A Microarray study of Carpet-Shell Clam (Ruditapes decussatus) shows common and organ-specific growth-related gene expression Differences in gills and digestive gland

Growth rate is one of the most important traits from the point of view of individual fitness and commercial production in mollusks, but its molecular and physiological basis is poorly known. We have studied differential gene expression related to differences in growth rate in adult individuals of the commercial marine clam Ruditapes decussatus. Gene expression in the gills and the digestive gland was analyzed in 5 fast-growing and five slow-growing animals by means of an oligonucleotide microarray containing 14,003 probes. A total of 356 differentially expressed genes (DEG) were found. We tested the hypothesis that differential expression might be concentrated at the growth control gene core (GCGC), i. e., the set of genes that underlie the molecular mechanisms of genetic control of tissue and organ growth and body size, as demonstrated in model organisms. The GCGC includes the genes coding for enzymes of the insulin/ insulin-like growth factor signaling pathway (IIS), enzymes of four additional signaling pathways (Raf/ Ras/ Mapk, Jnk, TOR, and Hippo), and transcription factors acting at the end of those pathways. Only two out of 97 GCGC genes present in themicroarray showed differential expression, indicating a very little contribution of GCGC genes to growth-related differential gene expression. Forty eight DEGs were shared by both organs, with gene ontology (GO) annotations corresponding to transcription regulation, RNA splicing, sugar metabolism, protein catabolism, immunity, defense against pathogens, and fatty acid biosynthesis. GO termenrichment tests indicated that genes related to growth regulation, development and morphogenesis, extracellular matrix proteins, and proteolysis were overrepresented in the gills. In the digestive gland overrepresented GO terms referred to gene expression control through chromatin rearrangement, RAS-related small GTPases, glucolysis, and energy metabolism. These analyses suggest a relevant role of, among others, some genes related to the IIS, such as the ParaHox gene Xlox, CCAR and the CCN family of secreted proteins, in the regulation of growth in bivalves.Direccion General de Investigacion Cientifica y Tecnica of the Spanish Government [AGL2010-16743, AGL2013-49144-C3-3-R]; COMPETE Program; Portuguese National Funds [PEst-255 C/MAR/LA0015/2011]; Portuguese FCT [UID/Multi/04326/2013]; Generalitat Valenciana; Ministry of Education, Culture, and Sports of the Spanish Government; Association of European Marine Biology Laboratoriesinfo:eu-repo/semantics/publishedVersio

Transcriptional profiling of populations in the clam Ruditapes decussatus suggests genetically determined differentiation in gene expression along parallel temperature gradients and between races of the Atlantic ocean and west Mediterranean sea

Ongoing ocean warming due to climate change poses new challenges for marine life and its exploitation. We have used transcriptomics to find genetically based responses to increased temperature in natural populations of the marine clam Ruditapes decussatus, which lives along parallel thermal gradients in southern Europe. Clams of the Atlantic and West Mediterranean races were collected in northern (cool) and a southern (warm) localities. The animals were kept in running seawater in the warm, southern Atlantic locality for a 15-week period. During this period, water temperature was raised to typical southern European summer values. After this period, an expression profile was obtained for a total of 34 clams and 11,025 probes by means of an oligonucleotide microarray. We found distinct transcriptional patterns for each population based on a total of 552 differentially expressed genes (DEGs), indicating innate differences which probably have a genetic basis. Race and latitude contributed significantly to gene expression differences, with very different sets of DEGs. A gene ontology analysis showed that races differed mainly in the genes involved in ribosomal function and protein biosynthesis, while genes related to glutathione metabolism and ATP synthesis in the mitochondria were the most outstanding with respect to north/south transcriptional differences.Grant AGL2010-16743;info:eu-repo/semantics/publishedVersio

