Lay summary: Candida albicans in different host niches

Iuliana Ene works in the Aberdeen Fungal Group at the University of Aberdeen. She and her supervisor, Prof. Alistair Brown, are interested in how available nutrients in host niches modulate the pathogenicity of C. albicans.

Dynamic environmental responses of Candida albicans that contribute to pathogenicity

Candida albicans is the most common fungal pathogen in humans, causing a variety of health problems ranging from mucosal to systemic infections. Generally harmless, it is present in 40-80% of the normal population, but in immunocompromised individuals it can proliferate and access different internal organs and tissues causing potentially fatal infections. C. albicans occupies a number of different niches in the human host. This is where the pathogen is exposed to a variety of nutrients, many of them different from more classical ones (e.g. glucose) which are the basis for most studies conducted so far. The shift from harmless commensal to opportunistic pathogen requires C. albicans’ ability to grow in poor nutrient niches and survive the diversity of stresses it encounters in the host.

Many of these stresses, such as therapeutic drugs or osmotic stress act on the cell wall of the pathogen. This is the main interface between C. albicans and its host, a multi-layered interface which proves to be extremely flexible and dynamic when exposed to different nutrients. We are studying how the variety of nutrients found in the host modulate adaptation and stress responses and how the cell wall must quickly adjust under these conditions. In doing so it relies on mechanisms of constant remodelling and maintenance of cell wall integrity. More importantly we have found that certain nutrients and in particular poor nutrient niches in the host provide a fitness advantage to the pathogen.  Having adapted to these niches, C. albicans also increases its resistance to a number of antifungals, which are currently the only available weapon against fungal infections.

In this study, we show how the nutrients taken up strongly influence the cell wall architecture and hence resistance of C. albicans to certain stresses. These findings are likely to have a major impact on the behaviour of this pathogen inside the human host and may be of major clinical importance.

Adaptări dinamice la condiţiile de mediu care contribuie la patogenicitatea  Candidei albicans

Candida albicans este agentul fungic patogen cel mai frecvent la om, provocând o varietate de probleme de sănătate de la nivelul mucoasei la infecţii sistemice. În general inofensiv,  acest patogen este prezent în 40-80% din populaţia normală, dar în cazul persoanelor imunocompromise poate prolifera şi avea acces la diferite organe interne şi ţesuturi, provocând infecţii potenţial letale.

C. albicans ocupă diferite nişe în gazda umană,  acest patogen fiind expus la o varietate de surse de carbon, multe dintre acestea diferind de zaharurile clasice (de exemplu, glucoză), care stau la baza majorităţii studiilor efectuate până în prezent. Trecerea de la comensalism la patogenicitate necesită abilitatea C. albicans de a prolifera în nişe sărace în nutrienţi şi de a supravieţui diversităţii de factori de stress întâlniţi în gazdă. Mulţi dintre aceşti factori de stress, cum ar fi agenţii terapeutici sau stresul osmotic, acţionează pe peretele celular al agentului patogen. Acesta constituie principala interfaţă dintre C. albicans şi gazdă, o interfaţă multi-strat, care se dovedeşte a fi extrem de flexibilă şi dinamică atunci când C. albicans este expus la diferiţi nutrienţi.  Acest proiect studiază modul în care varietatea de substanţe nutritive întâlnite în gazda umană modulează răspunsurile de adaptare la stres şi modul în care peretele celular se adaptează continuu acestor condiţii. În acest sens, se bazează pe mecanisme de remodelare constantă şi de menţinere a integrităţii peretelui celular.  Mai important, am constatat că anumiţi nutrienţi oferă un avantaj de supravieţuire agentului patogen. De asemenea, aceştia cresc rezistenţa la un număr de antifungice, care sunt în prezent disponibile ca singura arma împotriva infecţiilor fungice.

În acest studiu, vom arăta cum substanţele asimilate influenţează puternic arhitectura peretelui celular şi, prin urmare, rezistenţa C. albicans la anumiţi factori de stres. Aceste constatări pot avea un impact major asupra comportamentului acestui agent patogen în interiorul gazdei umane şi deci pot fi de importanţă clinică majoră.

Lay summary: Candida albicans and it's sweet tooth

The FINSysB researchers are preparing for the final workshop and conference in Italy in the next two weeks. In today's post, Iryna Bohovych describes where Candida albicans gets it sugar and how it is affected by the availabilty of different sugars. She is working at the University of Aberdeen in Prof. Al Brown's lab and is interested in what role of sugars in an infection.

