nematodes are among the large groups of the metazoans family

nematodes are among the large groups of the metazoans family
Sample Answer for nematodes are among the large groups of the metazoans family Included After Question
nematodes are among the large groups of the metazoans family
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. Methods Methods Worm Lysis Biology scholars can perform worm lysis on a single worm or numerous worms. A biology scholar can perform this process on a pool of worms (50-60). The consideration for worm lysis is that it breaks the cell worms and identifies the nucleus (Maggenti, 2020). The researchers working as a team for this research report inserted 20 worms into the PCR tube, followed by 33uL worm lysis. Later, he put two tubes in a freezer of -800, one with the worms and the other with no worms. The tube without worms was a negative control tube to utilize in the PCR reaction. The researchers used the new kit to perform worm lysis and DNA extraction to break the cell and access the nucleus by using the two tubes, one for the regular with worms and the other for the control. The regular tube contained 1-16 worms, 2ul extraction, 0.5ul tissue, and 2ul neutralization. PCR PCR is an acronym for polymerase chain reaction (PCR) and is a three-step process needed for any DNA synthesis reaction. These steps are denaturing the template into single strands, annealing primers to specific original strands for the new strand synthesis, and stretching the new DNA strands from the primers (Mubarak et al., 2020). The researchers performed PCR with the help of DreamTaq to determine the reliability of the method. They added 1.0ul 10uM SSU26R primer, 1.0ul 10uM SSU18R primer, 25ul DreamTaq PCR master mix, and 18ul dH20 in both tubes, one for negative control and the other with worms. Gel Electrophoresis and Gel Extraction It is a laboratory procedure to separate mixtures of proteins, DNA, or RNA depending on the molecular size. The procedure ensures that the electrical field pushes the molecules to be separated through gel with tiny pores (Green & Sambrook, 2019). Therefore, the researchers run the gel to determine the reliability of the PCR, where being able to observe the bands implicates the effectiveness of the gel. The researchers first made Gels by adding 50mL 1X TAE and 0.4g of agarose to 125mL Erlenmeyer flask and heating the contents in the microwave for 60 seconds at the interval of two in thirty-second increments. After that, they allowed the mixture to cool to hold the flask comfortably for about 10 seconds. After that, they added 2uL gel green into the flask and swirled the flask to mix the contents, build and set up the trays, and drain the contents into the prepared gel mold, allowing them to solidify. The researchers loaded Gels after making them by following a specific procedure. They prepared samples for loading while allowing the gel to cool and harden. They also prepared where to load the DNA ladder and each sample. Secondly, they placed the gel mold into the gel box, loosened the plastic screws, and lowered the mold sides. They added 1X TAE to the gel box until it reached a level 1cm higher than the top gel face. They added a 24uL sample to the intended wells and a 10uL DNA ladder and used electrodes to attach the lid. After that, they run the sample at 100mA or 100mv for roughly 40 minutes. Following this process suggests the possibility of easily observing 25 to 100ng of the DNA. DNA Sequencing It is the general laboratory method for determining the precise sequence of bases or nucleotides in a DNA molecule. DNA sequencing can be achieved through different methods like synthesis and single-molecule DNA sequencing (Green & Sambrook, 2019). Like the former procedures, the researchers performed worm lysis to identify the DNA by breaking the worm cell. They also run the gel thoroughly to determine the usefulness of the PCR. They performed the procedure of running the gels by making them and loading them for about 10-20 minutes to determine the band size. It will be easier for them to see 25-100ng of the DNA with fewer constraints. References Green, M. R., & Sambrook, J. (2019). Analysis of DNA by agarose gel electrophoresis. Cold Spring Harbor Protocols, 2019(1), pdb-top100388. Maggenti, A. R. (2020). General nematode morphology. In Manual of agricultural nematology (pp. 3-46). CRC Press. Mubarak et al. (2020). An optimization and common troubleshooting solving in polymerase chain reaction technique. Systematic Reviews in Pharmacy, 11(2), 427-436. 