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.     

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。     

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.     

Effect of predictor traits on accuracy of genomic breeding values for feed intake based on a limited cow reference population

The genomic breeding value accuracy of scarcely recorded traits is low because of the limited number of phenotypic observations. One solution to increase the breeding value accuracy is to use predictor traits. This study investigated the impact of recording additional phenotypic observations for predictor traits on reference and evaluated animals on the genomic breeding value accuracy for a scarcely recorded trait. The scarcely recorded trait was dry matter intake (DMI, n = 869) and the predictor traits were fat–protein-corrected milk (FPCM, n = 1520) and live weight (LW, n = 1309). All phenotyped animals were genotyped and originated from research farms in Ireland, the United Kingdom and the Netherlands. Multi-trait REML was used to simultaneously estimate variance components and breeding values for DMI using available predictors. In addition, analyses using only pedigree relationships were performed. Breeding value accuracy was assessed through cross-validation (CV) and prediction error variance (PEV). CV groups (n = 7) were defined by splitting animals across genetic lines and management groups within country. With no additional traits recorded for the evaluated animals, both CV- and PEV-based accuracies for DMI were substantially higher for genomic than for pedigree analyses (CV: max. 0.26 for pedigree and 0.33 for genomic analyses; PEV: max. 0.45 and 0.52, respectively). With additional traits available, the differences between pedigree and genomic accuracies diminished. With additional recording for FPCM, pedigree accuracies increased from 0.26 to 0.47 for CV and from 0.45 to 0.48 for PEV. Genomic accuracies increased from 0.33 to 0.50 for CV and from 0.52 to 0.53 for PEV. With additional recording for LW instead of FPCM, pedigree accuracies increased to 0.54 for CV and to 0.61 for PEV. Genomic accuracies increased to 0.57 for CV and to 0.60 for PEV. With both FPCM and LW available for evaluated animals, accuracy was highest (0.62 for CV and 0.61 for PEV in pedigree, and 0.63 for CV and 0.61 for PEV in genomic analyses). Recording predictor traits for only the reference population did not increase DMI breeding value accuracy. Recording predictor traits for both reference and evaluated animals significantly increased DMI breeding value accuracy and removed the bias observed when only reference animals had records. The benefit of using genomic instead of pedigree relationships was reduced when more predictor traits were used. Using predictor traits may be an inexpensive way to significantly increase the accuracy and remove the bias of (genomic) breeding values of scarcely recorded traits such as feed intake.     

Bayesian experimental design for nonlinear mixed-effects models with application to HIV dynamics

Bayesian experimental design is investigated for Bayesian analysis of nonlinear mixed-effects models. Existence of the posterior risk for parameter estimation is shown. When the same prior distribution is used for both design and inference, existence of the preposterior risk for design is also proven. If the prior distribution used in design is different from that used for inference, sufficient conditions are established for existence of the preposterior risk for design. A case study of design for an experiment in population HIV dynamics is provided.     

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.     

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.     

Comparison of funding and demand for the conservation of the charismatic koala with those for the critically endangered wombat <Emphasis Type="Italic">Lasiorhinus krefftii</Emphasis>

This study contrasts the actual conservation spending and the Australian public’s demand for conservation funding for two Australian mammal species, the koala and the northern hairy-nosed wombat. It involves a survey of 204 members of the Australian public. Willingness to fund conservation action to protect the northern hairy-nosed wombat was found to be higher than that for the koala despite the koala’s immense popularity. The critically endangered status of the northern-hairy nosed wombat and the more secure conservation status of the koala is a factor likely to have influenced the comparative willingness-to-pay decisions. Actual annual conservation expenditure for both species is lower than the estimated aggregate willingness-to-pay for their conservation. Furthermore, conservation funding for the koala is much more than that for the northern hairy-nosed wombat even though the estimated public willingness-to-pay (demand) for funding koala conservation was less than for this wombat species. Reasons for this are suggested. They may also help to explain misalignment between demand for conservation funding of other species involving differences in charisma and endangerment.     

Revised and extended serum cotinine cut-offs to classify smokers and non-smokers

Purpose: To revise and extend the previously published serum cotinine cut offs to classify smokers and non-smokers for US adolescents and adults.

Materials and methods: Cross-sectional data (N?=?10171) from National Health and Nutrition Examination Survey for 2011–2014 were used to compute serum cotinine cut-offs to classify smokers and non-smokers for US adults aged ≥20?years and 2007–2014 (N?=?4583) data were used to compute serum cotinine cut-offs for US adolescents aged 12–19?years.

Results: Specificities and sensitivities for the cut-offs among adults were ≥95% and ≥75% among adolescents. For adults, serum cotinine cut-offs in ng/mL to classify smokers from non-smokers were 3.3 for the total population, 4.13 for males, 2.99 for females, 4.03 for non-Hispanic whites, 8.85 for non-Hispanic blacks, 0.377 for Mexican Americans, 1.72 for other Hispanics and 1.41 for non-Hispanic Asians. For adolescents, serum cotinine cut-offs in ng/mL to classify smokers from non-smokers were 0.765 for the total population, 1.1 for males, 0.408 for females, 1.2 for non-Hispanic whites, 1.98 for non-Hispanic blacks, 0.215 for Mexican Americans and 0.321 for other Hispanics.

Conclusions: Serum cotinine cut-offs to distinguish smokers from non-smokers for US adults and adolescents were developed.     

