A wave from Quintay

Posted by on January 31st, 2012

The International course on Developmental Biology was a great experience, both instructive and mind-opening. All the students were shuttled to the remote and very small fishing village of Quintay, where the CIMARQ, the investigation centre where the course took place, is located. Originally a whaling station, this centre is dedicated to the instruction of professionals in the area of marine resources and has various branches of research mainly based in repopulation strategies of different species ranging from Sea Urchins to the delicious Conger eel or Sole fish. Their main objective is to provide small scale fish-farming to the general community. In fact, on the day of our arrival, after a Lecture on the history of and the main, original questions in Development by Dr. Roberto Mayor, we were given a short practical on Sea Urchin gamete harvesting and fertilization. This was followed by a very instructive tour of CIMARQ and its various projects, from seaweed culture (which is the main source of food for Sea Urchins) to the Conger and Cole fish tanks (see below). This course was unique in that it covered a wide range of developmental models instead of focusing on one or two: Throughout the twelve days of the course we had two days of each: Zebrafish, Xenopus, Planarian, Drosophila and Chick (plus a symposium and a first day tour). While including such a variety of different models may seem too optimistic (especially for just two days of each!), the truth is that the course was a huge success as proved by the fact that most of the experiments were successful. Our day schedule started with lectures and lab work in the morning. Then lunch, after which we spent most of the time in the lab and, after dinner, everyone attended presentations, by students, about their research. This part (the presentations) was a very good innovation this year and, given its success, it will probably continue in future courses. The discussions were very productive, and, from a student’s point of view, it was great having peak scientists listening, criticizing and suggesting experiments for my research. It was also good to share our areas of research between students since it was very different from the casual exchange of area of research in informal gossip. So, on to the course.

Zebrafish module

Zebrafish was coordinated by Dr. Kate Whitlock. The first Lecture was on Zebrafish basics (rearing and genetics) and embryo morphology. We then proceeded to the lab in which work consisted of cataloging the effects of different concentrations of alcohol in zebrafish development by observation under dissecting microscope of live embryo general morphology and craniofacial development. Afterwards, we carried out an immunohistochemistry protocol for the detection of neuron and neural crest markers so as to further characterize the effects of ethanol in early development. To sum up the results, I would say that the message ¨Vertebrate development and alcohol don’t mix¨ was extremely clear: The deleterious effects on general and craniofacial development were patent even without the need for immunohistochemistry. The second lecture by Kate focused on neural crest development and how neural crest cells migrate and interact with the neural tube and placodes to give origin to the olfactory system At the lab, we studied gene expression of three main neuron and neural-crest marker genes (shh, sox10 and six4b) using in-situ hybridization. Finally, we observed fluorescent-tagged transgenic lines and we compared the results with those of immunohistochemistry and hybridization.

Xenopus module

Xenopus was the next chapter in this course and, again, experiments were very successful (albeit with a lot of effort). We began with a lecture from Dr. John Gurdon on the history of Xenopus as a Development model and classic experiments followed by a focus on the regulation of induction by molecule gradients. In the lab, we tried some of those same experiments ourselves: After a brief introduction by Roberto Mayor on egg collection and fertilization, we injected GFP mRNA into two, four and eight cell embryos. The next step was to create Nieuwkoop recombinants by separating vegetable and animal poles from different embryos and then setting them one against the other so that the vegetable pole would induce growth and mesoderm tissue in the animal pole. The following task was to graft neural crest tissue from GFP labeled neurulas into normal ones. Although it took some practice, after a few hours we successfully observed neural crest cells migrating under the ectoderm. On the second day, Roberto took the stand for a lecture on the post-fertilization phenomena of the Xenopus embryo and on the development and function of the neural crest. The final (and most challenging) experiment was to perform a Spemann organizer graft. After about five or ten minutes of dissection, John Gurdon displayed, with a proud smile, a clean and very neat graft. Although John definitely made it look easy, I had like four or five embryos which attest to the contrary. This was the price of success however as, although most of us agreed that it was harder than it looked, we managed to come up with several grafts which, at least, looked quite tidy. Due to a power shortage (and consequent rise in temperature of the incubator) we were unable to photograph many of those embryos, but the truth is that we were all very satisfied with our achievements.

