Cloning and sequencing of IS1086, an Alcaligenes eutrophus insertion element related to IS30 and IS4351.

A new insertion sequence (IS), designated IS1086, was isolated from Alcaligenes eutrophus CH34 by being trapped in plasmid pJV240, which contains the Bacillus subtilis sacB and sacR genes. The 1,106-bp IS1086 element contains partially matched (22 of 28 bp) terminal-inverted repeats and a long open reading frame. Hybridization data suggest the presence of one copy of IS1086 in the strain CH34 heavy-metal resistance plasmid pMOL28 and at least two copies in its chromosome. Analysis of the IS1086 nucleotide sequence revealed striking homology with two other IS elements, IS30 and IS4351, suggesting that they are three close members in a family of phylogenetically related insertion sequences. One open reading frame of the Spiroplasma citri phage SpV1-R8A2 B was also found to be related to this IS family but to a lesser extent. Comparison of the G+C contents of IS30 and IS1086 revealed that they conform to their respective hosts (46 versus 50% for IS30 and Escherichia coli and 64.5% for IS1086 and A. eutrophus). The pressure on the AT/GC ratio led to a very different codon usage in these two closely related IS elements. Results suggesting that IS1086 transposition might be activated by some forms of stress are discussed.     

How the Nucleus and Mitochondria Communicate in Energy Production During Stress: Nuclear MtATP6, an Early-Stress Responsive Gene, Regulates the Mitochondrial F1F0-ATP Synthase Complex

A small number of stress-responsive genes, such as those of the mitochondrial F₁F₀-ATP synthase complex, are encoded by both the nucleus and mitochondria. The regulatory mechanism of these joint products is mysterious. The expression of 6-kDa subunit (MtATP6), a relatively uncharacterized nucleus-encoded subunit of F₀ part, was measured during salinity stress in salt-tolerant and salt-sensitive cultivated wheat genotypes, as well as in the wild wheat genotypes, Triticum and Aegilops using qRT-PCR. The MtATP6 expression was suddenly induced 3 h after NaCl treatment in all genotypes, indicating an early inducible stress-responsive behavior. Promoter analysis showed that the MtATP6 promoter includes cis-acting elements such as ABRE, MYC, MYB, GTLs, and W-boxes, suggesting a role for this gene in abscisic acid-mediated signaling, energy metabolism, and stress response. It seems that 6-kDa subunit, as an early response gene and nuclear regulatory factor, translocates to mitochondria and completes the F₁F₀-ATP synthase complex to enhance ATP production and maintain ion homeostasis under stress conditions. These communications between nucleus and mitochondria are required for inducing mitochondrial responses to stress pathways. Dual targeting of 6-kDa subunit may comprise as a mean of inter-organelle communication and save energy for the cell. Interestingly, MtATP6 showed higher and longer expression in the salt-tolerant wheat and the wild genotypes compared to the salt-sensitive genotype. Apparently, salt-sensitive genotypes have lower ATP production efficiency and weaker energy management than wild genotypes; a stress tolerance mechanism that has not been transferred to cultivated genotypes.     

Assessment of Heavy Metal Pollution and Human Health Risks Assessment in Soils Around an Industrial Zone in Neyshabur,Iran

Biological Trace Element Research - Heavy metal pollution of soils in industrial zones continues to attract attention because of its potential human health risks. The present research is an attempt...     

Occurrence and Characterization of the Bacterial Spot Pathogen Xanthomonas euvesicatoria on Pepper in Iran

We report in this study for the first time the occurrence of bacterial spot of pepper in Iran and both phenotypic and genetic characterization of its causal agent, Xanthomonas euvesicatoria. Pepper plants grown in 15 of 30 surveyed private gardens and commercial fields were infected by the pathogen in Marand County, East Azerbaijan Province, north‐western Iran. The obtained strains of X. euvesicatoria had different amylolytic and pectolytic activities compared with those reported for this species elsewhere. Pathogenicity tests showed that strains isolated from diseased pepper are able to infect tomato, in addition to pepper. Host range of the pathogen was assessed on eight annual plant species including crops and weeds by measuring the population dynamics. The host range assessment showed that in addition to pepper and tomato, known hosts of X. euvesicatoria, the Iranian strains were able to colonize a number of new hosts such as nightshade and common bean. In contrast, none of them were able to build up their population on cowpea, eggplant, bindweed and zucchini. All X. euvesicatoria strains obtained in this study were sensitive to copper sulphate and streptomycin at concentrations higher than 20 and 50 mg/l, respectively. Phylogenetic analyses of the strains using the sequences of gyrB and hrpB genes confirmed their species as X. euvesicatoria. Given a direct commercial trade of fresh solanaceous vegetables between Iran and Turkey, it is hypothesized that the pathogen entered north‐western Iran from eastern parts of Turkey through infected plant materials. Finally, the role of prevention – based on the use of healthy planting materials and resistant and/or tolerant plant varieties – to contain the potential disease epidemics is discussed.     

