The purpose of this summary is to present to “The Node” readers a recent update to the story which, in my opinion, is a quite interesting example of the phenomenon of programmed genome rearrangement (PGR) that occurs in the lamprey Petromyzon marinus.

Programmed genome rearrangement describes the regulated structural changes in the genome, which result in the generation of new coding sequences, changes in the control of genome functions and gene expression etc, within ontogeny (not to be confused with similar structural changes on the phylogenetic level). Although on a smaller scale, a form of PGR also occurs during the formation of the T- and B-cell progenitors in mammals, the V(D)J somatic recombination system, which generates the diversity of forms of the Ig- and T-cell receptors.

The PGR in P. marinus occurs during embryonic development and results in the differential deletion of hundreds of millions of base pairs specifically in the genomes of the somatic lineages, as contrasted to the germline. In effect, the germline retains sequences that are deleted in the soma. Of course, this is not the first known case in the Metazoan clade (it has been previously described in sciarid dipterans, nematodes, copepods, etc (see references in the articles cited below)) but according to the authors, it is the first known example of a genome rearrangement of such scale in vertebrates, which makes it especially important for better understanding the evolution and mechanisms of vertebrate gene regulation. Speculatively, lampreys eliminate particular sequences from the somatic tissues’ genomes, which are otherwise important for the complex meiotic rearrangements and pluripotency regulation in the germline, because misregulation of such sequences in the soma may lead to disruptions in genome integrity and defects in cell commitment/differentiation (e.g., tumorigenesis). However, DNA breaks are also visible at later stages of development, which suggests that further rearrangements probably do occur, possibly in a tissue-specific mode (as suggested by variation in the DNA content measured by flow cytometry), which may potentially lead not only to loss of function, but also to the assembly of new sequences (regulatory, coding, etc), that facilitate the differential development of the somatic lineages.

In the newer of the studies, the authors used a customized oligonucleotide microarray that targeted all available germline sequences and a small fraction of the somatic sequences. This revealed that nearly 13% of the screened germline sequences were deleted in the soma and that five of the promising candidate sequences were expressed in the juvenile and adult testes. A large fraction of the somatically deleted sequences are single-copy and protein-coding DNA, which argues against a predominant deletion of repeats. Intriguingly, the authors do not rule out the possibility that whole chromosome elimination may also contribute. Genes presented in the deleted regions include: APOBEC-1, cancer/testis antigen 68, WNT7A/B, SPOPL etc, which in other vertebrates have known roles in cell fate maintenance, proliferation and oncogenesis. Interestingly, some of the genes indentified in the germ-line specific fraction have homologs in other vertebrates where they are not known to function in germline development. I could easily hypothesize that those genes were recruited for germline functions during lamprey evolution or, alternatively, they were germline-specific in ancestral vertebrates but they were later deployed in somatic functions with concomitant loss of germline function. Or it simply means that our knowledge about vertebrate germline function genes is imperfect!

Despite this important differences in genome biology between lampreys and gnathostomes (as we know them), there are many fundamental similarities in embryonic development and gene content. It is expected that some of the factors involved in the lamprey’s PGR will have homologs in gnathostomes. I am curious whether these homologs perform similar functions in jawed vertebrates? Do such PGR mechanisms of a similar scale (excluding the V(D)J system) occur in gnathostomes as well?

From a broader view, these observations suggest that lampreys use an additional strategy for gene regulation as compared to the rest of vertebrates. However, it is important to note that similar PGRs also occur in hagfish (Myxini (please, see the references)). One is prompted to ask: “What is the extent of this process in Myxini? Do their PGRs specifically occur in the soma versus the germline, as in lampreys?” Considering the fact that both lampreys and hagfish use PGRs, it is legitimate to suggest that this strategy of gene regulation was an ancestral system for the early vertebrates, and that the evolution of a gene regulation system predominantly based on epigenetic modification of chromatin was a later invention. However, this is a pure speculation.

Whatever the case is, I imagine that there exist specific DNA sequences that recruit the recombineering machinery (RM) to those regions destined for deletion. Then, it should be of importance that these sequences are occupied by the RM in the particular somatic lineages only and not in the germline. This could be achieved by any of the mechanisms that regulate the function of other regulatory sequences, like enhancers for instance, and may include control of sequence accessibility via epigenetic modification on the chromatin. In addition, tissue-specific expression of the RM components could also be a factor.

