Sequence and comparative analysis of the genome of HSV-1 strain McKrae

Ocular infection by HSV-1 strain McKrae is neurovirulent in both mice and rabbits and causes fatal encephalitis in approximately 50% of animals. In addition, it spontaneously reactivates with high frequency relative to other HSV-1 strains in rabbits. We sequenced the McKrae strain genome and compared its coding protein sequences with those of six other HSV-1 strains. Most of the 74 predicted protein sequences are conserved; only eleven are less than 98% conserved. Eight proteins were identified to be unique for McKrae based on sequence homology bit score ratio (BSR). These include five proteins showing significant variations (RL1, RS1, UL49A, US7 and US11), two truncated proteins (UL36 and UL56) and one (US10) containing an extended open reading frame. The McKrae strain also has unique features in its 'a' sequence and non-coding sequences, such as LAT and miRNA. These data are indicative of strain variation but need further work to connect observed differences with phenotype effects.

Age-associated cartilage degeneration of the canine humeral head

The goal of this study was to determine if cartilage lesions of the humeral head in adult dogs are the consequence of osteochondrosis dissecans or degenerative joint disease. A gross and histologic survey was performed of humeral head cartilage lesions of 155 dogs ranging in age from 1 week to 19 years. The humeral head and cartilage lesion size were measured for each dog. Cartilage lesions were classified as fibrillation, fissures, erosion, and/or eburnation. The area of each lesion was multiplied by a severity score (fibrillation and fissures 1, erosion 2, and eburnation 3) to create a combined score for each humeral head. Correlations between this combined lesion score and age, humeral head size, body weight, and body condition score were assessed using a Bonferroni-corrected alpha of .01. Twenty-six humeral heads were also evaluated histologically. Of the 155 dogs, 80 (52%) had gross lesions of the articular cartilage. The presence and severity of the articular cartilage lesions were positively correlated with age, humeral head size, body weight, and body condition score. The average age of dogs with cartilage lesions was 8.8 years, and 77/105 (74%) of adult dogs had cartilage lesions. Fifty dogs were 3 years of age or younger; 3 of those had cartilage lesions, 1 of which was osteochondrosis. These data indicate that cartilage erosion of the caudal humeral head in dogs is a common degenerative lesion acquired in adult large breed dogs; osteochondrosis dissecans does not precede the lesion in the vast majority of cases.

Hierarchy of risk of childhood-onset rheumatoid arthritis conferred by HLA-DRB1 alleles encoding the shared epitope

OBJECTIVE

Associations between shared epitope (SE)-encoding HLA-DRB1 alleles and rheumatoid arthritis (RA) are well established. However, only a limited number of studies have investigated these alleles in patients with childhood-onset RA, which is defined as rheumatoid factor- and/or anti-citrullinated protein antibody-positive juvenile idiopathic arthritis. The aims of this study were to investigate the largest cohort of patients with childhood-onset RA for association with SE alleles and to determine whether there is a hierarchy of risk based on the amino acid sequence of the SE.

METHODS

High-resolution HLA-DRB1 genotypes were obtained for 204 patients with childhood-onset RA and 373 healthy control subjects. Odds ratios (ORs) and 95% confidence intervals (95% CIs) were calculated for different SE-encoding HLA-DRB1 alleles. In addition, genotype ORs were calculated for combinations of SE alleles classified into S(2) , S(3P) , or L alleles, based on amino acid sequences in position 70-74 of the DRβ1 chain, as proposed by Tezenas du Montcel et al.

RESULTS

We confirmed associations between HLA-DRB1 SE alleles and childhood-onset RA (76% of patients carried 1 or 2 SE alleles compared with 46% of control subjects; OR 3.81, 95% CI 2.4-6.0, P < 1 × 10(-7) ). We also observed associations between individual SE alleles (HLA-DRB1*0101, *0401, *0404, *0405, *0408, and *1001) and childhood-onset RA. Genotype-specific risk estimates suggested a hierarchy of risk, with the highest risk among individuals heterozygous for S(2) /S(3P) (OR 22.3, 95% CI 9.9-50.5, P < 0.0001).

