Article
Multidisciplinary Sciences
Arthur Viode, Patrick van Zalm, Kinga K. Smolen, Benoit Fatou, David Stevenson, Meenakshi Jha, Ofer Levy, Judith Steen, Hanno Steen
Summary: We present a cost-effective, robust high-throughput-compatible method for depleting plasma, enabling comprehensive profiling of plasma with detection of >1300 proteins per run and throughput of 60 samples per day. The method has been extensively validated, processing >3000 samples with no apparent batch effect, and costs around $2.5 per sample for the depletion step.
Article
Biochemistry & Molecular Biology
Limin Jiang, Fei Guo, Jijun Tang, Hui Yu, Scott Ness, Mingrui Duan, Peng Mao, Ying-Yong Zhao, Yan Guo
Summary: Efficient annotation of alterations in binding sequences of molecular regulators can help identify novel candidates for mechanisms study and offer original therapeutic hypotheses. SBSA is a powerful tool that annotates altered binding motifs/sequences, addressing diverse genomic variants and molecular regulators. Preloaded reference genomes for various species, including SARS-Cov-2 and other organisms, are supported by SBSA.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Clinical Neurology
Dora Batia Dyne Steel, Federica Rachele Danti, Mohamed Abunada, Benjamin Kamien, Sony Malhotra, Maya Topf, Marios Kaliakatsos, Jane Valentine, Andrea Hilary Nemeth, Sandeep Jayawant, Kimberley M. Reid, Kshitij Mankad, Sniya Sudhakar, Hilla Ben-Pazi, Katy Barwick, Manju A. Kurian
Summary: Birk-Landau-Perez syndrome is a genetic disorder caused by biallelic pathogenic variants in SLC30A9, presenting with a complex movement disorder, developmental regression, oculomotor abnormalities, and renal impairment. This study describes the clinical phenotype of 8 individuals from 4 unrelated families with SLC30A9-related disease. The findings expand the known phenotype of this syndrome.
Article
Biochemical Research Methods
Wun-Yi Huang, Kun-Pin Wu
Summary: Ectodomain shedding is an important cellular regulation process involved in various biological phenomena. To address the lack of comprehensive annotation in public protein databases, we constructed the SheddomeDB database through a literature review. After user feedback and advances in research, we revised and released a new version called SheddomeDB 2023. This database contains manually verified and curated protein entries, integrated cleavage and secretome information, and features a graphical presentation and user-friendly interface.
JOURNAL OF PROTEOME RESEARCH
(2023)
Article
Multidisciplinary Sciences
Koen F. Dekkers, Sergi Sayols-Baixeras, Gabriel Baldanzi, Christoph Nowak, Ulf Hammar, Diem Nguyen, Georgios Varotsis, Louise Brunkwall, Nynne Nielsen, Aron C. Eklund, Jacob Bak Holm, H. Bjorn Nielsen, Filip Ottosson, Yi-Ting Lin, Shafqat Ahmad, Lars Lind, Johan Sundstrom, Gunnar Engstrom, J. Gustav Smith, Johan Arnlov, Marju Orho-Melander, Tove Fall
Summary: In this study, the gut microbiota was found to explain up to 58% of the variance of individual plasma metabolites. This research sheds light on the close connection between the gut microbiome and individual health, providing a basis for targeted studies on perturbation of specific metabolites and identification of potential plasma biomarkers.
NATURE COMMUNICATIONS
(2022)
Article
Hematology
E. O. Artemenko, S. I. Obydennyi, K. S. Troyanova, G. A. Novichkova, D. Y. Nechipurenko, M. A. Panteleev
Summary: In this study, we investigated the adhesive properties of circulating plasma-derived and platelet-derived microvesicles (MVs) and their potential role in thrombus growth. The results showed that both types of MVs weakly bound fibrinogen but did not stably adhere to immobilized fibrinogen. Moreover, the presence of these MVs did not significantly affect thrombus formation. Therefore, MVs present in the plasma of healthy individuals are unlikely to directly contribute to thrombus formation under arterial flow conditions.
