Posts Tagged ‘Education’

MicrobiologyBytes Halloween House of Horror Part II: Monsters, microbiology and mathematics – the epidemiology of a zombie apocalypse

Thursday, October 31st, 2013

Zombie Generally speaking, I don’t “do” halloween, so it comes as a bit of a surprise to me that this is my second halloween post of the day, but this one really was too good to miss:

Monsters, microbiology and mathematics: the epidemiology of a zombie apocalypse. Journal of Biological Education 29 Oct 2013, doi: 10.1080/00219266.2013.849283
Abstract: The aim of this learning exercise was to harness current interest in zombies in order to educate audiences about the epidemiology of infectious disease. Participants in the activity were provided with an outbreak scenario, which they then used as the basis of play-based activities. By considering the mode and speed of transmission, size of outbreak and prevention/control strategy, participant groups were able to define parameters of their outbreak scenario. These were then input to SimZombie, a computer simulation program developed by the authors, which visually demonstrated the spread of infection through a population. The resulting animations were then used as the basis of in-depth discussion which, in turn, enabled the consideration of principles of disease transmission and control strategies. The activity provided an opportunity to engage a range of audiences through a variety of different delivery mechanisms, including role play, workshops and informal drop-in. Learning was evidenced by participation and feedback.


So why did I post this (apart from the obvious halloween angle)? The authors make a pretty strong case for this approach to communicating microbiology to a wider audience:

“Given the increasingly connected nature of the global community, there is a pressing need for a better public understanding of disease dynamics. In UK schools and colleges, knowledge of infectious diseases is indicated in the school science curriculum. For the general public, salient facts about infectious disease include principles of disease prevention and control and awareness of transmission routes. Public information is generally provided through the media, leaflets in surgeries/pharmacies and via the internet, but these are typically ‘one-way’ modes of communication, with no subsequent evaluation of learning acquisition. Engagement can therefore be enhanced by modifying the delivery system to use a novel vehicle or context, such as mixing science with art, literature,or games. Vampires, and other ‘monsters’ such as zombies and werewolves, potentially offer a focus for engagement with disease transmission and outbreaks. Thus, a workshop delivered for the 2010 Manchester Children’s Book Festival used the Twilight novel in that context. The workshop was set in a biology laboratory, with microscopes and slides of the cell cycle available for examination. Using readings from the novel and facilitated discussion, the participants identified routes of vampirism/disease transmission, and considered analogous methods of prevention (garlic as a representation of an antimicrobial; ‘not inviting them in’ representing behaviour modification).”

That’s the first time I’ve ever cited Twilight on MicrobiologyBytes: the horror, the horror. Don’t expect it happen again anytime soon :-)


What do you think a virus is?

Monday, September 23rd, 2013

Viruses Humans are exposed to viruses everywhere they live, play, and work. Yet people’s beliefs about viruses may be confused or inaccurate, potentially impairing their understanding of scientific information.

This study used semi-structured interviews to examine people’s beliefs about viruses, vaccines, and the causes of infectious disease. The authors compared people at different levels of science expertise: middle school students, teachers, and professional virologists. The virologists described more entities involved in microbiological processes, how these entities behaved, and why.

Quantitative and qualitative analyses revealed distinctions in the cognitive organization of several concepts, including infection and vaccination. For example, some students and teachers described viral replication in terms of cell division, independent of a host. Interestingly, most students held a mental model for vaccination in which the vaccine directly attacks a virus that is present in the body. The findings have immediate implications for how to communicate about infectious disease to young people.


Expert–novice differences in mental models of viruses, vaccines, and the causes of infectious disease.” Public Understanding of Science (2013) Public Understanding of Science 19 2013 doi: 0963662513496954

Major changes to Bioscience Horizons

Tuesday, April 23rd, 2013

Bioscience Horizons

1. Now the International Journal of Student Research – we accept papers from across the world

2. Now accepting papers from taught masters as well as undergraduate

3. Now accepting multiple authors (to include supervisors) although the student must be the primary author.


[Video] The Peter Wildy Prize for Microbiology Education 2013

Tuesday, April 2nd, 2013

Full length video of this great talk – make sure you watch this!


