Saturday, April 18, 2015

ClO2 Study - P. larvae Spores on Glass

From 4-15-15.

The colonies have begun to form on the MYPGP plates from the last ClO2 experiment. Initial colony counts seem to show a general trend of the more ClO2 reagent the spores were exposed to, the less colonies there were. However, I will wait an additional day or two before I report official colony counts. I have found that, especially with this P. larvae bacteria, the longer I wait to count colonies the more appear and the better they come in (can take up to a week before all colonies are seen).

Below are two images to be used in comparison of the effects of ClO2 on P. larvae spores on glass:

P. larvae spores exposed to 100 mg of ClO2 reagent (dilution 10^0)

P. larvae spores exposed to no ClO2 reagent (dilution 10^0)

//EWW

Friday, April 17, 2015

Wax Worm/P. larvae LD50

From 4-4-15.

Goal: Design a new method to use in determining the LD50 of the early instar wax worms to P. larvae spores.

Background: One of the issues I was having with the previous experiments was that the wax worms were not fed a high enough concentration of spores and I never actually was able to kill them. The B. thur spores were able to cause death in the wax worms after about three days, but all the P. larvae exposed wax worms still survived (or died due to other causes). However, signs of disease was observed in some of the wax worms exposed to P. larvae by day three, but cleared up by day six. The main reason that the early instar wax worms were not fed a high enough concentration of P. larvae spores was because my titers were not very high. Fortunately, I have increased my titer of P. larvae spores through use of the Columbian sheep's blood agar. The titers have increased from ~10^3 to ~10^6.

Another issue I had ran into previously was with storing numerous wax worms together that were in the same treatment group. The main concern with this was that frequently I would count surviving wax worms after each time point and there would be one completely missing from the container. I am extremely confident that the wax worm did not escape. My conviction in this statement was cemented after several small pieces of a wax worm's head was found inside the container (missing it's body). This was observed several times and upon further investigation I discovered that the wax worms will actually eat each other! They will eat organic material, including each other if the food source is scarce, which was also true since they were only provided the BAD spiked with spores as nutrients.

Also, there was some (more than I'd like) death in the early instar wax worms at Day 1. This was often attributed to either handling issues, which became reduced once I become more experienced moving the wax worms, or drowning of the wax worms in the diet. There were a number of wax worms that would be floating in the diet at Day 1. There was only a small volume pipetted into the container (between 5-10 uL), however they are VERY small early instar wax worms.

The last big issue I had with the previous experiment was the type of containers that was being used. There was no air transfer using those containers, and even though they were opened daily to count survival, humidity was noticeably building up inside the container. I am not sure how much oxygen an early instar wax worms needs for 24 hours, but I am pretty sure with 5-10 of them inside the small tightly sealed container, there wasn't enough. Coupled with the large amount of wax worms per container (between 5 -10 depending on the experiment) and the lack of air exchange the containers themselves became very inhospitable by the end of the experiments. 

Method: For this experiment, we wished to expose the wax worms to a higher concentration of P. larvae spores (in a decreased volume), store them individually in a 96 well plate, and use a breathable cover for the plate to facilitate air exchange. The next generation of wax worms have just began to hatch from their eggs a few days ago and are now a size that is easy to work with for this experiment.

1. Add a single piece of oat meal to the bottom of a well in a 96 well plate (I am not 100% sure if they WW will eat the oatmeal, but it is meant to serve as their nutrient source over the course of this experiment.
2. Serially dilute P. larvae spore stocks in sterile ddH2O and add a volume of 3 uL directly to the top of the piece of oatmeal inside the well. Allow the liquid to be absorbed into the oatmeal (~1 minute).
3. Add an early instar wax worm is then carefully transferred to the well using a forceps. Make sure it doesn't escape the well before it is covered.
4. Cover the wells using a metal sticky cover seal. Create a very small pin sized hole in the top of the film for the wax worms to breath and allow air to be exchanged.

The smiley bug is obviously a wax worm
5. Once all the wells are covered, tip the 96 well plate upside down and place inside a secondary container. Incubate the container at 37C and check survival of the wax worms every 24 hours.

Note: the reason the plates were not covered with a more permeable (or breathable) cover is because the WW will eat that material and escape the well. This is also the reason the plates were tipped upside down- to prevent them from leaving their wells.

For this experiment,

Control:
Negative - sterile ddH2O
Positive - B. thur spores (stock conc of 10^8 CFU/mL)

Experimental treatments:
P. larvae spores- stock (2.1x10^6 CFU/mL) and dilutions: 10^-1, 10^-2, 10^-3, 10^-4
Meaning the wax worms were fed 1000 spores, 100 spores, 10 spores, 1 spore, and essentially no spores (0.1 spore).



