Article
Oncology
Hiroko Nakajima, Jun Nakata, Kanako Imafuku, Hiromu Hayashibara, Kazuki Isokawa, Keiko Udaka, Fumihiro Fujiki, Soyoko Morimoto, Kana Hasegawa, Naoki Hosen, Yoshiko Hashii, Sumiyuki Nishida, Akihiro Tsuboi, Yoshihiro Oka, Yusuke Oji, Shinji Sogo, Haruo Sugiyama
Summary: This study identified three novel mouse Th epitope peptides that strongly induced and maintained WT1-specific CTLs, efficiently rejected WT1-expressing tumor cells, and showed that these CTLs played a central role in tumor rejection. The majority of WT1-specific CTLs induced by the co-immunization with WT1 CTL and the WT1-specific Th peptides were effector memory CD8(+) T cells, demonstrating their essential function in WT1-specific tumor immunity.
CANCER IMMUNOLOGY IMMUNOTHERAPY
(2021)
Article
Biochemistry & Molecular Biology
Om Rangacharya, Avanti Parab, Shrikant Adkine, Rahul Nagargoje
Summary: The scientific community is impressed with the efficacy, synthesis speed, and market speed of RNA-based vaccines. The self-amplifying mRNA vaccine addresses the limitations of traditional vaccines, such as the need for large doses or repeat injections. A thorough examination of the most antigenic component of the Nipah virus was conducted to design an antigen coding sequence that will provoke a virus-specific immune response. Epitopes from the NiV G-protein were predicted and evaluated, and structural compatibility was studied through docking between HLA alleles and epitopes. The designed vaccine has promising potential against the Nipah virus.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2023)
Article
Medicine, General & Internal
Sapna P. Patel, Megan Othus, Yuanbin Chen, G. Paul Wright, Kathleen J. Yost, John R. Hyngstrom, Siwen Hu-Lieskovan, Christopher D. Lao, Leslie A. Fecher, Thach-Giao Truong, Jennifer L. Eisenstein, Sunandana Chandra, Jeffrey A. Sosman, Kari L. Kendra, Richard C. Wu, Craig E. Devoe, Gary B. Deutsch, Aparna Hegde, Maya Khalil, Ankit Mangla, Amy M. Reese, Merrick I. Ross, Andrew S. Poklepovic, Giao Q. Phan, Adedayo A. Onitilo, Demet G. Yasar, Benjamin C. Powers, Gary C. Doolittle, Gino K. In, Niels Kokot, Geoffrey T. Gibney, Michael B. Atkins, Montaser Shaheen, James A. Warneke, Alexandra Ikeguchi, Jose E. Najera, Bartosz Chmielowski, Joseph G. Crompton, Justin D. Floyd, Eddy Hsueh, Kim A. Margolin, Warren A. Chow, Kenneth F. Grossmann, Eliana Dietrich, Victor G. Prieto, Michael C. Lowe, Elizabeth I. Buchbinder, John M. Kirkwood, Larissa Korde, James Moon, Elad Sharon, Vernon K. Sondak, Antoni Ribas
Summary: This study aimed to investigate whether giving pembrolizumab both before and after surgery would improve event-free survival in patients with resectable stage III or IV melanoma. Results showed that patients who received pembrolizumab both before and after surgery had significantly longer event-free survival. Overall rating: 9 out of 10.
NEW ENGLAND JOURNAL OF MEDICINE
(2023)
Article
Genetics & Heredity
Xingyu Jiang, Zhengtao Qian, Yu Chen, Tao Zhou, Can Zhao, Yongxiang Yin
Summary: CMTM7 is a potential tumor suppressor and regulator of PD-L1. It is correlated with immunomodulators, tumor-infiltrating immune cells, and immune checkpoints. Patients with high CMTM7 expression in breast cancer are more responsive to immunotherapy. CMTM7 can serve as a novel biomarker for identifying immunological characteristics and predicting immunotherapeutic response in breast cancer.
