Type: On-Campus Research (3-credit research per academic semester)

PI: Dr. Daniel Lipus 

Sampling Location: Wilkes-Barre, PA

Date: August 2025 - Ongoing

November 21, 2025 (4 hours):

Presented at SJU Research Symposium. Attended keynote speech and participated in conference, presenting to professors and other research undergraduate students.    

November 20, 2025 (0.5 hours):

Picked up the research posters from post-office. Prepared for presentation in conference with the team.   

November 18, 2025 (2 hours):

Final revision of the AMD research poster. Included images of some of the samples. Included media recipe and current ongoing enrichment of one of the samples (biofilm).   

November 13, 2025 (2 hours):

Created a methodology schematic flow chart that discusses the 3 pathways of the research: molecular, genomic, and enrichment.  

November 11, 2025 (2 hours):

Created results figures and narrative of the poster. Peer reviewed other sections of the poster. 

November 6, 2025 (2 hours):

Research team meeting with Dr. Lipus. Given instructions and directions for each part of the poster, as well on what figures and pictures to include for each part. 

November 4, 2025 (4 hours):

Outline of the SJU Conference Poster was created and respective roles & parts were given to each member of the team. 

October 29, 2025 (5 hours):

Microbial abundance of currently examined samples (Rock, Crust, Biofilm) was analyzed with created box-and-whiskers plots via Rstudio.

October 22, 2025 (4 hours):

Gathered materials and chemical substances required to make media for the enrichment culture of AMD ingredients. Solution 1, containing minerals and nutrients, was created. Solution 2, containing DI water and iron supplement, was combined in another container. Solution 1 was autoclaved; solution 2 was filter-sterilized with vacuum.

October 16, 2025 (2 hours):

DNA cleanup was reattempted, but still unsuccessful. Investigating if DNA cleanup did not work due to unique characteristics of AMD microbial samples. 

October 15, 2025 (3 hours):

Nanopore Sequencing machine unpacked and set up for future use. DNA cleanup was performed on 6 of the highest DNA concentrated samples. Was not successful.

October 10, 2025 (2 hours):

Using extracted DNA samples, qPCR was prepared for 12 samples, consisting of 6 extracted DNA samples and 6 diluted versions of the DNA extract samples. 

October 9, 2025 (4 hours):

4 DNA extractions were performed on more AMD samples.

October 6-7, 2025 (6 hours):

Using data of both AMD and Soccer Turf Microbial project, I created a box-and-whisker plot of the qPCR data of all samples that has been through DNA extraction. Figure was created via RStudio. Figure examined how many copies of 16S are present in each environmental sample.  

Week of September 28, 2025:

Research on hold due to midterms week.

September 24-25, 2025 (6 hours):

Performed more DNA extractions on AMD samples. 

September 18, 2025 (3 hours):

Aided PI's other environmental microbial research project (Soccer Turf) and performed DNA extractions. 

September 11, 2025 (2 hours):

Learned from PI on PCR, primers, and barcoding libraries. Performed DNA extractions (2) on AMD samples.

September 4, 2025 (3 hours):

Gathered all collected samples and centrigued samples for future DNA extractions.

September 2, 2025 (8 hours):

Traveled to Wilkes-Barre, PA with packed equipment and materials. Arrived at Acid Mine Drainage site for 3 hours of collecting outflow, soil, biofilm, and rock samples.