Sociologists,Archbishops, and ‘making a verb of a noun’

ABSTRACT

Contemporary discussion about race has a tendency to set off out without first checking the rear view mirror. In Theories of Race and Ethnicity: Contemporary Debates and Perspectives, in contrast, Murji and Solomos identify what has and has not been covered, and so appeal at the outset for a ‘more sustained’ account of changing research agendas of race and ethnic relations. Taken as a whole, the collection allows the editors to contemplate ‘what factors explain the mobilizing power of ideas about race and ethnicity in the contemporary environment?' and whether indeed ‘it is the “real” rather than race that should be placed in quotation marks’.     

Synthesis and moisture absorption and retention activities of a carboxymethyl and a quaternary ammonium derivative of α,α-trehalose

Carboxymethyl α,α-trehalose (CMT) and a quaternary ammonium derivative of α,α-trehalose (QT) were successfully prepared, and their moisture absorption and retention activities were assessed. Results showed that both CMT and QT had better moisture absorption abilities at 43% and 81% relative humidity (RH) than α,α-trehalose. In addition, the two α,α-trehalose derivatives had better moisture retention abilities than α,α-trehalose under three humidity conditions: 81% RH, 43% RH, and under dry conditions. Therefore, carboxymethylation and quaternarization could improve the moisture absorption and retention abilities of α,α-trehalose. CMT and QT showed better moisture absorption ability and moisture retention ability than that of hyaluronan (HA), and could potentially find a use as moisture retention ingredient, for example, in cosmetics.     

Cloning and characterization of a novel member of human β-1, 4-galactosyltransferase gene family

By using the EST strategy for identifying novel members belonging to homologous gene families, a novel full-length cDNA encoding a protein significantly homologous to UDP-Gal: N-acetylglucosamine β-1, 4-galactosyltransferase (GAlT) was isolated from a human testis cDNA library. A nucleotide sequence of 2 173 bp long was determined to contain an open reading frame of 1032 nucleotides (344 amino acids). In view of the homology to members of the galactosyltransferase gene family and especially the closest relationship to Gallus gallus GalT type I (CK I), the predicted product of the novel cDNA was designated as human β-1, 4-galactosyltransferase homolog I (HumGT-H1). Its mRNA is present in different degrees in 16 tissues examined. Southern analysis of human genomic DNA revealed its locus on chromosome 3.     

Purification, characterization and modular organization of a cellulose-binding protein, CBP105, a processive β-1,4-endoglucanase from Cellulomonas flavigena

A cellulose-binding protein of 105 kDa (CBP105) from Cellulomonas flavigena was purified and its gene was cloned. CBP105 is a processive endoglucanase with maximum activity on carboxymethyl cellulose (CMC) at pH 7.5 and 60°C. Limited proteolysis suggested that CBP105 is composed of one catalytic domain (CD) and two carbohydrate-binding modules (CBM). The nucleotide sequence of the cbp105 gene (AY729806) indicates that CBP105 is a modular enzyme with a family 9 glycoside hydrolase CD linked to a family 3 CBM, two fibronectin III-like domains and a family 2 CBM. This structural organization may be responsible for CBP105 processive CMC degradation.     

Structure, Mechanistic Action, and Essential Residues of a GH-64 Enzyme, Laminaripentaose-producing ��-1,3-Glucanase

