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"Stephan, Dietrich"
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Resolving Individuals Contributing Trace Amounts of DNA to Highly Complex Mixtures Using High-Density SNP Genotyping Microarrays
We use high-density single nucleotide polymorphism (SNP) genotyping microarrays to demonstrate the ability to accurately and robustly determine whether individuals are in a complex genomic DNA mixture. We first develop a theoretical framework for detecting an individual's presence within a mixture, then show, through simulations, the limits associated with our method, and finally demonstrate experimentally the identification of the presence of genomic DNA of specific individuals within a series of highly complex genomic mixtures, including mixtures where an individual contributes less than 0.1% of the total genomic DNA. These findings shift the perceived utility of SNPs for identifying individual trace contributors within a forensics mixture, and suggest future research efforts into assessing the viability of previously sub-optimal DNA sources due to sample contamination. These findings also suggest that composite statistics across cohorts, such as allele frequency or genotype counts, do not mask identity within genome-wide association studies. The implications of these findings are discussed.
Journal Article
More than a feeling: A global economic valuation of subjective wellbeing damages resulting from rising temperatures
When estimating economic and welfare effects from climate change, impact models must make broad assumptions because of a lack of data and the complexity of damage mechanisms. In this paper, we apply a novel approach to try and address this issue. We use an experienced utility approach to measure how extreme heat affects subjective wellbeing. The data comes from a life evaluation question collected on nationally representative surveys covering 160 countries, conducted annually for 13 years. We take advantage of 40 years of variation in daily land surface temperature data, finding that one additional exceptionally hot day significantly lowers wellbeing, by roughly 0.5% on average. This is equivalent to the wellbeing loss resulting from GDP decreasing by several percentage points. The effect size varies substantially between, and within, countries, highlighting the importance of having local data. Further, we analyze the source of wellbeing damages, by looking at income and non-income pathways. Suprisingly, we find that income pathways accounts for only a small proportion of wellbeing damages caused by extreme temperatures. This indicates current models that focus on income pathways are likely missing sources of climate-caused damages.
Journal Article
Economic development, weather shocks and child marriage in South Asia: A machine learning approach
Globally, 21 percent of young women are married before their 18th birthday. Despite some progress in addressing child marriage, it remains a widespread practice, in particular in South Asia. While household predictors of child marriage have been studied extensively in the literature, the evidence base on macro-economic factors contributing to child marriage and models that predict where child marriage cases are most likely to occur remains limited. In this paper we aim to fill this gap and explore region-level indicators to predict the persistence of child marriage in four countries in South Asia, namely Bangladesh, India, Nepal and Pakistan. We apply machine learning techniques to child marriage data and develop a prediction model that relies largely on regional and local inputs such as droughts, floods, population growth and nightlight data to model the incidence of child marriages. We find that our gradient boosting model is able to identify a large proportion of the true child marriage cases and correctly classifies 77% of the true marriage cases, with a higher accuracy in Bangladesh (92% of the cases) and a lower accuracy in Nepal (70% of cases). In addition, all countries contain in their top 10 variables for classification nighttime light growth, a shock index of drought over the previous and the last two years and the regional level of education, suggesting that income shocks, regional economic activity and regional education levels play a significant role in predicting child marriage. Given the accuracy of the model to predict child marriage, our model is a valuable tool to support policy design in countries where household-level data remains limited.
Journal Article
Whole Exome Sequencing in Females with Autism Implicates Novel and Candidate Genes
Classical autism or autistic disorder belongs to a group of genetically heterogeneous conditions known as Autism Spectrum Disorders (ASD). Heritability is estimated as high as 90% for ASD with a recently reported compilation of 629 clinically relevant candidate and known genes. We chose to undertake a descriptive next generation whole exome sequencing case study of 30 well-characterized Caucasian females with autism (average age, 7.7 ± 2.6 years; age range, 5 to 16 years) from multiplex families. Genomic DNA was used for whole exome sequencing via paired-end next generation sequencing approach and X chromosome inactivation status. The list of putative disease causing genes was developed from primary selection criteria using machine learning-derived classification score and other predictive parameters (GERP2, PolyPhen2, and SIFT). We narrowed the variant list to 10 to 20 genes and screened for biological significance including neural development, function and known neurological disorders. Seventy-eight genes identified met selection criteria ranging from 1 to 9 filtered variants per female. Five females presented with functional variants of X-linked genes (IL1RAPL1, PIR, GABRQ, GPRASP2, SYTL4) with cadherin, protocadherin and ankyrin repeat gene families most commonly altered (e.g., CDH6, FAT2, PCDH8, CTNNA3, ANKRD11). Other genes related to neurogenesis and neuronal migration (e.g., SEMA3F, MIDN), were also identified.
