Your browser doesn't support javascript.
Show: 20 | 50 | 100
Results 1 - 13 de 13
Filter
1.
Nat Genet ; 54(1): 1, 2022 01.
Article in English | MEDLINE | ID: covidwho-1626301
2.
Plant Biotechnol J ; 20(2): 360-373, 2022 02.
Article in English | MEDLINE | ID: covidwho-1621953

ABSTRACT

In the age of synthetic biology, plastid engineering requires a nimble platform to introduce novel synthetic circuits in plants. While effective for integrating relatively small constructs into the plastome, plastid engineering via homologous recombination of transgenes is over 30 years old. Here we show the design-build-test of a novel synthetic genome structure that does not disturb the native plastome: the 'mini-synplastome'. The mini-synplastome was inspired by dinoflagellate plastome organization, which is comprised of numerous minicircles residing in the plastid instead of a single organellar genome molecule. The first mini-synplastome in plants was developed in vitro to meet the following criteria: (i) episomal replication in plastids; (ii) facile cloning; (iii) predictable transgene expression in plastids; (iv) non-integration of vector sequences into the endogenous plastome; and (v) autonomous persistence in the plant over generations in the absence of exogenous selection pressure. Mini-synplastomes are anticipated to revolutionize chloroplast biotechnology, enable facile marker-free plastid engineering, and provide an unparalleled platform for one-step metabolic engineering in plants.


Subject(s)
Genetic Engineering , Plastids , Metabolic Engineering , Plants/genetics , Plastids/genetics , Synthetic Biology , Transgenes
3.
Nucleic Acids Res ; 50(D1): D1-D10, 2022 01 07.
Article in English | MEDLINE | ID: covidwho-1607482

ABSTRACT

The 2022 Nucleic Acids Research Database Issue contains 185 papers, including 87 papers reporting on new databases and 85 updates from resources previously published in the Issue. Thirteen additional manuscripts provide updates on databases most recently published elsewhere. Seven new databases focus specifically on COVID-19 and SARS-CoV-2, including SCoV2-MD, the first of the Issue's Breakthrough Articles. Major nucleic acid databases reporting updates include MODOMICS, JASPAR and miRTarBase. The AlphaFold Protein Structure Database, described in the second Breakthrough Article, is the stand-out in the protein section, where the Human Proteoform Atlas and GproteinDb are other notable new arrivals. Updates from DisProt, FuzDB and ELM comprehensively cover disordered proteins. Under the metabolism and signalling section Reactome, ConsensusPathDB, HMDB and CAZy are major returning resources. In microbial and viral genomes taxonomy and systematics are well covered by LPSN, TYGS and GTDB. Genomics resources include Ensembl, Ensembl Genomes and UCSC Genome Browser. Major returning pharmacology resource names include the IUPHAR/BPS guide and the Therapeutic Target Database. New plant databases include PlantGSAD for gene lists and qPTMplants for post-translational modifications. The entire Database Issue is freely available online on the Nucleic Acids Research website (https://academic.oup.com/nar). Our latest update to the NAR online Molecular Biology Database Collection brings the total number of entries to 1645. Following last year's major cleanup, we have updated 317 entries, listing 89 new resources and trimming 80 discontinued URLs. The current release is available at http://www.oxfordjournals.org/nar/database/c/.


Subject(s)
Databases, Factual , Molecular Biology , Animals , COVID-19 , Databases, Nucleic Acid , Databases, Protein , Genome, Microbial , Genome, Viral , Humans , Mice , Plants/genetics , Protein Processing, Post-Translational , Proteome , SARS-CoV-2/genetics , Signal Transduction
5.
PLoS One ; 16(9): e0257878, 2021.
Article in English | MEDLINE | ID: covidwho-1443847

ABSTRACT

Extracellular microRNAs (miRNAs) have been proposed to function in cross-kingdom gene regulation. Among these, plant-derived miRNAs of dietary origin have been reported to survive the harsh conditions of the human digestive system, enter the circulatory system, and regulate gene expression and metabolic function. However, definitive evidence supporting the presence of plant-derived miRNAs of dietary origin in mammals has been difficult to obtain due to limited sample sizes. We have developed a bioinformatics pipeline (ePmiRNA_finder) that provides strident miRNA classification and applied it to analyze 421 small RNA sequencing data sets from 10 types of human body fluids and tissues and comparative samples from carnivores and herbivores. A total of 35 miRNAs were identified that map to plants typically found in the human diet and these miRNAs were found in at least one human blood sample and their abundance was significantly different when compared to samples from human microbiome or cow. The plant-derived miRNA profiles were body fluid/tissue-specific and highly abundant in the brain and the breast milk samples, indicating selective absorption and/or the ability to be transported across tissue/organ barriers. Our data provide conclusive evidence for the presence of plant-derived miRNAs as a consequence of dietary intake and their cross-kingdom regulatory function within human circulating system.


