Article
Biochemistry & Molecular Biology
Yang Du, Meng Cai, Xiaofang Xing, Jiafu Ji, Ence Yang, Jianmin Wu
Summary: The PINA platform has been updated to version 3.0, integrating a unified human interactome with cancer type-specific RNA-seq transcriptomes and mass spectrometry-based proteomes. New analytical tools have been developed to help users identify cancer-specific protein expression, potential biomarkers, and therapeutic targets.
NUCLEIC ACIDS RESEARCH
(2021)
Review
Microbiology
Sonja Courtney Jun Hui Chua, Jianzhou Cui, David Engelberg, Lina Hsiu Kim Lim
Summary: Influenza virus causes 500,000 deaths worldwide annually. The elderly, children, and patients with chronic diseases are particularly vulnerable. Resistance against current antiviral drugs is growing, highlighting the need for novel treatments against resistant influenza strains. Host-directed therapies, which target host processes, may offer a potential strategy. In this review, the authors identified novel host pathways for host-directed therapy against influenza through viral-host interaction screens and bioinformatics analysis.
FRONTIERS IN MICROBIOLOGY
(2022)
Article
Dentistry, Oral Surgery & Medicine
W. W. Lau, M. Hardt, Y. H. Zhang, M. Freire, S. Ruhl
Summary: Saliva is now being used for on-site, remote, and real-time monitoring of oral and systemic health. The Human Salivary Proteome (HSP) Wiki is a public platform that integrates data from various sources to help researchers explore the protein composition of saliva.
JOURNAL OF DENTAL RESEARCH
(2021)
Article
Biochemistry & Molecular Biology
Simone Serrao, Cristina Contini, Giulia Guadalupi, Alessandra Olianas, Greca Lai, Irene Messana, Massimo Castagnola, Giulia Costanzo, Davide Firinu, Stefano Del Giacco, Barbara Manconi, Tiziana Cabras
Summary: Through mass spectrometry analysis, we found that the protein-protein interaction changes of the cystatin D-C(26) interactome are associated with systemic mastocytosis, providing a basis for future quantitative proteomic analysis and immune validation.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Review
Biochemical Research Methods
Tianjiao Zhang, Liang Chen, Rongzhen Li, Ning Liu, Xiaobing Huang, Garry Wong
Summary: PIWI-interacting RNAs (piRNAs) are short molecules found in various species, with the main function of monitoring and protecting the genome from transposons. They have limited bioinformatics resources compared to microRNAs (miRNAs). This review provides an overview of piRNA-specific and non-specific databases, computational models, and their role in disease associations, particularly in cancer and neurodegenerative conditions.
BRIEFINGS IN BIOINFORMATICS
(2022)
Article
Biochemical Research Methods
Georgios N. Dimitrakopoulos, Maria Klapa, Nicholas K. Moschonas
Summary: To enrich the human protein-protein interaction (PPI) meta-database, the PICKLE 3.0 upgrade incorporates mouse protein interactome data, utilizing ortholog gene pairs to extend the mouse interactome and compare mouse and human PPI networks. Despite 43.5% of experimental mouse PPIs lacking corresponding human orthologs, PICKLE 3.0 provides a comprehensive representation of the mouse protein interactome.
Article
Biochemical Research Methods
Yong-Zi Chen, Zhuo-Zhi Wang, Yanan Wang, Guoguang Ying, Zhen Chen, Jiangning Song
Summary: Lysine crotonylation (Kcr) has been reported to be involved in various pathophysiological processes, and several predictors have been developed for predicting Kcr sites, most of which are only suitable for histones or a mix of histone and nonhistone proteins. The proposed CNNrgb framework shows the best performance in predicting Kcr sites on nonhistone proteins and exhibits high computational efficiency.
BRIEFINGS IN BIOINFORMATICS
(2021)
Article
Chemistry, Multidisciplinary
Nimisha Ghosh, Indrajit Saha, Anna Gambin
Summary: COVID-19, caused by SARS-CoV-2, has been disrupting our lives for over two years. To combat the virus and its variants, understanding human-spike protein interactions and predicting new interactions is crucial. This study developed a pipeline to predict human-SARS-CoV-2 interactions and drug-protein interactions, resulting in the identification of potential drugs targeting human proteins.
Article
Biochemical Research Methods
Shayne D. Wierbowski, Siqi Liang, Yuan Liu, You Chen, Shagun Gupta, Nicole M. Andre, Steven M. Lipkin, Gary R. Whittaker, Haiyuan Yu
Summary: The emergence of new viral agents is driven by evolution of interactions between viral proteins and host targets, leading to increased infectivity of viruses such as SARS-CoV-2 through rapid evolution. State-of-the-art interface prediction and molecular docking were used to construct a three-dimensional structural interactome between SARS-CoV-2 and human, facilitating the study of how pathogen-host interactions impact transmission and virulence. The resource provided aims to aid in the development and testing of informed hypotheses for understanding the etiology and treatments of SARS-CoV-2.
