89 Works

Data from: Functionally reciprocal mutations of the prolactin signalling pathway define hairy and slick cattle

Matthew D. Littlejohn, Kristen M. Henty, Tiplady Kathryn, Thomas Johnson, Chad Harland, Thomas Lopdell, Richard G. Sherlock, Wanbo Li, Steven D. Lukefahr, Bruce C. Shanks, Dorian J. Garrick, Russel G. Snell, Richard J. Spelman & Stephen R. Davis
WGS Variants from 556 NZ Dairy Animals Chr23:30627379-40627379rtg_3.3.1_556_animal_Chr23:30627379-40627379_for_dryad.vcf.gzExome Variants in Multiple Breeds Chr20:34783594-42331973GATK-10MB-Window-Exomes.vcf.gzHairy syndrome genotypes and phenotypesGenotypes and phenotype used for genome-wide analysis of the hairy syndrome, Plink binary format (.bim .bed .fam)gen_phen_data_for_paper.zipHairy bull progeny TaqMan resultsHairy_bull_progeny_TaqMan_results.txtphysiological phenotypesphysiological_phenos.zipDFAM association results for 628,279 SNPDFAM_assoc_results.zipPhased genotypes and phenotypes for 82 Senepol crossbreedsphased_gen_phen_data_slick.zip

A new mechanism for a familiar mutation – bovine DGAT1 K232A modulates gene expression through multi-junction exon splice enhancement

Thomas Lopdell, Tania Fink, Kathryn Tiplady, Renee Handley, Thomas Johnson, Richard Spelman, Stephen Davis, Russell Snell & Mathew Littlejohn
The DGAT1 gene encodes an enzyme responsible for catalysing the terminal reaction in mammary triglyceride synthesis, and underpins a well-known pleiotropic quantitative trait locus (QTL) with a large influence on milk composition phenotypes. Since first described over 15 years ago, a protein-coding variant K232A has been assumed as the causative variant underlying these effects, following in-vitro studies that demonstrated differing levels of triglyceride synthesis between the two protein isoforms. In the current study, we used...

Data from: Non-additive association analysis using proxy phenotypes identifies novel cattle sydromes

Edwardo Reynolds & Mathew Littlejohn
Mammalian species carry ~100 loss-of-function variants per individual, where ~1-5 of these impact essential genes and cause embryonic lethality or severe disease when homozygous. The functions of the remainder are more difficult to resolve, though are assumed to impact fitness in less manifest ways. Here, we present data behind one of the largest sequence-resolution screens of cattle to date, targeting discovery and validation of non-additive effects in 130,725 animals. We highlight six novel recessive loci...

Red and processed meat intakes and cardiovascular disease and type 2 diabetes mellitus: An umbrella systematic review and assessment of causal relations using Bradford Hill’s criteria

Erica R. Hill, Lauren E. O’Connor, Yu Wang, Caroline M. Clark, Bethany S. McGowan, Michele R. Forman & Wayne W. Campbell
Observational research suggests higher red and processed meat intakes predict greater risks of developing or dying from cardiovascular diseases (CVD) and type 2 diabetes mellitus (T2DM), but this research limits causal inference. This systematic review of reviews utilizes both observational and experimental research findings to infer causality of these relations. Reviews from four databases were screened by two researchers. Reviews included unprocessed red meat (URM), processed meat (PM), or mixed URM + PM intake, and...

Organoids from patient biopsy samples can predict the response of BC patients to neoadjuvant chemotherapy

Dan Shu, Meiying Shen, Kang Li, Xiaojian Han, Han Li, Zhaofu Tan, Yu Wang, Yang Peng, Zhenrong Tang, Chi Qu, Aishun Jin & Shengchun Liu
Neoadjuvant chemotherapy has been widely used in locally advanced and inflammatory breast cancer. Generally, complete pathological response after neoadjuvant chemotherapy treatment predicts survival. Studies have shown that patient-derived organoids can be used in cancer research and drug development. Therefore, we aimed to generate a living organoid biobank from biopsy samples to predict the response of patients to neoadjuvant chemotherapy. We generated a living organoid biobank from locally advanced breast cancer patients receiving neoadjuvant chemotherapy. When...

Organoids from patient biopsy samples can predict the response of BC patients to neoadjuvant chemotherapy

Dan Shu, Meiying Shen, Kang Li, Xiaojian Han, Han Li, Zhaofu Tan, Yu Wang, Yang Peng, Zhenrong Tang, Chi Qu, Aishun Jin & Shengchun Liu
Neoadjuvant chemotherapy has been widely used in locally advanced and inflammatory breast cancer. Generally, complete pathological response after neoadjuvant chemotherapy treatment predicts survival. Studies have shown that patient-derived organoids can be used in cancer research and drug development. Therefore, we aimed to generate a living organoid biobank from biopsy samples to predict the response of patients to neoadjuvant chemotherapy. We generated a living organoid biobank from locally advanced breast cancer patients receiving neoadjuvant chemotherapy. When...

