Coisolation of genomic and organelle DNAs from 15 genera and 31 species of plants.
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DNA Fingerprinting↗
Biomedical subjects
Mehmet Karaca
Publications and source records attributed to Mehmet Karaca.
Exact tandem repeats analyzer (E-TRA): a new program for DNA sequence mining.
Exact Tandem Repeats Analyzer 1.0 (E-TRA) combines sequence motif searches with keywords such as 'organs', 'tissues', 'cell lines' and 'development stages' for finding simple exact tandem repeats as well as non-simple repeats. E-TRA has several advanced repeat search parameters/options compared to other repeat finder programs as it not only accepts GenBank, FASTA and expressed sequence tags (EST) sequence files, but also does analysis of multiple files with multiple sequences. The minimum and maximum tandem repeat motif lengths that E-TRA finds vary from one to one thousand. Advanced user defined parameters/options let the researchers use different minimum motif repeats search criteria for varying motif lengths simultaneously. One of the most interesting features of genomes is the presence of relatively short tandem repeats (TRs). These repeated DNA sequences are found in both prokaryotes and eukaryotes, distributed almost at random throughout the genome. Some of the tandem repeats play important roles in the regulation of gene expression whereas others do not have any known biological function as yet. Nevertheless, they have proven to be very beneficial in DNA profiling and genetic linkage analysis studies. To demonstrate the use of E-TRA, we used 5,465,605 human EST sequences derived from 18,814,550 GenBank EST sequences. Our results indicated that 12.44% (679,800) of the human EST sequences contained simple and non-simple repeat string patterns varying from one to 126 nucleotides in length. The results also revealed that human organs, tissues, cell lines and different developmental stages differed in number of repeats as well as repeat composition, indicating that the distribution of expressed tandem repeats among tissues or organs are not random, thus differing from the un-transcribed repeats found in genomes.
Cells, Cultured↗
Female adnexal tumor of probable Wolffian origin diagnosed during the staging evaluation of extranodal diffuse large B-cell lymphoma.
Female adnexal tumor of probable Wolffian origin (FATPWO) is a rare neoplasm arising within the leaves of broad ligament or hanging from it or a fallopian tube. A 55-year-old female patient with the diagnosis of non-Hodgkin lymphoma is presented. The staging procedure revealed a pelvic mass that was not regressed by chemotherapy. Explorative laparotomy showed FATPWO. The extremely rare coexistence of FATPWO in the staging evaluation of non-Hodgkin lymphoma is reported. According to our knowledge, this is the first case of FATPWO coexisting with extranodal diffuse large B-cell lymphoma in the English-language literature.
Antineoplastic Combined Chemotherapy Protocols↗
Mutation of GATA3 in human breast tumors.
GATA3 is an essential transcription factor that was first identified as a regulator of immune cell function. In recent microarray analyses of human breast tumors, both normal breast luminal epithelium and estrogen receptor (ESR1)-positive tumors showed high expression of GATA3. We sequenced genomic DNA from 111 breast tumors and three breast-tumor-derived cell lines and identified somatic mutations of GATA3 in five tumors and the MCF-7 cell line. These mutations cluster in the vicinity of the highly conserved second zinc-finger that is required for DNA binding. In addition to these five, we identified using cDNA sequencing a unique mis-splicing variant that caused a frameshift mutation. One of the somatic mutations we identified was identical to a germline GATA3 mutation reported in two kindreds with HDR syndrome/OMIM #146255, which is an autosomal dominant syndrome caused by the haplo-insufficiency of GATA3. The ectopic expression of GATA3 in human 293T cells caused the induction of 73 genes including six cytokeratins, and inhibited cell line doubling times. These data suggest that GATA3 is involved in growth control and the maintenance of the differentiated state in epithelial cells, and that GATA3 variants may contribute to tumorigenesis in ESR1-positive breast tumors.
Amino Acid Sequence↗
Statistical modeling for selecting housekeeper genes.
There is a need for statistical methods to identify genes that have minimal variation in expression across a variety of experimental conditions. These 'housekeeper' genes are widely employed as controls for quantification of test genes using gel analysis and real-time RT-PCR. Using real-time quantitative RT-PCR, we analyzed 80 primary breast tumors for variation in expression of six putative housekeeper genes (MRPL19 (mitochondrial ribosomal protein L19), PSMC4 (proteasome (prosome, macropain) 26S subunit, ATPase, 4), SF3A1 (splicing factor 3a, subunit 1, 120 kDa), PUM1 (pumilio homolog 1 (Drosophila)), ACTB (actin, beta) and GAPD (glyceraldehyde-3-phosphate dehydrogenase)). We present appropriate models for selecting the best housekeepers to normalize quantitative data within a given tissue type (for example, breast cancer) and across different types of tissue samples.
ATPases Associated with Diverse Cellular Activitie↗
A software program combining sequence motif searches with keywords for finding repeats containing DNA sequences.
