Primate population dynamics: variation in abundance over space and time

The rapid disappearance of tropical forests, the potential impacts of climate change, and the increasing threats of bushmeat hunting to wildlife, makes it imperative that we understand wildlife population dynamics. With long-lived animals this requires extensive, long-term data, but such data is often lacking. Here we present longitudinal data documenting changes in primate abundance over 45 years at eight sites in Kibale National Park, Uganda. Complex patterns of change in primate abundance were dependent on site, sampling year, and species, but all species, except blue monkeys, colonized regenerating forest, indicating that park-wide populations are increasing. At two paired sites, we found that while the primate populations in the regenerating forests had increased from nothing to a substantial size, there was little evidence of a decline in the source populations in old-growth forest, with the possible exception of mangabeys at one of the paired sites. Censuses conducted in logged forest since 1970 demonstrated that for all species, except black-and-white colobus, the encounter rate was higher in the old-growth and lightly-logged forest than in heavily-logged forest. Black-and-white colobus generally showed the opposite trend and were most common in the heavily-logged forest in all but the first year of monitoring after logging, when they were most common in the lightly-logged forest. Overall, except for blue monkey populations which are declining, primate populations in Kibale National Park are growing; in fact the endangered red colobus populations have an annual growth rate of 3%. These finding present a positive conservation message and indicate that the Uganda Wildlife Authority is being effective in managing its biodiversity; however, with constant poaching pressure and changes such as the exponential growth of elephant populations that could cause forest degradation, continued monitoring and modification of conservation plans are needed.     

Niche dynamics in space and time

Niche conservatism, the tendency of a species niche to remain unchanged over time, is often assumed when discussing, explaining or predicting biogeographical patterns. Unfortunately, there has been no basis for predicting niche dynamics over relevant timescales, from tens to a few hundreds of years. The recent application of species distribution models (SDMs) and phylogenetic methods to analysis of niche characteristics has provided insight to niche dynamics. Niche shifts and conservatism have both occurred within the last 100 years, with recent speciation events, and deep within clades of species. There is increasing evidence that coordinated application of these methods can help to identify species which likely fulfill one key assumption in the predictive application of SDMs: an unchanging niche. This will improve confidence in SDM-based predictions of the impacts of climate change and species invasions on species distributions and biodiversity.     

Cell-signalling dynamics in time and space

The specificity of cellular responses to receptor stimulation is encoded by the spatial and temporal dynamics of downstream signalling networks. Temporal dynamics are coupled to spatial gradients of signalling activities, which guide pivotal intracellular processes and tightly regulate signal propagation across a cell. Computational models provide insights into the complex relationships between the stimuli and the cellular responses, and reveal the mechanisms that are responsible for signal amplification, noise reduction and generation of discontinuous bistable dynamics or oscillations.     

Vegetation dynamics: patterns in time and space

This paper introduces the collection of contributions in this special volume on temporal and spatial patterns of vegetation dynamics. First, it is pointed out that the dynamics of any piece of vegetation, large or small, is always dependent on the degree of isolation of that piece towards its environment. Then ten types of island situation are treated ranging from very much to very little isolated: remote species-rich oceanic islands, remote species-poor islands, young big islands near a continent, small off-shore islands, emerging islands, isolated hills, landscape islands, isolated patches of vegetation, and gaps in stands of vegetation.Also, eight forms of vegetation dynamics are treated, ranging from short-term to long-term changes and involving larger and larger units: individuals, patches, communities, landscapes and vegetation regions. The forms of dynamics are fluctuation, gap dynamics, patch dynamics, cyclic succession, regeneration succession, secondary succession, primary succession, and secular succession. Each form of dynamics may occur under varying degrees of isolation.The general conclusion is that processes and patterns of vegetation dynamics cannot be generalized in any simple manner. The 20 papers collected in this volume, divergent as they are, express the complexity of vegetation dynamics.     

Control over DNA replication in time and space

DNA replication is precisely regulated in time and space, thereby safeguarding genomic integrity. In eukaryotes, replication initiates from multiple sites along the genome, termed origins of replication, and propagates bidirectionally. Dynamic origin bound complexes dictate where and when replication should initiate. During late mitosis and G1 phase, putative origins are recognized and become "licensed" through the assembly of pre-replicative complexes (pre-RCs) that include the MCM2-7 helicases. Subsequently, at the G1/S phase transition, a fraction of pre-RCs are activated giving rise to the establishment of replication forks. Origin location is influenced by chromatin and nuclear organization and origin selection exhibits stochastic features. The regulatory mechanisms that govern these cell cycle events rely on the periodic fluctuation of cyclin dependent kinase (CDK) activity through the cell cycle.     