1 Approach and Results Name Institutional Affiliation 2 Approach and Results Approach Worm lysis can be performed on a single or numerous worms of about fifty and sixty. Worm lysis breaks the cell worms and identifies the nucleus (Maggenti, 2020). The researchers, working as a team, put 20 worms into the PCR tube and later inserted 33uL worm lysis. After that, they inserted two tubes, one for negative control and the other for worms, in a freezer of 800. The new kit was used to perform worm lysis and DNA extraction to break the cell to access the nucleus by using two tubes, the regular tube with worms and the other with no worms, for the control. The regular tube had 1-16 worms, 2ul extraction, 0.5ul tissue, and 2ul neutralization. PCR It is a three-step process for DNA synthesis reaction. They are denaturing the template into single strands, annealing primers to specific original strands for the new strand synthesis, and stretching the new DNA strands from the primers (Mubarak et al., 2020). The researchers pursued this process by integrating DreamTaq to determine the reliability of the process. They added 1.0ul 10uM SSU26R primer, 25ul DreamTaq PCR master mix, and 18ul dH20 in the negative control and regular tubes. Gel Electrophoresis and Gel extraction The laboratory procedure was designed to separate mixed proteins, RNA, or DNA by molecular size. It forced the electrical field to push the molecules, separating them through Gel with tiny pores. The Gel was run to determine the reliability of the PCR. The Gel is effective if the bands are observable (Green & Sambrook, 2019). The Gels were first made by adding 50mL 1X TAE and 0.4g of agarose to the 125mL Erlenmeyer flask and heating the contents for sixty seconds at an interval of two in thirty-second increments. The mixture was then allowed to cool 3 so the flask could be held comfortably for ten seconds. 2uL gel green was then added into the flask and swirled to mix the contents and release the contents into the prepared get mold to allow them to solidify. A specific procedure then loaded gels. Samples were then prepared for loading while allowing the Gel to harden and cool. Loading of the DNA was also done at this point. The gel mold was then put into the gel box, loosened the plastic screws, and lowered the mold sides. 1X TAE was added to the gel box until it reached 1cm higher than the top gel face. 24uL sample was added to the intended wells, and a 10uL DNA ladder used electrodes to attach the lid. The sample was then run at 100mA or 100mv for about 40 minutes. DNA Sequencing It was performed to determine the precise sequence of the nucleotides or bases in the DNA molecule. Worm lysis was performed in this procedure to identify the DNA by breaking the worm cell. The Gel was run thoroughly to determine the significance of the PCR (Green & Sambrook, 2019). The process of running the gels was performed by designing them and loading them for about 20 minutes to determine the size of the band. It will be easier to observe 25100ng of the DNA. Summary of the Results Worm Lysis It was performed with DNA extraction to break the cell and get the nucleus. The process was performed in two tubes; one was designed for the negative control, while the other had 20 worms. After that, Gel was run to determine the effectiveness of the PCR. However, the Gel did not work for this study as no bands were visible. Below is an image illustrating the results of the process. 4 Figure 1: An illustration of bands invisible PCR PCR was performed with the help of DreamTaq to determine the effectiveness of the method (Green & Sambrook, 2019). The findings revealed that performing SapphireAmp Fast PCR Master Mix reduced total time if integrated with DreamTaq. It is more reliable than PCR Reaction Mix presented in the Extract-N-Amp XNAT2 kit. The Gel was correctly run to determine if PCR works, and it is possible if the bands are observable, and luckily, the PCR worked. Below is an image depicting how the PCR worked. Figure 2: An Image showing how the PCR worked. 5 DNA Sequencing It was achieved by performing worm lysis to identify the DNA by breaking the worm cell. The Gel was also run to determine the effectiveness of the PCR (Green & Sambrook, 2019). Unfortunately, the Gel failed to work because the wires were wrongly connected. They were connected in opposite directions. Conclusion The researchers examined the significance of worm lysis in genetics. It informs biology scholars that worm lysis can be performed on a single or many worms. Performing worm lysis together with DNA extraction is vital to breaking the cell to make it easy to access the nucleus. The Gel is always run to determine the effectiveness of the PCR, and it can be proved by observing the bands. Also, performing the PCR by integrating DreamTaq is ideal for determining 6 the appropriateness of the method, which can be confirmed by identifying the bands. The findings confirm the aim of this study wherein specifically cite that worm lysis is vital in genetic mapping. 