varAmpliCNV: analyzing variance of amplicons to detect CNVs in targeted NGS data

MOTIVATION

Computational identification of copy number variants (CNVs) in sequencing data is a challenging task. Existing CNV-detection methods account for various sources of variation and perform different normalization strategies. However, their applicability and predictions are restricted to specific enrichment protocols. Here, we introduce a novel tool named varAmpliCNV, specifically designed for CNV-detection in amplicon-based targeted resequencing data (Haloplex™ enrichment protocol) in the absence of matched controls. VarAmpliCNV utilizes principal component analysis (PCA) and/or metric dimensional scaling (MDS) to control variances of amplicon associated read counts enabling effective detection of CNV signals.

RESULTS

Performance of VarAmpliCNV was compared against three existing methods (ConVaDING, ONCOCNV and DECoN) on data of 167 samples run with an aortic aneurysm gene panel (n = 30), including 9 positive control samples. Additionally, we validated the performance on a large deafness gene panel (n = 145) run on 138 samples, containing 4 positive controls. VarAmpliCNV achieved higher sensitivity (100%) and specificity (99.78%) in comparison to competing methods. In addition, unsupervised clustering of CNV segments and visualization plots of amplicons spanning these regions are included as a downstream strategy to filter out false positives.

AVAILABILITY AND IMPLEMENTATION

The tool is freely available through galaxy toolshed and at: https://hub.docker.com/r/cmgantwerpen/varamplicnv. Supplementary Data File S1: https://tinyurl.com/2yzswyhh; Supplementary Data File S2: https://tinyurl.com/ycyf2fb4.

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.

Delineation of a new fibrillino-2-pathy with evidence for a role of FBN2 in the pathogenesis of carpal tunnel syndrome

BACKGROUND

Although carpal tunnel syndrome (CTS) is the most common form of peripheral entrapment neuropathy, its pathogenesis remains largely unknown. An estimated heritability index of 0.46 and an increased familial occurrence indicate that genetic factors must play a role in the pathogenesis.

METHODS AND RESULTS

We report on a family in which CTS occurred in subsequent generations at an unusually young age. Additional clinical features included brachydactyly and short Achilles tendons resulting in toe walking in childhood. Using exome sequencing, we identified a heterozygous variant (c.5009T>G; p.Phe1670Cys) in the fibrillin-2 (FBN2) gene that co-segregated with the phenotype in the family. Functional assays showed that the missense variant impaired integrin-mediated cell adhesion and migration. Moreover, we observed an increased transforming growth factor-β signalling and fibrosis in the carpal tissues of affected individuals. A variant burden test in a large cohort of patients with CTS revealed a significantly increased frequency of rare (6.7% vs 2.5%-3.4%, p<0.001) and high-impact (6.9% vs 2.7%, p<0.001) FBN2 variants in patient alleles compared with controls.

CONCLUSION

The identification of a novel FBN2 variant (p.Phe1670Cys) in a unique family with early onset CTS, together with the observed increased frequency of rare and high-impact FBN2 variants in patients with sporadic CTS, strongly suggest a role of FBN2 in the pathogenesis of CTS.

Multiple solvent elution, a method to counter the effects of coelution and ion suppression in LC-MS analysis in bottom up proteomics

On average a human cell type expresses around 10,000 different protein coding genes synthesizing all the different molecular forms of the protein product (proteoforms) found in a cell. In a typical shotgun bottom up proteomic approach, the proteins are enzymatically cleaved, producing several 100,000 s of different peptides that are analyzed with liquid chromatography-tandem mass spectrometry (LC-MSMS). One of the major consequences of this high sample complexity is that coelution of peptides cannot be avoided. Moreover, low abundant peptides are difficult to identify as they have a lower chance of being selected for fragmentation due to ion-suppression effects and the semi-stochastic nature of the precursor selection in data-dependent shotgun proteomic analysis where peptides are selected for fragmentation analysis one-by-one as they elute from the column. In the current study we explore a simple novel approach that has the potential to counter some of the effect of coelution of peptides and improves the number of peptide identifications in a bottom-up proteomic analysis. In this method, peptides from a HeLa cell digest were eluted from the reverse phase column using three different elution solvents (acetonitrile, methanol and acetone) in three replicate reversed phase LC-MS/MS shotgun proteomic analysis. Results were compared with three technical replicates using the same solvent, which is common practice in proteomic analysis. In total, we see an increase of up to 10% in unique protein and up to 30% in unique peptide identifications from the combined analysis using different elution solvents when compared to the combined identifications from the three replicates of the same solvent. In addition, the overlap of unique peptide identifications common in all three LC-MS analyses in our approach is only 23% compared to 50% in the replicates using the same solvent. The method presented here thus provides an easy to implement method to significantly reduce the effects of coelution and ion suppression of peptides and improve protein coverage in shotgun proteomics. Data are available via ProteomeXchange with identifier PXD011908.

pBRIT: gene prioritization by correlating functional and phenotypic annotations through integrative data fusion

Motivation

Computational gene prioritization can aid in disease gene identification. Here, we propose pBRIT (prioritization using Bayesian Ridge regression and Information Theoretic model), a novel adaptive and scalable prioritization tool, integrating Pubmed abstracts, Gene Ontology, Sequence similarities, Mammalian and Human Phenotype Ontology, Pathway, Interactions, Disease Ontology, Gene Association database and Human Genome Epidemiology database, into the prediction model. We explore and address effects of sparsity and inter-feature dependencies within annotation sources, and the impact of bias towards specific annotations.

