DNA Damage Repair System in Plants: A Worldwide Research Update

Exposure of Arabidopsis thaliana Mutants to Genotoxic Stress Provides New Insights for the Involvement of TDP1α and TDP1β genes in DNA-Damage Response

Genotoxic stress activates the DNA-damage response (DDR) signalling cascades responsible for maintaining genome integrity. Downstream DNA repair pathways include the tyrosyl-DNA phosphodiesterase 1 (TDP1) enzyme that hydrolyses the phosphodiester bond between the tyrosine of topoisomerase I (TopI) and 3'-phosphate of DNA. The plant TDP1 subfamily contains the canonical TDP1α gene and the TDP1β gene whose functions are not fully elucidated. The current study proposes to investigate the involvement of TDP1 genes in DDR-related processes by using Arabidopsis thaliana mutants treated with genotoxic agents. The phenotypic and molecular characterization of tdp1α, tdp1β and tdp1α/β mutants treated with cisplatin (CIS), curcumin (CUR), NSC120686 (NSC), zeocin (ZEO), and camptothecin (CPT), evidenced that while tdp1β was highly sensitive to CIS and CPT, tdp1α was more sensitive to NSC. Gene expression analyses showing upregulation of the TDP2 gene in the double mutant indicate the presence of compensatory mechanisms. The downregulation of POL2A gene in the tdp1β mutant along with the upregulation of the TDP1β gene in pol2a mutants, together with its sensitivity to replication inhibitors (CIS, CTP), point towards a function of this gene in the response to replication stress. Therefore, this study brings novel information relative to the activity of TDP1 genes in plants.

Engineered gamma radiation phytosensors for environmental monitoring

Nuclear energy, already a practical solution for supplying energy on a scale similar to fossil fuels, will likely increase its footprint over the next several decades to meet current climate goals. Gamma radiation is produced during fission in existing nuclear reactors and thus the need to detect leakage from nuclear plants, and effects of such leakage on ecosystems will likely also increase. At present, gamma radiation is detected using mechanical sensors that have several drawbacks, including: (i) limited availability; (ii) reliance on power supply; and (iii) requirement of human presence in dangerous areas. To overcome these limitations, we have developed a plant biosensor (phytosensor) to detect low-dose ionizing radiation. The system utilizes synthetic biology to engineer a dosimetric switch into potato utilizing the plant's native DNA damage response (DDR) machinery to produce a fluorescent output. In this work, the radiation phytosensor was shown to respond to a wide range of gamma radiation exposure (10-80 Grey) producing a reporter signal that was detectable at >3 m. Further, a pressure test of the top radiation phytosensor in a complex mesocosm demonstrated full function of the system in a 'real world' scenario.

A bibliometric review of grid parity, energy transition and electricity cost research for sustainable development

As the topic of sustainable development continues to prominence in global affairs, the case for renewable energy has never been stronger. To be regarded as a perfect alternative to conventional (non-renewable) energy sources in many climes, renewable energy, such as solar and wind, shows promise when considering concepts like grid parity. A significant number of studies have been devoted to understanding the concept. However, only a few studies have committed themselves to analysing the research activity carried out on it. This paper will present a bibliometric and empirical review of worldwide grid parity, energy transition, and electricity cost research. To situate the progress in this research area, a detailed search of Scopus was used to identify and situate research development in the field from 1965 until 2021. Using the data extracted from Scopus and VOSviewer for analysis, we explore different aspects of the publications, such as the volume, growth rate, and coverage of published documents, the most influential research papers and journals in this research area, and the most studied research themes in recent years. We also discuss Governmental policies in developed and developing economies that have accelerated the attainment of Grid parity in certain countries. Also, an empirical review of top-down, bottom-up, and artificial neural network approaches to evaluating grid parity was conducted. The study revealed a steady increase in the research articles focused on grid parity, energy transition, and electricity cost research from 2006. The geographic distribution of the publications shows that most of the publications on the subject originated from the USA, Germany, China, United Kingdom, and Spain, raking in 42.2% of the publications. Also, the top 7 authors with the highest document count from Scopus are from Finland, which coincidentally is one of the countries making significant progress in Grid parity attainment. Of the total document count from Scopus, only 0.02% are papers published from African Countries. Could this reluctance to publish research findings on energy transition be one of the reasons for the slow progression of sustainable energy for all in Africa? Therefore, it is imperative now more than ever for more research focusing on the attainment of grid parity, energy transition, and electricity costs for developing countries to be brought to the fore. This article provides a review of state-of-the-art research on the attainment of grid parity and energy transition with a focus on the Levelized Cost of Electricity (LCOE) models of renewable energy sources.

