Our jobs page was busy this month, with jobs advertised in the UK, France, Brazil, Finland and the USA! Here are the other highlights:

Research:

– Patrick told us the back story to his recent Nature paper that reported a common evolutionary origin for the external genitalia of a snake and the hindlimb of a mammal.

– Maiko and Hiroki posted about 2 recent papers from by their lab presenting new techniques for avian embryo research.

– Federico discussed his recent paper in Development that used the guinea pig to uncover a new neurogenic region of the brain.

– And Jiman discussed the potential of TALEN-mediated homologous recombination in the zebrafish.

Gurdon studentships:

In 2014 the British Society for Developmental Biology initiated the Gurdon Summer Studentship program, providing undergraduate students the opportunity to spend 8 weeks in a host lab engaging in practical research. A selection of posts from this year’s awardees will feature on the Node in the coming months, and the first two posts were published this month:

– Benedetta Carbone joined the Kaiji lab at the Centre for Regenerative Medicine in Edinburgh (UK) and wrote about her project using DNA adenine methyltransferase identification (DamID) to investigate Oct4 binding sites in mouse Embryonic Stem Cells.

– George Choa did his placement in the Stern lab , at University College London (UK), and his project focused on identifying ‘housekeeping’ gene in the chick embryo.

Also on the Node:

– How soft toys can be a great way to teach children (and adults!) about evolution and biodiversity- the new post in our outreach series.

– We reposted an interview with Chris Wylie and Janet Heasman, first published in Development.

– And if you missed the recent workshop ‘From Stem Cells to Human Development’, here is a video interviewing the organisers and attendees.

Happy reading!

(1 votes)

Loading...

2010 was declared the International Year of Biodiversity by the UN. At the Science & Culture Department of Montpellier University, which has designed science outreach and public engagement projects since 2000, we wanted to mark the occasion with an original project. We wanted a project that would:

    – talk about the methods rather than the results of the scientific process
    – explain the techniques used by naturalists to study biodiversity (past-present-future)
    – develop a do it at home project (with no need for an expedition to a remote deserted island)
    – have fun with disciplines often perceived as “dry”, such as taxonomy, phylogeny, classification…
    – work with kids and families (adults included)

 
As the result of a previous exhibition on evolution where we could evaluate the pedagogic potential of soft toys, we decided to create a fake (but highly serious) Société Française de Peluchologie-French Plushology Society, supposedly created in 1903, year of the creation of the first teddy bear. The idea being to study soft toys using the methods of a naturalist. Following this mysterious scientific discipline, kids (and adults) were encouraged to bring in and study specimens carefully. In the process they transformed a random collection of soft toys into scientific collections! Participants named specimens using Linnean binomial nomenclature (leading to very funny proposals), measured their specimens, compared them, and attempted to set up a real scientific collection and classification.

French Plushology Society, est 1903

The idea behind the project is that soft toys are part of every one of us (our first “transitional friend” was probably a soft toy [1]). Moreover, during childhood (and later for many of us…), stuffed animals are part of our “imaginary ecosystem”;

We created a 200m2 exhibition with display cabinets, interactive multimedia, and posters created in collaboration with master students in environmental sciences. We worked with a DNA phylogeny research group of researchers at our University on the classification process. We also convinced scientists to describe on a video their favourite soft toy, and use it to explain a specific aspect of evolution (bacteria soft toys and co-evolution, armadillo and genetic phylogeny, worms and parasitology…).

Our own collection has grown over time, by regular trips to second-hand shops and many spontaneous donations during activities. Some nice soft toys were also sent by collaborators all around the globe to illustrate local specimens. We have also collaborated with the 13th congress of the International Society of Ethnobiology (held in Montpellier in 2012), with conference attendees sharing with us their original toys…

Soft toys are really nice educational tools to explain a variety of biodiversity concepts. We start with specimen description: size, colour, material, label… Then, for the classification process, we list the characteristics without ordering them (colour, 4 legs, 2 legs, round ears, tail,…) coded by a O (absence)/1(presence) scale on a table. We then group the most similar specimens. I can tell you that agreements and deliberations within groups are not so far from discussions held in the genetic phylogeny labs! A plushology workshop on classification usually leads to many heated discussions: “let’s first classify by number of legs rather than colour”. This ability to re-invent a system collaboratively is a very interesting process..