Planarian module

Planarian was an interesting module in that it is a relatively new model and that we didn’t focus on embryogenesis but on regeneration instead (although we did have a very interesting lecture on planarian embryogenesis, which involves very rare and interesting processes). Planarians have unparalleled regeneration capacities and can regenerate a whole organism from a very small portion of the parent planarian. Dr. Alejandro Sánchez Alvarado was the scientist who established planarians as research models and it was great having him! Alejandro’s lecture on the establishment of planarians as regeneration research models and the similarities and differences between regeneration and embryogenesis was astounding. In the lab, we started out by cutting up worms in as many ways as we could think of. Over the following days, we got to see strange or downright weird forms of planarians as they regenerated the parts we had cut off. A second experimental part of this module consisted of dissociating cells, staining with Hoechst and observing  the cellular morphology of neoblasts (stem cells) among other cell types. In the third part we observed the differences in target proteins and tissue-specific markers between worms under normal conditions and worms either treated with RNAi or cut in half. I particularly enjoyed taking photos of these last worms showing the progressive regeneration of these systems and comparing the velocity and sequence of events that lead to the new worms. This was one of my favorite modules since I didn’t practically know anything about planarians past what I studied in an early zoology course (which seemed boring at the time) and, now, I can’t read enough about them!

Drosophila module

This module was taught by Drs Trudi Schüpbach, Eric Wieschaus and John Ewer. The first lecture, by Eric Wieschaus, was an interactive talk about fly genetics and fly crossing. We discussed the screen with which he identified genes that regulated embryogenesis. This was incredible and very instructive, because most of the time, we read about results without taking into account the real work that had to be done to obtain them. In the lab, we carried out several observational experiments: We were given embryos from unknown crosses and had to hypothesize what the parents´ phenotypes were by peeling embryos or bleaching them, followed by immersion in halocarbon oil or fixing in hoyers mountant. Another part of the practical consisted of analyzing mRNA expression (or localization) and observing embryo morphology and movement using transgenic lines. With the help of Trudi Schüpbach, we  also dissected ovaries and looked at oogenesis in transgenic lines with either GFP-tagged histones or a membrane-bound GFP. The second day, lead mainly by John Ewer, we focused on later stages of development. John gave a lecture about larval growth, physiology and metamorphosis concentrating on the reorganizing of the neural system during the pupal stage. In the lab we learned how to locate and remove imaginal discs from 3rd instar larvae and we watched the retraction and regrowth of sensory neuron axonal arbors and dendrites during the pupal stage Worthy of mention was Eric’s incredible enthusiasm with experiments and his loud cheering when the results were revealed (captured in photo). For me, all of the faculty of the course were extremely good professors: Their lectures were very clear and they were all very open to questions or doubts and were very watchful and helpful in the lab. Eric, however, was something else. I can’t actually explain how or why, but, as an example, he took it upon himself to single handedly sharpen most of our pincers to ease embryo peeling and larval dissection!

Chick module

The chick embryo was the last model and one of the most challenging, not only because of the complexity of dissection and grafting, but also because of how tired we were. After learning how to set up New cultures, we performed two experiments: Node grafts and cutting embryos in half. The first experiment, which is analogous to the one done in Xenopus, was intended to demonstrate how Hensen’s Node induces other tissues. In the second experiment we separated posterior and anterior halves of the embryo and observed their development, since the cells of each half reorganized and redefined the embryo axis. As professor Claudia Linker pointed out, in both of these experiments we had an impressive success rate (>90%), something most of us were very proud of! Additionally, we learned two other very useful techniques which were applied on embryos that were not removed from the egg: Embryo injection with either DNA or a fluorescent label and electroporation of the DNA-injected embryos. Although the success rate was lower, we did get to see some embryos with pretty neat dye labels and even a few good electroporations. Claudio Stern gave two more lectures on the molecular regulation and timing of neural specification and induction and a very interesting and comprehensive one integrating molecular and cellular processes that control, occur during and give rise to gastrulation.