FRONTIERS IN GENETICS
(2022)
Article
Medicine, General & Internal
Honghong Fan, Yuxin Shi, Huiyu Wang, Yuting Li, Jie Mei, Junying Xu, Chaoying Liu
Summary: This study found that the upregulation of guanylate binding protein 5 (GBP5) was associated with a good prognosis in non-small cell lung cancer (NSCLC) patients, and it was strongly correlated with the expression of many immune-related genes, TIIC levels, and PD-L1 expression. The results suggest that GBP5 may serve as a potential biomarker for predicting the outcome of NSCLC patients treated with immune checkpoint inhibitors (ICIs).
INTERNATIONAL JOURNAL OF GENERAL MEDICINE
(2023)
Article
Multidisciplinary Sciences
Jingyi Wu, Jianzuo Yao, Shu Jia, Xiaokun Yao, Jingping Shao, Weijuan Cao, Shuwei Ma, Xiaomin Yao, Hong Li
Summary: In this study, a prognostic cuproptosis-related lncRNA signature was constructed, which accurately and effectively predicted the prognosis of HCC. Tumors with high-risk signature had differences in TMB, tumor microenvironment, and tumor purity. High-risk patients had a poor response to immunotherapy.
Article
Biochemistry & Molecular Biology
Wenjun Zhu, Ziqi Chen, Min Fu, Qianxia Li, Xin Chen, Xiaoyu Li, Na Luo, Wenhua Tang, Feng Yang, Yiling Zhang, Yuanyuan Zhang, Xiaohong Peng, Guangyuan Hu
Summary: This study explored the relationship between cuprotosis and prognosis in low-grade glioma (LGG) patients. LGG patients were classified into two clusters based on expression of cuprotosis-related genes, with cluster A showing better prognosis. A cuprotosis-related prognostic signature was developed and validated, dividing LGG patients into high- and low-risk groups with significant differences in overall survival. The high-risk group also showed potential for benefiting from immunotherapy.
Article
Genetics & Heredity
Sibin Zhang, Xu Xiao, Yu Wang, Tianjun Song, Chenlong Li, Hongbo Bao, Qing Liu, Guiyin Sun, Xiaoyang Sun, Tianqi Su, Tianjiao Fu, Yujie Wang, Peng Liang
Summary: In this study, a novel immune-related signature was constructed to accurately predict prognosis and response to immunotherapy in patients with glioma. This has significant implications for improving the treatment outcomes of glioma patients.
FRONTIERS IN GENETICS
(2022)
Article
Oncology
Jie Mei, Guanyu Jiang, Yundi Chen, Yongrui Xu, Yuan Wan, Ruo Chen, Feng Liu, Wenjun Mao, Mingfeng Zheng, Junying Xu
Summary: This study identifies HLA-DRA as a potential biomarker for guiding immune checkpoint blockade therapy in NSCLC based on analysis of multiple immunotherapy datasets.
Article
Immunology
Junquan Song, Rongyuan Wei, Shiying Huo, Chenchen Liu, Xiaowen Liu
Summary: Studies have shown that VCAN expression plays an important role in the prognosis and response to treatment in gastric cancer patients. High VCAN expression is associated with poor prognosis, while low VCAN expression is associated with better response to adjuvant chemotherapy and chemoradiotherapy. Patients with high VCAN expression tend to be resistant to immunotherapy, suggesting that VCAN could be a promising indicator for predicting the response to immunotherapy.
FRONTIERS IN IMMUNOLOGY
(2022)
Article
Immunology
Qikai Tang, Zhengxin Chen, Jiaheng Xie, Chuangqi Mo, Jiacheng Lu, Qixiang Zhang, Zhangjie Wang, Wei Wu, Huibo Wang
Summary: This study investigates the role of ubiquitination genes in gliomas and identifies USP4 as a potential biomarker for glioma. The findings suggest that this research provides new insights for the treatment and immunotherapy of glioma.
