Evolutionary pressures and codon bias in low complexity regions of plasmodia

The biological meaning of low complexity regions in the proteins of Plasmodium species is a topic of discussion in evolutionary biology. There is a debate between selectionists and neutralists, who either attribute or do not attribute an effect of low-complexity regions on the fitness of these parasites, respectively. In this work, we comparatively study 22 Plasmodium species to understand whether their low complexity regions undergo a neutral or, rather, a selective and species-dependent evolution. The focus is on the connection between the codon repertoire of the genetic coding sequences and the occurrence of low complexity regions in the corresponding proteins. The first part of the work concerns the correlation between the length of plasmodial proteins and their propensity at embedding low complexity regions. Relative synonymous codon usage, entropy, and other indicators reveal that the incidence of low complexity regions and their codon bias is species-specific and subject to selective evolutionary pressure. We also observed that protein length, a relaxed selective pressure, and a broad repertoire of codons in proteins, are strongly correlated with the occurrence of low complexity regions. Overall, it seems plausible that the codon bias of low-complexity regions contributes to functional innovation and codon bias enhancement of proteins on which Plasmodium species rest as successful evolutionary parasites

Routine tests for both planning and evaluating image quality in tele-echocardiography

Both in real-time and "store & forward" tele-echocardiography (T-E), a coding process has to be applied to the echocardiography videoclips in order to limit the bandwidth needed and adapt it to the bandwidths furnished by network providers. The compression process degrades the videoclips, affecting thus the quality of the videoclips and potentially compromising the diagnostic accuracy of the T-E. In this work the authors investigated on the use of automatic tools for the video quality assessment by means of objective methods with particular care to the role of the system administrator. As the use of tests on video quality assessment (based on subjective methods) is hampered by the high number of needed resources (persons, laboratories and time). The use of valid objective methods is thus desirable. The study reviewed different tools with this specific aim. One of the more suitable tool was found to be represented by a software package designed by the Institute of Telecommunication Sciences and the National Telecommunication and Information Administration, the NTIA/ITS VQM tool. This tool gives back objective-quantitative data as outcomes, however embeds models emulating the subjective perception. This study reviewed and analyzed in depth the functionalities of the tool to improve the image quality in TE over the network. The tool was also found suitable for a more general process of T-E assessment, from a health technology assessment (HTA) perspective

The close relationship between the Golgi trafficking machinery and protein glycosylation

La glicosilazione è la più comune modifica post-traduzionale delle proteine; media la loro corretta piegatura e stabilità, nonché il loro trasporto attraverso il trasporto secretorio. I cambiamenti nei glicani legati all'N e all'O sono stati associati a molteplici condizioni patologiche tra cui disturbi congeniti della glicosilazione, malattie infiammatorie e cancro. La glicosilazione della glicoproteina al Golgi coinvolge l'azione coordinata di centinaia di glicosiltransferasi e glicosidasi, che vengono mantenute nella posizione corretta attraverso il traffico di vescicole retrograde tra le cisterne di Golgi. In questa recensione, descriviamo il macchinario molecolare coinvolto nel traffico di vescicole e nel tethering presso l'apparato di Golgi e gli effetti delle mutazioni nel contesto della biosintesi dei glicani e delle malattie umane.Glycosylation is the most common post-translational modification of proteins; it mediates their correct folding and stability, as well as their transport through the secretory transport. Changes in N- and O-linked glycans have been associated with multiple pathological conditions including congenital disorders of glycosylation, inflammatory diseases and cancer. Glycoprotein glycosylation at the Golgi involves the coordinated action of hundreds of glycosyltransferases and glycosidases, which are maintained at the correct location through retrograde vesicle trafficking between Golgi cisternae. In this review, we describe the molecular machinery involved in vesicle trafficking and tethering at the Golgi apparatus and the effects of mutations in the context of glycan biosynthesis and human diseases

Архієпископ Кримський Лука про способи духовного оздоровлення Кримської єпархії

In the past decade, mass-spectrometry-based methods have emerged for the quantitative profiling of dynamic changes in protein phosphorylation, allowing the behavior of thousands of phosphorylation sites to be monitored in a single experiment. However, when one is interested in specific signaling pathways, such shotgun methodologies are not ideal because they lack selectivity and are not cost and time efficient with respect to instrument and data analysis time. Here we evaluate and explore a peptide-centric antibody generated to selectively enrich peptides containing the cAMP-dependent protein kinase (PKA) consensus motif. This targeted phosphoproteomic strategy is used to profile temporal quantitative changes of potential PKA substrates in Jurkat T lymphocytes upon prostaglandin E2 (PGE2) stimulation, which increases intracellular cAMP, activating PKA. Our method combines ultra-high-specificity motif-based immunoaffinity purification with cost-efficient stable isotope dimethyl labeling. We identified 655 phosphopeptides, of which 642 (i.e. 98%) contained the consensus motif [R/K][R/K/X]X[pS/pT]. When our data were compared with a large-scale Jurkat T-lymphocyte phosphoproteomics dataset containing more than 10,500 phosphosites, a minimal overlap of 0.2% was observed. This stresses the need for such targeted analyses when the interest is in a particular kinase. Our data provide a resource of likely substrates of PKA, and potentially some substrates of closely related kinases. Network analysis revealed that about half of the observed substrates have been implicated in cAMP-induced signaling. Still, the other half of the here-identified substrates have been less well characterized, representing a valuable resource for future research

