Vegetative and generative dispersal capacity of field released transgenic aspen trees

Transfer of genes by pollen or wind-dispersed seed is considered a main potential risk when field release experiments with transgenic trees are initiated. In Germany, the first release experiment with genetically transformed trees was initiated in 1996. To ensure that the transgenic trees remained in the vegetative phase, the duration of the experiment was limited to 5 years. In total, 457 1-year-old trees including eight transgenic aspen lines carrying either the 35S- rolC or the rbcS- rolC gene construct, and three control clones were transferred to the field. In 1998 and 2000, 12 plants of transgenic lines all carrying the 35S- rolC gene construct formed female flower buds. Furthermore, one young aspen plant identified as a root sucker was observed in 1999 followed by an increasing number of root suckers derived from transgenic and non-transgenic trees in 2000 and 2001. In 2001, the last year of the field trial, 15 root suckers were detected outside the field. In total, 234 root suckers were harvested in 2000 and 2001 and analysed for their transgenic status. More than half of the roots suckers investigated showed the presence of the rbcS- rolC gene construct. We concluded that in addition to the widely accepted generative propagation, vegetative dispersal capacity of transgenic perennial plants is also important and must be included in risk assessment studies.     

Explanatory coherence and empirical adequacy: The problem of abduction, and the justification of evolutionary models

Foundationalist theories of justification for science were undermined by the theory-ladeness thesis, which has affinities with coherentist epistemologies. A challenge for defenders of coherentist theories of scientific justification is to specify coherence relations relevant to science and to show how these relations make the truth of their bearers likely. Coherence relations include characteristics that pick out better explanations in the implementation of abductive arguments. Empiricist philosophers have attacked abductive reasoning by claiming that explanatory virtues are pragmatic, having no implications regarding truth. However, empiricist's basic beliefs are subject to the same challenges facing abduction, both of which can be met by citing causally coherent etiologies, which are commonplace in biological explanations, and by demonstrating the relevance of causal coherence to truth.     

Formal language theory and DNA: An analysis of the generative capacity of specific recombinant behaviors

A new manner of relating formal language theory to the study of informational macromolecules is initiated. A language is associated with each pair of sets where the first set consists of double-stranded DNA molecules and the second set consists of the recombinational behaviors allowed by specified classes of enzymatic activities. The associated language consists of strings of symbols that represent the primary structures of the DNA molecules that may potentially arise from the original set of DNA molecules under the given enzymatic activities. Attention is focused on the potential effect of sets of restriction enzymes and a ligase that allow DNA molecules to be cleaved and reassociated to produce further molecules. The associated languages are analysed by means of a new generative formalism called a splicing system. A significant subclass of these languages, which we call the persistent splicing languages, is shown to coincide with a class of regular languages which have been previously studied in other contexts: the strictly locally testable languages. This study initiates the formal analysis of the generative power of recombinational behaviors in general. The splicing system formalism allows observations to be made concerning the generative power of general recombination and also of sets of enzymatic activities that include general recombination.     

A solution to limited genomic capacity: using adaptable binding surfaces to assemble the functional HIV Rev oligomer on RNA

Many ribonucleoprotein (RNP) complexes assemble into large, organized structures in which protein subunits are positioned by interactions with RNA and other proteins. Here we demonstrate that HIV Rev, constrained in size by a limited viral genome, also forms an organized RNP by assembling a homo-oligomer on the Rev response element (RRE) RNA. Rev subunits bind cooperatively to discrete RNA sites using an oligomerization domain and an adaptable protein-RNA interface, forming a complex with 500-fold higher affinity than the tightest single interaction. High-affinity binding correlates strongly with RNA export activity. Rev utilizes different surfaces of its alpha-helical RNA-binding domain to recognize several low-affinity binding sites, including the well-characterized stem IIB site and an additional site in stem IA. We propose that adaptable RNA-binding surfaces allow the Rev oligomer to assemble economically into a discrete, stable RNP and provide a mechanistic role for Rev oligomerization during the HIV life cycle.     

