Chaotic gene regulatory networks can be robust against mutations and noise

Robustness to mutations and noise has been shown to evolve through stabilizing selection for optimal phenotypes in model gene regulatory networks. The ability to evolve robust mutants is known to depend on the network architecture. How do the dynamical properties and state-space structures of networks with high and low robustness differ? Does selection operate on the global dynamical behavior of the networks? What kind of state-space structures are favored by selection? We provide damage propagation analysis and an extensive statistical analysis of state spaces of these model networks to show that the change in their dynamical properties due to stabilizing selection for optimal phenotypes is minor. Most notably, the networks that are most robust to both mutations and noise are highly chaotic. Certain properties of chaotic networks, such as being able to produce large attractor basins, can be useful for maintaining a stable gene-expression pattern. Our findings indicate that conventional measures of stability, such as damage propagation, do not provide much information about robustness to mutations or noise in model gene regulatory networks.     

Bayesian analysis of wildlife age-at-harvest data

SUMMARY: State and federal natural resource management agencies often collect age-structured harvest data. These data represent finite realizations of stochastic demographic and sampling processes and have long been used by biologists to infer population trends. However, different sources of data have been combined in ad hoc ways and these methods usually failed to incorporate sampling error. In this article, we propose a "hidden process" (or state-space) model for estimating abundance, survival, recovery rate, and recruitment from age-at-harvest data that incorporate both demographic and sampling stochasticity. To this end, a likelihood for age-at-harvest data is developed by embedding a population dynamics model within a model for the sampling process. Under this framework, the identification of abundance parameters can be achieved by conducting a joint analysis with an auxiliary data set. We illustrate this approach by conducting a Bayesian analysis of age-at-harvest and mark-recovery data from black bears (Ursus americanus) in Pennsylvania. Using a set of reasonable prior distributions, we demonstrate a substantial increase in precision when posterior summaries of abundance are compared to a bias-corrected Lincoln-Petersen estimator. Because demographic processes link consecutive abundance estimates, we also obtain a more realistic biological picture of annual changes in abundance. Because age-at-harvest data are often readily obtained, we argue that this type of analysis provides a valuable strategy for wildlife population monitoring.     

Herbaceous vegetation change in variable rangeland environments: The relative contribution of grazing and climatic variability

Abstract. A 44‐yr record of herbaceous vegetation change was analysed for three contrasting grazing regimes within a semi‐arid savanna to evaluate the relative contribution of confined livestock grazing and climatic variability as agents of vegetation change. Grazing intensity had a significant, directional effect on the relative composition of short‐ and mid‐grass response groups; their composition was significantly correlated with time since the grazing regimes were established. Interannual precipitation was not significantly correlated with response group composition. However, interannual precipitation was significantly correlated with total plant basal area while time since imposition of grazing regimes was not, but both interannual precipitation and time since the grazing regimes were established were significantly correlated with total plant density. Vegetation change was reversible even though the herbaceous community had been maintained in an altered state for ca. 60 yr by intensive livestock grazing. However, ca. 25 yr were required for the mid‐grass response group to recover following the elimination of grazing and recovery occurred intermittently. The increase in mid‐grass composition was associated with a significant decrease in total plant density and an increase in mean individual plant basal area. Therefore, we failed to reject the hypotheses based on the proportional change in relative response group composition with grazing intensity and the distinct effects of grazing and climatic variability on response group composition, total basal area and plant density. Long‐term vegetation change indicates that grazing intensity established the long‐term directional change in response group composition, but that episodic climate events defined the short‐term rate and trajectory of this change and determines the upper limit on total basal area. The occurrence of both directional and non‐directional vegetation responses were largely a function of (1) the unique responses of the various community attributes monitored and (2) the distinct temporal responses of these community attributes to grazing and climatic variation. This interpretation supports previous conclusions that individual ecosystems may exist in equilibrial and non‐equilibrial states at various temporal and spatial scales.     

