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  • April 11, 2011
  • 09:00 AM

Agricultural diversity improves health

by Jeremy in Agricultural Biodiversity Weblog

Here’s a turn-up for the books. A newspaper article headlined New farming practices grow healthier children actually delivers some specifics. The article reports on a project called Soils, Food and Healthy Communities, a joint effort by Canada and Malawi, and I’m ashamed to say (or can I blame the project’s communications?) that I knew nothing [...]... Read more »

  • April 11, 2011
  • 07:00 AM

April 11, 2011

by Erin Campbell in HighMag Blog

Normal 0 false false false EN-US X-NONE X-NONE MicrosoftInternetExplorer4 ... Read more »

  • April 11, 2011
  • 06:34 AM

Antrozoins: pallid bats, Van Gelder's bat, Rhogeessa... Baeodon!! (vesper bats part XI)

by Darren Naish in Tetrapod Zoology

Vesper bats. Well done with sticking with it all so far - I have lots of non-bat stuff I want to cover, but (for reasons soon to be explained) I need to get this series finished. With this article - part XI in the series (XI) - we are not at the end. But we are at the beginning of the end. Look at the cladogram below to see where we are, and follow the links below if you want to know what happened before. We arrive now at Antrozoini... Read the rest of this post... | Read the comments on this post...... Read more »

Baker, R. J. (1984) Mammalian sympatric, cryptic species: a new species of Rhogeessa (Chiroptera: Vespertilionidae). Systematic Zoology, 178-183. info:/

  • April 11, 2011
  • 01:13 AM

The Fly Tree of Life – Big Science, Big Results?

by Morgan Jackson in Biodiversity in Focus

This post is going to be longer and a little more technical than normal; feel free to jump in and out, or just check out some of the photos on your way to the conclusions. Although I may come across as critical and occasionally cynical at times, I’m not picking on anyone just to be [...]... Read more »

Wiegmann BM, Trautwein MD, Winkler IS, Barr NB, Kim JW, Lambkin C, Bertone MA, Cassel BK, Bayless KM, Heimberg AM.... (2011) Episodic radiations in the fly tree of life. Proceedings of the National Academy of Sciences of the United States of America, 108(14), 5690-5. PMID: 21402926  

  • April 10, 2011
  • 11:09 AM

Hey Hey We're All Monkeys

by ianmisner in LaneLab@URI

Discussion of primate phylogeny... Read more »

Perelman P, Johnson WE, Roos C, Seuánez HN, Horvath JE, Moreira MA, Kessing B, Pontius J, Roelke M, Rumpler Y.... (2011) A molecular phylogeny of living primates. PLoS genetics, 7(3). PMID: 21436896  

