Marker-based parentage analysis facilitates low input ‘breeding without breeding’ strategies for forest trees

Controlled crosses and progeny testing are important components of tree breeding programs. Recently, a new approach, ‘breeding without breeding’ (BWB), has been proposed to obtain structured pedigrees for the breeding and testing from wind-pollinated progenies; the technique uses high-resolution markers instead of conventional approaches. The BWB approach is attractive for outcrossing conifers where the breeding cycle is long and reproductive maturity is often delayed. For the application of the BWB approach, the accurate assignment of parents is essential. The first step in the application of the BWB approach is to conduct tests into the reliability of paternity and parent-pair exclusion procedures in complex situations. In this study we conducted multi-locus-based empirical and simulation analyses for a Scots pine seed orchard crop, in order to develop the appropriate parentage assignment techniques for BWB and to investigate whether pedigrees from a seed orchard crop can be determined with sufficient accuracy. The results were promising, as 93–97% of the seeds generated by mating among the seed orchard clones were correctly assigned to a parent-pair. When mating occurred with foreign pollen, the success rate of identifying mother clones was 60–78%. Based on these results, we propose three novel low input breeding strategies for forest trees. The principles of the different options and their potential benefits and costs are described and discussed using Scots pine as a case study.     

春玉米持续干旱过程中常用气孔导度模型的比较研究

气候变化背景下,干旱频发导致的土壤水分变化将影响气孔导度模型的适用性,进而影响生态系统碳-氮-水循环模拟的准确性。基于春玉米持续干旱田间模拟试验资料,比较了常用气孔导度模型在干旱条件下的模拟效果,评价了土壤水分响应函数对气孔导度模型效果的影响,并探讨了气孔导度模型的适用土壤水分范围。结果表明,在持续干旱过程中,模型模拟效果表现为BBL模型最优,其次是USO模型和BWB模型,Jarvis模型最差;引入土壤水分响应函数,提高了BWB模型和USO模型的模拟效果,而降低了Jarvis模型和BBL模型模拟效果,模型模拟效果表现为USO修正模型最优,其次是BBL修正模型和BWB修正模型,Jarvis修正模型最差。在持续干旱过程中,Jarvis模型和BWB模型的剩余气孔导度较大,而BBL模型和USO模型的剩余气孔导度相对较小,表明BBL模型和USO模型在干旱条件下具有一定的稳定性。基于95%置信区间判断表明:Jarvis模型、BBL模型和USO模型在土壤相对湿度范围为33%—83%条件下适用,而BWB模型的适用土壤相对湿度范围为33%—76%,引入水分响应函数后可在试验条件下适用。研究结果可为干旱条件下选取合适的气孔导度模型以准确模拟陆地生态系统碳循环和水循环提供依据,并为改善农业水资源的有效使用和评估提供支撑。     

Textiles wastewater treatment using anoxic filter bed and biological wriggle bed-ozone biological aerated filter

In this study, the performance of the anoxic filter bed and biological wriggle bed-ozone biological aerated filter (AFB-BWB-O₃-BAF) process treating real textile dyeing wastewater was investigated. After more than 2 month process operation, the average effluent COD concentration of the AFB, BWB, O₃-BAF were 704.8 mg/L, 294.6 mg/L and 128.8 mg/L, with HRT being 8.1-7.7 h, 9.2 h and 5.45 h, respectively. Results showed that the effluent COD concentration of the AFB decreased with new carriers added and the average removal COD efficiency was 20.2%. During operation conditions, HRT of the BWB and O₃-BAF was increased, resulting in a decrease in the effluent COD concentration. However, on increasing the HRT, the COD reduction capability expressed by the unit carrier COD removal loading of the BWB reactor increased, while that of the O₃-BAF reactor decreased. This study is a beneficial attempt to utilize the AFB-BWB-O₃-BAF combine process for textile wastewater treatment.     

