Article
Physiology
Xiaoting Yao, Tian Jing, Tianxing Wang, Chenxin Gu, Xi Chen, Fengqiang Chen, Hao Feng, Huiying Zhao, Dekun Chen, Wentao Ma
Summary: By integrating two microarray datasets, this study identified 38 common DEGs in PAH, highlighting hub genes, TFs, and miRNAs. Protein-drug interactions revealed potential compounds impacting PAH candidate biomolecules, with molecular signatures predominantly localized in extracellular and nuclear areas. These lung tissue-derived molecular signatures could offer novel insights into the mechanisms of PAH and aid in the development of diagnostic and therapeutic strategies.
FRONTIERS IN PHYSIOLOGY
(2021)
Article
Plant Sciences
Islam El-Sharkawy, Ahmed Ismail, Ahmed Darwish, Walid El Kayal, Jayasankar Subramanian, Sherif M. Sherif
Summary: This study identified a GA signaling gene PslSLY1 in Japanese plum, which plays a crucial role in fruit development and plant growth regulation; PslSLY1 interacts with downstream GA signaling components, promoting overall plant growth. These findings provide important insights into the growth mechanism and GA signaling network in commercially important perennial crops.
JOURNAL OF EXPERIMENTAL BOTANY
(2021)
Article
Microbiology
Ine Storaker Myrbraten, Gro Anita Stamsas, Helena Chan, Danae Morales Angeles, Tiril Mathiesen Knutsen, Zhian Salehian, Volha Shapaval, Daniel Straume, Morten Kjos
Summary: Cell division and cell wall synthesis in Staphylococcus aureus are complex processes that require the coordination of multiple proteins. In this study, a protein called SmdA was found to play a critical role in cell division. Proper levels of SmdA were necessary for septum formation and cell splitting. SmdA also interacted with other proteins involved in cell division and cell wall synthesis, and affected susceptibility to cell wall targeting antibiotics.
Article
Biochemical Research Methods
Sadaf Dadashkhan, Seyed Amir Mirmotalebisohi, Hossein Poursheykhi, Marzieh Sameni, Sepideh Ghani, Maryam Abbasi, Sima Kalantari, Hakimeh Zali
Summary: This study utilized systems biology and high-throughput technologies to analyze the molecular components of multiple sclerosis (MS) pathophysiology. By combining data from multiple omics sources, potential biomarkers and therapeutic targets were identified, along with repurposed drugs for MS treatment. The study identified differentially expressed genes associated with MS using GEO microarray datasets and MS proteomics data, and constructed protein-protein interaction networks to investigate crucial molecules. Furthermore, a drug-gene interaction network was created to propose medications. The findings provide insights into the pathophysiology of MS and suggest potential targets for treatment.
JOURNAL OF PROTEOMICS
(2023)
Article
Biochemical Research Methods
Taner Arslan, Yanbo Pan, Georgios Mermelekas, Mattias Vesterlund, Lukas M. Orre, Janne Lehtio
Summary: The subcellular localization of a protein is crucial for understanding its functions. In this study, a mass spectrometry- and bioinformatics-based pipeline was developed to generate a comprehensive resource for protein subcellular localization in multiple human cancer cell lines. The protocol includes a detailed wet-lab procedure, quantitative MS-data analysis, machine learning-based classification, and visualization of the output. The pipeline was evaluated using different peptide pre-fractionation approaches and proved to be straightforward and robust, with the entire process being completed within 1-2 weeks.
Article
Biochemistry & Molecular Biology
Ella Doron-Mandel, Indrek Koppel, Ofri Abraham, Ida Rishal, Terika P. Smith, Courtney N. Buchanan, Pabitra K. Sahoo, Jan Kadlec, Juan A. Oses-Prieto, Riki Kawaguchi, Stefanie Alber, Eitan Erez Zahavi, Pierluigi Di Matteo, Agostina Di Pizio, Didi-Andreas Song, Nataliya Okladnikov, Dalia Gordon, Shifra Ben-Dor, Rebecca Haffner-Krausz, Giovanni Coppola, Alma L. Burlingame, Pavel Jungwirth, Jeffery L. Twiss, Mike Fainzilber
Summary: Nucleolin is a multifunctional RNA Binding Protein (RBP) that can be found in various subcellular locations thanks to its glycine arginine rich (GAR) domain. This domain is responsible for driving subcellular localization through protein-protein interactions and mediating interactions with the plasma membrane. Additionally, the GAR domain plays a crucial role in nucleolin transport to axons and growth control of sensory neurons.
Article
Biotechnology & Applied Microbiology
Chongyang Ma, Kai Yan, Zisong Wang, Qiuyun Zhang, Lianyin Gao, Tian Xu, Jiayang Sai, Fafeng Cheng, Yuqiong Du
Summary: The study revealed a complex relationship between hypertension and NAFLD, identifying shared genes and potential mechanisms. The genes were associated with inflammatory, metabolic, and endocrine signals, suggesting a multi-target therapeutic strategy for future clinical research.
