Article
Nanoscience & Nanotechnology
Peng Qi, Ya-ling Zeng, Xu Ye, Ya-mei Li, Feng-jiao Wang, Wang-yang Pu, Rong Zhang, Min Li, Li Xiao, Gang Huang, Sirois Pierre, Jun Chuan, Jingjing Luo, Duan-fang Liao, Hongyan Wen, Kai Li
Summary: In this study, several strategies were tested to limit or abolish self-ligation of next generation sequencing adapters. Experimental data showed that these strategies can significantly reduce or completely eliminate self-ligation. Minimizing or eliminating self-ligation is crucial in improving the sensitivity, efficiency, and reproducibility of enzyme-mediated methylation assays. These strategies may also have applications in other nanotechnologies.
JOURNAL OF BIOMEDICAL NANOTECHNOLOGY
(2023)
Editorial Material
Cell Biology
Kyunghee Yu, Jiung Kang, Sunmi Jung, Jina Lee, Younhee Park
Summary: The HLA-DQB1*03:454 allele differs from the HLA-DQB1*03:01:01:01 allele by a single nucleotide at codon 227.
Article
Computer Science, Artificial Intelligence
Jae Won Cho, Dawit Mureja Argaw, Youngtaek Oh, Dong-Jin Kim, In So Kweon
Summary: This work empirically studies the use of adapters for debiased Visual Question Answering (VQA) and explores the possibility of preserving in-distribution performance while reducing bias. The study shows that a single fully connected layer can capture and model the debiasing information from different methods, and different placements of adapters are required for different debiasing techniques. The findings highlight the potential of using adapters for debiasing in VQA.
COMPUTER VISION AND IMAGE UNDERSTANDING
(2023)
Article
Engineering, Biomedical
Tairan Liu, Yuzhu Li, Hatice Ceylan Koydemir, Yijie Zhang, Ethan Yang, Merve Eryilmaz, Hongda Wang, Jingxi Li, Bijie Bai, Guangdong Ma, Aydogan Ozcan
Summary: An automated plaque assay leveraging lens-free holographic imaging and deep learning rapidly and accurately detects the cell-lysing events caused by viral replication.
NATURE BIOMEDICAL ENGINEERING
(2023)
Review
Biochemistry & Molecular Biology
Domenico Tierno, Gabriele Grassi, Serena Scomersi, Marina Bortul, Daniele Generali, Fabrizio Zanconati, Bruna Scaggiante
Summary: The poor survival of triple-negative breast cancer (TNBC) is attributed to its aggressive behavior, large heterogeneity, and high risk of recurrence. Next-generation sequencing (NGS) has been used to investigate the molecular characteristics of TNBC, revealing recurrent pathogenic alterations in TP53, immunocheckpoint response genes, and PIK3CA and DNA repair pathways. NGS has also identified potential personalized treatments and novel biomarkers such as AURKA, MYC, and JARID2 mutations. Additionally, NGS studies have identified ethnicity-specific alterations in African and African American TNBC, including EZH2 overexpression, BRCA1 alterations, and a BRCA2-delaAAGA mutation. The development of long-read sequencing methods and their combination with optimized short-read techniques hold promise for improving the efficiency of NGS approaches in future clinical use.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Chemistry, Analytical
Yue Sun, Zhenzi Xu, Feifang Zhang, Zongying Li, Bingcheng Yang
Summary: In this study, a reagent-free acid-base titration method was developed using an online electrodialytic titrant generator (ETG) that produced high purity titrants. By manipulating current, a series of titrants with different concentrations could be accurately obtained, showing good accuracy and precision in titration results. The utility of ETG was demonstrated in measuring the pKa-differentiated capacity of anion exchange resins.
Article
Engineering, Electrical & Electronic
Mohamed Ouameur, Boubacar Abdourahamane Kassoum, Francois Ziade, Djamel Allal
Summary: This article presents a high-frequency approach to evaluate the impedance characteristics of resistors at frequencies up to a few megahertz. By using specific adapters, the amplitude and phase of resistors can be measured within the frequency range.
