February 20

Reviewing Annotations and Group Abstract Writing 2/18/19

Reviewing Annotations and Group Abstract Writing 2/18/19

Rationale

The rationale behind these procedures is to ensure that all annotations on NapoleonB are correct and that abstracts are prepared for Scholar’s Day.

Tools/Procedure

  1. Several annotations were marked as potentially erroneous and were reexamined
  2. Genes were reexamined using:
    • NCBI was used to BLAST amino acid sequences against a large database of recorded sequences
    • Starterator and genemark were used to determine if the genes ought to be altered to include more or fewer base pairs
  3. The information gathered was used to verify the gene calls that were previously made
  4. Then in order to have an abstract prepared several lab members collaborated to create an abstract

Results

This image shows the unchanged gene 66 after it was reviewed

The abstract that was created by group collaboration is written below:

“Bacteriophage phage represent a widely diverse and understudied population of microorganisms. In order to further aid in the effort to understand the mechanics behind bacteriophages, the 2018-2019 Phage Hunter class of Baylor University isolated Arthrobacter phages from soil samples collected throughout Waco, Texas. The samples were washed and the resulting lysates were plated to test for phage presence. Phage presence was indicated by a series of plaque assays, spot tests, PCR and gel electrophoresis. Once phage presence was confirmed, the process of purification and amplification was used to achieve a high titer lysate which was then archived for DNA extraction. DNA was extracted from NapoleonB, sequenced, and late annotated using DNAMaster and other bioinformatics tools. In bench research, NapoleonB was found to constantly display two distinct plaque morphologies and appeared to be a Myoviridae in the AM phage cluster. In silico research revealed that NapoleonB contains a linear double-stranded DNA genome with approximately 97 genes composed of 57846 base pairs. Future research can be used to determine the exact mechanics behind NapoleonB’s many functions.”

Conclusion

There is not a lot of information from which to draw conclusions, but I am able to assert that gene 66 was called correctly.

Future Plans

In the future, I will use the annotations of NapoleonB to be able to research my own questions and hopefully add in someway to knowledge about phage.

February 20

DNA Day 9

18 February 2019 ✷ NapoleonB DNA Annotation Corrections + Abstracts

Rationale:  NapoleonB’s genes were assigned to each student to annotate and record in order to complete the genome annotation for the phage. Annotations for several genes were called into question by the TAs and group members double checked their annotations to ensure accuracy.

Procedure

  • DNA master was opened and NapoleonB was auto-annotated
  • PhageNotes was opened and each aspect of the DNA annotations for gene 23 was rechecked for the start codon. It was ultimately decided the start would not be moved because of the RBS scores and agreement with Starterator.
  • Abstracts for research performed last semester and this semester were crafted prior to lab and members of the group combined the best parts of each abstract into one strong one
  • Cooper’s abstract was used as the foundation for the group’s abstract, but the procedure from Kathryn’s was very strong and was included in the final draft. My introduction and final numerical values were included from my abstract, and Nathan’s procedure was also included.

Results

final annotation for gene 23:

 

 

 

 

 

 

The group’s abstract:

            ” Bacteriophages are a diverse, vast part of our biosphere that still have relatively little known about them. The 2018-2019 Baylor University SEA-PHAGES Cohort worked to isolate a collection of Arthrobacter phages and then annotated the genome of Arthrobacter phage NapoleonB. This study was conducted in order to discover and sequence a new bacteriophage. By collecting, purifying, and isolating the phage in a high-titer lysate, the fully sequenced genome of the phage was able to be annotated and analyzed. As a result of the annotations, completed on DNA Master, the annotations of NapoleonB showed 71 genes without a known function and 26 with a confirmed function. Among these 26, 7 genes suggested functions relating to tail proteins while 1 gene coded for holin, which makes NapoleonB the only phage in the AM cluster to have this gene. The genes that showed a function were supported by NCBI BLASTp, HHPred, and synteny from the Phamerator AM cluster phages and known phams. The unknown genes either showed ambiguous results or no significant results from an NCBI or PhagesDB BLAST, while the called genes showed evidence of basic bacteriophage functional proteins. The results of this sequencing and annotating suggest that while many different species, types, and clusters of bacteriophages have been discovered and analyzed thoroughly, there is much more to be discovered. However, the annotation of NapoleonB provides useful evidence that improves the general understanding of bacteriophages.”