//EWW

Thursday, April 16, 2015

Germinant Receptors in P. larvae - Bioinformatics

From 4-13-15.

Downloaded Stampy & BWA from http://www.well.ox.ac.uk/software-download-registration.

From the website:

Description: Stampy is a package for the mapping of short reads from illumina sequencing machines onto a reference genome. It's recommended for most workflows, including those for genomic resequencing, RNA-Seq and Chip-seq. Stampy excels in the mapping of reads containing that contain sequence variation relative to the reference, in particular for those containing insertions or deletions. It can map reads from a highly divergent species to a reference genome for instance. Stampy achieves high sensitivity and speed by using a fast hashing algorithm and a detailed statistical model. Stampy has the following features:
  • Maps single, paired-end and mate pair Illumina reads to a reference genome
  • Fast: about 20 Gbase per hour in hybrid mode (using BWA)
  • Low memory footprint: 2.7 Gb shared memory for a 3Gbase genome
  • High sensitivity for indels and divergent reads, up to 10-15%
  • Low mapping bias for reads with SNPs
  • Well calibrated mapping quality scores
  • Input: Fastq and Fasta; gzipped or plain
  • Output: SAM, Maq's map file
  • Optionally calculates per-base alignment posteriors
  • Optionally processes part of the input
  • Handles reads of up to 4500 bases

The reference paper for the package can be found here.

I plan to use Stampy & BWA to map all my downloaded sequences to a reference strain of P. larvae DSM 25430, which I have also downloaded the fasta file from NCBI for.

//EWW

Wednesday, April 15, 2015

ClO2 Study - P. larvae Spores on Glass

From 4-14-15.

Repeated ClO2 gas exposure to P. larvae spores on glass cover slips as before using different weights of ClO2 reagents. The previous time this experiment was ran I used a lot of ClO2 reagents for the reactions (200 mg and 2000 mg) which resulted in a lot of spore killing as evident by the lack of colony formation on the MYPGP agar after. The 2000 mg weight actually resulted in total killing of the spores and the 200 mg almost had the same result. So, this time I will be using less ClO2 reagent.

The total dry weights of ClO2 reagents used in this experiment were 100 mg, 50 mg, 25 mg, and 0 mg. P. larvae spore stock #15 was used in this experiment.

The spores on the glass cover slips were exposed to the ClO2 gas inside the modified anaerobic chambers inside the fume hood for six hours once again.

The spores were re-suspended after and plated on MYPGP agar as before. Plates were incubated at 37C for three days.

//EWW

Tuesday, April 14, 2015

ClO2 Study - P. larvae Spores on Glass

From 4-11-15.

Visible P. larvae colonies have begun to form on the MYPGP agar





How to calculate CFU/mL

(CFU * Dilution Factor * Volume Factor)

or

(# CFU) * ( 1 / 10^ dilution factor) * ( 1 / volume plated in mL) = CFU / mL

ex:

3 * ( 1 / 10^ (-4)) *  ( 1 / 0.01mL) = 3x10^6 CFU /mL


Unfortunately, there were no colony growth on the 2000 mg ClO2 weight concentration, even at the least dilute plate (10^-1). This isn't overly surprising as that concentration was relatively very high. So high in fact that it turned the plastic of the anaerobic chamber and the water inside a yellow tint. Fortunately, the yellow tint has disappeared from the container after a couple of days.
There were countable colonies in the No ClO2 and 200 mg treatment groups. Below is a graph illustrating the differences between CFU in those treatment groups:

Raw Data

Colony Counts:


Dilution Factor
ClO2 Conc 0 -1 -2 -3 -4
None TNTC TNTC 9 3 0
TNTC TNTC 9 1 0
TNTC TNTC 11 9 0
TNTC TNTC 13 3 0
TNTC TNTC 9 2 0
TNTC TNTC 13 2 0
TNTC TNTC 16 3 0
TNTC TNTC 9 1 0
TNTC TNTC 5 0 0
TNTC TNTC 7 4 0
TNTC TNTC 13 2 0
TNTC TNTC 11 3 0
TNTC TNTC 9 1 0
TNTC TNTC 7 3 0
TNTC TNTC 10 0 0
200 mg 1 0 0 0 0
2 0 0 0 0
1 0 0 0 0
1 0 0 0 0
0 0 0 0 0
3 0 0 0 0
2 0 0 0 0
0 0 0 0 0
1 0 0 0 0
1 0 0 0 0
1 0 0 0 0
0 0 0 0 0
2 0 0 0 0
0 0 0 0 0
4 0 0 0 0