IEEE TRANSACTIONS ON INSTRUMENTATION AND MEASUREMENT
(2022)
Article
Cardiac & Cardiovascular Systems
Jishnu Malgie, Pascal R. D. Clephas, Hans-Peter Brunner-La Rocca, Rudolf A. de Boer, Jasper J. Brugts
Summary: Multiple landmark trials in the past decade have significantly advanced the treatment of heart failure with reduced ejection fraction (HFrEF). The introduction of four main drug classes, including angiotensin-receptor neprilysin inhibitors/angiotensin-converting-enzyme inhibitors, beta-blockers, mineralocorticoid receptor antagonists, and sodium-glucose cotransporter-2 inhibitors, into the latest ESC guideline has proven their life-saving effect. Rapid drug implementation and up-titration have been shown to be superior to the traditional step-by-step approach, and various strategies have been proposed to reduce the time needed for the titration process.
HEART FAILURE REVIEWS
(2023)
Article
Immunology
Mark Itsko, Nadav Topaz, Sani Ousmane, Micheal Popoola, Rasmata Ouedraogo, Kadidja Gamougam, Adodo Yao Sadji, Abass Abdul-Karim, Christine Lascols, Xin Wang
Summary: Genomic surveillance for meningococcal meningitis can be significantly improved using culture-free methods to increase data representativeness and monitor changes in epidemiological landscape, especially for countries with low culture rate.
JOURNAL OF INFECTIOUS DISEASES
(2022)
Article
Biotechnology & Applied Microbiology
Marcela A. Johnson, Boris A. Vinatzer, Song Li
Summary: Climate change may result in the emergence of new plant diseases caused by unknown pathogens. Surveillance for emerging plant diseases is crucial to reduce threats to food security. Machine learning can be used for reference-free detection of plant pathogens using genomic sequencing.
APPLIED AND ENVIRONMENTAL MICROBIOLOGY
(2023)
Article
Multidisciplinary Sciences
Xuemei Cao, Cansu Kose, Christopher P. Selby, Aziz Sancar
Summary: The XR-seq method is widely used for mapping nucleotide excision repair genome-wide. It captures and sequences excised oligomers carrying DNA damage, and aligns their sequences to the genome. Researchers have successfully used ultraviolet light-irradiated plasmids as substrates for repair experiments in Escherichia coli and mammals, and found common excision product characteristics in both systems. This approach helps understand the effects of epigenetics and other cellular factors on DNA repair.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Article
Genetics & Heredity
Jada Lindsay Nix, Gustavo Pimenta Schettini, Fernando Henrique Biase
Summary: This article introduces the methods of using RNA-sequencing data or PCR assays to determine the presence of the chromosome Y in samples and emphasizes the importance of these methods for studying biological variation due to sexual dimorphism. The authors successfully identified a set of genes exclusively expressed in male tissues using the sequence of the cattle ChrY and transcriptome data, and used them to determine the sex of 22 cattle blastocysts. Additionally, they accurately identified the sex of cattle blastocysts using a pair of oligonucleotides in a PCR assay. These methods have important applications for researchers using RNA-sequencing data or DNA to determine the sex of samples. Evaluation: 9 points.
FRONTIERS IN GENETICS
(2023)
Letter
Oncology
Nick Veltmaat, Yujie Zhong, Filipe Montes de Jesus, Geok Wee Tan, Johanna A. A. Bult, Martijn M. Terpstra, Pim G. N. J. Mutsaers, Wendy B. C. Stevens, Rogier Mous, Joost S. P. Vermaat, Martine E. D. Chamuleau, Walter Noordzij, Erik A. M. Verschuuren, Klaas Kok, Joost L. Kluiver, Arjan Diepstra, Wouter J. Plattel, Anke Van den Berg, Marcel Nijland
Summary: The study investigates the use of cfDNA for genomic profiling of PTLD, and explores its potential as a screening tool. Analysis showed that 41% of patients had EBV-positive tumors and 76% had stage IV disease. The study provides important insights into the genetic variations and EBV infection in PTLD.
JOURNAL OF HEMATOLOGY & ONCOLOGY
(2023)
Article
Plant Sciences
Miroslav Glasa, Richard Hancinsky, Katarina Soltys, Lukas Predajna, Jana Tomasechova, Pavol Hauptvogel, Michaela Mrkvova, Daniel Mihalik, Thierry Candresse
Summary: Recent advances in high throughput sequencing (HTS) have provided new possibilities for studying the diversity and complexity of plant viromes, with mixed infections of multiple viruses commonly observed in plant samples. This study highlights the challenges involved in precisely identifying PVY isolates in mixed infections, showcasing the complexity of PVY infection in some host plants.
