Review
Microbiology
Yuping Li, Joseph Bondy-Denomy
Summary: Bacteriophages encode diverse anti-CRISPR (Acr) proteins that inhibit CRISPR-Cas immunity during infection of their bacterial hosts. Instead of a single phage shutting down CRISPR-Cas immunity, a community of acr-carrying phages cooperate to suppress bacterial immunity, displaying low phage autonomy. Enzymatic Acr proteins with novel mechanisms have been recently revealed and are predicted to enhance phage autonomy, while phage DNA protective measures offer the highest phage autonomy observed. These varied Acr mechanisms and strengths also have unexpected impacts on the bacterial populations and competing phages.
CELL HOST & MICROBE
(2021)
Article
Physics, Multidisciplinary
D. Wellnitz, G. Preisser, V. Alba, J. Dubail, J. Schachenmayer
Summary: The study investigates the operator entanglement of the density matrix of 1D many-body models undergoing dissipative evolution, and finds that under the dissipative mechanism of dephasing, the operator entanglement can increase logarithmically at long times.
PHYSICAL REVIEW LETTERS
(2022)
Article
Humanities, Multidisciplinary
Salva Duran-Nebreda, Michael J. O'Brien, R. Alexander Bentley, Sergi Valverde
Summary: This study explores the relationship between diversity and innovation in cultural evolution, finding that when a cultural domain expands to the point of exceeding the supply of experts, diversity decreases and information redundancy increases, with imitation replacing invention. The model predictions are validated through case studies, revealing the dynamics of boom and bust in innovation.
HUMANITIES & SOCIAL SCIENCES COMMUNICATIONS
(2022)
Editorial Material
Environmental Sciences
John P. Dunne
Summary: This article suggests that the vertical migration of tiny phytoplankton provides an unrecognized resiliency to climate warming, which is critical for carbon storage and living marine resources.
NATURE CLIMATE CHANGE
(2022)
Article
Multidisciplinary Sciences
Marten Scheffer, Ingrid van de Leemput, Els Weinans, Johan Bollen
Summary: The research suggests that there has been a gradual increase in the use of words associated with rationality in books since 1850, while words related to human experience have decreased. In recent decades, this pattern has reversed, accompanied by a shift from collectivism to individualism and changes in the ratio between sentiment and rationality flag words. Overall, there has been a marked shift in public interest from collective to individual, and from rationality towards emotion in recent decades.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Chemistry, Physical
Marco Baiesi, Stefano Iubini, Enzo Orlandini
Summary: A mean-field kinetic model suggests that the relaxation dynamics of wormlike micellar networks is a long and complex process, with subtle end-recombination dynamics that may not be easily detected in rheology experiments. The relaxation time scale is exponential and related to the free energy of an end cap and branching free energy.
JOURNAL OF CHEMICAL PHYSICS
(2021)
Article
Environmental Sciences
Valenti Rull
Summary: Mangrove forests are essential ecosystems for biodiversity and carbon mitigation, but they are highly threatened. The CARMA database has analyzed past environmental shifts and the response of mangroves in the Caribbean region. The diversity and composition of Caribbean mangroves were shaped by evolutionary and climate changes, and human activities have led to significant deforestation. Urgent conservation actions are needed to prevent the disappearance of these ancient ecosystems.
SCIENCE OF THE TOTAL ENVIRONMENT
(2023)
Article
Ecology
Dominic McAfee, Sean D. Connell
Summary: This article discusses the expansion of non-native Pacific oysters into the former distribution areas of native oyster species worldwide, and the challenges and opportunities they bring to society and ecosystems.
FRONTIERS IN ECOLOGY AND THE ENVIRONMENT
(2021)
Article
Astronomy & Astrophysics
Marcel Lotz, Klaus Dolag, Rhea-Silvia Remus, Andreas Burkert
Summary: Post-starburst (PSB) galaxies represent a transition population between star-forming and quiescent galaxies, evolving through mergers, black hole activity, and AGN feedback. Field PSBs are primarily quenched by AGN feedback, while cluster PSBs are mostly shut down by environmental mechanisms such as ram-pressure stripping.
