Review
Biochemical Research Methods
Zhaoqian Liu, Jingtong Feng, Bin Yu, Qin Ma, Bingqiang Liu
Summary: Bacterial genomes are recognized to closely interact with cellular processes. Researchers focus on uncovering organizational mechanisms of bacterial genomes to reveal potential cellular activities. Advances in experimental techniques and computational models provide opportunities for understanding these mechanisms, including local structures such as operons/transcription units and global constraints shaping bacterial genomes.
BRIEFINGS IN BIOINFORMATICS
(2021)
Article
Physics, Multidisciplinary
Luc Ciompi, Wolfgang Tschacher
Summary: This paper explores the affect-logic approach to schizophrenia in light of general complexity theories of cognition, suggesting that emotional tension may play a role in the transition from normal to psychotic functioning in vulnerable individuals. Additionally, the free energy principle proposes that psychotic symptoms correspond to alternative ways of minimizing free energy, leading to distorted perceptions of the body, self, and reality.
Article
Plant Sciences
Senjie Lin, Bo Song, David Morse
Summary: The genome architecture, evolution, and function in dinoflagellates are enigmatic and continuously inspire scientific quests. Recent research has shed light on the spatial organization of symbiodiniacean genomes, hinting at potential evolutionary trends in chromosome number decrease and length increase. Despite remaining mysteries, these findings provide new starting points for future inquiries.
JOURNAL OF PHYCOLOGY
(2021)
Article
Microbiology
Khandaker Rayhan Mahbub, Caroline Chenard, Steven Batinovic, Steve Petrovski, Federico M. Lauro, Md Hafizur Rahman, Mallavarapu Megharaj, Ashley E. Franks, Maurizio Labbate
Summary: This study compared the genomes of three metal-resistant bacteria isolated from mercury-contaminated soil. Diverse and novel mobile genetic elements (MGEs) were found, with evidence of lateral gene transfer (LGT) events shaping the genomic structure and heavy metal resistance. The strains Sphingobium sp SA2 and Sphingopyxis sp SE2 were resistant to multiple metals, while Pseudoxanthomonas sp SE1 showed resistance to mercury only. Whole genome sequencing revealed that the Sphingobium and Sphingopyxis strains contained multiple chromosomes and plasmids, while the Pseudoxanthomonas strain had one circular chromosome. Metal resistance genes were associated with various MGEs, including genomic islands (GIs), integrative conjugative elements (ICEs), transposons, insertion sequences (IS), recombinase in trio (RIT) elements, and group II introns. The study highlights the importance of LGT in the evolution of metal resistance in bacteria.
ENVIRONMENTAL MICROBIOLOGY
(2023)
Review
Chemistry, Physical
Peng Zhou, Chengqian Yuan, Xuehai Yan
Summary: Self-assembled peptide hydrogel is a promising biomaterial that exhibits unique properties in molecular design, hydrogel structure, and control strategies. Computational methods have played an important role in understanding the self-assembly process and morphologies of peptide hydrogels.
CURRENT OPINION IN COLLOID & INTERFACE SCIENCE
(2022)
Review
Physiology
Andrea Behanova, Anna Klemm, Carolina Waehlby
Summary: Interpreting tissue architecture is crucial for understanding healthy tissue development and disease. This review discusses novel molecular detection and imaging techniques that enable the mapping and localization of various objects in tissue space. It presents several methods for quantification and statistical verification of observed patterns in tissue architecture, categorized into three groups based on the type of objects. The review also explores four hypotheses related to the ability of these methods to distinguish between random and non-random distributions of objects, and provides information on openly available tools for these methods. Other spatial statistics methods compatible with different types of input data are also discussed.
FRONTIERS IN PHYSIOLOGY
(2022)
Article
Evolutionary Biology
Nitish Malhotra, Aswin Sai Narain Seshasayee
Summary: Bacterial genome organization is influenced by chromosomal replication and the presence of long identical DNA repeats. The positioning of long DNA repeats in the genome is under selection, as it affects bacterial fitness and growth rate. A study found that the distribution of long DNA repeats differs between fast- and slow-growing bacteria, suggesting that their positioning is a major constraint in maintaining the genome organization and minimizing disruption.
