The case for the anticode

The present paper will focus on the developments in our lab related to the origin of the code since the Israel meeting (1,2). Principally these items are: (a) a new set of correlations (3) which include ranked hydrophobicities of amino acids and dinucleotides; (b) binding constants (4) of Phe for the four mononucleotides; and (c) binding constants (5) of Phe, Leu, Ile, Val, and Gly for polyadenylic acid (poly A). The data continue to support a model for the origin of the code based on relationships between amino acids and their anticodons.     

Identification of Mx gene nucleotide dimorphism (G/A) as genetic marker for antiviral activity in Egyptian chickens

Egyptian chickens, representing 2 breeds and 7 strains, were genotyped using the PCR-RFLP and sequencing techniques for detection of a non-synonymous dimorphism (G/A) in exon 14 of chicken Myxovirus resistance (Mx) gene. This dimorphic position is responsible for altering Mx protein’s antiviral activity. Polymerase Chain reactions were performed using Egyptian chickens DNA and specific primer set to amplify Mx DNA fragments of 299 or 301?bp, containing the dimorphic position. Amplicons were cut with restriction enzyme Hpy81. Genotype and allele frequencies for the resistant allele A and sensitive allele G were calculated in all the tested chickens. Results of PCR-RFLP were confirmed by sequencing. The three genotypes AA, AG, GG at the target nucleotide position in Mx gene were represented in all the studied Egyptian chicken breeds and strains except Baladi strain which showed only one genotype AA. The average allele frequency of the resistant A allele in the tested birds (0.67) was higher than the sensitive G allele average frequency in the same birds (0.33). Appling PCR-RFLP technique in the breeding program can be used to select chickens carrying the A allele with high frequencies. This will help in improving poultry breeding in Egypt by producing infectious disease-resistant chickens.     

Decolorization,degradation and detoxification of carcinogenic sulfonated azo dye methyl orange by newly developed biofilm consortia

Metabolites of azo dyes are often carcinogenic, teratogenic, mutagenic and recalcitrant in nature. In this study, four biofilm consortia such as C1 (Vitreoscilla sp. ENSG301, Acinetobacter lwoffii ENSG302, Klebsiella pneumoniae ENSG303 and Pseudomonas fluorescens ENSG304), C2 (Escherichia coli ENSD101, Enterobacter asburiae ENSD102 and E. ludwigii ENSH201), C3 (E. asburiae ENSD102, Vitreoscilla sp. ENSG301 and Bacillus thuringiensis ENSW401), and C4 (E. coli ENSD101, E. ludwigii ENSH201 and B. thuringiensis ENSW401) were applied to degrade and detoxify methyl orange (MO), a carcinogenic, sulfonated mono azo dye, used in textile dyeing industry worldwide. The consortia of C1, C2, C3 and C4 showed 97.30, 98.75, 99.51 and 99.29% decolorization, respectively in yeast extract peptone (YEP) broth containing 200 mg L⁻¹ MO within 60 h of incubation in static condition. The optimum pH and temperature for decolorization was 7.0 and 28 °C, respectively. Some divalent metal ions including Mg²⁺, Ca²⁺, Zn²⁺ and Mn²⁺ could stimulate MO decolorization. UV–Vis spectral analysis showed that the absorption peak at 465 nm originated from the azo (N N) bond was completely disappeared within 60 h of incubation. Fourier transform infrared spectroscopy (FTIR) results also revealed that several major peaks including azo bond peak at 1602.6 cm⁻¹ are completely or partly vanished, deformed or shifted. Activities of azoreductase, NADH-DCIP reductase and laccase were significantly increased in the bacterial cells within 60 h of incubation in comparison to that of control (0 h). The chemical oxygen demand was incredibly reduced by 85.37 to 91.44% by these consortia. Accordingly, plant (wheat seed germination) and microbial (growth of the plant probiotic bacteria such as Pseudomonas cedrina ESR12 and Bacillus cereus ESD3 on biodegraded products) toxicity studies showed that biodegraded products of MO are non-toxic. Thus, all these consortia can be utilized in bioremediation of MO from wastewater for safe disposal into environment. To our knowledge, this is the first report on degradation and detoxification of MO from wastewater by bacterial biofilm consortia.     