MONTHLY NOTICES OF THE ROYAL ASTRONOMICAL SOCIETY
(2021)
Article
Plant Sciences
Guillermo Benitez, Marco Leonti, Barbara Bock, Simon Vulfsons, Amots Dafni
Summary: Mandrake, a famous medicinal plant, has a long history of medical use and is still used in popular medicine today. Although its role in popular medicine has diminished, mandrake-derived natural products such as atropine and scopolamine, as well as their semi-synthetic derivatives, continue to play an important role in medicine. This study aims to trace the historical and scientific events that led to the abandonment of mandrake as a medicine. The findings suggest a decrease in versatility and a more consolidated use pattern over time, possibly due to the reproduction of classic textual sources and reduced popularity of mandrake in medicine, while atropine gained importance in surgical interventions.
JOURNAL OF ETHNOPHARMACOLOGY
(2023)
Article
Development Studies
Douglas A. Irwin
Summary: Import substitution, once believed to be the best trade strategy to promote industrialization and economic growth in developing countries in the 1950s, faced widespread disenchantment by the mid-1960s. Early advocates of import substitution were cautious in their support and among the first to question its effectiveness based on country experiences.
Review
Microbiology
Sandra C. Garrett
Summary: CRISPR-Cas is a unique prokaryotic immune system that provides sequence-specific adaptive protection and can be updated in response to new threats. This system stores DNA fragments from invading genetic elements and continuously updates them, while regulating spacer uptake, residency, and loss for optimized immunity.
FRONTIERS IN MICROBIOLOGY
(2021)
Review
Cardiac & Cardiovascular Systems
James S. Lawson
Summary: This review explores the decline in coronary heart disease and its relation to atherosclerosis and tobacco smoking. The prevalence of coronary atherosclerosis rose dramatically between 1900 and 1960 but fell equally dramatically between 1960 and 2010. The decline in atherosclerosis can be attributed to the reduction in tobacco smoking and the control of hypertension and high serum total cholesterol.
FRONTIERS IN CARDIOVASCULAR MEDICINE
(2023)
Editorial Material
Biochemistry & Molecular Biology
Thomas J. Matthews
Summary: Islands serve as platforms for various remarkable evolutionary phenomena, such as the island rule - the tendency for animals to either shrink or enlarge in size. A recent study on insular mammals reveals that these size shifts make these evolutionary marvels more susceptible to extinction.
Article
Multidisciplinary Sciences
Chakresh Kumar Singh, Emma Barme, Robert Ward, Liubov Tupikina, Marc Santolini
Summary: The rise and fall of scientific fields follow a common evolutionary pattern, with early stages characterized by interdisciplinary works and small teams, while late stages involve specialized, large teams building on previous works. This method provides a foundation for quantitatively exploring generic patterns in the evolution of research fields, with implications for innovation studies.
Article
Multidisciplinary Sciences
Sofie M. Castelein, Tom F. Aarts, Juergen Schleppi, Ruud Hendrikx, Amarante J. Boettger, Dominik Benz, Maude Marechal, Advenit Makaya, Stan J. J. Brouns, Martin Schwentenwein, Anne S. Meyer, Benjamin A. E. Lehner
Summary: In-situ resource utilization is essential for sustainable extra-terrestrial colonies, with the use of self-reproducing bacteria showing promise for resource extraction. Combining bacterial treatment and magnetic extraction can significantly improve the quantity and concentration of extracted materials.
Article
Multidisciplinary Sciences
Sam P. B. van Beljouw, Anna C. Haagsma, Alicia Rodriguez-Molina, Daan F. van den Berg, Jochem N. A. Vink, Stan J. J. Brouns
Summary: The study presents a novel type III-E effector, Sb-gRAMP, which uses CRISPR RNA to guide target RNA recognition and cleavage, and potentially gains viral immunity through target RNA-induced protease activity.
