The CrispR revolution

Emmanuelle Charpentier and Jennifer Doudna have just won the Nobel Prize for Chemistry. They have been my picks for the prize for years now. Nobel Prizes are often awarded decades after the fact, but CrispR has been such an obvious winner that it is a surprise it took until 2020 to be awarded. (Largely, I guess, due to the politics of several competing claims and patents, that have been going through the courts). 

This Noble is a well-deserved recognition of one of the seminal breakthroughs in biology of the last several decades. The award recognises elegant basic biological experiments that identified a novel immune mechanism that bacteria use to fight off viruses. The key insight is that the chemistry of this system allowed simple modifications to rewire this bacterial system into a tool to edit the genome of essentially any living being. A striking example of blue-skies research on basic science having an incredible translational effect. The CrispR system ranks up there with identifying the structure of DNA or the sequencing of the human genome - indeed, for the first time it allows us to really use the information gained by these earlier revolutions. CrispR tools are used daily across the globe to create new vaccines, generate gene therapy, design bacteria to help industrial processes. Essentially, the discovery of CrispR as a genome-modification tool has put biology on steroids - dramatically accelerating the pace of both basic research and translational applications

Fact-checking COVID-19 claims

From a recent interview with a fact-checking journalist:

Claim: Alcohol-based hand sanitiser shouldn't be used day after day as it breaks down the first immune barrier of the body: the lipid bacteria of the skin.

Verdict: Misleading. Alcohol-based gels do reduce the number of skin-resident bacteria and can start to cause some damage to the skin with prolonged use, in some individuals. However, the skin barrier is irrelevant to COVID-19, and alcohol-based gels also eliminate viruses from the skin, preventing transmission to surfaces and your face. Overall there is a clear benefit to use frequent hand-washing, and the negatives can be countered with moisturising.

Claim: We can strengthen our immune system in weeks or even days (for young people), which would mean that if one does contract COVID-19, it's more likely going to be a mild case which does not require hospitalisation.

Verdict: False. First of all, it is misleading to talk about "strengthening" the immune system. The immune system could be considered more like taste. You can increase how spicy food is, or increase how sweet food is - both are "strengthening" the taste but mean different things. Different "flavours" of the immune response are optimal in different circumstances, so there is no such thing as a generic increase in how strong the immune system is. It is also completely unclear as to whether we actually want a "stronger" immune response in COVID-19 - there is good evidence that an excessive immune response of one particular "flavour" is causing the immune pathology. We want to train the immune response in a particular direction (e.g. through vaccines) not generically increase its power (even if that was possible, which it isn't).

Claim: A well functioning immune system is dependent on the quality of our intestinal flora. This is why we should avoid eating refined "industrial" food.

Verdict: Half true. There is an interaction between the gut bacteria and the immune system, and this is modified by the food we eat. It is not very well understood, and it is likely too early to say whether the net effect of the consequences is generally good or generally bad. It is certainly too early to say whether it makes a positive or negative effect in the case of COVID-19. As general advice, eating fresh and unprocessed foods, high in vegetables and low is red meat is good health advice, regardless of what it does to the immune system.

Claim: Fasting strengthens the immune system in only 3 days.

Verdict: False. Fasting modifies the immune system slightly, which could be advantageous in some circumstances and detrimental in others. It is a minor effect though, and certainly it would not be advised that someone with symptomatic COVID-19 undergoes extensive fasting. The body needs resources to fight an infection.

Claim: Herbal supplements such as echinacea and elderberry strengthen the immune system in a matter of weeks.

Verdict: False. There are active compounds in all plants, which can modify aspects of the immune system if given in high enough doses in a dish. That does not mean that eating a few pills does anything at all. It is very important for people to understand that supplements and medicines are regulated completely differently. "Supplements" are allowed to make essentially any claim, without any evidence, as long as that claim is vague. This is why you get garbage claims about "immune boosting": they are vague enough that they are legally allowed to be made without evidence. Actual medicines, on the other hand, can only make extremely specific claims that are backed up by evidence. All claims about herbal supplements should essentially be treated as advertising material. 

