Article
Biochemistry & Molecular Biology
Sander Plessers, Vincent Van Deuren, Rob Lavigne, Johan Robben
Summary: The study combined phage display technology with high-throughput sequencing to examine library diversity and selection dynamics, focusing on two homologous proteins. Short-read sequencing and nanopore sequencing revealed unexpected findings and highlighted the impact of amplification bias on the clones in the library.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Review
Biochemistry & Molecular Biology
Jasper Verwilt, Pieter Mestdagh, Jo Vandesompele
Summary: RNA sequencing has become influential in various research fields. However, the reverse transcription reaction in most protocols often leads to biases and artifacts in the resulting cDNA pool, which are overlooked in the literature. This review discusses these issues and provides solutions and good practices for RNA sequencing experiments, aiming to contribute to scientifically sound RNA studies.
Article
Agricultural Engineering
Mengxiao Xu, Hanchi Xu, Yalin Sui, Xiaoxiao Yan, Zhaojun Wang, Hong Cui, Hongying Zhang
Summary: A novel member of the homeodomain leucine zipper IV family, NtHDZIPIV9, was found to play a crucial role in the development of the epidermal cuticles in tobacco. Overexpression of NtHDZIPIV9 increased cuticle thickness, pigment content, and leaf surface exudates, while knockout of NtHDZIPIV9 significantly reduced these characteristics.
INDUSTRIAL CROPS AND PRODUCTS
(2023)
Article
Genetics & Heredity
Ke Ding, Shanwen Sun, Yang Luo, Chaoyue Long, Jingwen Zhai, Yixiao Zhai, Guohua Wang
Summary: Chromatin accessibility is crucial for understanding genetic regulatory networks and key biological processes. A comprehensive plant chromatin accessibility database, PlantCADB, has been developed for 37 species with 649 samples, covering abiotic stress-related, development-related, and tissue-specific categories. This database provides annotations and analysis tools to aid in the understanding of genetic regulatory networks in plants.
GENOMICS PROTEOMICS & BIOINFORMATICS
(2023)
Article
Multidisciplinary Sciences
Maik Pietzner, Robert Lorenz Chua, Eleanor Wheeler, Katharina Jechow, Julian D. S. Willett, Helena Radbruch, Saskia Trump, Bettina Heidecker, Hugo Zeberg, Frank L. Heppner, Roland Eils, Marcus A. Mall, J. Brent Richards, Leif-Erik Sander, Irina Lehmann, Soeren Lukassen, Nicholas J. Wareham, Christian Conrad, Claudia Langenberg
Summary: This study integrates genomic, proteomic, and single-cell data to identify ELF5 as a candidate risk gene for severe COVID-19. ELF5 shows consistent associations with different outcome definitions and is specifically expressed in respiratory epithelial cells, which are likely targets of SARS-CoV-2.
NATURE COMMUNICATIONS
(2022)
Article
Medicine, General & Internal
Bo-Wei Han, Xu Yang, Shou-Fang Qu, Zhi-Wei Guo, Li-Min Huang, Kun Li, Guo-Jun Ouyang, Geng-Xi Cai, Wei-Wei Xiao, Rong-Tao Weng, Shun Xu, Jie Huang, Xue-Xi Yang, Ying-Song Wu
Summary: A deep-learning pipeline, AECT, designed for transcription start site coverage profiles showed superior performance in improving TSS coverage accuracy and capturing latent biological features. Classifiers built using AECT-imputed shallow sequencing data for breast and rectal cancer detection performed close to high-depth sequencing, suggesting that AECT could offer a broadly applicable noninvasive screening approach with high accuracy and moderate cost.
FRONTIERS IN MEDICINE
(2021)
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
Michaela A. Boti, Panagiotis G. Adamopoulos, Panagiotis Tsiakanikas, Andreas Scorilas
Summary: Elf-3, a member of the ETS family, is crucial in epithelial cell differentiation, development, and cancer. This study identified 25 new ELF3 mRNA transcript variants and two novel exons, laying the foundation for further research on the biological function of these variants and protein isoforms.
