Photosynthetic physiology and primary productivity of phytoplankton in the Australian sector of the Southern Ocean

第2回極域科学シンポジウム　共通セッション「海氷圏の生物地球化学」 11月16日（水） 統計数理研究所 3階セミナー

Performance of a photogrammetric digital elevation model in a tropical montane forest environment

Digital photogrammetry has advanced to the point where digital elevation models (DEMs) can be derived in full automation from stereo images, offering new opportunities in various fields including forestry. However, the performance and limitations of digital photogrammetry need to be carefully investigated in forest environments where both scientific studies and forest management depend on accurate information. We evaluated the performance of a photogrammetric digital surface model (photo-DSM) derived from small-format aerial photographs over approximately 2000 ha of tropical montane forest in northern Borneo, Malaysia. The accuracy of the photo-DSM was evaluated by using a reference dataset derived from airborne laser scanning (ALS) with an approximate density of 15 pulses/m2. The vertical accuracy over the total area (18,349,288 pixels) was represented by a mean error of 0.006 m and RMSE of 3.003 m, with 61.1% of all measured heights accurate to within ±1 m, 81.9% accurate to within ±2 m, and 88.7% accurate to within ±3 m. More detailed local accuracy evaluation was conducted at block level: 31 1-ha blocks and one 0.25-ha block located over different forest types and characterized by the mean canopy height (range=8.4-41.1 m) and standard deviation (range=2.0-9.8 m) of the ALS-canopy height model (ALS-CHM). RMSE of the forest blocks ranged from 1.01 to 4.19 m, and this variance in RMSE could be explained by 78.6% of standard deviation of the ALS-CHM. Canopy slope and dark areas also had an effect on the RMSE: in areas of higher canopy slope and in darker areas within the forest blocks, the RMSE increased by up to 8.6 and 5.8 m, respectively. No-data areas accounted for 3.24% in the forest blocks and were also influenced by canopy slope and darker areas. RMSE of non-forest areas was 0.39 m (n=5243 pixels). Research and development on image-matching algorithms (which achieved 86.1% successful alignment of the aerial photographs in our study), cameras, unmanned aerial vehicles, and flight parameters are ongoing; as a result, digital photogrammetry and its capacity for use in various forestry applications are also continuing to improve

Changes in growth of marbled sole Pseudopleuronectes yokohamae between high and low stock-size periods in Tokyo Bay, Japan

We examined the age and growth of the marbled sole Pseudopleuronectes yokohamae collected from Tokyo Bay, Japan, during two study periods between 2002 and 2008, when the stock size was consistently low. The von Bertalanffy growth equations were found to differ significantly between sexes, and females attained a larger standard length than males of the same age. These results were then compared with those reported for 1974?1983 and 1986?1988, two study periods when the stock size was high. The growth of both sexes of marbled sole in Tokyo Bay during the 2000s was found to be significantly higher than that in the 1970s and 1980s. To explore possible factors causing these changes in the growth, we examined bottom water temperature and population density. We found that the population density decreased and the bottom water temperature increased between the late 1970s and the late 2000s. However, despite evidence of changes in population densities and water temperatures, further study is needed to determine the main factors causing the observed changes in growth

Estimation of above-ground biomass of a tropical forest in Northern Borneo using high-resolution satellite image

Estimating above-ground biomass is important in establishing an applicable methodology of Measurement, Reporting and Verification (MRV) System for Reducing Emissions from Deforestation and Forest Degradation-Plus (REDD+). We developed an estimation model of diameter at breast height (DBH) from IKONOS-2 image that led to above-ground biomass estimation (AGB). The IKONOS image was preprocessed with dark object subtraction and topographic effect correction prior to watershed segmentation for tree crown delineation. Compared to the field observation, the overall segmentation accuracy was 64%. Crown detection percent had a strong negative correlation to tree density. In addition, satellite-based crown area had the highest correlation with the field measured DBH. We then developed the DBH allometric model that explained 74% of the data variance. In average, the estimated DBH was very similar to the measured DBH as well as for AGB. Overall, this method can potentially be applied to estimate AGB over a relatively large and remote tropical forest in Northern Borneo

Comparison between surface-reading and cross-section methods using sagittal otolith for age determination of the marbled sole Pseudopleuronectes yokohamae

To find an appropriate method for age determination in the marbled sole Pseudopleuronectes yokohamae in Tokyo Bay, Japan, sagittal otoliths of 1,343 individuals were observed by surface-reading and cross-section methods and the results were compared. Opaque zones occurred once a year and were regarded as annuli in both methods. The surface-reading method sometimes provided a lower count of the number of annuli than the cross-section method, and the frequency of this discrepancy was highest in older fish (males above 5 years, females above 4 years). The oldest female fish was estimated to be age 10 years by the cross-section method but 8 years by the surface-reading method. The cross-section method could provide a more accurate estimate of age and is therefore likely to be indispensable to estimations of longevity. In contrast, the surface-reading method is superior in terms of cost and time efficiency but is likely to underestimate the ages of older fish. However, growth equations based on age estimated by the surface-reading method were sufficiently accurate if males ?5 years and females ?4 years were combined as specific, single age groups of 5+ and 4+, respectively

