We are looking for a PhD student for behavioral experiments with Drosophila fruit flies with manipulated FoxP function.

The human orthologues of the fly FoxP gene are the FOXP1-4 genes. Mutations in the FOXP2 gene cause verbal dyspraxia, a form of articulation impairment. Humans learn to articulate phonemes and words by a form of motor learning we can model in flies. Supporting the conceptual analogy of motor learning in humans and flies, manipulations of the fly FoxP gene also lead to impairments in motor learning.

In the past year, graduate student Ottavia Palazzo used CRISPR/Cas9 to edit the FoxP gene locus, tagging the gene with reporters. These reporters allow us to manipulate not only the gene, but also the neurons which express FoxP. The candidate will work closely with Ottavia to design behavioral experiments characterizing the various manipulations of the different neuronal populations for their involvement in the form of motor learning we use, operant self-learning at the torque meter:

The position is fully funded by a grant from the German funding agency DFG, with full healthcare, unemployment, etc. benefits. It includes admission and tuition to the “Regensburg International Graduate School of Life Sciences“. Starting date is as soon as convenient.

The successful candidate will have a Master’s degree or equivalent. They will be proficient in English as our group is composed of international members. The ideal candidate will have some training in behavioral experiments in Drosophila or other animals, some coding experience and an inclination towards electronics. However, all of these skills can also be learned during the project.

We are a small, international  group consisting of a PI (Björn Brembs), a postdoc (Anders Eriksson), one more graduate student besides Ottavia (Christian Rohrsen) and a technician. We are an open science laboratory and so one aspect of the project will involve a new open science initiative in our laboratory, where we have developed a simple method to make our behavioral data openly accessible automatically, i.e., without any additional efforts by the experimenter. This entails at least two advantages for the candidate in addition to doing science right: the data are automatically backed up and there is no need for a data management plan.

Regensburg is a university town in Bavaria, Germany with about 120k inhabitants and a vibrant student life, due to the 20k students enrolled here. The University of Regensburg is an equal opportunity employer.

Interested candidates should contact Björn Brembs with a CV and a brief letter of motivation.

Data 1:

Monica:

Anokhi:

 

Yellow 1 (Positive Control): Gr28bd-G4, TrpA1-G4

Parameters: Light: intensity (500 Lux side, 1000 Lux bottom); frequency = 20Hz; Delay = 1 ms; Duration = 9.9 ms; volts = 6.4

> Worked on the ping pong ball machine in the last week.
IMG_2907 (1)

The text file looks something like this: Not very sure how to interpret it because there is no column header.

> Did not find any RU486 fly lines in the Brembs fly stock.
What is RU486 and why are we using it? It is a conditional transactivation method that gets activated when introduced with Mifepristone/RU486 and works on the UAS promoter (Roman et al, 2001).

The genes we are knocking down:
1) SERCA gene
2) Ryr gene

LMC L1 and L2 Paper

(Coombe, P.E., 1986)

ERG

1. mass electrical response of the eye
2. waveform consisting of summed extracellular potentials produced by retinula cells and postsynaptic neurons
3. recorded by electrodes
4. waveform consists of on transient, negative sustained potential and off transient

L1 and L2

1. Two main reasons to select study upon these two:
   1. Only lamina neurons which are known electrophysiology
   2. Intracellular waveforms roughly correspond to ERG transients

Vam mutants

1. Vam = Vacuolar medulla
2. Semi-dominant mutation (Incomplete dominance)
3. Characterized by formation of large vacuoles and absence of ERG transients

(Electron Micrographs from the lamina) (ERG)

ERG waveform and LMC degeneration

1. No wt showed degeneration of LMC
2. Negative nonlinear relationship between % of LMC degeneration and the size of on/off transients in Vam flies

 

Results

1. Previous work has shown age-specific degeneration of LMC in the lamina.
2. Signs of degeneration start to appear in the form of large vacuoles in medulla and lamina.
3. LMC may be responsible for ERG transients

plotting the mean ratio of flies which stay in the middle during experiment.

 

Yellow 1 (Positive Control):  Gr28bd-G4, TrpA1-G4

Parameters:
Light: intensity (500 Lux side, 1000 Lux bottom)

frequency = 20Hz

Delay = 1 ms

Duration = 9.9 ms

volts = 6.4

Yellow 1 (Positive Control):  Gr28bd-G4, TrpA1-G4

Parameters:
Light: intensity (500 Lux side, 1000 Lux bottom)

frequency = 20Hz

Delay = 1 ms

Duration = 9.9 ms

volts = 6.4

Yellow 1 (Positive Control):  Gr28bd-G4, TrpA1-G4

Light: intensity (500 Lux side, 1000 Lux bottom), frequency (20Hz)

Arnim Jenett (Janelia Farm Research Campus), Kazunori Shinomiya, Kei Ito (both Tokyo University), and other anatomists made a great site with a 3D-viewer of adult Drosophila brains available. You have the chance to scroll threw a whole mount stack while ticking different brain areas. Those brain areas are listed next to the stack. Different areas are coloured differently, so that you can look at the location of several areas in the same brain. On the main page you can find simply explained tutorials about the usage of the site. It is correlated to the anatomical search engine of the Janelia farm GAL4 collection.
Because it was very helpful to me to learn all the synonyms of relevant areas and because I think it is very helpful to learn more about the structure of the Drosophila brain in general I wanted to advertise the site here.
http://www.virtualflybrain.org/site/vfb_site/overview.htm

I was on a meetup of corporate semantic web last Tuesday. These people are using semantic web technologies (making machine readable content based on ontological terms and relation between these terms) to improve the efficacy of private companies. For instance, they work on ways to improve wiki contents which may be produced in a company. This corresponds at using ontological term to annotate the wiki content and other related technologies. This can be used to find an expert in one category (=somebody who’s posts are rarely corrected on a specific subject).

What is the scientific community (the one which should be leading the way actually) doing during that time: we use text search in “keywords” and titles to find the appropriate literature, that we have to read thouroughly to drive our one conclusions about these different parts… At least, that is what we do 90% of the time, and we all know how inaccurate this can be. Experimental results may be translated into a machine readable content, why aren’t we doing it (it could make everything that much simpler, faster and more accurate)?

The answer: 1. there is no tool nor database where we could do it. 2. Scientists do not have the time to do it, they are over-pressurized to produce data, not to make it reusable or machine readable.
How to push people to use the semantic web technologies, how to ease this use, should it be done by the authors or by the community, pre or post publication, what ontology tool to use,… What can we do? Is anyone asking these questions around? Does a platform like researchgate be a way to introduce this, or should we go for a public solution, inside pubmed for example?

Is any of you asking/answering these questions?

By the way, this post is tagged by none-ontological terms, a shame?