An Investigation on Strains of Clavibacter michiganensis subsp. michiganensis in North and North West of Iran

Tomato bacterial canker disease was first reported from Urmiyeh in West Azerbaijan province in Iran. The disease causes lesion (canker), wilting and dryness of infected plants, leaf and fruit spots and the decline of the whole plant. Out of 102 isolates obtained from the fields in the major tomato producing areas of understudy regions, 98 were found Gram positive, yellow‐pigmented isolates, identified as Clavibacter michiganensis subsp. michiganensis based on the morphological and biochemical characteristics described in previous studies. Among these strains, 64 were virulent and 34 showed poor virulence. A strain of Cmm (NCPPB382) was used as a check (standard) in all steps of this study. DNA fingerprinting with repetitive‐sequence‐based PCR (rep‐PCR) (BOX primer) carried out among 11 representative strains (eight strains from West Azerbaijan, two from Golestan and one as standard). The most virulent strain was chosen as representative in each location. Dendrograms were prepared using NTSYS‐pc version 2/o2e software, unweighted pair group with arithmetic average method and simple matching similarity coefficient. According to the site of cut‐off line, three groups (clusters) with 82/5% similarity and six groups with 55% similarity were separated based on biochemical and SDS‐PAGE data, and rep‐PCR reactions respectively. Low similarity among groups (55%) can be explained as high genetic diversity among the strains. One strain of west Azerbaijan and the strains of Golestan, clustered in the same group suggesting that they may have been originated from a common source. Other strains of west Azerbaijan were clustered into different groups including II, III, IV, V and VI, suggesting the possibility of occurrence of different populations in a geographical region.     

MicroRNA Profiling in Intraocular Medulloepitheliomas

Purpose

To study the differential expression of microRNA (miRNA) profiles between intraocular medulloepithelioma (ME) and normal control tissue (CT).

Material and Methods

Total RNA was extracted from formalin fixed paraffin embedded (FFPE) intraocular ME (n=7) and from age matched ciliary body controls (n=8). The clinical history and phenotype was recorded. MiRNA profiles were determined using the Affymetrix GeneChip miRNA Arrays analyzed using expression console 1.3 software. Validation of significantly dysregulated miRNA was confimed by quantitaive real-time PCR. The web-based DNA Intelligent Analysis (DIANA)-miRPath v2.0 was used to perform enrichment analysis of differentially expressed (DE) miRNA gene targets in Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway.

Results

The pathologic evaluation revealed one benign (benign non-teratoid, n=1) and six malignant tumors (malignant teratoid, n=2; malignant non-teratoid, n = 4). A total of 88 miRNAs were upregulated and 43 miRNAs were downregulated significantly (P<0.05) in the tumor specimens. Many of these significantly dysregulated miRNAs were known to play various roles in carcinogenesis and tumor behavior. RT-PCR validated three significantly upregulated miRNAs and three significantly downregulated miRNAs namely miR-217, miR-216a, miR-216b, miR-146a, miR-509-3p and miR-211. Many DE miRNAs that were significant in ME tumors showed dysregulation in retinoblastoma, glioblastoma, and precursor, normal and reactive human cartilage. Enriched pathway analysis suggested a significant association of upregulated miRNAs with 15 pathways involved in prion disease and several types of cancer. The pathways involving significantly downregulated miRNAs included the toll-like receptor (TLR) (p<4.36E-16) and Nuclear Factor kappa B (NF-κB) signaling pathways (p<9.00E-06).

Conclusions

We report significantly dysregulated miRNAs in intraocular ME tumors, which exhibited abnormal profiles in other cancers as well such as retinoblastoma and glioblastoma. Pathway analysis of all dysregulated miRNAs shared commonalities with other cancer pathways.     

Procurement and Supply Management System for MDR-TB in Nigeria: Are the Early Warning Targets for Drug Stock Outs and Over Stock of Drugs Being Achieved?

Background

The World Health Organisation (WHO) introduced the twelve early warning indicators for monitoring and evaluating drug Procurement and Supply management (PSM) systems, intended to prevent drug stock-outs and overstocking. Nigeria- one of the high Multi Drug Resistant Tuberculosis (MDR-TB) burden countries, scaled-up treatment in 2012 with the concurrent implementation of a PSM system.

Method

We evaluated how well this system functioned using the WHO indicators, including all seven MDR-TB treatment centres in the country that were functional throughout 2013.

Results

The quantity of MDR-TB drugs ordered for 2013 matched the annual forecast and all central orders placed during the year were delivered in full and on time. Drug consumption was 81%–106% of the quantity allocated for routine consumption. Timely submission of complete inventory reports ranged from 86–100%, late submissions being 5–15 days late. Forty to 71% of treatment centres placed a drug order when stock was below the minimum level of three months. The proportion of drug orders received at the treatment centres in full and on time ranged from 29–80%, late orders being 1–19 days late.

Conclusion

The PSM was found to be performing well in terms of forecasting and procurement of MDR-TB drugs, but there were shortcomings in drug distribution, reporting at treatment centre level and in drug order placements. Despite these gaps, there were no stock outs. These findings indicate that where it matters most, namely ensuring that no drug stock outs affect patient management, the PSM system is effective. Addressing the observed shortcomings will help to strengthen the existing PSM system in anticipation of a growing MDR-TB case burden in the country.