Some recent lab journal clubs

It’s been a while since I updated on our regular lab journal clubs (I’ll blame grants and paper writing). So here are a few of the papers we’ve discussed in recent weeks. Although they each tackle a different research question, they highlight the versatility of Drosophila genetics to uncover key mechanisms governing animal physiology – the power and simplicity of the Drosophila genetic toolkit, means that the only major limitations to discovery are our ideas. Each of these papers has some very clever ideas.

Muscle mitohormesis promotes longevity via systemic repression of insulin signaling. Owusu-Ansah E, Song W, Perrimon N. Cell. 2013 Oct 24;155(3):699-712.

A very nice paper showing how limited mitochondrial stress in adult Drosophila muscle can extend lifespan, in part by limiting systemic insulin signaling.

 

Cell-nonautonomous effects of dFOXO/DAF-16 in aging. Alic N, Tullet JM, Niccoli T, Broughton S, Hoddinott MP, Slack C, Gems D, Partridge L. Cell Rep. 2014 Feb 27;6(4):608-16.

A clever study delineating the differential non-autonmous requirements for FOXO on controlling lifespan and metabolism in adult flies

 

Sensing of amino acids in a dopaminergic circuitry promotes rejection of an incomplete diet in Drosophila. Bjordal M, Arquier N, Kniazeff J, Pin JP, Léopold P. Cell. 2014 Jan 30;156(3):510-21

A paper that elegantly combines genetics, behavioural measurements and neural imaging to identify a role for the AA-regulate kinase GCN2 in the neuronal and behavioral response to limitation of dietary amino acids

 

Changes in rRNA transcription influence proliferation and cell fate within a stem cell lineage. Zhang Q, Shalaby NA, Buszczak M. Science. 2014 Jan 17;343(6168):298-301

This paper adds to a growing literature that points to the importance of differential regulation of mRNA translation and protein synthesis in controlling the behaviour of stem cells. The importance of this paper is that it suggests that rRNA synthesis and Pol I function may be an important control point in the regulation of stem cell protein synthesis.

Lab Journal Club: A holidic diet for Drosophila Melanogaster

In our last lab journal club, we discussed the recent paper from Matt Piper (@piperlab) (along with the Ribeiro (@RibeiroLab), Partridge and Pletcher labs) in which they define a holidic diet for Drosophila research:

A holidic medium for Drosophila Melanogaster (2013) Nat Methods

Variations in fly food between different labs (and even within labs) can profoundly influence organismal phenotypes, particularly behavioural, lifespan and stress responses. So, this very nice, meticulous paper provides an important, defined set of dietary conditions upon which to carry out these type of experiments.

As larval growth researchers, we were particularly interested in the finding that on the holidic diet, larvae took several days longer to pupate than on a ‘normal’ yeast/sugar-based food. Moreover, this delayed development could be abrogated by adding a small amount of yeast extract to the holidic diet. So what is the magic yeast ingredient?  A gustatory cue? An olfactory cue?  – (given the recent paper from the Banerjee lab – coming up next on lab journal club – on how olfactory cues can influence physiological responses in larvae). Also Or83B (olfactory receptor) mutant larvae show a (modest) delay in development, which is more pronounced when they have to compete with wildtype flies to forage for food (from – Vosshall lab @pollyp1)

Lab Journal Club: Diet-induced insulin resistance and tumors in Drosophila

In a recent journal club, we discussed a paper from the Cagan lab: Transformed Drosophila cells evade diet-mediated insulin resistance through wingless signaling.

This paper continues with a theme from a previous lab journal club and describes how diet-induced changes in fly physiology can influence localized imaginal tissue growth caused by altered oncogene/tumor suppressor signaling pathways. Here, the Cagan lab show that rasv12/csk- clones  show little or no growth phenotype in flies fed their ‘standard’ lab diet, but on a high sugar diet, these clones show massive overgrowth and invasive behaviour. The authors go on to show that this high sugar-phenotype can be explained in part by elevated Wg signaling in the rsv12/csk- cells, which leads to increased expression of the fly insulin receptor (InR) and increased insulin/PI3K signaling. Given that InR is also a transcriptional target of FOXO, we wondered whether some of the phenotype in RasV12/csk- may be explained by interactions with PI3K-FOXO signaling.

