University of Mary Washington Biology Paper

University of Mary Washington Biology Paper

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1 Literature Review This proposal builds on worm lysis and the 18S gene, and it consists of two parts: listing relevant articles plus summaries of valuable information from them. Part 1: List of Potentially Relevant Articles The articles will be drawn from two main databases, PubMed and Wormbase. The articles from PubMed will provide articles that deliberate about the 18S gene and worm lysis. The search terms 18S ribosomal RNA and gene result RN 18S will be used to search 18S gene. The search terms Lysis buffer and genotyping worms will be used to search for worm lysis. The search process will be achieved by integrating the Boolean operators’ strategy. The strategy focuses on customizing the search (Scells et al., 2018). For instance, keywords like ‘Lysis buffer’ AND ‘genotyping worms’ will be used to identify worm lysis. Wormbase is the second resourceful database that has a reference part. Accessing the database will identify pertinent publications regarding 18Sgene and worm lysis. The database also includes meeting abstracts from the international worm meeting. However, these abstracts are unreliable because they are always written months before a meeting, viewed as personal communication, and grounded on preliminary data. Therefore, it will be needful to examine the articles listed. Part 2: Summaries of Relevant Information Wang et al. (2022) performed a study to design a single-worm RNA-seq method that includes five steps. They are cDNA synthesis, RNA extraction, worm lysis, sequencing, library 2 preparation, and sequence data analysis. Designing the single-worm RNA-seq method would be made it possible for the authors to profile gene expression effectively. Following the five steps of designing the single-worm RNA-seq method allows scholars to identify and differentiate joint and individual gene practices in isogenic people. This article relates to the proposal because the proposal deliberates on worm lysis and 18S genes. Similarly, the article deliberates on the worm lysis role when integrated with other steps to form a single-worm RNA-seq method. The singleworm RNA-seq method is effective in profiling gene expression in individual C. researchers can also rely on the method to study the responses of the pathogen infection. This article is useful for this proposal as it provides pertinent information regarding the significance of worm lysis. Borges et al. (2022) researched 18S genes and determined that order Trypanosomatida parasites are known following their medical relevance. Previous researchers have been trying to understand the evolution of these parasites, yet there are numerous questions requiring serious phylogenetic markers to augment the resolution of trees. The authors add that Homology modeling predicted individual 18S RNA gene secondary structures. 18S RNA gene secondary structures act as a supplemental source of phylogenetic information. Therefore, using 18S RNA data can help researchers to infer alignments and trees. Fuerst and Booton (2020) comment that the data by 18S RNA ensures the accuracy and robustness of the reconstructed phylogenies. The usefulness of the 18S RNA data could be because of how it concurrently infers alignments and multigene trees. The article by Borges et al. will be useful in this proposal by providing pertinent information regarding the 18S RNA gene’s role in reconstructing vigorous phylogenetic trees. 3 References Borges et al. (2021). 18S rRNA gene sequence-structure phylogeny of the Trypanosomatida (Kinetoplastea, Euglenozoa) with special reference to Trypanosoma. European Journal of Protistology, 81, 125824. https://doi.org/10.1016/j.ejop.2021.125824 Fuerst, P. A., & Booton, G. C. (2020). Species, sequence types and alleles: dissecting genetic variation in Acanthamoeba. Pathogens, 9(7), 534. Scells et al. (2019, May). Automatic Boolean query refinement for systematic review literature search. In The world wide web conference (pp. 1646-1656). Wang et al. (2022). Using single-worm RNA sequencing to study C. elegans responses to pathogen infection. BMC genomics, 23(1), 1-16. 1 Research Proposal 1A Introduction/ Background Maggenti (2020) states that nematodes are among the large groups of the metazoans family. Roughly less than 4% of nematode organisms are scientifically known, with worldwide species richness of approximately 106 and 108. Most of the nematode species are parasitic and are harmful to the health of plants and animals globally. For instance, the World Health Organization (WHO) released a report which revealed that global infections because of soiltransmitted nematodes account for the human disease problem of 3.8 million years lost because of disabilities (Maggenti, 2020). It is important to work with nematodes because they enhance soil quality by mineralizing nutrients into plant-available forms, controlling the population of soil organisms, consuming disease-causing organisms, and offering a food source for them. The transformations in DNA sequencing approaches have seen precise and rapid identification of many organisms like nematodes. Scientific scholars have attempted to address the genetic taxonomy of nematodes with the help of the 18S rRNA. Worm lysis and the 18S gene are commonly studied topics in biology. Abbreviated as 18 rRNA, 18ribosomal RNA forms part of the ribosomal RNA. 18S rRNA is a eukaryotic cytosolic 16S ribosomal RNA homolog in plastids and prokaryotes. 