Mutations at the conserved N-Terminal of the human Rhinovirus capsid gene VP4, and their impact on the immune response.

Rhinoviruses (RV) are the major cause of chronic obstructive pulmonary disease and are associated with exacerbation development as well as community-acquired pneumonia in children, leading to substantial morbidity, mortality, and hospital admission. Here we have examined how changes at the amino terminal of the conserved VP4 epitope of different RV serotypes may affect pulmonary cytokine and chemokine responses and disease severity. Samples positive for rhinovirus were used for genetic characterization, followed by profiling gene expression of pulmonary Th1 and Th2 cytokines/chemokines by RT-PCR arrays. Genetic sequencing and homology 3D modeling revealed changes at the amino terminal of the conserved viral protein 4 (VP4) epitope in the RV-A101 serotype, especially serine at several positions that are important for interactive binding with the host immune cells. We found dysregulation of pulmonary gene expression of Th1- and Th2-related cytokines and chemokines in RV-A 101 and RV-C 8 pneumonia patients. These findings might contribute to a better understanding of RV immunity and the potential mechanisms underlying the pathogenesis of severe RV infections, but further functional studies are needed to confirm the causal relationship.

Zinc (Zn) mitigates copper (Cu) toxicity and retrieves yield and quality of lettuce irrigated with Cu and Zn-contaminated simulated wastewater.

Owing to a competitive interaction, zinc (Zn) contained in highly Cu-contained wastewater was hypothesized to mitigate Cu toxicity-induced negative effects on the growth and quality of lettuce. Thus, growth, metal accumulation and biochemical responses of lettuce irrigated with simulated wastewater (SW, control), Cu-contaminated SW (CuSW, 20 mg Cu L-1), Zn-contaminated SW (ZnSW, 100 mg Zn L-1) and both Cu- and Zn-contaminated SW (CuZnSW, 20 mg Cu and 100 mg Zn L-1) were evaluated. Results revealed that irrigation with CuSW negatively affected growth (dry matters, root length and plant height) and quality (low mineral concentrations) of lettuce, which were associated with higher Cu uptake. Irrigation with Zn + Cu-contaminated SW retrieved Cu toxicity and improved root and shoot dry matters and root length by 13.5%, 46% and 19%, respectively compared to that with alone Cu-contaminated SW. Moreover, CuZnSW improved lettuce leaf quality compared to CuSW and increased concentrations of Mg (30%), P (15%), Ca (41%), Mn (24%) and Fe (23%). Moreover, compared to CuSW, CuZnSW improved flavonoids (54%), total polyphenolic compounds (1.8-fold), polyphenolic acids (77%) and antiradical activities (16.6%). Most importantly, Zn addition boosted up lettuce Cu tolerance index by 18% under Cu-contaminated SW treatment. Pearson's correlation analysis among various growth and mineral parameters demonstrated that shoot Zn concentration was positively related to elemental concentrations, phytochemical contents and antioxidant activity under Cu-contaminated environment. Thus, it is concluded that Zn supplementation retrieves negative effects of Cu toxicity to lettuce grown with Cu-contaminated wastewater.

Integrated use of phosphorus fertilizer and farmyard manure improves wheat productivity by improving soil quality and P availability in calcareous soil under subhumid conditions.

