Fine scale structural variants distinguish the genomes of Drosophila melanogaster and D. pseudoobscura

BACKGROUND: A primary objective of comparative genomics is to identify genomic elements of functional significance that contribute to phenotypic diversity. Complex changes in genome structure (insertions, duplications, rearrangements, translocations) may be widespread, and have important effects on organismal diversity. Any survey of genomic variation is incomplete without an assessment of structural changes. RESULTS: We re-examine the genome sequences of the diverged species Drosophila melanogaster and D. pseudoobscura to identify fine-scale structural features that distinguish the genomes. We detect 95 large insertion/deletion events that occur within the introns of orthologous gene pairs, the majority of which represent insertion of transposable elements. We also identify 143 microinversions below 5 kb in size. These microinversions reside within introns or just upstream or downstream of genes, and invert conserved DNA sequence. The sequence conservation within microinversions suggests they may be enriched for functional genetic elements, and their position with respect to known genes implicates them in the regulation of gene expression. Although we found a distinct pattern of GC content across microinversions, this was indistinguishable from the pattern observed across blocks of conserved non-coding sequence. CONCLUSION: Drosophila has long been known as a genus harboring a variety of large inversions that disrupt chromosome colinearity. Here we demonstrate that microinversions, many of which are below 1 kb in length, located in/near genes may also be an important source of genetic variation in Drosophila. Further examination of other Drosophila genome sequences will likely identify an array of novel microinversion events

Discovery of malathion resistance QTL in Drosophila melanogaster using a bulked phenotyping approach

Drosophila melanogaster has proved an effective system with which to understand the evolutionary genetics and molecular mechanisms of insecticide resistance. Insecticide use has left signatures of selection in the fly genome, and both functional and quantitative genetic studies in the system have identified genes and variants associated with resistance. Here, we use D. melanogaster and leverage a bulk phenotyping and pooled sequencing “extreme quantitative trait loci” approach to genetically dissect variation in resistance to malathion, an organophosphate insecticide. We resolve 2 quantitative trait loci, one of which implicates allelic variation at the cytochrome P450 gene Cyp6g1, a strong candidate based on previous work. The second shows no overlap with hits from a previous genome-wide association study for malathion resistance, recapitulating other studies showing that different strategies for complex trait dissection in flies can yield apparently different architectures. Notably, we see no genetic signal at the Ace gene. Ace encodes the target of organophosphate insecticide inhibition, and genome-wide association studies have identified strong Ace-linked associations with resistance in flies. The absence of quantitative trait locus implicating Ace here is most likely because our mapping population does not segregate for several of the known functional polymorphisms impacting resistance at Ace, perhaps because our population is derived from flies collected prior to the widespread use of organophosphate insecticides. Our fundamental approach can be an efficient, powerful strategy to dissect genetic variation in resistance traits. Nonetheless, studies seeking to interrogate contemporary insecticide resistance variation may benefit from deriving mapping populations from more recently collected strains

Genomes, expression profiles, and diversity of mitochondria of the White-footed Deermouse Peromyscus leucopus, reservoir of Lyme disease and other zoonoses.

The cricetine rodents Peromyscus leucopus and P. maniculatus are key reservoirs for several zoonotic diseases in North America. We determined the complete circular mitochondrial genome sequences of representatives of 3 different stock colonies of P. leucopus, one stock colony of P. maniculatus and two wild populations of P. leucopus. The genomes were syntenic with that of the murids Mus musculus and Rattus norvegicus. Phylogenetic analysis confirmed that these two Peromyscus species are sister taxa in a clade with P. polionotus and also uncovered a distinction between P. leucopus populations in the eastern and the central United States. In one P. leucopus lineage four extended regions of mitochondrial pseudogenes were identified in the nuclear genome. RNA-seq analysis revealed transcription of the entire genome and differences from controls in the expression profiles of mitochondrial genes in the blood, but not in liver or brain, of animals infected with the zoonotic pathogen Borrelia hermsii. PCR and sequencing of the D-loop of the mitochondrion identified 32 different haplotypes among 118 wild P. leucopus at a Connecticut field site. These findings help to further establish P. leucopus as a model organism for studies of emerging infectious diseases, ecology, and in other disciplines

