Archive for September, 2009

Diseases of dinosaurs

Wednesday, September 30th, 2009

Tyrannosaurus rex Paleontologists have found that Tyrannosaurus rex and its close relatives suffered from a potentially life-threatening infectious disease similar to one that occurs in living birds known as trichomonosis. Trichomonas gallinae infections are most prevalent in pigeons which are generally immune.  Birds of prey are particularly susceptible to trichomonosis if they eat infected pigeons. Adult birds can then pass the disease to their nestlings through beak-to-beak contact. Tell-tale symptoms of trichomonosis include swellings and holes in the back of the lower jaw.  The disease is prevented from infecting the entire interior of the bone by the innate immune response that localizes infections as a result of the actions of a unique avian white blood cell called the heterophil. Some of the world’s most famous T. rex specimens, such as “Sue” at the Field Museum in Chicago, and the holotype specimen at the Carnegie Museum of Natural History in Pittsburgh have holes like these in their lower jaw. The holes in tyrannosaur jaws occur in exactly the same place as in modern birds with trichomonosis.  The shape of the holes and the way that they merge into the surrounding bone is very similar in both animals. The cause of these holes in tyrannosaurs has previously been attributed to tooth gouges from biting or bacterial infections, but a trichomonosis-type disease is more likely given the position and nature of the holes.

The disease appeared to be quite common in tyrannosaurs and could have been deadly to those that were infected. As the parasites take hold in serious infections, lesions form around the jaw and inside the throat, eventually eating away the bone. As the lesions grow, the animal has trouble swallowing food and may eventually starve to death. Tyrannosaurs are so far the only dinosaurs that appear to have had this disease.  The researchers therefore faced the problem of explaining how it was spread. In addition to other routes through which infection may have spread, tyrannosaurs might have facilitated infection by biting each other or even through cannibalism. Cannibalism has been tentatively suggested in other studies of theropod behaviour and this certainly could have been a route of transmission for the infection, but other scenarios were more frequent. Fighting and specifically head-biting would have been an ideal mechanism for spreading the disease among tyrannosaurs. It is unlikely to be a coincidence that a significant number of adult tyrannosaur specimens show both face-biting marks and evidence of a trichomonosis-like disease.  Previous studies have shown that up to 60% of tyrannosaur specimens display evidence of face-biting. Bone pathology is hard to find in any specimen, and bone diseases are relatively uncommon.  Finding both types of pathologies in a high proportion of individuals strongly suggests that they could be linked.

There are similarities with what has been happening to Tasmanian devils recently, where a debilitating oral cancer is being spread by animals fighting and biting each other’s faces.  This disease may eventually wipe out this iconic Australian mammal. It is ironic to think that an animal as mighty as T. rex probably died as a result of a parasitic infection. The link in disease is not surprising given the evolutionary relationship of dinosaurs to birds.  But the discovery of a likely candidate for such a disease represents a major step forward in our understanding of disease origins in birds and their dinosaur precursors. The discovery gives us an insight into the dinosaur immune system.  The response of tyrannosaurs to this trichomonosis-like disease is almost identical to that found in living birds. These simple holes in tyrannosaur jaws give us a dramatic example of an avian-like defence system in action.

Common Avian Infection Plagued the Tyrant Dinosaurs. PLoS ONE 4(9): e7288 doi:10.1371/journal.pone.0007288
Tyrannosaurus rex and other tyrannosaurid fossils often display multiple, smooth-edged full-thickness erosive lesions on the mandible, either unilaterally or bilaterally. The cause of these lesions in the Tyrannosaurus rex specimen FMNH PR2081 (known informally by the name ‘Sue’) has previously been attributed to actinomycosis, a bacterial bone infection, or bite wounds from other tyrannosaurids. We conducted an extensive survey of tyrannosaurid specimens and identified ten individuals with full-thickness erosive lesions. These lesions were described, measured and photographed for comparison with one another. We also conducted an extensive survey of related archosaurs for similar lesions. We show here that these lesions are consistent with those caused by an avian parasitic infection called trichomonosis, which causes similar abnormalities on the mandible of modern birds, in particular raptors. This finding represents the first evidence for the ancient evolutionary origin of an avian transmissible disease in non-avian theropod dinosaurs. It also provides a valuable insight into the palaeobiology of these now extinct animals. Based on the frequency with which these lesions occur, we hypothesize that tyrannosaurids were commonly infected by a Trichomonas gallinae-like protozoan. For tyrannosaurid populations, the only non-avian dinosaur group that show trichomonosis-type lesions, it is likely that the disease became endemic and spread as a result of antagonistic intraspecific behavior, consumption of prey infected by a Trichomonas gallinae-like protozoan and possibly even cannibalism. The severity of trichomonosis-related lesions in specimens such as Tyrannosaurus rex FMNH PR2081 and Tyrannosaurus rex MOR 980, strongly suggests that these animals died as a direct result of this disease, mostly likely through starvation.

