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Biomedical subjects

P Karnik

Publications and source records attributed to P Karnik.

8 recordsLinked to original sources
PubMed2005

MAGIC Tool: integrated microarray data analysis.

SUMMARY: Several programs are now available for analyzing the large datasets arising from cDNA microarray experiments. Most programs are expensive commercial packages or require expensive third party software. Some are freely available to academic researchers, but are limited to one operating system. MicroArray Genome Imaging and Clustering Tool (MAGIC Tool) is an open source program that works on all major platforms, and takes users 'from tiff to gif'. Several unique features of MAGIC Tool are particularly useful for research and teaching. AVAILABILITY: http://www.bio.davidson.edu/MAGIC

Algorithms↗
PubMed1998

Loss of heterozygosity at chromosome 11p15 in Wilms tumors: identification of two independent regions.

Loss of heterozygosity (LOH) on the short arm of chromosome 11 is the most frequent genetic alteration in Wilms tumors, indicating that one or more tumor suppressor genes that map to this chromosomal region are involved in the development of the disease. The WT1 gene located on 11p13 has been characterized but mutations in this gene occur in only about 10% of Wilms tumors. A second locus (WT2) at chromosome 11p15 has also been described in Wilms tumors but thus far efforts to clone the WT2 gene(s) have been frustrated by the large size (approximately 10 Mb) of this region. Using a high-density marker LOH analysis of 11p15.5-15.4, we have refined the location of a Wilms tumor suppressor gene between the markers D11S1318-D11S1288 (approximately 800 kb) within 11p15.5. We have also identified a second, novel region of LOH that spans the markers D11S1338-D11S1323 (approximately 336 kb) at 11p15.5-p115.4. Thus a second distinct locus, in addition to the previously defined WT2, on chromosome 11p15.5, appears to play a role in the development of Wilms tumors.

Adolescent↗
PubMed1998

Two distinct tumor suppressor loci within chromosome 11p15 implicated in breast cancer progression and metastasis.

Chromosome 11p15 has attracted considerable attention because of the biological importance of this region to human disease. Apart from being an important tumor suppressor locus showing loss of heterozygosity (LOH) in several adult and childhood cancers, 11p15 has been shown by linkage analysis to harbor the gene(s) for the Beckwith-Wiedemann syndrome. Furthermore, the clustering of known imprinted genes in the 11p15.5 region suggests that the target gene may also be imprinted. However, positional cloning efforts to identify the target genes have been complicated by the large size (approximately 10 Mb) and complexity of LOH at 11p15. Here, we have analyzed 94 matched normal and breast tumor samples using 17 polymorphic markers that map to 11p15.5-15.4. We have defined precisely the location of a breast tumor suppressor gene between the markers D11S1318 and D11S4088 (approximately 500 kb) within 11p15.5. LOH at this region occurred in approximately 35-45% of breast tumors analyzed. In addition, we have fine-mapped a second, critical region of LOH, that spans the markers D11S1338-D11S1323 (approximately 336 kb) at 11p15.5-p15.4, that is lost in approximately 55-60% of breast tumors. There is a striking correlation between the loss of the two 11p loci and the clinical and histopathological features of breast tumors. LOH at region 1 correlated significantly (P = 0.016) with early events in malignancy and invasiveness. In contrast, the loss of the more proximal region 2, is highly predictive (P = 0.012) of aggressive metastatic disease. Thus, two distinct tumor suppressor loci on chromosome 11p15 may contribute to tumor progression and metastasis in breast cancer. The fine mapping of this intriguing chromosomal region should facilitate the cloning of the target genes and provide critical clues to understanding the mechanisms that contribute to the evolution of adult and childhood cancers.

Breast↗
PubMed1995

Microsatellite instability at a single locus (D11S988) on chromosome 11p15.5 as a late event in mammary tumorigenesis.

Replication errors at microsatellite repeats are markers for genomic instability in hereditary nonpolyposis colon carcinoma and in some sporadic cancers. Microsatellite sequences may show alterations in one or both alleles in some tumors, suggesting an error in the DNA replication of dinucleotide repeats. We have investigated microsatellite instability (MSI) in sporadic breast tumors at several loci on the short arm of chromosome 11. Among microsatellites studied we found a high frequency of MSI at one specific locus, D11S988 on chromosome 11p15.5. Most colorectal tumors that exhibit MSI display abnormalities of at least one other locus and usually more. By contrast we have detected only one abnormal microsatellite in all the tumors examined. This marker lies between the TH and HBB genes, a subregion previously suggested to harbor a putative tumor suppressor gene for breast cancer. Loss of heterozygosity for chromosome markers at 11p15 has earlier been correlated with poor prognosis. In an unselected panel of primary breast tumors, we observed that 20 of 69 showed mobility shifts of D11S988 in tumor compared with corresponding normal DNA samples. Tumors with instability at D11S988 were rapidly proliferating compared with tumors without MSI. DNA aneuploidy, estrogen receptor positivity and moderate to poorly differentiated tumor phenotype were also characteristics of tumors with MSI at this locus and the majority also exhibited loss of heterozygosity at one or more of the six 11p loci analyzed. Taken together these data suggest that MSI at the D11S988 locus is a late event in mammary tumorigenesis and may be associated with progression of breast carcinomas.

