Article
Biotechnology & Applied Microbiology
Ryan M. Mulqueen, Dmitry Pokholok, Brendan L. O'Connell, Casey A. Thornton, Fan Zhang, Brian J. O'Roak, Jason Link, Galip Gurkan Yardimci, Rosalie C. Sears, Frank J. Steemers, Andrew C. Adey
Summary: The s3 technology, using a uracil-based adapter switching approach, significantly improves the usable reads per cell in single-cell genomics assays, especially in chromatin accessibility analysis. Compared with other methods, s3 demonstrates higher efficiency and resolution in single-cell whole-genome sequencing and chromatin conformation analysis.
NATURE BIOTECHNOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Wenting Zong, Hongen Kang, Zhuang Xiong, Yingke Ma, Tong Jin, Zheng Gong, Lizhi Yi, Mochen Zhang, Song Wu, Guoliang Wang, Yiming Bao, Rujiao Li
Summary: Single-cell bisulfite sequencing methods have been widely used to study epigenomic heterogeneity in cell states. Data generated from these methods have deepened our understanding of epigenetic regulation in various biological processes. scMethBank is the first open access database dedicated to single-cell DNA methylation data, providing researchers with access to a large number of samples for analysis and visualization.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Multidisciplinary Sciences
Euxhen Hasanaj, Jingtao Wang, Arjun Sarathi, Jun Ding, Ziv Bar-Joseph
Summary: Cell type assignment is a major challenge in high throughput single cell data analysis. To address this issue, researchers have developed Cellar, a software tool that provides interactive support for cell type assignment and dataset comparison.
NATURE COMMUNICATIONS
(2022)
Article
Biotechnology & Applied Microbiology
Simon Mages, Noa Moriel, Inbal Avraham-Davidi, Evan Murray, Jan Watter, Fei Chen, Orit Rozenblatt-Rosen, Johanna Klughammer, Aviv Regev, Mor Nitzan
Summary: Transferring annotations of single-cell-, spatial- and multi-omics data is challenging due to technical limitations and biological variations. We present TACCO, a computational framework for annotation transfer, which utilizes continuous mixtures of cells or molecules to annotate a wide variety of data. TACCO achieves high accuracy while reducing computational requirements and scales to larger datasets.
NATURE BIOTECHNOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Raphael Gollnisch, Joel Wallenius, Kristin E. Gribble, Dag Ahren, Karin Rengefors
Summary: Sequencing of reduced representation libraries allows for genotyping of many individuals in population genomic studies. However, it cannot be applied directly on single cells and requires high amounts of DNA, which limits its use on most microbes. To address this limitation, we developed a method called single amplified genomes followed by restriction-site-associated DNA sequencing, which avoids labor-intensive culturing and culturing bias, enabling population genomic studies on unicellular eukaryotes and providing insights into genetic diversity, gene flow, adaptation, dispersal, and biogeography of previously unexplored species.
MOLECULAR BIOLOGY AND EVOLUTION
(2023)
Article
Multidisciplinary Sciences
Xinrui Lin, Yingwen Chen, Li Lin, Kun Yin, Rui Cheng, Xin Lin, Xiaoyu Wang, Ye Guo, Zhaorun Wu, Yingkun Zhang, Jin Li, Chaoyong Yang, Jia Song
Summary: mitoSplitter is an algorithm that uses mitochondrial RNA variants to demultiplex samples in large scale scRNA-seq data. It can accurately analyze multiple samples and cells in a short time, and accelerate the application of scRNA-seq assays in biomedical research.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Article
Chemistry, Multidisciplinary
Kun Yin, Shanqing Huang, Weidong Ruan, Haopai Wei, He Dong, Dianyi Liang, Meijuan Zhao, Wei Qi, Chaoyong Yang, Zhi Zhu
Summary: Iso-seq is a rapid and uniform single-cell whole-genome sequencing method that uses a specially designed dual-well structure and a capillary-based centrifugal-driven droplet generator to isolate single cells and compartmentalize their genomes in droplets within 3 minutes. Iso-seq achieves high mapping ratio, broad coverage of the genome, and low coefficient of variation, making it promising for a wide variety of biological applications.
Article
Biochemical Research Methods
Miao Yu, Armen Abnousi, Yanxiao Zhang, Guoqiang Li, Lindsay Lee, Ziyin Chen, Rongxin Fang, Taylor M. Lagler, Yuchen Yang, Jia Wen, Quan Sun, Yun Li, Bing Ren, Ming Hu
Summary: SnapHiC is a computational tool for improving the detection of chromatin loops from single-cell Hi-C data, allowing high-resolution and accurate identification of chromatin loops. It can be used to analyze cell type-specific chromatin architecture and gene regulatory programs.
