Graph-Theoretical Analysis of Cleavage Pattern: Graph Developmental System and Its Application to Cleavage Pattern of Ascidian Egg

The skeletal structure of the embryo is represented by the graph. In the graph, the cells and the connectivities between the cells are reduced to the nodes and edges, respectively. Along cleavage history, the series of graphs is obtained. In this paper I propose a new graph developmental system(GDS) which develops the series of graphs. And I represent and analyze the cleavage pattern of the ascidian egg by GDS. In order to represent it by GDS, at first, the connectivities between the cells are labeled according to the developments of the connectivities at the next time step, and next the cells are labeled. But there are two ways of labeling the cells, then two types of GDS are defined: (1) to label according to the pattern of the connectivities of their descendant cells after two time steps (G-GDS), (2) to label according to the cell fates (C-GDS). The C-GDS of the ascidian egg produces 16 cleavage patterns at 64-cell stage non-deterministically. If some labels are distinguished at 16-cell stage, the C-GDS becomes deterministic at 64-cell stage.
GDS will be useful to simulate morphogenesis by the computer graphics.     

Establishment of the Embryo-derived Stem (ES) Cell Lines from Mouse Blastocysts: Effects of the Feeder Cell Layer.

The ES ceii lines are embryo-derived stem cell lines directly isolated from the inner cell mass of mouse blastocysts using feeder cell layer. We have established a number of ES cell lines from 129 or C57BL/6 strain mice by using the feeder layer of the STO cells (from ATCC) or the primary embryonic fibroblasts, which was obtained by trypsinizing the 16-day-old BALB/c mouse fetus. The ES cell lines established on the STO feeder layer showed differentiation into various tissues in solid tumors when injected into syngenic mice. Karyotype was, however, nearly tetraploid. The ES cell lines established on the primary fibroblasts exhibited differentiation into larger variety of tissues in solid tumors. Karyotype was almost diploid and majority of the cells kept normal set of chromosomes in G-banding. We conclude that the primary fibroblasts are better feeder layer than the STO cells for establishment and maintenance of the ES cell lines.     

K-Casein Suppresses Melanogenesis in Cultured Pigment Cells

The effects of bovine milk proteins on melanogenesis in B16 cells were examined. Both whey protein isolate and casein exhibited depigmenting properties. Among the major protein components of milk—including β-lactoglobulin, α-lactalbumin, α-, β-, and k-casein—only K-casein exhibited the depigmenting effect. However, the carboxyl terminal peptide of K-casein, glycomacropeptide, did not show this activity. Also, K-casein promoted the proliferation of the cells and inhibited the activity of tyrosinase in the cells. These results indicate that K-casein acts as a melanogenesis-suppressing modulator.     

Enhanced Melanogenesis Induced by Tyrosinase Gene-Transfer Increases Boron-Uptake and Killing Effect of Boron Neutron Capture Therapy for Amelanotic Melanoma

Specific and powerful cancer killing effect for melanoma by boron neutron capture therapy (BNCT) using DOPA analogue, ¹⁰B-p-boronophenylalanine (¹⁰B-BPA), has been established, but amelanotic melanoma is insufficiently responsive to ¹⁰B-BPA BNCT in comparison with actively melanin-producing melanoma. Although the accumulation mechanism of ¹⁰B-BPA within melanoma was not established, we have recently obtained findings suggesting that melanin monomers, key intermediates for melanin polymer formation, play a critical role in ¹⁰B-BPA accumulation. In addition, there are some kinds of human amelanotic melanomas, such as MEL2A, in which expression of tyrosinase is repressed or lacking though tyrosinase-related protein (TRP)-l and TRP-2 are well expressed. Thus, by using a similarly tyrosinase-lacking mouse amelanotic melanoma cell line, A1059, we constructed TA1059 cells by transfecting human tyrosinase-cDNA into these cells. TA1059 cells acquired higher DOPA-oxidase and DOPAchrome tautomerase activity as well as eumelanin content at even higher levels than those of B16F10 cells. TA1059 cells showed about 2.5 times higher ^p-boronophenylalanine (BPA) uptake than A1059 cells in culture. In animal experiments, by using these cell lines, tumor growth of TA1059 was significantly suppressed by ¹⁰B-BPA BNCT as compared with A1059. These findings indicate that the induction of active melanin biosynthesis by melanogenic gene-transfer effectively improves the treatment of amelanotic melanoma by BNCT.     

