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Journals Archives of Biochemistry and B...

Archives of Biochemistry and Biophysics

https://read.qxmd.com/read/38768746/histone-demethylase-kdm3b-mediates-matrix-stiffness-induced-osteogenic-differentiation-of-adipose-derived-stem-cells
#1
JOURNAL ARTICLE
Huangshui Ma, Tao Zhang
Biomechanical signals in the extracellular niche are considered promising for programming the lineage specification of stem cells. Recent studies have reported that biomechanics, such as the microstructure of nanomaterials, can induce adipose-derived stem cells (ASCs) to differentiate into osteoblasts, mediating gene regulation at the epigenetic level. Therefore, in this study, transcriptome expression levels of histone demethylases in ASCs were screened after treatment with different matrix stiffnesses, and histone lysine demethylase 3B (KDM3B) was found to promote osteogenic differentiation of ASCs in response to matrix stiffness, indicating a positive modulatory effect on this biological process...
May 18, 2024: Archives of Biochemistry and Biophysics
https://read.qxmd.com/read/38750923/structural-and-functional-characterization-of-avian-influenza-h9n2-virus-neuraminidase-with-a-combination-of-five-novel-mutations
#2
JOURNAL ARTICLE
Deeksha S Tare, Shailesh D Pawar, Pratip Shil, Nitin M Atre
The influenza virus neuraminidase (NA) protein is responsible for actively cleaving the sialic acid (SA) bound to the viral hemagglutinin. In the present study we identified a combination of five novel amino acid substitutions in the NA, conferring increased substrate binding and altered surface characteristics to a low pathogenic avian influenza (LPAI) H9N2 strain. The H9N2 virus strain reported from India, namely, A/Environmental/India/1726265/2017 (H9N2-1726265) showed the combination of amino acid substitutions T149I, R249W, G346A, W403R and G435R, which were in the vicinity of the enzyme active site cavity...
May 13, 2024: Archives of Biochemistry and Biophysics
https://read.qxmd.com/read/38750922/arg40-is-critical-for-stability-and-activity-of-adenylosuccinate-lyase-a-purine-salvage-enzyme-from-leishmania-donovani
#3
JOURNAL ARTICLE
Jigneshkumar A Mochi, Jani Jaykumar, Kiran Tak, Lodhi Krishna, Gayathri Pananghat, Anju Pappachan
Purine salvage enzymes have been of significant interest in anti-Leishmanial drug development due to the parasite's critical dependence on this pathway for the supply of nucleotides in the absence of a de novo purine synthesis pathway. Adenylosuccinate lyase (ADSL) one of the key enzymes in this pathway is a homo-tetramer, where the active site is formed by residues from three distinct subunits. Analysis of the subunit interfaces of LdADSL, revealed a conserved Arg40 forming critical inter-subunit interactions and also involved in substrate binding...
May 13, 2024: Archives of Biochemistry and Biophysics
https://read.qxmd.com/read/38750921/down-regulation-of-c1q-tumor-necrosis-factor-related-protein-6-is-associated-with-increased-risk-of-breast-cancer
#4
JOURNAL ARTICLE
Samia F Hamed, Nivin A Hassan, Samia A Shouman, Tohamy A Tohamy, Hussein Fakhry, Eman Radwan
C1q tumor necrosis factor-related protein 6 (CTRP6), a member of the C1q tumor necrosis factor-related protein (CTRP) family, is reported to be associated with the progression of different malignancies, however, its expression levels and role in breast cancer (BC) are yet unknown. In this study, we investigated the levels of circulating CTRP6 in BC patients and evaluated its role as a potential diagnostic biomarker in BC patients. Then we investigated the effect of recombinant CTRP6 on cellular viability in MCF-7 cells along with its effects on the expression of inflammatory cytokines, interleukin 6 (IL-6), tumor necrosis factor alpha (TNF-α) in addition to the expression of vascular endothelial growth factor (VEGF) as a marker of angiogenesis...
May 13, 2024: Archives of Biochemistry and Biophysics
https://read.qxmd.com/read/38750920/quantitation-of-oxidized-and-reduced-albumin-in-mammals-an-intriguing-analytical-question
#5
JOURNAL ARTICLE
Giorgia Gambardella, Sara Notari, Emanuele Criscuolo, Olga Lai, Antonella Nardoni, Renato Massoud, Laura Micheli, Alessio Bocedi, Giorgio Ricci
Oxidized albumin is considered a short-term biomarker of oxidative stress and its measurement in blood contributes to evaluate the impact of diseases, drugs, dialytic treatments, physical activity, environmental contaminants etc. on the red-ox balance of humans as well as of other mammalians. Nevertheless, the most common methods for quantifying these proteins are costly and time-consuming. Furthermore, there is a dearth of information regarding the proper ways to store human serum or plasma samples in order to prevent inaccurate quantification of these various albumin forms...
