Holes in the ice…

Research bloggingCRYOCONITE (‘ice dust’) holes are small pock-like depressions that are strewn over the surface of glaciers, looking much like a pristine snow drift after you’ve thrown a handful of gravel at it. Such melt-holes have been documented on glaciers at both poles, and on other glaciated regions such as Iceland, Greenland, Canada and the Himalayas. According to one account, at least, cryoconite holes  have been a bane to scientists working on the Greenland ice sheet, the holes being typically full of slushy ice, and big enough to step in by accident. However, cryoconite holes have been the subject of much debate in recent years; a debate centring on their role as contributors to glacial melting. Continue reading “Holes in the ice…”

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Bug eat bug…

This post was chosen as an Editor's Selection for ResearchBlogging.orgAS if it’s not hard enough at the bottom of the food chain, being cannibalised by your own bottom-dwelling compatriots must add insult to injury. The soil dwelling Gram-positive bacterium Bacillus subtilis is fully equipped to take appropriate action when faced with food shortages; a sub-population of cells initiate a process of dormancy by turning themselves into hardy, robust spores. In this form the bacteria are capable of enduring temporary, or prolonged, harsh environmental conditions.

However, this is not a process entered into without some careful deliberation. Sporulation, the act of forming a spore, is an energy intensive process that results in the formation of the essentially inactive spore, and the death of the ‘mother’ cell producing it. It comes as no surprise, therefore, to discover that B. subtilis has evolved a means of delaying sporulation as long as possible.

In an alternative strategy,  a sub-population have a genetic pre-disposition to become cannibals.

Continue reading “Bug eat bug…”

Risk taking and audacity in science…

Research bloggingIn the October edition of Cell1, Amy Maxmen, a New York based science writer, discusses how tackling long-standing scientific problems (i.e. studies that have been prone to failure), or refuting dogma, are perceived to be a poor strategy for early-career researchers; and contends that perhaps they shouldn’t be.

One of the reasons for this is down to the policies of research grant committees.

A common complaint among researchers is that in order to be funded, they feel they must submit conservative grants filled with so much preliminary data that their predictions aren’t quite predictions any more. As Venter says, “The problem in [grant] study sections is the philosophy of proposals being reviewed as contracts instead of ideas.”

My own thoughts are that sometimes the amount of preliminary data required in a grant submission is so great that you’re half way to addressing the research goals at the first base, but only at the cost of the remnants of the last grant, which were used to finance the preliminary studies for the next. It’s as if the research councils are looking for a sure thing, a guarantee of success.

This is not how science should work.

Continue reading “Risk taking and audacity in science…”

A shortcut to mushrooms…

Research bloggingI REFER in this case not to one of the opening chapters of the Fellowship of the Rings, but in fact to the September edition of Trends in Microbiology, in which a Dutch research team lead by Luis Lugones describe some interesting work with mushrooms.

Building upon an earlier patent by Lugones, the paper by Elsa Berends1, proposes for the first time the use of mushroom-forming fungi (the basidiomycetes) to produce N-glycosylated therapeutic proteins, an important class of protein-based therapeutic drug that represent a multi-billion dollar market.

‘Glycoproteins’ (proteins that have been processed by attaching a small string of sugars) are often prescribed to plug gaps in the metabolism of patients who for various reasons were born with, or have developed, errors of metabolism; these include insulin for treatment of diabetes, erythropoietin for treatment of anaemia, blood-clotting factors for haemophilia and a further 93 products (as of 2007).

Continue reading “A shortcut to mushrooms…”

The cutting edge…

This post was chosen as an Editor's Selection for ResearchBlogging.orgI HAD barely started reading this week’s edition of Nature when in the Research Highlights1 section a study really piqued my interest.

Surgeons operating to remove malignant tumours often struggle to differentiate such tumours from surrounding healthy tissues. To ensure the complete removal of a tumour, surgeons also need to remove some of the surrounding healthy tissue, which of course isn’t desirable, especially in the brain.

