Genetic parameter estimates in a clonally replicated progeny test of teak (Tectona grandis Linn. f.)

Teak (Tectona grandis Linn. f.) has been planted extensively in the tropics for its highly valued timber. We analysed data from a 3.5-year-old teak progeny test with clonal replication located in northern Australia. Additive and non-additive genetic variances were estimated for commercially important traits. Trees originating from seedlings were on average 2% taller and 4% straighter than those of the same genotype originating from cuttings. Non-additive genetic variance represented 35–50% of total genetic variance for growth traits and 63% of total genetic variance for incidence of flowering. Narrow-sense heritability was 0.22 for diameter, 0.18 for height and volume, 0.07 for stem straightness, 0.05 for insect defoliation, 0.03 for epicormic sprouts and 0.30 for incidence of flowering (estimated on an assumed underlying continuous scale). Broad-sense heritability was 0.37 for diameter, 0.28 for height, 0.35 for volume, 0.12 for stem straightness, 0.06 for insect defoliation, 0.12 for epicormic sprouts and 0.71 for incidence of flowering. Positive correlations were found between tree volume and flowering and between tree volume and stem straightness. The presence of sizeable non-additive variance supports the selection and deployment of clones to capture the full extent of genetic variation in commercially important traits.     

A preliminary investigation of some Maruthamalai forest plants for phytochemical compounds

Twenty five plant species from the Maruthamalai hills, Coimbatore, were screened for the presence of phytoconstituents. Among 25 plants, 19 gave positive tests for flavonoids, 23 for alkaloids, 20 for saponins, 25 for tannins, 22 for steroids and terpenoids, 23 for phenolic compounds, and tests indicated the presence of rotenoids in all the plants.     

RFLP mapping of QTLs for yield and related characters in rice (Oryza sativa L.)

Quantitative triat loci (QTLs) for yield and related traits in rice were mapped based on RFLP maps from two indica/indica F₂ populations, Tesanai 2/CB and Waiyin 2/CB. In Tesanai 2/CB, 14 intervals carrying QTLs for eight traits were detected, including 3 for grain weight per plant (GWT), 2 for number of panicles per plant (NP), 2 for number of grains per panicle (NG), 1 for total number of spikelets per panicle (TNS), 1 for spikelet fertility (SF), 3 for 1000-grain weight (TGWT), 1 for spikelet density (SD), and 1 for number of first branches per main panicle. The 3 QTLs for GWT were located on chromosomes 1, 2, and 4, with 1 in each chromosome. The additive effect of the single locus ranged from 2.0 g to 9.1 g. A major gene (np4) for NP was detected on chromosome 4 within the interval of RG143–RG214, about 4cM for RG143, and this locus explained 26.1% of the observed phenotypic variance for NP. The paternal allele of this locus was responsible for reduced panicles per plant (3 panicles per plant). In another population, Waiyin 2/CB, 12 intervals containing QTLs for six of the above-mentioned traits were detected, including 3 for GWT, 2 for each of NP, TNS, TGWT and SD, 1 for SF. Three QTLs for GWT were located on chromosome 1, 4, and 5, respectively. The additive effect of the single locus for GWT ranged from 6.7 g to 8.8 g, while the dominance effect was 1.7–11.5 g. QTL mapping in two populations with a common male parent is compared and discussed.     

Comparison of pure Holsteins to crossbred Holsteins with Norwegian Red cattle in first and second generations

