Weeds as hosts of Mycocentrospora acerina

Weeds were collected from carrot fields and some other sites at 27 localities in seven counties in Norway during August and September of 1986 and 1987. Leaf and petiole lesions were microscopically examined for Mycocentrospora acerina. Viola arvensis and Viola tricolor were commonly observed with the pathogen. The fungus was also registered on Fumaria officinalis, Galium aparine, Matricaria inodora, Matricaria matricarioides, Ranunculus repens, Senecio vulgaris and Stachys palustris. In inoculation experiments in the greenhouse, M. acerina infected carrot leaves and 13 of 16 species of weeds. The symptoms on the various susceptible plants showed some variation, but were essentially of the same pattern. The investigation indicates that weeds are common hosts of M. acerina. A list of 23 host weed species is given.     

Mycocentrospora acerina in carrots; Effects of crop rotation on disease incidence

Four experimental sites located in different climatic regions in Norway were inoculated with Mycocentrospora acerina in 1985. In 1986, crop rotation experiments including carrot, barley, grass, red clover, onion and potato, were established at these sites. Incidence of M. acerina on the foliage and the roots of carrots after storage were recorded in 1989/90 and 1994/95. The 3 yr rotation only slightly reduced the inoculum of M. acerina in the soil. Red clover and grass were the most effective crops in reducing the inoculum, potato and barley were less effective, and onion had no effect on the inoculum. Differences in M. acerina infection on carrots between 3, 6 and 8 yr of rotation with barley and grass were not statistically significant.     

侧孢短芽孢杆菌S2-31拮抗下细辛叶枯病菌转录组差异表达分析

通过分析侧孢短芽孢杆菌拮抗作用下叶枯病菌的转录组学特征,研究差异表达基因(DEGs)和代谢通路的富集情况,初步探索侧孢短芽孢杆菌拮抗叶枯病菌的分子机制.首先利用S2-31与叶枯病菌的对峙培养观察其拮抗作用,然后利用转录组测序探究侧孢短芽孢杆菌拮抗下和正常生长下的叶枯病菌的基因表达水平差异,并进行RT-qPCR验证,最后...     

The influence of the fungal pathogen Mycocentrospora acerina on the proteome and polyacetylenes and 6-methoxymellein in organic and conventionally cultivated carrots (Daucus carota) during post harvest storage

Many carrots are discarded during post harvest cold storage due to development of fungal infections, caused by, e.g., Mycocentrospora acerina (liquorice rot). We compared the susceptibility of carrots grown under conventional and organic agricultural practices. In one year, organically cultivated carrots showed 3 × to 7 × more symptoms than conventionally cultivated, when studying naturally occurring disease at 4 and 6 months, respectively. On the other hand, we have developed a bioassay for infection studies of M. acerina on carrots and observed that organic roots were more susceptible after one month of storage than conventional ones, but no differences were apparent after four or six months storage. Levels of polyacetylenes (falcarinol, falcarindiol and falcarindiol-3-acetate) did not change, whereas the isocoumarin phytoalexin (6-methoxymellein) accumulated in infected tissue as well as in healthy tissue opposite the infection. The proteomes of carrot and M. acerina were characterized, the intensity of 33 plant protein spots was significantly changed in infected roots including up regulation of defence and stress response proteins but also a decrease of proteins involved in energy metabolism. This combined metabolic and proteomic study indicates that roots respond to fungal infection through altered metabolism: simultaneous induction of 6-methoxymellein and synthesis of defence related proteins.     

Effects of the Plant-pathogenic Fungus Mycocentrospora acerina (Hartig) Deighton on Growth and Competition of Viola arvensis (Murr.) in Spring Wheat

Mycocentrospora acerina (Hartig) Deighton can kill or suppress the growth of Viola arvensis (Murr.) in spring wheat in pot-grown plants in both glasshouse and outdoor studies. The level of damage to V. arvensis and the effect on its competition with wheat were affected by inoculum density and environmental conditions. High inoculum density (105 macroconidia/ml) caused high mortality in V. arvensis and eliminated its competitive effect on wheat. At a lower density (104 macroconidia/ml), the V. arvensis fresh weight and its competition with the wheat were suppressed by up to 38 and 28% respectively, depending on environmental conditions.     

神经网络在蛋白质二级结构预测中的应用

介绍了蛋白质二级结构预测的研究意义,讨论了用在蛋白质二级结构预测方面的神经网络设计问题,并且较详尽地评述了近些年来用神经网络方法在蛋白质二级结构预测中的主要工作进展情况,展望了蛋白质结构预测的前景。     

幽门螺杆菌感染诊断方法的比较

目的:考核各种H.pylori感染诊断方法,试图证明分离培养仍是细菌性感染诊断的最可靠方法.方法:315例胃十二指肠疾病患者同时进行胃活检组织分离培养,病理切片找菌,快速脲酶试验,14CO2呼气试验检查,比较它们之间的检出率差异.结果:四种方法各自的总检出率差异无显著性.以分离培养为金标准,其他方法的误诊误治率可达12.06%～22.22%.各种诊断方法对H.pylori感染的实际检出率差异存在着显著性.结论:本研究提示,分离培养应为H.pylori感染临床诊断的金标准.     

