Animals and Plants have hundreds of miRNAs with diverse roles in gene regulation. In humans, each miRNA family can control up to several hundred genes (or up to 500 to be exact, in humans). A loss of function in one, can lead to an array of developmental defects & diseases. The same goes for plants. However, many plant miRNAs only have one target, which is frequently a transcription factor that in turn, controls many genes itself. It’s really like a house of cards. An mutant with a loss of function in one miRNA can have a full range of phenotypes.

Focusing on one miRNA pathway in plants:

Arabidopsis miR159, which only has 2 validated targets which are functionally redundant transcription factors (MYB33, MYB65).

mir159ab mutant v.s. wild type: (personal images)

The mir159ab mutant plant is smaller and the leaves curl upwards. Flowers are also affected, and fertility is reduced in the mutant. All because miR159 is no longer active, and it’s targets MYB33 and MYB65 are at free rein to meddle in regular development. miRNA mutants are quite revealing on how miRNAs ‘switch off’ target genes that would otherwise inhibit development.

miR159 targets actually have an important role in pollen development. Loss of function mutants in MYB33/MYB65 lead to male sterility in plants. Pollen is also the only tissues/cells where miR159 isn’t expressed, so the plant needs active MYB33 and 65 for fertility. Seems a bit wasteful to express MYB33/65 in the entire plant, if they appear to only have a role in the pollen. Also, what’s the point of expressing them and having a miR159 ‘switch’ em off?

It’s speculated that they have additional roles in programmed cell death (PCD) that’s associated with plant defense. It’s seemingly unrelated to pollen development. Bizarre, but MYB33/65 are actually transcription factors that up-regulate the genes involved in PCD. To connect the dots: PCD has a role in pollen development: it causes the degeneration of tissue that impede growth past a certain stage. Additionally, when a plant is challenged with a virus, infected cells & tissues will undergo PCD in an attempt to stop its spread. Many viruses are known to suppress siRNA and miRNA production. In addition to roles in its own development, gene silencing is used by plants to quell viral replication. If the virus attack the plant’s RNAi machinery, to halt defensive siRNA production, it also influences endogenous miRNAs. Thus, it could be possible that the miR159-MYB33/65 system is involved in this as a sort of viral sensor. If miR159 is no longer active, MYB33/65 will begin to trigger PCD.

All this, for one miRNA-target gene connection.

It’s a bit like playing Jenga. One piece may only touch 3-4 others, but if you remove the essential one, all 20 pieces fall down because they were all connected. (Image: Flikr CC, Jenga, by Paul_Carvill)

It gets more complex if key proteins in miRNA biogenesis & action are rendered function-less. Initially, before RNAi was more established, researchers believed they were dealing with a multitude of proteins with various functions..when really it was just a few participating in one show. Loss of one RNAi-related protein can translate into the loss of function in hundreds of miRNAs. Moreover, miRNAs aren’t actually the effectors of regulation, they are simply the guides. The proteins do the dirty work, from making miRNAs to making use of them..

Arabidopsis Dicer like 1 (DCL1) a one significant protein in miRNA biogenesis. It cuts out the mature miRNA strand from it’s precursory hairpin structure (the pri-miRNA). Furthermore, in plants at least, miRNA precursors come in many different hairpin shapes and lengths, so DCL1 is often forced to cut them up differently. And so a mutation in any of DCL1’s sequences can lead to diverse interruptions in plant development. For DCL1 alone, there are up to 10 different mutant alleles with variations in severity and phenotype. At first, research groups thought they were dealing with 3 different proteins and their mutant alleles. They all had different phenotypes and names, suspensor-1 (sus-1) was arrested in embryo development and was embryonic lethal. Carpel factory-1 (caf-1) overproduces carpels (female parts in the flowers) and has sterile anthers (male parts). Eventually, by virtue of gene mapping they began to connect the dots. Cloning of the DCL1 gene years later also verified this. The history of DCL1 and it’s mutants is summed up an article artfully called, “DICER-LIKE1: blind men and elephants in Arabidopsis development”.

Carpel factory-1, aka dcl1-9, flower versus a wild type flower (Images: Laufs et al. 2004, published in Development).

