A Sea Of Boxes

That’s what my life has turned into. I am moving to Plymouth in just a few weeks time now to take up a new job there. My office at work is a sea of boxes of my books, lab equipment and suchlike and my front parlour at home is similar. Removal men will be packing everything for me the day of the move but there’s stuff I want to do myself.

Never offer to take up a job so quickly that you have 8 weeks to pack your shit and move 200 miles whilst finishing off a lot of laboratory work, a patent and writing two manuscripts whilst reviewing and editing a dozen or so more. It is NOT A GOOD IDEA.

So, given the chaos, I’ll not be blogging until after I’ve moved really. I can’t justify the time. Still ranting away on Twitter as per normal, mind.

"Go west! Life is peaceful there!"

Some readers will know this already but, now that I have the contract signed and the resignation letter written, I can finally announce that I am leaving the University of Warwick in early 2012 to take up as post as Lecturer in Ecology and Environmental Biology at Plymouth University. 

It is a time of great excitement and opportunity and the last month has been a complete whirlwind - I cannot wait to get started on my next adventure early next year! It will be very sad to leave behind some frankly amazing friends here in Coventry but quite simply, I would’ve been a complete idiot to say no!

This is where the magic happens. This is my lab bench. It’s been my bench since 2009. Before that, I worked in the lab next door. Before that, I worked in the lab I’m in now but on the bench to the right of this one (the other side of a freezer and a door). Before that, I was on the end of a tiny bench, making do with not much space, but only for a few months.

To the left of my bench is a Ph.D student and behind me is our technician. To my right is a freezer - a normal, domestic one - containing all my frozen samples for storage and the lab’s general supply of chemicals that need to be kept frozen, like enzymes. Next to that is the door to the teaching block and then the place we hang out coats.

Top Shelf (from left)

First we have two Windogradsky Columns, made in Feb 2006 using sediment from the Colne Estuary, Essex mixed with seawater from the L4 Sampling Station off the coast of Plymouth and spiked with powdered chalk, potassium sulfate, a piece of scrap A4 paper torn into shreds and some crab chitin. It’s been going for over 5 years now and is a beautiful example of Cyanobacteria, Purple sulfur Bacteria, Purple non-sulfur Bacteria and Green sulfur Bacteria. They get dragged out once a year for the Second Year Microbiology lab class to have a look at - they used to make their own but now time is against them so they do other things instead.

Next are lots of boxes containing filtration apparatus, generously given to us by a friend who was closing down her lab. They’re not in the boxes any more - they’re all in use!

Second Shelf (from left)

First there are two boxes containing 25-mL volumetric flasks. There are about 200 of them in total and they are used when assaying thiosulfate or polythionates by the cyanolytic method. You need lots and lots of these flasks for those assays and I have lots and lots of them, which is good!

Then there are trays of scintillation vials for liquid scintillation counting - some have fluid in them already, waiting for use, but most are empty. There is foil on the ones that are full because the fluid degrades in sunlight, turning brown, which makes it give weird results in the counter. The fluid is a mixture of organic solvents and a fluorescent purple dye. When radiation his the big solvent molecules, it excites their electrons, which are passed on to the dye, which, becomes excited for a tiny, tiny period of time before the excited electron drops to ground state, emitting the excess energy as a photon of light. This allows us to convert radiation to light - one beta particle or alpha particle should, theoretically convert to one photon and these can easily be measured with a light detector, allowing us to count how radioactive samples are.

Third Shelf (from left)

First there are filters for harvesting Bacteria from cultures then my solutions and equipment for scanning electron microscopy, which includes red sticks of sealing wax, which you can just about see. Next are trace elements, microscopy stains and bottles of sterile culture media and metal stock solutions. In real labs, we just write on the glass with a marker - we don’t print nice neat labels like they do on TV - there just isn’t time to make things pretty.

