Terrier köpek normal ve tümörlü meme dokusu EST Kütüphanelerinden SSR’ların belirlenmesi

Dogs share a common environment with humans and knowledge of the specific dog breed diseases is very useful in developing a model for human cancer studies. ESTs represent part of the transcribed genome of an organism and are an important resource for identifying microsatellites. Simple Sequence Repeats (SSRs), or microsatellites, which contain repetitive DNA sequences, are among the most powerful genetic markers known. The development of EST-SSRs has become a fast, efficient, and low-cost option for genomic studies. In this study, to determine SSRs from EST libraryof mammary gland tissue of the Terrier dog that has 2304 ESTs; SSRIT and IMEx software, which have web-based versions and are easily accessible, were used. SSRIT finds motifs from 2 to 10 base lengths and adjusts the minimum number of repeats by eliminating single nucleotide motifs. IMEx finds perfect and imperfect microsatellites separately. It can find motifs of different lengths from 1 to 6 and the minimum number of repeats can be set. In addition, the appropriate primer for the desired SSR region can be designed. The 2, 3, 4, 5 and 6 nucleotide motifs were found for normal tissue ESTs whereas 5 nucleotide motifs were not found for tumoral tissue ESTsKöpekler, insanlarla ortak bir çevreyi paylaşır ve belirli köpek ırklarının hastalıkları hakkında bilgi, insan kanser çalışmaları için bir model geliştirmede çok yararlıdır. EST'ler, bir organizmanın transkribe edilen genomunun bir parçasını temsil eder ve mikrosatellitleri tanımlamak için önemli bir kaynaktır. Tekrarlayan DNA dizilerini içeren Basit Dizi Tekrarları (SSR'ler) veya mikrosatellitler, bilinen en güçlü genetik belirteçler arasındadır. EST-SSR'lerin gelişimi, genomik çalışmalar için hızlı, verimli ve düşük maliyetli bir seçenek haline gelmiştir. Bu çalışmada, 2304 EST içeren Terrier köpeğin meme bezi dokusunun EST koleksiyonundan SSR'lerin belirlenmesi için; Web tabanlı sürümleri olan ve kolayca erişilebilen SSRIT ve IMEx yazılımları kullanılmıştır. SSRIT, 2 ila 10 baz uzunluğundaki motifleri bulur ve tekli nükleotid motiflerini ortadan kaldırarak minimum tekrar sayısını ayarlar. IMEx mükemmel ve kusurlu mikrosatellitleri ayrı ayrı bulur. Farklı uzunluklarda 1 ile 6 arasındaki motifleri bulabilir ve minimum tekrar sayısı ayarlanabilir. Ek olarak, istenen SSR bölgesi için uygun primer tasarlanabilir. Normal doku EST'leri için 2, 3, 4, 5 ve 6 nükleotidli motifler bulunurken, tümörlü doku EST'leri için 5 nükleotidli motif bulunamamıştır

Generation and Analysis of Expressed Sequence Tags from Olea europaea L.

Olive (Olea europaea L.) is an important source of edible oil which was originated in Near-East region. In this study, two cDNA libraries were constructed from young olive leaves and immature olive fruits for generation of ESTs to discover the novel genes and search the function of unknown genes of olive. The randomly selected 3840 colonies were sequenced for EST collection from both libraries. Readable 2228 sequences for olive leaf and 1506 sequences for olive fruit were assembled into 205 and 69 contigs, respectively, whereas 2478 were singletons. Putative functions of all 2752 differentially expressed unique sequences were designated by gene homology based on BLAST and annotated using BLAST2GO. While 1339 ESTs show no homology to the database, 2024 ESTs have homology (under 80%) with hypothetical proteins, putative proteins, expressed proteins, and unknown proteins in NCBI-GenBank. 635 EST's unique genes sequence have been identified by over 80% homology to known function in other species which were not previously described in Olea family. Only 3.1% of total EST's was shown similarity with olive database existing in NCBI. This generated EST's data and consensus sequences were submitted to NCBI as valuable source for functional genome studies of olive

Preparing and Analyzing Expressed Sequence Tags (ESTs) Library for the Mammary Tissue of Local Turkish Kivircik Sheep

Kivircik sheep is an important local Turkish sheep according to its meat quality and milk productivity. The aim of this study was to analyze gene expression profiles of both prenatal and postnatal stages for the Kivircik sheep. Therefore, two different cDNA libraries, which were taken from the same Kivircik sheep mammary gland tissue at prenatal and postnatal stages, were constructed. Total 3072 colonies which were randomly selected from the two libraries were sequenced for developing a sheep ESTs collection. We used Phred/Phrap computer programs for analysis of the raw EST and readable EST sequences were assembled with the CAP3 software. Putative functions of all unique sequences and statistical analysis were determined by Geneious software. Total 422 ESTs have over 80% similarity to known sequences of other organisms in NCBI classified by Panther database for the Gene Ontology (GO) category. By comparing gene expression profiles, we observed some putative genes that may be relative to reproductive performance or play important roles in milk synthesis and secretion. A total of 2414 ESTs have been deposited to the NCBI GenBank database (GW996847-GW999260). EST data in this study have provided a new source of information to functional genome studies of sheep

Whole-Exome Sequencing (WES) results of 50 patients with chronic kidney diseases: a perspective of Alport syndrome

OBJECTIVE: Chronic kidney disease (CKD) remains one of the major common health problems, and the number of people affected by the disease is progressively increasing in Turkey and worldwide. This study aimed to investigate molecular defects in Alport syndrome (AS) and other genes in patients with clinically suspected CKD using whole-exome sequencing (WES).METHODS: Patients with clinical suspicion of CKD were included in the study. Molecular genetic analyses were performed on genomic DNA by using WES.RESULTS: A total of 15 with 5 different pathogenic or likely pathogenic variants were identified in CKD patients, with a diagnostic rate of 30%. Eight variants of uncertain significance were also detected. In this study, 10 variants were described for the first time. As a result, we detected variants associated with CKD in our study population and found AS as the most common CKD after other related kidney diseases.CONCLUSIONS: Our results suggest that in heterogeneous diseases such as CKD, WES analysis enables accurate identification of underlying molecular defects promptly. Although CKD accounts for 10-14% of all renal dysfunction, molecular genetic diagnosis is necessary for optimal long-term treatment, prognosis, and effective genetic counseling