GO Explorer: A gene-ontology tool to aid in the interpretation of shotgun proteomics data

Background  

Spectral counting is a shotgun proteomics approach comprising the identification and relative quantitation of thousands of proteins in complex mixtures. However, this strategy generates bewildering amounts of data whose biological interpretation is a challenge.     

A Failure Reveals Success

Although environmental education and education for sustainable development have become well‐established areas of scholarship and practice, there has not been a similar development focused on “industrial ecology education.” A review of the historical context and guiding philosophies for each of these areas finds many similarities, as well as key differences. Environmental education traces its modern roots to the idealism of the 1960s and 1970s. It has focused mostly on improving environmental conditions. Education for sustainable development arose along with international concerns about social justice. It has emphasized general education as well as education about sustainability as necessary to ensure human prosperity. Industrial ecology, in its contemporary form, evolved as an applied approach to address environmental concerns and to meet sustainability goals. It has developed into a diverse, multifaceted approach to address the complexity inherent in industrial society. Education focused on industrial ecology remains decentralized, with core principles and tools being integrated into existing disciplinary programs as well as development of industrial‐ecology–specific curricula. These efforts have not coalesced into a formalized, industrial ecology education. Rather than reflecting a shortcoming, this potentially offers a more robust method for applying industrial ecology principles and tools widely.     

Evidence of nanobacterial-like structures in calcified human arteries and cardiac valves

Mechanisms mediating vascular calcification remain incompletely understood. Nanometer scale objects hypothesized to be a type of bacteria (nanobacteria) are associated with calcified geological specimens, human kidney stones, and psammona bodies in ovarian cancer. Experiments were designed to evaluate human vascular tissue for the presence of similar nanometer-scale objects. Calcified human aneurysms (n = 8), carotid plaques (n = 2), femoral arterial plaques (n = 2), and cardiac valves (n = 2) and noncalcified aneurysms from patients with bicuspid aortic valve disease (n = 2) were collected as surgical waste from the Heart Hospital of Austin, Austin, Texas, and Mayo Clinic, Rochester, Minnesota. Whole mounts or adjacent sections from each specimen were examined by electron microscopy, stained for calcium phosphate, or stained with a commercially available antibody (8D10). Filtered (0.2 microm) homogenates of aneurysms were cultured and costained with 8D10 antibody followed by PicoGreen to detect DNA or incubated with [3H]uridine. Staining for calcium phosphate was heterogeneously distributed within all calcified tissues. Immunological staining with 8D10 was also heterogeneously distributed in areas with and without calcium phosphate. Analysis of areas with positive immunostaining identified spheres ranging in size from 30 to 100 nm with a spectral pattern of calcium and phosphorus (high-energy dispersive spectroscopy). Nanosized particles cultured from calcified but not from noncalcified aneurysms were recognized by a DNA-specific dye and incorporated radiolabeled uridine, and, after decalcification, they appeared via electron microscopy to contain cell walls. Therefore, nanometer-scale particles similar to those described as nanobacteria isolated from geological specimens and human kidney stones can be visualized in and cultured from calcified human cardiovascular tissue.     

Industrial Ecology Education at Wuhan University

China requires industrial ecology (IE) skills and knowledge to deal with the contradiction between rapid economic growth and subsequent environmental pollution and resource depletion. Industrial ecology education was introduced in China in 1997 and now a few Chinese universities offer IE courses. Wuhan University is one of them and since 1999 has committed itself to promoting IE education. The university offers different curricula for different majors at all levels: undergraduate, master's, and doctoral. Between 1999 and 2004 more than 5,000 students received IE education at Wuhan University. Although inadequate human resources and a lack of relevant textbooks present challenges to further developing IE education in China, as more universities pay attention to IE, more courses will be developed. It is believed that IE education in China will blossom in the near future.     

Identification within the simian virus 40 genome of a chromosomal loop attachment site that contains topoisomerase II cleavage sites.

We demonstrate that the simian virus 40 genome contains a single MAR (matrix association region) that maps within a large T-antigen coding region (nucleotides 4071 to 4377). This region contains topoisomerase II cleavage sites, exhibits sequence similarity with cellular MARs, and recognizes the same evolutionarily conserved, abundant nuclear binding sites seen by cellular MARs.     

The identification of two novel prostaglandins and a thromboxane

6,15-Dioxo-PGF_1α, 6-15-dioxo-13,14-dihydro-PGF_1α and 15-oxo-thromboxane B₂ have been identified in incubates of ram seminal vesicle homogenates with added arachidonic acid or in the perfusate from sensitised challenged guinea pig lungs. These compounds are probably related to 6-oxo-PGF_1α and thromboxane B₂. The structures have been determined by gas chromatography mass spectrometry, following suitable chemical derivatisation.