Future exploration of the PGR phenomenon will surely provide better understanding of the mechanisms that regulate genome stability, with important implications for cancer biology as well.

References:

Genetic consequences of programmed genome rearrangement, Current Biology, August 21 2012

http://www.cell.com/current-biology/retrieve/pii/S0960982212006732

Programmed loss of millions of base pairs from a vertebrate genome, PNAS, July 7 2009

http://www.pnas.org/content/106/27/11212.long

(5 votes)

Loading...

Here are the highlights from the current issue of Development:

Retinoic acid’s developmental role illuminated

The role of all-trans retinoic acid (RA) in hindbrain development and other developmental processes is usually studied by blocking endogenous RA synthesis and then continuously supplying exogenous RA by soaking embryos in all-trans RA or by implanting RA-soaked beads. Now, on p. 3355, David Bensimon and colleagues use photo-isomerisation of 13-cis RA to all-trans RA and vice versa to manipulate RA activity spatiotemporally in zebrafish embryos. In embryos in which all-trans RA synthesis is impaired, they report, brief incubation in all-trans RA or in 13-cis RA followed by UV illumination before the bud stage rescues hindbrain development. By contrast, rescue is impaired in embryos treated with all-trans RA and then exposed to UV light. Notably, activation of all-trans RA via photo-isomerisation of 13-cis RA at the end of gastrulation in head, but not tail, precursor cells rescues hindbrain development. These results suggest that all-trans RA is sequestered in embryos during normal development. Furthermore, they illustrate how RA activity can be spatiotemporally controlled in developing zebrafish embryos.

Branching out studies of dendritic patterning

The dendritic arbours of neurons in the central nervous system have highly diverse morphologies that determine neuronal connectivity and, consequently, brain function. But how is dendritic architecture sculpted during development? On p. 3442, Kazuto Fujishima, Mineko Kengaku and co-workers investigate this question by combining computer simulations and time-lapse imaging of cultured mouse cerebellar Purkinje cells. The researchers show that the characteristic Purkinje cell space-filling dendritic arbour of non-overlapping branchlets is shaped by several reproducible dynamic processes, including constant tip elongation, stochastic terminal branching and retraction triggered by contacts between growing dendrites. This last process, they report, is regulated by protein kinase D signalling. Their computer simulation of dendrite branch dynamics, which incorporates their experimental measurements, reproduces dendritic development in live Purkinje cells and confirms the important contribution that dendritic retraction makes to the formation of the Purkinje cell dendritic arbour. Further development of this two-pronged approach, suggest the researchers, will help to clarify the fundamental mechanisms of dendrite patterning in the developing brain.

Pancreatic development keeps its Sox on

All mature pancreatic cell types arise from a pool of organ-specific multipotent progenitor cells. Cell-intrinsic and cell-extrinsic cues promote the proliferation and cell fate commitment of these progenitor cells but what integrates these cues during pancreatic morphogenesis? Maike Sander and co-workers now report that the transcription factor Sox9 forms the centrepiece of a gene regulatory network that controls pancreatic development (see p. 3363). Pancreatic progenitor-specific ablation of Sox9 during early mouse pancreatic development, they report, leads to cell-autonomous loss of fibroblast growth factor receptor 2b (Fgfr2b), which is required to transduce mesenchymal Fgf10 signals. In turn, Fgf10 is required to maintain progenitor expression of Sox9 and Fgfr2b. Perturbation of this Sox9/Fgfr2b/Fgf10 feed-forward expression loop results in pancreas-to-liver fate conversion. Given that Fgf signalling is necessary for pancreatic progenitor cell proliferation, the researchers propose that a Sox9/Fgf feed-forward loop coordinately controls organ fate commitment and progenitor cell expansion in the developing pancreas, a finding that may advance efforts to generate insulin-producing cells for therapeutic use.

COP1 sheds light on root development

Although the roots of most plant species are not directly exposed to light, root growth is controlled by light and integrated with the growth of above-ground organs. Here (p. 3402), Teva Vernoux, Jian Xu and colleagues uncover a novel long-distance mechanism by which light signals through the master photomorphogenesis repressor COP1 to coordinate root and shoot development in Arabidopsis. The authors show that, in the shoot, COP1 regulates shoot-to-root transport of auxin by controlling transcription of the auxin efflux carrier gene PIN-FORMED1 (PIN1). In addition, they report, COP1 regulates auxin transport and cell proliferation in the root apical meristem by modulating the intracellular distribution of PIN1 and PIN2 in the root, thereby ensuring rapid and precise tuning of root growth to the light environment. Together, these results identify auxin as a long-distance signal in light-regulated plant development and show how spatially separated control mechanisms can converge on a single signalling system to coordinate development at the whole plant level.

