Article
Environmental Sciences
Shuangjian Qin, Boru Li, Runbing Li, Ying Cai, Kai Zheng, Haiyan Huang, Fang Xiao, Ming Zeng, Xinyun Xu
Summary: Proteomics and bioinformatics were used to investigate the differential expression of proteins induced by PM2.5 in hepatocytes. The study identified key proteins involved in metal ion response and lipoprotein metabolism. The findings suggest potential biomarkers for PM2.5-induced carcinogenesis.
ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY
(2021)
Article
Environmental Sciences
Boru Li, Shuangjian Qin, Ying Cai, Kai Zheng, Bingyu Wang, Runbing Li, Haiyan Huang, Ming Zeng, Fang Xiao, Xinyun Xu
Summary: The study used proteomics and bioinformatics to screen the differentially expressed proteins (DEPs) in HK-2 cells exposed to PM2.5 from Shenzhen and Taiyuan. Significant changes in DEPs expression were observed after exposure to PM2.5 from both cities, indicating a potential correlation between DEPs differences and PM2.5 components in Shenzhen and Taiyuan.
ENVIRONMENTAL TOXICOLOGY AND PHARMACOLOGY
(2021)
Article
Engineering, Chemical
Shu Zhang, Qi Ge, Liang Chen, Keping Chen
Summary: The study analyzed the potential synergistic mechanism of Mulberry Leaf and Radix Astragali in treating diabetes, identifying common genes and proteins and speculating on their main pathways of action in maintaining glucose homeostasis by affecting various biological processes.
Article
Biochemical Research Methods
Shannon P. Smyth, Brett Nixon, Amanda L. Anderson, Heather C. Murray, Jacinta H. Martin, Lily A. MacDougall, Sarah A. Robertson, David A. Skerrett-Byrne, John E. Schjenken
Summary: This study reports a new method for preparing seminal vesicle fluid (SVF) and identifies 126 proteins in SVF, including 83 previously undetected proteins. The most abundant proteins in SVF belong to the seminal vesicle secretory protein family. Functional analysis reveals that inflammation and formation of the vaginal plug are the most prominent biological processes associated with SVF proteins. Other processes include modulation of sperm function and regulation of the female reproductive tract immune environment. These findings provide a robust methodological framework for future SVF studies and identify novel proteins with potential to influence both male and female reproductive physiology.
Article
Rheumatology
Jun Inamo
Summary: This study investigated the relationship between different types of autoantibodies and gene expression profiles in skin lesions of patients with Systemic Sclerosis (SSc), identifying specific dysregulated pathways associated with each autoantibody type. By analyzing gene expression data, the study revealed potential new therapeutic targets for SSc based on specific autoantibody profiles.
Article
Medicine, General & Internal
Guan Lin, Zhang Xinhe, Tian Haoyu, Li Yiling
Summary: This study identified aberrantly methylated-differentially expressed genes and related pathways involved in cholangiocarcinoma (CCA). The analysis of mRNA expression and methylation profiling data revealed a number of genes that showed differential expression and methylation in CCA. Functional enrichment analysis and protein-protein interaction network analysis identified several pathways and hub genes associated with these genes. The findings of this study provide potential biomarkers for the accurate diagnosis and treatment of CCA.
Article
Toxicology
Kai Zheng, Ying Cai, Yuandi Lei, Yanping Liu, Zhanbing Sun, Ye Wang, Xinyun Xu, Zhaohui Zhang
Summary: By analyzing the proteomic data of Sprague Dawley rats exposed to beryllium sulfate, differentially expressed proteins were identified in lung tissue and serum, with some proteins like Akt1, Prpf19, Cct2, and Rpl18 showing potential as biomarkers for lung cancer and regulators of cell cycle and apoptosis.
TOXICOLOGY RESEARCH
(2021)
Article
Veterinary Sciences
Eimear M. Donnellan, Jean-Philippe Perrier, Kate Keogh, Miriam Stiavnicka, Caitriona M. Collins, Elaine M. Dunleavy, Eli Sellem, Naomi C. Bernecic, Patrick Lonergan, David A. Kenny, Sean Fair
Summary: This study identified potential biomarkers for bull fertility by characterizing the spermatozoa transcriptome of high and low fertility bulls. The differentially expressed genes and miRNAs were related to embryonic development and gene expression regulation, providing new insights for assessing semen quality and bull fertility improvement.
