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I am a Microbiologist/Molecular Biologist. Trained in medical microbiology, I have recently gained employment as an environmental microbiologist, studying the microbial population structures in wastewater and riparian zones. I am also working on projects revolving around bio-based energy.
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- October 7, 2010
- 10:52 AM
- 291 views
It's a Micro World after all - RB: Waste Not, Want Not.
by Thomas Joseph in It's a Micro World after all (LabSpaces Edition)
Welcome to my first Research Blogging post here at LabSpaces! I'm not sure if this is a first for LabsSpaces, or simply a first for It's a Micro World after all, but regardless ... you're here now and you may as well stay for the fun! I grabbed a paper which caught my eye, and certainly generated a fair amount of buzz in the news, probably because it highl; (read more)
Source: Thomas Joseph - Discipline: Research... Read more »
Cuéllar, A., & Webber, M. (2010) Wasted Food, Wasted Energy: The Embedded Energy in Food Waste in the United States. Environmental Science , 44(16), 6464-6469. DOI: 10.1021/es100310d
- October 7, 2010
- 01:00 AM
- 311 views
Featured - RB: Waste Not, Want Not.
by Thomas Joseph in It's a Micro World after all (LabSpaces Edition)
Welcome to my first Research Blogging post here at LabSpaces! I'm not sure if this is a first for LabsSpaces, or simply a first for It's a Micro World after all, but regardless ... you're here now and you may as well stay for the fun! I grabbed a paper which caught my eye, and certainly generated a fair amount of buzz in the news, probably because it highl; (read more)
Source: Thomas Joseph - Discipline: Research... Read more »
Cuéllar, A., & Webber, M. (2010) Wasted Food, Wasted Energy: The Embedded Energy in Food Waste in the United States. Environmental Science , 44(16), 6464-6469. DOI: 10.1021/es100310d
- January 4, 2010
- 10:46 AM
- 445 views
What's your name?
by TomJoe in (It's a ...) Micro World (... after all)
I figured to start off the new year I'd do something a little different. As I've written about before, I'm intrigued by how people come up with the names of the organisms they identify. So, I'm going to start a once-monthly blog entry (we'll see how long I can keep it up) highlighting some of the more interesting ones I come across.The best resource for this is the International Journal of Systemic and Evolutionary Microbiology, so it will be the journal a majority of my citations come from. You'll notice that I'm running a year behind in the journal because for some reason our institution doesn't carry this journal *grumble*. I guess this qualifies as a Research Blogging entry as well, no? So here goes... our main entry:1. Halorhabdus tiamatea - (ti.a.ma.te'a. N.L. fem. adj. tiamatea belonging to, or related to, Tiamat, the ancient Mesopotamian goddess of ‘the primal abyss’ and salty water). Named after a Mesopotamian goddess, this organism is extremely halophilic.... and now for a few others ...2. Nocardioides daphniae - (daph'ni.ae. N.L. gen. n. daphniae pertaining to the water flea genus Daphnia, as the type strain was isolated from Daphnia cucullata). Self-explanatory.3. Salinicoccus iranensis - I doubt this one will come as much of a surprise, looking at the species name ... (i.ran.en'sis. N.L. masc. adj. iranensis from Iran, where the organism was isolated). Yep, no brainer there.4. The next group got to name the genus AND species of this organism, Perlucidibaca piscinae. Perlucidibaca - Per.lu.ci.di.ba'ca. L. adj. perlucidus transparent, pellucid; L. fem. n. baca a small round fruit, a berry; N.L. fem. n. Perlucidibaca a transparent berry, and piscinae - pis.ci'nae. L. gen. n. piscinae "of a fish-pond".5. Methylobacterium iners - (i'ners. L. neut. adj. iners inactive, lazy). I guess this fellow isn't very motile.Primary ArticleAntunes, A., Taborda, M., Huber, R., Moissl, C., Nobre, M., & da Costa, M. (2008). Halorhabdus tiamatea sp. nov., a non-pigmented, extremely halophilic archaeon from a deep-sea, hypersaline anoxic basin of the Red Sea, and emended description of the genus Halorhabdus. INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, 58 (1), 215-220 DOI: 10.1099/ijs.0.65316-0... Read more »
Antunes, A., Taborda, M., Huber, R., Moissl, C., Nobre, M., & da Costa, M. (2008) Halorhabdus tiamatea sp. nov., a non-pigmented, extremely halophilic archaeon from a deep-sea, hypersaline anoxic basin of the Red Sea, and emended description of the genus Halorhabdus. INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, 58(1), 215-220. DOI: 10.1099/ijs.0.65316-0
- December 7, 2009
- 02:10 PM
- 530 views
Chimera! (Part 1)
by TomJoe in (It's a ...) Micro World (... after all)
NOTE: I've been sitting on this for quite awhile, and while I wanted to add to it, i figure I may as well post this now, and then followup at a later date. I think it can hold up on its own for the purposes of discussing the problem. So I'll call this post "Part 1" for now.To the left is the mythical creature known as the chimera. Though, to be honest, do you know how hard it is to find an actual drawing of what the mythical chimera was described as? It was a fire-breathing creature with the body of a lion, with a tail ending with a snake's head. On top of that a goat head sprouts up from the middle of the back. Weird creature, eh? And you wouldn't think that's too terribly hard to draw, but that's not typically how artists do it. I dunno, artistic license and all that jazz, eh? But anyways, that's a bit of an aside, as I don't really intend to hearken back to my geeky AD&D-playing teenage years to talk about mythical creatures. Rather, I want to talk about the phenomenon that gene jockeys who do microbial community analysis face when doing 16S rDNA gene sequence analysis. Yes, I'm talking about that chimera.It's a problem, and depending on who you read, it's a very BIG problem at that. I'm going to cite a couple of papers to illustrate. The first is by Kevin Ashelford et al. who titled a 2005 AEM article: At Least 1 in 20 16S rRNA Sequence Records Currently Held in Public Repositories Is Estimated To Contain Substantial Anomalies. Quoting from their abstract (this article should be in the public domain by now, so I'll link to it down below):A new method for detecting chimeras and other anomalies within 16S rRNA sequence records is presented. Using this method, we screened 1,399 sequences from 19 phyla, as defined by the Ribosomal Database Project, release 9, update 22, and found 5.0% to harbor substantial errors. Of these, 64.3% were obvious chimeras, 