THROMBOSIS RESEARCH
(2024)
Article
Biochemistry & Molecular Biology
David S. Wishart, Brendan Bartok, Eponine Oler, Kevin Y. H. Liang, Zachary Budinski, Mark Berjanskii, AnChi Guo, Xuan Cao, Michael Wilson
Summary: MarkerDB is a free electronic database that consolidates information on known clinical and selected pre-clinical molecular biomarkers. It provides various information related to biomarkers, and users can browse the data by disease, biomarker type, and more.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Biochemistry & Molecular Biology
Hongyan Lai, Yuchen Li, Hena Zhang, Jia Hu, Jiatao Liao, Ying Su, Qin Li, Bing Chen, Caiping Li, Zhen Wang, Yan Li, Jialei Wang, Zhiqiang Meng, Zhaohui Huang, Shenglin Huang
Summary: Extracellular vesicles contain diverse RNA species with specialized functions, and exoRBase 2.0 is an updated database that stores EV long RNAs derived from various human body fluids. This database not only integrates and compares exLR expression profiles, but also visualizes functional changes and origins of circulating EVs in different physiological and pathological conditions.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Biochemistry & Molecular Biology
Suvarna Nadendla, Rebecca Jackson, James Munro, Federica Quaglia, Balint Meszaros, Dustin Olley, Elizabeth T. Hobbs, Stephen M. Goralski, Marcus Chibucos, Christopher John Mungall, Silvio C. E. Tosatto, Ivan Erill, Michelle G. Giglio
Summary: ECO is a community resource providing an ontology of terms to capture evidence supporting biomedical annotations. Its consistent usage allows for provenance tracking, quality control, and evidence-based data mining. ECO is freely available for download and released under a CC0 1.0 Universal license.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Mathematical & Computational Biology
Min Zhao, Yining Liu, Hong Qu
Summary: This study highlights the significance of circRNA as a stable and specific biomarker for cancer diagnosis and prognosis, showing differential expression in various cancer types. By curating data across multiple platforms, the authors identified numerous circRNAs with potential impact on patient survival, providing valuable insights for cancer research and personalized medicine.
DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION
(2021)
Article
Biochemistry & Molecular Biology
Lianmin Chen, Daria Zhernakova, Alexander Kurilshikov, Sergio Andreu-Sanchez, Daoming Wang, Hannah E. Augustijn, Arnau Vich Vila, Rinse K. Weersma, Marnix H. Medema, Mihai G. Netea, Folkert Kuipers, Cisca Wijmenga, Alexandra Zhernakova, Jingyuan Fu
Summary: The study analyzed a large number of individuals to reveal the influence of an individual's genetics, diet, and gut microbiome on their plasma metabolome, and used Mendelian randomization and mediation analyses to unveil causal relationships between them.
Article
Biochemistry & Molecular Biology
Enrico Prenesti, Silvia Berto, Fabio Gosmaro, Marco Bagnati, Giorgio Bellomo
Summary: This study investigated the relationship between the total antioxidant capacity (TAC) and the concentrations of redox-active biomolecules in the human plasma of healthy and cardiopathic individuals. The results showed that around 80% of the TAC in both groups comes from endogenous compounds, with different contributions from exogenous compounds. γ-tocopherol played a different role in the chemical models developed for the two groups.
Article
Medicine, General & Internal
Annalisa Palmieri, Dorina Lauritano, Agnese Pellati, Luca Scapoli, Claudio Arcuri, Luigi Baggi, Roberto Gatto, Francesco Carinci
Summary: Oral cavity and oropharynx cancer associated with human papilloma virus infection is a serious public health problem, especially in young people continuously exposed to the virus. Studies showed newly acquired oral oncogenic HPV infections in healthy population are rare, but more research is needed to clarify HPV infection prevalence and guide prevention efforts.
JOURNAL OF CLINICAL MEDICINE
(2022)
Article
Engineering, Biomedical
Wenqin Yang, Ning Ding, Ran Luo, Qian Zhang, Zhenhua Li, Fengchun Zhao, Shuixian Zhang, Xuyang Zhang, Tengyuan Zhou, Haomiao Wang, Long Wang, Shengli Hu, Guixue Wang, Hua Feng, Rong Hu
Summary: Exosomes derived from young healthy human plasma can improve functional recovery in mice with intracerebral hemorrhage (ICH) by reducing brain injury and cell ferroptosis. MicroRNA-25-3p (miR-25-3p) in the exosomes plays a crucial role in mediating the neuroprotective effect against ferroptosis by regulating the P53/SLC7A11/GPX4 pathway. These findings provide a potential therapeutic strategy for ICH patients using plasma exosomes.
BIOACTIVE MATERIALS
(2023)
Article
Cell Biology
Valentina Siino, Ashfaq Ali, Giulia Accardi, Anna Aiello, Mattia E. Ligotti, Sergio Mosquim Junior, Giuseppina Candore, Calogero Caruso, Fredrik Levander, Sonya Vasto
Summary: The study of healthy human aging is crucial for understanding the molecular mechanisms behind aging and preventing age-related disorders. In this study, an unbiased mass spectrometry-based approach was used to investigate age-related protein changes in a healthy Sicilian plasma cohort. The findings confirmed previously known proteins associated with age and discovered novel proteins that could be a unique signature for healthy aging.