FRONTIERS IN VETERINARY SCIENCE
(2022)
Article
Biology
Meiyu Duan, Yueying Wang, Ya Qiao, Yangyang Wang, Xingyuan Pan, Zhuyu Hu, Yanyue Ran, Xian Fu, Yusi Fan, Lan Huang, Fengfeng Zhou
Summary: The transcriptome is a comprehensive reflection of gene expression in a sample. This study proposes a novel approach to understanding the regulatory relationships between transcription factors (TFs) and their target genes (mRNAs) by quantitatively analyzing the differences in their expression levels. By using a multi-input multi-output regression model, this study explores the quantitative transcription regulation relationships of metabolism-related genes. The findings suggest that certain genes can exhibit differential regulation patterns even when their expression levels do not differ significantly, and these "dark biomarkers" may have important implications for disease detection and classification.
COMPUTERS IN BIOLOGY AND MEDICINE
(2022)
Article
Biochemistry & Molecular Biology
Fernando Moreto, Artur J. T. Ferron, Fabiane V. Francisqueti-Ferron, Alfonsina D'Amato, Jessica L. Garcia, Mariane R. Costa, Carol Cristina V. A. Silva, Alessandra Altomare, Camila Renata Correa, Giancarlo Aldini, Ana Lucia A. Ferreira
Summary: This study revealed the impact of NASH on rats, showing altered biological processes and functions related to lipid metabolism, oxidative stress response, and other pathways.
JOURNAL OF BIOCHEMICAL AND MOLECULAR TOXICOLOGY
(2021)
Article
Andrology
Jing Ma, Ruiyu Han, Bo Sun, Jiajie Lin, Peipei Deng, Shusong Wang, Shaoguang Sun
Summary: This study identified 39 differentially expressed miRNAs in testicular tissues of rats with hyperuricaemia-induced male infertility. These miRNAs could shed light on the mechanism of hyperuricaemia-induced male infertility.
Article
Agriculture, Dairy & Animal Science
Chunhuan Ren, Zhipeng Sun, Yale Chen, Jiahong Chen, Shijia Wang, Qingqing Liu, Penghui Wang, Xiao Cheng, Zijun Zhang, Qiangjun Wang
Summary: Sperm cryopreservation is a key procedure in artificial insemination technology, and the survival rate of frozen sperm has been improved with the development of cryopreservation technology. This study aimed to identify biomarkers associated with sperm freezing tolerance in rams at the proteome level. The results revealed proteins and pathways associated with high and low cryopreservation recovery ratios, providing insights into the molecular mechanisms of sperm resistance to low temperatures and potential directions for cryopreservation of high-quality semen.
Review
Andrology
Manesh Kumar Panner Selvam, Saradha Baskaran, Ashok Agarwal, Ralf Henkel
Summary: Proteomics and bioinformatics analysis can reveal the molecular etiologies associated with poor semen quality in varicocele patients, particularly mitochondrial dysfunction. Through proteomic studies, potential reproductive biomarkers can be identified in varicocele patients, offering possibilities for the development of noninvasive diagnostic and therapeutic strategies.
Article
Agriculture, Dairy & Animal Science
Ivan Cunha Bustamante-Filho, Manoela Pasini, Arlindo Alencar Moura
Summary: With the development of proteomics technologies, our understanding of the roles of protein composition in semen and their potential as biomarkers has expanded greatly.
ANIMAL REPRODUCTION SCIENCE
(2022)
Article
Oncology
Wesley Ladeira Caputo, Milena Cremer de Souza, Caroline Rodrigues Basso, Valber de Albuquerque Pedrosa, Fabio Rodrigues Ferreira Seiva
Summary: This study provides a comprehensive analysis of differentially expressed genes in hepatocellular carcinoma (HCC), identifying potential therapeutic targets and opportunities for drug repurposing.
Article
Environmental Sciences
Gayatri Mohanty, Soumya Ranjan Jena, Sujata Kar, Luna Samanta
Summary: HSPA2 is a testis-specific molecular chaperone that plays a key role in spermatogenesis. Computational analysis revealed 18 deleterious nsSNPs in the HSPA2 gene, suggesting its potential impact on reproductive outcomes. Additionally, gene-gene interaction study identified a close association with antioxidant enzyme SOD1, providing insight into the oxidative scavenging regulatory mechanism in RPL patients.
ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH
(2022)
Article
Public, Environmental & Occupational Health
Laila A. Damiati, Sami Bahlas, Ahmed Aljohaney, Yasser Bawazir, Mohammad Mustafa, Iuliana Denetiu, Peter N. Pushparaj
Summary: This study examined the differential regulation of clinical, hematologic, and inflammatory biomarkers in COVID-19 patients of different age groups. Laboratory parameters such as GGT, creatinine, BUN, CRP, procalcitonin, ferritin, and D-dimer were found to be differentially regulated, potentially serving as clinical predictors of disease severity in the population. Age was identified as an important factor influencing the severity of COVID-19.
