Identification of novel bacterial species capable of degrading dalapon using 16S rRNA sequencing

2,2-dichloropropionic acid (2,2DCP) is used as herbicide in agricultural industry and it is one of the halogenated organic compounds distributed widely in the world causing contamination. In this study, a bacterial strain isolated from contaminated soil where halogenated pesticides applied in Universiti Teknologi Malaysia and it was named “JHA1”. Bacterium JHA1 was able to utilize 2,2 dichloropropionate 2,2-DCP or (Dalapon) as a source of carbon and energy. Based on 16S rRNA analysis, the isolate showed 87% identity to Terrabacter terrae strain PPLB. The identity score was lower than 98% so that it was suggested to be new organisms that worth for further investigations if it will be proven that this is novel. Therefore, current isolate was designated as Terrabacter terrae JHA1. The isolate grew in the minimal media containing 10 mM, 15 mM, 20 mM and 25 mM of 2,2- DCP as the sole energy and carbon source and the best growth rate was in 20 mM as the optimum concentration of 2,2-DCP while bacterial growth was inhibited in medium with 30 mM 2,2-DCP

A single epitope of Epstein-Barr virus stimulate IgG production in mice

Background: Epstein-Barr virus (EBV) is closely associated with the high incidence of nasopharyngeal carcinoma in worldwide. Vaccination is one strategy with the potential to prevent the occurrence of EBV-associated cancers, but a suitable vaccine is yet to be licensed. Much vaccine development research focuses on the GP350/220 protein of EBV as it contains an immunogenic epitope at residues 147–165, which efficiently stimulates IgG production in vitro. We examined the ability of this epitope (EBVepitope) to induce IgG production in mice. Methods: The antibody binding pattern of the epitope was analyzed using bioinformatics tools. The IgG production in mice were examined by FACS Calibur™ Flow cytometer. Results: The epitope bound the 72A1 monoclonal antibody at the same site as GP350/220 protein, indicating that the epitope should stimulate B cells to produce antibody. Moreover, in vivo administration of EBVepitope successfully induced IgG expression from B cells, compared with controls. Further investigation indicated that the relative number of B cells expressing IgE in EBVepitope-treated mice was lower than controls. Conclusions: Our data suggest that this EBV GP350 epitope is able to induce IgG expression in vivo without causing allergic reactions, and represents a potential EBV vaccine candidate

The single nucleotide polymorphisms rs11761556 and rs12706832 of the leptin gene are associated with type 2 diabetes mellitus in the Iraqi population

This study was conducted to assess the potential association between leptin (LEP) gene polymorphisms and type 2 diabetes mellitus (T2DM) in Iraqi patients. Genomic DNA was extracted from 120 diabetic subjects and 100 controls. Three specific PCR fragments were designed to flank three highly frequent single nucleotide polymorphism (SNP)s within LEP, rs11761556, rs12706832 and rs2167270. The amplified loci were genotyped by PCR-single-strand conformation polymorphism (SSCP) followed by Sanger sequencing for representative genotypes. Logistic regression analysis was performed to detect the association between the targeted genetic variants and T2DM. PCR-SSCP genotyping showed three banding patterns for all three targeted SNPs. Individuals with the AA genotype in both rs11761556 and rs12706832 SNPs showed significantly higher (P<0.05) body mass index (BMI), waist circumference (WC), fasting blood glucose (FBG), hemoglobin A1c (HbA1c), homeostatic model assessment for insulin resistance (HOMA-IR), insulin, low-density lipoprotein cholesterol (LDL-C) and triglyceride (TG) values than those with other genotypes. Association analysis revealed that individuals with the A allele exhibited a greater risk of T2DM. Data of the present investigation indicated that both rs11761556 and rs12706832 SNPs exerted a noticeable association with T2DM. The study suggests implementing both rs11761556 and rs12706832 SNPs in the early detection of T2DM

Macronutrient concentration in stem, leaf and petiole of wild grown water spinach (Ipomea Aquatic Forsk.) and its relationship with pond water

Water spinach (Ipomoea aquatic Forsk.) is a food for human beings and animals. It is rich in minerals, protein, dietary fibre, with high moisture content. The work was undertaken to determine contents of K, Ca, Mg, Na & P in the stems, leaves and petioles of water spinach. Atomic absorption spectrometry (AAS) and Inductive Couple Plasma (ICP) were used to determine concentration of nutrients, where one way ANOVA was applied to analyse if there is any significant differences in the macronutrient contents amongst the leaves, petioles and stems of the water spinach. If any of the results showed significant differences, Turkey post-hoc HSD test (p<0.05%) was adopted to separate the means. In addition, Pearson's Correlation Coefficient Test was conducted between the plant macronutrients samples (leaves + stem + petioles combined) and water macronutrients data run to determine their relationships. In addition, purpose of this study is to highlight to the public which parts of the plant should be consumed and also to indicate the relationship of Water Spinach with its growing medium. The K concentration was higher than the other elements and maximum concentration was in petioles (432+27.45 mg•L-1) and stems (424.60+14.19 mgL-1). The element with the least concentration was Na (3.10+0.40 mgL-1), in the petiole. There was no difference in Mg content in leaves, petioles and stems (avg. 28.55+1.61 mgL-1). High amounts of Ca (150+0.10 mgL-1) and low amounts of P (41.11+0.01 mgL-1) were in pond water. A positive correlation of each nutrient occurred between water spinach and pond water