 

We liked this paper, which like the previous PTEN paper, is built upon an interesting finding that diet can interact with genotype to influence tissue growth. These two papers in particular illustrate the utility and power of fly genetics to explore how the micro and macro–environment can influence tissue growth.

This weeks lab journal club: nutrient restriction and PTEN-regulated growth, @elife

For our first journal club after the summer we picked an interesting paper from Hugo Stocker and co:

“Nutrient restriction enhances the proliferative potential of cells lacking the tumor suppressor PTEN in mitotic tissues”  published in elife.

The paper describes the interesting behaviour of pten mutant imaginal disc cells under different dietary protein (yeast) conditions. In rich food (high yeast) pten mutant cells overgrow compared to neighboring wild-type cells (which was already known). However, under nutrient-restricted conditions (low yeast) , the pten cells show massive overgrowth and a strong proliferative advantage versus their wildtype neighbours. This over-poliferation requires amino acid import and TOR signaling, but appears distinct from the cell competition and supercompetitor effects of factors such as Myc (e.g. see Moreno and Basler or De La Cova et al). Interestingly, under nutrient restrictive conditions the overgrowth of pten mutant cell clones in the eye disc triggered a systemic growth impairment  (other tissues such as the wing and fat body were smaller – although marginally so)

We liked this paper a lot. A few quick comments and thoughts that we tried to wrap our heads around:

– Do PTEN cells actively upregulate their AA or nutrient import under nutrient-deprivation conditions? It would be interesting (although difficult) to measure nutrient uptake in pten cells to see if they actively switch (upregulate) to ‘nutrient scavenging mode’ upon a switch to poor food, or whether their basal level of nutrient uptake is already high under rich food and just remains so when nutrients are scarce.

-what underlies the switch from hypertrophic growth (rich nutrients) to hyperplastic growth (poor nutrients) in pten cell clones? Is it simply due to increased cellular nutrient import? Or is there some ‘organ-level’ control of growth?

– What underlies the systemic growth impairment? Is it the case that the pten cells are very efficient at nutrient and growth factor ‘scavenging’ that growth in other tissues is reduced? The systemic growth impairment didn’t appear marked, so this ‘scavenging’ explanation may be right. Alternatively, is there some kind of signaling triggered by pten cells that induces a systemic endocrine response – similar to dilp8 release from damaged discs, which influences ecdysone release and whole body development (Colombani et al , Carelli et al)

– what about tsc1 mutant cells? they have overactive TOR signaling – would they phenocopy the pten cells with respect to growth in rich vs poor food? The editor/reviewer comments did suggest that the authors address this, and intriguingly, in their response, the authors indicated that the experiments were done but that the story was ‘rather complex’ – we look forward to hearing about this complex story.

Finally, we enjoyed reading the paper in elife, especially with the transparent reviewer comments and author responses. All journals should adopt this policy.

This week’s lab journal club: CRISPR/Cas9 mutagenesis in Drosophila

This week we finally got around to talking about the recent CRISPR/Cas9 papers in Drosophila. We mostly focused on Bassett et al, but also discussed Gratz et al.

Like other Drosophila researchers we’ve talked to, we are excited by these techniques and we can’t wait to try them out in the lab (Our new postdoc, Byoungchun Lee will be doing a lot of the work here) – CRISPR/Cas9-mediated mutagenesis will very likely develop into a “must-have” genetic technique for model organism labs.