Article
Biochemical Research Methods
Hongqiang Lyu, Erhu Liu, Zhifang Wu, Yao Li, Yuan Liu, Xiaoran Yin
Summary: scHiCPTR is an unsupervised graph-based algorithm for inferring pseudotime from single-cell Hi-C contact matrices. It achieves high performance in pseudotime inference and exhibits reasonable biological significance by optimizing graph structure and handling developmental trajectories with multiple topologies.
Review
Parasitology
Dania Nanes Sarfati, Pengyang Li, Alexander J. Tarashansky, Bo Wang
Summary: Research on schistosomes has revealed a complex life cycle with different cell types, which can inform new therapeutic and preventive strategies against the disease.
TRENDS IN PARASITOLOGY
(2021)
Article
Chemistry, Multidisciplinary
Yingfei Wang, Yanyun Fang, Yu Zhu, Shiyi Bi, Ying Liu, Huangxian Ju
Summary: By developing a hydrogel microbead-based strategy, simultaneous sensitive quantification of multiple miRNAs in single cells is achieved. The porous structure of the hydrogel microbeads effectively avoids nonspecific cross-reactions and enables successful differentiation of cellular heterogeneity and subpopulation discrimination in liver cancer cells and normal liver cells.
Article
Biotechnology & Applied Microbiology
Ruochi Zhang, Tianming Zhou, Jian Ma
Summary: Higashi is an algorithm based on hypergraph representation learning that outperforms existing methods for embedding and imputation of scHi-C data, and can identify multiscale 3D genome features in single cells. Furthermore, Higashi can incorporate epigenomic signals jointly profiled in the same cell, leading to improved embeddings for single-nucleus methyl-3C data.
NATURE BIOTECHNOLOGY
(2022)
Article
Biotechnology & Applied Microbiology
Hansen Cheng, Wenhao Ma, Kun Wang, Han Chu, Guangchao Bao, Yu Liao, Yawen Yuan, Yixiong Gou, Liting Dong, Jian Yang, Haoyang Cai
Summary: This study introduces an algorithm called ATACAmp that uses ATAC-seq data to detect ecDNA/HSRs in tumor genomes. The algorithm achieves high accuracy by enriching ecDNA and reducing chromosomal DNA interference. The method outperforms other tools in terms of accuracy and also supports single-cell analysis.
Article
Oncology
Veronique G. LeBlanc, Diane L. Trinh, Shaghayegh Aslanpour, Martha Hughes, Dorothea Livingstone, Dan Jin, Bo Young Ahn, Michael D. Blough, J. Gregory Cairncross, Jennifer A. Chan, John J. P. Kelly, Marco A. Marra
Summary: Glioblastomas (GBMs) are highly heterogeneous brain tumors, and patient-derived models have been used to study this heterogeneity. However, the extent to which these models recapitulate GBM genomic features is still unclear. In this study, the researchers analyzed the genomes and transcriptomes of GBM tumors and patient-derived models, and found that the models exhibit genetic similarities to the tumors and retain varying gene expression characteristics. These findings provide valuable insights for using GBM-derived models to study cellular heterogeneity.
Article
Multidisciplinary Sciences
Ignacio Belda, Thomas C. Williams, Miguel de Celis, Ian T. Paulsen, Isak S. Pretorius
Summary: Synthetic metagenomics has the potential to reveal the complexity of microbial ecosystems by showing the simplicity of microbial communities captured in a single cell. Conceptually, a yeast cell carrying a representative synthetic metagenome could uncover the complexity of interactions between multiple species, as illustrated here with wine ferments.
NATURE COMMUNICATIONS
(2021)
Article
Biochemical Research Methods
David Feldman, Luke Funk, Anna Le, Rebecca J. Carlson, Michael D. Leiken, FuNien Tsai, Brian Soong, Avtar Singh, Paul C. Blainey
Summary: The combination of efficient genetic engineering and high-resolution phenotypic readouts has greatly accelerated the discovery of genetic components underlying fundamental and disease-related processes. Optical pooled screens using in situ sequencing provide a scalable integration of barcoded lentiviral libraries with high-content imaging assays, enabling single-cell resolution and accurate sequence reads for large-scale genetic screens.
