bluuebunny/crossref_metadata_2025 huggingface dataset:
Population growth rate and its determinants: an overview
Authors: Sibly Richard M. , Hone Jim
Published: October 2002

We argue that population growth rate is the key unifying variable linking the various facets of population ecology. The importance of population growth rate lies partly in its central role in forecasting future population trends; indeed if the form of density dependence were constant and known, then the future population dynamics could to some degree be predicted. We argue that population growth rate is also central to our understanding of environmental stress: environmental stressors should be defined as factors which when first applied to a population reduce population growth rate. The joint action of such stressors determines an organism's ecological niche, which should be defined as the set of environmental conditions where population growth rate is greater than zero (where population growth rate =r= loge(Nt+1/Nt)). While environmental stressors have negative effects on population growth rate, the same is true of population density, the case of negative linear effects corresponding to the well–known logistic equation. Following Sinclair, we recognize population regulation as occurring when population growth rate is negatively density dependent. Surprisingly, given its fundamental importance in population ecology, only 25 studies were discovered in the literature in which population growth rate has been plotted against population density. In 12 of these the effects of density were linear; in all but two of the remainder the relationship was concave viewed from above.

Alternative approaches to establishing the determinants of population growth rate are reviewed, paying special attention to the demographic and mechanistic approaches. The effects of population density on population growth rate may act through their effects on food availability and associated effects on somatic growth, fecundity and survival, according to a 'numerical response', the evidence for which is briefly reviewed. Alternatively, there may be effects on population growth rate of population density in addition to those that arise through the partitioning of food between competitors; this is 'interference competition'. The distinction is illustrated using a replicated laboratory experiment on a marine copepod,Tisbe battagliae. Application of these approaches in conservation biology, ecotoxicology and human demography is briefly considered. We conclude that population regulation, density dependence, resource and interference competition, the effects of environmental stress and the form of the ecological niche, are all best defined and analysed in terms of population growth rate.
Demographic, mechanistic and density–dependent determinants of population growth rate: a case study in an avian predator
Authors: Hone Jim , Sibly Richard M.
Published: October 2002

Identifying the determinants of population growth rate is a central topic in population ecology. Three approaches (demographic, mechanistic and density–dependent) used historically to describe the determinants of population growth rate are here compared and combined for an avian predator, the barn owl (
Tyto alba
). The owl population remained approximately stable (
r
≈ 0) throughout the period from 1979 to 1991. There was no evidence of density dependence as assessed by goodness of fit to logistic population growth. The finite (λ) and instantaneous (
r
) population growth rates were significantly positively related to food (field vole) availability. The demographic rates, annual adult mortality, juvenile mortality and annual fecundity were reported to be correlated with vole abundance. The best fit (
R
2
= 0.82) numerical response of the owl population described a positive effect of food (field voles) and a negative additive effect of owl abundance on
r
. The numerical response of the barn owl population to food availability was estimated from both census and demographic data, with very similar results. Our analysis shows how the demographic and mechanistic determinants of population growth rate are linked; food availability determines demographic rates, and demographic rates determine population growth rate. The effects of food availability on population growth rate are modified by predator abundance.
Pattern of variation in avian population growth rates
Authors: Sæther Bernt–Erik , Engen Steinar
Published: October 2002

A central question in population ecology is to understand why population growth rates differ over time. Here, we describe how the long–term growth of populations is not only influenced by parameters affecting the expected dynamics, for example form of density dependence and specific population growth rate, but is also affected by environmental and demographic stochasticity. Using long–term studies of fluctuations of bird populations, we show an interaction between the stochastic and the deterministic components of the population dynamics: high specific growth rates at small densitiesr1are typically positively correlated with the environmental variance σe2. Furthermore, θ, a single parameter describing the form of the density regulation in the theta–logistic density–regulation model, is negatively correlated withr1. These patterns are in turn correlated with interspecific differences in life–history characteristics. Higher specific growth rates, larger stochastic effects on the population dynamics and stronger density regulation at small densities are found in species with large clutch sizes or high adult mortality rates than in long–lived species. Unfortunately, large uncertainties in parameter estimates, as well as strong stochastic effects on the population dynamics, will often make even short–term population projections unreliable. We illustrate that the concept of population prediction interval can be useful in evaluating the consequences of these uncertainties in the population projections for the choice of management actions.
Estimating density dependence in time–series of age–structured populations
Authors: Lande R. , Engen S. , Sæther B.–E.
Published: October 2002

For a life history with age at maturity α, and stochasticity and density dependence in adult recruitment and mortality, we derive a linearized autoregressive equation with time–lags of from 1 to α years. Contrary to current interpretations, the coefficients for different time–lags in the autoregressive dynamics do not simply measure delayed density dependence, but also depend on life–history parameters. We define a new measure of total density dependence in a life history,D, as the negative elasticity of population growth rate per generation with respect to change in population size,D= –∂lnλT/∂lnN, where λ is the asymptotic multiplicative growth rate per year,Tis the generation time andNis adult population size. We show thatDcan be estimated from the sum of the autoregression coefficients. We estimatedDin populations of six avian species for which life–history data and unusually long time–series of complete population censuses were available. Estimates ofDwere in the order of 1 or higher, indicating strong, statistically significant density dependence in four of the six species.
Determinants of human population growth
Authors: Lutz Wolfgang , Qiang Ren
Published: October 2002

