Design and analysis of biodiversity field experiments

The design and analysis of field experiments have figured prominently in the current debate about biodiversity and ecosystem function. These debates have identified important issues about species traits, functional groups, and community assembly, but a broader debate needs to include discussions about the scale (grain and extent) of experiments relative to natural spatial and temporal heterogeneity. In addition, alternative statistical analyses need to be explored that focus on comparison among several statistical models rather than simple hypothesis testing. Analyses of the first 2 years of data from a new biodiversity field experiment are used to illustrate these concepts. A traditional one-way ANOVA demonstrates the expected increase in aboveground biomass with higher levels of vascular plant diversity. Further analysis demonstrates that this relationship is absent when the community contains either Arrhenatherum elatius or Holcus lanatus, two dominant species of grass. Variance in biomass is also a function of diversity and both spatial and temporal heterogeneity are significant factors in the analysis despite precautions taken to minimize them. These examples illustrate the degree to which the analysis of a field experiment influences the interpretation of the observed results. Ultimately, results from field experiments must be validated through continued comparisons among field experiments, mathematical models, laboratory trials, and mesocosm experiments.     

Identifying the scales of variability in stream macroinvertebrate abundance, functional composition and assemblage structure

1. Many natural ecosystems are heterogeneous at scales ranging from microhabitats to landscapes. Running waters are no exception in this regard, and their environmental heterogeneity is reflected in the distribution and abundance of stream organisms across multiple spatial scales. 2. We studied patchiness in benthic macroinvertebrate abundance and functional feeding group (FFG) composition at three spatial scales in a boreal river system. Our sampling design incorporated a set of fully nested scales, with three tributaries, two stream sections (orders) within each tributary, three riffles within each section and ten benthic samples in each riffle. 3. According to nested anova s, most of the variation in total macroinvertebrate abundance, abundances of FFGs, and number of taxa was accounted for by the among‐riffle and among‐sample scales. Such small‐scale variability reflected similar patterns of variation in in‐stream variables (moss cover, particle size, current velocity and depth). Scraper abundance, however, varied most at the scale of stream sections, probably mirroring variation in canopy cover. 4. Tributaries and stream sections within tributaries differed significantly in the structure and FFG composition of the macroinvertebrate assemblages. Furthermore, riffles in headwater (second order) sections were more variable than those in higher order (third order) sections. 5. Stream biomonitoring programs should consider this kind of scale‐dependent variability in assemblage characteristics because: (i) small‐scale variability in abundance suggests that a few replicate samples are not enough to capture macroinvertebrate assemblage variability present at a site, and (ii) riffles from the same stream may support widely differing benthic assemblages.     

Software sensor design considering oscillating conditions as present in industrial scale fed‐batch cultivations

Investigations of inhomogeneous dynamics in industrial‐scale bioreactors can be realized in laboratory simulators. Such studies will be improved by on line observation of the growth of microorganisms and their product synthesis at oscillating substrate availability which represents the conditions in industrial‐scale fed‐batch cultivations. A method for the kinetic monitoring of such processes, supported by on line measurements accessible in industrial practice, is proposed. It consists of a software sensor (SS) system composed of a cascade structure. Process kinetics are simulated in models with a structure including time‐varying yield coefficients. SSs for measured variable kinetics have classical structures. The SS design of unmeasured variables is realized after a linear transformation using a logarithmic function. For these software sensors, a tuning procedure is proposed, at which an arbitrary choice of one tuning parameter value that guarantees stability of the monitoring system allows the calculation of the optimal values of six parameters. The effectiveness of the proposed monitoring approach is demonstrated with experimental data from a glucose‐limited fed‐batch process of Bacillus subtilis in a laboratory two‐compartment scale down reactor which tries to mimic the conditions present in industrial scale nutrient‐limited fed‐batch cultivations. Biotechnol. Bioeng. 2013; 110: 1945–1955. © 2013 Wiley Periodicals, Inc.     

