“Bacterial Fortresses” and “gene-trafficking phages”, in my picks of the week from RB

Another week has gone by and some very interesting molbio blog posts have been aggregated to Researchblogging.org. Every week [see my opening post on the matter], I'll select some blog posts I consider particularly interesting in the field of molecular biology [see here to get a sense of the criteria that will be used], briefly describe them and list them here for you to check out.

Note that I'm only taking into consideration the molbio-related blog posts aggregated under "Biology".

Congratulations to everyone who got their post selected.

1) As I’ve commented before, in a previous issue of my Picks of the Week, under certain conditions bacteria can cooperate as a population to create biofilms, which consist of “sessile aggregates of bacteria embedded in a self-made extracellular polymeric matrix”.
Interestingly, this matrix can act as “tough physical barriers that are immune to attacks by many antibiotics and other bacteriocidal agents”, including the action of the host defence system.

Pseudomonas aeruginosa, an opportunistic pathogen, is capable of forming such biofilms, and Lab Rat discusses an interesting new article reporting that biofilm P. aeruginosa cells can react to the presence of polymorphonuclear neutrophilic leukocytes (phagocytic cells which are important players in the innate immune response since they produce a range of antimicrobial molecules able to kill pathogens) by producing a “shield” made of a particular glycolipid biosurfactant called rhamnolipid, which can cause lysis of these immune cells. Interestingly, the synthesis of these lipids is under control of the quorum-sensing system.

2) Hundreds of bacterial genomes have been sequenced and are now available for comparative genomics. Perhaps one of the most fascinating discoveries has been that the genomic diversity, even among the genomes of closely related species, can be enormous.
Bacteriophages have played an important role in shaping bacterial genomes, particularly by contributing to lateral gene transfer through transduction.

From the article:

“Bacteriophages have the ability to manipulate the life histories and evolution of their hosts and evolved many adaptation and defence mechanisms for efficient survival and multiplication. Most of these involve manipulation of the host DNA, as well as the incorporation, into the phage genomes, of bacterial genes that encode proteins with a potential to facilitate bacteriophage reproduction” (my emphasis)

Apparently, the latter is the case with cyanophages and cyanobacteria, as discussed by Iddo Friedberg at Byte Size Bio. He comments on a recent (and purely bioinformatic) Nature article reporting “the presence of photosystem I (PSI) genes in the genomes of viruses that infect marine cyanobacteria, [by] using pre-existing metagenomic data from a global ocean sampling expedition as well as from viral biomes”. Further, they show (by modeling) that apparently, the use of one of these proteins encoded in the phage genome can make the bacterial PSI function more efficiently.


That's it for this week. Stay tuned for more MolBio Research Highlights!

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Some of the articles discussed in this week's selected posts:

Alhede M, Bjarnsholt T, Jensen PØ, Phipps RK, Moser C, Christophersen L, Christensen LD, van Gennip M, Parsek M, Høiby N, Rasmussen TB, & Givskov M (2009). Pseudomonas aeruginosa recognizes and responds aggressively to the presence of polymorphonuclear leukocytes. Microbiology (Reading, England), 155 (Pt 11), 3500-8 PMID: 19643762


Sharon, I., Alperovitch, A., Rohwer, F., Haynes, M., Glaser, F., Atamna-Ismaeel, N., Pinter, R., Partensky, F., Koonin, E., Wolf, Y., Nelson, N., & Béjà, O. (2009). Photosystem I gene cassettes are present in marine virus genomes Nature, 461 (7261), 258-262 DOI: 10.1038/nature08284

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Peer review during WWII: HILARIOUS

Even the Führer has to deal with some annoying reviewers....

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“Hey! Where’s that cancer cell going?” and “M-cells, gateways to the mucosal immune system”, in my picks of the week from RB

Another week has gone by and some very interesting molbio blog posts have been aggregated to Researchblogging.org. Every week [see my opening post on the matter], I'll select some blog posts I consider particularly interesting in the field of molecular biology [see here to get a sense of the criteria that will be used], briefly describe them and list them here for you to check out.

