Potential implications of the glycosylation patterns in collagen α1(I) and α2(I) chains for fibril assembly and growth.

O-Glycosylation of hydroxylysine (Hyl) in collagen occurs at an early stage of biosynthesis before the triple-helix has formed. This simple post-translational modification (PTM) of lysine by either a galactosyl or glucosylgalactosyl moiety is highly conserved in collagens and depends on the species, type of tissue and the collagen amino acid sequence. The structural/functional reason why only specific lysines are modified is poorly understood, and has led to increased efforts to map the sites of PTMs on collagen sequences from different species and to ascertain their potential role in vivo. To investigate this, we purified collagen type I (Col1) from the skins of four animals, then used mass spectrometry and proteomic techniques to identify lysines that were oxidised, galactosylated, glucosylgalactosylated, or glycated in its mature sequence. We found 18 out of the 38 lysines in collagen type Iα1, (Col1A1) and 7 of the 30 lysines in collagen type Iα2 (Col1A2) were glycosylated. Six of these modifications had not been reported before, and included a lysine involved in crosslinking collagen molecules. A Fourier transform analysis of the positions of the glycosylated hydroxylysines showed they display a regular axial distribution with the same d-period observed in collagen fibrils. The significance of this finding in terms of the assembly of collagen molecules into fibrils and of potential restrictions on the growth of the collagen fibrils is discussed.

A simple but precise method for quantitative measurement of the quality of the laser focus in a scanning optical microscope.

We report a method for characterizing the focussing laser beam exiting the objective in a laser scanning microscope. This method provides the size of the optical focus, the divergence of the beam, the ellipticity and the astigmatism. We use a microscopic-scale knife edge in the form of a simple transmission electron microscopy grid attached to a glass microscope slide, and a light-collecting optical fibre and photodiode underneath the specimen. By scanning the laser spot from a reflective to a transmitting part of the grid, a beam profile in the form of an error function can be obtained and by repeating this with the knife edge at different axial positions relative to the beam waist, the divergence and astigmatism of the postobjective laser beam can be obtained. The measured divergence can be used to quantify how much of the full numerical aperture of the lens is used in practice. We present data of the beam radius, beam divergence, ellipticity and astigmatism obtained with low (0.15, 0.7) and high (1.3) numerical aperture lenses and lasers commonly used in confocal and multiphoton laser scanning microscopy. Our knife-edge method has several advantages over alternative knife-edge methods used in microscopy including that the knife edge is easy to prepare, that the beam can be characterized also directly under a cover slip, as necessary to reduce spherical aberrations for objectives designed to be used with a cover slip, and it is suitable for use with commercial laser scanning microscopes where access to the laser beam can be limited.

Energy shedding during nonlinear self-focusing of optical beams.

Self-focusing of intense laser beams and pulses of light in real nonlinear media is in general accompanied by material losses that require corrections to the conservative Nonlinear Schrödinger equations describing their propagation. Here we examine loss mechanisms that exist even in lossless media and are caused by shedding of energy away from the self-trapping beam making it to relax to an exact solution of lower energy. Using the conservative NLS equations with absorbing boundary conditions we show that energy shedding not only occurs during the initial reshaping process but also during oscillatory propagation induced by saturation of the nonlinear effect. For pulsed input we also show that, depending on the sign and magnitude of dispersion, pulse splitting, energy shedding, collapse or stable self-focusing may result.

Increased signals from short-wavelength-excited fluorescent molecules using sub-Ti:Sapphire wavelengths.

