bluuebunny/crossref_metadata_2025 huggingface dataset:
Structural basis of filamin A functions
Authors: Nakamura Fumihiko , Osborn Teresia M. , Hartemink Christopher A. , Hartwig John H. , Stossel Thomas P.
Published: December 2007

Filamin A (FLNa) can effect orthogonal branching of F-actin and bind many cellular constituents. FLNa dimeric subunits have N-terminal spectrin family F-actin binding domains (ABDs) and an elongated flexible segment of 24 immunoglobulin (Ig) repeats. We generated a library of FLNa fragments to examine their F-actin binding to define the structural properties of FLNa that enable its various functions. We find that Ig repeats 9–15 contain an F-actin–binding domain necessary for high avidity F-actin binding. Ig repeats 16–24, where most FLNa-binding partners interact, do not bind F-actin, and thus F-actin does not compete with Ig repeat 23 ligand, FilGAP. Ig repeats 16–24 have a compact structure that suggests their unfolding may accommodate pre-stress–mediated stiffening of F-actin networks, partner binding, mechanosensing, and mechanoprotection properties of FLNa. Our results also establish the orientation of FLNa dimers in F-actin branching. Dimerization, mediated by FLNa Ig repeat 24, accounts for rigid high-angle FLNa/F-actin branching resistant to bending by thermal forces, and high avidity F-actin binding and cross-linking.
Biogenesis of γ-secretase early in the secretory pathway
Authors: Kim Jinoh , Kleizen Bertrand , Choy Regina , Thinakaran Gopal , Sisodia Sangram S. , Schekman Randy W.
Published: December 2007

γ-Secretase is responsible for proteolytic maturation of signaling and cell surface proteins, including amyloid precursor protein (APP). Abnormal processing of APP by γ-secretase produces a fragment, Aβ42, that may be responsible for Alzheimer's disease (AD). The biogenesis and trafficking of this important enzyme in relation to aberrant Aβ processing is not well defined. Using a cell-free reaction to monitor the exit of cargo proteins from the endoplasmic reticulum (ER), we have isolated a transient intermediate of γ-secretase. Here, we provide direct evidence that the γ-secretase complex is formed in an inactive complex at or before the assembly of an ER transport vesicle dependent on the COPII sorting subunit, Sec24A. Maturation of the holoenzyme is achieved in a subsequent compartment. Two familial AD (FAD)–linked PS1 variants are inefficiently packaged into transport vesicles generated from the ER. Our results suggest that aberrant trafficking of PS1 may contribute to disease pathology.
Megf10 regulates the progression of the satellite cell myogenic program
Authors: Holterman Chet E. , Le Grand Fabien , Kuang Shihuan , Seale Patrick , Rudnicki Michael A.
Published: December 2007

We identify here the multiple epidermal growth factor repeat transmembrane protein Megf10 as a quiescent satellite cell marker that is also expressed in skeletal myoblasts but not in differentiated myofibers. Retroviral expression of Megf10 in myoblasts results in enhanced proliferation and inhibited differentiation. Infected myoblasts that fail to differentiate undergo cell cycle arrest and can reenter the cell cycle upon serum restimulation. Moreover, experimental modulations of Megf10 alter the expression levels of Pax7 and the myogenic regulatory factors. In contrast, Megf10 silencing in activated satellite cells on individual fibers or in cultured myoblasts results in a dramatic reduction in the cell number, caused by myogenin activation and precocious differentiation as well as a depletion of the self-renewing Pax7+/MyoD− population. Additionally, Megf10 silencing in MyoD−/− myoblasts results in down-regulation of Notch signaling components. We conclude that Megf10 represents a novel transmembrane protein that impinges on Notch signaling to regulate the satellite cell population balance between proliferation and differentiation.
Hepatic IGFBP1 is a prosurvival factor that binds to BAK, protects the liver from apoptosis, and antagonizes the proapoptotic actions of p53 at mitochondria
Authors: Leu J. I-Ju , George Donna L.
Published: December 2007

Liver is generally refractory to apoptosis induced by the p53 tumor suppressor protein, but the molecular basis remains poorly understood. Here we show that p53 transcriptional activation leads to enhanced expression of hepatic IGFBP1 (insulin-like growth factor-binding protein-1). Exhibiting a previously unanticipated role, a portion of intracellular IGFBP1 protein localizes to mitochondria where it binds to the proapoptotic protein BAK and hinders BAK activation and apoptosis induction. Interestingly, in many cells and tissues p53 also has a direct apoptotic function at mitochondria that includes BAK binding and activation. When IGFBP1 is in a complex with BAK, formation of a proapoptotic p53/BAK complex and apoptosis induction are impaired, both in cultured cells and in liver. In contrast, livers ofIGFBP1-deficient mice exhibit spontaneous apoptosis that is accompanied by p53 mitochondrial accumulation and evidence of BAK oligomerization. These data support the importance of BAK as a mediator of p53’s mitochondrial function. The results also identify IGFBP1 as a negative regulator of the BAK-dependent pathway of apoptosis, whose expression integrates the transcriptional and mitochondrial functions of the p53 tumor suppressor protein.
Dnmt3b promotes tumorigenesis in vivo by gene-specific de novo methylation and transcriptional silencing
Authors: Linhart Heinz G. , Lin Haijiang , Yamada Yasuhiro , Moran Eva , Steine Eveline J. , Gokhale Sumita , Lo Grace , Cantu Erika , Ehrich Mathias , He Timothy , Meissner Alex , Jaenisch Rudolf
Published: December 2007