7 References Green, M. R., & Sambrook, J. (2019). Analysis of DNA by agarose gel electrophoresis. Cold Spring Harbor Protocols, 2019(1), pdb-top100388. Maggenti, A. R. (2020). General nematode morphology. In Manual of agricultural nematology (pp. 3-46). CRC Press. Mubarak et al. (2020). An optimization and common troubleshooting solving in polymerase chain reaction technique. Systematic Reviews in Pharmacy, 11(2), 427-436. Interpretation of the Results Interpretation of the Results Significance Statement Summary of Results The study aimed to determine the significance of worm lysis in genetics. This study is significant because it will inform readers and future researchers about the role of worm lysis in genetics. The findings revealed that Gel did not work for worm lysis because no bands could be seen. I performed the PCR by using DreamTaq to determine its effectiveness. The findings confirmed that performing SapphireAmp Fast PCR Master Mix minimized the total time, proving the PCR’s functionality. Regarding DNA sequencing, I performed worm lysis to identify the DNA by breaking the worm cell. I performed this test by running Gel to determine the effectiveness of the PCR. Unfortunately, the Gel did not work because the Gel was running in opposite directions. Interpretation I performed worm lysis three times to see if the PCR worked. Procedurally, I started with worm lysis through PCR, Gel Electrophoresis, and Gel extraction through DNA sequencing. PCR works by denaturing the template into single strands, annealing primers to separately original strands for new strand synthesis, and extending the new DNA strands from the primers (Fuerst & Booton, 2020). I first performed the process with DNA extraction to break the cell and get the nucleus. I added 33 uL worm lysis buffer into the PCR tube and inserted twenty worms. I then run Gel to determine the effectiveness of the PCR, but it did not work because no bands could be observed. As Fuerst and Booton put it, Gel helps to analyze PCR products suggesting why it was used in the lab (2020). Therefore, failing to observe the bands could imply that the PCR was ineffective. Secondly, I performed the PCR process by following the three required steps in synthesizing DNA reaction. I used DreamTaq to perform the PCR. Using SapphireAmp Fast PCR Master Mix worked by minimizing the total time integrated with DreamTaq. After that, I run the Gel correctly to determine if PCR works. The bands were observable, meaning that the PCR worked. From the findings, it could be possible that the effectiveness of the PCR may have been drawn from the consideration of DreamTaq. However, in the first experiment, DreamTaq and SapphireAmp Fast PCR Master Mix were not acknowledged, and PCR did not work. From the findings, it could be possible that DreamTaq and SapphireAmp Fast PCR Master Mix promoted the effectiveness of the PCR. They are known as catalysts as they fasten the PCR process (Maggenti, 2020). It implies that the PCR process becomes effective when catalyzed. Lastly, I determined DNA sequencing by performing worm lysis to identify the DNA by breaking the worm cell. I also run the Gel to determine the effectiveness of the PCR, but Gel did not work because it was running in the opposite directions. Had the Gel been running correctly, it would have been easier to determine DNA sequencing. Therefore, results for this test were not obtained. Recommendations Researchers should be mindful when performing tests. I performed a series of tests where only one test generated desired results. For instance, the last test did not work because I was not attentive when running the Gel, and it is impossible to make conclusions without obtaining results. However, from the collected results, PCR seems effective when integrated with catalysts. Therefore, it would be meaningful for biologists to engage SapphireAmp Fast PCR Master Mix and DreamTaq catalysts as they not only speed up the process but account for the effectiveness of the PCR. Future researchers should explore questions on the significance of DreamTaq in promoting the effectiveness of PCR. References Fuerst, P. A., & Booton, G. C. (2020). Species, sequence types and alleles: dissecting genetic variation in Acanthamoeba. Pathogens, 9(7), 534. Maggenti, A. R. (2020). General nematode morphology. In Manual of agricultural nematology (pp. 3-46). CRC Press. Outline of Proposed Future Directions 11/18/2022 