Search

Fungi can acquire and store nutrients through decomposing and converting organic matter into fatty acids. This research demonstrates for the first time that the white-rot fungus Trametes versicolor has the ability to secrete extracellular droplets which can contain a high concentration of long-chain fatty acids and unsaturated fatty acids as well as monosaccharides and polysaccharides. The concentration and composition of the fatty acids varied according to the age of the droplet and the feedstock used for growth of the fungi. The results raise the possibility that these droplets could be harvested offering a new approach for the microbial generation of oil from waste.

Funder: FP7 Ideas: European Research Council (FP7 Ideas); Id: http://dx.doi.org/10.13039/100011199; Grant(s): 338060, Genetically identical individuals in bacterial populations can display significant phenotypic variability. This variability can be functional, for example by allowing a fraction of stress prepared cells to survive an otherwise lethal stress. The optimal fraction of stress prepared cells depends on environmental conditions. However, how bacterial populations modulate their level of phenotypic variability remains unclear. Here we show that the alternative sigma factor σV circuit in Bacillus subtilis generates functional phenotypic variability that can be tuned by stress level, environmental history and genetic perturbations. Using single‐cell time‐lapse microscopy and microfluidics, we find the fraction of cells that immediately activate σV under lysozyme stress depends on stress level and on a transcriptional memory of previous stress. Iteration between model and experiment reveals that this tunability can be explained by the autoregulatory feedback structure of the sigV operon. As predicted by the model, genetic perturbations to the operon also modulate the response variability. The conserved sigma‐anti‐sigma autoregulation motif is thus a simple mechanism for bacterial populations to modulate their heterogeneity based on their environment.

Beneficial insect communities on farms are influenced by site- and landscape-level factors, with pollinator and natural enemy populations often associated with semi-natural habitat remnants. They provide ecosystem services essential for all agroecosystems. For smallholders, natural pest regulation may be the only affordable and available option to manage pests. We evaluated the beneficial insect community on smallholder bean farms (Phaseolus vulgaris L.) and its relationship with the plant communities in field margins, including margin trees that are not associated with forest fragments. Using traps, botanical surveys and transect walks, we analysed the relationship between the floral diversity/composition of naturally regenerating field margins, and the beneficial insect abundance/diversity on smallholder farms, and the relationship with crop yield. More flower visits by potential pollinators and increased natural enemy abundance measures in fields with higher plant, and particularly tree, species richness, and these fields also saw improved crop yields. Many of the flower visitors to beans and potential natural enemy guilds also made use of non-crop plants, including pesticidal and medicinal plant species. Selective encouragement of plants delivering multiple benefits to farms can contribute to an ecological intensification approach. However, caution must be employed, as many plants in these systems are introduced species.

Female individuals of dioecious plants invest their resources more in storage and defence, and the males have higher nitrogen content invested in the production of pollen grains. An unresolved problem is whether this strategy occurs only in sexually mature plants or can also occur in juvenile plants. To answer this, Taxus baccata (L.) needles from the mature plants and rooted cuttings (juveniles) in a pot experiment were compared for the content of carbon, nitrogen, starch, total non-structural carbohydrates (TNC), and total phenolic compounds (TPhC). The results indicate that the differences between sexes occurred mainly in sexually mature plants, where the starch content was higher in females and nitrogen in males. However, the novelty of the results is that TPhC was generally higher in females than males in both adults and juveniles, suggesting that defence is a priority for females from an early age. We do not know if this is an innate trait because the strobili production (albeit at a very low level) of juveniles was observed in all individuals after the autumn of the first year. We found no effect of fertilization on sex-specific response in the pot experiment, which may be related to the lower reproductive effort of juveniles.

Made available in DSpace on 2021-06-25T10:24:35Z (GMT). No. of bitstreams: 0 Previous issue date: 2021-12-01 Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP) Biotechnology and Biological Sciences Research Council Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES) Although reference genes have previously been used in the expression analysis of genes involved in sugarcane flowering they had not been experimentally validated for stability and consistency of expression between different samples over a wide range of experimental conditions. Here we report the analysis of candidate reference genes in different tissue types, at different temporal time-points, in both short and long day photoperiodic treatments. The stability of the candidate reference genes in all conditions was evaluated with NormFinder, BestKeeper, and RefFinder algorithms that complement each other for a more robust analysis. As the Normfinder algorithm was more appropriate for our experimental conditions, greater emphasis was placed on Normfinder when choosing the most stable genes. UBQ1 and TUB were shown to be the most stable reference genes to use for normalizing RT-qPCR gene expression data during floral induction, whilst 25SrRNA1 and GAPDH were the least stable. Their use as a reference gene pair was validated by analyzing the expression of two differentially expressed target genes (PIL5 and LHP1). The UBQ1/TUB reference genes combination was able to reveal small significant differences in gene expression of the two target genes that were not detectable when using the least stable reference gene combination. These results can be used to inform the choice of reference genes to use in the study of the sugarcane floral induction pathway. Our work also demonstrates that both PIL5 and LHP1 are significantly up-regulated in the initial stages of photoperiodic induction of flowering in sugarcane. Faculdade de Ciências Agrárias e Veterinárias UNESP, Campus Jaboticabal Universidade Estadual de Campinas UNICAMP Instituto de Ciência e Tecnologia da Universidade Federal de São Paulo Departamento de Biotecnologia Escola de Engenharia de Lorena/Universidade de São Paulo EEL/USP Instituto Agronômico de Campinas Centro de Cana School of Life Sciences University of Warwick, Gibbet Hill Faculdade de Ciências Agrárias e Veterinárias UNESP, Campus Jaboticabal FAPESP: 2016/02679-9 Biotechnology and Biological Sciences Research Council: 2018/08380-0 CAPES: Finance Code 001

Dendrobium lineale is an Indonesian native orchid from the Spatulata section in Orchidaceae Family. This orchid is important because it is usually used as a parental plant in orchid breeding and is predicted to have a potential phytochemistry compound. In addition, in their natural habitat, this orchid is threatened due to forest exploitation and natural disaster. Therefore the precision mass propagation techniques for this orchid need to be conducted. Biotechnological approaches through inserting embryo gene such as AtRKD4 from Arabidopsis thaliana has already been successfully conducted. This study aims to check the integration stability of T-DNA harboring 35S::GR::AtRKD4 from ten selection transformants and to detect the existence of AtRKD4 protein after induction by Dexamethasone and/ Thidiazuron. The result showed that T-DNA were stably integrated into the genome of D. lineale transformants and the AtRKD4 protein with a molecular weight of 28.53 kDa was detected in D. lineale transformant plants after being induced by 15 µM DEX and 3 mgL-1 TDZ for 5 days.

During aging, mitochondrial membrane potential, a key indicator for bioenergetics of cells, depolarizes in a wide range of species-from yeasts, plants to animals. In humans, the decline of mitochondrial activities can impact the high-energy-consuming organs, such as the brain and heart, and increase the risks of age-linked diseases. Intriguingly, a mild depolarization of mitochondria has lifespan-extending effects, suggesting an important role played by bioelectricity during aging. However, the underpinning biophysical mechanism is not very well understood due in part to the difficulties associated with a multiscale process. Budding yeast Saccharomyces cerevisiae could provide a model system to bridge this knowledge gap and provide insights into aging. In this perspective, we overview recent studies on the yeast mitochondrial membrane electrophysiology and aging and call for more electrochemical and biophysical studies on aging.

Genetic studies aimed at onion improvement have been limited because of high heterozygosity, a very large genome size with a high level of repetitive DNA and a biennial life cycle. Onion bulb initiation is daylength-dependent, which places a significant barrier to adapting new varieties for growth at different latitudes. Compared to the photoperiodic regulation of flowering, relatively little is known about genetic regulation of the bulbing process. This study aims to identify the role of gene sequences involved in daylength-regulated bulb formation and tissue specific expression of onion. A comprehensive set of developmental and spatial quantitative mRNA expression experiments were carried out to investigate expression of onion FLOWERING LOCUS T (AcFT), LEAFY (AcLFY) and GIBBERELLIN-3 OXIDASE (GA3ox1) during the bulbing response. Bulbing ratios were used to measure the response of onion plants under long day (LD) and short day (SD) conditions. AcFT1 was expressed in LD, which induces bulb formation, while AcFT4 was expressed in SD, which inhibits bulb formation. AcFT5 and AcFT6 were expressed in LD and might also be involved in bulb formation itself. All AcFT, AcLFY and GA3ox1 genes showed distinctive patterns of tissue specific expression in onion, with AcFT genes found primarily in the sites of perception in the leaf and LFY in the basal tissues, the site of response. The results are consistent with AcFT1 expression being the signal for LD-induced bulb initiation and AcFT4, being involved in suppressing bulbing in SD.

