Motivation: 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, clustering coefficient, diameter, and relative graphlet frequency 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.

Results: 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 of graphlets with 2--5 nodes, but it is easily extendible to a greater number of constraints (i.e. graphlets), if necessary, and the extensions are limited only by the available CPU. Furthermore, we show a way to combine the 73 graphlet degree distributions into a network 'agreement' measure which is a number between 0 and 1, where 1 means that networks have identical distributions and 0 means that they are far apart. Based on this new network agreement measure, we show that almost all of the 14 eukaryotic PPI networks, including human, resulting from various high-throughput experimental techniques, as well as from curated databases, are better modeled by geometric random graphs than by Erdos--Reny, random scale-free, or Barabasi--Albert scale-free networks.

Availability: Software executables are available upon request.

Contact: natasha@ics.uci.edu

pdf/biological-network-comparison-using-graphlet-degree-101en0jrqn.pdf

Biological network comparison using graphlet degree distribution

In mammals, cadmium is widely considered as a non-genotoxic carcinogen acting through a methylation-dependent epigenetic mechanism. Here, the effects of Cd treatment on the DNA methylation patten are examined together with its effect on chromatin reconfiguration in Posidonia oceanica. DNA methylation level and pattern were analysed in actively growing organs, under short- (6 h) and long- (2 d or 4 d) term and low (10 mM) and high (50 mM) doses of Cd, through a Methylation-Sensitive Amplification Polymorphism technique and an immunocytological approach, respectively. The expression of one member of the CHROMOMETHYLASE (CMT) family, a DNA methyltransferase, was also assessed by qRT-PCR. Nuclear chromatin ultrastructure was investigated by transmission electron microscopy. Cd treatment induced a DNA hypermethylation, as well as an up-regulation of CMT, indicating that de novo methylation did indeed occur. Moreover, a high dose of Cd led to a progressive heterochromatinization of interphase nuclei and apoptotic figures were also observed after long-term treatment. The data demonstrate that Cd perturbs the DNA methylation status through the involvement of a specific methyltransferase. Such changes are linked to nuclear chromatin reconfiguration likely to establish a new balance of expressed/repressed chromatin. Overall, the data show an epigenetic basis to the mechanism underlying Cd toxicity in plants.

/pdf/in-posidonia-oceanica-cadmium-induces-changes-in-dna-3cu7uj83mr.pdf

In Posidonia oceanica cadmium induces changes in DNA methylation and chromatin patterning

Plant tissue culture has become one of the fundamental tools of plant science research. It is extensively employed in the production, conservation and improvement of plant resources. The presence of somaclonal variation in populations derived from tissue culture is affecting the use of tissue culture negatively and has remained a major problem. Conversely, it is a source of new desirable clones/variants with better agronomic traits. In this review, we summarize the possible causes, detection methods and desirability of variants. Somaclonal variation is one of the most researched and reviewed topics. Hence, we restricted ourselves to outlining various examples which may be used as important references for researchers who intend to identify and/or characterize somaclonal variants while using tissue culture for research and production. Emphasis is placed on the negative effects of somaclonal variation. However, this review also includes examples of some useful variants generated as a result of somaclonal variation.

Somaclonal variation in plants: causes and detection methods

Morpho-physiological disorders in in vitro culture of plants

The role of activated charcoal in plant tissue culture.

A scheme for commercial propagation of ornamental plants by tissue culture

The metabolism and the in vitro effects of the cytokinin N6-(3-hydroxybenzyl)adenine (meta-topolin, mT) were compared with those of N6-benzyladenine (BA), N6-benzyl-9-(2-tetrahydropyranyl)adenine (BPA) and N6-benzyladenine-9-riboside ([9R]BA) in micropropagated Spathiphyllum floribundum Schott cv. Petite. In vitro, BA, BPA and [9R]BA were mainly converted into the stable derivative N6-benzyladenine-9-glucoside ([9G]BA), located at the basal part of the plant. N6-(3-O-β-D-glucopyranosyl)benzyladenine-9-riboside {(OG)[9R]mT} was the main derivative of mT. This new cytokinin-O-glucoside, which was present in all plant parts, was metabolized much faster than [9G]BA during acclimatization. The effect of BA and mT on in vitro shoot and root production and post vitro rooting was compared. Only mT combined a good shoot production with in vitro root formation. The plants that developed on medium with 10 µM or more mT rooted better during acclimatization than those developed on medium with equimolar concentrations of BA.

Meta‐topolin, an alternative to benzyladenine in tissue culture?

In order to save manual labour in plant tissue propagation, we tried adding liquid media to established, exhausted cultures, instead of transplanting the tissues to a fresh medium This has been investigated for the elongation and for root induction stages with Cordyline, Philodendron, Magnolia and Spathiphyllum The salt concentration and the application time are important factors, determining the success of this method Charcoal added to the liquid stage IIIa medium eliminated the residual effects of BA applied during stage II

Liquid medium additions to established tissue cultures to improve elongation and rooting in vivo

Shootlets of Rosa multiflora L. cv. Montse were cultured in vitro with four different levels of sucrose (0, 1, 3 and 5%). Chloroplasts of shootlets grown in a medium without sucrose contained numerous, large plastoglobuli and were lacking in starch granules. The size and number of starch granules increased with the level of sucrose in the culture medium. Starch content in leaves of shootlets grown with 5% sucrose was higher (ca 1, 3%) than those grown with 3% (ca 0, 45%) and 1% sucrose (ca 0, 27%). Starch might be used by the in vitro shootlets during the acclimation period.

Effects of sucrose on starch accumulation and rate of photosynthesis in Rosa cultured in vitro

Subcultured explants of Magnolia soulangeana Soul, were incubated in tissue culture containers fitted with different types of closures. Type of closure affected the CO2 concentration, with levels as high as 14% CO2 being detected. The ethylene concentration increased gradually with time, to as much as 2–3 ppm after 9 weeks. There was a large variation in the composition of the atmosphere within the containers of any one type. The way by which a container was closed influenced exchange of the inner gas phase with the surrounding atmosphere and was important in determining the development of the cultured tissues.

Carbon dioxide and ethylene evolution in the culture atmosphere of Magnolia cultured in vitro

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