A sweet way to become stronger: an example from human fungal pathogen Candida albicans

 
There are more than 300,000 known species of fungi, but only a few of them can cause human infections. One of them, Candida albicans, is a relatively harmless organism, which can occupy the skin, oral cavity gastrointestinal tract and genitalia of healthy people. However, this fungus can take and advantage of immune system defects and cause a wide range of affections from mild superficial thrush to fatal systemic infections. There are lots of factors which make C. albicans so effective pathogen; among them are the ability to consume different nutrients (e.g. sugars) and to resist to different stresses.

When C. albicans cells enter the bloodstream, they are attacked by host cells, phagocytes, which cause oxidative stress to fungal cells. Also, in the human they are exposed to glucose in the bloodstream. Thus, we hypothesized that nutrients sensing might influence stress responses. Indeed, in laboratory environment C. albicans cell, exposed to glucose, became more resistant different stresses. Also, it was less sensitive to killing by neutrophils, cells isolated from human donors, when glucose was added. Using different types of modified glucose we have been able to prove that C. albicans cells just need to sense glucose, not necessarily to consume it, in order to become more resistance to oxidative stress. C.albicans, like other yeasts, has 3 distinct mechanisms for glucose sensing, which form a complicated network. We are now investigating the role of major components of this network in the phenomenon of glucose-enhanced oxidative stress resistance.

Сладкий способ стать сильнее: пример патогена человека  Candida albicans

Среди 300 000 известных видов грибов только несколько способны вызывать заболевания человека. В их числе относительно безвредный организм Candida albicans, населяющий кожу, ротовую полость, желудочно-кишечный тракт и половые органы человека. В условиях дефектов иммунной системы этот грибок может вызывать целый ряд заболевания человека, от легкой поверхностной молочницы и до летальных системных инфекций. C. albicans является настолько эффективным патогенном благодаря целому ряду факторов, среди которых способность употреблять разнообразные питательные вещества (например, сахара) и противостоять стрессам.

Когда C. albicans попадает в кровь, ее сразу же атакуют клетки хозяина, фагоциты, которые подвергают клетки грибка оксидативному стрессу. В то же время в организме человека этот микроорганизм сталкивается с глюкозой. Таким образом, у нас возникла гипотеза о влиянии сенсинга (опознания) питательных веществ на ответ на стресс. Действительно, в лабораторных условиях, клетки C. albicans после короткой инкубации с глюкозой ставали более резистентными к разным видам стресса. Также эти клетки были менее чувствительны к уничтожению нейтрофилами, изолированными со здоровых доноров. Использую разные типы модифицированной глюкозы, нам удалось доказать, что для клеток C. albicans необходимо всего лишь определить наличие глюкозы в среде для того, чтобы стать более резистентными к оксидативному стрессу. C. albicans, как и другие дрожжи, имеет 3 разных пути сенсинга глюкозы, объединенные в сложную сеть. Мы пытаемся изучить роль основных компонентов этой сети в феномене повышенной резистентности к оксидативному стрессу в ответ на наличие глюкозы.

Солодкий спосіб стати сильнішим: приклад патогена людини Candida albicans

З-понад 300 000 відомих видів грибів лише кілька можуть викликати захворювання людини. Одним з них є Candida albicans, відносно безпечний організм, що може населяти шкіру, ротову порожнину, шлунково-кишковий тракт та статеві органи здорової людини. Однак за умов порушень роботи імунної системи цей грибок може викликати ряд захворювань, від легкої поверхневої молочниці і до фатальних системних інфекцій. C. albicans є настільки ефективним патогеном за рахунок цілої низки факторів, серед яких є здатність споживати різноманітні поживні речовини (наприклад, цукри) та протистояти стресам.