We report the use of an all-solid-state ultrashort pulsed source specifically for two-photon microscopy at wavelengths shorter than those of the conventional Ti:Sapphire laser. Our approach involves sum-frequency mixing of the output from an optical parametric oscillator (λ= 1400-1640 nm) synchronously pumped by a Yb-doped fibre laser (λ= 1064 nm), with the residual pump radiation. This generated an fs-pulsed output tunable in the red spectral region (λ= 620-636 nm, ~150 mW, 405 fs, 80 MHz, M(2) ~ 1.3). We demonstrate the performance of our ultrashort pulsed system using fluorescently labelled and autofluorescent tissue, and compare with conventional Ti:Sapphire excitation. We observe a more than 3-fold increase in fluorescence signal intensity using our visible laser source in comparison with the Ti:Sapphire laser for two-photon excitation at equal illumination peak powers of 1.16 kW or less.

A search for predictive biomarkers of ovine pre-partum vaginal prolapse.

Ovine pre-partum vaginal prolapse (known as bearings in sheep) occurs within a few weeks prior to lambing and unless treated both ewes and unborn lambs will die. It is a worldwide problem with no clear aetiology. Rates of prolapse in New Zealand typically vary from 0.1 to 2% per annum, varying between seasons and farms. In order to determine preclinical changes leading to prolapse, blood samples were collected prior to prolapse occurring and analysed for changes in both protein and specific hormone and vitamin levels. 650 ewes were ear tagged and blood samples were taken one month prior to the beginning of lambing; 28 of these ewes subsequently prolapsed. Using an improved proteomic method plasma samples were subjected to 2D DIGE (two dimensional differential in gel electrophoresis) to determine if there were differences between the pre-prolapse and non-prolapsing ewes. Acidic isoforms of haptoglobin, a major acute phase protein in ruminants, increased approximately 3-fold in ewes prior to prolapse occurring. Total haptoglobin quantitation was confirmed with an independent assay. Although another plasma protein, α-1B-glycoprotein, was down regulated close to prolapse, the biological significance of this is unknown. While vitamin D levels were not associated with subsequent prolapse there was, however, a negative correlation between cortisol and days to prolapse from sampling (r2 = 0.36); i.e. ewes sampled closest to prolapse had higher plasma cortisol concentrations than controls. This raises the possibility that the ewes which prolapsed may have been suffering from chronic stress. Further research is needed.

Relaxed damage threshold intensity conditions and nonlinear increase in the conversion efficiency of an optical parametric oscillator using a bi-directional pump geometry.

A novel bi-directional pump geometry that nonlinearly increases the nonlinear optical conversion efficiency of a synchronously pumped optical parametric oscillator (OPO) is reported. This bi-directional pumping method synchronizes the circulating signal pulse with two counter-propagating pump pulses within a linear OPO resonator. Through this pump scheme, an increase in nonlinear optical conversion efficiency of 22% was achieved at the signal wavelength, corresponding to a 95% overall increase in average power. Given an almost unchanged measured pulse duration of 260 fs under optimal performance conditions, this related to a signal wavelength peak power output of 18.8 kW, compared with 10 kW using the traditional single-pass geometry. In this study, a total effective peak intensity pump-field of 7.11 GW/cm(2) (corresponding to 3.55 GW/cm(2) from each pump beam) was applied to a 3 mm long periodically poled lithium niobate crystal, which had a damage threshold intensity of 4 GW/cm(2), without impairing crystal integrity. We therefore prove the application of this novel pump geometry provides opportunities for power-scaling of synchronously pumped OPO systems together with enhanced nonlinear conversion efficiency through relaxed damage threshold intensity conditions.

Assessment of pelt quality in leather making using a novel non-invasive sensing approach.

Excessive removal of structural material from skin during leather processing results in unattractive crease formation in leather. It is difficult to detect this in pelts at an early processing stage as it only becomes really apparent once the skin is made into leather. There would be great advantages in detecting the problem at the pickled pelt stage (skins treated with sodium sulphide and lime, bated with enzymes, and then preserved in NaCl and sulphuric acid) so that adjustments to the processing could be made to mitigate the effect. A novel bio-sensor for inspection of pickled lamb pelts has been fabricated and developed. The sensor has the planar Interdigital structure. The experimental results show that the sensor has a great potential to predict the quality of leather in a non-invasive and non-destructive way.

