First report of pulmonary disease associated with Nicoletella semolina in a horse in New Zealand.

Case history: A 9-year-old warmblood gelding with a history of chronic intermittent tachypnoea and dyspnoea was presented for evaluation and removal of a mass on the left side of the neck. A fibrous mass adherent to the left jugular vein developed and was removed surgically 6 weeks later, at which time the owner requested an evaluation of the cause of the persistent respiratory signs first noted on primary admission. Clinical findings and treatment: Clinical findings included coarse lung sounds on thoracic auscultation, tracheal wheeze, and an abnormal trans-tracheal aspirate. These findings, in addition to the results of ultrasonographic imaging of the thorax and transtracheal cytology, were suggestive of bacterial bronchopneumonia. Initial antimicrobial therapy included I/M 22 mg/kg procaine penicillin every 12 hours and I/V 6.6 mg/kg gentamicin sulphate every 24 hours. The horse's clinical signs improved within 36 hours. It was discharged after 6 days, and at the owner's request antimicrobial therapy was changed to 25 mg/kg trimethoprim/sulphadimidine to be given orally every 12 hours for 10 days. One month later, the horse had recovered and there were no further complications reported by the owner except for an occasional cough while grazing Laboratory findings: Bacterial culture of transtracheal wash fluid resulted in the isolation of Nicoletella semolina as the sole organism, later confirmed by genotyping. Attempts to subculture the organism for antimicrobial susceptibility testing were unsuccessful. Diagnosis: Infectious bronchopneumonia associated with Nicoletella semolina Clinical relevance: Further work is required to determine whether N. semolina is acting as an opportunistic commensal of the equine respiratory tract or a primary pathogen. However, this article reports the first instance in New Zealand of an association between the presence of this organism and respiratory disease in a horse.

Infrared spectroscopy of serum fails to identify early biomarker changes in an equine model of traumatic osteoarthritis.

OBJECTIVE: to determine the accuracy of infrared (IR)-based serum biomarker profiling to differentiate horses with early inflammatory changes associated with a traumatically induced model of equine carpal osteoarthritis (OA) from controls. METHOD: unilateral carpal OA was induced in 9 of 17 healthy Thoroughbred fillies, while the remainder served as sham operated controls. Serum samples were obtained before induction of OA (Day 0) and weekly thereafter until Day 63 from both groups. Films of dried serum were created, and IR absorbance spectra acquired. Following pre-processing, partial least squares discriminant analysis (PLSDA) and principal component analysis (PCA) were used to assess group and time differences and generate predictive models for wavenumber ranges 1300-1800 â€‹cm-1 and 2600-3700 â€‹cm-1. RESULTS: the overall correct classification rate when classifying samples by group (OA or Sham) was 52.7% (s.d. â€‹= â€‹12.8%), while it was 94.0% (s.d. â€‹= â€‹1.4%) by sampling Day. The correct classification results by group-sampling Day combinations with pre-intervention serum (Day 0) was 50.5% (s.d. â€‹= â€‹21.7%). CONCLUSION: with the current approach IR spectroscopic analysis could not differentiate serum of horses with induced carpal OA from that of controls. The high classification rate obtained by Day of sampling may reflect the effect of exercise on the biomarker profile. A longer study period (advanced disease) or naturally occurring disease may provide further information on the suitability of this technique in horses.

A high-pressure flow through test vessel for neutron imaging and neutron diffraction-based strain measurement of geological materials.

Neutron scattering and neutron imaging have emerged as powerful methods for experimentally investigating material deformation and fluid flow in the interior of otherwise inaccessible or opaque structures. This paper describes the design and provides example uses of a pressure cell developed for investigating such behaviors within geological materials. The cell can accommodate cylindrical samples with diameters up to 38.1 mm and lengths up to 154 mm. Ports in the cell and a pressure isolating sleeve around the sample allow the independent application of confining pressure up to 69 MPa and axial pressure up to 34.5 MPa. Two material versions of the cell have been manufactured and used to date. An aluminum version is typically used for temperatures below 40 °C, because of its relative transparency to neutrons, while a titanium version, which is comparatively more neutron attenuating, is used for experiments requiring triaxial pressurization under conditions up to 350 °C. The pressure cells were commissioned at the VULCAN engineering diffractometer at the Oak Ridge National Laboratory (ORNL), Spallation Neutron Source, and have since been used at the ORNL high flux isotope reactor CG1-D imaging beamline, National Institute of Standard and Technology (NIST) BT-2, and NIST NG6 imaging beamlines.

Trace fossils from the athabasca oil sands, alberta, Canada.

A diverse and well-preserved ichnofossil suite has been identified from surface exposures of the middle and upper parts of the Lower Cretaceous McMurray Formation. The suite, consisting of representatives of at least ten ichnogenera, is one of the few clues to the original biotic component of the deposit. The distribution and abundance of these biogenic structures present strong evidence that the deep channel complex in which the sediments were deposited was closely associated with a nearby marine shoreline.

