Article
Biochemistry & Molecular Biology
Jungkyun Seo, D. Dewran Kocak, Luke C. Bartelt, Courtney A. Williams, Alejandro Barrera, Charles A. Gersbach, Timothy E. Reddy
Summary: The AP-1 transcription factor dimer is involved in regulating various biological processes and environmental responses, with flexible binding between its subunits. The study revealed that AP-1 hotspots predict cell type-specific gene expression and genomic responses to glucocorticoid signaling.
Article
Multidisciplinary Sciences
Alexandra D. Brown, Kyle Lynch, David N. Langelaan
Summary: This study characterizes the interactions between the C-terminal MITF transactivation domain and CBP/p300 and provides molecular details of how MITF interacts with CBP/p300 through multiple redundant interactions. The findings have important implications for understanding the function of MITF in melanocytes and melanoma.
SCIENTIFIC REPORTS
(2023)
Editorial Material
Cell Biology
Yibin Kang, Charlotte Kuperwasser
Summary: Selective pressure and signals from the tissue microenvironment play a crucial role in driving metastasis and determining the survival of metastatic tumor cells at distant organs. By utilizing CRISPR-mediated evolving barcode technology, researchers are able to elucidate the impact of the bone microenvironment on the evolution of breast cancer metastasis.
DEVELOPMENTAL CELL
(2021)
Review
Genetics & Heredity
Gang Wang, Heng Ye, Xuchao Wang, Binbin Liu
Summary: The epigenetic landscape plays a crucial role in determining cell fate during heart development, with Polycomb repressive complex 2 (PRC2) mediating histone methyltransferase activity. PRC2-deficient mice exhibit congenital heart malformations, highlighting the importance of PRC2 in cardiac cell differentiation. Specific long noncoding RNAs (lncRNAs) have been reported to regulate PRC2 recruitment, but promiscuous RNA binding by PRC2 also plays a role in cardiac cell fate decision. This review focuses on the RNA-mediated PRC2 recruitment machinery and the roles of individual lncRNAs and promiscuous RNA binding in heart development.
FRONTIERS IN GENETICS
(2022)
Editorial Material
Chemistry, Physical
Amos Martinez, Hui Deng
Summary: Professor Hui Deng from the University of Michigan discusses the evolution of polariton physics research in recent years and the role of emerging materials in creating a landscape full of challenges and possibilities.
News Item
Biochemistry & Molecular Biology
Anastasia Liuzzi, Ditlev E. Brodersen
Summary: Studies show that prokaryotic genomes contain highly similar toxin-antitoxin modules, which need to be balanced between protection and diversification. Research on paralogous modules now reveals how evolution secures insulation between related systems without compromising toxin inhibition.
NATURE CHEMICAL BIOLOGY
(2021)
Article
Computer Science, Artificial Intelligence
Xinming Shi, Leandro L. Minku, Xin Yao
Summary: Based on reconfigurable memristive units (RMUs), we propose an evolvable memristive reservoir circuit capable of adaptive evolution for varying tasks, avoiding the device variance of the memristors. We also propose a scalable algorithm for evolving the proposed circuit, addressing the scalability issue and ensuring circuit feasibility through sparse topology optimization. Experimental results demonstrate the feasibility and superiority of our proposed evolvable memristive reservoir circuit.
IEEE TRANSACTIONS ON NEURAL NETWORKS AND LEARNING SYSTEMS
(2023)
Article
Multidisciplinary Sciences
He Ma, Arunachalam Narayanaswamy, Patrick Riley, Li Li
Summary: The article introduces a new framework called SyFES, which automatically constructs accurate functionals in symbolic form. It is more explainable and easier to integrate than other machine learning functionals. The framework is also capable of evolving new functionals from existing ones.
Review
Chemistry, Multidisciplinary
Zhenzhen Wu, Yuhui Tian, Hao Chen, Liguang Wang, Shangshu Qian, Tianpin Wu, Shanqing Zhang, Jun Lu
Summary: Lithium-air batteries have attracted significant attention due to their high energy density and renewable features. However, the lack of critical electrode materials and a thorough understanding of the chemistry has hindered their development. Recent research has focused on systematic electrode design, fabrication, and modification, as well as comprehensive electrolyte selection. Future development requires further exploration and optimization.