Garzon, R., Marcucci, G., & Croce, C. (2010). Targeting microRNAs in cancer: rationale, strategies and challenges Nature Reviews Drug Discovery, 9 (10), 775-789 DOI: 10.1038/nrd3179

Allen, R., Li, J., Stahle, M., Dubroue, A., Gubler, F., & Millar, A. (2007). From the Cover: Genetic analysis reveals functional redundancy and the major target genes of the Arabidopsis miR159 family Proceedings of the National Academy of Sciences, 104 (41), 16371-16376 DOI: 10.1073/pnas.0707653104

Alonso-Peral, M., Li, J., Li, Y., Allen, R., Schnippenkoetter, W., Ohms, S., White, R., & Millar, A. (2010). The MicroRNA159-Regulated GAMYB-like Genes Inhibit Growth and Promote Programmed Cell Death in Arabidopsis PLANT PHYSIOLOGY, 154 (2), 757-771 DOI: 10.1104/pp.110.160630

Schwab, R., & Voinnet, O. (2009). miRNA processing turned upside down The EMBO Journal, 28 (23), 3633-3634 DOI: 10.1038/emboj.2009.334

SCHAUER, S., JACOBSEN, S., MEINKE, D., & RAY, A. (2002). : blind men and elephants in development Trends in Plant Science, 7 (11), 487-491 DOI: 10.1016/S1360-1385(02)02355-5

Laufs, P. (2004). MicroRNA regulation of the CUC genes is required for boundary size control in Arabidopsis meristems Development, 131 (17), 4311-4322 DOI: 10.1242/dev.01320

(1 votes)

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The Royal Society has uploaded audio files of almost all the talks of their Discussion Meeting last October: “2010: What Next for Stem Cell Biology?”.

Unfortunately there are no slides to look at (as far as I can tell) so some of the more technical talks may be hard to follow, but if you’re already familiar with the work of some of the speakers, hearing them speak may help put things in context, even without seeing the slides. The abstracts of the talks are all in the programme booklet, which you can download from their site as well.

I attended this meeting in person, and was impressed with both the variety of the talks as well as the overlap between them. If you’re trying to answer the RSc’s question posed in the meeting title, then the common thread of many of the talks suggests that what’s next for stem cell biology is mainly to get a complete picture of reprogramming. But the variety of the talks indicates that there are many ways to approach this: finding out how to make one particular cell type for therapeutic means (addressed by several speakers), finding out the mathematical concepts behind reprogramming to define a formal theory (Sui Huang’s talk), or even calculating the cost of reprogramming when setting up a company that relies on iPS cells for research (Cathy Prescott’s talk). There’s still a lot of work to be done, but hopefully the collective approaches will reveal a clear picture of reprogramming in the next few years.

(2 votes)

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I’ll save the thousand words.  Here’s the link:

J Vis Exp. 2011;47 http://www.jove.com/details.stp?id=2466

Holmes KE, Wyatt MJ, Shen Y, Thompson DA, Barald KF. Direct Delivery of MIF Morpholinos Into the Zebrafish Otocyst by Injection and Electroporation Affects Inner Ear Development.  J Vis Exp. 2011;47 http://www.jove.com/details.stp?id=2466 doi: 10.3791/2466.

(4 votes)

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The modENCODE project (model organism encyclopedia of DNA elements) is a collaborative effort to identify all sequence-based functional elements of Drosophila and C. elegans. The project has now produced almost a thousand data sets with information about transcription, epigenetics, replication and gene regulation across different developmental stages and multiple cell lines.

Just before the holidays, the modENCODE teams published several analyses of these data sets in a number of papers across four journals. Because the data were collected across multiple developmental stages, they give information that cannot be gathered from looking at just one point in development.

In a CSHL podcast, modENCODE team member Thomas Gingeras describes work from his group that was published in Science. They used the modENCODE data to confirm that 90% of all 17 thousand predicted protein coding regions in Drosophila indeed correspond to RNA expression. At any given point along the developmental timeline, this percentage would of course be a lot smaller, as genes switch on and off. In addition, they found almost two thousand previously unannotated genes.

Another result relevant to developmental biologists is covered in one of the Nature papers: An analysis of different chromatin states in Drosophila revealed a more complex pattern of Polycomb target regulation than was previously suspected.

Worm researchers also have a lot of new information to work with. For example, a Science paper describes the mapping of transcription factor binding sites in C. elegans and reports that some regions of the worm genome – which they called HOT regions – were bound by more than 15 transcription factors!

