JCB

ASCB 2008: The meeting report

Today sees the online release of the JCB's official report of the ASCB annual meeting 2008 that took place last month in San Francisco. The print version will be in the January 26th issue of the journal. Of course, we covered the meeting at the time here on biowrites. But in the intervening month, we've been busy picking out our favorite talks, speaking to the people involved, and - new this year - compiling reports from symposium chairs on the highlights of their own particular sessions.

As a result, we've ended up with far more material than we could possibly fit in the journal. So while you can check out the official meeting report here, we've also published some extra stuff on the blog: some additional session reports from the moderators involved and some longer versions of articles that had to be trimmed for the journal. We also have a special ASCB edition of our biobytes podcast for your listening pleasure. You can find all our posts on ASCB 2008 from both last month and this, here.

biobytes: ASCB 2008 special edition

This special issue of biobytes brings you highlights of the 2008 annual meeting of the American Society for Cell Biology. We learn how bone marrow transplants might stall neurodegeneration (Craig Montell, Johns Hopkins University Medical School, Baltimore, MD). JCB News Editor, Ben Short, tells us about David Boettiger's (University of Pennsylvania, PA) work on the extracellular matrix and cell signaling. We hear how cancer cells find their way into the brain (Joan Massagué, Memorial Sloan-Kettering Cancer Center, New York, NY). And lastly, we learn that fly phagocytes get the midnight munchies for certain bugs (Mimi Shirasu-Hiza, Stanford University, CA) and that breast cancer cells can have very intimate living arrangements (Michael Overholtzer, Memorial Sloan-Kettering Cancer Center, New York, NY). The show was written, presented and produced by Ruth Williams.

Lipid Dynamics: A field of study that’s moving

Story contributed by Ken Jacobson (University of North Carolina, Chapel Hill)  and Ivan R. Nabi (University of British Colombia).

This Minisymposium focused on membrane domains and included discussions on caveolar and non-caveolar domains, invadopodia, lectins in dendritic cells, CD36 diffusion, and nanoscopic raft domains. 

• Ken Jacobson (University of North Carolina, Chapel Hill) introduced the session by describing the challenges of elucidating structure-function relationships in domains of varying protein-lipid composition, stressing the importance of lipid protein interactions.
• Ivan Nabi (University of British Colombia) demonstrated that non-caveolar caveolin-1 domains functionally regulate raft-dependent endocytosis of the ganglioside GM1, and also presented proteomics data defining the differential protein composition of caveolar and non-caveolar raft domains.
• Giuisi Caldieri’s (Consorzio Mario Negri Sud, Santa Maria Imbaro, Italy) talk addressed invadopodia, cholesterol-rich domains whose formation and ability to degrade the extracellular matrix depends on caveolin-1 regulation of cholesterol homeostasis in the plasma membrane. 
• Raman Deep Singh (Mayo Clinic, Rochester, MN) described how sialic acid residues of cell surface gangliosides support the structural integrity of caveolae and maintain caveolar endocytosis.
• Aaron Neumann (University of North Carolina, Chapel Hill) discussed properties of DC-SIGN, CD206 and dectin, transmembrane lectins that can be mulitiplexed within the same pathogen recognition domains in dendritic cells. These domains lead to the appearance of a novel protrusive structure, called a fungipod, when yeast particles are phagocytosed.
• Khuloud Jaqaman (The Scripps Research Institute, La Jolla, CA) presented single particle tracking studies of the CD36 receptor in macrophages (Jaqaman, K. et al., 2008). Accomplished within a field that contains many particles, analysis of CD36 movement demonstrated an unexpected, linearly constrained diffusion of this receptor. Channeled by the actin and microtubule cytoskeletons, movement of CD36 facilitates receptor oligomerization and enhances requisite downstream signaling upon ligand binding.
• Christian Eggling (Max-Planck Institute for Biophysical Chemistry, Göttingen, Germany) elegantly demonstrated that sphingolipids and GPI-anchored proteins, but not phospholipids, are selectively trapped in cholesterol dependent nanodomains for around 10 ms using STED microscopy (Eggeling et al., 2008). These ‘raft’ domains are less than 30 nm in dimension—consistent with the concept that the elementary lipid raft is a dynamic nanoscale domain.

