An ancient enzyme finds a new home: Prevalence and neofunctionalization of trypsin in marine phytoplankton

Trypsin is an ancient protease best known as a digestive enzyme in animals, and traditionally believed to be absent in plants and protists. However, our recent studies have revealed its wide presence and important roles in marine phytoplankton. Here, to gain a better understanding on the importance of trypsin in phytoplankton, we further surveyed the distribution, diversity, evolution and potential ecological roles of trypsin in global ocean phytoplankton. Our analysis indicated that trypsin is widely distributed both taxonomically and geographically in marine phytoplankton. Furthermore, by systematic comparative analyses we found that algal trypsin could be classified into two subfamilies (trypsin I and trypsin II) and exhibited highly duplicated and diversified during evolution. We also observed markedly different domain sequences and organizations between and within the subfamilies, suggesting potential neofunctionalization. Diatoms contain both subfamilies of trypsin, with higher numbers of genes and more environment-responsive expression of trypsin than other lineages. The duplication and subsequent neofunctionalization of the trypsin family may be important in diatoms for adapting to dynamical environmental conditions, contributing to diatoms' dominance in the coastal oceans. This work advances our knowledge on the distribution and neofunctionalization of this ancient enzyme and creates a new window of research on phytoplankton biology.     

基于拉曼技术的单细胞生长检测方法

目的 单细胞生长检测可以更加科学地揭示微生物代谢变化的规律,为后期微生物工程应用提供指导。针对微生物生长应用于食品安全期和最佳食用期的精准检测问题,本文提出一种基于拉曼技术的单细胞生长检测方法。方法 首先,通过同步培养实验采集了枯草芽孢杆菌两个批次共900个单细胞拉曼光谱（SCRS）数据,其中600个用于训练和测试,另一批次300个用于模型验证。其次,基于主成分分析的特征关系矩阵,提出CP-SP特征评估方法以筛选SCRS特征用于模型检测。再基于XGBoost构建检测模型,并应用网格搜索和交叉验证对检测模型进行调优。最后,应用混淆矩阵、ROC曲线评估模型对细胞滞后期、对数期和稳定期的检测准确率、敏感性和特异性。结果 选用CP-SP筛选的第一、第二和第四主成分较特征贡献率前3个主成分的分类性能提高了3.1%,调优后的细胞生长检测模型测试准确率为96.0%,验证准确率为92.3%。结论 基于拉曼技术的单细胞生长检测方法能准确识别单细胞生长状态且具有较高的泛化能力,可为食品安全和保鲜制定精准调控机制提供科学指导。     

THE MEASUREMENT OF SELECTION ON QUANTITATIVE TRAITS: BIASES DUE TO ENVIRONMENTAL COVARIANCES BETWEEN TRAITS AND FITNESS

The use of regression techniques for estimating the direction and magnitude of selection from measurements on phenotypes has become widespread in field studies. A potential problem with these techniques is that environmental correlations between fitness and the traits examined may produce biased estimates of selection gradients. This report demonstrates that the phenotypic covariance between fitness and a trait, used as an estimate of the selection differential in estimating selection gradients, has two components: a component induced by selection itself and a component due to the effect of environmental factors on fitness. The second component is shown to be responsible for biases in estimates of selection gradients. The use of regressions involving genotypic and breeding values instead of phenotypic values can yield estimates of selection gradients that are not biased by environmental covariances. Statistical methods for estimating the coefficients of such regressions, and for testing for biases in regressions involving phenotypic values, are described.     

Excess of nutrients results in plant stress and decreased grass miner performance

We studied the relationship between plant stress intensity and herbivore response in the grass miner Chromatomyia milii (Kaltenbach) (Diptera: Agromyzidae) on nutrient stressed plants. We subjected the host grass Holcus lanatus (Poaceae) to a range of nutrient treatments (0%, 25%, 50%, 100%, and 200% Hoagland nutrient solution) and recorded plant stress intensity (plant growth and foliar chlorophyll a and b levels) and offspring performance of C. milii. Plant growth and foliar chlorophyll a and b levels decreased from the 25% treatment to the 200% treatment. The plant stress intensity from the 0% treatment was equal to or only slightly higher than the 25% treatment. Offspring survival of C. milii was lower on the 100% and the 200% treatments than on the other treatments. Offspring development time and pupal mass did not differ between the nutrient treatments. Offspring survival of C. milii showed a monotonic non‐linear increase with decreasing plant stress intensity. These results clearly show that an excess of nutrients may result in plant stress and reduced herbivore performance.     

