Article
Biology
Colleen M. Palmateer, Catherina Artikis, Savannah G. Brovero, Benjamin Friedman, Alexis Gresham, Michelle N. Arbeitman
Summary: Reproductive behaviors in Drosophila melanogaster are controlled by fruitless neurons. Single-cell RNA sequencing on pupal neurons revealed sex-specific gene expression patterns, with over 113 distinct clusters identified. Marker gene analyses showed enrichment of specific functional groups, including circadian clock neurons, mushroom body Kenyon cells, neurotransmitter-producing neurons, and those expressing doublesex. The presence of both male and female neurons in most clusters suggests common gene expression programs, with sex-specific differences overlaying these programs to generate diverse behaviors.
Article
Biotechnology & Applied Microbiology
Collin B. Merrill, Austin B. Montgomery, Miguel A. Pabon, Andrey A. Shabalin, Aylin R. Rodan, Adrian Rothenfluh
Summary: This study applied ATAC-seq and RNA-seq to investigate chromatin regions and gene expression changes in response to insulin signaling pathway in Drosophila cells. The results showed correlations between accessible chromatin regions and gene expression, especially for enhancer regions. Cloning of candidate enhancer regions demonstrated the potential of insulin-inducible reporter gene expression.
Article
Biotechnology & Applied Microbiology
Malarvizhi Sathasivam, Basavalingayya K. K. Swamy, Kushagra Krishnan, Rita Sharma, Spurthi N. N. Nayak, D. S. Uppar, Ravikumar Hosamani
Summary: This study investigates the molecular basis of enhanced root growth under hypergravity conditions by analyzing root transcriptome. The results reveal significant changes in transcript expression, including increased cell division, demand for cell wall constituents, and enhanced hormonal responses.
Article
Genetics & Heredity
Jiaqi Li, Jingjing Wang, Peijing Zhang, Renying Wang, Yuqing Mei, Zhongyi Sun, Lijiang Fei, Mengmeng Jiang, Lifeng Ma, E. Weigao, Haide Chen, Xinru Wang, Yuting Fu, Hanyu Wu, Daiyuan Liu, Xueyi Wang, Jingyu Li, Qile Guo, Yuan Liao, Chengxuan Yu, Danmei Jia, Jian Wu, Shibo He, Huanju Liu, Jun Ma, Kai Lei, Jiming Chen, Xiaoping Han, Guoji Guo
Summary: This study generated single-cell whole-body expression landscapes of zebrafish, Drosophila, and earthworm using Microwell-seq. By integrating cell landscapes from eight representative species, the researchers developed a deep-learning-based strategy, Nvwa, to predict gene expression and identify regulatory programs. Conserved genetic regulation in vertebrates and invertebrates were revealed through comparison of cell-type-specific transcription factors. This work provides a valuable resource and a new strategy for studying regulatory grammar in diverse biological systems.
Article
Food Science & Technology
Yuxuan Liang, Xiaomei Zhan, Xiaoyi Wei, Jing Zhong, Jie Deng, Yongchun Chen, Luyi Pan, Jiawei Zhang, Meiying Li, Riming Huang, Hong Wang, Yuanming Sun
Summary: The study investigated the material basis and mechanism of Daylily in improving sleep. The results showed that both aqueous and ethanol extracts of Daylily prolonged the total sleep time of insomnia fruit flies, with ethanol extracts having more significant effects. Quercetin, linoleic acid, phenethyl caffeate, L-methionine, and γ-aminobutyric acid were identified as core active metabolites. Transcriptomics analysis revealed 368 differentially expressed genes, with the neuroactive ligand-receptor interaction pathway being deduced as the main pathway. These findings contribute to the development of functional foods related to Daylily.
FOOD RESEARCH INTERNATIONAL
(2023)
Article
Biotechnology & Applied Microbiology
Florencia Schlamp, Sofie Y. N. Delbare, Angela M. Early, Martin T. Wells, Sumanta Basu, Andrew G. Clark
Summary: The immune response requires rapid initiation and maintenance, while also being balanced with other physiological processes. Tight control of initiation kinetics and shutdown dynamics for specific immune genes has been observed. In D. melanogaster, a trade-off between immune genes and metabolic genes was identified, with metabolic genes showing recovery to pre-infection levels before the immune response was fully resolved.
