Systems genetics identifies miRNA-mediated regulation of host response in COVID-19.

BACKGROUND: Individuals infected with SARS-CoV-2 vary greatly in their disease severity, ranging from asymptomatic infection to severe disease. The regulation of gene expression is an important mechanism in the host immune response and can modulate the outcome of the disease. miRNAs play important roles in post-transcriptional regulation with consequences on downstream molecular and cellular host immune response processes. The nature and magnitude of miRNA perturbations associated with blood phenotypes and intensive care unit (ICU) admission in COVID-19 are poorly understood. RESULTS: We combined multi-omics profiling-genotyping, miRNA and RNA expression, measured at the time of hospital admission soon after the onset of COVID-19 symptoms-with phenotypes from electronic health records to understand how miRNA expression contributes to variation in disease severity in a diverse cohort of 259 unvaccinated patients in Abu Dhabi, United Arab Emirates. We analyzed 62 clinical variables and expression levels of 632 miRNAs measured at admission and identified 97 miRNAs associated with 8 blood phenotypes significantly associated with later ICU admission. Integrative miRNA-mRNA cross-correlation analysis identified multiple miRNA-mRNA-blood endophenotype associations and revealed the effect of miR-143-3p on neutrophil count mediated by the expression of its target gene BCL2. We report 168 significant cis-miRNA expression quantitative trait loci, 57 of which implicate miRNAs associated with either ICU admission or a blood endophenotype. CONCLUSIONS: This systems genetics study has given rise to a genomic picture of the architecture of whole blood miRNAs in unvaccinated COVID-19 patients and pinpoints post-transcriptional regulation as a potential mechanism that impacts blood traits underlying COVID-19 severity. The results also highlight the impact of host genetic regulatory control of miRNA expression in early stages of COVID-19 disease.

Microbial inoculation and fertilizer application on growth of cowpea and spore-based assemblages of arbuscular mycorrhizal fungi in its rhizophere.

In this study, the effect of microbial inoculants and fertilizer application on cowpea (BRS Pujante) growth and on the structure and composition of arbuscular mycorrhizal fungi (AMF) assemblages were evaluated. A completely randomized experiment was set up involving 17 treatments: four with AMF, three with nodulating bacteria, six with AMF + nodulating bacteria, two with phosphorus, one with nitrogen and one control (reference) in five replicates. Plant growth and nutritional content, mycorrhizal colonization, glomerospores number, spore-based AMF assemblages and ecological indices were evaluated. Mycorrhizal inoculants associated with Bradyrhizobium BR3267 strain were more effective than the Microvirga BR3296 strain. Multidimensional scaling analysis showed that Acaulospora longula treatments were more similar among themselves, and distinct from the other treatments. A difference was observed in the structure of AMF community assemblage between treatments with G. albida + Bradyrhizobium BR 3267 and A. longula, with greater Shannon diversity and Pielou equitability indices in the first treatment and greater dominance in the treatment with A. longula only. Long-term studies are required to determine if the successful establishment of A. longula among indigenous species persists over time and if its dominant behavior is not deleterious to the AMF native community.

AtNOT1 is required for gametophyte development in Arabidopsis.

In flowering plants, pollen development is under a dynamic and well-orchestrated transcriptional control, characterized by an early phase with high transcript diversity and a late post-mitotic phase skewed to a cell-type-specific transcriptome. Such transcriptional changes require a balance between synthesis and degradation of mRNA transcripts, the latter being initiated by deadenylation. The CCR4-NOT complex is the main evolutionary conserved deadenylase complex in eukaryotes, and its function is essential during germline specification in animals. We hypothesized that the CCR4-NOT complex might play a central role in mRNA turnover during microgametogenesis in Arabidopsis. Disruption of NOT1 gene, which encodes the scaffold protein of the CCR4-NOT complex, showed abnormal seed set. Genetic analysis failed to recover homozygous progeny, and reciprocal crosses confirmed reduced transmission through the male and female gametophytes. Concordantly, not1 embryo sacs showed delayed development and defects in embryogenesis. not1 pollen grains exhibited abnormal male germ unit configurations and failed to germinate. Transcriptome analysis of pollen from not1/+ mutants revealed that lack of NOT1 leads to an extensive transcriptional deregulation during microgametogenesis. Therefore, our work establishes NOT1 as an important player during gametophyte development in Arabidopsis.

