The cell centered database project: an update on building community resources for managing and sharing 3D imaging data

Databases have become integral parts of data management, dissemination, and mining in biology. At the Second Annual Conference on Electron Tomography, held in Amsterdam in 2001, we proposed that electron tomography data should be shared in a manner analogous to structural data at the protein and sequence scales. At that time, we outlined our progress in creating a database to bring together cell level imaging data across scales, The Cell Centered Database (CCDB). The CCDB was formally launched in 2002 as an on-line repository of high-resolution 3D light and electron microscopic reconstructions of cells and subcellular structures. It contains 2D, 3D, and 4D structural and protein distribution information from confocal, multiphoton, and electron microscopy, including correlated light and electron microscopy. Many of the data sets are derived from electron tomography of cells and tissues. In the 5 years since its debut, we have moved the CCDB from a prototype to a stable resource and expanded the scope of the project to include data management and knowledge engineering. Here, we provide an update on the CCDB and how it is used by the scientific community. We also describe our work in developing additional knowledge tools, e.g., ontologies, for annotation and query of electron microscopic data.     

ATP scavenging by the intracellular pathogen Porphyromonas gingivalis inhibits P2X7-mediated host-cell apoptosis

The purinergic receptor P2X₇ is involved in cell death, inhibition of intracellular infection and secretion of inflammatory cytokines. The role of the P2X₇ receptor in bacterial infection has been primarily established in macrophages. Here we show that primary gingival epithelial cells, an important component of the oral innate immune response, also express functional P2X₇ and are sensitive to ATP-induced apoptosis. Porphyromonas gingivalis, an intracellular bacterium and successful colonizer of oral tissues, can inhibit gingival epithelial cell apoptosis induced by ATP ligation of P2X₇ receptors. A P. gingivalis homologue of nucleoside diphosphate kinase (NDK), an ATP-consuming enzyme, is secreted extracellularly and is required for maximal suppression of apoptosis. An ndk -deficient mutant was unable to prevent ATP-induced host-cell death nor plasma membrane permeabilization in the epithelial cells. Treatment with purified recombinant NDK inhibited ATP-mediated host-cell plasma membrane permeabilization in a dose-dependent manner. Therefore, NDK promotes survival of host cells by hydrolysing extracellular ATP and preventing apoptosis-mediated through P2X₇.     

Community‐level spatial structure supports a model of stochastic geometry in species‐rich shrublands

In some ecosystems a small suite of species can determine community‐level patterns of species richness by acting as either ‘accumulators’ or ‘repellers’; that is, the richness of the immediate neighbourhood of such species departs from that expected on the basis of a given null model. Using the individual species‐area approach, we evaluated community‐level spatial pattern in four species‐rich shrublands (two 40 × 40 m and two 30 × 30 m plots) by assessing the frequency of accumulator and repeller species and whether any such species were associated with specific life‐history characteristics. Few species departed from the expectations of the null spatial model that we used, although, at three of the four sites, accumulators were more common than repellers. Departures from the null model we assessed were most prevalent within just 1 m of focal individuals and were not consistently associated with specific life‐history traits. Model‐based clustering suggests that there are distinct sub‐communities in each of the four communities, but while internally spatially cohesive, these sub‐communities intermingle and their membership is not predictable from the life‐history traits of their constituent species. Comparable analyses in other species‐rich systems have also detected a similar absence of spatial interactions. The disturbance regime in the shrubland communities we consider is markedly different from those in the forest ecosystems where previous studies have been concentrated (recurrent fire versus infrequent gap‐phase dynamics) and resources are more limiting. Thus, our results provide further support for the generality of a model of stochastic geometry, likely underpinned by stochastic dilution effects, in species‐rich plant communities.     

Implications of childhood obesity for adult health: findings from thousand families cohort study

ObjectiveTo determine whether being overweight in childhood increases adult obesity and risk of disease.DesignProspective cohort study.SettingCity of Newcastle upon Tyne.Participants932 members of thousand families 1947 birth cohort, of whom 412 attended for clinical examination age 50.ResultsBody mass index at age 9 years was significantly correlated with body mass index age 50 (r=0.24, P<0.001) but not with percentage body fat age 50 (r=0.10, P=0.07). After adult body mass index had been adjusted for, body mass index at age 9 showed a significant inverse association with measures of lipid and glucose metabolism in both sexes and with blood pressure in women. However, after adjustment for adult percentage fat instead of body mass index, only the inverse associations with triglycerides (regression coefficient= −0.21, P<0.01) and total cholesterol (−0.17, P<0.05) in women remained significant.ConclusionsLittle tracking from childhood overweight to adulthood obesity was found when using a measure of fatness that was independent of build. Only children who were obese at 13 showed an increased risk of obesity as adults. No excess adult health risk from childhood or teenage overweight was found. Being thin in childhood offered no protection against adult fatness, and the thinnest children tended to have the highest adult risk at every level of adult obesity.