Almost any aspect of evolution can be easily explored with the right soft toy specimens: adaptation can be explained by soft toys with magnets, that are able to invade the fridge ecosystem; convergence can be explained using different striped soft toys; antique and recent teddy bears can introduce concepts of evolution; a souvenir moose soft toy can be an endemic species of Canada; extinction can be explained using a dodo soft toy from the island of Mauritius; classification challenges can be illustrated using a platypus soft toy; examples of invasive species are the Olympic games or world cup mascots (and of course Hello Kitty); and so on…

We take great care to preserve the poetry and emotions of soft toys, especially with the youngest public. However, it is REALLY important not to mix real and imaginary animals : the soft toys have to be studied as “soft objects” and not as dolphins or tigers…

Looking at soft toys can give an unrealistic vision of “real“ biodiversity. For example, the soft toy ecosystem has a considerable mammal content (especially bears!) but almost no insects. In the wild, biodiversity is mostly composed of insects (600,000 species) and the mammal proportion (6,000 species) is very small… So, soft toys diversity can deliver an incorrect idea of the variety of living species surrounding us.

However, the differences between the world of soft toys and real biodiversity can be the starting point to introduce concepts in an original way. One of the things that you may have spotted is that soft toys do not reproduce sexually. However, it is quite easy to explain that the vast majority of them are industrially cloned in China, and artists still create some of them manually (often made from natural material such as mohair and alpaca). In fact, the supply and demand laws of economics, designer inspiration and buyers’ tastes are perfectly Darwinian in our opinion. As an example: teddy bears’ forearms shortened during World War I due to the scarcity of raw materials.

This project is highly flexible and can be adapted to many different kinds of events. We have presented our project in a street theatre festival that focused on the theme of “Monsters” (setting up a monster soft toy collection), as well as in a municipal biodiversity fiesta (installing soft toys in a tree and organizing a binocular-assisted study of the zone, as well as tree climbing). We have even organized the first “plushology masters exam”. One of the question asked to draw the hotspots and deserts of soft toys on a blank worldmap. A diploma ceremony (in collaboration with the head of studies) even took place at the University.

The success and experience acquired in these activities gave us the idea to invade the web with our project. We decided to launch a collaborative platform where anyone can geo-localize their preferred toy and share their discoveries with the plushologist community. To date (November 2014), 1618 specimens have been described. The number is of course less important than the process…

 
A masters student at Montpellier University has also decided to work out the “king of soft toys” teddy bear classification. One can discover online which family his/hers favourite teddy belongs to, progressing step by step through a friendly cladistic tree.

Plushology is a wonderful and open-ended collaborative experiment. An original way to explore (bio)diversity through the scientific study of an imaginary ecosystem. The Plushologist community is growing worldwide, and the national Portuguese Science Explainers Association is currently launching a local project. Plushology is a great way to involve kids in science activities, and a really fun way to approach not so funny disciplines such as taxonomy, phylogeny, cladistics and classification.

And remember: “everyone has a soft toy story to tell”…

Videos (in french):

And also this video.

Links:

Mission Peluche website: http://www.peluche.um2.fr

Article: Plushology, a soft science (in French) : http://ocim.revues.org/1015

A collaboration with “Improbable Research”: http://www.improbable.com/2013/07/05/towards-a-taxonomy-of-teddy-bears/

Reference:

1- Transitional object explanation, on wikipedia: http://en.wikipedia.org/wiki/Comfort_object

This post is part of a series on science outreach. You can read the introduction to the series here and read other posts in this series here.

(8 votes)

Loading...

In 2014, the BSDB has initiated the Gurdon Summer Studentship program with the intention to provide highly motivated students with exceptional qualities and a strong interest in Developmental Biology an opportunity to engage in practical research. The 10 successful applicants spent 8 weeks in the research laboratories of their choices, and the feedback we received was outstanding. Please, read the student report kindly sent to us by George Choa.

Is there such thing as a housekeeping gene?

This summer I undertook an internship in the Research Department of Cell and Developmental Biology (CDB) at University College London (UCL). Joining the Organiser subgroup, my project involved determining the existence of a “housekeeping” gene (HKG), a gene that has both ubiquitous and uniform expression across different tissues types, no matter normal or diseased tissue, no matter the stage of embryo development, and no matter the model system used. HKGs act as reference genes in cases where magnitude of expression is required to be normalised, for example in RT-PCRs and northern blotting.

