Review
Environmental Sciences
Chuxiong Deng, Guangye Zhang, Yaojun Liu, Xiaodong Nie, Zhongwu Li, Junyu Liu, Damei Zhu
Summary: Terracing has been important for soil conservation and agricultural production for thousands of years, providing benefits such as reduced runoff and sediment, increased crop yields, and soil moisture. However, as terraces age, they may lead to environmental issues such as interference with water circulation.
INTERNATIONAL SOIL AND WATER CONSERVATION RESEARCH
(2021)
Review
Biochemistry & Molecular Biology
Ola Habanjar, Mona Diab-Assaf, Florence Caldefie-Chezet, Laetitia Delort
Summary: The 3D culture system has become essential in cancer research and tissue engineering for its ability to mimic tumor microenvironment and provide better biocompatibility. Different types of natural supports, synthetic strategies, and methods for generating normal and tumor spheroids are key factors in constructing ideal 3D models.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Review
Chemistry, Multidisciplinary
Andrew Jordan, Patrick Stoy, Helen F. Sneddon
Summary: This review discusses the reasons behind the widespread use of chlorinated solvents in chemistry laboratories, the increasing drive to minimize their usage, and the current alternatives available.
Review
Nutrition & Dietetics
Rebecca Olson, Breda Gavin-Smith, Chiara Ferraboschi, Klaus Kraemer
Summary: Food fortification is a cost-effective strategy that helps reduce micronutrient deficiencies and improve social and economic benefits. Despite ongoing debates globally and in some countries, successful food fortification programs require partnerships that include the public, private sector, and other stakeholders to address challenges effectively.
Review
Chemistry, Analytical
Briza Perez-Lopez, Monica Mir
Summary: The current situation of the Covid-19 pandemic is characterized by a high number of infections, high lethality, and rapid spread, severely affecting the global economy. Rapid diagnosis and testing are crucial in fighting the pandemic and maintaining public health. Various biosensing and diagnostic technologies are being developed and used to monitor the spread of the virus, with in vitro diagnosis companies striving to validate and deploy their technology quickly in the international market.
Article
Engineering, Environmental
Shuyao Zhu, Bingqing Yang, Yuqian Jia, Feiyu Yu, Zhiqiang Wang, Yuan Liu
Summary: This study aimed to explore the impact of different disinfectants on the horizontal transfer of antibiotic resistance genes (ARGs) and their underlying mechanisms. The results showed that quaternary ammonium salt, organic halogen, alcohol, and guanidine disinfectants significantly facilitated the conjugative transfer, while heavy metals, peroxides, and phenols displayed an inhibitory effect. Furthermore, guanidine disinfectants promoted conjugation through increased cell membrane permeability, over-production of reactive oxygen species (ROS), enhanced SOS response, and altered expression of conjugative transfer-related genes. Moreover, guanidine disinfectants also promoted bacterial energy metabolism and flagellum motility. These findings highlight the potential risks caused by the massive use of guanidine disinfectants, especially during the COVID-19 pandemic.
JOURNAL OF HAZARDOUS MATERIALS
(2023)
Review
Pharmacology & Pharmacy
Patrycja Kleczkowska, Dorota Sulejczak, Malgorzata Zaremba
Summary: Disulfiram is a well-known anti-alcohol agent that also shows potential in treating other forms of drug addiction, but it carries the greatest risk of pharmacological interactions compared to other drugs used in alcohol dependence.
EUROPEAN JOURNAL OF PHARMACOLOGY
(2021)
Article
Biotechnology & Applied Microbiology
Joshua G. Philips, Elena Martin-Avila, Andrea V. Robold
Summary: This review provides updated evidence on the likelihood, factors, and barriers for horizontal gene transfer in genetically modified plants, and presents the legislation and frameworks followed by the Australian Gene Technology Regulator in considering the risks posed by horizontal gene transfer.
FRONTIERS IN BIOENGINEERING AND BIOTECHNOLOGY
(2022)
Review
Polymer Science
Mateus Manabu Abe, Julia Ribeiro Martins, Paula Bertolino Sanvezzo, Joao Vitor Macedo, Marcia Cristina Branciforti, Peter Halley, Vagner Roberto Botaro, Michel Brienzo
Summary: The production of bioplastics, mainly from polysaccharides such as starch, has become a growing strategy to mitigate the environmental impacts of plastic waste. The use of plasticizers, blends, and reinforcement with lignocellulosic components has shown promising and environmentally safe alternatives for overcoming the limitations of bioplastics.
Article
Environmental Sciences
Shuai Zhang, Wen-Long Sun, Hai-Liang Song, Ting Zhang, Minghao Yin, Qilin Wang, XiaoJun Zuo
Summary: Voltage has the potential to affect bacterial mutation frequency and the transfer frequency of ARGs. This is likely due to the induction of oxidative reactions and increased cell membrane permeability caused by electrical stimulation.
