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Papers to read
Good place to paste interesting papers, or group talk papers!
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# Web Link Hits
1   Link   2009: Single molecule sequencing of a human genome
Where next-gen sequencing is heading...
2   Link   The single kinin receptor signals to separate and independent physiological pathways in Malpighian tubules of the yellow fever mosquito
Latest from Beyenbach lab
3   Link   2010: Tumor suppressors Sav/scrib and oncogene ras regulate stem-cell transformation in adult Drosophila malpighian tubules
Latest on stem cells in tubules from the Hou lab
4   Link   Inhibition of tyramine signaling by cGMP in Drosophila Malpighian tubules
Argues that cGMP inhibits LK response
5   Link   The kinin receptor is expressed in the Malpighian tubule stellate cells in the mosquito Aedes aegypti (L.): A new model needed to explain ion transport?
Directly opposes Beyenbach's model for kinin action, and supports ours.
6   Link   Light sheet microscopy
This is a new form of microscopy that claims to offer advantages like spinning-disc : clearer than confocal, but with a fraction of the irradiation of your precious specimen.
7   Link   Interactions between detoxification mechanisms and excretion in Malpighian tubules of Drosophila melanogaster
Insects have long been known to excrete toxins via the Malpighian (renal) tubules. In addition, exposure to natural or synthetic toxins is commonly associated with increases in the activity of detoxification enzymes such as the P450 monoxygenases (P450s) and the glutathione-S-transferases (GSTs). We examined the links between mechanisms for detoxification and excretion in adult Drosophila melanogaster using functional assays and measurements of changes in gene expression by quantitative reverse transcriptase PCR in response to dietary exposure to compounds known to alter activity or gene expression of P450s and GSTs. Dietary exposure to phenol, which alters gene expression for multiple GSTs after seven to 10 generations, was also associated with an increase (more than twofold) in secretion of the organic anion methotrexate (MTX) by isolated tubules. Dietary exposure to the insecticide synergist piperonyl butoxide (PBO) was associated with reduced expression of two P450 genes (Cyp4e2, Cyp4p1) and two GST genes (GstD1, GstD5) in the tubules, as well as increased expression of Cyp12d1 and GstE1. Thin layer chromatographic analysis of fluid secreted by isolated tubules indicated that dietary exposure to PBO resulted in increased levels of an MTX metabolite. In addition, exposure to PBO altered the expression of transporter genes in the tubules, including a Drosophila multidrug resistance-associated protein, and was associated with a 73% increase in MTX secretion by isolated tubules. The results suggest that exposure of Drosophila to toxins evokes a coordinated response by the Malpighian tubules, involving both alterations in detoxification pathways as well as enhanced transport.
8   Link   Claudin-2 Forms Homodimers and Is a Component of a High Molecular Weight Protein Complex
Useful for folks working on junctions.
9   Link   Proximity ligation assay
This is a remarkable technique that allows proximity of native proteins (i.e. not epitope tagged or overexpressed)to be detected by a form of linear PCR. Two antibodies are tagged with secondaries with oligos attached, ligated together, and then PCR'ed.
10   Link   The best reference gene for qPCR is...
...alpha-tubulin. Told you so. It's another insect, but they compared males, females and midgut,. Malpighian tubules, so similar to us.
They also found that the very expensive geNorm software gave results indistinguishable from the free NormFinder (http://www.mdl.dk/publicationsnormfinder.htm).
11   Link   Differential transcription of cytochrome P450s and glutathione S transferases in DDT-susceptible and -resistant Drosophila melanogaster strains in response to DDT and oxidative stress
Asks the question are the responses to stressors similar or not?
12   Link   PhD of the day...
13   Link   High-Throughput Multiplex Sequencing to Discover Copy Number Variants in Drosophila
Suggests that 8% of Drosophila genes are duplicated (i.e. more than diploid), especially those involved in toxin response...like Cyp6g1.
14   Link   Drosophila Ras/MAPK signalling regulates innate immune responses in immune and intestinal stem cells
From the Boutros lab.
See also the commentary at:
15   Link   The Ussing chamber - a little bit of history
Now you know what that strange bit of perspex on the shelf of my office is for.
16   Link   GM mosquitoes in the news - and Nature
Very interesting - group talk, someone?
Nature article is in:
17   Link   Metabolomics, systems biology, toxicology in Drosophila
Systems-Scale Analysis Reveals Pathways Involved in Cellular Response to Methamphetamine
18   Link   DNA Sudoku!
For lots of applications, Next-gen sequencing is massive overkill. Rather than get 7 million reads of the same thing, it can be good to multiplex several reactions by using unique sequences in the primers (barcodes) for each template. However, this only works for up to a few dozen templates. DNA sudoku uses a clever system of multiple pools of DNA, that allows thousands of separate samples to be sequenced at once!
19   Link   Light sheet microscopy- the future of very expensive microscopy
20   Link   Insulin Production and Signaling in Renal Tubules of Drosophila Is under Control of Tachykinin-Related Peptide and Regulates Stress Resistance
The insulin-signaling pathway is evolutionarily conserved in animals and regulates growth, reproduction, metabolic homeostasis, stress resistance and life span. In Drosophila seven insulin-like peptides (DILP1-7) are known, some of which are produced in the brain, others in fat body or intestine. Here we show that DILP5 is expressed in principal cells of the renal tubules of Drosophila and affects survival at stress. Renal (Malpighian) tubules regulate water and ion homeostasis, but also play roles in immune responses and oxidative stress. We investigated the control of DILP5 signaling in the renal tubules by Drosophila tachykinin peptide (DTK) and its receptor DTKR during desiccative, nutritional and oxidative stress. The DILP5 levels in principal cells of the tubules are affected by stress and manipulations of DTKR expression in the same cells. Targeted knockdown of DTKR, DILP5 and the insulin receptor dInR in principal cells or mutation of Dilp5 resulted in increased survival at either stress, whereas over-expression of these components produced the opposite phenotype. Thus, stress seems to induce hormonal release of DTK that acts on the renal tubules to regulate DILP5 signaling. Manipulations of S6 kinase and superoxide dismutase (SOD2) in principal cells also affect survival at stress, suggesting that DILP5 acts locally on tubules, possibly in oxidative stress regulation. Our findings are the first to demonstrate DILP signaling originating in the renal tubules and that this signaling is under control of stress-induced release of peptide hormone
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