Major G-Quadruplex Form of HIV-1 LTR Reveals a (3 + 1) Folding Topology Containing a Stem-Loop

Nucleic acids can form noncanonical four-stranded structures called G-quadruplexes. G-quadruplex-forming sequences are found in several genomes including human and viruses. Previous studies showed that the G-rich sequence located in the U3 promoter region of the HIV-1 long terminal repeat (LTR) folds into a set of dynamically interchangeable G-quadruplex structures. G-quadruplexes formed in the LTR could act as silencer elements to regulate viral transcription. Stabilization of LTR G-quadruplexes by G-quadruplex-specific ligands resulted in decreased viral production, suggesting the possibility of targeting viral G-quadruplex structures for antiviral purposes. Among all the G-quadruplexes formed in the LTR sequence, LTR-III was shown to be the major G-quadruplex conformation in vitro. Here we report the NMR structure of LTR-III in K+ solution, revealing the formation of a unique quadruplex-duplex hybrid consisting of a three-layer (3 + 1) G-quadruplex scaffold, a 12-nt diagonal loop containing a conserved duplex-stem, a 3-nt lateral loop, a 1-nt propeller loop, and a V-shaped loop. Our structure showed several distinct features including a quadruplex-duplex junction, representing an attractive motif for drug targeting. The structure solved in this study may be used as a promising target to selectively impair the viral cycle

Conserved G-quadruplexes regulate the immediate early promoters of human alphaherpesviruses

Human Alphaherpesviruses comprise three members, herpes simplex virus (HSV) 1 and 2 and varicella zoster virus (VZV). These viruses are characterized by a lytic cycle in epithelial cells and latency in the nervous system, with lifelong infections that may periodically reactivate and lead to serious complications, especially in immunocompromised patients. The mechanisms that regulate viral transcription have not been fully elucidated, but the master role of the immediate early (IE) genes has been established. G-quadruplexes are non-canonical nucleic-acid structures that control transcription, replication, and recombination in many organisms including viruses and that represent attractive antiviral targets. In this work, we investigate the presence, conservation, folding and activity of G-quadruplexes in the IE promoters of the Alphaherpesviruses. Our analysis shows that all IE promoters in the genome of HSV-1, HSV-2 and VZV contain fully conserved G-quadruplex forming sequences. These comprise sequences with long loops and bulges, and thus deviating from the classic G-quadruplex motifs. Moreover, their location is both on the leading and lagging strand and in some instances they contain exuberant G-tracts. Biophysical and biological analysis proved that all sequences actually fold into G-quadruplex under physiological conditions and can be further stabilized by the G-quadruplex ligand BRACO-19, with subsequent impairment of viral IE gene transcription in cells. These results help shed light on the control of viral transcription and indicate new viral targets to design drugs that impair the early steps of Alphaherpesviruses. In addition, they validate the significance of G-quadruplexes in the general regulation of viral cycles

Sobre a Existência e a Estabilidade de Movimentos Periódicos em Sistemas Com Vibro-impacto Com Folga Simétrica

Este trabalho apresenta a modelagem matemática de um sistema com vibro-impacto e excitação harmônica de base. O sistema tem sido estudado por vários pesquisadores que exploraram muitos aspectos da dinâmica global. No entanto, eles supuseram um único padrão de movimentos periódicos, isto é, um movimento com o mesmo período que a força de excitação. Este trabalho mostra que vários padrões de movimentos periódicos podem ocorrer e as condições de existência e estabilidade destes deve ser estudada cuidadosamente. As condições de periodicidade são aplicadas sobre o estado nos instantes de impactos a fim de obter um mapa do próximo impacto baseado no estado da anterior. Este mapa não-linear é aplicado para obter as condições de existência dos movimentos periódicos com padrões específicos. Aplicando as condições de existência, a estabilidade do movimento pode ser realizada por meio da análise dos autovalores do mapa, tendo em conta estas restrições. Palavras-chave: oscilações não-lineares, sistema mecânico não-suave, vibro-impacto, movimentos periódicos, estabilidade. ABSTRAC