Conclusion

Many of the genes annotated were no known function or tail proteins, so the study of the phage is largely centered around that.

Future plans

The annotation of NapoleonB’s genome will be completed, checked, and submitted to phagesdb. The information gathered from the annotation of the genome will lead to the creation of a research question and thus further research into phage biology involving NapoleonB.

February 20

2.18.19 NapoleonB Annotation Checking & Abstracts

2.18.19 NapoleonB Annotation Checking & Abstracts

Rationale: Since the genome annotations were completed for NapoleonB, it was possible to check the annotations that had been done. Therefore, it was pertinent to do so to ensure that no incomplete or inaccurate information was being placed in the database. Furthermore, abstracts were also presented to the group to begin to finalize the submission to the Scholar’s Week conference.

Tools/Procedure:

  • DNA Master
  • HHPred
  • PhageNotes
  • NCBI Blast
  • PhagesDB Blast

In the lab, genes that were listed to have questionable calls were checked over. For my group, genes 50, 1, and 2 were examined. A new gene was added and confirmed with Lathan. After these calls had been made, the abstracts were edited and submitted for the group rather than individually.

Results:

Gene 50 was determined to have been called correctly. Genes 1 & 2 had a large gap which was examined and eventually determined that there was supposed to be a reverse gene to account for the large gap. This gene’s annotation is found below. Apart from these two calls, the genes appeared to have been done correctly.

SSC:372 – 569, CP:No No coding potential was present, SCS:Neither, ST:NA, BLAST-Start:Aligns with circum gp2 NCBI BLAST q1:s1 100 2E-41, Aligns with Tribby gp2 PhagesDB BLAST q1:s1 1 6E-35, Gap:first gene, LO:Yes, RBS:Kibbler7 and Karlin Medium 3.263 -2.059 Yes, F:NKF, SIF-BLAST:NKF, SIF-HHPred:NKF, SIF-Syn:NKF

Conclusions:

Since the genome was checked in part by everyone, it can be assumed that NapoleonB has been fully sequenced and is close to being ready to submit with annotations. The abstract was also successfully assembled, which means that the group is closer to developing Scholar’s Week work.

Next Steps: Scholar’s Week work will be continued and abstracts/posters will continue to be developed throughout the week.

February 20

2.18.19 Annotation Proofing and Abstract Editing

Rationale:

To check the annotation of the phage NapoleonB and to edit/create an abstract for our assigned group.

Procedure:

  1. Using an already auto annotated version of NapoleonB on DNA Master and the NapoleonB phage notes, gene 18 was checked to ensure the LORF was correct.
  2. Using different elements from each of our own abstracts, a group abstract was compiled and submitted.

Results:

Gene 18 was verified as having the correct LORF. Our abstract included both Kathryn and Cooper’s abstracts as the basis for the structure, while elements of my material and methods and Lily’s introduction were also used.

Conclusions:

It can be concluded that the current annotation of gene 18 is correct and that our abstract matches up with the expectations set forth.

Next Steps:

The next step will be to continue working on a class abstract for our scholars week poster presentation and to begin working on our independent research project.

February 19

Annotation of NapoleonB gene 44 and Abstract

Rationale:

Corrected NapoleonB gene 44 and combined abstracts with other group members for a possible poster abstract.

Procedure:

Opened DNA Master and phage notes. Checked for errors in gene 44 with the help of Genemark, DNA Master, NCBI BLAST, PhageDB, HHpred, and phage notes. The start codon was changed and the product was placed into NCBI BLASTp to check for possible functions.

Results:

Conclusions:

Start codon pulled to 30372 and the product was checked in HHpred, NCBI BLASTp, and PhageDb to see the known function. Few sentences from my abstract were added into Brandon’s abstract, and grammatical errors were fixed as a group. Working in groups can be very beneficial since you will be able to see from multiple points of views, and also helps avoid confirmation bias.

Future Plans:

Start individual projects and designs for conferences.

February 19

NapoleonB Gene 26 and Abstracts (2/18/19)

Rationale:

Corrected NapoleonB gene 26 and combined abstracts from other group members for a possible poster abstract.

