Review
Biochemistry & Molecular Biology
Julia D. D. Meredith, Michael J. J. Gray
Summary: The pseudohypohalous acid hypothiocyanite/hypothiocyanous acid (OSCN-/HOSCN) has been widely investigated for its antimicrobial properties in mammalian immunity. Generated by peroxidase enzymes from thiocyanate (SCN-) and hydrogen peroxide (H2O2), HOSCN has potential applications in food preservation, pathogen control, and oral care. However, the mechanisms by which bacteria sense and respond to HOSCN remain largely unknown. This review summarizes the current knowledge on the role of HOSCN in host-pathogen interactions and discusses recent findings regarding bacterial responses to this antimicrobial agent, focusing on three model organisms: Escherichia coli, Streptococcus spp., and Pseudomonas aeruginosa.
MOLECULAR MICROBIOLOGY
(2023)
Review
Biochemistry & Molecular Biology
Sohyoung Lee, Sean Inzerillo, Gi Young Lee, Erick M. Bosire, Saroj K. Mahato, Jeongmin Song
Summary: Glycans play a crucial role in bacterial pathogenesis and host responses against pathogens. Interactions between bacterial and host glycans can benefit the pathogen, host, or both. Technological advances in glycoscience have accelerated research and offer valuable insights into antibacterial strategies to combat drug-resistant pathogens on a global scale.
TRENDS IN MICROBIOLOGY
(2022)
Review
Plant Sciences
Christian-Frederic Kaiser, Alessia Perilli, Guido Grossmann, Yasmine Meroz
Summary: Plant roots integrate sensory information over space and time to respond to non-uniform environmental conditions. The complexity of soil poses challenges for studying root metabolism, growth, development, and interactions with the rhizosphere. Microdevices offer opportunities to observe, analyze, and manipulate plant roots, and provide a better understanding of their physiology and development in soil-like conditions.
JOURNAL OF EXPERIMENTAL BOTANY
(2023)
Article
Biochemistry & Molecular Biology
Ekaterina Chernevskaya, Natalia Klimenko, Alisa Pautova, Irina Buyakova, Alexander Tyakht, Natalia Beloborodova
Summary: The study investigated the features of gut microbiota and profile of certain metabolites in chronically critically ill patients with neurological disorders. Specific associations between bacterial taxa in fecal samples, neurological status, and serum metabolites suggest potential for regulating brain function through impacting gut microbiota and their metabolism.
Review
Immunology
Annika Hausmann, Wolf-Dietrich Hardt
Summary: Host-microbe interactions are highly dynamic during infections, and utilizing genetic tags with stochastic population dynamic models allows for more precise quantification of these interactions. This approach can help predict the effects of immunodeficiencies or therapies on populations, generating new experimental hypotheses.
Review
Virology
Vladimir Chulanov, Anastasiya Kostyusheva, Sergey Brezgin, Natalia Ponomareva, Vladimir Gegechkori, Elena Volchkova, Nikolay Pimenov, Dmitry Kostyushev
Summary: CRISPR/Cas technology plays a crucial role in studying viral infections and identifying potential antiviral genes through screening methods. The development of CRISPR screens has helped in uncovering novel drug candidates for treating viral infections.
Article
Engineering, Biomedical
Min Beom Kim, Soonho Hwangbo, Sungho Jang, Yun Kee Jo
Summary: The recent increase in complex physiological host-microbe interactions has led to a demand for in vitro models that replicate the microbial microenvironment in the human body. Organoids, an in vitro culture system that closely mimics the structure, function, and genetic features of human organs, are emerging as a promising tool for studying host-microbe interactions. Co-cultures of organoids with microbes show great potential in simulating complex host-microbe interactions and advancing related fields. This review provides an overview of bioengineering approaches for microbe-co-cultured organoids and highlights the latest developments in their applications for studying human physiology and pathophysiology.
MATERIALS TODAY BIO
(2022)
Editorial Material
Microbiology
Kaitlin M. Gold
Summary: Plant disease sensing is an emerging discipline that holds great promise for modern agriculture by utilizing proximal and/or remote sensing for disease detection and diagnosis. Despite its revolutionary potential, challenges remain in both fundamental research and field application for plant disease sensing.
Review
Immunology
Emily R. Wahlenmayer, Daniel E. Hammers
Summary: The genus Streptococcus encompasses a wide range of bacteria that can colonize hosts and cause diseases. Streptococci produce peptides that manipulate the host immune system and environment, allowing them to survive and cause diseases. Understanding the functions of these peptides is crucial for developing therapeutic approaches against Streptococcal infections.