Article
Multidisciplinary Sciences
Jurre A. Steens, Yifan Zhu, David W. Taylor, Jack P. K. Bravo, Stijn H. P. Prinsen, Cor D. Schoen, Bart J. F. Keijser, Michel Ossendrijver, L. Marije Hofstra, Stan J. J. Brouns, Akeo Shinkai, John van der Oost, Raymond H. J. Staals
Summary: Type III CRISPR-Cas systems recognize and cleave target RNAs and produce signalling molecules. Here the authors discover that both processes are governed by a flexible seed region, ultimately resulting in SCOPE, a SARSCoV-2 diagnostic assay with atto-molar sensitivity.
NATURE COMMUNICATIONS
(2021)
Article
Biochemistry & Molecular Biology
Balwina Koopal, Ana Potocnik, Sumanth K. Mutte, Cristian Aparicio-Maldonado, Simon Lindhoud, Jacques J. M. Vervoort, Stan J. J. Brouns, Daan C. Swarts
Summary: In this study, we identified SPARTA as a prokaryotic immune system that reduces cell viability by RNA-guided detection of invading DNA.
Article
Biochemistry & Molecular Biology
Rebecca E. McKenzie, Emma M. Keizer, Jochem N. A. Vink, Jasper van Lopik, Ferhat Bueke, Vera Kalkman, Christian Fleck, Sander J. Tans, Stan J. J. Brouns
Summary: The study reveals that CRISPR interference is fast and has a narrow distribution of clearance times. However, invaders with escaping mutations show large cell-to-cell variability, which stems from primed CRISPR adaptation. The growth rate, cell division, and Cascade levels of bacteria influence the chances of clearance by interference or priming.
MOLECULAR SYSTEMS BIOLOGY
(2022)
Article
Multidisciplinary Sciences
Jack P. K. Bravo, Cristian Aparicio-Maldonado, Franklin L. Nobrega, Stan J. J. Brouns, David W. Taylor
Summary: This study provides insights into the activation and phage DNA recognition mechanism of the widespread antiviral defense system by determining the structure of the core DISARM complex.
NATURE COMMUNICATIONS
(2022)
Article
Genetics & Heredity
Wen Y. Wu, Simon A. Jackson, Cristobal Almendros, Anna C. Haagsma, Suzan Yilmaz, Gerrit Gort, John van der Oost, Stan J. J. Brouns, Raymond H. J. Staals
Summary: This study characterized CRISPR adaptation of the type V-A system from Francisella novicida and the type V-B system from Alicyclobacillus acidoterrestris using a high-throughput sequencing approach. It was found that Cas12 nucleases are dispensable for spacer acquisition in both systems, with only Cas1 and Cas2 (type V-A) or Cas4/1 and Cas2 (type V-B) being necessary. Cas4 activity was shown to be required for protospacer adjacent motif selection and prespacer trimming. The study also revealed a preference for spacers derived from foreign DNA rather than the host chromosome.
Review
Microbiology
Sam P. B. van Beljouw, Jasper Sanders, Alicia Rodriguez-Molina, Stan J. J. Brouns
Summary: This review summarizes the current understanding of RNA-targeting CRISPR-Cas systems. The composition and properties of type III and type VI systems are detailed, and the cellular defense processes initiated upon viral RNA sensing are outlined. The broad RNA-activated immune responses are explained as an effective strategy to combat viral infection.
NATURE REVIEWS MICROBIOLOGY
(2023)
Review
Biotechnology & Applied Microbiology
Marina Mahler, Ana Rita Costa, Sam P. B. van Beljouw, Peter C. Fineran, Stan J. J. Brouns
Summary: In recent years, there has been increasing interest in using phage therapy to treat antibiotic-resistant bacterial infections, which has boosted bacteriophage research. There is also a desire to use phages and their unique proteins for specific biocontrol applications and diagnostics. However, manipulating phage genomes to understand and control gene functions, as well as altering phage properties such as host range, has been challenging due to a lack of universal selectable markers.
TRENDS IN BIOTECHNOLOGY
(2023)
Article
Biology
Daan F. van den Berg, Baltus A. van der Steen, Ana Rita Costa, Stan J. J. Brouns, Ruben L. Gonzalez
Summary: Transfer RNAs (tRNAs) encoded by bacteriophages have been found in bacterial hosts of different genera, but their exact function has been unclear for more than 50 years. The most widely accepted hypothesis is codon compensation, which suggests that phages encode tRNAs that supplement less frequently used codons by the host. However, our study proposes a new hypothesis that phage-encoded tRNAs counteract the tRNA-depleting strategies of the host using enzymes such as VapC, PrrC, Colicin D, and Colicin E5 to defend against viral infection.
