ALBERT

Description: Motivation: Trans -acting small interfering RNAs (ta-siRNAs) play an essential role in the regulation of plant gene expression, but relevant reports are still limited. Bioinformatic analyses indicate that many ta-siRNA-producing loci (TASs) are present in plants, implying the existence of as yet undiscovered ta-siRNAs and related regulatory pathways. To expand our knowledge of these plant gene regulators, we applied high-throughput computational and experimental methods to grapevine ( Vitis vinifera L.). Results: Based on bioinformatic predictions, we identified 49 TASs from 49 055 small RNA clusters. Using RNA degradome analysis, we experimentally validated 5 TASs, 22 ta-siRNAs and 37 ta-siRNA targets. The cis- activities of ta-siRNAs were also confirmed, which suggested an inactive mechanism of TAS transcription, and a produced mechanism of multiple forms of small RNA from same TAS. We examined the conservation of newly identified ta-siRNA regulatory cascades and found that while the cascade related to vviTAS3 was conserved, cascades related to vviTAS7, vviTAS8, vviTAS9 and vviTAS10 were grape-specific. These results broaden the known scope of ta-siRNA regulation. Contact: zhang_chq2002@sohu.com Supplementary information: Supplementary data are available at Bioinformatics online.

Description: We propose the use of the kinetic Sunyaev–Zel'dovich (kSZ) effect to probe the circumgalactic medium (CGM), with the aid of a spectroscopic survey covering the same area of a SZ survey. It is possible to design an optimal estimator of the kSZ effect of the CGM with a matched filter, and to construct the cross-correlation between the estimator and the peculiar velocity recovered from the galaxy survey, which can be measured by stacking a number of galaxies. We investigate two compelling profiles for the CGM – the Maller–Bullock (MB) profile and the β profile – and we estimate the detectability against the synergy of a fiducial galaxy survey with number density 10 –3 h 3 Mpc –3 and an Atacama Cosmology Telescope-like SZ survey. We show that the shape of the filter does not change much with redshift for the β profile, while there are significant side lobes at z  〈 0.1 for the MB profile. By stacking ~10 4 Milky Way-size haloes around z  ~ 0.5, we can obtain 1 signal-to-noise ratio (S/N) for both profiles. The S/N increases with decreasing redshift before it reaches a maximum (~7.5 at z ~= 0.12 for the MB profile and ~19 at z ~= 0.03 for the β profile). Because of the large beam size, a Planck-like cosmic microwave background survey can marginally detect the kSZ signal by stacking the same number of galaxies at z  〈 0.1. The search for the CGM in realistic surveys will involve dividing the galaxies into subsamples with similar redshift and mass of host haloes, and scaling the results presented here to obtain the S/N.

Description: Author(s): L. Fang, Y. J. Zhang, J. Fang, and Y. Zhu We show by direct numerical simulations (DNSs) that in different types of isotropic turbulence, the fourth-order statistical invariants have approximately a linear relation, which can be represented by a straight line in the phase plane, passing two extreme states: the Gaussian state and the restric… [Phys. Rev. E 94, 023114] Published Tue Aug 30, 2016

Description: Xeroderma pigmentosum group D (XPD/ERCC2) encodes an ATP-dependent helicase that plays essential roles in both transcription and nucleotide excision repair of nuclear DNA, however, whether or not XPD exerts similar functions in mitochondria remains elusive. In this study, we provide the first evidence that XPD is localized in the inner membrane of mitochondria, and cells under oxidative stress showed an enhanced recruitment of XPD into mitochondrial compartment. Furthermore, mitochondrial reactive oxygen species production and levels of oxidative stress-induced mitochondrial DNA (mtDNA) common deletion were significantly elevated, whereas capacity for oxidative damage repair of mtDNA was markedly reduced in both XPD-suppressed human osteosarcoma (U2OS) cells and XPD-deficient human fibroblasts. Immunoprecipitation-mass spectrometry analysis was used to identify interacting factor(s) with XPD and TUFM, a mitochondrial Tu translation elongation factor was detected to be physically interacted with XPD. Similar to the findings in XPD-deficient cells, mitochondrial common deletion and oxidative damage repair capacity in U2OS cells were found to be significantly altered after TUFM knock-down. Our findings clearly demonstrate that XPD plays crucial role(s) in protecting mitochondrial genome stability by facilitating an efficient repair of oxidative DNA damage in mitochondria.

