159 research outputs found

    The zebrafish transcriptome during early development

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    <p>Abstract</p> <p>Background</p> <p>The transition from fertilized egg to embryo is accompanied by a multitude of changes in gene expression, and the transcriptional events that underlie these processes have not yet been fully characterized. In this study RNA-Seq is used to compare the transcription profiles of four early developmental stages in zebrafish (<it>Danio rerio</it>) on a global scale.</p> <p>Results</p> <p>An average of 79 M total reads were detected from the different stages. Out of the total number of reads 65% - 73% reads were successfully mapped and 36% - 44% out of those were uniquely mapped. The total number of detected unique gene transcripts was 11187, of which 10096 were present at 1-cell stage. The largest number of common transcripts was observed between 1-cell stage and 16-cell stage. An enrichment of gene transcripts with molecular functions of DNA binding, protein folding and processing as well as metal ion binding was observed with progression of development. The sequence data (accession number ERP000635) is available at the European Nucleotide Archive.</p> <p>Conclusion</p> <p>Clustering of expression profiles shows that a majority of the detected gene transcripts are present at steady levels, and thus a minority of the gene transcripts clusters as increasing or decreasing in expression over the four investigated developmental stages. The three earliest developmental stages were similar when comparing highly expressed genes, whereas the 50% epiboly stage differed from the other three stages in the identity of highly expressed genes, number of uniquely expressed genes and enrichment of GO molecular functions. Taken together, these observations indicate a major transition in gene regulation and transcriptional activity taking place between the 512-cell and 50% epiboly stages, in accordance with previous studies.</p

    Transposon- and Genome Dynamics in the Fungal Genus Neurospora: Insights from Nearly Gapless Genome Assemblies

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    A large portion of nuclear DNA is composed of transposable element (TE) sequences, whose transposition is controlled by diverse host defense strategies in order to maintain genomic integrity. One such strategy is the fungal-specific Repeat-Induced Point mutation (RIP) that hyper-mutates repetitive DNA sequences. While RIP is found across Fungi, it has been shown to vary in efficiency. The filamentous ascomycete Neurospora crassa has been a pioneer in the study of RIP, but data on TEs and RIP from other species in the genus is limited. In this study, we investigated 18 nearly gapless genome assemblies of ten Neurospora species, which diverged from a common ancestor about 7 MYA, to determine and compare genome-wide TE distribution and their associated RIP patterns. Four of these assemblies, generated by PacBio technology, represent new genomic datasets. We showed that the TE contents between 8.7-18.9% covary with genome sizes that range between 37.8-43.9 Mb. Degraded copies of Long Terminal Repeat (LTR) retrotransposons were abundant among the identified TEs, and these are distributed across the genome at varying frequencies. In all investigated Neurospora genomes, TE sequences had signs of numerous C-to-T substitutions, suggesting that RIP occurred in all species, and accordingly, RIP signatures correlated with TE-dense regions in all genomes. In conclusion, essentially gapless genome assemblies allowed us to identify TEs in Neurospora genomes, and reveal that TEs contribute to genome size variation in this group. Our study suggests that TEs and RIP are highly correlated in each examined Neurospora species, and hence, the pattern of interaction is conserved over the investigated evolutionary timescale. Finally, with our results, we verify that RIP signatures can be used to facilitate the identification of TE-rich region in the genome. The comprehensive genomic dataset of Neurospora is a rich resource for further in-depth analyses of fungal genomes by the community

    O CONSTITUCIONALISMO ANDINO E A UNASUL: UMA INTEGRAÇÃO PELA CONSTITUIÇÃO

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    O presente estudo tem por objeto a análise sobre o Constitucionalismo Andino, inaugurado pelas Constituições do Equador (2008) e da Bolívia (2009), e suas características que trouxeram novas luzes para o Direito Constitucional mundial, como o reconhecimento aos direitos da natureza, ao pluralismo jurídico, à democracia participativa e aos direitos humanos, com ênfase em uma política do “buen vivir”. Em seguida abordar-se-á sobre a UNASUL, como mais recente tentativa de integração regional sul-americana, traçando-se, por fim, um paralelo entre ambos, pontuando-se como o Constitucionalismo Andino pode contribuir para o processo de integração almejado pela UNASUL. Cuida-se, portanto, de uma pesquisa bibliográfica e legislativa que conclui que, não obstante ser tanto o Constitucionalismo Andino como a UNASUL movimentos em construção, ambos assentam especial relevância para uma política de redução das desigualdades que tanto afetam a América Latina, na busca constante de sociedades verdadeiramente democráticas e pluralistas. O presente estudo visa apontar a possibilidade de a UNASUL, como novo projeto de integração sul-americana em vigor, ser ponte para uma união regional que ultrapasse o viés meramente econômico e possa enfim lograr êxito na construção de uma identidade sul-americana verdadeiramente preocupada com o bem-estar do homem em sua integralidade

