Tuesday, 27 March 2012

Who Should Be Able To Read Your DNA?

DNA sequencing of a human genome (20-25 000 genes)was first achieved in 2003 by the Human Genome Project after 10 years of work and only 30 years after the first gene was sequenced (Bacteriophage MS2). At that time the dream was established that we would all be able to have our own genome sequenced and thus to be able to find out the sequence of all of our gene DNA. This would reveal a lot about what illnesses each of us are prone to, what we might develop as we age and in some cases hidden illnesses we may pass on to our children. 


USB memory stick - size genome sequencing device
Millions of us having our DNA sequenced seemed very unlikely back then, but now, 10 years further on we are about to start seeing that dream realised as genomes can be generated relatively quickly and cheaply. We can do hundreds in a few weeks to order. The NEXT improvement in sequencing technology promises to go a much further. A sequencing machine the size of a USB memory stick! Costing £600 each! A whole genome sequenced in a day! - all hold the possibility that everyone will be able to have the ultimate 'health screen' very soon - the technology claims to be ready by end of this year.


History has taught us the incredibly powerful technology that can massively influence our lives is also a potential hazard that must be controlled. Who should have access to your DNA sequence? Your health service? Your government? Your family (who have many of the same genes as you) Or just you? This is an ethical dilemma we have to consider and quickly.


This flood of information will need a whole new breed of supercomputer to analyse the information, and of course our clinical researchers stand to learn a huge amount from knowing what genes all of their patients have - many illnesses will be strongly influenced by the specific genes and their mutations carried by everyone.


We will also soon learn that under the skin we are all carrying mutations, we are all part of the huge genetic variation that gives us our individuality but also binds us together as the human race - far more in common with each other than we generally appreciate now.


The US government are starting to hold discussion with the public to try to come to a concensus to try to answer some of these questions. We are already debating the issues with our patients groups (Yahoo, Facebook) - feel free to join in!


Breaking news - have a look at this TV programme for a compelling examination of the effect genomic testing will have on our lives http://www.youtube.com/watch?v=oRz5M0WUkzo


Monday, 26 March 2012

Aspergillus Goes Banana's!

Fungal endophyte (green) growing into plant cells
Many fungi can live in close partnerships (endophytes) with some plant species, sometimes resulting in  exchange of mutually beneficial metabolites e.g. Aspergillus fumigatus and Cynodon dactylon(Link). Far from damaging the plant, Aspergillus in these circumstances can be of great benefit to the plant:- suggestions vary but include the endophyte providing protection from attack by parasites e.g. by providing antibacterial substances or chemicals toxic to insects and 'giving' them to the plant.
There are also examples of Aspergillus providing growth hormones when the plant is put under stress, helping the plant to grow when under drought conditions for example.

This information has recently been put to use by researchers trying to help banana farmers overcome Fusarium Wilt, a disease currently devastating banana plantations in The Phillipines. Fusarium is a fungus that causes rapid death of banana plants and renders the soil unable to support further growth for 10 years - extremely bad news if you are a small farmer.

Researchers have found that certain local strains of Aspergillus can be grown with plants to help prevent Fusarium Wilt - plants do much better in Fusarium-infected soils if they have been treated with Aspergillus. Aspergillus apparently grows around the roots causing a physical barrier and considering what we know about how this fungus works as an endophyte may well produce chemicals that help encourage growth and even produce chemicals toxic to Fusarium.

This technique along with several other techniques also being investigated should go a long way to reducing the threat from Fusarium Wilt for poor banana farmers.

Saturday, 24 March 2012

New Way to Detect Adverse Drug Effects



A study published recently (Tatonetti et. al. 2012) has looked at the huge problem of detecting adverse side effects of medications and in detecting the potential problems caused when one drug interacts with another if the prescribed courses run at the same time. The paper is summarised by Heidi Ledford in a recent copy of Nature magazine.

The US drug control body Food and Drug Administration (FDA) are the recipients of hundreds of thousands of reports of adverse side effects every year and the new research provides a way to sift those reports and arrive at a listing of new adverse events.

