April 26

Lab 14: Final Poster and Abstract

 

Grace Seevers

26 April 2019

Purpose:

The objective of this lab was to upload soil metadata results to the excel sheet and label DNA samples in order to choose one to be sent for sequencing. Our groups finalized the lab posters for the symposium next week. A final draft of the abstract was written and posted on Box.

 

Procedure:

  1. Fill out the shared excel spreadsheet with soil metadata.
  2. Vote on Cillicure logo design.
  3. Obtain and label soil and DNA samples “DPS22_Sp19”
  4. Complete final draft of abstract and upload to box.
  5. Complete final draft of poster and upload to Box.

Data:

 

Abstract

Ciliates are unicellular eukaryotic organisms that reside in freshwater or soil ecosystems. Ciliates are an important factor within the ecosystem because they consume different bacteria and protozoa, and act as a source of nutrition for organisms at higher trophic levels. The enormous discrepancy between the amount of research conducted on ciliates living in marine biomes versus ones living in the soil is due to a general lack of interest and/or knowledge of their importance. This experiment was conducted over the course of fourteen weeks in an effort to fill the gap between the amount of information known about marine and soil biodiversity by determining the overall composition of ciliates living in the rhizosphere of different trees across Baylor University’s campus. The V4 region of the 18S rRNA was observed because it is conserved within all eukaryotes and is unique to each specific organism. Soil samples were collected from the rhizosphere, where the highest concentration of ciliates are presumed to inhabit because of its abundance of nutrients and gas availability. After collection, the soil was searched for the presence of ciliates. Once the ciliates were isolated, their DNA was extracted and purified. The pure DNA was amplified through a polymerase chain reaction and ran through gel electrophoresis to determine whether or not eukaryotic DNA was present. Although our sample contained a very minute amount of DNA, if substantial DNA had been found, it would be sequenced using an online bioinformatics platform- QIIME2, to determine the specific organisms in our sample.

 

Conclusion:

In conclusion, our group worked together to submit our soil and DNA results and finalized our abstract and poster in preparation for the symposium. Our group is prepared to present our research and answer questions about ciliate biodiversity in the soil on Baylor’s Campus. In the future, a sample will be chosen to be sent off and next years class will analyze the results.

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April 26

Revised Lab 14 4/25/19

Date of Experiment: April 25, 2019

Objectives:

  • Develop an abstract for the scientific poster
  • Finalize metadata spreadsheet and poster presentations
  • Determine sample for Illumina sequencing

Purpose: Determine which sample will be sequenced based on compiled metadata and learn the components of an abstract

Materials:

  • Abstract
  • Scientific Poster
  • Frozen soil samples
  • Experimental sample
  • Illumina sequencing

Methods:

  1. Choose candidate samples based on suitable metadata
  2. Complete DNA extraction and send for Illumina sequencing
  3. Develop an abstract for the poster based on methods, procedures, results, and the conclusion
  4. Submit to class Box file

Observations:

Soil ID:  SS25_6SP19

Soil Bag Label: BSQS

GPS Location: -97.1135, 31.5491

Tree Species: Pinus taeda

BHD: 70 cm

Soil Texture: Silt loam

Extraction Method: Chelex

DNA Concentration: 112.1 ng/uL

PCR: Positive

Results:

Samples considered for sequencing either underwent Chelex extraction, or followed the PowerSoil protocol. While an abstract follows the pattern of a scientific poster or research paper, it merely summarizes the scientific findings into few, concise sentences.

Conclusion:

The sample sent for sequencing will be compared to those in a genetic database. Here, the relatedness of organisms can be seen among those that have already been analyzed. Developing an abstract is useful for summarizing the overall motives and procedure for conducting a specific experiment.

Category: Britney Somaly-32 | LEAVE A COMMENT
April 26

Lab 14 4/25/19

Date of Experiment: April 25, 2019

Objectives:

  • Develop an abstract for the scientific poster
  • Finalize metadata spreadsheet and poster presentations
  • Determine sample for Illumina sequencing

Purpose: Determine which sample will be sequenced based on compiled metadata and learn the components of an abstract

Materials:

  • Abstract
  • Scientific Poster
  • Frozen soil samples
  • Experimental sample
  • Illumina sequencing

Methods:

  1. Choose candidate samples based on suitable metadata
  2. Complete DNA extraction and send for Illumina sequencing
  3. Develop an abstract for the poster based on methods, procedures, results, and the conclusion
  4. Submit to class Box file

Observations:

N/A

Results:

Only two samples were suitable considerations for sequencing; where one sample underwent Chelex extraction, the other followed the PowerSoil protocol. While an abstract follows the pattern of a scientific poster or research paper, it merely summarizes the scientific findings into few, concise sentences.