选择容量价值:一个新的生态系统服务价值指标

对生态系统服务进行价值评估有助于落实生态系统的科学管理和推动生态补偿的科学实施。然而,传统的生态系统服务价值评估方法在管理实践应用中存在明显的局限性。为了规避这些局限性,另辟一条对生态系统服务价值评估的新思路,提出了描述生态系统服务价值的新指标——"选择容量价值"。选择容量价值以两个事实为基本依据:1)如果失去了任何一项生存所必需的生态系统服务(比如氧气、水),那么人类就无法生存,亦即人类经济社会活动所产生的价值是建立在消费该生态系统服务的基础上的;2)如果没有人类活动的存在,那么生态系统就给人类提供不了任何价值,亦即生态系统服务价值的度量是建立在生态系统服务所支持的人类经济社会活动所产生的价值上的。选择容量价值是指,一项人类生存生产所必需的生态系统服务,其总量为消费该生态系统服务的消费活动所提供的选择自由度(即选择容量)与该消费活动所产生的经济社会活动总价值的乘积,用非货币单位来计量。通过一个案例——对珠江流域的水资源供应的选择容量价值的估算,揭示选择容量价值对理解和量化生态系统服务价值的新洞察。结果显示,选择容量价值能够直观而综合地反映生态系统服务总量、生态系统服务消费量、社会经济...     

Model adequacy: A bayesian viewpoint

We present a BAYEsian theory for testing model adequacy which provides exact results whether the model is linear or nonlinear in the parameters. We consider two cases: (a) replicated data exists, and (b) no replicated data exists but an external estimate of the variance is available. Furthermore, we derive a useful approximation for testing model adequacy when the model is nonlinear in the parameters.     

Competitive exclusion and coexistence of universal grammars

Universal grammar (UG) is a list of innate constraints that specify the set of grammars that can be learned by the child during primary language acquisition. UG of the human brain has been shaped by evolution. Evolution requires variation. Hence, we have to postulate and study variation of UG. We investigate evolutionary dynamics and language acquisition in the context of multiple UGs. We provide examples for competitive exclusion and stable coexistence of different UGs. More specific UGs admit fewer candidate grammars, and less specific UGs admit more candidate grammars. We will analyze conditions for more specific UGs to outcompete less specific UGs and vice versa. An interesting finding is that less specific UGs can resist invasion by more specific UGs if learning is more accurate. In other words, accurate learning stabilizes UGs that admit large numbers of candidate grammars.     

Information,complexity and generative replication

The established definition of replication in terms of the conditions of causality, similarity and information transfer is very broad. We draw inspiration from the literature on self-reproducing automata to strengthen the notion of information transfer in replication processes. To the triple conditions of causality, similarity and information transfer, we add a fourth condition that defines a “generative replicator” as a conditional generative mechanism, which can turn input signals from an environment into developmental instructions. Generative replication must have the potential to enhance complexity, which in turn requires that developmental instructions are part of the information that is transmitted in replication. Demonstrating the usefulness of the generative replicator concept in the social domain, we identify social generative replicators that satisfy all of the four proposed conditions.

Mobile Link Organisms and Ecosystem Functioning: Implications for Ecosystem Resilience and Management

Current natural resource management seldom takes the ecosystem functions performed by organisms that move between systems into consideration. Organisms that actively move in the landscape and connect habitats in space and time are here termed “mobile links.” They are essential components in the dynamics of ecosystem development and ecosystem resilience (that is, buffer capacity and opportunity for reorganization) that provide ecological memory (that is, sources for reorganization after disturbance). We investigated the effects of such mobile links on ecosystem functions in aquatic as well as terrestrial environments. We identify three main functional categories: resource, genetic, and process linkers and suggest that the diversity within functional groups of mobile links is a central component of ecosystem resilience. As the planet becomes increasingly dominated by humans, the magnitude, frequency, timing, spatial extent, rate, and quality of such organism-mediated linkages are being altered. We argue that global environmental change can lead to (a) the decline of essential links in functional groups providing pollination, seed dispersal, and pest control; (b) the linking of previously disconnected areas, for example, the spread of vector-borne diseases and invasive species; and (c) the potential for existing links to become carriers of toxic substances, such as persistent organic compounds. We conclude that knowledge of interspatial exchange via mobile links needs to be incorporated into management and policy-making decisions in order to maintain ecosystem resilience and hence secure the capacity of ecosystems to supply the goods and services essential to society. Received 23 April 2001; accepted 17 June 2002.     

