Extinction threshold for spatial forest dynamics with height structure

We present a pair-approximation model for spatial forest dynamics defined on a regular lattice. The model assumes three possible states for a lattice site: empty (gap site), occupied by an immature tree, and occupied by a mature tree, and considers three nonlinearities in the dynamics associated to the processes of light interference, gap expansion, and recruitment. We obtain an expression of the basic reproduction number R₀ which, in contrast to the one obtained under the mean-field approach, uses information about the spatial arrangement of individuals close to extinction. Moreover, we analyze the corresponding survival-extinction transition of the forest and the spatial correlations among gaps, immature and mature trees close to this critical point. Predictions of the pair-approximation model are compared with those of a cellular automaton.     

When are cellular oscillators sufficient for sequential segmentation?

Sequential segmentation during embryogenesis involves the generation of a repeated pattern along the embryo, which is concurrently undergoing axial elongation by cell division. Most mathematical models of sequential segmentation involve inherent cellular oscillators, acting as a segmentation clock. The cellular oscillation is assumed to be governed by the cell's physiological age or by its interaction with an external morphogen gradient. Here, we address the issue of when cellular oscillators alone are sufficient for predicting segmentation, and when a morphogen gradient is required. The key to resolving this issue lies in how cells determine positional information in the model - this is directly related to the distribution of cell divisions responsible for axial elongation. Mathematical models demonstrate that if axial elongation occurs through cell divisions restricted to the posterior end of the unsegmented region, a cell can obtain its positional information from its physiological age, and therefore cellular oscillators will suffice. Alternatively, if axial elongation occurs through cell divisions distributed throughout the unsegmented region, then positional information can be obtained through another mechanism, such as a morphogen gradient. Two alternative ways to establish a morphogen gradient in tissue with distributed cell divisions are presented - one with diffusion and the other without diffusion. Our model produces segment polarity and a distribution of segment size from the anterior-to-posterior ends, as observed in some systems. Furthermore, the model predicts segment deletions when there is an interruption in cell division, just as seen in heat shock experiments, as well as the growth and final shrinkage of the presomitic mesoderm during somitogenesis.     

Decision making of the p53 network: Death by integration

The tumor suppressor protein p53 plays a central role in the multiple response pathways activated by DNA damage. In particular, p53 is involved in both the pro-survival response of cell cycle arrest and DNA repair, and the pro-death response of apoptosis. How does the p53 network coordinate the different pathways that lead to the opposite cell fates and what is its strategy in making the life-death decisions? To address these questions, we develop an integrated mathematical model that embraces three key modules of the p53 network: p53 core regulation, p53-induced cell cycle arrest and p53-dependent apoptosis initiation. Our analyses reveal that different aspects of the nuclear p53 dynamic profile are being used to differentially regulate the pro-survival and the pro-death modules. While the activation of the pro-survival module is dependent on the current or recent status of the DNA damage, the activation of the pro-death module relies on the accumulation or integration of the damage level over time. Thus, the cell will take the death fate if it cannot recover from the damage within a time period that is inversely proportional to the damage level. This “adaptive timer” strategy is likely to be adopted in other stress response systems.     

Benzopyrazine derivatives: A novel class of growth factor receptor bound protein 7 antagonists

Growth factor receptor bound protein 7 (Grb7) is an adapter protein that functions as a downstream effector of growth factor mediated signal transduction. Over-expression of Grb7 has been implicated in a variety of cancers such as breast, blood, pancreatic, esophageal, and gastric carcinomas. Inhibition of Grb7 has been shown to reduce the migratory and proliferative potential of these cancers, making it an attractive therapeutic target. Starting with a known peptide antagonist, the present work reports the application of a succession of computational ligand design tools comprising a ligand shape based similarity search, molecular docking and a 2D-similarity search to identify small molecular antagonists of the Grb7-SH2 domain from the NCI chemical database. Binding to the Grb7-SH2 domain was then experimentally tested using melting point shift assays and isothermal titration calorimetry. Overall, a total of 11 benzopyrazine based small molecular antagonists were identified with affinity for the Grb7-SH2 domain. Representative compounds tested using ITC were revealed to possess moderate binding affinity in the low micromolar range. Finally, the lead compound (NSC642056) was found to reduce the growth of a Grb7-expressing breast cancer cell line with an IC₅₀ of 86 ??M. It is expected that the identified antagonists will be useful additions to further explore the function of Grb7 and for the development of inhibitors with therapeutic potential.     

