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JOURNAL ARTICLE
Matilde Grupe Frost, Kristoffer Jarlov Jensen, Espen Jimenez-Solem, Camilla Qvortrup, Tine Plato Kuhlmann, Jon Lykkegaard Andersen, Estrid Høgdall, Tonny Studsgaard Petersen
OBJECTIVE: This study aims to evaluate the developments in the testing of Kirsten Rat Sarcoma viral oncogene homolog (KRAS) and v-Raf murine sarcoma viral oncogene homolog B1 (BRAF) mutations across different cancer types and regions in Denmark from 2010 to 2022. STUDY DESIGN AND SETTING: Using comprehensive data from the Danish health registries, we linked molecular test results from the Danish Pathology Registry with cancer diagnoses from the Danish National Patient Registry between 2010 and 2022...
April 2024: Genes, Chromosomes & Cancer
#2
JOURNAL ARTICLE
Arti Rathour, Shamli S Gupte, Divya Gupta, Shubham Singh, Sadhana Shrivastava, Deepa Yadav, Sangeeta Shukla
Oxidative injury is concerned with the pathogenesis of several liver injuries, including those from acute liver failure to cirrhosis. This study was designed to explore the antioxidant activity of Bacopa monnieri (BM) on Aflatoxin B1 (AFB1) induced oxidative damage in Wistar albino rats. Aflatoxin B1 treatment (200 μg/kg/day, p.o.) for 28 days induced oxidative injury by a significant alteration in serum liver function test marker enzymes (AST, ALT, ALP, LDH, albumin and bilirubin), inflammatory cytokines (IL-6, IL-10 and TNF-α), thiobarbituric acid reactive substances (TBARS) along with reduction of antioxidant enzymes (GSH, SOD, CAT), GSH cycle enzymes and drug-metabolizing enzymes (AH and AND)...
April 2024: Toxicology Research
#3
JOURNAL ARTICLE
Haiyan Gong, Sichen Zhang, Xiaotong Zhang, Yang Chen
For many years, multi-scale models of chromatin domains, such as A/B compartments, sub-compartments, topologically associated domains (TADs), sub-TADs, and loops have been popular. However, existing methods can only identify structures at a single scale and cannot partition multi-scale structures. In this paper, we proposed a method (TORNADOES) for chromatin domain partitioning based on hypergraph clustering. First, we use a density clustering algorithm to identify TADs at different scales based on Hi-C data with different resolutions...
December 2024: Computational and Structural Biotechnology Journal
#4
JOURNAL ARTICLE
Qingbin Hou, Jinping Jiang, Kun Na, Xiaolin Zhang, Dan Liu, Quanmin Jing, Chenghui Yan, Yaling Han
Coronavirus disease (COVID-19) and pulmonary hypertension (PH) are closely correlated. However, the mechanism is still poorly understood. In this article, we analyzed the molecular action network driving the emergence of this event. Two datasets (GSE113439 and GSE147507) from the GEO database were used for the identification of differentially expressed genes (DEGs).Common DEGs were selected by VennDiagram and their enrichment in biological pathways was analyzed. Candidate gene biomarkers were selected using three different machine-learning algorithms (SVM-RFE, LASSO, RF)...
April 23, 2024: Scientific Reports
#5
JOURNAL ARTICLE
Mariko Takahashi, Harrison B Chong, Siwen Zhang, Tzu-Yi Yang, Matthew J Lazarov, Stefan Harry, Michelle Maynard, Brendan Hilbert, Ryan D White, Heather E Murrey, Chih-Chiang Tsou, Kira Vordermark, Jonathan Assaad, Magdy Gohar, Benedikt R Dürr, Marianne Richter, Himani Patel, Gregory Kryukov, Natasja Brooijmans, Aliyu Sidi Omar Alghali, Karla Rubio, Antonio Villanueva, Junbing Zhang, Maolin Ge, Farah Makram, Hanna Griesshaber, Drew Harrison, Ann-Sophie Koglin, Samuel Ojeda, Barbara Karakyriakou, Alexander Healy, George Popoola, Inbal Rachmin, Neha Khandelwal, Jason R Neil, Pei-Chieh Tien, Nicholas Chen, Tobias Hosp, Sanne van den Ouweland, Toshiro Hara, Lillian Bussema, Rui Dong, Lei Shi, Martin Q Rasmussen, Ana Carolina Domingues, Aleigha Lawless, Jacy Fang, Satoshi Yoda, Linh Phuong Nguyen, Sarah Marie Reeves, Farrah Nicole Wakefield, Adam Acker, Sarah Elizabeth Clark, Taronish Dubash, John Kastanos, Eugene Oh, David E Fisher, Shyamala Maheswaran, Daniel A Haber, Genevieve M Boland, Moshe Sade-Feldman, Russell W Jenkins, Aaron N Hata, Nabeel M Bardeesy, Mario L Suvà, Brent R Martin, Brian B Liau, Christopher J Ott, Miguel N Rivera, Michael S Lawrence, Liron Bar-Peled
Cysteine-focused chemical proteomic platforms have accelerated the clinical development of covalent inhibitors for a wide range of targets in cancer. However, how different oncogenic contexts influence cysteine targeting remains unknown. To address this question, we have developed "DrugMap," an atlas of cysteine ligandability compiled across 416 cancer cell lines. We unexpectedly find that cysteine ligandability varies across cancer cell lines, and we attribute this to differences in cellular redox states, protein conformational changes, and genetic mutations...
