MicrobiologyBytes

The introduction of antibiotics is one of the most important medical interventions with regard to reducing human morbidity and mortality. However, the intensive use of antibiotics (which was estimated in 2002 to be 100,000–200,000 tonnes per annum worldwide and which is, in total, well over 1 million tonnes since the 1940s) has dramatically increased the frequency of resistance among human pathogens and threatens a loss of therapeutic options and a post-antibiotic era in which the medical advances to date are negated. Resistance dramatically reduces the possibility of treating infections effectively and increases the risk of complications and of a fatal outcome.

Most antibiotic resistance mechanisms are associated with a fitness cost that is typically observed as a reduced bacterial growth rate. The magnitude of this cost is the main biological parameter that influences the rate of development of resistance, the stability of the resistance and the rate at which the resistance might decrease if antibiotic use were reduced. These findings suggest that the fitness costs of resistance will allow susceptible bacteria to outcompete resistant bacteria if the selective pressure from antibiotics is reduced. Unfortunately, the available data suggest that the rate of reversibility will be slow at the community level. This paper reviews the factors that influence the fitness costs of antibiotic resistance, the ways by which bacteria can reduce these costs and the possibility of exploiting them. A better understanding of fitness costs and compensatory evolution and their impact on the emergence and spread of resistant bacteria should allow us to make better quantitative predictions about the rate and trajectory of the evolution of resistance towards new and old drugs and offers possibilities to prevent this evolution.

Antibiotic resistance and its cost: is it possible to reverse resistance? Nature Reviews Microbiology 8, 260 (2010) doi:10.1038/nrmicro2319

Related:

• The clinical consequences of antibiotic resistance
• Antibiotics, your gut, and you
• Resistance to Widely-Used Antibiotics among Inhabitants of Remote South American Villages

Tuesday 30 March 2010

Follow this event on Twitter: #sgmed10

When asked what they are looking for in a microbiology graduate, employers often stipulate a well-rounded individual who is self-motivated, can solve problems and interacts productively with fellow scientists. This symposium, organised jointly by the SGM and the HE Academy UK Centre for Bioscience, will give you the opportunity to discuss innovative approaches to delivering this paragon. The first half will look at how we can foster the key skills of creativity, problem-solving and enquiry-based learning in the laboratory and field. This will include a keynote presentation about an exciting ‘Phage-Hunting’ project from the University of Pittsburgh, which allows students from a range of educational backgrounds to engage in authentic scientific enquiry. We will then explore the impact of social networking tools, both on our students’ learning and on our own teaching practice. The symposium should be of interest to anyone involved in teaching microbiologists who wants to learn how to exploit the power of emerging approaches and technologies. If you think Twitter is just for chatting to celebrities, it’s time to take a fresh look!

Promoting key skills in microbiology teaching:
0830 Carol Wakeford, University of Manchester: A culture of creativity: techniques to foster new ideas.
0930 Tina Overton, Higher Education Academy, Hull Problem solving.
1100 Gus Cameron, eBioLabs, University of Bristol: Laboratory skills.
1400 Graham Hatfull, University of Pittsburgh: Where there’s smoke there’s PHIRE: authentic research projects for novice researchers.

Using Web2.0 technologies for teaching microbiology: information overload or filter failure?
1500 Cameron Neylon, STFC Rutherford Appleton Laboratory, Didcot: Information overload or filter failure?
1530 Vincent Racaniello, Columbia University Medical Center, New York: Social media in microbiology education and research.
1630 Kevin Emamy / Jason Hoyt, CiteULike, London / Mendeley, London: Automated discovery of scientific literature.

