New levels of sophistication in the transcriptional landscape of bacteria

An extra layer of complexity in the regulation of gene expression in bacteria is now apparent through previously unanticipated roles of noncoding and antisense RNAs.     

Application of Box-Behnken Design to Hybrid Electrokinetic-Adsorption Removal of Mercury from Contaminated Saline-Sodic Clay Soil

A hybrid electrokinetic-adsorption (HEKA) technique using uniform electric field and granular activated carbon (GAC) produced from date palm pits was investigated for the removal of mercury from natural saline-sodic clay heavily contaminated with heavy metals, phenol, and kerosene. Response surface methodology (RSM) was employed to model, optimize, and interpret the results obtained with the aid of Design Expert software. According to the Box-Behnken experimental design, 15 experiments were conducted each with residence time of three weeks. The effects of voltage gradient (0.2–1 V/cm), initial Hg concentration (mg/Kg), and polarity reversal interval (0-48 hours) on Hg removal efficiency and energy consumed for Hg removal were investigated. Respectively, the responses fitted reduced cubic (R² = 99.3%) and quadratic models (R² = 92.3%) with the overall relative contributions of the investigated parameters on the responses following the order: voltage gradient > initial Hg concentration > polarity reversal interval based on analysis of variance (ANOVA). The optimal conditions obtained with desirability of 90% aimed at maximizing Hg removal were 24 hours polarity reversal interval, 0.2 V/cm voltage gradient, and 100 mg/kg initial Hg concentration. This optimum operating condition yielded good removal of Hg (99.5%) at reduced energy consumption of 50.1kWh.m^?3mg^?1. Experimental validation of the models showed good prediction of Hg removal efficiency (0.0368% prediction error). The results presented herein suggest that HEKA technology could be utilized effectively for the removal of Hg from contaminated, low permeable soils under extreme soil and contamination conditions.     

Assessment of Natural Radioactivity Levels and Potential Radiological Risks of Common Building Materials Used in Bangladeshi Dwellings

The concentrations of primordial radionuclides (²²⁶Ra, ²³²Th and ⁴⁰K) in commonly used building materials (brick, cement and sand), the raw materials of cement and the by-products of coal-fired power plants (fly ash) collected from various manufacturers and suppliers in Bangladesh were determined via gamma-ray spectrometry using an HPGe detector. The results showed that the mean concentrations of ²²⁶Ra, ²³²Th and ⁴⁰K in all studied samples slightly exceeded the typical world average values of 50 Bq kg⁻¹, 50 Bq kg⁻¹ and 500 Bq kg⁻¹, respectively. The activity concentrations (especially ²²⁶Ra) of fly-ash-containing cement in this study were found to be higher than those of fly-ash-free cement. To evaluate the potential radiological risk to individuals associated with these building materials, various radiological hazard indicators were calculated. The radium equivalent activity values for all samples were found to be lower than the recommended limit for building materials of 370 Bq kg^-1, with the exception of the fly ash. For most samples, the values of the alpha index and the radiological hazard (external and internal) indices were found to be within the safe limit of 1. The mean indoor absorbed dose rate was observed to be higher than the population-weighted world average of 84 nGy h^–1, and the corresponding annual effective dose for most samples fell below the recommended upper dose limit of 1 mSv y^–1. For all investigated materials, the values of the gamma index were found to be greater than 0.5 but less than 1, indicating that the gamma dose contribution from the studied building materials exceeds the exemption dose criterion of 0.3 mSv y^-1 but complies with the upper dose principle of 1 mSv y⁻¹.     

Transformation von Deoxynivalenol durch die Darmflora des Schweines — In-vitro Untersuchungen zur Adaptation in Abhängigkeit von der Darreichungsform

To examine the biotransformation of Deoxynivalenol (DON) by the normal gut flora of pigs (in reliance on toxin-source) an in-vitro system was established. Suspensions of rectum contents from different treated animals were incubated with pure DON. Despite fast adaptation of microflora (Deepoxidation of DON) of animals fed wheat diet, no effects on reduced feed consumption and weight gain were seen. Even fast adaptation of microflora (lower intestine) couldn’t avoid DON-effects in vivo.     

Differentiation of adult-type Leydig cells occurs in gonadotrophin-deficient mice

During mammalian testis development distinct generations of fetal and adult Leydig cells arise. Luteinising hormone (LH) is required for normal adult Leydig cell function and for the establishment of normal adult Leydig cell number but its role in the process of adult Leydig cell differentiation has remained uncertain. In this study we have examined adult Leydig cell differentiation in gonadotrophin-releasing hormone (GnRH)-null mice which are deficient in circulating gonadotrophins. Adult Leydig cell differentiation was assessed by measuring expression of mRNA species encoding four specific markers of adult Leydig cell differentiation in the mouse. Each of these markers (3β-hydroxysteroid dehydrogenase type VI (3βHSD VI), 17β-hydroxysteroid dehydrogenase type III (17βHSD III), prostaglandin D (PGD)-synthetase and oestrogen sulphotransferase (EST)) is expressed only in the adult Leydig cell lineage in the normal adult animal. Real-time PCR studies showed that all four markers are expressed in adult GnRH-null mice. Localisation of 3βHSD VI and PGD-synthetase expression by in situ hybridisation confirmed that these genes are expressed in the interstitial tissue of the GnRH-null mouse. Treatment of animals with human chorionic gonadotrophin increased expression of 3βHSD VI and 17βHSD III within 12 hours further indicating that differentiated, but unstimulated cells already exist in the GnRH-null mouse. Thus, while previous studies have shown that LH is required for adult Leydig cell proliferation and activity, results from the present study show that adult Leydig cell differentiation will take place in animals deficient in LH.     

