AbstractGlobal climate change has driven breeding programs to develop abiotic stress‐resilient plant varieties. Traditionally, assessing drought resilience involves labor‐intensive and time‐consuming processes. This study used an unmanned aerial system (UAS) to predict key phenotyping traits in maize (Zea mays L.) and monitor plant response to drought during the crop cycle. We grew transgenic maize hybrids in two trials, one irrigated and another subjected to drought stress, and used a drone equipped with red–green–blue (RGB) and multispectral sensors to capture images of the plots over time. Machine learning models and various prediction scenarios revealed significant correlations between vegetation indices over time. Interestingly, the RGB sensor outperformed the multispectral sensor in trait prediction. Prediction accuracy across scenarios with untested genotypes and environments ranged from 0.40 to 0.70 for grain yield, 0.43 to 0.69 for days to anthesis, 0.51 to 0.67 for days to silking, and 0.35 to 0.57 for plant height. Ridge and random forest models consistently delivered the most accurate predictions across traits and environments. The vegetation indices normalized green–red difference index, VARI, and RCC also effectively predicted and captured the plant response to drought. This study highlights the value of UAS phenotyping as a practical tool for assessing abiotic stress due to its straightforward implementation.

Microbial communities can vary as a function of seasonal precipitation and the phenotypic characteristics of the prevailing plant species in an ecosystem. The Brazilian campos rupestres (CRs) host a unique flora adapted to harsh conditions, including severe droughts and nutrient-poor soils. Velloziaceae, a dominant angiosperm family in CRs, exhibit contrasting drought adaptive strategies, prominently desiccation tolerance and dehydration avoidance. Here, we created a comprehensive dataset of microbial composition and dynamics of bulk soil and distinct plant compartments (leaf blade, dry sheath, aerial root, and underground root) from two desiccation-tolerant and two dehydration-avoiding, non-desiccation-tolerant Vellozia species, across four seasons (beginning and end of rainy and dry seasons) through 16S rRNA gene sequencing of 374 samples. This dataset also includes 38 soil metagenomes encompassing dry and rainy seasons from both drought adaptive strategies. Exploring an overlooked aspect of CRs biology offers significant potential for understanding plant-microbial associations and adaptations to water availability in tropical regions. The genetic data and metadata support further research for hypothesis testing and cross-study comparisons.

Chapter 19 Nervous and Locomotor System Darin M. Madson, Darin M. MadsonSearch for more papers by this authorPaulo H.E. Arruda, Paulo H.E. ArrudaSearch for more papers by this authorBailey L. Arruda, Bailey L. ArrudaSearch for more papers by this author Darin M. Madson, Darin M. MadsonSearch for more papers by this authorPaulo H.E. Arruda, Paulo H.E. ArrudaSearch for more papers by this authorBailey L. Arruda, Bailey L. ArrudaSearch for more papers by this author Book Editor(s):Jeffrey J. Zimmerman, Jeffrey J. ZimmermanSearch for more papers by this authorLocke A. Karriker, Locke A. KarrikerSearch for more papers by this authorAlejandro Ramirez, Alejandro RamirezSearch for more papers by this authorKent J. Schwartz, Kent J. SchwartzSearch for more papers by this authorGregory W. Stevenson, Gregory W. StevensonSearch for more papers by this authorJianqiang Zhang, Jianqiang ZhangSearch for more papers by this author First published: 29 March 2019 https://doi.org/10.1002/9781119350927.ch19Citations: 5 AboutPDFPDF ToolsRequest permissionExport citationAdd to favoritesTrack citation ShareShareShare a linkShare onFacebookTwitterLinked InRedditWechat Summary Disorders, diseases, and deficits related to mentation and locomotion are both production and welfare concerns. Nervous disorders commonly occur with sudden onset or acute outbreaks, whereas most disorders of the skeletal system can be insidious, with faulty bone formation, structural loss, poor conformation, protracted inflammation, or trauma all contributing. Locomotor disorders contribute to losses in all stages of production with considerable variation between individual farms and are associated with numerous contributing risk factors. The primary purpose of the neurological examination is to determine the extent of the neurologic deficits and the potential anatomical location affected. Congenital and newborn locomotor diseases can result from myriad insults affecting gestating sows or newborn pigs. Hypoglycemia is a common problem, both in weak newborn pigs who do not nurse regularly and in sows with limited functional mammary glands. Hydrocephalus is an accumulation of cerebrospinal fluid within the brain. Citing Literature Diseases of Swine, Eleventh Edition RelatedInformation