Tools:

  • DNA Master
  • NCBI
  • PhagesDB
  • GeneMark
  • HHpred
  • phage notes

Procedure:

  1. Opened DNA Master and phage notes.
  2. Checked for mistakes in NapoleonB gene 26 with GeneMark, “Choose ORF start” window in DNA Master, NCBI, PhagesDB, and HHpred.
  3. Corrected the start coordinates.

Results:

The picture below shows the corrected annotation for NapoleonB gene 26.

Conclusion:

The start coordinates were corrected to 24802 bp.  Cooper’s and Lily’s introductory sentences, Nathan’s methods part, and my results sections were combined into an abstract. Working in groups can be a great tool when brainstorming ideas for a presentation; however, groups are not as effective when it comes to writing. One interesting finding placed in the abstract was that NapoleonB is the only AM clustered phage to have a gene with the holin function.  This gene might be the reason why NapoleonB had an extremely high titer relatively fast.

Future Work:

Start individual research projects and design a poster to show at conferences.

February 18

February 18 2019 Checking Annotations and Abstracts

Purpose: The purpose of this lab is to check the annotations for NapoleonB and write abstracts for Scholars Week.

Tools/Procedures:

Tools:

  • DNA Master
  • NCBI
  • PhagesDB
  • HHpred
  • Phamerator

Procedures

  1. The gap between genes 1 and 2 for NapoleonB was analyzed and it was determined that a reverse gene should be inserted.
  2. Annotations for gene 1B were completed and added to PhageNotes.
  3. Annotations for other genes were checked and corrections were made if necessary.
  4. Abstract for Scholars Week was edited and submitted.

Results:
Gene 1B was added to NapoleonB. This gene, while it is a reverse gene in a forward area, is common to many other AM cluster phages.

Annotation for Gene 1B:

SSC:372 – 569, CP:No No coding potential was present, SCS:Neither, ST:NA, BLAST-Start:Aligns with circum gp2 NCBI BLAST q1:s1 100 2E-41, Aligns with Tribby gp2 PhagesDB BLAST q1:s1 1 6E-35, Gap:first gene, LO:Yes, RBS:Kibbler7 and Karlin Medium 3.263 -2.059 Yes, F:NKF, SIF-BLAST:NKF, SIF-HHPred:NKF, SIF-Syn:NKF

Conclusions:
In conclusion, gene 1B was added to PhageNotes and annotated were complete. The other assigned annotations were checked to make sure they are correct and also updated on PhageNotes. The group abstract for Scholars Week was edited and completed. At this point, all of the gene annotations should have been checked.

Future Work:
Future work will include continuing to check NapoleonB’s annotations, as they need to all be correct. Also, we will continue to prepare for Scholars Week and create the poster.

