VPS13D bridges the ER to mitochondria and peroxisomes via Miro

Mitochondria, which are excluded from the secretory pathway, depend on lipid transport proteins for their lipid supply from the ER, where most lipids are synthesized. In yeast, the outer mitochondrial membrane GTPase Gem1 is an accessory factor of ERMES, an ER–mitochondria tethering complex that contains lipid transport domains and that functions, partially redundantly with Vps13, in lipid transfer between the two organelles. In metazoa, where VPS13, but not ERMES, is present, the Gem1 orthologue Miro was linked to mitochondrial dynamics but not to lipid transport. Here we show that Miro, including its peroxisome-enriched splice variant, recruits the lipid transport protein VPS13D, which in turn binds the ER in a VAP-dependent way and thus could provide a lipid conduit between the ER and mitochondria. These findings reveal a so far missing link between function(s) of Gem1/Miro in yeast and higher eukaryotes, where Miro is a Parkin substrate, with potential implications for Parkinson’s disease pathogenesis.     

Notes on the genus Orobanche in Italy: 3. Taxa described by A. Bertoloni

Abstract

Original material of the 12 taxa described as new by Bertoloni has been examined, and typification of their names is discussed. Lectotypes are designated for 11 of Bertoloni's names, one (O. densiflora Bertol.) had been lectotypified before. Orobanche bicolor Bertol. (non C. A. Mey.) belongs to O. cernua L., O. cruenta Bertol. to O. gracilis Sm., O. stricta Moris ex Bertol. to O. schultzii Mutel, O. thyrsoidea Moris ex Bertol to O. rigens Loisel., O. crithmi Bertol. to O. minor Sm., O. vitalbae Bertol. to O. artemisiae-campestris Gaudin, O. fragrantissima Bertol. to O. lutea Baumg., O. laurina Bertol. to O. hederae Duby, O. yuccae Savi f. ex Bertol. to O. hederae Duby (not to O. minor Sm.), O. centaurina Bertol. to O. litorea Guss. (not to O. artemisiae-campestris Gaudin). O. australis Moris ex Bertol., included by Beck in O. canescens C. Presl, is a good species restricted to Sardinia. O. densiflora Bertol. must not, as is customary, be ascribed to Reuter who republished it later.     

A phytosociological analysis of abandoned terraced olive grove shrublands in the Tyrrhenian district of Central Italy

ABSTRACT

A phytosociological study of the shrubland communities which colonise abandoned terraced olive groves in the Tyrrhenian district of Central Italy is presented here. The vegetational analysis was carried out using the Braun Blanquet phytosociological approach. Two main types of shrubland communities characterising distinct environmental conditions occur within abandoned terraced olive groves. On the one hand, there are those scrub types which tend to occupy the central part of the terrace; on the other hand, there are the scrubs types which develop along the stone walls bordering the terrace. Different phytosociological associations, sub-associations, and variants ranging from Pistacio-Rhamnetalia alaternii to Prunetalia spinosae are recognised and described. In the warm dry areas, both Myrto-Lentiscetum and Rhamno-Euphorbietum dendroidis occur. Also, a new Oleo-Ceratonion sub-association (Myrto-Lentiscetum spartietosum junceii) is presented here for the first time. In the inner zones of the study area, a range of aspects characterising a new Pruno-Rubion ulmifolii community type (Roso-Rubetum ulmifolii ass. nova) are identified.     

Analisi citologica di alcune specie del genere Vicia

Abstract

Karyology of some species of Vicia. The species studied are: Vicia articulata, Vicia monantha, Vicia narbonensis and Vicia ervilia.

The chromosome number 2n = 14 counted for the first three species agrees with that reported in literature; that of Vicia monantha (2n=14) agrees with that quoted by Heitz, while Senn finds 2n=12.

Karyotypes of V. narbonensis and V. ervilia show appreciable differences from those reported in literature.     

Aegilops (Poaceae) in Italy: taxonomy,geographical distribution,ecology, vulnerability and conservation

ABSTRACT

Aegilops L. includes wild species from which, over millennia, man has cultivated forms of Triticum L. Ten species of Aegilops occur in Italy. Three species are allochthonous and eight out of ten species are recorded in the Apulia region. Five out of the ten species have been included in Red Lists. Each taxon is presented and discussed, citing old and new sites of occurrence, by examining specimens from many different herbaria, and describing their ecology and habitats, according to the Directive 92/43 EEC. A new taxonomic key, for the identification of all Aegilops species growing in Italy, is provided. The occurrence of Aegilops caudata L., A. peregrina (Hack. in J. Fraser) Maire & Weiller and A. speltoides Tausch in Italy is doubtful.     