Results

pBRIT models feature dependencies and sparsity by an Information-Theoretic (data driven) approach and applies intermediate integration based data fusion. Following the hypothesis that genes underlying similar diseases will share functional and phenotype characteristics, it incorporates Bayesian Ridge regression to learn a linear mapping between functional and phenotype annotations. Genes are prioritized on phenotypic concordance to the training genes. We evaluated pBRIT against nine existing methods, and on over 2000 HPO-gene associations retrieved after construction of pBRIT data sources. We achieve maximum AUC scores ranging from 0.92 to 0.96 against benchmark datasets and of 0.80 against the time-stamped HPO entries, indicating good performance with high sensitivity and specificity. Our model shows stable performance with regard to changes in the underlying annotation data, is fast and scalable for implementation in routine pipelines.

Availability and implementation

http://biomina.be/apps/pbrit/; https://bitbucket.org/medgenua/pbrit.

Supplementary information

Supplementary data are available at Bioinformatics online.

Association and expression of the antigen-processing gene PSMB8, coding for low-molecular-mass protease 7, with vitiligo in North India: case-control study

BACKGROUND

Vitiligo is a multifactorial, autoimmune, depigmenting disorder of the skin where aberrant presentation of autoantigens may have a role.

OBJECTIVES

To study the association of two antigen-processing genes, PSMB8 and PSMB9, with vitiligo.

METHODS

In total 1320 cases of vitiligo (1050 generalized and 270 localized) and 752 healthy controls were studied for the PSMB9 exon 3 G/A single-nucleotide polymorphism (SNP), PSMB8 exon 2 C/A SNP and PSMB8 intron 6 G/T SNP at site 37 360 using polymerase chain reaction (PCR)-restriction fragment length polymorphism. Real-time PCR was used for transcriptional expression of PSMB8 and cytokines. Expression of ubiquitinated proteins and phosphorylated-p38 (P-p38) was studied by Western blotting.

RESULTS

Significant increases in PSMB8 exon 2 allele A (P < 2.07 × 10^-6 , odds ratio 1·93) and genotypes AA (P < 1.03 × 10^-6 , odds ratio 2·51) and AC (P < 1.29 × 10^-6 , odds ratio 1·63) were observed in patients with vitiligo. Interferon-γ stimulation induced lower expression of PSMB8 in peripheral blood mononuclear cells of cases compared with controls, suggesting impaired antigen processing, which was confirmed by accumulation of ubiquitinated proteins in both lesional and nonlesional skin of patients with vitiligo. Expression of proinflammatory cytokines - interleukin (IL)-6, IL-1β and IL-8 - was higher in the lesional skin. P-p38 expression was variable but correlated with the amount of ubiquitinated proteins in the lesional and nonlesional skin, suggesting that the inflammatory cytokine responses in lesional skin could be a result of both P-p38-dependent and -independent pathways.

CONCLUSIONS

The PSMB8 exon 2 SNP is significantly associated with vitiligo. Accumulation of ubiquitinated proteins in skin of cases of vitiligo suggests their aberrant processing, which may promote the development of the disease.

Mutations in two large pedigrees highlight the role of ZNF711 in X-linked intellectual disability

Intellectual disability (ID) affects approximately 1-2% of the general population and is characterized by impaired cognitive abilities. ID is both clinically as well as genetically heterogeneous, up to 2000 genes are estimated to be involved in the emergence of the disease with various clinical presentations. For many genes, only a few patients have been reported and causality of some genes has been questioned upon the discovery of apparent loss-of-function mutations in healthy controls. Description of additional patients strengthens the evidence for the involvement of a gene in the disease and can clarify the clinical phenotype associated with mutations in a particular gene. Here, we present two large four-generation families with a total of 11 males affected with ID caused by mutations in ZNF711, thereby expanding the total number of families with ID and a ZNF711 mutation to four. Patients with mutations in ZNF711 all present with mild to moderate ID and poor speech accompanied by additional features in some patients, including autistic features and mild facial dysmorphisms, suggesting that ZNF711 mutations cause non-syndromic ID.

Premedication in an autistic, combative child: Challenges and nuances

Children with autistic spectrum disorders are often encountered in anesthesia practice mainly for outdoor procedural sedation or anesthesia in endoscopy and magnetic resonance imaging suites. We describe a case of a 7-year-old autistic boy who required management of dental caries. He had a phobia to intravenous cannulation, displayed increasing anxiety and became combative on the day of surgery. With parental involvement and distraction, we succeeded in giving oral midazolam by concealing it, with the intent of avoiding intramuscular injection or unnecessary restraint. Lack of knowledge about the medical condition of such a patient can lead to inadequate preoperative preparation and use of restraint on the patient, which might cause anxiety or panic attacks in the operative room. To effectively manage children with special needs one needs to have clear guidelines on the management of uncooperative children, involve parents perioperatively, plan ahead with an emphasis on perioperative analgesia and sometimes incorporate the ethical use of restraint.

High-Sensitivity Measurement of Density by Magnetic Levitation

This paper presents methods that use Magnetic Levitation (MagLev) to measure very small differences in density of solid diamagnetic objects suspended in a paramagnetic medium. Previous work in this field has shown that, while it is a convenient method, standard MagLev (i.e., where the direction of magnetization and gravitational force are parallel) cannot resolve differences in density <10(-4) g/cm(3) for macroscopic objects (>mm) because (i) objects close in density prevent each other from reaching an equilibrium height due to hard contact and excluded volume, and (ii) using weaker magnets or reducing the magnetic susceptibility of the medium destabilizes the magnetic trap. The present work investigates the use of weak magnetic gradients parallel to the faces of the magnets as a means of increasing the sensitivity of MagLev without destabilization. Configuring the MagLev device in a rotated state (i.e., where the direction of magnetization and gravitational force are perpendicular) relative to the standard configuration enables simple measurements along the axes with the highest sensitivity to changes in density. Manipulating the distance of separation between the magnets or the lengths of the magnets (along the axis of measurement) enables the sensitivity to be tuned. These modifications enable an improvement in the resolution up to 100-fold over the standard configuration, and measurements with resolution down to 10(-6) g/cm(3). Three examples of characterizing the small differences in density among samples of materials having ostensibly indistinguishable densities-Nylon spheres, PMMA spheres, and drug spheres-demonstrate the applicability of rotated Maglev to measuring the density of small (0.1-1 mm) objects with high sensitivity. This capability will be useful in materials science, separations, and quality control of manufactured objects.