So what’s next for the modENCODE project? There is still a year of funding left, and much of that time will be spent adding more annotations for newly found functional regions, as well as integrating different types of data for a more complete picture.

Of course, the worm and fly are not the only organisms to be mapped. Let’s not forget ourselves! The (human) ENCODE project, which in fact precedes modENCODE, hopes to publish a full genome analysis next year.
(more…)

(3 votes)

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Cancer and stem cells are two very loaded biology concepts, and more frequently can be found in the same discussion.  Stem cells within tumors are able to divide and provide the various differentiated cell types that a tumor requires to thrive.  And, identifying how a normal stem cell divides, or stops dividing, can help further the understanding of tumorigenesis.  Along these lines, a paper from the December 15 issue of Development describes a pathway involved in intestinal stem cell proliferation.

Intestinal stem cells (ISCs) normally divide to replace differentiated intestinal cells at a rate that supports tissue homeostasis.  This rate of ISC division quickly increases when intestinal cells suffer injury due to damage, disease, or exposure to pathogens or chemical agents.  Recently, Karpowicz and colleagues investigated this switch from normal to “acute regeneration” of intestinal cells in Drosophila midgut epithelium, a great model for ISC self-renewal.  In this paper, the authors find that ISC proliferation is constitutively controlled by Hippo, a member of a pathway involved in organ growth and cancer.  In addition, injury disrupts this regulation of Hippo, which in turn activates Yorkie, a Hippo pathway target.  The authors find that this cell-autonomous role for the Hippo pathway is crucial for regulation of ISC proliferation.

Images above show regions of control (top) and Yorkie-depleted (bottom) Drosophila midgut tissue.  Yorkie depletion causes fewer ISC divisions, as seen as fewer cells positive for Escargot (Esg; green), a known transcription factor expressed in ISCs.

For a more general description of this image, see my post on EuroStemCell, the European stem cell portal.

Karpowicz, P., Perez, J., & Perrimon, N. (2010). The Hippo tumor suppressor pathway regulates intestinal stem cell regeneration Development, 137 (24), 4135-4145 DOI: 10.1242/dev.060483

(5 votes)

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Message from the BSDB, reposted with permission. Keep in mind that the funding opportunities are for BSDB members only, and the final deadline is very, very soon. The poster for the course was posted on the Node earlier.

We have the unique opportunity to provide UK BSDB members with funded opportunities to attend an intensive practical and theoretical course on embryonic stem cells and mammalian development in Mexico this March. This was to be explained in the upcoming newsletter, but as it is late, we would like to make sure that BSDB members don’t miss this opportunity and therefore we are sending this unusual email to the membership. There are up to 8 funded places open to students, post docs, or young principle investigators. The website is www.escellslatinamerica.org and you can either apply on line by the 5th of January or submit applications as a single PDF file to either Josh Brickman (josh.brickman@ed.ac.uk) or Jenny Nichols (jn270@cscr.cam.ac.uk), by Saturday the 8th of January at 5 PM. If you apply via an email to either Josh or Jenny, then you will need to include your education and research experience (one page, include all degrees and classifications), a list of publications (for PhD students with little experience this is not important), a letter explaining why you want to attend the course (no more than 500 words) and a letter from your supervisor or department head explaining why you should be considered for the course. If you are unable to get in touch with your supervisor this week, because of the holiday, then please contact us for alternative directions.

The course, “ES Cells as a Model System for Embryonic Development,” is organized every two years at different sites in Latin America. It is a practical and theoretical course on mouse development and embryonic stem cell technologies. The course strives to simultaneously teach and build international collaborative relationships. This year it will be held in March 2011 in Mexico (Feb 27th to March 17th, 2011). The course has funding to send from 5-8 PhD students, post docs or young faculty members from the UK to Mexico to participate in both the course and its associated scientific symposium, at which all participants will be expected to give a short talk.

