Owner: Twisted Bacteria URL:http://twistedbacteria.blogspot.com Join Date: Mon, 16 Jul 2007 20:04:13 -0500 Rating:0 Site Description: A science blog. Microbiology, with an emphasis on actinomycetes (a group of bacteria) and the biosynthesis of natural products of pharmaceutical interest. Site statistics:Click here
Romans, dried figs and Streptomyces 2007-07-12 13:39:00 In the year 79 AD, the Roman towns of Herculaneum and Pompeii were devastated by a terrible eruption of Mount Vesuvius. As a result, the towns were buried under many meters of volcanic ash, which left buildings, food remains and human bodies in a remarkable state of preservation. This allows to study the state of health of ancient Romans
and its relationship to nutrition and other environmental conditions. For instance, analysis of human remains from Herculaneum showed lesions typically produced by tuberculosis and, especially, brucellosis. The high frequency of brucellosis has been related to the eating of contaminated cheese: Herculaneum had an important production of goat's milk and cheese. Remarkably, the study of carbonized cheese showed particles of the right size and shape, suggesting that they were bacteria of the Brucella group.However, the Herculaneum inhabitants appeared to suffer few non-specific infections, which were common in antiquity due to poor sanitary conditions. A
Can you write? 2007-07-08 14:45:00 Well, at least many scientists need some writing classes (yes, I'm first on the list!). If you're interested in this topic, I recommend Time for a change - Linda Cooper's blog at Nature Network. In her own words:"In this blog I suggest that there's a better way to write a scientific article. Currently, published articles are unnecessarily difficult to read and researchers need to be trained in how to write about their research so that others can understand (...)"Additionally, from her article Reinventing the science paper - How impenetrable writing harms science, at LabLit:"Researchers need to be trained to write naturally and persuasively – that is, clearly, completely, and without making assumptions about what readers know about a topic"I wish I had such a training... but it's never too late to learn.(Image source: Wikipedia)
Feeds and clouds 2007-07-07 12:07:00 I'm playing around with some widgets here. I have added a couple of new feeds from Connotea to the side bar: my own bookmarks, and Connotea bookmarks tagged with "microbiology" (social bookmarks). Perhaps you find something that suits your taste.Besides, my previous tag cloud (from Technorati, see below, left image) was not very satisfactory: by clicking on a tag you were directed to a Technorati page that didn't always show the expected result (consisting of all my posts tagged with the said label). So I'm using now a tag cloud for Blogger (below, right): if you click on a tag, it will show you directly the expected posts. Font sizes and colors are customizable. Thanks to phydeaux3![These are just plain images. The real ("clickable") feeds and the tag cloud are located on the sidebar]
Journal of Visualized Experiments 2007-07-02 16:57:00 The Journal
of Visualized Experiments (JoVE) seems to be a very interesting initiative. Already in its fourth issue, it's been launched as "an online research journal employing visualization to increase reproducibility and transparency in biological sciences". The performance of several microbiology-related techniques can be directly watched on the available videos, including: microscopic observation of termite microbial symbionts, large-scale screening of metagenomic libraries, and bacterial gene expression analysis using microarrays. Other biological disciplines are also covered, such as neuroscience, developmental biology, cellular biology and plant biology.Definitely, a visual experience of a real experiment goes beyond any written description of the procedure. The central concept in JoVE is very appealing, but I have several doubts concerning its practical success:Is a majority of the scientific community willing to participate in such a transparency effort?Will you uncover all t
Thinking Blogger Awards (en español) 2007-06-28 16:56:00 "The Translator" de Rosetta Rants es el culpable de haberme nominado para un Thinking Blogger
