Literary Analysis by Jori Paradis

Literary Analysis by Jori Paradis https://padlet.com/joriparadis/edonprv4dkh21lt8 An outline of articles flow to understand how to write a scientific paper. en-us 2023-01-27 19:40:49 UTC 2023-03-09 03:04:37 UTC hello@padlet.com https://padlet.net/icons/png/1f4a1.png Introduction joriparadis https://padlet.com/joriparadis/edonprv4dkh21lt8/wish/2459408827 1. Broad IDEA: Different yeasts can drive fermentation. The Common yeasts found in spontaneous and innoculated fermentation is S. cerevisiae because it has a high tolerance to alcohol and low oxygen ( even in low abundance).
2. What past studies have found: Other yeasts also contribute to the wine flavour, aroma, and texture. They also included specific yeasts commonly found in early fermentation stages.
4. What is currently being researched: Spontaneous fermentation can produce complex wines where non traditional yeasts lead fermentation.
5. BIG IDEA: Indigenous yeasts are affected by geography, soil, climate, and vineyard management.
6. What is known about big idea: They have found unique microbial diversity in different regions. Lists places where yeast communities have been documented. Introduction to microbial terroir and how it is a combination of indigenous yeast and the wine characteristics and how there is an increasing interest in spontaneous fermentation
10. Brief explanation and validation of methods: Explains how sequencing is the best way to characterize microbial communities. They used two different sequencing to elliminate bias. Explains the benefits of each type of sequencing.
13. Why the study is important: It will provide this vineyard a better understanding of the yeast community and how to use non traditional yeasts and spontaneous fermentation to market a more regionally unique wine.
14. The purpose of the study: To document the yeast communities before and after spontaneous fermentation.

]]> 2023-01-27 19:43:57 UTC https://padlet.com/joriparadis/edonprv4dkh21lt8/wish/2459408827 Methods joriparadis https://padlet.com/joriparadis/edonprv4dkh21lt8/wish/2459409200 They were broken into five different sub headings.
1. Sample collection, preparation, and processing
They explained where the samples came from, how they were collected, the volume of the samples, and what the conditions were during fermentation. They also included how often they took measurements and what determined the end of fermentation.
2. DNA extraction and PCR
They explained when they extracted DNA and what protocol they followed. They also included the sequence of the forward and reverse primers used for PCR amplification.
3. Sequencing and sequence data processing
They disclosed what sequencing company they used and what region of DNA they used to identify the species (ITS2). They explained what the results consisted of and that they are deposited in various archive systems. They explained how they filtered the data and what databases they used. They also used phylogenetic binning to clarify the taxonomy of the saccharomyces. They went on to explain all the sources they used (including NCI BLAST) to identify the species and what they did if they couldn't.
4. Chemical and sensory evaluation of wines
They explained all the chemical components they assessed and how they limited their errors and what contributed to them. They also explained how they avoided any bias in the rating of the flavor and provided the list of the different sensory attributes they used.
5. Statistical analyses and data visualization
They explain that they used R to analyze their data and which specific packages they used to create various graphs.

OVERALL SUMMARY OF METHODS
The methods progressed in a chronological order and went into detail about how everything was performed. They broke it up into different sub headings to make the flow of information more clear. ]]> 2023-01-27 19:44:17 UTC https://padlet.com/joriparadis/edonprv4dkh21lt8/wish/2459409200 Results joriparadis https://padlet.com/joriparadis/edonprv4dkh21lt8/wish/2459409751 The results were broken into 5 different sections
1. Yeast community composition before and after spontaneous fermentation based on Illumina sequencing (Individual)

Components included:
- Total number of sequences before and after fermentation.
- Individual library sizes of before and after.
- Number of species overall with a breakdown of how specific. This many to phylum, genus, order, class, etc.
- Number of phylum grouped " this many were saccromyses, this many were ascomycete"
- Break down of number Species present before and fermentation along as a comparison between the relative amount of species between each year and how many they had in common.
- How many species were found after fermentation but not initially.
- What the yeast communities consisted of before and after fermentation ( Fig.1).

2. Yeast community composition before and after spontaneous fermentation based on PacBio sequencing (Individual)
This section included the same components as above.

3. Fungal community based on Illumina and PacBio sequencing (Comparison of similarities)
- This consisted of the overall abundances of different species based on both sequencing results for both before and after sequencing results.