A total of 1922 first generation crossbred cows born between 2005 and 2012 produced by inseminating purebred Israeli Holstein cows with Norwegian Red semen, and 7487 purebred Israeli Holstein cows of the same age in the same 50 herds were analyzed for production, calving traits, fertility, calving diseases, body condition score, abortion rate and survival under intensive commercial management conditions. Holstein cows were higher than crossbreds for 305-day milk, fat and protein production. Differences were 764, 1244, 1231 for kg milk; 23.4, 37.4, 35.6 for kg fat, and 16.7, 29.8, 29.8 for kg protein; for parities 1 through 3. Differences for fat concentration were not significant; while crossbred cows were higher for protein concentration by 0.06% to 0.08%. Differences for somatic cells counts were not significant. Milk production persistency was higher for Holstein cows by 5, 8.3 and 8% in parities 1 through 3. Crossbred cows were higher for conception status by 3.1, 3.6 and 4.7% in parities 1 through 3. Rates of metritis for Holsteins were higher than the crossbred cows by 7.8, 4.6 and 3.4% in parities 1 to 3. Differences for incidence of abortion, dystocia, ketosis and milk fever were not significant. Holstein cows were lower than crossbred cows for body condition score for all three parities, with differences of 0.2 to 0.4 units. Contrary to comparisons in other countries, herd-life was higher for Holsteins by 79 days. A total of 6321 Holstein cows born between 2007 and 2011 were higher than 765 progeny of crossbred cows backcrossed to Israeli Holsteins of the same ages for milk, fat and protein production. Differences were 279, 537, 542 kg milk; 10.5, 17.7, 17.0 kg fat and 6.2, 12.9, 13.2 kg protein for parities 1 through 3. Differences for fat concentration were not significant, while backcross cows were higher for protein percentage by 0.02% to 0.04%. The differences for somatic cell score, conception rate, and calving diseases other than metritis, were not significant. Holstein cows were lower than backcross cows by 1.5% to 2.5% for conception status in parities 1 to 3 and lower for body condition score for parities 1 and 2, with differences in the range of 0.06 to 0.09 units. Culling rates were higher, and herd-life lower for the crossbred cows. The gains obtained in secondary traits for crossbred cows did not compensate for the major reduction in production.     

Genetic parameters estimation for preweaning traits and their relationship with reproductive,productive and morphological traits in alpaca

The aim of this study was to estimate the genetic parameters for preweaning traits and their relationship with reproductive, productive and morphological traits in alpacas. The data were collected from 2001 to 2015 in the Pacomarca experimental farm. The data set contained data from 4330 females and 3788 males corresponding to 6396 and 1722 animals for Huacaya and Suri variants, respectively. The number of records for Huacaya and Suri variants were 5494 and 1461 for birth weight (BW), 5429 and 1431 for birth withers height (BH), 3320 and 896 for both weaning weight (WW) and average daily gain (DG) from birth to weaning, 3317 and 896 for weaning withers height (WH), and 5514 and 1474 for survival to weaning. The reproductive traits analyzed were age at first calving and calving interval. The fiber traits were fiber diameter (FD), standard deviation of FD (SD), comfort factor and coefficient of variation of FD and the morphological traits studied were density, crimp in Huacaya and lock structure in Suri, head, coverage and balance. Regarding preweaning traits, model of analysis included additive, maternal and residual random effects for all traits, with sex, coat color, number of calving, month–year and contemporary group as systematic effects, and age at weaning as linear covariate for WW and WH. The most relevant direct heritabilities for Huacaya and Suri were 0.50 and 0.34 for WW, 0.36 and 0.66 for WH, 0.45 and 0.20 for DG, respectively. Maternal heritabilities were 0.25 and 0.38 for BW, 0.18 and 0.32 for BH, 0.29 and 0.39 for WW, 0.19 and 0.26 for WH, 0.27 and 0.36 for DG, respectively. Direct genetic correlations within preweaning traits were high and favorable and lower between direct and maternal genetic effects. The genetic correlations of preweaning traits with fiber traits were moderate and unfavorable. With morphological traits they were high and positive for Suri but not for Huacaya and favorable for direct genetic effect but unfavorable for maternal genetic effect with reproductive traits. If the selection objective was meat production, the selection would have to be based on the direct genetic effect for WW but not on the maternal genetic effect that has been shown to have less relevance. Other weaning traits such as WH or DG would be indirectly selected.     

