Biology posts
- November 5, 2009
- 07:19 PM
- 1,575 views
The Genomic Ark: 10,000 vertebrate genomes
by Iddo Friedberg in Byte Size Biology
The first bioinformatics meeting I went to was in 1996 at the Nachsholim resort, north of Tel Aviv. I received a fellowship for the duration, and shared a room with the brilliant Golan Yona, then a grad student at the Hebrew University. I was doing biochemistry at the time and knew next to nothing about [...]... Read more »
, . (2009) Genome 10K: A Proposal to Obtain Whole-Genome Sequence for 10 000 Vertebrate Species. Journal of Heredity. DOI: 10.1093/jhered/esp086
Check Hayden, E. (2009) 10,000 genomes to come. Nature, 462(7269), 21-21. DOI: 10.1038/462021a
- November 5, 2009
- 04:05 PM
- 1,477 views
Plants and Bacteria 'Talk' to Thwart Disease
by Pamela Ronald in Tomorrow's Table
In plant and animal innate immunity, like many of the dances of life, it takes two to tango. A receptor molecule in the plant pairs up with a specific molecule on the invading bacteria and, presto, the immune system swings into action to defend against the invasion of the disease-causing microbe.
Unwrapping some of the mystery from how plants and bacteria communicate in this dance of immunity, hardworking scientists in my laboratory here at the University of California, Davis, have identified the bacterial molecule that matches up with a specific receptor in rice plants to ward off a devastating disease known as bacterial blight of rice.
The publication describing these results will appear tomorrow in the journal Science.
Read the rest of this post... | Read the comments on this post...... Read more »
Sang-Won Lee, Sang-Wook Han, Malinee Sririyanum, Chang-Jin Park, Young-Su Seo, & Pamela C. Ronald. (2009) A Type I–Secreted, Sulfated Peptide Triggers XA21-Mediated Innate Immunity . Science Magazine, 850-853. info:/DOI: 10.1126/science.1173438
- November 5, 2009
- 10:52 AM
- 515 views
“A fantastic exhibition of lymphocyte gymnastics”
by iayork in Mystery Rays from Outer Space
A truly amazing paper in today’s Nature1 shows 2-photon microscopy videos of T cells entering the brain in search of their target antigen. The title of this post is taken from the commentary,2 also in Nature.
Disease-causing T cells first adhere to the inner walls of the pial vessels and then crawl in continuous contact with [...]... Read more »
Bartholomäus, I., Kawakami, N., Odoardi, F., Schläger, C., Miljkovic, D., Ellwart, J., Klinkert, W., Flügel-Koch, C., Issekutz, T., Wekerle, H.... (2009) Effector T cell interactions with meningeal vascular structures in nascent autoimmune CNS lesions. Nature, 462(7269), 94-98. DOI: 10.1038/nature08478
Ransohoff, R. (2009) Immunology: In the beginning. Nature, 462(7269), 41-42. DOI: 10.1038/462041a
- November 5, 2009
- 09:44 AM
- 605 views
What you call this? Linguistic morphology of chemical names and lost in translation
by Abhishek Tiwari in Fisheye Perspective
Here is a real world example how Linguistic morphology of chemical names may have unwanted secondary effects. For example, English search engines such as Google and Yahoo! are unable to find "chlorobenzene" by searching for "benzene". Interestingly, in other languages such as Chinese, Japanese, or Korean (CJK languages), this is less of a problem, where for example the Japanese "(chlorobenzene) can usually be found by querying for"(benzene).So next time you visit Japan and wish to buy an Aspirin be sure what you are asking for. Similarly when chemical names fluorescin and fluorescein transliterated to Japanese their distinction is totally lost. Phenylacetate and phenyl acetate are different compounds but again indistinguishable in Japanese because it does not retain a notion of whitespace. In fact when it comes to chemical naming there is an endless list for this type of linguistic confusions.Indeed Mr Bob may not be only one who is lost in translationDirector [in Japanese, to the interpreter]: The translation is very important, O.K.? The translation. Interpreter [in Japanese, to the director]: Yes, of course. I understand. Director [in Japanese, to Bob]: Mr. Bob. You are sitting quietly in your study. And then there is a bottle of Suntory whisky on top of the table. You understand, right? With wholehearted feeling, slowly, look at the camera, tenderly, and as if you are meeting old friends, say the words. As if you are Bogie in Casablanca, saying, "Here's looking at you, kid," -- Suntory time! Interpreter [In English, to Bob]: He wants you to turn, look in camera. O.K.? Bob: Is that all he said?Reference:Sayle, R. (2009). Foreign Language Translation of Chemical Nomenclature by Computer Journal of Chemical Information and Modeling, 49 (3), 519-530 DOI: 10.1021/ci800243w
Original article is
available at Fisheye Perspective blog. Stay
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... Read more »
Sayle, R. (2009) Foreign Language Translation of Chemical Nomenclature by Computer. Journal of Chemical Information and Modeling, 49(3), 519-530. DOI: 10.1021/ci800243w
- November 5, 2009
- 09:02 AM
- 745 views
It Was The Worst of Times, It Was the Best of Times
by Moselio Schaechter in Small Things Considered
by Elio
At the end of the Permian period, about 250 million years ago and not long before the dinosaurs appeared, life on Earth experienced its greatest catastrophe: a mass extinction that did away with the vast majority of life forms on land and sea. The question arises, who ate the carcasses of the deceased? Surely bacteria and protozoa digested the animal corpses, most likely reaching unusually high population sizes as the result. But who took care of the masses of dead plant material? Fungi are quite good at digesting plants, especially woody plants. So, did the fungi also become prevalent after the catastrophe?