Note that I'm only taking into consideration the molbio-related blog posts aggregated under "Biology".

Congratulations to everyone who got their post selected.

1) As we’ve discussed before, tissue invasion and metastasis are hallmarks of cancer. Cells from primary tumor masses can travel and colonize the same or different organ sites leading to the formation of secondary tumors. Importantly, these “metastases” are the cause of 90% of human cancer-related deaths.
The first step towards metastasis involves the “movement of cancer cells into tissue surrounding the tumour, and the vasculature”. This generates lots of questions: What makes cancer cells motile? How do these cells move?

Lab Rat discusses a review commenting on the mechanisms underlying the motility of cancer cells.

2. In the gastrointestinal tract, the largest mucosal membrane surface in the human body, the highly specialized M-cells play an important sentinel role by sampling and transporting antigens from the lumen of the small intestine, to underlying mucosal lymphoid tissues (in a process called antigen transcytosis), where antigen-specific immune responses are evoked. Despite the importance of this process, the molecular mechanisms underlying this antigen uptake are largely unknown.

Geek discusses a recent article in Nature reporting “that glycoprotein 2, specifically expressed on the apical plasma membrane of M cells among enterocytes, serves as a transcytotic receptor for mucosal antigens” by recognizing a component of type I pili on bacteria.


That's it for this week. Stay tuned for more MolBio Research Highlights!

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Some of the articles discussed in this week's selected posts:

SAHAI, E. (2005). Mechanisms of cancer cell invasion Current Opinion in Genetics & Development, 15 (1), 87-96 DOI: 10.1016/j.gde.2004.12.002

Hase, K., Kawano, K., Nochi, T., Pontes, G., Fukuda, S., Ebisawa, M., Kadokura, K., Tobe, T., Fujimura, Y., Kawano, S., Yabashi, A., Waguri, S., Nakato, G., Kimura, S., Murakami, T., Iimura, M., Hamura, K., Fukuoka, S., Lowe, A., Itoh, K., Kiyono, H., & Ohno, H. (2009). Uptake through glycoprotein 2 of FimH+ bacteria by M cells initiates mucosal immune response Nature, 462 (7270), 226-230 DOI: 10.1038/nature08529

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Science Laughs: Science Comedian Brian Malow

This is just a preview. You can watch the full video here.

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The Cartoon Lab Archives

I was checking Twitter while I waited for a PCR to finish and I found these nice cartoons by Ed Himelblau at the Promega site (you can follow Promega here). I selected a few, but you should check them all out!

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Bacterial signaling and studying diseases through exome sequencing, in my picks of the week from RB

Another week has gone by and some very interesting molbio blog posts have been aggregated to Researchblogging.org. Every week [see my opening post on the matter], I'll select some blog posts I consider particularly interesting in the field of molecular biology [see here to get a sense of the criteria that will be used], briefly describe them and list them here for you to check out.

Note that I'm only taking into consideration the molbio-related blog posts aggregated under "Biology".

Congratulations to everyone who got their post selected.

1) All cells (including free-living organisms), can modulate their gene expression profiles in response to changes in their surroundings.

In bacteria, extracellular signals are transduced into the cell predominantly by two-component systems, but “bacteria also contain multi-component systems, for both inter- and intra-cellular signaling”.
Lab Rat discusses a recent article presenting a comprehensive census of signal transduction proteins encoded in 167 bacterial and archaeal genomes, which reveals some very interesting trends regarding their phylogenetic distribution and numbers. It also points to some unique features exclusive to bacterial signaling systems.

From the article:

“The complexity of signaling systems differs even among closely related organisms. Still, it usually can be correlated with the phylogenetic position of the organism, its lifestyle, and typical environmental challenges it encounters”

2. Keith Robison at Omics! Omics! discusses a new paper reporting the first application of exome sequencing to uncover the affected gene responsible for a rare mendelian disorder of unknown cause, Miller syndrome. The authors identified a single candidate gene, DHODH, which encodes a key enzyme in the pyrimidine de novo biosynthesis pathway.