Pten-less neuroblasts stop en route

Neuronal precursors in the subventricular zone (SVZ) of the adult rodent brain differentiate into neuroblasts and migrate through the rostral migratory stream (RMS) to the olfactory bulb, where they differentiate into interneurons. Diverse extracellular cues control neuroblast migration but what are the intracellular pathways that respond to these cues? On p. 3422, Suzanne Baker and colleagues identify a role for Pten, a negative regulator of phosphoinositide 3-kinase (PI3K) signalling, in mouse neuroblast development. The PI3K-Akt-mTorc1 pathway is inactivated in migrating neuroblasts in the SVZ and RMS, they report, but activated when the cells reach the olfactory bulb. Postnatal deletion of Pten, they show, causes aberrant activation of PI3K-Akt-mTorc1 signalling, premature termination of neuroblast migration, neuroblast differentiation and enlargement of the SVZ and RMS. Notably, live imaging of slice cultures shows that, although some Pten-null neuroblasts lack directional migration and have a non-polarised morphology, others migrate normally towards the olfactory bulb. Thus, the researchers suggest, the neuroblast migration defect associated with Pten loss is secondary to precocious neuroblast differentiation.

Haploid ESCs: a future in the germline

Parthenogenetic haploid embryonic stems cells (ESCs), which have recently been established through chemical activation of unfertilised mouse cells, give rise to a wide range of differentiated cell types in embryos and in vitro. But can they contribute to the germline, which is the defining hallmark of mouse diploid ESCs? Here (p. 3301), Martin Leeb, Anton Wutz and co-workers show that parthenogenetic haploid mouse ESCs have a robust germline potential and that transgenic mouse strains can be produced from genetically modified haploid ESCs. Differentiation of haploid ESCs in chimeric embryos, they report, correlates with the acquisition of a diploid karyotype by the ESCs through endoreduplication. By contrast, haploid ESCs induced to differentiate to an extra-embryonic fate by expression of the transcription factor Gata6 retain their haploid content. Parthenogenetic haploid mouse ESCs, the researchers conclude, are authentic pluripotent ESCs that can, potentially, be used to elucidate new details about developmental pathways through extension of genetic screens and manipulations directly into mouse models.

Plus…

Left-right patterning: conserved and divergent mechanisms

This Development At a Glance poster by Nakamura and Hamada summarizes the common and divergent mechanisms by which LR asymmetry is established in vertebrates.

Review: Principles and roles of mRNA localization in animal development

Intracellular targeting of mRNAs, which has long been recognised as a means to produce proteins locally, has recently emerged as a mechanism used to polarise various cell types. Here, Florence Besse and colleagues review the regulation and functions of RNA localisation during animal development. See Review on p. 3263

Review: Partitioning the heart: mechanisms of cardiac septation and valve development

On p. 3277, Zhou, Chang, and colleagues review the morphogenetic events and genetic networks that regulate spatiotemporal interactions between the cells that partition the heart.

(No Ratings Yet)

Loading...

Let’s take a very close look at the inside of a fish!

A recent paper in the Journal of Cell Biology describes a technique for generating large, composite, images from electron microscopy data. Frank Faas, Raimond Ravelli, and colleagues at the Leiden University Medical Center developed a method to computationally collect and align EM images. In the data viewer accompanying the paper, they show a large section of a zebrafish embryo, 5 days post-fertilisation, which is comprised of 26,434 individual images! The total size of the composite image is 921,600 pixels by 380,928 pixels. (For reference, the screenshots below are 500 pixels wide.)

In these screenshots you can see the overall fish in the bottom right, with the red area indicating where the larger, detailed, view is located. These are two different magnifications of the (edge of the) eye. In the bottom image you can also see the edge of the composite image, and appreciate how many individual images there are, and how well they connect.

To find out more about the method, and its practical applications, read the full paper and editorial at JCB.

Faas FG, Avramut MC, M van den Berg B, Mommaas AM, Koster AJ, & Ravelli RB (2012). Virtual nanoscopy: Generation of ultra-large high resolution electron microscopy maps. The Journal of cell biology, 198 (3), 457-69 PMID: 22869601

(2 votes)

Loading...