Claim: Vitamins and minerals strengthen the immune system.

Verdict: Misleading. Vitamins and minerals are different from other supplements. They are needed by the body in extremely low quantities, and if they are absent then health problems arise. For people who are actually deficient, taking vitamins and minerals will improve health, including the immune system. However, almost no one in the developed world is actually deficient, and certainly having a balanced diet of fresh food will give you more than enough of every known vitamin and mineral. Unless you have an exceptionally limited diet, taking these tablets doesn't do anything.  

Claim: Fear is a powerful immunodepressant.

Verdict: Half-true. Anxiety can modify the immune system, and can give poorer health outcomes during some types of infection. The effect is weak to moderate, but it is measurable. This should not be used as an excuse not to spread awareness of the COVID-19 pandemic, however: some degree of anxiety is rational and protective, where it supports valid infection-avoidance behaviours (e.g., hand-washing, wearing a mask, avoiding crowded areas).

Claim: Practicing yoga strengthens the immune system.

Verdict: Misleading. There is nothing special about yoga. There are, however, weak to moderate beneficial effects of exercise and the alleviation of anxiety on infection outcomes. For some people, they may get this through yoga. Others may get it through gardening, or a daily run, or the ritual of a cup of tea. We should look after our mental health, which means cultivating habits that make us happy. The idea that one particular solution like yoga or mediation has any special properties beyond this is completely unsupported. Keep it up if you enjoy it, but it doesn't replace medicine and won't work for every person.

Unpopular opinion: the scientific publication system is not the problem

Scientific publishing is undergoing radical change. Nothing surprising there, scientific publishing has been constantly evolving and constantly improving. Innovation and change are needed to improve, although not all innovations end up being useful. I'm on record for saying that the DORA approach, for example, is ideologically well meaning, but so little consideration has been made of the practicalities that the implementation is damaging. Open-access is another example: an excellent ambition, however the pay-to-publish model used for implementation turbo-charged the fake journal industry. I am glad that we have advocates pushing on various reforms to publishing: pre-print, open-access, retractions, innovations in accreditation, pre-registration, replication journals, trials in blind reviewing, publishing reviews, etc. The advocates do seem, to me, to have far too much belief that their particular reform is critical and often turn a blind eye to the potential downsides. That is also okay: the system needs both passionate advocates and dubious skeptics in order to push changes, throw out the ones that don't work and tweak the ones that do work in order to get the best cost/benefit ratio of implementation. Fundamentally, though, the publication system is not broken. Oh, it is certainly flawed and improvements are needed and welcomed. But even if every flaw was fixed (which is probably impossible: some ambitions in publishing are at heart mutually contradictory) I don't think it will have the huge benefits that many advocates assume. Because at the heart of it, the problem is not the publication system, but the other systems that publishing flows into. Let's take two examples:

• Careers. Probably the main reason why flaws in the publishing system drive so much angst is that scientific publication is the main criteria used in awarding positions and grants. So issues with prestige journals, impact factors and so forth have real implications that damage people's lives and destroy careers. DORA is the ambition to not do that, without the solution of an alternative. Perhaps one day we will find a better system (I happen to believe it lies in improving metrics, and valuing a basket of different metrics for different roles, not in pretending metrics don't exist). But even a perfect system (again, probably impossible) won't fix the issue in career anxiety. Because in the end the issue is that the scientific career structure is broken: it is under-funded, built based on short-term perspectives, and operates on the pressure-cooker approach to milking productivity out of people until they break. From a broader perspective, the scientific career structure is not operating in a vacuum - it is part of a capitalist economy which again fuels these anxieties. Why are people so worried about losing their place in the academic pipeline? Because in our economy changing careers is really, really scary. Fixing publishing doesn't actually fix any of those downstream issues.

Dieet met veel suiker verhoogt risico op pancreaskanker

Knack

Suikerrijke voeding veroorzaakt de ontwikkeling van alvleesklierkanker en verhoogt de kans op een dodelijke afloop. Tot die bevinding zijn onderzoekers van het Vlaams Instituut voor Biotechnologie (VIB) en de KU Leuven gekomen.

