February 17

The Forgotten Cure (Chapters 1-4)

  1. D’Herelle had took samples from patients from the war who suffered from dysentery, took the bacteria cultures and tested them out onto agar plates. He noticed that there were clear spots on the plate not just from dysentery patients, but also from locusts. He later made a filtrate, a test tube containing bacterial cells from his samples. During these experiments he saw that the dysentery bacteria “dissolved like sugar in water.” He later found out that there could be something that can infect bacteria. He also used this discovery to prove that his dysentery patient can recovered from it, which one patient did in fact, led to a wide discovery and a hunt for more bacteriophages from different places in the world.
  2. D’Herelle and Eliava were both hard workers that laid their foundation for the future bacteriophage institute. The co workers said that D’Herelle was very hard working and would always arrive on time each day. They said that he was a “virtuoso” and insisted on doing everything with his own hands. This shows that he is very diligent in his work and is a perfectionist. Eliava was hardworking like D’Herelle in terms of the research. Sadly Eliva and his wife supported the wrong side of the Russians and were eventually executed.
  3. War encourage the hunt for bacteriophages because many of the soldiers suffered from diseases and plaque spread among the people. Soldiers are needed to continue the war and the government needed a strong army, a cure is needed. Since the discovery of bacteriophages and its effects on bacteria cells, phage therapy was created for treatments. Politics had its pros and cons about phage therapy. In Elivas’ casem he used politics to help fund research, but also got him executed.
  4. Antibiotics came around and eventually won favor over bacteriophages. Due to new technology and research, everyone started to use more antibiotics than phage therapy.
  5. Delbruck and Luria worked on x-ray crystallography which lead to their interest in bacteriophages. They later joined Phage group. They also discovered the replication mechanism and the structure of phages with other members. The group members’ interest in phages started to fade away as they wanted to examine larger organisms. Therefore, the phage biology started to die out.
Category: Soo-Un Jeong | LEAVE A COMMENT
February 17

The Forgotten Cure: Chapters 1-4

The Forgotten Cure was a fascinating book that introduced topics and background to discoveries that I had not known to exist. World War I was consuming the countries, as many families had loved ones who were being put in unsanitary and unsafe conditions throughout the years. Dysentery had begun to impact many involved in the war, leading to a greater need for a cure to be found. The book revealed that the outbreak of dysentery caused by close quarters and a lifestyle susceptible to the transmitting of diseases allowed for the breakthrough to be made on bacteriophage discovery. Felix d’Herelle had previously seen “plaques” in his own experiments concerning locusts; however, when he began researching dysentery, the presence of plaques occurred again. d’Herelle began to realize the importance of his discovery when it was observed that phage presence in the body began to cure the effects of dysentery. This allowed for the world to turn an eye to the presence and discovery of the bacteriophages.

It was evident that d’Herelle possessed a thirst for knowledge and a passion for the sciences, rather than using it was a means for a career. He took up an unpaid position at a point in his life because he enjoyed the field, which showed that he was not swayed by other motives. d’Herelle displayed dedication and drive for his passions, which was evident in his works. Georgy Eliava was also a scientist that expressed drive and hard work for what he was passionate about. Eliava seemed to conduct himself in a more outgoing manner than d’Herelle however. The Elivia’s ultimately faced death due to the regime of the Soviet Union.

War and politics ultimately played a large role in the spread of phage therapy. War dramatically increased the number of diseases and problems present in the world. With the increase of problems came an increase in the need for a solution in troubling times. The discovery of bacteriophages and phage therapy during the time period allowed for their application and presence on the minds of others. War increased the use and demand for phage therapy to combat the problems being presented. However, while the presence of phage therapy was spread, little was done to advance the knowledge on the topic. Politics during the time period was very tense in all aspects. Many different countries and sides wanted an edge on the newest innovation and technology. I would imagine that scientific phage research was another aspect that many countries were trying to grasp and understand in order to not be behind in the race to discovery.

In my opinion, a major contributor as to why the spread of phage therapy failed was the lack of understanding of the topic. Its presence was known, as well as its potential uses, however, it is not nearly to the extent that it is today. Due to a large number of unknowns, alternatives to phage therapy were used instead to attempt to combat the diseases present, such as the use of antibiotics. While there were some means of spreading new knowledge about phage therapy, there was also a lack of media present during the time. In the present day, new scientific discoveries are extremely accessible to anyone who so chooses to find it. Back during that era, it was significantly harder to communicate and spread knowledge on the topic.