A few months ago, we published an interview with Stephen Fleenor, who won the poster award at the BSDB meeting. He won attendance to the SDB meeting in Montreal, where he passed on the baton and interviewed the winner of the SDB poster prize, John Young:

Stephen Fleenor: In which lab do you work?

John Young: I work in Richard Harland’s lab, at UC Berkeley.

SF: How long have you been there?

JY: I’ve been in his lab for four years, but I’ve been a student for five, because we do rotations the first year.

SF: I see. Well, congratulations on winning the poster prize. What was the crux of the poster?

JY: I’m interested in morphogens. I took a class from Mike Levine when I was a first-year student, and I was totally taken by the dorsal gradient and eve stripe enhancers, and I wanted to do something similar in vertebrates. So I chose to look at the neural plate. The neural plate is first induced to become neural tissue, and then it’s patterned by factors like Wnt, Fgf and retinoic acid. I chose to study Wnt and have been looking at Wnt-responsive genes in neuralized ectoderm. I first looked for direct transcriptional targets of Wnt signalling, and once I found those, I looked for the regulatory regions that mediated Wnt responses in these targets.

SF: And have you found regulatory regions?

JY: Using ChIP-qPCR with beta-catenin I found one regulatory region for one of my candidates that looks really good. Based on that I’m now doing ChIp-Seq with the beta-catenin antibody. I found a lot of direct targets of Wnt signalling, and a number of them showed specific expression in the posterior neural tissue. The two that I followed up with suggest that they modulate AP patterning.

The targets that I followed up after the screen were sall1 and sall4. I chose to work on these two because sall4 is a stem cell factor, and Sall1 has a human mutation associated with it. No one had yet looked at their roles in neural patterning in frogs, though, so I thought they’d be good ones to follow up on.

SF: Sounds like a pretty solid story

JY: It’s coming along!

SF: Have you ever won a poster prize before?

JY: Just at a retreat, and that was second place. This is real!

SF: Was it for the same work?

JY: Yes, it was, but it was a while ago, before things had been fleshed out.

SF: What was the element of your poster that now made it prize-worthy on an international scale?

JY: I think it was that I had knocked down the second Sall gene as well. At first I only had sall1, but now I’m working on both sall1 and 4. And at that time I didn’t have any of the ChIP data either. My project was first to find direct targets, and then I decided to look for the regulatory regions. Finding direct targets was really cool in itself, but it was only half the story.

SF: You’re four years into your PhD research. What are your plans?

JY: I’m going to do a postdoc in Cliff Tabin’s lab. I’m so excited about that, but it’s not until next summer. Now I have a year to finish up this story, and I also need to finish this completely separate project, looking at noggin mutants that I induced in Xenopus tropicalis.

SF: Do you think you’re close to closing the door on the Wnt project?

JY: I think so. I think once we get the beta-catenin ChIP-Seq data back that we can make a nice story out of that. The noggin stuff is not too far off either, so I can get it done in a year.

SF: Are you going to go to the BSDB meeting in Warwick?

JY: Absolutely! I’ve only been to Europe twice – once when I was 15, and in Oslo a number of years ago. I haven’t been to Europe much at all, so I’m looking forward to this opportunity.

At the BSDB meeting in 2013, John will, in turn, interview the winner of the BSDB poster prize.

(3 votes)

Loading...

I’ve just returned from this year’s Santa Cruz Developmental Biology meeting. Some of you may have seen the tweets I was sending out from there (see Storify for the collected set), but a combination of limited ability to multitask and limited laptop battery life meant I didn’t cover all the talks. So to add to what I missed, and for those who prefer more than 140 characters of coverage, here’s a summary of some of the highlights.

SCDB is a bi-annual broad developmental biology meeting, held at the beautiful wooded campus of UC Santa Cruz. With only around 180 participants, it’s a fairly small and very friendly event, with plenty of opportunity for informal discussions. This year, it was organised by Bob Goldstein, Amander Clark and John Tamkun, and topics discussed at the meeting ranged from the evolution of segmentation in arthropods (Mike Akam, University of Cambridge) to ligand/receptor interactions in axon guidance (Elke Stein, Yale University), with pretty much every model organism, tissue and process in between.

