SARS-CoV-2, the novel coronavirus behind COVID-19 pandemic is acquiring new mutations in its genome. Although some mutations provide benefits to the virus against human immune response, a number of them may result in their reduced pathogenicity and virulence. By analyzing more than 3000 high-coverage, complete genome sequences deposited in the GISAID database, here I report a unique 28881-28883:GGG>AAC trinucleotide-bloc mutation in the SARS-CoV-2 genome that results in two sub-strains, described here as SARS-CoV-2g (28881-28883:GGG genotype) and SARS-CoV-2a (28881-28883:AAC genotype). Computational analysis and literature review suggest that this bloc mutation would bring 203-204:RG(arginine-glycine)>KR(lysine-arginine) amino acid changes in the nucleocapsid (N) protein affecting the SR (serine-arginine)-rich motif of the protein, a critical region for the transcription of viral RNA and replication of the virus. Thus, 28881-28883:GGG>AAC bloc-mutation is expected to modulate the pathogenicity of the SARS-CoV-2. Remarkably, SARS-CoV-2g and SARS-CoV-2a strains can be linked with the heterogeneity of COVID-19 cases across different regions within and between countries by analyzing existing data. Sequence analysis suggests that severely affected cities, such as Milan, Lombardy, New York, Paris have the predominant presence of SARS-CoV-2g strains, whereas less affected places like Abruzzo, Lyon, Valencia have a relatively higher presence of SARS-CoV-2a, an indication that the latter strain may contribute to the reduced cases of COVID-19. A similar relationship is observed when Netherlands, Portugal are compared with Spain, France and Germany. These analyses suggest that the SARS-CoV-2 has already evolved into a less infective SARS-CoV-2a affecting COVID-19 cases in different regions. The time a country or region needs to acquire SARS-CoV-2a strains may be indicative to the time it would need to overcome the peak of the COVID-19 cases. To confirm these assumptions, prompt retrospective and prospective epidemiological studies should be conducted in different countries to understand the course of pathogenicity of the SARS-CoV-2a and SARS-CoV-2g. Potential drugs can be designed targeting 28881-28883 region of the N protein to modulate virus pathogenicity.

Heavy metal accumulation in soils used for agricultural purposes is a major issue as it can affect the growth of plants and contain health risks as plants containing heavy metals are taken as food. This study provided the potential of three Bacillus pumilus strains (C-2PMW-8, C-1 SSK-8, and C-1PWK-7) for mitigation of the health factors related to heavy metals on lettuce (Lactuca sativa) grown in chromium contaminated soil from activities related to mining. Lettuce seeds inoculated with B. pumilus strains were grown in pots with garden soil amended with varying amount of chromite mine soil (2.27%, 4.65%, 7.14%). Growth indicators like days to germination, percentage of germination, leaf weight, leaf area and rate of survival decreased with incremental soil chromium levels but improved highly with inoculation of B. pumilus compared to uninoculated controls. When B. pumilus strains were provided, there was also a decreased level in the buildup of chromium in soil as well as lettuce shoots. The results explains that plant growth-promoting B. pumilus strains may be able to lower down the detrimental effects of chromium on lettuce development, hence increment in the effectiveness of phytoremediation.

Objective: The aim of this study was to optimize the fermentation process of Radix Ranunculi ternate via microbial fermentation and analyze the changes in the contents of the main components, the antioxidant and hypoglycemic capacities of the extract before and after fermentation. Methods: The solid-state fermentation process was optimized using single-factor tests and the response surface method, with the yield of the alcohol extract of R. ternate as an evaluation index. Results: The best fermentation process was optimized using solid-state endophytic fungus fermentation technology as follows: strain addition ratio of Chaetomium globosum/Fusarium equiseti =1:1, fermentation for 5 d, sieve size of 40 mesh, liquid/material ratio of 0.8:1 mL·g−1, fermentation temperature of 31 °C, and inoculation amount of 7.5%. Under the optimized conditions, the contents of the water-soluble extract and total polysaccharides decreased by 12.71% and 12.95%, respectively, in the fermentation, The contents of ethanol-soluble-extract, flavonoids, saponins, polyphenols, organic acids, and total amino acids of fermented R. ternate increased by 19.77%, 57.14%, 79.67%, 14.29%, 17.63% and 3.82%, respectively, and the scavenging rate for DPPH, ABTS+, ·OH free radicals and inhibitory rate for α-amylase also increased by 19.02%, 14.17%, 7.53% and 34.54%, respectively, compared with unfermented R. ternate. Conclusions: Solid-state fermentation opens new avenues for the development and application of R. ternate as natural antioxidant and hypoglycemic food.