Conclusion:

The sample sent for sequencing will be compared to those in a genetic database. Here, the relatedness of organisms can be seen among those that have already been analyzed. Developing an abstract is useful for summarizing the overall motives and procedure for conducting a specific experiment.

Category: Britney Somaly-32 | LEAVE A COMMENT
April 26

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

Megan Hudson                                                                                               April 25, 2019

BIO 1106-22

Lab #14: Poster Presentation and Abstract Submission

 

Section I: Objective

The purpose of this lab was to edit and submit our final abstract and poster for the CURES Symposium presentation. We also ensured that all metadata was recorded for the soil samples to allow Dr. Adair to pick the most viable sample to send off for sequencing.

 

Section II: Procedure

  1. Vote on CILI-CURE Logo for possible merchandise
  2. Record sample identifier, GPS location, tree species, BHD (cm), pH, soil texture, extraction method, DNA concentration, volume, PCR results (+ or -), and soil label on bag into Metadata File Spreadsheet
  3. Label DNA tube with AHM22_5Sp19, concentration, and volume of sample
  4. Place the tube with a new label into microfuge tube rack
  5. Take the remainder of the lab to edit poster and abstract within lab groups.

 

Section III: Results

 

Metadata File:

Group Members: Megan Hudson, Madison Ambrose, Kelsey Menzie
Section 22
Group 5
Soil ID AHM22_5Sp19
GPS Location -97.1203258, 31.5467120
Tree Species Quercus virginiana
BHD (cm) 188.4
pH 6.5
Soil Texture Sandy Clay
Extraction Method Silica
DNA Concentration 1.44
Volume 30 ul
PCR –
Soil Label on Bag KRM22S19

 

Abstract:

The biodiversity of microorganisms within terrestrial ecosystems is dependent on the viability of the community profile. Soil microbiomes and the influence of eukaryotes within is largely unexplored. The following field experiment analyzes soil collected from the rhizosphere of a Quercus virginiana to attempt to further classify ciliates and understand the diversity of one of the most controversial monophyletic groups, SAR. Metadata regarding soil texture, percent water content, and pH were obtained from each soil sample. The MNH soil sample was identified as sandy loam and KRM and MAA soil samples were identified as sandy clay. The samples were then isolated and eDNA was extracted using silica beads. The eDNA was then cleaned with 80% isopropanol alcohol and primed with an 18S V4 primer to isolate the V4 region of DNA in eukaryotes. The MNH and KRM samples underwent gel electrophoresis to attempt to view bands of DNA and KRM sample was amplified using a polymerase chain reaction (PCR). Results from the PCR amplification were analyzed using the NanoDrop 2000 Spectrophotometer and the MBC C305 UV gel imager. The MNH sample yielded an A260/280 concentration of 1.3 and the KRM sample yielded 1.44, indicating that DNA was present in the sample. Though it was shown that DNA was present, gel electrophoresis images produced no visible bands. These results indicate that soil collected from the rhizosphere surrounding the Quercus virginiana did not contain quantifiable eDNA for eukaryotes, despite ciliates being observed and cultured before soil eDNA was extracted.

 

Final Poster:

FINAL- Analysis of Soil and eDNA from the Rhizosphere of a Quercus virginiana; Megan Hudson, Madison Ambrose, Kelsi Menzie (1)-2jauozb

 

Section IV: Where your sample was stored

All soil sample bags were labeled at the beginning of the semester and stored under the fume hood and samples that produced positive PCR and gel electrophoresis results were put into deep freeze.

 

Section V: Conclusion and Discussion

Posters and abstracts were finalized and submitted so the poster could be printed, and the abstract could be uploaded to the brochure for CURES Symposium next week. Metadata was recorded in the class spreadsheet so samples that are viable enough to send off for sequencing have proper data for future studies. In both the KRM and MNH soil samples, results from the NanoDrop indicated a presence of eDNA, but when we ran our gels and performed PCR, results were negative and did not show a presence of DNA. Since our results were negative for eDNA abundance, most likely our samples will not be sent for sequencing. Although my groups’ samples did not produce positive results, we still were able to establish a methodology for DNA extraction and PCR amplification for future CILI-CURE labs. Moving forward, my group plans to practice presenting our poster so we are prepared for CURES next Friday. As the semester comes to an end, I am grateful for all the research experience and scientific writing skills I have learned in CILI-CURE.