十种一碳代谢关键产物的HPLC-MS/MS 定量检测方法

目的:利用HPLC-MS/MS方法对十种一碳代谢相关产物进行定量分析。方法:采用Aglient ZORBAX SB-AQ C18柱(2.1mm×100 mm,3.5 m)、电喷雾离子源(ESI),以多离子反应监测方式(MRM)进行正离子检测。对游离叶酸(FA)、5-甲酰四氢叶酸(5-FT)、5-甲基四氢叶酸(5-MT)、S-腺苷蛋氨酸(SAM)、S-腺苷同型半胱氨酸(SAH)、胱硫醚(CYSTA)、组氨酸(HIS)、丝氨酸(SER)、蛋氨酸(MET)、同型半胱氨酸(HCY)进行定量分析。结果:FA、5-FT、5-MT、SAM、SAH、CYSTA、HIS、SER、MET、HCY的检测限分别为0.1 ng.L-1、0.25 ng.L-1、0.1 ng.L-1、0.1 ng.L-1、0.25 ng.L-1、0.25 ng.L-1、0.1 ng.L-1、0.025 ng.L-1、0.1 ng.L-1、0.1 ng.L-1。FA、5-FT、5-MT、SAH、CYSTA浓度测定方法线性范围为2~50 ng.L-1,SER、SAM浓度测定方法线性范围20~500 ng.L-1,MET、HCY浓度测定方法线性范围200~5000 ng.L-1,HIS浓度测定方法线性范围为400~10000 ng.L-1,r均在0.993以上,全部涵盖了已报道的血清中指标的含量范围。结论:建立了HPLC-MS/MS方法,可同时分析十种一碳代谢通路的关键产物,所需样品量少,检测速度快,同时实现分项检测,可为多种代谢性疾病系统性地检测一碳代谢中间产物体液分析方法建立实验条件基础。     

Assessment of Hazardous and Essential Elements in a Food Crop Irrigated with Municipal Sewage Water: Risk Appraisal for Public Health

To assess the impact of sewage water on metal accretion in selected diverse varieties of wheat (i.e., Lasani-2008, ARRI-10, Faisalabad-83, Punjab-85, Aas-2010, and Sehar-2006), their seeds were sown in pots containing soil. The results showed that the concentration of heavy metals in grains from the wheat plants supplied with sewage water was considerably higher than the plants supplied with canal irrigation water (control). In canal water irrigated wheat grains the metal concentrations (mg/kg) ranged from 2.20–3.5 for Cu, 12.50–32.4 for Zn, 22.45–35.22 for Mn, 0.05–0.15 for Pb, 0.012–0.029 for Cd, 2.5–5.3 for Ni, 18.16–29.63 for Fe, and 0.90–3.64 for Cr in different wheat varieties, whereas the wheat grains raised from sewage water, had metal concentrations (mg/kg): 3.8–5.30 for Cu, 29.60–40.50 for Zn, 32.9–50.40 for Mn, 1.14–7.50 for Pb, 0.26–0.42 for Cd, 3.90–7.55 for Ni, 32.21–40.35 for Fe, and 2.88–7.84 for Cr. Since these metals bioaccumulate in wheat grains with unremitting use of metal-enriched wastewater, care has to be taken for irrigating wheat plants with household wastewater for a longer time, particularly in those soils where this crop is grown regularly.     

Site-dependent Life-Cycle Impact Assessment in Sweden (5 pp)

Goal, Scope and Background Although LCA is traditionally a site-independent tool, there is currently a trend towards making LCA more site-dependent if not site-specific. For Europe, site-dependent impact factors have been calculated on a country basis for acidification, terrestrial eutrophication and toxicological impacts. It is, however, an open question whether this is the optimum level for site-dependent factors. The aim of this paper is to develop site-dependent characterisation factors for different parts of Sweden for air emissions of NOx, SOx and particulates regarding ecosystem and human health impacts. Based on experiences from a case-study, the usability of the site-dependent factors for LCA are discussed, as well as the appropriate level of site-dependency for ecosystem and human health impacts. Method logy. The Ecosense model is used for calculating site-dependent factors for some atmospheric pollutants. Characterisation factors are calculated for four different places in Sweden with two different stack heights. Results and Conclusions The characterisation factors for ecosystem impacts show fairly small differences between different parts of Sweden (within a factor of two). For health impacts, the differences between different parts of the country were larger and more significant (up to one order of magnitude). Also the difference between low and high stack heights may be relevant, especially in densely populated areas. These results suggest that for ecosystems, site-dependent characterisation factors for the considered atmospheric pollutants on a country level may be sufficient for most applications. However, for health impacts, site-dependent factors on a country level may be inappropriate. Beside LCA, the calculated factors and the methodology used should also be useful for other environmental system analysis tools, such as Strategic Environmental Assessment, Cost-Benefit Analysis and Environmental Management Systems.     