Pathology of experimental infection by Pasteurella multocida serotype A: 1 in buffalo calves

Pasteurella multocida serotype A:3 has been mostly implicated in pneumonic pasteurellosis in ruminants. In contrast, our previous studies have reported that both serotypes A:1 and A:3 were responsible for respiratory diseases in cattle and buffaloes. However, the pathology and pathogenesis of P. multocida serotype A:1 (Pm A:1) infection have not been studied in ruminants. In the present study, 12- to 15-week-old buffalo calves (Bubalus bubalis) infected by Pm A:1 had fibrinous and suppurative bronchopneumonia with focal areas of coagulation necrosis typical of pneumonic pasteurellosis. For the first time, this study reports the lung pathology and pathogenecity of Pm A:1 infection in calves.

GOParGenPy: a high throughput method to generate gene ontology data matrices

BACKGROUND

Gene Ontology (GO) is a popular standard in the annotation of gene products and provides information related to genes across all species. The structure of GO is dynamic and is updated on a daily basis. However, the popular existing methods use outdated versions of GO. Moreover, these tools are slow to process large datasets consisting of more than 20,000 genes.

RESULTS

We have developed GOParGenPy, a platform independent software tool to generate the binary data matrix showing the GO class membership, including parental classes, of a set of GO annotated genes. GOParGenPy is at least an order of magnitude faster than popular tools for Gene Ontology analysis and it can handle larger datasets than the existing tools. It can use any available version of the GO structure and allows the user to select the source of GO annotation. GO structure selection is critical for analysis, as we show that GO classes have rapid turnover between different GO structure releases.

CONCLUSIONS

GOParGenPy is an easy to use software tool which can generate sparse or full binary matrices from GO annotated gene sets. The obtained binary matrix can then be used with any analysis environment and with any analysis methods.

Trend in decline in leprosy disabilities of a LEPRA project in Malkangiri district, Odisha, India

This a retrospective analysis of the changes in 646 disabilities occurred amongst 3979 cases registered during 19 years from 1992 to 2010 in Malkangiri district. This amounted to 16.2% of cases with disability segregated to 310 (48%) Grade 1 and 336 (52%) Grade 2. In this project, managed by LEPRA India, POD care was in practice from the year 1992 and records were updated regularly. An analysis of the annual records showed that the next year-end balance increased up to the year 2001 followed by gradual decline. Within this period the total cases with disabilities declined by about 369 (57%) due to death by aging 204 (55%), migration from the area 77 (21%) and reversing to normal 88 (24%) in cases. Deletion due to recovery to normal especially with sensory impairment is fairly good with or without steroid. Disability percentage in new cases declined steadily especially Grade 2 from 30% to 1%, initial high rate attributed mostly to backlog cases. In later years the rate is erratic high amongst low number of new cases. Absolute number indicates the situation better. Such study helps to roughly extrapolate the existing disability load in a particular area and assists in planning for care and prevention.

Genome sequencing of the plant pathogen Taphrina deformans, the causal agent of peach leaf curl

Taphrina deformans is a fungus responsible for peach leaf curl, an important plant disease. It is phylogenetically assigned to the Taphrinomycotina subphylum, which includes the fission yeast and the mammalian pathogens of the genus Pneumocystis. We describe here the genome of T. deformans in the light of its dual plant-saprophytic/plant-parasitic lifestyle. The 13.3-Mb genome contains few identifiable repeated elements (ca. 1.5%) and a relatively high GC content (49.5%). A total of 5,735 protein-coding genes were identified, among which 83% share similarities with other fungi. Adaptation to the plant host seems reflected in the genome, since the genome carries genes involved in plant cell wall degradation (e.g., cellulases and cutinases), secondary metabolism, the hallmark glyoxylate cycle, detoxification, and sterol biosynthesis, as well as genes involved in the biosynthesis of plant hormones. Genes involved in lipid metabolism may play a role in its virulence. Several locus candidates for putative MAT cassettes and sex-related genes akin to those of Schizosaccharomyces pombe were identified. A mating-type-switching mechanism similar to that found in ascomycetous yeasts could be in effect. Taken together, the findings are consistent with the alternate saprophytic and parasitic-pathogenic lifestyles of T. deformans.

IMPORTANCE

Peach leaf curl is an important plant disease which causes significant losses of fruit production. We report here the genome sequence of the causative agent of the disease, the fungus Taphrina deformans. The genome carries characteristic genes that are important for the plant infection process. These include (i) proteases that allow degradation of the plant tissues; (ii) secondary metabolites which are products favoring interaction of the fungus with the environment, including the host; (iii) hormones that are responsible for the symptom of severely distorted leaves on the host; and (iv) drug detoxification enzymes that confer resistance to fungicides. The availability of the genome allows the design of new drug targets as well as the elaboration of specific management strategies to fight the disease.

Is abdominal aortic calcification score a cost-effective screening tool to predict atherosclerotic carotid plaque and cardiac valvular calcification in patients with end-stage renal disease?