Dissecting Complex Traits Using the Drosophila Synthetic Population Resource

For most complex traits we have a poor understanding of the positions, phenotypic effects, and population frequencies of the underlying genetic variants contributing to their variation. Recently, several groups have developed multi-parent advanced intercross mapping panels in different model organisms in an attempt to improve our ability to characterize causative genetic variants. These panels are powerful and are particularly well suited to the dissection of phenotypic variation generated by rare alleles and loci segregating multiple functional alleles. We describe studies using one such panel, the Drosophila Synthetic Population Resource, and the implications for our understanding of the genetic basis of complex traits. In particular, we note that many loci of large effect appear to be multiallelic. If multiallelism is a general rule, analytical approaches designed to identify multiallelic variants should be a priority for both genome wide association studies and multi-parental panels

High thermoelectric performance of bornite through control of the Cu(II) content and vacancy concentration

The thermoelectric performance of the p-type semiconductor bornite, Cu5FeS4, is greatly enhanced through chemical substitution. Non-stoichiometric materials in which the Cu:Fe ratio and overall cation-vacancy con-tent were adjusted are reported and a figure of merit, ZT = 0.79, is achieved at temperatures as low as 550 K in Cu4.972Fe0.968S4. All materials were synthesised mechanochemically and characterised by powder X-ray diffrac-tion, DSC and thermal and electrical transport property measurements. Single-phase behaviour is retained in copper deficient phases, Cu5-xFeS4, for vacancy levels up to x = 0.1, while in materials Cu5+yFe1-yS4, in which the Cu:Fe ratio is varied whilst maintaining full occupancy of cation sites, single-phase behaviour persists for y≤0.08. Adjusting the Cu:Fe ratio at a constant cation-vacancy level of 0.06 in Cu4.94+zFe1-zS4, leads to single-phases for z ≤0.04. DSC measurements indicate the temperature of the intermediate- (2a) to high-temperature (a) phase transition shows a more marked dependence on the Cu:Fe ratio than the lower temperature 4a to 2a transition. The thermoelectric power factor increases almost linearly with increasing Cu(II) content. The maximum figures of merit are obtained for materials with Cu(II) contents in the range 0.10 to 0.15 (corresponding to 2.0 – 2.8 % Cu(II)) which simultaneously contain ca .1 % of cation vacancies

The potential of decarbonising rice and wheat by incorporating carbon capture, utilisation and storage into fertiliser production

This paper aims to evaluate the reduction on greenhouse gas emissions in rice and wheat and their supply chains by incorporating carbon capture, utilisation, and storage into fertiliser production mainly from ammonia process, which is the section of fertiliser that produces the most carbon dioxide. Greenhouse gas emissions of these grains without carbon capture, utilisation and storage are provided from the results of life cycle assessment in the literatures. After that, a carbon dioxide emission from fertiliser production is quantified. The alternative considered for utilisation is enhanced oil recovery and it is compared with conventional way of oil production. The effect of carbon capture, utilisation, and storage in greenhouse gas reduction are presented in term of rice and wheat’s supply chains to make people conscious about the use and optimisation of food. The reduction of greenhouse gas is around 6-7% in rice supply chain e.g. rice milk, spoons of uncooked rice and 14-16% in wheat supply chain e.g. pasta, one slice of bread. Although the alternative with carbon dioxide storage demonstrates marginally higher greenhouse gas reduction, enhanced oil recovery may offer economic incentive from additional oil production that could reduce the cost of rice and wheat

Abundance and Distribution of Transposable Elements in Two Drosophila QTL Mapping Resources