A comparison of two methods for prediction of response and rates of inbreeding in selected populations with the results obtained in two selection experiments

Selection programmes are mainly concerned with increasing genetic gain. However, short-term progress should not be obtained at the expense of the within-population genetic variability. Different prediction models for the evolution within a small population of the genetic mean of a selected trait, its genetic variance and its inbreeding have been developed but have mainly been validated through Monte Carlo simulation studies. The purpose of this study was to compare theoretical predictions to experimental results. Two deterministic methods were considered, both grounded on a polygenic additive model. Differences between theoretical predictions and experimental results arise from differences between the true and the assumed genetic model, and from mathematical simplifications applied in the prediction methods. Two sets of experimental lines of chickens were used in this study: the Dutch lines undergoing true truncation mass selection, the other lines (French) undergoing mass selection with a restriction on the representation of the different families. This study confirmed, on an experimental basis, that modelling is an efficient approach to make useful predictions of the evolution of selected populations although the basic assumptions considered in the models (polygenic additive model, normality of the distribution, base population at the equilibrium, etc.) are not met in reality. The two deterministic methods compared yielded results that were close to those observed in real data, especially when the selection scheme followed the rules of strict mass selection: for instance, both predictions overestimated the genetic gain in the French experiment, whereas both predictions were close to the observed values in the Dutch experiment.     

Kernel machine approach to testing the significance of multiple genetic markers for risk prediction

There is growing evidence that genomic and proteomic research holds great potential for changing irrevocably the practice of medicine. The ability to identify important genomic and biological markers for risk assessment can have a great impact in public health from disease prevention, to detection, to treatment selection. However, the potentially large number of markers and the complexity in the relationship between the markers and the outcome of interest impose a grand challenge in developing accurate risk prediction models. The standard approach to identifying important markers often assesses the marginal effects of individual markers on a phenotype of interest. When multiple markers relate to the phenotype simultaneously via a complex structure, such a type of marginal analysis may not be effective. To overcome such difficulties, we employ a kernel machine Cox regression framework and propose an efficient score test to assess the overall effect of a set of markers, such as genes within a pathway or a network, on survival outcomes. The proposed test has the advantage of capturing the potentially nonlinear effects without explicitly specifying a particular nonlinear functional form. To approximate the null distribution of the score statistic, we propose a simple resampling procedure that can be easily implemented in practice. Numerical studies suggest that the test performs well with respect to both empirical size and power even when the number of variables in a gene set is not small compared to the sample size.     

The Effect of CO2 Enrichment on the Growth of Nodulated and Non-Nodulated Isogenic Types of Soybean Raised Under Two Nitrogen Concentrations

To find the effects of CO₂ enrichment on plant development and photosynthetic capacity of nodulated (line A62-1) and non-nodulated (line A62-2) isogenic lines of soybean (Glycine max Merr.), we examined the interactions among two CO₂ treatments (36±3 Pa = AC and 70±5 Pa = EC), and two nitrogen concentrations [0 g(N) m⁻²(land area) = 0N; 30 g(N) m⁻²(land area) = 30N]. Nodules were found in both CO₂ treatments in 0N of A62-1 where the number and dry mass of nodules increased from AC to EC. While the allocation of dry mass to root and shoot and the amount of N in each organ did not differ between the growth CO₂ concentrations, there was larger N allocation to roots in 0N than in 30N for A62-2. The CO₂-dependence of net photosynthetic rate (P _N) for A62-1 was unaffected by both CO₂ and N treatments. In contrast, the CO₂-dependence of P _N was lower in 0N than in 30N for A62-2, but it was independent of CO₂ treatment. P _N per unit N content was unaffected by CO₂ concentrations. The leaf area of both soybean lines grown in 30N increased in EC. But in 0N, only the nodulated A62-1 showed an increase in leaf area in EC. Nitrogen use efficiency of plants, NUE [(total dry mass of the plant)/(amount of N accumulated in the plant)] in 30N was unaffected by CO₂ treatments. In 0N, NUE in EC was lower than in AC in A62-1, and was higher than that at AC in A62-2. Hence, the larger amount and/or rate of N fixation with the increase of the sink-size of symbiotic microorganisms supplied adequate N to the plant under EC. In EC, N deficiency caused the down-regulation of the soybean plant. This revised version was published online in June 2006 with corrections to the Cover Date.     

