Use of models for integrated assessment of ecosystem health

An argument is presented for a greater use of numerical models in integrated assessment of ecosystem health. Ecosystem health has many facets which are interconnected and interact, and which can only be measured in integrated assessments. Modelling is an essential feature of integrated assessment being one of the few ways human groups can form a consensus understanding of the complex dynamics which occur. Functional assumptions are made explicit. The argument is expanded in response to a series of key questions: What is ecosystem health? How do we do integrated assessments? What is modelling? What are some successful examples? What should one conclude? The answers are illustrated with references to the International Joint Commission's program to develop and implement Remedial Action Plans for the Great Lakes' Areas of Concern, particularly in the Bay of Quinte, Lake Ontario. Three recommendations are offered: (i) Increase the use of models, (ii) Build models with existing data and hypotheses before initiating new programs, and (iii) Allow for iterative model development but be prepared to build a new model when a new problem arises.     

Why, when, and how biochemists should use least squares.

One of the most commonly used methods for the analysis of experimental data in the biochemical literature is nonlinear least squares (regression). This group of methods are also commonly misused. The purpose of this article is to review the assumptions inherent in the use of least-squares techniques and how these assumptions govern the ways that least-squares techniques can and should be used. Since these assumptions pertain to the nature of the experimental data to be analyzed they also dictate many aspects of the data collection protocol. The examination of these assumptions includes a discussion of questions like: Why would a biochemist want to use nonlinear least-squares techniques? When is it appropriate for a biochemist to use nonlinear least-squares techniques? What confidence can be assigned to the results of a nonlinear least-squares analysis?     

A note on serological interpretations1

This paper deals with the interpretation of binary serological data. It attempts to render exact and answer two questions: 1) What are all the serological interpretations of a given set of data? 2) How can different interpretations be distinguished serologically? It is hoped that the formal analysis of serology presented herein will prove to be helpful to those working with complex immunological systems.     

The Rad51 and Dmc1 recombinases: a non-identical twin relationship

A double-strand break in genomic DNA that remains unrepaired can be lethal for a cell. Indeed, the integrity of the genome is paramount for survival. It is therefore surprising that some cells deliberately introduce double-strand breaks at certain times during their life cycle. Why might they do this? What are the benefits? How are these breaks repaired? The answers to these questions lie in understanding the basis of meiotic recombination, the process that leads to genetic variation. This review summarizes the key roles played by the two recombinases, Dmc1 and Rad51, in the faithful repair of DNA breaks.     

Fifteen compelling open questions in plant cell biology

As scientists, we are at least as excited about the open questions—the things we do not know—as the discoveries. Here, we asked 15 experts to describe the most compelling open questions in plant cell biology. These are their questions: How are organelle identity, domains, and boundaries maintained under the continuous flux of vesicle trafficking and membrane remodeling? Is the plant cortical microtubule cytoskeleton a mechanosensory apparatus? How are the cellular pathways of cell wall synthesis, assembly, modification, and integrity sensing linked in plants? Why do plasmodesmata open and close? Is there retrograde signaling from vacuoles to the nucleus? How do root cells accommodate fungal endosymbionts? What is the role of cell edges in plant morphogenesis? How is the cell division site determined? What are the emergent effects of polyploidy on the biology of the cell, and how are any such “rules” conditioned by cell type? Can mechanical forces trigger new cell fates in plants? How does a single differentiated somatic cell reprogram and gain pluripotency? How does polarity develop de-novo in isolated plant cells? What is the spectrum of cellular functions for membraneless organelles and intrinsically disordered proteins? How do plants deal with internal noise? How does order emerge in cells and propagate to organs and organisms from complex dynamical processes? We hope you find the discussions of these questions thought provoking and inspiring.

We asked 15 experts to address what they consider to be the most compelling open questions in plant cell biology and these are their questions.     

