Mapping‐by‐sequencing in complex polyploid genomes using genic sequence capture: a case study to map yellow rust resistance in hexaploid wheat

Previously we extended the utility of mapping‐by‐sequencing by combining it with sequence capture and mapping sequence data to pseudo‐chromosomes that were organized using wheat–Brachypodium synteny. This, with a bespoke haplotyping algorithm, enabled us to map the flowering time locus in the diploid wheat Triticum monococcum L. identifying a set of deleted genes (Gardiner et al., 2014). Here, we develop this combination of gene enrichment and sliding window mapping‐by‐synteny analysis to map the Yr6 locus for yellow stripe rust resistance in hexaploid wheat. A 110 MB NimbleGen capture probe set was used to enrich and sequence a doubled haploid mapping population of hexaploid wheat derived from an Avalon and Cadenza cross. The Yr6 locus was identified by mapping to the POPSEQ chromosomal pseudomolecules using a bespoke pipeline and algorithm (Chapman et al., 2015). Furthermore the same locus was identified using newly developed pseudo‐chromosome sequences as a mapping reference that are based on the genic sequence used for sequence enrichment. The pseudo‐chromosomes allow us to demonstrate the application of mapping‐by‐sequencing to even poorly defined polyploidy genomes where chromosomes are incomplete and sub‐genome assemblies are collapsed. This analysis uniquely enabled us to: compare wheat genome annotations; identify the Yr6 locus – defining a smaller genic region than was previously possible; associate the interval with one wheat sub‐genome and increase the density of SNP markers associated. Finally, we built the pipeline in iPlant, making it a user‐friendly community resource for phenotype mapping.     

Environmental Enrichments for a Group of Captive Macaws: Low Interaction Does Not Mean Low Behavioral Changes

Environmental enrichment has been widely used to improve conditions for nonhuman animals in captivity. However, there is no consensus about the best way to evaluate the success of enrichments. This study evaluated whether the proportion of time spent interacting with enrichments indicated the proportion of overall behavioral changes. Six environmental enrichments were introduced in succession to 16 captive macaws, and interaction of the animals with them as well as the behaviors of the group were recorded before and during the enrichments. All of the enrichments affected the proportions of time spent in different behaviors. Macaws interacted more with certain items (hibiscus and food tree) than with others (a toy or swings and stairs), but introduction of the enrichments that invoked the least interaction caused as many behavioral changes as those that invoked the most. Moreover, feeding behavior was only affected by the enrichment that invoked the least interaction, a change not detected by a general analysis of enrichment effects. In conclusion, little interaction with enrichment does not mean little change in behavior, and the effects of enrichments are more complex than previously considered.     

Long-Term Macroevaluation of Environmental Enrichment in Three Brown Bears (Ursus arctos) at Barcelona Zoo

The evaluation of enrichment programs is important to determine their effect on nonhuman animal welfare. The daily activity pattern and use of space of 3 brown bears (Ursus arctos) were used for long-term macroevaluation of enrichment to compare the baseline and enrichment phases. Focal sampling methods were used for data collection, and instantaneous scans were made at 2-min intervals during 15 sessions of 1 hr for each animal during the 2 study periods. The enrichment devices were categorized as feeding, occupational, and sensorial. The long-term macroevaluation in 3 bears showed statistically significant differences in some types of activity but not in others. There were also statistically significant differences for the use of space in 4 of the 8 zones in which the enclosures were divided. A more homogenous pattern in the use of space was only observed during the enrichment phase in the old female. The 3 brown bears followed different patterns concerning the enrichment program.     

Health risk assessment of heavy metals and metalloids via dietary intake of a potential vegetable (Coriandrum sativum L.) grown in contaminated water irrigated agricultural sites of Sargodha,Pakistan

Levels of Mo, As, Se, Fe, Cu, Zn, Ni, and Pb were determined in a vegetable commonly consumed in Pakistan. Samples were collected from three different sites (Ratokala, Phularwan, and Mailowal) supplied with three different water sources. Mo and Pb in water and Mo and As in C. sativum were higher than the suggested standards at the international level. Lower bioconcentration factor and pollution load index were seen at Site-I than at other sites. A positive association was found between the rhizosphere metals and those of the vegetable at all three sites. Enrichment factor at three sites ranged from 0.28 to 10.39. The highest value of daily intake of metals was found for Fe (0.245 mg/kg/day) and of the health risk index for As (70.41) at the wastewater inundated site. It is inferred that uptake of Mo, As, Cu, Ni, and Pb through C. sativum represents a high health danger to the individuals using this vegetable.     

Pharmacophore modeling and structure-based virtual screening to identify potent inhibitors targeting LuxP of Vibrio harveyi

The main aim of the study is to identify molecules that can disrupt quorum sensing (QS) system of Vibrio harveyi and therefore perhaps the production of toxins. Recently, a novel class of dioxazaborocane derivatives has been found to block AI-2 QS by targeting LuxPQ, but the mechanism of protein inhibition is still unclear. In order to investigate the possible binding modes, all the derivatives were docked into the binding site of LuxP using induced fit docking (IFD). The computed binding affinity is in good agreement with the experimental data. Resultant protein–ligand complexes were simulated using Desmond module and the result revealed better binding of ligands in the binding site of LuxP. Both pharmacophore- and structure-based virtual screening was performed to identify novel hits against LuxP. A filtering protocol, including lipinski filters, number of rotatable bonds and three levels of docking precisions were used for the selection of hits with specific properties. The virtual screening results were then combined and analyzed, which retrieved six hits with significant Glide score, binding affinity toward LuxP. The pharmacokinetic properties of the retrieved hits are in the acceptable range. Enrichment calculation was performed to validate the final hits, to discriminate the active compounds from the inactive compounds. The identified hits could serve as a base for further drug development against LuxP of Vibrio harveyi.     