Performance evaluation of the prospects and challenges of effective power generation and distribution in Nigeria

Effective Electric Power Generation and Distribution result in the overall increase in efficiency in an economy. Nigeria generates 4500 MW for a population of 200 million people; hence, more than 50% of the population has no electricity access, and those with access experience power outages. Inasmuch as Nigeria is blessed with a vast amount of renewable energy sources, the country heavily relies on Natural Gas for power Generation. With regards to Power Generation, it is seen that the Power Generated is not evacuated efficiently. The purpose of this study is to access the growth of the Nigerian Power Sector from 1898 till date. This is achieved by evaluating the Power Sector Reforms enacted by different government to analyze their effectiveness. Furthermore, the study reviews strategically research that have discussed the strengths and weakness of the Nigerian Power Sector to be able to suggest hidden opportunities and reveal threats to the attainment of sustainable energy for all in 2030. Some of the Challenges discovered were energy user challenges, financial challenges, and energy losses. Some solutions and opportunities are the use of distributed generation, smart meters and the implemented of a smart grid system. In the long run, the authors propose that viable renewable energy sources in each State of the federation be tapped for Power Generation this would enable each State to the self-reliant and contributors to the Nigerian Power Generation Pool. It is believed that this actions would promote economic, social and technological benefits for the every stakeholder.

Evaluation of morpho-physiological responses and genotoxicity in Eruca sativa (Mill.) grown in hydroponics from seeds exposed to X-rays

Due to its potential applications in cultivated plants, ionizing radiation (IR) and its effect on organisms is increasingly studied. Here we measured the effects of ionizing radiation on Eruca sativa by analyzing plants from irradiated seeds (1 and 10 Gy) grown in hydroponics. We measured several morpho-physiological traits and genotoxicity. Radiation stress induced a noticeable variability of the morpho-physiological traits highlighting decreased plant vigor. Shoot length and leaf number were significantly higher in 1 Gy-treated samples, whereas root length was significantly higher in 10 Gy treated plants. Stomata number significantly increased with IR dose, whereas both pigment and Rubisco content decreased under radiation stress. Phenol content significantly increased in 1 Gy treated samples, otherwise from total antioxidants, which were not different from control. Most results could find a feasible explanation in a hormesis-like pattern and in a decreased plant vigor under radiation stress. IR induced genotoxic damage, evaluated by ISSR markers, in 15 day old leaves; specifically, a severe decrease in the genome template stability was observed. However, a partial recovery occurred after 2 weeks, especially under the lowest dose (i.e., 1 Gy), suggesting that DNA damage detection and repair mechanisms are active. Pigment content and genotoxic damage may serve as proxies for evaluating plant responses to IR stress, since they show univocal dose-dependent trends. The use of more checkpoints for analyses and more doses over a wider range, as well as the focus on different metabolites, could help elucidate plant response in terms of morpho-physiological changes.

Worldwide Research Trends on Milk Containing Only A2 β-Casein: A Bibliometric Study

Simple Summary

A1 β-casein has been correlated with adverse health outcomes, and, as a consequence, milk containing only A2 β-casein has emerged on the market. There has been a relevant increase in publications in this area since 2010. Food Science Technology and Agriculture were the main research areas of this topic. The term β-casomorphin was the most frequently used. The USA, New Zealand, and Australia were the most productive countries, though the most productive research institutions were, in absolute terms, from India, France, and Germany. The majority of the most cited studies that refer to A2 β-casein and health were reviews, and a few clinical trials have also been published.