More information

Within the past century, a number of “emerging viruses” with pathogenic properties, such as HIV-1, SARS-CoV, and several novel reassortments of influenza A, have entered the human population on a large scale. However, novel pathogenic viral infections of humans are not unique to modern history. “Paleovirology” is the study of ancient extinct viruses (called “paleoviruses”) and the effects that these agents have had on the evolution of their hosts. Thus far, the study of these viruses has mostly been limited to endogenous retroviruses that can be directly identified from their remnants in host genomes. However, one can infer the existence of other paleoviruses from their evolutionary pressures on host genes. This paper suggests that selection to survive the pathogenic effects of these viruses has shaped our repertoire of antiviral defenses in ways that impact our resistance or susceptibility to modern-day emerging viruses.

Paleovirology – Modern Consequences of Ancient Viruses. 2010 PLoS Biol 8(2): e1000301 doi:10.1371/journal.pbio.1000301

Related:

• Phoenix from the ashes: The 5 million year old virus
• The Island of Fossil Viruses

Poxviruses are considered to be unique among DNA viruses because their infection cycle is carried out exclusively in the host cytoplasm. Such an infection strategy is of interest, because it necessitates generation of elaborate factories in which viral replication and assembly are promoted. By using imaging techniques, researchers showed that the infection cycle of the largest virus currently identified, the Acanthamoeba polyphaga Mimivirus, similarly occurs exclusively in the host cytoplasm. Newly synthesized mRNAs accumulate at discrete cytoplasmic sites that are distinct from the sites where virus replication occurs, and this is also observed in vaccinia infection. By revealing substantial physiologic similarity between poxviruses and Mimivirus and thus, implying that an entirely cytoplasmic viral replication might be more common than generally considered, these findings underscore the ability of DNA viruses to generate large and elaborate replication factories.

Vaccinia-like cytoplasmic replication of the giant Mimivirus. PNAS USA March 15 2010 doi: 10.1073/pnas.091273710

Related:

• DNA Viruses
• Marvellous mimivirus
• Marine mimivirus relatives are large algal viruses
• Mimivirus and the Stargate

Most of my work over the last few years has been involved with science education, and much of the online effort has gone into surfacing aspects of the scientific literature by making it accessible to a student audience, and indeed the general public, should they be interested. Mostly, this has meant developing the MicrobiologyBytes website, along with its Twitter, Friendfeed and Facebook satellites. In my “education hat on” guise, I write frequently online about my work on Science of the Invisible, Twitter and Friendfeed. So why would I need another public outlet?

Open notebook science (ONS) is the practice of making the primary record of a research project publicly available online as it is generated. This involves placing the personal, or laboratory, notebook of the researcher(s) online along with all raw and processed data, and any associated material. The approach can be summed up by the slogan “no insider information”. This is far from the norm of scientific practice, but over the last year of talking to some of the leading practitioners of ONS, notably Jean-Claude Bradley and Cameron Neylon, I have become convinced that I would like to try it. One part of our feasibility test is a new blog, a space where our part-formed thoughts, ideas, planning, and general commentary on ONS stuff will appear. The other part is our open notebook on Wikispaces, where all the data will be posted. If you want to follow our progress, subscribe to the RSS feed for this blog, or go to this page and subscribe with the feed reader of your choice. If you prefer, you can receive updates via your email account.

Open or closed? It’s not that simple. There are many flavours of ONS, and it’s not clear yet which one(s) we want or are able to pursue. Indeed, our style of “open” is one of the first things we need to work out about this project. For a variety of reasons, not all of the research done in our laboratory will switch to ONS. Initially, we intend to try it out with a new project we are developing (which is described below). Thus our approach to ONS is itself an experiment. Only time will tell if we are able or willing to continue in this format. Apart from funding, it depends whether this idea wins hearts and minds – not only in our lab, but beyond it. In part, that depends how much interaction we receive. the project we are beginning is a new field for us, so we don’t expect the world to be queuing up to help us, but to be successful, the downside risk of ONS needs to be balanced by the upside of helpful positive interactions from interested observers.

So what about the science?

