3/25/19

Rational:

To come up with several different ideas for a research question that can be used for the group poster.

Procedure:

• Found parts of NapoleonB that were interesting (such as proteins, genes, or any other part of the genome)
• Came up with a few questions relating to these interests
• These interests included the holin gene whch was not found n many other phage in the cluster, gene 2 with defies the guiding principles for genes, and the reasoning behind the many tail proteins found in the genome
• Ordered the questions in order to the best to worst

Observations:

• The first and top question was about the holin gene’s structure and mechanism and comparing it to other Arthrobacter phage
• The second queston was looking at whether gene two was an actual gene or not
• The third was looking at whether there are other phage that have a reverse gene that also seems to break the guiding principles
• The last was about the many tail proteins in NapoleonB and comparing it to other Arthrobacter phage

Conclusion:

Our group came up with four possible research questions and the question about the holin gene in NapoleonB’s genome was our group’s first choice. Next lab we will start to figure out how we are going to research this question or whatever question we choose.

3/20/19

Ratonal:

To fix the last few details of the poster and to start looking at reasearch topics for the individual poster.

Procedure:

• Disscused the individual posters
• Looked at the different resources available for research
• Added the red and green circles indicating deleted and inserted genes onto the new phamerator
• Answered the QTM questions

Fig.11 – This image shows the new phamerator that was inserted into the poster. The red circles indicate deleted genes and the green circles indicate inserted genes.

Conclusion:

Fininshed the last details of the class poster and started on the individual posters. Next lab we will decide on a research topic and start working on the research.

3/18/19

Ratonal:

To finish the class poster by editing the text and fixing any formatting that needs fixing.

Procedure:

• The parts of the poster that needed work
• Formatted the boxes surrounding the texts and figures to make them the same size
• Changed all of the text to arial
• Added red circles indcatng deleted genes to the phamerator
• Added green circles indicatng inserted genes to the phamerator

Fig.10 – This image shows the final poster after all the edits have been made

Concluson:

The class poster was for the most part finished and only needs a few more details to be fixed. Next lab we will be put into groups and start working on our group posters.

Russia’s state health care was not very good and often the things that doctors and patents needed were not always available. The book mentioned that in Russia they didn’t always have the means to produce all of the antibiotics that were produced in other countries. Often, they would be able to stock a far smaller variety of antibiotics and a smaller quantity of those antibiotics. This meant that the medicine that was need at times was not always available and alternatives needed to be used. Russia itself pushed for the use of herbal medicine to make up for the medicine that they didn’t have. Phage therapy also became more popular and was sometimes used in place of the antibiotics that doctors didn’t always have available.

The outcome of these 2 centers is very different because Eliava Institute was successful in the beginning and its initial struggles were a result of financial collapse. Hirszfelds Institute had different struggles and that was mostly persecution. There is also the perception from the outside world that is different. The Eliava Institute does not focus on bringing this research to people around the world as much as the Hirszfelds Institute does. Also, Eliava Institutes has some stigmatism of Russian medicine attached to it so people may be more wary of it than if it were coming from Hirszfelds Institute.

They first used lambda phage they isolated a sample to help the phage get past the liver and spleen by first tang blood samples from the animals. They then increased the amount of phage present in that sample and reinjected the sample back into the organism. They did this several times before they had a sample of phages that were the most specific to the organism and disease they were combating. Mice were then injected with E. coli and three groups were created one where the original sample of phage was used, another where the new sample was used, and a control group. They then recorded the results of their experiment.

Phage therapy has more of a market now especially since scientists and doctors are becoming increasingly concerned about antibiotic resistance and superbugs. Phage therapy could be used with antibiotics to increase their effectiveness when against a bacteria that is resistant to it. There are also other cases that phage therapy can become more of a use for one example is my grandma who is not able to take antibiotics. My grandma a couple of years ago got sick and while she got better she s unable to take antibiotics anymore. This is because I believe the bacteria is still n her body just in an amount that is not dangerous at the moment but would become dangerous if she were to take antibiotics. I believe that the research that needs to be done on phage therapy could include how effective it is against superbugs as well as researching quicker ways to be able to produce a phage sample specific to the strain of disease a patient has.