Increased methylation of CpG islands and silencing of affected target genes is frequently found in human cancer; however, in vivo the question of causality has only been addressed by loss-of-function studies. To directly evaluate the role and mechanism of de novo methylation in tumor development, we overexpressed the de novo DNA methyltransferases Dnmt3a1 and Dnmt3b1 in ApcMin/+ mice. We found that Dnmt3b1 enhanced the number of colon tumors in ApcMin/+ mice approximately twofold and increased the average size of colonic microadenomas, whereas Dnmt3a1 had no effect. The overexpression of Dnmt3b1 caused loss of imprinting and increased expression of Igf2 as well as methylation and transcriptional silencing of the tumor suppressor genes Sfrp2, Sfrp4, and Sfrp5. Importantly, we found that Dnmt3b1 but not Dnmt3a1 efficiently methylates the same set of genes in tumors and in nontumor tissues, demonstrating that de novo methyltransferases can initiate methylation and silencing of specific genes in phenotypically normal cells. This suggests that DNA methylation patterns in cancer are the result of specific targeting of at least some tumor suppressor genes rather than of random, stochastic methylation followed by clonal selection due to a proliferative advantage caused by tumor suppressor gene silencing.
The hematopoietic stem cell and its niche: a comparative view
Authors: Martinez-Agosto Julian A. , Mikkola Hanna K.A. , Hartenstein Volker , Banerjee Utpal
Published: December 2007

Stem cells have been identified as a source of virtually all highly differentiated cells that are replenished during the lifetime of an animal. The critical balance between stem and differentiated cell populations is crucial for the long-term maintenance of functional tissue types. Stem cells maintain this balance by choosing one of several alternate fates: self-renewal, commitment to differentiate, and senescence or cell death. These characteristics comprise the core criteria by which these cells are usually defined. The self-renewal property is important, as it allows for extended production of the corresponding differentiated cells throughout the life span of the animal. A microenvironment that is supportive of stem cells is commonly referred to as a stem cell niche. In this review, we first present some general concepts regarding stem cells and their niches, comparing stem cells of many different kinds from diverse organisms, and in the second part, we compare specific aspects of hematopoiesis and the niches that support hematopoiesis in Drosophila, zebrafish and mouse.
Control of sex-specific apoptosis in C. elegans by the BarH homeodomain protein CEH-30 and the transcriptional repressor UNC-37/Groucho
Authors: Peden Erin , Kimberly Elizabeth , Gengyo-Ando Keiko , Mitani Shohei , Xue Ding
Published: December 2007

Apoptosis is essential for proper development and tissue homeostasis in metazoans. It plays a critical role in generating sexual dimorphism by eliminating structures that are not needed in a specific sex. The molecular mechanisms that regulate sexually dimorphic apoptosis are poorly understood. Here we report the identification of the ceh-30 gene as a key regulator of sex-specific apoptosis in Caenorhabditis elegans. Loss-of-function mutations in ceh-30 cause the ectopic death of male-specific CEM neurons. ceh-30 encodes a BarH homeodomain protein that acts downstream from the terminal sex determination gene tra-1, but upstream of, or in parallel to, the cell-death-initiating gene egl-1 to protect CEM neurons from undergoing apoptosis in males. The second intron of the ceh-30 gene contains two adjacent cis-elements that are binding sites for TRA-1A and a POU-type homeodomain protein UNC-86 and acts as a sensor to regulate proper specification of the CEM cell fate. Surprisingly, the N terminus of CEH-30 but not its homeodomain is critical for CEH-30’s cell death inhibitory activity in CEMs and contains a conserved eh1/FIL domain that is important for the recruitment of the general transcriptional repressor UNC-37/Groucho. Our study suggests that ceh-30 defines a critical checkpoint that integrates the sex determination signal TRA-1 and the cell fate determination and survival signal UNC-86 to control the sex-specific activation of the cell death program in CEMs through the general transcription repressor UNC-37.
The mechanism of an exceptional case of reinitiation after translation of a long ORF reveals why such events do not generally occur in mammalian mRNA translation
Authors: Pöyry Tuija A.A. , Kaminski Ann , Connell Emma J. , Fraser Christopher S. , Jackson Richard J.
Published: December 2007

