The Complex Mixture of Bugs Behind Cider Making

Cider is an alcoholic beverage made from apples and, depending on country or region of origin, ranges from a clear, amber colour, to turbid brown-green. It is usually highly carbonated. The powerhouses of cider production in Europe are Ireland and Britain, France, Slovenia and Spain. While many might regard cider as the poor man of the fermentation world, lacking the subtleties associated with beer formulation such as choice of malts to include, which, when and how much hops to use, the microbiology of the traditional cider fermentation rivals only that of wine in its complexity. Indeed, many of the yeasts involved in the conversion of apple must (a fancy word for juice) into cider are also present in the context of winemaking, the source for these yeasts being the skins of apple and grape respectively.

Some of the yeasts in question are Brettanomyces anomalus, B. bruxellensis, Dekkera polymorphus, Hanseniaspora uvarum, Metschnikowia pulcherrima; Hansenula anomola, H. fermentas, H. guilliermondii, Saccharomycodes ludwigii and Saccharomyces cerevisiae (the yeast behind beer and wine’s primary fermentation). As with many of the fermentations where non-Saccharomyces yeast form an important component of the microflora, the fermentation of a traditionally brewed cider is sequential, with one trophic group of organisms kicking things off, altering the must chemically so that their own survival becomes compromised. Another layer then takes over the fermentation, using the metabolites produced by the first group as energy and nutrient sources, until they themselves are replaced.

In a study of the role of indigenous yeasts in traditional Irish cider, Morrissey et al. (2004) divided the fermentation in three broad phases. During the first phase, the fruit yeast phase, species that were shown to arise from the apples’ surface dominated the fermentation. Among these was H. uvarum, which accounted for 80% of the yeast cells during the fermentation’s short lag phase and which reached counts of six million per millilitre. As fermentation proceeded and other species took over, H. uvarum was no longer detectable after twelve days. S. cerevisiae became the dominant yeast during the second fermentation phase. This phase witnessed a rise in levels of ethanol, and numbers of S. cerevisiae reaching eight million cells per millilitre. Among the possible reasons attributed to the overgrowth of S. cerevisiae at the expense of other organisms were: S. cerevisiae‘s excretion of ethanol; oxygen depletion in the must; increasing levels of must carbon dioxide; S. cerevisiae‘s faster growth rate and outcompeting of other yeasts for nutrients and sugars; and the flocculation (clumping together) of non-Saccharomyces species. During the third maturation phase, Dekkera/Brettanomyces species came to replace others, accounting for 90% of the yeast by day twenty-two of the fermentation. These species were shown to enter the must from installations in the press house (termed “resident yeast” by the authors), and to a lesser extent the surfaces of the apples, and contribute greatly to the organoleptic quality (taste and flavour) of the finished product. This is why there are commonalities in the flavour profiles of traditional ciders and Belgian lambic beer, where Brettanomyces also play an important role. Dekkera/Brettanomyces species are also encountered at this stage in French cider.

This traditional form of cider making incorporates neither temperature control nor deliberate inoculation. The organisms entering the must all come from the apples and what could be considered to be the “conditioned” environment of the cider house. Temperatures vary widely during the fermentation, determining as well as being determined by the particular yeasts dominating the fermentation at any point of time. Because of the loose control the traditional cider brewer exerts over the process, quality control is compromised, with large batch-batch variation. Additionally, seasonal variations in the microflora present on apples (as well as seasonal variations in ambient temperature) lend an extra layer of chance to the process. So, just as in the case of winemaking, we could talk about a good vintage of a particular brand of traditionally made cider.

 

Morrissey W.F., Davenport B., Querol A., Dobson A.D.W. (2004) ‘The role of indigenous yeasts in traditional Irish cider fermentations’, Journal of Applied Microbiology, 97,647–655.

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Lectins

ConArainbowsquareWe often think that it is only us animals that have sophisticated defence mechanisms against the microbes that would like to make a meal of us. While the mammalian immune system is highly complex and functions as a co-ordinated network of different cell types and the molecules they produce, shows the ability to learn and boasts a memory function, the defences plants possess are no less complex and effective. Plants do not have a circulatory system as we mammals have — they have no blood or lymph to move soldier cells to zones under attack — but they do possess an array of molecules which could only be described as agents of chemical warfare to protect them from viruses, bacteria, moulds and insects.