Alleles↗
PubMed1987

3'-terminal polyadenylate sequences of Escherichia coli tryptophan synthetase alpha-subunit messenger RNA.

Our earlier studies have shown that the mRNA from many bacterial species, including Escherichia coli and Bacillus subtilis, is extensively polyadenylated, but with shorter poly(A) segments than those associated with eukaryotic mRNA. In this paper, we show that about 40% of the mRNA for the tryptophan synthetase alpha-subunit (TrpA) of E. coli carries a 3'-terminal polyadenylate sequence of 15 to 20 residues. This conclusion was supported by several independent lines of evidence. About 40% of trpA mRNA bound to oligo(dT)-cellulose at high ionic strength and was eluted with water. Treatment with RNase H in the presence of oligo(dT)12-18 destroyed the ability of trpA mRNA to bind to oligo(dT)-cellulose, presumably through the degradation of the poly(A) tract. trpA mRNA could be used as template for complementary DNA synthesis with reverse transcriptase in a reaction that was absolutely dependent on oligo(dT)12-18 as primer. The identity of the cDNA product as a complement to trpA mRNA was established by specific hybridization. In addition, it was possible to synthesize polyadenylated trpA mRNA in toluene-permeabilized cells of E. coli transformed with a recombinant plasmid carrying the trpA gene. In view of the fact that the trpA gene and its 3'-untranslated region contain no continuous deoxyadenylate sequences larger than five nucleotides, one can conclude that the polyadenylate moiety is added post-transcriptionally.

DNA, Bacterial↗
PubMed1987

Messenger ribonucleic acid for the lipoprotein of the Escherichia coli outer membrane is polyadenylated.

Earlier studies had shown that a large portion of bacterial messenger RNA carries 3'-terminal polyadenylate sequences, albeit of somewhat shorter length than those associated with eukaryotic mRNA. In this paper, we show for the first time that a specific prokaryotic mRNA is polyadenylated. Three independent lines of evidence demonstrate that a 3'-terminal polyadenylate sequence 10 to 15 nucleotides in length is associated with about 40% of the mRNA of the outer membrane lipoprotein of Escherichia coli: 40% of lipoprotein mRNA binds to oligodeoxythymidylate-substituted cellulose at high ionic strength and is eluted by water; treatment of lipoprotein mRNA with oligodeoxythymidylate and ribonuclease H destroys its ability to bind to oligodeoxythymidylate-cellulose; and in the presence of oligodeoxythymidylate, lipoprotein mRNA can serve as template for the synthesis of DNA complementary to lipoprotein mRNA by reverse transcriptase. In view of the fact that the lpp gene and its downstream-flanking region contain no continuous deoxyadenylate sequences longer than five nucleotides, the polyadenylate moiety must be added post-transcriptionally. It was possible to demonstrate the synthesis of polyadenylated lipoprotein mRNA in toluene-permeabilized cells of E. coli, opening the way for the study of its biosynthesis.

Bacterial Outer Membrane Proteins↗
PubMed1986

Construction of a cDNA library from polyadenylated RNA of Bacillus subtilis and the determination of some 3'-terminal sequences.

We had found previously that polyadenylated RNA constitutes a surprisingly large fraction of mRNA in both Escherichia coli and Bacillus subtilis [Gopalakrishna et al., Nucl. Acids Res. 9 (1981) 3545-3554; Biochem. 21 (1982) 2724-2729]. We have also shown [Gopalakrishna and Sarkar, J. Biol. Chem. 257 (1982) 2747-2750] that polyadenylated RNA from B. subtilis can serve as a template for the synthesis of complementary DNA by reverse transcriptase using oligo(dT) as primer. In this work, we show that the cDNA thus synthesized contains sequences representative of poly(A)+RNA and can serve as template for double-stranded (ds) cDNA synthesis. The ds cDNA could be inserted into the PstI site of pBR322 and cloned in E. coli DH1. The cDNA inserts from a few cloned recombinant pBR322 plasmids were transferred to M13mp18 bacteriophage for sequence determination. Six cDNA species had terminal oligo(dT) sequences, indicating that they represented the complement of poly(A)+RNA. This constitutes independent and direct evidence for the existence of bacterial polyadenylated mRNA and opens the way for studying the nucleotide sequences that control polyadenylation.

Bacillus subtilis↗