The 20th century has seen unprecedented growth of the human population on this planet. While at the beginning of the century the Earth had an estimated 1.6 billion inhabitants, this number grew to 6.1 billion by the end of the century, and further significant growth is a near certainty. This paper tries to summarize what factors lie behind this extraordinary expansion of the human population and what population growth we can expect for the future. It discusses the concept of demographic transition and the preconditions for a lasting secular fertility decline. Recent fertility declines in all parts of the world now make it likely that human population growth will come to an end over the course of this century, but in parts of the developing world significant population growth is still to be expected over the coming decades. The slowing of population growth through declining birth rates, together with still increasing life expectancy, will result in a strong ageing of population age structure. Finally, this paper presents a global level systematic analysis of the relationship between population density on the one hand, and growth and fertility rates on the other. This analysis indicates that in addition to the well–studied social and economic determinants, population density also presents a significant factor for the levels and trends of human birth rates.
Two complementary paradigms for analysing population dynamics
Authors: Krebs Charles J.
Published: October 2002

To understand why population growth rate is sometimes positive and sometimes negative, ecologists have adopted two main approaches. The most common approach is through the density paradigm by plotting population growth rate against population density. The second approach is through the mechanistic paradigm by plotting population growth rate against the relevant ecological processes affecting the population. The density paradigm is applieda posteriori, works sometimes but not always and is remarkably useless in solving management problems or in providing an understanding of why populations change in size. The mechanistic paradigm investigates the factors that supposedly drive density changes and is identical to Caughley's declining population paradigm of conservation biology. The assumption that we can uncover invariant relationships between population growth rate and some other variables is an article of faith. Numerous commercial fishery applications have failed to find the invariant relationships between stock and recruitment that are predicted by the density paradigm. Environmental variation is the rule, and non–equilibrial dynamics should force us to look for the mechanisms of population change. If multiple factors determine changes in population density, there can be no predictability in either of these paradigms and we will become environmental historians rather than scientists with useful generalizations for the population problems of this century. Defining our questions clearly and adopting an experimental approach with crisp alternative hypotheses and adequate controls will be essential to building useful generalizations for solving the practical problems of population management in fisheries, wildlife and conservation.
Complex numerical responses to top–down and bottom–up processes in vertebrate populations
Authors: Sinclair A. R. E. , Krebs Charles J.
Published: October 2002

Population growth rate is determined in all vertebrate populations by food supplies, and we postulate bottom–up control as the universal primary standard. But this primary control system can be overridden by three secondary controls: top–down processes from predators, social interactions within the species and disturbances. Different combinations of these processes affect population growth rates in different ways. Thus, some relationships between growth rate and density can be hyperbolic or even have multiple nodes. We illustrate some of these in marsupial, ungulate and rabbit populations. Complex interactions between food, predators, environmental disturbance and social behaviour produce the myriad observations of population growth in nature, and we need to develop generalizations to classify populations. Different animal groups differ in the combination of these four processes that affect them, in their growth rates and in their vulnerability to extinction. Because conservation and management of populations depend critically on what factors drive population growth, we need to develop universal generalizations that will relieve us from the need to study every single population before we can make recommendations for management.
The numerical response: rate of increase and food limitation in herbivores and predators
Authors: Bayliss Peter , Choquenot David
Published: October 2002

Two types of numerical response function have evolved since Solomon first introduced the term to generalize features of Lotka–Volterra predator–prey models: (i) the demographic numerical response, which links change in consumer demographic rates to food availability; and (ii) the isocline numerical response, which links consumer abundanceper seto food availability. These numerical responses are interchangeable because both recognize negative feedback loops between consumer and food abundance resulting in population regulation. We review how demographic and isocline numerical responses have been used to enhance our understanding of population regulation of kangaroos and possums, and argue that their utility may be increased by explicitly accounting for non–equilibrium dynamics (due to environmental variability and/or biological interactions) and the existence of multiple limiting factors. Interferential numerical response functions may help bridge three major historical dichotomies in population ecology (equilibrium versus non–equilibrium dynamics, extrinsic versus intrinsic regulation and demographic versus isocline numerical responses).
Populations in variable environments: the effect of variability in a species' primary resource
Authors: Davis Stephen A. , Pech Roger P. , Catchpole Edward A.
Published: October 2002

