Article
Multidisciplinary Sciences
Virginie Pascal, Marine Dupont, Paco de Rouault, David Rizzo, Delphine Rossille, Robin Jeannet, Thomas Daix, Bruno Francois, Steve Genebrier, Marie Cornic, Guillaume Monneret, Fabienne Venet, Juliette Ferrant, Mikael Roussel, Florian Reizine, Mathieu Le Souhaitier, Jean-Marc Tadie, Kartin Tarte, Jean Feuillard, Michel Cogne
Summary: To investigate the immune response architecture in COVID-19 patients and understand the factors that can cause or prevent ARDS, we analyzed the B cell responses using flow cytometry and Ig repertoire analysis. Flow cytometry with FlowSOM analysis revealed changes associated with COVID-19 inflammation, including an increase in double-negative B cells and ongoing plasma cell differentiation. We also found the expansion of two disconnected B cell repertoires. Analysis of Ig repertoire patterns showed an early expansion of IgG1 clonotypes with atypical CDR3 characteristics, which correlated with ARDS severity. Additionally, we observed a convergent response with progressively increasing somatic hypermutation and normal or short CDR3 in anti-SARS-CoV-2 clonotypes, which persisted until the memory B cell stage after recovery.
Article
Oncology
Glykeria Gkoliou, Andreas Agathangelidis, Georgos Karakatsoulis, Chrysavgi Lalayanni, Apostolia Papalexandri, Alejandro Medina, Elisa Genuardi, Katerina Chlichlia, Evdoxia Hatjiharissi, Maria Papaioannou, Evangelos Terpos, Cristina Jimenez, Ioanna Sakellari, Simone Ferrero, Marco Ladetto, Ramon Garcia Sanz, Chrysoula Belessi, Kostas Stamatopoulos
Summary: The analysis of the immunogenetic background in multiple myeloma (MM) patients reveals distinct features in the IGH gene repertoires and somatic hypermutation (SHM). Differences were found in the IG gene repertoire and SHM between IgA and IgG MM cases, suggesting distinct immune trajectories. These findings emphasize the role of external drive in the natural history of MM.
FRONTIERS IN ONCOLOGY
(2023)
Article
Food Science & Technology
Rahul Mehra, Shiv Kumar, Nishant Verma, Naveen Kumar, Rajat Singh, Anuradha Bhardwaj, Varij Nayan, Harish Kumar
Summary: By conducting a chemometric study on the colostrum of Himachali Pahari cow breed in India, significant variations in physicochemical and immunological properties were observed between high and low altitudes as well as within different districts. Principal component analysis reduced 16 variables into 3 principal components, explaining a large portion of the variance.
LWT-FOOD SCIENCE AND TECHNOLOGY
(2021)
Review
Genetics & Heredity
Vinicius A. C. de Abreu, Jose Perdigao, Sintia Almeida
Summary: Antimicrobial resistance is a significant global public health issue, primarily caused by pathogens acquiring resistance genes through horizontal gene transfer. High-throughput sequencing technologies and metagenomics have helped identify community antimicrobial resistance, with challenges in analyzing microbial diversity, functional gene analysis, and searching for relevant resistome databases.
FRONTIERS IN GENETICS
(2021)
Article
Materials Science, Multidisciplinary
S. Rezaei, Shahram Rezapour, Jehad Alzabut, Robert de Sousa, B. M. Alotaibi, S. A. El-Tantawy
Summary: This paper constructs various solutions to nonlinear Schrodinger's equations using two efficient analytical techniques. Numerical simulations and graphical representations are used to gain a deeper understanding of the nonlinear phenomena described by these solutions. The obtained results are new and have implications for the study of nonlinear phenomena in plasma physics and fluid mechanics.
RESULTS IN PHYSICS
(2022)
Article
Immunology
Mark Chernyshev, Mateusz Kaduk, Martin Corcoran, Gunilla B. Karlsson Hedestam
Summary: This study quantified VDJ gene usage levels in the unmutated IgM repertoires of 45 macaques, revealing similar patterns of gene usage among macaque subgroups and individuals. Unlike humans, macaques showed a higher usage of IGHV4 family genes and evidence of evolutionary expansion of this gene family.
FRONTIERS IN IMMUNOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Yana Safonova, Sung Bong Shin, Luke Kramer, James Reecy, Corey T. Watson, Timothy P. L. Smith, Pavel A. Pevzner
Summary: An important challenge in vaccine development is understanding why vaccines work differently in different individuals. A study of 204 calves vaccinated against bovine respiratory disease found that variations in immunoglobulin genes and somatic hypermutations can impact vaccine response efficacy. This study represents the largest personalized immunogenomics study to date and has implications for selecting cattle for breeding programs.
