Establishment Probability in Fluctuating Environments: A Branching Process Model

We study the establishment probability of invaders in stochastically fluctuating environments and the related issue of extinction probability of small populations in such environments, by means of an inhomogeneous branching process model. In the model it is assumed that individuals reproduce asexually during discrete reproduction periods. Within each period, individuals have (independent) Poisson distributed numbers of offspring. The expected numbers of offspring per individual are independently identically distributed over the periods. It is shown that the establishment probability of an invader varies over the reproduction periods according to a stable distribution. We give a method for simulating the establishment probabilities and approximations for the expected establishment probability. Furthermore, we show that, due to the stochasticity of the establishment success over different periods, the expected success of sequential invasions is larger then that of simultaneous invasions and we study the effects of environmental fluctuations on the extinction probability of small populations and metapopulations. The results can easily be generalized to other offspring distributions than the Poisson.     

INFERRING THE RATES OF BRANCHING AND EXTINCTION FROM MOLECULAR PHYLOGENIES

Molecular techniques provide ancestral phylogenies of extant taxa with estimated branching times. Here we studied the pattern of ancestral phylogeny of extant taxa produced by branching (or cladogenesis) and extinction of taxa, assuming branching processes with time-dependent rates. (1) If the branching rate b and extinction rate c are constant, the semilog plot of the number of ancestral lineages over time is not a straight line but is curvilinear, with increasing slope toward the end, implying that ancestral phylogeny shows apparent increase in the branching rate near the present. The estimate of b and c based on nonlinear fitting is examined by computer simulation. The estimate of branching rate can be usable for a large phylogeny if b is greater than c, but the estimate of extinction rate c is unreliable because of large bias and variance. (2) Gradual decrease in the slope of the semilog plot of the number of ancestral lineages over time, as was observed in a phylogeny of bird families based on DNA hybridization data, can be explained equally well by either the decreasing branching rate or the increasing extinction rate. Infinitely many pairs of branching and extinction rates as functions of time can produce the same ancestral phylogeny. (3) An explosive branching event in the past would appear as a quick increase in the number of ancestral lineages. In contrast, mass extinction occurring in a brief period, if not accompanied by an increase in branching rate, does not produce any rapid change in the number of ancestral lineages at the time. (4) The condition in which the number of ancestral lineages of extant species changes in parallel with the actual number of species in the past is derived.     

The Role of Individual Domains and the Significance of Shedding of ATP6AP2/(pro)renin Receptor in Vacuolar H+-ATPase Biogenesis

The ATPase 6 accessory protein 2 (ATP6AP2)/(pro)renin receptor (PRR) is essential for the biogenesis of active vacuolar H⁺-ATPase (V-ATPase). Genetic deletion of ATP6AP2/PRR causes V-ATPase dysfunction and compromises vesicular acidification. Here, we characterized the domains of ATP6AP2/PRR involved in active V-ATPase biogenesis. Three forms of ATP6AP2/PRR were found intracellularly: full-length protein and the N- and C-terminal fragments of furin cleavage products, with the N-terminal fragment secreted extracellularly. Genetic deletion of ATP6AP2/PRR did not affect the protein stability of V-ATPase subunits. The extracellular domain (ECD) and transmembrane domain (TM) of ATP6AP2/PRR were indispensable for the biogenesis of active V-ATPase. A deletion mutant of ATP6AP2/PRR, which lacks exon 4-encoded amino acids inside the ECD (Δ4M) and causes X-linked mental retardation Hedera type (MRXSH) and X-linked parkinsonism with spasticity (XPDS) in humans, was defective as a V-ATPase-associated protein. Prorenin had no effect on the biogenesis of active V-ATPase. The cleavage of ATP6AP2/PRR by furin seemed also dispensable for the biogenesis of active V-ATPase. We conclude that the N-terminal ECD of ATP6AP2/PRR, which is also involved in binding to prorenin or renin, is required for the biogenesis of active V-ATPase. The V-ATPase assembly occurs prior to its delivery to the trans-Golgi network and hence shedding of ATP6AP2/PRR would not affect the biogenesis of active V-ATPase.     

Identification of Biological Properties of Intralymphatic Tumor Related to the Development of Lymph Node Metastasis in Lung Adenocarcinoma

Background

Intralymphatic tumors in the extratumoral area are considered to represent the preceding phase of lymph node metastasis. The aim of this study was to clarify the biological properties of intralymphatic tumors susceptible to the development of lymph node metastasis, with special reference to the expression of cancer initiating/stem cell (CIC/CSC) related markers in cancer cells and the number of infiltrating stromal cells.