One category of molecule the plant uses to defend itself are lectins. Plant seeds, especially legumes, are packed with these. Your lectin is like a cross between a molecular limpet and super glue. Lectins recognise the sugar molecules out of which the capsids of viruses, the walls of bacteria and the exoskeletons of insects are made of and stick to them like barnacles. Many thousands of lectins working together form a glue around invading bugs, immobilising them and preventing their movement and growth. Some lectins will also enter the cells to which they have attached and work their toxic magic on them. Each lectin will recognise a specific sugar group: wheat germ agglutinin sticks to N-acetyl-D-glucosamine and sialic acid; concanavalin A binds to α-D-mannosyl and α-D-glucosyl residues; peanut agglutinin has a liking for Galβ1-3GalNAcα1-Ser/Thr.

As has been the case with other immunity molecules such as antibodies, biotechnologists have harnessed the specificity of lectins for their experimental systems. There is an array of bioassays based on the ability of lectins to bind to a specific pattern of carbohydrate (known as a ligand). In a complex system a researcher might wish to light up specific cells or molecules with a fluorescent lectin and so gain an insight into structure or function. I myself have used concanavalin A tagged with a fluorescent marker to bind with reasonable specificity to enteric bacteria, and so light them up for cytometry and microscopy. Many blood group antigens are recognised by lectins, which form the basis of assays for typing. It is very common for lectins to be used as tools for the of imaging proteins for microscopy. Just check out Thermo Fisher’s lectin catalogue if you want an idea of the extent to which lectins are used by research scientists.

Of course, human beings being what there are, some lectins have been put to nefarious uses. We are all familiar with ricin — a lectin from the seed of the castor oil plant and highly toxic. Less than 2 milligrams can see off the average person. Many governments over the years have developed weapons systems for delivering ricin to the battlefield or unsuspecting civilian populations. During the Cold War, both blocks had stores of weaponised ricin. Thankfully, it has never been used in a wartime setting. Given that it is relatively easy to produce (compared to say botulism or synthetic nerve toxins) and that castor beans are easy to acquire or grow (in fact, the castor oil plant is a common ornamental species), ricin is something of the agent of choice for terrorist organisations, death cults and disturbed would-be mass murderers.

Colony Forming Units

img_0685.jpgMicrobiologists are always interested in knowing how many bacteria are present in a sample. You could say they’re obsessed with establishing how many invisible little bugs are growing in whatever system they happen to be studying. My job is to know how many nasties are in milk, its derivatives — whey powder, cheese, skim milk, et cetera — and the equipment used to process it. Numbers of bacteria per millilitre or gram or square centimetre is not a particularly easy thing to establish, and sometimes how to do so, gives me sleepless nights. But that’s for another blog.

When microbiologists speak about levels of bacteria in food or water or soil we do not refer to X number of bacteria per gram: we use colony forming units (CFUs). The CFU has been used since the very start of analytical microbiology, and when you learn of how the vast majority of quantitative assays are carried out by microbiologists as well as the nature of microbial growth you will understand just how rational it is to use CFUs. From the late nineteenth century, when agar-based solid media began to be used for growing bugs, and with the Petri dish becoming established as the format of choice for holding the media, microbiologists have observed that bacteria tend to form colonies on such nutritive solid surfaces.

A colony is simply the visible glob made up of billions of bacteria and which arises from the rapid, ceaseless exponential growth of a single founding cell (or cluster of cells — more anon). If you put any* live microbial cell on a solid growth medium which contains the correct balance of salts, proteins, energy sources and vitamins and incubate at the bug’s optimal temperature and with the right mix of gases (some bugs don’t like oxygen — the strict anaerobes) you will have a visible colony in a day or two. Now, some bugs are incredibly fussy, and it has taken the best part of a century to work out what media suit their growth (species of Mycobacterium are notoriously hard to grow), but for the majority of the bugs of interest to your average food microbiologist there are media which will have your lads forming colonies in double quick time.

The discovery of colonial growth was a huge step forward for microbiology. Prior to this, the only way to count bugs was by eye. “But they’re microscopic!” I hear you say. Indeed and they are! Prior to the days of the Petri dish, you put your sample on a special gridded slide, stained the bugs as best you could, hunkered down over your microscope and got counting until your eyeball dried up! Not pleasant work. And not very accurate. We humans are subjective and tend to make mistakes. Was that a rod or a coccus or just a salt crystal? It is far, far easier to take a sample, say a swab from the surface of a meat counter, get the bacteria into suspension in water or a solution such as Ringer’s which has salts that will help keep the bugs alive, and put that suspension to grow on a dish. You come back the next day and count the colonies and you know how many bugs were in the sample. Simple, isn’t it?

