March 1

feb 25 + 27

Print Friendly, PDF & Email

FEBRUARY 25TH 2019

-OBJECTIVE: 

  • Create an outline for posters 
  • PROCEDURE:
  • Class was broken into groups of three
  • Posters from previous years were analyzed 
  • Within those groups, a piece of paper was used to outline the layout of the poster
  • RESULTS:
  • Layouts were created and passed in
  • CONCLUSION:
  • Students will understand the layout of their own poster 
  • FUTURE STEPS: 
  • Design a the poster on PowerPoint 
  • FEBRUARY 27TH 2019
  • OBJECTIVE:
  • Create a more finalized version of posters
  • PROCDURE:
  • A PowerPoint file was created where a layout for the poster, along with the information was added 
  • END RESULT: 
  • A semi-finished poster was created (see figure below)
  • CONCLUSION:
  • Poster layout has been determined, but information must be added 
  • FUTURE STEPS:
  • More information will be added to the poster, and a color scheme will be picked 
February 22

FEB 18th-20th labs

Print Friendly, PDF & Email
  • FEBRUARY 18TH, 2019
  • OBJECTIVE:
    • Double check annotation starts, work on abstracts 
  • PROCEDURE: 
    • DNA master and gene mark were used to double check starts and stops of genes
    • A google doc was created in order to work on a group-made abstract 
  • RESULTS: 
    • Submitted abstract that was constructed as a group
    • No start codons were changed 
  • CONCLUSION:
    • Gene starts have been double checked and, abstract was constructed 
  • FUTURE STEPS: 
    • Edit the abstract if corrections are necessary 
  • FEBRUARY 20TH, 2019
  • OBJECTIVE: 
    • Understand poster design, and go over hard calls on Napoleon B
  • PROCDURE:
    • DNA master was use to examine the ORF’s of questionable genes 
    • Example posters were viewed in order to understand design 
  • RESULTS: 
    • Questionable genes were edited 
    • Important components of a poster were noted 
  • CONCLUSION: 
    • Students understand the fundamental layout of posters 
  • FUTURE STEPS:
    • Deign a poster 
February 18

The Forgotten Cure 1

Print Friendly, PDF & Email

Lauren Foley 

Dr. Adair 

BIO 1406

18 February 2019

The Forgotten Cure 1

Locusts, dysentery, and war all remarkably led to the discovery and progression made in the bacteriophage field. Locusts can ultimately take responsibility for the discovery of the bacteriophage. Of Course like many of the great discoveries of our time, phages were discovered by accident! Scientist d’Herelle discovered phages while studying sick locusts. During his experiments he noticed clear, spherical spots on his bacterial cultures. He investigated the spots but noticed nothing significant. Little did he know several years later while studying dysentery, these clear little spots would appear once again. In 1916, while at the Pasteur institute in Paris, d’Herelle was sent in investigate a breakout of dysentery that had spread among the troops in Paris. He cultured the samples from the sick patients, and to his surprise there they were again- those little clear spots. D’Herelle noticed the little clear spots were only seen in recuperating patients, and decide to investigate further. A new patient was admitted to the hospital and he decided to closely monitor her. During the first 3 days of observing her cultures- nothing. The tubes were full of bacterial growth, and opaque. On the fourth day he noticed something remarkable- one of the tubes was completely clear! When d’Herelle went to the hospital he found the patient had recovered. Dysentery and war go hand and hand in pushing for the discovery of phage, and ultimately led to this major breakthrough. When war erupts, all energy goes into the war efforts- even the scientific community’s efforts. At the end of the day its all about who is willing to pay for research and if the government wants to pay to help end a disease that is wiping out troops, then thats where the research will be conducted.It ultimately led to this major breakthrough in terms of phage discovery. 

