Review
Biochemistry & Molecular Biology
J. Craig Venter, John I. Glass, Clyde A. Hutchison, Sanjay Vashee
Summary: Synthetic genomics involves synthesizing complete genomes or chromosomes to create viruses, bacteria, and eukaryotic cells. This field has revolutionized viral reverse genetics, vaccine design, and bacterial resistance. Future advances in DNA synthesis will open up extraordinary opportunities in medicine, industry, agriculture, and research.
Article
Chemistry, Physical
Xueying Luo, Xiaowei Wang, Yuan Yao, Xin Gao, Lu Zhang
Summary: This study has elucidated the template-dependent inhibitory mechanism of remdesivir on SARS-CoV-2 RdRp and identified the molecular mechanism of drug resistance caused by the V557L mutation.
JOURNAL OF PHYSICAL CHEMISTRY LETTERS
(2022)
Article
Multidisciplinary Sciences
Hong Zhan, Nuruddin Unchwaniwala, Andrea Rebolledo-Viveros, Janice Pennington, Mark Horswill, Roma Broadberry, Jonathan Myers, Johan A. den Boon, Timothy Grant, Paul Ahlquist
Summary: Positive-strand RNA viruses replicate their genomes in virus-induced membrane vesicles, and the resulting RNA replication complexes are a major target for virus control. Using cryoelectron microscopy, researchers have discovered that mature nodavirus crowns are composed of two stacked 12-mer rings of viral RNA replication protein A, demonstrating the multifunctionality and flexibility of viral proteins.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Article
Ecology
Francisco Martinez-Hernandez, Awa Diop, Inmaculada Garcia-Heredia, Louis-Marie Bobay, Manuel Martinez-Garcia
Summary: Viral genetic microdiversity has critical impacts on the viral-host arms race, microbial community structure, and biogeochemical cycles. Single-virus genomics has discovered abundant microdiversity in an ocean virus infecting marine bacteria, with up to 1,500 viral strains and 30 related species found in a single sample. The maintenance of viral microdiversity over space and time, and the impact of recombination on virus and host speciation have been demonstrated.
Article
Virology
Camila Perdoncini Carvalho, Ruifan Ren, Junping Han, Feng Qu
Summary: Natural selection influences cellular organisms by ensuring advantageous mutations gain phenotypic advantage. However, its mechanism in plus-strand RNA viruses remains unclear. Recent studies suggest that these viruses may use the BIAS mechanism to select and isolate beneficial mutations, explaining superinfection exclusion.
ANNUAL REVIEW OF VIROLOGY
(2022)
Review
Virology
Rui-Zhu Shi, Yuan-Qing Pan, Li Xing
Summary: RNA helicase A (RHA) is a DExH-box helicase that unwinds double-stranded RNA and plays a crucial role in RNA metabolism, especially in the replication of RNA viruses.
Article
Microbiology
Gaspar Bruner-Montero, Carlos M. M. Luque, Cassia Siqueira Cesar, Shuai Dominique Ding, Jonathan P. P. Day, Francis Michael Jiggins
Summary: By establishing infected insect cells and a simple virus detection method, we successfully isolated La Jolla virus and Newfield virus. These viruses have harmful effects on the host and can sterilize fruit flies, with potential for biocontrol of the crop pest Drosophila suzukii.
Review
Microbiology
Melia Bonnamy, Stephane Blanc, Yannis Michalakis
Summary: The replication of plant-infecting single-stranded DNA viruses, Geminiviridae and Nanoviridae, involves rolling-circle replication (RCR) and recombination-dependent replication (RDR) mechanisms. RCR relies on a virus-encoded Replication-associated protein (Rep) and specific sequences called iterons, while RDR is also observed in some double-stranded DNA viruses. This article provides a synthesis of the current understanding of these replication modes and discusses the potential role of gene copy number regulation in viral gene expression.
Review
Microbiology
Chonghui Xu, Jizheng Chen, Xinwen Chen
Summary: Hepatitis viruses are the primary causative agents of hepatitis and pose a major public health issue globally. The host innate immune system acts as the first line of defense against these viruses. However, hepatitis viruses evade host immune surveillance through various strategies, compromising the innate immune response and creating a favorable environment for viral replication.
FRONTIERS IN MICROBIOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Yunshan Zhang, Min Zhu, Xing Zhang, Kun Dai, Zi Liang, Jun Pan, Ziyao Zhang, Manman Cao, Renyu Xue, Guangli Cao, Xiaolong Hu, Chengliang Gong
Summary: This study demonstrates that Bombyx mori cypovirus can generate viral circRNAs, and one of these circRNAs translates into a micropeptide that regulates viral replication.
INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES
(2022)
Article
Plant Sciences
Arjun Khakhar, Daniel F. Voytas
Summary: The tools of synthetic biology offer great potential to uncover fundamental mechanisms in plant development and metabolism, but typically require transgenesis. Delivery of foreign genetic material to plants using systemically mobile RNA virus vectors can minimize transgenesis, revolutionizing plant synthetic biology by reducing costs, accelerating experimental timescales, and making genetic manipulation easier.
