Gene expression in cell cycle of Cyanidioschyzon merolae_1
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ABSTRACT: To analyze mitotic cycle and organelle proliferation cycle, we investigated C.merolae cells across two cell cycles synchronized by light and dark cycles. C.merolae has one nucleus, mitochondria and chloroplast (Kuroiwa et al,1993. Protoplasma). Their division are strictly regulated by cell cycle and can be synchronized by light/dark cycle (Misumi et al,2005. Plant Physiol). These characteristics enable microarray system to analyze the proliferation cycle of not only the nucleus but also organelle. Keywords: Time course in cell cycle
Project description:To analyze mitotic cycle and organelle proliferation cycle, we investigated C.merolae cells across two cell cycles synchronized by light and dark cycles. C.merolae has one nucleus, mitochondria and chloroplast (Kuroiwa et al,1993. Protoplasma). Their division are strictly regulated by cell cycle and can be synchronized by light/dark cycle (Misumi et al,2005. Plant Physiol). These characteristics enable microarray system to analyze the proliferation cycle of not only the nucleus but also organelle. Keywords: Time course in cell cycle Analysis of C.merolae cells across two cell cycles, a length of 50 hours after onset of synchronizied culture by light/dark cycles. Gene expression examined at 2-hours intervals.
Project description:Germinal centers (GCs) are the sites of affinity maturation, the process by which antibodies improve their affinity for antigen over time (Cyster and Allen, 2019; De Silva and Klein, 2015; Eisen, 2014; Mesin et al., 2016; Rajewsky, 1996; Shlomchik et al., 2019; Victora and Nussenzweig, 2012). For efficient affinity maturation, GC B cells must cycle between two major transcriptional states, associated with localization of B cells to each of the two microanatomical “zones” of the GC. When in the dark zone (DZ), B cells proliferate vigorously while they mutate their immunoglobulin genes by somatic hypermutation (SHM). After transition to the light zone (LZ), B cells bearing advantageous mutations are selectively driven to clonally expand, based at least in part on their ability to bind and present antigen to GC-resident T follicular helper (Tfh) cells (Victora et al., 2010). Successive cycles of somatic hypermutation and affinity-based selection ultimately enrich for higher-affinity cells in among the GC B cell population, in a process known as cyclic re-entry (MacLennan, 1994; Victora and Nussenzweig, 2012).
Project description:Brachyury (or T) is expressed in the primitive streak, tailbud and notochord of the early mouse embryo (Herrmann et al., 1990; Wilkinson et al., 1990). It plays a key role in early development: mouse embryos lacking functional Brachyury protein fail to gastrulate properly, do not form a differentiated notochord, and lack structures posterior to somite seven (Chesley, 1935; Dobrovolskaïa-Zavadskaïa, 1927; Naiche et al., 2005; Wilson et al., 1995; Wilson et al., 1993; Yanagisawa et al., 1981) We apply a ChIP-on-chip approach to identify targets of Brachyury during mouse ES cell differentiation. ES cells provide an abundant source of differentiating cells and the identification of Brachyury targets in such cells will shed light on the mechanisms of ES cell differentiation and, by analyzing the targets in the developing embryo, will reveal to what extent they provide a bone fide model of early mouse development.
Project description:Genome wide rhythmic transcription under light/dark cycles is associated with sequential transcription of specific biological processes genes in Ostreococcus tauri. Transcriptional profiling of Ostreococcus tauri under light/dark cycles. In order to identify genes with a diurnal rhythm, cells entrained under 12:12 light/dark cycles were sampled every 3 hours for 27 hours with two overlapping time points at Time 9 (Light ON at Time 9; Light OFF at Time 21) in 3 independent experiments.