Despite covering the whole breadth of the field, there were some definite themes running through the meeting – aside those defined by the program. Multiple talks dealt with the germline: how you make it, put it in the right place and maintain it. Both Diana Laird (UCSF) and Jeremy Nance (NYU Skirball Institute) focussed on the earliest stages of gonad formation in the mouse and the worm respectively. Diana’s work looks at the interactions between migrating primordial germ cells and the various niches they encounter during migration through the embryo, while Jeremy presented data on the mechanisms by which C. elegans germ cells are internalised during gastrulation. Moving to later stages of the nematode, Jane Hubbard (NYU Skirball) demonstrated that nutrient status is a key determinant in regulating germ cell proliferation. The importance of environmental signals was echoed by Timothy Kelliher (Walbot lab, Stanford), who showed that hypoxia triggers germ cell formation in maize (where there is no pre-defined germline as in animals). Perhaps most spectacularly, Bruce Draper (UC Davis) presented his latest work on how mature germ cells influence sex determination in zebrafish: look out for his upcoming paper on sex-changing fish!

As is becoming standard in developmental biology meetings these days, talks were filled with beautiful movies of everything from early stage Drosophila embryos (Dan Kiehart, Duke University and Jen Zallen, Sloan Kettering) to regenerating axolotl (Saori Haigo, Center for Regenerative Therapies Dresden and UCSF) and mouse neural tube closure (Lee Niswander, University of Colorado Denver). But all were (or at least claimed to be!) put in the shade by Eric Betzig’s keynote lecture on super-resolution in vivo imaging: for unprecedented intracellular resolution in developing tissues, the future apparently lies with the Bessel beam.

In a third recurring theme, several speakers discussed the regulation of cell division and its impact on cell fate. Asako Sugimoto (Tohoku University) showed beautiful work on spindle assembly in C. elegans, directly comparing oocyte meiotic division, where the spindle is small and acentrosomic, with the following first zygotic mitosis, in which both centrosomes and chromatin direct microtubule assembly and spindle formation. Laurie Smith (UCSD) uses stomatal development in maize as a model to study asymmetric division, and shared her latest insights into the pathways regulating this process in plants. Finally, Roel Nusse (Stanford University) presented a tour-de-force study on the regulation of embryonic stem cell division by Wnt signalling – another paper to keep an eye out for in the future.

Away from the lecture theatre, the poster sessions were very lively and interactive – congratulations to poster prize winners Shawn Chavez (human blastocyst development), Harshani Peiris (planarian stem cells) and Jacqueline Tabler (ciliopathy models in mouse), although I’m sure there could have been many more winners among the great posters I saw. The Friday evening wine tasting and social session was also enlivened by the surprise entertainment: I’m not sure how many companies get called up and asked if they would sponsor a Mariachi band, but Nikon stepped up to the plate and delivered.

All of this means that the next set of organisers for this meeting – Jeremy Nance, Diana Laird and Amy Ralston – have a lot to live up to: not just in topping the Mexican minstrels, but mainly in putting together a fantastic and diverse set of speakers and fostering a welcoming and collaborative atmosphere. Look out for SCDB2014: I’m sure it’ll be a good’un!

(9 votes)

Loading...

Decisions, decisions.  Stem cells face the task to self-renew or differentiate, a decision made out of the combination and coordination of numerous regulators.  With the activation or suppression of transcriptional activators and the activation or suppression of repressors, it’s easy to see how understanding this process is anything BUT easy.  Today’s images are from a Development paper that describes the importance REST in neural stem/progenitor self-renewal and differentiation.

Neural development begins with neural stem cells and progenitor cells, and follows a specific time-line of differentiation involving neurons and glial cells.  The orderly progression through cell fates requires a complex network of regulators, but the specifics are unclear.  A recent paper in Development describes the importance of REST, a transcriptional repressor of neuronal genes, in the development of the nervous system.  REST, along with its co-repressor CoREST, suppresses neural fates in cells outside of the nervous system.  In this paper, Covey and colleagues found that REST maintains neural stem/progenitor (NS/P) cell self-renewal, and limits maturation into neural and glial cell fates.  In addition, a high level of REST in embryonic stem (ES) cells is important in suppressing transcription of neuronal genes, but is not required for ES pluripotency.  NS/P cells lacking REST have reduced self-renewal capacity and precocious neuronal differentiation.  As seen in the images above, REST heterozygote (middle) and homozygote knockout (right) ES cell-derived neurospheres have increased numbers of neurons (red, TUJ1) compared with control neurospheres (left).  REST null neurospheres also produced fewer astrocytes (green, GFAP).