Yes, but it comes with a proviso. While bacteria are single-celled organisms, not all bacteria exist as single cells. Some bugs grow in chains, others in clusters (Staphylococcus aureus is characterised by “bunch of grape” clusters under microscopic examination), and others exist as pairs or triplets. And then there are biofilms: huge, sometimes macroscopic amalgamations of bacteria trapped in their extracellular secretions. So, when you get your sample of suspended bacteria and plate it out on a Petri dish you are generally not dealing of a uniform suspension of single cells. And when these lads land on the surface of the agar and begin to grow it can be anything from one cell to dozens that give rise to your colony. Hence, to be strictly correct, each colony that has grown up is not evidence of the outgrowth of a single cell — it is evidence of the outgrowth of a colony forming unit. And the number that your microbiologist comes up with is an estimate, because they can never know how many bugs make up a colony forming unit.

 

*Not really any. Molecular studies have shown that perhaps less than 1% of microbial species have been ever grown on artificial media. It is really only the bacteria that are capable of growth on artificial media that us microbiologists know much about. But luckily, it is the ones of interest to us medically, environmentally and biotechnologically that have tended to be amenable to our trying to grow them. The rest of the microbial world are something resembling dark matter: we know they are there, but not very much else.

Some Irish Microbes

Hibernicus

The beautiful silica shell of the diatom Campylodiscus hibernicus

For the day that’s in it I’m going to dedicate this blog to talking about bacteria and other microbes named in honour of Ireland. I’ve spoken about naming and organising bacteria before, and those who have been attentive will have realised that this is no trivial matter. The anoraks in charge of bacterial taxonomy won’t just let you name your newly discovered bacteria after your girlfriend or your dog; you won’t see Citrobacter sharonii or Staphylococcus fidonis for example! However, there is a long tradition of naming bugs after the city or country in which they were first isolated or characterised, although stuffy microbial taxonomy being stuffy microbial taxonomy, there are strict rules governing the use of the latinised place names. The International Code of Nomenclature of Bacteria has an official list of country and region names (europaeus, africanus, asiaticus, ibericus, italicus, romanus, germanicus, britannicus, hibernicus [Ireland], indicus [India], arabicus [Arabia], gallicus [France], polonicus, hungaricus, graecus [Greece], hellenicus [Hellas, classical Greece], hispanicus [Spain], rhenanus [Rhineland], frisius [Friesland], saxonicus [Saxony], bavaricus [Bavaria], bretonicus [Brittany], balticus [Baltic Sea), mediterraneus [Mediterranean Sea], et cetera) and cities (Lucentum [Alicante], Argentoratum [Strasbourg], Lutetium [Paris], Traiectum [Utrech], Ratisbona [Regensburg], Eboracum [York], Londinium [London], Hafnia [Copenhagen]) and a convention for turning less well-known or New World cities into Latin.

 

I’ll get the baddies out of the way first. The most well-known bug named in honour of the Emerald Isle is a cousin of a bacterium familiar to you all — salmonella. The confusingly named Salmonella enterica subsp. enterica serovar Dublin is a nasty enteric (intestine-colonising) wee lad who is primarily associated with salmonellosis in cattle. As if causing fever, diarrhoea and all the rest of it in poor old Daisy the cow is not enough, Salmonella Dublin (to call him by his short name) is also zoonotic; it can cross over to humans. There have been some large foodborne outbreaks of non-typhoidal salmonellosis caused by Salmonella Dublin, with 700 cases in Glasgow in 1979 associated with the drinking of contaminated milk.

Another bug bearing the Dublin moniker is Candida dubliniensis (the iensis bit of dubliniensis means “of Dublin”). This colleen is a yeast, and like many other species of Candida, but not all (there are some Candida species that are responsible for adding to the fine flavours in lambic beer, for example), it is an opportunistic pathogen of humans. Among other things, it can cause oral candidosis in immuno-compromised patients. This bug was isolated and characterised by David Coleman and his group from Trinity College Dublin in 1995 and you can read all about their ingenious hard work and get a flavour for the hoops researchers must jump through to classify and characterise a newly discovered bug here.

A researcher called Niall Mullane is credited with characterising a fellow called Cronobacter dublinensis (note the ensis rather than iensis, following Dublin: there’s some rules being broken somewhere!). This bacterium was isolated from a milk powder production facility — worryingly, given that Cronobacter species have been linked with incidences of neonatal bacteraemia, meningitis and necrotising enterocolitis. The legal limits for Cronobacter in infant formula are very strict: if one bug per 10 g of formula is found, your manufacturing facility might be shut down.

