Using simulations to optimize genetic diversity in Prunus avium seed harvests

Conservation of forest genetic resources has drawn much attention in the last decades, as it prevents negative effects of genetic erosion on adaptability potential of material used for afforestation. According to the German Act on Forest Reproductive Material, seed harvesting must occur in certified stands. Seed lots must stem from a minimum number of seed-trees, although the effect of this limit on genetic diversity has not been addressed. In this study, we aimed at understanding the effect of seed harvesting strategies on genetic diversity. We used the simulation model Eco-Gene and real molecular data to disentangle the effects of number of seed-trees and harvesting method in three wild cherry (Prunus avium) stands. Our results outline the importance of harvesting genetically different or distant seed-trees in maintaining genetic diversity. Besides optimal sampling strategy, we also recommend minimum harvesting of 25 seed-trees to reach 90 % of genetic diversity available within the stand. The outcomes of these results for the practice are also discussed.     

Optimization of combined genetic gain and diversity for collection and deployment of seed orchard crops

Genetic gain and diversity of seed orchards’ crops are determined by the number of parents, their breeding values and relatedness, within-orchard pollination efficiency, and level of pollen contamination. These parameters can be manipulated at establishment by varying clonal representation (e.g., linear deployment), during orchard development by genetic thinning, or by selective harvesting. Since clonal fecundities are known to vary both within and among years, then each seed crop has a unique genetic composition and, therefore, crops should be treated on a yearly basis. Here we present an optimization protocol that maximizes crop’s genetic gain at any desired genetic diversity through the selection of a subset of the crop that meets both parameters. The genetic gain is maximized within the biological limit set by each clone’s seed-cone production and effective population size is used as a proxy to genetic diversity whereby any relationship among clones is considered. The optimization was illustrated using 3 years’ reproductive output data from a first-generation western larch seed orchard and was tested under various scenarios including actual male and female reproductive output and male reproductive output assumed to be either equal to that of female or a function of clonal representation. Furthermore, various levels of co-ancestry were assigned to the orchard’s clones in supplementary simulations. Following the optimization, all solutions were effective in creating custom seedlots with different gain and diversity levels and provided the means to estimate the genetic properties of composite seedlots encompassing the remaining “unused” seed from a number of years.     

马尾松二代无性系种子园子代父本分析及花粉散布

目前国内较早建立的马尾松(Pinus massoniana)二代种子园正陆续进入正常开花结实期。研究马尾松二代种子园花粉散布和自由授粉子代的父本组成, 可为生产上指导马尾松高世代种子园的规划设计和遗传管理提供理论依据。该文利用筛选的11对SSR引物, 对马尾松二代无性系种子园内8个无性系单株的320个自由授粉子代和48个候选父本进行了扩增, 并采用最大似然法对子代进行父本分析。结果表明: 11个位点共检测到61个等位基因, 每个位点的等位基因数在2-11之间, 平均为5.55个。试验亲本和子代群体的总平均观测杂合度(H_o)、期望杂合度(H_e)及多态信息含量(PIC)分别为0.428、0.433和0.387。在80%的可信度水平下可为232 (72.50%)个子代确定其父本。平均每个采种母树与19个父本产生子代。在自由授粉状态下, 马尾松二代种子园自交率为1.72%, 自交现象很弱, 其交配方式以异交为主。绝大多数亲本无性系的雄性繁殖适合度在1.00%-4.00%之间, 候选父本平均繁殖适合度为2.17%, 平均形成5个后代。马尾松有效花粉的散布距离和固定交配距离的父本繁殖适合度均符合正态分布, 两者呈极显著负相关, 其主要散布距离集中在0-100 m, 而检测到的最大散布距离为192 m。种子园花粉污染率较低, 仅为4.06%。总体看来, 树冠南面子代亲本交配距离较北面有增加的趋势, 但树冠南、北面子代父本组成数并未表现明显的规律。     

Mating patterns and pollen dispersal in a Japanese larch(Larix kaempferi) clonal seed orchard: a case study

