VirF Relieves the Transcriptional Attenuation of the Virulence Gene icsA of Shigella flexneri Affecting the icsA mRNA-RnaG Complex Formation

VirF is the master activator of virulence genes of Shigella and its expression is required for the invasion of the human intestinal mucosa by pathogenic bacteria. VirF was shown to directly activate the transcription of virB and icsA, which encode two essential proteins involved in the pathogenicity process, by binding their promoter regions. In this study, we demonstrate by band shift, enzymatic probing and cross-linking experiments that VirF, in addition to DNA, can also bind the icsA transcript and RnaG, an antisense non-coding small RNA that promotes the premature termination of icsA mRNA through a transcriptional attenuation mechanism. Furthermore, we show that VirF binds in vitro also other species of RNAs, although with lower specificity. The existence of VirF-RnaG and VirF-icsA mRNA complexes is confirmed in a pulldown assay carried out under experimental conditions that very close reproduce the in vivo conditions and that allows immobilized VirF to "fish" out RnaG and icsA mRNA from a total RNA extract. The VirF binding sites identified on both icsA mRNA and RnaG contain a 13 nucleotides stretch (5'-UUUUaGYcUuUau-3') that is the RNA-converted consensus sequence previously proposed for the VirF-DNA interaction. Band-shift assays with a synthetic RNA molecule whose sequence perfectly matches the consensus indicate that this signature plays a key role also in the VirF-RNA interaction, in particular when exposed in a stem-loop structure. To further explore the icsA-RnaG-VirF regulatory system, we developed an in vitro test (RNA-RNA Pairing Assay) in which pairing between icsA mRNA and synthetic RNAs that reproduce the individual stem-loop motifs of RnaG, was analyzed in the presence of VirF. This assay shows that this protein can prevent the formation of the kissing complex, defined as the initial nucleation points for RNA heteroduplex formation, between RnaG and icsA mRNA. Consistently, VirF alleviates the RnaG-mediated repression of icsA transcription in vitro. Therefore VirF, by hindering the icsA transcript-RnaG interaction, exhibits an activity opposed to that usually displayed by proteins, which generally assist the RNA-RNA interaction; this quite uncommon and new function and the regulatory implications of VirF as a potential RNA-binding protein are discussed

Iron-Fortified Drinking Water Studies for the Prevention of Children's Anemia in Developing Countries

Anemia and iron deficiency should receive special attention considering their high prevalence and serious consequences. For prevention, globally it is recommended to increase dietary iron intake, iron fortification of industrialized foods, and medical iron supplementation. Food fortification for the prevention of iron deficiency in developing countries should consider carriers locally available and consumed daily, requiring limited infrastructure and technology. Drinking water is the iron carrier we have been working for years for the prevention of iron deficiency and anemia in small children in Brazil. It was shown that studies with iron-fortified drinking water were proved to be effective on children's anemia prevention. Water is found everywhere, consumed daily by everyone may be easily fortified with simple technology, is low priced and was effective on the prevention of children's anemia. Fortification of drinking water with iron was locally implemented with the direct participation of the government and community. Government authorities, health personnel and population were part of the project and responsible for its community implementation. The mayor/municipality permitted and supported the proposal to supply it to children at their day-care centers. To keep the children drinking water iron fortified supply an officially authorized legislation was also approved

Giant Shape-Persistent Tetrahedral Porphyrin System: Light-Induced Charge Separation

Tetraphenylmethane appended with four pyridylpyridinium units works as a scaffold to self-assemble four ruthenium porphyrins in a tetrahedral shape-persistent giant architecture. The resulting supramolecular structure has been characterised in the solid state by X-ray single crystal analysis and in solution by various techniques. Multinuclear NMR spectroscopy confirms the 1 : 4 stoichiometry with the formation of a highly symmetric structure. The self-assembly process can be monitored by changes of the redox potentials, as well as by modifications in the visible absorption spectrum of the ruthenium porphyrin and by a complete quenching of both the bright fluorescence of the tetracationic scaffold and the weak phosphorescence of the ruthenium porphyrin. An ultrafast photoinduced electron transfer is responsible for this quenching process. The lifetime of the resulting charge separated state (800 ps) is about four times longer in the giant supramolecular structure compared to the model 1 : 1 complex formed by the ruthenium porphyrin and a single pyridylpyridinium unit. Electron delocalization over the tetrameric pyridinium structure is likely to be responsible for this effect

