solid tumours with similar efficiency. Selected complexes were also tested against non-cancer ARPE-19 cells. The RuI2L2 complexes are more potent than the RuCl2L2 analogues, and also more selective towards cancer cells with a selectivity factor >7-fold.
    • Bis-pyrene probes of foldamer conformation in solution and in phospholipid bilayers

      Lister, F.G.A.; Eccles, N.; Pike, Sarah J.; Brown, R.A.; Whitehead, G.F.S.; Raftery, J.; Webb, S.J.; Clayden, J. (2018-07)
      Exploring the detailed structural features of synthetic molecules in the membrane phase requires sensitive probes of conformation. Here we describe the design, synthesis and characterization of bis(pyrene) probes that report conformational changes in membrane-active dynamic foldamers. The probes were designed to distinguish between left-handed (M) and right-handed (P) screw-sense conformers of 310-helical α-aminoisobutyric acid (Aib) peptide foldamers, both in solution and in bilayer membranes. Several different bis(pyrene) probes were synthesized and ligated to the C-terminus of Aib tetramers that had different chiral residues at the N-terminus, residues that favored either an M or a P screw-sense in the 310-helix. The readily synthesized and conveniently incorporated N-acetyl-1,2-bis(pyren-1′-yl)ethylenediamine probe proved to have the best properties. In solution, changes in foldamer screw-sense induced substantial changes in the ratio of excimer/monomer fluorescence emission (E/M) for this reporter of conformation, with X-ray crystallography revealing that opposite screw-senses produce very different interpyrene distances in the reporter. In bilayers, this convenient and sensitive fluorescent reporter allowed, for the first time, an investigation of how the chirality of natural phospholipids affects foldamer conformation.
    • Bitumen in Neolithic Iran: Biomolecular and isotopic evidence.

      Gregg, M.W.; Brettell, Rhea C.; Stern, Ben (2007)
      This paper presents the results of the chemical analysis of materials recovered from two of the earliest agricultural villages in southwestern Iran and a late Neolithic pastoral encampment in nearby Khuzistan. Gas chromatography - mass spectrometry (GC-MS) revealed biomarker compounds characteristic of bitumen in residues from ceramic vessels supporting the excavators¿ contention that the interior surfaces of some vessels were coated with a thin layer of such material and confirmed that ¿fragments¿ collected during excavation were indeed bitumen. Biomolecular and isotopic analysis of the bitumen indicated that the sources utilized lie in the Susa and Deh Luran regions of southwestern Iran.
    • Black flags and black trowels: embracing anarchy in interpretation and practice

      Fitzpatrick, Alexandra L. (2018-12)
      The concept of an "anarchist archaeological framework" is not new; anarchy and archaeology have been explored in many forms together, including conference sessions (see SAA 2015 conference), special journal issues (Borck and Sanger 2017) and, more recently, as the focus of a manifesto written by a group known as the Black Trowel Collective (2016). This coincides with a broader movement across academia (and in general politics) calling for self-reflection and critical engagement with the problematic foundations that many of our disciplines have been based on, specifically with regards to sexism, racism, and colonisation. This paper continues this discussion by critically engaging with past attempts to utilise anarchist theory in archaeological interpretation, as well as expanding these arguments further by applying them to archaeological practice as well. I argue that engaging with anarchist theory in both interpretation and practice is a form of further detaching ourselves from the problematic foundations of our discipline and moving forward towards a more equitable archaeology that can imagine both a different past and future.
    • Blood Residues on Archaeological Objects - A Conservation Perspective

      Wilson, Andrew S.; Tuross, N.; Wachowiak, M.J. (1996)
    • Blunted epidermal l-tryptophan metabolism in vitiligo affects immune response and ROS scavenging by Fenton chemistry, part 1: epidermal H2O2/ONOO−-mediated stress abrogates tryptophan hydroxylase and dopa decarboxylase activities, leading to low serotonin and melatonin levels.

      Schallreuter, Karin U.; Salem, Mohamed M.A.; Gibbons, Nick C.; Martinez, A.; Slominski, Radomir; Lüdemann, J.; Rokos, Hartmut (2012-06)
      Vitiligo is characterized by a progressive loss of inherited skin color. The cause of the disease is still unknown. To date, there is accumulating in vivo and in vitro evidence for massive oxidative stress via hydrogen peroxide (H2O2) and peroxynitrite (ONOO−) in the skin of affected individuals. Autoimmune etiology is the favored theory. Since depletion of the essential amino acid l-tryptophan (Trp) affects immune response mechanisms, we here looked at epidermal Trp metabolism via tryptophan hydroxylase (TPH) with its downstream cascade, including serotonin and melatonin. Our in situ immunofluorescence and Western blot data reveal significantly lower TPH1 expression in patients with vitiligo. Expression is also low in melanocytes and keratinocytes under in vitro conditions. Although in vivo Fourier transform-Raman spectroscopy proves the presence of 5-hydroxytryptophan, epidermal TPH activity is completely absent. Regulation of TPH via microphthalmia-associated transcription factor and l-type calcium channels is severely affected. Moreover, dopa decarboxylase (DDC) expression is significantly lower, in association with decreased serotonin and melatonin levels. Computer simulation supports H2O2/ONOO−-mediated oxidation/nitration of TPH1 and DDC, affecting, in turn, enzyme functionality. Taken together, our data point to depletion of epidermal Trp by Fenton chemistry and exclude melatonin as a relevant contributor to epidermal redox balance and immune response in vitiligo.
    • Blunted epidermal l-tryptophan metabolism in vitiligo affects immune response and ROS scavenging by Fenton chemistry, part 2: epidermal H2O2/ONOO−-mediated stress in vitiligo hampers indoleamine 2,3-dioxygenase and aryl hydrocarbon receptor-mediated immune response signaling.