Article
Immunology
Yingyu Zhang, Wanwei Zhang, Jingyao Zhao, Takamasa Ito, Jiacheng Jin, Alexis O. Aparicio, Junsong Zhou, Vincent Guichard, Yinshan Fang, Jianwen Que, Joseph F. Urban, Jacob H. Hanna, Sankar Ghosh, Xuebing Wu, Lei Ding, Uttiya Basu, Yuefeng Huang
Summary: Huang and colleagues demonstrate that the m(6)A mRNA modifications mediated by METTL3 are crucial for the transcriptional activity of activated ILC2s. This study reveals that METTL3 deletion has limited effects on ILC homeostasis or cytokine-induced ILC1 or ILC3 responses, but significantly impairs ILC2 proliferation, migration, and effector cytokine production, resulting in impaired antihelminth immunity. The m(6)A RNA modification specifically supports cell enlargement and transcriptional activity in activated ILC2s, which is mediated by the m(6)A methylation of the transcription factor GATA3 gene.
Article
Biochemistry & Molecular Biology
Ana Ramon-Laca, Ramon Gallego, Krista M. Nichols
Summary: Biomonitoring surveys utilize metabarcoding tools to identify species through sequencing results against public genomic databases. However, incomplete mitochondrial genomic reference data and unsuitable existing sequence data pose challenges in species level resolution. This study presents a cost-effective workflow using long fragment sequencing and mitochondrial DNA enrichment to generate complete fish mitogenomes, allowing for the expansion of fish mitochondrial databases to nonmodel or understudied species.
MOLECULAR ECOLOGY RESOURCES
(2023)
Article
Biochemistry & Molecular Biology
Peerapat Khamwachirapithak, David Guillaume-Schoepfer, Pakkanan Chansongkrow, Sarah A. Teichmann, Philip A. Wigge, Varodom Charoensawan
Summary: This study combines ChIP-seq and RNA-seq to investigate the effects of global and local H3 depletion on gene transcription, as well as the interaction between the transcription factor Rap1 and H3. The results provide a working model and testable hypotheses regarding the impact of H3 depletion on transcriptional changes.
JOURNAL OF MOLECULAR BIOLOGY
(2023)
Article
Genetics & Heredity
Zhijun Zhang, Tingting Zhang, Lei Ma
Summary: This study constructed a weighted gene co-expression network using gene expression profile data of Arabidopsis under abiotic stress. Three gene modules primarily associated with cold stress, heat stress, and salt stress were identified. Functional enrichment analysis revealed the involvement of these modules in biological processes such as protein binding and stress response. Transcription factor enrichment analysis identified the crucial regulatory role of the BPC6 transcription factor in the key modules. Differential gene expression and protein interaction network analysis supported the interactions between BPC6 and other key genes within the modules.
FRONTIERS IN GENETICS
(2023)
Article
Green & Sustainable Science & Technology
Feifei Wu, Xiaohua Yang, Zhenyao Shen, Dehui Bian, Pius Babuna
Summary: The study assessed the sustainability and decoupling effects of natural capital utilization in 30 provinces of China by modifying an EF model. Results showed that China's ecological deficit peaked in 2015, and the dominant sustainability types of provinces changed over time. Despite an increase in sustainability in 6 provinces, overall sustainability in China decreased.
JOURNAL OF CLEANER PRODUCTION
(2021)
Article
Agriculture, Dairy & Animal Science
Lina Goransson, Stefan Gunnarsson, Anna Wallenbeck, Jenny Yngvesson
Summary: This study examined the behavior and free-range use of two slower-growing hybrids on Swedish organic farms, finding that the chickens spent most of their time sitting and that the outdoor areas lacked sufficient vegetation cover or artificial shelters. The research suggests that key improvements to both indoor and outdoor environments could enhance broiler welfare.
Article
Plant Sciences
Murat Aycan, Lutfun Nahar, Marouane Baslam, Toshiaki Mitsui
Summary: Salinity is a major problem in agriculture, limiting plant yield in half the fields. The hst1 gene improves salt tolerance in rice by reducing Na+ ions and lipid peroxidation, increasing proline and antioxidant enzyme activities, and regulating transporter and transcription factor genes. These findings provide insight into the salt tolerance mechanisms in rice and the development of salt-tolerant crops for food security during climate change.
