Article
Plant Sciences
Liam Le Lievre, Sreejith P. Chakkatu, Shiny Varghese, Robert C. Day, Sarah M. Pilkington, Lynette Brownfield
Summary: Pollen development is a complex process involving coordinated differentiation and functions of different cell types. However, studying gene expression during early stages of pollen development is challenging due to its inaccessibility. To overcome this, researchers have developed a protocol called SA RNA-Seq, which allows for the transcriptome analysis of isolated pollen from a single anther. This protocol has been successfully applied to Arabidopsis and kiwifruit, providing valuable insights into gene expression during pollen development.
FRONTIERS IN PLANT SCIENCE
(2023)
Article
Biochemical Research Methods
Massimo Andreatta, Ariel J. Berenstein, Santiago J. Carmona
Summary: scGate is a bioinformatics task in single-cell data analysis that automates the purification of a cell type or cell population of interest. It uses a set of markers to purify the cell population and outperforms other single-cell classifiers. scGate can be applied to multiple modalities of single-cell data and is integrated with the Seurat framework, providing an intuitive tool.
Article
Biology
Julia Eve Olivieri, Roozbeh Dehghannasiri, Peter L. Wang, SoRi Jang, Antoine de Morree, Serena Y. Tan, Jingsi Ming, Angela Ruohao Wu, Tabula Sapiens Consortium, Stephen R. Quake, Mark A. Krasnow, Julia Salzman
Summary: The study utilized a new statistical approach called SpliZ to detect and validate cell-type-specific splicing in multiple human tissues, demonstrating that splicing is regulated at the level of cell type.
Article
Cell Biology
Shuai Ma, Shuhui Sun, Jiaming Li, Yanling Fan, Jing Qu, Liang Sun, Si Wang, Yiyuan Zhang, Shanshan Yang, Zunpeng Liu, Zeming Wu, Sheng Zhang, Qiaoran Wang, Aihua Zheng, Shuguang Duo, Yang Yu, Juan Carlos Izpisua Belmonte, Piu Chan, Qi Zhou, Moshi Song, Weiqi Zhang, Guang-Hui Liu
Summary: The research indicates that aging is associated with increased systemic inflammation and compromised virus defense in the cardiopulmonary system. With age, expression of the SARS-CoV-2 receptor ACE2 increases, while the accumulation of the cytokine IL7 induces ACE2 expression. Treatment with vitamin C can block IL7-induced ACE2 expression, suggesting that geroprotective strategies may reduce the severity of COVID-19 in the elderly.
Article
Biochemistry & Molecular Biology
Andrew C. Adey
Summary: Tagmentation has become the preferred method for sequencing library construction over the past decade, due to its simplicity and high efficiency. It has fueled the development of single-cell assays and the hope is that it will inspire the creation of innovative molecular tools to explore the regulatory landscape of single cells further.
Review
Chemistry, Multidisciplinary
Wenpeng Liu, Fei Yue, Luke P. Lee
Summary: The global outbreaks of deadly infectious diseases have urged the need for rapid and accurate pathogen detection. While nucleic acid amplification tests provide a shorter turnaround time to identify pathogens, the complex sample preparation steps remain a bottleneck for modern molecular diagnostic devices.
ACCOUNTS OF CHEMICAL RESEARCH
(2021)
Article
Biochemical Research Methods
Yiming Wang, Xiaojie Wang, Tingrui Pan, Baoqing Li, Jiaru Chu
Summary: This technology utilizes real-time cellular recognition and microfluidic impact printing to efficiently isolate single cells in a label-free manner, with high efficiency and survival rate demonstrated in experiments. It has significant potential in various fields including single-cell omics, tissue engineering, and cell-line development.
Article
Biochemical Research Methods
Sally Anderson, Ben Hadwen, Chris Brown
Summary: The latest development in TFT-DMF technology, aQdrop (TM), shows promising applications in molecular diagnostics, including COVID-19 testing. With 41,000 independently addressable electrodes, TFT-DMF can manipulate droplets of any size and shape to perform multiple parallel reactions, demonstrating its potential for complex assays and sample processing.