Common variations in the pretest environment influence genotypic comparisons in models of anxiety

The behavioral characterization of rodent strains in different studies and laboratories can provide unreplicable results even when genotypes are kept constant and environmental control is maximized. In the present study, the influence of common laboratory environmental variables and their interaction with genotype on the results of behavioral tests of anxiety/emotionality were investigated. To this end, the inbred rat strains Lewis (LEW) and spontaneously hypertensive rats (SHR), which are known to differ for numerous emotionality-related behaviors, were tested in the open field (OF), elevated plus maze (EPM) and black/white box (BWB), while three environmental factors were systematically controlled and analyzed: (1) the experimenter handling the animal (familiar or unfamiliar); (2) the position of the home cage (top or bottom shelf of the rack) and (3) the behavioral state of the animal immediately before the test (arousal or rest). Experimenter familiarity did not alter the behavior of rats in the OF. Cage position, on the other hand, influenced the behavior in the OF and BWB, with rats housed in top cages appearing less anxious than those housed in the bottom. In the BWB (but not in the OF), these effects were genotype dependent. Finally, the behavioral state of the animals prior to testing altered the results of the EPM in a strain-dependent manner, with some anxiety-related genotypic differences being found only among rats that were aroused in their home cages. This study showed that common variations in the laboratory environment interact with genotype in behavioral tests of anxiety/emotionality. Recognizing and understanding such variations can help in the design of more effective experiments.     

Partitioning of pulmonary resistance in calves

Nine right apical lobes of healthy Friesian calves and 10 right apical lobes of double-muscled calves of Belgian White and Blue (BWB) breed were suspended in an airtight box, inflated at a constant transpulmonary pressure (Ptp), and subjected to quasi-sinusoidal pressure changes (amplitude: 0.5 kPa) at a frequency of 30 cycles/min. Lobar resistance (RL) was partitioned at six different lung volumes into three components: central airway resistance (Rc), small airway resistance (Rp), and tissue resistance (Rt). Pressure in small airways (2-3 mm ID) was measured with a retrograde catheter. Alveolar pressure was sampled in capsules glued onto the punctured pleural surface. RL was minimal at values of Ptp comprised between 0.5 and 0.7 kPa and increased at higher and lower values of Ptp. At a Ptp of 0.5 kPa, Rc, Rp, and Rt represented 30, 15, and 55% of RL, respectively, in Friesian calves and 25, 25, and 50% in BWB calves. Rp increased markedly at low lung volumes. Rt was responsible for the increase of RL at high Ptp. Rc tended to decrease at high Ptp. The significantly higher values of Rp in BWB calves (P less than 0.05) might explain the sensitivity of this breed to severe bronchopneumonia.     

A new phytoplasma detected in the South Australian native perennial shrub, Allocasuarina muelleriana

Allocasuarina muelleriana shrubs growing in natural sclerophyll roadside vegetation near Willalooka in the upper south‐east of South Australia have a high incidence of a yellowing disorder in either all or part of the foliage, combined in some cases with a shortening and curling of the leaf‐bearing stems. Samples from symptomatic and adjacent asymptomatic plants were tested for phytoplasmas by the polymerase chain reaction (PCR) assay. All but one asymptomatic plant were negative for phytoplasmas, whereas about half of the symptomatic plants were positive. Restriction fragment polymorphism analysis of PCR products indicated that the phytoplasma was related to the buckthorn witches.‐broom (BWB) and apple proliferation (AP) groups of phytoplasmas, members of which have not been previously reported in Australia. Further evidence from the sequence of the 16S rRNA gene and the use of PCR primers specific to the AP and pear decline (PD) phytoplasmas confirmed the close relationship to the BWB and AP group phytoplasmas.     

