RNA-seq analysis reveals narrow differential gene expression in MEP and MVA pathways responsible for phytochemical divergence in extreme genotypes of Thymus daenensis Celak.

BACKGROUND: Here, we investigated the underlying transcriptional-level evidence behind phytochemical differences between two metabolically extreme genotypes of Thymus daenensis. The genotypes 'Zagheh-11' (thymol/carvacrol type, poor in essential oil [EO] [2.9%] but rich in triterpenic acids) and 'Malayer-21' (thymol type and rich in EO [3.8%]) were selected from an ongoing breeding program and then clonally propagated for further experimental use. MATERIALS AND METHODS: GC-MS, GC-FID, and HPLC-PDA were utilized to monitor the fluctuation of secondary metabolites at four phenological stages (vegetative, bud burst, early, and full-flowering stages). The highest phytochemical divergence was observed at early flowering stage. Both genotypes were subjected to mRNA sequencing (approximately 100 million paired reads) at the aforementioned stage. The expression patterns of four key genes involved in the biosynthesis of terpenoids were also validated using qRT-PCR. RESULTS: Carvacrol content in 'Zagheh-11' (26.13%) was approximately 23 times higher than 'Malayer-21' (1.12%). Reciprocally, about 10% higher thymol was found in 'Malayer-21' (62.15%). Moreover, the concentrations of three major triterpenic acids in 'Zagheh-11' were approximately as twice as those found in 'Malayer-21'. Transcriptome analysis revealed a total of 1840 unigenes that were differentially expressed, including terpene synthases, cytochrome P450, and terpenoid backbone genes. Several differentially expressed transcription factors (such as MYB, bZIP, HB-HD-ZIP, and WRKY families) were also identified. These results suggest that an active cytosolic mevalonate (MVA) pathway may be linked to higher levels of sesquiterpenes, triterpenic acids, and carvacrol in 'Zagheh-11'. The chloroplastic pathway of methyl erythritol phosphate (MEP) may have also contributed to a higher accumulation of thymol in Malayer-21. Indeed, 'Zagheh-11' showed higher expression of certain genes (HMGR, CYP71D180, ß-amyrin 28-monooxygenase, and sesquiterpene synthases) in the MVA pathway, while some genes in the MEP pathway (including DXR, ispG, and γ-terpinene synthase) were distinctly expressed in Malayer-21. Future efforts in metabolic engineering of MVA/MEP pathways may benefit from these findings to produce increased levels of desired secondary metabolites at commercial scale.

Optimizing an efficient ensemble approach for high-quality de novo transcriptome assembly of Thymus daenensis.

Non-erroneous and well-optimized transcriptome assembly is a crucial prerequisite for authentic downstream analyses. Each de novo assembler has its own algorithm-dependent pros and cons to handle the assembly issues and should be specifically tested for each dataset. Here, we examined efficiency of seven state-of-art assemblers on ~ 30 Gb data obtained from mRNA-sequencing of Thymus daenensis. In an ensemble workflow, combining the outputs of different assemblers associated with an additional redundancy-reducing step could generate an optimized outcome in terms of completeness, annotatability, and ORF richness. Based on the normalized scores of 16 benchmarking metrics, EvidentialGene, BinPacker, Trinity, rnaSPAdes, CAP3, IDBA-trans, and Velvet-Oases performed better, respectively. EvidentialGene, as the best assembler, totally produced 316,786 transcripts, of which 235,730 (74%) were predicted to have a unique protein hit (on uniref100), and also half of its transcripts contained an ORF. The total number of unique BLAST hits for EvidentialGene was approximately three times greater than that of the worst assembler (Velvet-Oases). EvidentialGene could even capture 17% and 7% more average BLAST hits than BinPacker and Trinity. Although BinPacker and CAP3 produced longer transcripts, the EvidentialGene showed a higher collinearity between transcript size and ORF length. Compared with the other programs, EvidentialGene yielded a higher number of optimal transcript sets, further full-length transcripts, and lower possible misassemblies. Our finding corroborates that in non-model species, relying on a single assembler may not give an entirely satisfactory result. Therefore, this study proposes an ensemble approach of accompanying EvidentialGene pipelines to acquire a superior assembly for T. daenensis.

Modeling and optimizing concentration of exogenous application of γ-aminobutyric acid on NaCl-stressed pineapple mint (Mentha suaveolens) using response surface methodology: an investigation into secondary metabolites and physiological parameters.