Een suikerrijk dieet verhoogt niet alleen de kans op het ontwikkelen van pancreaskanker. Het stimuleert ook de agressieve groei van tumoren. Tot die conclusie komen onderzoekers van VIB-KU Leuven en collega's van het Babraham Institute van de Britse universiteit Cambridge.

De resultaten zijn gepubliceerd in het tijdschrift Cell Reports.

Alvleesklierkanker is een zeldzame maar dodelijke vorm van kanker door late detectie en een slecht begrip van risicofactoren. Bekende risicofactoren zijn obesitas, voeding en diabetes type 2, maar door de lage incidentie en de onderlinge samenhang is hun individuele bijdrage moeilijk in te schatten.

De onderzoekers voltooiden een uitgebreid project met experimenteel werk bij muizen en menselijke gegevens. Bij de dieren werd de progressie van pancreaskanker beïnvloed door voedingssuiker, met een snellere tumorgroei en verhoogde dodelijkheid.

Het effect bij mensen blijkt hetzelfde. Bij 500 deelnemers aan de studie onderzochten de onderzoekers de interactie tussen genen en voeding en ontdekten dat hoge niveaus van voedingssuiker het risico op alvleesklierkanker verhoogden. 'We hebben jarenlang gekeken naar verschillende voedings- en genetische veranderingen en niets komt in de buurt van de nadelige gevolgen van een dieet met veel suiker', zegt James Dooley, senior wetenschapper bij het Babraham Institute.

Plantaardige voeding met een equivalent van een avocado per dag vermindert het risico op pancreaskanker met tien procent.

Today in Cell

Not a bad day for the VIB Brain and Disease department...

  

New role for white blood cells in the developing brain

Whether white blood cells can be found in the brain has been controversial, and what they might be doing used to be complete mystery. In a seminal study published in Cell, an international team of scientists led by Prof. Adrian Liston (VIB-KU Leuven, Belgium & Babraham Institute, UK) describe a population of specialized brain-resident immune cells discovered in the mouse and human brain, and show that the presence of white blood cells is essential for normal brain development in mice.

Like a highly fortified headquarters, our brain enjoys special protection from what is circulating in the rest of our body through the blood-brain barrier. This highly selective border makes sure that passage from the blood to the brain is tightly regulated.

The blood-brain barrier also separates the brain from our body’s immune system, which is why it has its own resident immune cells, called microglia, which trigger inflammation and tissue repair. Microglia arrive in the brain during embryonic development, and later on, the population becomes self-renewing.

Yet, white blood cells—which are part of our immune system—have been found to play a role in different brain diseases, including multiple sclerosis, Alzheimer’s and Parkinson’s disease or stroke. Whether or not white blood cells can be found in healthy brains as well, and what they might be doing there, has been subject of intense debate. An interdisciplinary team of scientists led by Prof. Adrian Liston (VIB-KU Leuven, Babraham Institute) set out to find the answers.

White blood cells in the brain

"A misconception about white blood cells comes from their name,” explains Dr. Oliver Burton (Babraham Institute). “These 'immune cells' are not just present in the blood. They are constantly circulating around our body and enter all of our organs, including—as it turns out—the brain. We are only just starting to discover what white blood cells do when they leave the blood. This research indicates that they act as a go-between, transferring information from the rest of the body to the brain environment"

The team quantified and characterized a small but distinct population of brain-resident T helper cells present in mouse and human brain tissue. T cells are a specific type of white blood cells specialized for scanning cell surfaces for evidence of infection and triggering an appropriate immune response. New technologies allowed the researchers to study the cells in great detail, including the processes by which circulating T cells entered the brain and began to develop the features of brain-resident T cells.

Dr. Carlos Roca (Babraham Institute): “Science is becoming increasingly multidisciplinary. Here, we didn't just bring in expertise from immunology, neuroscience and microbiology, but also from computer science and applied mathematics. New approaches for data analysis allow us to reach a much deeper level of understanding of the biology of the white blood cells we found in the brain.”

