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   

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   

Wheat grain quality under increasing atmospheric CO₂ concentrations in a semi-arid cropping system     

Nimesha Fernando  Joe Panozzo  Michael Tausz  Robert M. Norton  Glenn J. Fitzgerald  Samuel Myers  Cassandra Walker  James Stangoulis  Saman Seneweera 《Journal of Cereal Science》2012

We investigated wheat (Triticum aestivum) grain quality under Free Air CO₂ Enrichment (FACE) of 550 ± 10% CO₂ μmol mol⁻¹. In each of two full growing seasons (2008 and 2009), two times of sowing were compared, with late sowing designed to mimic high temperature during grain filling. Grain samples were subjected to a range of physical, nutritional and rheological quality assessments. Elevated CO₂ increased thousand grain weight (8%) and grain diameter (5%). Flour protein concentration was reduced by 11% at e[CO₂], with the highest reduction being observed at the late time of sowing in 2009, (15%). Most of the grain mineral concentrations decreased under e[CO₂] - Ca (11%), Mg (7%), P (11%) and S (7%), Fe (10%), Zn (17%), Na (19%), while total uptake of these nutrients per unit ground area increased. Rheological properties of the flour were altered by e[CO₂] and bread volume reduced by 7%. Phytate concentration in grains tended to decrease (17%) at e[CO₂] while grain fructan concentration remained unchanged. The data suggest that rising atmospheric [CO₂] will reduce the nutritional and rheological quality of wheat grain, but at high temperature, e[CO₂] effects may be moderated. Reduced phytate concentrations at e[CO₂] may improve bioavailability of Fe and Zn in wheat grain.  相似文献   

Design and development of a geothermal temperature control system for broodstock management of channel catfish Ictalurus punctatus     

Steven G. Hall  James Finney  R. Paul Lang  Terrence R. Tiersch 《Aquacultural Engineering》2002,26(4):277-289

A control system was designed to raise and maintain water temperatures within 0.03-ha earthen ponds to a range conducive for spawning (24–30 °C) channel catfish Ictalurus punctatus. Heating was done during February 2001 to April 2001, when temperatures would have otherwise prohibited spawning (<24 °C). Temperature was increased from 10 °C (ambient) by 2 °C per day, and maintained at 27 °C, by the addition of geothermally warmed water (36 °C). The control system substantially increased the controllability and precision of heating ponds compared to manual operation. Systems were designed to control sets of four ponds. In designing this control system, consideration of biological constraints was essential. Reproduction in channel catfish is most strongly influenced by temperature. Because cold fronts are common during the winter and early spring (January–March), it was essential to ensure that pond temperatures did not fall below the range for spawning. Constraints on the heating rate and temperature variability to maintain fish health and stimulate spawning behavior were considered. Components of the control system included temperature measurement devices (type-T thermocouples), a central electronic control unit, electronic switches and electrically actuated ball valves. In response to the temperature sensed by each thermocouple, the controller sent a message to close or open the valve. When the valve was opened, warm water was added to the pond to increase the average pond temperature. Hardware and algorithm design and initial system testing were the major components of this project. The final design incorporated information on relevant biological parameters and safety features including peak pond temperature, independent aeration and water pressure control mechanisms. Initial results indicate successful control of this biological system, and ongoing studies suggest similar mechanisms may be used for additional control objectives. In particular, this system could be used to vary pond temperatures to study biological responses and to cool ponds by addition of well water during summer months.  相似文献   

Soil nitrogen availability alters rhizodeposition carbon flux into the soil microbial community     

Yaying Li  Juan Wang  Fuxiao Pan  Stephen James Chapman  Huaiying Yao 《Journal of Soils and Sediments》2016,16(5):1472-1480

  相似文献   

土壤增氧方式对其氮素转化和水稻氮素利用及产量的影响   总被引：7，自引：3，他引：7  

胡继杰  朱练峰  胡志华  钟楚  林育炯  张均华  曹小闯  Allen Bohr James  禹盛苗  金千瑜 《农业工程学报》2017,33(1):167-174