Article
Biochemistry & Molecular Biology
Fanjie Zong, Chenyu Long, Wanxin Hu, Shuang Chen, Wentao Dai, Zhi-Xiong Xiao, Yang Cao
Summary: The utilization of high-throughput sequencing for B-cell receptor immune repertoire analysis has become widespread, but the sheer volume of sequences generated poses challenges. To address this, Abalign, a standalone program specifically designed for ultrafast multiple sequence alignment of BCR/antibody sequences, is introduced. Benchmark tests demonstrate that Abalign achieves comparable or even better accuracy than state-of-the-art tools, with remarkable advantages in terms of speed and memory consumption. In addition to alignment capabilities, Abalign offers a broad range of BCR analysis features and can be easily run on personal computers. Overall, Abalign is an easy-to-use and effective tool for analyzing massive BCR/antibody sequences, leading to new discoveries in immunoinformatics. The software is freely available.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Genetics & Heredity
Christoph Hahn, Nicholas P. Howard, Dirk C. Albach
Summary: In this study, we analyzed the interrelationships, population structures, and genetic diversity of 72 kale and cabbage varieties using SPLoSH data. The results revealed four distinct groups of kale varieties and validated the use of SPLoSH information for analyzing interrelations in kale.
Article
Mechanics
Jinling Zhao, Hongli Ji, Jinhao Qiu, Chao Zhang, Chongcong Tao, Jianping Zhao, Nian Li
Summary: In this paper, a novel method is developed to directly relate ultrasonic wave velocities to the stiffness coefficients of anisotropic composites. The method allows for efficient sensitivity analysis and provides good explanations for the sensitivity behaviors using wave structure properties. Numerical sensitivity analysis and experiments are conducted to reconstruct the material properties based on measured wave velocities.
COMPOSITE STRUCTURES
(2023)
Review
Microbiology
Ho-Jin Gwak, Seung Jae Lee, Mina Rho
Summary: Microorganisms play vital roles in ecosystems, particularly in soil, ocean, and human gut environments. With the advancement of next-generation sequencing technology, researchers have been exploring the relationship between microbial communities and disease development, developing various methods to investigate microbiomes.
JOURNAL OF MICROBIOLOGY
(2021)
Review
Pharmacology & Pharmacy
Paolo Gresele, Stefania Momi
Summary: Platelets are crucial in thrombotic events caused by ruptured atherosclerotic plaques, making antiplatelet agents the main treatment for preventing myocardial infarction, atherothrombotic ischemic stroke, and critical limb ischemia. Despite advancements in antiplatelet drugs, important medical needs such as insufficient efficacy and high incidence of hemorrhagic complications remain. However, understanding the molecular mechanisms regulating platelet function and progress in pharmaceutical design have led to the identification of new drugs for existing targets and the development of novel targets. Clinical testing of innovative approaches, including GPVI antagonism, PAR4 antagonism, and PI3K inhibition, has shown promising preliminary results. This review discusses the current and developing pharmacologic approaches to platelet inhibition and their effects on platelet activation and thrombosis in vitro, animal models, and humans. The ultimate goal is to develop an antithrombotic agent that selectively targets pathological thrombus formation without affecting normal hemostasis, which would be a significant advancement in preventing ischemic cardiovascular events.
BIOCHEMICAL PHARMACOLOGY
(2022)
Article
Engineering, Marine
Yancheng Yang, Haixiao Liu
Summary: This study investigates the behavior of gravity installed anchors (GIAs) in multi-layered clays using theoretical and numerical approaches. The results show that both theoretical and numerical models can effectively predict the anchor behavior, revealing the complexity and variety of anchor behaviors in multi-layered clays.
Article
Immunology
Xaquin Castro Dopico, Marco Mandolesi, Gunilla B. Karlsson Hedestam
Summary: Immunoglobulin (IG) genes encoding B cell receptors (BCRs) are crucial for the immune system in recognizing diverse antigens and generating antibody responses. Understanding the impact of IG genetic diversity on host traits, disease susceptibility, and antibody recall responses is of great interest. Studying IG genetics can help decipher preferences for IG gene or allele usage and improve our understanding of antibody responses at the population level.