GENOME BIOLOGY AND EVOLUTION
(2022)
Article
Multidisciplinary Sciences
Mayank N. K. Choudhary, Kara Quaid, Xiaoyun Xing, Heather Schmidt, Ting Wang
Summary: Transposable elements (TEs), previously considered as junk DNA, contribute to species-specific 3D-genome structure by providing binding sites for CTCF protein. These elements play a role in gene regulation during mammalian evolution.
NATURE COMMUNICATIONS
(2023)
Article
Management
Jan Youtie, Robert Ward, Philip Shapira, R. Sandra Schillo, E. Louise Earl
Summary: This study explores a novel method using media sources and social networks to identify innovation ecosystems, and conducts an empirical study in the agri-food industry in Winnipeg, Canada. The results show that plant-based protein firms have a higher innovation orientation compared to conventional food processors, and have more ecosystem associations with industry, government, and other agricultural companies.
TECHNOLOGY ANALYSIS & STRATEGIC MANAGEMENT
(2023)
Review
Gastroenterology & Hepatology
Charles H. Danan, Kay Katada, Louis R. Parham, Kathryn E. Hamilton
Summary: The complex nature of the intestinal mucosa requires a spatial approach to study gut transcriptomics. Spatial transcriptomic techniques have become increasingly accessible and popular in the gut, allowing for the construction of spatial transcriptional maps at pseudosingle-cell resolution. These techniques have led to previously unattainable discoveries in the field.
AMERICAN JOURNAL OF PHYSIOLOGY-GASTROINTESTINAL AND LIVER PHYSIOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Mingyang Liu, Yun Li, Hongzhe Li
Summary: Researchers developed a deep learning method, e-DeepBGC, for detecting BGCs and their biosynthetic classes in bacterial genomes. Compared to previous methods, e-DeepBGC can accurately identify BGCs and improve the sensitivity of BGC detection while reducing false positive rates. The researchers applied e-DeepBGC to a large dataset of bacterial genomes and summarized the functional classes and distribution of predicted BGCs in different bacterial phyla.
JOURNAL OF MOLECULAR BIOLOGY
(2022)
Review
Chemistry, Multidisciplinary
Vinayak Bhat, Connor P. Callaway, Chad Risko
Summary: Computational methods can complement experimental observations and provide deep physicochemical insights into the structure-processing-property relationships of organic semiconductors. This Review traces the evolution of these methods in the field of organic semiconductors, highlighting their limitations and the creation of sophisticated frameworks to overcome these limitations. Through various examples, this Review demonstrates the applications of computational methods in accelerating the deployment of organic semiconductors in various technologies.
Article
Multidisciplinary Sciences
Daniel Dar, Nina Dar, Long Cai, Dianne K. Newman
Summary: The par-seqFISH method allows for recording gene expression and spatial context of microbial populations, revealing diverse physiological states coexisting within the same biofilm with high spatial resolution when studying Pseudomonas aeruginosa.
Article
Multidisciplinary Sciences
Mostafa M. H. Ellabaan, Christian Munck, Andreas Porse, Lejla Imamovic, Morten O. A. Sommer
Summary: Antibiotic resistance spreads among bacteria through horizontal transfer of antibiotic resistance genes. Researchers identified potential mobilization elements and other features associated with ARG transfer among bacterial clades, predicting the potential future dissemination of known ARGs.
NATURE COMMUNICATIONS
(2021)
Article
Biology
Xavier Didelot, Julian Parkhill
Summary: In recent years, the practicality of sequencing whole genomes from a large number of bacterial isolates has increased significantly, providing new insights into the evolution and epidemiology of bacterial pathogens. This article presents a step-by-step approach for large-scale genomic epidemiology analyses, focusing on the construction and application of dated phylogenies. The key advantage of this approach is its computational scalability, allowing for the analysis of hundreds or thousands of genomes within a short period of time.
PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES
(2022)
Article
Microbiology
Peter H. Culviner, Isabel Nocedal, Sarah M. Fortune, Michael T. Laub
Summary: A global analysis of 9 endoribonuclease toxins from E. coli revealed that these toxins use low-information cleavage motifs to cut a significant proportion of mRNAs and inhibit ribosome biogenesis, disrupting translation.
Article
Multidisciplinary Sciences
Marcin J. Szafran, Tomasz Malecki, Agnieszka Strzalka, Katarzyna Pawlikiewicz, Julia Dulawa, Anna Zarek, Agnieszka Kois-Ostrowska, Kim C. Findlay, Tung B. K. Le, Dagmara Jakimowicz
Summary: Bacteria of the genus Streptomyces have a linear chromosome and undergo substantial rearrangement during sporulation, transitioning from an 'open' to a 'closed' conformation, similar to eukaryotes.
NATURE COMMUNICATIONS
(2021)
Article
Biology
Monica S. Guo, Ryo Kawamura, Megan L. Littlehale, John F. Marko, Michael T. Laub
Summary: The GapR-seq method allows high-resolution mapping of positive supercoiling in genomes, revealing its widespread presence, association with transcription, and enrichment between certain genes. This approach provides new insights into chromosome structure and organization that are not accessible with existing methods like Hi-C.
Article
Biology
Adam S. B. Jalal, Ngat T. Tran, Clare E. M. Stevenson, Afroze Chimthanawala, Anjana Badrinarayanan, David M. Lawson, Tung B. K. Le
Summary: The study reveals that Caulobacter crescentus ParB escapes from the nucleation site and spreads on neighboring DNA by using cytidine triphosphate. The findings suggest a gating mechanism operated by CTP to regulate the processes of nucleation, spreading, and recycling of ParB.
Article
Biochemistry & Molecular Biology
Mary K. Thompson, Isabel Nocedal, Peter H. Culviner, Tong Zhang, Kevin R. Gozzi, Michael T. Laub
Summary: Through the study of SymE, it is found that it can bind to DNA and drive nucleoid condensation, leading to inhibition of DNA and RNA synthesis and causing DNA damage. SymE may belong to a new class of nucleoid-associated proteins widely distributed in bacteria.
MOLECULAR MICROBIOLOGY
(2022)
Article
Multidisciplinary Sciences
Ross D. Jones, Yili Qian, Katherine Ilia, Benjamin Wang, Michael T. Laub, Domitilla Del Vecchio, Ron Weiss
Summary: Phosphorylation networks play a crucial role in complex cellular decision making. This study engineers synthetic phosphorylation devices with feedback regulation in mammalian cells and demonstrates their tunable and robust control over cell behaviors. By using bacterial two-component signaling proteins, the authors develop synthetic phosphoregulation devices that can precisely regulate target gene expression and withstand perturbations in mammalian cells. The work lays the foundation for establishing tunable, precise, and robust control over cell behavior with synthetic signaling networks.
NATURE COMMUNICATIONS
(2022)
Article
Ecology
David Ding, Anna G. Green, Boyuan Wang, Thuy-Lan Vo Lite, Eli N. Weinstein, Debora S. Marks, Michael T. Laub
Summary: Neutral mutations in proteins can influence future mutational possibilities and functions. In a study of a bacterial toxin-antitoxin system, researchers identified enabling mutations that allow the toxin to tolerate mutations in the antitoxin. These enabling mutations expand mutational paths and have implications for protein design and evolutionary forecasting.
NATURE ECOLOGY & EVOLUTION
(2022)
Article
Biology
Isabel Nocedal, Michael T. Laub
Summary: Gene duplication is important for generating new signaling pathways during evolution. In this study, the researchers used ancestral sequence reconstruction to resurrect a bacterial two-component signaling system that duplicated in alpha-proteobacteria. They determined the interaction specificities of the signaling proteins before and after the duplication event and identified key mutations responsible for establishing specificity in the two systems. These findings suggest that protein-protein interactions with latent potential may be easily duplicated and diverged.
