Comparative context analysis of codon pairs on an ORFeome scale

Codon context is an important feature of gene primary structure that modulates mRNA decoding accuracy. We have developed an analytical software package and a graphical interface for comparative codon context analysis of all the open reading frames in a genome (the ORFeome). Using the complete ORFeome sequences of Saccharomyces cerevisiae, Schizosaccharomyces pombe, Candida albicans and Escherichia coli, we show that this methodology permits large-scale codon context comparisons and provides new insight on the rules that govern the evolution of codon-pair context.     

Effects of Acibenzolar-S-methyl on the specific activities of peroxidase, chitinase and phenylalanine ammonia-lyase and phenolic content of host leaves in cucumber-powdery mildew interaction

One of the properties of systemic acquired resistance in plants is its concomitance with the biochemical changes including enhancement of activities of defense-related enzymes. In this study, the effects of Acibenzolar-S-methyl (ACI) on the some of defense responses of the cucumber plants (healthy or inoculated with spore suspension of Podosphaerafusca, the causal agent of cucumber powdery mildew) were surveyed via in vivo tests. Changes of defense responses in ACI-treated cucumber plants, inoculated with pathogen or not, were studied and compared with those of non-treated control plants. Results indicated that specific activity of peroxidase increased significantly in treated plants. Increase in enzyme activity was higher in pathogen-inoculated than non-inoculated plants, thus pathogen attack stress to plant plays a role in enhancement of enzyme activity. Specific activity of phenylalanine ammonialyase showed no changes in ACI-treated non-inoculated plants, but in inoculated plants it Increased due to interaction between ACI treatment and pathogen attack stress. Specific activity of chitinase increased in both inoculated and non-inoculated ACI-treated plants at 24 hours after treatment onwards, and pathogen attack stress did not affect it. Phenolic content of ACI-treated plant tissues, despite of small fluctuations, did not show any definite pattern of changes.     

Patterns of Evolution in Iranian Tribal Textiles

Ever since the publication of The Origin of Species, anthropologists and archaeologists have been in turns enchanted and repulsed by the idea that cultural diversity can be explained by a Darwinian model of descent with modification. Over the last decade, this debate has intensified following the publication of a number of studies that have sought to reconstruct cultural histories using modern computational methods of phylogenetic analysis imported from biology. In this paper, I focus on evolution of tribal textile assemblages in Iran and Central Asia. Using cladistic phylogenetic analysis, I show that similarities and differences among the assemblages can be largely explained in terms of descent with modification from ancestral assemblages. Interestingly, the phylogenetic signal in design characters is just as strong (if not stronger) than the signal in technical characters. This may seem surprising given that techniques, like genes, are transmitted “vertically” from mothers to daughters whereas designs are frequently transmitted “horizontally” among peers. However, a closer examination reveals that the transmission of designs between weavers mainly occurs within, rather than between groups, and that, as in many cultures past and present, there are important constraints on the latter. This highlights that differences in the ways in which genes and cultural traits are transmitted among individuals should not be assumed to lead to differences in macro-level patterns of evolution, as many archaeologists and anthropologists have supposed.     

An Ustilago maydis chassis for itaconic acid production without by-products

Ustilago maydis is a promising yeast for the production of a range of valuable metabolites, including itaconate, malate, glycolipids and triacylglycerols. However, wild-type strains generally produce a potpourri of all of these metabolites, which hinders efficient production of single target chemicals. In this study, the diverse by-product spectrum of U. maydis was reduced through strain engineering using CRISPR/Cas9 and FLP/FRT, greatly increasing the metabolic flux into the targeted itaconate biosynthesis pathway. With this strategy, a marker-free chassis strain could be engineered, which produces itaconate from glucose with significantly enhanced titre, rate and yield. The lack of by-product formation not only benefited itaconate production, it also increases the efficiency of downstream processing improving cell handling and product purity.     