PLANT PHYSIOLOGY AND BIOCHEMISTRY
(2023)
Article
Biochemistry & Molecular Biology
Nathan Lawlor, Joshy George, Mohan Bolisetty, Romy Kursawe, Lili Sun, V. Sivakamasundari, Ina Kycia, Paul Robson, Michael L. Stitzel
Review
Nutrition & Dietetics
YingYing He, Nathan T. Lawlor, David S. Newburg
ADVANCES IN NUTRITION
(2016)
Review
Genetics & Heredity
Nathan Lawlor, Shubham Khetan, Duygu Ucar, Michael L. Stitzel
TRENDS IN GENETICS
(2017)
Article
Multidisciplinary Sciences
Nathan Lawlor, Ahrim Youn, Romy Kursawe, Duygu Ucar, Michael L. Stitzel
SCIENTIFIC REPORTS
(2017)
Article
Genetics & Heredity
Ina Kycia, Brooke N. Wolford, Jeroen R. Huyghe, Christian Fuchsberger, Swarooparani Vadlamudi, Romy Kursawe, Ryan P. Welch, Ricardo d'Oliveira Albanus, Asli Uyar, Shubham Khetan, Nathan Lawlor, Mohan Bolisetty, Anubhuti Mathur, Johanna Kuusisto, Markku Laakso, Duygu Ucar, Karen L. Mohlke, Michael Boehnke, Francis S. Collins, Stephen C. J. Parker, Michael L. Stitzel
AMERICAN JOURNAL OF HUMAN GENETICS
(2018)
Article
Endocrinology & Metabolism
Shubham Khetan, Romy Kursawe, Ahrim Youn, Nathan Lawlor, Alexandria Jillette, Eladio J. Marquez, Duygu Ucar, Michael L. Stitzel
Article
Multidisciplinary Sciences
Donghyung Lee, Anthony Cheng, Nathan Lawlor, Mohan Bolisetty, Duygu Ucar
SCIENTIFIC REPORTS
(2018)
Article
Cell Biology
Nathan Lawlor, Eladio J. Marquez, Peter Orchard, Narisu Narisu, Muhammad Saad Shamim, Asa Thibodeau, Arushi Varshney, Romy Kursawe, Michael R. Erdos, Matt Kanke, Huiya Gu, Evgenia Pak, Amalia Dutra, Sheikh Russell, Xingwang Li, Emaly Piecuch, Oscar Luo, Peter S. Chines, Christian Fuchbserger, Praveen Sethupathy, Aviva Presser Aiden, Yijun Ruan, Erez Lieberman Aiden, Francis S. Collins, Duygu Ucar, Stephen C. J. Parker, Michael L. Stitzel
Review
Endocrinology & Metabolism
Nathan Lawlor, Michael L. Stitzel
MOLECULAR METABOLISM
(2019)
Article
Biochemical Research Methods
Nathan Lawlor, Eladio J. Marquez, Donghyung Lee, Duygu Ucar
Article
Immunology
Nathan Lawlor, Djamel Nehar-Belaid, Jessica D. S. Grassmann, Marlon Stoeckius, Peter Smibert, Michael L. Stitzel, Virginia Pascual, Jacques Banchereau, Adam Williams, Duygu Ucar
Summary: This study introduced a cost-effective high-throughput multiplexed single-cell RNA-seq method to examine the immune cell responses to classic T cell and monocyte activators. The results demonstrated that anti-CD3/CD28 treatment activated various lymphocyte classes, while LPS specifically targeted monocytes.
FRONTIERS IN IMMUNOLOGY
(2021)
Article
Multidisciplinary Sciences
Jinxiu Rui, Songyan Deng, Ana Luisa Perdigoto, Gerald Ponath, Romy Kursawe, Nathan Lawlor, Tomokazu Sumida, Maya Levine-Ritterman, Michael L. Stitzel, David Pitt, Jun Lu, Kevan C. Herold
Summary: In Type 1 diabetes, beta cells may contribute to their own demise through the expression of Tet2, which regulates immune killing. Tet2-KO mice receiving WT bone marrow transplants develop insulitis but not diabetes, and Tet2 deletion protects beta cells by reducing expression of inflammatory genes needed to activate diabetogenic T cells. These findings suggest that Tet2 plays a crucial role in controlling damaging inflammatory pathways and interactions between beta cells and immune cells in autoimmune diabetes.
NATURE COMMUNICATIONS
(2021)
Article
Biotechnology & Applied Microbiology
Asa Thibodeau, Alper Eroglu, Christopher S. McGinnis, Nathan Lawlor, Djamel Nehar-Belaid, Romy Kursawe, Radu Marches, Daniel N. Conrad, George A. Kuchel, Zev J. Gartner, Jacques Banchereau, Michael L. Stitzel, A. Ercument Cicek, Duygu Ucar
Summary: Detecting multiplets in single nucleus (sn)ATAC-seq data is challenging, but AMULET shows high precision and recall compared to alternatives, especially when a certain read depth of 25K median valid reads per nucleus is achieved.
Article
Oncology
Nathan Lawlor, Alec Fabbri, Peiyong Guan, Joshy George, R. Krishna Murthy Karuturi
CANCER INFORMATICS
(2016)