The oldest macroborers: lower cambrian of labrador.

We have discovered numerous borings of Trypanites penetrating skeletons and synsedimentary cemented limestones in archaeocyathid reefs of the Forteau formation in southern Labrador. These are, to date, the oldest known macroborings. The discovery of these structures extends the record of large endolithic organisms 100 million years from the Lower Ordovician to the Lower Cambrian. This immediately postdates the appearance of metazoans with hard parts and confirms that endoliths have played a role in reef formation since the early Cambrian.

Determination of the Settling Rate of Clay/Cyanobacterial Floccules.

The mechanisms underpinning the deposition of fine-grained, organic-rich sediments are still largely debated. Specifically, the impact of the interaction of clay particles with reactive, planktonic cyanobacterial cells to the sedimentary record is under studied. This interaction is a potentially major contributor to shale depositional models. Within a lab setting, the flocculation and sedimentation rates of these materials can be examined and measured in a controlled environment. Here, we detail a protocol for measuring the sedimentation rate of cyanobacterial/clay mixtures. This methodology is demonstrated through the description of two sample experiments: the first uses kaolin (a dehydrated form of kaolinite) and Synechococcus sp. PCC 7002 (a marine coccoid cyanobacteria), and the second uses kaolin and Synechocystis sp. PCC 6803 (a freshwater coccoid cyanobacteria). Cyanobacterial cultures are mixed with varying amounts of clay within a specially designed tank apparatus optimized to allow continuous, real-time video and photographic recording. The sampling procedures are detailed as well as a post-collection protocol for precise measurement of chlorophyll a from which the concentration of cyanobacterial cells remaining in suspension can be determined. Through experimental replication, a profile is constructed that displays sedimentation rate.

Factor VIII S373L: mutation at P1' site confers thrombin cleavage resistance, causing mild haemophilia A.

A novel CRM+ mutation, factor VIII position 373 serine to leucine substitution (FVIII 373-Leu) was identified during a survey of Factor VIII (FVIII) mutations. We have purified the variant protein from the patient's plasma in order to allow further characterisation of the molecule. The CRM+ plasma contained 120% Factor VIII antigen (FVIII:Ag) and 6% Factor VIII coagulant activity (FVIII:C). After purification the mutant FVIII was subjected to thrombin proteolysis, and was thereby activated 5.6-fold compared with 7-fold for wild type molecule. Subsequently, spontaneous inactivation of the mutant was much slower than noted for wild type FVIII. Western blot analysis using monoclonal antibodies demonstrated that thrombin cleavage of FVIII 373-Leu at positions 740 and 1689 were normal but that cleavage at position 372 was completely absent. Crystallographic coordinates of the active site of thrombin complexed to fibrinopeptide A were used to explore possible mechanistic reasons for the failure of thrombin to cleave the mutant FVIII at position 372. Steric hindrance between the mutant side chain and the side chain of the P1 residue was apparent. We conclude that the functional defect of FVIII 373-Leu results from the inability of thrombin to cleave the mutant at position 372-373, and propose that this is due to steric hindrance by the side chain of leucine 373, preventing correct formation of the enzyme substrate complex.

Antibody coated bacteria in urine of patients with recent spinal injury.

Twenty patients with an acute spinal injury were prospectively studied to assess the clinical importance of antibody coated bacteria (ACB) in the urine and the association among the different bacterial species with a positive antibody coated bacteria test. Clinical urinary tract infection was associated with a positive ACB test on 45% of occasions. Three hundred and ninety nine urine samples containing 541 bacterial isolates were assessed for the presence of ACB; 13% were found to be positive and 87% negative for ACB; 67% of urines contained a single bacterial isolate. Pseudomonas aeruginosa was most commonly associated with clinical urinary tract infection, found in 25% of episodes, followed by Proteus mirabilis (17.5%), Klebsiella sp (12.5%), and Proteus morganii (10%). Providencia stuartii, however, was most commonly associated with a positive ACB test (found in 17%). Other bacteria associated with a positive ACB test included Klebsiella sp (14%), Acinetobacter sp (12.5%), Pseudomonas aeruginosa (12%), Citrobacter sp (11.5%). A positive ACB test is not to be expected from a patient with spinal injury who has a catheter in place, and the test may provide a useful guide to identify those patients with an invasive infection. It is doubtful that a decision to treat or not treat bacteriuria could rest on the identification of the bacterial species alone.

Genetic research as therapy: implications of "gene therapy" for informed consent.

Authors argue that characterization of gene transfer research as "gene therapy" has compromised informed consent in the current environment of regulatory exceptions, routinized consent, fostered therapeutic misconceptions, and oversold research.