Category: Megan Hudson-34 | LEAVE A COMMENT
April 26

Lab 14: Final Poster and Abstract 04.26.19

Purpose: The purpose of this lab was to make changes on our poster one more time, work on our abstract and record our metadata on the spreadsheet.

Title: Modified techniques to extract and amplify soil DNA for studying ciliate biodiversity

Abstract:

Ciliates are some of the most abundant and diverse protozoans; however, they are relatively under researched and little is known about how they affect the environment. This study was conducted in order develop a way to consistently and confidently determine the ciliate biodiversity in soil. The goal was to use the results from the biodiversity profiles to make inferences about the relationship between ciliate biodiversity and soil health. Metadata was collected from each sample to determine the conditions of the soil such as percent water, soil texture, and pH. Then, DNA was extracted, purified, ran through gel electrophoresis, and underwent a PCR reaction. DNA was present in the soil and was measure on the spectrophotometry results; however, after the PCR reaction was conducted, the results were only positive for five out of eight samples. Due to DNA being present in all samples, it appears that the DNA collection method works. The negative PCR result may be caused by impurities in specific samples that were not present in all samples.

Final Poster:

Fimal Powerpoint Presentation (5)-1aqokoh

Metadata recorded:

Group Members: Myrnalid Zapata, Tyler Bewley

Section: 21

Group: 1

SOIL-ID: BZ21_1Sp19

GPS Location: -97.1191, 31.5444

Tree Species: Brazilian Bluewood

BDH (cm): 46

pH: 6.5

Soil Texture: Sand

Extraction Method: Silica Bead

DNA concentration: 169.6 ng/ul

Volume: Missing

PCR: Negative (-)

Soil Label on Bag: Myrnalid Zapata Section 21

Next Steps: Our poster are going to get printed and next week we will be presenting them.

Conclusion: We filled out the Soil eDNA Metadata Spring 2019 spreadsheet, label our tubes correctly, work on our abstract and we made corrections to our posters one last time and turn it in. The posters are going to get print and next Friday we will be presenting them.

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April 26

Lab 14: Poster Presentation and Abstract Submission 4/26/2019

Madison Ambrose

1106-22

Purpose/Rationale/Objective:

The purpose of this lab was to finalize our groups abstract and poster for the CURE symposium.  The objective of this lab was to make edits to our poster as well as document and relabel the original soil samples with the new ID.

Procedure:

  1. Vote on the CILI-CURE logo and preferred merchandise.
  2. Fill out the information on the spreadsheet.
  3. Relabel DNA and soil samples with new ID AHM22_5Sp19.
  4. Edit the recommendations made by the TA to the poster.
  5. Edit Abstract drafts with the group.
  6. Submit Abstract and poster title to QTM 14 assignment.
  7. Upload abstract and poster to class Drop Box.

Data:

Abstract:

The biodiversity of microorganisms within terrestrial ecosystems is dependent on the viability of the community profile. Soil microbiomes and the influence of eukaryotes within is largely unexplored. The following field experiment analyzes soil collected from the rhizosphere of a Quercus virginiana to attempt to further classify ciliates and understand the diversity of one of the most controversial monophyletic groups, SAR. Metadata regarding soil texture, percent water content, and pH was obtained from each soil sample. The MNH soil sample was identified as sandy loam and KRM and MAA soil samples were identified as sandy clay. The samples were then isolated and eDNA was extracted using silica beads. The eDNA was then cleaned with 80% isopropanol alcohol and primed with an 18S V4 primer to isolate the V4 region of DNA in eukaryotes. The MHK and KRM samples underwent gel electrophoresis to attempt to view bands of DNA and KRM sample was amplified using a polymerase chain reaction (PCR). Results from the PCR amplification were analyzed using the NanoDrop 2000 Spectrophotometer and the MBC C305 UV gel imager. The MNH sample yielded an A260/280 concentration of 1.3 and the KRM sample yielded 1.44, indicating that DNA was present in the sample. Though it was shown that DNA was present, gel electrophoresis images produced no visible bands. These results indicate that soil collected from the rhizosphere surrounding the Quercus virginiana did not contain quantifiable eDNA for eukaryotes, despite ciliates being observed and cultured before soil eDNA was extracted.

