Modelling faunal responses to climatic gradients with GIS: land snails as a case study

Abstract. This study describes and exemplifies a multivariate approach based on geographical information system (GIS) technology for the analysis of faunal responses to climatic gradients. The approach is particularly suitable for the analysis of museum collections, and it combines the data reduction capabilities of multivariate techniques (ordination and classification) with GIS tools for the manipulation of geographically referenced data. The specific steps of the analysis are (1) construction of a grid covering the study area at an appropriate resolution, (2) overlaying the grid with a data base of spatially referenced species records, (3) determining the number of times each species was recorded in each cell, (4) constructing a matrix of grid cells by species where each entry indicates the number of records of a particular species in a particular cell, (5) removing cells whose total number of records is lower than some threshold (to be determined) from the matrix, (6) analysis of the reduced matrix using ordination and classification techniques, (7) construction of maps representing the results of the multivariate analyses, and (8) analysis of these maps with respect to digital maps of relevant climatological factors. The applicability of this approach was evaluated by analysing the response of the land snail fauna of Israel to regional variation in mean annual rainfall. As was expected, patterns of faunal variation were significantly correlated with underlying variation in rainfall. However, the per-unit effect of rainfall on the composition of the studied fauna was much greater in dry regions than in more rainy areas. Above 450 mm, no relationships could be detected between the observed patterns of faunal variation and rainfall. These patterns were consistent over a wide range of grid cell sizes (5–20 km), and were robust to outliers. The overall results indicate that the integration of GIS tools with standard multivariate techniques may serve as a valuable methodology for the identification and interpretation of regional patterns of faunal variation.     

Cellular signaling identifiability analysis: A case study

Two primary purposes for mathematical modeling in cell biology are (1) simulation for making predictions of experimental outcomes and (2) parameter estimation for drawing inferences from experimental data about unobserved aspects of biological systems. While the former purpose has become common in the biological sciences, the latter is less common, particularly when studying cellular and subcellular phenomena such as signaling—the focus of the current study. Data are difficult to obtain at this level. Therefore, even models of only modest complexity can contain parameters for which the available data are insufficient for estimation. In the present study, we use a set of published cellular signaling models to address issues related to global parameter identifiability. That is, we address the following question: assuming known time courses for some model variables, which parameters is it theoretically impossible to estimate, even with continuous, noise-free data? Following an introduction to this problem and its relevance, we perform a full identifiability analysis on a set of cellular signaling models using DAISY (Differential Algebra for the Identifiability of SYstems). We use our analysis to bring to light important issues related to parameter identifiability in ordinary differential equation (ODE) models. We contend that this is, as of yet, an under-appreciated issue in biological modeling and, more particularly, cell biology.     

Cellular responses to excess phospholipid

Phosphatidylcholine (PtdCho) is the major membrane phospholipid in mammalian cells, and its synthesis is controlled by the activity of CDP:phosphocholine cytidylyltransferase (CCT). Enforced CCT expression accelerated the rate of PtdCho synthesis. However, the amount of cellular PtdCho did not increase as a result of the turnover of both the choline and glycerol components of PtdCho. Metabolic labeling experiments demonstrated that cells compensated for elevated CCT activity by the degradation of PtdCho to glycerophosphocholine (GPC). Phospholipase D-mediated PtdCho hydrolysis and phosphocholine formation were unaffected. Most of the GPC produced in response to excess phospholipid production was secreted into the medium. Cells also degraded the excess membrane PtdCho to GPC when phospholipid formation was increased by exposure to exogenous lysophosphatidylcholine or lysophosphatidylethanolamine. The replacement of the acyl moiety at the 1-position of PtdCho with a non-hydrolyzable alkyl moiety prevented degradation to GPC. Accumulation of alkylacyl-PtdCho was associated with the inhibition of cell proliferation, demonstrating that alternative pathways of degradation will not substitute. GPC formation was blocked by bromoenol lactone, implicating the calcium-independent phospholipase A2 as a key participant in the response to excess phospholipid. Owing to the fact that PtdCho is biosynthetically converted to PtdEtn, excess PtdCho resulted in overproduction and exit of GPE as well as GPC. Thus, general membrane phospholipid homeostasis is achieved by a balance between the opposing activities of CCT and phospholipase A2.     

