Gene regulatory networks are a major focus of interest in molecular biology. A crucial question is how complex regulatory systems are encoded and controlled by the genome. Three recent publications have raised the question of what can be learned about gene regulatory networks from microarray experiments on gene deletion mutants. Using this indirect approach, topological features such as connectivity and modularity have been studied.
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http://dx.doi.org/10.1002/cfg.220 | DOI Listing |
Am J Pathol
December 2024
International Ocular Surface Research Center, Key Laboratory for Regenerative Medicine, Institute of Ophthalmology, Jinan University, Guangzhou 510632, China; Department of Ophthalmology, The First Affiliated Hospital of Jinan University, Jinan University, Guangzhou 510630, China. Electronic address:
The gut microbiota plays a crucial regulatory role in various physiological processes, yet its impact on corneal homeostasis remains insufficiently understood. Here, we investigate the effects of antibiotic-induced gut dysbiosis (AIGD) and germ-free (GF) conditions on circadian gene expression, barrier integrity, nerve density, and immune cell activity in the corneas of mice. Through RNA sequencing, we found that both AIGD and GF conditions significantly disrupted the overall transcriptomic profile and circadian transcriptomic oscillations in the cornea.
View Article and Find Full Text PDFFish Shellfish Immunol
December 2024
Institute of Aquatic Biotechnology, College of Life Sciences, Qingdao University, Qingdao, 266071, China; Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao Marine Science and Technology Center, Qingdao, Shandong 266237, China. Electronic address:
N6-methyladenosine (m6A) is the most prevalent RNA modification and a multifaceted regulator capable of affecting various aspects of mRNA metabolism, thereby playing important roles in numerous physiological processes. However, it is still unknown whether, when, and to what extent m6A modulation are implicated in the immune response of an economically important aquaculture fish, half-smooth tongue sole (Cynoglossus semilaevis). Herein, we systematically profiled and characterized the m6A epitranscriptome and transcriptome in C.
View Article and Find Full Text PDFInt J Biol Macromol
December 2024
State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China. Electronic address:
Intrauterine growth retardation (IUGR) has become a difficult problem in animal husbandry and is often accompanied by the occurrence of metabolic syndrome. tRNA-derived small RNAs (tsRNAs) are a novel class of regulatory small noncoding RNAs. However, the involvement of tsRNA in regulating the mechanism of IUGR remains unclear.
View Article and Find Full Text PDFJ Biol Chem
December 2024
Physiology & Biomedical Engineering, Mayo Clinic College of Medicine & Science, Rochester, MN, 55906; Nephrology & Hypertension, Mayo Clinic College of Medicine & Science, Rochester, MN, 55906. Electronic address:
The chloride transporter-channel SLC26A9 is mediated by a reciprocal regulatory mechanism through the interaction between its cytoplasmic STAS domain and the R domain of CFTR. In vertebrate Slc26a9s, the STAS domain structures are interrupted by a disordered loop which is conserved in mammals but is variable in non-mammals. Despite the numerous studies involving the STAS domains in SLC26 proteins, the role of the disordered loop region has not been identified.
View Article and Find Full Text PDFLeuk Res
December 2024
Ankara Yıldırım Beyazıt University, Hematology Clinic, Ankara, Turkey.
CD47 interacts with signal regulatory protein alpha (SIRPα) on macrophages to deliver an anti-phagocytic signal, enabling tumor cells to evade immune destruction. This study explores the relationship between CD47 and SIRPα expression and key clinical prognostic factors, microvascular density (MVD), and tumor-infiltrating lymphocytes (TIL) in Diffuse Large B Cell Lymphoma (DLBCL) cases. We analyzed tissue samples from 122 DLBCL cases using tissue microarray (TMA) blocks and immunohistochemical staining for CD47, SIRPα, CD31, and CD3.
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