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

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

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

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

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

Differences in Gene Expression between Mouse and Human for Dynamically Regulated Genes in Early Embryo

Peer reviewe

High-throughput mutational screening adds clinically important information in myelodysplastic syndromes and secondary or therapy-related acute myeloid leukemia

Non peer reviewe

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

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

The TLR signalling adaptor TRIF/TICAM-1 has an N-terminal helical domain with structural similarity to IFIT proteins

TRIF/TICAM-1 (TIR domain-containing adaptor inducing interferon-beta/TIR domain-containing adaptor molecule 1) is the adaptor protein in the Toll-like receptor (TLR) 3 and 4 signalling pathway that leads to the production of type 1 interferons and cytokines. The signalling involves TIR (Toll/interleukin-1 receptor) domain-dependent TRIF oligomerization. A protease-resistant N-terminal region is believed to be involved in self-regulation of TRIF by interacting with its TIR domain. Here, the structural and functional characterization of the N-terminal domain of TRIF (TRIF-NTD) comprising residues 1-153 is reported. The 2.22 angstrom resolution crystal structure was solved by single-wavelength anomalous diffraction (SAD) using selenomethionine-labelled crystals of TRIF-NTD containing two additional introduced Met residues (TRIF-NTDA66M/L113M). The structure consists of eight antiparallel helices that can be divided into two subdomains, and the overall fold shares similarity to the interferon-induced protein with tetratricopeptide repeats (IFIT) family of proteins, which are involved in both the recognition of viral RNA and modulation of innate immune signalling. Analysis of TRIF-NTD surface features and the mapping of sequence conservation onto the structure suggest several possible binding sites involved in either TRIF auto-regulation or interaction with other signalling molecules or ligands. TRIF-NTD suppresses TRIF-mediated activation of the interferon-beta promoter, as well as NF-kappa B-dependent reporter-gene activity. These findings thus identify opportunities for the selective targeting of TLR3- and TLR4-mediated inflammation

iGentifier: indexing and large-scale profiling of unknown transcriptomes

Development and refinement of methods to analyse differential gene expression has been essential in the progress of molecular biology. A novel approach called iGentifier is presented for profiling known and unknown transcriptomes, thus bypassing a major limitation in microarray analysis. The iGentifier technology combines elements of fragment display (e.g. Differential Display or RMDD) and tag sequencing (e.g. SAGE, MPSS) and allows for analysis of samples in high throughput using current capillary electrophoresis equipment. Application to epidermal tissue of wild-type and mlo5 barley (Hordeum vulgare) plants, infected with powdery mildew [Blumeria graminis (DC.) E.O. Speer f.sp.hordei], led to the identification of several 100 genes induced or repressed upon infection with many well known for their response to fungal pathogens or other stressors. Ten of these genes are suggested to be classified as marker genes for durable resistance mediated by the mlo5 resistance gene