There is evidence for this belief. ... Read more »
Sephton, M., Visscher, H., Looy, C., Verchovsky, A., & Watson, J. (2009) Chemical constitution of a Permian-Triassic disaster species. Geology, 37(10), 875-878. DOI: 10.1130/G30096A.1
- November 5, 2009
- 07:27 AM
- 1,162 views
Artemether: Entity of the Month
by Duncan Hull in O'Really?
November’s entity of the month at ChEBI is the antimalarial drug Artemether. This accompanies release 62 of ChEBI, not just yet another incremental release but an increase of more than twentyfold in the number of entities in ChEBI, thanks to merging of data between an updated ChEBI [1] and ChEMBL [2]. ChEBI now (as of [...]... Read more »
de Matos, P., Alcantara, R., Dekker, A., Ennis, M., Hastings, J., Haug, K., Spiteri, I., Turner, S., & Steinbeck, C. (2009) Chemical Entities of Biological Interest: an update. Nucleic Acids Research. DOI: 10.1093/nar/gkp886
Warr, W. (2009) ChEMBL. An interview with John Overington, team leader, chemogenomics at the European Bioinformatics Institute Outstation of the European Molecular Biology Laboratory (EMBL-EBI). Journal of Computer-Aided Molecular Design, 23(4), 195-198. DOI: 10.1007/s10822-009-9260-9
Singh, N., & Panwar, V. (2006) Case Report of a Pituitary Macroadenoma Treated With Artemether. Integrative Cancer Therapies, 5(4), 391-394. DOI: 10.1177/1534735406295311
Wu, Z., Gao, C., Wu, Y., Zhu, Q., Yan Chen, ., Xin Liu, ., & Chuen Liu, . (2009) Inhibitive Effect of Artemether on Tumor Growth and Angiogenesis in the Rat C6 Orthotopic Brain Gliomas Model. Integrative Cancer Therapies, 8(1), 88-92. DOI: 10.1177/1534735408330714
- November 5, 2009
- 05:55 AM
- 1,396 views
Making commercial plantations better for birds
by Rob Goldstein in Conservation Maven
From palm oil to eucalyptus to rubber, researchers have generally found that commercial plantations are bad for biodiversity compared to natural forests. Now a new study in the journal Conservation Biology finds that increasing the structural complexity of plantations could make them better for birds.
The study reflects a pragmatic way of thinking on the part of many conservationists who accept the reality that plantations are here to stay and maybe they can complement protected areas in conserving biodiversity.... Read more »
NÁJERA, A., & SIMONETTI, J. (2009) Enhancing Avifauna in Commercial Plantations. Conservation Biology. DOI: 10.1111/j.1523-1739.2009.01350.x
- November 4, 2009
- 08:39 PM
- 481 views
Tumor TRegs are more focused than I expected
by iayork in Mystery Rays from Outer Space
TRegs infiltrate into a tumor
One of the reasons the immune system doesn’t destroy tumors is the presence of regulatory T cells (TRegs) that actively shut down the anti-tumor response. For once, there’s a little bit of encouraging news on that front.