Article
Multidisciplinary Sciences
Saumya Jain, Ying Lin, Yerbol Z. Kurmangaliyev, Javier Valdes-Aleman, Samuel A. LoCascio, Parmis Mirshahidi, Brianna Parrington, S. Lawrence Zipursky
Summary: Integration of a global temporal transcriptional module with cell-type-specific transcription factors influences neuronal wiring and synaptic connectivity in the fly visual system. The steroid hormone ecdysone induces a cascade of transcription factors in all fly visual system neurons, regulating the expression of a common set of targets required for synaptic maturation and cell-type-specific targets enriched for cell-surface proteins regulating wiring specificity. Disruption of the ecdysone pathway leads to specific defects in dendritic and axonal processes and synaptic connectivity, with sequential expression of transcription factors correlating with wiring steps. Shared targets of a cell-type-specific transcription factor and the ecdysone pathway regulate wiring specificity. Neurons integrate temporal transcriptional regulation and cell-type-specific regulation to generate cell-type-specific patterns of cell recognition molecules influencing neuronal wiring.
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
George P. Kapali, Viviane Callier, Samuel J. L. Gascoigne, Jon F. Harrison, Alexander W. Shingleton
Summary: In fruit flies, the steroid hormone ecdysone regulates growth and body size development under hypoxic conditions by suppressing the insulin/IGF-signaling pathway. This suggests the existence of growth-regulatory mechanisms that respond to general environmental perturbation rather than individual environmental factors.
SCIENTIFIC REPORTS
(2022)
Article
Entomology
Si-Pei Liu, Hao-Dong Yin, Wen-Jie Li, Zhuang-Hui Qin, Yi Yang, Zheng-Zhong Huang, Le Zong, Xiao-Kun Liu, Zhong Du, Wei-Li Fan, Ya-Qiong Zhang, Dan Zhang, Yong E. Zhang, Xing-Yue Liu, Ding Yang, Si-Qin Ge
Summary: Advanced morphological techniques have been used to study the developmental process of the fruit fly's thoracic anatomical structures, uncovering the transformation of muscles, nerves, and gut during development. The study found changes in muscle position, shape, and bundle numbers during development. Early appearance and smooth development of flight muscles were observed, possibly to achieve full functionality. Sexual differences were also found, while the midguts of larvae and adults were found to be similar.
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
Environmental Sciences
Qing Zhang, Lichong Hao, Yu Hong
Summary: The study revealed that Triclosan has negative impacts on the development, reproduction, and behavior of Drosophila, with high concentrations causing impaired metamorphosis, decreased fertility, and potential damage to larval intestinal cells.
SCIENCE OF THE TOTAL ENVIRONMENT
(2021)
Article
Biotechnology & Applied Microbiology
Michelle Prioli Miranda Soares, Daniel Guariz Pinheiro, Flavia Cristina de Paula Freitas, Zila Luz Paulino Simoes, Marcia Maria Gentile Bitondi
Summary: The study analyzed 30 honeybee transcriptomes to identify gene expression for wing and thoracic dorsum construction from larval wing discs. Gene expression in wing discs and descendant structures showed differential expression profiles during developmental phases, highlighting caste-specific differences.
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
Biotechnology & Applied Microbiology
Jase Gehring, Jong Hwee Park, Sisi Chen, Matthew Thomson, Lior Pachter
NATURE BIOTECHNOLOGY
(2020)
Article
Biotechnology & Applied Microbiology
Pall Melsted, A. Sina Booeshaghi, Lauren Liu, Fan Gao, Lambda Lu, Kyung Hoi (Joseph) Min, Eduardo da Veiga Beltrame, Kristjan Eldjarn Hjorleifsson, Jase Gehring, Lior Pachter
Summary: The preprocessing workflow for single-cell RNA-seq data achieves near-optimal speed and high efficiency, demonstrating flexibility and scalability for large datasets.
NATURE BIOTECHNOLOGY
(2021)
Article
Biophysics
Gennady Gorin, Lior Pachter
Summary: In this study, the impact of splicing cascades on expression dynamics is investigated. The authors examine a class of processes and associated distributions that arise from bursty promoters coupled to directed acyclic graphs of splicing. They provide time-dependent joint distributions for various species, offering insights into how splicing can regulate expression dynamics. The findings are validated through the analysis of long-read sequencing data.
