JCB biowrites

New Issue: Dec 29th

Hope all of you have enjoyed the holidays and managed to get a break from the lab for a few days at least. No break from the JCB though, as we publish our latest issue today. The full table of contents is here, but I've picked out a few selected highlights...

Our festive-looking cover is taken from the paper by Sugimura et al., which shows that the DNA repair protein PARP-1 helps slow down DNA replication forks at sites of DNA damage. As explained in this summary, PARP-1 does this by allowing access to the proteins that repair DNA double-stranded breaks by the process of homologous recombination. The initiation of this pathway delays progression of the replication fork until the DNA is repaired.

Two papers in this issue look at the microtubule plus-end binding protein CLIP-170.Thomas Surrey's group uses an in vitro reconstitution system to study how CLIP-170 and another plus-end binding protein, EB1, dynamically track the growing end of a microtubule. They show that, while EB1 can independently recognize the growing end of a microtubule, CLIP-170 depends on binding to both EB1 and tubulin. Torsten Wittmann discusses the implications of these results in a commentary piece. Meanwhile, Lewkowicz et al. look at the function of CLIP-170 during phagocytosis in macrophages. They find that CLIP-170 is essential for the process and that it regulates actin polymerization by directly recruiting the actin-nucleating protein mDia1.

Away from the cytoskeleton, Gerard Karsenty and colleagues dissect a complicated pathway by which the hormone leptin inhibits the release of insulin from the pancreas. In addition to acting directly on insulin secretion, it seems that leptin also signals via the sympathetic nervous system to stimulate expression of a gene called Esp in bone cells. Esp inhibits the activity of another protein produced by bone cells -osteocalcin - that would usually stimulate pancreatic beta cells to produce insulin. This roundabout route to suppression of insulin is nicely summarized by Mitch here.

Mitch also has a summary of a paper from Sidney Strickland's lab, that shows how degradation of the extracellular matrix can lead to brain damage. It was known that degradation of the ECM protein laminin contributed to neuronal death by overexcitation. But, surprisingly, the group found that mice lacking laminin were actually MORE resistant to brain damage than wild type mice. It turns out that rather than the loss of laminin, it's the proteolytic fragments of the ECM protein that contribute to overexcitation by causing a neuronal receptor called KA1 to be upregulated. Overstimulation of this receptor is likely to be the main cause of cell death.

Finally, I'll just point you in the direction of a great mini-review by Mattias Belting and Anders Wittrup on how nucleic acids are transferred between cells. It's a really quick read and a great introduction to a relatively new field that you may not have read much about. It explains how nucleic acids are transferred between cells through structures such as exosomes, tunneling nanotubes, and apoptotic bodies. These all have implications in both development and diseases such as cancer. Highly recommended!

Plenty more stuff in the issue as well, so take a look. And, of course, have a happy - and successful - New Year!

New biosights: Dictyostelium lay a trail

Didn't have time to mention this before now, but there's a new episode of biosights available. This time, Ruth Williams and Justin Paul look at how Dictyostelium cells migrate in an orderly head-to-tail arrangement: they leave a trail of vesicles (thought to contain chemoattractant) for their fellow cells to follow. There's some really amazing videos of the Dictyostelium cells migrating and leaving this 'bread-crumb' trail behind them. If you haven't read the original paper by Kriebel et al., you should really watch the video and let senior author Carole Parent explain all...

ASCB 2008: Wednesday

It might have been the last day of ASCB 2008, but there was still a busy schedule in store. I managed to catch some of the morning symposium on “Gene Regulation and Non-coding RNAs”. For me, the coolest talk in the session was from Gisela Storz (NICHD, Bethesda) on a subject I hadn’t really heard much about before: small, non-coding RNAs in bacteria. Regulatory RNAs were first identified in bacteria long before their presence in eukaryotes was appreciated. Techniques such as microarrays have now detected around 80 small RNAs in E. coli, which represents about 2% of the genome.