基于叶片尺度观测数据的气孔导度模型评价

气孔导度(g)是控制冠层与大气之间能量和水分交换的重要因素。空气湿度是控制植物叶片气孔导度的一个关键环境因子。在过去的十几年中,普遍得到应用的是Ball-Woodrow-Berry(BWB)模型和Leuning模型中气孔导度与湿度的关系。本研究使用一个诊断变量f(H),基于农田叶片水平的光合-气孔导度观测数据,对BWB模型、Leuning模型以及新发展的power-h模型和power-D模型进行了气孔导度模拟效果的比较和评价。结果表明:BWB模型描述的是g和相对湿度(hs)之间的一种线性关系,当空气较为湿润时,模拟结果存在较大的低估;Leuning模型中反映的是g与饱和水汽压差(Ds)的非线性函数,降低了模拟结果的误差,但仍然不能很好地描述g在较湿状况下的显著升高;相比之下,两个新的模型,即Ds的指数函数和(1-hs)的指数函数形式模型能提高模拟结果的精度。这个研究结果也表明基于Ds的模型模拟效果要好于基于hs的模型。     

Inhibitors of arachidonic acid metabolism reduce DNA and nuclear fragmentation induced by TNF plus cycloheximide in U937 cells

U937 human myeloid leukemia cells are induced to apoptosis by tumour necrosis factor (TNF) plus cycloheximide (CHX). We have analysed the effect of various inhibitors of the arachidonic acid (AA) metabolism on several features of this process. The formation of high molecular weight and oligonucleosomal DNA fragments as well as nuclear fragmentation were reduced by inhibitors of 5-lipoxygenase (BWA4C and BWB70C), 5-LO activating protein (MK-886), and cytosolic PLA2 (AACOCF3). None of these agents blocked the morphological changes detected by microscopy or flow cytometry, phosphatidylserine exposure on the cell surface or Caspase 3-like activation. AA also induced nuclear fragmentation at a concentration of 1-20 microM. However, the mechanisms by which these inhibitors act, remain unexplained since there was no 5-LO expression in the U937 cells and no AA release followed their stimulation with TNF plus CHX.     

极端干旱区多枝柽柳叶片气孔导度的环境响应模拟

气孔通过调节植物体水分散失和CO₂吸收在植物适应环境变化和环境胁迫中发挥重要作用。该文在对极端干旱区多枝柽柳(Tamarix ramosissma)叶片气体交换参数观测的基础上, 引入诊断函数f(H)对BWB模型和BBL模型提出的气孔导度(g_s)模型中的空气湿度(h_s或D_s)进行了评价, 并将评价结果引入叶子飘和于强推导出的g_s机理模型。结果表明: (1) BWB和BBL模型对h_s (或D_s)的模拟效果存在很大差异: BWB模型拟合效果较好(R² = 0.5354), BBL模型的结果显著但效果较差(R² = 0.1103)。试验结果显示: 随h_s(或D_s)的增大, g_s呈先增大后减小的趋势, 可用Gauss模型进行拟合, R²分别为0.593和0.258, 说明g_s与h_s的关系要比D_s更密切; (2)叶子飘和于强给出的简化模型(Simple模型)和该文给出的指数模型(Gauss-h模型)均具有较好的模拟效果(R²分别为0.8707和0.8286), η值分别为0.1245和0.0171, 其值均介于0-1之间; (3)模型验证中Gauss-h模型较Simple模型明显低估了观测值, 当观测条件无限趋近于Simple模型的假设时, Simple模型的拟合效果可得到显著提高(R² = 0.9606)。     

Protein production and secretion in an Aspergillus nidulans mutant impaired in glycosylation

O-glycosylation has been considered a limiting factor in protein secretion in filamentous fungi. Overexpression of the yeast DPM1 gene encoding dolichylphosphate mannose synthase (DPMS) in an Aspergillus nidulans mutant (BWB26A) deficient in O-glycosylation caused an increase in the number of secretory vesicles and changes in protein secretion. However, the secretory proteins, primarily O-mannosylated glucoamylase and N-glycosylated invertase, were mainly trapped in the periplasmic space. Different glycoforms of invertase were found insite the cells, in the periplasmic space and in the cultivation medium. Our data point to the importance of the cell wall as a barrier in protein secretion.     

