Fittonia verschaffeltii Response to Artificial Light Treatments: BIOMASS, Nutrient Concentrations and Physiological Changes

The purpose of the present study was to evaluate the effects of different light treatments on biomass, nutrient concentrations and physiological parameters of Fittonia verschaffeltii (Lem) Van Houtte. The aim was to establish a methodology to evaluate the effect of photosynthetically active radiation (PAR) emitted by lamps on biomass. The light treatments used were tube luminescent Dunn (TL-D), tube luminescent Dunn + light emitting diodes (LEDs) and Tube luminescent 5 (TL-5). At the end of the experimental period, biomass, nutritional, biochemical, and physiological parameters were assessed. A clear reduction in total plant dry weight under TL-D + LEDs at the end of the experiment was recorded. With respect to nutrient concentration in the different organs assessed, there was no clear response under the different light treatments. The growth under TL-D lamps resulted in the highest concentration of total soluble sugars and starch in leaves, whereas the highest value of indole 3-acetic acid concentration was under TL-5 lamps. Plants grown under TL-D + LEDs showed the lowest values of chlorophyll a, b and a + b. The relationship proposed between integrated use of spectral energy (IUSE) and total dry weight (TDW) showed a good correlation with an R2 value of 0.86, therefore we recommend this methodology to discern the effects of the different spectral qualities on plant biomass

Evidence for the Concerted Evolution between Short Linear Protein Motifs and Their Flanking Regions

BACKGROUND: Linear motifs are short modules of protein sequences that play a crucial role in mediating and regulating many protein-protein interactions. The function of linear motifs strongly depends on the context, e.g. functional instances mainly occur inside flexible regions that are accessible for interaction. Sometimes linear motifs appear as isolated islands of conservation in multiple sequence alignments. However, they also occur in larger blocks of sequence conservation, suggesting an active role for the neighbouring amino acids. RESULTS: The evolution of regions flanking 116 functional linear motif instances was studied. The conservation of the amino acid sequence and order/disorder tendency of those regions was related to presence/absence of the instance. For the majority of the analysed instances, the pairs of sequences conserving the linear motif were also observed to maintain a similar local structural tendency and/or to have higher local sequence conservation when compared to pairs of sequences where one is missing the linear motif. Furthermore, those instances have a higher chance to co-evolve with the neighbouring residues in comparison to the distant ones. Those findings are supported by examples where the regulation of the linear motif-mediated interaction has been shown to depend on the modifications (e.g. phosphorylation) at neighbouring positions or is thought to benefit from the binding versatility of disordered regions. CONCLUSION: The results suggest that flanking regions are relevant for linear motif-mediated interactions, both at the structural and sequence level. More interestingly, they indicate that the prediction of linear motif instances can be enriched with contextual information by performing a sequence analysis similar to the one presented here. This can facilitate the understanding of the role of these predicted instances in determining the protein function inside the broader context of the cellular network where they arise

Geostatistical modelling of a coal seam for resource risk assessment

The evaluation of a coal seam for profitable extraction requires the estimation of its thickness and quality characteristics together with the spatial variability of these variables. In many cases the only data available for the estimation are from a limited number of exploration and feasibility drill holes. Spatial variability can be quantified by geostatistical modelling, which provides the basis for estimation (kriging). In cases where the spatial variability of the seam thickness and quality characteristics has a significant impact on how the coal is extracted and stored, geostatistical simulation may be preferable to geostatistical kriging methods. The aim of this paper is to present an improved approach to resource risk assessment by propagating the uncertainty in semi-variogram model parameters into the spatial variability of coal variables. We show that a more realistic assessment of risk is obtained when the uncertainty of semi-variogram model parameters is taken into account. The methodology is illustrated with a coal seam from North-western Spain. © 2012 Elsevier B.V.E. Pardo-Igúzquiza, P.A. Dowd, J.M. Baltuille, M. Chica-Olm

Correction of Errors During The Manufacture by Computer Numerical Control (CNC) of Blades for an Axial Hydrokinetic Turbine

