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  • 1
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    A method for de novo nucleic acid diagnostic target discovery (2014)
    Oxford University Press
    Details
    Publication Date: 2014-11-07
    Description: Motivation: A proper target or marker is essential in any diagnosis (e.g. an infection or cancer). An ideal diagnostic target should be both conserved in and unique to the pathogen. Currently, these targets can only be identified manually, which is time-consuming and usually error-prone. Because of the increasingly frequent occurrences of emerging epidemics and multidrug-resistant ‘superbugs’, a rapid diagnostic target identification process is needed. Results: A new method that can identify uniquely conserved regions (UCRs) as candidate diagnostic targets for a selected group of organisms solely from their genomic sequences has been developed and successfully tested. Using a sequence-indexing algorithm to identify UCRs and a k -mer integer-mapping model for computational efficiency, this method has successfully identified UCRs within the bacteria domain for 15 test groups, including pathogenic, probiotic, commensal and extremophilic bacterial species or strains. Based on the identified UCRs, new diagnostic primer sets were designed, and their specificity and efficiency were tested by polymerase chain reaction amplifications from both pure isolates and samples containing mixed cultures. Availability and implementation: The UCRs identified for the 15 bacterial species are now freely available at http://ucr.synblex.com . The source code of the programs used in this study is accessible at http://ucr.synblex.com/bacterialIdSourceCode.d.zip Contact: yazhousun@synblex.com Supplementary Information: Supplementary data are available at Bioinformatics online.
    Print ISSN: 1367-4803
    Electronic ISSN: 1460-2059
    Topics: Biology , Computer Science , Medicine
    Published by Oxford University Press
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  • 2
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    Phospholipid transfer protein (PLTP) deficiency accelerates memory dysfunction through altering amyloid precursor protein (APP) processing in a mouse model of Alzheimer's disease (2015)
    Oxford University Press
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    Publication Date: 2015-09-12
    Description: Phospholipid transfer protein (PLTP) is a widely expressed lipid transfer protein participating in the transport of cholesterol and other lipids in the plasma and peripheral tissues. Recently, elevated amyloid β (Aβ) in young and aged PLTP-deficient brains had been reported. However, the role of PLTP in amyloid precursor protein (APP) processing and Alzheimer's disease (AD) pathology remains elusive. Here we first found that deficiency of PLTP accelerated memory dysfunction in APP/PS1E9 AD model mice at the age of 3 months. Further characterization showed that PLTP deficiency increased soluble Aβ peptides, and intracellular accumulation of Aβ was illustrated, which might be due to disrupted APP turnover and the enhanced amyloidogenic pathway. Besides, reduced brain-derived neurotrophic factor (BDNF) was found in PLTP-deficient APP/PS1E9 mice, and the BDNF level was negatively correlated with Aβ42 content, instead of Aβ40 content. In addition, autophagic dysfunction was found in the PLTP-deficient APP/PS1E9 mice. Our data presented a novel model to link phospholipid metabolism to APP processing and also suggested that PLTP played an important role in Aβ metabolism and would be useful to further elucidate functions of PLTP in AD susceptibility.
    Print ISSN: 0964-6906
    Electronic ISSN: 1460-2083
    Topics: Biology , Medicine
    Published by Oxford University Press
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  • 3
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    A study of the high-inclination population in the Kuiper belt - I. The Plutinos (2013)
    Oxford University Press
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    Publication Date: 2013-12-06
    Description: The dynamics of the high-inclination Plutinos is systematically studied. We first present the peculiar features of the 2:3 Neptune mean motion resonance (NMMR) for inclined orbits, especially for the correlation of resonant amplitude A with inclination i . Using the numerical integrations for the age of the Solar system, the dynamical structure of the 2:3 NMMR is mapped out on the plane of semimajor axis versus i for different eccentricities. We have shown that i of stable resonant orbits could be as high as 90°; and the stable region is roughly surrounded by the contours of A  = 120°. These new findings allow us to further explore the 2:3 NMMR capture and retention of planetesimals with initial inclinations i 0  ≤ 90° in the frame of the planet migration model. We find that the outward transportation of Plutinos is possible for any inclined or even perpendicular orbits. The role of i 0 in the formation of Plutinos during Neptune's migration is highlighted and interesting results are obtained: (1) the capture efficiency of the 2:3 NMMR decreases drastically first with the increase of i 0 , but it then raises instead when i 0 exceeds ~50°; (2) the magnitude of i -variation is limited to less than 5° for any i 0 , and moreover, for Plutinos with i   48°, their i are forced to decrease throughout the outward migration; (3) Plutinos with i   48° are certainly outside the Kozai mechanism, since an inclination increase is prohibited by the migrating 2:3 NMMR; (4) the 7:11 inclination-type NMMR could be responsible for nearly circular Plutinos, and a minimum i 0  ~ 15° is required to intrigue this mechanism.