A Flexible and Accurate Genotype Imputation Method for the Next Generation of Genome-Wide Association Studies

Genotype imputation methods are now being widely used in the analysis of genome-wide association studies. Most imputation analyses to date have used the HapMap as a reference dataset, but new reference panels (such as controls genotyped on multiple SNP chips and densely typed samples from the 1,000 Genomes Project) will soon allow a broader range of SNPs to be imputed with higher accuracy, thereby increasing power. We describe a genotype imputation method (IMPUTE version 2) that is designed to address the challenges presented by these new datasets. The main innovation of our approach is a flexible modelling framework that increases accuracy and combines information across multiple reference panels while remaining computationally feasible. We find that IMPUTE v2 attains higher accuracy than other methods when the HapMap provides the sole reference panel, but that the size of the panel constrains the improvements that can be made. We also find that imputation accuracy can be greatly enhanced by expanding the reference panel to contain thousands of chromosomes and that IMPUTE v2 outperforms other methods in this setting at both rare and common SNPs, with overall error rates that are 15%–20% lower than those of the closest competing method. One particularly challenging aspect of next-generation association studies is to integrate information across multiple reference panels genotyped on different sets of SNPs; we show that our approach to this problem has practical advantages over other suggested solutions

Reconstructing Bioinvasion Dynamics Through Micropaleontologic Analysis Highlights the Role of Temperature Change as a Driver of Alien Foraminifera Invasion

Invasive alien species threaten biodiversity and ecosystem structure and functioning, but incomplete assessments of their origins and temporal trends impair our ability to understand the relative importance of different factors driving invasion success. Continuous time-series are needed to assess invasion dynamics, but such data are usually difficult to obtain, especially in the case of small-sized taxa that may remain undetected for several decades. In this study, we show how micropaleontologic analysis of sedimentary cores coupled with radiometric dating can be used to date the first arrival and to reconstruct temporal trends of foraminiferal species, focusing on the alien Amphistegina lobifera and its cryptogenic congener A. lessonii in the Maltese Islands. Our results show that the two species had reached the Central Mediterranean Sea several decades earlier than reported in the literature, with considerable implications for all previous hypotheses of their spreading patterns and rates. By relating the population dynamics of the two foraminifera with trends in sea surface temperature, we document a strong relationship between sea warming and population outbreaks of both species. We conclude that the micropaleontologic approach is a reliable procedure for reconstructing the bioinvasion dynamics of taxa having mineralized remains, and can be added to the toolkit for studying invasions

Acute rejection features in dual kidney transplant recipients from elderly donors: comparison of calcineurin inhibitor-based and calcineurin inhibitor-free immunosuppressive protocols.

Features of acute rejection in dual kidney transplant have not been studied. The aim of this study is to compare acute rejections in dual kidney transplant recipients from elderly donors on different immunosuppressive protocols. Sixty-nine patients were evaluated: 28 received calcineurin inhibitor-based (group 1) and 41 received calcineurin inhibitor-free immunosuppression (group 2). Histology of all donor kidneys was evaluated before implantation. All rejections showed tubulitis in both groups, and were classified as T cell-mediated acute rejections. Incidence and Banff grade of rejections in the two groups were not significantly different. Late rejections however, were observed in group 1 ( P < 0.01) whereas steroid-resistant rejections occurred in group 2 ( P < 0.03). C4d deposition was only observed in group 2. Occurrence of acute rejection was significantly associated with graft loss due to interstitial fibrosis/tubular atrophy in both groups. In group 1 mean serum creatinine levels of patients with rejections at six months and one year were higher than those of patients without rejections ( P < 0.03 and P < 0.009, respectively). In group 2 they were higher at six months ( P < 0.01) but not at one year. In addition, graft loss due to interstitial fibrosis/tubular atrophy occurred in 3/28 patients in group 1 (10.7%, OR= 1.95, 95%CI 1.02–3.71), and in 1/41 patients in group 2 (2.4%, OR= 0.41, 95%CI 0.07–2.24). Taken together these results suggest better renal function in patients on calcineurin inhibitor-free immunosuppression. In conclusion, acute rejections were detrimental irrespective of the type of immunosuppression, but different features were observed with each therapy. A tailored approach should be advantageous for prevention and treatment of acute rejections