Gas chromatographic–tandem mass spectrometric determination of anabolic steroids and their esters in hair: Application in doping control and meat quality control

We have developed a powerful and simple sensitive method for testing hair for anabolic steroids and their esters. A 100-mg amount of powdered hair was treated with methanol in an ultrasonic bath for extraction of esters, then alkaline digested with 1 M NaOH for an optimum recovery of other drugs. The two liquid preparations were subsequently extracted with ethyl acetate, pooled, then finally highly purified using a twin solid-phase extraction on amino and silica cartridges. The residue was derivatized with N-methyl-N(trimethylsilyl)-trifluoracetamide (MSTFA) prior to injection. Analysis was conducted by gas chromatography coupled to a triple quadrupole mass spectrometer. The generally chosen parent ion was the molecular ion while two daughter ions were selected for each compound with collision energies ranging from −16 to −21 eV. Internal standards were nandrolone d₃ for non-esterified drugs and testosterone phenyl propionate for esters. The limits of detection calculated from an analysis of the blanks (n=30) were 0.08 pg/mg for nandrolone, 6.20 pg/mg for boldenone, 0.07 pg/mg for methyl testosterone, 0.15 pg/mg for ethinyl estradiol, 2.10 pg/mg for metandienone, 0.86 pg/mg for testosterone propionate, 0.95 pg/mg for testosterone cypionate, 1.90 pg/mg for nandrolone decanoate, 3.10 pg/mg for testosterone decanoate and 4.80 pg/mg for testosterone undecanoate. Application to doping control has been demonstrated. In a series of 18 sportsmen, two tested positive for anabolic steroids in hair whereas urinalysis was negative for both of them. The first positive case was nandrolone and the second case concerned the identification of testosterone undecanoate. Measured in 10 white males aged between 22 and 31 years, the testosterone concentration was in the range 1.7–9.2 pg/mg (mean=5.0 pg/mg). The method was also applied in meat quality control. Of the 187 analyses realized based upon hair and urine sampling in slaughter houses, 23 were positive for anabolic steroids in hair: one case for boldenone, one case for metandienone, two cases for testosterone propionate, three cases for nandrolone, five cases for testosterone decanoate and 11 cases for methyl testosterone. In the meantime, urinalysis was always negative for these drugs or their metabolites.     

Cloning Vectors for Rice

We developed various binary vectors that can be used for expressing a foreign gene in rice. Vectors pGA3426, pGA3436, and pGA3626 are intended for overexpression of a gene using the maize Ubiquitin promoter, whereas pGA3780 is for rather mild expression of a gene using the rice Actin1 promoter. Vector pGA3777 is for expressing two genes simultaneously. We also developed binary vectors for expressing a fusion protein with a tag. Four vectors (pGA3427, pGA3428, pGA3429, and pGA3438) are for protein tags with sGFP, HA, His, and Myc, respectively. Vector pGA3383 is for analyzing promoter activity using the GUS reporter. In this vector, multiple cloning sites in front of GUS can be utilized for accepting a promoter fragment. We also generated transient expression vectors for studying the subcellular localization of a protein. Vectors pGA3452, pGA3651, and pGA3652 are for GFP fusion; pGA3574 for RFP fusion; pGA3697 for Myc tag; and pGA3698 for HA tag. In addition, we generated pGA3506, pGA3516, pGA3592, and pGA3593 for facilitating the subcloning of full-length cDNA clones into our binary vectors.     

Analysis of QTL×environment interaction for yield components and plant height in rice

 An F₂ and two equivalent F₃ populations of an indica-indica cross of rice, Tesanai 2/CB, were constructed and grown in different environments. The identification of quantitative trait loci (QTL) for yield components and plant height and an analysis of QTL×environment interaction were conducted for three trials. Interval mapping of QTL for eight traits was employed with a threshold of LOD=2 using the computer package MAPMAKER/QTL. A total of 44 QTL were detected in 18 intervals of nine chromosomes, including 3 for the number of panicles (NP), 5 for the number of filled grains (NFG), 6 for total number of spikelets (TNS), 3 for spikelet fertility (SF), 7 for 1000-grain weight (TGWT), 5 for grain weight per plant (GWT), 8 for plant height (PH) and 7 for panicle length (PL). The numbers of QTL detected in two or three trials were 1 for NP, 1 for NFG, 1 for TNS, none for SF, 4 for TGWT, 3 for GWT, 2 for PH and 5 for PL, making a total of 17. When a QTL was detected in more than one trial the direction and magnitude of its additive effect, the dominance effect and the degree of dominance were generally in good agreement. In all three trials, QTL were frequently detected for related traits in the same intervals. The directions of additive effect of QTL for related traits in a given interval were in agreement with few exceptions, no matter whether they were detected in the same trial or not. This result suggested that pleiotropism rather than close linkage of different QTL was the major reason why QTL for different traits were frequently detected in the same intervals. When gene pleiotropism was considered, 23 of the 29 QTL for yield and its components and 9 of the 15 QTL for plant stature were detected in more than one trial. This indicated that the detection of chromosomal segments harboring QTL was hardly affected by environmental factors. Received: 30 January 1997 / Accepted: 21 March 1997     

