Archive for the ‘Podcast’ Category

Sleep and susceptibility to the common cold

Monday, January 19th, 2009

Human rhinovirus Sleep quality is thought to be an important predictor of immunity and, in turn, susceptibility to the common cold. A new article examines whether sleep duration and efficiency in the weeks preceding virus exposure are associated with cold susceptibility. A total of 153 healthy men and women (age range, 21-55 years) volunteered to participate in the study. For 14 consecutive days, they reported their sleep duration and sleep efficiency (percentage of time in bed actually asleep) for the previous night and whether they felt rested. Average scores for each sleep variable were calculated over the 14-day baseline. Subsequently, participants were quarantined, administered nasal drops containing a rhinovirus, and monitored for the development of a clinical cold (infection in the presence of objective signs of illness) on the day before and for 5 days after exposure.
Results: There was a graded association with average sleep duration: participants with less than 7 hours of sleep were 2.94 times more likely to develop a cold than those with 8 hours or more of sleep. The association with sleep efficiency was also graded: participants with less than 92% efficiency were 5.50 times more likely to develop a cold than those with 98% or more efficiency. These relationships could not be explained by differences in prechallenge virus-specific antibody titers, demographics, season of the year, body mass, socioeconomic status, psychological variables, or health practices. The percentage of days feeling rested was not associated with colds.
Conclusion: Poorer sleep efficiency and shorter sleep duration in the weeks preceding exposure to a rhinovirus were associated with lower resistance to illness.

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Sleep habits and susceptibility to the common cold. 2009 Arch Intern Med. 169(1): 62-67

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I’m healthy, but hospitals are sick

Monday, January 12th, 2009

Hosptial I recently spent some time as a patient on a ward in an NHS hospital where I had been admitted for some tests. Thankfully, all the results were negative and I was diagnosed as being quite healthy for a person of my advanced age :-)

As anyone who has ever spent any time as an NHS patient knows only too well, one of the defining features of the experience is an awful lot of waiting around. I spent just under a day on a Clinical Decisions Unit ward where patients are admitted for testing and then either discharged or moved on to longer stay wards for treatment. There were a lot of very sick people on the ward, but I was feeling fine, so there wasn’t much I could do other than sit and observe the goings on, which is how I discovered that

Infection control in hospitals is broken

“Hospital superbugs” such as Staphylococcus aureus MRSA, Clostridium difficile and Noroviruses feature prominently in the news media and consequently on MicrobiologyBytes, with claim and counterclaim about increasing, static or declining infection rates constantly being batted backwards and forwards, and the Department of Health publishes endless guidance on infection control procedures. Apart from quack claims of miracle cures, the formal response to hospital-acquired infections are procedures for infection control such as cleaning, disinfection and sterilization, protective equipment and surveillance of infection rates. As an observer on a busy ward I was able to watch what happened as patients and staff came and went.

The care I received was exemplary, and for the most part, the ancillary, nursing and medical staff worked hard and clearly cared about the welfare of the patients. But that’s not enough. The reality is that the complexity of the system pushed all the staff beyond their limits, and damaged morale. As a simple example, I watched a domestic ancillary employed as bed maker drifting around looking for beds to make. She was once about to make one when she was called away, and when she came back, the nurses had made the bed. I listened to the nurses grumble about how the ancillaries didn’t do their jobs properly, and the ancillaries grumble about the nurses. And of course, everyone grumbled about the medical staff. Morale was at a low ebb. But it gets worse. Time and time again I watched ward staff strip the linen from beds which had been vacated by patients and painstakingly disinfect the mattress and the bed before remaking the bed with fresh linen. What’s wrong with that? No-one cleaned the bedside chairs. When the next patient arrived, they kicked their bags around on the floor for a while before putting them on the chair, which the nurses dumped the fresh linen on before making the beds.

In less than 24 hours, I was treated by dozens of medical staff and wheeled all over the hospital for various tests. The ward was like a motorway, with staff, patients and visitors constantly moving from ward to ward, street to common areas, canteens and homes. Flawed understanding of basic microbiology is not compensated for by mandated infection control procedures rigidly-applied without any thought or appreciation. Errors are compounded by a totemic belief in the miracle properties of alcohol hand rubs which adorn every bed but which distract from more effective handwashing procedures. Did I need to be visited by the person flitting from ward to ward to fiddle with the TV/radio/phone console above every bed? Even if they did spend several seconds squirting alcohol gel on their hands before moving on to the next patient? I don’t think so.

Infection control in hospitals is broken by the complexity of the system

So how can you fix it? Apart from better microbiology training, the system needs to be radically simplified so that staff and patients are not constantly moving around. Wards should be much more autonomous with a limited number of staff responsible for them, and allowed to do their jobs properly. This would allow much better standards of care arising from the evident motivation they have. There’s no need for people to flit constantly from ward to ward, delivering meals, borrowing equipment, chasing test results and spreading contamination. Simplify. Let people do the jobs they have been trained for and to feel pride in themselves. Back to basics.

