April 26

Lab 14: Poster Presentation and Abstract Draft

April 26th, 2019

Rationale: 

The purpose of this lab was to revise our poster presentations as well as write our abstract drafts.

Procedure: 

  • We began lab by editing our poster
    • The conclusion section was elaborated upon
    • The introduction was reorganized and shortened
    • A few of the figures were deleted and reconfigured
  • Next, the abstract draft was written and submitted

Observations/Data:

Final Poster:

 

 

 

 

 

 

 

 

Abstract:

There are many standard methods for extracting Ciliate eDNA but not all are effective and cost efficient.

Ciliates are protozoa in the Kingdom Protista. They play many different roles within soil and aquatic ecosystems. There has been very little research done on ciliate behavior and interactions within the soil. Our study targeted ciliates within the rhizosphere. The rhizosphere plays a key role in the cycling of nutrients as well as plant growth. Ciliates shape the diversity of microorganisms within the rhizosphere, thus their presence is vital to a healthy ecosystem.

The purpose of this study was to investigate new methods for eDNA extraction of ciliates.

Creating this new method was achieved by researching different ways to extract eDNA. These different methods were then combined to maximize the amount of eDNA collected. Metadata was collected regarding the soil sample and the environment it was collected from. Gels were run to determine the amount of DNA collected. The samples that contained an abundance of DNA underwent PCR in order to amplify the strand so they could more easily be sequenced.

The samples were loamy sand, with a pH of 6.5. The concentration of DNA in the sample was 1125 ng/ul and the A260/A280 value was 1.33. The DNA sequenced not only belonged to ciliate species, but fungal and bacterial species as well.

These results gave reason to believe the use of charcoal and Silica beads was effective in the extraction of DNA.

Conclusion:

Our posters are ready to be presented. In order to explain our experiment, it is important that as a group we review our procedures and findings. We must understand our work completely so that we are able to communicate clearly with listeners the importance of our research.

Category: Uncategorized | LEAVE A COMMENT
April 26

Lab 14: Poster Presentation and Abstract Submission (4/26/19)

Purpose: The purpose of this lab was to discuss how we improve and revise our posters using the comments we received from the TA/instructor, and input our soil meta-data into a shared excel sheet. We also gathered all the information and samples we had so we can send our samples to be sequenced so it can analyzed later.

Procedure:

  1. Vote on Ciliate logo
  2. Fill out soil meta-data excel sheet
  3. Do final edits on poster for presentation next week
  4. Revise and edit abstract for the poster
  5. Insert poster and abstract into class Box file

Soil Meta-data:

Meta-data 1:

Meta-data 2:

Poster:

Abstract:

Title: Analysis of eDNA from a Soil Sample in the Search for Soil Ciliate DNA

Soil ciliates are crucial organisms in the rhizosphere as they perform many important roles contributing to soil health. Currently, research concerning topics related to soil ciliate diversity is limited. Conventionally, ciliates have been identified and categorized through morphological characteristics and behaviors due to a lack of a standard genomic method for easy identification. This study aims to explore a standard method for ciliate identification through metabarcoding. For this, soil was collected and environmental DNA was extracted using the Silica Bead grinding method followed by Column Purification. Polymerase Chain Reaction was used to amplify the V4 region of the 18s rRNA subunit. Gel electrophoresis results showed that PCR amplified the eDNA. The image taken of the gel showed a concentrated band of DNA from the eDNA sample. Nano-drop analysis of the eDNA showed a 250.2 ng/ml of the DNA while it had a purification of 1.46 A260/280. The eDNA extraction method conducted appears to be the best option for extracting DNA due to the amount of DNA replicated. Metabarcoding of the V4 region of the 18s rRNA subunit was conducted using the eDNA to identify what kind of ciliates were extracted from the environmental sample and sequence. Bioinformatics (Cyverse/QIIME2) will be used to analyze how successful the V4 region can be in the identification of ciliates.

Conclusion/Future Steps: After this lab, we plan to do a practice presentation of our poster to the class next week to do last minute critique for how its presented. We also plan on presenting the poster at CURE so we can share our data to other people on what we learned from our research. After we send our samples to be sequenced, we can later analyze these samples using Cy-verse/QIIME2, seeing what kind of ciliates were found in the DNA solution. This lab should prepare us for the presentation so we know all the information we must present to our peers. This lab help us make crucial changes to the poster so we won’t make any major mistakes on our poster presentation.