14.3% were unidentified sequencing errors, and 21.4% were highly degenerate.Translation: Our sequence databases (which start with GenBank) are a mess. Then there is this study by Hugenholtz and Huber from 2003 in IJSEM entitled: Chimeric 16S rDNA sequences of diverse origin are accumulating in the public databases. Quoting their abstract (I believe this is also a freely accessible article) they state:A significant number of chimeric 16S rDNA sequences of diverse origin were identified in the public databases by partial treeing analysis. This suggests that chimeric sequences, representing phylogenetically novel non-existent organisms, are routinely being overlooked in molecular phylogenetic surveys despite a general awareness of PCR-generated artefacts amongst researchers.Now, this article was written a little over 6 years ago, but it continues to be a problem. These sequences are still in the databases and will no doubt remain there in perpetuity. So yah, we're stuck with the mistakes and total messes that people have submitted in the past. What needs to stop happening is adding to the problem in the future. That doesn't seem to be happening though. In 2006 Ashelford published again in AEM that recent large library submissions contained high percentages of chimeric sequences.Defining a large library as one containing 100 or more sequences of 1,200 bases or greater, we screened 25 of the 28 libraries and found that all but three contained substantial anomalies. Overall, 543 anomalous sequences were found. The average anomaly content per clone library was 9.0%, 4% higher than that previously estimated for the public repository overall. In addition, 90.8% of anomalies had characteristic chimeric patterns, a rise of 25.4% over that found previously. One library alone was found to contain 54 chimeras, representing 45.8% of its content. These figures far exceed previous estimates of artifacts within public repositories and further highlight the urgent need for all researchers to adequately screen their libraries prior to submission.In this article they talk about a program called Mallard which they use for chimera detection. As a matter of fact, there are a number of programs that can be used to identify 16S rDNA gene chimeras. Two of the most well-known programs are Chimera_Check and Bellerophon. Bellerophon is, of course, the mythical Greek who slew the chimera. All these programs work well, and they do what they are intended to do, under the proper conditions. I add that caveat because as most people who use these know, the conditions are important.For instance, Chimera Check and Bellerophon are champs at chimera detection when looking at full length 16S rDNA gene sequence. That means that your sequences should be roughly in the 1,500 basepair ballpark. So when you want to analyze sequences in the 300 to 600 base pair size range, those sequences will likely get thrown out by those programs. Chimera Check goes so far as to flat out state that sequences less than 400 base pairs in size may not be reliably analyzed, so it's definitely a case of "buyer beware". So, if you are someone who likes to look at a couple of variable regions (and there is good reason to narrow down your focus, which I hopefully will get to in another blog entry) you're going to have to find another way to check for chimeric sequences.ReferencesAshelford, K., Chuzhanova, N., Fry, J., Jones, A., & Weightman, A. (2005). At Least 1 in 20 16S rRNA Sequence Records Currently Held in Public Repositories Is Estimated To Contain Substantial Anomalies Applied and Environmental Microbiology, 71 (12), 7724-7736 DOI: 10.1128/AEM.71.12.7724-7736.2005 (PDF, 13 pages).Hugenholtz and Huber. Chimeric 16S rDNA sequences of diverse origin are accumulating in the public databases. 2003. IJSEM. 53: 289-93. (PDF, 5 pages).Ashelford et al. New Screening Software Shows that Most Recent Large 16S rRNA Gene Clone Libraries Contain Chimeras. 2006. AEM. 72(9): 5734-41. (PDF, 8 pages)... Read more »
Ashelford, K., Chuzhanova, N., Fry, J., Jones, A., & Weightman, A. (2005) At Least 1 in 20 16S rRNA Sequence Records Currently Held in Public Repositories Is Estimated To Contain Substantial Anomalies. Applied and Environmental Microbiology, 71(12), 7724-7736. DOI: 10.1128/AEM.71.12.7724-7736.2005
- October 5, 2009
- 11:09 AM
- 751 views
To all you knuckle crackers ...
by TomJoe in (It's a ...) Micro World (... after all)
... you can sleep easier tonight. Knuckle cracking does not lead to arthritis. So why would I bother to blog about this today? For one simple reason. After a 50 year, single participant study, results have demonstrated that habitual knuckle cracking does not lead to arthritis. This research has advanced the field so much that it was given a 2009 Ig Nobel award. The original research (see citation below) was published in 1998. A link directly to the Letter to the Editor of the journal Arthritis and Rheumatism can be found here (PDF, 2 pages).Donald Unger, an allergist in Thousand Oaks, California, earned the medicine prize for addressing another timeless question: does cracking knuckles really cause arthritis, as his mother warned him it would? As a child, he naturally thought his mother omniscient, but as a teenager he learned about science and started questioning received wisdom of this kind.To resolve the issue Unger embarked on a long-term controlled experiment, and began cracking the knuckles on his left hand twice a day, but not those on his right (Arthritis and Rheumatism, vol 41, p 949). He has done so for more than 60 years, and never suffered arthritis in either hand. "Mother, you were wrong," he says, looking heavenwards. What he now wants to know is: "Was it really necessary for me to eat my broccoli?"In the reported "study" the following was observed:For 50 years, the author cracked the knuckles of his left hand at least twice a day, leaving those on the right as a control. Thus, the knuckles on the left were cracked at least 36,500 times, while those on the right cracked rarely and spontaneously. At the end of the 50 years, the hands were compared for the presence of arthritis.There was no arthritis in either hand, and no apparent differences between the two hands.Therefore, rest assured knuckle crackers (of whom I am one), your habit is not detrimental.ReferenceUnger DL (1998). Does knuckle cracking lead to arthritis of the fingers? Arthritis and rheumatism, 41 (5), 949-50 PMID: 9588755... Read more »
Unger DL. (1998) Does knuckle cracking lead to arthritis of the fingers?. Arthritis and rheumatism, 41(5), 949-50. PMID: 9588755
- August 13, 2009
- 05:18 PM
- 635 views
Boobies!