CONCLUSION

We confirm the association between SE-encoding HLA-DRB1 alleles and susceptibility to childhood-onset RA. The excess risk conferred by carriage of the combination of S(2) and S(3P) risk alleles suggests that children with DRβ1 chains containing the KRAA and QRRAA or RRRAA sequences are especially susceptible to RA.

Host utilization of field-caged native and introduced thistle species by Rhinocyllus conicus

Rhinocyllus conicus Fröelich was introduced from Europe into North America as a biological control agent of the exotic weed Carduus nutans L. Concern exists over the feeding of this weevil on at least 25 species of native Cirsium thistles. Beginning in 2008, cage studies isolating adults of R. conicus on buds and flower heads of all eight thistle species (native and introduced) recorded from Tennessee were conducted to test if R. conicus could use these species for reproduction and what impacts larval feeding of R. conicus may have on seed production. Larvae of R. conicus completed development in heads of the native species C. carolinianum (Walter) Fernald and Schubert. and C. horridulum Michaux, and significant reductions in seed numbers of both species occurred during 2008. Rhinocyllus conicus oviposited on both C. carolinianum and C. horridulum at significantly greater levels than the introduced species C. arvense (L.) Scopoli and C. vulgare (Savi) Tenore. Infested heads of C. carolinianum contained numbers of R. conicus per centimeter of plant head width similar to Ca. nutans in 2008, and both native species contained numbers of R. conicus per centimeter of plant head width similar to C. arvense and C. vulgare in 2009. Body length was similar between R. conicus reared on native thistles and its target host Ca. nutans. This report is the first documentation of R. conicus feeding and reproducing on C. carolinianum and C. horridulum. Although R. conicus has been observed only on introduced thistles in naturally occurring populations in this region, the utilization of C. carolinianum and C. horridulum as host species in controlled conditions warrants continued monitoring of field populations and further investigation into factors that may influence nontarget feeding in the future.

Role of essential oils in control of Rhizoctonia damping-off in tomato with bioactive Monarda herbage

Plants in the genus Monarda produce complex essential oils that contain antifungal compounds. The objectives of this research were to identify selections of monarda that reduce Rhizoctonia damping-off of tomato, and to determine relationships between essential oil composition of 13 monarda herbages (dried and ground leaves) and disease suppression. Herbages were grouped into five chemotypes, based on essential oil composition and effective concentrations for reducing growth by 50% for Rhizoctonia solani. Replicated and repeated disease control assays were conducted with monarda herbages in greenhouse medium, with or without Rhizoctonia. Percent survival, seedling height, and stem diameter were evaluated at 8 weeks. Survival, seedling height, and stem diameter in herbage-only treatments were not different from the control (no-herbage, no-pathogen) for most herbage treatments. In the pathogen control (no-herbage + Rhizoctonia), seedling survival was 10% that of the control. In pathogen-infested media, seedling survival ranged from 65 to 80% for treatments with thymol chemotypes and 55 to 65% for carvacrol chemotypes. Effective control of Rhizoctonia damping-off was correlated with phenolic monoterpenes; herbages classified as carvacrol chemotypes effectively protected tomato seedlings from Rhizoctonia damping-off disease without phytotoxicity. This study provides evidence that monarda herbages have potential as growing media amendments for control of Rhizoctonia damping-off disease.

Agreement between values for arterial and end-tidal partial pressures of carbon dioxide in spontaneously breathing, critically ill dogs

OBJECTIVE

To determine agreement between arterial partial pressures of carbon dioxide (PaCO(2)) and end-tidal partial pressures of carbon dioxide (PETCO(2)) measured with a nasal catheter in spontaneously breathing, critically ill dogs.

DESIGN

Validation study.

ANIMALS

26 client-owned dogs admitted to an intensive care unit for various conditions.