All Shiny and New – the all new, all singing, all dancing Society for General Microbiology Website

Monday, March 25th, 2013


As we hardy British microbiologists frolic in the snow in what passes for Spring in Manchester, the Society for General Microbiology has just launched its brand new website, where all the microbiology information you need is only a click away:

Society for General Microbiology website


Virology Weekly Newsletter 22.03.2013 – Bumper End of Term Prion Edition!

Friday, March 22nd, 2013

Principles of molecular virology Students taking my virology course at the University of Leicester get a weekly newsletter containing extra links relevant to the lectures. This week we have been looking at sub-viral agents and the class notes are from Principles of Molecular Virology, chapter 10.



The Importance of Prions. (2013) PLoS Pathogens 9(1): e1003090
While agent host-range and strain properties convinced early researchers of a viral etiology, the once unorthodox postulate that prion transmission occurs by conformational corruption of host-encoded cellular prion protein (PrPC) by a pathogenic isoform (PrPSc) is now widely accepted. Indeed, conformational templating is increasingly understood to be a general mechanism of protein-mediated information transfer and pathogenesis. The high infectivity of prions, their capacity to cause neurodegeneration in genetically tractable animal models, as well as the ability to culture prions in cells, or under cell-free conditions using defined components, provide finely controlled experimental settings in which to elucidate general mechanisms for all diseases involving protein conformational templating, and thus to develop integrated therapeutic approaches.

Unusual infectious agents

Proteins behind mad-cow disease also help brain to develop
Prions are best known as the infectious agents that cause ‘mad cow’ disease and the human versions of it, such as variant Creutzfeldt–Jakob disease. But the proteins also have at least one known useful function, in the cells that insulate nerves, and are suspected to have more. Now researchers have provided the first direct evidence that the proteins play an important role in neurons themselves, lending a hand in forming neuronal connections.

Susan Lindquist: Protein Folding and Prions

Behavior of Prions in the Environment: Implications for Prion Biology. (2013) PLoS Pathogens 9(2): e1003113
The basic parameters of prion environmental interactions are only beginning to be described, and the effect of these interactions on prion transmission and pathogenesis are poorly understood. The interaction of prions in the environment is complex and must include consideration of the route of introduction for prions to the environment as well as the effects of soil properties and prion strain on prion interaction with soil. Once bound to soil, prions do not readily disassociate from the soil particle and remain highly infectious. The implications of these important observations are that prions immobilized to soil may persist at the surface where transmission to a naïve host would be more likely to occur. Strain-specific interactions with the environment may result in preferential selection of strains that have properties that favor environmental persistence and transmission.

Kuru: The Science and The Sorcery

Acquisition of Drug Resistance and Dependence by Prions. (2013) PLoS Pathogens 9(2): e1003158
Prions consist of PrPSc, an aggregated conformer of the host protein PrPC. PrPSc multiplies by catalyzing the conformational conversion of PrPC into a likeness of itself. Prions present as distinct strains that have the same primary amino acid sequence but differ in their conformation. Many distinct mouse-derived prions strains, for example RML, 22L or Me7, have been isolated. Prions can adapt to their environment. We investigated whether propagation of swainsonine-sensitive RML prions in the presence of the drug would yield swainsonine-resistant variants. Propagation of prions in the presence of an inhibitory drug may not only cause the selection of drug-resistant prions but even of stable prion variants that propagate more efficiently in the presence of the drug. These adaptations are most likely due to conformational changes of the abnormal prion protein.