by TomJoe in (It's a ...) Micro World (... after all)
Came across this article in the New Scientist. It's a lovely piece of modern day molecular biology doing some forensic work to rediscover a species that was thought to have died out a couple of hundred years ago. The bird in question is the Tasman Booby (Sula tasmani).It has been speculated that this bird has been extinct since around 1790, though evidence has suggested that these birds might still be around. From my reading of the papers, it appears that the call for extinction of the Tasman Booby was based on the examination of fossil material. However the authors believe that the previous study was instead looking at fossil remains of S. dactylatra, the Masked Booby, that were in the upper size range of that species.The authors first performed morphometric data. Their results were presented as follows:Contrary to van Tets et al. (1988), our comparison of new skeletal material revealed a size overlap between modern and fossil specimens for all standard humerus measurements.Such an overlap was not seen by van Tets et al. (see Table 1 reproduced below).So how does that happen? The authors of this manuscript state that van Tets et al. in their studies made a bit of a faux pas. Seems that they "failed to acknowledge" the fact that all the fossil specimens in their study were female, and the modern specimens in their study were male. Like a number of birds, the Booby presents with what is known as reversed sexual size dimorphism. In other words, the females are larger than the males. Whoops.Anywhoo ... Steeves et al. complement the morphometric data with genetic data by performing mitochondrial DNA sequencing. Phylogenetic analysis of these sequences revealed that mitochondrial DNA extracted from three of the six fossil specimens (nothing was recoved from the remaining fossils) were identical to an existing species of Booby, Sula dactylatra fullagari. Based on this, they proposed that all North Tasman Sea boobies should be known as Sula dactylatra tasmani. With this Steeves et al. have extracted the Tasman Booby from the Book of the Dead!ReferenceSteeves, T., Holdaway, R., Hale, M., McLay, E., McAllan, I., Christian, M., Hauber, M., & Bunce, M. (2009). Merging ancient and modern DNA: extinct seabird taxon rediscovered in the North Tasman Sea Biology Letters DOI: 10.1098/rsbl.2009.0478... Read more »
Steeves, T., Holdaway, R., Hale, M., McLay, E., McAllan, I., Christian, M., Hauber, M., & Bunce, M. (2009) Merging ancient and modern DNA: extinct seabird taxon rediscovered in the North Tasman Sea. Biology Letters. DOI: 10.1098/rsbl.2009.0478
- June 23, 2009
- 08:47 AM
- 757 views
Opportunities Lost
by TomJoe in (It's a ...) Micro World (... after all)
AKA: Why we need to protect the environment.... this past weekend I was invited out to dinner. While there I was engaged in a very interesting discussion with some other people about the environment and alternative fuel sources. One person suggested that we damn up all the local rivers and use them for hydroelectric power. I commented that this would disrupt local ecosystems, which in turn would have a detrimental effect on a number of species in those locales, possibly resulting in extinction of more than a few of them. Some of which we may not even know exist.The reply? If they can't manage to get around the dams, to hell with them.This report is support for my own position. Once we start damaging ecosystems, we run the risk of losing species. When we do so, we may actually be reducing our own ability to identify and develop extremely useful treatments for our own medical benefit. In addition, there is a massive largely, currently untapped, repository of bacterial species, currently unclassified ... most not even known to exist ... which may carry defenses which we could develop for antimicrobial therapies. That is supported by this manuscript. Metagenomics will eventually be able to identify such antimicrobials, but if we wipe out those environments before we ever get to test them ... it is an opportunity lost.ReferencesMangoni, M., Maisetta, G., Di Luca, M., Gaddi, L., Esin, S., Florio, W., Brancatisano, F., Barra, D., Campa, M., & Batoni, G. (2007). Comparative Analysis of the Bactericidal Activities of Amphibian Peptide Analogues against Multidrug-Resistant Nosocomial Bacterial Strains Antimicrobial Agents and Chemotherapy, 52 (1), 85-91 DOI: 10.1128/AAC.00796-07Okuyama-Nishida et al. Prevention of Death in Bacterium-Infected Mice by a Synthetic Antimicrobial Peptide, L5, through Activation of Host Immunity. Antimicrobial Agents and Chemotherapy, 2009; 53 (6): 2510 DOI: 10.1128/AAC.00863-08... Read more »
Mangoni, M., Maisetta, G., Di Luca, M., Gaddi, L., Esin, S., Florio, W., Brancatisano, F., Barra, D., Campa, M., & Batoni, G. (2007) Comparative Analysis of the Bactericidal Activities of Amphibian Peptide Analogues against Multidrug-Resistant Nosocomial Bacterial Strains. Antimicrobial Agents and Chemotherapy, 52(1), 85-91. DOI: 10.1128/AAC.00796-07
- June 11, 2009
- 09:13 AM
- 785 views
When the irresistable force meets the immoveable object ...