Award (Premio al ¿Blogger Pensador?). Como suelo leer blogs tanto en inglés como en español, voy a seguir esta cadena (blog meme suena bien en inglés, pero en castellano suena a memez) de forma bilingüe (la versión en inglés está aquí).Éstos son cinco blogs (entre otros) que me hacen pensar:Small Things Considered, de Moselio (Elio) Schaechter [en inglés]. El Blog de los Microorganismos.Xkcd, de Randall Munroe [en inglés]. Un cómic con fantasía, sarcasmo, matemáticas y lenguaje.El PaleoFreak, de El PaleoFreak (no tuvo infancia, tuvo prehistoria). Comentarios sobre evolución.MalaCiencia, de Alfonso de Terán Riva. Disparates, barbaridades y patadas a la ciencia, en noticias, películas o incluso en el saber general.Malatraducción, de Laertes. Sobre las traducciones al español de libros (principalmente), películas y tebeos.¡Enhorabuena, habéis ganado un "Thinking Blogger Awa Read more:Awards
Thinking Blogger Awards 2007-06-28 16:37:00 The Translator at Rosetta Rants should be blamed for nominating me for a Thinking Blogger
Award. As I use to read blogs in either English or Spanish, I'm continuing the blog meme in a bilingual fashion (a Spanish version of this post can be found here).These are five blogs (among others) that make me think:Small Things Considered, by Moselio (Elio) Schaechter. The Microbe Blog.Xkcd, by Randall Munroe. A webcomic of romance, sarcasm, math, and language.El PaleoFreak [in Spanish], by El PaleoFreak (he didn't have a childhood but a prehistory). Comments on evolution.MalaCiencia [in Spanish], by Alfonso de Terán Riva. Pieces of science nonsense found in news, films or common knowledge.Malatraducción [in Spanish/English], by Laertes. On Spanish translations of (mostly) books, films and comics.Congratulations, you won a Thinking Blogger Award!Should you choose to participate, please make sure you pass this list of rules to the blogs you are tagging. The participation rules are simple:If, Read more:Awards
The new Scientific American 2007-06-24 13:42:00 Scientific American
has been redesigned, and the complete July issue is available for download. It's a free download until June 30, so get it now! The only microbiology-related article deals with inflammation and its relation to cancer: A Malignant Flame, by Gary Stix. And a lot more of science reading is inside.(Did I mention it's free?)(Hey, free is good)
Read more:Scientific
, Scientific American
Microbiology Open House 2007-06-23 14:38:00 Just for fun, a short video (3:20) by Timothy Leung (TGokou2001). Enjoy images and music!(Video URL: Microbiology Open House
)
Natural products at Nature Chemical Biology 2007-06-23 12:22:00 The current issue of Nature Chemical Biology is centered on natural products, with an emphasis on terpenes. I found the following articles most interesting:One pathway, many products, by M.A. Fischbach & J. Clardy [Nat. Chem. Biol. (2007) 3, 353-355]. Primary metabolic pathways make single products, while secondary pathways generally make a variety of products, not just one. Why?The function of terpene natural products in the natural world, by J. Gershenzon & N. Dudareva [Nat. Chem. Biol. (2007) 3, 408-414]. Terpenes are the largest class of natural products, and we are just beginning to understand the biological roles of a few of them.Mining and engineering natural-product biosynthetic pathways, by B. Wilkinson & J. Micklefield [Nat. Chem. Biol. (2007) 3, 379-386]. With the purpose of developing new therapeutic agents, recent advances in the field come from improved screening technologies, genome mining, expression of entire biosynthetic gene clusters in suitable hosts, gene synthesis Read more:Natural
Combinatorial biosynthesis, but not as we know it 2007-06-18 15:43:00 Combinatorial biosynthesis can be understood as a special case of metabolic engineering, where genes responsible for individual metabolic reactions from different organisms are combined to generate hybrid metabolic pathways. An ideal result consists of a genetically-modified organism (or a collection of such microorganisms) that is useful for in vivo production of novel compounds. Nevertheless, there are examples of in vitro combinatorial biosynthesis (*), such as glycorandomization (a biocatalytic technique that uses purified enzymes to activate and attach sugars to natural products).One step beyond, a recent report in ACS Chemical Biology describes a new in vitro approach for the generation of combinatorial libraries of compounds derived from natural products. As a proof of concept, the authors combined three type-III polyketide synthases (PKSs), 16 different precursors (acyl-CoA esters) and three post-PKS tailoring enzymes. Remarkably, this strategy was adapted to a convenient micro