Description: With the avalanche of biological sequences generated in the post-genomic age, one of the most challenging problems in computational biology is how to effectively formulate the sequence of a biological sample (such as DNA, RNA or protein) with a discrete model or a vector that can effectively reflect its sequence pattern information or capture its key features concerned. Although several web servers and stand-alone tools were developed to address this problem, all these tools, however, can only handle one type of samples. Furthermore, the number of their built-in properties is limited, and hence it is often difficult for users to formulate the biological sequences according to their desired features or properties. In this article, with a much larger number of built-in properties, we are to propose a much more flexible web server called Pse-in-One ( http://bioinformatics.hitsz.edu.cn/Pse-in-One/ ), which can, through its 28 different modes, generate nearly all the possible feature vectors for DNA, RNA and protein sequences. Particularly, it can also generate those feature vectors with the properties defined by users themselves. These feature vectors can be easily combined with machine-learning algorithms to develop computational predictors and analysis methods for various tasks in bioinformatics and system biology. It is anticipated that the Pse-in-One web server will become a very useful tool in computational proteomics, genomics, as well as biological sequence analysis. Moreover, to maximize users’ convenience, its stand-alone version can also be downloaded from http://bioinformatics.hitsz.edu.cn/Pse-in-One/download/ , and directly run on Windows, Linux, Unix and Mac OS.

Description: Genomic structural variation (GSV) is a ubiquitous phenomenon observed in the genomes of Saccharomyces cerevisiae strains with different genetic backgrounds; however, the physiological and phenotypic effects of GSV are not well understood. Here, we first revealed the genetic characteristics of a widely used industrial S. cerevisiae strain, ZTW1, by whole genome sequencing. ZTW1 was identified as an aneuploidy strain and a large-scale GSV was observed in the ZTW1 genome compared with the genome of a diploid strain YJS329. These GSV events led to copy number variations (CNVs) in many chromosomal segments as well as one whole chromosome in the ZTW1 genome. Changes in the DNA dosage of certain functional genes directly affected their expression levels and the resultant ZTW1 phenotypes. Moreover, CNVs of large chromosomal regions triggered an aneuploidy stress in ZTW1. This stress decreased the proliferation ability and tolerance of ZTW1 to various stresses, while aneuploidy response stress may also provide some benefits to the fermentation performance of the yeast, including increased fermentation rates and decreased byproduct generation. This work reveals genomic characters of the bioethanol S. cerevisiae strain ZTW1 and suggests that GSV is an important kind of mutation that changes the traits of industrial S. cerevisiae strains.

Description: In order to investigate the operation performance of ground-coupled heat-pump (GCHP) system, an analytical simulation model of GCHP system on short time-step basis and a computer program based on this model to predict system operating parameters are developed in this study. Besides, detailed on-site experiments on GCHP test rig installed in a temperate region of China are carried out. The temperature distributions of borehole as well as ground around borehole at different depths are evaluated. Operation parameters of GCHP system such as circulating water temperature, heat rejection into ground and system power consumption when the system operated in intermittent and continuous modes are investigated. The accuracy of proposed simulation model is validated by experimental data. The advantage of GCHP technology in energy efficiency over other conventional air-conditioning systems is proved to be obvious and the performance of GCHP system is found to be affected by its operation modes.