FRONTIERS IN IMMUNOLOGY
(2022)
Article
Oncology
Lu Yuan, Xixi Wu, Longshan Zhang, Mi Yang, Xiaoqing Wang, Wenqi Huang, Hua Pan, Yuting Wu, Jihong Huang, Wenyu Liang, Jiaxin Li, Xiaodi Zhu, Shuang Wang, Jian Guan, Laiyu Liu
Summary: SFTPA1 protein plays a critical role in maintaining lung tissue homeostasis and the innate immune response, with its high expression associated with a favorable prognosis in lung adenocarcinoma. It may serve as a potential biomarker for predicting a positive response to immunotherapy in lung cancer patients.
CANCER IMMUNOLOGY IMMUNOTHERAPY
(2022)
Article
Biotechnology & Applied Microbiology
Yize Mao, Weisheng Cheng, Qiuxia Yang, Liqin Li, Wanming Hu, Zeyu Shuang, Dejun Fan, Xinlei Jiang, Feng Gao, Shengping Li, Wei Wang
Summary: In this study, a robust and convenient biomarker (ECC score) based on cell cycle genes RASAL2 and ASPM was developed to predict chemotherapy response in PDAC patients. Patients with high ECC scores exhibited shortened recurrence-free survival (RFS) and overall survival (OS) rates. It was also found that adjuvant chemotherapy significantly improved outcomes for ECC-high patients, while ECC-low patients did not benefit. Moreover, ECC-high patients showed less immune cell infiltration and elevated expression of immune suppressor genes compared to ECC-low patients.
Review
Oncology
Noel E. Donlon, Maria Davern, Conall Hayes, Robert Power, Andrew D. Sheppard, Claire L. Donohoe, Joanne Lysaght, John V. Reynolds
Summary: The perioperative period is a critical time for tumor micrometastasis progression, and the timing of introducing cancer therapies is crucial. Through exploring perioperative immune events at a cellular level and reviewing clinical trials, this study extrapolates the effects of oncological surgery on the perioperative immune milieu. The review focuses on perioperative immunosuppression, identifies potential modifiable factors, and discusses the combination of immunotherapy and major oncological gastrointestinal surgery.
CRITICAL REVIEWS IN ONCOLOGY HEMATOLOGY
(2022)
Article
Neurosciences
Chaoyou Fang, Houshi Xu, Yibo Liu, Chenkai Huang, Xiaoyu Wang, Zeyu Zhang, Yuanzhi Xu, Ling Yuan, Anke Zhang, Anwen Shao, Meiqing Lou
Summary: Through bioinformatic analysis, we found that aberrations of TRP family genes in glioma were correlated to prognosis, identified 10 hub genes that may play a crucial role in glioma, and demonstrated their significant association with patient prognosis.
Article
Chemistry, Multidisciplinary
Mohammad Bagher Ghoshoon, Mohammad Javad Raee, Mohammad Reza Shabanpoor, Zahra Dehghan, Narjes Ebrahimi, Aydin Berenjian, Manica Negahdaripour, Shiva Hemmati, Issa Sadeghian, Younes Ghasemi
Summary: The study found that immobilizing Escherichia coli cells in calcium alginate beads can increase the secretory production and enzyme activity of recombinant L-asparaginase, while also improving plasmid stability.
SEPARATION SCIENCE AND TECHNOLOGY
(2022)
Article
Chemistry, Multidisciplinary
Farid Reza Firoozi, Mohammad Javad Raee, Neha Lal, Alireza Ebrahiminezhad, Saeed Hosseini Teshnizi, Aydin Berenjian, Younes Ghasemi
Summary: The study demonstrates that immobilizing S. cerevisiae cells with L-lysine-coated magnetite nanoparticles is a promising method for ethanol production, with magnetically immobilized yeast cells successfully separated using an integrated magnetic separation process.
SEPARATION SCIENCE AND TECHNOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Mehrdad Ameri, Maedeh Alipour, Mobina Madihi, Navid Nezafat
Summary: In this study, an integrated approach was used to analyze hub genes in AML, and the important role of PPBP as a potential drug target in AML was discovered through the investigation of its structure and function.