    Print ISSN: 0035-8711
    Electronic ISSN: 1365-2966
    Topics: Physics
    Published by Oxford University Press
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  • 4
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    An association study of TOLL and CARD with leprosy susceptibility in Chinese population (2013)
    Oxford University Press
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    Publication Date: 2013-10-09
    Description: Previous genome-wide association studies (GWASs) identified multiple susceptibility loci that have highlighted the important role of TLR (Toll-like receptor) and CARD (caspase recruitment domain) genes in leprosy. A large three-stage candidate gene-based association study of 30 TLR and 47 CARD genes was performed in the leprosy samples of Chinese Han. Of 4363 SNPs investigated, eight SNPs showed suggestive association ( P 〈 0.01) in our previously published GWAS datasets (Stage 1). Of the eight SNPs, rs2735591 and rs4889841 showed significant association ( P 〈 0.001) in an independent series of 1504 cases and 1502 controls (Stage 2), but only rs2735591 (next to BCL10 ) showed significant association in the second independent series of 938 cases and 5827 controls (Stage 3). Rs2735591 showed consistent association across the three stages ( P 〉 0.05 for heterogeneity test), significant association in the combined validation samples (P corrected = 5.54 x 10 –4 after correction for 4363 SNPs tested) and genome-wide significance in the whole GWAS and validation samples ( P = 1.03 x 10 –9 , OR = 1.24). In addition, we demonstrated the lower expression of BCL10 in leprosy lesions than normal skins and a significant gene connection between BCL10 and the eight previously identified leprosy loci that are associated with NFB, a major regulator of downstream inflammatory responses, which provides further biological evidence for the association. We have discovered a novel susceptibility locus on 1p22, which implicates BCL10 as a new susceptibility gene for leprosy. Our finding highlights the important role of both innate and adaptive immune responses in leprosy.
    Print ISSN: 0964-6906
    Electronic ISSN: 1460-2083
    Topics: Biology , Medicine
    Published by Oxford University Press
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  • 5
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    MethHC: a database of DNA methylation and gene expression in human cancer (2015)
    Oxford University Press
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    Publication Date: 2015-01-16
    Description: We present MethHC ( http://MethHC.mbc.nctu.edu.tw ), a database comprising a systematic integration of a large collection of DNA methylation data and mRNA/microRNA expression profiles in human cancer. DNA methylation is an important epigenetic regulator of gene transcription, and genes with high levels of DNA methylation in their promoter regions are transcriptionally silent. Increasing numbers of DNA methylation and mRNA/microRNA expression profiles are being published in different public repositories. These data can help researchers to identify epigenetic patterns that are important for carcinogenesis. MethHC integrates data such as DNA methylation, mRNA expression, DNA methylation of microRNA gene and microRNA expression to identify correlations between DNA methylation and mRNA/microRNA expression from TCGA (The Cancer Genome Atlas), which includes 18 human cancers in more than 6000 samples, 6548 microarrays and 12 567 RNA sequencing data.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
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  • 6
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    Degradation of phenol wastewater by a new electromagnetic induction photo-catalytic reactor (2016)
    Institute of Physics (IOP)
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    Publication Date: 2016-09-03
    Description: A new inductive photo-catalytic reactor was obtained by the alternative magnetic field and optical coupling, which was driven by AC supply. In the cylinder reactor, UV-LED lights with the wavelength of 375-380nm were evenly distributed, and the phenol solution was used as simulated wastewater. The effects of initial phenol concentration, pH, TiO 2 , H 2 O 2 , alternative magnetic frequency, current, and reaction time on the phenol degradation were investigated under an imposed alternative magnetic field. The optimized conditions and results were as follows: phenol concentrations of 15mg/L, pH of 7, H 2 O 2 of 15μL, TiO 2 of 0.18g and alternative magnetic frequency of 12 KHz and current of 2A. With these conditions, the phenol degradation ratio reached 47.1% in 1 h reaction time. The new reactor is very promising for the effective treatment of refractory organic pollutants.
    Print ISSN: 1755-1307
    Electronic ISSN: 1755-1315
    Topics: Geography , Geosciences , Physics
    Published by Institute of Physics (IOP)
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  • 7
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    Study on optimized algorithm for mileage wheel of magnetic flux leakage detector (2017)
    Institute of Physics (IOP)
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    Publication Date: 2017-07-22
    Description: Pipeline integrity is significant to safe operation of long-range pipeline. To avoid critical failure of the pipeline, which may lead to great loss of property and life, MFL_PIG is often used to detect the corrosion and leakage of the pipeline. To accurately locate the defects, mileage pulses emitted by the mileage wheel are used to and emit signal to single-chip microcomputer for position. This paper investigates the factors that may affect the precision of mileage wheel, an important part of pipeline corrosion and leakage detector (MFL_PIG), investigate its working principle and present an optimized algorithm for mileage wheel to increase the precision of detection.
