“Let another man praise thee, and not thine own mouth; a stranger, and not thine own lips.” — Proverbs 27:2
“What-ever” – Me
In PLoS Computational Biology this week, a trio of researchers provides a review of the challenges that metagenomics might ― and already do ― pose for bioinformaticians. The authors refer to metagenomic sequencing data [...]... Read more »
This is pretty neat: scientists have apparently discovered the first example of truly anaerobic animal life (i.e. an animal that can survive in the absence of oxygen). This isn't some sort of fuzzy critter, though; instead, these are tiny (less than 1 mm in length) animals that were found on the floor of the Mediterranean Sea. Significantly, these animals lack mitochondria, the sub-cellular organelles where oxygen is employed to produce ATP in aerobic (oxygen-dependent) life.
You can check out the original paper by Danovaro et al. (and two accompanying commentary articles) at BMC Biology: Read the rest of this post... | Read the comments on this post...... Read more »
Danovaro, R., Dell'Anno, A., Pusceddu, A., Gambi, C., Heiner, I., & Kristensen, R. (2010) The first metazoa living in permanently anoxic conditions. BMC Biology, 8(1), 30. DOI: 10.1186/1741-7007-8-30
Mentel, M., & Martin, W. (2010) Anaerobic animals from an ancient, anoxic ecological niche. BMC Biology, 8(1), 32. DOI: 10.1186/1741-7007-8-32
This was a very interesting article I came across in Cancer Research while looking for something else. Serendipity is a great thing sometimes. A quote in the abstract caught my eye: "We have conducted a small interfering RNA (siRNA) screen...... Read more »
Higgins, G., Prevo, R., Lee, Y., Helleday, T., Muschel, R., Taylor, S., Yoshimura, M., Hickson, I., Bernhard, E., & McKenna, W. (2010) A Small Interfering RNA Screen of Genes Involved in DNA Repair Identifies Tumor-Specific Radiosensitization by POLQ Knockdown. Cancer Research, 70(7), 2984-2993. DOI: 10.1158/0008-5472.CAN-09-4040
by Mary in OpenHelix
As much as I love computational aspects of biology, there are times when the sort of flat and binary nature of the discipline leaves me craving some more three-dimensional, real live cellular work. My background was in cell biology and microtubule-associated proteins before I moved to the computational side of biology. And there are days when I would love to see more linkage between the digital and the dimensional. And days when I’d love to look around in the scope at mitosis and mitotic spindles again.
Today I saw it. And I’m going to show you where. We’ll be looking at the MitoCheck database. Below I’ll offer some discussion of the associated research papers, and in the movie I’ll show you how to navigate around the MitoCheck site a bit to find their data online.
It was actually coverage on the BBC* that tipped me off to this resource. And then I went looking for more. A press release on the work provided details and links. And then the Nature News article added additional information.
In short, this group of researchers used a couple of different genomics approaches to examine what happens to HeLa cells when you mess with the mitotic apparatus and processes. They transform cells with either RNA interference constructs, or GFP-tagged proteins, and film what happens to the cells over time. They analyze the movies, and make all this data available in the MitoCheck resource. As we say here in Boston–this is wicked cool.
But now, on to the papers: these researchers have 2 articles out that talk about the work, one focused more on the RNAi approach, and a separate one on the tagged proteins. I’ll address them separately below.
RNA interference experiments:
In this series of experiments, the MitoCheck team started with over 20,000 protein coding genes in humans, transformed HeLa cells with the siRNAs, and let the cells divide over a couple of days. The nuclei of the cells could be illuminated by a GFP-histone protein that they had already placed in the cells. They could light up the cells and film them, and monitor whether cell division looked normal or not. They were able to identify a number of cases where things were going awry. And they were going wrong in various ways. Sometimes there was cell death. Other times they could see a variety of phenotypes such as delayed mitosis, binuclear, poly-lobed, or “grape” looking aberrations. Some cells were too large. These could all be categorized, and compared, quantified, and are now stored as movies, processed data, and phenotypic assignment in the MitoCheck database.
