February 22, 2012

The University of Aberdeen Fungal Group was awarded £5.1M to tackle fungal infections



The University of Aberdeen Fungal Group has been a awarded a Wellcome Trust Strategic Award to lead a  UK collaboration to bring fungal science closer to treating infection.

The new Medical Mycology and Fungal Immunology Consortium aims to train a new generation of scientists and clinicians but also to promote greater public awareness of fungal infections.

Professor Al Brown (right), a chair in Microbiology at the University of Aberdeen and Co-Director of this Consortium, also coordinates the FINSysB Network. 

Read more about the award on BBC or the University website.

October 02, 2011

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.

September 30, 2011

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.

September 28, 2011

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.

September 27, 2011

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.

September 25, 2011

The flash game Pandemic 2 let's YOU be the infectious disease!

To effectively fight any enemy, you have to understand it first. This is one of the most basic principles when you are trying to prevent infectious diseases. But every disease and its causative agent are different. Modes of infection, transmission, outside host survivability, symptoms and especially the underlying molecular biology is hard to pin down and explain with only one model. But there are still a couple of basic principles that are very nicely illustrated in the game Pandemic 2 below.



































In this game you take on the role of an infectious disease. You can choose between being a virus, bacteria or a parasite (no fungi though, sorry). Then you are directly thrown on a world map. Congratulations, you just infected your first human in a random region of the world. Each region is characterized by a set of variables and measures taken by the government to control your disease. Many regions have ship yards and airports that are instrumental in spreading the infection. Also, national water supplies and hospitals are important factors.

While randomly occuring natural disasters helps you, governments will  hinder you by taking increasingly drastic measures.

The effectiveness of your disease depends basically on three variables. Lethality does exactly what it says on the box, a measure of how fast your disease kills an average human. Infectivity tells you how well the disease is transmitted and spreads through a population. Finally, Visibility determines how fast authorities react to your disease by closing airports, harbors, public transport and so on. For example, in the games term, the Ebola virus would have a high lethality, a medium infectivity but it would be very visible while HIV/AIDS would have a low visibility with medium infectivity and lethality. You can increase these variables by buying new traits with evolution points that are awarded for meeting certain milestones (number of infected, spread to a new region etc.).

Buying new symptoms, resistances and ways of transmission will affect the three key variables in different ways.

The game is relatively straight forward and has a good tutorial so just give it a try and see how you do. But it makes you realize how easily diseases can develop and spread. You also notice how hard the job of national and international health organizations like the WHO is to actually contain and combat a disease. So next time someone asks you what you did in your coffee break, just say you wiped out mankind. But remember, Madagaskar is always the hardest place to get. Enjoy!



July 26, 2011

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.

July 15, 2011

FINSysB video

This week we have something very special for you. During our last workshops in Berlin and Jena a video for our public dissemination video was shot. With Kate, Neelam and Francesco as our stars, the video gives an overview of what we do and why we do it. Have a look and let us know what you think. Next week, Kate will explain more about her project in her lay summary. Stay tuned and enjoy.


June 15, 2011

Lay summary: Candida albicans and cells of the immune system

Today's lay summary is about how the immune system is dealing with Candida albicans cells if they are encountered. Pedro Miramón is working at the HKI in Jena under the supervision of Professor Bernhard Hube. He is trying to understand the interplay between Candida albicans and specific immune cells, called neutrophils. His summary is available in english, spanish and german. Incidently, it is also Pedro's birthday to day so happy Birthday and keep up the good work!






Understanding the response of the human fungal pathogen Candida albicans to the attack by immune cells




Candida albicans is a fungus commonly associated with humans without causing any harm. The reason this fungus is usually harmless is because immune cells constantly patrol the sites in the body where the fungus lives; for example, the oral cavity or the gut. However, under certain circumstances, C. albicans is able to surpass the vigilance of the immune system, causing a variety of diseases ranging from superficial non-lethal manifestations to life-threatening deep-seated infections.


The purpose of this project is to understand how C. albicans is recognised and eliminated from the host. To this end, we are studying how the cells of the immune system fight against the pathogen. The key players involved in eliminating not only fungal, but pathogens in general, are phagocytes – specialised cells from the immune system which engulf and kill microorganisms. We know that C. albicans responds differently to the several kinds of cells found in blood. The cells that evoke the most dramatic response from the fungus are the so called neutrophils, cells of the immune system that play a major role in inflammation and the clearance of pathogens.