These RNAs can be put into several different categories. The most analogous to eukaryotic siRNAs are the type encoded in trans that have limited complementarity to their targets. These small RNAs can promote degradation, block translation, or activate translation of their bacterial target mRNAs to regulate such diverse processes as sugar metabolism and outer membrane composition. A second category is encoded in cis within their target in an antisense orientation. Storz showed an example of this type where a small antisense RNA promoted the cleavage of a long mRNA containing multiple genes, which probably alters the stability of the cleavage products. A third type of small RNAs mimic the structure of another nucleic acids – one RNA folds to look like an open DNA promoter, and therefore titrates out RNA polymerase from the real promoters! Finally, Storz pointed out that, as in eukaryotes, some ‘non-coding’ RNAs may turn out to encode small polypeptides after all…

Most of this stuff was new to me and I found it fascinating!

For the final session of ASCB 2008, I headed over to see the minisymposium on “Membrane Heterogeneity and Trafficking”, co-chaired by Jennifer Stow (U. of Queensland, Australia) and Karin Reinisch (Yale).

ASCB 2008: Tuesday

As I may have mentioned before, ASCB is big...really big. But, happily, I've still managed to bump into a few old friends, some of whom I haven't seen for years. On the down side, I haven't had too long to stop and chat,as there's been so much stuff to go and see. Tuesday promised to be the busiest day yet.

Things started off this morning with the symposium on 'Cytoskeletal Dynamics' - a slightly nebulous title that was reflected in the breadth of topics covered. Toshio Yanagida (Osaka U., Japan) began things with a talk on studying actin and myosin using single molecule nanotechnology. Myosin walks along actin filaments in a processive, 'hand-over-hand' fashion. It seems that the myosin head domain moves along the actin by brownian motion, where the direction of movement is biased to the forwards direction by intramolecular tension. The implication of this is that complex biological systems can economize their energy usage by making us of brownian motion. Yanagida then described how this has led to a collaboration aimed at building more sophisticated robots (!?!) and showed a video of a quite life-like robot interacting with humans...definitely one of the strangest digressions I've ever seen in a cell biology talk!

Back to the cytoskeleton... Claire Walczak (Indiana U., Bloomington) looks at mitotic spindle assembly and how chromosomes congress to align at the metaphase plate. RNAi knockdown of a protein called Nuf2 - a component of the Ndc80 complex that attaches spindle microtubules to kinetochores - results in the failure of chromosomes to align during metaphase. Surprisingly, normal alignment is restored by the simultaneous knockdown of a kinesin motor called HSET (which usually crosslinks and slides spindle microtubules across one another). In the double RNAi, microtubules associate with kinetochores laterally rather than end-on, and no tension is generated between the kinetochores on sister chromatids. It's already been shown that chromosomes only attached to one spindle pole can align at the metaphase plate in a process requiring the plus-end directed microtubule motor CENP-E. This same motor also seems to be required for the chromosome alignment in Nuf2/HSET double knockdown cells. It seems that chromosomes have more than one way to move around the cell during mitosis.

CellSlam 2008

Fresh from receiving the E.B. Wilson medal, Nobel laureates Martin Chalfie and Roger Tsien received an even bigger honor: places on the judging panel for CellSlam 2008, the ASCBs competition for scientists willing to make fools of themselves mix education with entertainment.

Compered by the brilliant Randy Hampton (UCSD), the competition featured 5 biologists presenting their work through the media of comedy, song, or dance. Alun Hughes (U. of Aberdeen, UK) gave a dark and gothic monologue on his work on bone morphogenesis while Jennifer Shieh (Stanford), with a little audience participation, presented the "Three Dances of Neuronal Migration".

Yu Li (Cell Signalling Technology) got third place for his really funny talk on how to prevent prostate cancer (Hint), while Geoff Hunt (Princeton) rapped about his life as a PhD student.

