Axial spatial distribution focusing: improving MALDI-TOF/RTOF mass spectrometric performance for high-energy collision-induced dissociation of biomolecules.

RATIONALE: For the last two decades, curved field reflectron technology has been used in matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometers, assisting in the generation of post-source-decay (PSD) or collision-induced dissociation (CID) without decelerating precursor ions, producing true high-energy CID spectra. The result was the generation of product ion mass spectra with product ions typical of high-energy (10 keV and beyond) collision processes. The disadvantage of this approach was the lack of resolution in CID spectra resulting from the excess laser energy deposition used to generate those MS/MS spectra. The work presented in this study overcomes this limitation and includes comprehensive examples of high-energy and high-resolution CID MALDI-MS/MS spectra of biomolecules. METHODS: The devices used in this study are TOF/RTOF instruments equipped with a high-vacuum MALDI ion source. High-resolution and high-energy CID spectra result from the use of axial spatial distribution focusing (ASDF) in combination with curved field reflectron technology. RESULTS: A CID spectrum of the P14 R1 peptide exhibits product ion resolution in excess of 10,000 (FWHM) but at the same time yields typical high-energy product ions such as w- and [y-2]-type ion series. High-energy CID spectra of lipids, exemplified by a glycerophospholipid and triglyceride, demonstrate C-C backbone fragmentation elucidating the presence of a hydroxyl group in addition to double-bond positioning. A complex high mannose carbohydrate (Man)8 (GlcNAc)2 was also studied at 20 keV collision energy and revealed further high-energy product ions with very high resolution, allowing unambiguous detection and characterization of cross-ring cleavage-related ions. CONCLUSIONS: This is the first comprehensive study using a MALDI-TOF/RTOF instrument equipped with a curved field reflectron and an ASDF device prior to the reflectron. © 2015 The Authors. Rapid Communications in Mass Spectrometry published by John Wiley & Sons Ltd.

Tooth microwear formation rate in Gasterosteus aculeatus.

Tooth microwear feature densities were significantly increased in a population of laboratory-reared three-spined stickleback Gasterosteus aculeatus in four days, after they were transferred from a limnetic feeding regime to a benthic feeding regime. These results show that even in aquatic vertebrates with non-occluding teeth, changes in feeding can cause changes in tooth microwear in just a few days, as in mammals.

Behavioural thermoregulation in two freshwater fish species.

In the presence of a vertical thermal gradient, juvenile three-spined sticklebacks Gasterosteus aculeatus and minnows Phoxinus phoxinus positioned themselves higher in the water column compared with adult conspecifics. This result was consistent regardless of whether age cohorts were tested separately or together. Furthermore, juveniles but not adult fishes positioned themselves higher in water column in the presence of a thermal gradient compared with those in the absence of a thermal gradient. Juvenile G. aculeatus and adult fish of both species did opt to position themselves higher in the water column in the hours immediately following a feeding event relative to their positions in the same gradient when they had not fed.

Shoal and prey patch choice by co-occurring fishes and prawns: inter-taxa use of socially transmitted cues.

Animals can use socially transmitted information to learn about the distribution and quality of resources without incurring the costs associated with having to search for and sample them first hand. Recently, it has been shown that the use of chemical social information specific to patterns of diet and habitat use is an important mechanism underpinning recognition and social organization in shoaling fishes. In this study we revealed that the use of resource-specific chemical information is not limited to conspecifics, or even members of the same taxon. In a series of laboratory experiments, we showed that threespine sticklebacks (Gasterosteus aculeatus) could recognize similar patterns of habitat use in common prawns (Leander serratus), preferentially orientating towards groups of prawns exposed to the same habitats as themselves, and even selecting foraging patches located close to them. Prawns were seen to use habitat-specific cues generated by conspecifics, but not by sticklebacks, suggesting that the benefits of forming these heterospecific social association patterns may be unequal for prawns and fishes. Our findings suggest that some species might use co-occurring, unrelated species as information centres in order to orient and locate resources within their surroundings.

Crystallization of an endochitinase from Hordeum vulgar L. seeds.