We aim to identify components of the fungal cell (proteins or enzymatic activities) that are involved in the response towards the attack by neutrophils, in order to better understand the response of the fungus and the strategies it uses to overcome and survive attack by neutrophils.


We have found that C. albicans responds in a different manner depending on whether it is inside or only touching the neutrophils. For instance, inside the neutrophils, we have observed that C. albicans produces proteins that neutralise potent oxidants that could kill the fungus. Some of these proteins are produced even before the fungus comes in contact with the neutrophil, preparing itself to encounter the oxidants and hence, survive. When the fungus is unable to produce these proteins, its survival is decreased in the presence of neutrophils. We have also observed that the fungus changes its metabolism to adapt to the nutrient-deficient environment inside the neutrophil.


Understanding the response of the fungus when confronted with phagocytes will allow us to identify the most important steps that lead to a proper response in order to contain the growth and dissemination of this opportunistic pathogen.


Entendiendo la respuesta del patógeno humano Candida albicans al ataque de células del sistema inmune.



Candida albicans es un hongo comúnmente asociado a los humanos sin causar daño alguno. La razón por la cual este hongo es generalmente inofensivo es porque las células del sistema inmune vigilan constantemente los sitios del cuerpo donde el hongo vive, por ejemplo, la cavidad oral o el intestino.

Sin embargo, bajo ciertas circunstancias, C. albicans es capaz de evadir la vigilancia del sistema inmune, provocando una variedad de enfermedades que van desde manifestaciones superficiales no letales hasta infectiones profundas que ponen en riesgo la vida.


El objetivo de este proyecto es entender cómo C. albicans es reconocida y eliminada del huesped. Para este fin estamos estudiando cómo las células del sistema inmune luchan contra el patógeno. Los principales actores involucrados en la eliminación de patógenos en general, no solo hongos, son los fagocitos – células especializadas del sistema inmune, encargadas de atrapar y matar microorganismos. Sabemos que C. albicans responde diferencialmente a los ditintos tipos de células que se encuentran en la sangre. El tipo de células que induce la respuesta más dramática por parte del hongo son los llamados neutrófilos, células del sistema inmune que juegan un papel muy importante durante procesos inflamatorios y durante la eliminación de patógenos.


Nuestro objetivo es identificar componentes del hongo (proteínas o actividades enzimáticas) involucrados en la respuesta hacia el ataque de los neutrófilos para comprender mejor esta respuesta, así como las estrategias empleadas para superar y sobrevivir al ataque de los neutrófilos.


Hemos encontrado que C. albicans responde de formas distintas dependiendo de si se encuentra dentro o sólo en contacto con los neutrófilos. Por ejemplo, dentro de los neutrófilos, hemos observado que C. albicans produce proteínas que neutralizan potentes oxidantes capaces de matar al hongo. Algunas de esta proteínas son producidas incluso antes de que el hongo entre en contacto con el neutrófilo, preparándose para encontrarse con oxidantes y, de esta manera, sobrevivir. Cuando el hongo es incapaz de producir esta proteínas, su sobrevivencia está disminuida en presencia de los neutrófilos. Hemos observado también que el hongo cambia su metabolismo para adaptarse a las condiciones deficientes en nutrientes dentro del neutrófilo.


Al comprender la respuesta del hongo cuando se enfrenta a los fagocitos, podremos identificar los eventos clave que llevan a una respuesta correcta para contener el crecimiento y la diseminación de este patógeno oportunista.



Wie der humanpathogene Pilz Candida albicans die Attacken des Immunsystems übersteht



Candida albicans ist ein Hefepilz, der häufig als harmloser Besiedler der menschlichen Haut und Schleimhäute vorkommt und unter normalen Umständen keinerlei gesundheitliche Schäden verursacht. In der Mundhöhle oder im Darm verhindern die Zellen des menschlichen Immunsystems effektiv, dass der Pilz Schaden anrichtet. Unter bestimmten Bedingungen kann C. albicans aber der Kontrolle des Immunsystems entgehen und dann verschiedenste Erkrankungen hervorrufen. Diese reichen von oberflächlichen und vergleichsweise harmlosen Verlaufsformen bis hin zu lebensbedrohlichen, systemischen Infektionen, die den ganzen Körper und verschiedene Organe betreffen.


