Systematic characterization of nuclear proteome during apoptosis: a quantitative proteomic study by differential extraction and stable isotope labeling

Identification and characterization of the nuclear proteome is important for detailed understanding of multiple signaling events in eukaryotic cells. Toward this goal, we extensively characterized the nuclear proteome of human T leukemia cells by sequential extraction of nuclear proteins with different physicochemical properties using three buffer conditions. This large scale proteomic study also tested the feasibility and technical challenges associated with stable isotope labeling by amino acids in cell culture (SILAC) to uncover quantitative changes during apoptosis. Analyzing proteins from three nuclear fractions extracted from naive and apoptotic cells generated 780,530 MS/MS spectra that were used for database searching using the SEQUEST algorithm. This analysis resulted in the identification and quantification of 1,174 putative nuclear proteins. A number of known nuclear proteins involved in apoptosis as well as novel proteins not known to be part of the nuclear apoptotic machinery were identified and quantified. Consistent with SILAC-based quantifications, immunofluorescence staining of nucleus, mitochondria, and some associated proteins from both organelles revealed a dynamic recruitment of mitochondria into nuclear invaginations during apoptosis.     

Induction of tumor necrosis factor alpha in human neuronal cells by extracellular human T-cell lymphotropic virus type 1 Tax.

To examine the role of human T-lymphotropic virus type 1 (HTLV-1) Tax1 in the development of neurological disease, we studied the effects of extracellular Tax1 on gene expression in NT2-N cells, postmitotic cells that share morphologic, phenotypic, and functional features with mature human primary neurons. Treatment with soluble HTLV-1 Tax1 resulted in the induction of tumor necrosis factor alpha (TNF-alpha) gene expression, as detected by reverse-transcribed PCR and by enzyme-linked immunosorbent assay. TNF-alpha induction was completely blocked by clearance with anti-Tax1 monoclonal antibodies. Furthermore, cells treated with either a mock bacterial extract or with lipopolysaccharide produced no detectable TNF-alpha. Synthesis of TNF-alpha in response to soluble Tax1 occurred in a dose-dependent fashion between 0.25 and 75 nM and peaked within 6 h of treatment. Interestingly, culturing NT2-N cells in the presence of soluble Tax1 for as little as 5 min was sufficient to result in TNF-alpha production, indicating that the induction of TNF-alpha in NT2-N does not require Tax1 to be continually present in the culture medium. Treatment of the undifferentiated parental embryonal carcinoma cell line NT2 with soluble Tax1 did not result in TNF-alpha synthesis, suggesting that differentiation-dependent, neuron-specific factors may be required. These results provide the first experimental evidence that neuronal cells are sensitive to HTLV-1 Tax1 as an extracellular cytokine, with a potential role in the pathology of HTLV-1-associated/tropical spastic paraparesis.     

Temporal oscillations in neuronal nets

Summary A model for the interactions of cortical neurons is derived and analyzed. It is shown that small amplitude spatially inhomogeneous standing oscillations can bifurcate from the rest state. In a periodic domain, traveling wave trains exist. Stability of these patterns is discussed in terms of biological parameters. Homoclinic and heteroclinic orbits are demonstrated for the space-clamped system.The research reported in this paper was supported in part by NIH GM2037     

High-Level Diversity of Tailed Phages,Eukaryote-Associated Viruses,and Virophage-Like Elements in the Metaviromes of Antarctic Soils

The metaviromes of two distinct Antarctic hyperarid desert soil communities have been characterized. Hypolithic communities, cyanobacterium-dominated assemblages situated on the ventral surfaces of quartz pebbles embedded in the desert pavement, showed higher virus diversity than surface soils, which correlated with previous bacterial community studies. Prokaryotic viruses (i.e., phages) represented the largest viral component (particularly Mycobacterium phages) in both habitats, with an identical hierarchical sequence abundance of families of tailed phages (Siphoviridae > Myoviridae > Podoviridae). No archaeal viruses were found. Unexpectedly, cyanophages were poorly represented in both metaviromes and were phylogenetically distant from currently characterized cyanophages. Putative phage genomes were assembled and showed a high level of unaffiliated genes, mostly from hypolithic viruses. Moreover, unusual gene arrangements in which eukaryotic and prokaryotic virus-derived genes were found within identical genome segments were observed. Phycodnaviridae and Mimiviridae viruses were the second-most-abundant taxa and more numerous within open soil. Novel virophage-like sequences (within the Sputnik clade) were identified. These findings highlight high-level virus diversity and novel species discovery potential within Antarctic hyperarid soils and may serve as a starting point for future studies targeting specific viral groups.     

