Plant Biosystems Research Articles

Exploring Multifaceted Roles of Nitroreductases in Bacterial, Animal and Plant Biosystems and their Detection using Fluorescent Probes

AbstractNitroreductases are the enzymes that can convert nitroaromatic substances including explosives like TNT to their corresponding nitrite, hydroxylamine or amino derivatives with reduced NADH or NADPH as an electron donor. A wide range of nitroreductases are known to present in bacterial genomes that are explored for their potential in the reduction of nitroaromatic compounds and they are used in converting prodrugs to toxic hydroxylamine derivatives causing tumor cell killing. Likewise, in cancer cells, the low oxygen condition called hypoxia is a characteristic of solid tumors and during hypoxia nitroreductase gene expression occurs. Moreover, due to the ability of nitroreductases to reduce nitroaromatic compounds, phytoremediation potential of plants was inspected by expressing bacterial nitroreductase genes in plants through genetic engineering. Due to its diversity and widespread applications in different biosystems, its detection has gained momentum among the scientific community. Designing fluorescent probes for detecting nitroreductases has emerged as a beneficial tool compared to conventional monitoring approaches due to their high sensitivity, selectivity, and real‐time monitoring ability. This review aims to provide an understanding of the activity and the status of nitroreductases in bacteria, plants and animal cells as well as the significance of fluorescent imaging‐related studies by employing recently designed probes.

Advances in the Application of Single-Cell Transcriptomics in Plant Systems and Synthetic Biology.

Plants are complex systems hierarchically organized and composed of various cell types. To understand the molecular underpinnings of complex plant systems, single-cell RNA sequencing (scRNA-seq) has emerged as a powerful tool for revealing high resolution of gene expression patterns at the cellular level and investigating the cell-type heterogeneity. Furthermore, scRNA-seq analysis of plant biosystems has great potential for generating new knowledge to inform plant biosystems design and synthetic biology, which aims to modify plants genetically/epigenetically through genome editing, engineering, or re-writing based on rational design for increasing crop yield and quality, promoting the bioeconomy and enhancing environmental sustainability. In particular, data from scRNA-seq studies can be utilized to facilitate the development of high-precision Build-Design-Test-Learn capabilities for maximizing the targeted performance of engineered plant biosystems while minimizing unintended side effects. To date, scRNA-seq has been demonstrated in a limited number of plant species, including model plants (e.g., Arabidopsis thaliana), agricultural crops (e.g., Oryza sativa), and bioenergy crops (e.g., Populus spp.). It is expected that future technical advancements will reduce the cost of scRNA-seq and consequently accelerate the application of this emerging technology in plants. In this review, we summarize current technical advancements in plant scRNA-seq, including sample preparation, sequencing, and data analysis, to provide guidance on how to choose the appropriate scRNA-seq methods for different types of plant samples. We then highlight various applications of scRNA-seq in both plant systems biology and plant synthetic biology research. Finally, we discuss the challenges and opportunities for the application of scRNA-seq in plants.

Dose-dependent Effects of Bio-AgNPs on Rubia tinctorum Callus and Root Biomass

Silver nanoparticles have frequently been used in many areas of biotechnology. These nanomaterials, especially biologically synthetized silver nanoparticles (bio-AgNPs), have some beneficial effects on plant biosystems because of their ethylene-inhibiting and auxin-stimulating effects which make them practical and cost-effective alternatives for synthetic plant growth regulators. The variety of the plants’ responses to bio-AgNPs is dose-dependent, and the effects show a wide variety for every plant, explant and culture types. In our study, bio-AgNPs derived from Syzygium aromaticum flowers were used in stem cultures of Rubia tinctorum. At 0–30 mg/L concentrations, their efficacies were evaluated on the basis of biomass and chemical accumulations. Bio-AgNPs affected the growth parameters and content of biomass depending on their concentrations. The highest biomass accumulations were detected at 10 mg/L concentration (up to 3.4 times higher compared to control). Callus and root regenerations were triggered at 5 and 10 mg/L concentrations. Total phenolic concentrations were detected at the highest level (16.54 and 18.86 mg GAE/g, respectively) at 15 mg/l concentration, whereas total flavonoid concentrations were the highest at 15 and 20 mg/L concentrations (5.63 and 5.42 mg QE/g, respectively). Total antioxidant capacity and radical scavenging activity enhanced in response to bio-AgNPs. The highest total antioxidant capacity was detected at 107.53 mg AAE/g at 1 mg/L concentration in root biomass (1.6 times higher than the control). Total anthraquinone concentrations reached their highest values at 30 mg/L bio-AgNP concentration in both callus and root tissues. The results revealed that bio-AgNPs acted as elicitors or/and biomass enhancers in response to their concentrations.

Plant Biosystems Design Research Roadmap 1.0.