An evolutionary role

When T helper cells are absent from the brain, the scientists found that the resident immune cells – microglia – in the mouse brain remained suspended between a fetal and adult developmental state. Observationally, mice lacking brain T cells showed multiple changes in their behavior. The analysis points to an important role for brain-resident T cells in brain development. If T cells participate in normal brain development in mice, could the same be true in humans?

“In mice, the wave of entry of immune cells at birth triggers a switch in brain development,” says Liston. “Humans have a much longer gestation than mice though, and we don't know about the timing of immune cell entry into the brain. Does this occur before birth? Is it delayed until after birth? Did a change in timing of entry contribute to the evolution of enhanced cognitive capacity in humans?”

The findings open up a whole new range of questions about how the brain and our immune system interact. "It has been really exciting to work on this project. We are learning so much about how our immune system can alter our brain, and how our brain modifies our immune system. The two are far more interconnected than we previously thought," says Dr. Emanuela Pasciuto (VIB-KU Leuven).

The study also brings in a connection with the gut microbiome, says Liston: “There are now multiple links between the bacteria in our gut and different neurological conditions, but without any convincing explanations for what connects them. We show that white blood cells are modified by gut bacteria, and then take that information with them into the brain. This could be the route by which our gut microbiome influences the brain.” 

Taken together, the results contribute towards the increasing recognition of the role of immune cells in the brain and shed new light on its involvement in a range of neurological diseases.

Check out the full article here

Witte bloedcellen ook belangrijk voor ons brein

Witte bloedcellen maken deel uit van ons immuunsysteem dat ons tegen ziektes beschermt.  Of ze ook in de hersenen terug te vinden zijn, en wat ze daar dan zouden doen bleef tot nog toe een raadsel. Een internationaal team van wetenschappers onder leiding van professor Adrian Liston (VIB-KU Leuven, België en Babraham Institute, VK) toont nu aan dat witte bloedcellen wel degelijk voorkomen in de hersenen van zowel muizen als mensen, en dat hun aanwezigheid essentieel is voor normale hersenontwikkeling. De resultaten verschijnen deze week in het prestigieuze vakblad Cell.

Onze hersenen worden als een versterkte burcht ommuurd door de bloed-hersenbarrière. Die moet vermijden dat stoffen die in onze bloedbaan circuleren zomaar in onze hersenen terechtkomen. Via de bloed-hersenbarrière worden onder strikte controle enkel welbepaalde stoffen uitgewisseld.

De bloed-hersenbarrière schermt de hersenen ook af van ons immuunsysteem, dat de rest van ons lichaam patrouilleert om bijvoorbeeld bacteriële of virale indringers op te sporen en uit te schakelen. Precies daarom heeft het brein z’n eigen immuuncellen: microglia.

Toch blijken witte bloedcellen ook een rol te spelen bij verschillende hersenaandoeningen. Denk maar aan MS, alzheimer, parkinson of een beroerte. Hierbij gaat het wel telkens om ziek of ‘beschadigd’ hersenweefsel, waar mogelijk ook de bloed-hersenbarrière is aangetast. De vraag bleef dus of – en waarom – witte bloedcellen nu werkelijk aanwezig zijn in hersenen die normaal en gezond zijn.

Witte bloedcellen in de hersenen

Een interdisciplinair team van wetenschappers onder leiding van prof. Adrian Liston (VIB-KU Leuven, Babraham Institute) heeft nu een kleine maar belangrijke groep van T-helpercellen ontdekt in hersenweefsel afkomstig van muizen en van mensen. T-helpercellen zijn een specifiek type witte bloedcellen, gespecialiseerd in het scannen van celoppervlakken op aanwijzingen van infectie en in het op gang trekken van een aangepaste immuunreactie. Aan de hand van de laatste technologie konden de wetenschappers de T-helpercellen tot in detail bestuderen, inclusief hoe en wanneer ze in de hersenen terecht komen.

Dr. Emanuela Pasciuto (VIB-KU Leuven), postdoctoraal onderzoeker in het team van Liston benadrukt het belang van interdisciplinair onderzoek: “Om de rol van witte bloedcellen in het brein in kaart te brengen hebben we niet alleen expertise van immunologie, neurowetenschappen en microbiologie bij elkaar gebracht, maar ook van informatica en toegepaste wiskunde. Nieuwe benaderingen voor data-analyse stellen ons in staat om een ​​veel dieper begrip te krijgen van de biologie van de witte bloedcellen die we in de hersenen hebben gevonden.”

