Assessing patterns of metazoans in the global ocean using environmental DNA.

Documenting large-scale patterns of animals in the ocean and determining the drivers of these patterns is needed for conservation efforts given the unprecedented rates of change occurring within marine ecosystems. We used existing datasets from two global expeditions, Tara Oceans and Malaspina, that circumnavigated the oceans and sampled down to 4000 m to assess metazoans from environmental DNA (eDNA) extracted from seawater. We describe patterns of taxonomic richness within metazoan phyla and orders based on metabarcoding and infer the relative abundance of phyla using metagenome datasets, and relate these data to environmental variables. Arthropods had the greatest taxonomic richness of metazoan phyla at the surface, while cnidarians had the greatest richness in pelagic zones. Half of the marine metazoan eDNA from metagenome datasets was from arthropods, followed by cnidarians and nematodes. We found that mean surface temperature and primary productivity were positively related to metazoan taxonomic richness. Our findings concur with existing knowledge that temperature and primary productivity are important drivers of taxonomic richness for specific taxa at the ocean's surface, but these correlations are less evident in the deep ocean. Massive sequencing of eDNA can improve understanding of animal distributions, particularly for the deep ocean where sampling is challenging.

Chromosome-scale pearl millet genomes reveal CLAMT1b as key determinant of strigolactone pattern and Striga susceptibility.

The yield of pearl millet, a resilient cereal crop crucial for African food security, is severely impacted by the root parasitic weed Striga hermonthica, which requires host-released hormones, called strigolactones (SLs), for seed germination. Herein, we identify four SLs present in the Striga-susceptible line SOSAT-C88-P10 (P10) but absent in the resistant 29Aw (Aw). We generate chromosome-scale genome assemblies, including four gapless chromosomes for each line. The Striga-resistant Aw lacks a 0.7 Mb genome segment containing two putative CARLACTONOIC ACID METHYLTRANSFERASE1 (CLAMT1) genes, which may contribute to SL biosynthesis. Functional assays show that P10CLAMT1b produces the SL-biosynthesis intermediate methyl carlactonoate (MeCLA) and that MeCLA is the precursor of P10-specific SLs. Screening a diverse pearl millet panel confirms the pivotal role of the CLAMT1 section for SL diversity and Striga susceptibility. Our results reveal a reason for Striga susceptibility in pearl millet and pave the way for generating resistant lines through marker-assisted breeding or direct genetic modification.

Mpox virus infection and drug treatment modelled in human skin organoids.

Mpox virus (MPXV) primarily infects human skin to cause lesions. Currently, robust models that recapitulate skin infection by MPXV are lacking. Here we demonstrate that human induced pluripotent stem cell-derived skin organoids are susceptible to MPXV infection and support infectious virus production. Keratinocytes, the predominant cell type of the skin epithelium, effectively support MPXV infection. Using transmission electron microscopy, we visualized the four stages of intracellular virus particle assembly: crescent formation, immature virions, mature virions and wrapped virions. Transcriptional analysis showed that MPXV infection rewires the host transcriptome and triggers abundant expression of viral transcripts. Early treatment with the antiviral drug tecovirimat effectively inhibits infectious virus production and prevents host transcriptome rewiring. Delayed treatment with tecovirimat also inhibits infectious MPXV particle production, albeit to a lesser extent. This study establishes human skin organoids as a robust experimental model for studying MPXV infection, mapping virus-host interactions and testing therapeutics.

Aroma Components in Horticultural Crops: Chemical Diversity and Usage of Metabolic Engineering for Industrial Applications.