Evidence for chemical changes on the root surface of tall fescue in response to infection with the fungal endophyte Neotyphodium coenophialum

Endophyte-infected (E+) tall fescue (Festuca arundinacea Schreb.) plants grown in phosphorus (P) deficient soils accumulate more P in roots and shoots than noninfected isolines. In a growth chamber experiment, four tall fescue genotypes DN2, DN4, DN7, and DN11, infected with their naturally occurring strains of Neotyphodium coenophialum (Morgan-Jones & Gams) Glenn, Bacon & Hanlin, and their noninfected isolines (E-), were cultivated in nutrient solution at two P levels: 31 ppm (P+) and 0 ppm (P-) for 4 wk. The Fe³⁺ reducing activity of extracellular reductants and intact root tissues, and total phenolic concentration in roots and shoots were measured. Endophyte infection significantly increased Fe³⁺ reducing activity rate of extracellular reductants (9.6 × 10^-3 mol Fe³⁺ h-1 g-1 root FW) when compared to E- plants (3.9 × 10^-3) and Fe³⁺ reduction rate of intact root tissues (6.16 and 4.48 mol Fe³⁺ h-1 g-1 root FW, respectively for E+ and E- plants). In response to P deficiency, Fe³⁺ reduction rate of intact root tissues increased in E+ plants by 375% when compared to E- plants, whereas no significant differences were observed when P was provided. Total phenolic concentration was 20% greater in shoots of E+ plants than in E- plants. In response to P deficiency, total phenolic concentration significantly increased in roots of E+ plants by 7%, and decreased in roots of E- plants by 10%. The most active Fe³⁺ reducing zones were located along branching of secondary and tertiary roots. The Fe³⁺ reducing activity on the root surface and total phenolic concentration in roots and shoots increased dramatically in response to endophyte infection, especially under P limiting conditions.Visiting Scientist sponsored by the Fulbright Program No. 21133     

Tables for Testing the Equality of Two Proportions when Prior Information on their Common Value May be Available

In testing the equality of two proportions, one may define a rejection point T? such that if the test statistic T (in this paper, the ordinary Pearsonian chi-squared) exceeds T? then the hypothesis may safely be rejected, whatever the common value p of the two proportions may be; and similarly define an acceptance point A? such that if T ≦ T? then one may safely accept. These points may be refined if prior information is available, for example that p must lie in the central interval (c, 1 – c) or one of the extremal intervals (v, w) and (1 – w, 1 – v). Smallsample tables are provided both for the unrestricted case and for situations where one has such prior information.     

Effects of Natural and Synthetic Auxins on the Gravitropic Growth Habit of Roots in Two Auxin-Resistant Mutants of Arabidopsis, axr1 and axr4: Evidence for Defects in the Auxin Influx Mechanism of axr4

Arabidopsis thaliana, axr4 , was restored by the addition of 30–300 nM 1-naphthaleneacetic acid (NAA) to the growth medium. Neither indole-3-acetic acid (IAA) nor 2,4-dichlorophenoxyacetic acid (2,4-D) showed such an effect. Growth of axr4 roots was resistant to IAA and 2,4-D, but not at all to NAA. The differential effects of the three auxins suggest that the defects of axr4 result from a lower auxin influx into its cells. The partially agravitropic growth habit of axr1 roots, which was less severe than that of axr4 roots, was only slightly affected by the three auxins in the growth medium at concentrations up to 300 nM; growth of axr1 roots was resistant to all three of the auxins. These results suggest that the lesion of axr1 mutants is different from that of axr4. Received 9 June 1999/ Accepted in revised form 16 August 1999     

Evaluation of stool antigen test, PCR on ORAL samples and serology for the noninvasive detection of Helicobacter pylori infection in children

BACKGROUND: Endoscopy represents the gold standard for the diagnosis of Helicobacter pylori infection. We evaluated three noninvasive tests in a group of children: the immunoassay for detection of H. pylori stool antigen, the polimerase chain reaction for identification of bacterial DNA on the oral cavity and the serum specific antibodies. MATERIALS AND METHODS: One hundred and ninety children underwent endoscopy for various gastrointestinal symptoms. H. pylori stool antigen and anti-H. pylori antibodies were assayed by commercial kits. The bacterial DNA on saliva and oral plaque was detected by a seminested PCR. RESULTS: Based on the positivity of culture or urease rapid test and histology, infection was detected in 47 patients. The statistical analysis showed that, for the detection of the infection, stool antigen assay is more effective in sensitivity and negative predictive value (91.5% and 96.5%), whereas specificity and positive predictive values appear slightly better in serology (89.6% and 76.0%). Correlations between serum IgG both with patients' age (r = 0.21, p < .05) and H. pylori stool antigen (r = 0.47, p < .01) were found. The search for bacterial DNA on oral samples proved to be very specific (99.1% on saliva and 98.2% on plaque), but insensitive (22.2% and 25.7%). CONCLUSIONS. In children H. pylori stool antigen represents a sensitive test, suitable for detecting H. pylori infection. Serum IgG proved to be more specific; the PCR on the oral cavity resulted as being a very specific, but insensitive test.     

