Construction of oligonucleotide arrays on a glass surface using a heterobifunctional reagent, N-(2-trifluoroethanesulfonatoethyl)-N-(methyl)-triethoxysilylpropyl-3-amine (NTMTA)

A rapid method for construction of oligonucleotide arrays on a glass surface, using a novel heterobifunctional reagent, N-(2-trifluoroethanesulfonatoethyl)-N-(methyl)-triethoxysilylpropyl-3-amine (NTMTA), has been described. The heterobifunctional reagent, NTMTA, carries two different thermoreactive groups. The triethoxysilyl group on one end is specific towards silanol functions on the virgin glass surface, while the trifluoroethanesulfonyl (tresyl) group on the other end of the reagent reacts specifically with aminoalkyl- or mercaptoalkyl- functionalized oligonucleotides. Immobilization of oligonucleotides on a glass surface has been realized via two routes. In the first one (A), 5'- aminoalkyl- or mercaptoalkyl-functionalized oligonucleotides were allowed to react with NTMTA to form a oligonucleotide-triethoxysilyl conjugate which, in a subsequent reaction with unmodified (virgin) glass microslide, results in surface-bound oligonucleotides. In the second route (B), the NTMTA reagent reacts first with a glass microslide whereby it generates trifluoroethanesulfonate ester functions on it, which in a subsequent step react with 5'-aminoalkyl or mercaptoalkyl oligonucleotides to generate support-bound oligonucleotides. Subsequently, the oligonucleotide arrays prepared by both routes were analyzed by hybridization experiments with complementary oligonucleotides. The constructed microarrays were successfully used in single and multiple nucleotide mismatch detection by hybridizing these with fluorescein-labeled complementary oligonucleotides. Further more, the proposed method was compared with the existing methods with respect to immobilization efficiency of oligonucleotides.

The annual risk of tuberculous infection in the eastern zone of India

SETTING

Rural and urban areas of eight selected districts in the eastern zone of India.

OBJECTIVES

To estimate the annual risk of tuberculous infection (ARTI).

STUDY DESIGN

A community-based, cross-sectional tuberculin survey was conducted among children aged 1-9 years residing in a sample of rural and urban areas. Stratified two-stage cluster sampling was adopted for selection of rural and urban clusters. A total of 40964 children in 515 clusters underwent tuberculin testing and reading with 1TU PPD RT23 with Tween 80; the maximum transverse diameter of induration was measured about 72 h after the test.

RESULTS

A bacille Calmette-Gúerin (BCG) scar was observed in 51.5% of the test-read children. The frequency distribution of tuberculin reaction size among 19332 children without BCG scar was found to be bimodal, with the mode of reactions attributable to infection with tubercle bacilli at 20 mm. The prevalence of infection was estimated as 6.9%. The ARTI computed from the estimated prevalence was 1.3%. Children residing in the urban areas were found to be at a significantly higher risk of infection than those residing in rural areas.

CONCLUSION

The high rate of ARTI in the eastern zone of India suggests a need for committed, sustained action in provision of quality tuberculosis control services.

Estimation of annual risk of tuberculosis infection (ARTI) among children aged 1-9 years in the south zone of India

OBJECTIVE

To estimate the annual risk of tuberculosis infection (ARTI) among children aged 1-9 years in the south zone of India.

SETTING

The survey was carried out in a representative sample of villages and census enumeration blocks of towns in four south Indian states, as a part of a nationwide tuberculin survey.

DESIGN

Six districts were selected through systematic random sampling. Four hundred and twenty rural clusters and 180 urban clusters were selected from these districts on the basis of the rural-urban ratio in the entire zone. To obtain the required sample of 12,000 children without bacille Calmette-Guérin (BCG) vaccination, 51,000 had to be covered. Eighty-five children from each cluster were tuberculin tested and read for reaction sizes. The ARTI was computed from the estimated prevalence of TB infection among children without a BCG scar.

RESULT

Among 52,951 children registered for the study, 50,846 (96%) had a tuberculin test result. The BCG coverage for the study population was about 65%. Among 17,811 children without a BCG scar, the prevalence of infection was 5.9% (95%CI 4.0-7.7%); the corresponding ARTI was 1.0% (95%CI 0.7-1.4%) [correction].

CONCLUSION

The estimated ARTI for the south zone is 1.0%, as compared to the national average of 1.7% used for programme evaluation. This baseline information should be useful for the assessment of future trends.