TRegs are normal parts of the immune system. They actively prevent other T cells (and [...]... Read more »
Bonertz, A., Weitz, J., Pietsch, D., Rahbari, N., Schlude, C., Ge, Y., Juenger, S., Vlodavsky, I., Khazaie, K., Jaeger, D.... (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
- November 4, 2009
- 01:44 PM
- 1,717 views
Sexual Attraction, Health and Evolution: It's a Rocky Road
by Daniel Hawes in Ingenious Monkey | 20-two-5
Which physical characteristics make for attraction? Many popular science reports evoke evolutionary psychology arguments as explanations of why modern humans supposedly respond to these attractiveness cues, but often times these reports fail to consider conflicting data realities as well as the many subtle limitations that are generally involved in research...... Read more »
Weeden J, & Sabini J. (2005) Physical attractiveness and health in Western societies: a review. Psychological bulletin, 131(5), 635-53. PMID: 16187849
- November 4, 2009
- 11:02 AM
- 968 views
Lowering Pharma firewalls: Just for Bioinformatics or Chemoinformatics also
by Abhishek Tiwari in Fisheye Perspective
Notion of pre-competitive collaboration has been in under experiment steadily for quite sometime now. Notable examples are the Airbus consortium of European aircraft manufacturers, the Sematech consortium of US semiconductor manufacturers, banks working together to launch Visa and Mastercard, our recent moon lust and many more. But this was never a case for pharmaceutical industry until now which is now lowering industry firewalls to shift funding and focus from early- to late-stage projects by developing cooperation in the areas with little potential for differentiation most notably a shared informatics infrastructure through public–private partnerships. Pre-competitive collaboration in this process means that everyone will have same common pool of data and resources. Competition will be still there but for better ideas, for better models and to discover first.Pre-competitive informatics initiativesA very interesting opinion piece appeared in September issue of Nature Reviews Drug Discovery discussing the importance of pre-competitive informatics initiatives in drug discovery. Article suggest that many companies are already beginning to embrace this idea, and that for some companiesthe focus has moved from the vigorous pursuit of intellectual property towards exploration of pre-competitive cross-industry collaborations and engagement with the public domain.This was a very timely review in the wake of several initiatives such a Innovative Medicines Initiative (IMI), EBI industry programme, Pistoia Alliance and many others. The idea of lowering industry firewalls caught more attention after the announcement of Sage Bionetworks, a non-profit medical research organization established this year with initiatives of Merck duo Eric Schadt and Stephen Friend. A similar kind of effort Open Source Drug Discovery(OSDD) was launched by CSIR, India earlier this year with a initial investment of US $38 million. OSDD consortium is trying to implement open source model for Drug Discovery and public-private partnership is one of the major focus of this initiative. Exciting isn't it? But wait there is a twist in story, there are no definitive answers for what type of data is pre-competitive and what is not? The definition of of pre-competitive is fluidic and it depends on several factors, one of them is whether data belongs to biology or chemistry. Article suggests that any data and tools used by biologists should be under consideration for pre-competitive sharing but those used by chemist should remain the competitive or proprietary (which is very much according to current trends). I could not find any rational reason behind this argument except the fact that there is overwhelming amount of public data in biology domain and day by day companies and institution are finding it hard to manage, integrate and use them for drug discovery. I will go further and suggest that much of these initiatives serves no benefits unless otherwise the data and tools belonging to chemistry domain is also considered as pre-competitive. Ironically much of the data and tools released by pharmaceutical companies under these initiatives are yet to proof their importance. For instance much hyped Life Science Grid released by Eli Lilly (which went open source in year 2008) failed to attract even an average user base. Lilly released only the biology side of the grid which includes a selected group of non proprietary plug-ins, including those for Gene Browser, NCBI Entrez, and Gene Ontology. Forgive me but there are already better tools for the biology in public domain. In my opinion unhindered access to data and tool is prerequisite for the success of the pre-competitive landscape which require more active contributions from the industry participants. Currently the systems is evolving and for now something is better than nothing.Apart from the issues related to definition of pre-competitive boundaries there are several other bottlenecks, for instance the who will fund the long-term maintainability of such an infrastructure, those remain unresolved . Reference:Barnes, M., Harland, L., Foord, S., Hall, M., Dix, I., Thomas, S., Williams-Jones, B., & Brouwer, C. (2009). Lowering industry firewalls: pre-competitive informatics initiatives in drug discovery Nature Reviews Drug Discovery, 8 (9), 701-708 DOI: 10.1038/nrd2944
Original article is
available at Fisheye Perspective blog. Stay
tuned for more posts and subscribe the RSS feed.
... Read more »
Barnes, M., Harland, L., Foord, S., Hall, M., Dix, I., Thomas, S., Williams-Jones, B., & Brouwer, C. (2009) Lowering industry firewalls: pre-competitive informatics initiatives in drug discovery. Nature Reviews Drug Discovery, 8(9), 701-708. DOI: 10.1038/nrd2944
- November 4, 2009
- 10:35 AM
- 1,288 views
Zinc inhibits rhinovirus replication
by Vincent Racaniello in virology blog
The title of this post should not come as a surprise to readers of virology blog – it was shown in 1974 that zinc could interfere with replication of rhinoviruses (see “Zinc and the common cold“). I am referring to the result of my first experiment to study the mechanism of zinc inhibition – something I promised I would document on these pages.