Laminaripentaose-producing β-1,3-glucanase (LPHase), a member of glycoside hydrolase family 64, cleaves a long-chain polysaccharide β-1,3-glucan into specific pentasaccharide oligomers. The crystal structure of LPHase from Streptomyces matensis DIC-108 was solved to 1.62 Å resolution using multiple-wavelength anomalous dispersion methods. The LPHase structure reveals a novel crescent-like fold; it consists of a barrel domain and a mixed (α/β) domain, forming a wide-open groove between the two domains. The liganded crystal structure was also solved to 1.80 Å, showing limited conformational changes. Within the wide groove, a laminaritetraose molecule is found to sit in an electronegatively charged central region and is proximal to several conserved residues including two carboxylates (Glu¹⁵⁴ and Asp¹⁷⁰) and four other sugar-binding residues (Thr¹⁵⁶, Asn¹⁵⁸, Trp¹⁶³, and Thr¹⁶⁷). Molecular modeling using a laminarihexaose as a substrate suggests roles for Glu¹⁵⁴ and Asp¹⁷⁰ as acid and base catalysts, respectively, whereas the side chains of Thr¹⁵⁶, Asn¹⁵⁸, and Trp¹⁶³ demarcate subsite +5. Site-directed mutagenesis of Glu¹⁵⁴ and Asp¹⁷⁰ confirms that both carboxylates are essential for catalysis. Together, our results suggest that LPHase uses a direct displacement mechanism involving Glu¹⁵⁴ and Asp¹⁷⁰ to cleave a β-1,3-glucan into specific α-pentasaccharide oligomers.Glycoside hydrolases (GHs,³ EC 3.2.1.x) hydrolyze the glycosidic bond between two or more carbohydrates or between a carbohydrate and non-carbohydrate moiety (1). These enzymes play diverse roles in nature; they breakdown cellulose into smaller carbohydrates (i.e. during biomass degradation by cellulases), they function during pathogenesis such as the activity of influenza virus neuraminidase (2), and they are engaged in normal cellular metabolic processes that involve the formation and breakage of glycosidic bonds along with glycosyl transferase (3). GHs can be classified as exo- or endo-type of glycoside hydrolases that catalyze the hydrolysis of the glycosidic bond from the end or at the middle, respectively, of a polysaccharide chain. GHs can also be classified as the inverting or the retaining enzymes with respect to their distinct stereochemical mechanisms during catalysis (3). Sequence-based classification of GHs into various families has been proposed by Henrissat et al. (4, 5). Additionally, numerous structures of GHs have revealed details of their catalytic mechanisms as well as the basis for their diverse substrate specificity (6). Based on sequence comparisons and structural analyses, the carbohydrate-active enzymes data base (CAZy) provides continuously updated information on the GH families (7).Two key residues among GHs, generally found as carboxylates, are involved in the hydrolysis of the glycosidic bond: a proton donor and a nucleophile/base (3). In either the retaining or the inverting enzymes, the position of the proton donor is found within hydrogen-bonding distance of the glycosidic oxygen. Active sites that consist of the key residues have been classified into three topologies by Davies and Henrissat (1): (i) a pocket or a crater that preferentially recognizes a saccharide molecule with a non-reducing end, presenting the exo-type hydrolysis, (ii) a cleft or groove that accommodates a large substrate for endo-type cleavage, and (iii) a tunnel that enables a polysaccharide chain to be threaded through for efficient endo-hydrolase processivity.Among the current 114 families of GHs, β-1,3-glucanases, namely exo-β-1,3-glucanases, (E.C. 3.2.1.58) and endo-β-1,3-glucanases (E.C 3.2.1.39) that degrade β-1,3-glucans into smaller biological response modifiers (8) are found in seven families. GH-3 and GH-5 are found to be exo-type; GH-16 and GH-17 are in the endo-type category. Both endo- and exo-type enzymes are found in GH-55. However, GH-64 and GH-81 remain unclear (7). Three-dimensional structures of members from GH-3, GH-5, GH-16, GH-17, and GH-55 have been solved, providing detailed structure-activity information (9–13). Members of the GH-5 and GH-17 families contain a (β/α)₈ architecture, whereas GH-16 family members fold as a β-jelly roll. Barley β-d-glucan exohydrolase, a member of the GH-3 family has an N-terminal TIM-barrel domain and a C-terminal 6-stranded β-sandwich. Notably, glucanases from these families are retaining enzymes. The newly resolved structure of Lam55A, an inverting enzyme in GH-55 family (13), has two β-helical domains, separated by a long linker region, that form a ribcage-like structure. To date, no structure has been reported for GH-64 and GH-81, and thus detailed information on the mode of catalysis is lacking.Laminaripentaose-producing β-1,3-glucanase (LPHase) cleaves a long-chain polysaccharide, β-1,3-glucan, including laminarin, into a specific pentasaccharide oligomer “laminaripentaose” (14, 15). Of interest, β-1,3-glucans such as laminarin, which constitute the cell walls of plants and fungi have interesting biological roles in immune modulation (8, 16, 17). Biochemical characterization of LPHase from Streptomyces matensis DIC-108 showed that the enzyme belongs to the GH-64 family and is an inverting enzyme (14, 15). This enzyme is unique that it releases mainly laminaripentaose as the end product, as compared with that exo-type enzymes produce much smaller sugars (monosaccharides or disaccharides) (18–20) while endo-type enzymes yield heterogeneous forms of oligosaccharides. This atypical product specificity, to our knowledge, has not been reported for other glucanases. Here we report the three-dimensional structures for the apo and complex LPHase of S. matensis. Structural analysis, modeling, and mutagenesis results revealed a novel crescent-fold structure containing Glu¹⁵⁴ and Asp¹⁷⁰ involved in the cleavage of a long-chain oligosaccharide from the reducing end.     

