RNA, Genome Output and Input

RNA, the transcriptional output of genomes, not only templates protein synthesis or directly engages in catalytic functions, but can feed back to the genome and serve as regulatory input for gene expression. Transcripts affecting the RNA abundance of other genes act by mechanisms similar to and in concert with protein factors that control transcription. Through recruitment or blocking of activating and silencing complexes to specific genomic loci, RNA and protein factors can favor transcription or lower the local gene expression potential. Most regulatory proteins enter nuclei from all directions to start the search for increased affinity to specific DNA sequences or to other proteins nearby genuine gene targets. In contrast, RNAs emerge from spatial point sources within nuclei, their encoding genes. A transcriptional burst can result in the local appearance of multiple nascent RNA copies at once, in turn increasing local nucleic acid density and RNA motif abundance before diffusion into the nuclear neighborhood. The confined initial localization of regulatory RNAs causing accumulation of protein co-factors raises the intriguing possibility that target specificity of non-coding, and probably coding, RNAs is achieved through gene/RNA positioning and spatial proximity to regulated genomic regions. Here we review examples of positional cis conservation of regulatory RNAs with respect to target genes, spatial proximity of enhancer RNAs to promoters through DNA looping and RNA-mediated formation of membrane-less structures to control chromatin structure and expression. We speculate that linear and spatial proximity between regulatory RNA-encoding genes and gene targets could possibly ease the evolutionary pressure on maintaining regulatory RNA sequence conservation

Electron microprobe analysis of cryolite

Comunicação apresentada em: EMAS 2013 : 13th European Workshop on Modern Developments and Applications in Microbeam Analysis, Centro de Congressos da Alfândega do Porto, Portugal, 12 to 16 May 2013A sample of cryolite was studied with a JEOL JXA 8500-F electron microprobe under several operating conditions. A TAP crystal was used to analyse Na and Al and a LDE1 crystal to analyse F. As F and Na are both highly "volatile" elements, special care must be taken during analysis. The measurement order of Na, F and Al is not irrelevant and optimum conditions may also result in different combinations of accelerating voltage, beam current, beam size or counting times. Relevant X-ray signals were recorded in order to investigate the behaviour of the Na Ka and F Ka counts with elapsed time. The incident beam current was also recorded at the same time. In a clear contrast to what has normally been reported in the EPMA analysis of aluminosilicates and silicate glasses, we found that the Na X-ray counts increase with time. This increment of X-rays intensities for sodium in cryolite depends on the operating conditions and is accompanied by a strong migration of fluorine from the beam excitation volume, leading to a decrease in F X-ray counting rates. It was also observed that higher incident beam currents induce higher radiation damage in the mineral. The current instability is consistent with possible electron induced dissociation in the cryolite structure. An analytical protocol was achieved for 6 kV and 15kV accelerating voltage for the correct EPMA analysis of cryolite

Copper Acts Synergistically With Fluconazole in Candida glabrata by Compromising Drug Efflux, Sterol Metabolism, and Zinc Homeostasis

Funding Information: This work was supported by (1) Project LISBOA-01-0145-FEDER-007660 (“Microbiologia Molecular, Estrutural e Celular”) funded by FEDER funds through COMPETE2020 – “Programa Operacional Competitividade e Internacionalização” (POCI); (2) “Fundação para a Ciência e a Tecnologia” (FCT) through programme IF (IF/00124/2015) to CP; (3) the European Union’s Horizon 2020 Research and Innovation Programme under grant agreement No. 810856; (4) COST Action CA15133, supported by COST (European Cooperation in Science and Technology); and (5) PPBI – Portuguese Platform of BioImaging (PPBI-POCI-01-0145-FEDER-022122) co-funded by national funds from OE – “Orçamento de Estado” and by FEDER. AG-C was supported by a FCT Ph.D. fellowship (SFRH/BD/118866/2016), and CA and VP by a FCT contract according to DL57/2016 (SFRH/BPD/74294/2010 and SFRH/BPD/87188/2012, respectively). Publisher Copyright: Copyright © 2022 Gaspar-Cordeiro, Amaral, Pobre, Antunes, Petronilho, Paixão, Matos and Pimentel.The synergistic combinations of drugs are promising strategies to boost the effectiveness of current antifungals and thus prevent the emergence of resistance. In this work, we show that copper and the antifungal fluconazole act synergistically against Candida glabrata, an opportunistic pathogenic yeast intrinsically tolerant to fluconazole. Analyses of the transcriptomic profile of C. glabrata after the combination of copper and fluconazole showed that the expression of the multidrug transporter gene CDR1 was decreased, suggesting that fluconazole efflux could be affected. In agreement, we observed that copper inhibits the transactivation of Pdr1, the transcription regulator of multidrug transporters and leads to the intracellular accumulation of fluconazole. Copper also decreases the transcriptional induction of ergosterol biosynthesis (ERG) genes by fluconazole, which culminates in the accumulation of toxic sterols. Co-treatment of cells with copper and fluconazole should affect the function of proteins located in the plasma membrane, as several ultrastructural alterations, including irregular cell wall and plasma membrane and loss of cell wall integrity, were observed. Finally, we show that the combination of copper and fluconazole downregulates the expression of the gene encoding the zinc-responsive transcription regulator Zap1, which possibly, together with the membrane transporters malfunction, generates zinc depletion. Supplementation with zinc reverts the toxic effect of combining copper with fluconazole, underscoring the importance of this metal in the observed synergistic effect. Overall, this work, while unveiling the molecular basis that supports the use of copper to enhance the effectiveness of fluconazole, paves the way for the development of new metal-based antifungal strategies.publishe

