Article
Biochemical Research Methods
Julian Dosch, Holger Bergmann, Vinh Tran, Ingo Ebersberger
Summary: FAS is a scoring method that integrates features from multiple annotation sources and resolves redundancies in architecture comparison. It consistently provides more plausible architecture similarities compared to other methods in large-scale evaluation. Three case studies demonstrate its utility in various applications.
Article
Biochemistry & Molecular Biology
Elizabeth Martinez-Perez, Matyas Pajkos, Silvio C. E. Tosatto, Toby J. Gibson, Zsuzsanna Dosztanyi, Cristina Marino-Buslje
Summary: DisProt is a curated database of Intrinsically Disordered Proteins (IDPs) with strong experimental support. Transferring annotations regarding disorder state and functions to homologous proteins in other species is important for understanding their biological roles. With the use of a pipeline, it is possible to transfer annotations from DisProt proteins to their orthologs, resulting in a large number of transferred terms by homology.
Article
Plant Sciences
Jin-Wook Choi, Ha-Eun Kim, Seungill Kim
Summary: This study conducted genome-wide re-annotation of bZIP genes in the Solanaceae family, revealing structural and functional diversity, as well as putative functional differences in response to abiotic stresses. These findings provide important evidence for understanding the roles of bZIP genes in Solanaceae plants.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Chemistry, Multidisciplinary
Thomas Gobbato, Giulia Alice Volpato, Andrea Sartorel, Marcella Bonchio
Summary: The conversion of light into chemical energy is crucial for the transition to renewable and clean solar fuels. The success of photosynthesis depends not only on the performance of individual components, but also on their integration in optimized structures. The cellular structure of natural photosynthesis can inspire the design of artificial photosynthesis. This article presents a case study on the design of artificial photosynthetic systems, highlighting the importance of molecular structures in enhancing overall performance.
Article
Biochemistry & Molecular Biology
Lilian Mbaisi Ang'ang'o, Jeremy Keith Herren, Ozlem Tastan Bishop
Summary: This research developed a robust bioinformatics annotation pipeline to annotate hypothetical proteins (HPs) from Vittaforma corneae. Various steps were used to retrieve sequences and homologs, perform physicochemical characterization, protein family classification, motif and domain identification, protein-protein interaction network analysis, and homology modeling. In total, 162 out of 2034 HPs were fully annotated, providing insights into the functions of microsporidian HPs.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Review
Biochemistry & Molecular Biology
Yusuke Nakasone, Masahide Terazima
Summary: This review describes the reactions of three BLUF proteins with similar EAL functional groups or with a separated target protein using time-resolved diffusion technique.
PHOTOCHEMICAL & PHOTOBIOLOGICAL SCIENCES
(2022)
Article
Computer Science, Hardware & Architecture
Syed M. Raza, Boyun Jang, Huigyu Yang, Moonseong Kim, Hyunseung Choo
Summary: This paper proposes an Improved Generative Adversarial Network with Fact Forcing (iGAN-FF) for mobility prediction, which reduces the need for training data and achieves higher accuracy through adversarial learning. Experimental results confirm the superiority of the iGAN-FF method.
JOURNAL OF NETWORK AND COMPUTER APPLICATIONS
(2022)
Review
Chemistry, Multidisciplinary
Xiao-Zhen Li, Chong-Bin Tian, Qing-Fu Sun
Summary: Lanthanide supramolecular chemistry is a rapidly growing and fascinating research field. Polymetallic lanthanide supramolecular assemblies offer more structural and functional advantages. This review summarizes the design principles of polynuclear Ln structures, emphasizing the importance of water solubility and chirality, and discusses strategies for improving luminescent properties and applications.
