Owner: Blogging for Bacteriophage URL:http://www.thewanderingminstral.blogspot.com Join Date: Mon, 24 Mar 2008 13:51:43 -0500 Rating:0 Site Description: A look into modern developments of microbiology, and the ramifications they have on health and technology. Site statistics:Click here
Research Synopsis 2008-04-05 17:04:39 So my grad school application process continues. This is part of my personal statement....it is a synopsis of my research. Let me know what you think, any changes I should make, etc. Thanks in advance!For the past two and a half years, I have had the privilege to work as an undergraduate researcher in the lab of Dr. Graham Hatfull at the University of Pittsburgh. Dr. Hatfull is one of a unique group of researchers adamantly recruiting young students into biological research. Students as young as 6th and 7th grade are able to work in his lab through his Phagehunting program. Although I did not begin my work in the program at that young of an age, many would consider my start as a college freshman early compared to most. I began my research in January of my freshman year. The first pro Read more:Research
Intro to Bacteriophages 2008-04-05 17:04:22 So, Tim studies bacteriophages...well, what the heck are they anyway. Here's a very brief introduction as to what they are and do. There may be some links around the site that will tell you more.A bacteriophage (from 'bacteria' and the Greek "phagein", meaning 'to eat') is any one of a number of virus-like agents that infect only bacteria. The term is commonly used in its shortened form, phage.Typically, bacteriophages consist of an outer protein hull enclosing genetic material. The genetic material can be dsRNA, ssDNA, or dsDNA between 5 and 500 kilo base pairs long with either circular or linear arrangement. Bacteriophages are much smaller than the bacteria they destroy - usually between 20 and 200 nm in size.Phages are estimated to be the most widely distributed and diverse entities in
Phage Therapy 2008-04-05 17:04:08 Phage therapy is the use of bacteriophages (usually purely lytic) to treat pathogenic bacterial infections. Phages are viruses that invade only bacterial cells and, in the case of lytic phages, cause the bacterium to burst and die, thus releasing more phages. Phage therapy is a potential alternative to antibiotics, being developed for clinical use in the 21st century by many research groups in Europe and the US. After having been extensively used and developed mainly in former Soviet Union countries for about 90 years, phage therapy is now becoming more available in other countries such as USA for a variety of bacterial infections.Phage therapy has many applications in human medicine as well as dentistry, veterinary science and agriculture.An important benefit of phage therapy is that bact Read more:Therapy
Phage Therapy's Positive Attributes 2008-04-05 17:03:49 Let's discuss now what makes phages ideal for human therapy and food treatment.1. Phages are very specific with what they infect.They only infect bacterial cells, never your cells! They also only have the ability to usually infect one type of bacteria as well. This means that a phage used to kill off harmful gut bacteria, isn't likely to kill off beneficial bacteria. We can also easily make cocktails of different phages to ensure that the harmful bacteria are completely destroyed.Current antibiotics do not differentiate between harmful and beneficial bacteria. Phages do. 2. Phages don't harmfully interact with your cells.Unlike some antibiotics, you won't experience any negative affects directly from exposure to a bacteriophage. For one, they are already ubiquitous to the environment. Stud Read more:Attributes
, Positive
, Therapy
I'll Have My Bacteria Extra-CRISPR 2008-04-05 17:03:33 The microbial cold war between species has been widely studied and is, in my opinion, one of the most interesting topics in current biology. Fungi make compounds to destroy bacteria, bacteria make compounds to destroy fungi. But it doesn't stop there. Phages mutate constantly to evade bacterial defenses. We've known about a handful of bacterial defenses against phage-- repressor systems, restriction enzymes, receptor modification, DNA modification, etc. We have utlized these systems to our advantage--our first effective antibiotic (Penicillin G) came from the fungus Penicllium, a vital antifungal (cyclohexamide) comes from the bacteria Streptomyces, our ability to clone and subclone is only useful because we can specifically cut DNA with restriction enzymes, etc..... But now, Read more:Bacteria
, Extra
Myxoma virus: From Rabbits to Cancer 2008-04-05 17:03:04 More than half a million individuals in the US died in 2004 from cancer and more than 10.8 million Americans are living with the disease.(CDC 2008) The number of cancer deaths each year continues to decline, due to advances in medical technologies. With the advent of a cervical cancer vaccine,Gardasil this number promises to continue to drop dramatically. Furthermore, there are new treatments in development that promise to revolutionize the effective treatment of cancer. One of these, which I am currently fascinated by, is oncolytic virotherapy. This is a summary of a review article by Grant McFadden at the University of Florida.Oncolytic virotherapy is the use of live virus
es to kill malignant cells in situ. The use of viruses holds potential to not only be a direct treatment of cancer, b Read more:Cancer