Category: Chris Amezcua-31 | LEAVE A COMMENT
April 26

Lab 14: Poster Presentation and Abstract Submission 4/25/19

Objective

The objective for this lab was to refine our posters and prepare our Abstracts so that we can present our findings next Friday. We also voted on a logo and ensured our metadata was entered correctly.

Purpose

The purpose of this lab was to prepare our presentations for the CILI-CURE Symposium next Friday. We also wrote a short Abstract that compressed the entirety of this semester’s research into a paragraph. Additionally, we checked our metadata to ensure the accuracy of our findings and hopefully have our sample be sent off for genetic sequencing.

Procedure/Data

When we first got to the lab, we voted on a logo for CILI-CURE. After this, we worked in our groups to compose an Abstract for our poster that was approximately 250 words long and that accurately depicted the research we had done in the last semester. Once this Abstract was completed, we focused on editing our poster and addressing comments that could be easily fixed. We altered the organization to make it more aesthetically pleasing and clarified the purpose of our research in the introduction and conclusion.

Conclusion

We were able to draft an accurate Abstract as well as edit the poster to be much better than before. I must say I am looking forward to presenting during the symposium, as I am confident in my knowledge of all the processes and procedures that we performed this semester.

Category: Austin Ruiz-34 | LEAVE A COMMENT
April 26

Lab #14: Poster Presentation and Submitting the Abstract

Lab #14: Poster Presentation and Submitting the Abstract – 4/26/19

Objective/Rationale

The main goal for this weeks lab was to prepare for our poster presentations at the cure symposium next week by writing our abstracts and adding last-minute corrections to our posters before they are sent for printing. We want to be as ready as possible for symposium so it is important for us to make sure that the posters are perfect. We will also be presenting our posters next week in lab so we need to be ready for that as well.

Methods

Working in our lab groups, we used a template given to us by our instructor so that we would be able to write an abstract appropriate for symposium. Each group made sure to include information relevant to each section of the poster so that the abstract was basically a spark notes version of the poster.

Results

Here is a copy of our finalized abstract:

Currently, there is very little information on soil ciliates because they do not directly impact humans and are difficult to culture. This study was conducted to test specific DNA extraction protocols, obtain metadata from trees on Baylor’s campus, and to compare the sequenced DNA of soil ciliates to other sequenced genomes. Various soil metadata were obtained such as pH, percent water content, soil texture, location of the tree, breast height diameter of the tree, and tree species. Ciliates were cultured from the soil in order to extract the DNA and have it sequenced. A chelex extraction protocol was used to isolate the DNA from the ciliate culture. Nanodrop and gel were used to quantify DNA concentration. PCR was used to amplify the 18S V4 ribosomal region and visualized using a DNA gel. The soil had a water percent content of 26.1%, pH of 6.5, texture classified as silt loam, BHD of 43 cm, location within Baylor campus, and the species of the tree was determined to be Pinus taeda. The concentration of the DNA was 112 ng/ul. PCR resulted in bands appearing in the DNA gel. This project resulted in successful eukaryotic DNA isolation. With positive PCR results and the appearance of banding in the gel, these findings will contribute to the minimal literature on soil ciliates.

The title of our abstract is: Extraction of Soil Ciliate DNA and Amplification with PCR Primers

Metadata information
Group Members (Names) Section Group “SOIL-ID;Student(s) initials: Last names in alphabetical order Section-group-semester-year Example for section 21, group 1, Tyler Kingston, Daphne Simo, Johanna Warner=   KSW21_1Sp19” GPS location Tree Species BHD (cm) pH Soil Texture Extraction Method DNA concentrationng/µl ~volume µl PCR SOIL label on Bag Column1
+ CT25Sp19
Britney Somaiy, Quinn Strassheim 25 6 SS25_2SP19 -97.1135,31.5491 Pinus taeda 70 6.5 Silt Loam Chelex 112.1 1 + BSQS
Final pster draft

Conclusion

I think that the template was very helpful, our abstract flows very nicely and delivers the information concisely, as an abstract should.  We also had a lot of very useful help from our instructors which was superrrrr great. I feel like we are prepared enough to present next week.

Future Goals

My main goal is to focus heavily on preparing for the presentation next week. I hope that it goes well.

