Comparative Analysis of the Saccharomyces cerevisiae and Caenorhabditis elegans Protein Interaction Network

Protein interaction networks aim to summarize the complex interplay of proteins in an organism. Early studies suggested that the position of a protein in the network determines its evolutionary rate but there has been considerable disagreement as to what extent other factors, such as protein abundance, modify this reported dependence. We compare the genomes of Saccharomyces cerevisiae and Caenorhabditis elegans with those of closely related species to elucidate the recent evolutionary history of their respective protein interaction networks. Interaction and expression data are studied in the light of a detailed phylogenetic analysis. The underlying network structure is incorporated explicitly into the statistical analysis. The increased phylogenetic resolution, paired with high-quality interaction data, allows us to resolve the way in which protein interaction network structure and abundance of proteins affect the evolutionary rate. We find that expression levels are better predictors of the evolutionary rate than a protein's connectivity. Detailed analysis of the two organisms also shows that the evolutionary rates of interacting proteins are not sufficiently similar to be mutually predictive. It appears that meaningful inferences about the evolution of protein interaction networks require comparative analysis of reasonably closely related species. The signature of protein evolution is shaped by a protein's abundance in the organism and its function and the biological process it is involved in. Its position in the interaction networks and its connectivity may modulate this but they appear to have only minor influence on a protein's evolutionary rate.Comment: Accepted for publication in BMC Evolutionary Biolog

SNPSTR: a database of compound microsatellite-SNP markers

There has been widespread and growing interest in genetic markers suitable for drawing population genetic inferences about past demographic events and to detect the effects of selection. In addition to single nucleotide polymorphisms (SNPs), microsatellites (or short tandem repeats, STRs) have received great attention in the analysis of human population history. In the SNPSTR database () we catalogue a relatively new type of compound genetic marker called SNPSTR which combines a microsatellite marker (STR) with one or more tightly linked SNPs. Here, the SNP(s) and the microsatellite are less than 250 bp apart so each SNPSTR can be considered a small haplotype with no recombination occurring between the two individual markers. Thus, SNPSTRs have the potential to become a very useful tool in the field of population genetics. The SNPSTR database contains all inferable human SNPSTRs as well as those in mouse, rat, dog and chicken, i.e. all model organisms for which extensive SNP datasets are available

Modeling the distribution of phosphine in cylindrical grain silos with CFD methods for precision fumigation: Poster

In the present study, the distribution of phosphine gas in a cylindrical silo was modeled and compared with available sensor data. The cylindrical silo was filled with wheat and a recirculation system was used to enhance the diffusion of phosphine throughout the grain volume. A Computational Fluid Dynamics (CFD) model was developed with OpenFoam software, which accounted for gas transport in porous media and sorption effects of phosphine into the grain. A time-dependent source was used to model the phosphine release from Aluminum Phosphide bags. Furthermore, simulation results were obtained for insect mortality as a function of their exposure to phosphine gas. The phosphine concentration measurements were available from calibrated wireless sensors provided by Centaur Analytics, placed near the silo walls at various heights. As the agreement of phosphine measured data with the simulation results was satisfying, it led to considering that the proposed CFD model (equations, boundary conditions, grain properties, recirculation system approach, etc.) was accurate. Utilizing the capabilities of fumigation modeling, the phosphine concentration could then be determined for every location inside the storage volume and at any given time, thus a prediction method for fumigation duration and success could be enabled. Additionally, as the CFD model correlates phosphine exposure with insect mortality, a methodology for planning precision fumigations can now be established.In the present study, the distribution of phosphine gas in a cylindrical silo was modeled and compared with available sensor data. The cylindrical silo was filled with wheat and a recirculation system was used to enhance the diffusion of phosphine throughout the grain volume. A Computational Fluid Dynamics (CFD) model was developed with OpenFoam software, which accounted for gas transport in porous media and sorption effects of phosphine into the grain. A time-dependent source was used to model the phosphine release from Aluminum Phosphide bags. Furthermore, simulation results were obtained for insect mortality as a function of their exposure to phosphine gas. The phosphine concentration measurements were available from calibrated wireless sensors provided by Centaur Analytics, placed near the silo walls at various heights. As the agreement of phosphine measured data with the simulation results was satisfying, it led to considering that the proposed CFD model (equations, boundary conditions, grain properties, recirculation system approach, etc.) was accurate. Utilizing the capabilities of fumigation modeling, the phosphine concentration could then be determined for every location inside the storage volume and at any given time, thus a prediction method for fumigation duration and success could be enabled. Additionally, as the CFD model correlates phosphine exposure with insect mortality, a methodology for planning precision fumigations can now be established

