bluuebunny/crossref_metadata_2025_split huggingface dataset:
Drivers of canine distemper virus exposure in dogs at a wildlife interface in Janos, Mexico
Authors: Almuna Rocío , López‐Pérez Andrés M. , Sarmiento Rosa E. , Suzán Gerardo 
Published: May 2021

AbstractBackgroundHuman population expansion has increased the contact between domestic animals and wildlife, thereby increasing the transmission of infectious diseases including canine distemper virus (CDV). Here, we investigated the risk factors associated with CDV exposure in domestic and wild carnivores from the Janos Biosphere Reserve (JBR), Mexico.MethodsA cross‐sectional household questionnaire study was performed in four rural towns to investigate the risk factors associated with the presence of CDV in domestic and wild carnivores from the JBR, Mexico. In addition, we tested serum samples from 70 dogs and three wild carnivores, including one bobcat (Lynx rufus), one striped skunk (Mephitis mephitis)and one gray fox (Urocyon cinereoargenteus) for CDV antibodies using immunochromatographic and viral neutralization assays.ResultsOverall, 62% of domestic dogs were seropositive for CDV, and the presence of antibodies was significantly higher in free‐roaming owned dogs than dogs with restricted movement. Among the wild carnivores, only the bobcat was seropositive. The rate of vaccination against CDV in dogs was low (7%), and there was a high rate of direct interactions between domestic dogs and wild carnivores.ConclusionOur serological assays show that CDV is circulating in both domestic dogs and wild carnivores, suggesting cross‐species transmission. Our finding of low vaccination rates, high number of unrestrained owned dogs and direct interactions between wildlife and domestic animals reported in the region may be perpetuating the high prevalence of the virus and increasing the risk of CDV transmission between wild and domestic carnivores. Therefore, long‐term longitudinal studies are recommended in order to monitor infectious diseases at the domestic‐wildlife interface in this highly biodiverse region.
Detailed Method for Performing the ExSTA Approach in Quantitative Bottom-Up Plasma Proteomics
Authors: Percy Andrew J. , Borchers Christoph H. 
Published: May 2021

AbstractThe use of stable isotope-labeled standards (SIS) is an analytically valid means of quantifying proteins in biological samples. The nature of the labeled standards and their point of insertion in a bottom-up proteomic workflow can vary, with quantification methods utilizing curves in analytically sound practices. A promising quantification strategy for low sample amounts is external standard addition (ExSTA). In ExSTA, multipoint calibration curves are generated in buffer using serially diluted natural (NAT) peptides and a fixed concentration of SIS peptides. Equal concentrations of SIS peptides are spiked into experimental sample digests, with all digests (control and experimental) subjected to solid-phase extraction prior to liquid chromatography tandem mass spectrometry (LC-MS/MS) analysis. Endogenous peptide concentrations are then determined using the regression equation of the standard curves. Given the benefits of ExSTA in large-scale analysis, a detailed protocol is provided herein for quantifying a multiplexed panel of 125 high-to-moderate abundance proteins in undepleted and non-enriched human plasma samples. The procedural details and recommendations for successfully executing all phases of this quantification approach are described. As the proteins have been putatively correlated with various noncommunicable diseases, quantifying these by ExSTA in large-scale studies should help rapidly and precisely assess their true biomarker efficacy.
Quantitative Cross-Linking of Proteins and Protein Complexes
Authors: Barth Marie , Schmidt Carla 
Published: May 2021

