Time scales of memory, learning, and plasticity

After only about 10 days would the storage capacity of our nervous system be reached if we stored every bit of input. The nervous system relies on at least two mechanisms that counteract this capacity limit: compression and forgetting. But the latter mechanism needs to know how long an entity should be stored: some memories are relevant only for the next few minutes, some are important even after the passage of several years. Psychology and physiology have found and described many different memory mechanisms, and these mechanisms indeed use different time scales. In this prospect we review these mechanisms with respect to their time scale and propose relations between mechanisms in learning and memory and their underlying physiological basis.     

Prey patchiness, predator survival and fish recruitment

A simple mathematical model is presented for the population dynamics of fish larvae when the main food supply, in this case copepods, is spatially patchy in its distribution. Encounters by an individual predator (larva) with prey patches, and with individual prey within patches, are represented by Poisson processes. It is demonstrated analytically, and confirmed by numerical experiments, that prey patchiness fails to alter mean predator-prey encounter rates from their values for homogeneous prey distributions. Individual variance in encounter rate is, however, much affected. This has significant consequences for the (small) numbers of larvae surviving to metamorphosis and recruitment to the adult fish population.     

Carrion fly community dynamics: patchiness, seasonality and coexistence

ABSTRACT. 1. An outdoor cage experiment was conducted to test the theory that localized interactions facilitate coexistence of species breeding in ephemeral habitats. The same amount of larval resource (50 g of liver) but divided into one, two, four, eight or sixteen pieces was placed into each of fifteen cages once a week from June to September for 4 years.
2. The cage populations were initially mixtures of thirteen species but after 4 years only Lucilia illustris (Meig.), Sarcophaga scoparia Pand. and S.aratrix Pand. remained. Lucilia illustris , by far the most abundant species in the field, predominated in every cage.
3. Sarcophaga went extinct in most cages, but they survived in five cages in which the larval resource was much divided, in agreement with the theoretical prediction.
4. Lucilia silvarum (Meig.) emerged about a week later than L.illustris in early summer; this phenological difference gave rise to a competitive asymmetry between the two species. This difference appears to explain why L.silvarum went extinct in the cages in 3 years, and it may explain why L.silvarum has consistently been less abundant than L.illustris in the natural community.
5. Other differences in phenology, voltinism and rate of development in the flies are described, and such differences are suggested to facilitate regional coexistence of many species in seasonal environments.     

Stomatal patchiness and task-performing networks

BACKGROUND: Patchy stomatal conductance is a poorly understood and little-studied phenomenon. It is relatively common, yet it appears to be detrimental to water-use efficiency under some conditions and has no immediately obvious physiological function of any kind. Much of the difficulty in studying patchy stomatal conductance is tied to its unpredictability, both in occurrence and in characteristics. SCOPE AND CONCLUSIONS: Statistical analyses of the variability of stomatal patchiness reveal remarkable similarities to structures and behaviours found in locally connected networks of dynamic units that perform tasks. Such systems solve problems that reside at the level of the entire network despite the absence of a central processor or a mechanism for directly sharing information over the entire system. Frequently, task performance is emergent, in the sense that no unit independently performs the task. Because each unit in the network can communicate with only its immediate neighbours, problem solving is accomplished by the states of the individual units self-organizing into synchronized, collective patterns. In some cases, patches of states form and move coherently over the network, thus providing a means for distantly separated parts of the network to communicate. Often, exactly what form these patches take and how they move as the units synchronize is highly unpredictable. In analogy with such networks, it is suggested that stomatal patchiness may be a signature that plants optimize gas exchange in a more sophisticated and adaptive manner than if performed by their individual stomata independently.     

