Biochemistry and Biophysics Reports最新文献_第4页

Three sample-sparing techniques to estimate the molar absorption coefficient of luminescent dyes

IF 2.3

Biochemistry and Biophysics Reports Pub Date : 2025-03-08 DOI: 10.1016/j.bbrep.2025.101971

Jeffrey M. Schaub, Quinn A. Best, Cheng Zhao, Richard A. Haack, Qiaoqiao Ruan

{"title":"Three sample-sparing techniques to estimate the molar absorption coefficient of luminescent dyes","authors":"Jeffrey M. Schaub, Quinn A. Best, Cheng Zhao, Richard A. Haack, Qiaoqiao Ruan","doi":"10.1016/j.bbrep.2025.101971","DOIUrl":"10.1016/j.bbrep.2025.101971","url":null,"abstract":"<div><div>Luminescent dyes are commonly modified to improve their solubility, permeability, or spectral properties. However, changing the chemical structure influences the absorption of light and thus the compound-specific molar absorption coefficient (<em>ε</em>), which also confounds the compound's concentration in solution. The accurate determination of the molar absorption coefficient of new luminescent molecules is labor intensive and challenging when a limited amount of material is available for testing. To address this problem, we developed three techniques combined with UV–Vis spectrophotometry to closely approximate the molar absorption coefficient of various light-emitting dyes. The first technique uses Electrospray Mass Spectrometry to obtain a high-resolution incorporation ratio of a dye-labeled protein. The second approach utilizes covalent linking of the unknown dye to a dye with a known absorption coefficient. In the third method, we used fluorescence correlation spectroscopy to determine the fluorophore concentration in solution. We test each method with well-characterized fluorescent dyes and an uncharacterized chemilumiphore. Each technique produced calculated absorption coefficients comparable to the published reference values, although each presented unique limitations that reduced accuracy under certain conditions. Nevertheless, the techniques could be incorporated into current compound evaluation workflows and require only a small amount of sample, two significant advantages over traditional methods for characterizing new luminescent compounds.</div></div>","PeriodicalId":8771,"journal":{"name":"Biochemistry and Biophysics Reports","volume":"42 ","pages":"Article 101971"},"PeriodicalIF":2.3,"publicationDate":"2025-03-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143579902","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Machine learning unravels the mysteries of glioma typing and treatment

IF 2.3

Biochemistry and Biophysics Reports Pub Date : 2025-03-07 DOI: 10.1016/j.bbrep.2025.101969

Ying Dang , Youhu Chen , Jie Chen , Guoqiang Yuan , Yawen Pan

{"title":"Machine learning unravels the mysteries of glioma typing and treatment","authors":"Ying Dang , Youhu Chen , Jie Chen , Guoqiang Yuan , Yawen Pan","doi":"10.1016/j.bbrep.2025.101969","DOIUrl":"10.1016/j.bbrep.2025.101969","url":null,"abstract":"<div><div>Gliomas, which are complex primary malignant brain tumors known for their heterogeneous and invasive nature, present substantial challenges for both treatment and prognosis. Recent advancements in whole-genome studies have opened new avenues for investigating glioma mechanisms and therapies. Through single-cell analysis, we identified a specific cluster of cancer cell-related genes within gliomas. By leveraging diverse datasets and employing non-negative matrix factorization (NMF), we developed a glioma subtyping method grounded in this identified gene set. Our exploration delved into the clinical implications and underlying regulatory frameworks of the newly defined subtype classification, revealing its intimate ties to glioma malignancy and prognostic outcomes. Comparative assessments between the identified subtypes revealed differences in clinical features, immune modulation, and the tumor microenvironment (TME). Using tools such as the <em>limma</em> R package, weighted gene co-expression network analysis (WGCNA), machine learning methodologies, survival analyses, and protein-protein interaction (PPI) networks, we identified key driver genes influencing subtype differentiation while quantifying associated outcomes. This study not only sheds light on the biological mechanisms within gliomas but also paves the way for precise molecular targeted therapies within this intricate disease landscape.</div></div>","PeriodicalId":8771,"journal":{"name":"Biochemistry and Biophysics Reports","volume":"42 ","pages":"Article 101969"},"PeriodicalIF":2.3,"publicationDate":"2025-03-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143563669","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Exploring the role of exosomal and non-exosomal non-coding RNAs in Kawasaki disease: Implications for diagnosis and therapeutic strategies against coronary artery aneurysms