I have some minor concerns about how knocked-down the transcripts are–they say that the values of the target mRNAs drop a lot, but these numbers vary quite a bit (the amount of supplemental data with the paper is excruciating….). It’s also hard to be sure what that means for the protein levels at this point. Also, HeLa cells have some characteristics that may not be average. But that said–as a general method and a hunting license to find genes to assess in more detail, I think this is a very excellent strategy. If I was still in the lab, I’d try the same thing with the cell system I used to study: C2C12 cells for muscle development. You could track whether cell fusion and myotube formation was disrupted….man, sometimes I do crave the lab still….
Tagged protein experiments:
In a second paper from the research teams, they use a similar strategy of monitoring the behavior of cells during mitosis via movies. But this time instead of knocking down a gene, they put a GFP tag on some selected proteins (mostly mouse proteins) that they put into the HeLa cells. These are stably-transfected tagged proteins on BACs, and they call this BAC TransgeneOmics (ahem, another -omics?). They look for where these proteins end up in dividing cells. Again, they have movies of this available now in their database. They also pull down protein complexes and look at them in more detail with other techniques.
Again, I have minor questions about the approach: mouse proteins in HeLa cells, and the bulky GFP tag affecting interactions, expression levels, etc. But again, as a hunting-license sort of effort, I think this is a very neat way to move downstream from digital genomics to real cells. And it’s worth it. The team demonstrates that you can begin to characterize the functions of unknown proteins with this strategy.
So, for this week’s tip of the week I show you MitoCheck. I’ll show how to access this data so you can take it further if you like. One technical note: I did have all of the issues that they talked about in their “troubleshooting” document (PDF) on my Windows machine. I had to do all 4 of the things they recommend in there to get the movies to run. FYI.
MitoCheck site: http://mitocheck.org/
Nature paper with RNAi data:
Neumann, B., Walter, T., Hériché, J., Bulkescher, J., Erfle, H., Conrad, C., Rogers, P., Poser, I., Held, M., Liebel, U., Cetin, C., Sieckmann, F., Pau, G., Kabbe, R., Wünsche, A., Satagopam, V., Schmitz, M., Chapuis, C., Gerlich, D., Schneider, R., Eils, R., Huber, W., Peters, J., Hyman, A., Durbin, R., Pepperkok, R., & Ellenberg, J. (2010). Phenotypic profiling of the human genome by time-lapse microscopy reveals cell division genes Nature, 464 (7289), 721-727 DOI: 10.1038/nature08869
Sciencexpress article with protein and complexes data:
Hutchins, J., Toyoda, Y., Hegemann, B., Poser, I., Heriche, J., Sykora, M., Augsburg, M., Hudecz, O., Buschhorn, B., Bulkescher, J., Conrad, C., Comartin, D., Schleiffer, A., Sarov, M., Pozniakovsky, A., Slabicki, M., Schloissnig, S., Steinmacher,... Read more »
Neumann, B., Walter, T., Hériché, J., Bulkescher, J., Erfle, H., Conrad, C., Rogers, P., Poser, I., Held, M., Liebel, U.... (2010) Phenotypic profiling of the human genome by time-lapse microscopy reveals cell division genes. Nature, 464(7289), 721-727. DOI: 10.1038/nature08869
Hutchins, J., Toyoda, Y., Hegemann, B., Poser, I., Heriche, J., Sykora, M., Augsburg, M., Hudecz, O., Buschhorn, B., Bulkescher, J.... (2010) Systematic Localization and Purification of Human Protein Complexes Identifies Chromosome Segregation Proteins. Science. DOI: 10.1126/science.1181348
A few months ago, I asked Why Do We Sleep?That post was about sleep researcher Jerry Siegel, who argues that sleep evolved as a state of "adaptive inactivity". According to this idea, animals sleep because otherwise we'd always be active, and constant activity is a waste of energy. Sleeping for a proportion of the time conserves calories, and also keeps us safe from nocturnal predators etc.Siegel's theory in what we might call minimalist. That's in contrast to other hypotheses which claim that sleep serves some kind of vital restorative biological function, or that it's important for memory formation, or whatever. It's a hotly debated topic.But Siegel wasn't the first sleep minimalist. J. Allan Hobson and Robert McCarley created a storm in 1977 with The Brain As A Dream State Generator; I read somewhere that it provoked more letters to the Editor in the American Journal of Psychiatry than any other paper in that journal.Hobson and McCarley's article was so controversial because they argued that dreams are essentially side-effects of brain activation. This was a direct attack on the Freudian view that we dream as a result of our subconscious desires, and that dreams have hidden meanings. Freudian psychoanalysis was incredibly influential in American psychiatry in the 1970s.Freud believed that dreams exist to fulfil our fantasies, often though not always sexual ones. We dream about what we'd like to do - except we don't dream about it directly, because we find much of our desires shameful, so