Small World 2007-06-16 05:15:00 This is a beautiful collection of video clips and stills of microscopic pond life (length 8:48), by Jon Grove. Combined with Beethoven's "Moonlight" sonata as soundtrack, it's just stunning!(Video URL: SmallWorld
)
Read more:Small World
Congratulations! It's a Scintilla! 2007-06-14 17:29:00 The guys at Nature Publishing Group are trying hard to build "the definitive" Web 2.0 for scientists: Connotea (online reference management service), Nature Network (online meeting place for scientists), and now Scintilla.Scintilla is an aggregator of science weblogs, news stories and publication databases, with two remarkable features. First, sources are manually selected to be related only to science. And second, you can rate and recommend stories to other people (which can be organized in groups according to their interests, for instance microbiology). Some comments are available on Nascent, bbgm and MicrobiologyBytes.(Twisted note no. 1) Nature Network (network.nature.com) is not the same as Nature Network (www.naturenetwork.net [live imagery and sound from cameras set up in Nature throughout the world]), which is also different to Nature Network (www.naturenetwork.org [platform to help developing countries for economic development and environmental protection]).(Twisted note no. Read more:Congratulations
Time travel 2007-06-08 18:24:00 You may know Google News Archive Search. I enjoy using it to search for old, historical stories. Soon I noticed that the oldest (free) stories came from the archives of Time Magazine, which are fully available for searching and reading (don't miss the covers!). Looking for articles containing the words "Streptomyces" or "actinomycete" in the complete Time archive, I got only five hits. Remarkably, they were written on 1948, 1949, 1950 and 1963. (So sad, it seems nothing related to these terms has happened in almost 50 years!)The Time articles, which deal with the discovery of antibiotics from actinomycetes, are:Antibiotic for Plants (Nov. 22, 1948). Actidione, now better known as cycloheximide, a product of Streptomyces griseus.Man of the Soil (April 4, 1949). Neomycin. You may have guessed that the "man" refers to Selman Waksman, the Father of Antibiotics.The Healing Soil (Nov. 7, 1949). Entertaining, long article about antibiotics (actinomycin, streptomycin, etc) and Waksman*.New An
Actinomycetes and Actinobacteria 2007-06-04 15:37:00 For some people, Actinomycetes and Actinobacteria are the same thing. Try and search Wikipedia with the word "actinomycete", and you will be redirected to the Actinobacteria page. And the first sentence in the definition is: "The Actinobacteria or Actinomycetes are a group of Gram-positive bacteria with high G+C ratio". OK, that's not authoritative enough for you. Then go to the NCBI Taxonomy Browser and search for "actinomycetes". As a result, a single entry is displayed: Actinobacteria (class). If you dig further into the Actinobacteria (class) entry, you see this:That's it, Actinomycetes and Actinobacteria (class) are synonyms! So, if we search for "actinobacteria" at the NCBI Taxonomy browser, we will arrive to the same "Actinobacteria (class) = Actinomycete" entry, right? Nope! We come to a different place called: "Actinobacteria, phylum, actinobacteria". Oh, I see, the "Actinobacteria (class) = Actinomycetes" is just a part of a greater Actinobacteria (phylum).But, wait, there
Microbiology Today: Actinobacteria 2007-06-03 05:40:00 Actinobacteria* are the stars in the May issue of Microbiology Today
, the magazine of the Society for General Microbiology. This is a good opportunity to learn the basics and review hot topics in the field. Relevant articles:An introduction to the actinobacteria. By Sir David Hopwood.Streptomyces: not just antibiotics. By Rosemary Loria, Madhumita Joshi & Simon Moll.Good, bad, but beautiful: the weird and wonderful actinobacteria. By Paul A. Hoskisson.Corynebacteria: the good guys and the bad guys. By Michael Bott.The mycobacteria. By Matt Hutchings.Good reading!(*) My next post will deal with the use of the terms "actinobacteria" and "actinomycetes".