Plants produce an incredible variety of volatile organic compounds (VOCs) that assist the interactions with their environment, such as attracting pollinating insects and seed dispersers and defense against herbivores, pathogens, and parasites. Furthermore, VOCs have a significant economic impact on crop quality, as well as the beverage, food, perfume, cosmetics and pharmaceuticals industries. These VOCs are mainly classified as terpenoids, benzenoids/phenylpropanes, and fatty acid derivates. Fruits and vegetables are rich in minerals, vitamins, antioxidants, and dietary fiber, while aroma compounds play a major role in flavor and quality management of these horticultural commodities. Subtle shifts in aroma compounds can dramatically alter the flavor and texture of fruits and vegetables, altering their consumer appeal. Rapid innovations in -omics techniques have led to the isolation of genes encoding enzymes involved in the biosynthesis of several volatiles, which has aided to our comprehension of the regulatory molecular pathways involved in VOC production. The present review focuses on the significance of aroma volatiles to the flavor and aroma profile of horticultural crops and addresses the industrial applications of plant-derived volatile terpenoids, particularly in food and beverages, pharmaceuticals, cosmetics, and biofuel industries. Additionally, the methodological constraints and complexities that limit the transition from gene selection to host organisms and from laboratories to practical implementation are discussed, along with metabolic engineering's potential for enhancing terpenoids volatile production at the industrial level.

Overexpression of GmWRKY172 enhances cadmium tolerance in plants and reduces cadmium accumulation in soybean seeds.

Introduction: Cadmium (Cd) stress is a significant threat to soybean production, and enhancing Cd tolerance in soybean is the focus of this study. The WRKY transcription factor family is associated with abiotic stress response processes. In this study, we aimed to identify a Cd-responsive WRKY transcription factor GmWRKY172 from soybean and investigate its potential for enhancing Cd tolerance in soybean. Methods: The characterization of GmWRKY172 involved analyzing its expression pattern, subcellular localization, and transcriptional activity. To assess the impact of GmWRKY172, transgenic Arabidopsis and soybean plants were generated and examined for their tolerance to Cd and Cd content in shoots. Additionally, transgenic soybean plants were evaluated for Cd translocation and various physiological stress indicators. RNA sequencing was performed to identify the potential biological pathways regulated by GmWRKY172. Results: GmWRKY172 was significantly upregulated by Cd stress, highly expressed in leaves and flowers, and localized to the nucleus with transcriptional activity. Transgenic plants overexpressing GmWRKY172 showed enhanced Cd tolerance and reduced Cd content in shoots compared to WT. Lower Cd translocation from roots to shoots and seeds was also observed in transgenic soybean. Under Cd stress, transgenic soybean accumulated less malondialdehyde (MDA) and hydrogen peroxide (H2O2) than WT plants, with higher flavonoid and lignin contents, and peroxidase (POD) activity. RNA sequencing analysis revealed that many stress-related pathways were regulated by GmWRKY172 in transgenic soybean, including flavonoid biosynthesis, cell wall synthesis, and peroxidase activity. Discussion: Our findings demonstrated that GmWRKY172 enhances Cd tolerance and reduces seed Cd accumulation in soybean by regulating multiple stress-related pathways, and could be a promising candidate for breeding Cd-tolerant and low Cd soybean varieties.

Genome-Wide Identification, Characterization, and Expression Analysis of SPIRAL1 Family Genes in Legume Species.

The SPIRAL1 (SPR1) gene family encodes microtubule-associated proteins that are essential for the anisotropic growth of plant cells and abiotic stress resistance. Currently, little is known about the characteristics and roles of the gene family outside of Arabidopsis thaliana. This study intended to investigate the SPR1 gene family in legumes. In contrast to that of A. thaliana, the gene family has undergone shrinking in the model legume species Medicago truncatula and Glycine max. While the orthologues of SPR1 were lost, very few SPR1-Like (SP1L) genes were identified given the genome size of the two species. Specifically, the M. truncatula and G. max genomes only harbor two MtSP1L and eight GmSP1L genes, respectively. Multiple sequence alignment showed that all these members contain conserved N- and C-terminal regions. Phylogenetic analysis clustered the legume SP1L proteins into three clades. The SP1L genes showed similar exon-intron organizations and similar architectures in their conserved motifs. Many essential cis-elements are present in the promoter regions of the MtSP1L and GmSP1L genes associated with growth and development, plant hormones, light, and stress. The expression analysis revealed that clade 1 and clade 2 SP1L genes have relatively high expression in all tested tissues in Medicago and soybean, suggesting their function in plant growth and development. MtSP1L-2, as well as clade 1 and clade 2 GmSP1L genes, display a light-dependent expression pattern. The SP1L genes in clade 2 (MtSP1L-2, GmSP1L-3, and GmSP1L-4) were significantly induced by sodium chloride treatment, suggesting a potential role in the salt-stress response. Our research provides essential information for the functional studies of SP1L genes in legume species in the future.

