Bacterial polysaccharide synthesis and gene nomenclature

Gene nomenclature for bacterial surface polysaccharides is complicated by the large number of structures and genes. We propose a scheme applicable to all species that distinguishes different classes of genes, provides a single name for all genes of a given function and greatly facilitates comparative studies.

Understanding the Effects of Ionicity in Salts, Solvates, Co-Crystals, Ionic Co-Crystals, and Ionic Liquids, Rather than Nomenclature, Is Critical to Understanding Their Behavior

The incorporation of active pharmaceutical ingredients (APIs) into multicomponent solid forms (such as salts and co-crystals) or liquid forms (such as ionic liquids (ILs) or deep eutectic mixtures) is important in optimizing the efficacy and delivery of APIs. However, there is a current debate regarding the classification of these multicomponent systems based on their ionicity which could interfere with their consideration in important applications. Multicomponent systems of intermediate ionicity can show a combination of properties, leading to behavior that is neither strictly typical of either purely ionic or purely neutral compounds, nor easily described as intermediate between the two. In this perspective, we attempt to illustrate the problems in classifying multicomponent APIs based on one of two categories by discussing selected literature regarding solid and liquid multicomponent APIs and presenting the crystal structures of some relevant systems as case studies. It is clear that a focus on restrictive nomenclature carries with it the risk that a thorough examination of the physicochemical properties of the compounds will be overlooked.

Novel brevinins from Chinese piebald odorous frog (Huia schmackeri) skin deduced from cloned biosynthetic precursors

Antimicrobial peptides represent the most characterized and diverse class of peptides within the defensive skin secretions of anuran amphibians. With an ever expanding database of primary structures, the current accepted rules for nomenclature have become increasingly difficult to apply to peptides whose primary structural attributes are either unique or that fall between those that define existing groups. An additional factor that adds to the confusion is the regular re-classification or revision of existing taxa. In the present study, we have identified five new antimicrobial peptide homologs in the defensive skin secretion of the Chinese piebald odorous frog, Huia schmackeri (formerly Rana (Odorrana) schmackeri), by cloning of their respective biosynthetic precursors. As these peptides are obvious homologs of the brevinin-1 and brevinin-2 families we have named these in accordance: (1) brevinin-1HS1, (2) brevinin-2HS1, (3) brevinin-2HS2, (4) brevinin-2HS3 and (5) brevinin-1HS2. The reasons for adopting these names are discussed. It is clear that with an ever-increasing number of amphibian skin antimicrobial peptides appearing in the literature that a consistent nomenclature scheme needs to be established.

Recessive congenital methaemoglobinaemia: cytochrome b(5) reductase deficiency

Some 60 years ago, Quentin Gibson reported the first hereditary disorder involving an enzyme when he deduced that familial methaemoglobinaemia was caused by an enzymatic lesion associated with the glycolysis pathway in red blood cells. This disorder, now known as recessive congenital methaemoglobinaemia (RCM), is caused by NADH-cytochrome b5 reductase (cb(5)r) deficiency. Two distinct clinical forms, types I and II, have been recognized, both characterized by cyanosis from birth. In type II, the cyanosis is accompanied by neurological impairment and reduced life expectancy. Cytochrome b(5) reductase is composed of one FAD and one NADH binding domain linked by a hinge region. It is encoded by the CYB5R3 (previously known as DIA1) gene and more than 40 mutations have been described, some of which are common to both types of RCM. Mutations associated with type II tend to cause incorrect splicing, disruption of the active site or truncation of the protein. At present the description of the sequence variants of cb(5)r in the literature is confusing, due to the use of two conventions which differ by one codon position. Herein we propose a new system for nomenclature of cb(5)r based on recommendations of the Human Genome Variation Society. The development of a heterologous expression system has allowed the impact of naturally occurring variants of cb(5)r to be assessed and has provided insight into the function of cb(5)r.

Structural basis for the platelet-collagen interaction - The smallest motif within collagen that recognizes and activates platelet glycoprotein VI contains two glycine-proline-hydroxyproline triplets

Collagen-related peptide is a selective agonist for the platelet collagen receptor Glycoprotein VI. The triple helical peptide contains ten GPO triplets/strand (single letter amino acid nomenclature, where O is hydroxyproline) and so over-represents GPO compared with native collagen sequence. To investigate the ability of Glycoprotein VI to recognize GPO triplets in a setting more representative of the collagens, we synthesized a set of triple helical peptides containing fewer GPO triplets, varying their number and spacing within an inert (GPP)(n) backbone. The adhesion of recombinant human Glycoprotein VI ectodomain, like that of human platelets, to these peptides increased with their GPO content, and platelet adhesion was abolished by the specific anti-Glycoprotein VI-blocking antibody, 10B12. Platelet aggregation and protein tyrosine phosphorylation were induced only by cross-linked peptides and only those that contained two or more GPO triplets. Such peptides were less potent than cross-linked collagen-related peptide. Our data suggest that both the sequences GPOGPO and GPO center dot center dot center dot center dot center dot center dot center dot center dot center dot GPO represent functional Glycoprotein VI recognition motifs within collagen. Furthermore, we propose that the (GPO)(4) motif can support simultaneous binding of two glycoprotein VI molecules, in either a parallel or anti-parallel stacking arrangement, which could play an important role in activation of signaling.

The contours of memory in post-conflict societies: enacting public remembrance of the bomb in Omagh, Northern Ireland

Drawing on the theoretical insights of Paul Ricoeur this paper investigates the geographies of public remembrance in a post-conflict society. In Northern Ireland, where political divisions have found expression through acts of extreme violence over the past 30 years, questions of memory and an amnesty for forgetting have particular resonance both at the individual and societal level, and render Ricoeur’s framework particularly prescient. Since the signing of the Belfast Agreement in 1998, initiating the Peace Process through consociational structures, discovering a nomenclature and set of practices which would aid in the rapprochement of a deeply divided society has presented a complex array of issues. In this paper I examine the various practices of public remembrance of the 1998 bombing of Omagh as a means of understanding how memory-spaces evolve in a post-conflict context. In Omagh there were a variety of commemorative practices instituted and each, in turn, adopted a different contour towards achieving reconciliation with the violence and grief of the bombing. In particular the Garden of Light project is analysed as a collective monument which, with light as its metaphysical centre, invited the populace to reflect backward on the pain of the bombing while at the same time enabling the society to look forward toward a peaceful future where a politics of hope might eclipse a politics of despair.

The geriatric minimum data set for clinical trials (GMDS)

To overcome the weak evidence base coming from often poor and insufficient clinical research in older people, a minimum data set to achieve harmonisation is highly advisable. This will lead to uniform nomenclature and to the standardisation of the assessment tools. Our primary objective was to develop a Geriatric Minimum Data Set (GMDS) for clinical research.