Article
Biochemistry & Molecular Biology
Benjamin A. Adler, Marena Trinidad, Daniel Bellieny-Rabelo, Elaine Zhang, Hannah M. Karp, Petr Skopintsev, Brittney W. Thornton, Rachel F. Weissman, Peter H. Yoon, Linxing Chen, Tomas Hessler, Amy R. Eggers, David Colognori, Ron Boger, Erin E. Doherty, Connor A. Tsuchida, Ryan Tran, Laura Hofman, Honglue Shi, Kevin M. Wasko, Zehan Zhou, Chenglong Xia, Muntathar J. Al-Shimary, Jaymin R. Patel, Vienna C. J. X. Thomas, Rithu Pattali, Matthew J. Kan, Anna Vardapetyan, Alana Yang, Arushi Lahiri, Michaela F. Maxwell, Andrew G. Murdock, Glenn C. Ramit, Hope R. Henderson, Roland W. Calvert, Rebecca S. Bamert, Gavin J. Knott, Audrone Lapinaite, Patrick Pausch, Joshua C. Cofsky, Erik J. Sontheimer, Blake Wiedenheft, Peter C. Fineran, Stan J. J. Brouns, Dipali G. Sashital, Brian C. Thomas, Christopher T. Brown, Daniela S. A. Goltsman, Rodolphe Barrangou, Virginius Siksnys, Jillian F. Banfield, David F. Savage, Jennifer A. Doudna
Summary: CRISPR-Cas enzymes play a crucial role in bacterial immunity and genome editing. CasPEDIA is a comprehensive database that summarizes the enzymatic properties of Cas enzymes, providing valuable resources for researchers.
NUCLEIC ACIDS RESEARCH
(2023)
Review
Microbiology
Sam P. B. van Beljouw, Jasper Sanders, Alicia Rodriguez-Molina, Stan J. J. Brouns
Summary: This review summarizes the current understanding of RNA-targeting CRISPR-Cas systems, focusing on the composition, properties, and cellular defense processes initiated upon viral RNA sensing. The broad RNA-activated immune responses are described as an effective strategy to combat viral infections.
NATURE REVIEWS MICROBIOLOGY
(2023)
Review
Microbiology
Julia E. Egido, Ana Rita Costa, Cristian Aparicio-Maldonado, Pieter-Jan Haas, Stan J. J. Brouns
Summary: This article explores the defense mechanisms of bacteriophages and their relevance for the potential clinical use of bacteriophages as therapeutic agents, suggesting new directions for research.
FEMS MICROBIOLOGY REVIEWS
(2022)
Article
Multidisciplinary Sciences
Chunyi Hu, Cristobal Almendros, Ki Hyun Nam, Ana Rita Costa, Jochem N. A. Vink, Anna C. Haagsma, Saket R. Bagde, Stan J. J. Brouns, Ailong Ke
Summary: Prokaryotes adapt to challenges from mobile genetic elements by integrating spacers from foreign DNA into the CRISPR array. Cas4 nuclease, which contains a Fe-S cluster, is crucial in ensuring that spacers are acquired from DNA with a protospacer adjacent motif (PAM) and inserted unidirectionally. This intricate molecular interaction between Cas4 and Cas1-Cas2 is essential for selecting PAM-containing prespacers for integration and establishing directionality.
Article
Biotechnology & Applied Microbiology
Jochem N. A. Vink, Jan H. L. Baijens, Stan J. J. Brouns
Summary: This study uses metagenomic sequence databases to map a large number of unique CRISPR spacers and identify over 200 unique PAM sequences associated with specific CRISPR-Cas subtypes. The study reveals subtype-specific preferences for targeting different strands of open reading frames, as well as evidence of shared adaptation machinery and arrays between different CRISPR-Cas systems. This has implications for understanding how CRISPR-Cas systems function in various organisms.