Article
Biochemistry & Molecular Biology
Chia-Ming Chang, Yao-Feng Li, Hsin-Chung Lin, Kai-Hsi Lu, Tzu-Wei Lin, Li-Chun Liu, Kuo-Min Su, Cheng-Chang Chang
Summary: This study utilized integrated analysis to explore gene expression profiles of BOTs and its subtypes. Key dysregulated biomolecular functions were identified, including immune response, cell membrane, cell cycle, and cell metabolism-related functions, contributing to the pathogenesis of BOTs. Relevant genes involved in these functions were identified, highlighting the potential roles of immunological functionome and metabolic pathways in the tumorigenesis of BOTs.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Cell Biology
Yi Xin (Iris) Tu, Andrew M. Sydor, Etienne Coyaud, Estelle M. N. Laurent, Diana Dyer, Nora Mellouk, Jonathan St-Germain, Robert M. Vernon, Julie D. Forman-Kay, Taoyingnan Li, Rong Hua, Kexin Zhao, Neale D. Ridgway, Peter K. Kim, Brian Raught, John H. Brumell
Summary: This study identified a network of interactions among core human macroautophagy proteins using proximity-dependent biotin identification, highlighting the critical role of OSBPL family members in the macroautophagy process.
Review
Biochemistry & Molecular Biology
Roman Roy, Joshua Wilcox, Andrew J. Webb, Kevin O'Gallagher
Summary: Nitric oxide (NO) plays important roles in regulating various functions in the cardiovascular system. Different isoforms of nitric oxide synthase (NOS) have distinct functions and localizations, and may have different pathophysiological roles. Modulating NOS activity is a potential therapeutic approach for cardiovascular diseases. This review summarizes recent advances in understanding the physiological role of NOS isoforms and discusses the possibility of targeting NO and NOS activity for novel cardiovascular therapeutics.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Microbiology
Qijun Wu, Yingying Lei, Ya Zuo, Ji Zhang, Fenglin Guo, Weize Xu, Tanghui Xie, Dang Wang, Guiqing Peng, Xiangru Wang, Huanchun Chen, Zhenfang Fu, Gang Cao, Jinxia Dai
Summary: This study elucidates the protein-protein interaction (PPI) network between African swine fever virus (ASFV) and host immune pathways, exploring the differences between domestic pigs and warthogs, and investigating the potential functions of ASFV-host PPI in immune regulation.
Article
Plant Sciences
Lixin Cheng, Yonglun Zeng, Shuai Hu, Ning Zhang, Kenneth C. P. Cheung, Baiying Li, Kwong-Sak Leung, Liwen Jiang
Summary: This study identified autophagy-related modules in Arabidopsis using a systems-level algorithm, revealing that newly identified genes in these modules are upregulated and coexpressed during senescence. Additionally, the Golgi apparatus autophagy-related module, ARM13, was found to function in the autophagy process through module clustering and functional analysis.
Article
Genetics & Heredity
Limei Wang, Weixin Xie, Kongning Li, Zhenzhen Wang, Xia Li, Weixing Feng, Jin Li
Summary: Dysregulated Pathway Identification Analysis (DysPIA) addresses limitations of current pathway analysis methods by incorporating individual level product correlation and constructing a more comprehensive gene-pair background. It demonstrates high accuracy in identifying causal pathways in simulation studies and outperforms other methods in analyzing p53 mutation data. DysPIA's practical applications in breast cancer datasets further highlight its effectiveness and biological significance.
FRONTIERS IN GENETICS
(2021)
Article
Obstetrics & Gynecology
Valentina Vannuzzi, Caterina Bernacchioni, Angela Muccilli, Francesca Castiglione, Filippo Nozzoli, Silvia Vannuccini, Tommaso Capezzuoli, Marcello Ceccaroni, Paola Bruni, Chiara Donati, Felice Petraglia
Summary: This study found a significant dysregulation of the S1P signaling axis in adenomyosis, and the expression of ACTA2, which is associated with fibrosis, was positively correlated. This suggests that S1P may serve as a potential biomarker for adenomyosis.
REPRODUCTIVE BIOMEDICINE ONLINE
(2022)
Article
Toxicology
Barbara Fuezi, Neann Mathai, Johannes Kirchmair, Gerhard F. Ecker
Summary: In silico methods, specifically data science and knowledge-based methods, are increasingly important in computational risk assessment. These methods allow for the use of existing data to find correlations, build hypotheses, and generate new knowledge. When predicting toxicity, the complexity of the endpoint and available data are vital factors to consider. For complex endpoints like hepatotoxicity, a systemic approach can be beneficial.
TOXICOLOGY LETTERS
(2023)
Review
Pharmacology & Pharmacy
Emmanuel Boadi Amoafo, Philomena Entsie, Ying Kang, Ilaria Canobbio, Elisabetta Liverani
Summary: Sepsis is a complex pathological response to severe infection, characterized by a strong systemic inflammatory response involving multiple components of the immune system. Blood platelets, known for their role in haemostasis, have also been found to be involved in inflammation in septic patients. Antiplatelet therapy with P2Y(12) antagonists has been explored as a potential treatment for sepsis, but studies have yielded conflicting results regarding its effectiveness. This review discusses the role of platelets in sepsis and the potential of targeting P2Y(12) signalling pathways as a therapeutic approach.
