1st Midland Molecular Microbiology Meeting

The 1st Midland Molecular Microbiology Meeting will take place over the 15th and 16th September @ the University of Birmingham. Midlands Molecular Microbiology Meeting

The Conference will focus on a wide range of topics from metagenomics to host-pathogen interactions. The goal of this conference is to act as a conduit for fostering collaboration among leading scientists who study the molecular biology of prokaryotes and fungi and to promote the exchange of ideas between the next generation of microbiologists.

Expect great talks from keynote speakers:

  • Dlawer Ala’Aldeen (University of Nottingham)
  • Gurdyal Besra (University of Birmingham)
  • Weng Chan (University of Nottingham)
  • Stewart Cole École Polytechnique Fédérale de Lausanne
  • Ian Connerton (University of Nottingham)
  • Ross Dalbey (Ohio State University)
  • Aaron Darling (University of Technology, Sydney)
  • Scott Hultgren (Washington University, St. Louis)
  • Linda Kenney (University of Illinois, Chicago)
  • Robin May (University of Birmingham)
  • Søren Molin (Technical University of Denmark)
  • Laura Piddock (University of Birmingham)
  • Natividad Ruiz (Ohio State University)
  • Torsten Seemann

See you all there!

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The end of the Summer School …..for this year!

……..and as with all things, the Summer School came to an end! The biggest eye opener was the skills and enthusiasm that this bunch of A-level students possessed – and how, for a group of students who didn’t know each other at the start of the week, they bonded into a great cohesive bunch!

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Dave (aka Simon P) and Anne-Marie say – a big thank you to the students for being great, the IMI demonstrators (far too many to list!) for giving up their precious time to teach the students and especially to the School of Biosciences teaching lab staff for setting up the labs and making the summer school into a great event!

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Thanks to Saj, Mala, Amy, Indira, Sophie, Troy and Bob :-)

 

 

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The final task – to purify some DNA

Despite the summer school students having never used a pipette before, and not talking about μl volumes of liquid on a daily basis (like the majority of the IMI do!), we set them the challenge of purifying some plasmids from a bacterial culture. Armed with a team of 7 demonstrators, Dr David Lee set about helping the students follow a Qiagen mini-prep protocol to purify the DNA, which they then cut with a variety of restriction enzymes.

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An agonizing overnight step later and it was time to analyse the DNA on an agarose gel (after a few practice loads on some spare gels!).

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Lets just say – we were very impressed!

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Picking worms, feeding worms

During the Summer School, the students also got the chance to work with a bacterial eating worm called Caenorhabditis elegans, under the expert tutelage of Drs Tim Wells, Becky Hall and Leanne Smith. The task set was to gaze through a microscope and pick the 1-2 millimeter long worms, which were grazing on a nice lawn of bacteria, with a small metal hook, and transplant them to a fresh plate for further analysis.

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Expecting this to take a while to master was a mistake! the students were experts within 5 minutes and rose to the challenge by picking 3 1mm long worms using a metal hook in 24 seconds! Thankfully, a talk from Dr Kerstin Voeltz, on Zebrafish as a model organism, and a demonstration on how other model organisms work saved our blushes for underestimating the students skills!

After the worms had had a good feed on the fresh E. coli for a day or so, the students were back to pick them to view under a higher magnification microscope. Great results were obtained, with a group of students capturing an image of a worm next to 3 eggs, with about 6 eggs still in its abdomen. 20140724_11432820140724_114600

 

 

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Which bugs are lurking in your house – and how do we get rid of them??

What happens when you give a bunch of A-level students some swab kits, and send them home to swab various parts of their homes? Answer: a pretty disgusting set of agar plates!

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Analysing environmental swabs

 

 

 

 

 

Studious students examining their agar plates

 

No part of the home was spared: the garage, kitchen, bathroom, bedroom – underwear drawer (should be clean you’d think!) and even the family car were checked for bugs.

What we found were an interesting array of bacteria and fungi: thanks to Dr Katie Hardy of the IMI for helping us to ID them. These including:

Escherichia coli residing in cars

Plenty of α and β haemolytic bacteria – pretty much everywhere!

