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In accordance with earlier findings, we observed a highly tissue-specific expression pattern for all tissues analyzed. The brain was found to express the highest number of tissue-specific miRNAs, followed by testis.
Notably, our experiments also revealed robust strain-specific differential miRNA expression in the liver that is caused by genetic variation between the strains. Finally, we identified two types of germline-specific piRNAs in testis, mapping either to transposons or in strand-specific clusters.
Strain and tissue-specific expression patterns furthermore provide a strong basis for studying the role of small RNAs in regulatory networks as well as biological process like physiology and neurobiology that are extensively studied in this model system.
The target spectrum of a miRNA is mostly defined by the seed, i. Thousands of mRNAs are expected to be under regulatory control of miRNAs [ 12 , 13 ] and the presence or absence of a single miRNA has been shown to affect, albeit modestly, the level of thousands of proteins [ 14 , 15 ].
Thus, miRNAs form a complex regulatory network affecting the majority of genes. A second developmentally vital class of small RNAs are the piwi-interacting pi RNAs [ 16 , 17 ], which play a role in the formation of the germ line. The pre-pachytene piRNAs, which are repeat- and transposon-derived, likely play a role in guiding DNA methylation to repeats, thereby silencing transposons [ 20 ] and preventing genome instability.
Conversely, the pachytene piRNAs are mostly derived from a selected set of genomic clusters that show a very strong strand bias. The function of these genomic clusters, however, remains elusive [ 18 - 21 ]. The laboratory rat Rattus norvegicus is a model organism in which organ-systems physiology has been studied for decades [ 25 ]. Recent advances in techniques to genetically modify the rat [ 26 - 30 ] enables detailed analyses of rat physiology at molecular levels.
Furthermore, well-established genetic systems, such as congenic, consomic and recombinant inbred lines are versatile tools for studying the effect of genetic variation on quantitative traits such as blood pressure [ 31 ] or gene expression [ 32 ] corresponding to quantitative trait loci QTLs and expression e QTLs, respectively. Comprehensive small RNA inventories and profiles are instrumental in such genetical genomics and systems biological approaches, as they serve as a resource for annotation of the genome.
Small RNAs are important players in many regulatory processes and are thus important for understanding disease etiology. The rat small RNA inventory described here will also be important for understanding human disease, since many rat models were selected to reflect clinical symptoms [ 33 ]. Conserved expression specificity of miRNAs has been described for a number of organ systems or cell cultures, based on deep sequencing approaches [ 34 - 36 ].
Simultaneously, species-specific miRNAs have been identified in closely related species [ 34 , 36 - 38 ], indicating that miRNAs are evolutionary dynamic. The availability of comprehensive species-specific miRNA profiles of different tissues and organ systems is an important requirement for elucidating the biological roles that miRNAs fulfill.
More exhaustive profiling will likely improve existing profiles and increase insight in the basis of quantitative and qualitative variations in miRNA expression.
Thirty-one of these pre-miRNAs were not previously characterized in rat, but were found to be homologous to mouse or human loci; 30 novel candidate pre-miRNA loci do not have an apparent homologue in these species. Finally, we identified thousands of piRNAs in the testis samples. The dataset described here greatly contributes to our understanding of miRNA divergence, variation and expression and may be a valuable resource in evolutionary analyses as well as in the interpretation of regulatory networks and functional genomics experiments in the rat.
Of all raw reads, The length distribution of the vast majority of small RNA reads was between 18 and 23 nt, corresponding with the expected size for miRNAs. We aimed to address global profiling as well as RNA editing and for profiling we only included perfectly mapping reads 6.
Each tissue dataset consisted out of approximately , miRNA reads. We assume that our global expression profiles allowed us to detect most miRNAs. This is likely due to the absence of the miRNA in the investigated tissues, or highly specific expression in a limited number of cells.
Therefore, we treated miRNAs derived from either hairpin arm as individual entities for further analysis steps. Seed nt or overlaps with known miRBase miRNAs showed that the majority of miRNAs is conserved; are conserved in rodents, whereas comparison to all categorized vertebrates shows that seeds are conserved.
Likely, the higher number of seed conservation in all vertebrates is due to the poor miRNA annotation in most rodents. Seventy-seven miRNAs Additional file 7 , File S5 contain seeds without known homologues in vertebrates, of which twenty-four are derived from the opposite strand of known miRNAs. These may represent rat-specific miRNAs, although it cannot be excluded that these remain to be detected in other species. In order to understand the function of miRNAs in specific tissues, it may therefore be helpful to identify global miRNA profiles.
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In accordance with earlier findings, we observed a highly tissue-specific expression pattern for all tissues analyzed. The brain was found to express the highest number of tissue-specific miRNAs, followed by testis. Notably, our experiments also revealed robust strain-specific differential miRNA expression in the liver that is caused by genetic variation between the strains. Finally, we identified two types of germline-specific piRNAs in testis, mapping either to transposons or in strand-specific clusters.
Small RNA expression and strain specificity in the rat
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