Identification of novel mutations in SARS-COV-2 isolates from Turkey.

SARS-CoV-2 was first detected in the city of Wuhan, Hubei Province, China. In this study, we identified 11 unique mutations in viral SARS-COV-2 isolates from Turkey. Nine of them cause structural alterations in the S protein, nsp2, nsp3, nsp4 and nsp12 regions. The mutations identified here might have significant functional implications that need to be addressed in future studies in the context of vaccine engineering and therapeutic interventions. Moreover, transmission and phylogenetic analysis revealed multiple independent sources of introductions of SARS-CoV-2 into Turkey and a close relationship to the isolates from Saudi Arabia.

Genome Wide Identification and Comparative Analysis of the Serpin Gene Family in Brachypodium and Barley.

Serpins (serine protease inhibitors) constitute one of the largest and most widely distributed superfamilies of protease inhibitors and have been identified in nearly all organisms. To gain significant insights, a comprehensive in silico analysis of the serpin gene family was carried out in the model plant for temperate grasses Brachypodium distachyon and barley Hordeum vulgare using bioinformatic tools at the genome level for the first time. We identified a total of 27 BdSRPs and 25 HvSRP genes in Brachypodium and barley, respectively, showing an unexpectedly high gene number in these model plants. Gene structure, conserved motifs and phylogenetic comparisons of serpin genes supported the role of duplication events in the expansion and evolution of serpin gene family. Further, purifying selection pressure was found to be a main driving force in the evolution of serpin genes. Genome synteny analysis indicated that BdSRP genes were present in syntenic regions of barley, rice, sorghum and maize, suggesting that they evolved before the divergence of these species from common ancestor. The distinct expression pattern in specific tissues further suggested a specialization of functions during development and in plant defense. These results suggest that the LR serpins (serpins with Leu-Arg residues at P2-P1') identified here can be utilized as candidates for exploitation in disease resistance, pest control and preventing stress-induced cell death. Additionally, serpins were identified that could lead to further research aimed at validating and functionally characterizing the role of potential serpin genes from other plants.

An overview on red algae bioactive compounds and their pharmaceutical applications.

Objectives To review red algae bioactive compounds and their pharmaceutical applications. Content Seaweed sources are becoming attractive to be used in health and therapeutics. Among these red algae is the largest group containing bioactive compounds utilized in cosmetic, pharmaceutical, food industry, manure and various supplements in food formula. Various significant bioactive compounds such as polysaccharides (aginate, agar, and carrageenan), lipids and polyphenols, steroids, glycosides, flavanoids, tannins, saponins, alkaloids, triterpenoids, antheraquinones and cardiac glycosides have been reported in red algae. The red algae have rich nutritional components Different polysaccharides of red algae possess the antiviral potential namely agarans, carrageenan, alginate, fucan, laminaran and naviculan. Sulfated polysaccharides and carraginans of red algae are rich source of soluble fibers which can account for antitumor activities depending upon chemistry of various secondary metabolites and metabolism of cell line. Flavons-3-ols containing catechins from many red algae block the telomerase activity in colon cancer cells. Contraceptive agents were tested from red algae as a source for post-coital. Lectin of red algae showed pro-healing properties and anti-ulcerogenic activities. Carragenates from red algae also conferred a positive influence on diabetes. Red algae depicted a reducing effect on plasma lipids and obesity. Porphyran from red alga can act as anti-hyperlipidemic agent also reduces the apolipoprotein B100 via suppression of lipid synthesis in human liver. Summary The polyphenolic extracts of Laurencia undulate, Melanothamnus afaqhusainii and Solieria robusta extract show anti-inflammatory effects against multiple genera of devastating fungi. Antioxidants such as phlorotannins, ascorbic acids, tocopherols, carotenoids from red algae showed toxicity on some cancer cells without side effects. Red algae Laurencia nipponica was found insecticidal against mosquito larvae. Red algae fibers are very important in laxative and purgative activities. Gracilaria tenuistipitat resisted in agricultural lands polluted with cadmium and copper. Outlook In the recent decades biotechnological applications of red algae has been increased. Polysaccharides derived from red algae are important tool for formulation of drugs delivery system via nanotechnology.

Xanthophyll: Health benefits and therapeutic insights.