Course includes lectures and workshops with:
Alejandro Schinder (Buenos Aires, AR)
Alfonso Martinez-Arias (Cambridge, UK)
Andrew Smith (Edinburgh, UK)
Austin Smith (Cambridge, UK)
Heiko Lickert (Neuherberg, GER)
Ivan Velasco (Mexico City, Mexico)
James Briscoe (London, UK)
Janet Rossant (Toronto, CA)
Jennifer Nichols (Cambridge, UK)
José Xavier Neto (Campinas, BR)
Joshua Brickman (Edinburgh, UK)
Luis Covarrubias (Cuernavaca, Mexico)
Meng Li (London, UK)
Peter Andrews (Sheffield, UK)
Philippe Soriano (New York, USA)
Robin Lovell-Badge (London, UK)
Sally Lowell (Edinburgh, UK)
Simon Tomlinson (Edinburgh, UK)
Tariq Enver (London, UK)
Tetsuya Taga (Tokyo, Japan)
Tilo Kunath (Edinburgh, UK)
Wendy Bickmore (Edinburgh, UK)
Yann Barrandon (Lausanne, Switzerland)
Diana Escalante-Alcalde (Mexico City, Mexico)
Chris Wood (Cuernavaca, Mexico)
Guillermo Lanuza (Buenos Aires, AR)

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But you know he’ll always keep movin’
You know he’s never gonna stop movin’
Cause he’s rollin’, he’s a rollin’ stone

~ Baker Street, by Gerry Rafferty (Link to Song on Youtube)

Something to ponder. whether you’re a rock star or researcher, you’re bound to be on the road at some point. Seldom do researchers remain in one facility, city or continent, with some exceptions. I’d always been told that labs prefer to have personnel with some experience abroad. It’s likely because this brings some fresh perspective and techniques.

(Image: Flikr CC by Katerha)

Scottish Rocker Gerry Rafferty recently passed (Obituary in the Telegraph here). He penned a couple of famous rock songs, such as Stuck in the middle with you (terribly 70s MV), and Baker Street. (I get the feeling I’ll get a few disgruntled rock fans stumbling into this post after a keyword search).

A couple of bloggers have drawn parallels between rockers and scientists before. Eva even has a blog on it.

Listening to Rafferty’s Baker Street got me thinking of another thing or two Researchers & Rock Stars have in common. Usually, neither enjoy stable careers. You can have a few hits or articles in high impact journals..then wind up languishing in anonymity or worse..without a grant for several rounds. (Some will undergo career changes). Often times, success comes from luck, and not merely just talent & hard work. You also have to know what’s currently “hot” & attractive to the masses (or government agencies & publishers).

Many researchers have expertise & research interests that aren’t always high in demand. It’s part of the onus to travel, pursuing one contract after another after grad school. So many PIs, Postdocs and students in Australia are actually internationals on PR or VISAs, for instance. In my department alone at the ANU, there’s a dozen Germans & Austrians, half a dozen from Spain or Latin America and scores of Asians and South East Asians. Even the Aussies in the dept are well-travelled, having lived in 2-3 continents before returning home. Many PIs, I’ve noticed, travelled the world but eventually return their alma maters, the universities that fostered their education & training.

You used to think that it was so easy
You used to say that it was so easy
But you’re tryin’, you’re tryin’ now
Another year and then you’d be happy
Just one more year and then you’d be happy

…And it’s taken you so long to find out you were wrong
When you thought it held everything

This set of lyrics reminds me of two PhD Comics Strips, Origin of the theses (brings so many grad students to their knees), and Your Life Ambition (which takes a nose dive after you enter grad school and find that most of your projects aren’t working, troubleshooting is a b***, your results don’t add up, and your paper got scooped etc. Wonder how many feel jaded after they’ve reached their postdoc). Every year except the one you’re in, seems to offer endless time for you to find your answers and provide evidence for them.

Winding your way down on Baker Street
Light in your head and dead on your feet
Well another crazy day, you’ll drink the night away
and forget about everything

After a hard day or week, (possibly contemplating the above ideas) everyone enjoys their happy hours and drinks at the pubs. It’s the times they get to take a break from work, unwind and not worry about a thing. This could apply to anyone really, who’s had a tough bout in their jobs, which is probably why Baker Street continues to be an iconic 70s rock song. The lyrics themselves are so universal.

To end on a less :( note…

And when you wake up it’s a new morning
The sun is shining, it’s a new morning
But you’re going…

Research (& Music) offers the appeal of travel and change. Work will never be stagnant for long. If the current situation drags or isn’t ideal..you apply for the next position, fellowship and/or contract somewhere else. At least for research, you’re never bound to one country or job by your career. You’re not even bound to your field.

