A novel GUCY2D mutation, V933A, causes central areolar choroidal dystrophy

Purpose: To identify the genetic cause of central areolar choroidal dystrophy (CACD) in a large Northern Irish family.
Methods: We previously reported linkage of the locus for CACD in this family to an interval of approximately 5 cM on chromosome 17p13 flanked by polymorphic markers D17S1810 and CHLC GATA7B03. We undertook sequence capture, massively-parallel sequencing and computational alignment, base-calling and annotation to identify a causative mutation. Conventional sequencing was used to confirm the results.
Results: Deep sequencing identified a single-base substitution in guanylate cyclase 2D, membrane (retina-specific) (GUCY2D). The novel mutation segregated with the disease phenotype and resulted in substitution of valine by alanine at position 933, within the catalytic domain of the protein. It altered a motif that is strongly conserved in a large number of distantly related proteins across several species, and was predicted to have a damaging effect on protein activity.
Conclusion: Mutations in GUCY2D have previously been associated with dominant cone rod dystrophies (CORD6) and recessive forms of Leber's congenital amaurosis (LCA). This is the first report of GUCY2D mutation causing CACD and adds to our understanding of genotype-phenotype correlation in this heterogeneous group of choroidoretinal dystrophies.

Association Testing of Previously Reported Variants in a Large Case-Control Meta-analysis of Diabetic Nephropathy

We formed the GEnetics of Nephropathy–an International Effort (GENIE) consortium to examine previously reported genetic associations with diabetic nephropathy (DN) in type 1 diabetes. GENIE consists of 6,366 similarly ascertained participants of European ancestry with type 1 diabetes, with and without DN, from the All Ireland-Warren 3-Genetics of Kidneys in Diabetes U.K. and Republic of Ireland (U.K.-R.O.I.) collection and the Finnish Diabetic Nephropathy Study (FinnDiane), combined with reanalyzed data from the Genetics of Kidneys in Diabetes U.S. Study (U.S. GoKinD). We found little evidence for the association of the EPO promoter polymorphism, rs161740, with the combined phenotype of proliferative retinopathy and end-stage renal disease in U.K.-R.O.I. (odds ratio [OR] 1.14, P = 0.19) or FinnDiane (OR 1.06, P = 0.60). However, a fixed-effects meta-analysis that included the previously reported cohorts retained a genome-wide significant association with that phenotype (OR 1.31, P = 2 × 10-9). An expanded investigation of the ELMO1 locus and genetic regions reported to be associated with DN in the U.S. GoKinD yielded only nominal statistical significance for these loci. Finally, top candidates identified in a recent meta-analysis failed to reach genome-wide significance. In conclusion, we were unable to replicate most of the previously reported genetic associations for DN, and significance for the EPO promoter association was attenuated.

Investigating Hydraulically Active Fractures in A Shallow Meta-Sedimentary Bedrock Aquifer Using Single Well Tracer Testing, Mount Stewart, Northern Ireland

Knowledge of groundwater flow/mass transport, in poorly productive aquifers which underlie over 65% of the island of Ireland, is necessary for effective management of catchment water quality and aquatic ecology. This research focuses on a fractured low-grade Ordovician/Silurian greywacke sequence which underlies approximately 25% of the northern half of Ireland. Knowledge of the unit’s hydrogeological properties remain largely restricted to localised single well open hole “transmissivity” values. Current hydrogeological conceptual models of the Greywacke view the bulk of groundwater flowing through fractures in an otherwise impermeable bedrock mass.
Core analysis permits fracture characterisation, although not all identified fractures may be involved in groundwater flow. Traditional in-situ hydraulic characterisation relies on cumbersome techniques such as packer testing or geophysical borehole logging (e.g. flowmeters). Queen’s University Belfast is currently carrying out hydraulic characterization of 16 boreholes at its Greywacke Hydrogeological Research Site at Mount Stewart, Northern Ireland.
Development of dye dilution methods, using a recently-developed downhole fluorometer, provided a portable, user-friendly, and inexpensive means of detecting hydraulically active intervals in open boreholes. Measurements in a 55m deep hole, three days following fluorescent dye injection, demonstrated the ability of the technique to detect two discrete hydraulically active intervals corresponding to zones identified by caliper and heat-pulse flowmeter logs. High resolution acoustic televiewer logs revealed the zones to correspond to two steeply dipping fractured intervals. Results suggest the rock can have effective porosities of the order of 0.1%.
Study findings demonstrate dye dilution’s utility in characterizing groundwater flow in fractured aquifers. Tests on remaining holes will be completed at different times following injection to identify less permeable fractures and develop an improved understanding of the structural controls on groundwater flow in the uppermost metres of competent bedrock.