Bromine oxidation of methyl α- and β-pyranosides of D-galactose,D-glucose,and D-mannose

Methyl α- and β-pyranosides of D-galactose, D-glucose, and D-mannose have been oxidized with bromine in aqueous solution at various pH values. The resulting keto glycosides were converted into their more-stable O-methyloxime derivatives which were characterized by spectroscopy and chromatography. Oxidation at a ring carbon atom where the hydrogen is axial is hindered by bulky substituents in syn (i.e., a 1,3) diaxial relationship. Thus, the aglycon group in the α anomers protects position 3, the axial HO-4 in galactopyranosides protects position 2, and the axial HO-2 in mannopyranosides protects position 4 from oxidation.     

Rates of entry and oxidation of acetate,glucose, d(?)-β-hydroxybutyrate,palmitate, oleate and stearate,and rates of production and oxidation of propionate and butyrate in fed and starved sheep

1. Rates of entry and oxidation of a range of metabolites have been measured in tracheostomized sheep (diet, 800g. of lucerne chaff and 100g. of maize/day) by combining isotope-dilution techniques with the continuous measurement of total respiratory gas exchange, and ¹⁴CO₂ production during the intravenous or intraruminal infusion of ¹⁴C-labelled substrates. 2. Mean entry rates in fed and starved (24hr.) sheep respectively, expressed as mg./min./kg. body wt.^0·75, were: glucose, 5·0 (range 4·8–5·1, 2 observations) and 3·8 (3·2–4·2, 4); acetate, 10·8 (9·1–13·5, 4) and 5·8 (1); d(−)-β-hydroxybutyrate, 1·4 (1) and 1·5 (0·8–2·4, 4); palmitate, oleate and stearate (starved sheep only) 1·0 (0·6–1·9, 7), 0·9 (0·2–1·6, 10) and 0·9 (0·5–1·1, 11) respectively. 3. Production rates of propionate and butyrate in continuously feeding sheep were 6·4 (4·7–8·3, 4) and 4·3 (3·4–6·1, 4) mg./min./kg.^0·75 respectively, and in starved (24hr.) sheep were 2·5 (2·2–2·9, 2) and 1·0 (0·8–1·2, 2) mg./min./kg.^0·75 respectively. 4. Calculated terminal values for the specific radioactivity of respiratory ¹⁴CO₂ during measurements of entry rates and production rates were used to calculate the contributions of individual substrates to overall oxidative metabolism. Mean values for fed and starved sheep respectively were: glucose, 9·1 (8·6–9·6, 2) and 11·2 (5·9–15·1, 4)%; acetate, 31·6 (26·8–38·1, 4) and 22·1 (1)%; d(−)-β-hydroxybutyrate, 10·4 (1) and 4·8 (1·9–7·7, 4)%; propionate, 23·0 (13·8–29·9, 4) and 7·1 (6·8–7·4, 2)%; butyrate, 16·5 (13·7–20·5, 4) and 5·3 (5·2–5·3, 2)%; palmitate, oleate and stearate (starved sheep only), 4·7 (2·0–7·7, 7), 4·0 (1·2–6·6, 10) and 4·4 (3·8–5·8, 9)% respectively. The sum of these values for individual substrates in fed and starved sheep, excluding that of β-hydroxybutyrate and after correction of the glucose value for the known interrelations of this substrate with propionate, accounted for 76% and 58% respectively of total production of carbon dioxide. 5. Calculations based on the proportion of substrate entry directly oxidized indicated that the substrates studied accounted for 63% (fed sheep) and 43% (starved sheep) of total energy expenditure measured by oxygen uptake. The contribution of β-hydroxybutyrate was excluded, and corrections were made for glucose–propionate interrelations, and for the different rates of oxidation of the methyl and carboxyl fragments of acetate. 6. The present results have been combined with those obtained earlier in this Laboratory to examine the relationships between rates of substrate entry and oxidation, and concentrations of substrate in blood. Rates of entry of acetate, glucose, d(−)-β-hydroxybutyrate, palmitate and oleate (but not stearate) were well correlated with concentration in blood, and substrate contribution to production of carbon dioxide showed a similar correlation to blood concentration, except with glucose. 7. It was concluded that the general technique is of potential value in providing valid quantitative parameters of animal metabolism.     