Mechanistic models for herbivore populations responding to rainfall–driven pasture are used to explore the effect of temporal variability in a primary resource on the abundance and distribution of a species. If the numerical response of the herbivore to pasture is a convex function, then gains made over time intervals with above average rainfall do not compensate for losses incurred when rainfall is below average. Populations therefore fare worse when rainfall is variable compared with when rainfall is reliable. It is demonstrated that this result is independent of the distribution of rainfall. Sensitivity of a species to variability, and hence the limit to its distribution in variable environments, is directly proportional to the difference between population growth rate under ideal conditions and the estimated rate of decline as the species' resource tends to zero. When density dependence is included in the numerical response, the average abundance of a species declines with increasing variability in its primary resource. However, a model for the dynamics of pasture and rabbits (
Oryctolagus cuniculus
) and red foxes (
Vulpes vulpes
) in southern Australia, is used to illustrate that trophic interactions can reverse the effect of variability: in the absence of foxes, the mean abundance of rabbits declines with variability as expected, but in the full model the mean abundance of rabbits increases.
Trophic interactions and population growth rates: describing patterns and identifying mechanisms
Authors: Hudson Peter J. , Dobson Andy P. , Cattadori Isabella M. , Newborn David , Haydon Dan T. , Shaw Darren J. , Benton Tim G. , Grenfell Bryan T.
Published: October 2002

While the concept of population growth rate has been of central importance in the development of the theory of population dynamics, few empirical studies consider the intrinsic growth rate in detail, let alone how it may vary within and between populations of the same species. In an attempt to link theory with data we take two approaches. First, we address the question 'what growth rate patterns does theory predict we should see in time–series?' The models make a number of predictions, which in general are supported by a comparative study between time–series of harvesting data from 352 red grouse populations. Variations in growth rate between grouse populations were associated with factors that reflected the quality and availability of the main food plant of the grouse. However, while these results support predictions from theory, they provide no clear insight into the mechanisms influencing reductions in population growth rate and regulation. In the second part of the paper, we consider the results of experiments, first at the individual level and then at the population level, to identify the important mechanisms influencing changes in individual productivity and population growth rate. The parasitic nematodeTrichostrongylus tenuisis found to have an important influence on productivity, and when incorporated into models with their patterns of distribution between individuals has a destabilizing effect and generates negative growth rates. The hypothesis that negative growth rates at the population level were caused by parasites was demonstrated by a replicated population level experiment. With a sound and tested model framework we then explore the interaction with other natural enemies and show that in general they tend to stabilize variations in growth rate. Interestingly, the models show selective predators that remove heavily infected individuals can release the grouse from parasite–induced regulation and allow equilibrium populations to rise. By contrast, a tick–borne virus that killed chicks simply leads to a reduction in the equilibrium. When humans take grouse they do not appear to stabilize populations and this may be because many of the infective stages are available for infection before harvesting commences. In our opinion, an understanding of growth rates and population dynamics is best achieved through a mechanistic approach that includes a sound experimental approach with the development of models. Models can be tested further to explore how the community of predators and others interact with their prey.
Behavioural models of population growth rates: implications for conservation and prediction
Authors: Sutherland William J. , Norris Ken
Published: October 2002

Conservation biologists often wish to predict how vertebrate populations will respond to local or global changes in conditions such as those resulting from sea–level rise, deforestation, exploitation, genetically modified crops, global warming, human disturbance or from conservation activities. Predicting the consequences of such changes almost always requires understanding the population growth rate and the density dependence. Traditional means of directly measuring density dependence are often extremely difficult and have the problem that if the environment changes then it is necessary to remeasure the density dependence. We describe an alternative approach that does not require such long datasets and can be used to predict the density dependence under novel conditions. Game theory can be used to describe behavioural decisions that individuals make in response to interference, prey depletion, territorial behaviour or social dominance, and the resultant fitness consequences. It is then possible to predict how survival or reproductive output changes with population size. From this we can then make predictions about the responses of populations to environmental changes. We will illustrate how this can be applied to a range of species and a range of applied problems.
Comparative ungulate dynamics: the devil is in the detail
Authors: Clutton–Brock T. H. , Coulson T.
Published: October 2002

Attempts to relate species differences in population dynamics to variation in life histories rely on the assumption that the causes of contrasts in demography are sufficiently simple to be derived from first principles. Here, we investigate the causes of contrasts in dynamics between two ungulate populations on Hebridean islands (red deer and Soay sheep) and show that differences in stability, as well as in the effects of variation in density and climate, are related to differences in timing of reproduction relative to seasonal variation in resource abundance. In both populations, attempts to predict changes in population size sufficiently accurately for the results to be useful for management purposes require a knowledge of the responses of different age and sex categories to changes in density and climate, as well as of population structure.
Population growth rate as a basis for ecological risk assessment of toxic chemicals
Authors: Forbes Valery E. , Calow Peter
Published: October 2002