Adopt an Actinomycete! 2007-06-02 06:28:00 These are image samples from Adopt a Microbe, by Emma Lurie. If you don't know her blog yet, you should visit it right now. Very nice cartoons and brief texts on (mostly) pathogenic bacteria. And viruses are coming soon!
Size and shape in the genomes of actinomycetes 2007-05-20 17:08:00 A new genome sequence of an antibiotic-producing actinomycete has been recently published in Nature Biotechnology. This seems to me a good excuse to highlight some peculiar aspects of genome evolution in this group of bacteria.The mentioned microorganism is Saccharopolyspora erythraea, known as an industrial source for erythromycin. The size of the genome, 8.2 Mbp (Mbp = megabasepairs = million base pairs), is similar to that of Streptomyces coelicolor (8.7 Mbp) and Streptomyces avermitilis (9 Mbp). These are some of the largest genomes in bacteria, although much smaller genomes are found in other actinomycetes. An example of the latter is Bifidobacterium adolescentis, with only 2.1 Mbp (not to mention the obligate parasite Tropheryma whipplei, the causative agent of Whipple's disease, with a tiny 0.9-Mbp genome).In the Sac. erythraea chromosome, the majority of conserved, essential genes are contained in a region extending either side of the origin of replication (the "core"). This
Intertwined lives: symbiosis 2007-05-12 12:43:00 Some actinomycetes are known for establishing symbioses with other organisms. A typical example is the formation of nodules on the roots of certain plants by soil bacteria of the genus Frankia. Although these microbes can also be found as free forms in the soil, the nodule constitutes a comfortable home for Frankia, with abundance of carbon sources. Additionally, it's an adequate environment for an activity that greatly benefits the plant: nitrogen fixation. This is a process by which atmospheric nitrogen is converted into ammonia, nitrate and other compounds. Hence, the actinomycete fixes nitrogen and fertilizes its host plant. Recently, the genomes of three Frankia strains have been sequenced, which will help to understand how different strains are able to select and colonize certain plant hosts but not others.(Image: Nodule from Alnus incana subsp. rugosa, about 1.5 cm diameter; D. R. Benson)In other actinomycetal symbioses, the second partner is an insect, for instance a beewolf
Actinomycetes, natural drug factories 2007-05-05 15:27:00 Actinomycetes are Gram-positive bacteria with a high GC-content in their DNA. Among others, representative genera include Corynebacterium, Micrococcus, Mycobacterium, Nocardia, Propionibacterium, and Streptomyces. Many actinomycetes, such as Streptomyces, grow as branching filaments and live in soil, as fungi do. Because of this resemblance, actinomycetes were originally classified as fungi. This was reflected on their name, where "mycetes" comes from the Greek for "mushroom, fungus".Some actinomycetes are pathogenic, such as Mycobacterium tuberculosis. However, many others are extremely useful due to their ability to produce compounds with pharmaceutical properties (antibiotic, antifungal, antitumor, immunosuppressive). The genus Streptomyces is well known precisely for this ability.In this blog, I intend to post mainly about the biology of actinomycetes, especially those aspects related to the biosynthesis of natural products of pharmaceutical interest. However, I may occasionally
Microbial Life, Second Edition 2007-07-18 18:39:00 A new microbiology textbook is available that I find interesting: Microbial
Life, SecondEdition
, by James T. Staley, Robert P. Gunsalus, Stephen Lory and Jerome J. Perry. It is written for sophomore to senior undergraduates who have a general understanding of chemical concepts and biochemistry. Some free samples are available from the book, including two complete chapters in pdf format (Structure and Function of Bacteria and Archaea, and Taxonomy of Bacteria and Archaea), some figures and a powerpoint lecture. A companion website additionally provides interesting learning resources. After checking the free samples, it seems to me that the book has been edited taking great care to content, illustrations and general aspect.
