28 research outputs found
Pooled RNAi Screens - Technical and Biological Aspects
RNA interference (RNAi) screens have recently emerged as an exciting new tool for studying gene function in mammalian cells. In order to facilitate those studies, short hairpin RNA (shRNA) expression libraries covering the entire human transcriptome have become commercially available. To make use of the full potential of such large-scale shRNA libraries, microarray-based methods have been developed to analyze complex pooled RNAi screens. In terms of microarray analysis, different strategies have been pursued by different research groups, largely influenced by the employed shRNA library. In this review, we compare the three major shRNA expression libraries with a focus on their suitability for a microarray-based analysis of pooled screens. We analyze and compare approaches previously used to perform pooled RNAi screens and point out their advantages as well as limitations
Microarray study of gene expression in uterine leiomyoma
Uterine leiomyoma is a most common benign neoplasm in women of reproductive age. It arises from the myometrial compartment of the uterus and may transform in some cases to a malignant phenotype. Aim: To identify the genes involved in pathogenesis of uterine leiomyoma. Methods: We have studied differential gene expression in matched tissue samples of leiomyoma and normal myometrium from the very same people utilizing a cDNA microarray screening method. We also compared our results with previously published microarray data to identify the overlapping gene alterations. Results: Based on this comparison we can divide genes deregulated in our study into two groups. The first group comprises genes that to our knowledge have not been previously reported as deregulated in fibroids: CLDN1, FGF7 (KGF), HNRPM, ISOC1, MAGEC1 (CT7), MAPK12, RFC, TIE1, TNFRSF21 (DR6). The second group consists of genes identified also in previous studies: CCND1 (BCL1), CDKN1A (P21), CRABP2, FN1 and SOX4 (EVI16). In our study FN1 was the most up-regulated gene, occupying the place between the myometrium and fibroids ranging from 2.07 to 3.64, depending of the probe molecule used for detection. Conclusions: Newly identified genes may be regarded as potential diagnostic or prognostic markers of uterine leiomyoma and thus may be very useful as new therapeutic candidates.ΠΠ΅ΠΉΠΎΠΌΠΈΠΎΠΌΠ° ΠΌΠ°ΡΠΊΠΈ ΡΠ²Π»ΡΠ΅ΡΡΡ ΠΎΠ΄Π½ΠΈΠΌ ΠΈΠ· Π½Π°ΠΈΠ±ΠΎΠ»Π΅Π΅ ΡΠ°ΡΠΏΡΠΎΡΡΡΠ°Π½Π΅Π½Π½ΡΡ
Π΄ΠΎΠ±ΡΠΎΠΊΠ°ΡΠ΅ΡΡΠ²Π΅Π½Π½ΡΡ