Een evolutionaire rol

De onderzoekers stelden vast dat in muizenhersenen zonder T-helpercellen de ontwikkeling van de typische immuuncellen van het brein (de microglia) bleef hangen ergens tussen een foetale en volwassen ontwikkelingsstatus. De muizen zonder T-helpercellen in de hersenen vertoonden bovendien verschillende gedragsafwijkingen, wat wijst op een belangrijke rol voor de T-helpercellen bij de normale hersenontwikkeling. En als dat geldt voor muizen, zou hetzelfde dan ook waar zijn voor mensen?

“We zien dat de toestroom van immuuncellen in de hersenen bij de geboorte van muizen leidt tot een omslag in het ontwikkelingsproces,” zegt Liston. “Maar de zwangerschap bij mensen is veel langer dan bij muizen, en we weten niet wanneer de immuuncellen dan toekomen in het menselijk brein. Gebeurt het nog vóór de geboorte? Is het uitgesteld tot na de geboorte? Kan een verandering in de timing bijgedragen hebben aan de evolutie van de uitzonderlijke hersencapaciteit van mensen?”

De bevindingen openen een heel nieuw gamma aan vragen over de wisselwerking tussen ons brein en ons immuunsysteem. “We leren nog elke dag bij over hoe ons immuunsysteem ons brein kan beïnvloeden en vice versa. De twee zijn veel meer met elkaar verbonden dan we eerder dachten,” zegt Pasciuto.

Darmen en hersenen

De studie legt ook nieuwe verbanden tussen ons brein en onze darmflora, aldus Liston: “Heel wat neurologische aandoeningen worden in verband gebracht met bacteriën in onze darmen, maar zonder overtuigende verklaringen voor die connectie. Onze resultaten laten zien dat darmbacteriën witte bloedcellen kunnen beïnvloeden, die deze ‘informatie’ vervolgens mee nemen naar de hersenen. Dit zou de manier kunnen zijn waarop onze darmflora onze hersenen beïnvloeden. ”

De nieuwe resultaten dragen enorm bij tot de groeiende kennis over de rol van immuuncellen in de hersenen, zowel tijdens de normale ontwikkeling als bij verschillende ziekteprocessen.

Dietary sugar drives pancreatic cancer

Research using mice and human data shows how diet affects disease risk

Eating a diet high in sugar increases the likelihood of developing pancreatic cancer in some individuals and also drives the aggressive growth of tumours, a study by researchers from the Babraham Institute, Cambridge, UK, and VIB-KU Leuven, Belgium, has found.

The researchers completed a comprehensive project using experimental work in mice and human data, including from pancreatic cancer patients, to understand the influence of different dietary components on the development and progression of pancreatic cancer. The research is published today in the journal Cell Reports.

Pancreatic cancer is a rare but fatal form of cancer, due to late detection and a poor understanding of the risk factors. Known risk factors include obesity, diet and type 2 diabetes, however the low incidence rate and interconnection of these factors mean that it is difficult to tease apart their individual contribution.

The researchers first studied the effects of obesity, diet and diabetes on pancreatic cancer development, growth and lethality in mice. In parallel they analysed the effect of diet using data from the European Prospective Investigation into Cancer and Nutrition (EPIC) study, which followed over half a million Europeans for 20 years.

The researchers found that obesity, diet and diabetes had profound and differing impacts on cancer incidence and growth. Using mice, the results indicated that obesity, dietary animal fats and dietary sugar were independent drivers of different facets of pancreatic cancer progression. In particular the results shed light on how pancreatic cancer might be affected by dietary sugar, with more rapid tumour growth and escalated lethality.

The effect of dietary sugars on pancreatic cancer development was preserved between mice and humans. In 500 study participants with pancreatic cancer, the researchers explored the interaction between genes and diet and found that high levels of dietary sugar increased pancreatic cancer risk in individuals with a certain genetic variation (found in 6% of the population).

