Error-correcting microarray design

We describe a microarray design based on the concept of error-correcting codes from digital communication theory. Currently, microarrays are unable to efficiently deal with "drop-outs," when one or more spots on the array are corrupted. The resulting information loss may lead to decoding errors in which no quantitation of expression can be extracted for the corresponding genes. This issue is expected to become increasingly problematic as the number of spots on microarrays expands to accommodate the entire genome. The error-correcting approach employs multiplexing (encoding) of more than one gene onto each spot to efficiently provide robustness to drop-outs in the array. Decoding then allows fault-tolerant recovery of the expression information from individual genes. The error-correcting method is general and may have important implications for future array designs in research and diagnostics.

Studies on the electrical characteristics of thoron (220Rn) progeny

Electrical characteristics of thoron (220Rn) progeny under various low ampere (< 1 mA) DC voltages applied to a calibration facility (CF) has been studied. About 30 y old thorium hydroxide was used as the source for the generation of thoron and its decay products. The study has revealed that under a low ventilation rate (approximately 1 air charge per hour) and at high equilibrium equivalent concentration (EER) of thoron, above 275 Bq m(-3) (> 1 WL), a considerable fraction of 212Pb nuclides are negatively charged. It was also concluded that 212Pb has lesser charge (per ion) than 212Bi and is more susceptible to an electric field. There is a linear relationship between the activity collected and the voltage applied and the activity collected is proportional to the area of the collecting surface. Under the experimental conditions, when a voltage of +/- 2500 V is simultaneously applied, the activity concentration can be reduced by a factor of 100.

Measurement of 40k as an indicator of body potassium: implication for diabetes and other disease conditions

Potassium (K) content in 408 male workers of a rare earths processing plant was estimated using a shadow shield whole body counter. The average K content in the non-vegetarian and vegetarian group was found to be 1.5 g kg(-1) and 2.1 g kg(-1) respectively. The absorbed dose due to 40K is determined as 0.18 +/- 0.02 mGy. While the K content was found to be proportional to body build index, it is inversely proportional to slenderness. Body K was maximum in the middle aged group (35-45 y) and a minimum in younger and older persons. The correlation of potassium content with some disease patterns was also studied. Diabetes mellitus patients were observed to have low K content of 0.9 +/- 0.2 g kg(-1) and those who suffer from cardiovascular disorders were found to have high K content 2.7 +/- 0.3 g kg(-1). The studies showed that the depletion of body K content takes place a few years prior to the clinical detection of diabetes and it builds up a few years before the clinical detection of cardiovascular disorders. It is stressed that the medical information is preliminary as the number of subjects studied was not very large. Wider and in depth study by various groups can hopefully strengthen the observation.

Chemical fate of arsenic and other metals in groundwater of Bangladesh: experimental measurement and chemical equilibrium model

The presence of toxic level of inorganic arsenic in groundwater used for drinking in Bangladesh and neighboring India is unfolding as one of the worst natural disaster in the region. The purpose of this work is to ascertain the chemical fate of arsenic and other metals in groundwater of Bangladesh. A combination of techniques was used to measure 24 metals, 6 anions, Eh, pH, dissolved oxygen, conductivity, and temperature to understand the distribution of components which were then used in computational chemical equilibrium model, MINEQL+, for detailed speciation. It was found that the fate of arsenic and its speciation were inextricably linked to the formation of hydrous ferric oxide (HFO) and its kinetic. The HFO induced natural attenuation removes 50-75% of total arsenic in first 24 h through a first order kinetics. Adsorption on HFO is the predominant mode of removal of arsenic, iron, manganese, and most trace metals. The equilibrium model points to the presence of excess active sites for the removal of arsenic. MINEQL+ shows that significantly higher concentration of HFO forming iron is required to remove arsenic below maximum contamination level (MCL) of 50 microg/L than predicted by stoichiometry. The practical implication of this work is the prediction of water quality based on models.