  • April 9, 2011
  • 05:21 PM

A spider in ant disguise

by Africa Gomez in BugBlog

My young daughter does not like ants. This is a bit troublesome at this time of the year when garden ants are everyhwere. Yesterday, she pointed at something on the ground. I looked at I saw what looked like an ant carrying another ant running very fast. It must have looked a bit odd as I stopped the "ant" putting my hand in front of it. She hid underneath and I slowly lifted my hand and took a couple of shots. Only when revising the shots did I realised that the ant was only an illusion: it was a spider, but one that strongly resembles an ant not only in size, general shape, shininess, but also in posture and behaviour. She carried her front legs raised so that it looks like its got antennae and six legs, and its movements were most reminiscent of the manic running of ants in hot weather.In her review of ant mimicry in spiders Paula Cushing stated referring to morphological spider modifications to resemble ants:They include a variety of color and body-form modifications that give the spider the appearance of having three body segments instead of two and of having long, narrow legs instead of shorter, more robust legs. Mandibles, compound eyes and even stings are sometimes mimicked by the spiders through modifications in the chelicerae, pigmentation in the cuticle, or special positioning of the spinnerets. In many cases, the extent to which the mimics resemble a particular model is extraordinaryThe following table helps in dispelling the notion that this ant resemblance is just a fantasy of the observer.There are many species of invertebrates that have evolved to resemble ants including crickets, bugs, beetles, springtails, and even flies. At least 100 species of spiders of 12 families mimic ants. The formal name for this phenomenon is ant mimicry or myrmecomorphy. But why would a spider evolve to look like an ant? A few spiders resembles ants in order to get close to them and eat them (aggressive mimicry), but the most ant mimic spiders benefit from visual predators taking them for ants, and avoid eating them. This is a case of protective or Batesian mimicry, the mimic imitating a dangerous model. Ants can be distasteful or aggressive or both, with biting mandibles, a spray of formic acid and a sting. Given that the deception is visual the selective agent must be highly visual: birds, wasps, hunter spiders that normally avoid ants would avoid an ant mimic in the same way, therefore a small spider may have much to gain from resembling a common local ant. My little ant-spider is most likely Micaria pulicaria, a widespread species in the U.K. often found running in the company of common garden ants. It is not reported that it preys on ants so, the reason for its ant mimicry, most likely involves Batesian mimicry. Interestingly, it is the only diurnal genus in a mostly nocturnal hunter spider family - Gnaphosidae, for an example see this post - and ant mimicry might have help this spider lineage conquer and diversify in a diurnal niche.ReferencesCushing, P. (1997). Myrmecomorphy and Myrmecophily in Spiders: A Review. The Florida Entomologist, 80 (2) DOI: 10.2307/3495552Reiskind, J. (1977). Ant-Mimicry in Panamanian Clubionid and Salticid Spiders. (Araneae: Clubionidae, Salticidae) Biotropica, 9 (1) DOI: 10.2307/2387854... Read more »

  • April 9, 2011
  • 10:32 AM

The Meaning of Mastodon Tusks

by Laelaps in Laelaps

Until recently, I did not fully appreciate fossil teeth. Their significance for identifying species and narrowing down the general diet of extinct animals was obvious, but I didn’t understand that teeth also hold intricate records of an individual animal’s life. Tiny pits and scratches on enamel can reveal what a creature was eating around the [...]... Read more »

  • April 9, 2011
  • 05:25 AM

Detecting pathogens in medieval Venice

by Michelle Ziegler in Contagions

Medieval Venice was a trading empire, one of the busiest ports of the late medieval world. As a hub of commerce waves of plague visited and revisited Venice in 1348, 1462, 1485, 1506, 1575-1577, and 1630-1632 with the last two producing mortality rates around 30% of the population (Tran et al, 2011). As we all [...]... Read more »

Fournier PE, Ndihokubwayo JB, Guidran J, Kelly PJ, & Raoult D. (2002) Human pathogens in body and head lice. Emerging infectious diseases, 8(12), 1515-8. PMID: 12498677  

Foucault C, Brouqui P, & Raoult D. (2006) Bartonella quintana characteristics and clinical management. Emerging infectious diseases, 12(2), 217-23. PMID: 16494745  

  • April 8, 2011
  • 10:45 PM

Yes We C(r)an(berry)!

by James Byrne in Disease Prone

That title is awful I know but I'm tired. Cut me some slack :)  I ran into a something that I have heard about before but assumed was rubbish and never really looked into it properly. A friend of mine insisted it was the case so I looked it up and I have to say, I was a little surprised.

So this is what cranberries look like. I never knew.
Cranberry juice is apparently very good at prevent urinary tract infection, particularly in women. There have been a few studies approaching it from different angles but, disappointingly, the studies all use different types of cranberry product, different doses and dosing techniques but despite all this the message seems to be pretty clear. Cranberries prevent urinary tract infections kicking in.
Before we can consider how this occurs its important to define what we are talking about. Urinary tract infections or UTIs are generally caused by a strain of Escherichia coli called Uropathogenic E. coli (UPEC) and it gets there by moving from the colon…ew. For this reason men rarely have to worry about them while they can be a chronic problem for women around the world, however the insertion of urinary catheters is a major risk factor for both genders. Clinical symptoms include burning sensation during urination and cloudy urine but these are only really evident once the bacteria have ascended the urethra into the bladder causing urethritis and cystitis respectively. If you want to feel real pain however let the little bastards work their way into your kidneys where kidney infection (or pyelonephritis) results in the above symptoms plus back pain and fever and the possibility of systemic spread.
So the first step in the infective process is generally stable colonisation of the colon. This step is often overlooked but without a source of UPEC it’s hard to get a proper infection going. The next step is invasion of the vaginal microbiota. Not an insignificant task since the vaginal niche is normally fully occupied by lactobacilli and other innocuous strains. Only once this has occurred can the UPEC ascend the urethra.