Dr James DooleyDr James Dooley, senior staff scientist in the Immunology programme at the Babraham Institute, said: "Our study raises concern about the remarkable toxicity of sugar in our diet. We spent years looking at different dietary and genetic changes, and nothing has anywhere near the detrimental impact of a high sugar diet. Our findings suggest that it drives pancreatic cancer onset and makes it a more aggressive and lethal tumour."

Analysis of the human-derived data from the large EPIC study suggested that dietary plant fats reduced the risk of pancreatic cancer, estimating a 10% decrease in risk when eating the equivalent of an avocado a day.

Professor Adrian Liston, senior group leader at the Babraham Institute, said: "This study shows the power of combining animal research with the study of patients. We were able to use epidemiology and large patient-based resources to find a link in humans, and then go back to an animal model to formally test the direction of causality. Finding the same gene-diet link in both mice and humans makes us confident that diet is modifying disease risk, and gives us the tools to test preventative and therapeutic interventions."

Proliferating pancreatic cancer cells in mice fed high sugar dietsWhile the impact of nutrition on cancer development continues to be explored and debated, this study provides a vital foundation for further studies and important indications to explore. Armed with this knowledge, clinicians could be supported to identify individuals at increased risk for screening and individuals with a high-risk genetic background could take pro-active dietary changes to reduce their risk of pancreatic cancer.

Ali Stunt FRSA, Founder and Chief Executive of Pancreatic Cancer Action, concurs: "Here at Pancreatic Cancer Action, we strongly advocate for high quality research into this neglected cancer. Dr Liston and his team have made a major contribution into understanding how diet and genetics changes the risk for pancreatic cancer. Healthy lifestyle choices, such as avoiding sugar-sweetened beverages and choosing a diet rich in vegetables, can reduce your risk of pancreatic cancer, and may be especially important in families with a history of the disease."

Read the original article here.

AutoSpill: a method for calculating spillover coefficients in high-parameter flow cytometry

I am really thrilled to release AutoSpill onto BioRxiv. AutoSpill is a novel method for applying compensation to flow cytometry data, which reduces the error by ~100,000-fold. It is thanks to AutoSpill that we can push machines to their max colours, and actually get good quality 40+ parameter flow cytometry data. AutoSpill is a beautiful example of what maths can add to #immunology, led by the talented Dr Carlos Roca.

So how does AutoSpill work? If you just want to compensate your data, simply upload your single colour controls to https://autospill.vib.be and then copy the spillover matrix to your flow cytometry program of choice. Dr Carly Whyte made this easy two minute tutorial:

If you program your flow cytometry analysis in R, we have also released the AutoSpill full code, so you can add this to your bioinformatics pipeline.

Here are a few examples of the error reduction you can get with AutoSpill:

In high dimensional flow cytometry traditional compensation errors create artefacts. AutoSpill creates a perfect spillover matrix. What does a "perfect" spillover matrix mean? An error reduction of 100,000-fold on average, to the point where error is practically zero. (if you are using the script, you can reduce the error further - we stop the improvement at this point because it is functionally perfect). This means the large over/under-compensation effects can be completely removed from your data. If you want to run 28 colour flow cytometry on a 28 colour machine, you can spend hours-upon-hours compensating your data by hand, or 2 minutes with AutoSpill. AutoSpill is designed to run through the same operations that a skilled flow user does, just faster. But always remember - the compensation can still only be as good as the quality of the single colour controls!

How does AutoSpill work? It is a huge surprise to me, but with the enormous effort over decades to add extra lasers and new flurophores onto machines, the mathematics behind compensation hasn't been updated since 1993, where it was designed for 3 colour flow on computers with 100,000-fold less capacity. For decades we've been building more-and-more expensive machines, and haven't updated the basic maths that the machines run on!

Traditional compensation defines a positive and a negative population, finds the slope and uses that as the spillover matrix. It still works okay in most cases, it is just that the small errors start piling up when you are making 250+ calculations on a high parameter dataset.