The chytrid fungus Batrachochytrium dendrobatidis (Bd) is an emerging pathogen of amphibians worldwide. The aquatic zoospores of this primitive fungus infect larval or adult amphibians, and, depending on the host species and other factors as yet unknown, may cause anything from 0-100% mortality. Coupled with climate change, pollution and habitat loss, chytridiomycosis (or “chytrid”, pronounced “kit-rid”) is a serious threat to many amphibian species. Bd research has moved from obscurity to prominence very rapidly over the past few years, and two complete genome sequences are available (JAM81, JEL423):

http://dan.corlan.net/medline-trend.html

So where do we fit in?

We are trying to leverage our existing skills in molecular biology, antibody production, protein chemistry and microbiology to study this organism. In part, this is because of an interest in the environmental impact of this emerging pathogen, but we are also interested in studying Bd as a model organism to examine aspects of fungal biology and pathogenesis. We are currently interested in developing work in the following areas:

Phage lambda is one of the key model organisms on which molecular biology was built. Such a wealth of existing knowledge on this organism makes it an ideal test model for systems biology. In this article in Microbiology Today (pdf) Rosalind Allen explores the usefulness of this bacteriophage to systems biology and vice versa:

Phage lambda, discovered in 1950, infects sensitive strains of E. coli. For a genome of only 48.5kb, packed into a particle of only 50nm diameter, this phage has attracted a lot of attention. Phage lambda became one of the key model organisms on which modern molecular biology was built. Over a period of intense study lasting 40 years, the genes in the phage lambda genome, the proteins encoded by them and the interactions between these genes and proteins were investigated in great detail. The humble phage lambda was the source of discoveries such as repression and activation mechanisms for gene regulation, chaperone proteins, DNA recombination and restriction enzymes, which microbiologists and many others now take for granted. This huge body of knowledge makes it the ideal test case for systems biology modelling.

Related:

• Bugs Against Biofilms
• Bacteriophages for plant disease control
• Bacteriophage lysogeny

MicroRNAs (miRNAs) are a class of small, ~22 nt regulatory RNAs that modulate a diverse array of cellular activities. Through recognition of sequence complementary target elements found most often in the 3′ untranslated region (UTR) of cellular mRNAs, miRNAs post-transcriptionally regulate numerous cellular processes by way of mRNA translation inhibition or, less commonly, by catalytic mRNA degradation. It is thought that upwards of one-third of all human mRNAs are regulated by the over 700 human miRNAs that are currently known. Many miRNAs can have tissue-specific localizations and, in addition, some are now known to have cancer-specific signatures. The mechanisms by which a miRNA regulates a given mRNA are influenced by parameters such as the degree of sequence homology and target site multiplicity as well as by features of the mRNA itself, including target site secondary structure and location. In addition, the cellular machinery used to translate mRNAs is thought to profoundly affect miRNA regulation. While capped mRNAs are known to be amenable to both catalytic miRNA-induced cleavage and miRNA-mediated translational repression, it has been suggested that uncapped mRNAs that rely on an IRES (Internal Ribosome Entry Site) for translation initiation (such as picornavirus genomes) are not susceptible to translational repression.

Virus host range is shaped by cellular determinants such as transcription factors and receptor expression. In addition, tissue-specific microRNAs can be utilized to direct the specificity of a replication competent picornavirus, Coxsackievirus A21. This report demonstrates the mechanism by which microRNAs are able to directly influence oncolytic viruses, an important class of anticancer agents. It show that microRNA expression is an important determinant of permissivity to picornavirus replication, but the actual abundance of that expression is far more important. There are actually multiple different stages in the life cycle of a replication competent picornavirus that are amenable to regulation by cellular microRNAs. microRNAs can regulate virus tropism in vivo, but circulating high virus titers in the blood can overcome this mechanism of conferring tissue specificity. MicroRNAs are well known to have both oncogenic or oncosuppressive activities in human cancers. Tissue-specific microRNA expression can thus be used to modulate the efficacy of viral anticancer therapeutics.

