INDIGO-DataCloud: a Platform to Facilitate Seamless Access to E-Infrastructures

[EN] This paper describes the achievements of the H2020 project INDIGO-DataCloud. The project has provided e-infrastructures with tools, applications and cloud framework enhancements to manage the demanding requirements of scientific communities, either locally or through enhanced interfaces. The middleware developed allows to federate hybrid resources, to easily write, port and run scientific applications to the cloud. In particular, we have extended existing PaaS (Platform as a Service) solutions, allowing public and private e-infrastructures, including those provided by EGI, EUDAT, and Helix Nebula, to integrate their existing services and make them available through AAI services compliant with GEANT interfederation policies, thus guaranteeing transparency and trust in the provisioning of such services. Our middleware facilitates the execution of applications using containers on Cloud and Grid based infrastructures, as well as on HPC clusters. 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Perturbation of the Dimer Interface of Triosephosphate Isomerase and its Effect on Trypanosoma cruzi

Most of the enzymes of parasites have their counterpart in the host. Throughout evolution, the three-dimensional architecture of enzymes and their catalytic sites are highly conserved. Thus, identifying molecules that act exclusively on the active sites of the enzymes from parasites is a difficult task. However, it is documented that the majority of enzymes consist of various subunits, and that conservation in the interface of the subunits is lower than in the catalytic site. Indeed, we found that there are significant differences in the interface between the two subunits of triosephosphate isomerase from Homo sapiens and Trypanosoma cruzi (TcTIM), which causes Chagas disease in the American continent. In the search for agents that specifically inhibit TcTIM, we found that 2,2′-dithioaniline (DTDA) is far more effective in inactivating TcTIM than the human enzyme, and that its detrimental effect is due to perturbation of the dimer interface. Remarkably, DTDA prevented the growth of Escherichia coli cells that had TcTIM instead of their own TIM and killed T. cruzi epimastigotes in culture. Thus, this study highlights a new approach base of targeting molecular interfaces of dimers

Distinct colonization patterns and cDNA-AFLP transcriptome profiles in compatible and incompatible interactions between melon and different races of Fusarium oxysporum f. sp. melonis

Background: Fusarium oxysporum f. sp. melonis Snyd. & Hans. (FOM) causes Fusarium wilt, the most important infectious disease of melon (Cucumis melo L.). The four known races of this pathogen can be distinguished only by infection on appropriate cultivars. No molecular tools are available that can discriminate among the races, and the molecular basis of compatibility and disease progression are poorly understood. Resistance to races 1 and 2 is controlled by a single dominant gene, whereas only partial polygenic resistance to race 1,2 has been described. We carried out a large-scale cDNA-AFLP analysis to identify host genes potentially related to resistance and susceptibility as well as fungal genes associated with the infection process. At the same time, a systematic reisolation procedure on infected stems allowed us to monitor fungal colonization in compatible and incompatible host-pathogen combinations. Results: Melon plants (cv. Charentais Fom-2), which are susceptible to race 1,2 and resistant to race 1, were artificially infected with a race 1 strain of FOM or one of two race 1,2 w strains. Host colonization of stems was assessed at 1, 2, 4, 8, 14, 16, 18 and 21 days post inoculation (dpi), and the fungus was reisolated from infected plants. Markedly different colonization patterns were observed in compatible and incompatible host-pathogen combinations. Five time points from the symptomless early stage (2 dpi) to obvious wilting symptoms (21 dpi) were considered for cDNA-AFLP analysis. After successful sequencing of 627 transcript-derived fragments (TDFs) differentially expressed in infected plants, homology searching retrieved 305 melon transcripts, 195 FOM transcripts expressed in planta and 127 orphan TDFs. RNA samples from FOM colonies of the three strains grown in vitro were also included in the analysis to facilitate the detection of in planta-specific transcripts and to identify TDFs differentially expressed among races/strains. Conclusion: Our data suggest that resistance against FOM in melon involves only limited transcriptional changes, and that wilting symptoms could derive, at least partially, from an active plant response. We discuss the pathogen-derived transcripts expressed in planta during the infection process and potentially related to virulence functions, as well as transcripts that are differentially expressed between the two FOM races grown in vitro. These transcripts provide candidate sequences that can be further tested for their ability to distinguish between races. Sequence data from this article have been deposited in GenBank, Accession Numbers: HO867279-HO867981

A simple method to obtain essential oils from Salvia triloba L. and Laurus nobilis L. by using microwave-assisted hydrodistillation

A microwave-assisted hydrodistillation protocol was modified to extract essential oils from leaves of Salvia triloba L. and Laurus nobilis L. The essential oils of these plants are generally obtained by hydrodistillation or steam distillation. The volatile compounds obtained by microwave-assisted hydrodistillation and hydrodistillation methods were analyzed by GC and GC/MS. Both distillation methods and analytical results were compared. 1,8-Cineole (46.8-54.2%) was the main component in the leaf oils of both samples. Although the distillation was accomplished in a shorter time, oil yields and 1,8-cineole contents were slightly higher in the microwave-assisted hydrodistillation compared to usual hydrodistillation. Microwave-assisted hydrodistillation appears to be an effective method for the production of essential oils

Determining anatomical localizations of cervical esophagus, hiatal clamp and esophagogastric junction with esophagogastroduodenoscopy

Background: In this study, the purpose was to determine the anatomical localizations of the cervical esophagus length, hiatal clamp, and esophagogastric junction depending on age and gender in patients who undergo Esophagogastroduodenoscopy (EGD). Materials and methods: The images of the patients who underwent EGD between 2018 and 2020 were analyzed retrospectively in this study. The distance of the anatomical localizations of the cervical esophagus length, hiatal clamp, and esophagogastric junction to the anterior incisors, and the relations of this distance with the demographic characteristics and clinical manifestations of the patients were investigated on the esophagogastroduodenoscopy data. Results: A total of 298 patients (174 women/124 men) were included in the study. The cervical esophagus length and the distance of the esophagogastric junction and  hiatal clamp localization of the patients were found to be 15.06±0.57 cm, 37.51±2.23 cm and 38.62±2.23 cm, respectively. It was also found that the mean values ​​of all lengths in males were higher at a statistically significant level than in females (p<0.001; p<0.01). Conclusions: Knowing these anatomical localizations may be important in predicting complications that may occur in this region in EGD and planning the precautions to be taken. We also believe that it will guide clinicians in determining hiatal hernia and related deficiencies