The perceived effects and comfort of various body armour systems on police officers while performing occupational tasks.

BACKGROUND: The nature of police work often necessitates use of Individual Light Armour Vests (ILAVs) for officer protection. Previous research has demonstrated various biomechanical and physical performance impacts of ILAVs, however, little knowledge exists on the individual officer's perceptions of ILAV. The aim of this study was to investigate officers' perceptions of the impacts of three different ILAVs and normal station wear whilst performing police occupational tasks. METHODS: A prospective, within subjects, repeated measures design was employed in which 11 serving police officers wore each of three different types of body armour (ILAV A, ILAV B or ILAV C) and normal station wear for a full day while performing tasks including a simulated victim drag, a patrol vehicle exit and a marksmanship shoot. Ratings of Perceived Exertion (RPE) and a Visual Analogue Scale (VAS; - 10 to + 10) were used to examine officer perceptions of each ILAV. Finally, officers were asked to indicate areas of both discomfort and comfort of each ILAV on a mannequin chart. RESULTS: Officers perceived less effort was required for the victim drag whilst wearing ILAV B (RPE = 3.6/10) when compared to ILAV A, ILAV C and even station wear (RPE = 4.7/10, 4.0/10, 3.8/10, respectively). A positive impact on performance was perceived for ILAV B (VAS = + 0.26) when performing a patrol vehicle exit and sprint task but not for the other two ILAVs (VAS = - 3.58, - 0.55, - 0.85, respectively). Officers perceived a positive impact of ILAV B (VAS = + 2.7) and station wear (VAS = + 1.4) and a negative impact of ILAVs A and C (VAS = - 2.1, - 1.7 respectively) on marksmanship. Despite all armour types being criticized for discomfort, ILAV B received lower ratings of discomfort overall, and some positive comments regarding both comfort and performance. CONCLUSIONS: Officers perceived ILAV B to have positive effects on task performance. It was also rated more comfortable than the other two, possibly due to a longer torso design which shifted load from the shoulders to the hips and pelvis. Officer perceptions of comfort and effects on occupational performance should be considered when designing and procuring armour systems. Although ILAVs may be similar, perceived impacts may vary between officers.

The three-dimensional structure of PNGase F, a glycosylasparaginase from Flavobacterium meningosepticum.

BACKGROUND: Peptide:N-glycosidase F (PNGase F) is an enzyme that catalyzes the complete removal of N-linked oligosaccharide chains from glycoproteins. Often called an endoglycosidase, it is more correctly termed an amidase or glycosylasparaginase as cleavage is at the asparagine-sugar amide linkage. The enzyme is widely used in structure-function studies of glycoproteins. RESULTS: We have determined the crystal structure of PNGase F at 1.8 A resolution. The protein is folded into two domains, each with an eight-stranded antiparallel beta jelly roll configuration similar to many viral capsid proteins and also found, in expanded form, in lectins and several glucanases. Two potential active site regions have been identified, both in the interdomain region and shaped by prominent loops from one domain. Exposed aromatic residues are a feature of one site. CONCLUSIONS: The finding that PNGase F is based on two jelly roll domains suggests parallels with lectins and other carbohydrate-binding proteins. These proteins either bind sugars on the concave face of the beta-sandwich structure (aided by loops) or amongst the loops themselves. Further analysis of the function and identification of the catalytic site should lead to an understanding of both the specificity of PNGase F and possibly also the recognition processes that identify glycosylation sites on proteins.

Conceptual framework for outcomes research studies of hepatitis C: an analytical review.