Project description:Our aim is to study the circadian expression of genes to aid in our attempt of modelling the Arabidopsis circadian clock. Circadian microarray data have previously been published for plants after white light (WL)-dark cycles, using the 8k chip (Harmer et al. 2000). We intend to repeat this experiment using the 26k chips and are coordinating with Dr. Harmer, who is pursuing complementary experiments in UC Davis. Plants will be transferred to continuous WL after entrainment to 12h:12h light dark cycles. RNAs will be harvested every 4 hours over two days, with the same accession and sampling intervals used previously by Harmer et al. The two days of sampling provide internal replication. Our experience shows that this is the most economical design: it is easier to identify rhythms over a two-day timecourse than in two replicates of a single day. Hence: 13 RNA samples on 13 chips in total. METHOD: Seed was sown on MS agar plates with 3% sucrose, imbibed at 4 C for 96 hours. Seed was then entrained for 7 days at 22C, in cycles of 12 hours white light, 12 hours darkness. After 7 days they were transferred to constant white light at 22 C: this is time 0h. Tissue harvested at the time points shown after time 0. Experimenter name = Kieron Edwards Experimenter phone = 024 7652 8374 Experimenter fax = 024 7652 3701 Experimenter department = Department of Biological Sciences Experimenter institute = University of Warwick Experimenter address = Department of Biological Sciences Experimenter address = University of Warwick Experimenter address = Gibbet Hill Road Experimenter address = Coventry Experimenter zip/postal_code = CV4 7AL Experimenter country = UK Keywords: time_series_design, growth_condition_design
Project description:Series of 6 repetitions of hybridization of treatment (L30min) and control (0h) each. Comparison of plants exposed to light for 30 min after a 12 h dark period versus 12 h dark adapted plants. E. Richly et al., EMBO Rep. 4 (2003), pp. 491–498 Keywords: repeat sample
Project description:Series of 6 repetitions of hybridization of treatment (laf6_L_1h) and control (WT_D) each. Comparison of Arabidopsis laf6 mutant lacking the atABC1-transporter versus WT. laf6 exposed to normal light for 1 h after dark adaptation, WT dark adapted. S.G. Moeller et al., Genes Dev 15 (2001), pp. 90-103 Keywords: repeat sample
Project description:Series of 8 repetitions of hybridization of treatment (gun5) and control (WT) each. Comparison of Arabidopsis gun5 mutant lacking a ChlH subunit of Mg-chelatase versus WT. R.E. Susek et al., Cell 74 (1993), pp. 787-799; N. Mochizuki et al., Proc Natl Acad Sci U S A 98 (2001), pp. 2053-2058 Keywords: repeat sample
Project description:The wild type strain of Halobacterium salinarium strain NRC-1 was used for the diel growth experiments. Culturing from colony was done under constant light in a liquid Complete Medium (CM; at 37 ºC with shaking at 220 rpm). For experiment, cultures were started at an OD = 0.005. Cultures were grown aerobically (shaking at 120 rpm) and a temperature of 37° C under light:dark cycles (12:12 hrs) for 72 hours then grown in complete darkness. Light intensity was 150 μE/m2/sec. Time course sampling began after the 72 hour light:dark phase. A second culture was also sampled as a control and was grown under complete darkness (no light:dark cycle) before sampling began. Samples from both the experimental and control cultures were collected after 83 hours of exposure to the light:dark cycle every 1 to 3 hours for another 25 hours. Aliquots of the cultures were centrifuged and the cell pellet flash-frozen in liquid nitrogen after decanting the supernatant. RNA extractions were performed using the Stratagene Absolute RNA kit and RNA quality checked with the Agilent Bioanalyzer and with PCR. Microarrays were fabricated at the Institute for Systems Biology Microarray Facility. The arrays contain 4 spots per unique 70-mer oligonucleotides for each of 2400 non-redundant genes in Halobacterium NRC-1. Labeling, hybridization and washing have been previously described (Baliga et al. 2002) with 5 μg of RNA from the sample and reference. Bias in dye incorporation was accounted for by reversing the labeling dyes (dye-flip). Raw data was processed and converted into log10 ratios with lambda (λ) values determined by a maximum likelihood method. Baliga, N. S., Pan, M., Goo, Y. A., Yi, E. C., Goodlett, D. R., Dimitrov, K., Shannon, P., Aebersold, R., Ng, W. V. & Hood, L. (2002) Proc Natl Acad Sci U S A 99:14913-84. Keywords: environmental response
Project description:Previous studies have shown that a considerable proportion of the Arabidopsis genome cycles under circadian and/or diurnal conditions (Edwards et al., 2006 PMID: 16473970, Blaesing et al., 2005 PMID 16299223). It is likely that the correct phasing of gene expression plays an important role in improving the growth of the model plant (Dodd et al., 2005 PMID: 16040710). A key question is whether similar regulation is occurring in other higher plant species. In this study we measure the diurnal expression pattern of genes in the T89 clone of the hybrid aspen (Populus tremula L. x P. tremuloides Michx.) using the Affymetrix Poplar array. Samples (leaf blades) were taken at 4h intervals over the course of 2 diurnal cycles (18h Light: 6h Dark). Time-points were labelled relative to dawn (time 0) on the first day of sampling. T89 was selected as it has routinely been used for genetic modification since 1992 (Nilsson et al.) and is the genetic background for a large number of transgenic trees created in order to investigate the function of aspen genes, providing potential for genetic manipulations during our further studies. We also measured the diurnal expression pattern of genes in trees with a compromised circadian clock. Trees with less expressed LATE ELONGATED HYPOCOTYL 1 (LHY1) and LHY2 by RNA interference (lhy) line that was created in T89 clone of the aspen hybrid (Populus tremula L. x P. tremuloides Michx.) using the Affymetrix Poplar array. Samples (leaf blades) were taken at 4h intervals over the course of 2 diurnal cycles (18h Light: 6h Dark) as described above. Thus, time-points are labelled relative to dawn (time 0) on the first day of sampling. The data obtained from using a RNAi line in central Clock components complements the study of wild type T89, since they were grown and sampled at the same time under the same conditions.