Although the name, Mycobacterium hiberniae, might scare the bejaysus out of you given the fierceness of its cousins, Mycobacterium tuberculosis and Mycobacterium leprae, it is in terms of human health an innocuous spalpeen. It is a Class I microbe, considered safe enough to work on without the need for special precautions such as a biosafety hood. The same could be said for Aerobacter hibernicus, which is so obscure (and presumably harmless) that it has been renamed (either Klebsiella hibernicus or Enterobacter hibernicus), and this author has not been able to confirm its new handle. Believe me, if the former Aerobacter hibernicus was up to scratch in terms of either being of harm or benefit to humanity, I’d google the boyo as fast as the widow O’Neill would have her butter churned. (You may have noticed that I’m tossing uncalled-for and random Far and Away-type Irishisms into this blog — for the craic, no less, to be sure, to be sure!)

Cyanobacteria are neither baddies nor obscure. It is a group of bacteria that are capable of photosynthesis. In the oceans, as part of the microplankton, they float around and convert sunlight into energy, producing oxygen in the process, while on the land they hang around in niches in the soil, oxygenating roots and gobbling up pesticides and the like. So, as well as the lungs of the planet, they can be considered to be the livers. I came across a study concerning cyanobacteria in — wait for it — paddy fields of all things, where a lassie called Hapalosiphon hibernicus was doing her bit for mother earth. Unfortunately, for the authors, she did not produce the antimicrobials they were screening for.

And finally, I will wrap up by giving mention to a couple of oddballs (for what are we Irish if not odd?!): the diatom Campylodiscus hibernicus and the basidiomycete Oligoporus hibernicus. Diatoms are protists, unicellular algae covered by a shell made up of silica, and form part of the ocean’s phytoplankton. These are definitely goodies: they make up the productive base of the oceanic food chain. Under the microscope their shells are revealed to be among the most architecturally beautiful objects produced by nature. Basidiomycete is a fancy name for a fungus which produces an above-ground structure which may resemble a mushroom. Oligoporus hibernicus, however, does not produce anything as impressive or functional as the toad stool upon which a leprechaun might sit. Its fruiting body is described as “crust-like”. You see these fellows growing on rotting trunks or branches. Not very Darby O’Gill!

A happy St Patrick’s Day to all my readers.

Histamine in Food

HistamineMany people are aware of the relatively common food poisoning phenomenon whereby a meal (usually fish is involved) is eaten and within minutes the unfortunate victim is experiencing symptoms which indicate that toxic amounts of histamine have been ingested: headache, vomiting, increased blood pressure and even allergic reactions of strong intensity. There may be a tell-tale reddening of the face, neck and chest and an unpleasant nausea and confusion. Histamine, and a trio of other related compounds — the biogenic amines, tyramine, putrescine and cadaverine — have vasoactive (meaning they affect the control of the flow of blood) and psychoactive properties.

How do these nasties make their way into our food?

The answer is: through a wide array of bacteria whose levels have been allowed to increase to dangerous levels by poor food hygiene and storage.

There is a world of foodborne bacteria out there who are capable of synthesising histamine and other biogenic amines. Some of these, such as Enterococcus species, are normally not considered food poisoning organisms, but if allowed to grow in food to unusually high levels they are capable of generating biogenic amines. In the case of dairy products, it can even be the starter microflora that can produce the toxins. (Let me stress that this starter-culture-gone-bad scenario is extremely rare.)

Bacteria do not produce histamine and the other biogenic amines out of any inherent badness or psychopathy! They’re just trying to get by, to metabolise, grow and reproduce. The wee bugs take common amino acids found in all high-protein foods cut a bit off the molecule in a process called decarboxylation, gain a bit of energy in the process and spit out a biogenic amine. The amino acid, histamine is converted to histidine, tyrosine to tyramine, et cetera. It is curious that it is a bacterial metabolite — an excretion product, if your like — that does us unsuspecting plaice-eaters the damage!

So common is biogenic amine food poisoning caused by eating fish, that this has been given its own name: scombroid poisoning. An important fact to take into account is that biogenic amines are heat stable. They survive the cooking and in some cases the canning processes. Therefore, cooking inappropriately stored fish, while masking off flavours somewhat, will not inactivate any toxins that might be present. There have even been reported cases of canned tuna (which will have been pressure-cooked to within an inch of its life as part of the canning procedure) causing scombroid poisoning.

The standard treatment for breathing difficulties brought on by biogenic amines is the administration of intramuscular epinephrine, while intravenous antihistamine may be given if needed.

 

What is a Type Strain?

