#stemcellfacts – Tweeting stem cell research

Posted by on February 16th, 2012

Twitter logoAt the start of February, EuroStemCell used our Twitter page @eurostemcell in a new way: We posted a series of fascinating facts and ‘test your knowledge’ questions about stem cells, using the hashtag #stemcellfacts. The tweets covered a lot of ground, from embryonic stem cells and blastocysts to skin stem cells, gut stem cells, heart cells and regeneration.

Thanks to Kate Blair for developing the #stemcellfacts concept and researching the content for the 30 tweets. You can see all the tweets collated with responses from other tweeters in our Storify summary.

We’ve got off to a flying start in 2012 with lots of other activities too - new blogs, translation into Italian, new educational tools and articles about embryonic stem cells. Find out more in our February newsletter. And as ever, we’re keen to hear you feedback at www.eurostemcell.org/contact.
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Freeware for scientists

Posted by on February 6th, 2012

After commenting on a previous post, I’ve decided to make my own post about freeware I use regularly that other scientists might find useful. All of these are available for Windows, Mac and Linux as far as I’m aware and come with various price plans if you want more storage space/functionality. You’ll need to create an account for some of them, but again that’s free.

Libre Office – I use my own laptop in the lab and as a result of that I don’t have some common software like Photoshop, Illustrator and most annoyingly, Microsoft Office. Rather than paying out of my nose for a productivity suite like Office, I chose to have a go at some open source alternatives. LibreOffice is an open source productivity suite that’s spent around 20 years in development, so it’s pretty stable. It comes with the same kind of programs as Office, a word processor, spreadsheets, presentation maker, drawing tools etc. It’s also compatible with MO as well, so you can open documents you created in program with the other. Migrating from Microsoft to LibreOffice was pretty easy and most of the layout and functionality is the same. I’ve been using this for a year or so now and I think whilst it still lacks the polish of Microsoft Office, it works just as well.

AlternativesGoogle Docs, laTEX (this is supposed to be specific for creating manuscripts)

Dropbox – I mentioned this in a comment on a previous post, but I’ll go into a little more detail here. Dropbox is basically a file syncronisation tool that you can download as a client program. Once installed, if you place a file in your Dropbox folder, it syncs it with your account so you can access that file from anywhere with an internet connection. It’s very easy to use and once you set up your Dropbox folder, you can share it with anyone. The syncronisation between folders on different computers is very fast, you can upload a file onto a shared Dropbox folder and within seconds the other person receives the file. This is very useful for collaborations or even just sharing data in a lab.

The servers they use to store files are very secure and you can create multiple sub-folders that you can share with various people. You get 2GB free storage but if you invite other people to share your folders or install it on another computer you get some extra storage.

AlternativesSugarsync

Mendeley – Mendeley is a web based reference manager that also has a desktop app you can download to organise PDFs and documents on your computer. The web app lets you build a library with an easy to use web importer that works as a plug-in to your browser. Mendeley also store pdfs on the (up to 500MB) and you can retrieve them from any computer or share them with other users by forming groups.

The Mendeley desktop app organises and indexed your PDFs that are stored on your computer. You can also annotate, highlight and add sticky notes to your files. As I begin to write my thesis, I’m finding this part increasingly useful. There is also a toolbar you can install in Microsoft Word or LibreOffice to cite papers whilst writing.

Unlike Endote, it’s free (although you can pay for more cloud storage) and unlike Papers, it’s a cross-platform tool (available for Windows, Mac and Linux), making it very useful for collaborations. I find the interface really easy to use and within half-hour of downloading it, I had most of my references stored on the desktop app. Also the ability to annotate and make notes on papers is proving to be invaluable.

Alternatives - Zotero

Reflect – This is a useful look-up tool when reading papers online. Basically, it’s a plugin for your browser that highlights proteins/molecules/biological concepts in any text. You can click on the highlighted text to show a pop-up window which displays some basic information such as what the molecule is, it’s role, structure and what it interacts with. The information displayed is community driven so for really obscure proteins and molecules there might not be a lot of information displayed, but the makers are keen on the community using it to edit and add more information.

