Identification of phylogenetically conserved sequence motifs in microRNA 5' flanking sites from C. elegans and C. briggsae

<p>Abstract</p> <p>Background</p> <p>MicroRNAs (miRNAs) are small, noncoding RNA molecules that act as post-transcriptional regulators of gene expression. Studies concerning transcriptional regulation of miRNAs have so far concentrated on those located within the intergenic region of the genome and the search for putative promoters, thus leaving open the question of the existence of possible regulatory elements common to all miRNAs including those located in introns of protein coding genes.</p> <p>Results</p> <p>In this study, we initially searched for motifs occurring in the area 1000 bp upstream from all miRNAs independent of their genomic location. We discovered a previously unknown sequence motif GANNNNGA that displayed a conserved distribution in the nematode worms <it>Caenorhabditis elegans </it>and <it>Caenorhabditis briggsae</it>. This motif had a peak occurrence at 500 bp upstream, with a sharp drop-off toward the miRNA start site. Further analysis indicated that this motif was locally restricted and not enriched 1000–5000 bp upstream or 0–2000 bp downstream of the miRNA start site. In addition, this motif was observed to be most abundant in the upstream sequences of two important miRNAs, <it>mir-1 </it>and <it>mir-124</it>. This abundance was also conserved in phylogenetically distant species including human and mouse.</p> <p>Conclusion</p> <p>The results show that the motif GANNNNGA is conserved close to miRNA precursor start sites, suggesting that it may be involved in miRNA sequence recognition or regulation. This data provides important knowledge for the identification and computational prediction of miRNA sequences.</p

From a Hiding Place to the Eternal Glory : Thomas Aquinas’s Saintly Presence in Dominican Liturgy

Non peer reviewe

The Medieval Offices of Saint Thomas Aquinas

Peer reviewe

Tuomas Akvinolaiselle omistetut keskiaikaiset rukoushetket

Peer reviewe

Terveyskasvatuksen harharetket

The justification of health education is based on medicine and the research results achieved through it. By nature, it has been paternalistic, underestimating a person’s capacity to think and act for himself. ln addition, health education includes elements of persuasion and manipulation. And yet health education ought to be able to take into account the logic of a person’s own actions and his internal preferences. This is something that the present-day health education in Finland does not have a sufficient knowledge and skill base for. ln her analysis of Finland’s misguided health education, the author places emphasis on the firm connection that exists between mental and physical wellbeing.Terveyskasvatuksen oikeutus perustuu lääketieteeseen ja sen avulla saavutettuihin tutkimustuloksiin. Se on ollut luonteeltaan paternistista, ihmisiä holhoavaa ja heidän ajatteluja harkintakykyään aliarvioivaa. Siinä on myös suostuttelun ja manipuloinnin piirteitä. Terveyskasvatuksen tulisi kuitenkin pystyä ottamaan huomioon ihmisen oman toiminnan logiikka ja sisäiset preferenssit. Siihen nykyisellä terveyskasvatuksella ei ole riittäviä tiedollisia ja taidollisia edellytyksiä. Analysoidessaan terveyskasvatuksen harharetkiä artikkeli painottaa myös ihmisen psyykkisen ja fyysisen hyvinvoinnin kesken vallitsevaa kiinteää yhteyttä

Functional characterization of endogenous siRNA target genes in Caenorhabditis elegans

<p>Abstract</p> <p>Background</p> <p>Small interfering RNA (siRNA) molecules mediate sequence specific silencing in RNA interference (RNAi), a gene regulatory phenomenon observed in almost all organisms. Large scale sequencing of small RNA libraries obtained from <it>C. elegans </it>has revealed that a broad spectrum of siRNAs is endogenously transcribed from genomic sequences. The biological role and molecular diversity of <it>C. elegans </it>endogenous siRNA (endo-siRNA) molecules, nonetheless, remain poorly understood. In order to gain insight into their biological function, we annotated two large libraries of endo-siRNA sequences, identified their cognate targets, and performed gene ontology analysis to identify enriched functional categories.</p> <p>Results</p> <p>Systematic trends in categorization of target genes according to the specific length of siRNA sequences were observed: 18- to 22-mer siRNAs were associated with genes required for embryonic development; 23-mers were associated uniquely with post-embryonic development; 24–26-mers were associated with phosphorus metabolism or protein modification. Moreover, we observe that some argonaute related genes associate with siRNAs with multiple reads. Sequence frequency graphs suggest that different lengths of siRNAs share similarities in overall sequence structure: the 5' end begins with G, while the body predominates with U and C.</p> <p>Conclusion</p> <p>These results suggest that the lengths of endogenous siRNA molecules are consequential to their biological functions since the gene ontology categories for their cognate mRNA targets vary depending upon their lengths.</p