In addition to that one of the things that really surprised me was how early phages were actually being used to treat diseases. I had always thought that phage research, and therapies were something that started in the 2000’s, not the early 1900’s. To find out that scientists were using phages before they could even see them. D’Herelles predictions and insight into what he believed bacteriophages were, is absolutely astounding to me and show true creative thinking, considering he couldn’t even see the bacteriophages. With the invention of the electron microscope in 1940, which provided a visual insight into bacteriophages. When Luria first viewed what he referred to as “tadpole-shaped particles” they were shocked- because all scientist had assumed they were sphere shaped before this time. This then lead scientists to wonder, how did phages infect bacteria? This question then gave way to the famous Hershey and Chase experiment that altered the field of bacteriophages forever. 

February 15

FEBUARY 11TH AND 13TH- LABS

Print Friendly, PDF & Email

FEBUARY 11TH, 2019 

  • OBJECTIVE: 
    • Annotate assigned Napoleon B genes 
  • PROCEDURE
    • FasA file of Napoleon B was run through gene mark, and was downloaded into DNA Master 
    • The file in DNA master was auto-annotated
    • Genemark was analyzed to determine the start of gene 5
  • Phages DB was used to determine the protein function, and was used to determine the relation to phage Tribby 
  • RESULTS: 
    • Gene 5 

SSC:2458 – 2826, CP:Yes, SCS:Both, ST:NI, BLAST-Start:Aligns with  gp NCBI BLAST q:s  , Aligns with Tribby gp6 PhagesDB BLAST q1:s1 1 6E-67, Gap:25bp gap, LO:Yes, RBS:Kibbler7 and Karlin Medium 2.869 -3.568 No, F:NKF, SIF-BLAST:NKF Supported by PhagesDB BLAST Tribby gp6   , , SIF-HHPred:NKF, SIF-Syn:NKF

  • CONCLUSION:
    • Gene 5 is partially annotated and needs to be finished
  • FUTURE STEPS: 
    • Finish annotating gene 5, and the 3 other assigned genes 
  • FEBRUARY 13TH, 2019
  • ABSENT 
February 8

FEB- 4TH AND 6TH LABS

Print Friendly, PDF & Email
  • FEBRUARY 4TH, 2019 
  • OBJECTIVE: 
  • Work on protein function annotation 
  • PROCEDURE: 
  • HH Pred was used to run protein sequence to determine proteins potential function 
  • This step was also repeated using BLAST 
  • DNA master was used to go and fix annotations 
  • RESULT:
  • It was found neither gene had a function 
  • CONCLUSION: 
  • Function of proteins produced by gene 8 and 9 was determined 
  • FUTURE STEPS: 
  • Learn more about proper protein annotation, and continue to work on annotation of gene 8 and 9
  • FEBUARY 6TH, 2019
  • OBJECTIVE:
  • Fix previous annotations, and learn about annotation of tRNA
  • PROCDURE:
  • Google sheets was used as template for annotation 
  • DNA master was used to view genes and aid in annotation 
  • Phamerator was used to show relation between phage’s genomes
  • ARAGORN was used to learn about the function of tRNAs
  • RESULTS:
  • See images below 
  • CONCLUSION 
  • Genes 8 and 9 were annotated 
  • FUTURE STEPS: 
  • Work on annotating more genes and working on perfecting annotations 
February 1