Regulating the dynamics of EGF receptor signaling in space and time

The epidermal growth factor receptor (EGFR) signaling cascade represents one of the cardinal pathways that transmits information between cells during development in a broad range of multicellular organisms. Most of the elements that constitute the core EGFR signaling module, as well as a variety of negative and positive modulators, have been identified. Although this molecular pathway is utilized multiple times during development, the spatial and temporal features of its signaling can be modified to fit a particular developmental setting. Recent work has unraveled the various mechanisms by which the EGFR pathway can be modulated.     

Cellular changes in early development of regenerating thin cell layer-explants of rapeseed analyzed by light and electron microscopy

Cellular changes in thin cell layer (TCL) explants of stem origin of Brassica napus L. cv. Vega were studied from 0 to 15 day by light and transmission electron microscopy. Apical and basal ends of the old explants were analysed separately. Quantitative and qualitative analyses showed that during the first culture day the parenchyma cells enlarged significantly as did the cytoplasm/vacuole ratio. The cytoplasm contained increased rough endoplasmic reticulum (RER), polysomes and dictyosomes associated with both coated and uncoated vesicles. The cell enlargement continued during the first 5 days of culture. The structural organization of the cell wall became somewhat loose and inhomogeneous. Parenchyma in the basal end divided frequently, resulting in several centres of division, while cell division in apical cells was less frequent and cells there remained enlarged. Starch accumulation started on the first day and increased until the third day. i. e. until cell divisions became more frequent. The starch content of dividing cells gradually decreased and starch was almost totally lacking in 15-day-old explants. Starch grains remained numerous, however, in the large non-dividing apical cells, except in those cells adjacent to the medium. Cell divisions started close to medium in explants containing vascular tissue, but closer to the epidermis in the explants without vascular tissue.
The results show how rapid (one day) striking changes in the cells take place and suggest that optimal hormone concentration and intertissue relations between epidermis and parenchyma and between parenchyma and vascular tissues as well as intercellular relations among parenchyma cells determine the first cell division sites and planes in the explants. Although the cells change from elongated to spheroid, their original polarity remains as evidenced by the formation of more numerous basal shoot primordia than in apical shoot primordia.     

High resolution scanning electron microscopy of the cell

The scanning electron microscope (SEM) has become a powerful tool for ultrastructural research with improvement of the instrument's resolution and progress in specimen preparation techniques. With regard to resolution, it has been improved step-by-step in this decade and, in 1985, an ultra-high resolution SEM (UHS-T1) was developed, with a resolution of 0.5 nm. Concerning specimen preparation, the osmium-DMSO-osmium method, which is effective for revealing intracellular structures, has come to be widely used. Techniques for observing smaller objects, such as bacteriophages, viruses, and biological macromolecules, have also been devised in recent years. As a result of these preparation techniques and the availability of the ultra-high resolution SEM, the application of SEM in biology is expanding rapidly. In this paper, an outline of the ultra-high resolution SEM, techniques for specimen preparation, findings of some biological materials by these techniques, and guidelines to making the specimens, are described.     

Determination of bacterial cell number and cell volume by means of flow cytometry, transmission electron microscopy, and epifluorescence microscopy

Comparative measurements of bacterial total counts and volumes of flow cytometry (FCM), transmission electron (TEM), and epifluorescence microscopy (EFM), were undertaken during a four week mesocosm experiment. Total counts of bacteria measured by TEM, EFM, and FCM were in the range of 1 · 10⁶−6 cells ml⁻¹, 1 · 10⁶−3 · 10¹⁶ cells ml⁻¹, and 5 · 10⁵ cells ml⁻¹ respectively. The mean volume of the bacterial community, measured by means of EFM and TEM, increased from 0.12–0.15 μm³ at the start of the experiment to 0.39–0.53 μm³ at the end. Generally, there was good agreement between the two methods and regression analyses gave r = 0.87 (p < < 0.01) for cell volume and r = 0.97 (p < < 0.01) for cell number. DAPI stained bacteria with volumes less than 0.2 μm³ were not detected by flow cytometry and these were generally an order of magnitude lower than counts made by TEM and EFM. For samples where the mean bacterial cell volume was longer than 0.3 μm³, all three methods were in agreement both with respect to counts and volume estimates.     