AbstractCross-linking, in general, involves the covalent linkage of two amino acid residues of proteins or protein complexes in close proximity. Mass spectrometry and computational analysis are then applied to identify the formed linkage and deduce structural information such as distance restraints. Quantitative cross-linking coupled with mass spectrometry is well suited to study protein dynamics and conformations of protein complexes. The quantitative cross-linking workflow described here is based on the application of isotope labelled cross-linkers. Proteins or protein complexes present in different structural states are differentially cross-linked using a “light” and a “heavy” cross-linker. The intensity ratios of cross-links (i.e., light/heavy or heavy/light) indicate structural changes or interactions that are maintained in the different states. These structural insights lead to a better understanding of the function of the proteins or protein complexes investigated. The described workflow is applicable to a wide range of research questions including, for instance, protein dynamics or structural changes upon ligand binding.
Synthesis of Fluorescently Labeled Antibodies Using Non-Canonical Amino Acids in Eukaryotic Cell-Free Systems
Authors: Stech Marlitt , Rakotoarinoro Nathanaël , Teichmann Tamara , Zemella Anne , Thoring Lena , Kubick Stefan 
Published: May 2021

AbstractCell-free protein synthesis (CFPS) enables the development of antibody conjugates, such as fluorophore conjugates and antibody-drug conjugates (ADCs), in a rapid and straightforward manner. In the first part, we describe the cell-free synthesis of antibodies containing fluorescent non-canonical amino acids (ncaa) by using pre-charged tRNA. In the second part, we describe the cell-free synthesis of antibodies containing ncaa by using an orthogonal system, followed by the site-specific conjugation of the fluorescent dye DyLight 650-phosphine. The expression of the antibodies containing ncaa was analyzed by SDS-PAGE, followed by autoradiography and the labeling by in-gel fluorescence. Two different fluorescently labeled antibodies could be generated.
Strategies for Engineering Photosynthesis for Enhanced Plant Biomass Production
Authors: Yamori Wataru 
Published: May 2021

AbstractCrop productivity would have to increase by 60–110% compared with the 2005 level by 2050 to meet both the food and energy demands of the growing population. Although more than 90% of crop biomass is derived from photosynthetic products, photosynthetic improvements have not yet been addressed by breeding. Thus, it has been considered that enhancing photosynthetic capacity is considered a promising approach for increasing crop yield. Now, we need to identify the specific targets that would improve leaf photosynthesis to realize a new Green Revolution. This chapter summarizes the various genetic engineering approaches that can be used to enhance photosynthetic capacity and crop productivity. The targets considered for the possible candidates include Rubisco, Rubisco activase, enzymes of the Calvin–Benson cycle, and CO2 transport, as well as photosynthetic electron transport. Finally, it describes the importance of considering ways to improve photosynthesis not under the stable environmental conditions already examined in many studies with the aim of improving photosynthetic capacity, but under natural conditions in which various environmental factors, and especially irradiation, continually fluctuate.
Green Super Rice (GSR) Traits: Breeding and Genetics for Multiple Biotic and Abiotic Stress Tolerance in Rice
Authors: Ali Jauhar , Anumalla Mahender , Murugaiyan Varunseelan , Li Zhikang 
Published: May 2021

AbstractThe frequent fluctuations in global climate variability (GCV), decreases in farmland and irrigation water, soil degradation and erosion, and increasing fertilizer costs are the significant factors in declining rice productivity, mainly in Asia and Africa. Under GCV scenarios, it is a challenging task to meet the rice food demand of the growing population. Identifying green traits (tolerance of biotic and abiotic stresses, nutrient-use efficiency, and nutritional grain quality) and stacking them in high-yielding elite genetic backgrounds is one promising approach to increase rice productivity. To this end, the Green Super Rice (GSR) breeding strategy helps to pool multi-stress-tolerance traits by stringent selection processes and to develop superior GSR cultivars within a short span of 4–5 years. In the crossing and selection process of GSR breeding, selective introgression lines (SILs) derived from sets of early backcross BC1F2bulk populations through both target traits and non-target traits were selected. Genotyping of SILs with high-density SNP markers leads to the identification of a large number of SNP markers linked with the target green traits. The identified SILs with superior trait combinations were used for designed QTL pyramiding to combine different target green traits. The GSR breeding strategy also focused on nutrient- and water-use efficiency besides environment-friendly green features primarily to increase grain yield and income returns for resource-poor farmers. In this chapter, we have highlighted the GSR breeding strategy and QTL introgression of green traits in rice. This breeding strategy has successfully dissected many complex traits and also released several multi-stress-tolerant varieties with high grain yield and productivity in the target regions of Asia and Africa.
Growing Rice with Less Water: Improving Productivity by Decreasing Water Demand
Authors: Singh Balwant , Mishra Shefali , Bisht Deepak Singh , Joshi Rohit 
Published: May 2021