植物气孔导度的环境响应模拟及其尺度扩展

气孔导度是衡量植物和大气间水分、能量及CO2平衡和循环的重要指标,探讨气孔导度与环境因子的关系及其模拟,以及气孔导度在叶片、冠层及区域尺度间的尺度转换及累积效应,对更好地认识植被与大气间的水热运移过程,合理评价植被在陆面过程中的地位和作用都具有重要意义。从植物气孔导度与环境因子的关系、气孔导度模拟以及尺度扩展三个方面,对前人的研究成果进行了概括总结。从叶片和冠层两个尺度出发,归纳总结了前人对于不同植物气孔导度与环境因子关系的研究成果,发现由于不同植物的遗传特性、测定时的环境、时间尺度的不同,以及未考虑各个环境因子的相互作用对气孔导度的影响,由此得到的气孔导度与环境因子之间的关系也不尽一致。对各单一环境因子与气孔导度的关系,给出了生理学解释,从根本上说明了环境因子变化对气孔导度的影响,而研究环境因子对气孔导度的综合影响时,应对各环境因子进行系统控制与同步观测。模拟计算植物气孔导度的模型主要有Jarvis模型和BWB模型两类,这些模型的模拟能力随着研究对象、试验区域、环境条件的改变而存在一定的差异,在具体使用时应结合实际情况选择最优模型进行模拟。除上述常用模型外,还总结了其他学者分别从不同角度提出的新的模型,对现有气孔导度模型进行了全面的总结。从叶片-冠层、冠层-区域两个方面归纳总结了前人关于气孔导度尺度扩展的研究成果,发现叶片-冠层的尺度扩展研究较成熟而冠层-区域的尺度扩展在模拟精度的验证方面存在困难。针对以下几个方面提出了今后气孔导度的研究重点:(1)结合研究对象所在的区域及环境条件,选择最优模型进行模拟;(2)综合考虑环境因子之间的相互作用及其对气孔导度的累积影响;(3)BWB模型与光合模型的耦合;(4)提高大尺度范围内的气孔导度模拟精度。     

三种经验模型模拟荒漠河岸柽柳叶片气孔导度

植物叶片气孔是控制水分和CO_2出入的通道,是植物水分蒸腾和气体交换的门户。植物叶片气孔导度地准确模拟,对于植物蒸腾作用地有效模拟以及植物与大气间能量和质量平衡的研究至关重要。基于黑河下游阿拉善群落水热平衡综合观测场实际观测数据,采用LI-COR 6400光合作用测定系统,对荒漠河岸柽柳叶片气孔导度进行观测,分析晴朗天气条件下气孔导度日变化特征,同时,结合微气象及植物生理相关数据,运用学术界3种最常用的(半)经验模型对柽柳叶片气孔导度进行模拟,结果表明:(1)柽柳叶片气孔导度日变化大致呈先升高后降低的趋势。上午随着太阳辐射逐渐增强,气温逐渐升高,气孔导度值逐渐升高,蒸腾速率也逐渐增大,在10:00—12:00时间段内达到最大值。绝大部分观测日内12:00前后气孔导度呈现出一定的波动,原因在于温度过高致使叶片气孔关闭。随后,太阳辐射减弱,气温逐渐降低,空气中相对湿度增加,柽柳叶片内外水汽压差减小,气孔导度减小导致蒸腾速率下降。(2)通过3种最常用的(半)经验模型(Jarvis、Ball-Woodrow-Berry(BWB)和Ball-Berry-Leuning(BBL))模拟气孔导度的结果可以看出,Jarvis模型的修正效率系数(0.775、0.891)、修正一致系数(0.887、0.945)和决定系数(0.590、0.645)在3个模型中均是最高或次最高的,说明其模拟精度最高。(3)BWB模型与BBL模型的模拟精度相近,说明水汽压差、大气湿度与气孔导度的密切程度相近,没有明显的区别。     