Macronutrient concentration in stem, leaf and petiole of wild grown water spinach (ipomea aquatic forsk.) and its relationship with pond water

Water spinach (Ipomoea aquatic Forsk.) is a food for human beings and animals. It is rich in minerals, protein, dietary fibre, with high moisture content. The work was undertaken to determine contents of K, Ca, Mg, Na & P in the stems, leaves and petioles of water spinach. Atomic absorption spectrometry (AAS) and Inductive Couple Plasma (ICP) were used to determine concentration of nutrients, where one way ANOVA was applied to analyse if there is any significant differences in the macronutrient contents amongst the leaves, petioles and stems of the water spinach. If any of the results showed significant differences, Turkey post-hoc HSD test (p<0.05%) was adopted to separate the means. In addition, Pearson’s Correlation Coefficient Test was conducted between the plant macronutrients samples (leaves + stem + petioles combined) and water macronutrients data run to determine their relationships. In addition, purpose of this study is to highlight to the public which parts of the plant should be consumed and also to indicate the relationship of Water Spinach with its growing medium. The K concentration was higher than the other elements and maximum concentration was in petioles (432+27.45 mg∙L-1) and stems (424.60+14.19 mgL-1). The element with the least concentration was Na (3.10+0.40 mgL-1), in the petiole. There was no difference in Mg content in leaves, petioles and stems (avg. 28.55+1.61 mgL- 1). High amounts of Ca (150+0.10 mgL-1) and low amounts of P (41.11+0.01 mgL-1) were in pond water. A positive correlation of each nutrient occurred between water spinach and pond water

Identification of Pseudomonas sp. strain S3 based on small subunit ribosomal RNA gene sequences

Pseudomonas sp. strain S3 was isolated from Paddy (rice) field agricultural area. This organism, which can utilize a halogenated compound of D,L-2-Chloropropionic acid as sole carbon and energy source, catalyses the hydrolytic dehalogenation of both D- and L- isomers of 2-Chloropropionic acid. Identification of Pseudomonas sp. S3 is still ambiguous due to the lack of basic studies, especially their molecular genetic information. In this study, the amplified 16S rRNA gene sequence of Pseudomonas sp. S3 (Accession No. FJ968758) was compared to other nine selected gene sequences from the same group of Pseudomonas sp. and/or dehalogenase producing bacteria using in silico method. Their phylogenetic relationships were then determined. The results were analysed using MEGA4 software to ascertain its evolutionary distance by reconstructing a phylogenetic tree of these organisms. The evolutionary history and bootstrap consensus tree were inferred using the Neighbour-Joining method from 500 replicates. The tree is drawn to scale, with branch lengths (next to the branches) in the same units as those of the evolutionary distances used to infer the phylogenetic tree. The evolutionary distances were computed using the p-distance method and were in the units of the number of base substitutions per site. Based on this analysis, Pseudomonas sp. S3 16S rRNA gene was closely related to the Pseudomonas chlororaphis with genetic distance 0.170 base substitutions per site. S3 gene was also compared among known dehalogenase producing bacteria 16S rRNA genes. Results suggested that S3 was closely related to the Pseudomonas sp. R1 with a genetic distance 0.040 base substitutions per site. From present study, evolutionary relationships of 16S rRNA gene of Pseudomonas sp. S3 were elegantly illustrated by phylograms, comparable to a pedigree showing which microorganisms are most closely related

Molecular prediction of dehalogenase producing microorganism using 16S rDNA Analysis of 2,2-dichloropropionate (dalapon) degrading bacterium isolated from volcanic soil