Salinity, a severe worldwide issue, compromises the economic production of medicinal plants including mints and causes drug-yield decline. γ-Aminobutyric acid (GABA) is a tolerance-inducing signaling bio-molecule in various plant physiological processes. Pineapple mint (Mentha suaveolens Ehrh.) is a valuable medicinal herb with an exhilarating scent of citrus fruit. Piperitenone oxide is the major bioactive constituent of its essential oil, having significant demand by pharmaceutical industries. Nonetheless, modeling and optimizing the effective concentration of GABA remain within twin foci of interest. Therefore, a two factor-five level (NaCl 0-150 mM and GABA 0-2.4 mM) central composite design was conducted to model and optimize drug yield and physiological responses of M. suaveolens. Based on the design of experiments (DoE) approach, different linear, quadratic, cubic, and quartic models were assigned to the response variables. Change trends of shoot and root dry weights followed a simple linear model, whereas sophisticated models (i.e., multiple polynomial regression) were fitted to the other traits. NaCl stress inevitably reduced root and shoot dry weight, piperitenone oxide content, relative water content, pigments content, and maximum quantum yield of PSII. However, content of malondialdehyde (MDA) and total flavonoid, and DPPH radical scavenging activity were increased under salinity. Under severe NaCl stress (150 mM), the essential oil content (0.53%) was increased three times in comparison with control (0.18%). Optimization analysis demonstrated that the highest amount of essential oil (0.6%) and piperitenone oxide (81%) as a drug yield-determining component would be achievable by application of 0.1-0.2 mM GABA under 100 mM NaCl. The highest dry weight of root and shoot was predicted to be achieved at 2.4 mM GABA. Overall, extremely severe NaCl stress (i.e., more than 100 mM) in which a sharp drop in yield components value was observed seemed to be out of M. suaveolens salinity tolerance range. Hence, it is rationale to compensate the decrease of drug yield by foliar application of a dilute GABA solution (i.e., 0.1-0.2 mM) under 100 mM NaCl stress or lower levels.

The interaction mechanism of plasma iron transport protein transferrin with nanoparticles.

In the biological systems, exposure to nanoparticles (NPs) can cause complicated interactions with proteins, the formation of protein corona and structural changes to proteins. These changes depend not only on NP physicochemical properties, but also on the intrinsic stability of protein molecules. Although, the formation of protein corona on the surface of NPs and the underlying mechanisms have been fully explored in various studies, no comprehensive review has discussed the direct biochemical and biophysical interactions between NPs and blood proteins, particularly transferrin. In this review, we first discussed the interaction of NPs with proteins to comprehend the effects of physicochemical properties of NPs on protein structure. We then overviewed the transferrin structure and its direct interaction with NPs to explore transferrin stability and its iron ion (Fe3+) release behavior. Afterwards, we surveyed the various biological functions of transferrin, such as Fe3+ binding, receptor binding, antibacterial activity, growth, differentiation, and coagulation, followed by the application of transferrin-modified NPs in the development of drug delivery systems for cancer therapy. We believe that this study can provide useful insight into the design and development of bioconjugates containing NP-transferrin for potential biomedical applications.

Zinc Application Mitigates Copper Toxicity by Regulating Cu Uptake, Activity of Antioxidant Enzymes, and Improving Physiological Characteristics in Summer Squash.

Zinc (Zn) and copper (Cu) are essential micronutrients for the plant's growth, development, and metabolism, but in high concentrations, the elements disrupt normal metabolic processes. The present study investigated the effects of different concentrations (added to a Hogland-based solution) of zinc (control, 5, 10 mg L-1 ZnSO4) and copper (control, 0.1, 0.2 mg L-1 CuSO4) on the growth characteristics and biochemical indices of summer squash (Cucurbita pepo L.). Compared with control, a single application of Cu or Zn at both concentrations significantly declined fruit yield, growth traits, pigments content, and high content of these minerals and values of stress-related indices. Increased Cu concentration in the nutritional solutions reduced the activity of ascorbate peroxidase (APX) and guaiacol peroxidase (GPX). Copper at high concentrations intensified ROS production, aggravated oxidative stresses, and decreased the plant yield and productivity. Nonetheless, combining Cu and Zn could alleviate stress intensity by boosting antioxidant enzymes, redox regulation, and a resultant diminishment in the content of H2O2, proline, malondialdehyde, and minerals. The obtained results corroborate that the co-application of zinc in Cu-contaminated areas can improve the plant's economic yield and physiological parameters by hindering copper toxicity and enhancing the photosynthetic capacity.

