Article
Biochemistry & Molecular Biology
Yuexu Jiang, Lei Jiang, Chopparapu Sai Akhil, Duolin Wang, Ziyang Zhang, Weinan Zhang, Dong Xu
Summary: The study introduces a new web application based on MULocDeep, which has improved performance, result interpretation, and visualization, for predicting protein localization and understanding its mechanisms. By transferring the original model into species-specific models, MULocDeep achieves competitive prediction performance at the subcellular level compared to other state-of-the-art methods. Besides localization prediction, the web service quantifies the contribution of single amino acids to localization for individual proteins and derives common motifs or potential targeting-related regions for a group of proteins. The visualizations of targeting mechanism analyses can be downloaded for publication-ready figures. The MULocDeep web service is available at https://www.mu-loc.org/.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Plant Sciences
Anna T. Olek, Phillip S. Rushton, Daisuke Kihara, Peter Ciesielski, Uma K. Aryal, Zicong Zhang, Cynthia Stauffacher, Maureen C. McCann, Nicholas C. Carpita
Summary: This study investigated two plant-unique sequences in cellulose synthases and found that certain amino acid residues within these sequences play a crucial role in their function, while others do not.
Review
Computer Science, Information Systems
Neha Agarwal, Geeta Sikka, Lalit Kumar Awasthi
Summary: With the advancement of web 2.0 and the development of the Internet of Things (IoT), web services play a crucial role in supporting the successful journey of IoT. However, managing and discovering web services presents challenges, and web service clustering techniques can enhance the process of service discovery and selection. This paper conducts a systematic literature review to investigate and analyze state-of-the-art techniques based on web service clustering, providing insights into future research directions.
COMPUTER SCIENCE REVIEW
(2022)
Article
Environmental Sciences
Huaqiao Xing, Haihang Wang, Jinhua Zhang, Dongyang Hou
Summary: Land cover change has significant impacts on global climate change, energy cycle, carbon cycle, and water cycle, affecting human well-being. Web service-based online change detection applications have been developed for monitoring land cover change. However, the integration and sharing of services in the land cover domain have been overlooked, making it difficult for end-users to access LCC information in a timely manner.
Article
Multidisciplinary Sciences
Ovinu Kibria Islam, Israt Islam, Otun Saha, Md. Mizanur Rahaman, Munawar Sultana, Dirk P. Bockmuehl, M. Anwar Hossain
Summary: The resistance of Pseudomonas aeruginosa to antimicrobials and its virulence is due to the multifactorial nature of biofilm development and genomic variabilities. Extensive research on genetic determinants is required to inhibit the formation of biofilms or disrupt already formed ones. A study on 20 multidrug-resistant clinical isolates of P. aeruginosa revealed their varying abilities to form biofilms, with some strains showing strong, moderate, or weak biofilm-forming tendencies. Genome sequencing of representative strains showed that most biofilm-related genes had high sequence identity with the reference strain PAO1. However, variations in the sequences and structures of pel operon proteins were found to affect the biofilm phenotypes of certain strains. The findings highlight the importance of studying genomic divergence in P. aeruginosa strains to better understand and combat biofilm formation.
SCIENTIFIC REPORTS
(2023)
Article
Computer Science, Information Systems
Andy Neumann, Nuno Laranjeiro, Jorge Bernardino
Summary: An analysis of 500 websites claiming to provide REST web service APIs revealed trends and discrepancies, with only a small percentage strictly adhering to all REST principles. The results can assist practitioners in developing guidelines for higher quality services and identifying deficiencies in current deployments.
IEEE TRANSACTIONS ON SERVICES COMPUTING
(2021)
Article
Computer Science, Information Systems
Lalit Purohit, Sandeep Kumar
Summary: This study proposed a method for web service selection based on QoS parameters, which combines prefiltering, improved PROMETHEE method, and Maximizing Deviation Method to select the most suitable web services for end users, achieving better performance in terms of user satisfaction and efficiency in experiments compared to existing similar approaches.
IEEE TRANSACTIONS ON SERVICES COMPUTING
(2021)
Article
Biology
Thomas G. Bartholow, Terra Sztain, Ashay Patel, D. John Lee, Megan A. Young, Ruben Abagyan, Michael D. Burkart
Summary: Bartholow et al. conducted a comprehensive residue-by-residue comparison of the protein-protein interactions in de novo fatty acid biosynthesis that occurs in E. coli using structural and computational analysis. This study provides insights into molecular events that occur in carrier protein-dependent pathways.