Delbruck’s and Luria’s work and collaboration enabled them to be introduced to the world. While searching for organisms to research, the two physicists came across bacteriophages and became integrated into the Phage Group. The pair, along with the collaborations with Hershey, won a Nobel Prize for their work. They became known for their strides in bacteriophage mutations and their genetic structure. Phage biology began to die out due to the lack of work being conducted on the subject. Delbruck and Luria ultimately moved on from their work on phages and other scientists devoted their time elsewhere.

Category: Emily Gaw | LEAVE A COMMENT
February 17

The Forgotten Cure: Chapters 1-4

The Forgotten Cure: Chapters 1-4

Describe the role that locusts, dysentery and war had in the discovery of bacteriophage.

Locusts, dysentery, and war played a unique role in the discovery of bacteriophage. During World War I, troops struggled as dysentery plagued their ranks as they lived in incredibly tight quarters with shared space, food, and water. This created a sense of desperation surrounding the situation of dysentery, as troops were suffering major losses and were unable to perform at their peak capacity. Felix d’Herelle, a microbiologist of the time, was working with bacteria cultures when he noticed strange clearings that appeared “randomly” on the plates. Upon further investigation, d’Herelle developed methods to consistently obtain these clearings and he concluded that there was a specimen so small that could be considered invisible that was infecting the bacteria and killing them. When he proved that this specimen was capable of curing individuals rather rapidly of dysentery, the discovery was lauded and the new specimen gained immense popularity, which led to many more people becoming interested and studying bacteriophage.

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?

Felix d’Herelle consistently displayed that he was devoted to the field of science above all else. This dedication allowed him to gain experience in a variety of ways, such as d’Herelle taking an unpaid position at a prestigious scientific organization. His curiosity and drive to learn provided a large basis of his skills that made him a successful scientist. Furthermore, d’Herelle was also very confident and extraordinarily particular about how his lab work was performed. These qualities made for a scientist who was suited for publishing new concepts, as his confidence allowed him to display resilience even when critical articles or other roadblocks were in his way. Georgi Eliava was similar to d’Herelle in regard to their upbringing and interests, but was different in their mannerisms. Both shared very privileged upbringings, which provided the initial resources to explore science and develop interests in such fields. These interests were very strong in both of their lives, and it led to their bond as scientists who worked passionately in the same field. Their mannerisms were described to be very different, as Eliava was said to be smooth, with pomaded hair and a way with women whereas d’Herelle was said to be particular and very serious. Eventually, the Eliava’s met their demise at the hands of the Russian regime, as Eliava fell on the wrong side of a Russian political leader, which led to his imprisonment and execution.

Discuss the influence war and politics had on the spread of phage therapy.

War had a very important influence on the spread of phage therapy. Due to the magnitude of the diseases that occurred, an effective and sustainable solution was needed to cure the troops of the disorders that they encountered. This led to the birth of phage therapy, and also the development as the technologies were refined as they were put into practice. Politics had an arguably more influential effect on the spread of phage therapy. Joseph Stalin felt that the Russians were far behind the rest of the developed nations in terms of science and technology – he estimated that they had fallen behind between fifty and one hundred years, and if they were not to make up that difference in the next ten years, they would be rather permanently at a disadvantage. This led to Stalin looking favorably upon the establishment of a phage institute in Georgia, which was established and run by Georgi Eliava. As resources were funneled into this field, more and more discoveries were made that enhanced the understanding of bacteriophages and furthered them as a possible treatment.

What are some of the reasons that the spread of phage therapy failed?