From the article:

(…) deep resequencing of all human genes for discovery of allelic variants could potentially identify the gene underlying any given rare monogenic disease. Massively parallel DNA sequencing technologies have rendered the whole-genome resequencing of individual humans increasingly practical, but cost remains a key consideration. An alternative approach involves the targeted resequencing of all protein-coding subsequences (that is, the exome), which requires 5% as much sequencing as a whole human genome.

Keith comments on the results, methodology and on the economic feasibility to use this approach to study the genetic basis of a large number of still uncharacterized rare diseases.

That's it for this week. Stay tuned for more MolBio Research Highlights!

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Some of the articles discussed in this week's selected posts:

Galperin MY (2005). A census of membrane-bound and intracellular signal transduction proteins in bacteria: bacterial IQ, extroverts and introverts. BMC microbiology, 5 PMID: 15955239

Ng, S., Buckingham, K., Lee, C., Bigham, A., Tabor, H., Dent, K., Huff, C., Shannon, P., Jabs, E., Nickerson, D., Shendure, J., & Bamshad, M. (2009). Exome sequencing identifies the cause of a mendelian disorder Nature Genetics DOI: 10.1038/ng.499

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Let's have “Organizer's picks” at Scientific Meetings

I’ve just received an email from F1000 which got me thinking about something I’ve considered in the past. I won’t go into the details of the email, as these are private communications, but it reinforced my idea that this project could actually work.

I’m not sure that this hasn’t been done before, but to my knowledge, and in the context of my limited number of international meetings, I’ve yet to see it. Anyway, if this has already been implemented somewhere, I'll appreciate your thoughts and comments, so we can start using it at our meetings here in Chile.

My idea is to include in the conference book (the one that includes all the abstracts and is given to all the attendees), “Organizer’s picks”, which highlight a few posters of the ones that will be presented at the meeting. I consider this to be a useful addition to the book.

The way I think this could be done, is as follows: abstracts are sent as part of the normal application process, but authors could also include a slightly lengthier summary (with a limited number of words), describing in a little more detail the context of the research, the results and its implications. Both this “author summary” and the abstract, are reviewed by a panel of scientists involved in the meeting (i.e the organizers) and select a few they consider particularly interesting under a particular criteria, like “broadness of interest”, “significant technical advance” or whatever. This picks are then included in the conference book under “Organizer’s picks” or selections. Shall the writing of the author summary or its reviewing be considered as “too much work”, then the reviewing could be done based solely on the regular abstract.

I remember that the RNA Society Meeting has something similar, in which “selected talks” are scheduled on the first day, to start off the meeting. I’ve always considered this to be a fascinating idea.

While discussing this idea in my lab, someone argued that this may immediately unveil the potential winners of the “best poster presentation”, which may be considered a bad thing, as it takes the surprise away and may be discouraging for some presenters.

I argue that some posters may look good in “paper”, but are not nearly as exciting once you go see it and talk to the presenter (which is something conference organizers must do in order to award the prize). On the other hand, some posters may have a “low profile” abstract but may be particularly interesting, to the degree of being among the candidates to win the award. So, being included in the organizer’s selection does not necessarily guarantee that one of those posters will be awarded the prize. Further, the categories can be selected in a way such that they don't highlight the "best poster", but can be something along the lines of "broadness of interest”, “innovative technique”, etc, as I mentioned before, which won't get in the way of the aforementioned award.

Anyway, this is just an idea and I welcome your input, so tell me what you think, suggest ideas on how to improve it or express your concerns about its applicability.

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[Image credit: Association of College & Research Libraries]

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Cry for help: help me win a free bioKM account!

Dear readers,

I come to you today, asking for your help. As you know, I'm a "scientwist", a scientist that tweets [see Labelling the molecular biologist (who tweets)].

Recently, BioData started a Twitter Challenge. The prize? A free lifetime account at BioKM, "a secured internet application designed to meet the everyday needs of researchers in an academic lab environment".

In order to win, scientwists must be nominated by other twitter users.

I REALLY want to win this account, so please nominate me!