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Dissecting the Cell Entry Pathway of Dengue Virus

Monday, January 5th, 2009

Dengue virus Dengue virus (DENV) is the most common arthropod-borne infection worldwide with 50–100 million cases annually. Despite its high clinical impact, little is known about the infectious cell entry pathway of the virus. Previous studies have shown conflicting evidence about whether the virus fuses directly with the cell plasma membrane or enters cells by receptor-mediated endocytosis.

Entry of DENV into hosts cells is mediated by the virus envelope glycoprotein E, which is organized in 90 homodimers on the surface of the virion. The E glycoprotein is involved in interaction with cellular receptors as well as the subsequent membrane fusion process. In vitro studies show that membrane fusion is triggered on exposure of the virus to low pH, when the E proteins undergo a dramatic re-organization which leads to the formation of trimers. The crystal structure of the E protein has been solved in its dimeric pre-fusion, and trimeric post-fusion configurations. Although much is known about the molecular mechanisms involved in the membrane fusion process, many critical questions regarding the cell entry pathway of flaviviruses remain unanswered.

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A recent paper dissects the cell entry pathway of DENV by tracking single fluorescently-labeled DENV particles in living cells expressing various fluorescent cellular markers, using real-time multi-color fluorescence microscopy (Dissecting the Cell Entry Pathway of Dengue Virus by Single-Particle Tracking in Living Cells. 2008 PLoS Pathog 4(12): e1000244). It shows that DENV particles are delivered to pre-existing clathrin-coated pits by diffusion along the cell surface. Following clathrin-mediated uptake, the majority of DENV particles are transported to early endosomes, which mature into late endosomes, where membrane fusion occurs. This is the first study that describes the cell entry process of DENV at the single particle level and therefore provides unique mechanistic and kinetic insights into the route of entry, endocytic trafficking behavior, and membrane fusion properties of individual DENV particles in living cells.

This work opens new avenues in flavivirus biology and will lead toward a better understanding of the critical determinants in DENV infection. Single-particle tracking has substantially enriched our knowledge of virus cell entry mechanisms and has revealed previously unknown aspects of virus-host interactions. The mechanistic and kinetic insights offered by this technique provide a better understanding of disease pathogenesis and may lead to a rational design of antiviral drugs and vaccines.

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MicrobiologyBytes 2008 – Review of the Year

Monday, December 22nd, 2008

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It’s been another busy year at MicrobiologyBytes, with more than 300 posts this year, and over half a million page views, so here’s a whistle-stop tour of just some of the topics we’ve looked at during the last year:

January

February

March

April

May

June

July

August


September

October

November

December

So what’s going to happen in 2009? Watch the video, and keep reading MicrobiologyBytes!

UK Norovirus Outbreak December 2008

Friday, December 19th, 2008

Noroviruses The BBC is reporting that thousands of people across the UK suffer from Norovirus infection, which causes vomiting and diarrhoea, so this is the time to remind you of the information I posted about these viruses in January 2007:

Hardly a day goes by without another outbreak of Norovirus infection being reported in the news. That’s particularly true at this time of year, and it’s no accident that the consequences of Norovirus infection used to be known as “winter vomiting disease”, although infections occur year round. And yet, in spite of how common they are, these viruses are not household names in the same way as influenza and polio, so MicrobiologyBytes comes to the rescue!

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Historically, noroviruses have been named after the places where outbreaks occurred. By far the most famous Norovirus is Norwalk virus, named after an outbreak of acute gastroenteritis in children at an elementary school in Norwalk, Ohio, in November 1968. These viruses remained poorly understood however, since for the most part, they do not grow in the laboratory. The taxonomy of these viruses became confused and they were previously grouped on the basis of their appearance in the electron microscope, and this led to the name “Small Round-Structured Viruses”. By adding labelled antibodies and performing immune electron microscopy (IEM), it became possible to be a bit more specific which virus was being studied. However, it was not until the genomes of these viruses were cloned and sequenced in the 1990s that the situation became clearer. Based on this molecular information, Norwalk virus and its troublesome little friends became a new genus, Norovirus, in the Calicivirus family, with which they share similarities.

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Molecular approaches to bioremediation

Monday, December 15th, 2008

Oil spill Bioremediation can be defined as a process that uses microorganisms, fungi, green plants or their enzymes to return the natural environment altered by contaminants to its original condition. A major advantage of bioremediation is its reduced cost compared to conventional cleanup techniques – the cost of remediation for all contaminated sites in the USA alone is estimated to be $1.7 trillion (Molecular approaches in bioremediation. Curr Opin Biotechnol. Nov 12 2008). In addition, bioremediation is often a permanent solution providing complete transformation of the pollutant to its molecular constituents like carbon dioxide and water rather than a partial method that transfers wastes from one phase to another. Unfortunately, there are many man-made compounds that lack good biological catalysts, and many instances where good biocatalysts fail to transform pollutants in the environment.