Oncogenic roles of GOLPH3 in the physiopathology of cancer

Golgi phosphoprotein 3 (GOLPH3), un effettore del fosfatidilinositolo 4-fosfato [PI (4) P] al Golgi, è necessaria per il mantenimento della struttura del nastro del Golgi, il traffico di vescicole e la glicosilazione del Golgi. GOLPH3 è stato convalidato come oncoproteina combinando la genomica integrativa con l'analisi clinopatologiche e funzionali. È spesso amplificato in diversi tipi di tumori solidi tra cui melanoma, cancro ai polmoni, cancro al seno, glioma e cancro del colon-retto. La sovraespressione di GOLPH3 è correlata a una prognosi infausta in più tipi di tumore, compreso il 52% dei tumori al seno e dal 41% al 53% del glioblastoma. I ruoli di GOLPH3 nella tumorigenesi possono essere correlati a diverse attività cellulari, tra cui: (i) regolazione del traffico dal Golgi alla membrana plasmatica e contributo a fenotipi secretori maligni; (ii) controllare l'internalizzazione e il riciclaggio di molecole di segnalazione chiave o aumentare la glicosilazione delle glicoproteine ​​rilevanti per il cancro; e (iii) influenzare la risposta al danno al DNA e il mantenimento della stabilità genomica. Qui riassumiamo le attuali conoscenze sui percorsi oncogeni che coinvolgono GOLPH3 nel cancro umano, l'influenza di GOLPH3 sul metabolismo del tumore e sullo stroma circostante e il suo possibile ruolo nella formazione di metastasi tumorali.Golgi phosphoprotein 3 (GOLPH3), a Phosphatidylinositol 4-Phosphate [PI(4)P] effector at the Golgi, is required for Golgi ribbon structure maintenance, vesicle trafficking and Golgi glycosylation. GOLPH3 has been validated as an oncoprotein through combining integrative genomics with clinopathological and functional analyses. It is frequently amplified in several solid tumor types including melanoma, lung cancer, breast cancer, glioma, and colorectal cancer. Overexpression of GOLPH3 correlates with poor prognosis in multiple tumor types including 52% of breast cancers and 41% to 53% of glioblastoma. Roles of GOLPH3 in tumorigenesis may correlate with several cellular activities including: (i) regulating Golgi-to-plasma membrane trafficking and contributing to malignant secretory phenotypes; (ii) controlling the internalization and recycling of key signaling molecules or increasing the glycosylation of cancer relevant glycoproteins; and (iii) influencing the DNA damage response and maintenance of genomic stability. Here we summarize current knowledge on the oncogenic pathways involving GOLPH3 in human cancer, GOLPH3 influence on tumor metabolism and surrounding stroma, and its possible role in tumor metastasis formation

On "Ergodicity and Central Limit Theorem in Systems with Long-Range Interactions" by Figueiredo et al

In the present paper we refute the criticism advanced in a recent preprint by Figueiredo et al [1] about the possible application of the $q$-generalized Central Limit Theorem (CLT) to a paradigmatic long-range-interacting many-body classical Hamiltonian system, the so-called Hamiltonian Mean Field (HMF) model. We exhibit that, contrary to what is claimed by these authors and in accordance with our previous results, $q$-Gaussian-like curves are possible and real attractors for a certain class of initial conditions, namely the one which produces nontrivial longstanding quasi-stationary states before the arrival, only for finite size, to the thermal equilibrium.Comment: 2 pages, 2 figures. Short version of the paper, accepted for publication in Europhysics Letters, (2009) in pres

Fungal Biosorption, An Innovative Treatment for the Decolourisation and Detoxification of Textile Effluents

Textile effluents are among the most difficult-to-treat wastewaters, due to their considerable amount of recalcitrant and toxic substances. Fungal biosorption is viewed as a valuable additional treatment for removing pollutants from textile wastewaters. In this study the efficiency of Cunninghamella elegans biomass in terms of contaminants, COD and toxicity reduction was tested against textile effluents sampled in different points of wastewater treatment plants. The results showed that C. elegans is a promising candidate for the decolourisation and detoxification of textile wastewaters and its versatility makes it very competitive compared with conventional sorbents adopted in industrial processes

Invariant measures of the 2D Euler and Vlasov equations

We discuss invariant measures of partial differential equations such as the 2D Euler or Vlasov equations. For the 2D Euler equations, starting from the Liouville theorem, valid for N-dimensional approximations of the dynamics, we define the microcanonical measure as a limit measure where N goes to infinity. When only the energy and enstrophy invariants are taken into account, we give an explicit computation to prove the following result: the microcanonical measure is actually a Young measure corresponding to the maximization of a mean-field entropy. We explain why this result remains true for more general microcanonical measures, when all the dynamical invariants are taken into account. We give an explicit proof that these microcanonical measures are invariant measures for the dynamics of the 2D Euler equations. We describe a more general set of invariant measures, and discuss briefly their stability and their consequence for the ergodicity of the 2D Euler equations. The extension of these results to the Vlasov equations is also discussed, together with a proof of the uniqueness of statistical equilibria, for Vlasov equations with repulsive convex potentials. Even if we consider, in this paper, invariant measures only for Hamiltonian equations, with no fluxes of conserved quantities, we think this work is an important step towards the description of non-equilibrium invariant measures with fluxes.Comment: 40 page