Contamination level and risk assessment of heavy metal deposited in street dusts in Khamees-Mushait city,Saudi Arabia

Abstract

The levels of some potentially toxic metals (Cr, Mn, Fe, Co, Cu, Zn, Cd, and Pb) were quantified in 60 street dust samples from Khamees-Mushait city, Saudi Arabia. Samples were taken from three locations at each functional area (total 18 including traffic, industrial, residential, and workshops) and at each control area (total two including a park and a new domestic planner). Heavy metals concentrations were quantified in less than 106 µm particle-size using inductively-coupled plasma-optical emission spectrometer after microwave wet digestion. The total concentrations (µg/g) were in the ranges of Cr 128.48–277.53, Mn 589.43–1091.45, Fe 43478.26–99151.63, Co 23.04–55.22, Cu 10.46–176.13, Cd 0.30–1.99, and Pb 9.36–340.56. The accuracy of results was examined using standard quality control samples, spiking, and a certified reference material. The overall recovery was in the range of 86.2–113.3%. The enrichment factors and the geoaccumulation indices, besides principal component analysis, reveal various levels of enrichment by Fe, Cu, Zn, and Pb from functional areas of congested traffic, commercial activities, and metallic workshops activities. In contrast, no significant enrichment by Cr, Mn, and Co was recorded. The cluster analysis revealed that the metallic workshops and the vehicle scrap workshops are the hottest functional areas.     

Metabolism of carbosulfan II. Human interindividual variability in its in vitro hepatic biotransformation and the identification of the cytochrome P450 isoforms involved

This study aims to characterize interindividual variability and individual CYP enzymes involved in the in vitro metabolism of the carbamate insecticide carbosulfan. Microsomes from ten human livers (HLM) were used to characterize the interindividual variability in carbosulfan activation. Altogether eight phase I metabolites were analyzed by LC–MS. The primary metabolic pathways were detoxification by the initial oxidation of sulfur to carbosulfan sulfinamide (‘sulfur oxidation pathway’) and activation via cleavage of the nitrogen sulfur bond (N–S) to give carbofuran and dibutylamine (‘carbofuran pathway’). Differences between maximum and minimum carbosulfan activation values with HLM indicated nearly 5.9-, 7.0, and 6.6-fold variability in the k_m, V_max and CL_int values, respectively. CYP3A5 and CYP2B6 had the greatest efficiency to form carbosulfan sulfinamide, while CYP3A4 and CYP3A5 were the most efficient in the generation of the carbofuran metabolic pathway. Based on average abundances of CYP enzymes in human liver, CYP3A4 contributed to 98% of carbosulfan activation, while CYP3A4 and CYP2B6 contributed 57 and 37% to detoxification, respectively. Significant correlations between carbosulfan activation and CYP marker activities were seen with CYP3A4 (omeprazole sulfoxidation), CYP2C19 (omeprazole 5-hydroxylation) and CYP3A4 (midazolam 1′-hydroxylation), displaying r² = 0.96, 0.87 and 0.82, respectively. Activation and detoxification pathways were inhibited by ketoconazole, a specific CYP3A4 inhibitor, by 90–97% and 47–94%, respectively. Carbosulfan inhibited relatively potently CYP3A4 and moderately CYP1A1/2 and CYP2C19 in pooled HLM. These results suggest that the carbosulfan activation pathway is more important than the detoxification pathway, and that carbosulfan activation is predominantly catalyzed in humans by CYP3A4.     

Global soil nitrogen cycle pattern and nitrogen enrichment effects: Tropical versus subtropical forests