The subgenomic mRNA of feline caliciviruses is bicistronic with the two cistrons overlapping by four nucleotides, ..AUGA. The upstream cistron encodes a 75-kDa major capsid protein precursor (pre-VP1), and the downstream cistron a 10-kDa minor capsid protein. The kinetics of translation in reticulocyte lysates show that the downstream cistron is translated by a termination–reinitiation process, which is unusual in not requiring eIF4G or the eIF4F complex. Reinitiation requires the 3′-terminal 87 nucleotides (nt) of the pre-VP1 ORF, but no other viral sequences. The reinitiation site is selected by virtue of its proximity to this 87-nt element, and not its proximity to the pre-VP1 ORF stop codon, although this must be located not more than ∼30 nt downstream from the restart codon. This 87-nt element was shown to bind 40S ribosomal subunits and initiation factor eIF3, and addition of supplementary eIF3 enhanced reinitiation efficiency. Mutants defective in reinitiation showed reduced affinity for eIF3 or defective 40S subunit binding (or both). These results suggest a mechanism in which some of the eIF3/40S complexes formed during disassembly of post-termination ribosomes bind to this 87-nt element in a position appropriate for reinitiation following acquisition of an eIF2/GTP/Met-tRNAiternary complex.
Testing Spatial and Nonspatial Learning Using a Morris Water Maze
Authors: Paul Carol Ann , Beltz Barbara , Berger-Sweeney Joanne
Published: December 2007

INTRODUCTION

Animal studies of memory have used many different types of mazes and tasks, where the animal is required to learn the demands of the test and then perform correctly until a predetermined performance criterion is reached. Traditional studies have relied on water or food deprivation to motivate the animal to do the test using food or water rewards. In 1984, Richard Morris introduced the water maze. The maze consists of a large cylindrical tank of water with a hidden platform; the animal has to swim until it finds the platform. The animal generally uses cues outside the maze (extramaze cues) to develop a spatial map of the environment and guide its performance. This maze avoids the problems associated with food or water deprivation, because the animal’s goal is to find the hidden platform so that it can stop swimming. Many types of memory can be studied by varying the visual cues, the placement of the platform, and the starting point of the animal. This protocol describes the use of the water maze to test rats in two behavioral tasks: a spatial task and a nonspatial, visual task.
Hydroxyl-Radical Footprinting
Authors: Carey Michael , Smale Stephen T.
Published: December 2007

INTRODUCTION

The hydroxyl-radical footprinting methodology has wide applications to studying protein-DNA interactions, as well as structural perturbations (e.g., bending) that occur in DNA during protein binding. Hydroxyl radicals cleave DNA by abstracting a hydrogen atom from C4 of the sugar in the minor groove. Protein binding over the minor groove generally protects the sugar from cleavage. Because a hydroxyl radical molecule is small and thus is not subject to the same steric restrictions as other agents (such as DNase I), hydroxyl-radical footprinting can give detailed information on protein binding to the minor groove. In this protocol, the radical is generated by Fe(II) EDTA, which cleaves hydrogen peroxide into a hydroxyl radical and a hydroxide ion. The radical then cleaves the sugar in a diffusion limited reaction. Ascorbic acid is included to regenerate the active Fe(II).
Phosphate Ethylation Interference Assay: Figure 1.
Authors: Carey Michael , Smale Stephen T.
Published: December 2007

INTRODUCTION

In the ethylation interference assay, ethyl nitrosourea is used to ethylate phosphates within 32P-end-labeled DNA molecules that contain a protein recognition site; the reaction is optimized to yield approximately one ethyl group per DNA molecule. The DNA is then incubated with barely saturating concentrations of a DNA-binding protein, but the ethylated phosphates interfere with proteins coming into close proximity to the minor groove or phosphate backbone of the binding site on the DNA molecule. Because ethylation makes the DNA susceptible to piperidine-induced cleavage, the protein recognition site can be identified by analyzing the cleavage products (from modified DNA molecules with bound protein versus modified DNA molecules without bound protein) on a polyacrylamide/urea gel alongside a sequencing ladder. Two points are critical for success with this assay. First, only about 10% of the molecules should be ethylated, which avoids having a significant number of molecules with multiple ethylations. This can be determined by modifying the DNA until ~10% of the starting probe is converted to a ladder of bands. It is critical that each DNA molecule be modified only once, so that it is clear that the modification being detected--the one nearest to the 32P-labeled end--is the one responsible for interference. Second, only barely saturating amounts of protein should be bound to the DNA. Barely saturated amounts are used because although the ethylation decreases binding, it does not always abolish it. High concentrations of protein may overcome the deleterious effect of the modification.
Chemical Two-Photon Uncaging
Authors: Pettit Diana L. , Augustine George J.
Published: December 2007

INTRODUCTION

Chemical two-photon uncaging is useful for a wide range of applications, including both mapping of receptor location and localized photostimulation of neurons via activation of excitatory glutamate receptors. Experimental preparations could include brain slices, cultured neurons, and, among other possibilities, whole brains in vivo. This protocol documents the utility of chemical two-photon uncaging in examining glutamate receptors of pyramidal neurons in hippocampal slices.
Ex Ovo Electroporation of DNA Vectors into Pre-gastrulation Avian Embryos
Authors: Cui Cheng , Rongish Brenda , Little Charles , Lansford Rusty
Published: December 2007