Outline of Proposed Future Directions Worm Lysis a. Worm lysis is performed on either a single worm or numerous worms. b. The process can be performed on a pool of worms (50-60). c. 20 worms are inserted into a PCR tube, followed by 33uL worm lysis. d. Two tubes are kept in a freezer of -800; one has worms, while the other has no worms (Green & Sambrook, 2019). e. The one with worms is labeled as a regular tube, while the other with no worms is meant for control. f. The regular tube contained 1-16 worms, 2ul extraction, 0.5ul tissue, and 2ul neutralization. PCR a. It is an acronym for polymerase chain reaction (PCR) and is a three-step process needed for any DNA synthesis reaction. b. The steps are denaturing the template into single strands, annealing primers to specific original strands for the new strand synthesis, and stretching the new DNA strands from the primers (Maggenti, 2020). c. PCR is performed with the help of DreamTaq to determine the reliability of the method. They added 1.0ul 10uM SSU26R primer, 1.0ul 10uM SSU18R primer, 25ul DreamTaq PCR master mix, and 18ul dH20 in both tubes, one for negative control and the other with worms. Gel Electrophoresis and Gel Extraction a. It is a laboratory procedure to separate mixtures of proteins, DNA, or RNA depending on the molecular size. b. The procedure ensures that the electrical field pushes the molecules to be separated through gel with tiny pores. c. The gel is run to determine the reliability of the PCR, where being able to observe the bands implicates the effectiveness of the gel (Mubarak et al., 2020). d. It is made by adding 50mL 1X TAE and 0.4g of agarose to 125mL Erlenmeyer flask and heating the contents in the microwave for 60 seconds at an interval of two in thirty-second increments. e. The mixture is allowed to cool to hold the flask comfortably for about 10 seconds. f. Finally, 2uL gel green is added into the flask and swirled to mix the contents, build and set up the trays, and drain the contents into the prepared gel mold, allowing them to solidify (Mubarak et al., 2020). g. Gels are loaded after making them by following a specific procedure. h. Gel mold is placed into the gel box, loosened the plastic screws, and lowered the mold sides. i. 1X TAE is added to the gel box until it reaches 1cm higher than the top gel face. j. 24uL sample is added to the intended wells, and a 10uL DNA ladder and used electrodes to attach the lid. After that, they run the sample at 100mA or 100mv for roughly 40 minutes. DNA Sequencing a. It is the general laboratory method for determining the precise sequence of bases or nucleotides in a DNA molecule. b. DNA sequencing is achieved through synthesis and single-molecule DNA sequencing (Green & Sambrook, 2019). c. Worm lysis is performed to identify the DNA by breaking the worm cell. d. The gels are run by making them and loading them for about 10-20 minutes to determine the band size. References Green, M. R., & Sambrook, J. (2019). Analysis of DNA by agarose gel electrophoresis. Cold Spring Harbor Protocols, 2019(1), pdb-top100388. Maggenti, A. R. (2020). General nematode morphology. In Manual of agricultural nematology (pp. 3-46). CRC Press. Mubarak et al. (2020). An optimization and common troubleshooting solving in polymerase Research Report Rubric. MBRI Final Assignment 130 points Introduction/background:content (30 points) • broad introduction to: your project, nematodes, benefits of working with nematodes in the classroom and/or course-based research projects, and other specifics. • Deeper introduction: o For groups 1: introduction to gene targeted by PCR, why chosen, existence in other species, potentially with a figure about the region we are amplifying. Group 1 – a lot more on nematode diversity and purpose of finding nematodes. • Research question/problem/ or hypothesis statement along the lines of: “Cloning the 18S rDNA as a positive control for PCR is possible and useful; supporting BIOL121 will benefit students and generate data on nematode diversity; Behavior tests can be used in 121 to characterize and compare nematode species and allow introductory students to design experiments and analyze data; Genetics students will benefit from an introduction to nematodes and RNAi that has identifiable phenotypes. (students: please refine these, as its your ideas to articulate and I only wanted to give example ideas). • The molecular mechanism should be incorporated into this section, or possibly referenced as being in the appendix. • Ends with a statement about how this study will add knowledge to the field / benefit classes. • Figures or tables that are part of the background may also be