Коли C. albicans потрапляє в кров, то її одраз ж атакують клітини господаря, фагоцити, що спричинюють оксидативний стрес клітин грибка. В той же час в організмі людини цей мікроорганізм стикається з глюкозою. Таким чином, у нас виникла гіпотеза про вплив сенсингу (впізнання) поживних речовин на відповідь на стрес. Дійсно, в лабораторних умовах, клітини C. albicans після короткої інкубації з глюкозою ставали більш резистентними до різних видів стресу. Також ці ж клітини були менш чутливими до знищення нейтрофілами, ізольованими зі здорових донорів. З використанням різних типів модифікованої глюкози нам вдалося довести, що для клітин C. albicans необхідно лише виявити наявність глюкози в середовищі для того, щоб стати більш опірною до оксидативного стресу. C. albicans, як і інші дріжджі, має 3 окремі шляхи сенсингу глюкози, що об’єднані в складну сітку. Ми намагаємося з’ясувати роль основних компонентів цієї сітки у феномені підвищеної резистентності до оксидативного стресу у відповідь на наявність глюкози.

Lay summary: Clinical relevant stresses and the cell wall

Another day, another lay summary. Today, Alice Sorgo, working at the Universiteit van Amsterdam in the Netherlands. In the group of Dr. Frans Klis she is interested in how Candida albicans copes with medical relevant stresses that it encounters in the patient. This research will lead in the future to better targeting of new antifungals and a more effective therapy regime.

Dynamics of cell wall and secreted proteins of the pathogenic fungus Candida albicans in response to clinically relevant stress conditions

The fungus Candida albicans is living in the majority of the human population usually without having any effect on their health. Sometimes it causes relatively mild superficial infections. Nevertheless, when the host’s immune system is severely weakened, C. albicans can gain access to the bloodstream and spread throughout the whole body. If not detected and properly treated in time a bloodstream infection is able to rapidly kill the patient. Conventional methods for diagnosis take two days, making faster diagnostics necessary. New resistances emerge against the already existing antifungal drugs resistances, hence new antifungal treatments are needed.

The wall proteins and secreted proteins of C. albicans are very dynamic under changing environmental conditions. These proteins play an important role for C. albicans fitness and virulence. They serve fundamental roles, like tissue adhesion and invasion, biofilm formation, nutrient acquisition and defense against the host’s immune system. In the human host C. albicans has to cope with a variety of challenges. It grows in sites where oxygen levels are high, like on the skin, as well in niches where very low oxygen levels are found, such as in the gut. C. albicans is able to acquire iron, which is rarely found in a freely available form in the human body but is essential for its survival. It also adapted to survive in the presence of antifungal drugs and at high temperatures, like during fever.

We are investigating how the cell wall and secreted proteins of C. albicans contribute to the fungus’ survival and virulence under these medically relevant stress conditions. We are applying mass spectrometry to measure qualitative as well as quantitative changes of these proteins that might help C. albicans adapting to these conditions. Our research will improve the understanding of how C. albicans copes with various infection-associated stress conditions as well as how cell wall and secreted protein levels are controlled. Importantly it might lead to the identification of new potential targets for vaccine development and diagnostic markers.

Dynamik der Zellwandproteine und sekretierten Proteine des pathogenen Pilzes Candida albicans als Antwort auf klinisch relevante Stressbedingungen

Candida albicans ist ein Pilz der in den meisten Menschen lebt ohne Einfluss auf deren Gesundheit zu haben. Manchmal kann er jedoch eine oberflächliche Infektion der Schleimhäute verursachen. Bei Patienten deren Immunsystem ernsthaft geschwächt ist kann C. albicans bis in die Blutbahn vordringen und sich im ganzen Körper ausbreiten. Wenn eine solche Infektion nicht rasch diagnostiziert und richtig behandelt wird endet das in den meisten Fällen tödlich für den Patienten. Herkömmliche Diagnosen nehmen zwei Tage in Anspruch, was die Entwicklung schnellerer Methoden notwendig macht. Gegen die kommerziell verfügbaren Antimykotika entwickeln sich immer mehr resistente Pilzstämme, somit ist es notwendig ständig nach neuen Antimykotika and Behandlungsarten zu suchen.