INTRODUCTION

The transfection of GFP-expressing constructs into early embryos permits key developmental events such as gastrulation to be dynamically imaged using time-lapse video-microscopy. This protocol describes the ex ovo electroporation of a DNA plasmid into avian embryos as young as stage X, nearly 24 h earlier in development than most electroporation protocols. Compared to in ovo electroporation, the ex ovo method allows easier embryo orientation (the posterior half of the embryo is darker than the anterior half). Thus, positioning of the specimen and consistency of the electroporation site between embryos is improved. Furthermore, nearly all embryos can be electroporated at the same stage using the ex ovo method: If some embryos have not reached a desired stage, it is possible to temporally stop development of those embryos already at the desired stage by keeping them at room temperature while incubating the rest at 37°C until they develop. The method described here uses relatively low voltage, and the electroporation chamber can be made easily, with no specialized equipment required.
Preparation of Cells in 96-Well Plates for siRNA Transfection and High-Content Analysis
Authors: Roquemore Elizabeth P.
Published: December 2007

INTRODUCTION

RNA interference using siRNA libraries is a powerful technology for elucidating gene function by downregulating gene expression at the post-transcriptional level. Phenotypic changes associated with siRNA knockdown can be monitored using cell lines expressing fluorescent reporter proteins. Test siRNAs are transiently transfected into the reporter cell line and behavior of the fluorescent reporter probe is monitored using a high-content imaging system. A range of cell features and additional fluorescent probes can be monitored to assess the effects of knockdown. This article details how to perform siRNA transfection in multiwell plates for subsequent high-content analysis.
Optimization of siRNA Knockdown in EGFP-Expressing Cell Lines Using High-Content Analysis
Authors: Roquemore Elizabeth P.
Published: December 2007

INTRODUCTION

RNA interference using siRNA libraries is a powerful technology for elucidating gene function by downregulating gene expression at the post-transcriptional level. Phenotypic changes associated with siRNA knockdown can be monitored using cell lines expressing fluorescent reporter proteins. Test siRNAs are transiently transfected into the reporter cell line and behavior of the fluorescent reporter probe is monitored using a high-content imaging system. A range of cell features and additional fluorescent probes can be monitored to assess the effects of knockdown. This article describes how to optimize siRNA knockdown in EGFP-expressing cell lines.
Organotypic Slice Culture of Embryonic Brain Tissue: Figure 1.
Authors: Daza Ray A.M. , Englund Chris , Hevner Robert F.
Published: December 2007

INTRODUCTION

This protocol describes how to dissect, assemble, and cultivate mouse embryonic (E) brain tissue from age E11.5 to E18.5 (days) for organotypic slice culture. These preparations can be used for a variety of assays and studies including coculture of different brain regions, cell migration assays, axon guidance assays, and DNA electroporation experiments. During electroporation, an electric current is applied to the surface of a specific target area of the brain slice in order to open holes in the plasma membrane and introduce a plasmid of coding DNA. The floating slice-on-membrane construct helps to preserve the structural integrity of the brain slices, while maintaining easy experimental access and optimal viability. Experiments can be monitored in living slices (e.g., with confocal imaging), and further studies can be completed using slices that have been fixed and cryosectioned at the end of the experiment. Any region of embryonic brain or spinal tissue can be used in this protocol.
Fate-Mapping Technique: Using Carbocyanine Dyes for Vital Labeling of Cells in Gastrula-Stage Mouse Embryos Cultured In Vitro
Authors: Bildsoe Heidi , Franklin Vanessa , Tam Patrick P.L.
Published: December 2007

INTRODUCTION

The allocation of different progenitor populations to embryonic structures can be visualized by tracking the distribution of cells to specific tissues in the live embryo. A critical prerequisite for cell tracking is to identify unambiguously the progenitors and their descendants during morphogenesis. This can be achieved by using molecular markers that are expressed from transgenes integrated into the genome or as episomal DNA constructs, or by tagging the cells with exogenous markers that are incorporated into the cell membrane or cytoplasmic components of the cells. These labels can be introduced by dye-labeling the membrane, injecting marker enzyme into the cytoplasm, or integrating reporter constructs by transfection or electroporation. This protocol describes how to label cells in the endoderm (which, at this stage of development, is the superficial tissue layer) of live mouse embryos at 7.0-7.5 days post-coitum (dpc), using two carbocyanine dyes (DiI and DiO).
Combining population genetics and demographical approaches in evolutionary studies of plant mating systems
Authors: Cheptou Pierre‐Olivier , J. Schoen Daniel
Published: December 2007

The striking amount of variation in the mating systems of higher plants has stimulated fruitful research by both ecologists and population geneticists. Historically, these two schools of thought have developed independent theoretical treatments and empirical approaches to account for the evolution of such diversity. We highlight the approach adopted by each field. Population geneticists have developed an approach centred on gene properties of individuals and their role on the evolution of self‐fertilisation (transmission rules and the deleterious role of mutations), while ecologists have mostly focused on demographic properties of self‐fertilisation (seed production, colonisation ability of selfers). As a result, the two approaches sometimes use conflicting notions of fitness. The recent empirical advances on inbreeding depression, a topic typically motivated by population genetic questions, have emphasized the need to adopt a demographical perspective for fitness. In this paper, we suggest generalizing this approach in mating system evolution and we expect further improvements by integrating demographic and genetics perspectives.
Increasing isolation reduces predator:prey species richness ratios in aquatic food webs
Authors: Shulman Rachel S. , Chase Jonathan M.
Published: December 2007