Having ascended the urethra the UPEC are not in the free and clear because the bladder and urethra have a formidable barrier to infection, the waterfall of flushing, cleansing urine that washes away all in its path. To overcome this UPEC have developed powerful adhesins, proteins used adherence of the bacterium to a surface and in this case specifically to the urinary epithelial tissue.
Adhesins are found in most pathogenic bacterial species but the array and strength of the UPEC adhesins is staggering. Among the most important adhesins produced by the UPEC are the pili. Pili are hair-like structures on the bacterial surface that are often capped with sticky (in the molecular sense) ends that facilitate adhesion. Importantly for UPEC possessing three different sticky caps (S, P and Type 1 pili) increases the chances of binding.
The S pili tend to be more important for adhesion outside of the gentio-urinary tract and so may play a part in systemic spread. In the urine however these pili bind the mannose filled protein uromodulin. Because of this S pili are called mannose sensitive pili and its thought that the ability to bind uromodulin, the most abundant protein in urine, possibly results in bacterial clumping and this allows a better opportunity for the P and Type 1 pili to do their thing. These two pili are responsible for the binding in the urethra and bladder.
Initially the Type 1 pili bind mannose sugars on the surface of the bladder cells allowing the bacteria to get some traction on the bladder/urethra walls before the P pili bind to a different sugar group to cement the interaction. The ability of P pili to bind non-mannose sugars has earned them the alternative title mannose resistant pili whereas type 1 pili are grouped with the mannose sensitive S pili.

The pili are the hairy bits on the picture of E. coli. The paper this pic is from is referenced at the bottom.
Once adhered to the host surface the UPEC can invade the epithelial cells but the bladder’s defence against this is to kick those invaded cells into the urine. A good defence strategy but it may contribute to tissue damage in the urinary tract when infections are recurrent. Also it seems some bacteria can prevent this expulsion of the cell they have invaded and in doing so remain as a reservoir of infection out of the way of the immune system and most antibiotic treatments.
Invasion does not always occur and instead some UPEC strains are able to release toxins directly onto the host epithelial surface due to the close interaction between bacterium and host. These toxins, as well as one of my boss’s favourite little molecules lipopolysaccharide (LPS) cause the inflammation that goes with the UTI.
So that’s the UTI side of things but where does Cranberry juice come into this story?
Cranberries (Vaccinium macrocarpon if you don’t mind) together with blueberries and Concord grapes constitute the only native fruit species to the US and Canada. Bet you didn’t know that, or maybe you did but I didn’t. In any case often the best way to work out what the native flora is capable of you have to look back to the indigenous peoples and, surprise surprise, Native Americans have known about and utilised the medicinal properties of cranberries for many years. Commonly used in different preparations to treat blood disorders, stomach issues, liver trouble and fevers.
By the 1880’s people were trying to work out what was doing what with cranberries and some German researchers found benzoic acid in cranberries. Then as now it was known to be a potent antiseptic and was included in a number of medicines and topical anti-bacteria treatments. This observation set researchers down the wrong path from the get go as the real power of cranberries lies in other activities of other compounds.
Continuing research into the antibacterial properties of cranberries found the benzoic acid was converted to hippuric acid, another antibacterial agent that also has a role in acidifying the urine. Everyone thought they were onto a winner. A powerful antibacterial compound excreted in the urine because you ate some cranberries. This is open and closed right? Well…

Could I be any clearer... Read more »

  • April 8, 2011
  • 08:19 PM

100 sextillion stars wasn't enough

by Cyc in The Rantings of a Gothic Atheist

100 sextillion. Or if you like visual aids 100,000,000,000,000,000,000,000. This has been the estimated number of stars in the visible universe. Or at least it was until recently. A study by a team headed by Van Dokkum, using Hawaii's Keck Observatory, have just tripled this number.