A 'terror of tyrannosaurs': the first trackways of tyrannosaurids and evidence of gregariousness and pathology in Tyrannosauridae.

The skeletal record of tyrannosaurids is well-documented, whereas their footprint record is surprisingly sparse. There are only a few isolated footprints attributed to tyrannosaurids and, hitherto, no reported trackways. We report the world's first trackways attributable to tyrannosaurids, and describe a new ichnotaxon attributable to tyrannosaurids. These trackways are from the Upper Cretaceous (Campanian - Maastrichtian) of northeastern British Columbia, Canada. One trackway consists of three tridactyl footprints, and two adjacent trackways consist of two footprints each. All three trackways show animals bearing southeast within an 8.5 meter-wide corridor. Similarities in depth and preservation of the tyrannosaurid tracks indicate that these three trackways were made by track-makers walking concurrently in the same direction. These trackways add significantly to previous osteology-based hypotheses of locomotion and behavior in Tyrannosauridae by providing ichnologic support for gregariousness in tyrannosaurids, and the first record of the walking gait of tyrannosaurids.

Increase of activated factor VIIA and haemostatic molecular markers in juvenile chronic arthritis.

Activated factor VIIa (FVIIa), von Willebrand factor antigen (vWF:Ag), D-dimer and thrombin-antithrombin III complex (TAT) were measured to monitor coagulation status in patients with juvenile chronic arthritis (JCA). Subjects included 14 patients with systemic JCA, 16 with pauciarticular JCA and 16 with polyarticular JCA without disseminated intravascular coagulopathy, thrombosis or liver dysfunction. All types of JCA showed an increase of FVIIa, D-dimer and TAT, indicating enhanced activation of coagulation. In systemic JCA only there was also characteristically an elevation of vWF:Ag. We conclude that all types of JCA constitute a state of subclinical hypercoagulopathy caused by tissue damage and that additionally systemic JCA involves a prothrombotic state associated with or precipitated by vasculitis.

Anti-neutrophil cytoplasmic antibodies (ANCA) from patients with systemic vasculitis recognize restricted epitopes of proteinase 3 involving the catalytic site.

ANCA with specificity for proteinase 3 (PR3), a neutrophil primary granule enzyme, are of diagnostic value in Wegener's granulomatosis (WG) and certain other forms of systemic vasculitis. There is evidence to suggest that they play a pathogenic role in disease, and that the interaction of ANCA with PR3 is likely to be important. We showed, using a resonant mirror biosensor, that C-ANCA from different patients recognized the same or closely related epitopes on PR3. Studies using linear peptides in the SPOT system confirmed the highly restricted nature of this interaction and identified five linear epitopes. Fluid-phase inhibition studies, using a different set of peptides, validated the sequences involved. Using a computer-generated model of the structure of PR3, four of five epitopes were shown to be intimately linked with the catalytic site. The restricted number of epitopes, and their location at the catalytic site, has important implications for the role of C-ANCA in the pathogenesis of vasculitis.

A molecular model of the serine protease domain of activated protein C: application to the study of missense mutations causing protein C deficiency.

A molecular model of the serine protease domain of protein C was constructed by standard comparative methods. Individual missense mutations were inserted into the model and plausible explanations for their interference with protein C structure/function were derived through consideration of location, steric effects and protein stability. A hydrophilic cluster of many Arg and Lys residues, found adjacent to the active site cleft, is proposed to be involved in thrombomodulin and/or protein S interactions. Analysis of comparative binding studies also suggested the presence of an extended substrate binding pocket in the model.

Single-strand conformation polymorphism (SSCP) analysis of the molecular pathology of hemophilia B.

In the present study, we report the application of polymerase chain reaction-single-strand conformation polymorphism (PCR-SSCP) analysis to the screening of seven functionally important factor IX gene (FIX) regions (total length 2.66 kb) in 9 unrelated haemophilia B patients of Portuguese or African origin. In eight of the patients an altered migration pattern of single-stranded DNA was observed. Direct sequencing of the relevant DNA fragments unveiled the following sequence alterations: two novel mutations, namely FIXBarcelos Thr-380-Pro and FIXLousada 9bp insertion at position 31,309 or 31,318; five mutations previously reported in other ethnic groups (FIXPorto Arg-145-His, FIXLuanda Gly-207-Arg, FIXPenafiel Arg-248-Gln, FIXSesimbra Arg-333-Gln, FIXCascais Arg-333-Stop); and a normal variant, G-->T transvertion at position 6,596 in intron 2. We propose hypothetical models for the generation of the 9 bp duplication (FIXLousada). We have performed molecular modeling studies in order to predict the structure of the variant FIX molecules.

A molecular model for the triplicated A domains of human factor VIII based on the crystal structure of human ceruloplasmin.