BIOTECHNOLOGY AND APPLIED BIOCHEMISTRY
(2022)
Editorial Material
Immunology
Mehrdad Ameri, Navid Nezafat, Sedigheh Eskandari
EXPERT REVIEW OF VACCINES
(2022)
Article
Biochemistry & Molecular Biology
Saeed Taghizadeh, Amir Savardashtaki, Cambyz Irajie, Mohammad Reza Rahbar, Younes Ghasemi
Summary: The increase in antibiotic-resistant bacteria cases is a pressing global health issue. Scorpion venom is a promising candidate for the development of new antimicrobial drugs. This study successfully expressed and purified BmTXKS2 antimicrobial peptide, demonstrating potent inhibitory effects against multiple strains of bacteria.
INTERNATIONAL JOURNAL OF PEPTIDE RESEARCH AND THERAPEUTICS
(2022)
Article
Biochemistry & Molecular Biology
Seyedeh-Masoumeh Taghizadeh, Alireza Ebrahiminezhad, Mohammad Javad Raee, Hamidreza Ramezani, Aydin Berenjian, Younes Ghasemi
Summary: This study investigated the impacts of L-lysine-coated iron oxide nanoparticles (lys@IONPs) on the growth and biofilm formation of Chlorella vulgaris cells. The results demonstrated that low concentrations of nanoparticles can promote cell growth and biofilm formation, while higher concentrations have adverse effects on microalgal communities. The adaptability of cells to nanoparticles is concentration- and exposure time-dependent.
MOLECULAR BIOTECHNOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Seyedeh-Masoumeh Tagizadeh, Alireza Ebrahiminezhad, Mohammad Bagher Ghoshoon, Ali Dehshahri, Aydin Berenjian, Younes Ghasemi
Summary: Magnetic immobilization is a viable technique that can be effectively applied in eukaryotic expression systems without adverse effects on cell growth and metabolic status.
MOLECULAR BIOTECHNOLOGY
(2022)
Article
Food Science & Technology
Milad Mohkam, Shiva Ghasemi Firoozabadi, Younes Ghasemi, Ahmad Gholami
Summary: Probiotic characterization of lactic acid bacteria (LAB) isolated from Souro, a traditional food in Iran, was studied. The research found that Souro had high protein and lipid content. The isolated LABs showed good physiological traits and safety evaluation, indicating their potential for use in human diet and probiotic food formulations.
JOURNAL OF MICROBIOLOGY BIOTECHNOLOGY AND FOOD SCIENCES
(2022)
Article
Food Science & Technology
Marzieh Alizadeh, Ersin Demir, Nida Aydogdu, Najmeh Zare, Fatemeh Karimi, S. Masoud Kandomal, Hassan Rokni, Younes Ghasemi
Summary: This study provides a comprehensive review of the latest developments in the electrochemical impressions of important dyestuffs, specifically amaranth and carminic acid. Electroanalytical methods, particularly voltammetric techniques, have been successfully used for the determination of these food colors due to their quick analysis durations, high precision and accuracy, and great selectivity.
FOOD AND CHEMICAL TOXICOLOGY
(2022)
Article
Cell Biology
Marjan Khorsand, Sahar Khajeh, Mahboobeh Eslami, Navid Nezafat, Younes Ghasemi, Vahid Razban, Zohreh Mostafavi-Pour
Summary: This study aimed to investigate the effects of Telmisartan, a novel N-cadherin antagonist, on cell migration of cancer cells. The results showed that Telmisartan and ADH-1 significantly reduced cell attachment to N-cadherin coated plate in different cancer cell lines. Telmisartan and Docetaxel also showed significant inhibitory effects on cell migration. Moreover, Telmisartan exerted its anti-proliferation and anti-migration effects by targeting antagonistically N-cadherin, suggesting its potential use as an alternative to ADH-1 in enhancing the anticancer effects of Docetaxel.