our minds disguise the wishes behind layers of metaphor etc. "Steep inclines, ladders and stairs, and going up or down them, are symbolic representations of the sexual act..." Interpreting the symbolism of dreams can therefore shed light on the depths of the mind.Hobson and McCarley argued that during REM sleep, our brains are active in a similar way to when we are awake; many of the systems responsible for alertness are switched on, unlike during deep, dreamless, non-REM sleep. But of course during REM there is no sensory input (our eyes are closed), and also, we are paralysed: an inhibitory pathway blocks the spinal cord, preventing us from moving, except for our eyes - hence why it's Rapid Eye Movement sleep.Dreams are simply a result of the "awake-like" forebrain - the "higher" perceptual, cognitive and emotional areas - trying to make sense of the input that it's receiving as a result of waves of activation arising from the brainstem. A dream is the forebrain's "best guess" at making a meaningful story out of the assortment of sensations (mostly visual) and concepts activated by these periodic waves. There's no attempt to disguise the shameful parts; the bizarreness of dreams simply reflects the fact that the input is pretty much random.Hobson and McCarley proposed a complex physiological model in which the activation is driven by the giant cells of the pontine tegmentum. These cells fire in bursts according to a genetically hard-wired rhythm of excitation and inhibition.The details of this model are rather less important than the fact that it reduces dreaming to a neurological side effect. This doesn't mean that the REM state has no function; maybe it does, but whatever it is, the subjective experience of dreams serves no purpose.A lot has changed since 1977, but Hobson seems to have stuck by the basic tenets of this theory. A good recent review came out in Nature Neuroscience last year, REM sleep and dreaming. In this paper Hobson proposes that the function of REM sleep is to act as a kind of training system for the developing brain.The internally-generated signals that arise from the brainstem (now called PGO waves) during REM help the forebrain to learn how to process information. This explains why we spend more time in REM early in life; newborns have much more REM than adults; in the womb, we are in REM almost all the time. However, these are not dreams per se because children don't start reporting experiencing dreams until about the age of 5.Protoconscious REM sleep could therefore provide a virtual world model, complete with an emergent imaginary agent (the protoself) that moves (via fixed action patterns) through a fictive space (the internally engendered environment) and experiences strong emotion as it does so.This is a fascinating hypothesis, although very difficult to test, and it begs the question of how useful "training" based on random, meaningless input is.While Hobson's theory is minimalist in that it reduces dreams, at any rate in adulthood, to the status of a by-product, it doesn't leave them uninteresting. Freudian dream re-interpretation is probably ruled out ("That train represents your penis and that cat was your mother", etc.), but if dreams are our brains processing random noise, then they still provide an insight into how our brains process information. Dreams are our brains working away on their own, with the real world temporarily removed.Of course most dreams are not going to give up life-changing insights. A few months back I had a dream which was essentially a scene-for-scene replay of the horror movie Cloverfield. It was a good dream, scarier than the movie itself, because I didn't know it was a movie. But I think all it tells me is that I was paying attention when I watched Cloverfield.On the other hand, I have had several dreams that have made me realize important things about myself and my situation at the time. By paying attention to your dreams, you can work out how you really think, and feel, about things, what your preconceptions and preoccupations are. Sometimes.Hobson JA, & McCarley RW (1977). The brain as a dream state generator: an activation-synthesis hypothesis of the dream process. The American journal of psychiatry, 134 (12), 1335-48 PMID: 21570Hobson, J. (2009). REM sleep and dreaming: towards a theory of protoconsciousness Nature Reviews Neuroscience, 10 (11), 803-813 DOI: 10.1038/nrn2716... Read more »
Hobson JA, & McCarley RW. (1977) The brain as a dream state generator: an activation-synthesis hypothesis of the dream process. The American journal of psychiatry, 134(12), 1335-48. PMID: 21570
Hobson, J. (2009) REM sleep and dreaming: towards a theory of protoconsciousness. Nature Reviews Neuroscience, 10(11), 803-813. DOI: 10.1038/nrn2716
Researchers from New York have presented an approach to help teachers better integrate conservation biology into the high school classroom. This is important because teaching conservation biology to students could play a key role in influencing people to "pursue careers or live lifestyles that would reduce the negative impact of humans on the world."
