Article
Biology
Stefanny Villalobos-Cantor, Ruth M. Barrett, Alec F. Condon, Alicia Arreola-Bustos, Kelsie M. Rodriguez, Michael S. Cohen, Ian Martin
Summary: Controlled protein synthesis is crucial for regulating gene expression in a cell type-specific manner. We developed a new method to specifically label and visualize newly-synthesized proteins in targeted cell populations in the fly brain, allowing for quantitative analysis of protein synthesis states in vivo.
Article
Multidisciplinary Sciences
Alessandro T. Caputo, Oliver M. Eder, Hana Bereznakova, Heleen Pothuis, Albert Ardevol, Janet Newman, Stewart Nuttall, Thomas S. Peat, Timothy E. Adams
Summary: The study demonstrates that structure-guided manipulation of PAC can enhance the secretion of recombinant proteins in cell lines while reducing selection stringency.
SCIENTIFIC REPORTS
(2021)
Article
Multidisciplinary Sciences
Bin Shao, Jayan Rammohan, Daniel A. Anderson, Nina Alperovich, David Ross, Christopher A. Voigt
Summary: Accurate measurements of promoter activities are crucial for predictably building genetic systems. This study reports a method to simultaneously count plasmid DNA, RNA transcripts, and protein expression in single living bacteria to infer promoter activity in units of RNAP/s. This quantitative assessment can improve the precision of cellular engineering.
NATURE COMMUNICATIONS
(2021)
Article
Biochemistry & Molecular Biology
Cody N. Heiser, Victoria M. Wang, Bob Chen, Jacob J. Hughey, Ken S. Lau
Summary: dropkick is a fully automated software tool for quality control and filtering of single-cell RNA sequencing data, which outperforms conventional thresholding approaches and EmptyDrops in recovering rare cell types and excluding uninformative barcodes. It provides a fast and reproducible solution for cell identification critical to downstream analysis, compatible with popular single-cell Python packages.
Review
Biochemical Research Methods
Kenong Su, Tianwei Yu, Hao Wu
Summary: Cell clustering is a crucial task in single-cell RNA sequencing (scRNA-seq) data analysis, with feature selection playing a key role in improving clustering accuracy. The study evaluates the impact of feature selection on cell clustering accuracy and introduces a new algorithm named FEAture SelecTion (FEAST) for selecting more representative features. Applying FEAST to 12 public scRNA-seq datasets demonstrates a significant improvement in clustering accuracy when combined with existing clustering tools.
BRIEFINGS IN BIOINFORMATICS
(2021)
Article
Multidisciplinary Sciences
Bianca Dumitrascu, Soledad Villar, Dustin G. Mixon, Barbara E. Engelhardt
Summary: Single-cell technologies allow for characterization of complex cell populations at unprecedented scale and resolution. The method proposed in this study uses linear programming for supervised genetic marker selection and provides a Python package scGeneFit for implementation.
NATURE COMMUNICATIONS
(2021)
Article
Genetics & Heredity
Sarah J. J. Pickett, Gavin Hudson, Laura C. C. Greaves
Summary: Single large-scale mitochondrial DNA deletions result in a range of diseases with varying levels of severity and tissue expression. Examining single-cell deletion levels through multi-modal cellular readouts allows for better understanding of hematopoietic cell fate and disease manifestation.
Article
Immunology
Zoe Steier, Dominik A. Aylard, Laura L. McIntyre, Isabel Baldwin, Esther Jeong Yoon Kim, Lydia K. Lutes, Can Ergen, Tse-Shun Huang, Ellen A. Robey, Nir Yosef, Aaron Streets
Summary: Streets, Yosef, Robey and colleagues used multiomics analysis to establish a comprehensive timeline of the development of CD4(+) and CD8(+) T cells lineage commitment. They identified sequential waves of TCR signaling that initiate CD4(+) T cell lineage differentiation followed by CD8(+) T cell lineage specification. Their findings provide valuable insights into cell fate decisions and suggest a sequential selection process in guiding lineage choice.
Article
Multidisciplinary Sciences
Doina Ciobanu, Alicia Clum, Steven Ahrendt, William B. Andreopoulos, Asaf Salamov, Sandy Chan, C. Alisha Quandt, Brian Foster, Jan P. Meier-Kolthoff, Yung Tsu Tang, Patrick Schwientek, Gerald L. Benny, Matthew E. Smith, Diane Bauer, Shweta Deshpande, Kerrie Barry, Alex Copeland, Steven W. Singer, Tanja Woyke, Igor Grigoriev, Timothy Y. James, Jan-Fang Cheng
Summary: This study outlines a pipeline for targeted single-cell sequencing of poorly studied and uncultivated eukaryotic microorganisms found at low abundance. The pipeline consists of seven steps, each with quality review measures to ensure high genome quality at low cost. Genomes generated through this pipeline are shown to be almost as good as complete reference genomes for functional and comparative genomics of environmental microbial eukaryotes.
