Rationale: Work on parts of poster as a class to compete a final version

Process:

1. began working in graphic design group to design small images to put onto the poster
   1. Main contributions:
      1. created the worst design that was too small
      2. found the exact code for the color used on the poster
2. Joined Ram’s group to help create data figures for in silico results
   1. main contributions:
      1. created a c++ program that parsed through a text block generated from a pharmerator image to extract different NapoleonB information

Results:

code:

#include <iostream>
#include <fstream>
#include <cctype>
#include <string>

using namespace std;

struct Entry {
    string id;
    int code;
    int num;
};


int main() {
     ifstream in;


     in.open("data.txt");


     int count = 0;
     int ecap = 100;
     Entry *entries = new Entry[ecap];

     string save[5000];
     int scnt = 0;
     char name[40];
     char num[10];
     int nc = 0;
     char a[40];
     char *b;

     while ( in >> a ) {
         save[scnt] = a;
         char *da = a;

         while (*da != '\0')
         {
             if (*da == 'i')
             {
                 da++;
                 if (*da == 'd') {
                     da++;

                     if (*da == '=')
                     {
                         char *dname = name;
                         da += 2;

                         while (*da != '"') {
                             *dname = *da;
                             dname++;
                             da++;
                         }

                         *dname = '\0';
                         //cout << name << endl;
                         entries[count].id = name;
                         count++;
                         //cout << entries[count].id << endl;
                     }
                 }
             }
             da++;
         }

         if ( a[0] == '(' )
         {
             //cout << save[scnt -1] << endl;

             char *na = a;
             char *dnum = num;

             na++;

             while ( *na != ')' )
             {
                 *dnum = *na;
                 dnum++;
                 na++;
             }
             *dnum = '\0';

             entries[nc].num = atoi( num );

             string codeLine = save[scnt-1];

             string codeS = codeLine.substr(codeLine.find(">") + 1);


             entries[nc].code = stoi( codeS );
             //cout << entries[nc].code << " " << nc << endl;
             nc++;

         }

         scnt++;

     }

     in.close();

     //bubble sort

    Entry temp;
    bool madeAswap;

    do
    {
        madeAswap = false;
        for ( int i = 0; i < 100; i++ )
        {
            if ( entries[i].num > entries[i + 1].num )
            {
                temp = entries[i];
                entries[i] = entries[i+1];
                entries[i+1]= temp;
                madeAswap = true;
            }
        }
    } while ( madeAswap );

    for ( int i = 0; i < 100; i++ )
    {
        cout << entries[i].num << ","
             << entries[i].id << ","
             << entries[i].code << endl;
    }





