The Prediction and Validation of Small CDSs Expand the Gene Repertoire of the Smallest Known Eukaryotic Genomes

The proper prediction of the gene catalogue of an organism is essential to obtain a representative snapshot of its overall lifestyle, especially when it is not amenable to culturing. Microsporidia are obligate intracellular, sometimes hard to culture, eukaryotic parasites known to infect members of every animal phylum. To date, sequencing and annotation of microsporidian genomes have revealed a poor gene complement with highly reduced gene sizes. In the present paper, we investigated whether such gene sizes may have induced biases for the methodologies used for genome annotation, with an emphasis on small coding sequence (CDS) gene prediction. Using better delineated intergenic regions from four Encephalitozoon genomes, we predicted de novo new small CDSs with sizes ranging from 78 to 255 bp (median 168) and corroborated these predictions by RACE-PCR experiments in Encephalitozoon cuniculi. Most of the newly found genes are present in other distantly related microsporidian species, suggesting their biological relevance. The present study provides a better framework for annotating microsporidian genomes and to train and evaluate new computational methods dedicated at detecting ultra-small genes in various organisms.     

Determining “safe” levels of exposure: The validity of the use of 10X safety factors

The current guideline for risk assessment of chemicals having a toxic end point routinely uses the reference dose (RfD) approach based on uncertainty factors of 10. With this method the quality of individual risk assessment varies among chemicals, often resulting in either an over‐ or under‐estimation of adverse health risk. The purpose of this investigation is to evaluate whether the magnitude of the 10X uncertainty factors have scientific merit against data from published experimental studies. A compilation and comparison of ratios between LOAEL/NOAEL (Lowest Observed Adverse Effect Level/No Observed Adverse Effect Level), subchronic/chronic, and animal/human values were made. The results of the present investigation revealed that the use of default factors could be over‐conservative or unprotective. More reasonable estimates of the risk to human health would result in a reduction of unnecessary, and expensive over‐regulation. In addition to the LOAEL to NOAEL, and subchronic to chronic ratios, the adequacy of uncertainty factors for animal to human extrapolations were examined. Although a 10‐fold uncertainty factor (UF) is most commonly used in the risk assessment process, an examination of the literature for the compounds presented here suggests that the use of different values is scientifically justifiable.     

RETRACTED ARTICLE: Influence of arbuscular mycorrhizal fungi and copper on growth, accumulation of osmolyte, mineral nutrition and antioxidant enzyme activity of pepper (Capsicum annuum L.)

The effect of arbuscular mycorrhizal (AM) fungi inoculation on pepper (Capsicum annuum L. cv. Zhongjiao 105) plant growth and on some physiological parameters in response to increasing soil Cu concentrations was studied. Treatments consisted of inoculation or not with Glomus mosseae and the addition of Cu to soil at the concentrations of 0 (control), 2 (low), 4 (medium), and 8 (high) mM CuSO₄. AM fungal inoculation decreased Cu concentrations in plant organs and promoted biomass yields as well as the contents of chlorophyll, soluble sugar, total protein, and the concentrations of P, K, Ca, and Mg. Plants grown in high Cu concentration exhibited a Cu-induced proline accumulation and also an increase in total free amino acid contents; however, both were lower in mycorrhizal pepper. Cu-induced oxidative stress by increasing lipid peroxidation rates and the activity of superoxide dismutase, catalase, ascorbate peroxidase and glutathione reductase, and AM symbiosis enhanced these antioxidant enzyme activities and decreased oxidative damage to lipids. In conclusion G. mosseae was able to maintain an efficient symbiosis with pepper plants in contaminated Cu soils, improving plant growth under these conditions, which is likely to be due to reduced Cu accumulation in plant tissues, reduced oxidative stress and damage to lipids, or enhanced antioxidant capacity.     

Interactions between Nile tilapia (Oreochromis niloticus) and cladocerans in ponds (Khartoum,Sudan)

Juvenile Nile tilapia (Oreochromis niloticus) are omnivorous, and the question asked in this study is how they affect on their environment? Do they mainly act as predators on the cladoceran zooplankton or do they compete with the cladocerans for phytoplankton? This problem was studied in three ponds with and three ponds without small tilapia (3–5 cm). The fish growth rate, the succession of plankton species and the changes in abiotic conditions, were monitored over a period of 67 days. The fish biomass was kept low and the mean was approximately constant (12.6 g m^?2) during the experiment. Phosphate was added to avoid phytoplankton nutrient limitation. Although the diet of Nile tilapia contained both phytoplankton and zooplankton, the fish affected the ecosystem in a similar way as zooplanktivorous fish. The fish ponds got more phytoplankton due to increase of Chlorophyta. Effects on the other phytoplankton groups Euglenophyta, Bacillariophyta, Cryptophyta and Cyanophyta could not be registered. The ponds without fish had higher densities of Daphnia lumholtzi and D. barbata. The other Cladocerans seemed less influenced by fish presence. The relative fish growth rate was most positively correlated with the density of Daphnia lumholtzi, Diaphanosmoa excisum and Bosmina longirostris. Tilapia seemes to have two feeding modes: (1) preying on large zooplankton and (2) unselective filtration of small planktonic organisms such as phytoplankton. In our experiment the first feeding mode affected the ecosystem more than the second.     

