Screening for diabetes among presumptive tuberculosis patients at a tertiary care centre in Pondicherry, India

SETTING

Designated microscopy centre (DMC) attached to a tertiary care centre in Pondicherry, India.

OBJECTIVES

To determine 1) the proportion of diabetes mellitus (DM), 2) the additional yield of newly diagnosed DM cases, and 3) the number needed to screen (NNS) to find a new case of DM among presumed TB patients.

DESIGN

An institution-based cross-sectional study was carried out among 650 presumed TB patients attending the DMC. Capillary blood glucose was measured using fasting blood sugar and/or oral glucose tolerance test, and evaluated according to the World Health Organization criteria.

RESULTS

Of 570 presumed TB patients evaluated for DM, 121 (21.2%) were found to be diabetic. Of these, 69 were previously known to have DM, while 52 were newly diagnosed. The additional yield of diabetes was 43%. The NNS to detect a new case of DM was 11; among those aged >40 years, the NNS was 9.3, and among smear-positive TB patients it was 4.6.

CONCLUSION

One fifth of the presumed TB patients had diabetes, and nearly half of these patients were newly diagnosed. Opportunity screening of presumed TB patients for DM in routine care will help in early detection of diabetes and pre-diabetes.

Single versus double blade technique for skin incision and deep dissection in surgery for closed fracture: a prospective randomised control study

PURPOSE

To compare blade cultures in surgery for closed fracture using a single or double blade technique to determine whether the current practice of double blade technique is justified.

METHODS

155 men and 29 women aged 20 to 60 (mean, 35) years who underwent surgery for closed fracture with healthy skin at the incision site were included. Patients were block randomised to the single (n=92) or double (n=92) blade technique. Blades were sent for bacteriological analysis. Outcome measures were early surgical site infection (SSI) within 30 days and cultures from the blades.

RESULTS

The 2 groups were comparable in baseline characteristics. In the single blade group, 6 surgical blades and 2 control blades showed positive cultures; 4 patients developed SSI, but only one had a positive culture from the surgical blade (with different organism isolated from the wound culture). In the double blade group, 6 skin blades, 7 deep blades, and 0 control blade showed positive culture; only 2 patients had the same bacteria grown from both skin and deep blade. Five patients developed SSI, but only one patient had a positive culture from the deep blade (with different organism isolated from the wound culture). The difference in incidence of culture-positive blade or SSI between the 2 groups was not significant. The relative risk of SSI in the single blade group was 0.8. Positive blade culture was not associated with SSI in the single or double blade group.

CONCLUSION

The practice of changing blade following skin incision has no effect on reducing early SSI in surgery for closed fracture in healthy patients with healthy skin.

Complete chloroplast genome sequence of MD-2 pineapple and its comparative analysis among nine other plants from the subclass Commelinidae

BACKGROUND

Pineapple (Ananas comosus var. comosus) is known as the king of fruits for its crown and is the third most important tropical fruit after banana and citrus. The plant, which is indigenous to South America, is the most important species in the Bromeliaceae family and is largely traded for fresh fruit consumption. Here, we report the complete chloroplast sequence of the MD-2 pineapple that was sequenced using the PacBio sequencing technology.

RESULTS

In this study, the high error rate of PacBio long sequence reads of A. comosus's total genomic DNA were improved by leveraging on the high accuracy but short Illumina reads for error-correction via the latest error correction module from Novocraft. Error corrected long PacBio reads were assembled by using a single tool to produce a contig representing the pineapple chloroplast genome. The genome of 159,636 bp in length is featured with the conserved quadripartite structure of chloroplast containing a large single copy region (LSC) with a size of 87,482 bp, a small single copy region (SSC) with a size of 18,622 bp and two inverted repeat regions (IRA and IRB) each with the size of 26,766 bp. Overall, the genome contained 117 unique coding regions and 30 were repeated in the IR region with its genes contents, structure and arrangement similar to its sister taxon, Typha latifolia. A total of 35 repeats structure were detected in both the coding and non-coding regions with a majority being tandem repeats. In addition, 205 SSRs were detected in the genome with six protein-coding genes contained more than two SSRs. Comparative chloroplast genomes from the subclass Commelinidae revealed a conservative protein coding gene albeit located in a highly divergence region. Analysis of selection pressure on protein-coding genes using Ka/Ks ratio showed significant positive selection exerted on the rps7 gene of the pineapple chloroplast with P less than 0.05. Phylogenetic analysis confirmed the recent taxonomical relation among the member of commelinids which support the monophyly relationship between Arecales and Dasypogonaceae and between Zingiberales to the Poales, which includes the A. comosus.

