Description: The Maritime Continent (MC) forms the western boundary of the tropical Pacific Ocean, and relatively small changes in this region can impact the climate locally and remotely. In the mid-Piacenzian warm period of the Pliocene (mPWP; 3.264 to 3.025 Ma) atmospheric CO2 concentrations were ∼ 400 ppm, and the subaerial Sunda and Sahul shelves made the land–sea distribution of the MC different to today. Topographic changes and elevated levels of CO2, combined with other forcings, are therefore expected to have driven a substantial climate signal in the MC region at this time. By using the results from the Pliocene Model Intercomparison Project Phase 2 (PlioMIP2), we study the mean climatic features of the MC in the mPWP and changes in Indonesian Throughflow (ITF) with respect to the preindustrial. Results show a warmer and wetter mPWP climate of the MC and lower sea surface salinity in the surrounding ocean compared with the preindustrial. Furthermore, we quantify the volume transfer through the ITF; although the ITF may be expected to be hindered by the subaerial shelves, 10 out of 15 models show an increased volume transport compared with the preindustrial. In order to avoid undue influence from closely related models that are present in the PlioMIP2 ensemble, we introduce a new metric, the multi-cluster mean (MCM), which is based on cluster analysis of the individual models. We study the effect that the choice of MCM versus the more traditional analysis of multi-model mean (MMM) and individual models has on the discrepancy between model results and data. We find that models, which reproduce modern MC climate well, are not always good at simulating the mPWP climate anomaly of the MC. By comparing with individual models, the MMM and MCM reproduce the preindustrial sea surface temperature (SST) of the reanalysis better than most individual models and produce less discrepancy with reconstructed sea surface temperature anomalies (SSTA) than most individual models in the MC. In addition, the clusters reveal spatial signals that are not captured by the MMM, so that the MCM provides us with a new way to explore the results from model ensembles that include similar models.

Description: 〈jats:p〉Abstract. The mid-Pliocene warm period (3.264–3.025 Ma) is the most recent geological period in which the atmospheric CO2 concentration was approximately equal to the concentration we measure today (ca. 400 ppm). Sea surface temperature (SST) proxies indicate above-average warming over the North Atlantic in the mid-Pliocene with respect to the pre-industrial period, which may be linked to an intensified Atlantic Meridional Overturning Circulation (AMOC). Earlier results from the Pliocene Model Intercomparison Project Phase 2 (PlioMIP2) show that the ensemble simulates a stronger AMOC in the mid-Pliocene than in the pre-industrial. However, no consistent relationship between the stronger mid-Pliocene AMOC and either the Atlantic northward ocean heat transport (OHT) or average North Atlantic SSTs has been found. In this study, we look further into the drivers and consequences of a stronger AMOC in mid-Pliocene compared to pre-industrial simulations in PlioMIP2. We find that all model simulations with a closed Bering Strait and Canadian Archipelago show reduced freshwater transport from the Arctic Ocean into the North Atlantic. This contributes to an increase in salinity in the subpolar North Atlantic and Labrador Sea that can be linked to the stronger AMOC in the mid-Pliocene. To investigate the dynamics behind the ensemble's variable response of the total Atlantic OHT to the stronger AMOC, we separate the Atlantic OHT into two components associated with either the overturning circulation or the wind-driven gyre circulation. While the ensemble mean of the overturning component is increased significantly in magnitude in the mid-Pliocene, it is partly compensated by a reduction in the gyre component in the northern subtropical gyre region. This indicates that the lack of relationship between the total OHT and AMOC is due to changes in OHT by the subtropical gyre. The overturning and gyre components should therefore be considered separately to gain a more complete understanding of the OHT response to a stronger mid-Pliocene AMOC. In addition, we show that the AMOC exerts a stronger influence on North Atlantic SSTs in the mid-Pliocene than in the pre-industrial, providing a possible explanation for the improved agreement of the PlioMIP2 ensemble mean SSTs with reconstructions in the North Atlantic. 〈/jats:p〉

Description: Numerical modeling enables a comprehensive understanding not only of the Earth's system today, but also of the past. To date, a significant amount of time and effort has been devoted to paleoclimate modeling and analysis, which involves the latest and most advanced Paleoclimate Modelling Intercomparison Project phase 4 (PMIP4). The definition of seasonality, which is influenced by slow variations in the Earth's orbital parameters, plays a key role in determining the calculated seasonal cycle of the climate. In contrast to the classical calendar used today, where the lengths of the months and seasons are fixed, the angular calendar calculates the lengths of the months and seasons according to a fixed number of degrees along the Earth's orbit. When comparing simulation results for different time intervals, it is essential to account for the angular calendar to ensure that the data for comparison are from the same position along the Earth's orbit. Most models use the classical calendar, which can lead to strong distortions of the monthly and seasonal values, especially for the climate of the past. Here, by analyzing daily outputs from multiple PMIP4 model simulations, we examine calendar effects on surface air temperature and precipitation under mid-Holocene, Last Interglacial, and pre-industrial climate conditions. We came to the following conclusions. (a) The largest cooling bias occurs in boreal autumn when the classical calendar is applied for the mid-Holocene and Last Interglacial, due to the fact that the vernal equinox is fixed on 21 March. (b) The sign of the temperature anomalies between the Last Interglacial and pre-industrial in boreal autumn can be reversed after the switch from the classical to angular calendar, particularly over the Northern Hemisphere continents. (c) Precipitation over West Africa is overestimated in boreal summer and underestimated in boreal autumn when the classical seasonal cycle is applied. (d) Finally, month-length adjusted values for surface air temperature and precipitation are very similar to the day-length adjusted values, and therefore correcting the calendar based on the monthly model results can largely reduce the artificial bias. In addition, we examine the calendar effects in three transient simulations for 6–0 ka by AWI-ESM, MPI-ESM, and IPSL-CM. We find significant discrepancies between adjusted and unadjusted temperature values over continents for both hemispheres in boreal autumn, while for other seasons the deviations are relatively small. A drying bias can be found in the summer monsoon precipitation in Africa (in the classical calendar), whereby the magnitude of bias becomes smaller over time. Overall, our study underlines the importance of the application of calendar transformation in the analysis of climate simulations. Neglecting the calendar effects could lead to a profound artificial distortion of the calculated seasonal cycle of surface air temperature and precipitation.

