2,329 research outputs found
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
AM-OER: An Agile Method for the Development of Open Educational Resources
Open Educational Resources have emerged as important elements of education in the contemporary society, promoting life-long and personalized learning that transcends social, eco- nomic and geographical barriers. To achieve the potential of OERs and bring impact on education, it is necessary to increase their development and supply. However, one of the current challenges is how to produce quality and relevant OERs to be reused and adapted to different contexts and learning situations. In this paper we proposed an agile method for the development of OERs – AM-OER, grounded on agile practices from Software Engineering. Learning Design practices from the OULDI project (UK Open University) are also embedded into the AM-OER aiming at improving quality and facilitating reuse and adaptation of OERs. In order to validate AM-OER, an experiment was conducted by applying it in the development of an OER on software testing. The results showed preliminary evidences on the applicability, effectiveness and ef ciency of the method in the development of OERs
CplexA: a Mathematica package to study macromolecular-assembly control of gene expression
Summary: Macromolecular assembly vertebrates essential cellular processes,
such as gene regulation and signal transduction. A major challenge for
conventional computational methods to study these processes is tackling the
exponential increase of the number of configurational states with the number of
components. CplexA is a Mathematica package that uses functional programming to
efficiently compute probabilities and average properties over such
exponentially large number of states from the energetics of the interactions.
The package is particularly suited to study gene expression at complex
promoters controlled by multiple, local and distal, DNA binding sites for
transcription factors. Availability: CplexA is freely available together with
documentation at http://sourceforge.net/projects/cplexa/.Comment: 28 pages. Includes Mathematica, Matlab, and Python implementation
tutorials. Software can be downloaded at http://cplexa.sourceforge.net
Stochastic dynamics of macromolecular-assembly networks
The formation and regulation of macromolecular complexes provides the
backbone of most cellular processes, including gene regulation and signal
transduction. The inherent complexity of assembling macromolecular structures
makes current computational methods strongly limited for understanding how the
physical interactions between cellular components give rise to systemic
properties of cells. Here we present a stochastic approach to study the
dynamics of networks formed by macromolecular complexes in terms of the
molecular interactions of their components. Exploiting key thermodynamic
concepts, this approach makes it possible to both estimate reaction rates and
incorporate the resulting assembly dynamics into the stochastic kinetics of
cellular networks. As prototype systems, we consider the lac operon and phage
lambda induction switches, which rely on the formation of DNA loops by proteins
and on the integration of these protein-DNA complexes into intracellular
networks. This cross-scale approach offers an effective starting point to move
forward from network diagrams, such as those of protein-protein and DNA-protein
interaction networks, to the actual dynamics of cellular processes.Comment: Open Access article available at
http://www.nature.com/msb/journal/v2/n1/full/msb4100061.htm
A manual of suggestions adapting the instructional materials in the social studies to the reading abilities of slow learning children in the fifth grade.
Thesis (M.A.)--Boston Universit
Bound states in the continuum: localization of Dirac-like fermions
We report the formation of bound states in the continuum for Dirac-like
fermions in structures composed by a trilayer graphene flake connected to
nanoribbon leads. The existence of this kind of localized states can be proved
by combining local density of states and electronic conductance calculations.
By applying a gate voltage, the bound states couple to the continuum, yielding
a maximum in the electronic transmission. This feature can be exploited to
identify bound states in the continuum in graphene-based structures.Comment: 7 pages, 5 figure
Controlling the layer localization of gapless states in bilayer graphene with a gate voltage
Experiments in gated bilayer graphene with stacking domain walls present
topological gapless states protected by no-valley mixing. Here we research
these states under gate voltages using atomistic models, which allow us to
elucidate their origin. We find that the gate potential controls the layer
localization of the two states, which switches non-trivially between layers
depending on the applied gate voltage magnitude. We also show how these bilayer
gapless states arise from bands of single-layer graphene by analyzing the
formation of carbon bonds between layers. Based on this analysis we provide a
model Hamiltonian with analytical solutions, which explains the layer
localization as a function of the ratio between the applied potential and
interlayer hopping. Our results open a route for the manipulation of gapless
states in electronic devices, analogous to the proposed writing and reading
memories in topological insulators
- …