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
Reductive Evolution in Mycobacterium leprae 2008-03-23 14:24:58 Mycobacterium leprae is quite an interesting bug. It is significantly related to M. tuberculosis (the causative agent of TB), yet leprosy is a very different illness.Unlike other mycobacteria, M. leprae is unique in the fact that it is an obligate intracellular parasite. Replication of the bacterium cannot occur outside of host cells. To date, no synthetic media has been able to support M. leprae replication. Since M. leprae is required to parasitize, it stands to reason that discovering the genetic components of this lifestyle will provide possible venues for drug therapy against this debilitating illness.It is clear that M. leprae is closely related to the other mycobacteria, this paperby Cole et al. analyzes the genetic sequence of M. leprae and compares it to M. tuberculosis. By doing Read more:Evolution
I'll Have My Bacteria Extra-CRISPR 2008-03-22 12:18:31 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
Research Synopsis 2008-03-19 19:15:53 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
Phage Therapy 2008-03-19 19:01:36 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 2008-03-19 19:00:04 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
Intro to Bacteriophages 2008-03-19 18:58:17 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
Steelers and Life 2007-10-18 08:05:18 Steelers have are 3-0 for the first time since Bill Cowher's first season as head coach.Mike Tomlin appears to be doing quite an impressive job as his first year as head coach. But we will have to see if they can improve to 4-0 when they face the Cardinals next week. In other news, classes are surprisingly difficult this year. Microbial Physiology, Western Civilization, Origins of Christianity, Intro to Modern Art, Ecology, and Tae Kwon Do. It's gonna be a crazy semester.Aside from classes, I've been applying to grad schools. This is a vain attempt to continue on my way to a PhD. Schools I am looking at include: Albert Einstein College of Medicine- Bronx, NY; University of Florida; Emory University- Atlanta, GA; U. of Wisconsin-Madison; Stanford U.; and Harvard U. Apps are due the first we Read more:Steelers
What's up with Life? 2007-09-24 21:14:46 Ahhh! This week is going to be crazy. Quite crazy as a matter of fact.Christianity exam tomorrow....Modern Art exam on Wends....and then Microbial Phys on Thurs.Ugh. And my tuberculosis cultures aren't growing very well at all. They are supposed to be growing slow....but not this slow. It is quite sad. Maureen seems unhappy right now too. I am not sure why. But, I am sure that I will be trying to make smile until she gets out of her funk.Thats all for now...time to go back to studying. Maybe take a walk and grab a drink!
Myxoma virus: From Rabbits to Cancer 2008-03-28 07:03:02 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
RecQ's Role in Illegitimate Recombination 2008-04-02 22:13:24 Genetic recombination is a ubiquitous event that occurs in every species; it is necessary for the production of unique gametes, it is involved in DNA damage repair, it provides a mechanism for evolution, and it is a required action for many viruses and phages to undergo nucleic acid replication.(My discussion here will focus entirely on recombination in prokaryotes and their viruses)There are three different types of recombination: homologous recombination--where DNA of significant sequence similarity recombines, non-homologous recombination--where DNA without significant sequence similarity recombines (usually along gene boundaries), and finally there is illegitimate recombination--where DNA recombines randomly.Although DNA is surprisingly fluid, there are enzymes that mediate recombinati
Just For Phun! 2008-04-05 13:20:29 I found this in my photo archives, I thought some of you may enjoy it! (2005)
Recombineering: A Practical Application of Phage Biology 2008-04-05 13:07:18 The most obvious use of phages is of course direct phage therapy. Although exciting, there are many other uses of phage that are just as revolutionary, but tend to slip by. In my last article, I hinted at a method in molecular biology called “recombineering.” (Short for homology-dependent, recombination-mediated, genetic engineering) This is a method whereby phage proteins are used to catalyze homologous recombination. The ramifications are huge. Mutations can be made; whole genes and operons can be knocked out with relative ease, and much more. In fact, some may say that this recently described process revolutionized E. coli genetics.Since this system was so successful in E. coli, the Hatfull Lab at the University of Pittsburgh set out to develop this system in the Mycobacteria. Befor Read more:Application
, Practical
Phages With Horns?! What's Next? 2008-04-07 16:16:03 In the world of phage, uniqueness rules. The total number of phages in the biosphere is dramatic, with estimates numbering the population at 1031! Despite such high numbers, since the discovery of phage no identical phage has been found in the environment twice. They have often been termed "Nature's Most Successful Experiment." Their genomes are in constant flux amoung themselves and their hosts. It therefore should no longer surprise us when we discover a phage that doesn't quite fit the mold.In this paper by Pope, et al. they describe a phage (named Syn5) of the cyanobacteria that comes equipped with a "horn." Described as a "slender elongated fibrous protrusion," the horn clocks in at 50nm in length. To put perspective on this, the horn is almost as long as the capsid is wide (60nm) and Read more:Horns