N-(3-Trifluoroethanesulfonyloxypropyl)anthraquinone- 2-carboxamide: a new heterobifunctional reagent for immobilization of biomolecules on a variety of polymer surfaces

A new heterobifunctional reagent, N-(3-trifluoroethanesulfonyloxypropyl)anthraquinone-2-carboxamide (NTPAC) has been developed, useful for making bioconjugates and immobilization of biomolecules, viz., oligonucleotides, peptides, proteins, etc., on a variety of carbon-containing solid surfaces. Its trifluoroethanesulfonate ester group reacts with aminoalkyl or mercaptoalkyl functions present in biomolecules, and the anthraquinone structure reacts with a variety of carbon-containing polymers under ultraviolet irradiation (365 nm). The reagent has been used in two ways. First, the reagent, NTPAC, was first brought in contact with the above said supports and exposed to long wavelength ultraviolet light (365 nm), thereby generating active trifluoroethanesulfonate ester functions on the support, which subsequently react with appropriate mercaptoalkyl- or aminoalkyl-containing biomolecules to fix them on the supports. In another route, the proposed reagent was allowed to react first with proteins or 5'-aminoalkyl- or mercaptoalkyl-modified oligonucleotides to form the appropriate biomolecule-anthraquinone conjugate, which was then brought in contact with a variety of carbon-containing polymers, viz., modified controlled pore glass (CPG), modified glass microslides, cross-linked polystyrene, nylon, cross-linked polysaccharides, polypropylene (PP), polyethylene (PE), etc., and exposed to long wavelength ultraviolet light (365 nm), resulting in immobilization of the conjugates on the support. Both of the routes work satisfactorily and we could successfully immobilize a number of enzymes and modified oligonucleotides on a variety of supports.

Reduced bone mineral density in human immunodeficiency virus-infected patients and its association with increased central adiposity and postload hyperglycemia

Reduced bone mineral density (BMD) and abnormalities in fat redistribution, glucose homeostasis, and lipid metabolism are prevalent among HIV-infected patients on highly active antiretroviral therapy (HAART). The relationship between the metabolic and skeletal complications of HIV is unclear. Fifty-one HIV patients on HAART (aged 30-54 yr, 86% male) and 21 HIV-negative control subjects (aged 31-51 yr, 82% male) were examined with oral glucose tolerance testing, a fasting lipid profile, and dual x-ray absorptiometry, and markers of bone formation (serum osteocalcin) and resorption (urinary deoxypyridinoline). HIV-infected subjects had a higher prevalence of either osteopenia or osteoporosis (World Health Organization criteria) at the spine, hip, or forearm, compared with HIV-negative controls (63% vs. 32%, P = 0.02) and evidence of increased bone resorption (urine deoxypyridinoline, 14.7 +/- 6.5 vs. 10.9 +/- 2.5 nmol/mmol creatinine, P = 0.012). Among the HIV-infected patients, those with reduced bone mineral density (n = 32) were similar to the group with normal BMD (n = 19) in the use of protease inhibitors, duration of HAART therapy, or other demographic variables. Plasma glucose 2 h after a glucose load (odds ratio 1.02 per 1 mg/dl increase, 95% confidence interval 1.01-1.05, P = 0.009) and central adiposity (trunk fat/total fat) (odds ratio 1.09 per 1% ratio increase, 95% confidence interval 1.00-1.18, P = 0.012) were associated with reduced BMD. These associations remained significant in a multivariate model including age and body mass index. Bone resorption was associated with female gender (P < 0.001) and non-high-density lipoprotein cholesterol (P = 0.034) in a multivariate linear regression model controlling for age, body mass index, protease inhibitor use, duration of HAART, and extremity fat. Reduced BMD is prevalent in HIV-infected patients on HAART and is related to central adiposity and postload hyperglycemia. Bone resorption is independently associated with female gender and dyslipidemia. HIV-infected patients with metabolic abnormalities may represent a population that would benefit from bone density screening.

A randomized controlled trial of sodium bicarbonate in neonatal resuscitation—effect on immediate outcome

Very little evidence is available that supports or disproves the use of medications in neonatal resuscitation. In this randomized controlled trial, we evaluated the effect of sodium bicarbonate given during neonatal resuscitation, on survival and neurological outcome at discharge.

SUBJECTS AND METHODS

Consecutively born asphyxiated neonates continuing to need positive pressure ventilation at 5min of life received either sodium bicarbonate or 5% dextrose. The study group was given intravenous sodium bicarbonate solution 4ml/kg (1.8meq./kg) over 3-5min. This solution was prepared by diluting 7.5% sodium bicarbonate (0.9meq./ml) with distilled water in a 1:1 ratio. The placebo group received 4ml/kg of undiluted 5% dextrose at a similar rate. The surviving neonates were evaluated for their neurological status at discharge. Primary outcome variable: Death or abnormal neurological examination at discharge. Secondary outcome variables: Encephalopathy, multi-organ dysfunction, intraventricular haemorrhage (IVH) and arterial pH at 6h.