Higher plants contain several constitutively expressed proteins for protection against infections by viruses, bacteria and fungi. Here we report the crystallization of a polypeptide with antifungal activity, a 26,000 dalton endochitinase from barley (Hordeum vulgare L.) seeds, in a form suitable for high-resolution X-ray analysis. Crystals were grown by vapor diffusion under several different conditions. The best crystals, obtained with ammonium sulfate as the precipitant, belong to the tetragonal space group P4(1)2(1)2 (P4(3)2(1)2), with cell dimensions a = b = 62.9 A and c = 96.0 A. The cell dimensions are consistent with one endochitinase molecule per asymmetric unit, and the crystals diffract to at least 2.0 A resolution.

The refined crystal structure of an endochitinase from Hordeum vulgare L. seeds at 1.8 A resolution.

Class II chitinases (EC 3.2.1.14) are plant defense proteins. They hydrolyze chitin, an insoluble beta-1,4-linked polymer of N-acetylglucosamine (NAG), which is a major cell-wall component of many fungal hyphae. We previously reported the three-dimensional structure of the 26 kDa class II endochitinase from barley seeds at 2.8 A resolution, determined using multiple isomorphous replacement (MIR) methods. Here, we report the crystallographic refinement of this chitinase structure against data to 1.8 A resolution using rounds of hand rebuilding coupled with molecular dynamics (X-PLOR). The final model has an R-value of 18.1% for the 5.0 to 1.8 A data shell and 19.8% for the 10.0 to 1.8 A shell, and root-mean-square deviations from standard bond lengths and angles of 0.017 A and 2.88 degrees, respectively. The 243 residue molecule has one beta-sheet, ten alpha-helices and three disulfide bonds; 129 water molecules are included in the final model. We show structural comparisons confirming that chitinase secondary structure resembles lysozyme at the active site region. Based on substrate binding to lysozyme, we have built a hypothetical model for the binding of a hexasaccharide into the pronounced active site cleft of chitinase. This provides the first view of likely substrate interactions from this family of enzymes; the model is consistent with a lysozyme-like mechanism of action in which Glu67 acts as proton donor and Glu89 is likely to stabilize the transition state oxycarbonium ion. These binding site residues, and many hydrophobic residues are conserved in a range of plant chitinases. This endochitinase structure will serve as a model for other plant chitinases, and that catalytic models based on this structure will be applicable to the entire enzyme family.

Crystallization of a chitosanase from Streptomyces N174.

Chitosanases are produced by many soil fungi and bacteria to degrade chitosan present in fungal cell walls. Here, we report the crystallization of a 29,500 dalton protein with chitosan endo-hydrolase activity isolated from Streptomyces N174. The crystals were grown by vapor diffusion. They are mechanically strong and diffract to at least 1.9 A resolution. The crystals belong to the monoclinic space group P2(1) with unit cell parameters a = 56.4 A, b = 59.6 A, c = 86.1 A and beta = 96.6 degrees. Cell parameters and crystal density are consistent with two chitosanase molecules per asymmetric unit.

Crystal structure of an endochitinase from Hordeum vulgare L. seeds.

Higher plants contain multiple constitutively expressed proteins for defense against infection by viruses, bacteria, and fungi. One such class of proteins, the chitinases, are effective antifungal agents because they hydrolyze the insoluble beta-1,4-linked polymer of N-acetylglucosamine (chitin), which is the major component of the mycelial cell wall of many fungi. We report here the three-dimensional, 2.8 A, crystal structure of a 26 kDa endochitinase from barley (Hordeum vulgare L.) seeds. The 243 amino acid residue molecule is rich in alpha-helices and has three disulfide bonds. A prominent elongated cleft runs the length of the molecule, and is presumably the region responsible for substrate binding and catalysis. Endochitinases from various species of plants show a high degree of similarity in their amino acid sequences. It is therefore likely that the barley endochitinase structure can serve as a model for other plant endochitinases and that catalytic models based on that structure will be applicable to the entire enzyme family.

Crystallization of the B chain of Shiga-like toxin I from Escherichia coli.

Shiga-like toxin I (SLT-I) is produced by several pathogenic strains of Escherichia coli associated with diarrheal disease. The toxin consists of an A chain, which attacks eukaryotic ribosomes, inhibiting protein synthesis, and multiple copies of a 69 amino acid B chain. The B subunit mediates cell binding and uptake through its interactions with cell surface carbohydrate moieties. Here we report that the B chain has been crystallized in a form suitable for high-resolution X-ray analysis. The space group is P2(1)2(1)2(1), with a = 56.2 A, b = 59.9 A and c = 102.5 A. A rotation function using three-dimensional diffraction data suggests that the asymmetric unit is a tetramer.