Human life intimately depends on plants for food, biomaterials, health, energy, and a sustainable environment. Various plants have been genetically improved mostly through breeding, along with limited modification via genetic engineering, yet they are still not able to meet the ever-increasing needs, in terms of both quantity and quality, resulting from the rapid increase in world population and expected standards of living. A step change that may address these challenges would be to expand the potential of plants using biosystems design approaches. This represents a shift in plant science research from relatively simple trial-and-error approaches to innovative strategies based on predictive models of biological systems. Plant biosystems design seeks to accelerate plant genetic improvement using genome editing and genetic circuit engineering or create novel plant systems through de novo synthesis of plant genomes. From this perspective, we present a comprehensive roadmap of plant biosystems design covering theories, principles, and technical methods, along with potential applications in basic and applied plant biology research. We highlight current challenges, future opportunities, and research priorities, along with a framework for international collaboration, towards rapid advancement of this emerging interdisciplinary area of research. Finally, we discuss the importance of social responsibility in utilizing plant biosystems design and suggest strategies for improving public perception, trust, and acceptance.

Plant Biosystems Design for a Carbon-Neutral Bioeconomy.

Our society faces multiple daunting challenges including finding sustainable solutions towards climate change mitigation; efficient production of food, biofuels, and biomaterials; maximizing land-use efficiency; and enabling a sustainable bioeconomy. Plants can provide environmentally and economically sustainable solutions to these challenges due to their inherent capabilities for photosynthetic capture of atmospheric CO2, allocation of carbon to various organs and partitioning into various chemical forms, including contributions to total soil carbon. In order to enhance crop productivity and optimize chemistry simultaneously in the above- and belowground plant tissues, transformative biosystems design strategies are needed. Concerted research efforts will be required for accelerating the development of plant cultivars, genotypes, or varieties that are cooptimized in the contexts of biomass-derived fuels and/or materials aboveground and enhanced carbon sequestration belowground. Here, we briefly discuss significant knowledge gaps in our process understanding and the potential of synthetic biology in enabling advancements along the fundamental to applied research arc. Ultimately, a convergence of perspectives from academic, industrial, government, and consumer sectors will be needed to realize the potential merits of plant biosystems design for a carbon neutral bioeconomy.

Gymnocoronis spilanthoides

Gymnocoronis spilanthoides

The influence of mechanolysis on the activaton of nanocomplexes of heteropolysaccharides and proteins of plant biosystems in developing of nanotechnologies

A nanotechnology of protein plant supplements in the form of puree of peas was developed that is based on the processes of deep processing of raw materials. Finely dispersed grinding and steam and thermal processing were used in this work as the innovation. When using traditional methods of raw materials processing, biological potential is not used in full. It was found that during deep processing of plant raw materials (dried peas), which is based on comprehensive effect of steam and thermal processing and finely dispersed grinding on the raw material in obtaining nanostructured puree, the processes of mechanical destruction and mechanical chemistry occur. These processes are accompanied by non–ezymatic biocatalysis – mechanolysis (destruction) of hard soluble biopolymers and nanocomplexes of biopolymers (proteins, heteropolysaccharides, namely, pectins, cellulose, starch) with their transformation to monomers (35...55 %) into soluble easily absorbed form (almost 2 times higher compared to the original raw material in a hidden form). The mechanism of protein mechanical destruction and its nanocomplexes, which is associated with the mechanical cracking, was discovered. It was found that the steam and thermal processing and finely dispersed grinding of peas, while obtaining finely dispersed puree, leads to the destruction of polysaccharides by the non–enzymatic catalysis, namely cellulose and starch (30...35 %), protopectin (50 %), to separate monomers. It is shown that in parallel there is an increase of glucose in nanopuree of peas (1.0 g. …10.0 g/100 g, i. e. by10 times). Integrated application of these processes is accompanied by mechanical destruction, mechanical activation and mechanolysis of biopolymers of nanocomplexes (protein, heteropolysaccharides, etc.) to α–amino acids, glucose, etc. (48…55 %).

PENGOLAHAN AIR LIMBAH DOMESTIK DENGAN BIOSISTEM TANAMAN BASAH (CONTRUCTED WETLAND) DI BANDARA NGURAH RAI

Research has been conducted on domestic wastewater Ngurah Rai Wet Plant Biosystems (BTB) This study aims to determine the characteristics of the waste water, the effectiveness and capacity of the BTB’s decreased levels of BOD, COD and Ammonia. The experimental research method is using the media of sand and coral and plants Cattail. Data collection was performed every 6 hours for 48 hours and the pH, temperature, and analysis of BOD, COD, ammonia UPT done in the Bali Provincial Health Laboratory. Data were analyzed by descriptive statistics and regression .. The results showed that the initial wastewater characteristics exceed Standards of quality, effectiveness of the BBT in lowering BOD in wastewater WWTP Ngurah Rai have been effective (37.21%) of the Quality Standards (BM = 18.92 %), while the effectiveness of the process is still not less than 50% effective. As for changes in the levels of COD in a state that has not demonstrated effectiveness towards a decrease of 69.66% reduction in ammonia and BOD reduction in the highest capacity = 55.08 g . day. and ammonia = 42.24 g day. While in lowering the COD has not shown a decrease towards