Characteristics of insect populations on habitat fragments: A mini review

Modern human-dominated landscapes are typically characterized by intensive land-use and high levels of habitat destruction, often resulting in sharply contrasted habitat mosaics. Fragmentation of remaining habitat is a major threat to biodiversity. In the present paper, we focus on the different features of habitat fragmentation. First we discuss the importance of pure habitat loss, fragment size, fragment isolation and quality, edge effects, and the importance of landscape structure. Second, we characterize life-history features of fragmentation-sensitive species, showing that rare, specialized, little dispersing species are most affected, as well as species characterized by high population variability and a high trophic position, while the effect of body size is unclear. Third, we discuss the conservation value of habitat fragments. The question arises how to relate studies on population survival to those of community structure and studies on biodiversity to those on ecologicalal functions. Despite the general superiority of large to small reserves, only small or medium-sized reserves are available in many human-dominated landscapes. A great number of small habitats covering a wide range of geographic area should maximize beta diversity and spreading of risk and may be very important for the regional conservation of biodiversity, in contrast to the prevailing arguments in favor of large habitats. Finally, landscape context influences community structure of fragments, and communities are composed of species that experience the landscape on a broad range of spatial scales. Spatial arrangement of habitat fragments in a landscape appears to be important only in simple, not complex landscapes.     

Additive partitioning of rarefaction curves and species-area relationships: unifying alpha-, beta- and gamma-diversity with sample size and habitat area

Additive partitioning of species diversity is widely applicable to different kinds of sampling regimes at multiple spatial and temporal scales. In additive partitioning, the diversity within and among samples ( α and β ) is expressed in the same units of species richness, thus allowing direct comparison of α and β . Despite its broad applicability, there are few demonstrated linkages between additive partitioning and other approaches to analysing diversity. Here, we establish several connections between diversity partitions and patterns of habitat occupancy, rarefaction, and species–area relationships. We show that observed partitions of species richness are equivalent to sample-based rarefaction curves, and expected partitions from randomization tests are approximately equivalent to individual-based rarefaction. Additive partitions can also be applied to species–area relationships to determine the relative contributions of factors influencing the β -diversity among habitat fragments.     

Same but different–Scale up and numbering up in electrobiotechnology and photobiotechnology

Facing energy problems, there is a strong demand for new technologies dealing with the replacement of fossil fuels. The emerging fields of biotechnology, photobiotechnology and electrobiotechnology, offer solutions for the production of fuels, energy, or chemicals using renewable energy sources (light or electrical current e.g. produced by wind or solar power) or organic (waste) substrates. From an engineering point of view both technologies have analogies and some similar challenges, since both light and electron transfer are primarily surface‐dependent. In contrast to that, bioproduction processes are typically volume dependent. To allow large scale and industrially relevant applications of photobiotechnology and electrobiotechnology, this opinion first gives an overview over the current scales reached in these areas. We then try to point out the challenges and possible methods for the scale up or numbering up of the reactors used. It is shown that the field of photobiotechnology is by now much more advanced than electrobiotechnology and has achieved industrial applications in some cases. We argue that transferring knowledge from photobiotechnology to electrobiotechnology can speed up the development of the emerging field of electrobiotechnology. We believe that a combination of scale up and numbering up, as it has been shown for several photobiotechnological reactors, may well lead to industrially relevant scales in electrobiotechnological processes allowing an industrial application of the technology in near future.     