24 Páginas Daucus has traditionally been estimated to comprise 21–25 species, but a recent study expanded the genus to c. 40 species. The present study uses ten nuclear orthologues to examine 125 accessions, including 40 collections of 11 species (D. annuus, D. arcanus, D. decipiens, D. durieua, D. edulis, D. gracilis, D. minusculus, D. montanus, D. pumilus, D. setifolius and D. tenuissimus) newly examined with nuclear orthologues. As in previous nuclear orthologue studies, Daucus resolves into two well-defined clades, and groups different accessions of species together. Maximum likelihood and maximum parsimony analyses provide concordant results, but SVD quartets reveals many areas of disagreement of species within these two major clades. With maximum likelihood and maximum parsimony analyses Daucus montanus (hexaploid) is resolved as an allopolyploid between D. pusillus (diploid) and D. glochidiatus (tetraploid), whereas with SVD quartets it is resolved as an allopolyploid between D. glochidiatus and an unknown Daucus sp. We propose the new combination Daucus junceus (Durieua juncea) for a neglected species endemic to the south-western Iberian Peninsula often referred to as D. setifolius, and we place D. arcanus in synonymy with D. pusillus. Three lectotypes are also designated. INTRODUCTION. MATERIAL AND METHODS. RESULTS. DISCUSSION. NOMENCLATURAL PROPOSALS. REFERENCES

The alarming current and predicted species extinction rates have galvanized conservationists in their efforts to avoid future biodiversity losses, but for species extinct in the wild, few options exist. We posed the questions, can these species be restored, and, if so, what role can ex situ plant collections (i.e., botanic gardens, germplasm banks, herbaria) play in the recovery of plant genetic diversity? We reviewed the relevant literature to assess the feasibility of recovering lost plant genetic diversity with using ex situ material and the probability of survival of subsequent translocations. Thirteen attempts to recover species extinct in the wild were found, most of which used material preserved in botanic gardens (12) and seed banks (2). One case of a locally extirpated population was recovered from herbarium material. Eight (60%) of these cases were successful or partially successful translocations of the focal species or population; the other 5 failed or it was too early to determine the outcome. Limiting factors of the use of ex situ source material for the restoration of plant genetic diversity in the wild include the scarcity of source material, low viability and reduced longevity of the material, low genetic variation, lack of evolution (especially for material stored in germplasm banks and herbaria), and socioeconomic factors. However, modern collecting practices present opportunities for plant conservation, such as improved collecting protocols and improved cultivation and storage conditions. Our findings suggest that all types of ex situ collections may contribute effectively to plant species conservation if their use is informed by a thorough understanding of the aforementioned problems. We conclude that the recovery of plant species currently classified as extinct in the wild is not 100% successful, and the possibility of successful reintroduction should not be used to justify insufficient in situ conservation.Colecciones Ex Situ y su Potencial para la Restauración de Plantas Extintas Resumen Las alarmantes tasas de extinción actuales y pronosticadas han incitado a los conservacionistas a esforzarse para evitar las futuras pérdidas de biodiversidad, pero para las especies que ya se encuentran extintas en vida silvestre existen pocas opciones. Nos preguntamos si estas especies pueden ser restauradas, y de ser así, qué papel pueden desempeñar las colecciones ex situ de plantas (es decir, jardines botánicos, bancos de germoplasma, herbarios) en la recuperación de la diversidad genética de las plantas. Revisamos la literatura relevante para evaluar la factibilidad de la recuperación de la diversidad genética perdida y la probabilidad de supervivencia subsecuente de las reubicaciones. Encontramos 13 intentos por recuperar especies extintas en vida silvestre, la mayoría de los cuales usó material preservado en jardines botánicos (12) y en bancos de semillas (2). También hubo un caso de una población eliminada localmente que fue recuperada con material de un herbario. Ocho (60%) de estos casos fueron reubicaciones exitosas o parcialmente exitosas de la especie o población focal; los otros cinco fallaron o era demasiado pronto para poder determinar el resultado. Los factores que limitan el uso de material proveniente de colecciones ex situ para la restauración de la diversidad genética de las plantas en vida silvestre incluyen la escasez de material original, la baja viabilidad y la longevidad reducida del material, la baja variación genética, la falta de evolución (especialmente para el material almacenado en herbarios y bancos de germoplasma) y los factores socioeconómicos. A pesar de esto, las prácticas modernas de colección representan una oportunidad para la conservación de las plantas, como los protocolos mejorados de recolección y las condiciones acrecentadas de cultivo y almacenamiento. Nuestros hallazgos sugieren que todos los tipos de colecciones ex situ pueden contribuir efectivamente a la conservación de especies de plantas si su uso está respaldado por un entendimiento a fondo de los problemas antes mencionados. Concluimos que la recuperación de especies de plantas que actualmente están clasificadas como extintas en vida silvestre no es 100% exitosa y que la posibilidad de una reintroducción exitosa no debería utilizarse para justificar una conservación in situ insuficiente.

WEE1 regulates the cell cycle by inactivating cyclin dependent protein kinases (CDKs) via phosphorylation. In yeast and animal cells, CDC25 phosphatase dephosphorylates the CDK releasing cells into mitosis, but in plants, its role is less clear. Expression of fission yeast CDC25 (Spcdc25) in tobacco results in small cell size, premature flowering and increased shoot morphogenetic capacity in culture. When Arath;WEE1 is over-expressed in Arabidopsis, root apical meristem cell size increases, and morphogenetic capacity of cultured hypocotyls is reduced. However expression of Arath;WEE1 in tobacco plants resulted in precocious flowering and increased shoot morphogenesis of stem explants, and in BY2 cultures cell size was reduced. This phenotype is similar to expression of Spcdc25 and is consistent with a dominant negative effect on WEE1 action. Consistent with this putative mechanism, WEE1 protein levels fell and CDKB levels rose prematurely, coinciding with early mitosis. The phenotype is not due to sense-mediated silencing of WEE1, as overall levels of WEE1 transcript were not reduced in BY2 lines expressing Arath;WEE1. However the pattern of native WEE1 transcript accumulation through the cell cycle was altered by Arath;WEE1 expression, suggesting feedback inhibition of native WEE1 transcription.

The basement membrane is a specialized extracellular matrix substrate responsible for support and maintenance of epithelial and endothelial structures. Engineered basement membrane-like hydrogel systems have the potential to advance understanding of cell-cell and cell-matrix interactions by allowing precise tuning of the substrate or matrix biochemical and biophysical properties. In this investigation, we developed tunable hydrogel substrates with conjugated bioactive peptides to modulate cell binding and growth factor signaling by endothelial cells. Hydrogels were formed by employing a poly(ethylene glycol) crosslinker to covalently crosslink gelatin polymers and simultaneously conjugate laminin-derived YIGSR peptides or vascular endothelial growth factor (VEGF)-mimetic QK peptides to the gelatin. Rheological characterization revealed rapid formation of hydrogels with similar stiffnesses across tested formulations, and swelling analysis demonstrated dependency on peptide and crosslinker concentrations in hydrogels. Levels of phosphorylated VEGF Receptor 2 in cells cultured on hydrogel substrates revealed that while human umbilical vein endothelial cells (HUVECs) responded to both soluble and conjugated forms of the QK peptide, conditionally-immortalized human glomerular endothelial cells (GEnCs) only responded to the conjugated presentation of the peptide. Furthermore, whereas HUVECs exhibited greatest upregulation in gene expression when cultured on YIGSR- and QK-conjugated hydrogel substrates after 5 days, GEnCs exhibited greatest upregulation when cultured on Matrigel control substrates at the same time point. These results indicate that conjugation of bioactive peptides to these hydrogel substrates significantly influenced endothelial cell behavior in cultures but with differential responses between HUVECs and GEnCs.