Description: The Maritime Continent (MC) forms the western boundary of the tropical Pacific Ocean, and relatively small changes in this region can impact the climate locally and remotely. In the mid-Piacenzian warm period of the Pliocene (mPWP; 3.264 to 3.025 Ma) atmospheric CO2 concentrations were ∼ 400 ppm, and the subaerial Sunda and Sahul shelves made the land–sea distribution of the MC different to today. Topographic changes and elevated levels of CO2, combined with other forcings, are therefore expected to have driven a substantial climate signal in the MC region at this time. By using the results from the Pliocene Model Intercomparison Project Phase 2 (PlioMIP2), we study the mean climatic features of the MC in the mPWP and changes in Indonesian Throughflow (ITF) with respect to the preindustrial. Results show a warmer and wetter mPWP climate of the MC and lower sea surface salinity in the surrounding ocean compared with the preindustrial. Furthermore, we quantify the volume transfer through the ITF; although the ITF may be expected to be hindered by the subaerial shelves, 10 out of 15 models show an increased volume transport compared with the preindustrial. In order to avoid undue influence from closely related models that are present in the PlioMIP2 ensemble, we introduce a new metric, the multi-cluster mean (MCM), which is based on cluster analysis of the individual models. We study the effect that the choice of MCM versus the more traditional analysis of multi-model mean (MMM) and individual models has on the discrepancy between model results and data. We find that models, which reproduce modern MC climate well, are not always good at simulating the mPWP climate anomaly of the MC. By comparing with individual models, the MMM and MCM reproduce the preindustrial sea surface temperature (SST) of the reanalysis better than most individual models and produce less discrepancy with reconstructed sea surface temperature anomalies (SSTA) than most individual models in the MC. In addition, the clusters reveal spatial signals that are not captured by the MMM, so that the MCM provides us with a new way to explore the results from model ensembles that include similar models.

Description: Diamond–Blackfan anemia (DBA) was the first ribosomopathy associated with mutations in ribosome protein (RP) genes. The clinical phenotypes of DBA include failure of erythropoiesis, congenital anomalies and ca...

Description: Journal of the American Chemical Society DOI: 10.1021/ja406484v

Description: Background: Orange-spotted grouper, Epinephelus coioides, is one of the most valuable fish species in China. Commercial production of orange-spotted grouper could be increased by developing higher growth rates and improving commercially important traits. Information on genetic markers associated with quantitative trait loci (QTL) can be used in breeding programs to identify and select individuals carrying desired traits. A high-density genetic linkage map is the basis for QTL study, and multiplexed shotgun genotyping (MSG) facilitates the development of single nucleotide polymorphisms (SNPs) and genotyping. In this study, the first high-density genetic linkage maps for groupers were generated on the basis of the MSG method. Results: The sex-averaged map contained a total of 4,608 SNPs, which spanned 1581.7 cM, with a mean distance between SNPs of 0.34 cM. The 4,608 SNPs were located in 2,849 unique locations on the linkage map, with an average inter-location space at 0.56 cM. There were 2,516 SNPs on the female map, and the number of unique locus was 1,902. However, the male map contained more numbers of SNP (2,939) and unique locations (2,005). The total length of the female and male maps was 1,370.9 and 1,335.5 cM, respectively. Conclusions: The high-resolution genetic linkage maps will be very useful for QTL analyses and marker-assisted selection (MAS) for economically important traits in molecular breeding of the orange-spotted grouper.

Description: Organic Letters DOI: 10.1021/acs.orglett.8b00622

Description: Background: DNA methylation plays important biological roles in plants and animals. To examine rice genomic methylation landscape and assess its functional significance, we generated the single-base resolution DNA methylome maps for Asian cultivated rice Oryza sativa ssp. japonica, indica and their wild relatives, Oryza rufipogon and Oryza nivara. Results: The overall methylation level of rice genomes is four times higher than that of Arabidopsis. Consistent with the results reported for Arabidopsis, methylation in promoters represses gene expression while gene-body methylation generally appears to promote gene expression. Interestingly, we discovered that methylation in gene transcriptional termination regions (TTRs) can significantly repress gene expression, and the effect is even stronger than that of promoter methylation. Through integrated analysis of genomic, DNA methylomic and transcriptomic differences between cultivated and wild rice, we found that DNA sequence divergence may be the major determinant of methylational differences at the whole genome level, but DNA methylational difference can only account for limited gene expression variation between cultivated and wild rice. We also identified a number of genes with significant difference in methylation level between the wild and cultivated rice. Conclusions: The single-base resolution methylomes of rice obtained in this study have not only broadened our understanding of the mechanism and function of DNA methylation in plant genomes, but also provided valuable data for future studies on rice epigenetics as well as on epigenetic differentiation between wild and cultivated rice.

Description: Organic Letters DOI: 10.1021/ol401251u