Abdominal aortic calcification (AAC), cardiac valvular calcification (CVC), and atherosclerotic carotid plaque (CP) are known cardiovascular risk factors. The accuracy of the AAC score in predicting CP and CVC in patients with end-stage renal disease (ESRD) is assessed in this study. Twenty-two consecutive prevalent dialysis patients (group 1) and 26 consecutive nondialysis stage V chronic kidney disease patients (group 2) were assessed for their demographic and laboratory variables. Lateral radiograph of the lumbosacral spine was used to assess the AAC score. CP and CVC were assessed using carotid sonography and echocardiogram, respectively. Prevalence of AAC, CP, and CVC in groups 1 and 2 was, respectively, 72.7%, 81.8%, and 72.7% and 76.9%, 80.8%, and 57.7%. AAC was strongly associated with CP and CVC in both groups (P < 0.001). Tests of accuracy for the AAC score as a predictor of CP and CVC showed sensitivity, specificity, positive predictive value, negative predictive value, likelihood ratio of a positive test, and likelihood ratio of a negative test, respectively, in group 1: 83%, 75%, 93%, 50%, 3.32, and 0.23 and 85%, 77%, 87%, 70%, 4.5, and 0.29, and in group 2: 90%, 95%, 83%, 69%, 3.9, 0.41, and 82%, 91%, 77%, 71%, 4.1, and 0.21. Reproducibility of the AAC score among observers was acceptable. The AAC score can predict CP and CVC with moderate accuracy in ESRD patients. However, as our study was underpowered, the findings need validation in larger, adequately powered studies.

Molecular characterization of Avian strains of Pasteurella multocida serogroup-A:1 based on amplification of repetitive regions by PCR

Repetitive extragenic palindromic (REP)-PCR (polymerase chain reaction), enterobacterial repetitive intergenic consensus (ERIC)-PCR, and single primer PCR assays were employed to characterize 66 strains of Pasteurella multocida serogroup A:1 isolated from avian species belonging to different regions of India. REP-PCR resulted in amplification of REP sequences from the genome which were in the range of approximately 200 to approximately 3000 bp and accounted for a total of 54 distinguishing profiles (D=0.99). ERIC-PCR analysis also generated amplified products in the range of approximately 200 to approximately 3200 bp categorizing strains into a total of 50 different profiles (D=0.98). Amplification of repetitive regions using a microsatellite primer (GTG)(5), resulted in clear distinctive bands ranging from approximately 200 to approximately 2400 bp. Strains were assigned to 43 profiles (D=0.96). No correlation could be drawn between genotypic profiles and avian hosts with their geographical area of origin. Avian strains of P. multocida serogroup A:1 were found to be highly heterogeneous with diverse profiles. REP-PCR was found to be highly discriminatory and simple method for differentiation of phenotypically similar strains. The present study also indicated that PCR based amplification of repetitive regions of P. multocida is a rapid technique with good discrimination and could be employed directly for routine typing of field isolates from fowl cholera outbreaks.

REP-PCR analysis of Pasteurella multocida isolates from wild and domestic animals in India

Repetitive extragenic palindromic sequence-based PCR (REP-PCR) was used to characterize 67 field isolates of Pasteurella multocida originating from different animal species and geographical regions of India. REP-PCR was found to be rapid and reproducible (three repeats were done). These isolates yielded different 23 profiles which were clustered into eight groups. The discrimination index was moderate (D value 0.83). Somatic and antigenic typing of the isolates did not reveal any correlation with REP-PCR profiles. There was no host-specific, type-specific, region-specific or pathenogenicity-specific pattern. The REP profiles of isolates obtained from wild animals were similar to those obtained from domestic animals. Two common bands were present in all the isolates irrespective of somatic or antigenic types. The results were not comparable with earlier findings, which had shown high discrimination index and correlation with disease presentation.

Comparative sequence analysis of 16S rRNA gene of Pasteurella multocida serogroup B isolates from different animal species

The phylogenetic relationships of five isolates of Pasteurella multocida serotype B:2 belonging to buffalo, cattle, pig, sheep and goat were investigated by comparative sequence analysis of 16S rRNA gene. The 1468bp fragment of 16S rRNA gene sequence comparison showed that the isolates of cattle (PM75), pig (PM49) and sheep (PM82) shared 99.9% homology with the buffalo isolate (vaccine strain P52) whereas, the goat isolate (PM86) shared 99.8% homology with the vaccine strain. The 16S rRNA gene sequences of these isolates were also found monophyletic with type B reference strain NCTC 10323 of P. multocida subsp. multocida. The present study indicated the close relationships of haemorrhagic septicaemia causing P. multocida serotype B:2 isolates of buffalo and cattle with other uncommon hosts (pig, sheep and goat).

Identification of avian strains of Pasteurella multocida in India by conventional and PCR assays

The prevalence of capsular and somatic serotypes were studied among 123 Pasteurella multocida strains isolated from chickens (n=94), ducks (22), quails (4), turkeys (2) and geese (1) from different geographical regions of India. All strains exhibited similar cultural and morphological characteristics. Ninety-two of the isolates belonged to serotype A:1, the most prevalent serotype, with serotypes A:3, A:1,3, D:3 and F:3 having two isolates each. Only one isolate was positive for serotypes A:4 and D:1. Twenty isolates were untyped. A multiplex capsular PCR assay generated amplicons of sizes approximately 460, approximately 1044, approximately 657 and approximately 854 bp in 106 isolates identified as capsular serotype-A, 15 in serotype D and two in serotype F. Capsular types B and E were not detected in any of the avian isolates studied. The present findings suggest that a multiplex capsular PCR assay may be suitable for the rapid initial identification serotypes P. multocida during epidemiological studies of fowl cholera.

Evaluation of a recombinant LipL41 antigen of Leptospira interrogans serovar Canicola in ELISA for serodiagnosis of bovine Leptospirosis

The efficacy of a recombinant leptospiral lipoprotein LipL41 as an antigen for conducting enzyme-linked immunosorbent assay (ELISA) for diagnosis of bovine leptospirosis was evaluated. Using known positive and known negative cattle sera the recombinant antigen was found to be highly reactive in the concentration of 100 ng/well. Using a total of 321 field cattle sera the sensitivity of ELISA as compared to microscopic agglutination test (MAT) was calculated to be 100% whereas the specificity was 85.3%. The seropositivity of leptospirosis among bovine population was found to be 21.18% having the predominance of serovars Sejroe and Pomona. It was concluded that rLipL41 protein could be a putative diagnostic candidate for serodiagnosis of bovine leptospirosis.