FRONTIERS IN CELLULAR AND INFECTION MICROBIOLOGY
(2023)
Article
Microbiology
Muhammad Siddique Afridi, Ali Fakhar, Ashwani Kumar, Sher Ali, Flavio H. Medeiros, Muhammad Atif Muneer, Hina Ali, Muhammad Saleem
Summary: The rhizosphere is a dynamic region of plant root-soil interfaces that plays a crucial role in plant health and stress tolerance. Engineering the rhizosphere microbiome using omics tools and gene-editing techniques can enhance plant growth and disease management. This review explores the complex interactions within the rhizosphere microbiome and the potential for ecological engineering to improve plant fitness and increase crop production.
MICROBIOLOGICAL RESEARCH
(2022)
Review
Microbiology
Ying Zhao, Yan Zeng, Dong Zeng, Hesong Wang, Mengjia Zhou, Ning Sun, Jinge Xin, Abdul Khalique, Danish Sharafat Rajput, Kangcheng Pan, Gang Shu, Bo Jing, Xueqin Ni
Summary: This paper discusses the roles of probiotics and miRNAs in host-microbe interactions, proposes the association of probiotics with altered miRNAs in intestinal diseases and potential mechanisms, and provides a perspective on the probiotics-miRNA-host/gut microbiota axis for disease management highly associated with the gut microbiome in future studies.
FRONTIERS IN MICROBIOLOGY
(2021)
Article
Cell Biology
Belinda L. Spillings, Christopher J. Day, Albert Garcia-Minambres, Anupriya Aggarwal, Nicholas D. Condon, Thomas Haselhorst, Damian F. J. Purcell, Stuart G. Turville, Jennifer L. Stow, Michael P. Jennings, Johnson Mak
Summary: This study reveals that HIV is captured near the lymphocyte surface in a virion-glycan-dependent manner. Removing certain glycans impairs virus-cell binding and interfering with glycan interactions reduces HIV infectivity. These findings provide new insights into the interaction between HIV and host cells.
Article
Multidisciplinary Sciences
Hazel McLellan, Sarah E. Harvey, Jens Steinbrenner, Miles R. Armstrong, Qin He, Rachel Clewes, Leighton Pritchard, Wei Wang, Shumei Wang, Thomas Nussbaumer, Bushra Dohai, Qingquan Luo, Priyanka Kumari, Hui Duan, Ana Roberts, Petra C. Boevink, Christina Neumann, Nicolas Champouret, Ingo Hein, Pascal Falter-Braun, Jim Beynon, Katherine Denby, Paul R. J. Birch
Summary: By studying the interaction between pathogen effectors and nonhost plants, we revealed the mechanism behind nonhost resistance and demonstrated the crucial role of disrupting this interaction in immune response.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Automation & Control Systems
Talha Burak Alakus, Ibrahim Turkoglu
Summary: This study predicted viral-host interactions between SARS-CoV-2 virus and human proteins using computational-based approaches. Protein sequences were converted into numerical expressions and a deep learning model was designed for classification. The entropy-based method showed the best performance, followed by the Z-scale method.
CHEMOMETRICS AND INTELLIGENT LABORATORY SYSTEMS
(2022)
Review
Plant Sciences
Danillo O. Alvarenga, Kathrin Rousk
Summary: Mosses play a crucial role in ecosystems, forming symbiotic relationships with bacteria that significantly impact carbon and nitrogen cycles. They can store a large amount of carbon and contribute to nitrogen input in ecosystems through microbial interactions.
JOURNAL OF EXPERIMENTAL BOTANY
(2022)
Article
Biotechnology & Applied Microbiology
Tobias Strittmatter, Sabina Egli, Adrian Bertschi, Richard Plieninger, Daniel Bojar, Mingqi Xie, Martin Fussenegger
Summary: In this study, a gene switch using l-glucose and d-idonate to regulate gene expression was designed and successfully utilized to control the production of rituximab.
BIOTECHNOLOGY AND BIOENGINEERING
(2021)
Article
Biochemistry & Molecular Biology
Luc Thomes, Daniel Bojar
Summary: This study examines the distribution and characteristics of fucose-containing glycan motifs across different taxa, revealing clear differences in fucose usage among various groups, even within the same domain, based on the physiology and habitat of organisms. The differences in fucose-containing motifs between vertebrates and invertebrates are highlighted, as well as the importance of fucose-containing motifs in molecular mimicry, as shown with pathogenic and non-pathogenic strains of Escherichia coli. This research sheds light on an important class of glycan motifs and provides new insights into the role of fucosylated glycans in symbiosis, pathogenicity, and immunity.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2021)
Article
Biochemistry & Molecular Biology
Daniel Bojar, Lawrence Meche, Guanmin Meng, William Eng, David F. Smith, Richard D. Cummings, Lara K. Mahal
Summary: Glycans play critical roles in biology and medicine, but the specificity of lectins, which are key proteins in glycans binding, has not been well-defined. In this study, machine learning algorithms and expert annotation were used to define the lectin specificity for 57 unique lectins. This research provides important insights into the complex binding features of commercially available lectins.