High-performance liquid chromatographic method to screen and quantitate seven selective serotonin reuptake inhibitors in human serum

A high-performance liquid chromatographic screening method (HPLC) is described for the determination of seven selective serotonin reuptake inhibitors (SSRIs) (fluvoxamine, milnacipran, paroxetine, sertraline, fluoxetine, citalopram, venlafaxine) and for three pharmacologically active N-demethylated metabolites (desmethylcitalopram, didesmethylcitalopram and norfluoxetine). A tricyclic antidepressant, clomipramine, was used as an internal standard. The method consists of liquid extraction of serum after alcalinisation at pH 9.50, followed by chromatography on a Beckman C₁₈ reversed-phase column. Compounds were detected at 200.4 nm. The standard curves were linear over a working range of 50–1000 ng/ml for fluvoxamine, 15–1000 ng/ml for fluoxetine, 25–500 ng/ml for norfluoxetine, 50–500 ng/ml for sertraline, 20–500 ng/ml for paroxetine, 25–550 ng/ml for citalopram, 25–750 ng/ml for desmethylcitalopram, 25–800 ng/ml for didesmethylcitalopram, 25–650 ng/ml for milnacipran, and 25–500 ng/ml for venlafaxine. The quantitation limits of the method were 15 ng/ml for fluoxetine, 20 ng/ml for paroxetine, 25 ng/ml for venlafaxine, norfluoxetine and citalopram, and its metabolites, 40 ng/ml for sertraline and 50 ng/ml for fluvoxamine. No interferences were noted with this sensitive and specific method which can be used for therapeutic drug monitoring.     

Procedures for microencapsulation of enzymes, cells and genetically engineered microorganisms

Methods to microencapsulate enzyme, cells, and genetically engineered cells have been described in this article. More specific examples of enzyme encapsulation include the microencapsulation of xanthine oxidase for Lesch-Nyhan disease; phenylalanine ammonia lyase for pheny, ketonuria and microencapsulation of multienzyme systems with cofactor recycling for multistep enzyme conversions. Methods for cell encapsulation include the details for encapsulating hepatocytes for liver failure and for gene therapy. This also includes the details of a novel two-step method for encapsulation of high concentrations of smaller cells. Another new approach is the detailed method of the encapsulation of genetically engineered Escherichia coli DH5 cells for lowering urea, ammonia, and other metabolites in kidney or, liver failure and other diseases.     

Polymorphism of a complex resistance gene candidate family in wild populations of common bean (Phaseolus vulgaris) in Argentina: comparison with phenotypic resistance polymorphism

Fifteen populations of wild bean (Phaseolus vulgaris), located in three provinces in Argentina, were analysed for their polymorphism for a complex resistance gene candidate (RGC) family clustered on the genome and for resistance phenotypes to strains of Colletotrichum lindemuthianum. Results indicate that RGC polymorphism is high. Population structure obtained for markers related to resistance was compared to population structure obtained for RAPD markers in order to infer the evolutionary forces driving polymorphism for resistance in wild populations at both molecular and phenotypic levels. Hierarchical analysis of differentiation showed that, within provinces, populations were differentiated for RAPD as well as for molecular and phenotypic markers of resistance. In contrast, provinces were differentiated only for RAPD and RGC markers and not for resistance phenotypes. The discrepancies found between diversity structures for molecular markers (RAPD and RGCs) and for resistance phenotypes suggest an effect of selection and indicate that diversity for resistance may not be driven by the same selective forces at the molecular and phenotypic levels. We further discuss whether specific selective forces are exerted on RGC markers and underline the importance of spatial scale of analysis for demonstrating an impact of selection.     