Aquaporins influence water flow in plants, yet little is known of their involvement in the water‐driven process of seed germination. We therefore investigated their role in seeds in the laboratory and under field and global warming conditions. We mapped the expression of tonoplast intrinsic proteins (TIPs) during dormancy cycling and during germination under normal and water stress conditions. We found that the two key tonoplast aquaporins, TIP3;1 and TIP3;2, which have previously been implicated in water or solute transport, respectively, act antagonistically to modulate the response to abscisic acid, with TIP3;1 being a positive and TIP3;2 a negative regulator. A third isoform, TIP4;1, which is normally expressed upon completion of germination, was found to play an earlier role during water stress. Seed TIPs also contribute to the regulation of depth of primary dormancy and differences in the induction of secondary dormancy during dormancy cycling. Protein and gene expression during annual cycling under field conditions and a global warming scenario further illustrate this role. We propose that the different responses of the seed TIP contribute to mechanisms that influence dormancy status and the timing of germination under variable soil conditions., Aquaporins influence water flow in plants, yet little is known of their involvement in the water‐driven process of seed germination. We therefore investigated their role in seeds, both in the laboratory and field. We mapped the expression of tonoplast intrinsic proteins during germination in normal and water stress conditions. We found that the two key tonoplast aquaporins, TIP3;1 and TIP3;2, act antagonistically to modulate the response to ABA, with TIP3;1 being a positive and TIP3;2 a negative regulator. A third isoform, TIP4;1, which is normally expressed upon completion of germination, was found to play an earlier role during water stress. Seed TIPs also regulate the depth of primary dormancy and differences in the induction of secondary dormancy in a similar manner. We propose that the different responses of the seed TIP constitute a mechanism to influence germination under water stress and dormancy cycling in variable soil conditions.

Adenylyl cyclases (ACs) catalyze the formation of the second messenger cAMP from ATP. Here we report the characterization of an Arabidopsis thaliana leucine-rich repeat (LRR) protein (At3g14460; AtLRRAC1) as an adenylyl cyclase. Using an AC-specific search motif supported by computational assessments of protein models we identify an AC catalytic center within the N-terminus and demonstrate that AtLRRAC1 can generate cAMP in vitro. Knock-out mutants of AtLRRAC1 have compromised immune responses to the biotrophic fungus Golovinomyces orontii and the hemibiotrophic bacteria Pseudomonas syringae, but not against the necrotrophic fungus Botrytis cinerea. These findings are consistent with a role of cAMP-dependent pathways in the defense against biotrophic and hemibiotrophic plant pathogens.

High-throughput sequencing technology was used to establish the OTU (Operational Taxonomic Units) composition and diversity of bacteria and fungi in the gut of three family groups of Hainan gibbons (Nomascus hainanus) in the Bawangling National Nature Reserve on Hainan Island, southern China. Firmicutes (47.23%) and Bacteroidetes (36.54%) predominated at the phylum level, while the predominant genera were Prevotella-7 (15.30%), Lachnospiraceae_NK3A20_group (12.49%), and uncultured_bacterium_f_Erysipelotrichaceae (11.79%). At the phylum level, the dominant fungi were Ascomycota (66.41%), as well as Hanseniaspora (23.33%), Schwanniomyces (13.44%), and Pichia (5.43%) at the genus level. We found significant differences in the bacterial OTU diversity (Shannon index) between family groups living in Tropical Lowland or Tropical Montane Rain Forest, compared to those inhabiting Tropical Montane Evergreen Forest at higher altitudes. Bacterial OTU community composition also differed between family groups, unraveling significant differences among the 30 most dominant bacterial core taxa. Furthermore, we unraveled a significant difference of OTU richness in the fungal microbiome (Chao 1) between family groups living at lower altitudes, i.e., Tropical Lowland or Tropical Montane Rain Forest and those inhabiting the Tropical Montane Evergreen Forest. Our analysis further indicated significant differences in the fungal OTU community composition between the three family groups, especially regarding the three most dominant fungal core taxa. Subsequently, two habitat factors, and nine environmental and anthropogenic variables were used to explore possible causes of disparity in the microbial flora of gibbon groups. A factor reduction procedure resulted into three principal components which were correlated to bacterial and fungal OTU richness and diversity using Spearman's rank-order correlations. Bacterial and fungal OTU diversity was high in areas of high altitude, steep slopes, high tree density, but low tree height, while high fungal OTU richness corresponded to high altitude habitats, i.e., in the Tropical Montane Evergreen Forest. Distance to human settlements and to the next water body showed no significant relation with bacterial and fungal richness and diversity.

The genus Vitex is also known as a chaste tree, in which it is a large shrub native to the tropical and subtropical regions of the world. A diverse range of species is distributed throughout Southern Europe, the Mediterranean, and Central Asia. The Vitex tree, including its leaves and fruits, has been used for herbal remedies in the form of pastes, decoctions, and dried fruits since ancient times. This article aimed to prepare a comprehensive review of traditional uses and secondary metabolites derived from Vitex sp., including the chemical compounds, biological activities, application of Vitex in human clinical trials, toxicology and safety, marketed products, and patents. The scientific findings were obtained using a number of search engines and databases, including Google Scholar, PMC, and ScienceDirect. Vitex species are well known in pharmacology to have medicinal values, such as anti-inflammatory, antibacterial, antifungal, antimicrobial, antioxidant, and anticancer properties. Previous studies reported that some species are proven to be effective in treating diseases, such as diabetes, and improving female health. A total of 161 compounds from different Vitex species are reported, covering the literature from 1982 to 2022. A chemical analysis report of various studies identified that Vitex exhibited a wide range of phytoconstituents, such as iridoid, diterpenoid, ecdysteroid, and flavonoid and phenolic compounds. Apart from that, the review will also discuss the application of Vitex in human clinical trials, toxicology and safety, marketed products, and patents of the genus. While the extracts of the genus have been made into many commercial products, including supplements and essential oils, most of them are made to be used by women to improve menstrual conditions and relieve premenstrual syndrome. Among the species, Vitex agnus-castus L. is the only one that has been reported to undergo clinical trials, mainly related to the use of the genus for the treatment of mastalgia, menstrual bleeding problems, amenorrhea, menorrhagia, luteal insufficiency, and premenstrual syndrome. Overall, the review addresses recent therapeutic breakthroughs and identifies research gaps that should be explored for prospective research work.

Asian rice (Oryza sativa L.) is consumed by more than half of the world’s population. Despite its global importance, the process of early rice domestication remains unclear. During domestication, wild rice (O. rufipogon Griff.) acquired non-seed-shattering behaviour, allowing humans to increase grain yield. Previous studies argued that the sh4 mutation triggered a reduction in seed shattering during rice domestication; but our experiments using wild introgression lines of O. rufipogon show that the domesticated sh4 allele alone is insufficient for shattering loss. Here, we identified the interaction between three key mutations associated with the interruption of abscission layer formation and panicle architecture that were causal in early rice domestication. An interruption of abscission layer formation requires both sh4 and qSH3 mutations, presenting an apparent barrier to the selection of shattering loss. We identified a causal single-nucleotide polymorphism at qSH3 within the seed-shattering gene OsSh1, which is conserved in indica and japonica subspecies but absent in the circum-aus group of rice. Through harvest experiments, we demonstrated that seed shattering alone did not significantly impact yield; rather yield increases were observed with closed panicle formation controlled by SPR3, which is further augmented by the integration of sh4 and qSH3 alleles. Complementary manipulation of seed shattering and panicle shape result in a mechanically stable panicle structure. We propose a stepwise route for the earliest phase of rice domestication, wherein selection of visible SPR3-controlled closed panicle morphology was instrumental in the sequential recruitment of sh4 and qSH3, which led to the loss of shattering.Significance StatementRice is one of the most important crops worldwide. Loss of seed shattering in domesticated rice, previously attributed to single mutations such as those in sh4, is considered the principal genetic change which resulted in yield increases. However, we show that sh4 alone is insufficient and other genes, such as qSH3, are required to cause abscission layer disruption. The evolution of non-seed-shattering therefore required multiple mutations. Furthermore, shattering loss in genetic backgrounds of wild rice does not correspondingly increase yields. We have identified an interaction in which a second trait, closed panicle formation controlled by SPR3, that both increases the yield and facilitates recruitment of sh4 and qSH3, which synergistically augment yield, leading to a stepwise model for rice domestication.

