Deducing topology of protein-protein interaction networks from experimentally measured sub-networks.

BackgroundProtein-protein interaction networks are commonly sampled using yeast two hybrid approaches. However, whether topological information reaped from these experimentally-measured sub-networks can be extrapolated to complete protein-protein interaction networks is unclear.ResultsBy analyzing various experimental protein-protein interaction datasets, we found that they are not random samples of the parent networks. Based on the experimental bait-prey behaviors, our computer simulations show that these non-random sampling features may affect the topological information. We tested the hypothesis that a core sub-network exists within the experimentally sampled network that better maintains the topological characteristics of the parent protein-protein interaction network. We developed a method to filter the experimentally sampled network to result in a core sub-network that more accurately reflects the topology of the parent network. These findings have fundamental implications for large-scale protein interaction studies and for our understanding of the behavior of cellular networks.ConclusionThe topological information from experimental measured networks network as is may not be the correct source for topological information about the parent protein-protein interaction network. We define a core sub-network that more accurately reflects the topology of the parent network

The physiology and genetics of stomatal adjustment under fluctuating and stressed environments

Stomata are pores in the leaf that allow gas exchange where water vapor leaves the plant and carbon dioxide enters. Under natural condition, plants always experience at a fluctuating light regime (shade-/sun-fleck) and due to global climate change, occasionally extreme high temperature and CO2 enrichment will be inevitable occurred, which dramatically affects stomatal response, and trade-off between water-use efficiency and photosynthesis. Response of stomata to fluctuating and stressed environments determines optimized strategy of plants directing to water save or photosynthesis. Dynamic adjustments of stomata play an equivalent role as steady-state stomatal characteristics. Evolutionary approach indicated that stomatal-dynamic adjustments interacting with historical environments or life histories could be genetically controlled and environmentally selected. In this article, we reviewed physiological response of stomatal dynamic to changing enironments including our previous works, and discussed the possibility of genetic improvements on stomatal adjustments by estimating broad-sense heritability and SNP heritability of stomatal pattern. To gain insight into the framework of stomatal genetics, we highlighted the importance of combining multidisciplinary techniques, such as mathematic modeling, quantitative genetics, molecular biology and equipments developments

Comparative analyses of bidirectional promoters in vertebrates

<p>Abstract</p> <p>Background</p> <p>Orthologous genes with deep phylogenetic histories are likely to retain similar regulatory features. In this report we utilize orthology assignments for pairs of genes co-regulated by bidirectional promoters to map the ancestral history of the promoter regions.</p> <p>Results</p> <p>Our mapping of bidirectional promoters from humans to fish shows that many such promoters emerged after the divergence of chickens and fish. Furthermore, annotations of promoters in deep phylogenies enable detection of missing data or assembly problems present in higher vertebrates. The functional importance of bidirectional promoters is indicated by selective pressure to maintain the arrangement of genes regulated by the promoter over long evolutionary time spans. Characteristics unique to bidirectional promoters are further elucidated using a technique for unsupervised classification, known as ESPERR.</p> <p>Conclusion</p> <p>Results of these analyses will aid in our understanding of the evolution of bidirectional promoters, including whether the regulation of two genes evolved as a consequence of their proximity or if function dictated their co-regulation.</p

Experimental Testing and Validation of P-band Bi-static Remote Sensing of Soil Moisture in 137-138MHz Range

Remote sensing using readily available communication signal transmitted by ORBCOMM satellites at very high frequency (VHF) range (137-138MHz) is a promising method for detecting the root zone soil moisture content. The radio wave reflectivity of soil is strongly correlated to soil moisture content. Therefore, if we were able to measure the reflectivity, we might be able to estimate the soil moisture content. In this preliminary study, we analyze direct signal data from the satellites to investigate and verify communication channels in frequency range of interest and their characteristics (bandwidth, pattern, etc.). The analysis of direct signal data is also used for calibrating signal collection systems and compensating for the subtle differences of systems. After comparing the satellite geometry and spectrum from raw signal, we verified that ORBCOMM has 13 channels in our frequency range of interest. It was also verified that among these 13 channels, the channel with center frequency at 137.56MHz is a public channel shared by all satellites and is not suitable for reflectivity computation in that multiple satellites could be in sight by our antenna and the signal reflecting region cannot be determined. In our long duration (~12 hours) analysis, we observed the visible duration and period of the satellites. Conclusively, using ORBCOMM communication signal for sensing the soil moisture is viable. Further study is needed to build up model that relates soil moisture content to reflectivity and a lot of technical issues need to be resolved

Using an agent-based sexual-network model to analyze the impact of mitigation efforts for controlling chlamydia

Chlamydia trachomatis (Ct) is the most reported sexually transmitted infection in the United States with a major cause of infertility and pelvic inflammatory disease among women. Despite decades of screening women for Ct, rates increase among young African Americans (AA). We create and analyze an agent-based network model to understand the spread of Ct. We calibrate the model parameters to agree with survey data showing Ct prevalence of 12% of the women and 10% of the men in the 15-25 year-old AA in New Orleans, Louisiana. Our model accounts for long-term and casual partnerships. The network captures assortative mixing of individuals by preserving the joint-degree distributions observed in the data. We compare the efficiency of intervention strategies of randomly screening men, partner notification, which includes partner treatment, partner screening, and rescreening for infection. We compare the difference between treating partners of an infected person both with and without testing them. We observe that although increased Ct screening, rescreening and treating most of the partners of infected people will reduce the prevalence, these mitigations alone are not sufficient to control the epidemic. The current practice is to treat the partners of an infected individual, without first testing them for infection. The model predicts that if a sufficient number of the partners of all infected people are tested and treated, then there is a threshold condition where the epidemic can be mitigated. This threshold results from the expanded treatment network created by treating the partners of the infected partners of an individual. Although these conclusions can help design future Ct mitigation studies, we caution the reader that these conclusions are for the mathematical model, not the real world, and are contingent on the validity of the model assumptions