Article
Biochemical Research Methods
Kalyani Dhusia, Carlos Madrid, Zhaoqian Su, Yinghao Wu
Summary: The interactions between ectodomains of cell surface proteins play important roles in various cellular processes, but little progress has been made in studying these extracellular interactions. In this study, we present an online database called EXCESP, which is based on computational modeling and contains experimentally determined and computationally predicted interactions among type-I transmembrane proteins in humans. The database also includes additional information such as protein expression levels and signaling pathways.
JOURNAL OF PROTEOME RESEARCH
(2022)
Article
Biochemical Research Methods
Raghav Kataria, Rakesh Kaundal
Summary: The study constructed a database called WeCoNET, which provides functional annotations of pathogen proteins and host-pathogen interactions for the molecular mechanisms of common bunt infection in wheat. The database also includes various functional annotations and predictions to assist molecular biologists and breeders.
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.
Article
Biochemistry & Molecular Biology
Patricia Mirela Bota, Altair C. Hernandez, Joan Segura, Oriol Gallego, Baldo Oliva, Narcis Fernandez-Fuentes
Summary: According to recent estimations, the human interactome consists of around half a million interactions, but only a small fraction of them have available three-dimensional structural information. This study presents CM2D3, a relational database containing structural models of the entire human interactome derived from both comparative modeling and data-driven docking. By using computational methods, structural models were derived from a consensus interactome integrated from multiple interactomics databases. CM2D3 complements existing resources by providing models derived from free-docking, expanding the available structural information on protein complexes.
JOURNAL OF MOLECULAR BIOLOGY
(2023)
Article
Plant Sciences
Merve Yilmaz, Merle Paulic, Thorsten Seidel
Summary: This study reports a protein-protein interaction network of Arabidopsis thaliana, combining various types of information such as subcellular localization, gene ontologies, biochemical properties, and co-expression. The resulting network shows enrichment in nuclear, cytosolic, and plasma membrane proteins, while being depleted in extracellular and mitochondrial proteins. Additionally, proteins involved in transcription are highly abundant in the network.
Review
Chemistry, Multidisciplinary
Ciaran P. Seath, Aaron D. Trowbridge, Tom W. Muir, David W. C. MacMillan
Summary: Biomolecular interactions are crucial for cellular processes, with a focus on protein-protein interactions playing a key role in cellular signaling pathways. Recent advancements in creating reactive intermediates that cross-link neighboring proteins have provided insights into the biomolecular makeup of cellular environments, accelerating the understanding of PPIs and their impact on cellular physiology.
CHEMICAL SOCIETY REVIEWS
(2021)
Review
Dentistry, Oral Surgery & Medicine
Camilla Vieira Esteves, Wladimir Gushiken de Campos, Juliana Amorim dos Santos, Solange Kobayashi Velasco, Eliete Neves Silva Guerra, Walter L. Siqueira, Celso Augusto Lemos
CLINICAL ORAL INVESTIGATIONS
(2020)
Article
Nanoscience & Nanotechnology
Claudia Viviane Guimaraes Pellissari, Carlos Eduardo Vergani, Elson Longo, Ana Claudia Pavarina, Paula Volpato Sanita, Walter Luiz Siqueira, Janaina Habib Jorge
JOURNAL OF NANOMATERIALS
(2020)
Article
Dentistry, Oral Surgery & Medicine
David Zuanazzi, Yizhi Xiao, Walter L. Siqueira
Summary: The study found that the composition of the salivary pellicle was more complex on rough surfaces (SLA and SLActive). Despite variation in protein composition between surfaces, most proteins were detected on more than one surface, indicating limited surface specificity for protein binding. The salivary pellicle formed on SLActive had a larger number of proteins associated with immune response, biological adhesion, and biomineralization.
CLINICAL ORAL INVESTIGATIONS
(2021)
Article
Dentistry, Oral Surgery & Medicine
Claudia Viviane Guimaraes Pellissari, Janaina Habib Jorge, Lina Maria Marin, Robinson Sabino-Silva, Walter Luiz Siqueira
Summary: The study evaluated the effect of statherin and its naturally occurring peptides on Candida albicans metabolism and biofilm development. The peptides were found to decrease the viability and proliferation of Candida albicans, with IT-32 showing the most significant reduction in cell proliferation and biomass. These results suggest that statherin peptides have potential in reducing Candida albicans colonization and biofilm proliferation.