First place, however, deservedly went to Stanley Cohn (DePaul U.) for his hilarious, charming, yet strangely informative 'G-Protein Samba'.All in all, CellSlam was a great way to end a long day of serious science talks. Congratulations to everyone who got involved...

Celldance 2008

Tuesday saw the awards ceremony for Celldance 2008 - the ASCB cell image and movie contest. There were 3 categories of awards with first prizes of $500 in each! Alexander Bird (Max-Planck Institute, Dresden) won the still images category with his images of U2OS cells in metaphase and anaphase. The public outreach video award went to Rachid Sougrat (NIHCD, Bethesda) for his animation of ER to Golgi transport, using images constructed from electron tomography studies. First prize in the science video section went to Janet Iwasa (Harvard Medical School), for her animation of clathrin mediated endocytosis, set to the music of 'Flight of the Bumblebee', with adapter proteins and dynamin buzzing around constructing the vesicle. You can see all of the winners here, including my personal favorite, a reenactment of mitosis by synchronized swimmers...

New biobytes podcast available

Image: Narendra et al.

Ruth Williams and Justin Paul provide our monthly installment of biobytes, featuring interviews with the scientists behind recent papers in the JCB and the JEM. Ruth speaks with Eline Luning Prak from the University of Pennsylvania about antibody gene editing and autoimmunity (Panigrahi et al., JEM), and Richard Youle (NIH, Bethesda) tells us how a protein associated with Parkinson's disease prompts the destruction of damaged mitochondria (Narenda et al., JCB). Meanwhile, Justin talks to Christina Mitchell and Megan McGrath from Monash University in Melbourne, Australia, who explain how a protein called FHL1 makes muscle cells mighty (Cowling et al., JCB). You can subscribe to biobytes on iTunes here.

DataViewer: The Movie

Steve Jobs eat your heart out - this short movie shows off our new DataViewer and all it can do. It's been running all week at the JCB booth here at ASCB and - if you'll allow us to blow our own trumpet for a moment - the response has been fantastic. People are really excited by the new opportunities the DataViewer offers to the presentation of your own work and the understanding of others'. Still not sure exactly what the DataViewer is? Just watch the movie above and it should all be clear...You can watch a higher quality version here.

ASCB 2008: Monday

"What do you think integrins talk to?"

With this question - addressed to those who don't consider the extracellular matrix (ECM) important - Mina Bissell (Lawrence Berkeley National Laboratory) opened the minisymposium on "Signaling from the extracellular matrix". She followed this with a talk on the role of ECM in determining the state of metastatic breast cancer cells, touching on many aspects of her work over the last several years. She illustrated in many ways her idea that 'phenotype is dominant over genotype', malignant cells can be reverted to a more normal phenotype by many different treatments. Changes in the ECM can also induce tumors and increase genomic instability. Bissell now showed that the matrix metalloproteinase MMP9 is upregulated in malignant cells, that its activation messes up the organization of non-malignant cells and that its knockdown by RNAi can revert malignant cells back to normal. She ended her talk with a challenge: that we currently no nothing about 'the language and alphabet of form'.

The following talks attempted to add some letters to this alphabet. Bill Frazier (Washington U., St. Louis) described how the ECM ligand thrombospondin-1 (TSP-1) and it's receptor CD47 inhibit nitric oxide signaling. The NO signaling pathway promotes mitochondrial biogenesis, and Frazier showed that CD47 knockout mice have increased numbers of mitochondria in their skeletal muscle and therefore have enhanced endurance. The KO tissue is also healthier, as the mitochondria produce less superoxides.

