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Further evidence for the genetic association between CACNA1I and schizophrenia

Background Recent large-scale genome-wide association studies (GWAS) have showed that the neuronal calcium signaling has pivotal roles in schizophrenia (SCZ) in populations of European of ancestry. However, it is not known if calcium signaling pathway genes are also associated with SCZ in Han Chinese population. Methods Here we investigated the association between genetic...

Integrated intracellular metabolic profiling and pathway analysis approaches reveal complex metabolic regulation by Clostridium acetobutylicum

Background Clostridium acetobutylicum is one of the most important butanol producing strains. However, environmental stress in the fermentation process usually leads to a lower yield, seriously hampering its industrialization. In order to systematically investigate the key intracellular metabolites that influence the strain growth and butanol production, and find out the critical...

Identifying causal regulatory SNPs in ChIP-seq enhancers

Di Huang 0 Ivan Ovcharenko 0 0 Computational Biology Branch, National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health , Bethesda, MD 20892 , USA

Moxibustion Alleviates Injury in a Rat Focal Segmental Glomerulosclerosis Model

. Chunling Zhang designed the experiments and wrote the manuscript. Ke Wang wrote the manuscript. Peicheng Shen, Di Huang, Wen Ma, and Jin Zhang designed the experiments. Lin Li performed experiments. Liqun He

A Meta-Analysis of Randomized Controlled Trials of Yiqi Yangyin Huoxue Method in Treating Diabetic Nephropathy

Screening Literature screening was performed by two authors (Di Huang and Jian Dong Gao) independently. They screened literature on the inclusion criteria. All identified abstracts and full texts of ... . Competing Interests The authors declare that there is no conflict of interests regarding the publication of this paper. Authors’ Contributions Jiao Ying Ou and Di Huang contributed equally to this work

Enhancer modeling uncovers transcriptional signatures of individual cardiac cell states in Drosophila

Here we used discriminative training methods to uncover the chromatin, transcription factor (TF) binding and sequence features of enhancers underlying gene expression in individual cardiac cells. We used machine learning with TF motifs and ChIP data for a core set of cardiogenic TFs and histone modifications to classify Drosophila cell-type-specific cardiac enhancer activity. We...

High-resolution genome-wide DNA methylation maps of mouse primary female dermal fibroblasts and keratinocytes

Background Genome-wide DNA methylation at a single nucleotide resolution in different primary cells of the mammalian genome helps to determine the characteristics and functions of tissue-specific hypomethylated regions (TS-HMRs). We determined genome-wide cytosine methylation maps at 91X and 36X coverage of newborn female mouse primary dermal fibroblasts and keratinocytes and...

Genome-scale metabolic network guided engineering of Streptomyces tsukubaensis for FK506 production improvement

Background FK506 is an important immunosuppressant, which can be produced by Streptomyces tsukubaensis. However, the production capacity of the strain is very low. Hereby, a computational guided engineering approach was proposed in order to improve the intracellular precursor and cofactor availability of FK506 in S. tsukubaensis. Results First, a genome-scale metabolic model of S...

Development and application of an automatic measurement method for nozzle orifice diameter and length

Diesel sprays are important to engine combustion and emission formation processes, however, their behaviors are difficult to predict as they are very sensitive to the internal geometries of the nozzle. Based on synchrotron radiation X-ray tomography, a novel method is presented for measuring automatically the orifice diameter and length of fuel nozzles. According to this method...

Model-Driven Redox Pathway Manipulation for Improved Isobutanol Production in Bacillus subtilis Complemented with Experimental Validation and Metabolic Profiling Analysis

To rationally guide the improvement of isobutanol production, metabolic network and metabolic profiling analysis were performed to provide global and profound insights into cell metabolism of isobutanol-producing Bacillus subtilis. The metabolic flux distribution of strains with different isobutanol production capacity (BSUL03, BSUL04 and BSUL05) drops a hint of the importance of...

Rational improvement of the engineered isobutanol-producing Bacillus subtilis by elementary mode analysis

Background Isobutanol is considered as a leading candidate for the replacement of current fossil fuels, and expected to be produced biotechnologically. Owing to the valuable features, Bacillus subtilis has been engineered as an isobutanol producer, whereas it needs to be further optimized for more efficient production. Since elementary mode analysis (EMA) is a powerful tool for...

Endoplasmic Reticulum Stress-Unfolding Protein Response-Apoptosis Cascade Causes Chondrodysplasia in a col2a1 p.Gly1170Ser Mutated Mouse Model

thank LetPub for its linguistic assistance during the preparation of this manuscript. Conceived and designed the experiments: PS Dongsheng Huang. Performed the experiments: GL CL Di Huang AL YP WY ZW

Machine learning classification of cell-specific cardiac enhancers uncovers developmental subnetworks regulating progenitor cell division and cell fate specification

The Drosophila heart is composed of two distinct cell types, the contractile cardial cells (CCs) and the surrounding non-muscle pericardial cells (PCs), development of which is regulated by a network of conserved signaling molecules and transcription factors (TFs). Here, we used machine learning with array-based chromatin immunoprecipitation (ChIP) data and TF sequence motifs to...

Lin28 Induces Epithelial-to-Mesenchymal Transition and Stemness via Downregulation of Let-7a in Breast Cancer Cells

The RNA-binding protein Lin28 is known to promote malignancy by inhibiting the biogenesis of let-7, which functions as a tumor suppressor. However, the role of the Lin28/let-7 axis in the epithelial-to-mesenchymal transition (EMT) and stemness in breast cancer has not been clearly expatiated. In our previous study, we demonstrated that let-7 regulates self-renewal and...

Bioactive composite gradient coatings of nano-hydroxyapatite/polyamide66 fabricated on polyamide66 substrates

Tightly bonding of bioactive coating is the first crucial need for orthopaedic implants. This study describes a novel and convenient technique to prepare bioactive coating with high adhesion on orthopaedic substitutes made of polymeric matrix. Here, a chemical corrosion method has been adopted to fabricate a coating on the surface of injection-moulded polyamide66 (PA66...

Design and Selection of a Camelid Single-Chain Antibody Yeast Two-Hybrid Library Produced De Novo for the Cap Protein of Porcine Circovirus Type 2 (PCV2)

Nanobodies (or variable domain of the heavy chain of the heavy-chain antibodies, VHHs) are single-domain antigen-binding fragments derived from camelid heavy chain antibodies. Their comparatively small size, monomeric behavior, high stability, high solubility, and ability to bind epitopes inaccessible to conventional antibodies make them especially suitable for many therapeutic...

MicroRNA-Integrated and Network-Embedded Gene Selection with Diffusion Distance

Gene network information has been used to improve gene selection in microarray-based studies by selecting marker genes based both on their expression and the coordinate expression of genes within their gene network under a given condition. Here we propose a new network-embedded gene selection model. In this model, we first address the limitations of microarray data. Microarray...

DNA Polymorphisms and Biocontrol of Bacillus Antagonistic to Citrus Bacterial Canker with Indication of the Interference of Phyllosphere Biofilms

Citrus bacterial canker caused by Xanthomonas axonopodis pv. citri is a devastating disease resulting in significant crop losses in various citrus cultivars worldwide. A biocontrol agent has not been recommended for this disease. To explore the potential of bacilli native to Taiwan to control this disease, Bacillus species with a broad spectrum of antagonistic activity against...