Preparation and characterization of a novel polymorph of indiplon, Form α

A new polymorph α of indiplon was discovered, initially prepared by two methods, and further characterized by various means including single-crystal X-ray diffraction (SCXRD), powder X-ray diffraction (PXRD), variable temperature powder X-ray diffraction (VT-PXRD), differential scanning calorimetry (DSC), thermogravimetry analysis (TGA), Fourier transform Raman (FT-Raman) spectroscopy and solubility determination. The crystal structure of Form α as analyzed by SCXRD differ from the three previously reported polymorphs, Form I, II, and III. In addition, PXRD and solubility measurements could clearly distinguish between Form α and Form I. Slight differences between the two forms were also detected by FT-Raman. No differences between Form α and I were observed by DSC, which was explained by VT-PXRD results showing a solid-solid phase change from Form α to Form I during the heating process. Solubility measurements at various temperatures showed that the two polymorphs were mutually monotropic and that Form I was the relatively thermodynamically stable crystal form.     

A comprehensive ex vivo functional analysis of human NKT cells reveals production of MIP1-α and MIP1-β, a lack of IL-17, and a Th1-bias in males

NKT cells contribute to the modulation of immune responses and are believed to be important in the pathogenesis of autoimmune and infectious diseases, as well as cancer. Variations in the composite NKT cytokine response may determine individual disease susceptibility or severity. Due to low frequencies in peripheral blood, knowledge of the breadth of ex vivo human NKT cell functions has been limited. To bridge this gap, we studied highly purified NKT cells from PBMC of healthy donors and assessed the production of 27 effector functions using sensitive Elispot and multiplex bead assays. We found the ex vivo human NKT cell response is predominantly comprised of the chemokines MIP1-α, and MIP1-β as well as the Th1 cytokines IFN-γ and TNF-α. Although lower in magnitude, there was also significant production of IL-2, IL-4, and perforin after mitogen stimulation. Surprisingly, little/no IL-5, IL-6, IL-10, or IL-13 was detected, and no subjects' NKT cells produced IL-17. Comparison of the NKT functional profiles between age-matched male and female subjects revealed similar IL-4 responses, but higher frequencies of cells producing IFN-γ and MIP1-α, from males. There were no gender differences in the circulating NKT subset distribution. These findings implicate chemokines as a major mechanism by which NKT cells control responses in humans. In addition, the panoply of Th2 and Th17 cytokine secretion by NKT cells from healthy donors may not be as pronounced as previously believed. NKT cells may therefore contribute to the gender bias found in many diseases.     

Structure and stability of Gyuba, a β-lactoglobulin chimera

β-lactoglobulin (LG) contains nine β-strands (strands A-I) and one α-helix. Strands A-H form a β-barrel. At neutral pH, equine LG (ELG) is monomeric, whereas bovine LG (BLG) is dimeric, and the I-strands of its two subunits form an intermolecular β-sheet. We previously constructed a chimeric ELG in which the sequence of the I-strand was replaced with that of BLG. This chimera did not dimerize. For this study, we constructed the new chimera we call Gyuba (which means cow and horse in Japanese). The amino acid sequence of Gyuba includes the sequences of the BLG secondary structures and those of the ELG loops. The crystal structure of Gyuba is very similar to that of BLG and indicates that Gyuba dimerizes via the intermolecular β-sheet formed by the two I-strands. Thus, the entire arrangement of the secondary structural elements is important for LG dimer formation.     