Π½ΠΎΠ²ΠΎΠΎΠ±ΡΠ°Π·ΠΎΠ²Π°Π½ΠΈΠΉ ΠΆΠ΅Π½ΡΠΊΠΎΠΉ ΡΠ΅ΠΏΡΠΎΠ΄ΡΠΊΡΠΈΠ²Π½ΠΎΠΉ
ΡΡΠ΅ΡΡ. Π Π½Π΅ΠΊΠΎΡΠΎΡΡΡ
ΡΠ»ΡΡΠ°ΡΡ
ΠΎΡΠΌΠ΅ΡΠ°ΡΡ Π·Π»ΠΎΠΊΠ°ΡΠ΅ΡΡΠ²Π΅Π½Π½ΡΡ ΡΡΠ°Π½ΡΡΠΎΡΠΌΠ°ΡΠΈΡ Π΄Π°Π½Π½ΠΎΠ³ΠΎ Π½ΠΎΠ²ΠΎΠΎΠ±ΡΠ°Π·ΠΎΠ²Π°Π½ΠΈΡ. Π¦Π΅Π»Ρ: ΠΈΠ΄Π΅Π½ΡΠΈΡΠΈΠΊΠ°ΡΠΈΡ
Π³Π΅Π½ΠΎΠ², Π²ΠΎΠ²Π»Π΅ΡΠ΅Π½Π½ΡΡ
Π² ΠΏΠ°ΡΠΎΠ³Π΅Π½Π΅Π· Π»Π΅ΠΉΠΎΠΌΠΈΠΎΠΌΡ. ΠΠ΅ΡΠΎΠ΄Ρ: ΠΏΡΠΎΠ²Π΅Π΄Π΅Π½ Π°Π½Π°Π»ΠΈΠ· Π΄ΠΈΡΡΠ΅ΡΠ΅Π½ΡΠΈΠ°Π»ΡΠ½ΠΎΠΉ ΡΠΊΡΠΏΡΠ΅ΡΡΠΈΠΈ Π³Π΅Π½ΠΎΠ² Π²
ΠΎΠ±ΡΠ°Π·ΡΠ°Ρ
Π»Π΅ΠΉΠΎΠΌΠΈΠΎΠΌΡ ΠΈ Π½ΠΎΡΠΌΠ°Π»ΡΠ½ΠΎΠ³ΠΎ ΠΌΠΈΠΎΠΌΠ΅ΡΡΠΈΡ ΠΎΠ΄Π½ΠΈΡ
ΠΈ ΡΠ΅Ρ
ΠΆΠ΅ ΠΏΠ°ΡΠΈΠ΅Π½ΡΠΎΠ² ΠΌΠ΅ΡΠΎΠ΄ΠΎΠΌ ΠΠΠ-Π±ΠΈΠΎΡΠΈΠΏ-Π³ΠΈΠ±ΡΠΈΠ΄ΠΈΠ·Π°ΡΠΈΠΈ ΠΈ ΠΏΡΠΎΠ²Π΅Π΄Π΅Π½ΠΎ
ΡΡΠ°Π²Π½Π΅Π½ΠΈΠ΅ ΠΏΠΎΠ»ΡΡΠ΅Π½Π½ΡΡ
ΡΠ΅Π·ΡΠ»ΡΡΠ°ΡΠΎΠ² Ρ Π΄Π°Π½Π½ΡΠΌΠΈ, ΠΎΠΏΡΠ±Π»ΠΈΠΊΠΎΠ²Π°Π½Π½ΡΠΌΠΈ ΡΠ°Π½Π΅Π΅. Π Π΅Π·ΡΠ»ΡΡΠ°ΡΡ: Π²ΡΡΠ²Π»Π΅Π½Ρ ΡΠ°Π·Π»ΠΈΡΠΈΡ Π² ΡΠΊΡΠΏΡΠ΅ΡΡΠΈΠΈ
ΡΡΠ΄Π° Π³Π΅Π½ΠΎΠ², ΠΊΠΎΡΠΎΡΡΠ΅ ΠΌΠΎΠΆΠ½ΠΎ ΡΠ°Π·Π΄Π΅Π»ΠΈΡΡ Π½Π° Π΄Π²Π΅ Π³ΡΡΠΏΠΏΡ. ΠΠΏΠ΅ΡΠ²ΡΠ΅ Π²ΡΡΠ²Π»Π΅Π½Π° ΠΏΠΎΠ²ΡΡΠ΅Π½Π½Π°Ρ ΡΠΊΡΠΏΡΠ΅ΡΡΠΈΡ Π³Π΅Π½ΠΎΠ² CLDN1, FGF7 (KGF),
HNRPM, ISOC1, MAGEC1 (CT7), MAPK12, RFC, TIE1 ΠΈ TNFRSF21 (DR6) Π² ΡΠΊΠ°Π½ΠΈ Π»Π΅ΠΉΠΎΠΌΠΈΠΎΠΌΡ ΠΏΠΎ ΡΡΠ°Π²Π½Π΅Π½ΠΈΡ Ρ Π½ΠΎΡΠΌΠ°Π»ΡΠ½ΡΠΌ
ΠΌΠΈΠΎΠΌΠ΅ΡΡΠΈΠ΅ΠΌ. ΠΠΎ Π²ΡΠΎΡΠΎΠΉ Π³ΡΡΠΏΠΏΠ΅ ΠΌΠΎΠΆΠ½ΠΎ ΠΎΡΠ½Π΅ΡΡΠΈ Π³Π΅Π½Ρ CCND1 (BCL1), CDKN1A (P21), CRABP2, FN1 ΠΈ SOX4 (EVI16), ΡΠΆΠ΅
ΡΠΏΠΎΠΌΠΈΠ½Π°Π²ΡΠΈΠ΅ΡΡ Π² ΡΠ²ΡΠ·ΠΈ Ρ ΠΏΠ°ΡΠΎΠ³Π΅Π½Π΅Π·ΠΎΠΌ Π»Π΅ΠΉΠΎΠΌΠΈΠΎΠΌΡ Π² ΡΡΠ΄Π΅ ΠΏΡΠ΅Π΄ΡΠ΄ΡΡΠΈΡ
ΠΈΡΡΠ»Π΅Π΄ΠΎΠ²Π°Π½ΠΈΠΉ. ΠΠ°ΠΈΠ±ΠΎΠ»ΡΡΠΈΠΌ ΠΈΠ·ΠΌΠ΅Π½Π΅Π½ΠΈΠ΅ΠΌ ΡΡΠΎΠ²Π½Ρ ΡΠΊΡΠΏΡΠ΅ΡΡΠΈΠΈ
(Π² 2,07β3,64 ΡΠ°Π· Π² Π·Π°Π²ΠΈΡΠΈΠΌΠΎΡΡΠΈ ΠΎΡ Π·ΠΎΠ½Π΄Π°) Ρ
Π°ΡΠ°ΠΊΡΠ΅ΡΠΈΠ·ΠΎΠ²Π°Π»ΡΡ Π³Π΅Π½ ΡΠΈΠ±ΡΠΎΠ½Π΅ΠΊΡΠΈΠ½Π° FN1. ΠΡΠ²ΠΎΠ΄Ρ: ΠΈΠ΄Π΅Π½ΡΠΈΡΠΈΡΠΈΡΠΎΠ²Π°Π½Π½ΡΠ΅
Π³Π΅Π½Ρ ΠΌΠΎΠ³ΡΡ ΡΠ°ΡΡΠΌΠ°ΡΡΠΈΠ²Π°ΡΡΡΡ Π² ΠΊΠ°ΡΠ΅ΡΡΠ²Π΅ ΠΏΠΎΡΠ΅Π½ΡΠΈΠ°Π»ΡΠ½ΡΡ
Π΄ΠΈΠ°Π³Π½ΠΎΡΡΠΈΡΠ΅ΡΠΊΠΈΡ
ΠΈ ΠΏΡΠΎΠ³Π½ΠΎΡΡΠΈΡΠ΅ΡΠΊΠΈΡ
ΠΌΠ°ΡΠΊΠ΅ΡΠΎΠ² Π»Π΅ΠΉΠΎΠΌΠΈΠΎΠΌΡ ΠΌΠ°ΡΠΊΠΈ
Multiplex approaches in protein microarray technology
The success of genome sequencing projects has provided the basis for systematic analysis of protein function and has led to a shift from the description of single molecules to the characterization of complex samples. Such a task would not be possible without the provision of appropriate high-throughput technologies, such as protein microarray technology. In addition, the increasing number of samples necessitates the adaptation of such technologies to a multiplex format. This review will discuss protein microarray technology in the context of multiplex analysis and highlight its current prospects and limitations
Corrigendum to "Functional analysis of <i>Trypanosoma brucei</i> PUF1" [Mol. Biochem. Parasitol. 150 (2006) 340β349]