 

Category: Quinn Strasshelm-32 | LEAVE A COMMENT
April 26

lab notebook 14?

Lab 14: posters and abstracts

Adriana Robledo

4-26-19

purpose:

The purpose of this lab was to finish revising your abstract, add our metadata to a , to fix any mistakes that were made when creating your poster, and vote on a label for our cilicure lab.

procedure:

  1. Vote on cilicure logo
  2. Enter metadata into the online collaborative file
  3. Label you DNA sample tube with your last initial (of the group) in alphabetical order, section number, a underscore, then “2Sp19”
  4. Obtain the concentration from the tube and replace it on the rack
  5. Head over to the computer lab and use the time to work on the group’s abstract.
section group label GPS location species BHD pH Soil texture Extraction DNA concentration
25 4 GRS25_2Sp19 -97.1182, 31.5498 Quercus virginiana 57cm 6.4 clay loam silica bead 262.1

Title:

Soil eDNA analysis targeting the V4 region using 18S primer.

Abstract:

Soil ciliates are a diverse group of eukaryotes that play an important role in the environment but are understudied due to a lack of standard methods used to extract them from soil.The purpose of this experiment was to determine ciliate biodiversity in soil samples taken from the rhizosphere of Baylor trees. The protocols used were ones that have yet to be perfected in hopes of establishing them as universal method such as silica bead extraction of DNA and the chelex extraction method.DNA was extracted and purified from the soil collected using the ‘silica bead method’. The DNA concentration was obtained using a nanodrop and gel electrophoresis by running against a mass standard, and used PCR to amplify the 18s V4 region.The Polymerase Chain Reaction yielded a negative result, indicated by a ‘smear’ of DNA rather than a band. The nanodrop showed the concentration of DNA to be 262.1 ng/µl with the  A260/280 to be 1.5. Despite negative results, the experiment showed the validity of results that can be found through silica bead and chelex DNA extraction; however, the lack of positive results was most likely due to an improper dilution or a degradation of DNA. Additionally, further research can be done using bioinformatics to visualize the ciliate diversity.

Conclusion:

This lab was extremely helpful in the way that it helped us to finish two big pieces of our final presentation in one lab. We all came together and brought little parts of the abstract that we independently worked on and asked for help perfecting the message and wording. We split up the work among the group and were able to successfully complete everything that we needed to do.

future steps:

In the future, we will present our presentations to the class and then at the symposium.

storage:

Return the tubes to the rack and any other miscellaneous supplies.

Category: Adriana Robledo-34 | LEAVE A COMMENT
April 26

Lab #14 Final Abstract and Poster

Megan Tran

4/26/19

Objective:

The purpose of this lab was to analyze the metadata we’ve acquired throughout this lab and to put it onto a spreadsheet. We also made final corrections to our scientific poster and our created a refined abstract for our experiment.

Procedure:

  1. Vote on a logo for CILI-CURE.
  2. Finish total metadata for the class.
  3. Revise scientific poster and abstract.
  4. Upload these documents to our Baylor Box.

Metadata:

Megan Tran, Daniel Shin, Andrea Huynh-Duong 21 6 HST21_6Sp19 -97.1147, 31.5489 Quercus virginiana 115.59 6 Clay Loam Silica Bead 884.6 10 – Andrea Huynh-Duong 21

Title of poster:

Extraction and Analysis of Ciliate eDNA from Soil Ecosystems

Abstract:

Soil ciliates have very little research done in its field, especially measuring the biodiversity of ciliates. Biodiversity of organisms, especially microorganisms in any ecosystem, is an important component to the stability of the ecosystem. Thus, this study was done in order to measure and quantify the measure of biodiversity of ciliates in soil ecosystems using a new method to extract eDNa, also giving us an idea if this new method, the silica bead method, is a viable one to extract eDNA in future studies. The silica bead method was utilized for the actual extraction of eDNA from the selected soil sample. Gel electrophoresis, the nanodrop spectrophotometer, and PCR were all effectively used to determine if the extraction of DNA from the soil sample was successful or not. After performing the eDNA extraction and the tests, the presence of DNA in our tests were negative, meaning we were unable to effectively extract eDNA from our soil sample. The DNA concentration was 7.1ng/ul as shown by the nanodrop spectrophotometer, an extremely low concentration. The gel electrophoresis fluorescent imaging found that there was no DNA in any of our lanes in both the pre-PCR imaging and the post-PCR imaging. The silica bead method was done correctly, without fail, leading us to analyze the metadata of our soil to determine if any of the other environmental factors prevented us from extracting eDNA. From the following results, we can reasonably conclude that there was no eDNA to extract from the soil sample or that there were certain factors surrounding the soil sample that prevented us from extracting the eDNA.

