Application Deadline: 27 January 2017

Apply here

Details
Prof Richard Baines of Manchester University and Dr Adam Claridge-Chang of A*STAR, Singapore are offering an exciting doctoral project to identify novel anticonvulsant compounds for the analysis and treatment of epilepsy. Doctoral research will be conducted in both Manchester (years 1 and 4) and Singapore (years 2 and 3). 

Current antiepileptic drugs are effective for only two-thirds of patients and are associated with significant side-effects. Better drugs are needed, but a lack of novel drug targets and good screening methods are significant barriers. The fruit fly (Drosophila melanogaster) offers the prospect to develop high-throughput screens to identify novel anticonvulsant compounds. Single gene mutations exist that increase the severity and duration of induced seizures in flies; seizures that respond well to treatment using existing antiepileptic drugs. This, and other studies, shows that the underlying biological basis of seizure in flies is remarkably similar to humans. 

In the first year, you will learn to work with Drosophila seizure mutants, using behavioral methods and calcium imaging to observe activity of central neurons. In the second year, you will implement advanced behavioral analysis methods (machine vision) to quantify seizure severity and dynamics. In the third year, you will use the behavioral analysis systems to screen for novel anticonvulsant compounds. These will include venom peptides that may block voltage-gated sodium channels and/or other excitatory ionic currents. In the final year, you will apply calcium-imaging and electrophysiology to determine mode-of-action for interesting anticonvulsant compounds identified.

This is an interdisciplinary research project that combines the quantitative analysis of seizure behaviours, drug-screening and in vivo physiology in Drosophila seizure models. As an ideal candidate, you would need to have an interest in epilepsy causes and treatments, along with the aptitude to learn a range of experimental techniques spanning neurogenetics, neurophysiology, computer-aided imaging and testing of compounds in whole-animal seizure screens. Both labs offer conscientious scientific mentorship, rigorous technical training and highly collaborative environments. 

Funding Notes
The project is available to UK/EU candidates. Funding covers fees (UK/EU rate) and stipend for four years. Overseas candidates can apply providing they can pay the difference in fees and are from an eligible country. Please check the website for information on eligibility. Candidates will be required to split their time between Manchester and Singapore, as outlined on our website. Applications should be submitted online and candidates should make direct contact with the Manchester supervisor to discuss their application directly.

References
1.Streit AK, Fan YN, Masullo L and Baines RA (2016) Calcium imaging of neuronal activity in Drosophila can identify anticonvulsive compounds. PLOS One DOI:10.1371/journal.pone.0148461  February 10, 2016. 
2.Giachello CNG and Baines RA (2015) Inappropriate neural activity during a sensitive period in embryogenesis results in persistent seizure-like behaviour. Curr. Biol. 25:2964-2968. 
3.Lin WH, He M and Baines RA (2015) Seizure suppression through manipulating splicing of a voltage-gated sodium channel. Brain 138:891-901. 
4. Alnabulsi S, Santina E, Russo I, Hussein B, Kadirvel M, Chadwick A, Bichenkova EV, Bryce RA, Nolan K, Demonacos C, Stratford IJ, Freeman S (2016) Non-symmetrical furan-amidines as novel leads for the treatment of cancer and malaria. Eur. J. Med. Chem.111:33–45. 
5. Emsley HC, Appleton RE, Whitmore CL, Jury F, Lamb JA, Martin JE, Ollier WE, de la Morandière KP, Southern KW and Allan SM (2014) Variations in inflammation-related genes may be associated with childhood febrile seizure susceptibility. Seizure 23:457-61

The anion channelrhodopsins from the algae Guillardia theta are highly effective at inhibiting neuronal activity in flies. Our manuscript is now available as a preprint.

Why do I need to do this?
A lot of biology involves (1) doing an experiment where you make an intervention and (2) measuring what effect the intervention has.

If you are living in the Dark Age of P, you assume your intervention has had absolutely no effect, and then calculate the probability of seeing your data (or more extreme data), under that assumption of zero effect. Since you likely did the experiment because you thought there would be an effect, it seems super weird and slightly depressing to then go assuming zero effect when you start analyzing your data.

​If you use estimation, a far more sensible method, you want to estimate the size of the effect of your intervention. The most straightforward effect size is the difference between the control mean and the intervention mean ('mean difference'), along with its confidence interval.

I've got confidence interval error bars, is that enough?
It's a good start to have CI error bars on your observed data plots. However, you also need to be able to say things like:
     "when we made the intervention to flies their behavior X
​     increased by +54% [95CI +35, +78], P = 0.01."
You need (1) know what your delta variable is and (2) know how to get these numbers.


What statistics are essential?
The three essential statistics are:

• Mean difference (your 'delta variable')
• Confidence interval of the mean difference
• Sample sizes (N)

Figure out how to calculate these numbers, and work them into your writing, especially in the figure legend, and also in the main text when you want to highlight an effect. It's simply not enough to say "behavior X increased," or worse, "behavior X increased significantly" without putting an effect size number on that statement, either immediately in the Results section or in the relevant Figure legend. If you have this you can import it into a Google Spreadsheet and share with your co-authors, one sheet per Figure or Panel.

What statistics are nice to have?