Tropical and subtropical forest biomes are a main hotspot for the global nitrogen (N) cycle. Yet, our understanding of global soil N cycle patterns and drivers and their response to N deposition in these biomes remains elusive. By a meta-analysis of 2426-single and 161-paired observations from 89 published ¹⁵ N pool dilution and tracing studies, we found that gross N mineralization (GNM), immobilization of ammonium ($I_{{\mathrm{NH}}_4}$) and nitrate ($I_{{\mathrm{NO}}_3}$), and dissimilatory nitrate reduction to ammonium (DNRA) were significantly higher in tropical forests than in subtropical forests. Soil N cycle was conservative in tropical forests with ratios of gross nitrification (GN) to $I_{{\mathrm{NH}}_4}$ (GN/$I_{{\mathrm{NH}}_4}$) and of soil nitrate to ammonium (NO₃⁻/NH₄⁺) less than one, but was leaky in subtropical forests with GN/$I_{{\mathrm{NH}}_4}$ and NO₃⁻/NH₄⁺ higher than one. Soil NH₄⁺ dynamics were mainly controlled by soil substrate (e.g., total N), but climatic factors (e.g., precipitation and/or temperature) were more important in controlling soil NO₃⁻ dynamics. Soil texture played a role, as GNM and $I_{{\mathrm{NH}}_4}$ were positively correlated with silt and clay contents, while $I_{{\mathrm{NO}}_3}$ and DNRA were positively correlated with sand and clay contents, respectively. The soil N cycle was more sensitive to N deposition in tropical forests than in subtropical forests. Nitrogen deposition leads to a leaky N cycle in tropical forests, as evidenced by the increase in GN/$I_{{\mathrm{NH}}_4}$, NO₃⁻/NH₄⁺, and nitrous oxide emissions and the decrease in $I_{{\mathrm{NO}}_3}$ and DNRA, mainly due to the decrease in soil microbial biomass and pH. Dominant tree species can also influence soil N cycle pattern, which has changed from conservative in deciduous forests to leaky in coniferous forests. We provide global evidence that tropical, but not subtropical, forests are characterized by soil N dynamics sustaining N availability and that N deposition inhibits soil N retention and stimulates N losses in these biomes.     

Possible gastrointestinal disorders for athletes during Ramadan: an overview

Ramadan is considered to be the month of the stomach break. It has been reported that Ramadan has some health benefits. In most Muslims countries, there is a huge modification in the diet during this month. These changes could induce some gastrointestinal (GI) disorders (e.g. diarrhea, cramps, fullness, nausea). The aims of the present overview were to present some challenges that could be observed for athletes during the training sessions or competition and present some practical recommendations to avoid GI disorders during Ramadan. Based on previous studies, we could advance that the prevalence of GI disorders will be more pronounced when athletes travel for international competitions during Ramadan. Besides, GI disorders are more frequent for athletes when there is a huge modification in the training load. Dehydration observed during Ramadan is one of the factors that may induce GI disorders. The latter could be exacerbated by sweat loss during training sessions. Carbohydrate is frequently used by athletes to improve performance and is associated with some GI disorders. Therefore, during Ramadan, coaches and athletes should be advised to maintain the same diet and a good hydration as before the fasting month, and avoid air travel when preparing for competitions.     

Piecewise Whittle estimator for trabecular bone radiograph characterization

Osteoporosis is a disease in which low bone mass and microarchitectural deterioration of bone tissue lead to increased bone fragility and a consequent increase in fracture risk. The objective of this paper is to develop and validate a new method to assess bone microarchitecture on radiographs. Taking into account the piecewise fractal nature of bone radiograph images, an appropriate fractal model (piecewise fractional Brownian motion) is used to characterize the trabecular bone network. Based on the Whittle estimator, a new method for calculating the Hurst exponent H is developed to better consider the piecewise fractal nature of the data. Different estimators are used and compared to the proposed method to discriminate two populations composed of healthy controls and osteoporotic patients. Our findings demonstrate that the new estimator proposed here provides effective results in terms of discrimination of the subjects and is better adapted to bone radiograph image analysis.     

Mitochondrial DNA structure in the Arabian Peninsula

Background  

Two potential migratory routes followed by modern humans to colonize Eurasia from Africa have been proposed. These are the two natural passageways that connect both continents: the northern route through the Sinai Peninsula and the southern route across the Bab al Mandab strait. Recent archaeological and genetic evidence have favored a unique southern coastal route. Under this scenario, the study of the population genetic structure of the Arabian Peninsula, the first step out of Africa, to search for primary genetic links between Africa and Eurasia, is crucial. The haploid and maternally inherited mitochondrial DNA (mtDNA) molecule has been the most used genetic marker to identify and to relate lineages with clear geographic origins, as the African Ls and the Eurasian M and N that have a common root with the Africans L3.