Article
Plant Sciences
Mengdi Zhang, Shuai Hu, Fang Yi, Yanli Gao, Dongmei Zhu, Yizhu Wang, Yi Cai, Dan Hou, Xinchun Lin, Jinbo Shen
Summary: A protoplast transient gene expression system was established in moso bamboo, generating multicolored fluorescent markers for analyzing subcellular localization and functional study of unknown proteins. This system will promote rapid progress in diverse areas of research in bamboo plants.
FRONTIERS IN PLANT SCIENCE
(2021)
Review
Engineering, Biomedical
Hanmei Li, Yao Wang, Qi Tang, Dan Yin, Chuane Tang, En He, Liang Zou, Qiang Peng
Summary: The formation of a protein corona (PC) on nanoparticles (NPs) in the blood can influence their behavior. Strategies to reduce PC formation or exploit it to enhance NP functions are discussed in this review. Studying protein-NP interactions can provide insights into their clinical activity in health and disease.
ACTA BIOMATERIALIA
(2021)
Article
Computer Science, Artificial Intelligence
Peizhen Bai, Filip Miljkovic, Bino John, Haiping Lu
Summary: DrugBAN is a deep bilinear attention network framework that explicitly learns the local interactions between drugs and targets, and adapts to out-of-distribution data. It achieves the best performance on three benchmark datasets compared to five state-of-the-art baseline models. The visualized bilinear attention map provides interpretable insights from prediction results.
NATURE MACHINE INTELLIGENCE
(2023)
Article
Biochemistry & Molecular Biology
Asker Y. Khapchaev, D. Martin Watterson, Vladimir P. Shirinsky
Summary: The subcellular localization of S-MLCK can be altered by phosphorylation of specific residues within its actin-binding domain, providing insight into its involvement in various cellular processes.
BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH
(2021)
Article
Biochemistry & Molecular Biology
Jinlong Chang, Ze Song, Shoupeng Wei, Yunxia Zhou, Jun Ju, Peijia Yao, Youheng Jiang, Hui Jin, Xinjin Chi, Ningning Li
Summary: Aberrant expression of GPR158 is linked to various central nervous system diseases, but the underlying mechanism is unclear. Researchers generated a GPR158 tagged mouse model and found that it is mainly expressed in neurons. Protein interaction analysis and RNA sequencing revealed potential interacting proteins and their involvement in chloride channel complex and synaptic vesicle membrane composition. This model will be valuable for future studies related to GPR158.
Article
Cell Biology
Qin-Li Liang, Lan-Bi Nie, Ting-Ting Li, Hany M. Elsheikha, Li-Xiu Sun, Zhi-Wei Zhang, Dan-Yu Zhao, Xing-Quan Zhu, Jin-Lei Wang
Summary: This study investigated the subcellular localization of 17 PSPs in the apicomplexan protozoan Toxoplasma gondii and examined their role in the pathogenicity of the parasite. The results showed that some PSPs play a crucial role in the invasion and infection process of T. gondii.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2022)
Article
Biochemical Research Methods
Qiao Liu, Bohyun Lee, Lei Xie
Summary: This study constructed a disease-centric microbial interaction network and developed an accurate algorithm for predicting the effects of microbes on human health and diseases. The study found potential drug targets in microbial proteins and demonstrated that pathogenic microbes have specific drug targets in periplasmic and cellular outer membrane proteins. This research opens a new avenue for the small-molecule drug discovery of the microbiome.
BMC BIOINFORMATICS
(2022)
Article
Biotechnology & Applied Microbiology
Diogo Tavares, Jan R. van der Meer
Summary: Periplasmic binding proteins are promising for designing sensor proteins with new recognition specificities, but computational design of new ligand-binding properties ignores the more general properties of these proteins. This study focused on the subcellular localization of ribose-binding protein (RbsB) in Escherichia coli and found that designed variants had defects in proper localization, which could impair sensor signaling.
APPLIED AND ENVIRONMENTAL MICROBIOLOGY
(2022)
Article
Cell Biology
Shalini Elangovan, Thomas J. Borody, R. M. Damian Holsinger
Summary: Alzheimer's disease (AD) is a progressive neurodegenerative disorder with no known treatment or cure, but fecal microbiota transplantation (FMT), a widely accepted treatment for other diseases, has shown potential as an AD therapeutic. In a mouse model, a 7-day FMT treatment demonstrated plaque-reducing and behavior-modifying effects in AD mice, with donor age affecting treatment efficacy. Further investigation in human trials is needed.