长白山各植被带主要树种凋落物分解速率及模型模拟的试验研究

2001～2003年在长白山自然保护区内3个垂直植被带的典型群落红松阔叶林、云冷杉林和岳桦林内,利用网袋埋藏法对群落内的6个主要优势乔木树种凋落物进行埋藏分解试验,研究凋落物分解速率及其变化动态;同时利用分解模型,模拟预测凋落物的分解进展,为深入研究这6个树种的营养策略、群落养分循环等奠定基础,也为森林生态系统管理提供理论依据.研究结果表明,所研究的6个树种凋落物都表现出随时间进程失重率增大的现象,但失重率并不与时间呈线性相关.在分解的638d（1.75a）后,6种叶凋落物的分解速率明显升高.到分解实验结止时（699d）,叶凋落物干重剩余率从小至大依次为白桦（24.56%）、紫椴（24.81%）、红松（38.48%）、鱼鳞云杉（41.15%）、岳桦（41.53%）和臭冷杉（42.62%）.枝凋落物分解速率明显低于叶,枝干重剩余率从小至大依次为紫椴（44.98%）、臭冷杉（64.62%）、红松（72.07%）、鱼鳞云杉（73.51%）、白桦（77.37%）和岳桦（80.35%）.在同一海拔高度,阔叶树种叶凋落物分解速率大于针叶树种.并且随着海拔的升高,叶凋落物分解速率逐渐减慢.模型分析预测结果表明,长白山北坡各垂直植被带的优势树种叶凋落物分解95%需4.5～8.0a;年分解系数为紫椴（0.686）〉白桦（0.624）〉 红松（0.441）〉 鱼鳞云杉（0.406）〉 臭冷杉（0.397）〉岳桦（0.385）;枝凋落物分解95%需7.8～29.3a,不同树种间的差异明显.枝年分解系数为紫椴（0.391）〉臭冷杉（0.204）〉红松（0.176）＞鱼鳞云杉（0.157）〉白桦（0.148）〉 岳桦（0.102）.     

Identifying and Controlling for Variation in Canid Harvest Data

An accurate understanding of harvest trends is required for effective wildlife management. Trapper harvest data represent valuable long-term data for evaluating patterns and trends for wildlife species at broad spatiotemporal scales. Inferring accurate trends from harvest data, however, first requires identifying and controlling for confounding factors that vary independent of abundance. We investigated trends in 43 years of trapper harvest data (1976–2018) from Illinois, USA, for red fox (Vulpes vulpes), gray fox (Urocyon cinereoargenteus), and coyote (Canis latrans) while controlling for factors that may affect trapper effort, including number of effective (i.e., successful) trappers, pelt price, gasoline price, winter unemployment, and winter weather conditions. Annual trapper harvest for red and gray foxes declined and was affected by gasoline price and winter unemployment, whereas annual trapper harvest for coyotes increased and was not strongly affected by other covariates. After adjusting for pelt price, harvest of red foxes was relatively stable, but harvest of gray foxes declined and harvest of coyotes increased. Effects of covariates on harvest per successful trapper varied by species; nevertheless, we detected an increasing trend for coyotes and decreasing trends for gray foxes and red foxes. Concordance across indices for gray foxes and coyotes was consistent with hypothesized declines for gray foxes and increases for coyotes in the midwestern United States. Trends for red foxes varied depending on how we accounted for potential confounding factors and it is unclear if these trends suggest population declines or distribution shifts to urban areas with reduced trapping susceptibility. Our results highlight the importance of understanding sources of variation in harvest data and that their effects can vary across species. © 2020 The Wildlife Society.     

Structure prediction of biological assemblies using GALAXY in CAPRI rounds 38-45

We participated in CARPI rounds 38-45 both as a server predictor and a human predictor. These CAPRI rounds provided excellent opportunities for testing prediction methods for three classes of protein interactions, that is, protein-protein, protein-peptide, and protein-oligosaccharide interactions. Both template-based methods (GalaxyTBM for monomer protein, GalaxyHomomer for homo-oligomer protein, GalaxyPepDock for protein-peptide complex) and ab initio docking methods (GalaxyTongDock and GalaxyPPDock for protein oligomer, GalaxyPepDock-ab-initio for protein-peptide complex, GalaxyDock2 and Galaxy7TM for protein-oligosaccharide complex) have been tested. Template-based methods depend heavily on the availability of proper templates and template-target similarity, and template-target difference is responsible for inaccuracy of template-based models. Inaccurate template-based models could be improved by our structure refinement and loop modeling methods based on physics-based energy optimization (GalaxyRefineComplex and GalaxyLoop) for several CAPRI targets. Current ab initio docking methods require accurate protein structures as input. Small conformational changes from input structure could be accounted for by our docking methods, producing one of the best models for several CAPRI targets. However, predicting large conformational changes involving protein backbone is still challenging, and full exploration of physics-based methods for such problems is still to come.     