CONCLUSIONS

The complete sequence of the chloroplast of pineapple provides insights to the divergence of genic chloroplast sequences from the members of the subclass Commelinidae. The complete pineapple chloroplast will serve as a reference for in-depth taxonomical studies in the Bromeliaceae family when more species under the family are sequenced in the future. The genetic sequence information will also make feasible other molecular applications of the pineapple chloroplast for plant genetic improvement.

Development of ESTs and data mining of pineapple EST-SSRs

Improving the quality of the non-climacteric fruit, pineapple, is possible with information on the expression of genes that occur during the process of fruit ripening. This can be made known though the generation of partial mRNA transcript sequences known as expressed sequence tags (ESTs). ESTs are useful not only for gene discovery but also function as a resource for the identification of molecular markers, such as simple sequence repeats (SSRs). This paper reports on firstly, the construction of a normalized library of the mature green pineapple fruit and secondly, the mining of EST-SSRs markers using the newly obtained pineapple ESTs as well as publically available pineapple ESTs deposited in GenBank. Sequencing of the clones from the EST library resulted in 282 good sequences. Assembly of sequences generated 168 unique transcripts (UTs) consisting of 34 contigs and 134 singletons with an average length of ≈500 bp. Annotation of the UTs categorized the known proteins transcripts into the three ontologies as: molecular function (34.88%), biological process (38.43%), and cellular component (26.69%). Approximately 7% (416) of the pineapple ESTs contained SSRs with an abundance of trinucleotide SSRs (48.3%) being identified. This was followed by dinucleotide and tetranucleotide SSRs with frequency of 46 and 57%, respectively. From these EST-containing SSRs, 355 (85.3%) matched to known proteins while 133 contained flanking regions for primer design. Both the ESTs were sequenced and the mined EST-SSRs will be useful in the understanding of non-climacteric ripening and the screening of biomarkers linked to fruit quality traits.

Characterization of 10 novel microsatellite loci for the brown marbled grouper, Epinephelus fuscoguttatus (Serranidae)

Epinephelus fuscoguttatus is a commercially important marine fish species in southeast Asia. Due to overfishing and water pollution, this species has been declared as near-threatened. Thus, to provide information to help maintain and preserve the species, microsatellites were developed, using an enriched genomic library method. Thirty individuals were collected from the hatchery of the Fishery Research Institute, Terengganu, Malaysia. These individuals, from four to six years old, originated from Sabah and are maintained in captive culture as broodstock. Genomic DNA was extracted from the fins of selected individuals that weighed 3-8 kg. Ten microsatellite loci were found to be polymorphic in this population, with 5 to 21 alleles per locus. Observed and expected heterozygosities ranged from 0.53 to 0.97 and 0.59 to 0.95, respectively. Only one locus deviated significantly from Hardy-Weinberg equilibrium and no significant linkage disequilibrium was found among the pairs of loci. These polymorphic microsatellite loci will be used by the Malaysian Fishery Research Institute for investigating genetic diversity and for developing breeding strategies.

Smoking-Related Gene Expression in Laser Capture-Microdissected Human Lung

PURPOSE: Interindividual differences in quantitative expression could underlie a propensity for lung cancer. To determine precise individual gene expression signatures on a lung compartment-specific basis, we investigated the expression of carcinogen metabolism genes encoding cytochromes P450 (CYP) 1B1, 2A13, GSTP1, and a tumor suppressor gene p16 in laser capture-microdissected samples of human alveolar compartment (AC) and bronchial epithelial compartment (BEC) lung tissue from 62 smokers and nonsmokers. EXPERIMENTAL DESIGN: Tobacco exposure was determined by plasma nicotine, cotinine, and smoking history. Precise mRNA expression was determined using our RNA-specific qRT-PCR strategy, and correlated with detailed demographic and clinical characteristics. RESULTS: Several correlations of mRNA expression included (a) CYP1B1 in AC (positively with plasma nicotine level, P = 0.008; plasma cotinine level, P = 0.001), (b) GSTP1 in AC (positively with plasma cotinine level, P = 0.003), and (c) GSTP1 in BEC (negatively with smoke dose, P = 0.043; occupational risk, P = 0.019). CYP2A13 was rarely expressed in AC and not expressed in BEC. p16 expression was not correlated with any measured factor. For each gene, subjects showed expression that was individually concordant between these compartments. No clear association of mRNA expression with lung cancer risk was observed in this pilot analysis. CONCLUSIONS: The association between lung mRNA expression and tobacco exposure implies that gene-tobacco interaction is a measurable quantitative trait, albeit with wide interindividual variation. Gene expression tends to be concordant for alveolar and bronchial compartments for these genes in an individual, controlling for proximate tobacco exposure. (Clin Cancer Res 2009;15(24):7562-70).