COMMUNICATIONS BIOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Yuping Liu, Siting Pan, Xinshuai Zhang, Hua Huang
Summary: Pantothenic acid is converted to beta-alanine and (R)-pantoate, and then (R)-pantoate is transformed to aldopentoate in a reconstituted pathway identified through genomic enzymology strategy. The pathway genes, common in Proteobacterial genomes, are responsible for the biodegradation of pantothenic acid.
ACS CHEMICAL BIOLOGY
(2021)
Article
Green & Sustainable Science & Technology
R. Kanesaraj Ramasamy, Fang-Fang Chua, Su-Cheng Haw, Chin-Kuan Ho
Summary: This study addresses the challenges of web service composition in service-oriented computing and proposes solutions for data type matching. By dividing the composition process into three phases, dynamic and adaptable web service composition can be achieved.
Article
Biochemistry & Molecular Biology
Laiyi Fu, Yingxin Cao, Jie Wu, Qinke Peng, Qing Nie, Xiaohui Xie
Summary: UFold is a deep learning-based method for RNA secondary structure prediction, which uses a novel image-like representation of RNA sequences to achieve accurate predictions in a short time, outperforming previous methods on within-family datasets and showing similar performance on distinct RNA families.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Biochemistry & Molecular Biology
Mihaly Varadi, Stephen Anyango, David Armstrong, John Berrisford, Preeti Choudhary, Mandar Deshpande, Nurul Nadzirin, Sreenath S. Nair, Lukas Pravda, Ahsan Tanweer, Bissan Al-Lazikani, Claudia Andreini, Geoffrey J. Barton, David Bednar, Karel Berka, Tom Blundell, Kelly P. Brock, Jose Maria Carazo, Jiri Damborsky, Alessia David, Sucharita Dey, Roland Dunbrack, Juan Fernandez Recio, Franca Fraternali, Toby Gibson, Manuela Helmer-Citterich, David Hoksza, Thomas Hopf, David Jakubec, Natarajan Kannan, Radoslav Krivak, Manjeet Kumar, Emmanuel D. Levy, Nir London, Jose Ramon Macias, Madhusudhan M. Srivatsan, Debora S. Marks, Lennart Martens, Stuart A. McGowan, Jake E. McGreig, Vivek Modi, R. Gonzalo Parra, Gerardo Pepe, Damiano Piovesan, Jaime Prilusky, Valeria Putignano, Leandro G. Radusky, Pathmanaban Ramasamy, Atilio O. Rausch, Nathalie Reuter, Luis A. Rodriguez, Nathan J. Rollins, Antonio Rosato, Luis Serrano, Gulzar Singh, Petr Skoda, Carlos Oscar S. Sorzano, Jan Stourac, Joanna Sulkowska, Radka Svobodova, Natalia Tichshenko, Silvio C. E. Tosatto, Wim Vranken, Mark N. Wass, Dandan Xue, Daniel Zaidman, Janet Thornton, Michael Sternberg, Christine Orengo, Sameer Velankar
Summary: PDBe-KB is an open collaboration platform that aims to integrate functional and biophysical annotations from world-leading specialist data resources, serving the Protein Data Bank. By developing standardized data exchange formats and integrating functional annotations from partner resources, PDBe-KB aims to place macromolecular structure data in a biological context and provide valuable biological insights.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Computer Science, Software Engineering
Remaci Zeyneb Yasmina, Hadjila Fethallah, Lahfa Fadoua
Summary: Web services are increasingly used for complex tasks, with users searching for compositions that meet QoS requirements. The challenge lies in the growing number of services and their uncertain QoS, but with a heuristic approach and constraint programming search, optimal compositions can be selected efficiently.
CONCURRENCY AND COMPUTATION-PRACTICE & EXPERIENCE
(2022)
Article
Computer Science, Information Systems
Lalit Purohit, Santosh Singh Rathore, Sandeep Kumar
Summary: In this study, a web service selection model called CPSky is proposed, consisting of a Prefilter layer and a Selection layer. The Prefilter layer filters potent services through quality pruning and clustering, while the Selection layer uses the improved Skyline-Plus approach to select appropriate web services. Experimental results demonstrate that the proposed approach performs better than existing methods in terms of efficiency and user satisfaction.