Die Zusammensetzung der Zellwandproteine und sekretierten Proteine ändert sich je nach der Umgebung in der C. albicans sich befindet. Außerdem sind diese Proteine unverzichtbar für Fitness und Virulenz des Pilzes. Sie dienen grundlegenden Funktionen, wie etwa der Anhaftung und Einwanderung in das Gewebe, der Bildung von Biofilmen, der Aufnahme von Nährstoffen und der Verteidigung gegen das Immunsystem des Wirtes. Das Leben in einem Wirt bringt viele Herausforderungen mit sich. C. albicans wächst an sauerstoffreichen Orten, wie etwa der Haut, aber auch an Orten an denen Sauerstoffarmut vorherrscht, wie etwa im Darm. C. albicans ist außerdem in der Lage das für das Überleben notwendige Eisen zu erlangen, obwohl dieses im Wirt kaum frei zugänglich ist. Der Pilz hat sich so weit angepasst, dass es ihm sogar möglich ist in der Gegenwart von Antimykotika und hohen Temperaturen, wie zum Beispiel während eines Fiebers, zu überleben. 

Wir erforschen wie Zellwandproteine und sekretierte Proteine dem Überleben und der Virulenz dieses Pathogens während medizinisch relevanter Stressbedingungen dienen. Mittels Massenspektrometrie messen wir qualitative und quantitative Veränderungen in der Zusammensetzung dieser Proteine, welche dem Pilz bei der Anpassung an diese Bedingungen hilft. Unsere Forschung wird das generelle Verständnis darüber verbessern wie C. albicans verschiedene Stressbedingungen bewältigt und wie Zellwandproteine und sekretierte Proteine kontrolliert werden. Schlussendlich könnten neue Angriffspunkte für die Impfstoffentwicklung und Diagnose von Candida Infektionen ermittelt werden.

Lay summary: Zinc uptake in Candida albicans

In our continuing coverage of our FINSysB film stars, today Dr. Francesco Citiulo.  He is working at the Hans-Knoell-Institute in Jena, Germany in Prof. Hube's group. He is trying to understand how Candida albicans aquires zinc in the host where it is kept scarce.

Characterization of molecular mechanism used by fungal pathogens to uptake Zinc from host cells during the infection

Fungal pathogens are a significant cause of morbidity and mortality and resistance to current antifungals limits the effectiveness of treatment. Targeting the access of the fungus to host nutrients represents an exciting new area of therapeutic development. A variety of metals are important for pathogenic fungi to grow and to establish an infection. For example, iron is known to be sequestered by the host to prevent the growth of pathogens in a process known as nutritional immunity. However, Candida albicans is able to acquire host iron, and the molecular mechanisms underlying this have begun to be unraveled.

Zinc is an important metal for both the host and any invading pathogen. Recently, it has been shown that the natural antimicrobial peptide, calprotectin, is highly expressed in the human body in response to infection and chelates zinc. This points to the possibility of an important role of host zinc for the pathogen to establish an infection.

Using C. albicans as a model, our aim is to characterize the molecular mechanisms that pathogenic fungi use to acquire zinc from the host. By an in silico analysis on the C. albicans secretome we identified multiple Zn binding domains in 35 kD secreted protein , this protein is interestingly highly conserved throughout the fungal kingdom. Using a deletion strain for this protein and other molecular tools, including a gene reporter we have already shown that zinc is important for C. albicans growth and that the 35 kD secreted protein plays a pivotal role in host cell damage via Zn-acquisition.

Therefore, we have begun to uncover the molecular mechanism by which C. albicans acquires Zn from host cells. The future goal will be to fully characterize the molecular bases of the mechanism that C. albicans uses to sequester Zn, useful for growth, from the host. The knowledge obtained from these studies will lay the foundation for the future creation of peptides that could inhibit Zn uptake from the host by pathogenic fungi restricting their ability to establish an infection.

Caratterizzazione dei meccanismi molecolari usati dai funghi patogeni per catturare Zinco dall’ospite durante il processo d’infezione.

I funghi patogeni sono una significativa causa di malattia e mortalità, la resistenza che essi sviluppano agli antifungini limita l’efficacia dei trattamenti odiernamente usati per eradicarne l’infezione. Un’interessante area di ricerca sullo sviluppo di nuove terapie per le infezioni fungine è basata sulla creazione di molecole che impediscono al fungo l’acquisizione di nutrienti dall’ospite. L´accesso ai metalli dell’ospite da parte del fungo è, infatti, uno step molto importante per il processo d’infezione; per esempio il ferro è sequestrato dall’ospite per prevenire la crescita del patogeno, in un processo conosciuto come immunità nutrizionale. Candida albicans ha sviluppato meccanismi per circonvenire questo processo e acquisire ferro dall’ospite; le basi molecolari di questo meccanismo sono in corso di studio.

