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  • 1
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    Robust detection of alternative splicing in a population of single cells (2016)
    Oxford University Press
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    Publication Date: 2016-05-06
    Description: Single cell RNA-seq experiments provide valuable insight into cellular heterogeneity but suffer from low coverage, 3' bias and technical noise. These unique properties of single cell RNA-seq data make study of alternative splicing difficult, and thus most single cell studies have restricted analysis of transcriptome variation to the gene level. To address these limitations, we developed SingleSplice, which uses a statistical model to detect genes whose isoform usage shows biological variation significantly exceeding technical noise in a population of single cells. Importantly, SingleSplice is tailored to the unique demands of single cell analysis, detecting isoform usage differences without attempting to infer expression levels for full-length transcripts. Using data from spike-in transcripts, we found that our approach detects variation in isoform usage among single cells with high sensitivity and specificity. We also applied SingleSplice to data from mouse embryonic stem cells and discovered a set of genes that show significant biological variation in isoform usage across the set of cells. A subset of these isoform differences are linked to cell cycle stage, suggesting a novel connection between alternative splicing and the cell cycle.
    Keywords: Computational Methods, Genomics
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
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  • 2
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    A feasible energy-saving analysis of a new system for CO2 cryogenic capture (2016)
    Oxford University Press
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    Publication Date: 2016-05-27
    Description: A new CO 2 cryogenic capture and liquefaction system has been proposed previously in order to separate CO 2 from exhausted gases and make it as a resource for industry. This system combines CO 2 cryogenic capture with N 2 /O 2 separation together. Its energy consumption is lower than the traditional amine solution capture process as theoretical analysis. In this study, the simulation of the proposed system with several improvements was carried out aiming to reduce the energy consumption further. Many heat exchangers were introduced and the heat exchanger arrangements were optimized to recycle the refrigeration capacity from the returned N 2 after the N 2 /O 2 separation. The discharge pressure of mixture gas from the compressor was reduced from 10 to 3.493 MPa. The simulation results showed that the compression work could be greatly reduced and the energy consumption of CO 2 capture in this new system after these improvements reached 2.884 GJ/ton CO 2 . The new system is promising because not only liquid or solid CO 2 could be produced but also N 2 and O 2 could be separated.
    Print ISSN: 1748-1317
    Electronic ISSN: 1748-1325
    Topics: Energy, Environment Protection, Nuclear Power Engineering , Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics
    Published by Oxford University Press
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  • 3
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    Engineering a ribozyme cleavage-induced split fluorescent aptamer complementation assay (2016)
    Oxford University Press
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    Publication Date: 2016-06-03
    Description: Hammerhead ribozymes are self-cleaving RNA molecules capable of regulating gene expression in living cells. Their cleavage performance is strongly influenced by intra-molecular loop–loop interactions, a feature not readily accessible through modern prediction algorithms. Ribozyme engineering and efficient implementation of ribozyme-based genetic switches requires detailed knowledge of individual self-cleavage performances. By rational design, we devised fluorescent aptamer-ribozyme RNA architectures that allow for the real-time measurement of ribozyme self-cleavage activity in vitro . The engineered nucleic acid molecules implement a split Spinach aptamer sequence that is made accessible for strand displacement upon ribozyme self-cleavage, thereby complementing the fluorescent Spinach aptamer. This fully RNA-based ribozyme performance assay correlates ribozyme cleavage activity with Spinach fluorescence to provide a rapid and straightforward technology for the validation of loop–loop interactions in hammerhead ribozymes.
    Keywords: Synthetic Biology and Assembly Cloning, RNA characterisation and manipulation
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
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  • 4
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    limma powers differential expression analyses for RNA-sequencing and microarray studies (2015)
    Oxford University Press
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    Publication Date: 2015-04-21
    Description: limma is an R/Bioconductor software package that provides an integrated solution for analysing data from gene expression experiments. It contains rich features for handling complex experimental designs and for information borrowing to overcome the problem of small sample sizes. Over the past decade, limma has been a popular choice for gene discovery through differential expression analyses of microarray and high-throughput PCR data. The package contains particularly strong facilities for reading, normalizing and exploring such data. Recently, the capabilities of limma have been significantly expanded in two important directions. First, the package can now perform both differential expression and differential splicing analyses of RNA sequencing (RNA-seq) data. All the downstream analysis tools previously restricted to microarray data are now available for RNA-seq as well. These capabilities allow users to analyse both RNA-seq and microarray data with very similar pipelines. Second, the package is now able to go past the traditional gene-wise expression analyses in a variety of ways, analysing expression profiles in terms of co-regulated sets of genes or in terms of higher-order expression signatures. This provides enhanced possibilities for biological interpretation of gene expression differences. This article reviews the philosophy and design of the limma package, summarizing both new and historical features, with an emphasis on recent enhancements and features that have not been previously described.