不同属性人群对原风景的景观偏好研究

原风景是指人们在18岁之前由于在某一地域中长期生活而形成的对该地域永恒的定影景象。本文作者采用问卷调查的方法,分析了不同属性人群对原风景的景观偏好。结论如下：1）通过T检验得出总分频数分布图显示在10~14左右取得最大值,表明不同属性人群都具有一定的原风景意识;2）原风景对人群的行为、认知、情感的影响依次减弱;3）不同属性人群对原风景的景观偏好存在明显差异,表现为：①性别：男性>女性;②年龄：51~60岁>31~40岁>18~30岁>41~50岁;③生活环境（18岁之前）：农村>城市>县城：④地区：北方地区>南方地区;⑤学历：大专、本科>初中及以下>硕士及以上>中专及职高;⑥职业：企业职员>事业单位职员>其他>学生>个体及自由职业者。通过分析不同属性人群的景观偏好特征,发掘其不同特性,旨在为城市发展基于“乡愁”的景观规划设计提供理论指导。     

土地整理的生态系统服务价值评估与生态设计策略——以吉林省大安市土地整理项目为例

土地整理作为土地利用变化的重要驱动因素,显著改变土地利用和景观格局,对区域生态系统功能及其服务价值产生影响.本文以吉林省大安市的土地整理项目为例,利用生态服务价值模型计算了村域、镇域和县域尺度下土地整理区的生态服务价值及其总量变化.结果表明: 以增加耕地为目标的土地整理项目易造成草地和湿地等具有较高生态服务价值的地类减少,导致不同尺度下土地整理区生态服务价值总量出现不同程度的下降.村域尺度下,整理后研究区总的生态服务价值为796.14万元,较整理前减少10.5%;镇域尺度下,整理后总的生态服务价值为84301.26万元,较整理前减少14.2%;县域尺度下,整理后总的生态服务价值为120585.76万元,较整理前减少33.1%.根据土地整理的生态服务价值评估,从提高生态功能入手,最后提出了土地整理的景观生态设计策略,以期为土地整理的持续发展提供决策依据.     

Standard survey designs drive bias in the mapping of upland swamp communities

Vegetation maps are critical biodiversity planning instruments, but the classification of vegetation for mapping can be strongly biased by survey design. Standardization of survey design across different vegetation types is therefore increasingly recommended for vegetation mapping programs. However, some vegetation types have complex small‐scale vegetation patterns that are important in characterizing these vegetation types, and standard designs will often not capture these patterns. The objective of this paper was to investigate the magnitude of potential map bias that results from survey design standardization and recommend approaches to deal with this bias. We surveyed upland swamps of the Greater Blue Mountains World Heritage Area Australia using two contrasting survey designs, including the standard 400 m² single quadrat design recommended and used by authorities. We then derived a classification for these swamps and tested the effect of survey design on this classification, species richness and the type of species detected (obligate or facultative swamp species). Species richness and species type were not significantly different among survey techniques. However, more than 40% of swamps clustered differently among survey designs. Thus, one of the 10 derived communities (which is floristically consistent with a previously mapped endangered community) was indistinct, and some individual swamps misclassified using the standard survey design. An effect of landscape position on swamp floristic patterns and a significant trend for high similarity scores among swamps surveyed with multiple small quadrats compared to the standard survey design was also determined. Australian upland swamps are classified at the global scale as shrub‐dominated wetlands, and complex floristic patterns have been recorded in shrub‐dominated wetlands in both northern and southern hemispheres. We therefore advocate either multiple survey designs or different survey standards for upland swamp communities and other vegetation types that have complex floristic patterns at small scales.     

大尺度生物多样性评价

如何在减小采样付出和获取真实信息之间取得平衡,是大尺度生物多样性评价的一个主要问题。本文首先给出了大尺度评价的定义,然后回顾其历史并指出了其中存在的问题。接着从采样空间策略、代理物种、评价指标、快速评价技术、遥感技术5个方面对评价设计方法学作了总结,最后引入了多尺度生物多样性评价体系,作为解决问题的思路。该体系要求在一系列空间尺度上对生物多样性的特征值进行采样和计算,其核心是中间尺度的构建,可以采用自底向上和自顶向下两种思路构建中间尺度。对于多样性的保育来说,中间尺度至关重要,生物多样性的评价、管理规划和实践的整合需要在中间尺度上进行。大尺度生物多样性变化可以作为整合的背景,而小尺度是保育管理行动的合适尺度。     