Diagnosing and assessing uncertainties of terrestrial ecosystem models in a multimodel ensemble experiment: 2. Carbon balance

This paper examines carbon stocks and their relative balance in terrestrial ecosystems simulated by Biome‐BGC, LPJ, and CASA in an ensemble model experiment conducted using the Terrestrial Observation and Prediction System. We developed the Hierarchical Framework for Diagnosing Ecosystem Models to separate the simulated biogeochemistry into a cascade of functional tiers and examine their characteristics sequentially. The analyses indicate that the simulated biomass is usually two to three times higher in Biome‐BGC than LPJ or CASA. Such a discrepancy is mainly induced by differences in model parameters and algorithms that regulate the rates of biomass turnover. The mean residence time of biomass in Biome‐BGC is estimated to be 40–80 years in temperate/moist climate regions, while it mostly varies between 5 and 30 years in CASA and LPJ. A large range of values is also found in the simulated soil carbon. The mean residence time of soil carbon in Biome‐BGC and LPJ is ～200 years in cold regions, which decreases rapidly with increases of temperature at a rate of ～10 yr °C^?1. Because long‐term soil carbon pool is not simulated in CASA, its corresponding mean residence time is only about 10–20 years and less sensitive to temperature. Another key factor that influences the carbon balance of the simulated ecosystem is disturbance caused by wildfire, for which the algorithms vary among the models. Because fire emissions are balanced by net ecosystem production (NEP) at steady states, magnitudes, and spatial patterns of NEP vary significantly as well. Slight carbon imbalance may be left by the spin‐up algorithm of the models, which adds uncertainty to the estimated carbon sources or sinks. Although these results are only drawn on the tested model versions, the developed methodology has potential for other model exercises.     

Constraining rooting depths in tropical rainforests using satellite data and ecosystem modeling for accurate simulation of gross primary production seasonality

Accurate parameterization of rooting depth is difficult but important for capturing the spatio-temporal dynamics of carbon, water and energy cycles in tropical forests. In this study, we adopted a new approach to constrain rooting depth in terrestrial ecosystem models over the Amazon using satellite data [moderate resolution imaging spectroradiometer (MODIS) enhanced vegetation index (EVI)] and Biome-BGC terrestrial ecosystem model. We simulated seasonal variations in gross primary production (GPP) using different rooting depths (1, 3, 5, and 10 m) at point and spatial scales to investigate how rooting depth affects modeled seasonal GPP variations and to determine which rooting depth simulates GPP consistent with satellite-based observations. First, we confirmed that rooting depth strongly controls modeled GPP seasonal variations and that only deep rooting systems can successfully track flux-based GPP seasonality at the Tapajos km67 flux site. Second, spatial analysis showed that the model can reproduce the seasonal variations in satellite-based EVI seasonality, however, with required rooting depths strongly dependent on precipitation and the dry season length. For example, a shallow rooting depth (1–3 m) is sufficient in regions with a short dry season (e.g. 0–2 months), and deeper roots are required in regions with a longer dry season (e.g. 3–5 and 5–10 m for the regions with 3–4 and 5–6 months dry season, respectively). Our analysis suggests that setting of proper rooting depths is important to simulating GPP seasonality in tropical forests, and the use of satellite data can help to constrain the spatial variability of rooting depth.     