Introduction: Low soil fertility and high fertilizer costs are constraints to wheat production, which may be resolved with integrating fertilizer phosphorus (P) and farm-yard manure (FYM). Study objectives were to evaluate P source impacts on soil, P efficiency, and wheat growth in a calcareous soil. Methods: Treatments included P fertilizer (0, 17, 26, or 39 kg P ha-1) and/or FYM (0 or 10 T ha-1) in a: 1) incubation experiment and 2) wheat (Triticum aestivum spp.) field experiment. Results and Discussion: Soil organic matter increased (30-72%) linearly for both fertilizer and FYM, whereas pH decreased (0.1-0.3 units) with fertilizer only. Addition of fertilizer and FYM increased plant available P (AB-DTPA extractable soil P) an average of 0.5 mg P kg-1 soil week-1 with incubation. The initial increase was 1-9 mg P kg-1, with further increase after 84 d of ~3-17 mg P kg-1. There was also a significant increase of available P in the soil supporting plants in the field study, although the magnitude of the increase was only 2 mg kg-1 at most for the highest fertilizer rate + FYM. Grain (66 to 119%) and straw (25-65%) yield increased significantly, peaking at 26 kg P ha-1 + FYM. The P Absorption Efficiency (PAE), P Balance (PB), and P Uptake (PU) increased linearly with P rate, with the highest levels at the highest P rate. The P Use Efficiency (PUE) was highest at the lowest rates of P, with general decreases with increasing P, although not consistently. Principal component analysis revealed that 94.34 % of the total variance was accounted for with PC1 (84.04 %) and PC2 (10.33 %), with grain straw yield significantly correlated to SOM, PU, and PAE. Regression analysis showed highly significant correlation of PB with P-input (R2= 0.99), plant available P (R2= 0.85), and PU (R2= 0.80). The combination of FYM at the rate of 10 T ha-1 and fertilizer P at 26 kg P ha-1 was found as the optimum dose that significantly increased yield. It is concluded that FYM concoction with fertilizer-P not only improved SOM and residual soil P, but also enhanced wheat yields with reasonable P efficiency.

Effect of soil texture and zinc oxide nanoparticles on growth and accumulation of cadmium by wheat: a life cycle study.

Cadmium (Cd) is getting worldwide attention due to its continuous accumulation in agricultural soils which is due to anthropogenic activities and finally Cd enters in food chain mainly through edible plants. Cadmium free food production on contaminated soils is great challenge which requires some innovative measures for crop production on such soils. The current study evaluated the efficiency of zinc oxide nanoparticles (ZnONPs) (0, 150 and 300 mg/kg) on the growth of wheat in texturally different soils including clay loam (CL), sandy clay loam (SCL), and sandy loam (SL) which were contaminated with were contaminated with 25 mg/kg of Cd before crop growth. Results depicted that doses of ZnONPs and soil textures significantly affected the biological yields, Zn and Cd uptake in wheat plants. The application of 300 mg/kg ZnONPs caused maximum increase in dry weights of shoot (66.6%), roots (58.5%), husk (137.8%) and grains (137.8%) in CL soil. The AB-DTPA extractable Zn was increased while Cd was decreased with doses of NPs depending upon soil textures. The maximum decrease in AB-DTPA extractable Cd was recorded in 300 mg/kg of ZnONPs treatment which was 58.7% in CL, 33.2% in SCL and 12.1% in SL soil as compared to respective controls. Minimum Cd concentrations in roots, shoots, husk and grain were found in 300 mg/kg ZnONPs amended CL soil which was 58%, 76.7%, 58%, and 82.6%, respectively. The minimum bioaccumulation factor (0.14), translocation index (2.46) and health risk index (0.05) was found in CL soil with the highest dose of NPs. The results concluded that use of ZnONPs significantly decreased Cd concentration while increased Zn concentrations in plants depending upon doses of NPs and soil textures.

Growth and Distribution of Boron in Oilseed Rape (Brassica napus L.) as Affected by Boron Supply.

Oilseed rape (Brassica napus L.) is one of the most important oilseed crops. It has relatively high boron (B) requirements for growth. In this study, a hydroponic experiment was performed to determine the critical B requirement and B distribution in B. napus. The plants were grown for four weeks at a range of B levels (from 0.25 to 1000 µM) supplied in a nutrient solution. The results showed significant differences in the root and shoot dry matter and B accumulation in these tissues among the supplied B levels. Severe visible symptoms of B deficiency were observed on the leaves at levels lower than 1 µM B and toxicity at 1000 µM B in the nutrient solution. The maximum shoot and root dry matter were recorded at 25 µM B in the nutrient solution. The plants supplied with the lowest and the highest B levels produced 35% and 37% less shoot dry matter than those supplied with 25 µM B, while the corresponding decreases in the root dry matter were 48% and 36%, respectively. The critical concentration of B, which is the lowest concentration at which plants produce 90% of the maximum shoot dry matter, was proven to be 1 µM B for oilseed rape. At this level of external B supply, the B concentration in the shoot was 26.9 mg kg-1 DM. It was found that with the increase in B levels in the nutrient solution, the relative distribution of B between the roots and the shoots shifted in favor of the shoots.