Keeping a parameter-sparse concept in agroforestry modeling while integrating new processes and dynamics: new developments in yield-safe

info:eu-repo/semantics/publishedVersio

Complex architecture and regulated expression of the Sox2ot locus during vertebrate development

The Sox2 gene is a key regulator of pluripotency embedded within an intron of a long noncoding RNA (ncRNA), termed Sox2 overlapping transcript (Sox2ot), which is transcribed in the same orientation. However, this ncRNA remains uncharacterized. Here we show that Sox2ot has multiple transcription start sites associated with genomic features that indicate regulated expression, including highly conserved elements (HCEs) and chromatin marks characteristic of gene promoters. To identify biological processes in which Sox2ot may be involved, we analyzed its expression in several developmental systems, compared to expression of Sox2. We show that Sox2ot is a stable transcript expressed in mouse embryonic stem cells, which, like Sox2, is down-regulated upon induction of embryoid body (EB) differentiation. However, in contrast to Sox2, Sox2ot is up-regulated during EB mesoderm-lineage differentiation. In adult mouse, Sox2ot isoforms were detected in tissues where Sox2 is expressed, as well as in different tissues, supporting independent regulation of expression of the ncRNA. Sox2dot, an isoform of Sox2ot transcribed from a distal HCE located >500 kb upstream of Sox2, was detected exclusively in the mouse brain, with enrichment in regions of adult neurogenesis. In addition, Sox2ot isoforms are transcribed from HCEs upstream of Sox2 in other vertebrates, including in several regions of the human brain. We also show that Sox2ot is dynamically regulated during chicken and zebrafish embryogenesis, consistently associated with central nervous system structures. These observations provide insight into the structure and regulation of the Sox2ot gene, and suggest conserved roles for Sox2ot orthologs during vertebrate development

Immediate and long-term microshear bond strength of resin-based cements to core build-up materials

To evaluate the microshear bond strength (?-SBS) between resin-based cements and core build-up materials after water storage. Material and Methods: Cylinders (1x1 mm) of conventional dual-cure resin cement (RelyX ARC, 3M ESPE), universal du

Canopy insect herbivores in the Azorean Laurisilva forests: key host plant species in a highly generalist insect community

Copyright © ECOGRAPHY 2005.This article explores patterns of insect herbivore distribution in the canopy of the Laurisilva forests on seven islands in the Azores archipelago. To our knowledge, this is one of the first extensive studied of this type in tree or shrub canopies of oceanic island ecosystems. One of the most frequently debated characteristics of such ecosystems is the likely prevalence of vague, ill-defined niches due to taxonomic disharmony, which may have implications for insect-plant interactions. For instance, an increase in ecological opportunities for generalist species is expected due to the lack of predator groups and reduced selection for chemical defence in host plants. The following two questions were addressed: 1) Are specialists rare species, and insect herbivore species randomly distributed among host plant species in the Azores? 2) Are the variances in insect herbivore species composition, frequency and richness explained by host plants or by regional island effects? We expect a proportional distribution of herbivore species between host plants, influenced by host frequency and distinct island effects; otherwise, deviation from expectation might suggest habitat preference for specific host tree crowns. Canopy beating tray samples were performed on seven islands, comprising 50 transects with 1 to 3 plant species each (10 replicates per species), giving 1320 samples from ten host species trees or shrubs in total. From a total of 129 insect herbivore species, a greater number of herbivore species was found on Juniperus brevifolia (s=65) and Erica azorica (s=53). However, the number of herbivore species per individual tree crown was higher for E. azorica than for any other host, on all islands, despite the fact that it was only the fourth more abundant plant. In addition, higher insect species richness and greater insect abundance were found on the trees of Santa Maria Island, the oldest in the archipelago. Insect species composition was strongly influenced by the presence of E. azorica, which was the only host plant with a characteristic fauna across the archipelago, whereas the fauna of other plant crowns was grouped by islands. The great insect occurrence on E. azorica reflects strong habitat fidelity, but only four species were clearly specialists. Our findings indicate a broadly generalist fauna. The simplicity of Azorean Laurisilva contributed to the understanding of insect-plant mechanisms in canopy forest habitats

Androgen responsive intronic non-coding RNAs

BACKGROUND: Transcription of large numbers of non-coding RNAs originating from intronic regions of human genes has been recently reported, but mechanisms governing their biosynthesis and biological functions are largely unknown. In this work, we evaluated the existence of a common mechanism of transcription regulation shared by protein-coding mRNAs and intronic RNAs by measuring the effect of androgen on the transcriptional profile of a prostate cancer cell line. RESULTS: Using a custom-built cDNA microarray enriched in intronic transcribed sequences, we found 39 intronic non-coding RNAs for which levels were significantly regulated by androgen exposure. Orientation-specific reverse transcription-PCR indicated that 10 of the 13 were transcribed in the antisense direction. These transcripts are long (0.5–5 kb), unspliced and apparently do not code for proteins. Interestingly, we found that the relative levels of androgen-regulated intronic transcripts could be correlated with the levels of the corresponding protein-coding gene (asGAS6 and asDNAJC3) or with the alternative usage of exons (asKDELR2 and asITGA6) in the corresponding protein-coding transcripts. Binding of the androgen receptor to a putative regulatory region upstream from asMYO5A, an androgen-regulated antisense intronic transcript, was confirmed by chromatin immunoprecipitation. CONCLUSION: Altogether, these results indicate that at least a fraction of naturally transcribed intronic non-coding RNAs may be regulated by common physiological signals such as hormones, and further corroborate the notion that the intronic complement of the transcriptome play functional roles in the human gene-expression program