Genome Science and Biological Exploration - Essay Example

 Genome Science and Biological Exploration Qn. 1 Gene Expression in the yeast Saccharomyces cerevisiae on a genome-wide level Advancement in technology in the field of genome science has been instrumental in the current revolution in the approaches used in biological exploration, which allows the study of organisms in a genomic-wide level. The use of DNA microarrays in characterising the whole genome expression has been instrumental in the provision of a picture of the genome of an organism in action, which reveals thousands of genes in action at a time. A 1997 study by Derisi et al. used DNA microarrays to follow the process through which yeast cells naturally transitioned from their stage of fermentative metabolism to the final stage of respiration in order to study the changes in gene expressions on a global level. The use of microarray technology to study gene-expressions in yeast S. cerevisiae first involves the construction of microarrays in four steps. The first of these steps involves generation of target DNA for spotting. The S. cerevisiae genome contains PCR products that significantly predict opening reading frames whose standard conditions and sequence-specific primers are essential in intensifying the reading frame and the intergenic sequencing of the S. cerevisiae (Hayward, et al., 2000). The second step involves the preparation of slides before engaging in carrying out the printing process. Importantly, these slides must be of high quality. Thereafter, printing the arrays takes place with the final step involving the processing of the microarrays after printing. In this step, the spotted DNA must be prevented from the nonspecific binding of probe DNA by using chemicals to block the unbound lysine on the surface of the slide (Hayward, et al., 2000). After the construction of the microarrays, it is important to highlight the importance of the steps that guide the process of the experiment such as establishing the appropriate conditions for strains and growth conditions for microarray experiments. In addition, the establishment of an experimental design in order to choose the appropriate dose of a stimulus and measure the timing of a response of a cell, which requires effective investigations. In line with this step, a microarray-referencing sample should be chosen in order to ensure that there is collection of adequate sample during the experiment procedure. Following the selection of the sample, the next step involves the isolation of RNA and probe generation. In this case, it involves lysing the frozen samples, centrifuging the emulsion obtained after incubation to remove any debris, and then proceeding with the extraction of the aqueous state. Finally, this process culminates in the precipitation of the total RNA that undergoes incubation, centrifugation, and resuspension to provide RNA that was pure in protein. After obtaining these samples of total RNA, the next step involves amplification of the total RNA to obtain double stranded cDNA that undergoes hybridation and a sequence of three washes in order to increase the stringency (Wang, et al., 2000). Qn. 2 a) Importance of the yeast Saccharomyces cerevisiae as a model organism in the study of the cell cycle Model organisms are crucial in research since they provide researchers the opportunity to develop frameworks that facilitate standardized methods for analysis. The yeast S. cerevisiae as a model in the study of cell cycle is important since the “cells lack the dense cortical actin cytoskeleton, which in mammalian cells gives structural support to the plasma membrane and maintains the cell shape” (Kaksonen, n.d, p.86). In addition, these cells are not capable of movement and are free of the extensive membrane-associated actin structures that power migration of cells in animal cells. In addition, these cells represent a wider class of living beings that can investigate any phenomenon among living things (Karathia, et al., 2011). 2. b) Bacterial Adaptation to Stress in a Biofilm Bacterial cells that are growing in biofilms are exposed to nutrients that reach them through the water channels within the matrix EPS, which helps the cells to resist the shear force from the flow of blood and the washing by saliva of an organism. On the other hand, the structure of the biofilm allows the bacterial cells to be close to each other, which facilitates intercellular communication, which is essential for bacteria cells to respond in a collective approach by signalling pathways in order to adapt to changes in the environment. On the other hand, biofilm components provide bacteria cells living inside the animal host with protection and resistance from “biocides, antibiotic treatment, and host immune response” (An, Dong and Zhang, n.d, p.214). Qn. 2 c) Properties of Zymomonas spp Zymomonas mobilis is an aerobe that is tolerant to air and its growth requires pH levels that were above 3.4 with the concentration of ethanol at 10% (w/v). This gram-negative bacterium produces equimolar amounts of ethanol and carbon dioxide while also having the capabilities of fermenting sucrose, fructose, and glucose in quantitative levels. On the other hand, these species of bacteria do not have the characteristics of fermenting maltose and maltotriose, which signifies its inability to cause wort infection. On the other hand, this species of bacteria produces high levels of hydrogen sulphide and acetaldehydes that causes change in odour and loss of sweetness (Sakamoto and Konings, n.d.). Qn. 3 Cell Division in Escherichia coli Replication of E. coli