     return 0;
}

Generated List:
1,NAPOLEONB_DRAFT_30,8973
1,NAPOLEONB_DRAFT_46,2172
2,NAPOLEONB_DRAFT_18,17808
2,NAPOLEONB_DRAFT_28,620
2,NAPOLEONB_DRAFT_82,9032
3,NAPOLEONB_DRAFT_29,9160
3,NAPOLEONB_DRAFT_80,6235
4,NAPOLEONB_DRAFT_35,5503
4,NAPOLEONB_DRAFT_64,23957
4,NAPOLEONB_DRAFT_66,14746
6,NAPOLEONB_DRAFT_43,14427
6,NAPOLEONB_DRAFT_96,5481
7,NAPOLEONB_DRAFT_94,16425
8,NAPOLEONB_DRAFT_78,7010
8,NAPOLEONB_DRAFT_88,16636
9,NAPOLEONB_DRAFT_90,2220
10,NAPOLEONB_DRAFT_17,15199
10,NAPOLEONB_DRAFT_89,17851
11,NAPOLEONB_DRAFT_27,20203
11,NAPOLEONB_DRAFT_40,2745
11,NAPOLEONB_DRAFT_65,15086
12,NAPOLEONB_DRAFT_55,3201
13,NAPOLEONB_DRAFT_63,16469
14,NAPOLEONB_DRAFT_21,1334
14,NAPOLEONB_DRAFT_22,5598
14,NAPOLEONB_DRAFT_31,1350
14,NAPOLEONB_DRAFT_32,12456
14,NAPOLEONB_DRAFT_33,7647
14,NAPOLEONB_DRAFT_34,13454
14,NAPOLEONB_DRAFT_36,15534
14,NAPOLEONB_DRAFT_4,24501
14,NAPOLEONB_DRAFT_41,4750
14,NAPOLEONB_DRAFT_45,15236
14,NAPOLEONB_DRAFT_47,9175
14,NAPOLEONB_DRAFT_48,21289
14,NAPOLEONB_DRAFT_49,8333
14,NAPOLEONB_DRAFT_50,4594
14,NAPOLEONB_DRAFT_51,5790
14,NAPOLEONB_DRAFT_52,2845
14,NAPOLEONB_DRAFT_57,11576
14,NAPOLEONB_DRAFT_59,11096
14,NAPOLEONB_DRAFT_6,21245
14,NAPOLEONB_DRAFT_60,15626
14,NAPOLEONB_DRAFT_67,6336
14,NAPOLEONB_DRAFT_68,7770
14,NAPOLEONB_DRAFT_70,9736
14,NAPOLEONB_DRAFT_72,9734
14,NAPOLEONB_DRAFT_73,24174
14,NAPOLEONB_DRAFT_74,19891
14,NAPOLEONB_DRAFT_75,12457
14,NAPOLEONB_DRAFT_76,8135
14,NAPOLEONB_DRAFT_79,18042
14,NAPOLEONB_DRAFT_83,18383
14,NAPOLEONB_DRAFT_84,23835
14,NAPOLEONB_DRAFT_85,11536
14,NAPOLEONB_DRAFT_86,9686
14,NAPOLEONB_DRAFT_91,2726
14,NAPOLEONB_DRAFT_92,23725
14,NAPOLEONB_DRAFT_93,6962
15,NAPOLEONB_DRAFT_1,23265
15,NAPOLEONB_DRAFT_25,10017
15,NAPOLEONB_DRAFT_37,3102
15,NAPOLEONB_DRAFT_39,14856
16,NAPOLEONB_DRAFT_26,25449
17,NAPOLEONB_DRAFT_87,21252
19,NAPOLEONB_DRAFT_10,1045
20,NAPOLEONB_DRAFT_11,17557
21,NAPOLEONB_DRAFT_53,15168
21,NAPOLEONB_DRAFT_69,24820
23,NAPOLEONB_DRAFT_95,24540
24,NAPOLEONB_DRAFT_56,24917
32,NAPOLEONB_DRAFT_54,12742
36,NAPOLEONB_DRAFT_13,9387
37,NAPOLEONB_DRAFT_58,8182
38,NAPOLEONB_DRAFT_24,19229
38,NAPOLEONB_DRAFT_38,24858
41,NAPOLEONB_DRAFT_23,1881
46,NAPOLEONB_DRAFT_42,15962
46,NAPOLEONB_DRAFT_77,9657
47,NAPOLEONB_DRAFT_71,9303
56,NAPOLEONB_DRAFT_97,17850
62,NAPOLEONB_DRAFT_8,15225
83,NAPOLEONB_DRAFT_3,13517
84,NAPOLEONB_DRAFT_12,943
84,NAPOLEONB_DRAFT_2,2026
84,NAPOLEONB_DRAFT_44,24949
85,NAPOLEONB_DRAFT_100,24878
85,NAPOLEONB_DRAFT_15,12693
85,NAPOLEONB_DRAFT_19,21786
85,NAPOLEONB_DRAFT_20,17763
85,NAPOLEONB_DRAFT_5,4824
85,NAPOLEONB_DRAFT_61,19831
85,NAPOLEONB_DRAFT_62,19129
85,NAPOLEONB_DRAFT_7,9738
85,NAPOLEONB_DRAFT_81,24076
85,NAPOLEONB_DRAFT_9,16027
85,NAPOLEONB_DRAFT_98,20968
85,NAPOLEONB_DRAFT_99,1026
114,NAPOLEONB_DRAFT_14,4461
114,NAPOLEONB_DRAFT_16,4461