Article
Medicine, General & Internal
Md. Khabir Uddin Ahamed, Md Manowarul Islam, Md. Ashraf Uddin, Arnisha Akhter, Uzzal Kumar Acharjee, Bikash Kumar Paul, Mohammad Ali Moni
Summary: COVID-19 is a severe respiratory contagious disease that has spread globally. This article proposes a deep learning-based model to detect COVID-19 cases using chest X-ray images dataset. The accuracy of the model can assist radiologists in rapid detection and diagnosis of COVID-19 cases.
Article
Computer Science, Information Systems
Md. Alamin Talukder, Khondokar Fida Hasan, Md. Manowarul Islam, Md. Ashraf Uddin, Arnisha Akhter, Mohammand Abu Yousuf, Fares Alharbi, Mohammad Ali Moni
Summary: Network intrusion detection systems (NIDSs) are vital for computer network security, with anomaly-based automated detection mechanisms outperforming others significantly. However, handling large amounts of data remains a challenge for anomaly-based NIDS development. In this research, we propose a hybrid model that combines machine learning and deep learning to enhance detection rates and ensure dependability. Our method employs SMOTE for data balancing and XGBoost for feature selection, resulting in excellent performance on KDDCUP'99 and CIC-MalMem-2022 datasets, achieving accuracy of 99.99% and 100% respectively, without overfitting or Type-1 and Type-2 issues.
JOURNAL OF INFORMATION SECURITY AND APPLICATIONS
(2023)
Article
Chemistry, Medicinal
Quy-Susan Huynh, R. M. Damian Holsinger
Summary: Neurotrophic factors alone are not enough for sustained neural regeneration in neural tissue engineering scaffolds. We attempted to induce neuroblastoma cells to express trophic factors by electrical stimulation. Electrically stimulating human SH-SY5Y neuroblastoma cells cultured on electrospun nanofibers resulted in changes in nuclear morphology and brain-derived neurotrophic factor (BDNF) expression. Fiber orientation played a significant role in both nuclear deformation and BDNF expression.
Article
Biotechnology & Applied Microbiology
Sadia Afrin Bristy, Md Arju Hossain, Md Imran Hasan, S. M. Hasan Mahmud, Mohammad Ali Moni, Md Habibur Rahman
Summary: Moraxella catarrhalis is a unique bacterium in humans, acting as a symbiotic organism while also causing mucosal infections. It is a major contributor to acute middle ear infections in children, and its resistance to multiple drugs poses a challenge in treatment. This study used a computational approach to understand the processes leading to antibiotic resistance in M. catarrhalis by analyzing 12 strains from the NCBI-Genome database. The study found 74 antimicrobial-resistant genes and explored their interaction network, revealing their involvement in antibiotic inactivation, target replacement, alteration, and efflux pump processes. Several genes, such as rpoB, atpA, fusA, groEL, and rpoL, were identified as potential therapeutic targets for novel medications. Overall, this study provides valuable insights into the antimicrobial resistance system of M. catarrhalis.
BRIEFINGS IN FUNCTIONAL GENOMICS
(2023)
Review
Biochemistry & Molecular Biology
Fatima Javed Mirza, Saadia Zahid, R. M. Damian Holsinger
Summary: Carnosic acid is a diterpenoid found in plants of the Lamiaceae family, known for its antioxidant, anti-inflammatory, and anticarcinogenic activities. It has been identified as a neuroprotective agent and may have potential therapeutic applications in neurodegenerative disorders. This review summarizes the current understanding of the neuroprotective mode of action of carnosic acid and its implications for novel therapeutic approaches.
Review
Biochemistry & Molecular Biology
Edward O. O. Olufunmilayo, Michelle B. B. Gerke-Duncan, R. M. Damian Holsinger
Summary: Neurodegenerative disorders are a significant aspect in neurological diseases, with a pivotal role in public health. The pathophysiology involves the complex interaction between general and disease-specific factors leading to neuronal degeneration and clinical manifestations. Oxidative stress, characterized by an imbalance between pro-oxidant species and antioxidants, has been identified as a crucial factor in the progression of neurodegenerative conditions. This article reviews the impact of oxidative stress on the central nervous system and its influence on Alzheimer's disease, Parkinson's disease, Amyotrophic Lateral Sclerosis, and Huntington's disease, and discusses potential therapeutic approaches to mitigate oxidative stress and halt disease progression for clinical benefits.
Article
Computer Science, Interdisciplinary Applications
Md. Jamal Uddin, Md. Martuza Ahamad, Prodip Kumar Sarker, Sakifa Aktar, Naif Alotaibi, Salem A. Alyami, Muhammad Ashad Kabir, Mohammad Ali Moni
Summary: Autism Spectrum Disorder (ASD) is a neurological impairment condition that severely affects cognitive, linguistic, object recognition, interpersonal, and communication skills. Our machine learning (ML) architecture effectively analyzes autistic children's datasets and accurately classifies and identifies ASD traits. Early diagnosis using our proposed framework could be helpful for clinicians and reduce medical costs.