The saccharopine pathway (SacPath) and the pipecolate pathway (PipPath) catabolize lysine to α-aminoadipate. Although the PipPath has been highlighted as the prominent route operating in the brain, recent work has demonstrated that the SacPath plays a major role in lysine catabolism in the brain. The first two enzymatic steps of the SacPath involve the bifunctional enzyme α-aminoadipate semialdehyde synthase (AASS) harboring the lysine-ketoglutarate reductase (LKR) and the saccharopine dehydrogenase (SDH) domains that convert lysine to α-aminoadipate semialdehyde. Thereafter, the semialdehyde is converted to α-aminoadipate by α-aminoadipate semialdehyde dehydrogenase (AASADH). Mutations abolishing the enzymatic activities of LKR, SDH, and AASADH lead to the genetic diseases hyperlysinemia type I and II, and pyridoxine-dependent epilepsy (PDE), respectively. Hyperlysinemia type I accumulates lysine and causes a benign phenotype without clinical significance. Hyperlysinemia type II accumulates saccharopine, which leads to neuronal disorders and intellectual disability. PDE accumulates α-aminoadipate semialdehyde and its cyclic isomer piperideine-6-carboxylate, which binds pyridoxal 5′-phosphate, disturbs synapses, and causes seizures along with developmental disorders. Another genetic disease, glutaric aciduria type I (GA1), localizes just downstream of the SacPath and is caused by mutations abolishing the enzymatic activity of glutaryl-CoA dehydrogenase (GCDH). GA1 accumulates glutarate and 3-hydroxyglutarate, which are neurotoxic molecules that cause irreversible brain damage. Downregulation of LKR has been shown to reduce the metabolic flux through SacPath and alleviate PDE and GA1 symptoms. This review discusses the role of SacPath and its enzymes as potential targets for developing drugs to treat PDE and GA1, as well as other diseases.

AbstractIn recent years, microbiomes and their potential applications for human, animal or plant health, food production and environmental management came into the spotlight of major national and international policies and strategies. This has been accompanied by substantial R&D investments in both public and private sectors, with an increasing number of products entering the market. Despite widespread agreement on the potential of microbiomes and their uses across disciplines, stakeholders and countries, there is no consensus on what defines a microbiome application. This often results in non‐comprehensive communication or insufficient documentation making commercialisation and acceptance of the novel products challenging. To showcase the complexity of this issue we discuss two selected, well‐established applications and propose criteria defining a microbiome application and their conditions of use for clear communication, facilitating suitable regulatory frameworks and building trust among stakeholders.

In contrast to its close homolog PLANT UNCOUPLING MITOCHONDRIAL PROTEIN 1 (UCP1), which is an abundant carrier protein in the mitochondria, UCP2 localizes to the Golgi.

Recent advances in genome editing have enormously enhanced the effort to develop biotechnology crops for more sustainable food production. CRISPR/Cas, the most versatile genome-editing tool, has shown the potential to create genome modifications that range from gene knockout and gene expression pattern modulations to allele-specific changes in order to design superior genotypes harboring multiple improved agronomic traits. However, a frequent bottleneck is the delivery of CRISPR/Cas to crops that are less amenable to transformation and regeneration. Several technologies have recently been proposed to overcome transformation recalcitrance, including HI-Edit/IMGE and ectopic/transient expression of genes encoding morphogenic regulators. These technologies allow the eroding of the barriers that make crops inaccessible for genome editing. In this review, we discuss the advances in genome editing in crops with a particular focus on the use of technologies to improve complex traits such as water use efficiency, drought stress, and yield in maize.