IMMUNOLOGY LETTERS
(2023)
Article
Engineering, Environmental
Sun-Hwa Nam, Tae-Yang Lee, Sang A. Kim, Youn-Joo An
Summary: Microplastics are a significant environmental concern due to their widespread presence. This study examined the toxicity data of microplastics in marine water and analyzed their species sensitivity distribution curves and hazardous concentrations. The results showed that non-traditional toxicity endpoints had stronger HC values, better fit, and more variable toxicity sensitivity compared to traditional values. The use of non-traditional toxicity and marine water toxicity data can expand the marine water toxicity database and provide valuable information about the toxicity of various types of microplastics.
JOURNAL OF HAZARDOUS MATERIALS
(2023)
Article
Biochemistry & Molecular Biology
William Lees, Christian E. Busse, Martin Corcoran, Mats Ohlin, Cathrine Scheepers, Frederick A. Matsen, Gur Yaari, Corey T. Watson, Andrew Collins, Adrian J. Shepherd
NUCLEIC ACIDS RESEARCH
(2020)
Article
Multidisciplinary Sciences
Palash C. Maity, Mayas Bilal, Marvyn T. Koning, Marc Young, Cornelis A. M. van Bergen, Valerio Renna, Antonella Nicolo, Moumita Datta, Eva Gentner-Goebel, Rob S. Barendse, Sebastiaan F. Somers, Ruben A. L. de Groen, Joost S. P. Vermaat, Daniela Steinbrecher, Christof Schneider, Eugen Tausch, Tamara Bittolo, Riccardo Bomben, Andrea Nicola Mazzarello, Giovanni del Poeta, Wilma G. M. Kroes, J. Tom van Wezel, Katharina Imkeller, Christian E. Busse, Massimo Degano, Tamam Bakchoul, Axel Ronald Schulz, Henrik Mei, Paolo Ghia, Konstantia Kotta, Kostas Stamatopoulos, Hedda Wardemann, Antonella Zucchetto, Nicholas Chiorazzi, Valter Gattei, Stephan Stilgenbauer, Hendrik Veelken, Hassan Jumaa
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2020)
Article
Biochemistry & Molecular Biology
Rajagopal Murugan, Stephen W. Scally, Giulia Coste, Ghulam Mustafa, Elaine Thai, Tizian Decker, Alexandre Bosch, Katherine Prieto, Elena A. Levashina, Jean-Philippe Julien, Hedda Wardemann
Article
Immunology
Johanna Kabbert, Julia Benckert, Tim Rollenske, Thomas C. A. Hitch, Thomas Clavel, Vuk Cerovic, Hedda Wardemann, Oliver Pabst
JOURNAL OF EXPERIMENTAL MEDICINE
(2020)
Article
Multidisciplinary Sciences
Cristina Lorenzo, Pilar Delgado, Christian E. Busse, Alejandro Sanz-Bravo, Inmaculada Martos-Folgado, Elena Bonzon-Kulichenko, Alessia Ferrarini, Ileana B. Gonzalez-Valdes, Sonia M. Mur, Raquel Roldan-Montero, Diego Martinez-Lopez, Jose L. Martin-Ventura, Jesus Vazquez, Hedda Wardemann, Almudena R. Ramiro
Summary: Atherosclerosis, an inflammatory disease that can remain asymptomatic for long periods, is the main cause of cardiovascular events. Research shows that certain autoantibodies can recognize target antigens in atherosclerotic plaques and potentially delay plaque formation in mice, suggesting therapeutic potential in cardiovascular disease.
Article
Virology
Julia Butt, Rajagopal Murugan, Theresa Hippchen, Sylvia Olberg, Monique van Straaten, Hedda Wardemann, Erec Stebbins, Hans-Georg Krausslich, Ralf Bartenschlager, Hermann Brenner, Vibor Laketa, Ben Schoettker, Barbara Mueller, Uta Merle, Tim Waterboer
Summary: The emergence of the SARS-CoV-2 pandemic has highlighted the urgent need for specific and sensitive high-throughput serological assays to assess the epidemiology of SARS-CoV-2. Researchers have developed a fluorescent-bead based SARS-CoV-2 multiplex serology assay to detect antibody responses to the SARS-CoV-2 proteome. This assay demonstrated high sensitivity and specificity in COVID-19 patients, allowing for epidemiological research and explorative analyses regarding disease progression and antibody response.
