Dynamic root growth and architecture responses to limiting nutrient availability: linking physiological models and experimentation

In recent years the study of root phenotypic plasticity in response to sub-optimal environmental factors and the genetic control of these responses have received renewed attention. As a path to increased productivity, in particular for low fertility soils, several applied research projects worldwide target the improvement of crop root traits both in plant breeding and biotechnology contexts. To assist these tasks and address the challenge of optimizing root growth and architecture for enhanced mineral resource use, the development of realistic simulation models is of great importance. We review this research field from a modeling perspective focusing particularly on nutrient acquisition strategies for crop production on low nitrogen and low phosphorous soils. Soil heterogeneity and the dynamics of nutrient availability in the soil pose a challenging environment in which plants have to forage efficiently for nutrients in order to maintain their internal nutrient homeostasis throughout their life cycle. Mathematical models assist in understanding plant growth strategies and associated root phenes that have potential to be tested and introduced in physiological breeding programs. At the same time, we stress that it is necessary to carefully consider model assumptions and development from a whole plant-resource allocation perspective and to introduce or refine modules simulating explicitly root growth and architecture dynamics through ontogeny with reference to key factors that constrain root growth. In this view it is important to understand negative feedbacks such as plant–plant competition. We conclude by briefly touching on available and developing technologies for quantitative root phenotyping from lab to field, from quantification of partial root profiles in the field to 3D reconstruction of whole root systems. Finally, we discuss how these approaches can and should be tightly linked to modeling to explore the root phenome.     

Bayesian Statistics-Based Procedure for Sampling of Contaminated Sites

A variable density sampling pattern based on Bayesian statistics is presented and compared to a uniform density statistical pattern and a judgmental approach in a real case study. The Bayesian statistics, supported by a software tool, supplied a soil sampling plan similar to the judgmental one, especially for the number of sampling points and their location. It allowed statistical goals to be set and expert judgment to be included in the sampling strategy in a transparent and systematic procedure. For these reasons, it appears quite suitable for inclusion into Quality Assurance Quality Control plans.     

Indirect nontarget effects of host-specific biological control agents: Implications for biological control

Classical biological control of weeds currently operates under the assumption that biological control agents are safe (i.e., low risk) if they do not directly attack nontarget species. However, recent studies indicate that even highly host-specific biological control agents can impact nontarget species through indirect effects. This finding has profound implications for biological control. To better understand the causes of these interactions and their implications, we evaluate recent case studies of indirect nontarget effects of biological control agents in the context of theoretical work in community ecology. We find that although particular indirect nontarget effects are extremely difficult to predict, all indirect nontarget effects of host specific biological control agents derive from the nature and strength of the interaction between the biological control agent and the pest. Additionally, recent theoretical work suggests that the degree of impact of a biological control agent on nontarget species is proportional to the agent’s abundance, which will be highest for moderately successful control agents. Therefore, the key to safeguarding against indirect nontarget effects of host-specific biological control agents is to ensure the biological control agents are not only host specific, but also efficacious. Biological control agents that greatly reduce their target species while remaining host-specific will reduce their own populations through density-dependent feedbacks that minimize risks to nontarget species.     

Relationship of CSF neurotransmitter metabolite levels to disease severity and disability in multiple sclerosis

Axonal degeneration and brain tissue loss occur during disease progression in multiple sclerosis (MS) and are expected to influence neurotransmitter activities, with consequences on neurologic and psychiatric symptomatology. We searched for relationships of disease duration, disability, and severity of MS patients to CSF levels of the major metabolites of noradrenaline, dopamine, and serotonin, MHPG, methoxyhydroxyphenylglycol (MHPG), homovanillic acid, and 5-hydroxyindoleacetic acid (5-HIAA), respectively, in 39 patients with relapsing–remitting (RR) MS in remission, and 26 patients with progressive (PR) MS. Disability and Disease Severity were assessed by the Expanded Disability Status Scale (EDSS) and the Multiple Sclerosis Severity Score (MSSS). Compared with the levels of 50 control subjects, MHPG levels were not different in either MS group, correlated negatively to duration of illness and number of relapses in the RRMS group, but not to EDSS score or to MSSS. Homovanillic acid levels were significantly lower only in the PRMS group, with a negative correlation to duration of illness, and a strong negative correlation to EDSS score, but not to MSSS. 5-HIAA was significantly lower in both RRMS and PRMS groups. In the RRMS group, 5-HIAA levels were negatively related to EDSS and to MSSS. Multiple regression analyses revealed a significant association of MHPG to duration of illness, and a strong negative association of 5-HIAA to MSSS rather than to EDSS. The strong negative correlation of MSSS to CSF 5-HIAA levels in RRMS group of patients indicates that deficits in central serotonergic activity are related to the rate of disability accumulation in RRMS, and could be linked to the reported reduction of disease activity by serotonergic drugs.     

Study design and parameter estimability for spatial and temporal ecological models

The statistical tools available to ecologists are becoming increasingly sophisticated, allowing more complex, mechanistic models to be fit to ecological data. Such models have the potential to provide new insights into the processes underlying ecological patterns, but the inferences made are limited by the information in the data. Statistical nonestimability of model parameters due to insufficient information in the data is a problem too‐often ignored by ecologists employing complex models. Here, we show how a new statistical computing method called data cloning can be used to inform study design by assessing the estimability of parameters under different spatial and temporal scales of sampling. A case study of parasite transmission from farmed to wild salmon highlights that assessing the estimability of ecologically relevant parameters should be a key step when designing studies in which fitting complex mechanistic models is the end goal.     