CHEMICAL SOCIETY REVIEWS
(2022)
Article
Optics
Baolei Liu, Fan Wang, Chaohao Chen, Fei Dong, David Mcgloin
Summary: Ghost imaging captures 2D images using a point detector instead of an array sensor, offering the potential to image objects in turbid media and bypass offline processing. The self-evolving ghost imaging strategy evaluates and generates illumination patterns in real time, updating the object's image at a rapid rate. SEGI demonstrates robust imaging capabilities for static and moving objects, surpassing traditional computational ghost imaging in terms of imaging power and adaptability.
Review
Chemistry, Multidisciplinary
Yutan D. Y. L. Getzler, Robert T. Mathers
Summary: This paper discusses the evolution of environmentally responsible research in polymer chemistry and proposes solutions for achieving sustainability. The authors provide a historical overview and trace their own responses and research projects. They suggest moving beyond qualitative use of the 12 Principles of Green Chemistry and adopting a portfolio of metrics. The authors also propose the creation of a national Life Cycle Assessment center.
ACCOUNTS OF CHEMICAL RESEARCH
(2022)
Review
Cell Biology
Claudia C. S. Chini, Julianna D. Zeidler, Sonu Kashyap, Gina Warner, Eduardo Nunes Chini
Summary: NAD and NADP have diverse roles beyond co-factors in oxidation-reduction reactions, including signaling pathways, post-translational modifications, epigenetic changes, and RNA regulation. Recent studies have shown that NAD metabolism is highly dynamic with a short halflife in some tissues, and new concepts are emerging in the roles of NAD pathway metabolites in various disease states. Resolving open questions in NAD biology will lead to significant advancements in the field.
Article
Computer Science, Artificial Intelligence
Yujing Wang, Yaming Yang, Zhuo Li, Jiangang Bai, Mingliang Zhang, Xiangtai Li, Jing Yu, Ce Zhang, Gao Huang, Yunhai Tong
Summary: In this paper, a novel and generic evolving attention mechanism is proposed, which models the evolution of inter-token relationships through a chain of residual convolutional modules. Experimental results show that the networks equipped with this mechanism achieve superior performance in various applications.
IEEE TRANSACTIONS ON PATTERN ANALYSIS AND MACHINE INTELLIGENCE
(2023)
Article
Computer Science, Artificial Intelligence
Amanda O. C. Ayres, Fernando J. Von Zuben
Summary: This article introduces a new evolving fuzzy-rule-based algorithm named extreme value evolving predictor (EVeP), which offers a statistically well-founded approach to improve the prediction performance of rules by using evolving fuzzy granules and fuzzy structural relationships. It outperforms the state-of-the-art evolving algorithms in terms of prediction performance.
IEEE TRANSACTIONS ON FUZZY SYSTEMS
(2022)
Article
Computer Science, Information Systems
Edwin Lughofer
Summary: In this paper, an evolving multi-label fuzzy classifier (EFC-ML) is proposed, which is capable of self-adapting and self-evolving its structure for the problem of multi-label classification. The EFC-ML is based on a multi-output Takagi-Sugeno type architecture and integrates a locally weighted incremental correlation-based algorithm with recursive fuzzily weighted least squares and Lasso-based regularization. Antecedent learning is achieved through product-space clustering, resulting in a compact rule base for better interpretability. Furthermore, the approach includes an online active learning strategy for updating the classifier on a selected subset of samples, making it suitable for applications with sparsely labeled data.
INFORMATION SCIENCES
(2022)
Article
Immunology
Karin Hjort, Pontus Juren, Juan Carlos Toro, Sven Hoffner, Dan Andersson, Linus Sandegren
Summary: Whole-genome sequencing of Mycobacterium tuberculosis from a single patient over 9 years of disease and treatment revealed that antibiotic treatment was the main driver of sequence evolution, leading to stepwise accumulation of resistance mutations to various antibiotics. The study highlighted the dynamic nature of M. tuberculosis infection, population structure, and resistance evolution, emphasizing the importance of rapid antibiotic susceptibility tests in combating this pathogen.
JOURNAL OF INFECTIOUS DISEASES
(2022)
Article
Microbiology
Clara Atterby, Marie Nykvist, Ulrika Lustig, Dan Andersson, Josef D. Jarhult, Linus Sandegren
Summary: Exposure to sub-MIC levels of ciprofloxacin can lead to enrichment of Escherichia coli with reduced susceptibility to ciprofloxacin in wildlife, highlighting the potential impact of antibiotic pollution on the environment. The study found that in vivo selection of gyrA mutants occurred in mallards during exposure to ciprofloxacin concentrations found in aquatic environments, with resistance plasmids readily transferring between strains in the intestines of the mallards. Ultimately, the findings underscore the importance of reducing antibiotic contamination to curb the spread of resistance.