Doodle – Doodle is a web-based time management tool that you can use to co-ordinate meetings. It does this by creating simple polls where everyone can vote on when they are free. You can use various calender programs like iCal, Microsoft Outlook or Google Calender to track dates and organise meetings with other people. I’ve never used it professionally, only with friends to organise some camping trips and it’s a pretty handy tool that saves on a lot of emails.

Alternatives -  Timebridge

OMERO –  OMERO is an microscopy image management tool created especially for scientists. It’s designed by the Open Microscopy Enviroment team which is based in multiple sites across the globe. Once you have an account set up and downloaded the programs, you can upload your images to a central server and process/analyse images and even make them ready for publication with a nice figure making tool. The Journal of Cell Biology has a data viewer based on OMERO that allows authors to upload images as they were acquired and users can look through z-stacks, time lapses and individual channels in these images.

If you have any tips for other useful freeware let us know in the comments section below.
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Society Journals and the Research Works Act

Posted by on January 31st, 2012

This post about the Research Works Act and the effect on society journals was written for, and first published on, Reciprocal Space. Reposted with permission, and edited to add a correction.

Much has been said about the RWA, and the involvement of big name publishers. Less discussed, but very important for many scientists, is the role that scientific societies and their journals have, and the impact of current or future publishing practices. Some societies, such as the American Association of Immunologists (AAI), the American Society of Nephrology (ASN), the American Heart Association (AHA), and the American Society for Clinical Investigation (ASCI), publish their own journals. Of these, very few (in this list only the ASCI), have an open access policy. Other societies, such as the Society for Developmental Biology (SDB), publish in journals operated by big publishers, such as Elsevier (in the case of SDB’s journal, Developmental Biology). So where do these societies and their journals stand on RWA?

Well in some cases it’s crystal clear. In letters that responded to a “Request for Information” (RFI) by the Office of Science and Technology Policy, Executive Office of the President, regarding “Public Access to Peer- Reviewed Scholarly Publications Resulting from Federally Funded Research””, the AAI wrote:

“…working in partnership with professional societies and other scholarly publishers offers the federal government the most cost-effective and efficient way of ensuring that private sector, scholarly journals survive, preserving their crucially important service of providing independent, expert peer review (accomplished at publishers’ expense) of government-funded scientific research.”

This refers to their perceived duplication of efforts in having PubMedCentral duplicating published manuscripts. The statement might make sense, if the journals were to offer free access after 12 months. But they continue with:

“…want to express our clear opposition to government mandates which require private sector publishers to make their legally-owned property (i.e., journal manuscripts, published articles and associated data) available online on sites other than our own, or to comply with a government-determined embargo period. These mandates allow the government to take private property without owner authorization or compensation, and threaten the sustainability of our nation’s premier peer-review publishing system.”

So, not so happy about providing free access. They also claim that PMC is an inferior means of disseminating and archiving published material. This is highly debatable, especially the permanence of published work. Finally, they answer many questions posed by the RFI, and include this delightful gem, which we’ve heard from Congresswoman Maloney:

“…increased “free” access is likely to benefit scientists in other nations, whether allies or enemies. In some instances, this will enhance international cooperation in the sciences, but it is not necessarily beneficial to the U.S. economy as even our friendly competitors will gladly take our research findings for free….. Neither publishers, nor the U.S. scientific enterprise, nor the U.S. taxpayer benefits from the “giving away” of our peer-reviewed publications.”

Oh dear. The point really is, these societies make most of their money from their publications, and of course feel threatened.

But then how does ASCI do it, publishing all papers in JCI for free? I don’t have the answer, but perhaps these societies should talk to each other…

In the case of the SDB, it’s a bit more complicated. They too make most of their revenue from their journal. But in this case, they fall under Elsevier’s control, and only receive a fraction of the journal’s revenues (around 10%). What can they do, stuck between a rock and a hard place? Currently they are debating what to do, so the jury is out. The SDB does provide an OA option stemming from agreements with HHMI and Wellcome Trust, that allows researchers to make their paper available as OA for a fee of $3,000. (The Company of Biologists, who publish Development, have a similar hybrid model and offer OA for a fee.)