precedes cell division in this bacteria cell. Importantly, the process of replication takes about forty minutes for the cells to consist of more than a copy of the chromosomes with this process of replication starting at random regions of the grandmother cells in the bacterium. Thereafter, the first signs of septation start appearing with the end of the process of chromosomal replication and the process that involves the separation of the nucleoid in the E. coli cell. The division of the cell involves the joint activity of various gene products such as the product of ftsZ, which is essential in the early stage of cell division, and the ftsA, which is crucial for the terminal stage of cell division. Activities of cell mutation that occurs in the fts genes results to filaments through the process of allowing growth and replication while preventing septation. After septation, the next activity involves cell separation through the production of envA. Thereafter, the newly formed poles become an active site for cell division and are consequently inactivated through the action of minC, B, and E products (Ayala, Garrido, De Pedro and Vicente, 1994). Chromosomes are allocated in the daughter cells during the process of cell division. Importantly, the process of mitosis is responsible for ensuring that “two daughter cells have the same type of genome” that are a copy of the chromosomes (Richards and Hawley, 2011). In this case, it is crucial to point out that the mechanism of cytokinesis divides the cells into two daughter cells since this is the mechanism where cell division occurs during the process of mitosis. Qn. 4 Mechanisms of the Evolution of Bacterial Genomes and Plasmids Bacterial genomes and plasmids can evolve under various mechanisms. In this regard, each mechanism involves various products and different processes in order for the genomes and plasmids to undergo a complete evolution. First, bacterial genomes and plasmids can undergo evolution through the mechanism of gene duplication. In this case, gene duplication will entail the duplication of a gene in a region of the DNA coding. Importantly, gene duplication may occur as an error that results to the evolution of plasmids and bacterial genomes under the process involving a homologous combination, duplication of the whole chromosome, or even as a retrotransportation event (Taylor and Raes, 2004). Bacterial genomes and plasmids can evolve under the mechanism of mutation. In this regard, the outcome of mutation is an increase or deletion of nucleotide bases by the process that involves a change in the sequence nucleotide sequence of the bacterial genome or plasmids. It is important to point out that mutation results from the process that involves unrepaired damage of DNA or RNA genomes or from errors that occurred during the process of replication of a bacterial genome or a plasmid. In effect, this results to changes in the genome with these changes being easily identifiable or at other times challenging to discern (Clark, 2005). Exon shuffling is another mechanism through which bacterial genomes and plasmids have evolved. In this case, this mechanism involves the creation of new genes in the bacterial genome or the plasmids. The process occurs in two different approaches that involve a combination of two different exons or the duplication of an exon, which changes the bacterial genome or the plasmid (Clark, 2005). Qn. 5 VNBC state In genetics, the term “viable but nonculturable” (VNBC) defines the state at which bacterial cells cannot be recovered despite these bacterial cells holding features that make these bacterial cells viable. The two distinct features that these bacterial cells hold, which make them viable despite their state of not being recoverable are cellular integrity feature and the other feature being the ability of the cells to have some activities (McDougald, Rice, Weichart and Kjelleberg, 1998). Experts interpret the non-recoverable state of these bacteria as state in which the bacteria is dormant. However, it is important to point out that a state in which a cell is dormant does not indicate any important activity in a cell with the definition of dormancy being a phenomenon that is reversible with the dormant cells being inactive and culturable (Kaprelyants, Gottschal and Kell, 1993). Hence, it is possible to deduce that a bacteria cell in VBNC state is a refractory state and not a dormant state whereby a cell is in a state of debilitation awaiting its death. In effect, this implies that the state of VBNC is an adaptation state of the cell. Cells in the state of VNBC are in a state of injury resulting from various processes, which effectively implies that these cells have the ability to attain and retain a viable state for some degree of time. Nonetheless, it is important to point out that the state of a cell becoming stable and achieving integrity are not effective indicators for defining survival in a cell (Kell, et al., 1998). In effect, this implies that cells that are in a state of VNBC are in an adaptation state and they are not weak due to the injured state, which means that the cells are not nearing their death. References Ayala, J. A., Garrido, T., De Pedro, M. and Vicente, M., 1994. Molecular Biology of Bacterial Septation. In J. M. Ghuysen and R. Hakenbeck, eds. 1994. Bacterial Cell Wall. Amsterdam: Elsevier Science B.V. Ch. 5. An, S., Dong, Y. H. and Zhang, L. H., n.d. The Impact and Molecular Genetics of Bacterial Biofilms. In: W. T. Liu and J. K. Jansson, eds. 2010. Environmental Molecular Microbiology. 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