Interaction of Sulforaphane with DNA and RNA

Sulforaphane (SFN) is an isothiocyanate found in cruciferous vegetables with anti-inflammatory, anti-oxidant and anti-cancer activities. However, the antioxidant and anticancer mechanism of sulforaphane is not well understood. In the present research, we reported binding modes, binding constants and stability of SFN–DNA and -RNA complexes by Fourier transform infrared (FTIR) and UV–Visible spectroscopic methods. Spectroscopic evidence showed DNA intercalation with some degree of groove binding. SFN binds minor and major grooves of DNA and backbone phosphate (PO₂), while RNA binding is through G, U, A bases with some degree of SFN–phosphate (PO₂) interaction. Overall binding constants were estimated to be K_(SFN–DNA)=3.01 (± 0.035)×10⁴ M^-1 and K_(SFN–RNA)= 6.63 (±0.042)×10³ M^-1. At high SFN concentration (SFN/RNA = 1/1), DNA conformation changed from B to A occurred, while RNA remained in A-family structure.     

Spatial and technological variability in the carbon footprint of durum wheat production in Iran

Purpose

The purpose of this study was to quantify the spatial and technological variability in life cycle greenhouse gas (GHG) emissions, also called the carbon footprint, of durum wheat production in Iran.

Methods

The calculations were based on information gathered from 90 farms, each with an area ranging from 1 to 150 ha (average 16 ha). The carbon footprint of durum wheat was calculated by quantifying the biogenic GHG emissions of carbon loss from soil and biomass, as well as the GHG emissions from fertilizer application and machinery use, irrigation, transportation, and production of inputs (e.g., fertilizers, seeds, and pesticides). We used Spearman’s rank correlation to quantify the relative influence of technological variability (in crop yields, fossil GHG emissions, and N₂O emissions from fertilizer application) and spatial variability (in biogenic GHG emissions) on the variation of the carbon footprint of durum wheat.

Results and discussion

The average carbon footprint of 1 kg of durum wheat produced was 1.6 kg CO₂-equivalents with a minimum of 0.8 kg and a maximum of 3.0 kg CO₂-equivalents. The correlation analysis showed that variation in crop yield and fertilizer application, representing technological variability, accounted for the majority of the variation in the carbon footprint, respectively 76 and 21%. Spatial variation in biogenic GHG emissions, mainly resulting from differences in natural soil carbon stocks, accounted for 3% of the variation in the carbon footprint. We also observed a non-linear relationship between the carbon footprint and the yield of durum wheat that featured a scaling factor of ?2/3. This indicates that the carbon footprint of durum wheat production (in kg CO₂-eq kg^?1) typically decreases by 67% with a 100% increase in yield (in kg ha^?1 year^?1).

Conclusions

Various sources of variability, including variation between locations and technologies, can influence the results of life cycle assessments. We demonstrated that technological variability exerts a relatively large influence on the carbon footprint of durum wheat produced in Iran with respect to spatial variability. To increase the durum wheat yield at farms with relatively large carbon footprints, technologies such as site-specific nutrient application, combined tillage, and mechanized irrigation techniques should be promoted.

     

Isolation and partial characterization of bacteria with potential antimicrobial activity from the Caspian Sea

Due to the constant increasing of bacterial resistance against known antibiotics, it is now necessary to find new sources of antimicrobials including the marine environment. The aim of this study was to evaluate antimicrobial activity of bacterial strains isolated from different coastal regions of the Caspian Sea and to provide phylogenetic analyses of antibiotic producing strains. Water samples collected from the Caspian Sea were serially diluted and plated on selective media. Isolates were tested against a panel of reference strains (Streptococcus pyogenes, Staphylococcus aureus, Escherichia coli, and Pseudomonas aeruginosa) by microbial antagonism and disc diffusion assay. Unweighted Pair Group Method with Arithmetic Mean (UPGMA) method was also employed to produce a phylogenetic tree based on 16S rDNA sequences. Amongst 162 isolates, 8 strains (4.93%) showed antibacterial activity. Isolated bacteria displayed more activity against gram-positive bacteria than gram-negative bacteria. Moreover, the 16S sequences obtained for the 8 selected strains were compared using a BLAST algorithm and allowed us to determine the strains genus as followed: Bacillus (RS28, RS54, RS56, RS82, RS116, and NS53), Brevundimonas (RS32), and Arthrobacter (NS25). The findings of the present study recommend that culturally marine bacteria collected from the Caspian Sea might be a potent source of novel bioactive compounds such as antibiotics.     

Analysis of Y-chromosomal short tandem repeat (STR) polymorphism in an Iranian Sadat population

The molecular genotyping of individuals and reconstruction of kinship through short and highly polymorphic DNA markers, so called short tandem repeats (STR), has become one of the important and efficient methods in anthropology studies and forensic science. Although many populations have been analyzed, no study has yet been carried out on Sadat populations who are putative descendents of Prophet Mohammad (peace be upon him). Polymorphisms of 6 Y-STR loci (DYS19, DYS385a/b, DYS389II, DYS390, DYS392, and DYS393) have been studied in an unrelated population of Sadat males. The aim of this study was to find possible similarities within Sadat males, resided in Iran. Among Sadat, DYS385b was proved to be the most polymorphic (GD = 0.8588), and DYS392 showed the lowest polymorphism (GD = 0.3527). In 50 samples, 45 different haplotypes were found, of which 39 haplotypes were unique. In the study, three samples had multi-allelic patterns. Haplotype diversity, in regard to these 7 markers was 0.9942.     