Results of antiretroviral treatment interruption and intensification in advanced multi-drug resistant HIV infection from the OPTIMA trial

Background

Guidance is needed on best medical management for advanced HIV disease with multidrug resistance (MDR) and limited retreatment options. We assessed two novel antiretroviral (ARV) treatment approaches in this setting.

Methods and Findings

We conducted a 2×2 factorial randomized open label controlled trial in patients with a CD4 count ≤300 cells/µl who had ARV treatment (ART) failure requiring retreatment, to two options (a) re-treatment with either standard (≤4 ARVs) or intensive (≥5 ARVs) ART and b) either treatment starting immediately or after a 12-week monitored ART interruption. Primary outcome was time to developing a first AIDS-defining event (ADE) or death from any cause. Analysis was by intention to treat. From 2001 to 2006, 368 patients were randomized. At baseline, mean age was 48 years, 2% were women, median CD4 count was 106/µl, mean viral load was 4.74 log₁₀ copies/ml, and 59% had a prior AIDS diagnosis. Median follow-up was 4.0 years in 1249 person-years of observation. There were no statistically significant differences in the primary composite outcome of ADE or death between re-treatment options of standard versus intensive ART (hazard ratio 1.17; CI 0.86–1.59), or between immediate retreatment initiation versus interruption before re-treatment (hazard ratio 0.93; CI 0.68–1.30), or in the rate of non-HIV associated serious adverse events between re-treatment options.

Conclusions

We did not observe clinical benefit or harm assessed by the primary outcome in this largest and longest trial exploring both ART interruption and intensification in advanced MDR HIV infection with poor retreatment options.

Trial Registration

Clinicaltrials.gov {"type":"clinical-trial","attrs":{"text":"NCT00050089","term_id":"NCT00050089"}}NCT00050089     

Upregulation of vascular inducible nitric oxide synthase mediates the hypotensive effect of ethanol in conscious female rats.

Previous reports from our laboratory have shown that ethanol elicits hypotension in female but not in male rats and that this effect of ethanol is estrogen dependent (El-Mass MM and Abdel-Rahman AA. Alcohol Clin Exp Res 23: 624-632, 1999; El-Mass MM and Abdel-Rahman AA. Clin Exp Hypertens 21: 1429-1445, 1999). In the present study, we tested the hypothesis that ethanol lowers blood pressure in female rats via upregulation of the inducible nitric oxide synthase (iNOS) in vascular tissues. The effects of pretreatment with NG-nitro-L-arginine (NOARG; nonselective nitric oxide synthase inhibitor) or aminoguanidine (selective iNOS inhibitor) on hemodynamic responses elicited by intragastric (ig) ethanol were determined in conscious female rats. Changes in vascular (aortic) iNOS protein expression evoked by ethanol in the presence and absence of aminoguanidine were also measured by immunohistochemistry. Compared with control (water treated) female rats, ethanol (1 g/kg ig) elicited hypotension that was associated with a significant increase in the aortic iNOS activity. The hypotensive effect of ethanol was virtually abolished in rats infused with the nitric oxide synthase inhibitor NOARG, suggesting a role for nitric oxide in ethanol hypotension. The inability of ethanol to lower blood pressure in NOARG-treated rats cannot be attributed to the presence of elevated blood pressure in these rats because ethanol produced hypotension when blood pressure was raised to comparable levels with phenylephrine infusion. Selective inhibition of iNOS by aminoguanidine (45 mg/kg ip), which had no effect on baseline blood pressure, abolished both the hypotensive action of subsequently administered ethanol and the associated increases in aortic iNOS content. These findings implicate vascular iNOS, at least partly, in the acute hypotensive action of ethanol in female rats.     

Buffalo species identification and delineation using genetic barcoding markers

Enrichment of barcode databases with mitochondrial cytochrome c oxidase subunit I (COI) barcode sequences in different animal taxa has become important for identification of animal source in food samples to prevent commercial fraud. In this study, COI barcode sequence in seventy one river buffalo samples were determined, analyzed and deposited in Genbank barcode database and barcode of life database (BOLD) to contribute for construction of public reference library for COI barcode sequence in river buffalo. Moreover COI barcode sequence was used to identify the closely related buffalo groups: river buffalo, swamp buffalo, lowland anoa and African buffalo. Results indicated the success of the COI barcode in the identification of each of the tested groups. Whereas a suggested sequence of other mitochondrial segment representing two successive transfer RNA (tRNA) genes; tRNA-Threonine (MT-TT) and tRNA-Proline (MT-TP) was failed to be used as a barcode marker for differentiation between the tested buffalo groups.