CNplot: visualizing pre-clustered networks

SUMMARY: CNplot is a simple technique for the visualization of global connectivity within pre-clustered network data. CNplot is easy to implement and in most cases produces informative and satisfactory summary of the data. AVAILABILITY: A Java implementation is available that allows users to modify graphics parameters and produces a LaTeX output. This software is free and is available at http://csb.stanford.edu/nbatada/VCN.html     

The antidepressant-like effect of Ocimum basilicum in an animal model of depression

We investigated the efficacy of Ocimum basilicum (OB) essential oils for treating depression related behavioral, biochemical and histopathological changes caused by exposure to chronic unpredictable mild stress (CUMS) in mice and to explore the mechanism underlying the pathology. Male albino mice were divided into four groups: controls; CUMS; CUMS plus fluoxetine, the antidepressant administered for pharmacological validation of OB; and CUMS plus OB. Behavioral tests included the forced swim test (FST), elevated plus-maze (EPM) and the open ?eld test (OFT); these tests were performed at the end of the experiment. We assessed serum corticosterone level, protein, gene and immunoexpression of brain-derived neurotropic factor (BDNF) and glucocorticoid receptors (GRs) as well as immunoexpression of glial fibrillary acidic protein (GFAP), Ki67, caspase-3 in the hippocampus. CUMS caused depression in the mice as evidenced by prolonged immobility in the FST, prolonged time spent in the open arms during the EPM test and reduction of open field activity in the OFT. OB ameliorated the CUMS induced depressive status. OB significantly reduced the corticosterone level and up-regulated protein and gene expressions of BDNF and GR. OB reduced CUMS induced hippocampal neuron atrophy and apoptosis, and increased the number of the astrocytes and new nerve cells. OB significantly increased GFAP-positive cells as well as BDNF and GR immunoexpression in the hippocampus.     

Spatial regulation and the rate of signal transduction activation

Of the many important signaling events that take place on the surface of a mammalian cell, activation of signal transduction pathways via interactions of cell surface receptors is one of the most important. Evidence suggests that cell surface proteins are not as freely diffusible as implied by the classic fluid mosaic model and that their confinement to membrane domains is regulated. It is unknown whether these dynamic localization mechanisms function to enhance signal transduction activation rate or to minimize cross talk among pathways that share common intermediates. To determine which of these two possibilities is more likely, we derive an explicit equation for the rate at which cell surface membrane proteins interact based on a Brownian motion model in the presence of endocytosis and exocytosis. We find that in the absence of any diffusion constraints, cell surface protein interaction rate is extremely high relative to cytoplasmic protein interaction rate even in a large mammalian cell with a receptor abundance of a mere two hundred molecules. Since a larger number of downstream signaling events needs to take place, each occurring at a much slower rate than the initial activation via association of cell surface proteins, we conclude that the role of co-localization is most likely that of cross-talk reduction rather than coupling efficiency enhancement.     

The impact of the nucleosome code on protein-coding sequence evolution in yeast

Coding sequence evolution was once thought to be the result of selection on optimal protein function alone. Selection can, however, also act at the RNA level, for example, to facilitate rapid translation or ensure correct splicing. Here, we ask whether the way DNA works also imposes constraints on coding sequence evolution. We identify nucleosome positioning as a likely candidate to set up such a DNA-level selective regime and use high-resolution microarray data in yeast to compare the evolution of coding sequence bound to or free from nucleosomes. Controlling for gene expression and intra-gene location, we find a nucleosome-free "linker" sequence to evolve on average 5-6% slower at synonymous sites. A reduced rate of evolution in linker is especially evident at the 5' end of genes, where the effect extends to non-synonymous substitution rates. This is consistent with regular nucleosome architecture in this region being important in the context of gene expression control. As predicted, codons likely to generate a sequence unfavourable to nucleosome formation are enriched in linker sequence. Amino acid content is likewise skewed as a function of nucleosome occupancy. We conclude that selection operating on DNA to maintain correct positioning of nucleosomes impacts codon choice, amino acid choice, and synonymous and non-synonymous rates of evolution in coding sequence. The results support the exclusion model for nucleosome positioning and provide an alternative interpretation for runs of rare codons. As the intimate association of histones and DNA is a universal characteristic of genic sequence in eukaryotes, selection on coding sequence composition imposed by nucleosome positioning should be phylogenetically widespread.     

Productivity of forests in the Eurosiberian boreal region and their potential to act as a carbon sink –- a synthesis