Wireless UV-A LEDs-driven AOP in the treatment of agro-industrial wastewaters.

A wireless UV-A LEDs lab-scale reactor powered by a resonant inductive coupling (RLC) system was built to maximize the UV photon absorption of agro-industrial wastewaters. The UV-A LEDs (λ = 365 nm) energy was supplied through a magnetic field generated inside of the photoreactor by induction coils placed on the external wall made of polyvinyl chloride. Immersing the light sources in the wastewater increases the photon transfer efficiency and the reaction rate. Maximum magnetic field and optical irradiance were obtained at 26.8 and 27.0 kHz, respectively. As proof-of-concept, elderberry wastewater (EW), olive washing wastewater (OWW) and white and red winery wastewaters (WWW and RWW) were treated combining the wireless UV-A LEDs with the Advanced Oxidation Process (AOP) - Fenton reagent. Fenton experiments were performed using [Fe2+] = 10 mg L-1, [H2O2] = 500 mg L-1, pH = 3 and a reaction time of 4 h. With EW a DOC removal of 35% (k = 0.0696 h-1) was achieved, whereas adding the wireless UV-A LEDs (f = 26.8 kHz) 53% was attained (k = 0.1722 h-1). The Electric Energy per Order (EEO) for the wireless UV-A LEDs consumption was calculated (EEO LEDs = 48.7 kWh m-3 order-1) and for all the remain equipment (air pump, RC box and power amplifier), EEO total = 495 kWh m-3 order-1. Experiments with OWW presented a DOC removal of 62% and a EEO LEDs = 40.5 kWh m-3 order-1; RWW shown 40% of DOC removal and a EEO LEDs = 68.4 kWh m-3 order-1, while with WWW 35% of DOC removal and a EEO LEDs = 79.8 kWh m-3 order-1 were obtained. This work shows that wireless UV-A LEDs can be a promising alternative to conventional UV lamps and wired LEDs in the treatment of real wastewaters. However, optimization of the induction system is still needed, as well as the number and wavelength of the LEDs (e.g. UV-C LEDs) to reduce the overall treatment costs.

Photocatalytic degradation of an agro-industrial wastewater model compound using a UV LEDs system: kinetic study.

An ultraviolet light emitting diode (UV-A LED) system was built to test the capability of performing heterogeneous photocatalysis using TiO2 P25. The LEDs maximum wavelength is 365 nm with an irradiance power of 85 W m-2. The device was tested in batch and continuous (CSTR) mode in a laboratorial scale reactor. The degradation of an agro-industrial wastewater model compound (p-hydroxybenzoic acid, pHBA) was investigated, assessing the effect of different experimental conditions such as pH, pHBA and TiO2 concentration keeping constant the UV-A LEDs power and temperature. The photodegradation of different concentrations of pHBA with [TiO2] = 500 mg L-1, IUV = 85 W m-2 and a T = 21 °C were analysed by pseudo-first order kinetics. The results were applied to the Langmuir-Hinshelwood model yielding kc = 0.885 mg L-1 min-1 and kLH = 0.217 L mg-1. In a comparative experiment the UV-A LEDs system showed faster kinetics (k = 0.0134 min-1) than solar radiation (IUV = 23 W m-2; k = 0.0077 min-1), with [pHBA] = 75 mg L-1 and [TiO2] = 500 mg L-1. The values of the Electric Energy per Order (EEO) = 115 kWh m-3 order-1 and the Specific Applied Energy (ESAE) = 318 kWh mol-1 order-1 were obtained with [TiO2] = 1000 mg L-1 and [pHBA] = 50 mg L-1. Analogous results were obtained ([TiO2] = 500 mg L-1) in a CSTR with a slight decrease in the first order kinetic constant due to the "non-ideal" reactor: from 0.0284 to 0.0158 min-1 and from 0.0143 to 0.00825 min-1 with [pHBA] = 50 mg L-1 and 75 mg L-1, respectively. This work shows that photocatalytic reactors with UV-A LEDs can advantageously replace conventional UV mercury lamps based reactors in the photodegradation of phenolic compounds.