A Concept Model about Allometric Scaling of Hierarchical Energy Flow through Plant Biosystems

Ecologists have long sought a general metabolic scaling law (e.g., the 3/4 power law), although the size-independent mass-special metabolic ratemay have been selected for over evolutionary time. Here, we outline four hierarchical energy processes along the path of energy flow. These processes are represented as the scaling exponents of mass-dependent energy flow (e.g., a 1/4-scaling rule for individuals and a 1/3-scaling rule for populations). Individuals and populations have evolved as the conduits of energy flow. Interestingly, the mass-dependent hierarchical energy flow can help explain the development of a tree population. Our theory highlights that mass-dependent hierarchical energy flow may act as a metabolic integrator and suggests an energetic explanation of the evolution of plant biosystems from the individual to the community level.

New trends in biodiversity informatics

Plant Biosystems dedicated a special issue to present and discuss new trends in biodiversity and informatics. The definition and theoretical framework of this challenging and stimulating research field are delineated together with several examples that illustrate data collection, organisation, dissemination, analysis and application.

New trends in plant cytogenetics and cytoembryology: Dedicated to the memory of Emilio Battaglia

A survey of all the 154 scientific publications of Emilio Battaglia (1917–2011) is presented, grouped in three main research interests – plant embryology, cytogenetics in plants and cytological terminology – plus other less relevant contributions. Battaglia's past and present role in these disciplines is briefly discussed, in the light of current research on these topics, partly reviewed also in other contributions of the present Plant Biosystems issue.

Ludwigia grandiflora and L. peploides Onagraceae – Water primroses

<i>Ludwigia grandiflora</i> and <i>L. peploides</i> Onagraceae – Water primroses

Evolution and applications of plant pathway resources and databases

Plants are important sources of food and plant products are essential for modern human life. Plants are increasingly gaining importance as drug and fuel resources, bioremediation tools and as tools for recombinant technology. Considering these applications, database infrastructure for plant model systems deserves much more attention. Study of plant biological pathways, the interconnection between these pathways and plant systems biology on the whole has in general lagged behind human systems biology. In this article we review plant pathway databases and the resources that are currently available. We lay out trends and challenges in the ongoing efforts to integrate plant pathway databases and the applications of database integration. We also discuss how progress in non-plant communities can serve as an example for the improvement of the plant pathway database landscape and thereby allow quantitative modeling of plant biosystems. We propose Good Database Practice as a possible model for collaboration and to ease future integration efforts.

Induced resistance: destined to remain on the sidelines of crop protection?

Dale Ronald Walters was born in Tenby in the United Kingdom in 1957 and spent his childhood in Trinidad, West Indies, attending Queen’s Royal College from 1969–1975. He obtained a BSc in Plant Science from Wye College, University of London in 1978 and studied for a PhD at Lancaster University from 1978–1981, under the supervision of Peter Ayres. The PhD (on root function in powdery mildew-infected barley) was followed by a postdoctoral period at Lancaster working on photosynthesis and nitrogen metabolism in mildew-infected barley. Walters moved to the West of Scotland Agricultural College (later to become part of the Scottish Agricultural College) in August 1982 as a lecturer in plant physiology and immediately started research on physiological responses of diseased plants. This research included much work on polyamine metabolism, as well as work, starting in 1987, on induced resistance. Promotion to senior lecturer in 1990 was followed by appointment as Head of the Department of Plant Biology in 1997. He was elected to a Fellowship of the Institute of Biology in 1998, was awarded a DSc by Lancaster University for his work on host–pathogen physiology in 1999, and was awarded a personal professorship in 2000. He is currently leader of the Plant Pathology Team at the Scottish Agricultural College in Edinburgh, where he is also Manager for Research Postgraduate Studies. Walters has been an Honorary Lecturer at the University of Glasgow since 1985. Publications: 116 refereed publications, plus 136 other publications, edited three books, currently writing a textbook; Senior Editor of Physiological & Molecular Plant Pathology since 1992, on the Editorial Board of the UK Institute of Biology journal Biologist, and has been on the Editorial Board of Mycological Research and the Italian journal Plant Biosystems. Current research: Induced resistance to plant disease, especially in relation to field implementation; fitness and ecological costs associated with induced resistance; novel approaches to control of plant disease; physiological responses of plants to pathogens. Phytoparasitica (2010) 38:1–4 DOI 10.1007/s12600-009-0067-y

EMFs and DNA effects: potential mechanism elucidated.

