24 September 2006

Light sensing response in Prochlorococcus marinus MED4

A new article is about to be published in the Journal of Bacteriology, describing a whole genome analysis of the response of Prochlorococcus marinus MED4 to different light conditions (light quantities and wavelengths). The microarray analysis reveals that this phototroph probably uses the same light sensing mechanism to respond to high-intensity white and blue light. This enables it to thrive over a wide range of depths, up to 200 meters where only blue part of the light spectrum can be utilised for photosynthesis. The response involves differential gene expression of genes possibly encoding bacterial chryptochromes and alterations of the redox state of the electron transport chain.

Microarrays is a really great technique to investigate environmental response of cyanobacteria. It's huge importance emerges when investigating organisms like Prochlorococcus, which is a dominating photosynthetic organism in huge areas of the open ocean, contributing up to 50% of the primary production in the oligotrophic gyres of the open ocean between 40..N and 40..S). In addition, MED4 has the smallest genome of a free-living photoautotroph (1716 genes), a third of which have not been functionally characterized, which makes it easier and more interesting to analyse, assuming that during the billions of years of evolution, the redundant genetic material was shed, turning MED4 into a perfectly adapted organism to low-nutrient environments, such as oligotrophic ocean.

Of course, my interest is elicited by the fact that MED4 is also a model organism in my research ;).


Prochlorococcus MED4 has, with a total of only 1716 annotated protein-coding genes, the most compact genome of a free-living photoautotroph. Although light quality and quantity play an important role in regulating the growth rate of this organism in its natural habitat, the majority of known light-sensing proteins are absent from its genome. To explore the potential for light-sensing in this phototroph, we measured its global gene expression pattern in response to different light qualities and quantities using high density Affymetrix microarrays. Though seven different conditions were tested, only blue light elicited a strong response. In addition, hierarchical clustering revealed that the response to high white light and blue light was very similar, and different from that of the lower intensity of white light, suggesting that the actual sensing of high light is mediated via a blue light receptor. Bacterial cryptochromes seem to be good candidates for the blue light sensors. The existence of a signaling pathway for the redox state of the photosynthetic electron transport chain was suggested by the presence of genes that responded similarly to red and blue light, as well as genes that responded to the addition of DCMU, a specific inhibitor of photosystem II-mediated electron transport.
Link (subscription access)

Technorati tags:

Microbiology, Environment, Microarrays, Prochlorococcus, MED4

02 July 2006

Linkie Winkie

Linkie Winkie

Had to Wink! :)

Invasive Species Newsflash!

Seems like no habitat, regardless of how isolated and inappropriate for human colonisation, is not spared of the invasive species plague. New Scientist reports on invasive species becoming a problem even on Antarctica (registration required):

New Scientist SPACE - Premium- Alien species at the gates of Antarctica - Breaking News: "ALIENS are invading Antarctica. The battle is on to prevent them from wreaking havoc, but it may not be enough. Non-native species are already establishing themselves in what is one of the world's last great wildernesses.

At the Antarctic Treaty Consultative Meeting (ATCM) in Edinburgh, UK, last week, 45 nations agreed measures aimed at stopping non-native microbes, plants and animals from invading the Antarctic. Visiting ships are being urged not to dump ballast water from other oceans, and the invading aliens problem was given top priority for research."

Technorati tags:

Ecology, Environment, Invasive Species, Biodiversity

14 June 2006

Reshuffling regulons

When discussing mobile elements in DNA, we usually talk about jumping genes, meaning open reading frames, or even better - fully functional proteins whose encoding genes can either transfer themselves from one place to the other inside its genome or copy itself, thereby creating apparently redundant amount of genetic material.

