Imputation of missing genotypes from low‐ to high‐density SNP panel in different population designs

Imputation of missing genotypes, in particular from low density to high density, is an important issue in genomic selection and genome‐wide association studies. Given the marker densities, the most important factors affecting imputation accuracy are the size of the reference population and the relationship between individuals in the reference (genotyped with high‐density panel) and study (genotyped with low‐density panel) populations. In this study, we investigated the imputation accuracies when the reference population (genotyped with Illumina BovineSNP50 SNP panel) contained sires, halfsibs, or both sires and halfsibs of the individuals in the study population (genotyped with Illumina BovineLD SNP panel) using three imputation programs (fimpute v2.2, findhap v2, and beagle v3.3.2). Two criteria, correlation between true and imputed genotypes and missing rate after imputation, were used to evaluate the performance of the three programs in different scenarios. Our results showed that fimpute performed the best in all cases, with correlations from 0.921 to 0.978 when imputing from sires to their daughters or between halfsibs. In general, the accuracies of imputing between halfsibs or from sires to their daughters were higher than were those imputing between non‐halfsibs or from sires to non‐daughters. Including both sires and halfsibs in the reference population did not improve the imputation performance in comparison with when only including halfsibs in the reference population for all the three programs.     

Effects of drought on nutrient and ABA transport in Ricinus communis

We studied the effects of variations of water flux through the plant, of diurnal variation of water flux, and of variation of vapour pressure deficit at the leaf on compensation pressure in the Passioura-type pressure chamber, the composition of the xylem sap and leaf conductance in Ricinus communis. The diurnal pattern of compensation pressure showed stress relaxation during the night hours, while stress increased during the day, when water limitation increased. Thus compensation pressure was a good measure of the momentary water status of the root throughout the day and during drought. The bulk soil water content at which predawn compensation pressure and abscisic acid concentration in the xylem sap increased and leaf conductance decreased, was high when the water usage of the plant was high. For all xylem sap constituents analysed, variations in concentrations during the day were larger than changes in mean concentrations with drought. Mean concentrations of phosphate and the pH of the xylem sap declined with drought, while nitrate concentration remained constant. When the measurement leaf was exposed to a different VPD from the rest of the plant, leaf conductance declined by 400mmol m^?2 s^?1 when compensation pressure increased by 1 MPa in all treatments. The compensation pressure needed to keep the shoot turgid, leaf conductance and the abscisic acid concentration in the xylem were linearly related. This was also the case when the highly dynamic development of stress was taken into account.     

Water movement through Quercus rubra I. Leaf water potential and conductance during polycyclic growth

Two experiments examined simultaneous changes in leaf area (A_L), root length (L_r), stomatal conductance (g_s), leaf water potential (Ψ_L), transpiration and hydraulic plant conductance per unit leaf area (G) during the first three shoot cycles of northern red oak (Quercus rubra L.) grown under favourable and controlled conditions. Each shoot cycle consisted of bud swell, stem elongation, leaf expansion and rest; roots grew almost continuously. The g_s of all leaves decreased substantially while leaves of the newest flush were expanding and increased modestly when seedling leaf area remained constant. Overall, g_s decreased. The Ψ_L of mature leaves decreased during leaf expansion and increased by an equivalent amount during intervening periods. Possible explanations for the paired changes in g_s and Ψ_L are considered. Changes in G closely paralleled those of canopy g_s. These parallel changes during polycyclic seedling growth should act to keep seedling Ψ_L relatively constant as plant size increases and thereby help prevent Ψ_L from dropping to levels that would cause runaway embolism.     

The roles of history: age and prior exploitation in aquatic container habitats have immediate and carry‐over effects on mosquito life history

1. Per‐capita resource availability in aquatic habitats is influenced directly by consumer density via resource competition and indirectly via delayed resource competition when temporally non‐overlapping cohorts of larvae exploit the same resources. In detritus‐based systems, resources are likely to be influenced by the age of the aquatic habitat, as detritus changes in quality over time and may be replenished by new inputs. 2. For aquatic insects that exploit detritus‐based habitats, feeding conditions experienced during immature stages can influence fitness directly via effects on development and survivorship, but also indirectly by influencing adult traits such as fecundity and longevity. 3. Larval habitat age and prior resource exploitation were manipulated in a field experiment using the container mosquito Aedes triseriatus. 4. It was found that A. triseriatus from older habitats had greater larval survival, faster development and greater adult longevity. Exploitation of larval habitats by a prior cohort of larvae had a significant negative effect on subsequent cohorts of larvae by delaying development. 5. It is suggested that extended conditioning of detritus probably resulted in conversion of recalcitrant resources to more available forms which improved the quality of the habitat. 6. In a parallel study, evidence was found of carry‐over effects of habitat age and prior exploitation on adult longevity for A. triseriatus and Aedes japonicus collected from unmanipulated aquatic habitats. 7. These results indicate the importance of detritus dynamics and the discontinuous nature of resource competition in these mosquito‐dominated aquatic systems.     

Perfusion culture apparatus for suspended mammalian cells

A variety of processes have been proposed for mammalian cell culture in the commercial production of useful substances (e.g., monoclonal antibodies, therapeutic and diagnostics proteins). Among them, the perfusion culture of suspended non-immobilized cells is the most advantageous. Perfusion culture can be classified by the separation process of suspended cells from the culture mixture into three types, namely filtration, gravitational settling and centrifugation. From a commercial point of view, the present situation and technical problems of suspended-cell perfusion culture will be reviewed based on the three types, The recent development of perfusion culture has been carried out mainly on the filtration separation process, but the centrifugation process seems to have a promising future because of operation stability and scale-up feasibility. The reasons will be explained in details.     