This is not an easy task. There are many variables to take in for account whenever an adverse event is reported; age, gender, health status all vary tremendously and profoundly affect conclusions.
The example Heidi uses is one where there are high rates of heart attack reported in people taking a particular drug (compared with the general population). That sounds like an adverse effect of that drug! However if we delve a bit deeper we find that only older people take the drug, and of course amongst older people there are far higher rates of heart attack - the impression that this drug is causing heart attack as a side effect is merely a coincidence.

 How do we tell if an adverse effect is the real thing? In this case we would compare older people who don't take the drug with older people who do take the drug - if there are still more cases of heart attack amongst the people taking the drug then we have found a genuine adverse effect.

The computer software developed by Tatonetti et. al. looks at all of the reported adverse effects and carries out comparisons using corrections for the type of bias I just described. This approach has successfully identified hundreds of previously unknown side effects and drug interactions in only 1332 of the drugs currently on the market. Application of this software should reveal many more when run against all of the drugs currently on the market, making us all more aware of the hazards of taking all drugs, separately OR in combination.

Friday, 23 March 2012

Newsbite:Aspergillus & Aspergillosis Newsletter Published

The Aspergillus Newsletter is published once per month and contains much of the most recent news from the Aspergillus Website, The national Aspergillosis Centre and other resources. more...

Thursday, 15 March 2012

Gates Foundation Supporting Eradication of Mycotoxin in 3rd World Food

There is a well known and  long standing problem in the developing world that it is difficult to grow enough food to adequately feed the growing population. The Bill Gates Foundation recently announced another  $200 million in grants to small farmers in poorer parts of  Africa and Asia to allow them to improve productivity - far better to enable farmers to feed their own people than have to ship in food supplies from outside when famine strikes.

There are several aspects of increasing food productivity that this money addresses, including

  • Supported the release of 34 new varieties of drought-tolerant maize
  • Delivered vaccines to tens of millions of livestock
  • Trained more than 10,000 agro-dealers to equip and train farmers
New foundation grants will go to support:
  • Breaking down gender barriers so women farmers can increase productivity
  • Controlling contamination that affects 25 percent of world food crops
  • Creating an innovative system to monitor the effects of agricultural productivity on the population and environment
A major focus is on preventing contamination of food stocks, mainly by aflatoxins produced when Aspergillus species infect stored grain (PACA), and when crops in the field are damaged by drought, wind or insect infestations.
PACA aims to adapt proven solutions, and identify new ones, that will work for smallholder farmers in Sub-Saharan Africa. Comprehensive solutions will be developed, addressing the health, nutrition, trade, and agricultural impacts of aflatoxin.  Solutions will include effective measures to control aflatoxin along the value chain, from crop production to processing, and food preparation to consumption.  For instance, native strains of beneficial fungi have been shown to dramatically reduce the prevalence of aflatoxin in the field and in storage. Proper drying and storage can help further control aflatoxin. Many other measures can be taken to reduce aflatoxin exposure to local consumers and improve opportunities to sell aflatoxin-safe crops to markets, but measures need to be supported by appropriate policy and regulatory actions.  It is expected that comprehensive and feasible solutions being developed for the African small farmer context will also be useful for other regions where aflatoxin is a problem.  

As can be seen from these figures (25% of world food crops) this is a massive problem, much of it preventable if the grain can be dried and stored correctly. Partly this requires investment in communal drying equipment, partly training of farmers to do the right things. Regardless, the highlighting of this issue by high profile organisations like the Gates Foundation can only do good.



Tuesday, 13 March 2012

Newsbite: Warning for Nut Allergy Sufferers

Vigantoletten (1000 IU Colecalciferol) Tablets (containing vitamin D3) marketed by Merck Serono contain traces of nut oil and should be avoided by people with nut allergy. This warning was issued by UK government drug safety agency MHRA. It is issued partly because the pack information (and warning) is written in the German language and thus difficult to understand for English speakers. more...

Newsbite: We are on Facebook!


After a long period of partially engaging with the Facebook community we have finally taken the plunge. The Aspergillus Website and Aspergillosis Patients Support are now available to join on Facebook

Support for Aspergillosis patients & carers: https://www.facebook.com/groups/aspergillussupport/

Aspergillus and Aspergillosis:
https://www.facebook.com/Aspergillus.and.Aspergillosis

Fungal Research Trust: https://www.facebook.com/FungalResearchTrust

It helps our efforts if you 'Like' and 'Share' from these pages.