Can Bacterial Endophytes Be Used as a Promising Bio-Inoculant for the Mitigation of Salinity Stress in Crop Plants?-A Global Meta-Analysis of the Last Decade (2011-2020).

Soil salinity is a major problem affecting crop production worldwide. Lately, there have been great research efforts in increasing the salt tolerance of plants through the inoculation of plant growth-promoting endophytic bacteria. However, their ability to promote plant growth under no-stress and salinity-stress conditions remains largely uncertain. Here, we carried out a global meta-analysis to quantify the plant growth-promoting effects (improvement of morphological attributes, photosynthetic capacity, antioxidative ability, and ion homeostasis) of endophytic bacteria in plants under no-stress and salinity-stress conditions. In addition, we elucidated the underlying mechanisms of growth promotion in salt-sensitive (SS) and salt-tolerant (ST) plants derived from the interaction with endophytic bacteria under no-stress and salinity-stress conditions. Specifically, this work encompassed 42 peer-reviewed articles, a total of 77 experiments, and 24 different bacterial genera. On average, endophytic bacterial inoculation increased morphological parameters. Moreover, the effect of endophytic bacteria on the total dry biomass, number of leaves, root length, shoot length, and germination rate was generally greater under salinity-stress conditions than no-stress conditions. On a physiological level, the relative better performance of the bacterial inoculants under the salinity-stress condition was associated with the increase in total chlorophyll and chlorophyll-b, as well as with the decrease of 1-aminocylopropane-1-carboxylate concentration. Moreover, under the salinity-stress condition, bacterial inoculation conferred a significantly higher increase in root K+ concentration and decrease in leaf Na+ concentration than under the no-stress condition. In SS plants, bacterial inoculation induced a higher increase in chlorophyll-b and superoxide dismutase activity, as well as a higher decrease in abscisic acid content, than in ST plants. Under salinity-stress, endophytic bacterial inoculation increased root K+ concentration in both SS and ST plants but decreased root Na+ concentration only in ST plants. Overall, this meta-analysis suggests that endophytic bacterial inoculation is beneficial under both no salinity-stress and salinity-stress conditions, but the magnitude of benefit is definitely higher under salinity-stress conditions and varies with the salt tolerance level of plants.

Elevated Expression Levels of Lung Complement Anaphylatoxin, Neutrophil Chemoattractant Chemokine IL-8, and RANTES in MERS-CoV-Infected Patients: Predictive Biomarkers for Disease Severity and Mortality.

The complement system, a network of highly-regulated proteins, represents a vital part of the innate immune response. Over-activation of the complement system plays an important role in inflammation, tissue damage, and infectious disease severity. The prevalence of MERS-CoV in Saudi Arabia remains significant and cases are still being reported. The role of complement in Middle East Respiratory Syndrome coronavirus (MERS-CoV) pathogenesis and complement-modulating treatment strategies has received limited attention, and studies involving MERS-CoV-infected patients have not been reported. This study offers the first insight into the pulmonary expression profile including seven complement proteins, complement regulatory factors, IL-8, and RANTES in MERS-CoV infected patients without underlying chronic medical conditions. Our results significantly indicate high expression levels of complement anaphylatoxins (C3a and C5a), IL-8, and RANTES in the lungs of MERS-CoV-infected patients. The upregulation of lung complement anaphylatoxins, C5a, and C3a was positively correlated with IL-8, RANTES, and the fatality rate. Our results also showed upregulation of the positive regulatory complement factor P, suggesting positive regulation of the complement during MERS-CoV infection. High levels of lung C5a, C3a, factor P, IL-8, and RANTES may contribute to the immunopathology, disease severity, ARDS development, and a higher fatality rate in MERS-CoV-infected patients. These findings highlight the potential prognostic utility of C5a, C3a, IL-8, and RANTES as biomarkers for MERS-CoV disease severity and mortality. To further explore the prediction of functional partners (proteins) of highly expressed proteins (C5a, C3a, factor P, IL-8, and RANTES), the computational protein-protein interaction (PPI) network was constructed, and six proteins (hub nodes) were identified.

Amplicon and Metagenomic Analysis of Middle East Respiratory Syndrome (MERS) Coronavirus and the Microbiome in Patients with Severe MERS.