Comparison of techniques for the measurement of skin temperature during exercise in a hot,humid environment

Exercising or working in a hot, humid environment can results in the onset of heat-related illness when an individual''s temperature is not carefully monitored. The purpose of the present study was to compare three techniques (data loggers, thermal imaging, and wired electrodes) for the measurement of peripheral (bicep) and central (abdominal) skin temperature. Young men and women (N = 30) were recruited to complete the present study. The three skin temperature measurements were made at 0 and every 10-min during 40-min (60% VO₂max) of cycling in a hot (39±2°C), humid (45±5% RH) environment. Data was statistically analyzed using the Bland-Altman method and correlation analysis. For abdominal skin temperature, the Bland-Altman limits of agreement indicated that data loggers (1.5) were a better index of wired than was thermal imaging (3.5), For the bicep skin temperature the limits of agreement was similar between data loggers (1.9) and thermal (1.9), suggesting the both were suitable measurements. We also found that when skin temperature exceeded 35°C, we observed progressively better prediction between data loggers, thermal imaging, and wired skin sensors. This report describes the potential for the use of data loggers and thermal imaging to be used as alternative measures of skin temperature in exercising, human subjects.     

Comparison of gas phase intrinsic properties of cytosine and thymine nucleobases with their O-alkyl adducts: different hydrogen bonding preferences for thymine versus O-alkyl thymine

In recent years, there has been increasing interest in damaged DNA and RNA nucleobases. These damaged nucleobases can cause DNA mutation, resulting in various diseases such as cancer. Alkylating agents are mutagenic and carcinogenic in a variety of prokaryotic and eukaryotic organisms. The present study employs density functional theory (DFT/B3LYP) with the 6-311++G(d,p) basis set to investigate the effect of chemical damage in O-alkyl pyrimidines such as O⁴-methylthymine, O²-methylcytosine and O²-methylthymine. We compared the intrinsic properties, such as proton affinities, gas phase acidities, equilibrium tautomerization and nucleobase pair’s hydrogen bonding properties, of these molecules with those in the normal nucleobases thymine and cytosine. The results are of interest for chemical reasons and also possibly for biological purposes since biological media can be quite non-polar. Furthermore, we found that N1-H of O⁴-methylthymine is less acidic than N1-H of thymine, suggesting that alkyl DNA glycosylase enzyme cannot discriminate this damaged nucleobase from a normal thymine nucleobase. This result indicates that the conjugated base anion of O⁴-methylthymine would be a worse leaving group and O⁴-methylthymine is repaired in genome by demethylation rather than enzyme-catalyzed excision at N1.     

Soil‐nutrient availability under a global‐change scenario in a Mediterranean mountain ecosystem

Changes in rainfall availability will alter soil‐nutrient availability under a climate‐change scenario. However, studies have usually analyzed the effect of either drier or wetter soil conditions, despite the fact that both possibilities will coexist in many climatic regions of the world. Furthermore, its effect may vary across the different habitats of the ecosystem. We experimentally investigated the effect of three contrasting climatic scenarios on different carbon (C), nitrogen (N), and phosphorus (P) fractions in soil and microbial compartments among three characteristic habitats in a Mediterranean‐type ecosystem: forest, shrubland, and open areas. The climatic scenarios were dry summers, according to the 30% summer rainfall reduction projected in the Mediterranean; wet summer, simulating summer storms to reach the maximum historical records in the study area; and current climatic conditions (control). Sampling was replicated during two seasons (spring and summer) and 2 years. The climatic scenario did not affect the nutrient content in the litter layer. However, soil and microbial nutrients varied among seasons, habitats, and climatic scenarios. Soil‐nutrient fractions increased with lower soil‐moisture conditions (dry scenario and summer), whereas microbial nutrients increased under the wet summer scenario and spring. This pattern was consistent both studied years, although it was modulated by habitat, differences being lower with denser plant cover. Holm oak seedlings, used as live control of the experiment, tended to increase their N and P content (although not significantly) with water availability. Thus, the results support the idea that higher rainfall boosts microbial and plant‐nutrient uptake, and hence nutrient cycling. By contrast, a rainfall reduction leads to an accumulation of nutrients in the soil, increasing the risk of nutrient loss by leaching or erosion. These results show that the projected climate change will have significant effects on nutrient cycles, and therefore will have important implications on the ecosystem functioning.     

The prevalence of polycystic ovary syndrome in a community sample of Iranian population: Iranian PCOS prevalence study

Background  

Despite the heavy burden and impact of the polycystic ovary syndrome (PCOS) in reproduction and public health, estimates regarding its prevalence at community levels are limited. We aimed to ascertain prevalence of PCOS in a community based sample using the National Institute of Health (NIH), the Rotterdam consensus (Rott.) and the Androgen Excess Society (AES) criteria.