Article
Biotechnology & Applied Microbiology
Shisi Xing, Dan Deng, Wen Wen, Wei Peng
Summary: This study investigated the differences in gene expression in the female midgut between mated and virgin Drosophila suzukii. The results showed that mating had significant effects on metabolism and immune system in the midgut, which may contribute to supplying the female with nutrients and energy required for egg production.
Article
Parasitology
Lei Liu, Fen Yan, Lu Zhang, Zhi-feng Wu, De-yong Duan, Tian-yin Cheng
Summary: This study analyzed the tick/host protein components in the hemolymph of Haemaphysalis flava and identified numerous tick- and host-derived proteins. The protein profile revealed the important physiological functions of these proteins in blood coagulation, digestion of blood meal, and innate immunity. Further investigations are needed to characterize tick-derived proteins in hemolymph.
PARASITES & VECTORS
(2022)
Article
Multidisciplinary Sciences
Xu Shi, Xiao Wang, Andrew F. Neuwald, Leena Halakivi-Clarke, Robert Clarke, Jianhua Xuan
Summary: BayesDenovo addresses the challenge of de novo transcriptome assembly by accurately reconstructing splicing graphs using a read-guided and Bayesian strategy, achieving higher accuracy and reducing false positives, especially for alternatively spliced genes and highly/lowly expressed transcripts. Additionally, it is more robust on multiple replicates and can identify phenotype-specific transcripts associated with breast cancer recurrence.
SCIENTIFIC REPORTS
(2021)
Article
Multidisciplinary Sciences
August Guang, Mark Howison, Felipe Zapata, Charles Lawrence, Casey W. Dunn
Summary: treeinform is a method that utilizes phylogenetic information across species to improve transcriptome assemblies within species. It helps identify and correct the error of mistaking different transcripts of the same gene as transcripts from multiple closely related genes.
Article
Biochemical Research Methods
Qianqian Zhang, Xing Xu, Li Lin, Jian Yang, Xing Na, Xin Chen, Lingling Wu, Jia Song, Chaoyong Yang
Summary: Cilo-seq is a high-performance platform for single-cell RNA sequencing library construction. It utilizes digital microfluidics in a single device, enabling convenient single-cell isolation, efficient nucleic acid amplification, low-loss nucleic acid purification, and high-quality library preparation.
Article
Multidisciplinary Sciences
Chaoqiong Ding, Xiang Yan, Mengying Xu, Ran Zhou, Yuancun Zhao, Dan Zhang, Zongyao Huang, Zhenzhong Pan, Peng Xiao, Huifang Li, Lu Chen, Yuan Wang
Summary: This study reports the full-length transcriptome of mouse neural stem cells (NSCs) at different developmental stages, providing an important resource for studying NSC fate determination, neural development, and disease in the neuroscience community.
Article
Cell Biology
Di Wu
Summary: The germinal vesicle (GV) stage is a critical transition point in mammalian oocyte development that determines oocyte quality through active RNA degradation and transcriptome reprofiling. Oocyte RNA-seq has revealed differences between non-surrounded nucleolus (NSN) and surrounded nucleolus (SN) phases. Single oocyte RNA-seq (soRNA-seq) shows higher reproducibility and a better illustration of gene changes during oocyte development.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2022)
Article
Evolutionary Biology
Camilla A. Santos, Gabriel G. Sonoda, Thaina Cortez, Luiz L. Coutinho, Sonia C. S. Andrade
Summary: Understanding how selection shapes population differentiation and local adaptation in marine species is a major challenge in evolutionary biology. This study analyzed the gene expression profiles of the marine gastropod Littoraria flava from different locations in Southeast Brazil, identifying differentially expressed genes and those related to local adaptation.
GENOME BIOLOGY AND EVOLUTION
(2021)
Article
Biotechnology & Applied Microbiology
Muchun Niu, Wenjian Cao, Yongcheng Wang, Qiangyuan Zhu, Jiayi Luo, Baiping Wang, Hui Zheng, David A. Weitz, Chenghang Zong
Summary: The profiling of individual synapses reveals molecular heterogeneity, which is crucial for signal transmission and shows considerable morphological and electrophysiological heterogeneity. However, there is currently a lack of high-throughput methods to analyze the molecular heterogeneity among individual synapses.