Assessing the ecological risks of toxic chemicals is most often based on individual–level responses such as survival, reproduction or growth. Such an approach raises the following questions with regard to translating these measured effects into likely impacts on natural populations. (i) To what extent do individual–level variables underestimate or overestimate population–level responses? (ii) How do toxicant–caused changes in individual–level variables translate into changes in population dynamics for species with different life cycles? (iii) To what extent are these relationships complicated by population–density effects? These issues go to the heart of the ecological relevance of ecotoxicology and we have addressed them using the population growth rate as an integrating concept. Our analysis indicates that although the most sensitive individual–level variables are likely to be equally or more sensitive to increasing concentrations of toxic chemicals than population growth rate, they are difficult to identify
a priori
and, even if they could be identified, integrating impacts on key life–cycle variables via population growth rate analysis is nevertheless a more robust approach for assessing the ecological risks of chemicals. Populations living under density–dependent control may respond differently to toxic chemicals than exponentially growing populations, and greater care needs to be given to incorporating realistic density conditions (either experimentally or by simulation) into ecotoxicological test designs. It is impractical to expect full life–table studies, which record changes in survival, fecundity and development at defined intervals through the life cycle of organisms under specified conditions, for all relevant species, so we argue that population growth rate analysis should be used to provide guidance for a more pragmatic and ecologically sound approach to ecological risk assessment.
Population growth rates: issues and an application
Authors: Godfray H. Charles J. , Rees Mark
Published: October 2002

Current issues in population dynamics are discussed in the context of The Royal Society Discussion Meeting 'Population growth rate: determining factors and role in population regulation'. In particular, different views on the centrality of population growth rates to the study of population dynamics and the role of experiments and theory are explored. Major themes emerging include the role of modern statistical techniques in bringing together experimental and theoretical studies, the importance of long-term experimentation and the need for ecology to have model systems, and the value of population growth rate as a means of understanding and predicting population change. The last point is illustrated by the application of a recently introduced technique, integral projection modelling, to study the population growth rate of a monocarpic perennial plant, its elasticities to different life-history components and the evolution of an evolutionarily stable strategy size at flowering.
Smad3 allostery links TGF-β receptor kinase activation to transcriptional control
Authors: Qin Bin Y. , Lam Suvana S. , Correia John J. , Lin Kai
Published: October 2002

Smad3 transduces the signals of TGF-βs, coupling transmembrane receptor kinase activation to transcriptional control. The membrane-associated molecule SARA (Smad Anchor for Receptor Activation) recruits Smad3 for phosphorylation by the receptor kinase. Upon phosphorylation, Smad3 dissociates from SARA and enters the nucleus, in which its transcriptional activity can be repressed by Ski. Here, we show that SARA and Ski recognize specifically the monomeric and trimeric forms of Smad3, respectively. Thus, trimerization of Smad3, induced by phosphorylation, simultaneously activates the TGF-β signal by driving Smad3 dissociation from SARA and sets up the negative feedback mechanism by Ski. Structural models of the Smad3/SARA/receptor kinase complex and Smad3/Ski complex provide insights into the molecular basis of regulation.
The Arabidopsis HOBBIT gene encodes a CDC27 homolog that links the plant cell cycle to progression of cell differentiation
Authors: Blilou Ikram , Frugier Florian , Folmer Saskia , Serralbo Olivier , Willemsen Viola , Wolkenfelt Harald , Eloy Núbia B. , Ferreira Paulo C.G. , Weisbeek Peter , Scheres Ben
Published: October 2002

In plant meristems, dividing cells interpret positional information and translate it into patterned cell differentiation. Here we report the molecular identification of the Arabidopsis HOBBIT gene that is required for cell division and cell differentiation in meristems. We show that it encodes a homolog of the CDC27 subunit of the anaphase-promoting complex (APC). HOBBIT partially complements a yeast nuc2/cdc27 mutant. Unlike other CDC27 homologs inArabidopsis, its transcription is cell cycle regulated. Furthermore, hobbit mutants show a reduction inDR5 :: GUS auxin reporter gene expression and accumulate the AXR3/IAA17 repressor of auxin responses. HOBBIT activity may thus couple cell division to cell differentiation by regulating cell cycle progression in the meristem or by restricting the response to differentiation cues, such as auxin, to dividing cells.
Parallel Construction of Orthologous Sequence-Ready Clone Contig Maps in Multiple Species
Authors: Thomas James W. , Prasad Arjun B. , Summers Tyrone J. , Lee-Lin Shih-Queen , Maduro Valerie V.B. , Idol Jacquelyn R. , Ryan Joseph F. , Thomas Pamela J. , McDowell Jennifer C. , Green Eric D.
Published: October 2002