Characterization of avian strains of Pasteurella multocida by restriction endonuclease and amplified fragment length polymorphism

Avian strains of Pasteurella multocida were typed by employing restriction endonuclease analysis (REA) and single enzyme-amplified fragment length polymorphism (AFLP) to evaluate their applicability for epidemiological studies of fowl cholera outbreaks. A total of 72 strains isolated from different avian species (chicken, duck, turkey, quail and goose) belonging to various geographical regions of India were characterized. REA using two different enzymes HhaI and HpaII produced 9 and 18 clusters respectively, whereas Single enzyme-AFLP recognized 32 patterns out of 72 strains typed. The study indicated that REA using HpaII is a simple and resource efficient method, however, further typing with more stringent and rapid method like Single enzyme-AFLP, could drastically enhance investigation in epidemiological studies of fowl cholera outbreaks.

Detection of Pasteurella multocida in experimentally infected embryonated chicken eggs by PCR assay

Applicability of polymerase chain reaction (PCR) assay to detect Pasteurella multocida in experimentally infected embryonated chicken egg was assessed in the present study. PCR assay rapidly and specifically detected the genome of P. multocida in amniotic fluid, allantoic fluid and homogenates of infected embryo and its membranes. The sensitivity of detection was as low as 20 bacterial cells/ml of allantoic or amniotic fluids. Detection of P. multocida in dead embryos by PCR was possible up to 6 and 30 days or more following storage of dead embryos at 37 degrees C, and at 4 degrees C as well as at -20 degrees C, respectively. The study revealed that PCR assays could be employed directly for detection and confirmation of P. multocida infection in experimentally infected chicken embryos.

Detection of multiple strains ofPasteurella multocidain fowl cholera outbreaks by polymerase chain reaction-based typing

Applicability of molecular methods for the detection and differentiation of Pasteurella multocida strains involved in two separate fowl cholera outbreaks in a single poultry farm was investigated. A total of 12 and 18 strains of P. multocida obtained from two separate outbreaks were subjected to phenotypic and genotypic characterization. Phenotypically, all strains were similar; however, DNA-based techniques by employing polymerase chain reaction (PCR) assays were found to be highly specific and sensitive for rapid detection and differentiation of strains. All 30 strains gave amplicons of approximately 460 bp and approximately 1,044 bp specific for P. multocida and capsular serogroup A in the Multiplex Capsular PCR typing system. Molecular typing techniques such as repetitive extragenic palindromic PCR, enterobacterial repetitive intergenic consensus PCR and single primer PCR differentiated all 30 strains into different profiles. However, similar patterns of genome fragments were observed among all strains following restriction endonuclease analysis using the enzyme HpaII. The current investigation revealed involvement of the same and multiple strains of P. multocida in two outbreaks. The results also indicated that molecular methods of detection and typing are rapid in comparison with conventional methods for epidemiological investigations of fowl cholera outbreaks.

Ribotyping of Indian Isolates of Pasteurella multocida Based on 16S and 23S rRNA Genes

The applicability of ribotyping based on 16S and 23S rRNA was evaluated for molecular epidemiological studies. Forty-eight isolates of Pasteurella multocida isolated from different hosts and geographical locations and one reference isolate were ribotyped. Only four ribotypes were found. All the isolates including reference isolate from wild carnivores had the same ribotype, though they had different serotypes. The isolate from a tiger had one band in addition to the bands present in the major ribotype. The isolates from lions represented two ribotypes; of these ribotypes, one (r2) had an additional band of 3.6 kbp, which was absent in all other ribotypes. The second ribotype (r4) from a lion had one band missing (6 kbp) that was present in the other ribotypes. These isolates were further typed using ERIC-PCR and REP-PCR. With ERIC-PCR and REP-PCR, higher D values of 0.83 and 0.89 were obtained. The current study revealed that ribotyping is not a very efficient typing tool for use in molecular epidemiology for differentiation of isolates.

Cost and efficiency of HIV voluntary counselling and testing centres in Andhra Pradesh, India

BACKGROUND

[corrected] As part of the effort to control HIV/AIDS, the number of HlV voluntarycounselling and testingcentres (VCTCs) is increasing rapidly in the public health system of the Indian state of Andhra Pradesh, which is estimated to have one of the highest rates of HIV infection in India. However, systematic data on the cost and efficiency of providing VCT services in India are not available to help guide efficient use of resources for these services.

METHODS

We used standardized methods to obtain detailed cost and output data for the 2002-03 fiscal year from written records and interviews in 17 VCTCs in the public health system in Andhra Pradesh. We calculated the economic cost per client receiving VCT services, and analysed the variation and determinants of total and unit costs across VCTCs. We used multivariate regression techniques to estimate incremental unit costs. We assessed hurdles towards serving an optimal number of clients by VCTCs.

RESULTS

In the 2002-03 fiscal year, 32 413 clients received the complete sequence of services at the 17 VCTCs, including post-HIV test counselling. The number of clients served by each VCTC ranged from 334 to 7802 (median 979). The overall HIV-positive rate in post-test counselled clients was 20.5% (range 5.4%-52.6%). The cost per client for the complete VCT sequence varied 6-fold between VCTCs (range Rs 141.5-829.6 [US 2.92-17.14 dollars], median Rs 363.5 [US 7.51 dollars]). The cost per client was significantly lower at VCTCs with more clients (p < 0.001, R2 = 0.83; power function) due to substantial fixed costs. Personnel made up the largest component of cost (53.7%). The cost per client had a significant direct relation with percent personnel cost for VCTCs (p < 0.001, R2 = 0.58; exponential function). A multiple regression model revealed that the incremental cost of providing complete VCT services to each HIV-positive and -negative client was Rs 123.5 (US 2.54 dollars) and Rs 59.2 (US 1.22 dollars), respectively. Fourteen VCTCs (82.4%) reported that they could serve more clients with the available personnel and infrastructure, and that inadequate demand for their services was the main hurdle towards achieving this.