Effect of Carbon Substrates on Rock Phosphate Solubilization by Bacteria from Composts and Macrofauna

Five of the 207 isolates from different composts, farm waste compost (FWC), rice straw compost (RSC), Gliricidia vermicompost (GVC), and macrofauna, showed rock phosphate (RP) solubilization in buffered medium in plate culture. When tested in RP broth medium, all five strains, Enterobacter cloacae EB 27, Serratia marcescens EB 67, Serratia sp. EB 75, Pseudomonas sp. CDB 35, and Pseudomonas sp. BWB 21, showed gluconic acid production and solubilized RP. Based on cellulose-degrading and P-solubilizing ability, two strains were selected for further studies. In the presence of different carbon sources, both strains showed a drop in pH and solubilized RP. P released was maximum with glucose (1212 and 522 μmol) and minimum with cellobiose (455 and 306 μmol) by S. marcescens EB 67 and Pseudomonas sp. CDB 35, respectively. Glucose dehydrogenase (GDH) activity was 63 and 77% with galactose and 35 and 46% with cellobiose when compared to glucose (100%) by EB 67 and CDB 35, respectively. Both strains solubilized RP in the presence of different crop residues. EB 67 and CDB 35 showed maximum cellulase activity (0.027 units) in the presence of rice straw and a mixture of rice straw and root. P solubilized from RP in the presence of pigeonpea root was 134 and 140 μmol with EB 67 and CDB 35. Significantly, these bacteria isolated from composts and macrofauna solubilized rock phosphate in the presence of various pure carbon substrates and crop residues and their importance in soil/rhizosphere conditions is discussed.     

Biological Control of Chickpea Collar Rot by Co-inoculation of Antagonistic Bacteria and Compatible Rhizobia

Two hundred and seven bacteria were isolated from composts and macrofauna and screened for plant growth promoting and antagonistic traits. Seven of the 207 isolates showed antagonistic activity against Sclerotium rolfsii in plate culture. Inhibition of S. rolfsii by the bacterial isolates ranged between 61 and 84%. Two of the seven isolates were Bacillus sp. and rest belonged to Pseudomonas sp. Two isolates, Pseudomonas sp. CDB 35 and Pseudomonas sp. BWB 21 was compatible with chickpea Rhizobium sp. IC 59 and IC 76 in plate culture conditions. Increase in plant biomass (dry weight) ranged between 18 and 30% on application of these bacteria by seed coating and seed priming methods. However, by seed-priming there was an increase in plant biomass by 5–7% compared to seed coating. Number of nodules and the nodule weight was similar by both seed coating and seed priming methods. Disease incidence was reduced up to 47% in treatments where captan (fungicide) or antagonistic Pseudomonas sp. CDB 35 was applied. Increase in shoot weight was 36% by seed coating with Rhizobium sp. IC 59 and Pseudomonas sp. CDB 35 when compared to captan application. Whereas by seed priming with IC 59 and CDB 35 increased shoot weight by 3 and 39% increase in nodulation was observed.     

High-throughput analysis of GST-fusion protein expression and activity-dependent protein interactions on GST-fusion protein arrays with a spectral surface plasmon resonance biosensor

We modified gold arrays with a glutathione (GSH) surface, and investigated high-throughput protein interactions with a spectral surface plasmon resonance (SPR) biosensor. We fabricated the GSH exterior on gold surfaces by successive modification with aminoethanethiol, 4-maleimidobutyric acid N-hydroxysuccinimide ester and GSH. We immobilized GST-Rac1, GST-RhoA, the GST-Rho-binding domain of rhotekin and the GST-p21-binding domain of PAK1 onto the GSH surface, and observed specific antigen-antibody interactions on the GST-fusion protein arrays. We determined the expression of GST-fusion proteins in Escherichia coli on the GSH surface with the SPR biosensor. We then analyzed the interactions of tissue transglutaminase (tTGase), a Ca2+-dependent enzyme, with RhoA and Rac1 on the GST-fusion protein arrays with the SPR biosensor. We found that tTGase interacted with RhoA and Rac1 in a Ca2+-dependent manner, indicating that the interactions were dependent on tTGase activity. In addition, transamidation of Rac1 by tTGase was dependent on Ca2+ concentration. We obtained similar results with GST pull-down assays. Thus, protein arrays prepared on the GSH surface provide a useful system for the high-throughput analysis of GST-fusion protein expression and activity-dependent protein interactions with the spectral SPR biosensors.     

