Option three was more appealing to me since it talked about accelerate innovation. Lots of things were said that could help with climate change. In the discussion, we talked a lot about how little steps are being made towards a “green” world. We talked about how the majority of us will have to give in to the cause, whether that is big or small. Things talked about in option one seemed huge on many levels. One of the examples of what could be done stated to require the use of electrical cars. We have made steps in that direction, but it would take time to give up something that is so useful in our society. An interesting topic was discussed in our group on how nuclear plants should be the way the go since they are easy to make, and not as much pollution, such as nitrogen. Public deliberation in the community is a great way to spread the word of an important topic that will have an effect on many lives. It is where the community can come to one and talk about real world issues in that community or in that state/country. Having more of these in a classroom setting would only help the class benefit from many things such as: learning something new, broaden your scope on how you viewed a certain topic, and connecting with your classmates. Option three on the what can be done example stated ease regulation to bring new “green” technologies to the market more quickly could have an effect on the environment. It is like asking yourself, “which is “eco-friendlier”? the paper bag or the plastic bag?” It depends on your prospective on this since both have its pros and cons.

The global rise of multi-drug resistant bacteria has resulted many concerns for this antibiotic resistance is fast approaching. This had led many scientists to review the forgotten cure that was forgotten in the west but not the east. The long clinical history of phage therapy in Eastern Europe, combined with more recent in vitro and in vivo success, shows potential for phage based antibacterial agents. Despite the fact that phage therapy is not yet approved by FDA, phages have already been used to save lives in experimental treatments. A patient who suffered from antibiotic-resistant bacteria was reported in San Diego. Tom Patterson was infected by a multidrug-resistent Acinetobacter baumannii. He was quickly flown back to California and treated with antibiotics, but he near got better. He was saved by a cocktail of phages purified from sewage in Texas. In the near future, as antibiotics lose their effectiveness, we might see more stories like this one. One day, phage might move from our last resort against antibiotic-resistant bacteria to our first line of defense, bringing the “forgotten cure” back to life.

With the multiple lives saved from phage therapy, phage therapy should be tested on humans for other diseases and not AIDS first. I see phage one day becoming a big help to save lives, but not as a first resort, but definitely not last. Once FDA approves phage therapy for a disease on humans, I see more and more experiments run to test these forgotten cures, but only when hard data supports this, phage therapy will just be a “last resort”. Once experimenters have enough data to show that researchers have found a cure for a particular cure, then human trails can start, which will then have to convince the public that “hey this is actually good”. Animal trials would be done first before the start of any human trials. Even with growing antibiotic-resistance, researchers are still producing new antibiotics that work, but only for a short period of time, making the bacteria stronger. Even if phage therapy were to be “the go-to cure”, I see that one day the bacteria to grow an immunity and would research go back to antibiotics? Possibly an endless loop of resistance.

Phages are not used since in the discovery of penicillin in 1928 that shifted modern medicine in the west. To produce phage, scientists have to grow large quantity of bacteria that is the natural host of the phage. Bacteria is then infected with phage, but the problem lies with the isolation of live phages. I would look at other ways of isolating phages and not from multitude of dead bacteria corpses, since this could lead to a deadly immune response. Phage also take a lot of time, time that patients do not have – especially when phages are used as a last resort. Last, other concerns about phage therapy are centered on its safety and efficacy. Since the western world abandoned phage therapy, little data is available. However, institutes like Phage Therapy, Phage Biotics, GangaGen, Exponential Biotherapies continue to provide research on the forgotten cure, and from their studies, phage therapy does not exhibit major safety concerns.

Rationale: Start codons for all Arthrobacter phage tape measure proteins, minor tail proteins, and major tail proteins were analyzed.

Procedure: DNA Master and PhagesDB were used to gather data. Obtained DNA Master file from PhagesDB and uploaded onto DNA Master. Protein sequence was analyzed, size of gene, and the cluster were all documented onto a google sheet. Abstract for independent research was written using Word.

Results:

Future work/Conclusions: Couple of reverse genes that is uncharacteristic of tail proteins. Majority of the major tail proteins have the start “ATG” with a couple of “GTG” with only one “TTG”. Make graphs for presentation representing the hard data, and look into the reverse genes, and what makes them unique. Only one reverse gene from the major tail proteins 1/154 genes that were analyzed. Further work will be needed to be done to analyze this reverse gene as long as other reverse genes found.

Rationale: Create an outline for CURES presentation and finish hard data for minor tail proteins.

Procedure: Word document was made and outline was made. Reviewed primary literature to help construct both an abstract and introduction. Google sheets, DNA Master, and PhagesDB were used to help analyze the starts of the Arthrobacter phage minor tail proteins. The last few minor tail protein starts preferences were entered.