Using the spectrometer at the Keck Observatory, the team analyzed eight near by elliptical galaxies. When it comes to galaxies, the term 'near by' can seem a bit misleading. In this case they were between around 50 and 300 million light years away. In these, the largest of galaxies, the team went looking for Red Dwarfs, relatively small stars with long life-spans. In the case of stars, the smaller the star, the longer the life span. This is due to the effects of gravity spurring on the fusion that rules the lives of stars, with a size of .075 solar masses, this makes for an increadibly long life. Due to the vast distances involved, the signatures of Red Dwarfs were previously impossible to detect. To get around this problem, an estimate of the number of Red Dwarfs in our own galaxy was taken and this number was extrapolated to other galaxies.

In our own galaxy, the Milky Way, there are about 100 Red Dwarfs for every other star. However this new data revealed that the far larger elliptical galaxies had closer to 1,000 Red Dwarfs for every one other type star. In an article at, Van Dokkum stated:

Elliptical galaxies are some of the largest galaxies in the universe. The largest of these galaxies were thought to hold more than 1 trillion stars (compared with the 400 billion stars in our Milky Way). The new finding suggests there may be five to 10 times as many stars inside elliptical galaxies than previously thought, which would triple the total number of known stars in the universe, researchers said.
Besides the obviously implications about the prevalence of star formation in massive galaxies, there are two other important extrapolations from this data. This first being planet formation. It is already known that planets can and do form around Red Dwarfs. Recently a Venus like "Super-Earth" was found orbiting one of these small stars. With such a grand increase in the number of available stars, the number of planets is increased dramatically as well. While there is still some debate as to the habitability of planets orbiting Red Dwarfs, some hope is given in their long, stable lives. Where as our own star, Sol, has a life span around 10 billion years, the average Red Dwarf is expected to maintain fusion for 10 trillion years.

The next repercussion has to do with a quandary involving Dark Matter. Before this discovery, the amount of Dark Matter in elliptical galaxies was thought to be higher than in other types of galaxies. This was detected by the strong gravitational lensing seen around such galaxies. Gravitational lensing being the effect of light being bent around massive objects, the greater the bend, the more massive the object. But with the mass of the increased number of Red Dwarfs factored in, the amount of Dark Matter seems to be more along the expected amounts.

van Dokkum, P., & Conroy, C. (2010). A substantial population of low-mass stars in luminous elliptical galaxies Nature, 468 (7326), 940-942 DOI: 10.1038/nature09578

... Read more »

  • April 8, 2011
  • 12:25 PM

Microbiome Studies: We Are More than the Sum of our Parts

by Isobel in Promega Connections

What if you could help protect yourself from certain diseases by populating your gut with “good” bacteria, or selectively getting rid of “bad” ones? Two news articles suggesting this possibility caught my eye this week. The articles both summarized results from the microbiome project–a research effort geared towards developing a deep understanding of how the [...]... Read more »

Wang, Z., Klipfell, E., Bennett, B., Koeth, R., Levison, B., DuGar, B., Feldstein, A., Britt, E., Fu, X., Chung, Y.... (2011) Gut flora metabolism of phosphatidylcholine promotes cardiovascular disease. Nature, 472(7341), 57-63. DOI: 10.1038/nature09922  

  • April 8, 2011
  • 12:00 PM

Is it time for a sustainable pet movement?

by Southern Fried Scientist in Southern Fried Science

The world is rapidly approaching 7 billion people and the challenges of food supply, security, and sustainability will, along with climate change, be the defining issues of the 21st century. While the issues of the wealthiest nations revolve around the quality of our food, the environmental impact or our farming practices, and the value we place [...]... Read more »

Sleeman JM, Keane JM, Johnson JS, Brown RJ, & Woude SV. (2001) Feline leukemia virus in a captive bobcat. Journal of wildlife diseases, 37(1), 194-200. PMID: 11272497  

Roelke ME, Forrester DJ, Jacobson ER, Kollias GV, Scott FW, Barr MC, Evermann JF, & Pirtle EC. (1993) Seroprevalence of infectious disease agents in free-ranging Florida panthers (Felis concolor coryi). Journal of wildlife diseases, 29(1), 36-49. PMID: 8445789  