Reticulons are a large family of integral membrane proteins that are ubiquitous in eukaryotes and play a key role in functional remodelling of the endoplasmic reticulum membrane. The reticulon family is especially large in plants, with the Arabidopsis thaliana genome containing twenty-one isoforms. Reticulons vary in length but all contain a conserved C-terminal reticulon homology domain (RHD) that associates with membranes. An understanding of the structure and membrane interactions of RHDs is key to unlocking their mechanism of function, however no three-dimensional structure has been solved. We believe that this is, in part, due to difficulties in obtaining reticulon proteins in yields sufficient for structural study. To address this, we report here the first bacterial overexpression, purification, and biophysical investigation of a reticulon protein from plants, the RTNLB13 protein from A. thaliana. RTNLB13 is the smallest plant reticulon and is made up of a single RHD. We used circular dichroism, SDS-PAGE and analytical ultracentrifugation to reveal that RTNLB13 is 45% α-helical in a number of detergent environments, monomeric at low concentrations, and capable of self-association at higher concentrations. We used solution-state NMR to screen the effect of detergent type on the fold of isotopically-enriched RTNLB13, and found that ∼60% of the expected protein peaks were broadened due to slow dynamics. This broadening points toward a large network of protein-membrane interactions throughout the sequence. We have interpreted our results in light of current literature and suggest a preliminary description of RTNLB13 structure and topology.

While the changes in starch physicochemical properties resulting from typical dry ball milling (usually requiring hours) have been widely studied, there has been limited knowledge regarding how wet ball milling (with liquid media) affects starch structure and properties. This work was to investigate the effect of wet ball milling on the multiscale structures and pasting behavior of indica rice starch. For this starch, increasing ball-milling time resulted in decreases in particle size, crystallinity, and double-helix content and increases in single-helix and amorphous contents. Only 15 min of ball milling effectively destroyed the semicrystalline lamellar structure and resulted in the cleavage of long chains from amylose and amylopectin backbones and marked decreases in pasting temperature and viscosity, while ball milling for an even longer duration did not cause significant changes in these aspects. Thus, this work shows the high efficacy of wet ball milling for modifying rice starch structure and properties.

Background and Aims Genetically controlled self-incompatibility (SI) mechanisms constrain selfing and thus have contributed to the evolutionary diversity of flowering plants. In homomorphic gametophytic SI (GSI) and homomorphic sporophytic SI (SSI), genetic control is usually by the single multi-allelic locus S. Both GSI and SSI prevent self pollen tubes reaching the ovary and so are pre-zygotic in action. In contrast, in taxa with late-acting self-incompatibility (LSI), rejection is often post-zygotic, since self pollen tubes grow to the ovary, where fertilization may occur prior to floral abscission. Alternatively, lack of self fruit set could be due to early-acting inbreeding depression (EID). The aim of our study was to investigate mechanisms underlying the lack of selfed fruit set in Handroanthus heptaphyllus in order to assess the likelihood of LSI versus EID. Methods We employed four full-sib diallels to study the genetic control of LSI in H. heptaphyllus using a precociously flowering variant. We also used fluorescence microscopy to study the incidence of ovule penetration by pollen tubes in pistils that abscised following pollination or initiated fruits. Key Results All diallels showed reciprocally cross-incompatible full sibs (RCIs), reciprocally cross-compatible full sibs (RCCs) and non-reciprocally compatible full sibs (NRCs) in almost equal proportions. There was no significant difference between the incidences of ovule penetrations in abscised pistils following self- and cross-incompatible pollinations, but those in successful cross-pollinations were around 2-fold greater. Conclusions A genetic model postulating a single S locus with four S alleles, one of which, in the maternal parent, is dominant to the other three, will produce RCI, RCC and NRC full sib situations each at 33 %, consistent with our diallel results. We favour this simple genetic control over an EID explanation since none of our pollinations, successful or unsuccessful, resulted in partial embryo development, as would be expected under a whole-genome EID effect.

Climate change from elevated [CO2] may reduce water availability to crops through changes in precipitation and higher temperatures. However, agriculture already accounts for 70% of human consumption of water. Stomata, pores in the leaf surface, mediate exchange of water and CO2 for the plant. In crops including barley, the speed of stomatal response to changing environmental conditions is as important as maximal responses and can thus affect water use efficiency. Wild barleys and landraces which predate modern elite lines offer the breeder the potential to find unexploited genetic diversity. This study aimed to characterize natural variation in stomatal anatomy and leaf physiology and to link these variations to yield. Wild, landrace and elite barleys were grown in a polytunnel and a controlled environment chamber. Physiological responses to changing environments were measured, along with stomatal anatomy and yield. The elite barley lines did not have the fastest or largest physiological responses to light nor always the highest yields. There was variation in stomatal anatomy, but no link between stomatal size and density. The evidence suggests that high photosynthetic capacity does not translate into yield, and that landraces and wild barleys have unexploited physiological responses that should interest breeders.

Pathogens modulate plant cell structure and function by secreting effectors into host tissues. Effectors typically function by associating with host molecules and modulating their activities. This study aimed to identify the host processes targeted by the RXLR class of host-translocated effectors of the potato blight pathogen Phytophthora infestans. To this end, we performed an in planta protein-protein interaction screen by transiently expressing P. infestans RXLR effectors in Nicotiana benthamiana leaves followed by co-immunoprecipitation (co-IP) and liquid chromatography tandem mass spectrometry (LC-MS/MS). This screen generated an effector-host protein interactome matrix of 59 P. infestans RXLR effectors x 586 N. benthamiana proteins. Classification of the host interactors into putative functional categories revealed over 35 biological processes possibly targeted by P. infestans. We further characterized the PexRD12/31 family of RXLR-WY effectors, which associate and co-localize with components of the vesicle trafficking machinery. One member of this family, PexRD31, increased the number of FYVE positive vesicles in N. benthamiana cells. FYVE positive vesicles also accumulated in leaf cells near P. infestans hyphae, indicating that the pathogen may enhance endosomal trafficking during infection. We anticipate that the interactome dataset we generated will serve as a useful community resource for functional studies of P. infestans effectors and of effector-targeted host processes.

Dimethylsulfoniopropionate (DMSP) is an abundant and ubiquitous organosulfur molecule in marine environments with important roles in global sulfur and nutrient cycling. Diverse DMSP lyases in some algae, bacteria, and fungi cleave DMSP to yield gaseous dimethyl sulfide (DMS), an infochemical with important roles in atmospheric chemistry. Here, we identified a novel ATP-dependent DMSP lyase, DddX. DddX belongs to the acyl-CoA synthetase superfamily and is distinct from the eight other known DMSP lyases. DddX catalyses the conversion of DMSP to DMS via a two-step reaction: the ligation of DMSP with CoA to form the intermediate DMSP-CoA, which is then cleaved to DMS and acryloyl-CoA. The novel catalytic mechanism was elucidated by structural and biochemical analyses. DddX is found in several Alphaproteobacteria, Gammaproteobacteria, and Firmicutes, suggesting that this new DMSP lyase may play an overlooked role in DMSP/DMS cycles., eLife digest The global sulfur cycle is a collection of geological and biological processes that circulate sulfur-containing compounds through the oceans, rocks and atmosphere. Sulfur itself is essential for life and important for plant growth, hence its widespread use in fertilizers. Marine organisms such as bacteria, algae and phytoplankton produce one particular sulfur compound, called dimethylsulfoniopropionate, or DMSP, in massive amounts. DMSP made in the oceans gets readily converted into a gas called dimethyl sulfide (DMS), which is the largest natural source of sulfur entering the atmosphere. In the air, DMS is converted to sulfate and other by-products that can act as cloud condensation nuclei, which, as the name suggests, are involved in cloud formation. In this way, DMS can influence weather and climate, so it is often referred to as ‘climate-active’ gas. At least eight enzymes are known to cleave DMSP into DMS gas with a few by-products. These enzymes are found in algae, bacteria and fungi, and are referred to as lyases, for the way they breakdown their target compounds (DMSP, in this case). Recently, researchers have identified some bacteria that produce DMS from DMSP without using known DMSP lyases. This suggests there are other, unidentified enzymes that act on DMSP in nature, and likely contribute to global sulfur cycling. Li, Wang et al. set out to uncover new enzymes responsible for converting the DMSP that marine bacteria produce into gaseous DMS. One new enzyme called DddX was identified and found to belong to a superfamily of enzymes quite separate to other known DMSP lyases. Li, Wang et al. also showed how DddX drives the conversion of DMSP to DMS in a two-step reaction, and that the enzyme is found across several classes of bacteria. Further experiments to characterise the protein structure of DddX also revealed the molecular mechanism for its catalytic action. This study offers important insights into how marine bacteria generate the climatically important gas DMS from DMSP, leading to a better understanding of the global sulfur cycle. It gives microbial ecologists a more comprehensive perspective of these environmental processes, and provides biochemists with data on a family of enzymes not previously known to act on sulfur-containing compounds.