April 17, 2024: Cell
#6
JOURNAL ARTICLE
Min Yu, Xiaoling Zhou, Dongyue Chen, Yuan Jiao, Guomin Han, Fang Tao
Aspergillus flavus is a fungus notorious for contaminating food and feed with aflatoxins. As a saprophytic fungus, it secretes large amounts of enzymes to access nutrients, making endoplasmic reticulum (ER) homeostasis important for protein folding and secretion. The role of HacA, a key transcription factor in the unfolded protein response pathway, remains poorly understood in A. flavus. In this study, the hacA gene in A. flavus was knockout. Results showed that the absence of hacA led to a decreased pathogenicity of the strain, as it failed to colonize intact maize kernels...
April 4, 2024: International Journal of Food Microbiology
#7
JOURNAL ARTICLE
Ming-Rui Li, En-Xiang Chen, Zhuo-Hang Li, Hong-Lan Song, Yi Zhang, Fang-Fang Li, You-Long Xie, Jing Tang, Yu-Bin Ding, Li-Juan Fu
OBJECTIVE: The purpose of this study is to investigate the role of high mobility group protein B1 (HMGB1) in placental development and fetal growth. METHODS: We employed the Cre-loxP recombination system to establish a placenta-specific HMGB1 knockout mouse model. Breeding HMGB1flox/flox mice with Elf5-Cre mice facilitated the knockout, leveraging Elf5 expression in extra-embryonic ectoderm, ectoplacental cone, and trophoblast giant cells at 12.5 days of embryonic development...
April 22, 2024: Biology of Reproduction
#8
JOURNAL ARTICLE
J Stewart New, Brian L P Dizon, John F Kearney, R Glenn King
Using an Ig H chain conferring specificity for N-acetyl-d-glucosamine (GlcNAc), we developed transgenic (VHHGAC39 TG) mice to study the role of self-antigens in GlcNAc-reactive B-1 B cell development. In VHHGAC39 TG mice, GlcNAc-reactive B-1 B cell development during ontogeny and in adult bone marrow was normal. However, adult TG mice exhibited a block at transitional-2 immature B cell stages, resulting in impaired allelic exclusion and accumulation of a B cell subset coexpressing endogenous Ig gene rearrangements...
April 22, 2024: Journal of Immunology
#9
JOURNAL ARTICLE
Huimin Liu, Ye Zheng, Shaoning Kan, Ming Hao, Huan Jiang, Shuangji Li, Rong Li, Yinyu Wang, Dongxu Wang, Weiwei Liu
Tongue squamous cell carcinoma (TSCC) occupies a high proportion of oral squamous cell carcinoma. TSCC features high lymph node metastasis rates and chemotherapy resistance with a poor prognosis. Therefore, an effective therapy strategy is needed to improve patient prognosis. Melatonin (MT) is a natural indole compound shown to have anti-tumor effects in several cancers. This study focused on the role and mechanism of MT in TSCC cells. The results of the study suggest that MT could inhibit cell proliferation in CRL-1623 cells...
April 30, 2024: Heliyon
#10
JOURNAL ARTICLE
Yue Lv, Chengrui Zhao, Qiuyan Jiang, Yilin Rong, Mingfeng Ma, Lili Liang, Weiping Li, Jiuxuan Zhang, Ning Xu, Huiwen Wu
BACKGROUND: Obesity is associated with a wide variety of metabolic disorders that impose significant burdens on patients and society. The "browning" phenomenon in white adipose tissue (WAT) has emerged as a promising therapeutic strategy to combat metabolic disturbances. However, though the anti-diabetic drug dapagliflozin (DAPA) is thought to promote "browning," the specific mechanism of this was previously unclear. METHODS: In this study, C57BL/6 J male mice were used to establish an obesity model by high-fat diet feeding, and 3T3-L1 cells were used to induce mature adipocytes and to explore the role and mechanism of DAPA in "browning" through a combination of in vitro and in vivo experiments...