Article
Ecology
Mantas Sereika, Francesca Petriglieri, Thomas Bygh Nymann Jensen, Artur Sannikov, Morten Hoppe, Per Halkjaer Nielsen, Ian P. G. Marshall, Andreas Schramm, Mads Albertsen
Summary: Cable bacteria are centimeter-long filamentous bacteria capable of long-distance electron transfer. They are currently classified into two candidate genera: Candidatus Electronema, found in freshwater, and Candidatus Electrothrix, found in saltwater. To address the lack of complete genomic information, researchers performed Nanopore long-read and Illumina short-read shotgun sequencing, resulting in the recovery of multiple cable bacteria genomes. Phylogenomic analysis classified two circular genomes as novel species: Ca. Electronema halotolerans and Ca. Electrothrix laxa. The discovery of Ca. Electronema halotolerans in brackish-water sediment suggests its evolutionary link between marine and freshwater cable bacteria lineages.
Article
Environmental Sciences
Hesham Amin, Ian P. G. Marshall, Randi J. Bertelsen, Inge M. Wouters, Vivi Schlunssen, Torben Sigsgaard, Tina Santl-Temkiv
Summary: By improving the efficiency of DNA extraction, we have successfully increased the DNA yield of bacterial components collected by the passive sampling device EDC, enabling further research on airborne bacterial and fungal communities. We have also developed a method for simultaneous extraction of DNA and endotoxin, which can be used in large-scale epidemiological studies.
SCIENCE OF THE TOTAL ENVIRONMENT
(2023)
Article
Chemistry, Multidisciplinary
Tessa Lund Biel-Nielsen, T. Alan Hatton, Sebastian N. B. Villadsen, Jan S. Jakobsen, Jacob L. Bonde, Alfred M. Spormann, Philip L. Fosbol
Summary: The unprecedented increase in atmospheric CO2 levels requires efficient, sustainable, and cost-effective technologies for CO2 removal. Future CO2 technologies are expected to follow the trend towards electrified systems, driven by declining electricity prices, expansion of renewable energy infrastructure, and advancements in carbon electrotechnologies. Reviewing selected electrochemical technologies, further development is needed within the next decade to meet ambitious climate goals.
Article
Multidisciplinary Sciences
Rebecca J. Carlson, Michael D. Leiken, Alina Guna, Nir Hacohen, Paul C. Blainey
Summary: This study used high-throughput imaging technology and genome-wide CRISPR knockout screening to identify regulators of IRF3 translocation, Sendai virus localization, and peroxisomal biogenesis. The study also found that the ER-localized P5A-type ATPase ATP13A1 is essential for viral sensing and is involved in promoting the localization of MAVS to mitochondrial membranes.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Article
Multidisciplinary Sciences
Jesper J. Bjerg, Jamie J. M. Lustermans, Ian P. G. Marshall, Anna J. Mueller, Signe Brokjaer, Casper A. Thorup, Paula Tataru, Markus Schmid, Michael Wagner, Lars Peter Nielsen, Andreas Schramm
Summary: Cable bacteria are filamentous microbes that conduct electrons via internal wires and couple sulfide oxidation between sediment layers. Other bacteria swarm around the anoxic part of oxygen-respiring cable bacteria and seem to transfer electrons to cable bacteria via soluble metabolites. This association and interaction with diverse partners may explain how oxygen from cable bacteria affects microbial communities and processes in anoxic environments.
NATURE COMMUNICATIONS
(2023)
Article
Multidisciplinary Sciences
Sri Gowtham Thakku, Jackson Lirette, Kanagavel Murugesan, Julie Chen, Grant Theron, Niaz Banaei, Paul C. Blainey, James Gomez, Sharon Y. Wong, Deborah T. Hung
Summary: This study presents a new method called WATSON that can detect microbial cell-free DNA (cfDNA) for diagnosing infection. WATSON utilizes pooled amplification and CRISPR/Cas13-based detection to improve the detection of cfDNA compared to traditional methods. This approach shows potential for point-of-care diagnostic tests for infectious diseases.
NATURE COMMUNICATIONS
(2023)
Article
Microbiology
Jamie J. M. Lustermans, Jesper J. J. Bjerg, Laurine D. W. Burdorf, Lars Peter Nielsen, Andreas Schramm, Ian P. G. Marshall
Summary: Cable bacteria are filamentous bacteria that play a major role in sediment geochemistry and microbial communities. Our study investigated the timing and drivers of flocking in a culture of freshwater cable bacteria. We found that flocking always occurred, regardless of the overall abundance or activity of the cable bacteria. Flocking was linked to the individual cable bacteria's electron conducting activity.