Next Steps:

Begin individual project

1. In the 1940s, Winston Churchill, Josef Stalin, and Franklin Delano Roosevelt agreed to introduce antibiotics to the USSR in order to generate more antibiotic production sites during the war. Because this was funded by other countries, it worked temporarily. After the war, however, the USSR had to rely on their own resources to fund antibiotic production and the state funding system was no help to this. The state’s priorities very much played a role in medicine in the following years. The political climate at the time prompted the Russian state to direct their priorities to weapon manufacturing and pushed medicine aside. This resulted in insufficient supplies of antibiotics in hospitals which were in high demand once the population caught word of the new medicine. To cope with this, the state manipulated the population by presenting antibiotics as foreign compared to the traditional natural remedies that were far cheaper. This set the stage perfectly for an increase in bacteriophage use.

2. Ludwik Hirszfeld and his family were some of the many Jewish Poles sent to a ghetto occupied by Russia. There, Ludwik had a medical background which he continued to exercise in the ghetto. He and his family were able to escape and survive with false documents, but his daughter fell ill and died, a tragedy that left Ludwik feeling very distraught about his life work and the political situation he had been forced into where his family could not even go by there real names. Ludwik then moved to Wroclaw and became dean of the medical school. At the time, the Stalin supported idea of Lysenkoism, that genes did not exist and acquired traits were inherited proved to be an obstacle for Ludwik who’s studies were based off genes. He feared for his own persecution until Stalin’s sudden death, which actually enable him to start his own institute. The institute then became a leading center for phage therapy. This is starkly different from the Elavia institute in which Russian politics also played a part. The Eliava institute had been widely successful across the soviet when antibiotics were too expensive and more traditional, cheaper medications were favored by the state. However, when the soviet disbanded, there was not enough cliental to sustain the institute and it fell apart. I think the differences in success exist because Eliava Institute was located in Russia which became very unstable after the war. Hirszfield was located in Poland and was able to receive support from European Union.

3. Merrils early experiments were hampered by the livers and spleens of the mice he was testing. Phages that he introduced into their systems were quickly rendered useless caught inside these organs. He hypothesized that this was the reason phage therapy had historically received poor scientific support. To breed more effective phages that could evade the liver and spleen he tested lamda phage on mice. Lamda phage was chosen because it was the most well known phage and had the most background information available. Lamda was inserted into the mice and then bacteriophages were harvested from the blood stream hours later. These harvested phages were reinjected into mice and the same process was repeated 8 times. In the end, Merril had a wild type phage that could avoid the liver and spleen with a survival rate 1000 times higher than the parent phage. The paper that Merril and his team published showed that over the course of 25 hours, the derived phages named argo1 and argo2 began at a higher concentration in the blood stream and decreased concentration at significantly slower rate. When different groups of mice were injected with the parent strand in comparison to argo1, both phages rid the mouse of disease when the control group resulted in death. The main difference was the effectiveness of the injection. Argo1 was more effective and the mice reached recovery sooner and had symptoms that did not go much past the 1 rating whereas the mice injected with the parent strand showed symptoms up to the 3 rating.

4. GangaGen is a startup company developing ectolysins or highly-specific therapeutic proteins to target bacteria. Their leading ectolysin, p128, is a derived from a phage and can rapidly degrade a bacteria’s cell wall with only making contact with the outside and not having to enter the cell. In order to effectively test p128 by FDA standards, the drug must be administered in three different phases, showing promising results from each one. It must be delivered alongside a control to measure progress, and also used at various concentrations to farther measure effect. It would probably work in GangaGen’s favor to attempt combination trials to see if results could reach an even higher level of effectiveness.

Rationale: Continue creating poster on powerpoint

Steps:

1. Joined groups with Copper, Josef, and Henry and added to the poster together

Result:

Final Draft of PowerPoint Poster

Next Steps:

Begin to create a poster as a class

Rationale: Begin creating poster on powerpoint

Steps:

1. Selected “create your own” 48 x 48 poster template from
   1. https://www.posterpresentations.com/free-poster-templates.html
2. Reconstructed layout and began to find the necessary information
3. Inserted information in a visually pleasing manner

Result:

Next Steps:

Continue to edit poster

Rationale: Start planning poster with small group

Process:

After going over over posters as a class, created a quick sketch of poster design and color scheme.

