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2. Quartet RNA reference materials improve the quality of transcriptomic data through ratio-based profiling

Author

Yu, Ying, Hou, Wanwan, Liu, Yaqing, Wang, Haiyan, Dong, Lianhua, Mai, Yuanbang, Chen, Qingwang, Li, Zhihui, Sun, Shanyue, Yang, Jingcheng, Cao, Zehui, Zhang, Peipei, Zi, Yi, Liu, Ruimei, Gao, Jian, Zhang, Naixin, Li, Jingjing, Ren, Luyao, Jiang, He, Shang, Jun, Zhu, Sibo, Wang, Xiaolin, Qing, Tao, Bao, Ding, Li, Bingying, Li, Bin, Suo, Chen, Pi, Yan, Wang, Xia, Dai, Fangping, Scherer, Andreas, Mattila, Pirkko, Han, Jinxiong, Zhang, Lijun, Jiang, Hui, Thierry-Mieg, Danielle, Thierry-Mieg, Jean, Xiao, Wenming, Hong, Huixiao, Tong, Weida, Wang, Jing, Li, Jinming, Fang, Xiang, Jin, Li, Xu, Joshua, Qian, Feng, Zhang, Rui, Shi, Leming, and Zheng, Yuanting

Published
2024
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7. Extend the benchmarking indel set by manual review using the individual cell line sequencing data from the Sequencing Quality Control 2 (SEQC2) project

Author

Gong, Binsheng, Li, Dan, Zhang, Yifan, Kusko, Rebecca, Lababidi, Samir, Cao, Zehui, Chen, Mingyang, Chen, Ning, Chen, Qiaochu, Chen, Qingwang, Dai, Jiacheng, Gan, Qiang, Gao, Yuechen, Guo, Mingkun, Hariani, Gunjan, He, Yujie, Hou, Wanwan, Jiang, He, Kushwaha, Garima, Li, Jian-Liang, Li, Jianying, Li, Yulan, Liu, Liang-Chun, Liu, Ruimei, Liu, Shiming, Meriaux, Edwin, Mo, Mengqing, Moore, Mathew, Moss, Tyler J., Niu, Quanne, Patel, Ananddeep, Ren, Luyao, Saremi, Nedda F., Shang, Erfei, Shang, Jun, Song, Ping, Sun, Siqi, Urban, Brent J., Wang, Danke, Wang, Shangzi, Wen, Zhining, Xiong, Xiangyi, Yang, Jingcheng, Yin, Lihui, Zhang, Chao, Zhang, Ruolan, Bhandari, Ambica, Cai, Wanshi, Eterovic, Agda Karina, Megherbi, Dalila B., Shi, Tieliu, Suo, Chen, Yu, Ying, Zheng, Yuanting, Novoradovskaya, Natalia, Sears, Renee L., Shi, Leming, Jones, Wendell, Tong, Weida, and Xu, Joshua

Published
2024
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10. Mouse auditory cortex sub-fields receive neuronal projections from MGB subdivisions independently

Author

Chi Wang, Zhen-yu Jiang, Jian-yuan Chai, Hong-suo Chen, Li-xia Liu, Tong Dang, and Xian-mei Meng

Subjects
Mouse auditory cortex, Neuronal circuits, Belt area, Thalamus projection, Optical imaging, Medicine, Science
Abstract

Abstract Mouse auditory cortex is composed of six sub-fields: primary auditory field (AI), secondary auditory field (AII), anterior auditory field (AAF), insular auditory field (IAF), ultrasonic field (UF) and dorsoposterior field (DP). Previous studies have examined thalamo-cortical connections in the mice auditory system and learned that AI, AAF, and IAF receive inputs from the ventral division of the medial geniculate body (MGB). However, the functional and thalamo-cortical connections between nonprimary auditory cortex (AII, UF, and DP) is unclear. In this study, we examined the locations of neurons projecting to these three cortical sub-fields in the MGB, and addressed the question whether these cortical sub-fields receive inputs from different subsets of MGB neurons or common. To examine the distributions of projecting neurons in the MGB, retrograde tracers were injected into the AII, UF, DP, after identifying these areas by the method of Optical Imaging. Our results indicated that neuron cells which in ventral part of dorsal MGB (MGd) and that of ventral MGB (MGv) projecting to UF and AII with less overlap. And DP only received neuron projecting from MGd. Interestingly, these three cortical areas received input from distinct part of MGd and MGv in an independent manner. Based on our foundings these three auditory cortical sub-fields in mice may independently process auditory information.

