91 posts · 71,059 views
The idea of the blog was to provide accurate and interesting information and reflections on science from somebody currently in the field.
Lab Rat
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- August 26, 2012
- 04:00 AM
- 206 views
Tiny RNA fragments control bacterial infections
There is more than one type of genetic material within the cell. As well as DNA, which stores the code for making cellular protiens, there is also RNA, which contains similar snatches of code but is less stable and more mobile than DNA. If DNA is a library of books which are not allowed to be removed, then RNA is little buts of paper containing copies of pages that are spread around for people to read.... Read more »
Mann B, van Opijnen T, Wang J, Obert C, Wang YD, Carter R, McGoldrick DJ, Ridout G, Camilli A, Tuomanen EI.... (2012) Control of Virulence by Small RNAs in Streptococcus pneumoniae. PLoS pathogens, 8(7). PMID: 22807675
- June 16, 2012
- 03:46 AM
- 287 views
How bacteria in the vagina change during pregnancy
One thing that becomes more clear with each piece of research is that the human body is a hive of mostly harmless bacteria that live in any crevice they can reach while affecting their human host as little as possible. In some cases these bacteria can be very beneficial – preventing more dangerous bacteria from taking up residence in places like the stomach and throat. In some cases they can occasionally go rogue, get into places they shouldn’t be, and cause havoc.... Read more »
Kjersti Aagaard, Kevin Riehle, Jun Ma, Nicola Segata4, Toni-Ann Mistretta, Cristian Coarfa, Sabeen Raza, Sean Rosenbaum, Ignatia Van den Veyver, Aleksandar Milosavljevic, Dirk Gevers, Curtis Huttenhower, Joseph Petrosino, James Versalovic. (2012) A Metagenomic Approach to Characterization of the Vaginal Microbiome Signature in Pregnancy. PloS one, 7(6). DOI: 10.1016/j.ajog.2010.10.087
Maria G. Dominguez-Bello, & et al. (2010) Delivery mode shapes the acquisition and structure of the initial microbiota across multiple body habitats in newborns. Proceedings of the National Academy of Sciences, 107(26). DOI: 10.1073/pnas.1002601107
- May 27, 2012
- 08:10 AM
- 268 views
The Bacteria that Commit Honourable Suicide
In multicellular organisms it is essential that every cell behaves and does the job it was produced to perform. The survival of a multicellular organism depends on this - every cell in your body is tightly controlled in terms of how big it can grow (fairly big), when it can reproduce (almost never) and what sort of metabolic processes it may carry out. And, like a dystopian sci-fi future, any cell that steps out of line is put to death. Not by surrounding cells, but by it’s own internal p........ Read more »
Lewis, K. (2000) Programmed Death in Bacteria. Microbiology and Molecular Biology Reviews, 64(3), 503-514. DOI: 10.1128/MMBR.64.3.503-514.2000
Robinson, R. (2012) In E. coli, Interrupting One Death Pathway Leads You Down Another. PLoS Biology, 10(3). DOI: 10.1371/journal.pbio.1001278
- May 12, 2012
- 06:00 AM
- 320 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
- February 7, 2012
- 10:00 AM
- 342 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
- 421 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
- September 23, 2011
- 06:00 AM
- 559 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
- August 24, 2011
- 12:00 PM
- 894 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
- June 22, 2011
- 01:27 PM
- 883 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
- June 16, 2011
- 06:22 PM
- 988 views
Plant Defence 3 - Acquired Resistance
In posts one and two of this mini-series I explored how plants can defend against bacteria by releasing dangerous chemicals and by killing off cells. This post looks at how surviving one bacterial attack can make plants more able to survive subsequent ones with both local and systemic acquired resistance.Locally acquired resistance is the simplest to manage, and provides a clear advantage. If cells have been attacked once it makes sense to defend them in case of a second attack. Plants achieve t........ Read more »
Brisson, L., Tenhaken, R., & Lamb, C. (1994) Function of Oxidative Cross-Linking of Cell Wall Structural Proteins in Plant Disease Resistance. The Plant Cell, 6(12), 1703. DOI: 10.2307/3869902
Durrant, W., & Dong, X. (2004) SYSTEMIC ACQUIRED RESISTANCE. Annual Review of Phytopathology, 42(1), 185-209. DOI: 10.1146/annurev.phyto.42.040803.140421
Shulaev, V., Silverman, P., & Raskin, I. (1997) Airborne signalling by methyl salicylate in plant pathogen resistance. Nature, 385(6618), 718-721. DOI: 10.1038/385718a0
- June 14, 2011
- 01:53 PM
- 1,154 views
Plant defence 2 - Honourable Suicide