IF 2.3

Biochemistry and Biophysics Reports Pub Date : 2025-03-06 DOI: 10.1016/j.bbrep.2025.101970

Negar Jafari , Ali Zolfi Gol , Venus Shahabi Rabori , Mohammadreza Saberiyan

{"title":"Exploring the role of exosomal and non-exosomal non-coding RNAs in Kawasaki disease: Implications for diagnosis and therapeutic strategies against coronary artery aneurysms","authors":"Negar Jafari , Ali Zolfi Gol , Venus Shahabi Rabori , Mohammadreza Saberiyan","doi":"10.1016/j.bbrep.2025.101970","DOIUrl":"10.1016/j.bbrep.2025.101970","url":null,"abstract":"<div><div>Kawasaki disease (KD) is an acute vasculitis primarily affecting children, with a potential risk of developing coronary artery aneurysms (CAAs) and cardiovascular complications. The emergence of non-coding RNAs (ncRNAs), including microRNAs (miRNAs), long non-coding RNAs (lncRNAs), and circular RNAs (circRNAs), has provided insights into Kawasaki disease pathogenesis and opened new avenues for diagnosis and therapeutic intervention. Furthermore, polymorphism analysis of ncRNA genes offers significant insights into genetic predisposition to Kawasaki disease, facilitating tailored treatment approaches and risk assessment to improve patient outcomes. Exosomal ncRNAs, which are ncRNAs encapsulated within extracellular vesicles, have garnered significant attention as potential biomarkers for Kawasaki disease and CAA due to their stability and accessibility in biological fluids. This review comprehensively discusses the biogenesis, components, and potential of exosomal and non-exosomal ncRNAs in Kawasaki disease diagnosis and prognosis prediction. It also highlights the roles of non-exosomal ncRNAs, such as miRNAs, lncRNAs, and circRNAs, in Kawasaki disease pathogenesis and their implications as therapeutic targets. Additionally, the review explores the current diagnostic and therapeutic approaches for Kawasaki disease and emphasizes the need for further research to validate these ncRNA-based biomarkers in diverse populations and clinical settings.</div></div>","PeriodicalId":8771,"journal":{"name":"Biochemistry and Biophysics Reports","volume":"42 ","pages":"Article 101970"},"PeriodicalIF":2.3,"publicationDate":"2025-03-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143549568","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Alterations of renal polyamine metabolism in mice with folic acid-induced chronic kidney disease

IF 2.3

Biochemistry and Biophysics Reports Pub Date : 2025-03-05 DOI: 10.1016/j.bbrep.2025.101967

Cheng Xue , Jiaxin Chen , Xinming Li , Chenchen Zhou , Zhiguo Mao

引用次数: 0

Designing of an efficient DC-inducing multi-epitope vaccine against Epstein Barr virus targeting the GP350 using immunoinformatics and molecular dynamic simulation

IF 2.3

Biochemistry and Biophysics Reports Pub Date : 2025-03-03 DOI: 10.1016/j.bbrep.2025.101966

Golzar Fatahi , Maasoume Abdollahi , Zahra Nashtahosseini , Shima Minoo , Mehrnaz Mostafavi , Kholoud Saeidi

{"title":"Designing of an efficient DC-inducing multi-epitope vaccine against Epstein Barr virus targeting the GP350 using immunoinformatics and molecular dynamic simulation","authors":"Golzar Fatahi , Maasoume Abdollahi , Zahra Nashtahosseini , Shima Minoo , Mehrnaz Mostafavi , Kholoud Saeidi","doi":"10.1016/j.bbrep.2025.101966","DOIUrl":"10.1016/j.bbrep.2025.101966","url":null,"abstract":"<div><div>The findings underscore the critical role of Epstein-Barr virus (EBV) in the onset of various cancers. In response to the lack of effective treatments or vaccines for EBV infection, this investigation employed immunoinformatics approaches to develop a potent vaccine targeting multiple epitopes of the EBV glycoprotein 350 (Gp350), a key surface protein. Utilizing computational methods, we designed a comprehensive multi-epitope vaccine featuring 11 CTL and HTL epitopes, totaling 324 amino acids and covering five distinct EBV strains such as B95-8, P3HR-1, GD1, AG876, and Akata. To enhance immunogenicity, the 50S ribosomal protein L7/L12 (rplL) was included as an adjuvant at the vaccine's N-terminal. The vaccine was evaluated for its physicochemical and immunological properties, demonstrating stability, potency, solubility, hydrophilicity, non-allergenicity, and non-toxicity. Molecular docking studies have shown that the vaccine interacts with Toll-like receptor 4 (TLR4). Simulations performed using GROMACS confirmed the stability of the system over 100ns. Immune simulations indicated that the vaccine elicited robust humoral and cellular responses, activating both innate and adaptive immunity. The findings indicate that the multi-epitope vaccine is highly immunogenic and shows significant potential for further experimental validation.</div></div>","PeriodicalId":8771,"journal":{"name":"Biochemistry and Biophysics Reports","volume":"42 ","pages":"Article 101966"},"PeriodicalIF":2.3,"publicationDate":"2025-03-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143534807","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Intestinal antibody repertoire is altered by diabetes and varies depending on the pathogenesis