Insulin regulation of glucose uptake: a complex interplay of intracellular signalling pathways

Insulin-stimulated glucose uptake in adipose tissue and striated muscle is critical for reducing post-prandial blood glucose concentrations and the dysregulation of this process is one hallmark of Type II (non-insulin-dependent) diabetes mellitus. It has been well established that the insulin-stimulated redistribution of the insulin responsive glucose transporter, GLUT-4, from intracellular storage sites to the plasma membrane depends on the production of phosphoinositide 3,4,5 trisphosphate by the Class IA Phosphatidylinositol 3' kinase. Recent discoveries however, have shown the presence of a second insulin signalling pathway leading to GLUT-4 translocation, a pathway dependent on insulin receptor signalling emanating from caveolae or lipid rafts at the plasma membrane. This pathway begins with the phosphorylation of the adaptor protein Cbl by the insulin receptor, and results in the activation of a small GTP binding protein, TC10, a member of the Rho family. TC10 is able to modulate actin structure in 3T3L1 adipocytes, and its overexpression inhibits insulin-stimulated GLUT-4 translocation, an inhibition completely dependent on localization of TC10 to the caveolae or lipid rafts. The spatial compartmentalization of insulin signalling from caveolae or lipid rafts provides a novel signalling pathway that functions in concert with general signalling mechanisms in the control of actin dynamics regulating insulin-dependent GLUT-4 translocation.

Statistical analysis of multiplex brain gene expression images

Analysis of variance (ANOVA) was employed to investigate 9,000 gene expression patterns from brains of both normal mice and mice with a pharmacological model of Parkinson's disease (PD). The data set was obtained using voxelation, a method that allows high-throughput acquisition of 3D gene expression patterns through analysis of spatially registered voxels (cubes). This method produces multiple volumetric maps of gene expression analogous to the images reconstructed in biomedical imaging systems. The ANOVA model was compared to the results from singular value decomposition (SVD) by using the first 42 singular vectors of the data matrix, a number equal to the rank of the ANOVA model. The ANOVA was also compared to the results from non-parametric statistics. Lastly, images were obtained for a subset of genes that emerged from the ANOVA as significant. The results suggest that ANOVA will be a valuable framework for insights into the large number of gene expression patterns obtained from voxelation.

Solid phase microextraction: measurement of volatile organic compounds (VOCs) in Dhaka City air pollution

A solid phase microextraction (SPME) technique was applied for the sampling of volatile organic compounds (VOCs) in ambient air polluted by two stroke autorickshaw engines and automobile exhausts in Dhaka city, Bangladesh. Analysis was carried out by capillary gas chromatography (GC) and GC-mass spectrometry (MS). The methodology was tested by insitu sampling of an aromatic hydrocarbon mixture gas standard with a precision of +/-5% and an average accuracy of 1-20%. The accuracy for total VOCs concentration measurement was about 7%. VOC's in ambient air were collected by exposing the SPME fiber at four locations in Dhaka city. The chromatograms showed signature similar to that of unburned gasoline (petrol) and weathered diesel containing more than 200 organic compounds; some of these compounds were positively identified. These are normal hydrocarbons pentane (n-C5H2) through nonacosane (n-C29H60), aromatic hydrocarbons: benzene, toluene, ethylbenzene, n-propylbenzene, n-butylbenzene, 1,3,5-trimethylbenzene, xylenes, and 1-isocyanato-3-methoxybenzene. Two samples collected near an autorickshaw station contained 783000 and 1479000 microg/m3 of VOCs. In particular, the concentration of toluene was 50-100 times higher than the threshold limiting value of 2000 microg/m3. Two other samples collected on street median showed 135000 microg/m3 and 180000 microg/m3 of total VOCs. The method detection limit of the technique for most semi-volatile organic compounds was 1 microg/m3.

Characterization of pathogenic mutations in 21-hydroxylase gene of Pakistani patients with congenital adrenal hyperplasia and their family members--a preliminary report

OBJECTIVE

To characterize specific mutations within the 21-hydroxylase gene (CYP21-B) using ARMS-PCR assay in patients with congenital adrenal hyperplasia (CAH) and to compare it with that reported in other populations.

SUBJECTS AND METHODS

Five families, having an index case with CAH diagnosed on the basis of clinical and biochemical findings volunteered to give blood samples for analysis. A strategy, based on ARMS-PCR (Amplified Refractory Mutation System) was employed for the detection of mutations in 21-hydroxylase gene. The products of ARMS-PCR were resolved on agarose gels and the PCR products were visualized over ultra violet illumination.