AbstractRice is a staple food for more than half of the global population. With the increasing population, the yield of rice must correspondingly increase to fulfill the requirement. Rice is cultivated worldwide in four different types of ecosystems, which are limited by the availability of irrigation water. However, water-limiting conditions negatively affect rice production; therefore, to enhance productivity under changing climatic conditions, improved cultivation practices and drought-tolerant cultivars/varieties are required. There are two basic approaches to cultivation: (1) plant based and (2) soil and irrigation based, which can be targeted for improving rice production. Crop plants primarily follow three mechanisms: drought escape, avoidance, and tolerance. Based on these mechanisms, different strategies are followed, which include cultivar selection based on yield stability under drought. Similarly, soil- and irrigation-based strategies consist of decreasing non-beneficial water depletions and water outflows, aerobic rice development, alternate wetting and drying, saturated soil culture, system of rice intensification, and sprinkler irrigation. Further strategies involve developing drought-tolerant cultivars through marker-assisted selection/pyramiding, genomic selection, QTL mapping, and other breeding and cultivation practices such as early planting to follow escape strategies and decreasing stand density to minimize competition with weeds. Similarly, the identification of drought-responsive genes and their manipulation will provide a technological solution to overcome drought stress. However, it was the Green Revolution that increased crop production. To maintain the balance, there is a need for another revolution to cope with the increasing demand.
Crop Establishment in Direct-Seeded Rice: Traits, Physiology, and Genetics
Authors: Quilloy Fergie Ann , Labaco Benedick , Casal Carlos , Dixit Shalabh 
Published: May 2021

AbstractThe changing climate and water availability strongly affect the current state of agricultural production. While the global temperature rises, the occurrence of extreme climatic conditions becomes erratic. This current scenario has driven the development of rice varieties and cultivation practices that require less water and favor mechanization. Although puddled transplanted rice has been more widely used in the past, direct seeding has been gaining popularity in recent years, especially due to its water- and labor-saving features. This technique allows full crop establishment from seeds that were directly sown in the field, thus avoiding puddling, transplanting, and maintaining standing water. Consequently, it offers promising positive environmental effects including decreasing the release of greenhouse gases and increasing water-use efficiency. Historically, rice varieties bred for transplanting are also used in direct seeding, which limits the maximum yield potential of field trials. The success of direct seeding relies strongly on the development of rice varieties with robust crop establishment. Anaerobic germination, seed longevity, and early seedling vigor are the key traits required to achieve this. This chapter expounds on the physiology, molecular mechanisms, genetics, and relevance of the enumerated traits for direct seeding. A brief discussion of breeding for rice varieties with improved germination under direct seeding is also provided.
Microbial Growth and its Effects on Inorganic Heritage Materials
Authors: Pinna Daniela 
Published: May 2021

AbstractCultural heritage objects composed of inorganic materials, such as metals and stones, support microbial life. Many factors affect the growth of microorganisms: moisture, pH, light, temperature, nutrients. Their colonization relates closely to the nature of the substrata as well as to the characteristic of the surrounding environment. This chapter contains an overview of the complex relationships among microbial growth, materials, and the environment. It emphasizes issues on bioreceptivity of stones and the factors influencing biological colonization, focusing on the biological alteration of inorganic heritage objects and on the agents of biodeterioration. It outlines the effect of biofilms and lichens in terms of degradation of substrata and includes a discussion on an important topic, the bioprotection of stones by biofilms and lichens. In summary, this chapter aims to discuss these issues and review the recent literature on (i) biofilms and lichens colonizing inorganic materials, (ii) the limiting factors of this colonization, (iii) the deteriorative aspects, and (iv) the protective effects of the colonization.
Sustainable Restoration Through Biotechnological Processes: A Proof of Concept
Authors: Sprocati Anna Rosa , Alisi Chiara , Migliore Giada , Marconi Paola , Tasso Flavia 
Published: May 2021

