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Lab Rat
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- February 7, 2012
- 10:00 AM
- 39 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
- 129 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
- 121 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 a........ 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
- 118 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 ........ 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
- 294 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 medic........ 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
- 203 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
- 200 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
- 238 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 an........ 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
- 182 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 ........ 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
- 187 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
- 213 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
- 230 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 com........ 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
- 261 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
- 297 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 ........ 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
- August 24, 2011
- 12:00 PM
- 440 views
How cytomegalovirus evades the immune system
The human immune system is a large and complex beast, but in general it has two roles. Firstly, to prevent an infection from causing any harm and secondly to protect the body against a repeat attack. For many diseases protection against reinfection happens very efficiently, and this is the principle on which vaccines are based. By exposing your body to a non-harmful sample of the disease your immune system can built up resistance. For cytomegalovirus however the immune system seems mysteriously ........ Read more »
Hansen, S., Powers, C., Richards, R., Ventura, A., Ford, J., Siess, D., Axthelm, M., Nelson, J., Jarvis, M., Picker, L.... (2010) Evasion of CD8 T Cells Is Critical for Superinfection by Cytomegalovirus. Science, 328(5974), 102-106. DOI: 10.1126/science.1185350
Nigro, G., Adler, S., La Torre, R., & Best, A. (2005) Passive Immunization during Pregnancy for Congenital Cytomegalovirus Infection. New England Journal of Medicine, 353(13), 1350-1362. DOI: 10.1056/NEJMoa043337
- August 4, 2011
- 10:00 AM
- 474 views
Bacterial Traitors
by Lab Rat in Lab Rat Blog
Aphids are small insects that are a major pest in crop production. Dealing with these aphid pests often involves the use of pesticides, however growing resistance to these pesticides means that many farmers are now looking to use natural predators such as ladybirds or hoverflies to stop aphids destroying crops.... Read more »
Leroy PD, Sabri A, Heuskin S, Thonart P, Lognay G, Verheggen FJ, Francis F, Brostaux Y, Felton GW, & Haubruge E. (2011) Microorganisms from aphid honeydew attract and enhance the efficacy of natural enemies. Nature communications, 348. PMID: 21673669
Wootton L. (2011) Microbial ecology: Bacterial volatiles give the game away. Nature reviews. Microbiology. PMID: 21785449
- July 25, 2011
- 11:00 PM
- 410 views
Making bacteria visible
by Lab Rat in Lab Rat Blog
For a microbiologist, viewing bacteria is rarely a problem. When I look at bacteria in the lab they are samples that I have grown specially, in aseptic conditions to stop any other bacteria getting in. They will all be the same species of bacteria, grown in media that favours them exclusively and is designed to make them easy to see under a microscope.... Read more »
Ning X, Lee S, Wang Z, Kim D, Stubblefield B, Gilbert E, & Murthy N. (2011) Maltodextrin-based imaging probes detect bacteria in vivo with high sensitivity and specificity. Nature materials, 10(8), 602-7. PMID: 21765397
- July 21, 2011
- 10:30 AM
- 228 views
When virus's and bacteria unite!
by Lab Rat in Lab Rat Blog
Illnesses have a tendency to clump together. An attack of the flu can bring on bacterial lung infections; in the USA almost half of all cases of bacterial sepsis occur following viral infections in the lungs. This is a problem at the best of times as it means that patients spend longer in hospitals, but in times of a viral pandemic it becomes incredibly deadly.... Read more »
Beadling, C., & Slifka, M. (2004) How do viral infections predispose patients to bacterial infections?. Current Opinion in Infectious Diseases, 17(3), 185-191. DOI: 10.1097/00001432-200406000-00003
Kim YG, Park JH, Reimer T, Baker DP, Kawai T, Kumar H, Akira S, Wobus C, & Núñez G. (2011) Viral infection augments nod1/2 signaling to potentiate lethality associated with secondary bacterial infections. Cell host , 9(6), 496-507. PMID: 21669398
Brundage, J. (2006) Interactions between influenza and bacterial respiratory pathogens: implications for pandemic preparedness. The Lancet Infectious Diseases, 6(5), 303-312. DOI: 10.1016/S1473-3099(06)70466-2
- July 11, 2011
- 10:30 AM
- 260 views
Communicating with electricity
by Lab Rat in Lab Rat Blog
Bacteria that communicate by producing an electric current.... Read more »
Reguera, G., McCarthy, K., Mehta, T., Nicoll, J., Tuominen, M., & Lovley, D. (2005) Extracellular electron transfer via microbial nanowires. Nature, 435(7045), 1098-1101. DOI: 10.1038/nature03661
Nielsen, L., Risgaard-Petersen, N., Fossing, H., Christensen, P., & Sayama, M. (2010) Electric currents couple spatially separated biogeochemical processes in marine sediment. Nature, 463(7284), 1071-1074. DOI: 10.1038/nature08790
Nealson, K. (2010) Geomicrobiology: Sediment reactions defy dogma. Nature, 463(7284), 1033-1034. DOI: 10.1038/4631033a
- June 22, 2011
- 01:27 PM
- 440 views
Vaccines and viral evolution
This is the first time in ten years that I haven't had an exam around summer-time. It feels odd, everyone around me is either exam-stressed or post-exam-relaxed, it's turning to summer and there's a definite final term feeling but this time I'm not really part of it. It's been an interesting year this year, since January I've not been involved in any part of research science, other than writing about it.However luckily I'm still surrounded by lectures, seminars, talks and various other interesti........ Read more »
Witter RL. (2001) Protective efficacy of Marek's disease vaccines. Current topics in microbiology and immunology, 57-90. PMID: 11217428
Witter RL. (1997) Increased virulence of Marek's disease virus field isolates. Avian diseases, 41(1), 149-63. PMID: 9087332
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