... Read more »
KORANT, B., KAUER, J., & BUTTERWORTH, B. (1974) Zinc ions inhibit replication of rhinoviruses. Nature, 248(5449), 588-590. DOI: 10.1038/248588a0
- November 4, 2009
- 08:00 AM
- 1,082 views
The impact from recreational power boating on freshwater turtles
by Rob Goldstein in Conservation Maven
Attention all boaters, please slow down for wildlife! A new study finds that recreational power boating can pose serious threats to freshwater turtles.
Researchers from the University of Ontario measured the occurrence of power boating injuries to northern map turtles ... Read more »
Bulté, G., Carrière, M., & Blouin-Demers, G. (2009) Impact of recreational power boating on two populations of northern map turtles ( ) . Aquatic Conservation: Marine and Freshwater Ecosystems. DOI: 10.1002/aqc.1063
- November 4, 2009
- 07:45 AM
- 1,340 views
Tip of the Week: CHOP CNV database
by Mary in OpenHelix
One of the hottest searches we see all the time is for more information on CNVs, or copy number variations. These intriguing structural variants in our genomes explain a lot of the reason that SNP hunting for complex diseases like schizophrenia and autism weren’t able to elucidate the problems as most people expected. These spectrum sorts of conditions were just not going to turn out as straightforward as the sickle-cell variation or the cystic fibrosis stories.
Resources to catalog and look at CNVs have developed. We have had a tutorial on DGV, the Database of Genomic Variants for some time (subscription required for tutorial). Just the other day I was looking around at the NCBI tool called dbVar, which has a nice diagrammatic overview of the kinds of structural variations CNVs represent (but I’m not sure I understand how to use the database yet–I’ll keep you posted ). Now there is also CHOP CNV.
Today I’ll be introducing you to the CHOP CNV resource. I heard about it at ASHG a couple of weeks ago, and decided to look into it. I had remembered hearing about the tool at one of the trainings we did at CHOP, but I wasn’t sure it was publicly available. Now I’m sure it is!
The publication associated with the CHOP CNV resource provides an overview of the strategy. The authors highlight the reason they developed this one–to use a uniform technology (Illumina chips to start, and then subsequent validation with other techniques) and to have a large sample set. They examine the genomes of over 2000 healthy individuals. The point of looking at healthy folks is that they form the reference set essentially: you can now take the samples from affected patients and subtract the things that healthy folks appear to share. This helps to narrow down your search for CNVs that might cause disease conditions. They offer various statistics on the types and sizes of the structural variants observed in the healthy population. It reminded me of another talk I heard at ASHG called “The first map of dispensable regions in the human genome” by T. Vrijenhoek et al–which was a cool talk that began with a Facebook chat that had us all giggling–but the serious message was there’s a lot of missing genome healthy people appear to tolerate just fine….
The paper goes on to describe the creation of their web interface. Although I couldn’t find it mentioned in the paper, I asked one of the authors and my suspicion that it was based on GBrowse was confirmed–I thought the tracks and controls appeared “GBrowsy” to me. It shows the variations on the graphical display. The deletions are red, the duplications are blue. There is also a table that contains the data which you can color code to indicate uniqueness with green. And the table provides a column that summarizes the genes in that region (if there are some), and links to the UCSC Genome Browser in that region so you can choose to go there and examine the other genomic features in that region. When you have that loaded at UCSC, the data becomes a custom track that you can then examine with all the UCSC tools, including detailed queries with the table browser. It’s a nice example of a big data set from a publication getting displayed at UCSC for further query options.
Another nice feature of the tabular display is that it also links to FABLE. FABLE is a literature mining tool (Fast Automated Biomedical Literature Extraction) that will be searched for papers relating to the genes you find in that region–so you can quickly assess what’s known about a given gene in a CNV region.
They also include a compelling “application” as a way to illustrate how you can use the CHOP CNV resource to make discoveries. There was a clinical sample of a patient with a number of congenital anomalies. The CNV detection of the genomic sample indicated that 32 of the 35 variations this patient had existed in the healthy controls–which means that targeting the remaining 3 for further study provides a much more helpful focus on the likely issues. There were a couple of other examples of utility as well.
When I asked the CHOP CNV team some questions about their Figure 1 in the paper (it showed what appeared to be lab group names with data sets), I was told that new versions will be coming that will offer some new features–including an option to upload your own samples to compare them to their data set.