Hepatitis C virus infection is one of the main causes of chronic liver disease worldwide. Until recently, the standard antiviral regimen for hepatitis C was a combination of an interferon derivative and ribavirin, but a plethora of new antiviral drugs is becoming available. While these new drugs have shown great efficacy in clinical trials, observational studies are needed to determine their effectiveness in clinical practice. Previous observational studies have shown that multiple factors, besides the drug regimen, affect patient outcomes in clinical practice. Here, we provide an analytical review of published outcomes studies of the management of hepatitis C virus infection. A conceptual framework defines the relationships between four categories of variables: health care system structure, patient characteristics, process-of-care, and patient outcomes. This framework can provide a starting point for outcomes studies addressing the use and effectiveness of new antiviral drug treatments.

Preliminary crystallographic studies on human apo-lactoferrin in its native and deglycosylated forms.

Human apo-lactoferrin in both native and deglycosylated forms has been purified, and crystals obtained by dialysis against low ionic strength buffer solutions. The crystals of native apo-lactoferrin are orthorhombic, space group P2(1)2(1)2(1) with cell dimensions a = 222.0 A, b = 115.6 A, c = 77.8 A and have two protein molecules per asymmetric unit. Two crystal forms of deglycosylated apo-lactoferrin have been obtained. One is orthorhombic, space group P2(1)2(1)2(1), with cell dimensions a = 152.1 A, b = 94.6 A, c = 55.8 A. The second is tetragonal, space group I4, with cell dimensions a = b = 189.4 A, c = 55.1 A. Both of the latter have only one molecule per asymmetric unit, and are suitable for high-resolution X-ray structure analysis.

Structure of azurin from Alcaligenes denitrificans at 2.5 A resolution.

The structure of the blue copper protein, azurin, from Alcaligenes denitrificans has been determined from an electron density map at a nominal resolution of 3.0 A. Four isomorphous heavy-atom derivatives, prepared with KAu(CN)2, uranyl acetate, Hg(NH3)2Cl2 and KAu(CN)2 + uranyl acetate (a double derivative) were used to calculate phases by the method of isomorphous replacement. The overall figure of merit was 0.61. The two molecules in the asymmetric unit are related by an approximate 2-fold axis. Independent interpretations of the density were made for the two molecules, and the structures have since been partially refined. After 12 refinement cycles, using the Hendrickson-Konnert restrained least-squares program, the R factor is 0.318 for data to 2.5 A resolution and there are no major conformational differences between the two molecules. Refinement is continuing. Eight extended strands of the polypeptide chain form a beta-barrel structure whose topology is the same as that of plastocyanin and the alternative folding proposed for Pseudomonas aeruginosa azurin. As in the latter two proteins, the copper atom forms three short bonds, with His-46 N delta 1, His117 N delta 1 and Cys112 S gamma, and one longer bond, with Met121 S delta, these four ligands forming a very distorted tetrahedron. A possible additional interaction, between copper and the carbonyl oxygen of Gly45, cannot be discounted at the present stage of the analysis. A surface hydrophobic patch, around the edge of the imidazole ring of His117 appears the most likely electron transfer locus. The sequences of azurin and plastocyanin have been aligned and the homology between the two proteins is discussed.

Structure of human lactoferrin: crystallographic structure analysis and refinement at 2.8 A resolution.