However, one recent paper that caught my eye is describing a slightly different picture: it is not the gene that is jumping, it is the promoter:

The genome of Tolypothrix sp. PCC 7601 carries two copies of a novel insertion sequence, ISTosp1. One of the two copies is located upstream of the gene encoding glutamyl-tRNA synthetase, an enzyme playing a key role in protein and pigment synthesis. The tnpA gene of the IS element and gltX were co-transcribed and their expression was transiently upregulated upon retrieval of the ammonium source irrespective of whether nitrate or no nitrogen source were available. The second copy is also transcribed and shows a similar regulatory pattern. Structural elements of the promoter (-10 and -35 sequences) directing the expression of the tnpA-gltX operon have been localized within the IS. Regulatory sequences involving the NtcA transcription factor in the control of tnpA-gltX expression were found both within and in sequences upstream of the insertion element. The expression of gltX in a closely related cyanobacterium, Nostoc sp. PCC 7120, which lacks the insertion upstream of gltX, decreased upon ammonium retrieval, a regulatory pattern that markedly differs from that observed in Tolypothrix sp. PCC 7601. ISTosp1 constitutes a good example of how cells can make use of a transposable element to evolve an original regulatory mechanism.

It is quite an interesting concept. Just imagine a nitrogen response element being able to jump from place to place in cyanobacterial genome and regulate a different sets of genes every time, in response to a nitrogen stress. One can only assume that the number of different regulatory possibilities would be huge and that different variants produced by the regulon shifting would have different fitness levels at different nutrient stress conditions. For example, a variant whose nitrogen response element has inserted itself before the genes for photosynthetic complexes would be able to decrease the level of photosynthetic activity in response to the lack of nitrogen, in addition to its previous abilities to regulate the photosynthesis in response to light conditions. Such variant would have much greater fitness than the non-shuffled "wildtype". This removes a whole dimension of randomality from the shoulders of the evolution of microorganisms...

SAR11 - update

OK, so here is the long promised SAR11 update. Actually it is quite a nice story.

While looking for material about the way bacteria adapt to oligotrophic environment, i stumbled upon mention of a convention that took place in Berlin in 1979. The name of convention was Dahlem Konferenzen and the topic was "Strategies of Microbial Life in Extreme Environments". It was impossible to find proceedings from the conference since they were definitely not to be found online or in any other digital format. I went to consult the professor responsible for the course i was taking and he had the proceedings on his shelf! Go figure.

Anyways, in one of the sessions of the conference called "Life under conditions of low nutrient concentrations", the participants tried to list a number of general traits that would be typical of an microorganism in oligotrophic conditions. So i thought it would be cool to take the predictions from 1979 and see whether they are confirmed in the case of SAR11. So here is what i came up with:

1979 Dahlem Konferenzen Prediction



A high surface-to-volume ratio

SAR11 is one of the smallest known prokaryotes. Its’ bean shaped cell is about 0.5 µm long and 0.2 µm wide


Preferential usage of metabolic energy for nutrient uptake

SAR11 has an average of 62% more genes encoding membranal transporters than any other bacteria with a sequenced genome. From 50% of total transporters and almost all of the nutrient uptake related transporters are ABC transporters, meaning that they are using ATP in order to bring in the nutrients from the outside.


Possession of high-affinity, low-specificity transport systems

ABC transporters are considered to generally be a high affinity enzymes with a very high turnover number. Additionally, genome sequence analysis of SAR11 shows that it posseses both high affinity transporters (Ammonia, Urea, Simple amino acids, Spermidine (co-factor), Putrescine (growth factor) transporters) as well as low specificity transporters (Sugars, Branched amino acids, Dicarboxylic acids, Tricarboxylic acids, Osmolytes (glycine, betaine, proline, mannitol, etc.)


Establishment of accumulation reserves following nutrient uptake

SAR11 was found to accumulate several types of metabolites after the uptake, such as amino acids and DMSP


Biosynthetic rates regulated in accordance with the nutrient uptake rate

Genome sequence analysis of SAR11 shows a large number of different regulatory proteins:

  • PhoR/PhoB/PhoC homologues (phosphate limitation response regulators)
  • NtrY/NtrX homologues (nitrogen limitation response regulators)
  • Fur (iron limitation response regulator)
  • envZ/OmpR homologues (osmotic stress regulator)
  • RegB/RegA homologues (redox stress regulator)


Cool, no ?

