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Lab Rat
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- May 12, 2012
- 06:00 AM
- 90 views
Ancient Diseases of Human Ancestors
I’ve written before about ancient diseases of the ice age, but this time I’m going even further back in time, to diseases that were present in the first human-like hominids. Although many human infections only developed after human settlements and animal domistication, early human ancestors would still have been fighting off bacteria and other nasty diseases. Some of these diseases are still around today.... Read more »
Trueba G, & Dunthorn M. (2012) Many neglected tropical diseases may have originated in the Paleolithic or before: new insights from genetics. PLoS neglected tropical diseases, 6(3). PMID: 22479653
Monot, M., Honoré, N., Garnier, T., Zidane, N., Sherafi, D., Paniz-Mondolfi, A., Matsuoka, M., Taylor, G., Donoghue, H., Bouwman, A.... (2009) Comparative genomic and phylogeographic analysis of Mycobacterium leprae. Nature Genetics, 41(12), 1282-1289. DOI: 10.1038/ng.477
Diavatopoulos DA, Cummings CA, Schouls LM, Brinig MM, Relman DA, & Mooi FR. (2005) Bordetella pertussis, the causative agent of whooping cough, evolved from a distinct, human-associated lineage of B. bronchiseptica. PLoS pathogens, 1(4). PMID: 16389302
- May 5, 2012
- 05:30 AM
- 96 views
Pathogens that feed off human blood
by Lab Rat in Lab Rat Blog
Bacteria may be tiny little micro-organisms but like any other living creature there are certain molecules that they need for survival. No matter what niche a bacterial colony occupies, it eventually requires a source of iron. For bacteria that live within the human body, there is one incredibly iron-rich molecule that circulates throughout the human body and can be found permeating the tissues.... Read more »
Pishchany G, & Skaar EP. (2012) Taste for blood: hemoglobin as a nutrient source for pathogens. PLoS pathogens, 8(3). PMID: 22412370
Pishchany, G., McCoy, A., Torres, V., Krause, J., Crowe, J., Fabry, M., & Skaar, E. (2010) Specificity for Human Hemoglobin Enhances Staphylococcus aureus Infection. Cell Host , 8(6), 544-550. DOI: 10.1016/j.chom.2010.11.002
- March 12, 2012
- 10:00 AM
- 179 views
Deadly cocktails for killing bacteria
by Lab Rat in Lab Rat Blog
As a general rule in life there is always a bigger fish – for every predator there is a bigger one lurking that is ready to eat it. However it is also worth remembering that there is usually always a smaller fish as well; for every small irritating parasite there is something that can infect it. Bacteria are no exception.... Read more »
Gu J, Liu X, Li Y, Han W, Lei L, Yang Y, Zhao H, Gao Y, Song J, Lu R.... (2012) A method for generation phage cocktail with great therapeutic potential. PloS one, 7(3). PMID: 22396736
- March 1, 2012
- 11:00 AM
- 185 views
How to form a species (in the world of the Very Small)
by Lab Rat in Lab Rat Blog
A species is one of those things that is harder to define than it looks. While it’s clear that (for example) a rat is a different species than a dog, the more closely related animals get, the harder it is to properly put them into species. Usual definitions involve the sharing of physical characteristics (although the physical characteristics shared between a Great Dane and a Shih Tzu can be harder to ascertain…) and the fundamental idea of breeding. If two species can interbreed to produce fertile offspring they are usually considered the same species. This still runs into problems; some animals can interbreed but just don’t (for example if they live on opposite sides of a mountain range) some animals can interbreed and produce mostly asterile offspring with the occasional random fertile quirk, while some animals could potentially interbreed but it’s rather hard to imagine (again, with the Great Dane and the Shih Tzu)... Read more »
Cadillo-Quiroz H, Didelot X, Held NL, Herrera A, Darling A, Reno ML, Krause DJ, & Whitaker RJ. (2012) Patterns of gene flow define species of thermophilic archaea. PLoS biology, 10(2). PMID: 22363207
- February 26, 2012
- 05:50 AM
- 175 views
Gastric ulcer bacteria hide from the immune system
by Lab Rat in Lab Rat Blog
A while ago, I wrote about how Helicobacter pylori, the bacteria that cause stomach ulcers and are implicated in certain stomach cancers, cause the cells of the stomach wall to die. H. pylori kills cells very sneakily, by releasing a chemical that causes them to commit suicide. It turns out that this is not the only sneaky trick H. pylori has, it can also hide from the immune system by changing its outer cell membrane.... Read more »
Cullen TW, Giles DK, Wolf LN, Ecobichon C, Boneca IG, & Trent MS. (2011) Helicobacter pylori versus the host: remodeling of the bacterial outer membrane is required for survival in the gastric mucosa. PLoS pathogens, 7(12). PMID: 22216004
- February 12, 2012
- 11:10 AM
- 168 views
How the TB bacteria bursts your cells
by Lab Rat in Lab Rat Blog
The bacteria that causes Tuberculosis is a nasty little beast. The white blood cells that clear infection in your body work by ingesting bacteria and then breaking them up, and the TB escapes this by letting itself get ingested and then sitting inside your white blood cells. They don’t sit passively, however, they burst out of the cell and recruit a whole host of other blood cells which surround the infection and form what’s called a granuloma. The bacteria stay inside the granuloma and become dormant, but if they escape they can set up other sites of infection throughout the body.... Read more »