JAN 28TH AND 30TH- LABS

Print Friendly, PDF & Email
  • JANUARY 28TH, 2019
  • OBJECTIVE: 
    • Alter Annotation settings 
  • PROCEDURE: 
    • The description settings were copied from a Canvas page 
    • Those setting were then copied and pasted into DNA Master 
  • RESULTS: 
    • The settings were updated, and it now allows for the notes section to contain each part that must be completed for annotation (as seen in the figure below) 
  • CONCLUSION: 
    • Settings were successfully updated 
  • FUTURE STEPS: 
    • Start to annotate Elear’s genome 
  • JANUARY 30TH, 2019
  • OBJECTIVE: 
    • Learn how to annotate genes, and attempt to successfully annotate genes 8 and 9 
  • PROCEDURE: 
    • DNA master was used to view and annotate genes 
    • Phages DB was used to BLAST genes 
  • RESULTS: 
    • Gene 8
      • Original Glimmer call @bp 6224 has strength 11.15
      • SSC:6224.6583 CP:yes SCS:both ST: BLAST-Start: Minl,40, function unknown, 60%, Phages DB GAP: LO: RBS:Kibler7, Karlin Medium, 3.067,  -2.451, no
    • Gene 9 
      • Original Glimmer call @bp 6552 has strength 13.86
      • SSC:6552.7511 CP:yes SCS:both ST: BLAST-Start: Aligns With Ryan, 10, q17:s1, 52%, phages DB GAP: overlap, 329bp LO:yes RBS:Kibler 7, Karlin Medium, 1.145,-6.385, no
  • CONCLUSION: 
    • Genes 8 and 9 were annotated 
  • FUTURE STEPS: 
    • Continue to work on learning how to annotate, and continue to annotate ore of Elesar’s genes 
January 25

January 25th labs

Print Friendly, PDF & Email
  • JANUARY 25th, 2018
  • OBJECTIVE:
    • To auto-annotate the genome of Elesar, and learn how to calculate gaps and overlaps within the genome
  • PROCEDURE: 
    • DNA master was downloaded 
    • And a word document was copied and pasted into DNA master for annotation settings
  • RESULTS: 
    • Error code kept occurring when attempting to auto-annotate Elesar’s genome
  • CONCLUSION: 
    • Annotation settings were successful updated
  • FUTURE STEPS: 
    • Work on finding reason why DNA master will not auto-annotate
January 18

JANUARY 16TH LAB

Print Friendly, PDF & Email
  • JANUARY 16th, 2018
  • OBJECTIVE: 
    • To download DNA Master onto laptop and run the auto connotation of Elesar’s genome. 
  • PROCEDURE: 
    • DNA Master was downloaded from a file online 
    • Elesar’s genome file was downloaded from phagedb.com 
  • RESULTS: 
    • DNA Master was downloaded 
    • Elesar’s genome file was downloaded off of phagedb.com 
    • The file was then uploaded onto DNA Master 
  • CONCLUSION: 
    • DNA Master was downloaded and Elesar’s genome was uploaded 
  • FUTURE STEPS: 
    • Auto annotate the genome, and start annotating from there 
November 30

NOVEMBER 26TH AND 28TH- Labs

Print Friendly, PDF & Email
  • NOVEMBER 26TH, 2018
    • OBJECTIVE: 
      • Plate high titer in order to flood plates and get more lysate for DNA extraction 
    • PROCEDURE: 
      • Tables were cleaned and lamps were lit 
      • The dilutions from last lab were used, and the following amounts were placed into a tube with .5mL of Arthrobacter for 15 minutes:
        • 10^-2 45𝝁L  
        • 10^-2 45𝝁L
        • 10^-1 4.5𝝁L 
      • During the 15 minutes a large test tube was filled with: 
        • 8mL LB
        • 90𝝁L  CaCl2 
        • 10mL 2X TA 
      • Then 4.5mL of the 2X TA solution was pipetted into the tube containing lysate and Arthrobacter, then the tube was poured onto a plate
      • The previous step was repeated for all the tubes containing lysate and Arthrobacter 
      • For the control 4.5mL of the 2X TA solution was pipetted onto a plate
      • The plates were then left to solidify for 10 minutes, before being inverted and placed into the incubator 
    • RESULTS: 
      • The Results can be viewed in Figure 26 
    • CONCLUSION: 
      • Minimal to no plaques grew due to how old the lysate was. As the lysate ages, the bacteriophage most likely lost infectivity.
    • NEXT STEPS:
      • Use original lysate to get a high titer plate
  • NOVEMBER 28TH, 2018 
    • OBJECTIVE: 
      • Use lysate from flooded plate (on 12/19) to create serial dilutions and get a high titer
    • PROCEDURE:
      • Tables were cleaned and lamps were lit
      • Six micro-centrifuge tubes were labeled according to the dilution (10^0 through 10^-5)
      • The tube labeled 10^0 was filled with 100𝝁L of phage buffer and tubes 10^-1 through 10^-6 were filled with 90𝝁L of phage buffer 
      • 100𝝁L of lysate was pipetted into the 10^-0 micro centrifuge tube
      • Then 10𝝁L of the 10^0 dilution was pipetted into the 10^-1 tube, then 10𝝁L of solution from the 10^-1 tube was pipetted into the 10^-2 tube, and so on until a dilution of 10^-5 was reached
    • The following amounts of dilutions were placed into a tube with .5mL of Arthrobacter for 15 minutes:
      • 10^-2 45𝝁L  
      • 10^-4 10𝝁L 
      • 10^-1 4.5𝝁L 
      • 10^-2 10𝝁L 
      • 10^-5 10𝝁L 
      • During the 15 minutes a large test tube was filled with: 
        • 14mL LB
        • 157.5𝝁L  CaCl2 
        • 17.5mL 2X TA 
      • Then 4.5mL of the 2X TA solution was pipetted into the tube containing lysate and Arthrobacter, then the tube was poured onto a plate
      • The previous step was repeated for all the tubes containing lysate and Arthrobacter 
      • For the control 4.5mL of the 2X TA solution was pipetted onto a plate
      • The plates were then left to solidify for 10 minutes, before being inverted and placed into the incubator 
    • RESULTS: 
      • Waiting for results 
    • CONCLUSION: 
      • Waiting for results 
    • NEXT STEPS:
      • Wait for results, if high titer was not achieved a TEM will be ran on lysate available, if high titer is achieved plates will be flooded and DNA extraction will be run 
November 23