In diesem Projekt soll daher versucht werden, die Erkennung und die Bekämpfung von C. albicans durch den Wirt besser zu verstehen. Wir untersuchen dazu, welche Mechanismen die Zellen des Immunsystems entwickelt haben, um C. albicans zu kontrollieren. Besonders wichtig sind dabei die sogenannten Phagozyten, Fresszellen des angeborenen Immunsystems, die Mikroorganismen in sich aufnehmen und dann zerstören können. Sie sind auch die ersten Immunzellen, mit denen C. albicans (und auch andere Krankheitserreger) im Wirt in Kontakt kommen sobald der Pilz in Gewebe eindringt. Dabei reagiert C. albicans in unterschiedlicher Weise auf die einzelnen Zelltypen der Immunabwehr. Besonders die neutrophilen Granulozyten, die an Entzündungsprozessen und an der Beseitigung von Pathogenen beteiligt sind, führen zu einer deutlichen Antwort des Pilzes.


Wir wollen deshalb Bestandteile der Pilzzelle (insbesondere Proteine und aktive Enzyme) identifizieren, die an der Interaktion von C. albicans mit neutrophilen Granulozyten beteiligt sind. Das soll uns ermöglichen, die Reaktionen des Pilzes besser zu verstehen – und damit seine Strategien, den Kontakt mit Immunzellen zu überleben.


Wir konnten schon zeigen, dass C. albicans – je nachdem, ob sich der Pilz im Inneren der Neutrophilen befindet oder nur an deren Oberfläche – unterschiedlich reagiert. Beispielsweise haben wir beobachten können, dass C. albicans innerhalb der Immunzellen ein Protein bildet, das Oxidantien unschädlich macht, die sonst den Pilz abtöten können. Einige dieser Proteine werden vom Pilz sogar schon gebildet, bevor er überhaupt mit Neutrophilen in Kontakt kommt. So kann er sich vor oxidativem Stress schützen und sein Überleben sichern. Ohne diese Proteine überleben deutlich weniger C. albicans-Zellen den Kontakt mit neutrophilen Granulozyten. Außerdem haben wir beobachten können, dass C. albicans seinen Stoffwechsel an die nährstoffarme Umgebung innerhalb der Neutrophilen anpassen kann.


In Zukunft wollen wir so die Reaktion von C. albicans auf Immunzellen besser verstehen und dadurch diejenigen Mechanismen identifizieren, die das Wachstum und die Ausbreitung des Pilzes im Körper ermöglichen.



Pedro Miramón

April 13, 2011

Lay summary: Wall proteins of Candida albicans

Today will be the launch of a series of posts that will focus on the particular work of individual scientists of the FINSysB network. We are trying to describe our work as easy as possible for the lay men to understand and as a special treat the summaries will be translated in the researcher's mother tongue below. We hope you enjoy reading the summaries as much as we enjoy doing the research.




Wall proteins of Candida albicans as new targets for diagnostics and treatment of systemic fungal infections



Patients with a weakened immune system and especially in intensive care units are increasingly contracting fungal infections. These infections are often life-threatening. Candida albicans is the most common of these infectious fungi. Depending on how suppressed the immune response is, this can lead to unpleasant infections of the skin and mucosa, but also invasive, blood stream infections. Usually, almost half of these infections are fatal within a week, highlighting the need for faster diagnostics and better preventative measures, i.e. a vaccine.


The first contact with the host cell is established by proteins on the wall of the fungus. They have been shown to play a crucial role in both infections and resistance to the immune system. We are particularly interested in this layer of proteins that is directly attached to the cell wall of the fungus or is released into the environment. Environment specific changes are important for C. albicans to thrive in different niches in the host during an infection. We also are interested in how the predominant growth form change in C. albicans, from spheric yeast cells to elongated hyphal cells, affect the proteins on the wall.


The goals of my project are three fold. Firstly, we want to increase the basic understanding of these attached wall proteins and the secreted proteins and how their composition and abundance changes in infection related conditions. To this end, we want to quantify the wall proteins using mass spectrometry. Secondly, we want to develop methods that allow faster diagnostics based on these secreted proteins that are abundant in many growth conditions. Thirdly, we want to identify targets for the development of a vaccine against C. albicans. To identify parts of the proteins that are suitable for vaccine development, we will use prediction algorithms to assess their ability to elicit an immune response. Using these results we will assemble and test a vaccine protein that is comprised of the most immune-stimulating peptides of these proteins.




