Other recent F1000 evaluations

I have not recently updated my blog to include my F1000 evaluations; I now include these missing evaluations here for the benefit of those who do not subscribe to F1000. All of the following were first published on F1000 Prime in the last 12 months.

The GTPase IFT27 is involved in both anterograde and retrograde intraflagellar transport.

Huet D, Blisnick T, Perrot S, Bastin P. elife 2014; 3:e02419 PMID: 24843028 DOI: 10.7554/eLife.02419.001

This fascinating paper exploits Trypanosomes as a model system to define a role for the intraflagellar transport (IFT) protein IFT27 in flagellar function. IFT27 is a known component of the IFT-B particle mediating transport from the flagellar base to tip (anterograde IFT); here, the authors show that the GTPase function of IFT27 is also required to load the retrograde IFT particle (IFT-A) and its associated motor (dynein-2) into cilia. As such, this work defines IFT27 as a critical control point not only for anterograde but also for retrograde IFT. A key point is that IFT27 is a small Rab-like GTPase, and the authors convincingly demonstrate a role for this enzyme activity in the transport process. In some ways this provides further analogy between IFT-mediated transport and canonical membrane trafficking steps in which Rab proteins have critical roles in controlling timing and directionality.

 

Proteins of the Ciliary Axoneme Are Found on Cytoplasmic Membrane Vesicles during Growth of Cilia.

Wood CR, Rosenbaum JL. Curr Biol 2014 May 19; 24(10):1114-20 PMID: 24814148 DOI: 10.1016/j.cub.2014.03.047

This paper provides good evidence that structural proteins of the ciliary axoneme are transported into cilia on vesicular structures. Using Chlamydomonas as a model system, the data show that axonemal components and intraflagellar transport (IFT) particle proteins are delivered to the base of cilia on the surface of vesicles. These then associate with transitional fibres at the point of contact with the cell membrane. The process is particularly evident during cilia formation when a burst of synthesis of the ciliary components must be matched by an upregulation of their delivery. The work suggests an important and ongoing association of axonemal proteins with membranes. This and other work also support the maintained association of IFT proteins with membranes during transport within the cilium. This is therefore a significant paper in that it provides an integrated model for the transport of both membrane and axonemal proteins into cilia.

 

SNARE and regulatory proteins induce local membrane protrusions to prime docked vesicles for fast calcium-triggered fusion.

Bharat TA, Malsam J, Hagen WJ, Scheutzow A, Söllner TH, Briggs JA. EMBO Rep 2014 Mar 1; 15(3):308-14 PMID: 24493260 DOI: 10.1002/embr.201337807

The paper provides strong supporting evidence in favour of a membrane deformation event early in soluble N-ethylmaleimide-sensitive factor attachment protein receptor (SNARE)-dependent fusion. I concur entirely with what has already been said by Liangyi Chen and Junmei Fan and especially by Robert Burgoyne in his evaluation. Providing a mechanistic basis for some early electron microscopy (EM) is a lovely way to close the loop.

 

An Unconventional Secretory Pathway Mediates the Cilia Targeting of Peripherin/rds.

Tian G, Ropelewski P, Nemet I, Lee R, Lodowski KH, Imanishi Y. J Neurosci 2014 Jan 15; 34(3):992-1006 PMID: 24431457 DOI: 10.1523/JNEUROSCI.3437-13.2014

This paper provides some further evidence for the somewhat controversial idea of a non-conventional secretion pathway operating from the early secretory pathway to the cilium. Evidence on this originally came from the Witzgall lab looking at the trafficking of polycystin-2 {1}. Here, the authors use cell culture models and Xenopus to show that Peripherin-2/rds seems to be trafficked in a similar manner. Key evidence for this comes from glycosylation assays monitoring sensitivity to endoglycosidase H (EndoH). Canonical trafficking of glycoproteins results in an acquisition of EndoH resistance as a result of sugar chain modification in the Golgi. While there is some potential for slightly different interpretations, the data are broadly consistent with the idea of a non-canonical pathway operating in the delivery of cargo to the cilium.

