From Structure Prediction to Genomic Screens for Novel Non-Coding RNAs

Non-coding RNAs (ncRNAs) are receiving more and more attention not only as an abundant class of genes, but also as regulatory structural elements (some located in mRNAs). A key feature of RNA function is its structure. Computational methods were developed early for folding and prediction of RNA structure with the aim of assisting in functional analysis. With the discovery of more and more ncRNAs, it has become clear that a large fraction of these are highly structured. Interestingly, a large part of the structure is comprised of regular Watson-Crick and GU wobble base pairs. This and the increased amount of available genomes have made it possible to employ structure-based methods for genomic screens. The field has moved from folding prediction of single sequences to computational screens for ncRNAs in genomic sequence using the RNA structure as the main characteristic feature. Whereas early methods focused on energy-directed folding of single sequences, comparative analysis based on structure preserving changes of base pairs has been efficient in improving accuracy, and today this constitutes a key component in genomic screens. Here, we cover the basic principles of RNA folding and touch upon some of the concepts in current methods that have been applied in genomic screens for de novo RNA structures in searches for novel ncRNA genes and regulatory RNA structure on mRNAs. We discuss the strengths and weaknesses of the different strategies and how they can complement each other

Population genomics of the Wolbachia endosymbiont in Drosophila melanogaster

Wolbachia are maternally-inherited symbiotic bacteria commonly found in arthropods, which are able to manipulate the reproduction of their host in order to maximise their transmission. Here we use whole genome resequencing data from 290 lines of Drosophila melanogaster from North America, Europe and Africa to predict Wolbachia infection status, estimate cytoplasmic genome copy number, and reconstruct Wolbachia and mtDNA genome sequences. Complete Wolbachia and mitochondrial genomes show congruent phylogenies, consistent with strict vertical transmission through the maternal cytoplasm and imperfect transmission of Wolbachia. Bayesian phylogenetic analysis reveals that the most recent common ancestor of all Wolbachia and mitochondrial genomes in D. melanogaster dates to around 8,000 years ago. We find evidence for a recent incomplete global replacement of ancestral Wolbachia and mtDNA lineages, which is likely to be one of several similar incomplete replacement events that have occurred since the out-of-Africa migration that allowed D. melanogaster to colonize worldwide habitats.Comment: 41 pages, 5 figure

Short-Lived Trace Gases in the Surface Ocean and the Atmosphere

The two-way exchange of trace gases between the ocean and the atmosphere is important for both the chemistry and physics of the atmosphere and the biogeochemistry of the oceans, including the global cycling of elements. Here we review these exchanges and their importance for a range of gases whose lifetimes are generally short compared to the main greenhouse gases and which are, in most cases, more reactive than them. Gases considered include sulphur and related compounds, organohalogens, non-methane hydrocarbons, ozone, ammonia and related compounds, hydrogen and carbon monoxide. Finally, we stress the interactivity of the system, the importance of process understanding for modeling, the need for more extensive field measurements and their better seasonal coverage, the importance of inter-calibration exercises and finally the need to show the importance of air-sea exchanges for global cycling and how the field fits into the broader context of Earth System Science

The streamlined genome of Phytomonas spp. relative to human pathogenic kinetoplastids reveals a parasite tailored for plants

Members of the family Trypanosomatidae infect many organisms, including animals, plants and humans. Plant-infecting trypanosomes are grouped under the single genus Phytomonas, failing to reflect the wide biological and pathological diversity of these protists. While some Phytomonas spp. multiply in the latex of plants, or in fruit or seeds without apparent pathogenicity, others colonize the phloem sap and afflict plants of substantial economic value, including the coffee tree, coconut and oil palms. Plant trypanosomes have not been studied extensively at the genome level, a major gap in understanding and controlling pathogenesis. We describe the genome sequences of two plant trypanosomatids, one pathogenic isolate from a Guianan coconut and one non-symptomatic isolate from Euphorbia collected in France. Although these parasites have extremely distinct pathogenic impacts, very few genes are unique to either, with the vast majority of genes shared by both isolates. Significantly, both Phytomonas spp. genomes consist essentially of single copy genes for the bulk of their metabolic enzymes, whereas other trypanosomatids e.g. Leishmania and Trypanosoma possess multiple paralogous genes or families. Indeed, comparison with other trypanosomatid genomes revealed a highly streamlined genome, encoding for a minimized metabolic system while conserving the major pathways, and with retention of a full complement of endomembrane organelles, but with no evidence for functional complexity. Identification of the metabolic genes of Phytomonas provides opportunities for establishing in vitro culturing of these fastidious parasites and new tools for the control of agricultural plant disease. © 2014 Porcel et al