Read more:Second Edition
Choose your preferred definition 2007-07-17 15:14:00 In a previous post, I've already complained about the undefined definition of the word "actinomycete". Today I might even weep a little. Using Dictionary.com and Reference.com as sources, I've learnt that an actinomycete can be understood as a bacterium belonging to:order Actinomycetales [1,2,3,4], orphylum Actinobacteria [5,6], orphylum Chlamydobacteriae, or order Actinomycetales [7], orgenus Actinomyces, or family Actinomycetaceae, or order Actinomycetales [8]But don't put the blame on dictionary writers. There isn't a unified definition for "actinomycete" since the word lost its status as a class in bacterial nomenclature, long time ago. Anyway, dictionaries are really entertaining, aren't they?[1] The American Heritage® Dictionary of the English Language, Fourth Edition.[2] WordNet® 3.0.[3] Merriam-Webster's Medical Dictionary.[4] Crystal Reference Encyclopedia.[5] The American Heritage® Science Dictionary.[6] Wikipedia, the free encyclopedia.[7] Dictionary.com Unabridged Read more:preferred
Yondelis: from the seas to the pharmacy 2007-07-20 15:01:00 Yondelis (trabectedin, ecteinascidin-743, ET-743) is an anticancer natural product isolated from a marine organism, the tunicate Ecteinascidia turbinata. The compound has been extracted from the naturally growing and farmed tunicate, but now it's manufactured by semi-synthesis from a structurally-related metabolite produced by the bacteria Pseudomonas fluorescens. Probably, the actual producer of Yondelis may be a symbiotic bacterium living in close relationship to the tunicate. The drug is being developed by PharmaMar, a Spanish biopharmaceutical company subsidiary of the Zeltia Group. For several years, Yondelis has being studied in clinical trials for treatment of several cancer types.This morning, finally, good news: the European Medicines Agency has recommended Yondelis be approved by the European Comission, which means that the drug should be available to treat soft tissue sarcomas by the end of the year. I want to cite the words of José María Fernández Sousa (president of Ze
Science is my life... 2007-08-11 04:16:00 Sorry, I couldn't stop myself...(Image from Lab Bratz, a web comic by Ed Dunphy & Max Velati)(Via The Scientist: Pass the comics -- No, the science ones, by Edyta Zielinska)
Read more:Science
Streptomyces: they're twisted! 2007-08-10 13:39:00 I'm back from vacation, and trying to catch up. Perhaps this is a good moment for a brief, personal overview of Streptomyces biology, summarizing some important aspects.Although they may look like molds, Streptomyces organisms are bacteria (eubacteria). There are essential differences at the cell and molecular levels between fungi (which are eukaryotes) and bacteria (which are prokaryotes). The similarities found between streptomycetes and fungi are the result of convergent evolution, adapting to similar environments as saprophytic soil microorganisms.Streptomyces has a complex life cycle that includes formation of spores and other cell types. Typically, a spore germinates under the right conditions to generate a vegetative or substrate mycelium. This consists of a net of branching hyphae that grow and "dig" into the substrate to reach nutrients. Remarkably, there are few partition walls in the substrate mycelium: as a result, several copies of the genome are contained in every "cell"
Make Love (and Proteins), Not War 2007-08-14 15:07:00 "Protein Synthesis: An Epic on the Cellular Level" is an educational film directed in 1971 by Robert Alan Weiss. It seems that the movie has been viewed by generations of science students in the United States. Now, thanks to the internet, we all can enjoy. The film starts with a three-minute introduction by Professor Paul Berg (who later shared half of the 1980 Nobel Prize for Chemistry with the team of Walter Gilbert and Frederick Sanger). The screen then fills with a bunch of people dancing, singing and having fun... and making proteins. Ribosomal subunits, initiation or elongation factors, messenger or transfer RNAs, are impersonated by dancers in colored costumes.Music sound track: "Protein Jive Sutra".Yes, this is a true "molecular happening"!The video is available for download from the web of Kenyon College (MP4 format, 38 MB, a lengthy download).Or watch the video again at YouTube.