JOURNAL OF INFECTION AND PUBLIC HEALTH
(2022)
Article
Pediatrics
Muhammad Imran Naseer, Peter Natesan Pushparaj, Angham Abdulrahman Abdulkareem, Osama Y. Muthaffar
Summary: This case report study presents two pediatric patients with biotinidase deficiency and clinical features of neuromyelitis optica. The intake of biotin resulted in clinical improvement, highlighting that biotinidase deficiency is a treatable cause of neuromyelitis optica.
FRONTIERS IN PEDIATRICS
(2022)
Review
Orthopedics
Ursule Kalvaityte, Csaba Matta, Eiva Bernotiene, Peter Natesan Pushparaj, Ata M. Kiapour, Ali Mobasheri
Summary: This article reviews the biological roles of clusterin in cartilage, chondrocytes, and other synovial joint tissues, and discusses its potential as a biomarker in synovial and systemic fluids of patients with rheumatoid arthritis (RA) or osteoarthritis (OA). Clusterin has cytoprotective functions and may serve as a biomarker of early repair responses in OA.
JOURNAL OF ORTHOPAEDIC TRANSLATION
(2022)
Article
Biochemistry & Molecular Biology
Soumya Ranjan Jena, Ganeswar Dalei, Subhraseema Das, Jasmine Nayak, Manoranjan Pradhan, Luna Samanta
Summary: This study fabricated biomimetic bioscaffolds using dialdehyde alginate and xanthan gum, which displayed an ideal porous network structure and exhibited good performance, promoting cell adhesion and proliferation, and demonstrating antibacterial activity. The effectiveness of these scaffolds in tissue engineering applications was confirmed through experimental results.
INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES
(2022)
Article
Fisheries
Bibekananda Panda, Gopi Krishna Ogirala, Sanjeet Manna, Dhananjay Kumar Verma, Luna Samanta, Padmanav Routray
Summary: This study assessed the seasonal changes in germ cells and maturation of Labeo rohita and Oreochromis niloticus. It revealed different spawning behaviors and germ cell proliferation patterns in the two species. The study provided insights into the reproductive status of fish in response to seasonal climate changes and proposed comparative models for germ cell proliferation and maturation. Scanning electron microscope analysis also showed different developmental stages of germ cells in different seasons.
TURKISH JOURNAL OF FISHERIES AND AQUATIC SCIENCES
(2022)
Article
Immunology
Soumya Ranjan Jena, Jasmine Nayak, Sugandh Kumar, Sujata Kar, Luna Samanta
Summary: Recent evidence suggests that male factors may be involved in recurrent pregnancy loss (RPL), as paternally expressed genes are predominant in the placenta. In this study, proteome profiling was carried out on seminal extracellular vesicles (SEVs), extracellular vesicle free seminal plasma (EVF-SP), and spermatozoa from RPL patients and fertile donors. The differentially expressed proteins in these samples were found to be associated with inflammatory response, immune cell signaling, and apoptosis. This suggests that altered cytokine levels in seminal components may contribute to impaired immune response and improper placental development in RPL.
AMERICAN JOURNAL OF REPRODUCTIVE IMMUNOLOGY
(2023)
Article
Environmental Sciences
Falguni Panda, Samar Gourav Pati, Taslima Nasim Anwar, Luna Samanta, Biswaranjan Paital
Summary: Studies on oxidative stress physiology on molluscs to monitor the aquatic environment, influenced by pollutants and stressors are very limited in general and in Indian apple snails, P. globosa in particular. The main focus of the present study was to establish the baseline data on a redox regulatory system in P. globosa sampled across the Indian subcontinent. Snails were sampled from different zones of India in three seasons (rainy, summer and winter) and the redox regulatory system (levels of antioxidant enzyme activities and small redox regulatory molecules) and oxidative stress indicator (lipid peroxidation) were analyzed. The observed elevated lipid peroxidation level in the summer season accompanied with elevated pH, salinity and temperature indicates induction of stress. In the summer season, the activities of superoxide dismutase (SOD), catalase (CAT) and glutathione reductase (GR) enzymes were augmented, whereas the level of the free -SH group and the activities of glutathione peroxidase (GPx) and glutathione-S-transferase (GST) were found to be increased. Similarly, correlation analysis between the antioxidant system and aquatic parameters revealed that SOD, CAT and GR were influenced by pH as well as salinity, whereas CAT was strongly correlated with temperature. Collectively, our data indicate the use of P. globosa as a model organism to monitor and access the freshwater environment by determining the redox regulatory status of this animal.