May 13, 2024: Archives of Biochemistry and Biophysics
https://read.qxmd.com/read/38740275/sequence-similarity-network-analysis-of-drug-and-dye-modifying-azoreductase-enzymes-found-in-the-human-gut-microbiome
#6
JOURNAL ARTICLE
Audrey R Long, Emma L Mortara, Brisa N Mendoza, Emma C Fink, Francis X Sacco, Matthew J Ciesla, Tyler M M Stack
Drug metabolism by human gut microbes is often exemplified by azo bond reduction in the anticolitic prodrug sulfasalazine. Azoreductase activity is often found in incubations with cell cultures or ex vivo gut microbiome samples and contributes to the xenobiotic metabolism of drugs and food additives. Applying metagenomic studies to personalized medicine requires knowledge of the genes responsible for sulfasalazine and other drug metabolism, and candidate genes and proteins for drug modifications are understudied...
May 11, 2024: Archives of Biochemistry and Biophysics
https://read.qxmd.com/read/38729594/single-nucleus-rna-transcriptome-profiling-reveals-murine-adipose-tissue-endothelial-cell-proliferation-gene-networks-involved-in-obesity-development
#7
JOURNAL ARTICLE
Zhimin Lu, Ling Ding, Xing Jiang, Sen Zhang, Min Yan, Guangxin Yang, Xuewen Tian, Qinglu Wang
Endothelial cells play an important role in the metabolism of adipose tissue (AT). This study aimed to analyze the changes that adipose tissue in AT endothelial cells undergo during the development of obesity, using single-nucleus RNA sequence (snRNA-seq). Mouse paraepididymal AT cells were subjected to snRNA-seq with the 10X Genomics platform. The cell types were then clustered using t-distributed stochastic neighbor embedding and unbiased computational informatics analyses. Protein-protein interactions network was established using the STRING database and visualized using Cytoscape...
May 8, 2024: Archives of Biochemistry and Biophysics
https://read.qxmd.com/read/38724316/special-issue-extracellular-fine-particles-in-life-death-and-disease
#8
EDITORIAL
Shinya Toyokuni
No abstract text is available yet for this article.
May 8, 2024: Archives of Biochemistry and Biophysics
https://read.qxmd.com/read/38718957/heterologous-expression-of-nattokinase-in-e-coli-biochemical-characterization-and-functional-analysis-of-fibrin-binding-residues
#9
JOURNAL ARTICLE
Ankush Jain, Nishi Sondhi, Kashmir Singh, Jagdeep Kaur
Heterologous expression of nattokinase, a potent fibrinolytic enzyme, has been successfully carried out in various microorganisms. However, the successful expression of this enzyme as a soluble protein was not achieved in E. coli. This study delves into the expression of nattokinase in E. coli as a soluble protein followed by its biochemical characterization and functional analysis for fibrinolytic activity. E. coli BL21 C41 and pET32a vector host strain with pGro7 protein chaperone induced with IPTG at 16°C 180rpm for 16 h enabled the production of recombinant nattokinase in soluble fraction...
May 6, 2024: Archives of Biochemistry and Biophysics
https://read.qxmd.com/read/38705227/staphylococcal-peroxidase-inhibitor-spin-residue-level-investigation-of-the-helical-bundle-domain
#10
JOURNAL ARTICLE
Soheila Fatehi, Timothy J Herdendorf, Nicoleta T Ploscariu, Brian V Geisbrecht
Myeloperoxidase is a critical component of the antibacterial arsenal of neutrophils, whereby it consumes H2 O2 as an oxidant to convert halogen and pseudohalogen anions into cytotoxic hypohalous acids. Following phagocytosis by neutrophils, the human pathogen Staphylococcus aureus secretes a potent myeloperoxidase inhibitory protein, called SPIN, as part of its immune evasion repertoire. The matured S. aureus SPIN polypeptide consists of only 73 residues yet contains two functional domains: whereas the 60 residue C-terminal helical bundle domain is responsible for MPO binding, the 13 residue N-terminal domain is required to inhibit MPO...