HIV-1 Nucleocapsid Protein Unfolds Stable RNA G-Quadruplexes in the Viral Genome and Is Inhibited by G-Quadruplex Ligands

The G-quadruplexes that form in the HIV-1 RNA genome hinder progression of reverse transcriptase in vitro, but not in infected cells. We investigated the possibility that the HIV-1 nucleocapsid protein NCp7, which remains associated with the viral RNA during reverse transcription, modulated HIV-1 RNA G-quadruplex stability. By electrophoresis, circular dichroism, mass spectrometry, and reverse transcriptase stop assays, we demonstrated that NCp7 binds and unfolds the HIV-1 RNA G-quadruplexes and promotes DNA/RNA duplex formation, allowing reverse transcription to proceed. The G-quadruplex ligand BRACO-19 was able to partially counteract this effect. These results indicate NCp7 as the first known viral protein able to unfold RNA G-quadruplexes, and they explain how the extra-stable HIV-1 RNA G-quadruplexes are processed; they also point out that the reverse transcription process is hindered by G-quadruplex ligands at both reverse transcriptase and NCp7 level. This information can lead to the development of more effective anti-HIV-1 drugs with a new mechanism of action

Dynamics of Saccharomyces cerevisiae strains isolated from vine bark in vineyard: Influence of plant age and strain presence during grape must spontaneous fermentations

In this study, two vineyards of different age were chosen. During three years, a sampling campaign was performed for isolating vineyard-associated Saccharomyces cerevisiae (S. cerevisiae) strains. Bark portions and, when present, grape bunches were regularly collected from the same vine plants during the overall sampling period. Each bark portion was added to a synthetic must, while each grape bunch was manually crushed, and fermentations were run to isolate S. cerevisiae strains. All collected yeasts were identified at different species and strain levels to evaluate the genetic variability of S. cerevisiae strains in the two vineyards and strains dynamics. Moreover, bark-associated strains were compared with those isolated from spontaneous fermentations of grapes collected during the two harvests. Regarding the youngest vineyard, no S. cerevisiae was identified on bark and grape surface, highlighting the importance of vine age on yeast colonization. Results reported the isolation of S. cerevisiae from vine bark of the old vineyard at all sampling times, regardless of the presence of the grape bunch. Therefore, this environment can be considered an alternative ecological niche that permanently hosts S. cerevisiae. Bark-associated strains were not found on grape bunches and during pilot-scale vinifications, indicating no significative strain transfer from vine bark to the grape must. Commercial starters were identified as well both in vineyards and during vinifications

Deficiency of vitamins C and E in women of childbearing age in Brazil: a systematic review and meta-analysis

Background: Despite current policies of salt iodination, iodine deficiency is still a global public health problem, especially in women. So far, conflicting evidence has been suggested for the prevalence of iodine deficiency in Brazil. Objective: To estimate the prevalence of iodine deficiency and associated factors in women of childbearing age in Brazil. Methods: A systematic review was conducted using databases (PubMed, LILACS, WHO, Scopus, and Capes dissertation and thesis), from inception to May 2020. Meta-analyses of proportions were performed using the variance inverse for the fixed model. Reporting and methodological quality were assessed using the Joanna Briggs Institute tool to prevalence studies. Results: Our review identified seven studies published between 2002 e 2017, including 1354 participants, especially pregnant women. All studies presented at least one quality limitation, mainly regarding the sampling method (i.e., convenience) and small sample size. The prevalence of iodine deficiency ranged among studies from 16% to 62%. In contrast, the meta-analysis identified a mean prevalence of 40% (95% confidence interval, CI 37%-43%) for pregnant women and 13% (95% CI 4%-24%) for non-pregnant women. Cumulative meta-analysis suggests a tendency of higher iodine deficiency prevalence from 2018 in pregnant women. Conclusions: Although this systematic review identified studies with poor methodological and reporting quality, a high prevalence of iodine deficiency was identified in pregnant women, reinforcing the importance of national nutritional policies for monitoring iodine status in this population. Future studies should consider random probabilistic sampling, appropriate sample size, and pre-defined subgroup analysis to adequately inform the prevalence of iodine deficiency and associated factors in women of childbearing age and support health policies