There are some other things that make this microorganism such a success in oligotropich oceans:

  • the number of active genes in the genome is brought to the minimum - 1354 ORFs
  • the amount of the non-coding DNA was reduced to the astonishing 3 basepairs in average! That is the most reduced known genome in the world!
  • the G:C to A:T ratio was reduced to a point of 29.7% G:C content, which means about 30% less nitrogen atoms per DNA molecule needed.
  • some of its preferred metabolites serve also as osmolites, which adaptes SAR11 to oligotrophic saline environments
  • they seem to have dual energy production system: its genome shows both genes for aerobic respiration and light-driven proteorhodopsin. It is assumed that the proteorhodopsin gives SAR11 advantage over other organisms in the conditions of organic electron donor scarcity

I am generally fascinated by the mechanisms used by microorganisms to adopt to extreme conditions, especially the minimized metabolic pathways and greatly reduced genomic content. SAR11 seems to be a champion of both strategies and can present an important evolutionary example of mechanisms of adaptation driven by extreme environmental conditions

BTW the if anyone wants to search for the Dahlem Konferenzen article, here is the citation:

Hirsch, P, Bernhard, M, Cohen, SS, Ensign, JC, Jannasch, HW, Koch, AL, Marshall, KC Poindexter, JS, Rittenberg, SC, Smith, DC, Veldkamp, H (1979); "Life under conditions of low nutrient concentrations." In: Strategies of Microbial Life in Extreme Environments, Dahlem Konferenzen, Berlin, pp 357-372

11 May 2006

Invasive Species

It was written extensively about the ways we affect our surroundings. The media is full of headlines screaming about global warming, rainforest decimation, oil spills and ozone depletion, but there is one major risk to the world's biodiversity that we are the major cause of and that is not being spoken about so often: invasive species.

Invasive species are defined as:

species introduced deliberately or unintentionally outside their natural habitats where they have the ability to establish themselves, invade, outcompete natives and take over the new environments. They are widespread in the world and are found in all categories of living organisms and all types of ecosystems. However, plants, mammals and insects comprise the most common types of invasive alien species in terrestrial environments.

Invasion of novel species is not a new concept. It is probabbly a sort of human disturbance that has changed the course of human history in the strongest manner: The balance of power today would probably be completely different, had the New World natives been resistant to some of the strains of disease that the Old World colonist brought with them. Colonization of the unexplored lands has brought the dramatic increase in the number and impact of alien species on the pristine niches, when the colonists brought the native species of plants and animals for their use in the New World. Since then, the things are just going downhill and invasive species is now part of the infamous top 3 damaging effects that we extend over our environment, joining pollution and habitat destruction.

Islands are the most vulnerable habitat in regards to invasive species effect. Due to the lack of space, animal and plant species on islands are made out of smaller number of smaller populations. Extremely strong speciation, due to the isolation, makes this habitat prone to huge disturbances due to novel species mainly introduced by humans. Some of the most striking examples to this phenomenon are invasion of the Brown Tree Snake (Boiga irregularis) to Guam and historical invasion of rabbits to Australia.

Plants are much more common invasive species than animals, due to their widespread use as food, building material and in horticulture. Botanical gardens are often hotspots for novel species that spread from there and invade hosting countries' habitats. An extreme example is invasion of Acacia Saligna in several countries with Mediterranean-type climate, such as South Africa or Israel.

In addition to the damage that alien species can inflict to the local biodiversity, they can pose great threat to the human health and economy. In addition to the mentioned infective diseases brought by European colonists to the New World, one of the more recent examples is a spread of the dengue fever in the US, through the far-east native Asian Tiger Mosquito (Aedes albopictus) brought into the country inside of imported tires.

The economical impact of invasive species is hard to measure in the majority of the cases due to several reasons:
  • the delayed effect - sometimes it can take years for an introduced species to become alien and start affecting the local biodiversity

  • the multi-level impact - due to their effect on often key players in the food webs, it is impossible to estimate the total effect on the whole of the ecosystem. Sometimes it is just one link in the chain that is affected, sometimes it is the whole chain that collapses.