Title: Analysis of Soil and eDNA from the Rhizosphere of a Quercus virginiana​

Group Members Section Group Soil ID GPS Location Tree Species BHD (cm)
Madison Ambrose, Megan Hudson, Kelsi Menzie 22 5 AHM22_5Sp19

-97.1203258,

31.5467120

 Quercus virginiana 188.4

 

pH Soil Texture Extraction Method DNA concentration Volume PCR Soil Label on Bag
6.5 Sandy Clay Silica Bead 1.44 30ul – KRM22S19

 

Poster:

 

Storage:

Make sure the lab bench is clean, turn in your QTM, submit the abstract, and upload the poster and abstract to the Drop Box.

Conclusion/Interpretation/Future Steps:

This lab allowed us to wrap up the semester by making our final poster edits and prepare for the CURE symposium.  By setting our poster aside for a few weeks then returning to it at the end of the semester allowed us to make modifications with a fresh perspective of the experiment.  Additionally, due to the practice we had with the Qiime2 program allowed us to have a more mature understanding of the conclusion and discussion section, specifically on the future steps we can take with the experiment we performed. The edits along with recommendations from our TA and LA were very beneficial and allowed us to perfect the poster for the CURE symposium next week. Going forward I am curious to see what the results from the PCR sequencing will tell us about our community profile and if we will find ciliates that have never been identified before. Lastly, although our eDNA sample had negative results course was a valuable learning experience I can aspects of further into my academic career.

Category: Madison Ambrose-34 | LEAVE A COMMENT
April 26

Lab 14: Final Poster and Abstract

Lauren langston

4/26/19

The purpose of this lab was to prepare ourselves for the CILI-CURE symposium and to finish our posters and abstracts.

Title:

Isolation and Purification of Ciliate DNA from Ilex Vomitoria

FINAL ABSTRACT:

Nearly 85% of ciliate diversity has not been accounted for, yet ciliates play a crucial role in soil ecosystems, ensuring the cycling of materials and energy flow of other microorganisms and serving as predators regulating the environment. This study was conducted to develop a well-defined methodology that could be used to explore soil ciliates on a molecular level via sequencing. Soil samples were taken from an Ilex vomitoria and DNA was extracted using the silica bead extraction method. Metadata anaylsis of the soil showed that the soil type was sandy loam and had a pH level of 6.5. Gel electrophoresis showed that crude DNA was extracted from the soil samples and PCR was able to amplify an 18S V4 region of the DNA. From the Nanodrop analysis, performed after the extraction of a crude DNA sample and DNA purification, the extracted DNA had a purity of 1.46 (A260/A280), which is the expected score of a pure sample. The utilization of this less costly and more efficient protocol can yield DNA samples of a good purity that can be used for future sequencing and taxonomic identification of organisms within a collected sample.

META DATA:

FINAL POSTER:

Conclusion and future goals

I was able to fix along with my group members the amount of words on my poster and reorganize several of my elements on my poster. in the future I wish to have a successful presentation at the symposium.

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April 26

Lab 14: Poster Presentation and Abstract Submission

Lab 14: Poster Presentation and Abstract Submission

 

The purpose and objective:

The objective of this lab is to complete the metadata form, final draft abstract and scientific poster.

 

Date: 04/26/2019

 

Procedures:

  1. Fill in the form of soil metadata through Excel;
  2. Discuss and write the abstract, and edit the scientific poster;
  3. Upload file on Canvas and box.

 

Data:

  • Metadata
Group Members Section Group Soil ID GPS location Tree Species
Michelle Nguyen, Lauren Langston, Zihan Yuan 22  6  LNY22_6Sp19  -97.11,31.55 Ilex Vomitoria
BHD(cm) pH Soil Texture Extraction Method DNA Concentration/µl Volume µl PCR Soil Label On Bag
38.1 6.5 Sandy Clay Loam Silica Bead 1.46 10 + LNY22_6Sp19

 

  • Abstract

Isolation and Purification of Ciliate DNA from Ilex Vomitoria

Nearly 85% of ciliate diversity has not been accounted for, yet ciliates play a crucial role in soil ecosystems, ensuring the cycling of materials and energy flow of other microorganisms and serving as predators regulating the environment. This study was conducted to develop a well-defined methodology that could be used to explore soil ciliates on a molecular level via sequencing. Soil samples were taken from an Ilex vomitoria and DNA was extracted using the silica bead extraction method. Metadata analysis of the soil showed that the soil type was sandy clay loam and had a pH level of 6.5. Gel electrophoresis showed that crude DNA was extracted from the soil samples and PCR was able to amplify an 18S V4 region of the DNA. From the Nanodrop analysis, performed after the extraction of a crude DNA sample and DNA purification, the extracted DNA had a purity of 1.46 (A260/A280), which is the expected score of a pure sample. The utilization of this less costly and more efficient protocol can yield DNA samples of a good purity that can be used for future sequencing and taxonomic identification of organisms within a collected sample.