If you are interested in structural variations in the genome you should check out the CHOP CNV database. You might find some helpful information for your project! I almost forgot to note–you can download all the data as well, and use it with other data you may have or for other analysis tools.
Direct to the site: http://cnv.chop.edu/
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Shaikh, T., Gai, X., Perin, J., Glessner, J., Xie, H., Murphy, K., O’Hara, R., Casalunovo, T., Conlin, L., D’Arcy, M., Frackelton, E., Geiger, E., Haldeman-Englert, C., Imielinski, M., Kim, C., Medne, L., Annaiah, K., Bradfield, J., Dabaghyan, E., Eckert, A., Onyiah, C., Ostapenko, S., Otieno, F., Santa, E., Shaner, J., Skraban, R., Smith, R., Elia, J., Goldmuntz, E., Spinner, N., Zackai, E., Chiavacci, R., Grundmeier, R., Rappaport, E., Grant, S., White, P., & Hakonarson, H. (2009). High-resolution mapping and analysis of copy number variations in the human genome: A data resource for clinical and research applications Genome Research, 19 (9), 1682-1690 DOI: 10.1101/gr.083501.108
... Read more »
Shaikh, T., Gai, X., Perin, J., Glessner, J., Xie, H., Murphy, K., O'Hara, R., Casalunovo, T., Conlin, L., D'Arcy, M.... (2009) High-resolution mapping and analysis of copy number variations in the human genome: A data resource for clinical and research applications. Genome Research, 19(9), 1682-1690. DOI: 10.1101/gr.083501.108
- November 4, 2009
- 07:17 AM
- 1,780 views
MM#07 Answer: Haplosporidia -- spores with lids
by Psi Wavefunction in Skeptic Wonder
Johan, our resident micropaleontologist, got this past week's Mystery Micrograph - congratulations! The answer was: Haplosporidia. Johan went the extra mile and identified its genus: Minchinia. This one is M.mercenariae, from Ford et al. 2009 JEM:Minchinia mercenariae (Haplosporidian) from the clam Mercenaria mercenaria; 13 - SEM of spore with arrow pointing to the opening; 12 - spore with a closed hinged lid; 2 - Minchinia's 'habitat' in the clam connective tissue (which it has taken over), while the digestive epithelia (DE) remain untouched. (Ford et al. 2009 JEM)Haplosporidia are unicellular parasites known for their peculiar jug-with-a-lid spores. Presumably those spores get inside the host and the hinged lid opens (cute!), releasing the organism, but I was unable to find any details of their invasion process. After finding their way inside the host and excysting, they exist in an amoeboid stage for a while, perhaps to quickly spread throughout the host. They then proceed to form multinuclear plasmodia inside host tissues and form spores via palintomy (cellularisation) (kinda like apicomplexans and some dinos), and release the spores.Many of them are commercially important due to their taste in shellfish. However, they seem to linger in obscurity despire that fact. In fact, one wonders whether their complete life cycles are known yet. Parasites are notorious for spanning multiple species at times, and it's hard to rule out a secondary host of some sort. However, the presence of what seems to be a complete set of life cycle stages within one sample suggest a single host at the moment, but intermediates remain possible (Azavedo et al. 2008 J Parasitol).TEM of Haplosporidium lusitanicum; Nu - nucleus; Sp - 'spherule' (multivesicular body) Hp - haplosporosome; Op - operculum ('lid'). Right: drawing of H.montforti; w- spore wall, F - filament (Left: Azevedo 1984 J Parasitol; Right: Azavedo et al. 2006 J Invert Pathol)There are three major genera of Haplosporidia, which are quite distinct morphologically. See this nice page describing them, with pictures (thanks, Johan!). They used to be categorised based on spore ornamentation, but that turned out to be rather messy. Haplosporidia reside in Rhizaria (TC-S & Chao 2002), close to Cercozoa, as shown in the aforementioned website and in the Pawlowski & Burki 2009 tree. Rhizarians have gote so much cool stuff it ain't funny.Next up we will have a glimpse of Paramyxids, which seem to be related to today's topic. They also have really interesting lifestyles. TC-S and Chao (2002, 2003) place them in "Ascetosporea" (Sprague 1979), sister to Haplosporidians, and Pawlowski (2008) doesn't seem to mind, so that's enough excuse to talk about them. I mean, I just READ a few paragraphs of TC-S, we can't let that effort go to waste! Besides, not like a little bit of long branch attraction has ever harmed anyone...But that'll be later this week. I shouldn't really be reviewing Rhizaria right now or anything, even though that would be kinda fun!References:Azevedo, C. (1984). Ultrastructure of the Spore of Haplosporidium lusitanicum sp. n. (Haplosporida, Haplosporidiidae), Parasite of a Marine Mollusc The Journal of Parasitology, 70 (3) DOI: 10.2307/3281564AZEVEDO, C., BALSEIRO, P., CASAL, G., GESTAL, C., ARANGUREN, R., STOKES, N., CARNEGIE, R., NOVOA, B., BURRESON, E., & FIGUERAS, A. (2006). Ultrastructural and molecular characterization of Haplosporidium montforti n. sp., parasite of the European abalone Haliotis tuberculata Journal of Invertebrate Pathology, 92 (1), 23-32 DOI: 10.1016/j.jip.2006.02.002Azevedo, C., Casal, G., & Montes, J. (2008). U... Read more »
