Atmospheric turbulence and land - atmosphere energy transfer characteristics in the surface layer of the Northern slope of Mt. Qomolangma area : abstract

Based on the turbulent data collected at Quzong site, on the northern slope of Mt. Qomolangma, from April 2005 to March 2006, macro-scale turbulent statistical characteristics and land-atmosphere energy transfer before and after the onset of southwest monsoon were acquired by the eddy correlation method. It was found that Monin-Obukhov similarity theory is applicable for Mt. Qomolangma area. The relationship between normalized wind speed standard deviation and atmospheric stability, variances of normalized temperature and humidity standard deviation with atmospheric stability were simulated in the study. It was also found that energy balance components (net radiation flux, sensible heat flux, latent heat flux and soil heat flux) and surface heating filed had evident diurnal and seasonal changes. Especially under the influence of southwest monsoon, the sensible heat flux and latent heat flux in Quzong area have evident opposite changing trends. The variation characteristics of other surface parameters (surface reflectance and Bowen ratio) is very clear before and after the breakout of southwest monsoon

Genome-Wide Transcriptome and Antioxidant Analyses on Gamma-Irradiated Phases of Deinococcus radiodurans R1

Adaptation of D. radiodurans cells to extreme irradiation environments requires dynamic interactions between gene expression and metabolic regulatory networks, but studies typically address only a single layer of regulation during the recovery period after irradiation. Dynamic transcriptome analysis of D. radiodurans cells using strand-specific RNA sequencing (ssRNA-seq), combined with LC-MS based metabolite analysis, allowed an estimate of the immediate expression pattern of genes and antioxidants in response to irradiation. Transcriptome dynamics were examined in cells by ssRNA-seq covering its predicted genes. Of the 144 non-coding RNAs that were annotated, 49 of these were transfer RNAs and 95 were putative novel antisense RNAs. Genes differentially expressed during irradiation and recovery included those involved in DNA repair, degradation of damaged proteins and tricarboxylic acid (TCA) cycle metabolism. The knockout mutant crtB (phytoene synthase gene) was unable to produce carotenoids, and exhibited a decreased survival rate after irradiation, suggesting a role for these pigments in radiation resistance. Network components identified in this study, including repair and metabolic genes and antioxidants, provided new insights into the complex mechanism of radiation resistance in D. radiodurans

Monitoring Water and Energy Cycles at Climate Scale in the Third Pole Environment (CLIMATE-TPE)

A better understanding of the water and energy cycles at climate scale in the Third Pole Environment is essential for assessing and understanding the causes of changes in the cryosphere and hydrosphere in relation to changes of plateau atmosphere in the Asian monsoon system and for predicting the possible changes in water resources in South and East Asia. This paper reports the following results: (1) A platform of in situ observation stations is briefly described for quantifying the interactions in hydrosphere-pedosphere-atmosphere-cryosphere-biosphere over the Tibetan Plateau. (2) A multiyear in situ L-Band microwave radiometry of land surface processes is used to develop a new microwave radiative transfer modeling system. This new system improves the modeling of brightness temperature in both horizontal and vertical polarization. (3) A multiyear (2001–2018) monthly terrestrial actual evapotranspiration and its spatial distribution on the Tibetan Plateau is generated using the surface energy balance system (SEBS) forced by a combination of meteorological and satellite data. (4) A comparison of four large scale soil moisture products to in situ measurements is presented. (5) The trajectory of water vapor transport in the canyon area of Southeast Tibet in different seasons is analyzed, and (6) the vertical water vapor exchange between the upper troposphere and the lower stratosphere in different seasons is presented

The oyster genome reveals stress adaptation and complexity of shell formation

The Pacific oyster Crassostrea gigas belongs to one of the most species-rich but genomically poorly explored phyla, the Mollusca. Here we report the sequencing and assembly of the oyster genome using short reads and a fosmid-pooling strategy, along with transcriptomes of development and stress response and the proteome of the shell. The oyster genome is highly polymorphic and rich in repetitive sequences, with some transposable elements still actively shaping variation. Transcriptome studies reveal an extensive set of genes responding to environmental stress. The expansion of genes coding for heat shock protein 70 and inhibitors of apoptosis is probably central to the oyster's adaptation to sessile life in the highly stressful intertidal zone. Our analyses also show that shell formation in molluscs is more complex than currently understood and involves extensive participation of cells and their exosomes. The oyster genome sequence fills a void in our understanding of the Lophotrochozoa. © 2012 Macmillan Publishers Limited. All rights reserved