Abstract

The protein fraction of β-casein may play a key role in the manifestation of a new intolerance: milk protein intolerance. The most common forms of β-casein among dairy cattle breeds are A1 and A2 β-casein. During gastrointestinal digestion of A1 β-casein, an opioid called peptide β-casomorphin-7 (BCM-7) is more frequently released, which can lead to adverse health outcomes. For that reason, novel products labelled as “A2 milk” or “A1-free dairy products” have appeared on the market. In this context, a bibliometric analysis on A2 β-casein research was carried out through the Web of Science (WoS) database. The main objective of this work was to provide an overview of the state of the art in the field of β-casein A2 by analyzing the number of publications per year, trends in thematic content, the most frequently used terms, and the most important institutions and countries in the field. This bibliometric study showed that a greater effort is needed to determine the possible implications of this novel product for human health and the market.

Identification and Characterization of SOG1 (Suppressor of Gamma Response 1) Homologues in Plants Using Data Mining Resources and Gene Expression Profiling

SOG1 (Suppressor of the Gamma response 1) is the master-regulator of plant DNA damage response (DDR), a highly coordinated network of DNA damage sensors, transducers, mediators, and effectors, with highly coordinated activities. SOG1 transcription factor belongs to the NAC/NAM protein family, containing the well-conserved NAC domain and five serine-glutamine (SQ) motifs, preferential targets for phosphorylation by ATM and ATR. So far, the information gathered for the SOG1 function comes from studies on the model plant Arabidopsis thaliana. To expand the knowledge on plant-specific DDR, it is opportune to gather information on other SOG1 orthologues. The current study identified plants where multiple SOG1 homologues are present and evaluated their functions by leveraging the information contained in publicly available transcriptomics databases. This analysis revealed the presence of multiple SOG1 sequences in thirteen plant species, and four (Medicago truncatula, Glycine max, Kalankoe fedtschenkoi, Populus trichocarpa) were selected for gene expression data mining based on database availability. Additionally, M. truncatula seeds and seedlings exposed to treatments known to activate DDR pathways were used to evaluate the expression profiles of MtSOG1a and MtSOG1b. The experimental workflow confirmed the data retrieved from transcriptomics datasets, suggesting that the SOG1 homologues have redundant functions in different plant species.

Exploring microRNA Signatures of DNA Damage Response Using an Innovative System of Genotoxic Stress in Medicago truncatula Seedlings

One of the challenges that living organisms face is to promptly respond to genotoxic stress to avoid DNA damage. To this purpose, all organisms, including plants, developed complex DNA damage response (DDR) mechanisms. These mechanisms are highly conserved among organisms and need to be finely regulated. In this scenario, microRNAs (miRNAs) are emerging as active players, thus attracting the attention of the research community. The involvement of miRNAs in DDR has been investigated prominently in human cells whereas studies in plants are still scarce. To experimentally investigate the involvement of plant miRNAs in the regulation of DDR-associated pathways, an ad hoc system was developed, using the model legume Medicago truncatula. Specific treatments with camptothecin (CPT) and/or NSC120686 (NSC), targeting distinct components of DDR, namely topoisomerase I (TopI) and tyrosyl-DNA phosphodiesterase 1 (TDP1), were used. Phenotypic (germination percentage and speed, seedling growth) and molecular (cell death, DNA damage, and gene expression profiles) analyses demonstrated that the imposed treatments impact DDR. Our results show that these treatments do not influence the germination process but rather inhibit seedling development, causing an increase in cell death and accumulation of DNA damage. Moreover, treatment-specific changes in the expression of suppressor of gamma response 1 (SOG1), master-regulator of plant DDR, were observed. Additionally, the expression of multiple genes playing important roles in different DNA repair pathways and cell cycle regulation were differentially expressed in a treatment-specific manner. Subsequently, specific miRNAs identified from our previous bioinformatics approaches as putatively targeting genes involved in DDR processes were investigated alongside their targets. The obtained results indicate that under most conditions when a miRNA is upregulated the corresponding candidate target gene is downregulated, providing an indirect evidence of miRNAs action over these targets. Hence, the present study extends the present knowledge on the information available regarding the roles played by miRNAs in the post-transcriptional regulation of DDR in plants.