In order to confine the number of candidate genes for the project, specific criteria were applied to two sets of chick RNA data – quantitative expression values from microarray screens and RNASeq tissue assays, which were collected over time at both the Stern Lab at UCL and the Streit Lab at King’s College London (KCL). Simply done on Microsoft Excel, variance for each mRNA was calculated across samples of a variety of chick tissue types and stages, to which they were ranked. The least variant 5% (P = 0.05) and 1% (P = 0.01) mRNAs from microarray and RNASeq data, respectively, were selected. As this still left us with a total of more than 1500 mRNA HKG candidates, further filtration was applied, for example comparing the candidates to existing results in expression databases such as ZFin. This criteria resulted in a selection of 14 candidate HKGs, including genes that encode ribosomal proteins (RPS25) and channel proteins (KCNJ4). On top of this, an additional 9 probes that are considered conventional HKGs were also tested to confirm their reliability as HKGs; these conventional genes are commonly used as a baseline for a multitude of developmental studies, for example GAPDH and ACTB. All these probes were presented by box plots and heat maps using R, composed by me, taught by the Stern lab bioinformatician at the time; these were used in my end-of-project presentation.

The more practical side of my project came next. My first week consisted of firstly learning to harvest chick embryos. This required a lot of patience and resolution, something I’ve come to appreciate to be two of the most important features of working as a researcher in science. One of the biggest challenges was the application of different techniques when harvesting embryos of different stages; some could be harvested quickly, most others took time and extreme delicacy. It was easy competing with myself from the previous day as each day I matured my technique, collecting dozens in one sitting, easily collecting over 150 different embryos of different Hamburger Hamilton (HH) stages over my first six weeks.

Following learning the tricks of the embryology trade, I dove into the more molecular side of my project – in situ hybridisation (ISH). Probes were synthesised and purified, and harvested chick embryos were processed, both by Stern lab protocols, ready to be stained. From this, the probes that appeared convincingly uniform in expression, as well as a variety of the conventionally used HKGs, were processed through wax sectioning to gain a better, more comprehensive look at the extent of the staining, before, and after, which they were documented.

A range of data (115 embryos) were collected by the end of my project, and with the several-odd wax section images, I found that none of the candidate genes matched the requirements of a HKG; even those that were sectioned due to convincing ubiquitous expression, which includes those conventional HKGs that hitherto are being used to normalise expression data.

Having collected all my data and completed my project to the best of my abilities, I presented my work in one of the many lab meetings I had the opportunity to attend. It was without doubt odd to sum my eight weeks spent researching into a 15 minute PowerPoint, but it was also wholly rewarding to see all I accomplished over my time at the Stern lab. Data collected from my project seem quite cogent in that there is probably no such thing as a HKG, which the lab hopes to publish in the near future.

Going into my final year of my Biomedical Sciences degree, I cannot thank everyone in the lab enough for the guidance, support and endless conversation that kept conducting my project so lively and enjoyable. I must however thank in particular my principal investigator Claire and Tutor Claudio for being so patient with me throughout the whole endeavour, and I hope one day I will return to the lab to take on my own PhD.

George Choa, BSc Biomedical Sciences, UCL

(7 votes)

Loading...

In 2014, the BSDB has initiated the Gurdon Summer Studentship program with the intention to provide highly motivated students with exceptional qualities and a strong interest in Developmental Biology an opportunity to engage in practical research. The 10 successful applicants spent 8 weeks in the research laboratories of their choices, and the feedback we received was outstanding. Please, read the student report kindly sent to us by Benedetta Carbone.

I am Benedetta, an undergraduate student studying Molecular Genetics at the University of Edinburgh. This summer I had the amazing opportunity to spend 8 weeks in a research lab working on stem cells.

It all started out because after 3 years of studying Biology and an interest in building a career in research, I didn’t really know what the job of a full time researcher looked like. So, encouraged by University professors, I started investigating fields and topics that I had liked the most during my studies.

I was doing some research on induced pluripotent stem cells when I came across Dr. Kaji’s lab at the Centre for Regenerative Medicine in Edinburgh. Their work focuses on the Biology of Reprogramming, the molecular changes that occur in reprogramming cells and how the process can be further understood and improved.

I contacted him to ask if I could join the lab for the summer. He offered me a place for an internship and designed a project focusing on DNA adenine methyltransferase identification (DamID). DamID is a technique based on the bacterial protein DNA adenine methyltransferase (Dam). This protein recognises GATC sequences and methylates position 6 of the adenine. DamID works by tethering Dam to a DNA-binding protein. The target protein binds to DNA localising Dam to the same sites within the genome. Thus, Dam has a higher chance of methylating GATC sequences around the binding site of the target protein.DamID is hence used to detect DNA-binding sites for target proteins, producing data similar to ChIP-seq. As a result, DamID does not require the use of any antibody, reducing the amount of time necessary to process DNA and the amount of cells required as starting material.