Questions/comments we had: We mostly talked about how we would use this technique for our lab, with our favorite genes. In the Bassett et al paper the efficiency and frequency of mutagenesis for y and w looked good (although there was a high level of lethality – even in the non-injected controls ?!). But will this high efficiency hold true for all genes? Will genomic/chromatin context matter? (some of our favorite genes are in heterochromatic regions) Also, what’s the most efficient fly injecting/crossing scheme to generate stable mutant stocks (especially if the mutation efficiency ends up being quite low for some genes)? Finally, we’re interested to see how well the combination of CRISPR/Cas9 with donor oligos can be used to engineer specific alterations in our favourite genes. Gratz et al did a great job of using the approach to introduce attP sites into yellow, and presumably a similar approach can be used to introduce specific nucleotide substitutions into our favourite genes (e.g. to generate serine-to-alanine mutations at known phosphorylation sites).

Overall, two great papers. Exciting times ahead for fly genetics!

This weeks Lab Journal Club..Mlx-Mondo transcriptional regulation and sugar tolerance in larvae

This week in JC we discussed a recent paper on high sugar tolerance in larvae from the Hietakangas lab:

Mondo/ChREBP-Mlx-regulated transcriptional network is essential for dietary sugar tolerance in Drosophila. Havula E, Teesalu M, Hyötyläinen T, Seppälä H, Hasygar K, Auvinen P, Orešič M, Sandmann T, Hietakangas V. PLoS Genet. 2013 Apr;9(4):e1003438.

The paper describes how the Mlx-Mondo transcriptional complex is required for larvae to tolerate a high sugar diet –  Mlx mutants can develop to pupae on normal food, but show reduced larval growth and fail to pupate on a high sugar diet. The paper goes on to describe alterations in carbohydrate and lipid metabolism that may account for the high sugar sensitivity in mlx mutants. In particular, two targets of Mondo-Mlx – the transcription factor cabut and the detoxifying enzyme Aldehyde dehydrogenase type III  – are required for high sugar tolerance.

Overall, we liked this paper. We think a lot about how dietary protein can influence larval growth via insulin/TOR signaling. But clearly alterations in dietary sugar, and probably changes in the ratio of sugar: protein, can have important effects on larval physiology and growth.

Questions we had: How do larvae sense and respond to high sugar? via changes in insulin signaling? (see Pasco and Leopold, 2012). Does Mondo-Mlx transcriptional activity respond to changes in diet and/or insulin signaling? (increased expression? increased DNA localization?). Do Mondo-Mlx mutants show altered responses to dietary amino acids and do alterations in the relative balance of dietary sugar: protein influence larval growth?

This weeks lab journal club

We usually pick recent papers, but occasionally we’ll discuss older papers that we may have missed or that have become relevant to our research.

This week we discussed a 2008 Genes Dev paper from the Calvi lab: Endocycling cells do not apoptose in response to DNA rereplication genotoxic stress (picked By Mahsa) – Free access:

http://genesdev.cshlp.org/content/22/22/3158.full.pdf+html

Calvi et al describe how re-replication (triggered by overexpression of Dup, double-parked) can induce DNA damage in both mitotic and endocycling cells, but only the mitotic cells die. They suggest that the pro-apoptotic genes (hid, grim, reaper) maybe silenced in endoreplicating cells and hence cannot be upregulated by DNA damage cues (Chk2- and p53-dependent). Overall we found this to be an interesting paper. Questions that came up: Why don’t endoreplicating cells die? Can larval endocycling cells tolerate DNA damage and still function? What is the silencing mechanism operating in endoreplicating cells? Why do different endocycling cells behave differently (e.g. hs/gal4-expression of propapoptic genes killed salivary gland cells but had no effect on fat body cells)?

Lab Journal Club

Every couple of weeks we have a lab journal club in which we discuss, comment, critique and enjoy (usually!) recent papers in our field. I’ll update with new papers as we discuss them. But here are some of the papers we’ve discussed (and usually liked) over the last year or so:

Biochemical membrane lipidomics during Drosophila development.

