41 research outputs found
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
Transcriptome Analysis of the Thymus in Short-Term Calorie-Restricted Mice Using RNA-seq
Calorie restriction (CR), which is a factor that expands lifespan and an important player in immune response, is an effective protective method against cancer development. Thymus, which plays a critical role in the development of the immune system, reacts to nutrition deficiency quickly. RNA-seq-based transcriptome sequencing was performed to thymus tissues of MMTV-TGF-α mice subjected to ad libitum (AL), chronic calorie restriction (CCR), and intermittent calorie restriction (ICR) diets in this study. Three cDNA libraries were sequenced using Illumina HiSeq™ 4000 to produce 100 base pair-end reads. On average, 105 million clean reads were mapped and in total 6091 significantly differentially expressed genes (DEGs) were identified (p<0.05). These DEGs were clustered into Gene Ontology (GO) categories. The expression pattern revealed by RNA-seq was validated by quantitative real-time PCR (qPCR) analysis of four important genes, which are leptin, ghrelin, Igf1, and adinopectin. RNA-seq data has been deposited in NCBI Gene Expression Omnibus (GEO) database (GSE95371). We report the use of RNA sequencing to find DEGs that are affected by different feeding regimes in the thymus
Preparing and Analyzing Expressed Sequence Tags (ESTs) Library for the Mammary Tissue of Local Turkish Kivircik Sheep
WOS: 000394141500001PubMed ID: 28239610Kivircik 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.Yildiz Technical University Scientific Research Projects Coordination DepartmentYildiz Technical University [27-01-07-02]This research has been supported by Yildiz Technical University Scientific Research Projects Coordination Department (Project no. 27-01-07-02)
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
Analysis of Expressed Genes in Normal and Tumoral Mammary Gland Tissue of the Terrier Dog
WOS: 000429197900005Mammary gland tumor is the most common type of tumor in female dogs. Data on genes that are involved in tumorigenesis and mechanism of tumor development are insufficient. Comparative studies have been conducted in order to see if tumorigenesis studies in the dog could be a model for human mammary gland tumors. In this study, we constructed two different cDNA libraries from mammary tissue, which were collected from a normal mammary tissue of a healthy Terrier dog and a tumoral mammary tissue of a sick dog. A total 2304 colonies which are randomly picked out from the two libraries were sequenced for developing a dog mammary gland ESTs collection. Raw EST data were analyzed with Phred/Phrap programs and readable EST sequences were assembled with the CAP3 program. All of EST sequences were grouped into 45 contig and 2203 singletons. Putative functions of all unique sequences were designated by NCBI BLAST based on gene homology and annotated by BLAST2GO. The results of this study are a very valuable resource for functional genome studies of the dogs
Hepatit C tedavisinde karşılaşılan telaprevir ilişkili DRESS sendromu
Kronik hepatit C tedavisinde telaprevir yüksek kalıcı viral yanıt ve kısa süreli tedavi özelliğiyle dikkat çekmektedir, ancak özellikle çeşitli cilt yan etkileri olmak üzere yeni yan etkilerle ilişkilidir. Biz telaprevir bazlı hepatit C tedavisi esnasında sistemik semptomlar ve eozinofilinin eşlik ettiği ilaç reaksiyonu gelişen 66 yaşında bir kadın hasta sunduk. Hastanın tüm antiviralleri kesildi ve destek tedavi verildi. Takibinde sistemik ve cilt bulguları düzeldi. Nadir olmasına rağmen telaprevir bazlı tedavi esnasında ciddi cilt reaksiyonları akılda tutulmalıdırIn chronic hepatitis C patients telaprevir attracts attention with high sustained virologic response and short term treatment however it is associated a new spectrum of adverse events, especially several cutaneous manifestations. We report a 66-year-old female patient developed drug reaction with eosinophilia and systemic symptoms during telaprevir based hepatitis C treatment. All antivirals were discontinued and she was treated with supportive care. Systemic and cutaneous symptoms resolved in follow-up. Although rare, clinicians should be aware of potentially severe cutaneous skin reactions during telaprevir -based therapy. J Microbiol Infect Dis 2015;5(1): 36-3