Neuroendocrine aspects of primary endogenous depression. II. Serum dexamethasone concentrations and hypothalamic-pituitary-adrenal cortical activity as determinants of the dexamethasone suppression test response.

To determine the contribution of serum dexamethasone concentrations and hypothalamic-pituitary-adrenal cortical activity before dexamethasone administration to the dexamethasone suppression test (DST) response, a series of stepwise discriminant function analyses were performed for 40 patients with definite endogenous depression and 40 matched normal control subjects. The 24-hour serum cortisol concentration before dexamethasone administration and the serum dexamethasone concentrations at 8, 16, and 24 hours after administration served as the independent variables, and the DST "escaper"/"suppressor" dichotomy served as the dependent variable. While both types of independent variables significantly influenced the DST response, the major factor that contributed to the discrimination of escapers from suppressors was the 24-hour cortisol concentration before dexamethasone administration. Sixteen hours after dexamethasone administration, when the DST had the highest positive predictive value, serum dexamethasone concentrations significantly influenced DST outcome only when they were below a certain threshold level. At this time, hypothalamic-pituitary-adrenal cortical hyperactivity before dexamethasone administration accounted for approximately two thirds of the incidence of DST nonsuppression.

Subunit asymmetry in the three-dimensional structure of a human CuZnSOD mutant found in familial amyotrophic lateral sclerosis.

The X-ray crystal structure of a human copper/zinc superoxide dismutase mutant (G37R CuZnSOD) found in some patients with the inherited form of Lou Gehrig's disease (FALS) has been determined to 1.9 angstroms resolution. The two SOD subunits have distinct environments in the crystal and are different in structure at their copper binding sites. One subunit (subunit[intact]) shows a four-coordinate ligand geometry of the copper ion, whereas the other subunit (subunit[broken]) shows a three-coordinate geometry of the copper ion. Also, subunit(intact) displays higher atomic displacement parameters for backbone atoms ((B) = 30 +/- 10 angstroms2) than subunit(broken) ((B) = 24 +/- 11 angstroms2). This structure is the first CuZnSOD to show large differences between the two subunits. Factors that may contribute to these differences are discussed and a possible link of a looser structure to FALS is suggested.

Uclacyanins, stellacyanins, and plantacyanins are distinct subfamilies of phytocyanins: plant-specific mononuclear blue copper proteins.

The cDNAs encoding plantacyanin from spinach were isolated and characterized. In addition, four new cDNA sequences from Arabidopsis ESTs were identified that encode polypeptides resembling phytocyanins, plant-specific proteins constituting a distinct family of mononuclear blue copper proteins. One of them encodes plantacyanin from Arabidopsis, while three others, designated as uclacyanin 1, 2, and 3, encode protein precursors that are closely related to precursors of stellacyanins and a blue copper protein from pea pods. Comparative analyses with known phytocyanins allow further classification of these proteins into three distinct subfamilies designated as uclacyanins, stellacyanins, and plantacyanins. This specification is based on (1) their spectroscopic properties, (2) their glycosylation state, (3) the domain organization of their precursors, and (4) their copper-binding amino acids. The recombinant copper binding domain of Arabidopsis uclacyanin 1 was expressed, purified, and shown to bind a copper atom in a fashion known as "blue" or type 1. The mutant of cucumber stellacyanin in which the glutamine axial ligand was substituted by a methionine (Q99M) was purified and shown to possess spectroscopic properties similar to uclacyanin 1 rather than to plantacyanins. Its redox potential was determined by cyclic voltammetry to be +420 mV, a value that is significantly higher than that determined for the wild-type protein (+260 mV). The available structural data suggest that stellacyanins (and possibly other phytocyanins) might not be diffusible electron-transfer proteins participating in long-range electron-transfer processes. Conceivably, they are involved in redox reactions occurring during primary defense responses in plants and/or in lignin formation.

A missing link in cupredoxins: crystal structure of cucumber stellacyanin at 1.6 A resolution.