Additional file 1 of Transcutaneous electrical acupoint stimulation for high-normal blood pressure: study protocol for a randomized controlled pilot trial

Yu Wang, Guang-Xia Shi, Zhong-Xue Tian, Jun-Hong Liu, You-Sheng Qi, Jian-Feng Tu, Jing-Wen Yang, Li-Qiong Wang & Cun-Zhi Liu
Additional file 1. Completed Standard Protocol Items: Recommendation for Interventional Trials (SPIRIT) 2013 Checklist: items addressed in this clinical trial protocol.

Integrative analysis of a novel 5 methylated snoRNA genes prognostic signature in patients with glioma

Bing Zhao, Erbao Bian, Deran Zhang, Zhiwei Wang, Yu Wang, Zhigang Cheng, Zhihao Yang, Lianxin Li, Yinfei Zheng & Xiaoyu Yue
Supplementary Table 1 | Genes associated with risk scores.
Supplementary Table 2 | Expression levels and methylation levels of SNORA71B in gliomas (TCGA Database). Supplementary Table 3 | Fold change values of the 5 methylated snoRNA genes (TCGA Database).
Supplementary Table 4 | Methylation levels of five snoRNAs in gliomas (TCGA Database).
Supplementary Table 5 Clinic-pathological characteristics of 13 glioma patients.

Genome-wide association analysis reveals QTL and candidate mutations involved in white spotting in cattle

Swati Jivanji, Gemma Worth, Thomas J. Lopdell, Anna Yeates, Christine Couldrey, Edwardo Reynolds, Kathryn Tiplady, Lorna McNaughton, Thomas J.J. Johnson, Stephen R Davis, Bevin Harris, Richard Spelman, Russell G Snell, Dorian Garrick & Mathew D. Littlejohn
Background White spotting of the coat is a characteristic trait of various domestic species including cattle and other mammals. It is a hallmark of Holstein-Friesian cattle, and several previous studies have detected genetic loci with major effects for white spotting in animals with Holstein-Friesian ancestry. Here, our aim was to better understand the underlying genetic and molecular mechanisms of white spotting, by conducting the largest mapping study for this trait in cattle, to date. Results...

Folic acid-modified ROS-responsive nanoparticles encapsulating luteolin for targeted breast cancer treatment

Yu Wang, Qianmei Wang, Wei Feng, Qian Yuan, Xiaowei Qi, Sheng Chen, Pu Yao, Qing Dai, Peiyuan Xia, Dinglin Zhang & Fengjun Sun
Luteolin (Lut) is a natural flavonoid polyphenolic compound with multiple pharmacological activities, such as anti-oxidant, anti-inflammatory, and anti-tumor effects. However, the poor aqueous solubility and low bioactivity of Lut restrict its clinical translation. Herein, we developed a reactive oxygen species (ROS)-responsive nanoplatforms to improve the bioactivity of Lut. Folic acid (FA) was employed to decorate the nanoparticles (NPs) to enhance its targeting ability. The size of Lut-loaded ROS-responsive nanoparticles (Lut/Oxi-αCD NPs) and FA-modified Lut/Oxi-αCD NPs...

MICALL2 as a substrate of ubiquitinase TRIM21 regulates tumorigenesis of colorectal cancer

Pushuai Wen, Huade Wang, Yi Li, Xinyao Sui, Zhijuan Hou, Xiaoyan Guo, Wanying Xue, Dahua Liu, Yu Wang & Jing Gao
Abstract Background Molecule interacting with CasL-like protein 2 (MICALL2) is believed to regulate cytoskeleton dynamics, tight junction formation, and neurite outgrowth. However, its biological role and the underlying mechanism in colorectal cancer (CRC) remain largely elusive. Methods qRT-PCR, Western blotting and immunohistochemistry assays were used to detect the expression levels of different genes. Next, mass spectrometry, co-immunoprecipitation and immunofluorescence staining were used to detect the interactions of proteins. Furthermore, MTT assay, colony formation assay, wound-healing...

Additional file 11 of Deficiency of exchange protein directly activated by cAMP (EPAC)-1 in mice augments glucose intolerance, inflammation, and gut dysbiosis associated with Western diet

Preeti Dinesh Virwani, Lin Cai, Patrick Ka Kit Yeung, Gordon Qian, Yingxian Chen, Lei Zhou, Jason Wing Hon Wong, Yu Wang, Joshua Wing Kei Ho, Kui Kai Lau, Pei-Yuan Qian & Sookja Kim Chung
Additional file 11: Table S9. KEGG orthology IDs.