JOURNAL OF CELLULAR AND MOLECULAR MEDICINE
(2022)
Article
Food Science & Technology
Fatemeh Karimi, Ersin Demir, Nida Aydogdu, Moein Shojaei, Mohammad A. Taher, Padideh Naderi Asrami, Marzieh Alizadeh, Younes Ghasemi, Somaye Cheraghi
Summary: This review discusses the properties, applications, and electrochemical determinations of brown HT and carmoisine, which are synthetic food colorants. The paper compares sensor types, detection limits, and analytical applications in the developed electrochemical strategies for both substances. The benefits of using electrochemical techniques for the determination of these food colors are summarized. Future perspectives in electrochemical strategy for brown HT and carmoisine are also provided.
FOOD AND CHEMICAL TOXICOLOGY
(2022)
Article
Immunology
Yasaman Mohammadi, Navid Nezafat, Manica Negahdaripour, Sedigheh Eskandari, Mozhdeh Zamani
Summary: In this study, a mRNA vaccine against BK virus (BKV) was designed using a reverse vaccinology approach. Potential immunogenic epitopes were predicted and selected based on several evaluation criteria. The designed vaccine was antigenic, non-toxic, non-allergenic, and had a high population coverage worldwide. Molecular dynamic simulation studies showed strong interactions between the vaccine and toll-like receptor 4 (TLR4). In silico immune simulation analyses demonstrated increased immune responses following repeated exposure to the vaccine.
IMMUNOLOGIC RESEARCH
(2023)
Review
Immunology
Manica Negahdaripour, Bahare Vakili, Navid Nezafat
Summary: Exosome-based vaccines have emerged as promising tools for delivering a wide range of antigens and immunomodulatory properties. Studies have shown their potential in tackling infectious diseases and cancers both in vitro and in vivo.
INTERNATIONAL IMMUNOPHARMACOLOGY
(2022)
Article
Immunology
Bahareh Vakili, Mahboubeh Karami-Darehnaranji, Esmaeil Mirzaei, Farnaz Hosseini, Navid Nezafat
Summary: Graphene, as a new type of vaccine adjuvant, has been found to enhance antigen immunogenicity and stimulate immune responses. However, its injection may lead to oxidative stress and inflammation, thereby requiring modifications to reduce adverse effects.
INTERNATIONAL IMMUNOPHARMACOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Farzaneh Vahedi, Younes Ghasemi, Amir Atapour, Kamiar Zomorodian, Maryam Ranjbar, Ahmad Monabati, Navid Nezafat, Amir Savardashtaki
Summary: In this study, a diagnostic kit for detecting Candida albicans with high sensitivity and specificity was designed using a bioinformatics approach. The designed construct, derived from eight antigenic proteins of Candida albicans, showed promising results in identifying the fungus in serum samples of patients with invasive candidiasis.
INTERNATIONAL JOURNAL OF PEPTIDE RESEARCH AND THERAPEUTICS
(2022)
Article
Biology
Iain Hunter, Raz Leib
Summary: Natural movement is related to health, but it is difficult to measure. Existing methods cannot capture the full range of natural movement. Comparing movement across different species helps identify common biomechanical and computational principles. Developing a system to quantify movement in freely moving animals in natural environments and relating it to life quality is crucial. This study proposes a theoretical framework based on movement ability and validates it in Drosophila.
JOURNAL OF THEORETICAL BIOLOGY
(2024)
Article
Biology
Andy Gardner
Summary: Fisher's geometric model is a useful tool for predicting key properties of Darwinian adaptation, and here it is applied to predict differences between the evolution of altruistic versus nonsocial phenotypes. The results suggest that the effect size maximizing probability of fixation is smaller in the context of altruism and larger in the context of nonsocial phenotypes, leading to lower overall probability of fixation for altruism and higher overall probability of fixation for nonsocial phenotypes.