RESULTS

Twenty-seven babies were randomized to receive sodium bicarbonate (bicarb group) and 28 to receive 5% dextrose. Eighteen of the 27 (66.7%) babies in the bicarb group and 19 of the 28 babies (68%) in the dextrose group survived to discharge ( P=0.84 ). Twenty-eight percent of the survivors in the bicarb group and 32% of the survivors in the dextrose group were neurologically abnormal at discharge ( P=0.10 ). The composite primary outcome of death or abnormal neurological examination at discharge was similar in both groups (52% versus 54%, P=0.88 ). The incidence of encephalopathy (74% versus 63%), cerebral oedema (52% versus 30%), need for inotropic support (44% versus 29%), intraventricular haemorrhage (IVH) and the mean arterial pH at 6hrs were similar between the two groups.

CONCLUSION

Administration of sodium bicarbonate during neonatal resuscitation did not help to improve survival or immediate neurological outcome.

Evidence based paediatrics: review of BTS guidelines for the management of community acquired pneumonia in children

Community acquired pneumonia is a common illness with significant morbidity and mortality in children and a high cost to society. Guidelines for management in the UK were issued by the British Thoracic Society in 2002 [Thorax 57 (2002) 1]. This review summarises the guidelines with emphasis on aetiology, investigations and antibiotic treatment.

Indirect sensing of insulin-induced hypoglycaemia by the carotid body in the rat

The most physiologically important sensors for systemic glucoregulation are located in extra-cranial sites. Recent evidence suggests that the carotid body may be one such site. We assessed rat carotid body afferent neural output in response to lowered glucose, indirectly by measurement of ventilation, and directly by recording single or few-fibre chemoafferent discharge, in vitro. Insulin (0.4 Ukg(-1)min(-1))-induced hypoglycaemia (blood glucose reduced by ca 50% to 3.4 +/- 0.1 mmoll(-1)) significantly increased spontaneous ventilation in sham-operated animals but not in bilateral carotid sinus nerve sectioned (CSNX) animals. In both groups, metabolic rate (measured as ) was almost doubled during hypoglycaemia. The ventilatory equivalent was unchanged in the sham group leading to a maintained control level of P(a, CO(2)), but was significantly reduced in the CSNX group, giving rise to an elevation of 6.0 +/- 1.3 mmHg in P(a, CO(2)). When pulmonary ventilation in sham animals was controlled and maintained, phrenic neural activity increased during hypoglycaemia and was associated with a significant increase in P(a, CO(2)) of 5.1 +/- 0.5 mmHg. Baseline chemoreceptor discharge frequency, recorded in vitro, was not affected, and did not increase when the superfusate [glucose] was lowered from 10 mm to 2 mm by substitution with sucrose: 0.40 +/- 0.20 Hz to 0.27 +/- 0.15 Hz, respectively (P > 0.20). We suggest therefore that any potential role of the carotid bodies in glucose homeostasis in vivo is mediated through its transduction of some other metabolically derived blood-borne factor rather than glucose per se and that this may also provide the link between exercise, metabolic rate and ventilation.

Recent advances in oligonucleotide synthesis and their applications

Short synthetic oligonucleotides are finding wide variety of applications in area of genomics and medicinal chemistry. Since the isolation of nucleic acids to the mapping of human genome, chemical synthesis of nucleic acids has undergone tremendous advancements. Further improvements in this area such as, introduction of high throughput synthesizers, better coupling reagents, improved polymer supports, newer sets of protecting groups for exocyclic amino groups of nucleic bases and introduction of universal polymer supports have completely revolutionized the entire field of nucleic acids chemistry. Most of these developments have been targeted to assemble these molecules more efficiently in a cost-effective manner and rapidly. Preparation of oligonucleotide conjugates has further helped in identifying the newer areas of their applications. A number of conjugates with biological and abiological ligands have been discussed in this article along with their possible wide spectrum of applications. Recently developed microarray technology, which refers to attachment of short oligonucleotides on a solid/polymeric surface, has proved to be useful for screening of genetic mutations, study of polymorphism, as diagnostics, etc. The major developments in these areas are presented in the review.

Annual risk of tuberculous infection in Khammam a tribal district of Andhra Pradesh

A tuberculin survey to estimate annual risk of tuberculosis was conducted in Khammam tribal district during 2001-2002. A total of 8637 children were test-read--2991 without BCG scar and 5442 with BCG scar. The tests were performed using ITU PPD RT23 and the maximum size of induration was recorded at about 72 hours after the test. Based on the frequency distribution of reaction size, cut-off point for infection with tubercle bacilli was considered at 12 mm. Using this criterion, the prevalence of infection was estimated at 11.8% among children without BCG scar and 10.6% among children with BCG scar. This difference was found to be statistically insignificant. ARTI rates computed from the prevalence estimates among children without and with BCG scar were 1.6% and 1.5% respectively. It was computed as 1.5% from the prevalence in the combined group i.e. irrespective of BCG scar status.