Fourth Shelf (from left)

Sodium thiosulfate in two big white jars - this is the main energy source I use to grow my bugs and I also use it as a starting material to synthesise polythionates - which are in the jars next to these. Amongst these jars are auric chloride - one of few gold compounds and it’s used to kill my bugs in controls. Normally folk use mercuric chloride but some of my bugs resist it and give strange results but gold kills all of them very effectively. The little plastic bottles with green lids are water for molecular biology (ultraclean!) and then there’s the business card of a Romanian collaborator then trace element solutions in dark glass with green lids, then more polythionates, protein stains and an indium standard solution. In a lot of work I have metal analyses done by an external contractor. To ensure the data are accurate, I add a known amount of indium (not found in huge amounts in nature) and then when I get the results back, if only 50% of the indium could be found, I know I need to double all the other results because 50% of everything else was lost in the sample preparation too. Above this are the switches for the air conditioning and a network socket to the right, which doesn’t work.

Front of the yellow shelf, from left.

Stopclock on a magnet holding up a bit of paper with a medium recipe on it; another stopclock; my Gilson pipettes; my Biochemical Society membership card; a newspaper clipping and accompanying note from a friend to tell me about a new brand of gin and then the plug for the freezer to my right! Hanging underneath are rolls of yellow insulation tape (for labelling), masking and autoclave tape (has a dye in it that turns black when heated to the same temperature/pressure that things need to be in the autoclave to render them sterile). These are hanging from gas taps and water-fed vacuum pumps.

On the bench, from left

Just visible are metal cans in which glass pipettes are sterilised by baking in the oven repeatedly. Next to these are rows and rows of Universal bottles with 10× stock solutions of different substrates to grow my bugs on. Then there are some conical flasks with cultures in them, topped with foam bungs covered in aluminium foil or with a red rubber vaccine stopper, which you can inject through. I use these when working with gases or toxins that I wouldn’t want to escape. In front of these are my blue notebooks and adjacent are boxes with very accurate glass syringes for small volumes like 0.01mL and suchlike. At the back are some Petri dishes containing bright yellow agar - probably had thiosulfate and a pH indicator and turned yellow after the bugs made acid. The bench has a glass plate on it to give a flat, wipe-clean surface. It’s a piece of window-glass, nowt special. Behind it are a beaker for waste like tips and filters and a beaker with pens, loops, spatulas etc and two bottles of agar that can be remelted and poured when needed. Big bottle is trace elements solution (such a chore to make, this one, I do 2L at a time, which makes about 200L of culture medium). In front of that is a tray of respirometry flasks, needles and bungs, ready to take to the radioisotope lab.

In Praise of Escherichia coli

Ok - this post includes frankly childish and graphic commentary on the effects of food poisoning - you have been warned! This is in response to two things - both extending from Twitter! One is that @flylilypad blogged the full version of something I’d laughed at that she’d done last week and so now it’s my turn I guess and also because @anglais_in_sete has similar problems at the moment and I thought a good laugh might cheer her up!