Article
Evolutionary Biology
Joshua T. Smith, Cheryl P. Andam
Summary: Members of the genus Staphylococcus have been historically classified into coagulase-positive and coagulase-negative based on the presence of the coagulase protein. While horizontal gene transfer has been well-studied in CoPS species like Staphylococcus aureus, this study sheds light on the importance of these processes in CoNS evolution. CoNS species serve as reservoirs of transferrable genes associated with antimicrobial resistance, with certain species acting as hubs of gene flow and genetic diversity for the entire genus.
GENOME BIOLOGY AND EVOLUTION
(2021)
Article
Biochemical Research Methods
Le Yuan, Hongzhong Lu, Feiran Li, Jens Nielsen, Eduard J. Kerkhoven
Summary: In this study, a computational toolbox called HGTphyloDetect was developed, which combines high-throughput analysis with phylogenetic inference to accurately identify horizontal gene transfer (HGT) events and illustrate the transmission pathway among evolutionarily distant or closely related species. The HGTphyloDetect toolbox is user-friendly, capable of detecting HGT events with high efficiency and low false discovery rate.
BRIEFINGS IN BIOINFORMATICS
(2023)
Review
Biochemistry & Molecular Biology
Wiktoria Wrobel, Emilia Pach, Iwona Ben-Skowronek
Summary: Achondroplasia is a genetic disorder caused by a mutation in the FGFR3 gene, leading to short stature. Treatment is necessary to improve quality of life and reduce complications, with recombinant human growth hormone being the current best option. Other drugs are still in early stages of clinical trials.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Medicine, General & Internal
Malgorzata Wierzbicka, Witold Szyfter, Grazyna Greczka, Wojciech Gawecki
Summary: The study showed that the 3D exoscope provides excellent, highly magnified, and well-illuminated high-definition images of the surgical field, outperforming the traditional operating microscope in various aspects. However, limitations were also observed, including decreased depth perception in deep areas of the tympanic cavity and reduced visibility in a narrow surgical field, leading to the need to switch to an operating microscope in select cases.
JOURNAL OF CLINICAL MEDICINE
(2021)
Review
Immunology
Meiying Tan, Chuan Liao, Lina Liang, Xueli Yi, Zihan Zhou, Guijiang Wei
Summary: This article provides an overview of the principle, advantages, and disadvantages of a nucleic acid amplification method called recombinase polymerase amplification (RPA). The specific applications of RPA in detecting bacteria, fungi, viruses, parasites, drug resistance genes, genetically modified foods, and SARS-CoV-2 are described.
FRONTIERS IN CELLULAR AND INFECTION MICROBIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Fanny E. Hartmann, Sandra Lorena Ament-Velasquez, Aaron A. Vogan, Valerie Gautier, Stephanie Le Prieur, Myriam Berramdane, Alodie Snirc, Hanna Johannesson, Pierre Grognet, Fabienne Malagnac, Philippe Silar, Tatiana Giraud
Summary: The study reveals the presence of nonrecombining regions around the mating-type locus in the fungus Podospora anserina and related species, leading to occasional recombination due to the labile and polymorphic nature of these regions. The size and location of the nonrecombining region vary between strains and species, resulting in differences in heterozygosity levels. Low levels of heterozygosity suggest low but nonnull outcrossing rates in nature for these pseudohomothallic fungi, contributing to our understanding of mating-type chromosome evolution and mating systems.
MOLECULAR BIOLOGY AND EVOLUTION
(2021)
Article
Ecology
Ivain Martinossi-Allibert, Carl Veller, S. Lorena Ament-Velasquez, Aaron A. Vogan, Claus Rueffler, Hanna Johannesson
Summary: Meiotic drivers (MDs) are selfish genetic elements that can spread in a population due to their transmission advantage, even if they impose fitness costs on their host organisms. The ability of an MD to invade and coexist in a population depends on the host organism's biology and the specific fitness effects of the driving allele on the host.
Article
Biochemistry & Molecular Biology
Aaron A. Vogan, S. Lorena Ament-Velasquez, Eric Bastiaans, Ola Wallerman, Sven J. Saupe, Alexander Suh, Hanna Johannesson
Summary: The study reports the discovery of a giant tyrosine-recombinase-mobilized DNA transposon named Enterprise, and the finding that the Spok block not only has meiotic driving ability but also transposition capability. Additionally, experimental evidence demonstrates the deleterious effects of the Spok block in Podospora.
Article
Mycology
Aaron A. Vogan, Ivain Martinossi-Allibert, S. Lorena Ament-Velasquez, Jesper Svedberg, Hanna Johannesson
Summary: During meiosis, the phenomenon of meiotic drive allows certain genes to manipulate the inheritance of alleles, resulting in a higher frequency of one allele over the other. In ascomycete fungi, meiotic drive is known as spore killing and has recently been studied extensively at the genetic, genomic, and molecular levels. This review summarizes the known diversity of spore killers and explores their impacts on genome architecture, resistance mechanisms, population dynamics, speciation, and gene flow. The authors suggest that spore killing is common but under-observed in natural populations, and they encourage further research on this remarkable genetic phenomenon.