The Importance of Biodiversity E-infrastructures for Megadiverse Countries.

Addressing the challenges of biodiversity conservation and sustainable development requires global cooperation, support structures, and new governance models to integrate diverse initiatives and achieve massive, open exchange of data, tools, and technology. The traditional paradigm of sharing scientific knowledge through publications is not sufficient to meet contemporary demands that require not only the results but also data, knowledge, and skills to analyze the data. E-infrastructures are key in facilitating access to data and providing the framework for collaboration. Here we discuss the importance of e-infrastructures of public interest and the lack of long-term funding policies. We present the example of Brazil's speciesLink network, an e-infrastructure that provides free and open access to biodiversity primary data and associated tools. SpeciesLink currently integrates 382 datasets from 135 national institutions and 13 institutions from abroad, openly sharing ~7.4 million records, 94% of which are associated to voucher specimens. Just as important as the data is the network of data providers and users. In 2014, more than 95% of its users were from Brazil, demonstrating the importance of local e-infrastructures in enabling and promoting local use of biodiversity data and knowledge. From the outset, speciesLink has been sustained through project-based funding, normally public grants for 2-4-year periods. In between projects, there are short-term crises in trying to keep the system operational, a fact that has also been observed in global biodiversity portals, as well as in social and physical sciences platforms and even in computing services portals. In the last decade, the open access movement propelled the development of many web platforms for sharing data. Adequate policies unfortunately did not follow the same tempo, and now many initiatives may perish.

Predictors of Arbuscular Mycorrhizal Fungal Communities in the Brazilian Tropical Dry Forest.

Arbuscular mycorrhizal fungi (AMF) are symbiotic fungi with a broad distribution, and many taxa have physiological and ecological adaptations to specific environments, including semiarid ecosystems. Our aim was to address regional distribution patterns of AMF communities in such semiarid environments based on spore morphological techniques. We assessed AMF spores at the bottom and top of inselbergs distributed throughout the tropical dry forest in the Northeast region of Brazil. Across 10 replicate inselbergs and the surrounding area, spanning a range of altitude between 140 and 2000 m, we scored the AMF soil diversity and properties in 52 plots. We fitted parsimonious ordination analyses and variance partitioning models to determine the environmental factors which explained the variation in AMF community, based on morphological spore analysis. The diversity of AMF was similar at the bottom and top of inselbergs; however, we detected high variation in abundance and richness across sites. We formulated a parsimonious richness model that used physical soil factors as predictors. The AMF community structure could be best explained through the variables coarse and total sand, iron, organic matter, potassium, silt, and sodium which together accounted for 17.8% of total variance. Several AMF species were indicators of either deficiency or high values of specific soil properties. We demonstrated that habitat isolation of the inselbergs compared with surrounding areas did not trigger differences in AMF communities in semiarid regions of Brazil. At the regional scale, soil predictors across sites drove the distribution of symbiotic mycorrhizal fungi.

Intercellular communication in Arabidopsis thaliana pollen discovered via AHG3 transcript movement from the vegetative cell to sperm.

An Arabidopsis pollen grain (male gametophyte) consists of three cells: the vegetative cell, which forms the pollen tube, and two sperm cells enclosed within the vegetative cell. It is still unclear if there is intercellular communication between the vegetative cell and the sperm cells. Here we show that ABA-hypersensitive germination3 (AHG3), encoding a protein phosphatase, is specifically transcribed in the vegetative cell but predominantly translated in sperm cells. We used a series of deletion constructs and promoter exchanges to document transport of AHG3 transcripts from the vegetative cell to sperm and showed that their transport requires sequences in both the 5' UTR and the coding region. Thus, in addition its known role in transporting sperm during pollen tube growth, the vegetative cell also contributes transcripts to the sperm cells.

Integrated aerobic biological-chemical treatment of winery wastewater diluted with urban wastewater. LED-based photocatalysis in the presence of monoperoxysulfate.