Stellacyanins are blue (type I) copper glycoproteins that differ from other members of the cupredoxin family in their spectroscopic and electron transfer properties. Until now, stellacyanins have eluded structure determination. Here we report the three-dimensional crystal structure of the 109 amino acid, non-glycosylated copper binding domain of recombinant cucumber stellacyanin refined to 1.6 A resolution. The crystallographic R-value for all 18,488 reflections (sigma > 0) between 50-1.6 A is 0.195. The overall fold is organized in two beta-sheets, both with four beta-stands. Two alpha-helices are found in loop regions between beta-strands. The beta-sheets form a beta-sandwich similar to those found in other cupredoxins, but some features differ from proteins such as plastocyanin and azurin in that the beta-barrel is more flattened, there is an extra N-terminal alpha-helix, and the copper binding site is much more solvent accessible. The presence of a disulfide bond at the copper binding end of the protein confirms that cucumber stellacyanin has a phytocyanin-like fold. The ligands to copper are two histidines, one cysteine, and one glutamine, the latter replacing the methionine typically found in mononuclear blue copper proteins. The Cu-Gln bond is one of the shortest axial ligand bond distances observed to date in structurally characterized type I copper proteins. The characteristic spectroscopic properties and electron transfer reactivity of stellacyanin, which differ significantly from those of other well-characterized cupredoxins, can be explained by its more exposed copper site, its distinctive amino acid ligand composition, and its nearly tetrahedral ligand geometry. Surface features on the cucumber stellacyanin molecule that could be involved in interactions with putative redox partners are discussed.

Cloning, expression, and spectroscopic characterization of Cucumis sativus stellacyanin in its nonglycosylated form.

The cDNA encoding the 182 amino acid long precursor stellacyanin from Cucumis sativus was isolated and characterized. The protein precursor consists of four sequence domains: I, a 23 amino acid hydrophobic N-terminal signal peptide with features characteristic of secretory proteins; II, a 109 amino acid copper-binding domain; III, a 26 amino acid hydroxyproline- and serine-rich peptide characteristic of motifs found in the extension family, extracellular structural glycoproteins found in plant cell walls; and IV, a 22 amino acid hydrophobic extension. Maturation of the protein involves posttranslational processing of domains I and IV. The copper-binding domain (domain II), which shares high sequence identity with other stellacyanins, has been expressed without its carbohydrate attachment sites, refolded from the Escherichia coli inclusion bodies, purified, and characterized by electronic absorption, EPR, ESEEM, and RR spectroscopy. Its spectroscopic properties are nearly identical to those of stellacyanin from the Japanese lacquer tree Rhus vernicifera, the most extensively studied and best characterized stellacyanin, indicating that this domain folds correctly, even in the absence of its carbohydrate moiety. The presence of a hydroxyproline- and serine-rich domain III suggests that stellacyanin may have a function other than that of a diffusible electron transfer protein, conceivably participating in redox reactions localized at the plant cell wall, which are known to occur in response to wounding or infection of the plant.

Age-specific differences in the winter foraging strategies of rooks Corvus frugilegus.

Foraging efficiency and intraspecific competition were compared between wild adult and immature rooks Corvus frugilegus with respect to flock size. Behavioural time budgets, and observations of prey selection and prey energetic values revealed that adult rooks in large flocks (> 50 individuals) consumed smaller, less profitable prey, but allocated more time to feeding and fed at a faster rate and with greater success than adults in small flocks. By contrast, immature rooks in flocks of more than 30 individuals allocated proportionally less time to feeding, fed at a lower rate and fed with no increase in success rate than when foraging in smaller flocks. Agonistic encounters and the avoidance of adults by immature rooks appeared responsible for such inefficient foraging. Hence immature rooks showed a preference for smaller flocks (< 50 individuals) with low adult: immature ratios while adults preferred larger flocks (> 50 individuals). We discuss the possible influence of competitive disadvantages on immature rook distribution, flock composition and post-natal dispersal.

Mating interactions between two biotypes of the whitefly, Bemisia tabaci (Hemiptera: Aleyrodidae) in Australia.

The biological consequences of mating interactions between indigenous and exotic biotypes of Bemisia tabaci (Gennadius) in Australia were studied using a combination of field and laboratory experiments. The key results of the interaction between the B and eastern Australian biotypes were reduced population increase, a marked increase in the proportion of male progeny, fewer eggs produced by females paired with males of different biotype and no difference in the numbers of eggs per unmated female and females paired with males of the same biotype. In addition, there was no change in the proportion of eggs hatching, mixed biotype pairs spent more time courting than single biotype pairs and a low level of hybridization in field cages and small containers was observed. These observations suggest three possibilities. The first is the 'distracting male hypothesis' in which mating pairs made up of different biotypes apportion more time to courtship and less time to egg laying than single biotype pairs. The second invokes the 'single-locus complementary sex determination model' in which the production of non-viable diploid male zygotes may explain the reduction in eggs laid. The third is cytoplasmic incompatibility between biotypes caused by Wolbachia. The results also suggest that the geographical distribution of clusters of related biotypes both overseas and in Australia may be explained by between-biotype interactions leading to the formation of parapatric populations.