Comparison is a fundamental tool for analyzing DNA sequence. Interspecies sequence comparison is particularly powerful for inferring genome function and is based on the simple premise that conserved sequences are likely to be important. Thus, the comparison of a genomic sequence with its orthologous counterpart from another species is increasingly becoming an integral component of genome analysis. In ideal situations, such comparisons are performed with orthologous sequences from multiple species. To facilitate multispecies comparative sequence analysis, a robust and scalable strategy for simultaneously constructing sequence-ready bacterial artificial chromosome (BAC) contig maps from targeted genomic regions has been developed. Central to this approach is the generation and utilization of “universal” oligonucleotide-based hybridization probes (“overgo” probes), which are designed from sequences that are highly conserved between distantly related species. Large collections of these probes are used en masse to screen BAC libraries from multiple species in parallel, with the isolated clones assembled into physical contig maps. To validate the effectiveness of this strategy, efforts were focused on the construction of BAC-based physical maps from multiple mammalian species (chimpanzee, baboon, cat, dog, cow, and pig). Using available human and mouse genomic sequence and a newly developed computer program (soop) to design the requisite probes, sequence-ready maps were constructed in all species for a series of targeted regions totaling ∼16 Mb in the human genome. The described approach can be used to facilitate the multispecies comparative sequencing of targeted genomic regions and can be adapted for constructing BAC contig maps in other vertebrates.
Plasticity of the Human Auditory Cortex Induced by Discrimination Learning of Non-Native, Mora-Timed Contrasts of the Japanese Language
Authors: Menning Hans , Imaizumi Satoshi , Zwitserlood Pienie , Pantev Christo
Published: October 2002

In this magnetoencephalographic (MEG) study, we examined with high temporal resolution the traces of learning in the speech-dominant left-hemispheric auditory cortex as a function of newly trained mora-timing. In Japanese, the “mora” is a temporal unit that divides words into almost isochronous segments (e.g.,na-ka-mu-ra and to-o-kyo-o each comprises four mora). Changes in the brain responses of a group of German and Japanese subjects to differences in the mora structure of Japanese words were compared. German subjects performed a discrimination training in 10 sessions of 1.5 h each day. They learned to discriminate Japanese pairs of words (in a consonant, anni–ani; and a vowel,kiyo–kyo, condition), where the second word was shortened by one mora in eight steps of 15 msec each. A significant increase in learning performance, as reflected by behavioral measures, was observed, accompanied by a significant increase of the amplitude of the Mismatch Negativity Field (MMF). The German subjects' hit rate for detecting durational deviants increased by up to 35%. Reaction times and MMF latencies decreased significantly across training sessions. Japanese subjects showed a more sensitive MMF to smaller differences. Thus, even in young adults, perceptual learning of non-native mora-timing occurs rapidly and deeply. The enhanced behavioral and neurophysiological sensitivity found after training indicates a strong relationship between learning and (plastic) changes in the cortical substrate.
Induction of Mitochondrial Alternative Oxidase in Response to a Cell Signal Pathway Down-Regulating the Cytochrome Pathway Prevents Programmed Cell Death
Authors: Vanlerberghe Greg C. , Robson Christine A. , Yip Justine Y.H.
Published: October 2002

Treatment of tobacco (Nicotiana tabacum L. cv Petit Havana SR1) cells with cysteine (Cys) triggers a signal pathway culminating in a large loss of mitochondrial cytochrome (cyt) pathway capacity. This down-regulation of the cyt path likely requires events outside the mitochondrion and is effectively blocked by cantharidin or endothall, indicating that protein dephosphorylation is one critical process involved. Generation of reactive oxygen species, cytosolic protein synthesis, and Ca2+ flux from organelles also appear to be involved. Accompanying the loss of cyt path is a large induction of alternative oxidase (AOX) protein and capacity. Induction of AOX allows the cells to maintain high rates of respiration, indicating that the lesion triggered by Cys is in the cyt path downstream of ubiquinone. Consistent with this, transgenic (AS8) cells unable to induce AOX (due to the presence of an antisense transgene) lose all respiratory capacity upon Cys treatment. This initiates in AS8 a programmed cell death pathway, as evidenced by the accumulation of oligonucleosomal fragments of DNA as the culture dies. Alternatively, wild-type cells remain viable and eventually recover their cyt path. Induction of AOX in response to a chemical inhibition of the cyt path (by antimycin A) is also dependent upon protein dephosphorylation and the generation of reactive oxygen species. Common events required for both down-regulation of the cyt path and induction of AOX may represent a mechanism to coordinate the biogenesis of these two electron transport paths. Such coordinate regulation may be necessary, not only to satisfy metabolic demands, but also to modulate the initiation of a programmed cell death pathway responsive to mitochondrial respiratory status.
Barley Cbf3 Gene Identification, Expression Pattern, and Map Location
Authors: Choi Dong-Woog , Rodriguez Edmundo M. , Close Timothy J.
Published: October 2002