Establishing gene function by mutagenesis in Arabidopsis thaliana

The nuclear genome of Arabidopsis thaliana was sequenced to near completion a few years ago, and ahead lies the challenge of understanding its meaning and discerning its potential. How many genes are there? What are they? What do they do? Computer algorithms combined with genome array technologies have proven efficient in addressing the first two questions as shown in a recent report ( Yamada et al., 2003 ). However, assessing the function of every gene in every cell will require years of careful analyses of the phenotypes caused by mutations in each gene. Current progress in generating large numbers of molecular markers and near‐saturation insertion mutant collections has immensely facilitated functional genomics studies in Arabidopsis. In this review, we focus on how gene function can be revealed through the analysis of mutants by either forward or reverse genetics. These mutants generally fall into two distinct classes. The first class typically includes point mutations or small deletions derived from chemical or fast neutron mutagenesis whereas the second class includes insertions of transferred‐DNA or transposon elements. We describe the current methods that are used to identify the gene corresponding to these mutations, which can then be used as a probe to further dissect its function.     

Germination of Spores of Bacillus Species: What We Know and Do Not Know

Spores of Bacillus species can remain in their dormant and resistant states for years, but exposure to agents such as specific nutrients can cause spores'' return to life within minutes in the process of germination. This process requires a number of spore-specific proteins, most of which are in or associated with the inner spore membrane (IM). These proteins include the (i) germinant receptors (GRs) that respond to nutrient germinants, (ii) GerD protein, which is essential for GR-dependent germination, (iii) SpoVA proteins that form a channel in spores'' IM through which the spore core''s huge depot of dipicolinic acid is released during germination, and (iv) cortex-lytic enzymes (CLEs) that degrade the large peptidoglycan cortex layer, allowing the spore core to take up much water and swell, thus completing spore germination. While much has been learned about nutrient germination, major questions remain unanswered, including the following. (i) How do nutrient germinants penetrate through spores'' outer layers to access GRs in the IM? (ii) What happens during the highly variable and often long lag period between the exposure of spores to nutrient germinants and the commitment of spores to germinate? (iii) What do GRs and GerD do, and how do these proteins interact? (iv) What is the structure of the SpoVA channel in spores'' IM, and how is this channel gated? (v) What is the precise state of the spore IM, which has a number of novel properties even though its lipid composition is very similar to that of growing cells? (vi) How is CLE activity regulated such that these enzymes act only when germination has been initiated? (vii) And finally, how does the germination of spores of clostridia compare with that of spores of bacilli?     

“国际生物多样性观察年（IBOY）”核心项目——内容介绍及建议

生物多样性观察年（IBOY）的核心项目包括4个大的主题：1）全球生物多样性现状;2）生物多样性的变化方式;3）生物多样性对人类生活的价值;4）人类如何保护生物多样性。本文对这些主题内的不同课题进行了介绍,同时对我国生物多样性科学的发展提出了相应的建议。     

Interactions between intrinsic membrane protein and electric field. An approach to studying nerve excitability

We have approached the problem of nerve excitability through three questions: (a) What is the diagram for a channel? That is, what conformational states can the protein assume, and what transitions between these conformations are permitted? (b) What is the channel conductance associated with each conformation the channel can assume? (c) How do the rates for conformational transition depend upon membrane potential? These three questions arise from a standard statistical mechanical treatment of a nerve membrane containing several classes of identical, independent channels. Gating of channels, in this view, is associated with conformational changes of the channel protein, and it is assumed these conformations are distinct. The precise formulation of these questions is presented in terms of the theoretical treatment, and the approaches we have taken to answer the questions are indicated. Our present results indicate: Transition rates should depend exponentially on membrane potential over a limited voltage range, but probably will show a more complex dependence for extremes of the range; channels probably can take on only two conductances, open and shut, but more complicated situations are not entirely excluded; the diagram for a channel cannot be determined from standard voltage clamp data alone, but by studying gating currents and conductance fluctuations, it should be possible to select between alternative plausible physical mechanisms.     

The genetics and molecular biology of the titin/connectin-like proteins of invertebrates