Xanthophylls constitute a major part of carotenoids in nature. They are an oxidized version of carotenoid. Xanthophyll has widely drawn scientists' attentions in terms of its functionality, bioavailability and diversity. An assortment of xanthophyll varieties includes lutein, zeaxanthin, ß-cryptoxanthin, capsanthin, astaxanthin, and fucoxanthin. Chemically, lutein and zeaxanthin are dipolar carotenoids with hydroxyl groups at both ends of their molecules that bestow hydrophilic properties to them. Hydrophilic affinity in lutein and zeaxanthin makes better bioavailability in reaction with singlet oxygen in water phase, whereas non-polar carotenoids have shown to have less efficiency in scavenging free radicals. Xanthophylls have been studied for their effects in a wide variety of diseases including neurologic, ophthalmologic, oral, allergic and immune diseases. This review highlights pharmaco-pharmaceutical applications of xanthophylls as well asits drug interactions with beta-carotene. Different types of xanthophylls have been shown to have neuroprotective effects. Fucoxanthin demonstrated potent antiplasmodial activity. Lutein and zeaxanthin prevent the progression of age related macular degeneration. They have also demonstrated promising effects on uveitis, retinitis pigmentosa, scleritis, cataracts, glaucoma, retinal ischemia and choroideremia. Astaxanthin showed to have skin protecting effects against ultraviolet light injury. Astaxanthin have anti-allergic activity against the contact dermatitis especially to treat the patients having adverse reactions induced by steroids. Astaxanthin has been reported to exert beneficial effects in preventing oral lichen planus and early stage cancers. ß-cryptoxanthin has been considered a good candidate for prevention of bone loss via osteoblastic bone formation and inhibiting osteoclastic bone resorption. There is also some concern that higher dose of xanthophylls may be linked to increased risk of skin cancer and gastric adenocarcinoma. However this increased risk was not statistically significant when adjusted for confounding factors. Further researches including clinical studies are needed to better evaluate the efficacy and safety of xanthophylls in prevention and treatment of different diseases.

In vitro antioxidant and anti-cancer activities and phytochemical analysis of Commelina benghalensis L. root extracts

Objective: To explore antioxidant potential, anti-cancer activity, and phytochemicals of Commelina benghalensis L. Methods: The roots of Commelina benghalensis were extracted in different solvents (methanol, ethanol, benzene, chloroform, n-hexane) with a range of polarity. Antioxidant activity was evaluated by reducing power assay, DPPH radical scavenging activity and phosphomolybdenum method, cytotoxicity by MTT assay, apoptotic and cell cycle analysis by flow cytometry, migratory and invasive potential by wound scratch assay and invasion assay, respectively, functional groups analysis by FT-IR spectroscopy and phytochemicals by aluminum chloride colorimetric and Folin-Ciocalteu methods. Results: The extracts showed worthy antioxidant potential. The chloroform extract demonstrated the most significant cytotoxic effect on MDA-MB-231 (breast cancer) cell line, induced apoptosis and reduced migratory and invasive potential of MDA-MB-231 cells. Methanol and ethanol extracts presented good yield of total phenolic and total flavonoid contents. The FTIR spectroscopic studies revealed different characteristic peak values with various functional compounds such as alkenes, alkanes, aliphatic amines, aromatics, alkyl halides, carboxylic acid, alcohols, ester, aldehydes and ketones. Conclusions: The results demonstrate the potential use of Commelina benghalensis as a good antioxidant with significant anti-cancer effect.

Expression analysis of the polyphenol oxidase gene in response to signaling molecules, herbivory and wounding in antisense transgenic tobacco plants.

KEY MESSAGE: We provide evidence that the expression of the PPO gene was significantly reduced in response to wounding, MeJ and herbivory in transgenic tobacco under wound-inducible OsRGLP2 promoter in an anti-sense orientation. ABSTRACT: Polyphenol oxidase (PPO) genes play an important role in plant defense mechanisms against biotic and abiotic stresses. In the present study, a 655 bp core sequence of the potato PPO gene was placed under the control of wound-inducible OsRGLP2 promoter in an anti-sense direction to evaluate its potential effects during biotic (Trialeurodes vaporariorum's infestation) and various abiotic (wounding, MeJ, ABA) stresses. Transcriptional profiling of PPO gene by real-time PCR (qRT-PCR) in transgenic tobacco revealed a significant suppression (3.5-fold) of PPO in response to wounding than control plants after 24 h. In response to MeJ at different concentrations (100 µM and 200 µM), the PPO expression was greatly down-regulated by 4.7-fold after 6 h at 100 µM MeJ, and a non-significant expression was observed with ABA treatment. Moreover, significant levels of PPO reduction (sixfolds) was found in whitefly feeding assay indicating that expression of potato PPO in an anti-sense orientation had down-regulated the PPO activity. This down-regulation of PPO by wounding, MeJ and whitefly infestation clearly links the specific expression of PPO in biotic and abiotic stresses. In the future, PPO gene suppression in transgenic plants using anti-sense potato PPO gene construct can be used to inhibit enzymatic browning in fruits and vegetables, e.g., potato.

Expression analysis of proteinase inhibitor-II under OsRGLP2 promoter in response to wounding and signaling molecules in transgenic Nicotiana benthamiana.