Summing up…

As a student, I was extremely grateful to have had the opportunity to participate in this course. All the faculty were extremely helpful, friendly and sympathetic. In my experience, the closest I can get to scientists of the stature as the faculty of this course is by asking questions at lectures (if I’m extremely lucky). Sharing at least two days with them was very productive and actually giving them) a short presentation was incredible! I was given very good advice on how to guide my research and I also had some very interesting questions (the sort of that great minds usually ask)! Apart from the advantages/tricks/advice I learned for the model I currently work with, this course was very mind-opening: I learned about models that I practically had never heard of before and I feel comfortable about working, for example, with Zebrafish , Xenopus or Chick, three models I never though I would do experiments with! I’m currently thinking about how I can relate my research to one of these models and, hopefully, get my hands dirty working a few months in a lab which uses such models. I would strongly recommend this course for anyone with a strong curiosity and willing to take a look ¨outside the box¨. Please contact me at gersabio@gmail.com if you have any particular doubts about the course or this article and this is the course website: http://biodesarrollo.unab.cl/I wanted to shout out a special thanks for the three organizers: Alfredo Molina, Ariel Reyes and Roberto Mayor, without whom this course would not have occurred, for their dedication and very good will.


Germán Sabio
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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:




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Emergence and evolution of developmental patterns; APPLICATION DEADLINE EXTENDED TO 29 JAN 2012

Posted by on January 25th, 2012

Conference page: http://www.cnrs.fr/insb/cjm/2012/Vincent_e.html
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Interested in writing for the Node?

Posted by on January 24th, 2012

New readers of the Node, did you know that you can contribute to the site as well? If not, see the registration page for more information.

But what if you already have an account, and would love to write for the Node, but just don’t know what to write about?

So far, we have occasionally contacted people individually to ask if they would be interested in writing about a particular topic, or posted general calls on Facebook and Twitter, but some people may have missed out on these emails and messages.

So here’s something new, specifically for those of you with (approved) Node accounts who would like to be kept in the loop about specific writing opportunities:


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Science Online North Carolina

Posted by on January 19th, 2012

If you’re interested in the role of the internet in science and science communication, you should keep an eye on Twitter from today until Saturday. Specifically, the tag #scio12, which is being used by the annual Science Online conference in North Carolina.  (Here’s the link to see the newest tweets tagged #scio12, but I’ve also collected a few interesting ones in the Storify shown at the end of this post.)

I’m not attending this year, but I’ve been a few times before. The meeting is very broad, covering scientific publishing, data sharing, blogging, science journalism, science art and everything in between. The thing that sets it apart most from many scientific conferences is that many of the participants know each other very well, personally, but have never met. The meeting originated as “science blogging” conference, and brought together people who had been talking to each other online for months or years. As a result, in between serious discussions titled “Self-censorship in physician writers” or “Using altmetrics to track the online impact of your research” the schedule leaves room for social events, and participants have been planning podcasts and chocolate swaps for months. For many people, this conference is the event of the year, where they get to see old friends again. For others, it’s a place to promote their latest science book, to introduce their new software for scientists, to recruit science communicators, or simply to take a step back from their research and look at science from a new angle.

The several hundred tickets for the conference sold out within minutes, so there’s a good chance that, like me, you’re not there. I’ll do my best to follow the meeting over Twitter the next few days, and collect the most interesting things in the Storify below. Join me in following along with Science Online online!

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Dates for your calendar

Posted by on January 16th, 2012

Conference season is about to kick off, so here are a few registration dates for various meetings you might want to attend. If you know of any others, please leave a comment below. And of course keep checking the events calendar (and add any events not on there yet - see the help page for instructions on creating accounts and adding events)

 

January 16 (today!) - early registration deadline for the Sixth International Symposium on Vertebrate Sex Determination. They’re based in Hawaii, so you may still make the early registration deadline.
January 20 - early registration deadline for Drosophila Meeting (final deadline on February 29)
February 8 - registration/abstracts deadline for the 12th International Conference on Limb Development and Regeneration
March 1 - Application deadline for “The Stem Cell Niche - Development and Disease” in Copenhagen (see poster below)
March 23 - Early registration deadline for the BSDB/BSCB/JSDB meeting

To celebrate the opening of the Copenhagen Stem Cell Centre (DanStem), the foundation is hosting a conference from June 25 to 27. If you’re selected as participant, they will cover hotel, registration, local transport and meals. See poster below for speaker list.
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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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Wellcome PhD – Lab 3: Pigs that fly

Posted by on December 8th, 2011



This is my personal report on the last of three laboratory projects which I have undertaken during the rotation year of my 4-year Wellcome Trust PhD. I studied how flies depend on Pigs to fly.