References

Polycystin-2 takes different routes to the somatic and ciliary plasma membrane.

Hoffmeister H, Babinger K, Gürster S, Cedzich A, Meese C, Schadendorf K, Osten L, de Vries U, Rascle A, Witzgall R. J Cell Biol 2011 Feb 21; 192(4):631-45 PMID: 21321097 DOI: 10.1083/jcb.201007050

 

A Regulator of Secretory Vesicle Size, Kelch-Like Protein 12, Facilitates the Secretion of Apolipoprotein B100 and Very-Low-Density Lipoproteins.

Butkinaree C, Guo L, Ramkhelawon B, Wanschel A, Brodsky JL, Moore KJ, Fisher EA. Arterioscler Thromb Vasc Biol 2013 PMID: 24334870 DOI: 10.1161/ATVBAHA.113.302728

This article is important in that it extends our understanding of the molecular mechanisms governing the formation of large COPII vesicles at the endoplasmic reticulum (ER). Previously, the Rape lab has shown that the ubiquitin conjugation cofactor Klhl12 is required for the COPII-dependent formation of procollagen containing carriers {1}, likely through ubiquitylation of the outer layer COPII subunit Sec31. Here, Fisher and colleagues show that another atypically large cargo, apolipoprotein particles, also require Klhl12. While the paper does not fully explore the similarities or potential differences in mechanisms, the data do support a role for Klhl12 more generally in the export of unusually large cargo from the ER.

References

Ubiquitin-dependent regulation of COPII coat size and function.

Jin L, Pahuja KB, Wickliffe KE, Gorur A, Baumgärtel C, Schekman R, Rape M. Nature 2012 Feb 23; 482(7386):495-500 PMID: 22358839 DOI: 10.1038/nature10822

 

Microtubules that form the stationary lattice of muscle fibers are dynamic and nucleated at Golgi elements.

Oddoux S, Zaal KJ, Tate V, Kenea A, Nandkeolyar SA, Reid E, Liu W, Ralston E. J Cell Biol 2013 Oct 28; 203(2):205-13 PMID: 24145165 DOI: 10.1083/jcb.201304063

This article shows that static Golgi elements in flexor digitorum brevis (FDB) muscle fibers organize the microtubule network. The surprising finding is that this is not through a Golgi-nucleated microtubule mechanism involving proteins such as AKAP450 and GCC185 but instead through centrosomal proteins pericentrin and gamma-tubulin.
These experiments stemmed from the observation of microtubule bundles in these cells where an apparently stable microtubule lattice was seen to be decorated with dynamic EB3 puncta along their length. EB3 is known to only decorate growing microtubule ends. This was then explained through the good use of super-resolution microscopy (in this case gated stimulated emission depletion [GSTED]). Here, Oddoux and colleagues showed the presence of microtubule bundles emanating from clearly definable hubs. These hubs turned out to be Golgi elements, nucleating new microtubules which then grew alongside pre-existing ones. These in vitro data are also supported by in vivo data from intravital imaging. These experiments convincingly demonstrate the relevance of these findings in vivo.

The data are very carefully quantified and present a compelling case. The story adds nicely to our understanding of the relationship between the Golgi and centrosomal proteins in an interesting and important model system. The authors are now also well placed to determine the relevance of this organization and these mechanisms to Duchenne muscular dystrophy where loss of microtubule organization is thought to underlie the disease pathology {1}.

References

Microtubules underlie dysfunction in duchenne muscular dystrophy.

Khairallah RJ, Shi G, Sbrana F, Prosser BL, Borroto C, Mazaitis MJ, Hoffman EP, Mahurkar A, Sachs F, Sun Y, Chen YW, Raiteri R, Lederer WJ, Dorsey SG, Ward CW. Sci Signal 2012; 5(236):ra56  PMID: 22871609 DOI: 10.1126/scisignal.2002829

 

Asymmetric inheritance of centrosome-associated primary cilium membrane directs ciliogenesis after cell division.