Bridging Engineering and Life Sciences: “Cool” next generation tools for cell biology

Contributed by Jean Schwarzbauer (Princeton University, Princeton, NJ)

Microdevices, micropatterns, particle tracking, cantilevers, and spinning discs are just some of the technologies with potential to lead to novel diagnostic techniques through basic cell biological applications.  This Special Interest Subgroup hosted by the National Cancer Institute brought together biologists, physicists, chemists, and engineers to showcase multidisciplinary approaches for studying and controlling complex cellular processes.

“Micro” technologies are providing cool new tools to examine cell activities such as cell adhesion and migration.  In one approach, cell-adhesive proteins in linear patterns generated by laser ablation of non-adhesive materials were shown to guide cell migration in one-dimension.  High-resolution microscopic analyses of cells migrating along these lines are now providing new information about cell shapes, membrane projections, and intracellular distributions of cellular organelles during cell movement.  A second strategy, microetched migration channels with hooks, provides a unique substrate to separate motile cells by geometry.  Cell types that extend long thin protrusions at the leading edge are able to grab onto hook tips bent in the direction of migration whereas cells with wide lamelli migrate toward hook tips allowing small numbers of cells to be sorted by their migratory behaviors.

How micro technologies can extend into the diagnostic realm was well illustrated with the integrated blood barcode chip.  This unique protein detection system is built by decorating single-stranded DNA barcode arrays with DNA-tagged antibodies.  This array is then assembled into a microfluidic device to generate an antibody barcode chip with the ability to capture target proteins from solutions flowing by.  As proof of principle, small amounts of proteins in blood taken from a finger prick were identified and measured showing the chip’s capacity to analyze complex samples (Fan, R. et al., 2008).

These highlights cover only a smattering of the techniques and interdisciplinary tools discussed in this subgroup.  However, they illustrate how innovative applications of emerging technologies are providing new insights into biological problems and new potential for translation to the clinic. 

Cellular Response to Infectious Agents: The "ins" and "outs" of pathogen invasion

New imaging technologies have aided virus particle trafficking studies over the past decade (Campbell, E.M. et al. (2008) J. Cell Biol. 180:549)

Contributed by Gisou van der Goot (Polytechnique Fédérale de Lausanne, Switzerland)

Participants in this Minisymposium reported novel aspects of host-pathogen interactions, from crossing barriers, to infection and viral spreading, and the host response to pathogen invasion.

Two talks illustrated how pathogens breech barriers.  Thomas Hope (Northwestern University, Chicago, IL) presented studies using a fluorescently labeled HIV that revealed it can penetrate the epithelial barriers of the female genital tract to a depth where the virus could interact with and potentially infect target cells of the immune system.  These results suggest that normal weaknesses in the barrier caused by cell turnover allow the virus to enter the intact tissue and show that the epithelium is not as robust a barrier as generally thought. Using the gerbil and a new knock-in mouse line, Marc Lecuit (Institut Pasteur, Paris, France) showed that two well-characterized species-specific invasion proteins of Listeria monocytogenes, InlA and InlB, act in a conjugated manner to allow the bacteria to cross the placenta, providing the first molecular mechanism to explain how a pathogen can cross this barrier (Disson, O., et al., 2008).