Article
Biochemistry & Molecular Biology
Zongliang Yue, Eric Zhang, Clark Xu, Sunny Khurana, Nishant Batra, Son Do Hai Deng, James J. Cimino, Jake Y. Chen
Summary: PAGER-CoV is a new web-based database that assists biomedical researchers in interpreting coronavirus-related functional genomic study results using a vast collection of PAGs. By exploring relationships between PAGs, users can gain deeper insights into the research information. This database can help researchers find molecular biology mechanisms and tailored therapeutics for treating COVID-19 patients.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Biochemistry & Molecular Biology
Abtar Mishra, Assirbad Behura, Ashish Kumar, Abhirupa Ghosh, Lincoln Naik, Shradha Mawatwal, Subhashree Subhasmita Mohanty, Amit Mishra, Sudipto Saha, Sujit K. Bhutia, Ramandeep Singh, Rohan Dhiman
Summary: The study revealed that soybean lectin (SBL) induced autophagy exerts an anti-mycobacterial effect through a P2RX7-NF-kappa B dependent pathway generating ROS. These findings provide important insights for developing new therapeutic interventions.
BIOCHIMICA ET BIOPHYSICA ACTA-GENERAL SUBJECTS
(2021)
Article
Medical Informatics
Thanh Nguyen, Tongbin Zhang, Geoffrey Fox, Sisi Zeng, Ni Cao, Chuandi Pan, Jake Y. Chen
Summary: This study demonstrated the use of clinical information and electronic medical records to support precision medicine research and clinical decision-making on complex diseases. Through integration of public omic databases and advanced machine learning techniques, the study successfully addressed issues such as patient stratification, significant associations between clinical information and diseases, and potential linkages between clinical information and genomic data.
BMC MEDICAL INFORMATICS AND DECISION MAKING
(2021)
Article
Biochemistry & Molecular Biology
Moumita Bhowmik, Moumita Biswas Sarkar, Rajat Kanti Sarkar, Angira Dasgupta, Sudipto Saha, Kuladip Jana, Gaurab Sircar, Swati Gupta Bhattacharya
Summary: Papaya allergen Cari p 2 is identified as a new allergen that can induce allergic reactions through fruit consumption and respiratory hazards through pollen exposure. The study found that rCari p 2 displayed IgE-reactivity with the majority of papaya allergic individuals and showed allergenic activity.
MOLECULAR IMMUNOLOGY
(2021)
Article
Engineering, Biomedical
Sudipto Bhattacharjee, Banani Saha, Parthasarathi Bhattacharyya, Sudipto Saha
Summary: LHSPred is a web-based tool that evaluates CT scans and predicts the risk of pneumonia without radiologist intervention. It can help in early assessment of lung health severity and monitoring the post-COVID lung health for recovered patients.
BIOMEDICAL SIGNAL PROCESSING AND CONTROL
(2022)
Article
Multidisciplinary Sciences
Deepika Chaudhary, Avantika Singh, Mardiana Marzuki, Abhirupa Ghosh, Saqib Kidwai, Tannu Priya Gosain, Kiran Chawla, Sonu Kumar Gupta, Nisheeth Agarwal, Sudipto Saha, Yashwant Kumar, Krishan Gopal Thakur, Amit Singhal, Ramandeep Singh
Summary: This study identified small molecule inhibitors targeting homoserine acetyl transferase from Mycobacterium tuberculosis, which were effective in inhibiting the growth of drug-resistant bacteria. These inhibitors have the potential to be developed into new broad-spectrum antibacterial agents for treating drug-resistant bacterial infections.
SCIENTIFIC REPORTS
(2022)
Article
Microbiology
Amar Chandra Mahatha, Srijon Kaushik Banerjee, Abhirupa Ghosh, Suruchi Lata, Sudipto Saha, Joyoti Basu, Manikuntala Kundu
Summary: This study reveals the important role of RegX3 in the adaptation of Mycobacterium tuberculosis to hypoxia. Gene expression analysis and validation experiments confirm the regulation of a group of hypoxia-associated genes by RegX3, and identify the involvement of the RegX3-Rv0195 and RegX3-Rv3334 axis in the response of M. tuberculosis to low oxygen conditions.
Article
Computer Science, Interdisciplinary Applications
Sudipto Bhattacharjee, Banani Saha, Parthasarathi Bhattacharyya, Sudipto Saha
Summary: This study developed machine learning models to classify obstructive and non-obstructive pulmonary diseases based on spirometry data, achieving good accuracy. The results suggest that these machine learning models could serve as early prediction tools for clinicians and patients.