The number of species that live in a habitat typically declines as that habitat becomes more isolated. However, the influence of habitat isolation on patterns of food web structure, in particular the ratio of predator to prey species richness, is less well understood. We placed aquatic mesocosms at varying distances from ponds that acted as sources of potential colonists; then we examined how isolation affected the ratio of predator:prey species richness in the communities that assembled. In the final sampling, a total of 21 species (12 prey and 9 predators) of insects, crustaceans, and amphibians had colonized the mesocosms. We found that total species richness, as well as the richness of predators and prey, declined with increasing isolation. However, predator richness declined more rapidly than prey richness with increasing isolation, which lead to decreasing predator:prey ratios. This result conflicts with prior demonstrations of invariant predator:prey ratios in freshwater communities.
Serins with intermediate brightness have a higher survival in the wild
Authors: Figuerola Jordi , Carlos Senar Juan
Published: December 2007

More ornamented individuals are supposed to signal their superior quality and health, however the development of larger ornaments or brighter plumages can affect their survival probabilities. The survival of male serins Serinus serinus in relation to the color characteristics of carotenoid‐derived breast coloration was analyzed in a six‐year capture–recapture study in northeastern Spain. A total of 210 males were individually marked generating 340 captures, between 1997 and 2003. The model with the best fit indicated a quadratic relationship between brightness of carotenoid‐derived coloration and survival, independent of time and age of the birds, so that individuals with intermediate plumage brightness survived longer. Hence, results stress that plumage color in male serins is under stabilizing natural selection, with reduced survival both in drabber and brighter individuals. While lower condition of drabber individuals can explain their lower survival, brighter birds can suffer more from predation risk or from a higher investment of resources into mate attraction and/or reproduction.
Vole–vegetation interactions in an experimental, enemy free taiga floor system
Authors: Rammul Üllar , Oksanen Tarja , Oksanen Lauri , Lehtelä Jouko , Virtanen Risto , Olofsson Johan , Strengbom Joachim , Rammul Ivi , Ericson Lars
Published: December 2007

Vole–vegetation interactions in a predation‐free taiga environment of northern Fennoscandia were studied by transferring vegetation from natural Microtus habitats into a greenhouse, where three habitat islands of about 30 m2 were created. The ‘islands’ were subjected to simulated summer conditions and a paired female field vole, Microtusagrestis, was introduced to each ‘island’. The development of the female and her young was followed by recurrent live trapping. The development of the vegetation was followed by recurrent marking and censusing of plant shoots at intervals of five days. In the next growing season, two ‘islands’ were subjected to a new grazing treatment to study the impacts of repeated grazing on the vegetation and on the growth and reproduction of voles. Plant biomasses were harvested at the end of each trial. In all trials, the biomasses of graminoids and non‐toxic herbs other than ferns, fireweeds and rosaceous plants were profoundly decimated. Even the biomass of a toxic herb Aconitum lycoctonum decreased largely at pace with the palatable herbs. The least preferred plant categories maintained their biomasses at control levels. Their neutral collective response was created by opposite species‐level trends. Species typical for moist and nutrient‐rich forests suffered from vole grazing, whereas the biomass of species adapted to disturbed habitats increased.

In spite of the dramatic changes in the vegetation, the introduced female voles survived throughout the trials and reproduced normally. The young of their first litters survived well and reached the final weights typical for individuals starting to winter as immatures. We conclude that most of the plant biomass found on productive boreal forest floors is potential food for field voles and remains palatable for them even when subjected to recurrent, severe grazing. If nothing else than summer resources were limiting the growth of the field vole populations, the plants currently dominating moist and nutrient‐rich taiga floors could not survive in this habitat.
Coping with predators and food limitation: testing life history theory for sex–specific larval development
Authors: Johannes Mikolajewski Dirk , Joop Gerrit , Wohlfahrt Bianca
Published: December 2007

For animals with complex life cycles, recent models of sexual size‐dimorphism at maturity assume three key variables to optimise larval life history: activity in the larval stage, development time, and size at maturation. However, model predictions remain largely untested. In the territorial dragonfly Libellula depressa (Odonata) exhibiting a flexible development time we tested for male‐biased sexual size‐dimorphism and sex differences in larval activity, development time, and growth rate. Based on models we predicted that males achieved their larger size compared to females by a longer development rather than being more active. Results revealed that males took longer to develop and achieved a larger size than females but were not more active. Compared to males, females exhibited a higher growth rate which was not achieved by an activity‐mediated increased food intake. We conclude that sexual size‐dimorphism in species with a flexible development time is mediated by differences in developmental length but not activity. Furthermore, sexes differ in their plastic responses to food availability and predator presence making it necessary to consider sex‐specific differences in testing further life history responses.
Multi‐scale regulated plant community dynamics: mechanisms and implications
Authors: Szabó Péter , Meszéna Géza
Published: December 2007