饲料中狐狸、水貂、貉子和狗源性的五重实时荧光PCR检测方法的建立

为了快速鉴别饲料中的狐狸、水貂、貉子和狗源性成分,根据线粒体16S r DNA种间保守序列,设计合成针对狐狸、水貂、貉子和狗的特异性引物和探针,通过对荧光PCR反应体系和反应条件的优化筛选,建立了多重实时荧光PCR方法,在同一PCR反应体系中可以同时完成4种动物源性成分检测。通过对15种其他物种的源性成分的检测,结果表明所设计的引物和探针具有很好的物种特异性,且灵敏度高,狐狸、水貂、貉子和狗的DNA检出限为0.01ng。对40份样品检测,其中5份检测出貉子、狐狸和水貂源性成分。结果表明,该方法可以有效地鉴别出饲料中狐狸、水貂、貉子和狗源性成分,同时适用于相关动物产品中。     

Binding of [H][D-Ala, MePhe, Gly-ol] Enkephalin, [H][D-Pen, D-Pen]Enkephalin, and [H]U-69,593 to Airway and Pulmonary Tissues of Normal and Sensitized Rats

Bhargava, H. N., V. M. Villar, J. Cortijo and E. J. Morcillo. Binding of [³H][D-Ala², MePhe⁴, Gly-ol⁵]enkephalin, [³H][D-Pen², D-Pen⁵]enkephalin, and [³H]U-69,593 to airway and pulmonary tissues of normal and sensitized rats. Peptides 18(10) 1603–1608, 1997.—The role of endogenous opioid peptides in the regulation of bronchomotor tone, as well as in the pathophysiology of asthma is uncertain. We have studied the binding of highly selective [³H]labeled ligands of μ-([D-Ala², MePhe⁴, Gly-ol⁵]enkephalin; DAMGO), δ ([D-Pen², D-Pen⁵]enkephalin; DPDPE), and κ-(U-69,593) opioid receptors to membranes of trachea, main bronchus, lung parenchyma and pulmonary artery obtained from normal (unsensitized) and actively IgE-sensitized rats acutely challenged with the specific antigen. [³H]DAMGO, [³H]DPDPE and [³H]U-69,593 bound to membranes of normal and sensitized tissues at a saturable, single high-affinity site. The rank order of receptor densities in normal tissues was δ- ≥ κ- ≥ μ-, with lung parenchyma exhibiting the greatest binding capacity for δ- and μ- receptors compared to the other regions examined. The K_d values showed small differences between ligands and regions tested. The μ- and δ-opioid receptor densities were decreased in sensitized main bronchus and lung parenchyma, respectively, compared to normal tissues. By contrast, κ-opioid receptor density was augmented in sensitized lung parenchyma but an increase in K_d values was also observed. These differential changes in the density and affinity of opioid receptor types may be related to alterations in endogenous opioid peptides during the process of sensitization.     

VIP in cerebrospinal fluid of patients with multiple sclerosis

The concentration of VIP was measured radioimmunochemically in cerebrospinal fluid (CSF) from 14 healthy volunteers and from 22 patients with multiple sclerosis. Significantly lower levels of VIP was obtained in the patients (18 +/- 3 pmol/l) than in controls (37 +/- 4 pmol/l). There was no correlation between the level of VIP in CSF and other CSF parameters such as albumin. IgG or cell content; nor between VIP concentration and the physical handicap or neuropsychiatric symptoms. There was a trend towards lower values of VIP in patients with steadily progressing rather than intermittent course of the disease but the difference between the groups was not significant.     

Using patterns of variability to test for multiple community states on rocky intertidal shores

Predictions based on theory of multiple stable states suggest that larger perturbations should lead to more unpredictable patterns of succession. This prediction was tested in the Gulf of Maine using data from 60 intertidal plots of varying size that were experimentally cleared of the rockweed Ascophyllum nodosum and from 14 benchmark sites from throughout the Gulf. Rockweed was removed from the experimental clearings ranging from 1 to 8 m in diameter in 1996 and data collected in 2004 were used to test effects of clearing size and location on divergence and variability in species composition. Benchmark data were collected in 2005, and the 14 sites were from a dataset on 53 sites throughout the Gulf of Maine. The selected sites were randomly chosen from all sites with > 80% canopy cover by A. nodosum and were expected to be similar to uncleared control plots from the experiment. Experimental removal of A. nodosum resulted in clearings at 12 sites within 4 bays. Abundances of gastropods, barnacles, mussels, and fucoid algae and the percentage cover of barnacles, mussels, fucoid algae, bare space, and other species were sampled. CAP and PERMDISP analyses revealed significant differences in multivariate dispersion and variability with both clearing size and location. Variability generally increased with clearing size and location effects were related to the north-south positioning of the sites. Benchmark sites were similar to the experimental control plots but as variable as the largest clearings. Results suggest that succession in larger clearings has been more unpredictable than in small clearings. The pattern of variability in the experimental clearings is consistent with the predictions of multiple stable states. However, the large amount of variation among the benchmark sites was due to mussels and was unexpected. This unexpected variability underscores the importance of sampling benchmark sites as part of experiments.