Lo zinco è un metallo importante sia per l’ospite sia per il patogeno. Recentemente è stato dimostrato che la calprotettina, un peptide a funzione antibiotica prodotto dall’uomo, è altamente espressa durante un infezione microbica o fungina ed essa sequestra lo zinco. Questo mette in evidenza la possibilità che l’accesso allo zinco dell’ospite da parte del patogeno giochi un ruolo chiave nell’infezione.

Usando C. albicans come organismo modello, il nostro scopo è quello di caratterizzare i meccanismi molecolari che i funghi patogeni usano per acquisire lo zinco dall’ospite. Mediante un’analisi in silico del secretoma di C. albicans abbiamo identificato una proteina di 35kD, con omologhi in altri funghi patogeni, che contiene multipli siti di legame per lo zinco. Usando un ceppo di C. albicans deleto per questa proteina e altri tool molecolari incluso un gene reporter, abbiamo dimostrato che lo zinco è essenziale per la crescita di C. albicans e che la proteina 35kD ha un ruolo chiave nel processo d’infezione, rendendo lo zinco dell’ospite accessibile al fungo.

Il nostro futuro goal è quello di caratterizzare le basi molecolari di questo meccanismo che permette a C. albicans di sequestrare lo zinco dell’ospite. Le conoscenze derivanti da questo studio saranno le basi per la sperimentazione di nuovi composti che consentiranno di bloccare l’accesso di varie specie di funghi patogeni allo zinco dell’ospite limitando così la loro capacità di creare un infezione.

Lay summary: Antifungal drug development

As promised, this week it is Kate's turn to summarize her work. Kate is working with F2G Ltd. in Manchester to develop antifungal drugs based on essential genes.

Investigating new drug leads for fungal infections



Aspergillus fumigatus and Candida albicans are fungal species that can cause serious, often fatal, disease in the vulnerable, especially cancer and AIDS patients. Current medicines to treat these infections have many drawbacks including serious side effects and limited effectiveness. This project aims to find new leads in the fight against these kinds of infection. A molecular approach has been used to find proteins that are essential for the survival of both A. fumigatus and C. albicans. The theory is that if these essential proteins are disabled the fungal cells will die. Therefore it is hoped that finding chemicals that disrupt these proteins will provide chemical leads for antifungal drug discovery.

To date 3 proteins have been identified that are essential for the survival of both types of fungi. The 3 essential proteins have been made in large quantities using bacterial cells and screens are being developed to test for activity of the protein. Measuring activity of the protein in the presence of a library of small molecule compounds will enable identification of chemical inhibitors. Chemicals that disrupt both A. fumigatus and C. albicans proteins will be analysed in further detail to identify the best starting points for drug design. It is important that a new drug has the ability to enter cells in order to disrupt the protein inside the cell and cause cell death. This will be tested by mixing the chemicals of interest with whole cells to see if they can enter and then kill the cells. It is also important that the chemicals are not toxic to human cells. One way of testing this is to grow mammalian cells in a test tube in the presence of the chemicals and see if the cells stay alive. Other considerations are how easily the drug compounds can be manufactured, costs and intellectual property surrounding the work.

This study should result in new broad-spectrum antifungal drug leads to fight two of the most medically important fungi. Newer, effective antifungal medicines will result in huge benefits to human health.

Scientific collaborations

Science doesn't happen in a vaccum. Despite the fact that scientist are usually depicted as recluses that spend the majority of their days (and nights) in the lab chasing new ideas and doing experiments, scientists are actually quite communicative. You could almost refer to them as social butterflies (in their field at least). The reason for that is quite simple. Specialization is the key not only in science but also in real life. Or, in other words, would you preferred to have your taxes done by an accountant or your butcher?

Most scientists are specialist in a defined field so that they can focus on solving a particular problem. The problem with too much specialization is that you lose track of the big picture and neglect to integrate your research with other results. Collaborations are the remedy to this problem. If scientists encounters a phenomenon that can not fully describe by their methods and experiments in which they are specialized, they turn to other experts in their field that have access to other methods, instruments or area of expertise. Of course, as a young researcher you don't have a large network available to you but usually you are introduced by your supervisor, make contact after talks or poster sessions at conferences or just have a drink with the people you want to talk to at the hotel bar. Scientists are a very open group of people because we all share the same idealism about research and progress. The pictures in this blog post show the scientific collaborations in the World and Europe from 2005 to 2009 and are courtesy of Oliver Beauchesne and flowing data.com. Also check out the zoomable worldmap here.