MOTIVATION: One of the most interesting features of genomes (both coding and non-coding regions) is the presence of relatively short tandemly repeated DNA sequences known as tandem repeats (TRs). We developed a new PC-based stand-alone software analysis program, combining sequence motif searches with keywords such as organs, tissues, cell lines or development stages for finding exact, inexact and compound, TRs. Tandem Repeats Analyzer 1.5 (TRA) has several advanced repeat search parameters/options over other repeat finder programs as it does not only accept GenBank, FASTA and expressed sequence tag (EST) sequence files but also does analysis of multifiles with multisequences. Advanced user-defined parameters/options let the researchers use different motif lengths search criteria for varying motif lengths simultaneously. The outputs show statistical results to be evaluated by the user. The discovery of TRs in ESTs could be useful for both gene mapping and association studies and discovering TRs located in coding regions of important genes that are expressed under various conditions of environment, stress, organ, tissue and development stage. RESULTS: In this paper, we demonstrated applications of TRA using 175 899 ESTs sequences for three Arabidopsis spp. downloaded from GenBank. The EST-SSRs/ESTs ratios were found 43.1%, 15.3% and 2.34% in A.lyrata, A.thaliana and A.halleri, respectively. Analysis revealed that organs, tissues and development stages possessed different amounts of repeats and repeat compositions. This indicated that the distribution of TRs among the tissues or organs may not be random differing from the untranscribed repeats found in genomes. AVAILABILITY: The program can be obtained free by anonymous FTP from ftp.akdeniz.edu.tr/Araclar/TRA.
Arabidopsis↗
Universal Reference RNA as a standard for microarray experiments.
BACKGROUND: Obtaining reliable and reproducible two-color microarray gene expression data is critically important for understanding the biological significance of perturbations made on a cellular system. Microarray design, RNA preparation and labeling, hybridization conditions and data acquisition and analysis are variables difficult to simultaneously control. A useful tool for monitoring and controlling intra- and inter-experimental variation is Universal Reference RNA (URR), developed with the goal of providing hybridization signal at each microarray probe location (spot). Measuring signal at each spot as the ratio of experimental RNA to reference RNA targets, rather than relying on absolute signal intensity, decreases variability by normalizing signal output in any two-color hybridization experiment. RESULTS: Human, mouse and rat URR (UHRR, UMRR and URRR, respectively) were prepared from pools of RNA derived from individual cell lines representing different tissues. A variety of microarrays were used to determine percentage of spots hybridizing with URR and producing signal above a user defined threshold (microarray coverage). Microarray coverage was consistently greater than 80% for all arrays tested. We confirmed that individual cell lines contribute their own unique set of genes to URR, arguing for a pool of RNA from several cell lines as a better configuration for URR as opposed to a single cell line source for URR. Microarray coverage comparing two separately prepared batches each of UHRR, UMRR and URRR were highly correlated (Pearson's correlation coefficients of 0.97). CONCLUSION: Results of this study demonstrate that large quantities of pooled RNA from individual cell lines are reproducibly prepared and possess diverse gene representation. This type of reference provides a standard for reducing variation in microarray experiments and allows more reliable comparison of gene expression data within and between experiments and laboratories.
Animals↗
A novel root-specific gene, MIC-3, with increased expression in nematode-resistant cotton (Gossypium hirsutum L.) after root-knot nematode infection.
A full-length cDNA, MIC-3, has been identified from a lambda ZAPII cDNA library constructed from the mRNA of nematode-resistant cotton (Gossypium hirsutum L.) roots after infection with root-knot nematode (Meloidogyne incognita). The putative open reading frame of MIC-3 encoded a protein of 141 amino acids with a calculated molecular mass of 15.3 kDa. Seven alternative polyadenylation sites have been identified for the MIC-3 transcripts, and the major transcripts are the longest ones. The MIC-3 gene contains a single intron within its coding region and belongs to a novel, multi-gene family containing up to six members. Expression of MIC-3 is root localized and specifically enhanced in the nematode induced, immature galls of resistant cotton line M-249, suggesting that MIC-3 may play a critical role in the resistance response to root-knot nematode.
Adhesins, Bacterial↗
The comprehensive midtrimester test: high-sensitivity Down syndrome test.
OBJECTIVE: The purpose of this study was to develop a highly sensitive algorithm for midtrimester Down syndrome detection. STUDY DESIGN: Urine (hyperglycosylated human chorionic gonadotropin, beta-core fragment of human chorionic gonadotropin), serum (alpha-fetoprotein, human chorionic gonadotropin and unconjugated estriol [uE(3)]), and ultrasound biometry (nuchal thickness, humerus length, the presence of gross ultrasonographic anomalies), and maternal age were measured at genetic amniocentesis. Stepwise logistic regression analysis was used to identify the most significant markers. A multivariate Gaussian algorithm plus age was used to derive patient-specific Down syndrome risk. Sensitivity and false-positive rates at different risk thresholds and the area under the receiver-operating characteristic curve were determined. A probability value of <.05 was significant. RESULTS: There were 568 study cases with 17 Down syndrome cases (3.0%). The mean (+/-SD) maternal and gestational ages for the study group were 36.9 (+/-3.5) years and 16.2 (+/-1.4) weeks, respectively. The significant markers were nuchal thickness (P =.0001), hyperglycosylated human chorionic gonadotropin(P <.001), and beta-core fragment (P <.002). Neither maternal age nor gross sonographic anomaly contributed significantly to Down syndrome detection. The comprehensive midtrimester test was extremely efficient for Down syndrome detection in advanced maternal age only cases with a sensitivity of 92.3% at a 0.8% false-positive rate. In women <35 years old, all the Down syndrome cases were detected at 2.2% false positive rate. For the overall population, the sensitivity was 93.7% at 5% false-positive rate. CONCLUSION: In a preliminary study, the comprehensive midtrimester test appeared highly sensitive in different age groups. Gross anomaly detection was not required for high performance, which makes the comprehensive midtrimester test potentially suitable for low-risk screening and as an alternative to amniocentesis in women who wish to avoid the procedure. This was a small study; thus, the clinical value of this test can only be established in large trials.
Adult↗