Article
Cell Biology
Lianguang Shang, Xiaoxia Li, Huiying He, Qiaoling Yuan, Yanni Song, Zhaoran Wei, Hai Lin, Min Hu, Fengli Zhao, Chao Zhang, Yuhua Li, Hongsheng Gao, Tianyi Wang, Xiangpei Liu, Hong Zhang, Ya Zhang, Shuaimin Cao, Xiaoman Yu, Bintao Zhang, Yong Zhang, Yiqing Tan, Mao Qin, Cheng Ai, Yingxue Yang, Bin Zhang, Zhiqiang Hu, Hongru Wang, Yang Lv, Yuexing Wang, Jie Ma, Quan Wang, Hongwei Lu, Zhe Wu, Shanlin Liu, Zongyi Sun, Hongliang Zhang, Longbiao Guo, Zichao Li, Yongfeng Zhou, Jiayang Li, Zuofeng Zhu, Guosheng Xiong, Jue Ruan, Qian Qian
Summary: By studying the pan-genomes of large natural populations, we can uncover the genetic diversity and complexity of rice. We have created a super pan-genome of rice using long-read assembly and identified extensive structural variations and gene presence/absence variations. Additionally, we have discovered genetic variants associated with various traits in rice and identified a common set of genes that have played a role in adaptation and domestication in Asian and African rice.
Article
Biology
Thunyarat Surasiang, Chalongrat Noree
Summary: The study confirmed that the effect of A6E mutation on the protein expression levels of asparagine synthetase is common in both unicellular and multicellular eukaryotes, suggesting yeast could be a model of asparagine synthetase deficiency. The A6E mutation could be introduced into the ASNS gene of acute lymphoblastic leukemia patients to inhibit the upregulation of ASNS by cancer cells, reducing the risk of developing resistance to asparaginase treatment.
Article
Dermatology
Jason Thomson, Findlay Bewicke-Copley, Chinedu Anthony Anene, Abha Gulati, Ai Nagano, Karin Purdie, Gareth J. Inman, Charlotte M. Proby, Irene M. Leigh, Catherine A. Harwood, Jun Wang
Summary: This study conducted the largest AK whole exome sequencing study to date and found significant similarities between AK and cSCC in terms of genetic mutations, copy number alterations, driver gene mutations, and mutational signatures. The research identified 44 significantly mutated AK driver genes and suggested that dysregulated TGFf3 signaling may play an important role in AK-cSCC progression.
JOURNAL OF INVESTIGATIVE DERMATOLOGY
(2021)
Article
Multidisciplinary Sciences
Pengbo Beck, Barbara Selle, Lukas Madenach, David T. W. Jones, Christian Vokuhl, Apurva Gopisetty, Arash Nabbi, Ines B. Brecht, Martin Ebinger, Jenny Wegert, Norbert Graf, Manfred Gessler, Stefan M. Pfister, Natalie Jaeger
Summary: Pediatric renal cell carcinomas (RCC) differ from their adult counterparts in histologic subtypes, clinical characteristics, and outcome. Whole-exome and transcriptome sequencing analyses revealed limited genomic overlap between pediatric RCC and adult RCC, even within the same histologic subtype. Recurrent somatic mutations in genes not previously reported in RCC were detected, and papillary pediatric RCCs exhibited distinct genomic subtypes compared to MiT-RCC and adult RCC.
Article
Multidisciplinary Sciences
Feng Zhu, Zhong-Tao Yin, Zheng Wang, Jacqueline Smith, Fan Zhang, Fergal Martin, Denye Ogeh, Maxwell Hincke, Fang-Bing Lin, David W. Burt, Zheng-Kui Zhou, Shui-Sheng Hou, Qiang-Sen Zhao, Xiao-Qin Li, Si-Ran Ding, Guan-Sheng Li, Fang-Xi Yang, Jing-Pin Hao, Ziding Zhang, Li-Zhi Lu, Ning Yang, Zhuo-Cheng Hou
Summary: This study provides insights into avian evolution and the genetics of oviparity through genome analysis of domestic ducks. It discovers new protein-coding genes and a rich resource of variants potentially related to commercial traits improvement in ducks.
NATURE COMMUNICATIONS
(2021)
Article
Hematology
Zhenhua Li, Ti-Cheng Chang, Jacob J. Junco, Meenakshi Devidas, Yizhen Li, Wenjian Yang, Xin Huang, Dale J. Hedges, Zhongshan Cheng, Mary Shago, Andrew J. Carroll, Nyla A. Heerema, Julie Gastier-Foster, Brent L. Wood, Michael J. Borowitz, Lauren Sanclemente, Elizabeth A. Raetz, Stephen P. Hunger, Eleanor Feingold, Tracie C. Rosser, Stephanie L. Sherman, Mignon L. Loh, Charles G. Mullighan, Jiyang Yu, Gang Wu, Philip J. Lupo, Karen R. Rabin, Jun J. Yang
Summary: This study investigates the genomics of Down syndrome-related acute lymphoblastic leukemia (DS-ALL) and identifies 15 molecular subtypes, as well as abnormal activation of key genes. It also reveals the common occurrence of somatic genomic abnormalities mediated by gene rearrangements in DS-ALL and the association between subtype heterogeneity and prognosis. These findings provide important insights into the biology of DS-ALL and offer opportunities for individualized treatment.
Article
Environmental Sciences
Seyed Jamaleddin Shahtaheri, Zahra Goodarzi, Esmaeil Karami, Ali Khavanin, Mahmoud Ghazi Khansari, Mehrafarin Kiani, Ali Rashidy-Pour
Summary: This study investigated the impact of acute exposure to white noise and Al2O3 NPs, alone and in combination, on the hearing and structural functions of the cochlea in rats. The results showed that both independent and combined exposure to white noise and Al2O3 NPs damaged the hearing and structural functions of the cochlea, leading to an increase in temporary threshold shift (TTS) and permanent threshold shift (PTS).
ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH
(2023)
Article
Biochemical Research Methods
Mengyuan Yang, Yiya Ke, Pora Kim, Xiaobo Zhou
Summary: Exon skipping is a common alternative splicing event that can contribute to human diseases. ExonSkipAD database provides functional annotation of ES events in AD and identifies potential therapeutic targets.
BRIEFINGS IN BIOINFORMATICS
(2021)
Article
Oncology
Hidenari Hirata, Atsushi Niida, Nobuyuki Kakiuchi, Ryutaro Uchi, Keishi Sugimachi, Takaaki Masuda, Tomoko Saito, Shun-Ichiro Kageyama, Yushi Motomura, Shuhei Ito, Tadamasa Yoshitake, Daisuke Tsurumaru, Yusuke Nishimuta, Akira Yokoyama, Takanori Hasegawa, Kenichi Chiba, Yuichi Shiraishi, Junyan Du, Fumihito Miura, Masaru Morita, Yasushi Toh, Masakazu Hirakawa, Yoshiyuki Shioyama, Takashi Ito, Tetsuo Akimoto, Satoru Miyano, Tatsuhiro Shibata, Masaki Mori, Yutaka Suzuki, Seishi Ogawa, Kousei Ishigami, Koshi Mimori
Summary: A study sequencing 52 tumor samples from 33 ESCC patients who received radiotherapy combined with 5-fluorouracil/platinum revealed the impact of chemoradiotherapy on clonal evolution, with MYC gain potentially serving as a marker for therapy resistance. The findings enhance understanding of therapeutic resistance and support the rationale for precision chemoradiotherapy.
Article
Fisheries
Zijie Lin, Sota Yoshikawa, Masaomi Hamasaki, Takashi Koyama, Kiyoshi Kikuchi, Sho Hosoya
Summary: This study compared four possible replacement diets for tiger pufferfish, and found that replacing fishmeal with yeast meal can promote growth without inducing severe deleterious effects.
Article
Biochemistry & Molecular Biology
Renying Wang, Peijing Zhang, Jingjing Wang, Lifeng Ma, E. Weigao, Shengbao Suo, Mengmeng Jiang, Jiaqi Li, Haide Chen, Huiyu Sun, Lijiang Fei, Ziming Zhou, Yincong Zhou, Yao Chen, Weiqi Zhang, Xinru Wang, Yuqing Mei, Zhongyi Sun, Chengxuan Yu, Jikai Shao, Yuting Fu, Yanyu Xiao, Fang Ye, Xing Fang, Hanyu Wu, Qile Guo, Xiunan Fang, Xia Li, Xianzhi Gao, Dan Wang, Peng-Fei Xu, Rui Zeng, Gang Xu, Lijun Zhu, Lie Wang, Jing Qu, Dan Zhang, Hongwei Ouyang, He Huang, Ming Chen, Shyh-Chang Ng, Guang-Hui Liu, Guo-Cheng Yuan, Guoji Guo, Xiaoping Han
Summary: By using single-cell RNA sequencing, researchers mapped organism-level cell landscapes for mice, zebrafish, and Drosophila. They identified structural inflammation and mitochondrial dysfunction as common hallmarks of organism aging.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Cell Biology
Carolin Sailer, Jasmin Jansen, Kamil Sekulski, Victor E. Cruz, Jan P. Erzberger, Florian Stengel
Summary: In this study, a comprehensive interaction map of ribosome biogenesis factors (RBFs) during 60S maturation was derived using quantitative proteomics and crosslinking coupled to mass spectrometry. The results were validated by mapping the catalytic activity of methyltransferases and provide a valuable resource for future studies of ribosome biogenesis.
Article
Biochemistry & Molecular Biology
Meiling Zhang, Zhe Jiang, Yichen Ma, Wenqing Liu, Yuan Zhuang, Bo Lu, Kai Li, Jinying Peng, Chengqi Yi
Summary: In this study, a method called "PRAISE" was developed to quantitatively assess the abundance of pseudouridine (psi) in the human transcriptome. The approach involved selective chemical labeling of psi with bisulfite, which induced a nucleotide deletion signature during reverse transcription. The results revealed a median modification level of about 10% for 2,209 confident psi sites in HEK293T cells. The method was also used to identify differential mRNA targets of pseudouridine synthases and quantified pseudouridine sites in mitochondrial mRNA catalyzed by PUS1.
NATURE CHEMICAL BIOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Jingwen Zhu, Pan Chu, Xiongfei Fu
Summary: Global regulation of cell growth rate on gene expression perturbs gene networks and impacts cell-fate determination. Using a synthetic circuit, researchers discovered that growth rates can induce a bifurcation in the landscape, leading to changes in cell-fate decisions. This bifurcation is caused by unbalanced gene expression response to growth variations. These findings highlight the importance of growth regulation in cell-fate determination processes.
NATURE CHEMICAL BIOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Leah Pollet, Luke Lambourne, Yu Xia
Summary: Protein interfaces play crucial roles in protein-protein interactions by determining their structure and function. Interfacial residues are more conserved and understanding the evolutionary constraints imposed by the microenvironment surrounding them can provide insights into the design principles of protein-protein interactions. Different structure-based measures of residue interfacial involvement impact evolutionary rate prediction in interfaces, with change in RSA playing a dominant role.
JOURNAL OF MOLECULAR BIOLOGY
(2022)