Lilly Bourguignon (UCSF) looked at another ECM ligand, hyaluronan (HA, the major glycosaminoglycan in most tissues) and its cognate plasma membrane receptor, CD44. Bourguignon showed that in the epithelial cell line MCF-7, HA binding to CD44 induces the ES cell transcription factor NANOG to translocate to the nucleus where it activates its target genes. Strangely, HA also promotes an interaction between CD44 and NANOG. When questioned on this, Bourguignon said that NANOG bound to CD44, was phosphorylated, and then translocated to the nucleus, but didn't give any more details. Binding of HA to CD44 has other effects as well: it stimulates expression of the multiple drug resistance gene, MDR1, and also promotes the formation of a complex of the MDR1 protein with CD44 and the cytoskeletal anchor protein ankyrin. Cell lines stimulated with HA therefore have increased drug resistance. Frankly, this was all rather confusing, but since NANOG is overexpressed in many breast cancers, HA-CD44 signaling may be critical to both tumor progression and drug resistance.

ECM signaling isn't just a matter of a ligand binding to its receptor however: Joachim Spatz (U. of Heidelberg, Germany) gave a nice talk on how the spatial arrangement of the ligand provides information to the cell as well. His group uses nanolithography to array RGD peptides (which bind integrins) on a surface in defined patterns and with a defined distance from one another. It was quite amazing to see how differently fibroblasts behave depending on the arrangement of the RGD peptides and therefore the arrangement of their integrins: fibroblasts on RGD peptides 58 nm apart were fairly immobile and proliferative. Increasing the distance by just 15 nm to 73 nm made the fibroblasts highly motile and susceptible to apoptosis. If the peptides were closer together, the cells could more easily cluster their integrins and generate cell adhesive force. Fibroblasts can even sense a 1 nm difference in the spacing of the RGD peptides and preferentially move towards the smaller spacing, so the arrangement of the ECM has the potential to induce cell migration.

New Issue: Dec 15th

We have a new issue out today. You can find the full table of contents here, but these are a few highlights…

A paper from Margaret Gardel, Clare Waterman and colleagues (our cover story, no less) looks at the relationship between the speed of F-actin flow and the traction forces of a migrating cell. It turns out that the relationship is biphasic: at the cell’s leading edge, slower flow means higher traction, while further back slower flow means lower traction. Simultaneously measuring both traction forces and actin speeds is an amazing technical achievement so if, like me, you find words such as ‘traction’, ‘stress’, and ‘retrograde flow’ a little bit scary, I highly recommend Ruth’s summary of the paper.

Hot on the heels of last month's paper on ankyrinG and neuronal polarity comes an article from Bénédicte Dargent’s lab, showing that the protein kinase CK2 promotes the interaction of ankyrinG with sodium channels. By phosphorylating the channels, CK2 ensures that they are correctly organized within the axon at the initial segment and nodes of Ranvier.  Matthew Rasband has written a comment piece for us, and our summary of the paper is here.

Sticking with neurons, Dominique Muller’s group has an article looking at the roles of PSD-95 and nitric oxide signaling in synaptogenesis. It seems that PSD-95 recruits Nitric Oxide Synthase to the post-synapse, where the production of NO stimulates the formation of contacts with pre-synapses. For a few more details, click here.

Another form of cell-cell contacts are adherens junctions, and a paper from Kathryn Harris and Ulrich Tepass looks at how these junctions are regulated during Drosophila neuroblast formation. The polarity protein Cdc42 acts through the Par complex to regulate endocytosis and junction stability: loss of Cdc42 results in an increase in apical endocytosis and a loss of junctions. Mark Peifer, along with Mara Duncan, puts this into context for us with an excellent commentary piece.

Finally for today, I’ll also point you in the direction of a paper on the regulation of skeletal muscle mass from Christina Mitchell’s lab (a slightly longer summary here). The group found that transgenically expressing a protein called FHL1 produces mice with bigger and stronger muscles. It seems to do this by regulating the transcription factor NFATc1. What’s more, FHL1 is mutated in several human myopathies and may cause the disease by blocking NFATc1 signaling.

Lots of other interesting papers in the issue that unfortunately I haven’t got time to mention, so go take a look…