One of the PhD students in Dr. Kaji’s Lab, Luca Tosti, has been working with DamID and the aim of my summer project was to test the DamID technology by generating my own Dam expressing cell line to investigate Oct4 binding sites in mouse Embryonic Stem Cells (mESCs).

And so my internship began. At first I was a bit overwhelmed and I found myself confused by very simple things. It quickly got a lot better, thanks to everyone in the lab (especially Luca!): they were all very friendly, helpful and patient!

I started by cloning the expression vectors and I gained experience in basic molecular biology techniques such as restriction enzyme digestions and ligations, bacterial transformations, extraction of plasmid DNA and gel electrophoresis. I also familiarised myself with the ApE software to design cloning strategies.

I generated several vectors to test different levels of Dam expression in order to get a good signal-to-noise ratio. Indeed, one of the main issues related to this technology is the high background signal arising from the intrinsic DNA-binding activity of the Dam protein.

Afterward, I was introduced to tissue culture where I worked with mouse ESCs (mESCs). I learned how to maintain mESCs in culture and how to passage them when confluent. I also gained experience on plasmid transfection, picking colonies, freezing and thawing cells. I transfected mESCs with the vectors I had previously generated and I used the antibiotic resistance cassette I had cloned into the constructs to select for cells expressing the transgene.

As a part of the project, I also wanted to check how the adenine methylation signal changes when mESCs differentiate, and for this purpose I performed retinoic acid (RA) differentiation of mESCs. After removing Leukaemia Inhibitory Factor (LIF, a signalling molecule important for maintaining the undifferentiated state of mESCs) and adding RA to the medium (for 9 days), I was able to observe significant morphological changes.

I then went back to the lab bench: I learned how to extract RNA and how to perform RT-qPCR to determine gene expression patterns. Using this approach I could confirm that differentiated cells had switched off pluripotency markers. I also learned how to extract genomic DNA and how to use enzymatic digestion coupled to qPCR to quantify the methylation levels of DNA around GATC sequences. My results were very encouraging. I managed to get good expression of the Dam-Oct4 fusion protein and to observe good positive signal correlating well with published ChIP-seq datasets.

This internship has been an amazing experience for me. I found the work of a researcher both challenging and rewarding and it definitely encouraged me to pursue a career in science. I would recommend this experience to any Biology student who wants to learn how real research is carried forward.

Benedetta Carbone

(11 votes)

Loading...

The BSDB committee are inviting applications and nominations for a post doctoral representative to join the committee. We already have a Graduate Student representative and feel that the post doctoral community should also be represented. This position is available immediately and would be for a two year  term and we would like someone in place by the New Year ideally. The post doc rep would attend committee meetings twice a year, one at the annual Spring BSDB-BSCB meeting and one in London in the fall. They would act as a voice and conduit for the postdoc community within the BSDB. This a great opportunity to gain insight and understanding of how a learned Society is run and could serve as a valuable addition to a CV. Please send applications and nominations to the BSDB Secretary : secretary@bsdb.org

(2 votes)

Loading...

A fully funded studentship (fees and RCUK-level stipend) open to EU students is available under the supervision of Dr Thomas Butts in the School of Biological and Chemical Sciences at Queen Mary, University of London.

The studentship is to study the evolution of neural development within vertebrates, particularly in relation to the control of neurogenesis. Within this broad area of interest in the lab, the details of the project will be dependent upon the interests of the student. More info is available at:

www.sbcs.qmul.ac.uk/prospectivestudents/research/projects/143399.html.

Informal enquiries by email (thomas.butts@qmul.ac.uk) are welcomed. The closing date for applications is 31st January, 2015.

(1 votes)

Loading...

We are recruiting researchers at different levels to join a 4-years international project, DEVODIVERSITY, funded by the French Agence Nationale de la Recherché (ANR) and the São Paulo Research Foundation (FAPESP). The Brown Lab at the Instituto de Biociências in Brazil (USP) and the Tiozzo Lab at the Villefranche-sur-Mer Developmental Biology Laboratory in France (CNRS-UPMC) will study the evolution of regeneration, asexual reproduction, and clonality in several species of ascidians (Urochordata), and examine how ecological factors affect distribution ranges, evolution of life cycles, and developmental strategies.

DEVODIVERSITY has the following aims:

1.  To resolve the phylogenetic relationships and evolutionary transitions between strictly sexual reproduction to budding or high regenerative abilities among Styelidae (Ascidiacea) species.
2. To provide a morphological and ecological understanding of asexual propagation (budding). We will generate detailed anatomical and developmental descriptions of budding processes, and explore if environmental conditions are associated with the use of particular budding modes.
3. To compare gene pathways involved in cell function or trans/de-differentiation processes of budding and regeneration by in silico analysis of transcriptomic data.
4. To launch a comparative genomic approach if styelid ascidians to better understand the evolution of major life history transitions in marine chordates, in particular the evolutionary transition from sexual to asexual propagation.