Understanding avian responses to forest boundaries: a case study with chickadee winter flocks

Avian species diversity and territory location are often associated with sharp forest edges, or boundaries. However, our understanding of behaviours underlying avian distribution near forest boundaries, especially species with large home ranges, remains poor. In a two-year study, we measured chickadee flock movements in forests at 0–300 m from boundaries in an agricultural landscape near Edmonton, Alberta, Canada. Even though flocks foraged in all forested parts of the study area, only six of the 53 flocks studied foraged further from forest boundaries than expected if they had used their home range irrespectively of the distance to boundaries. We found no evidence that the association of chickadee flocks to forest boundaries resulted from vegetation changes near boundaries, or to changes in their foraging sites and foraging success near boundaries. However, chickadee flocks moved parallel to boundaries (<75 m away) twice as frequently as expected from random movement, thus suggesting that forest boundaries act as movement conduits. Even when birds do not apparently seek special features near forest boundaries, they may be closely associated with them, simply because their passive movements are constrained by habitat barriers defined by boundaries.     

Cellular responses to enteropathogenicEscherichia coli infection

EnteropathogenicEscherichia coli (EPEC), first described in the 1940's and 1950's, remain an important cause of severe infantile diarrhoea in many parts of the developing world. EPEC do not produce enterotoxins and are not invasive; instead their virulence depends upon exploitation of host cell signalling pathways and the host cell cytoskeleton both as a means of colonizing mucosal surfaces of the small intestine and causing diarrhoea. Following initial mucosal attachment, EPEC secrete signalling proteins and expresss a surface adhesin, intimin, to produce attaching & effacing lesions in the enterocyte brush border membrane characterised by localised destruction of brush border microvilli, intimate bacterial adhesion and cytoskeletal reorganisation and accretion beneath attached bacteria. The pathophysiology of EPEC diarrhoea is also complex and probably results from a combination of epithelial cell responses including both electrolyte secretion and structural damage.     

Cellular responses to extracellular guidance cues

Extracellular guidance cues have a key role in orchestrating cell behaviour. They can take many forms, including soluble and cell‐bound ligands (proteins, lipids, peptides or small molecules) and insoluble matrix substrates, but to act as guidance cues, they must be presented to the cell in a spatially restricted manner. Cells that recognize such cues respond by activating intracellular signal transduction pathways in a spatially restricted manner and convert the extracellular information into intracellular polarity. Although extracellular cues influence a broad range of cell polarity decisions, such as mitotic spindle orientation during asymmetric cell division, or the establishment of apical–basal polarity in epithelia, this review will focus specifically on guidance cues that promote cell migration (chemotaxis), or localized cell shape changes (chemotropism).     

Cellular responses to extreme water loss: The water-replacement hypothesis

The previously advanced hypothesis that desiccation resistance involves the replacement of water adjacent to intracellular surfaces with polyhydroxy compounds has been supported by experiments on cysts of the brine shrimp, Artemia, and in a model system of albumin-glycerol-water, using nuclear magnetic resonance spectroscopy, microwave dielectrics, and density measurements. We have also considered other problems that cells face when large fractions of their total water content are removed. Observations by other investigators have indicated that a variety of mammalian cells can lose roughly 50% of their water and survive; for a given cell type death occurs if its volume is reduced below a certain minimum level. Membrane damage has previously been suggested to be a major cause of dehydration damage. We have proposed some additional plausible mechanisms that might also be involved.     

Cellular and tissue responses to heavy ions: Basic considerations

Summary Responses of the S/S variant of the L5178Y murine leukemic lymphoblast, the photoreceptor cell of the rabbit retina and the lenticular epithelium of the rabbit to heavy ions (²⁰Ne,²⁸Si,⁴⁰Ar and⁵⁶Fe) are described and discussed primarily from the standpoint of the need for a comprehensive theory of cellular radiosensitivity from which a general theory of tissue radiosensitivity can be constructed.The radiation responses of the very radiosensitive, repair-deficient S/S variant during the G₁- and early S phases of the cell cycle were found to be unlike those of normally radioresistant cells in culture: the relative biological effectiveness (RBE) did not increase with the linear energy transfer (LET) of the incident radiation. Such behavior could be anticipated for a cell which is lacking the repair system that operates in other (normal) cells when they are exposed to ionizing radiations in the G₁ phase of the cell cycle. The S/S variant does exhibit a peak of radioresistance to X-photons mid-G₁ + 8 h into the cell cycle, however, and as the LET was increased, the repair capacity responsible for that radioresistance was reduced progressively.Sensory cells (photoreceptors) in the retina of the New Zealand white (NZW) rabbit are very radioresistant to ionizing radiations, and several years elapsed after localized exposure (e.g., 5–10 Gy) to heavy ions (²⁰Ne,⁴⁰Ar) before photoreceptor cells were lost from the retina. During the first few weeks after such irradiations, damage to DNA in the photoreceptor cells was repaired to a point where it could not be demonstrated by reorienting gradient sedimentation under alkaline conditions, a technique that can detect DNA damage produced by <0.1 Gy of X-photons. Restitution of DNA structure was not permanent, however, and months or years later, butbefore loss of photoreceptor cells from the retina could be detected, progressive deterioration of the DNA structure began.     