Article
Biochemistry & Molecular Biology
Camilla Ferrari, Nicolas Manosalva Perez, Klaas Vandepoele
Summary: In this study, we developed MINI-EX, an integrative approach to infer cell-type-specific networks in plants. MINI-EX uses single-cell transcriptomic data to define expression-based networks and integrates TF motif information to filter the inferred regulons, resulting in networks with increased accuracy. The method successfully identifies key regulators controlling the development of specific cell types in plants, enhancing our understanding of cell-type-specific regulation.
Article
Chemistry, Analytical
Zhihang Yu, Jing Jin, Siyuan Chen, Lingling Shui, Huaying Chen, Liuyong Shi, Yonggang Zhu
Summary: This paper presents a smart droplet microfluidic system that allows for single-cell selective lysis and real-time sorting. By applying voltage and injection pressure to the oil-water interface, the efficiency of droplet injection is greatly improved and the cell lysis solution can be selectively injected into target single-cell droplets. The system function is explored by introducing complex cell samples, achieving a high success rate in treating target cells.
ANALYTICAL CHEMISTRY
(2023)
Article
Cell Biology
Lihua Zhang, Shihua Zhang
Summary: Single-cell RNA sequencing (scRNA-seq) is a powerful tool for determining gene expression patterns in individual cells, but analyzing the data remains challenging due to technical noise and dropout events. The PBLR method proposed in this study effectively imputes dropouts, improves data representation and recovery of gene relationships, and automatically detects cell sub-populations.
JOURNAL OF MOLECULAR CELL BIOLOGY
(2021)
Article
Food Science & Technology
Mirian Labrador, Carlota Gimenez-Rota, Carmen Rota
Summary: A real-time PCR method has been developed for quantifying Listeria monocytogenes on meat products through the gene hlyA, achieving high efficiency and specificity. The method, combined with matrix lysis, showed excellent correspondence with the reference method and higher precision and sensitivity at low concentrations of the pathogen, demonstrating potential for routine control in the meat industry.
Review
Chemistry, Multidisciplinary
Kuangwen Hsieh, Kathleen E. Mach, Pengfei Zhang, Joseph C. Liao, Tza-Huei Wang
Summary: Antimicrobial resistance is a global threat, and there is an urgent need for rapid identification and antimicrobial susceptibility testing technologies to combat the rise of multi-drug-resistant pathogens. Utilizing droplet microfluidics, high-sensitivity detection and rapid response to single cells can be achieved.
ACCOUNTS OF CHEMICAL RESEARCH
(2022)
Article
Biotechnology & Applied Microbiology
Tianyi Sun, Dongyuan Song, Wei Vivian Li, Jingyi Jessica Li
Summary: scDesign2 is a transparent simulator that can simultaneously preserve genes, capture gene correlations, and generate any number of cells with varying sequencing depths, making it advantageous for generating high-fidelity synthetic data for multiple single-cell gene expression count-based technologies.
Article
Multidisciplinary Sciences
Aleksandr Ianevski, Anil K. Giri, Tero Aittokallio
Summary: We developed a computational platform, ScType, for automated and fast cell-type identification using scRNA-seq data and a comprehensive cell marker database. ScType provides unbiased and accurate cell type annotations by ensuring the specificity of marker genes across cell clusters and types. It can also distinguish between healthy and malignant cell populations based on single-nucleotide variant calling.
NATURE COMMUNICATIONS
(2022)
Article
Neurosciences
Rocio Valle-Bautista, Berenice Marquez-Valadez, Gabriel Herrera-Lopez, Ernesto Griego, Emilio J. Galvan, Nestor-Fabian Diaz, Jose-Antonio Arias-Montano, Anayansi Molina-Hernandez
Summary: The transient histaminergic system, activated through H-1 receptor, plays a role in the differentiation of deep-layer cortical neurons. Blocking H-1 receptors with chlorpheniramine during neurogenesis leads to decreased levels of deep-layer cortical neurons and impairs learning, wakefulness, and nociception. This study evaluated the long-lasting effects of chlorpheniramine on the differentiation of deep-layer cortical neurons in neonates and 21-day-old pups. The results showed altered expression and distribution of cortical markers, as well as impaired dendritic arborization and lower excitability in response to histamine. These findings suggest the importance of H1 receptors in cortical neurogenesis and its impact on motor activity and cognition.
