ALBERT

Description: Although millions of RNA editing events have been reported to modify hereditary information across the primate transcriptome, evidence for their functional significance remains largely elusive, particularly for the vast majority of editing sites in noncoding regions. Here, we report a new mechanism for the functionality of RNA editing—a crosstalk with PIWI-interacting RNA (piRNA) biogenesis. Exploiting rhesus macaque as an emerging model organism closely related to human, in combination with extensive genome and transcriptome sequencing in seven tissues of the same animal, we deciphered accurate RNA editome across both long transcripts and the piRNA species. Superimposing and comparing these two distinct RNA editome profiles revealed 4,170 editing-bearing piRNA variants, or epiRNAs, that primarily derived from edited long transcripts. These epiRNAs represent distinct entities that evidence an intersection between RNA editing regulations and piRNA biogenesis. Population genetics analyses in a macaque population of 31 independent animals further demonstrated that the epiRNA-associated RNA editing is maintained by purifying selection, lending support to the functional significance of this crosstalk in rhesus macaque. Correspondingly, these findings are consistent in human, supporting the conservation of this mechanism during the primate evolution. Overall, our study reports the earliest lines of evidence for a crosstalk between selectively constrained RNA editing regulation and piRNA biogenesis, and further illustrates that such an interaction may contribute substantially to the diversification of the piRNA repertoire in primates.

Description: In this paper, we prove that the Cauchy problem for a non-linear wave equation (1) has a unique global generalized solutions in and a unique global classical solution in . We also prove that the Cauchy problem for the equation (1) admits a unique global generalized solution in C 2 ([0, ); W m , p ( R )   L ( R ))( m  ≥ 0 is an integer,1 ≤  p  ≤ ) and a unique global classical solution in .

Description: The non-coding RNA 7SK is the scaffold for a small nuclear ribonucleoprotein (7SKsnRNP) which regulates the function of the positive transcription elongation factor P-TEFb in the control of RNA polymerase II elongation in metazoans. The La-related protein LARP7 is a component of the 7SKsnRNP required for stability and function of the RNA. To address the function of LARP7 we determined the crystal structure of its La module, which binds a stretch of uridines at the 3'-end of 7SK. The structure shows that the penultimate uridine is tethered by the two domains, the La-motif and the RNA-recognition motif (RRM1), and reveals that the RRM1 is significantly smaller and more exposed than in the La protein. Sequence analysis suggests that this impacts interaction with 7SK. Binding assays, footprinting and small-angle scattering experiments show that a second RRM domain located at the C-terminus binds the apical loop of the 3' hairpin of 7SK, while the N-terminal domains bind at its foot. Our results suggest that LARP7 uses both its N- and C-terminal domains to stabilize 7SK in a closed structure, which forms by joining conserved sequences at the 5'-end with the foot of the 3' hairpin and has thus functional implications.

Description: Whole-genome duplication (WGD), or polyploidy, is a major force in plant genome evolution. A duplicate of all genes is present in the genome immediately following a WGD event. However, the evolutionary mechanisms responsible for the loss of, or retention and subsequent functional divergence of polyploidy-derived duplicates remain largely unknown. In this study we reconstructed the evolutionary history of the glutathione S-transferase (GST) gene family from the soybean genome, and identified 72 GST duplicated gene pairs formed by a recent Glycine -specific WGD event occurring approximately 13 Ma. We found that 72% of duplicated GST gene pairs experienced gene losses or pseudogenization, whereas 28% of GST gene pairs have been retained in the soybean genome. The GST pseudogenes were under relaxed selective constraints, whereas functional GSTs were subject to strong purifying selection. Plant GST genes play important roles in stress tolerance and detoxification metabolism. By examining the gene expression responses to abiotic stresses and enzymatic properties of the ancestral and current proteins, we found that polyploidy-derived GST duplicates show the divergence in enzymatic activities. Through site-directed mutagenesis of ancestral proteins, this study revealed that nonsynonymous substitutions of key amino acid sites play an important role in the divergence of enzymatic functions of polyploidy-derived GST duplicates. These findings provide new insights into the evolutionary and functional dynamics of polyploidy-derived duplicate genes.