Sound mining in the North : a guide to environmental regulation and best practices supporting social sustainability

Julkaistu versi

Ohjeita järvien ja jokien pohjaeläimistöseurannan näytteenottoon ja raportointiin

Ohje on laadittu ympäristökeskusten alueilla tapahtuvaa, lähinnä velvoitetarkkailuihin kuuluvaa pohjaeläinseurantaa varten. Ohje on tarkoitettu sekä konsulttien että aluekeskuksissa velvoitetarkkailuja hoitavien käyttöön ja sitä voidaan hyödyntää mm. tarkkailuohjelmien laadintavaiheessa. Ohjeen avulla pyritään yhdenmukaistamaan pohjaeläinseurantoja, koskien lähinnä pohjaeläimistön näytteenottoa. Tulosten raportointia ja käsittelyä ei ole ohjeistettu kovin pitkälle, mutta olennaisimmat huomioitavat tekijät on kerrottu. Lisäksi on esitetty lisätietolähteitä ja keskeisin pohjaeläimistön määrityskirjallisuus

Methylmercury exposure increases lipocalin related (lpr) and decreases activated in blocked unfolded protein response (abu) genes and specific miRNAs in Caenorhabditis elegans

Methylmercury (MeHg) is a persistent environmental and dietary contaminant that causes serious adverse developmental and physiologic effects at multiple cellular levels. In order to understand more fully the consequences of MeHg exposure at the molecular level, we profiled gene and miRNA transcripts from the model organism Caenorhabditis elegans. Animals were exposed to MeHg (10µM) from embryo to larval 4 (L4) stage and RNAs were isolated. RNA-seq analysis on the Illumina platform revealed 541 genes up- and 261 genes down-regulated at a cutoff of 2-fold change and false discovery rate-corrected significance q < 0.05. Among the up-regulated genes were those previously shown to increase under oxidative stress conditions including hsp-16.11 (2.5-fold), gst-35 (10.1-fold), and fmo-2(58.5-fold). In addition, we observed up-regulation of 6 out of 7 lipocalin related (lpr) family genes and down regulation of 7 out of 15 activated in blocked unfolded protein response (abu) genes. Gene Ontology enrichment analysis highlighted the effect of genes related to development and organism growth. miRNA-seq analysis revealed 6–8 fold down regulation of mir-37-3p, mir-41-5p, mir-70-3p, and mir-75-3p. Our results demonstrate the effects of MeHg on specific transcripts encoding proteins in oxidative stress responses and in ER stress pathways. Pending confirmation of these transcript changes at protein levels, their association and dissocation characteristics with interaction partners, and integration of these signals, these findings indicate broad and dynamic mechanisms by which MeHg exerts its harmful effects

Chemical Characterization of Gas- and Particle-Phase Products from the Ozonolysis of alpha-Pinene in the Presence of Dimethylamine

Amines are recognized as key compounds in new particle formation (NPF) and secondary organic aerosol (SOA) formation. In addition, ozonolysis of a-pinene contributes substantially to the formation of biogenic SOAs in the atmosphere. In the present study, ozonolysis of a-pinene in the presence of dimethylamine (DMA) was investigated in a flow tube reactor. Effects of amines on SOA formation and chemical composition were examined. Enhancement of NPF and SOA formation was observed in the presence of DMA. Chemical characterization of gas and particle-phase products by high-resolution mass spectrometric techniques revealed the formation of nitrogen containing compounds. Reactions between ozonolysis reaction products of a-pinene, such as pinonaldehyde or pinonic acid, and DMA were observed. Possible reaction pathways are suggested for the formation of the reaction products. Some of the compounds identified in the laboratory study were also observed in aerosol samples (PM1) collected at the SMEAR II station (Hyytiala, Finland) suggesting that DMA might affect the ozonolysis of a-pinene in ambient conditions.Peer reviewe