The hemophilia A mutation database lists more than 160 missense mutations: each represents a molecular defect in the FVIII molecule, resulting in the X-linked bleeding disorder hemophilia A with a clinical presentation varying from mild to severe. Without a three-dimensional FVIII structure it is in most cases impossible to explain biological dysfunction in terms of the underlying molecular pathology. However, recently the crystal structure of the homologous human plasma copper-binding protein ceruloplasmin (hCp) has been solved, and the A domains of FVIII share approximately 34% sequence identity with hCp. This advance has enabled the building of a molecular model of the A domains of FVIII based on the sequence identity between the two proteins. The model allows exploration of predictions regarding the general features of the FVIII molecule, such as the binding-sites for factor IXa and activated protein C; it has also allowed the mapping of more than 30 selected mutations with known phenotype from the database, and the prediction of hypothetical links to dysfunction in all but a few cases. A computer-generated molecular model such as that reported here cannot substitute for a crystal structure. However, until such a structure for FVIII becomes available, the model represents a significant advance in modeling FVIII; it should prove a useful tool for exploiting the increasing amount of information in the hemophilia A mutation database, and for selecting appropriate targets for investigation of the structure-function relationships via mutagenesis and expression in vitro.

The molecular basis for cross-reacting material-positive hemophilia A due to missense mutations within the A2-domain of factor VIII.

Factor VIII (FVIII) is the protein defective in the bleeding disorder hemophilia A. Approximately 5% of hemophilia A patients have normal amounts of a dysfunctional FVIII protein and are termed cross-reacting material (CRM)-positive. The majority of genetic alterations that result in CRM-positive hemophilia A are missense mutations within the A2-domain. To determine the mechanistic basis of the genetic defects within the A2-domain for FVIII function we constructed six mutations within the FVIII cDNA that were previously found in five CRM-positive hemophilia A patients (R527W, S558F, I566T, V634A, and V634M) and one CRM-reduced hemophilia A patient (DeltaF652/3). The specific activity for each mutant secreted into the conditioned medium from transiently transfected COS-1 cells correlated with published data for the patients plasma-derived FVIII, confirming the basis of the genetic defect. Sodium dodecyl sulfate-polyacrylamide gel electrophoresis analysis of immunoprecipitated FVIII protein radiolabeled in COS-1 cells showed that all CRM-positive mutant proteins were synthesized and secreted into the medium at rates similar to wild-type FVIII. The majority of the DeltaF652/3 mutant was defective in secretion and was degraded within the cell. All mutant FVIII proteins were susceptible to thrombin cleavage, and the A2-domain fragment from the I566T mutant had a reduced mobility because of use of an introduced potential N-linked glycosylation site that was confirmed by N-glycanase digestion. To evaluate interaction of FVIII with factor IXa, we performed an inhibition assay using a synthetic peptide corresponding to FVIII residues 558 to 565, previously shown to be a factor IXa interaction site. The concentration of peptide required for 50% inhibition of FVIII activity (IC50) was reduced for the I566T (800 mumol/L) and the S558F (960 mumol/L) mutants compared with wild-type FVIII (> 2,000 mumol/L). N-glycanase digestion increased I566T mutant FVIII activity and increased its IC50 for the peptide (1,400 mumol/L). In comparison to S558F, a more conservative mutant (S558A) had a sixfold increased specific activity that also correlated with an increased IC50 for the peptide. These results provided support that the defects in the I566T and S558F FVIII molecules are caused by steric hindrance for interaction with factor IXa.

Molecular defects in CRM+ factor VII deficiencies: modelling of missense mutations in the catalytic domain of FVII.

The molecular defects causing CRM+ factor VII deficiency were investigated in seven unrelated subjects and several members of their families. Four missense mutations located in the catalytic domain of factor VII were found. The previously reported 304Arg-->Gln substitution was present in the homozygous and heterozygous forms, with different polymorphic haplotypes, thus demonstrating that it is recurrent and frequent in the Italian population. The 310Cys-->Phe substitution was found in the homozygous form and in the compound heterozygous condition with the nonsense mutation 356Trp-->stop. Two missense mutations, 298Met-->Ile and 342Gly-->Arg, were found in the homozygous and in the heterozygous condition respectively. Molecular heterogeneity was further increased by finding of the 353Arg-->Gln polymorphism in the doubly heterozygous condition with the 304 and 342 mutations. Plausible explanations for loss of FVII function were found by inspecting a model of the serine protease domain of factor VIIa. Inefficient activation of the catalytic site is predicted for 298Met-->Ile. 342Gly-->Arg would directly distort the geometry of the 'oxyanion hole' preventing formation of a substrate enzyme intermediate. 310Cys-->Phe is predicted to have an adverse effect on tissue factor interaction. These mutations point to important regions of the factor VII molecule.