Article
Oncology
Tamotsu Sugai, Mitsumasa Osakabe, Takeshi Niinuma, Ryo Sugimoto, Makoto Eizuka, Yoshihito Tanaka, Naoki Yanagawa, Koki Otsuka, Akira Sasaki, Takayuki Matsumoto, Hiromu Suzuki
Summary: This study identified specific miRNA/mRNA networks that contribute to the progression of colorectal tumors, providing insights into the molecular tumorigenesis of these tumors.
FRONTIERS IN ONCOLOGY
(2022)
Article
Biochemical Research Methods
Sylwester Swat, Artur Laskowski, Jan Badura, Wojciech Frohmberg, Pawel Wojciechowski, Aleksandra Swiercz, Marta Kasprzak, Jacek Blazewicz
Summary: This study proposes a new genome-scale de novo assembler, ALGA, based on the overlap graph approach, which can generate more accurate contigs in a short amount of time. ALGA outperforms nine state-of-the-art assemblers in terms of overall quality of genome reconstruction, achieving a good balance between genome coverage, accuracy, and length of resulting sequences.
Article
Multidisciplinary Sciences
Johnathan Wong, Lauren Coombe, Vladimir Nikolic, Emily Zhang, Ka Ming Nip, Puneet Sidhu, Rene L. Warren, Inanc Birol
Summary: Current state-of-the-art de novo long read genome assemblers often require excessive RAM. Our work introduces GoldRush, a new algorithm with linear time complexity that achieves efficient genome assembly using a dynamic data structure. We tested GoldRush on different datasets and demonstrated its scalability and effectiveness in producing high-quality assembly scaffolds within a day.
NATURE COMMUNICATIONS
(2023)
Article
Chemistry, Medicinal
Beiwei Liang, Chunlai Li, Zhan Zhou, Yubo Xie
Summary: This study aimed to investigate the effect of hydromorphone on the growth of human gastric cancer cells. The results showed that within a certain concentration range, hydromorphone can suppress the growth of human gastric cancer cells, and the inhibitory effect is enhanced with longer incubation time and higher concentrations. Hydromorphone inhibits the growth of human gastric cancer cells through cell cycle arrest and induction of apoptosis.
DRUG DESIGN DEVELOPMENT AND THERAPY
(2023)
Article
Multidisciplinary Sciences
Aritra Sarkar, Zaid Al-Ars, Koen Bertels
Summary: This article introduces QuASeR, a reference-free DNA sequence reconstruction method using quantum computation. Each step of the implementation is explained with proof-of-concept examples to target genomics research community and quantum application developers. The limitations of current classical simulation and available quantum hardware systems are also highlighted.
Article
Multidisciplinary Sciences
Anastassia A. Vorobieva, Paul White, Binyong Liang, Jim E. Horne, Asim K. Bera, Cameron M. Chow, Stacey Gerben, Sinduja Marx, Alex Kang, Alyssa Q. Stiving, Sophie R. Harvey, Dagan C. Marx, G. Nasir Khan, Karen G. Fleming, Vicki H. Wysocki, David J. Brockwell, Lukas K. Tamm, Sheena E. Radford, David Baker
Summary: Through computational design, researchers successfully developed novel TMBs with no homology to known TMBs, which can reversibly insert and fold into synthetic lipid membranes, and exhibit experimental structures highly similar to computational models. This advancement is expected to facilitate the custom design of pores for various applications.
Article
Biochemistry & Molecular Biology
Wentao Kong, Yuanchao Qian, Philip S. Stewart, Ting Lu
Summary: Synthetic biology has demonstrated the potential to program living microorganisms for various applications. However, current engineering practices mainly focus on planktonic cells, while microbes in nature constantly alternate their lifestyles. This study presents a synthetic genetic program that regulates bacterial life cycle and enables phase-specific gene expression. The program utilizes an engineered protein as the biofilm matrix building block and allows controlled biofilm assembly and decomposition as well as responsive planktonic-biofilm phase transition. By coupling with synthesis modules, it can be programmed for various functional realizations. This work establishes a versatile platform for microbial engineering and gene circuit applications in complex environments.
NATURE CHEMICAL BIOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Hong Yu, Tao Lin, Xiangbing Meng, Huilong Du, Jingkun Zhang, Guifu Liu, Mingjiang Chen, Yanhui Jing, Liquan Kou, Xiuxiu Li, Qiang Gao, Yan Liang, Xiangdong Liu, Zhilan Fan, Yuntao Liang, Zhukuan Cheng, Mingsheng Chen, Zhixi Tian, Yonghong Wang, Chengcai Chu, Jianru Zuo, Jianmin Wan, Qian Qian, Bin Han, Andrea Zuccolo, Rod A. Wing, Caixia Gao, Chengzhi Liang, Jiayang Li
Summary: The study presents a strategy for de novo domestication of wild allotetraploid rice and establishes necessary resources for this purpose, demonstrating the rapid improvement of agronomically important traits through gene editing.