FRONTIERS IN PLANT SCIENCE
(2021)
Article
Multidisciplinary Sciences
Rommel J. Gestuveo, Jamie Royle, Claire L. Donald, Douglas J. Lamont, Edward C. Hutchinson, Andres Merits, Alain Kohl, Margus Varjak
Summary: The authors developed mosquito cell lines expressing Zika virus (ZIKV) capsid and conducted proteomics experiments, identifying 157 protein interactors, with 8 shown to act as pro-viral factors, demonstrating the transitional endoplasmic reticulum 94 (TER94) and its human ortholog VCP target ZIKV capsid to proteasomal degradation to facilitate infection.
NATURE COMMUNICATIONS
(2021)
Article
Biochemistry & Molecular Biology
Andrew H. Mack, Georgina Menzies, Alex Southgate, D. Dafydd Jones, Thomas R. Connor
Summary: The RNA-dependent RNA polymerase of SARS-CoV-2 is prone to errors, but these errors can be corrected by the exonuclease proofreading mechanism. The interplay between replicase fidelity and environmental pressures affects virus mutagenesis and evolutionary trajectory. A single distal mutation in NSP14 has been shown to significantly impact proofreading, leading to increased mutation accumulation and elevated evolutionary rate. Understanding these changes is crucial for understanding the population-wide evolution of the virus.
MOLECULAR BIOLOGY AND EVOLUTION
(2023)
Article
Physics, Multidisciplinary
M. Henstridge, M. Foerst, E. Rowe, M. Fechner, A. Cavalleri
Summary: Nonlinear phononics is a method for creating transient structural changes in solids. This study extends nonlinear phononics to propagating polaritons, separating the functional response from the optical drive.
Article
Microbiology
Jennifer Gribble, Laura J. Stevens, Maria L. Agostini, Jordan Anderson-Daniels, James D. Chappell, Xiaotao Lu, Andrea J. Pruijssers, Andrew L. Routh, Mark R. Denison
Summary: Recombination is essential for coronavirus diversity and the emergence of new strains. The mechanisms of CoV recombination are not well understood, but studies have shown extensive and diverse recombination products in CoVs during replication. The nsp14-ExoN protein is crucial for native recombination in CoVs, highlighting its potential as a target for inhibitors to control SARS-CoV-2 and future emerging zoonotic CoVs.
Article
Biochemical Research Methods
Veronica Aragones, Flavio Aliaga, Fabio Pasin, Jose-Antonio Daros
Summary: The JoinTRV vector system based on tobacco rattle virus (TRV) is introduced in this study, which simplifies gene silencing and genome editing. The system demonstrates successful applications in tobacco plants, allowing efficient delivery of single-guide RNAs and achieving high somatic cell editing efficiencies in Cas9 transgenic hosts.
BIOTECHNOLOGY JOURNAL
(2022)
Review
Plant Sciences
Manuel Rodriguez-Concepcion, Jose-Antonio Daros
Summary: Enriching food with health-promoting compounds like carotenoids is an effective approach to combat unhealthy eating habits. Carotenoids are precursors of vitamin A and can reduce the risk of various chronic diseases. Recent advances in transient expression systems have provided valuable insights into the synthesis and storage of carotenoids in plants, enabling efficient biofortification of plant tissues.
CURRENT OPINION IN PLANT BIOLOGY
(2022)
Article
Plant Sciences
Mireia Uranga, Jose-Antonio Daros
Summary: Using plant RNA viruses as transient delivery vectors is an improved method for CRISPR-Cas genome editing, allowing for rapid editing in a short period of time. This method shows potential for enhancing plant resistance using CRISPR-Cas technology. However, there are still challenges and limitations to be addressed.
Article
Mathematics, Interdisciplinary Applications
Angel Calsina, Silvia Cuadrado, Blai Vidiella, Josep Sardanyes
Summary: The impact of space on ecosystem dynamics, especially in relation to transients and bifurcations, has been the subject of ongoing debate in theoretical ecology. In this study, a simple model with intra-specific cooperation and habitat loss is used to explore the effects of diffusion on ghost extinction transients near a saddle-node bifurcation. The results show that while transients typically increase in length near the bifurcation, at extreme values of diffusion, both small and large, extinction times remain long and similar to well-mixed results. However, at intermediate diffusion rates, the influence of ghosts decreases, leading to a dramatic reduction in transients' length. These findings remain robust for different initial spatial distributions of cooperators, and a two-patch metapopulation model is introduced to summarize the main results. The study also provides analytical results for the model's passage times and scaling in a normal form. The implications of these findings are discussed within the context of ecological transients.
CHAOS SOLITONS & FRACTALS
(2023)
Editorial Material
Biology
Josep Sardanyes, Filip Ivancic
PHYSICS OF LIFE REVIEWS
(2023)
Review
Biology
Beltran Ortola, Jose-Antonio Daros
Summary: This article reviews the discovery and current understanding of viroid biology, including the structure and classification of viroid molecules, viroid genome replication and movement mechanisms, transmission between plants, and how they cause disease. The article also discusses the potential biotechnological applications of viroid molecules.
