Article
Multidisciplinary Sciences
Shenji Wu, Jinqiang Huang, Yongjuan Li, Lu Zhao, Zhe Liu
Summary: In this study, the skin transcriptomes of yellow mutant rainbow trout were analyzed to explore the temporal expression patterns of pigmentation-related genes. Numerous differentially expressed genes associated with pigmentation were identified, including those involved in pteridine and carotenoid synthesis as well as melanin synthesis pathways. The results enhance our understanding of the molecular mechanism underlying skin pigmentation in yellow mutant rainbow trout.
SCIENTIFIC REPORTS
(2022)
Article
Biology
Donard S. Dwyer
Summary: Protein receptors are proposed to evolve from self-binding peptides, which are encoded by self-interacting gene segments widely dispersed in the genome. The construction modules for receptors are duplicated, dispersed and maintained in the genome due to structure/function relationships. Receptor genes exhibit more gene-gene interactions, possibly indicating greater evolutionary conservation and involvement in active gene relocation areas for functional block formation.
Article
Oncology
Piaopiao Li, Yingxia Li, Lei Ma
Summary: This study investigated the biological roles and mechanisms of chimeric genes in pigs using weighted co-expression network analysis. The results showed that most protein domains of chimeric genes were derived from fused pre-genes and were involved in negative regulation of cell proliferation and protein localization to centrosomes. Additionally, chimeric genes were related to the growth factor-beta superfamily and played a key role in regulating T cell pathways.
WORLD JOURNAL OF SURGICAL ONCOLOGY
(2021)
Article
Automation & Control Systems
Karthik Raghavan Ramaswamy, Giulio Bottegal, Paul M. J. Van den Hof
Summary: The method presented in the paper uses regularized kernel-based methods for identification, reducing computational complexity and showing potential in local module identification.
Review
Biochemistry & Molecular Biology
Thai Q Tran, Chrissa Kioussi
Summary: Homeobox genes encode SSTFs that regulate organogenesis in eukaryotes, while Pitx genes, belonging to the highly conserved homeobox genes, mainly regulate LR asymmetry and organ development and symmetry. Mutations in Pitx genes can cause various congenital defects and cancers, but also have the potential to play a role in regenerative medicine.
CELLULAR AND MOLECULAR LIFE SCIENCES
(2021)
Article
Energy & Fuels
Wei Zhou, Pengjun Wang, Ali Asghar Heidari, Xuehua Zhao, Hamza Turabieh, Majdi Mafarja, Huiling Chen
Summary: This study proposes an enhanced spherical evolution algorithm based on a novel dynamic sine-cosine mechanism to improve the efficiency and accuracy of parameter identification for PV cells and modules. Experimental results demonstrate that the algorithm outperforms other competing algorithms in terms of performance.
Article
Automation & Control Systems
Sina Jahandari, Donatello Materassi
Summary: This article presents a systematic algorithm for consistently identifying specific transfer functions in a dynamic network from observational data. The algorithm selects auxiliary measurements by minimizing an appropriate cost function. The article shows that the conditions for consistent identification of a single transfer function are equivalent to the concept of minimum cut in an augmented graph. Different approaches, such as graph theory algorithms, distributed algorithms, or optimization-based procedures, can be used to find the optimal set of auxiliary measurements that minimize the cost. The results are also extended to the scenario of simultaneously identifying multiple transfer functions.
IEEE TRANSACTIONS ON AUTOMATIC CONTROL
(2022)
Article
Chemistry, Multidisciplinary
Yanhui Chen, Yun Hu, Jinhui Liu, Yu Wang, Aiting Li
Summary: Based on the reorganization mechanism and synaptic adaptability in brain science, a bionic dynamic synaptic model is proposed and applied to motif and brain-like network models. By studying the synchronization characteristics and analyzing the effects of synchronous discharge activities on effective links, a path selection strategy is designed to maximize the information transmission capacity between nodes. The results show that the phase information carried by the stimulus signal regulates the path selection, and the paths in the network have different phase preferences.