Yet, in the United States - and probably many other countries - few secondary schools have specific classes in conservation biology. ... Read more »
WYNER, Y., & DESALLE, R. (2010) Taking the Conservation Biology Perspective to Secondary School Classrooms. Conservation Biology. DOI: 10.1111/j.1523-1739.2010.01478.x
In a world in which numerous species are declining towards extinction, conservationists are forced to make the difficult choice of where to spend limited resources. Some scientists are taking an interesting approach to prioritization by focusing on the evolutionary distinctiveness of species - i.e. the extent to which a given species is lacking in close relatives. Their approach is based on the idea that maintaining evolutionary diversity should be an important objective...... Read more »
Cadotte, M., & Jonathan Davies, T. (2010) Rarest of the rare: advances in combining evolutionary distinctiveness and scarcity to inform conservation at biogeographical scales. Diversity and Distributions. DOI: 10.1111/j.1472-4642.2010.00650.x
A little while back I wrote an article about a recent study which largely blamed farmed Tilapia for the loss of native biodiversity in Fijian waterways. I have since received e-mails from Gerald Billings, the Head of Aquaculture at the Ministry of Fisheries and Forests in Fiji. He expressed his concern over the paper's intent and subsequent findings. As a scientist, I believe strongly in impartiality, so I've posted the entirety of his response to the study after the fold for you to read if you wish. I don't like the idea of supporting bickering between governments and conservation organizations, but in this case, I feel the need to comment more on this paper. Indeed, there are many sides to the story here, and my first pass was a little short-sighted.
I am a conservationist at heart, so I was clearly drawn to the message of the Tilapia study. I instantly agreed with the idea that our actions are having negative consequences in ways we haven't even thought of, and that we need to be more careful when we throw species around the globe.
But, Mr. Billings brings up counter points to the study that cannot be ignored. Indeed, as he states, there is a growing need to feed people that cannot be met by the current native species, and the authors management plan does not include any way of dealing with this issue. To be fair (to myself), I did bring this up in my review. To quote myself on the issue (which is a very strange thing to do),
It's a good plan for the native fish, but as the human populations continue to expand, countries like Fiji will, out of necessity, rely more and more heavily on compact, efficient means of producing food like fish farms. As they do so, it will be harder and harder to keep the fish in the farms from escaping and damaging the surrounding habitat. While this paper serves to warn of the downsides of aquaculture, it unfortunately doesn't provide a solution to the underlying problem of too many mouths to feed on limited resources.
But Mr. Billings also brings up another valid point that I didn't recognize the first time I read the study. It's my age-old pet peeve, and this time, I failed to properly critique the authors: correlation isn't causation.
The paper looked at a number of variables and correlated them to native fish density and diversity. To summarize the entire paper super-quickly, the researchers found that where tilapia lived, native fish didn't. They suggested that this was due to tilapia's voracious appetite. What they didn't do is actually justify that position - they provided no data to show that tilapia introduction in a previously tilapia free waterway caused a drop in native fish density.