Zellwandproteine als Ziele für neue Diagnose- und Therapieansätze gegen systemische Pilzinfektionen durch Candida albicans


Patienten mit geschwächtem Immunsystem und speziell auf Intensivstationen erkranken immer häufiger an Pilzinfektionen. Diese Infektionen sind oft lebensbedrohlich. Candida albicans ist der am häufigsten vorkommende Erreger von Pilzerkrankungen. Abhängig vom Immunstatus der Patienten können unangenehme, aber relativ harmlose Infektionen der Haut und Schleimhäute, aber auch zu invasive, lebensbedrohliche Blutbahninfektionen auftreten. Üblicherweise verlaufen fast die Hälfte aller Blutstrominfektionen bei nicht rechtzeitiger Behandlung innerhalb einer Woche tödlich. Diese Tatsache unterstreicht die Notwendigkeit zur Entwicklung neuer und schnellerer Diagnoseverfahren und besseren Präventionsstrategien, zum Beispiel durch die Entwicklung eines Impfstoffes.


Der Erstkontakt zur Wirtszelle wird durch Proteine auf der Zellwand des Pilzes etabliert. Es wurde bereits gezeigt dass, diese Proteine eine essentielle Rolle beim Widerstand von C. albicans gegen das Immunsystem und bei Infektionen spielen. Unserer besonderes Interesse gilt hierbei jenen Proteinen, welche direkt an die Zellwand gebunden sind oder in die Umgebung abgegeben werden. Umgebungsbedingte Veränderungen dieser Proteine sind wichtig für C. albicans um in den verschiedensten Nischen des Wirts während einer Infektion zu florieren. Weiterhin sind wir daran interessiert, wie die wichtigste Veränderung in der Wuchsform, von runden Hefezellen zu verlängerten Hyphen, die Proteine der Zellwand beeinflusst.


Es gibt drei Hauptziele meines Projekts. Erstens, wollen wir die gebundenen Zellwandproteine und die sekretierten Proteine sowie Änderungen in ihrer Zusammensetzung und Menge unter Infektionsbedingungen grundlegend besser verstehen. Zu diesem Zweck setzen wir Massenspektrometrie ein um die Zellwandproteinmenge zu bestimmen. Zweitens, wollen wir basierend auf sekretierten Proteinen, die in vielen Wachstumsbedingungen gehäuft vorkommen, diagnostische Marker und Methoden entwickeln. Drittens, wollen wir vielversprechende Ziele zur Impfstoffentwicklung identifizieren. Mithilfe von Prognosealgorhythmen, bestimmen wir Teile dieser Proteine die in der Lage sind eine starke Immunreaktion auszulösen. Basierend auf diesen Ergebnissen stellen wir ein Impfstoffprotein zusammen, das aus den am immune-stimulierendsten Teilen dieser Proteine besteht, um es anschliessend zu testen.

March 04, 2011

Databases: The Facebook of the Molecules involved in Life

The objective of biomedical scientists is to discover new medicines to cure diseases and to be able to detect them with new techniques which are more rapid, cheap and precise. In this field of research an enormous amount of information is generated with very powerful equipments (such as the ones used for the HUMAN GENOME PROJECT), producing huge files containing the sequence of nucleic acids (DNA, RNA) and protein sequences, protein 3D structures, and so on. So, where can we store all of this information? And how can we access them quickly? Where can we read scientific articles without going to the local library? The answer to all of these questions is the same: databases.

The databases are mainly maintained by big research associations such as EBI (the European Bioinformatics Institute) which is European or the NCBI (National Center for biotechnology information) which is American. As it was mentioned previously in our Scientific Collaborations article, the interaction between different organisms allows this to be possible.

