Article
Biotechnology & Applied Microbiology
Tianyuan Zhang, Hanzhou Li, Silin Ma, Jian Cao, Hao Liao, Qiaoyun Huang, Wenli Chen
Summary: This study evaluated the performance of ONT R10.4.1 16S amplicon and found that it had a lower error rate and better results in synthetic communities. Moreover, the analysis of environmental samples using ONT R10.4.1 showed a similar composition to Pacbio data. Based on these findings, ONT R10.4.1 16S amplicon can also be used for environmental samples.
APPLIED AND ENVIRONMENTAL MICROBIOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Hugo B. C. Kleikamp, Mario Pronk, Claudia Tugui, Leonor Guedes da Silva, Ben Abbas, Yue Mei Lin, Mark C. M. van Loosdrecht, Martin Pabst
Summary: The novel de novo metaproteomics approach introduced in this study does not rely on constructing protein sequence databases, allowing for rapid quantitative profiling of microbial communities and capturing unsequenced community members.
Article
Computer Science, Artificial Intelligence
Rui Qiao, Ngoc Hieu Tran, Lei Xin, Xin Chen, Ming Li, Baozhen Shan, Ali Ghodsi
Summary: The research team presents a neural network-based method that can handle sequencing data of any resolution while improving the accuracy of predicted sequences. Increasing resolution in mass spectrometry provides better data for sequencing, but also raises the challenge of computational complexity in data analysis.
NATURE MACHINE INTELLIGENCE
(2021)
Article
Virology
Zhuozhuang Lu, Yongjin Wang, Xiaohui Zou, Tao Hung
Summary: In this study, the transcriptome of fowl adenovirus 4 (FAdV-4) was analyzed using deep sequencing. 39 novel open reading frames (ORFs) and 18 viral promoters and 15 polyadenylation signals were identified. These findings provide a foundation for studying viral gene function, virulence, and evolution.
Article
Multidisciplinary Sciences
Yi Yang, Guoquan Yan, Siyuan Kong, Mengxi Wu, Pengyuan Yang, Weiqian Cao, Liang Qiao
Summary: This study developed a DIA-based glycoproteomics workflow with stringent statistical controls to accurately identify intact glycopeptides. By benchmarking the method on yeast and human serum samples, it was demonstrated that DIA with GproDIA outperforms traditional data-dependent acquisition methods in terms of capacity and accuracy of glycoproteomic analysis.
NATURE COMMUNICATIONS
(2021)
Article
Biology
Zelin Liu, Changyu Tao, Shiwei Li, Minghao Du, Yongtai Bai, Xueyan Hu, Yu Li, Jian Chen, Ence Yang
Summary: circFL-seq is a novel method for full-length circRNA sequencing, allowing accurate identification and quantification of complete circRNA sequences with significant advantages at the isoform level. This method enables large-scale screening of functional circRNAs.
Article
Multidisciplinary Sciences
A. Hoarfrost, A. Aptekmann, G. Farfanuk, Y. Bromberg
Summary: Computational methods for analyzing microbial systems often rely on reference databases that do not fully capture the functional diversity of these systems. In this study, the authors develop a deep learning model that is capable of transferring its learned knowledge to multiple tasks, resulting in biologically relevant models. The model, called LookingGlass, can provide useful representations of unknown and unannotated sequences, shedding light on the microbial dark matter that dominates life on Earth.
NATURE COMMUNICATIONS
(2022)
Article
Chemistry, Multidisciplinary
Weishan Wang, Chenghong Zhu, Bin Zhang, Yi Feng, Yan Zhang, Jinbo Li
Summary: Researchers have developed a near-infrared photoactivatable nano-PROTAC (NAP) that enables remote control of protein degradation in tumors. NAP, formed by molecular self-assembly, can be activated by NIR photoirradiation to selectively degrade proteins in tumor regions.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2023)
Article
Endocrinology & Metabolism
Beidi Lan, Yuan Bai, Xiaoyi Chang, Xiaoxia Zhang
Summary: The joint effect of leukocyte telomere length (LTL) and type 2 diabetes (T2D) on the risk of all-cause death was explored. Participants with high telomere length and diabetes showed the highest possibility of death compared with other groups.
FRONTIERS IN ENDOCRINOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Pengfei Zhang, Dike Jiang, Yin Wang, Xueping Yao, Yan Luo, Zexiao Yang
Summary: This study compared different assembly strategies for Haemophilus parasuis, a bacterium causing Glasser's disease in swine, and found that assembly with PacBio or ONT reads followed by polishing with Illumina reads resulted in high-quality genome reconstruction. Additionally, correction with Homopolish after ONT-only assembly was equally effective. Aligning transcripts to assembled genomes revealed that ONT assembly errors were mainly insertions and deletions in homopolymer regions, affecting protein prediction. Polishing can fill indels and correct mistakes.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Biotechnology & Applied Microbiology
Vincent Hahaut, Dinko Pavlinic, Walter Carbone, Sven Schuierer, Pierre Balmer, Mathieu Quinodoz, Magdalena Renner, Guglielmo Roma, Cameron S. Cowan, Simone Picelli
Summary: FLASH-seq (FS) is a full-length single-cell RNA sequencing method that offers increased sensitivity and reduced hands-on time compared to Smart-seq3. It can be easily automated and miniaturized to decrease resource consumption.
NATURE BIOTECHNOLOGY
(2022)
Article
Chemistry, Physical
Mengbiao Guo, Zhou Songyang, Yuanyan Xiong
Summary: ChArmTelo is a computational toolbox for analyzing telomeres at the chromosome arm level in humans and other animals. It has been demonstrated to reveal population-specific differences in arm-level telomere lengths and identify liver cancer signatures. It also suggests that disruption of DNA replication origin may play a role in cancer by affecting telomere lengths.
Article
Biochemical Research Methods
Roberta Lucchi, Maria C. Lucana, Montserrat Escobar-Rosales, Cristina Diaz-Perlas, Benjami Oller-Salvia
Summary: Antibody therapeutics have potential to treat various diseases, but side effects limit their safe dosage. Conditionally-active antibodies provide additional selectivity for improved safety. In this study, a versatile approach to conditionally mask antibody derivatives was proposed and successfully applied to cancer stem cells in multiple tumors. This method enables rapid activation of antibodies with different internal or external stimuli.
Article
Biotechnology & Applied Microbiology
Victoria Probst, Arman Simonyan, Felix Pacheco, Yuliu Guo, Finn Cilius Nielsen, Frederik Otzen Bagger
Summary: The study evaluated four different plate-based scRNA-seq protocols and found that G&T had the highest gene detection per single cell, while SS3 was the most cost-effective option. Takara, although user-friendly, was the most expensive, and NEB was a more affordable alternative to other commercial kits.
Article
Microbiology
Isabel Abellan-Schneyder, Annemarie Siebert, Katharina Hofmann, Mareike Wenning, Klaus Neuhaus
Summary: Full-length SSU rRNA gene sequencing allows for species-level identification of diverse microorganisms in milk samples, with improved species-level classification compared to short amplicon sequencing. This approach may be useful for detecting potential mastitis-causing species and controlling spoilage-related microorganisms. The method is easy to conduct, standardized, and compatible with Illumina sequencing machines for microbiome screening.