Paridaen JTML, Wilsch-Bräuninger M, Huttner WB. Cell 2013 Oct 10; 155(2):333-44 PMID: 24120134 DOI: 10.1016/j.cell.2013.08.060

This is one of those papers that has such a simple underpinning observation that one wonders how it has not been seen before. The authors identify an Arl13b-positive membrane that is endocytosed from the primary cilium as the cell enters mitosis. This associates selectively with the mother centriole and gives this a head-start in terms of ciliogenesis and therefore in the ability to respond to sonic hedgehog signals. The paper demonstrates this in a number of different ways, both in vitro and in vivo, and shows some evidence for the importance of this asymmetric ciliogenesis in stem cell function.
Many questions remain as a result of this work. The evidence here strongly supports a model where this internalized Arl13b-positive membrane acts as a primer for ciliogenesis. Not only will it be important to define how this selective association occurs but whether and how selective biosynthetic trafficking to this compartment reinforces this process to drive subsequent cilia formation on exit from mitosis. I strongly recommend a look at the accompanying mini-review from Hoerner and Stearns as well {1}.

References

Remembrance of cilia past. Hoerner C, Stearns T. Cell 2013 Oct 10; 155(2):271-3 PMID: 24120128 DOI: 10.1016/j.cell.2013.09.027

 

Cerebral organoids model human brain development and microcephaly.

Lancaster MA, Renner M, Martin CA, Wenzel D … Homfray T, Penninger JM, Jackson AP, Knoblich JA.  Nature 2013 Sep 19; 501(7467):373-9 PMID: 23995685 DOI: 10.1038/nature12517

This is an outstanding manuscript that demonstrates not only the development of a system to model the human brain in vitro but also then applies this technique to prove that it can model complex human brain diseases. The authors develop what they term ‘cerebral organoids’ through differentiation of human pluripotent stem cells in a 3D culture system. They also develop organoids from patient-derived stem cells to show that the observed microcephaly caused by mutation in CDK5RAP2 is recapitulated in this system. The microcephaly phenotype is also evident after short hairpin RNA (shRNA) knockdown of CDK5RAP2, further demonstrating the applicability of this method. This paper provides an outstanding example for teaching purposes and of course will likely be widely applied to human developmental brain disorders.

 

A conserved role for atlastin GTPases in regulating lipid droplet size.

Klemm RW, Norton JP, Cole RA, Li CS … Farese RV Jr, Blackstone C, Guo Y, Mak HY.  Cell Rep 2013 May 30; 3(5):1465-75 PMID: 23684613 DOI: 10.1016/j.celrep.2013.04.015

The concept that atlastin is important for lipid metabolism raises new questions about the way that mutations in this protein cause human disease. The paper also points to a key link between endoplasmic reticulum morphology and lipid droplet biogenesis, which could have important implications for many other studies in this field.

 

ER exit sites are physical and functional core autophagosome biogenesis components.

Graef M, Friedman JR, Graham C, Babu M, Nunnari J. Mol Biol Cell 2013 PMID: 23904270 DOI: 10.1091/mbc.E13-07-0381

This paper convincingly identifies a key role for endoplasmic reticulum (ER) exit sites (ERESs) in autophagosome formation in Saccharomyces cerevisiae. These data show that autophagosomes form in close proximity to these specialised invaginations of the ER where COPII vesicles assemble.

Using a broad-ranging forward proteomics approach, Graef et al. defined multiple protein-protein interactions between autophagy proteins and vesicle trafficking proteins, most notably those that comprise the COPII coat. Key interactions were defined between COPII and proteins of the PI3-kinase and Atg9 complexes that initiate autophagosome formation. It is notable that the Sec23 subunit of the COPII coat appears to be at the hub of this network of interactions. This subunit also interacts with other key cellular machineries directing multiple functions of COPII and ensuring a directional flow to traffic (see {1}). Fluorescence imaging showed that early autophagosome structures formed adjacent to ERESs. Consistent with a key role for ERESs in this process, inhibiting ERES function using a temperature-sensitive form of Sec12 inhibited autophagic flux.