CONCLUSION

These data suggest that the efforts of the National AIDS Control Organisation of India and the Andhra Pradesh State AIDS Control Society in increasing VCTCs could yield even higher benefit if the demand for these services was enhanced, as this would increase the number of clients served and reduce the cost per client. Ongoing systematic cost-efficiency analysis is necessary to help guide efficient use of HIV-control resources in India.

Antibiotic Sensitivity Patterns among Indian Strains of Avian Pasteurella multocida

An investigation was carried out to study the antibiotic sensitivity of avian strains of Pasteurella multocida and to select an effective antimicrobial agent for control of avian pasteurellosis in India. A total of 123 strains of P. multocida recently isolated from different avian species (chicken, duck, turkey, quail, and goose), from different regions of India were subjected to antibiotic sensitivity tests using 20 different antibiotics. Absolute resistance was observed against sulfadiazine. The studies indicated that the strains were most sensitive to chloramphenicol (73.98%), followed by enrofloxacin (71.54%), lincomycin (64.23%), norfloxacin (61.79%) and doxycycline-HCl (56.91%). The majority of the strains were found to exhibit intermediate sensitivity. Chloramphenicol was selected and suggested for treatment. Antibiogram studies also revealed the emergence of multidrug-resistant strains of P. multocida among Indian poultry.

Prevalent Serotypes of Pasteurella multocida Isolated from Different Animal and Avian Species in India

Identification and estimation of the prevalence of Pasteurella multocida organisms in different animal and avian species in India during November 2000 to July 2003 was carried out. Out of 418 samples collected from different outbreaks suspected to be caused by P. multocida, a total of 206 bacterial cultures were identified as P. multocida on the basis of cultural, morphological and biochemical characteristics. All the 206 cultures were isolated from different domestic animal species (cattle, buffalo, sheep, goat, pig and rabbit), avian species (chicken, duck, quail, turkey, goose) and wild animals such as leopard and deer. Serotyping of P. multocida cultures revealed the presence of various serotypes (A:1, A:3, A:1,3, A:4, B:2, D:1 and -:1) among the livestock population. P. multocida polymerase chain reaction (PCR) assay applied on different forms of bacterial cultures (bacterial culture lysate, direct bacterial colony and mixed bacterial culture lysate) yielded an amplified product of approximately 460 bp specific for P. multocida. The results of PCR assay correlated well with conventional methods of identification. The present investigation revealed the presence of varied serotypes among livestock and PCR assay was found to be useful for rapid, sensitive and specific diagnosis of pasteurellosis in animals and avian species.

Molecular variability among strains of Pasteurella multocida isolated from an outbreak of haemorrhagic septicaemia in India

The applicability of conventional and molecular methods for rapid detection and differentiation of Pasteurella multocida serogroup B isolates involved in an outbreak of haemorrhagic septicaemia affecting Indian buffaloes, was studied. Five isolates were obtained and were subjected to phenotypic and genotypic characterization. None of the five isolates could be differentiated on the basis of cultural, biochemical, pathogenicity and antimicrobial sensitivity patterns. Polymerase chain reaction (PCR)-based techniques were found to be specific and sensitive for rapid detection and differentiation of isolates. Repetitive extragenic palindromic (REP-) PCR, enterobacterial repetitive intergenic consensus (ERIC-) PCR and single-primer PCR differentiated all the five isolates into different profiles. All the isolates involved in the outbreak were found to have a genetic profile different from standard P. multocida strain (P52). However, three isolates had similar profiles, whereas each of the remaining two had a different profile. The study indicates the involvement of multiple strains of P. multocida in a single outbreak of haemorrhagic septicaemia in buffaloes. The results also indicate that molecular methods of detection and typing are superior to conventional methods for rapid epidemiological investigations of haemorrhagic septicaemia.

Specific identification of Pasteurella multocida serogroup-A isolates by PCR assay

A polymerase chain reaction (PCR) assay targeting the hyaC-hyaD gene was developed and used to identify strains of Pasteurella multocida belonging to serogroup-A. A set of serogroup-specific-PCR primers amplified a 564 bp product from genomic DNA prepared from bacterial cells or directly from bacterial colonies. This method detected as low as 10 ng of bacterial DNA and had a specificity of 100% for P. multocida serogroup-A. A nested PCR method yielded a single 374 bp product. All fifty isolates were also shown to be identical by restriction fragment length polymorphism (RFLP) analysis of the PCR products after digestion with BglII.

Fatal intentional poisoning cases admitted to the University Hospitals of Leuven, Belgium from 1993 to 1996

Between January 1993 and July 1996, a total of 2827 intentional cases of poisoning were registered in the University Hospitals of Leuven, Belgium. Ten of these cases were fatal. This study was set up to evaluate the substances involved, the circumstances, the features and the characteristics of the patients who died due to intentional poisoning. The male to female ratio of these fatal cases was 9 : 1. The median age was 43 years. Two groups of substances were revealed to be associated with fatal outcome. The first group consisted of chemicals (seven lethal cases): cholinesterase inhibitors ( =3), methanol ( =2) and paraquat ( =2). The second group consisted of benzodiazepines (three lethal cases). In the cases of poisoning with chemicals, death was directly related to product toxicity and the severity of the poisoning, whilst with benzodiazepines, which are considered to be relatively safe drugs even when taken in overdose, there was a clear relationship between a fatal outcome and a delay between ingestion and medical support. Product toxicity, complications and a delay in medical support may be considered as predictors for the effectiveness and efficacy of treatment and may influence which medical treatments need to be administered.