Additional file 2 of Deficiency of exchange protein directly activated by cAMP (EPAC)-1 in mice augments glucose intolerance, inflammation, and gut dysbiosis associated with Western diet

Preeti Dinesh Virwani, Lin Cai, Patrick Ka Kit Yeung, Gordon Qian, Yingxian Chen, Lei Zhou, Jason Wing Hon Wong, Yu Wang, Joshua Wing Kei Ho, Kui Kai Lau, Pei-Yuan Qian & Sookja Kim Chung
Additional file 2. R scripts used for bioinformatics analysis.

Data from: Sequence-based association analysis reveals an MGST1 eQTL with pleiotropic effects on bovine milk composition

Mathew D. Littlejohn, Kathryn Tiplady, Tania A. Fink, Klaus Lehnert, Thomas Lopdell, Thomas Johnson, Christine Couldrey, Michael D. Keehan, Richard G. Sherlock, Chad Harland, Andrew Scott, Russell G. Snell, Stephen R. Davis & Richard J. Spelman
GWAS_pop_dataChromosome 5 Illumina BovineHD genotypes and phenotypes for the milk fat percentage GWAS population.RNAseq_pop_imputed_seq_dataChromsome 5 imputed sequence and gene expression data used for eQTL mappingRNAseq_pop_imputed_seq_data_with_gap_varsChromsome 5 imputed sequence and gene expression data used for eQTL mapping - with reference gap variantsLarge_pop_imputed_seqChromsome 5 imputed sequence and phenotype data used for milk composition association mappingRNAseq_pop_del_haplotypeGene expression (phenotypes), pedigree, and diplotype (haplotype pair) data for analysis of the CNV-proxy haplotypeZipped library of Supplementary files 1-12A zipped collection of...

Additional file 5 of Deficiency of exchange protein directly activated by cAMP (EPAC)-1 in mice augments glucose intolerance, inflammation, and gut dysbiosis associated with Western diet

Preeti Dinesh Virwani, Lin Cai, Patrick Ka Kit Yeung, Gordon Qian, Yingxian Chen, Lei Zhou, Jason Wing Hon Wong, Yu Wang, Joshua Wing Kei Ho, Kui Kai Lau, Pei-Yuan Qian & Sookja Kim Chung
Additional file 5: Table S4. Relative abundance of orders detected through 16S rRNA gene sequencing using fecal DNA.

Additional file 7 of Deficiency of exchange protein directly activated by cAMP (EPAC)-1 in mice augments glucose intolerance, inflammation, and gut dysbiosis associated with Western diet

Preeti Dinesh Virwani, Lin Cai, Patrick Ka Kit Yeung, Gordon Qian, Yingxian Chen, Lei Zhou, Jason Wing Hon Wong, Yu Wang, Joshua Wing Kei Ho, Kui Kai Lau, Pei-Yuan Qian & Sookja Kim Chung
Additional file 7: Table S6. Relative abundance of genera detected through 16S rRNA gene sequencing using fecal DNA.

Additional file 9 of Deficiency of exchange protein directly activated by cAMP (EPAC)-1 in mice augments glucose intolerance, inflammation, and gut dysbiosis associated with Western diet

Preeti Dinesh Virwani, Lin Cai, Patrick Ka Kit Yeung, Gordon Qian, Yingxian Chen, Lei Zhou, Jason Wing Hon Wong, Yu Wang, Joshua Wing Kei Ho, Kui Kai Lau, Pei-Yuan Qian & Sookja Kim Chung
Additional file 9: Table S7. Relative abundance of bacterial species determined through shotgun sequencing.

Additional file 10 of Deficiency of exchange protein directly activated by cAMP (EPAC)-1 in mice augments glucose intolerance, inflammation, and gut dysbiosis associated with Western diet

Preeti Dinesh Virwani, Lin Cai, Patrick Ka Kit Yeung, Gordon Qian, Yingxian Chen, Lei Zhou, Jason Wing Hon Wong, Yu Wang, Joshua Wing Kei Ho, Kui Kai Lau, Pei-Yuan Qian & Sookja Kim Chung
Additional file 10: Table S8. Gene coverage of various functional KEGG genes detected through shotgun sequencing.

Photoelectrochemical Immunosensor Based on ZnIn2S4/Bi2Se3 Nanocomposite for the Determination of Cardiac Troponin I

Wanxin Dong, Xinxin Mo, Yu Wang, Qin Lei & He Li
In this work, a novel flexible photoelectrochemical immunosensor is developed to determine cardiac troponin I (cTnI) in serum. The flower-like ZnIn2S4 nanospheres (ZIS), as signal amplification material, were successfully synthesized by a solvothermal method. The ZIS and Bi2Se3 were modified on the indium tin oxide- polyethylene terephthalate (ITO-PET) electrode, which effectively accelerates the electronic transition and improved the photocurrent conversion efficiency (signal on). However, the binding of antigen–antibody proteins blocks the electron transfer, resulting in...