Description: Aims Ecosystem carbon models often require accurate net ecosystem exchange of CO 2 (NEE) light-response parameters, which can be derived from the Michaelis–Menten equation. These parameters include maximum net ecosystem exchange (NEE max ), apparent quantum use efficiency ( α ) and daytime ecosystem respiration rate ( R e ). However, little is known about the effects of land conversion between steppe and cropland on these parameters, especially in semi-arid regions. To understand how these parameters vary in responses to biotic and abiotic factors under land conversions, seasonal variation of light-response parameters were evaluated for a steppe and a cropland of Inner Mongolia, China, during three consecutive years (2006–08) with different precipitation amounts. Methods NEE was measured over a steppe and a cropland in Duolun, Inner Mongolia, China, using the eddy covariance technique, and NEE light-response parameters (NEE max , α and R e ) were derived using the Michaelis–Menten model. Biophysical regulations of these parameters were evaluated using a stepwise regression analysis. Important Findings The maximum absolute values of NEE max occurred in the meteorological regimes of 15°C ≤ T a 〈 25°C, vapor pressure deficit (VPD) 〈 1 KPa and 0.21 m 3 m – 3 ≤ volumetric soil water content at 10 cm (SWC) 〈 0.28 m 3 m – 3 for both the steppe and the cropland ecosystems. The variations of α and R e showed no regular variation pattern in different T air , VPD and SWC regimes. Under the same regime of T air , VPD and SWC, the cropland had higher absolute values of NEE max than the steppe. Canopy conductance and leaf area index (LAI) were dominant drivers for variations in NEE light-response parameters of the steppe and the cropland. The seasonal variation of NEE light-response parameters followed the variation of LAI for two ecosystems. The peak values of all light-response parameters for the steppe and the cropland occurred from July to August. The values of NEE light-response parameters (NEE max , α and R e ) were lower in the driest year (2007). Seasonally averaged NEE light-response parameters for the cropland surpassed those for the steppe. Land conversion from steppe to cropland enhanced NEE light-response parameters during the plant growing period. These results will have significant implications for improving the models on regional NEE variation under climate change and land-use change scenarios.

Description: The photoionization cross-sections of Ti 2+ in the ground state ([Ne]3s 2 3p 6 3d 2 3 F e ) are calculated using both non-relativistic ( LS -coupling) and relativistic (Breit–Pauli) R -matrix methods for the photon energy from 27.49 eV (I.P.) to 48.00 eV. The results show that, in this energy range, the photoionization cross-sections are dominated by resonances 3p 5 3d 3 , 3p 5 3d 2 4d and 3p 5 3d 2 4s, which are labelled by LS -terms by combining with the multiconfiguration Dirac-Fock calculations. Moreover, from the fractional parentage coefficients and the percentages (the square of the configuration interaction expansion coefficients) of the LS -terms involved in the final resonance states, the relative strength of the resonances have been explained qualitatively in a general way. The present results should be of great help in the modelling and diagnostic of astrophysical plasmas as well as laboratory plasmas.

Description: The emerging environmental spread of antibiotic-resistance genes (ARGs) and their subsequent acquisition by clinically relevant microorganisms is a major threat to public health. Animal manure has been recognized as an important reservoir of ARGs; however, the dissemination of manure-derived ARGs and the impacts of manure application on the soil resistome remain obscure. Here, we conducted a microcosm study to assess the temporal succession of total bacteria and a broad spectrum of ARGs in two contrasting soils following manure application from cattle that had not been treated with antibiotics. High-capacity quantitative PCR detected 52 unique ARGs across all the samples, with β-lactamase as the most dominant ARG type. Several genes of soil indigenous bacteria conferring resistance to β-lactam, which could not be detected in manure, were found to be highly enriched in manure-treated soils, and the level of enrichment was maintained over the entire course of 140 days. The enriched β-lactam resistance genes had significantly positive relationships with the relative abundance of the integrase intI1 gene, suggesting an increasing mobility potential in manure-treated soils. The changes in ARG patterns were accompanied by a significant effect of cattle manure on the total bacterial community compositions. Our study indicates that even in the absence of selective pressure imposed by agricultural use of antibiotics, manure application could still strongly impact the abundance, diversity and mobility potential of a broad spectrum of soil ARGs. Our findings are important for reliable prediction of ARG behaviors in soil environment and development of appropriate strategies to minimize their dissemination.