Middle East respiratory syndrome coronavirus (MERS-CoV) is a zoonotic infection that emerged in the Middle East in 2012. Symptoms range from mild to severe and include both respiratory and gastrointestinal illnesses. The virus is mainly present in camel populations with occasional zoonotic spill over into humans. The severity of infection in humans is influenced by numerous factors, and similar to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), underlying health complications can play a major role. Currently, MERS-CoV and SARS-CoV-2 are coincident in the Middle East and thus a rapid way of sequencing MERS-CoV to derive genotype information for molecular epidemiology is needed. Additionally, complicating factors in MERS-CoV infections are coinfections that require clinical management. The ability to rapidly characterize these infections would be advantageous. To rapidly sequence MERS-CoV, an amplicon-based approach was developed and coupled to Oxford Nanopore long read length sequencing. This and a metagenomic approach were evaluated with clinical samples from patients with MERS. The data illustrated that whole-genome or near-whole-genome information on MERS-CoV could be rapidly obtained. This approach provided data on both consensus genomes and the presence of minor variants, including deletion mutants. The metagenomic analysis provided information of the background microbiome. The advantage of this approach is that insertions and deletions can be identified, which are the major drivers of genotype change in coronaviruses. IMPORTANCE Middle East respiratory syndrome coronavirus (MERS-CoV) emerged in late 2012 in Saudi Arabia. The virus is a serious threat to people not only in the Middle East but also in the world and has been detected in over 27 countries. MERS-CoV is spreading in the Middle East and neighboring countries, and approximately 35% of reported patients with this virus have died. This is the most severe coronavirus infection so far described. Saudi Arabia is a destination for many millions of people in the world who visit for religious purposes (Umrah and Hajj), and so it is a very vulnerable area, which imposes unique challenges for effective control of this epidemic. The significance of our study is that clinical samples from patients with MERS were used for rapid in-depth sequencing and metagenomic analysis using long read length sequencing.

Lithium: Perspectives of nutritional beneficence, dietary intake, biogeochemistry, and biofortification of vegetables and mushrooms.

Although lithium (Li) is not an essential nutrient for humans, low Li intakes are associated with increased suicide and homicide rates, aggressive behaviors, unipolar/bipolar disorders, acute mania, etc. On the other hand, Li is one of the most effective psychopharmacological agents used for the treatment of these psycho-behavioral disorders. The beneficial normothymic effect of Li could be achieved at lower doses, therefore, modern psychiatry has called to consider Li biofortification of foods to improve its dietary intake. The concept of agronomic biofortification of crops with Li is juvenile and there exist a limited number of studies, mainly focused on vegetables or mushrooms. This review, first of its kind, discusses the nutritional beneficence and dietary intake of Li, its biogeochemistry, and opportunities and challenges in the Li biofortification of food crops. Literature showed that dietary intake of Li in many countries of the world is insufficient, compared to the provisional recommended dietary allowance (RDA) of 1.0 mg day-1 for a 70 kg adult. Lithium contents of soils are widely variable and the metal has high mobility in soils, making it more prone to leaching, and available for plant uptake. Biofortification studies reveal that plants can accumulate significant quantities of Li in their edible tissues without yield loss and quality associated negative effects. At lower application rates, Li tissue concentration could reach to the level that consuming 100-200 g of Li-biofortified fresh vegetables or mushrooms could support its RDA. It seems impossible to enrich the plants with Li to the levels that allow their application in psychiatric treatments, which requires the dosage of 600-1200 mg day-1. However, there is need to refine the methods of Li biofortification strategies to obtains plant specific concentration of Li in edible parts so that consuming a specific amount could provide the proposed dietary intake requirement.

Influenza co-infection associated with severity and mortality in COVID-19 patients.