Studies on mobilization of chromium with reference to its plant availability – Role of organic acids

Metal-organic acid interactions with special reference to their plant availability have been studied. The role of organic acids in the mobilization of Cr by converting it into labile organically bound form, enhancing its availability, is highlighted. Pot experiments are conducted to investigate the effect of various organic acids on the uptake and translocation of root absorbed trivalent and hexavalent chromium by maize (z. mays) plants grown in sand and soil culture. Statistically significant increases in chromium accumulation from CrIII-treated plants in the presence of increasing concentrations of organic acid suggest the existence of CrIII – organic acid interactions in the soil plant system. In order to support the above mentioned hypothesis of formation of organically bound CrIII in the presence of various organic acids (carboxylic and amino acids), separate experiments have been performed to synthesize and estimate its respective organically bound forms. Amendments with organic acids, however, do not appear to markedly affect chromium accumulation from CrVI treatment. The results are discussed on the basis of the potential of organic acids to form complexes with CrIII.     

A free-air enrichment system for exposing tall forest vegetation to elevated atmospheric CO2

A free-air CO₂ enrichment (FACE) system was designed to permit the experimental exposure of tall vegetation such as stands of forest trees to elevated atmospheric CO₂ concentrations ([CO₂]_a) without enclosures that alter tree microenvironment. We describe a prototype FACE system currently in operation in forest plots in a maturing loblolly pine (Pinus taeda L.) stand in North Carolina, USA. The system uses feedback control technology to control [CO₂] in a 26 m diameter forest plot that is over 10 m tall, while monitoring the 3D plot volume to characterize the whole-stand CO₂ regime achieved during enrichment. In the second summer season of operation of the FACE system, atmospheric CO₂ enrichment was conducted in the forest during all daylight hours for 96.7% of the scheduled running time from 23 May to 14 October with a preset target [CO₂] of 550 μmol mol^–1, ≈ 200 μmol mol^–1 above ambient [CO₂]. The system provided spatial and temporal control of [CO₂] similar to that reported for open-top chambers over trees, but without enclosing the vegetation. The daily average daytime [CO₂] within the upper forest canopy at the centre of the FACE plot was 552 ± 9 μmol mol^–1 (mean ± SD). The FACE system maintained 1-minute average [CO₂] to within ± 110 μmol mol^–1 of the target [CO₂] for 92% of the operating time. Deviations of [CO₂] outside of this range were short-lived (most lasting < 60 s) and rare, with fewer than 4 excursion events of a minute or longer per day. Acceptable spatial control of [CO₂] by the system was achieved, with over 90% of the entire canopy volume within ± 10% of the target [CO₂] over the exposure season. CO₂ consumption by the FACE system was much higher than for open-top chambers on an absolute basis, but similar to that of open-top chambers and branch bag chambers on a per unit volume basis. CO₂ consumption by the FACE system was strongly related to windspeed, averaging 50 g CO₂ m^–3 h^–1 for the stand for an average windspeed of 1.5 m s^–1 during summer. The [CO₂] control results show that the free-air approach is a tractable way to study long-term and short-term alterations in trace gases, even within entire tall forest ecosystems. The FACE approach permits the study of a wide range of forest stand and ecosystem processes under manipulated [CO₂]_a that were previously impossible or intractable to study in true forest ecosystems.     

Effect of CO2 Concentration Doubling on the Leaf Morphology and Structure of 10 Species in Gramineae

The effects of CO2 concentration on leaf thickness, chloroplast manbers in the bundle sheath cell, epidermal cell density, stomatal density, stomatal index, stomatal size were compared in 10 species in Gramineae: Triticum aestivum L., T. aestivum ssp. tibeticum, Hordeum vulgare L., H. brevisubulatum ( Trin. ) Link, Oryza sativa L., O. meyeriana ssp. granulata, Setaria italica (L.) Beauv, S. viridis (L.) Beauv, Sorghum vulgare Pers., Zea mays L. following their exposure to doubled carbon dioxide (700μL/L) and ambient carbon dioxide concentration (350μL/L). The results indicated that different species of plants might vary in their response to doubled CO2. In general, the leaves became thicker under the elevated CO2 condition. The mean stomatal density of the C3 species was decreased in doubled CO2, whereas the results of C4 species showed an inverse trend. The epidermal cell density and the chloroplast numbers of the bundle sheath cell in the wild plant species were less than those in the control under CO2 enrichment. The stomatal density was positively correlated with the stomatal index. Finally, the general pattern of structural variation under different CO2 concentrations was proposed, and their implication to the research of global change was discussed as well.     

鹅掌楸苗期动态生命表

报道了鹅掌楸在苗圃播种后的出苗率和幼苗存活率,根据定期观察数据编制了苗期动态生命表。结果表明,4个种源的出苗率都很低(1.64%～3.05%),比其各自的饱满种子率低得多;天然种源的出苗率高于栽培的种源,但前者的出苗数占饱满种子数的比例却低于后者。至一个生长季以后,幼苗存活率仅占出苗数的16%～27%,而黄山种源与庐山种源的交配后代则高达60%,明显地高于其亲本和其它种源。种子大小对于出苗率和幼苗存活率没有直接影响。最后讨论了遗传因素和生存环境对幼苗存活的影响,并认为种子和幼苗适合度低是鹅掌楸致濒的重要原因之一。