  • April 8, 2011
  • 06:29 AM

The genetics of renal cell carcinoma

by Danielle Stevenson in BHD Research Blog

As mentioned in the blog last week, high-throughput DNA sequencing is helping to identify novel mutations related to a number of different genetic disorders. A recent example of this can be seen in a study by Varela et al. (2011), … Continue reading →... Read more »

Kenneth, N., Mudie, S., van Uden, P., & Rocha, S. (2008) SWI/SNF Regulates the Cellular Response to Hypoxia. Journal of Biological Chemistry, 284(7), 4123-4131. DOI: 10.1074/jbc.M808491200  

Reisman, D., Glaros, S., & Thompson, E. (2009) The SWI/SNF complex and cancer. Oncogene, 28(14), 1653-1668. DOI: 10.1038/onc.2009.4  

Varela, I., Tarpey, P., Raine, K., Huang, D., Ong, C., Stephens, P., Davies, H., Jones, D., Lin, M., Teague, J.... (2011) Exome sequencing identifies frequent mutation of the SWI/SNF complex gene PBRM1 in renal carcinoma. Nature, 469(7331), 539-542. DOI: 10.1038/nature09639  

Xia, W., Nagase, S., Montia, A., Kalachikov, S., Keniry, M., Su, T., Memeo, L., Hibshoosh, H., & Parsons, R. (2008) BAF180 Is a Critical Regulator of p21 Induction and a Tumor Suppressor Mutated in Breast Cancer. Cancer Research, 68(6), 1667-1674. DOI: 10.1158/0008-5472.CAN-07-5276  

  • April 8, 2011
  • 12:44 AM

Friday Weird Science: The measure of a man, not quite what you’d think.

by Scicurious in Neurotic Physiology

Of COURSE this awesome paper would blow up the internets on a Monday, and of course, as you know, Sci is never funny on Mondays. She is only funny on Fridays. Should you ever find Sci funny on any other day of the week, you are delusional. But now I have the paper, and I’d [...]... Read more »

  • April 7, 2011
  • 09:30 PM

Australasian big-eared bats, and how to (perhaps) single-handedly wipe out an entire species, 1890s-style (vesper bats part X)

by Darren Naish in Tetrapod Zoology

About 12 species of big-eared Australasian bats are known as the, err, Australian big-eared bats and New Guinean bats. More formally, they are the Nyctophilus species. They're also known from some of the islands that surround New Guinea (like the Lesser Sundas), and also from New Caledonia (an endemic New Caledonian species, N. nebulosus, was named in 2002). Their presence has also been claimed for Fiji, but the evidence for this (based on specimens stored at the Natural History Museum in London) is inconclusive (J. E. Hill, in Parnaby 2002). Together with the New Guinea big-eared bat or Thomas's big-eared bat Pharotis imogene, these bats have often been given their own 'subfamily' (Nyctophilinae) or 'tribe' (Nyctophilini) (e.g., Tate 1942, Koopman & Jones 1970, McKenna & Bell 1997). I'll be referring to both Nyctophilus and Pharotis as the nyctophilins. Yes, we're now on part X of the vesper bat series: for the other parts, follow the links given below [adjacent photo shows a Mount Missim big-eared bat N. shirleyae, a species named as new in 2009]. Read the rest of this post... | Read the comments on this post...... Read more »

Volleth, M., & Tidemann, C. R. (1991) The origin of the Australian Vespertilioninae bats, as indicated by chromosomal studies. Zeitschrift für Säugetikerkunde, 321-330. info:/

  • April 7, 2011
  • 08:30 PM

Sex and mosquitoes – transmitting the Zika virus

by Captain Skellett in A Schooner of Science

When Brian Foy returned home to America from a field trip in Senegal, Africa, he didn’t know he was infected with the mosquito spread Zika virus. But just a few days later he was sick with extreme fatigue and joint pain, and so was his wife Chilson. A new study coauthored by the pair and [...]... Read more »

  • April 7, 2011
  • 03:45 PM

Beyond the Bacterial Microcompartment

by Merry Youle in Small Things Considered

Bacterial microcompartments were a great innovation. As Alan Derman explained, these protein-bounded structures assist with diverse metabolic processes by housing the requisite enzymes along with their substrates, sequestering potentially toxic intermediates, and allowing the products to exit. But the story does not end there. Enter the nanocompartment.