Although cold and drought adaptation in cereals and other plants involve the induction of a large number of genes, inheritance studies in Triticeae (wheat [Triticum aestivum], barley [Hordeum vulgare], and rye [Secale cereale]) have revealed only a few major loci for frost or drought tolerance that are consistent across multiple genetic backgrounds and environments. One might imagine that these loci could encode highly conserved regulatory factors that have global effects on gene expression; therefore, genes encoding central regulators identified in other plants might be orthologs of these Triticeae stress tolerance genes. The CBF/DREB1 regulators, identified originally in Arabidopsis as key components of cold and drought regulation, merit this consideration. We constructed barley cDNA libraries, screened these libraries and a barley bacterial artificial chromosome library using rice (Oryza sativa) and barley Cbf probes, found orthologs of ArabidopsisCBF/DREB1 genes, and examined the expression and genetic map location of the barley Cbf3 gene,HvCbf3. HvCbf3 was induced by a chilling treatment. HvCbf3 is located on barley chromosome 5H between markers WG364b and saflp58 on the barley cv Dicktoo × barley cv Morex genetic linkage map. This position is some 40 to 50 cM proximal to the winter hardiness quantitative trait locus that includes the Vrn-1H gene, but may coincide with the wheat 5A Rcg1 locus, which governs the threshold temperature at which cor genes are induced. From this, it remains possible that HvCbf3 is the basis of a minor quantitative trait locus in some genetic backgrounds, though that possibility remains to be thoroughly explored.
Using Genomic Resources to Guide Research Directions. The Arabinogalactan Protein Gene Family as a Test Case
Authors: Schultz Carolyn J. , Rumsewicz Michael P. , Johnson Kim L. , Jones Brian J. , Gaspar Yolanda M. , Bacic Antony
Published: October 2002

Arabinogalactan proteins (AGPs) are extracellular hydroxyproline-rich proteoglycans implicated in plant growth and development. The protein backbones of AGPs are rich in proline/hydroxyproline, serine, alanine, and threonine. Most family members have less than 40% similarity; therefore, finding family members using Basic Local Alignment Search Tool searches is difficult. As part of our systematic analysis of AGP function in Arabidopsis, we wanted to make sure that we had identified most of the members of the gene family. We used the biased amino acid composition of AGPs to identify AGPs and arabinogalactan (AG) peptides in the Arabidopsis genome. Different criteria were used to identify the fasciclin-like AGPs. In total, we have identified 13 classical AGPs, 10 AG-peptides, three basic AGPs that include a short lysine-rich region, and 21 fasciclin-like AGPs. To streamline the analysis of genomic resources to assist in the planning of targeted experimental approaches, we have adopted a flow chart to maximize the information that can be obtained about each gene. One of the key steps is the reformatting of the Arabidopsis Functional Genomics Consortium microarray data. This customized software program makes it possible to view the ratio data for all Arabidopsis Functional Genomics Consortium experiments and as many genes as desired in a single spreadsheet. The results for reciprocal experiments are grouped to simplify analysis and candidate AGPs involved in development or biotic and abiotic stress responses are readily identified. The microarray data support the suggestion that different AGPs have different functions.
ADP-Ribosylation Factor 1 of Arabidopsis Plays a Critical Role in Intracellular Trafficking and Maintenance of Endoplasmic Reticulum Morphology in Arabidopsis
Authors: Lee Mi Hee , Min Myung Ki , Lee Yong Jik , Jin Jing Bo , Shin Dong Han , Kim Dae Heon , Lee Kwang-Hee , Hwang Inhwan
Published: October 2002

ADP-ribosylation factors (Arf), a family of small GTP-binding proteins, play important roles in intracellular trafficking in animal and yeast cells. Here, we investigated the roles of two Arf homologs, Arf1 and Arf3 of Arabidopsis, in intracellular trafficking in plant cells. We generated dominant negative mutant forms of Arf 1 and Arf3 and examined their effect on trafficking of reporter proteins in protoplasts. Arf1[T31N] inhibited trafficking of H+-ATPase:green fluorescent protein (GFP) and sialyltransferase (ST):GFP to the plasma membrane and the Golgi apparatus. In addition, Arf1[T31N] caused relocalization of the Golgi reporter protein ST:GFP to the endoplasmic reticulum (ER). In protoplasts expressing Arf1[T31N], ST:red fluorescent protein remained in the ER, whereas H+-ATPase:GFP was mistargeted to another organelle. Also, expression of Arf1[T31N] in protoplasts resulted in profound changes in the morphology of the ER. The treatment of protoplasts with brefeldin A had exactly the same effect as Arf1[T31N] on various intracellular trafficking pathways. In contrast, Arf3[T31N] did not affect trafficking of any of these reporter proteins. Inhibition experiments using mutants with various domains swapped between Arf1 and Arf3 revealed that the N-terminal domain is interchangeable for trafficking inhibition. However, in addition to the T31N mutation, motifs in domains II, III, and IV of Arf1 were necessary for inhibition of trafficking of H+-ATPase:GFP. Together, these results strongly suggest that Arf1 plays a role in the intracellular trafficking of cargo proteins in Arabidopsis, and that Arf1 functions through a brefeldin A-sensitive factor.
Loss-of-Function Mutations in the Ethylene ReceptorETR1 Cause Enhanced Sensitivity and Exaggerated Response to Ethylene in Arabidopsis
Authors: Cancel Jesse D. , Larsen Paul B.
Published: October 2002

