The DAWGPAWS pipeline for the annotation of genes and transposable elements in plant genomes     

James C Estill  Jeffrey L Bennetzen 《Plant methods》2009,5(1):8-11

Background  

High quality annotation of the genes and transposable elements in complex genomes requires a human-curated integration of multiple sources of computational evidence. These evidences include results from a diversity of ab initio prediction programs as well as homology-based searches. Most of these programs operate on a single contiguous sequence at a time, and the results are generated in a diverse array of readable formats that must be translated to a standardized file format. These translated results must then be concatenated into a single source, and then presented in an integrated form for human curation.  相似文献   

Image processing-based study of soil porosity and its effect on water movement through Andosol intact columns     

B. Prado  C. Duwig  P. Delmas  J. James 《Agricultural Water Management》2009,96(10):1377-1386

The soil pore network and marcoporosity are important factors affecting water and solute transport. The transfer of contaminants to water resources is of particular importance in the Valle de Bravo watershed as it provides 10% of the drinking water for the 20 million inhabitants of Mexico City. This watershed is composed mainly of Andosols with unique mineralogical and physical characteristics. Soil porosity is usually examined on thin sections, using various image analysis techniques. We propose a novel methodology combining image analysis and a displacement experiment to study relationships between soil structure and water tracer transport parameters. H₂¹⁸O displacement experiments were conducted through intact soil columns sampled at three depths from a representative cultivated Andosol profile. The soil structure and pore characteristics were obtained by image analysis on thin sections obtained from each column at the end of the displacement experiment. The total 2D porosity (for pores larger than 50 μm) varied from 80% of the total section area in the topsoil to around 60% in the subsoil. Tubular pores were the most abundant in the soil profile, but ploughing of the topsoil had destroyed sections of these pores and replaced them with packing pores. Water transport in the intact subsoil columns was always in physical non-equilibrium, showing the existence of preferential flow pathways. In the topsoil, one column out of three showed no preferential flow, demonstrating that soil ploughing also homogenised pore connections. Pore connectivity was larger in the ploughed topsoil than in their deeper soil horizon counterparts. Our methodology offers a 2D quantitative characterisation of the macroporous network at 50 μm resolution and the determination of water transport parameters on the same intact soil samples. 3D characterisation of soil porosity using X-ray computed tomography (CT) gives a better picture of pore connection but usually has lower spatial resolution and a larger cost.  相似文献   

Can giant clam (Tridacna squamosa) populations be restored on Singapore's heavily impacted coral reefs?     

James R. Guest  Peter A. Todd  Eugene Goh  Balasubramaniam S. Sivalonganathan  Konda P. Reddy 《水产资源保护:海洋与淡水生态系统》2008,18(5):570-579

• 1. Giant clams have been a sustainable resource for millennia, but unregulated harvesting has led to local extinctions within the Indo‐Pacific region. Giant clam mariculture can produce large numbers of juveniles for restocking wild populations where natural recruitment is low or absent.
• 2. Singapore is surrounded by more than 60 small islands, many with fringing reefs. These reefs, however, experience increased turbidity and sedimentation resulting from massive coastal development projects and regular dredging of shipping lanes.
• 3. Seven reefs off Singapore's southern islands were surveyed (9670 m²) for giant clams. Also, an experiment was conducted to determine the growth of Tridacna squamosa reared in aquaria under three light treatments: ～50% ambient photosynthetically active radiation (PAR); ～25% ambient PAR; and ～12% ambient PAR. Finally, 144 clams (T. squamosa) were transplanted to four reefs around Singapore to study survival and growth in a heavily impacted environment.
• 4. A total of 23 adult clams from three species were found during the survey, representing a mean density of 0.24 per 100 m². Most clams were found at Raffles Lighthouse, Singapore's ‘best’ reef. No juvenile clams were encountered. In the aquarium experiment, clam growth was significantly different among the three light treatments, with growth greatest in the ～50% ambient PAR treatment. Of the 144 transplanted clams, 116 (80.6%) were recovered after 7 months. All specimens had increased in size, with growth rates among reefs ranging from 3.3 mm month^?1 (SD=1.3 mm) to 4.8 mm month^?1 (SD=1.6 mm).
• 5. Results suggest that, despite high levels of sedimentation and turbidity on Singapore's reefs, giant clams can survive and grow well. Restocking efforts using maricultured clams may be effective in enhancing the dwindling local populations. It is not clear, however, whether a self‐sustaining community can be established as high sedimentation may hinder larval settlement and survival.

Copyright © 2007 John Wiley & Sons, Ltd.  相似文献   

Loggerhead turtle (Caretta caretta) bycatch in Canadian pelagic longline fisheries: Relative importance in the western North Atlantic and opportunities for mitigation     

John C. Brazner  James McMillan 《Fisheries Research》2008,91(2-3):310-324

Little is known about the ecology of loggerhead turtles, Caretta caretta, in Canadian waters. However, Canada's eastern waters off the Scotian Shelf, Georges Bank and Grand Banks appear to be seasonal foraging habitats based on dates and locations where they have been captured as fishery bycatch. Estimates derived from data recorded by the international observer program (IOP) and used for this study suggest that thousands of mostly immature loggerheads have been captured in the Canadian pelagic longline fishery (PLF) in the western North Atlantic since 1999. These data suggest that the PLFs for tuna and swordfish are among the most important causes of incidental capture. Although U.S. and Canadian bycatch estimation methods differ and uncertainty associated with the estimates is high, it is clear from the IOP data that bycatch in the Canadian PLF is substantial and roughly within the same magnitude as that reported for the entire U.S. fleet in the North Atlantic for the same period (1999–2005). Analysis of bycatch observer data from the Canadian PLF and other empirical data suggests that fishing at temperatures below 20 °C using fish rather than squid bait and size-18 circle hooks could reduce loggerhead bycatch and mortality. However, research is needed to identify the best options and their commercial viability. Loggerheads that use Canadian Maritime waters are one of the least studied groups of loggerheads in the world, so systematic long-term studies on the ecology of loggerheads in Canada would help fill important information gaps and assist in developing effective recovery plans for this species.  相似文献   