by TomJoe in (It's a ...) Micro World (... after all)
So this conversation that has been going on over at The Intersection, and which I blogged on yesterday about this abhorrent Japanese game, got me thinking (imagine that). One of the commenters on the original thread, and which I reposted in the comment section of my own entry said:The other issue with a game like this is that it appears that every rapist goes through an escalation process, mimicked in the game by the forced fondling prior to the rape. It seems to me fairly obvious that this game would serve as that escalation process. No “normal” man wants to rape. Therefore, anyone who buys this game already has rape fantasies that could escalate.Which got me to thinking about the whole virtual child pornography issue because it seems that the two cover similar ground. I couldn't remember what the legal rulings were on it, so I googled and it turns out SCOTUS considered it protected "free speech". However, I came across an article (PDF, 6 pages) that discussed the issue and it seems that it is equally (if not more so) applicable in the issue we're discussing today.The abstract for Neil Levy's paper reads as follows:The United States Supreme Court has recently ruled that virtual child pornography is protected free speech, partly on the grounds that virtual pornography does not harm actual children. I review the evidence for the contention that virtual pornography might harm children, and find that it is, at best, inconclusive. Saying that virtual child pornography does not harm actual children is not to say that it is completely harmless, however. Child pornography, actual or virtual, necessarily eroticizes inequality; in a sexist society it therefore contributes to the subordination of women.Bold emphasis mine. If you change the words "child pornography" with "rape" it reads: Rape, actual or virtual, necessarily eroticizes inequality; in a sexist society it therefore contributes to the subordination of women. Now, I'm not a lawyer, but could one reasonable argue then that protection of "free speech" in the cases of these software may come at the price of harming the equality of women? What would happen in such a case? Would free speech win out?Onto some of the points made by the paper:Though it is obvious that no child is harmed by the manufacture of virtual child pornography, supporters of the act typically maintain that it remains harmful to children, and ought to be prohibited for this reason. They advance several arguments, designed to showthat real children are harmed by virtual pornography:(1) Child pornography causes child abuse;(2) Virtual child pornography will be used to seduce actual children;(3) Allowing virtual child pornography makes laws banning real child pornography unenforceable;(4) Child pornography, actual or virtual, on the Internet allows isolated pedophiles and potential pedophiles to contact each other and reinforce each other’s desires. It thus increases the probability of offenses.He then goes on to address each point. I think #4 is pertinent since these software games often include "inviting friends" to engage in the acts to win you further points in the game. To this effect Neil Levy states:(4) I turn lastly to the argument that permitting child pornography on the Internet allows isolated pedophiles and potential pedophiles to contact one another, and thereby mutually reinforce each others’ pedophilic tendencies. This is a variant on the first argument, that child pornography causes child abuse, but it is worth treating separately, on the grounds that it gives the argument a new, Internet-focused, twist. Perhaps merely viewing pictures or films of (apparent) children engaged in sexual activity does not cause child abuse, but talking to other people who are engaged in, or who are considering, child abuse, can make this deviant activity seem quite normal. As Roger Darlington, chairman of the Internet Watch Foundation, notes,On the net you gain access to a community that legitimises your views. If you are operating in the real world, then meeting other paedophiles will require some organisation and will be difficult, but online you’ll find hundreds of thousands of people who share your views worldwide.This is but one aspect of a wider problem: the radicalization of people who meet and talk only to the likeminded, through the medium of the Internet. Carl Sunstein, whose book Republic.com is largely devoted to it and related problems, calls this the phenomenon of group polarization. Dicussion only with the likeminded encourages extremism and contempt for the opinions of others. Because the Internet enables and encourages such discussion, even for those with minority tastes who would otherwise be isolated from one another, it becomes a breeding ground for hate groups, political radicals – and pedophiles.This of course leads to an interesting turn of the discussion in the paper:If group polarization is a serious problem, it is a problem which arises largely out of speech; out of the discussions among the likeminded, and not significantly out of the viewing of images. If group polarization is a significant risk among those who have pedophilic desires, this gives us a reason to limit what they may say to each other, even to prevent them seeking one another out. This makes the problem more, not less, troubling, since it brings the right to freedom of speech into direct conflict with the right we all have to forestall clear and present dangers.Which essentially is the point of this post. Which one would win? Would the burden be too much to prove that rape software presents a clear and present danger? Neil Levy essentially closes with the following: Now, we have seen that the evidence that virtual child [pornography] harms actual children is weak. But we have good reason to believe that the eroticization of inequality harms women. Obtaining equal status for all women requires, inter alia, a new sexuality: a sexuality in which inequality is not a condition of sexual pleasure for men or women. It requires that sexual relations be conducted between equals. But since child pornography is necessarily an eroticization of inequality, allowing it undermines efforts to forge this new sexuality. Perhaps, then, it is because of harm to actual women, and not children, that virtual child pornography is objectionable.One could reasonably, I presume, argue that virtual rape software likewise eroticizes inequality, and as such, actually harms women. Neil Levy does not discuss whether this harm is sufficient for banning virtual child pornography (or in this case, virtual rape software), but I think it warrants serious consideration.ReferenceNeil Levy (2002). Virtual child pornography: The eroticization of inequality Ethics and Information Technology, 4, 319-323... Read more »
Neil Levy. (2002) Virtual child pornography: The eroticization of inequality. Ethics and Information Technology, 319-323. DOI: http://www.springerlink.com/content/l13412g37682p358/fulltext.pdf
- May 14, 2009
- 08:11 AM
- 852 views
The Origin of Life: RNA?
by TomJoe in (It's a ...) Micro World (... after all)
Discussion of a new paper by M.W. Powner et al.... Read more »
Powner, M., Gerland, B., & Sutherland, J. (2009) Synthesis of activated pyrimidine ribonucleotides in prebiotically plausible conditions. Nature, 459(7244), 239-242. DOI: 10.1038/nature08013