PROCEDURES

PaCO(2) was measured with a commercial blood gas analyzer, and PETCO(2) was measured with a sidestream capnograph attached to a nasal catheter. Measurements were obtained twice (ie, with and without supplemental oxygen). Paired values were compared by means of the Pearson correlation method. Level of agreement was assessed by means of the Bland-Altman method.

RESULTS

Mean difference between PaCO(2) and PETCO(2) when dogs did not receive supplemental oxygen (mean +/- SD, 3.95 +/- 4.92 mm Hg) was significantly lower than mean difference when dogs did receive supplemental oxygen (6.87 +/- 6.42 mm Hg). Mean difference in dogs with a condition affecting the respiratory system (8.55 +/- 5.43 mm Hg) was significantly higher than mean difference in dogs without respiratory tract disease (3.28 +/- 3.23 mm Hg). There was a significant linear correlation and good agreement between measured values of PaCO(2) and PETCO(2). Catheter size, ventilatory status, and outcome were not significantly associated with mean difference between PaCO(2) and PETCO(2).

CONCLUSIONS AND CLINICAL RELEVANCE

Results suggested that nasal capnography is a clinically relevant method of estimating PaCO(2) in spontaneously breathing, critically ill dogs, but that values should be interpreted with caution in dogs receiving supplemental oxygen and in dogs with conditions affecting the respiratory system.

Biomarkers in rheumatologic disease: a review

Rheumatologic disorders are in many ways heterogeneous diseases.They have an array of clinical manifestations, involve multiple organs, produce unpredictable flares, and have widely varying clinical outcomes. Diagnosing rheumatologic diseases and predicting outcomes in a reliable way could lead to new therapeutic strategies and optimization of care. This article reviews the current literature on biological and clinical markers related to diagnosing disease, assessing for disease activity, and predicting outcomes for selected rheumatologic conditions.

Premature atherosclerosis in pediatric systemic lupus erythematosus: risk factors for increased carotid intima-media thickness in the atherosclerosis prevention in pediatric lupus erythematosus cohort

OBJECTIVE

To evaluate risk factors for subclinical atherosclerosis in a population of patients with pediatric systemic lupus erythematosus (SLE).

METHODS

In a prospective multicenter study, a cohort of 221 patients underwent baseline measurements of carotid intima-media thickness (CIMT) as part of the Atherosclerosis Prevention in Pediatric Lupus Erythematosus (APPLE) trial. SLE disease measures, medications, and traditional risk factors for atherosclerosis were assessed. A standardized protocol was used to assess the thickness of the bilateral common carotid arteries and the mean maximal IMT of 12 segments. Univariable analysis identified potential associations with CIMT, which were examined in multivariable linear regression modeling.

RESULTS

Based on the mean-mean common or the mean-max CIMT as the dependent variable, univariable analysis showed significant associations of the following variables with increased CIMT: increasing age, longer SLE duration, minority status, higher body mass index (BMI), male sex, increased creatinine clearance, higher lipoprotein(a) level, proteinuria, azathioprine treatment, and prednisone dose. In multivariable modeling, both azathioprine use (P=0.005 for the mean-mean model and P=0.102 for the mean-max model) and male sex (P<0.001) were associated with increases in the mean-max CIMT. A moderate dosage of prednisone (0.15-0.4 mg/kg/day) was associated with decreases in the mean-max CIMT (P=0.024), while high-dose and low-dose prednisone were associated with increases in the mean-mean common CIMT (P=0.021) and the mean-max CIMT (P=0.064), respectively. BMI (P<0.001) and creatinine clearance (P=0.031) remained associated with increased mean-mean common CIMT, while increasing age (P<0.001) and increasing lipoprotein(a) level (P=0.005) were associated with increased mean-max CIMT.

CONCLUSION

Traditional as well as nontraditional risk factors were associated with increased CIMT in this cohort of patients in the APPLE trial. Azathioprine treatment was associated with increased CIMT. The relationship between CIMT and prednisone dose may not be linear.