Guan XL, Cestra G, Shui G, Kuhrs A, Schittenhelm RB, Hafen E, van der Goot FG, Robinett CC, Gatti M, Gonzalez-Gaitan M, Wenk MR.Dev Cell. 2013 Jan 14;24(1):98-111.

dMyc expression in the fat body affects DILP2 release and increases the expression of the fat desaturase Desat1 resulting in organismal growth.

Parisi F, Riccardo S, Zola S, Lora C, Grifoni D, Brown LM, Bellosta P.Dev Biol. 2013 Apr 19

A histone mutant reproduces the phenotype caused by loss of histone-modifying factor Polycomb.

Pengelly AR, Copur Ö, Jäckle H, Herzig A, Müller J. Science. 2013 Feb 8;339(6120):698-9.

 

Transcription in the absence of histone H3.2 and H3K4 methylation.

Hödl M, Basler K.Curr Biol. 2012 Dec 4;22(23):2253-7

 

The oscillating miRNA 959-964 cluster impacts Drosophila feeding time and other circadian outputs.

Vodala S, Pescatore S, Rodriguez J, Buescher M, Chen YW, Weng R, Cohen SM, Rosbash M.  Cell Metab. 2012 Nov 7;16(5):601-12.

 

A secreted decoy of InR antagonizes insulin/IGF signaling to restrict body growth in Drosophila.

Okamoto N, Nakamori R, Murai T, Yamauchi Y, Masuda A, Nishimura T. Genes Dev. 2013 Jan 1;27(1):87-97.

 

Drosophila cytokine unpaired 2 regulates physiological homeostasis by remotely controlling insulin secretion.

Rajan A, Perrimon N. Cell. 2012 Sep 28;151(1):123-37

 

Intramyocellular fatty-acid metabolism plays a critical role in mediating responses to dietary restriction in Drosophila melanogaster.

Katewa SD, Demontis F, Kolipinski M, Hubbard A, Gill MS, Perrimon N, Melov S, Kapahi P.Cell Metab. 2012 Jul 3;16(1):97-103 

 

Conserved microRNA miR-8 controls body size in response to steroid signaling in Drosophila.

Jin H, Kim VN, Hyun S.Genes Dev. 2012 Jul 1;26(13):1427-32.

 

Insulin/IGF signaling drives cell proliferation in part via Yorkie/YAP.

Straßburger K, Tiebe M, Pinna F, Breuhahn K, Teleman AA. Dev Biol. 2012 Jul 15;367(2):187-96.

 

Secreted peptide Dilp8 coordinates Drosophila tissue growth with developmental timing.

Colombani J, Andersen DS, Léopold P. Science. 2012 May 4;336(6081):582-5.

 

Imaginal discs secrete insulin-like peptide 8 to mediate plasticity of growth and maturation.

Garelli A, Gontijo AM, Miguela V, Caparros E, Dominguez M. Science. 2012 May 4;336(6081):579-82

 

Direct sensing of systemic and nutritional signals by haematopoietic progenitors in Drosophila.

Shim J, Mukherjee T, Banerjee U. Nat Cell Biol. 2012 Mar 11;14(4):394-400.

 

Insulin signaling regulates fatty acid catabolism at the level of CoA activation.

Xu X, Gopalacharyulu P, Seppänen-Laakso T, Ruskeepää AL, Aye CC, Carson BP, Mora S, Orešič M, Teleman AA. PLoS Genet. 2012 Jan;8(1):

 

FOXO regulates organ-specific phenotypic plasticity in Drosophila.

Tang HY, Smith-Caldas MS, Driscoll MV, Salhadar S, Shingleton AW. PLoS Genet. 2011 Nov;7(11)

 

Enteric neurons and systemic signals couple nutritional and reproductive status with intestinal homeostasis.

Cognigni P, Bailey AP, Miguel-Aliaga I. Cell Metab. 2011 Jan 5;13(1):92-104.