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41 posts · 44,572 views
Currently, Tim is a Microbiology and Molecular Genetics graduate student at Emory University, studying host innate immune signaling suppression by Francisella. Undergraduate work was done in the Hatfull Lab at the U. of Pittsburgh studying bacteriophage genetics and as agents of gene transfer in the Mycobacteria.
The Times Microbial
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- April 6, 2010
- 08:00 AM
- 1,063 views
Speculation Surrounding Sporulation in the Mycobacteria
by Tim Sampson in The Times Microbial
by TimThe Mycobacteria are quite the unique genus; not quite Gram-positive due to their waxy mycolic acids on their outer surface, but certainly not Gram-negative as they do not have an outer lipid bilayer. (Although, there are some interesting micrographs showing a structural feature that does look a lot like a typical Gram-negative outer membrane on the surface of Mycobacteria.) Much slower growing than the average bacteria studied in the lab and not so easily manipulated genetically (though s........ Read more »
Ghosh, J., Larsson, P., Singh, B., Pettersson, B., Islam, N., Sarkar, S., Dasgupta, S., & Kirsebom, L. (2009) Sporulation in mycobacteria. Proceedings of the National Academy of Sciences, 106(26), 10781-10786. DOI: 10.1073/pnas.0904104106
Traag, B., Driks, A., Stragier, P., Bitter, W., Broussard, G., Hatfull, G., Chu, F., Adams, K., Ramakrishnan, L., & Losick, R. (2009) Do mycobacteria produce endospores?. Proceedings of the National Academy of Sciences, 107(2), 878-881. DOI: 10.1073/pnas.0911299107
- March 8, 2010
- 08:30 AM
- 1,240 views
A Role for the Host-Microbe Interface in Obesity
by Tim Sampson in The Times Microbial
by TimOur bodies are home to 10 times more bacterial cells than human cells. With such sheer numbers, we have developed an intricate balance with the mutualists living on our skin and in our guts. Their mere presence is vital for protection from pathogenic species; but at the same time, our immune system must keep their numbers in check to prevent overgrowth. Those bacteria within our guts perform important roles in fermenting carbohydrates and producing essential nutrients like vitamin K and bi........ Read more »
Vijay-Kumar, M., Aitken, J., Carvalho, F., Cullender, T., Mwangi, S., Srinivasan, S., Sitaraman, S., Knight, R., Ley, R., & Gewirtz, A. (2010) Metabolic Syndrome and Altered Gut Microbiota in Mice Lacking Toll-Like Receptor 5. Science. DOI: 10.1126/science.1179721
- March 5, 2010
- 09:00 AM
- 963 views
Noisy and Bistable Gene Expression: Hedging Your Bets
by Tim Sampson in The Times Microbial
Often times resistance to antibiotics has a genetic basis. That is, a bacteria encodes a protein that functions to export, degrade, or otherwise block the function of a given antibiotic compound. However in the last few years, the observation of non inherited antibiotic resistance has come into view. One of my favorite articles describing the phenomenon is one by Nathalie Balaban et al, in Science back in 2004, particularly due to her super cool use of microfluidics and single cell imaging.
F........ Read more »
Nathalie Q. Balaban, Jack Merrin, Remy Chait, Lukasz Kowalik, Stanislas Leibler. (2004) Bacterial Persistence as a Phenotypic Switch . Science, 305(5690), 1622-1625. info:/http://www.sciencemag.org/cgi/content/full/305/5690/1622
- December 28, 2009
- 09:00 AM
- 1,298 views
Not All Mice Are Created Equal When it Comes to Gonorrhea
by Tim Sampson in The Times Microbial
Neisseria gonorrhoeae, the causative agent of the sexually transmitted infection, gonorrhea, is a Gram-negative diplococcus and an obligate human pathogen. An estimated 800,000 cases of gonorrhea occur each year in the United States (1). The most common sites of infection are the cervix and the male urethra, and symptomatic infection is characterized by a purulent exudate composed of numerous polymorphonuclear leukocytes (PMNs) containing intracellular gonococci (3).