A Systematic Analysis on DNA Methylation and the Expression of Both mRNA and microRNA in Bladder Cancer

Background: DNA methylation aberration and microRNA (miRNA) deregulation have been observed in many types of cancers. A systematic study of methylome and transcriptome in bladder urothelial carcinoma has never been reported. Methodology/Principal Findings: The DNA methylation was profiled by modified methylation-specific digital karyotyping (MMSDK) and the expression of mRNAs and miRNAs was analyzed by digital gene expression (DGE) sequencing in tumors and matched normal adjacent tissues obtained from 9 bladder urothelial carcinoma patients. We found that a set of significantly enriched pathways disrupted in bladder urothelial carcinoma primarily related to "neurogenesis" and "cell differentiation" by integrated analysis of -omics data. Furthermore, we identified an intriguing collection of cancer-related genes that were deregulated at the levels of DNA methylation and mRNA expression, and we validated several of these genes (HIC1, SLIT2, RASAL1, and KRT17) by Bisulfite Sequencing PCR and Reverse Transcription qPCR in a panel of 33 bladder cancer samples. Conclusions/Significance: We characterized the profiles between methylome and transcriptome in bladder urothelial carcinoma, identified a set of significantly enriched key pathways, and screened four aberrantly methylated and expressed genes. Conclusively, our findings shed light on a new avenue for basic bladder cancer research

Integrated Profiling of MicroRNAs and mRNAs: MicroRNAs Located on Xq27.3 Associate with Clear Cell Renal Cell Carcinoma

Background: With the advent of second-generation sequencing, the expression of gene transcripts can be digitally measured with high accuracy. The purpose of this study was to systematically profile the expression of both mRNA and miRNA genes in clear cell renal cell carcinoma (ccRCC) using massively parallel sequencing technology. Methodology: The expression of mRNAs and miRNAs were analyzed in tumor tissues and matched normal adjacent tissues obtained from 10 ccRCC patients without distant metastases. In a prevalence screen, some of the most interesting results were validated in a large cohort of ccRCC patients. Principal Findings: A total of 404 miRNAs and 9,799 mRNAs were detected to be differentially expressed in the 10 ccRCC patients. We also identified 56 novel miRNA candidates in at least two samples. In addition to confirming that canonical cancer genes and miRNAs (including VEGFA, DUSP9 and ERBB4; miR-210, miR-184 and miR-206) play pivotal roles in ccRCC development, promising novel candidates (such as PNCK and miR-122) without previous annotation in ccRCC carcinogenesis were also discovered in this study. Pathways controlling cell fates (e. g., cell cycle and apoptosis pathways) and cell communication (e. g., focal adhesion and ECM-receptor interaction) were found to be significantly more likely to be disrupted in ccRCC. Additionally, the results of the prevalence screen revealed that the expression of a miRNA gene cluster located on Xq27.3 was consistently downregulated in at least 76.7% of similar to 50 ccRCC patients. Conclusions: Our study provided a two-dimensional map of the mRNA and miRNA expression profiles of ccRCC using deep sequencing technology. Our results indicate that the phenotypic status of ccRCC is characterized by a loss of normal renal function, downregulation of metabolic genes, and upregulation of many signal transduction genes in key pathways. Furthermore, it can be concluded that downregulation of miRNA genes clustered on Xq27.3 is associated with ccRCC

Comparative mRNA and microRNA Expression Profiling of Three Genitourinary Cancers Reveals Common Hallmarks and Cancer-Specific Molecular Events

Genome-wide gene expression profile using deep sequencing technologies can drive the discovery of cancer biomarkers and therapeutic targets. Such efforts are often limited to profiling the expression signature of either mRNA or microRNA (miRNA) in a single type of cancer.Here we provided an integrated analysis of the genome-wide mRNA and miRNA expression profiles of three different genitourinary cancers: carcinomas of the bladder, kidney and testis.Our results highlight the general or cancer-specific roles of several genes and miRNAs that may serve as candidate oncogenes or suppressors of tumor development. Further comparative analyses at the systems level revealed that significant aberrations of the cell adhesion process, p53 signaling, calcium signaling, the ECM-receptor and cell cycle pathways, the DNA repair and replication processes and the immune and inflammatory response processes were the common hallmarks of human cancers. Gene sets showing testicular cancer-specific deregulation patterns were mainly implicated in processes related to male reproductive function, and general disruptions of multiple metabolic pathways and processes related to cell migration were the characteristic molecular events for renal and bladder cancer, respectively. Furthermore, we also demonstrated that tumors with the same histological origins and genes with similar functions tended to group together in a clustering analysis. By assessing the correlation between the expression of each miRNA and its targets, we determined that deregulation of 'key' miRNAs may result in the global aberration of one or more pathways or processes as a whole.This systematic analysis deciphered the molecular phenotypes of three genitourinary cancers and investigated their variations at the miRNA level simultaneously. Our results provided a valuable source for future studies and highlighted some promising genes, miRNAs, pathways and processes that may be useful for diagnostic or therapeutic applications