甘肃永登县土地利用景观格局的空间尺度效应

依据“斑块-廊道-基质”模式,研究了甘肃省兰州市永登县景观格局的空间尺度效应.结果表明:草地为整个研究区景观结构的基质;廊道包括道路和河流;其余景观组分(耕地、林地、园地,住宅用地、工矿用地、公共管理与服务用地和其他土地)均为斑块.斑块类型水平指数与景观水平指数均表现出明显的空间幅度依赖性.不同景观组分的斑块类型指数的尺度效应在不同幅度区间存在差异性,景观水平指数的尺度效应在不同幅度区间也存在差异性.在1～20 km幅度区间,尺度效应的组分类型、指标类型之间差异最为明显;在21～90 km幅度区间,尺度效应的组分类型、指标类型之间差异较小;在>90 km幅度后,尺度效应消失.90 km×90 km为研究景观格局尺度依赖性的有效幅度.     

生态学中的尺度问题：内涵与分析方法

尺度问题已成为现代生态学的核心问题之一.尺度问题主要涉及3个方面：尺度概念、尺度分析和尺度推绎.主要评述前两个方面.生态学尺度有三重概念：维数、种类和组分,其中每重概念又包含了多个定义,有必要进行澄清、分类和统一.尺度分析涉及尺度效应分析和多尺度空间格局分析.格局、过程及它们之间的关系,以及某些景观特性均表现出尺度效应,因此多尺度研究非常必要和重要.多尺度空间格局分析（尤其是特征尺度的识别）是进行尺度效应分析和跨尺度推绎的基础.多尺度分析需要特定的方法,景观指数法是最常用和最简单的方法,但也常产生误导;空间统计学方法（如半方差分析法、尺度方差分析法、空隙度指数法和小波分析法等）和分维分析法在最近十几年发展起来,并逐渐应用于生态学,在尺度分析上具有很大的应用潜力.各种方法在尺度分析上各有优势和不足,有必要同时使用两种或两种以上方法进行比较和评估.总之,有关尺度分析的研究需要进一步加强,从而为下一步的尺度推绎提供可靠的依据.     

Development of a scale down cell culture model using multivariate analysis as a qualification tool

In characterizing a cell culture process to support regulatory activities such as process validation and Quality by Design, developing a representative scale down model for design space definition is of great importance. The manufacturing bioreactor should ideally reproduce bench scale performance with respect to all measurable parameters. However, due to intrinsic geometric differences between scales, process performance at manufacturing scale often varies from bench scale performance, typically exhibiting differences in parameters such as cell growth, protein productivity, and/or dissolved carbon dioxide concentration. Here, we describe a case study in which a bench scale cell culture process model is developed to mimic historical manufacturing scale performance for a late stage CHO‐based monoclonal antibody program. Using multivariate analysis (MVA) as primary data analysis tool in addition to traditional univariate analysis techniques to identify gaps between scales, process adjustments were implemented at bench scale resulting in an improved scale down cell culture process model. Finally we propose an approach for small scale model qualification including three main aspects: MVA, comparison of key physiological rates, and comparison of product quality attributes. © 2013 American Institute of Chemical Engineers Biotechnol. Prog., 30:152–160, 2014     

Trickle-bed root culture bioreactor design and scale-up: growth, fluid-dynamics, and oxygen mass transfer

