Australia and New Zealand renal gene panel testing in routine clinical practice of 542 families

Genetic testing in nephrology clinical practice has moved rapidly from a rare specialized test to routine practice both in pediatric and adult nephrology. However, clear information pertaining to the likely outcome of testing is still missing. Here we describe the experience of the accredited Australia and New Zealand Renal Gene Panels clinical service, reporting on sequencing for 552 individuals from 542 families with suspected kidney disease in Australia and New Zealand. An increasing number of referrals have been processed since service inception with an overall diagnostic rate of 35%. The likelihood of identifying a causative variant varies according to both age at referral and gene panel. Although results from high throughput genetic testing have been primarily for diagnostic purposes, they will increasingly play an important role in directing treatment, genetic counseling, and family planning

Beta Cell Hubs Dictate Pancreatic Islet Responses to Glucose

N.R.J. was supported by a Diabetes UK RW and JM Collins Studentship (12/0004601). J.B. was supported by a European Foundation for the Study of Diabetes (EFSD) Albert Renold Young Scientist Fellowship and a Studienstiftung des deutschen Volkes PhD Studentship. D.T. was supported by an Advanced Grant from the European Research Commission (268795). G.A.R. was supported by Wellcome Trust Senior Investigator (WT098424AIA) and Royal Society Wolfson Research Merit Awards, and by MRC Programme (MR/J0003042/1), Biological and Biotechnology Research Council (BB/J015873/1), and Diabetes UK Project (11/0004210) grants. G.A.R. and M.W. acknowledge COST Action TD1304 Zinc-Net. D.J.H. was supported by Diabetes UK R.D. Lawrence (12/0004431), EFSD/Novo Nordisk Rising Star and Birmingham Fellowships, a Wellcome Trust Institutional Support Award, and an MRC Project Grant (MR/N00275X/1) with G.A.R. D.J.H and G.A.R. were supported by Imperial Confidence in Concept (ICiC) Grants. J.F. was supported by an MRC Programme grant (MR/L02036X/1). L.P. provided human islets through collaboration with the Diabetes Research Institute, IRCCS San Raffaele Scientific Institute (Milan), within the European islet distribution program for basic research supported by JDRF (1-RSC-2014-90-I-X). P.M. and M.B. were supported by the Innovative Medicine Initiative Joint Undertaking under grant agreement no. 155005 (IMIDIA), resources of which are composed of financial contribution from the European Union’s Seventh Framework Programme (FP7/2007-2013) and EFPIA companies in kind contribution, and by the Italian Ministry of University and Research (PRIN 2010-2012). D.B. and E.B. provided human islets through the European Consortium for Islet Transplantation sponsored by JDRF (1-RSC-2014-100-I-X)

The Loss of Species: Mangrove Extinction Risk and Geographic Areas of Global Concern

Mangrove species are uniquely adapted to tropical and subtropical coasts, and although relatively low in number of species, mangrove forests provide at least US $1.6 billion each year in ecosystem services and support coastal livelihoods worldwide. Globally, mangrove areas are declining rapidly as they are cleared for coastal development and aquaculture and logged for timber and fuel production. Little is known about the effects of mangrove area loss on individual mangrove species and local or regional populations. To address this gap, species-specific information on global distribution, population status, life history traits, and major threats were compiled for each of the 70 known species of mangroves. Each species' probability of extinction was assessed under the Categories and Criteria of the IUCN Red List of Threatened Species. Eleven of the 70 mangrove species (16%) are at elevated threat of extinction. Particular areas of geographical concern include the Atlantic and Pacific coasts of Central America, where as many as 40% of mangroves species present are threatened with extinction. Across the globe, mangrove species found primarily in the high intertidal and upstream estuarine zones, which often have specific freshwater requirements and patchy distributions, are the most threatened because they are often the first cleared for development of aquaculture and agriculture. The loss of mangrove species will have devastating economic and environmental consequences for coastal communities, especially in those areas with low mangrove diversity and high mangrove area or species loss. Several species at high risk of extinction may disappear well before the next decade if existing protective measures are not enforced

The use of phylogeny to interpret cross-cultural patterns in plant use and guide medicinal plant discovery: an example from Pterocarpus (Leguminosae)