NATURE BIOTECHNOLOGY
(2023)
Article
Biotechnology & Applied Microbiology
Wenxiang Lu, Qin Zhou, Yi Chen
Summary: RNA sequencing is an innovative technology for studying transcriptomes, but clinical specimens face challenges due to sample degradation. This study replicated the process of RNA degradation and found that even slight levels of degradation can significant affect RNA expression.
Article
Parasitology
Min Kyu Sang, Hongray Howrelia Patnaik, Jie Eun Park, Dae Kwon Song, Jun Yang Jeong, Chan Eui Hong, Yong Tae Kim, Hyeon Jun Shin, Liu Ziwei, Hee Ju Hwang, So Young Park, Se Won Kang, Seung-Hwan Park, Sung-Jae Cha, Jung Ho Ko, E. Hyun Shin, Hong Seog Park, Yong Hun Jo, Yeon Soo Han, Bharat Bhusan Patnaik, Yong Seok Lee
Summary: The study used high-throughput sequencing and data analysis to explore the genetic resources and potential adaptation-related genes of Haemaphysalis flava ticks. The researchers identified various gene families and repetitive sequences, providing valuable information for studying tick biology and disease transmission.
PARASITES & VECTORS
(2023)
Article
Multidisciplinary Sciences
Peijie Zhou, Shuxiong Wang, Tiejun Li, Qing Nie
Summary: MuTrans is a method based on multiscale reduction technique that can identify the underlying stochastic dynamics governing cell-fate transitions, construct cell-fate dynamical manifold, distinguish stable and transition cells, and quantify transition probabilities between cell states. The method is consistent with Langevin equation and transition rate theory, and has been shown to robustly unravel complex cell fate dynamics induced by transition cells in various systems. It bridges data-driven and model-based approaches for single-cell resolution analysis of cell-fate transitions.
NATURE COMMUNICATIONS
(2021)
Article
Multidisciplinary Sciences
Jun Zhang, Mayra Ahmad, Rongrong Xie, Hongbo Gao
Summary: In multicellular organisms, cellular heterogeneity, which refers to the differences in developmental programming and environmental responses among different cell types or even within cells, is a significant phenomenon. Recent advances in single-cell and cell-type isolation combined with next-generation sequencing techniques have provided valuable tools for studying biological processes at single-cell resolution. However, isolating plant cells is more challenging due to the presence of plant cell walls, limiting the application of single-cell approaches in plant studies.
JOVE-JOURNAL OF VISUALIZED EXPERIMENTS
(2023)
Article
Biochemistry & Molecular Biology
Bijayalaxmi Sahoo, Balaram Mishra, Rakesh Bhaskar, Y. N. V. Vikas, Anushri Umesh, Praveen Kumar Guttula, Mukesh Kumar Gupta
Summary: This study investigated the effect of heparin on in vitro capacitation and spermatozoal RNA (spRNA) population in goats. The results showed that heparin enhanced sperm motility and induced capacitation by upregulating the spRNA population and oxidative stress pathway.
INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES
(2023)
Article
Plant Sciences
Yang Liu, Xiaomei Fang, Tian Tang, Yudong Wang, Yinhuan Wu, Jinyu Luo, Haotian Wu, Yingqian Wang, Jian Zhang, Renwu Ruan, Meiliang Zhou, Kaixuan Zhang, Zelin Yi
Summary: This study sequenced the transcriptome of common buckwheat and Ukrainian daliqiao using high-throughput sequencing technology, obtaining a large amount of gene information and differentially expressed genes. SSR and EST-SSR loci were also detected. The clustering results verified the genetic relationship between common buckwheat and Ukrainian daliqiao. These findings are important for enriching the genetic information and marker-assisted selection breeding of buckwheat.