Proteinase inhibitor-II (PI-II) genes are important defense related genes that play critical regulatory roles in plant growth and development. In the present study, the expression of tomato PI-II gene was investigated under the control of a wound-inducible OsRGLP2 (Oryza sativa root germin like protein 2) promoter in transgenic tobacco plants after wounding, ABA and MeJA applications. Transcript level of target gene in transgenic plants was confirmed by quantitative real time PCR (qPCR). In response to ABA treatment at different concentrations, PI-II gene was strongly induced under OsRGLP2 promoter at higher concentration (100 µM), while considerable level of target gene expression was observed with MeJA application at 50 µM concentration. Upon wounding, relatively high PI-II gene expression was observed after 36-h treatment. Correspondingly, high GUS activity was detected at 36 h with histochemical assay and microscopic analysis in the vascular regions of leaves, stem and roots in wounded transgenic plants. This inducibility of PI-II gene by wounding, ABA and MeJA indirectly indicates its role in plant defense mechanism against biotic and abiotic stresses. Moreover, it was also suggested that ABA and MeJA dependent signaling pathways are involved in stimulation of PI-II gene. To the best of our knowledge, this is the first report describing the induction of PI-II gene under the regulation of OsRGLP2 promoter under stress conditions. The results of present research are useful for potential role of PI-II gene to improve stress tolerance in transgenic crops. Thus, efficacy of this gene can potentially be exploited to test the responses of different plants to various environmental stresses.

Rumex dentatus Inhibits Cell Proliferation, Arrests Cell Cycle, and Induces Apoptosis in MDA-MB-231 Cells through Suppression of the NF-κB Pathway.

Background:Rumex dentatus, commonly known as tooth docked, is widely used in traditional system of medicines. Although it is well reported for its biological activities and medicinal value, only few studies have been carried out to assess its anticancer potential. Purpose: This study seeks to evaluate the anticancer activity of leaf extracts of R. dentatus against breast cancer MDA-MB-231 cell line, a triple negative human breast cancer cell line with invasive properties and to identify the molecular targets underlying its mechanism of action. Methods: Cytotoxicity of plant extracts was determined against breast cancer cells, using the MTT assay. Flow cytometry was performed to analyze the changes in cell cycle and apoptotic effect, if any. Cells were also studied for their wound healing and invasive potential as well as for Western blotting of apoptotic genes and nuclear factor-kappaB (NF-κB) pathway. Results: The results revealed that R. dentatus methanol (RM) and chloroform (RC) extracts of R. dentatus had the highest inhibition of cell proliferation in a concentration- and time-dependent manner. This inhibitory effect was found to be linked to arrest of cell cycle at the G0/G1 phase, along with induction of apoptosis and accumulation in the sub-G1 phase. Moreover, it was shown that both RM and RC inhibited the proliferation of the malignant cells and induced apoptosis by repressing the activation of NF-κB and its subsequent transcripts, Bcl-xl, Bcl-2, Cyclin D1, survivin, and XIAP. Apoptosis was also confirmed in the cells as suggested by caspase-3 detection. RM and RC also abrogated IκBa phosphorylation in the malignant cells as well as reduced the invasive and migratory capabilities of these cells. Conclusion: Our findings suggest that the methanol and chloroform extracts of R. dentatus may have anti-cancer compounds that are potentially useful in the treatment of human breast cancer.

Structural and functional characteristics of plant proteinase inhibitor-II (PI-II) family.

Plant proteinase inhibitor-II (PI-II) proteins are one of the promising defensive proteins that helped the plants to resist against different kinds of unfavorable conditions. Different roles for PI-II have been suggested such as regulation of endogenous proteases, modulation of plant growth and developmental processes and mediating stress responses. The basic knowledge on genetic and molecular diversity of these proteins has provided significant insight into their gene structure and evolutionary relationships in various members of this family. Phylogenetic comparisons of these family genes in different plants suggested that the high rate of retention of gene duplication and inhibitory domain multiplication may have resulted in the expansion and functional diversification of these proteins. Currently, a large number of transgenic plants expressing PI-II genes are being developed for enhancing the defensive capabilities against insects, bacteria and pathogenic fungi. Much emphasis is yet to be given to exploit this ever expanding repertoire of genes for improving abiotic stress resistance in transgenic crops. This review presents an overview about the current knowledge on PI-II family genes, their multifunctional role in plant defense and physiology with their potential applications in biotechnology.

Computational analysis of atpB gene promoter from different Pakistani apple varieties.

Apple is the fourth most important fruit crop grown in temperate areas of the world belongs to the family Rosaceae. In the present study, the promoter (∼1000bp) region of atpB gene was used to evaluate the genetic diversity and phylogeny of six local apple varieties. atpB gene is one of the large chloroplastic region which encodes ß-subunit of ATP synthase and previously it had been used largely in phylogenetic studies. During the present study, atpB promoter was amplified, sequenced and analyzed using various bioinformatics tools including Place Signal Scan, MEGA6 and BLASTn. During the phylogenetic analysis, obtained phylogram divided the studied varieties into two clusters revealing the monophyletic origin of studied apple varieties. Pairwise distance revealed moderate genetic diversity that ranges from 0.047-0.170 with an average of 0.101. While identifying different cis-acting elements present in the atpB promoter region, results exhibited the occurrence of 56 common and 20 unique cis-regulatory elements among studied varieties. The identified cis-acting regulatory elements were mapped as well. It was observed that Kala Kulu has the highest unique features with reference to the availability of cis-acting elements. Moreover, the possible functions of all regulatory elements present on the promoter sequence of atpB gene were predicted based on already reported information regarding their in vivo role.