JOURNAL OF COMPUTATIONAL SCIENCE
(2022)
Article
Microbiology
Abhirupa Ghosh, Sudipto Saha
Summary: In this study, the taxonomic and functional components of the sputum microbiome in different airway diseases were studied. Specific markers were identified for each airway disease, as well as microbial features like specific gene families, pathways, and metabolites. These findings can contribute to improved diagnosis and therapy.
JOURNAL OF MEDICAL MICROBIOLOGY
(2022)
Article
Genetics & Heredity
Deepika Gaur, Navinder Kumar, Abhirupa Ghosh, Prashant Singh, Pradeep Kumar, Jyoti Guleria, Satinderdeep Kaur, Nikhil Malik, Sudipto Saha, Thomas Nystrom, Deepak Sharma
Summary: Hsp70 plays a critical role in the Hsp90 chaperoning pathway. Novel mutations in the nucleotide-binding domain of yeast Ssa1 Hsp70 have been identified, which adversely affect Hsp90 client maturation. These mutations result in better binding with Ydj1 and poor growth support in the absence of Sti1. Furthermore, downregulation of pathways involved in signaling, signal transduction, and protein phosphorylation was observed in cells expressing the mutant Hsp70. The study shows that Ydj1 interaction at the nucleotide-binding domain of Ssa1 Hsp70 influences Hsp90 function.
Article
Oncology
Subhadip Pati, Sumon Mukherjee, Saikat Dutta, Aharna Guin, Dia Roy, Sayantan Bose, Silpita Paul, Sudipto Saha, Sankar Bhattacharyya, Pratyush Datta, Jayati Chakraborty, Diptendra K. Sarkar, Gaurisankar Sa
Summary: B cells play a vital role in humoral immunity by producing antigen-specific antibodies to eliminate pathogens. However, patients with breast cancer have low levels of serum IgG despite an increase in B cell numbers. Through high-dimensional flow cytometry analysis, a tumor-specific subset of B regulatory (Breg) cells expressing CD19+CD24hiCD38hi IL10 was identified. The identification and isolation of viable Breg cells were hindered by the intracellular nature of IL10 and the high expression of CD24 and CD38. Transcriptomic analysis revealed CD39-negativity as a sorting-friendly surface marker for tumor-associated Breg cells. The identified CD19+CD39-IL10+ B cell population exhibited suppressive properties, limiting T helper cell proliferation, cytokine production, T effector cell survival, and promoting regulatory T cell generation. These tumor-associated Breg cells also restricted T follicular helper cell expansion and IL21 secretion, impairing germinal transcript formation and class-switch recombination involved in antibody production. This abnormality in isotype switching hindered B cell differentiation into memory B cells and plasma B cells, leading to weakened IgG-mediated antibody responses in cancer patients.
CANCER IMMUNOLOGY RESEARCH
(2023)
Article
Genetics & Heredity
N. Saran, Sudipto Saha
Summary: Mycobacteria develops resistance to fluoroquinolones antibiotics through various mechanisms, and the PRP MfpA contributes to intrinsic resistance. The distribution and arrangement of mfp conservon in Mycobacteriaceae were surveyed, and its promoter elements were predicted. The mfpA gene was observed in different forms, and the first 158 bases of the intergenic region showed the highest promoter activity.
Review
Neurosciences
Radomir M. Slominski, Chander Raman, Jake Y. Chen, Andrzej T. Slominski
Summary: During oncogenesis, tumors can affect local and systemic homeostasis by producing cytokines, immune mediators, neurotransmitters, and other substances. They can control the central neuroendocrine and immune systems to promote their own growth and expansion.
TRENDS IN NEUROSCIENCES
(2023)
Article
Mathematical & Computational Biology
Shazia Firdous, Abhirupa Ghosh, Sudipto Saha
Summary: Cancer stem cells play vital roles in cancer recurrence, metastasis, and drug resistance. BCSCdb is a database collecting information on CSC biomarkers, including various types of markers and clinical biomarkers.
DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION
(2022)
Article
Genetics & Heredity
Thanh Minh Nguyen, Jacob John Jeevan, Nuo Xu, Jake Y. Chen
Summary: The Polar Gini Curve is a method for characterizing cluster markers by analyzing single-cell RNA sequencing data, which helps users understand the shape and density distribution of cells in a particular cluster. By combining gene expression and spatial information, it can detect uniformity patterns within clustered cells and identify biomarkers with consistent gene expression patterns across clusters.
GENOMICS PROTEOMICS & BIOINFORMATICS
(2021)