The first post of this mini-series covered how plants can defend themselves against bacterial attack by releasing chemicals, either on a regular basis or as a specific response to the attack. This post will explore the hypersensitive response, which allows plants to rapidly kill of cells around the area of infection, starving the bacteria of nutrients to prevent it spreading. The end result is a small area of dead plant matter, with the rest of the organism unaffected.One of the main differences........ Read more »
Lam, E., Kato, N., & Lawton, M. (2001) Programmed cell death, mitochondria and the plant hypersensitive response. Nature, 411(6839), 848-853. DOI: 10.1038/35081184
Pontier, D., Balagué, C., & Roby, D. (1998) The hypersensitive response. A programmed cell death associated with plant resistance. Comptes Rendus de l'Académie des Sciences - Series III - Sciences de la Vie, 321(9), 721-734. DOI: 10.1016/S0764-4469(98)80013-9
- June 10, 2011
- 12:55 PM
- 567 views
Plant defence 1 - Deadly Chemicals
Although I've never officially studied immunology, my second year course in Pathology left me with a pretty solid idea of how humans defend themselves against bacterial attack. Even without a university course I've always been vaguely aware of the presence of immune cells; the B and T cells that make up the adaptive immune system, the clotting response, and the symptoms of inflammation around the site of infection.How plants responded to bacterial attack was still a complete mystery though. One ........ Read more »
Papadopoulou, K. (1999) Compromised disease resistance in saponin-deficient plants. Proceedings of the National Academy of Sciences, 96(22), 12923-12928. DOI: 10.1073/pnas.96.22.12923
Nürnberger, T., & Scheel, D. (2001) Signal transmission in the plant immune response. Trends in Plant Science, 6(8), 372-379. DOI: 10.1016/S1360-1385(01)02019-2
- April 27, 2011
- 12:04 PM
- 1,356 views
Social Evolution in Bacteria - SGM series
This is the fourth post in my latest SGM series.
The social behaviour of bacteria is something that I get very excited about. From the wolf-pack hunting strategies of Myxococcus xanthus to the terminal differentiation of cyanobacteria, it's something that I never get tired of writing about. As well as providing interesting quirks of bacterial behaviour, living within a colony also gives new scope for exploring the evolution of bacteria; not just as single entities but as a fully functioning so........ Read more »
Sandoz, K., Mitzimberg, S., & Schuster, M. (2007) From the Cover: Social cheating in Pseudomonas aeruginosa quorum sensing. Proceedings of the National Academy of Sciences, 104(40), 15876-15881. DOI: 10.1073/pnas.0705653104
Paterson S, Vogwill T, Buckling A, Benmayor R, Spiers AJ, Thomson NR, Quail M, Smith F, Walker D, Libberton B.... (2010) Antagonistic coevolution accelerates molecular evolution. Nature, 464(7286), 275-8. PMID: 20182425
- April 22, 2011
- 05:30 AM
- 1,414 views
Life at zero growth rate - SGM series
This is the third post in my latest SGM series.One of the first topics that I learnt in Biology was that there are two types of things; living things, and dead things. Living things are given a whole host of distinguishing characteristics (growth, reproduction and, my favourite, irritability) where as dead things are defined as everything else. Biology was usually defined as the study of living things.As I grew older, I found that there were many complications to this neat little classification......... Read more »
Kana BD, Gordhan BG, Downing KJ, Sung N, Vostroktunova G, Machowski EE, Tsenova L, Young M, Kaprelyants A, Kaplan G.... (2008) The resuscitation-promoting factors of Mycobacterium tuberculosis are required for virulence and resuscitation from dormancy but are collectively dispensable for growth in vitro. Molecular microbiology, 67(3), 672-84. PMID: 18186793
Davies AP, Dhillon AP, Young M, Henderson B, McHugh TD, & Gillespie SH. (2008) Resuscitation-promoting factors are expressed in Mycobacterium tuberculosis-infected human tissue. Tuberculosis (Edinburgh, Scotland), 88(5), 462-8. PMID: 18440866
- April 13, 2011
- 12:37 PM
- 1,066 views
Insect Symbiosis - SGM series
This is the second post from my latest SGM series.It's a pretty well known fact now that the human body contains lots of bacteria. Bacteria live on your skin and in your throat and gut, for the most part completely harmlessly, protecting your body from more dangerous invaders.But something that doesn't get mentioned quite so often is that humans are not the only animals with a corresponding posse of bacteria. Other animals have them as well, including insects. From a bacterial point of view both........ Read more »
Wilson AC, Ashton PD, Calevro F, Charles H, Colella S, Febvay G, Jander G, Kushlan PF, Macdonald SJ, Schwartz JF.... (2010) Genomic insight into the amino acid relations of the pea aphid, Acyrthosiphon pisum, with its symbiotic bacterium Buchnera aphidicola. Insect molecular biology, 249-58. PMID: 20482655