The price of patchiness

Patchy distribution of animals, on a large or small scale, is a common phenomenon. Various explanations have been given for this spatial and temporal heterogeneity, but in many cases the causes are obscure. Patchy distribution of zooplankton is not understood and was not even expected in the fast turbulent currents of the well mixed tidal channels of the Wadden Sea. This patchiness is shown here for a number of plankton species. Methods commonly used for monitoring plankton usually neglect the fact of patchy distribution, and thus results suffer. Interpretation of such data can be highly misleading, particularly when used to assess the environmental status of an area: an overestimate or underestimate of population density may be the result. Sound quantitative data can only be obtained by making great efforts in terms of work and money. The costs entailed by such studies must be valued accordingly. Presented at the VI International Wadden Sea Symposium (Biologische Anstalt Helgoland, Wattenmeerstation Sylt, D-2282 List, FRG, 1–4 November 1988)     

Time and length scales of autocrine signals in three dimensions

A model of autocrine signaling in cultures of suspended cells is developed on the basis of the effective medium approximation. The fraction of autocrine ligands, the mean and distribution of distances traveled by paracrine ligands before binding, as well as the mean and distribution of the ligand lifetime are derived. Interferon signaling by dendritic immune cells is considered as an illustration.     

Trade-offs between and within scales: environmental persistence and within-host fitness of avian influenza viruses

Trade-offs between different components of a pathogen''s replication and transmission cycle are thought to be common. A number of studies have identified trade-offs that emerge across scales, reflecting the tension between strategies that optimize within-host proliferation and large-scale population spread. Most of these studies are theoretical in nature, with direct experimental tests of such cross-scale trade-offs still rare. Here, we report an analysis of avian influenza A viruses across scales, focusing on the phenotype of temperature-dependent viral persistence. Taking advantage of a unique dataset that reports both environmental virus decay rates and strain-specific viral kinetics from duck challenge experiments, we show that the temperature-dependent environmental decay rate of a strain does not impact within-host virus load. Hence, for this phenotype, the scales of within-host infection dynamics and between-host environmental persistence do not seem to interact: viral fitness may be optimized on each scale without cross-scale trade-offs. Instead, we confirm the existence of a temperature-dependent persistence trade-off on a single scale, with some strains favouring environmental persistence in water at low temperatures while others reduce sensitivity to increasing temperatures. We show that this temperature-dependent trade-off is a robust phenomenon and does not depend on the details of data analysis. Our findings suggest that viruses might employ different environmental persistence strategies, which facilitates the coexistence of diverse strains in ecological niches. We conclude that a better understanding of the transmission and evolutionary dynamics of influenza A viruses probably requires empirical information regarding both within-host dynamics and environmental traits, integrated within a combined ecological and within-host framework.     

Time scales and mechanisms of estuarine variability,a synthesis from studies of San Francisco Bay

This review of the preceding papers suggests that temporal variability in San Francisco Bay can be characterized by four time scales (hours, days-weeks, months, years) and associated with at least four mechanisms (variations in freshwater inflow, tides, wind, and exchange with coastal waters). The best understood component of temporal variability is the annual cycle, which is most obviously influenced by seasonal variations in freshwater inflow. The winter season of high river discharge is characterized by: large-scale redistribution of the salinity field (e.g. the upper estuary becomes a riverine system); enhanced density stratification and gravitational circulation with shortened residence times in the bay; decreased tissue concentrations of some contaminants (e.g. copper) in resident bivalves; increased estuarine inputs of river-borne materials such as dissolved inorganic nutrients (N, P, Si), suspended sediments, and humic materials; radical redistributions of pelagic organisms such as copepods and fish; low phutoplankton biomass and primary productivity in the upper estuary; and elimination of freshwater-intolerant species of macroalgae and benthic infauna from the upper estuary. Other mechanisms modulate this river-driven annual cycle: (1) wind speed is highly seasonal (strongest in summer) and causes seasonal variations in atmosphere-water column exchange of dissolved gases, resuspension, and the texture of surficial sediments; (2) seasonal variations in the coastal ocean (e.g. the spring-summer upwelling season) influence species composition of plankton and nutrient concentrations that are advected into the bay; and (3) the annual temperature cycle influences a few selected features (e.g. production and hatching of copepod resting eggs). Much of the interannual variability in San Francisco Bay is also correlated with freshwater inflow: wet years with persistently high river discharge are characterized by persistent winter-type conditions.Mechanisms of short-term variability are not as well understood, although some responses to storm events (pulses in residual currents from wind forcing, erosion of surficial sediments by wind waves, redistribution of fish populations) and the neap-spring tidal cycle (enhanced salinity stratification, gravitational circulation, and phytoplankton biomass during neap tides) have been quantified. In addition to these somewhat predictable features of variability are (1) largely unexplained episodic events (e.g. anomalous blooms of drift macroalgae), and (2) long-term trends directly attributable to human activities (e.g. introduction of exotic species that become permanent members of the biota).     