Ethylene signaling in Arabidopsis begins at a family of five ethylene receptors that regulate activity of a downstream mitogen-activated protein kinase kinase kinase, CTR1. Triple and quadruple loss-of-function ethylene receptor mutants display a constitutive ethylene response phenotype, indicating they function as negative regulators in this pathway. No ethylene-related phenotype has been described for single loss-of-function receptor mutants, although it was reported that etr1 loss-of-function mutants display a growth defect limiting plant size. In actuality, this apparent growth defect results from enhanced responsiveness to ethylene; a phenotype manifested in all tissues tested. The phenotype displayed by etr1 loss-of-function mutants was rescued by treatment with an inhibitor of ethylene perception, indicating that it is ethylene dependent. Identification of an ethylene-dependent phenotype for a loss-of-function receptor mutant gave a unique opportunity for genetic and biochemical analysis of upstream events in ethylene signaling, including demonstration that the dominant ethylene-insensitive phenotype of etr2-1 is partially dependent on ETR1. This work demonstrates that mutational loss of the ethylene receptor ETR1 alters responsiveness to ethylene in Arabidopsis and that enhanced ethylene response in Arabidopsis not only results in increased sensitivity but exaggeration of response.
Independent Activation of Cold Acclimation by Low Temperature and Short Photoperiod in Hybrid Aspen
Authors: Welling Annikki , Moritz Thomas , Palva E. Tapio , Junttila Olavi
Published: October 2002

Temperate zone woody plants cold acclimate in response to both short daylength (SD) and low temperature (LT). We were able to show that these two environmental cues induce cold acclimation independently by comparing the wild type (WT) and the transgenic hybrid aspen (Populus tremula × Populus tremuloides Michx.) line 22 overexpressing the oat (Avena sativa) PHYTOCHROME A gene. Line 22 was not able to detect the SD and, consequently, did not stop growing in SD conditions. This resulted in an impaired freezing tolerance development under SD. In contrast, exposure to LT resulted in cold acclimation of line 22 to a degree comparable with the WT. In contrast to the WT, line 22 could not dehydrate the overwintering tissues or induce the production of dehydrins (DHN) under SD conditions. Furthermore, abscisic acid (ABA) content of the buds of line 22 were the same under SD and long daylength, whereas prolonged SD exposure decreased the ABA level in the WT. LT exposure resulted in a rapid accumulation of DHN in both the WT and line 22. Similarly, ABA content increased transiently in both the WT and line 22. Our results indicate that phytochrome A is involved in photoperiodic regulation of ABA and DHN levels, but at LT they are regulated by a different mechanism. Although SD and LT induce cold acclimation independently, ABA and DHN may play important roles in both modes of acclimation.
A Novel Plant Homeodomain Protein Interacts in a Functionally Relevant Manner with a Virus Movement Protein
Authors: Desvoyes Bénédicte , Faure-Rabasse Sandrine , Chen Min-Huei , Park Jong-Won , Scholthof Herman B.
Published: October 2002

Tomato bushy stunt virus and its cell-to-cell movement protein (MP; P22) provide valuable tools to study trafficking of macromolecules through plants. This study shows that wild-type P22 and selected movement-defective P22 amino acid substitution mutants were equivalent for biochemical features commonly associated with MPs (i.e. RNA binding, phosphorylation, and membrane partitioning). This generated the hypothesis that their movement defect was caused by improper interaction between the P22 mutants and one or more host factors. To test this, P22 was used as bait in a yeast (Saccharomyces cerevisiae) two-hybrid screen with a tobacco (Nicotiana tabacum) cDNA library, which identified a new plant homeodomain leucine-zipper protein that reproducibly interacted with P22 but not with various control proteins. These results were confirmed with an independent in vitro binding test. An mRNA for the host protein was detected in plants, and its accumulation was enhanced upon Tomato bushy stunt virusinfection of two plant species. The significance of this interaction was further demonstrated by the failure of the homeodomain protein to interact efficiently with two of the well-defined movement-deficient P22 mutants in yeast and in vitro. This is the first report, to our knowledge, that a new plant homeodomain leucine-zipper protein interacts specifically and in a functionally relevant manner with a plant virus MP.
Variable-temperature studies of the 4-isopropylphenol crystal structure from X-ray diffraction. Comparison of thermal expansion and molecular dynamics with spectroscopic results
Authors: Wójcik Grażyna , Holband Jolanta
Published: October 2002

Crystalline 4-isopropylphenol, C9H12O, an optically non-linear material, was studied by X-ray diffraction in order to determine its structure at several temperatures in the 95–300 K range. The thermal expansion coefficients have been calculated from the lattice parameters' dependence on temperature. The rigid-body analysis of the anisotropic displacement parameters including the correlation with the internal motion of large amplitude provided the values of the molecular translation and libration tensors at the temperatures studied and was used to characterize the torsional motion of the isopropyl group. The calculated normal modes and internal torsion frequency were compared with the wave numbers at the maximum of bands in the low-frequency Raman scattering, FTIR and inelastic neutron scattering spectra.
Crystal structure prediction of small organic molecules: a second blind test
Authors: Motherwell W. D. Sam , Ammon Herman L. , Dunitz Jack D. , Dzyabchenko Alexander , Erk Peter , Gavezzotti Angelo , Hofmann Detlef W. M. , Leusen Frank J. J. , Lommerse Jos P. M. , Mooij Wijnand T. M. , Price Sarah L. , Scheraga Harold , Schweizer Bernd , Schmidt Martin U. , van Eijck Bouke P. , Verwer Paul , Williams Donald E.
Published: October 2002