IF 2.3

Biochemistry and Biophysics Reports Pub Date : 2025-03-02 DOI: 10.1016/j.bbrep.2025.101964

Miho Chikazawa, Ken-Ichiro Minato

引用次数: 0

A novel anti-mouse CXCR1 monoclonal antibody, Cx1Mab-8, demonstrates nanomolar affinity in flow cytometry

IF 2.3

Biochemistry and Biophysics Reports Pub Date : 2025-03-01 DOI: 10.1016/j.bbrep.2025.101965

Guanjie Li, Hiroyuki Suzuki, Tomohiro Tanaka, Hiroyuki Satofuka, Mika K. Kaneko, Yukinari Kato

{"title":"A novel anti-mouse CXCR1 monoclonal antibody, Cx1Mab-8, demonstrates nanomolar affinity in flow cytometry","authors":"Guanjie Li, Hiroyuki Suzuki, Tomohiro Tanaka, Hiroyuki Satofuka, Mika K. Kaneko, Yukinari Kato","doi":"10.1016/j.bbrep.2025.101965","DOIUrl":"10.1016/j.bbrep.2025.101965","url":null,"abstract":"<div><div>CXC chemokine receptor 1 (CXCR1) is an important regulator for neutrophil granulocyte activation through binding to the ligand interleukin-8 (IL-8). Upon binding to IL-8, CXCR1 activates downstream signaling, critical for innate and adaptive immune responses. The IL-8-CXCR1 axis also plays an important role in tumor progression, especially in the tumor microenvironment. CXCR1 antagonists or anti-IL-8 monoclonal antibodies (mAbs) have been developed and evaluated in clinical trials for inflammatory diseases and tumors. In this study, we developed novel mAbs for mouse CXCR1 (mCXCR1) using the N-terminal peptide immunization. Among the established anti-mCXCR1 mAbs, Cx<sub>1</sub>Mab-8 (rat IgG<sub>2b</sub>, kappa) recognized mCXCR1-overexpressed Chinese hamster ovary-K1 (CHO/mCXCR1) and mCXCR1-overexpressed LN229 (LN229/mCXCR1) by flow cytometry. The dissociation constant (<em>K</em><sub>D</sub>) values of Cx<sub>1</sub>Mab-8 for CHO/mCXCR1 and LN229/mCXCR1 were determined as 4.1 × 10<sup>−10</sup> M and 1.5 × 10<sup>−9</sup> M, respectively. These results indicated that Cx<sub>1</sub>Mab-8 is useful for detecting mCXCR1 by flow cytometry with high affinity and could contribute to obtaining the proof of concept in preclinical studies.</div></div>","PeriodicalId":8771,"journal":{"name":"Biochemistry and Biophysics Reports","volume":"42 ","pages":"Article 101965"},"PeriodicalIF":2.3,"publicationDate":"2025-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143521306","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Corrigendum to “A non-invasive screening method using Caenorhabditis elegans for early detection of multiple cancer types: A prospective clinical study” [Biochem. and Biophys. Rep. 39 (2024) 101778]

IF 2.3

Biochemistry and Biophysics Reports Pub Date : 2025-03-01 DOI: 10.1016/j.bbrep.2024.101883

Hideyuki Hatakeyama, Masayo Morishita, Aya Hasan Alshammari, Umbhorn Ungkulpasvich, Junichi Yamaguchi, Takaaki Hirotsu, Eric di Luccio

引用次数: 0

The C-terminal end of PLIN1 displays structural disorder

IF 2.3

Biochemistry and Biophysics Reports Pub Date : 2025-02-28 DOI: 10.1016/j.bbrep.2025.101963