 

  • Poster

 

Conclusion and The future goal:

In this lab, based on discussion, suggestions and comments, we edited and finished our final abstract and poster successful. In the future, we will do a presentation of our scientific poster next week and I am looking forward it!

 

 

Category: Zihan Yuan-32 | LEAVE A COMMENT
April 26

Lab 14: Poster Presentation and Abstract Submission

Lauren langston

4/26/19

The purpose of this lab was to prepare ourselves for the CILI-CURE symposium and to finish our posters and abstracts.

Title:

Isolation and Purification of Ciliate DNA from Ilex Vomitoria

FINAL ABSTRACT:

Nearly 85% of ciliate diversity has not been accounted for, yet ciliates play a crucial role in soil ecosystems, ensuring the cycling of materials and energy flow of other microorganisms and serving as predators regulating the environment. This study was conducted to develop a well-defined methodology that could be used to explore soil ciliates on a molecular level via sequencing. Soil samples were taken from an Ilex vomitoria and DNA was extracted using the silica bead extraction method. Metadata anaylsis of the soil showed that the soil type was sandy loam and had a pH level of 6.5. Gel electrophoresis showed that crude DNA was extracted from the soil samples and PCR was able to amplify an 18S V4 region of the DNA. From the Nanodrop analysis, performed after the extraction of a crude DNA sample and DNA purification, the extracted DNA had a purity of 1.46 (A260/A280), which is the expected score of a pure sample. The utilization of this less costly and more efficient protocol can yield DNA samples of a good purity that can be used for future sequencing and taxonomic identification of organisms within a collected sample.

META DATA:

FINAL POSTER:

Conclusion and future goals

I was able to fix along with my group members the amount of words on my poster and reorganize several of my elements on my poster. in the future I wish to have a successful presentation at the symposium.

Category: Uncategorized | LEAVE A COMMENT
April 26

Lab 14: Poster Presentation and Abstract Submission 4/25/2019

Objective:

The objective of today’s lab is to finalize our poster presentations for the CURE symposium.

Purpose:

The purpose of today’s lab is to prepare for the CURE symposium.

What did we do?:

Poster Title: Environmental DNA in the Rhizosphere Surrounding Quercus incana

Final Abstract

Both marine and soil ciliates are eukaryotic microorganisms that play an integral part in the health and prosperity of aquatic and terrestrial food chains, respectively. Marine ciliates are often the targets of biodiversity research, but soil ciliates are often overlooked in scientific studies. This field experiment focuses on using metabarcoding to detect the presence of the V4 region of the 18s ribosomal subunit, a genetic sequence unique only to eukaryotic organisms. The soil sample we collected was from a Bluejack Oak, or Quercus incana, near Earle Hall and East Village on Baylor University’s campus. The sample was brought back to the lab to be tested for different types of metadata, such as pH and soil texture. For DNA extraction, we used silica beads to break open the cell membrane of the microorganisms, DNA extraction buffer to pull the DNA from the lysed cells, and activated charcoal powder to remove impurities from the new DNA sample. Once we obtained a purified DNA sample, we performed a polymerase chain reaction to amplify the eDNA. This amplified DNA was used in gel electrophoresis, where we determined both the mass of our DNA and the length of each sequence.  We also performed a nanodrop experiment in which we found the concentration of DNA. Based on our results, we were able to confirm the presence of the 18s ribosomal subunit, thus signifying that ciliates are present in our sample. Our DNA can be sequenced and analyzed in conjunction with our metadata to increase our understanding of soil ciliate biodiversity.

Conclusion:

I fixed some of the organization issues in the poster and added “why does this matter” statements to the intro and the conclusion.

Future Goals:

I hope to have a successful presentation at the symposium.

 

Category: Anthony Capili-34 | LEAVE A COMMENT