Biomedical subjects

Adnan Ali

Publications and source records attributed to Adnan Ali.

7 recordsLinked to original sources

PubMed2006

Array of informatics: Applications in modern research.

The advent of microarray technology in the past decade has greatly enhanced gene expression studies and allowed for the acquisition of a vast amount of information simultaneously. Microarrays have been used in numerous scientific fields to identify new genes, to determine the transcriptional activity of cells, and to discover downstream targets of different loci. Recently, DNA microarrays have also been utilized in disease studies to determine outcomes at many levels including diagnosis, prognosis, and drug therapy. The promise of protein microarrays is to allow us to study the molecular interactions of protein, lipids, small molecules, and carbohydrates. They can be exploited to analyze a single protein pair interaction, to address changes in multiple protein levels as a response to treatment (i.e., drug or radiation), or in a pathological condition. Tissue microarrays allow the analysis of numerous tumor samples simultaneously. Finally, live cell-based microarrays provide an opportunity to study the function of the entire proteome en masse within living cells. However, these exciting new areas still have to overcome many inherent problems. In this review, we discuss novel microarray-based approaches that are in development and that have potential in applications for medicine, biotechnology, and basic research.

Animals↗

PubMed2005

Altered gene expression in human hepatoma HepG2 cells exposed to low-level 2,4-dichlorophenoxyacetic acid and potassium nitrate.

2,4-dichlorophenoxyacetic acid (2,4-D) and nitrate are agricultural contaminants found in rural ground water. It is not known whether levels found in groundwater pose a human or environmental health risk, nor is the mechanism of toxicity at the molecular/cellular level understood. This study focused on determining whether 2,4-D or nitrate at environmentally realistic levels elicit gene expression changes in exposed cells. cDNA microarray technology was used to determine the impact of 2,4-D and nitrate in an in vitro model of exposure. Human hepatoma HepG2 cells were incubated with 2,4-D or nitrate alone for 24 h. Cell viability (neutral red assay) and proliferation (BrdU incorporation) were assessed following exposure. Total RNA from treated and control cells were isolated, reverse transcribed and reciprocal labelled with Cy3 or Cy5 dyes, and hybridized to a human cDNA microarray. The hybridized microarray chips were scanned, quantified and analyzed to identify genes affected by 2,4-D or nitrate exposure based on a two-fold increase or decrease in gene expression and reproducibility (affected in three or more treatments). Following filtering, normalization and hierarchical clustering initial data indicate that numerous genes were found to be commonly expressed in at least three or more treatments of 2,4-D or nitrate tested. The affected genes indicate that HepG2 cells respond to environmental, low-level exposure and produce a cellular response that is associated with alterations in the expression of many genes. The affected genes were characterized as stress response, cell cycle control, immunological and DNA repair genes. These findings serve to highlight new pathway(s) in which to further probe the effects of environmental levels of 2,4-D and nitrate.

2,4-Dichlorophenoxyacetic Acid↗

PubMed2005

Spot detection and image segmentation in DNA microarray data.

Following the invention of microarrays in 1994, the development and applications of this technology have grown exponentially. The numerous applications of microarray technology include clinical diagnosis and treatment, drug design and discovery, tumour detection, and environmental health research. One of the key issues in the experimental approaches utilising microarrays is to extract quantitative information from the spots, which represent genes in a given experiment. For this process, the initial stages are important and they influence future steps in the analysis. Identifying the spots and separating the background from the foreground is a fundamental problem in DNA microarray data analysis. In this review, we present an overview of state-of-the-art methods for microarray image segmentation. We discuss the foundations of the circle-shaped approach, adaptive shape segmentation, histogram-based methods and the recently introduced clustering-based techniques. We analytically show that clustering-based techniques are equivalent to the one-dimensional, standard k-means clustering algorithm that utilises the Euclidean distance.

Algorithms↗

PubMed2003

Negative regulation of phosphatidylinositol 3-kinase and Akt signalling pathway by PKC.