Result:

The rough layout for mine and Lucy F’s poster.

The color scheme brainstorm for our poster.

Next Steps:

Begin creating poster on powerpoint

Rationale: Visually review fully annotated genomes and double check start codons

Process:

The class went through the entire genome and looked at genes that seemed off – for example having too large gaps, too much overlap, or not the longest ORF.

Result:

Several gene start codons were corrected.

Next Steps:

Refine abstract and begin poster.

Rationale: Check annotations and answer Lathan’s questions as well as construct abstracts.

Process:

Within groups, we double checked our annotations according to Lathan’s suggestions.

We then worked on constructing an abstract within out group.

Result:

My group changed a start codon of one of the genes and submitted an abstract.

Next Steps:

Refine abstract and begin poster.

The Forgotten Cure Part 1

In the first 4 chapters of The Forgotten Cure we learn about the early discoveries of phage, phage therapy, and phage biology.  Blog about which ideas or observations presented in the first 4 chapters surprised or shocked you concerning the process of scientific discovery? You may use these examples or comment on your own ideas.

• Describe the role that locusts, dysentery and war had in the discovery of bacteriophage.
  • d’Herelle was studying sick locusts and by chance, also discovered bacteriophages in the form of clear circles on plates streaked with bacterial cultures. When WWI started  not long after, there was a pressing need for medicine to treat bacterial diseases such as dysentery. d’Herelle was tasked with analyzing dysentery outbreaks and begin examining stool samples. Again he witnessed the same clear spots on agar streaked with samples of recovering patients and this launched him into hos study of bacteriophages.

• Discuss the characteristics of d’Herelle that led him to be a successful scientist. How did he compare to Georgi Eliava?  What happened to the Eliava’s?
  • d’Herelle was a stubborn, self-educated scientist who was known for being “self-confident, idealistic, outspoken and unafraid of controversy”. These personality traits helped phage therapy gain popular attention worldwide, but not in the scientific community. Georgia Eliava shared a similar privileged upbringing and was able to go to med school. Unlike d’Herelle, Eliava was charming and polished. d’Herelle became a mentor and friend to Eliava and the together they pushed the limits of phage therapy research. Eliava was later arrested and shot to death in the Republic of Georgia where he maintained a risky foreign and aristocrat status in a communist society paranoid of losing power to rebellion and resorting to using fear methods to control the population.

• Discuss the influence war and politics had on the spread of phage therapy.
  • War provided a dire need for treatment against bacterial disease- both in troops and recovering countries. In the case of the Republic of Georgia, the soviet was far behind the leading countries in medicine and science and desperately wanted to catch up. This provided a perfect opportunity for Eliava and d’Herelle to gain support and funding to further study and advance phage therapy.

• What are some of the reasons that the spread of phage therapy failed?
  • One of the main reasons phage therapy fizzled out was the lack of sound scientific testing. Scientists and physicians needed to produce double-bind tests with control groups to effectively demonstrate the capacities of phage therapy. However, it was difficult for doctors to leave out a control group when they wanted to an administer a promising drug to everyone who needed it. Other studies used multiple methods for treatment, leaving it unclear how much part of the recovery phage therapy held. Overall, there were too many conflicting reports on the topic and when antibiotics emerged, it quickly stole the spotlight from phage therapy.