You can also join the general community by becoming our 'Friends' at https://www.facebook.com/DrGrahamAtherton

Monday, 5 March 2012

Genetic Link Suspected in Kakapo Death by Aspergillosis

The death of a young male kakapo last week – the fifth since September – may be linked to poor genetics, prompting the Kakapo Recovery team to consider removing Basil, an Anchor Island-based bird, from the breeding programme.
Rooster, who hatched in 2008, was flown off Whenua Hou/Codfish Island on February 29 for veterinary care at Auckland Zoo, after suffering weight loss and loss of appetite. He died the next day, with initial post mortem results indicating a fungal infection – aspergillosis – was widespread throughout his body, including his lungs.
Kakapo Recovery programme manager Deidre Vercoe Scott said the team was investigating the cause and also looking into whether there could be a link with genetics. Of the six young kakapo to die in recent times (birds aged 1-9 years old since 2004), four had been fathered by Basil. Two, Rooster and Purity, had died since September.
“We also know that, of all the dead embryos and hatched chicks of known paternity, 24% of the 33 were fathered by Basil.”
Kakapo Recovery scientist Dr Ron Moorhouse said statistically, the probability of Basil fathering that number of dead chicks by chance, was one in a hundred. Otago University geneticist Dr Bruce Robertson would be looking at Basil’s offspring relative to other kakapo, examining their DNA for variation at the MHC allele. This was the part of the DNA involved with immune response to pathogens, Dr Moorhouse said.
“If we can get to the bottom of it we might, ultimately, be able to identify males likely to produce poor quality progeny before, rather than after, the fact.”
He said it was inevitable that some young kakapo would be genetically compromised because of the very low genetic variation in the parental population.
“We are using artificial insemination and DNA fingerprinting to minimise the loss of genetic diversity from the kakapo population and improve the genetic quality of kakapo chicks.”

The Importance of Science to Britain and the World: Richard Dimbleby Lecture

The BBC commemorates the life of one of its brightest stars by presenting an annual lecture entitled the Richard Dimbleby Lecture in his honour. The lecture is delivered by speakers from a variety of backgrounds and talk about many different subjects.

This year the topic was 'The Wonder of Science' delivered by Sir Paul Nurse, recipient of the Nobel Prize in 2001 and who proved to be a passionate supporter and promoter of science.

In this talk he advocates the importance of science and engineering and of a strong science base in the UK for the future of British industry, medical advancement, our climate, our environment and growing enough food for us all to have sufficient to eat.

He also points out to the UK government and private industry that compared to our major competitors we spend around half as much on research, raising the point that even as we all must take care over spending during this current economic downturn, we must also pay heed to the financial demands of ensuring that  our future is better for many years to come.

Watch the Richard Dimbleby Lecture on BBC iPlayer

Thursday, 1 March 2012

FUNGUS - FRIEND or FOE? How Schoolchildren Will Make The Link Through Art and Music

A competition – the first of its kind to explore the relationship between fungi and and the illnesses that they cause using art and music – launches this week across the region’s schools.

For the next ten weeks thousands of young people in more than 400 schools in the North West and North Wales will be invited to interpret how they see the deadly role fungus can play in human diseases through creative arts and music.

Project Director, Professor David Denning explains: “Fungi are beautiful and fascinating they are essential to our ecosystem in the carbon and nitrogen cycles, and are valuable in commerce. Many industries use “good” fungi, for example in the making of alcohol, bread and cheese. However some fungi can also cause human infection. Fungal infections are mostly hidden and diagnosis is often missed. As many as 300 million people worldwide are affected, in many different forms of illness, some of which are deadly. This is an exciting project because never before has the mystery and beauty of microscopic fungi been explored in art and music.”

The competition is being run by LIFE Worldwide which has three fundamental aims:
Ø  To promote awareness of LIFE and its aims through the work of young artists and musicians
Ø  To give budding artists and musicians the recognition they deserve by promoting their talents
Ø  To educate young people about fungi and how they can cause illness.

The project, which is open to all young people aged between 13 and 18 and has a deadline of April 29th , is supported by the UK charity the Fungal Research Trust and the University Hospital of South Manchester. This is based at Wythenshawe Hospital, and the Manchester Academic Health Science Centre.