Oncolytics: Not just for Myxoma Virus 2008-04-24 14:52:25 In a previous article, I discussed the use of Myxoma Virus as an oncolytic therapy against malignant gliomas.Recently, I came across a post from The Evilutionary Biologist, pointing to an article describing a modified Herpes Virus as treatment against human sarcomas.This continues to show us that viruses can be highly beneficial to our society. Antibacterial therapy and cancer therapy are just two of the many advances that viruses have been crucial in development.It is my opinion that we should begin seriously exploring the potential therapies that Nature has already created for us, rather than concentrate on de novo synthesis of treatments. There are an infinite number of mechanisms and pathways in Nature that could provide groundbreaking technologies.It is just up to us to find them and
Where the Wild Microbes Are: A New Theory on How Pathogens Survive Food Processing 2008-04-26 11:09:03 Produce borne diseases have recently been gracing the front pages of our media. Our spinach has E. coli, our onions have Hepatitis A virus and E. coli, our strawberries have Listeria, and our tomatoes and peanut butter have Salmonella. Not to mention the countless tons of ground beef tainted with pathogenic E. coli. Common sense says that washing and proper handling of our food should simply be enough to prevent illness outbreaks. It has now been hypothesized that many bacteria were able to "hide" within and among the plant cells, protected by their sturdy cell wall. Or even that some pathogenic bacteria were able to enter the cells and remain protected from traditional washing methods.An article in this month's Applied and Environmental Microbiology looks at a much different method of bac Read more:Processing
, Theory
Happy Birthday Elio Schaechter! 2008-04-26 07:42:52 Blogging for Bacteriophages would like to take a moment to wish Elio Schaechter at Small Things Considered a very happy 80th Birthday
.Small Things Considered is a joint collaboration between Elio Schaechter and Merry Youle. These fine writers post on the wonders within the world of microbes. Their American Society for Microbiology blog is always entertaining and informative, and serves as a unique looking glass at "the Small Things."
Read more:Happy
, Happy Birthday
Got Phage? 2008-05-09 17:37:17 A little bacteriophage graphic that I designed, and placed on some merchandise. I thought that some here may find it interesting / entertaining.The Blogging for Bacteriophages "Got Phage?" store is selling some T-Shirts and some random things. I think the "Ringer T-Shirt" looks really good, and I also recommend the clock, stickers, and pillow.Feel free to check it out and enjoy! I'll try to move some images to this site soon.
Mosaicism: The World of Horizontal Gene Transfer (Part 1) 2008-05-09 13:29:13 Commonly, gene transfer is thought of as a vertical line from parent to offspring, along which all evolutionary traits are passed. However, as we began delving into genomic sequences, we found that this may not be true and that the lines between "species," especially on the microbial level, are quite fuzzy.Horizontal
gene transfer is the transfer of genetic elements between species. The microbial world is filled with examples of this phenomenon. This article is the first in a 3 part series that will explore the ever fluctuating genetic world of our microbial majority.Escherichia coli is perhaps the most well studied and utilized bacterial organism on the planet. This bug also has the capability for a wide range of illness in humans including: non-pathogenic, enterohemorrhagic (such as popu Read more:World
Mosaicism: Life on a Small, Ever-Changing Scale (Part 2) 2008-05-19 19:31:34 In the my last article, I briefly discussed the role of horizontal gene transfer in bacteria...specifically the development of mosaic pathogenicity islands in Escherichia coli. However, the formation of mosaics are not just limited to operons within bacterial genomes. In fact, we can see such events in phage and viral genomes. This article is part two in a brief series on genomic mosaicism.Current Read more:Changing
, Scale
, Small
Walking the Line Between Grades and Experience: My Life as an Undergraduate Researcher (Part 1) 2008-05-23 17:54:57 From the moment I began looking for a university to attend after high school, I knew I wanted to do biology research. "Experience is key" I was told, in order to do anything after receiving a 4yr degree. So although I was unsure what it was I truly wanted to pursue after getting my BS in Microbiology, I KNEW that I would need research experience to succeed.And so, I sent out my first requests to v Read more:Researcher
, Undergraduate
, Walking
Walking the Line Between Grades and Experience: My Life as an Undergraduate Researcher (Part 2) 2008-05-23 17:52:01 Continued from Part 1 I finished my sophomore year with a B-average, and went into the summer with my mind set on losing myself in my research again. I was doing some really cool assays with M. tb and M. bovis BCG (I was the only undergraduate in the lab taking advantage of our facilities). This work spring boarded me into a highly competative fellowship from HHMI. Since this was quite a some of m Read more:Researcher
, Undergraduate
, Walking
Winogradsky Column (Day 1) 2008-05-26 10:58:10 I have decided that my microbiology education would be incomplete without experiencing first hand the creation of a Windogradsky Column
.I must apologize for not having any sort of dissecting/micro scope to closely examine the succession over time. This column was started yesterday with mud/silt from Panther Hollow "Lake,"and no extra nutrients or minerals were added. It's currently sitting in my
2008 ASM General Meeting, Boston MA 2008-05-28 20:19:48 On June 1st through 5th, I have the distinct pleasure of attending my third ASM General
Meeting, in as many years. My poster titled "Novel Generalized Transducing Phages of the Mycobacteria" is number M-005. Feel free to come and chat about esoteric microbiology topics.I plan on writing on a handful of interesting topics presented. It should be a great time for all!