- April 6, 2009
- 01:28 PM
- 1,150 views
Biochar: Carbon Mitigation from the Ground Up
by TomJoe in (It's a ...) Micro World (... after all)
Was doing one of my weekly Scopus searches for new articles and came across the following review (PDF, 4 pages) on biochar, and it seems rather timely given that I've highlighted this topic recently. The title of this blog is taken from the title of the article, and it talks about the terra preta soils of the Amazon.The soils are proof of concept that burying biochar (biomass-derived charcoal) in the soils will both: increase soil productivity/fertility; and trap carbon for long periods of time in the soil. Quoting the work of Christoph Steiner, one of the leading experts in the area of biochar, the article relates that: ... charcoal-mediated enhancement of soil caused a 280-400% increase in plant uptake of nitrogen, an element essential for crop production.So how did the terra preta come about? There are competing theories:Anna Roosevelt, a professor of anthropology at the University of Illinois at Chicago, believes terra preta was created accidentally through the accumulation of garbage. The dark soil, she says, is full of human cultural traces such as house foundations, hearths, cemeteries, food remains, and artifacts, along with charcoal. In contrast, Erickson says he’s sure the Amazonian peoples knew exactly what they were doing when they developed this rich soil. As evidence, he says, "All humans produce and toss out garbage, but the terra preta phenomenon is limited to a few world regions." As I've mentioned before though, not all biochar is identical, and this article highlights some research pointing out this fact:However, not all biochar performs the same. The importance of biochar’s variable chemical composition was illustrated in studies by Goro Uehara, a professor of soil science at the University of Hawaii, who grew plants both with and without biochar made from macadamia nutshells. He says, "As we added more [biochar], the plants got sicker and sicker." Uehara’s colleague, University of Hawaii extension specialist Jonathan Deenik, says that when they repeated the experiment with a more highly carbonized version of the nutshell biochar, which contained lower levels of volatile compounds, "preliminary results in a greenhouse study showed that low-volatility [biochar] supplemented with fertilizer outperformed fertilizer alone by 60%, in a statistically significant difference." This research was presented at the October 2008 annual meeting of the Soil Science Society of America.From my particular vantage point, some biochars will act as a chelator (e.g., activated carbon) and pull essential nutrients (e.g., calcium, zinc, copper, iron) out of the soil, making them unavailable for plants and microbes.However, in terms of storage capabilities, what does biochar bring to the table?The calculations for potential carbon storage can be estimated downward from the amount of atmospheric carbon that photosynthesis removes from the air each year; using figures from the Intergovernmental Panel on Climate Change, Amonette estimates that number at 61.5 billion metric tons. He says the best estimates are presented in four scenarios for carbon storage calculated by the nonprofit International Biochar Initiative (IBI), a consortium of scientists and others who advocate for research/development and commercialization of biochar technology. The IBI’s "moderate" scenario assumed that 2.1% of the annual total photosynthesized carbon would be available for conversion to biochar containing 40% of the carbon in the original biomass, and that incorporating this charcoal in the soil would remove half a billion metric tons of carbon from the atmosphere annually. Because the heat and chemical energy released during pyrolysis could replace energy derived from fossil fuels, the IBI calculates the total benefit would be equivalent to removing about 1.2 billion metric tons of carbon from the atmosphere each year. That would offset 29% of today’s net rise in atmospheric carbon, which is estimated at 4.1 billion metric tons, according to the Energy Information Administration.Pretty significant, eh?An additional beauty to biochar is that it technically doesn't take a sophisticated setup to produce it:Among other projects, the students made their own biochar in a 55-gallon drum and found that positioning the drum horizontally produced the best burn.But biochar alone cannot solve our problems ... we need to better use our existing resources, and recycle!As a carbon mitigation strategy, most biochar advocates believe biochar should be made only from plant waste, not from trees or plants grown on plantations. "The charcoal should not come from cutting down the rainforest and growing eucalyptus," says Amonette.Now, all we need to do is get cracking and get into long-term field studies.ReferenceTenenbaum, D.J. (2009). Biochar: Carbon mitigation from the ground up. Environmental Health Perspectives, 117 (2): A70-A73.... Read more »
Tenenbaum, D.J. (2009) Biochar: Carbon mitigation from the ground up. Environmental Health Perspectives, 117(2). DOI: http://www.ehponline.org/members/2009/117-2/innovations.html
- March 16, 2009
- 03:39 PM
- 871 views
Garbage, garbage everywhere ...
by TomJoe in (It's a ...) Micro World (... after all)
I don't know, I guess I'm a sucker for poor defenseless animals, and I guess I believe that we, as humans, should hold ourselves to a higher accountability when it comes to being proper stewards of our great planet Earth. So when I come across manuscripts like this one ... damn it, it pisses me off! Here is the abstract:The leatherback, Dermochelys coriacea, is a large sea turtle that feeds primarily on jellyfish. Floating plastic garbage could be mistaken for such prey. Autopsy records of 408 leatherback turtles, spanning 123 years (1885–2007), were studied for the presence or absence of plastic in the GI tract. Plastic was reported in 34% of these cases. If only cases from our first report (1968) of plastic were considered, the figure was 37%. Blockage of the gut by plastic was mentioned in some accounts. These findings are discussed in the context of removal of top predators from poorly understood food chains.Check out the following figure ...Whiskey Tango Foxtrot folks! Look at 1950 and on. That's all us ... humans ... contributing to these incident rates. What part of "Do not throw your trash in the ocean" can't people seem to understand? The authors have a pretty sobering point as well when they state:Looking further ahead, we do not know what impact, if any, an increased demand for jellyfish by Asian markets could have on leatherback turtles. It has been speculated that leatherbacks off the coast of France take in more plastic in cooler months when jellyfish are scarcer. If it is correct that commercial harvests of jellyfish reduce the availability of this prey item, will ingestion of plastic by leatherbacks increase?One can only hope not.ReferenceMrosovsky, N., Ryan, G., & James, M. (2009). Leatherback turtles: The menace of plastic Marine Pollution Bulletin, 58 (2), 287-289 DOI: 10.1016/j.marpolbul.2008.10.018... Read more »
Mrosovsky, N., Ryan, G., & James, M. (2009) Leatherback turtles: The menace of plastic. Marine Pollution Bulletin, 58(2), 287-289. DOI: 10.1016/j.marpolbul.2008.10.018
- February 9, 2009
- 12:00 AM
- 1,138 views
No talking in class!