included. Methods (20 points) • Covers the techniques used. If a technique was used multiple times, it covers the various changes and iterations of the technique used. • Includes the sources of all commercial reagents. Standard reagents made in house (like TAE) can just be described in general terms, such as “1X TAE was used with agarose (commercial source) to make 0.8% agarose gel.” Kits can be briefly described and deviations from kit protocols can be noted. Results (30 points) • Describes the approach used • Includes organized presentation of data in Figures. • Figures & Tables • formatted properly (as described in the guidelines) and easy to understand. • Group 1: PCR results, DNA gel images, MEGA alignments and phylogenies. Also, generate a figure diagraming what you achieved. For example, the cloning you have completed and if you have finished cloning your gene into the pGEM T Easy vector, you should build a plasmid diagram in SerialCloner and include it in your report. • Group 2: Includes: PCR results DNA gel image, gene cloned into plasmid depiction, blue-white screening results • Group 3: Includes Tables of results, illustrations or photos of experimental set up, potentially other figures. • Group 4: Includes Tables of results, photos of phenotypes • Stand alone – all figures understandable without the accompanying paper • Each result is presented in the context of a specific smaller question that the experiment is designed to address, a description of the result, • Includes simple interpretations of figures (longer interpretations in discussion) • Past tense Discussion and (Future Directions or Appendix) (20 points) • Data interpreted and contextualized. Includes references. • • • • Relates back to the Introduction and to existing theory and knowledge How does your work relate to scholarship in biology education or how does it relate to what we know about building plasmids or DNA sequencing? Speculation is appropriate if it is so identified. Suggestions for the improvement of techniques or experimental design may also be included here. o Sequencing and bioinformatics group (1): Based on what you accomplished so far, what are the next steps? Also, instructions for MEGA could be an appendix. o Cloning group (2): If your gene has not been cloned, you should list approaches that will be taken to get it cloned (as if you had more time). If it has been cloned, what can be done next? o Behavior group (3): What else could be explored with the tools we have? Will students in introductory biology that complete behavior tests be able to do statistical analysis? Complete multiple experiments (repeats or new designs) in a semester? o RNAi group (4): What else could be explored with the tools we have? What will genetics students learn from this lab? What other ideas would you explore with more time? Organization o 1st paragraph typically contains another general significance statement followed by a brief summary of the results. o Subsequent paragraphs either expand upon the interpretation of specific experiments or promote conclusions relevant to multiple experiments (integration of the results). It is not uncommon to see citations in this section if the results: a) disprove a previous paper, b) agree with a previous result, c) are supported by a parallel experiment in another system. o Final paragraph – This is a good place to propose models, suggest important future questions etc. In the context of a lab report (or a progress report to a PhD committee), this last section is typically expanded. If you are generating an Appendix, refer to it here. Most of this section should be in the present tense. References (10 points) • Follow the reference guidelines beginning on page 15-10 of the lab manual • Accessed and read various articles as you developed the background section • Citations support background appropriately. • Use original sources-peer reviewed articles and reviews, not just Wormbase, reputable sources Style (20 points) • Correct title page • clear connections between 1) the background and proposed research and 2) the information presented in the different paragraphs (i.e. use transitions between paragraphs). • Sentences well structured • Includes proper scientific terminology, such as italicized gene and species names, along with proper notation of scientific quantities. • Organized, understandable presentation of material. • Followed feedback from previous drafts of the proposal
nematodes are among the large groups of the metazoans family
A Sample Answer For the Assignment: nematodes are among the large groups of the metazoans family
Title: nematodes are among the large groups of the metazoans family