Sugarcane (Saccharum officinarum, Poaceae) is cultivated on a large scale in (sub)tropical regions such as Brazil and has considerable economic value for sugar and biofuel production. The plant is a rich substrate for endo- and epiphytic fungi. Black yeasts in the family Herpotrichiellaceae (Chaetothyriales) are colonizers of human-dominated habitats, particularly those rich in toxins and hydrocarbon pollutants, and may cause severe infections in susceptible human hosts. The present study assessed the diversity of Herpotrichiellaceae associated with sugarcane, using in silico identification and selective isolation. Using metagenomics, we identified 5833 fungal sequences, while 639 black yeast-like isolates were recovered in vitro. In both strategies, the latter fungi were identified as members of the genera Cladophialophora, Exophiala, and Rhinocladiella (Herpotrichiellaceae), Cyphellophora (Cyphellophoraceae), and Knufia (Trichomeriaceae). In addition, we discovered new species of Cladophialophora and Exophiala from sugarcane and its rhizosphere. The first environmental isolation of Cladophialophora bantiana is particularly noteworthy, because this species up to now is exclusively known from the human host where it mostly causes fatal brain disease in otherwise healthy patients.

The recalcitrance exhibited by many maize (Zea mays) genotypes to traditional genetic transformation protocols poses a significant challenge to the large-scale application of genome editing (GE) in this major crop species. Although a few maize genotypes are widely used for genetic transformation, they prove unsuitable for agronomic tests in field trials or commercial applications. This challenge is exacerbated by the predominance of transformable maize lines adapted to temperate geographies, despite a considerable proportion of maize production occurring in the tropics. Ectopic expression of morphogenic regulators (MRs) stands out as a promising approach to overcome low efficiency and genotype dependency, aiming to achieve ’universal’ transformation and GE capabilities in maize. Here, we report the successful GE of agronomically relevant tropical maize lines using a MR-based, Agrobacterium-mediated transformation protocol previously optimized for the B104 temperate inbred line. To this end, we used a CRISPR/Cas9-based construct aiming at the knockout of the VIRESCENT YELLOW-LIKE (VYL) gene, which results in an easily recognizable phenotype. Mutations at VYL were verified in protoplasts prepared from B104 and three tropical lines, regardless of the presence of a single nucleotide polymorphism (SNP) at the seed region of the VYL target site in two of the tropical lines. Three out of five tropical lines were amenable to transformation, with efficiencies reaching up to 6.63%. Remarkably, 97% of the recovered events presented indels at the target site, which were inherited by the next generation. We observed off-target activity of the CRISPR/Cas9-based construct towards the VYL paralog VYL-MODIFIER, which could be partly due to the expression of the WUSCHEL (WUS) MR. Our results demonstrate efficient GE of relevant tropical maize lines, expanding the current availability of GE-amenable genotypes of this major crop.

Mitochondrial retrograde signaling is an important component of intracellular stress signaling in eukaryotes. UNCOUPLING PROTEIN (UCP)1 is an abundant plant inner-mitochondrial membrane protein with multiple functions including uncoupled respiration and amino-acid transport1,2 that influences broad abiotic stress responses. Although the mechanism(s) through which this retrograde function acts is unknown, overexpression of UCP1 activates expression of hypoxia (low oxygen)-associated nuclear genes.3,4 Here we show in Arabidopsis thaliana that UCP1 influences nuclear gene expression and physiological response by inhibiting the cytoplasmic PLANT CYSTEINE OXIDASE (PCO) branch of the PROTEOLYSIS (PRT)6 N-degron pathway, a major mechanism of oxygen and nitric oxide (NO) sensing.5 Overexpression of UCP1 (UCP1ox) resulted in the stabilization of an artificial PCO N-degron pathway substrate, and stability of this reporter protein was influenced by pharmacological interventions that control UCP1 activity. Hypoxia and salt-tolerant phenotypes observed in UCP1ox lines resembled those observed for the PRT6 N-recognin E3 ligase mutant prt6-1. Genetic analysis showed that UCP1 regulation of hypoxia responses required the activity of PCO N-degron pathway ETHYLENE RESPONSE FACTOR (ERF)VII substrates. Transcript expression analysis indicated that UCP1 regulation of hypoxia-related gene expression is a normal component of seedling development. Our results show that mitochondrial retrograde signaling represses the PCO N-degron pathway, enhancing substrate function, thus facilitating downstream stress responses. This work reveals a novel mechanism through which mitochondrial retrograde signaling influences nuclear response to hypoxia by inhibition of an ancient cytoplasmic pathway of eukaryotic oxygen sensing.