Virology Weekly Newsletter 15.03.2013

Friday, March 15th, 2013

Principles of molecular virology Students taking my virology course at the University of Leicester get a weekly newsletter containing extra links relevant to the lectures. This week the class notes are from Principles of Molecular Virology, chapter 7.



Antiviral drugs

Antivirals versus vaccines

Antivirals versus vaccines

Viruses and Cancer

Viruses and Cancer

NEWS: Receptor for new coronavirus-EMC identified
The cell receptor for the coronavirus-EMC, which has so far infected 15 humans with 9 deaths, has been identified as dipeptidyl peptidase 4 (DPP4). Nice work. Evidence:
- Soluble DPP4 blocks infection of susceptible cells with CoV-EMC.
- Expression of DPP4 in non-susceptible cells renders them susceptible to infection.
- Antibody to DPP4 blocks infection of cells with CoV-EMC.
- Purified DPP4 protein binds CoV-EMC and inhibits infection.



Virology Weekly Newsletter 08.03.2013 – Virus Infection

Friday, March 8th, 2013

Principles of molecular virology Students taking my virology course at the University of Leicester get a weekly newsletter containing extra links relevant to the lectures. This week we have been looking at virus genomes and the class notes are from Principles of Molecular Virology, chapter 6.


Biology of Plant Virus Infection:


A virological view of innate immune recognition
Innate immune recognition The innate immune system uses multiple strategies to detect viral infections. Because all viruses rely on host cells for their synthesis and propagation, the molecular features used to detect viral infections must be unique to viruses and absent from host cells. Research in the past decade has advanced our understanding of various cell-intrinsic and cell-extrinsic modes of virus recognition. This review examines the innate recognition from the point of view of virus invasion and replication strategies, and places innate sensors in the context of detecting viral genome, replication intermediate, transcriptional by-product, and other viral invasion strategies. On the basis of other unique features common to viral infections, undiscovered areas of virus detection are discussed.
A virological view of innate immune recognition. (2012) Annu Rev Microbiol. 66: 177-196

This relates back to defective virus genomes, which we covered earlier in the course:
Defective viruses are viral particles with genetic mutations or deletions that eliminate essential functions, so that they cannot complete their life cycles independently. They can reproduce only by co-infecting host cells with functional viruses and ‘borrowing’ their functional elements. Defective viruses have been observed for many human pathogens, but they have not been thought to impact epidemiological outcomes. Recently it was reported that a lineage of defective dengue virus spread through humans and mosquitoes in Myanmar for at least 18 months in 2001–2002. This study investigates the emergence and epidemiological impact of this defective lineage by combining genetic sequence analyses with mathematical models. It shows that the defective lineage emerged from circulating dengue viruses between June 1998 and February 2001, and that it spreads because its presence causes functional dengue viruses to transmit more efficiently. This study demonstrates the potential for defective viruses to affect the epidemiology of infectious diseases.
Phylodynamic Analysis of the Emergence and Epidemiological Impact of Transmissible Defective Dengue Viruses. (2013) PLoS Pathog 9(2): e1003193. doi:10.1371/journal.ppat.1003193


Virology Journal Club 07.03.2013

Thursday, March 7th, 2013

HepG2 cells infected with the hepatitis B virus This term students taking my virology course at the University of Leicester are doing a series of tutorials involving reading and explaining research papers in virology. This is the sort of exercise which is common in graduate schools and regularly performed by researchers, and is known as a “journal club”. We cannot give students access to the facilities or equipment to study dangerous human viruses at the forefront of research, so gaining an deep understanding of the way into which research is currently being conducted in this area is the closest we can come to allowing them to be “real virologists”. Today, we are looking at the following paper:

Sodium taurocholate cotransporting polypeptide is a functional receptor for human hepatitis B and D virus. (2012) eLife, 1: e00049


How do you read a research paper? Start with a quick scan: what’s this all about?