At the root of almost any microbiological study is a type strain. Lay people always ask what this is. In brief, a type strain is a particular strain (or breed) of a microbe that presents all of the characteristics that define a species. A perfect specimen, if you like. Using a type strain allows the microbiologist to perform studies on a particular species that will have relevance to all of the (sometimes thousands) of strains that make up that species. In my work on Bacillus cereus, an age ago, I used a couple of type strains in order to show that the staining techniques I developed would apply to the majority of B. cereus isolates that might be found in rice or milk or lasagna. It would have been folly to isolate my own bugs from a slice of ham from the local deli and then try and extrapolate that particular bug’s heat resistance, for example, to B. cereus stains that find their way into food all around the world.

Let’s extend the type strain concept to human beings. A perfect specimen person should display all the characteristics that define the what being Homo sapiens means: (s)he should walk upright, have 32 teeth, neither be a dwarf nor a giant, not be a diabetic, have a blood pressure within the normal range et cetera, et cetera. The perfect specimen should also be clonable and be amenable to cryopreservation so that they can be bulked up and sent around the world to participate in studies! And be genderless — just like bacteria. In other words, human type strains do not exist, and thus the execution of clinical trials and the like involving real people are peppered with layers of complexity and issues of extrapolation to the general population that us microbiologists don’t have to deal with.

Just as is the case with the classification of bacteria, the designation of a particular strain as the type strain is controversial. You come across grand debates in the scientific journals arguing why one wee fellow should be defrocked of his status as type strain, and another cheeky lad handed the crown. The type strain in question may not display the salt tolerance typical of the entire species, or may have a biochemical pathway untypical of the rest of his brethren. He may munch pentose sugars and spit out acetone, whereas the rest of the strains making up the species might turn their noses up at five-carbon sugars, and find nail polish remover inimical. That’s why when I do my studies, I like to have a couple of type strains. Just in case one of the wee fellows is about to lose his title. I also like to have some local isolates — fellows I’ve hunted down myself, grown up in the lab and done the necessary tests on to prove that they show the defining traits of the species. Using isolates from the particular foodstuff or environment that I am studying give the study more robustness.

The rules that govern the designation of a strain as a type strain are laid out very solemnly in a document called the International Code of Nomenclature of Bacteria. Very often type strains were defined in the early twentieth century and have stood the test of time, which is a tribute to the precision and diligence of previous generations of microbiologists.

An obvious question is: how do microbiologists get their hands on type strains? Well, just as there are seed banks all around the world where seeds are stored for many reasons, only one of which is the frightening scenario of the post-apocalypse re-seeding of the planet, there are collections of type strains. The most well known of such bodies is the ATCC — the American Type Culture Collection — which started out in the McCormick Institute in Chicago but is now located in Manassas, Virginia, and boasts 18,000 sq ft and 200 megafreezers of storage. The main European culture collections are the DSMZ (Deutsche Sammlung von Microorganismen und Zellkulturen), located in Braunschweig, Germany and the UK’s NCIMB (National Collection of Industrial Food and Marine Bacteria). If I want a particular type (or even a non-type) strain, I just browse these organisations’ on-line catalogues, pick my strain and place an order. (A single “dose” of type strain will cost less than $200). A vial of freeze-dried bacteria promptly arrives (because of their cell wall, most bugs survive freeze drying), sometimes even in super-convenient “quick stick” formats (a plastic tube with an applicator; you just twist it open and you have your resuspended bugs at the end of a cotton bud thing), and it is then up to me to carefully revive the small fellows. They go into a light broth at a temperature that suits their growth, and the next day I have trillions of cells to work with.

Bacteria are perfectly suited to storage in such facilities as the ATCC. They are so amenable to cryopreservation that even the most modestly resourced microbiology lab can freeze cultures down and feel safe in the knowledge that the critters will survive for decades in such a frozen state. And because bacteria divide by binary fission, a daughter cell is (with a few qualifications) a clone of its mother. You can be cock sure as a microbiologist that a vial of E. coli, for example, frozen by an éminence gris in the 1930s will, when slowly thawed, give rise to a viable culture which will perform exactly the same biochemically and physiologically as the colony forming units that were scooped up and placed in glycerol (a cryoprotectant which stops ice microcrystals from damaging the structure of cells as they freeze down) all those years ago.

It is a tribute to scientists’ willingness to share and co-operate across international boundaries that bodies such as the ATCC exist. It is individual microbiologists who send their newly discovered and characterised strains to culture collections and it is usually public money that supports such facilities. An impoverished microbiologist does not necessarily have to shell out for her type strains. Most of us will send a strain on to a colleague when politely asked. These are referred to as “gifts” in the scientific literature.