Simeone R, Bobard A, Lippmann J, Bitter W, Majlessi L, Brosch R, & Enninga J. (2012) Phagosomal Rupture by Mycobacterium tuberculosis Results in Toxicity and Host Cell Death. PLoS pathogens, 8(2). PMID: 22319448
- February 7, 2012
- 10:00 AM
- 175 views
Sticky bacteria and the benefits of staying still
I’ve written before about the many ways that bacteria can move around. Considering that they’re just one cell long, micro-organisms have a whole range of ways to travel through their little world. Movement is useful for finding food and for changing your environment when all nearby resources have been exhausted. For bacteria that can’t move, however, or that don’t want to move, there is a second option; they can park themselves on a nearby surface and settle down to wait.... Read more »
Busscher HJ, & van der Mei HC. (2012) How do bacteria know they are on a surface and regulate their response to an adhering state?. PLoS pathogens, 8(1). PMID: 22291589
- January 10, 2012
- 01:00 AM
- 262 views
Discrete steps to antibiotic resistance
I’ve been getting so exited about the awesome powers of bacteria on this blog lately that I’ve been neglecting to cover the nasty bacteria. More specifically the fascinating world of antibiotics, the antimicrobial elements that bacteria and fungi produce and that humans exploit, manufacture and synthesise in order to protect against bacterial infections.... Read more »
Toprak, E., Veres, A., Michel, J., Chait, R., Hartl, D., & Kishony, R. (2011) Evolutionary paths to antibiotic resistance under dynamically sustained drug selection. Nature Genetics, 44(1), 101-105. DOI: 10.1038/ng.1034
- January 4, 2012
- 11:00 PM
- 297 views
How bacteria sneak into your blood through your mouth
by Lab Rat in Lab Rat Blog
The inside of the human body is a bacteria-free zone. Bacteria are certainly within you, but they exist only in areas that have a direct channel to the outside world, such as the mouth, intestines and the surface of the skin. These areas are well protected by a layer of cells (epithilial cells) which form a protective barrier to keep away the nasties of the outside world. That’s why there are healthy stomach bacteria, but no healthy liver bacteria. From a certain point of view your lungs and digestive tract still are the outside world, which is why bacteria can get in and live there, sometimes perfectly happily without causing any trouble at all.... Read more »
Fardini, Y., Wang, X., Témoin, S., Nithianantham, S., Lee, D., Shoham, M., & Han, Y. (2011) Fusobacterium nucleatum adhesin FadA binds vascular endothelial cadherin and alters endothelial integrity. Molecular Microbiology, 82(6), 1468-1480. DOI: 10.1111/j.1365-2958.2011.07905.x
- November 16, 2011
- 06:00 AM
- 296 views
Bacteria with bodies – multicellular prokaryotes
by Lab Rat in Lab Rat Blog
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Bacteria with bodies – multicellular prokaryotes
By S.E. Gould | November 16, 2011 |
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Bacterial cells are fundamentally different to the cells of multicellular animals such as humans. They are far smaller, with less internal organisation and no nucleus (they have DNA but it is not packaged safely within a membrane). Because of this bacteria are almost exclusively single-celled organisms, with their own autonomy and often mobility.... Read more »
Flores, E., & Herrero, A. (2009) Compartmentalized function through cell differentiation in filamentous cyanobacteria. Nature Reviews Microbiology, 8(1), 39-50. DOI: 10.1038/nrmicro2242
- November 14, 2011
- 08:02 AM
- 487 views
How cancer-causing bacteria force your cells to die
by Lab Rat in Lab Rat Blog
The discovery that stomach ulcers are caused by bacteria is quite recent and was proved fairly conclusively in 1984 when the Australian scientist Barry Marshall drank a petri-dish full of the bacteria Helicobacter pylori and five days later developed serious gastritis, which cleared after antibiotic treatment. As stomach ulcers are quite common, and can be a major source of duodenal ulcers and stomach cancer, the discovery that they could be treated by a course of antibiotics was of major medical importance.... Read more »
Jain P, Luo ZQ, & Blanke SR. (2011) Helicobacter pylori vacuolating cytotoxin A (VacA) engages the mitochondrial fission machinery to induce host cell death. Proceedings of the National Academy of Sciences of the United States of America, 108(38), 16032-7. PMID: 21903925
- November 2, 2011
- 07:00 PM
- 364 views
How to explore a protein
by Lab Rat in Lab Rat Blog
I’m doing a journal club presentation tomorrow, where I take a paper apart in front of my lab through the medium of powerpoint. It’s a nice short little paper but it does bring up some interesting points and also works as a prime example of a very common way that scientists go about exploring how a particular protein works. There are many ways to do this, but this one is quite a common one and if everything works it can generate very nice results.