The rapid expansion of oil palm (OP) has led to its emergence as a commodity of strategic global importance. Palm oil is used extensively in food and as a precursor for biodiesel. The oil generates export earnings and bolsters the economy of many countries, particularly Indonesia and Malaysia. However, oil palms are prone to basal stem rot (BSR) caused by Ganoderma boninense which is the most threatening disease of OP. The current control measures for BSR management including cultural practices, mechanical and chemical treatment have not proved satisfactory. Alternative control measures to overcome the G. boninense problem are focused on the use of biological control agents and many potential bioagents were identified with little proven practical application. Planting OP varieties resistant to G. boninense could provide the ideal long-term solution to basal stem rot. The total resistance of palms to G. boninense has not yet been reported, few examples of partial resistances have been observed. Importantly, basidiospores are now recognized as the method by which the disease is spread, and control methods require to be revaluated because of this phenomenon. Many methods developed to prevent the spread of the disease effectively are only tested at nursery levels and are only reported in the national journal inhibiting the development of useful techniques globally. The initial procedures employed by the fungus to infect the OP require consideration in terms of the physiology of the growth of the fungus and its possible control. This review assesses critically the progress that has been made in BSR development and management in OP., The authors thank the Ministry of Higher Education (MOHE) Malaysia for providing financial support under the project Fundamental Research Grant Scheme (FRGS/1/2019/STG05/UPM02/22) and University Putra Malaysia. We are also thankful to Dr Yuvarani Naidu from Malaysian Palm Oil Board for providing images of Basal Stem Rot disease symptoms from her personal collection. Professor Paterson is grateful for his second IOI Professorial Chair 2018/19., info:eu-repo/semantics/publishedVersion

Duncan V. Mifsud is the grateful recipient of an Endeavour Scholarship (Republic of Malta). The Endeavour Scholarship Scheme is part-financed by the European Union – European Social Fund (ESF): Operational Programme II – Cohesion Policy 2014-20. Emissions from traffic over the past few decades have become a significant source of air pollution. Among the pollutants emitted are nitrogen oxides (NOx), exposure to which can be detrimental to public health. Recent studies have shown that nitrogen (N) stable isotope ratios in tree-rings and foliage express a fingerprint of their major N source, making them appropriate for bio-monitoring purposes. In this study, we have applied this proxy to Aleppo pines (Pinus halepensis) at three distances from one of the busiest roads in Malta, a country known to suffer from intense traffic pollution. Our results showed that N and organic carbon (C) stable isotope ratios in tree-rings do not vary over the period 1980–2018 at any of the investigated sites; however, statistically significant spatial trends were apparent in both tree-rings and foliage. The roadside and transitional sites exhibited more positive δ15N and more negative δ13C values compared to those at a rural control site. This is likely due to the incorporation of 15N-enriched NOx and 13C-depleted CO2 from traffic pollution. Sampled top-soil also exhibited the δ15N trend. Our results constitute the first known application of dendrogeochemistry to atmospheric pollution monitoring in Malta. Postprint

Cassava productivity is hampered by pests and diseases including cassava mosaic disease (CMD) and cassava brown streak disease (CBSD). The main objective of this study was to identify stable superior genotypes that combine disease re-sistance and high yield. Sixteen cassava genotypes were planted in a randomized complete block design with three replications for six planting seasons (years) at five sites in Tanzania. The genotypes were assessed using the additive main effect and multiplicative interaction (AMMI) analysis, and highly significant (

The rhizosphere microbiome is considered to play a key role in determining crop health. However, current understanding of the factors which shape assembly and composition of the microbiome is heavily biased toward bacterial communities, and the relevance for other microbial groups is unclear. Furthermore, community assembly is determined by a variety of factors, including host genotype, environment and agricultural management practices, and their relative importance and interactions remain to be elucidated. We investigated the impact of nitrogen fertilization on rhizosphere bacterial, fungal, nematode and protist communities of 10 contrasting oilseed rape genotypes in a field experiment. We found significant differences in the composition of bacteria, fungi, protist and nematode communities between the rhizosphere and bulk soil. Nitrogen application had a significant but weak effect on fungal, bacterial, and protist community composition, and this was associated with increased relative abundance of a complex of fungal pathogens in the rhizosphere and soil, including Mycosphaerella sp. and Leptosphaeria sp. Network analysis showed that nitrogen application had different effects on microbial community connectivity in the soil and rhizosphere. Crop genotype significantly affected fungal community composition, with evidence for a degree of genotype specificity for a number of pathogens, including L. maculans, Alternaria sp., Pyrenopeziza brassicae, Olpidium brassicae, and L. biglobosa, and also potentially beneficial Heliotales root endophytes. Crop genotype had no significant effect on assembly of bacteria, protist or nematode communities. There was no relationship between genetic distance of crop genotypes and the extent of dissimilarity of rhizosphere microbial communities. Field disease assessment confirmed infection of crops by Leptosphaeria sp., P. brassicae, and Alternaria sp., indicating that rhizosphere microbiome sequencing was an effective indicator of plant health. We conclude that under field conditions soil and rhizosphere nutrient stoichiometry and crop genotype are key factors determining crop health by influencing the infection of roots by pathogenic and mutualistic fungal communities, and the connectivity and stability of rhizosphere microbiome interaction networks.

Methods for screening combinations of lignin-degrading enzymes and accessory enzymes for product release from polymeric lignin have been developed, using two colorimetric assays that can be applied in microtiter plate format. A set of 3 bacterial DyP-type peroxidase enzymes fromPseudomonas fluorescens,Comamonas testosteroniandAgrobacteriumsp., two bacterial multi-copper oxidase enzymes CueO fromOchrobactrumsp. and CopA fromPseudomonas putida, andSphingobacteriumsp. T2 manganese superoxide dismutase have been tested in combination with one LigEβ-etherase enzyme fromAgrobacteriumsp., two dihydrolipoamide dehydrogenase enzymes fromSphingobacteriumsp. T2,Burkholderia cenocepaciaperoxiredoxin, andDesulfitobacterium hafniensearylsulfotransferase. Combinations ofAgrobacteriumLigE with DyP-type peroxidases gave 4–10 enhancement in low molecular weight product release from technical lignins, and enhancements in product release were observed for all lignins tested, using different accessory enzymes. Analysis of products formed by reverse phase HPLC verified increases in concentrations of specific low molecular weight products.

Gene expression noise influences organism evolution and fitness but is poorly understood. There is increasing evidence that the functional roles of components of the translation machinery influence noise intensity. In addition, modulation of the activities of at least some of these same components affects the replicative lifespan of a broad spectrum of organisms. In a novel comparative approach, we modulate the activities of the translation initiation factors eIFG1 and eIF4G2, both of which are involved in the process of recruiting ribosomal 43S preinitiation complexes to the 5’ end of eukaryotic mRNAs. We show that tagging of the cell wall using a fluorescent dye allows us to follow gene expression noise as different yeast strains progress through successive cycles of replicative ageing. This procedure reveals a relationship between global protein synthesis rate and gene expression noise (cell‐to‐cell heterogeneity), which is accompanied by a parallel correlation between gene expression noise and the replicative age of mother cells. An alternative approach, based on microfluidics, confirms the interdependence between protein synthesis rate, gene expression noise and ageing. We additionally show that it is important to characterize the influence of the design of the microfluidic device on the nutritional state of the cells during such experiments. Analysis of the noise data derived from flow cytometry and fluorescence microscopy measurements indicates that both the intrinsic and the extrinsic noise components increase as a function of ageing.\ud \ud

Sand–clay mixtures can be encountered in both natural soils (e.g., residual soils, clay deposits and clinosols) and artificial fills. The method of utilising biopolymers in ground improvement for sand–clay mixtures has emerged recently. However, a full understanding of the strengthening effect of biopolymer-treated sand–clay mixtures has not yet been achieved due to a limited number of relevant studies. In this study, xanthan gum (XG), as one of the eco-friendly biopolymers, was used to treat reconstituted sand–clay mixtures that had various compositions in related to clay (or sand) content and clay type (kaolin and bentonite). A series of laboratory unconfined compression strength (UCS) tests were conducted to probe the performances of XG-treated sand–clay mixtures from two aspects, i.e., optimum treatment conditions (e.g., XG content and initial moisture content) to achieve the maximum strengthening effect and strengthening efficiency for the sand–clay mixtures with different compositions. The experimental results indicated that the optimum initial moisture content decreased as the sand content increased. The optimum XG content, which also decreased with the increasing sand content, remained approximately 3.75% for all sand–kaolin mixtures and 5.75% for all sand–bentonite mixtures if calculated based on clay fraction. While untreated sand–kaolin mixtures and sand–bentonite mixtures had comparable UCS values, XG-treated sand–kaolin mixtures seemed to have better improved mechanical strength due to higher ionic (or hydrogen) bonds with XG and low-swelling properties compared with bentonite. The deformation modulus of XG-treated sand–clay mixtures were positively related with UCS. The variation in UCS and stiffness for each treatment condition increased as the sand content was elevated for both sand-kaolin and sand-bentonite mixtures. An increment in the proportion of the heterogeneous composite formed by irregular sand particles conglomerated with the XG–clay matrix in total soil might be responsible for this phenomenon.