Edgar D. Páez-Pérez , Miriam Livier Llamas-García , Gabriela M. Montero-Morán , Samuel Lara-González

{"title":"The C-terminal end of PLIN1 displays structural disorder","authors":"Edgar D. Páez-Pérez , Miriam Livier Llamas-García , Gabriela M. Montero-Morán , Samuel Lara-González","doi":"10.1016/j.bbrep.2025.101963","DOIUrl":"10.1016/j.bbrep.2025.101963","url":null,"abstract":"<div><div>Lipid droplets (LDs) serve as crucial organelles for lipid storage and metabolism, with their proteome significantly influencing their regulation. Perilipins (PLINs), in particular PLIN1, play vital role in LD metabolism by orchestrating lipolysis. The C-terminal end of PLIN1 regulates lipolysis through interactions with coactivators such as the CGI-58 protein. Despite its importance, the structural characterization of this domain remains limited. Here, we present a comprehensive bioinformatic and biophysical analysis of the C-terminal end of mouse PLIN1 (mPLIN1C). Our findings suggest that mPLIN1C behaves as an intrinsically disordered region (IDR), exhibiting context-dependent properties of the coil-like or pre-molten globule type. Structural analysis reveals a predominance of disordered secondary structure, with circular dichroism spectroscopy indicating a high coil content. Interaction studies with SDS micelles suggest a conformational transition towards a pre-molten globule state. Furthermore, the analysis of molecular recognition features (MoRFs) identifies the EPESE sequence spanning residues 413–417 as a potential binding site for partner molecules. Overall, our findings shed light on the structural properties and potential interaction mechanisms of mPLIN1C, providing insight into its functional role in LD metabolism.</div></div>","PeriodicalId":8771,"journal":{"name":"Biochemistry and Biophysics Reports","volume":"42 ","pages":"Article 101963"},"PeriodicalIF":2.3,"publicationDate":"2025-02-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143510839","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Development and analytical performance of a new research use only (RUO) GP73 automated immunoassay

IF 2.3

Biochemistry and Biophysics Reports Pub Date : 2025-02-25 DOI: 10.1016/j.bbrep.2025.101961

Shaohua Ning , Enfu Liu , Fanju Meng , Fei Chen , James Hartnett , Zhihong Lin , Bailin Tu , David J. Hawksworth , Bryan C. Tieman , De Yu Mao , Ryan Piktel , Amit Kumar , You Pan , Philip M. Hemken

{"title":"Development and analytical performance of a new research use only (RUO) GP73 automated immunoassay","authors":"Shaohua Ning , Enfu Liu , Fanju Meng , Fei Chen , James Hartnett , Zhihong Lin , Bailin Tu , David J. Hawksworth , Bryan C. Tieman , De Yu Mao , Ryan Piktel , Amit Kumar , You Pan , Philip M. Hemken","doi":"10.1016/j.bbrep.2025.101961","DOIUrl":"10.1016/j.bbrep.2025.101961","url":null,"abstract":"<div><div>Golgi protein 73 (GP73) is a serum marker with potential applications in the assessment of chronic liver disease progression. We developed a research use only (RUO) GP73 immunoassay to detect serum GP73 concentration. A pair of internal antibodies that most effectively capture and detect GP73 were used to develop a prototype assay. An internal recombinant GP73 standard was used to prepare the assay calibrator and controls. The stability performance of the antibodies and GP73 calibrator were evaluated. We analyzed assay performance on the automated Alinity i system, including precision, sensitivity, linearity, endogenous interference, and HAMA/RF interference. The RUO Alinity i GP73 immunoassay showed good stability when the reagent kit was stored on board the instrument for more than 30 days without recalibration. The internal GP73 calibrator was stable at 2–8 °C for 28 days. Total %CV for 20 days was ≤3 %. The limit of quantitation (LoQ) at 20 % CV was 0.20 ng/mL or lower. Dilution analysis yielded a linear result within the range of 2.1 ng/mL – 1000.0 ng/mL. No interference was observed from common endogenous interferents at each test interference level. These findings support the reliability and robustness of the RUO Alinity i GP73 immunoassay for measuring serum GP73 concentration.</div></div>","PeriodicalId":8771,"journal":{"name":"Biochemistry and Biophysics Reports","volume":"41 ","pages":"Article 101961"},"PeriodicalIF":2.3,"publicationDate":"2025-02-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143480166","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0