In the NCBI database you can explore the gene region (literally walking among the chromosomes , as if you were using Google Maps), see the variations among people, check the protein database, You can also find PubMed, the bibliographic database; GenBank, the nucleotide sequence database; and the BLAST algorithm for sequence comparison, and so on. Similar results can be found in the Ensembl database.
If you are interested in proteins, you can check out the uniprot/swissprot database, where you can find biological information, the secondary structure of the protein (based on real-life experiments), the sequence of the protein and the bibliography. And even more interestingly, you can check the 3D structure of the proteins (based on real-life experiments as well) in the Protein Data Bank, you can find related information of the protein, bibliographic references, and the most exciting part, you can play with the Jmol viewer, moving the protein, and if you have the right pair of glasses, you can watch it in real 3D (yes, like in Avatar).

And exactly as on Facebook, you can check the “Friends” list of the molecule of interest, which could be the protein coded by this gene, related publications, gene ontology (gene and gene product information in several species), and so on, because all of this information is interconnected. The swissprot database is famous for having the links well up-to-dated. Moreover, you can find the “Photos” of the molecule of interest. 

Before spending a lot of time and money in crazy experiments you can take a look on this databases to see if somebody else did the same experiment on the same molecule before or in a similar one which you can transfer information from. The best part is that if you don't know how to use these tools you can just click on the tutorial link and they have even videos where you can learn how to play with them! Scientists use these tools everyday in the lab before designing an experiment or when analyzing  results, and even more, bioinformaticians (nerdy scientists than only use computers for their research) can even publish articles only by analyzing the information of this databases and using other programs to generate predictions, models or deep analysis of this information.

To summarize, databases are a user-friendly and open access way to obtain biologically relevant information which is used worldwide in research institutes, hospitals, industries and universities.

Diana Rosentul

February 25, 2011

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...

February 11, 2011

Paul Stamets on 6 ways mushrooms can save the world

An interesting yet lively talk from TED - Paul Stamets believes that mushrooms can save our lives, restore our ecosystems and "terraform other worlds in our galaxy by sowing a mix of fungal spores and other seeds to create an ecological footprint on a new planet"

January 31, 2011

Let's talk about Candida albicans!

After starting this blog with a couple of posts about scientific concepts and a few ways to play with biological information let me tell you a bit more about our research interest today. Candida albicans is the core focus of the european FINSysB research network. It is comprised of eleven internationally renowned labs from all over Europe as well as an industrial partner, F2G Ltd. ,for quick translation into the clinic. Usually, most research papers in our field start with a statement such as: "C. albicans is ordinarily found as a commensal yeast colonizing the human gastrointestinal tract."; "The opportunistic fungal pathogen Candida albicans is a leading cause of death in patients with fungal infections." or "Candida albicans is commonly found as a benign commensal in many warm-blooded animals. In humans it mainly resides on the skin and on mucosal surfaces without causing significant harm to the host."

But what does this actually tell you. Not a lot I guess. Basically, there is no reason to be afraid of Candida albicans if you are healthy and your immune system is in good shape. And even if not you shouldn't be alarmed because in most cases C. albicans is kept in check by the immune system. Some studies say that more than 80% of all humans carry Candida albicans on their mucosal surfaces and the gut. Most cases of fungal infections are either oral or vaginal thrush which are easily treatable by a capable physician and are unpleasant but not deadly.
The picture changes when C. albicans penetrates into the blood stream and/or the immune system is severely compromised as in ICU patients after major surgery or HIV patients. Here the mortality is going up to 40%, mainly because diagnostics are not fast enough and there are not enough effective antifungals available. The main problem here is that the fungal infection quickly disseminates to other organs, especially the kidneys, and destroys the tissue. In addition, in recent times Candida albicans is developing resistances to the few effective antifungals we have and evades treatment that way.
So the FINSysB consortium has several goals in which we hope to help treating clinicians as well as researchers in understanding both the inner workings of C. albicans as well as new treatment options. For that we defined four basic research areas: The "Fungal Armoury" is all about finding out how C. albicans is able to attack our cells and penetrate healthy tissue. Our body defends itself with "Defensive Shields"that kill of the fungus and prevent the infection from spreading. This battle is quite dynamic and a back and forth on the "Key Battlefields", mainly the surface of both C. albicans and our cells. Finally, we want to help to "Defeat the Enemy" by developing faster diagnostic methods, effective antifungals and ultimately a vaccine.
So have a look at our website, read about us in the European parliament magazine (page 78) or just comment if you have questions. But read our disclaimer first to avoid disappointment.

January 16, 2011

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.


November 25, 2010

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!

November 21, 2010

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.