For a more general description of this image, see my imaging blog within EuroStemCell, the European stem cell portal.

Covey MV, Streb JW, Spektor R, & Ballas N (2012). REST regulates the pool size of the different neural lineages by restricting the generation of neurons and oligodendrocytes from neural stem/progenitor cells. Development (Cambridge, England), 139 (16), 2878-90 PMID: 22791895

(2 votes)

Loading...

48 anatomical structures of the presented mouse embryo atlas are shown in 3D.

Here is the backdrop for our recent paper in Development, “A novel 3D mouse embryo atlas based on micro-CT”.   With the human genome project complete, the sequence and the location of each gene in the genome is understood.  However, the understanding of gene function and the corresponding expressed phenotype for all the genes in the human genome is still in its infancy.  Most of the research aimed to tackle this question will be carried out in the mouse due to the 99% genetic homology between mice and humans and the available techniques to manipulate mice genetically.  Over the last decade, the efforts of a world wide consortium, the International Knockout Mouse Consortium (IKMC, www.knockoutmouse.org), has embarked on a mission to knock out each of the ~23,000 genes in the mouse genome, one at a time, and generate the resultant mice.  With this effort now close to completion another world-wide effort, the International Mouse Phenotyping Consortium (IMPC, www.mousephenotype.org), has been established and the plan on how to phenotype the resultant mice from the IKMC project is being formulated.  What is well understood is that ~30% of the gene knockout mice strains will be embryonic lethal, further accentuating the need for an assay to phenotype mouse embryos throughout development.

If you have two groups of mouse embryos, one wild-type and one mutant, with a single gene knockout, how do you find out what’s different about them?  How do you get clues to the function of the knocked out gene and its role in mouse embryo development?  The most intuitive answer would be to look at the two groups of mouse embryos with a microscope and see if you can find any gross differences in morphology in the mutant group.  You could hypothesize that the organ or structure that shows an aberration in comparison with the wild-type group is an area where that particular gene function is important and carry on with more focused phenotyping assays from there.

This is the exact premise of our recent paper in Development.   Our aim was to eliminate the human bias and time needed to parse through thousands of high-resolution images by developing automated computer methods that could export volume measures of each of the major organ structures within the mature mouse embryo.   We used advanced high-resolution 3D imaging called Micro-CT to image 35 E15.5 C57/Bl6 mouse embryos and developed sophisticated computer software to automatically calculate the mean volumes and standard deviation of 48 structures inside the mouse embryo.  To achieve this, each of the 48 structures within a representative average image of all 35 mouse embryo images were manually painted by one individual, totalling ~400 hours of work.  Through this we acquired baseline volumetric measurements of wild-type mice to determine how tight the variation is among controls.  The resulting labeled data set (the above figure) exists as an E15.5 mouse embryo atlas for which all future mutant strains can be compared with and automatic volume measurements can be executed.  The results presented in this paper, in our opinion, is an important step in demonstrating the feasibility of using 3D imaging as a primary screen in the IMPC pipeline and provides a robust tool that can handle and analyze the large volume of images that will be acquired.

Wong MD, Dorr AE, Walls JR, Lerch JP, & Henkelman RM (2012). A novel 3D mouse embryo atlas based on micro-CT. Development (Cambridge, England), 139 (17), 3248-56 PMID: 22872090

(11 votes)

Loading...

I just came across a press release that looked like it might be interesting to some of you: 1DegreeBio has launched a Stem Cell Portal on its site, that allows you to easily find user reviews and protocols for antibodies used in stem cell research.

1DegreeBio is a relatively new company and the database of reviews is still incomplete, but they do have long lists of antibodies for various targets, and an easy interface for search queries. For example, of the more than two hundred listed antibodies against POU5F1, only two have currently been reviewed by users, and another three were linked to relevant publications.

The search screen

The resource is free to use, though, and if you submit your own reviews of the antibodies you use, you can earn points that you can then spend in their shop, on Amazon gift cards or geeky toys, or donate to charity.

As the number of reviews on the site grow, you’ll be able to make more accurate assessments on the functionality of various antibodies. It seems especially useful for antibodies from certain companies that don’t do any quality testing themselves, but that are sometimes unavoidable when no other supplier sells the antibody you need. I do wonder how 1DegreeBio will be able to ensure that all reviews are done by actual independent researchers, and not left by employees of the companies selling the products, but that is something that might also be less of an issue as the number of reviews grows.

