3,201 research outputs found
Composition and regulation of maternal and zygotic transcriptomes reflects species-specific reproductive mode
Background
Early embryos contain mRNA transcripts expressed from two distinct origins; those expressed from the mother's genome and deposited in the oocyte (maternal) and those expressed from the embryo's genome after fertilization (zygotic). The transition from maternal to zygotic control occurs at different times in different animals according to the extent and form of maternal contributions, which likely reflect evolutionary and ecological forces. Maternally deposited transcripts rely on post-transcriptional regulatory mechanisms for precise spatial and temporal expression in the embryo, whereas zygotic transcripts can use both transcriptional and post-transcriptional regulatory mechanisms. The differences in maternal contributions between animals may be associated with gene regulatory changes detectable by the size and complexity of the associated regulatory regions.
Results
We have used genomic data to identify and compare maternal and/or zygotic expressed genes from six different animals and find evidence for selection acting to shape gene regulatory architecture in thousands of genes. We find that mammalian maternal genes are enriched for complex regulatory regions, suggesting an increase in expression specificity, while egg-laying animals are enriched for maternal genes that lack transcriptional specificity.
Conclusions
We propose that this lack of specificity for maternal expression in egg-laying animals indicates that a large fraction of maternal genes are expressed non-functionally, providing only supplemental nutritional content to the developing embryo. These results provide clear predictive criteria for analysis of additional genomes.Molecular and Cellular Biolog
Serially-regulated biological networks fully realize a constrained set of functions
We show that biological networks with serial regulation (each node regulated
by at most one other node) are constrained to {\it direct functionality}, in
which the sign of the effect of an environmental input on a target species
depends only on the direct path from the input to the target, even when there
is a feedback loop allowing for multiple interaction pathways. Using a
stochastic model for a set of small transcriptional regulatory networks that
have been studied experimentally, we further find that all networks can achieve
all functions permitted by this constraint under reasonable settings of
biochemical parameters. This underscores the functional versatility of the
networks.Comment: 9 pages, 3 figure
CD24 cell surface expression in Mvt1 mammary cancer cells serves as a biomarker for sensitivity to anti-IGF1R therapy
IGF1R-KD significantly reduced the metastatic capacity of CD24+ cells. (A) Representation of lung metastasis following 4Ă weeks of 10,000 cells inoculation into WT mice tail vein. (B) Average of macrometastasis per lung in each group is displayed in the bar graph. Mann-Whitney test performed to compare the difference between the groups. **PĂąÂÂ<ĂąÂÂ0.005. (PPTX 537 kb
Biological network comparison using graphlet degree distribution
Analogous to biological sequence comparison, comparing cellular networks is
an important problem that could provide insight into biological understanding
and therapeutics. For technical reasons, comparing large networks is
computationally infeasible, and thus heuristics such as the degree distribution
have been sought. It is easy to demonstrate that two networks are different by
simply showing a short list of properties in which they differ. It is much
harder to show that two networks are similar, as it requires demonstrating
their similarity in all of their exponentially many properties. Clearly, it is
computationally prohibitive to analyze all network properties, but the larger
the number of constraints we impose in determining network similarity, the more
likely it is that the networks will truly be similar.
We introduce a new systematic measure of a network's local structure that
imposes a large number of similarity constraints on networks being compared. In
particular, we generalize the degree distribution, which measures the number of
nodes 'touching' k edges, into distributions measuring the number of nodes
'touching' k graphlets, where graphlets are small connected non-isomorphic
subgraphs of a large network. Our new measure of network local structure
consists of 73 graphlet degree distributions (GDDs) of graphlets with 2-5
nodes, but it is easily extendible to a greater number of constraints (i.e.