Based on review and original data, this synthesis investigates carbon pools and fluxes of Siberian and European forests (600 and 300 million ha, respectively). We examine the productivity of ecosystems, expressed as positive rate when the amount of carbon in the ecosystem increases, while (following micrometeorological convention) downward fluxes from the atmosphere to the vegetation (NEE = Net Ecosystem Exchange) are expressed as negative numbers. Productivity parameters are Net Primary Productivity (NPP=whole plant growth), Net Ecosystem Productivity (NEP = CO₂ assimilation minus ecosystem respiration), and Net Biome Productivity (NBP = NEP minus carbon losses through disturbances bypassing respiration, e.g. by fire and logging). Based on chronosequence studies and national forestry statistics we estimate a low average NPP for boreal forests in Siberia: 123 gC m^–2 y^–1. This contrasts with a similar calculation for Europe which suggests a much higher average NPP of 460 gC m^–2 y^–1 for the forests there. Despite a smaller area, European forests have a higher total NPP than Siberia (1.2–1.6 vs. 0.6–0.9 × 10¹⁵ gC region^–1 y^–1). This arises as a consequence of differences in growing season length, climate and nutrition. For a chronosequence of Pinus sylvestris stands studied in central Siberia during summer, NEE was most negative in a 67-y old stand regenerating after fire (– 192 mmol m^–2 d^–1) which is close to NEE in a cultivated forest of Germany (– 210 mmol m^–2 d^–1). Considerable net ecosystem CO₂-uptake was also measured in Siberia in 200- and 215-y old stands (NEE:174 and – 63 mmol m^–2 d^–1) while NEP of 7- and 13-y old logging areas were close to the ecosystem compensation point. Two Siberian bogs and a bog in European Russia were also significant carbon sinks (– 102 to – 104 mmol m^–2 d^–1). Integrated over a growing season (June to September) we measured a total growing season NEE of – 14 mol m^–2 summer^–1 (– 168 gC m^–2 summer^–1) in a 200-y Siberian pine stand and – 5 mol m^–2 summer^–1 (– 60 gC m^–2 summer^–1) in Siberian and European Russian bogs. By contrast, over the same period, a spruce forest in European Russia was a carbon source to the atmosphere of (NEE: + 7 mol m^–2 summer^–1 = + 84 gC m^–2 summer^–1). Two years after a windthrow in European Russia, with all trees being uplifted and few successional species, lost 16 mol C m^–2 to the atmosphere over a 3-month in summer, compared to the cumulative NEE over a growing season in a German forest of – 15.5 mol m^–2 summer^–1 (– 186 gC m^–2 summer^–1; European flux network annual averaged – 205 gC m^–2 y^–1). Differences in CO₂-exchange rates coincided with differences in the Bowen ratio, with logging areas partitioning most incoming radiation into sensible heat whereas bogs partitioned most into evaporation (latent heat). Effects of these different surface energy exchanges on local climate (convective storms and fires) and comparisons with the Canadian BOREAS experiment are discussed. Following a classification of disturbances and their effects on ecosystem carbon balances, fire and logging are discussed as the main processes causing carbon losses that bypass heterotrophic respiration in Siberia. Following two approaches, NBP was estimated to be only about 13–16 mmol m^–2 y^–1 for Siberia. It may reach 67 mmol m^–2 y^–1 in North America, and about 140–400 mmol m^–2 y^–1 in Scandinavia. We conclude that fire speeds up the carbon cycle, but that it results also in long-term carbon sequestration by charcoal formation. For at least 14 years after logging, regrowth forests remain net sources of CO₂ to the atmosphere. This has important implications regarding the effects of Siberian forest management on atmospheric concentrations. For many years after logging has taken place, regrowth forests remain weaker sinks for atmospheric CO₂ than are nearby old-growth forests.     

Using wintergreen oil for mounting mosquito larvae: a safer alternative to xylene

Permanent mounting of fourth instar mosquito larvae is essential for identifying Aedes spp. This procedure requires extensive exposure to xylene, a clearing agent in the mounting process. We investigated wintergreen oil as a substitute for xylene. Five hundred larvae were mounted on slides to evaluate shrinkage or expansion of specimens after clearing using xylene or wintergreen oil. We examined the ventral brush and siphonal hair tufts for species identification and for preservation of morphological characteristics after clearing specimens in xylene or wintergreen oil. Shrinkage of the length of whole larvae and width of the head, thorax and abdomen after mounting was significantly greater after clearing with xylene than with wintergreen oil. The length of the comb scale nearest the ventral brush was similar for both clearing agents. The clarity of the specimens after mounting was improved by clearing with wintergreen oil, but the integrity of the ventral brush and siphonal hair tufts were similar for both clearing agents.     

Stratus not altocumulus: a new view of the yeast protein interaction network

Systems biology approaches can reveal intermediary levels of organization between genotype and phenotype that often underlie biological phenomena such as polygenic effects and protein dispensability. An important conceptualization is the module, which is loosely defined as a cohort of proteins that perform a dedicated cellular task. Based on a computational analysis of limited interaction datasets in the budding yeast Saccharomyces cerevisiae, it has been suggested that the global protein interaction network is segregated such that highly connected proteins, called hubs, tend not to link to each other. Moreover, it has been suggested that hubs fall into two distinct classes: "party" hubs are co-expressed and co-localized with their partners, whereas "date" hubs interact with incoherently expressed and diversely localized partners, and thereby cohere disparate parts of the global network. This structure may be compared with altocumulus clouds, i.e., cotton ball-like structures sparsely connected by thin wisps. However, this organization might reflect a small and/or biased sample set of interactions. In a multi-validated high-confidence (HC) interaction network, assembled from all extant S. cerevisiae interaction data, including recently available proteome-wide interaction data and a large set of reliable literature-derived interactions, we find that hub-hub interactions are not suppressed. In fact, the number of interactions a hub has with other hubs is a good predictor of whether a hub protein is essential or not. We find that date hubs are neither required for network tolerance to node deletion, nor do date hubs have distinct biological attributes compared to other hubs. Date and party hubs do not, for example, evolve at different rates. Our analysis suggests that the organization of global protein interaction network is highly interconnected and hence interdependent, more like the continuous dense aggregations of stratus clouds than the segregated configuration of altocumulus clouds. If the network is configured in a stratus format, cross-talk between proteins is potentially a major source of noise. In turn, control of the activity of the most highly connected proteins may be vital. Indeed, we find that a fluctuation in steady-state levels of the most connected proteins is minimized.