Article
Chemistry, Multidisciplinary
Subhrajit Mohanty, Binita Tirkey, Soumya Ranjan Jena, Luna Samanta, Usharani Subuddhi
Summary: Despite the medicinal benefits of curcumin, its practical applications are limited due to poor solubility and bioavailability. Biosurfactant-based micellar systems have emerged as a promising method for enhancing curcumin's efficacy. This study investigates the effect of different steroidal surfactants on curcumin's photophysical properties and its potential as a drug carrier. The results show that the surfactant's structure significantly influences curcumin's photophysics, solubility, stability, and cytotoxicity. Among the tested surfactants, CHAPS, a zwitterionic derivative of cholic acid, offers the best solubility, stability, and enhanced bioavailability for curcumin. Thus, CHAPS-based colloids hold promise as effective drug carriers for curcumin.
Article
Medicine, General & Internal
Peter Natesan Pushparaj, Mahmood Rasool, Muhammad Imran Naseer, Kalamegam Gauthaman
Summary: In this study, bleomycin was examined for its cellular, molecular, and toxicological mechanisms using next-generation knowledge discovery (NGKD) tools. By analyzing gene expression data and using iPathwayGuide, differentially regulated signaling pathways, biological processes, cellular and molecular functions, and upstream regulators induced by bleomycin were identified.
PAKISTAN JOURNAL OF MEDICAL SCIENCES
(2023)
Article
Biochemistry & Molecular Biology
Roland Takacs, Judit Vago, Szilard Poliska, Peter Natesan Pushparaj, Laszlo Ducza, Patrik Kovacs, Eun-Jung Jin, Richard Barrett-Jolley, Roza Zakany, Csaba Matta
Summary: Chondrogenesis is a complex process involving the differentiation of cartilage progenitor cells. In this study, the researchers used RNA sequencing to investigate the gene expression patterns during cartilage formation in micromass cultures of embryonic limb bud-derived progenitors. They identified differentially expressed genes and confirmed their involvement in chondrogenic differentiation. Transient gene silencing experiments revealed the role of ATOH8 and EBF1 in regulating key osteochondrogenic marker genes during chondrogenesis. These findings provide a comprehensive understanding of the molecular mechanism of chondrogenesis and offer new insights for cartilage tissue engineering.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Immunology
Patrik Kovacs, Peter Natesan Pushparaj, Roland Takacs, Ali Mobasheri, Csaba Matta
Summary: This study mapped and analyzed the network of clusterin in osteoarthritis (OA) using STRING database and Cytoscape. Results showed that the clusterin network predominantly involved intracellular chaperones, aggregate-forming proteins, apoptosis regulators, and complement proteins. Additional interacting partners, including serum proteins, apolipoproteins, and heat shock proteins, were identified. These findings contribute to the identification of potential biomarker panels for prognosis and diagnosis of OA.
FRONTIERS IN IMMUNOLOGY
(2023)
Correction
Oncology
Gauthaman Kalamegam, Khalid Hussein Wali Sait, Farid Ahmed, Roaa Kadam, Peter Natesan Pushparaj, Nisreen Anfinan, Mahmood Rasool, Mohammad Sarwar Jamal, Muhammed Abu-Elmagd, Mohammed Al-Qahtani
FRONTIERS IN ONCOLOGY
(2023)
Article
Mathematical & Computational Biology
Hussein Algahtani, Bader Shirah, Angham Abdulrhman Abdulkareem, Fehmida Bibi, Peter Natesan Pushparaj, Muhammad Imran Naseer
Summary: Leber hereditary optic neuropathy (LHON) is a rare mitochondrial disorder that primarily affects young male adults. It is characterized by progressive bilateral vision loss and has distinguishing features from other optic neuritis-causing diseases.
Article
Biochemistry & Molecular Biology
Etimad Huwait, Nouf Al-Gharawi, Maryam A. Al-Ghamdi, Mamdooh Gari, Alexandre Prola, Peter Natesan Pushparaj, Gauthaman Kalamegam
Summary: This study evaluated the effects of Thymoquinone (TQ) on key pathogenic stages of atherosclerosis and identified potential molecular targets and signaling mechanisms using in-vitro experiments and in-silico analysis. The results suggest that TQ has anti-inflammatory effects and may be a potential nutraceutical candidate for the prevention and treatment of atherosclerosis.
CURRENT ISSUES IN MOLECULAR BIOLOGY
(2022)