BRITISH JOURNAL OF PHARMACOLOGY
(2023)
Article
Multidisciplinary Sciences
Pankaj Kumar Chauhan, Ramanathan Sowdhamini
Summary: Cardiomyopathies are a common and progressive cause of heart failures. These diseases have complex interactions with other diseases, and understanding their molecular mechanisms is essential. By using network medicine techniques, we identified candidate genes associated with cardiomyopathies and found strong associations with brain, cancer, and metabolic diseases. Through integrated analysis of molecular pathways and experimental data, we identified important candidate genes related to abnormal heart phenotype. This study expands our understanding of the genetic associations of cardiomyopathies with other diseases and holds significant potential in cardiomyopathy research.
SCIENTIFIC REPORTS
(2022)
Article
Cell Biology
Fettah Erdogan, Tudor Bogdan Radu, Anna Orlova, Abdul Khawazak Qadree, Elvin Dominic de Araujo, Johan Israelian, Peter Valent, Satu M. Mustjoki, Marco Herling, Richard Moriggl, Patrick Thomas Gunning
Summary: This study conducted a comprehensive review and in silico analysis of reported data on STAT-linked diseases, proposing rational targeting approaches for therapeutic intervention in major cancer categories. The study also revealed member-specific STAT activity and identified surprising roles for EGFR family members and sex steroid hormone receptor ESR1 in oncogenic STAT function.
JOURNAL OF CELLULAR AND MOLECULAR MEDICINE
(2022)
Article
Cell Biology
Adriana Marcelo, Ines T. Afonso, Ricardo Afonso-Reis, David V. C. Brito, Rafael G. Costa, Ana Rosa, Joao Alves-Cruzeiro, Benedita Ferreira, Carina Henriques, Rui J. Nobre, Carlos A. Matos, Luis Pereira de Almeida, Clevio Nobrega
Summary: Spinocerebellar ataxia type 2 (SCA2) is an incurable genetic neurodegenerative disorder characterized by progressive degeneration of brain regions. Mutations in the ATXN2 gene lead to toxic polyglutamine segment in ataxin-2 protein. This study suggests autophagy plays a crucial role in SCA2 pathology and targeting this pathway could be a potential treatment strategy.
CELL DEATH & DISEASE
(2021)
Article
Oncology
Qingzhu Gao, Bin Cheng, Chang Chen, Chong Lei, Xue Lin, Dan Nie, Jingjing Li, Luyi Huang, Xiaosong Li, Kai Wang, Ailong Huang, Ni Tang
Summary: This study found that GSTZ1 deficiency contributes to HCC metastasis by promoting UDP-GlcUA accumulation and stabilizing TGFβR1 mRNA to activate TGFβ/Smad signaling pathway. UGDH and UDP-GlcUA may serve as prognostic markers for HCC, and targeting UGDH could be a promising strategy for HCC therapy.
CLINICAL AND TRANSLATIONAL MEDICINE
(2022)
Article
Multidisciplinary Sciences
Linlin Li, Aidong Zhou, Yanjun Wei, Feng Liu, Peng Li, Runping Fang, Li Ma, Sicong Zhang, Longqiang Wang, Jinze Liu, Hope T. Richard, Yiwen Chen, Hengbin Wang, Suyun Huang
Summary: In this study, a previously unidentified oncogenic lncRNA called lncEPAT was discovered to mediate the integration of the dysregulated EGFR pathway with H2A deubiquitination in tumorigenesis. LncEPAT interacts with deubiquitinase USP16 and inhibits its recruitment to chromatin, thereby blocking USP16-mediated H2A deubiquitination and repressing target gene expression. Depletion of lncEPAT promotes USP16-induced cell cycle arrest and cellular senescence, and represses tumor formation in GBM cells.
Article
Biochemical Research Methods
Md Shahriare Satu, Md Imran Khan, Md Rezanur Rahman, Koushik Chandra Howlader, Shatabdi Roy, Shuvo Saha Roy, Julian M. W. Quinn, Mohammad Ali Moni
Summary: This study identified infectome, diseasome, and comorbidities between COVID-19 and cancer, highlighting the synergistic complexities of SARS-CoV-2 infections for cancer patients through gene set enrichment and semantic similarity. The bioinformatics approach revealed commonly dysregulated genes, gene ontology, and molecular pathways between SARS-CoV-2 infections and cancers, emphasizing the interconnections in terms of significant genes, GO, and pathways. Ribosome biogenesis, Wnt signaling pathway, ribosome, chemokine, and cytokine pathways were commonly deregulated in cancers and COVID-19, indicating potential avenues for further research and therapeutic interventions.
BRIEFINGS IN BIOINFORMATICS
(2021)
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)