Stage one: Find your gene... Read more »
Scharf DH, Remme N, Habel A, Chankhamjon P, Scherlach K, Heinekamp T, Hortschansky P, Brakhage AA, & Hertweck C. (2011) A dedicated glutathione S-transferase mediates carbon-sulfur bond formation in gliotoxin biosynthesis. Journal of the American Chemical Society, 133(32), 12322-5. PMID: 21749092
- November 2, 2011
- 07:00 PM
- 377 views
How to explore a protein
by Lab Rat in Lab Rat Blog
I’m doing a journal club presentation tomorrow, where I take a paper apart in front of my lab through the medium of powerpoint. It’s a nice short little paper but it does bring up some interesting points and also works as a prime example of a very common way that scientists go about exploring how a particular protein works. There are many ways to do this, but this one is quite a common one and if everything works it can generate very nice results.
Stage one: Find your gene... Read more »
Scharf DH, Remme N, Habel A, Chankhamjon P, Scherlach K, Heinekamp T, Hortschansky P, Brakhage AA, & Hertweck C. (2011) A dedicated glutathione S-transferase mediates carbon-sulfur bond formation in gliotoxin biosynthesis. Journal of the American Chemical Society, 133(32), 12322-5. PMID: 21749092
- November 1, 2011
- 01:00 AM
- 423 views
Modelling a werewolf epidemic
by Lab Rat in Lab Rat Blog
The field of bacteriology is a wide-reaching one. Blogging about bacteria means that I get to explore many different fields of science; from the highly molecular world of biochemistry and synthetic biology to the larger and more human-centred land of the pathologists and immunologists.
One area that I don’t go into so much is epidemiology; the study of how diseases spread through a population. It’s an important area of research and leads to vital discoveries about immunisations and population load. By modelling how diseases spread through a population you can look at potential ways to stop them.... Read more »
Philip Munz, Ioan Hudea, Joe Imad, Robert J. Smith. (2009) When Zombies attack!: Mathematical modelling of an outbreak of zombie infection. Infectious Disease Modelling Research Progress. info:other/978-1-60741-347-9
- October 26, 2011
- 10:00 PM
- 336 views
Plastic from bacteria – now in algae!