    Keywords: Computational Methods
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
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  • 5
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    Glycogen synthase kinase 3 beta inhibits microRNA-183-96-182 cluster via the {beta}-Catenin/TCF/LEF-1 pathway in gastric cancer cells (2014)
    Oxford University Press
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    Publication Date: 2014-03-13
    Description: Glycogen synthase kinase 3 beta (GSK3β) is a critical protein kinase that phosphorylates numerous proteins in cells and thereby impacts multiple pathways including the β-Catenin/TCF/LEF-1 pathway. MicroRNAs (miRs) are a class of noncoding small RNAs of ~22 nucleotides in length. Both GSK3β and miR play myriad roles in cell functions including stem cell development, apoptosis, embryogenesis and tumorigenesis. Here we show that GSK3β inhibits the expression of miR-96, miR-182 and miR-183 through the β-Catenin/TCF/LEF-1 pathway. Knockout of GSK3β in mouse embryonic fibroblast cells increases expression of miR-96, miR-182 and miR-183, coinciding with increases in the protein level and nuclear translocation of β-Catenin. In addition, overexpression of β-Catenin enhances the expression of miR-96, miR-182 and miR-183 in human gastric cancer AGS cells. GSK3β protein levels are decreased in human gastric cancer tissue compared with surrounding normal gastric tissue, coinciding with increases of β-Catenin protein, miR-96, miR-182, miR-183 and primary miR-183-96-182 cluster (pri-miR-183). Furthermore, suppression of miR-183-96-182 cluster with miRCURY LNA miR inhibitors decreases the proliferation and migration of AGS cells. Knockdown of GSK3β with siRNA increases the proliferation of AGS cells. Mechanistically, we show that β-Catenin/TCF/LEF-1 binds to the promoter of miR-183-96-182 cluster gene and thereby activates the transcription of the cluster. In summary, our findings identify a novel role for GSK3β in the regulation of miR-183-96-182 biogenesis through β-Catenin/TCF/LEF-1 pathway in gastric cancer cells.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
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  • 6
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    A novel role for the mono-ADP-ribosyltransferase PARP14/ARTD8 in promoting homologous recombination and protecting against replication stress (2015)
    Oxford University Press
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    Publication Date: 2015-04-02
    Description: Genomic instability, a major hallmark of cancer cells, is caused by incorrect or ineffective DNA repair. Many DNA repair mechanisms cooperate in cells to fight DNA damage, and are generally regulated by post-translational modification of key factors. Poly-ADP-ribosylation, catalyzed by PARP1, is a post-translational modification playing a prominent role in DNA repair, but much less is known about mono-ADP-ribosylation. Here we report that mono-ADP-ribosylation plays an important role in homologous recombination DNA repair, a mechanism essential for replication fork stability and double strand break repair. We show that the mono-ADP-ribosyltransferase PARP14 interacts with the DNA replication machinery component PCNA and promotes replication of DNA lesions and common fragile sites. PARP14 depletion results in reduced homologous recombination, persistent RAD51 foci, hypersensitivity to DNA damaging agents and accumulation of DNA strand breaks. Our work uncovered PARP14 as a novel factor required for mitigating replication stress and promoting genomic stability.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
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  • 7
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    Probing modified gravity theories with ISW and CMB lensing (2014)
    Oxford University Press
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    Publication Date: 2014-06-10
    Description: We use the optimized skew-spectrum as well as the skew-spectra associated with the Minkowski functionals to test the possibility of using the cross-correlation of the integrated Sachs–Wolfe effect (ISW) and lensing of the cosmic microwave background (CMB) radiation to detect deviations in the theory of gravity away from General Relativity (GR). We find that the although both statistics can put constraints on modified gravity, the optimized skew-spectra are especially sensitive to the parameter B 0 that denotes the Compton wavelength of the scalaron at the present epoch. We investigate three modified gravity theories, namely the post-parametrized Friedmann formalism; the Hu–Sawicki model and the Bertschinger–Zukin (BZ) formalism. Employing a likelihood analysis for an experimental setup similar to ESA's Planck mission, we find that, assuming GR to be the correct model, we expect the constraints from the first two skew-spectra, $S_{\ell }^{(0)}$ and $S_{\ell }^{(1)}$ , to be the same: B 0  〈 0.45 at 95 per cent confidence level (CL) and B 0  〈 0.67 at 99 per cent CL in the BZ model. The third skew-spectrum does not give any meaningful constraint. We find that the optimal skew-spectrum provides much more powerful constraint, giving B 0  〈 0.071 at 95 per cent CL and B 0  〈 0.15 at 99 per cent CL, which is essentially identical to what can be achieved using the full bispectrum.
