The RGG domain in the C-terminus of the DEAD box helicases Dbp2 and Ded1 is necessary for G-quadruplex destabilization

The identification of G-quadruplex (G4) binding proteins and insights into their mechanism of action are important for understanding the regulatory functions of G4 structures. Here, we performed an unbiased affinity-purification assay coupled with mass spectrometry and identified 30 putative G4 binding proteins from the fission yeast Schizosaccharomyces pombe. Gene ontology analysis of the molecular functions enriched in this pull-down assay included mRNA binding, RNA helicase activity, and translation regulator activity. We focused this study on three of the identified proteins that possessed putative arginine-glycine-glycine (RGG) domains, namely the Stm1 homolog Oga1 and the DEAD box RNA helicases Dbp2 and Ded1. We found that Oga1, Dbp2, and Ded1 bound to both DNA and RNA G4s in vitro. Both Dbp2 and Ded1 bound to G4 structures through the RGG domain located in the C-terminal region of the helicases, and point mutations in this domain weakened the G4 binding properties of the helicases. Dbp2 and Ded1 destabilized less thermostable G4 RNA and DNA structures, and this ability was independent of ATP but dependent on the RGG domain. Our study provides the first evidence that the RGG motifs in DEAD box helicases are necessary for both G4 binding and G4 destabilization.     

Genetic structure of Chrysanthemum genotypes from Iran assessed by AFLP markers and phenotypic traits

Chrysanthemum is popular worldwide as cut flower, potted plant and perennial garden plant. This study used amplified fragment length polymorphism and phenotypic traits to assess genetic diversity and population structure in Chrysanthemum. Results for the phenotypic traits of ray floret number, tubular floret number, flower number, pedicel length, leaflet number on pedicel and days to visible flower bud had high level (i.e., >30 %) evaluations for genotypic coefficient of variation and phenotypic coefficient of variation; thus, heritability for various phenotypic traits ranged from 45.30 to 94.55 %. Phenotypic data clustered the genotypes into four separate groups. Twenty-five primer combinations were used for molecular analysis. On average, each primer combination produced 83.96 polymorphic DNA bands, ranging from 33 to 122 bands. Polymorphic percentage (99.3 %), polymorphism information content (0.43) and Shannon’s information index (0.45) evaluated high levels of genetic variation in the tested genotypes. The Neighbor-Joining (NJ) method grouped genotypes into six clusters, which were in part confirmed by principal coordinate analysis. A Bayesian structure analysis identified four clusters, in which 30 individuals were maintained within the admixed clusters. Results from this study provide appropriate information applicable to designing effective breeding programs and other analyses associated with future studies of Chrysanthemum.     

Metronidazole aryloxy,carboxy and azole derivatives: Synthesis,anti-tumor activity,QSAR, molecular docking and dynamics studies

A series of novel metronidazole aryloxy, carboxy and azole derivatives has been synthesized and their cytotoxic activities on three cancer cell lines were evaluated by MTT assay. Compounds 4m, 4l and 4d showed the most potent cytotoxic activity (IC₅₀s?less than?100?µg/mL). Apoptosis was also detected for these compounds by flow cytometry. Docking studies were performed in order to propose the probable target protein. In the next step, molecular dynamics simulation was carried out on the proposed target protein, focal adhesion kinase (FAK, PDB code: 2ETM), bound to compound 4m. As, 4m showed a potent cytotoxic activity and an acceptable apoptotic effect, it can be a potential anticancer candidate that may work through inhibition of FAK.     

QTLs mapping of physiological traits related to salt tolerance in young rice seedlings

Oryza sativa L. F₂ population and F_2:3 derived from a cross between salt tolerance cv. Tarommahali and salt sensitive cv. Khazar were used in this study. A linkage map based on F₂ population was constructed (74 SSR markers on 192 individuals), which covered a total of 1231.50 cM with an average two locus interval of 19.83 cM. Two QTLs related to Na⁺/K⁺ ratio were found on chromosome 3 and 6. qDM-3 and qDM-8 (for dry mass of shoot) are major QTLs with very large effects explained 20.90 and 17.72 % of the total phenotypic variance, respectively. Major locus for DM (qDM-3) was bracketed by RM1022 — RM6283 spread over 13.6 cM on chromosome 3. Major part of the variability for standard tolerance ranking (STR) was explained by the qSTR-6 flanked by RM3727 — RM340 on chromosome 6, which exhibited phenotypic variance of 17.25 % and peak likelihood ratio (LR) of 17.51. The length of this QTL is 8.8 cM and identification of any tightly linked markers in this region will serve as a candidate gene for fine-mapping. qSTR-3 overlapped with qNA-3 and qNAK-3. The qSTR-3 may contain a new major gene for salt stress tolerance at seedling stage in rice. Major QTLs identified in this paper, after fine-mapping, could be used for marker assisted selection.     

Effect of different muscle contraction mode on the expression of Myostatin,IGF-1, and PGC-1 alpha family members in human Vastus Lateralis muscle

Molecular Biology Reports - Muscle contraction stimulates a transient change of myogenic factors, partly related to the mode of contractions. Here, we assessed the response of IGF-1Ea, IGF-1Eb,...     

Green synthesis of selenium nanoparticles using Rosmarinus officinalis and investigated their antimicrobial activity

BioMetals - The interest of many has been attracted by plant-mediated synthesizing procedures for nanoparticles since they provide certain qualities including being cost-effective, quick, and...     

Superior adaptation of aerobic rice under drought stress in Iran and validation test of linked SSR markers to major QTLs by MLM analysis across two years

Molecular Biology Reports - Drought is one of the biggest challenges for rice (Oryza sativa L.) production in rainfed areas. Developing “aerobic rice” cultivars could be a valuable...     

In Vivo Occupancy of Mitochondrial Single-Stranded DNA Binding Protein Supports the Strand Displacement Mode of DNA Replication

Mitochondrial DNA (mtDNA) encodes for proteins required for oxidative phosphorylation, and mutations affecting the genome have been linked to a number of diseases as well as the natural ageing process in mammals. Human mtDNA is replicated by a molecular machinery that is distinct from the nuclear replisome, but there is still no consensus on the exact mode of mtDNA replication. We here demonstrate that the mitochondrial single-stranded DNA binding protein (mtSSB) directs origin specific initiation of mtDNA replication. MtSSB covers the parental heavy strand, which is displaced during mtDNA replication. MtSSB blocks primer synthesis on the displaced strand and restricts initiation of light-strand mtDNA synthesis to the specific origin of light-strand DNA synthesis (OriL). The in vivo occupancy profile of mtSSB displays a distinct pattern, with the highest levels of mtSSB close to the mitochondrial control region and with a gradual decline towards OriL. The pattern correlates with the replication products expected for the strand displacement mode of mtDNA synthesis, lending strong in vivo support for this debated model for mitochondrial DNA replication.     

Inflammatory,antioxidant and glycemic status to different mode of high-intensity training in type 2 diabetes mellitus

Molecular Biology Reports - Exercise has traditionally been used and prescribed as an effective and suitable way to treat type 2 diabetics Mellitus (T2DM). In this regard, we compared inflammatory,...