The authors conclude that ERESs act in the mechanical process of ERS formation and suggest that one role could be to tether the nascent autophagosome as it expands. While it is not yet clear exactly how ERESs function in autophagosome formation, the work places ERESs as acting downstream of Atg1 kinase complex localisation and speculate that ERESs provide membrane, and/or somehow scaffold, autophagosome assembly.

Interestingly, the authors extended their findings to higher eukaryotic cells, showing similar co-localisation between autophagy components and ERESs (labelled with mCherry-Sec16B) in Cos-7 cells. Exactly how ERESs direct autophagosome assembly, the identity of the proposed ERES-tether complex, and how the autophagosome is eventually released from its association with the ER remain to be defined.

References

Coordination of COPII vesicle trafficking by Sec23. Fromme JC, Orci L, Schekman R. Trends Cell Biol 2008 Jul; 18(7):330-6 PMID: 18534853 DOI: 10.1016/j.tcb.2008.04.006

 

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Microscopy – a painful transition to Windows 7…..stalled

Volocity does not drive a Coolsnap HQ2 under Windows 7

I am posting this in case it pops up in anyone’s Internet searches for similar issues:

We have a pretty standard fixed cell imaging system running on a Windows XP PC.

It has a Photometrics Coolsnap HQ2

We use Perkin-Elmer (formerly Improvision) Volocity software to drive the system. We do however run an older version of the software having run out of money to maintain the continuous upgrade path (known as a Software Maintenance Agreement with Perkin Elmer). Microsoft has now forced us to switch from Windows XP to a newer OS. I could normally cope with this – reinstall a few things, update some drivers and off you go.

Sadly, in this case, no.

The Coolsnap HQ2 is supported under Windows 7

Volocity (even version 5.4) will run on Windows 7

Unfortunately the cnombination doesn’t work:

Volocity does not drive a Coolsnap HQ2 under Windows 7

I should add that Perkin-Elmer, Photometrics, and our own University IT guys have bee great through the process but to no avail.

Perkin Elmer are investigating whether there could be a solution but for now at least, there isn’t. Unless we change to Micromanager. Which we could but isn’t as simple and user-friendly for a broad lab like ours….We may have to do this and so be it.

Comments on: The Microtubule-Binding Protein Ensconsin Is an Essential Cofactor of Kinesin-1.

I evaluated the following article for F1000 Prime.

The Microtubule-Binding Protein Ensconsin Is an Essential Cofactor of Kinesin-1.

Barlan K, Lu W, Gelfand VI.

Curr Biol 2013 PMID: 23394833 DOI: 10.1016/j.cub.2013.01.008

This paper defines the microtubule binding protein ensconsin as an obligate co-factor for kinesin-1 drive in motility in Drosophila. In a series of elegant experiments, the authors show that ensconsin is not required for the recruitment of kinesin to membranes but is in some way involved in activating the motor. Ensconsin does not seem to affect the amount of membrane-bound kinesin in cells so the authors sought to define its role in motor activation. Kinesin-1 normally exists in an auto-inhibited confirmation in cells. In a key experiment the authors showed that removal of this auto-inhibition within the kinesin-1 motor by mutation eliminates the requirement for ensoconsin in vivo. These data suggest a model in which ensconsin acts to relieve the auto-inhibition. An important point is that this function of ensconsin did not require its own microtubule binding activity. The authors postulate that spatial restriction of ensconsin to microtubules acts to refine the spatial activation of kinesin-1, adding to the diversity of mechanisms that control the spatial and temporal organization of microtubule motor activation.

Note: Ensconsin is also known as E-MAP-115 and MAP7.

These comments also appear on Faculty of 1000 Prime

Art competition entries 2012

I entered a few of my images into our Faculty Art Competition this year. They didn’t win but I thought I would post them here anyway.

Click on the images for a larger view.