Published
2024
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11. Author Correction: Quartet RNA reference materials improve the quality of transcriptomic data through ratio-based profiling

Author

Yu, Ying, Hou, Wanwan, Liu, Yaqing, Wang, Haiyan, Dong, Lianhua, Mai, Yuanbang, Chen, Qingwang, Li, Zhihui, Sun, Shanyue, Yang, Jingcheng, Cao, Zehui, Zhang, Peipei, Zi, Yi, Liu, Ruimei, Gao, Jian, Zhang, Naixin, Li, Jingjing, Ren, Luyao, Jiang, He, Shang, Jun, Zhu, Sibo, Wang, Xiaolin, Qing, Tao, Bao, Ding, Li, Bingying, Li, Bin, Suo, Chen, Pi, Yan, Wang, Xia, Dai, Fangping, Scherer, Andreas, Mattila, Pirkko, Han, Jinxiong, Zhang, Lijun, Jiang, Hui, Thierry-Mieg, Danielle, Thierry-Mieg, Jean, Xiao, Wenming, Hong, Huixiao, Tong, Weida, Wang, Jing, Li, Jinming, Fang, Xiang, Jin, Li, Xu, Joshua, Qian, Feng, Zhang, Rui, Shi, Leming, and Zheng, Yuanting

Published
2024
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27. Precursor-directed production of water-soluble red Monascus pigments with high thermal stability via azaphilic addition reaction-based semi-synthesis

Author

Linman He, Cai Liu, Suo Chen, Jialan Zhang, Mengxiang Gao, and Li Li

Subjects
Monascus pigments, Semi-synthesis, Azaphilic addition reaction, Water solubility, Thermal stability, Nutrition. Foods and food supply, TX341-641, Food processing and manufacture, TP368-456
Abstract

Red Monascus pigments (MPs) are a large group of polyketides from the fungus Monascus which have been widely used as food colorants. In this study, a variety of red MPs congeners were prepared to explore promising water-soluble candidates for application in liquid food formulations. The results showed that by combining the two-stage, low-pH fermentation strategy with a downstream purification step of fractional crystallization, precursors of red MPs, namely monascorubrin and rubropunctatin, were obtained with a purity of 91.9%. Then, via the azaphilic addition reaction, 18 types of red MPs congeners carrying different amino acid moieties (MPs-aa) were semi-synthesized. Compared to rubropunctamine and monascorubramine, the water solubility, pH and thermal stability of MPs-aa were improved greatly. MPs-His, MPs-Phe, MPs-Tyr and MPs-Trp were identified to be the most resistant to pasteurization. These findings provide water-soluble red MPs candidates with high thermal stability and an attractive approach for their large scale production.

Published
2023
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28. Non-invasive early detection of cancer four years before conventional diagnosis using a blood test.

Author

Chen, Xingdong, Gole, Jeffrey, Gore, Athurva, He, Qiye, Lu, Ming, Min, Jun, Yuan, Ziyu, Yang, Xiaorong, Jiang, Yanfeng, Zhang, Tiejun, Suo, Chen, Li, Xiaojie, Cheng, Lei, Zhang, Zhenhua, Niu, Hongyu, Li, Zhe, Xie, Zhen, Shi, Han, Zhang, Xiang, Fan, Min, Wang, Xiaofeng, Yang, Yajun, Dang, Justin, McConnell, Catie, Zhang, Juan, Wang, Jiucun, Yu, Shunzhang, Ye, Weimin, Gao, Yuan, Zhang, Kun, Liu, Rui, and Jin, Li

Subjects
Humans, Neoplasms, Genetic Markers, Sensitivity and Specificity, Longitudinal Studies, Reproducibility of Results, DNA Methylation, Adult, Aged, Aged, 80 and over, Middle Aged, China, Female, Male, Early Detection of Cancer, Young Adult, Epigenomics, High-Throughput Nucleotide Sequencing, Healthy Volunteers, Biomarkers, Tumor, Circulating Tumor DNA
Abstract

Early detection has the potential to reduce cancer mortality, but an effective screening test must demonstrate asymptomatic cancer detection years before conventional diagnosis in a longitudinal study. In the Taizhou Longitudinal Study (TZL), 123,115 healthy subjects provided plasma samples for long-term storage and were then monitored for cancer occurrence. Here we report the preliminary results of PanSeer, a noninvasive blood test based on circulating tumor DNA methylation, on TZL plasma samples from 605 asymptomatic individuals, 191 of whom were later diagnosed with stomach, esophageal, colorectal, lung or liver cancer within four years of blood draw. We also assay plasma samples from an additional 223 cancer patients, plus 200 primary tumor and normal tissues. We show that PanSeer detects five common types of cancer in 88% (95% CI: 80-93%) of post-diagnosis patients with a specificity of 96% (95% CI: 93-98%), We also demonstrate that PanSeer detects cancer in 95% (95% CI: 89-98%) of asymptomatic individuals who were later diagnosed, though future longitudinal studies are required to confirm this result. These results demonstrate that cancer can be non-invasively detected up to four years before current standard of care.