Mr. Billings is right: just because they're at the scene of the crime doesn't mean they committed it. Another perfectly plausible explanation for the correlation between tilapia presence and low native fish density is that, like many invasive and introduced species, tilapia is quick to fill ecological gaps. Instead of the tilapia eating their way through freshwater streams, it's possible that some other disturbance created ecological holes that the fast-breeding, adaptable tilapia gladly filled.
That's not to say that studies like this one shouldn't be done: indeed, understanding what is happening in an ecosystem is the first step in understanding why it is happening. I still believe this paper is interesting and vital to understanding the role invasive species may play in ecosystem decay, but some of the authors' conclusions must be taken with a grain of salt. At minimum, they must be supported by further research into the interaction of tilapia and native fish. Read the rest of this post... | Read the comments on this post...... Read more »
Jenkins, A., Jupiter, S., Qauqau, I., & Atherton, J. (2010) The importance of ecosystem-based management for conserving aquatic migratory pathways on tropical high islands: a case study from Fiji. Aquatic Conservation: Marine and Freshwater Ecosystems, 20(2), 224-238. DOI: 10.1002/aqc.1086
A leopard (Panthera pardus). Image from Wikipedia.
SK-54 is a curious fossil. The 1.5 million year old skullcap represents a juvenile Paranthropus robustus, one of the heavy-jawed hominins which lived in prehistoric South Africa, but there is something that makes this skull fragment particularly special. Near one of the sutures along the back of the skull are two neat puncture marks, the hallmark of a leopard.
Even though it was initially proposed that SK-54 had been murdered by another australopithecine wielding a weapon of bone or horn, in the late 1960's the paleontologist C.K. Brain was able to demonstrate that the holes almost precisely fitted with the lower canine teeth of a leopard. What's more, Brain determined that many of the accumulations of bones found in the South African cave deposits were attributable to the activities of predators, meaning that for a long span of time our ancient relatives (particularly juveniles) may have regularly been cat food. Nor were hominins the only primate fossils to be found in these accumulations. It seems that the prehistoric leopards had a taste for primates, just as some living leopards do.
In the Tai Forest of Cote d'Ivoire, leopards frequently kill and consume primate prey. It is rare that scientists observe an attack in progress, but the primate remains in big cat scat confirm that primates are a major part of the leopard diet in this forest. Along with what we know from the fossil record, these prey preferences have raised an interesting question. Have the hunting habits of leopards influenced primate evolution? Read the rest of this post... | Read the comments on this post...... Read more »
Managing for stability just doesn’t work.
This epiphany has helped forge the development of ecosystem based management (EBM), theoretically a more holistic approach to natural resource management that is more in tune with natural processes. However, we still haven’t worked out the kinks so something good in theory often falls flat. A couple of recent [...]... Read more »
GRANEK, E., POLASKY, S., KAPPEL, C., REED, D., STOMS, D., KOCH, E., KENNEDY, C., CRAMER, L., HACKER, S., BARBIER, E.... (2010) Ecosystem Services as a Common Language for Coastal Ecosystem-Based Management. Conservation Biology, 24(1), 207-216. DOI: 10.1111/j.1523-1739.2009.01355.x
PETERSON, M., HALL, D., FELDPAUSCH-PARKER, A., & PETERSON, T. (2010) Obscuring Ecosystem Function with Application of the Ecosystem Services Concept. Conservation Biology, 24(1), 113-119. DOI: 10.1111/j.1523-1739.2009.01305.x
Researchers have discovered three species of Loricifera living in an oxygen-starved basin at the bottom of the Mediterranean Sea. Loricifera are marine sediment-dwelling animals consisting of a head, mouth, digestive system and outer shell called a lorica.
... Read more »
Roberto Danovaro, Antonio Dell'Anno, Antonio Pusceddu, Cristina Gambi, Iben Heiner, & Reinhardt Mobjerg Kristensen. (2010) The first metazoa living in permanently anoxic conditions. BMC Biology, 8(3). info:/
Scientists validate a new drug target, the Trypanosoma brucei enzyme N-myristoyltransferase, in the fight against sleeping sickness, and have already identified and tested an inhibitor against this enzyme that successfully cures T. brucei infection in mice.