Transcriptome analysis of the phosphate starvation response sheds light on strigolactone biosynthesis in rice.

Phosphorus (P) is a major element required for plant growth and development. To cope with P shortage, plants activate local and long-distance signaling pathways, such as an increase in the production and exudation of strigolactones (SLs). The role of the latter in mitigating P deficiency is, however, still largely unknown. To shed light on this, we studied the transcriptional response to P starvation and replenishment in wild-type rice and a SL mutant, dwarf10 (d10), and upon exogenous application of the synthetic SL GR24. P starvation resulted in major transcriptional alterations, such as the upregulation of P TRANSPORTER, SYG1/PHO81/XPR1 (SPX) and VACUOLAR PHOSPHATE EFFLUX TRANSPORTER. Gene Ontology (GO) analysis of the genes induced by P starvation showed enrichment in phospholipid catabolic process and phosphatase activity. In d10, P deficiency induced upregulation of genes enriched for sesquiterpenoid production, secondary shoot formation and metabolic processes, including lactone biosynthesis. Furthermore, several genes induced by GR24 treatment shared the same GO terms with P starvation-induced genes, such as oxidation reduction, heme binding and oxidoreductase activity, hinting at the role that SLs play in the transcriptional reprogramming upon P starvation. Gene co-expression network analysis uncovered a METHYL TRANSFERASE that displayed co-regulation with known rice SL biosynthetic genes. Functional characterization showed that this gene encodes an enzyme catalyzing the conversion of carlactonoic acid to methyl carlactonoate. Our work provides a valuable resource to further studies on the response of crops to P deficiency and reveals a tool for the discovery of SL biosynthetic genes.

Bioengineering Techniques to Improve Nitrogen Transformation and Utilization: Implications for Nitrogen Use Efficiency and Future Sustainable Crop Production.

Nitrogen (N) is crucial for plant growth and development, especially in physiological and biochemical processes such as component of different proteins, enzymes, nucleic acids, and plant growth regulators. Six categories, such as transporters, nitrate absorption, signal molecules, amino acid biosynthesis, transcription factors, and miscellaneous genes, broadly encompass the genes regulating NUE in various cereal crops. Herein, we outline detailed research on bioengineering modifications of N metabolism to improve the different crop yields and biomass. We emphasize effective and precise molecular approaches and technologies, including N transporters, transgenics, omics, etc., which are opening up fascinating opportunities for a complete analysis of the molecular elements that contribute to NUE. Moreover, the detection of various types of N compounds and associated signaling pathways within plant organs have been discussed. Finally, we highlight the broader impacts of increasing NUE in crops, crucial for better agricultural yield and in the greater context of global climate change.

Hydropriming and Osmotic Priming Induce Resistance against Aspergillus niger in Wheat (Triticum aestivum L.) by Activating ß-1, 3-glucanase, Chitinase, and Thaumatin-like Protein Genes.