The structure of human lactoferrin has been refined crystallographically at 2.8 A (1 A = 0.1 nm) resolution using restrained least squares methods. The starting model was derived from a 3.2 A map phased by multiple isomorphous replacement with solvent flattening. Rebuilding during refinement made extensive use of these experimental phases, in combination with phases calculated from the partial model. The present model, which includes 681 of the 691 amino acid residues, two Fe3+, and two CO3(2-), gives an R factor of 0.206 for 17,266 observed reflections between 10 and 2.8 A resolution, with a root-mean-square deviation from standard bond lengths of 0.03 A. As a result of the refinement, two single-residue insertions and one 13-residue deletion have been made in the amino acid sequence, and details of the secondary structure and tertiary interactions have been clarified. The two lobes of the molecule, representing the N-terminal and C-terminal halves, have very similar folding, with a root-mean-square deviation, after superposition, of 1.32 A for 285 out of 330 C alpha atoms; the only major differences being in surface loops. Each lobe is subdivided into two dissimilar alpha/beta domains, one based on a six-stranded mixed beta-sheet, the other on a five-stranded mixed beta-sheet, with the iron site in the interdomain cleft. The two iron sites appear identical at the present resolution. Each iron atom is coordinated to four protein ligands, 2 Tyr, 1 Asp, 1 His, and the specific Co3(2-), which appears to bind to iron in a bidentate mode. The anion occupies a pocket between the iron and two positively charged groups on the protein, an arginine side-chain and the N terminus of helix 5, and may serve to neutralize this positive charge prior to iron binding. A large internal cavity, beyond the Arg side-chain, may account for the binding of larger anions as substitutes for CO3(2-). Residues on the other side of the iron site, near the interdomain crossover strands could provide secondary anion binding sites, and may explain the greater acid-stability of iron binding by lactoferrin, compared with serum transferrin. Interdomain and interlobe interactions, the roles of charged side-chains, heavy-atom binding sites, and the construction of the metal site in relation to the binding of different metals are also discussed.

Preliminary crystallographic studies of the amino terminal half of human lactoferrin in its iron-saturated and iron-free forms.

The amino terminal half of human lactoferrin (LfN) produced from transfected baby hamster kidney cells has been crystallized in its iron-saturated and iron-free forms. The crystals of glycosylated LfN and deglycosylated LfN are monoclinic, space group C2, with cell dimensions a = 133.0 A, b = 58.3 A, c = 58.3 A, alpha = 90.0 degrees, beta = 114.7 degrees, gamma = 90.0 degrees, and one molecule per asymmetric unit. Crystals of apo LfN have also been prepared using deglycosylated protein. These crystals are tetragonal, space group P4(1)2(1)2 (or P4(3)2(1)2), with cell dimensions of a = b = 58.4 A and c = 217.2 A and one molecule per asymmetric unit. Both the iron-saturated and the iron-free crystals are suitable for high resolution X-ray analysis.

Purification and crystallization of the endoglycosidase PNGase F, a peptide:N-glycosidase from Flavobacterium meningosepticum.

The endoglycosidase peptide: N-glycosidase, secreted by the Gram-negative bacterium Flavobacterium meningosepticum (PNGase F), has been isolated, purified to homogeneity and crystallized from polyethylene glycol solutions using vapour diffusion and seeding techniques. The crystals are orthorhombic, space group P2(1)2(1)2, with unit cell dimensions a = 85.07 A, b = 85.14 A, c = 48.50 A, and are suitable for high resolution X-ray structure analysis.

Crystallization of the C-terminal domain of rabbit serum hemopexin.

The C-terminal domain of rabbit serum hemopexin, comprising residues 215 to 435, has been crystallized following removal of the attached carbohydrate using the endoglycosidase Endo F. The crystals, grown by vapour diffusion from solutions containing polyethylene glycol 1500, are orthorhombic, with cell dimensions a = 41.0 A, b = 64.2 A, c = 85.2 A, space group P2(1)2(1)2(1), and one molecule in the asymmetric unit. The crystals diffract to 2.4 A resolution and are suitable for X-ray structure analysis.

Domain closure in lactoferrin. Two hinges produce a see-saw motion between alternative close-packed interfaces.

