Evaluation of genetic diversity among some Iranian wild asparagus populations using morphological characteristics and RAPD markers

An evaluation of genetic diversity in 39 wild asparagus populations was carried out using morphological and RAPD markers. A combination of morphological traits and random RAPD primers was used to examine the level of genetic variation and polymorphisms among the populations. A factor analysis using Ward's method on mean values of morphological characteristics indicated seven main factors resulting in four groups. Analysis of polymorphic bands using Jaccard's similarity coefficient indicated that genetic similarity ranged between 0.71 and 0.29. At a similarity level of 0.64, the populations were divided in three sub-clusters, containing 34, four and one populations, respectively. Significant regression associations were found between 21 morphological characteristics and 18 RAPD markers, revealing some informative markers associated with some traits. The highest R² was related to 18 RAPD markers associated with gender (53.5%) that among them BA-04₂₀₀₀ had a maximum R². The results showed that Iranian wild asparagus with its high levels of genetic variation could be considered as a valuable gene pool for future asparagus breeding programs. Furthermore, it could be inferred that morphological characteristics and RAPD markers are suitable tools to discriminate asparagus populations for the evaluation of genetic diversity.     

Anaesthetic efficacy of eugenol on iridescent shark,Pangasius hypophthalmus (Sauvage, 1878) in different size classes

Anaesthetic efficacy of eugenol was investigated on iridescent shark, Pangasius hypophthalmus. Fish (2, 5, 10 and 20 g) subjected to 20–200 mg L^?1 eugenol and behavioural response as well as induction and recovery times were recorded. Induction and recovery times were significantly affected by eugenol concentration as well as fish weight (P < 0.05). Generally, 27–300 s after exposure to 20–200 mg L^?1 eugenol, iridescent sharks reached stage 3 anaesthesia (suitable for general handling). Fish entered stage 4 anaesthesia (suitable for surgery and blood sampling) over 54–710 s exposure to such concentrations. Recovery time was 109–600 s in all weight classes as well as eugenol concentrations. Mortality (44–100%) was only observed in 2 g fish when subjected to 110–170 mg L^?1 eugenol. This study, for the first time, showed behavioural response of iridescent shark to anaesthesia as well as effectiveness of eugenol as anaesthetic in this important aquaculture‐ornamental species. According to the models obtained in this study, minimum eugenol concentrations to induce anaesthesia over less than 3 min were 53.8–81.5 mg L^?1 in 2–20 g fish. Likewise, maximum eugenol concentrations in which fish recovered over less than 5 min were 65.9–105.8 mg L^?1 in 2–20 g fish.     

Microsatellite and mitochondrial DNA analyses reveal no genetic difference between two pufferfish species torafugu <Emphasis Type="Italic">Takifugu rubripes</Emphasis> and karasu <Emphasis Type="Italic">T. chinensis</Emphasis>

It has been reported that the nucleotide sequences of the mitochondrial and nuclear genes of Takifugu pufferfish torafugu T. rubripes and karasu T. chinensis show 99–100% sequence identity, indicating a very close relationship between the two species. To further investigate this genetic relationship, we compared genetic variation at four microsatellite loci and at the mitochondrial control region (CR) (561 bp) between groups of T. rubripes caught at two locations [TrG, caught in the Genkai Sea off Tsushima Island in 2003 (n = 50); TrS, caught in the Suwo Sea off Kita-Kyushu in 2008 (n = 50)] and T. chinensis caught at one location (TcK, caught off the east coast of Korea in 2004; n = 50). Analyses using microsatellite loci showed that genetic diversity index values of the TrG, TrS and TcK groups were 0.9505, 0.9350 and 0.9335, respectively, while values of genetic distance and genetic differentiation between TrG and TcK (0.0543 and 0.0189, respectively) were smaller than those between TrG and TrS (0.0857 and 0.0194, respectively). Analyses using CR for the same specimens showed that genetic distances were consistent with those obtained using microsatellite loci. These results, together with our previous observations, suggest that T. rubripes and T. chinensis are very closely related and possibly can be regarded as the same species.     

Metagenomic analysis using 16S ribosomal RNA genes of a bacterial community in an urban stream,the Tama River,Tokyo

In an effort to determine genus- or species-level taxonomic profiles and diversity of bacterial consortia in the Tama River around urban Tokyo, next-generation sequencing technology targeting a 16S ribosomal RNA (rRNA) gene amplicon was employed. Metagenomic analysis performed by an Ion Personal Genome Machine after sequentially filtering samples through 5-, 0.8- and 0.2-μm filters yielded 1.48 Gb of 16S sequences (average 2.38 M reads/sample). The results indicated that half of the bacterial sequences belonged to Proteobacteria, followed by Bacteroidetes, Actinobacteria and Cyanobacteria. Flavobacterium (Bacteroidetes), possibly including a potential fish pathogen, was the most numerous genera in the Tama River metagenome, and accounted for?~?16% of assigned 16S reads, followed by Mycobacterium. Other dominant bacterial genera including Zoogloea, Sediminibacterium, Hyphomicrobium, Sphingopyxis, Thiothrix and Lysobacter, were thought to be associated with waste water and sludge. MiSeq metagenomic analysis revealed that environmental factors, particularly water temperature, influenced the bacterial composition throughout the year, with a strong negative correlation observed for Proteobacteria and a positive correlation for Bacteroidetes. In terms of bacterial genera, Flavobacterium was positively correlated with temperature, while Polaromonas, Pseudomonas and Bradyrhizobium were negatively correlated with this, suggesting dynamic change in the free-living bacterial population throughout the year and versatile adaptation strategies in relation to environmental factors.     