Pollination dynamics highly determines the genetic quality of seed orchard crops. However, there is less research about the effect of mating patterns on seed productivity of orchard crops. So far, clonal seed orchards have been producing genetically improved seedlings used for most Japanese larch(Larix kaempferi(Lamb.) Carr.) plantations in China. In the present study, a total of 17 highly variable simple sequence repeat(SSR) markers were used for genotyping a progeny trial population consisting of 647 open-pollinated progenies germinated from seeds which were collected from 63 maternal clones with 140 potential paternal clones in a Japanese larch clonal seed orchard in China. Paternity analysis was used in the present case study in order to evaluate the level of paternal gametic contribution, estimate pollen contamination and selfing rates, and investigate pollination patterns,pollen dispersal patterns and the impact of mating patterns on seed productivity of orchard crops. We observed 93.7% of the success rate of the parental assignment, unequal paternal gametic contribution(0–12.4%) with 6.3% of the progenies derived from pollen contamination or unsampled pollen donors, and absence of evidence for selfing. We also found that pollination rate highly depended on the distance between pollen donors and maternal parents, the majority of the identified crossing(65.7%)occurred between clones within a 150-m radius, and large variations in growth performance existed among the paternal halfsiblings. Progeny growth performance(diameter at breast(DBH) and height(HGT)) was measured at Age-20 in order to investigate the impact of mating patterns on timber production of orchard crops. As either the paternal or maternal, two clones(i.e., clones Z38 and Z62) were identified to have produced progenies with higher average stem volume breeding values than that of all of the progenies. Specifically, the genetic gains for volume were 3.53% for the two clones as paternal parents, and 8.26% as the maternal parents at Age-20. Thus, both elite clones were ideal candidates for the construction of next-generation clonal seed orchards due to their synchronous reproductive phenology with greater crossing rate and higher genetic gain. These results improved the pedigree information to provide solid evidence of mating patterns for future design and effective management of seed orchards and for the development of viable long-term breeding strategies for other coniferous species.     

Performance of microsatellites for parentage assignment following mass controlled pollination in a clonal seed orchard of loblolly pine (Pinus taeda L.)

Mass controlled pollination (MCP), involving large-scale application of pollen on physically isolated female reproductive organs, has been a lower cost alternative to controlled pollination for the commercial production of genetically improved seeds. Nevertheless, rare are the studies that examined the efficacy of operational MCP and no such assessment has been done in loblolly pine to date. The success of MCP was assessed by a microsatellite-based investigation of the realized versus expected parentage of a set of 300 Pinus taeda offspring in 19 families generated in two subsequent rounds of MCP in 2005 and 2006 in a clonal seed orchard in Brazil. Multi-locus combined probability of parentage exclusion both theoretical and realized from actual testing was >99 % for single parent and parent pair testing when using nine or ten markers. Parentage assignments carried out under a maximum likelihood framework revealed a significantly higher success rate of MCP in 2006 (84 %) following technical improvements adopted to minimize pollen contamination and maximize male reproductive success, although significant variability in the correct maternity and full parentage was seen among individual families. The observed patterns of unexpected parentage indicated that this variability likely resulted from mislabeling of clonal ramets of the parents used in the crosses which impacted both maternity and paternity. Preventing pollen contamination will not be sufficient for successful MCP if inaccuracies exist in the identity of the clonal plants that ultimately provide pollen and female strobili, showing that DNA marker auditing and correction of identity of all ramets in a clonal seed orchard should be a standard practice in the operational implementation of MCP.     

Efficient classification of complete parameter regions based on semidefinite programming

Background  

Current approaches to parameter estimation are often inappropriate or inconvenient for the modelling of complex biological systems. For systems described by nonlinear equations, the conventional approach is to first numerically integrate the model, and then, in a second a posteriori step, check for consistency with experimental constraints. Hence, only single parameter sets can be considered at a time. Consequently, it is impossible to conclude that the "best" solution was identified or that no good solution exists, because parameter spaces typically cannot be explored in a reasonable amount of time.     

红松种子园种群表型多样性研究

为揭示红松（Pinus koraiensis Sieb.et Zucc.）不同种群的表型分化程度和变异规律,以吉林省露水河红松种子园6个种群红松为研究对象,采用巢式方差分析、多重比较、变异系数和聚类分析等方法对红松的叶片、球果和种子共15个表型性状进行了系统分析。结果表明：（1）红松15个表型性状在种群间和种群内均存在着极显著的差异,红松种群遗变异比较丰富,在松属植物中属于中等水平,其中纬度最低的露水河种群在其中10个表型性状均值上表现出最高值;（2）红松种群间的表型分化系数（Vst）均值为12.39%,种群内的变异（87.61%）大于种群间的变异（12.39%）,种群内的变异是主要变异来源;（3）各表型性状平均变异系数为13.28%,变幅为6.16%-31.48%,叶片、球果、种子的平均变异系数依次为：球果17.86% > 针叶11.19% > 种子9.87%,种子性状最小,成为最稳定的表型性状,带岭和丰林种群表型性状遗传多样性要高于其他种群;（4）利用欧氏平均距离对红松种群进行UPGMA聚类分析,红松种群的表型性状按照地理距离而聚类,可将红松种子园6个种群分为4类,其表型性状跟地形（东北山脉）有一定的契合。红松种群具有中等水平的表型遗传多样性,种群间和种群内均存在丰富的表型变异,研究结果为顺利开展红松种质资源收集、保存,以及良种选育等工作提供依据。     