      Schallreuter, Karin U.; Salem, Mohamed M.A.; Gibbons, Nick C.; Maitland, Derek J.; Marsch, E.; Elwary, Souna M.A.; Healey, Andrew R. (2012-06)
      Vitiligo is characterized by a mostly progressive loss of the inherited skin color. The cause of the disease is still unknown, despite accumulating in vivo and in vitro evidence of massive oxidative stress via hydrogen peroxide (H2O2) and peroxynitrite (ONOO−) in the skin of affected individuals. The most favored hypothesis is based on autoimmune mechanisms. Since depletion of the essential amino acid l-tryptophan (Trp) severely affects various immune responses, we here looked at Trp metabolism and signaling in these patients. Our in vivo and in vitro data revealed total absence of epidermal Trp hydroxylase activities and the presence of H2O2/ONOO− deactivated indoleamine 2,3-dioxygenase. Aryl hydrocarbon receptor signaling is severely impaired despite the ligand (Trp dimer) being formed, as shown by mass spectrometry. Loss of this signal is supported by the absence of downstream signals (COX-2 and CYP1A1) as well as regulatory T-lymphocytes and by computer modeling. In vivo Fourier transform Raman spectroscopy confirmed the presence of Trp metabolites together with H2O2 supporting deprivation of the epidermal Trp pool by Fenton chemistry. Taken together, our data support a long-expressed role for in loco redox balance and a distinct immune response. These insights could open novel treatment strategies for this disease.—Schallreuter, K. U., Salem, M. A. E. L., Gibbons, N. C. J., Maitland, D. J., Marsch, E., Elwary, S., Healey, A. R. Blunted epidermal l-tryptophan metabolism in vitiligo affects immune response and ROS scavenging by Fenton chemistry, part 2: epidermal H2O2/ONOO−-mediated stress in vitiligo hampers indoleamine 2,3-dioxygenase and aryl hydrocarbon receptor-mediated immune response signaling.
    • BMP signaling induces cell-type-specific changes in gene expression programs of human keratinocytes and fibroblasts

      Fessing, Michael Y.; Atoyan, R.; Shander, B.; Mardaryev, Andrei N.; Botchkarev, V.V. Jr; Poterlowicz, Krzysztof; Peng, Yonghong; Efimova, T.; Botchkarev, Vladimir A. (2010)
      BMP signaling has a crucial role in skin development and homeostasis, whereas molecular mechanisms underlying its involvement in regulating gene expression programs in keratinocytes and fibroblasts remain largely unknown. We show here that several BMP ligands, all BMP receptors, and BMP-associated Smad1/5/8 are expressed in human primary epidermal keratinocytes and dermal fibroblasts. Treatment of both cell types by BMP-4 resulted in the activation of the BMP-Smad, but not BMP-MAPK pathways. Global microarray analysis revealed that BMP-4 treatment induces distinct and cell type-specific changes in gene expression programs in keratinocytes and fibroblasts, which are far more complex than the effects of BMPs on cell proliferation/differentiation described earlier. Furthermore, our data suggest that the potential modulation of cell adhesion, extracellular matrix remodeling, motility, metabolism, signaling, and transcription by BMP-4 in keratinocytes and fibroblasts is likely to be achieved by the distinct and cell-type-specific sets of molecules. Thus, these data provide an important basis for delineating mechanisms that underlie the distinct effects of the BMP pathway on different cell populations in the skin, and will be helpful in further establishing molecular signaling networks regulating skin homeostasis in health and disease.
    • BMPR-II deficiency elicits pro-proliferative and anti-apoptotic responses through the activation of TGFbeta-TAK1-MAPK pathways in PAH

      Nasim, Md. Talat; Ogo, T.; Chowdhury, H.M.; Zhao, L.; Chen, C-n.; Rhodes, C.; Trembath, R.C. (2012)
      Pulmonary arterial hypertension (PAH) is a cardiovascular disorder associated with enhanced proliferation and suppressed apoptosis of pulmonary arterial smooth muscle cells (PASMCs). Heterozygous mutations in the type II receptor for bone morphogenetic protein (BMPR2) underlie the majority of the inherited and familial forms of PAH. The transforming growth factor beta (TGFbeta) pathway is activated in both human and experimental models of PAH. However, how these factors exert pro-proliferative and anti-apoptotic responses in PAH remains unclear. Using mouse primary PASMCs derived from knock-in mice, we demonstrated that BMPR-II dysfunction promotes the activation of small mothers against decapentaplegia-independent mitogen-activated protein kinase (MAPK) pathways via TGFbeta-associated kinase 1 (TAK1), resulting in a pro-proliferative and anti-apoptotic response. Inhibition of the TAK1-MAPK axis rescues abnormal proliferation and apoptosis in these cells. In both hypoxia and monocrotaline-induced PAH rat models, which display reduced levels of bmpr2 transcripts, this study further indicates that the TGFbeta-MAPK axis is activated in lungs following elevation of both expression and phosphorylation of the TAK1 protein. In ex vivo cell-based assays, TAK1 inhibits BMP-responsive reporter activity and interacts with BMPR-II receptor. In the presence of pathogenic BMPR2 mutations observed in PAH patients, this interaction is greatly reduced. Taken together, these data suggest dysfunctional BMPR-II responsiveness intensifies TGFbeta-TAK1-MAPK signalling and thus alters the ratio of apoptosis to proliferation. This axis may be a potential therapeutic target in PAH.