The oxidation of Winery Wastewater (WW) by conventional aerobic biological treatment usually leads to inefficient results due to the presence of organic substances, which are recalcitrant or toxic in conventional procedures. This study explores the combination of biological and chemical processes in order to complete the oxidation of biodegradable and non-biodegradable compounds in two sequential steps. Thus, a biological oxidation of a diluted WW is carried out by using the activated sludge process. Activated sludge was gradually acclimated to the Diluted Winery Wastewater (DWW). Some aspects concerning the biological process were evaluated (kinetics of the oxidation and sedimentation of the sludge produced). The biological treatment of the DWW led to a 40-50% of Chemical Oxygen Demand (COD) removal in 8 h, being necessary the application of an additional process. Different chemical processes combining UVA-LEDs radiation, monoperoxysulfate (MPS) and photocatalysts were applied in order to complete the COD depletion and efficient removal of polyphenols content, poorly oxidized in the previous biological step. From the options tested, the combination of UVA, MPS and a novel LaCoO3-TiO2 composite, with double route of MPS decomposition through heterogeneous catalysis and photocatalysis, led to the best results (95% of polyphenol degradation, and additional 60% of COD removal). Initial MPS concentration and pH effect in this process were assessed.

Modelization and Statistical Optimization of Coagulation-Flocculation Treatment of an Old Leachate.

Coagulation/flocculation process was studied using the response surface methodology (RSM) and central composite design (CCD), to design the experiments, develop models, evaluate the relationship between operating factors (FeCl3 dose [m] and pH), and provide an efficient method for the treatment of old leachates. The quadratic polynomial models developed for chemical oxygen demand (COD) and turbidity responses indicated that the optimum conditions were m of 0.82 g/L at pH 5.33 with coefficient of determination R2 of 98.88 and 99.84%, and adjusted R2 of 98.09 and 99.73% for both COD and turbidity. The experimental data and model predictions agreed well. Chemical oxygen demand, turbidity, lead and copper removal efficiency of 76.4, 98.9, 99 and 99%, respectively, were reached.

Changes in Microbial Community Structure and Soil Biological Properties in Mined Dune Areas During Re-vegetation.

The aim of this study was to describe the impact of re-vegetation on the restoration of microbial community structure and soil microbiological properties in sand dunes that had been affected by mining activity. Soil samples were collected during the dry and rainy seasons from a chronosequence (1, 9, 21 years) of re-vegetated dunes using a single preserved dune as a reference. The composition of the fatty acid methyl esters and soil microbial properties were evaluated. The results showed that the changes in microbial community structure were related to seasonal variations: biomarkers of Gram-positive bacteria were higher than Gram-negative bacteria during the dry season, showing that this group of organisms is more tolerant to these stressful conditions. The microbial community structure in the natural dune was less affected by seasonal variation compared to the re-vegetated areas, whereas the opposite was observed for microbiological properties. Thus, in general, the proportion of saprobic fungi was higher in the natural dune, whereas Gram-negative bacteria were proportionally more common in the younger areas. Although over time the re-vegetation allows the recovery of the microbial community and the soil functions, these communities and functions are different from those found in the undisturbed areas.

Arabidopsis tetraspanins are confined to discrete expression domains and cell types in reproductive tissues and form homo- and heterodimers when expressed in yeast.

Tetraspanins are evolutionary conserved transmembrane proteins present in all multicellular organisms. In animals, they are known to act as central organizers of membrane complexes and thought to facilitate diverse biological processes, such as cell proliferation, movement, adhesion, and fusion. The genome of Arabidopsis (Arabidopsis thaliana) encodes 17 members of the tetraspanin family; however, little is known about their functions in plant development. Here, we analyzed their phylogeny, protein topology, and domain structure and surveyed their expression and localization patterns in reproductive tissues. We show that, despite their low sequence identity with metazoan tetraspanins, plant tetraspanins display the typical structural topology and most signature features of tetraspanins in other multicellular organisms. Arabidopsis tetraspanins are expressed in diverse tissue domains or cell types in reproductive tissues, and some accumulate at the highest levels in response to pollination in the transmitting tract and stigma, male and female gametophytes and gametes. Arabidopsis tetraspanins are preferentially targeted to the plasma membrane, and they variously associate with specialized membrane domains, in a polarized fashion, to intercellular contacts or plasmodesmata. A membrane-based yeast (Saccharomyces cerevisiae) two-hybrid system established that tetraspanins can physically interact, forming homo- and heterodimer complexes. These results, together with a likely genetic redundancy, suggest that, similar to their metazoan counterparts, plant tetraspanins might be involved in facilitating intercellular communication, whose functions might be determined by the composition of tetraspanin complexes and their binding partners at the cell surface of specific cell types.