Yield of willow (Salix spp.) grown in short rotation coppice mixtures in a long‐term trial

Salix spp. genotypes were grown in random intimate mixtures comprising 5, 10, 15 and 20 components at 3 planting densities (10 000, 15 000 and 20 000 cuttings ha^?1). Planted in 1994/95, plots were harvested every 3 years in 1998/99 (previously reported), 2001/02, 2004/05 and 2007/08. Each individual stool in both mono‐ and mixture plots was weighed. The total yield from mixture plots was consistently higher than the mean of the components in mono‐plots and with only limited exceptions higher than the yield of any of the individual components grown in mono‐plots. This occurred despite the loss of a number of disease‐susceptible genotypes. When a stool died the remaining plants were able to colonise the vacant space and compensate for the loss. There was no clear benefit in increasing the number of components from 10 to 15 or 20 although host diversity is considered to be an important contributor to the effectiveness of a mixture both in disease reduction and yield enhancement. It is argued that the use of Salix spp. mixtures is highly advantageous, even in the absence of any disease pressure, and that mixtures increase the sustainability of a willow plantation.     

Gradients of Intercellular CO(2) Levels Across the Leaf Mesophyll

Most current photosynthesis models, and interpretations of many wholeleaf CO₂ gas exchange measurements, are based on the often unstated assumption that the partial pressure of CO₂ is nearly uniform throughout the airspaces of the leaf mesophyll. Here we present measurements of CO₂ gradients across amphistomatous leaves allowed to assimilate CO₂ through only one surface, thus simulating hypostomatous leaves. We studied five species: Eucalyptus pauciflora Sieb. ex Spreng., Brassica chinensis L., Gossypium hirsutum L., Phaseolus vulgaris L., and Spinacia oleracea L. For Eucalyptus, maximum CO₂ pressure differences across the leaf mesophyll were 73 and 160 microbar when the pressures outside the lower leaf surface were 310 and 590 microbar, respectively. Using an approximate theoretical calculation, we infer that if the CO₂ had been supplied equally at both surfaces then the respective mean intercellular CO₂ pressures would have been roughly 12 and 27 microbar less than the pressures in the substomatal cavities in these cases. For ambient CO₂ pressures near 320 microbar, the average and minimum pressure differences across the mesophyll were 45 and 13 microbar. The corresponding mean intercellular CO₂ pressures would then be roughly 8 and 2 microbar less than those in the substomatal cavities. Pressure differences were generally smaller for the four agricultural species than for Eucalyptus, but they were nevertheless larger than previously reported values.     

Response of microbial adhesives and biofilm matrix polymers to chemical treatments as determined by interference reflection microscopy and light section microscopy.

The polymers involved in the adhesion of Pseudomonas fluorescens H2S to solid surfaces were investigated to determine whether differences between cell surface adhesives and biofilm matrix polymers could be detected. Two optical techniques, i.e., interference reflection microscopy (IRM) and light section microscopy (LSM), were used to compare the responses of the two types of polymer to treatment with electrolytes, dimethyl sulfoxide (DMSO), and Tween 20. To evaluate initial adhesive polymers, P. fluorescens H2S cells were allowed to attach to glass cover slip surfaces and were immediately examined with IRM, and their response to chemical solutions was tested. With IRM, changes in cell-substratum separation distance between 0 and ca. 100 nm are detectable as changes in relative light intensity of the image; a contraction of the polymer would be detected as a darkening of the image, whereas expansion would appear as image brightening. To evaluate the intercellular polymer matrix in biofilms, 3-day-old biofilms were exposed to similar solutions, and the resultant change in biofilm thickness was measured with LSM, which measures film thicknesses between 10 and 1,000 microns. The initial adhesive and biofilm polymers were similar in that both appeared to contract when treated with electrolytes and to expand when treated with Tween 20. However, with DMSO treatment, the initial adhesive polymer appeared to contract, whereas there was no change in thickness of the biofilm polymer. These results indicate that both polymers bear acidic groups and thus act electrostatically with cations and are able to enter into hydrophobic interactions.(ABSTRACT TRUNCATED AT 250 WORDS)