CFU/mL:

0 -1 -2 -3 -4
None N/A N/A 9.0E+04 3.0E+05 N/A
N/A N/A 9.0E+04 1.0E+05 N/A
N/A N/A 1.1E+05 9.0E+05 N/A
N/A N/A 1.3E+05 3.0E+05 N/A
N/A N/A 9.0E+04 2.0E+05 N/A
N/A N/A 1.3E+05 2.0E+05 N/A
N/A N/A 1.6E+05 3.0E+05 N/A
N/A N/A 9.0E+04 1.0E+05 N/A
N/A N/A 5.0E+04 0.0E+00 N/A
N/A N/A 7.0E+04 4.0E+05 N/A
N/A N/A 1.3E+05 2.0E+05 N/A
N/A N/A 1.1E+05 3.0E+05 N/A
N/A N/A 9.0E+04 1.0E+05 N/A
N/A N/A 7.0E+04 3.0E+05 N/A
N/A N/A 1.0E+05 0.0E+00 N/A
200 mg 1.0E+01 N/A N/A N/A N/A
2.0E+01 N/A N/A N/A N/A
1.0E+01 N/A N/A N/A N/A
1.0E+01 N/A N/A N/A N/A
0.0E+00 N/A N/A N/A N/A
3.0E+01 N/A N/A N/A N/A
2.0E+01 N/A N/A N/A N/A
0.0E+00 N/A N/A N/A N/A
1.0E+01 N/A N/A N/A N/A
1.0E+01 N/A N/A N/A N/A
1.0E+01 N/A N/A N/A N/A
0.0E+00 N/A N/A N/A N/A
2.0E+01 N/A N/A N/A N/A
0.0E+00 N/A N/A N/A N/A
4.0E+01 N/A N/A N/A N/A






Averages:

0 -1 -2 -3 -4
None
Avg N/A N/A 1.0E+05 2.5E+05 N/A
Std N/A N/A 2.8E+04 2.2E+05 N/A
200 mg
Avg 1.3E+01 N/A N/A N/A N/A
Std 1.2E+01 N/A N/A N/A N/A


The average recovery of spores from the No ClO2 exposure group is listed above, meaning that the recovery of the P. larvae spores from the glass cover slip was between 35.7% to 89.3% (from the 2.8x10^5 CFU/mL). Which isn't too bad, but not the best either.

Graph (using the -2 data from the No ClO2 group since it had the lowest Std)

//EWW



Monday, April 13, 2015

Germinant Receptors in P. larvae - Bioinformatics

From 4-6-15.

I want to convert all the .sra files to .fastq files using the sra toolkit. I did not want to convert each of them

Fortunately, I received assistance from Oleksandr M. with the command line script to convert the formats after many hours of attempts and failures on my own.

Converting .sra to .fastq

  1. In order to convert all of my .sra files to .fastq in one go, rather than type them all in individually I had to first navigate to the directory (in the command terminal) where all the executable files for the sra toolkit were located.
    1. It is found in the sratoolkit.2.4.5-2-mac64 / bin
  2. Once there, I entered  $ pwd    and was told that directory's location. 
    1. The pwd was " /Users/Elliott/sratoolkit.2.4.5-2-mac64/bin "
  3. After the source directory was identified, I navigated to the location where all the .sra files were located.
    1. It is found in ncbi / public / sra
  4. Once there, I entered the command to begin converting all the .sra files found in this directory to .fastq using the command $ /Users/Elliott/sratoolkit.2.4.5-2-mac64/bin/fastq-dump *.sra
    1. The first part indicates the source (the sra toolkit in this case) and asterisk (*) indicates to perform that action to ALL the .sra files found in that directory. I believe I could have also told it to put all the newly converted .fastq files into a different directory, but instead it just put them in the current one with the .sra files.
    2. All the .fastq files were generated into the ncbi / public / sra
  5. All of the .fastq files were then manually moved from the sra directory into the newly created fastq directory located in ncbi / public/ fastq
//EWW

Saturday, April 11, 2015

ClO2 Study - P. larvae Spores on Glass

Goal: Expose P. larvae spores on a glass surface to chlorine dioxide gas in order to determine the gas's effect on the spores. The glass surface will serve as somewhat of a control, as metal, plastic, and possibly wood surfaces will be implemented in the future.