It is vital that the cells that make up your body’s tissues are correctly organised. If cells can’t differentiate between up and down (or inside and outside) they can’t possibly organise themselves into the complex structures we need to function. For the final rotation in the first year of my 4-year Wellcome Trust PhD I joined Dr Katja Röper’s lab to work with fruit flies (Drosophila melanogaster), investigating the complex and unusual nature of an organiser protein – the brilliantly titled ‘Pickled eggs’ (Pigs for short).

As I have discussed in some of my previous posts, cells contain a network of internal scaffolding known as the cytoskeleton, which helps to control cell shape and movement. It also provides transport routes to help move molecules and organise everything within a cell. Different parts of the cytoskeleton perform different functions, differentiated by the size of the structures they form and the proteins they are made of. The thinnest are microfilaments, made of actin, responsible for cell shape (they also allow muscles to work). The thickest are microtubules, made of tubulin, which form the major transport routes within a cell. Other animals (but not flies) contain further intermediate filaments that have primarily structural roles.

Although these different parts of the cytoskeleton have been studied independently for many years, it has only recently been discovered that they often work together. It turns out that there are many components needed to make these interactions possible. One of these components in fruit flies is the protein Pigs, a ‘GAS2-like protein’ related to four known human proteins. Pigs is thought to interact with both microfilaments and microtubules, forming a bridge that holds the different structures together.

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Senescent cell rejuvenation – you(r cells) are never too old for pluripotency!

Posted by on December 3rd, 2011

 



In 2007, a group let by Takahashi and Yamanaka from Kyoto University successfully generated pluripotent cells from human adult fibroblasts.  They were able to induce a pluripotent state in differentiated cells by introducing four transcription factors, OCT4, SOX2, c-MYC, and KLF4 by retroviral infection, hence the name “induced pluripotent stem cells (iPSCs).”  Although the mechanism of how these factors induced pluripotency in somatic cells is not completely understood, it is clear that the endogenous pluripotency genes OCT4, SOX2 and NANOG were activated and, in turn, re-activated the autoregulatory loop that could maintain the pluripotent state independent of the transgenes. iPS cells showed many characteristics of human embryonic stem cells (hESCs) such as expression of pluripotency markers, reactivation of telomerase and the ability to form teratomas, demonstrating a potential to redifferentiate into descendants of all three embryonic lineages.

However, follow-up studies suggested that the reprogramming of iPS cells was incomplete. Some epigenetic imprinting remained, the telomeres length was not fully restored, and the descendants of these cells entered senescence prematurely. Additionally, it was reported that cells from older donors were difficult to convert to iPS cells.

As people age the number of cells that are senescent increases.  Senescence is defined as an irreversible cell proliferation arrest and occurs in response to various stresses, including activation of oncogenes, shortened telomeres, DNA damage, oxidative stress and mitochondrial dysfunction.  Common features of senescence include activation of the p53/p21 and p16/pRb pathways and formation of senescence-associated heterochromatic foci (SAHF).

Conversion of somatic cells to iPS cells occurs at very low frequency in any given cell population, but because older individuals have a higher number of senescent cells it has proved to be difficult to convert cells from older-aged donors. In an effort to overcome this barrier some researchers tried an alternative four-factor combination, substituting NANOG and LIN28 for c-MYC and KLF4, but without much improvement. Researchers began to wonder whether cellular aging was a barrier to iPS cell conversion.

In a recent paper published the November issue of Genes in Development, entitled “Rejuvenating senescent and centenarian human cells by reprogramming through the pluripotent state,” Lapasset and colleagues from the Institute of Functional Genomics in France report that they have overcome this barrier and generated iPS cells from human donors as old as 101 years.  What’s more, the converted cells showed no signs of premature aging and appeared “rejuvenated” – iPS cells converted from nearly senescent donor cells regained their replicative potential and, when re-differentiated to fibroblasts, by all accounts resembled young proliferative cells.

The key was to use six transcription factors, not four, combining OCT4, SOX2, c-MYC, KLF4, NANOG and LIN28. Initially, they took fibroblasts from a 74-year-old man and induced them into replicative senescence by serial passaging. Senescence was confirmed by FACS analysis showing cell cycle arrest, increase in molecular markers characteristic of senescence, and formation of SAHF.