Facilitation, competition, and vegetation patchiness: from scale free distribution to patterns

A new technique for the modeling of perennial vegetation patchiness in the arid/semiarid climatic zone is suggested. Incorporating the stochasticity that affects life history of seedlings and the deterministic dynamics of soil moisture and biomass, this model is flexible enough to yield qualitatively different forms of spatial organization. In the facilitation-dominated regime, scale free distribution of patch sizes is observed, in correspondence with recent field studies. In the competition controlled case, on the other hand, power-law statistics is valid up to a cutoff, and an intrinsic length scale appears.     

Universal multifractals and ocean patchiness: phytoplankton, physical fields and coastal heterogeneity

We argue that a wide-range scaling approach is demanded by standardStommel diagrams and that it can unify the treatment of phytoplanktonvariability over wide ranges of scales. By investigating theeffects of coastal heterogeneity on the variability of in situsalinity (S), oxygen (     

Time scales of change in the San Francisco Bay benthos

Results from multi-year investigations in the San Francisco Bay estuary show that large abundance fluctuations within benthic macroinvertebrate populations reflect both (1) within-year periodicity of reproduction, recruitment, and mortality that is not necessarily coincident with seasonal changes of the environment (e.g., the annual temperature cycle), and (2) aperiodic density changes (often larger than within-year fluctuations) following random perturbations of the environment.Density peaks of the small, short-lived estuarine invertebrates that comprise the vast majority of individuals in the bay's relatively homogeneous benthic community normally occur between spring and autumn depending on the species, in large part a reflection of reproductive periodicity. However, because mild winters permit reproductive activity in some of the common species throughout much of the year, other factors are important to within-year density fluctuations in the community. Seasonally predictable changes in freshwater inflow, wind and tidal mixing, microalgal biomass, and sediment erosion/deposition patterns all contribute to observed seasonal changes in abundance. For example, the commonly observed decline in abundance during winter reflects both short-lived species that die after reproducing and the stress of winter conditions (e.g., inundation by less saline, sediment-laden water and the decline in both planktonic and benthic algal biomass — a direct source of food for the shallow-water benthos). On the other hand, data from several studies suggest that observed recruitment and mortality may in fact be the migration of juveniles and adults to and from study sites. For example, the common amphipod Ampelisca abdita apparently moves from shallow to deep water, or from up-estuary to down-estuary locations, coincident with periods of high river runoff in winter. Growth of individuals within the few studied species populations is also highly seasonal, and appears to be coincident with seasonal increases in the abundance of planktonic and/or benthic microalgae.Two multi-year studies have shown that, in addition to within-year periodicity, major restructuring of the benthic community can occur as a result of anomalous (usually climate-related) perturbations of the benthic habitat. For example, during wet years freshwater-intolerant species disappear from the upper part of the estuary and from shallow areas of the bay. During a two-year drought these same species colonized the extreme upper end of the estuary in large numbers. Other aperiodic perturbations include localized instances of sediment erosion or deposition and algal mat accumulations that greatly depress abundance. Additionally, there is evidence (observations that the clam Macoma balthica establishes large populations only when the amphipod A. abdita is not abundant) that species interactions can contribute greatly to interannual variations. Thus, while community composition may change little over the long term, year-to-year predictability of species abundances is low.     