Emerging role of mesenchymal stromal cells (MSCs)-derived exosome in neurodegeneration-associated conditions: a groundbreaking cell-free approach.

Accumulating proofs signify that pleiotropic effects of mesenchymal stromal cells (MSCs) are not allied to their differentiation competencies but rather are mediated mainly by the releases of soluble paracrine mediators, making them a reasonable therapeutic option to enable damaged tissue repair. Due to their unique immunomodulatory and regenerative attributes, the MSC-derived exosomes hold great potential to treat neurodegeneration-associated neurological diseases. Exosome treatment circumvents drawbacks regarding the direct administration of MSCs, such as tumor formation or reduced infiltration and migration to brain tissue. Noteworthy, MSCs-derived exosomes can cross the blood-brain barrier (BBB) and then efficiently deliver their cargo (e.g., protein, miRNAs, lipid, and mRNA) to damaged brain tissue. These biomolecules influence various biological processes (e.g., survival, proliferation, migration, etc.) in neurons, oligodendrocytes, and astrocytes. Various studies have shown that the systemic or local administration of MSCs-derived exosome could lead to the favored outcome in animals with neurodegeneration-associated disease mainly by supporting BBB integrity, eliciting pro-angiogenic effects, attenuating neuroinflammation, and promoting neurogenesis in vivo. In the present review, we will deliver an overview of the therapeutic benefits of MSCs-derived exosome therapy to ameliorate the pathological symptoms of acute and chronic neurodegenerative disease. Also, the underlying mechanism behind these favored effects has been elucidated.

Introducing Three New Fruit-Scented Mints to Farmlands: Insights on Drug Yield, Essential-Oil Quality, and Antioxidant Properties.

Mint species are one of the most traded medicinal plants with a wide array of applications in the food, pharmaceutical, and perfumery industries. Here, a field experiment based on completely randomized block design (RCBD) aimed to compare drug yield, antioxidant properties, and essential-oil (EO) quality of three newly introduced mints (i.e., ginger mint, pineapple mint, and grapefruit mint) with a chiefly cultivated one (i.e., peppermint). The results manifested that dry-weight yield and EO yield of grapefruit mint (310 g/m2 and 5.18 g/m2, respectively) was approximately 2 times more than that of others. The highest EO content (i.e., 3.12%, v/w)) was obtained from the ginger mint; however, there were no significant differences among the other three mints. The highest total flavonoids content and 2,2-diphenyl-1-picrylhydrazyl (DPPH) scavenging activity of both methanolic and ethanolic extracts were found in pineapple and grapefruit mint. Methanolic extract of ginger mint yielded the highest total polyphenol content, whereas the ethanolic extract of pineapple mint showed the highest total polyphenol content. According to mean comparisons, the EO of ginger mint exhibited the highest antioxidant activity (EC50 value = 2.23 µL/mL), while EO of peppermint showed the lowest antioxidant activity (EC50 value = 48.23 µL/mL). Gas chromatography analysis identified four EO types among these mints: (i) grapefruit mint EO rich in linalool (51.7%) and linalyl acetate (28.38%); (ii) ginger mint EO rich in linalool (59.16%); (iii) pineapple mint EO rich in piperitone oxide (77.65%); and (iv) peppermint EO rich in menthol (35.65%). The findings of the present study provide new insights into the cultivation of preferable mints possessing desired characteristics for food and drug industries.

Natural diversity in fatty acids profiles and antioxidant properties of sumac fruits (Rhus coriaria L.): Selection of preferable populations for food industries.

The current study screened the oil content, fatty acids profile, and antioxidant properties of twelve Iranian sumac fruit accessions. The oil contents were variable among the investigated populations (ranging from 5.15 to 16.70%). Oleic acid (32.3-47.41%), palmitic acid (18.90-36.29%), and linoleic acid (10.31-35.39%) were the predominant fatty acids in the oil samples. According to principal component and cluster analysis, sumac germplasms were categorized into three groups: i.e., group I (five populations rich in linoleic acid), group II (four populations rich in oleic acid), group III (three populations rich in palmitic acid). The highest fruits weight, oil percentage, and linoleic acid content was obtained from Arasbaran population. Arasbaran population possessed the highest ∑PUSFA (i.e, 34.53%) and ∑UNSFA: ∑SFA ratio. Meanwhile, Paveh population possessed the highest antioxidant attributes. Such variabilities provide the possibility of using elite populations containing a high ratio of unsaturated fatty acids and antioxidant compounds in the food industry.