You can see the winners here.

3D rendering of ciliated cells

3D rendering of ciliated cells. LLC-PK1 (pig kidney epithelial) cells were grown on a round micropattern to constrain growth. Cilia are in green with the Golgi in magenta and nuclei in blue. The image is a 3D rendering of a deconvolved z-series acquired using widefield microscopy.

Image of Aequorea victoria.

A pseudocoloured image of the jellyfish Aequorea victoria from which Green Fluorescent Protein was isolated. The pseudocolouring illustrates the diverse colour palette of GFP variants that we now have available.
The image is a photograph taken by me at Monterey Bay aquarium in 2003. There is only one jellyfish in the original photo, this image is a montage.

PhD studentship opportunity in our lab

We have a potential PhD studentship available to start in October 2013.

This studentship is part of the MRC Doctoral Training Programme at the University of Bristol. As such you apply to the Programme and the selection process is in competition with all other advertised projects. You can find full details on the programme, including the other available projects here:

MRC Doctoral Training Programme at the University of Bristol.

This is an exciting inter-disciplinary project bridging ongoing work in Biochemistry and Physics. The project would suit a graduate in biochemistry, cell biology, or biophysics. Full training will be provided and the training elements can be tailored to the interests of the successful candidate.

Please note the eligibility criteria: Only applicants from the UK/EU are eligible for this programme.

Title: Analysis Of Integration Between Membrane And Cytoskeleton Dynamics Using Advanced Light Microscopy

Supervisors: Professor David Stephens (Biochemistry) & Dr Henkjan Gersen (Physics)

To apply for this project please select ‘Faculty of Medical and Veterinary Sciences’ and ‘Biochemistry (PhD)(4-yr)’. Please also identify ‘MRCDTG’ as your fee payer in the Funding section of the online application.

The intricate relationship between endomembranes and cytoskeletal filaments governs the spatial organization, morphology, and function or organelles. Multiple cellular functions that coalesce around Golgi membranes are governed by small GTPases of the Rho family, Cdc42 being the most significant Rho GTPase at the Golgi (1). Recent years have seen the emergence of the septins as a critical component of this system; Cdc42 is known to dictate septin filament organization (2). Septin filaments act in concert with microtubules to direct trafficking around the Golgi (3). Septins also dictate the formation and function of primary cilia, a “cellular antenna” that integrates key signalling pathways essential to normal organism development and tissue function (4, 5, 6). Through selective disruption of Cdc42, Golgi, or septin function, we will define how the classical structure of the Golgi apparatus is defined by septin filaments and vice versa.

Septins adopt a highly conserved structural organization within filaments that can be detected by polarization fluorescence microscopy (7, 8), allowing the subunit architecture of septin filaments to be analysed in an intact cell context. This advanced bioimaging approach will form a core training aspect of the work and would suit a biomedical science graduate with a keen interest in imaging or a biophysics graduate with a strong interest in cell biology. The project bridges the Biochemistry and Physics departments at the University of Bristol. You would be based in the Stephens lab in the School of Biochemistry within newly refurbished cell biology laboratories and the project will involve considerable mammalian cell biology using gene silencing and advanced light microscopy. The Gersen lab, located a short distance away, will provide training in development and application of novel optical microscopy methods, notably fluorescence polarization. Successful PhD training is ensured through links to existing cell biology and nanoscience students in both labs as well as international collaboration.

Informal enquires to David Stephens (david.stephens@bristol.ac.uk) or Henkjan Gersen (H.Gersen@bristol.ac.uk) are welcome.