Article
Chemistry, Analytical
Rosa Marquez-Costa, Roser Montagud-Martinez, Maria-Carmen Marques, Eliseo Albert, David Navarro, Jose-Antonio Daros, Raul Ruiz, Guillermo Rodrigo
Summary: This study presents a novel nucleic acid detection strategy based on CRISPR-Cas9, which enables the detection of different viruses, including the novel respiratory virus SARS-CoV-2. The results show that CRISPR-Cas9 allows the simultaneous detection of different DNA amplicons, and engineered DNA logic circuits can process the detected signals. This platform has the potential for diagnosis and biocomputing.
ANALYTICAL CHEMISTRY
(2023)
Editorial Material
Biochemistry & Molecular Biology
Jose-Antonio Daros, Fabio Pasin, Fernando Merwaiss
Article
Multidisciplinary Sciences
J. Tomas Lazaro, Tomas Alarcon, Carlos P. Garay, Josep Sardanyes
Summary: Slowing down occurs in dynamical systems close to bifurcations or phase transitions. We numerically investigated the effect of intrinsic noise on the deterministic picture and found a more complicated scaling law. Using a Wentzel-Kramers-Brillouin asymptotic approximation and the Master Equation, we provide a theoretical basis for this new law with two models of cooperation. Our approach allows for useful theoretical predictions of transient times in stochastic systems close to a bifurcation.
PROCEEDINGS OF THE ROYAL SOCIETY A-MATHEMATICAL PHYSICAL AND ENGINEERING SCIENCES
(2023)
Article
Biochemistry & Molecular Biology
Olivia Costantina Demurtas, Maria Sulli, Paola Ferrante, Paola Mini, Maricarmen Marti, Veronica Aragones, Jose-Antonio Daros, Giovanni Giuliano
Summary: Crocins, a type of glycosylated apocarotenoids found in saffron, have strong coloring power and various health benefits. The CsCCD2 enzyme, which catalyzes carotenoid cleavage, shows a preference for zeaxanthin and can be used in planta to produce saffron crocins.
Article
Biochemical Research Methods
Mireia Uranga, Veronica Aragones, Jose-Antonio Daros, Fabio Pasin
Summary: Viral vectors are powerful tools for editing plant genomes. This protocol describes a method for assembling plant viral vectors for sgRNA delivery, allowing rapid assessment of design effectiveness and the generation of heritable mutations.
Article
Biochemistry & Molecular Biology
Adriana E. Cisneros, Tamara Martin-Garcia, Anamarija Primc, Wojtek Kuziuta, Javier Sanchez-Vicente, Veronica Aragones, Jose-Antonio Daros, Alberto Carbonell
Summary: This study analyzed the structural and sequence requirements for producing artificial microRNAs (amiRNAs) in plants, and found that highly effective and accurately processed amiRNAs can be produced from minimal precursors. The viral vectors containing minimal amiRNA precursors can be applied in a transgene-free manner to induce whole-plant gene silencing.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Agronomy
Beltran Ortola, Alberto Urbaneja, Marcelo Eiras, Meritxell Perez-Hedo, Jose-Antonio Daros
Summary: The study demonstrates the potential of dsRNA molecules as oral insecticides in medfly.
PEST MANAGEMENT SCIENCE
(2023)
Article
Plant Sciences
Lucia Morote, Angela Rubio-Moraga, Alberto Jose Lopez Jimenez, Veronica Aragones, Gianfranco Diretto, Olivia Constantina Dermutas, Sarah Frusciante, Oussama Ahrazem, Jose-Antonio Daros, Lourdes Gomez-Gomez
Summary: In this study, eight enzymes involved in the biosynthesis of crocins were identified in two Verbascum species. Four of them were similar to enzymes found in Buddleja and were identified to be involved in crocin biosynthesis. These enzymes were able to efficiently produce crocins using beta-carotene and zeaxanthin as substrates in bacterial and plant systems. The discovery of these enzymes, which have a broad substrate spectrum, provides new opportunities for biotechnological production of apocarotenoids.
Article
Biotechnology & Applied Microbiology
Fernando Merwaiss, Enrique Lozano-Sanchez, Joao Zulaica, Luciana Rusu, Marta Vazquez-Vilar, Diego Orzaez, Guillermo Rodrigo, Ron Geller, Jose-Antonio Daros
Summary: Researchers have developed genetically encoded multivalent viral nanoparticles that can recognize and neutralize SARS-CoV-2 Spike protein. These nanoparticles exhibited higher neutralization activity compared to the corresponding nanobodies in a dimeric format. The ability to produce VNP cocktails in plants makes them an attractive alternative to standard antibodies for multiple applications in diagnosis and therapeutics.
PLANT BIOTECHNOLOGY JOURNAL
(2023)