Post-Magmatic Fluids Dominate the Mineralization of Dolomite Carbonatitic Dykes Next to the Giant Bayan Obo REE Deposit, Northern China

The Bayan Obo rare earth element (REE) deposit in Inner Mongolia, northern China, is the largest REE deposit in the world, whose mineralization process remains controversial. There are dozens of carbonatite dykes that are tightly related to the deposit. Here we report the petrological and mineralogical characteristics of a typical dolomite carbonatite dyke near the deposit. The dolomite within the dyke experienced intense post-emplacement fluids metasomatism as evidenced by the widespread hydrothermal REE-bearing minerals occurring along the carbonate mineral grains. REE contents of bulk rocks and constituent dolomite minerals (>90 vol.%) are 1407–4184 ppm and 63–152 ppm, respectively, indicating that dolomite is not the dominant mineral controlling the REE budgets of the dyke. There are three types of apatite in the dyke: Type 1 apatite is the primary apatite and contains REE2O3 at 2.35–4.20 wt.% and SrO at 1.75–2.19 wt.%; Type 2 and Type 3 apatites are the products of replacement of primary apatite. The REE2O3 (6.10–8.21 wt.%) and SrO (2.83–3.63 wt.%) contents of Type 2 apatite are significantly elevated for overprinting of REE and Sr-rich fluids derived from the carbonatite. Conversely, Type 3 apatite has decreased REE2O3 (1.17–2.35 wt.%) and SrO (1.51–1.99 wt.%) contents, resulting from infiltration of fluids with low REE and Na concentrations. Our results on the dyke suggest that post-magmatic fluids expelled from the carbonatitic melts dominated the REE mineralization of the Bayan Obo deposit, and a significant fluid disturbance occurred but probably provided no extra REEs to the deposit

The Pedogenesis of Soil Derived from Carbonate Rocks along a Climosequence in a Subtropical Mountain, China

Revealing the pedogenesis of soil on carbonate rocks is a key step in determining the boundaries of soil types along a climosequence. However, related research is lacking for a subtropical mountain. In this study, eight pedons were sampled across an elevation gradient (789–2322 m) having large variation in mean annual precipitation (MAP) (1189–1764 mm) and mean annual temperature (MAT) (5.7–14.9 °C). General processes were performed, including physical, chemical, and morphological characterizations, X-ray diffraction (XRD), total elements’ content, and soil classification of the carbonate rock. In the climo-toposequence, the illite had been transformed into illite-smectite below 1300–1500 m of elevation, 1300–1370 mm of MAP, and above 10.5–11.5 °C of MAT, and into vermiculite above this climate. These findings indicated that the effects of temperature on soil mineral transformation had weakened with the gradual increases in elevation. The pedon at 861 m of elevation, 1206 mm of MAP, and 14.5 °C of MAT, which accounted for the argic horizons, was divided into Argosols after human activities. The finding revealed that changes from forest to cultivated land could potentially accelerate the formation of argic horizons, and it provided a theoretical basis for global carbonate rocks’ weathering conditions and ecological problems in subtropical mountains. When the soils reached approximately 1100–1200 m of elevation, 1250–1300 mm of MAP, and 11.5–13.5 °C of MAT, the argic horizons of the soil could be accounted for, as evolved from the Cambosols in Chinese Soil Taxonomy (CST) (Inceptisols in Soil Taxonomy (ST), Cambisols in the World Reference Base for Soil Resources (WRB)) to the Argosols in CST (Alfisols in ST, Luvisols or Alisols in WRB) under natural vegetation. Therefore, it was indicated that the soil types changed significantly in the CST, ST, and WRB with increases of MAP and decreases of MAT, which provides a reference for determining the boundaries of the soil types along a climosequence in subtropical mountains