Azevedo, C. (1984) Ultrastructure of the Spore of Haplosporidium lusitanicum sp. n. (Haplosporida, Haplosporidiidae), Parasite of a Marine Mollusc. The Journal of Parasitology, 70(3), 358. DOI: 10.2307/3281564
AZEVEDO, C., BALSEIRO, P., CASAL, G., GESTAL, C., ARANGUREN, R., STOKES, N., CARNEGIE, R., NOVOA, B., BURRESON, E., & FIGUERAS, A. (2006) Ultrastructural and molecular characterization of Haplosporidium montforti n. sp., parasite of the European abalone Haliotis tuberculata. Journal of Invertebrate Pathology, 92(1), 23-32. DOI: 10.1016/j.jip.2006.02.002
Azevedo, C., Casal, G., & Montes, J. (2008) Ultrastructural Developmental Cycle of Haplosporidium montforti (Phylum Haplosporidia) in its Farmed Abalone Host, Haliotis tuberculata (Gastropoda). Journal of Parasitology, 94(1), 137-142. DOI: 10.1645/GE-1177.1
Cavalier-Smith, T., & Chao, E. (2003) Phylogeny of Choanozoa, Apusozoa, and Other Protozoa and Early Eukaryote Megaevolution. Journal of Molecular Evolution, 56(5), 540-563. DOI: 10.1007/s00239-002-2424-z
FORD, S., STOKES, N., BURRESON, E., SCARPA, E., CARNEGIE, R., KRAEUTER, J., & BUSHEK, D. (2009) Minchinia mercenariae n. sp. (Haplosporidia) in the Hard Clam Mercenaria mercenaria Implications of a Rare Parasite in a Commercially Important Host . Journal of Eukaryotic Microbiology, 56(6), 542-551. DOI: 10.1111/j.1550-7408.2009.00432.x
- November 4, 2009
- 06:59 AM
- 478 views
Changing patterns of investment in biofuels
by Ciaran O'Neill in Biotechnology for Biofuels
The research and development of biofuels is beginning to attract investment from large international companies, including those traditionally associated with their fossil fuel predecessors.
A series of news articles published in Nature evaluate recent shifts in interest and investment in jatropha and algae as biofuel feedstocks, as well as techniques to produce cellulosic ethanol and liquid fuel directly from biomass (content requires subscription or payment).
With the announcement this summer that BP had pulled out of a $160 million joint venture with D1 oils to accelerate the cultivation of jatropha curcus, the prospect of further large scale investment in the shrub as a biofuel feedstock faded.
Due to its ability to grow on land unsuitable for agriculture, cultivating jatropha was previously touted as a way of avoiding competition for resources with food
crops. However, a recent controversial study suggests that jatropha requires much more water than other prospective bioenergy crops.
Despite falling investment in jatropha over the last year, various remaining projects suggest that the crop could still play a role in meeting future sustainable energy needs. Their scope is broad ranging, from genetic research on the development of high yielding seed strains, to initiatives operating on a local scale which incentivise farmers to cultivate jatropha alongside existing crops. A novel
method of jatropha oil transesterification for use in biodiesel synthesis was reported in Biotechnology for Biofuels earlier this year.
While interest and investment in Jatropha has waned, algal biofuels have emerged very quickly as perhaps the most promising source of biofuel for the future. The willingness of oil companies to invest was punctuated by the announcement in July that ExxonMobil would join J. Craig Venter’s Synthetic Genomics Inc. in a project (potentially worth $600-million) attempting to up-scale the production of biofuels from algae (see our previous blog post here). BP & Chevron have also invested in Martek Biosciences and NREL respectively. The potential benefits of algae as a ‘green’ source of energy are several fold; they can be cultured using land and water unsuitable for agriculture, and consume carbon dioxide during photosynthetic growth. Scientific advance in algal biofuel technology is difficult to gauge, however, as private companies withhold their research from peer review and publication.