Time scales of circulation and mixing processes of San Francisco Bay waters

Conceptual models for tidal period and low-frequency variations in sea level, currents, and mixing processes in the northern and southern reaches of San Francisco Bay describe the contrasting characteristics and dissimilar processes and rates in these embayments: The northern reach is a partially mixed estuary whereas the southern reach (South Bay) is a tidally oscillating lagoon with density-driven exchanges with the northern reach.The mixed semidiurnal tides are mixtures of progressive and standing waves. The relatively simple oscillations in South Bay are nearly standing waves, with energy propagating down the channels and dispersing into the broad shoal areas. The tides of the northern reach have the general properties of a progressive wave but are altered at the constriction of the embayments and gradually change in an upstream direction to a mixture of progressive and standing waves. The spring and neap variations of the tides are pronounced and cause fortnightly varying tidal currents that affect mixing and salinity stratification in the water column.Wind stress on the water surface, freshwater inflow, and tidal currents interacting with the complex bay configuration are the major local forcing mechanisms creating low-frequency variations in sea level and currents. These local forcing mechanisms drive the residual flows which, with tidal diffusion, control the water-replacement rates in the estuary. In the northern reach, the longitudinal density gradient drives an estuarine circulation in the channels, and the spatial variation in tidal amplitude creates a tidally-driven residual circulation. In contrast, South Bay exhibits a balance between wind-driven circulation and tidally-driven residual circulation for most of the year. During winter, however, there can be sufficient density variations to drive multilayer (2 to 3) flows in the channel of South Bay.Mixing models (that include both diffusive and dispersive processes) are based on time scales associated with salt variations at the boundaries and those associated with the local forcing mechanisms, while the spatial scales of variations are dependent upon the configuration of the embayments. In the northern reach, where the estuarine circulation is strong, the salt flux is carried by the mean advection of the mean salt field. Where large salinity gradients are present, the tidal correlation part of the salt flux is of the same order as the advective part. Our knowledge of mixing and exchange rates in South Bay is poor. As this embayment is nearly isohaline, the salt flux is dominated entirely by the mean advection of the mean salt field. During and after peaks in river discharge, water mixing becomes more dynamic, with a strong density-driven current creating a net exchange of both water mass and salt. These exchanges are stronger during neap tides.Residence times of the water masses vary seasonally and differ between reaches. In the northern reach, residence times are on the order of days for high winter river discharge and of months for summer periods. The residence times for South Bay are fairly long (on the order of several months) during summer, and typically shorter (less than a month) during winter when density-driven exchanges occur.     

A simple model for plankton patchiness

Recent work on zooplankton spatial variability shows that thepower spectrum of the wave-number variance is flatter than thatfor chlorophyll, as a consequence of greater fine structurein the herbivores. The relative slopes of the power spectracan result from white noise forcing of simple coupled phytoplankton-herbivoremodels with diffusion.     