AutoSpill is actually fairly simple at heart:

1. Draw an automatic live cell gate
2. Use linear regression to take into account every cell, not just the two data points of average positive and average negative
3. Calculate the error left, using the sum of errors in every compensation pair 
4. Use the residual error and return to step 2
5. Repeat the tweaking of the matrix until error is gone

The underlying mathematics is tougher though (never thought I'd write a paper  discussing "the linearity of the quantum mechanical nature of photons"!), because AutoSpill was built for actual flow cytometry users, not as a computational exercise. Carlos built the original pipeline, and then we extensively beta-tested it on 1000+ datasets over 20 months. Something as simple as a live gate becomes complex when you want it to robustly work on any dataset, cells or beads, collected on any machine. I'll spare you the details, but two stage tesselation and a 33% density estimation using a convex hull does the trick, successfully spotting the cells or beads even with heavy debris:

There are many advantages to using linear regression to calculate compensation. Why through out the data from 40,000 cells and instead turn it into two points, the way traditional compensation does? If you use linear regression you can use all of the data, which means AutoSpill works even if you have mostly negative or mostly positive data, just a shoulder of positive events or even a smear. So you can use the real antibodies on real cells to calculate your single colour compensations, rather than using beads or anti-CD4 in every channel.

As an added advantage to this approach, AutoSpill can remove most of the autofluroscence from your flow cytometry sample. For people working on cancer or myeloid cells this can be a complete game-changer. It turns out that while cells have different amounts of autofluorescence, the spectrum of that autofluirescence is fairly constant. You can collect empty data in the worst autofluorescent channel. The single in this channel can be used to calculate the autofluorescent spectrum, which can then be calculated on a per-cell basis and used to compensate it out of every other channel.

Here are two examples:

1. Back when I was a post-doc, there were many published reports of Foxp3 expression in macrophages, epithelium, cancer, etc. All autofluorescent artefacts that wasted years of research.  
AutoSpill removes this autofluorescence specifically from the macrophages:

2. Now we work on microglia, and it is still argued in the literature as to whether they express low levels of MHCII at homeostasis. Using AutoSpill to remove the autofluorescent signal it is quite simple - no they don't.

Of course, AutoSpill is a tool to get an optimal solution for good data. It can't turn bad data into good data. You should always work with your Core Facility staff to optimise the machines and run high quality single colour controls.

If you like AutoSpill, and you come from a math, computer science or data science background, why not come and join the lab? We have a position open for a data science post-doc or senior scientist for another two weeks.

Training the PhD supervisors

I just completed another "training the PhD supervisors" course, in anticipation of my first Cambridge PhD students. I have a few thoughts on training supervisors, but first my credentials and context: 

1. Unlike most science professors, I took formal training in higher education, through a two year part-time Graduate Certificate program, and have published on PhD training.

2. 26 PhD students as supervisor (16) or co-supervisor (10). Of these, 18 graduations, 6 students still in progress and 2 drop-outs. Some easy experiences, where the students flew though. Some wonderful experiences, where I really got to help the student grow and flourish. Some steep learning curves, where the student and I took longer to get it together, but ultimately we both learned from the experience and the student suceeded. Some nightmares, that had me on the edge of quitting and occasionally still give me insomnia. I am a better supervisor today than I was 10 years ago, and hopefully I will be a better PhD supervisor in 10 years than I am today.

3. I see the PhD as a program where you create the environment that gives the student the opportunity to grow. This is difficult, since it involves understanding the student and pushing them just the right amount to stimulate them without intimidating them. The PhD for me is a highly versatile program, and I am happy for it to steer towards many different outcomes based on what the student is aiming for (academia, industry, etc).

So, my thoughts on training programs for PhD supervisors

First, they are necessary. The messages end up being fairly simple. Remember your PhD student is a person as well as a student. Learn that your student has different needs and expectations that you did as a PhD student. Learn to listen to their expectations, learn to be explicit in your expectations, be prepared to discuss and compromise. Document and revisit discussions. Learn the boundaries of reasonable expectations on both sides. Learn when to bring in extra help, learn where that help can come from. While these messages are simple, for many PhD supervisors it will be the first time they've explicitly heard them, and often new supervisors rely excessively on the lessons of their own n=1 PhD. 