Plant competition is not a direct interaction, but operates via environmental feedback loops, which interconnect population densities and environmental regulating variables. It is suggested that due to scale dependent elements of these feedback loops, competition may occur eventually on very different scales, necessitating a cross‐scale extension of plant competition theory. After introducing the concept of cross‐scale competition, we incorporate its elements into a metacommunity model and study its implications on community organization. It is found that both the equilibrium community composition, regarding coexisting functional types, and its stability depend on scale dependent attributes of environmental feedback loops and disturbance regimes. We argue that plant communities are likely to exhibit properties, which are in line with the hierarchical ecosystem concept. Environmental feedback loops on different scales act as distinct organizational levels, what can be affected by disturbances of corresponding spatial extent.
What regulate and limit reindeer populations in Norway?
Authors: Tveraa Torkild , Fauchald Per , Gilles Yoccoz Nigel , Anker Ims Rolf , Aanes Ronny , Arild Høgda Kjell
Published: December 2007

An understanding of how species are affected by top‐down and bottom‐up processes in food webs, and how these forces interact with climatic conditions is crucial for how ecosystems should be managed. In Norway large carnivores are effectively removed from extensive areas to protect livestock, leaving human harvesting as the only significant top‐down force on ungulate populations. We examined the relative role of top‐down and bottom‐up processes for 58 semi‐domesticated reindeer populations in Norway subjected to contrasting climatic regimes over the period 1981–2005. Intensive herding and international agreement have resulted in a situation where some populations are unable to undertake seasonal migration to the interior to escape the unfavourable climatic conditions that rule the coastal region in the winter, a critical season for northern ungulates. We used this natural manipulation to contrast between populations with ‘poor’ and ‘good’ winter conditions. For populations with good winter conditions, average body size increased with harvesting, suggesting that some top‐down process was necessary to avoid food limitation. Time‐series analyses revealed that direct regulation of population size was only evident in populations subjected to intensive harvesting. The lack of direct regulation in populations subjected to low harvesting resulted in high vulnerability to harsh winter weather. The body size and climate vulnerability of populations with poor winter conditions was unaffected of harvesting, but average densities was positively related to overall vegetation productivity as indexed by satellite images (NDVI). Top‐down processes appeared to be necessary to dampen the effect of harsh winters in populations with generally good winter conditions. Conversely, populations subjected to generally poor winter conditions appeared to be more influenced by bottom‐up processes and buffered climatic perturbations by increasing body size.
Stoichiometry of nutrient excretion by fish: interspecific variation in a hypereutrophic lake
Authors: Torres Lisette E. , Vanni Michael J.
Published: December 2007

This study investigates how nutrient cycling rates and ratios vary among fish species, with a particular focus on comparing an ecologically dominant detritivore (gizzard shad) to other fishes in a productive lake. We also examined how nutrient cycling rates are mediated by body size (as predicted by allometry theory), and how variation in nutrient cycling is related to body and food nutrient contents (according to predictions of ecological stoichiometry). As predicted by allometry, per capita nitrogen and phosphorus excretion rates increased and mass‐specific excretion rates decreased, with increasing mass. Body phosphorus content was correlated with body mass only in one species, bluegill. Contrary to stoichiometric predictions, there was no relationship between body P and mass‐normalized P excretion rate, or between body N:P and excreted N:P, when all individuals of all species were considered.

However, at the species level, we observed some support for a body nutrient content effect on excretion as predicted by stoichiometry theory. For example, gizzard shad had lower body P (high body N:P) and also excreted P at higher rates (lower N:P) than bluegill, which had high body P (lower body N:P). We applied the Sterner (1990) homeostatic stoichiometry model to the two most common species in the study – gizzard shad and bluegill and found that food N:P had a greater effect than consumer body N:P on excreted N:P. This indicates that, in terms of variation among these species, nutrient excretion may be more of a function of food nutrient content than the nutrient content of the consumer. These results suggest that stoichiometry can provide a framework for variation among species in nutrient cycling and for evaluating the ecosystem consequences of biodiversity loss.
Stream mosses as chemically‐defended refugia for freshwater macroinvertebrates
Authors: Parker John D. , Burkepile Deron E. , Collins Dwight O. , Kubanek Julia , Hay Mark E.
Published: December 2007