New molecular arrays based on a tin(IV) porphyrin scaffold

Two new porphyrin arrays-a hexamer and a nonamer-have been synthesized and characterized by elemental analysis as well as mass, (1)H NMR, and UV-vis spectroscopic methods. The scheme of construction of these arrays employs a synthetic protocol involving sequential "organic" and "inorganic" reactions conducted, respectively, at the peripheral meso-phenyl ring and the central tin(IV) ion of the porphyrin scaffold. The architecture of the hexamer is such that it is based on a covalently linked tin(IV) porphyrin dimer, with each of the two tin(IV) centers trans-axially ligated to two free-base porphyrins, while the higher homologue features a tin(IV) porphyrin trimer as the basal unit, with its central metalloid ions having two free-base porphyrins as axial ligands. This extended, "axial-bonding"-type architecture of the new arrays has been investigated by the (1)H NMR method, which reveals characteristic ring-current-induced shifts and coupling patterns for the resonances due to protons of the axial free-base porphyrin subunits. The presence of any ring-ring (basal-basal, basal-axial, or axial-axial) interaction in these arrays is not obvious from their UV-vis and redox potential data, which are close to those of the corresponding constituent monomeric species. On the other hand, their singlet-state activities are quite different from those of the precursor reference compounds as probed by steady-state fluorescence. The results of the detailed investigations carried out on these hybrid, "bichromophoric" arrays have been interpreted in terms of the occurrence of intraarray, interchromophore energy- and electron-transfer reactions.

Ocular and systemic lesions in children with HIV

The spectrum of ocular lesions in children with HIV infection is different from that seen in adults. Ocular lesions in pediatric AIDS patients have not been studied in India. We analyzed the clinical profile, demographic characteristics, ocular and systemic lesions in children with AIDS seen in a referral eye institute in India. The clinical profile and demographic features were studied and complete ocular examination was done. Systemic findings were evaluated at an AIDS care center and recorded in a precoded proforma. Out of the 218 cases of HIV infection seen at our hospital between December 1993 and October 1999, 12 (5.50%) were below 15 years of age. Seven (58.33%) were males and 5 (41.66%) were females with the mean age of 6.5 years and median age of 6.2 years. Vertical transmission was the most common mode of infection (58.33%). Seven (58.33%) of these patients had systemic infection, the most common being pulmonary tuberculosis (42.85%). Ocular lesions were found in 6 (50%) patients. The most common ocular lesions were anterior uveitis and cytomegalovirus retinitis (CMV) (33%) followed by retinal detachment (16.66%) and vitreous hemorrhage (16.66%). High prevalence of ocular lesions in pediatric AIDS patients in India in a referral eye centre was observed. The most common lesions were anterior uveitis followed by CMV retinitis. The management in such cases was often challenging in a developing country like India.

Electrical impedance cardiography using artificial neural networks

This study evaluates the use of artificial neural networks to estimate stroke volume from pre-processed, thoracic impedance plethysmograph signals from 20 healthy subjects. Standard back-propagation was used to train the networks, with Doppler stroke volume estimates as the desired output. The trained networks were then compared to two classical biophysical approaches. The coefficient of determination (R2 x 100%) between the biophysical approaches and the Doppler was 8.20% and 9.90%, while it was 77.38% between the best neural network and the Doppler. Among these methods, only the neural network residuals had a significant zero mean Gaussian distribution (alpha=0.05). Our results indicate that an invertible relationship may exist between thoracic bioimpedance and stroke volume, and that artificial neural networks may offer a potentially advantageous approach for estimating stroke volume from thoracic electrical impedance, both because of their ease of use and their lack of confounding assumptions.

The effect of paroxetine on thiothixene pharmacokinetics

OBJECTIVE

In this study healthy volunteers received thiothixene with and without a 3-day pretreatment with paroxetine to determine if paroxetine decreased the clearance of thiothixene.

METHOD

Ten healthy medication-free volunteers (4 women and 6 men, mean age 38 +/- 12 years) were randomized to receive a single 20 mg oral dose of thiothixene on two separate occasions. On one occasion thiothixene was given concurrently, and following 3 days of pre-treatment with oral paroxetine (20 mg/day). On the other occasion thiothixene was given without paroxetine pre-treatment. The two study days were separated by a minimum period of 2 weeks. On both study days, after the administration of thiothixene, 10 ml blood samples were collected over the next 72 h.

RESULTS

None of the pharmacokinetic parameters of thiothixene were significantly altered by a 3-day treatment with paroxetine.

DISCUSSION

It is likely that the CYP2D6 isoenzyme is not responsible for a high proportion of thiothixene clearance, but one cannot exclude the possibility that a longer paroxetine pretreatment might have caused some inhibition of thiothixene clearance.

Cryosurgery of prostate cancer. Use of adjuvant hormonal therapy and temperature monitoring--A one year follow-up

OBJECTIVE

To determine the clinical outcomes at one year of Stages T2-T3 prostate cancer by cryosurgery utilizing pretreatment with total androgen ablation therapy and temperature monitoring to control the freezing process. Study Group To date, 347 patients have had 356 cryosurgical procedures, 280 have reached one year post treatment. Of these 131 had re-evaluation with prostatic biopsy and serum PSA.

METHODS

Transrectal ultrasound (TRUS) measurement of tumor size and biopsy of extraprostatic space was used to stage patients into two main groups: confined (66.6%) versus nonconfined (19.3%). Radiation failures (14.1%) formed a separate group. Failure rates for the 131 men include all cancer diagnosed during the one year period following cryosurgery.

RESULTS

The one year failure rate for the study group was 19.8% (26/131). For stages T2a, T2h C, T3 and radiation failures, the rates of positive biopsies were 13.9%, 12.9%, 33.3% and 35%, respectively. For those with local control of cancer (negative biopsy), 80% had prostate specific antigen (PSA) levels of < 0.5 ng/ml. The statistical variables for persistent cancer with prostate specific antigen > 0.5 ng/ml were: sensitivity of 66.7%, PPV of 16.7%, NPV of 98% and specificity of 83.7%. A statistically significant difference exist between stages T2 vs T3 and radiation failures (p = < 0.5). Major complications of rectal fistula and total incontinence for previously non-treated cancer versus radiation failures were 0.33% and 8.7% respectively, a 26 times greater risk.