Mmf1p, a novel yeast mitochondrial protein conserved throughout evolution and involved in maintenance of the mitochondrial genome

A novel protein family (p14.5, or YERO57c/YJGFc) highly conserved throughout evolution has recently been identified. The biological role of these proteins is not yet well characterized. Two members of the p14.5 family are present in the yeast Saccharomyces cerevisiae. In this study, we have characterized some of the biological functions of the two yeast proteins. Mmf1p is a mitochondrial matrix factor, and homologous Mmf1p factor (Hmf1p) copurifies with the soluble cytoplasmic fraction. Δmmf1 cells lose mitochondrial DNA (mtDNA) and have a decreased growth rate, while Δhmf1 cells do not display any visible phenotype. Furthermore, we demonstrate by genetic analysis that Mmf1p does not play a direct role in replication and segregation of the mtDNA. rho(+) Δmmf1 haploid cells can be obtained when tetrads are directly dissected on medium containing a nonfermentable carbon source. Our data also indicate that Mmf1p and Hmf1p have similar biological functions in different subcellular compartments. Hmf1p, when fused with the Mmf1p leader peptide, is transported into mitochondria and is able to functionally replace Mmf1p. Moreover, we show that homologous mammalian proteins are functionally related to Mmf1p. Human p14.5 localizes in yeast mitochondria and rescues the Δmmf1-associated phenotypes. In addition, fractionation of rat liver mitochondria showed that rat p14.5, like Mmf1p, is a soluble protein of the matrix. Our study identifies a biological function for Mmf1p and furthermore indicates that this function is conserved between members of the p14.5 family

First results of the Kourovka Planet Search: discovery of transiting exoplanet candidates in the first three target fields

We present the first results of our search for transiting exoplanet candidates as part of the Kourovka Planet Search (KPS) project. The primary objective of the project is to search for new hot Jupiters which transit their host stars, mainly in the Galactic plane, in the $R_c$ magnitude range of 11 to 14 mag. Our observations were performed with the telescope of the MASTER robotic network, installed at the Kourovka astronomical observatory of the Ural Federal University (Russia), and the Rowe-Ackermann Schmidt Astrograph, installed at the private Acton Sky Portal Observatory (USA). As test observations, we observed three celestial fields of size $2\times2$ deg$^2$ during the period from 2012 to 2015. As a result, we discovered four transiting exoplanet candidates among the 39000 stars of the input catalogue. In this paper, we provide the description of the project and analyse additional photometric, spectral, and speckle interferometric observations of the discovered transiting exoplanet candidates. Three of the four transiting exoplanet candidates are most likely astrophysical false positives, while the nature of the fourth (most promising) candidate remains to be ascertained. Also, we propose an alternative observing strategy that could increase the project's exoplanet haul.Comment: 11 pages, 16 figures; Accepted for publication in Monthly Notices of the Royal Astronomical Society 201

Low-energy Coulomb excitation of 94Zr

Recent state-of-the-art Monte Carlo shell-model calculations predict shape coexistence in Zr isotopes. In this context, the 94Zr nucleus is particularly interesting since some experimental investigations have already suggested the possible coexistence of spherical and oblate shapes, however, no definitive conclusion on its deformation has been reported to date. As such, a dedicated experiment to study collectivity and configuration coexistence in 94Zr by means of a low-energy Coulomb excitation was performed. This study was performed at the INFN Legnaro National Laboratory with the GALILEO-SPIDER setup, which, in this instance, was further augmented with 6 Lanthanum Bromide scintillators (LaBr3:Ce) in order to to maximize the γ-ray detection efficiency