What is already known on this topic

Many studies have found that body mass index in childhood is significantly correlated with body mass index in adulthoodObese children have been found to have higher all cause mortality as adults

What this study adds

No excess health risk from childhood overweight was foundChildhood body mass index was linked to adulthood body mass index but not percentage body fatOnly children who were obese at 13 showed a significant increased risk of obesity as adultsPeople who were thinnest as children and fattest as adults tended to have the highest adult risk     

Herbivory, serotiny and seedling defence in Western Australian Proteaceae

We examined how acceptability characteristics displayed by 28-day-old seedlings of 12 species of Western Australian Proteaceae affect the likelihood of seedling herbivory in the field. The seedling attributes quantified were cotyledon phenolic, cyanide and nitrogen concentrations, and cotyledon area, thickness and specific leaf area. Only phenolic content was significantly correlated (negatively) with field rates of herbivore attack. This finding shows that the phenomenon of selective herbivore attack on seedlings may be influenced by a specific plant life-history trait, (in this case cotyledon phenolic concentration). In addition, we also studied the interaction between fire, serotiny and herbivory in matched burned and unburned plots. Although herbivore activity was greater in unburned plots, weakly serotinous species were as prone to defoliation as congeneric, strongly serotinous species, even though their seedlings recruit successfully in the absence of fire. This result suggests that seedlings of species able to establish between fires are not better defended against the higher levels of herbivory normally associated with unburned vegetation.     

Spontaneous preterm labour and delivery at under 34 weeks' gestation.

The management and outcome of 242 infants delivered between 26 and 34 weeks'' gestation in an obstetrical and neonatal regional referral centre as a result of spontaneous preterm labour were recorded prospectively. Results of the survey show that the decision to intervene and delay delivery will depend on the availability of neonatal intensive care facilities. Infants likely to require intensive neonatal care should be transferred in utero to a centre with these facilities. The use of steroids reduces the mortality of preterm infants. The maximum effect occurs between 30 and 32 weeks'' gestation, and there is no benefit after 34 weeks. If the weight is over 1500 g the mode of delivery of the preterm infant presenting by the breech does not influence outcome; if under 1500 g a caesarean section improves survival over those infants born by vaginal breech delivery.     

Isolation and characterization of three class II MHC genomic clones from the chicken

A genomic library was constructed from sperm DNA from an individual of the inbred chicken line G-B2, MHC haplotype B6. The library was screened with a chicken class II probe (beta 2 exon specific) and three MHC class II beta chain genomic clones were isolated. The restriction maps of the three clones showed that each of the three clones was unique. The position of the beta chain sequence was located in each of the three genomic clones by Southern blot hybridization. Subclones containing the beta chain gene were produced from each of the genomic clones and the orientation of the leader peptide, beta 1, beta 2, transmembrane, and cytoplasmic exons was determined by Southern blot hybridization and nucleotide sequencing. The complete nucleotide sequence of two of the three subclones was determined. Comparison of the nucleotide and predicted amino acid sequences of the two subclones with other class II beta chain sequences showed that the B6 chicken beta chain genes are evolutionarily related to the class II beta chain genes from chickens of other MHC haplotypes, and to class II beta chain genes from other species. Analysis of Southern blots of B6 chicken DNA, as well as the isolation of the three beta chain genes, suggests that chickens of the B6 haplotype possess at least three MHC class II beta chain genes.     

Membrane topology of epoxide hydrolase

The amino acid sequences of epoxide hydrolase from rat, rabbit and human have been subjected to hydropathy analysis and a novel model for the membrane topology of this enzyme is presented. The enzyme would appear to be retained in microsomal membranes by a single transmembrane segment located at the N-terminus and the majority (96%) of the protein is exposed at the cytosolic membrane surface. This model is significantly different from a scheme suggested by analysis of the rat enzyme alone which proposed six transmembrane domains (Porter et al. (1988) Arch. Biochem. Biophys. 248, 121-129). Experiments with rat microsomal membranes were conducted to distinguish between the two models and used proteolytic enzymes and non-permeant chemical probes. Epoxide hydrolase of intact and permeabilised membranes was resistant to digestion by a number of proteinases. However, this is likely to be related to a compact fold of the protein rather than membrane association since purified, delipidated enzyme preparations were also resistant to proteolysis. While the use of proteinases did not provide useful membrane topological information, experiments with the fluorescent probe, 3-azido-2,7-naphthalenedisulphonate strongly support the view that the majority of the protein is indeed exposed at the cytosolic surface of the membranes. The analysis illustrates the caution which must be employed in the formulation of topological models based on hydropathy plots alone and the value of considering homologous proteins.