April 21, 2024: Molecular Biology Reports
#11
JOURNAL ARTICLE
Ying Chen, Ming-Fei Wu, Man-Man Xie, Yang Lu, Chao Li, Shuai-Shuai Xie, Wen-Xian Ma, Ming-Lu Ji, Rui Hou, Ze-Hui Dong, Ruo-Bing He, Meng-Meng Zhang, Hao Lu, Li Gao, Jia-Gen Wen, Juan Jin, Xiao-Wu Dong, Jin-Xin Che, Xiao-Ming Meng
Acute kidney injury (AKI) is defined as sudden loss of renal function characterized by increased serum creatinine levels and reduced urinary output with a duration of 7 days. Ferroptosis, an iron-dependent regulated necrotic pathway, has been implicated in the progression of AKI, while ferrostatin-1 (Fer-1), a selective inhibitor of ferroptosis, inhibited renal damage, oxidative stress and tubular cell death in AKI mouse models. However, the clinical translation of Fer-1 is limited due to its lack of efficacy and metabolic instability...
April 19, 2024: Acta Pharmacologica Sinica
#12
JOURNAL ARTICLE
Zhiqiang Xiao, Shanshan Wang, Liang Luo, Wenkai Lv, Peiran Feng, Yadong Sun, Quanli Yang, Jun He, Guangchao Cao, Zhinan Yin, Meixiang Yang
γδ T cells play a crucial role in immune surveillance and serve as a bridge between innate and adaptive immunity. However, the metabolic requirements and regulation of γδ T-cell development and function remain poorly understood. In this study, we investigated the role of liver kinase B1 (Lkb1), a serine/threonine kinase that links cellular metabolism with cell growth and proliferation, in γδ T-cell biology. Our findings demonstrate that Lkb1 is not only involved in regulating γδ T lineage commitment but also plays a critical role in γδ T-cell effector function...
April 19, 2024: Cellular & Molecular Immunology
#13
JOURNAL ARTICLE
Yin Yang, Li Liu, Haley O Tucker
B-cell Chronic Lymphocytic Leukemia (B-CLL) is a malignancy caused by the clonal expansion of mature B lymphocytes bearing a CD5+ CD19+ (B1) phenotype. However, the origin of B-CLL remains controversial. We showed previously that STYK1/NOK transgenic mice develop a CLL-like disease. Using this model system in this study, we attempt to define the stage of CLL initiation. Here, we show that the phenotype of STYK1/NOK-induced B-CLL is heterogeneous. The expanded B1 lymphocyte pool was detected within peripheral lymphoid organs and was frequently associated with the expansions of memory B cells...
July 2024: Biochemistry and Biophysics Reports
#14
JOURNAL ARTICLE
Wei Zhang, Cuixiang Li, Yangyong Lv, Shan Wei, Yuansen Hu
Aspergillus flavus colonization on agricultural products during preharvest and postharvest results in tremendous economic losses. Inspired by the synergistic antifungal effects of essential oils, the aims of this study were to explore the mechanism of combined cinnamaldehyde and nonanal (SCAN ) against A. flavus and to evaluate the antifungal activity of SCAN loading into diatomite (DM). Shriveled mycelia were observed by scanning electron microscopy, especially in the SCAN treatment group. Calcofluor white staining, transmission electron microscopy, dichloro-dihydro-fluorescein diacetate staining and the inhibition of key enzymes in tricarboxylic acid cycle indicated that the antifungal mechanism of SCAN against A...
August 2024: Food Microbiology
#15
JOURNAL ARTICLE
Wenping Ding, Yanqun Li, Xingyu Li, Songbiao Shi, Jiajia Yin, Xinpeng Tian, Min Xiao, Si Zhang, Hao Yin
Bafilomycins are macrocyclic polyketides with intriguing structures and therapeutic value. Genomic analysis of Streptomyces sp. SCSIO 66814 revealed a type I polyketide synthase biosynthetic gene cluster (BGC), namely blm, which encoded bafilomycins and featured rich post-modification genes. The One strain many compounds (OSMAC) strategy led to the discovery of six compounds related to the blm BGC from the strain, including two previously undescribed 6,6-spiroketal polyketides, streptospirodienoic acids D (1) and E (2), and four known bafilomycins, bafilomycins P (3), Q (4), D (5), and G (6)...
