We have continued our work in collaboration with Dr. Minoru Ko (LG-NIA) to characterize developmental pathways induced in mouse embryonic stem cells using transcription factor manipulation. We were able to establish a differentiation assay based on morphology alone, using phase-contrast imaging without specific markers. We were able to show that differentiation can be tracked over time, and that morphological similarities between differentiating cells are established early and maintained for several days of differentiation. An important milestone is that we were able to establish a conditions where cell lines showed consistent grouping by gene function over several independent experiments. Additionally, we were able to expand this analysis to compare the morphologies of 56 cell lines. These results are being prepared for publication. We have continued work characterizing the molecular basis of morphological age-state transitions during the C. elegans life-span. In previous published work we used WND-CHARM to identify distinct morphological aging states in C. elegans. We used this technique to sort worms based on their age state during a transition period where an aging population is evenly divided between individuals in Stage I and Stage II. The worms were identical genetically, by chronological age, by growth conditions, and by visual appearance, and could only be sorted into age-states using WND-CHARM. Micro-array experiments performed on these two sub-populations revealed several hundred genes with significantly altered expression profiles. By comparing our gene lists with those from other aging studies in C. elegans, we were able to identify several gene families and functional groups that were unique to our study, as well as several important aging genes that were identified previously. The results of this study are being prepared for publication. In the next stage of this study, we will begin to screen through our gene list using RNAi libraries to shift the timing of the Stage I - Stage II transition.
| Shamir, Lior; Rahimi, Salim; Orlov, Nikita et al. (2010) Progression analysis and stage discovery in continuous physiological processes using image computing. EURASIP J Bioinform Syst Biol 2010:107036 |
| Shamir, Lior; Ling, Shari; Rahimi, Salim et al. (2009) Biometric identification using knee X-rays. Int J Biom 1:365-370 |
| Shamir, L; Ling, S M; Scott, W et al. (2009) Early detection of radiographic knee osteoarthritis using computer-aided analysis. Osteoarthritis Cartilage 17:1307-12 |
| Shamir, Lior; Eckley, D Mark; Delaney, John et al. (2009) An Image Informatics Method for Automated Quantitative Analysis of Phenotype Visual Similarities. IEEE NIH Life Sci Syst Appl Workshop 2009:96-99 |
| Nishiyama, Akira; Xin, Li; Sharov, Alexei A et al. (2009) Uncovering early response of gene regulatory networks in ESCs by systematic induction of transcription factors. Cell Stem Cell 5:420-33 |
| Shamir, Lior; Ling, Shari M; Scott Jr, William W et al. (2009) Knee x-ray image analysis method for automated detection of osteoarthritis. IEEE Trans Biomed Eng 56:407-15 |
| Shamir, Lior; Wolkow, Catherine A; Goldberg, Ilya G (2009) Quantitative measurement of aging using image texture entropy. Bioinformatics 25:3060-3 |
| Tadeu, Ana Mafalda Baptista; Ribeiro, Susana; Johnston, Josiah et al. (2008) CENP-V is required for centromere organization, chromosome alignment and cytokinesis. EMBO J 27:2510-22 |