The next two speakers, Jing Jin from Walther Mothes’ laboratory (Yale University, New Haven, CT) and Taro Ohkawa from Matthew Welch's lab (University of California, Berkeley), discussed virus infection and dispersal.  Jin addressed the mechanism by which cell-cell contact enhances retroviral spreading. Applying 4D imaging to visualize viral release from living cells, she demonstrated that viral budding is polarized towards sites of cell-cell contact, allowing viruses to exit one host cell headed straight for their nearest neighbor. Ohkawa demonstrated that baculoviruses harness actin polymerization machinery to drive virus transport to the nucleus and back to the cellular periphery, whereas many other viruses are transported within the cell cytoplasm using the microtubule cytoskeleton.  They hypothesize that actin-mediated transport to the nucleus speeds virus replication, whereas transport to the periphery, bypassing slower microtubule-based motors, enables rapid repackaging and transmission of virus to other cells.

In the last two presentations, cellular responses to pathogens were also addressed. Gisou van der Goot (Polytechnique Fédérale de Lausanne, Switzerland) revealed the multitude of signaling pathways that are activated by bacterial pore forming toxins upon induction of membrane damage, which include inflammasome mediated activation of lipid metabolic pathways, transient arrest in protein synthesis and MAPkinase activation and recovery of ion homeostasis. Finally, Craig Roy (Yale University, New Haven, CT) found that the obligate intracellular bacterium Coxiella burnetii inhibits host cell apoptosis by translocating the effector protein AnkG using its type IV secretion system. Remarkably, he found that AnkG inhibits apoptosis by a novel mechanism that involves binding to a host protein called p32, which interferes with an alternative splicing reaction required for production of the pro-apoptotic Bcl-xS protein.

Cell Polarity and Epithelial Morphogenesis: Approaches from multiple directions

Contributed by Ian Macara (University of Virginia, Charlottesville)

 

Crumbs (blue) localize to the apical domain of epithelial cells. 

It is hard to find any biological process that is not linked in some way to cell polarity, and defects in polarization play key roles in many developmental and infectious diseases, and in cancer.  This Minisymposium, co-chaired by Elisabeth Knust and Ian Macara, highlighted the extraordinary range of processes in which cell polarity is manifested.  Model organisms from nematodes to mouse mammary glands and human cancer cells were represented. 

Two speakers discussed specialized types of polarized cell migration, and screens to identify genes involved in these processes.  Joshua Ziel from the Sherwood laboratory (Duke University, Durham, NC) discussed a powerful in vivo model for studying invasion of cells through basement membranes (Ziel, J. et al., 2008).  During vulval development in C. elegans, the anchor cell penetrates the basement membrane so as to contact underlying vulval epithelial cells.  Unexpectedly, a factor called netrin, which has been implicated in axon guidance, promotes invasion by polarizing the netrin receptor to the basal side of the anchor cell.  The receptor activates the Rac GTPase, which nucleates actin polymerization to form a specialized cortical domain, from which proteases are secreted that degrade the adjacent basement membrane.  This mechanism highlights an unexpected function for netrin that may be conserved through evolution. 

An interesting talk by Todd Nystul from the Spradling laboratory (Carnegie Institute, Troy, MI) concerned a different type of polarized cell migration, which governs the maintenance of follicle stem cells within the Drosophila germarium at either side of each ovariole.  Strikingly, a stem cell lost on one side of the ovariole can be replaced by a stem cell daughter, produced on the other side.  The replacement cell migrates between the two niches in a process regulated by Notch signaling.  A genetic screen for mutations that perturb this replacement identified a cell adhesion molecule, CRELD1, as being an important regulator of this process.

Loss of cell polarity is a key event in cancer progression, and Patrick Humbert (Peter MacCallum Cancer Centre, Melbourne, Australia) discussed the role of the Scribble polarity protein as a tumor suppressor in mammary epithelial cells.  Over-expression of Scribble can suppress transformation by oncogenic Ras, and an RNAi screen for genes involved in this suppression revealed a variety of other polarity proteins and signaling components that may function downstream of Scribble.