Article
Materials Science, Multidisciplinary
Tian Xue, Ankit Jain, Xiaobao Cao, David Hess, Stavros Stavrakis, Andrew de Mello
Summary: This article describes a valve-based droplet-on-demand generator that can generate femtoliter-volume water-in-oil droplets stably under controlled conditions. This method allows for high-precision droplet dilution and programmable droplet pairing/merging operations, as well as rapid low-volume titrations. Therefore, this generator enables a range of automated and multi-step droplet-based manipulations.
ADVANCED MATERIALS TECHNOLOGIES
(2023)
Article
Biochemistry & Molecular Biology
Sara Beier, Anders F. Andersson, Pierre E. Galand, Corentin Hochart, Juerg B. Logue, Katherine McMahon, Stefan Bertilsson
Editorial Material
Oncology
Zhengbo Song, Chenyu Lu, Chun-Wei Xu, Zongli Zheng
JOURNAL OF THORACIC ONCOLOGY
(2021)
Article
Biology
Karin Holmfeldt, Emelie Nilsson, Domenico Simone, Margarita Lopez-Fernandez, Xiaofen Wu, Ino de Bruijn, Daniel Lundin, Anders F. Andersson, Stefan Bertilsson, Mark Dopson
Summary: Investigating the deep terrestrial virosphere reveals unique viral communities associated with Firmicutes and Patescibacteria, impacting ecological dynamics through viral predation and nutrient recycling. The presence of 'kill-the-winner' oscillations and 'boom and burst' cycles suggest complex interactions within deep groundwater ecosystems.
COMMUNICATIONS BIOLOGY
(2021)
Article
Ecology
Conny Sjoqvist, Luis Fernando Delgado, Johannes Alneberg, Anders F. Andersson
Summary: Bacterioplankton in the Baltic Sea exhibit significant genomic diversity and population structures correlated with environmental factors, with more pronounced differentiation over spatial scales. The study highlights genes that have adapted to different salinity regimes and emphasizes the importance of physiological barriers in shaping bacterioplankton species.
Article
Medicine, General & Internal
Amir Sohrabi, Joar Franzen, Nikolaos Tertipis, Ulrika Zagai, Wanxin Li, Zongli Zheng, Weimin Ye
Summary: The study evaluated the LAMP assay for H. pylori detection using noninvasive and self-sampling methods, showing high specificity and sensitivity for potential clinical applications. The combination of LAMP assay with noninvasive sampling methods has the potential to be a useful point-of-care testing approach for detecting H. pylori infection in clinic settings and screening programs.
Article
Oncology
Zhengbo Song, Shifeng Lian, Silvia Mak, Maggie Zi-Ying Chow, Chunwei Xu, Wenxian Wang, Hoi Yee Keung, Chenyu Lu, Firaol Tamiru Kebede, Yanqiu Gao, Wah Cheuk, William Chi Shing Cho, Mengsu Yang, Zongli Zheng
Summary: Gene fusion variants in ALK-rearranged NSCLC may predict patient outcomes and the efficacy of targeted therapy. Multiple fusion isoforms may lead to worse survival rates, and treatment may result in temporal changes of fusion isoforms.
JOURNAL OF THORACIC ONCOLOGY
(2022)
Article
Biochemical Research Methods
Nikolay L. Malinin, GaHyun Lee, Cicera R. Lazzarotto, Yichao Li, Zongli Zheng, Nhu T. Nguyen, Matthew Liebers, Ved V. Topkar, A. John Iafrate, Long P. Le, Martin J. Aryee, J. Keith Joung, Shengdar Q. Tsai
Summary: GUIDE-seq is a sensitive, unbiased, genome-wide method for defining the specificity of genome-editing nucleases in living cells, allowing for the identification of off-target sites and ranking them by nuclease activity.