From the Abstract:

  • Human hepatitis B virus (HBV) infection and HBV-related diseases remain a major public health problem. Individuals coinfected with satellite hepatitis D virus (HDV) have more severe disease.
  • Cellular entry of both viruses is mediated by HBV envelope proteins. The pre-S1 domain of the large envelope protein is a key determinant for receptor(s) binding.
  • Near zero distance photo-cross-linking and tandem affinity purification [What is this?] revealed that the receptor-binding region of pre-S1 specifically interacts with sodium taurocholate cotransporting polypeptide (NTCP), a multiple transmembrane transporter predominantly expressed in the liver.
  • Silencing [RNA interference] NTCP inhibited HBV and HDV infection, while exogenous NTCP expression made a non-susceptible hepatocarcinoma cell line susceptible to infection.
  • Replacing amino acids 157–165 of nonfunctional monkey NTCP with the human counterpart conferred the ability to support infection.


At this stage it is useful to scan though the figures and explanatory figure legends in the paper to get an overview of the data:


Figure 1. Developing photoreactive peptide ligands and an antibody for identifying pre-S1 binding partner(s) by zero distance cross-linking
A) Monoclonal antibody (mAb) 2D3 binding epitope (grey box) and modified peptides for cross linking. UV cross-linking converts non-covalent interactions between proteins or simply their proximity into covalent bonds.
B) Binding of mutant HDV L proteins to cells (PTH: primary Tupaia hepatocytes).
C) Peptide inhibition of HDV binding.
D) Peptide inhibition of HBV and HDV infection.
E) Epitope mapping of 2D3 antibody.

Figure 2. Identification of pre-S1 binding protein on primary Tupaia hepatocytes with photoreactive peptide Myr-47/WTb
A) Western blot of bound protein.
B) WT but not mutant peptide competes for binding.
C) The abundance of the target protein(s) in PTH cells decreases over time.
D) Cross linked target protein.
E) Purification of target protein(s) for mass spectrometry analysis.
F) Sequence of target protein.

Figure 3. Binding of NTCP to N-terminal peptide of pre-S1 and HDV virions
A) Western blots from 293T cells transfected with hNTCP or tsNTCP expression vectors.
B) Confocal microscopy of 293T cells [human embryonic kidney cell line] transfected with hNTCP or tsNTCP expression vectors.
C) FACS analysis of FITC-labeled pre-S1 peptide binding to hNTCP transiently transfected Huh-7 cells.
D) HDV binding to Huh-7 cells transfected with hNTCP or tsNTCP expression vectors.

Figure 4. HDV and HBV infection of hepatocytes requires NTCP
A) HDV and HBV infection of PTHs is inhibited by tsNTCP siRNA knockdown.
B) HDV and HBV infection of HepaRG is inhibited by NTCP siRNA knockdown.
C) Knockdown of hNTCP in primary human hepatocytes (PHH) hampers HBV infection.

Figure 5. NTCP expression confers Huh-7 susceptibility to HDV infection
A) NTCP mRNA expression levels.
B) Transfected cells stained with 4G5 antibody to HDV delta antigen.
C) Inhibition of HDV infection of Huh-7 cells transfected with hNTCP.
D) HDV RNAs detected by RT-PCR.
E) HCV moi dose response. [Efficiency of infection is low, ~10%]
F) Infection response to hNTCP level.

Figure 6. NTCP expression confers susceptibility to HBV infection [See response to referees comments]
A) Intracellular expression of HBsAg in HBV-infected HepG2-hNTCP stable cells.
B) Secreted HBeAg levels in the supernatants of HBV-infected cells.
C) Dose response of HBV infection.
D) Southern blot analysis of cccDNA
E-F) Kinetic analysis of HBV cccDNA and RNAs in HBV-infected HepG2-hNTCP cells.