Visual tracking of plant virus infection and movement using a reporter MYB transcription factor that activates anthocyanin biosynthesis.

Insertion of reporter genes into plant virus genomes is a common experimental strategy to research many aspects of the viral infection dynamics. Their numerous advantages make fluorescent proteins the markers of choice in most studies. However, the use of fluorescent proteins still has some limitations, such as the need of specialized material and facilities to detect the fluorescence. Here, we demonstrate a visual reporter marker system to track virus infection and movement through the plant. The reporter system is based on expression of Antirrhinum majus MYB-related Rosea1 (Ros1) transcription factor (220 amino acids; 25.7 kD) that activates a series of biosynthetic genes leading to accumulation of colored anthocyanins. Using two different tobacco etch potyvirus recombinant clones tagged with Ros1, we show that infected tobacco (Nicotiana tabacum) tissues turn bright red, demonstrating that in this context, the sole expression of Ros1 is sufficient to induce pigment accumulation to a level readily detectable to the naked eye. This marker system also reports viral load qualitatively and quantitatively by means of a very simple extraction process. The Ros1 marker remained stable within the potyvirus genome through successive infectious passages from plant to plant. The main limitation of this marker system is that color output will depend on each particular plant host-virus combination and must be previously tested. However, our experiments demonstrate accurate tracking of turnip mosaic potyvirus infecting Arabidopsis (Arabidopsis thaliana) and either tobacco mosaic virus or potato X virus infecting Nicotiana benthamiana, stressing the general applicability of the method.

Mycorrhizal technology and phosphorus in the production of primary and secondary metabolites in cebil (Anadenanthera colubrina (Vell.) Brenan) seedlings.

BACKGROUND: The application of arbuscular mycorrhizal fungi (AMF) can increase the growth and concentration of primary and secondary metabolites in several plant species. Cebil (Anadenanthera colubrina), a medicinal plant, benefits from mycorrhizal association, but the influence of the symbiosis on the production of its bioactive compounds is unknown. In this study the effect of mycorrhizal inoculation and phosphorus (P) supply on the production of primary and secondary metabolites in cebil seedlings was determined. RESULTS: The production of proteins and carbohydrates in terms of both concentration and content was enhanced by inoculation with AMF, but this benefit was mitigated at higher levels of P (30 and 50 mg dm(-3) soil). The concentration of phenols, flavonoids and total tannins was favoured by mycorrhizal inoculation even at the highest levels of P (30 and 50 mg dm(-3) soil). CONCLUSION: The production of primary and secondary metabolites in leaves of A. colubrina can be maximised by mycorrhization, with the benefit depending on supplementation of soil phosphate.

RNA-Binding Proteins: A Role in Neurotoxicity?

Despite sustained efforts to treat neurodegenerative diseases, little is known at the molecular level to understand and generate novel therapeutic approaches for these malignancies. Therefore, it is not surprising that neurogenerative diseases are among the leading causes of death in the aged population. Neurons require sophisticated cellular mechanisms to maintain proper protein homeostasis. These cells are generally sensitive to loss of gene expression control at the post-transcriptional level. Post-translational control responds to signals that can arise from intracellular processes or environmental factors that can be regulated through RNA-binding proteins. These proteins recognize RNA through one or more RNA-binding domains and form ribonucleoproteins that are critically involved in the regulation of post-transcriptional processes from splicing to the regulation of association of the translation machinery allowing a relatively rapid and precise modulation of the transcriptome. Neurotoxicity is the result of the biological, chemical, or physical interaction of agents with an adverse effect on the structure and function of the central nervous system. The disruption of the proper levels or function of RBPs in neurons and glial cells triggers neurotoxic events that are linked to neurodegenerative diseases such as spinal muscular atrophy (SMA), amyotrophic lateral sclerosis (ALS), fragile X syndrome (FXS), and frontotemporal dementia (FTD) among many others. The connection between RBPs and neurodegenerative diseases opens a new landscape for potentially novel therapeutic targets for the intervention of these neurodegenerative pathologies. In this contribution, a summary of the recent findings of the molecular mechanisms involved in the plausible role of RBPs in RNA processing in neurodegenerative disease is discussed.