关于植物DNA条形码研究技术规范

DNA条形码是利用标准的基因片段对物种进行快速鉴定的技术,已经成功用于生物物种分类和鉴定、生态学调查和生物多样性评估等研究领域。尽管生命条形码数据（BOLD）系统提供了主要针对动物类群DNA条形码研究的技术规范,但由于植物本身的生物学特性与所使用的条形码不同,因此已有技术规范并不完全适用于植物DNA条形码的研究。本文根据植物DNA条形码研究的特点与我国的实际情况,编写了植物DNA条形码研究技术标准和规范指南,具体包括十个方面的内容,即植物DNA条形码研究的样品采集策略;植物标本和野外数据的采集规范;植物标本图像信息的采集规范;植物DNA材料的采集规范;植物DNA材料的干燥与保存规范;植物总DNA的质量标准及保存规范;植物标准DNA条形码的选择与通用引物;DNA条形码的扩增与测序;DNA条形码数据的命名、编辑和提交规范;以及DNA条形码数据分析。我们期望通过这些标准规范的实施和在实践中的不断修订和完善,能为我国学者开展植物DNA条形码和iFlora研究提供参考和借鉴。
关键词：植物DNA条形码;技术规范;物种鉴定;标准;新一代植物志     

The Scalpel and the Butterfly: The Conflict between Animal Research and Animal Protection Deborah Rudacille

ABSTRACT

Although there is a substantial body of research on inter-human empathy and inter-animal empathy, there is a dearth of research comparing humans' empathic reactions to humans and animals. To address this issue, three experiments were conducted in which participants read a scenario about a human or animal abuse victim in need of medical attention, and indicated the degree of empathy they had on an emotional response scale. In Experiment 1, women had significantly more empathy for animals than for humans, whereas men tended to express more empathy for humans than for animals. In Experiment 2, adult women expressed the same degree of empathy for a child as for a puppy. Similarly, in Experiment 3, adult men and women expressed the same degree of empathy for a baby as for a puppy. Overall, results indicated that people feel at least as much empathy for animals as for humans. We suggest that an animal target elicits a great deal of empathy partly because it is perceived as not being responsible for having caused the need situation. Future research will show whether empathy for animals translates to prosocial behavior toward them as well.     

Roots of Stylosanthes hamata create macropores in the compact layer of a sandy soil

A field experiment with five lime rates (0, 3.75, 7.50, 11.25, and 15.00 Mg ha^–1) was maintained on a red soil (Ultisol) for 15 years to determine changes of soil acidity and effect on crop yields. The soil acidity decreased while exchangeable Ca in plough layer (0–20 cm) increased with lime rate and time. The decreased subsoil (20–60 cm) acidity started to occur four years after liming, and the extent of decreased soil acidity increased with lime rate and time. The increased ranges of exchangeable Mg²⁺ in subsoil were greater than that of exchangeable Ca²⁺, suggesting that downward movement of Mg²⁺ into the subsoil was faster than that of Ca²⁺. Lime application significantly increased the yields of crops studied. During the period of experiment, the maximum yield increased 4.67 times for barley, 2.24 times for mungbean, 57.3% for wheat, 53.4% for sesame, 52.8% for broad bean, 44.1% for potato, 35.1% for rapeseed, 32.1% for cotton, 28.4% for corn, 18.5% for watermelon, 11.0% for cowpea and 8.8 % for soybean. Liming at the highest rate was in favor to the decline in subsoil acidity and yield increase, especially for the later period of the experiment. Residual effects of reducing soil acidity by liming for the treatments of 0.5 L, 1.0 L, 1.5 L, and 2.0 L could last for 5, 7, 12, and 14 years, respectively, and the effects of lime application on the yields could last for more than 15 years.