A glycan of Ψ-factor from Dictyostelium discoideum contains a bisecting-GlcNAc, an intersecting-GlcNAc, and a core α-1,6-fucose

A secretory glycoprotein named Ψ-factor that we have purified and cloned from Dictyostelium discoideum is prespore cell-inducing factor. To address its functional significance, it is necessary to examine the attached sites and structures of its glycans as well as its protein structure. Here we identified and isolated a tryptic glycosylated peptide with the 71st to 89th amino acids of Ψ-factor that contained the consensus amino acid sequence for an N-linked glycan (N-T-T). MALDI-TOF mass spectrometry indicated that the major protonated molecular ions, [M+H](+), of the glycopeptide were present at m/z 3,806, the minor m/z 3,603 and 3,400 ions corresponding to the loss of one and two N-acetylhexosamines respectively. Digestion of it with N-glycosidase F gave a molecular mass of 1,766.9 for the whole glycan moiety, which accounts for its composition of five hexoses, four N-acetylhexosamines, and a deoxyhexose. Further digestion experiments on the basis of the substrate specificity of α-mannosidase and β-N-acetylhexosaminidase allowed us to elucidate the unique structure of the glycan, which contains a bisecting and an intersecting GlcNAc and a core α1,6-fucosyl moiety.     

Production, Characterization, and Properties of β-Glucosidase and β-Xylosidase from a Strain of Aureobasidium sp.

-Glucosidase and -xylosidase production by a yeastlike Aureobasidium sp. was carried out during solid-state and submerged fermentation using different carbon sources and crude enzymes were characterized. -Glucosidase and -xylosidase exhibited optimum activities at pH 2.0–2.5 and 3.0, respectively. These enzymes had the maximum activities at 65°C and were stable in a wide pH range and at high temperatures.     

Recombinant expression,characterization, and pulp prebleaching property of a Phanerochaete chrysosporium endo-β-1,4-mannanase

A Phanerochaete chrysosporium cDNA predicted to encode endo-1,4-β-d-mannanase, man5D, was cloned and expressed in Aspergillus niger. The coding region of the gene man5D was predicted to contain, in order from the N-terminal: a secretory signal peptide, cellulose-binding domain, linker region, and glycosyl hydrolase family 5 catalytic site. The enzyme was purified from culture filtrate of A. niger transformants that carried the recombinant man5D. Recombinant Man5D had an apparent molecular size of about 65 kDa by SDS-PAGE, and optimal activity at pH 4.0–6.0 and 60 °C. It was stable from pH 4.0 to 8.0 and up to 60 °C. The enzyme showed affinity for Avicel cellulose, suggesting that the predicted cellulose-binding domain is biologically functional. The specific activities of Man5D on mannan, galactomannan, and glucomannan at pH 5 and 60 °C ranged from 160 to 460 μmol/(min mg), with apparent K_m values from 0.54 to 2.3 mg/mL. Product analysis results indicated that Man5D catalyzes endo-cleavage, and appears to have substantial transglycosylase activity. When used to treat softwood kraft pulp, Man5D hydrolyzed mainly glucomannan and exhibited a positive effect as a prebleaching agent. Compared to a commercial prebleaching with xylanase, the prebleaching effect of Man5D was weaker but with reduced loss of fibre yield as determined by the release of solubilized sugars.     

Antigenic similarity between the β-subunits of the ATPases of a bacterium,a yeast and a higher plant

Antiserum raised against the β-subunit of wheat (Triticum aestivum) chloroplast ATPase cross-reacts with a 51000 protein located in the membrane fraction of Escherichia coli. The differential solubility of this polypeptide after chloroform treatment of unc⁺ and uncD409 strains indicates that this cross-reacting polypeptide is the bacterial β-subunit of ATPase. Thus a high degree of conservation of antigenic determinant sites exists between a bacterial β-subunit and the β-subunit of a monocot. This conservation also seems to extend to the β-subunit of mitochondrial ATPase of yeast (Saccharomyces cerevisiae).     