Epithelial cells polarize in an apical/basal direction, but in tissues can also polarize within the plane of the epithelial sheet – a process called planar cell polarity (PCP).  In mammals the PCP pathway controls many steps in development including cell movements during gastrulation and the organization of hair cells in the inner ear.  A talk byPadmashree Rida from the Chen laboratory (Emory University, Atlanta, GA) described a novel protein, TBC1d19, which interacts with the PCP protein Vangl2 and plays an important role in both of these processes.  TBC1d19 may provide the missing link believed to couple the PCP pathway to microtubules and cilia.

Two other talks covered apical/basal polarity mechanisms.  Eli Knust (Max-Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany) discussed the role of Crumbs in photoreceptor development in flies (Bulgakova, N.A. et al., 2008).  Crumbs is a transmembrane protein that forms a complex at the apical junction of epithelial cells with the polarity proteins Stardust and Patj.  Defects in these genes result in light-induced retinal degeneration.  Luke McCaffrey, in Ian Macara’s laboratory (University of Virginia, Charlottesville), described a new model for studying gene function, in which murine mammary stem cells are transduced with lentivirus to knockdown gene expression, then transplanted back into a host mouse to permit mammary gland regeneration.  Silencing of Par3 expression in this system blocks normal progenitor cell differentiation and duct formation.

Overall, the minisymposium provided a fascinating overview of the wide-ranging functions of cell polarization in animal development.  The take home message was that there is still much to learn about the signaling pathways responsible for directed migration, invasion, planar or apical/basal polarity, and cell fate determination. 

A crash course in Wikipedia for cell biologists

  Contributed by Aimee deCathelineau (JCB).

For the first time, this year ASCB offered a workshop on creating and editing articles on Wikipedia for cell biologists. 

“Contributions from experts are desperately needed to improve the quality of cell and molecular biology articles on Wikipedia and to ensure the information is accurate, correctly cited, and well-presented”, says Tim Vickers (Washington University, St. Louis, MO).  Vickers heads the Molecular and Cell Biology (MCB) WikiProject, a domain in Wikipedia that coordinates article coverage for a given subject area.  At the invitation of David L. Ennist, Director of Digital Resources for ASCB, Vickers hosted the workshop together with William Wedemeyer (Michigan State University, East Lansing, MI).  The workshop provided an overview of the Wikipedia site and had several Wikipedians on-hand to assist attendees with creating a Wiki account.  Participants then learned how to edit existing articles, and were given guidelines for the desired structure for Wiki articles when creating new ones. 

Currently, scientific articles such as the “immune system” draw nearly 2600 viewers a day (one million hits per year). Like this article, many articles on cell biology-related topics have achieved the Wikipedia “gold standard”, or “feature article” status.  However, literally thousands of other articles haven’t been so lucky.  There are more than 2 million entries in MCB-related fields, but the majority of these have been abandoned as “stubs” - meaning the site was initiated but contains minimal amounts of information.  For example, a Wikipedia article for every enzyme with an EC number has been generated, but most of these articles are underdeveloped and not annotated, and so are not helpful to the average Wikipedia user. 

The MCB WikiProject, which currently has more than 200 members, aims to increase the quality of scientific articles on MCB related topics.  The MCB portal highlights selected articles and images, biographies, and news.  The site also lists articles that need expansion, clean-up, or peer-review.  The group has created a prioritized list of articles in need of expert attention, such as “cell division” and “B-cell receptor”. In addition, the MCB WikiProject selects a “collaboration of the month”, which encourages authors to work together to improve an article to “feature article status”. 

Several groups have sought advice and worked together with the MCB WikiProject to create new Wikipedia sites.  Andrew Su and colleagues (The Novartis Institute for Genome Research, San Diego, CA) created software that automatically drops a ‘skeleton’ for each gene identified through the human genome project onto Wikipedia (Huss, J.W. III, et al., 2008).  Jennifer Daub, who works on the Rfam database run by Alex Bateman (UK Wellcome Trust Sanger Institute, Cambridgeshire, England), also contacted MCB wikipedians for guidance to establish similar sites for non-coding RNAs.  This collaboration, like the genome project started by Su, seeks to provide an open-access and centralized information source for the scientific community.  In turn, a new journal, RNA Biology, is collaborating with the Rfam consortium, and will require authors to generate a Wiki article when a new family of non-coding RNAs is identified (Butler, D, 2008). In both cases, the ongoing and active participation of experts will be important for site development and maintenance. 