At Risk

Today being a Sunday, my alarms went off at 0855. First my iPhone alarm, then the radio alarm (BBC Coventry & Warwickshire), then SleepCycle alarm (on my iPhone too), all about 30s apart, for extra annoyance, which helps get me out of bed. Once I’m awake, I slowly propped myself up, checking for dislocations and subluxations that happen during my sleep. My right hand was a mess, as per, and needed cracking back into position. I seem to sleep on my front a lot at the moment, which crushes my right hand between my breastbone and the bed. I then took my first doses of pain relief for the day whilst listening to the 0900 radio news. I heard that Marco Simoncelli had been killed in a motorcycle Grand Prix accident. I’d never heard the name before as I don’t follow motorcycle sports - the only sport I pay attention to is the rugby and sometimes winter sports. After an hour or so of reading in bed I decided to read the BBC News website and saw a picture of a quite beautiful young man with kind eyes. It was him. I felt sad - the same way I feel sad when anyone young dies. Then I read about how it happened and the “that’s such a high-risk job” thought went through my mind. I once said this to a friend of mine who is now a Captain in the Army, back when he was a mere 2Lt. He was about to go on his first tour of duty in Afghanistan and I feared for him - though of course I never told him that - but I think he knew. He said to me “I know my career is dangerous - but look at yours!”. I’d quite honestly never looked at it before and I guess, yes, there are dangers. The poisons - arsenic, thallium, mercury, cadmium, FCCP, CCCP, DCCD, cyanide, diisopropylfluorophosphate - which is a close relative of sarin - all lovingly stored in neat alphabetical rows in a locked cupboard hidden away. The explosives - methane, propane, butane, picric acid - all in their sturdy metal cabinet. The radiation - carbon-14 and uranium-235/238, spewing alpha, beta and gamma radiation but shielded inside leaded perspex when not in active use. The physical dangers - dangling on a rope in a 30m pit, the bottom of which is lined with two iron girders; sitting in an underground chamber with deadly levels of carbon dioxide and hydrogen sulfide all around me; falling 2m onto solid rock whilst 40m underground in the wilds of Romania… The list goes on. I doubt any career or anything in life is truly without risk, but I feel that the risks in my profession are relatively well controlled compared to those in other professions (IEDs can’t be predicted; no matter how carefully you ride your motorcycle or car, it could always have problems). 

I guess nothing in life is without risk and we’re all just ephemera where the universe is concerned. With something so fragile, we should live for every moment.

Reality of Disability

[This is a follow-on from Kaliya Franklin’s superb Guardian article]

I’m sat sitting eating my lunch, which is the 30 mins of the day that I catch up on personal emails, blog, catch up on twitter/blogs and generally have some non-science-time - it’s very much a break and also the only part of the day in which my office door is closed and phone/work email ignored until my break is over. I just read Kaliya’s Guardian article on the reality of disability and I thought I’d share some of my views since this is such a hot topic at the moment.

Like Kaliya, I have Ehlers-Danlos Syndrome (EDS). This means that our collagen (the stretchy protein that is found in nearly all our cells) is a bit different to how it “should” be - in fact, in some ways, it’s a bit better, because it’s really, really stretchy. This means we can do interesting things like stretch our skin further than other people. Collagen is also found in our joints, so they’re extra stretchy too, but this unfortunately means that whilst we can lick our elbows and put our feet behind our heads without much effort, every step we take dislocates something to some degree and we spend our time shoving joints back into place.

Though Kaliya and I have the same condition, we’re a good example of why regulations/considerations for disabled people can’t be blanket-like. Kaliya requires a wheelchair; I don’t. Kaliya’s joints dislocate every few steps that she takes; mine don’t. Kaliya is so ill that she is unable to work; I am not. I use a walking stick to get around now and started using it this year. Since I have begun to do so, things have become much easier for me. Nearly 10 years ago, when I was a student, I started to get a lot of lower back/left hip pain and the doctor at the time told me it was muscular and gave me dihydrocodeine and diclofenac and told me to keep it warm and it’d be ok in a few weeks. It didn’t improve and so I saw a rheumatologist (a medic who deals in joints and immune system disorders like arthritis and lupus) and after many scans and x-rays, they couldn’t find much wrong with the joint that was causing the pain, other than it being inflamed, though not by very much. EDS was mentioned and then forgotten and I continued to put up with the pain for several more years.

After a year of severe joint and muscular pain in my face, neck, spine and pelvis and neurological problems in my arms - all of which started after a viral infection - I eventually saw a rheumatologist again (after seeing maxilo-facial surgeons, neurologists, neurophysiologists and dermatologists) and he finally diagnosed me with having had EDS since birth. He gave me pamphlets on it and the pain disorders that I have due to EDS and sent me on my way for some more scans to try and understand which areas are causing the most problems. I’m seeing him again next week to get some answers and suggestions for what I can do to help myself. 