The reticulon family of integral membrane proteins are conserved across all eukaryotes and typically localize to the endoplasmic reticulum (ER), where they are involved in generating highly-curved tubules. We recently demonstrated that Reticulon-like protein B13 (RTNLB13) from Arabidopsis thaliana contains a curvature-responsive amphipathic helix (APH) important for the proteins’ ability to induce curvature in the ER membrane, but incapable of generating curvature by itself. We suggested it acts as a feedback element, only folding/binding once a sufficient degree of curvature has been achieved, and stabilizes curvature without disrupting the bilayer. However, it remains unclear whether this is unique to RTNLB13 or is conserved across all reticulons—to date, experimental evidence has only been reported for two reticulons. Here we used biophysical methods to characterize a minimal library of putative APH peptides from across the 21 A. thaliana isoforms. We found that reticulons with the closest evolutionary relationship to RTNLB13 contain curvature-sensing APHs in the same location with sequence conservation. Our data reveal that a more distantly-related branch of reticulons developed a ~ 20-residue linker between the transmembrane domain and APH. This may facilitate functional flexibility as previous studies have linked these isoforms not only to ER remodeling but other cellular activities.

Iron–sulfur (Fe–S) clusters are ubiquitous cofactors in all life and are used in a wide array of diverse biological processes, including electron transfer chains and several metabolic pathways. Biosynthesis machineries for Fe–S clusters exist in plastids, the cytosol, and mitochondria. A single monothiol glutaredoxin (GRX) is involved in Fe–S cluster assembly in mitochondria of yeast and mammals. In plants, the role of the mitochondrial homolog GRXS15 has only partially been characterized. Arabidopsis (Arabidopsis thaliana) grxs15 null mutants are not viable, but mutants complemented with the variant GRXS15 K83A develop with a dwarf phenotype similar to the knockdown line GRXS15amiR. In an in-depth metabolic analysis of the variant and knockdown GRXS15 lines, we show that most Fe–S cluster-dependent processes are not affected, including biotin biosynthesis, molybdenum cofactor biosynthesis, the electron transport chain, and aconitase in the tricarboxylic acid (TCA) cycle. Instead, we observed an increase in most TCA cycle intermediates and amino acids, especially pyruvate, glycine, and branched-chain amino acids (BCAAs). Additionally, we found an accumulation of branched-chain α-keto acids (BCKAs), the first degradation products resulting from transamination of BCAAs. In wild-type plants, pyruvate, glycine, and BCKAs are all metabolized through decarboxylation by mitochondrial lipoyl cofactor (LC)-dependent dehydrogenase complexes. These enzyme complexes are very abundant, comprising a major sink for LC. Because biosynthesis of LC depends on continuous Fe–S cluster supply to lipoyl synthase, this could explain why LC-dependent processes are most sensitive to restricted Fe–S supply in grxs15 mutants.

The Mediator complex controls transcription of most eukaryotic genes with individual subunits required for the control of particular gene regulons in response to various perturbations. In this study, we reveal the roles of the plant Mediator subunits MED16, MED14, and MED2 in regulating transcription in response to the phytohormone abscisic acid (ABA) and we determine which cis elements are under their control. Using synthetic promoter reporters we established an effective system for testing relationships between subunits and specific cis-acting motifs in protoplasts. Our results demonstrate that MED16, MED14, and MED2 are required for the full transcriptional activation by ABA of promoters containing both the ABRE (ABA-responsive element) and DRE (drought-responsive element). Using synthetic promoter motif concatamers, we showed that ABA-responsive activation of the ABRE but not the DRE motif was dependent on these three Mediator subunits. Furthermore, the three subunits were required for the control of water loss from leaves but played no role in ABA-dependent growth inhibition, highlighting specificity in their functions. Our results identify new roles for three Mediator subunits, provide a direct demonstration of their function and highlight that our experimental approach can be utilized to identify the function of subunits of plant transcriptional regulators., publishedVersion

The use of plant-derived natural products for the treatment of tropical parasitic diseases often has ethnopharmacological origins. As such, plants grown in temperate regions remain largely untested for novel anti-parasitic activities. We describe here a screen of the PhytoQuest Phytopure library, a novel source comprising over 600 purified compounds from temperate zone plants, against in vitro culture systems for Plasmodium falciparum, Leishmania mexicana, Trypanosoma evansi and T. brucei. Initial screen revealed 6, 65, 15 and 18 compounds, respectively, that decreased each parasite’s growth by at least 50% at 1–2 µM concentration. These initial hits were validated in concentration-response assays against the parasite and the human HepG2 cell line, identifying hits with EC50 &lt, 1 μM and a selectivity index of &gt, 10. Two sesquiterpene glycosides were identified against P. falciparum, four sterols against L. mexicana, and five compounds of various scaffolds against T. brucei and T. evansi. An L. mexicana resistant line was generated for the sterol 700022, which was found to have cross-resistance to the anti-leishmanial drug miltefosine as well as to the other leishmanicidal sterols. This study highlights the potential of a temperate plant secondary metabolites as a novel source of natural products against tropical parasitic diseases.

Extracts of the tropical Cinderella plantSynedrella nodifloraare used traditionally to manage convulsive conditions in the West African sub-region. This study sought to determine the neuronal basis of the effectiveness of these plant extracts to suppress seizure activity. Using the hippocampal slice preparation from rats, the ability of the extract to depress excitatory synaptic transmission andin vitroseizure activity were investigated. Bath perfusion of the hydro-ethanolic extract ofSynedrella nodiflora(SNE) caused a concentration-dependent depression of evoked field excitatory postsynaptic potentials (fEPSPs) recorded extracellularly in the CA1 region of the hippocampus with maximal depression of about 80% and an estimated IC50of 0.06 mg/ml. The SNE-induced fEPSP depression was accompanied by an increase in paired pulse facilitation. The fEPSP depression only recovered partially after 20 min washing out. The effect of SNE was not stimulus dependent as it was present even in the absence of synaptic stimulation. Furthermore, it did not show desensitization as repeat application after 10 min washout produced the same level of fEPSP depression as the first application. The SNE effect on fEPSPs was not via adenosine release as it was neither blocked nor reversed by 8-CPT, an adenosine A1receptor antagonist. In addition, SNE depressedin vitroseizures induced by zero Mg2+and high K+-containing artificial cerebrospinal fluid (aCSF) in a concentration-dependent manner. The results show that SNE depresses fEPSPs and spontaneous bursting activity in hippocampal neurons that may underlie its ability to abort convulsive activity in persons with epilepsy.

Boron has essential roles in plant growth and development. BOR proteins are key in the active uptake and distribution of boron, and regulation of intracellular boron concentrations. However, their mechanism of action remains poorly studied. BOR proteins are homologues of the human SLC4 family of transporters, which includes well studied mammalian transporters such as the human Anion Exchanger 1 (hAE1). Here we generated Arabidopsis thaliana BOR1 (AtBOR1) variants based (i) on known disease causing mutations of hAE1 (S466R, A500R) and (ii) a loss of function mutation (D311A) identified in the yeast BOR protein, ScBOR1p. The AtBOR1 variants express in yeast and localise to the plasma membrane, although both S466R and A500R exhibit lower expression than the WT AtBOR1 and D311A. The D311A, S466R and A500R mutations result in a loss of borate efflux activity in a yeast bor1p knockout strain. A. thaliana plants containing these three individual mutations exhibit substantially decreased growth phenotypes in soil under conditions of low boron. These data confirm an important role for D311 in the function of the protein and show that mutations equivalent to disease-causing mutations in hAE1 have major effects in AtBOR1. We also obtained a low resolution cryo-EM structure of a BOR protein from Oryza sativa, OsBOR3, lacking the 30 C-terminal amino acid residues. This structure confirms the gate and core domain organisation previously observed for related proteins, and is strongly suggestive of an inward facing conformation.