  • the lack of ability to put an exact price tag on biodiversity loss
However there are some well documented cases that can just give an example of the possible costs of invasion of alien species. Zebra Mussels (Dreissena polymorpha), native to the Caspian Sea, have been noticed in the Great Lakes area in the late 80-s. They have probably arrived with the ballast water released by the commercial cargo ships coming through the Hudson River. Due to their ability to multiply almost exponentially, they have quickly started to affect the local mollusk species. In addition to the biodiversity impact, the relatively small Zebra Mussel, has found its way into the drains and water pipes of lake shore cities in US and Canada and started causing immense damage. In 1989 there was even a case of a complete three day long water supply shortage in a city of Monroe, MI. Totally US Fish and Wildlife Service estimates the cost of the damage caused by Zebra Mussels in the next 10 years to about $5 billion in the US and Canada alone.

There are quite a few ways of dealing with this problem and the best one is obviously prevention. Appropriate legal measures should be taken in order to prevent any introduction, intentional and unintentional, into the country. Laws protecting biodiversity should be introduced. A good example of a country that takes its invasive species seriously is New Zealand that has introduced its Biosecurity Act which provides the border officials with extensive authorities in goal of prevention of introductions. This is understandable taken that New Zealand is specialy vulnerable to introduction of alien species being an isolated island.

All in all, if we do not take this problem seriously in any country we occupy, they may pretty soon look very bland due to the extensive loss of biodiversity brought upon by the introduction of alien plants and animals

01 May 2006

Malaria resistant mosquitoes

As the Science magazine reports, a group of scientists from the U of Minnesota, the Fred Hutchinson Cancer Research Center in Seattle, Washington, Princeton University, and the University of Bamako in Mali have discovered that the 22 out of 100 known pedigrees of Anopheles gambiae mosquitoes--Africa's most important malaria vector--are already resistant to Plasmodium falciparum, the malaria parasite.

The resistance comes, as reported, from a single cluster of genes:

They discovered that a small region on the 2L chromosome of A. gambiae played an all-important role. The Plasmodium Resistance Island, as they dubbed it, contains almost 1000 genes. Using several techniques to shake out genes of relevance, they pinpointed one gene, APL1, that appears to play a particularly important role; when its action was blocked using RNA interference, mosquitoes became vulnerable to infection. Still, other nearby genes may be involved as well, says lead author Kenneth Vernick of the University of Minnesota, St. Paul.
This discovery brings up possibilities of novel ways of dealing with the disease: since there is already a fungi that attacks predominantly malaria-infected mosquitoes, it is possible to try and eradicate only those mosquitoes that do not posses the resistant allele of the APL1 gene.

Let's just hope that we have not tapped into this opportunity in the middle of the evolutionary arms race between the Plasmodium and Anopheles and that there are no parasites out there that are already capable of getting around the natural defenses of the resistant mosquitoes.


30 April 2006

Not junk after all

From IBM press releases page:

IBM today announced its researchers have discovered numerous DNA patterns shared by areas of the human genome that were thought to have little or no influence on its function and those areas that do. If verified experimentally, the discovery suggests a potential connection between these coding and non-coding parts of the human genome that could have a profound impact on genomic research and provide important insights on the workings of cells.

“Our goal is to apply advanced computational techniques to analyze the workings of processes and systems, in this case the function of the human genome,” said Ajay Royyuru, head of the Computational Biology Center at IBM Research. “Using these tools, we’ve been able to shed new light on parts of the DNA that were traditionally thought of as not having a specific purpose. We believe the innovative application of technology can provide further understanding in the life sciences at large.”

The findings will be published in the next PNAS issue. Here is the abstract of the publication:

