Using Pan RNA-Seq Analysis to Reveal the Ubiquitous Existence of 5′ and 3′ End Small RNAs

In this study, we used pan RNA-seq analysis to reveal the ubiquitous existence of both 5′ and 3′ end small RNAs (5′ and 3′ sRNAs). 5′ and 3′ sRNAs alone can be used to annotate nuclear non-coding and mitochondrial genes at 1-bp resolution and identify new steady RNAs, which are usually transcribed from functional genes. Then, we provided a simple and cost effective way for the annotation of nuclear non-coding and mitochondrial genes and the identification of new steady RNAs, particularly long non-coding RNAs (lncRNAs). Using 5′ and 3′ sRNAs, the annotation of human mitochondrial was corrected and a novel ncRNA named non-coding mitochondrial RNA 1 (ncMT1) was reported for the first time in this study. We also found that most of human tRNA genes have downstream lncRNA genes as lncTRS-TGA1-1 and corrected the misunderstanding of them in previous studies. Using 5′, 3′, and intronic sRNAs, we reported for the first time that enzymatic double-stranded RNA (dsRNA) cleavage and RNA interference (RNAi) might be involved in the RNA degradation and gene expression regulation of U1 snRNA in human. We provided a different perspective on the regulation of gene expression in U1 snRNA. We also provided a novel view on cancer and virus-induced diseases, leading to find diagnostics or therapy targets from the ribonuclease III (RNase III) family and its related pathways. Our findings pave the way toward a rediscovery of dsRNA cleavage and RNAi, challenging classical theories

Spatio-Temporal Characteristics of Global Warming in the Tibetan Plateau during the Last 50 Years Based on a Generalised Temperature Zone - Elevation Model

Temperature is one of the primary factors influencing the climate and ecosystem, and examining its change and fluctuation could elucidate the formation of novel climate patterns and trends. In this study, we constructed a generalised temperature zone elevation model (GTEM) to assess the trends of climate change and temporal-spatial differences in the Tibetan Plateau (TP) using the annual and monthly mean temperatures from 1961-2010 at 144 meteorological stations in and near the TP. The results showed the following: (1) The TP has undergone robust warming over the study period, and the warming rate was 0.318°C/decade. The warming has accelerated during recent decades, especially in the last 20 years, and the warming has been most significant in the winter months, followed by the spring, autumn and summer seasons. (2) Spatially, the zones that became significantly smaller were the temperature zones of -6°C and -4°C, and these have decreased 499.44 and 454.26 thousand sq km from 1961 to 2010 at average rates of 25.1% and 11.7%, respectively, over every 5-year interval. These quickly shrinking zones were located in the northwestern and central TP. (3) The elevation dependency of climate warming existed in the TP during 1961-2010, but this tendency has gradually been weakening due to more rapid warming at lower elevations than in the middle and upper elevations of the TP during 1991-2010. The higher regions and some low altitude valleys of the TP were the most significantly warming regions under the same categorizing criteria. Experimental evidence shows that the GTEM is an effective method to analyse climate changes in high altitude mountainous regions

K13 blocks KSHV lytic replication and deregulates vIL6 nad hIL6 expression: A model of lytic replication induced clonal selection in viral oncogenesis

Background. Accumulating evidence suggests that dysregulated expression of lytic genes plays an important role in KSHV (Kaposi's sarcoma associated herpesvirus) tumorigenesis. However, the molecular events leading to the dysregulation of KSHV lytic gene expression program are incompletely understood. Methodoloxy/Principal Findings. We have studied the effect of KSHV-encoded latent protein vFLIP K13, a potent activator of the NF-κB pathway, on lytic reactivation of the virus. We demonstrate that K13 antagonizes RTA, the KSHV lytic-regulator, and effectively blocks the expression of lytic proteins, production of infectious virions and death of the infected cells. Induction of lytic replication selects for clones with increased K13 expression and NF-κB activity, while siRNA-mediated silencing of K13 induces the expression of lytic genes. However, the suppressive effect of K13 on RTA-induced lytic genes is not uniform and it falls to block RTA-induced viral IL6 secretion and cooperates with RTA to enhance cellular IL-6 production, thereby dysregulating the lytic gene expression program. Conclusions/Significance. Our results support a model in which ongoing KSHV, lytic replication selects for clones with progressively higher levels of K13 expression and NF-κB activity, which in turn drive KSHV tumorigenesis by not only directly stimulating cellular survival and proliferation, but also indirectly by dysregulating the viral lytic gene program and allowing non-lytic production of growth-promoting viral and cellular genes. Lytic Replication-Induced Clonal Selection (LyRICS) may represent a general mechanism in viral oncogenesis. 2007 Zhao et al