Then the final question is for those of us who are members of these societies. Do we boycott our own society journals? Do we engage the leadership to try to convey our views? There is no clear answer, but it should be something. The editors of the journals are scientists, just like us. They understand, and they will listen. The societies have existed for a long time, and are an important part of science, in assembling scientists with shared interests in the form of conferences and journals, promoting scientific education, amongst other laudable goals. But many have their survival inextricably linked with their closed access journals.

As scientists we must ask ourselves how to help our scientific societies, while promoting open access.


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Would you use a digital lab notebook?

Posted by on January 26th, 2012

Nature featured a news article about digital lab notebooks, which launched a discussion in various places (including the comments of the article itself) about whether or not they’re useful.

What do you think? Would you use a digital lab notebook in your lab, or would you rather keep your old paper notebook? Or maybe you already keep all your notes in a digital format only. You’re all web-savvy Node readers, of course, but let’s see how digital you are when it comes to benchwork. Here’s a poll:




Read the rest of this entry »
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Stem cells, cellules souches, Stammzellen: taking research to Europe’s public

Posted by on December 22nd, 2011

It’s been a busy year for EuroStemCell: Europe’s stem cell hub - see www.eurostemcell.org for more information on who we are. We’d like to wish The Node community a happy festive season and a great start to 2012. But before we say goodbye to 2011, we thought you might be interested to know about some of the things we’ve been doing recently…

EuroStemCell goes multilingual


eurostemcell.org is multilingual! Or tri-lingual, at least.

The EuroStemCell website is now available in 2 additional languages, German and French, with Italian and Spanish coming soon. Just click on the flag icons to the right of any page on the website to give the newly translated interface a whirl.

Read more about our translation project, or go straight to the French or German homepage.


Research updates from EU-funded stem cell projects

Our research updates keep you informed about progress in public-funded European stem cell research. Here’s a recent example from our partner, NeuroStemcell.


Using stem cells to develop new therapies for Parkinson’s and Huntington’s diseases


NeuroStemcell brings stem cell biology and clinical science together to develop and test new approaches to stem-cell-based therapy. We study Parkinson’s (PD) and Huntington’s (HD) diseases, which are degenerative diseases of the brain.

Read more about NeuroStemcell

 

Italy meets the UK to discuss the future of stem cells in the clinic




Over 100 Italian and UK scientists and politicians came together on 12 December for a Summit on Regenerative Medicine organized by the Italian Embassy in London and the School of Science Technology and Health, University Campus Suffolk. Their aim: to bring the collective expertise of academics, industry and the political world to bear on the question of how to take basic stem cell research towards the clinic.

We went along to the meeting - read our report on the discussions



Inside the lab

We’ve got two new guest bloggers on our site: Anestis Tsakiridis is sharing his insider’s view of stem cell research in his blogs, Behind the Bench: A series about researchers and their rituals; and we’re delighted to welcome Alzheimer’s researcher Selina Wray, who posted her first blog, A fish out of water, on our site just last week.

Meet the stem cell scientists

We’ve also been busy talking to experts across the stem cell field. Read our interviews with Cedric Blanpain, Yann Barrandon, Christine Mummery, Doug Sipp, Karen English and Nick Barker on the site now and keep your eye out for our chats with Jane Visvader, Connie Eaves and others in the New Year.

Stem cell factsheets


We’ve got an ever-growing set of fact sheets giving quick access to the key facts about different areas of stem cell and regenerative medicine research. The content is written by researchers and  reviewed by senior scientists.  The fact sheets are designed for non-specialists but why not check them out next time for a quick overview next time someone asks you about something a little outside your own field? Take a look at the whole collection (13 published so far, some in French & German too), but here’s one of our latest…

Type 1 Diabetes: How could stem cells help?

Diabetes is a common life-long condition and the number of children being diagnosed with type 1 diabetes is increasing. The symptoms can be controlled but there is no cure. For many, diabetes means living with daily insulin injections and the possibility of long-term damage to their health. How might stem cells help?Read our factsheet about stem cells and diabetes


 

Keep up with Europe’s stem cell news

Sign up to our newsletter to stay in touch with all the latest news from the EuroStemCell project. From February 2012 we’ll be sending out a  monthly newsletter. For more regular updates, you can follow us on Twitter, check out our Facebook page or subscribe to our RSS feeds.  And if you haven’t visited the site for a while, do take a look and get in touch with your feedback and ideas.
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Let’s make a developmental biology bingo game!