I Got You Phage 2008-04-05 17:01:48 Back in August of 2006, I wrote and performed this song for a lab meeting to summarize my work I had done that summer and the previous year (All regarding a bacteriophage called BPs).Some of the lyrics are hard to catch, you can find them below the embed. Enjoy! LyricsWill I find you? Well, I don't know.I won't find out until my smeg will grow.I scraped the dirt right off my shoeYou were there and phage, I found you.(Chorus)Phage, I got you phage. I got you phage. I got you phage.They say you won't kill TB, you'll only infect Bovis BCGI can tell from your lack of spotsYou won't infect all the bacteria we got(Chorus)You have recE in your genesYou have Halo on your teamAnd when your cruising round the townBateria die when you're around.So let them say your tail's too longI don't care, I wrot
Wild Bacteria That Eat Our Antibiotics? Of Course! 2008-04-10 07:05:49 Antibiotics were invented by bacteria and fungi during thier conception in this universe. Used to control microbial niche environments, it wasn't until 1928 that Fleming (and subsequently Florey and Chain) began the widespread use of the antibiotic penicillin to control bacterial infections in humans. And so, the antibiotic revolution began. Subsequent use (and misuse) of antibiotics has given rise to various resistant strains. These are becoming a vast problem in the treatment of diseases that once were "easily" curable, including the well-publisized MRSA and XDR-TB, as well as many others.This paper, coming out of Harvard University, describes the isolation of bacterial strains that can live on antibiotics as their sole carbon source. Current thought states that resistance in a bacterial Read more:Antibiotics
, Bacteria
A Fatty Acid Synthetase is Necessary for Active TB Infection 2008-04-11 12:43:10 Mycobacterium tuberculosis is the most common infectious agent in the world. Nearly 1/3 of the world population is infected, and a drastic number of these are increasingly antibiotic resistant. MDR-TB and XDR-TB are becoming more commonplace everyday, especially in regions that are combating HIV infections. As such, it is incredibly important to study how this bug works. It is one of the most difficult organisms to work with due to a wide variety of factors. These include: slow growth rate, pathogenicity, very waxy cell walls, high levels of illegitimate recombination, and a bunch of other nuances that make the mycobacteria unique among its relatives. One unique feature of the mycobacteria, is their unique acid-fast staining pattern. It has been shown that when treated with isoniazid Read more:Active
, Fatty
, Necessary
Molecular and Cell Biology Carnival #1 2008-04-14 07:05:21 Announcement:The inaugural Molecular
and Cell Biology Carnival
has been published. Hosted over at The Skeptical Alchemist, this edition highlights some current topics in MCB. This is the first of (hopefully) many, so feel free to submit your articles for future inclusion over at Blog Carnival.Enjoy!
Monthly Book List, First Edition 2008-04-14 07:05:02 Here are a variety of books that may interest some of you. Many of these are personal favorites, some are entertaining and educational, others just educational, but rife with knowledge.The Hot Zone: A Terrifying True Story Follow the story of the Ebola virus. This book brought me into the world of virology. Exciting and educational...not many people know that we had an Ebola virus outbreak right in Virginia.The Demon in the Freezer: A True StoryAnother book by Richard Preston, this time centering around the bioterrorist threat of smallpox and anthrax. Although quite embellished, this is an entertaining read and definatly worthy of its place on my bookshelf.Biohazard: The Chilling True Story of the Largest Covert Biological Weapons Program in the World--Told from Inside by the Man Who Ran I Read more:Edition
, First
, First Edition
, Monthly
The Definition of Life; and, Taxonomy as We Know It 2008-04-15 20:38:16 In order to make sense of our surroundings, we, as humans, constantly group things into discrete catagories--states of matter, times of day, types of clothes, etc. Since Linnaeus, we have consistantly grouped life in boxes-within-boxes, based on physical characteristics. The advent of nucleic acid sequencing changed some of these early notions of taxonomy. But now, as we discover more about life, specifically of our microbial counterparts and their viruses, we are coming to the realization that Linnaein taxonomy is not sufficient. Especially if our motivation for using taxonomy is to deduce evolutionary relationships.Viral taxonomy has some very specific shortfalls. Researchers in this 2002 Journal of Bacteriology article, lay out these shortcomings. One striking point is that with viruses Read more:Definition
Seminar Time 2008-04-14 21:40:02 You know you've sat through lectures at seminars or conferences that sounded like this. Read more:Seminar