Marine and terrestrial studies show that small, sedentary herbivores that utilize plants as both food and habitat can gain enemy‐free space by living on hosts that are chemically defended from larger, generalist consumers. Although large herbivores are increasingly recognized as important consumers of macrophytes in freshwater communities, the potential indirect effects of herbivory on plant‐associated macroinvertebrates have rarely been studied. Here, we show that the large, generalist consumers in a riverine system, Canada geese, Branta canadensis, and crayfish, Procambarus spiculifer, both selectively consumed riverweed, Podostemum ceratophyllum, over an aquatic moss, Fontinalis novae‐angliae, even though moss comprised 89% of the total plant biomass on riverine rocky shoals. Moss supported twice as many plant‐associated macroinvertebrates as riverweed, suggesting that it might provide a spatial refuge from consumption by these larger consumers. Bioassay‐guided fractionation of moss extracts led to the isolation of a C18 acetylenic acid, octadeca‐9,12‐dien‐6‐ynoic acid, that deterred crayfish feeding. In contrast to results with Canada geese and crayfish, both the amphipod Crangonyx gracilis and the isopod Asellus aquaticus consumed significant amounts of moss but rejected riverweed in laboratory feeding assays. Moreover, neither amphipod nor isopod feeding was deterred by the crude organic extract of Fontinalis, suggesting that these mesograzers tolerate or circumvent the chemical defenses that deterred larger consumers. Thus, herbivory by large, generalist herbivores may drive freshwater plant community structure towards chemically defended plants and favor the ecological specialization of smaller, less mobile herbivores on unpalatable hosts that represent enemy‐free space.
Interactions between dispersal, competition, and landscape heterogeneity
Authors: North Ace , Ovaskainen Otso
Published: December 2007

It is widely acknowledged that space has an important role in population regulation, yet more specific knowledge into how the relevant factors interact attains little consensus. We address this issue via a stochastic, individual based model of population dynamics, in a continuous space continuous time framework. We represent habitat quality as a continuously varying surface over the two‐dimensional landscape, and assume that the quality affects either fecundity (rate of propagule production) or probability of propagule establishment. We control the properties of the landscape by two parameters, which we call the patch size (the characteristic length scale in quality variation), and the level of heterogeneity (the characteristic quality difference between poor quality and high quality areas). In addition to such exogenous variability, we also account for endogenous factors causing spatial variation by assuming localised dispersal and competition. We find that heterogeneity has a general positive effect on population density, and hence it is beneficial to improve best quality habitat at the expense of worst quality habitat. With regards to patch size, we find an intermediate optimum, due to a conflict between minimising the loss of propagules to low quality regions and maximising the benefits of heterogeneity. We address the consequences of regional stochasticity by allowing the environmental conditions change in time. The cost of having to continuously track where the favourable conditions have moved to ultimately reduces population size.
Synergism between mutational meltdown and Red Queen in parthenogenetic biotypes of the freshwater planarian Schmidtea polychroa
Authors: Bruvo Ruža , Schulenburg Hinrich , Storhas Martin , K. Michiels Nico
Published: December 2007

Do parasites and accumulation of deleterious mutations act synergistically in balancing the costs of sex? We addressed this possibility in the freshwater planarian flatworm Schmidtea polychroa. Sexual and parthenogenetic forms of this species sometimes coexist but show no ecological separation. Previous studies indicate that in a mixed sexual/ parthenogenetic population in Lago di Caldonazzo (N. Italy) parthenogens get more frequently infected with parasites. At the same time, they suffer from higher embryo mortality, which has been interpreted as a sign of accumulation of deleterious mutations. In the present study, we test whether these two factors are correlated, by focusing on the differences among the clonal lineages of a predominantly parthenogenetic subpopulation. Our results suggest that, for two out of three parasite types found, the infections are positively associated with the indirect measure of host mutation load.
Species evenness and invasion resistance of experimental grassland communities
Authors: Brett Mattingly W. , Hewlate Rachel , Reynolds Heather L.
Published: December 2007

Concern for biodiversity loss coupled with the accelerated rate of biological invasions has provoked much interest in assessing how native plant species diversity affects invasibility. Although experimental studies extensively document the effects of species richness on invader performance, the role of species evenness in such studies is rarely examined. Species evenness warrants more attention because the relative abundances of species can account for substantially more of the variance in plant community diversity and tend to change more rapidly and more frequently in response to disturbances than the absolute numbers of species. In this study, we experimentally manipulated species evenness within native prairie grassland mesocosms. We assessed how evenness affected primary productivity, light availability and the resistance of native communities to invasion. The primary productivity of native communities increased significantly with species evenness, and this increase in productivity was accompanied by significant decreases in light availability. However, evenness had no effect on native community resistance to invasion by three common exotic invasive species. In this study, niche complementarity provides a potential mechanism for the effects of evenness on productivity and light availability, but these effects apparently were not strong enough to alter the invasibility of the experimental communities. Our results suggest that species evenness enhances community productivity but provides no benefit to invasion resistance in otherwise functionally diverse communities.
Pedigree relatedness, not greenbeard genes, explains eusociality
Authors: Helanterä Heikki , Bargum Katja
Published: December 2007

The evolution of eusociality, where some individuals altruistically forgo reproduction, poses a dilemma which can be solved by kin selection, i.e. by considering relatedness among cooperating individuals. Most often, such relatedness is caused by pedigree relationships between family members. However, an alternative explanation has recently emerged in an article byWilson and Hölldobler (2005). Wilson and Hölldobler see the ecological benefit of group living as the principal reason for sociality. In their scenario, individuals sharing the same altruistic allele (analogous to a greenbeard gene) preferentially interact with each other, regardless of pedigree relatedness. We argue that empirical evidence has the potential to answer the question of whether pedigree relatedness plays a role in the evolution of eusociality. We conclude that both phylogenetic studies and studies of intra‐genomic conflict support the importance of pedigree relatedness in the evolution of eusociality.
A tree in the eyes of a moth – temporal variation in oak leaf quality and leaf‐miner performance
Authors: Gripenberg Sofia , Salminen Juha‐Pekka , Roslin Tomas
Published: December 2007