Most scientific papers that are written are not the product of a single group of researchers in one lab but by a number of groups that all contribute. These contacts are mainly made during scientific conferences or in research networks (like the european FINSysB network). By pooling their resources researchers are able to produce more and better research than they could if they were working alone. The exchange of ideas is at the very core of science right next to the scientific method and peer review. So the next time you see a single scientist saving the world in his small lab without ever talking to anyone in a movie or on television, you know how likely that is...

Playing with DNA can be fun!

Happy New Year to everyone and although it is a little late (I know, I know) I thought we start it with a play section again. I am sure there was an uproar among all the geneticists that I choose a protein game for the first play post and not something with DNA. Also, the last game was a bit on the complicated side so today I want to introduce you to Phylo.

Phylo is a small flash game written by researchers from McGill University. They gave an important tool of genetic scientists, the so called Multiple Sequence Alignments, a bit more playful note. Multiple Sequence Alignments are used to see how similiar sequences from different species are and are therefore used to construct a tree of life starting from the origin of life. By seeing how similar sequences are, the relationship of species is revealed and how on species evolved out of another.



Since DNA is only composed of the four bases (Adenine, Cytosine, Guanine and Thymidine), Phylo replaces these building blocks by colored bricks. Your task is now to align two or more sequences to each other in that way that gaps in the sequence are minimized and a maximum of bricks of the same color are aligned. The program automatically scores you against a target value.

Normally this is done by computers which are good for a random aligning brute force approach but the human mind is a master in pattern recognition. Sometimes people can score higher than the computer just by intuition and a general feeling of what looks right. So to avoid spending an ungodly amount of money, they just harvest your free brainpower when you are taking a break and just wanna play something. So give it a try and see if you can help science in your lunch break.

How YOU can help science by solving puzzles

The last few posts were mainly focused on concepts in science but today I just want to let everyone know of an easy way of helping biological science. The folding and conformation of proteins is essential for their function. From the DNA sequence, we can translate out of which amino acids the protein is made up and in which order they have to go. But the final structure is much more complicated to understand because a larger number of chemical bonds and interactions have to be take into account.

The program Foldit is a distributed computing application (like SETI@home where unused processing time of your computer is donated to sorting through radiotelescope data.) The difference between SETI@home and Foldit is that Foldit is looking to the smaller structure and therefore inward instead of outward. Foldit tries to simulate how a protein will fold when it is finished. The computer time you donate will be used to calculate the possible and impossible conformations for the protein.

Even better, you can even interact! Foldit is not a passive activity but fully interactive. because they are also trying to see if humans can improve computer predictions. Each protein is given to you first in an unfolded version (much like the translated product coming from the ribosomes). With a few tutorials and tools you are already able to fold proteins in their proper and most stable form. The picture below shows you the beginning of protein puzzle 48 (taken from Fold.it, links below).

The goal now is to fold it into the correct conformation as seen below.

Try it for yourself and see if you like it. Maybe next time instead of solving a crossword puzzle or doing a Sudoku, try folding some proteins and help science!

Koch's Postulates

In my last post I was describing how scientists use the scientific method to keep their research objective. One of the best examples of applying the scientific method are Koch's Postulates. Robert Koch (1843-1910, left) was a german physician who was interested in how diseases are spread. He is considered the founder of modern microbiology and bacteriology together with his contemporary, Louis Pasteur (1822-1895, right).

In the course of his career, he developed countless microbial techniques that are still in use today. The Petri dish is named after his assistant. He identified the causative agents of Tuberculosis (Mycobacterium tuberculosis), Anthrax (Bacillus anthracis) and Cholera (Vibrio cholera). This earned him the Nobel prize for medicine in 1905.

One of his greatest contributions to microbiology was the formulation of the four Postulates that now carry his name. The postulates are step wise, each postulate based on the previous finding.
In order to establish that an organism causes a disease the following requirements have to be fullfilled:

Step 1: Association- The organism and the disease are observed together consistently.

Step 2: Isolation - The organism can be isolated from the diseased.

Step 3: Inoculation - The isolated organism causes the disease in a healthy individuum.

Step 4: Re-isolation - The organism can be re-isolated from the infected individuum.