RESULTS

Twenty-six specimens were analyzed for common point mutations in the 21-hydroxlase genes at the nucleotide positions 659, 1004 and 1688. Seven samples belonged to index cases with CAH. Of these 7, the assigned sex was male in 5 and female in 2 cases. However, genotypic sex was 3 males and 4 females. The mean age was 8 months in 5 cases while the median 17-OH Progesterone levels was 273.2 ng/ml. Vomiting, precocious puberty and ambiguous genitalia were the presenting features in 2, 1 and 4 cases respectively. Analysis for mutation at 659, 100 and 1688 was performed on 7 index cases and the family members of 5 index cases. The mutation analysis for the family members of index case 6 and 7 was not performed due to non-availability of their blood specimens. Index case No. 1, 4 and 7 showed homozygosity for splice mutations at nucleotide position 659, intron 2 with a sequence change of A to G, while the index case No. 2 and 6 showed heterozygosity for the same mutation. No mutation was found at 659, 1004 or 1688 in index case No. 3 and 4 at the analyzed nucleotide position. Nineteen family members of Case Nos. 1-5 were also analyzed for the same mutations. (Family No. 1, 2, 3, 4 and 5 included 3, 2, 7, 4 and 5 members respectively). These included 8 males and 11 females. All were asymptomatic. Both the parents of index case 1 and 4 were heterozygous at 659 while the father of index case No. 2 was heterozygous at 659 and mother was normal.

CONCLUSION

Our results demonstrated the A to G transition at nucleotide 659 causing aberrant splicing, reported for some other populations as the most commonly identified point mutations. All cases were appropriately assigned to paternal or maternal chromosomes.

Multiplex three-dimensional brain gene expression mapping in a mouse model of Parkinson's disease

To facilitate high-throughput 3D imaging of brain gene expression, a new method called voxelation has been developed. Spatially registered voxels (cubes) are analyzed, resulting in multiple volumetric maps of gene expression analogous to the images reconstructed in biomedical imaging systems. Using microarrays, 40 voxel images for 9000 genes were acquired from brains of both normal mice and mice in which a pharmacological model of Parkinson's disease (PD) had been induced by methamphetamine. Quality-control analyses established the reproducibility of the voxelation procedure. The investigation revealed a common network of coregulated genes shared between the normal and PD brain, and allowed identification of putative control regions responsible for these networks. In addition, genes involved in cell/cell interactions were found to be prominently regulated in the PD brains. Finally, singular value decomposition (SVD), a mathematical method used to provide parsimonious explanations of complex data sets, identified gene vectors and their corresponding images that distinguished between normal and PD brain structures, most pertinently the striatum.

Gene expression tomography

Gene expression tomography, or GET, is a new method to increase the speed of three-dimensional (3-D) gene expression analysis in the brain. The name is evocative of the method's dual foundations in high-throughput gene expression analysis and computerized tomographic image reconstruction, familiar from techniques such as positron emission tomography (PET) and X-ray computerized tomography (CT). In GET, brain slices are taken using a cryostat in conjunction with axial rotation about independent axes to create a series of "views" of the brain. Gene expression information obtained from the axially rotated views can then be used to recreate 3-D gene expression patterns. GET was used to successfully reconstruct images of tyrosine hydroxylase gene expression in the mouse brain, using both RNase protection and real-time quantitative reverse transcription PCR (QRT-PCR). A Monte-Carlo analysis confirmed the good quality of the GET image reconstruction. By speeding acquisition of gene expression patterns, GET may help improve our understanding of the genomics of the brain in both health and disease.

High-throughput imaging of brain gene expression

Voxelation is a new method for acquisition of three dimensional (3D) gene expression patterns in the brain. It employs high-throughput analysis of spatially registered voxels (cubes) to produce multiple volumetric maps of gene expression analogous to the images reconstructed in biomedical imaging systems. Using microarrays, 24 voxel images of coronal hemisections at the level of the hippocampus of both the normal human brain and Alzheimer's disease brain were acquired for 2000 genes. The analysis revealed a common network of coregulated genes, and allowed identification of putative control regions. In addition, singular value decomposition (SVD), a mathematical method used to provide economical explanations of complex data sets, produced images that distinguished between brain structures, including cortex, caudate, and hippocampus. The results suggest that voxelation will be a useful approach for understanding how the genome constructs the brain.

