Trees on networks: resolving statistical patterns of phylogenetic similarities among interacting proteins

Background  

Phylogenies capture the evolutionary ancestry linking extant species. Correlations and similarities among a set of species are mediated by and need to be understood in terms of the phylogenic tree. In a similar way it has been argued that biological networks also induce correlations among sets of interacting genes or their protein products.     

Moving forward with the primate microbiome: Introduction to a special issue of the American Journal of Primatology

Primate microbiome research is a quickly growing field with exciting potential for informing our understanding of primate biology, ecology, and evolution as well as host‐microbe interactions more broadly. This introductory essay to a special section of the American Journal of Primatology provides a cross‐sectional snapshot of current activity in these areas by briefly summarizing the diversity of contributed papers and their relationships to key themes in host‐associated microbiome research. It then uses this survey as a foundation for consolidating a set of key research questions to broadly guide future research. It also argues for the importance of methods standardization to facilitate comparative analyses and the identification of generalizable patterns and relationships. While primatology will benefit greatly from the integration of microbial datasets, it is uniquely positioned to address important questions regarding microbiology and macro‐ecology and evolution more generally. We are eager to see where the primate microbiome leads us.     

Depicting the Spatial Distribution of Proteins in Human Tumor Tissue Combining SELDI and MALDI Imaging and Immunohistochemistry

Carcinoma tissue consists of not only tumor cells but also fibroblasts, endothelial cells or vascular structures, and inflammatory cells forming the supportive tumor stroma. Therefore, the spatial distribution of proteins that promote growth and proliferation in these complex functional units is of high interest. Matrix-assisted laser desorption/ionization imaging mass spectrometry is a newly developed technique that generates spatially resolved profiles of protein signals directly from thin tissue sections. Surface-enhanced laser desorption/ionization mass spectrometry (MS)combined with tissue microdissection allows analysis of defined parts of the tissue with a higher sensitivity and a broader mass range. Nevertheless, both MS-based techniques have a limited spatial resolution. IHC is a technique that allows a resolution down to the subcellular level. However, the detection and measurement of a specific protein expression level is possible only by semiquantitative methods. Moreover, prior knowledge about the identity of the proteins of interest is necessary. In this study, we combined all three techniques to gain highest spatial resolution, sensitivity, and quantitative information. We used frozen tissue from head and neck tumors and chose two exemplary proteins (HNP1–3 and S100A8) to highlight the advantages and disadvantages of each technique. It could be shown that the combination of these three techniques results in congruent but also synergetic data. (J Histochem Cytochem 58:929–937, 2010)     

Subcellular localization of acetyl-CoA synthetase in leaf protoplasts of Spinacia oleracea

The localization of acetyl-CoA synthetase in the spinach leaf cell was examined. When the different compartments of lysed spinach protoplasts were assayed for marker enzymes and acetyl-CoA synthetase, it was determined that the synthetase was totally localized in the chloroplast compartment. Analysis of spinach leaf for free acetate revealed that this acid was present at a 1 mm level in the leaf cell. It is suggested that free acetate probably derived from a number of sources in the cell diffuses into the chloroplast stroma compartment where it is converted to acetyl-CoA and thence employed for biosynthetic reactions. Thus, free acetate is metabolically inert in the leaf cell until it is transported to the only compartment that contains acetyl-CoA synthetase, namely the chloroplast.     

Utility of [16 alpha-125I] iodoestradiol for autoradiography for the study of cellular and regional distribution of receptors

We demonstrate the utility of [16 alpha-125I]iodoestradiol for thaw-mount autoradiography with 2 micron and 4 micron thick sections of rat and mouse uterus, pituitary, and brain after in vivo administration. Under the conditions of the experiments, short-term autoradiography with exposure times between 3 and 14 days provides optimal cellular resolution, whereas long-term autoradiography with 1-2 months of exposure may be used to obtain topographic-regional surveys of distribution.     

Nuclear receptors for 1,25(OH)2 vitamin D3 in thymus reticular cells studied by autoradiography

Summary After injection of ³H 1,25(OH)₂ vitamin D₃ to rats fed a vitamin D-deficient diet, nuclear concentration and retention of radioactivity exists in reticular cells of the thymus medulla and cortex, as well as outer cells of developing Hassal's corpuscles. Lymphocytes do not show nuclear concentration of radioactivity. Nuclear concentration in reticular cells is prevented by prior injection of excess 1,25(OH)₂ vitamin D₃. The results indicate that reticular-endothelial cells contain nuclear receptors for 1,25(OH)₂ vitamin D₃ and suggest that effects of 1,25(OH)₂ vitamin D₃ on immune response and lymphocyte differentiation are indirect and mediated through genomic modulation of reticular cell functions such as messenger secretion.     

Ontogeny of gonadotropin releasing hormone and gonadotropin immunoreactivity in brain and pituitary of normal and estrogen-treated guppies,Poecilia reticulata Peters

Summary Gonadotropin releasing hormone (GnRH) and gonadotropic hormone (GTH) were identified by immunohistochemistry in the brains and pituitaries of neonate, juvenile and adult guppies. GTH was present in some cells of the pars intermedia (pi) and proximal pars distalis (ppd) of all animals. GnRH was found in the perikarya of the nucleus olfactoretinalis. In the pituitaries of juvenile 30-day-old guppies, GnRH-immunoreactive cells existed in a juvenile pattern, whereas in adult animals GnRH was recognized in only a few cells. GnRH-immunoreactive fibers were seen in the pituitaries of animals that were 30 days or older. In adult guppies, the ventral and lateral ppd (the gonadotropic region) contained a dense network of GnRH-immunoreactive fibers. Pituitary cells staining for either GnRH or GTH were located in different places. After immunohistochemical double staining of adult pituitaries, none of the GnRH-immunoreactive cells were LH-immunoreactive, although both cell types were often found in close proximity. After 20 days or more of ethinylestradiol treatment, less immunoreactive GnRH was detected in the pituitary cells of juvenile guppies, and fewer animals exhibited the juvenile pattern of GnRH-immunoreactive pituitary cells, when compared with untreated controls. The results indicate that GnRH-immunoreactive pituitary cells in the guppy are distinct from gonadotropes and that these cells are involved in regulatory processes along the juvenile brain-pituitary-gonad axis.