Now look at each of these steps carefully and think about what they require you to do. Did you notice it? Between each of the steps the principles of the scientific method are applied. Here is a more graphic representation of the application of Koch's Postulates.

By putting clearly defined rules for what defines a disease causing organism (today referred to as a pathogenic organism or just pathogen), Koch made a major contribution to the then raging discussion about the cause and origin of diseases.

Before Kochs discovery of the Cholera bacterium, there was a heated discussion between the Contagionists and the Anticontagionists. The Anticontagionists (Max von Pettenkoffer was one of them, see also this post) argued that in their theory human-to-human transmission was only a very minor component. They were strong opponents of quarantine and disinfection because it inhibited trade and was less effective than local solutions like improved sanitation. You can read more about it here.

Koch's Postulates proved that transmissibility played an important role in epidemics and quarantines and disinfection was indeed a suitable method to counter both. In the end, everyone benefited from the discussion because it improved both local and global safety against infectious diseases. Getting scientists to agree to something is quite difficult but using the right arguments derived from proper use of the scientific method and you have a good chance of succeeding.

Next week I will write about the central dogma of molecular biology and why it is not so dogmatic anymore.

The scientific method

In my previous post I was talking about the difficulty that scientists face to keep their research objective and unbiased. Luckily, smarter people than me have developed a basic set of concepts that help do that. All these concepts are mainly based on the Aristotelian laws of logic from the third century BC. Most of the ideas that define the scientific method nowadays are already described there. The scientific method is at the heart of science as a set of rules to make research as objective as possible. It is usually described in four basic steps.

Step 1: Observation and description of a phenomenon or group of phenomena.

Step 2: Formulation of a hypothesis to explain the phenomena.

Step 3: Use of the hypothesis to predict the existence of other phenomena, or to predict quantitatively the results of new observations.

Step 4: Performance of experimental tests of the predictions by several independent researchers and properly performed experiments.

Actually, people use these steps almost instinctively to predict cause and effect and adapt accordingly. For example, when you wake up in the morning, you look out of the window and see people on the street in cold weather clothing (Step 1, observation). Your hypothesis (Step 2) is that people are wearing warm clothes because it is cold outside (Step 3, prediction). To test your prediction you open a window or look at a thermometer (Step 4, Experiment). Usually the laymen abstain from enlisting independent researchers to do control experiments.

The scientific method has been refined over the centuries but the core of it is still untouched. The setup that is usually used as a checklist for adherence to the scientific method is the following:

1. Define the question
2. Gather information and resources (observe)
3. Form hypothesis
4. Perform experiment and collect data
5. Analyze data
6. Interpret data and draw conclusions serving as a starting point for new hypothesis
7. Publish results
8. Retest (frequently done by other scientists)

Notice point 6 which clearly shows that you normally refine your hypothesis based on the outcome of your first results. Most hypotheses defined by scientists continuously cycle between step 3 and 6 before they are ever published. The picture below describes the usual approach.

It is also important to note, that the scientific method doesn’t allow the absolute verification of a hypothesis. Einstein himself said: "No amount of experimentation can ever prove me right; a single experiment can prove me wrong." Especially physicists have a tendency to postulate an unknown factor, like the Higgs-Boson, to resolve issues with current theories. The current interest at the large colliders in Switzerland (Large Hadron Collider, CERN) and the US (Tevatron, Fermilab) is to experimentally proof whether or not the Higgs-Boson actually exists and has the properties that are required to make the theory behind it work.

If the Higgs-Boson could not be experimentally proven in the predicted range, most theoretical models of physics would have to be reexamined. I think that makes it slightly more understandable why there is so much money going into this kind of research because entirely rethinking physics sounds like a huge headache to me.

You can easily test what I said about the instinctive use of the scientific method. Just watch yourself and observe how your brain works and you draw conclusions about your environment. Or ask people how they arrived at the conclusion that it won’t rain today. But don’t let them get away with: “It never rains when I have an umbrella with me.” Maybe you can disprove that to them using the scientific method.

Have a nice weekend and keep on thinking!

Personal opinion and bias in science

In my last post I was writing about how scientists are constantly looking for the big picture and more pieces of the puzzle. But how do we do that? What tools and techniques do we use? In the future we will describe specific techniques like imaging or mass spectrometry in this blog. But for now I would like to give a short introduction into the theoretical groundwork that every scientist uses. I hope that by explaining basic concepts in science it will help you to understand (and reality check) some or most of the news items that are published in non-scientific journals.

