Service and cloud computing supporting genomic analysis of the mammalian species

 This research focused on building Software as a Service clouds to support mammalian genomic applications such as personalized medicine. Outcomes of this research included a Software as a Service cloud framework, the Uncinus research cloud and novel genomic analysis software. Results have been published in high ranking peer-reviewed international journals.

A survey of cloud-based service computing solutions for mammalian genomics

Cloud-based service computing has started to change the way how research in science, in particular biology, medicine, and engineering, is being carried out. Researchers in the area of mammalian genomics have taken advantage of cloud computing technology to cost-effectively process large amounts of data and speed up discovery. Mammalian genomics is limited by the cost and complexity of analysis, which require large amounts of computational resources to analyse huge amount of data and biology specialists to interpret results. On the other hand the application of this technology requires computing knowledge, in particular programming and operations management skills to develop high performance computing (HPC) applications and deploy them on HPC clouds. We carried out a survey of cloud-based service computing solutions, as the most recent and promising instantiations of distributed computing systems, in the context their use in research of mammalian genomic analysis. We describe our most recent research and development effort which focuses on building Software as a Service (SaaS) clouds to simplify the use of HPC clouds for carrying out mammalian genomic analysis.

Intense predation of non-colonial, ground-nesting bird eggs by corvid and mammalian predators

Context Loss of eggs to predators is a major cause of reproductive failure among birds. It is especially pronounced among ground-nesting birds because their eggs are accessible to a wide range of predators. Few studies document the main causes of clutch fate of ground-nesting birds. Aims The main objective of the present study was to identify the major egg predator of red-capped plovers (Charadrius ruficapillus). We also investigated the effectiveness of the following two primary strategies available to the plovers to avoid egg predation: (1) the placement of clutches under vegetative cover and (2) avoiding predators by nesting outside the peak season of predator occurrence. Methods Remote-sensing cameras were deployed on plover nests to identify egg predators and nests were monitored over four breeding seasons to document reproductive success and fate. An experiment using false clutches with model eggs investigated the influence of nest cover on the risk of egg predation throughout the year. Line-transect surveys were conducted to estimate the abundance of egg predators in and around the wetlands. Key results The little raven (Corvus mellori) was the major egg predator identified in 78.6% of red-capped plover clutches and in 92.4% of false clutches that were camera-monitored. The hatching success of plover eggs was not influenced by nest cover (P≤0.36), but model egg survival in false clutches improved significantly with the presence of nest cover (P≤0.02). The abundance of little ravens increased during the plover breeding season and was highly negatively correlated with false clutch survival (rpearson≤-0.768, P≤0.005). Conclusions Little ravens were the major predator of red-capped plover eggs and their abundance increased significantly during the plover breeding season. Any influence of nest cover on hatching success of eggs may have been masked by the extremely high rate of egg loss associated with the increased little raven abundance during the plover breeding season. Implications The high rate of egg predation is likely to have negative consequences on the local red-capped plover population, suggesting management is warranted. Little raven populations have expanded and, thus, their impact as egg predators needs to be investigated especially on threatened species. Journal compilation

Studies to prevent degradation of recombinant fc-fusion protein expressed in mammalian cell line and protein characterization

Clipping of recombinant proteins is a major issue in animal cell cultures. A recombinant Fc-fusion protein, VEGFR1(D1-D3)-Fc expressed in CHOK1SV GS-KO cells was observed to be undergoing clippings in lab scale cultures. Partial cleaving of expressed protein initiated early on in cell culture and was observed to increase over time in culture and also on storage. In this study, a few parameters were explored in a bid to inhibit clipping in the fusion protein The effects of culture temperature, duration of culture, the addition of an anti-clumping agent, ferric citrate and use of protease inhibitor cocktail on inhibition of proteolysis of the Fc fusion were studied. Lowering of culture temperature from 37 to 30 °C alone appears to be the best solution for reducing protein degradation from the quality, cost and regulatory points of view. The obtained Fc protein was characterized and found to be in its stable folded state, exhibiting a high affinity for its ligand and also biological and functional activities.

Analysis of mammalian cell proliferation and macromolecule synthesis using deuterated water and gas chromatography-mass spectrometry.

Deuterated water (²H₂O), a stable isotopic tracer, provides a convenient and reliable way to label multiple cellular biomass components (macromolecules), thus permitting the calculation of their synthesis rates. Here, we have combined ²H₂O labelling, GC-MS analysis and a novel cell fractionation method to extract multiple biomass components (DNA, protein and lipids) from the one biological sample, thus permitting the simultaneous measurement of DNA (cell proliferation), protein and lipid synthesis rates. We have used this approach to characterize the turnover rates and metabolism of a panel of mammalian cells in vitro (muscle C2C12 and colon cancer cell lines). Our data show that in actively-proliferating cells, biomass synthesis rates are strongly linked to the rate of cell division. Furthermore, in both proliferating and non-proliferating cells, it is the lipid pool that undergoes the most rapid turnover when compared to DNA and protein. Finally, our data in human colon cancer cell lines reveal a marked heterogeneity in the reliance on the de novo lipogenic pathway, with the cells being dependent on both 'self-made' and exogenously-derived fatty acid.