Positions available:

•  2 Postdoctoral positions (a2-year postdoc in France and a 3-year postdoc in Brazil): (1)candidate with experience in cell and molecular biology, some genomic experience will be favored and (2) candidate with experience in ecology, phylogenetics, and systematics.
• 4 Doctoral positions (two 3-year positions both in France and Brazil respectively):highly motivated candidates should have an internationally recognized Master degree.
• 1 Bioinformatician position (4-year position, only available in Brazil): the candidate must have strong competence in computer sciences or related areas. S/he should have either completed his/her doctorate OR should have five years of proven experience in information technology.
• Several Master positions (both in France and Brazil): candidates should have completed their undergraduate degrees, and preferably with some research experience.

The successful candidates will join either the Brown lab in São Paulo (Brazil) or the Tiozzo lab in Villefranche-sur-Mer (France) and will have the opportunity to do laboratory and fieldwork in both countries.

Research position salaries and applications procedures are distinct for Brazil and France; these follow the general guidelines of either FAPESP (Brazil) or ANR (France) respectively. Please submit your letter of interest, updated CV, and contact information of three references to either Federico Brown (Brazil) or Stefano Tiozzo (France). Review of applications will begin on December 2014 and continue until the positions are filled. Start date should ideally be in early or mid-2015.

Contacts

Stefano Tiozzo (tiozzo@obs-vlfr.fr):http://biodev.obs-vlfr.fr/~tiozzo/tiozzo-lab.

LBDV: http://biodev.obs-vlfr.fr/en/index.html

Federico Brown (fdbrown@usp.br): http://www.ib.usp.br/zoologia/evodevo

Instituto Biociências (in Portuguese only): http://www.ib.usp.br/

(1 votes)

Loading...

There is a fully funded PhD studentship opening in Barbara Jennings’s group at Oxford Brookes University (starting September 2015) to investigate developmental gene regulation in Drosophila.

For further details about the studentship and how to apply please see

http://bms.brookes.ac.uk/research/studentships/transcriptional-elongation

The deadline for applications is December 14th 2014.

(No Ratings Yet)

Loading...

Applications are sought for the role of Reviews Editor on The Journal of Experimental Biology, based in Cambridge, UK.

Joining an experienced and successful team, this newly created role is an exciting opportunity for a talented scientific editor to make a significant contribution to the leading journal in comparative animal physiology.

The Journal of Experimental Biology publishes papers on the form and function of living organisms at all levels of biological organisation ­­– from the molecular and subcellular to the integrated whole animal – in an evolutionary and environmental context.  In addition to core primary research articles, the journal has a well-regarded and dynamic front section of review and news content, and continues to expand its services to authors and readers.

Applicants will have a PhD in a relevant scientific field. Post-doctoral and/or previous editorial experience are highly desirable, although we will provide on-the-job training.

Core responsibilities:

– Commissioning, handling peer review and developmental editing of review material for the front section of the journal.

– Representation of the journal at international conferences and within the wider scientific community.

– Creative involvement in the journal’s development.

The successful candidate will have a broad interest in science, the scientific community and publishing. Excellent interpersonal and literary skills, enthusiasm and commitment are also essential requirements for the position.

The Reviews Editor will work alongside an experienced in-house team, including the Publishing Editor and News & Views Editor, as well as with our international team of academic editors. Additional responsibilities may be provided for the right candidate.

The position represents a unique opportunity to gain experience on a highly successful life-science journal and offers an attractive salary and benefits. The position is full time (although part-time working may be considered) and will be based in our offices in Cambridge, UK.

The Company of Biologists is a not-for-profit organisation and publishes three internationally renowned, established journals – The Journal of Experimental Biology, Development and Journal of Cell Science –as well as two newer Open Access journals – Disease Models & Mechanisms and Biology Open. The organisation has an active programme of charitable giving for the further advancement of biological research, including travelling fellowships for junior scientists and contributions to academic societies and conferences.

Applicants should send a CV, along with a covering letter that summarises their relevant experience, why they are enthusiastic about the role, and their salary expectations, by email to hr@biologists.com no later than 3 December 2014. Please direct informal enquiries to Miriam Ganczakowski on +44 (0)1223 426164.

Applicants must be eligible to work in the UK and be able to travel internationally.

(No Ratings Yet)

Loading...