This is the raison d'être of these training programs, and the central work is typically done well. There are several common failings, however:

1. Pedagogy has a teaching problem. Education is an advanced academic field, with a highly specialised language, just like other fields. Unfortunately, many education experts use this language when training PhD supervisors. It is a major turn-off, especially to STEM academics, where even common humanities terms can be opaque or even just mystifying. Most supervisors are going to get less than one undergrad credit worth of education training - the use of specialist language is unnecessary and a barrier to concept uptake. I fully acknowledge that STEM disciplines have the same language barrier. I hope that one day there is a concerted effort to bring knowledge from STEM into humanities - and at that point we will need to learn the language of humanities to effectively communicate. But during supervisor training the onus is clearly on the trainer to use discipline-neutral language.

2. Humanities and STEM are just too different. The PhD programs are so different, in style, outcome and supervision, that examples and advice end up being so generic it is of little value, or it jars completely with one of the fields. Just split up these training courses into humanities and STEM, replicate the common content and specialise the field-specific content. 

3. Supervisor training programs are too reactionary. A common mistake for new supervisors is to focus on correcting problems that they experienced during their own PhD. It can result in them being blindsided by different challenges. Ironically, the very classes that teach this are often guilty of the same problem. These courses are designed around the failings of current senior faculty. It is almost "what do we wish our senior lecturers had been taught 20 years ago?" in content and context. In STEM, the biggest failure in the senior supervisor population is the "sink or swim" mentality, which essentially assumes that any student who struggles is not cut out for a PhD (i.e., the failure is entirely in the student). This is demonstrably incorrect and propogates major problems of inequality. However, while this flaw is common in senior supervisors, it is becoming extremely rare in junior supervisors. When given problem examples, junior supervisors tend to first assume the failures are entirely in the supervisor. I have seen more issues arise from junior supervisors trying to be a friend to their students, or over-committing their time to a single student, then I have from junior supervisors neglecting their students. This is not to say that neglect is not a problem - it is, and needs to be addressed. However training courses for junior supervisors should better reflect the problems that are common in junior supervisors. 

4. Training programs are less valuable because they are siloed. This training is focused on the well-being of the student, and is essentially dedicated entirely to situations where the student has a problem that can be fixed by behaviour-change in the supervisor. We know, however, that junior faculty are under enormous stress, rife with anxiety. One of the biggest sources of stress can be the very rare cases of problem students. This situation, of a problem that requires behaviour-change in the student, is almost entirely neglected in supervisor training. We are trying to fix one side of the equation in this training, and the other side is often entirely neglected or dealt with in a generic "stress resilience" training course (which also assumes the flaw is in the faculty not being able to deal with the stress). What we need is integrated training. Pitch us the same problem scenario twice, but with different missing context. Walk through the problem scenario with missing context A, where you need to change. Walk through the problem scenario with missing context B, where the student needs to change. Discuss how to identify developing problems, how to reflect on whether you are dealing with a context A or context B issue, and what practical steps to take in each context. I really dislike the problem scenarios where we are expected to take a one paragraph description at face value - real lab problems are never that simple, and always involve looking at a problem from multiple perspectives. Real solutions always involve trade-offs. Let's not pretend to junior supervisors that they will be in a situation where they can just invest limitless time - there needs to be hard barriers to stop work-life imbalance on their side. Let's also not pretend that a supervisor-student relationship exists in isolation - it has impacts on the entire lab, and trade-offs are always required. Perhaps this comes from a STEM vs humanities divide, but I see the concept of the team/lab almost entirely neglected in problem scenarios and trouble-shooting.

Finally, a little self-reflection. I would give this particular training course a 9/10 - probably the best I've been through. And yet 90% of what I wrote is a criticism. Occupational hazard? I think in STEM we move very quickly on from the success to trying to fix the failures. I know that when I run evaluations I need to force myself to stop, and say "well done on X, Y and Z. These are important. Congratulations. Now let's talk about A, B and C, which need some improvement...... Again, well done on X, Y and Z."