May 3, 2024: Archives of Biochemistry and Biophysics
https://read.qxmd.com/read/38703803/role-of-fxr-in-the-development-of-nafld-and-intervention-strategies-of-small-molecules
#11
REVIEW
Jiachan Long, Yuanhang Xu, Xuerong Zhang, Bingxing Wu, Caiyan Wang
Non-alcoholic fatty liver disease (NAFLD) remains a prevailing etiological agent behind hepatocyte diseases like chronic liver disease. The spectrum of processes involved in NAFLD stages includes hepatic steatosis, non-alcoholic fatty liver, and non-alcoholic steatohepatitis (NASH). Without intervention, the progression of NASH can further deteriorate into cirrhosis and ultimately, hepatocellular carcinoma. The cardinal features that characterize NAFLD are insulin resistance, lipogenesis, oxidative stress and inflammation, extracellular matrix deposition and fibrosis...
May 2, 2024: Archives of Biochemistry and Biophysics
https://read.qxmd.com/read/38697344/virtually-identical-does-not-mean-exactly-identical-discrepancy-in-energy-metabolism-between-glucose-and-fructose-fermentation-influences-the-reproductive-potential-of-yeast-cells
#12
JOURNAL ARTICLE
Roman Maslanka, Sabina Bednarska, Renata Zadrag-Tecza
The physiological efficiency of cells largely depends on the possibility of metabolic adaptations to changing conditions, especially on the availability of nutrients. Central carbon metabolism has an essential role in cellular function. In most cells is based on glucose, which is the primary energy source, provides the carbon skeleton for the biosynthesis of important cell macromolecules, and acts as a signalling molecule. The metabolic flux between pathways of carbon metabolism such as glycolysis, pentose phosphate pathway, and mitochondrial oxidative phosphorylation is dynamically adjusted by specific cellular economics responding to extracellular conditions and intracellular demands...
April 30, 2024: Archives of Biochemistry and Biophysics
https://read.qxmd.com/read/38697343/extracellular-vesicles-powered-immunotherapy-unleashing-the-potential-for-safer-and-more-effective-cancer-treatment
#13
JOURNAL ARTICLE
Pratiksha Tiwari, Krishna Yadav, Ravi Prakash Shukla, Avijit Kumar Bakshi, Dilip Panwar, Sweety Das, Prabhat Ranjan Mishra
Cancer treatment has seen significant advancements with the introduction of Onco-immunotherapies (OIMTs). Although some of these therapies have received approval for use, others are either undergoing testing or are still in the early stages of development. Challenges persist in making immunotherapy widely applicable to cancer treatment. To maximize the benefits of immunotherapy and minimize potential side effects, it's essential to improve response rates across different immunotherapy methods. A promising development in this area is the use of extracellular vesicles (EVs) as novel delivery systems...
April 30, 2024: Archives of Biochemistry and Biophysics
https://read.qxmd.com/read/38692471/the-role-of-labile-iron-on-brain-proteostasis-could-it-be-an-early-event-of-neurodegenerative-disease
#14
JOURNAL ARTICLE
Aiyarin Kittilukkana, Jannarong Intakhad, Chalermchai Pilapong
Iron deposits in the brain are a natural consequence of aging. Iron accumulation, especially in the form of labile iron, can trigger a cascade of adverse effects, eventually leading to neurodegeneration and cognitive decline. Aging also increases the dysfunction of cellular proteostasis. The question of whether iron alters proteostasis is now being pondered. Herein, we investigated the effect of ferric citrate, considered as labile iron, on various aspects of proteostasis of neuronal cell lines, and also established an animal model having a labile iron diet in order to evaluate proteostasis alteration in the brain along with behavioral effects...
April 30, 2024: Archives of Biochemistry and Biophysics
https://read.qxmd.com/read/38688397/a-structure-based-pharmacophore-modelling-approach-to-identify-and-design-new-neprilysin-nep-inhibitors-an-in-silico-based-investigation
#15
JOURNAL ARTICLE
Shikha Thakur, Apurba Sinhari, Anil Bhanudas Gaikwad, Hemant R Jadhav
Neutral endopeptidase or neprilysin (NEP) cleaves the natriuretic peptides, bradykinin, endothelin, angiotensin II, amyloid β protein, substance P, etc., thus modulating their effects on heart, kidney, and other organs. NEP has a proven role in hypertension, heart disease, renal disease, Alzheimer's, diabetes, and some cancers. NEP inhibitor development has been in focus since the US FDA approved a combination therapy of angiotensin II type 1 receptor inhibitor (valsartan) and NEP inhibitor (sacubitril) for use in heart failure...