Posted by on December 5th, 2011

Ever noticed how each field has its own jargon?

Benchfly, a site with free video protocols and other resources for researchers, has created “Group Meeting Bingo”. The site generates bingo cards with the particular phrases common to various fields of research. They have cards for biochemistry, cell biology, and various other fields, but no developmental biology…yet!

So, let’s make a developmental biology bingo game!

Over the next few weeks (until we have enough words), you can leave a comment below (no registration required) with your suggestions for typical words that regularly show up in developmental biology talks. Benchfly will then turn our suggestions into a playable bingo game!

They suggest taking out the cards during meetings, but I’ve enjoyed just refreshing the existing cards on the site and marveling at all the field-specific words.


Section of one of the cell biology bingo cards. Of course some of the words from other fields can appear on the developmental biology cards as well!

Looking forward to see what you all come up with for the developmental biology game!

NB: The Node does not endorse playing bingo at the expense of paying attention to talks. Personally I’ve played a similar game at a conference where the meeting organizers handed out the cards, and encouraged everyone to play. I found it very easy to pay attention to the talks there, take notes, learn things, and still win the game. It’s actually easier to spot the words if you are paying attention!
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Parenting in Science

Posted by on October 31st, 2011

After the interview with Ottoline Leyser was posted last week, a discussion on Twitter focussed on the last part of the interview, about parenting.

That interview question referred to a little booklet Leyser published a few years ago, after winning the Royal Society Rosalind Franklin Award in 2007. The book, called “Mothers in Science: 64 ways to have it all” features interviews with mothers who have managed to maintain a career in science while raising children. (Here is a link to the PDF on the Royal Society website.) In the booklet, all featured scientists have a page with a timeline showing the important events in their career and family life. They’re all unique stories, because every situation is different.

When I wanted to address the ensuing Twitter discussion (which you can read in the Storify embedded below) I thought I could add a poll to ask how other people have managed to combine their career with children, or perhaps to ask how others have failed to do so. But I quickly realised that there is no question I could possibly ask for which the answer can be reduced to a set of multiple choice answers. The possible answers would need to include all combinations of which family members are scientists, what the other partner’s job is, the age difference between parents (e.g. one is a postdoc, one a PI), working hours, who took the main child-rearing responsibilities or whether there is a balance, gender, which country you’re in, competition in the field of research, how close together the kids are, and much, much more.

Even a quick show of hands, just to ask who has children or not, would be meaningless if it didn’t account for gender, age, career stage, country, family situation, and desire to even have children in the first place.

So there is no poll. There is no poll because clearly there isn’t one clear-cut problem, and because there is not just one type of family unit.

What Ottoline Leyser’s book did is showcase a group of women who all managed to combine a family with a career in their own way. It’s an example to show that it can be done, but it’s not a collection of recipes for success. Each case really is different, and this Twitter discussion between @fishscientist and @David_S_Bristol tells a different story. (Text continues after the embedded file.)



So are there solutions? One promising step was made last week in the UK, when the Research Excellence Framework (REF) announced that “UK funding bodies have taken an early decision on the arrangements for taking account of maternity leave in the REF. … researchers may reduce the number of outputs in a submission by one, for each period of maternity leave taken during the REF period.”

That doesn’t help most of you, but it positively affects the career progress of a few mothers, and at least changes their stories.

If you have your own story to add, please leave a comment, as a poll was just too complicated….


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Ada Lovelace Day

Posted by on October 6th, 2011

October 7 is Ada Lovelace Day, celebrating women in science and technology. This international day to promote gender equality in these fields was first held in 2009, and is named after Ada Lovelace. Ada Lovelace is considered to be the world’s first computer programmer - although in the 19th century, they weren’t called “computers” yet! Ada wrote algorithms for Charles Babbage’s “Analytical Engine”.