Article
Multidisciplinary Sciences
Mohamed Awad, Xiangchao Gan
Summary: This paper introduces GALA, a computational framework for chromosome-based sequencing data separation and gap-free de novo assembly. It allows integration of different data sources and addresses the challenge of achieving gap-free chromosome-scale assemblies using current workflows for long-read platforms. The method is demonstrated through the assembly of various genomes.
NATURE COMMUNICATIONS
(2023)
Article
Multidisciplinary Sciences
Lifu Song, Feng Geng, Zi-Yi Gong, Xin Chen, Jijun Tang, Chunye Gong, Libang Zhou, Rui Xia, Ming-Zhe Han, Jing-Yi Xu, Bing-Zhi Li, Ying-Jin Yuan
Summary: The study introduces a novel DNA strand assembly algorithm, DBGPS, that utilizes de Bruijn graph and greedy path search to tackle errors commonly encountered in DNA data storage. DBGPS demonstrates significant advantages in handling DNA breaks, rearrangements, and indels, and its robustness is demonstrated through various tests.
NATURE COMMUNICATIONS
(2022)
Article
Pathology
Kai Song, Qi Yang, Yu Yan, Xiaoyan Yu, Kanlun Xu, Jinghong Xu
Summary: The study revealed that different mucin phenotypes in early differentiated gastric adenocarcinomas in a Chinese cohort are associated with histological classification, transition process, depth of invasion, and other clinicopathological features. The gastric phenotype exhibits aggressive biological behavior in early differentiated gastric adenocarcinomas.
DIAGNOSTIC PATHOLOGY
(2021)
Article
Chemistry, Multidisciplinary
Jianhuan Qi, Fan Mo, Ni A. An, Tingwei Mi, Jiaxin Wang, Jun-Tian Qi, Xiangshang Li, Boya Zhang, Longkuo Xia, Yingfei Lu, Gaoying Sun, Xinyue Wang, Chuan-Yun Li, Baoyang Hu
Summary: The study identified a human-specific de novo gene, SP0535, which is preferentially expressed in the ventricular zone of the human fetal brain and plays an important role in cortical development and function. Knockout of SP0535 in human embryonic stem cell-derived cortical organoids compromises their growth and neurogenesis. In SP0535 transgenic mice, expression of SP0535 induces fetal cortex expansion and formation of sulci and gyri-like structures. SP0535 also promotes unique proliferation and differentiation of progenitors and neurons in the mouse cortex. SP0535 TG adult mice exhibit improved cognitive ability and working memory. Mechanistically, SP0535 interacts with the membrane protein Na+/K+ ATPase subunit alpha-1 (ATP1A1) and releases Src from the ATP1A1-Src complex, promoting cell proliferation.
Article
Multidisciplinary Sciences
Maria Gladysheva-Azgari, Kristina Petrova, Svetlana Tsygankova, Irina Mitrofanova, Anatoliy Smykov, Eugenia Boulygina, Natalia Slobodova, Sergey Rastorguev, Fedor Sharko
Summary: This paper presents the assembly of the P. persica cv. 'Sovetskiy' genome using a hybrid assembly approach with Oxford Nanopore long reads and Illumina short reads. The unique cultivars from the Nikitsky Botanical Garden are essential for a more comprehensive assessment of the peach genome in Crimea and southern Russia.
Article
Medicine, General & Internal
Choong-Kyun Noh, Eunyoung Lee, Bumhee Park, Sun Gyo Lim, Sung Jae Shin, Kee Myung Lee, Gil Ho Lee
Summary: This study investigated the long-term effect of Helicobacter pylori eradication on the prevention of metachronous gastric neoplasm after endoscopic submucosal dissection (ESD) of gastric adenoma. The results showed that eradication of H. pylori did not increase the risk of metachronous gastric neoplasm after ESD.
JOURNAL OF CLINICAL MEDICINE
(2023)
Article
Multidisciplinary Sciences
Prasun Kumar, Neil G. Paterson, Jonathan Clayden, Derek N. Woolfson
Summary: The alpha-helix is important in structural biology and protein folding. This study shows that synthetic peptide assemblies can be built from 3(10)-helices, which are less common in natural proteins. The research provides principles and rules for designing in this unexplored region of protein structure.