When examined at any moment in time, different parts of an individual oak tree exhibit almost as large differences in quality as different trees. But how consistent are such patterns in time? In this paper, we use intraclass correlations to assess the temporal consistency of host plant quality at several spatial scales. As measures of quality, we use both individual chemical attributes (phenolic contents) and the overall performance (larval survival) of the host‐specific leaf‐minerTischeria ekebladella. Concentrations of 24 phenolic compounds were monitored on seven trees throughout a season. Variation in mine initiation and larval survival rates was assessed for individuals transplanted to another set of trees early versus later in the season, while year‐to‐year variation in larval survival was studied through stratified surveys of wild individuals during three years. At all time scales considered, measures of host quality were moderately consistent: a tree favourable in quality at one point in time often remained so, but there was abundant variation around this relationship (ρ=0.4–0.6). One hierarchical level deviated from this general pattern: on individual branches, larval survival rates varied randomly among years (ρ=0). Our study suggests that the quality of trees, and in particular of smaller units within trees, may be difficult to predict both in space and in time. To account for this, insects might benefit from adopting a bet‐hedging strategy when selecting resources.
Architectural and growth traits differ in effects on performance of clonal plants: an analysis using a field‐parameterized simulation model
Authors: Wildová Radka , Gough Laura , Herben Tomáš , Hershock Chad , Goldberg Deborah E.
Published: December 2007

Individual traits are often assumed to be linked in a straightforward manner to plant performance and processes such as population growth, competition and community dynamics. However, because no trait functions in isolation in an organism, the effect of any one trait is likely to be at least somewhat contingent on other trait values. Thus, to the extent that the suite of trait values differs among species, the magnitude and even direction of correlation between values of any particular trait and performance is likely to differ among species. Working with a group of clonal plant species, we assessed the degree of this contingency and therefore the extent to which the assumption of simple and general linkages between traits and performance is valid. To do this, we parameterized a highly calibrated, spatially explicit, individual‐based model of clonal plant population dynamics and then manipulated one trait at a time in the context of realistic values of other traits for each species. The model includes traits describing growth, resource allocation, response to competition, as well as architectural traits that determine spatial spread. The model was parameterized from a short‐term (3 month) experiment and then validated with a separate, longer term (two year) experiment for six clonal wetland sedges, Carex lasiocarpa, Carex sterilis, Carex stricta, Cladium mariscoides, Scirpus acutus and Scirpus americanus. These plants all co‐occur in fens in southeastern Michigan and represent a spectrum of clonal growth forms from strong clumpers to runners with long rhizomes.

Varying growth, allocation and competition traits produced the largest and most uniform responses in population growth among species, while variation in architectural traits produced responses that were smaller and more variable among species. This is likely due to the fact that growth and competition traits directly affect mean ramet size and number of ramets, which are direct components of population biomass. In contrast, architectural and allocation traits determine spatial distribution of biomass; in the long run, this also affects population size, but its net effect is more likely to be mediated by other traits. Such differences in how traits affect plant performance are likely to have implications for interspecific interactions and community structure, as well as on the interpretation and usefulness of single trait optimality models.
Adaptive significance of maternal induction of density‐dependent phenotypes
Authors: Meylan Sandrine , Clobert Jean , Sinervo Barry
Published: December 2007

Density has been demonstrated to impact life history traits such as growth, fecundity and survival. Some authors have proposed that morphological and behavioral traits have evolved in response to density conditions. To escape the adverse effect of density, individuals can either adapt to crowding or avoid crowding by dispersing. The aim of this work is to study the interplay between local adaptation and dispersal in four populations of the common lizard,Lacerta vivipara,where densities of both the maternal and juvenile environment have been experimentally manipulated. Density was decreased in the spring by removing a quarter of the population at two sites and was un‐manipulated in two other sites. One month later, we caught some pregnant females and kept them in the laboratory until parturition. To manipulate density of postnatal neonates and juveniles, we divided each clutch into two, and released half of the juveniles either in a reduced density site or in a control one. We then recaptured individuals a year after release and recorded their size and weight. When density was reduced, females increased their clutch size, but produced offspring of lower body condition than in the control sites. The conspicuous ventral color of females was likewise increased when density was reduced. However, offspring growth rate, local survival and dispersal were not influenced by maternal density. Juvenile females released in the reduced‐density site had lower survival rate than those released in the control density site. Contrary to expectations, offspring dispersal was significantly higher at the reduced compared to control density sites. There was no interaction between maternal density habitat and the juvenile release habitat indicating that maternal effects did not influence juvenile life history traits in a different way according to the level of density. Moreover, clutch size and offspring size had no effect on juvenile growth or survival.