Computational approaches to study protein unfolding: Hen egg white lysozyme as a case study

Four methods are compared to drive the unfolding of a protein: (1) high temperature (T-run), (2) high pressure (P-run), (3) by imposing a gradual increase in the mean radius of the protein using a penalty function added to the physical interaction function (F-run, radial force driven unfolding), and (4) by weak coupling of the difference between the temperature of the radially outward moving atoms and the radially inward moving atoms to an external temperature bath (K-run, kinetic energy driven unfolding). The characteristic features of the four unfolding pathways are analyzed in order to detect distortions due to the size or the type of the applied perturbation, as well as the features that are common to all of them. Hen egg white lysozyme is used as a test system. The simulations are analyzed and compared to experimental data like ¹H-NMR amide proton exchange-folding competition, heat capacity, and compressibility measurements. © 1995 Wiley-Liss, Inc.     

Temperature-body size responses in insects: a case study of British Odonata

1. Body size is highly correlated with physiological traits, fitness, and trophic interactions. These traits are subject to change if there are widespread reductions of body size with warming temperatures, which is suggested as one of the ‘universal’ ecological responses to climate change. However, general patterns of body size response to temperature in insects have not yet emerged. 2. To address this knowledge gap, we paired the wing length (as a proxy for body size) of 5331 museum specimens of 14 species of British Odonata with historical temperature data. Three sets of analyses were performed: (i) a regression analysis to test for a relationship between wing length and mean seasonal temperature within species and subsequent comparisons across species and suborders; (ii) an investigation of whether the body size of species has an effect on sensitivity to warming temperature; and (iii) a linear-mixed effects model to investigate factors that potentially affect temperature–size response. 3. The regression analysis indicated that wing length is negatively correlated with mean seasonal temperatures for Zygoptera, whereas Anisoptera showed no significant correlation with temperature. 4. There is a significant decline in wing length of all Zygoptera (but not Anisoptera) with collection date, suggesting that individuals emerging later in the season are smaller. 5. Life-cycle type was not important for predicting wing length–temperature responses, whereas sex, species, and suborder were indicated as important factors affecting the magnitude of temperature–size responses in Odonata. 6. Overall, wing lengths of Zygoptera are more sensitive to temperature and collection date than Anisoptera.     

Plant responses to extracellular nucleotides: Cellular processes and biological effects

Higher plants exhibit cellular responsiveness to the exogenous application of purine nucleotides in a manner consistent with a cell–cell signaling function for these molecules. Like animals, plants respond to extracellular ATP, ADP, and stable analogues (e.g., ATPγS and ADPβS) by increasing the cytoplasmic concentration of calcium. Agonist substrate specificity and concentration dependency suggest receptor mediation of these events, and, although the identity of the plant receptor is currently unknown, pharmacological analysis points to the involvement of a plasma membrane-localized calcium channel. Extracellular ATP can also induce the production of reactive oxygen species and stimulate an increase in the mRNA levels of a number of stress- and calcium-regulated genes, suggesting a role for nucleotide-based signaling in plant wound and defense responses. Furthermore, the growth and development of plants can also be altered by the application of external ATP. Recent studies are only beginning to uncover the complexities of plant signaling networks activated in response to extracellular ATP and how these might interact to affect plant physiological processes.     

Proteomics and systems biology to tackle biological complexity: Yeast as a case study

In this note we discuss how, by using budding yeast as model organism (as has been done in the past for biochemical, genetics and genomic studies), the integration of "omics" sciences and more specifically of proteomics with systems biology offers a very profitable approach to elucidating regulatory circuits of complex biological functions.     