4. Statistical differences in vineyard yeast community compositions based on Illumina and PacBio sequencing( Comparison of differences)
- This section included the statitstical tests ran.

5. Chemical and sensory evaluation of wines

Summary of Results
They divided their results into the different types of sequences and then compared together. The last part included the sensory evaluation which was the final part of the study. They have consistently conveyed this information in the same order throughout the paper. ]]> 2023-01-27 19:44:51 UTC https://padlet.com/joriparadis/edonprv4dkh21lt8/wish/2459409751 Discussion joriparadis https://padlet.com/joriparadis/edonprv4dkh21lt8/wish/2459409847 1. Summary statement of overall results
2. Reference to past studies: What yeasts were found in past yeast community studies.
3. Addressed which yeast phylum was most abundant in pre fermentation: In this case it was basidiomycete.
4. Most significant results in order from most to least: Talked about the most abundant genus of Basidiomycete which was Filobasidium and addressed where it was found and in what climate.
5. Addressed how yeasts would affect wine quality: Addressed how the three most abundant yeasts would affect wine quality specifically.
- Also revealed a possible explanation for why 2018 was more liked than 2019.
6. Talked about the Post -fermentation community found, where they are found and how they attribute to wine flavor, and acknowledged limitations of the analysis along with a possible explanation.
7.Other methods used in similar studies: However, they both provided similar results.
8. Talks about potential bias/ errors in the study.
9. Explains how their study has added to the knowledge gap and how it can be applied.

SUMMARY OF DISCUSSION
The discussion followed the guidelines of going from narrow to broad. They addressed the significance of their specific results in the same order they were presented throughout the paper. When applicable they mentioned any limitations to the study and gave a plausible explanation for their results. In the concluding paragraphs they cited other literature and compared their results. Lastly, they explained how their study adds to the knowledge gap and can be used in the future. ]]> 2023-01-27 19:44:58 UTC https://padlet.com/joriparadis/edonprv4dkh21lt8/wish/2459409847 ARTICLE #1: Yeast communities before and after spontaneous fermentation of wine grapes: a case study from Nova Scotia joriparadis https://padlet.com/joriparadis/edonprv4dkh21lt8/wish/2459416563 Citation:
Bunbury-Blanchette, A., Fan, L., English, M., & Kernaghan, G. (2022). Yeast communities before and after spontaneous fermentation of wine grapes: a case study from Nova Scotia. Canadian Journal of Microbiology. https://doi.org/10.1139/cjm-2022-0179 ]]> 2023-01-27 19:52:30 UTC https://padlet.com/joriparadis/edonprv4dkh21lt8/wish/2459416563 Summary of introduction joriparadis https://padlet.com/joriparadis/edonprv4dkh21lt8/wish/2459456406 There were a lot of moving pieces within the introduction but they were able to funnel it down very well. They started out by talking about yeast in general and then went step by step through all of the factors that influence the communities of yeasts in different regions. They introduced and validated the methods the study would be using and then concluded with the purpose and goal of the study.]]> 2023-01-27 20:43:28 UTC https://padlet.com/joriparadis/edonprv4dkh21lt8/wish/2459456406 Article #2 joriparadis https://padlet.com/joriparadis/edonprv4dkh21lt8/wish/2460489252
Citation:
Díaz, C., Molina, A. M., Nähring, J., & Fischer, R. (2013). Characterization and Dynamic Behavior of Wild Yeast during Spontaneous Wine Fermentation in Steel Tanks and Amphorae. BioMed Research International, 2013, 540465. https://doi.org/10.1155/2013/540465

]]> 2023-01-29 18:51:45 UTC https://padlet.com/joriparadis/edonprv4dkh21lt8/wish/2460489252 Introduction joriparadis https://padlet.com/joriparadis/edonprv4dkh21lt8/wish/2460495760 1. Broad IDEA: Spontaneous Fermentation is becoming more popular among wine makers.
2. Transition: Spontaneous fermentation relies on natural flora
3. BIG IDEA: Yeasts affect wine aroma and flavor.
4. Methods of analysis: qPCR is the most common way to identify and quantify yeast communities.
5. Purpose of the study: To identify the yeast species during spontaneous fermentation.

SUMMARY of the INTRODUCTION:
This author began their research by introducing a broad statement and then transitioning into more detailed topics related to the broad statement. Additionally they introduced the best way to investigate these topics and concluded with the goals/purpose of the study.