Beauty inside a cell 2007-08-30 16:10:00 You must see this paper at PLoS ONE, describing the application of a new electron microscopy technique (electron cryotomography) to reconstruct the 3D inner structure of a simple photosynthetic eukaryote, Ostreococcus tauri.Watch the video*. See the figures. You can even read the paper (open access).When science is good, it's great. But when science is good and beautiful, it's wonderful!Citation:Henderson GP, Gan L, Jensen GJ (2007)3-D Ultrastructure of O. tauri: Electron Cryotomography of an Entire Eukaryotic Cell.PLoS ONE 2(8): e749. doi:10.1371/journal.pone.0000749(*) Alternatively, you can watch the video at YouTube.
Read more:Beauty
, inside
Viruses help to culture "the unculturable" 2007-08-29 15:27:00 You probably know it: less than 1% of bacteria from environmental samples can be culture
d in the laboratory; so, the 99% silent majority is called the "unculturable bacteria". But let's make it clear: "unculturable" only means that we haven't found a way to grow them yet. The word "unculturable" is impressive and widely used, although perhaps misleading, and might be replaced by "yet to be cultured", "uncultured" or "uncultivated". Why are most microorganisms so fastidious, not growing in common media? Possible reasons: a required nutrient or "growth factor" is missing (perhaps produced in the natural environment by other bacteria), a component of the medium is toxic, or other bacteria in the sample produce an inhibitory substance.One obvious method of eliminating common microorganisms of a complex sample is by the addition of antibiotics to the culture media. Hence, for the isolation of actinomycetes, cycloheximide and nalidixic acid can be used to inhibit the growth of fungi and Gr Read more:Viruses
Twisted Picks 2007-09-25 14:45:00 This is the first of a series of posts where I plan to gather some links from my Connotea library that other people (you?) might find interesting. They'll mainly consist of links to research news or original articles, but don't expect many big headlines (that you can read anywhere). Links to research news will be preferred, as they are more readable by a wider audience. Most of the links will be microbe-centric but others may be related to biology fields beyond microbiology. So, there we go.Microbes and spaceships, great combination! I thought that microorganisms were too small to be bothered by terrestrial gravity, but I was wrong. For instance, Salmonella can get more virulent during a space trip (not very good news for astronauts): Spaceflight shown to alter ability of bacteria to cause disease. Other researchers are studying the effects of microgravity on mutation and DNA recombination rates in microbes (including some streptomycetal astronauts!): Russian rocket carries experimen Read more:Twisted
Bacterial sex: quarantined! 2007-09-21 07:29:00 You might have noticed several feeds on the sidebar. One of them (Connotea: csrsanchez''s bookmarks) lists the last five references added to my Connotea library. Last Tuesday I added a new reference: Bacterial
solutions to the problem of sex, from PLoS Biology. "The problem of sex" refers to the difficulties to find a fully satisfactory explanation to why sexual reproduction appeared and what its consequences were (from a scientific, evolutionary perspective). After a couple of days, I noticed that the reference did not come out on my sidebar, while later-added entries did. The explanation is that the sexy reference was quarantined by Connotea, due to the repeated use of the word "sex", I guess. This is not a complaint, I understand the use of automatic filters to avoid submission of inappropriate links (and, of course, Connotea has all the right to define "inappropriateness" in the use of its FREE service). Given that automatic filters may be widespread in academic sites and e-mail
Your favorite life science blogs? 2007-09-20 04:50:00 The Scientist is making a survey to find the most popular life science blogs: Vote for your favorite life science blogs. Anyone can vote and add a comment. This is an opportunity to discover new interesting blogs, too!
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