A surgical electrode is a popular means to bisect (cut out) tissues. This makes use of a high-frequency electric current that is focussed into a highly localised ‘blade’ that effectively evaporates biological tissue as it comes into contact: water in the cells rapidly boils, proteins are precipitated and the membranes of the cells disintegrate forming a gaseous cloud of molecular ions of the major tissue components.

An innovative study MSpublished by team of researchers in Budapest, lead by Zoltán Takáts2, makes use of the fact that thermal evaporation of different tissues results in gaseous clouds with potentially different ion signatures. The team coupled a suction tube to a surgical electrode, and when cutting begins the tube draws the ions into an instrument called a mass spectrometer, something with which all CSI fans should be familiar. Using this process Takáts’ team found they could differentiate between healthy and malignant tissues, which provides a great basis for real-time tissue analysis under the knife, so to speak.

Continue reading “The cutting edge…”

Addicted to DNA…

Research bloggingBACTERIA can find themselves in the rather undesirable position of being addicted to parasites. The parasites in question are not of the blood-sucking sort however, but rather of the gene-sucking sort.

In nature there are numerous genetic entities, various forms of DNA, that parasitise bacteria:

  • bacteriophages (viruses that infect only bacteria),
  • plasmids (usually a circular strand of DNA that exists separately to the bacteria’s chromosome),
  • transposons (a unit that consists of a collection of genes that inserts itself into the host’s chromosome, but can cut itself free and reinsert itself elsewhere on the chromosome) and conjugative transposons (also capable of transferring themselves from cell to cell between bacteria),
  • genomic islands (again, a collection of genes that usually encode particular functions – disease-causing factors or antibiotic resistance – that have arrived from another organism and have become fixed in the chromosome).

We also have integrative conjugative elements (ICEs) that, like conjugative transposons, insert themselves into the host’s chromosome where they are replicated along with the host’s DNA, but then periodically (often under stress) cut themselves free and mail a copy off to another host cell.

Transfer of any of the above genetic entities can result in a bacterial cell acquiring new and desirable traits as such as the ability to consume new food sources, or resist antibiotics, or be more invasive. These traits have been picked up via the many occasions that these elements have jumped into and out of bacterial chromosomes, taking bits of those chromosomes with them.

The transfer of new traits by these genetic entities is referred to as Horizontal Gene Transfer (HGT), which is a term that is perhaps easier to understand if we consider that sexual reproduction, the process by which your parents produced you, is a form of vertical gene transfer; so too is the division of a single bacterial cell to produce a copy of itself and a ‘daughter’ cell. By comparison, horizontal gene transfer might be likened to you reaching out to touch your cousin and acquiring his or her ginger hair and freckles.

The thing that unites these genetic elements is that, being parasites, they need the host cell in order to produce more of themselves. Sometimes these elements don’t provide anything useful to the cell, sometimes they’re more of a burden, but some of these genetic parasites have evolved ways to ensure that the cell doesn’t toss them aside.

Continue reading “Addicted to DNA…”

Mimicry: survival or flattery?…

This post was chosen as an Editor's Selection for ResearchBlogging.orgIF you hadn’t guessed already, I’m busy trying to write a paper at the moment. This being the case, I have managed to successfully postpone this onerous task by spending time reading other people’s papers. I’m now going to spend a little more time explaining one of them you, my lovely readers.

Many years ago, when I was a grad student, I found myself at an otherwise rather dull conference on nucleic acid research; but fortunately it was not a complete wash-out, a chance conversation with a grad student who happened to be presenting a poster on the adjacent board to mine introduced me to the world of molecular mimicry.

Hoverfly (via David Packman, hampshirecam.co.uk)So what is mimicry and why is it important in the natural world? Mimicry is the imitation of one species by another, with the most well known purpose being to avoid being eaten. Most people will have encountered hoverflies, and may in the first instance have mistaken them for a wasp or a bee; from an evolutionary perspective, predators such as birds have also learnt to associate these warning (aposematic) colours with a stinging or poisonous prey, and so the Hoverfly gets to fly another day.

Continue reading “Mimicry: survival or flattery?…”