April 28, 2024: Archives of Biochemistry and Biophysics
https://read.qxmd.com/read/38677505/lncrna-dlg5-as1-facilitates-breast-cancer-cell-proliferation-and-invasion-by-promoting-ezh2-mediated-transcriptional-silencing-of-sfrp1
#16
JOURNAL ARTICLE
Yun Cai, Yi Liu, Ye Sun, Yu Ren
Rapid proliferation and metastasis of breast cancer contributed to poor clinical prognosis. Accumulating evidence revealed that the dysregulation of long noncoding RNAs (lncRNAs) was associated with breast cancer progression. However, the role of lncRNA DLG5-AS1 in breast cancer has not been established. Here, we investigated the mechanisms of DLG5-AS1 in the development of breast cancer. We found that the expression of DLG5-AS1 was significantly upregulated in breast cancer tissues and cell lines. DLG5-AS1 interference markedly restrained AU565 cell proliferation, invasion, the expression of apoptosis related (caspase3 and caspase8) and Wnt/β-catenin pathway related proteins (wnt5a, β-Catenin and c-Myc), as well as promoted cell apoptosis, whereas DLG5-AS1 overexpression showed an opposite effects...
April 25, 2024: Archives of Biochemistry and Biophysics
https://read.qxmd.com/read/38670301/exploring-the-diagnostic-value-of-endothelial-cell-and-angiogenesis-related-genes-in-hashimoto-s-thyroiditis-based-on-transcriptomics-and-single-cell-rna-sequencing
#17
JOURNAL ARTICLE
Yihang Li, Xiaokai Lu, Weihan Cao, Nianqiu Liu, Xin Jin, Yuting Li, Shiying Tang, Ling Tao, Qian Zhu, Hongmin Liang
(1) BACKGROUND: Hashimoto's thyroiditis (HT) can cause angiogenesis in the thyroid gland. However, the molecular mechanism of endothelial cells and angiogenesis related genes (ARGs) has not been extensively studied in HT. (2) METHODS: The HRA001684, GSE29315 and GSE163203 datasets were included in this study. Using single-cell analysis, weighted gene co-expression network analysis (WGCNA), functional enrichment analysis, machine learning algorithms and expression analysis for exploration. And receiver operator characteristic (ROC) curves was draw...
April 24, 2024: Archives of Biochemistry and Biophysics
https://read.qxmd.com/read/38658208/corrigendum-to-epicatechin-prevents-tnf%C3%AE-induced-activation-of-signaling-cascades-involved-in-inflammation-and-insulin-sensitivity-in-3t3-l1-adipocytes-arch-biochem-biophys-2012-nov-15-527-2-113-8-doi-10-1016-j-abb-2012-02-019-epub-2012-mar-8
#18
Marcela A Vazquez-Prieto, Ahmed Bettaieb, Fawaz G Haj, César G Fraga, Patricia I Oteiza
No abstract text is available yet for this article.
April 24, 2024: Archives of Biochemistry and Biophysics
https://read.qxmd.com/read/38663796/structural-features-and-substrate-engagement-in-peptide-modifying-radical-sam-enzymes
#19
REVIEW
Lilly E Cheek, Wen Zhu
In recent years, the biological significance of ribosomally synthesized, post-translationally modified peptides (RiPPs) and the intriguing chemistry catalyzed by their tailoring enzymes has garnered significant attention. A subgroup of bacterial radical S-adenosylmethionine (rSAM) enzymes can activate C-H bonds in peptides, which leads to the production of a diverse range of RiPPs. The remarkable ability of these enzymes to facilitate various chemical processes, to generate and harbor high-energy radical species, and to accommodate large substrates with a high degree of flexibility is truly intriguing...
April 23, 2024: Archives of Biochemistry and Biophysics
https://read.qxmd.com/read/38649133/multifunctionality-of-arginine-residues-in-the-active-sites-of-non-canonical-d-amino-acid-transaminases
#20
JOURNAL ARTICLE
Alina K Bakunova, Ilya O Matyuta, Mikhail E Minyaev, Tatiana Y Isaikina, Konstantin M Boyko, Vladimir O Popov, Ekaterina Yu Bezsudnova
Structure-function relationships are key to understanding enzyme mechanisms, controlling enzyme activities, and designing biocatalysts. Here, we investigate the functions of arginine residues in the active sites of pyridoxal-5'-phosphate (PLP)-dependent non-canonical D-amino acid transaminases, focusing on the analysis of a transaminase from Haliscomenobacter hydrossis. Our results show that the tandem of arginine residues R28* and R90, which form the conserved R-[RK] motif in non-canonical D-amino acid transaminases, not only facilitates effective substrate binding but also regulates the catalytic properties of PLP...
April 20, 2024: Archives of Biochemistry and Biophysics
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