Conclusions A substantial amount of information has been gathered about the structure and function of twitchin/titin-related proteins in the invertebrates. This has been obtained through sequence analysis and the analysis of loss-offunction phenotypes inC. elegans andDrosophila. Nevertheless, a number of fascinating questions remain, including: (i) Why are these invertebrate proteins all of approx. 700–800 kDa? In terms of sarcomeric organization, what is the significance of this size? (ii) Why do three of these proteins consist of a mixture of Ig and Fn domains, whereas UNC-89 contains only Ig domains? This is even more interesting because the structures of Ig and Fn domains are very similar (118). What is the significance of the repeating pattern of groups of Ig and Fn domains (e.g. Fn-Fn-Ig)? (iii) How are twitchin and the synchronous muscle isoform of projectin situated on the surface of thick filaments? That is, do they form polymers or are they located at discrete locations with intervening gaps? (iv) What is the mechanism by which the fundamentally similar projectin isoforms get localized to different sarcomeric locations? (v) If the data onAplysia twitchin can be extended to the muscles of other invertebrates, what is the mechanism by which twitchin inhibits the rate of relaxation? How does phosphorylation of twitchin relieve this inhibition? (vi) What are the substrates for the protein kinase domains of nematode twitchin and insect projectin? If rMLCs are indeed the substrates, how would and why does this phosphorylation take place for the IFM isoform of projectin, which resides primarily in the I band? If rMLCs are the substrates, given the stoichiometry of approx. 1∶50 for twitchin:myosin, and the likely fixed position of twitchin along the thick filament, how does phosphorylation of just a few rMLCs result in a physiological effect (e.g. inhibition of relaxation)? What is the true activator for the twitchin and projectin kinases? (vii) How does UNC-89 participate in M-line assembly? (viii) What are the biochemical and physiological functions of intestinal brush border twitchin? A number of investigators will enjoy pursuing these and other questions for some time in the future.     

Regulation of phospholipase C by G proteins

Specific phospholipase C enzymes can hydrolyse phosphatidylinositol 4,5-bisphosphate into two products: inositol 1,4,5-trisphosphate, which regulates the release of intracellular calcium stores, and diacylglycerol, which can stimulate protein kinase C. A new group of G proteins, the G_q subfamily, have recently been shown to mediate the regulation of this activity by a variety of hormones. How do different members of this family modulate unique phospholipase C isozymes? What is the mechanism of this regulation? How might the G_q subfamily act to modulate other important second messenger pathways? The tools to answer these questions are being rapidly developed.     

Reconstruction of paleoclimates by isotopic analysis: What can the fossil isotopic record tell us about the plant life of past environments?

The last two decades of scientific research have seen a pronounced increase in studies of abrupt climatic change. Understanding past shifts in climate becomes a priority as we examine reasons for climatic change and the interrelationship between the biosphere and the atmosphere-ocean-cryosphere. The realisation that modern climate appears to be changing at a rapid rate has challenged scientists to look at past records of abrupt climate change. How rapidly can vegetation respond to climate shifts? What magnitude of vegetation change has been seen in the past? How widespread were these changes and how do they compare with shifts in the polar ice cores and the ocean? A selection of vegetation records, for which the isotopic signatures reflect environmental changes, are examined here. This paper focuses on the type of paleoclimatic interpretation that can be made: qualitative information with or without temporal constraint or even, in the best instances, the possibility of reaching a quantitative reconstruction.     

Endocytosis and signaling: a relationship under development

The ability to internalize macromolecules by endocytosis is a property of all eukaryotic cells. Frontline research on endocytosis has been presented in a successful series of biannual meetings in Europe. This year's meeting on "Membrane Dynamics in Endocytosis" was held September 13-18 in Acquafredda di Maratea, on the coast of southern Italy. Four key questions were addressed: What are the molecular mechanisms of endocytic membrane trafficking? How does endocytosis modulate receptor signaling and vice versa? What is the importance of endocytosis during development? How do endocytic organelles contribute to immunity or susceptibility to pathogens?     

Food vs Fuel

Cover illustration: This special issue of BTJ, edited by Dr. Stefan Nordhoff (Marl, Germany), highlights the potential but also the drawbacks of biotechnology in energy production. What are the economics behind sustainable energy production? How can we face the competition for the use of biomaterials for food or for mobility? What are new developments in the field? How much agricultural land can be converted and where should water for irrigation come from? What are alternative solutions to the world's energy problem? Cover images © Corbis Digital Stock and Brand X Pictures.     