APPLIED SCIENCES-BASEL
(2023)
Editorial Material
Biochemistry & Molecular Biology
Han Han, Wenqi Wang
Summary: In a recent study published in The EMBO Journal, Qi et al (2023) propose a new model for the Hippo kinase cascade, shedding light on the long-standing question of its precise organization.
Article
Biochemistry & Molecular Biology
Taylor M. Weiskittel, Choong Y. Ung, Cristina Correia, Cheng Zhang, Hu Li
Summary: Despite the limited understanding of individual disease etiology and therapeutics, a novel computational pipeline has been proposed to collect potent disease gene cooperative pathways for individualized disease etiology and therapies. The importance of mutated genes in specific patients and the synthetic penetrance of these genes across patients can be elucidated through individualized disease modules. This study reveals the fluctuation of importance for notorious cancer drivers in breast cancers and the high disease module importance of rarely mutated genes in specific individuals. Furthermore, customized singular and combinatorial target therapies can be devised through individualized module disruption, emphasizing the need for precision therapeutics pipelines. This analysis demonstrates the power of individualized disease modules for precision medicine, offering deep novel insights on the activity of diseased genes in individuals.
Article
Plant Sciences
Mengping Li, Keun Pyo Lee, Tong Liu, Vivek Dogra, Jianli Duan, Mengshuang Li, Weiman Xing, Chanhong Kim
Summary: Salicylic acid-related transcription coregulators, SIB1 and LSD1, have antagonistic effects on the activity of GLK1/2 transcription factors, thereby regulating chloroplast development and stress response. SIB1 and LSD1 interact with GLK1/2 to enhance or repress the expression of PhANGs, modulating the ROS homeostasis and cell death in chloroplasts.
Article
Biochemical Research Methods
Ran Wang, Xubin Zheng, Fangda Song, Man Hon Wong, Kwong Sak Leung, Lixin Cheng
Summary: Human gut microbiota dysbiosis is associated with various diseases, and it is crucial to uncover the associations between gut microbiota and disease states along with other factors. Existing methods may lead to false associations, so we propose a new method to investigate gut microbiota using groups of related taxa instead of individual taxa. The results show that this method can better explain the relationships between gut microbiota and clinical factors, and it demonstrates effectiveness in identifying microbial modules.
Article
Biology
Catia Pereira, Jimmy Larsson, Karin Hjort, Johan Elf, Dan Andersson
Summary: Bacterial populations can exhibit heteroresistance, where an antibiotic resistant subpopulation is present within a susceptible population. This phenomenon is often underestimated in clinical isolates, leading to treatment failure. Understanding the dynamics of resistant subpopulations in the presence and absence of selection can provide insights for more effective diagnostics and treatment of infections caused by heteroresistant bacteria.
COMMUNICATIONS BIOLOGY
(2021)
Article
Multidisciplinary Sciences
Jay Vornhagen, Emily K. Roberts, Lavinia Unverdorben, Sophia Mason, Alieysa Patel, Ryan Crawford, Caitlyn L. Holmes, Yuang Sun, Alexandra Teodorescu, Evan S. Snitkin, Lili Zhao, Patricia J. Simner, Pranita D. Tamma, Krishna Rao, Keith S. Kaye, Michael A. Bachman
Summary: This study identifies several genes reproducibly associated with progression to infection in patients colonized by diverse Klebsiella. Patient variables, such as comorbidities, partially explain which patients will progress to Klebsiella infection, with colonization of the gut acting as a reservoir. Little is known, however, regarding Klebsiella genes that may increase risk of disease in colonized individuals.
NATURE COMMUNICATIONS
(2022)
Article
Biochemistry & Molecular Biology
Julien Martinez, Lisa Klasson, John J. Welch, Francis M. Jiggins
Summary: Cytoplasmic incompatibility is a selfish manipulation of reproduction induced by the endosymbiont Wolbachia in arthropods. The genes cifA and cifB, strongly associated with cytoplasmic incompatibility, are found in many Wolbachia genome sequences with up to seven copies in each genome. These genes undergo gain, loss, and recombination processes, supporting evolutionary models of cytoplasmic incompatibility.
MOLECULAR BIOLOGY AND EVOLUTION
(2021)