Read more:Boston
Free Hydrogen--Algal Biofuel Production 2008-05-30 18:20:01 Blogging for Bacteriophages is proud to give you it's first guest post. This article comes from M. McGuirk., a biochemistry student at Chatham University.Green algae are photosynthetic microorganisms capable of using protons as a reductant and producing molecular hydrogen. As technology advances, these organisms might provide an efficient, cost-effective method to mass produce hydrogen gas to be u Read more:Production
Evolution of Phage Capsid and Genome Size 2008-06-08 15:32:01 Viruses come in all shapes and sizes. From the very small, such as the picornaviruses or the parvoviruses, to the very large like mimivirus, or the herpesviruses, and poxviruses. These large viruses are not just large in physical size, but in the size of their genomes as well.At the recent 2008 ASM General Meeting, Roger Hendrix of the University of Pittsburgh, laid forth a rather interesting hypo Read more:Evolution
, Genome
A Brief Bit More on Reductive Evolution in M. leprae 2008-06-13 08:24:48 In a previous post I discussed the evidence for reductive evolution in Mycobacterium leprae, an interesting obligate intracellular parasite.At the 2008 ASM General Meeting, the Division U keynote lecture was headed by Tom Gillis of the National Hansen's Disease Program. His talk described the same work I cited in the previous article, which showed the immense amount of pseudogenes in the M. leprae Read more:Brief
, Evolution
Suggested Reading Lists 2008-06-27 16:51:33 I have compiled a list of the books Debbie has ordered for the lab in recent years. You may find some of these titles interesting and useful. I have included the ISBNs for easy access and ordering through whichever venue you use. In many cases I have included a link to Amazon for current new/used prices and a description. Hope you find this helpful!-TimPlease feel free to comment on any of these b Read more:Lists
, Reading
, Suggested
Apology 2008-08-19 18:45:00 I need to apologize for my lack of activity recently....things got a little out of hand, but now that I have finished a rather large move and am settling in to things, there should be more content in the near future!Thanks!Tim
Read more:Apology
How Far Do Those Phages Stretch? 2008-09-19 17:53:15 The number of viruses in the biosphere has been estimated to be anywhere from 1030 to 1032. But what does this number really mean? How big is 1031? (The number I see most commonly cited as the number of phages in the biosphere)Roger Hendrix gives a great list of examples, and one of these is "How far will 1031 phages stretch if laid end to end?" I thought I would do the calculation for myself (and Read more:Stretch
Altruism in Bacteria? Allowing Yourself to Die for the Good of the Species 2008-09-19 12:37:12 Altruism in general is an interesting concept from an evolutionary perspective. As defined by Dictionary.com, altruism is "the principle or practice of unselfish concern for or devotion to the welfare of others," or more specifically, it is "behavior by an animal that may be to its disadvantage but that benefits others of its kind, such as a warning cry that reveals the location of the caller to a Read more:Bacteria
, Yourself
A MAP to Crohn's Disease; Revisiting Koch's Postulates 2008-10-06 09:48:06 The fundamental principle of infectious disease is Koch'sPostulate. To be brief, he set forth the qualifications that must be fulfilled in order to associate a pathogen with an illness. This includes the isolation of the organism from diseased tissue, the ability to grow the organism in pure culture, and the recreation of the disease in a healthy individual following introduction of the purified Read more:Crohn
The Brillant Dance of the Starvation Response 2008-09-20 21:40:13 Another dorky song that only a microbiologist could love. This one is about the amazing regulation of the starvation response in E. coli during sugar starvation. Some of the details may be skipped through, but the core concept is there.This is dedicated to undergraduate Microbial Physiology, instructed by Jeffery Lawrence.The Brillant Dance
of the Starvation Response
(To the tune of Dashboard Conf
It's Gonna Be There (The E. Coli Song) 2008-10-23 16:49:09 I'm back again with a dorky song. Written originally years ago for undergraduate Microbiology Lab, this song was in response to the many outbreaks of E. coli (specifically those occuring in spinach and other produce).I hope you find this song as enjoyable as I do.I would love to hear some feedback on this and the other "performances" I have posted under the "Phage Fun" heading. Feel free to e-mail
The Origins of Antibiotic Resistance 2008-10-17 17:21:10 Antibiotic resistance is becoming an increasingly important plight that we face in our treatment against bacterial infections. The acronyms MRSA and XDR-TB have become headlines across the world; and the number of untreatable infections is on the rise. But even as we learn more about the increase in antibiotic resistance and what we must do to overcome this, we must also look into past evolutionar Read more:Origins
, Resistance
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