Genome-scale engineering and custom synthetic genomes are reshaping the next generation of industrial yeast strains. The Cre-recombinase mediated chromosomal rearrangement mechanism of designer synthetic Saccharomyces cerevisiae chromosomes, known as SCRaMbLE, is a powerful tool which allows rapid genome evolution upon command. This system is able to generate millions of novel genomes with potential valuable phenotypes, but the excessive loss of essential genes often results in poor growth or even the death of cells with useful phenotypes. In this study we expanded the versatility of SCRaMbLE to industrial strains, and evaluated different control measures to optimise genomic rearrangement, whilst limiting cell death. To achieve this, we have developed RED (Rapid Evolution Detection), a simple colorimetric plate-assay procedure to rapidly quantify the degree of genomic rearrangements within a post-SCRaMbLE yeast population. RED-enabled semi-synthetic strains were mated with haploid progeny of industrial yeast strains to produce stress tolerant heterozygous diploid strains. Analysis of these heterozygous strains with the RED-assay, genome sequencing and custom bioinformatics scripts demonstrated a correlation between RED-assay frequencies and physical genomic rearrangements. Here we show that RED is a fast and effective method to evaluate optimal SCRaMbLE induction times of different Cre-recombinse expression systems for the development of industrial strains.

The World Health Organization has identified antimicrobial resistance as a public health emergency and developed a global priority pathogens list of antibiotic-resistant bacteria that can be summarized in the acronym ESKAPE (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa and Enterobacterales species), reminding us of their ability to escape the effect of antibacterial drugs. We previously tested new heteroaryl-ethylene compounds in order to define their spectrum of activity and antibacterial capability. Now, we focus our attention on PB4, a compound with promising MIC and MBC values in all conditions tested. In the present study, we evaluate the activity of PB4 on selected samples of ESKAPE isolates from nosocomial infections: 14 S. aureus, 6 E. faecalis, 7 E. faecium, 12 E. coli and 14 A. baumanii. Furthermore, an ATCC control strain was selected for all species tested. MICs were performed according to the standard method, with some modifications. PB4 MIC values were within very low ranges regardless of bacterial species and resistance profiles: from 0,12 to 2 mg/L for S. aureus, E. faecalis, E. faecium and A. baumannii. For E. coli, the MIC values obtained were slightly higher (4-64 mg/L), butstill promising. The PB4 heteroaryl-ethylenic compound was able to counteract the bacterial growth of both high-priority Gram-positive and Gram-negative clinical strains. In the future, it would be interesting to evaluate the activity of PB4 in animal models to test for its toxicity.

Between 25 and 30% of the nearly one million military personnel who participated in the 1991 Persian Gulf War became ill with chronic symptoms ranging from gastrointestinal to nervous system dysfunction. This disorder is now referred to as Gulf War Illness (GWI) and the underlying pathophysiology has been linked to exposure-based neuroinflammation caused by organophosphorous (OP) compounds coupled with high circulating glucocorticoids. In a mouse model of GWI we developed, corticosterone was shown to act synergistically with an OP (diisopropylflurophosphate) to dramatically increase proinflammatory cytokine gene expression in the brain. Because not all Gulf War participants became sick, the question arises as to whether differential genetic constitution might underlie individual differences in susceptibility. To address this question of genetic liability, we tested the impact of OP and glucocorticoid exposure in a genetic reference population of 30 inbred mouse strains. We also studied both sexes. The results showed wide differences among strains and overall that females were less sensitive to the combined treatment than males. Furthermore, we identified one OP-glucocorticoid locus and nominated a candidate gene—Spon1—that may underlie the marked differences in response.