Spatial dynamics of lions and their prey along an environmental gradient

Establishing the ecological determinants of the spatial dynamics of large African savanna mammals is necessary for understanding the cumulative impacts on the suitability and resilience of their natural habitats, of progressive habitat fragmentation and temporal shifts in climate, fire regimes and elephant browsing. Systematic directional gradients and small‐scale spatial dependence were evident in rainfall, herbivore biomass and lion density in the Masai Mara National Reserve during September 1990 to July 1992. Lion density, the biomass of resident and all herbivore species were autocorrelated within 4.3, 4.1 and 3.3 km, respectively, and peaked in areas of relatively low rainfall but higher microtopographic and vegetation heterogeneity and complexity and more diverse drainage systems. Rainfall influenced herbivore biomass and hence lion density non‐linearly and that influence was apparently modified by forage mineral nutrients, structural habitat complexity, degree of drainage and distance to waterpoints. Lion density was related to the biomass of resident herbivores, even after controlling for rainfall and spatial trends. Persistence of the recent decline in Mara woodlands and increasing human population along the reserve–ranch boundary would likely reduce the reserve's lion population because most lions spent the daytime within the vegetation mosaic fringing drainage lines, away from humans and domestic livestock.     

Comparative seed ecology of the endangered shrub, Pimelea spicata and a threatening weed, Bridal Creeper: Smoke, heat and other fire-related germination cues

Summary Pimelea spicata R. Br. is a nationally listed endangered Australian shrub threatened with extinction by habitat fragmentation and environmental weed invasion. Bridal Creeper (Asparagus asparagoides L. W. Wight) is the primary weed threat to the largest remaining populations of P. spicata in the Cumberland Plain. Fire, as part of an integrated pest management program, offers the potential to stimulate P. spicata populations while controlling Bridal Creeper. It is important, therefore, to understand how the components of fire affect the germination and growth of both species. Using laboratory experiments we investigated the effects of smoke, heat, ash and/or light on the germination of P. spicata and Bridal Creeper. We found a significant promotive effect of smoke and indication of an inhibitory heat shock (90°C for 10 min) effect on the germination of P. spicata seeds. The response of Bridal Creeper seeds to the same factors was complex; while the results of one experiment suggested an inhibitory effect of smoke and a promotive effect of heat, subsequent trials were contradictory, implying that Bridal Creeper, like many weeds, is able to germinate under a wide range of environmental conditions. Other experiments investigated the optimal germination temperature and innate dormancy of P. spicata in the absence of fire‐related germination cues. Of the incubation temperatures investigated, the optimal diurnally fluctuating regime for P. spicata germinations was 10°C and 20°C in the night and day, respectively. The innate dormancy of freshly produced seeds disappeared after 3 months. In contrast to Bridal Creeper, we found a persistent germinable seed bank of about 97 P. spicata seeds/m² located in the top 5 cm of the soil profile. While fire alone is unlikely to kill Bridal Creeper plants, fire may help to manage local infestations of the weed by limiting germination and providing opportunity for herbicide treatment of regrowth.     

Early needle senescence and thinning of the crown structure of Picea abies as induced by chronic SO2 pollution. II. Field data basis, model results and tolerance limits

Field data on the sulphur and cation budget of growing Norway spruce canopies (Picea abies [L.] Karst.) are summarized. They are used to test a spruce decline model capable of quantifying effects of chronic SO₂ pollution on spruce forests. At ambient SO₂ concentrations, acute SO₂ damage is rare, but exposure to polluted air produces reversible thinning of the canopy structure with a half-time of a few years. Canopy thinning in the spruce decline model is highest (i) at elevated SO₂ pollution, (ii) in the mountains, (iii) at unfertilized sites with poor K⁺, Mg²⁺ or Zn²⁺ supply, (iv) at low spruce litter decomposition rates, and (v) acidic, shallow soils at high annual precipitation rates in the field and vice versa. Model application using field data from Würzburg (moderate SO₂ pollution, alkaline soils, no spruce decline) and from the Erzgebirge (extreme SO₂ pollution, acidic soils in the mountains, massive spruce decline) predicts canopy thinning by 2–11% in Würzburg and by 45–70% in the Erzgebirge. The model also predicts different SO₂-tolerance limits for Norway spruce depending on the site elevation and on the nutritional status of the needles. If needle loss of more than 25% (damage class 2) is taken to indicate ‘real damage’ exceeding natural variances, then for optimum soil conditions SO₂ tolerance limits range from (27.3 ± 7.4) μg m^?3 to (62.6 ± 16.5) μg m^?3. For shallow and acidic soils, SO₂ tolerance limits range from (22.0 ± 5.5) μg m^?3 to (37.4 ± 7.5) μ m^?3. These tolerance limits, which are calculated on an ecophysiological data basis for Norway spruce are close to epidemiological SO₂-toIerance limits as recommended by the IUFRO, UN-ECE and WHO. The observed statistical regression slope of the plot (damaged spruce trees vs. SO₂-pollution) in west Germany is confirmed by modelling (6% error). Model application to other forest trees allows deduction of the observed sequence of SO₂-sensitivity: Abies > Picea > Pinus > Fagus > Quercus. Thus, acute phytotoxicity of SO₂ seems not to be involved in ‘forest decline’. Chronic SO₂-pollution induces massive canopy thinning of Abies alba and Picea abies only at unfavourable sites, where natural stress factors and secondary effects of SO₂pollution act together to produce tree decline.     

