Man-Seok Kim

Fusarium verticillioides is recognized as an important stalk rot pathogen of maize worldwide, but our knowledge of genetic mechanisms underpinning this pathosystem is limited. Previously, we identified a striatin-like protein Fsr1 that plays an important role in stalk rot. To further characterize transcriptome networks downstream of Fsr1, we performed next-generation sequencing (NGS) to investigate relative read abundance and also to infer co-expression networks utilizing the preprocessed expres

Intercellular mitochondrial transfer in the tumor microenvironment (TME) is a paradigm-shifting process that redefines cancer-T cell crosstalk. This review explores its dual nature as both a tumor immune evasion strategy and a promising therapeutic avenue. Crucially, oxidative stress acts as a key regulator, inducing tunneling nanotube (TNT) formation to facilitate this organelle exchange. Tumors exploit this by transferring dysfunctional, reactive oxygen species (ROS) generating mitochondria to

Fusarium verticillioides is a fungal pathogen that triggers stalk rots and ear rots in maize. In this study, we performed a comparative analysis of wild type and loss-of-virulence mutant F. verticillioides co-expression networks to identify subnetwork modules that are associated with its pathogenicity. We constructed the F. verticillioides co-expression networks from RNA-Seq data and searched through these networks to identify subnetwork modules that are differentially activated between the wild

BACKGROUND: Maize, a crop of global significance, is vulnerable to a variety of biotic stresses resulting in economic losses. Fusarium verticillioides (teleomorph Gibberella moniliformis) is one of the key fungal pathogens of maize, causing ear rots and stalk rots. To better understand the genetic mechanisms involved in maize defense as well as F. verticillioides virulence, a systematic investigation of the host-pathogen interaction is needed. The aim of this study was to computationally identif

Interest in metformin as a potential anticancer agent for colorectal cancer (CRC) has increased. However, compelling epidemiological links and strong preclinical evidence suggest that metformin has variable efficacy in patients with CRC. This variability highlights the need to identify the patients who are most likely to benefit from effective stratification. We aimed to review the evidence concerning the diverse roles of metformin in CRC prevention and treatment, focusing on identifying and val

Spatial transcriptomics (ST) is emerging as a powerful technology that transforms our understanding of thyroid cancer by offering a spatial context of gene expression within the tumor tissue. In this review, we synthesize the recent applications of ST in thyroid cancer research, with a particular focus on the heterogeneity of the tumor microenvironment, tumor evolution, and cellular interactions. Studies have leveraged the spatial information provided by ST to map distinct cell types and express

BACKGROUND: Multi-target therapeutics has been shown to be effective for treating complex diseases, and currently, it is a common practice to combine multiple drugs to treat such diseases to optimize the therapeutic outcomes. However, considering the huge number of possible ways to mix multiple drugs at different concentrations, it is practically difficult to identify the optimal drug combination through exhaustive testing. RESULTS: In this paper, we propose a novel stochastic search algorithm,

A pterygium is a common conjunctival degeneration and inflammatory condition. It grows onto the corneal surface or limbus, causing blurred vision and cosmetic issues. Ultraviolet is a well-known risk factor for the development of a pterygium, although its pathogenesis remains unclear, with only limited understanding of its hereditary basis. In this study, we collected RNA-seq from both pterygial tissues and conjunctival tissues (as controls) from six patients (a total of twelve biological sample

Fear memory is a critical adaptive process that enables organisms to avoid potential threats and survive in complex environments. Traditionally viewed as a neuronal phenomenon, emerging evidence has demonstrated that astrocytes play a fundamental role in fear memory acquisition, consolidation, extinction, and retrieval across the distributed neural network encompassing the amygdala, hippocampus, and prefrontal cortex. This review presents recent advances in our understanding of the molecular mec

Pathways such as VEGF, EGF and mTOR are known to be one of the major mechanisms of tumorigenesis including kidney cancer. To identify potential signaling pathway proteins, we performed differential/correlation analyses of mTOR-associated genes from three public datasets. AKT1 protein, one of the PI3K/AKT/mTOR pathways, turned out to be the potential by showing a consistent discrepancy between ccRCC-associated conditions as well as strong correlation with other mTOR-associated genes across the da

Recent advances in sequencing technology and big data analytics are moving plant pathology into a new era where we are now pursuing a deeper systems-level understanding of host–pathogen associations. For past several decades, scientists have predominantly tried to delineate and streamline these interactions into single pathogen–single host model systems, using reductionist experimental approaches. As many of us are aware, there have been several significant proposed ideas and models to help simp

α-Gustducin (Gα-gust) is the α subunit of the heterotrimeric G-protein complex specific for taste receptor cells of the tongue. However, it has been shown to be present in ectopic regions, such as airways and digestive tract. Recently, Gα-gust was found within neurons in various regions of the mouse brain. In this study, we tested whether Gα-gust is expressed in the mammalian retina. Gα-gust was identified in mouse, rat, and rabbit retinas by western blot and immunohistochemistry analyses. Doubl

The LPS-induced inflammation model is widely used for studying inflammatory processes due to its cost-effectiveness, reproducibility, and faithful representation of key hallmarks. While researchers often validate this model using clinical cytokine markers, a comprehensive understanding of gene regulatory mechanisms requires extending investigation beyond these hallmarks. Our study leveraged multiple whole-blood bulk RNA-seq datasets to rigorously compare the transcriptional profiles of the well-

Myopia is a substantial global public health concern primarily linked to the elongation of the axial length of the eyeball. While numerous animal models have been employed to investigate myopia, the specific contributions of genetic factors and the intricate signaling pathways involved remain incompletely understood. In this study, we conducted RNA-seq analysis to explore genes and pathways in two distinct myopia-inducing mouse models: form-deprivation myopia (FDM) and lens-induced myopia (LIM).

Emerging evidence suggests that the timing of eating and exercise over the course of the day is paramount to metabolism and physical function. This review highlights seminal studies showing that adipocyte AMPKα2 signaling controls circadian adipose tissue-skeletal muscle communication. Day-restricted feeding has been shown to improve exercise performance via adipocyte-specific activation of AMPKα2, which controls fat-muscle crosstalk in a time-of-day dependent manner. This review also discusses