Editorial Material
Biochemistry & Molecular Biology
Emile Gluck-Thaler, Aaron A. Vogan, Sara Branco
Summary: A new study identifies HEPHAESTUS as a large, horizontally transferred mobile genetic element in fungi that carries cargo and confers tolerance to multiple metals.
Article
Biochemistry & Molecular Biology
Emile Gluck-Thaler, Timothy Ralston, Zachary Konkel, Cristhian Grabowski Ocampos, Veena Devi Ganeshan, Anne E. Dorrance, Terry L. Niblack, Corlett W. Wood, Jason C. Slot, Horacio D. Lopez-Nicora, Aaron A. Vogan
Summary: Accessory genes in a species can vary and act as a reservoir of adaptive functions. This study discovered a group of massive mobile elements called Starships in fungi that facilitate genome content variation. These Starships have shaped fungal genomes for millions of years and represent a new route for evolution in eukaryotes.
MOLECULAR BIOLOGY AND EVOLUTION
(2022)
Article
Genetics & Heredity
Clement Goubert, Rory J. Craig, Agustin F. Bilat, Valentina Peona, Aaron A. Vogan, Anna Protasio
Summary: This paper provides a set of detailed computer protocols, software recommendations, and video tutorials for those aiming to manually curate transposable elements (TEs). The proposed programs and tools make the process of manual curation achievable and accessible to all researchers, especially those new to the field of TEs.
Correction
Genetics & Heredity
Clement Goubert, Rory J. Craig, Agustin F. Bilat, Valentina Peona, Aaron A. Vogan, Anna V. Protasio
Article
Ecology
S. Lorena Ament-Velasquez, Aaron A. Vogan, Alexandra Granger-Farbos, Eric Bastiaans, Ivain Martinossi-Allibert, Sven J. Saupe, Suzette de Groot, Martin Lascoux, Alfons J. M. Debets, Corinne Clave, Hanna Johannesson
Summary: Genetic, ecological and simulation data demonstrate that the origin and coexistence of reproductively isolated sympatric groups in a fungus is driven by pleiotropic vegetative incompatibility genes under balancing selection.
NATURE ECOLOGY & EVOLUTION
(2022)
Article
Ecology
Aaron A. Vogan, Jesper Svedberg, Magdalena Grudzinska-Sterno, Hanna Johannesson
Summary: This study reveals the role of meiotic drive in the formation of Bateson-Dobzhansky-Muller (BDM) incompatibilities. Using the model fungus Neurospora, the researchers demonstrate that the large meiotic drive haplotypes Sk-2 and Sk-3 contain putative sexual incompatibilities. Their experiments show that when strains of N. intermedia carry Sk-2 or Sk-3, the proportion of viable progeny drops substantially, indicating the contribution of meiotic drive to reproductive isolation and speciation.
Editorial Material
Biochemistry & Molecular Biology
S. Lorena Ament-Velasquez, Aaron A. Vogan
TRENDS IN MICROBIOLOGY
(2022)
Article
Biochemical Research Methods
Pouyan Chamanian, Paul G. Higgs
Summary: We present simulations of non-enzymatic template-directed RNA synthesis and find that virtual circle genomes do not emerge naturally and functional sequences cannot be encoded on a virtual circle. Additionally, sequence scrambling occurs in populations of protocells, causing the loss of functional sequences even under positive selection.
PLOS COMPUTATIONAL BIOLOGY
(2022)
Article
Biology
Felipe Rivera-Madrinan, Katherine Di Iorio, Paul G. Higgs
Summary: The rolling circle mechanism is a possible way for replication to begin in the RNA World. In this study, simulations were conducted to investigate the replication process of rolling circle RNAs in populations of protocells. The presence of self-cleaving ribozymes, such as hammerheads, is crucial for this mechanism. Errors in copying the hammerhead sequence can lead to the creation of strands that are multiple times the length of the minimal sequence, providing space for the origin of new genes. If a beneficial gene appears in this new space, it can be selected and evolve into a longer circle, even though it replicates more slowly.
Article
Virology
Hyunjin Park, Saven Denha, Paul G. G. Higgs
Summary: RNA viruses can be monopartite, multipartite, or segmented. This article explores the competition between a complete monopartite virus and two defective viruses that have complementary genes. Stochastic models are used to study the replication and transmission of these viruses. The formation of segmented particles is influenced by the speed of assembly of the defective viruses, and different scenarios determine whether the monopartite or segmented virus can eliminate the other. Conditions of excess protein or RNA resources favor different types of viruses. The study also investigates the impact of deleterious mutations on virus behavior.
Article
Chemistry, Multidisciplinary
Varun Kitson, Quentin Sanders, Avinash V. Dass, Paul G. Higgs
Summary: This article discusses the theoretical models and experimental results of RNA polymerization, showing the differences in mechanisms and effects when different types of phosphates are involved. It suggests that the presence of 5'-triphosphates can lead to a circular reaction flux in RNA polymerization, resembling a metabolism pathway.