The impact of climate change on the geographical distribution of two vectors of Chagas disease: implications for the force of infection

Chagas disease, caused by the parasite Trypanosoma cruzi, is the most important vector-borne disease in Latin America. The vectors are insects belonging to the Triatominae (Hemiptera, Reduviidae), and are widely distributed in the Americas. Here, we assess the implications of climatic projections for 2050 on the geographical footprint of two of the main Chagas disease vectors: Rhodnius prolixus (tropical species) and Triatoma infestans (temperate species). We estimated the epidemiological implications of current to future transitions in the climatic niche in terms of changes in the force of infection (FOI) on the rural population of two countries: Venezuela (tropical) and Argentina (temperate). The climatic projections for 2050 showed heterogeneous impact on the climatic niches of both vector species, with a decreasing trend of suitability of areas that are currently at high-to-moderate transmission risk. Consequently, climatic projections affected differently the FOI for Chagas disease in Venezuela and Argentina. Despite the heterogeneous results, our main conclusions point out a decreasing trend in the number of new cases of Tr. cruzi human infections per year between current and future conditions using a climatic niche approach.     

Effects of shading and powdery mildew infection on senescence of the root cortex and coleoptile of wheat and barley seedlings,and implications for root- and foot-rot fungi

Summary Nuclear and cytoplasmic staining methods were used to study natural senescence of the root cortex and coleoptile of wheat and barley seedlings grown in glasshouse conditions. Coleoptiles of barley senesced more slowly than those of wheat, paralleling the known difference in rates of root cortex senescence in these cereals. The coleoptiles and root cortices of both cereals senesced more slowly in shaded than in unshaded conditions, but infection of the shoots of barley byErysiphe graminis had little effect on root cortex senescence. The results are discussed in relation to infection by root- and foot-rot fungi. Previous reports on the effects of illumination on take-all infection (Gaeumannomyces graminis) are explained. It is suggested that natural senescence of the coleoptile might affect establishment of infection by the eyespot fungus,Pseudocercosporella herpotrichoides, either directly or through the activities of competing microorganisms.     

A rapid method for quantitative prediction of high affinity CTL epitopes: QSAR studies on peptides having affinity with the class I MHC molecular HLA-A*0201

Summary It would be useful to develop a method to rapidly identify peptide epitopes for vaccine development. In this paper, empirical three-dimensional quantitative structure-affinity relationship (3D-QSAR) methods were used to study the relationship between the three dimensional structural parameters (the isotropic surface area, ISA, and the electronic charge index, ECI) of the HLA-A^*0201 binding peptide and the HLA-A^*0201/peptide binding affinities. A set of 102 peptides having affinity with the class I MHC HLA-A^*0201 molecule was used as training set. A test set of 40 peptides was used to determine the predictive value of the models. The 3D-QSAR models gave aq ²=0.5724 and highr _pred ² =0.6955. According to the standard regression coefficients, it is known that the hydrophobic interactions (in these studies, the ISA is highly correlative with the hydrophobic property) play a dominant role in peptide-MHC molecule binding, and also which amino acid residue with what property is needed at specific position of the peptide. The approach we have taken is highly complementary to the many excellent methods described in references and appears highly predictive. It is a rapid and convenient method for detecting high affinity peptide epitopes.     

A rapid method for quantitative prediction of high affinity CTL epitopes: QSAR studies on peptides having affinity with the class I MHC molecular HLA-A*0201

Summary  It would be useful to develop a method to rapidly identify peptide epitopes for vaccine development. In this paper, empirical three-dimensional quantitative structure-affinity relationship (3D-QSAR) methods were used to study the relationship between the three dimensional structural parameters (the isotropic surface area, ISA, and the electronic charge index, ECI) of the HLA-A^*0201 binding peptide and the HLA-A^*0201/peptide binding affinities. A set of 102 peptides having affinity with the class I MHC HLA-A^*0201 molecule was used as training set. A test set of 40 peptides was used to determine the predictive value of the models. The 3D-QSAR models gave aq ²=0.5724 and highr _pred ² =0.6955. According to the standard regression coefficients, it is known that the hydrophobic interactions (in these studies, the ISA is highly correlative with the hydrophobic property) play a dominant role in peptide-MHC molecule binding, and also which amino acid residue with what property is needed at specific position of the peptide. The approach we have taken is highly complementary to the many excellent methods described in references and appears highly predictive. It is a rapid and convenient method for detecting high affinity peptide epitopes.