Analysis of the molecular variation between and within cultivated and wild Pistacia species using AFLPs

Knowledge of pistachio genetic diversity is necessary for the formulation of appropriate management strategies for the conservation of these species. We analysed amplified fragment length polymorphisms in a total of 216 pistachio accessions, which included seven populations from three wild species (Pistacia vera, Pistacia khinjuk and Pistacia atlantica subsp. kurdica) and most of the important cultivars from Iran, together with some foreign cultivars. High levels of genetic diversity were detected within the Iranian cultivars, and they showed a clear separation from foreign cultivars, as revealed by unweighted pair group method with arithmetic averaging and supported by analysis of molecular variance. The lowest amount of polymorphism was observed in P. atlantica subsp. kurdica, which showed the lowest number of total bands as compared to the other species. This revealed strong genetic erosion of P. atlantica subsp. kurdica, which reflected a severe decline in habitat and over-exploitation. Based on these findings, strategies are proposed for the genetic conservation and management of pistachio species and cultivars.     

Vibrio cholerae O139 persists in Dhaka,Bangladesh since 1993

BackgroundAfter a multi-country Asian outbreak of cholera due to Vibrio cholerae serogroup O139 which started in 1992, it is rarely detected from any country in Asia and has not been detected from patients in Africa.Methodology/Principal findingsWe extracted surveillance data from the Dhaka and Matlab Hospitals of International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b) to review trends in isolation of Vibrio cholerae O139 in Bangladesh. Data from the Dhaka Hospital is a 2% sample of > 100,000 diarrhoeal patients treated annually. Data from the Matlab Hospital includes all diarrhoeal patients who hail from the villages included in the Matlab Health and Demographic Surveillance System. Vibrio cholerae O139 was first isolated in Dhaka in 1993 and had been isolated every year since then except for a gap between 2005 and 2008. An average of thirteen isolates was detected annually from the Dhaka Hospital during the last ten years, yielding an estimated 650 cases annually at this hospital. During the last ten years, cases due to serogroup O139 represented 0.47% of all cholera cases; the others being due to serogroup O1. No cases with serogroup O139 were identified at Matlab since 2006. Clinical signs and symptoms of cholera due to serogroup O139 were similar to cases due to serogroup O1 though more of the O139 cases were not dehydrated. Most isolates of O139 remained sensitive to tetracycline, ciprofloxacin, and azithromycin, but they became resistant to erythromycin starting in 2009.Conclusions/SignificanceCholera due to Vibrio cholerae serogroup O139 continues to cause typical cholera in Dhaka, Bangladesh.     

Buckyballs conjugated with nucleic acid sequences identifies microorganisms in live cell assays

Background

Rapid identification of bacteria can play an important role at the point of care, evaluating the health of the ecosystem, and discovering spatiotemporal distributions of a bacterial community. We introduce a method for rapid identification of bacteria in live cell assays based on cargo delivery of a nucleic acid sequence and demonstrate how a mixed culture can be differentiated using a simple microfluidic system.

Methods

C60 Buckyballs are functionalized with nucleic acid sequences and a fluorescent reporter to show that a diversity of microorganisms can be detected and identified in live cell assays. The nucleic acid complexes include an RNA detector, targeting a species-specific sequence in the 16S rRNA, and a complementary DNA with an attached fluorescent reporter. As a result, each bacterium can be detected and visualized at a specific emission frequency through fluorescence microscopy.

Results

The C60 probe complexes can detect and identify a diversity of microorganisms that include gram-position and negative bacteria, yeast, and fungi. More specifically, nucleic-acid probes are designed to identify mixed cultures of Bacillus subtilis and Streptococcus sanguinis, or Bacillus subtilis and Pseudomonas aeruginosa. The efficiency, cross talk, and accuracy for the C60 probe complexes are reported. Finally, to demonstrate that mixed cultures can be separated, a microfluidic system is designed that connects a single source-well to multiple sinks wells, where chemo-attractants are placed in the sink wells. The microfluidic system allows for differentiating a mixed culture.

Conclusions

The technology allows profiling of bacteria composition, at a very low cost, for field studies and point of care.