    Print ISSN: 0035-8711
    Electronic ISSN: 1365-2966
    Topics: Physics
    Published by Oxford University Press
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  • 8
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    Adapt-Mix: learning local genetic correlation structure improves summary statistics-based analyses (2015)
    Oxford University Press
    Details
    Publication Date: 2015-06-14
    Description: Motivation: Approaches to identifying new risk loci, training risk prediction models, imputing untyped variants and fine-mapping causal variants from summary statistics of genome-wide association studies are playing an increasingly important role in the human genetics community. Current summary statistics-based methods rely on global ‘best guess’ reference panels to model the genetic correlation structure of the dataset being studied. This approach, especially in admixed populations, has the potential to produce misleading results, ignores variation in local structure and is not feasible when appropriate reference panels are missing or small. Here, we develop a method, Adapt-Mix, that combines information across all available reference panels to produce estimates of local genetic correlation structure for summary statistics-based methods in arbitrary populations. Results: We applied Adapt-Mix to estimate the genetic correlation structure of both admixed and non-admixed individuals using simulated and real data. We evaluated our method by measuring the performance of two summary statistics-based methods: imputation and joint-testing. When using our method as opposed to the current standard of ‘best guess’ reference panels, we observed a 28% decrease in mean-squared error for imputation and a 73.7% decrease in mean-squared error for joint-testing. Availability and implementation: Our method is publicly available in a software package called ADAPT-Mix available at https://github.com/dpark27/adapt_mix . Contact: noah.zaitlen@ucsf.edu
    Print ISSN: 1367-4803
    Electronic ISSN: 1460-2059
    Topics: Biology , Computer Science , Medicine
    Published by Oxford University Press
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  • 9
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    Engineering of a 3'-sulpho-Gal{beta}1-4GlcNAc-specific probe by a single amino acid substitution of a fungal galectin (2015)
    Oxford University Press
    Details
    Publication Date: 2015-03-28
    Description: Among sulphated glycans, little is known about 3'-sulphation because of the lack of useful probes. In the course of molecular engineering of a fungal galectin from Agrocybe cylindracea , we found that a single substitution of Glu86 with alanine resulted in acquisition of specific binding for the 3'-sulpho-Galβ1-4GlcNAc structure. Extensive glyco-technological analysis revealed that this property was obtained in a ‘loss-of-function’ manner. Though this mutant (E86A) had low total affinity, it showed substantial binding to a naturally occurring N -glycan, of which the terminal galactose is 3-sulphated. Moreover, E86A specifically bound to HeLa cells, in which galactose-3- O -sulfotransferases (Gal3ST2 or Gal3ST3) were over-expressed.
    Print ISSN: 0021-924X
    Electronic ISSN: 1756-2651
    Topics: Biology , Chemistry and Pharmacology
    Published by Oxford University Press on behalf of The Japanese Biochemical Society (JBS).
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  • 10
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    Genome-wide association study in Chinese identifies novel loci for blood pressure and hypertension (2015)
    Oxford University Press
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    Publication Date: 2015-01-13
    Description: Hypertension is a common disorder and the leading risk factor for cardiovascular disease and premature deaths worldwide. Genome-wide association studies (GWASs) in the European population have identified multiple chromosomal regions associated with blood pressure, and the identified loci altogether explain only a small fraction of the variance for blood pressure. The differences in environmental exposures and genetic background between Chinese and European populations might suggest potential different pathways of blood pressure regulation. To identify novel genetic variants affecting blood pressure variation, we conducted a meta-analysis of GWASs of blood pressure and hypertension in 11 816 subjects followed by replication studies including 69 146 additional individuals. We identified genome-wide significant ( P 〈 5.0 x 10 –8 ) associations with blood pressure, which included variants at three new loci ( CACNA1D , CYP21A2 , and MED13L ) and a newly discovered variant near SLC4A7 . We also replicated 14 previously reported loci, 8 ( CASZ1 , MOV10 , FGF5 , CYP17A1 , SOX6 , ATP2B1 , ALDH2 , and JAG1 ) at genome-wide significance, and 6 ( FIGN , ULK4 , GUCY1A3 , HFE , TBX3-TBX5 , and TBX3 ) at a suggestive level of P = 1.81 x 10 –3 to 5.16 x 10 –8 . These findings provide new mechanistic insights into the regulation of blood pressure and potential targets for treatments.
    Print ISSN: 0964-6906
    Electronic ISSN: 1460-2083
    Topics: Biology , Medicine
    Published by Oxford University Press
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