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"Elvin, Mark"
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Sediments of time : environment and society in Chinese history
Written by some of the world's leading experts, 'Sediments of Time' offers a survey of the environmental history of China. Crystallising a new and distinct field of research, the book studies the effect of human social systems on the natural world.
Book
retreat of the elephants
This is the first environmental history of China during the three thousand years for which there are written records. It is also a treasure trove of literary, political, aesthetic, scientific, and religious sources, which allow the reader direct access to the views and feelings of the Chinese people toward their environment and their landscape.Elvin chronicles the spread of the Chinese style of farming that eliminated the habitat of the elephants that populated the country alongside much of its original wildlife; the destruction of most of the forests; the impact of war on the environmental transformation of the landscape; and the re-engineering of the countryside through water-control systems, some of gigantic size. He documents the histories of three contrasting localities within China to show how ecological dynamics defined the lives of the inhabitants. And he shows that China in the eighteenth century, on the eve of the modern era, was probably more environmentally degraded than northwestern Europe around this time.Indispensable for its new perspective on long-term Chinese history and its explanation of the roots of China's present-day environmental crisis, this book opens a door into the Chinese past.
eBook
VIVID interacts with the WHITE COLLAR complex and FREQUENCY-interacting RNA helicase to alter light and clock responses in Neurospora
The photoreceptor and PAS/LOV protein VIVID (VVD) modulates blue-light signaling and influences light and temperature responses of the circadian clock in Neurospora crassa. One of the main actions of VVD on the circadian clock is to influence circadian clock phase by regulating levels of the transcripts encoded by the central clock gene frequency (frq). How this regulation is achieved is unknown. Here we show that VVD interacts with complexes central for circadian clock and blue-light signaling, namely the WHITE-COLLAR complex (WCC) and FREQUENCY-interacting RNA helicase (FRH), a component that complexes with FRQ to mediate negative feedback control in Neurospora. VVD interacts with FRH in the absence of WCC and FRQ but does not seem to control the exosome-mediated negative feedback loop. Instead, VVD acts to modulate the transcriptional activity of the WCC.
Journal Article
Trichome morphology relates to taxonomic diversity in Monardella (Lamiaceae) in the lower Snake River Watershed of Idaho and Oregon, USA: Taxonomic studies in Monardella (Lamiaceae) VI
Monardella is a western North America genus ranging from the Rocky Mountains to the Pacific Ocean and from southern Canada to the southern tip of Baja California Sur. The levels of unrecognized and cryptic taxa within Monardella are similar to other taxonomically complicated western North American genera, such as Eriogonum (Polygonaceae), Penstemon (Plantaginaceae), and Oreocarya (Boraginaceae). We present variation in trichome morphology as a taxonomic tool within Monardella, being comparable in importance to trichome variation in other plant families and genera (e.g., Brassicaceae, Draba; Loasaceae, Mentzelia; Solanaceae, Solanum). Trichome morphology within Monardella is a useful character to differentiate taxa and resolve taxonomic ambiguities. We present nomenclatural novelties and revisions for Monardella occurring in the Hells Canyon region along the lower Snake River of west-central Idaho and northeastern Oregon. We introduce the following taxonomic and nomenclatural changes. Monardella odoratissima Benth. var. neglecta Cronquist is recognized as a later homonym; a new name and rank are presented for it: M. perplexans Elvin, R. B. Kelley, & B. T. Drew. Two new species are described: M. kruckebergii Elvin, R. B. Kelley, & B. T. Drew and M. walwaamaxsia Elvin, R. B. Kelley, & B. T. Drew.
Journal Article
Cryptic genetic variation of expression quantitative trait locus architecture revealed by genetic perturbation in Caenorhabditis elegans
Genetic perturbation in different genetic backgrounds can cause a range of phenotypes within a species. These phenotypic differences can be the result of the interaction between the genetic background and the perturbation. Previously, we reported that perturbation of gld-1, an important player in the developmental control of Caenorhabditis elegans, released cryptic genetic variation (CGV) affecting fitness in different genetic backgrounds. Here, we investigated the change in transcriptional architecture. We found 414 genes with a cis-expression quantitative trait locus (eQTL) and 991 genes with a trans-eQTL that were specifically found in the gld-1 RNAi treatment. In total, we detected 16 eQTL hotspots, of which 7 were only found in the gld-1 RNAi treatment. Enrichment analysis of those 7 hotspots showed that the regulated genes were associated with neurons and the pharynx. Furthermore, we found evidence of accelerated transcriptional aging in the gld-1 RNAi–treated nematodes. Overall, our results illustrate that studying CGV leads to the discovery of hidden polymorphic regulators.
