miRAS: a data processing system for miRNA expression profiling study

<p>Abstract</p> <p>Background</p> <p>The study of microRNAs (miRNAs) is attracting great considerations. Recent studies revealed that miRNAs play as important regulators of gene expression and some even as cancer players or inhibitors. Many studies try to discover new miRNAs and reveal the miRNA expression profile in cancer using a SAGE-based total RNA clone method. However, the data processing of this method is labor-intensive with several different biological databases and more than ten data processing steps involved.</p> <p>Results</p> <p>With miRAS, miRNAs and possible miRNA candidates contained in the submitted sequencing data were obtained together with their expression profile. The functions of known and predicted miRNAs were then analyzed by miRNA target prediction followed by target gene annotations. Finally, to extract the biological significance of the miRNAs in the samples, further annotations of the known miRNA and target genes were performed by collecting the public expression datasets of miRNA and target genes in normal and cancer tissues.</p> <p>Conclusion</p> <p>We introduce a web-based analysis platform called miRNA Analysis System (miRAS), for processing and analyzing of the sequence data obtained from the total RNA clone method. The system was built on generalizing the study of a liver cancer cell line total RNA sequencing project. miRAS is freely available on the web.</p

Research progress in plant molecular systematics of lauraceae

Lauraceae is a large family of woody plants with high ecological and economic value. The tribal and generic division and phylogenetic relationship of Lauraceae have long been contro-versial. Based on morphological and molecular evidence, phylogenetic relationships within the Cinnamomeae, Laureae and Perseeae tribes, also called ‘the Core Lauraceae’, have arisen particular attention. In this review, we comprehensively collated the literatures on the phylogeny of Lau-raceae published in recent years and summarized progress made in molecular systematic researches employing gene fragments, chloroplast genomes and DNA barcodings analyses. We clarified the phylogenetic relationships and main controversies of ‘the Core Lauraceae’, the systemic position of fuzzy genera (Neocinnamomum, Caryodaphnopsis and Cassytha) and the development of chloroplast genome and DNA barcodes. We further suggested and proposed the whole genome analysis and different inflorescence types would be possible to provide more information for further research on phylogenetic relationships and taxonomy of Lauraceae

The oldest oil accumulation in China: Meso-proterozoic Xiamaling Formation bituminous sandstone reservoirs

Based on analysis on the coexistent relationship between igneous rock intrusion and bituminous sandstone of the Xiamaling Formation in northern Hebei (Qnx), the accumulation time of the Xiamaling Formation bituminous sandstone reservoir is defined by the methods of organic petrology and isotope chronology. According to field investigation, observation of thin-section and the shallow drilling show, and based on the previous results of oil seepages and bitumen spots in the Qnx base sandstone, thirty-one new oil seepages (bitumen spots), including twenty-one visible black bitumen spots, were discovered in the Qnx. The distribution of paleo-reservoirs in the Qnx bituminous sandstone was identified, and 4 paleo-reservoirs, i.e. Shuangdong paleo-reservoir in Pingquan, Longtangou paleo-reservoir in Lingyuan, Lujiazhuang paleo-reservoir and Tashan paleo-reservoir in Kuancheng, have been named. The reserves of the paleo-reservoirs are 0.7-1.0 billion tons, which are calculated by the volume method with the solid bitumen content. Organic petrology analysis shows that two kinds of solid bitumen with diferent reflectivity characteristics were developed. Class structure of natural coke is discovered in solid bitumen, which is the first direct evidence to prove that severe thermal alteration occurs in the Qnx base sandstone bitumen. The age of Qnx gabbro-diabase baddeleyite by SHRIMP U-Pb dating is 1 327 Ma±2 Ma, which indicates that the accumulation time of the Xiamaling Formation bituminous sandstone is 1 400 Ma to 1 327 Ma. So, it is the oldest oil accumulation in China. 摘要: ：从冀北坳陷下马岭组（Qnx）沥青砂岩与火成岩侵入体的共存关系入手，利用有机岩石学、同位素年代学方法准确厘定Qnx沥青砂岩油藏的成藏时限。根据野外调查、实验室薄片镜下观察及浅钻结果，在前人已发现Qnx底砂岩油苗/沥青点的基础上，新发现Qnx油苗/沥青点31处（其中肉眼可见黑色沥青点21处），基本查明了Qnx沥青砂岩油藏平面分布规律并命名了4个古油藏：平泉双洞、凌源龙潭沟、宽城芦家庄和宽城塌山古油藏。根据沥青含量，采用体积法估算Qnx沥青砂岩古油藏的规模在7´108～10´108 t。大量样品的有机岩石学分析发现，Qnx沥青砂岩中发育两类具有不同反射率特征的固体沥青，在固体沥青中发现了类天然焦结构，首次以直接证据证实Qnx底砂岩沥青遭受过严重的热蚀变效应。Qnx辉长辉绿岩斜锆石SHRIMP U-Pb测年结果为1 327 Ma±2 Ma，限定Qnx沥青砂岩油藏的成藏时间为1 400～1 327 Ma，确定Qnx沥青砂岩油藏是迄今为止中国最古老的油藏。图7表1参30 Key words: bituminous sandstone, Mesoproterozoic-Neoproterozoic, Xiamaling Formation, igneous rock, oldest reservoir, accumulation time, Yansha