以3种不同生态型水稻品种中浙优1号(水稻)、IR45765-3B(深水稻)和中旱221(旱稻)为材料,比较研究了不同增氧方式(T1-增施过氧化钙、T2-微纳气泡水增氧灌溉、T3-表土湿润灌溉和CK-淹水对照)下稻田土壤氮素转化和水稻氮素吸收利用特性。结果表明:1)增氧处理明显改善土壤氧化还原状况,3种增氧方式下土壤氧化还原电位均高于CK。稻田增氧促进土壤氮素硝化,在分蘖期和齐穗期T1、T2和T3的土壤硝化强度和脲酶活性均显著高于CK,反硝化强度显著低于CK。2)不同增氧处理对水稻氮素吸收的影响不同,在拔节期、齐穗期和完熟期3品种的植株氮素积累量均表现为T1、T2显著高于CK,而T3显著低于CK;在完熟期,T1处理下中浙优1号、IR45765-3B和中旱221植株氮素积累量分别较CK增加了21.2%、13.2%和17.0%,而T2处理下3品种的植株氮素积累量分别较CK增加了14.3%、6.9%和9.1%。3)与CK相比,T1和T2显著提高水稻籽粒产量和收获指数,氮素籽粒生产效率与CK无显著差异,而T3显著增加水稻氮素干物质生产效率和氮素籽粒生产效率。可见,施用过氧化钙和微纳气泡水增氧灌溉能有效改善稻田土壤氧化还原状况,不仅显著提高水稻产量,而且显著增强稻田氮的硝化而减少氮素损失,从而提高水稻氮素积累量和氮素收获指数。  相似文献   

Crop management effects on soil carbon sequestration on selected farmers’ fields in northeastern Ohio     

Marek K. Jarecki  Rattan Lal  Randy James 《Soil & Tillage Research》2005,81(2):265-276

Soil organic carbon (SOC) pool is the largest among terrestrial pools. The restoration of SOC pool in arable lands represents a potential sink for atmospheric CO₂. Restorative management of SOC includes using organic manures, adopting legume-based crop rotations, and converting plow till to a conservation till system. A field study was conducted to analyze soil properties on two farms located in Geauga and Stark Counties in northeastern Ohio, USA. Soil bulk density decreased with increase in SOC pool for a wide range of management systems. In comparison with wooded control, agricultural fields had a lower SOC pool in the 0–30 cm depth. In Geauga County, the SOC pool decreased by 34% in alfalfa (Medicago sativa L.) grown in a complex rotation with manuring and 51% in unmanured continuous corn (Zea mays L.). In Stark County, the SOC pool decreased by 32% in a field systematically amended with poultry manure and 40% in the field receiving only chemical fertilizers. In comparison with continuous corn, the rate of SOC sequestration in Geauga County was 379 kg C ha⁻¹ year⁻¹ in no-till corn (2 years) previously in hay (12 years), 760 kg C ha⁻¹ year⁻¹ in a complex crop rotation receiving manure and chemical fertilizers, and 355 kg C ha⁻¹ year⁻¹ without manuring. The rate of SOC sequestration was 392 kg C ha⁻¹ year⁻¹ on manured field in Stark County.  相似文献   

Characterization of glomalin as a hyphal wall component of arbuscular mycorrhizal fungi   总被引：1，自引：0，他引：1  

James D. Driver 《Soil biology & biochemistry》2005,37(1):101-106

Arbuscular mycorrhizal fungi (AMF) produce a protein, glomalin, quantified operationally in soils as glomalin-related soil protein (GRSP). GRSP concentrations in soil can range as high as several mg g⁻¹ soil, and GRSP is highly positively correlated with aggregate water stability. Given that AMF are obligate biotrophs (i.e. depending on host cells for their C supply), it is difficult to explain why apparently large amounts of glomalin would be produced and secreted actively into the soil, since the carbon could not be directly recaptured by the mycelium (and benefits to the AMF via increased soil structure would be diffuse and indirect). This apparent contradiction could be resolved by learning more about the pathway of delivery of glomalin into soil; namely, does this occur via secretion, or is glomalin tightly bound in the fungal walls and only released after hyphae are being degraded by the soil microbial community? In order to address this question, we grew the AMF Glomus intraradices in in vitro cultures and studied the release of glomalin from the mycelium and the accumulation of glomalin in the culture medium. Numerous protein-solubilizing treatments to release glomalin from the fungal mycelium were unsuccessful (including detergents, acid, base, solvents, and chaotropic agents), and the degree of harshness required to release the compound (autoclaving, enzymatic digestion) is consistent with the hypothesis that glomalin is tightly bound in hyphal and spore walls. Further, about 80% of glomalin (by weight) produced by the fungus was contained in hyphae and spores compared to that released into the culture medium, strongly suggesting that glomalin arrives mainly in soil via release from hyphae, and not primarily through secretion. These results point research on functions of glomalin and GRSP in a new direction, focusing on the contributions this protein makes to the living mycelium, rather than its role once it is released into the soil.  相似文献