Rebecca Lancefield

Microbiology has very few female superheroes. Hell, science has very few superwomen. Names that role off the tongue, that are synonymous with high achievement, brilliance, genius even. There’s Marie Skłodowska Curie and maybe Dian Fossey and, and, and . . . Whereas there are dozens of men whose fame is so great that even the most scientifically illiterate member of the public could rattle off their names. From my own field of microbiology we have Louis Pasteur, Julius Richard Petri, Robert Koch, Alexander Fleming, Edward Jenner. That is why, when I was doing some research on streptococci recently, I was delighted to come across Rebecca Lancefield, a woman whose talent and brilliance should serve as an inspiration to all aspiring female scientists, and who was a giant in the field of clinical microbiology for many a decade of the twentieth century.

Rebecca Lancefield’s influence on her field was so great that she is one of those special breeds of scientists whose name has become immortalised in the jargon of her speciality. Just as Petri gave his name to that indispensable round culture dish, and Joseph Lister his to a genus of nasty little bugs, Rebecca Lancefield will forever be remembered when microbiologists speak of streptococci. She gave us the Lancefield Group.

Microbiologists are obsessed with giving their bugs names. It can seem from the outside that much of the microbiological scientific literature is concerned with classifying, re-classifying and de-classifying strains. Scientists who learned their trade in the 1990s and beyond are often perplexed by the new names given to old, familiar bugs and the manner in which whole groups are shifted around on the evolutionary tree. Remember Enterobacter sakazakii — a lad whose presence in infant formulas and bottled water put the fear of God in parents, regulatory authorities and manufacturers alike? (It can kill those with under-developed immune systems.) Well, it’s now Chronobacter sakazakii. The field of bacterial taxonomy (or systematics) — organising the invisible little critters into species, genus, families and all that based on genetic relatedness and phenotypic traits — is in constant ferment (excuse the pun). Many articles in this field are infused with defensive, passive-aggressive righteousness and generate a series of ever escalating letters to the unfortunate editor of the scientific journal in which the article has appeared. The joke goes: how do you define a bacterial taxonomist? Someone who disagrees with another bacterial taxonomist.

But, naming bugs is vital. A matter of life and death. Which brings me back to Rebecca Lancefield.

Rebecca Lancefield spent her life, before and after getting her PhD from Colombia University in 1925 studying a group of bacteria familiarly called the streptococci. We are all familiar with the strep throat — an infection caused by a species called Streptococcus pyogenes. There are dozens of other Streptococcus species, as well as cousins, in-laws and out-laws who can cause far more damage than making you sound like Tom Waits for a couple of days. Scarlet fever and rheumatic fever and many opportunistic infections are caused by streptococci. For a doctor to diagnose and treat a particular infection suspected of being caused by a streptococcus, she must identify the particular strain involved. This is not an easy task. Under even the most powerful microscope and with the most advanced staining techniques, one Streptococcus pretty much looks like another. There are a raft of biochemical tests that can be used to designate a strain, but these are growth-based and, therefore, slow; the bug in question is inoculated into a special medium and must grow to sufficient numbers to metabolise the compound that gives the colour change. This can take days in some cases. Rebecca Lancefield devised a rapid system of designating streptococci — the Lancefield Grouping. Bacteria’s reactions to special antisera allowed their placing into groups from A to S. This greatly aided the treatment and study of streptococcal infections. A doctor would take a swab of an infected area, or a blood sample, grow it up, and add a colony of bugs to a few drops of antiserum. If there was a reaction — coagulation — the doctor knew exactly what nasty she was dealing with and could proceed accordingly.

To this day, the Lancefield Grouping is in use, making doctors’ jobs easier and saving lives. Its inventor serves as an example to all women who have a passion for microbiology and wish to have a career in the field. She had an extremely lengthy career, spending from 1918 until 1980 at Rockefeller University and, in a pre-molecular biology world, achieved a remarkable amount of detailed characterisation of her “babies”, the streptococci. Although honoured by her peers (President of the Society of American Bacteriologists, President of the American Association of Immunologists and elected to the National Academy of Sciences as one of only ten women among more than one thousand men) her name is not, unfortunately, as widely known as it deserves to be. For a woman who was known in microbiology circles as the “Sherlock Holmes of the streptococci”, this is a great pity. We can all do our bit to honour Rebecca Lancefield: croak her name every time we have a strep throat!

Machines in Science

We’re currently trying to offload an old cell sorter — a MoFlo — which although has seen better days, could still churn out some pure cells for someone willing to give the machine a wee bit of TLC. Organising the MoFlo’s sale, shipping and replacement has got me thinking about research scientists’ relationships with the machines (or to be posher about it, instruments) they work with.