An insight into the mechanism of DNA damage response in plants- role of SUPPRESSOR OF GAMMA RESPONSE 1: An overview

Because of their sessile lifestyle, plants are inescapably exposed to various kinds of environmental stresses throughout their lifetime. Therefore, to regulate their growth and development, plants constantly monitor the environmental signals and respond appropriately. However, these environmental stress factors, along with some endogenous metabolites, generated in response to environmental stress factors often induce various forms of DNA damage in plants and thus promote genome instability. To maintain the genomic integrity, plants have developed an extensive, sophisticated and coordinated cellular signaling mechanism known as DNA damage response or DDR. DDR evokes a signaling process which initiates with the sensing of DNA damage and followed by the subsequent activation of downstream pathways in many directions to repair and eliminate the harmful effects of DNA damages. SUPPRESSOR OF GAMMA RESPONSE 1 (SOG1), one of the newly identified components of DDR in plant genome, appears to play central role in this signaling network. SOG1 is a member of NAC [NO APICAL MERISTEM (NAM), ARABIDOPSIS TRANSCRIPTION ACTIVATION FACTOR (ATAF), CUP-SHAPED COTYLEDON (CUC)] domain family of transcription factors and involved in a diverse array of function in plants, encompassing transcriptional response to DNA damage, cell cycle checkpoint functions, ATAXIA-TELANGIECTASIA-MUTATED (ATM) or ATAXIA TELANGIECTASIA AND RAD3-RELATED (ATR) mediated activation of DNA damage response and repair, functioning in programmed cell death and regulation of induction of endoreduplication. Although most of the functional studies on SOG1 have been reported in Arabidopsis, some recent reports have indicated diverse functions of SOG1 in various other plant species, including Glycine max, Medicago truncatula, Sorghum bicolour, Oryza sativa and Zea mays, respectively. The remarkable functional diversity shown by SOG1 protein indicates its multitasking capacity. In this review, we integrate information mainly related to functional aspects of SOG1 in the context of DDR in plants. Considering the important role of SOG1 in DDR and its functional diversity, in-depth functional study of this crucial regulatory protein can provide further potential information on genome stability maintenance mechanism in plants in the context of changing environmental condition.

Alternative Splicing and DNA Damage Response in Plants

Plants are exposed to a variety of abiotic and biotic stresses that may result in DNA damage. Endogenous processes - such as DNA replication, DNA recombination, respiration, or photosynthesis - are also a threat to DNA integrity. It is therefore essential to understand the strategies plants have developed for DNA damage detection, signaling, and repair. Alternative splicing (AS) is a key post-transcriptional process with a role in regulation of gene expression. Recent studies demonstrate that the majority of intron-containing genes in plants are alternatively spliced, highlighting the importance of AS in plant development and stress response. Not only does AS ensure a versatile proteome and influence the abundance and availability of proteins greatly, it has also emerged as an important player in the DNA damage response (DDR) in animals. Despite extensive studies of DDR carried out in plants, its regulation at the level of AS has not been comprehensively addressed. Here, we provide some insights into the interplay between AS and DDR in plants.

Worldwide Research Trends on Wheat and Barley: A Bibliometric Comparative Analysis

Grain cereals such as wheat, barley, rice, and maize are the nutritional basis of humans and animals worldwide. Thus, these crop plants are essential in terms of global food security. We conducted a bibliometric assessment of scientific documents and patents related to wheat and barley through the Scopus database. The number of documents published per year, their affiliation and corresponding scientific areas, the publishing journals, document types and languages were metricized. The main keywords included in research publications concerning these crops were also analysed globally and clustered in thematic groups. In the case of keywords related to agronomy or genetics and molecular biology, we considered documents dated up to 1999, and from 2000 to 2018, separately. Comparison of the results obtained for wheat and barley revealed some remarkable different trends, for which the underlying reasons are further discussed.

Analysis of Global Research on Malaria and Plasmodium vivax

Background: Malaria is one of the infectious diseases of greatest interest to the scientific community and of greatest concern to international health authorities. Traditionally, the focus has been on Plasmodium falciparum, the parasite that causes the most severe form of the disease in Africa. However, in the last twenty years, the Plasmodium vivax parasite, responsible for a large number of cases in Latin America, the Middle East, South and Southeast Asia, the Horn of Africa, and Oceania, has also generated enormous interest due, among other things, to the published evidence that it can cause severe malaria. Methods: In this paper, the international scientific publication on malaria and P. vivax has been analyzed using the Scopus database to try to define global trends in this field of study. Results: It has been shown that events such as the emergence of resistance to certain drugs can break a trend. The important role of non-malaria-endemic countries such as the USA or Switzerland in malaria research is also evident. Conclusions: International cooperation will be essential for the eradication of the disease. Moreover, in this sense, the general vision given by the bibliometric analysis of malaria caused by P. vivax is fundamental to paint the picture regarding the current situation and encourage international cooperation and control efforts.