These are the simplest variation known so far on the theme of bacterial compartments. Like the micro version, these nano structures are thin, icosahedral protein shells that enclose a specific protein payload.... Read more »

Sutter M, Boehringer D, Gutmann S, Günther S, Prangishvili D, Loessner MJ, Stetter KO, Weber-Ban E, & Ban N. (2008) Structural basis of enzyme encapsulation into a bacterial nanocompartment. Nature structural , 15(9), 939-47. PMID: 19172747  

  • April 7, 2011
  • 10:01 AM

Re-Defining Science Communication: Emerging Best Practices that Empower the Public

by Matthew C. Nisbet in Age of Engagement

Over the past few years, scholars and scientists have been re-examining both the goals and the nature of science communication initiatives.  In a guest post today, Melanie Gade reviews much of this recent discussion and innovation.  Gade is a graduate student in this semesters course on "Science ...Read More... Read more »

Nisbet, M., Hixon, M., Moore, K., & Nelson, M. (2010) Four cultures: new synergies for engaging society on climate change. Frontiers in Ecology and the Environment, 8(6), 329-331. DOI: 10.1890/1540-9295-8.6.329  

Groffman, P., Stylinski, C., Nisbet, M., Duarte, C., Jordan, R., Burgin, A., Previtali, M., & Coloso, J. (2010) Restarting the conversation: challenges at the interface between ecology and society. Frontiers in Ecology and the Environment, 8(6), 284-291. DOI: 10.1890/090160  

  • April 7, 2011
  • 07:00 AM

April 7, 2011

by Erin Campbell in HighMag Blog

What do you have in common with a worm? A lot, and you should be thankful! The worm C. elegans is used as a model system that allows researchers to learn an amazing amount about the genetic pathways and development in many systems, including our own. Thankfully for HighMag, the worms are quite photogenic too. Our germ line is the line of cells that are responsible for passing on our genetic material to the next generation. The germline is composed of gametes (eggs and sperm), as well as the cells that divide to give rise to gametes. The cytoplasm of germ cells contain special aggregates of proteins and RNA called germ granules, yet their formation and function are not completely understood. A recent paper was published describing work on the germ granules, called P-granules, in the nematode C. elegans. Updike and colleagues probe further into the comparison of P-granules to nuclear pores and provide new information on the roles of different P-granule proteins. Interestingly, P-granules establish a size-exclusion barrier and are held together by hydrophobic interactions, similar to nuclear pores. Images above show the germ lines of a wild-type worm (left) and a worm with decreased levels of the P-granule protein GLH-1 (right). Without normal levels of GLH-1, the P-granules (green) were not able to localize to the surface of the nuclei (blue).Updike, D., Hachey, S., Kreher, J., & Strome, S. (2011). P granules extend the nuclear pore complex environment in the C. elegans germ line originally published in The Journal of Cell Biology, 192 (6), 939-948 DOI: 10.1083/jcb.201010104... Read more »

Updike, D., Hachey, S., Kreher, J., & Strome, S. (2011) P granules extend the nuclear pore complex environment in the C. elegans germ line. originally published in The Journal of Cell Biology, 192(6), 939-948. DOI: 10.1083/jcb.201010104  

  • April 7, 2011
  • 06:40 AM

A new view on eye development

by Eva Amsen in the Node

How do you make an eye? In the developing embryo, this process begins with the formation of the optic vesicle from the neural tube. This optic vesicle then invaginates to form an optic cup, which in turn develops into the outer pigmented layer of the retina and the inner neurosensory layer. Normally, this all takes [...]... Read more »

Eiraku, M., Takata, N., Ishibashi, H., Kawada, M., Sakakura, E., Okuda, S., Sekiguchi, K., Adachi, T., & Sasai, Y. (2011) Self-organizing optic-cup morphogenesis in three-dimensional culture. Nature, 472(7341), 51-56. DOI: 10.1038/nature09941  

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