The study of traditional knowledge of medicinal plants has led to discoveries that have helped combat diseases and improve healthcare. However, the development of quantitative measures that can assist our quest for new medicinal plants has not greatly advanced in recent years. Phylogenetic tools have entered many scientific fields in the last two decades to provide explanatory power, but have been overlooked in ethnomedicinal studies. Several studies show that medicinal properties are not randomly distributed in plant phylogenies, suggesting that phylogeny shapes ethnobotanical use. Nevertheless, empirical studies that explicitly combine ethnobotanical and phylogenetic information are scarce.In this study, we borrowed tools from community ecology phylogenetics to quantify significance of phylogenetic signal in medicinal properties in plants and identify nodes on phylogenies with high bioscreening potential. To do this, we produced an ethnomedicinal review from extensive literature research and a multi-locus phylogenetic hypothesis for the pantropical genus Pterocarpus (Leguminosae: Papilionoideae). We demonstrate that species used to treat a certain conditions, such as malaria, are significantly phylogenetically clumped and we highlight nodes in the phylogeny that are significantly overabundant in species used to treat certain conditions. These cross-cultural patterns in ethnomedicinal usage in Pterocarpus are interpreted in the light of phylogenetic relationships.This study provides techniques that enable the application of phylogenies in bioscreening, but also sheds light on the processes that shape cross-cultural ethnomedicinal patterns. This community phylogenetic approach demonstrates that similar ethnobotanical uses can arise in parallel in different areas where related plants are available. With a vast amount of ethnomedicinal and phylogenetic information available, we predict that this field, after further refinement of the techniques, will expand into similar research areas, such as pest management or the search for bioactive plant-based compounds

Hadley circulation and precipitation changes control black shale deposition in the Late Jurassic Boreal Seaway

New climate simulations using the HadCM3L model with a paleogeography of the Late Jurassic [155.5 Ma], and proxy-data corroborate that warm and wet tropical-like conditions reached as far north as the UK sector of the Jurassic Boreal Seaway [~35oN]. This is associated with a northern hemisphere Jurassic Hadley cell and an intensified subtropical jet which both extend significantly polewards than in the modern (July-September). Deposition of the Kimmeridge Clay Formation [KCF] occurred in the shallow, storm-dominated, epeiric Boreal Seaway. High resolution paleo-environmental proxy data from the Kimmeridge Clay Formation [KCF; ~155–150 Ma], UK are used to test for the role of tropical atmospheric circulation on meter-scale heterogeneities in black shale deposition. Proxy and model data show that the most organic-rich section [eudoxus to mid-hudlestoni zones] is characterised by a positive δ13Corg excursion and up to 37 wt% total organic carbon [%TOC]. Orbital-modulation of organic carbon burial primarily in the long eccentricity power band combined with a clear positive correlation between %TOC carbonate-free and the kaolinite/illite ratio supports peak organic carbon burial under the influence of very humid climate conditions, similar to the modern tropics. This re-interpretation of large-scale climate relationships, supported by independent modelling and geological data, has profound implications for atmospheric circulation patterns and processes affecting marine productivity and organic carbon burial further north along the Boreal Seaway, including the Arctic

Massively parallel sequencing and targeted exomes in familial kidney disease can diagnose underlying\ua0genetic disorders

Inherited kidney disease encompasses a broad range of disorders, with both multiple genes contributing to specific phenotypes and single gene defects having multiple clinical presentations. Advances in sequencing capacity may allow a genetic diagnosis for familial renal disease, by testing the increasing number of known causative genes. However, there has been limited translation of research findings of causative genes into clinical settings. Here, we report the results of a national accredited diagnostic genetic service for familial renal disease. An expert multidisciplinary team developed a targeted exomic sequencing approach with ten curated multigene panels (207 genes) and variant assessment individualized to the patient's phenotype. A genetic diagnosis (pathogenic genetic variant[s]) was identified in 58 of 135 families referred in two years. The genetic diagnosis rate was similar between families with a pediatric versus adult proband (46% vs 40%), although significant differences were found in certain panels such as atypical hemolytic uremic syndrome (88% vs 17%). High diagnostic rates were found for Alport syndrome (22 of 27) and tubular disorders (8 of 10), whereas the monogenic diagnostic rate for congenital anomalies of the kidney and urinary tract was one of 13. Quality reporting was aided by a strong clinical renal and genetic multidisciplinary committee review. Importantly, for a diagnostic service, few variants of uncertain significance were found with this targeted, phenotype-based approach. Thus, use of targeted massively parallel sequencing approaches in inherited kidney disease has a significant capacity to diagnose the underlying genetic disorder across most renal phenotypes