• Hedges' g
  
• P

It's nice to have Hedges' g, because this effect size is in units of standard deviations, which is sort of a universal currency. Most scientists will know what it means for an intervention to produce a 1 SD shift in the mean, and have an intuition that this is a large effect. Report P for pro forma purposes only and state "no significance tests were conducted, P was reported pro forma." This will satisfy reviewers wanting to see P while avoiding significance testing.

What text style should I follow?
The text format we are using for mean difference with its confidence interval is:
     -1.5 [95CI -1.2, -1.8]
     or
      +1.5 [95CI +1.2, +1.8] 
Note the use of the +/- signs to denote that this is a measure of the change in the variable, not a measure of the variable itself. I prefer '95CI' instead of '95%CI' as I find the latter to be cluttered.
 
Often it is useful to write something like this.
     ∆weight = +1.5 µg [95CI +1.2, +1.8] 
to remind the reader of the change variable (∆weight) and the units (µg). The confidence interval bounds are contained within square brackets [], and this generally follows the mean difference closely in text. It is then followed by the supporting statistics. For example:

     ∆VO2 = -1.5 µl/fly/min [95CI -1.2, -1.9], N = 65, 62
     or
     ∆VO2 = -1.5 µl/fly/min [95CI -1.2, -1.9], g = 0.56, P = 0.01, N = 65, 62

The g statistic was invented by Larry Hedges, so Hedges' g uses a possessive apostrophe after the 's.' The 'g' is italicized. P should be italicized and capitalized by default. 

What graphical style should I follow in charts?
Instead of the little stars, you can put the effect size right next to your difference marker. In this case, simplicity is a virtue. You can write '∆ = -1.5' next to the first marker, then just the numbers without the '∆ =' for the rest of the markers in that Figure.

When using Google Docs, there are a few tricks. 

• Use Paperpile for references.
• Follow Practical Typography where possible.
• Margins larger than 1 inch. Narrower text columns are easier to read.
• Never use Arial, use Helvetica Neue instead if Arial is required.
• If Arial not required, use Source Serif Pro and Source Sans Pro.
• Use Serif for the body text, Sans for headers and figure legends.
• Use the Text Styles menu to style each paragraph by typeface, margins, type weight, and paragraph spacing.
• Main text paragraphs should have no space before, and a space afterwards.
• Paragraph headers should have no spaces before or after.
• Text Styles allows you to auto-generate a Table of  Contents. 
• Use 200-300 dpi PNG files for figures.
• When discussing a project, use Basecamp. When discussing the details of a manuscript, use the Docs Comment function. I admit there is a lot of overlap between the two.
• Try to avoid using email to discuss either.

How might a fly model of anxiety help us understand the genetic causes of anxiety disorders? Read the paper (PDF).

Back in January, Nature Methods ran our letter that defined and explained 'estimation statistics.' Since journal policy allows posting an e-print of the accepted manuscript 6 months after publication, here is the manuscript version of  "Estimation should replace significance testing."

​This e-print is also available at Zenodo, http://dx.doi.org/10.5281/zenodo.60156.

Some notes on gene and protein nomenclature, based on this extensive guide here.

1. For genes use 'genename' when the original allele was recessive and 'Genename' for genes found with a dominant allele. Always italicize.
2. Gene abbreviations are similar, e.g. 'gen' or 'Gen'.
3. The name for the protein product of that gene is 'Genename' (regardless of capitalization in the gene's name), while the symbol for the protein product is 'Gen'. Never italicize if you are referring to a protein.
4. Use the gene name and abbreviation given by Flybase, even if most of the field uses something else.
5. A UAS transgene is a gene too, so use 'UAS-genename' or 'UAS-gen' to refer to it, i.e. italicize. The same goes for 'gen-Gal4'.
6. Separate chromosomes with a ';' between the names of alleles carried on those chromosomes e.g. "w; gen-Gal4; UAS-gen". If there is ambiguity about the chromosome and it is important, you can add a superfluous semicolon, e.g. "gen-Gal4; ;UAS-gen" to indicate the Gal4 is on the X and the UAS is on III.
7. Gene naming rules are different in other species, look up their nomenclature if you have to.
8. Please tell me if you catch me breaking these guidelines.

Using Illustrator to make figures give nice results, but is a pain to collate into a single pdf repeatedly during the drafting process, requiring the use of Adobe Acrobat Pro's Create PDF > Merge Files into a Single PDF, clicking "Add Files", then selecting the files you want to collate into a pdf.

A faster way is to use pdftk server, a command line tool that is made for pdfs, but seems to work fine for .ai files also. From the examples given on the pdftk page, doing this is as simple as launching Terminal and typing the relevant version of this:

$ cd yourdirectory
$ pdftk input1.ai input2.ai cat output new.pdf

The resulting pdf files still ends up pretty big (as large as doing the same operation in Acrobat), so one still has to reduce file size in Preview (File > Export... > Quartz Filter: Reduce File Size, click Save).

You can download and install pdftk server here.

For repeated collation, you can save your command lines into a text file for later use.

*Note that you can find yourdirectory by using the Finder to find one of the relevant files and pressing Command-I to get information. Then highlight and copy the path information under "Where" in the information window.

Here is a guide to installing Python for data analysis on a Mac, along with a few extra tips to get going.