Topology Analysis of Social Networks Extracted from Literature

In a world where complex networks are an increasingly important part of science, it is interesting to question how the new reading of social realities they provide applies to our cultural background and in particular, popular culture. Are authors of successful novels able to reproduce social networks faithful to the ones found in reality? Is there any common trend connecting an author’s oeuvre, or a genre of fiction? Such an analysis could provide new insight on how we, as a culture, perceive human interactions and consume media. The purpose of the work presented in this paper is to define the signature of a novel’s story based on the topological analysis of its social network of characters. For this purpose, an automated tool was built that analyses the dialogs in novels, identifies characters and computes their relationships in a time-dependent manner in order to assess the network’s evolution over the course of the story.     

ECERIFERUM2-LIKE Proteins Have Unique Biochemical and Physiological Functions in Very-Long-Chain Fatty Acid Elongation

The extension of very-long-chain fatty acids (VLCFAs) for the synthesis of specialized apoplastic lipids requires unique biochemical machinery. Condensing enzymes catalyze the first reaction in fatty acid elongation and determine the chain length of fatty acids accepted and produced by the fatty acid elongation complex. Although necessary for the elongation of all VLCFAs, known condensing enzymes cannot efficiently synthesize VLCFAs longer than 28 carbons, despite the prevalence of C28 to C34 acyl lipids in cuticular wax and the pollen coat. The eceriferum2 (cer2) mutant of Arabidopsis (Arabidopsis thaliana) was previously shown to have a specific deficiency in cuticular waxes longer than 28 carbons, and heterologous expression of CER2 in yeast (Saccharomyces cerevisiae) demonstrated that it can modify the acyl chain length produced by a condensing enzyme from 28 to 30 carbon atoms. Here, we report the physiological functions and biochemical specificities of the CER2 homologs CER2-LIKE1 and CER2-LIKE2 by mutant analysis and heterologous expression in yeast. We demonstrate that all three CER2-LIKEs function with the same small subset of condensing enzymes, and that they have different effects on the substrate specificity of the same condensing enzyme. Finally, we show that the changes in acyl chain length caused by each CER2-LIKE protein are of substantial importance for cuticle formation and pollen coat function.The extension of fatty acids to lengths greater than 28 carbons (C28) is an exceptional process in plant metabolism in that it requires unique biochemical machinery, and the elongation products are used for the synthesis of specialized plant metabolites. Derivatives of C30 to C34 fatty acids make up the bulk of plant cuticular wax, which coats all of a plant’s primary aerial surfaces. Cuticular wax serves as a barrier against transpirational water loss (Riederer and Schreiber, 2001) and protects the plant from both biotic (Eigenbrode, 1996) and abiotic (Grace and van Gardingen, 1996) stresses. C30 to C34 fatty acid-derived lipids are also components of the pollen coat, where they function in pollen hydration and germination on dry stigma (Elleman et al., 1992; Preuss et al., 1993).The core complex that elongates long-chain fatty acids (C16–C18) to very-long-chain fatty acids (VLCFAs; C20–C34) consists of four interacting proteins localized to the endoplasmic reticulum (ER). β-Keto-acyl-CoA synthases (KCSs), also known as condensing enzymes, catalyze the first reaction required for VLCFA elongation, condensing malonyl-CoA with an acyl-CoA (n) to produce a β-keto-acyl-CoA (n + 2). Condensation is both a specific and rate-limiting step in elongation (Millar and Kunst, 1997). Chain length specificity of KCSs is of particular importance because VLCFA length determines the downstream use of the fatty acid (for review, see Joubès et al., 2008; Haslam and Kunst, 2013a). There are two families of condensing enzymes in Arabidopsis (Arabidopsis thaliana). The ELONGATION-DEFECTIVE (ELO)-LIKE family is homologous to yeast (Saccharomyces cerevisiae) ELOs, and has putative functions in sphingolipid biosynthesis (Quist et al., 2009). Although our current understanding of plant ELO-LIKE physiological function and biochemical activity is limited, the mechanism of yeast Elo protein activity has been thoroughly investigated (Denic and Weissman, 2007). The FATTY ACID ELONGATION1 (FAE1)-type family is homologous to the first condensing enzyme identified in Arabidopsis, which is required for the synthesis of C20 to C22 VLCFAs in Arabidopsis oilseeds. Many of the 21 FAE1-type condensing enzymes of Arabidopsis have been characterized using reverse genetics and heterologous expression in yeast (Trenkamp et al., 2004; Blacklock and Jaworski, 2006; Paul et al., 2006; Tresch et al., 2012). This work has revealed the intriguing caveat that, although FAE1-type KCSs are involved in the synthesis of diverse downstream metabolites and use a broad range of acyl chain lengths, none are able to efficiently elongate VLCFAs beyond C28 (for review, see Haslam and Kunst, 2013a), which is essential for the production of cuticular wax components.Eceriferum2 (cer2) and glossy2 (gl2) mutants of Arabidopsis and Zea mays, respectively, are deficient in specific VLCFA-derived waxes longer than C28 (Bianchi et al., 1975; McNevin et al., 1993; Jenks et al., 1995). Both mutations were mapped to genes that do not resemble any component of the elongase complex (Tacke et al., 1995; Xia et al., 1996), but are homologous to the BAHD family of acyltransferases (St-Pierre et al., 1998). However, site-directed mutagenesis of conserved acyltransferase catalytic site amino acids in CER2 revealed that this motif is not required for CER2 function in cuticular wax synthesis (Haslam et al., 2012).CER6 is a condensing enzyme necessary for the accumulation of stem cuticular waxes in Arabidopsis, but when expressed in yeast, CER6 can only elongate VLCFAs to C28. When CER2 is expressed in yeast, it has no elongation activity. However, coexpression of CER2 and CER6 results in efficient production of C30 VLCFAs. Coexpression of CER2 with LfKCS45, a condensing enzyme from the crucifer Lesquerella fendleri that generates C28 and a small amount of C30 VLCFAs (Moon et al., 2004), does not alter product chain length (Haslam et al., 2012). Based on these observations, it was hypothesized that CER2 modifies the chain length specificity of the core elongase complex by interaction with specific KCS enzymes (Haslam et al., 2012).CER2 homologs are found in diverse flowering plant lineages, and many species have multiple CER2 homologs (Tuominen et al., 2011). A BLAST search of proteins from Arabidopsis identified two sequences with substantial similarity to CER2. {"type":"entrez-protein","attrs":{"text":"NP_193120","term_id":"15236357","term_text":"NP_193120"}}NP_193120 is 36% identical to CER2, and is encoded by the gene At4g13840. We named this gene CER2-LIKE1 (also known as CER26) (Pascal et al., 2013). {"type":"entrez-protein","attrs":{"text":"NP_566741","term_id":"18403923","term_text":"NP_566741"}}NP_566741 is 38% identical to CER2, and is encoded by the gene At3g23840. We named this gene CER2-LIKE2 (also named CER26-LIKE) (Pascal et al., 2013). Characterization of a cer2-like1 null mutant revealed a role for the CER2-LIKE1 protein in the elongation of leaf wax precursors beyond C30, analogous to the role of CER2 in C28 elongation in stems (Haslam et al., 2012; Pascal et al., 2013). cer2 cer2-like1 double mutants are deficient in the formation of wax components longer than C28 in both stems and leaves. As the cer2 single mutant has no leaf wax phenotype, the additive effect of these two mutations on leaf wax composition indicates that there is partial functional redundancy between the two genes.A comprehensive investigation of the biochemical and physiological functions of CER2-LIKE proteins is necessary. Beyond the value of knowing the specific roles of each homolog, such an investigation has potential to elucidate the nature of CER2-LIKE protein function. With this objective, we used our data to address the following questions: (1) Do CER2-LIKE proteins function with CER6 alone, or can they modify the activity of other FAE1-type condensing enzymes? (2) Do CER2-LIKE proteins have different effects on the substrate specificity of the same condensing enzyme, or is substrate specificity determined exclusively by the condensing enzyme? (3) What is the physiological relevance of the subtle changes in acyl lipid chain length that CER2-LIKE proteins induce?     

