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Wednesday, 12 September 2018

Historical review on Metagenomics by one of its pioneers

Norman Pace, one of the pioneers of metagenomics is offering us an historical review of his own contribution to the field,  here.

A few citations from the master:
Only in recent decades has the microbial world been recognized as a driver of global biology, deeply intertwined with the health and functions not only of ourselves but of the biosphere at large.

Despite this, he acknowledges that we still poorly undestand the microbial world, and conclude that
The Golden Age of microbiology is still ahead of us

Enjoy! 

Wednesday, 27 June 2018

Nitrogen fixing Planctomycetes uncovered

In a TARA metagenomes reconstruction exercise,
Delmont et al., Nature Microbio 2018 report the discovery of nitrogen fixing in Planctomycetes. This is the first report of such diazotrophes in this exciting phylum.

In addition, they report that the proportion of genes of unknown function was 27.6% (±2.63%) for the proteobacterial HBDs and 49.3% (±0.5%) as compared to for the 27.6% (±2.63%) for the proteobacterial, highlight the fact that we still poorly understand the functioning of these bacteria.

Also, the set of nitrogen fixation genes were very divergent, suggesting that they were not the result of a lateral gene transfer from more classical diazotrphes.

Looking forward to more discovery in this field.

Thursday, 21 September 2017

Decision making to be a sustainable scientist

Excellent advices to be a sustainable scientist The “want to–need to” matrix is excellent advice:
Say yes only to the things you both need and want to do, and say no if you either do not need or do not want to do something
If you are like most of us looking for time optimization, this is the way to go.

Thursday, 9 March 2017

Tom Rapaport just reported that Organelle shape can be generated by a surprisingly small set of proteins in Powers et al., Nature 2017. It is well known that the eukaryotic endomembrane system is composed of various compartments with very specific function and shape. The development of such a complex system during evolution is expected to be complex and requiring many molecular players. This new report demonstrate that just a few component can induce a tubular network from proteoliposomes. The use of GTP hydrolysis inhibitor demonstrate that maintenance of this network requires continuous membrane fusion. Conclusions from the authors:
Our results show that organelle shape can be generated by a surprisingly small set of proteins and represents an energy-dependent steady state between formation and disassembly.
Thus, it appears that evolutionarily speaking, the development of an endomembrane system might require fewer players than previously expected.  

Thursday, 9 February 2017

Keynote speakers, please try harder

Excellent comment prompting for a better preparation keynote speakers, but also speakers in general, in Nature by Judy Ford.
Best part is probably the following:

Speakers, it is likely that my registration fees have contributed to your travel, so I expect you to demonstrate that you have given a lot of thought to your talk and prepared each slide carefully rather than simply recycling it. I have come to listen to you, the expert, so I expect to enjoy a well-organized, possibly brilliant, presentation, in which creative visuals amplify your words and enhance my understanding.

But anyway, those are comments that we could all take into account.

Thursday, 21 July 2016

Biologists should specialize, not hybridize

Why computational biologists should specialize in their dry skills and not learn other 'stuff', like wet biology, is excellently explained in this column by Assaf Zritsky in this issue of Nature.
As I use to say, computers are just tools like any other ones, such as microscopes or mass spectrometers. You don't ask your favorite microscope specialist to be also an expert in cloning or cell culture. Same thing with computers, we should collaborate not work in isolation.

Friday, 8 April 2016

Randomly distribution grants?

Randomly determining which grants are funded and which ones are not. This looks like a terrible idea, isn't it?
Well, may be not that bad, as suggested by J. Sills in this recent insight in Science. Indeed, currents systems have their limitations and randomly assigning money to the not so bad, but also not so good grants, the middle 60% might not be such a bad idee. Similar ideas have also been proposed to fix our 'democratic' system by example by D. van Reybrouck in his book 'Against the elections'. Why not the same in science?

Monday, 8 February 2016

Did mitochondria arrive late in eukaryogenesis?

Gabaldon just published an interesting phylogenetic analysis of eukaryotic signature proteins. The evolutionary signal that they could recover for those proteins does not support an early aquisition of mitochondria during eukaryogenesis, but to the opposite a late one, suggesting that most of the ancestral eukaryotic cell was already quite complex, when the mitochondria was aquired.

Thursday, 26 March 2015

Where ideas come from

Creativity is all important in science. In this previously unpublished note, SciFi author Isaac Asimov analyses some of his reflexions on the act of creating new ideas.

Friday, 26 September 2014

Organizing the second PVC conference

Just to tell you quickly that we started organizing the second conference entirely dedicated to PVC bacteria research.

It will be held from the 2nd to the 4th of June 2015 in Carmona , a very lovely town close to Sevilla, Andalucia, Spain.

The first PVC conference was already successful and we are all looking forward to the second one.

So please start saving the dates. More information soon.