Material and Methods

Primary lung adenocarcinomas with lymphatic permeation in the extratumoral area were retrospectively examined (n = 107). We examined the expression levels of CIC/CSC related markers including ALDH1, OCT4, NANOG, SOX2 and Caveolin-1 in the intralymphatic cancer cells to evaluate their relationship to lymph node metastasis. Moreover, the number of infiltrating stromal cells expressing CD34, α-smooth muscle actin, and CD204 were also evaluated.

Results

Among the intralymphatic tissues, low ALDH1 expression in cancer cells, high SOX2 expression in cancer cells, and a high number of CD204(+) macrophages were independent predictive factors for lymph node metastasis (P = 0.004, P = 0.008, and P = 0.028, respectively). Among these factors, only low ALDH1 expression in cancer cells was significantly correlated with the farther spreading of lymph node metastasis (mediastinal lymph node, pathological N2) (P = 0.046) and the metastatic lymph node ratio (metastatic/resected) (P = 0.028). On the other hand, in the primary tumors, ALDH1 expression in the cancer cells was not associated with lymph node metastasis. Intralymphatic cancer cells expressing low ALDH1 levels exhibited lower E-cadherin expression levels than cancer cells with high levels of ALDH1 expression (P = 0.015).

Conclusions

Intralymphatic cancer cells expressing low levels of ALDH1 and infiltrating macrophages expressing CD204 have a critical impact on lymph node metastasis. Our study also highlighted the significance of evaluating the biological properties of intralymphatic tumors for tumor metastasis.     

Longitudinal distribution and microhabitat use of young Japanese eel Anguilla japonica in a small river flowing through paddy areas

Although the Japanese eel Anguilla japonica is a commercially important species, its habitat use is not well understood during its life stages in the river. In this study, we investigated the longitudinal distribution and microhabitat use of young Japanese eels (<200 mm in total length [TL], which correspond to elver and early yellow stages) using 180 quadrates (1 m × 1 m) in six stations in a small river (approximately 11.5 km long, 3.0–25.0 m wide) that flows through paddy areas in Fukushima Prefecture, Japan. No differences were observed in the TL of eels among the sampling stations. The analysis using generalized linear models showed that eel density increased as number of weirs decreased. The analysis using generalized additive models showed that water depth, current velocity, and substrate complexity were important factors determining microhabitat use. Eels used shallow habitats (<35 cm) with slow currents (5–40 cm/s) and high complex riverbeds (>0.35 in index of substrate complexity). These findings provide useful information to conserve and manage wild eels inhabiting small rivers flowing through paddy areas.     

Phosphatidylinositol 3-Kinase Class II α-Isoform PI3K-C2α Is Required for Transforming Growth Factor β-induced Smad Signaling in Endothelial Cells

We have recently demonstrated that the PI3K class II-α isoform (PI3K-C2α), which generates phosphatidylinositol 3-phosphate and phosphatidylinositol 3,4-bisphosphates, plays crucial roles in angiogenesis, by analyzing PI3K-C2α knock-out mice. The PI3K-C2α actions are mediated at least in part through its participation in the internalization of VEGF receptor-2 and sphingosine-1-phosphate receptor S1P₁ and thereby their signaling on endosomes. TGFβ, which is also an essential angiogenic factor, signals via the serine/threonine kinase receptor complex to induce phosphorylation of Smad2 and Smad3 (Smad2/3). SARA (Smad anchor for receptor activation) protein, which is localized in early endosomes through its FYVE domain, is required for Smad2/3 signaling. In the present study, we showed that PI3K-C2α knockdown nearly completely abolished TGFβ1-induced phosphorylation and nuclear translocation of Smad2/3 in vascular endothelial cells (ECs). PI3K-C2α was necessary for TGFβ-induced increase in phosphatidylinositol 3,4-bisphosphates in the plasma membrane and TGFβ receptor internalization into the SARA-containing early endosomes, but not for phosphatidylinositol 3-phosphate enrichment or localization of SARA in the early endosomes. PI3K-C2α was also required for TGFβ receptor-mediated formation of SARA-Smad2/3 complex. Inhibition of dynamin, which is required for the clathrin-dependent receptor endocytosis, suppressed both TGFβ receptor internalization and Smad2/3 phosphorylation. TGFβ1 stimulated Smad-dependent VEGF-A expression, VEGF receptor-mediated EC migration, and capillary-like tube formation, which were all abolished by either PI3K-C2α knockdown or a dynamin inhibitor. Finally, TGFβ1-induced microvessel formation in Matrigel plugs was greatly attenuated in EC-specific PI3K-C2α-deleted mice. These observations indicate that PI3K-C2α plays the pivotal role in TGFβ receptor endocytosis and thereby Smad2/3 signaling, participating in angiogenic actions of TGFβ.     