The six transcription factors were introduced by lentiviral infection. A week after infection,  the SAHF disappeared (see figure above, left panel) and after 40 days colonies appeared that looked like hES cells (see figure above, right panel). Lapasset et al. examined individual clones and found that endogenous pluripotency gene expression was activated and the promoters of OCT4 and NANOG, which are usually heavily methylated in differentiated cells, were demethylated in the newly converted iPS cells.  Individual clones were able to differentiate into cells expressing markers of all three germ layers as well as form teratomas with organ-like structures typical of all three embryonic lineages.

The authors then repeated this procedure with cells from donors 92, 94, 96 and 101 years of age and again were successful in generating iPS cells with the same efficiency, making these the oldest human donors so far whose cells were reprogrammed for pluripotency.

They extensively tested whether the iPS cells retained marks of aging similar to cells they originated from. They found that unlike parental cells, p16 and p21 expression in iPS cells was downregulated, similar to hES cells.  Additionally, telomere length was restored and maintained after numerous population doublings.  Because previous reports using the 4-factor induction method reported that iPS cells induced from  aged donor cells have chromosomal abnormalities the authors examined the karyotypes of the iPS, but found that in all cases they were normal.

They went on to compare the transcriptomes of the iPS cells with those of the hES cells and the parental cell types. The result was that the iPS cells gene expression profile had much more in common with hES cells and very little with the parental cells.

The final question they addressed was whether reprogramming of senescent cells and cells from long-lived donors to a pluripotent state leads to the production of “young” cells upon redifferentiation. Previous studies of fibroblasts derived from iPS cells showed that they have limited replicative potential and entered senescence early. In this study, when the iPS cells derived from 74-year-old and 96-year-old donors were redifferentiated to fibroblasts their rate of proliferation was similar to young proliferative fibroblasts.  The cells had regained replicative potential and were able to go through additional 60 population doublings before re-entering senescence, in contract to the sencescent cells they were derived from, which were no longer capable of replicating.

Transcriptome analysis of the newly differentiated fibroblasts showed that they resembled young proliferative embryonic fibroblasts derived from hES cells rather than their parental cell types. They also had less oxidative stress and better mitochondrial function than the parental cells.  The authors concluded that the cells were “rejuvenated” as a result of reprogramming through the pluripotent state.

This paper represents a significant advance in the field of iPS cells, demonstrating that cellular aging is not a barrier to generating pluripotent cells, bringing us one step closer to cell-based therapies for aged patients.

 

ResearchBlogging.org
Lapasset L, Milhavet O, Prieur A, Besnard E, Babled A, Aït-Hamou N, Leschik J, Pellestor F, Ramirez JM, De Vos J, Lehmann S, & Lemaitre JM (2011). Rejuvenating senescent and centenarian human cells by reprogramming through the pluripotent state. Genes & development, 25 (21), 2248-53 PMID: 22056670
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Development: New Executive Editor

Posted by on November 30th, 2011

I’m the new Executive Editor at Development, taking over after Jane Alfred’s eight years at the journal, and I’d like to take this opportunity to introduce myself. I’m starting here fresh off the plane from Heidelberg, Germany, where I have been working as a scientific editor at The EMBO Journal for the last three years, handling manuscripts in the fields of developmental and cell biology. Before then, my research life is probably best described as “trying to understand how to make an eye”: firstly during my PhD with Matthew Freeman at the Laboratory of Molecular Biology in Cambridge working with Drosophila (where I published my first ever paper in Development!), and subsequently studying morphogenesis of the fish retina in Jochen Wittbrodt’s lab at EMBL Heidelberg.

While I’m no longer in the lab, I’m still fascinated by the subject, and am excited to be getting back to my developmental biologist roots here at the journal. To me, Development is all about publishing by and for the community, and The Node is a big part of that: I’ve been reading it since its inception last year, and I look forward to playing a more active role from now on – I’m sure you’ll be hearing more from me in the future. I also hope to be meeting many of you in person over the coming months and years. For now, though, all that remains is for me to thank Jane for the fantastic job she’s done here: I have big boots to fill, but I hope I’m up to the challenge!
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