RecQ's Role in Illegitimate Recombination 2008-04-14 19:51:08 Genetic recombination is a ubiquitous event that occurs in every species; it is necessary for the production of unique gametes, it is involved in DNA damage repair, it provides a mechanism for evolution, and it is a required action for many viruses and phages to undergo nucleic acid replication.(My discussion here will focus entirely on recombination in prokaryotes and their viruses)There are three different types of recombination: homologous recombination--where DNA of significant sequence similarity recombines, non-homologous recombination--where DNA without significant sequence similarity recombines (usually along gene boundaries), and finally there is illegitimate recombination--where DNA recombines randomly.Although DNA is surprisingly fluid, there are enzymes that mediate recombinati
Recombineering: A Practical Application of Phage Biology 2008-04-14 19:49:35 The most obvious use of phages is of course direct phage therapy. Although exciting, there are many other uses of phage that are just as revolutionary, but tend to slip by. In my last article, I hinted at a method in molecular biology called “recombineering.” (Short for homology-dependent, recombination-mediated, genetic engineering) This is a method whereby phage proteins are used to catalyze homologous recombination. The ramifications are huge. Mutations can be made; whole genes and operons can be knocked out with relative ease, and much more. In fact, some may say that this recently described process revolutionized E. coli genetics.Since this system was so successful in E. coli, the Hatfull Lab at the University of Pittsburgh set out to develop this system in the Mycobacteria. Befor Read more:Application
, Practical
Just For Phun! 2008-04-14 19:46:34 I found this in my photo archives, I thought some of you may enjoy it! (2005)
Phages With Horns?! What's Next? 2008-04-14 19:46:04 In the world of phage, uniqueness rules. The total number of phages in the biosphere is dramatic, with estimates numbering the population at 1031! Despite such high numbers, since the discovery of phage no identical phage has been found in the environment twice. They have often been termed "Nature's Most Successful Experiment." Their genomes are in constant flux amoung themselves and their hosts. It therefore should no longer surprise us when we discover a phage that doesn't quite fit the mold.In this paper by Pope, et al. they describe a phage (named Syn5) of the cyanobacteria that comes equipped with a "horn." Described as a "slender elongated fibrous protrusion," the horn clocks in at 50nm in length. To put perspective on this, the horn is almost as long as the capsid is wide (60nm) and Read more:Horns
A Fatty Acid Synthetase is Necessary for Active TB Infection 2008-04-14 19:44:49 Mycobacterium tuberculosis is the most common infectious agent in the world. Nearly 1/3 of the world population is infected, and a drastic number of these are increasingly antibiotic resistant. MDR-TB and XDR-TB are becoming more commonplace everyday, especially in regions that are combating HIV infections. As such, it is incredibly important to study how this bug works. It is one of the most difficult organisms to work with due to a wide variety of factors. These include: slow growth rate, pathogenicity, very waxy cell walls, high levels of illegitimate recombination, and a bunch of other nuances that make the mycobacteria unique among its relatives.One unique feature of the mycobacteria, is their unique acid-fast staining pattern. It has been shown that when treated with isoniazid (the m Read more:Active
, Fatty
, Necessary
Wild Bacteria That Eat Our Antibiotics? Of Course! 2008-04-14 07:06:04 Antibiotics were invented by bacteria and fungi during thier conception in this universe. Used to control microbial niche environments, it wasn't until 1928 that Fleming (and subsequently Florey and Chain) began the widespread use of the antibiotic penicillin to control bacterial infections in humans. And so, the antibiotic revolution began. Subsequent use (and misuse) of antibiotics has given rise to various resistant strains. These are becoming a vast problem in the treatment of diseases that once were "easily" curable, including the well-publisized MRSA and XDR-TB, as well as many others.This paper, coming out of Harvard University, describes the isolation of bacterial strains that can live on antibiotics as their sole carbon source. Current thought states that resistance in a bacterial Read more:Antibiotics
, Bacteria
Molecular and Cell Biology Carnival #1 2008-04-14 07:05:21 Announcement:The inaugural Molecular
and Cell Biology Carnival
has been published. Hosted over at The Skeptical Alchemist, this edition highlights some current topics in MCB. This is the first of (hopefully) many, so feel free to submit your articles for future inclusion over at Blog Carnival.Enjoy!
Monthly Book List, First Edition 2008-04-14 07:05:02 Here are a variety of books that may interest some of you. Many of these are personal favorites, some are entertaining and educational, others just educational, but rife with knowledge.The Hot Zone: A Terrifying True Story Follow the story of the Ebola virus. This book brought me into the world of virology. Exciting and educational...not many people know that we had an Ebola virus outbreak right in Virginia.The Demon in the Freezer: A True StoryAnother book by Richard Preston, this time centering around the bioterrorist threat of smallpox and anthrax. Although quite embellished, this is an entertaining read and definatly worthy of its place on my bookshelf.Biohazard: The Chilling True Story of the Largest Covert Biological Weapons Program in the World--Told from Inside by the Man Who Ran I Read more:Edition
, First
, First Edition
, Monthly
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