ANTIMICROBIAL AGENTS AND CHEMOTHERAPY
(2021)
Article
Genetics & Heredity
Michael Knopp, Arianne M. Babina, Jonina S. Gudmundsdottir, Martin Douglass, M. Stephen Trent, Dan Andersson
Summary: Random sequences can generate novel antibiotic resistance determinants de novo, which act via specific peptide-protein interactions in the transmembrane domain. These peptides may potentially evolve as bona fide resistance determinants in natura.
Article
Microbiology
Roderich Roemhild, Dan I. Andersson
Article
Multidisciplinary Sciences
Komal Umashankar Rao, Domhnall Iain Henderson, Nitya Krishnan, Manoj Puthia, Izabela Glegola-Madejska, Lena Brive, Fanny Bjarnemark, Anna Millqvist Fureby, Karin Hjort, Dan I. Andersson, Erik Tenland, Erik Sturegard, Brian D. Robertson, Gabriela Godaly
Summary: A fungal peptide was found to effectively reduce tuberculosis load and synergize with current TB drugs. The peptide remained stable in circulation and showed efficacy against drug-resistant bacteria.
SCIENTIFIC REPORTS
(2021)
Article
Infectious Diseases
Jessica Howard-Anderson, Michelle Davis, Alexander M. Page, Chris W. Bower, Gillian Smith, Jesse T. Jacob, Dan Andersson, David S. Weiss, Sarah W. Satola
Summary: This study investigated the prevalence of colistin heteroresistance in carbapenem-resistant Pseudomonas aeruginosa (CRPA) and its association with clinical outcomes. The results showed that colistin heteroresistance was present in up to 26% of CRPA patients, but it did not have a significant impact on 90-day mortality.
JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY
(2022)
Article
Immunology
Greta Zaborskyte, Erik Wistrand-Yuen, Karin Hjort, Dan I. Andersson, Linus Sandegren
Summary: Medical device-related biofilms are a major cause of hospital-acquired infections. The 3D-printed device (FlexiPeg) presented in this study is a robust and easy-to-use tool for studying biofilms, with versatile applications.
FRONTIERS IN CELLULAR AND INFECTION MICROBIOLOGY
(2022)
Article
Food Science & Technology
Konstantinos Koutsoumanis, Ana Allende, Avelino Alvarez-Ordonez, Declan Bolton, Sara Bover-Cid, Marianne Chemaly, Robert Davies, Alessandra De Cesare, Lieve Herman, Friederike Hilbert, Roland Lindqvist, Maarten Nauta, Giuseppe Ru, Marion Simmons, Panagiotis Skandamis, Elisabetta Suffredini, Dan I. Andersson, Vasileios Bampidis, Johan Bengtsson-Palme, Damien Bouchard, Aude Ferran, Maryline Kouba, Secundino Lopez Puente, Marta Lopez-Alonso, Soren Saxmose Nielsen, Alena Pechova, Mariana Petkova, Sebastien Girault, Alessandro Broglia, Beatriz Guerra, Matteo Lorenzo Innocenti, Ernesto Liebana, Gloria Lopez-Galvez, Paola Manini, Pietro Stella, Luisa Peixe
Summary: EFSA and EMA collaborated to assess the specific concentrations of sulfonamides in non-target feed for food-producing animals and their impact on bacterial resistance and growth promotion. However, due to lack of data, conclusions could not be drawn, and further studies are needed to fill the gaps.
Article
Food Science & Technology
Konstantinos Koutsoumanis, Ana Allende, Avelino Alvarez-Ordonez, Declan Bolton, Sara Bover-Cid, Marianne Chemaly, Robert Davies, Alessandra De Cesare, Lieve Herman, Friederike Hilbert, Roland Lindqvist, Maarten Nauta, Giuseppe Ru, Marion Simmons, Panagiotis Skandamis, Elisabetta Suffredini, Dan Andersson, Vasileios Bampidis, Johan Bengtsson-Palme, Damien Bouchard, Aude Ferran, Maryline Kouba, Secundino Lopez Puente, Marta Lopez-Alonso, Soren Saxmose Nielsen, Alena Pechova, Mariana Petkova, Sebastien Girault, Alessandro Broglia, Beatriz Guerra, Matteo Lorenzo Innocenti, Ernesto Liebana, Gloria Lopez-Galvez, Paola Manini, Pietro Stella, Luisa Peixe
Summary: The EFSA collaborated with the EMA to assess specific concentrations of amoxicillin and penicillin V in non-target feed for food-producing animals. The study aimed to understand the effects on bacterial resistance and growth promotion. New assessment models were recommended for addressing antimicrobial resistance, along with the need for further data to fill the gaps in calculations.