I’ve seen Pain Management specialists too. They don’t tell you how to cope with pain or tell you to strap a pair on - they inject you full of Botox to deaden the nerves and give you prescriptions for drugs far stronger than morphine to try and give you your life back. Or at least…they used to. My primary care trust no longer funds Botox injections or about 10 other procedures for pain - apparently pain is “just pain” and we should learn to live with it. A vial of Botox costs £170 and I need it 4 times per year - apparently I’m not worth that and so instead I’m doped up with Tapentadol and Pregabalin all of the time - which probably costs about the same. Idiotic policies, as always, dreamt up by the bean counters and pen pushers who’ve never actually spoken to a patient at any stage. There is, of course, some manner of appeal process to essentially beg for funding but it takes months - they don’t seem to grasp that patients need answers fast. Pain isn’t “just pain” - people kill themselves because of it. I’ve come close myself.

Since I’ve started to walk with a stick, I no longer limp on my left leg (putting weight on that leg causes a lot of pain), which means my pelvis isn’t diagonal and my spine is no longer twisted - so I get far less spinal pain too. I’ve had a few problems of accessibility by on the whole it’s not been too bad. No one ever offers me their seat on the bus though and I had a stand-off with a pregnant woman who seemed to think she needed to sit down more than I did without even knowing why I had a stick or how far I was travelling. I sat elsewhere in the end but not before pointing out that those nice seats at the front of the bus are for “elderly and disabled” people - last time I checked, pregnancy wasn’t a disability. By all means sit there, but if a disabled or elderly person asks you to move, it’s because we genuinely need to sit down. I can stand on the bus and often do, but when I ask for a seat, it’s because I really, really need it.

This week I went Somewhere New and it was into a building that I was told had a lift, as I was going to have to go to the top floor, so I checked in advance and told them why I was asking. When I got there, it turned out the lift was broken (and had been for a while) and they were trying to fix it but it was too late for me. Thankfully, one of the staff there was very kind and held my briefcase for me so that I had a free hand to get up the narrow, steep stairs. It wasn’t too bad but the building was very old and the stairs were very steep, narrow and had wooden banisters that you couldn’t really lean on without breaking them. Normally, I can cope with stairs but that morning I was in a lot of pain and those stairs had a rise far higher than I’m used to, so it hurt. The lady who helped me was very kind and I thanked her for going out of her way to help me, but, I was disappointed that no one had bothered to tell me that the lift wasn’t working or that no one had checked, given that I had asked. There was also no attempt to try anything like moving the venue to the ground floor, it was just assumed I would be okay, even though I’d specifically made a point of phoning to ask about the lift. I don’t expect special treatment - I expect the same as everyone else - i.e. to be able to access the venue. I managed (though it was painful) but I can imagine many people would not’ve coped.

Once I got to where I was going, I had to apologise as Pregabalin makes me forget words and I stop mid-sentence like I’m about to fall asleep and have to describe the thing I’ve forgotten. I didn’t remember to mention this beforehand so I had to apologise when it happened the first time which gets me funny looks.

I got to and from on the train. Two trains, in fact, as I had to change. Kaliya had train issues in her blog post, but I cope just fine on the train and walking about. Not so good in crowds, but otherwise ok.

Both of us have the same diagnosis and both of us are of similar ages. One of us can’t walk or work; one of us can. One of us uses a stick; one of us uses a wheelchair. One of us takes lots of pain relief all the time; one of us takes it when needed. 

We’re very different though we both have effectively the same diagnosis and prognosis. How can disability benefits be issued “fairly” when people with the same diagnosis can be so different? One could assess Kaliya and say “well, if Rich can go to work, so can you” but at the same time, why not say “Rich, give up your job, you need to stay at home”. Which is right? The truth is, neither. We have very, very different needs and that is what needs to be assessed. There’s no sense asking what we can’t do - it’s what we can do that matters. If I can walk to the bus stop and go to work, I don’t need mobility allowance - what would it buy me? A new stick?! I don’t need care allowance as I can care for myself - but some money for physio would be nice as the NHS doesn’t seem to want to pay for it in the form that I need.