Responses of Antarctic marine ecosystems to global environmental changes with carbonate systems (RAMEEC) – Preliminary report of JARE52 -

第2回極域科学シンポジウム　共通セッション「海氷圏の生物地球化学」 11月16日（水） 統計数理研究所 3階セミナー

Integrative Annotation of 21,037 Human Genes Validated by Full-Length cDNA Clones

The human genome sequence defines our inherent biological potential; the realization of the biology encoded therein requires knowledge of the function of each gene. Currently, our knowledge in this area is still limited. Several lines of investigation have been used to elucidate the structure and function of the genes in the human genome. Even so, gene prediction remains a difficult task, as the varieties of transcripts of a gene may vary to a great extent. We thus performed an exhaustive integrative characterization of 41,118 full-length cDNAs that capture the gene transcripts as complete functional cassettes, providing an unequivocal report of structural and functional diversity at the gene level. Our international collaboration has validated 21,037 human gene candidates by analysis of high-quality full-length cDNA clones through curation using unified criteria. This led to the identification of 5,155 new gene candidates. It also manifested the most reliable way to control the quality of the cDNA clones. We have developed a human gene database, called the H-Invitational Database (H-InvDB; http://www.h-invitational.jp/). It provides the following: integrative annotation of human genes, description of gene structures, details of novel alternative splicing isoforms, non-protein-coding RNAs, functional domains, subcellular localizations, metabolic pathways, predictions of protein three-dimensional structure, mapping of known single nucleotide polymorphisms (SNPs), identification of polymorphic microsatellite repeats within human genes, and comparative results with mouse full-length cDNAs. The H-InvDB analysis has shown that up to 4% of the human genome sequence (National Center for Biotechnology Information build 34 assembly) may contain misassembled or missing regions. We found that 6.5% of the human gene candidates (1,377 loci) did not have a good protein-coding open reading frame, of which 296 loci are strong candidates for non-protein-coding RNA genes. In addition, among 72,027 uniquely mapped SNPs and insertions/deletions localized within human genes, 13,215 nonsynonymous SNPs, 315 nonsense SNPs, and 452 indels occurred in coding regions. Together with 25 polymorphic microsatellite repeats present in coding regions, they may alter protein structure, causing phenotypic effects or resulting in disease. The H-InvDB platform represents a substantial contribution to resources needed for the exploration of human biology and pathology

Guidelines for the use and interpretation of assays for monitoring autophagy (3rd edition)

In 2008 we published the first set of guidelines for standardizing research in autophagy. Since then, research on this topic has continued to accelerate, and many new scientists have entered the field. Our knowledge base and relevant new technologies have also been expanding. Accordingly, it is important to update these guidelines for monitoring autophagy in different organisms. Various reviews have described the range of assays that have been used for this purpose. Nevertheless, there continues to be confusion regarding acceptable methods to measure autophagy, especially in multicellular eukaryotes. For example, a key point that needs to be emphasized is that there is a difference between measurements that monitor the numbers or volume of autophagic elements (e.g., autophagosomes or autolysosomes) at any stage of the autophagic process versus those that measure fl ux through the autophagy pathway (i.e., the complete process including the amount and rate of cargo sequestered and degraded). In particular, a block in macroautophagy that results in autophagosome accumulation must be differentiated from stimuli that increase autophagic activity, defi ned as increased autophagy induction coupled with increased delivery to, and degradation within, lysosomes (inmost higher eukaryotes and some protists such as Dictyostelium ) or the vacuole (in plants and fungi). In other words, it is especially important that investigators new to the fi eld understand that the appearance of more autophagosomes does not necessarily equate with more autophagy. In fact, in many cases, autophagosomes accumulate because of a block in trafficking to lysosomes without a concomitant change in autophagosome biogenesis, whereas an increase in autolysosomes may reflect a reduction in degradative activity. It is worth emphasizing here that lysosomal digestion is a stage of autophagy and evaluating its competence is a crucial part of the evaluation of autophagic flux, or complete autophagy. Here, we present a set of guidelines for the selection and interpretation of methods for use by investigators who aim to examine macroautophagy and related processes, as well as for reviewers who need to provide realistic and reasonable critiques of papers that are focused on these processes. These guidelines are not meant to be a formulaic set of rules, because the appropriate assays depend in part on the question being asked and the system being used. In addition, we emphasize that no individual assay is guaranteed to be the most appropriate one in every situation, and we strongly recommend the use of multiple assays to monitor autophagy. Along these lines, because of the potential for pleiotropic effects due to blocking autophagy through genetic manipulation it is imperative to delete or knock down more than one autophagy-related gene. In addition, some individual Atg proteins, or groups of proteins, are involved in other cellular pathways so not all Atg proteins can be used as a specific marker for an autophagic process. In these guidelines, we consider these various methods of assessing autophagy and what information can, or cannot, be obtained from them. Finally, by discussing the merits and limits of particular autophagy assays, we hope to encourage technical innovation in the field