CONCLUSION

Results of cryosurgery for all stages of prostate cancer at one year are encouraging, being 80% free of disease (biopsy and prostate specific antigen). The morbidity of the previously non-treated cancers from this procedure for us was minimal with high patient acceptance. For radiation failures a local control rate of 65% was achieved. However, early in our experience significant morbidity did occur and our enthusiasm for attempted salvage was initially tempered.

Genotoxicity testing of two red dyes in the somatic and germ line cells of Drosophila

Two red dyes, rhodamine B and amaranth, were tested for their genotoxic effects in the somatic (wing primordia) and germ line cells of Drosophila melanogaster following the wing spot and the sex-linked recessive lethal tests. Second- and third-instar larvae, carrying suitable genetic markers, were subjected to chronic exposure to different concentrations of the test dyes. The results indicate that rhodamine is genotoxic in both somatic and germ line cells and amaranth is non-genotoxic.

Genotoxicity of 2,4-dichlorophenoxyacetic acid tested in somatic and germ-line cells of Drosophila

The genotoxic potential of 2,4-dichlorophenoxyacetic acid, a commonly used chlorophenoxy herbicide, was tested in Drosophila somatic and germ-line cells following the protocols of the wing spot test and the sex-linked recessive lethal test. In the wing spot test second- and third-instar larvae, carrying genetic markers mwh and flr3, were exposed to different concentrations of the herbicide so that induced genetic changes would be phenotypically expressed as mosaic spots on the wings of eclosing adults. The Basc (Muller-5) standard technique but with larval exposure was followed for the sex-linked recessive lethal test. The results obtained indicate that the test compound is genotoxic both in the somatic and germ-line cells of Drosophila.

Expression of recombinant human plasminogen in mammalian cells is augmented by suppression of plasmin activity

We present evidence that over-expression of human plasminogen, the precursor to the serine protease plasmin, can be cytotoxic to mammalian cells. When an expression vector containing plasminogen cDNA is transfected into baby hamster kidney cells, the number of drug-resistant colonies as well as the levels of plasminogen secreted by those colonies is lower than observed in similar transfections of other protease precursor genes. The recombinant plasminogen accumulates intracellularly as degraded NH2-terminal fragments. In contrast, a mutant of plasminogen that produces inactive plasmin (active site Ser740 changed to Ala) is synthesized by these cells as a full-length plasminogen molecule, and the colony numbers and expression levels are normal. Thus, the generation of plasmin activity is responsible for the cytotoxic phenomena and the degradation associated with plasminogen expression. In addition, experiments using a plasminogen mutant that cannot be activated to plasmin (activation cleavage site Arg560 to Gly) or using coexpression of antisense urokinase RNA indicate that an endogenous plasminogen activator is responsible for converting newly synthesized plasminogen to plasmin. Finally, coexpression of plasminogen with alpha 2-plasmin inhibitor, a serpin which is the physiologic inhibitor of plasmin, prevents the toxic effects of intracellular plasmin activity and allows the synthesis and secretion of native human plasminogen.

Stereotactic brain biopsy in the diagnosis of malignant lymphoma

Fifteen patients with cerebral involvement by malignant non-Hodgkin's lymphoma were identified, among more than 200 patients who underwent stereotactic biopsy at The Johns Hopkins Hospital. All but one of these cases were diagnosed accurately by the stereotactic biopsy procedure. In 12 of 14 patients, the material was adequate to classify the lymphoma according to the Working Formulation. Because all but one of the lesions were intermediate or high-grade neoplasms, a diagnosis of lymphoma was often possible by conventional light microscopic examination alone. Monotypic light chain expression was demonstrated by immunohistochemical techniques in six patients, and positivity for B-cell markers was observed in an additional case. In one instance, two stereotactic biopsy specimens were interpreted as being suggestive of lymphoma, but necrosis and inflammation prevented a definitive diagnosis. Nine patients had no known risk factors for cerebral lymphoma, and the diagnosis often was unsuspected clinically.

Endoproteolytic processing of the human protein C precursor by the yeast Kex2 endopeptidase coexpressed in mammalian cells

The human protein C precursor undergoes extensive co- and posttranslational modification during its biosynthesis in the liver. These modifications include glycosylation, gamma-carboxylation, and beta-hydroxylation of specific amino acids and endoproteolytic processing to remove the pre- and propeptides as well as the pair of basic amino acids which connect the light and heavy chains in the precursor. Previous studies with a recombinant mammalian expression system have indicated that the endopeptidase in several mammalian cell types which recognizes and cleaves this dibasic site has a substrate specificity for sites which also include a basic amino acid in the -4 position (Foster et al., 1990). Since the human protein C precursor has His154 in the -4 position, it is poorly and incompletely cleaved in BHK and several other mammalian cell lines and also apparently secreted from the liver as a mixed population of mature two-chain and precursor one-chain molecules. In the present study, a mammalian expression system has been used to study the effect of coexpressing the protein C precursor together with the yeast Kex2 endopeptidase which is known to recognize and process dibasic pairs within peptide precursors in yeast. Coexpression of the KEX2 gene resulted in complete conversion of the protein C precursor to the mature two-chain form. Amino-terminal sequencing of the cleavage products has indicated that the cleavage occurs in the correct location and that this site is preferentially recognized by the yeast endopeptidase within the context of the mammalian cell secretory pathway.

Artificial intelligence for medical decision making

Artificial intelligence techniques find extensive applications in medical decision making and other aspects of health care. A number of successful expert systems have been developed in various disciplines of medicine. This paper gives an overview of expert system techniques, describes some practical systems, and discusses the relevance of such systems in clinical diagnosis and management of diseases.