Optimal foraging and community structure: implications for a guild of generalist grassland herbivores

A particular linear programming model is constructed to predict the diets of each of 14 species of generalist herbivores at the National Bison Range, Montana. The herbivores have body masses ranging over seven orders of magnitude and belonging to two major taxa: insects and mammals. The linear programming model has three feeding constraints: digestive capacity, feeding time and energy requirements. A foraging strategy that maximizes daily energy intake agrees very well with the observed diets. Body size appears to be an underlying determinant of the foraging parameters leading to diet selection. Species that possess digestive capacity and feeding time constraints which approach each other in magnitude have the most generalized diets. The degree that the linear programming models change their diet predictions with a given percent change in parameter values (sensitivity) may reflect the observed ability of the species to vary their diets. In particular, the species which show the most diet variability are those whose diets tend to be balanced between monocots and dicots. The community-ecological parameters of herbivore body-size ranges and species number can possibly be related to foraging behavior.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/47765/1/442_2004_Article_BF00377109.pd

Rain-induced subsurface airflow and Lisse effect

Water-level increase after rainfall is usually indicative of rainfall recharge to groundwater. This, however, may not be true if the Lisse effect occurs. This effect represents the water-level increase in a well driven by airflow induced by an advancing wetting front during highly intensive rains. The rainwater, which may behave like a low-permeability lid, seals the ground surface so that the air pressure beneath the wetting front is increased because of air compression due to downward movement of the wetting front. A rapid and substantial rise of the water level in the well screened below water table, which bears no relationship to groundwater recharge, can be induced when various factors such as soil properties and the rain-runoff condition combine favorably. A transient, three-dimensional and variably saturated flow model was employed to study the air and groundwater flows in the soil under rain conditions. The objectives of this paper are two-fold: to evaluate the reliability of the theory of the Lisse effect presented by Weeks to predict its magnitude in modeled situations that mimic the physical complexity of real aquifers, and to conduct parametric studies on the sensitivity of the water-level rise in the well to soil properties and the rain event. The simulation results reveal that the magnitude of the Lisse effect increases with the ponding depth. Soil permeability plays a key role in generating the Lisse effect. The water-level rise in the well is delayed relative to the air-pressure rise in the unsaturated zone when the soil permeability is low, and the maximum water-level rise is less than the maximum air pressure induced by rain infiltration. The simulation also explores the sensitivity of the Lisse effect to the van Genuchten parameters and the water table depth. Copyright 2008 by the American Geophysical Union.link_to_subscribed_fulltex

Control of Tamarix in the western United States: Implications for water salvage, wildlife use, and riparian restoration

Non-native shrub species in the genus Tamarix (saltcedar, tamarisk) have colonized hundreds of thousands of hectares of floodplains, reservoir margins, and other wetlands in western North America. Many resource managers seek to reduce saltcedar abundance and control its spread to increase the flow of water in streams that might otherwise be lost to evapotranspiration, to restore native riparian (streamside) vegetation, and to improve wildlife habitat. However, increased water yield might not always occur and has been substantially lower than expected in water salvage experiments, the potential for successful revegetation is variable, and not all wildlife taxa clearly prefer native plant habitats over saltcedar. As a result, there is considerable debate surrounding saltcedar control efforts. We review the literature on saltcedar control, water use, wildlife use, and riparian restoration to provide resource managers, researchers, and policy-makers with a balanced summary of the state of the science. To best ensure that the desired outcomes of removal programs are met, scientists and resource managers should use existing information and methodologies to carefully select and prioritize sites for removal, apply the most appropriate and cost-effective control methods, and then rigorously monitor control efficacy, revegetation success, water yield changes, and wildlife use. © 2005 Springer Science+Business Media, Inc