Article
Microbiology
Kaichao Chen, Miaomiao Xie, Edward Wai-Chi Chan, Sheng Chen
Summary: This study investigates the molecular mechanisms underlying the plasmid fusion process mediated by insertion sequence (IS) elements, by monitoring the interactions between a helper plasmid and two common mobile genetic elements (MGEs). The use of MinION single-molecule long-read sequencing technology provides valuable information on genetic polymorphism and plasmid heterogeneity in different multidrug resistance (MDR) encoding bacteria.
FRONTIERS IN MICROBIOLOGY
(2022)
Article
Multidisciplinary Sciences
Sohrab Salehi, Farhia Kabeer, Nicholas Ceglia, Mirela Andronescu, Marc J. Williams, Kieran R. Campbell, Tehmina Masud, Beixi Wang, Justina Biele, Jazmine Brimhall, David Gee, Hakwoo Lee, Jerome Ting, Allen W. Zhang, Hoa Tran, Ciara O'Flanagan, Fatemeh Dorri, Nicole Rusk, Teresa Ruiz de Algara, So Ra Lee, Brian Yu Chieh Cheng, Peter Eirew, Takako Kono, Jenifer Pham, Diljot Grewal, Daniel Lai, Richard Moore, Andrew J. Mungall, Marco A. Marra, Andrew McPherson, Alexandre Bouchard-Cote, Samuel Aparicio, Sohrab P. Shah
Summary: Progress in defining genomic fitness landscapes in cancer, particularly those associated with copy number alterations (CNAs), has been hindered by the absence of time-series single-cell sampling and temporal statistical models. This study generated a large number of genomes from long-term time-series single-cell whole-genome sequencing of breast epithelium and primary triple-negative breast cancer (TNBC) patient-derived xenografts, revealing the impact of TP53 mutation and cisplatin chemotherapy on clonal fitness dynamics defined by CNAs. The findings show that TP53 mutation alters the fitness landscape, redistributing fitness across different clones associated with distinct CNAs, and that drug treatment can lead to the emergence of drug-resistant clones while eradicating high-fitness clones in untreated settings.
Article
Biochemical Research Methods
Yunpei Xu, Hong-Dong Li, Cui-Xiang Lin, Ruiqing Zheng, Yaohang Li, Jinhui Xu, Jianxin Wang
Summary: Single-cell RNA sequencing (scRNA-seq) is a powerful tool for dissecting biological tissues. This study presents CellBRF, a feature selection method that considers the relevance of genes to cell types, improving single-cell clustering accuracy. CellBRF outperforms existing methods in terms of clustering accuracy and consistency, and has been successfully applied to cell differentiation stage identification, non-malignant cell subtype identification, and rare cell identification.
Article
Multidisciplinary Sciences
Thomas Hu, Mayar Allam, Shuangyi Cai, Walter Henderson, Brian Yueh, Aybuke Garipcan, Anton V. Ievlev, Maryam Afkarian, Semir Beyaz, Ahmet F. Coskun
Summary: The authors developed a framework for joint protein-metabolite profiling at the single-cell level in human tissue combining targeted multiplexed protein imaging and untargeted spatial metabolomics in a single pipeline.
NATURE COMMUNICATIONS
(2023)
Article
Chemistry, Analytical
Xin Geng, Zi-Ang Zhou, Yang Mi, Chunhong Wang, Meng Wang, Chenjia Guo, Chongxiao Qu, Shilun Feng, Inyoung Kim, Miao Yu, Hongming Ji, Xiang Ren
Summary: The study presents an innovative cyclic conical constricted (CCC) microfluidic device for better differentiation of glioma cells from normal glial cells. Compared with traditional microchannels, the CCC channels gradually deform cells and obtain their biomechanical characteristics, achieving the goal of distinguishing different cell types.
ANALYTICAL CHEMISTRY
(2023)
Article
Mathematics
Ilmari Kangasniemi
Summary: The study demonstrates that certain manifolds do not admit a non-constant, non-injective uniformly quasiregular self-map, providing the first example of a quasiregularly elliptic manifold not uniformly quasiregularly elliptic. Conformally formal manifolds are introduced, and it is shown that they have similarities to existing studies of geometrically formal manifolds.
ADVANCES IN MATHEMATICS
(2021)