Article
Biochemical Research Methods
Julien Tremblay, Lars Schreiber, Charles W. Greer
Summary: In this study, real data was used to conduct detailed benchmarking of shallow shotgun metagenomics. The results show that shallow sequencing has the potential to obtain reliable results regarding microbial community structures, and high-depth sequencing does not provide additional ecological interpretation. However, ultra-deep sequencing and maximizing the usage of all data can be beneficial for generating metagenome-assembled genomes.
BRIEFINGS IN BIOINFORMATICS
(2022)
Article
Biochemistry & Molecular Biology
Guanjun Li, Qingchuan Shi, Yanqiu He, Jie Zhu, Mingluan Zhong, Lingjie Tong, Huaping Li, Yanfang Nie, Yunfeng Li
Summary: This study analyzed the secretome of Magnaporthe oryzae and identified 3315 non-redundant secreted proteins, with 9.6% classified as classical secreted proteins and 24.7% as non-classical secreted proteins. Additionally, 60.0% of the proteins were secreted through an unknown pathway. Functional analysis revealed 257 proteins as extracellular enzymes and 90 proteins as candidate effectors. Experimental validation showed that 18 candidate effectors are involved in the pathogenicity of M. oryzae.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Biochemistry & Molecular Biology
Charles Pouchon, Carlos G. Boluda
Summary: Researchers have developed a tool called REFMAKER that can extract nuclear genomes from genome sequencing data for phylogenetic analysis in plant systematics. The tool constructs a catalog, selects nuclear regions, removes duplicate sequences, and generates consensus sequences from low-coverage sequencing data. The results demonstrate that REFMAKER is able to successfully reconstruct phylogenetic trees from low-coverage sequencing data.
MOLECULAR PHYLOGENETICS AND EVOLUTION
(2023)
Article
Microbiology
Wojtek Bazant, Ann S. S. Blevins, Kathryn Crouch, Daniel P. P. Beiting
Summary: The study presents a tool called CORRAL for identifying eukaryotes in shotgun metagenomic data. It utilizes eukaryote-specific marker genes and Markov clustering to automate the detection of eukaryotes, even those not represented in the reference marker gene set, such as novel strains.
Article
Biochemistry & Molecular Biology
Guobao Wang, Jiangrun Wang, Lei Nie
Summary: This study employed RNA-seq to investigate the transcriptome profile of the central nervous system (CNS) of Antheraea pernyi, revealing the neuropeptides and neuropeptide receptors involved in regulating various behaviors and physiological processes. Comparison of gene expression patterns between the brain and ventral nerve cord (VNC) showed higher expression levels in the brain. Additionally, differentially expressed genes were screened and analyzed, providing a foundation for further research into their functions.
INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES
(2023)
Article
Multidisciplinary Sciences
Komwit Surachat, Todd Duane Taylor, Wanicbut Wattanamatiphot, Sukgamon Sukpisit, Kongpop Jeenkeawpiam
Summary: RNA-seq is a sequencing technique that studies the entire transcriptome of a biological sample using NGS, but the command-line interfaces of NGS are obstacles for biologists and researchers. To simplify the RNA-seq data analysis, the aTAP platform integrates various bioinformatics workflows, providing a user-friendly graphical interface for researchers to more easily analyze transcriptome data.
Article
Biochemistry & Molecular Biology
Jingrong Ma, Chuang Pan, Haiming Chen, Weijun Chen, Wenxue Chen, Ming Zhang, Qiuping Zhong
Summary: This study investigated the proteome of coconut meat using shotgun proteomics and protein-based bioinformatic analysis. A total of 1686 proteins were identified, including antioxidant proteins and globulins. Network analysis revealed the associations of globulins with Cupin and Oleosin sub-networks, and antioxidant proteins with glutathione metabolism and peroxisome sub-networks. The study also discovered that bioactive peptides, with antioxidant and emulsifying properties, can be obtained through in-silico digestion.
Article
Endocrinology & Metabolism
Yuwei Deng, Nan Luo, Ming Xie, Ling He, Ruixue Jiang, Nan Hu, Jin Wen, Xinquan Jiang
Summary: This study compared periodontal tissues from different stages of mice and found that tissue development, energy metabolism, and immune response were critical processes in periodontal remodeling. The developmental and adult stages showed different gene expression patterns. These findings contribute to a deeper understanding of periodontal development and remodeling, and may provide references for periodontal regeneration.
FRONTIERS IN ENDOCRINOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Ramon E. Rivera-Vicens, Catalina A. Garcia-Escudero, Nicola Conci, Michael Eitel, Gert Woerheide
Summary: The use of RNA sequencing and de novo transcriptome assembly is crucial for ecological and evolutionary studies, especially for nonmodel organisms lacking genome information. A multi-assembler approach, followed by a reduction step, is often employed to improve the assembly quality. TransPi is a comprehensive pipeline for de novo transcriptome assembly that achieves higher completeness percentages and reduces duplication rates compared to single assembler approaches. It is easy to configure and can be seamlessly deployed using Conda, Docker, and Singularity.
MOLECULAR ECOLOGY RESOURCES
(2022)
Article
Physiology
Wenhong Li, Zhimo Li, Xiang Yang, Xinyi Wang, Mingwei Yang, Chunyang Huang, Yueping He
Summary: In this study, neuropeptide signaling genes of the predatory stink bug Picromerus lewisi were comprehensively identified, providing valuable information for understanding its biology and behavior, as well as for developing improved pest management strategies.