The interaction of mitochondria with cellular components evolved differently in plants and mammals; in plants, the organelle contains proteins such as ALTERNATIVE OXIDASES (AOXs), which, in conjunction with internal and external ALTERNATIVE NAD(P)H DEHYDROGENASES, allow canonical oxidative phosphorylation (OXPHOS) to be bypassed. Plant mitochondria also contain UNCOUPLING PROTEINS (UCPs) that bypass OXPHOS. Recent work revealed that OXPHOS bypass performed by AOXs and UCPs is linked with new mechanisms of mitochondrial retrograde signaling. AOX is functionally associated with the NO APICAL MERISTEM transcription factors, which mediate mitochondrial retrograde signaling, while UCP1 can regulate the plant oxygen-sensing mechanism via the PRT6 N-Degron. Here, we discuss the crosstalk or the independent action of AOXs and UCPs on mitochondrial retrograde signaling associated with abiotic stress responses. We also discuss how mitochondrial function and retrograde signaling mechanisms affect chloroplast function. Additionally, we discuss how mitochondrial inner membrane transporters can mediate mitochondrial communication with other organelles. Lastly, we review how mitochondrial metabolism can be used to improve crop resilience to environmental stresses. In this respect, we particularly focus on the contribution of Brazilian research groups to advances in the topic of mitochondrial metabolism and signaling.

Increasing knowledge of the microbiome has led to significant advancements in the agrifood system. Case studies based on microbiome applications have been reported worldwide and, in this review, we have selected 14 success stories that showcase the importance of microbiome research in advancing the agrifood system. The selected case studies describe products, methodologies, applications, tools, and processes that created an economic and societal impact. Additionally, they cover a broad range of fields within the agrifood chain: the management of diseases and putative pathogens; the use of microorganism as soil fertilizers and plant strengtheners; the investigation of the microbial dynamics occurring during food fermentation; the presence of microorganisms and/or genes associated with hazards for animal and human health (e.g., mycotoxins, spoilage agents, or pathogens) in feeds, foods, and their processing environments; applications to improve HACCP systems; and the identification of novel probiotics and prebiotics to improve the animal gut microbiome or to prevent chronic non-communicable diseases in humans (e.g., obesity complications). The microbiomes of soil, plants, and animals are pivotal for ensuring human and environmental health and this review highlights the impact that microbiome applications have with this regard.

The substrates of the Brazilian campos rupestres, a grassland ecosystem, have extremely low concentrations of phosphorus and nitrogen, imposing restrictions to plant growth. Despite that, this ecosystem harbors almost 15% of the Brazilian plant diversity, raising the question of how plants acquire nutrients in such a harsh environment. Here, we set out to uncover the taxonomic profile, the compositional and functional differences and similarities, and the nutrient turnover potential of microbial communities associated with two plant species of the campos rupestres-dominant family Velloziaceae that grow over distinct substrates (soil and rock). Using amplicon sequencing data, we show that, despite the pronounced composition differentiation, the plant-associated soil and rock communities share a core of highly efficient colonizers that tend to be highly abundant and is enriched in 21 bacterial families. Functional investigation of metagenomes and 522 metagenome-assembled genomes revealed that the microorganisms found associated to plant roots are enriched in genes involved in organic compound intake, and phosphorus and nitrogen turnover. We show that potential for phosphorus transport, mineralization, and solubilization are mostly found within bacterial families of the shared microbiome, such as Xanthobacteraceae and Bryobacteraceae. We also detected the full repertoire of nitrogen cycle-related genes and discovered a lineage of Isosphaeraceae that acquired nitrogen-fixing potential via horizontal gene transfer and might be also involved in nitrification via a metabolic handoff association with Binataceae. We highlight that plant-associated microbial populations in the campos rupestres harbor a genetic repertoire with potential to increase nutrient availability and that the microbiomes of biodiversity hotspots can reveal novel mechanisms of nutrient turnover.