Subject(s)
Computational Biology/methods , MicroRNAs/genetics , Plants/genetics , Sequence Analysis, RNA/methods , Animal Feed/analysis , Animals , Brain Chemistry , Carnivora/genetics , Diet , Female , Herbivory/genetics , Humans , Milk, Human/chemistry , Organ Specificity , RNA, Plant/genetics , Sample Size
6.
Front Immunol ; 12: 673723, 2021.
Article in English | MEDLINE | ID: covidwho-1389183

ABSTRACT

Reprogramming of primary virus-infected cells is the critical step that turns viral attacks harmful to humans by initiating super-spreading at cell, organism and population levels. To develop early anti-viral therapies and proactive administration, it is important to understand the very first steps of this process. Plant somatic embryogenesis (SE) is the earliest and most studied model for de novo programming upon severe stress that, in contrast to virus attacks, promotes individual cell and organism survival. We argued that transcript level profiles of target genes established from in vitro SE induction as reference compared to virus-induced profiles can identify differential virus traits that link to harmful reprogramming. To validate this hypothesis, we selected a standard set of genes named 'ReprogVirus'. This approach was recently applied and published. It resulted in identifying 'CoV-MAC-TED', a complex trait that is promising to support combating SARS-CoV-2-induced cell reprogramming in primary infected nose and mouth cells. In this perspective, we aim to explain the rationale of our scientific approach. We are highlighting relevant background knowledge on SE, emphasize the role of alternative oxidase in plant reprogramming and resilience as a learning tool for designing human virus-defense strategies and, present the list of selected genes. As an outlook, we announce wider data collection in a 'ReprogVirus Platform' to support anti-viral strategy design through common efforts.


Subject(s)
COVID-19/prevention & control , Cellular Reprogramming Techniques/methods , Plant Somatic Embryogenesis Techniques/methods , SARS-CoV-2/genetics , COVID-19/pathology , Gene Expression Regulation, Developmental/genetics , Gene Expression Regulation, Plant/genetics , Humans , Mitochondrial Proteins/metabolism , Oxidoreductases/metabolism , Plant Development/genetics , Plant Proteins/metabolism , Plants/embryology , Plants/genetics , Reactive Oxygen Species/metabolism
7.
Heredity (Edinb) ; 125(6): 431-436, 2020 12.
Article in English | MEDLINE | ID: covidwho-1327195

ABSTRACT

Student career aspirations are directly linked to the careers that they are exposed to and the esteem that they are given in society. Where schools are located in areas with low visibility of scientific careers this will have an impact on student aspirations. This project is demonstrating that aspirations can be altered by engaging 16-18-year-old A level biologists in sustained research. A total of 20 students from schools across Jersey are attempting to sequence the chloroplast genomes from daffodils that they have collected from non-cultivated locations using Oxford Nanopore Technologies' MinION. Despite site closures due to COVID-19 control measures, the project has developed insight into different scientific careers through experience and ownership of the entire project pipeline. This project demonstrates an opportunity for schools and academics to collaborate to further science and potentially improve student outcomes.


Subject(s)
Coronavirus Infections/epidemiology , Education/trends , Pandemics , Plants/genetics , Pneumonia, Viral/epidemiology , Adolescent , Betacoronavirus/pathogenicity , COVID-19 , Coronavirus Infections/virology , Humans , Pneumonia, Viral/virology , SARS-CoV-2 , Students
8.
Curr Opin Plant Biol ; 62: 102057, 2021 08.
Article in English | MEDLINE | ID: covidwho-1253456

ABSTRACT

In the last two decades, advances in network science have facilitated the discovery of important systems' entities in diverse biological networks. This graph-based technique has revealed numerous emergent properties of a system that enable us to understand several complex biological processes including plant immune systems. With the accumulation of multiomics data sets, the comprehensive understanding of plant-pathogen interactions can be achieved through the analyses and efficacious integration of multidimensional qualitative and quantitative relationships among the components of hosts and their microbes. This review highlights comparative network topology analyses in plant-pathogen co-expression networks and interactomes, outlines dynamic network modeling for cell-specific immune regulatory networks, and discusses the new frontiers of single-cell sequencing as well as multiomics data integration that are necessary for unraveling the intricacies of plant immune systems.


Subject(s)
Plant Immunity , Plants , Biology , Plant Immunity/genetics , Plants/genetics
10.
Viruses ; 13(1)2020 12 22.
Article in English | MEDLINE | ID: covidwho-1000349

ABSTRACT

Severe virus outbreaks are occurring more often and spreading faster and further than ever. Preparedness plans based on lessons learned from past epidemics can guide behavioral and pharmacological interventions to contain and treat emergent diseases. Although conventional biologics production systems can meet the pharmaceutical needs of a community at homeostasis, the COVID-19 pandemic has created an abrupt rise in demand for vaccines and therapeutics that highlight the gaps in this supply chain's ability to quickly develop and produce biologics in emergency situations given a short lead time. Considering the projected requirements for COVID-19 vaccines and the necessity for expedited large scale manufacture the capabilities of current biologics production systems should be surveyed to determine their applicability to pandemic preparedness. Plant-based biologics production systems have progressed to a state of commercial viability in the past 30 years with the capacity for production of complex, glycosylated, "mammalian compatible" molecules in a system with comparatively low production costs, high scalability, and production flexibility. Continued research drives the expansion of plant virus-based tools for harnessing the full production capacity from the plant biomass in transient systems. Here, we present an overview of vaccine production systems with a focus on plant-based production systems and their potential role as "first responders" in emergency pandemic situations.