Scientific Poster:

Conclusion/Future Goals: In today’s lab, we were able to complete our metadata for our entire class. After looking at the comments on our final poster draft, we adjusted our mistakes and made our poster ready for presentation. In the future, hopefully I will be able to explain our research throughout this semester thoroughly at the symposium with my fellow group members.

 

Category: Megan Tran-31 | LEAVE A COMMENT
April 26

Lab 14

Mackenzie Singer

4/25/19

Objective:

The purpose of this lab was to vote on a logo, create a final abstract, and complete our final poster so that they are ready to be presented.

Procedure:

  1. Vote on a logo
  2. Put soil metadata into the class spreadsheet
  3. Label soil samples
  4. Create a final abstract
  5. Finish up the poster and make necessary changes

Data:

Abstract:

Ciliates play a major role in the food web which impacts all hierarchies of life. There is vast biodiversity in the rhizosphere of Earth, containing ciliates and other microorganisms (1). Little is known about the abundance of organisms that reside in the soil of terrestrial environments. This study was conducted to determine the diversity of soil ciliates in the rhizosphere on Baylor University’s campus. The process included collection, extraction, and amplification of ciliate DNA from the soil samples (2). The sample was retrieved from a Quercus Virginiana tree on Baylor’s campus in sandy loam soil. Our PCR for the 18S V4 primer resulted in a positive DNA band although the DNA concentration was not completely pure. Our results indicate that there is a large concentration of ciliates in the rhizosphere of trees on Baylor University’s campus.

Storage:

Soil tubes were placed in the rack.

Conclusion and future steps:

This lab was very productive in finishing up the posters. We finished them and submitted them for printing. Future steps will be to present these posters at the symposium. We also voted on a logo so that we can make cool stuff to wear.

Category: Uncategorized | LEAVE A COMMENT
April 26

Lab #14: Poster Presentation and Abstract Submission

Sara Rothrock

4/25/2019

Purpose:

The purpose of this lab was to enter the metadata we collected this semester to determine which samples to sequence, to edit our poster presentations and write an abstract with our groups.

Procedure:

  • Vote on a logo for stickers and t-shirts
  • Enter the metadata we collected into the class excel sheet
  • Revise our poster and write our abstract

Metadata:

Sara Rothrock, Rebekah Gerry, Andreea Loghin 22 7 GLR22_7Sp19 -97.1195413, 31.5495435

Quercus

Virginiana

 55.0064 6.5

Loamy

sand

Silica

bead

1125

ng/ul

 30 + GLR22_7Sp19

Abstract:

There are many standard methods for extracting Ciliate eDNA but not all are effective and cost efficient.

Ciliates are protozoa in the Kingdom Protista. They play many different roles within soil and aquatic ecosystems. There has been very little research done on ciliate behavior and interactions within the soil. Our study targeted ciliates within the rhizosphere. The rhizosphere plays a key role in the cycling of nutrients as well as plant growth. Ciliates shape the diversity of microorganisms within the rhizosphere, thus their presence is vital to a healthy ecosystem.

The purpose of this study was to investigate new methods for eDNA extraction of ciliates.

Creating this new method was achieved by researching different ways to extract eDNA. These different methods were then combined to maximize the amount of eDNA collected. Metadata was collected regarding the soil sample and the environment it was collected from. Gels were run to determine the amount of DNA collected. The samples that contained an abundance of DNA underwent PCR in order to amplify the strand so they could more easily be sequenced.

The samples were loamy sand, with a pH of 6.5. The concentration of DNA in the sample was 1125 ng/ul and the A260/A280 value was 1.33. The DNA sequenced not only belonged to ciliate species, but fungal and bacterial species as well.

These results gave reason to believe the use of charcoal and Silica beads was effective in the extraction of DNA.

