• Engineered hypoxia-responding Escherichia coli carrying cardiac peptide genes, suppresses tumor growth, angiogenesis and metastasis in vivo

    25 days ago - By Journal of Biological Engineering

    Development of engineered non-pathogenic bacteria, capable of expressing anti-cancer proteins under tumor-specific conditions, is an ideal approach for selectively eradicating proliferating cancer cells. Herei...
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  • CRISPR/Cas9 mediated T7 RNA polymerase gene knock-in in E. coli BW25113 makes T7 expression system work efficiently

    25 days ago - By Journal of Biological Engineering

    T7 Expression System is a common method of ensuring tight control and high-level induced expression. However, this system can only work in some bacterial strains in which the T7 RNA Polymerase gene resides in the...
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  • RNA Solutions: Synthesizing Information to Support Transcriptomics

    25 days ago - By Oxford Journals

    AbstractMotivationTranscriptomics is a common approach to identify changes in gene expression induced by a disease state. Standard transcriptomic analyses consider differentially expressed genes as indicative of disease states so only a few genes would be treated as signals when the effect size is small, such as in brain tissue. For tissue with small effect sizes, if the DEGs do not belong to a pathway known to be involved in the disease, there would be little left in the transcriptome for researchers to follow up with.ResultsWe developed RNA Solutions: Synthesizing Information to Support...
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  • XGBLC: An Improved Survival Prediction Model Based on Xgboost

    25 days ago - By Oxford Journals

    AbstractMotivationSurvival analysis using gene expression profiles plays a crucial role in the interpretation of clinical research and assessment of disease therapy programs. Several prediction models have been developed to explore the relationship between patients' covariates and survival. However, the high-dimensional genomic features limit the prediction performance of the survival model. Thus, an accurate and reliable prediction model is necessary for survival analysis using high-dimensional genomic data.ResultsIn this study, we proposed an improved survival prediction model based on...
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  • Multiomix: a cloud-based platform to infer cancer genomic and epigenomic events associated with gene expression modulation

    25 days ago - By Oxford Journals

    AbstractMotivationLarge-scale cancer genome projects have generated genomic, transcriptomic, epigenomic, and clinicopathological data from thousands of samples in almost every human tumor site. Although most omics data and their associated resources are publicly available, its full integration and interpretation to dissect the sources of gene expression modulation require specialized knowledge and software.ResultsWe present Multiomix, an interactive cloud-based platform that allows biologists to identify genetic and epigenetic events associated with the transcriptional modulation of...
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  • Single-cell landscape of nuclear configuration and gene expression during stem cell differentiation and X inactivation

    25 days ago - By Genome Biology

    Mammalian development is associated with extensive changes in gene expression, chromatin accessibility, and nuclear structure. Here, we follow such changes associated with mouse embryonic stem cell differentia...
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  • Primordial germ cells can be differentiated by retinoic acid and progesterone induction from embryonic stem cells

    25 days ago - By Journal of Biosciences

    Abstract
    This study aimed to examine the expression of the genes associated with different development stages of primordial germ cells in differentiating mouse embryonic stem cells. The cells were cultured in three groups of control, 10 −8 M of all-trans retinoic acid and the combination of 10 −7 M of Progesterone and retinoic acid for 7, 12, 17, and 22 days. Immunofluorescent and Quantitative RT-PCR were used to evaluate the effect of progesterone on the differentiation of mESCs into primordial germ cells. RA-treated cells exhibited increased expression of Fragilis , Stella , Dazl , Stra8...
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  • Boosting the power of transcriptomics by developing an efficient gene expression profiling approach

    25 days ago - By Wiley

    Summary
    Recent advances in plant genomics are scaling up gene expression profiling from the individual level to the population level, making transcriptomics a more powerful tool while deciphering the genome function. This study developed an efficient 3′RNA-seq method, Simplified Poly Anchored Sequencing , to perform large-scale experiments of gene expression quantification. Aside from being cost-effective, by conducting a comprehensive performance assessment of SiPAS in hexaploid wheat, we demonstrated that SiPAS is highly sensitive, accurate, and reproducible while quantifying gene...
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