In vivo visual screen for dopaminergic Rab ⇿ LRRK2-G2019S interactions in Drosophila discriminates Rab10 from Rab3

LRRK2 mutations cause Parkinson’s, but the molecular link from increased kinase activity to pathological neurodegeneration remains undetermined. Previous in vitro assays indicate that LRRK2 substrates include at least 8 Rab GTPases. We have now examined this hypothesis in vivo in a functional, electroretinogram screen, expressing each Rab with/without LRRK2-G2019S in selected Drosophila dopaminergic neurons. Our screen discriminated Rab10 from Rab3. The strongest Rab/LRRK2-G2019S interaction is with Rab10; the weakest with Rab3. Rab10 is expressed in a different set of dopaminergic neurons from Rab3. Thus, anatomical and physiological patterns of Rab10 are related. We conclude that Rab10 is a valid substrate of LRRK2 in dopaminergic neurons in vivo. We propose that variations in Rab expression contribute to differences in the rate of neurodegeneration recorded in different dopaminergic nuclei in Parkinson’s

Co-expression Network Analysis of Diverse Wheat Landraces Reveals Marker of Early Thermotolerance and Candidate Master-regulator of Thermotolerance Genes

Bread wheat (Triticum aestivum L.) is a crop, relied on by billions of people around the world as a major source of both income and calories. Rising global temperatures, however, pose a genuine threat to the livelihood of these people, as wheat growth and yields are extremely vulnerable to damage by heat stress. Here we present the YoGI wheat landrace panel, comprised of 342 accessions which show remarkable phenotypic and genetic diversity thanks to their adaptation to different climates. We quantified the abundance of 110,790 transcripts from the panel and used these data to conduct weighted co-expression network analysis and identify hub genes in modules associated with abiotic stress tolerance. We found that the expression of three hub genes, all heat shock proteins (HSPs), were significantly correlated with early thermotolerance in a validation panel of landraces. These hub genes belonged to the same module, with one (TraesCS4D01G207500.1) likely regulating the expression of the other two hub genes, as well as a suite of other HSPs and heat stress transcription factors (Hsfs). In this work, therefore, we identify three validated hub genes, whose expression can serve as markers of thermotolerance during early development, and suggest that TraesCS4D01G207500.1 is a potential master regulator of HSP and Hsf expression – presenting the YoGI landrace panel as an invaluable tool for breeders wishing to determine and introduce novel alleles into modern varieties, for the production of climate-resilient crops

Oilfield in a box: The Hutton Field Dataset. British Geological Survey. (Dataset).

This data includes all of the information provided to British Geological Survey through the National Hydrocarbon Data Archive for the Hutton Field. It includes: Production data and a 3D seismic survey in addition to borehole records from 65 wells across the Hutton Field

Interaction of LRRK2-G2019S with Rab GTPases in vivo

Previously, we identified an excitotoxic mechanism by which expression of mutant forms of LRRK2 in the dopaminergic neurons increased visual signalling in young flies, followed by the complete loss of visual response in old flies. We used this assay to screen for Rabs which interact with LRRK2. Our top hit is Rab10. In young flies, expressing both Rab10 and LRRK2-G2019S increases the lamina neural response ~20 fold. These changes in the neural response are independent of photoreception. Knockdown of Rab10 ameliorates the neurodegeneration seen in the visual system of old flies expressing LRRK2-G2019S in their dopamine neurons. GFP expression/antibody staining suggests that the dopamine neurons innervating the visual system (lobes and lamina) and suboesophageal zone (controlling the proboscis extension response) are Rab10+, but in other dopamine neurons (e.g. those controlling sleep/wake/circadian patterns) Rab10 is undetectable. We therefore tested dopaminergic knockdown of Rab10 and found it rescues movement G2019S-induced deficits in the proboscis movement. Neither LRRK2-G2019S nor Rab10-RNAi affect the circadian pattern. In dopaminergic neurons, not all Rabs are equal: Rab3 and Rab32 (the fly homolog of Rab29) affect LRRK2 in other ways. Neither are found in visual neurons. We conclude that differences in neurodegeneration between groups of dopaminergic neurons may be the consequence of their palette of Rab proteins

Genome sequence and genetic diversity of European ash trees

Eurofins MWG provided a discounted service for Illumina and 454 sequencing of the reference genome, funded by Natural Environment Research Council (NERC) Urgency Grant NE/K01112X/1 to R.J.A.B. The associative transcriptomic and metabolomic work was part of the ‘Nornex’ project led by J.A.D. funded jointly by the UK Biotechnology and Biological Sciences Research Council (BBSRC) (BBS/E/J/000CA5323) and the Department for Environment, Food & Rural Affairs. The Earlham Institute, Norwich, UK, sequenced ‘Tree 35’ funded by ‘Nornex’ and the European Diversity Panel funded by the Earlham Institute National Capability in Genomics (BB/J010375/1) grant. W. Crowther assisted with DNA extractions for the KASP assay; The John Innes Centre contributed KASP analyses. J. F. Miranda assisted with RNA extractions and quantitative PCR with reverse transcription (qRT–PCR) at the University of York. H. V. Florance, N. Smirnoff and the Exeter Metabolomics Facility developed metabolomic methods and ran samples, and T. P. Howard helped with statistics. L.J.K. and R.J.A.B. were partly funded by Living with Environmental Change (LWEC) Tree Health and Plant Biosecurity Initiative - Phase 2 grant BB/L012162/1 to R.J.A.B., S.L. and P. Jepson funded jointly by a grant from the BBSRC, Defra, Economic and Social Research Council, the Forestry Commission, NERC and the Scottish Government, under the Tree Health and Plant Biosecurity Initiative. G.W. was funded by Teagasc Walsh Fellowship 2014001 to R.J.A.B. and G.C.D. E.D.C. was funded by a Marie Skłodowska-Curie Individual Fellowship ‘FraxiFam’ (grant agreement 660003) to E.D.C. and R.J.A.B. E.S.A.S. and J.Z. were funded by the Marie Skłodowska-Curie Initial Training Network INTERCROSSING. J.A.D. received a John Innes Foundation fellowship. We thank A. Joecker for supervising E.S.A.S. at Qiagen and for helpful discussions. R.H.R.G. is supported by a Norwich Research Park PhD Studentship and Earlham Institute Funding and Maintenance Grant. This research used Queen Mary’s MidPlus computational facilities, supported by QMUL Research-IT and funded by Engineering and Physical Sciences Research Council grant EP/K000128/1 and NERC EOS Cloud. D.J.S. acknowledges the support of BBSRC grant BB/N021452/1, which partly supported M.G., C.M.S. and D.J.S. during this work