The Dynamics of Nestedness Predicts the Evolution of Industrial Ecosystems

In economic systems, the mix of products that countries make or export has been shown to be a strong leading indicator of economic growth. Hence, methods to characterize and predict the structure of the network connecting countries to the products that they export are relevant for understanding the dynamics of economic development. Here we study the presence and absence of industries at the global and national levels and show that these networks are significantly nested. This means that the less filled rows and columns of these networks' adjacency matrices tend to be subsets of the fuller rows and columns. Moreover, we show that nestedness remains relatively stable as the matrices become more filled over time and that this occurs because of a bias for industries that deviate from the networks' nestedness to disappear, and a bias for the missing industries that reduce nestedness to appear. This makes the appearance and disappearance of individual industries in each location predictable. We interpret the high level of nestedness observed in these networks in the context of the neutral model of development introduced by Hidalgo and Hausmann (2009). We show that, for the observed fills, the model can reproduce the high level of nestedness observed in these networks only when we assume a high level of heterogeneity in the distribution of capabilities available in countries and required by products. In the context of the neutral model, this implies that the high level of nestedness observed in these economic networks emerges as a combination of both, the complementarity of inputs and heterogeneity in the number of capabilities available in countries and required by products. The stability of nestedness in industrial ecosystems, and the predictability implied by it, demonstrates the importance of the study of network properties in the evolution of economic networks.Comment: 26 page

MRNA-Seq and microarray development for the Grooved carpet shell clam, Ruditapes decussatus:A functional approach to unravel host -parasite interaction

Abstract Background The Grooved Carpet shell clam Ruditapes decussatus is the autochthonous European clam and the most appreciated from a gastronomic and economic point of view. The production is in decline due to several factors such as Perkinsiosis and habitat invasion and competition by the introduced exotic species, the manila clam Ruditapes philippinarum. After we sequenced R. decussatus transcriptome we have designed an oligo microarray capable of contributing to provide some clues on molecular response of the clam to Perkinsiosis. Results A database consisting of 41,119 unique transcripts was constructed, of which 12,479 (30.3%) were annotated by similarity. An oligo-DNA microarray platform was then designed and applied to profile gene expression in R. decussatus heavily infected by Perkinsus olseni. Functional annotation of differentially expressed genes between those two conditionswas performed by gene set enrichment analysis. As expected, microarrays unveil genes related with stress/infectious agents such as hydrolases, proteases and others. The extensive role of innate immune system was also analyzed and effect of parasitosis upon expression of important molecules such as lectins reviewed. Conclusions This study represents a first attempt to characterize Ruditapes decussatus transcriptome, an important marine resource for the European aquaculture. The trancriptome sequencing and consequent annotation will increase the available tools and resources for this specie, introducing the possibility of high throughput experiments such as microarrays analysis. In this specific case microarray approach was used to unveil some important aspects of host-parasite interaction between the Carpet shell clam and Perkinsus, two non-model species, highlighting some genes associated with this interaction. Ample information was obtained to identify biological processes significantly enriched among differentially expressed genes in Perkinsus infected versus non-infected gills. An overview on the genes related with the immune system on R. decussatus transcriptome is also reported.Peer Reviewe

Degenerate Dynamical Systems

Dynamical systems whose symplectic structure degenerates, becoming noninvertible at some points along the orbits are analyzed. It is shown that for systems with a finite number of degrees of freedom, like in classical mechanics, the degeneracy occurs on domain walls that divide phase space into nonoverlapping regions each one describing a nondegenerate system, causally disconnected from each other. These surfaces are characterized by the sign of the Liouville's flux density on them, behaving as sources or sinks of orbits. In this latter case, once the system reaches the domain wall, it acquires a new gauge invariance and one degree of freedom is dynamically frozen, while the remaining degrees of freedom evolve regularly thereafter.Comment: 6 pages, 1 figure, two columns, revtex. Minor changes. Final version for J. Math. Phy

Understanding the complete reservoir of bacteriophage depolymerases against A. baumannii capsules