Validity of Messenger RNA Expression Analyses of Human Saliva

PURPOSE

The origins of expression microarray and reverse transcription-PCR (RT-PCR) signals in human saliva were evaluated.

EXPERIMENTAL DESIGN

The "RNA" extracts from human saliva samples were treated with vehicle, DNase, or RNase. Two-step amplification and hybridization to Affymetrix 133A cDNA microarrays were then done. Confirmatory RT-PCR experiments used conventionally designed PCR primer pairs for the reference housekeeper transcripts encoding 36B4, beta-actin, and glyceraldehyde-3-phosphate dehydrogenase (GAPDH) mRNA sequences, which are known to be homologous to genomic DNA pseudogene sequences. Negative controls included the omission of reverse transcriptase ("no-RT") to detect any DNA-derived signal. Finally, an RNA-specific RT-PCR strategy eliminated confounding signals from contaminating genomic DNA.

RESULTS

Microarray experiments revealed that untreated, DNase-treated, and RNase-treated "RNA" extracts from saliva all yielded negligible overall signals. Specific microarray signals for 36B4, beta-actin, and GAPDH were low, and were unaffected by RNase. Real-time quantitative RT-PCR reactions using conventional, non-RNA-specific primers on saliva samples yielded PCR products for 36B4, beta-actin, and GAPDH; DNase-treated saliva samples did not yield a PCR product, and the "no-RT" and "+RT" conditions yielded similar amounts of PCR product. The RNA-specific RT-PCR strategy, across all conditions, yielded no PCR product from saliva.

CONCLUSIONS

The combination of (a) a minimal microarray signal, which was unaffected by RNase treatment, (b) the presence of a conventional RT-PCR housekeeper product in both RNase-treated and no-RT saliva samples, (c) the absence of a conventional RT-PCR housekeeper product in DNase-treated conditions, and (d) the absence of a RNA-specific RT-PCR product shows that any microarray or RT-PCR signal in the saliva must arise from genomic DNA, not RNA. Thus, saliva extracts do not support mRNA expression studies.

Haplotype-environment interactions that regulate the human glutathione S-transferase P1 promoter

Phase II detoxification of carcinogens is reported to mediate some of the anticarcinogenesis effects of candidate chemopreventive agents. We explored the interaction between sequence variation in the GSTP1 gene promoter and candidate chemopreventive exposure in regulating human GSTP1 expression. Polymorphisms along 1.8 kb of the GSTP1 promoter were identified in leukocytes [peripheral blood mononuclear cells (PBMC)] from 40 Caucasian subjects. Ten promoter polymorphisms (9 previously unreported) displayed strong linkage disequilibrium, yielding identification of three frequently observed haplotypes [HAP1 (43%), HAP2 (36%), and HAP3 (8%)]. Each haplotype was cloned into luciferase reporter constructs and transfected into normal human bronchial epithelial cells. Basal HAP3 reporter activity was significantly elevated (1.8-fold) but decreased to the same levels as HAP2 and HAP1 with increasing concentrations of sulforaphane, benzyl isothiocyanate (BITC), and epigallocatechin gallate (EGCG). To confirm native HAP3 functionality, we quantitated mRNA expression in uncultured PBMCs and in laser microdissected normal lung epithelial cells (MNLEC) from the same patients. Basal mRNA expression was higher in HAP3 individuals [1.8-fold (PBMC) and 4-fold (MNLEC) for HAP3 heterozygotes and 2.3-fold (PBMC), and 15-fold (MNLEC) for the HAP3 homozygote] than in the other genotypes. PBMC GSTP1 mRNA expression correlated to MNLEC expression (R2 = 0.77). After culture and in vitro exposure to sulforaphane, BITC, or EGCG, the elevated GSTP1 mRNA expression of PBMCs from HAP3 individuals decreased to common expression levels. Elevated HAP3 function was confirmed at the protein level in PBMCs (5-fold higher for HAP3 heterozygotes and 7.6-fold for the HAP3 homozygote). These data suggest a potentially protective GSTP1 promoter haplotype and unpredicted inhibitory chemopreventive agent-haplotype interactions.