Simulating long-term effect of Hyrcanian forest loss on phosphorus loading at the sub-watershed level

Conversion of forest land to farmland in the Hyrcanian forest of northern Iran increases the nutrient input, especially the phosphorus(P) nutrient, thus impacting the water quality. Modeling the effect of forest loss on surface water quality provides valuable information for forest management. This study predicts the future impacts of forest loss between 2010 and 2040 on P loading in the Tajan River watershed at the sub-watershed level. To understand drivers of the land cover, we used Land Change Modeler(LCM) combining with the Soil Water Assessment Tool(SWAT) model to simulate the impacts of land use change on P loading. We characterized priority management areas for locating comprehensive and cost-effective management practices at the sub-watershed level. Results show that agricultural expansion has led to an intense deforestation. During the future period 2010–2040, forest area is expected to decrease by 34,739 hm~2. And the areas of pasture and agriculture are expected to increase by 7668 and 27,071 hm~2, respectively. In most sub-watersheds, P pollution will be intensified with the increase in deforestation by the year 2040. And the P concentration is expected to increase from 0.08 to 2.30 mg/L in all of sub-watersheds by the year 2040. It should be noted that the phosphorous concentration exceeds the American Public Health Association′s water quality standard of 0.2 mg/L for P in drinking water in both current and future scenarios in the Tajan River watershed. Only 30% of sub-watersheds will comply with the water quality standards by the year 2040. The finding of the present study highlights the importance of conserving forest area to maintain a stable water quality.     

Nutritional and Functional Properties of Two Dried Brown Seaweeds Sirophysalis trinodis and Polycladia myrica

Sirophysalis trinodis and Polycladia myrica, two brown seaweeds present on the southeast coast of Iran, were evaluated for their nutritional and functional properties after drying. Fourier transform-infrared spectroscopy (FTIR) analysis of crude polysaccharides revealed the characteristic absorption bands of phenol, O–H, C–H, C–O–S, C–O, C=O, C–H groups, and β-glycosidic linkages from cellulose, with the sulfate contents estimated as 4.89 ± 0.11% and 6.96 ± 0.05% of SO₄^?2. Results of nutritional profiles revealed all of the essential amino acids, especially methionine, isoleucine, leucine, lysine, threonine, valine, phenyl alanine, and arginine. In addition, important fatty acids such as linolenic acid, palmitic acid, and oleic acid were found in high amounts. The other nutritional components present in high amounts were proline and minerals such as calcium, magnesium, iron, manganese, copper, and zinc. The antibacterial activity was weak, but the result of antioxidant activities (hydroxyl and superoxide radicals scavenging and ferrous-ion chelating ability) of crude polysaccharides was considerable. In general, the findings of this study recommend that S. trinodis and P. myrica dried seaweeds have a potent nutritional value and might be used as a valuable source of nutrient supplements for humans and animals.     

Photooxidation Properties of Photosensitizer/Direct Dye Patterned Polyester/Cotton Fabrics

Towards the goal of developing anti-infective textiles based on a photodynamic inactivation mechanism, here we present the design, dyeing procedure, characterization, substrate photooxidation studies, and antibacterial efficacy of methylene blue-dyed polyester fabrics, termed MB-polyester. Dye-uptake and apparent K/S (absorption and scattering coefficient) values as a function of MB concentration % (o.w.f) were determined, and were found to correlate. Photooxidation studies employing the model substrate 1,5-dihydroxynaphthalene (1,5-DHN) revealed that the MB-polyester fabrics were able to generate singlet oxygen in an illumination time-dependent manner. Antibacterial efficacy was evaluated against Staphylococcus aureus (ATCC-29213), with our best results achieving a 99.89 % (~3 log units) reduction in Colony-Forming Units (CFU)/mL after only 30 min illumination (Xenon lamp, 3500 mW/cm², 420–780 nm). On the basis of these results with MB-polyester, we subsequently designed patterned dual-dyed polyester/cotton fabrics, wherein an alternating pattern of MBdyed polyester was combined with direct dyes-dyed cotton, and showed that their ability to sensitize singlet oxygen (¹O²) in the photooxidation reaction of 1,5-DHN was maintained. Taken together, these findings suggest that MB is a suitable photosensitizer (PS) against S. aureus for the practical development of low-cost polyester-based antimicrobial textiles, and can potentially be used in the production of diverse form-patterned textiles that possess a photodynamic antimicrobial inactivation mechanism.     