All you have to do is tweet the following: +1 @aemonten @bioKM

and you'll be helping me towards this goal. I look forward to your tweets!!

Oh... and remember to follow me on Twitter :-).

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Spine-independent immunology, “PAMP” it up and more, in my Picks of the Week from RB

Another week has gone by and some very interesting molbio blog posts have been aggregated to Researchblogging.org. Every week [see my opening post on the matter], I'll select some blog posts I consider particularly interesting in the field of molecular biology [see here to get a sense of the criteria that will be used], briefly describe them and list them here for you to check out.

Note that I'm only taking into consideration the molbio-related blog posts aggregated under "Biology".

Congratulations to everyone who got their post selected.

1) Sea urchins get by without an adaptive immune system. Nevertheless, they partly compensate this deficiency by exhibiting an “unprecedented complexity of innate immune recognition receptors, relative to other animal species”. Lucas Brouwers at Thoughtomics gives some “genomic insights” into the immune system of these organisms.

2) The recognition of “pathogen-associated molecular patterns” (PAMPs) by particular plant receptors, triggers a series of defense responses with the aim of neutralizing the invading microorganism and halting the infection. Pamela Ronald at Tomorrow’s Table, presents her recent Science paper reporting the identification of a PAMP from Xanthomonas oryzae pv. oryzae, the causal agent of rice bacterial blight disease.

3) The next article was recently selected by Francisco and I to be included in the 27th issue of the Cancer Research Blog Carnival, which we hosted and published last Friday here at MolBio Research Highlights [see Cancer Research Blog Carnival #27]. I’ll quote what we wrote about it then:

Regulatory T –cells (TReg cells) help control immune responses, playing a key role in immune homeostasis. Interestingly, it has been proposed that these cells facilitate tumors' escape from immune monitoring. Further, these TReg cells have been shown to be antigen-specific. Ian York at Mystery Rays from Outer Space takes a look at a recent article addressing an interesting question in the field: what are the tumor antigens that are driving the TRegs?

“I would have assumed that TRegs are looking at many, many tumor antigens, including both normal self antigens as well as classical tumor antigens. But a recent paper suggests, to my surprise, that this assumption is wrong. Instead, “TRegs in tumor patients were highly specific for a distinct set of only a few tumor antigens“. What’s more, eliminating TRegs cranked up the functional immune response, but only to those antigens TRegs recognized — as you’d expect, if the suppression is indeed antigen specific”

That's it for this week. Stay tuned for more MolBio Research Highlights!

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Some of the articles discussed in this week's selected posts:

Buckley KM, Terwilliger DP, & Smith LC (2008). Sequence variations in 185/333 messages from the purple sea urchin suggest posttranscriptional modifications to increase immune diversity. Journal of immunology (Baltimore, Md. : 1950), 181 (12), 8585-94 PMID: 19050278

Lee, S., Han, S., Sririyanum, M., Park, C., Seo, Y., & Ronald, P. (2009). A Type I-Secreted, Sulfated Peptide Triggers XA21-Mediated Innate Immunity Science, 326 (5954), 850-853 DOI: 10.1126/science.1173438

Bonertz, A., Weitz, J., Pietsch, D., Rahbari, N., Schlude, C., Ge, Y., Juenger, S., Vlodavsky, I., Khazaie, K., Jaeger, D., Reissfelder, C., Antolovic, D., Aigner, M., Koch, M., & Beckhove, P. (2009). Antigen-specific Tregs control T cell responses against a limited repertoire of tumor antigens in patients with colorectal carcinoma Journal of Clinical Investigation DOI: 10.1172/JCI39608

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Quotes from the science blogosphere

This one goes beyond the blogosphere world and into my Friendfeed account:

"(...) remember that reviewers comments, even editors, don't have to make sense"

-Mr Gunn


(To get a sense of what "Quotes from the science blogosphere" is all about, check this post)

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Cancer Research Blog Carnival #27

We are honored to have been invited to host this month’s Cancer Research Blog Carnival (CRBC), your monthly roundup of posts from the cancer blogosphere. This marks the 27th Edition of this successful Carnival and we are excited to be a part of it.