     

Effect of exposure to extremely low electro-magnetic field during prenatal period on mice spleen

Total body weight of newborns, the volume of spleen, and the number of megakaryocytes decreased following the exposure to ELF-MF (6 x 10(-3) T and 50 Hz) at 1-5, 6-10, 11-15, and 16-20 days of pregnancy of mice. The complete period of gestation was sensitive to ELF-MF exposure; the initial days were more prone to exposure. The results suggest that the use of ELF-MF producing instruments should be limited during gestation.     

RANTES gene mRNA expression and its -403 G/A promoter polymorphism in coronary artery disease

Objective

Increased RANTES expression has been described to have a role in atherosclerosis plaque formation. Functional polymorphisms within RANTES promoter region have shown association with increased risk of coronary atherosclerosis (CAD). The aim of this study was to examine the RANTES mRNA expression in patients with CAD compared to patients without CAD and its association with RANTES − 403 G/A polymorphism in an Iranian population.

Methods

The study was performed on 319 patients who underwent coronary artery angiography and patients with > 50% stenosis in vessels considered as case groups (CAD+) N = 191 and normal vessels group as control (CAD−) N = 128. In each group 20 patients were examined for RANTES mRNA expression.RANTES mRNA expression was examined using quantitative real-time PCR. Genotyping of − 403 polymorphism was performed using PCR-RFLP technique.

Results

We found that RANTES mRNA expression was increased to 1.37 fold in CAD patients compared to the controls but the difference was not statistically significant. Also comparing the RANTES mRNA expression in patients with different RANTES − 403 G/A polymorphism showed that in patients carrying AA genotype RANTES mRNA expression was increased to 1.74 fold compared to patients carrying GG genotype and to 1.51 fold compared to patients carrying GA genotype. No significant difference for allele and genotype frequencies of RANTES − 403 polymorphism was found between cases and controls.

Conclusion

More studies on larger number of samples are required to further evaluate role of RANTES in pathogenesis of CAD.     

Bioavailability and Concentration of Heavy Metals in the Sediments and Leaves of Grey Mangrove, <Emphasis Type="BoldItalic">Avicennia marina</Emphasis> (Forsk.) Vierh,in Sirik Azini Creek,Iran

The concentration and bioavailability of Ni, Cu, Cd, Zn, and Pb in the sediments and leaves of grey mangrove, Avicennia marina, were studied throughout Sirik Azini creek (Iran) with a view to determine heavy metals bioavailability, and two methods were used. Results show that Zn and Ni had the highest concentrations in the sediments, while Cd and Cu were found to have the lowest concentrations in the sediments. Compared to the mean concentrations of heavy metals in sedimentary rock (shales), Zn and Cu showed lower concentration, possibly indicating that the origin of these heavy metals is natural. A geo-accumulation index (I _geo) was used to determine the degree of contamination in the sediments. I _geo values for Zn, Cu, Pb, and Ni showed that there is no pollution from these metals in the study area. As heavy metal concentrations in leaves were higher than the bioavailable fraction of metals in sediments, it follows that bioconcentration factors (leaf/bioavailable sediment) for some metals were higher than 1.     

Comparing multiple ChIP-sequencing experiments

New high-throughput sequencing technologies can generate millions of short sequences in a single experiment. As the size of the data increases, comparison of multiple experiments on different cell lines under different experimental conditions becomes a big challenge. In this paper, we investigate ways to compare multiple ChIP-sequencing experiments. We specifically studied epigenetic regulation of breast cancer and the effect of estrogen using 50 ChIP-sequencing data from Illumina Genome Analyzer II. First, we evaluate the correlation among different experiments focusing on the total number of reads in transcribed and promoter regions of the genome. Then, we adopt the method that is used to identify the most stable genes in RT-PCR experiments to understand background signal across all of the experiments and to identify the most variable transcribed and promoter regions of the genome. We observed that the most variable genes for transcribed regions and promoter regions are very distinct. Gene ontology and function enrichment analysis on these most variable genes demonstrate the biological relevance of the results. In this study, we present a method that can effectively select differential regions of the genome based on protein-binding profiles over multiple experiments using real data points without any normalization among the samples.