The complete chloroplast genome of Phoebe minutiflora (Lauraceae)

Phoebe minutiflora H. W. Li, is a member of the Lauraceae family, while its generic relationship has been long-term controversial. The complete chloroplast (cp) genome of P. minutiflora was first reported in this paper. The cp genome was 152,654 bp in length with four typical quadripartite structures, which was consisted of a large single-copy (LSC) region of 93,697 bp, a small single-copy (SSC) region of 18,809 bp, and two inverted repeats (IRs) of 20,074 bp. In addition, there were a total of 112 unique genes, including 79 protein-coding genes, 29 tRNA genes, and four rRNA genes. The phylogenetic analysis indicated that P. minutiflora should be placed into Machilus

Magnesium sulfate reduces vascular endothelial cell apoptosis in rats with preeclampsia via the miR-218-5p/HMGB1 pathway

Objective This study aims to investigate the mechanism by which magnesium sulfate regulates the miR-218-5p/HMGB-pathway-mediated apoptosis of vascular endothelial cells (VECs) in rats with preeclampsia (PE). Methods Twenty pregnant rats were randomly divided into four groups: normal, PE, MgSO4, and high-mobility group protein B1 (HMGB1)-agomir groups. On the 14th day of each rat’s pregnancy, endotoxin was used to establish a PE model in the PE, MgSO4, and HMGB1-agomir groups. Then, the MgSO4 and HMGB1-agomir groups were treated with magnesium sulfate. Finally, HMGB1 overexpression was performed only in the HMGB1-agomir group. The rats’ urinary protein content and systolic blood pressure at 24 h were detected on the 11th, 13th, 15th, 17th, and 19th day of pregnancy. Results Compared with the PE group, 24-h urinary protein content, blood pressure, VEC apoptosis rate, apoptosis marker levels, and HMGB1 expression decreased while miR-218-5p levels increased in the MgSO4 group. The dual-luciferase assay revealed that HMGB1 can be targeted and regulated by miR-218-5p. Compared with the MgSO4 group, 24-h urinary protein content, blood pressure, VEC apoptosis rate, apoptosis marker levels, and HMGB1 expression increased while miR-218-5p levels decreased in the HMGB1-agomir group. Conclusion MgSO4 reduces VEC apoptosis in PE rats via the miR-218-5p/HMGB1 pathway and thus plays a role in treating PE

Insulin-Like Peptide Receptor-Mediated Signaling Pathways Orchestrate Regulation of Growth in the Pacific Oyster (Crassostrea gigas), as Revealed by Gene Expression Profiles

The involvement of insulin/insulin-like growth factor signaling (IIS) pathways in the growth regulation of marine invertebrates remains largely unexplored. In this study, we used a fast-growing Pacific oyster (Crassostrea gigas) variety “Haida No.1” as the material with which to unravel the role of IIS systems in growth regulation in oysters. Systematic bioinformatics analyses allowed us to identify major components of the IIS signaling pathway and insulin-like peptide receptor (ILPR)-mediated signaling pathways, including PI3K-AKT, RAS-MAPK, and TOR, in C. gigas. The expression levels of the major genes in IIS and its downstream signaling pathways were significantly higher in “Haida No.1” than in wild oysters, suggesting their involvement in the growth regulation of C. gigas. The expression profiles of IIS and its downstream signaling pathway genes were significantly altered by nutrient abundance and culture temperature. These results suggest that the IIS signaling pathway coupled with the ILPR-mediated signaling pathways orchestrate the regulation of energy metabolism to control growth in Pacific oysters

Long-Term (2017&ndash;2020) Aerosol Optical Depth Observations in Hohhot City in Mongolian Plateau and the Impacts from Different Types of Aerosol