Analysis Checklist

What did the authors want to find out or prove? Why? (Introduction)
HBV-related liver diseases remain a major public health problem, causing approximately 1 million deaths per year. Progress in HBV research has been impeded by the lack of understanding of HBV entry process by which the virus specifically infects human liver cells. HDV is a small satellite RNA virus of HBV carrying all three HBV envelope proteins and can only propagate when coexisting with HBV. The pre-S1 domain of the L protein is a key determinant for entry of both HBV and HDV and was believed to mediate viral interaction with the cellular receptor(s) on hepatocytes. An N-terminal myristoylated peptide corresponding to amino acids 2–48 of the pre-S1 domain of the L protein has been shown to block both HBV and HDV infection of hepatocytes. By using a synthetic modified peptide originating from the native aa 2–48 lipopeptide (Myr-47/WT) as a probe the authors set out to identify the HBV/HDV receptor.

What exactly did they do? (Methods)
HBV infects only primary hepatocytes in humans, chimpanzees and a primate-like animal called the treeshrew (Tupaia belangeri), but it does not infect other animals such as monkeys, rats, mice or rabbits. So far, no transformed or immortalized cell lines can be infected with HBV. HBV research is limited by the availability of primary hepatocytes from permissive hosts. The authors used primary hepatocytes from Tupaia and human liver and a number of cell lines to investigate HBV/HDV infection.
Infection of cells was measured by antibody staining and real time RT-PCR analysis of HDV genome and antigenome RNAs. HBV covalently closed circular DNA (cccDNA) was measured by Southern blot analysis and qPCR.
Expression vectors expression Tupaia and human PTH were made from cDNA libraries.
Photo-cross-linking of peptide ligand and tandem purification of the target molecule(s) was carried out. Cross-linked target proteins were identified by mass spectrometry and bioinformatic data bases.
Gene knockdowns of NTCP in cultured cells was performed by siRNA interference.

What were their results? (Results)
Photo-cross-linking of a synthetic peptide derived from the native pre-S1 peptide with certain residues replaced by nonnatural amino acids (L-photo-leucine, L-2-amino-4,4-azi-pentanoic acid) identified NTCP as a specific binding protein of pre-S1 (partial sequence obtained by mass spectrometry (MS) analysis).
This was confirmed by cloning and expressing human and Tupaia NTCP and showing that NTCP expression was required for HBV and HDV infection, and conversely that HBV/HDV infection is reduced by siRNA knockdown of NTCP.
NTCP expression made non-susceptible hepatocarcinoma cells (Huh-7 and HepG2) permissive for HDV and HBV infection.
Residues 157 to 165 of hNTCP are critical for pre-S1 binding and virus infection.

What do these results mean? (Discussion)
The liver bile acid transporter, NTCP, specifically interacts with a key region in the pre-S1 domain of the HBV envelope L protein, and functions as a major receptor of HBV/HDV.
Why this protein? NTCP is a multiple transmembrane glycoprotein presumed to span the cellular membrane up to 10 times with small extracellular loops and is mainly expressed in the liver consistent with the liver tropism of HBV and HDV.
NTCP is functionally conserved in mammalians, but protein sequences of NTCP vary among species, which is likely to contribute to the narrow species tropism of HBV infection.

What else could the authors have done? What should they do next? What are the strengths and weaknesses of this paper? Why does this research matter? (Synthesis)
Identification of NTCP as a functional receptor for HBV and HDV advances our understanding of their entry into host cells and may lead to new prevention and treatment strategies against these viruses and related diseases.

Interestingly, eLife is one of the new generation of scientific journals that publish referees comments on the submitted manuscript and the authors responses to these, a stage in scientific research is normally kept secret. In this case, there was an interesting discussion around the fact that the efficiency of infection is low (5-10%). Does this indicate that NTCP is not the only HBV receptor in vivo, that other soluble factors in the blood or other co-receptor/entry components boost the efficiency in vivo, or that the microenvironment and architecture of hepatocytes in the liver affects the infection process?

In any case, this paper is a major technical tour de force and a major advance in understanding HBV infection.