The development of whole ........ Read more »
Packiam M, Veit SJ, Anderson DJ, Ingalls RR, & Jerse AE. (2010) Mouse strain-dependent differences in susceptibility to Neisseria gonorrhoeae infection and induction of innate immune responses. Infection and immunity, 78(1), 433-40. PMID: 19901062
- December 21, 2009
- 09:00 AM
- 1,044 views
Noisy and Bistable Gene Expression: Why Genes and Environment Aren't Everything
by Tim Sampson in The Times Microbial
Classically, a cell's phenotype was thought to be a product of its genetic background and its environment. All changes within a cell would be due to the cell's genetic capability to react to the environmental changes happening around them. However, as we begin looking more in depth at cell populations at the single cell level, we are finding that this paradigm isn't always true.
In this two part series, I want to examine how genetically identical cells in equal environments can........ Read more »
Maamar H, Raj A, & Dubnau D. (2007) Noise in gene expression determines cell fate in Bacillus subtilis. Science (New York, N.Y.), 317(5837), 526-9. PMID: 17569828
- December 11, 2009
- 11:20 AM
- 1,195 views
Nitric Oxide Synthase Isn't Just Used by Our White Blood Cells...
by Tim Sampson in The Times Microbial
Phagehunter.org is proud to have J. Kandler, a microbiology graduate student at Emory University, present to us this interesting post on a defense feature common in our immune system, but being utilized by bacteria as well.After Halloween, I came across this spooky article in Science describing yet another way bacteria are dodging antibiotics. Don’t worry, there’s a silver lining! Gusarov and his colleagues may have found a new target for the antibiotic industry, bacterial nitric oxide synth........ Read more »
Gusarov I, Shatalin K, Starodubtseva M, & Nudler E. (2009) Endogenous nitric oxide protects bacteria against a wide spectrum of antibiotics. Science (New York, N.Y.), 325(5946), 1380-4. PMID: 19745150
- December 5, 2009
- 05:50 PM
- 1,213 views
How Helicobacter Gets Around
by Tim Sampson in The Times Microbial
Helicobacter pylori is the only bacterium (that I know of) that is capable of colonizing the rather intimidating environment of the human stomach. A very low pH, and a thick viscous and elastic mucus, make for a difficult niche to inhabit. But for a bacterium, the payoffs are huge: a constant supply for nutrients, no other prokaryotic competition, and little interaction with the immune system.It is well described that to survive the low pH, Helicobacter utilizes a urease system. Taking in urea ........ Read more »
Celli, J., Turner, B., Afdhal, N., Keates, S., Ghiran, I., Kelly, C., Ewoldt, R., McKinley, G., So, P., Erramilli, S.... (2009) Helicobacter pylori moves through mucus by reducing mucin viscoelasticity. Proceedings of the National Academy of Sciences, 106(34), 14321-14326. DOI: 10.1073/pnas.0903438106
- November 24, 2009
- 09:33 PM
- 1,259 views
Out With the Bad: Efflux in Klebsiella pneumoniae
by Tim Sampson in The Times Microbial
Blogging for Bacteriphages is proud to announce an article by guest author, E. Ohneck, of Emory University.The Resistance-Nodulation-Division (RND) family of efflux pumps is widely utilized, especially among Gram-negative bacteria, for the export of a diverse array of antimicrobial agents from the bacterial interior, making these efflux systems important in multidrug resistance (1). RND family pumps are composed of three parts: a transporter protein in the inner cytoplasmic membrane, an outer me........ Read more »
Padilla E, Llobet E, Doménech-Sánchez A, Martínez-Martínez L, Bengoechea JA, & Albertí S. (2009) Klebsiella pneumoniae AcrAB efflux pump contributes to antimicrobial resistance and virulence. Antimicrobial agents and chemotherapy. PMID: 19858254
- November 17, 2009
- 07:45 AM
- 879 views
A Home for the Bugs in Our Appendix
by Tim Sampson in The Times Microbial
The appendix has long been considered a useless, vestigial organ, primarily based on the fact that it can be removed with no visibly harmful effects on the appendectomy recipient and that it is rather susceptible to severe inflammation. In fact, many theories have been proposed for its ancient purpose, ranging from being a place to allow plant matter to ferment to being a locale for crushed bones to be dissolved.