M-Finder: Uncovering functionally associated proteins from interactome data integrated with GO annotations

Background

Protein-protein interactions (PPIs) play a key role in understanding the mechanisms of cellular processes. The availability of interactome data has catalyzed the development of computational approaches to elucidate functional behaviors of proteins on a system level. Gene Ontology (GO) and its annotations are a significant resource for functional characterization of proteins. Because of wide coverage, GO data have often been adopted as a benchmark for protein function prediction on the genomic scale.

Results

We propose a computational approach, called M-Finder, for functional association pattern mining. This method employs semantic analytics to integrate the genome-wide PPIs with GO data. We also introduce an interactive web application tool that visualizes a functional association network linked to a protein specified by a user. The proposed approach comprises two major components. First, the PPIs that have been generated by high-throughput methods are weighted in terms of their functional consistency using GO and its annotations. We assess two advanced semantic similarity metrics which quantify the functional association level of each interacting protein pair. We demonstrate that these measures outperform the other existing methods by evaluating their agreement to other biological features, such as sequence similarity, the presence of common Pfam domains, and core PPIs. Second, the information flow-based algorithm is employed to discover a set of proteins functionally associated with the protein in a query and their links efficiently. This algorithm reconstructs a functional association network of the query protein. The output network size can be flexibly determined by parameters.

Conclusions

M-Finder provides a useful framework to investigate functional association patterns with any protein. This software will also allow users to perform further systematic analysis of a set of proteins for any specific function. It is available online at http://bionet.ecs.baylor.edu/mfinder

     

Prognostic impact of coronary microcirculation abnormalities in systemic sclerosis: a prospective study to evaluate the role of non-invasive tests

Introduction

Microcirculation dysfunction is a typical feature of systemic sclerosis (SSc) and represents the earliest abnormality of primary myocardial involvement. We assessed coronary microcirculation status by combining two functional tests in SSc patients and estimating its impact on disease outcome.

Methods

Forty-one SSc patients, asymptomatic for coronary artery disease, were tested for coronary flow velocity reserve (CFR) by transthoracic-echo-Doppler with adenosine infusion (A-TTE) and for left ventricular wall motion abnormalities (WMA) by dobutamine stress echocardiography (DSE). Myocardial multi-detector computed tomography (MDCT) enabled the presence of epicardial stenosis, which could interfere with the accuracy of the tests, to be excluded. Patient survival rate was assessed over a 6.7- ± 3.5-year follow-up.

Results

Nineteen out of 41 (46%) SSc patients had a reduced CFR (≤2.5) and in 16/41 (39%) a WMA was observed during DSE. Furthermore, 13/41 (32%) patients showed pathological CFR and WMA. An inverse correlation between wall motion score index (WMSI) during DSE and CFR value (r = -0.57, P <0.0001) was observed; in addition, CFR was significantly reduced (2.21 ± 0.38) in patients with WMA as compared to those without (2.94 ± 0.60) (P <0.0001). In 12 patients with abnormal DSE, MDCT was used to exclude macrovasculopathy. During a 6.7- ± 3.5-year follow-up seven patients with abnormal coronary functional tests died of disease-related causes, compared to only one patient with normal tests.

Conclusions

A-TTE and DSE tests are useful tools to detect non-invasively pre-clinical microcirculation abnormalities in SSc patients; moreover, abnormal CFR and WMA might be related to a worse disease outcome suggesting a prognostic value of these tests, similar to other myocardial diseases.     

Manganese Tetraphenylporphyrins Catalyzed Selective Oxidation of Purine Derivatives

Abstract

The oxidation of purine derivatives using porphyrins as catalysts and dimethyldioxirane (DMDO) as oxygen atom donor is reported. The regioselectivity of the oxidation was found to be dependent on the presence of a free OH moiety on the N(9)-side chain of the substrate and on the structure of the catalyst.     

Synthesis of Novel 5′-Uridine-Head Amphiphiles as Model for DNA Molecular Recognition

Here we describe uridine functionalization in the 5′ position, which provides new classes of cationic and nonionic amphiphiles specifically designed as DNA transfection agents. The synthetic procedures developed to obtain the cationic uridine-head surfactants prevented intramolecular cyclization that occurs when uridine is functionalized in this position without using protecting groups in the uracil.