The study, published in the journal Nature, provides a much-needed boost to research into neglected tropical diseases, which are often associated with [...]... Read more »
Frearson, J., Brand, S., McElroy, S., Cleghorn, L., Smid, O., Stojanovski, L., Price, H., Guther, M., Torrie, L., Robinson, D.... (2010) N-myristoyltransferase inhibitors as new leads to treat sleeping sickness. Nature, 464(7289), 728-732. DOI: 10.1038/nature08893
The Harpy Eagle (Harpia harpyja) is a nasty scary-looking muppethugging monster of a carnivorous bird. Female harpies weigh 14-20 pounds, and males weigh 8.5-12 pounds. They stand between 2.9 and 3.5 feet tall. The wingspan of the harpy eagle can reach 6 feet, 7 inches. The talons – sharp claws to grasp onto [...]... Read more »
Gil-da-Costa R, Palleroni A, Hauser MD, Touchton J, & Kelley JP. (2003) Rapid acquisition of an alarm response by a neotropical primate to a newly introduced avian predator. Proceedings. Biological sciences / The Royal Society, 270(1515), 605-10. PMID: 12769460
A bunch of scientists build robots which blend in with a society by learning their languages and customs. The intention of these robots is to subvert the societies by changing the how the locals think and act.
Sounds like something from a bad sci-fi movie, right? A Tea Party speech, perhaps?
Welcome to the world of pest [...]... Read more »
Halloy, J., Sempo, G., Caprari, G., Rivault, C., Asadpour, M., Tache, F., Said, I., Durier, V., Canonge, S., Ame, J.... (2007) Social Integration of Robots into Groups of Cockroaches to Control Self-Organized Choices. Science, 318(5853), 1155-1158. DOI: 10.1126/science.1144259
The turritopsis nutricula species of jellyfish may, in fact, be the only immortal creature in the world.... Read more »
Piraino, S., Boero, F., Aeschbach, B., & Schmid, V. (1996) Reversing the Life Cycle: Medusae Transforming into Polyps and Cell Transdifferentiation in Turritopsis nutricula (Cnidaria, Hydrozoa). Biological Bulletin, 190(3), 302. DOI: 10.2307/1543022
People move animals around. It's what we do. Why are there Elk on Afognak island? Some guy thought it was a good idea at the time. Wildlife managers in the past were some of the biggest conduits for moving animals around, frequently en mass, back before biology really caught up with the profession. We can cite plenty of examples where moving animals around to do population rescues was a bad thing... Read more »
Haanes, H., Røed, K., Mysterud, A., Langvatn, R., & Rosef, O. (2010) Consequences for genetic diversity and population performance of introducing continental red deer into the northern distribution range. Conservation Genetics. DOI: 10.1007/s10592-010-0048-1
Much like internal waves, I always loved the idea of explosive radiation. Not the nasty, pernicious Chernobyl kind; I mean the rapid evolution of a whole bunch of species from a common ancestor, over a relatively short period of time. There's a few textbook examples of explosive radiations, but none so well-worn (possibly even hackneyed) as that of the cichlid fishes in the rift lakes of ... Read more »
Väinölä, R., Witt, J., Grabowski, M., Bradbury, J., Jazdzewski, K., & Sket, B. (2007) Global diversity of amphipods (Amphipoda; Crustacea) in freshwater. Hydrobiologia, 595(1), 241-255. DOI: 10.1007/s10750-007-9020-6
Elmer, K., Reggio, C., Wirth, T., Verheyen, E., Salzburger, W., & Meyer, A. (2009) Pleistocene desiccation in East Africa bottlenecked but did not extirpate the adaptive radiation of Lake Victoria haplochromine cichlid fishes. Proceedings of the National Academy of Sciences, 106(32), 13404-13409. DOI: 10.1073/pnas.0902299106
I love B-grade monster movies, and one of my all time favorites is the 1980 creature feature Alligator. As its title suggests, the film’s protagonist is a 40-foot-long alligator, literally pumped up on steroids from consuming the bodies of medical research lab animals which had been dumped in the sewers under Chicago, and it spends [...]... Read more »
Héctor E. RIVERA-SYLVA, Eberhard FREY, José Rubén GUZMÁN-GUTIÉRREZ. (2009) Evidence of predation on the vertebra of a hadrosaurid dinosaur from the Upper Cretaceous (Campanian) of Coahuila, Mexico. Notebooks on Geology, 1-6. info:/
