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Exact and Direct Modeling Technique for Rotor-Bearing Systems with Arbitrary Selected Degrees-of-Freedom

An exact and direct modeling technique is proposed for modeling of rotor-bearing systems with arbitrary selected degrees-of-freedom. This technique is based on the combination of the transfer and dynamic stiffness matrices. The technique differs from the usual combination methods in that the global dynamic stiffness matrix for the system or the subsystem is obtained directly by...

Chemical and genetic diversity of Astragalus mongholicus grown in different eco-climatic regions

Shilin Chen 1 0 Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College , Beijing , China , 2 Sustainability Department , Traditional Medicinals

miRNA-221 of exosomes originating from bone marrow mesenchymal stem cells promotes oncogenic activity in gastric cancer

miRNA-221 of exosomes originating from bone marrow mesenchymal stem cells promotes oncogenic activity in gastric cancer Min Ma,1,* Shilin Chen,1,* Zhuo Liu,1 Hailong Xie,2 Hongyu Deng,3 Song Shang,1 ... e a r c h Min Ma,1,* shilin chen, 1,* Zhuo liu, 1 hailong Xie, 2 hongyu Deng, 3 song shang, 1 http://dx.doi.org/10.2147/OTT.S143315 in future clinical medicine. Introduction It was reported that

Compensatory Base Changes in ITS2 Secondary Structures Correlate with the Biological Species Concept Despite Intragenomic Variability in ITS2 Sequences – A Proof of Concept

: Shilin Chen and Jingyuan Song have been supported by the Fundamental Research Funds for the Central Universities of China (No. 2012C02). The funders had no role in study design, data collection and

Processing Technology Investigation of Loquat (Eriobotrya japonica) Leaf by Ultra-Performance Liquid Chromatography-Quadrupole Time-of-Flight Mass Spectrometry Combined with Chemometrics

Ultra-performance liquid chromatography-quadrupole time-of-flight mass spectrometry (UPLC-QTOF/MS) and multivariate statistical analysis were used to investigate the processing technology of Loquat (Eriobotrya japonica) leaf (pipaye, PPY). The differences in samples processed using different methods were revealed by unsupervised principal component analysis (PCA). In the scores...

Characterisation of Caenorhabditis elegans sperm transcriptome and proteome

Background Although sperm is transcriptionally and translationally quiescent, complex populations of RNAs, including mRNAs and non-coding RNAs, exist in sperm. Previous microarray analysis of germ cell mutants identified hundreds of sperm genes in Caenorhabditis elegans. To take a more comprehensive view on C. elegans sperm genes, here, we isolate highly pure sperm cells and...

FastUniq: A Fast De Novo Duplicates Removal Tool for Paired Short Reads

The presence of duplicates introduced by PCR amplification is a major issue in paired short reads from next-generation sequencing platforms. These duplicates might have a serious impact on research applications, such as scaffolding in whole-genome sequencing and discovering large-scale genome variations, and are usually removed. We present FastUniq as a fast de novo tool for...

Transcriptome analysis reveals ginsenosides biosynthetic genes, microRNAs and simple sequence repeats in Panax ginseng C. A. Meyer

Background Panax ginseng C. A. Meyer is one of the most widely used medicinal plants. Complete genome information for this species remains unavailable due to its large genome size. At present, analysis of expressed sequence tags is still the most powerful tool for large-scale gene discovery. The global expressed sequence tags from P. ginseng tissues, especially those isolated...

Genome-wide identification and characterization of novel genes involved in terpenoid biosynthesis in Salvia miltiorrhiza

Terpenoids are the largest class of plant secondary metabolites and have attracted widespread interest. Salvia miltiorrhiza, belonging to the largest and most widely distributed genus in the mint family, is a model medicinal plant with great economic and medicinal value. Diterpenoid tanshinones are the major lipophilic bioactive components in S. miltiorrhiza. Systematic analysis...

Comprehensive transcriptome analysis reveals novel genes involved in cardiac glycoside biosynthesis and mlncRNAs associated with secondary metabolism and stress response in Digitalis purpurea

Background Digitalis purpurea is an important ornamental and medicinal plant. There is considerable interest in exploring its transcriptome. Results Through high-throughput 454 sequencing and subsequent assembly, we obtained 23532 genes, of which 15626 encode conserved proteins. We determined 140 unigenes to be candidates involved in cardiac glycoside biosynthesis. It could be...