Rest of the Baker Street Lyrics can be found here

(2 votes)

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Here are the research highlights from the new issue of Development:

Wnt/PCP signalling, microtubules and gastrulation

During vertebrate gastrulation, convergence and extension (C&E) movements shape the germ layers to form the anterioposteriorly elongated body axis of vertebrate embryos. Non-canonical Wnt/planar cell polarity (Wnt/PCP) signalling regulates C&E by polarising the morphology and behaviour of cells, which suggests that the Wnt/PCP pathway might influence the microtubule cytoskeleton. Here, Lila Solnica-Krezel and co-workers investigate this possibility by assessing the position of the centrosome/microtubule organising centre (MTOC) relative to the cell nucleus and the body axes during zebrafish gastrulation (see p. 543). They report that MTOCs occupy a polarised position within the plane of the ectoderm and mesoderm, becoming biased to the posterior and dorsal/medial side of the cell between mid and late gastrulation. This polarisation, they report, depends on intact Wnt/PCP signalling. Conversely, microtubule disruption experiments show that microtubules are required to initiate the anterior localisation of Prickle, a core PCP signalling component. These and other results suggest that reciprocal interactions between Wnt/PCP signalling and the microtubule cytoskeleton are required during C&E gastrulation movements.

Skin deep: Adam10 regulates Notch signalling

Notch signalling plays a crucial role in the development and maintenance of the epidermis: the stratified epithelium that forms the skin’s outer layer and protects organisms from dehydration, mechanical trauma and microbial invasion. Now, on p. 495, Carien Niessen, Paul Saftig and colleagues reveal that the disintegrin/metalloproteinase Adam10, a `sheddase’ involved in Notch processing, is essential for epidermal integrity and Notch-mediated epidermal signalling in mice. The researchers show that epidermal-specific deletion of Adam10 in mouse embryos leads to perinatal death, impairment of the skin’s barrier function and an absence of sebaceous glands. Moreover, deletion of Adam10 in adult mice causes hair loss, epidermal hyperproliferation and cyst formation. These phenotypes closely resemble those produced by epidermal inactivation of Notch signalling. Indeed, the researchers report that epidermal loss of Adam10 severely impairs Notch processing and signalling in the epidermis. Together, these data identify Adam10 as the major Notch processing enzyme in the epidermis in vivo and as a central regulator of skin development and maintenance.

SAD (kinase) tales of neural-specific glycans

Several aspects of neural development and function rely on the regulated expression of specific glycans, but what are the mechanisms that govern neural-specific glycosylation during embryogenesis? On p. 553, Michael Tiemeyer and colleagues report that Sugar-free frosting (Sff) – the Drosophila homologue of SAD kinase, which regulates synaptic vesicle tethering and neuronal polarity in nematodes and vertebrates – drives neural-specific glycan expression in the Drosophila embryo prior to synaptogenesis. They performed a genetic screen for mutations that affect the expression of neural-specific N-linked glycans known as HRP-epitopes; neural expression of HRP-epitopes requires ectodermal expression of Tollo, a Drosophila Toll-like receptor. Analysis of the sff mutant recovered from this screen reveals that Sff modulates glycan complexity by altering Golgi dynamics in neurons that respond to Tollo transcellular signals. The researchers propose that multiple protein kinases facilitate flux through divergent Golgi processing pathways, thereby sculpting tissue-specific glycan expression patterns during development.

nanos1: novel structure-based translational regulation

During development, translational control of mRNAs regulates gene expression. Translational control is usually achieved through binding of trans-acting factors to mRNA untranslated regions but, on p. 589, Mary Lou King and co-workers reveal a novel, structure-based mechanism for translational repression of Xenopus germline nanos1. Nanos translational repressors maintain primordial germ cell identity during development. nanos1 RNA is transcribed during early oogenesis and stored in germinal granules. Surprisingly, the researchers report that, unlike other mRNAs, nanos1 RNA translates poorly after injection into Xenopus oocytes. Thus, sequestration within germinal granules cannot explain translational control of nanos1 mRNA. Instead, they report, a secondary structural element immediately downstream of the mRNA start site is necessary and sufficient to repress the initiation of nanos1 translation through steric hindrance of ribosome scanning; insertion of 15 nucleotides between the start codon and this element relieves repression. Although structure-based translational regulation is common in prokaryotes it has not been observed before in eukaryotes and represents a new, developmentally important mode of nanos1 regulation.