Using psychological theory to inform methods to optimize the implementation of a hand hygiene intervention

ABSTRACT: BACKGROUND: Careful hand hygiene (HH) is the single most important factor in preventing the transmission of infections to patients, but compliance is difficult to achieve and maintain. A lack of understanding of the processes involved in changing staff behaviour may contribute to the failure to achieve success. The purpose of this study was to identify nurses' and administrators' perceived barriers and facilitators to current HH practices and the implementation of a new electronic monitoring technology for HH. METHODS: Ten key informant interviews (three administrators and seven nurses) were conducted to explore barriers and facilitators related to HH and the impact of the new technology on outcomes. The semi structured interviews were based on the Theoretical Domains Framework by Michie et al. and conducted prior to intervention implementation. Data were explored using an inductive qualitative analysis approach. Data between administrators and nurses were compared. RESULTS: In 9 of the 12 domains, nurses and administrators differed in their responses. Administrators believed that nurses have insufficient knowledge and skills to perform HH, whereas the nurses were confident they had the required knowledge and skills. Nurses focused on immediate consequences, whereas administrators highlighted long-term outcomes of the system. Nurses concentrated foremost on their personal safety and their families' safety as a source of motivation to perform HH, whereas administrators identified professional commitment, incentives, and goal setting. Administrators stated that the staff do not have the decision processes in place to judge whether HH is necessary or not. They also highlighted the positive aspects of teams as a social influence, whereas nurses were not interested in group conformity or being compared to others. Nurses described the importance of individual feedback and self-monitoring in order to increase their performance, whereas administrators reported different views. CONCLUSIONS: This study highlights the benefits of using a structured approach based on psychological theory to inform an implementation plan for a behavior change intervention. This work is an essential step towards systematically identifying factors affecting nurses' behaviour associated with HH.     

Using clonal replicates to explore genetic variation in a perennial plant species

Summary An experimental design is presented for estimating genetic parameters using a family structure with clonally replicated individuals. This experimental design provides a technique to quantify genetic variation in a population, with partial separation of additive, dominance and epistatic gene action. Our method is offered as an alternative to techniques for estimating epistatic gene action that require several generations and/or inbreeding. Such methods are not particularly useful for long-lived perennials with long generation cycles. An example of the analysis is given with a forest tree species, Populus deltoides Bartr., and parameter estimates are presented for traits measured over 8 years.     

Gene flow estimation with microsatellites in a Malagasy seed orchard of Eucalyptus grandis

Eucalyptus grandis has a mixed-mating reproductive system. Malagasy Eucalyptus seed orchards were established 15 years ago with two aims both based on panmixia: open-pollinated seed production and genetic improvement. The panmixia hypothesis has never been confirmed in the seed orchard. From a seedling seed-orchard stand comprising 349 trees and using data obtained with six selected microsatellite markers, paternity analysis was performed for 724 offspring collected on 30 adult trees. Paternity assignment, based on exclusion procedures and likelihood-ratio method, was achieved with high accuracy; the exclusion probability value was 0.997. The outcrossing rate was very high (96.7%). More than 50% of potential male trees (199 out of 349) in the seed orchard contributed to pollination for 440 offspring of 30 progenies (8.6% of the basic population). The pollination rate from outside the seed orchard was high (39.2%), but might be due to the small size of this seed orchard. This study showed that "panmixia-like pollination" can be assumed.     

Using the Golden Triangle to optimize clearance and oral absorption

The Golden Triangle is a visualization tool developed from in vitro permeability, in vitro clearance and computational data designed to aid medicinal chemists in achieving metabolically stable, permeable and potent drug candidates. Classifying compounds as permeable and stable and plotting molecular weight (MW) versus octanol:buffer (pH 7.4) distribution coefficients (log D) or estimated octanol:buffer (pH 7.4) distribution coefficients (elog D) reveals useful trends. Analysis of at least two orthogonal trends, such as permeability and clearance, can be extremely effective in balancing and optimizing multiple properties. In addition, molecular weight and log D impact potency-efficiency calculations, allowing potency, clearance and permeability to be optimized simultaneously.     