Utility of the trnH–psbA Intergenic Spacer Region and Its Combinations as Plant DNA Barcodes: A Meta-Analysis

Background The trnH–psbA intergenic spacer region has been used in many DNA barcoding studies. However, a comprehensive evaluation with rigorous sequence preprocessing and statistical testing on the utility of trnH–psbA and its combinations as DNA barcodes is lacking. Methodology/Principal Findings Sequences were searched from GenBank for a meta-analysis on the usefulness of trnH...

Comparative transcriptome sequencing of germline and somatic tissues of the Ascaris suum gonad

Background Ascaris suum (large roundworm of pigs) is a parasitic nematode that causes substantial losses to the meat industry. This nematode is suitable for biochemical studies because, unlike C. elegans, homogeneous tissue samples can be obtained by dissection. It has large sperm, produced in great numbers that permit biochemical studies of sperm motility. Widespread study of A...

De novo characterization of the root transcriptome of a traditional Chinese medicinal plant Polygonum cuspidatum

Various active components have been extracted from the root of Polygonum cuspidatum. However, the genetic basis for their activity is virtually unknown. In this study, 25600002 short reads (2.3 Gb) of P. cuspidatum root transcriptome were obtained via Illumina HiSeq 2000 sequencing. A total of 86418 unigenes were assembled de novo and annotated. Twelve, 18, 60 and 54 unigenes...

DNA Barcode Goes Two-Dimensions: DNA QR Code Web Server

The DNA barcoding technology uses a standard region of DNA sequence for species identification and discovery. At present, “DNA barcode” actually refers to DNA sequences, which are not amenable to information storage, recognition, and retrieval. Our aim is to identify the best symbology that can represent DNA barcode sequences in practical applications. A comprehensive set of...

The Complete Chloroplast Genome Sequence of the Medicinal Plant Salvia miltiorrhiza

Salvia miltiorrhiza is an important medicinal plant with great economic and medicinal value. The complete chloroplast (cp) genome sequence of Salvia miltiorrhiza, the first sequenced member of the Lamiaceae family, is reported here. The genome is 151,328 bp in length and exhibits a typical quadripartite structure of the large (LSC, 82,695 bp) and small (SSC, 17,555 bp) single...

Complete chloroplast genome sequence of Magnolia grandiflora and comparative analysis with related species

Magnolia grandiflora is an important medicinal, ornamental and horticultural plant species. The chloroplast (cp) genome of M. grandiflora was sequenced using a 454 sequencing platform and the genome structure was compared with other related species. The complete cp genome of M. grandiflora was 159623 bp in length and contained a pair of inverted repeats (IR) of 26563 bp separated...

Evaluating the feasibility of using candidate DNA barcodes in discriminating species of the large Asteraceae family

Chang Liu 0 Shilin Chen 0 0 Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College , Beijing , PR China 1 College of Life Sciences, Qingdao

Comparison of 454-ESTs from Huperzia serrata and Phlegmariurus carinatus reveals putative genes involved in lycopodium alkaloid biosynthesis and developmental regulation

Background Plants of the Huperziaceae family, which comprise the two genera Huperzia and Phlegmariurus, produce various types of lycopodium alkaloids that are used to treat a number of human ailments, such as contusions, swellings and strains. Huperzine A, which belongs to the lycodine type of lycopodium alkaloids, has been used as an anti-Alzheimer's disease drug candidate...

Transcriptome Analysis of Buds and Leaves Using 454 Pyrosequencing to Discover Genes Associated with the Biosynthesis of Active Ingredients in Lonicera japonica Thunb.

Background Lonicera japonica Thunb. is a plant used in traditional Chinese medicine known for its anti-inflammatory, anti-oxidative, anti-carcinogenic, and antiviral pharmacological properties. The major active secondary metabolites of this plant are chlorogenic acid (CGA) and luteoloside. While the biosynthetic pathways of these metabolites are relatively well known, the genetic...

Analysis of the transcriptome of Panax notoginseng root uncovers putative triterpene saponin-biosynthetic genes and genetic markers

Background Panax notoginseng (Burk) F.H. Chen is important medicinal plant of the Araliacease family. Triterpene saponins are the bioactive constituents in P. notoginseng. However, available genomic information regarding this plant is limited. Moreover, details of triterpene saponin biosynthesis in the Panax species are largely unknown. Results Using the 454 pyrosequencing...