Subject(s)
COVID-19/immunology , Plants/genetics , Viral Vaccines , Animals , COVID-19/prevention & control , COVID-19 Vaccines , Humans , Pandemics/prevention & control , Plant Viruses/genetics , Plants/metabolism , SARS-CoV-2 , Tobacco/immunology , Viral Vaccines/genetics , Viral Vaccines/immunology
11.
Methods Mol Biol ; 2225: 25-38, 2021.
Article in English | MEDLINE | ID: covidwho-893254

ABSTRACT

Various systems exist for the robust production of recombinant proteins. However, only a few systems are optimal for human vaccine protein production. Plant-based transient protein expression systems offer an advantageous alternative to costly mammalian cell culture-based systems and can perform posttranslational modifications due to the presence of an endomembrane system that is largely similar to that of the animal cell. Technological advances in expression vectors for transient expression in the last two decades have produced new plant expression systems with the flexibility and speed that cannot be matched by those based on mammalian or insect cell culture. The rapid and high-level protein production capability of transient expression systems makes them the optimal system to quickly and versatilely develop and produce vaccines against viruses such as 2019-nCoV that have sudden and unpredictable outbreaks. Here, expression of antiviral subunit vaccines in Nicotiana benthamiana plants via transient expression is demonstrated.


Subject(s)
Betacoronavirus/drug effects , Coronavirus Infections/prevention & control , Pandemics/prevention & control , Plants/immunology , Pneumonia, Viral/prevention & control , Vaccines, Subunit/administration & dosage , Vaccines, Subunit/biosynthesis , Betacoronavirus/immunology , Betacoronavirus/isolation & purification , COVID-19 , Coronavirus Infections/immunology , Coronavirus Infections/transmission , Coronavirus Infections/virology , Genetic Vectors , Humans , Plants/genetics , Pneumonia, Viral/immunology , Pneumonia, Viral/transmission , Pneumonia, Viral/virology , SARS-CoV-2
12.
Brief Bioinform ; 22(3)2021 05 20.
Article in English | MEDLINE | ID: covidwho-787100

ABSTRACT

Recent advances in transcriptomics have uncovered lots of novel transcripts in plants. To annotate such transcripts, dissecting their coding potential is a critical step. Computational approaches have been proven fruitful in this task; however, most current tools are designed/optimized for mammals and only a few of them have been tested on a limited number of plant species. In this work, we present NAMS webserver, which contains a novel coding potential classifier, NAMS, specifically optimized for plants. We have evaluated the performance of NAMS using a comprehensive dataset containing more than 3 million transcripts from various plant species, where NAMS demonstrates high accuracy and remarkable performance improvements over state-of-the-art software. Moreover, our webserver also furnishes functional annotations, aiming to provide users informative clues to the functions of their transcripts. Considering that most plant species are poorly characterized, our NAMS webserver could serve as a valuable resource to facilitate the transcriptomic studies. The webserver with testing dataset is freely available at http://sunlab.cpy.cuhk.edu.hk/NAMS/.


Subject(s)
Computational Biology/methods , Gene Expression Profiling/methods , Gene Expression Regulation, Plant , Internet , Molecular Sequence Annotation/methods , Plants/genetics , Genetic Code/genetics , Plants/classification , RNA, Messenger/genetics , RNA, Plant/genetics , Reproducibility of Results , Species Specificity , Support Vector Machine
13.
Genomics ; 112(6): 4322-4331, 2020 11.
Article in English | MEDLINE | ID: covidwho-701714

ABSTRACT

COVID-19 caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is devastative to the humankind for which neither vaccines nor precise therapeutic molecules for treatment are identified. The search for new drugs and repurposing of existing drugs are being performed; however, at the same time, research on plants to identify novel therapeutic compounds or testing the existing ones is progressing at a slower phase. In this context, genomics and biotechnology offer various tools and strategies to manipulate plants for producing those complex biopharmaceutical products. This review enumerates the scope for research on plant-based molecules for their potential application in treating SARS-CoV-2 infection. Strategies to edit gene and genome, overexpression and silencing approaches, and molecular breeding for producing target biomolecules in the plant system are discussed in detail. Altogether, the present review provides a roadmap for expediting research on using plants as a novel source of active biomolecules having therapeutic applications.


Subject(s)
Antiviral Agents/metabolism , Antiviral Agents/pharmacology , Genomics/methods , Plants/chemistry , Antiviral Agents/chemistry , COVID-19/drug therapy , Gene Editing , Humans , Plants/genetics , Plants/metabolism , Plants, Genetically Modified
SELECTION OF CITATIONS
SEARCH DETAIL