A phylogenetic analysis of an unknown strain AZZ2 isolated from volcanic area Gunung Sibayak Indonesia was performed. Their phylogenetic relationships were analysed using MEGA4 software® to ascertain its evolutionary distance by reconstructing a phylogenetic tree of these organisms. The evolutionary history and bootstrap consensus tree were inferred using the Neighbor-Joining method from 500 replicates. The tree is drawn to scale, with branch lengths (next to the branches) in the same units as those of the evolutionary distances used to infer the phylogenetic tree. The evolutionary distances were computed using the p-distance method and were in the units of the number of base substitutions per site. Based on the partial 16S rDNA sequence determination, the strain showed high sequence similarity to Citrobacter sp. strain JC73/SL7. AZZ2 gene was also compared among known dehalogenase producing bacteria 16S rDNA genes. The results suggested that AZZ2 was closely related to the Serratia marcescens HL1. On the basis of phylogenetic identification only, AZZ2 was subjected to grow on 2,2-dichloropropionate (2,2DCP). The results suggested that strain AZZ2 can degrade 2,2DCP as expected similar to the characteristic of strain HL1 that can grow on halogenated compound. From this study, there was a possibility to predict the phenotype of newly isolated bacteria. The present findings also show that the evolutionary relationships of 16S rDNA gene strain AZZ2 were illustrated by phylograms and both topology are not in good agreement and may suggest an uncertainty of the origin of dehalogenases in volcanic area

A Comparative Study of the Inorganic Nutrients in Different Types of Zea Mays L. Using Inductively Coupled Plasma Mass Spectrometry

Inductively coupled plasma-mass spectrometry (ICP-MS) was used in this study to perform a quantitative elemental analysis in order to compare the inorganic nutrients in commercial white and noncommercial yellow maize flours. ICP-MS measurements reveals that both white and yellow maize flours contains 20 different elements including toxic elements (Pb, Cd, As, Ni, Cr, Sr, U), essential elements (Ca, Co, Se, Zn, Cu, Fe, Mn, Mo) and probably essential elements (Mg, K, Na, Ba, Al) and their crossponding nutrients values were compared in detail. The ICP -MS analysis revealed that inorganic elements such as Al, As, Ba, Ca, Cd, Co, Cr, Cu, Fe, K, Mg, Mn, Mo, Na, Ni, Pb, U, Zn have concentration of 168.19, 0.17, 2.13, 1327.56, 0.04, 0.12, 9.14, 5.43, 82.03, 34.90, 99.62, 2.83, 0.74, 96.09, 4.5, 9.49, 6.12, 0.03, 6.47 µg/g in white and 200.05, 0.17, 2.53, 1290.27, 0.04, 0.145, 9.85, 11.46, 115.13, 914.98, 1594.14, 21.48, 1.71, 63.89, 6.08, 17.05, 5.23, 0.027, 33.89 µg/g in yellow maize flour, respectively. On the other hand toxic elements such as Cd or Pb in both white and yellow maize flours does not exceed their maximum limit set by the European Legislation or values recommended by the codex alimentarius

Antibacterial activity of PLAL synthesized nanocinnamon

Natural cinnamon containing polyphenolic compound is well known for diverse biological activities, broad range of pharmacological and therapeutic properties. However, the potential of nanocinnamon for antibacterial usage was not widely explored. Highly crystalline elliptical shaped cinnamon nanoparticles (CNPs) were prepared via pulse laser ablation in liquid (PLAL) by immersing a cinnamon target in methanol. Effects of varying laser fluence on the structure, morphology and optical properties of as-grown CNPs were determined. Samples were characterized via UV-Vis, FTIR, XRD, TEM, HRTEM, SAED, EDX, DLS and HPLC measurements. Methanol was found to be favorable for the growth of CNPs at optimum fluence of 5.73 J/cm2. These CNPs revealed robust antibacterial activity against Gram-negative and Gram-positive bacterial strains including Escherichia coli, Pseudomonas aeruginosa, Bacillus subtilis and Staphylococcus aureus. Antibacterial activity of CNPs was evaluated via agar well diffusion assay and optical density (OD600) tests. It was established that the PLAL may constitute a basis for the production CNPs with desired size distribution potential for nanomedicinal applications

© 2010 Asian Network for Scientific Information Cotyledon with Hypocotyl Segment as an Explant for the Production of Transgenic Citrullus vulgaris Schrad (Watermelon) Mediated by Agrobacterium tumefaciens

Abstract: In this study, we describe the successful production of transgenic watermelon using Agrobacterium tumefaciens after optimizing a couple of transformation parameters using cotyledon with hypocotyl segment from 5 day old in vitro seedlings as target tissues. It was found that the best condition for transformation of watermelon was using bacteria at a concentration of OD600 0.6, inoculation for 30 min and 3 day of co-cultivation. Addition of 200 µM acetosyringone in the medium helped to further increase the transformation efficiency. Agrobacterium tumefaciens strain EHA101 was found to be more effective to infect this watermelon variety as compared to LBA 4404 strain. Wounding of the explant meristems to induce multiple shoot was best carried out after 3 day. Transformed explants were selected on medium containing 5 mg LG 1 hygromycin. A total of 31 putative transformed plants were recovered with 25 shoots were found to be GUS positive after transformation of 110 cotyledons. A total of 15 GUS positive shoots amplified the hpt gene using PCR. However, only 7 shoots were successfully regenerated into whole plants