graphlets). Furthermore, we show a way to combine the 73 GDDs into a network
'agreement' measure. Based on this new network agreement measure, we show that
almost all of the 14 eukaryotic PPI networks, including human, are better
modeled by geometric random graphs than by Erdos-Reny, random scale-free, or
Barabasi-Albert scale-free networks.Comment: Proceedings of the 2006 European Conference on Computational Biology,
ECCB'06, Eilat, Israel, January 21-24, 200
ImmPort, toward repurposing of open access immunological assay data for translational and clinical research
Immunology researchers are beginning to explore the possibilities of reproducibility, reuse and secondary analyses of immunology data. Open-access datasets are being applied in the validation of the methods used in the original studies, leveraging studies for meta-analysis, or generating new hypotheses. To promote these goals, the ImmPort data repository was created for the broader research community to explore the wide spectrum of clinical and basic research data and associated findings. The ImmPort ecosystem consists of four componentsâPrivate Data, Shared Data, Data Analysis, and Resourcesâfor data archiving, dissemination, analyses, and reuse. To date, more than 300 studies have been made freely available through the ImmPort Shared Data portal , which allows research data to be repurposed to accelerate the translation of new insights into discoveries
Topology of biological networks and reliability of information processing
Biological systems rely on robust internal information processing: Survival
depends on highly reproducible dynamics of regulatory processes. Biological
information processing elements, however, are intrinsically noisy (genetic
switches, neurons, etc.). Such noise poses severe stability problems to system
behavior as it tends to desynchronize system dynamics (e.g. via fluctuating
response or transmission time of the elements). Synchronicity in parallel
information processing is not readily sustained in the absence of a central
clock. Here we analyze the influence of topology on synchronicity in networks
of autonomous noisy elements. In numerical and analytical studies we find a
clear distinction between non-reliable and reliable dynamical attractors,
depending on the topology of the circuit. In the reliable cases, synchronicity
is sustained, while in the unreliable scenario, fluctuating responses of single
elements can gradually desynchronize the system, leading to non-reproducible
behavior. We find that the fraction of reliable dynamical attractors strongly
correlates with the underlying circuitry. Our model suggests that the observed
motif structure of biological signaling networks is shaped by the biological
requirement for reproducibility of attractors.Comment: 7 pages, 7 figure
Structure of n-clique networks embedded in a complex network
We propose the n-clique network as a powerful tool for understanding global
structures of combined highly-interconnected subgraphs, and provide theoretical
predictions for statistical properties of the n-clique networks embedded in a
complex network using the degree distribution and the clustering spectrum.
Furthermore, using our theoretical predictions, we find that the statistical
properties are invariant between 3-clique networks and original networks for
several observable real-world networks with the scale-free connectivity and the
hierarchical modularity. The result implies that structural properties are
identical between the 3-clique networks and the original networks.Comment: 12 pages, 5 figure
Patterns of Interactions in Complex Social Networks Based on Coloured Motifs Analysis
Coloured network motifs are small subgraphs that enable to discover and interpret the patterns of interaction within the complex networks. The analysis of three-nodes motifs where the colour of the node reflects its high â white node or low â black node centrality in the social network is presented in the paper. The importance of the vertices is assessed by utilizing two measures: degree prestige and degree centrality. The distribution of motifs in these two cases is compared to mine the interconnection patterns between nodes. The analysis is performed on the social network derived from email communication
Identifying dynamical modules from genetic regulatory systems: applications to the segment polarity network
BACKGROUND
It is widely accepted that genetic regulatory systems are 'modular', in that the whole system is made up of smaller 'subsystems' corresponding to specific biological functions. Most attempts to identify modules in genetic regulatory systems have relied on the topology of the underlying network. However, it is the temporal activity (dynamics) of genes and proteins that corresponds to biological functions, and hence it is dynamics that we focus on here for identifying subsystems.
RESULTS
Using Boolean network models as an exemplar, we present a new technique to identify subsystems, based on their dynamical properties. The main part of the method depends only on the stable dynamics (attractors) of the system, thus requiring no prior knowledge of the underlying network. However, knowledge of the logical relationships between the network components can be used to describe how each subsystem is regulated. To demonstrate its applicability to genetic regulatory systems, we apply the method to a model of the Drosophila segment polarity network, providing a detailed breakdown of the system.
CONCLUSION
We have designed a technique for decomposing any set of discrete-state, discrete-time attractors into subsystems. Having a suitable mathematical model also allows us to describe how each subsystem is regulated and how robust each subsystem is against perturbations. However, since the subsystems are found directly from the attractors, a mathematical model or underlying network topology is not necessarily required to identify them, potentially allowing the method to be applied directly to experimental expression data
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