MicroRNA Antagonism of the Picornaviral Life Cycle: Alternative Mechanisms of Interference. 2010 PLoS Pathog 6(3): e1000820. doi:10.1371/journal.ppat.1000820
In addition to modulating the function and stability of cellular mRNAs, microRNAs can profoundly affect the life cycles of viruses bearing sequence complementary targets, a finding recently exploited to ameliorate toxicities of vaccines and oncolytic viruses. To elucidate the mechanisms underlying microRNA-mediated antiviral activity, we modified the 3′ untranslated region (3′UTR) of Coxsackievirus A21 to incorporate targets with varying degrees of homology to endogenous microRNAs. We show that microRNAs can interrupt the picornavirus life-cycle at multiple levels, including catalytic degradation of the viral RNA genome, suppression of cap-independent mRNA translation, and interference with genome encapsidation. In addition, we have examined the extent to which endogenous microRNAs can suppress viral replication in vivo and how viruses can overcome this inhibition by microRNA saturation in mouse cancer models.

Related:

• Five Questions about viruses and microRNAs
• Virus-encoded microRNAs in herpesvirus biology

RNA replicons are derived from either positive- or negative-strand RNA viruses, from which at least one gene encoding an essential structural protein has been deleted. RNA replicons can be regarded as disabled viruses unable to produce infectious progeny. Despite such gene deletions, the viral RNA is replicated and transcribed by the viral RNA polymerase. Any genetic information encoded by the replicon will be amplified many times, resulting in high levels of antigen expression. This property distinguishes RNA replicons from plasmid DNA-based vaccines, which rely on the initial levels of genetic information successfully delivered to the nucleus. The latter together with the characteristics of DNA replication can prove to be a major hurdle for advancing DNA vaccines. Vaccines based on DNA plasmids often contain regulatory sequences and antibiotic resistance genes. The potential integration of such sequences into the host genome by non-homologous recombination may represent an unknown risk. In contrast, replication/transcription of replicon RNA is strictly confined to the cytosol, and does not require any cDNA intermediates, nor is any recombination with or integration into the chromosomal DNA of the host required. Taken together, several safety issues are associated with DNA vaccines, which do not arise with the much more biosafe RNA-based vaccines. Due to autonomous RNA replication, RNA replicons are able to drive high level, cytosolic expression of recombinant antigens stimulating both the humoral and the cellular branch of the immune system. This review provides an update on the available literature covering influenza virus vaccines based on RNA replicons. The pros and cons of this vaccine strategies are discussed.

RNA Replicons – A New Approach for Influenza Virus Immunoprophylaxis. Viruses 2010, 2, 413-434

Related:

• Protective immunity against influenza
• Influenza vaccines from plants
• Animation of influenza replication

Malaria and alcohol consumption both represent major public health problems. Alcohol consumption is rising in developing countries and, as efforts to manage malaria are expanded, understanding the links between malaria and alcohol consumption becomes crucial. Our aim was to ascertain the effect of beer consumption on human attractiveness to malaria mosquitoes in semi field conditions in Burkina Faso. We used a Y tube-olfactometer designed to take advantage of the whole body odour (breath and skin emanations) as a stimulus to gauge human attractiveness to Anopheles gambiae (the primary African malaria vector) before and after volunteers consumed either beer (n = 25 volunteers and a total of 2500 mosquitoes tested) or water (n = 18 volunteers and a total of 1800 mosquitoes). Water consumption had no effect on human attractiveness to An. gambiae mosquitoes, but beer consumption increased volunteer attractiveness. Body odours of volunteers who consumed beer increased mosquito activation (proportion of mosquitoes engaging in take-off and up-wind flight) and orientation (proportion of mosquitoes flying towards volunteers’ odours). The level of exhaled carbon dioxide and body temperature had no effect on human attractiveness to mosquitoes. Despite individual volunteer variation, beer consumption consistently increased attractiveness to mosquitoes. These results suggest that beer consumption is a risk factor for malaria and needs to be integrated into public health policies for the design of control measures.

Beer Consumption Increases Human Attractiveness to Malaria Mosquitoes. PLoS ONE 5(3): e9546. doi:10.1371/journal.pone.0009546