Species accumulation over space and time in European Plio-Holocene mammals

The rate of increase in species number with sampled area is one issue of major interest in ecology. Species number increases with sampled time as well, though this kind of analysis is much rarer in literature. Species-area and species-time relationships have been recently integrated in a single model, which allows studying how time and area interact with each other in determining the cumulative increase in species richness. Here we studied species-area, species-time, and species-time-area relationships in Plio-Holocene large mammals of Western Eurasia, by using an extensive database including 184 species distributed in 685 fossil sites. We found that the increase of species number with time is much higher than with area. When sampling inequality of fossil localities in time and space is accounted for, time and area interact with each other in a negative, though non-linear fashion. The intense climatic changes that characterized the Plio-Holocene period apparently affected both species-area and species-time relationships in large mammals, by increasing the slope of the former during the Pliocene and middle Pleistocene, and of the latter during younger, climatically harsher, late Pleistocene times. This study emphasizes the importance of accounting for time and space in tracing paleodiversity curves.     

Coordinating cell polarity with cell division in space and time

Decisions of when and where to divide are crucial for cell survival and fate, and for tissue organization and homeostasis. The temporal coordination of mitotic events during cell division is essential to ensure that each daughter cell receives one copy of the genome. The spatial coordination of these events is also crucial because the cytokinetic furrow must be aligned with the axis of chromosome segregation and, in asymmetrically dividing cells, the polarity axis. Several recent papers describe how cell shape and polarity are coordinated with cell division in single cells and tissues and begin to unravel the underlying molecular mechanisms, revealing common principles and molecular players. Here, we discuss how cells regulate the spatial and temporal coordination of cell polarity with cell division.     

Phosphoinositides: key players in cell signalling, in time and space

Over the last few years, many reports have extended our knowledge of the inositol lipid metabolism and brought out some exciting information about the location, the variety and the role of phosphoinositides (PIs). Besides the so-called "canonical PI pathway" leading to the production of phosphatidylinositol 4,5-bisphosphate (PtdIns(4,5)P2), the precursor of the intracellular second messengers inositol 1,4,5-trisphosphate and diacylglycerol (DAG), many other metabolic pathways have been identified to produce seven different polyphosphoinositides. Several of these quantitatively minor lipid molecules appear to be specifically involved in the control of cellular events, such as the spatial and temporal organisation of key signalling pathways, the rearrangement of the actin cytoskeleton or the intracellular vesicle trafficking. This is consistent with the fact that many of the enzymes, such as kinases and phosphatases, involved in the tight control of the intracellular level of polyphosphoinositides, are regulated and/or relocated through cell surface receptors for extracellular ligands. The remarkable feature of PIs, which can be rapidly synthesised and degraded in discrete membrane domains or even subnuclear structures, places them as ideal regulators and integrators of very dynamic mechanisms of cell regulation. In this review, we will summarise recent studies on the potential location, the metabolic pathways and the role of the different PIs. Some aspects of the temporal synthesis of D3 PIs will also be discussed.     

Signalling in space and time: systems dynamics of intracellular communication

The second edition of the EMBO Spatial meeting took place in May 2011 in Engelberg, Switzerland. Although the work presented at the meeting covered a challengingly broad range of topics, it accomplished the rare goal of promoting interactions between cell biologists, neuroscientists, systems biologists and mathematicians, all united by a common interest in understanding how cells integrate signals in space and time.     

Polymer manipulation and nanofabrication in real time using transmission electron microscopy

Here we present time-resolved in situ transmission electron microscopy (TEM) observations and real-time manipulation of nematic ordered cellulose and ultradrawn polyethylene films. Drawn films of these two polymers exhibited a unique response to the low-dose electron beam. Electron beam damage was minimal based on retention of an organized electron diffraction pattern. Increased electron dosage appeared to melt the polymer with subsequent movement and attraction toward preferred electron concentrations within the beam. This discovery allowed the preferential, directed manipulation of polymer chain aggregates in two dimensions. These findings provide a basis for a new technique to manipulate and simultaneously observe dynamic assembly at the molecular level of structures using TEM.     