Priming is used as a method to improve plant growth and alleviate the detrimental effects of pathogens. The present study was conducted to evaluate the effects of different priming methods in the context of resistance to Aspergillus niger in wheat (Triticum aestivum L.). Here, we show that different priming treatments­viz., hydropriming, osmotic priming, halopriming, and hormonal priming techniques can induce disease resistance by improving the biochemical contents of wheat, including chlorophyll, protein, proline, and sugar. In addition, physiological parameters­such as root length, shoot length, fresh and dry root/shoot ratios, and relative water content were positively affected by these priming methods. In essence, hydropriming and osmotic priming treatments were found to be more potent for enhancing wheat biochemical contents, along with all the physiological parameters, and for reducing disease severity. Hydropriming and osmotic priming significantly decreased disease severity, by 70.59−75.00% and 64.71−88.33%, respectively. RT-PCR and quantitative real-time PCR analyses of potentially important pathogenesis-related (PR)-protein genes (Thaumatin-like protein (TLP), chitinase, and ß-1,3-glucanase) in primed plants were evaluated: ß-1,3-glucanase was most highly expressed in all primed plants; Chitinase and TLP exhibited higher expression in hormonal-, halo-, osmotic-, and hydro-primed plants, respectively. These results suggest that the higher expression of ß-1,3-glucanase, TLP, and chitinase after hydropriming and osmotic priming may increase disease resistance in wheat. Our study demonstrates the greater potential of hydropriming and osmotic priming for alleviating stress caused by A. niger inoculation, and enhancing resistance to it, in addition to significantly improving plant growth. Thus, these priming methods could be beneficial for better plant growth and disease resistance in other plants.

Identification of GOLDEN2-like transcription factor genes in soybeans and their role in regulating plant development and metal ion stresses.

The Golden 2-Like (G2-like or GLK) transcription factors are essential for plant growth, development, and many stress responses as well as heavy metal stress. However, G2-like regulatory genes have not been studied in soybean. This study identified the genes for 130 G2-Like candidates' in the genome of Glycine max (soybean). These GLK genes were located on all 20 chromosomes, and several of them were segmentally duplicated. Most GLK family proteins are highly conserved in Arabidopsis and soybean and were classified into five major groups based on phylogenetic analysis. These GmGLK gene promoters share cis-acting elements involved in plant responses to abscisic acid, methyl jasmonate, auxin signaling, low temperature, and biotic and abiotic stresses. RNA-seq expression data revealed that the GLK genes were classified into 12 major groups and differentially expressed in different tissues or organs. The co-expression network complex revealed that the GmGLK genes encode proteins involved in the interaction of genes related to chlorophyll biosynthesis, circadian rhythms, and flowering regulation. Real-time quantitative PCR analysis confirmed the expression profiles of eight GLK genes in response to cadmium (Cd) and copper (Cu) stress, with some GLK genes significantly induced by both Cd and Cu stress treatments, implying a functional role in defense responsiveness. Thus, we present a comprehensive perspective of the GLK genes in soybean and emphasize their important role in crop development and metal ion stresses.

Developing Genetic Engineering Techniques for Control of Seed Size and Yield.

Many signaling pathways regulate seed size through the development of endosperm and maternal tissues, which ultimately results in a range of variations in seed size or weight. Seed size can be determined through the development of zygotic tissues (endosperm and embryo) and maternal ovules. In addition, in some species such as rice, seed size is largely determined by husk growth. Transcription regulator factors are responsible for enhancing cell growth in the maternal ovule, resulting in seed growth. Phytohormones induce significant effects on entire features of growth and development of plants and also regulate seed size. Moreover, the vegetative parts are the major source of nutrients, including the majority of carbon and nitrogen-containing molecules for the reproductive part to control seed size. There is a need to increase the size of seeds without affecting the number of seeds in plants through conventional breeding programs to improve grain yield. In the past decades, many important genetic factors affecting seed size and yield have been identified and studied. These important factors constitute dynamic regulatory networks governing the seed size in response to environmental stimuli. In this review, we summarized recent advances regarding the molecular factors regulating seed size in Arabidopsis and other crops, followed by discussions on strategies to comprehend crops' genetic and molecular aspects in balancing seed size and yield.

Function of CTLGA9 Amino Acid Residue Leucine-6 in Modulating Cry Toxicity.