Drug administration errors: a prospective survey from three South African teaching hospitals

This prospective study was undertaken to determine the incidence of drug administration errors by anaesthetists at three tertiary South African hospitals. Hospitals A and C treat adults predominantly, whereas Hospital B is a paediatric hospital. Anaesthetists completed an anonymous study form for every anaesthetic performed over a six-month period. They were asked to indicate whether or not an error or near-miss had occurred and if so, the details thereof. A total of 30,412 anaesthetics were administered during the study period. The response rate and combined incidence of errors and near-misses was as follows: Hospital A 48.8% (1:320), B 81.3% (1:252) and C 48.1% (1:250). The overall response rate was 53% and the combined incidence was 1:274. Neither the experience of the anaesthetist nor emergency surgery influenced whether an error occurred or not. Most errors occurred during the maintenance phase of anaesthesia. The most common errors were those of substitution. At the paediatric hospital, incorrect dose was as frequent an error as substitution. Of all errors, 36.9% were due to drug ampoule misidentification; of these the majority (64.4%) were due to similar looking ampoules. Another 21.3% were due to syringe identification errors. No major complication attributable to a drug administration error was reported. Despite an increasing awareness of the problem together with suggestions in the literature to reduce the incidence, drug administration errors remain fairly common in South Africa. Failure to institute suggested solutions will continue to compromise patient safety.

Assessment and treatment of pulmonary arterial hypertension: an Australian perspective in 2006

Pulmonary arterial hypertension is a group of diseases which forms a small subset of those with elevated pulmonary artery pressure (pulmonary hypertension). The recent development of selective pulmonary vasodilator has lead to a substantial resurgence of interest in what have been previously regarded as rare and incurable diseases. This review aims to describe the spectrum of pulmonary vascular diseases, the evolving understanding as to pathogenesis, the evolving evidence of efficacy for drug therapies, trying to put this into a contemporary Australian context. Several key pathogenic pathways may be involved: prostacycline, Nitric Oxide-cGMP-phosphodiesterase 5 and endothelin- all of which are exploited for therapeutic benefit by newly available drug therapies. A recently modified classification system reasserts the importance of precise diagnosis. The cardinal symptom of exertional dyspnea warrants careful evaluation in an attempt to prevent (frequently occurring) substantial delay in diagnosis. Echocardiogram is the cornerstone of screening for pulmonary arterial hypertension; however, a detailed evaluation including a carefully performed right heart catheterisation with sufficient data to allow calculation of pulmonary vascular resistance is key to accurate diagnosis. These new approaches to therapy are already substantially improving quality of life and prognosis.

Outcomes of patients with interstitial lung disease referred for lung transplant assessment

BACKGROUND

Patients with interstitial lung disease (ILD) very frequently die before the opportunity to receive lung transplantation (LTx). This retrospective study describes the clinical course of 86 patients with ILD referred for LTx assessment between January 1999 and December 2002.

AIMS

(i) To describe the outcomes, (ii) to identify reasons of delay to transplantation, (iii) to describe the causes of death/complications and (iv) to assess the pathological diagnosis and concordance with explanted lung pathology.

METHODS

Data were collected from the case notes of all patients with ILD referred to the Alfred Hospital over a 4-year period.

RESULTS

Twenty women and 66 men, mean age of 55 +/- 8 years, were referred for LTx assessment. Forty-five patients were deemed not suitable for LTx and 41 were listed. Twenty-two patients underwent transplantation, 16 died on the waiting list and 7 are still on the waiting list. Complications were frequent (e.g. pulmonary embolism, malignancy and infection) and carried high mortality. Patients dying on the waiting list appeared generally to be in accelerated decline, dying shortly after listing, with no evidence in their lung function test assessment predicting them as a poor prognosis group.