A study of spatial variability of domoic acid in razor clams: recommendations for resource management on the Washington coast

Domoic acid (DA) levels in Washington State razor clams (Siliqua patula) have been extremely variable and unpredictable, resulting in emergency closures of harvest areas in 1991, 1998, and 1999. Information concerning toxin variability relative to sampling location is important in developing a more reliable plan for managing DA outbreaks. In November 1998, record levels of DA in razor clams (up to 295 ppm) were reported at Kalaloch beach, Washington. A razor clam resource survey conducted there during the summer of 1999, along with the long retention time of DA in the clams, permitted a study of DA levels as a function of tidal elevation and north-south beach location. During the summer low tides (28–31 July 1999) razor clams were collected from six east-west transects, approximately 1.6 km apart. Each clam was individually analyzed for DA to determine the distribution of toxin between (interspecific variability) and within (intraspecific variability) transects. While average DA levels were similar between transects, toxin levels varied substantially among individual clams. The coefficient of variation among all samples (n=445) was 122%, indicating that harvest closures based upon composite analyses of only six clams could be in error. Here we recommend a sampling strategy of razor clams for regulatory purposes that will result in DA measurements more representative of total population toxin values.     

Reversible coupling of individual phycobiliprotein isoforms during state transitions in the cyanobacterium Trichodesmium analysed by single-cell fluorescence kinetic measurements

In the non-heterocyst, marine cyanobacterium Trichodesmium nitrogen fixation is confined to the photoperiod and occurs coevally with oxygenic photosynthesis although nitrogenase is irreversibly inactivated by oxygen. In previous studies it was found that regulation of photosynthesis for nitrogen fixation involves Mehler reaction and various activity states with reversible coupling of photosynthetic components. We now investigated these activity states in more detail. Spectrally resolved fluorescence kinetic measurements of single cells revealed that they were related to alternate uncoupling and coupling of phycobilisomes from and to the photosystems, changing the effective cross-section of PSII. Therefore, we isolated and purified the phycobiliproteins of Trichodesmium via ion exchange chromatography and recorded their UV/VIS absorption, fluorescence excitation and fluorescence emission spectra. After describing these spectra by mathematical equations via the Gauss-Peak-Spectra method, we used them to deconvolute the in vivo fluorescence spectra of Trichodesmium cells. This revealed that the contribution of different parts of the phycobilisome antenna to fluorescence quenching changed during the daily activity cycle, and that individual phycobiliproteins can be reversibly coupled to the photosystems, while the expression levels of these proteins did not change much during the daily activity cycle. Thus we propose that variable phycobilisome coupling plays a key role in the regulation of photosynthesis for nitrogen fixation in Trichodesmium.     

Changes in adenosine 3',5'-monophosphate induced by parathyroid hormone and theophylline in the developing rat renal cortex

To test the biochemical responsiveness of developing rat renal cortex to parathyroid hormone (PTH), intracellular concentrations of adenosine 3′,5′-monophosphate (cyclic AMP) were measured. Renal cortical slices from 10-day-, 20-day-, and 12-week-old animals contained higher concentrations of cyclic AMP when incubated in the presence of theophylline than in its absence. In the absence of theophylline, tissue from all three age groups responded to PTH with dose-dependent increases in cyclic AMP. In the presence of theophylline the response of tissue from 10-day-old animals was greater than that of 12-week-old animals.It is suggested that the differential effect of theophylline with respect to age may be the result of higher turnover rates of cyclic AMP in the young animals.     

Citric acid and polyols production by Aspergillus niger at high glucose concentration in solid state fermentation on inert support

Summary Aspergillus niger cultures at high initial glucose concentration (up to 400 g/1) on Amberlite as inert support were carried out. Citric acid was accumulated in the support showing high concentration (94.54 g/l) and productivity (1.35 g/l h) without inhibition related to the presence of metals (Mn²⁺, Zn²⁺, Co²⁺, Cu²⁺, and Ca²⁺) at high concentrations. Citric acid accumulation was clearly associated with both, glycerol production and to the age of the culture. Glycerol and erythritol, the major osmoregulator metabolites, were also produced (8.16 and 24.57 g/l respectively) at 400 g/l of glucose.