Autotrophic Mycobacterium spp. - whatever next?!

One of the many genera within the Bacteria that I have worked on is Mycobacterium. When I tell people this, they often say “Oh, you work on TB?” and the answer is no. I’ve never worked on the tubercle bacillus, as TB stands, though I did apply to do a Ph.D on TB at the National Institute of Medical Research - I even went and had my TB vaccination done because I’d never been vaccinated (growing up in the Styx, it wasn’t necessary so we never had it done). The Mycobacterium strain that I worked on was called (by my own invention) DSQ3 and I’ll say a bit more about it in a minute. I read an article this past week in Frontiers in Microbial Physiology and Metabolism, our newest microbial physiology journal concerning autotrophic growth of two Mycobacterium spp. at the expense of elemental sulfur. This is very exciting as although autotrophy at the expense of hydrogen has been found in Mycobacterium spp. before (Lukins & Foster, 1963), the prospect of them using sulfur opens up a whole new set of doors…but I’m not really that surprised. You see - Mycobacterium is one of those genera (like Bacillus) that is just full of surprises and metabolic diversity (usually by way of pinching genes from other bugs) - it never ceases to amaze me. I myself discovered methylated amine use as a sole carbon and nitrogen source in Mycobacterium sp. DSQ3 (Boden et al. 2008) so I’ve seen first hand just how adaptable these bugs can be.

The genus Mycobacterium has been known about for over 100 years now, but diseases caused by some of its members have been around for far longer than that. Leprosy and tuberculosis are caused by M. leprae and M. tuberculosis (in man anyway, M. bovis in cattle) respectively and are probably two diseases that are immediately associated with particular periods of world history or particular parts of the globe. M. tuberculosis is the type species of the genus though M. leprae is an excellent example of an important organism that we can easily identify in its environment (living organisms!) but can’t actually grow in the lab (outside of a laboratory animal). The names of these species are rather boringly just Latinisations of “of [disease name]” but Mycobacterium itself tells you a lot about the genus. It very literally means “fungal rodlet” and that’s pretty much what the little swines look like - small rods and there’s something distinctly fungal about them. When they’re growing on solid media in the lab their colonies look very much more fungal than bacterial and the produce floating mats on complex broths which look a lot like fungi.

Now, the main thing about the Mycobacterium genus is that it’s stupidly large as genera go. There are at present 154 species of Mycobacterium, which is frankly idiotic and there are numerous non-Code divisions within the genus such as “fast”/”slow” and different “complexes” relating to different disease causing groups. What it really needs is a good spring-clean and a good sort out but, even as a taxonomist, I ain’t touching it. It’s way too far gone to get any real sense out of without moving some clinically important strains into different genera, which won’t help with diagnostics and, although it’ll make things systematically “right”, it could complicate things more in other ways. The species that I worked with was M. fluoranthenivorans, the type strain of which degrades fluoranthene (a polyaromatic hydrocarbon from coal tar), though my strain was never tested on it - mine grows pretty well on dimethylamine hydrochloride though (Hormisch et al., 2004; Boden et al., 2008) and came from the sediments of the River Thames.

The strains that have just been shown to grow on elemental sulfur are from the species M. cosmeticum and M. pallens and were isolated from sandstone at the Angkor Wat in Cambodia (Kasumi et al., 2011). The former was originally isolated from a sink in a nail salon in Atlanta and also from an infection under the skin of a Venezuelan woman who had undergone a minor invasive cosmetic procedure (Cooksey et al., 2004) - the name “cosmeticum” refers to cosmetics in general. The latter species came from soil in Hawaii and takes the name “pallens” from its pale yellow colour (Hennessee et al., 2009). In the original studies on these species, there is nothing to really make it obvious that the whole species could grow on sulfur - in fact, it could very well be just the strains from Angkor that can do it - but I can’t help wondering - how widespread is autotrophy in the genus Mycobacterium? What about these ones we can’t grow? What about M. leprae? I’d be willing to bet money on the fact that no one has tried these “obligate” pathogens on substrates such as sulfur or ammonium for autotrophic growth or even on things like methanol and things other than complex medical-microbiology broths. 