Trickle-bed root culture reactors are shown to achieve tissue concentrations as high as 36 g DW/L (752 g FW/L) at a scale of 14 L. Root growth rate in a 1.6-L reactor configuration with improved operational conditions is shown to be indistinguishable from the laboratory-scale benchmark, the shaker flask (mu=0.33 day(-1)). These results demonstrate that trickle-bed reactor systems can sustain tissue concentrations, growth rates and volumetric biomass productivities substantially higher than other reported bioreactor configurations. Mass transfer and fluid dynamics are characterized in trickle-bed root reactors to identify appropriate operating conditions and scale-up criteria. Root tissue respiration goes through a minimum with increasing liquid flow, which is qualitatively consistent with traditional trickle-bed performance. However, liquid hold-up is much higher than traditional trickle-beds and alternative correlations based on liquid hold-up per unit tissue mass are required to account for large changes in biomass volume fraction. Bioreactor characterization is sufficient to carry out preliminary design calculations that indicate scale-up feasibility to at least 10,000 liters.     

森林多目标经营单元的时空尺度扩展

森林多目标经营是我国林业发展的重要趋势,而森林本身的特性以及国内外的众多研究证明,森林多目标经营需要考虑多个时空尺度,以满足其生态、经济和社会效益的综合发挥。在界定多功能林业和森林多目标经营的概念及基础上,系统地分析了传统森林经营时空尺度和现代森林多目标经营时空尺度的联系与区别,提出现代森林多目标经营单元空间尺度上应该满足区域、景观和林分多尺度的需要,而在时间尺度上则要综合考虑短期、中期和长期,并以露水河林业局为例给出具体的研究思路,以期为我国开展森林多目标经营提供借鉴。     

鳞翅目昆虫鳞片的结构发育与眼斑的形成

从形态学和发育生物学角度上对鳞翅目昆虫翅面上的鳞片做了总体论述 ,重点讨论了鳞片的结构与发育和色素的沉淀等 ,并从遗传学角度对鳞翅目昆虫眼斑型的形成与决定做了介绍。     

Predation on reef-building corals: multiscale variation in the density of three corallivorous gastropods, Drupella spp.

 Feeding aggregations of three corallivorous gastropods, Drupella cornus, D. fragum and D. rugosa, have caused considerable coral damage on reefs across the Indo-West Pacific. Distribution and abundance of these three species were explored at Lizard Island, Great Barrier Reef, to determine within-reef variations in density, and spatial relationships between Drupella and their prey corals. The scales of greatest variation were between reef habitats (combinations of exposure and depth) and individual coral colonies. Density varied 12-fold among four habitats: exposed crests (2.55/m²), exposed slopes (0.22/m²), sheltered crests (0.34/m²) and sheltered slopes (2.07/m²). Species composition also varied markedly between habitats. Individuals were highly aggregated, usually forming small clusters (<10 individuals) on live coral colonies and other substrata, and occasional large aggregations of=200 to>2000. Five basic tenets for sampling Drupella are established, based on patterns of variation in density and species composition, and small-scale habitat use. Accepted: 8 February 1999     

Similarity networks of protein binding sites

An increasing attention has been dedicated to the characterization of complex networks within the protein world. This work is reporting how we uncovered networked structures that reflected the structural similarities among protein binding sites. First, a 211 binding sites dataset has been compiled by removing the redundant proteins in the Protein Ligand Database (PLD) (http://www-mitchell.ch.cam.ac.uk/pld/). Using a clique detection algorithm we have performed all-against-all binding site comparisons among the 211 available ones. Within the set of nodes representing each binding site an edge was added whenever a pair of binding sites had a similarity higher than a threshold value. The generated similarity networks revealed that many nodes had few links and only few were highly connected, but due to the limited data available it was not possible to definitively prove a scale-free architecture. Within the same dataset, the binding site similarity networks were compared with the networks of sequence and fold similarity networks. In the protein world, indications were found that structure is better conserved than sequence, but on its own, sequence was better conserved than the subset of functional residues forming the binding site. Because a binding site is strongly linked with protein function, the identification of protein binding site similarity networks could accelerate the functional annotation of newly identified genes. In view of this we have discussed several potential applications of binding site similarity networks, such as the construction of novel binding site classification databases, as well as the implications for protein molecular design in general and computational chemogenomics in particular.