BIOPHYSICAL JOURNAL
(2022)
Review
Biochemical Research Methods
Lambda Moses, Lior Pachter
Summary: This article reviews spatial transcriptomics research since 1987 and provides a detailed analysis of trends and applications of related technologies and methods. The study offers historical context and guidance for current research.
Correction
Biochemical Research Methods
Lambda Moses, Lior Pachter
Article
Biochemical Research Methods
Gennady Gorin, Meichen Fang, Tara Chari, Lior Pachter
Summary: We perform a thorough analysis of RNA velocity methods and propose an improved framework.
PLOS COMPUTATIONAL BIOLOGY
(2022)
Article
Multidisciplinary Sciences
Gennady Gorin, John J. Vastola, Meichen Fang, Lior Pachter
Summary: This study investigates how cell-to-cell differences in transcription rate affect RNA count distributions. The authors introduce quantitative models to compare and contrast two biologically plausible hypotheses about transcription rate variation. They propose a framework for analyzing these models and use Bayesian model selection to identify candidate genes in single-cell transcriptomic data.
NATURE COMMUNICATIONS
(2022)
Correction
Multidisciplinary Sciences
A. Sina Booeshaghi, Eduardo da Veiga Beltrame, Dylan Bannon, Jase Gehring, Lior Pachter
SCIENTIFIC REPORTS
(2023)
Article
Biochemical Research Methods
Tara Chari, Lior Pachter
Summary: Dimensionality reduction is a common method for filtering noise and identifying relevant features in large-scale data analysis. However, reducing high-dimensional datasets to just 2 or 3 dimensions can lead to significant distortion. This study shows that low-dimensional embedding of single-cell data can be counter-productive for exploratory biological analysis due to extensive distortions and inconsistent practices. Alternative approaches for targeted embedding and feature exploration are discussed to enable hypothesis-driven biological discovery.
PLOS COMPUTATIONAL BIOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Gennady Gorin, John J. Vastola, Lior Pachter
Summary: Recent experimental developments in genome-wide RNA quantification show great potential for systems biology. However, a unified mathematical framework is needed to comprehensively study the biology of living cells, taking into account technical variations in genomics assays and the stochasticity of single-molecule biology. In this paper, we review different models for RNA transcription processes and present a framework that integrates these phenomena through the manipulation of generating functions. Finally, we provide simulated scenarios and biological data to demonstrate the implications and applications of this approach.
Article
Biophysics
Gennady Gorin, Lior Pachter
Summary: Single-cell RNA sequencing data can be modeled using Markov chains to gain genome-wide insights into transcriptional physics. However, accurate analysis of the data requires careful consideration of noise sources. A length-based model of capture bias is proposed to explain the over-representation of long pre-mRNA transcripts in sequencing data, which may lead to false-positive observations. This model provides concordant parameter trends and helps identify systematic, mechanistically interpretable technical and biological differences in paired data sets.
BIOPHYSICAL REPORTS
(2023)
Article
Engineering, Electrical & Electronic
A. Sina Booeshaghi, Yeokyoung (Anne) Kil, Kyung Hoi (Joseph) Min, Jase Gehring, Lior Pachter
Summary: Colosseum is a low-cost, modular, and automated fluid sampling device that uses a single motor, can be built for less than $100, and assembled in less than an hour. Instructions and source files are available online.
Article
Biotechnology & Applied Microbiology
Johan Gustafsson, Jonathan Robinson, Jens Nielsen, Lior Pachter
Summary: This study introduces UMIs in single-cell RNA-seq assays to identify duplicated molecules, presenting an improved quantification method called BUTTERFLY based on unseen species modeling. This method effectively addresses the bias caused by the naive removal of duplicates by demonstrating its efficacy across cell types and genes, sometimes even inverting the relative abundance of genes.
Article
Physics, Fluids & Plasmas
Gennady Gorin, Lior Pachter
Article
Biotechnology & Applied Microbiology
Gennady Gorin, Valentine Svensson, Lior Pachter