In comparison to algae, the uptake from companies expected to be involved in the commercialization of cellulosic ethanol production (the conversion of agricultural residues and municipal waste into useful fuel), has been slow. Fewer investments than initially expected have been secured, due in part to the economic downturn and previous financial losses in maize ethanol.
This has resulted in an increased focus on the reduction of production costs; increasing the efficiency of fungal enzymes used in ethanol production and using engineered microorganisms that convert cellulose directly to ethanol are two approaches currently being explored. Attention has also turned to crops and industrial process by-products not previously considered or grown for use as feedstocks in bioethanol production. Research published in Biotechnology for Biofuels looks at spent grain from the brewing process, and blemished watermelons discarded from the annual crop.
In time, fuels derived from biomass which replicate the hydrocarbon fuels in use today might prove more attractive to investors than bioethanol. The technology to convert biomass to liquid fuel in this way is in its infancy, however the benefits of the approach include the generation of fuel products that would be tailored for the existing petrol-focused infrastructure. In 2008, Virunt and investor Royal Dutch Shell announced plans to develop technology for converting
plant sugars into hydrocarbons similar to those produced at petroleum refineries, and other companies including Chevron and Volkswagen have also invested in projects to develop biomass to liquid fuel technology.
Biotechnology for Biofuels welcomes high-quality studies describing technological and operational advances in the above production techniques, as well as others covered by the journal scope.
You can browse or search published articles, or submit your manuscript for consideration, online.
Gerbens-Leenes, W., Hoekstra, A., & van der Meer, T. (2009). The water footprint of bioenergy Proceedings of the National Academy of Sciences, 106 (25), 10219-10223 DOI: 10.1073/pnas.0812619106
Kumari, A., Mahapatra, P., Garlapati, V., & Banerjee, R. (2009). Enzymatic transesterification of Jatropha oil Biotechnology for Biofuels, 2 (1) DOI: 10.1186/1754-6834-2-1
Xiros, C., & Christakopoulos, P. (2009). Enhanced ethanol production from brewer's spent grain by a Fusarium oxysporum consolidated system Biotechnology for Biofuels, 2 (4) DOI: 10.1186/1754-6834-2-4
... Read more »
Gerbens-Leenes, W., Hoekstra, A., & van der Meer, T. (2009) The water footprint of bioenergy. Proceedings of the National Academy of Sciences, 106(25), 10219-10223. DOI: 10.1073/pnas.0812619106
Kumari, A., Mahapatra, P., Garlapati, V., & Banerjee, R. (2009) Enzymatic transesterification of Jatropha oil. Biotechnology for Biofuels, 2(1). DOI: 10.1186/1754-6834-2-1
Xiros, C., & Christakopoulos, P. (2009) Enhanced ethanol production from brewer's spent grain by a Fusarium oxysporum consolidated system. Biotechnology for Biofuels, 2(4). DOI: 10.1186/1754-6834-2-4
Fish, W., Bruton, B., & Russo, V. (2009) Watermelon juice: a promising feedstock supplement, diluent, and nitrogen supplement for ethanol biofuel production. Biotechnology for Biofuels, 2(18). DOI: 10.1186/1754-6834-2-18
- November 3, 2009
- 08:38 PM
- 944 views
Endangered Birds Share Traits with Extinct Species
There’s an old adage that pops up all the time not just in reference to conservation, but in the subject area of “you name it.” And for this very reason it has become quite ubiquitous. It goes something like “Those who do not study history are doomed to repeat it” or some variation there in [...]... Read more »
BOYER, A. (2009) Consistent Ecological Selectivity through Time in Pacific Island Avian Extinctions. Conservation Biology. DOI: 10.1111/j.1523-1739.2009.01341.x
- November 3, 2009
- 03:26 PM
- 761 views
Fish migrate to escape climate change
by Katie Kline in EcoTone
A study out today in the journal Marine Ecology Progress Series shows that global warming could have a major effect on the fishing industry by forcing large fish populations from their original habitats. About half of the fish stocks studied in the Atlantic ocean, many of them commercially valuable species, have shifted northward over the [...]