Phylogenetic diversity of stress signalling pathways in fungi

Open Access via PMC2666651Peer reviewedPublisher PD

Technical improvement of the Detia Degesch Phosphine Tolerance Test Kit: Presentation

Phosphine is the most important commonly used fumigant for the control of stored product insects in warehouses and processing facilities globally. However, the improper and extensive use has led to reduced susceptibility to phosphine for several insect species and strains in many parts of the world. To evaluate and quantify this phenomenon, Detia Degesch developed the Detia Degesch Phosphine Tolerance Test Kit (DDPTTK) more than 10 years ago. The use of DDPTTK is based on the exposure of the insects on a high concentration of phosphine (e.g. 3000 ppm) for short exposure periods (e.g. 8-15 min). This kit can be used on site by the fumigation and food industry, and can provide immediate results on the tolerance status of the insect strains that are to be treated. So far, the instructions of DDPTTK refer only to a six insect species. In this work, data for the expansion of knowledge about other species is provided, in order to broaden the spectrum of cases where the kit can be used. Moreover, certain improvements for the use of the kit are introduced, i.e. practical recommendations on the procedure and safety instructions.Phosphine is the most important commonly used fumigant for the control of stored product insects in warehouses and processing facilities globally. However, the improper and extensive use has led to reduced susceptibility to phosphine for several insect species and strains in many parts of the world. To evaluate and quantify this phenomenon, Detia Degesch developed the Detia Degesch Phosphine Tolerance Test Kit (DDPTTK) more than 10 years ago. The use of DDPTTK is based on the exposure of the insects on a high concentration of phosphine (e.g. 3000 ppm) for short exposure periods (e.g. 8-15 min). This kit can be used on site by the fumigation and food industry, and can provide immediate results on the tolerance status of the insect strains that are to be treated. So far, the instructions of DDPTTK refer only to a six insect species. In this work, data for the expansion of knowledge about other species is provided, in order to broaden the spectrum of cases where the kit can be used. Moreover, certain improvements for the use of the kit are introduced, i.e. practical recommendations on the procedure and safety instructions

Interaction of dental pulp stem cells with Biodentine and MTA after exposure to different environments

Objective: The aim of the present study was to evaluate and compare the cytotoxic effects of Biodentine and MTA on dental pulp stem cells (DPSCs) and to assess cell viability and adherence after material exposure to an acidic environment. Material and Methods: DPSCs were cultured either alone or in contact with either: Biodentine; MTA set for 1 hour; or MTA set for 24 hours. After 4 and 7 days, cell viability was measured using the MTT assay. Biodentine and MTA were also prepared and packed into standardized bovine dentin disks and divided into three groups according to the storage media (n=6/group): freshly mixed materials without storage medium (Group A); materials stored in saline (Group B); materials stored in citric acid buffered at pH 5.4 (Group C). After 24 hours, DPSCs were introduced in the wells and cell adherence, viability, and cellular morphology were observed via confocal microscopy after three days of culture. Cell viability was analyzed using repeated-measures analysis of variance test with Tukey's post hoc tests (α=0.05). Results: Biodentine expressed significantly higher cell viability compared with all other groups after 4 days, with no differences after 7 days. Notably, cell viability was significantly greater in 24-hour set MTA compared with 1-hour set MTA and control groups after 7 days. Material exposure to an acidic environment showed an increase in cell adherence and viability in both groups. Conclusions: Biodentine induced a significantly accelerated cell proliferation compared with MTA. Setting of these materials in the presence of citric acid enhanced DPSC viability and adherence