ARCHIVES OF ORAL BIOLOGY
(2021)
Article
Chemistry, Multidisciplinary
Yi Zhu, Lina M. Marin, Yizhi Xiao, Elizabeth R. Gillies, Walter L. Siqueira
Summary: Salivary proteins like histatins play important roles in tooth health. Chitosan nanoparticles show promise in protecting these proteins from enzymatic degradation in the oral environment, especially in acidic conditions. The results demonstrate their potential as carriers for oral applications.
Review
Chemistry, Medicinal
Gustavo Moraes, Carolina Zambom, Walter L. Siqueira
Summary: Nanoparticles have gained attention in dentistry for their potential in improving the diagnosis, prevention, and treatment of various oral diseases, as well as enhancing the properties of dental prostheses and implants. They can also be used to improve drug delivery through the oral mucosa. Studies from 2015 to 2020 have explored the wide range of potential applications of nanoparticles in dentistry.
Article
Biochemical Research Methods
Lina M. Marin, Jaime A. Cury, Walter L. Siqueira
Summary: In this study, an in vitro cariogenic Streptococcus mutans biofilm model was modified and validated by assessing the dose-response effect of fluoride on enamel demineralization. The model demonstrated a dose-response effect of fluoride in influencing enamel demineralization, showing the potential for assessing novel biotechnological strategies for caries prevention.
JOURNAL OF MICROBIOLOGICAL METHODS
(2022)
Article
Dentistry, Oral Surgery & Medicine
Sreenath Madathil, Walter L. Siqueira, Lina M. Marin, Farisa Banu Sanaulla, Nancy Faraj, Carlos R. Quinonez, Mary McNally, Michael Glogauer, Paul Allison
Summary: This study estimated the COVID-19 incidence rates among Canadian dentists and found a low infection rate, which should be reassuring to both dentists and the general community. It emphasizes the importance of continued disease surveillance data collection.
JOURNAL OF THE AMERICAN DENTAL ASSOCIATION
(2022)
Article
Dentistry, Oral Surgery & Medicine
Patricia Luciana Serra Nunes, Filipe Atahide Fonseca, Luiz Renato Paranhos, Cauane Blumenberg, Valentim Adelino Ricardo Barao, Elizabeth Soares Fernandes, Rebeca Garcia Ferreira, Walter Luiz Siqueira, Michelle Foigel Siqueira, Eduardo Buozi Moffa
Summary: Mucopolysaccharidosis (MPS) is a rare genetic disorder resulting from deficiency of lysosomal enzymes. The study found that the salivary levels of nitric oxide (NO) products can be used to monitor MPS disorders.
BRAZILIAN ORAL RESEARCH
(2022)
Review
Medicine, General & Internal
Pedro Urquiza Jayme Silva, Millena Barroso Oliveira, Walbert Vieira, Sergio Vitorino Cardoso, Cauane Blumenberg, Ademir Franco, Walter Luiz Siqueira, Luiz Renato Paranhos
Summary: The outcomes of this study suggest that the occurrence of oral pigmentation induced by chloroquine or hydroxychloroquine is associated with the dosage and treatment length, with a higher risk observed in long-term treatment with higher dosages.
Article
Microbiology
Lina Maria Marin, Yizhi Xiao, Jaime Aparecido Cury, Walter Luiz Siqueira
Summary: The engineered salivary peptide DR9-RR14 has been shown to effectively reduce enamel demineralization, but has no significant impact on biofilm biomass or the expression of cariogenic bacterial proteins. This suggests that DR9-RR14 may primarily control caries development through a physicochemical mechanism.
Review
Dentistry, Oral Surgery & Medicine
Paras Ahmad, Ahmed Hussain, Alonso Carrasco-Labra, Walter L. Siqueira
Summary: Salivary proteins play an important role in the repair of damaged tissues and the maintenance of oral health. This systematic review aimed to assess the association between caries and salivary proteins by comparing caries-free (CF) and caries-active (CA) individuals. The results showed that the levels of certain salivary proteins were significantly increased in CA patients, while others were significantly increased in CF subjects. However, there were conflicting results regarding the salivary levels of immunoglobulin-A and total proteins among CA and CF subjects. Due to significant heterogeneity among the included studies, no meta-analysis could be performed. Therefore, larger prospective studies are needed to verify the diagnostic value of salivary proteins as biomarkers for caries.
Article
Multidisciplinary Sciences
Dina G. Moussa, Walter L. Siqueira
Summary: Dental caries is a widespread chronic disease globally, and research on enamel pellicle (AEP) suggests its crucial role in protecting teeth by controlling bacterial adhesion and plaque formation. Novel hybrid constructs and the integration of functional domains of salivary proteins/peptides have shown promising multifunctional preventive effects against caries.