February 18

“The Forgotten Cure” Blog

Towards the beginning of the century, little to no knowledge was recorded of the presence of bacteriophage within the vast biosphere of our world. The exciting world of bacteriophages was brought about when Felix d’Herelle. D’Herelle developed a love for microbiology at a young age, but his decision to delve into field work when he noticed that he remained calm when he witnessed multiple people dying from yellow fever. He never received higher education in the sciences but he was self-taught. Due to his lack of education, he went straight into fieldwork. While working at the Pasteur Institute, he discovered bacteriophages on accident. He was observing locusts when he noticed clear spots on the cloudy background. His curiosity led him to have a desire to further study the strange event but he was unable to begin. His understanding of the strange spots began when he was ordered to analyze samples from the troops to detect any new form of the virulent infection. It was during this time that he observed that the strange spots appeared again; therefore, he was unable to claim these results were insignificant. One patient that entered the hospital in the Pasteur Institute was monitored for their progress through her illness and also through her recovery to locate the clear spots from her stool. Using different methods such as filtration and plates, he observed that the plate contained only dysentery bacteria after several days. After this observation, he was definite that a particle smaller than bacteria existed. After publishing his first paper, he faced a lot of controversy such as numerous explanations to reason that no such thing exists. The controversies behind phages continued into the early 1940s, but that did not prevent d’Herelle from visioning the potential behind bacteriophages against diseases in living organisms. Through numerous experiments on those who are sick, he received successful results from the insertion of bacteriophages within those who were infected with virulent diseases. After several years of moving around to promote the usage of bacteriophages as a weapon against virulent diseases, d’Herelle received an invitation from Georgi Eliava to establish a center in Tbilisi. Eliava entered d’Herelle’s life at a low point in his life. They both shared many things in common such as their passion for phages. However, they also had some differences. Eliava was relaxed and charming while d’Herelle was sharp and businesslike. The differences did not prevent them from becoming lifelong friends. As they were getting ready to open the bacteriophage institute in Tbilisi, Stalin gained control over the government which hindered their development of the center. Because of the growing fear in the Soviet Union, the Eliavas, after having been arrested two time times, were executed. Due to his death, the ties between the bacteriophage institute in the east and those of the west were cut. After d’Herelle’s death, the idea of bacteriophage was still not clearly defined. However, this problem did not leave to the decline in usage of bacteriophage; new medical discoveries were being brought about to prove to be more effective and cheaper such as the company Bayer making a new drug known as sulfanilamide. With increasing medical discoveries, more institutions began to lean towards these new discoveries which eventually led to the field of phage therapy to be forgotten. When the medical field abandoned the usage of bacteriophage, uses were found within other disciplines of science. Two men, Luria and Delbruck, who both found a passion for the integration of biology and physics, discovered the concept of using bacteriophage as a tool for studying genes which gave birth to the field of molecular biology.  With the history of the coming up of bacteriophages, it is really interesting how a man with no higher education was able to test for the presence of particles that make up a vast portion of the biosphere. It was also interesting how scientists have integrated the use of bacteriophages within many disciplines of science.

February 18

The Forgotten Cure 1

Lauren Foley 

Dr. Adair 

BIO 1406

18 February 2019

The Forgotten Cure 1

Locusts, dysentery, and war all remarkably led to the discovery and progression made in the bacteriophage field. Locusts can ultimately take responsibility for the discovery of the bacteriophage. Of Course like many of the great discoveries of our time, phages were discovered by accident! Scientist d’Herelle discovered phages while studying sick locusts. During his experiments he noticed clear, spherical spots on his bacterial cultures. He investigated the spots but noticed nothing significant. Little did he know several years later while studying dysentery, these clear little spots would appear once again. In 1916, while at the Pasteur institute in Paris, d’Herelle was sent in investigate a breakout of dysentery that had spread among the troops in Paris. He cultured the samples from the sick patients, and to his surprise there they were again- those little clear spots. D’Herelle noticed the little clear spots were only seen in recuperating patients, and decide to investigate further. A new patient was admitted to the hospital and he decided to closely monitor her. During the first 3 days of observing her cultures- nothing. The tubes were full of bacterial growth, and opaque. On the fourth day he noticed something remarkable- one of the tubes was completely clear! When d’Herelle went to the hospital he found the patient had recovered. Dysentery and war go hand and hand in pushing for the discovery of phage, and ultimately led to this major breakthrough. When war erupts, all energy goes into the war efforts- even the scientific community’s efforts. At the end of the day its all about who is willing to pay for research and if the government wants to pay to help end a disease that is wiping out troops, then thats where the research will be conducted.It ultimately led to this major breakthrough in terms of phage discovery. 

In addition to that one of the things that really surprised me was how early phages were actually being used to treat diseases. I had always thought that phage research, and therapies were something that started in the 2000’s, not the early 1900’s. To find out that scientists were using phages before they could even see them. D’Herelles predictions and insight into what he believed bacteriophages were, is absolutely astounding to me and show true creative thinking, considering he couldn’t even see the bacteriophages. With the invention of the electron microscope in 1940, which provided a visual insight into bacteriophages. When Luria first viewed what he referred to as “tadpole-shaped particles” they were shocked- because all scientist had assumed they were sphere shaped before this time. This then lead scientists to wonder, how did phages infect bacteria? This question then gave way to the famous Hershey and Chase experiment that altered the field of bacteriophages forever. 