Here we present computational machinery to efficiently and accurately identify transposable element (TE) insertions in 146 next-generation sequenced inbred strains of Drosophila melanogaster. The panel of lines we use in our study is composed of strains from a pair of genetic mapping resources: the Drosophila Genetic Reference Panel (DGRP) and the Drosophila Synthetic Population Resource (DSPR). We identified 23,087 TE insertions in these lines, of which 83.3% are found in only one line. There are marked differences in the distribution of elements over the genome, with TEs found at higher densities on the X chromosome, and in regions of low recombination. We also identified many more TEs per base pair of intronic sequence and fewer TEs per base pair of exonic sequence than expected if TEs are located at random locations in the euchromatic genome. There was substantial variation in TE load across genes. For example, the paralogs derailed and derailed-2 show a significant difference in the number of TE insertions, potentially reflecting differences in the selection acting on these loci. When considering TE families, we find a very weak effect of gene family size on TE insertions per gene, indicating that as gene family size increases the number of TE insertions in a given gene within that family also increases. TEs are known to be associated with certain phenotypes, and our data will allow investigators using the DGRP and DSPR to assess the functional role of TE insertions in complex trait variation more generally. Notably, because most TEs are very rare and often private to a single line, causative TEs resulting in phenotypic differences among individuals may typically fail to replicate across mapping panels since individual elements are unlikely to segregate in both panels. Our data suggest that “burden tests” that test for the effect of TEs as a class may be more fruitful

Genetic Dissection of the Drosophila melanogaster Female Head Transcriptome Reveals Widespread Allelic Heterogeneity

Modern genetic mapping is plagued by the “missing heritability” problem, which refers to the discordance between the estimated heritabilities of quantitative traits and the variance accounted for by mapped causative variants. One major potential explanation for the missing heritability is allelic heterogeneity, in which there are multiple causative variants at each causative gene with only a fraction having been identified. The majority of genome-wide association studies (GWAS) implicitly assume that a single SNP can explain all the variance for a causative locus. However, if allelic heterogeneity is prevalent, a substantial amount of genetic variance will remain unexplained. In this paper, we take a haplotype-based mapping approach and quantify the number of alleles segregating at each locus using a large set of 7922 eQTL contributing to regulatory variation in the Drosophila melanogaster female head. Not only does this study provide a comprehensive eQTL map for a major community genetic resource, the Drosophila Synthetic Population Resource, but it also provides a direct test of the allelic heterogeneity hypothesis. We find that 95% of cis-eQTLs and 78% of trans-eQTLs are due to multiple alleles, demonstrating that allelic heterogeneity is widespread in Drosophila eQTL. Allelic heterogeneity likely contributes significantly to the missing heritability problem common in GWAS studies.This work was supported by NIH R01 RR024862/OD010974 to SJM and ADL, an American Recovery and Reinvestment Act (ARRA) administrative supplement to this award, and F32 GM099382 to EGK. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript

Correlation between ankle-brachial index, symptoms, and health-related quality of life in patients with peripheral vascular disease

AbstractObjectiveImproving health-related quality of life (HRQL) is the main goal of surgery to treat peripheral vascular disease (PVD); however, HRQL is rarely measured directly. Rather, most surgeons use other measures, such as patient symptoms and ankle-brachial index (ABI) to determine the need for intervention in PVD. The accuracy of these surrogates in representing HRQL has been untested. The purpose of this study was to determine the correlation of these measures with HRQL in patients undergoing evaluation for intervention in symptomatic PVD.MethodsPatients (n = 108) referred to the vascular surgery service with symptoms of PVD were enrolled in a prospective study of HRQL. Patients completed two validated HRQL questionnaires: the short form-36 (SF-36) and the Walking Impairment Questionnaire (WIQ). All patients had symptoms consistent with PVD, including claudication (n = 69; 63.9%), ischemic rest pain (n = 17; 15.7%), or tissue loss (n = 22; 20.4%). ABI was measured at presentation.ResultsThe mean ABI was 0.53 (range, 0.00-0.98). The maximal correlation between SF-36 score and ABI was reflected in the Physical Component Summary score (r = 0.25). WIQ score also exhibited modest correlation with ABI, with maximal correlation noted for stair climbing (r = 0.26). Both SF-36 and WIQ scores exhibited a highly significant association with symptoms. Patients with more severe symptoms, such as lifestyle-limiting claudication or limb-threatening ischemia, had lower HRQL scores compared with patients with non-lifestyle-limiting claudication. Multivariate analysis demonstrated that SF-36 and WIQ physical summary scores are better predicted by symptoms than by ABI (P < .01).ConclusionsHRQL in patients with PVD correlates weakly with ABI, but exhibits a closer association with vascular symptoms. However, neither variable fully expresses patient HRQL. These data suggest that sole reliance on these surrogates may not accurately reflect the effect of PVD on HRQL, or the potential benefit of vascular surgery in improving HRQL