ACS CHEMICAL BIOLOGY
(2022)
Article
Chemistry, Multidisciplinary
Jon Lundstrom, Emma Korhonen, Frederique Lisacek, Daniel Bojar
Summary: LectinOracle model, combining transformer-based representations for proteins and graph convolutional neural networks for glycans, is able to predict protein-glycan interactions accurately and generalize well to new glycans and lectins. It has various applications in improving lectin classification, accelerating lectin directed evolution, predicting epidemiological outcomes, and analyzing host-microbe interactions.
Article
Biochemistry & Molecular Biology
Jon Lundstrom, Daniel Bojar
Summary: Despite their widespread presence in biological systems, glycans have historically received insufficient attention. Recent investigations have revealed the significance of glycans in regulating the human gut microbiota. This article provides a brief overview of current trends in computational and experimental research approaches, enhancing our understanding of host-microbe glycointeractions.
CURRENT OPINION IN STRUCTURAL BIOLOGY
(2022)
Review
Chemistry, Multidisciplinary
Daniel Bojar, Frederique Lisacek
Summary: The use of artificial intelligence methods in glycoinformatics is currently limited due to the unique challenges of glyco-data. However, with the accumulation of glycomics and glycan-binding data, as well as advancements in deep learning techniques, the future of glycoinformatics looks promising.
Article
Multidisciplinary Sciences
Rui Qin, Lara K. Mahal, Daniel Bojar
Summary: Glycosylation is a common occurrence in cells and is often dysregulated in diseases. Understanding the regulation and functional importance of different types of glycosylation at the cellular level is challenging experimentally. However, the use of multi-omics and single-cell measurements, such as SUGAR-seq, can help address this issue. In this study, a deep learning model was developed to predict glycan phenotypes of cells using transcriptomic data. The model interpretation process identified genes that are highly predictive and relevant to glycan biology. This work demonstrates the potential of interpretable deep learning models in uncovering novel functions and regulatory mechanisms of glycans from integrated transcriptomic and glycomic datasets.
Article
Chemistry, Multidisciplinary
Roman Joeres, Daniel Bojar, Olga V. Kalinina
Summary: Glycans are polysaccharides that play important roles in cellular processes. Their structures can be represented using IUPAC-condensed notation. However, there is a lack of an easy-to-use tool to convert IUPAC-condensed notation to SMILES for atomic-level representation.
JOURNAL OF CHEMINFORMATICS
(2023)
Article
Cell Biology
Luc Thomes, Viktoria Karlsson, Jon Lundstrom, Daniel Bojar
Summary: Milk oligosaccharides (MOs) are important constituents of breast milk and their biosynthesis and evolutionary relationships have been studied using a comprehensive dataset of >100 mammalian species. The study identified systematic glycome biases, biosynthetic restrictions and conserved biosynthetic modules, advancing our understanding of glycan biosynthesis and the evolution of breast milk.
Meeting Abstract
Biochemistry & Molecular Biology
Daniel Bojar
Meeting Abstract
Biochemistry & Molecular Biology
Daniel Bojar
Article
Biochemistry & Molecular Biology
Luc Thomes, Rebekka Burkholz, Daniel Bojar
Summary: Glycowork is an open-source Python package designed for glycan-related data science and machine learning, providing functions such as automatic annotation of glycan motifs and analysis of their distributions. It also includes visualization methods, routines to interact with stored databases, trained machine learning models, and learned glycan representations. The tool aims to extract further insights from glycan datasets for various biological contexts.
Article
Social Sciences, Mathematical Methods
Maximiliane Uhlich, Daniel Bojar
Summary: By using deep learning methods, facial and bodily emotion expression, and other features, we can assess the momentary relationship state of romantic couples. Our new model, DeepConnection, achieved an average accuracy of nearly 97%, demonstrating its potential for informing couples, advancing relationship research, and assisting in couple therapy.
JOURNAL OF COMPUTATIONAL SOCIAL SCIENCE
(2021)