Dissolution characteristics of 226Ra from phosphogypsum

The paper presents the results of the dissolution characteristics of 226Ra from phosphogypsum, a by-product from phosphate fertilizer industries. Leachability of 226Ra in distilled water and rainwater have been examined under different leaching conditions such as contact time, solid:liquid ratio and simulating natural conditions. The concentration of 226Ra activity in the leachates ranged from 0.07 to 0.53 Bq l(-1). Study indicated that leaching of radium may be slow in field conditions near the phosphogypsum stock piles.

Insulin stimulates actin comet tails on intracellular GLUT4-containing compartments in differentiated 3T3L1 adipocytes

Incubation of isolated GLUT4-containing vesicles with Xenopus oocyte extracts resulted in a guanosine 5'-[gamma-thio]triphosphate (GTP gamma S) and sodium orthovanadate stimulation of actin comet tails. The in vitro actin-based GLUT4 vesicle motility was inhibited by both latrunculin B and a dominant-interfering N-WASP mutant, N-WASP/Delta VCA. Preparations of gently sheared (broken) 3T3L1 adipocytes also displayed GTP gamma S and sodium orthovanadate stimulation of actin comet tails on GLUT4 intracellular compartments. Furthermore, insulin pretreatment of intact adipocytes prior to gently shearing also resulted in a marked increase in actin polymerization and actin comet tailing on GLUT4 vesicles. In addition, the insulin stimulation of actin comet tails was completely inhibited by Clostridum difficile toxin B, demonstrating a specific role for a Rho family member small GTP-binding protein. Expression of N-WASP/Delta VCA in intact cells had little effect on adipocyte cortical actin but partially inhibited insulin-stimulated GLUT4 translocation. Taken together, these data demonstrate that insulin can induce GLUT4 vesicle actin comet tails that are necessary for the efficient translocation of GLUT4 from intracellular storage sites to the plasma membrane.

Low-level lead exposure and blood lead levels in children: a cross-sectional survey

The authors studied 53 girls (44.5%) and 66 (55.5%) boys in Karachi, Pakistan, to determine their blood lead levels. The association between blood lead levels/water lead levels and the possible risk factors and symptoms associated with lead toxicity was explored. The mean lead level for the entire group was 7.9 microg/dl (standard deviation = 4.5 microg/dl). Thirty (25.2%) of the children had lead levels that exceeded 10 microg/dl; 12 (10.0%) of these had lead levels that exceeded 15 microg/dl. Thirteen (20.9%) of the children under the age of 6 yr (n = 62) had lead levels greater than 10 microg/dl, and 6 (9.6%) had levels in excess of 15 microg/dl. The authors found no association (p > .05) between high lead levels in water and blood lead levels in children. Mean blood lead levels were highest in the group of children exposed to various risk factors for lead absorption (e.g., exposure to paint, remodeling, and renovation; use of lead utensils; pica). There was a significant association between a history of exposure to paint/renovation activities and a history of pica. High blood lead levels in the children in Karachi stress the urgency for actions that control lead pollution. Screening programs should be instituted by the state. Individuals must become aware of lead's toxicity, and they must avoid substances that contain lead.

Fertility of the cysts of Echinococcus granulosus in domestic herbivores from Benghazi, Libya, and the reactivity of antigens produced from them

Unilocular cysts produced by Echinococcus granulosus were recovered from 110 domestic herbivores (60 sheep, 25 cattle, 20 goats and five camels) slaughtered in Benghazi. The proportion of the cysts from the sheep found to be fertile (75%) was higher than that of the cysts from the goats (55%), camels (40%), or cattle (0%). When tested in indirect haemagglutination assays (IHA) with eight sera from human cases of cystic echinococcosis, the fluid from the cattle cysts never gave a positive reaction. Antigens in the fluids collected from sheep or goat cysts did react with the sera, with antigens from each of the two sources giving similar titres with each serum. However, crude somatic antigens (prepared from protoscolices and brood capsules collected from sheep cysts) appeared to be more sensitive for the immunodiagnosis of human cystic echinococcosis than the cyst-fluid antigens.