Fast Nodal/Lefty movements set LR asymmetry

Nodal and its feedback inhibitor Lefty instruct left-right (LR) asymmetry in vertebrates, but what controls the spatial distribution of these ligands in the embryo? On p. 475, Lindsay Marjoram and Christopher Wright address this question by expressing functional epitope-tagged Nodal and Lefty from grafts implanted into tailbud Xenopus embryos. Both ligands move long distances along the extracellular matrix (ECM), they report, with Lefty moving faster than Nodal. Moreover, sulphated proteoglycans in the ECM seem to facilitate Nodal movement. Thus, the researchers propose, Nodal autoregulation aided by rapid ligand transport underlies the anteriorward shift of Nodal expression along the left lateral plate mesoderm (LPM), with higher levels of chondroitin-sulphate proteoglycan in more mature anterior regions providing directional transport cues. Finally, they report, Lefty moves from the left to the right LPM, a result that strengthens LR patterning models that involve active blocking of right-sided Nodal expression. Future molecular studies into how Nodal and Lefty interact with sulphated proteoglycan-rich ECM should provide additional insights into the establishment of LR asymmetry.

Moved to radial intercalation by PDGF-A

Radial intercalation – a common morphogenetic process in which cells from germ layers deep in developing embryos interdigitate into more superficial layers – is essential for the tissue rearrangements that occur during gastrulation. Here (p. 565), Erich Damm and Rudolf Winklbauer use scanning electron microscopy and time-lapse recordings to analyse radial intercalation in the prechordal mesoderm (PCM) during Xenopus gastrulation. They show that this process involves cell reorientation in response to a long-range platelet-derived growth factor A (PDGF-A) signal and directional intercellular migration towards the ectoderm, the source of this signal. The PCM, they report, fails to spread during gastrulation when endogenous PDGF-A signalling is inhibited. However, expression of a short-splicing isoform of PDGF-A, but not of a long-splicing form that binds to the extracellular matrix, rescues PCM radial intercalation. These results provide the first insights into the molecular basis of radial intercalation movements in the vertebrate gastrula and identify distinct roles for PDGF-A isoforms during gastrulation.

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As part of the Evolutionary crossroads in developmental biology series, Pauline Schaap introduces Dictyostelium discoideum, a social amoeboid that exists as both uni- and multicellular life forms, studies of which have provided key insights into the evolution of multicellularity.
See the Primer article on p. 387.

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Let me take you on a Bioluminescent journey across many kingdoms.

If you’re not well acquainted with the term, it’s the ability of living things to chemically produce light. It’s also a natural widespread feature to many organisms, from jellyfish to algae, fireflies to fungi. In recent years, it’s become a standard molecular biological tool for visualizing gene expression.

(Blue Jellyfish by Maaco. CC. link here.)

On some coasts (and even lakes), if you disturb the water you might notice the sudden appearance of hundreds of tiny bright lights in the water. Sometimes it’s observable in the crest of a powerful wave.

(bioluminescent wave, Phil Hart, CC, Ask Nature)

The light comes from the thousands of tiny unicellular algae, or dinoflagellates. The same species that cause deadly red tides (toxins released from the algae, which can cause paralysis in concentrated amounts. hence, never eat shellfish in red tide areas)

On land in fireflies, the luciferin pigments in their bodies can react with oxygen, to emit radiant light energy. This is catalyzed (or sped up) by the luciferase enzyme. Many biologists are probably familiar with Luciferase reporter genes, as markers for gene expression.

For instance, this reporter system can be used to track circadian rhythms in plants, by fusing the firefly luciferase gene to a plant one. The light signals are controlled by the plant genes, and are switched on by the plant itself during different parts of the day.

(Image: Firefly, by qmnonic)

The artificial lights cue researchers when the plant genes are switched on an off according to it’s circadian clock. Of course, the plants need a water with luciferin pigments, which they don’t naturally produce.

The idea of using bioluminescent genes & proteins (at least in plants) originated in tobacco in the late 80s. The moment was captured in Science & Time Magazine, it was so groundbreaking and breathtaking. Link here (Google Books) for the comparison of tobacco before and after “switching on” the luciferase action.