The competition website can be found at www.projectlifecompetition.org. It  includes videos of interviews with patients living with fungal disease and a photo gallery displaying the vast array of different types of disease causing fungi.

Winning entries to the competitions will be receive an individual winners cash prize and a separate cash prize will be awarded to their School. Other prizes will include the opportunity for valuable work experience in a clinical environment.  The panel of judges includes:
      Clark Rundell, Director of Contemporary Music and Head of Conducting at the Royal Northern College of Music in Manchester
      Dr Lizzie Burns, Director of Science to Life, Oxfordshire
      Sally Nash, a Landscape Architect with Gillespies in Manchester, and
       Bob Devereux, Poet, Artist and Gallery Director of the Salthouse Gallery in St Ives, Cornwall.


Background on LIFE:

LIFE is the international education and advocacy brainchild of the UK charity the Fungal Research Trust (www.fungalresearchtrust.org). The FRT was set up in 1991 and since then has distributed in excess of £3,500,000 in research grants resulting in more than 145 research publications in clinical and scientific aspects of fungal infection. It has contributed to the postgraduate training of more than 25 scientists and doctors in the UK and overseas, and provides travel grants to scientific congresses. It also supports the encyclopaedic Aspergillus Website at www.aspergillus.org.uk.  As well as being a key resource for clinicians and researchers, the website also devotes a section to patients and relatives to help them understand more about the disease.

Fungal infection
Over 300 million people are acutely or chronically infected by fungi, leading to death, long term illness, blindness, psychological problems and reduced work capacity. These diseases have mostly been neglected. Many recent improvements in diagnostics and treatment have not reached treating clinicians in all countries, and access to appropriate diagnostics and simple antifungal agents is far from universal.

Deaths from fungal infections
Ø  Cryptococcal meningitis – 10% death rate in the USA, >80% in Africa. 600,000 deaths annually. Diagnosis simple with antigen test, but often late and appropriate medication not available.
Ø  Invasive aspergillosis – 200,000+ cases annually; 50% mortality treated, 100% if not, >100,000 deaths. Diagnosis difficult; treatment often too late, and only partially effective.
Ø  Chronic pulmonary aspergillosis – ~3 million cases and 450,000 deaths; diagnosis often confused with TB, and requires radiology and aspergillus antibody test; 30% mortality in 6 months, often by coughing up blood. Treatment partially successful but long term.
Ø  Pneumocystis pneumonia - ~ 400,000 patients annually; ~15% mortality in UK in AIDS, ~50% non-AIDS, 100% if not diagnosed and treated. >80,000 deaths. Diagnosis difficult without PCR or fluorescence microscopy. Treatment straightforward and available.
Ø  Candida bloodstream infection – 300,000+ cases worldwide; ~40% mortality, treated. ~120,000 deaths. Diagnosis by blood culture. Treatment straightforward, best drugs expensive.
Ø  Severe asthma with fungal sensitization (SAFS) – probably over 3.5 million patients worldwide; increased risk of asthmatic death (estimated to be 100,000 annually worldwide).

Major fungal infections and their impact or health and wellbeing
Ø  Oral and oesophageal thrush – unpleasant, reduced food intake and weight loss.
Ø  Allergic bronchopulmonary aspergillosis (ABPA) [~4 million people worldwide] and SAFS – breathlessness with severe asthma, reducing work capability especially for manual workers, co-morbidity issues with smoke from home cooking – easy diagnosis (skin prick tests), if considered, antifungal treatment 60-80% effective.
Ø  Chronic pulmonary aspergillosis – progressive breathlessness and weight loss, with significant hospitalisation and medication costs (typically mis-directed).
Ø  Fungal eye infection – ~1 million cases annually; usually results in unilateral blindness as diagnosis late, good outcome if treated early. Diagnosis requires expert input; treatment intensive initially but unaffordable for most afflicted.
Ø  Candida vaginitis – ~75 million women with at least 4 attacks a year; mis-diagnosis and anxiety major problems; impaired sex life and therefore relationship issues.
Ø  Fungal hair infection – over 100 million children affected; most common in black children, who suffer patches of hair loss, exclusion from school and psychological problems as a result. Diagnosis and treatment usually straightforward and highly effective.

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