CONCLUSIONS

Serious complications and death on the waiting list of patients with idiopathic pulmonary fibrosis are high, not apparently because of delayed referral but usually in patients undergoing very rapid decline.

Contemporary referral of patients from community care to cardiology lack diagnostic and clinical detail

The quantity of referrals to secondary care is increasing. That the quality of medical referrals is decreasing is a common allegation yet has rarely been assessed. We report a time-limited, cross-sectional survey evaluating cardiological referral information quality. Referral letters (n = 218, excluding direct access pro formas) from GPs to the Cardiology Department at City Hospital, Birmingham, were collated and analysed over 2 months. A subset (n = 49) of these patients completed questionnaires assessing their knowledge and patient communication of the referral. Information quality was poor (length, diagnosis, expectation, prior treatment and investigation) with almost half of all letters containing only outline symptomatic complaints without diagnosis. The majority of patients referred had not been investigated or treated in any way before referral. Despite lack of understanding of the reason for referral, typically the majority of patients expressed themselves as satisfied with the process. Given most referrals are seen as appropriate, information exchange between secondary and primary care is crucial. By contrast, the standard of even basic clinical assessment communicated between primary care and secondary care was severely limited. The reason(s) why medical assessment is lacking are unclear but must be explored to give more support to primary care to complete basic medical task particularly if investment is to flow into this source.

Statistical analysis of real-time PCR data

BACKGROUND

Even though real-time PCR has been broadly applied in biomedical sciences, data processing procedures for the analysis of quantitative real-time PCR are still lacking; specifically in the realm of appropriate statistical treatment. Confidence interval and statistical significance considerations are not explicit in many of the current data analysis approaches. Based on the standard curve method and other useful data analysis methods, we present and compare four statistical approaches and models for the analysis of real-time PCR data.

RESULTS

In the first approach, a multiple regression analysis model was developed to derive DeltaDeltaCt from estimation of interaction of gene and treatment effects. In the second approach, an ANCOVA (analysis of covariance) model was proposed, and the DeltaDeltaCt can be derived from analysis of effects of variables. The other two models involve calculation DeltaCt followed by a two group t-test and non-parametric analogous Wilcoxon test. SAS programs were developed for all four models and data output for analysis of a sample set are presented. In addition, a data quality control model was developed and implemented using SAS.

CONCLUSION

Practical statistical solutions with SAS programs were developed for real-time PCR data and a sample dataset was analyzed with the SAS programs. The analysis using the various models and programs yielded similar results. Data quality control and analysis procedures presented here provide statistical elements for the estimation of the relative expression of genes using real-time PCR.

Relation of interlobar collaterals to radiological heterogeneity in severe emphysema

BACKGROUND

A study was undertaken to assess the prevalence of interlobar collateral ventilation in patients with severe emphysema to identify factors that may help to predict patients with significant collateral ventilation.

METHODS

Between April 2002 and August 2003, ex vivo assessment of the lungs 17 consecutive patients with smoking related severe emphysema was performed. To assess collateral flow, all lobes of explanted specimens were selectively intubated using a wedged cuffed microlaryngeal intubation tube and then manually ventilated using a bagging circuit. Interlobar collateral ventilation was defined as the ability to easily inflate a non-intubated lobe at physiological pressures. Pre-transplant demographic characteristics, physiological data, radiological results, and explant histology were assessed for retrospective relationships with the degree of interlobar collateral ventilation in the explanted lung.

RESULTS

A total of 23 lungs were evaluated, 15 of which (66%) had significant collateral interlobar airflow. There were no significant differences in any demographic, physiological, or pathological variables between patients with collateral ventilation and those with no collateral ventilation. However, there was a significant relationship between the presence of interlobar collateral ventilation and radiological scores (p<0.05).

CONCLUSIONS

Interlobar collateral ventilation occurs to a much greater extent in patients with radiologically homogeneous emphysema than in those with heterogeneous emphysema. Heterogeneity of emphysema may predict patients with a significantly reduced risk of interlobar collateral ventilation.