Article
Biology
Md Mahmodul Hasan, Muhammad Minoar Hossain, Mohammad Motiur Rahman, Akm Azad, Salem A. Alyami, Mohammad Ali Moni
Summary: This research develops a computer-assisted intelligent methodology for ultrasound lung image classification using a fuzzy pooling-based convolutional neural network. The Xception model achieves the best classification results when all pooling layers utilize fuzzy pooling.
COMPUTERS IN BIOLOGY AND MEDICINE
(2023)
Review
Genetics & Heredity
Edward O. Olufunmilayo, R. M. Damian Holsinger
Summary: Alzheimer's disease is the most common form of dementia, with a high prevalence worldwide. Various risk factors, including gene variants, have been identified for this disease. Microglial cells play a critical role in brain protection and cellular homeostasis, and the SHIP1 protein has effects on their signaling pathways. Polymorphisms of the INPP5D gene are associated with an increased risk of Alzheimer's disease. However, there is limited knowledge about the regulation of INPP5D/SHIP1 expression and its influence on microglial signaling processes in relation to AD pathophysiology.
Article
Computer Science, Information Systems
Md Jamal Uddin, Md Martuza Ahamad, Md Nesarul Hoque, Md Abul Ala Walid, Sakifa Aktar, Naif Alotaibi, Salem A. Alyami, Muhammad Ashad Kabir, Mohammad Ali Moni
Summary: Diabetes is a chronic disease with high blood sugar level, leading to other chronic diseases. Prompt detection and identification of risk factors are crucial in managing diabetes. This study used a questionnaire-based survey to examine diabetes prevalence in Bangladesh and proposed an ensemble-based machine learning framework for prompt detection. Experimental results showed the effectiveness of the ensemble technique (ET) and identified age, extreme thirst, and family history of diabetes as significant features. This method has great potential for clinicians to identify individuals at risk and provide timely intervention and care.
Review
Computer Science, Information Systems
Showmick Guha Paul, Arpa Saha, Mohammad Shamsul Arefin, Touhid Bhuiyan, Al Amin Biswas, Ahmed Wasif Reza, Naif M. Alotaibi, Salem A. Alyami, Mohammad Ali Moni
Summary: Green computing, or sustainable computing, focuses on developing and optimizing computer technology to be more energy efficient and have less negative impact on the environment. This study reviews and summarizes the advancements, challenges, and future research opportunities in green computing. It provides insights and ideas for organizations, researchers, and institutions conducting research in this field, as well as benefits environmental organizations, companies, and government agencies concerned with reducing carbon emissions and energy consumption.
Article
Health Care Sciences & Services
Md. Martuza Ahamad, Sakifa Aktar, Md. Jamal Uddin, Md. Rashed-Al-Mahfuz, A. K. M. Azad, Shahadat Uddin, Salem A. Alyami, Iqbal H. Sarker, Asaduzzaman Khan, Pietro Lio, Julian M. W. Quinn, Mohammad Ali Moni
Summary: Good vaccine safety and reliability are crucial for countering infectious diseases effectively. This study aims to reduce adverse reactions to COVID-19 vaccines by identifying common factors through patient data analysis and classification. Patient medical histories and postvaccination effects were examined, and statistical and machine learning approaches were used. The analysis revealed that prior illnesses, hospital admissions, and SARS-CoV-2 reinfection were significantly associated with poor patient reactions.
Article
Biotechnology & Applied Microbiology
Md. Tanvir Hasan, Md. Rakibul Islam, Md. Rezwan Islam, Baraa Riyadh Altahan, Kawsar Ahmed, Francis M. M. Bui, Sami Azam, Mohammad Ali Moni
Summary: This study conducted network analysis to explore genetic connections, functional enrichment, pathway analysis, miRNA-TF co-regulatory network, gene-disease associations, and therapeutic targets for CC. The findings suggest that CC has specific links with the progression of different tumors, and candidate drugs identified in this study could be effective for advanced CC treatment.
JOURNAL OF GENETIC ENGINEERING AND BIOTECHNOLOGY
(2023)
Review
Biochemistry & Molecular Biology
Julie-Anne T. Matheson, R. M. Damian Holsinger
Summary: Neurodegenerative diseases are prevalent and poorly understood, and attention has recently shifted toward investigating the gut microbiome as a potential target for therapeutic research. Alterations in the gut microbiome have been associated with various neurological disorders, and the restoration of a dysbiotic gut through fecal microbiota transplantation (FMT) has shown promise in improving disease conditions. This review aims to summarize neurodegenerative research that has used FMT and its implications for understanding pathogenesis.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