CML9, a multifunctional Arabidopsis thaliana calmodulin-like protein involved in stress responses and plant growth?

Plants have evolved complex signaling networks to respond to their fluctuating environment and adapt their growth and development. Calcium-dependent signaling pathways play key role in the onset of these adaptive responses. In plant cells, the intracellular calcium transients are triggered by numerous stimuli and it is supposed that the large repertory of calcium sensors present in higher plants could contribute to integrate these signals in physiological responses. Here, we present data on CML9, a calmodulin-like protein that appears to be involved in plant responses to both biotic and abiotic stress. Using a reverse genetic approach based on gain and loss of function mutants, we present here data indicating that this CML might also be involved in root growth control in response to the flagellin, a pathogen-associated molecular pattern (PAMP) also involved in plant immunity.     

Modeling the Winter–to–Summer Transition of Prokaryotic and Viral Abundance in the Arctic Ocean

One of the challenges in oceanography is to understand the influence of environmental factors on the abundances of prokaryotes and viruses. Generally, conventional statistical methods resolve trends well, but more complex relationships are difficult to explore. In such cases, Artificial Neural Networks (ANNs) offer an alternative way for data analysis. Here, we developed ANN-based models of prokaryotic and viral abundances in the Arctic Ocean. The models were used to identify the best predictors for prokaryotic and viral abundances including cytometrically-distinguishable populations of prokaryotes (high and low nucleic acid cells) and viruses (high- and low-fluorescent viruses) among salinity, temperature, depth, day length, and the concentration of Chlorophyll-a. The best performing ANNs to model the abundances of high and low nucleic acid cells used temperature and Chl-a as input parameters, while the abundances of high- and low-fluorescent viruses used depth, Chl-a, and day length as input parameters. Decreasing viral abundance with increasing depth and decreasing system productivity was captured well by the ANNs. Despite identifying the same predictors for the two populations of prokaryotes and viruses, respectively, the structure of the best performing ANNs differed between high and low nucleic acid cells and between high- and low-fluorescent viruses. Also, the two prokaryotic and viral groups responded differently to changes in the predictor parameters; hence, the cytometric distinction between these populations is ecologically relevant. The models imply that temperature is the main factor explaining most of the variation in the abundances of high nucleic acid cells and total prokaryotes and that the mechanisms governing the reaction to changes in the environment are distinctly different among the prokaryotic and viral populations.