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Leptospira – dawn of the molecular genetics era

Tuesday, September 29th, 2009

The first modern clinical description of leptospirosis was published by Weil in 1886, hence leptospirosis is frequently known as Weil’s disease. Over the past decade, outbreaks during sporting events, adventure tourism and disasters have underscored its ability to become a public health problem in non-traditional settings. However, leptospirosis is a neglected disease that places its greatest burden on impoverished populations from developing countries and tropical regions. In addition to being an endemic disease of subsistence farmers, leptospirosis has emerged as a widespread problem in urban slums, where inadequate sanitation has produced the conditions for rat-borne transmission. More than 500,000 cases of severe leptospirosis are reported each year, with case fatality rates exceeding 10%.

Leptospirosis

Leptospirosis is a zoonotic disease, transmitted from rats to humans via rodent urine, that has emerged as an important cause of morbidity and mortality among impoverished populations. One hundred years after the discovery of the causative spirochaetal agent, little is understood about Leptospira pathogenesis, which in turn has hampered the development of new intervention strategies to address this neglected disease. However, the recent availability of complete genome sequences for Leptospira spp. and the discovery of genetic tools for their transformation have led to important insights into the biology of these pathogens and their pathogenesis. This review discusses the life cycle of the bacterium, recent advances in understanding and the implications for the future prevention of leptospirosis.

Leptospira: the dawn of the molecular genetics era for an emerging zoonotic pathogen. 2009 Nature Reviews Microbiology 7: 736-747 doi:10.1038/nrmicro2208

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10 things you should know about E. coli O157

Monday, September 28th, 2009

<em>Escherichia coli</em> E. coli has been in the media a lot recently (Latest News), so MicrobiologyBytes thinks it’s time for:

10 things you should know about E. coli O157:

1. Escherichia coli (E. coli) is a normal inhabitant of the human gut. It’s been with us for millions of years and overall does us a lot of good, e.g. helping with digestion and providing vitamins we can’t make for ourselves.

2. There are many different strains of E. coli, which all look much alike. They are identified by the antigens on the surface of the cell. These include somatic (O antigens) on the surface of the cell, flagellar (H antigen) and capsular (K antigens) associated with polysaccharide capsules on some strains.

3. A few strains of E. coli are pathogenic and cause disease. Enterotoxigenic (ETEC) strains cause diarrhea but are non-invasive and do not leave the intestine. Enteropathogenic (EPEC) strains also cause diarrhea and enter epithelial cells around the intestine. Enteroinvasive (EIEC) strains cause severe diarrhea and high fever. Enterohemorrhagic (EHEC) strains such as E. coli O157:H7 cause bloody diarrhea, hemolytic-uremic syndrome and kidney failure.

4. E. coli O157:H7 infections often case to bloody diarrhea and occasionally acute kidney failure, especially in young children and elderly people.

5. Most infections are associated with eating undercooked, contaminated ground beef (e.g. burgers), drinking unpasteurized milk, swimming in or drinking contaminated water, and eating contaminated salad vegetables. Infection can also be aquired via direct contact with animal faeces, for example on farms.

6. A bit of dirt never did me any harm… E. coli O157:H7 is new. It was first recognized around 25 years ago and is now widespread, possibly due to agricultural practices.

7. Where did it come from? This strain of E. coli contains lysogenic bacteriophages which encode Shiga toxins (these strains are known as STECs: Shiga Toxin Producing Escherichia coli). E. coli O157:H7 has two stx toxins, stx1 and stx2.

8. How does it cause disease? E. coli O157:H7 is an EHEC strain which kills epithelial cells in the gut, resulting in bloody diarrhea. It also invades the urinary tract causing an ascending infection which damages the kidneys. But it gets worse. Broad spectrum fluoroquinolone antibiotics such as ciprofloxacin which are often used to treat infections cause an SOS response in E. coli cells which in turn induces the lytic cycle of the lysogenic toxin-carrying phages. This results in a thousand-fold increase in toxin expression. Treatment with some some beta-lactam antibiotics also increase stx toxin production.

9. Many people recover without antibiotics or other specific treatment in 5–10 days. There is no clinical evidence that antibiotics improve the course of disease, and some may make it much worse (see above). Haemolytic-uremic syndrome is a life-threatening condition usually treated in an intensive care unit. Blood transfusions and kidney dialysis are often required. Even with intensive care, the death rate for haemolytic uremic syndrome is 3%–5%.