Evaluating the impacts of climate and elevated carbon dioxide on tropical rainforests of the western Amazon basin using ecosystem models and satellite data

Forest inventories from the intact rainforests of the Amazon indicate increasing rates of carbon gain over the past three decades. However, such estimates have been questioned because of the poor spatial representation of the sampling plots and the incomplete understanding of purported mechanisms behind the increases in biomass. Ecosystem models, when used in conjunction with satellite data, are useful in examining the carbon budgets in regions where the observations of carbon flows are sparse. The purpose of this study is to explain observed trends in normalized difference vegetation index (NDVI) using climate observations and ecosystem models of varying complexity in the western Amazon basin for the period of 1984–2002. We first investigated trends in NDVI and found a positive trend during the study period, but the positive trend in NDVI was observed only in the months from August to December. Then, trends in various climate parameters were calculated, and of the climate variables considered, only shortwave radiation was found to have a corresponding significant positive trend. To compare the impact of each climate component, as well as increasing carbon dioxide (CO₂) concentrations, on evergreen forests in the Amazon, we ran three ecosystem models (CASA, Biome‐BGC, and LPJ), and calculated monthly net primary production by changing a climate component selected from the available climate datasets. As expected, CO₂ fertilization effects showed positive trends throughout the year and cannot explain the positive trend in NDVI, which was observed only for the months of August to December. Through these simulations, we demonstrated that the positive trend in shortwave radiation can explain the positive trend in NDVI observed for the period from August to December. We conclude that the positive trend in shortwave radiation is the most likely driver of the increasing trend in NDVI and the corresponding observed increases in forest biomass.     

Diurnal and seasonal variations in stomatal conductance of rice at elevated atmospheric CO2 under fully open‐air conditions

Understanding of leaf stomatal responses to the atmospheric CO₂ concentration, [CO₂], is essential for accurate prediction of plant water use under future climates. However, limited information is available for the diurnal and seasonal changes in stomatal conductance (g_s) under elevated [CO₂]. We examined the factors responsible for variations in g_s under elevated [CO₂] with three rice cultivars grown in an open‐field environment under flooded conditions during two growing seasons (a total of 2140 individual measurements). Conductance of all cultivars was generally higher in the morning and around noon than in the afternoon, and elevated [CO₂] decreased g_s by up to 64% over the 2 years (significantly on 26 out of 38 measurement days), with a mean g_s decrease of 23%. We plotted the g_s variations against three parameters from the Ball‐Berry model and two revised versions of the model, and all parameters explained the g_s variations well at each [CO₂] in the morning and around noon (R² > 0.68), but could not explain these variations in the afternoon (R² < 0.33). The present results provide an important basis for modelling future water use in rice production.     

Plasticity in the timing of a major life‐history transition and resulting changes in the age structure of populations of the salamander Hynobius retardatus

Variation in age and size at life‐history transitions is a reflection of the diversifying influence of biotic or abiotic environmental change. Examples abound, but it is not well understood how such environmental changes influence the age structure of a population. I experimentally investigated the effects of water temperature and food type on age and body size at metamorphosis in larvae of the salamander Hynobius retardatus. In individuals grown at a cold temperature (15 °C) or given Chironomidae as prey, the time to metamorphosis was significantly prolonged, and body size at metamorphosis was significantly enlarged, compared with individuals grown at a warmer temperature (20 °C) or fed larvae. I also examined whether larval density (a possible indicator of cannibalism in natural habitats) generated variation in the age structure of natural populations in Hokkaido, Japan, where the climate is subarctic. Natural ponds in Hokkaido may contain larvae that have overwintered for 1 or 2 years, as well as larvae of the current year, and I found that the number of age classes was related to larval density. Although cool water temperatures prolong the larval period and induce later metamorphosis, in natural ponds diet‐based enhancement of development translated into a shorter larval duration and earlier metamorphosis. Geographic variation in the frequency of cannibalism resulted in population differences in metamorphic timing in H. retardatus larvae. It is important to understand how environmental effects are ultimately transduced through individual organisms into population‐level phenomena, with the population response arising as the summation of individual responses. Without a thorough comprehension of the mechanisms through which population and individual responses to environmental conditions are mediated, we cannot interpret the relationship between population‐level and individual‐level phenomena. © 2010 The Linnean Society of London, Biological Journal of the Linnean Society, 2011, 102 , 100–114.