Article
Chemistry, Multidisciplinary
Shuiyan Cao, Anna Roslawska, Benjamin Doppagne, Michelangelo Romeo, Michel Feron, Frederic Cherioux, Herve Bulou, Fabrice Scheurer, Guillaume Schull
Summary: The funneling of energy within multichromophoric assemblies is essential for efficient solar energy conversion in plants. By using luminescence induced by scanning tunneling microscopy, researchers were able to probe model multichromophoric structures on a surface and mimic strategies developed by photosynthetic systems. This approach, based on organic chromophores, provides a powerful model to study fundamental physical processes in natural light-harvesting complexes.
Article
Genetics & Heredity
Gagandeep Singh, Dinesh Gupta
Summary: This study aims to characterize hypothetical proteins of the parasite to identify novel drug targets using a computational pipeline. The study reveals that out of the overall pool of hypothetical proteins, 266 proteins have conserved functional signatures, with 23 proteins playing essential roles in various biochemical, signalling and metabolic pathways.
FRONTIERS IN GENETICS
(2022)
Article
Biochemistry & Molecular Biology
Patricia P. Chan, Brian Y. Lin, Allysia J. Mak, Todd M. Lowe
Summary: tRNAscan-SE, a tool for predicting transfer RNA genes, has been widely used for over twenty years. Recent updates have greatly improved its ability to identify and classify tRNAs by creating nearly one hundred specialized isotype- and Glade-specific models.
NUCLEIC ACIDS RESEARCH
(2021)
Review
Microbiology
Zachary Ardern, Sagarika Chakraborty, Florian Lenk, Anne-Kristin Kaster
Summary: Annotating protein sequences is crucial for understanding microbial diversity and potential applications, but traditional methods are limited by the vast amount of 'omics' data. Hypothetical proteins (HPs) are a knowledge gap with hidden potential. Artificial intelligence (AI) and machine learning algorithms offer opportunities to leverage 'Big Data' for comprehensive genome annotations. This review explores the aims, methods, and recent research examples of protein annotation, with a focus on machine and deep learning algorithms.
FEMS MICROBIOLOGY REVIEWS
(2023)
Article
Chemistry, Multidisciplinary
Joao Felicidade, Fabio M. F. Santos, Jesus F. Arteaga, Patricia Remon, Rene Campos-Gonzalez, Ha-Chi Nguyen, Francisco Najera, Francisco Bosca, David Y. W. Ng, Pedro M. P. Gois, Uwe Pischel
Summary: A series of boronic-acid-derived salicylidenehydrazone (BASHY) complexes were synthesized in good yields through a versatile three-component reaction. These complexes exhibit fluorescence switching behavior by photoinduced electron transfer, which can be controlled by the addition of acid. In organic solvent, the fluorescence is observed in the green-to-orange region, while in water under physiological pH conditions, the fluorescence is observed in the red-to-NIR region with appreciable quantum yields and lifetimes. These characteristics make these dyes suitable for fluorescence lifetime imaging of live cells.
CHEMISTRY-A EUROPEAN JOURNAL
(2023)
Review
Chemistry, Multidisciplinary
Mingqiu Hu, Thomas P. Russell
Summary: This review highlights the developments in the past decade that used polymers with advanced architectures as multifunctional emulsifiers in various industries such as food, cosmetics, and pharmaceuticals. These emulsifiers have been utilized for encapsulation, delivery, and as templates for polymerization reactions.
MATERIALS CHEMISTRY FRONTIERS
(2021)
Article
Chemistry, Physical
Dou Luo, Zhengyan Jiang, Wanli Yang, Xugang Guo, Xuehui Li, Erjun Zhou, Gongqiang Li, Lanqing Li, Chenghao Duan, Chengwei Shan, Zhaojin Wang, Yuheng Li, Baomin Xu, Aung Ko Ko Kyaw
Summary: This study demonstrates a method to improve the efficiency of organic solar cells (OSCs) by using two tailor-made non-fused ring electron acceptors (NFREAs). By introducing an ambipolar NFREA as the third component, smooth charge transfer routes and additional carrier generation are achieved. The results show that, with similar molecular structure and enhanced molecular packing, the power conversion efficiency of the ternary blend is significantly higher than that of the binary devices.
