Article
Environmental Sciences
Halina Binde Doria, Pauline Hannappel, Markus Pfenninger
Summary: This study investigated the evolutionary adaptation and genomic basis of increased tolerance in Chironomus riparius to cadmium exposure. The results showed a strong genome-wide selective response in all replicates, with pathways related to microtubules and organelles and cellular movement being specifically selected by cadmium exposure.
SCIENCE OF THE TOTAL ENVIRONMENT
(2022)
Review
Cell Biology
Tamer Butto, Kanak Mungikar, Peter Baumann, Jennifer Winter, Beat Lutz, Susanne Gerber
Summary: In the last decade, there has been a significant increase in nuclei-based studies, especially in combination with next-generation sequencing. These studies aim to understand the molecular states in heterogeneous cell populations using more affordable sequencing approaches and optimized nuclei isolation methods. While these powerful new methods offer unprecedented insights, it is important to consider the associated challenges critically. This article provides a comprehensive overview of the rise of nuclei-based studies and discusses their advantages and disadvantages, with a specific focus on their utility for transcriptomic sequencing analyses. Improving experimental designs and using various strategies appropriately will lead to biologically accurate and meaningful information.
Article
Biochemistry & Molecular Biology
Sanjay Joshi, Hadia Awan, Priyanka Paul, Ran Tian, Sharyn E. Perry
Summary: AGL15, a member of the MADS-domain transcription factor family, primarily accumulates in plant embryos and promotes plant regeneration. Through the use of different technological platforms, researchers have identified an interaction between AGL15 and the brassinosteroid hormone signaling pathway.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Chemistry, Multidisciplinary
Na Zhao, Jiabao Cao, Jiayue Xu, Beibei Liu, Bin Liu, Dingqiang Chen, Binbin Xia, Liang Chen, Wenhui Zhang, Yuqing Zhang, Xuan Zhang, Zhimei Duan, Kaifei Wang, Fei Xie, Kun Xiao, Wei Yan, Lixin Xie, Hongwei Zhou, Jun Wang
Summary: Utilizing RNA sequencing and third-generation sequencing technology for pathogen identification can improve the ratio of microbial reads and accelerate clinical diagnosis, showing significant potential.
Review
Environmental Sciences
Tessa M. Page, Jonathan W. Lawley
Summary: As we enter the United Nations Decade of Ocean Science for Sustainable Development, efforts to reverse ocean health decline are urgent. Transcriptomic technologies are playing an increasingly important role in marine ecology research, providing researchers with valuable tools to understand genetic variation, cellular processes, and pathways.
FRONTIERS IN MARINE SCIENCE
(2022)
Article
Genetics & Heredity
Michael Schwabe, Sven Griep, Henrike Schmidtberg, Rudy Plarre, Alexander Goesmann, Andreas Vilcinskas, Heiko Vogel, Karina Brinkrolf
Summary: The clothes moth Tineola bisselliella is capable of digesting keratin, and the analysis of its gut transcriptome reveals various enzymes involved in keratin digestion. Additionally, the unstable intestinal microbiome of T. bisselliella larvae may play a role in keratin digestion.
Article
Behavioral Sciences
Miguel Fuentes-Ramos, Marta Alaiz-Noya, Angel Barco
Summary: Transcription and epigenetic changes play vital roles in neuronal response to stimulation, impacting enduring changes in animal behavior such as learning and memory. Yet, understanding the specific epigenetic changes occurring in these cells and their contribution to memory persistence remains a challenge despite recent research progress.
NEUROSCIENCE AND BIOBEHAVIORAL REVIEWS
(2021)
Article
Genetics & Heredity
Asra Almubarak, Dan Zhang, Mackenzie Kosak, Sarah Rathwell, Jasmine Doonanco, Alison J. Eaton, Peter Kannu, Joanna Lazier, Monique Lui, Karen Y. Niederhoffer, Melissa J. MacPherson, Melissa Sorsdahl, Oana Caluseriu
Summary: The study reviewed the approach to prenatal testing over a three-year period, with a total diagnostic yield of 30.4%. The majority of diagnoses were obtained using NGS technology, with 43.4% of them during ongoing pregnancies.