Article
Immunology
Ilka Wahl, Sandro Hoffmann, Rebecca Hundsdorfer, Julia Puchan, Stephen L. Hoffman, Peter G. Kremsner, Benjamin Mordmuller, Christian E. Busse, Hedda Wardemann
Summary: This study established a high-throughput platform for analyzing human TCR repertoires quantitatively and qualitatively, providing insights into the clonal and functional composition of CD4(+) and CD8(+) αβ T cells. The strategy is a powerful tool for qualitatively assessing differences between antigen receptors of phenotypically defined αβ T cell subsets, applicable in research on cancer, vaccination, infection, and autoimmune diseases.
EUROPEAN JOURNAL OF IMMUNOLOGY
(2022)
Review
Immunology
Ilka Wahl, Hedda Wardemann
Summary: This review summarizes our understanding of the molecular and cellular immune responses to Plasmodium falciparum circumsporozoite protein (PfCSP) in humans, and discusses the implications for vaccine design. However, the current efficacy of anti-PfCSP vaccine responses is limited. Therefore, this article reviews recent research efforts and discusses ways to overcome these limitations to improve vaccine effectiveness and long-term protection.
JOURNAL OF EXPERIMENTAL MEDICINE
(2022)
Article
Multidisciplinary Sciences
Tim Rollenske, Sophie Burkhalter, Lukas Muerner, Stephan von Gunten, Jolanta Lukasiewicz, Hedda Wardemann, Andrew J. Macpherson
Summary: In this study, recombinant dimeric monoclonal IgAs were used to map the intestinal plasma cell response to microbial colonization in mice, revealing distinct effects on microbial function and metabolism depending on the antigen specificity of the dimeric mIgAs. Even when targeting the same microbial antigen, different IgA epitope specificities led to varied microbial metabolic changes.
Article
Immunology
Katherine J. L. Jackson, Justin T. Kos, William Lees, William S. Gibson, Melissa Laird Smith, Ayelet Peres, Gur Yaari, Martin Corcoran, Christian E. Busse, Mats Ohlin, Corey T. Watson, Andrew M. Collins
Summary: The poorly characterized immunoglobulin genes in inbred mouse strains commonly used in models of antibody-mediated human diseases could compromise data analysis. This study used long-read SMRT sequencing to amplify VDJ-C sequences from BALB/c mice and identified strain variations in specific immunoglobulin genes. By computationally retrieving IGHV haplotypes, a set of expressed BALB/c IGHV germline gene sequences was established. The study also assessed the suitability of assemblies from the Mouse Genome Project for the determination of IGH loci genes.
FRONTIERS IN IMMUNOLOGY
(2022)
Article
Multidisciplinary Sciences
Fauzia K. Musasia, Irene N. Nkumama, Roland Frank, Victor Kipkemboi, Martin Schneider, Kennedy Mwai, Dennis O. Odera, Micha Rosenkranz, Kristin Fuerle, Domitila Kimani, James Tuju, Patricia Njuguna, Mainga Hamaluba, Melissa C. Kapulu, Hedda Wardemann, Faith H. A. Osier
Summary: The study shows that antibody-dependent phagocytosis of ring-stage P. falciparum parasites in semi-immune Kenyan adults is mediated by merozoite antigens and is a strong predictor of protection.
NATURE COMMUNICATIONS
(2022)
Article
Immunology
Ilka Wahl, Anna S. Obraztsova, Julia Puchan, Rebecca Hundsdorfer, Sumana Chakravarty, B. Kim Lee Sim, Stephen L. Hoffman, Peter G. Kremsner, Benjamin Mordmueller, Hedda Wardemann
Summary: T follicular helper (T-FH) cells are crucial for the development of B cell responses after infection and vaccination, but little is known about their clonal evolution and epitope targeting. This study investigated the dynamics and specificity of T-FH cells during malaria immunizations, revealing a polyclonal response to a limited number of epitopes and potential T cell supertope. However, vaccine-induced TCRs were limited to the vaccine strain, suggesting that parasite diversity may limit the effectiveness of T-FH cell response induced by vaccination.
SCIENCE IMMUNOLOGY
(2022)
Article
Computer Science, Information Systems
Scott Christley, Ademar Aguiar, George Blanck, Felix Breden, Syed Ahmad Chan Bukhari, Christian E. Busse, Jerome Jaglale, Srilakshmy L. Harikrishnan, Uri Laserson, Bjoern Peters, Artur Rocha, Chaim A. Schramm, Sarah Taylor, Jason Anthony Vander Heiden, Bojan Zimonja, Corey T. Watson, Brian Corrie, Lindsay G. Cowell
FRONTIERS IN BIG DATA
(2020)