Bacteria have enormous potential for cleaning up wastes; however, the interactions between bacteria and pollutants are complex and suitable outcomes do not always take place. Hence, molecular approaches are being applied to enhance bioremediation. One advance in bioremediation to improve the stability of the biocatalyst is to create a system where degradation occurs in the area near the roots of plants known as the rhizosphere. In rhizoremediation, the bacteria degrade the pollutants while the plant roots provide a niche for the microorganism and key nutrients. The advantages of rhizoremediation include the ability of plant roots to provide a large surface area for bacterial propagation and biofilm formation, the roots transport the bacteria through the contaminated soil, the roots provide a niche for the bacteria by providing nutrients, and the roots facilitate oxygen exchange. Successful rhizoremediation systems have been established for pollutants such as polycyclic aromatic hydrocarbons, polychlorinated biphenyls (PCBs), fuels, metals, and pesticides such as parathion.

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Directed evolution or DNA shuffling is a powerful mutagenesis technique that mimics the natural molecular evolution of genes in order to efficiently re-design them. Its power lies in the fact that it can introduce multiple mutations into a gene in order to create new enzymatic activity, which can be discovered by a suitable method of selection (bioassays). Family shuffling applies DNA shuffling to groups of related genes to combine them in a manner that accelerates directed evolution. Genome shuffling recombines the chromosomes of several bacteria to enhance the activity of the whole organism.

Metabolic engineering involves redirecting a cell’s metabolism to achieve a particular goal using recombinant engineering. This technique has been used to create bacterial strains that degrade chlorinated ethenes through the addition of several cloned enzymes to the cell. Metabolic engineering has also been used successfully to handle difficult mixtures of pollutants.

Whole-transcriptome profiling using DNA microarrays has the advantage that the relative amount of transcripts from the whole genome may be easily determined compared to such techniques like proteomics. To understand the metabolism of bacteria in the rhizosphere, researchers have begun to utilize whole-genome profiling.

Although a tremendous amount of work remains to be performed, significant advances have been made through protein engineering and through metabolic engineering for the purposes of bioremediation. However, even though whole-transcriptome profiling and proteomics are utilized routinely in some disciplines, they remain to be utilized extensively in bioremediation. Furthermore, it is important to ensure engineered strains for field use are competitive; rhizoremediation can provide a niche for these engineered bacteria. Chromosomal integration of introduced genes can limit horizontal gene transfer to other species, but this should also be empirically verified to ensure that no adverse environmental effects occur.

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New ways to beat malaria

Monday, December 1st, 2008

Malaria antigens One of the main problems in fighting malaria is the speed with which Plasmodium falciparum, the causative agent of human malaria, is able to vary its genetic makeup. This allows antigenic variation, which makes the creation of effective vaccines very difficult. Antigenic variability also gives P. falciparum the ability to persist in the face of an immune reaction and to reinfect people who have been previously exposed to the disease. Effective immunity to malaria requires repeated infections and is slow to develop, so children under ten years of age are most susceptible to illness. The entry of malaria parasites into red blood cells during the replication cycle creates two opportunities to evade host immunity. First, infected red blood cells do not induce a CTL response due to their lack of MHC I expression. Second, malaria antigens exposed on the surface of the cell are highly variable. The P. falciparum erythrocyte membrane protein 1 (PfEMP1) is a key virulence factor which is expressed on the surface of infected erythrocytes and causes the blood cells to stick to the walls of small blood vessels, preventing infected cells from going through the general circulation and to the spleen (see: Giving malaria the slip).

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Red blood cells infected with Plasmodium display immunodominant parasite antigens on their surface. The reason for this is not clear, but it may be to modify the physical properties of the host cells so that they are not trapped and destroyed in the spleen. The expression of the immunodominant surface protein PfEMP1 is also linked to suppression of host interferon-gamma in the early immune response to the parasite, and low interferon-gamma levels may improve parasite survival.

PfEMP1 is in fact a family of cell surface molecules, encoded by approximately 60 var genes. Antigenic variation is controlled by epigenetic factors including monoallelic var transcription in separate domains at the nuclear periphery, differential histones on otherwise identical var genes, and var gene silencing mediated by telomeres (Antigenic variation in Plasmodium falciparum. Annu Rev Microbiol. 2008 62: 445-470).

Targeting the mechanisms responsible for antigen switching could be a promising approach to tackle the malaria parasite without having to deal with phenotypic variation of the surface molecule. The development of specific biological assays that target antigenic variation could uncover crucial mechanisms required for export to the cell surface, repression of the var gene family, or switching to new variants and would allow the screening of drugs which block these essential processes. Plasmodium’s trump card could yet prove to be its undoing.