However, recent evidence posits that the appendix plays a crucial role in mainta........ Read more »
Smith HF, Fisher RE, Everett ML, Thomas AD, Bollinger RR, & Parker W. (2009) Comparative anatomy and phylogenetic distribution of the mammalian cecal appendix. Journal of evolutionary biology, 22(10), 1984-99. PMID: 19678866
- September 24, 2009
- 09:15 AM
- 1,059 views
The Next Steps in Synthetic Biology
by Tim Sampson in The Times Microbial
The advent of genome sequencing and analysis, coupled with the relative simplicity of DNA synthesis, has given rise to the field of synthetic biology. Described in 1974 by Waclaw Szybalski, the practice of synthetic biology would include the ability to "devise new control elements and add these new modules to the existing genomes or build up wholly new genomes."... Read more »
Lartigue, C., Vashee, S., Algire, M., Chuang, R., Benders, G., Ma, L., Noskov, V., Denisova, E., Gibson, D., Assad-Garcia, N.... (2009) Creating Bacterial Strains from Genomes That Have Been Cloned and Engineered in Yeast. Science. DOI: 10.1126/science.1173759
- September 24, 2009
- 09:15 AM
- 1,075 views
The Next Steps in Synthetic Biology
by Tim Sampson in The Times Microbial
The advent of genome sequencing and analysis, coupled with the relative simplicity of DNA synthesis, has given rise to the field of synthetic biology. Described in 1974 by Waclaw Szybalski, the practice of synthetic biology would include the ability to "devise new control elements and add these new modules to the existing genomes or build up wholly new genomes."More than 20 years later, this description is being realized. With the great minds and funds of the Venter Institute, we have seen the d........ Read more »
Lartigue, C., Vashee, S., Algire, M., Chuang, R., Benders, G., Ma, L., Noskov, V., Denisova, E., Gibson, D., Assad-Garcia, N.... (2009) Creating Bacterial Strains from Genomes That Have Been Cloned and Engineered in Yeast. Science. DOI: 10.1126/science.1173759
- May 14, 2009
- 10:41 AM
- 1,241 views
Prokaryotes Can Do Geometry, and Even Have Their Own Protractor
by Tim Sampson in The Times Microbial
Despite what once was a popular opinion, bacterial cells are not mere sacks of enzymes. Rather, we are discovering that they are highly structured. (Although, this probably should have been expected) Bacterial cells have to know where their poles are located in order to create such structures as E. coli’s chemotactic nose, Caulobacter’s stalk, and polar flagella. Cells must also be able to recognize where their midpoints are located in order to divide or differentiate properly. Furth........ Read more »
Ramamurthi, K., Lecuyer, S., Stone, H., & Losick, R. (2009) Geometric Cue for Protein Localization in a Bacterium. Science, 323(5919), 1354-1357. DOI: 10.1126/science.1169218
- May 9, 2009
- 03:16 PM
- 1,526 views
Throwing the Clutch (not the Brake) on a Bacterial Flagella
by Tim Sampson in The Times Microbial
For most my of readers, it is common knowledge that bacteria are more than just singled celled entities; and instead bacteria are complex organisms capable of undergoing large-scale, multicellular activities. Of particular interest to many current microbiologists, is the development of biofilms.These multicellular structures are likely how many bacteria exist in the environment, and are implemented in a variety of diseases. Taken alone, biofilms are fascinating, but I have a keen interest in und........ Read more »
Blair, K., Turner, L., Winkelman, J., Berg, H., & Kearns, D. (2008) A Molecular Clutch Disables Flagella in the Bacillus subtilis Biofilm. Science, 320(5883), 1636-1638. DOI: 10.1126/science.1157877
- May 9, 2009
- 01:40 PM
- 1,863 views
Phage Plus Metal = Battery
by Tim Sampson in The Times Microbial
By now, many people have read about Angela Belcher, a professor at MIT, and her lab's recent developments in the use of bacteriophages as a componant of batteries. Having had a very distinct privilage to hear her speak yesterday, I wish to share what I have learned.