While the cooking of rice into porridge or similar foods is widely practiced, how microwave treatment, a rapid heating technology, changes the structure of rice starch with excess water remains largely unexplored. This work describes the multiscale structural changes of indica rice starch (IRS) with high water contents (70, 80, and 90 wt %, wet basis) subjected to microwave treatment for 1–3 min. Microwave treatment destructed crystalline lamellae, changed the crystalline type from A to B+V, and decreased crystallinity and double-helix content. While these changes depend on both water content and treatment time, the former had a stronger effect due to combined effects of water and heat for starch gelatinization. Interestingly, a highly porous material can be obtained simply upon microwave treatment of IRS for 3 min at a water content of 90 wt %. Thus, this work presents a simple method for creating such material promising for encapsulation and delivery applications.\ud \ud

The Casparian strip (CS) constitutes a physical diffusion barrier to water and nutrients in plant roots, which is formed by the polar deposition of lignin polymer in the endodermis tissue. The precise pattern of lignin deposition is determined by the scaffolding activity of membrane-bound Casparian Strip domain proteins (CASPs), but little is known of the mechanism(s) directing this process. Here, we demonstrate that Endodermis-specific Receptor-like Kinase 1 (ERK1) and, to a lesser extent, ROP Binding Kinase1 (RBK1) are also involved in regulating CS formation, with the former playing an essential role in lignin deposition as well as in the localization of CASP1. We show that ERK1 is localized to the cytoplasm and nucleus of the endodermis and that together with the circadian clock regulator, Time for Coffee (TIC), forms part of a novel signaling pathway necessary for correct CS organization and suberization of the endodermis, with their single or combined loss of function resulting in altered root microbiome composition. In addition, we found that other mutants displaying defects in suberin deposition at the CS also display altered root exudates and microbiome composition. Thus, our work reveals a complex network of signaling factors operating within the root endodermis that establish both the CS diffusion barrier and influence the microbial composition of the rhizosphere. ispartof: PLANT AND CELL PHYSIOLOGY vol:62 issue:2 pages:248-261 ispartof: location:Japan status: published

Water hyacinth (Pontederia crassipes, also referred to as Eichhornia crassipes) is one of the most invasive weed species in the world, causing significant adverse economic and ecological impacts, particularly in tropical and sub-tropical regions. Large scale real-time monitoring of areas of chronic infestation is critical to formulate effective control strategies for this fast spreading weed species. Assessment of revenue generation potential of the harvested water hyacinth biomass also requires enhanced understanding to estimate the biomass yield potential for a given water body. Modern remote sensing technologies can greatly enhance our capacity to understand, monitor, and estimate water hyacinth infestation within inland as well as coastal freshwater bodies. Readily available satellite imagery with high spectral, temporal, and spatial resolution, along with conventional and modern machine learning techniques for automated image analysis, can enable discrimination of water hyacinth infestation from other floating or submerged vegetation. Remote sensing can potentially be complemented with an array of other technology-based methods, including aerial surveys, ground-level sensors, and citizen science, to provide comprehensive, timely, and accurate monitoring. This review discusses the latest developments in the use of remote sensing and other technologies to monitor water hyacinth infestation, and proposes a novel, multi-modal approach that combines the strengths of the different methods.

Prokaryotic cell-free coupled transcription–translation (TX-TL) systems are emerging as a powerful tool to examine natural product biosynthetic pathways in a test tube. The key advantages of this approach are the reduced experimental time scales and controlled reaction conditions. To realize this potential, it is essential to develop specialized cell-free systems in organisms enriched for biosynthetic gene clusters. This requires strong protein production and well-characterized synthetic biology tools. The Streptomyces genus is a major source of natural products. To study enzymes and pathways from Streptomyces, we originally developed a homologous Streptomyces cell-free system to provide a native protein folding environment, a high G+C (%) tRNA pool, and an active background metabolism. However, our initial yields were low (36 μg/mL) and showed a high level of batch-to-batch variation. Here, we present an updated high-yield and robust Streptomyces TX-TL protocol, reaching up to yields of 266 μg/mL of expressed recombinant protein. To complement this, we rapidly characterize a range of DNA parts with different reporters, express high G+C (%) biosynthetic genes, and demonstrate an initial proof of concept for combined transcription, translation, and biosynthesis of Streptomyces metabolic pathways in a single “one-pot” reaction.\ud \ud

Background The plant microbiome plays a vital role in determining host health and productivity. However, we lack real-world comparative understanding of the factors which shape assembly of its diverse biota, and crucially relationships between microbiota composition and plant health. Here we investigated landscape scale rhizosphere microbial assembly processes in oilseed rape (OSR), the UK’s third most cultivated crop by area and the world's third largest source of vegetable oil, which suffers from yield decline associated with the frequency it is grown in rotations. By including 37 conventional farmers’ fields with varying OSR rotation frequencies, we present an innovative approach to identify microbial signatures characteristic of microbiomes which are beneficial and harmful to the host. Results We show that OSR yield decline is linked to rotation frequency in real-world agricultural systems. We demonstrate fundamental differences in the environmental and agronomic drivers of protist, bacterial and fungal communities between root, rhizosphere soil and bulk soil compartments. We further discovered that the assembly of fungi, but neither bacteria nor protists, was influenced by OSR rotation frequency. However, there were individual abundant bacterial OTUs that correlated with either yield or rotation frequency. A variety of fungal and protist pathogens were detected in roots and rhizosphere soil of OSR, and several increased relative abundance in root or rhizosphere compartments as OSR rotation frequency increased. Importantly, the relative abundance of the fungal pathogen Olpidium brassicae both increased with short rotations and was significantly associated with low yield. In contrast, the root endophyte Tetracladium spp. showed the reverse associations with both rotation frequency and yield to O. brassicae, suggesting that they are signatures of a microbiome which benefits the host. We also identified a variety of novel protist and fungal clades which are highly connected within the microbiome and could play a role in determining microbiome composition. Conclusions We show that at the landscape scale, OSR crop yield is governed by interplay between complex communities of both pathogens and beneficial biota which is modulated by rotation frequency. Our comprehensive study has identified signatures of dysbiosis within the OSR microbiome, grown in real-world agricultural systems, which could be used in strategies to promote crop yield.

Plants can adjust their competitive traits for acquiring resources in response to the relatedness of their neighbours. Recently, it has been found that plants can alter their investment in traits of attracting pollinators based on kin-interaction. We build a mathematical model to study the optimal floral display to attract pollinators in a patch with kin structure. We show that when plants can attract pollinators to a whole patch through the magnet effect, the floral display should increase with the increasing relatedness of the plants in the patch. Our model also indicates that increasing investment into attracting pollinators is a form of altruism, reducing a plant’s own seed production but increasing the contribution of other plants to its fitness. We also predict that seed production should increase with increasing relatedness in the patch. Our model provides the explicit conditions when resource allocation to attract pollinators in response to neighbour relatedness can be favoured by kin selection, and a possible mechanism for the plants to deal with the consequent loss of pollinator diversity and abundance.