Pfold: RNA secondary structure prediction using stochastic context-free grammars

RNA secondary structures are important in many biological processes and efficient structure prediction can give vital directions for experimental investigations. Many available programs for RNA secondary structure prediction only use a single sequence at a time. This may be sufficient in some applications, but often it is possible to obtain related RNA sequences with conserved secondary structure. These should be included in structural analyses to give improved results. This work presents a practical way of predicting RNA secondary structure that is especially useful when related sequences can be obtained. The method improves a previous algorithm based on an explicit evolutionary model and a probabilistic model of structures. Predictions can be done on a web server at http://www.daimi.au.dk/~compbio/pfold.     

Unifying generative and discriminative learning principles

Background  

The recognition of functional binding sites in genomic DNA remains one of the fundamental challenges of genome research. During the last decades, a plethora of different and well-adapted models has been developed, but only little attention has been payed to the development of different and similarly well-adapted learning principles. Only recently it was noticed that discriminative learning principles can be superior over generative ones in diverse bioinformatics applications, too.     

Simple empirical intensity and buffering capacity measurements to predict potassium uptake by white clover

Summary This experiment examined the feasibility of predicting K uptake in white clover by the use of simple and relatively rapid tests that would dispense with the need of knowing the quantity of plant available potassium. Potassium uptake was found to correlate highly (R=>0.9) in linear bivariate regressions using K concentration in the soil solution displaced by centrifuging and an empirical estimate of potassium retention. There was no advantage in determining activity ratios because in at least some of the soils used the ratio law did not apply. Exchangeable potassium alone correlated rather poorly with uptake except at very low soil potassium status. This was not because nonexchangeable potassium was an important source of this nutrient to white clover but because of the large differences in the retention of K amongst the soils used.     

Clade support measures and their adequacy

In addition to hypothesis optimality, the evaluation of clade (group, edge, split, node) support is an important aspect of phylogenetic analysis. Here we clarify the logical relationship between support and optimality and formulate adequacy conditions for support measures. Support, S, and optimality, O, are both empirical knowledge claims about the strength of hypotheses, h₁, h₂, …h_n, in relation to evidence, e, given background knowledge, b. Whereas optimality refers to the absolute strength of hypotheses, support refers to the relative strength of hypotheses. Consequently, support and optimality are logically related such that they vary in direct proportion to each other, S(h | e,b) ∝ O(h | e,b). Furthermore, in order for a support measure to be objective it must quantify support as a function of explanatory power. For example, Goodman–Bremer support and ratio of explanatory power (REP) support satisfy the adequacy requirement S(h | e,b) ∝ O(h | e,b) and calculate support as a function of explanatory power. As such, these are adequate measures of objective support. The equivalent measures for statistical optimality criteria are the likelihood ratio (or log‐likelihood difference) and likelihood difference support measures for maximum likelihood and the posterior probability ratio and posterior probability difference support measures for Bayesian inference. These statistical support measures satisfy the adequacy requirement S(h | e,b) ∝ O(h | e,b) and to that extent are internally consistent; however, they do not quantify support as a function of explanatory power and therefore are not measures of objective support. Neither the relative fit difference (RFD; relative GB support) nor any of the parsimony (bootstrap and jackknife character resampling) or statistical [bootstrap character resampling, Markov chain Monte Carlo (MCMC) clade frequencies] support measures based on clade frequencies satisfy the adequacy condition S(h | e,b) ∝ O(h | e,b) or calculate support as a function of explanatory power. As such, they are not adequate support measures. © The Willi Hennig Society 2008.     

生态系统工程师：理论与应用

生物通过非同化--异化过程影响环境的事实普遍存在,生态学家对此也开展了大量的研究,但缺乏相应理论框架的指导,使得这些工作的潜在价值未能得到充分的体现.学者Clive G.Jones等提出的"生态系统工程师"概念,概括了此类生态学现象的一般特征,为认识生物对环境的影响提供了一种新的理论框架.介绍了生态系统工程师概念及相关的理论体系,包括3个术语、2类生态系统工程师、5种生态系统工程概念模型以及工程效应的测定方法.同时,论述了该概念在入侵生态学、保护生物学、恢复生态学等领域的应用前景.最后,讨论了未来的研究方向.可以预料,生态系统工程师概念及相关理论的不断发展将有助于对生态学本质的认识,并为生态系统管理提供新的思路.     

Genetic manipulation in plant breeding: somatic versus generative

Theoretical and Applied Genetics - A comparison is made between molecular/ in vitro/somatic and plant-level/generative approaches in the reconstruction of genotypes and reproductive systems....