Thomas GH, Zucker J, Macdonald SJ, Sorokin A, Goryanin I, & Douglas AE. (2009) A fragile metabolic network adapted for cooperation in the symbiotic bacterium Buchnera aphidicola. BMC systems biology, 24. PMID: 19232131
Schoenian I, Spiteller M, Ghaste M, Wirth R, Herz H, & Spiteller D. (2011) Chemical basis of the synergism and antagonism in microbial communities in the nests of leaf-cutting ants. Proceedings of the National Academy of Sciences of the United States of America, 108(5), 1955-60. PMID: 21245311
- March 1, 2011
- 06:04 AM
- 1,229 views
Signals for Infection
Neisseria meningitidis is a bacteria which lives in the throats of around 30% of the human population. In most cases it causes no problems at all and just exists as a normal part of the throat microbial flora. In some patients however it can start to colonise the bloodstream and brain, leading to cases of septicemia and meningitis which are highly dangerous and can be fatal.The invasion starts with individual bacteria, which adhere to the epithelial cells that cover the inside of the throat. Th........ Read more »
Chamot-Rooke J, Mikaty G, Malosse C, Soyer M, Dumont A, Gault J, Imhaus AF, Martin P, Trellet M, Clary G.... (2011) Posttranslational modification of pili upon cell contact triggers N. meningitidis dissemination. Science (New York, N.Y.), 331(6018), 778-82. PMID: 21311024
- February 21, 2011
- 01:33 PM
- 1,143 views
Multicellular signalling
I like studying bacteria. I find them fascinating, wonderful little creatures, able to do as much (and often more!) with a single cell as other organisms need whole multicellular bodies to achieve. I like exploring the places bacteria live, the things they can do, the ways they manage to exploit practically every niche on earth, and of course most importantly how I can exploit them.But not everyone loves bacteria, and at heart I am a biochemist which means, among other things, that I get to teac........ Read more »
Rajagopal S, Rajagopal K, & Lefkowitz RJ. (2010) Teaching old receptors new tricks: biasing seven-transmembrane receptors. Nature reviews. Drug discovery, 9(5), 373-86. PMID: 20431569
- January 16, 2011
- 09:18 AM
- 886 views
Targeting dormant bacteria
Antibiotics are effective against bacteria because they target and knock out specific functions that are vital for bacterial survival. As most bacterial infections involve rapid growth and division of the invading bacteria, many commercial antibiotics currently target metabolically active cells, by blocking enzymes needed for growth, reproduction, or cell wall synthesis. While these will kill acute bacterial infections they are often far less effective against dormant bacteria in longer-term per........ Read more »
Hurdle JG, O'Neill AJ, Chopra I, & Lee RE. (2011) Targeting bacterial membrane function: an underexploited mechanism for treating persistent infections. Nature reviews. Microbiology, 9(1), 62-75. PMID: 21164535
- December 24, 2010
- 07:34 AM
- 886 views
Levels of evolution
Eukaryotes - animals, plants, and other creatures with a nucleus, evolve relatively slowely. Genetic variation occurs through changes in the DNA between generations; each offspring will be a genetic product of their parents and nothing else. Genetic changes happen down the generations. In bacteria, however, everything is a little more insane. Because bacteria can change DNA with almost any other bacteria they come accross, there is less of a conserved genetic record. Genes are flying around all ........ Read more »
He, M., Sebaihia, M., Lawley, T., Stabler, R., Dawson, L., Martin, M., Holt, K., Seth-Smith, H., Quail, M., Rance, R.... (2010) Evolutionary dynamics of Clostridium difficile over short and long time scales. Proceedings of the National Academy of Sciences, 107(16), 7527-7532. DOI: 10.1073/pnas.0914322107
- December 9, 2010
- 03:24 PM
- 716 views
Guest post - Microbes and Madness
This guest post comes from my fiancé who is a Psychiatrist. I've been very excited about this post for a while, because unlike me, he is a published author who has written a book on Consciousness and the philosophy of mind.Microbes and MadnessAt first glance, it would be reasonable to assume that my profession and that of the author of this fabulous blog are poles apart. However, everything in nature has a connection, and so it is not surprising to discover a fascinating area where psychiatry a........ Read more »
Pfister D, Siegemund M, Dell-Kuster S, Smielewski P, Rüegg S, Strebel SP, Marsch SC, Pargger H, & Steiner LA. (2008) Cerebral perfusion in sepsis-associated delirium. Critical care (London, England), 12(3). PMID: 18457586
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