A few related resources to mark the day:
-The Journal of Cell Science’s “Women in Cell Science” interview series by Fiona Watt.
-“Mothers in Science: 64 ways to have it all”, a free eBook published by the Royal Society and produced by Ottoline Leyser (who has a bit more to say on the topic in an upcoming interview with Development, so watch this space in a few weeks.)

Who inspired you?
In many areas of science, women are underrepresented at all levels. In other fields, such as chemistry or molecular biology, the distribution is still quite even among students, and then drops dramatically among more senior scientists. Developmental biology, on the other hand, seems to suffer less from a lack of women than many other areas of science. In 2010, more than half of the presidents of national developmental biology societies were women! In addition, quite a few women have made significant seminal contributions to developmental biology over the years and are role models to many: Nicole Le Douarin, Christiane Nüsslein-Volhard, or Anne McLaren (see also here), to name just a few of them - but there are many others!

The organisers of Ada Lovelace Day are asking people to “share your story about a woman — whether an engineer, a scientist, a technologist or mathematician — who has inspired you to become who you are today.”   So who is your female role model?
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Company of Biologists Workshop – Growth, Division and Differentiation – Day 2

Posted by on September 26th, 2011

-By Nitin Sabherwal, Eugen Nacu, Heike Laman, Irene Gutierrez Vallejo and Anna Kicheva

The second day of the workshop has finished and it is the reporting time now.

We had a wonderful day with fantastic talks and a nice walk around the area. The weather had also been beautifully supportive for these kinds of excursions and this added to the joy of walking around such a splendid place.

The first session on the second day had talks with the general question and theme- is it possible to control the cell fate decisions, particularly in context of neural development, by manipulating/controlling the cell cycle?

The session started with a talk by Philipp Kaldis who investigated the brain of CDK2/CDK4 double knock out (DKO) mice embryos. He found that the brain of these mice showed similar gross structures as the normal brain from control mice, however, the cortical plate and the intermediate zone areas showed reduced thickness indicating reduced differentiation, while the subventricular zone and the ventricular zone containing progenitors were largely unaffected. His work conveyed 2 important points:

1)   in the absence of CDK2 and CDK4, cyclinD will pair up with CDK1 and CDK6 instead.



2)   CDK2 and CDK4 have an effect on differentiation of neural stem cells. The effect is mediated by a change in the length of cell cycle and potentially by a direct effect of CDK2 and CDK4 on differentiation.

In the second talk, Federico Calegari, followed up on the theme of “cell cycle length (particularly the length of the G1 phase) being a determinant of cell fate during division of neural stem cells in the developing mouse brain”.  He started by describing the process of neurogenesis in mice, which follows thepath: apical progenitor -> basal (intermediate) progenitor -> neuron. He followed with explanation of previous work that supported this idea; work which showed that:

1) the G1 length of neural progenitors increases during development

2) cortical areas with higher neurogenesis have a longer G1 than proliferating progenitors

3) an artificial lengthening of G1 induces premature differentiation.

4) shortening of G1 by CDK4 and cyclinD1 inhibits neurogenesis and promotes the expansion of basal progenitors during embryonic development

And finally he showed the amazing results that it is possible to conditionally control the expansion of NSC in the adult mouse brain by temporarily overexpressing CDK4 and cyclinD1 (called 4D), which would initially expand the progenitor pool and then, after stopping the 4D overexpression by genetic manipulation, the expanded pool would eventually differentiate into the neurons. In essence, this new system allows the increase of neuron number in the adult hippocampus, which may have important implications for understanding the role of adult neurogenesis in cognitive function and controlling this process for therapy of neurodegenerative diseases

So we found out that controlling cell cycle length by CDKs and cyclins influences fate decisions in neural progenitors. But the next bigger question becomes- what is downstream of these Cyclin/Cdk molecules responsible for the fate change? And here came Anna Philpott’s insightful talk to our rescue.She looked at the posttranslational modifications of Neurogenin2 which drives neurogenesis. Neurogenin2 has multiple sites for phosphorylation and these different sites show different sensitivity to Cyc/CDK levels, with more sites being phosphorylated at a higher level of CDK. These phosphorylations were shown to negatively affect the stability of Neurogenin promoter binding in a cumulative fashion. Anna nicely showed that the efficiency of Neurogenin2 induction of neuronal markers is inversely proportional to the number of phosphorylated residues.