JOURNAL OF THEORETICAL BIOLOGY
(2024)
Article
Biology
Thomas F. Pak, Joe Pitt-Francis, Ruth E. Baker
Summary: Cell competition is a process where cells interact in multicellular organisms to determine a winner or loser status, with loser cells being eliminated through programmed cell death. The winner cells then populate the tissue. The outcome of cell competition is context-dependent, as the same cell type can win or lose depending on the competing cell type. This paper proposes a mathematical framework to study the emergence of winner or loser status, highlighting the role of active cell death and identifying the factors that drive cell competition in a cell-based modeling context.
JOURNAL OF THEORETICAL BIOLOGY
(2024)
Article
Biology
Haruto Tomizuka, Yuuya Tachiki
Summary: Batesian mimicry is a strategy in which palatable prey species resemble unpalatable prey species to avoid predation. The evolution of this mimicry plays a crucial role in protecting the unpalatable species from extinction.
JOURNAL OF THEORETICAL BIOLOGY
(2024)
Article
Biology
Jason W. Olejarz, Martin A. Nowak
Summary: Gene drive technology shows potential for population control, but its release may have unpredictable consequences. The study suggests that the failure of suppression is a natural outcome, and there are complex dynamics among wild populations.
JOURNAL OF THEORETICAL BIOLOGY
(2024)
Article
Biology
Hamid Ravaee, Mohammad Hossein Manshaei, Mehran Safayani, Javad Salimi Sartakhti
Summary: Gene expression analysis is valuable for cancer classification and phenotype identification. IP3G, based on Generative Adversarial Networks, enhances gene expression data and discovers phenotypes in an unsupervised manner. By converting gene expression profiles into images and utilizing IP3G, new phenotype profiles can be generated, improving classification accuracy.
JOURNAL OF THEORETICAL BIOLOGY
(2024)
Article
Biology
Beatrix Rahnsch, Leila Taghizadeh
Summary: This study forecasts the evolution of the COVID-19 pandemic in Germany using a network-based inference method and compares it with other approaches. The results show that the network-inference based approach outperforms other methods in short-to mid-term predictions, even with limited information about the new disease. Furthermore, predictions based on the estimation of the reproduction number in Germany can yield more reliable results with increasing data availability, but still cannot surpass the network-inference based algorithm.
JOURNAL OF THEORETICAL BIOLOGY
(2024)
Article
Biology
Rongsheng Huang, Qiaojun Situ, Jinzhi Lei
Summary: Maintaining tissue homeostasis requires appropriate regulation of stem cell differentiation. Random inheritance of epigenetic states plays a pivotal role in stem cell differentiation. This computational model provides valuable insights into the intricate mechanism governing stem cell differentiation and cell reprogramming, offering a promising path for enhancing the field of regenerative medicine.
JOURNAL OF THEORETICAL BIOLOGY
(2024)
Article
Biology
Patrick Vincent N. Lubenia, Eduardo R. Mendoza, Angelyn R. Lao
Summary: This study compares insulin signaling in healthy and type 2 diabetes states using reaction network analysis. The results show similarities and differences between the two conditions, providing insights into the mechanisms of insulin resistance, including the involvement of other complexes, less restrictive interplay between species, and loss of concentration robustness in GLUT4.
JOURNAL OF THEORETICAL BIOLOGY
(2024)
Article
Biology
Nuverah Mohsin, Heiko Enderling, Renee Brady-Nicholls, Mohammad U. Zahid
Summary: Mathematical modeling is crucial in understanding radiobiology and designing treatment approaches in radiotherapy for cancer. This study compares three tumor volume dynamics models and analyzes the implications of model selection. A new metric, the point of maximum reduction of tumor volume (MRV), is introduced to quantify the impact of radiotherapy. The results emphasize the importance of caution in selecting models of response to radiotherapy due to the artifacts imposed by each model.
JOURNAL OF THEORETICAL BIOLOGY
(2024)
Article
Biology
Armindo Salvador
Summary: Michael Savageau's Biochemical Systems Analysis papers have had a significant impact on Systems Biology, generating core concepts and tools. This article provides a brief summary of these papers and discusses the most relevant developments in Biochemical Systems Theory since their publication.
JOURNAL OF THEORETICAL BIOLOGY
(2024)