BACKGROUND: In COVID-19 patients, undetected co-infections may have severe clinical implications associated with increased hospitalization, varied treatment approaches and mortality. Therefore, we investigated the implications of viral and bacterial co-infection in COVID-19 clinical outcomes. METHODS: Nasopharyngeal samples were obtained from 48 COVID-19 patients (29% ICU and 71% non-ICU) and screened for the presence of 24 respiratory pathogens using six multiplex PCR panels. RESULTS: We found evidence of co-infection in 34 COVID-19 patients (71%). Influenza A H1N1 (n = 17), Chlamydia pneumoniae (n = 13) and human adenovirus (n = 10) were the most commonly detected pathogens. Viral co-infection was associated with increased ICU admission (r = 0.1) and higher mortality (OR 1.78, CI = 0.38-8.28) compared to bacterial co-infections (OR 0.44, CI = 0.08-2.45). Two thirds of COVID-19 critically ill patients who died, had a co-infection; and Influenza A H1N1 was the only pathogen for which a direct relationship with mortality was seen (r = 0.2). CONCLUSIONS: Our study highlights the importance of screening for co-infecting viruses in COVID-19 patients, that could be the leading cause of disease severity and death. Given the high prevalence of Influenza co-infection in our study, increased coverage of flu vaccination is encouraged to mitigate the transmission of influenza virus during the on-going COVID-19 pandemic and reduce the risk of severe outcome and mortality.

One-Time Foliar Application and Continuous Resupply via Roots Equally Improved the Growth and Physiological Response of B-Deficient Oilseed Rape.

Oilseed rape (Brassica napus L.) is a high-boron (B)-demanding crop, and initially, normal growing plants might show B deficiency at advanced growth stages on soils with marginal B availability. Hence, we compared the effects of B resupply via roots and leaves on growth and physiological response, and relative expression of B transporters in B-deficient oilseed rape plants. Four-week-old plants initially grown with inadequate B (1 µM B for the first two weeks and 0.25 µM B for the next two weeks) were later grown either as such with 0.25 µM B, with 25 µM B in nutrient solution or foliar sprayed with 7 mL of 30, 60 and 150 mM B solution plant-1 as boric acid. Plants grown with 25 µM B in the nutrient solution from the beginning were included as adequate B treatment. Results showed that B resupply to B-deficient plants via roots and leaves (60 mM B) equally improved root and shoot dry matter, but not to the level of plants grown with adequate B supply. Foliar-applied 150 mM B proved toxic, causing leaf burn but not affecting dry matter. Resupply of B via roots increased B concentration in roots and leaves, while leaf-applied B did so only in leaves. Net carbon assimilation had a positive relationship with dry matter accumulation. Except for the highest foliar B level, B resupply via roots and leaves increased the accumulation of glucose, fructose and sucrose in leaves. Boron-deficient plants showed significant upregulation of BnaNIP5;1 in leaves and roots and of BnaBOR1;2 in roots. Boron resupply via roots reversed the B-deficiency-induced upregulation of BnaNIP5;1 in roots, whereas the expression of BnaBOR1;2 was reversed by both root and foliar B resupply. In leaves, B resupply by both methods reversed the expression of BnaNIP5;1 to the level of B-adequate plants. It is concluded that B resupply to B-deficient plants via roots and leaves equally but partially corrected B deficiency in B. napus grown in hydroponics.

Boron uptake and distribution by oilseed rape (Brassica napus L.) as affected by different nitrogen forms under low and high boron supply.

Ammonium (NH4+) and nitrate (NO3-) conversely alter pH of the rooting medium, and thus differentially affect the equilibrium between boric acid and borate in soil solution. This can alter boron (B) uptake by plants, which is passive under high, but facilitated (boric acid) or active (borate) under low B supply. Therefore, the effect of NH4+ and NO3- forms was investigated on the growth, 10B uptake rate and accumulation, and expression of B transporters in Brassica napus grown with low (1 µM) or high (100 µM) 10B for five days in the nutrient solution. At the low 10B level, NO3--fed plants had the same specific 10B uptake rate, 10B accumulation and xylem 10B concentration as NH4NO3-fed plants but these attributes were reduced at the high 10B level. BnaBOR1;2 and BnaNIP5;1 were upregulated in roots of NO3-fed plants at low 10B supply. NH4+-fed plants had substantially lower dry matters; due to nutrient solution acidification (2.0 units)-induced deficiency of nitrogen, potassium, magnesium, and iron in plant shoots. Reduced transpiration rates resulted in lower 10B uptake rate and accumulation in the roots and shoots of NH4+-fed plants. BnaNIP5;1 in roots, while both BnaBOR1;2 and BnaNIP5;1 in shoots were upregulated in NH4+-fed plants at low 10B level. Collectively, NH4+-induced acidity and consequent lowering of 10B uptake induced the upregulation of B transport mechanisms, even at marginal 10B concentrations, while NO3--induced alkalinization resulted in altered B distribution between roots and shoots due to restricted B transport, especially at higher 10B supply.