IEEE TRANSACTIONS ON SERVICES COMPUTING
(2023)
Review
Chemistry, Inorganic & Nuclear
Jordi Zamarreno Beas, Marco A. M. Videira, Ligia M. Saraiva
Summary: Haem b and sirohaem are two important prosthetic groups in bacterial proteins, synthesized through complex pathways with divergences at the formation of uroporphyrinogen III. The biosynthesis of these tetrapyrroles involves unstable or potentially hazardous intermediates and end-products, requiring tight control of cellular metabolic fluxes.
COORDINATION CHEMISTRY REVIEWS
(2022)
Article
Biochemistry & Molecular Biology
Malgorzata Rydzanicz, Malgorzata Wachowska, Erik C. Cook, Pawel Lisowski, Bozena Kuzniewska, Krystyna Szymanska, Sebastian Diecke, Alessandro Prigione, Krzysztof Szczaluba, Aleksandra Szybinska, Agnieszka Koppolu, Victor Murcia Pienkowski, Joanna Kosinska, Malgorzata Wiweger, Grazyna Kostrzewa, Malgorzata Brzozowska, Dorota Domanska-Pakiela, Elzbieta Jurkiewicz, Piotr Stawinski, Agnieszka Gromadka, Piotr Zielenkiewicz, Urszula Demkow, Magdalena Dziembowska, Jacek Kuznicki, Trevor P. Creamer, Rafal Ploski
EUROPEAN JOURNAL OF HUMAN GENETICS
(2019)
Article
Biotechnology & Applied Microbiology
Michal Reichert, Anna Lukasik, Piotr Zielenkiewicz, Marek Matras, Joanna Maj-Paluch, Magdalena Stachnik, Ewa Borzym
Article
Cell & Tissue Engineering
Marta Milewska, Anna Burdzinska, Katarzyna Zielniok, Katarzyna Siennicka, Slawomir Struzik, Piotr Zielenkiewicz, Leszek Paczek
STEM CELLS INTERNATIONAL
(2020)
Article
Multidisciplinary Sciences
Marta M. Stepniewska-Dziubinska, Piotr Zielenkiewicz, Pawel Siedlecki
SCIENTIFIC REPORTS
(2020)
Review
Biochemistry & Molecular Biology
Vasso Apostolopoulos, Joanna Bojarska, Tsun-Thai Chai, Sherif Elnagdy, Krzysztof Kaczmarek, John Matsoukas, Roger New, Keykavous Parang, Octavio Paredes Lopez, Hamideh Parhiz, Conrad O. Perera, Monica Pickholz, Milan Remko, Michele Saviano, Mariusz Skwarczynski, Yefeng Tang, Wojciech M. Wolf, Taku Yoshiya, Janusz Zabrocki, Piotr Zielenkiewicz, Maha AlKhazindar, Vanessa Barriga, Konstantinos Kelaidonis, Elham Mousavinezhad Sarasia, Istvan Toth
Summary: Peptides, as fragments of proteins, play vital roles in biological processes with unique characteristics and promising potentials in biotherapies. Current research focuses on short peptide-based therapeutic developments, covering disease treatments, biosynthesis, nanotechnology, peptide limitations overcoming, among others.
Article
Agriculture, Dairy & Animal Science
Malgorzata Habich, Bartosz Pawlinski, Maria Sady, Katarzyna Siewruk, Piotr Zielenkiewicz, Zdzislaw Gajewski, Pawel Szczesny
Article
Biochemistry & Molecular Biology
Norbert Odolczyk, Ewa Marzec, Maria Winiewska-Szajewska, Jaroslaw Poznanski, Piotr Zielenkiewicz
Summary: SARS-CoV-2 is responsible for COVID-19, but there is no specific treatment available. Short peptides designed based on ACE2 show potential in disrupting virus-host interactions and blocking viral infection.
Article
Immunology
Michal Konwerski, Agnieszka Gromadka, Adam Arendarczyk, Marta Koblowska, Roksana Iwanicka-Nowicka, Radoslaw Wilimski, Pawel Czub, Krzysztof Jerzy Filipiak, Piotr Hendzel, Piotr Zielenkiewicz, Grzegorz Opolski, Aleksandra Gasecka, Tomasz Mazurek
Summary: Perivascular release of inflammatory mediators may accelerate coronary lesion formation and contribute to plaque instability. The study revealed altered gene expression in PCAT of CAD patients, with upregulation of genes involved in inflammation and atherosclerosis, and downregulation of genes related to cardiac ischemia, remodeling, platelet function, and mitochondrial function. This suggests that genes in PCAT may play a role in CAD development and progression.