Article
Biology
Sriram Srikant, Chantal K. Guegler, Michael T. Laub
Summary: This study reveals the mechanism by which phages overcome bacterial defense systems through experimental evolution. The emergence of one counter-defense mechanism can lead to the loss of other mechanisms, thus constraining the host range of phages.
Article
Microbiology
Michele LeRoux, Sriram Srikant, Gabriella I. C. Teodoro, Tong Zhang, Megan L. Littlehale, Shany Boron, Mohsen Badiee, Anthony K. L. Leung, Rotem Sorek, Michael T. Laub
Summary: The DarTG toxin-antitoxin system protects bacteria against phage infection by ADP-ribosylating viral DNA. The system can be evaded by phages through mutation of their DNA polymerase or the gp61.2 anti-DarT factor. A bioinformatics search identified homologues of DarTG, a family of TA systems that provide strong protection against phages. The toxin of DarTG modifies viral DNA upon phage infection, preventing replication and virion production. Phages have evolved mutations to overcome DarTG defense. These findings suggest that phage defense may be a common function of TA systems.
NATURE MICROBIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Kevin Gozzi, Ngat T. Tran, Joshua W. Modell, Tung B. K. Le, Michael T. Laub
Summary: Gene transfer agents (GTAs) are prophage-like entities found in bacterial genomes that can transfer host genome fragments to recipient cells, potentially contributing to bacterial survival in certain conditions.
Article
Microbiology
Christopher N. Vassallo, Christopher R. Doering, Megan L. Littlehale, Gabriella I. C. Teodoro, Michael T. Laub
Summary: The study identified numerous new candidate defense systems in E. coli using an experimental selection scheme, demonstrating that intact prophages and mobile genetic elements are primary reservoirs and distributors of defense systems.
NATURE MICROBIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Kirill V. Sukhoverkov, Adam S. B. Jalal, James R. Ault, Frank Sobott, David M. Lawson, Tung B. K. Le
Summary: In Bacillus subtilis, a ParB-like protein called Noc binds specifically to Noc-binding sites (NBSs) on the chromosome to coordinate chromosome segregation and cell division. Noc forms large membrane-associated nucleoprotein complexes by binding to CTP, which physically inhibits the assembly of the cell division machinery. The structure of Noc bound to NBS DNA reveals important conformational changes that occur during the binding process.
JOURNAL OF BIOLOGICAL CHEMISTRY
(2023)
Article
Multidisciplinary Sciences
Dia A. Ghose, Kaitlyn E. Przydzial, Emily M. Mahoney, Amy E. Keating, Michael T. Laub
Summary: The evolution of novel functions in biology relies on gene duplication and divergence, creating large paralogous protein families. However, the specificity of these paralogs to their interaction partners can be sensitive to mutation. Through deep mutational scanning, it was demonstrated that a family of bacterial signaling proteins exhibits marginal specificity, with individual substitutions leading to substantial cross-talk between pathways. These findings suggest that the evolution of bacterial signaling proteins is constrained by sequence space crowding, and that evolution selects for good enough rather than optimized phenotypes in paralogs.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Article
Multidisciplinary Sciences
Aoshu Zhong, Xiaofang Jiang, Alison B. Hickman, Katherine Klier, Gabriella I. C. Teodoro, Fred Dyda, Michael T. Laub, Gisela Storz
Summary: Recombination-promoting nuclease (Rpn) proteins are toxin-antitoxin systems that combat phage infection. The small Rpn C-terminal domains block the activities of the toxic RpnL proteins. Plasmid-encoded RpnP2L protects Escherichia coli against certain phages. This discovery suggests that many more intragenic-encoded proteins with regulatory roles may remain to be discovered in all organisms.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