I often read something in the news about science that looks like a brilliant breakthrough and the journalist tries to suggest immediate applicability. In most cases it is just not as simple as that (especially not if it is written in the tabloids). Just because something was tested and worked in an animal model does not mean that it will work in exactly the same way in humans or soon. Sometimes it even has detrimental effects (London drug trial incident 2006). So I would like to explain a few basic concepts in science in my next posts. But first I want to highlight some problems that scientists face not only from without but also from within.

A major problem in science was (is?) the removal of personal opinion and bias. At some point people can get so invested in their idea that any other theory, observation or result must be wrong and can be explained away or faulted for some reason in some way. One of my favorite examples is the feud between Robert Koch and Max von Pettenkofer about the transmission of Cholera. Both brilliant scientists in their own right, they could never agree if Cholera, as it had been shown by Koch, can be transmitted from person to person and cause disease. This is one of Koch’s postulates, which I will address in a later post. Despite experimental evidence, Pettenkofer, aged 74, drank a pure culture of Vibrio cholerae, to show his opponent once and for all. He survived and just contracted light diarrhea and abdominal pain (he probably had contracted Cholera earlier in his life and this led to a lighter course of disease this time around). Pettenkofer saw that as irrefutable evidence that Koch was wrong.

Today we know differently but despite the fact that Pettenkofer was wrong in this instance he still was a brilliant scientist and one of the most important hygienists. The history of science is full of stories of personal animosity, spite and (now) hilariously wrong explanations. So besides being curious (as I stated in my last post), scientist also need to be critical. And first and foremost critical of their own work. If you can’t convince yourself based on your data how do you expect to convince others? Being impartial and objective is hard for everyone, but as a scientist it is even more important to not get too attached to your ideas and theories. Because they are just that until you have proof and other scientists can reproduce your results. I will also explain and discuss the peer review system in place for scientific journals which is trying to safeguard science against fraud.

But I think it is also very important that scientists adhere as strictly as possible to the scientific method, which I will discuss in my next post.

Clemens J. Heilmann

P.s.: Opinions, suggestions, theories, comments? Please let’s hear them below.

Motivation to do science

First of all, I would like to welcome every reader to our blog. We hope we can interest you at least a little in science and make it more understandable why people in the prime of their live like to spend time day, night and weekends in labs and in front of computers instead of partying and just having a good time. But actually, to be honest we do have a good time. And here is why…

The way people get into science is very diverse but we all share on basic trait that a scientist can’t do without, curiosity. Curiosity killed the cat but luckily the cat has nine lives. This analogy is actually truer than you would think. One of the first things you have to learn to deal with in science is failure. And frustration. So if you are not curious or enthusiastic about science you probably won’t make it. One of the things I think makes a good scientist is the ability to ask the question everyone in the room is thinking about but no one dares to voice. Call that curiosity for lack of a better word.

Children are the quintessential scientists. Full of enthusiasm and an insatiable curiosity for the world that surrounds them, they go forth and explore their world. And this curiosity is the hardest thing to conserve when you get older. Other, more important things start to enter the equation of what makes our life successful (family, money, power). So science is also escapism in a way. Because despite its rigorous rules for publication and proper research, most scientists are whimsical, funny and most importantly, curious. Basically, scientists didn’t really want to grow up but still made something out of their natural strengths.

But why do we accept to bear the common failures and frustrations of daily lab work? I think the reason is that we want to understand and we love it when all parts of a puzzle come together and form a stunning no picture of the world that surrounds us. And we are the first to have a glimpse. This glimmer of knowledge is what we are after. If you look into the past, you will always see that science is the great door opener to improving the human condition. Curing numerous diseases, developing clean, sustainable sources of electricity, increasing the quality of life for everyone on this planet are some of the key challenges for humanity. Science can solve or at least help to solve most of them.

Most scientists are not Marie Curie, Robert Koch, Louis Pasteur or Leonardo da Vinci. But we all strive for that flash of genius and that brilliant deduction about the world that surrounds us. Whenever we understand something, we want more. And we never give up. We always look for the next puzzle to solve or when we solve one, we only see it as a small part of an even bigger picture.

Clemens Heilmann