Aedes aegypti is a crucial vector for many arboviral diseases that cause millions of deaths worldwide and thus is of major public health concern. Crystal (Cry) proteins, which are toxins produced by Bacillus thuringiensis, are structurally organized into three-domains, of which domain II is the most variable in terms of binding towards various toxin receptors. The binding of Cry11Aa to putative receptor such as aminopeptidase-N (APN) is explicitly inhibited by midgut C-type lectins (CTLs). The similarity between the domain II fold of Cry11Aa toxin and the carbohydrate recognition domain in the CTLs is a possible structural basis for the involvement of Cry domain II in the recognition of carbohydrates on toxin receptors. In this study, a site-directed point mutation was introduced into the A. aegypti CTLGA9 gene on the basis of molecular docking findings, leading to substitution of the Leucine-6 (Leu-6) residue in the protein with alanine. Subsequently, functional monitoring of the mutated protein was carried out. Unlike the amino acid residues of wild-type CTLGA9, none of the residues of mutant (m) CTLGA9 were competed with Cry11Aa for binding to the APN receptor interface. Additionally, ligand blot analysis showed that both wild-type and mutant CTLGA9 had similar abilities to bind to APN and Cry11Aa. Furthermore, in the competitive ELISA in which labeled mutant CTLGA9 (10 nM) was mixed with increasing concentrations of unlabeled Cry11Aa (0-500 nM), the mutant showed no competition with Cry11Aa for binding to APN., By contrast, in the positive control sample of labeled wild type CTLGA9 mixed with same concentrations of Cry11Aa competition between the two ligands for binding to the APN was evident. These results suggest that Leucine-6 may be the key site involved in the competitive receptor binding between CTLGA9 and Cry11Aa. Moreover, according to the bioassay results, mutant CTLGA9 could in fact enhance the toxicity of Cry11Aa. Our novel findings provide further insights into the mechanism of Cry toxicity as well as a theoretical basis for enhancing the mosquitocidal activity of these toxin through molecular modification strategies.

Role of Lectin in the Response of Aedes aegypti Against Bt Toxin.

Aedes aegypti is one of the world's most dangerous mosquitoes, and a vector of diseases such as dengue fever, chikungunya virus, yellow fever, and Zika virus disease. Currently, a major global challenge is the scarcity of antiviral medicine and vaccine for arboviruses. Bacillus thuringiensis var israelensis (Bti) toxins are used as biological mosquito control agents. Endotoxins, including Cry4Aa, Cry4Ba, Cry10Aa, Cry11Aa, and Cyt1Aa, are toxic to mosquitoes. Insect eradication by Cry toxin relies primarily on the interaction of cry toxins with key toxin receptors, such as aminopeptidase (APN), alkaline phosphatase (ALP), cadherin (CAD), and ATP-binding cassette transporters. The carbohydrate recognition domains (CRDs) of lectins and domains II and III of Cry toxins share similar structural folds, suggesting that midgut proteins, such as C-type lectins (CTLs), may interfere with interactions among Cry toxins and receptors by binding to both and alter Cry toxicity. In the present review, we summarize the functional role of C-type lectins in Ae. aegypti mosquitoes and the mechanism underlying the alteration of Cry toxin activity by CTLs. Furthermore, we outline future research directions on elucidating the Bti resistance mechanism. This study provides a basis for understanding Bti resistance, which can be used to develop novel insecticides.

Rapid evolution of SARS-CoV-2 challenges human defenses.

The race between pathogens and their hosts is a major evolutionary driver, where both reshuffle their genomes to overcome and reorganize the defenses for infection, respectively. Evolutionary theory helps formulate predictions on the future evolutionary dynamics of SARS-CoV-2, which can be monitored through unprecedented real-time tracking of SARS-CoV-2 population genomics at the global scale. Here we quantify the accelerating evolution of SARS-CoV-2 by tracking the SARS-CoV-2 mutation globally, with a focus on the Receptor Binding Domain (RBD) of the spike protein determining infection success. We estimate that the > 820 million people that had been infected by October 5, 2021, produced up to 1021 copies of the virus, with 12 new effective RBD variants appearing, on average, daily. Doubling of the number of RBD variants every 89 days, followed by selection of the most infective variants challenges our defenses and calls for a shift to anticipatory, rather than reactive tactics involving collaborative global sequencing and vaccination.