FRONTIERS IN NEUROSCIENCE
(2022)
Article
Neurosciences
Nilton Akio Muto, Moises Hamoy, Chryslen Brenda da Silva Ferreira, Akira Otake Hamoy, David Cristian Rodrigues Lucas, Vanessa Joia de Mello, Herve Rogez
Summary: This study demonstrated the anticonvulsant protective properties of Euterpe oleracea stone extract (EEOS) through EEG profiling in induced convulsing rats. The mechanism of action of EEOS is similar to diazepam (DZP) and involves the benzodiazepine (BDZ) subunit of the GABAA receptor.
FRONTIERS IN CELLULAR NEUROSCIENCE
(2022)
Article
Microbiology
Maria Gisele Goncalves, Lucila Okuyama Fukasawa, Karoline Rodrigues Campos, Fabio Takenori Higa, Adele Caterino-de-Araujo
Summary: Brazil currently has the highest number of individuals infected with human T-lymphotropic virus 1- and 2- (HTLV-1 and HTLV-2) globally. Molecular protocols and commercial assays for HTLV-1/-2 diagnosis are not available or validated by the Brazilian regulatory agency. In this study, two in-house multiplex quantitative real-time PCR assays were developed and validated for HTLV-1/-2 diagnosis. The assays showed high sensitivity and specificity and could resolve issues with indeterminate and untyped results in HTLV western blotting.
FRONTIERS IN MICROBIOLOGY
(2022)
Article
Pharmacology & Pharmacy
Benjamin Hackl, Peter Lukacs, Janine Ebner, Krisztina Pesti, Nicholas Haechl, Matyas C. Foeldi, Elena Lilliu, Klaus Schicker, Helmut Kubista, Anna Stary-Weinzinger, Karlheinz Hilber, Arpad Mike, Hannes Todt, Xaver Koenig
Summary: Ivabradine acts as an atypical inhibitor of voltage-gated sodium channels, affecting heart rate and cardiac conduction system, which may provide potential basis for anti-arrhythmic effects.
FRONTIERS IN PHARMACOLOGY
(2022)
Article
Oncology
Ayman Osman, Malin Linden, Tobias Osterlund, Christoffer Vannas, Lisa Andersson, Mandy Escobar, Anders Stahlberg, Pierre Aman
Summary: DDIT3 is a transcription factor that plays a key role in cellular stress responses, cell cycle regulation, apoptosis, cell differentiation, and cancer development. It can bind to DNA and regulate target genes by forming heterodimers with other bZIP transcription factors. DDIT3 mainly binds to the promoter region of regulated genes and shows a strong overlap with H3K27 acetylation marks.
EXPERIMENTAL CELL RESEARCH
(2023)
Article
Biology
Serik Sagitov, Anders Stahlberg
Summary: This study utilizes molecular barcoding technology to detect extremely rare variant alleles, such as tumor DNA, within a complex mixture of DNA molecules, in order to avoid sequencing errors. They propose a random model to describe the random outcome of PCR barcoding and discover a remarkable asymptotic pattern under moderate PCR cycle numbers. The results of this model will assist users in drawing more accurate conclusions from the outcomes of different sequencing protocols.
JOURNAL OF THEORETICAL BIOLOGY
(2023)
Article
Chemistry, Analytical
Amin Forootan, Daniel Andersson, Soheila Dolatabadi, David Svec, Jose Andrade, Anders Stahlberg
Summary: This study used self-organizing maps technology to analyze cells from myxoid liposarcoma and Ewing sarcoma, and found that they have similar gene expression signatures, indicating that these two tumors exhibit similar cellular characteristics.