Iodine deficiency in women of childbearing age in Brazil: systematic review and meta-analysis

Background: Despite current policies of salt iodination, iodine deficiency is still a global public health problem, especially in women. So far, conflicting evidence has been suggested for the prevalence of iodine deficiency in Brazil. Objective: To estimate the prevalence of iodine deficiency and associated factors in women of childbearing age in Brazil. Methods: A systematic review was conducted using databases (PubMed, LILACS, WHO, Scopus, and Capes dissertation and thesis), from inception to May 2020. Meta-analyses of proportions were performed using the variance inverse for the fixed model. Reporting and methodological quality were assessed using the Joanna Briggs Institute tool to prevalence studies. Results: Our review identified seven studies published between 2002 e 2017, including 1354 participants, especially pregnant women. All studies presented at least one quality limitation, mainly regarding the sampling method (i.e., convenience) and small sample size. The prevalence of iodine deficiency ranged among studies from 16% to 62%. In contrast, the meta-analysis identified a mean prevalence of 40% (95% confidence interval, CI 37%-43%) for pregnant women and 13% (95% CI 4%-24%) for non-pregnant women. Cumulative meta-analysis suggests a tendency of higher iodine deficiency prevalence from 2018 in pregnant women. Conclusions: Although this systematic review identified studies with poor methodological and reporting quality, a high prevalence of iodine deficiency was identified in pregnant women, reinforcing the importance of national nutritional policies for monitoring iodine status in this population. Future studies should consider random probabilistic sampling, appropriate sample size, and pre-defined subgroup analysis to adequately inform the prevalence of iodine deficiency and associated factors in women of childbearing age and support health policies.</jats:p

Dyads of G-Quadruplex Ligands Triggering DNA Damage Response and Tumour Cell Growth Inhibition at Subnanomolar Concentration

Naphthalene diimide (NDI) dyads exhibiting a different substitution pattern and linker length have been synthesised and evaluated as G-quadruplex (G4) ligands, by investigating their cytotoxicity in selected cell lines. The dyads with the long C7 linker exhibit extremely low IC50 values, below 10\u2005nm, on different cancer cell lines. Contrary, the dyads with the shorter C4 linker were much less effective, with IC values increasing up to 1\u2005\u3bcm. Among the three dyads with the longest linker, small differences in the IC50 values emerge, suggesting that the linker length plays a more important role than the substitution pattern. We have further shown that the dyads are able to induce cellular DNA damage response, which is not limited to the telomeric regions and is likely the origin of their cytotoxicity. Both absorption titration and dynamic light scattering of the most cytotoxic dyads in the presence of hTel22 highlight their ability to induce effective G4 aggregation, acting as non-covalent cross-linking agents

Metodologia para padronizar informações climáticas dos cenários futuros no banco de dados geográfico do projeto CLIMAPEST.

Estudos sobre os impactos das mudanças climáticas globais são importantes para atenuar seus possíveis impactos negativos. O objetivo deste trabalho foi desenvolver metodologia para padronizar as informações fornecidas pelos modelos climáticos globais do Quarto Relatório do IPCC (Painel Intergovernamental sobre Mudanças Climáticas), utilizando métodos de interpolação de dados a fim de que os planos de informação no banco de dados do SIG possuam as mesmas características de resolução espacial e limites geográficos

Determination of the orbital moment and crystal field splitting in LaTiO3_{3}

Utilizing a sum-rule in a spin-resolved photoelectron spectroscopic experiment with circularly polarized light, we show that the orbital moment in LaTiO$_3$ is strongly reduced both below and above the N\'{e}el temperature. Using Ti $L_{2,3}$ x-ray absorption spectroscopy as a local probe, we found that the crystal field splitting in the $t_{2g}$ subshell is about 0.12-0.30 eV. This large splitting does not facilitate the formation of an orbital liquid