April 16, 2024: Phytochemistry
#16
JOURNAL ARTICLE
Brett M Frye, Jacob D Negrey, Corbin S C Johnson, Jeongchul Kim, Richard A Barcus, Samuel N Lockhart, Christopher T Whitlow, Kenneth L Chiou, Noah Snyder-Mackler, Thomas J Montine, Suzanne Craft, Carol A Shively, Thomas C Register
Mediterranean diets may be neuroprotective and prevent cognitive decline relative to Western diets, however the underlying biology is poorly understood. We assessed the effects of Western versus Mediterranean-like diets on RNAseq-generated transcriptional profiles in lateral temporal cortex and their relationships with longitudinal changes in neuroanatomy, circulating monocyte gene expression, and observations of social isolation and anxiety in 38 socially-housed, middle-aged female cynomolgus macaques (Macaca fascicularis)...
April 16, 2024: Brain, Behavior, and Immunity
#17
JOURNAL ARTICLE
Lu Zhang, Ying Liu, Qiongyi Zhang, Weiyu Yao, Zenghui Zhao, Xiao Wang, Yongzhan Bao, Wanyu Shi
Aflatoxin B1 (AFB1) is one of the common dietary contaminants worldwide, which can harm the liver of humans and animals. Salvia miltiorrhiza polysaccharide (SMP) is a natural plant-derived polysaccharide with numerous pharmacological activities, including hepatoprotective properties. The purpose of this study is to explore the intervention effect of SMP on AFB1-induced liver injury and its underlying mechanisms in rabbits. The rabbits were administered AFB1 (25 μg/kg/feed) and or treatment with SMP (300, 600, 900 mg/kg/feed) for 42 days...
April 17, 2024: Ecotoxicology and Environmental Safety
#18
JOURNAL ARTICLE
Zuzana Fabová, Barbora Loncová, Abdel Halim Harrath, Alexander V Sirotkin
The objective of this study was to elucidate the intricate interplay among miR-105-1, kisspeptin, and their synergistic influence on basic ovarian granulosa cell functions. The effects of miR-105-1 mimics or miR-105-1 inhibitor, kisspeptin (0, 1, and 10 ng/ml), and its combinations with miR-105-1 mimics on porcine granulosa cells were assessed. The expression levels of miR-105-1, viability, proliferation (accumulation of PCNA, cyclin B1, XTT-, and BrdU-positive cells), apoptosis (accumulation of bcl-2, bax, caspase 3, p53, TUNEL-positive cells), proportion of kisspeptin-positive cells, and the release of steroid hormones and IGF-I were analyzed...
April 17, 2024: Reproductive Sciences
#19
JOURNAL ARTICLE
Cody Bekkering, Shu Yu, Chih Chi Kuo, Li Tian
Mutants lacking functional HYD2 homoeologs showed improved seedling growth, but comparable or increased susceptibility to salt stress in tillering plants, suggesting a developmentally restricted role of HYD2 in salt response. Salinity stress threatens global food security by reducing the yield of staple crops such as wheat (Triticum ssp.). Understanding how wheat responds to salinity stress is crucial for developing climate resilient varieties. In this study, we examined the interplay between carotenoid metabolism and the response to salt (NaCl) stress, a specific form of salinity stress, in tetraploid wheat plants with mutations in carotenoid β-hydroxylase 1 (HYD1) and HYD2...
April 17, 2024: Plant Cell Reports
#20
JOURNAL ARTICLE
Haifen Huang, Bin Peng, Qingyong Chen, Yi Wang, Ren Li
BACKGROUND: Foam cell formation is an important step for atherosclerosis (AS) progression. We investigated the mechanism by which the long non-coding RNA (lncRNA) nuclear-enriched abundant transcript 1 (NEAT1) regulates foam cell formation during AS progression.Methods and Results: An in vivo AS model was created by feeding ApoE-/- mice a high-fat diet. Oxidized low-density lipoprotein (ox-LDL)-stimulated macrophages were used as a cellular AS model. Interactions between NEAT1, miR-17-5p, itchy E3 ubiquitin protein ligase (ITCH) and liver kinase B1 (LKB1) were analyzed...
April 16, 2024: Circulation Journal: Official Journal of the Japanese Circulation Society
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