If any of you are using the 1DegreeBio site and their stem cell portal, feel free to leave a comment about your experience. I didn’t sign up myself, because I’m no longer using antibodies, but I’ve gone through many, many vials during my PhD, and have emailed several companies to check species specificity (“Does your human antibody also work with mice?”). If this kind of “Yelp for antibodies” had existed back then I’m sure I would have left many reviews about extreme variation in batch strength, unidentified cross-reactivity, and the few unexpectedly perfect antibodies that saved my thesis.

(6 votes)

Loading...

POSTDOCTORAL  POSITIONS  in  Cell  and  Developmental  Biology  is available to study the cellular and molecular mechanisms controlling the development of the lymphatic vasculature using available mouse models  and  its  functional  roles  in  health  and  disease.  Highly motivated individuals who recently obtained a PhD. or MD degree and  have  a  strong  background  in  molecular  and  developmental biology are encouraged to apply. Interested individuals should send their curriculum vitae, a brief description of their research interests, and the names of three references to:

Guillermo Oliver, Ph.D (guillermo.oliver@stjude.org) Member

Department of Genetics

St. Jude Children’s Research Hospital

332 N. Lauderdale

Memphis, TN 38105

USA

www.stjude.org/departments/oliver.htm

(2 votes)

Loading...

Here are the highlights from the current issue of Development:

eIF4E-3 puts a cap on spermatogenesis

Gene expression is translationally regulated during many developmental processes. Translation is mainly controlled at the initiation step, which involves recognition of the mRNA 5′ cap structure by the eukaryotic initiation factor 4E (eIF4E). Eukaryotic genomes often encode several eIF4E paralogues but their biological relevance is largely unknown. Here (p. 3211), Paul Lasko and co-workers report that Drosophila eIF4E-3, one of eight fly eIF4E cognates, is essential for spermatogenesis. The researchers show that eIF4E-3 is a testis-specific protein and that male flies lacking eIF4E-3 are sterile. eIF4E-3 is required for meiotic chromosome segregation and cytokinesis, they report, and for nuclear shaping and sperm individualisation. The researchers also show that eIF4E-3 physically interacts with other components of the cap-binding complex. Furthermore, many proteins are expressed at different levels in wild-type and eIF4E-3 mutant testes, suggesting that eIF4E-3 has widespread effects on translation. These results add to the evidence that alternative forms of eIF4E add complexity to the control of gene expression during eukaryotic development.

SnoN regulates mammary alveologenesis and lactation

Mammary epithelial cells undergo structural and functional differentiation at late pregnancy and parturition to initiate milk secretion. TGF-β and prolactin signalling act antagonistically to regulate this process but what coordinates these pathways? On p. 3147, Kunxin Luo and colleagues report that SnoN, a member of the Ski family of pro-oncogenic and anti-oncogenic proteins, regulates both TGF-β and prolactin signalling to control alveologenesis and lactation in mice. The researchers show that the expression of SnoN, a negative regulator of TGF-β signalling, is induced at late pregnancy through the coordinated actions of TGF-β and prolactin. Heightened SnoN expression, they report, represses TGF-β signalling, which relieves TGF-β inhibition of the prolactin pathway. SnoN also directly promotes prolactin signalling by stabilising Stat5, a mediator of prolactin signalling. Consistent with these results, alveologenesis and lactogenesis are severely disrupted in SnoN^–/– mice and mammary epithelial cells from these mice fail to undergo proper morphogenesis in vitro unless rescued by active Stat5 expression. Together, these results identify a new role for SnoN in the regulation of lactation.

Co-operative neuronal migration

During the development of the central nervous system, neurons and/or neuronal precursors travel along diverse routes from the ventricular zones of the developing brain and integrate into specific brain circuits. Neuronal migration has been extensively studied in the forebrain but little is known about this key developmental event in the embryonic midbrain (mesencephalon). On p. 3136, Kwang-Soo Kim, Anju Vasudevan and co-workers remedy this situation by studying the migration of dopaminergic (DA) and GABAergic (GABA) neurons in the mouse mesencephalon. They show that DA and GABA neurons follow similar paths to the ventral mesencephalon (VM) in a temporally sequential manner. Interestingly, they report that in Pitx3-deficient (aphakia) mice, which have a defective DA neuron architecture, DA neuron migration is abnormal, stalled DA progenitors fail to reach the VM and GABA neurons also fail to migrate to the VM. These results suggest that pre-existing DA neurons modulate the migration of GABA neurons, thereby providing new insights into neuronal migration and the establishment of brain connectivity during mesencephalon development.