An Overview of Lipid Metabolism and Nonalcoholic Fatty Liver Disease

The occurrence of nonalcoholic fatty liver disease (NAFLD) is associated with major abnormalities of hepatic lipid metabolism. We propose that lipid abnormalities directly or indirectly contribute to NAFLD, especially fatty acid accumulation, arachidonic acid metabolic disturbance, and ceramide overload. The effects of lipid intake and accumulation on NAFLD and NAFLD treatment are explained with theoretical and experimental details. Overall, these findings provide further understanding of lipid metabolism in NAFLD and may lead to novel therapies

Fine Root Production and Soil Available Nutrients in Rubber Monoculture versus Rubber–Flemingia macrophylla Agroforestry

In the present study, we examined fine root production and soil available nutrients (N, P and K) across different soil depths in rubber monoculture and rubber–Flemingia macrophylla agroforestry of different stand ages. We used the ingrowth cores method and sampled 360 soil cores over four growth intervals, representing one year of growth for the present study. The results showed that root production and macronutrient concentrations generally decreased with increasing soil depth. Total fine root production was comparatively high in the youngest stand age (12 years) rubber monoculture; a similar trend was observed for the soil available P and K, but available N was greater in older than younger stand ages. Root growth and soil available P and K were all lower in the agroforestry system than the monoculture. Significant differences in fine root production with stand ages, management system and seasons suggest that fine root responses to the soil available nutrients are vital to understanding the precise response of above- and belowground biomass to environmental changes

Fine Root Production and Soil Available Nutrients in Rubber Monoculture versus Rubber–<i>Flemingia macrophylla</i> Agroforestry

In the present study, we examined fine root production and soil available nutrients (N, P and K) across different soil depths in rubber monoculture and rubber–Flemingia macrophylla agroforestry of different stand ages. We used the ingrowth cores method and sampled 360 soil cores over four growth intervals, representing one year of growth for the present study. The results showed that root production and macronutrient concentrations generally decreased with increasing soil depth. Total fine root production was comparatively high in the youngest stand age (12 years) rubber monoculture; a similar trend was observed for the soil available P and K, but available N was greater in older than younger stand ages. Root growth and soil available P and K were all lower in the agroforestry system than the monoculture. Significant differences in fine root production with stand ages, management system and seasons suggest that fine root responses to the soil available nutrients are vital to understanding the precise response of above- and belowground biomass to environmental changes

<it>De Novo</it> characterization of the banana root transcriptome and analysis of gene expression under <it>Fusarium oxysporum</it> f. sp. <it>Cubense</it> tropical race 4 infection

<p>Abstract</p> <p>Background</p> <p>Bananas and plantains (Musa spp.) are among the most important crops in the world due to their nutritional and export value. However, banana production has been devastated by fungal infestations caused by <it>Fusarium oxysporum</it> f. sp. <it>cubense</it> (Foc), which cannot be effectively prevented or controlled. Since there is very little known about the molecular mechanism of Foc infections; therefore, we aimed to investigate the transcriptional changes induced by Foc in banana roots.</p> <p>Results</p> <p>We generated a cDNA library from total RNA isolated from banana roots infected with Foc Tropical Race 4 (Foc TR 4) at days 0, 2, 4, and 6. We generated over 26 million high-quality reads from the cDNA library using deep sequencing and assembled 25,158 distinct gene sequences by <it>de novo</it> assembly and gap-filling. The average distinct gene sequence length was 1,439 base pairs. A total of 21,622 (85.94%) unique sequences were annotated and 11,611 were assigned to specific metabolic pathways using the Kyoto Encyclopedia of Genes and Genomes database. We used digital gene expression (DGE) profiling to investigate the transcriptional changes in the banana root upon Foc TR4 infection. The expression of genes in the Phenylalanine metabolism, phenylpropanoid biosynthesis and alpha-linolenic acid metabolism pathways was affected by Foc TR4 infection.</p> <p>Conclusion</p> <p>The combination of RNA-Seq and DGE analysis provides a powerful method for analyzing the banana root transcriptome and investigating the transcriptional changes during the response of banana genes to Foc TR4 infection. The assembled banana transcriptome provides an important resource for future investigations about the banana crop as well as the diseases that plague this valuable staple food.</p