Using biofeedback to optimize scapular muscle activation ratios during a seated resisted scaption exercise

Impairments in muscle activation have been linked to increased risk of developing shoulder pathologies such as subacromial impingement syndrome (SIS) and associated rotator cuff injuries. Individuals with SIS have demonstrated increased upper trapezius (UT) muscle activation and reduced serratus anterior (SA) and lower trapezius (LT) muscle activation, which can be collectively represented as ratios (UT/SA and UT/LT). Targeted exercise is an important component of shoulder rehabilitation programs to re-establish optimal muscle activation and ratios. Electromyography (EMG) biofeedback during exercise has been shown to reduce UT activation and favorably alter scapular muscle activation ratios, however, a literature gap exists regarding the efficacy of other types of biofeedback. Therefore, we compared the effects of three types of biofeedback (visual EMG, auditory, verbal cues) on UT/SA and UT/LT ratios during a seated resisted scaption exercise in fifteen subjects without shoulder pain. Baseline muscle activation was recorded and compared to real-time muscle activation during each randomized biofeedback trial. All biofeedback types showed improvements in the UT/SA and UT/LT ratios, with visual EMG demonstrating a significant change in UT/LT ratio (p < 0.05). These results suggest that biofeedback could be utilized as a component of rehabilitation programs to prevent or treat shoulder pain.     

Using severity factor as a parameter to optimize krill treatment under subcritical water conditions

The aim of this study was to optimize the conditions for subcritical water treatment of krill, as expressed with a single parameter: the severity factor (log R₀). Raw krill was treated under subcritical water conditions at various log R₀ values (1.54–3.75) by varying the treatment temperatures (120–180 °C) and times (0–10 min) in two different sizes of batch-type vessel (10 and 117 mL). The log R₀ value could efficiently describe changes in various properties of the obtained liquid extracts and solid residues. The most desirable shrimp-like flavor intensity and highest sensory preference were obtained for log R₀ values of 2.75–3.01. The results also proved that severity factor can be used as a single parameter to control subcritical water treatment conditions in differently sized batch-type vessels to produce shrimp-like flavor extract and residue from krill.     

利用模拟退火算法优化Biome-BGC模型参数

生态过程模型建立在明确的机理之上,能够较好地模拟陆地生态系统的行为和特征,但模型众多的参数,成为模型具体应用的瓶颈。本文以Biome-BGC模型为例,采用模拟退火算法,对其生理、生态参数进行优化。在优化过程中,先对待优化参数进行了选择,然后采取逐步优化的方法进行优化。结果表明,使用优化后的参数,模型模拟结果与实际观测更为接近,参数优化能有效地降低模型模拟的不确定性。文中参数优化的过程和方法,可为生态模型的参数识别和优化提供一种实例和思路,有助于生态模型应用区域的扩展。     

Low temperature seed germination of several tomato genotypes

Environmental stresses at particularly vulnerable stages during crop development may severely diminish productivity. At temperature of 10 °C or below cultivated tomato germinate slowly if at all. In this study, seven tomato genotypes bred at the Research Institute of Vegetable Crops were evaluated for germination time at 10 °C. Analysis identified that one genotype which has L. chilense in its pedigree, germinated most rapidly while four other genotypes germinated slower. After 21 days, four out of five of the genotypes resulted in seed germination from 81 to 98 %.     

Effective number of pollen parents in clonal seed orchards

Summary A method for quantifying mating behavior in clonal seed orchards of forest tree species is presented. It involves the estimation of effective numbers of pollen parents from seed samples collected from individual ramets in such orchards. These effective numbers are variance effective numbers for populations of male gametes that are successful in uniting with ovules to produce viable seed. Three such effective numbers are defined for clonal seed orchards:N _p (a) for male gamete populations for ramets within clones,N _p (b) for male gamete populations for clones, andN _p (c) for male gamete populations for entire orchards. Estimators for these effective numbers and for standardized variances of allele frequencies in the male gametic populations are presented. Expressions are also given for the confidence intervals for each of the three effective numbers. Estimates of these parameters and the corresponding confidence intervals for two seed orchards are presented and interpreted.     

利用氧化还原电位调控乳酸发酵

研究了控制不同氧化还原电位（oxidation—reduction potential,ORP）对乳酸发酵过程的影响。通过5L发酵罐分批发酵实验发现ORP水平控制在-170mV时最有利于乳酸生成,乳酸最高质量浓度达176g／L,糖酸转化率为94％,其平均乳酸产率3．7g/（L·h）,比ORP控制在-220mV和-120mV时分别高19％,37％;通过对发酵过程胞外有机酸浓度及代谢流分析发现氧化还原电位是通过影响细胞内代谢流分布来影响乳酸合成的。