Targeted transcriptional and proteomic studies explicate specific roles of Bacillus subtilis iturin A, fengycin, and surfactin on elicitation of defensive systems in mandarin fruit during stress

Application of Bacillus cyclic lipopeptides (CLPs); fengycin, iturin A and surfactin has shown a great potential in controlling the spread of green mold pathogen invasion (Penicillium digitatum) in wounded mandarin fruit during postharvest period. The limited defensive protein profiles followed specific expression of pivotal genes relating to plant hormone mediating signaling pathways of the CLPs’ action on stimulating host plant resistance have been exhibited. The present study aimed to elucidate the specific effect of individual CLP obtained from Bacillus subtilis ABS-S14 as elicitor role on activation of plant defensive system at transcriptional and proteomic levels with and without P. digitatum co-application in mandarin fruit. Fengycin and iturin A elevated the gene expression of PAL, ACS1, ACO, CHI, and GLU while significantly stimulating plant POD transcription was only detected in the treatments of surfactin both with and without following P. digitatum. An increase of LOX and PR1 gene transcripts was determined in the treatments of individual CLP with fungal pathogen co-application. Fengycin activated production of unique defensive proteins such as protein involved in ubiquinone biosynthetic process in treated flavedo without P. digitatum infection. Proteins involved in the auxin modulating pathway were present in the iturin A and surfactin treatments. CLP-protein binding assay following proteome analysis reveals that iturin A attached to 12-oxophytodienoate reductase 2 involved in the oxylipin biosynthetic process required for jasmonic acid production which is implicated in induced systemic resistance (ISR). This study suggests specific elicitor action of individual CLP, particularly iturin A showed the most powerful in stimulating the ISR system in response to stresses in postharvest mandarins.

Unaccompanied Minors: Worldwide Research Perspectives

Due to the globalisation of the economy, migratory flows have increased significantly. Unaccompanied foreign minors have become a growing problem in recent years. The objective of this study is to make an analysis from a bibliometric point of view and to identify the main research trends concerning this topic by clusters identification. It has been observed that, above all, there are two main subjects that dominate the scientific literature in this field, the social sciences and medicine. The first one is the clearest in terms of legal and political implications, but the second one is related to the field of determining the age of minors by means of diagnostic tests. As to clusters, the following have been identified: First as a refugee–asylum seeker, second as a refugees–psychology, third as migration, fourth as age determination, and fifth as health care. Finally, the following temporal evolution of the issues dealt with in relation to unaccompanied minors has been observed: War, stress, migration, immigration, risk factors, health, legal aspects and, more recently, vaccination or age determination.

The Identification of Scientific Communities and Their Approach to Worldwide Malaria Research

It is essential to establish a pattern to detect the strengths and weaknesses of working groups publishing on malaria, to promote coordination to facilitate the eradication of the disease. Given the complexity of the scientific network of groups and institutions studying malaria, it is necessary to use a mathematical algorithm that allows us to know the real structure of research on the disease in the world. In this work, articles with the word “malaria” in the title or author keywords gathered from Elsevier Scopus database were analyzed. By means of specific software, graphs were created. The analysis of the data allowed established different scientific communities, among which two were very diverse: one formed by those groups concerned about the vector transmission and control, and another one focused on the drug resistance of the parasite. Basic, applied, and operational research to eradicate malaria is an ambitious goal of the international institutions and the scientific community. The combination of effort and the establishment of a worldwide-scientific network that allows an effective interconnection (exchange) of knowledge, infrastructure technology, collaborators, financial resources, and datasets will contribute more effectively to end the disease.