Two reasons why the spread of phage therapy ultimately failed were the development of other technologies and a low level of comprehension. As the technology spread to the Western world, other technologies would be developed each time a swell of interest in phage therapy would occur. The development of sulfa drugs and penicillins both were considered to be more important and effective methods to treat bacterial infection despite evidence that both, especially penicillins, could result in antibiotic-resistant bacterial strains. While even phages share this problem (CRISPR-Cas9 bacterial defense system), they are more adaptable and present a lower risk due to their specificity. Despite this, the western world prioritized alternative methods of treating bacterial infections. Therefore, resources were not placed into phage research, which stunted its development. Alternatively, a lack of understanding of bacteriophages resulted in a halt of their spread. A series of unfavorable reviews from JAMA (Journal of American Medical Association), described phages as enzymes and proteins, which clearly is not the case. It also suggested that they had limited effectiveness in treating conditions. Moreover, studies about phages were conducted rather haphazardly, as scientists eager to save each patient lacked control groups in their study, which compromised the results that displayed encouraging feedback. Therefore, poor levels of understanding along with the development of other technologies and interests led to the deterioration of the spread of 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 joined the Phage Group in somewhat of a roundabout way. As a physicist, he attended a presentation where it was suggested that life was so complex that learning all of the intricacies would be nearly impossible. This challenge was interesting to him, and the idea that there may be a few laws that could govern all life motivated him to find a way to study biology. This led him to the radiation experiment on fruit fly genes, which mutated them and allowed Delbruck and the group studying the flies to conclude that genes are the basic unit of life – a belief held to this day. The knowledge of this experiment interested Luria, and he also became interested in biology. As Delbruck and Luria were looking for a new organism to examine the genome of, they turned to phages and ended up joining the Phage Group. Through this group and a series of experiments featuring Hershey (Hershey and Chase experiment), they studied the mechanism of bacteriophages and learned much more about their structure. However, after they had learned so much about phages, their interest was whittled down to seven specific types of bacteriophage, and then later it was changed to the examination of other organisms. Therefore, the examination of bacteriophages fell away from the forefront of science, and phage biology began to die out in the 70s.

Other Note:

The culture of the Phage Group sounded very fun and exciting. It sounded like the ideal summer camp – working hard to learn science during the day and enjoying swimming and play reenactments later at night! It would be fun to have a summer opportunity like this at Baylor, with a phage study group over the summer with a cohort similar to the one selected for BEARS in the SEA.

Category: Henry Burns | LEAVE A COMMENT
February 17

The Forgotten Cure Discussion Questions Chapters 1-4

  1. Describe the role that locusts, dysentery and war had in the discovery of bacteriophage.
    1. Felix d’Herelle, while working with how to control locusts with bacteria discovered what we now call plaques in the bacterial lawn of the locust killing bacteria he was investigating. Dysentery was what led d’Herelle to find the importance of these, at that point, unknown phages, as he observed patients rapidly cured of dysentery as a result of phage presence in their body. Subsequently because of the war dysentery was rampant amongst troops as were other diseases prompting governments to pump money and effort into researching the use of phages in fighting disease. Especially in the USSR were a significant effort was made in this regard, allowing Eliava to further study and research bacteriophages.
  2. 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?
    1. Felix d’Herelle was a successful scientist as a result of his curiosity, passion, hard work, and his unwillingness to conform to the accepted thought of the day. All of these things allowed d’Herelle to succeed in making discoveries and promising developments about bacteriophages. Eliava was similar in regards to the characteristics of d’Herelle which made him just as an impactful scientist in the USSR as well as a leader in the bringing of medical treatments to Georgia. Unfortunately, Eliava and his wife were executed as a result of the Great Purge.
  3. Discuss the influence war and politics had on the spread of phage therapy.
    1. With war, it encouraged the spread and development of phage therapy, as war and the many diseases it brought made governments desperate enough to look into and support any potentially promising treatment method, including phages. Politics, on the other hand, had both positive and negative impacts on the spread of phage therapy, as in Russia under Eliava he used political means to secure funding for his phage institute but it was also politics that got him killed in the purges.
  4. What are some of the reasons that the spread of phage therapy failed?
    1. The advent of antibiotics was a major reason phages failed to pick up as they were easily seen as successful far more often than phages, as well as more effective in the types of bacteria they could kill. This coupled with the fact that phages were hyped up to an extensive amount yet never amounted to the expectations set forth also led to scientists, governments, and the general public to all but abandon phages in favor of antibiotics.
  5. 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?
    1. They ended up as a part of Phage Group as a result of their work in x-ray crystallography which subsequently led them to become interested in phages. They ended up discovering the replication mechanism and genetic structure of bacteriophages along with Hershey, which the three of them received the Nobel prize for. However, the group’s members were ultimately more concerned with how higher organisms reproduced, resulting in the work on phages to die out.
Category: Nathan Newton, Uncategorized | LEAVE A COMMENT
February 17

The Forgotten Cure Post 1

In the first four chapters of Anna Kuchment’s The Forgotten Cure, the presented bacteriophage history offers two interesting themes relating to the process of scientific discovery. First, anybody who is passionate enough can participate in research, and second, society and politics will influence the science community’s views of what receives priority in publication.