Association between p53?Codon 72 (Arg72Pro) Polymorphism and Primary Open-Angle Glaucoma in Iranian Patients

Background: Glaucomatous neuropathy is a type of cell death due to apoptosis. The p53 gene is one of the regulatory genes of apoptosis. Recently, the association between the p53 gene encoding for proline at codon 72 and primary open-angle glaucoma (POAG) has been studied in some ethnic groups. This study is the first association analysis of POAG and p53 codon 72 polymorphism in Iranian patients. Methods: A cohort of 65 unrelated patients with POAG (age range from 12-62 years, mean ± SD of 40.16 ± 17.51 years) and 65 unrelated control subjects (without glaucoma, age range of 14-63 years, mean ± SD of 35.64 ± 13.61 years) were selected. In Iranian POAG patients and normal healthy controls, the p53 codon 72 polymorphism in exon 4 was amplified using polymerase chain reaction. The amplified DNA fragments were digested with the BstUI restriction enzyme, and the digestion patterns were used to identify the alleles for the polymorphic site. Results: Comparisons revealed significant differences in allele and genotype frequencies of Pro72Arg between POAG patients and control group. A higher risk of POAG was associated with allele Pro (OR = 2.1, 95% CI = 1.2–3.4) and genotype Pro/Pro (OR = 3.9, 95% CI = 0.13-12.7). Conclusion: The p53 Pro72 allele was more frequent in Iranian POAG patients than in the control group (P<0.05). The present findings show that the individuals with the Pro/Pro genotype may be more likely to develop POAG. However, additional studies are necessary to confirm this association. Key Words: Primary open-angle glaucoma (POAG), Glaucoma, p53, Codon 72, Iran     

Simultaneous Analysis of Multidrug Resistance 1(MDR1) C3435T,G2677T/A,and C1236T Genotypes in Hamadan City Population,West of Iran

Background: One of the limitations in the treatment of common diseases such as cancer chemotherapy is development of multidrug resistance (MDR). Polymorphisms could alter the expression level of MDR1 gene, which plays an important role in MDR. In this research, the frequency of C3435T, C1236T, and G2677T/A polymorphisms of MDR1 gene was investigated in a large group of population from Hamadan city to provide a sample data resource. Methods: Peripheral blood (2 ml) was taken, and DNA extraction was carried out. Multiplexed mutagenically separated PCR, which was followed by polyacrylamide gel electrophoresis and silver staining, was applied to detect the mentioned polymorphisms in 935 individuals. Sequencing performed for confirmation of gel electrophoresis resulted in 10 random cases. In total, alleles and genotypes of 933 persons (776 women and 157 men) were determined. Results: The most frequent alleles of the polymorphisms were: 3435T, C1236, and G2677. The most frequent genotypes were: 3435C/T, 1236C/T, and 2677G/A, and their concurrent presence was also found as the most frequent simultaneous genotypes. There was not any meaningful difference among the prevalence of these genotypes in groups of men and women. Conclusion: Our results were close to those of other studies performed in Iran and compared to the other ethnic groups, which showed more similarity to Asian peoples than Europeans. As an aspect of personalized medicine, it could be used by chemotherapists to improve the routine methods of cancer treatment.Key Words: Gene polymorphism, Multi-drug resistance, Neoplasm     

Association of tcdA+/tcdB+ Clostridium difficile Genotype with Emergence of Multidrug-Resistant Strains Conferring Metronidazole Resistant Phenotype

Background:

Reduced susceptibility of Clostridium difficile to antibiotics is problematic in clinical settings. There is new evidence indicating the cotransfer of toxin-encoding genes and conjugative transposons encoding resistance to antibiotics among different C. difficile strains. To analyze this association, in the current study, we evaluated the frequency of toxigenic C. difficile among the strains with different multidrug-resistant (MDR) profiles in Iran.

Methods:

Antimicrobial susceptibility patterns and minimal inhibitory concentrations (MIC) of the isolates were determined against metronidazole, imipenem, ceftazidime, amikacin, and ciprofloxacin by agar dilution method. The association of the resistance profiles and toxigenicity of the strains were studied by PCR targeting tcdA and tcdB genes.

Results:

Among 86 characterized strains, the highest and lowest resistance rates were related to ciprofloxacin (97%) and metronidazole (5%), respectively. The frequency of resistance to other antibiotics was as follow: imipenem (48%), ceftazidime (76%), and amikacin (76.5%). Among the resistant strains, double drug resistance and MDR phenotypes were detected in the frequencies of 10.4% and 66.2%, respectively. All of the metronidazole-resistant strains belonged to tcdA ⁺/tcdB ⁺ genotype with triple or quintuple drug resistance phenotypes. MIC₅₀ and MIC₉₀ for this antibiotic was equally ≤ 8 μg/ml.

Conclusion:

These results proposed the association of tcdA ⁺/tcdB ⁺ genotype of C. difficile and the emergence of resistance strains to broad-spectrum antibiotics and metronidazole. Key Words: Multidrug resistance, Clostridium difficile, Metronidazole