Increasing knowledge of the microbiome has led to significant advancements in the agrifood system. Case studies based on microbiome applications have been reported worldwide and, in this review, we have selected 14 success stories that showcase the importance of microbiome research in advancing the agrifood system. The selected case studies describe products, methodologies, applications, tools, and processes that created an economic and societal impact. Additionally, they cover a broad range of fields within the agrifood chain: the management of diseases and putative pathogens; the use of microorganism as soil fertilizers and plant strengtheners; the investigation of the microbial dynamics occurring during food fermentation; the presence of microorganisms and/or genes associated with hazards for animal and human health (e.g., mycotoxins, spoilage agents, or pathogens) in feeds, foods, and their processing environments; applications to improve HACCP systems; and the identification of novel probiotics and prebiotics to improve the animal gut microbiome or to prevent chronic non-communicable diseases in humans (e.g., obesity complications). The microbiomes of soil, plants, and animals are pivotal for ensuring human and environmental health and this review highlights the impact that microbiome applications have with this regard.

Sugarcane (Saccharum spp.) has been produced worldwide as a relevant source of food and sustainable energy. However, the constant need to increase crop yield has led to excessive use of synthetic agrochemical inputs such as inorganic fertilizers, herbicides, and pesticides in plant cultures. It is known that these conventional practices can lead to deleterious effects on health and the environment. Organic farming emerges as a sustainable alternative to conventional systems; however, farm management influences in plant-associated microbiomes remain unclear. Here, the aim is to identify the effects of farming systems on the sugarcane microbiota. To address this issue, we sampled the microbiota from soils and plants under organic and conventional farming from two crop fields in Brazil. Then, we evaluated their compositional, structural, and functional traits through amplification and sequencing of phylogenetic markers of bacteria (16S rRNA gene, V3-V4 region) and fungi (Internal Transcribed Spacer - ITS2). The data processing and analyses by the DADA2 pipeline revealed 12,839 bacterial and 3,222 fungal sequence variants. Moreover, differences between analogous niches were detected considering the contrasting farming systems, with samples from the conventional system showing a slightly greater richness and diversity of microorganisms. The composition is also different between the farming systems, with 389 and 401 differentially abundant taxa for bacteria and fungi, respectively, including taxa capable of promoting plant growth. The microbial co-occurrence networks showed structural changes in microbial communities, where organic networks were more cohesive since they had closer taxa and less modularity by niches. Finally, the functional prediction revealed enriched metabolic pathways, including the increased presence of antimicrobial resistance in the conventional farming system. Taken together, our findings reveal functional, structural, and compositional adaptations of the microbial communities associated with sugarcane plants in the field, according to farming management. With this, we point out the need to unravel the mechanisms driving these adaptations.

Atypical porcine pestivirus (APPV) is a cause of congenital tremors (CTs) in piglets and has been found in swine populations around the globe. Although systemic distribution of the virus has been reported, there is limited information regarding viral localization at the cellular level and distribution at the tissue level. We collected multiple tissues from 2-d-old piglets (n = 36) born to sows inoculated at 45 or 62 d of gestation with APPV via 3 simultaneous routes: intravenous, intranasal, and directly in amniotic vesicles. In addition, 2 boars from APPV-inoculated sows with CT were raised and euthanized when 11 mo old. In situ hybridization performed on tissue samples from piglets demonstrated a broad and systemic distribution of viral RNA including endothelial cells, fibroblasts, and smooth muscle. Labeling in tissues was more pronounced in piglet tissues compared to boars, with the notable exception of diffuse labeling of the cerebellum in boars. Presence of APPV in boar tissues well after resolution of clinical signs suggests persistence of APPV similar to other pestiviruses.