10. Wash your hands thoroughly with soap and warm water after contact with animals. Wash raw vegetables such as salads well before eating. Cook meat thoroughly all the way through, especially burgers and sasuages where external contamination of meat is transferred to the inside by mincing.

11. E. coli is a Gram-negative bacterium. IT’S NOT A VIRUS! So next time a journalist talks or writes about “the E. coli virus” – do us all a favour and yell at them!

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Heterosexual transmission of HIV in the UK

Friday, September 25th, 2009

HIV infection was first detected in the United Kingdom (as AIDS) in 1981–2 among men who have sex with men (MSM). Early outbreaks with UK sources include Scottish intravenous drug users (IDUs) dated to 1983 and haemophiliacs to 1984. All strains isolated initially were of the B subtype, both in MSM and IDUs and also in the small number of individuals infected through heterosexual contact during that decade. However within 10 years, multiple virus subtypes had been detected within the UK. From the mid 1990s increasing numbers of HIV infections in the UK were being found in heterosexuals, until the current situation was attained whereby this risk group comprises the majority of new HIV diagnoses. This increase coincided with increasing immigration from southern and Eastern Africa, particularly from South Africa, Uganda and Zimbabwe. Genetic characterisation of viruses from infected heterosexuals revealed that while subtype B was still observed in the majority of samples obtained during 1996/7, by the year 2000, subtype C was most common (35%) with subtype A at 15%, reflecting the main subtypes in those countries. Subtype B was present in only 25% of individuals. Thus, the heterosexual risk group in the UK has become strongly associated with non-B HIV subtypes. Recently there has been some evidence of limited crossover among risk groups.

HIV diagnoses

Since 1995, HIV among heterosexuals in the UK increased to the point where the total number of heterosexuals infected with HIV, predominantly of non-B subtypes, exceeds the number of HIV-positive homosexual men. To understand the dynamics of this epidemic, researchers applied phylodynamic techniques to the analysis of viral sequences taken in the course of routine clinical care from approximately 40% of the HIV-infected heterosexual population in the UK. Phylodynamics reconstructs the pattern of viral sequence divergence in time, revealing the size of transmission clusters and the dynamics of transmission within them.

Of 11,071 patients studied, 296 were linked to at least two others in the UK. There were 8 clusters comprising 10 or more individuals among these, yielding a total of 143 or 5% of all individuals with links, much lower than seen earlier among homosexual men (25%). HIV transmissions within clusters also occurred less rapidly, only 2% being dated to the first 6 months of infection, compared to 25% among homosexual men. Overall, transmission clusters exist in the UK heterosexual HIV epidemic but they are generally smaller than among homosexuals; onward transmission occurs less rapidly and is not associated with acute HIV infection. The study concludes that heterosexual transmission could be significantly reduced by early diagnosis and treatment. The slower dynamics of the heterosexual epidemic thus offer more opportunity for successful intervention, but it is essential that diagnosis is achieved as early as possible.

Molecular Phylodynamics of the Heterosexual HIV Epidemic in the United Kingdom. 2009 PLoS Pathog 5(9): e1000590 doi:10.1371/journal.ppat.1000590
The heterosexual risk group has become the largest HIV infected group in the United Kingdom during the last 10 years, but little is known of the network structure and dynamics of viral transmission in this group. The overwhelming majority of UK heterosexual infections are of non-B HIV subtypes, indicating viruses originating among immigrants from sub-Saharan Africa. The high rate of HIV evolution, combined with the availability of a very high density sample of viral sequences from routine clinical care has allowed the phylodynamics of the epidemic to be investigated for the first time. Sequences of the viral protease and partial reverse transcriptase coding regions from 11,071 patients infected with HIV of non-B subtypes were studied. Of these, 2774 were closely linked to at least one other sequence by nucleotide distance. Including the closest sequences from the global HIV database identified 296 individuals that were in UK-based groups of 3 or more individuals. There were a total of 8 UK-based clusters of 10 or more, comprising 143/2774 (5%) individuals, much lower than the figure of 25% obtained earlier for men who have sex with men (MSM). Sample dates were incorporated into relaxed clock phylogenetic analyses to estimate the dates of internal nodes. From the resulting time-resolved phylogenies, the internode lengths, used as estimates of maximum transmission intervals, had a median of 27 months overall, over twice as long as obtained for MSM (14 months), with only 2% of transmissions occurring in the first 6 months after infection. This phylodynamic analysis of non-B subtype HIV sequences representing over 40% of the estimated UK HIV-infected heterosexual population has revealed heterosexual HIV transmission in the UK is clustered, but on average in smaller groups and is transmitted with slower dynamics than among MSM. More effective intervention to restrict the epidemic may therefore be feasible, given effective diagnosis programmes.