February 18

Forgotten Cure Chapter 1-4

  1. While working with sick locusts, he observed that there was some clearing on his plates, which were called at the time taches vierges. With the discovery of these clearing lead to multiple tests, and at the time he thought he were somehow related to the locusts disease This would later lead to future test performed by d’Herelle and the publishing of his first paper, his results of his findings in these lytic creatures, that are smaller than bacteria. World war one started, and it mission of monitoring disease outbreaks and manufacturing commercial vaccines took on new urgency. This led to the hault of his recent discorvies, but the continuation of how these “clearing” were. Once asked to look into a new outbreak during the war, he performed multiple tests, and saw these taches vierges once again, and lead to many experiments and the publication of his paper.

 

  1. d’Herelle loved sciences as a child and taught himself microbiology/phage biology. As he was returning to Paris from Rio de Janeiro by ship, yellow fever broke out among the passengers and crew. At that moment, he saw something that would lead to him focusing of later to known as phage biology. Following in the footsteps of his hero Louis Pasteur where he would begin his studies studying fermentations. He was very driven by science, and so was Georgi Eliava. The two share many things in common such as they both came from privileged backgrounds. Their fathers were doctors from a well-connected family. Eliava was easily distracted and often carried away with many different ideas, which lead many of his lab experiments remained in his labs for weeks untouched. The two shared a warm friendship and the two published two papers together. Years later. Civil broke out in Spain and Eliava was arrested, which would cut all ties between Tbilisi’s Bacteriophage Institute and the West for more than 50 years.

 

  1. War helped d’Herelle realize that there was a correlation between his last two findings, and it helped him discover an agent that is smaller than bacteria. He performed many tests to prove his hypothesis, and soon he traveled all over the world to help cure diseases around the world. Governments in India changed to allow the use of bacteriophages since phage therapy proved to show success in lab and on humans. With the later wars like WWII and civil wars in the Eastern hemisphere, caused many ties with the western labs. The eastern labs were closed and scientists like Eliava were arrested. Politics and war played a great role with the spread of bacteriophage. If the two scientists were still sharing information during wars, the west might have kept up with bacteriophage. Since the west lost ties, the west found new ways to treating humans (antibodies) while the east kept up with bacteriophage, and they use antibodies as well.

 

  1. One reason that phage therapy failed was due to the fact articles that showed antibiotics were the new thing to cure diseases/illness pushed halted phage therapy in the western hemisphere, whereas phage therapy stopped in the east, but did not completely stop as in the west. Another reason why phage therapy failed in other parts of the country was due to the fact of multiple strains of the same bacteria were in different parts of the country. While d’Herelle helped heal thousands in Bombay, he sent his phage used to cure cholera in Egypt to India, but the phage did not work since the viruses isolated in Indochina didn’t work against the strain of phage bacteria active in Bombay. Without television or radio, word of outbreak of this new phage therapy spread slowly.

 

 

  1. The two scientists around the same time started bacteriophage research. Delbruck was searching for a way to apply the laws of physics to biology which lead him to bacteriophages. He and two other scientists aimed x-rays at the genes if Drosophila fruit flies and demonstrated that the genes mutated proportionally to given dose of radiation, which proved genes are “the ultimate units of life”. Like Delbruck, Luria began to think of a field that could bride the field of biology along with physics. After reading Delbruck’s paper on the genes, Luria discovered bacteriophages. The two became intrigued with bacteriophages, which lead to meetings that became known as the phage group. Through many talks, the question was if bacteriophages were really genes, like human genes, then it would give a new angle to look at human body genes. The two contributed to phage biology through there similar interests and what they saw in genes and how bacteriophages are the tools for studying genes. The group that was formed by the two introduced chemists, biologists and physicists to change and would be the birth of molecular biology. Phage biology died since scientists were intrigued with a new topic and that topic was how higher organisms reproduce and any role that phages might have once played in curing humans was viewed as a failed effort.

 

  1. Discovery of bacteriophage has come a long way and with the help of multiple scientists, phage have helped cure millions in the early 1900’s to 1950’s. It is amazing to see how much of a role politics plays in our lives. Politics “run” everything and it very important. Wars had a huge effect and how it prevented the spread of this wealth of knowledge. This first few chapters of the book were a really great read and it was very fascinating to see where bacteriophages have come from. We started this class without little to no knowledge about bacteriophage, let alone any of the history, and now we have come to understand a lot about bacteriophages.