Biosynthesis,cDNA and amino acid sequences of a precursor of conglutin δ, a sulphur-rich protein from Lupinus angustifolius

The biosynthesis of conglutin has been studied in developing cotyledons of Lupinus angustifolius L. Precursors of conglutin formed the major sink for [³⁵S]-cysteine incorporated by developing lupin cotyledons, and these precursors were rapidly sequestered into the endoplasmic reticulum. The sequence of a cDNA clone coding for one such precursor of conglutin was determined. The structure of the precursor polypeptide for conglutin predicted from the cDNA sequence contained an N-terminal leader peptide of 22 amino acids directly preceding a subunit polypeptide of M _r 4520, together with a linking region of 13 amino acids and a subunit polypeptide of M _r 9558 at the C-terminus. The amino acid sequence predicted from the cDNA sequence showed minor variations from that established by sequencing of the protein purified from mature dried seeds (Lilley and Inglis, 1986). These were consistent with the existence of a multi-gene family coding for conglutin . Comparison of the sequences of conglutin with those of other 2S storage proteins showed that the cysteines involved in internal disulphide bridges between the mature subunits of conglutin , were maintained throughout this family of proteins but that little else was conserved either at the protein or DNA level.     

Location of a cell-wall hydroxyproline-rich glycoprotein,cellulose and β-1,3-glucans in apical and differentiated regions of maize mycorrhizal roots

The cell-wall components of the interface compartment in functioning mycorrhizal roots of maize (Zea mays L. cv. W64A) have been investigated with the use of immunocytochemistry and enzyme/lectin-gold techniques. The distribution of specific cell-wall probes was determined in the apical and differentiated regions of maize roots in the presence and in the absence of the mycorrhizal fungus, Glomus versiforme. Labelling experiments showed that a maize hydroxyproline-rich glycoprotein (HRGP), identified with a specific antibody, was particularly abundant in the apical dividing cells of the root meristem. Cellulose, located with a cellobiohydrolase-gold complex, showed a similar labelling pattern in the walls of both meristematic and differentiated parts of the roots. When the cortex was colonized by the mycorrhizal fungus, the HRGP and cellulose were expressed in two sites: the wall and the interface area created by invagination of the host membrane around the developing fungus. In contrast, in uninfected roots of the same age, they were only present in the inner part of the wall. A specific antibody against -1,3-glucans demonstrated that these glucans were not laid down at the interface between the plant and fungus, while they appeared to be a skeletal component of the fungal wall, together with chitin.Abbreviations CBH I cellobiohydrolase - DAPI 4,6-diamino-2-phenylindole - HRGP hydroxyproline-rich glycoprotein The research was supported by the Italian Murst (40%) grant and by an International Project between Spain and Italy (Azioni Integrate).     

Structure and Properties of a Complex of α-Synuclein and a Single-Domain Camelid Antibody

The aggregation of the intrinsically disordered protein α-synuclein to form fibrillar amyloid structures is intimately associated with a variety of neurological disorders, most notably Parkinson's disease. The molecular mechanism of α-synuclein aggregation and toxicity is not yet understood in any detail, not least because of the paucity of structural probes through which to study the behavior of such a disordered system. Here, we describe an investigation involving a single-domain camelid antibody, NbSyn2, selected by phage display techniques to bind to α-synuclein, including the exploration of its effects on the in vitro aggregation of the protein under a variety of conditions. We show using isothermal calorimetric methods that NbSyn2 binds specifically to monomeric α-synuclein with nanomolar affinity and by means of NMR spectroscopy that it interacts with the four C-terminal residues of the protein. This latter finding is confirmed by the determination of a crystal structure of NbSyn2 bound to a peptide encompassing the nine C-terminal residues of α-synuclein. The NbSyn2:α-synuclein interaction is mediated mainly by side-chain interactions while water molecules cross-link the main-chain atoms of α-synuclein to atoms of NbSyn2, a feature we believe could be important in intrinsically disordered protein interactions more generally. The aggregation behavior of α-synuclein at physiological pH, including the morphology of the resulting fibrillar structures, is remarkably unaffected by the presence of NbSyn2 and indeed we show that NbSyn2 binds strongly to the aggregated as well as to the soluble forms of α-synuclein. These results give strong support to the conjecture that the C-terminal region of the protein is not directly involved in the mechanism of aggregation and suggest that binding of NbSyn2 could be a useful probe for the identification of α-synuclein aggregation in vitro and possibly in vivo.