Journal Article
Autism and Increased Paternal Age Related Changes in Global Levels of Gene Expression Regulation
A causal role of mutations in multiple general transcription factors in neurodevelopmental disorders including autism suggested that alterations in global levels of gene expression regulation might also relate to disease risk in sporadic cases of autism. This premise can be tested by evaluating for changes in the overall distribution of gene expression levels. For instance, in mice, variability in hippocampal-dependent behaviors was associated with variability in the pattern of the overall distribution of gene expression levels, as assessed by variance in the distribution of gene expression levels in the hippocampus. We hypothesized that a similar change in variance might be found in children with autism. Gene expression microarrays covering greater than 47,000 unique RNA transcripts were done on RNA from peripheral blood lymphocytes (PBL) of children with autism (n = 82) and controls (n = 64). Variance in the distribution of gene expression levels from each microarray was compared between groups of children. Also tested was whether a risk factor for autism, increased paternal age, was associated with variance. A decrease in the variance in the distribution of gene expression levels in PBL was associated with the diagnosis of autism and a risk factor for autism, increased paternal age. Traditional approaches to microarray analysis of gene expression suggested a possible mechanism for decreased variance in gene expression. Gene expression pathways involved in transcriptional regulation were down-regulated in the blood of children with autism and children of older fathers. Thus, results from global and gene specific approaches to studying microarray data were complimentary and supported the hypothesis that alterations at the global level of gene expression regulation are related to autism and increased paternal age. Global regulation of transcription, thus, represents a possible point of convergence for multiple etiologies of autism and other neurodevelopmental disorders.
Journal Article
From the dual cyclone harvest performance of single conidium powder to the effect of Metarhizium anisopliae on the management of Thaumastocoris peregrinus (Hemiptera: Thaumastocoridae)
Insect pests introduced in eucalyptus plantations in Brazil are mostly of Australian origin, but native microorganisms have potential for their management. High quality biopesticide production based on entomopathogenic fungi depends on adequate technologies. The objective of this study was to evaluate Mycoharvester® equipment to harvest and separating particles to obtain pure Metarhizium anisopliae conidia to manage Thaumastocoris peregrinus Carpintero & Dellapé, 2006 (Hemiptera: Thaumastocoridae). The Mycoharvester® version 5b harvested and separated M . anisopliae spores. The pure conidia were suspended in Tween 80® (0.1%) and calibrated to the concentrations of 1 x 10 6 , 10 7 , 10 8 and 10 9 conidia/ml to evaluate the pathogenicity, lethal concentration 50 and 90 (LC 50 , LC 90 ) and lethal time 50 and 90 (LT 50 , LT 90 ) of this fungus to T . peregrinus . This equipment harvested 85% of the conidia from rice, with production of 4.8 ± 0.38 x 10 9 conidia/g dry mass of substrate + fungus. The water content of 6.36% of the single spore powder (pure conidia) separated by the Mycoharvester® was lower than that of the agglomerated product. The product harvested at the concentrations of 10 8 and 10 9 conidia/ml caused high mortality to T . peregrinus third instar nymphs and adults. The separation of conidia produced by solid-state fermentation with the Mycoharvester® is an important step toward optimizing the fungal production system of pure conidia, and to formulate biopesticides for insect pest management.
Journal Article
Investigation on the Influence of Production and Incubation Temperature on the Growth, Virulence, Germination, and Conidial Size of Metarhizium brunneum for Granule Development
Important for the infection of an insect with an entomopathogenic fungus and its use as a plant protection agent are its growth, conidiation, germination, and virulence, which all depend on the environmental temperature. We investigated not only the effect of environmental temperature but also that of production temperature of the fungus. For this purpose, Metarhizium brunneum JKI-BI-1450 was produced and incubated at different temperatures, and the factors mentioned as well as conidial size were determined. The temperature at which the fungus was produced affects its subsequent growth and conidiation on granule formulation, the speed of germination, and the conidial width, but not its final germination or virulence. The growth and conidiation was at its highest when the fungus was produced at 25 °C, whereas when the germination was faster, the warmer the fungus was produced. The incubation temperature optimum of JKI-BI-1450 in relation to growth, speed of germination, and survival time was 25–30 °C and for conidiation 20–25 °C. Conidial length decreased with increasing incubation temperature. Although the fungus could not be adapted to unfavorable conditions by the production temperature, it was found that the quality of a biological control agent based on entomopathogenic fungi can be positively influenced by its production temperature.
Journal Article
Alzheimer's disease is associated with reduced expression of energy metabolism genes in posterior cingulate neurons
Alzheimer's disease (AD) is associated with regional reductions in fluorodeoxyglucose positron emission tomography (FDG PET) measurements of the cerebral metabolic rate for glucose, which may begin long before the onset of histopathological or clinical features, especially in carriers of a common AD susceptibility gene. Molecular evaluation of cells from metabolically affected brain regions could provide new information about the pathogenesis of AD and new targets at which to aim disease-slowing and prevention therapies. Data from a genome-wide transcriptomic study were used to compare the expression of 80 metabolically relevant nuclear genes from laser-capture microdissected non-tangle-bearing neurons from autopsy brains of AD cases and normal controls in posterior cingulate cortex, which is metabolically affected in the earliest stages; other brain regions metabolically affected in PET studies of AD or normal aging; and visual cortex, which is relatively spared. Compared with controls, AD cases had significantly lower expression of 70% of the nuclear genes encoding subunits of the mitochondrial electron transport chain in posterior cingulate cortex, 65% of those in the middle temporal gyrus, 61% of those in hippocampal CA1, 23% of those in entorhinal cortex, 16% of those in visual cortex, and 5% of those in the superior frontal gyrus. Western blots confirmed underexpression of those complex I-V subunits assessed at the protein level. Cerebral metabolic rate for glucose abnormalities in FDG PET studies of AD may be associated with reduced neuronal expression of nuclear genes encoding subunits of the mitochondrial electron transport chain.
Journal Article