Cited as the father of bacteriophages, Félix d’Herelle did not have the benefit of a college education. His discovery resulted from his intuition and curiosity. D’Herelle teaches himself and seeks after an unpaid research position. Through his careful observations of locust and stool samples while working as an unpaid assistant, his curiosity drove him to hypothesize why the phenomenon of plaques forming occurred. His desire to answer his hypothesis led him through trial and error in the lab. This resulted in his phage discovery and the development of phage therapy to cure dysentery patients. His curiosity caused him to continue to make effective therapies for Bubonic plague and cholera. Another bacteriophage researcher, Georgi Eliava shared d’Herelle’s same passion. He too observed the plaque-appearing phenomenon and which sparked his curiosity. Unlike d’Herelle, politics had a stronger influence on Eliava’s work. Eliava received government support through funding and expensive science instruments under Lenin. However, Eliava’s work came to an abrupt halt as Stalin’s xenophobia caused the deaths of many Soviet intellects.

One reason why most research goes unacknowledged by the scientific community is that the research is not published. If a scientist does not publish their work, they might as well never have conducted it. Authors such as Sinclair Lewis and Paul de Kruif reeducated the public about the realities of research institutions and practicing physicians. Researchers will rush to publish experiments that were not complete to beat their rivals to receive credit.  D’Herelle’s published work received bad publicity which greatly impacted the spread of phage therapy. As others tried or rush their experiments, they made published papers which argued against his findings. World War II made the scientific community made the military’s needs a priority. Since Fleming’s penicillin seemed more promising and negatively publicity left phage therapy’s effectiveness in question, many physicians turned to antibiotics for treatments.

In conclusion, it surprising what d’Herelle accomplished without a degree. The critical role of publication and the powerful influence of politics on the scientific community is also shocking.

Category: Kathryn Adkins | LEAVE A COMMENT
February 16

The Forgotten Cure Chapters 1-4

  1. Describe the role that locusts, dysentery, and war had in the discovery of bacteriophage.
    1. D’ Herelle was a scientist that was tasked with working with sickened locusts. By chance, when he was making bacterial assays from the locusts, he noticed that some of the spots had been cleared out on the plate. D’ Herelle named them “taches vierges.” He repeated the same procedure of making plaque assays and kept getting the same, cleared out circles on his plaque assays. He couldn’t replicate it anywhere else and essentially just left it alone until World War I when commercial vaccines started blossoming. French troops came down with a massive case of dysentery, and D’Herelle was assigned to analyzing their stool samples. It was then that he saw the clear spots on the bacterial assays again. He had proof that the clear spots appeared in more than one strain of bacteria, and that the spots only appeared in patients that were getting better from their disease. This led him to the belief that the clear spots were indicative of bacterial death
  2.  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?
    1. D’Herelle was a successful scientist due to his perseverance and passion for his newly discovered “taches vierges” and devoted his studies to understanding what could come out of it, rather than becoming frustrated and disregarding the practice completely. D’Herelle also used his discoveries for good, doing his best to make sure the public could benefit from his early form of gene therapy. Like D’Herelle, Eliava carried the same demeanor and attitude regarding phage therapy. They both were in the same headspace, with similar goals for phage therapy development. The Eliava’s were targeted because of their high profile and pre-Revolution education. The family was put into camps and eventually suppressed in order to fulfill the Soviet Socialist agenda of the time.
  3. Discuss the influence war and politics had on the spread of phage therapy.
    1. Much like the previous response, a political revolution had broken out in Eastern Europe along with a Civil War in Spain, which thickened the plot for Stalin. Personal affairs and politics got in the way of Eliava’s work during the war and caused the relationship between D’Herelle and Eliava to fade. D’Herelle started getting older and was settling down in Paris, beginning to wean himself off of his advocacy for the spread of phage therapy. The combination of the deteriorating relationship and the end of D’Herelle’s career marked the deterioration of the phage therapy revolution.
  4. What are some of the reasons that the spread of phage therapy failed?
    1. Along with politics and war, there were many other reasons why the spread of phage therapy fell short. For example, much of the research done on phages was flawed and conducted in an inconclusive manner, meaning no meaningful conclusions could be drawn. There was also a lot of misunderstanding and ambiguity as to what a bacteriophage was, many people believed it was some sort of enzyme that broke bacteria down. Obviously, this wasn’t the case, but the misunderstanding definitely led to confusion. Lastly, synthetic drugs started to make a rise in the scientific community, leading to a drought in scientific articles regarding phage therapy.
  5. 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?
    1. Delbruck, then a physicist, was interested in the way scientists observe organisms, and how technically an organism cannot be observed without modification. He collaborated with another group of scientists interested in genes and radioactive effects enacted on them by x-rays. They were published in an obscure journal but barely discovered by Schrodinger. Their bride between biology in physics took off from there, especially as Delbruck became more interested in biophysics as a result. In Rome, Luria decided his interest in physics was mostly “amateurish” and wished for something more, so he endeavored in biophysics, coming across Delbruck’s paper. He decided to try and test Delbruck’s ideas on genes and discovered bacteriophages. They both decided to devote their studies to bacteriophages and met at a convention. During their meetings, they established a loosely organized group called the Phage Group that was comprised of scientists of many different specialties. Their collaboration helped drive the spirit behind the group that eventually made progress in the bacteriophage world to the point where Luria, Delbruck, and Hershey won a joint Nobel Prize for their efforts and discoveries. Consequently, the Phage Groups discoveries raised doubts that bacteriophages could truly conquer bacteria. Due to this discovery, the research and new discoveries on phages hit a low and started slowing down. The scientists also started shifting their focus to other fields and more complex organisms.
Category: Cooper Johnson | LEAVE A COMMENT
February 15