In this edition, and in agreement with the spirit of our blog, MolBio Research Highlights, we’ve favored posts with a molecular biology/genetics orientation.

Let’s get down to business:

1) Approaches like linkage analysis or genome-wide association studies have enabled us to study the genetic basis of diseases like prostate cancer, one of the most prevalent types of cancer among men. Erin Cline at The Spittoon, discusses the reporting in Nature Genetics of new SNPs (single nucleotide polymorphisms) associated with this disease^(a)

"(…) researchers are turning to studies that include larger numbers of participants than ever before. The hard work is paying off, as can be seen in four recent reports published in the journal Nature Genetics. These analyses, based on the DNA of tens of thousands of men, have added at least 12 new variants to the roster of prostate cancer-associated SNPs"

2) Keith Robison at Omics! Omics! discusses a recent article on the topic of cancer genomics. Through the use of Illumina technology, a Canadian group sequenced both the genome and transcriptome of an oestrogen-receptor-alpha-positive metastatic lobular breast cancer and compared it to a primary tumor sample from the same patient, from 9 years earlier. These approaches showed that significant tumor evolution can occur with disease progression.

3) Regulatory T –cells (TReg cells) help control immune responses, playing a key role in immune homeostasis. Interestingly, it has been proposed that these cells facilitate tumors' escape from immune monitoring. Further, these TReg cells have been shown to be antigen-specific. Ian York at Mystery Rays from Outer Space takes a look at a recent article addressing an interesting question in the field: what are the tumor antigens that are driving the TRegs?

“I would have assumed that TRegs are looking at many, many tumor antigens, including both normal self antigens as well as classical tumor antigens. But a recent paper suggests, to my surprise, that this assumption is wrong. Instead, “TRegs in tumor patients were highly specific for a distinct set of only a few tumor antigens“. What’s more, eliminating TRegs cranked up the functional immune response, but only to those antigens TRegs recognized — as you’d expect, if the suppression is indeed antigen specific”

4) Cases of vertical transmission of tumors have been recorded in the literature, but it wasn’t until recently that evidence of a shared cancer clone between the mother and the child (i.e genetic evidence for mother-to-offspring transmission), was reported. How complex is fetal-maternal cell trafficking? Is this traffic bidirectional? How does this phenomenon impact on existing paradigms in cancer biology?
Alex at Hematopoiesis discusses a recent review addressing some of these questions.

5) Colin Hockings at Blue Genes gives us a very nice post about telomeres. Given that this year’s Nobel Prize in Physiology or Medicine was awarded to three American scientists "for the discovery of how chromosomes are protected by telomeres and the enzyme telomerase", it’s nice to have an overview of our current knowledge on this subject.

Simply put, telomere integrity is essential for the stability of chromosomes, which in turn determines the survival of the cell. As cells divide, telomeres get shorter which limits the number of divisions a cell can undergo. Notably, most types of cancer exhibit deregulations in telomere biology, which supports the limitless proliferative potential these cell harbor. Colin’s post is written in an amenable fashion and links to a recent review considering telomerase as a therapeutic target.


That's it for this month's Cancer Research Blog Carnival. We hope you've enjoyed reading it, just as much as we did putting it together. For older editions, visit the Carnival Homepage. Don't forget, the CRBC has subscription options; you can follow by email or RSS feed.

If you'd like to host a future edition, email bayblab@gmail.com


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^(a) By definition, a polymorphism is a nucleotide variant present in more than 1% of the studied population and, for a few years now, researchers have used these normally occurring variations to try to map risk factors for several complex diseases, including cancer.