AbstractAn understanding of the different microbial constellations or microbiomes, which every habitat and every organism harbor, will be the key to addressing many of the challenges humanity will face in the twenty-first century. Such comprehension could launch several innovations relating to natural and cultural capital, including historical and artistic heritage. In relation to cultural heritage, microorganisms are mainly known through their role as deteriogens, but the features creating damage can be exploited positively, attaining more sustainable restoration strategies, in accordance with the principles of compatibility and retreatability deriving from reflections on the Cultural Heritage inspired by the Charter of Venice (International charter for the Conservation and restoration of monument and sites (the Venice Chart 1964). In: ICOMOS, IInd International Congress of Architects and Technicians of Historic Monuments, 1964) onwards. In this article, we show a series of case studies, using both wild-type microorganisms and plant-based extracts, providing a comprehensive proof of concept of the feasibility of biotechnological solutions for a more sustainable restoration strategy, to replace the products in use which are often dangerous for operators, aggressive for works of art and no longer compatible with the environment. The overview of the case studies presented, many of which are still unpublished, responds to the need to go beyond the state of the art and has entirely sprung from suggestions by restorers, interested in learning about potential innovations and strongly determined to introduce non-toxic products in their daily work. In this perspective, the case studies dealt with two topics: bio-cleaning and disinfection. Noteworthy results were obtained on a platform of different types of artworks and different materials with compatible, harmless and selective products.
Siderophores and their Applications in Wood, Textile, and Paper Conservation
Authors: Rapti Stavroula , Boyatzis Stamatis C. , Rivers Shayne , Pournou Anastasia 
Published: May 2021

AbstractSince the 1950s, siderophores have been acknowledged as nature’s chelating powerhouse and have been given considerable attention concerning their crucial roles in microorganisms and plants for capturing non-bioavailable iron from aquatic and terrestrial environments, as well as for their applications in agriculture, health, and materials science and environmental research. In recent years, the exceptional affinity and complexing efficacy, as well as the high selectivity of these potent chelators towards iron(III), have led to investigations by researchers aiming at understanding their capacity for removing potentially harmful and aesthetically unacceptable iron stains from organic substrates in cultural heritage objects. In the context of the conservation of cultural heritage objects, potent chelators have been proposed to remove iron from surfaces by transferring it to the more soluble complexed phase. In this review, the origins and the types of bio-environments of siderophores as well as their structure and chemistry are investigated and related to the requirements of conservation. It is evident that, given the enormous potential that these chelators have, the research for their application in cultural heritage is at a preliminary level, and has to date been within the rather narrow context of cellulosic materials such as paper and wood. The results of research conducted to date are presented in this review and questions regarding the optimal use of siderophores as iron-removing agents are posed.
Organic Green Corrosion Inhibitors Derived from Natural and/or Biological Sources for Conservation of Metals Cultural Heritage
Authors: Argyropoulos Vasilike , Boyatzis Stamatis C. , Giannoulaki Maria , Guilminot Elodie , Zacharopoulou Aggeliki 
Published: May 2021