The human body is an environment like any other and yet medically-related organisms are usually treated and handled differently to how an “environmental” microbiologist would work. I think there’s probably a lot to gain by doing a bit of swapping of strains and trying some of these organisms that have “no sink in the environment” and are “obligate” pathogens or have to have a host on some of the less mainstream substrate combinations to see if they will grow at all. I’d be willing to bet that out of 154 species of Mycobacterium, more than two exhibit some degree of lithotrophy.

——

Boden et al., 2008. Environ. Microbiol. 10, 3225-3236.

Cooksey et al., 2004. Int. J. Syst. Evol. Microbiol. 54: 2385-2391.

Hennessee et al., 2009. Int. J. Syst. Evol. Microbiol. 59: 378-387.

Hormisch et al., 2006. Syst. Appl. Microbiol. 27, 653-660.

Kasumi et al., 2011. Frontiers Microbiol. Physiol. 2, 104. 

Lukins & Foster, 1963. Z. Allg. Mikrobiol. 3, 251–264.

Mrs Hunger-Weeping

I’ve blogged previously that, as a child, I lived for reading and spent pretty much every Saturday morning in the local lending library. At some point when I was in Junior School, I came home one day to find that my Mother had been into the town food shopping and to pay the Council Tax (no Direct Debits where my mother was concerned, she manually paid (or avoided paying) everything) and, whilst there, had noticed that the Library was having a sale of old books for Not Much Cash and had brought home a big bag of books for me.

Two of my most treasured books for many years that, unfortunately, I sold as a student when skint (and now deeply regret) were a pair of “Jepsons”, properly known as Biological Drawings With Notes, Volumes 1 and 2, by Maud Jepson M.Sc (Manchester). I can’t find out a lot about Maud on the internet, which is a shame, but I do know that the first volume was published in 1938 and that the two that I had were both first editions. They are a set of beautiful pen and ink drawings, annotated in probably the most beautiful hand I’ve ever seen (during 6th form, I sat down and learnt how to write like Jepson - unfortunately, it doesn’t work well when one has to write quickly and I soon forgot how to do it!). I remember particularly the painstakingly detailed images, page upon page, of rabbit dissection, layer by layer. I learnt an awful lot from these two books over the years and, even though most of the dissections had been removed from school teaching in the years between Jepson and I, I learnt most of it from her amazing drawings. These books really captured the romance of science and of discovery and detail - they were certainly something to do with my drive to become a scientist.

Another book in the pile that day was one that vanished from my possession at some point - probably when I left home and all the books I hadn’t taken with me went to the charity shop. It took me many years to trace it on the internet and eventually I managed to buy a second hand copy a few years ago. The book was The Maharajah Adventure by Irmelin Sandman-Lilius, a Swedish-speaking Finn. I didn’t know it was a “foreign” book at the time and it was originally published as Maharadjan av Scha-scha-scha slé (“The Maharajah from Scha-scha-scha slé”) in Swedish in 1964 (and in Finnish as Sasassaleen Viltias (“The Ruler of Sasassale”) and the version I had was Ian Rodger’s English translation from 1966. As with the more famous books of the more famous Swedish-speaking Finn, Tove Jansson, it was a fantasy set in the woods and mountains of Finland - all dark forbidding trees and friendly creatures. It was a children’s book, probably aimed at little girls given that the main character is a little girl who has a talking doll. Said girl was based on her own daughter, so I’m told by the various webpages about the author. She is obviously pretty famous in Finland but, of course, why would anyone know of her books in England? The basic plot of the book involves said girl and said doll meeting a Maharajah who has exiled himself from his homeland of Scha-Scha-Scha-Slé and taken up residence in the woods of the North of Finland. Somewhere along the line a chase ensues with the protagonists running away from what has to be one of the best named character in fiction: the blunderbuss-wielding Mrs Hunger-Weeping - a terrifying enormous woman who chases the protagonists through the blizzards and snow drifts of the Finnish north.