厚壳贻贝whirlin类贝壳基质蛋白的重组表达与功能分析

贝壳历来是生物工程和材料学研究的重要对象。贝壳中的贝壳基质蛋白质在贝壳的形成与发育过程中具有重要的调控作用。Whirlin类蛋白质(Whirlin-like protein,WLP)是一种从厚壳贻贝(Mytilus coruscus)中鉴定的新型贝壳基质蛋白质。序列分析结果显示,该蛋白质含有PDZ(postsynaptic density/Discs large/Zonula occludens)结构域,而该结构域对贝壳生物矿化的影响目前尚无报道。为深入了解WLP在贝壳形成中对碳酸钙晶体的影响,在序列分析基础上,采用密码子优化结合原核重组表达,获得其重组表达产物后,开展了重组WLP对碳酸钙晶体形貌及晶型的影响研究,结晶速度抑制以及碳酸钙晶体结合分析。分析结果表明,重组WLP能诱导文石型碳酸钙晶体的形貌和方解石型碳酸钙晶体的晶型发生改变;同时重组WLP对碳酸钙晶体具有结合作用,且能抑制碳酸钙晶体的结晶速度。上述结果表明,WLP对贝壳的形成及发育具有重要影响,并可能在贝壳肌棱柱层的形成中发挥了重要作用。     

Individually mark–mass release–resight study elucidates effects of patch characteristics and distance on host patch location by an insect herbivore

1. How organisms locate their hosts is of fundamental importance in a variety of basic and applied ecological fields, including population dynamics, invasive species management and biological control. However, tracking movement of small organisms, such as insects, poses significant logistical challenges. 2. Mass‐release and individual–mark–recapture techniques were combined in an individually mark–mass release–resight (IMMRR) approach to track the movement of over 2000 adult insects in an economically important plant–herbivore system. Despite its widespread use for the biological control of the invasive thistle Carduus nutans, the host‐finding behaviour of the thistle head weevil Rhinocyllus conicus has not previously been studied. Insects were released at different distances from a mosaic of artificially created host patches with different areas and number of plants to assess the ecological determinants of patch finding. 3. The study was able to characterize the within‐season dispersal abilities and between‐patch movement patterns of R. conicus. Weevils found host plant patches over 900 m away. Large patches, with tall plants, situated close to the nearest release point had the highest first R. conicus resights. Patch area and plant density had no effect on the number of weevils resighted per plant; however, R. conicus individuals were more likely to disperse out of small patches and into large patches. 4. By understanding how R. conicus locates host patches of C. nutans, management activities for the control of this invasive thistle can be better informed. A deeper mechanistic understanding of host location will also improve prediction of coupled plant–herbivore spatial dynamics in general.     

Estimation of density of gibbon groups by use of loud songs

The density of gibbon populations may be estimated by listening for the loud duetted songs of monogamous territorial groups. This method requires a correction factor which must be estimated from the frequency of singing of an adequate number of known study groups. The correction factor and its error were estimated for pileated gibbons (Hylobates pileatus) in Khao Soi Dao Wildlife Sanctuary in southeastern Thailand. Among 30 groups studied, 47% sang per day, on average, but the variation between days and the variation in singing frequency between groups were large. Weather conditions, especially windiness, explained some variation in singing. During an area-wide survey of groups in the sanctuary, unexplained variation in singing from day to day accounted for approximately half of the sample error of group density estimated from 1-day listening samples. Error due to day-to-day variability can be reduced by listening for more than one day at each site. Correction factors based on the cumulative proportion of groups heard during longer (2–5-day) sample periods of listening were closer to 1.0, therefore leaving less room for error and bias of the correction factor. © 1993 Wiley-Liss, Inc.     

High herkogamy but low reciprocity characterizes isoplethic populations of Jasminum malabaricum,a species with stigma‐height dimorphism

• Studies of floral polymorphisms have focused on heterostyly, while stigma‐height dimorphism has received considerably less attention. Few studies have examined the reproductive biology of species with stigma‐height dimorphism to understand how factors influencing mate availability and pollen transfer are related to morph ratios in populations.
• Floral morphological traits, especially herkogamy and reciprocity, pollinator visitation, breeding system and spatiotemporal mate availability, are known to affect inter‐morph pollination and morph ratios in species with stigma‐height dimorphism. In this study, we investigated the presence of stigma‐height dimorphism and estimated morph ratios in four naturally occurring populations of Jasminum malabaricum. We quantified morph‐ and population‐specific differences in the abovementioned factors in these populations to understand the observed morph ratios.
• The positions of anthers and stigmas were characteristic of stigma‐height dimorphism, the first report of this polymorphism in the genus. All study populations were isoplethic, implying equal fitness of both morphs. Herkogamy was higher in the short‐styled morph, while reciprocity was higher between the long‐styled stigma and short‐styled anthers. Long‐ and short‐tongued pollinators were common floral visitors, and we observed no differences between morphs in spatiotemporal mate availability or pollinator visitation. Neither morph exhibited self‐ or heteromorphic incompatibility.
• The short‐styled stigma had lower reciprocity but likely receives sufficient inter‐morph pollen from long‐tongued pollinators, and also by avoiding self‐pollination due to higher herkogamy. These results highlight the importance of sufficient effective pollinators and floral morphological features, particularly herkogamy, in maintaining isoplethy in species with stigma‐height dimorphism.