Out on a limb: HoxD chromatin topology

Anterior-posterior patterning of both the primary embryonic axis and the secondary body axis (limbs and digits) in mammals requires regulated Hox expression. Polycomb-mediated changes in chromatin structure control Hox expression during the first patterning event but are they also involved in the second? Here (p. 3157), Robert Hill, Wendy Bickmore and colleagues analyse the chromatin topology of the HoxD gene cluster in immortalised cell lines derived from posterior and anterior regions of distal E10.5 mouse limbs and in dissected E10.5 limb buds. They report that there is a loss of polycomb-catalysed histone methylation and a chromatin decompaction over HoxD in the distal posterior, compared with the anterior, limb. Moreover, the global control region spatially localises with the 5′ HoxD genomic region specifically in the distal posterior limb, a result that is consistent with chromatin looping between this long-range enhancer and its target genes. Thus, the researchers conclude, the development of the mammalian secondary body axis involves anterior-posterior differences in chromatin compaction and looping.

Developmental roles for ribosomal biogenesis genes

Mutations in the human Shwachman-Bodian-Diamond syndrome (SBDS) gene, which functions during maturation of the large 60S ribosomal subunit, cause a disorder characterised by exocrine pancreatic insufficiency, chronic neutropenia and skeletal defects. Steven Leach and colleagues have now refined a zebrafish model of this ‘ribosomopathy’ (see p. 3232). Knockdown of the zebrafish sbds orthologue, they report, fully recapitulates the developmental abnormalities of the human syndrome but, interestingly, unlike in other ribosomopathies, loss of p53 does not rescue these developmental defects. The researchers show that impaired proliferation of pancreatic progenitor cells is the primary defect underlying the pancreatic phenotype and report that loss of sbds results in widespread changes in the expression of genes related to ribosome biogenesis, rRNA processing and translational initiation, including ribosomal protein L3 and pescadillo. Notably, inactivation of either of these genes also impairs expansion of pancreatic progenitor cells in a p53-independent manner. Together, these results suggest new p53-independent developmental roles for ribosomal biogenesis genes.

Mapping the mouse embryo

The sequence and location of every gene in the human genome is now known but our understanding of the relationships between human genotypes and phenotypes is in its infancy. To better understand the role of every gene in the development of an individual, the International Mouse Phenotyping Consortium aims to phenotype targeted gene knockout mice throughout the genome (∼23,000 genes). Because many of these mice will be embryonic lethal, methods for phenotyping mouse embryos are needed. Michael Wong and colleagues are developing such an approach and, on p. 3248, they present a new three-dimensional atlas of the mouse embryo. To produce their atlas, the researchers combined micro-computed tomography images of 35 E15.5 mouse embryos into an average image using automated image registration software, and then manually segmented 48 anatomical structures. This atlas establishes baseline anatomical phenotypic measurements against which mutant mouse phenotypes can be assessed; in the future, a mutant embryo image can be registered to the atlas and its organ volumes calculated automatically.

Plus…

Making waves: the rise and fall and rise of quantitative developmental biology

The tenth annual RIKEN Center for Developmental Biology symposium ‘Quantitative Developmental Biology’ held in March 2012 covered a range of topics. As reviewed by Davidson and Baum, the studies presented at the meeting shared a common theme in which a combination of physical theory, quantitative analysis and experiment was used to understand a specific cellular process in development. See the Meeting Review on p. 3065

A computational image analysis glossary for biologists

Meyerowitz and colleagues present a glossary of image analysis terms to aid biologists and  discuss the importance of robust image analysis in developmental studies.

See the Primer article on p. 3071

Developmental and evolutionary diversity of plant MADS-domain factors: insights from recent studies

Members of the MADS-box transcription factor family play essential roles in almost every developmental process in plants. Kaufmann and colleagues review recent findings on MADS-box gene functions in Arabidopsis and discuss the evolutionary history and functional diversification of this gene family in plants.

See the Review article on p. 3081

(1 votes)

Loading...