Impacts of menopause hormone therapy on mood disorders among postmenopausal women

P. Feng, L. Lin, Y. Wang, L. Chen, J. Min, Y. Xie, M. Liu, S. Wei, S. Lin & Q. Yu
This study aimed to explore the modulatory effects of menopause hormone therapy (MHT) on mood disorders among postmenopausal women. A cross-sectional study was conducted to recruit postmenopausal women, including patients (arranged MHT for over 3 years as the medication group) and non-MHT controls. All participants were asked to respond to the Center for Epidemiological Studies Depression Scale (CES-D) and Generalized Anxiety Disorder Screener (GAD-7) questionnaires to assess their depression and anxiety status. A total of...

Folic acid-modified ROS-responsive nanoparticles encapsulating luteolin for targeted breast cancer treatment

Yu Wang, Qianmei Wang, Wei Feng, Qian Yuan, Xiaowei Qi, Sheng Chen, Pu Yao, Qing Dai, Peiyuan Xia, Dinglin Zhang & Fengjun Sun
Luteolin (Lut) is a natural flavonoid polyphenolic compound with multiple pharmacological activities, such as anti-oxidant, anti-inflammatory, and anti-tumor effects. However, the poor aqueous solubility and low bioactivity of Lut restrict its clinical translation. Herein, we developed a reactive oxygen species (ROS)-responsive nanoplatforms to improve the bioactivity of Lut. Folic acid (FA) was employed to decorate the nanoparticles (NPs) to enhance its targeting ability. The size of Lut-loaded ROS-responsive nanoparticles (Lut/Oxi-αCD NPs) and FA-modified Lut/Oxi-αCD NPs...

Additional file 1 of Failure pattern and suggestions for target volume delineation of carcinoma showing thymus-like differentiation treated with intensity-modulated radiotherapy

Fang-Fang Kong, Guang-Sen Pan, Rui-Ping Zhai, Cheng-Run Du, Xia-Yun He, Chun-Ying Shen, Xue-Guan Lu, Tuan-Qi Sun, Yu Wang, Qing-Hai Ji, Chao-Su Hu & Hong-Mei Ying
Supplementary Material 1

Accelerated Fatigue Model for Predicting Composite Restoration Failure

B. Yang, W. Aregawi, R. Chen, L. Zhang, Y. Wang & A.S.L. Fok
An empirical method is proposed to predict the clinical performance of resin composite dental restorations by using laboratory data derived from simple specimens subjected to chemical degradation and accelerated cyclic fatigue. Three resin composites were used to fill dentin disks (2-mm inner diameter, 5-mm outer diameter, and 2 mm thick) made from bovine incisor roots. The specimens (n = 30 per group) were aged with different durations of a low-pH challenge (0, 24, and 48...

Accelerated Fatigue Model for Predicting Composite Restoration Failure

B. Yang, W. Aregawi, R. Chen, L. Zhang, Y. Wang & A.S.L. Fok
An empirical method is proposed to predict the clinical performance of resin composite dental restorations by using laboratory data derived from simple specimens subjected to chemical degradation and accelerated cyclic fatigue. Three resin composites were used to fill dentin disks (2-mm inner diameter, 5-mm outer diameter, and 2 mm thick) made from bovine incisor roots. The specimens (n = 30 per group) were aged with different durations of a low-pH challenge (0, 24, and 48...

Transcutaneous electrical acupoint stimulation for high-normal blood pressure: study protocol for a randomized controlled pilot trial

Yu Wang, Guang-Xia Shi, Zhong-Xue Tian, Jun-Hong Liu, You-Sheng Qi, Jian-Feng Tu, Jing-Wen Yang, Li-Qiong Wang & Cun-Zhi Liu
Abstract Background High-normal blood pressure (BP) is associated with increased all-cause, cardiovascular mortality and frequently progresses to hypertension. Transcutaneous electrical acupoint stimulation (TEAS) might be a non-pharmaceutical therapy option to control BP. This trial aims to determine the effectiveness and safety of TEAS combined with lifestyle modification for high-normal BP. Methods/design This prospective, randomized, and parallel clinical trial will be conducted in a community service center in China. Sixty participants with high-normal BP will be...

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Affiliations

  • Livestock Improvement Corporation
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  • Tianjin Agricultural University
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  • Hainan Medical University
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  • West China Hospital of Sichuan University
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  • Zhejiang University
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  • Xuan Wu Hospital of the Capital Medical University
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  • Wenzhou Medical University
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  • Fudan University
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  • Capital Medical University
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