Tensions and perplexities within teacher education and P–12 schools for music teachers with visual impairments

We have written this article seeking to connect societal perceptions of disability with P–12 schools and higher education institutions toward the goal of greater understanding and equitable employment opportunities for music teachers with disabilities, specifically teacher candidates with visual impairment. In our investigation, we examine the following questions: (a) How have special education programs within P–12 schools, universities, and schools of music reflected societal perceptions of persons with disabilities and how do those in turn influence perceptions of teacher candidates? (b) How have the essential functions of teaching been articulated by accreditation programs and what tensions arise when music teachers with visual impairments are considered for employment? and (c) What are potential ways forward for P–12 education, teacher education programs, and schools of music? To disrupt binaries between able and disabled in schools, we recommend embracing a broader, interdependent view of music education, one that is defined by and includes all teaching professionals and school communities. Additionally, we support recruitment of teacher candidates with disabilities to music education programs and consistent advocacy through matriculation and job placement to encourage entry into P–12 schools.     

Analytical methods for detecting pesticide switches with evolution of pesticide resistance

After a pest develops resistance to a pesticide, switching between different unrelated pesticides is a common management option, but this raises the following questions: (1) What is the optimal frequency of pesticide use? (2) How do the frequencies of pesticide applications affect the evolution of pesticide resistance? (3) How can the time when the pest population reaches the economic injury level (EIL) be estimated and (4) how can the most efficient frequency of pesticide applications be determined? To address these questions, we have developed a novel pest population growth model incorporating the evolution of pesticide resistance and pulse spraying of pesticides. Moreover, three pesticide switching methods, threshold condition-guided, density-guided and EIL-guided, are modelled, to determine the best choice under different conditions with the overall aim of eradicating the pest or maintaining its population density below the EIL. Furthermore, the pest control outcomes based on those three pesticide switching methods are discussed. Our results suggest that either the density-guided or EIL-guided method is the optimal pesticide switching strategy, depending on the frequency (or period) of pesticide applications.     

Gazing at a giraffe gyroscope: where are we going?

Giraffe are popular animals to watch while on wildlife safaris, and feature prominently in zoos, advertisements, toys and cartoons. Yet, until recently, few field studies have focused on giraffe. We introduce this giraffe topic issue with a review essay that explores five primary questions: How many (sub) species of giraffe exist? What are the dynamics of giraffe herds? How do giraffe communicate? What is the role of sexual selection in giraffe reproduction? How many giraffe reside in Africa? A confluence of causes has produced drastic declines in giraffe population numbers in Africa, and we conclude that guiding giraffe conservation plans depends upon evaluation of the five key quandaries that we pose.     

Model use in phylogenetics: nine key questions

Models of character evolution underpin all phylogeny estimations, thus model adequacy remains a crucial issue for phylogenetics and its many applications. Although progress has been made in selecting appropriate models for phylogeny estimation, there is still concern about their purpose and proper use. How do we interpret models in a phylogenetic context? What are their effects on phylogeny estimation? How can we improve confidence in the models that we choose? That the phylogenetics community is asking such questions denotes an important stage in the use of explicit models. Here, we examine these and other common questions and draw conclusions about how the community is using and choosing models, and where this process will take us next.     

Dietary self-selection in fish: a new approach to studying fish nutrition and feeding behavior

The principles of modern aquaculture encourage the development of fish feeds containing low fish meal content and several types of plant ingredients plus nutrients to avoid depleting global fish stocks and to reduce costs. However, food constituents can affect animal nutrition and feeding behavior, so the effect of different diets on fish behavior and growth needs to be understood to optimize the use of nutrients and to improve fish welfare. The development of multiple-choice self-feeding systems led to a new perspective for investigating these issues in aquaculture species. Our purpose with this review is to summarize the information that has been published to date on this topic and to identify gaps in knowledge where research is needed. Key subjects are assessed under the following major headings: How do we study dietary selection in fish? What food signals do fish use to choose the right diet? and How do fish respond to food challenges? The present review will provide a picture of the main results obtained to date in these studies in aquaculture fish species, as well as perspectives for future research in the field.     

Morphogenesis of the Acanthocephala

Postzygotic development of acanthocephalans is described. The major conclusion that can be drawn is that there has been a great deal of speculation, and that there are still many questions left unanswered. For example, exactly when does the acanthor become a complete syncytium? Is the formulation of the central nuclear mass really homologous to gastrulation, and does this mass really represent endoderm? What is endoderm in an animal with no trace of a digestive system? What is the significance, if any, of the 90 degree change in polarity from the acanthor to the adult? How do a few giant nuclei determine the fate and function of a massive synctial body? These and other questions continue to intrigue and perplex the investigator. Perhaps by the time of ICOPA-VII we will have some of the answers.