Structural Mapping of Mutations in Spike, RdRp and Orf3a Genes of SARS-CoV-2 in Influenza Like Illness (ILI) Patients.

In December 2019, the emergence of SARS-CoV-2 virus in China led to a pandemic. Since both Influenza Like Illness (ILI) and COVID-19 case definitions overlap, we re-investigated the ILI cases using PCR for the presence of SARS-CoV-2 in 739 nasopharyngeal swabs collected from November 2019 to March 2020. SARS-CoV-2 RNA was found in 37 samples (5%) collected mostly during February 2020. It was followed by confirmation of evolutionary and spatial relationships using next generation sequencing (NGS). We observed that the overall incidence of ILI cases during 2019-2020 influenza season was considerably higher than previous years and was gradually replaced with SARS-CoV-2, which indicated a silent transmission among ambulatory patients. Sequencing of representative isolates confirmed independent introductions and silent transmission earlier than previously thought. Evolutionary and spatial analyses revealed clustering in the GH clade, characterized by three amino acid substitutions in spike gene (D614G), RdRp (P323L) and NS3 (Q57H). P323L causes conformational change near nsp8 binding site that might affect virus replication and transcription. In conclusion, assessment of the community transmission among patients with mild COVID-19 illness, particularly those without epidemiological link for acquiring the virus, is of utmost importance to guide policy makers to optimize public health interventions. The detection of SARS-CoV-2 in ILI cases shows the importance of ILI surveillance systems and warrants its further strengthening to mitigate the ongoing transmission of SARS-CoV-2. The effect of NS3 substitutions on oligomerization or membrane channel function (intra- and extracellular) needs functional validation.

One-time abscisic acid priming induces long-term salinity resistance in Vicia faba: Changes in key transcripts, metabolites, and ionic relations.

Abscisic acid (ABA) priming is known to enhance plant growth and survival under salinity. However, the mechanisms mediating this long-term acclimatization to salt stress are still obscure. Specifically, the long-term transcriptional changes and their effects on ion relations were never investigated. This motivated us to study the long-term (8 days) effect of one-time 24 h root priming treatment with 10 µM ABA on transcription levels of relevant regulated key genes, osmotically relevant metabolites, and ionic concentrations in Vicia faba grown under 50 mM NaCl salinity. The novelty of this study is that we could demonstrate long-term effects of a one-time ABA application. ABA-priming was found to prevent the salt-induced decline in root and shoot dry matter, improved photosynthesis, and inhibited terminal wilting of plants. It substantially increased the mRNA level of AAPK and 14-3-3 ABA inducible kinases and ion transporters (PM H+ -ATPase, VFK1, KUP7, SOS1, and CLC1). These ABA-induced transcriptional changes went along with altered tissue ion patterns. Primed plants accumulated less Na+ and Cl- but more K+ , Ca2+ , Zn2+ , Fe2+ , Mn2+ , NO3 - , and SO4 2- . Priming changed the composition pattern of organic osmolytes under salinity, with glucose and fructose being dominant in unprimed, whereas sucrose was dominant in the primed plants. We conclude that one-time ABA priming mitigates salt stress in Vicia faba by persistently changing transcription patterns of key genes, stabilizing the ionic and osmotic balance, and improving photosynthesis and growth.

Simultaneous Biofortification of Rice With Zinc, Iodine, Iron and Selenium Through Foliar Treatment of a Micronutrient Cocktail in Five Countries.