SCIENTIFIC REPORTS
(2021)
Review
Dentistry, Oral Surgery & Medicine
Renata Prata Cunha Bernardes Rodrigues, Walbert de Andrade Vieira, Walter Luiz Siqueira, Bernardo Antonio Agostini, Eduardo Buozi Moffa, Luiz Renato Paranhos
Summary: This study found that the reductions in salivary urea and creatinine levels after hemodialysis are similar to and correlated with the reductions in blood urea and creatinine levels among chronic kidney disease patients. All eligible studies showed significant reductions in both salivary and serum urea/creatinine levels with a low risk of bias. Meta-analysis demonstrated a moderate to high correlation between salivary and blood levels of urea and creatinine with very low certainty.
BRAZILIAN ORAL RESEARCH
(2021)
Meeting Abstract
Cell Biology
K. Quensel, J. Hutchenreuther, S. Xu, B. Hinz, W. Siqueira, D. O'Gorman, R. Stratton, A. Leask
WOUND REPAIR AND REGENERATION
(2020)
Article
Biochemical Research Methods
Tanushree Halder, Elke Stroeher, Hui Liu, Yinglong Chen, Guijun Yan, Kadambot H. M. Siddique
Summary: Improving the root system of wheat is crucial for enhancing grain yield and climate resilience. This study identified proteins associated with root length and root mass in wheat using label-free quantitative proteomics. The findings revealed potential biomarkers that could be used for improving the root system of wheat.
JOURNAL OF PROTEOMICS
(2024)
Article
Biochemical Research Methods
Yinhua Pan, Quanqing Zou, Wu Yin, Zhen Huang, Yingzhu Zhao, Zongming Mo, Lihui Li, Jianrong Yang
Summary: A prognostic model of BC based on LNM-related genes was established in this study, providing guidance for prognosis evaluation and precise treatment of BC. The genes related to lymph node metastasis in BC are largely unknown and need further exploration. Searching for potential lymph node metastasis-related genes of BC will provide meaningful biomarkers for BC treatment. Our model, based on TCGA-BRCA data, effectively predicted patient outcomes and classified BC patients. The identified feature genes might have a predictive function in immunotherapy. The results of this study provide a new reference for the prognosis and treatment of BC patients with lymph node metastasis.
JOURNAL OF PROTEOMICS
(2024)
Article
Biochemical Research Methods
Qiushi Liang, Joon M. Pijnenburg, Erikjan Rijkers, Arnold G. Vulto, Ans T. van der Ploeg, Niek P. van Til, Eva C. Vlaar, Jeroen A. A. Demmers, W. W. M. Pim Pijnappel
Summary: Pompe disease is a lysosomal storage disorder characterized by glycogen accumulation in skeletal muscle, leading to profound pathology. This study showed that lentiviral gene therapy with LV-IGF2.GAAco can nearly completely correct disease-associated proteomic changes, supporting its future clinical development as a new treatment option for Pompe disease.
JOURNAL OF PROTEOMICS
(2024)
Article
Biochemical Research Methods
Chuang Liu, Wenjing Zhang, Qianli Dong, Haipeng Liu
Summary: This study fills the knowledge gap about the matrix proteins involved in the formation of mineralized exoskeletons in decapod crustaceans. By comparing with well-studied molluscan biomineralization proteins, it is proposed that decapod crustaceans evolved novel proteins while sharing some proteins with molluscs. This study provides insights into the evolution and adaptation of crustaceans and molluscs in forming their exoskeletons.
JOURNAL OF PROTEOMICS
(2024)
Article
Biochemical Research Methods
Rania D. Baka, Josipa Kules, Angelo Beletic, Vladimir Farkas, Dina Resetar Maslov, Blanka Beer Ljubic, Ivana Rubic, Vladimir Mrljak, Mark McLaughlin, David Eckersall, Zoe Polizopoulou
Summary: This study analyzed serum samples from dogs with epilepsy and identified potential markers of epilepsy, proteins involved in nerve tissue regeneration, and proteins altered by antiepileptic medication. The findings provide insight into the pathogenesis of epilepsy and the effects of medication on extracellular matrix proteins.
JOURNAL OF PROTEOMICS
(2024)
Article
Biochemical Research Methods
Viviane M. Codognoto, Fabiana F. de Souza, Thais R. Cataldi, Carlos A. Labate, Laiza S. de Camargo, Pedro H. Esteves Trindade, Roberto R. da Rosa Filho, Diego J. B. de Oliveira, Eunice Oba
Summary: This study aimed to compare urine proteomics from non- and pregnant buffaloes to identify potential biomarkers of early pregnancy. A total of 798 proteins were reported in the urine considering all groups, and the differential proteins play essential roles during pregnancy.
JOURNAL OF PROTEOMICS
(2024)