Exfoliated buccal and microdissected lung cell expression of antioxidant enzymes

INTRODUCTION

An exfoliated buccal cell biomarker assay for antioxidant gene transcript levels was used to measure inter-tissue concordance with lung, and inter-subject variability in a lung cancer case-control study.

METHODS

First, qualitative RNA-specific RT-PCR was used to compare expression in exfoliated buccal cells with that in laser microdissected lung tissue remote from the tumor from 14 individuals providing both specimens.

RESULTS

There was complete [100% for quinone oxidoreductase 1 (NQO1), glutathione peroxidase (GPX), and superoxide dismutase 1 (SOD1)], or predominant [85.7% for catalase (CAT)] inter-tissue concordance for qualitative expression. Second, quantitative real-time RT-PCR for antioxidant enzyme transcript levels was performed in exfoliated buccal samples from these same 14 individuals, as well as 28 additional individuals providing buccal cells only, for a total of 42 buccal specimens (19 current smokers and 23 ex- or never-smokers), of whom 26 (61.39%) had a new diagnosis of lung cancer.

DISCUSSION

Wide inter-individual expression differences for each gene transcript (>10(1)-10(4)-fold) were observed in the exfoliated buccal cells, unrelated to smoking and case-control status. In multivariate analyses, family history of tobacco-related malignancy correlated inversely with buccal NQO1 and CAT mRNA levels (p=0.003, p<0.001, respectively). This antioxidant expression trait may relate to family risk of cancer, but is notably unrelated to oxidant challenges inherent in cigarette smoke.

Gene-environment interaction signatures by quantitative mRNA profiling in exfoliated buccal mucosal cells

Exfoliated cytologic specimens from mouth (buccal) epithelium may contain viable cells, permitting assay of gene expression for direct and noninvasive measurement of gene-environment interactions, such as for inhalation (e.g., tobacco smoke) exposures. We determined specific mRNA levels in exfoliated buccal cells collected by cytologic brush, using a recently developed RNA-specific real-time quantitative reverse transcription-PCR strategy. In a pilot study, metabolic activity of exfoliated buccal cells was verified by 3-[4,5-dimethylthiazol-2-yl]-2,5- diphenyltetrazolium assay in vitro. Transcriptional activity was observed, after timed in vivo exposure to mainstream tobacco smoke resulted in induction of CYP1B1 in serially collected buccal samples from the one subject examined. For a set of 11 subjects, mRNA expression of nine genes encoding carcinogen- and oxidant-metabolizing enzymes qualitatively detected in buccal cells was then shown to correlate with that in laser-microdissected lung from the same individuals (Chi2 = 52.91, P < 0.001). Finally, quantitative real-time reverse transcription-PCR assays for seven target gene (AhR, CYP1A1, CYP1B1, GSTM1, GSTM3, GSTP1, and GSTT1) and three reference gene [glyceraldehyde-3-phosphate dehydrogenase (GAPDH), beta-actin, and 36B4] transcripts were performed on buccal specimens from 42 subjects. In multivariate analyses, gender, tobacco smoke exposure, and other factors were associated with the level of expression of CYP1B1, GSTP1, and other transcripts on a gene-specific basis, but substantial interindividual variability in mRNA expression remained unexplained. Within the power limits of this pilot study, gene expression signature was not clearly predictive of lung cancer case or control status. This noninvasive and quantitative method may be incorporated into high-throughput human applications for probing gene-environment interactions associated with cancer.

Low doses of heavy metals disrupt normal structure and function of rat platelets

Aggregation, an important property of platelets, plays a key role in the coagulation of blood and is potentiated by ADP and adrenaline, whereas cAMP acts as a strong inhibitor. Because of the rise in the heavy metal load in the environment, more studies are necessary to look at its subtle effects in the animal system, wherein platelet structure and function can be targeted. We carried out structural analyses under phase contrast and scanning electronmicroscopy of the platelets prepared from 1/10 LD50 metal-treated rats. After mercury (Hg) and arsenic (As) treatment, the cell margins appeared irregular and wavy, with small pseudopodia-like protrusions from the surface. Cadmium (Cd) treatment caused loss of the general spindle shape, and the platelets assumed a round spongy appearance. All metal treatments effected enhanced collagen-induced aggregation and inhibited ADP- and arachidonic acid-induced aggregation, whereas epinephrine accelerated aggregation in Hg and Cd treatment but inhibited aggregation in As treatment. Cd proved a potent inhibitor of phosphodiesterase, increasing the cAMP level in in vitro treatments at equimolar (5, 10, and 20 pmoles) concentrations. The rate of aggregation was enhanced with all the agonists used in in vitro Hg and As treatments, with concomitant reduction in cAMP, while Cd inhibited platelet aggregation. Thus, we can conclude that cytosolic cAMP, which is decreased by the metal-induced inhibition of phosphodiesterase, is a regulator molecule in platelet aggregation. Furthermore, it is also abundantly clear that equimolar doses of metals are not always equitoxic. Therefore, the action of each xenobiotic is not only due to the concentration used but also to the type of xenobiotic depending on its unique mechanism of action.