Widespread malnutrition of zinc (Zn), iodine (I), iron (Fe) and selenium (Se), known as hidden hunger, represents a predominant cause of several health complications in human populations where rice (Oryza sativa L.) is the major staple food. Therefore, increasing concentrations of these micronutrients in rice grain represents a sustainable solution to hidden hunger. This study aimed at enhancing concentration of Zn, I, Fe and Se in rice grains by agronomic biofortification. We evaluated effects of foliar application of Zn, I, Fe and Se on grain yield and grain concentration of these micronutrients in rice grown at 21 field sites during 2015 to 2017 in Brazil, China, India, Pakistan and Thailand. Experimental treatments were: (i) local control (LC); (ii) foliar Zn; (iii) foliar I; and (iv) foliar micronutrient cocktail (i.e., Zn + I + Fe + Se). Foliar-applied Zn, I, Fe or Se did not affect rice grain yield. However, brown rice Zn increased with foliar Zn and micronutrient cocktail treatments at all except three field sites. On average, brown rice Zn increased from 21.4 mg kg-1 to 28.1 mg kg-1 with the application of Zn alone and to 26.8 mg kg-1 with the micronutrient cocktail solution. Brown rice I showed particular enhancements and increased from 11 µg kg-1 to 204 µg kg-1 with the application of I alone and to 181 µg kg-1 with the cocktail. Grain Se also responded very positively to foliar spray of micronutrients and increased from 95 to 380 µg kg-1. By contrast, grain Fe was increased by the same cocktail spray at only two sites. There was no relationship between soil extractable concentrations of these micronutrients with their grain concentrations. The results demonstrate that irrespective of the rice cultivars used and the diverse soil conditions existing in five major rice-producing countries, the foliar application of the micronutrient cocktail solution was highly effective in increasing grain Zn, I and Se. Adoption of this agronomic practice in the target countries would contribute significantly to the daily micronutrient intake and alleviation of micronutrient malnutrition in human populations.

Molecular Evolution and Structural Mapping of N-Terminal Domain in Spike Gene of Middle East Respiratory Syndrome Coronavirus (MERS-CoV).

The Middle East Respiratory Syndrome Coronavirus (MERS-CoV) is a lethal zoonotic pathogen circulating in the Arabian Peninsula since 2012. There is no vaccine for MERS and anti-viral treatment is generally not applicable. We investigated the evolution of the MERS-CoV spike gene sequences and changes in viral loads over time from patients in Saudi Arabia from 2105-2017. All the MERS-CoV strains belonged to lineage 5, and showed high sequence homology (99.9%) to 2017 strains. Recombination analysis showed a potential recombination event in study strains from patients in Saudi Arabia. The spike gene showed eight amino acid substitutions, especially between the A1 and B5 lineage, and contained positively selected codon 1020. We also determined that the viral loads were significantly (p < 0.001) higher in fatal cases, and virus shedding was prolonged in some fatal cases beyond 21 days. The viral concentration peaked during the first week of illness, and the lower respiratory specimens had higher levels of MERS-CoV RNA. The presence of the diversifying selection and the topologies with the structural mapping of residues under purifying selection suggested that codon 1020 might have a role in the evolution of spike gene during the divergence of different lineages. This study will im-prove our understanding of the evolution of MERS-CoV, and also highlights the need for enhanced surveillance in humans and dromedaries. The presence of amino acid changes at the N-terminal domain and structural mapping of residues under positive selection at heptad repeat 1 provides better insight into the adaptive evolution of the spike gene and might have a potential role in virus-host tropism and pathogenesis.

Antigenic drift of hemagglutinin and neuraminidase in seasonal H1N1 influenza viruses from Saudi Arabia in 2014 to 2015.

Antigenic drift of the hemagglutinin (HA) and neuraminidase (NA) proteins of the influenza virus cause a decrease in vaccine efficacy. Since the information about the evolution of these viruses in Saudi is deficient so we investigated the genetic diversity of circulating H1N1 viruses. Nasopharyngeal aspirates/swabs collected from 149 patients hospitalized with flu-like symptoms during 2014 and 2015 were analyzed. Viral RNA extraction was followed by a reverse transcription-polymerase chain reaction and genetic sequencing. We analyzed complete gene sequences of HA and NA from 80 positive isolates. Phylogenetic analysis of HA and NA genes of 80 isolates showed similar topologies and co-circulation of clades 6b. Genetic diversity was observed among circulating viruses belonging to clade 6B.1A. The amino acid residues in the HA epitope domain were under purifying selection. Amino acid changes at key antigenic sites, such as position S101N, S179N (antigenic site-Sa), I233T (antigenic site-Sb) in the head domain might have resulted in antigenic drift and emergence of variant viruses. For NA protein, 36% isolates showed the presence of amino acid changes such as V13I (n = 29), I314M (n = 29) and 12% had I34V (n = 10). However, H257Y mutation responsible for resistance to neuraminidase inhibitors was missing. The presence of amino acid changes at key antigenic sites and their topologies with structural mapping of residues under purifying selection highlights the importance of antigenic drift and warrants further characterization of recently circulating viruses in view of vaccine effectiveness. The co-circulation of several clades and the predominance of clade 6B.1 suggest multiple introductions in Saudi.