Annotation of NapoleonB Genes 11 and 12

2/15/19

Rational:

To annotate genes 11 and 12 for NapoleonB and enter them in PhageNotes

Procedure:

  • Dowloaded the fastA and auto-annotated NapoleonB
  • Entered the gene call after genes 11, 12 and 98 in the home tab for PhageNotes
  • Opened the genemark for NapleonB
  • Checked to see if the coding potential was covered by the current start and that it was the ongest ORF
  • Entered the start and stop codon
  • Entered who the start was call and chosen by
  • Checked phagesdb to see whether the gene’s start matches with the most called start (starterator)
  • BLASTed genes 11 and 12 through NBCI and Phagesdb
  • Ran the genes through HHpred
  • Entered the required information for the NBCI and phagesdb hit in PhageNotes
  • Calculated the gap/overlap for the gene and its upstream gene
  • Selected the gene to get the information needed for RBS
  • Entered the information for the hits in NBCI (BLAST and CDD), Phagesdb, and HHpred for the function
  • BLASTed the surrounding genes and looked at Phamarator to look for for SIF-Syn

Observations:

  • The genemark showed that the current start does not cover the coding potential for gene 11, but it is the LORF
  • The coding potential is covered for gene 12 and it was the LORF
  • Both genes were LORF
  • Gene 12 had a gap of more than 10 bp
  • Genes 11 and 12 both agreed with the starterator
  • For gene 11 the NBCI hit was Arcadia and phagesdb was Xenomorph
  • For gene 12 the NBCI hit was Arcadia and phagesdb was Xenomorph
  • Gene 11 had a overlap of 17 and gene 12 had an gap of 19
  • For both genes the SD score for the chosen start was not the best
  • The funtion for genes 11 and 12 is capsid maturation protease, however this was only supported by the NBCI BLAST for both genes

Fig.3 – The teal block shows gene 11 and the yellow and green blocks representing genes 10 and 12 for the phage KeanyLin do not show signs of synteny as they do not match the function of the genes 10 and 12 in NapoleonB.

Conclusion:
The genes 11 and 12 were finished and their function was found to likely be a a capsid maturation protease for both. Note the only source that supported this was the NBCI BLAST the Phagesdb, Phamerator, and HHpred did not. Next lab I will finish the annotation of  98 and help check any mistakes made.

 

Category: Emily Balint | LEAVE A COMMENT
February 15

2-13-19 — Consolidation of Annotations to PhageNotes

Consolidation of Annotations to PhageNotes

Date: 2-13-19

  • Rational
    • The rational for this lab is to consolidate all annotations into one google sheet for analysis.
  • Procedure
    • The notes section for genes 53-56 in DNAMaster were copied to the class PhageNotes google sheet.
  • Results
    • Annotations for every gene in phage NapoleonB are in one central document.
  • Future Plans
    • The next step is to check the annotated genes and analyze them further.
Category: Brandon Reider | LEAVE A COMMENT
February 15