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HIV-2 – a kinder AIDS virus?

Monday, November 24th, 2008

HIV-2 distribution HIV-2 is retrovirus a closely related to HIV-1, but seems to cause AIDS in only a minority of infected individuals (HIV-2: the forgotten AIDS virus. Trends in Microbiology 2008 Oct 27). Determining exactly why HIV-2 causes asymptomatic infection in most people could further our understanding of HIV immunopathogenesis. Studies to date have suggested that both enhanced immune responses and lower virus replication could play a role. Investigating immune responses in HIV-1-infected long-term nonprogressors (LTNPs) is one of the main approaches used to identify aspects of protective immunity to HIV, but the study of LTNPs is restricted by the small proportion of HIV-1-infected individuals who display slow or no progression to AIDS. In contrast, valuable insights might be gained into HIV immunopathogenesis from studies of HIV-2 cohorts with their high proportion of LTNPs.

HIV-2 is estimated to have entered the human population in 1940 (±16 years), approximately a decade after the introduction of HIV-1 into humans. The prevalence of this virus is highest in West Africa. Although the clinical features of HIV-2 AIDS mirror those of HIV-1, the AIDS-free survival rate at 5 years is significantly greater and the rate of CD4+ T cell decline was much slower than with HIV-1.

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HIV-2 does not appear to be an attenuated virus since it is able to replicate equally as well as HIV-1, however, virus load and plasma RNA levels during the asymptomatic stages of HIV-2 infection are approximately 30-fold lower than with HIV-1. The reason for this seems to be better host immune control of HIV-2 infection. There is evidence that innate, cellular and humoral immune responses might all be more effective at controlling HIV-2 infection than HIV-1. Immune activation is also lower in HIV-2 patients than HIV-1 patients, resulting in a lower rate of CD4+ T cell decline. Unfortunately, HIV-2 infection offers no protection against HIV-1.

HIV-2 offers tantalizing glimpses into how HIV-1-induced AIDS might be approached, although as yet this has not had any tangible practical benefits.

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Iron Uptake and Virulence

Monday, November 17th, 2008

Iron All living organisms need iron to survive. Iron is involved mainly in electron transfer reactions. Many parasites have a high iron requirement. In mammals, iron is closely regulated. Extracellular free iron is essentially unavailable and iron availability has a crucial role in the fight against pathogens. In plasma, circulating iron is bound to transferrin and in external secretions such as colostrum, iron is bound to lactoferrin. Therefore, microbial pathogens have developed specialized and effective mechanisms to acquire iron during infections (Crusade for iron: iron uptake in unicellular eukaryotes and its significance for virulence. Trends in Microbiology 2008 16: 261-268).

Pathogens use two general strategies for iron acquisition from their hosts. The first is direct contact between the pathogen and the host iron source (usually an iron-containing protein). The second strategy uses secretion and subsequent uptake of small iron-binding molecules called siderophores, which are able to remove iron from host proteins because of their high affinity for the metal. These systems have been studied in many different pathogens.

Iron-acquisition strategies of fungi essentially consist of siderophore production, reductive iron-uptake and haem-uptake systems. Some fungi make siderophores, others do not, including the pathogenic Candida albicans. However, even species which cannot produce any siderophores can take up xenosiderophores – siderophores produced by other organisms (bacteria and fungi).

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Trypanosoma brucei is a protozoan parasite responsible for sleeping sickness in humans and a disease Nagana in domestic livestock in Africa. Trypanosomes obtain iron from host transferrin, and encode a number of different transferrin receptors which vary in their affinities for transferrins from different host species. Leishmania are parasites that require a sand fly vector and a mammalian host to complete their life cycle. As expected from the diversity of the environments Leishmania encounters during its life cycle, this parasite is able to use iron from several sources, such as transferrin, lactoferrin or haemin.

Because of the importance of iron to pathogens, siderophore-blocking drugs could turn out to be effective antimicrobial compunds against organisms which rely on this method of iron uptake, although none are in use yet. Another mystery of pathogen iron metabolism is iron storage. Once the cell takes up iron, it must be safely sequestered or it would participate in the generation of reactive oxygen species. In most organisms, this is ensured by iron-storage proteins, mainly ferritin. The majority of unicellular eukaryotes, such as yeast and parasitic protists, do not possess ferritin and the mechanism of intracellular iron storage in these organisms is not clear. In yeasts, the vacuole seems to have the function of an iron-storage compartment. It is important to complete our knowledge of the mechanisms of iron metabolism in pathogens because this might lead to the development of novel chemotherapeutic strategies. Without effective mechanisms for acquisition and utilization of iron, no parasite can survive.

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