Log-linear Models for Polytomous Data

The present study discusses two variants of linear logistic models for polytomous variables for ?unordered”? and for ?ordered”? categories (polydimensional and one-dimensional model). The ML-estimation equations and the possibilities to test the validity of the model are given for both. A test for goodness-of-fit (external validity) and a test for equality of the parameter estimates for split data (interval validity) are suggested. In addition, statistical tests for the significance of individual parameters on the basis of the information matrix and likelihood ratio tests for one or more parameters are described. The presentation is completed by an empirical example from the area of audiology.     

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.     

Communalities for rates of diaphyseal elongation of short bones of the hand of children with Down syndrome

Communality indices for rates of elongation of diaphyses of short bones of the hand were computed from serial data for children with Down syndrome, 7 to 14 years of age. Communalities were larger for adjacent than for nonadjacent bones and also larger for bones grouped in rows rather than rays of the hand. This pattern is similar to that reported for normal children. Communality indices for rates of diaphyseal elongation for girls with Down syndrome were lower than those of boys with Down syndrome and normal children.     

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     

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     

Aerobactin production and plasmid distribution in Escherichia coli clinical isolates

The distribution of plasmids as a function of aerobactin production, antibiotic resistance and antimicrobial agents production was studied in 139 Escherichia coli strains obtained from clinical sources. Ninety eight per cent of the strains analyzed presented plasmids with a median value of 2.97 plasmids per cell. Differences in the number of plasmids were observed for aerobactin production (3.52 for aerobactin producing strains, 2.56 (for non-producing ones) and antibiotic resistance (3.19 for antibiotic resistant strains and 2.58 for the sensitive ones). But this was not the case for antibacterial agent production (2.96 for the producing strains, 2.98 for the non-producing ones. Ecological implications of these results are discussed.     

Aspects of the reproductive biology of two pelagic sharks in the eastern Atlantic Ocean

This study used data provided by the Chinese Longline Fishery Scientific Observer Programme from the tropical eastern Atlantic Ocean to estimate the reproductive parameters of the blue shark (Prionace glauca) and crocodile shark (Pseudocarcharias kamoharai). Sizes ranged from 80 to 298 cm fork length (FL) for blue sharks and from 48 to 99 cm FL for crocodile sharks. Sexual segregation was observed during different months for both sharks. The sex ratio for blue sharks was 1.38 F:1 M, and 1 F:2.79 M for crocodile sharks. The size of adult blue sharks ranged from 144 to 280 cm for males and from 174 to 298 cm for females; and that of crocodile sharks from 63 to 97 cm for males and 78–99 cm for females. The size at 50% of maturity for blue sharks was estimated at 191.7 cm FL for females and 197.5 cm FL for males, and that of crocodile sharks was assessed at 84.9 cm FL for females and 78.5 cm FL for males. Most sexually matured females were pregnant; their means were 207.2 ± 16.4 cm FL for blue sharks and 89.4 ± 4.3 cm FL for crocodile sharks. Mature sizes for both species were significantly different among months. Embryonic sizes also varied widely among months for crocodile sharks, but a slight change was recorded for those of blue sharks. The observed mean size at birth and litter size were 34.5 cm FL and 37 ± 12 for the blue sharks, and that of the crocodile sharks, 39.5 cm FL and a dominant four embryos in the uterus. Due to the observed increasing catch trend of blue sharks and the slow reproductive cycle of crocodile sharks, this study presents the need of implementing conservation measures to ensure the sustainability of both species in their habitat.     

放线菌和霉菌菌种保藏研究报告

用砂管法室温保藏放线菌244株29年。其存活率(%)为:6年96;9年91;11年88;14年78;15年76;17年74;20年70;22年59;25年47;27年40;29年37。保藏29年尚存活的放线菌的抗曾活性与保藏前基本相同。用麸曲法室温保藏木霉、曲霉和青霉等12属共216株,存活率因种而异。保藏12年,不同种属霉菌的存活率为0—100%;保藏至16年,全部失活。     

A gas chromatography/mass spectrometry assay to measure estradiol, catecholestradiols, and methoxyestradiols in plasma

We have developed a gas chromatography/mass spectrometry (GC/MS) assay to measure 17beta-estradiol (E) and its biologically active metabolites 2-hydroxyestradiol (2OHE) and 4-hydroxyestradiol (4OHE), and 2-methoxyestradiol (2MEOE) and 4-methoxyestradiol (4MEOE) in rat plasma. All analytes are well separated and show a linear relationship between concentration (0.25-5 pg/microl) and signal, and coefficients of variation (CVs) are low. Intra-assay CV for the lowest quality control samples (QCs) (0.375 pg/microl) were on average for 17beta-estradiol 20.5%, for 2-hydroxyestradiol 15.6%, for 4-hydroxyestradiol 16.5%, for 2-methoxyestradiol 16.5%, and for 4-methoxyestradiol 11.5%. The inter-assay CVs for the lowest QCs were for 17beta-estradiol 12.1%, for 2-hydroxyestradiol 7.1%, for 4-hydroxyestradiol 15.5%, for 2-methoxyestradiol 16.7%, and for 4-methoxyestradiol 9.7%. The highest sensitivity for this assay was observed for hydroxyestradiols followed by the methoxyestradiols and 17beta-estradiol. In summary, we describe a convenient, sensitive, and specific assay to measure 17beta-estradiol and its biologically active metabolites.