NOVEMBER 16TH and 19TH- LABS

Print Friendly, PDF & Email
  • NOVEMBER 16TH, 2018
    • OBJECTIVE:
      • To pick a plaque and create serial dilutions, so dilutions can be easily plated next time coming into lab 
    • PROCEDURE:
      • Tables were cleaned and lamps were lit
      • Seven micro-centrifuge tubes were labeled according to the dilution (10^0 through 10^-6)
      • The tube labeled 10^0 was filled with 100𝝁L of phage buffer and tubes 10^-1 through 10^-6 were filled with 90𝝁L of phage buffer 
      • The P4 plate was examined under a light microscope, where a plaque was picked using a micropipette 
      • The pipet tip was then swirled in 100𝝁L of phage buffer
      • Then 10𝝁L of the 10^0 dilution was pipetted into the 10^-1 tube, then 10𝝁L of solution from the 10^-1 tube was pipetted into the 10^-2 tube, and so on until a dilution of 10^-6 was reached 
      • After the plaque was picked 8mL of phage buffer was put onto the P4 plate, where the plate was then left to flood for 48 hours 
    • RESULTS: 
      • None
    • CONCLUSION: 
      • None 
    • NEXT STEPS: 
      • Plate dilutions and filter lysate from plate flooding 
  • NOVEMBER 19TH, 2018
    • OBJECTIVE: 
      • To plate serial dilutions and filter lysate
    • PROCEDURE: 
      • Tables were cleaned and lamps were lit 
      • A large test tube was filled with: 
        • 4mL LB
        • 5mL 2X TA
        • 45𝝁L of CaCl2
      • 4.5mL was then pipetted onto 2 plates, one plate where the serial dilutions will be tested, and the control 
      • After allowing 10 minutes for the plates to solidify, 10𝝁L of each dilution was pipetted onto the designated location on the plate 
      • After allowing 10 minutes to let the dilutions sit on the plate, the plate was placed right side up in the incubator
      • The contents of the flooded plate were poured into a top filter, and filtered out creating a new lysate
    • RESULTS: 
      • The results can be viewed in Figure 25 
    • CONCLUSION: 
      • The area on the plate labeled 10^-3 will be used as the high titer for the lysate 
    • NEXT STEPS: 
      • Calculate how much is needed to make a high titer, then plate the amount calculated