Some pseudomonas in a variety of places – mostly the bathroom

Some Staphylococcus, which looked like it was MRSA on indicator plates, but a bit of in depth MALDI-TOF thankfully confirmed that it was not MRSA!

And some Enterococcus faecium, which can be associated with faecal contamination, and some Proteus mirabilis, which can grow on urea- nice! (disclaimer – these two came from a car who’s owner regularly mucks out horses!)

Oh – and it turns out that underwear drawers, which you would think are full of clean clothes, are also full of bacteria!

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TSI slants and blood agar plates, used to try to work out what our bugs are

In addition to finding out which bugs live in the home, the students also collected a range of household cleaning products to see how antimicrobial they were. A simple experiment was set up, where a strain of Escherichia coli was spread onto an agar plate and onto it were placed disks soaked in cleaning product. E. coli might not be expected to be present in all of the places the products target – but you’d still expect them to kill it….right??

Not necessarily, it turns out!

Not wanting to brand-name drop, but some antibacterial soaps (that claim to kill 99.99% of bacteria) didn’t kill any bacteria! The best was one containing milk and honey – which didn’t actually claim to kill any bacteria!

Toothpaste – a very mixed bag of success! Some named brands didn’t kill any bacteria, whereas another brands most basic toothpaste was easily the best. Interestingly, as soon as this company gave their toothpaste super powers, like enamel strengthening or super whitening, the toothpastes were suddenly hopeless at killing bacteria!

Easily the best chemical we found for killing microbes was ……… Tea tree oil – which cleared more bacteria than undiluted bleach!

Easily the worst was a toilet cleaner which killed zero bacteria! The members of the IMI will not be buying that one anymore!!

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IMI Summer School First day

Written by Anna Schager of the IMI

It’s just after 10 am Monday morning 21st of July, 26 A level students are collected in the undercroft of the Biosciences building at University of Birmingham, munching cookies and drinking coffee and tea. They have all sacrificed one holy week of their precious summer vacation for the sake of science. For the next 5 days they will take part in the IMI Summer School, and will hopefully get some of those mysterious microbiology questions answered!  What is lurking in our houses, and how do we get rid of them? Are all microbes our enemies? How do you distinguish between different microbes? How do you purify DNA, and how can you visualize it? And most importantly, what does it really mean to be a scientist at IMI, and what do they do?

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First difficult task of the day – spell your name right on the name-tag!

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 Expectant students awaiting to take the dive into the amazing word of microbes.

But first things first, name-tags are on and it is time to get to know each other, a sort of team-building if you will. Creativity and thinking “outside the box” are nice words, but what do they mean practically? Well, after this morning there should be little doubt! Groups of students were sent out to collect items from a list where each successfully collected item generated certain points. Fair enough! Doesn’t seem so difficult. Let’s see: A painted face, something a million years old, a captured scent, a photograph of the whole team under water… wait, what?? A duet in harmony…. do we really have to sing???

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Item treasure hunt. Something from the list is obviously hiding in the ground. Perhaps something made from a worm, a footprint, something that can convert energy or perhaps even a completed sudoku?

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 Clusters of inventive brains in progress.

After this exhausting serious practice (winner to be announced) where creativity formally exploded and no thoughts were kept in any box, it was time for the tour of IMI…

 

Proud scientists proudly presented robots, all in different sizes. The smallest, no larger than a bar of soap, is actually capable of sequencing “a lot, lot, LOT of DNA bases in a VERY short time” – to quote Ashley Robinson! The biggest is able to screen literally thousands of chemical compounds for their antimicrobial effect, also in a very short time. What would we do without all those robots? There was also the opportunity to visit the newly built (and not in operation yet!) bio-safety lab – housing cat. 3 and 4 beasties such as HIV and Tuberculosis. Creepy…. Almost like the labs in the movies – all that was missing was the guys in white space suits!