With these initiatives already in progress, it is easy to imagine how Wikipedia may change some aspects of scientific communication in the future.  Wedemeyer notes that participation in the MCB WikiProject is a great way to network and may lead to new professional contacts as authors ask for and receive advice from their colleagues.  

As an open access source of information, Wikipedia provides immense potential for outreach by the scientific community.  Google searches for many scientific topics often result in Wikipedia as the first-listed site.  The Wikipedia audience is truly global, and includes not only your family, friends, and neighbors, but policy makers, granting agencies, voters, fellow scientists, and students.  Getting involved with Wikipedia or the MCB WikiProject is an excellent way to draw attention to your field of study, improve your writing and presentation skills, and collaborate with other scientists in order to contribute to the dissemination of accurate scientific information, and provide a valuable and lasting electronic resource for the general public.

If you are interested in becoming a Wikipedian, connect to the Wikipedia editing tutorial, and get started (once you are logged in with a user name- you can contact the MCB WikiProject for help)!  Wedemeyer has also posted video tutorials on YouTube.

Mitosis and Meiosis: Dividing cells are a win-win combination

 Story contributed by  Alexey Khodjakov (Wadsworth Institute, Albany, NY).

 

Spindly regulates kinetochore (green) attachment to microtubules (red) during mitosis in C. elegans (A. Desai).

This year’s ‘Mitosis and Meiosis’ session was especially memorable. Two of the speakers were recipients of major ASCB awards. Arshad Desai of the Ludwig Institute for Cancer Research and University of California at San Diego received the prestigious “Early Career Life Scientist Award”. Ekaterina (Katya) Grishchuk (University of Colorado, Boulder) was the leading author on the Molecular Biology of the Cell “Paper of the Year” (Grischuk, E.L., et al., 2007). 

Desai summarized work in the C. elegans embryo that led to the identification of the core microtubule-binding machinery of the kinetochore and described recent efforts that revealed a new mechanism regulating this machinery, which emerged from analysis of the conserved coiled-coil protein SPDL-1/Spindly. This protein, identified in RNAi screens for chromosome segregation defects, is required to recruit the dynein/dynactin motor complex to kinetochores and appears to mediate lateral interactions between unattached kinetochores and microtubules.

The importance of this type of kinetochore-microtubule interaction for chromosome positioning is becoming a hot topic in the field. In fact, this subject was also covered in another talk presented by Sadie Wignall (Stanford University) who demonstrated that chromosomes can properly align at the spindle equator in the absence of classic ‘end-on’ kinetochore attachments during meiosis in C. elegans oocytes (McIntosh, R. et al., 2008). In this system, Klp19-mediated sliding of kinetochores alongside microtubule bundles appears to be sufficient for chromosome congression.

In contrast, end-on attachments appear to be essential during anaphase, and a fascinating study presented by Katya Grishchuk revealed new details of the mechanism responsible for coupling of microtubule dynamics and chromosome movement. Based on a series of biophysical experiments, structural reconstructions, and computer simulations Grishchuk demonstrated that microtubule depolymerization produces a strong force that is transmitted to the chromosome through kinetochore protein complexes (Grischuk, E.L. et al. 2008). Intriguingly, transmission of force is several times more efficient if the kinetochore is attached via ring-like complexes (such as Dam1 in budding yeast) than if the coupler binds only one side of the microtubule (as in the case of the Ndc80 coupler in higher eukaryotes). This offers an explanation for why budding yeast, where individual kinetochores are attached to just one microtubule, utilize the ring-attachment.

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.