First off: modern science would come to a grinding halt without the machines we researchers use. Gone are the days when you could generate publishable data using just a calipers and a ball of yarn. I know of no field, bar perhaps ecology and psychology, where scientists just go out and measure things or count stuff or ask folks questions — et violà they have hard data they can write up into a Nature paper. Nowadays, the scientist’s possibilities of generating data (also know as finding stuff out) are as dependent on an array of high-tech machines as a teenager’s love life on his or her smartphone. Pull the plug on these instruments and our friend in the well-worn, off-white lab coat is thrown back to the days of Darwin, manually taking every data point, logging results into leather-bound notebooks by candlelight (with the aid of a quill and a bottle of ink, of course), and using snail- rather than e-mail to stay in contact with their peers. Mr D didn’t fare badly out of his enforced reliance on Victorian technology, but I don’t see me or my peers showing up at a Nobel ceremony and heaping praise on Uriah Smickenthorpe and Sons, their longstanding monocle and clock glass manufacturers “without whom we would never have proven the flatness of the Earth”.

Those esoteric machines that mooch in the corner of every lab, LEDs a-blink and fans a-whir, are indispensable to us boffins. Not only do they do things quicker, more efficiently, more accurately and more precisely than could be done decades ago, they also allow us to take measurements and perform reactions and generate data in ways that were unimaginable to previous generations of science. They have quickened the pace of scientific research and broadened the scope of what each and every field of inquiry can measure. Science is galloping forward, and in a large part it is due to the fantastic (and fantastical) new machines that seem to appear with greater regularity than new models of the Toyota Yaris.

There is a downside to this lightning-quick and unceasing innovation, though; it’s become an arms race. These magnificent machines do not generally come cheap. Let me talk about cytometry, a field I know well. A basic cytometer which can take six to eight measurements from a single cell comes in at forty grand. Add another couple of measurements and your up to eighty K. Three lasers and twelve parameters and you’re riding over the hundred K. And what about a five-laser machine that can generate 20 data points per cell? That’s heaps of money. Heaps of money not every lab or research institute can afford. And what happens if the Iranian National Frog Fertility Centre can afford a five-laser machine and their rivals in Perth’s Ranarium Research Facility only have a two-laser machine? Our down-under chums fall behind in their enquiry into amphibious immune systems and sperm motility, while Prof. J. Frogenstein of the INFFC gets paper after paper into Nature chock full of cytographs made possible by his twenty-colour panels.

Another issue is that our reliance on fancy machines can make us scientists less technically adept, lazier, less questioning even. Your modern machines are very often what the manufacturers call “black boxes”. The user doesn’t know how they work, maybe isn’t even passingly familiar with the principles upon which they work. They just feed their sample in one end and get an Excel file or graphic out the other. That can be dangerous. If you don’t know how a machine works, you don’t know how to fix it. Neither do you know how to spot rum data — stuff that’s out of spec, or weird looking because of some artifact. In fact, your whole relationship with your data is changed by not knowing very much about how it was generated. In this author’s humble opinion, a scientist should be able to stand over every point of data she generates. The words “Oh they’re just numbers the machine spits out when I put cells through” should never be used.

Which brings me back to our old MoFlo. The data (and cells) generated by this machine were the craft beer of the cell sorting world. The user of a MoFlo had to know pretty much everything about the machine and enough about the principles and theory of sorting (i.e. have read Howard Shapiro’s book from cover to cover at least three times) to be able to get a decent publishable graph and a smattering of pure cells. The system was so open, that everything that could possibly influence a cell’s journey (and the instrument’s recording of that journey) through the machine was manipulable. If something went wrong, you knew exactly why. And if something went right, you knew exactly how to repeat those conditions. The MoFlow straddled the world between hands-on, sleeves-rolled-up, DIY, gentleman and gentlewoman science and today’s sleek “just press acquire” instruments in a way that I loved. You got your twelve data points per cell, but boy did you work for it and boy did you know how you’d done it. I’m going to miss that ornery ol’ sorter!!

Coming Back

It is always said of footballers that they should never return to a club for which they used to play. “Never go back”, goes the hoary old cliché. And it mostly rings true. The list of fading stars who have returned to former clubs — sometimes the very clubs that nurtured them up through the ranks from academy to first team — and failed to impress is a long as your arm. Wayne Rooney returning to Everton? Damp squib Fernando Torres to Atlético Madrid? He might have well as chosen a nice retirement home by the Manzanares river! Even players at the top of their game don’t seem to do well on return to former clubs. Paul Pogba to Manchester United? The jury is still decidedly out.

