(It's a ...) Micro World (... after all)

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Previously known as Bio-Fuel!, (It's a ...) Micro World (... after all) is a blog dedicated to discussing scientific issues related (mostly) to microbiology and molecular biology. It'll primarily focus on matters of agricultural , bioenergy, and environmental importance, though I reserve the right to ramble on about any topics I wish to.

19 posts

Joko Hariyono
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  • January 4, 2010
  • 11:46 AM

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........ Read more »

  • December 7, 2009
  • 03:10 PM

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 bod........ Read more »

  • October 5, 2009
  • 12:09 PM

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 a........ Read more »

  • August 13, 2009
  • 06:18 PM


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 Bo........ 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
  • 09:47 AM

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 o........ 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
  • 10:13 AM

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........ Read more »

  • May 14, 2009
  • 09:11 AM

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 »

  • April 6, 2009
  • 02:28 PM

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 ........ Read more »

  • March 16, 2009
  • 04:39 PM

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 l........ 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
  • 01:00 AM

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 Che........ 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
  • 05:01 PM

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........ Read more »

  • September 4, 2008
  • 04:24 PM

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. Th........ 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
  • 10:23 AM

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, whi........ Read more »

  • July 14, 2008
  • 12:10 PM

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 impor........ 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
  • 06:14 PM

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 discu........ Read more »

  • July 9, 2008
  • 03:14 PM

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 potentia........ Read more »

  • July 7, 2008
  • 03:16 PM

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? Va........ Read more »

  • May 15, 2008
  • 12:17 PM

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'........ 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/

  • May 4, 2008
  • 03:08 PM

The Nitrogen Cycle

by TomJoe in (It's a ...) Micro World (... after all)

This is my first attempt at using Research Blogging, hope I don't mess this up. At any rate I've been reading a number of articles, for a paper I'm putting together, and I came across this review which I think is pretty good. It goes over the nitrogen cycle, of which I'm primarily concerned with nitrification and denitrification. Nitrification is the biological degradation of ammonia to nitrite and nitrates. Denitification takes nitrite and nitrate and reduces it to (hopefull........ Read more »

Masahito Hayatsu, Kanako Tago, & Masanori Saito. (2008) Various players in the nitrogen cycle: Diversity and functions of the microorganisms involved in nitrification and denitrification. Soil Science and Plant Nutrition, 33-45.

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