Multiplex genotyping system for efficient inference of matrilineal genetic ancestry with continental resolution

Abstract Background: In recent years, phylogeographic studies have produced detailed knowledge on the worldwide distribution of mitochondrial DNA (mtDNA) variants, linking specific clades of the mtDNA phylogeny with certain geographic areas. However, a multiplex genotyping system for the detection of the mtDNA haplogroups of major continental distribution that would be desirable for efficient DNA-based bio-geographic ancestry testing in various applications is still missing. Results: Three multiplex genotyping assays, based on single-base primer extension technology, were developed targeting a total of 36 coding-region mtDNA variants that together differentiate 43 matrilineal haplo-/paragroups. These include the major diagnostic haplogroups for Africa, Western Eurasia, Eastern Eurasia and Native America. The assays show high sensitivity with respect to the amount of template DNA: successful amplification could still be obtained when using as little as 4 pg of genomic DNA and the technology is suitable for medium-throughput analyses. Conclusions: We introduce an efficient and sensitive multiplex genotyping system for bio-geographic ancestry inference from mtDNA that provides resolution on the continental level. The method can be applied in forensics, to aid tracing unknown suspects, as well as in population studies, genealogy and personal ancestry testing. For more complete inferences of overall bio-geographic ancestry from DNA, the mtDNA system provided here can be combined with multiplex systems for suitable autosomal and, in the case of males, Y-chromosomal ancestrysensitive DNA markers

Global Mapping of Citizen Science Projects for Disaster Risk Reduction

Citizen science for disaster risk reduction (DRR) holds huge promise and has demonstrated success in advancing scientific knowledge, providing early warning of hazards, and contributed to the assessment and management of impacts. While many existing studies focus on the performance of specific citizen science examples, this paper goes beyond this approach to present a systematic global mapping of citizen science used for DRR in order to draw out broader insights across diverse methods, initiatives, hazards and country contexts. The systematic mapping analyzed a total of 106 cases of citizen science applied to DRR across all continents. Unlike many existing reviews of citizen science initiatives, relevance to the disaster risk context led us to ‘open up’ our mapping to a broader definition of what might constitute citizen science, including participatory research and narrative-based approaches. By taking a wider view of citizen science and opening up to other disciplinary practices as valid ways of knowing risks and hazards, we also capture these alternative examples and discuss their relevance for aiding effective decision-making around risk reduction. Based on this analysis we draw out lessons for future research and practice of citizen science for DRR including the need to: build interconnections between disparate citizen science methods and practitioners; address multi-dimensionality within and across hazard cycles; and develop principles and frameworks for evaluating citizen science initiatives that not only ensure scientific competence but also attend to questions of equity, responsibility and the empowerment of those most vulnerable to disaster risk

An efficient multiplex genotyping approach for detecting the major worldwide human Y-chromosome haplogroups

The Y chromosome is paternally inherited and therefore serves as an evolutionary marker of patrilineal descent. Worldwide DNA variation within the non-recombining portion of the Y chromosome can be represented as a monophyletic phylogenetic tree in which the branches (haplogroups) are defined by at least one SNP. Previous human population genetics research has produced a wealth of knowledge about the worldwide distribution of Y-SNP haplogroups. Here, we apply previous and very recent knowledge on the Y-SNP phylogeny and Y-haplogroup distribution by introducing two multiplex genotyping assays that allow for the hierarchical detection of 28 Y-SNPs defining the major worldwide Y haplogroups. PCR amplicons were kept small to make the method sensitive and thereby applicable to DNA of limited amount and/or quality such as in forensic settings. These Y-SNP assays thus form a valuable tool for researchers in the fields of forensic genetics and genetic anthropology to infer a man's patrilineal bio-geographic ancestry from DNA

A 12-month follow-up study of treating overweight schizophrenic patients with aripiprazole

Objective: To investigate the feasibility of switching overweight schizophrenic patients to aripiprazole and to assess the impact of 12 months of aripiprazole treatment on weight in routine practice. Method: This was a non-controlled cohort study in overweight schizophrenic patients. Data were collected before treatment with aripiprazole was started and at 12-month follow-up. Results: A total of 53 patients were included; of these 55% continued using aripiprazole for 12 months. Aripiprazole treatment for 12 months (P = 0.027) and stopping clozapine or olanzapine treatment (P = 0.038) predicted weight loss (>= 3 kg). Patients receiving aripiprazole monotherapy (n = 16, mean -3.0 kg) had similar weight loss than patients receiving aripiprazole in addition to another antipsychotic drug (n = 13, mean -4.4 kg). Conclusion: In routine practice once aripiprazole treatment was started, more than half of the patients remained on aripiprazole and most of them lost weight. Adding aripiprazole to clozapine gave similar weight loss as monotherapy with aripiprazole

Simultaneous Whole Mitochondrial Genome Sequencing with Short Overlapping Amplicons Suitable for Degraded DNA Using the Ion Torrent Personal Genome Machine

Whole mitochondrial (mt) genome analysis enables a considerable increase in analysis throughput, and improves the discriminatory power to the maximum possible phylo

National-Scale Rainfall-Triggered Landslide Susceptibility and Exposure in Nepal

Nepal is one of the most landslide-prone countries in the world, with year-on-year impacts resulting in loss of life and imposing a chronic impediment to sustainable livelihoods. Living with landslides is a daily reality for an increasing number of people, so establishing the nature of landslide hazard and risk is essential. Here we develop a model of landslide susceptibility for Nepal and use this to generate a nationwide geographical profile of exposure to rainfall-triggered landslides. We model landslide susceptibility using a fuzzy overlay approach based on freely-available topographic data, trained on an inventory of mapped landslides, and combine this with high resolution population and building data to describe the spatial distribution of exposure to landslides. We find that whilst landslide susceptibility is highest in the High Himalaya, exposure is highest within the Middle Hills, but this is highly spatially variable and skewed to on average relatively low values. Around 4 × 106 Nepalis (∼15\% of the population) live in areas considered to be at moderate or higher degree of exposure to landsliding (>0.25 of the maximum), and critically this number is highly sensitive to even small variations in landslide susceptibility. Our results show a complex relationship between landslides and buildings, that implies wider complexity in the association between physical exposure to landslides and poverty. This analysis for the first time brings into focus the geography of the landslide exposure and risk case load in Nepal, and demonstrates limitations of assessing future risk based on limited records of previous events