    Print ISSN: 1757-8981
    Electronic ISSN: 1757-899X
    Topics: Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics
    Published by Institute of Physics (IOP)
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  • 8
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    Establishment of magnetic sensors in above ground marking system (2017)
    Institute of Physics (IOP)
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    Publication Date: 2017-07-22
    Description: Magnetic sensors used in Above Ground Markers (AGM) to measure the magnetic field signals are one of the main parts of AGM. By collecting the change of magnetic field parameter using magnetic sensors, AGM can record the precise time when MFL_PIG is passing by the AGM. In this paper, the magnetic sensors, such as induced coil and magneto-resistive sensor, are investigated in characteristics and performance of measurement. With advantages of low cost, high resolution and wide range of measurement, the induced coil is adopted in a novel AGM. The traction test, seal ability test and temperature test show that the AGM with induced coil as magnetic sensor works well under extreme condition and reacts to change the magnetic field with high sensibility.
    Print ISSN: 1757-8981
    Electronic ISSN: 1757-899X
    Topics: Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics
    Published by Institute of Physics (IOP)
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  • 9
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    A study of the high-inclination population in the Kuiper belt - II. The Twotinos (2014)
    Oxford University Press
    Details
    Publication Date: 2014-07-24
    Description: As the second part of our study, in this paper, we proceed to explore the dynamics of the high-inclination Twotinos in the 1:2 Neptune mean motion resonance (NMMR). Depending on the inclination i , we show the existence of two critical eccentricities e a ( i ) and e c ( i ), which are lower limits of the eccentricity e for the resonant angle to exhibit libration and asymmetric libration, respectively. Accordingly, we have determined the libration centres 0 for inclined orbits, which are strongly dependent on i . With initial = 0 on a fine grid of ( e , i ), the stability of orbits in the 1:2 NMMR is probed by 4-Gyr integrations. It is shown that symmetric librators are totally unstable for i ≥ 30°; while stable asymmetric librators exist for i up to 90°. We further investigate the 1:2 NMMR capture and retention of planetesimals with initial inclinations i 0 ≤ 90° in the planet migration model using a time-scale of 2 x 10 7 yr. We find that: (1) the capture efficiency of the 1:2 NMMR decreases drastically with the increase of i 0 , and it goes to 0 when i 0 60°; (2) the probability of discovering Twotinos with i 〉 25°, beyond observed values, is roughly estimated to be 0.1 per cent; (3) more particles are captured into the leading rather than the trailing asymmetric resonance for i 0 ≤ 10°, but this number difference appears to be the opposite at i 0 = 20° and is continuously varying for even larger i 0 ; (4) captured Twotinos residing in the trailing resonance or having i 〉 15° are practically outside the Kozai mechanism, like currently observed samples.
    Print ISSN: 0035-8711
    Electronic ISSN: 1365-2966
    Topics: Physics
    Published by Oxford University Press
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  • 10
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    A Sensitive and Accurate protein domain cLassification Tool (SALT) for short reads (2013)
    Oxford University Press
    Details
    Publication Date: 2013-08-13
    Description: Motivation: Protein domain classification is an important step in functional annotation for next-generation sequencing data. For RNA-Seq data of non-model organisms that lack quality or complete reference genomes, existing protein domain analysis pipelines are applied to short reads directly or to contigs that are generated using de novo sequence assembly tools. However, these strategies do not provide satisfactory performance in classifying short reads into their native domain families. Results: We introduce SALT, a protein domain classification tool based on profile hidden Markov models and graph algorithms. SALT carefully incorporates the characteristics of reads that are sequenced from the domain regions and assembles them into contigs based on a supervised graph construction algorithm. We applied SALT to two RNA-Seq datasets of different read lengths and quantified its performance using the available protein domain annotations and the reference genomes. Compared with existing strategies, SALT showed better sensitivity and accuracy. In the third experiment, we applied SALT to a non-model organism. The experimental results demonstrated that it identified more transcribed protein domain families than other tested classifiers. Availability: The source code and supplementary data are available at https://sourceforge.net/projects/salt1/ Contact: yannisun@msu.edu Supplementary information: Supplementary data are available at Bioinformatics online.
    Print ISSN: 1367-4803
    Electronic ISSN: 1460-2059
    Topics: Biology , Computer Science , Medicine
    Published by Oxford University Press
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