by Lab Rat in Lab Rat Blog
Bacteria are capable of producing a wide range of exciting and important materials, and one of the most unusual is probably bacterial plastics. Used by the bacteria as an energy store, these bioplastics are of particular interest as not only could they be a non-oil-based form of plastic but they are also biodegradable. At the moment, they are still far more expensive than conventional plastics, but researchers are working on finding ways to make bacterial bioplastic a more viable alternative to synthetic plastics.... Read more »
Hempel F, Bozarth AS, Lindenkamp N, Klingl A, Zauner S, Linne U, Steinbuchel A, & Maier UG. (2011) Microalgae as bioreactors for bioplastic production. Microbial cell factories, 10(1), 81. PMID: 22004563
Rehm BH. (2003) Polyester synthases: natural catalysts for plastics. The Biochemical journal, 376(Pt 1), 15-33. PMID: 12954080
- October 6, 2011
- 01:00 AM
- 354 views
The evolution of bacterial energy centres
by Lab Rat in Lab Rat Blog
One of the first things you learn once you start taking biology as a subject is that life is split into two separate domains – prokeryotes and eukaryotes. Prokaryotes are small and blobby and have no nucleus or internal organisation, while eukaryotes are big and multicellular and contain not just a nucleus, but all sorts of other organelles inside the cell such as mitochondria, chloroplasts, vacuoles and exciting things with names like endoplasmic reticulum.... Read more »
Seufferheld, M. (2003) Identification of Organelles in Bacteria Similar to Acidocalcisomes of Unicellular Eukaryotes. Journal of Biological Chemistry, 278(32), 29971-29978. DOI: 10.1074/jbc.M304548200
Seufferheld, M., Kim, K., Whitfield, J., Valerio, A., & Caetano-Anolles, G. (2011) Evolution of vacuolar proton pyrophosphatase domains and volutin granules: clues into the early evolutionary origin of the acidocalcisome. Biology Direct, 6(1), 50. DOI: 10.1186/1745-6150-6-50
- October 2, 2011
- 12:00 PM
- 380 views
Sequencing the Impossible – working with ‘unculturable’ bacteria
by Lab Rat in Lab Rat Blog
Bacteria are everywhere. In the air, in the soil, in our bodies and, thanks to human-built rockets, even in space. While the number of different bacterial strains and species discovered is continually increasing some bacteria, particularly environmental ones, are often very difficult to work with. These so-called ‘unculturable’ bacteria don’t grow under laboratory conditions, making it impossible to characterise and understand them.... Read more »
Chitsaz H, Yee-Greenbaum JL, Tesler G, Lombardo MJ, Dupont CL, Badger JH, Novotny M, Rusch DB, Fraser LJ, Gormley NA.... (2011) Efficient de novo assembly of single-cell bacterial genomes from short-read data sets. Nature biotechnology. PMID: 21926975
- September 23, 2011
- 06:00 AM
- 357 views
Ancient resistance – ice-age bacteria that could fight off antibiotics
Antibiotic resistance is often seen as a modern phenomenon – an ability generated by bacteria in order to defend against the challenges of modern medicine. This is supported by the fact that bacteria from before the era of antibiotics are often more susceptible to their use. Which is why I found it intriguing that recent studies (ref below) have unearthed bacteria from 30 000-year old permafrost sediment and have found evidence of genes that provide resistance against three of the most common types of antibiotics used in hospitals: β-lactam, tetracycline and glycopeptide antibiotics.... Read more »
D'Costa VM, King CE, Kalan L, Morar M, Sung WW, Schwarz C, Froese D, Zazula G, Calmels F, Debruyne R.... (2011) Antibiotic resistance is ancient. Nature. PMID: 21881561
- September 19, 2011
- 08:00 AM
- 398 views
Synthetic DNA - now in yeast!
by Lab Rat in Lab Rat Blog
iGEM season is here and so to get into the spirit of things I thought I'd see if any interesting synthetic biology news had happened recently. It turns out that while I've been getting all excited about bacteria, people doing research on yeast have managed something pretty spectacular - they've replaced a whole section of a yeast chromosome with artificial DNA... Read more »
Dymond JS, Richardson SM, Coombes CE, Babatz T, Muller H, Annaluru N, Blake WJ, Schwerzmann JW, Dai J, Lindstrom DL.... (2011) Synthetic chromosome arms function in yeast and generate phenotypic diversity by design. Nature. PMID: 21918511
- September 13, 2011
- 12:00 PM
- 481 views
Genes for antibiotic resistance
by Lab Rat in Lab Rat Blog
Ever since the discovery and marketing of penicillin in 1928 by Alexander Fleming, bacteria have been developing resistance to antibiotics at an alarming rate. In many cases, resistant bacteria can be found lurking even before the new drug hits the market, making it only a matter of time before it becomes widespread.
Bacteria that are resistant to multiple antibiotics are commonly known as ‘superbugs’ and on one particularly virulent such bug is vancomycin-resistant Enterococcus faecium or VRE. VRE is an intestinal bacteria that lives in the human gut and is resistant to many antibiotics including vancomycin, which is currently one of the more powerful antibiotics used to treat other superbugs such as MRSA.... Read more »
Arias CA, Panesso D, McGrath DM, Qin X, Mojica MF, Miller C, Diaz L, Tran TT, Rincon S, Barbu EM.... (2011) Genetic basis for in vivo daptomycin resistance in enterococci. The New England journal of medicine, 365(10), 892-900. PMID: 21899450
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