by TomJoe in (It's a ...) Micro World (... after all)
For all microbiologists not living in a cave, we all know that we're really losing the war against pathogenic bacteria, at least on the antiobiotic front. Even the most potent antibiotics like vancomycin -- often considered the antibiotic of last resort -- have seen some organisms develop resistance to it. So, it's time for either new drugs, or a new approach. A New Scientist article discusses developing new antibiotics which target quorum sensing. The article is based on a communication in Chemical Communications, entitled: Towards quorum-quenching catalytic antibodies. The process of quorum sensing is described as following in the NS article:Individual bacteria monitor the concentration of signalling molecules, and when it reaches a certain level, change their behaviour. That concentration provides a rough indication of when the number of cells in a particular population has reached a certain critical mass – known as a quorum.So? This process, the authors hypothesize, can be targetted in what they call "antivirulence therapy".Bacterial antivirulence therapies seek to avoid the development of treatment-induced resistance.Thew NS article continues to explain:But hacking the bacterial communication system could make it possible to prevent this transformation, and leave the cells waiting in a safe form for an attack signal that never comes. That would give the immune system extra time to naturally clear the bacteria from the body, says David Spring at the University of Cambridge, UK.Of course, that does mean that the body needs to clear the infection on its own. In some circumstances, that may not be possible. But at any rate, how can they do it? They plan on designing antibodies to these quorum molecules. These antibodies will degrade the quorum molecules upon contact, or at least that is the hope/plan. ReferencePrashant B. Kapadnis, Evan Hall, Madeleine Ramstedt, Warren R. J. D. Galloway, Martin Welch, David R. Spring (2009). Towards quorum-quenching catalytic antibodies Chemical Communications (5) DOI: 10.1039/b819819e... Read more »
Prashant B. Kapadnis, Evan Hall, Madeleine Ramstedt, Warren R. J. D. Galloway, Martin Welch, & David R. Spring. (2009) Towards quorum-quenching catalytic antibodies. Chemical Communications, 538. DOI: 10.1039/b819819e
- September 9, 2008
- 04:01 PM
- 1,207 views
Mars - Making a case for life
by TomJoe in (It's a ...) Micro World (... after all)
Was doing Scopus searches for relevant articles in my field and saw the following article (entitled: The microbial case for Mars and its implication for human expeditions to Mars) and thought: Research Blogging! With a title as cool as that, it deserves to be blogged on!Gerda Horneck starts the Introduction by making a case for life on Mars. There are several factors which lean positively towards this being the case.1. The physical and chemical surfaces of the early Earth and Mars were similar.2. Early Mars (3.5 Ga ago) was wet and had a more temperate climate.3. Microbial life existed on Earth by 3.5 to 3.8 Ga ago.Water, Water EverywhereAccording to Horneck: As well as carbon based chemistry and an adequate energy source, water in liquid phase has been considered as one of the prerequisites for habitability. To which, is outlined the case for water on Mars.1. Erosional patterns on Mars.2. Presence of hematite, which is only formed in the presence of water.3. Presence of sodium chloride which also is only formed when water is present.4. The global mineralogical data (clay minerals) of Mars also points towards liquid water.Given Mars present, extremely cold, atmosphere, water is unable to persist in a liquid state on the surface. Therefore, Horneck states: The search for putative extant Martian life must therefore concentrate on the subsurface biological oases where liquid water still exists under the current conditions.Don't the current conditions suck?Well, for most life, the answer to that question is: Yep. However, there is always the exceptions to the rule. Section 3 lays the groundwork for the possibility of life on Mars by citing the many instances of life on Earth in very "inhospitable" places.Arid environmentsThough not cited directly by name, the organism Deinococcus radiodurans is one of my favorite examples of survival in one environment, providing protection in another. D. radiodurans has been shown to be quite resistant to extremely high levels of radiation, able to effectively stitch its DNA back together after receiving doses of radiation which would kill most everything else. And it's not that D. radiodurans grew up next to Chernobyl. This bacterium is often isolated in very arid environments, and such areas where dessication is a common threat, methods to repair such damage (which is very similar to radiation damage) were necessarily evolved. Horneck also speaks of cryptoendolithic microbial ecosystems in deserts which ... give an example how life has withdrawn into protected zones. They colonize sandstones a few millimeters below the surface, forming layers of algae and cyanobacteria as primary producers as well as fungi and bacteria as consumers, thereby producing their own microhabitate in an otherwise hostile arid environment.Cold environmentsPsychrophiles, one of my favorite groups of organisms. These organisms don't just live, they thrive in places where the warmest it gets is 0 degrees centigrade. Some have been shown to grow in Antarctica at temperatures below -20 C (-4 F). Nevermind the fact that long term storage of bacteria usually involves freezing at -80 C or in liquid nitrogen (-346 F).Salty environmentsHalophiles (salt loving) organisms thrive in areas where salt is abundant. Brine, salt lakes and inside rock salts. They have evolved to regulate osmotic flow to survive.Intense UV radiationHere Horneck states that during the Archean (3.8 to 2.5 billion years ago), UV irradiation has been calculated to be about 1000 times greater than it is today (we have photosynthesis and our ozone-ified atmosphere to thank for the protection). Yet, during this period, life still found a way to survive. Not only that, by UV radiation is a mutagen and could have promoted biological evolution. What it certainly did do, was force bacteria to evolve DNA repair mechanisms.Intense ionizing radiationHere Horneck cites the story of D. radiodurans (Dr), and says that while Dr can tolerate radiation does of 3 x 10^3 Gy, the dosages on Mars are 30,000 to 40,000 lower. Horneck also states: Recently, hyperthermophilic archaea have been described that exert a similar high radiation resistance as D. radiodurans. Even the more radiation sensitive spores of Bacillus subtilis or vegetative cells of Escherichia coli would be able to survive radiation exposure under Martian conditions for extended periods of time.So, as we can see ... there are many conditions on Earth where we wouldn't expect life, but it's there anyways. Can the same be the case for Mars? Could there perhaps be areas on Mars similar to these inhospitable areas on Earth which teem with life?So, where?Where are these, as Horneck calls them: putative Martian oases?There is a general consensus that the present surface of Mars is not likely to be a habitable place. Putative habitable regions may exist in the sub-surface of Mars, where liquid water might be present, temperature fluctuations are low and the harmful UV radiation is attenuated.Perhaps given such cruddy environmental conditions the microorganisms are currently "hiding out", as Horneck states: On Earth, microorganisms could survive for hundred thousand years or even longer in ice or permafrost. Bacterial