Some of this carnival's discussed articles:

Yeager, M., Chatterjee, N., Ciampa, J., Jacobs, K., Gonzalez-Bosquet, J., Hayes, R., Kraft, P., Wacholder, S., Orr, N., Berndt, S., Yu, K., Hutchinson, A., Wang, Z., Amundadottir, L., Feigelson, H., Thun, M., Diver, W., Albanes, D., Virtamo, J., Weinstein, S., Schumacher, F., Cancel-Tassin, G., Cussenot, O., Valeri, A., Andriole, G., Crawford, E., Haiman, C., Henderson, B., Kolonel, L., Le Marchand, L., Siddiq, A., Riboli, E., Key, T., Kaaks, R., Isaacs, W., Isaacs, S., Wiley, K., Gronberg, H., Wiklund, F., Stattin, P., Xu, J., Zheng, S., Sun, J., Vatten, L., Hveem, K., Kumle, M., Tucker, M., Gerhard, D., Hoover, R., Fraumeni, J., Hunter, D., Thomas, G., & Chanock, S. (2009). Identification of a new prostate cancer susceptibility locus on chromosome 8q24 Nature Genetics, 41 (10), 1055-1057 DOI: 10.1038/ng.444

Bonertz, A., Weitz, J., Pietsch, D., Rahbari, N., Schlude, C., Ge, Y., Juenger, S., Vlodavsky, I., Khazaie, K., Jaeger, D., Reissfelder, C., Antolovic, D., Aigner, M., Koch, M., & Beckhove, P. (2009). Antigen-specific Tregs control T cell responses against a limited repertoire of tumor antigens in patients with colorectal carcinoma Journal of Clinical Investigation DOI: 10.1172/JCI39608

Shay, J., & Keith, W. (2008). Targeting telomerase for cancer therapeutics British Journal of Cancer, 98 (4), 677-683 DOI: 10.1038/sj.bjc.6604209

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Quick, “on-the-go”, picks of the week from RB: Antifungal comes to the rescue and Protein tricks in cell regulatory networks

Another week has gone by and some very interesting molbio blog posts have been aggregated to Researchblogging.org. Every week [see my opening post on the matter], I'll select some blog posts I consider particularly interesting in the field of molecular biology [see here to get a sense of the criteria that will be used], briefly describe them and list them here for you to check out.

Note that I'm only taking into consideration the molbio-related blog posts aggregated under "Biology".

Despite all of this, too many experiments, TA assignments, undergrad mentoring and some other work-related stuff, have narrowed my time for writing this week’s post. In fact, I’m at the lab right now! (it’s 11.20 pm… hey, is that gel still running?).

I did read them all, though. My "limited time" only makes reference to the actual writing of the post.

Anyway, as you know, I like to give a nice intro to the selected posts (for example, see here), but this week I’ll just direct you to them. I promise to get back to my regular (more extended) format next week.

This week, two blog posts made the cut:

1) Prion diseases are neurodegenerative disorders characterized by the aggregation of a misfolded isoform of the cellular prion protein (PrP(C)). Interestingly, it has been reported that Amphotericin B, a common antifungal drug, has anti-prion activity, although its use has been limited due to its high toxicity.

Brian Appleby at CJD Bloggers discusses a somewhat recent article assessing anti-prion properties and toxicity of new amphotericin B analogues, in which the exocyclic carboxyl groups normally found in amphotericin B, have been replaced by methyl groups.

"This study is significant in that it demonstrates anti-prion activity of less toxic amphotericin analogues that may be further studied in regards to possible anti-prion disease treatments."

2) Nir London at Macromolecular Modeling Blog, summarizes the most important points of a recent review discussing “some of the many strategies that proteins in regulatory networks use to achieve the dynamic plasticity necessary to rapidly respond to diverse cellular needs”, integrating aspects of specificity, modularity, the role of post-translational modifications (particularly phosphorylation) and more!

That's it for this week. Stay tuned for more MolBio Research Highlights!

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Some of the articles discussed in this week's selected posts:

SOLER, L. (2008). Effects of new amphotericin analogues on the scrapie isoform of the prion protein Biochimica et Biophysica Acta (BBA) - General Subjects, 1780 (10), 1162-1167 DOI: 10.1016/j.bbagen.2008.07.005

Stein, A., Pache, R., Bernadó, P., Pons, M., & Aloy, P. (2009). Dynamic interactions of proteins in complex networks: a more structured view FEBS Journal, 276 (19), 5390-5405 DOI: 10.1111/j.1742-4658.2009.07251.x

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