Description: The temperature dependence of magnetic susceptibility ( –T curves) and magnetization ( M–T curves) has been used as a routine rock magnetic tool to characterize the magnetic mineralogy and magnetic granulometry of Chinese loess/palaeosols. However, palaeoclimatic interpretation of these thermomagnetic analyses remains controversial. In the present study, total organic carbon (TOC), thermomagnetic and low-temperature magnetic experiments on Mid-Late Pleistocene loess/palaeosols in Central Asia and the Chinese Loess Plateau (CLP) have been conducted. We found that the M ( T ) cooling curves at room temperature were mostly lower than the corresponding heating curves, whereas for the ( T ) analyses the cooling curves at room temperature were always much higher than the heating curves. Low-temperature magnetic measurements demonstrated that a large amount of superparamagnetic ferrimagnetic particles were produced during the thermal treatment and resulted in the aforementioned differences. This finding further indicated that the use of the M–T curves to estimate the relative content of maghemite in the loess/palaeosols from the CLP was problematic. In addition, a positive correlation exists between the TOC and the frequency-dependent susceptibility ( FD ) in the CLP, suggesting that stronger pedogenesis would result in the simultaneous increase in the content of both maghemite and organic matter. Consequently, the parameters 1 (representing the relative content of pedogenic maghemite), 2 ([ ph – ] + 1 ) and ph (related to the organic matter concentration), which can be calculated from the –T analyses, can potentially be used as new indicators of pedogenesis and palaeoclimate in Central Asia and the CLP.

Description: Increased synthesis of endothelin-1 (ET-1) by human vascular endothelial cells (HVECs) in response to hypoxia underscores persistent vasoconstriction observed in patients with pulmonary hypertension. The molecular mechanism whereby hypoxia stimulates ET-1 gene transcription is not well understood. Here we report that megakaryocytic leukemia 1 (MKL1) potentiated hypoxia-induced ET-1 transactivation in HVECs. Disruption of MKL1 activity by either a dominant negative mutant or small interfering RNA mediated knockdown dampened ET-1 synthesis. MKL1 was recruited to the proximal ET-1 promoter region (–81/+150) in HVECs challenged with hypoxic stress by the sequence-specific transcription factor serum response factor (SRF). Depletion of SRF blocked MKL1 recruitment and blunted ET-1 transactivation by hypoxia. Chromatin immunoprecipitation analysis of the ET-1 promoter revealed that MKL1 loss-of-function erased histone modifications consistent with transcriptional activation. In addition, MKL1 was indispensable for the occupancy of Brg1 and Brm, key components of the chromatin remodeling complex, on the ET-1 promoter. Brg1 and Brm modulated ET-1 transactivation by impacting histone modifications. In conclusion, our data have delineated a MKL1-centered complex that links epigenetic maneuverings to ET-1 transactivation in HVECs under hypoxic conditions.

Description: Aims Although many studies have reported net gains of soil organic carbon (SOC) after afforestation on croplands, this is uncertain for Chinese paddy rice croplands. Here, we aimed to evaluate the effects of afforestation of paddy rice croplands on SOC sequestration and soil respiration ( R s ). Such knowledge would improve our understanding of the effectiveness of various land use options on greenhouse gas mitigation in China. Methods The investigation was conducted on the Chongming Island, north subtropical China. Field sites were reclaimed from coastal salt marshes in the 1960s, and soils were homogeneous with simple land use histories. SOC stocks and R s levels were monitored over one year in a paddy rice cropland, an evergreen and a deciduous broad-leaved plantation established on previous paddy fields and a reference fallow land site never cultivated. Laboratory incubation of soil under fast-changing temperatures was used to compare the temperature sensitivity ( Q 10 ) of SOC decomposition across land uses. Important Findings After 15–20 years of afforestation on paddy fields, SOC concentration only slightly increased at the depth of 0–5cm but decreased in deeper layers, which resulted in a net loss of SOC stock in the top 40cm. Seasonal increase of SOC was observed during the rice-growing period in croplands but not in afforested soils, suggesting a stronger SOC sequestration by paddy rice cropping. However, SOC sequestered under cropping was more labile, as indicated by its higher contents of dissolved organic carbon and microbial biomass. Also, paddy soils had higher annual R s than afforested soils; R s abruptly increased after paddy fields were drained and plowed and remained distinctively high throughout the dry farming period. Laboratory incubation revealed that paddy soils had a much higher Q 10 of SOC decomposition than afforested soils. Given that temperature was the primary controller of R s in this region, it was concluded that despite the stronger SOC sequestration by paddy rice cropping, its SOC was less stable than in afforested systems and might be more easily released into the atmosphere under global warming.