FRONTIERS IN MICROBIOLOGY
(2023)
Article
Multidisciplinary Sciences
Miguel Reyes, Samantha M. Leff, Matteo Gentili, Nir Hacohen, Paul C. Blainey
Summary: Cells respond to various signals by adopting complex transcriptional states. Most single-cell profiling is done at baseline, ignoring cells' potential functional responses. Single-cell genomics combined with multiplexing techniques provide a useful tool for characterizing cell states across experimental conditions.
Article
Engineering, Environmental
Hesham Amin, Tina Santl-Temkiv, Christine Cramer, Kai Finster, Francisco Gomez Real, Thorarinn Gislason, Mathias Holm, Christer Janson, Nils Oskar Jogi, Rain Jogi, Andrei Malinovschi, Ian P. G. Marshall, Lars Modig, Dan Norback, Rajesh Shigdel, Torben Sigsgaard, Cecilie Svanes, Hulda Thorarinsdottir, Inge M. Wouters, Vivi Schlunssen, Randi J. Bertelsen
Summary: There is limited research on the factors influencing the indoor bacterial community. This study investigated the airborne microbiomes in the homes of 1038 participants from five cities in Northern Europe and identified environmental factors that affect the composition of indoor bacterial communities. The results showed that households in Tartu and Aarhus had higher bacterial load and diversity than those in Bergen and Reykjavik, possibly due to elevated concentrations of outdoor bacterial taxa associated with low precipitation and high wind speeds.
ENVIRONMENTAL SCIENCE & TECHNOLOGY
(2023)
Article
Multidisciplinary Sciences
Bingxu Liu, Rebecca J. Carlson, Ivan S. Pires, Matteo Gentili, Ellie Feng, Quentin Hellier, Marc A. Schwartz, Paul C. Blainey, Darrell J. Irvine, Nir Hacohen
Summary: The activation of STING leads to proton leakage from organelles, which triggers noncanonical lipidation of LC3B and inflammasome activation. Through structural analysis, it is suggested that STING functions as a proton channel. STING-induced proton flux in the Golgi and liposomes can be blocked by the STING agonist C53, leading to inhibition of LC3B lipidation and inflammasome activation. These findings demonstrate that the interferon-induction function of STING can be separated from its roles in LC3B lipidation and inflammasome activation.
Article
Ecology
Alexandra L. McCully, McKenna Loop Yao, Kara K. Brower, Polly M. Fordyce, Alfred M. Spormann
Summary: Our understanding of in situ microbial physiology is limited due to biases towards fast-growing and readily-isolable microbes. To overcome this, a high-throughput bacterial enrichment platform called GrowMiDE was developed, which allows cultivation of underrepresented taxa and slower-growing microbes. GrowMiDE prevents dominance of fast-growing species and enriches for more efficient strains. Moreover, it is compatible with fluorescence-activated cell sorting (FACS) for obtaining isolates. Overall, GrowMiDE + DE-FACS is a promising tool for diverse microbial enrichments or screens.
ISME COMMUNICATIONS
(2023)
Article
Chemistry, Multidisciplinary
Tessa Lund Biel-Nielsen, T. Alan Hatton, Sebastian N. B. Villadsen, Jan S. Jakobsen, Jacob L. Bonde, Alfred M. Spormann, Philip L. Fosbol
Summary: The unprecedented increase in atmospheric CO2 levels requires efficient, sustainable, and cost-effective technologies for CO2 removal. The future of CO2 technologies will likely be electrically-based, driven by decreasing electricity prices, renewable energy expansion, and advancements in carbon electrotechnologies. Initiatives such as electrochemical carbon capture integrated with Power-to-X applications show promise, but further development within the next decade is crucial for meeting ambitious climate goals.
Review
Materials Science, Multidisciplinary
Jo Philips, Luciano Procopio, Ian P. G. Marshall
Summary: This work reviews the metabolic capacities and extracellular electron transfer mechanisms of Shewanella strains, explaining the various mechanisms by which they induce and inhibit corrosion, and emphasizes the impact of medium composition on these mechanisms.
NPJ MATERIALS DEGRADATION
(2023)
Article
Microbiology
Jeanine S. Geelhoed, Casper A. Thorup, Jesper J. Bjerg, Lars Schreiber, Lars Peter Nielsen, Andreas Schramm, Filip J. R. Meysman, Ian P. G. Marshall
Summary: In this study, we identified a novel species of marine cable bacteria with a large diameter, named Candidatus Electrothrix gigas. The genomes of this species contain a gene encoding a novel actin-like protein (Bbp) that is also found in other giant bacteria. This suggests that there may be a genetic basis for large cell size. The Bbp protein may have a structural role in the cell or potentially facilitate intracellular transport.
MICROBIOLOGY SPECTRUM
(2023)