JOURNAL OF INFLAMMATION RESEARCH
(2021)
Article
Multidisciplinary Sciences
Melanie Faria da Cunha, Iwona Pranke, Ali Sassi, Christiane Schreiweis, Stephanie Moriceau, Dragana Vidovic, Aurelie Hatton, Mariane Sylvia Carlon, Geordie Creste, Farouk Berhal, Guillaume Prestat, Romain Freund, Norbert Odolczyk, Jean Philippe Jais, Christine Gravier-Pelletier, Piotr Zielenkiewicz, Vincent Jullien, Alexandre Hinzpeter, Franck Oury, Aleksander Edelman, Isabelle Sermet-Gaudelus
Summary: This study provides the first in vivo preclinical evidence of the efficacy of c407 in treating Cystic Fibrosis, correcting CFTR dysfunction and improving chloride conductance. Importantly, c407 was well tolerated and demonstrated no obvious toxicity after systemic administration.
SCIENTIFIC REPORTS
(2022)
Article
Pharmacology & Pharmacy
Kaja Kasarello, Iwona Koehling, Anna Kosowska, Katarzyna Pucia, Anna Lukasik, Agnieszka Cudnoch-Jedrzejewska, Leszek Paczek, Urszula Zielenkiewicz, Piotr Zielenkiewicz
Summary: Cross-kingdom gene expression regulation by xenomiRs, particularly from plants, has been found to have potential scientific significance. In this study, miR172a derived from Brassica oleracea was shown to decrease the levels of FAN protein in human and mouse cells. Furthermore, treatment with miR172a was found to mitigate inflammation in a mouse model of rheumatoid arthritis.
FRONTIERS IN PHARMACOLOGY
(2022)
Editorial Material
Biochemistry & Molecular Biology
Vasso Apostolopoulos, Joanna Bojarska, Tsun-Thai Chai, Jack Feehan, Krzysztof Kaczmarek, John M. Matsoukas, Octavio Paredes Lopez, Michele Saviano, Mariusz Skwarczynski, Jillian Smith-Carpenter, Mariano Venanzi, Wojciech M. Wolf, Piotr Zielenkiewicz, Zyta M. Ziora
Article
Biochemistry & Molecular Biology
Dorota Adamczyk-Szabela, Ewa Chrzescijanska, Piotr Zielenkiewicz, Wojciech M. M. Wolf
Summary: The aim of this study was to assess the influence of cadmium and zinc treatments on antioxidant activity and photosynthesis efficiency in lemon balm. The results showed a reduction in net photosynthesis for plants subjected to both zinc and cadmium treatments. The herbal extracts had exceptional antioxidant capacities and were good scavengers of free radicals and reactive oxygen species. In addition, the structural similarity of cadmium and zinc facilitated their mutual structural exchange and led to an expansion of phenolics under mixed zinc and cadmium treatments.
Article
Biochemistry & Molecular Biology
Aizhan Rakhmetullina, Aigul Akimniyazova, Togzhan Niyazova, Anna Pyrkova, Makpal Tauassarova, Anatoliy Ivashchenko, Piotr Zielenkiewicz
Summary: A database of human piRNAs has been created, allowing study of their interactions with disease-associated genes. In this study, piRNAs that can interact with candidate ESCC genes were identified. Bioinformatic analysis revealed that piRNAs only bind to the mRNAs of nine candidate genes. The organization of piRNA binding sites suggests an interdependence of gene expression through piRNAs. Individual piRNAs and sets of piRNAs are proposed for diagnosis and therapy of ESCC.
CURRENT ISSUES IN MOLECULAR BIOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Aizhan Rakhmetullina, Aigul Akimniyazova, Togzhan Niyazova, Anna Pyrkova, Saltanat Kamenova, Aida Kondybayeva, Alma-Gul Ryskulova, Anatoliy Ivashchenko, Piotr Zielenkiewicz
Summary: This study validated the interaction between more than eight million piRNAs and the SARS-CoV-2 genome using bioinformatic approaches. Several potential target sites for antiviral drug development were identified, and 16 synthetic piRNAs with strong binding energy to gRNA were proposed for the suppression of SARS-CoV-2 reproduction.
CURRENT ISSUES IN MOLECULAR BIOLOGY
(2023)
Letter
Medicine, General & Internal
Mariusz Niemczyk, Arkadiusz Gladki, Agnieszka Gromadka, Piotr Zielenkiewicz, Leszek Paczek
POLISH ARCHIVES OF INTERNAL MEDICINE-POLSKIE ARCHIWUM MEDYCYNY WEWNETRZNEJ
(2021)