Article
Evolutionary Biology
Niko Popitsch, Christian D. Huber, Ilana Buchumenski, Eli Eisenberg, Michael Jantsch, Arndt von Haeseler, Miguel Gallach
GENOME BIOLOGY AND EVOLUTION
(2020)
Article
Microbiology
Ines Ferreira, Stephan Beisken, Lukas Lueftinger, Thomas Weinmaier, Matthias Klein, Johannes Bacher, Robin Patel, Arndt von Haeseler, Andreas E. Posch
JOURNAL OF CLINICAL MICROBIOLOGY
(2020)
Review
Infectious Diseases
Norhan Mahfouz, Ines Ferreira, Stephan Beisken, Arndt von Haeseler, Andreas E. Posch
JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY
(2020)
Article
Biochemistry & Molecular Biology
Alina F. Leuchtenberger, Stephen M. Crotty, Tamara Drucks, Heiko A. Schmidt, Sebastian Burgstaller-Muehlbacher, Arndt von Haeseler
MOLECULAR BIOLOGY AND EVOLUTION
(2020)
Article
Biochemistry & Molecular Biology
Olga Chernomor, Lena Peters, Judith Schneidewind, Anita Loeschcke, Esther Knieps-Gruenhagen, Fabian Schmitz, Eric von Lieres, Roger Jan Kutta, Vera Svensson, Karl-Erich Jaeger, Thomas Drepper, Arndt von Haeseler, Ulrich Krauss
Summary: LPOR is essential for the synthesis of chlorophyll in bacteria, and our study shows that it is not only present in oxygenic phototrophic bacteria but also widespread in aerobic anoxygenic phototrophic bacteria, indicating complex evolutionary processes involving multiple horizontal gene transfer events.
MOLECULAR BIOLOGY AND EVOLUTION
(2021)
Article
Biochemistry & Molecular Biology
Tobias S. Kaiser, Arndt von Haeseler, Kristin Tessmar-Raible, David G. Heckel
Summary: Research shows that ecological divergence can occur in sympatry in the presence of gene flow, but this does not result in genome-wide genetic divergence.
Article
Multidisciplinary Sciences
Jason Sims, Giovanni Sestini, Christiane Elgert, Arndt von Haeseler, Peter Schloegelhofer
Summary: Despite vast differences between organisms, some characteristics of their genomes are conserved, such as the nucleolus organizing region (NOR). Using a combination of long- and short-read sequencing, researchers have identified tissue-specific variants of rRNA genes integrated into translating ribosomes in Arabidopsis NOR2 rDNA.
NATURE COMMUNICATIONS
(2021)
Article
Biochemistry & Molecular Biology
Bruno M. Fontinha, Theresa Zekoll, Mariam Al-Rawi, Miguel Gallach, Florian Reithofer, Alison J. Barker, Maximilian Hofbauer, Ruth M. Fischer, Arndt von Haeseler, Herwig Baier, Kristin Tessmar-Raible
Summary: Vertebrate behavior is greatly influenced by light receptors called opsins, with diverse functions across a wide range of species. Despite their widespread occurrence, the nonvisual functions of opsins remain largely unknown. Teleost fish have a large number of opsin genes, which play a key role in their diurnal behavior and ability to utilize complex light information underwater.
Article
Microbiology
Ines Ferreira, Sarah Lepuschitz, Stephan Beisken, Giuseppe Fiume, Katharina Mrazek, Bernhard J. H. Frank, Silke Huber, Miriam A. Knoll, Arndt von Haeseler, Arne Materna, Jochen G. Hofstaetter, Andreas E. Posch, Johannes Weinberger
Summary: The newly developed ARESdb AMR panel allows for comprehensive and sensitive detection of antimicrobial resistance markers. Compared to metagenomics sequencing, the capture-based workflow has higher sensitivity and lower sequencing depth requirements, with a limit of detection for specific pathogens in synovial fluid and urine samples of 1000 CFU/mL. It also enables culture-free detection of bacterial taxa and AMR markers with an average sensitivity of 99% in septic patient samples.