Fe-57 Mossbauer Spectroscopy of Ir-Fe Catalysts for Preferential CO Oxidation in H-2

New insights on the interaction between Ir and Fe oxide are reported. Three Ir-Fe catalysts were prepared by different impregnation sequences of an Al2O3 support. Co-impregnation gave a better catalyst for the preferential CO oxidation in H-2 (PROX) reaction. Microcalorimetry data showed that the adsorption of CO and H-2 were different. Quasi in situ Mossbauer data of the three catalysts after reduction, reoxidation, and PROX reaction showed that a strong interaction between Ir and Fe affected the redox properties of the Ir-Fe catalysts. CO conversion was proportional to the concentration of the Fe2+(a) species, thus, Fe2+(a) was an active site in the PROX reaction. The impregnation sequence influenced the interaction between Ir and Fe and consequently, the amount of the active Fe2+(a) species. A strong Ir-Fe interaction stabilized the active Fe2+ sites for activating O-2

Response of net primary productivity to precipitation exclusion in a savanna ecosystem

Declines in precipitation are expected to affect plant performance and ecosystem carbon uptake. The response of ecosystem productivity to declines in precipitation and potential underlying mechanisms have been well studied in many biomes; however, little is known about the role of declines in precipitation and the involved mechanisms in savanna ecosystems. In a 4-year field precipitation manipulation experiment, we simulated four levels of precipitation exclusion (control, 30%, 50% and 70%) to assess the effects of declines in precipitation on net primary productivity (NPP) in a savanna ecosystem in southwestern China. NPP was strongly correlated with soil water content during the experimental period. Precipitation exclusion significantly decreased the NPP of the entire vegetation including trees, shrubs, perennials and litterfall but significantly increased the NPP of annuals. Our results suggested that precipitation exclusion can reduce the productivity of savannas and that plant functional types differ in sensitivity to precipitation exclusion. These findings imply that future declines in precipitation in savanna regions may negatively impact carbon accumulation and may induce shifts in plant functional types to buffer the effects of declines in precipitation on productivity and stabilize ecosystem function in savannas

The influence of drought strength on soil respiration in a woody savanna ecosystem, southwest China

Drought is expected to be more frequent and more intense with global warming. Our aim was to investigate how soil respiration would respond to different levels of precipitation exclusion ('drought strength'). We conducted a two-year drought experiment in a woody savanna ecosystem in south west of China, which consisted of four treatments: a control treatment (CK); 30% precipitation exclusion (PE3), 50% precipitation exclusion (PE5) and 70% precipitation exclusion (PE7). The cumulative soil respiration rates were significantly decreased in both rainy and dry seasons as drought became more intense. The sensitivity of soil respiration to soil moisture decreased as drought severity increased. There were bursts of CO2 emission when dry soils were rewetted by rainfall after the dry season. Unlike most other exponential relationships between soil respiration and soil temperature, a parabolic function was observed in all treatments (P &lt; 0.05), which was due to higher soil temperature (&gt; 28 A degrees C) coinciding with insufficient soil water content (&lt; 11% Vol). Respiration rate is best represented by a model which combines soil moisture and temperature. Soil respiration rates were significantly decreased as drought enhanced. The response of soil respiration to drought in the dry season should not be ignored especially when evaluating the effect of drought on soil respiration in a whole year in savanna ecosystems. The quadratic relationship between soil respiration and soil temperature may be important for modeling the response of soil respiration to climate change (drought) in savanna ecosystems