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HIV – new vaccine, new hope?

Thursday, September 24th, 2009

In the news today:

What?

Researchers who carried out a trial of a new HIV vaccine in Thailand found the jab reduced the risk of being infected by nearly a third.

Why?

HIV infection causes AIDS. Although it may be possible to inhibit HIV infection from developing into AIDS, the best situation is to prevent people from becoming infected with the virus.

When?

This clinical trial began in October 2003 and studied more than 16,000 HIV-negative Thai men and women aged 18 to 30 judged to be at average risk of becoming infected.

How?

Half of the participants received four “priming doses” and two “booster doses” of the vaccine over six months. The other half received pacebo shots. All were given condoms, counselling and treatment for any sexually transmitted infections and were tested every six months for HIV. Any who became infected were given free treatment with antiviral medicines. Participants were followed for three years after vaccination ended.
Two different vaccines were used, each of which had been tested before and shown to be ineffective on its own. The priming vaccine was Alvac, which is based on bird virus canarypox genetically altered to express synthetic versions of three different HIV envelope genes. Canarypox cannot replicate in humans so is very safe. The booster vaccine was Aidsvax which consists of two different recombinant HIV gp120 envelope proteins.

The Good News

After 25 years of trying, this is the first vaccine scientifically proven to show some protection against HIV infection of humans. Although similar results have been obtained in animal studies, it has never before been possible to actually demonstrate that prevention of HIV infection (and hence AIDS) is possible in humans.

The Bad News

This candidate treatment will never come to the market. At a little over 30% effectiveness, it is not good enough. The significance of this story is that we now that protection against HIV is possible in practice, not just in theory. By studying how this vaccine works, researchers hope to produce more effective vaccines that will be used in humans, although that is at least several years away.

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Petri Dish Circus

Wednesday, September 23rd, 2009

Nice video from MicrobeWorld:

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Viruses causing childhood diarrhoea in the developing world

Tuesday, September 22nd, 2009

diarrhoea Globally, it is estimated that diarrhoeal disease results in about 1.87 million deaths in children less than 5 years, accounting for 19% of total child deaths. The majority of these diarrhoeal deaths (1.46 million, 76%) occur in the developing countries of Africa and south-east Asia. In industrialized countries, viral agents of gastroenteritis are the leading cause of acute watery diarrhoea in children. Recently, with improvements in hygiene, sanitation and water supply in developing countries, there has been a marked reduction in the number of bacterial pathogens, and an increasing proportion of diarrhoea hospitalizations that are attributed to viruses. This review focuses on recent studies that contribute to our understanding of the role of enteric viruses as important causes of diarrhoea in children in the developing world, examining epidemiology, pathogenesis and susceptibility.

With the use of sensitive molecular techniques, it is evident that a significant proportion of childhood diarrhoea is attributable to enteric viruses, with at least one viral agent in nearly 43% of samples from childhood diarrhoea in developing countries. Rotaviruses remain the most common pathogens in children, followed by noroviruses in almost all countries. There is increasing evidence that both rotaviruses and caliciviruses spread beyond the gut in a large proportion of infections. The review highlights the importance of viral agents of gastroenteritis in developing countries. Wider use of molecular techniques is resulting in rapid identification of new or emerging strains and in the detection of extra-intestinal spread. There is a need to better understand susceptibility and immune response to these agents to be able to design suitable interventions.

Viruses causing childhood diarrhoea in the developing world. 2009 Current Opinion in Infectious Diseases 22 (5): 477-82

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The killer in our midst – fighting to end tuberculosis

Monday, September 21st, 2009

Dr Helen McShane at the University of Oxford and the Oxford-Emergent Tuberculosis Consortium Ltd have received a Wellcome trust Strategic Award to part-fund the first trial to test efficacy of the new TB vaccine candidate, MVA85A, for potential efficacy in South African infants. In this film Dr McShane discusses the new vaccine candidate and these trials. www.wellcome.ac.uk

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Mushroom Expert

Saturday, September 19th, 2009

Mushroomexpert.com Mushroomexpert.com is a great website by Michael Kuo for anyone interested in identifying fungi, whether edible or poisonous! As well as Mushroom of the Month, the site also includes great sections on:

Although they are beautiful, there is no simple way of knowing which fungi are safe to eat and which poisonous. Do not experiment with edible fungi, and get expert advice if you are in any doubt. Do not trust visual identification alone, whether from books or websites, as fungi vary tremendously in size, shape, colour and sometimes even in growing habitat.

Why not grow your own?

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