Tuesday, 16 September 2014

Peptidoglycan in Chlamydia

Related to the discussion about the exceptional status of the PVC cell plan to which we dedicated two recent posts, on the TiM and AvL articles by Devos, and the latest by Fuerst's team, is a new article reporting detection of peptidoglycan in Chlamydia. Liechti et al. describe in Nature a new cell-wall labelling method that finally settles the 50 years old debate concerning the chlamydial anomaly. important question not answered by this manuscript is where is the PG located in Chlamydia? Is it in between the two membranes, where Devos suggests it should be, or is it found outside the outermost membrane, where Fuerst would have it? Although not directly addressed by the authors, it seems pretty clear that the green signal, marking the OM ring is located outside of the red signal, marking the PG (see Fig. 2 or supplementary figure 5). Thus, it seems that PG is located internal to the OM, supporting a more classical G- interpretation of the cell plan, at least in Chlamydia.

Improve your figure

Nice little paper in the '10 simple rules' collection of PLoS Comp. Bio. about drawing better figures.
We could all get something out of this paper. It also contain good references about how to make them colorblind friendly
Like most of the paper in the 10SR series, nice, short and useful.

Saturday, 9 August 2014

A call for a genomic catalog of all cultured Bacteria and Archaea

Microbes are the keys to everything. If you read this blog, you will agree. And genomes are the keys to those microbes. However, the current practice of deciding which genome to sequence is very much left to the major interest of each scientist. Now, Kyrpides et al., PLoS Biology 2014 call for a structured approach to the sequencing of micro-organisms. Of course this means money. However, great expectations are placed on such approach.
Here we call for the funding of a systematic effort to produce a comprehensive genomic catalog of all cultured Bacteria and Archaea by sequencing, where available, the type strain of each species with a validly published name (currently~11,000). This effort will provide an unprecedented level of coverage of our planet's genetic diversity, allow for the large-scale discovery of novel genes and functions, and lead to an improved understanding of microbial evolution and function in the environment.
Very nice article, timely. Let's hope the politics get the message.

Monday, 7 July 2014

Excellence vs diversity. Is it really?

In a post for European scientist, FS Labini is discussing the point of funding excellence vs diversity. But is it really? Do we really have to choose between excellence and diversity? Does this mean to imply that funding more diverse type of science mean abandoning excellence to turn towards more diverse but less good science? That is certainly not what is implied by the post. However, the title might be misleading in this sense. I would argue that to the opposite, there is certainly plenty of excellent science to be funded while exploring diversity, as opposed to all those big consorcium planned, lobbied, organised and composed by what begin to look like a feodal system of science in Europe, and elsewhere. Look at the ESFRI for example.

Wednesday, 2 July 2014

Introducing the Myojin parakaryote

Eukaryotes are derived from prokaryotes. This is demonstrated by the fact that eukaryotic endosymbionts are derived from prokaryotes. Opponents to this have objected that such a transition must have left intermediary organisms, the lack of which strongly weakened this possibility.
Such an organism has in fact been discovered. Yamaguchi et al., J. Electron Microscopy (2012) report the identification from deep see survey of an organism with features that appear to be intermediary between prokaryotes and eukaryotes. This organism, named "Parakaryon myojinensis" for its intermediary location, is big, >100 times bigger than  your usual prokaryote like E. coli. Its genome is composed of naked DNA fibers, instead of the classical eukaryotic chromosomes, and is surrounded by a single membrane instead of the classical double (single folded) membrane of eukaryotes. It also harbor various endosymbionts but no mitochondria. Thus, this organism appear neither to classify as eukaryote or prokaryote, but more like something in between.
The study is far from definitive. Indeed, there is no molecular identification of domain markers, like ribosomal RNA, or proteome oriented studies, most likely because of the lack of isolation and cultivation of this organism.
However, this is another example of the value of sampling the biodiversity that is out there.
Interesting article and I am looking forward to read more about this thought-provoking organism.

Monday, 24 March 2014

And Fuerst strikes back

Planctomycetes are definitively fascinating bacteria. In addition to other interesting characteristics, the exact definition of their cell plan appears to continues to baffle biologists. Initially, back at the end of last century and beginning of this one, Planctomycetes have been claimed to possess a particular cell plan, differentiating them from classical bacterial ones, mainly based on the work of Fuerst and colleagues.
Last year and beginning of this one (2013-14), Devos and associates have published a series of paper advocating that the cell plan of those bacteria is not so radically different, but a variation from, the classical Gram-negative cell plan (see previous posts on the subject here and there). This claim has been developed in various articles and was based on reconsideration of the previous data from Fuerst and others, taking into account novel data, including genomics and high resolution electron-microscopy. This claim had been voiced by others before (Speth et al., Front. Microbiol. 2012; Strous et al., Nature 2006; Lage et al AvL 2013), causing considerable trouble in the PVC community.
Now Fuerst just struck back with new electron-microscopy and immuno-localization data combined with a new model of division in Gemmata obscuriglobus, just published in Sagulenko et al., PLoS One 2014.
The data is highly interesting, including that in some of the supplementary movies, you can see the tubulovesicular network previously revealed by Acehan et al. (particularly in SMovie 2). However, they appear far from being conclusive and promise to fuel more controversy instead of settling it.
In addition, to the interesting data about the cell plan, the cell wall (Suppl. fig. 4), and the FtsK data, Fuerst present a re-evaluated model of cell division in Gemmata (see figure)
The presented three-dimensional reconstruction of a 'nuclear body' does indeed appear to confirm, at least in the presented case, the presence of such compartment in this organism, although more details about the metodology and data would have been needed to fully appreciate the accuracy and relevance of the model. However the data could also be interpreted in the tubulo-vesicular model of Acehan et al., were the DNA containing compartment would just be another of the connected vesicles that fill the cytoplasm, a derivation of the G- cell cycle, as proposed by Devos TiM 2014 (see figure).