Chronic scrotal hyperthermia induces azoospermia and severe damage to testicular tissue in mice.

Scrotal hyperthermia leads to altered spermatogenesis due to heat-related oxidative stress. One of the main causes of infertility in men is oxidative stress, which refers to an imbalance in the levels of reactive oxygen species (ROS) and antioxidants. Therefore, this study aimed to evaluate the effects of chronic scrotal hyperthermia on testicular tissue structure, sperm parameters, and oxidative stress in adult mice. Thirty adult NMRI male mice were divided into three groups: Control (n = 10), Sham (n = 10), and Hyperthermia (n = 10). At the end of the study animals were sacrificed for evaluations of biochemical, cellular and histological analysis. The Hyperthermia group revealed a significant reduction in sperm count and weight of testis when compared to the control and sham groups. Also, succinate dehydrogenase (SDH) activity, ROS, ATP production, glutathione disulfide (GSH), tiols metabolism and stereological parameters in the hyperthermia group showed a significant reduction compared to the control and sham groups. Our results also revealed that scrotal hyperthermia significantly increases ROS production, mitochondrial membrane permeability (MMP), malondialdehyde (MDA), oxidized glutathione (GSSG) and apoptotic cells in testicular tissue in the hyperthermia groups in comparison with the control and sham groups. Overall, our result indicated that chronic scrotal hyperthermia causes complete spermatogenic arrest, probably mainly throughout the induction of oxidative stress.

Iranian Society of Cardiac Surgeons COVID-19 task force version II, restarting elective surgeries.

Given the nature of heart disease and the importance of continuing heart surgery during the pandemic and its aftermath and in order to provide adequate safety for the surgical team and achieve the desired result for patients, as well as the optimal use of ICU beds, the medical team, blood, blood products, and personal protective equipment, it is essential to change the usual approach during the pandemic. There are still a lot of evidences and experiences needed to produce the perfect protocol. Some centers may have a special program for their centers during this period of epidemics that can be respected and performed. Generally, in pandemic conditions, the use of non-surgical approaches is preferred if similar outcomes can be obtained.

Effects of exogenous application of citrulline on prolonged water stress damages in hyssop (Hyssopus officinalis L.): Antioxidant activity, biochemical indices, and essential oils profile.

This study examined the effects of exogenous citrulline (control, 1 and 2 mM) and water availability (100%, 50% and 25% WA) on antioxidant attributes and essential oil constituents of Hyssopus officinalis L. in two successive harvests. Hyssop tolerantly responded to water deficiency by well-promoted antioxidant enzymes (i.e., superoxide dismutase, and catalase), strong DPPH-scavenging activity, and increasing polyphenols; however, the essential oil content was negatively reduced by water stress. External citrulline further increased the activity of antioxidant enzymes. Citrulline application at 2 mM under severe water stress could also improve essential oil (EO) content in the first and second harvests by about 15 and 30%, respectively. Furthermore, under severe drought, citrulline at 2 mM could obtain the highest yield of isopinocamphone (47%) as the main component of EO. The results showed the high potential of this novel applied metabolite agent to be used in a well-fulfilled production of this medicinal plant.

Betanin purification from red beetroots and evaluation of its anti-oxidant and anti-inflammatory activity on LPS-activated microglial cells.

Microglial activation can release free radicals and various pro-inflammatory cytokines, which implicates the progress of a neurodegenerative disease. Therefore suppression of microglial activation can be an appropriate strategy for combating neurodegenerative diseases. Betanin is a red food dye that acts as free radical scavenger and can be a promising candidate for this purpose. In this study, purification of betanin from red beetroots was carried out by normal phase colum chromatography, yielding 500 mg of betanin from 100 g of red beetroot. The purified betanin was evaluated by TLC, UV-visible, HPLC, ESI-MASS, FT-IR spectroscopy. Investigation on the inhibitory effect of betanin on activated microglia was performed using primary microglial culture. The results showed that betanin significantly inhibited lipopolysaccharide induced microglial function including the production of nitric oxide free radicals, reactive oxygen species, tumor necrosis factor-alpha (TNF-α), interleukin-6 (IL-6) and interleukin-1 beta (IL-1ß). Moreover, betanin modulated mitochondrial membrane potential, lysosomal membrane permeabilization and adenosine triphosphate. We further investigated the interaction of betanin with TNF-α, IL-6 and Nitric oxide synthase (iNOS or NOS2) using in silico molecular docking analysis. The docking results demonstrated that betanin have significant negative binding energy against active sites of TNF-α, IL-6 and iNOS.