Article
Food Science & Technology
Ana Allende, Konstantinos Koutsoumanis, Ana Allende, Avelino Alvarez-Ordonez, Declan Bolton, Sara Bover-Cid, Marianne Chemaly, Robert Davies, Alessandra De Cesare, Lieve Herman, Friederike Hilbert, Roland Lindqvist, Maarten Nauta, Giuseppe Ru, Marion Simmons, Panagiotis Skandamis, Elisabetta Suffredini, Dan Andersson, Vasileios Bampidis, Johan Bengtsson-Palme, Damien Bouchard, Aude Ferran, Maryline Kouba, Secundino Lopez Puente, Marta Lopez-Alonso, Soren Saxmose Nielsen, Alena Pechova, Mariana Petkova, Sebastien Girault, Alessandro Broglia, Beatriz Guerra, Matteo Lorenzo Innocenti, Ernesto Liebana, Gloria Lopez-Galvez, Paola Manini, Pietro Stella, Luisa Peixe
Summary: The European Food Safety Authority and the European Medicines Agency collaborated to assess the effects of antibiotic concentrations in feed on antimicrobial resistance and growth promotion. Due to data gaps, assessments for some antibiotics could not be completed, and further studies are recommended to fill these gaps.
Review
Microbiology
Roderich Roemhild, Tobias Bollenbach, Dan I. Andersson
Summary: This review discusses the importance of using combination antibiotics to enhance treatment efficacy and combat resistance evolution. While several promising strategies have been proposed, a deeper understanding of the physiological responses and genetic mechanisms underlying antibiotic interactions and their clinical applicability is still lacking.
NATURE REVIEWS MICROBIOLOGY
(2022)
Article
Immunology
Po-Cheng Tang, Olle Eriksson, Josefin Sjogren, Nikos Fatsis-Kavalopoulos, Johan Kreuger, Dan I. Andersson
Summary: Biofilms are a crucial mode of growth for bacteria, but how antibiotic resistance emerges and is selected in biofilms is poorly understood. This study developed and validated a microfluidic chip (Brimor) for studying the dynamics of antibiotic-resistant bacteria in biofilms. The chip was found to be easy to use and a relevant model for studying the selection of antibiotic resistance in bacterial biofilms, providing valuable insights into this area of research.
FRONTIERS IN CELLULAR AND INFECTION MICROBIOLOGY
(2022)
Article
Microbiology
Karin Hjort, Elin Fermer, Po-Cheng Tang, Dan I. Andersson
Summary: The use and misuse of antibiotics have led to the selection of difficult-to-treat resistant bacteria. This study compared the selection of antibiotic-resistant E. coli strains during planktonic and biofilm growth. The results showed that resistant mutants were selected at sub-minimal inhibitory concentrations (MICs) in both growth conditions, emphasizing the significance of low antibiotic concentrations in driving the emergence and enrichment of resistant bacteria.
Article
Biology
Arianne M. Babina, Serhiy Surkov, Weihua Ye, Jon Jerlstrom-Hultqvist, Marten Larsson, Erik Holmqvist, Per Jemth, Dan Andersson, Michael Knopp
Summary: The origins and evolution of small proteins with diverse physiological roles remain unclear. Recent genomic sequence analyses suggest that new functions encoded by small open reading frames (sORFs) may emerge de novo from noncoding sequences. This study shows that randomly generated sORFs can rescue Escherichia coli cells by upregulating hisB expression and that they bind to the 5' end regulatory region of the his operon mRNA, promoting structural rearrangements of the RNA for increased hisB expression. This provides experimental evidence that small proteins with selective benefits can originate from the expression of nonfunctional sequences.
Article
Biology
Ramith R. Nair, Dan I. Andersson
Summary: The dynamics of nitrofurantoin resistance selection in Escherichia coli is significantly affected by interspecies interactions with Bacillus subtilis. The presence of B. subtilis slows down the selection for resistant E. coli mutants by producing extracellular compounds, particularly the YydF peptide. This study highlights the importance of considering interspecies interactions in understanding and predicting the evolution of antibiotic resistance.
COMMUNICATIONS BIOLOGY
(2023)