2-11-19 Annotation of Phage NapoleonB Genes 53-56

Annotation of Phage NapoleonB Genes 53-56

Date: 2-11-19

  • Rational
    • The rational for this lab was to begin annotation of phage NapoleonB, starting with genes 53, 54, 55, 56.
  • Procedure
    1. DNA Master was opened.
    2. File > Open > Archived DNA Master File was used to open the NapoleonB FastA file from PhagesDB.
    3.  Gene 53 was selected through the listing of predicted genes, and the Product was copied.
    4. The amino acid sequence was loaded into the BLASTp feature on the NCBI website and the BLAST results were analyzed and recorded on the PhageNotes google sheet.
    5. The amino acid sequence was loaded into HHPRED, a program that evaluated the three-dimensional protein structure of the gene region and the results were analyzed and recorded.
    6. The starterator map on PhagesDB was evaluated by choosing gene 53 from the NapoleonB gene list and the information was recorded.
    7. Steps 3-6 were repeated for genes 54-56.
    8. Ctrl + Alt + F brought up the Frames of the genome, ORFS was selected to show the locate open reading frames, and RBS was selected to determine the ribosome binding site for the each gene.
    9. Genemark was used in order to determine if coding potential was covered.
    10. Using the acquired information, the 53rd-56th genes were annotated.
  • Results
    • The following annotations were made for gene 53:
      • Original GeneMark call @bp 33165
        SSC: 33165 – 33263, CP: Yes, SCS: Both, ST:SS, BLAST-Start: Aligns with Arthrobacter Phage Tribby gp53 NCBI BLAST q53:s1 1 5E-13, Aligns with Arthrobacter Phage Tribby gp53 PhagesDB BLAST q53:s1 1 1E-12, Gap: 4bp overlap, LO: Yes, RBS: Kibbler7 and Karlin Medium 3.263 -2.524 No, F: NKF, SIF-BLAST: NKF, SIF-HHPred: NKF, SIF-Syn: NKF

An image of the starterator report

An image of the RBS choices

An image of the PhagesDB BLAST results

An image of the NCBI BLAST results

An image of the HHPRED results

An image of the GeneMark results

  • The following annotations were made for gene 54:
    • Original Glimmer call @bp 33273 has strength 10.13
      SSC: 33273 – 33962, CP: Yes, SCS: Both, ST: SS, BLAST-Start: Aligns with Arthrobacter Phage Circum gp55 NCBI BLAST q54:s1 1 4E-167, Aligns with Arthrobacter Phage KeaneyLin gp52 PhagesDB BLAST q54:s2 1 1E-128, Gap: 9bp gap, LO: Yes, RBS: Kibbler7 and Karlin Medium 1.993 -4.759 No, F: NKF, SIF-BLAST: NKF, SIF-HHPred: NKF, SIF-Syn: NKF

An image of the starterator results

An image of the RBS choices

An image of the PhagesDB BLAST results

An image of the NCBI BLAST results

An image of the HHPRED results

Images of the GeneMark results

  • The following annotations were made for gene 55:
    • Original Glimmer call @bp 33955 has strength 0.38
      SSC: 33949 – 34173, CP: Yes, SCS: Both-CS, ST: SS, BLAST-Start: Aligns with Arthrobacter Phage Circum gp56 NCBI BLAST q55:s1 0.98 3E-44, Aligns with Arthrobacter Phage KeaneyLin gp53 PhagesDB BLAST q55:s2 0.98 7E-36, Gap: 14bp overlap, LO: No, RBS: Kibbler7 and Karlin Medium 1.391 -5.257 No, F: NKF, SIF-BLAST: NKF, SIF-HHPred: NKF, SIF-Syn: NKF

An image of the starterator results

An image of the RBS choices

An image of the PhagesDB BLAST results

An image of the NCBI BLAST results

An image of the HHPRED results

An image of the GeneMark results

  • The following annotations were made for gene 56:
    • Original Glimmer call @bp 34191 has strength 0.52
      SSC: 34191 – 34316, CP: Yes, SCS: Both, ST: SS, BLAST-Start: Aligns with Arthrobacter Phage Circum gp57 NCBI BLAST q56:s1 1 1E-20, Aligns with Arthrobacter Phage Circum gp57 PhagesDB BLAST q56:s3 1 2E-16, Gap: 17bp gap, LO: Yes, RBS: Kibbler7 and Karlin Medium 2.053 -5.205 No, F: NKF, SIF-BLAST: NKF, SIF-HHPred: NKF, SIF-Syn: NKF

An image of the starterator results

An image of the RBS choices

An image of the PhagesDB BLAST results

An image of the NCBI BLAST results

An image of the HHPRED results

An image of the GeneMark results

  • Conclusion
    • Phage NapoleonB has no known functions for genes 53-56.
  • Future Plans
    • The next step is to consolidate the gene annotations to the PhageNotes google sheet.
Category: Brandon Reider | LEAVE A COMMENT
February 15

FEBUARY 11TH AND 13TH- LABS

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 
Category: Lauren Foley | LEAVE A COMMENT