Using an unsupervised pattern-discovery method, we processed the human intergenic and intronic regions and catalogued all variable-length patterns with identically conserved copies and multiplicities above what is expected by chance. Among the millions of discovered patterns, we found a subset of 127,998 patterns, termed pyknons, which have additional nonoverlapping instances in the untranslated and protein-coding regions of 30,675 transcripts from 20,059 human genes. The pyknons arrange combinatorially in the untranslated and coding regions of numerous human genes where they form mosaics. Consecutive instances of pyknons in these regions show a strong bias in their relative placement, favoring distances of {approx}22 nucleotides. We also found pyknons to be enriched in a statistically significant manner in genes involved in specific processes, e.g., cell communication, transcription, regulation of transcription, signaling, transport, etc. For {approx}1/3 of the pyknons, the intergenic/intronic instances of their reverse complement lie within 380,084 nonoverlapping regions, typically 60–80 nucleotides long, which are predicted to form double-stranded, energetically stable, hairpin-shaped RNA secondary structures; additionally, the pyknons subsume {approx}40% of the known microRNA sequences, thus suggesting a possible link with posttranscriptional gene silencing and RNA interference. Cross-genome comparisons reveal that many of the pyknons have instances in the 3' UTRs of genes from other vertebrates and invertebrates where they are overrepresented in similar biological processes, as in the human genome. These unexpected findings suggest potential unique functional connections between the coding and noncoding parts of the human genome.

It is interesting that 98.5% of our genome is non-coding (meaning it does not encode functional proteins) and still, science does not leave it at that but keeps exploring and asking infinite questions about it, driven by simple reasoning: it is highly unlikable that the millions of years of evolution have left 98% of DNA that needs repairing, doubling, dragging to different sides of the cell in the process of replication, sifting through in the process of transcription etc., without any purpose for such a vast amount of nucleic acid. Finding a pattern in a chaos is usually a first step towards discovering a function.

IBM Research | Press Resources | IBM Discovery Could Shed New Light on Workings of the Human Genome

29 April 2006


SAR 11 is one of the most ubiquitous organisms on earth.
With it's 1.3 Mb genome, that was only recently sequenced and annotated, it is a smallest known bacteria (1/100th of the size of the average bacteria) and it thrives in the oligotrophic ocean. It's abundance is mind-boggling: 200,000 to 300,000 cells per milliliter! It is an aerobic heterotroph and only recently sucessfuly cultured in a lab. The comparative genomics is of particular interest, since it's genome can shed some additional light on the identity of the obligatory genes for survival in oligotrophic conditions, or if you like it, which of the genes were shed in the evolutionary reductive process.

This intriguing prokaryote is being researched at Stephen Giovannoni's lab in the Department of Microbiology at Oregon State University, where they had the honour of giving it its official proposed name: (Candidatus) Pelagibacter ubique.

I am presently writing a paper on the subject of "Adaptation of microorganisms to oligotrophic environment", so hopefully i will be able to write a comprehensive update on this topic soon.

28 April 2006

The Greatest Scientist

They say that it takes a good scientist to come up with the new theory, but only the great ones take the obvious things that are in fron tof our eyes and formulate it into a scientific theory.

Visit the Charles Darwin exhibit at the American Museum of Natural History. It may be a good starting point of a wonderful journey.


OK, here we go.

Of course i have heard of blogging and of course i had blogs and of course they ended after the third post. So what is different ?

I think that the difference is that now i would like to write about the topic that is my first love, my present time consumer and my future bread maker. Biology. If i have one advantage over a lot of people in my age group, it is the fact that i knew what i want to do with my life since about the age of five. It started with the chocolate bars that had animal stickers in them. Well, i used to throw away the chocolate. It continued with gathering water samples from puddles instead of splashing in them, bringing home lizards and insect, reading Brehm's Tierleben instead of Spiderman (well, in addition to...), watching the World of Survival every afternoon and wanting to become David Attenborough when i'm big.

It may sound nerdy to you, but i actually did not let go and proceeded to take biology as a major in high-school (together with computers) and am now at the end of my undergrad degree at Hebrew U in Jerusalem, majoring in biology and environmental sciences. I am in my last semester and are planning to continue next year into the graduate degree. During the years, my focus in biology has gotten smaller (molecular) and my love for the subject bigger. As someone smarter once wrote: "There is grandeur in this view of life"...

Here i am planning to write mainly about biology. Interesting stuff that i get exposed to in the course of my studies and my research, things i read on the net, new research and articles i stumble upon and interesting debates i read about on scientific blogs. There will be some personal stuff as well (only a little) and here and there computer/gadget/Internet related stuff.

Hope i will enjoy and persist in writing...