spores, which are reported to survive interim hostile conditions over millions of years, are another example of potential survivors over extreme intervals on Mars.Implications for human expeditions to MarsWhy do it? Horneck says that to search for life, it's really a task best suited for humans. Factors such as critical thinking, and real-time repairs play a role in any successful attempt at examining the planet. Of course, this comes with downsides as well, and Horneck focuses on three: the risk of contamination of astronauts by Martian microbes, the risk of contamination of Earth by Martian microbes on a return trip, and the risk of contaminating Mars with Earth microorganisms. It appears that NASA already has #3 in check, or is working on it. The issue is, as Horneck argues: Strict requirements to keep Mars clean can only be met with robotic missions to Mars. The scenario changes when humans are involved in the mission. Since humans carry vast amounts of microbes required to sustain important body functions, Mars will become inevitably contaminated with terrestrial microorganisms as soon humans arrive on its surface. Although the surface of Mars seems to be very hostile to microbial life, it cannot be excluded that some terrestrial microorganisms accidentally imported may find protective ecological niches where they could survive or even metabolize, grow and eventually propagate.ConclusionsI think Horneck summarizes the issue quite nicely in the closing paragraphs:Finally the question arises, whether the increasing robotic exploration of Mars and the eventual human exploration and settlement of that planet is likely to cause an environmental impact to scientifically important sites, regions of natural beauty and historically important regions, in the form of contamination with spacecraft parts and microbiota. Already the presence of crashed robots on Mars begs important questions on the type of wilderness ethic one may apply to Mars and how this ethic is emboided within practical environmental policy.Good points, all of them. I would argue that if we eventually "colonize" Mars, we're going to have to accept a certain level of contamination of Mars with terrestrial organisms. I'd say that it gives us a perfect opportunity to "do it right" with this second chance, which should minimize the extent of this contamination, but it's probably unavoidable.Overall though, this was a very interesting read. If you have access to the journal, it's definitely worth a download (PDF, 10 pages).ReferencesG HORNECK (2008). The microbial case for Mars and its implication for human expeditions to Mars Acta Astronautica, 63 (7-10), 1015-1024 DOI: 10.1016/j.actaastro.2007.12.002... Read more »
G HORNECK. (2008) The microbial case for Mars and its implication for human expeditions to Mars. Acta Astronautica, 63(7-10), 1015-1024. DOI: 10.1016/j.actaastro.2007.12.002
- September 4, 2008
- 03:24 PM
- 1,327 views
Periodic Table of Life - 68 "Elements"
by TomJoe in (It's a ...) Micro World (... after all)
A recent correspondence out of Nature - Cell Biology describes a sort of "periodic table of biology" revolving around 68 basic molecules which Dr. Jamey Marth refers to as the "molecular building blocks of life". While the illustration doesn't look like a periodic table, the figure provided in the correspondence (and here in this post, down below) does list all 68 molecules. These molecules revolve around 4 basic areas of cellular composition: 1)DNA & RNA; 2)Glycans; 3)Proteins; and 4)Lipids. The nucleotides and amino acids account for 28 of the 68 molecules, and most everyone how has taken a biology class will know of them. The glycans and lipids, though less well known, are just as important.Dr. Marth argues the following:As indivisible units of life, the cells of all organisms consist of four fundamental macromolecular components: nucleic acids (including DNA and RNA), proteins, lipids and glycans. From the construction, modification and interaction of these components, the cell develops and functions. The struggle to comprehend this interplay is the preoccupation of biologists, and more recently those engaged in systems biology. But do we readily take into account all of the components of biological systems to model health and disease accurately? To do this, the basic composition of all cells must be evident.The physical sciences developed the periodic table of the elements to convey the composition and relatedness of matter. A related construct for biology may provide a more balanced view of the cell and its biochemistry.And closes with the following:Defining the molecular building blocks of life provides a conceptual framework for biology that has the potential to enhance education and research by promoting the integration of knowledge. The insights afforded by bridging the divides that exist between disciplines can further moderate the view that researchers must invariably sacrifice breadth of knowledge to acquire depth of understanding. Cultivating this integration would reflect a more holistic and rigorous endeavour, which will ultimately be required if we are to perceive and most effectively manipulate the biological mechanisms of health and disease.It's an interesting concept. I'm not sure that the figure presented lends itself to easy memorization, a better understanding of the interactions of the molecules, or if it is as useful as the periodic table. Do we need to have better interdisciplinary collaborations? Most certainly. You see a fair amount of overlap (in some cases, not all) between the gene jockeys and protein chemists, but I think glycan and lipid research has lagged far behind (at least in the areas of microbiology to which I have been exposed). So, while an interesting concept, I'm not sure what traction this correspondence will obtain. Time will tell I suppose.Jamey D. Marth (2008). A unified vision of the building blocks of life Nature Cell Biology, 10 (9), 1015-1015 DOI: 10.1038/ncb0908-1015... Read more »
Jamey D. Marth. (2008) A unified vision of the building blocks of life. Nature Cell Biology, 10(9), 1015-1015. DOI: 10.1038/ncb0908-1015
- August 19, 2008
- 09:23 AM
- 1,254 views
Is The World Slowly Dying?
by TomJoe in (It's a ...) Micro World (... after all)
CNN has an article which reports on a peer reviewed manuscript published in Science which discusses the fact that the world's oceans contain over 400 dead zones. That's not a good thing.These dead zones are the result of eutrophication, when massive amounts of nutrients are released into an ecosystem. It is particularly bad when that ecosystem happens to be a coastal watershed, stream, river, pond or lake. These nutrients are typically runoff from agricultural lands, into adjacent waterways, which are then flushed into the oceans. Eutrophication is not a "Good Thing" as it typically leads to excessive plant, algae, and/or microbial growth, which in turn effectively chokes off the existing biodiversity in the area. That's bad.As Diaz and Rosenberg write:The worldwide distribution of coastal oxygen depletion is associated with major population centers and watersheds that deliver large quantities of nutrients (Fig. 1 and table S1). Most of these systems were not hypoxic when first studied, but it appears that from the middle of the past century, the DO concentrations of many coastal ecosystems have been adversely affected by eutrophication. The observed declines in DO have lagged about 10 years behind the increased use of industrially produced nitrogen fertilizer that began in the late 1940s, with explosive growth in the 1960s to 1970s (4). For marine systems with data from the first