Journal Article
Natural Genetic Variation Influences Protein Abundances in C. elegans Developmental Signalling Pathways
Complex traits, including common disease-related traits, are affected by many different genes that function in multiple pathways and networks. The apoptosis, MAPK, Notch, and Wnt signalling pathways play important roles in development and disease progression. At the moment we have a poor understanding of how allelic variation affects gene expression in these pathways at the level of translation. Here we report the effect of natural genetic variation on transcript and protein abundance involved in developmental signalling pathways in Caenorhabditis elegans. We used selected reaction monitoring to analyse proteins from the abovementioned four pathways in a set of recombinant inbred lines (RILs) generated from the wild-type strains N2 (Bristol) and CB4856 (Hawaii) to enable quantitative trait locus (QTL) mapping. About half of the cases from the 44 genes tested showed a statistically significant change in protein abundance between various strains, most of these were however very weak (below 1.3-fold change). We detected a distant QTL on the left arm of chromosome II that affected protein abundance of the phosphatidylserine receptor protein PSR-1, and two separate QTLs that influenced embryonic and ionizing radiation-induced apoptosis on chromosome IV. Our results demonstrate that natural variation in C. elegans is sufficient to cause significant changes in signalling pathways both at the gene expression (transcript and protein abundance) and phenotypic levels.
Journal Article
reGenotyper: Detecting mislabeled samples in genetic data
In high-throughput molecular profiling studies, genotype labels can be wrongly assigned at various experimental steps; the resulting mislabeled samples seriously reduce the power to detect the genetic basis of phenotypic variation. We have developed an approach to detect potential mislabeling, recover the \"ideal\" genotype and identify \"best-matched\" labels for mislabeled samples. On average, we identified 4% of samples as mislabeled in eight published datasets, highlighting the necessity of applying a \"data cleaning\" step before standard data analysis.
Journal Article
A fitness assay for comparing RNAi effects across multiple C. elegans genotypes
Background
RNAi technology by feeding of
E. coli
containing dsRNA in
C. elegans
has significantly contributed to further our understanding of many different fields, including genetics, molecular biology, developmental biology and functional genomics. Most of this research has been carried out in a single genotype or genetic background. However, RNAi effects in one genotype do not reveal the allelic effects that segregate in natural populations and contribute to phenotypic variation.
Results
Here we present a method that allows for rapidly comparing RNAi effects among diverse genotypes at an improved high throughput rate. It is based on assessing the fitness of a population of worms by measuring the rate at which
E. coli
is consumed. Critically, we demonstrate the analytical power of this method by QTL mapping the loss of RNAi sensitivity (in the germline) in a recombinant inbred population derived from a cross between Bristol and a natural isolate from Hawaii. Hawaii has lost RNAi sensitivity in the germline. We found that polymorphisms in
ppw-1
contribute to this loss of RNAi sensitivity, but that other loci are also likely to be important.
Conclusions
In summary, we have established a fast method that improves the throughput of RNAi in liquid, that generates quantitative data, that is easy to implement in most laboratories, and importantly that enables QTL mapping using RNAi.
Journal Article
A New Species of Monardella (Lamiaceae) from Southeastern Oregon and Adjacent Idaho, U.S.A
Monardella angustifolia Elvin, Ertter & Mansfield (Lamiaceae), a new species from southeastern Oregon and adjacent Idaho, is described and illustrated. It occurs on ash tuff outcrops in and near Leslie Gulch in the northern reaches of the Great Basin Desert. The new species is best distinguished by its calyx trichomes, fascicled leaves, and leaf and bract morphology. It is unique in the genus in having very narrow, conduplicate, and often fascicled leaves and being endemic to soils derived from ash tuff. It is most similar morphologically and ecologically to several perennial species of Monardella Benth. in the Mojave Desert ca. 900 km to the south. It shares with them a similar habit, pubescence, branching, and bract and glomerule morphologies.
Journal Article
Three New Subspecies of Monardella (Lamiaceae) from Southern California, U.S.A
Continuing work on the flora of California after the publication of The Jepson Manual: Vascular Plants of California has led to the discovery of three new Monardella Benth. (Lamiaceae) subspecies: M. australis Abrams subsp. gabrielensis Elvin & A. C. Sanders, M. australis subsp. occidentalis Elvin, R. A. Burgess & A. C. Sanders, and M. sinuata Elvin & A. C. Sanders subsp. gerryi Elvin, A. C. Sanders & R. A. Burgess. Monardella australis subsp. gabrielensis occurs in the central and western San Gabriel Mountains of the Transverse Ranges, and M. australis subsp. occidentalis occurs on Pine Mountain Ridge in the Western Transverse Ranges and the San Rafael Mountains of the adjacent southern portion of the South Coast Ranges. The two new subspecies of M. australis are most similar to the autonymic subspecies, but both differ in their bract and leaf morphology, pubescence on the stems and calyces, stature, and distribution. Monardella sinuata subsp. gerryi occurs in the Las Posas and Camarillo Hills in the coastal plain of Ventura County in the South Coast Region. The new subspecies is most similar to M. sinuata subsp. sinuata but differs in its stem, leaf, bract, and glomerule size and in its pubescence, nutlets, and ecological setting. Monardella neglecta Greene is transferred to a new rank as a subspecies of M. purpurea Howell, as M. purpurea subsp. neglecta (Greene) Elvin & A. C. Sanders. It is a diminutive, glabrous, serpentine endemic on the Marin and Tiburon peninsulas in northern California. A taxonomic assessment of names within the M. villosa Benth. complex results in the synonymy of M. franciscana Elmer to M. villosa subsp. villosa. Monardella villosa subsp. subserrata (Greene) Epling is recognized as the upland and interior taxon in this species. A lectotype is designated for M. purpurea Howell and recognized for both M. franciscana Elmer and M. neglecta Greene.
Journal Article