Methodology for estimating the abundance of rare animals: seabird nesting on north east Herald Cay

We discuss the problem of estimating the number of nests of different species of seabirds on North East Herald Cay based on the data from a 1996 survey of quadrats along transects and data from similar past surveys. We consider three approaches based on different plausible models, namely a conditional negative binomial model that allows for additional zeroes in the data, a weighting approach (based on a heteroscedastic regression model), and a transform-both-sides regression approach. We find that the conditional negative binomial approach and a linear regression approach work well but that the transform-both-sides approach should not be used. We apply the conditional negative binomial and linear regression approaches with poststratification based on data quality and availability to estimate the number of frigatebird nests on North East Herald Cay.     

Selection on insect immunity in the wild

The strength of selection on immune function in wild populations has only been examined in a few vertebrate species. We report the results from a study measuring selection on a key insect immune enzyme, phenoloxidase (PO), in a wild population of the damselfly Calopteryx xanthostoma. We followed individually marked males from the pre-reproductive adult phase and recorded their lifetime mating success. We found positive selection on PO activity in response to an immune insult, but no selection on wing-spot quality, a trait actively displayed to females during courtship. We suggest that positive selection on PO activity in the year of study may be explained by annual fluctuations in parasite loads.     

Inbreeding depression in pronghorn (Antilocapra americana) fawns

Although inbreeding depression affects survival, fitness and population viability, the extent of inbreeding depression in wild populations remains unclear. We examined inbreeding depression in the small, isolated National Bison Range (NBR), MT, pronghorn (Antilocapra americana) population following a bottleneck. We have studied the National Bison Range pronghorn extensively since 1981, and we have detailed birth, survival and mate choice data. We genotyped all animals in the population between 1999 and 2010 at 19 microsatellite loci, assigned paternities to all fawns based on genotype and constructed a genetic-based pedigree to calculate inbreeding coefficients (f). We found an increase in the frequency of inbreeding following the bottleneck. We detected evidence of inbreeding depression on fawn survival to weaning, birth mass, foot length and condition. We estimated the number of diploid lethal equivalents on survival to weaning as 24.17-28.72. Standardized heterozygosity (H) had a relatively small influence on survival, mass, length and condition compared with f, and H was not correlated with f. We conclude that for pronghorn, H was not a good predictor of pedigree-estimates of f.     

Is wildlife research useful for wildlife conservation in the tropics? A review for Borneo with global implications

The urgency of the tropical biodiversity crisis continues to be a major justification for wildlife research and its funding. To examine the benefits of this research for on-the-ground conservation, we focused on Borneo, where conservation has a long history and we have direct experience. We compiled, categorized and evaluated 284 publications from a broad variety of sources, 153 from peer-reviewed journals. We found that few studies address threats to species and fewer still provide input for or guidance to effective management. We consider various reasons for these shortcomings. Research is seldom judged on its relevance to pragmatic problem solving. Furthermore, many research programs lack the necessary long-term vision and organizational structure for useful applied research. We consulted conservation leaders about our conclusions and all responses suggest that our concerns are not unique to Borneo but reflect wider problems. We conclude that conservation research across most of the tropics is failing to address conservation needs. We make a number of recommendations based on our findings. Conservation biologists should place a higher priority on addressing practical conservation needs and goals.