half of the 20th century, declines in oxygen concentrations were first observed in the 1950s in the northern Adriatic Sea (5), between the 1940s and 1960s in the northwestern continental shelf of the Black Sea (6), and in the 1980s in the Kattegat (7). Localized declines of DO levels were noted in the Baltic Sea as early as the 1930s, but it wasn’t until the 1960s that hypoxia became widespread (7). Localized hypoxia had also been observed since the 1930s in the Chesapeake Bay (8) and since the 1970s in the northern Gulf of Mexico (9) and many Scandinavian coastal systems (7). Paleoindicators (foraminifera ratios and organic and inorganic compounds) show that hypoxia had not been a naturally recurring event in these ecosystems (10, 8). The number of dead zones has approximately doubled each decade since the 1960s (fig. S1 and table S1).DO stands for dissolved oxygen which is the measure of oxygen which is a measure of the level of oxygen saturation in a system. Since a sizeable portion of life relies on oxygen, a poor DO level is an ominous sign. There are several "levels of hypoxia", with about half of the dead zones being annual phenomenon, typically occurring once a year. An additional 25% have multiple hypoxic events each year. Some systems do not experience hypoxic episodes every year (~17% of the dead zones) but still are cause for concern. In all cases, these hypoxic events result in mortality for a portion of the existing organisms within the ecosystem.Light at the end of the tunnel?There is hope however. With effective nutrient management, several systems have reduced the dead zones in the surrounding ecosystems. As the authors relate:The management of nutrients and carbon inputs has virtually eliminated dead zones from several systems, including the Hudson and East Rivers in the United States and the Mersey and Thames Estuaries in England (31, 32). However, in other systems, such as the Chesapeake Bay, the management of nutrient input has not improved DO. Nevertheless, the management of sewage and pulp mill effluents has led to many small-scale reversals in hypoxia (table S1).There are several ways to help reduce eutrophication, such as building riparian zone buffers around farmland, organic farming, better fertilization practices, as well as sound and effective environmental policy. These steps, and many more, are going to be necessary in order to help the worlds oceans survive and continue to provide us with food and life.R. J. Diaz, R. Rosenberg (2008). Spreading Dead Zones and Consequences for Marine Ecosystems Science, 321 (5891), 926-929 DOI: 10.1126/science.1156401... Read more »
R. J. Diaz, & R. Rosenberg. (2008) Spreading Dead Zones and Consequences for Marine Ecosystems. Science, 321(5891), 926-929. DOI: 10.1126/science.1156401
- July 14, 2008
- 11:10 AM
- 1,069 views
Primum Non Nocere - Part IV (Scientists and the Media)
by TomJoe in (It's a ...) Micro World (... after all)
Scientists Generally Happy With Their Media Interaction. (Title compliments of Science Daily).The article cited is based on a report in Science, entitled Interactions with the mass media (see Reference).Key findings of the survey included:1. Increasing the public's perception of science was the most important benefit mentioned by scientists as an incentive to interact with the media, with 93% indicating that achieving 'a more positive public attitude towards research' was an important motivator;2.However, lack of control of media outcomes remains an issue fo... Read more »
H Peters, D Brossard, S de Cheveigne, S Dunwoody, M Kallfass, S Miller, & S Tsuchida. (2008) SCIENCE COMMUNICATION: Interactions with the Mass Media. Science, 321(5886), 204-205. DOI: 10.1126/science.1157780
- July 9, 2008
- 05:14 PM
- 1,046 views
Celebrity Death Match - Biodiesel vs Bioethanol (Part II)
by TomJoe in (It's a ...) Micro World (... after all)
When I first came up with the title "Celebrity Death Match" for this series, I was actually referring to a spat in the pages of Trends in Biotechnology, rather than biodiesel versus bioethanol. Specifically, I was speaking about the exchange between Lucas Reijnders and Yusuf Chisti, which I will cover in this blog entry. But hey, the shoe fits, so I'll take credit for the double entendre.I love these sorts of exchanges. Perhaps the romantic in me believes this is how science discuss was handled in days long gone. Scientists would converge at their respective Academies of Science an... Read more »
L REIJNDERS. (2008) Do biofuels from microalgae beat biofuels from terrestrial plants?. Trends in Biotechnology, 26(7), 349-350. DOI: 10.1016/j.tibtech.2008.04.001
Y CHISTI. (2008) Response to Reijnders: Do biofuels from microalgae beat biofuels from terrestrial plants?. Trends in Biotechnology, 26(7), 351-352. DOI: 10.1016/j.tibtech.2008.04.002
- July 9, 2008
- 02:14 PM
- 1,157 views
Celebrity Death Match - Biodiesel vs. Bioethanol (Part I)
by TomJoe in (It's a ...) Micro World (... after all)
A fight for the ages, and it's being waged through the pages of Trends in Biotechnology!In 2007, Yusuf Chisti published an opinion piece in Trends in Biotechnology with the title "Biodiesel from microalgae beats bioethanol" (see reference, below). In this article, Dr. Chisti laid out the rationale as to why we should seriously look at biodiesel from microalgae. In the abstract, Chisti states ...Biodiesel from microalgae seems to be the only renewable biofuel that has the potential to completely displace petroleum-derived transport fuels without adversely affecting supply of food a... Read more »
Y CHISTI. (2008) Biodiesel from microalgae beats bioethanol. Trends in Biotechnology, 26(3), 126-131. DOI: 10.1016/j.tibtech.2007.12.002
- July 7, 2008
- 02:16 PM
- 1,064 views
Ceftobiprole To The Rescue
by TomJoe in (It's a ...) Micro World (... after all)
Back when I was a Medical Technologist, and doing my microbiology clinical rotations, the lab director who was supervising me sat me down several times a week. During these sit downs, we went over various microbiological topics. One such topic was antibiotic resistance. I remember him quite clearly when he told me that if vancomycin-resistant organisms ever arose, we'd all be in deep poop. Well, there are organisms out there which are now vancomycin resistant. Why is this such a problem? Vancomycin is literally the last line of defense. It is the antibiotic which is given when no others are le... Read more »
M Chung, A Antignac, C Kim, & A Tomasz. (2008) Comparative study of the susceptibility of major epidemic clones of MRSA to oxacillin and to the new broad spectrum cephalosporin ceftobiprole. Antimicrobial Agents and Chemotherapy. DOI: 10.1128/AAC.00266-08
- May 15, 2008
- 11:17 AM
- 1,175 views
What the floc?
by TomJoe in (It's a ...) Micro World (... after all)
If you ever deal with wastewater, you'll notice that there are small bits of particulate matter floating in it. I'm not going to go into the gory details of what a portion of that matter is because I think your imagination can do a pretty good job of figuring it out on its own.However, a substantial portion of this matter is bacterial in nature. Some bacteria are free-floating, in that they don't adhere to other bacteria and exist in the environment independently. Others aren't so happy doing things that way, and they form films and flocculants to keep their communities together. ... Read more »
Yoshitaka Tago, & Akira Yokota. (2004) Comamonas badia sp. nov., a floc-forming bacterium isolated from activated sludge. Journal of General and Applied Microbiology, 50(5), 243-243. info:1349-8037/
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