Microbiocontrol of Mycogone perniciosa is focused on casing soil antagonists use. Since no industrial producer strains of polyfunctional biologics were used in previous studies, research goal was to characterize Bacillus subtilis B-10 and M-22 effect on mycopathogen and reveal its control possibilities. Interactions between producer strains and M. perniciosa were evaluated using well method and spraying. Mycoparasite colony area and its lysis zone were determined. Biological efficacy was characterized by lysis zone proportion in total area occupied by the micromycete mycelium. Statistical processing included W-test, ANOVA, means (M) and standard errors (±SEM) calculation. The significance was assessed by t-test. M. perniciosa development suppressing by producer strains was established, indicates a prolonged B-10 and M-22 effect on mycopathogen. High biological efficacy of both strains at the early stages of mycopathogen development by introducing into the wells and spraying was shown: B-10 – 50.9–99.6 % and M-22 – 57.5–99.2 % respectively (p ≤ 0.05). Significant differences between producer strains were not revealed, although during the first exposure day to developed M. perniciosa colonies M-22 has shown greater activity. Preventive treatment high efficiency when producer strains completely suppressed mycoparasite development, permit recommending them both to introduce when preparing casing for M. perniciosa control.

Ocular pathologies present significant challenges in achieving effective therapeutic re-sults due to various anatomical and physiological barriers. Natural products, such as flavonoids, alone or in association with allopathic drugs, present many therapeutical actions, including anti-cancer, anti-inflammatory, and antibacterial action. However, their clinical employment is chal-lenging for scientists due to their low water solubility. In this study, we designed a liquid formu-lation based on rutin/sulfobutylether-β-cyclodextrin (RTN/SBE-β-CD) inclusion complex for treating ocular infections. The correct stoichiometry and the accurate binding constant were de-termined by employing the SupraFit software on the Uv-vis titration experiment. A deep physical-chemical characterization of the RTN/SBE-β-CD inclusion complex was also performed; it con-firmed the predominant formation of a stable complex (Kc, 9660 M−1) in a 1:1 molar ratio, with high water solubility of 20 times (2.5 mg/mL) higher than the free molecule (0.125 mg/mL), per-mitting the dissolution of the solid complex within 30 min. NMR studies revealed the involve-ment of the bicyclic flavonoid moiety in the complexation, which was also confirmed by molecu-lar modeling studies. In vitro, the antibacterial and antibiofilm activity of the formulation was assayed against Staphylococcus aureus and Pseudomonas aeruginosa strains demonstrating a sig-nificant activity of the formulation to the free components.

The purpose of this work is to optimize angular extrusion for sever plastic deformation of tubular specimens. A finite element model (FEM) was built in Deform-3D^® for three extrusion dies and analyzed. The dies were ECAP (135°), TCAP with external groove of 90° (denoted as TCAP-e) and TCAP with internal groove of 90° (denoted as TCAP-i). The analysis for process parameters (such as coefficient of friction-μ, die angles-ѱ and φ, temperature - T, and radius ratio-R) showed that TCAP-i was the optimal die in processing Al6063 tubes based on strain and load distribution of the model. The TCAP-i die model was further optimized for different parameters namely die angles, coefficient of friction, deformation ratio and temperature. The results showed that at constant process temperature of 25 °C, the optimal TCAP-i has the following parameters: φ₂=80⁰, Ѱ₁=30⁰, Ѱ₂=80⁰, Ѱ₃=30⁰, μ =0.4 and R =1.5.

Pepino mosaic virus (PepMV) causes significant economic losses in tomato crops worldwide. Since its first detection infecting tomato in 1999, aggressive PepMV variants have emerged. This study aimed to characterize two aggressive PepMV isolates, PepMV-H30 and PepMV-KLP2. Both isolates were identified in South-Eastern Spain infecting tomato plants, which showed severe symptoms, including bright yellow mosaics. Full-length infectious clones were generated, and phylogenetic relationships were inferred using their nucleotide sequences and another 35 full-length sequences from isolates representing the five PepMV known strains. Our analysis revealed that PepMV-H30 and PepMV-KLP2 belong to the EU and CH2 strains, respectively. Amino acid sequence comparisons between these and mild isolates identified 8 and 15 amino acid substitutions for PepMV-H30 and PepMV-KLP2, respectively, potentially involved in severe symptom induction. None of the substitutions identified in PepMV-H30 had previously been described as symptom determinant. The E236K substitution, originally present in the PepMV-H30 CP, was introduced into a mild PepMV-EU isolate, resulting in a virus that causes symptoms similar to those induced by the parental PepMV-H30. In silico analyses revealed that this residue is located at the C-terminus of the CP and is solvent-accessible, suggesting its potential involvement in CP-host proteins interactions. We also examined the subcellular localization of PepGFPm2E236K in comparison to that of PepGFPm2, focusing on chloroplast affection, but no differences were observed in the GFP subcellular distribution between the two viruses. Due to the easily visible symptoms that PepMV-H30 and PepMV-KLP2 induce, these isolates represent valuable tools in programs destined to breeding resistance to PepMV in tomato.