    Digitalisering i dagligvarehandel – en studie om påvirkningsfaktorene ved bruk av selvbetjening

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    I dette studiet undersøker vi hvilke faktorer som påvirker forbrukeres evne og villighet til å ta i bruk selvbetjeningssystemer. Vi undersøker også endring i kjøpsatferd som følge av Covid- 19-pandemien, og bruker resultater fra disse for å konkludere i vår problemstilling. Strukturen i oppgaven følger vår egenutviklede modell, basert på teori fra flere fagartikler og litteratur. Analysen og resultatene baserer seg på svar fra 802 respondenter fordelt på forskjellige aldersgrupper fra hele landet. Metoden vi tar i bruk er et bekvemmelighetsutvalg gjennom en nettbasert spørreundersøkelse, distribuert gjennom ulike sosiale medier. Fra disse kartlegger vi viktigheten av flere attributter, samt deres egne formeninger om endring i kjøpsatferden. Vi har også innhentet sekundærdata fra Meny AS, for å underbygge påstandene i studiet. Ved bruk av illustrasjoner som den overordnede modellen og enkle diagrammer, gir vi leseren gode forutsetninger for å forstå innholdet i både analysene og studiet i sin helhet. Gjennom grundige analyser ved hjelp av Excel og SPSS, vurderer vi økt mottakelighet for selvbetjening etter pandemien. Dette baserer vi på funn i analysene, der vi ser tydelige korrelasjoner mellom funksjoner ved selvbetjeningssystemet, samt ulike variabler tilknyttet personlige faktorer. Resultatene vi avdekker er interessante og åpner for videre forskning og utviklingsmuligheter hos Meny AS

    Apparent non-canonical trans-splicing is generated by reverse transcriptase in vitro

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    Trans-splicing, the in vivo joining of two RNA molecules, is well characterized in several groups of simple organisms but was long thought absent from fungi, plants and mammals. However, recent bioinformatic analyses of expressed sequence tag (EST) databases suggested widespread trans-splicing in mammals^1-2^. Splicing, including the characterised trans-splicing systems, involves conserved sequences at the splice junctions. Our analysis of a yeast non-coding RNA revealed that around 30% of the products of reverse transcription lacked an internal region of 117 nt, suggesting that the RNA was spliced. The junction sequences lacked canonical splice-sites but were flanked by direct repeats, and further analyses indicated that the apparent splicing actually arose because reverse transcriptase can switch templates during transcription^3^. Many newly identified, apparently trans-spliced, RNAs lacked canonical splice sites but were flanked by short regions of homology, leading us to question their authenticity. Here we report that all reported categories of non-canonical splicing could be replicated using an in vitro reverse transcription system with highly purified RNA substrates. We observed the reproducible occurrence of ostensible trans-splicing, exon shuffling and sense-antisense fusions. The latter generate apparent antisense non-coding RNAs, which are also reported to be abundant in humans^4^. Different reverse transcriptases can generate different products of template switching, providing a simple diagnostic. Many reported examples of splicing in the absence of canonical splicing signals may be artefacts of cDNA preparation

    Dominant Mutations in GRHL3 Cause Van der Woude Syndrome and Disrupt Oral Periderm Development

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    Mutations in interferon regulatory factor 6 (IRF6) account for ∼70% of cases of Van der Woude syndrome (VWS), the most common syndromic form of cleft lip and palate. In 8 of 45 VWS-affected families lacking a mutation in IRF6, we found coding mutations in grainyhead-like 3 (GRHL3). According to a zebrafish-based assay, the disease-associated GRHL3 mutations abrogated periderm development and were consistent with a dominant-negative effect, in contrast to haploinsufficiency seen in most VWS cases caused by IRF6 mutations. In mouse, all embryos lacking Grhl3 exhibited abnormal oral periderm and 17% developed a cleft palate. Analysis of the oral phenotype of double heterozygote (Irf6+/−;Grhl3+/−) murine embryos failed to detect epistasis between the two genes, suggesting that they function in separate but convergent pathways during palatogenesis. Taken together, our data demonstrated that mutations in two genes, IRF6 and GRHL3, can lead to nearly identical phenotypes of orofacial cleft. They supported the hypotheses that both genes are essential for the presence of a functional oral periderm and that failure of this process contributes to VWS
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