For further details see:

http://www.bristol.ac.uk/biochemistry/stephens/index.html

http://www.bristol.ac.uk/physics/people/henkjan-gersen/index.html

References

  • S. Etienne-Manneville, Cdc42–the centre of polarity. J. Cell Sci. 117, 1291 (Mar 15, 2004).
  • G. Joberty et al., Borg proteins control septin organization and are negatively regulated by Cdc42. Nat. Cell Biol. 3, 861 (Oct, 2001).
  • E. T. Spiliotis, Regulation of microtubule organization and functions by septin GTPases. Cytoskeleton 67, 339 (Jun, 2010).
  • Q. Hu et al., A septin diffusion barrier at the base of the primary cilium maintains ciliary membrane protein distribution. Science 329, 436 (Jul 23, 2010).
  • J. R. Bowen, D. Hwang, X. Bai, D. Roy, E. T. Spiliotis, Septin GTPases spatially guide microtubule organization and plus end dynamics in polarizing epithelia. J. Cell Biol. 194, 187 (Jul 25, 2011).
  • E. T. Spiliotis, S. J. Hunt, Q. Hu, M. Kinoshita, W. J. Nelson, Epithelial polarity requires septin coupling of vesicle transport to polyglutamylated microtubules. J. Cell Biol. 180, 295 (Jan 28, 2008).
  • B. S. DeMay et al., Septin filaments exhibit a dynamic, paired organization that is conserved from yeast to mammals. The Journal of cell biology 193, 1065 (Jun 13, 2011).
  • S. A. Rosenberg, M. E. Quinlan, J. N. Forkey, Y. E. Goldman, Rotational Motions of Macromolecules by Single-Molecule Fluorescence Microscopy, . Accounts of Biochemical Research 38, 583 (2005).

Potential applicants are encouraged to contact David when applying.

The deadline for applications is Wednesday 16th January 2013 and interviews are likely to be in the weeks of 11th February and 18th February 2013.

Evaluated: Boncompain et al (2012) Synchronization of secretory protein traffic in populations of cells.

I evaluated this for F1000 (yes, I’ve been busy!). Looks like a really useful system for many, especially given its adaptability.

G Boncompain, S Divoux, N Gareil, H de Forges, A Lescure, L Latreche, V Mercanti, F Jollivet, G Raposo and F Perez  (2012) Synchronization of secretory protein traffic in populations of cells. Nature Methods 2012 9 PMID: 22406856 DOI: 10.1038/nmeth.1928

This paper presents an exciting and widely modifiable system to study organelle dynamics and secretory protein traffic in a controlled manner. The retention using selective hooks (RUSH) system is based on controlled retention of proteins in the endoplasmic reticulum (ER) allowing one to exploit any number of targets through genetic engineering of relevant reporters. There are many advantages over other systems that have been highlighted by the other evaluations. The system presents some great options for both image-based and biochemical assays. I entirely agree with their comments and look forward to seeing this system in wide use (I note there are no restrictions on academic use).

PowerPoint with embedded movies on the iPad

Having recently bought and iPad but not being a Mac user I found some issues with getting the content I wanted to loaded.

The simple thing was Powerpoint presentations with embedded movies. On my PC these are all WMV files which I generated from original AVI files.

I am sure there are 1001 ways of doing this but I thought I would share mine as clearly there are 1001 websites with conflicting info on there. The easy solution I found was to buy Keynote from the app store. This runs all my PowerPoint presentations easily it seems. The only issue was then getting the embedded movies in.
Solution was to convert them to MP4 for which I use the (free) Leawo MP4 Converter.

This was a very quick easy and free way to convert and enables batch conversion. The whole folder took about 10 mins. A couple did not convert but I think this is down to old codecs used to make them in the first place.

I then uploaded these to my iPad using iTunes (Photos folder, manually selecting which folders to use).

In Keynote on the iPad I then found I simply needed to deletee the embedded movie which wouldn’t run and insert (as a new item) the relevant MP4.
Bingo. Cost £6.99 for Keynote app, time taken ~ 2 hours to work it out and then achieve. Result, nice looking presentation on iPad. The display on the 2012 version is great for this.
The method which didn’t work was to use “replace” not delete and insert from scratch. Having looked at a variety of websites about this issue, this seems to be where some go wrong.

All good now – question remains when will I be brave enough to present using this alone and not take my trusty laptop with me? For the time being I can now load any presentation I have to at least show and discuss whenever I like.