Aerosol optical depth (AOD) measurements for 2017&ndash;2020 in urban Hohhot of the Mongolian plateau, a transition zone between the depopulated zone and East Asian urban agglomeration, were analyzed for the first time. Results show that annual AOD500 and &Aring;ngstr&ouml;m exponent &alpha;440-675 were 0.36 &plusmn; 0.09 and 1.11 &plusmn; 0.16 (2017), 0.41 &plusmn; 0.12 and 0.90 &plusmn; 0.28 (2018), 0.38 &plusmn; 0.09 and 1.13 &plusmn; 0.24 (2019), 0.38 &plusmn; 0.12 and 1.17 &plusmn; 0.22 (2020), respectively, representing a slightly polluted level with a mixed type of coarse dust aerosol and a fine urban/industrial aerosol. Throughout the year, depopulated-zone continental air flows predominated in Hohhot (i.e., NW-quadrant wind), accounting for 82.12% (spring), 74.54% (summer), 63.61% (autumn), and 100% (winter). The clean and strong NW-quadrant air flows induced by the south movement of a Siberian anticyclone resulted in a low 500-nm AOD of 0.30 &plusmn; 0.29, 0.20 &plusmn; 0.15, 0.24 &plusmn; 0.29, and 0.13 &plusmn; 0.08 from spring to winter. Meanwhile, the local emissions from Hohhot city, as well as anthropogenic urban/industrial aerosols transported by southern and western air masses, originating from southern urban agglomeration and western industrial cities (Baotou, Wuhai, etc.), contributed to the highest aerosol loading, with significant transformation rates of the secondary aerosols Sulfate-Nitrate-Ammonium (SNA) of 47.45%, 57.39%, 49.88%, and 45.16&ndash;47.36% in PM2.5 for each season. The extinction fraction of fine aerosols under these anthropogenic trajectories can be as high as 80%, and the largest fine aerosol size was around 0.2&ndash;0.25 &mu;m. Dust aerosols were suspending in urban Hohhot all year, although at different levels for different seasons, and the extinction fraction of dust aerosol during sandstorms was generally higher than 70%

Characterization of the first complete chloroplast genome sequence of Celtis sinensis (Cannabaceae) and its phylogenetic implications

Celtis sinensis Pers. is a popular garden landscape tree in riparian areas and a valuable resistant tree in many extreme environments. Here, we determined the first complete chloroplast genome of C. sinensis using high-throughput sequencing technology. Our results showed the chloroplast genome of C.sinensis was 159,092 bp long and displayed a typical quadripartite structure consisting of a pair of inverted repeats with a length of 26,895 bp and separating by two single-copy regions (LSC, 86,085 bp and SSC, 19,217 bp). Besides, the chloroplast genome of C. sinensis totally contained 131 genes, including 87 protein coding genes, 36 transfer RNAs and eight ribosomal RNAs. Additionally, a maximum likelihood phylogenetic analysis based on the 19 chloroplast genomes demonstrated the monophyly of Cannabaceae and C. sinensis formed a sister clade to Celtis biondii

Comparative Chloroplast Genomics of Litsea Lam. (Lauraceae) and Its Phylogenetic Implications

Litsea Lam. is an ecological and economic important genus of the “core Lauraceae” group in the Lauraceae. The few studies to date on the comparative chloroplast genomics and phylogenomics of Litsea have been conducted as part of other studies on the Lauraceae. Here, we sequenced the whole chloroplast genome sequence of Litsea auriculata, an endangered tree endemic to eastern China, and compared this with previously published chloroplast genome sequences of 11 other Litsea species. The chloroplast genomes of the 12 Litsea species ranged from 152,132 (L. szemaois) to 154,011 bp (L. garrettii) and exhibited a typical quadripartite structure with conserved genome arrangement and content, with length variations in the inverted repeat regions (IRs). No codon usage preferences were detected within the 30 codons used in the chloroplast genomes, indicating a conserved evolution model for the genus. Ten intergenic spacers (psbE–petL, trnH–psbA, petA–psbJ, ndhF–rpl32, ycf4–cemA, rpl32–trnL, ndhG–ndhI, psbC–trnS, trnE–trnT, and psbM–trnD) and five protein coding genes (ndhD, matK, ccsA, ycf1, and ndhF) were identified as divergence hotspot regions and DNA barcodes of Litsea species. In total, 876 chloroplast microsatellites were located within the 12 chloroplast genomes. Phylogenetic analyses conducted using the 51 additional complete chloroplast genomes of “core Lauraceae” species demonstrated that the 12 Litsea species grouped into four sub-clades within the Laurus-Neolitsea clade, and that Litsea is polyphyletic and closely related to the genera Lindera and Laurus. Our phylogeny strongly supported the monophyly of the following three clades (Laurus–Neolitsea, Cinnamomum–Ocotea, and Machilus–Persea) among the above investigated “core Lauraceae” species. Overall, our study highlighted the taxonomic utility of chloroplast genomes in Litsea, and the genetic markers identified here will facilitate future studies on the evolution, conservation, population genetics, and phylogeography of L. auriculata and other Litsea species