• How did the physicists Delbruck and Luria end up as part of the Phage Group? What contributions did they make to phage biology?  Why did phage biology die out in the 70’s?
  • Delbruck and Luria were both intrigued by the applications of physics in biology. Delbruck began by studying the effects of X-rays on DNA and published a paper that eventually reached Luria. Delbruck’s paper suggested that genes were tangible molecules and the “ultimate units of life”. Luria decided that the bacteriophage, the smallest presumably living thing would be the perfect specimen to test this on. After the two met at a conference, they shared ideas and began to work together. Together they founded a school to attract great scientists to study phage biology. It was the collaboration of this group that lead to the observation of the phage’s tadpole like structure with a head and a tail, and the very important scientific realization that genetic material is housed in DNA, not protein. In the 70’s, phage biology came to an end as antibiotics began to emerge. The phage group were more interested in studying phage to further understand DNA and not as a treatment for bacterial disease. With much stronger literary and scientific support for antibiotics on the rise, phage biology began to die out.

Rationale: Continue annotating assigned genes of NapoleonB

Process: Used DNA Master, GeneMark, NCBi Blast, NCBi cd, phagesdb, and HHPRED to annotate gene 82-84 of NapoleonB

• changed the start codon of gene 83 to include more coding potential
• no evidence of any function for all three genes

Result:

Gene 82:

SSC:48102 – 48746, CP:Yes, SCS:Both, ST:SS, BLAST-Start:Aligns with Arthrobacter phage KeaneyLin gp77 NCBI BLAST q1:s1 0.99 2E-145, Aligns with Arthobacter Phage KeaneyLin gp77 PhagesDB BLAST q1:s1 0.96 1E-114, Gap:27bp gap, LO:Yes, RBS:Kibbler7 and Karlin Medium 3.263 -2.348 Yes, F:NKF, SIF-BLAST:NKF, SIF-HHPred:NKF, SIF-Syn:NKF

Gene 83:

SSC:48743 – 48818, CP:Yes, SCS:BothGM, ST:SS, BLAST-Start:Aligns with Arhtrobacter Phage Circum gp82 NCBI BLAST q1:s1 0.76 1E-32, Aligns with Arhtobacter Phage Circum gp82 PhagesDB BLAST q1:s1 76%% 2E-28, Gap:4bp overlap, LO:NA, RBS:Kibbler7 and Karlin Medium 2.188 -4.267 Yes, F:NKF, SIF-BLAST:NKF, SIF-HHPred:NKF, SIF-Syn:NKF

Gene 84:

SSC:49015 – 49233, CP:Yes, SCS:Both, ST:SS, BLAST-Start:Aligns with Arthrobacter phage Cheesy gp84 NCBI BLAST q1:s1 0.98 4E-45, Aligns with Arthrobacter Phage Cheesy gp84 PhagesDB BLAST q1:s1 0.98 3E-36, Gap:65bp gap, LO:, RBS:Kibbler7 and Karlin Medium 1.98 -4.847 No, F:NKF, SIF-BLAST:NKF Supported by NCBI BLAST gp , NKF Supported by PhagesDB BLAST gp , , SIF-HHPred:NKF, SIF-Syn:NKF, upstream gene is , downstream gene is , just like in phage

Next Steps: continue annotating NapoleonB genes

Rationale: Begin annotating assigned genes of NapoleonB

Process: Used DNA Master, GeneMark, NCBi Blast, NCBi cd, phagesdb, and HHPRED to annotate gene 81 of NapoleonB

• covered all of coding potential and more so I did not change the start codon
• had an overlap of 6bp
• evidence that gene 81 could code for a helicase

Result:

SSC:46764 – 48074, CP:Yes, SCS:Both, ST:SS, BLAST-Start:Aligns with Arthrobacter Phage Circum gp80 NCBI BLAST q1:s1 0.99 0, Aligns with Arthrobacter Phage Circum gp80 PhagesDB BLAST q1:s1 0.99 0, Gap:6bp overlap, LO:NA, RBS:Kibbler7 and Karlin Medium 1.808 -5.07 No, F:Helicase, SIF-BLAST:ATP-dependent helicase Supported by NCBI BLAST Arthrobacter Phage Circum gp80 ALY08763.1 0.99 0, ATP-dependent helicase Supported by PhagesDB BLAST Circum gp80 KU160642 0.98 0, , SIF-HHPred:Predicted DNA helicase supported by KOG gpNA KOG1016 0.3166 , SIF-Syn:NKF

Next Steps: continue annotating NapoleonB genes 82-84