3/6/19

Rational:

To present the group poster and critique other group’s poster and decide which poster to use as a base.

Procedure:

• Critiqued every groups poster
• Presented the groups poster explaining each section and the reasoning behind the set up
• As a class decided on the base poster
• Made a list of the compoents from other posters to add to the base poster

Observations:

• As a class the doughnut figure showing the gene function list was decided on
• A smaller intro was decided on
• Decided to use a better figure to represent the soil metadata (more visually appealing)
• The figure of the tree on the map and the figure of the plate showing the plaque morphologies were kept

Fig.9 – This image shows the two figures that were kept by the class to be added the the final poster

Conclusion:

A base poster was decided on as well as important components to add. Next lab we will start making the final poster using the base poster and the components chosen.

3/4/19

Rational:

To combine the poster rough drafts that our large groups two smaller groups created.

Procudure:

• Used my group’s poster as the template poster
• Added information and figures to the rough draft
• Added some of the information from the other group’s poster to the final

Conclusion:

The final draft for our group’s poster was finished. Next lab each group will present their poster so that we can decide on the base for our classes final poster.

Fig.8 – This image shows the final draft that was created on Monday

2/27/19

Rational:

To start the rough draft of the poster using the drawing from last lab.

Procedure:

• Set up the different sections of the poster (introduction, title, methods and results, etc.)
• Added information under the sections
• Created figures for the poster

Observations:

• The poster is currently set up in rows (left to right), but columns might work better (top to bottom)

Fig.7 – This image shows the rough draft of the poster as of now.

Conclusion:

Started the rough draft of the poster and created figures for the poster. Next lab we will finish the rough draft of the poster and fix problems on the poster.

2/25/19

Rational:

To create the poster design for our first presentation with our assigned group.

Procedure:

• Disscussed different posters to get an idea of what works and what doesn’t
• With assigned group disscused how to set up the poster
• Drew the poster design
• Drew potential figure designs

Fig.6 – This image shows the sketch of the poster that was done, which outlines how the poster will be set up.

Conclusion:

A sketch of our poster was done showing how the poster will look. Next lab we will use this as a guide to make the rough draft of our poster.

2/20/19

Rational:

To check the annotations of NapoleonB in order to fix possible errors.

Procedure:

• Looked for gaps and overlaps that could indicate a mistake
• Rechecked GeneMark using the correct host
• Checked the coding potential for genes 9-12 and 98
• Checked the SCS for the genes

Observations:

• The host that was originally used for GeneMark was inncorrect which gave incorrect information for coding potential
• The answer for SCS was also changed for a few of the genes
• The answers for coding potential did not change

Fig.5 – This image shows that the GeneMark results show coding potential for gene 10, but not a gene

Conclusion:

The errors that were found in the assigned genes as well as the rest of the genes were fixed. Next lab we will work on the poster for the lab.

2/18/19

Rational:

To finish annotating gene 98. Also to write an abtract for the lab with my group using the abtracts we had written and brought to class.

Procedure:

• Checked GeneMark to make sure the coding potential was covered
• Entered the start and stop codons
• Checked phagesdb to make sure the starterator agreed with the called start
• BLASTed the gene in phagesdb and NBCI
• Entered the information about the BLAST-Start from the hit from phagesdb and NBCI
• Calculated the gap
• Entered the information about the RBS for gene 98
• Used NBCI, CDD, phagesdb, Synteny, and HHpred to find the gene’s function
• Wrote the finl draft of the abtract that my group wrote

Observations:

• The hit from phagesdb and NBCI was Mudcat
• The calculated gap was 2
• The SD score for RBS was not the best start
• The genes function was HTH DNA binding domain protein

Fig.4 – The red number under the final score column shows the score for the chosen start, but the highlighted portion shows a start with a score closer to zero. This means that the current start is not the best according to RBS.

Conclusion:

Gene 98 was annotated nd it function was determined to be an HTH DNA binding domain protein. Next lab I will check the annotaions for errors before it finished.