The ecosystem approach to environmental assessment: moving from theory to practice

The ecosystem approach to environmental management is viewed by many as being fundamental to the development of appropriate management strategies. While this approach represents a major advance in the way researchers view environmental assessment, the approach in itself does not provide practical information as to what questions to ask and what tools to use in assessing and managing ecosystems. Similarly, the concept of ecosystem health, as it is usually defined, has little practical value for ecosystem managers. We suggest the next stage in environmental assessment will be the development of specific frameworks designed to assess individual ecosystems. Of primary importance is the need to consider the basic structure and function of the ecosystem itself. Such consideration, together with explicit identification of anthropogenic stresses particular to the system, serves to identify those components most at risk and those issues most deserving of attention. Researchers should explore critical linkages between environmental stressors and their observable, measurable and predictable effects on ecological parameters and use this understanding to develop a management strategy that incorporates appropriate ecological indicators. The importance of these considerations will be illustrated using examples from the Northern River Basins Study.     

Discontinuities in technological and natural systems caused by exotic species

This discussion focuses on discontinuities in both natural and technological systems caused by the introduction of exotic species into areas which they would not have been able to reach without human assistance or other alterations to native communities. The case histories of both the Asian clam and the zebra mussel are particularly instructive because of their recent introductions and the dramatic impact they have had on both natural and technological systems. Control of these mollusc species in technological systems (e.g. water intake systems) is effective to a degree but requires constant attention and utilization of resources. If control is neglected there could be extremely serious consequences. At present, no inexpensive means exist for controlling their effects, and further geographical distribution in North America is highly probable. The mollusc case histories do not appear to be linear and, in some instances, may not be continuous. Some importations of exotic species were deliberate (such as the gypsy moth, Porthetria dispar), but their escape into natural systems has often been accidental or, a less charitable person might say, careless. A viable strategy for coping with discontinuities is elusive. Discontinuities will, undoubtedly, have a major effect on the possibility of sustainable use of the planet or, to use the currently popular term, sustainable development.     

Integrating conservation and development: incorporating vulnerability into biodiversity-assessment of areas

Protection of regional biodiversity requires that priority for protection of individual areas be based on both the contribution the area can make to representing overall biodiversity and the degree to which the area, in the absence of action, is vulnerable to loss of its biodiversity. Attempts to apply these criteria together largely have been ad hoc. A solution to this problem is presented for environmental surrogate data, based on environmental diversity (ED). ED uses a standard ecological continuum model to link environmental pattern to species-level biodiversity, so that a set of areas can be characterized by its relative expected biodiversity. This allows explicit incorporation of estimates of area-vulnerability, interpreted as the relative probability that any member species will not persist, into biodiversity assessments. The contribution of a given area to regional expected biodiversity is influenced not only by its own vulnerability value, but also by the vulnerability of other areas. Increasing the degree of protection of any area (reducing its vulnerability) will increase expected biodiversity: however, expected regional biodiversity sometimes may be maximized when limited resources for protection are directed to an area with lower vulnerability rather than to one with higher vulnerability.The allocation of land uses in a region need not be viewed as an all-or-nothing assignment of protection. The effect of a particular management regime on the biodiversity of a given area can be equated with some consequent degree of vulnerability; viewed positively, a management regime that offers some degree of biodiversity protection can make a measurable contribution to the protection of the biodiversity of a region.