Results: Outline and the end list of the minor tail proteins (613 minor tail proteins).

Future work: Start structure analysis and to examine start the start sites of all tail proteins. See correlation between the starts and length. and see why there was a reverse minor tail protein.

Conclusions: Finished the hard data and analysis of starts will be done 4/17. The overall process of collecting data took longer than expected. Figure out another way to gather data that would take less time i.e. Phamerator or code.

Rationale: Begin major tail protein structural analysis and to finish hard data for both minor tail proteins and tail proteins.

Procedure: DNA Master, PhagesDB, Google Sheets, and SWISS-MODEL Workspace were used to in major tail protein structural analysis. Obtained amino acid sequence from PhagesDB and uploaded the sequence to SWISS-MODEL Workspace and the structures were produced. Analysis of sturures were performed and lots of differences were found.

Results:  

Heisenberger 15 Major tail proteins both with the start AUG

some of the tail proteins hard data were obtained but not all. One of these tail proteins had a 399bP length, and that is really small for a tail protein. More research on this will have to be done to see why this particular protein is extremely small compared to the others.

Conclusions: When the Heisenberger 15 amino acid sequence was placed into SWISS-MODEL Workspace, these were 2 of the 3 structures produced. Two of the structures were the same but as you can see from the results, two are different, and they both have the same amino acid with the preferred starts. More work is being done to analysis the different structures of the major tail protein. Changing the starts of some tail proteins had no effect to the overall structures, but some proteins had different structures just from the preferred start site.

Future work: Begin tail protein and minor tail protein structural analysis. Finish both tail proteins and minor tail proteins hard data by using PhagesDB and DNA Master.

Procedure: Continue research on start site preferences for minor tail proteins.

Procedure: Met with the group to continue independent research. Data were obtained by using PhagesDB and DNA Master. Obtained FASTA file, and checked start site preferences on known minor tail proteins. Data was recorded onto a google spreadsheet so group members have access to data.

Results: 

Conclusions/Future work: Finish up data on google sheets and start structure analysis along with the manipulation of start sites for these tail proteins.

Rationale: Continue to find data and articles for the proposed question set for independent research

Procedures: Met with groups and started gathering data for starts of Tail protein found in Arthrobacter phages. Used PhagesDB to download FASTA file to determine starts and which genes where tail proteins. Two research articles were found to help support the significance of start sites in bacteriophage.

Results: 

:

Conclusions/Future work: continue to list all sequenced Arthrobacter phage and obtain FASTA files to check the start sites. Then manipulate the starts of the protein sequence and see if a change in structure had occurred.

Rationale: Refine the question made on 3/25 and create a procedure to test the research question.

Procedure: Questions were refined and ideas were bounced from group members to coach. Performed NCBI BLASTp on a tape measure protein to see other know bacteria to have the same known protein, and the starts of AM cluster tape measure proteins were determined.

Results: The following images below show the NCBI BLASTp and confirmation that all AM cluster phages have methionine as the first amino acid sequence.

Conclusions: NCBI BLASTp showed many hits with many known bacteria to have the same protein meaning there are similarities between them.

Future work: Test to see if these hits have the same start sequences. Find a database that can allow the manipulation of the starts to see if the change of the start site of the tape measure protein has an effect on the shape of the protein. See if there is a correlation between the starts and why certain proteins prefer this start sequence rather than the other two start sequences.

Rationale: Develop multiple questions that are testable for the final project.

Procedure: Got into groups and ideas were generated fro question topics. Everyone decided what topics the group had the most interest in. Four questions were generated and the questions were submitted to Canvas.

Results: Image shows the four questions that were generated.

Conclusions: Four questions were generated and three of the four could be potential research topics that could support the class poster.

Future work: Decide on the final question and start independent research.

Rationale: In groups, finish the final posters In-Silico results and become familiar with the new databases that would help with the independent research project.

Procedure: Groups from 3/18 worked to finish the In-Silico results, and the results were finished. In groups, each member looked at each module to help form some start to a testable research project. Group explored the bacteriophages genomics databases, and the databases helped narrow potential research question.

Results: Two topics were taken into consideration for a testable question that the group could further expand on.

Conclusions: Further analyzations need to be made in order to form two testable research questions for Monday’s lab. Other outside sources need to be brought in to help target the question. Potential independent research topic could compare the start site preferences of NapoleonB with other phages in AM cluster and the preferred ribosome binding sites could help bring other questions as well.

Future work: Poster will be updated to ensure the poster is ready for URSA. Form two testable questions that would help kick start independent research.