Stomatal patchiness in Mediterranean evergreen sclerophylls

Midday depression of net photosynthesis and transpiration in the Mediterranean sclerophylls Arbutus unedo L. and Quercus suber L. occurs with a depression of mesophyll photosynthetic activity as indicated by calculated carboxylation efficiency (CE) and constant diurnal calculated leaf intercellular partial pressure of CO₂ (C_i). This work examines the hypothesis that this midday depression can be explained by the distribution of patches of either wide-open or closed stomata on the leaf surface, independent of a coupling mechanism between stomata and mesophyll that results in a midday depression of photosynthetic activity of the mesophyll. Pressure infiltration of four liquids differing in their surface tension was used as a method to show the occurrence of stomatal patchiness and to determine the status of stomatal aperture within the patches. Liquids were selected such that the threshold leaf conductance necessary for infiltration through the stomatal pores covered the expected diurnal range of calculated leaf conductance (g) for these species. Infiltration experiments were carried out with leaves of potted plants under simulated Mediterranean summer conditions in a growth chamber. For all four liquids, leaves of both species were found to be fully infiltratable in the morning and in the late afternoon while during the periods leading up to and away from midday the leaves showed a pronounced patchy distribution of infiltratable and non-infiltratable areas. Similar linear relationships between the amount of liquid infiltrated and g (measured by porometry prior to detachment and infiltration) for all liquids clearly revealed the existence of pneumatically isolated patches containing only wide-open or closed stomata. The good correspondence between the midday depression of CE, calculated under the assumption of no stomatal patchiness, and the diurnal changes in non-infiltratable leaf area strongly indicates that the apparent reduction in mesophyll activity results from assuming no stomatal patchiness. It is suggested that simultaneous responses of stomata and mesophyll activity reported for other species may also be attributed to the occurrence of stomatal patchiness. In Quercus coccifera L., where the lack of constant diurnal calculated C_i and major depression of measured CE at noontime indicates different stomatal behavior, non-linear and dissimilar relationships between g and the infiltratable quantities of the four liquids were found. This indicates a wide distribution of stomatal aperture on the leaf surface rather than only wide-open or closed stomata.Dedicated to Professor Otto L. Lange on the occasion of his 65th birthday     

Phylogenetic distribution of large-scale genome patchiness

Background  

The phylogenetic distribution of large-scale genome structure (i.e. mosaic compositional patchiness) has been explored mainly by analytical ultracentrifugation of bulk DNA. However, with the availability of large, good-quality chromosome sequences, and the recently developed computational methods to directly analyze patchiness on the genome sequence, an evolutionary comparative analysis can be carried out at the sequence level.     

Vesicle trafficking and cell surface membrane patchiness.

Membrane proteins and lipids often appear to be distributed in patches on the cell surface. These patches are often assumed to be membrane domains, arising from specific molecular associations. However, a computer simulation (Gheber and Edidin, 1999) shows that membrane patchiness may result from a combination of vesicle trafficking and dynamic barriers to lateral mobility. The simulation predicts that the steady-state patches of proteins and lipids seen on the cell surface will decay if vesicle trafficking is inhibited. To test this prediction, we compared the apparent sizes and intensities of patches of class I HLA molecules, integral membrane proteins, before and after inhibiting endocytic vesicle traffic from the cell surface, either by incubation in hypertonic medium or by expression of a dominant-negative mutant dynamin. As predicted by the simulation, the apparent sizes of HLA patches increased, whereas their intensities decreased after endocytosis and vesicle trafficking were inhibited.     

Measles virus, immune control, and persistence

Measles remains one of the most important causes of child morbidity and mortality worldwide with the greatest burden in the youngest children. Most acute measles deaths are owing to secondary infections that result from a poorly understood measles-induced suppression of immune responses. Young children are also vulnerable to late development of subacute sclerosing panencephalitis, a progressive, uniformly fatal neurologic disease caused by persistent measles virus (MeV) infection. During acute infection, the rash marks the appearance of the adaptive immune response and CD8(+) T cell-mediated clearance of infectious virus. However, after clearance of infectious virus, MeV RNA persists and can be detected in blood, respiratory secretions, urine, and lymphoid tissue for many weeks to months. This prolonged period of virus clearance may help to explain measles immunosuppression and the development of lifelong immunity to re-infection, as well as occasional infection of the nervous system. Once MeV infects neurons, the virus can spread trans-synaptically and the envelope proteins needed to form infectious virus are unnecessary, accumulate mutations, and can establish persistent infection. Identification of the immune mechanisms required for the clearance of MeV RNA from multiple sites will enlighten our understanding of the development of disease owing to persistent infection.