Figure 4: A model for mechanism of cell division of G. obscuriglobus cells.
Step 1, the bud appears as a hump on the surface of a cell (Figures S5 and S6 in File S1). The nuclear body is divided, before or during the formation of a bud, forming two fully enveloped structures, as shown in step 2. Finally, one of the nuclear bodies migrates into a newly formed cell (step 3). Other riboplasm vesicles not containing nucleoid DNA are also transferred into the newly formed cell (Figure S6B in File S1). Cell wall is indicated in red; plasma membrane – blue; ICM – green; paryphoplasm – yellow; riboplasm – light blue; nucleoid – black; ribosomes – grey circles. doi:10.1371/journal.pone.0091344.g004.
This is the legend directly from the article. In the G- interpretation, Riboplasm=Cytoplasm; Paryphoplasm=Periplasm.
Despite the wealth of interesting data, some contradictions are found in the paper and it gives the impression to have been written in a haste, throwing together data that could have made it to a few independent paper if consolidated by more results. May be the most important contradiction is the comparison between the topology of the 'nuclear body' and the one of the eukaryotic nucleus, a subject very dear to Fuerst.
The authors constantly claim that the 'nuclear body' is mostly separated from the rest of the cytoplasm by a double membrane, including nice figures seemingly confirming this. However, it seems that this double membrane is in fact formed by the juxtaposition of the membranes of two vesicles or compartments, as acknowledged by the authors (see figure).
If we stick to this interpretation, then the 'nuclear-body' is mostly surrounded by a single-membrane, and not a double one. And as such, there is limited similarity with the eukaryotic nuclear envelope and the nucleus.
This has also implications for the mode of division of this bacteria that has lost the classical FtsZ-based division machinery and the proposed model definitively deserves consideration.
All together, a very interesting paper that deserves to be read very carefully. Even if it seems like a melting-pot of various subjects, the presented data are of considerable interest. However, it clearly does not settle the issue about PVC cell plan or its mode of division. The proposed models are at best tentative and more work is definitively required on both subjects.

I would very much like to encourage you to post a comment about your reaction to this paper and may be to start a discussion about it.

Thursday, 13 February 2014

Don't be a P-hacker

Excellent call about the correct usage of statistics in sciences in general, in Nature 12 February 2014 Editorial and News feature by Regina Nuzzo.
Is your analysis really significant?
Please see the related statistics for biologists web collection from Nature.  

Thursday, 6 February 2014

A tubulovesicular network in Gemmata

Damn it, aren't those bacteria surprising? The report by Acehan et al., in JCS 2014 reveals the presence of a network made of membrane tubules and vesicles in the periplasm of the planctomycetes Gemmata obscuriglobus. This is very surprising by itself, but even more because this tubulovesicular network (TVN) seems to connect the outer membrane to the inner one, so the cytoplasm is directly connected to the outside. How is that possible? In addition, this TVN is in close contact with the membrane coat proteins previously identified in the proteome of this organism based on structural similarities with proteins like clathrin or some nucleoporins. This is most likely directly related to the phenomenon of protein internalisation and degradation previously reported by Lonhienne et al., in PNAS 2010 in the same organism. All together, the presence of a TVN in contact with membrane coat proteins and related to endocytosis is pretty close to one of the possibilities of what is expected to have been present in the ancestral eukaryote.
All this is nicely covered in a JCS 'in this issue' highlight.

Advice to young scientists

Review of the book "Letters to a Young Scientist" by Edward O. Wilson (2013) in PLoS Biology 2013. Probably the most important advice given appears to be: "Be passionated".
Seems like a book we need to read, whatever the age.

Thursday, 2 January 2014

Plant Platypus sequenced

The genome of microbiology's platypus is still incomplete, but scientists have now sequenced the genome of the plant's platypus. It is a small plant called Amborella, endemic to the main island, Grande Terre, of New Caledonia in the South Pacific, probably unknown to most of us before that.
"In the same way that the genome sequence of the platypus – a survivor of an ancient lineage – can help us study the evolution of all mammals, the genome sequence of Amborella can help us learn about the evolution of all flowers," said co-author Dr Victor Albert of the University at Buffalo.
The genome will be very useful to decipher the changes of function upon gene duplication, as it provides conclusive evidence that the ancestor of all flowering plants, including Amborella, evolved following a ‘genome doubling event’ that occurred about 200 million years ago. It would be interesting to see what happened to those duplications. Plenty of other fascinating analysis are bound to come from this newly sequenced genome. The story is covered in the Sci-News.com post to Amborella. See also the Amborella database