The effects of incomplete protein interaction data on structural and evolutionary inferences

BACKGROUND: Present protein interaction network data sets include only interactions among subsets of the proteins in an organism. Previously this has been ignored, but in principle any global network analysis that only looks at partial data may be biased. Here we demonstrate the need to consider network sampling properties explicitly and from the outset in any analysis. RESULTS: Here we study how properties of the yeast protein interaction network are affected by random and non-random sampling schemes using a range of different network statistics. Effects are shown to be independent of the inherent noise in protein interaction data. The effects of the incomplete nature of network data become very noticeable, especially for so-called network motifs. We also consider the effect of incomplete network data on functional and evolutionary inferences. CONCLUSION: Crucially, when only small, partial network data sets are considered, bias is virtually inevitable. Given the scope of effects considered here, previous analyses may have to be carefully reassessed: ignoring the fact that present network data are incomplete will severely affect our ability to understand biological systems

Human rights arguments in investor-state arbitration

Ο σημαντικός ρόλος του διεθνούς δικαίου ανθρωπίνων δικαιωμάτων (IHRL) στην διεθνή επενδυτική διαιτησία γίνεται όλο και πιο έκδηλος και στους επενδυτές και στα κράτη υποδοχής. Οι εξελίξεις στο IHRL όχι μόνο δύνανται να ενημερώσουν το περιεχόμενο των εγγυήσεων και τα απροσδιόριστα δικαιώματα που προβλέπει μία διεθνής επενδυτική συμφωνία αλλά και να καλύψουν υπάρχοντα κενά στο καθεστώς των διεθνών επενδύσεων. Παράλληλα, η ενσωμάτωση ρητών προβλέψεων περί ανθρωπίνων δικαιωμάτων και προστασίας του περιβάλλοντος εντός των διεθνώς επενδυτικών συμφωνιών και η δυνατότητα υποβολής counterclaims από τα κράτη θα ενδυνάμωνε την άμυνα των κρατών και θα προήγαγε την ισότητα των όπλων στην διεθνή επενδυτική διαιτησία. Η παρούσα μελέτη επιδιώκει να ερευνήσει, μέσω μίας νομολογιακής προσέγγισης, την πορεία εξέλιξης των επιχειρημάτων-ισχυρισμών περί ανθρωπίνων δικαιωμάτων (human rights arguments-HRAs) στην διεθνή επενδυτική διαιτησία, την τελευταία δεκαετία, εξετάζοντας τις πιο πρόσφατες υποθέσεις και επισημαίνοντας τις ποιοτικές διαφορές στην επιχειρηματολογία περί ανθρωπίνων δικαιωμάτων που τα μέρη και τα διαιτητικά δικαστήρια έχουν αναπτύξει, συγκριτικά με παλαιότερες υποθέσεις. Αποσκοπεί σε μία κριτική αξιολόγηση των HRAs των μερών, ενώ παράλληλα υποδεικνύει την σπουδαιότητα της συμμετοχής τρίτων μέσω της υποβολής amicus curiae υπομνημάτων. Αρχικά, παρουσιάζεται το θεωρητικό πλαίσιο μέσα στο οποίο ζητήματα περί ανθρωπίνων δικαιωμάτων υπεισέρχονται στην διεθνή επενδυτική διαιτησία. Εν συνεχεία, οι ισχυρισμοί ανθρωπίνων δικαιωμάτων από πλευράς των επενδυτών ταξινομούνται βάσει του σκοπού που επιδιώκει η επίκλησή τους (η παραβίαση των ανθρωπίνων δικαιωμάτων του επενδυτή είτε ως ανεξάρτητος ισχυρισμός είτε προς υποστήριξη παραβίασης της επενδυτικής συμφωνίας, επιχειρήματα αναφορικά με την προστασία του περιβάλλοντος προς υποστήριξη παραβίασης της επενδυτικής συμφωνίας, και το δικαίωμα του επενδυτή στην ιθαγένεια προς θεμελίωση της ratione personae δικαιοδοσίας του δικαστηρίου). Ακολούθως, η έρευνα επικεντρώνεται στα HRAs των κρατών υποδοχής και των amici υπέρ του κράτους, παρουσιάζοντας case studies, στις οποίες τα κράτη είτε επικαλέστηκαν IHRL είτε στήριξαν την υπερασπιστική τους γραμμή αποκλειστικά σε εθνικές διατάξεις περί προστασίας ανθρωπίνων δικαιωμάτων και περιβάλλοντος. Τέλος, η έρευνα αυτή αποσκοπεί, να δώσει απαντήσεις στα ακόλουθα: Ποιες είναι οι κύριες οδοί που χρησιμοποιούνται, για να εισαχθούν HRAs στην διεθνή επενδυτική διαιτησία; Υπάρχουν ενδείξεις αλλαγής στην συχνότητα και στην ποιότητα των HRAs; Ποια τα χαρακτηριστικά που πρέπει να πληρούνται, για να έχει βάσιμες πιθανότητες ένα “human right argument”, να γίνει δεκτό;The significant role of international human rights law (IHRL) in investor-state arbitration becomes increasingly manifest for both the investors and the host States. Developments under IHRL not only can inform the indeterminate standards and rights provided under an IIA, but also fill a gap in the international investment regime. On the other hand, the incorporation of explicit human rights and environmental provisions into the IIAs, and the drafting of IIAs to permit closely related host States’ counterclaims would reinforce host State defenses, rebalance investment law and promote equity of weapons in investor-state arbitration. The present study aims to investigate, though a case law analysis approach, the course of development of human rights arguments (HRAs) in investor-state arbitration, over the last decade, looking into the most recent cases and highlighting the qualitative differences in human rights argumentation provided by the parties and in tribunals’ relevant analysis, compared to earlier cases. It aims at a critical appraisal of both parties’ HRAs, indicating, in parallel, the significance of amicus curiae submissions; it explores the different issues that evolve and provides further considerations. Initially, it presents an overview of the theoretical framework within which human rights issues become relevant in investor-state arbitration. Then, considering human rights as an investor’s sword, the classification of the investors’ HRAs is based on the different purposes their invocation serve (investors claiming their ‘human’ rights violation as independent human rights claims or in support of treaty violations, environmental arguments in support of investors’ claims, invocation of the right to a nationality to establish jurisdiction ratione personae). Subsequently, the paper focuses on HRAs raised by the host States and the amici in support of the host State defense, presenting both cases where the host States have invoked IHRL and cases where the host States have relied primarily in domestic human rights and environmental provisions. Finally, this study aims to give answers, inter alia, to the following: Which are the principal avenues used for inserting HRAs in investor-state arbitration? Is there any evidence to suggest a change in the frequency and quality of HRAs? What makes a strong human rights argument

Biometric and emotion identification: an ECG compression based method

We present an innovative and robust solution to both biometric and emotion identification using the electrocardiogram (ECG). The ECG represents the electrical signal that comes from the contraction of the heart muscles, indirectly representing the flow of blood inside the heart, it is known to convey a key that allows biometric identification. Moreover, due to its relationship with the nervous system, it also varies as a function of the emotional state. The use of information-theoretic data models, associated with data compression algorithms, allowed to effectively compare ECG records and infer the person identity, as well as emotional state at the time of data collection. The proposed method does not require ECG wave delineation or alignment, which reduces preprocessing error. The method is divided into three steps: (1) conversion of the real-valued ECG record into a symbolic time-series, using a quantization process; (2) conditional compression of the symbolic representation of the ECG, using the symbolic ECG records stored in the database as reference; (3) identification of the ECG record class, using a 1-NN (nearest neighbor) classifier. We obtained over 98% of accuracy in biometric identification, whereas in emotion recognition we attained over 90%. Therefore, the method adequately identify the person, and his/her emotion. Also, the proposed method is flexible and may be adapted to different problems, by the alteration of the templates for training the model.publishe