Using solute/ micro organism comparative tracer testing to investigate hydrogeological heterogeneity in a fluvioglacial sand and gravel aquifer.

Groundwater drawn from fluvioglacial sand and gravel aquifers form the principal source of drinking water in many part of central Western Europe. High population densities and widespread organic agriculture in these same areas constitute hazards that may impact the microbiological quality of many potable supplies. Tracer testing comparing two similarly sized bacteria (E.coli and P. putida) and the smaller bacteriophage (H40/1) with the response of non-reactive solute tracer (uranine) at the decametre scale revealed that all tracers broke through up to 100 times more quickly than anticipated using conventional rules of thumb. All microbiological tracer responses were less disperse than the solute, although bacterial peak relative concentrations consistently exceeded those of the solute tracer at one sampling location reflecting exclusion processes influencing micro biological tracer migration. Relative recoveries of H40/1 and E.coli proved consistent at both monitoring wells, while responses of H40/1 and P.putida differed. Examination of exposures of the upper reaches of the aquifer in nearby sand and gravel quarries revealed the aquifer to consist of laterally extensive layers of open framework (OW) gravel enveloped in finer grained gravelly sand. Granulometric analysis of these deposits suggested that the OW gravel was up to two orders of magnitude more permeable than the surrounding deposits giving rise to the preferential flow paths. By contrast fine grained lenses of silty sand within the OW gravels are suspected to play an important role in the exclusion processes that permit solutes to access them but exclude larger micro organisms.

Analysis of alteration of p75NTR processing and signalling by PS2 mutation and gamma-secretase inhibition

The presenilins (PSs) were identified as causative genes in cases of early-onset familial Alzheimer's disease (AD) and current evidence indicates that PSs are part of the gamma-secretase complex responsible for proteolytic processing of type I membrane proteins. p75NTR, a common neurotrophin receptor, was shown to be subject to gamma-secretase processing. However, it is not clear if the p75NTR downstream signal is altered in response to gamma-secretase cleavage, and further there is a possibility that AD-related PS mutations may affect this cleavage, resulting in pathogenic alterations in signal transduction. In this study, we confirmed that p75NTR downstream signalling is altered by PS2 mutation or gamma-secretase inhibition in SHSY-5Y cells. The activity of the small GTPase RhoA is strongly affected by these treatments. This study demonstrates that gamma-secretase and PS2 play an important role in regulating neurotrophin signal transduction and either mutation of PS2 or inhibition of gamma-secretase disturbs this function.

Autosomal dominant Alport syndrome caused by a COL4A3 splice site mutation

Alport syndrome (AS) is a clinically and genetically heterogeneous renal disorder, predominantly affecting the type IV collagen alpha 3/alpha 4/alpha 5 network of the glomerular basement membrane (GBM). AS can be caused by mutations in any of the three genes encoding these type IV collagen chains. The majority of AS families (85%) are X-linked (XL-AS) involving mutations in the COL4A5 gene. Mutations in the COL4A3 and COL4A4 genes cause autosomal recessive AS (AR-AS), accounting for approximately 14% of the cases. Recently, autosomal dominant AS (AD-AS) was linked to the COL4A3/COL4A4 locus in a large family.

Testing the Prebish-Singer hypothesis using second-generation panel data stationarity tests with a break

In this paper, we test the Prebish-Singer (PS) hypothesis, which states that real commodity prices decline in the long run, using two recent powerful panel data stationarity tests accounting for cross-sectional dependence and a structural break. We find that the hypothesis cannot be rejected for most commodities other than oil.