Although substantial studies have begun to explore the regulation of phosphatidylinositol 3-kinase/Akt cascade by different signalling pathways, whether protein kinase C (PKC) activity plays a crucial role remains as yet unclear. In this study, we found that in A549 and HEK293 cells non-selective PKC inhibitors Ro 31-8220 and bisindolylmaleimide VIII, and PKCbeta inhibitor LY 379196, caused Akt/PKB phosphorylation at Ser 473 and increased the upstream activator, integrin-linked kinase (ILK) activity. The increased Akt phosphorylation was blocked by phosphatidylinositol 3-kinase inhibitor wortmannin and the newly identified PIP(3)-dependent kinases (PDK) inhibitor SB 203580. In contrast to the Akt stimulation caused by PKC inhibitors, PMA attenuated Akt/PKB phosphorylation. We also found that this stimulating effect on Akt phosphorylation by PKC inhibitors was not the result of phosphatase inhibition, since treatment with PP2A, PP2B and tyrosine phosphatase inhibitors (okadaic acid, FK506 and sodium orthovanadate, respectively) had no effect. We conclude that phosphatidylinositol 3-kinase/Akt signalling pathway is regulated by PKC in a negative manner.

Androstadienes↗

PubMed2002

Developmental biology: an array of new possibilities.

Microarrays offer biologists comprehensive and powerful tools to analyze the involvement of genes in developmental processes at an unprecedented scale. Microarrays that employ defined sequences will permit us to elucidate genetic relationships and responses, while those that employ undefined DNA sequences (ESTs, cDNA, or genomic libraries) will help us to discover new genes, relate them to documented gene networks, and examine the way in which genes (and the process that they themselves control) are regulated. With access to broad new avenues of research come strategic and logistical headaches, most of which are embodied in the reams of data that are created over the course of an experiment. The solutions to these problems have provided interesting computational tools, which will allow us to compile huge data sets and to construct a genome-wide view of development. We are on the threshold of a new vista of possibilities where we might consider in comprehensive and yet specific detail, for example, the degree to which diverse organisms utilize similar genetic networks to achieve similar ends.

Journal Article↗

PubMed2002

Enhanced accumulation of constitutive heat shock protein mRNA is an initial response of eye tissue to mild hyperthermia in vivo in adult Xenopus laevis.

We have examined the effect of mild hyperthermia in vivo on heat shock transcription factor (HSF) binding activity and heat shock protein (hsp) gene expression in eye tissue of adult Xenopus laevis. A specific interaction between HSF and a synthetic oligonucleotide corresponding to the proximal heat shock element of the Xenopus hsp70B gene was greatly enhanced in eyes from hyperthermic animals compared with controls. Given these results, we examined the effect of hyperthermia in vivo on the expression of five hsp genes (hsp70, hsc70, BiP, hsp90, and hsp30) in eye tissue. Interestingly, at 28 degrees C constitutively expressed hsp genes hsc70, BiP, and hsp90 were strongly enhanced, with further accumulation at 30 degrees C. However, hsp70 and hsp30 mRNA accumulation were not detectable at 28 degrees C but were strongly induced at 30 degrees C. No enhancement of the relative levels of cytoskeletal actin mRNA was observed in the eye tissue of hyperthermic animals. These results suggest that one of the primary responses of eye tissue to hyperthermia in vivo is in the elevation of mRNAs encoding a set of constitutively expressed molecular chaperones.

Animals↗

PubMedDate not supplied

Accuracy of surgeon-performed abdominal utrasound for gallstones.

BACKGROUND: Gallstone disease is common in Pakistan. It is primarily diagnosed by ultrasonography. which is traditionally done by radiologists. If surgeons could perform ultrasonography, it would enable early diagnosis in one-stop clinic. This study was done to evaluate the accuracy of surgeon-performed abdominal ultrasonography to detect gallstones. METHODS: This study was carried out at Surgical A and Surgical C units of Ayub Teaching Hospital, Abbottabad from July, 2000 to December, 2002. One hundred fourty two patients with signs and symptoms of gallstone disease who had ultrasonography performed by a surgeon. trained in ultrasonography were exclusively studied. These patients were referred for further scanning by the radiologists who were unaware of the surgeon's interpretation. The results of surgeon and radiologist performed ultrasonography were compared. RESULTS: The interpretation of surgeon-performed ultrasonography was correct in 100 patients and incorrect in 42 patients. There were 100 True Positive, 41 True Negative, One False Negative and Zero False Positive scans yielding 99%, Sensitivity, 100% Specificity and 99.3%, Accuracy. Sensitivity of surgeon-performed ultrasonography in detecting gallstones compared to operative findings was 100%. CONCLUSIONS: Abdominal ultrasonography performed by an ultrasonography trained surgeon can detect gallstones as accurately as by a radiologist.

Adult↗