The meshless Petrov-Galerkin (MLPG) method is developed to analyse 2-D problems for flexoelectricity and thermoelectricity. Both problems are multiphysical and scale dependent. The size-effect is considered by the strain- and electric field-gradients in the flexoelecricity and higher-grade heat flux in the thermoelectricity. The variational principle is applied to de-rive the governing equations considered constitutive equations. The order of derivatives in governing equations is higher than in equations obtained from classical theory. The coupled governing partial differential equations (PDE) are satisfied in a local weak-form on small fic-titious subdomains with a simple test function. Physical fields are approximated by the mov-ing least-squares (MLS) scheme. Applying the spatial approximations in local integral equa-tions a system of algebraic is obtained for the nodal unknowns.

The stress imposed by ethanol to Saccharomyces cerevisiae cells are one of the most challenging limiting factors in industrial fuel-ethanol production. Consequently, the toxicity and tolerance to high ethanol concentrations has been the subject of extensive research, allowing the identification of several genes important for increasing the tolerance to this stress factor. However, most studies were performed with well characterized laboratory strains, and how the results obtained with these strains work in industrial strains remains unknown. In the present work we have tested three different strategies known to increase ethanol tolerance by laboratory strains in an industrial fuel-ethanol producing strain: overexpression of the TRP1 or MSN2 genes, or overexpression of a truncated version of the MSN2 gene. Our results show that the industrial CAT-1 strain tolerates up to 14% ethanol, and indeed the three strategies increased its tolerance to ethanol. When these strains were subjected to fermentations with high sugar content and cell-recycle, simulating the industrial conditions used in Brazilian distilleries, only the strain with overexpression of the truncated MSN2 gene showed improved fermentation performance, allowing the production of 16% ethanol from 33% of total reducing sugars present in sugarcane molasses. Our results highlight the importance of testing genetic modifications in industrial yeast strains under industrial conditions in order to improve the production of industrial fuel ethanol by S. cerevisiae.

Gastroenteritis cases associated with non-toxigenic strains of Vibrio parahaemolyticus have been reported in many countries, suggesting the contribution of novel virulence factors. One candidate is zonula occludens toxin (Zot), which increases the intestinal permeability by other bacteria. Recently we identified prophages belonging to the Inoviridae family encoding putative Zot-like toxins in Chilean strains. Based on this information we performed sequence-based analyses of these toxins, followed by phylogenetic and structural analyses using computational tools. Our results showed that Zots found in Chilean V. parahaemolyticus strains are grouped into three different phylogenetic clusters, sharing two conserved motifs (Walker A and B) in their N-terminal region. These motifs are also conserved in Zots from the human pathogens Vibrio cholerae, Neisseria meningitidis and Campylobacter concisus. Although Zots of V. parahaemolyticus do not possess the FCIGRL sequence responsible for the effects produced by V. cholerae, they do possess a conserved secondary structure within their C-terminal region with Zots proteins able to disrupt the intestinal barrier, which is interesting since it has been suggested that the structure and not the Zot sequence would be responsible for the biological effects. This preliminary study provides the basis to study the function of Zots found in V. parahaemolyticus on the intestinal barrier and their possible role as a virulence factor.