This work was supported by Specific Project for Strategic Biological Resources and Technology Supporting System from the Chinese Academy of Sciences (No. ZSZY-001), Chenshan Special Foundations from Shanghai Municipal Administration of Forestation and City Appearances (Nos. G162408, G172410, and G182409), the Science and Technology Program of Shanghai Science and Technology Committee (No. 20392000600), the Reserve Talents for Academic and Technical Leaders of Middle-aged and Young People in Yunnan Province (Grant No. 2018HB066), and Ten Thousand Talent Program of Yunnan Province (Grant No. YNWR-QNBJ-2018-174). Delayed autonomous selfing (DAS) provides reproductive assurance under conditions of pollinator and/or pollen-limitation. Few plant species have been investigated to determine if DAS is terminated when a flower is sufficiently pollinated by a pollen vector, thereby saving plant resources for other purposes. We examined this possibility in bumblebee-pollinated Salvia umbratica. We first showed that DAS resulting in high fruit set (100%) and seed set (>80%) per flower occurred in the absence of insect pollinators by means of style recurvature and was completed in 94% of flowers 72 h after they opened. In contrast, in flowers pollinated immediately after opening, DAS was prevented by corollas dropping away before styles recurve toward the upper thecae. We next showed that hand-pollination of flowers immediately after they opened resulted in high fruit set (100%) and seed set (>80%) when 5–10 pollen grains or more were deposited on their stigmas, whereas fruit set and seed set were reduced to 45.00 and 22.50%, respectively, when pollen loads were reduced to 1–3 pollen grains. Finally, we showed that on average single pollinator visits deposited 26 pollen grains on stigmas of flowers that had just opened, which is more than enough to ensure high fruit and seed set. Our results indicate that flower longevity is highly correlated with the pollinator environment and female fitness of S. umbratica, with extended flower longevity allowing DAS to occur being advantageous when pollinators are absent, while reduced floral longevity and prevention of DAS being favored when flowers are pollinated by pollinators. Thus, flower longevity in S. umbratica varies so as to optimize reproductive output and resource efforts, and is dependent on the availability and effectiveness of pollinators to pollinate flowers. Publisher PDF

Thematic Issue: Crystal Ball., Filamentous members of the phylum Actinobacteria are a remarkable source of natural products with pharmaceutical potential. The discovery of novel molecules from these organisms is, however, hindered because most of the biosynthetic gene clusters (BGCs) encoding these secondary metabolites are cryptic or silent and are referred to as orphan BGCs. While co-culture has proven to be a promising approach to unlock the biosynthetic potential of many microorganisms by activating the expression of these orphan BGCs, it still remains an underexplored technique. The marine actinobacterium Salinispora tropica, for instance, produces valuable compounds such as the anti-cancer molecule salinosporamide but half of its putative BGCs are still orphan. Although previous studies have used marine heterotrophs to induce orphan BGCs in Salinispora, its co-culture with marine phototrophs has yet to be investigated. Following the observation of an antimicrobial activity against a range of phytoplankton by S. tropica, we here report that the photosynthate released by photosynthetic primary producers influences its biosynthetic capacities with production of cryptic molecules and the activation of orphan BGCs. Our work, using an approach combining metabolomics and proteomics, pioneers the use of phototrophs as a promising strategy to accelerate the discovery of novel natural products from marine actinobacteria., A.C. was supported by an MIBTP PhD scholarship (BB/M01116X/1) and D.S. by a NERC CENTA DTP studentship (NE/L002493/1). J.A.C.-O was funded by a NERC Independent Research Fellowship NE/K009044/1 and Ramón y Cajal contract RYC-2017-22452 (funded by the Ministry of Science, Innovation and Universities, the National Agency of Research, and the European Social Fund). C.C. thanks BBSRC (grant BB/M022765/1) and European Union’s Horizon 2020 research No. 765147 for support. L.S. would like to acknowledge BBSRC (BB/M017982/1 and BB/R000689/1) and EPSRC (EP/P0305721/1) for financial support.

© The Author(s) 2021. Published by Oxford University Press on behalf of Nucleic Acids Research. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited., Although the RNA helicase Upf1 has hitherto been examined mostly in relation to its cytoplasmic role in nonsense mediated mRNA decay (NMD), here we report high-throughput ChIP data indicating genome-wide association of Upf1 with active genes in Schizosaccharomyces pombe. This association is RNase sensitive, correlates with Pol II transcription and mRNA expression levels. Changes in Pol II occupancy were detected in a Upf1 deficient (upf1Δ) strain, prevalently at genes showing a high Upf1 relative to Pol II association in wild-type. Additionally, an increased Ser2 Pol II signal was detected at all highly transcribed genes examined by ChIP-qPCR. Furthermore, upf1Δ cells are hypersensitive to the transcription elongation inhibitor 6-azauracil. A significant proportion of the genes associated with Upf1 in wild-type conditions are also mis-regulated in upf1Δ. These data envisage that by operating on the nascent transcript, Upf1 might influence Pol II phosphorylation and transcription., Wellcome Trust [9340/Z/09/Z, 202115/Z/16/Z]; Royal Society [RG170246]; DBT Ramalingaswami Grant [BT/RHD/35/02/2006]; Biotechnology and Biological Sciences Research Council [BBSRC BB/M022757/1, BBSRC BB/S017984/1, BBSRC BB/M]; Bangabandhu Science and Technology Fellowship Trust. Funding for open access charge: Fellowship Trust.

This paper explores the use of Convolutional Neural Networks in classifying images of date fruits as one of 9 varieties, creating several models with the highest achieving 97% accuracy. It contributes an original dataset of 1658 high-quality images taken in a controlled environment for use in both the computer vision and agricultural technology fields. A range of models is explored and trained, both with and without data augmentation, leading to high classification accuracy.

This chapter outlines isolation, detection and characterization methods for soft rot Pectobacteriaceae (SRP) and finishes with recommendations for diagnostics of SRP and perspectives for improved detection using metagenomic and pan-genomic approaches. For dilution plating and isolation of SRP, crystal violet pectate is still the medium of preference, although it is poorly selective. To improve the diagnostic sensitivity of detection methods, enrichment methods are used in which selective growth of the pathogen is enhanced by incubation in a pectate broth under low oxygen conditions. For molecular characterization, various finger printing techniques are described, but today analysis based on phylogenetic markers are preferred, in particular multi-locus sequence typing of housekeeping genes and comparative genetics using whole-genome sequences. For phenotypic characterization, methods are used based on serological, biochemical and physiological features. Currently the most precise phenotyping method is protein mass fingerprinting using a MALDI-TOF Mass Spectrometry. For detection of the pathogen, DNA-based amplification methods are generally used, including conventional PCR, real time (TaqMan) PCR assays and LAMP assays. They can detect the pathogen at a low density and allow recognition of the pathogens at different taxonomic levels. An inventory has been included of recently developed primer and probe combinations.

The effects of brassinosteroid signaling on shoot and root development have been characterized in great detail but a simple consistent positive or negative impact on a basic cellular parameter was not identified. In this study, we combined digital 3D single-cell shape analysis and single-cell mRNA sequencing to characterize root meristems and mature root segments of brassinosteroid-blind mutants and wild type. The resultant datasets demonstrate that brassinosteroid signaling affects neither cell volume nor cell proliferation capacity. Instead, brassinosteroid signaling is essential for the precise orientation of cell division planes and the extent and timing of anisotropic cell expansion. Moreover, we found that the cell-aligning effects of brassinosteroid signaling can propagate to normalize the anatomy of both adjacent and distant brassinosteroid-blind cells through non-cell-autonomous functions, which are sufficient to restore growth vigor. Finally, single-cell transcriptome data discern directly brassinosteroid-responsive genes from genes that can react non-cell-autonomously and highlight arabinogalactans as sentinels of brassinosteroid-dependent anisotropic cell expansion., This study combines digital 3D single-cell shape analysis and single-cell mRNA sequencing to characterize roots of brassinosteroid-blind mutants. The data demonstrate that brassinosteroid signaling is essential for precise cell division plane orientation and the extent and timing of anisotropic cell expansion. These cell-aligning brassinosteroid effects can propagate non-cell-autonomously, manifesting in arabinogalactan expression as sentinels of brassinosteroid-dependent anisotropic cell expansion.

Onion bulb initiation is photoperiod-dependent. Understanding this is crucial for adapting new varieties for growth at different latitudes, as well as aiding germplasm screening for the choice of current varieties. This study aims to gain further understanding of the molecular mechanisms involved in onion bulbing process based on the parallels with well-characterised functional clock genes in the Arabidopsis flowering pathway. A comprehensive set of diurnal quantitative expression experiments was carried out to investigate the bulbing response in two different onion varieties, namely Renate, a long-day variety and Hojem, a short-day variety under increasing intermediate day-lengths. All onion homologous to Arabidopsis flowering time genes showed clear diurnal expression patterns peaking at different times of the day for both long/short-day onions, indicating their role in daylength dependent bulbing process at molecular level. Under intermediate daylengths, AcFT1 expression level increased with daylengths in both varieties, while AcFT4 was expressed in all daylengths. The two genes showed complementary expression with AcFT4 peaking in the morning and AcFT1 in the evening in longer days. The results indicate that AcFT1 and AcFT4 are negatively co-regulated, but AcFT1 is the predominant regulator of bulb formation in response to daylength.