What about a normal Joe Soap like you and I returning to a former workplace? How does that usually work out?

Well, not only am I starting out on a new project, but I’m returning to a lab in which I formerly worked. Under a boss who was my boss the last time. A man under which I did my PhD, no less. That’s a lot of returning going on there!

Now, if I was fully over the moon about my post-doctoral position back in 2009, would I have left to pursue a fresh career as a cytometrist in Spain? If everything was perfect in my former/newly current lab almost ten years ago, would I have turned my back on it as readily as I did? The answer is a nuanced “no”.

In all honesty, I was a wee bit burned-out and-cheesed off upon leaving my former/current lab the previous time. Things had become a struggle. During my PhD, it had been a pleasure to work there: everything to myself, doing my own thing, minimal hassle. But when I finished and graduated up to post-doc, a lot changed. There was a huge influx of new post-grads and supervisors and some of them made working there difficult. There were queues to use pieces of equipment, untidiness, disagreements, politics. I just wanted to put my head down and research, but I was spending more and more time butting my head against those above and below me in the academic research food chain. And hand-holding underperforming post-docs. So I left, before I became too bitter.

But now I’m back. This time, I know what I’m getting myself into. Eyes wide open. I’m older and wiser, calmer, more patient. I’ll not let the silly things that got under my skin the last time get to me this time. Whatever person or set of circumstances gives me lemons this time, I’m gonna make lemonade.

I have to say, it’s weird being back in a lab you used to work in before. Much of this strangeness is a case of plus ça change, plus c’est la même chose: most of the equipment that was there when I left (much of it procured by my good self) is still there, some of it exactly the same, some the worst for wear. My handwriting is all over the place: since I helped commission the lab much of the signage and labelling was written by me. There’s old tip boxes, glassware, reagent bottles all with ULTAN written in thick marker. But, then there’s plenty of new equipment, new names, new faces.

And, as that chorus goes in the Cure’s “A Strange Day”, the faces, the faces, the faces. There’s plenty new people in my former/current workplace. But there’s also plenty of old ones too. And thanks be to God, that among these old faces are none of the ones that caused me grief the first time round. All the bad eggs have moved on, leaving their own mark on my former/new lab (samples in the -80, reagents in the cupboards, ice boxes and the like). The bad people never clean up after themselves!

 

So, this project, as much as it will be about the science and experiments described in the proposal, will be about proving that you can come back and make it work.

Starting

There’s always a frisson when you start a new project. Tension. Nervousness. A bit of self-doubt nagging away at you.

Will I be able for this?

What if . . .?

There are many what ifs. Enough to choke a horse.

GanttThe trick is to take it one day at a time, or even one task at a time. Looking at the Gantt chart over which you shed blood, sweat and tears during the drafting of the proposal is all well and good, but during the first days or weeks of your new project, extended study of its coloured bars and the bold lines that delineate tasks and milestones will do you no good. That way madness lies! You’ll be a slobbering wreck if your eyes and mind keep drifting to that complicated old bird!

You’re staring down the barrel of three years’ work and it’s all to do. A mountain of deadlines and deliverables. It will overwhelm you if you let it, crash down on you like a ton of bricks. Have you squirming and shivering in bed at four in the morning, reaching for your Rosary beads — or the bottle of Jameson. So put Mr Gantt out of your mind and reach for every comforting cliché in the research scientists’ manual.

Rome was not built in a day.

One day at a time, sweet Jesus.

Steady as she goes.

Less haste and more speed.

That’s what I’m telling myself now, anyway.

I’m keeping it simple for the moment. Starting from the ground up. Slowly, but surely.

The fancy stuff will come later, all those fine ideas and strategies that won over the evaluators and convinced them that I was the man to grant a whack of money to. Therefore, my first few days on the job are about building foundations: getting my computing set up; making my desk an ergonomic, nest-like haven where I wont feel the time go whenever I have to burn the midnight oil; setting up my bench space just the way I like it — clean, efficient, with everything useful at hand; getting to know the lab; ordering the things I think I’ll need during this start-up phase.

I know that as soon as I start making media and pouring plates and reviving freeze-dried type strains I won’t feel that nagging tension. Every little act I do in the lab will be a baby step closer to being along the route of the project plan, and in a few months I will have forgotten all about this feeling.

I keep telling myself that I’m a lucky so-and-so. Who else gets to do something that they love with a passion, something that excites, challenges and stimulates?

Very soon, I’ll be bug hunting!