MERS-CoV infection is associated with downregulation of genes encoding Th1 and Th2 cytokines/chemokines and elevated inflammatory innate immune response in the lower respiratory tract.

MERS-CoV, a highly pathogenic virus in humans, is associated with high morbidity and case fatality. Inflammatory responses have a significant impact on MERS-CoV pathogenesis and disease outcome. However, CD4+ T-cell induced immune responses during acute MERS-CoV infection are barely detectable, with potent inhibition of effector T cells and downregulation of antigen presentation. The local pulmonary immune response, particularly the Th1 and Th2-related immune response during acute severe MERS-CoV infection is not fully understood. In this study, we offer the first insights into the pulmonary gene expression profile of Th1 and Th2-related cytokines/chemokines (Th1 & Th2 responses) during acute MERS-CoV infection using RT2 Profiler PCR Arrays. We also quantified the expression level of primary inflammatory cytokines/chemokines. Our results showed a downregulation of Th2, inadequate (partial) Th1 immune response and high expression levels of inflammatory cytokines IL-1α and IL-1ß and the neutrophil chemoattractant chemokine IL-8 (CXCL8) in the lower respiratory tract of MERS-CoV infected patients. Moreover, we identified a high viral load in all included patients. We also observed a correlation between inflammatory cytokines, Th1, and Th2 downregulation and the case fatality rate. Th1 and Th2 response downregulation, high expression of inflammatory cytokines, and high viral load may contribute to lung inflammation, severe infection, the evolution of pneumonia and ARDS, and a higher case fatality rate. Further study of the molecular mechanisms underlying the Th1 and Th2 regulatory pathways will be vital for active vaccine development and the identification of novel therapeutic strategies.

Opportunities and challenges in the remediation of metal-contaminated soils by using tobacco (Nicotiana tabacum L.): a critical review.

The successful phytoextraction of potentially toxic elements (PTEs) from polluted soils can be achieved by growing non-food and industrial crops. Tobacco (Nicotiana tabacum L.) is one of the main industrial crops and is widely grown in many countries. Tobacco can uptake high concentrations of PTEs especially in aboveground biomass without suffering from toxicity. This review highlighted the potential of tobacco for the phytoextraction of heavy metals and tolerance mechanisms under metal stress. Different management practices have been discussed which can enhance the potential of this plant for metal extraction. Finally, suitable options for the management/disposal of biomass enriched in excess metal have been elaborated to prevent secondary pollution.

Split application of silicon in cadmium (Cd) spiked alkaline soil plays a vital role in decreasing Cd accumulation in rice (Oryza sativa L.) grains.

Food contamination with cadmium (Cd) is a serious health threat to humans worldwide and Cd accumulation by rice is a major source of Cd entrance to the food chain. Silicon (Si) application decreases the Cd content in rice but the timing of Si application may need further investigation. The present study investigated the effect of split application of Si in the soil (600 kg/ha of Si) at different growth stages of rice on the growth and Cd accumulation by rice under Cd stress. Rice plants were grown in the presence and absence of Cd and Si was applied in the soil at different growth stages of rice under Cd stress. The results indicated that Cd stress alone reduced the growth and photosynthesis and increased the Cd content in different tissues and grains of rice. Silicon application improved the plant growth and reduced the Cd accumulation, translocation factor, and bioaccumulation factor in rice especially in grains, whereas the response of Si varied with the application of Si at different growth stages. The application of Si in three splits (transplanting (S1), tillering (S2), panicle initiation (S3)) was the best in improving growth and reducing Cd concentrations in plants compared to other combinations of Si application. Silicon application in three splits (S1+S2+S3) reduced the grain Cd concentrations below the threshold level (0.2 mg/kg) and reduced the Cd health risk index under the experimental conditions. Overall, split application of Si at three growth stages may function as remediator and diminishes Cd uptake into rice grains.