Lactoferrin is an iron transport protein. Upon binding iron, the two domains in the N-terminal half of the molecule move together. Previous work has shown that this domain closure involves two hinges. Using the newly refined structure of the open form, the structural mechanism underlying this motion is analyzed here in detail. Upon closure the domains rotate 54 degrees essentially as rigid bodies. The axis of rotation passes through the two beta-strands linking the domains. These strands contain hinges in the sense that three large torsion angle changes are responsible for the bulk of the motion while smaller torsion angle changes in neighboring residues are responsible for the remainder of the motion. The rotation axes of these three torsion angle changes are nearly parallel to the axis of the overall 54 degrees rotation, so the local motion in the hinges can be directly related to the overall motion. A crucial feature of the hinge residues is that they have very few packing constraints on their main-chain atoms. The domains make different packing contacts with each other in the open and closed forms. These contacts form two interdomain interfaces arranged on either side of the hinges. Pivoting about the hinges produces a see-saw motion between the two interfaces. That is, when the domains close down, residues in the interface on one side of the hinges become buried and close-packed and residues on the other side become exposed. The situation is reversed when the domains open up. Lactoferrin provides a particularly clear example of the general features of hinged domain motion. It is compared to other instances of hinged domain closure and contrasted with instances of shear domain closure, where the overall motion is a summation of many small sliding motions between close-packed segments of polypeptide.

Altered domain closure and iron binding in transferrins: the crystal structure of the Asp60Ser mutant of the amino-terminal half-molecule of human lactoferrin.

The crystal structure of a site-specific mutant of the N-terminal half-molecule of human lactoferrin, Lf(N), in which the iron ligand Asp60 has been mutated to Ser, has been determined at 2.05 A resolution in order to determine the effects of the mutation on iron binding and domain closure. Yellow monoclinic crystals of the D60S mutant, in its iron-bound form, were prepared, and have unit cell dimensions a = 110.2 A, b = 57.0 A, c = 55.2 A, beta = 97.6 degrees, space group C2, with one molecule of 333 residues in the asymmetric unit. The structure was determined by molecular replacement, using the wild-type Lf(N) as search model, and was refined by restrained least-squares methods. The final model, comprising 2451 protein atoms (from residues 2 to 315) one Fe3+ and one CO2-(3), and 107 water molecules, gives an R-factor of 0.175 for all data in the resolution range 20.0 to 2.05 A. The model conforms well with standard geometry, having root-mean-square deviations of 0.014 A and 1.2 degrees from standard bond lengths and angles. The structure of the D60S mutant deviates in two important respects from the parent Lf(N) molecule. At the mutation site the Ser side-chain neither binds to the iron atom nor makes any interdomain contact as the substituted Asp does; instead a water molecule fills the iron coordination site and participates in interdomain hydrogen bonding. The domain closure is also changed, with the D60S mutant having a more closed conformation. Consideration of crystal packing suggests that the altered domain closure is a genuine molecular property but both the iron coordination and interdomain contacts are consistent with weakened iron binding in the mutant. The implications for iron binding in transferrins generally are discussed.

Preliminary crystallographic studies on bovine lactoferrin.

The purification of bovine lactoferrin, its crystallization at low ionic strength, and preliminary X-ray crystallographic data are reported. The crystals, which grow from a two-phase system, are radiation-stable and suitable for a medium-resolution X-ray analysis. They are orthorhombic, space group P2(1)2(1)2(1), with cell dimensions a = 138.4 A, b = 87.1 A, c = 73.6 A, and one protein molecule in the asymmetric unit.

Anticonvulsant activity of some 4-aminobenzanilides.

A series of 4-aminobenzanilides derived from ring-alkylated anilines were prepared and evaluated for anticonvulsant activity. These benzanilides were prepared in the course of studies designed to determine the relationship between the benzamide structure and anticonvulsant effects. The compounds were tested in mice against seizures induced by electroshock and metrazole (pentylenetetrazole) and in the rotorod assay for neurologic deficit. All of the 4-aminobenzanilides showed activity at doses of 300 mg/kg against maximal electroshock seizures (MES). The 4-aminobenzanilide derived from 2,6-dimethylaniline (8) was the most potent anti-MES compound with an ED50 of 2.60 mg/kg and a protective index of 5.77 (PI = TD50/ED50). The activity profile for 8 compares quite favorably with that for phenobarbital and phenytoin in the same assays.