A. baumannii is an important nosocomial and drug-resistant pathogen. The capsule is a major virulence factor that helps bacteria to avoid host immunity and viral predation. Acinetobacter phages can bind and degrade host capsules through capsular depolymerases with proven anti-virulence activity (1-3). Understanding the full reservoir of phage depolymerases against A. baumannii capsules, as well as relevant capsular types in clinical isolates, is crucial for developing depolymerase-based treatments. In this work, we 1) characterized 94 carbapenem-resistant A. baumannii Portuguese isolates; 2) isolated phages for relevant capsular types and characterized their depolymerases and 3) developed bioinformatic tools to collect the diversity of phage depolymerases. We show clonal shifts of A. baumannii KL2, KL7, KL9 and KL120 serotypes over time, with different virulence assessed in G. mellonella. Acinetobacter phages specific for particular k-types were isolated and several depolymerases (for KL1, KL2/KL19, KL9, KL30/KL45, KL32, KL38, KL44, KL67 types) characterized. We also demonstrate that most Acinetobacter phages encode capsular depolymerases (from 134 deposited in 2021, 73 contain capsular depolymerases), exclusively located in small viruses (<90 kb). To disclose the full genetic diversity, we developed PhageDPO (available in Galaxy uminho.pt server), a machine learning tool that identifies depolymerases in phages and bacteria genomes (prophages). We also present PhageKDB, a database that compiles available information of capsular depolymerases, retrieved through both manually and text-mining approaches, serving as an open portal to phage community. Overall, we present novel insights into A. baumannii isolates and phage depolymerase diversity and a collaborative tool to advance research in the field.info:eu-repo/semantics/publishedVersio

New di(hetero)arylethers and di(hetero)arylamines in the thieno[3,2-b]pyridine series: Synthesis, growth inhibitory activity on human tumor cell lines and non-tumor cells, effects on cell cycle and on programmed cell death

New fluorinated and methoxylated di(hetero)arylethers and di(hetero)arylamines were prepared functionalizing the 7-position of the thieno[3,2-blpyridine, using copper (C-O) or palladium (C N) catalyzed couplings, respectively, of the 7-bromothieno[3,2-blpyridine, also prepared, with ortho, meta and para fluoro or methoxy phenols and anilines. The compounds obtained were evaluated for their growth inhibitory activity on the human tumor cell lines MCF-7 (breast adenocarcinoma), NCI-H460 (non-small cell lung cancer), HCI15 (colon carcinoma), HepG2 (hepatocellular carcinoma) and HeLa (cervical carcinoma). The most active compounds, a di(hetero)arylether with a methoxy group in the meta position relative to the ether function and two di(hetero)arylamines with a methoxy group either in the ortho or in the meta position relative to the NH, were further tested at their GI(50) concentrations on NCI-H460 cells causing pronounced alterations in the cell cycle profile and a strong and significant increase in the programmed death of these cells. The fluorinated and the other methoxylated compounds did not show important activity, presenting high GI(50) values in all the cell lines tested. Furthermore, the hepatotoxicity of the compounds was assessed using porcine liver primary cells (PLP2), established by some of us. Results showed that one of the most active compounds was not toxic to the non-tumor cells at their GI(50) concentrations showing to be the most promising as antitumoral.The authors would like to thank to the Foundation for the Science and Technology (PCT Portugal) for financial support through the NMR Portuguese network (Bruker 400 Avance III-Univ Minho); to FCT and FEDER-COMPETE/QREN/EU for financial support through the research unities PEst-C/QUI/UI686/2011 and PEst-OE/AGR/UI0690/2011, the research project PTDC/QUI-QUI/111060/2009 and the post-Doctoral grants attributed to R.C.C. (SFRH/BPD/68344/2010) and R.T.L. (SRH/BPD/68787/2010). IPATIMUP is an Associate Laboratory of the Portuguese Ministry of Science, Technology and Higher Education and is partially supported by FCT

BVRI Light Curves for 29 Type Ia Supernovae

BVRI light curves are presented for 27 Type Ia supernovae discovered during the course of the Calan/Tololo Survey and for two other SNe Ia observed during the same period. Estimates of the maximum light magnitudes in the B, V, and I bands and the initial decline rate parameter m15(B) are also given.Comment: 17 pages, figures and tables are not included (contact first author if needed), to appear in the Astronomical Journa