No abstract available
Glucose triggers different global responses in yeast, depending on the strength of the signal, and transiently stabilizes ribosomal protein mRNAs
Glucose exerts profound effects upon yeast physiology. In general, the effects of high glucose concentrations (0.1%. We also show that cytoplasmic ribosomal protein mRNAs are transiently stabilized by glucose, indicating that both transcriptional and post-transcriptional mechanisms combine to accelerate the accumulation of ribosomal protein mRNAs. Presumably, this facilitates rapid ribosome biogenesis after exposure to glucose. However, our data indicate that yeast activates ribosome biogenesis only when sufficient glucose is available to make this metabolic investment worthwhile. In contrast, the regulation of metabolic functions in response to very low glucose signals presumably ensures that yeast can exploit even minute amounts of this preferred nutrient
Monitoring the Switch from Housekeeping to Pathogen Defense Metabolism in Arabidopsis thaliana Using cDNA Arrays
Plants respond to pathogen attack by deploying several defense reactions. Some rely on the activation of preformed components, whereas others depend on changes in transcriptional activity. Using cDNA arrays comprising 13,000 unique expressed sequence tags, changes in the transcriptome of Arabidopsis thaliana were monitored after attempted infection with the bacterial plant pathogen Pseudomonas syringae pv. tomato carrying the avirulence gene avrRpt2. Sampling at four time points during the first 24 h after infiltration revealed significant changes in the steady state transcript levels of ~650 genes within 10 min and a massive shift in gene expression patterns by 7 h involving ~2,000 genes representing many cellular processes. This shift from housekeeping to defense metabolism results from changes in regulatory and signaling circuits and from an increased demand for energy and biosynthetic capacity in plants fighting off a pathogenic attack. Concentrating our detailed analysis on the genes encoding enzymes in glycolysis, the Krebs cycle, the pentose phosphate pathway, the biosynthesis of aromatic amino acids, phenylpropanoids, and ethylene, we observed interesting differential regulation patterns. Furthermore, our data showed potentially important changes in areas of metabolism, such as the glyoxylate metabolism, hitherto not suspected to be components of plant defense