Feeding capability of black scraper <Emphasis Type="Italic">Thamnaconus modestus</Emphasis> on giant jellyfish <Emphasis Type="Italic">Nemopilema nomurai</Emphasis> evaluated through field observations and tank experiments

Although many fish species are known to feed on jellyfish, only a few quantitative studies on this subject have been conducted in the field or laboratory. We combined field observations and feeding experiments to quantitatively evaluate the potential feeding capability of the black scraper Thamnaconus modestus on giant jellyfish Nemopilema nomurai in a jellyfish-abundant area. Underwater observations revealed that shoals of T. modestus fed voraciously on jellyfish when the jellyfish were close to the fish’s seaweed habitat. Gut contents of field-collected T. modestus almost exclusively consisted of jellyfish. In tank trials, feeding activity of black scraper was high when light intensity was between about 1.1 lx and 50 × 10³ lx. The estimated feeding speed of T. modestus on the jellyfish in the Sea of Japan when the jellyfish bloom occurred was 10.0 ± 2.0 times fish body weight per day. The results support the prediction that T. modestus and probably other coastal medusivorous fishes have a substantial capability to eliminate jellyfish blooms. Considering that they are highly dependent on seaweed bed, protection of such habitats for these medusivores may be the most cost-efficient control method for jellyfish blooms.     

Growth and migration patterns of juvenile temperate seabass Lateolabrax japonicus in the Yura River estuary,Japan—combination of stable isotope ratio and otolith microstructure analyses

It is important to know the characteristics of migration pattern and vital rates of juveniles to understand the early life history and its effect on the population dynamics of fishes. The relationship between growth and migration pattern of juvenile temperate seabass Lateolabrax japonicus in the Yura River estuary was examined by combination of stable carbon isotope ratio (δ¹³C) and otolith microstructure. Gut fullness indices were also examined to know the feeding condition of juveniles. δ¹³C values of seabass juveniles in the lower estuary and surf zone (LES) were enriched, while those in freshwater zone (FW) were depleted, consistent with δ¹³C differences in prey items. The back-calculated growth rates of juveniles in FW were significantly lower than those of juveniles that resided in the LES from 50 days to 90 days old, implying that juveniles with poor growth ascended the river while those with better growth remained in the LES. However, the growth rates of the juveniles, which resided in FW for more than 1 month, caught up with and even overtook those of juveniles in LES within 1 month after ascended the river. The higher water temperature and better feeding conditions would contribute to better growth rates of juveniles in FW than those in LES.     

Modeling socio-economic aspects of ecosystem management and biodiversity conservation

For successful ecosystem management and biodiversity conservation, in addition to ecological and evolutionary processes, we need to consider social and economic influences on the management target. Here, we introduce several theoretical models that address economic and social aspects of the human society which are closely related to ecosystem management. The first model analyzes economic decisions on the use of the common fishing ground in Jeju Island, Korea, by traditional divers and tourists. We observe that the way the number of tourists increases with the availability of resources strongly influences how benefits are distributed among fishing ground stakeholders. The second model discusses activities that raise public awareness about biodiversity, which will help maintain public support for conservation in the future. Based on control theory, we derive the optimal investment in these activities to maximize the long-term quality of the conservation target. The third model analyzes punishment scheme as a mechanism to enforce people to follow the regulation on the use of common resource. An important aspect of successful management is “graduated punishment”, in which the severity of the punishment applied to deviators gradually increases with the amount of harm caused by deviation from the rule. We show that graduated punishment is the most efficient way to ensure cooperation when evaluation errors are unavoidable and when people are heterogeneous with respect to the sensitivity to utility differences. We conclude that socio-economic aspects related to ecosystem management are promising research foci of theoretical ecology.