Expression of cystic fibrosis transmembrane regulator Cl- channels in heart.

Cyclic AMP (cAMP)-dependent chloride channels modulate changes in resting membrane potential and action potential duration in response to autonomic stimulation in heart. A growing body of evidence suggests that there are marked similarities in the properties of the cAMP-dependent chloride channels in heart and cystic fibrosis transmembrane regulator (CFTR) chloride channels found in airway epithelia or in cells expressing the CFTR gene product. We isolated poly A+ mRNA from rabbit ventricle and converted it to cDNA for amplification using the polymerase chain reaction (PCR). A fragment corresponding to the nucleotide-binding domain 1 (NBD1) of the CFTR transcript was cloned. Comparison of the amino acid sequence of NBD1 of human CFTR with the deduced sequence of the rabbit heart PCR product indicated 98% identity. Northern blot analysis, using the heart amplification product as a cDNA probe, demonstrated expression of homologous transcripts in human atrium, guinea pig and rabbit ventricle, and dog pancreas. Xenopus oocytes injected with poly A+ mRNA extracted from rabbit and guinea pig ventricle or dog pancreas expressed robust time-independent chloride currents in response to an elevation of cAMP. We conclude that CFTR chloride channels are expressed in heart and are responsible for the observed cAMP-dependent chloride conductance.

Seasonal variation in hypothalamic content of gonadotropin-releasing hormone (GnRH), pituitary receptors for GnRH, and pituitary content of luteinizing hormone and follicle-stimulating hormone in the mare.

Seasonal changes in the hypothalamic-hypophyseal axis were investigated using tissue from 49 light-horse mares, of mixed breeding. Hypothalamic and pituitary tissues were collected at 5 intervals throughout the years 1981 and 1982, representing midbreeding season (July, n = 10), transition out of the breeding season (October, n = 11), midanestrus (December, n = 8), transition into the breeding season (March, n = 10), and again in the following midbreeding season (July, n = 10). The hypothalamic region was dissected into preoptic area, body and median eminence. Gonadotropin-releasing hormone (GnRH) was extracted from hypothalamic samples with methanol-formic acid and quantified by radioimmunoassay. The anterior pituitary was homogenized and receptors for GnRH were quantified in a crude membrane fraction. Concentrations of luteinizing hormone (LH) and follicle-stimulating hormone (FSH) were measured in the resulting supernatant. Content of GnRH in each of the 3 hypothalamic areas varied with season (P less than 0.01) and was lowest during midanestrus (P less than 0.05). There was no effect of season (P greater than 0.01) on either concentration or total number of receptors for GnRH, or concentration of FSH in the anterior pituitary. Concentrations of LH in the anterior pituitary varied with season (P less than 0.001). Means (+/- SEM) for the 5 collection times were 15.5 +/- 2.7, 9.7 +/- 2.4, 2.3 +/- 0.5, 2.7 +/- 0.4 and 11.7 +/- 1.5 microgram LH/mg anterior pituitary, respectively.(ABSTRACT TRUNCATED AT 250 WORDS)

Neonatal hypothyroidism: effect on the circadian variation of serum TSH in adult male rats.

Newborn rats were rendered hypothyroid during the first post-natal week and then studied as adults. At 80 days of age, groups of control and neonatally treated animals were sacrificed at the peak (13.00 h) and trough (07.00 h) of the serum thyroid stimulating hormone (TSH) circadian rhythm. Both control and treated animals showed the normal peak and trough fluctuation of serum TSH, although the animals made hypothyroid neonatally had serum TSH levels which were less than those of the control animals. Serum thyroxine (T4) levels of control and treated animals were similar at the trough of the serum TSH rhythm (07.00 h), but the (T4) levels of the neonatally hypothyroid animals were significantly lower than those found in the control animals at the peak of the TSH rhythm (13.00 h). The results of this experiment indicate that the central nervous system (CNS) regulation of the circadian pattern of serum TSH is maintained in adult animals made hypothyroid neonatally, and supports the results of previous studies which indicate an enhanced sensitivity of TSH secretion to feedback suppression by thyroid hormones.