Netrin-1 protects the SH-SY5Y cells against amyloid beta neurotoxicity through NF-κB/Nrf2 dependent mechanism

Molecular Biology Reports - Many evidence confirms that amyloid beta 1–42 fragment (Aβ1–42) causes neuroinflammation, oxidative stress, and cell death, which are related to...     

The effect of sub-lethal exposure to copper and the time course of recovery in clean water on biochemical changes in juvenile fish (Acipenser persicus)

This study reports the 96-h LC₅₀ value and tissue copper (Cu) levels and biochemical changes in juvenile fish (Acipenser persicus) exposed to 0.026?mg/l ambient Cu for 1, 7 and 14?days. It then examined the recovery of the same parameters after placing the juvenile fish in clean water for a further period of 28?days. The intestine, kidney and gill Cu levels, plasma glucose, total protein, triglyceride, cortisol, triiodothyronine and thyroxine concentrations, liver protein contents, liver catalase, superoxide dismutase (SOD) and glutathione S-transferase activities were studied. The 96-h LC₅₀ value of Cu was 0.502?mg/l for juvenile A. persicus. The results indicate that Cu exposure produced significant accumulations of Cu in gills and kidney over the treatment time. Sublethal dose of Cu resulted in a short-term increase in plasma glucose, total protein and cortisol levels that decreased with time. After the 28-day recovery phase, there were significant differences in kidney Cu levels and triglyceride concentrations as well as SOD activities between recovery fish treatments and their control groups on day 42. The 28-day recovery phase caused significant decreases in total protein levels and SOD activities of Cu-exposed fish on day 42 compared to day 14. The results suggest that 28?days are insufficient for complete recovery to Cu exposure by juveniles and a longer period would be required for full recovery. Moreover, the study showed that the recovery phase following Cu exposure could change biochemical parameters to levels that are not close to those seen during exposure or control levels.     

Integrative analysis of DNA methylation and gene expression through machine learning identifies stomach cancer diagnostic and prognostic biomarkers

DNA methylation is an early event in tumorigenesis. Here, by integrative analysis of DNA methylation and gene expression and utilizing machine learning approaches, we introduced potential diagnostic and prognostic methylation signatures for stomach cancer. Differentially-methylated positions (DMPs) and differentially-expressed genes (DEGs) were identified using The Cancer Genome Atlas (TCGA) stomach adenocarcinoma (STAD) data. A total of 256 DMPs consisting of 140 and 116 hyper- and hypomethylated positions were identified between 443 tumour and 27 nontumour STAD samples. Gene expression analysis revealed a total of 2821 DEGs with 1247 upregulated and 1574 downregulated genes. By analysing the impact of cis and trans regulation of methylation on gene expression, a dominant negative correlation between methylation and expression was observed, while for trans regulation, in hypermethylated and hypomethylated genes, there was mainly a negative and positive correlation with gene expression, respectively. To find diagnostic biomarkers, we used 28 hypermethylated probes locating in the promoter of 27 downregulated genes. By implementing a feature selection approach, eight probes were selected and then used to build a support vector machine diagnostic model, which had an area under the curve of 0.99 and 0.97 in the training and validation (GSE30601 with 203 tumour and 94 nontumour samples) cohorts, respectively. Using 412 TCGA-STAD samples with both methylation and clinical data, we also identified four prognostic probes by implementing univariate and multivariate Cox regression analysis. In summary, our study introduced potential diagnostic and prognostic biomarkers for STAD, which demands further validation.     

Moderate O3/O2 therapy enhances enzymatic and non-enzymatic antioxidant in brain and cochlear that protects noise-induced hearing loss

Mitochondrial damage and oxidative stress are known to contribute to the pathogenesis of noise-induced hearing loss (NIHL). In this study, we examined the protective effect of O₂/O₃ mixture (ozone/oxygen) therapy against mitochondrial induced damage and oxidative stress by noise exposure in rat brain and cochlear. For this purpose, rats were divided into four groups: 1 – control group; 2 – noise-exposed group (100?dB); 3 – noise?+?O₂/O₃, and 4 – O₂/O₃ (30 µg/ml). After 14 d, animals were anesthetised. Rat brain and cochlear tissue were removed for evaluation of the histopathological damages, oxidative stress, and mitochondrial dysfunction in both tissues. Our findings indicated that noise caused pathological damage, oxidative stress, and mitochondrial dysfunction in rat brain and cochlear. Also, daily administration of an O₂/O₃ therapy (30 µg/ml intravenous) efficiently increased enzymatic and non-enzymatic antioxidant in brain and cochlear that this action led to inhibition of pathological damages, oxidative stress, reactive oxygen species formation, mitochondrial membrane potential (MMP) collapse, mitochondrial swelling, and cytochrome c release resulting from noise. These findings suggest that the moderate O₂/O₃ therapy enhances the capacity of enzymatic and non-enzymatic antioxidant in brain and cochlear that protects against NIHL.