Microglial Activation in Metal Neurotoxicity: Impact in Neurodegenerative Diseases.

Neurodegenerative processes encompass a large variety of diseases with different pathological patterns and clinical features, such as Alzheimer's and Parkinson's diseases. Exposure to metals has been hypothesized to increase oxidative stress in brain cells leading to cell death and neurodegeneration. Neurotoxicity of metals has been demonstrated by several in vitro and in vivo experimental studies, and most probably, each metal has its specific pathway to trigger cell death. As a result, exposure to essential metals, such as manganese, iron, copper, zinc, and cobalt, and nonessential metals, including lead, aluminum, and cadmium, perturbs metal homeostasis at the cellular and organism levels leading to neurodegeneration. In this contribution, a comprehensive review of the molecular mechanisms by which metals affect microglia physiology and signaling properties is presented. Furthermore, studies that validate the disruption of microglia activation pathways as an essential mechanism of metal toxicity that can contribute to neurodegenerative disease are also presented and discussed.

Incorporation of SARS-CoV-2 spike NTD to RBD protein vaccine improves immunity against viral variants.

Emerging SARS-CoV-2 variants pose a threat to human health worldwide. SARS-CoV-2 receptor binding domain (RBD)-based vaccines are suitable candidates for booster vaccines, eliciting a focused antibody response enriched for virus neutralizing activity. Although RBD proteins are manufactured easily, and have excellent stability and safety properties, they are poorly immunogenic compared to the full-length spike protein. We have overcome this limitation by engineering a subunit vaccine composed of an RBD tandem dimer fused to the N-terminal domain (NTD) of the spike protein. We found that inclusion of the NTD (1) improved the magnitude and breadth of the T cell and anti-RBD response, and (2) enhanced T follicular helper cell and memory B cell generation, antibody potency, and cross-reactive neutralization activity against multiple SARS-CoV-2 variants, including B.1.1.529 (Omicron BA.1). In summary, our uniquely engineered RBD-NTD-subunit protein vaccine provides a promising booster vaccination strategy capable of protecting against known SARS-CoV-2 variants of concern.

Whole genome analysis of gene expression reveals coordinated activation of signaling and metabolic pathways during pollen-pistil interactions in Arabidopsis.

Plant reproduction depends on the concerted activation of many genes to ensure correct communication between pollen and pistil. Here, we queried the whole transcriptome of Arabidopsis (Arabidopsis thaliana) in order to identify genes with specific reproductive functions. We used the Affymetrix ATH1 whole genome array to profile wild-type unpollinated pistils and unfertilized ovules. By comparing the expression profile of pistils at 0.5, 3.5, and 8.0 h after pollination and applying a number of statistical and bioinformatics criteria, we found 1,373 genes differentially regulated during pollen-pistil interactions. Robust clustering analysis grouped these genes in 16 time-course clusters representing distinct patterns of regulation. Coregulation within each cluster suggests the presence of distinct genetic pathways, which might be under the control of specific transcriptional regulators. A total of 78% of the regulated genes were expressed initially in unpollinated pistil and/or ovules, 15% were initially detected in the pollen data sets as enriched or preferentially expressed, and 7% were induced upon pollination. Among those, we found a particular enrichment for unknown transcripts predicted to encode secreted proteins or representing signaling and cell wall-related proteins, which may function by remodeling the extracellular matrix or as extracellular signaling molecules. A strict regulatory control in various metabolic pathways suggests that fine-tuning of the biochemical and physiological cellular environment is crucial for reproductive success. Our study provides a unique and detailed temporal and spatial gene expression profile of in vivo pollen-pistil interactions, providing a framework to better understand the basis of the molecular mechanisms operating during the reproductive process in higher plants.