]]> 2023-01-29 19:02:08 UTC https://padlet.com/joriparadis/edonprv4dkh21lt8/wish/2460495760 Methods joriparadis https://padlet.com/joriparadis/edonprv4dkh21lt8/wish/2460507993 1. Sample collection

2. Isolating yeast from the winery environment before fermentation

3. How fermentation was monitored ( the parameters)

4. How the yeast species were identified ( including primers used and protocols followed)

5. How the yeasts were quantified using (qPCR)

6. Wild Yeast Dynamics during fermentation.

Summary of Methods:
This author took the approach of breaking the methods down into different sections. It appears that they broke it down in order of what they completed first to last. In each section they went into detail about the measurements, time, and procedures followed.

]]> 2023-01-29 19:21:43 UTC https://padlet.com/joriparadis/edonprv4dkh21lt8/wish/2460507993 Results joriparadis https://padlet.com/joriparadis/edonprv4dkh21lt8/wish/2460512151 1. Establishing the method for yeast identification

2. Natural Flora found in Vineyard and Cellar Environments: Includes specific yeasts found and where in the environment

3. Yeast Flora in steel-Tank Fermentations: Changes in the yeast community throughout spontaneous fermentation. Includes what musts were used and what methods. Also included basic quantitative analysis.

4. Real time PCR

5. Yeast Flora in Quevri Fermentations: Included which was the dominant species and less dominant species.

OVERALL SUMMARY of RESULTS
Similar to the methods section the results were explained in the same order they were mentioned in the methods section.

]]> 2023-01-29 19:28:44 UTC https://padlet.com/joriparadis/edonprv4dkh21lt8/wish/2460512151 Discussion joriparadis https://padlet.com/joriparadis/edonprv4dkh21lt8/wish/2460525949 1. Isolation and Identification of Predominant Yeast Species
- Discussed the significance of their findings, why they chose certain methods over others, and limitations/errors within the study.
- Discussed yeast found in cellar environment and potential reasons why they were found.

2. Dynamic Behavior of Wild Yeasts during spontaneous Fermentation in Qveris.
- Reiterated why the study is important
- Potential reasoning for results.
- Identified key factors of the study
- States what further research should be done on based on results of this paper.

Summary of Discussion
The author took a different route to discuss their results. They broke it down into the two different fermentations they were looking into which was congruent with the methods and results. To convey the information they discussed the significance of the results, defended the methods/restated purpose, and addressed limitations and errors.

]]> 2023-01-29 19:50:53 UTC https://padlet.com/joriparadis/edonprv4dkh21lt8/wish/2460525949 Comprehensive Summary of Article Number 1 joriparadis https://padlet.com/joriparadis/edonprv4dkh21lt8/wish/2460538889
This article was very easy to follow from the introduction to the discussion. It was clear to see how it was a story. In the introduction they moved from a broad idea to the purpose and reason for the study by going into detail about the different components of the big idea and including transitions. The methods section was easy to read because it was broken into sections in chronological order of completion. This was complimented by a very thorough analysis of the results presented in the same order as the methods. The correlation between the methods and the results was very clear because the sub titles were very similar and in the same order. To compliment everything the discussion talked about information that hadn't been presented previously in the paper and was significant. The discussion also lead the reader to a bigger purpose and a clear idea of how this research contributed to the bigger picture. Overall this paper was very well organized and written.

]]> 2023-01-29 20:14:23 UTC https://padlet.com/joriparadis/edonprv4dkh21lt8/wish/2460538889 Comprehensive Summary of Article #2 joriparadis https://padlet.com/joriparadis/edonprv4dkh21lt8/wish/2460543030 This article followed a similar structure to what we have been taught in class. The biggest aspect that hindered it's story was the lack of transitions and a bigger purpose. The introduction never mentioned why this study is important or what the benefit of doing it was. This was also reflected in the discussion. Without the purpose of the paper being known the discussion seemed to fizzle out and not matter. The other part of the paper that hindered it was it's repetition. Although they had the designated methods, results, and discussion sections, there was information in each section that overlapped making it seem very repetative and choppy. The area that the paper did well was with how it organized what it talked about in each section. The paper had various elements that it researched and it consistently addressed them in the same order in each section of the paper. This made it easier to follow and know the significance of what they were talking about. Overall the flow of the paper was harder to follow but because it stuck to a consistent order of events it was redeemable. ]]> 2023-01-29 20:21:47 UTC https://padlet.com/joriparadis/edonprv4dkh21lt8/wish/2460543030