Diclofenac sodium injection sterilized by autoclave and the occurrence of cyclic reaction producing a small amount of impurity

A known impurity is formed in the production of a parenteral dosage form of diclofenac sodium if terminally sterilized by autoclave. This impurity has been detected as 1-(2,6-dichlorophenyl) indolin-2qone, which is also an intermediate from which diclofenac sodium is generally synthesized. It is only the condition of the autoclave method (i.e., 123 +/- 2 degrees C) that enforces the intramolecular cyclic reaction of diclofenac sodium forming the indolinone derivative and sodium hydroxide. The formation of this impurity has been found to depend on the initial pH of the formulation. The reaction follows first-order kinetics, and the energy of activation is 5.34 kcal/mol. The other excipients in the formulation do not have a role in this reaction. The concentration of the impurity in the resultant product in the ampule goes beyond the limit of the raw materials in the pharmacopoeias. It is thus preferable to use an alternative sterilization method; that is, an aseptic filtration method in which the formation of this impurity can be avoided.

Recurrent infantile digital fibromatosis--a rare entity

We present here a rare case of Infantile Digital Fibromatosis in a six year old female child who presented with recurrent swelling over the phalanx of left middle finger.

Morphological spectrum of ophthalmic tumors in northern Pakistan

OBJECTIVE

The objective of the study was to assess the frequency and pattern of ophthalmic tumours in Northern Pakistan.

METHODS

This study included all ophthalmic tumours diagnosed during a one year period (January to December 1992).

RESULTS

One hundred and fourteen ophthalmic tumours were diagnosed at the Armed Forces Institute of Pathology (AFIP) and Pathology Department of the Army Medical College (AMC), Rawalpindi. Of these tumours, 70 were malignant (61.5%) and 44 were benign (38.5%). The age distribution of malignant ophthalmic tumours had two peaks. The first was seen in the paediatric age group and was mainly due to retinoblastoma. The second peak was seen above 50 years of age and was mainly due to conjunctival squamous cell carcinoma and malignant eyelid tumours which constituted 85% of the malignant ophthalmic tumours in paediatric age group. The average age at presentation of retinoblastoma was 3.8 years. The average age at presentation for squamous cell carcinoma was 56 years. Basal cell carcinoma was the most common malignant eyelid tumour (55%). The most common extraocular malignant orbital tumour was non-Hodgkin's lymphoma. Malignant melanoma of the uvea formed 22% of all melanomas diagnosed during this period. The most common benign tumours were naevi (33%), epidermal inclusion cysts (18%), choristomata (16%) and haemangioma (8%). The malignant ophthalmic tumours constituted 3% of all the malignant tumours diagnosed in Northern Pakistan during 1992 at AFIP and AMC, Rawalpindi.

CONCLUSION

The ophthalmic tumours, both benign and malignant are not infrequent in clinical practice in Northern Pakistan.

A study of the technologically modified sources of 222Rn and its environmental impact in an Indian U mineralised belt

These investigations present qualitative and quantitative assessments of the 222Rn contributing potential of the technologically modified sources, e.g. mine exhausts and tailings piles, arising due to the mining and processing of uraniferous minerals at Jaduguda, India. The overall geometric mean of the 222Rn flux from low-grade uranium (U) mill tailings being 1.19 Bq m-2 s-1, requisite attenuation of 37.8% to the recommended limit of 0.74 Bq m-2 s-1 can be attained by a typical clay coverage of 20 cm. Theoretically, feasible options for selection of overburden materials for stabilisation of the tailings piles are examined. Extrapolation studies with a turbulent diffusion model yield an atmospheric dispersion pattern of 222Rn in reasonable correspondence with the prevailing concentrations, especially for locations beyond a 4 km radius. The overall 222Rn contribution of the U complex to the ambient air is the same as that contributed by the adjoining land mass of 2.75 km radius in this mineralised terrain.

A genetic screen for novel behavioral mutations in mice

A genetic screen using mice was performed to identify dominant loci affecting behavior. Mice were mutagenized with ENU, then bred to examine their G1 offspring for behavioral abnormalities. Potentially mutant G1 pups were screened through a variety of behavioral assays, including tests of learning and memory, sensorimotor gating, fear and anxiety, nociception (pain perception) and locomotor activity. Mice falling outside the normal performance distribution in these tests were considered potential behavioral mutants and were bred for further analysis. Outliers included both animals with very discrete defects and animals with abnormal performance across a range of tests. To date, we have identified two confirmed mutants affecting sensorimotor gating. These results provide further impetus for the use of random mutagenesis screens as a tool for dissecting the genetic basis of brain and behavior.