AbstractIn the last decade, there has been an increase in research related to green corrosion inhibitors for conservation of metals cultural heritage to help promote sustainable practices in the field that are safe, environmentally friendly, and ecologically acceptable. The most common are organic substances derived either from natural and/or biological sources: plant extracts and oils, amino acids, microorganisms, and biopolymers. The chapter will provide a review of these substances as corrosion inhibitors for metals conservation, by discussing the state-of-the-art research to date, with a special focus on cysteine. Most of the research has focused on the examination of such inhibitors on metal coupons with or without corrosion products using electrochemical techniques or weight-loss measurements to determine their effectiveness. Some of these studies have also considered the conservation principles for practice, i.e., reversibility of the treatment and the visual aspect of the modification of the treated metal surface. However, before such green inhibitors can be routinely applied by conservators, more research is required on their application to real artefacts/monuments using in situ corrosion measurements. Furthermore, given that the composition of a green inhibitor is highly dependent on its extraction process, research must also involve identifying the specific adsorption models and involved mechanisms to ensure reproducibility of results.
Molecular-Based Techniques for the Study of Microbial Communities in Artworks
Authors: Sterflinger Katja , Piñar Guadalupe 
Published: May 2021

AbstractThanks to the revolutionary invention of the polymerase chain reaction and the sequencing of DNA and RNA by means of “Sanger sequencing” in the 1970th and 1980th, it became possible to detect microorganisms in art and cultural assets that do not grow on culture media or that are non-viable. The following generation of sequencing systems (next generation sequencing, NGS) already allowed the detection of microbial communities on objects without the intermediate step of cloning, but still most of the NGS technologies used for the study of microbial communities in objects of art rely on “target sequencing” linked to the selectivity of the primers used for amplification. Today, with the third generation of sequencing technology, whole genome and metagenome sequencing is possible, allowing the detection of taxonomic units of all domains and kingdoms as well as functional genes in the produced metagenome. Currently, Nanopore sequencing technology is a good, affordable, and simple way to characterize microbial communities, especially in the field of Heritage Science. It also has the advantage that a bioinformatic analysis can be performed automatically. In addition to genomics and metagenomics, other “-omics” techniques such as transcriptomics, proteomics, and metabolomics have a great potential for the study of processes in art and cultural heritage, but are still in their infancy as far as their application in this field is concerned.
New Perspectives Against Biodeterioration Through Public Lighting
Authors: Sanmartín Patricia 
Published: May 2021

AbstractThere is currently an increasing trend in urban centres towards the use of public outdoor lighting systems to illuminate historic and architecturally important buildings during evening hours, but for which there is no specific regulatory framework. Considering that the light is a key factor involved in regulating growth and physiological processes in photosynthetic organisms, it seems appropriate to address the effects that artificial light has on the organisms growing on the facades affected by public lighting. In this sense, despite scientific research in the fields of biological colonization of buildings surfaces and light technology has advanced greatly in recent years, the combination of both disciplines aimed at the correct handling of city public lighting remains uncharted territory with huge potential to provide innovative solutions for smart cities. Recent studies have examined how urban monuments are affected by night-time outdoor illumination in combination with natural sunlight and demonstrated that the use of suitable lighting can inhibit the development of biological colonization. In this frame, this chapter will look at ways of contribute to the long-term management of public illumination on monuments and other structures, while reducing negative impacts caused by night lighting.
Bioremoval of Graffiti in the Context of Current Biocleaning Research
Authors: Bosch-Roig Pilar , Sanmartín Patricia 
Published: May 2021

AbstractSome microorganisms can be used as bioremediation agents, in biocleaning treatments, to remove undesired sulphates, nitrates and organic matter from cultural heritage surfaces. Graffiti materials (mainly spray paints) are now included in the list of materials that can be biocleaned, with studies on this topic being initiated just over 5 years ago. Research on the bioremoval of graffiti is continuing and on a promising track. This chapter reports a critical analysis of studies of the bioremoval of graffiti carried out in recent years, which are compared with similar studies of the removal of salts (mainly nitrates and sulphates) and organic matter conducted in the last thirty years. Likewise, the present challenges and ways of overcoming them are addressed towards developing a complete protocol for the use of bioremediation to remove graffiti, with particular emphasis on the use of the method for cleaning facades and buildings.