Published
2020

43. Risk factors for progression to severe infection and prolonged viral clearance time in hospitalized elderly patients infected with the Omicron variant of SARS-CoV-2: a retrospective study at Shanghai Fourth People's Hospital, School of Medicine, Tongji University

Author

Tang, Siqi, primary, Man, Qiuhong, additional, Zhu, Dongliang, additional, Yu, Xueying, additional, Chen, Ruilin, additional, Wang, Shuo, additional, Lu, Yihan, additional, Shi, Qiqing, additional, Suo, Chen, additional, and Xiong, Lize, additional

Published
2024
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49. Purification of Polysaccharide Produced by the Haploid Yeast Strain of Tremella sanguinea and Its Antioxidant and Prebiotic Activities

Author

Yichi Liu, Suo Chen, Jialan Zhang, Mengxiang Gao, and Li Li

Subjects
Tremella sanguinea, the haploid yeast stage, polysaccharide, antioxidant, prebiotics, Organic chemistry, QD241-441
Abstract

Tremella sanguinea is a traditional Chinese medicinal and edible mushroom. Polysaccharides from Tremella mushrooms have received increasing amounts of research attention due to their diverse pharmacological activities. In this study, via the incubation of basidiospores collected from fresh artificially cultivated basidiocarps of T. sanguinea, a haploid yeast strain of T. sanguinea was obtained, and it was found to be a typical loose-slime-forming yeast capable of producing a large amount of exopolysaccharides (EPS). Using DEAE-52 cellulose column chromatography and Sephadex G-100 gel permeation chromatography, the major polysaccharide, named TSPS-1, was separated and purified from the EPS produced by the haploid yeast strain of T. sanguinea. TSPS-1 was a homogeneous polysaccharide with a molecular weight of 2.5 × 103 kDa and consisted of rhamnose, glucose, xylose, mannose and glucuronic acid at a molar ratio of 1: 0.7: 62.2: 24.6: 11.5. The bioactivity of the TSPS-1 polysaccharide was evaluated. The results show that TSPS-1 exhibited noticeable antioxidant activity by scavenging hydroxyl radicals (EC50 = 1.92 mg/mL) and superoxide radicals (EC50 = 1.33 mg/mL), and prebiotic activity by promoting the growth of different probiotic strains in the genus Lactobacillus and Bifidobacterium. These results suggest that the cultivation of the haploid yeast strain can be a promising alternative for the efficient production of valuable T. sanguinea polysaccharides with antioxidant and prebiotic potential.

Published
2023
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50. Impact of accelerated biological aging and genetic variation on esophageal adenocarcinoma: Joint and interaction effect in a prospective cohort.

Author

Zhao, Renjia, Yuan, Huangbo, Chen, Shuaizhou, Xu, Kelin, Zhang, Tiejun, Liu, Zhenqiu, Jiang, Yanfeng, Suo, Chen, and Chen, Xingdong

Abstract

Accelerated biological aging may be associated with increased risk of esophageal adenocarcinoma (EAC). However, its relationship with genetic variation, and its effect on improving risk population stratification, remains unknown. We performed an exposome association study to determine potential associated factors associated with EAC. To quantify biological age and its difference from chronological age, we calculated the BioAge10 and Biological Age Acceleration (BioAgeAccel) based on chronological age and nine biomarkers. Multivariable Cox regression models for 362,310 participants from the UK Biobank with a median follow‐up of 13.70 years were performed. We established a weighted polygenic risk score (wPRS) associated with EAC, to assess joint and interaction effects with BioAgeAccel. Four indicators were used to evaluate their interaction effects, and we fitted curves to evaluate the risk stratification ability of BioAgeAccel. Compared with biologically younger participants, those older had higher risk of EAC, with adjusted HR of 1.79 (95%CI: 1.52–2.10). Compared with low wPRS and biologically younger group, the high wPRS and biologically older group had a 4.30‐fold increase in HR (95% CI: 2.78–6.66), at meanwhile, 1.15‐fold relative excess risk was detected (95% CI: 0.30–2.75), and 22% of the overall EAC risk was attributable to the interactive effects (95% CI: 12%–31%). The 10‐year absolute incidence risk indicates that biologically older individuals should begin screening procedures 4.18 years in advance, while youngers can postpone screening by 4.96 years, compared with general population. BioAgeAccel interacted positively with genetic variation and increased risk of EAC, it could serve as a novel indicator for predicting incidence. [ABSTRACT FROM AUTHOR]

Published
2025
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