In vitro toxicity of mercury, cadmium, and arsenic to platelet aggregation: influence of adenylate cyclase and phosphodiesterase activity

In vitro effect of mercury (Hg2+), cadmium (Cd2+), and arsenic (As3+) on adenylate cyclase (AC) and phosphodiesterase (PDE) activity in relation to platelet aggregation (PA) was studied in rats. Cd(2+) significantly elevated cAMP (p < 0.005) in a dose-dependent (5, 10 and 20 pmoles) manner while Hg(2+) and As(3+) significantly reduced the cAMP level (p < 0.01 and p < 0.005, respectively). Our studies further reveal that Hg21 and As(3+) inhibit AC and stimulate PDE activity with a concomitant increase in the rate of PA. On the other hand, Cd(2+) stimulates AC and inhibits PDE activity with a decrease in the rate of PA. The present investigation suggests that cellular cAMP is a regulatory molecule in the event of PA and the disruption of its homeostasis is directly correlated to xenobiotic effects on PA. It is concluded that other than divalent heavy metal cations, As(3+) appears to be one of the most toxic xenobiotics to platelet function.

Pattern of opportunistic pulmonary infections in HIV sero-positive subjects: observations from Pondicherry, India

Prospective analysis for a period of six-and-a-half years was done in 190 patients with HIV infection, which showed post-primary tuberculosis with sputum positive for acid-fast bacilli in 65% of cases. Extrapulmonary forms of tuberculosis especially lymph nodes infection was more frequent. Cervical group of lymph node involvement was the commonest presentation. Procedures such as FNAC/biopsy of lymph nodes and pleura provided the immediate diagnostic yields. These procedures must be considered early in the course of illness of HIV infected patients with suspected extrapulmonary and disseminated tuberculosis. Tuberculosis constitutes a common pathology with an appreciable mortality in disseminated subjects. Majority of patients with tuberculosis responded to 2EHRZ/7HR therapy indicating infection by Mycobacterium tuberculosis rather than by atypical mycobacteria, without any serious adverse reactions. Retrospective analysis of two groups (February 1991-May 1994) and (June 1994-October 1997) shows a significant increase in disseminated tuberculosis and Pneumocystis carini pneumonia indicating late stage of HIV disease.

2',3'-Didehydro-2',3'-dideoxy-5-hydroxymethyluridine

The furanose ring in C10H12N2O5 adopts the O(4')-endo envelope conformation (0E) and the glycosidic torsion angle C(2)--N(1)--C(1')--O(4'), chi, is 245.2 (3) degrees. The pseudo-rotational parameters are P = 102.7 degrees and tau m = 5.2 degrees. The CH2OH group on C(5') has the t conformation [gamma = 179.2 (2) degrees].

Ocular manifestations of Hansen's disease

A detailed ophthalmic evaluation including slitlamp biomicroscopy, measurement of corneal sensitivity using Cochet and Bonnet aesthesiometer, Schirmer's test and Goldmann applanation tonometry was carried out in 89 patients of Hansen's disease attending the leprosy clinic with or without ocular symptoms and willing to undergo eye evaluation. Thirty-one patients had lepromatous leprosy (8 with erythema nodosum leprosum), 56 patients had borderline disease (13 with reversal reactions) and 2 had tuberculoid disease. In addition to the well documented changes of lagophthalmos (6.7%), uveitis (7.3%) and cataracts (19%), we noted prominent corneal nerves in 133 eyes (74.7%), beaded corneal nerves in 19 eyes (10.7%), corneal scarring in 10 eyes (5.6%), corneal hypoaesthesia in 51 eyes (28%) and dry eye in 18 eyes (13%). Beaded corneal nerves and/or stomal infiltrates occurred mainly in the lepromatous group (75%). Ocular hypotony (IOP less than 12 mm Hg) was not seen more frequently in Hansen's as compared to age and sex matched controls with refractive errors or cataracts (33.7%, vs. 37.8%, p = 0.33). Our study highlights the primary corneal involvement with corneal neuropathy as the predominant feature of Hansen's disease.