In a broad sense, the goal of her lab is to give inorganic compounds (batteries, medical devices, solar cells, etc), "genetic intelligence."... Read more »
Lee, Y., Yi, H., Kim, W., Kang, K., Yun, D., Strano, M., Ceder, G., & Belcher, A. (2009) Fabricating Genetically Engineered High-Power Lithium Ion Batteries Using Multiple Virus Genes. Science. DOI: 10.1126/science.1171541
- December 15, 2008
- 06:26 PM
- 707 views
Antibiotic Treatment: Increasing the Rates of Genetic Exchange
by Tim Sampson in The Times Microbial
The dangers of single antibiotic treatment are well known and well established. It is common knowledge that improper use of antibiotics can lead to the development of resistant strains in which the antibiotic was created to be used against.The development of these resistances in a population is most often thought to be due to direct selective pressure. That is, those cells containing mutations that resist the antibiotic, or those that contain a protein to export or degrade the antibiotic, are h........ Read more »
Prudhomme, M. (2006) Antibiotic Stress Induces Genetic Transformability in the Human Pathogen Streptococcus pneumoniae. Science, 313(5783), 89-92. DOI: 10.1126/science.1127912
- December 15, 2008
- 05:00 PM
- 951 views
Antibiotic Treatment: Increasing the Rate of Genetic Exchange
by Tim Sampson in The Times Microbial
The dangers of single antibiotic treatment are well known and well established. It is common knowledge that improper use of antibiotics can lead to the development of resistant strains in which the antibiotic was created to be used against. The development of these resistances in a population is most often thought to be due to direct selective pressure.However, there is a 2006 study, published in Science, which shows that antibiotic treatment does more than "merely" select for resistan........ Read more »
Prudhomme, M. (2006) Antibiotic Stress Induces Genetic Transformability in the Human Pathogen Streptococcus pneumoniae. Science, 313(5783), 89-92. DOI: 10.1126/science.1127912
- November 23, 2008
- 08:46 PM
- 943 views
Extracellular Membrane Vesicles in Bacteria: Taking Quorum Sensing in New Directions
by Tim Sampson in The Times Microbial
Bacterial quorum sensing is not a new phenomenon by any means. Although the term has only recently come into the existence, the concept has been around for decades.In 1964,Tomasz and Hotchkiss, out of Rockefeller, demonstrated the presence of a macromolecule responsible for induction of competence in pneumococcus when the cells reached a specific growth point in mid to late log phase.This concept has been vastly expanded upon and the ramifications of such diffusible communication molecules are v........ Read more »
Mashburn, L., & Whiteley, M. (2005) Membrane vesicles traffic signals and facilitate group activities in a prokaryote. Nature, 437(7057), 422-425. DOI: 10.1038/nature03925
- November 23, 2008
- 05:00 PM
- 1,137 views
Extracellular Membrane Vesicles in Bacteria: Taking Quorum Sensing in New Directions
by Tim Sampson in The Times Microbial
Bacterial quorum sensing is not a new phenomenon by any means. Although the term has only recently come into the existence, the concept has been around for decades.
In 1964,Tomasz and Hotchkiss, out of Rockefeller, demonstrated the presence of a macromolecule responsible for induction of competence in pneumococcus when the cells reached a specific growth point in mid to late log phase.
This concept has been vastly expanded upon and the ramifications of such diffusible communication molecules........ Read more »
Mashburn, L., & Whiteley, M. (2005) Membrane vesicles traffic signals and facilitate group activities in a prokaryote. Nature, 437(7057), 422-425. DOI: 10.1038/nature03925
- November 13, 2008
- 09:30 PM
- 592 views
Utilizing Natural Killers: Phage-Based Antimicrobials
by Tim Sampson in The Times Microbial
My last article on the origins of antibiotic resistance perked my interest in the current thinking of how we scientists are planning on overcoming this challange. The two answers that most people will consider are 1) develop new chemical analogs of current antibiotic compounds, and 2) discover novel compounds that act as antimicrobials.It is this second concept that appeals most to me. However, it raises the question, "Where do we look for novel antimicrobial compounds?"Some are taking a step ba........ Read more »
Rybniker, J., Plum, G., Robinson, N., Small, P., & Hartmann, P. (2008) Identification of three cytotoxic early proteins of mycobacteriophage L5 leading to growth inhibition in Mycobacterium smegmatis. Microbiology, 154(8), 2304-2314. DOI: 10.1099/mic.0.2008/017004-0
- November 13, 2008
- 05:00 PM
- 1,089 views
Utilizing Natural Killers: Phage-Based Antimicrobials
by Tim Sampson in The Times Microbial
My last article on the origins of antibiotic resistance perked my interest in the current thinking of how we scientists are planning on overcoming this challange. The two answers that most people will consider are 1) develop new chemical analogs of current antibiotic compounds, and 2) discover novel compounds that act as antimicrobials.
It is this second concept that appeals most to me. However, it raises the question, "Where do we look for novel antimicrobial compounds?"... Read more »
Rybniker, J., Plum, G., Robinson, N., Small, P., & Hartmann, P. (2008) Identification of three cytotoxic early proteins of mycobacteriophage L5 leading to growth inhibition in Mycobacterium smegmatis. Microbiology, 154(8), 2304-2314. DOI: 10.1099/mic.0.2008/017004-0
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