Article
Biochemistry & Molecular Biology
Chaya T. L. Yuen, Dawn G. L. Thean, Becky K. C. Chan, Peng Zhou, Cynthia C. S. Kwok, Hoi Yee Chu, Maggie S. H. Cheung, Bei Wang, Yee Man Chan, Silvia Y. L. Mak, Anskar Y. Leung, Gigi C. G. Choi, Zongli Zheng, Alan S. L. Wong
Summary: Researchers have enhanced editing accuracy and reduced off-target edits by re-engineering KKH-SaCas9 with a Y239H mutation and a set of additional mutations, demonstrating the feasibility of multi-domain combinatorial mutagenesis to optimize editing fidelity.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Biochemistry & Molecular Biology
Meike A. C. Latz, Vesna Grujcic, Sonia Brugel, Jenny Lycken, Uwe John, Bengt Karlson, Agneta Andersson, Anders F. Andersson
Summary: In this study, new primers targeting 18S and 28S rRNA were designed and evaluated in vitro and in vivo. The results showed that a new V6-V8 primer pair and the V4_Balzano primer pair performed well in short-read sequencing, while fewer differences were observed between long-read primer pairs. Long-read amplicons and ITS1 alone provided higher taxonomic resolution than V4. These findings provide a reference and guide for the selection of robust primers for research on and environmental monitoring of microbial eukaryotes.
MOLECULAR ECOLOGY RESOURCES
(2022)
Article
Multidisciplinary Sciences
Dawn G. L. Thean, Hoi Yee Chu, John H. C. Fong, Becky K. C. Chan, Peng Zhou, Cynthia C. S. Kwok, Yee Man Chan, Silvia Y. L. Mak, Gigi C. G. Choi, Joshua W. K. Ho, Zongli Zheng, Alan S. L. Wong
Summary: This study presents a machine learning-coupled combinatorial mutagenesis approach to reduce the experimental burden for engineering Cas9 genome editing enzymes. Using this approach, the authors identified a variant of Cas9 with enhanced editing activity in human cells. This research validates a feasible workflow for resource-efficient high-throughput engineering of genome editor's activity.
NATURE COMMUNICATIONS
(2022)
Article
Microbiology
Luis Fernando Delgado, Anders F. Andersson
Summary: This study evaluates three assembly strategies for generating gene catalogs from 124 Baltic Sea samples and finds that the mix-assembly approach results in a more extensive and functionally annotated gene set, making it a valuable resource for brackish water research.
Article
Biochemical Research Methods
Maria Prager, Daniel Lundin, Fredrik Ronquist, Anders F. Andersson
Summary: The ASV portal is a web interface that effectively integrates biodiversity data derived from DNA sequences into the Living Atlas platform.
BMC BIOINFORMATICS
(2023)
Article
Ecology
Elzbieta Iwaszkiewicz-Eggebrecht, Emma Granqvist, Mateusz Buczek, Monika Prus, Jan Kudlicka, Tomas Roslin, Ayco J. M. Tack, Anders F. Andersson, Andreia Miraldo, Fredrik Ronquist, Piotr Lukasik
Summary: Metabarcoding has shown promise as a cost-effective method for studying insect communities, but its performance varies among studies. This research evaluated the impact of DNA extraction protocols on metabarcoding results using mock community experiments. The results showed that a nondestructive, mild lysis approach is best for reconstructing species lists and approximate counts, while homogenization protocols are better for characterizing biomass composition. Species-specific reference data and adequate spike-in data were also important for accurate species abundance estimates.
METHODS IN ECOLOGY AND EVOLUTION
(2023)
Article
Multidisciplinary Sciences
Krzysztof T. Jurdzinski, Maliheh Mehrshad, Luis Fernando Delgado, Ziling Deng, Stefan Bertilsson, Anders F. Andersson
Summary: The crossing of environmental barriers poses adaptive challenges and bacterial communities in freshwater-marine transitions are rarely related to brackish counterparts. This study conducted a phylogenomic analysis of metagenome-assembled genomes to investigate the molecular adaptations facilitating cross-biome transitions. The results showed that cross-biome transitions were rare, ancient, and mostly directed toward the brackish biome, accompanied by systematic changes in proteomes and gene functions.
Article
Ecology
Alejandro Rodriguez-Gijon, Moritz Buck, Anders F. F. Andersson, Dandan Izabel-Shen, Francisco J. A. Nascimento, Sarahi L. L. Garcia
Summary: This study investigates the ecological implications of microbial genome size variation in benthic and pelagic habitats of the Baltic Sea. It finds that genome size is associated with depth and salinity, with benthic genomes being larger than pelagic genomes. Additionally, the study shows differences in functions, metabolic potential, and taxonomy between Bacteria inhabiting sediment and water column.
ISME COMMUNICATIONS
(2023)