Preservation of extracellular space during fixation of the brain for electron microscopy

Adult mammalian brain contains about 20% extracellular space, but fixatives cause the cellular processes to ingest the extracellular fluid, and the space is not preserved in electron micrographs prepared by any of the conventional methods. This distortion can be prevented by replacing part of the sodium chloride in the extracellular fluid by an impermeant solute such as sucrose. To do this, the blood-brain barrier can be opened by vascular perfusion at 300 mmHg pressure, or the barrier can be bypassed by immersion of thin slices of fresh brain in the impermeant solution. In either case, addition of aldehyde fixatives and conventional processing then leads to the preservation of extracellular space in electron micrographs. Both procedures are as easy to use for routine fixation as conventional methods. In well fixed tissue the cellular processes are different in size, shape and electron density from the inflated profiles seen after the ingestion of extracellular fluid that accompanies conventional fixation. Moreover, extracellular space is found to separate widely some cellular elements, while leaving others contiguous.     

Transmission electron microscopy, scanning tunneling microscopy, and atomic force microscopy of the cell envelope layers of the archaeobacterium Methanospirillum hungatei GP1.

Methanospirillum hungatei GP1 possesses paracrystalline cell envelope components including end plugs and a sheath formed from stacked hoops. Both negative-stain transmission electron microscopy (TEM) and scanning tunneling microscopy (STM) distinguished the 2.8-nm repeat on the outer surface of the sheath, while negative-stain TEM alone demonstrated this repeat around the outer circumference of individual hoops. Thin sections revealed a wave-like outer sheath surface, while STM showed the presence of deep grooves that precisely defined the hoop-to-hoop boundaries at the waveform nodes. Atomic force microscopy of sheath tubes containing entrapped end plugs emphasized the end plug structure, suggesting that the sheath was malleable enough to collapse over the end plugs and deform to mimic the shape of the underlying structure. High-resolution atomic force microscopy has revised the former idea of end plug structure so that we believe each plug consists of at least four discs, each of which is approximately 3.5 nm thick. PT shadow TEM and STM both demonstrated the 14-nm hexagonal, particulate surface of an end plug, and STM showed the constituent particles to be lobed structures with numerous smaller projections, presumably corresponding to the molecular folding of the particle.     

Population genetics of the aquatic fungus Tetracladium marchalianum over space and time

Aquatic hyphomycete fungi are fundamental mediators of energy flow and nutrient spiraling in rivers. These microscopic fungi are primarily dispersed in river currents, undergo substantial annual fluctuations in abundance, and reproduce either predominantly or exclusively asexually. These aspects of aquatic hyphomycete biology are expected to influence levels and distributions of genetic diversity over both spatial and temporal scales. In this study, we investigated the spatiotemporal distribution of genotypic diversity in the representative aquatic hyphomycete Tetracladium marchalianum. We sampled populations of this fungus from seven sites, three sites each in two rivers in Illinois, USA, and one site in a Wisconsin river, USA, and repeatedly sampled one population over two years to track population genetic parameters through two seasonal cycles. The resulting fungal isolates (N = 391) were genotyped at eight polymorphic microsatellite loci. In spite of seasonal reductions in the abundance of this species, genotypic diversity was consistently very high and allele frequencies remarkably stable over time. Likewise, genotypic diversity was very high at all sites. Genetic differentiation was only observed between the most distant rivers (∼450 km). Clear evidence that T. marchalianum reproduces sexually in nature was not observed. Additionally, we used phylogenetic analysis of partial β-tubulin gene sequences to confirm that the fungal isolates studied here represent a single species. These results suggest that populations of T. marchalianum may be very large and highly connected at local scales. We speculate that large population sizes and colonization of alternate substrates in both terrestrial and aquatic environments may effectively buffer the aquatic populations from in-stream population fluctuations and facilitate stability in allele frequencies over time. These data also suggest that overland dispersal is more important for structuring populations of T. marchalianum over geographic scales than expected.     

Phylogenetic analysis of community assembly and structure over space and time

Evolutionary ecologists are increasingly combining phylogenetic data with distributional and ecological data to assess how and why communities of species differ from random expectations for evolutionary and ecological relatedness. Of particular interest have been the roles of environmental filtering and competitive interactions, or alternatively neutral effects, in dictating community composition. Our goal is to place current research within a dynamic framework, specifically using recent phylogenetic studies from insular environments to provide an explicit spatial and temporal context. We compare communities over a range of evolutionary, ecological and geographic scales that differ in the extent to which speciation and adaptation contribute to community assembly and structure. This perspective allows insights into the processes that can generate community structure, as well as the evolutionary dynamics of community assembly.