espanolClostridioides difficile ( C. difficile) es una bacteria responsable de diarreas como consecuencia del efecto citotoxico de las toxinas A y B producidas tras la colonizacion del tubo digestivo de lechones neonatos. La comprension de los mecanismos de virulencia de C. difficile y como derivan en la aparicion de un cuadro diarreico, supone un pilar fundamental para implementar medidas preventivas en la sala de maternidad. Lo que parece evidente es que el conocimiento sobre la bacteria es cada vez mayor, y junto a un enfoque multifactorial cada vez se dispone de nuevas y mejores herramientas para la prevencion de la enfermedad. EnglishClostridioides difficile (C. difficile) is a bacterium responsible for diarrhea as a consequence of the cytotoxic effect of toxins A and B produced after colonization of the digestive tract of newborn piglets. Understanding the virulence mechanisms of C. difficile and how they lead to the appearance of diarrhea, is a fundamental pillar to implement preventive measures in the maternity ward. What seems evident is that knowledge about the bacteria is increasing, and together with a multifactorial approach, new and better tools are increasingly available for the prevention of the disease.

espanolClostridioides difficile (C. difficile) es una bacteria anaerobica vegetativa que forma parte de la microbiota comensal de los lechones, pero a la vez ocasiona episodios de diarrea neonatal. Esta particularidad hace que el diagnostico de la enfermedad suponga un reto complejo y a la vez fundamental para determinar medidas correctoras. Los signos clinicos se caracterizan por la presencia de una diarrea acuosa y amarillenta durante la primera semana de vida, ademas de lesiones macroscopicas en el intestino grueso (especialmente en el colon) debido al efecto citotoxico de las toxinas. En la mayoria de los casos sera preciso complementar el diagnostico con tecnicas laboratoriales como la PCR, ELISA o la histopatologia. EnglishClostridioides difficile (C. difficile) is a vegetative anaerobic bacterium that is part of the commensal microbiota of piglets, but also causes episodes of neonatal diarrhea. This particularity makes the diagnosis of the disease a complex challenge and at the same time fundamental to determine corrective measures. The clinical signs are characterized by the presence of a watery and yellowish diarrhea during the first week of life, in addition to macroscopic lesions in the large intestine (especially in the colon) due to the cytotoxic effect of toxins. In most cases it will be necessary to complement the diagnosis with laboratory techniques such as PCR, ELISA or histopathology.

espanolClostridioides difficile esta bien descrito como un patogeno nosocomial en humanos asociado a una disbiosis como consecuencia de antibioterapias, especialmente en edades avanzadas. En porcino se trata de un colonizador temprano del intestino del lechon neonato, que causa enfermedad enterica durante los primeros dias de vida. La prevencion de la enfermedad en porcino requiere un enfoque multifactorial entre un buen manejo en la sala de partos, la disminucion de la presion de infeccion en la sala de partos, la disminucion de la presion de infeccion e incrementar la capacidad de resistencia de los lechones. EnglishClostridioides difficile is well described as a nosocomial pathogen in humans associated with dysbiosis as a consequence of antibiotics, especially in advanced ages. In pigs, it is an early colonizer of the neonate piglet's intestine, causing enteric disease during the first days of life. Disease prevention in pigs requires a multifactorial approach between good management in the farrowing room, reducing the infection pressure in the farrowing room, reducing the infection pressure and increasing the resistance capacity of the piglets. .

Over the past decades, advances in plant biotechnology have allowed the development of genetically modified maize varieties that have significantly impacted agricultural management and improved the grain yield worldwide. To date, genetically modified varieties represent 30% of the world’s maize cultivated area and incorporate traits such as herbicide, insect and disease resistance, abiotic stress tolerance, high yield, and improved nutritional quality. Maize transformation, which is a prerequisite for genetically modified maize development, is no longer a major bottleneck. Protocols using morphogenic regulators have evolved significantly towards increasing transformation frequency and genotype independence. Emerging technologies using either stable or transient expression and tissue culture-independent methods, such as direct genome editing using RNA-guided endonuclease system as an in vivo desired-target mutator, simultaneous double haploid production and editing/haploid-inducer-mediated genome editing, and pollen transformation, are expected to lead significant progress in maize biotechnology. This review summarises the significant advances in maize transformation protocols, technologies, and applications and discusses the current status, including a pipeline for trait development and regulatory issues related to current and future genetically modified and genetically edited maize varieties.