I’ve re-read it as an adult and unfortunately, it’s not nearly as good as it was 20-odd years ago. Somehow Enid Blyton, Tolkien et al. all manage to hold up, but this one doesn’t. It’s still a nice story and I remember it really touched me as a child - Mrs Hunger-Weeping haunted my dreams for a while.

Free Graze Box

Link: Free Graze Box

As per just about everyone on the planet, I’ve got a free Graze code. I’ve been using them for just over a week - the food is delicious and more than enough for lunch/snacks during the day - the only gripe I have is that the delivery is unreliable because Royal Mail are involved and they just aren’t efficient enough to deliver things within 24-48h at times.

Click here to claim a free Graze box worth £3.49 and then £1.00 off another one if you order two. They arrive through your letterbox and provide you with 4 different things to nibble on that day - they’re advertised as snacks but in reality there’s enough for lunch. It’s not all bunnyfood either!

The Blackleg Miner - Part 2

In yesterday’s post about biomining, I mentioned I was involved in a second type of mining and that’s the subject of today’s post: genome mining.

Last week I submitted a manuscript that I had written to a journal for consideration for publication concerning the genome sequence of a strain of Methylomonas methanica. The manuscript has 27 authors based at 8 institutions in 5 different countries and is the biggest project in terms of number of authors that I have been involved in and, of those 27 authors, I’m at the front, because I pulled most of it together in the end, though I started out about 5th and gradually moved forwards, particularly as I ended up writing the manuscript itself - that wasn’t planned originally but that’s how it ended up. This is the second genome sequence that I have worked on - the first being that of Methylophaga thiooxydans, which I published earlier this year with a much smaller team. 

Both of these organisms are Bacteria found in the marine environment and, since they both have “Methylo-” generic names, they evidently have a lot in common. Members of the genus Methylomonas are methanotrophic, which means that they can grow on methane as a source of carbon. There is an apparent peculiarity amongst a lot of Bacteria that can grow on methane in that they seem to depend upon it - they’ve lost the ability to grow on pretty much anything else. Personally, I don’t think this makes evolutionary sense and I’m sure they can use other things though refuse to do so in the lab. Members of the genus Methylophaga are still fussy eaters but far less so - they can’t grow on methane but they can grow on methanol, methylated amines, dimethylsulfide and a lot of other “one-carbon” or “C1” compounds, in addition to fructose and a few other multicarbon compounds - they are methylotrophic. These C1 compounds are prevalent in seawater (yes, even methane) and it makes sense, therefore, that there is something out there eating them. After decades of C1 research around the world, we now know which enzymes and genes are responsible for the metabolism of a lot of these compounds but we’re still struggling with some of the details - which is why the genome sequences are so useful.

The Blackleg Miner - Part 1

Ok - this has nothing to do with the NACODS during the NUM strike or 19th century folk songs - no, this is about a different kind of mining.

Father and son, we’re both miners. My Father mined coal until the mid-1980s but me? I’m a different kind of miner - in fact, I’m TWO different kinds of miner, thinking about it. Firstly, I’m a biominer - I worked for a while mining copper using Bacteria. You might think that a bit far-fetched but, would you believe that gold, copper and uranium are often mined in this way? Amazing though it may seem, over 25% of all the copper mined in the world is mined by Bacteria (well, Archaea too but but let’s keep it simple!). It’s not even a new process either - the Romans discovered it around 2,000 years ago!