Review
Biochemistry & Molecular Biology
Lukas Lueftinger, Ines Ferreira, Bernhard J. H. Frank, Stephan Beisken, Johannes Weinberger, Arndt von Haeseler, Thomas Rattei, Jochen G. Hofstaetter, Andreas E. Posch, Arne Materna
Summary: This review summarizes the current developments in next-generation sequencing based predictive antibiotic susceptibility testing and discusses the potential and limitations for common PJI pathogens.
Review
Plant Sciences
Jason Sims, Fernando A. Rabanal, Christiane Elgert, Arndt Von Haeseler, Peter Schloegelhofer
Summary: Ribosomal RNA genes are organized in large domains of hundreds of rDNA units, with stable inheritance crucial for survival. During meiosis, rDNA loci are embedded within the nucleolus favoring non-homologous end joining as a repair mechanism, while rare homologous recombination events dynamically change rDNA unit numbers. The sequence heterogeneity and size stability of rDNA clusters in Arabidopsis thaliana show potential functional implications and drive further research into the mechanisms maintaining their metastable state.
FRONTIERS IN PLANT SCIENCE
(2021)
Article
Cell Biology
Michelle Huth, Laura Santini, Elena Galimberti, Julia Ramesmayer, Fabian Titz-Teixeira, Robert Sehlke, Michael Oberhuemer, Sarah Stummer, Veronika Herzog, Marius Garmhausen, Merrit Romeike, Anastasia Chugunova, Friederike Leesch, Laurenz Holcik, Klara Weipoltshammer, Andreas Lackner, Christian Schoefer, Arndt von Haeseler, Christa Buecker, Andrea Pauli, Stefan L. Ameres, Austin Smith, Andreas Beyer, Martin Leeb
Summary: Cell fate transitions depend on balanced rewiring of transcription and translation programs. This study reveals the regulatory role of NMD in the expression levels of the translation initiation factor Eif4a2 and its premature termination codon-encoding isoform, establishing a feedback loop between NMD and translation initiation. Furthermore, the severity of target deregulation and differentiation phenotypes in NMD effector KOs highlights heterodimer-independent functions for SMG5 and SMG7.
GENES & DEVELOPMENT
(2022)
Article
Biochemistry & Molecular Biology
Abel Vertesy, Oliver L. Eichmueller, Julia Naas, Maria Novatchkova, Christopher Esk, Meritxell Balmana, Sabrina Ladstaetter, Christoph Bock, Arndt von Haeseler, Juergen A. Knoblich
Summary: This study reveals that organoids experience cellular stress, but it is limited to specific subpopulations and does not affect neuronal specification or maturation. The researchers have developed an algorithm to identify and remove stressed cells, proving its usefulness in different organoid systems.
Article
Cell Biology
Joanna Kaczanowska, Florian Ganglberger, Olga Chernomor, Dominic Kargl, Bence Galik, Andreas Hess, Yoshan Moodley, Arndt von Haeseler, Katja Buehler, Wulf Haubensak
Summary: By studying the evolution of the human brain, we found that the cognitive demands of humans have become increasingly complex over time, accompanied by adaptive evolution in the areas of language and strategic thinking.
Article
Biochemistry & Molecular Biology
Marie-Therese Kurzbauer, Michael Peter Janisiw, Luis F. Paulin, Ignacio Prusen Mota, Konstantin Tomanov, Ondrej Krsicka, Arndt von Haeseler, Veit Schubert, Peter Schloegelhofer
Summary: The study shows that Arabidopsis ATM plays a role in multiple steps of meiosis, limiting the number of meiotic DSBs and affecting CO formation and SC organization. This extends our understanding of how ATM functions during plant meiosis.