Terrestrial algae are the group of photosynthetic organisms, which can survive in extreme conditions. pH is one of the most important factor, influencing on distribution of algae, both in aquatic and terrestrial ecosystems. The influence of different pH levels on cell volume and other morphological characters of authentic and reference strains of Chlorella vulgaris, Bracteacoccus minor, Pseudoccomyxa simplex, Chlorococcum infusionum, and Vischeria magna were studied. Chlorella vulgaris and Pseudoccomyxa simplex were the most resistant species, retaining its morphology in range of pH 4-11,5. The change of pH towards acidic and alkaline levels caused the increase of volume of Pseudoccomixa simplex and Vischeria magna cells according to polynomial regression model. Volume of Chlorella vulgaris cells increased from low to high pH according to linear regression model. Changes of pH levels did not have a significant impact on volume of Bracteacoccus minor and Chlorococcum infusionum cells. Low and high levels of pH caused thickening of cell walls of Chlorococcum infusionum and increase of oil containing substances in Vischeria magna and Bracteacoccus minor cells. Our study revealed a high resistance of studied species to extreme level of pH, which allow recommend these strains for broader use in biotechnology and natures protection.

A striking aspect of COVID-19 is the difference in the outcome of the infection between different countries, and different ethnic groups within one country. We surveyed the literature on SARS-CoV-2 complemented with comparative publications on SARS-CoV and other coronaviruses to capture the current understanding of virus – host interactions including virus subtypes, transmission, zoonotic aspects, and potential host determinants.

Natural products have long played a major role in medicine and science. The garden snail Cornu aspersa is a rich source of biologically active natural substances which might be an important source for new drugs to treat human disease. Based on our previous studies seven fractions containing compounds with Mw <3 kDa, <10 kDa, <20 kDa, >20 kDa, and between 3-5 kDa, 5-10 kDa, and 10-30 kDa were purified from the mucus of C. aspersa and analyzed by tandem mass spectrometry (MALDI-TOF/TOF). Seventeen novel peptides with potential antibacterial activity have been identified by de novo MS/MS sequencing using tandem mass spectrometry. The different fractions were tested for antibacterial activity against Gram─ (Pseudomonas aureofaciens and Escherichia coli) and Gram+ (Brevibacillus laterosporus) bacterial strains as well anaerobic bacterium Clostridium perfringens. These results revealed that the peptide fractions exhibit a predominant antibacterial activity against B. laterosporus, the fraction with Mw 10 – 30 kDa against E. coli, another peptide fraction <20 kDa against P. aureofaciens, and the protein fraction >20 kDa against the bacterial strain C. perfringens. The discovery of new antimicrobial peptides (AMPs) from natural sources is of great importance for public health due to their effective antimicrobial activities and low resistance rates.

Pulmonary hypertension (PH) has a high mortality, and few treatment options. Adaptive immune mediators of PH in mice challenged with antigen/particulate matter (antigen/PM) has been the focus of our prior work. We identified key roles of type 2 and type 17 responses in C57BL/6 mice. Here, we focused on type 2 response related cytokines, specifically Resistin-like-molecule (RELM)α, a critical mediator of hypoxia-induced PH. Because of strain differences in the immune responses to type 2 stimuli, we compared C57BL/6J and BALB/c mice. A model of intraperitoneal antigen sensitization with subsequent, intranasal challenges with antigen/PM (ovalbumin and urban ambient PM2.5) or saline was used in C57BL/6 and BALB/c wild type or RELMα-/- mice. Vascular remodeling was assessed by histology, right ventricular (RV) pressure, RV weights and cytokines were quantified. Upon challenge with antigen/PM2.5, both C57BL/6 and BALB/c mice developed pulmonary vascular remodeling; these changes were more prominent in the C57BL/6 strain. Compared to wild type mice, RELMα-/- had significantly reduced pulmonary vascular remodeling in BALB/c, but not in C57BL/6 mice. RV weights, RV IL-33 and RV ST2-IL-33-receptor were significantly increased in BALB/c wild type mice, but not in BALB/c-RELMα-/- or in C57BL/6-wild type or C57BL/6-RELMα-/- mice. RV systolic pressures (RVSP) were higher in BALB/c compared to C57BL/6J mice, and RELMα-/- were not different from their respective wild type controls. In BALB/c mice, RELMα was a key contributor to antigen/PM2.5 induced pulmonary vascular remodeling, RV thickening and RV cytokine responses, highlighting the significance of the genetic background. The RELMα-/- animals demonstrated significantly decreased expression of RELMβ and RELM which makes these mice comparable to a situation where human RELMα levels would be significantly modified, as humans only have one RELM molecule.