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==Week 11 Journal Assignment
==Week 11 Journal Assignment==
Week 11 Journal Assignment
- Motif- The smallest group of atoms in a polymer that, when under the influence of a rotation-translation operator, will assemble the rest of the atoms in the chain. 
- Biogenesis-The process in which life forms arise from similar life forms; living things can only be produced by another living thing, and not by a non-living thing. 
- Batch Culture- large-scale closed system culture in which cells are grown in a fixed volume of nutrient culture medium under specific environmental conditions (In this case: nutrient limits, temperature) up to a certain density in a tank or airlift fermentor, harvested and processed as a batch, especially before all nutrients are used up. 
- Catabolite- Product of catabolism, the breakdown of complex molecules into simpler ones. 
- Trehalose- a crystalline disaccharide (C12H22O11) that is found in various organisms that is about half as sweet as sucrose, and is sometimes used as a sweetener in commercially prepared foods 
- Gene Regulatory Protein- Any protein that interacts with dna sequences of a gene and controls its transcription. 
- Transcriptome- the complement of mature messenger RNAs produced in a given cell in a given moment of its life. 
- Up-regulation- process that increases ligand/receptor interactions due to an increase in the number of available receptors. 
- Down-regluation- the process that decreases ligand and receptor interactions or reduces the responsiveness of a cell to a stimulus following first exposure.
- Mannoprotein- yeast cell wall components that are proteins with large numbers of mannose groups attached; highly antigenic." 
Outline: Acclimation of Saccharomyces cerevisiae to Low Temperature: A Chemostat-based Transcriptome Analysis
- Yeast prefer to grow in temperature closer to 30°C compared to 12°C
- Gene expression changes in response to outside stimuli such as temperature change
- Experiments had been done in the past to check for 'cold shock' genes that are up-regulated when yeast are exposed to low temperatures
- These experiments did not use chemostats
- There are three main responses to cold temperature depending on the duration of the temperature
- Sudden Exposure leads to Adaptation
- Prolonged Exposure leads to Acclimation (used in this study)
- Very Long Exposure leads to Evolutionary Adaptation
- Dilution Rate: 0.03/h
- Temperature: One set at 12°C and another at 30°C
- Yeast grown in a steady-state chemostat instead of batches that had been used in previous experiments
- Anaerobic conditions
- Haploid yeast
- The two limited nutrients were glucose and ammonia each done separately at different temperatures making 4 data sets
- Three replicas were done for each of the four conditions
- Results were compared to results from previous batch experiments
- In previous experiments, yeast were exposed to cold shock; in this experiment yeast were grown at a lower temperature
- Adaptation vs. Acclimation
- P-Values calculated
- Venn Diagrams used
- The residual concentration of limiting reagents were lower at 12°C
- At 12°C there was also a higher transcription level of ribosome biogenesis genes
- Low temperature growth did not use Msn2/Msn4
- FIGURES AND TABLES
- Table 1: Biomass yields and fermentation rates in both temperature conditions did not change significantly; this shows that yeast can adapt to the colder environment.
- Figure 1: Shows number of differently regulated genes, a total of 1065 genes regulated differently.- In nitrogen limiting, 806 genes; In carbon limiting 494 genes. Of these genes 235 are regulated differently in both conditions.
- Figure 2: Heat map representing the transcript level ratio of 1065 differentially expressed genes. This figure shows in detail the functions of many of the genes that are up-regulated and down-regulated in different limiting conditions.
- Table 2: Shows amount of storage carbohydrate in yeast cells under the different limiting conditions. There is a much lower concentration of Trehalose in the 12°C yeast cells compared to the 30°C yeast cells.
- Table 3:
- A)5' upstream cis-regulatory motif. Motifs that are significantly overrepresented are shown here. Significantly overrepresented in this case means that they showed up much more often than they should have just by random.
- B)Significantly overrepresented promoter elements that bind known transcription factors (TF) or TF pairs.
- Figure 3: These are genes from other studies that were regulated differently in batch studies that went through adaptation instead of acclimation.
- Figure 4: Comparison of the transcript ratio of 259 genes common to three batch-culture low-temperature transcriptome datasets. There are surprisingly very few genes that are regulated differently in both this experiment and the batch experiments.
- Figure 5: A Venn diagram comparison of the genes specifically up- or down-regulated during acclimation(this study) or adaptation (overlap of the datasets. There are again very few genes shared between all the studies.
- Figure 6:
- A)Same Venn diagram figure as Figure 5, but the ESR (Environmental Shock Response) genes have been added to the diagram as well to show where they are similar to the batch studies of adaptation. There are not many similarities, but the are more similarities in terms of up-regulation and down-regulation.
- B)Same Venn diagram as A, but with this study's acclimation data. There is an opposite effect occurring with which genes are being up-regulated and down-regulated. It appears that ESR genes are more likely used in "cold shock" where there is a sudden change in temperature, but they are not necessarily used when the yeast are growing at a lower temperature. This could be because the yeast know that they are staying at a constant temperature and not possibly dropping below freezing.
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