Interaction of iron nanoparticles with nervous system: an in vitro study.

Nanoparticles (NPs) are one of the interesting and widely studying issues mainly because of their particular physico-chemical features and broad applications in the field of biomedical sciences, such as diagnosis and drug delivery. In this study, the interaction of iron nanoparticles (Fe-NPs) with Tau protein and PC12 cell, as potential nervous system models, was investigated with a range of techniques including dynamic light scattering, intrinsic fluorescence spectroscopy, circular dichroism, [(3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyl-tetrazolium-bromid] assay, and acridine orange/ethidium bromide (AO/EB) dual staining method. An inverse correlation between Stern and Volmer constant (KSV) and temperature indicated a probable static quenching mechanism occurred between Tau protein and Fe-NPs. The number of binding site (n = 0.86) showed that there is almost one binding site of Fe-NP per protein. The negative values of ∆H (-53.21 kJ/mol) and T∆S (-42.44 kJ/mol) revealed that Fe-NPs interacts with Tau protein with dominate role of hydrogen bonds and van der Waals interactions and this interaction was spontaneous (∆G = -10.77 kJ/mol). Also, Fe-NPs stabilized the random coil structure of Tau protein. Moreover, Fe-NPs reduced PC12 cells viability by fragmentation of DNA in an apoptotic manner. In conclusion, induced conformational changes of Tau protein and cytotoxicity of PC12 cells by Fe-NP were revealed to be in a concentration and time-dependent manner.

Bivalent flagellin immunotherapy protects mice against Pseudomonas aeruginosa infections in both acute pneumonia and burn wound models.

Pseudomonas aeruginosa infections are a serious challenge to therapy because of the complex pathogenesis and paucity of new effective antibiotics, thus renewing interest in antibody-based therapeutic strategies. Immunotherapy strategies typically target selected virulence factors that are expressed by the majority of clinical strains of P. aeruginosa, particularly because virulence factors mediate infection. Type a and b flagellins (flagellin a+b) of P. aeruginosa are acute virulence factors that play a major role in the establishment of infection. Here we evaluate the protective efficacy of antibodies raised against "flagellin a+b" in both acute pneumonia and burn models. A combination strategy using antibodies against "flagellin a+b" provided greater protection against cell invasion and enhanced opsono-phagocytosis and decreased motility of P. aeruginosa strains, compared to strategies using antibodies against a single flagellin. Antibodies against "flagellin a+b"-protected mice infected with P. aeruginosa strains significantly reduced bacterial dissemination from the site of infection to the liver and spleen. Passive immunization with antibodies against "flagellin a+b" led to an efficacious protection against P. aeruginosa infection in both acute pneumonia and burn models.

Impact of Angiotensin-converting enzyme inhibitors and Angiotensin receptor blockers on mortality of coronary artery bypass grafting.

BACKGROUND: There is controversy over the potential benefits/harms of the usage of angiotensin-converting enzyme inhibitors (ACEIs) or angiotensin receptor blockers (ARBs) as regards the postoperative mortality of coronary artery bypass grafting (CABG). This study investigates the correlation between the in-hospital mortality of CABG and the preoperative administration of ACEI/ARB. METHODS: Out of 10055 consecutive patients with isolated CABG from 2006 to 2009, 4664 (46.38%) patients received preoperative ACEI/ARB. Data were gathered from the Cardiac Surgery Registry of Tehran Heart Center. In-hospital mortality was defined as death within the same admission for surgery. Adjusted for confounders, multivariable logistic regression models were used to evaluate the impact of preoperative ACEI/ARB therapy on in-hospital death. RESULTS: The mean age of the patients was 60.04 ± 9.51 years and 7364 (73.23%) were male. Eighty-seven (0.86%) patients expired within 30 days. Multivariate analysis revealed that the administration of ACEI/ARB significantly protected against in-hospital deaths inasmuch as there were 33 (0.70%) vs. 54 (1.0%) deaths in the ACEI/ARB positive and negative groups, respectively (OR: 0.628; p value = 0.09). Patients without ACEI/ARB were more likely to have a higher global ejection fraction. CONCLUSION: Preoperative ACEI usage in patients undergoing CABG can be associated with decreased in-hospital mortality. Large-scale randomized clinical trials are suggested.