Predicting the age of fish using general and generalized linear models of biometric data: A case study of two estuarine finfish from New South Wales, Australia     

Faith A. Ochwada  James P. Scandol  Charles A. Gray 《Fisheries Research》2008,90(1-3):187-197

Direct ageing of fish can be a laborious and expensive task when age estimates from a large population are required, and often involves a degree of subjectivity. This study examined the application of general and generalized linear models that predict the age of fish from a range of efficiently and objectively measured covariates. The data sampled were from yellowfin bream (Acanthopagrus australis (Sparidae) (Owen, 1853)) and sand whiting (Sillago ciliata (Sillaginidae) Cuvier, 1829) populations from New South Wales, Australia. The covariates evaluated in the models were fish length, otolith weight, sex and location (the estuary from which the fish were sampled). Akaike Information Criteria were used for model selection and residual plots of the final models revealed a satisfactory fit to the observations. The best fitting model for each species included all covariates. An additional investigation considered whether general and generalized linear models that predict age from two different categories of biometric information outperform age-length keys with respect to subsequent estimates of total mortality from catch-curve analysis. The two categories of biometric information differed in the ease and cost with which the information could be collected. The first category only included fish length and location as covariates, whilst the second category also included otolith weight and sex. It was found that traditional age-length keys outperformed the predictive models that estimated age from only fish length and location, because the results from the models were prone to significant bias. However, when otolith weight and sex were added as covariates to the predictive models, some of them, including a generalized linear model with a Poisson-distributed response variable, performed similarly to the age-length key. Given that otolith weight and the sex of fish are cheaper to quantify than age from a sectioned otolith in many situations, general or generalized linear models may represent a cheaper and faster method of estimating mortality compared to age-length keys. Such models can also easily incorporate the influence of spatial, temporal and demographic variation.  相似文献   

Comparing mating designs to restore seed production of interspecific hybrids between Trifolium repens (white clover) and Trifolium uniflorum          下载免费PDF全文

Muhammad Naeem  Isabelle Marjorie Verry  Peter D. Kemp  James P. Millner  Warren Mervyn Williams 《Plant Breeding》2017,136(3):420-426

Interspecific hybrids between Trifolium uniflorum and cultivated white clover (Trifolium repens) have highly useful characteristics for temperate pastoral systems derived from both parent species. However, the early hybrids (F₁ and BC₁) also have unacceptably poor seed production for commerce. This study analysed the basis for the poor seed production and investigated breeding strategies for overcoming the problem. The BC₁F₁ generation produced lower‐than‐expected numbers of heads per plant and seeds per floret. Backcrossing of selected hybrids to white clover corrected these deficiencies and created new variation. Seed numbers were also returned to near target levels by recurrent selection within the BC₁ generation. Thus, it was possible to retain a theoretical average of 25% of T. uniflorum genome and still achieve high seed production per plant. The BC₁F₂ and BC₂F₁ generations produced high seed numbers per plant, along with reasonable variation. Both of these second‐generation hybrid forms have high reproductive potential and should be the focus for the selection of the desired combinations of agronomic and seed production traits.  相似文献   

Step-wise drops in modularity and the fragmentation of exploited marine metapopulations     

Tania S. Peña  James R. Watson  Laura I. González-Guzmán  Timothy H. Keitt 《Landscape Ecology》2017,32(8):1643-1656

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Environmental heterogeneity and biotic interactions as potential drivers of spatial patterning of shorebird nests     

Rose J. Swift  Amanda D. Rodewald  Nathan R. Senner 《Landscape Ecology》2017,32(8):1689-1703

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I,River?: New materialism,riparian non‐human agency and the scale of democratic reform          下载免费PDF全文

James L. Smith 《Asia Pacific viewpoint》2017,58(1):99-111

This article is a discussion of the “discourse on the unthinkable” surrounding potential future democratic engagements with rivers as non‐human persons or natural objects. In the context of the Asia–Pacific region, this article suggests that the developments in material philosophy entitled “new materialism” are essential tools in the reconceptualisation of rivers as democratic entities but that local socio‐historical conditions must also be taken into the account. In order to make its case, the article not only surveys the context for considering rivers as non‐human persons in a juridical context but also discusses the new material context that assists modern democracies in the renegotiation of the demos that forms the body politic of democracy – often in the face of neoliberal exploitation and a legacy of extremes in instrumentalism. The article argues that the incorporation of water in the democratic project of enfranchisement is an essential exercise born of many Western beliefs and ideals but articulated uniquely at a regional and national level.  相似文献   

Testing the ability of unmanned aerial systems and machine learning to map weeds at subfield scales: a test with the weed Alopecurus myosuroides (Huds)     

James PT Lambert  Dylan Z Childs  Rob P Freckleton 《Pest management science》2019,75(8):2283-2294

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