Linking the data together from Federico’s and Anna’s work, it is tempting to speculate that CDK4 and cyclinD1 induce proliferation of basal progenitors by decreasing the activity of Neurogenin2 and similar differentiation factors.

The last talk of the session was from Kristen Kroll who talked about the role of Geminin in setting up the epigenetic landscape for neural fate acquisition. Kris has long standing interests in how neural fate acquisitionis regulated by Geminin, which she cloned long time back in Mark Kirschner’s lab, as a regulator of both neurogenesis and cell cycle.  Kris nicely showed that knockdown of Geminin, a nuclear protein had no effect on the ability of ES cells to maintain or exit pluripotency, but when she overexpressed Geminin, it promoted neural fate acquisition, even in the presence of growth factors that normally antagonize neural induction. She followed this observation and showed that the mechanism behind Geminin’s ability for neural induction was due to its ability to maintain a hyperacetylated and open chromatin conformation at neural genes. She nicely showed that in ES cells, Geminin had the ability to enhance the histone acetylation on neural promoters and also it binds to the acetylated neural promoters and activate the expression of neural genes, leading to the neural fate acquisition caused by the Geminin overexpression. Thus Kris showed that Geminin functions as an intrinsic factor regulating the neural fate acquisition, by establishing an appropriate epigenetic signature on neural promoters.

During the Monday afternoon session we continued with two talks that link polarity and cell proliferation.  Dr. Helena Richardson presented her work in Drosophila eye imaginal discs about the role of lgl in proliferation.  lgl is a polarity protein that has been implicated in human cancers. Helena found that lgl mutant cells show an increase in proliferation without apparent defects in apical basal polarity. This proliferation mis-regulation is due to a perturbation of the Salvador/Warts/Hippo pathway, and she also presented her preliminary data on novel mechanisms that couple the polarity to the Hippo pathway.

Dr. Nancy Papalopulu spoke on her work on the early neural plate progenitor cells from Xenopus, In this system, cells with different apical-basal polarity properties showed different potentials for proliferation and differentiation. Her work shows that a membrane-bound, active form of aPKC, an apical polarity protein, is able to directly phosphorylate some components of the cell cycle regulatory machinery.  This caused protein destabilization with consequent effects on shortening the length of G1 phase, and promoting proliferation. She proposed that cell polarization is one mechanism that controls the length of the cell cycle, with consequent effects on the differentiation potential of the cells.

The fun (for scientists) continued in the evening with a mini grant writing session where five teams of randomly-paired discussants were asked to come up with a fundable proposal, that incorporated both team members expertise, in 15 minutes!! Proposals included microRNA regulation of oscillatory networks, proteomic screens on limb regeneration, uncovering links between patterning and proliferation, molecular requirements for NSC differentiation, and the importance of G2 phase.  Reflecting the current economic climate, none of the proposals was funded

 

 

 

 

 
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Stem cell research in Qatar

Posted by on July 11th, 2011

There’s an interesting interview in Nature News, with Abdelali Haoudi - the vice-president for research of the Qatar foundation. Qatar opened a biomedical research institute a few years ago, and is now looking to expand this with a stem cell institute.

The situation in Qatar is almost opposite of that of many other countries:  they have enough money to set up the institute, but not necessarily enough highly-skilled people to work there. They’ve sent six students abroad to learn about stem cells at top institutes, and expect them to come back to work in Qatar, but will they really all come back, or is this going to be a practical lesson in the risks of “brain drain”?

The interview also addresses the ethical aspects and Islamic views of stem cell research. The foundation organised a conference for Islamic scholars to determine the fatwa (official Islamic rules) concerning human embryonic stem cells, and they came up with a set of well-defined rules: “We can use tissues from embryos for up to 14 days after fertilization. We have to get the consent of the parents. We cannot create embryos specifically for research, and we cannot use the tissues for commercial purposes — only for basic research or to develop new therapies”, explains Haoudi.

Have a look at the entire interview.

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