Poster:

Conclusion:

This lab was extremely beneficial because I learned how to properly edit my poster to have all the information necessary about the research without too many words. My group was marked down mainly because the conclusion had to have more detail but edit out information that can be conveyed during the presentation and our introduction has irrelevant information to the specific research we did. After revising our poster, I feel confident in the poster we submitted and we were able to fix all the mistakes we had made.

Future Steps:

In the future, I hope to continue doing research and that my metadata is selected to be further sequenced because I think that it. would be really cool to see what is in my specific sample.

Category: Sara Rothrock-31 | LEAVE A COMMENT
April 26

Lab #14- Poster Presentation and Abstract

Chandler Opara 

April 25, 2019

Poster Presentation and Abstract

 

Objective/Purpose:

The objectives of the lab were to vote on a logo, complete our final abstract, and make the finishing touches to our poster. The purpose of completing the abstract and poster is to be able to present  it in the Symposium.

Procedures:

  1. Vote on logo design presented in the PowerPoint .
  2. Input all the metadata in the class Excel spreadsheet. Label the sample with the criteria stated in the spreadsheet.
  3. Finally, use the critiques from the rubric to revise and finalize the poster. Write out the abstract and edit the poster title if necessary. When finished, upload the poster to the Box and Canvas.

Data:

Abstract

Ciliates play a major role in the food web which impacts all hierarchies of life. There is vast biodiversity in the rhizosphere of Earth, containing ciliates and other microorganisms (1). Little is known about the abundance of organisms that reside in the soil of terrestrial environments. This study was conducted to determine the diversity of soil ciliates in the rhizosphere on Baylor University’s campus. The process included collection, extraction, and amplification of ciliate DNA from the soil samples (2). The sample was retrieved from a Quercus Virginiana tree on Baylor’s campus in sandy loam soil. Our PCR for the 18S V4 primer resulted in a positive DNA band although the DNA concentration was not completely pure. Our results indicate that there is a large concentration of ciliates in the rhizosphere of trees on Baylor University’s campus.

Storage:

Tubes were placed back in the rack after use.

Conclusion/Future Steps:

In conclusion, we were able to revise our poster based off of the critiques, draw better conclusions from our results, and fix any minor details. The next step would be to present our posters at the symposium on May 2.

Category: Chandler Opara-34 | LEAVE A COMMENT
April 26

Lab #14 Final Abstract and Poster 4/26/19

Abel Thomas

4/26/19

Purpose/Objective:

The purpose of this lab was to label and understand our metadata along with correcting our poster and our perfecting the final abstract for the poster.

Procedure:

  1. Vote on a logo
  2. Finish total metadata for the class
  3. Revise poster and the abstract

Metadata:

Bassam Ballout, Paul Nemer, Abel Thomas 21 7 BNT21_7Sp19 -97.1147539, 31.5489044 Quercus macrocarpa 71.34 6 Clay Loam Silica Bead 722.3 10 + Bassam Ballout BNT21_7Sp19

Title:

The Observation of Biodiversity on the Baylor Campus through Metabarcoding

Abstract:

Soil biodiversity plays an integral role within the soil microenvironment as well as the sustainability of the macroenvironment. As a field experiment, soil was collected and analyzed from the rhizosphere of Quercus macrocarpa for metabarcoding using the silica bead DNA extraction method. Using this protocol for DNA extraction, a positive PCR product with relatively pure eDNA confirms the presence of soil microorganisms, possibly ciliates. After collection, extraction, purification, gel electrophoresis, amplification of DNA using PCR, and gel electrophoresis of the amplified DNA, next generation sequencing and analysis are ready to be conducted by quantifying the diversity present through the QIIME2 application and basic bioinformatics tools. By quantifying the microorganisms present, we can better learn and understand the optimum environments for ciliates and other microorganisms for future application. Further testing is necessary to better understand the extent of biodiversity present in the soil of the rhizosphere on Baylor campus. Bioinformatics analysis will be further conducted in regard to quantifying and characterizing qualitatively the importance of biodiversity in the environment.

Poster:

Storage: After inputting the metadata, we went up to the computer lab and fixed up our poster and our abstract to be submitted into Box.

Conclusion/Future Goals: In lab we were able to complete our metadata for our entire class. And then using the computer lab we were able to complete and fix our errors in our abstract and our posters. With this information we would be able to send our information to a lab and eventually use QIIME to analyze it.

Category: Abel Thomas-33 | LEAVE A COMMENT