FRONTIERS IN PHYSIOLOGY
(2023)
Article
Genetics & Heredity
Diego A. A. Morais, Joao V. F. Cavalcante, Shenia S. Monteiro, Matheus A. B. Pasquali, Rodrigo J. S. Dalmolin
Summary: Metagenomic studies provide valuable insights into the taxonomic composition and functional characteristics of microbial communities. However, selecting and setting up the appropriate tools for comprehensive metagenomic analysis poses challenges. In this study, the researchers surveyed state-of-the-art tools, created simulated datasets, and performed benchmarks to develop an efficient and flexible metagenomic analysis pipeline called MEDUSA. Compared to existing tools, MEDUSA accurately identifies a greater number of species and is well-suited for functional analysis.
FRONTIERS IN GENETICS
(2022)
Article
Fisheries
Omer Can Unuvar, Ercan Selcuk Unlu
Summary: This study provides comprehensive transcriptome data for Tetradesmus obliquus and identifies conserved genes involved in lutein pigment biosynthesis. The data can be used for biotechnological applications related to T. obliquus, such as increasing pigment production.
TURKISH JOURNAL OF FISHERIES AND AQUATIC SCIENCES
(2022)
Article
Genetics & Heredity
Xiaoyan Zhang, Tong Xue, Zebing Hu, Xian Guo, Gaozhi Li, Yixuan Wang, Lijun Zhang, Liqun Xu, Xinsheng Cao, Shu Zhang, Fei Shi, Ke Wang
Summary: This study identifies hub genes and explores novel molecular mechanisms underlying microgravity-induced bone loss, providing potential targets for countermeasures against this condition.
FRONTIERS IN GENETICS
(2022)
Article
Medicine, General & Internal
Zhen-Chen Chu, Ting Cong, Jian-Yu Zhao, Jian Zhang, Zhi-Yuan Lou, Yang Gao, Xin Tang
Summary: This study identified three hub genes (HTRA1, P2RY6, and RCAN1) related to osteoarthritis through gene expression analysis and weighted gene co-expression network analysis. The expression levels of these genes were confirmed in osteoarthritis patients. The findings provide new insights for targeted treatment of osteoarthritis.
FRONTIERS IN MEDICINE
(2023)
Article
Biochemical Research Methods
Karel K. M. Koudijs, Stefan Bohringer, Henk-Jan Guchelaar
Summary: Transcriptome signature reversion (TSR) is widely used for drug repositioning in cancer treatment. However, the predictive utility of TSR is lower than previously reported and is mainly based on generic anti-proliferative drug effects, rather than targeting specific cancer pathways.
BRIEFINGS IN BIOINFORMATICS
(2023)
Article
Endocrinology & Metabolism
Xiaomeng Li, Charles Brighton Ndandala, Qi Zhou, Chunyan Huang, Guangli Li, Huapu Chen
Summary: This study investigated the role of estrogen receptors (ERs) in vitellogenesis (Vtgs) regulation in pompano fish. The findings suggest that E2 may regulate the expression of different subtypes of vtg through ERs, displaying a compensatory expression effect on the regulation of ers and vtgs. This provides a theoretical basis for further research on reproductive endocrinology in pompano fish.
GENERAL AND COMPARATIVE ENDOCRINOLOGY
(2024)
Article
Endocrinology & Metabolism
Norio Kansaku, Takeshi Ohkubo
Summary: Endocrine changes during bird reproduction, particularly the relationship between prolactin and incubation behavior, were investigated. The study monitored the physiological status and incubation behavior of Silkie hens over 1-2 years. The results showed that most mature hens exhibited incubation behavior multiple times, and there was a noticeable increase in nest occupancy 7-10 days before incubation onset. Protein analysis revealed that secreted prolactin during the reproductive cycle contains various isoforms, suggesting post-translational modifications like glycosylation and phosphorylation.
GENERAL AND COMPARATIVE ENDOCRINOLOGY
(2024)
Article
Endocrinology & Metabolism
Minghui Li, Lina Sun, Linyan Zhou, Deshou Wang
Summary: This article summarizes the importance of the Nile tilapia as an excellent animal model for studying reproductive endocrinology in fish, with a focus on the crucial role of estrogen in female development.
GENERAL AND COMPARATIVE ENDOCRINOLOGY
(2024)
Article
Endocrinology & Metabolism
Breanna N. Harris, Carolyn M. Bauer, James A. Carr, Caitlin R. Gabor, Jennifer L. Grindstaff, Caleigh Guoynes, Jennifer J. Heppner, Cris C. Ledon-Rettig, Patricia C. Lopes, Sharon E. Lynn, Carla B. Madelaire, Lorin A. Neuman-Lee, Maria G. Palacios, Paul Soto, Jennifer Terry
Summary: The COVID-19 pandemic had a significant impact on academics, particularly on those with minoritized identities or who were early career, caregivers, or had intersecting identities. The pandemic altered the impact factors of academia, including scholarly products, and affected the way individuals could respond. It is predicted that the pandemic will have long-term impacts on the population dynamics, composition, and landscape of the academic ecosystem. The number of journal submissions decreased, especially among women authors, and the pandemic heavily impacted women authors from Asia and the Middle East.
GENERAL AND COMPARATIVE ENDOCRINOLOGY
(2024)