Article
Biotechnology & Applied Microbiology
Tong Zhang, Jinxin Dong, Hua Jiang, Zuyao Zhao, Mengjiao Zhou, Tianting Yuan
Summary: This study proposes a new method, CNV-PCC, for detecting copy number variations (CNVs). By utilizing split read signals and a segmentation strategy, CNV-PCC improves the identification capabilities for low copy number duplications and small CNVs. The analysis of simulated data and real sequencing samples demonstrates that CNV-PCC outperforms other methods in sensitivity, F1-score, and breakpoint accuracy.
FRONTIERS IN BIOENGINEERING AND BIOTECHNOLOGY
(2022)
Article
Genetics & Heredity
Dingani Nkosi, Giby V. George, Huijie Liu, Meghan Buldo, Moises J. Velez, Zoltan N. Oltvai
Summary: DNA-only, small gene next-generation sequencing (sNGS) panels combined with ultra-rapid reflex testing using Idylla Genefusion assay provide a cost-effective and comprehensive testing modality for the majority of lung cancer cases, but additional reflex testing capability is needed for a small subset of lung cancers with rare variants and post-treatment resistance mutations.
Review
Immunology
Yan Zheng, Xiaojian Qiu, Ting Wang, Jie Zhang
Summary: Metagenomic next-generation sequencing (mNGS) technology has provided a promising means for pathogen-specific diagnosis of lower respiratory tract infections, but still faces technical difficulties in clinical applications.
FRONTIERS IN CELLULAR AND INFECTION MICROBIOLOGY
(2021)
Article
Parasitology
Banucicek Yucesan, Dilek Guldemir, Cahit Babur, Selcuk Kilic, Ayse Cakmak
Summary: This study successfully conducted whole-genome sequencing of T. gondii for the first time in Turkey, providing important data for better understanding this pathogen.
Article
Oncology
Tyler Shugg, Reynold C. Ly, Wilberforce Osei, Elizabeth J. Rowe, Caitlin A. Granfield, Ty C. Lynnes, Elizabeth B. Medeiros, Jennelle C. Hodge, Amy M. Breman, Bryan P. Schneider, S. Cenk Sahinalp, Ibrahim Numanagic, Benjamin A. Salisbury, Steven M. Bray, Ryan Ratcliff, Todd C. Skaar
Summary: This study assessed the accuracy of the Aldy computational method in extracting pharmacogenomics genotypes from whole genome sequencing (WGS) and whole exome sequencing (WES) data. The results showed that Aldy achieved over 99% accuracy in calling diplotypes for major pharmacogenes from both WGS and WES data, supporting its importance in clinical applications.
FRONTIERS IN ONCOLOGY
(2023)
Article
Microbiology
Ilayda Akacin, Seymanur Ersoy, Osman Doluca, Mine Gungormusler
Summary: This review provides a comprehensive overview of recent literature on the utilization of TGS and NGS technologies in microbial metagenomics research. It discusses the advantages and limitations of these technologies and presents real-time examples of novel applications in clinical microbiology and public health, food and agriculture, energy and environment, arts and space.
MICROBIOLOGICAL RESEARCH
(2022)
Article
Dermatology
Amanda M. Saracino, Daniel Kelberman, Georg W. Otto, Andrey Gagunashvili, David J. Abraham, Christopher P. Denton
Summary: This study found no primary somatic epidermal mosaicism in linear morphoea (LM) and identified potential disease-driving mechanisms, epidermal-dermal interactions, and differential gene expression in LM. The epidermis in LM showed enhanced proliferation, inflammation, and fibrosis, along with the activation of various signaling pathways. Enhanced epidermal-dermal communication and specific gene expression patterns were also observed. These findings provide insights into the pathogenesis of LM and potential targets for future therapies.
ARCHIVES OF DERMATOLOGICAL RESEARCH
(2023)