 

After lunch there was a talk by Prof. Steve Busby

Steve's talk

Steve’s talk

on the amazing world of bacteria, and then it was time for the students to meet the microbes! At five different stations there were demonstrations on how to ferment bacteria, and how to distinguish between Aspergillus and Penicillin. Students were taught in the skilful art of gram staining bacteria and how cryptococcus infecting macrophages can be visualised by fluorescence. It may look fairly harmless but the awful truth is that the small green dot on the screen inside the big macrophage is actually responsible for 650 000– 600 000 human deaths per year! 

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That’s a lot of tubes. Is there really a fermenter underneath?

Well, that was a looong day! A lot to take in. Time for some rest and prepare for a brand new day tomorrow. But not quite so, there is actually homework! Are you ever really alone? Time to see what is actually living there side by side with us, unseen to the naked eye. All students were sent home with the mission to swab surfaces of their home and cars

Kerstin swabs her radio

Kerstin swabs her radio

for bugs, only the imagination sets the limit. But also to bring with them for tomorrow, small samples of cleaning solutions, antimicrobial soaps and mouthwashes etc. they want, to determine how efficient they really are at killing bugs. OK, now you can go home! Except those of you who wants to see the really BIG robot in action one more time of course :-)

 

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The IMI Summer School is nearly here!

The IMI Summer School starts on Monday 21st July: a microbiology filled week which will 20130603_105649fuel the enthusiasm of A-level students for all things micro! The students will be finding and identifying the bugs that are lurking in their houses, on their iPads, on their smart phones and in the family car! They’ll also be testing how well the cleaning products that we all use around the house are at killing bacteria – watch this space for some scary results!

As well as all that the students will get the chance ‘to meet the microbes’, learn about biotechnology, see some worms eat some fluorescent bacteria, purify and identify some DNA and listen to some great talks from: Prof Steve Busby – The Amazing World Of Bacteria; Dr Andy Lovering – Extraordinary Microbes; and Dr Jess Blair – What Is A Superbug?

A total of 65 students applied to participate in our free course this year, the vast majority from schools within Birmingham, although we have participants from Stratford and Manchester! The IMI is very much looking forward to meeting them all and having a micro filled week!

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Prof Tim Mitchell’s Inaugural Lecture – Wednesday 4th June

Professor Tim Mitchell’s inaugural lecture, entitled “The Pneumococcus: Captain of the men of death” will take place on Wednesday 4th June at 4.30pm in the Leonard Deacon Lecture Theatre at the Medical School.

Tim Mitchell qualified with a BSc in Biological Sciences (Microbiology) from University of Birmingham in 1983. He was awarded a PhD from the same University in 1986. He obtained a Wellcome Trust Fellowship and spent 1 year at Erasmus University in Rotterdam. He returned to the UK as a post-doctoral researcher and then Wellcome Trust Fellow at University of Leicester. In 1992 he was awarded a Royal Society University Research Fellowship and in 1996 moved to the University of Glasgow where he was appointed to the Chair of Microbiology. He was elected a Fellow of the Royal College of Pathologists in 2004. In 2012 he returned to the University of Birmingham as Professor of Microbial Infection and Immunity. His research is focused on understanding the mechanisms by which bacteria cause disease and development of vaccines and therapeutic approaches to prevent pneumonia and meningitis.

For further information contact Yvonne Dawson (y.dawson@bham.ac.uk/0121 414 4054)

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Loman Lab to be one of the first recipients of the new Oxford Nanopore MinION sequencing platform

The Loman Lab has been chosen to be one of the first recipients of the new Oxford Nanopore MinION sequencing platform in their phase 1 early access programme. This is the much-hyped USB-stick sequencer which promises to be disposable and usable in the field, generating potentially unlimited read lengths and requiring little sample preparation. Nick expects theirs to arrive next month and will keep the IMI updated with their findings!

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Student success – Krachler lab

One of the first ever Krachler lab members, Cathy Hawley, was just accepted as a PhD student at the Royal Infirmary Hospital at Edinburgh. She spent the Summer 2012 with us, studying the effects of MAM-based adhesion inhibitors on wound healing. She was joint first author on a PLoS One paper we published last year and said this experience definitely boosted her ability to find a PhD position in these tough times. She will start her project in September, looking at tissue-resident macrophages.

 

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