... Read more »
Nye, J., Link, J., Hare, J., & Overholtz, W. (2009) Changing spatial distribution of fish stocks in relation to climate and population size on the Northeast United States continental shelf. Marine Ecology Progress Series, 111-129. DOI: 10.3354/meps08220
- November 3, 2009
- 09:54 AM
- 688 views
Components of green tea interfere with the physiologic role of the native prion protein and its conversion into the pathologic prion protein
by Brian Appleby in CJD Blogger
As I continue to catch up on my articles, this post is about an article by Rambold and colleagues that was published in the Journal of Neurochemistry. The researchers’ study was designed to identify compounds that would interfere with the propagation of the pathologic prion protein. The two compounds investigated in the present article were the main components of green tea, epigallocatechin gallate (EGCG) and gallocatechin gallate (GCG). This was an in vitro study that used scrapie-infected N2a (ScN2a) cells. Both EGCG and GCG reduced pathological prion protein in addition to decreasing native prion proteins. In comparison to similar compounds, the authors found that the gallate side chain was necessary for antiprion activity and that an additional hydroxyl group of the trihydroxyphenyl side chain increased depletion of native prion proteins. Their data also indicated that EGCG induced a conformational change in the native prion protein at the plasma membrane that resulted in a transitional conformation that led to internalization and lysosomal degradation. Thus native prion proteins were depleted which also resulted in a reduction of the pathologic prion proteins. An interesting side point was that EGCG decreased the stress-protective function of the native prion protein in uninfected cells. EGCG-treated cells showed an increased vulnerability to stressful conditions (i.e., subjected to excitotoxin kainate, an apoptotic agent) In summary, EGCG and GCG induces a conformation change of the native prion protein that causes it to be internalized and degraded, thereby decreasing its conversion to pathologic prion protein. In this process, the stress-protective activities of the native prion protein are diminished. Once again, the conundrum of pathologic function +/- loss of function questions emerge as the etiologic cause of the neuropathologic process in prion diseases. Rambold, A., Miesbauer, M., Olschewski, D., Seidel, R., Riemer, C., Smale, L., Brumm, L., Levy, M., Gazit, E., Oesterhelt, D., Baier, M., Becker, C., Engelhard, M., Winklhofer, K., & Tatzelt, J. (2008). Green tea extracts interfere with the stress-protective activity of PrP and the formation of PrP Journal of Neurochemistry, 107 (1), 218-229 DOI: 10.1111/j.1471-4159.2008.05611.x del.icio.us Tags: prion,biology,research,biochemistry ... Read more »
Rambold, A., Miesbauer, M., Olschewski, D., Seidel, R., Riemer, C., Smale, L., Brumm, L., Levy, M., Gazit, E., Oesterhelt, D.... (2008) Green tea extracts interfere with the stress-protective activity of PrP and the formation of PrP . Journal of Neurochemistry, 107(1), 218-229. DOI: 10.1111/j.1471-4159.2008.05611.x
- November 3, 2009
- 08:00 AM
- 858 views
The danger of restoring native plants using non-local sources
by Rob Goldstein in Conservation Maven
A new study on ecological restoration efforts in Minnesota illustrates the dangers of establishing native plant species using non-local sources.
For the last 30 years, organizations and landowners have been working to restore native vegetation to dunes at Park Point along the western shore of Lake Superior. At first glance, it might not seem like such a big deal that these projects have been planting American beachgrass in Minnesota using propagules from source populations in Michigan.
But the study led by Rebecca Holmstrom found evidence that the Michigan plants differ genetically from a Minnesota population already existing in the area, and this gives the non-local beachgrass a competitive advantage.... Read more »
Holmstrom, R., Etterson, J., & Schimpf, D. (2009) Dune Restoration Introduces Genetically Distinct American Beachgrass, , into a Threatened Local Population . Restoration Ecology. DOI: 10.1111/j.1526-100X.2009.00593.x
- November 2, 2009
- 08:37 PM
- 1,312 views
Hot News: Curry, Curcumin, Cancer & Cure
by Laika in Laika's Medliblog
*Hot* News via Twitter and various news media a few days ago. Big headlines tell the following in respectively The Sun, Herald, Ireland, BBC News / NHS Health and Reuters:
Curry is a ‘cure for cancer‘
Spices in curry may help cure cancer
Curry spice ‘kills cancer cells‘
Scientists say curry compound kills cancer cells
The message of these headlines [...]... Read more »
O'Sullivan-Coyne, G., O'Sullivan, G., O'Donovan, T., Piwocka, K., & McKenna, S. (2009) Curcumin induces apoptosis-independent death in oesophageal cancer cells. British Journal of Cancer, 101(9), 1585-1595. DOI: 10.1038/sj.bjc.6605308
López-Lázaro, M. (2008) Anticancer and carcinogenic properties of curcumin: Considerations for its clinical development as a cancer chemopreventive and chemotherapeutic agent. Molecular Nutrition . DOI: 10.1002/mnfr.200700238
Castedo, M., Perfettini, J., Roumier, T., Andreau, K., Medema, R., & Kroemer, G. (2004) Cell death by mitotic catastrophe: a molecular definition. Oncogene, 23(16), 2825-2837. DOI: 10.1038/sj.onc.1207528
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