18S rRNA is among the mostly used genes in phylogenetic studies. It is also a vital marker in environmental biodiversity screening (Borges et al., 2022). Precisely, it is an important marker by randomly targeting polymerase chain reaction (PCR). rRNA gene sequences are easily accessible because the highly flanking regions make it easier to use universal primers. The gene is recognized for reconstructing the 2 metazoan tree of life. It also contributed to the most existing revolutionary change in conceptualizing metazoan relationships. Research Question/ Problem/ Hypothesis Statement The primary research problem that this proposal intends to solve is determining the 18S RNA gene role in reconstructing vigorous phylogenetic trees. The study also focuses on the significance of worm lysis in genetics. The research questions are listed below: RQ1: What is the 18S RNA gene’s role in reconstructing vigorous phylogenetic trees? RQ2: What is the significance of worm lysis in genetics? This proposal is important because it will add knowledge regarding the 18S RNA gene’s role in reconstructing vigorous phylogenetic trees and the significance of worm lysis in genetics. Methods The study will perform a qualitative systematic review method to identify information about the studied topic from peer-reviewed sources (Williams et al., 2021). The method will uncover a new understanding of the subject. Results Borges et al. (2022) concluded that the 18S RNA gene is vital in reconstructing vigorous phylogenetic trees. On the other hand, Borges et al. (2022) concluded by citing that worm lysis is important in genetic mapping. 3 References Borges et al. (2021). 18S rRNA gene sequence-structure phylogeny of the Trypanosomatida (Kinetoplastea, Euglenozoa) with special reference to Trypanosoma. European Journal of Protistology, 81, 125824. https://doi.org/10.1016/j.ejop.2021.125824 Maggenti, A. R. (2020). General nematode morphology. In Manual of agricultural nematology (pp. 3-46). CRC Press. Williams et al. (2021). Re-examining systematic literature review in management research: Additional benefits and execution protocols. European Management Journal, 39(4), 521-533. 1 Research Proposal Part B Introduction/ Background Maggenti (2020) states that nematodes are among the large groups of the metazoans family. Roughly less than 4% of nematode organisms are scientifically known, with worldwide species richness of approximately 106 and 108. Most of the nematode species are parasitic and are harmful to the health of plants and animals globally. For instance, the World Health Organization (WHO) released a report which revealed that global infections because of soiltransmitted nematodes account for the human disease problem of 3.8 million years lost because of disabilities (Maggenti, 2020). It is important to work with nematodes because they enhance soil quality by mineralizing nutrients into plant-available forms, controlling the population of soil organisms, consuming disease-causing organisms, and offering a food source for them. The transformations in DNA sequencing approaches have seen precise and rapid identification of many organisms like nematodes. Scientific scholars have attempted to address the genetic taxonomy of nematodes with the help of the 18S rRNA. Worm lysis and the 18S gene are biology’s most commonly studied topics. Abbreviated as 18 rRNA, 18ribosomal RNA forms part of the ribosomal RNA. 18S rRNA is a eukaryotic cytosolic 16S ribosomal RNA homolog in plastids and prokaryotes. 18S rRNA is among the mostly used genes in phylogenetic studies. It is also a vital marker in environmental biodiversity screening (Borges et al., 2022). Precisely, it is an important marker by randomly targeting polymerase chain reaction (PCR). rRNA gene sequences are easily accessible because the highly flanking regions make it easier to use universal primers. The gene is recognized for 2 reconstructing the metazoan tree of life. It also contributed to the most existing revolutionary change in conceptualizing metazoan relationships. Research Question/ Problem/ Hypothesis Statement The primary research problem that this proposal intends to solve is determining the 18S RNA gene role in reconstructing vigorous phylogenetic trees. The study also focuses on the significance of worm lysis in genetics. The research questions are listed below: RQ1: What is the 18S RNA gene’s role in reconstructing vigorous phylogenetic trees? RQ2: What is the significance of worm lysis in genetics? This proposal is important because it will add knowledge regarding the 18S RNA gene’s role in reconstructing vigorous phylogenetic trees and the significance of worm lysis in genetics. 3 References Borges et al. (2021). 18S rRNA gene sequence-structure phylogeny of the Trypanosomatida (Kinetoplastea, Euglenozoa) with special reference to Trypanosoma. European Journal of Protistology, 81, 125824. https://doi.org/10.1016/j.ejop.2021.125824 Maggenti, A. R. (2020). General nematode morphology. In Manual of agricultural nematology (pp. 3-46). CRC Press.

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