Research ArticleOpen AccessEMFs and DNA effects: potential mechanism elucidated. Ernie Hood Ernie Hood Search for more papers by this author Published:1 May 2004https://doi.org/10.1289/ehp.112-a368bCited by:2AboutSectionsPDF ToolsDownload CitationsTrack Citations ShareShare onFacebookTwitterLinked InRedditEmail "EMFs and DNA effects: potential mechanism elucidated.." Environmental Health Perspectives, 112(6), p. A368FiguresReferencesRelatedDetailsCited By Makarov V and Khmelinskii I (2014) Modulation effect of low-frequency electric and magnetic fields on CO 2 production and rates of acetate and pyruvate formation in Saccharomyces cerevisiae cell culture , Electromagnetic Biology and Medicine, 10.3109/15368378.2014.902382, 34:1, (93-104), Online publication date: 2-Jan-2015. Bitonti M, Mazzuca S, Ting T and Innocenti A (2006) Magnetic field affects meristem activity and cell differentiation in Zea mays roots , Plant Biosystems - An International Journal Dealing with all Aspects of Plant Biology, 10.1080/11263500500511314, 140:1, (87-93), Online publication date: 1-Mar-2006. Vol. 112, No. 6 May 2004Metrics About Article Metrics Publication History Originally published1 May 2004Published in print1 May 2004 Financial disclosures License information EHP is an open-access journal published with support from the National Institute of Environmental Health Sciences, National Institutes of Health. All content is public domain unless otherwise noted. Note to readers with disabilities EHP strives to ensure that all journal content is accessible to all readers. However, some figures and Supplemental Material published in EHP articles may not conform to 508 standards due to the complexity of the information being presented. If you need assistance accessing journal content, please contact [email protected]. Our staff will work with you to assess and meet your accessibility needs within 3 working days.

Bacterial Canker and Decline of European Hazelnut.

HomePlant DiseaseVol. 86, No. 7Bacterial Canker and Decline of European Hazelnut PreviousNext OPENOpen Access licenseBacterial Canker and Decline of European HazelnutMarco ScortichiniMarco ScortichiniSearch for more papers by this authorAffiliationsAuthors and Affiliations Marco Scortichini , Istituto Sperimentale per la Frutticoltura, Rome, Italy Published Online:23 Feb 2007https://doi.org/10.1094/PDIS.2002.86.7.704AboutSectionsPDF ToolsAdd to favoritesDownload CitationsTrack Citations ShareShare onFacebookTwitterLinked InRedditEmailWechat DetailsFiguresLiterature CitedRelated Vol. 86, No. 7 July 2002SubscribeISSN:0191-2917e-ISSN:1943-7692 Metrics Article History Issue Date: 25 Jan 2008Published: 23 Feb 2007 Pages: 704-709 Information© 2002 The American Phytopathological SocietyPDF downloadCited byBacterial diseases in forest treesCorylus avellana (hazel)CABI Compendium, Vol. CABI CompendiumXanthomonas arboricola pv. juglandis and pv. corylina : Brothers or distant relatives? 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Hall, Ian B. Dry, Christopher L. Blanchard, and Melanie A. 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Kennelly, Francisco M. Cazorla, Antonio de Vicente, Cayo Ramos, and George W. Sundin16 February 2007 | Plant Disease, Vol. 91, No. 1Evidence for separate origins of the two Pseudomonas avellanae lineagesPlant Pathology, Vol. 55, No. 3Pseudomonas syringae pv. coryli, the Causal Agent of Bacterial Twig Dieback of Corylus avellanaMarco Scortichini, Maria Pia Rossi, Stefania Loreti, Adriana Bosco, Mario Fiori, Robert W. Jackson, David E. Stead, Andy Aspin, Ugo Marchesi, Maurizio Zini, and Jaap D. Janse5 February 2007 | Phytopathology®, Vol. 95, No. 11Clonal population structure of Pseudomonas avellanae strains of different origin based on multilocus enzyme electrophoresisMicrobiology, Vol. 149, No. 10New Considerations for Pruning in Management of Fire Blight in PearsD. Shtienberg, M. Zilberstaine, D. Oppenheim, S. Levi, H. Shwartz, and G. 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Bond graph models for plant biosystems

Computable dynamic models for plant biosystems permit the study of effects of environmental variables on plant growth and productivity. Using bond graphs, a comprehensive phenomenological model of a plant biosystem may be developed and used in computer simulations. Elements of a model studied in this paper include a gas diffusion network between the atmosphere and leaf cytoplasm, intracellular chemistry, and the translocation networks of the phloem. Bond graphs are shown to provide a conceptual basis for the development of biological subsystem and system models and lead to computable representations.