(CC from the Harmer Lab. Luciferase activity in a transgenic Arabidopsis plant)

Firefly luciferase is slightly different from GFP, a photoprotein. Photoproteins don’t require any special pigments, enzymes or chemicals to set it off. Once expressed, it simply needs mineral substrates to emit fluorescence. GFP was originally recruited from jellyfish. It has the same purpose as the luciferase enzyme in molecular biology, to mark the expression of select genes. At least in the lab, it GFP also requires you to shine blue light (or sometimes UV) for it to emit the green fluorescence. It’s such a standard tool now, in mice, plants, flies, fish studies. And it garnered it’s inventors the Nobel Prize for Chemistry in 2008.

In RNAi industry, it’s becoming a convenient diagnostic tool for tracking the efficiency of RNAi drugs. Previously, to gauge how well a target gene could be silenced by RNAi, substantial amounts of tissues needed to be extracted and ground up to conduct a quantitative RNA assay. this gave a numeric reading of how much was silenced compared to untreated tissues or model animals. However, this was a rather intensive method. Reporter genes, such a luciferase one, offer a non-invasive way of perceiving how strong the silencing is occurring.

Some fungi also naturally have a green glow at night. Their traditional names include jack-o-latern fungi, ghost fungi and foxfire (image on left, CC from the Cornell Mushroom Blog). Perhaps these guys were the original fairy rings 18th century cottagers thought they saw.

Thanks for reading & hope you enjoyed the show

(Image, CC from Hither & Thither).

References & Interesting Reading:

Luciferase in Tobacco:

OW, D., DE WET, J., HELINSKI, D., HOWELL, S., WOOD, K., & DELUCA, M. (1986). Transient and Stable Expression of the Firefly Luciferase Gene in Plant Cells and Transgenic Plants Science, 234 (4778), 856-859 DOI: 10.1126/science.234.4778.856

Luciferase in Arabidopsis for tracing circadian rhythms:
Harmer SL, Hogenesch JB, Straume M, Chang HS, Han B, Zhu T, Wang X, Kreps JA, & Kay SA (2000). Orchestrated transcription of key pathways in Arabidopsis by the circadian clock. Science (New York, N.Y.), 290 (5499), 2110-3 PMID: 11118138

New Developments with Luciferase in the Pink Tentacle Blog

Review on Fluorescence in Molecular Biology:

Mavrakis M, Pourquié O, & Lecuit T (2010). Lighting up developmental mechanisms: how fluorescence imaging heralded a new era. Development (Cambridge, England), 137 (3), 373-87 PMID: 20081186

Luciferase and RNAi Diagnostics:
McCaffrey, A., Meuse, L., Pham, T., Conklin, D., Hannon, G., & Kay, M. (2002). Gene expression: RNA interference in adult mice Nature, 418 (6893), 38-39 DOI: 10.1038/418038a

Just noticed that Wiki has a list of proposed uses of bioluminescence here (just have to scroll down a bit). Some original ones include using luciferase trees to line highways and save on electricity. Crops that light up when they’re thirsty. Glow in the dark pets. etc.

(1 votes)

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Each year in early December, the Howard Hughes Medical Institute hosts a series of educational seminars, called the Holiday Lectures, in which researchers explain the very basic concepts of their work. The lectures make a great introduction to a topic, and all past lectures are available on the HHMI Biointeractive site or as DVDs for teachers to use in the classroom. This year’s Holiday Lecture was on viral outbreaks, but a few past lectures have been on topics more closely related to developmental biology.

The Biointeractive site also features short videos and animations related to each year’s lectures, and the 2006 Holiday Lecture series on “Potent Biology: Stem Cells, Cloning, and Regeneration” offers many interesting clips for use in teaching developmental biology or stem cell science. For example, there’s an 11 minute mini documentary in which Alejandro Sanchez Alvarado explains planarian regeneration.

On the animation section of the Biointeractive site you can find, among other things, a short explanation about creating embryonic stem cell lines, also from the 2006 Holiday Lectures.

Have a look the lists of videos and animations on the site. There are too many to all watch, but it’s worth looking around just to see what’s there, especially if you’re teaching introductory courses. There’s even an interactive transgenic fly lab on the site, and a museum!

(Screencaps used with permission.)

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