Managing ski resorts to improve biodiversity conservation: Australian reptiles as a case study

Alpine/subalpine environments are diverse systems that support many endemic species. Worldwide, these ecosystems are under threat from ski resort disturbances – even in areas broadly designated for biodiversity conservation. The effects of ski resorts on reptiles are largely unknown, making it difficult to implement effective conservation actions. Many ski resorts do not currently address the needs of reptiles, even those listed as threatened, in their management plans. If reptiles are to continue inhabiting ski resorts in Australia, strategies must be implemented that target their conservation. To begin to address this problem, we summarise current research investigating the effects of ski resorts on reptiles. Based on this information, we recommend strategies that will enhance the conservation of reptiles in areas affected by ski‐related disturbances. Suggested strategies include (i) restricting intensive disturbances to already highly modified areas of Australian ski resorts, (ii) avoiding disturbance of remaining native vegetation and structural complexity in ski resorts and (iii) re‐establishing structural complexity at highly modified sites through revegetation programmes, or through the cessation of mowing during peak reptile activity periods. While these strategies are designed to facilitate the persistence of reptiles in ski resorts, their long‐term success can only be evaluated by monitoring their effectiveness.     

Cellular responses to postsegregational killing by restriction-modification genes

Plasmids that carry one of several type II restriction modification gene complexes are known to show increased stability. The underlying mechanism was proposed to be the lethal attack by restriction enzyme at chromosomal recognition sites in cells that had lost the restriction modification gene complex. In order to examine bacterial responses to this postsegregational cell killing, we analyzed the cellular processes following loss of the EcoRI restriction modification gene complex carried by a temperature-sensitive plasmid in an Escherichia coli strain that is wild type with respect to DNA repair. A shift to the nonpermissive temperature blocked plasmid replication, reduced the increase in viable cell counts and resulted in loss of cell viability. Many cells formed long filaments, some of which were multinucleated and others anucleated. In a mutant defective in RecBCD exonuclease/recombinase, these cell death symptoms were more severe and cleaved chromosomes accumulated. Growth inhibition was also more severe in recA, ruvAB, ruvC, recG, and recN mutants. The cells induced the SOS response in a RecBC-dependent manner. These observations strongly suggest that bacterial cells die as a result of chromosome cleavage after loss of a restriction modification gene complex and that the bacterial RecBCD/RecA machinery helps the cells to survive, at least to some extent, by repairing the cleaved chromosomes. These and previous results have led us to hypothesize that the RecBCD/Chi/RecA system serves to destroy restricted "nonself" DNA and repair restricted "self" DNA.     

Testing the island rule: primates as a case study

The island rule states that after island colonization, larger animals tend to evolve reduced body sizes and smaller animals increased sizes. Recently, there has been disagreement about how often, if ever, this rule applies in nature, and much of this disagreement stems from differences in the statistical tests employed. This study shows, how different tests of the island rule assume different null hypotheses, and that these rely on quite different biological assumptions. Analysis and simulation are then used to quantify the biases in the tests. Many widely used tests are shown to yield false support for the island rule when island and mainland evolution are indistinguishable, and so a Monte Carlo permutation test is introduced that avoids this problem. It is further shown that tests based on independent contrasts lack power to detect the island rule under certain conditions. Finally, a complete reanalysis is presented of recent data from primates. When head-body length is used as the measure of body size, reports of the island rule are shown to stem from methodological artefacts. But when skull length or body mass are used, all tests agree that the island rule does hold in primates.     

Cellular responses to endoplasmic reticulum stress and apoptosis

The endoplasmic reticulum (ER) is the cell organelle where secretory and membrane proteins are synthesized and folded. Correctly folded proteins exit the ER and are transported to the Golgi and other destinations within the cell, but proteins that fail to fold properly—misfolded proteins—are retained in the ER and their accumulation may constitute a form of stress to the cell—ER stress. Several signaling pathways, collectively known as unfolded protein response (UPR), have evolved to detect the accumulation of misfolded proteins in the ER and activate a cellular response that attempts to maintain homeostasis and a normal flux of proteins in the ER. In certain severe situations of ER stress, however, the protective mechanisms activated by the UPR are not sufficient to restore normal ER function and cells die by apoptosis. Most research on the UPR used yeast or mammalian model systems and only recently Drosophila has emerged as a system to study the molecular and cellular mechanisms of the UPR. Here, we review recent advances in Drosophila UPR research, in the broad context of mammalian and yeast literature.