The Higher Education Sustainability through Virtual Laboratories: The Spanish University as Case of Study

Education has been integrated into the globalization process supported by technological advances such as e-learning. The sustainability of the universities is one of the key points of the university survival, and they strongly depend on the number of students that can enroll in them. Thus, many of the educational institutions have had to develop their curricula based on the use new technologies. Without a doubt, virtual laboratories are the latest technology in this regard. The objective of this work is to determine which are the main institutions and research trends in relation to virtual laboratories. The methodology followed in this research was to perform a bibliometric analysis of the whole scientific production indexed in Scopus. The world’s scientific production has been analysed in the following domains: first the trend over time, types of publications and countries, second the main subjects and keywords, third main institutions and their main topics, and fourth the main journals and proceedings that publish on this topic. After that, a case study was analysed in detailed as a representative country (Spain). The most productive institution in this field, Universidad de Educación a Distancia (UNED). If the ranking is established by average citations per published paper, the first three institutions are from the USA: Massachusetts Institute of Technology (MIT), University of Washington (Seattle), and Carnegie Mellon University. The scientific categories at world level and in the case of study are similar. First, there is the field of engineering followed by computer science and above all it highlights the wide spectrum of branches of knowledge in which this topic is published, which indicates the great acceptance of this teaching methodology in all fields of education. Finally, community detection has been applied to the case study and six clusters have been found: Virtual Reality, Users, E-learning, Programming, Automatic-robotics, Computer Simulation and Engineering Education. As a main conclusion, bibliographic analysis confirms that research in virtual laboratories is a very active field, where scientific productivity has exponentially increased over recent years in tandem with universities growth. Therefore, expectations are high in this field for the near future. The possibility of virtual laboratories opens up new perspectives for higher education sustainability, where the educational policies of countries could be reoriented.

The Electric Bicycle: Worldwide Research Trends

The bicycle has gone from being an old-fashioned recreational product to a less polluting means of transport and a compact, ultra-light personal mobility tool. This is how electrical bicycles will be used as the pillar that could support individual public transport in large cities worldwide. The objective of this manuscript is to detect how worldwide research on the electric bicycle is being developed, and, especially, around which scientific domains is it clustered, to finally identify the main trends in the field. This study has been carried out based on the Scopus database, where all the publications related to the topic of the electric bicycle have been analyzed up to the year 2017. ¨Therefore, research on the global research trends of this topic was conducted. Its evolution over time shows that since 2008 the growth of publications is much higher than in the previous period. The main countries are China and the USA, and it can be inferred that there are two major trend countries with high environmental awareness, which also have a large population and that the electric bicycle is a suitable and sustainable form of transport. Among the main scientific fields, engineering leads in research. The keyword analysis shows that the central theme is electric, then battery and motor stand out. A community detection was applied to detect the six main clusters of this research, largely dedicated to the following topics: Transportation–Environment, Electrical Engineering, Safety, Batteries, Sporting Goods–Urban Planning, and Mechanical Engineering. This manuscript shows that global research trends about the electric bicycle are increasing, and that it should be considered a means of sustainable urban transport and will therefore contribute to energy saving and sustainable energy.

Trends in plant research using molecular markers

A deep bibliometric analysis has been carried out, obtaining valuable parameters that facilitate the understanding around the research in plant using molecular markers. The evolution of the improvement in the field of agronomy is fundamental for its adaptation to the new exigencies that the current world context raises. In addition, within these improvements, this article focuses on those related to the biotechnology sector. More specifically, the use of DNA markers that allow the researcher to know the set of genes associated with a particular quantitative trait or QTL. The use of molecular markers is widely extended, including: restriction fragment length polymorphism, random-amplified polymorphic DNA, amplified fragment length polymorphism, microsatellites, and single-nucleotide polymorphisms. In addition to classical methodology, new approaches based on the next generation sequencing are proving to be fundamental. In this article, a historical review of the molecular markers traditionally used in plants, since its birth and how the new molecular tools facilitate the work of plant breeders is carried out. The evolution of the most studied cultures from the point of view of molecular markers is also reviewed and other parameters whose prior knowledge can facilitate the approach of researchers to this field of research are analyzed. The bibliometric analysis of molecular markers in plants shows that top five countries in this research are: US, China, India, France, and Germany, and from 2013, this research is led by China. On the other hand, the basic research using Arabidopsis is deeper in France and Germany, while other countries focused its efforts in their main crops as the US for wheat or maize, while China and India for wheat and rice.