The first collaborative workshop on crystal structure prediction (CSP1999) has been followed by a second workshop (CSP2001) held at the Cambridge Crystallographic Data Centre. The 17 participants were given only the chemical diagram for three organic molecules and were invited to test their prediction programs within a range of named common space groups. Several different computer programs were used, using the methodology wherein a molecular model is used to construct theoretical crystal structures in given space groups, and prediction is usually based on the minimum calculated lattice energy. A maximum of three predictions were allowed per molecule. The results showed two correct predictions for the first molecule, four for the second molecule and none for the third molecule (which had torsional flexibility). The correct structure was often present in the sorted low-energy lists from the participants but at a ranking position greater than three. The use of non-indexed powder diffraction data was investigated in a secondary test, after completion of the ab initio submissions. Although no one method can be said to be completely reliable, this workshop gives an objective measure of the success and failure of current methodologies.
Reproducability and transferability of topological properties; experimental charge density of the hexapeptide cyclo-(D,L-Pro)_2–(L-Ala)_4 monohydrate
Authors: Dittrich B. , Koritsánszky T. , Grosche M. , Scherer W. , Flaig R. , Wagner A. , Krane H. G. , Kessler H. , Riemer C. , Schreurs A. M. M. , Luger P.
Published: October 2002

The charge density of a hexapeptide was determined from high-resolution CCD area-detector experiments at 100 K. Two datasets, one from a rotating anode and a second one from synchrotron radiation, were measured and the results are compared. The data are interpreted in terms of the `rigid pseudoatom' model. The topology of the experimental density is analyzed and compared with the topology of the constituting amino acids, and shows good agreement. All critical points of the electron density at the covalent and hydrogen bonds, as well as those of the Laplacian, were located. With respect to the transferability of electronic and bond topological properties the six peptide bonds were compared with values given in the literature.
CSDSymmetry: the definitive database of point-group and space-group symmetry relationships in small-molecule crystal structures
Authors: Yao Jing Wen , Cole Jason C. , Pidcock Elna , Allen Frank H. , Howard Judith A. K. , Motherwell W. D. Samuel
Published: October 2002

An algorithm that perceives molecular symmetry has been applied to ca. 200 000 entries from the Cambridge Structural Database (CSD). For each molecule, the perceived point group, together with crystallographic properties such as space group, occupied Wyckoff positions and number of residues in the asymmetric unit, have been placed in a relational database, CSDSymmetry, using Microsoft Access software. Database queries can be constructed easily to find occurrences of any combination of molecular or crystallographic attributes, and thereby to answer questions on relative distributions. Some typical example queries are given. The inclusion of CSD reference codes enables direct visualization of search results using the Cambridge Crystallographic Data Centre's three-dimensional structure visualizer, Mercury.
X-ray study and structure simulation of amorphous tungsten oxide
Authors: Lugovskaya L. A. , Aleshina L. A. , Kalibaeva G. M. , Fofanov A. D.
Published: October 2002

In this work, X-ray studies of the amorphous oxide films obtained by thermal evaporation of WO3 powder in a vacuum and by anodic oxidation were carried out. X-ray diffraction patterns were obtained in the symmetric reflection geometry on a DRON-4 diffractometer (Mo K
α radiation, LiF monochromator) in automatic mode. Molecular dynamics simulation of amorphous tungsten oxide atomic configurations has been carried out in the micro-canonical ensemble (NVE) for N = 208 atoms and N = 624 atoms, in a cubic cell, using pairwise Born–Mayer interaction potentials and periodic boundary conditions. One of the purposes of the present work is to analyze the influence of the parameters and the cutoff of the interaction potentials on the interatomic distances. The values obtained in the molecular dynamics simulation for the pair functions D(r) are compared with the experimental data for amorphous oxides in order to choose the most convenient aforesaid values. The values of the average interatomic distances and the coordination numbers obtained by both methods are also compared. The result shows that the tungsten subsystem can be well reproduced using the potential cutoff radius of about 4 Å, but the oxygen subsystem can be well reproduced when the cutoff of the potential for the W—O pairs is equal to 2.8 Å. The configuration built during the molecular dynamics experiment consists of distorted octahedra. These octahedra form chains, as in the WO3 phases of type ReO3, and hexagonal rings, of the same type as in the WO3(1/3)H2O phase, when we extract (1/3)O at every WO3 unit. The pair function D(r) and scattering intensity I(s) distribution curves calculated for simulation configurations show a satisfactory agreement with experiment.