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 see here and here for some recent advances), studying this important group of pathogens challenges a researcher's patience for results. (Imagine waiting a month or more for a colony to grow to see if a simple transformation was successful!)Neveretheless, the study of these bacteria is vital as the Mycobacteria represent one of the largest, global public health concerns. Over 1/3 of the world's population is thought to be infected with Mycobacterium tuberculosis, and a growing percentage of this population is exceedingly drug resistant. During infection, the bacterial population often enters a latent state, making antibiotic treatment (and diagnosis) difficult.In an effort to study this latent phase, a research group happened upon what appeared to be textbook endospores in very late stationary phase cultures of Mycobacterium marinum, a common model for acute Mycobacteria infection. As they closely examined cell morphology over long periods of time (2 months), they began to see forespore formation, and subsequent endospores. Utilizing TEM, the distinct outer coat and cortex of the spores could be identified in the M. marinum population.These researchers analyzed rRNA from the sporulating cells and identified it as M. marinum, ruling out contamination issues. Also, they demonstrated heat tolerance, malachite green staining, and the presence of dipicolinic acid an important compound necessary for heat resistance in most spore-forming species. Furthermore, their bioinformatic analysis revealed the presence of homologs of genes utilized in sporulation within the M. marinum genome. Taken all together, the authors hypothesize that M. marinum forms spores, and posit that these spores may be how Mycobacteria stay dormant in a host.However, here is where the speculation steps in...A group of rather prominent US labs in the field attempted to replicate M. marinum sporulation in their labs, and were unable to demonstrate sporulation by any of the methods used by the original researchers. Furthermore, in an attempt to see if spores were present during latent M. marinum infection as the original authors postulated, they attempted to isolate heat resistant cells from infected frogs. Although they could recover Bacillus spores from spiked tissue samples, they could never isolate M. marinum.Additionally, the authors demonstrate that the majority of the genes picked out by the original researchers as being sporulation homologs in Mycobacteria, are actually rather universal Gram-positive genes, with homologs present in a wide variety of species, without being used for sporulation. Some of these genes identified by the original group are also not necessary for sporulation, even in Bacillus sp. Finally, neither group of researchers could identify a group of coat proteins, in M. marinum, that are necessary for spore formation in Bacillus.The lack of this set of coat proteins could be explained by the hypothesis that M. marinum forms its coat differently. This would be a fine rationale, however the spores the original researchers imaged looked identical to those found in B. subtilis. This is of note, particularly because even within the Bacillus genus (with similar coat proteins), spores between species are highly dissimilar.With this set of data, the second set of researchers conclude that M. marinum does not form spores, and that the simplest solution is that the original authors were looking at Bacillus sp. spores, and not those of M. marinum.Looking at these two articles, what do you think? (It's time to stop reading articles that don't pertain to my thesis proposal and get back to studying for quals!)Sources: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.0904104106Traag, 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.0911299107Other Articles of Interest:A Fatty Acid Synthetase is Necessary for Active TB InfectionRecombineering: A Practical Application of Phage BiologyProkaryotes Can Do Geometry, And Even Have Their Own Protractor
... 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
Most studies on turbidity investigate freshwater ecosystems and few studies have focused on the impacts of turbidity on marine ecosystems. Eianne et al. (1999) showed that invertebrate planktivores (jellyfish) replaced planktivorous fish within Norwegian turbid fiords. This was likely to be because increased turbidity levels reduced the possibility of foraging in visually oriented fish, while tactile feeding in jellyfish allowed them to continue to feed under light-limited conditions.... Read more »
Eiane, K., Aksnes, D.L., Bagoien, E., & Kaartvedt, S. (1999) Fish or jellies - a question of visibility?. Limnology and Oceangraphy, 44(5), 1352-1357. info:/
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