Procedure:
  1. A 100 uL volume of P. larvae spore stock was added to the surface of a sterile glass cover slip. The volume was allowed to evaporate for about an hour inside the laminar flow hood. 
    1. For this experiment. I used Spore Stock #16 from 4-7-15, so each cover slip was inoculated with 2.8x10^5 spores.
      100 uL volume of P. larvae spore stock on glass cover slip

  2. The chlorine dioxide reagents (Part A & Part B) were weighed out using he analytical balance in the Pruess lab with reagents being temporarily stored in 1.5 mL eppendorf tubes. Note: Be careful not to mix the two reagents and to change out weigh paper and scoops between each reagent.
    1. For this experiment, there was only two experimental groups using chlorine dioxide- 100 mg and 1000 mg concentrations. Once the reagents are mixed their final weight concentration will be 200 mg and 2000 mg.
  3. The actual ClO2 gas exposure will take place inside of the modified anaerobic chambers as shown on 10-18-15 inside of a laminar flow hood. The exposure chambers were assembled and organized also similarly as to what had been previously done. A beaker containing 50 mL of ddH2O was added to the corner of the modified anaerobic chamber to increase humidity (higher humidity increases the rate at which ClO2 is generated). A metal stir bar in combination with a magnetic stir plate were utilized in order to evenly mix the gas once it is being generated. In order to get the metal stir bar to smoothly spin inside the chamber a number of glass microscopy slides were placed on the bottom of the chamber for the stir bar to spin on. Otherwise the stir bar would be spinning on the plastic.
    1. Set up anaerobic chamber similarly it what it was on 11-9-14. This image does not show the sachet containing the ClO2 reagents. Note: the metal stir bar in the center (blurry spot)- it is spinning on top of several glass microscope slides that have been placed on the bottom of the chamber.
      Chambers set up in laminar flow hood. The ClO2 exposure will be conducted within the hood. 

  4. The modified anaerobic chambers were closed and allowed to spin for an hour to build up humidity (and while I prepped everything else)
    1. How the modified anaerobic chamber was organized. Image created using Inkscape Software.
    2. After three hours of the chamber being closed and spinning the humidity was 77% and was a temperature of 26.2C.
  5. The glass cover slips containing the dried P. larvae spores were aseptically transferred to the modified anaerobic chambers using sterile forceps. The cover slips (three per container) were placed inside a sterile petri plate.
  6. The chlorine dioxide gas reagents were quickly and thoroughly mixed inside small sachet bags and added to the modified anaerobic chambers. The tops of the sachet bags were pinched in the opening of the chamber lid and sealed shut. The light in the hood was turned off and the opening to the hood was sealing using foam boards

    1. Hood sealed with foam board to protect the anaerobic chambers from reaction - ClO2 will not be generated as efficiently in the presence of light. 

  7. The exposure continued for six hours inside the sealed laminar flow hood with the lights off and metal stir bar spinning.
  8. After six hours, the chlorine gas concentrations was measured in each modified anaerobic chamber using chlorine gas detection tubes (previously described 10-8-14) in conjugation with the GasTec (Link) pump. A total volume of 200 mL was removed from the container.
    1. For this experiment, there was significantly more chlorine gas present in the anaerobic chamber with the larger weight of chlorine dioxide gas reagent, which makes logical sense. In the container with only 200 mg the Cl detection tube only detected 75 ppm Cl. In the container with 2000 mg, there was over 500 ppm of chlorine present. The detection tube was unable to determine exactly how much Cl was present in this container since it was beyond what the detection column could detect.
    Chlorine gas detection tubes from each of the experimental groups, the left is from the container with 200 mg total of reagent (100 mg each), and the right is from the container with 2000 mg total weight.
    In fact, the concentration of Cl was so high in the one container that the container itself turned yellow. Even the water inside that container turned yellow. The below image shows the difference between the two containers - there is no trick with the lighting, the container on the right now has a yellow tint to it compared to the one on the left.
    Notice the color differences between the two chambers that were exposed to different levels of ClO2 gas

    1. Additionally, the temperature inside the hood, but not the containers, after 6 hours was 30.4C.

9. The anaerobic chamber was opened inside the laminar flow hood and the cover slips containing the P. larvae spores were aseptically transferred to a 50 mL conical tube containing 1.0 mL of sterile ddH2O. The glass cover slip was broken (shattered) using a sterile forceps while inside the tube.

10. The tube and contents were vigorously vortexed for 30 seconds and allowed to incubate at room temperature for 5 minutes.

11. The re-suspended spores were diluted in sterile ddH2O and plated on MYPGP agar. Plates were incubated at 37C for three days until colonies can be counted and spore concentration can determined.



//EWW