Densovirus Oil Suspension Significantly Improves the Efficacy and Duration of Larvicidal Activity against Aedes albopictus.

Aedes albopictus is the sole vector for various mosquito-borne viruses, including dengue, chikungunya, and Zika. Ecofriendly biological agents are required to reduce the spread of these mosquito-borne infections. Mosquito densoviruses (MDVs) are entomopathogenic mosquito-specific viruses, which can reduce the capacity of isolated vectors and decrease mosquito-borne viral disease transmission. However, their variable pathogenicity restricts their commercial use. In the present study, we developed a series of novel larvicide oil suspensions (denoted Bacillus thuringiensis (Bti) oil, Ae. albopictus densovirus (AalDV-5) oil, and a mixture of AalDV-5+Bti oil), which were tested against Ae. albopictus larvae under experimental semi-field and open-field conditions. The effect of AalDV-5 on non-target species was also evaluated. The combined effect of AalDV-5+Bti was greater than that of individual toxins and was longer lasting and more persistent compared with the laboratory AalDV-5 virus strain. The virus was quantified on a weekly basis by quantitative polymerase chain reaction (qPCR) and was persistently detected in rearing water as well as in dead larvae. Wildtype densovirus is not pathogenic to non-target organisms. The present findings confirm the improved effect of a mixed microbial suspension (AalDV-5+Bti oil) larvicide against Ae. albopictus. The development and testing of these products will enable better control of the vector mosquitoes.

Comprehensive Genomic Survey, Evolution, and Expression Analysis of GIF Gene Family during the Development and Metal Ion Stress Responses in Soybean.

The GIF gene family is one of the plant transcription factors specific to seed plants. The family members are expressed in all lateral organs produced by apical and floral meristems and contribute to the development of leaves, shoots, flowers, and seeds. This study identified eight GIF genes in the soybean genome and clustered them into three groups. Analyses of Ka/Ks ratios and divergence times indicated that they had undergone purifying selection during species evolution. RNA-sequence and relative expression patterns of these GmGIF genes tended to be conserved, while different expression patterns were also observed between the duplicated GIF members in soybean. Numerous cis-regulatory elements related to plant hormones, light, and stresses were found in the promoter regions of these GmGIF genes. Moreover, the expression patterns of GmGIF members were confirmed in soybean roots under cadmium (Cd) and copper (Cu) stress, indicating their potential functions in the heavy metal response in soybean. Our research provides valuable information for the functional characterization of each GmGIF gene in different legumes in the future.

Recombinant Mosquito Densovirus with Bti Toxins Significantly Improves Pathogenicity against Aedes albopictus.

Mosquito densoviruses (MDVs) are mosquito-specific viruses that are recommended as mosquito bio-control agents. The MDV Aedes aegypti densovirus (AeDNV) is a good candidate for controlling mosquitoes. However, the slow activity restricts their widespread use for vector control. In this study, we introduced the Bacillus thuringiensis (Bti) toxin Cry11Aa domain II loop α8 and Cyt1Aa loop ß6-αE peptides into the AeDNV genome to improve its mosquitocidal efficiency; protein expression was confirmed using nanoscale liquid chromatography coupled to tandem mass spectrometry (nano LC-MS/MS). Recombinant plasmids were transfected into mosquito C6/36 cell lines, and the expression of specific peptides was detected through RT-PCR. A toxicity bioassay against the first instar Aedes albopictus larvae revealed that the pathogenic activity of recombinant AeDNV was significantly higher and faster than the wild-type (wt) viruses, and mortality increased in a dose-dependent manner. The recombinant viruses were genetically stable and displayed growth phenotype and virus proliferation ability, similar to wild-type AeDNV. Our novel results offer further insights by combining two mosquitocidal pathogens to improve viral toxicity for mosquito control.