Article
Orthopedics
Bernhard Springer, Robin Dreisbach, Klaus-Dieter Schatz, Bernd Kubista, Wenzel Waldstein
Summary: This study evaluated the information quality of YouTube videos regarding postoperative patient information and rehabilitation after arthroscopic rotator cuff repair. Most of the videos were of poor quality, with videos uploaded by medically trained professionals offering better information. The findings suggest that physicians should provide alternative sources of high-quality information to patients.
ARTHROSCOPY-THE JOURNAL OF ARTHROSCOPIC AND RELATED SURGERY
(2023)
Review
Biotechnology & Applied Microbiology
Eva Pasquier, Jennifer Rosendahl, Amalie Solberg, Anders Stahlberg, Joakim Hakansson, Gary Chinga-Carrasco
Summary: Breast cancer is a common cancer among women, and the efficiency of available treatments varies. Current 2D models overestimate drug efficiency, leading to higher failure rates in later clinical trials. Therefore, new model systems are needed for drug screening. 3D printed hydrogels with active components provide interesting candidates for next generation cancer cell models.
BIOENGINEERING-BASEL
(2023)
Article
Multidisciplinary Sciences
Kieran D. O'Malley, Henry Schofield, Patrick G. R. Wright, Daniel Hargreaves, Tom Kitching, Marina Bollo Palacios, Fiona Mathews
Summary: Identifying peaks of bat activity through acoustic monitoring can help locate bat colonies, and a triage system based on this method can be used to prioritize survey efforts. This study successfully developed a methodology for predicting woodland occupancy by barbastelle bats using acoustic data, and validated it through citizen science surveys and specialist tracking surveys.
Article
Multidisciplinary Sciences
Elin Schoultz, Shawn Liang, Therese Carlsson, Stefan Filges, Anders Stahlberg, Henrik Fagman, Clotilde Wiel, Volkan Sayin, Mikael Nilsson
Summary: It is found that tumor development and progression differ significantly in lung and thyroid targeted by Braf mutation. Even with similar levels of Braf mutation in both tissues, non-induced mutants only developed multiple lung adenocarcinomas, while thyroid tumors were rare and constrained. This indicates that BRAF(V600E)-induced tumorigenesis follows organ-specific traits that might be modified differently by a shared lineage factor.
Article
Oncology
Vasu R. Sah, Henrik Jespersen, Joakim Karlsson, Lisa M. Nilsson, Mattias Bergqvist, Iva Johansson, Ana Carneiro, Hildur Helgadottir, Max Levin, Gustav Ullenhag, Anders Stahlberg, Roger Olofsson Bagge, Jonas A. Nilsson, Lars Ny
Summary: The 2-year follow-up of the PEMDAC trial showed that patients with high levels of CCL21 in blood had better treatment response and survival. The expression of CCL21 in tumors and the presence of TLS-like regions were also associated with longer survival.
CANCER RESEARCH COMMUNICATIONS
(2023)
Article
Agriculture, Dairy & Animal Science
Jianfei Chen, Ziwei Chen, Jilong Zhang, Wuchao Zhuang, Xiaotong Zheng
Summary: This study utilized different algorithms to evaluate the stability of internal reference genes in the gastrointestinal tract of chickens. The most suitable reference genes for each type of GI tissue were identified. Commonly used internal reference genes exhibited poor stability and are not recommended for future gene expression studies in the GI region.
Article
Mycology
Relber Aguiar Goncales, Igor Godinho Portis, Thaila Fernanda dos Reis, Luiz Roberto Basso Junior, Roberto Martinez, Heng Zhu, Maristela Pereira, Celia Maria de Almeida Soares, Paulo Sergio Rodrigues Coelho
Summary: In this study, expression analysis of GPI-anchored proteins in Paracoccidioides brasiliensis was conducted. The findings revealed increased expression levels of certain proteins in the mycelium and yeast forms, and these proteins showed immune reactivity against sera obtained from PCM patients. These results provide valuable information about the function of GPI-anchored proteins and their potential as diagnostic markers.
FRONTIERS IN FUNGAL BIOLOGY
(2023)