The design and manufacture of new systems for providing electric power to non-interconnected areas is one of the challenges for engineering. There are several alternatives, including water or wind-power generation systems, where hydrokinetic turbines are highlighted. This work establishes the methodology, identification and correction of errors generated during the manufacture by machining, using CAD/CAPP/CAM techniques, for an axial hydrokinetic turbine. During the manufacturing process, the generation of an error on the edges of the blades was identified, which was attributed to problems in the design of the model since the degrees of freedom of the manufacturing system used were not considered. For the manufacture of complex surfaces in the design of models, the most extreme points of the surfaces in contact must match the tangent edges to ensure that the tools of machining can reach them with the trajectories generated from the CAM

A tree-based conservation scoring method for short linear motifs in multiple alignments of protein sequences

<p>Abstract</p> <p>Background</p> <p>The structure of many eukaryotic cell regulatory proteins is highly modular. They are assembled from globular domains, segments of natively disordered polypeptides and short linear motifs. The latter are involved in protein interactions and formation of regulatory complexes. The function of such proteins, which may be difficult to define, is the aggregate of the subfunctions of the modules. It is therefore desirable to efficiently predict linear motifs with some degree of accuracy, yet sequence database searches return results that are not significant.</p> <p>Results</p> <p>We have developed a method for scoring the conservation of linear motif instances. It requires only primary sequence-derived information (e.g. multiple alignment and sequence tree) and takes into account the degenerate nature of linear motif patterns. On our benchmarking, the method accurately scores 86% of the known positive instances, while distinguishing them from random matches in 78% of the cases. The conservation score is implemented as a real time application designed to be integrated into other tools. It is currently accessible via a Web Service or through a graphical interface.</p> <p>Conclusion</p> <p>The conservation score improves the prediction of linear motifs, by discarding those matches that are unlikely to be functional because they have not been conserved during the evolution of the protein sequences. It is especially useful for instances in non-structured regions of the proteins, where a domain masking filtering strategy is not applicable.</p

A PP2A-B55-Mediated Crosstalk between TORC1 and TORC2 Regulates the Differentiation Response in Fission Yeast

Extracellular cues regulate cell fate, and this is mainly achieved through the engagement of specific transcriptional programs. The TORC1 and TORC2 complexes mediate the integration of nutritional cues to cellular behavior, but their interplay is poorly understood. Here, we use fission yeast to investigate how phosphatase activity participates in this interplay during the switch from proliferation to sexual differentiation. We find that loss of PP2A-B55$^{Pab1}$ enhances the expression of differentiation-specific genes and leads to premature conjugation. $\textit{pab1}$ deletion brings about a transcriptional profile similar to TORC1 inactivation, and deletion of $\textit{pab1}$ overcomes the repression of differentiation genes in cells overexpressing TORC1. Importantly, we show that this effect is mediated by an increased TORC2-AKT (Gad8) signaling. Under nutrient-rich conditions, PP2A-B55$^{Pab1}$ dephosphorylates Gad8 Ser546, repressing its activity. Conversely, TORC1 inactivation upon starvation leads to the inactivation of PP2A-B55$^{Pab1}$ through the Greatwall-Endosulfin pathway. This results in the activation of Gad8 and the commitment to differentiation. Thus, PP2A-B55$^{Pab1}$ enables a crosstalk between the two TOR complexes that controls cell-fate decisions in response to nutrient availability.We thank Dominique Helmlinger and Sergio Moreno for sharing unpublished results and strains, and for stimulating discussion. We thank Janni Petersen, Ronit Weisman, Kazuhiro Shiozaki, Mitsuhiro Yanagida, and Hisao Masukata for strains, constructs, and antibodies. We thank Toni Hurtado and Beata Grallert for critical reading of the manuscript. This work was supported by NFR FRIMEDBIO grant 214049. M.P. is the recipient of a Kreftforeningen postdoctoral fellowship (grant 5843744). N.C. has received funding from the European Union Seventh Framework Programme (FP7-PEOPLE-2013-COFUND) under grant agreement 609020 - Scientia Fellows. J.M. was supported by BBSRC research grants BB/N007697/1 and BB/M021483/1