Processes of organic carbon in mangrove ecosystems

In addition to carbon accumulation in plants, processes of organic carbon in mangrove ecosystems include origins of sediment organic carbon, carbon fluxes between mangroves and their adjacent systems (coastal waters and atmosphere), and cycling processes. Sediment organic carbon originates from suspending solids in coastal waters, mangrove plants and benthic algae. In mangroves with low organic carbon content in sediments, tidal seawater is the main origin of sediment organic carbon, while in mangroves with high sediment organic carbon contents, sediment organic carbon mainly originates from mangrove plants. Due to tidal flush, there is large material exchange between mangrove ecosystems and their adjacent coastal waters. In China, exports of organic carbon in litter falls and dissolved organic carbon from mangroves to their adjacent coastal waters have not been documented. Processes of mangrove litter falls, including production, decomposition, export and animal consumption, determine linkages among organic carbon among mangrove plants, secondary production and coastal ocean. Consumers especially benthic animals may influence organic carbon in mangrove ecosystems, because (1) their consumption rates are high, and their selective feeding on some food sources will change the relative quantities of export, bury and mineralization of organic carbon from different origins; (2) their consumption is much more than assimilation, resulting in the changes in sizes, forms and qualities of non-assimilated organic matters, and then the changes in availability of export, consumption or mineralization of organic carbon. Respiration and sulfate reduction are important mineralization processes of organic carbon in mangrove sediments. Mineralization rates of organic carbon in mangrove sediments are influenced by quantities, activities and particle sizes of organic matters, and other factors such as forest ages, root activities and animal burrowing activities. Researches on processes of mangrove organic carbon should be based on open systems, and ecological processes of organic carbon should be coupled with vegetation restoration.     

Directional positive feedback and pattern at an alpine tree line

Abstract. The spatial pattern at alpine tree line may be part of a feedback process in which wind plays a central role. The basic aspects of such a feedback were embedded in a cellular automaton. Spatial metrics of the patterns generated by this simulation and those of observed patterns at a windy tree line site were ordinated using Principal Component Analysis. Only the simulations that included a directionally weighted feedback fell close to the observed sites in ordination space. MANOVA indicated that the directionally weighted feedback is most important in structuring the tree line pattern, but that random hotspots for establishment and the overall steepness of the environmental gradient from forest to tundra in space also have an effect. The importance of wind in determining feedback with the spatial pattern of a canopy indicates that nonlinear reactions to climatic change are likely.     

On a periodic-like behavior of a delayed density-dependent branching process

Most of natural populations seem to be regulated in their sizes in complex ways. Particularly, the sizes of some populations change in time or generation roughly periodically. There are many theoretical studies on such population dynamics. This paper develops stochastic population models for a periodic-like population dynamics. To see the nature of such mechanism, we consider simple models of a delayed density-dependent branching process, and present by numerical simulations how such a branching process shows periodic population changes. The effects of randomly changing stationary environments on the population dynamics are also considered.     

Recycling of nitrogen in herbivore feces: plant recovery,herbivore assimilation,soil retention,and leaching losses

Herbivores directly and indirectly affect ecosystem functioning in forests. Feces deposition is a direct effect that supplies ephemeral N pulses to soils. Herbivore-mediated changes in plant N allocation and uptake are indirect effects that can also influence soil N availability. These effects may interact if defoliation influences the ability of plants to recover fecal N, and this may affect subsequent generations of herbivores. We added ¹⁵N-enriched insect feces (frass) to a series of replicated red oak, Quercus rubra, mesocosms that had been damaged experimentally and then followed the frass N over the course of 2 years. In the first season, some frass N was mineralized in the soil and leached in organic form from the mesocosms within 1 week of deposition. Within 1 month, frass N had been acquired by the oaks and enriched the foliage; late-season herbivores assimilated the frass N within the same growing season. In the second season, herbivore damage from the previous year lowered total leaf N contents and ¹⁵N recovered in the foliage. A subsequent cohort of early-season herbivores fed on this foliage consequently derived less of their N from the previous year’s frass, and feral leaf rollers colonized fewer of these saplings. The 0- to 5-cm soil fraction was the largest N sink measured, and 42% of the frass N was recovered in the soil. The results demonstrate that: (1) some frass N can be recycled rapidly into foliage and assimilated by successive cohorts of herbivore within the same season; (2) damage can affect N allocation in the following year’s foliage, influencing N availability to and host selection by herbivores; and (3) leaching losses occur soon after deposition but are buffered by soil pools, which are the largest sinks for frass N.     

Characterization of an alternative splice variant of human nucleoside triphosphate diphosphohydrolase 3 (NTPDase3): a possible modulator of nucleotidase activity and purinergic signaling

Nucleoside triphosphate diphosphohydrolase 3 (NTPDase3) is a cell surface, membrane-bound enzyme that hydrolyzes extracellular nucleotides, thereby modulating purinergic signaling. An alternatively spliced variant of NTPDase3 was obtained and analyzed. This alternatively spliced variant, termed "NTPDase3beta", is produced through the use of an alternative terminal exon (exon 11) in place of the terminal exon (exon 12) in the full-length NTPDase3, now termed "NTPDase3alpha". This results in an expressed protein lacking the C-terminal cytoplasmic sequence, the C-terminal transmembrane helix, and apyrase conserved region 5. The cDNA encoding this truncated splice variant was detected in a human lung library by PCR. Like the full-length NTPDase3alpha, the alternatively spliced NTPDase3beta was expressed in COS cells after transfection, but only the full-length NTPDase3alpha is enzymatically active and properly trafficked to the plasma membrane. However, when the truncated NTPDase3beta was co-transfected with full-length NTPDase3alpha, there was a significant reduction in the amount of NTPDase3alpha that was properly processed and trafficked to the plasma membrane as active enzyme, indicating that the truncated form interferes with normal biosynthetic processing of the full-length enzyme. This suggests a role for the NTPDase3beta variant in the regulation of NTPDase3 nucleotidase activity, and therefore the control of purinergic signaling, in those cells and tissues expressing both NTPDase3alpha and NTPDase3beta.