Description: The telomerase is responsible for adding telomeric repeats to chromosomal ends and consists of the reverse transcriptase TERT and the RNA subunit TERC. The expression and activity of the telomerase are tightly regulated, and aberrant activation of the telomerase has been observed in 〉85% of human cancers. To better understand telomerase regulation, we performed immunoprecipitations coupled with mass spectrometry (IP-MS) and identified cold inducible RNA-binding protein (CIRP or hnRNP A18) as a telomerase-interacting factor. We have found that CIRP is necessary to maintain telomerase activities at both 32°C and 37°C. Furthermore, inhibition of CIRP by CRISPR-Cas9 or siRNA knockdown led to reduced telomerase activities and shortened telomere length, suggesting an important role of CIRP in telomere maintenance. We also provide evidence here that CIRP associates with the active telomerase complex through direct binding of TERC and regulates Cajal body localization of the telomerase. In addition, CIRP regulates the level of TERT mRNAs. At the lower temperature, TERT mRNA is upregulated in a CIRP-dependent manner to compensate for reduced telomerase activities. Taken together, these findings highlight the dual roles that CIRP plays in regulating TERT and TERC, and reveal a new class of telomerase modulators in response to hypothermia conditions.

Description: 1, 3-Butadiene (BD) is a high-efficiency carcinogen in rodents and was classified as a human carcinogen in 2008 by the International Agency for Research on Cancer. However, its ability to induce genetic damage and the influence of metabolic polymorphisms to such damage in humans are both controversial claims. This study was conducted to investigate the relationships between exposure to BD, the polymorphisms of metabolic genes and the chromosomal damage in 45 pairs of occupationally exposed workers in a BD product workshop and matched control workers in an administrative office and circulatory water workshop in China. Exposure to BD was evaluated by personal sampling and stationary sampling. Different chromosomal damage endpoints in peripheral blood lymphocytes were determined using the cytokinesis-blocked micronucleus (CBMN) cytome assay; polymorphisms of metabolic genes [cytochrome P450 2E1 ( CYP2E1 ), glutathione S -transferases ( GST ) and microsomal epoxide hydrolase ( mEH )] in BD-exposed group were detected by polymerase chain reaction (PCR) or PCR–restriction fragment length polymorphism analysis. The results show that the average BD measurements of the exposed group were significantly higher than those for the control group (a personal sampling and stationary sampling, respectively). The BD-exposed workers exhibited increased frequencies of micronuclei (MNi) (8.00 ± 3.78 versus 5.62 ± 2.41) and nucleoplasmic bridges (NPBs) (2.58 ± 2.79 versus 1.13 ± 1.34) and a decreased nuclear division index (2.20 ± 0.14 versus 2.35 ± 0.27) when compared subjects in the control group. Meanwhile, BD-exposed workers carrying CYP2E1 c1c2/c2c2 or mEH intermediate (I)/high (H) group had a significantly higher NPB frequency than those carrying CYP2E1 c1c1 [frequency ratio (FR) = 2.60, 95% confidence interval (CI) 1.72–3.93; P 〈 0.0001) or the mEH low(S) group (FR = 2.06, 95% CI% 1.17–3.62; P 〈 0.05), respectively. Our study suggests that MNi and NPB frequency in CBMN cytome assay could be potential genotoxic biomarkers for BD exposure in humans. The polymorphism of CYP2E1 and mEH could also affect the chromosomal instability of BD workers.

Description: Aims Estimation of gross primary production (GPP) from remote sensing data is an important approach to study regional or global carbon cycle. However, for a given algorithm, it usually has its limitation on applications to a wide range of vegetation types and/or under diverse environmental conditions. This study was conducted to compare the performance of two remote sensing GPP algorithms, the MODIS GPP and the vegetation photosynthesis model (VPM), in a semiarid temperate grassland ecosystem. Methods The study was conducted at a typical grassland site in Ujimuqin of Inner Mongolia, North China, over 2 years in 2006 and 2007. Environmental controls on GPP measured by the eddy covariance (EC) technique at the study site were first investigated with path analysis of meteorological and soil moisture data at a daily and 8-day time steps. The estimates of GPP derived from the MODIS GPP and the VPM with site-specific inputs were then compared with the values of EC measurements as ground truthing at the site. Site-specific max (α) was estimated by using rectangular hyperbola function based on the 7-day flux data at 30-min intervals over the peak period of the growing season (May to September). Important Findings Between the two remote sensing GPP algorithms and various estimates of the fraction of absorbed photosynthetic active radiation (FPAR), the VPM based on FPAR derived from the enhanced vegetation index (EVI) works the best in predicting GPP against the ground truthing of EC GPP. A path analysis indicates that the EC GPP in this semiarid temperate grassland ecosystem is controlled predominantly by both soil water and temperature. The site water condition is slightly better simulated by the moisture multiplier in the VPM than in the MODIS GPP algorithm, which is a most probable explanation for a better performance of the VPM than MODIS GPP algorithm in this semiarid grassland ecosystem.