Prediction of peak pressure from clinical and radiological measurements in patients with diabetes

Background

Various structural and functional factors of foot function have been associated with high local plantar pressures. The therapist focuses on these features which are thought to be responsible for plantar ulceration in patients with diabetes. Risk assessment of the diabetic foot would be made easier if locally elevated plantar pressure could be indicated with a minimum set of clinical measures.

Methods

Ninety three patients were evaluated through vascular, orthopaedic, neurological and radiological assessment. A pressure platform was used to quantify the barefoot peak pressure for six forefoot regions: big toe (BT) and metatarsals one (MT-1) to five (MT-5). Stepwise regression modelling was performed to determine which set of the clinical and radiological measures explained most variability in local barefoot plantar peak pressure in each of the six forefoot regions. Comprehensive models were computed with independent variables from the clinical and radiological measurements. The difference between the actual plantar pressure and the predicted value was examined through Bland-Altman analysis.

Results

Forefoot pressures were significant higher in patients with neuropathy, compared to patients without neuropathy for the whole forefoot, the MT-1 region and the MT-5 region (respectively 138 kPa, 173 kPa and 88 kPa higher: mean difference). The clinical models explained up to 39 percent of the variance in local peak pressures. Callus formation and toe deformity were identified as relevant clinical predictors for all forefoot regions. Regression models with radiological variables explained about 26 percent of the variance in local peak pressures. For most regions the combination of clinical and radiological variables resulted in a higher explained variance. The Bland and Altman analysis showed a major discrepancy between the predicted and the actual peak pressure values.

Conclusion

At best, clinical and radiological measurements could only explain about 34 percent of the variance in local barefoot peak pressure in this population of diabetic patients. The prediction models constructed with linear regression are not useful in clinical practice because of considerable underestimation of high plantar pressure values. Identification of elevated plantar pressure without equipment for quantification of plantar pressure is inadequate. The use of quantitative plantar pressure measurement for diabetic foot screening is therefore advocated.     

Graphical analysis of pH-dependent properties of proteins predicted using PROPKA

Background  

Charge states of ionizable residues in proteins determine their pH-dependent properties through their pK_a values. Thus, various theoretical methods to determine ionization constants of residues in biological systems have been developed. One of the more widely used approaches for predicting pK_a values in proteins is the PROPKA program, which provides convenient structural rationalization of the predicted pK_a values without any additional calculations.     

A genetic study on C5-TRAF1 and progression of joint damage in rheumatoid arthritis

IntroductionThe severity of joint damage progression in rheumatoid arthritis (RA) is heritable. Several genetic variants have been identified, but together explain only part of the total genetic effect. Variants in Interleukin-6 (IL-6), Interleukin-10 (IL-10), C5-TRAF1, and Fc-receptor-like-3 (FCRL3) have been described to associate with radiographic progression, but results of different studies were incongruent. We aimed to clarify associations of these variants with radiographic progression by evaluating six independent cohorts.MethodsIn total 5,895 sets of radiographs of 2,493 RA-patients included in six different independent datasets from the Netherlands, Sweden, Spain and North-America were studied in relation to rs1800795 (IL-6), rs1800896 (IL-10), rs2900180 (C5-TRAF1) and rs7528684 (FCRL3). Associations were tested in the total RA-populations and in anti-citrullinated peptide antibodies (ACPA)-positive and ACPA-negative subgroups per cohort, followed by meta-analyses. Furthermore, the associated region C5-TRAF1 was fine-mapped in the ACPA-negative Dutch RA-patients.ResultsNo associations were found for rs1800795 (IL-6), rs1800896 (IL-10) and rs7528684 (FCRL3) in the total RA-population and after stratification for ACPA. Rs2900180 in C5-TRAF1 was associated with radiographic progression in the ACPA-negative population (P-value meta-analysis = 5.85 × 10⁻⁷); the minor allele was associated with more radiographic progression. Fine-mapping revealed a region of 66Kb that was associated; the lowest P-value was for rs7021880 in TRAF1. The P-value for rs7021880 in meta-analysis was 6.35 × 10⁻⁸. Previous studies indicate that the region of rs7021880 was associated with RNA expression of TRAF1 and C5.ConclusionVariants in IL-6, IL-10 and FCRL3 were not associated with radiographic progression. Rs2900180 in C5-TRAF1 and linked variants in a 66Kb region were associated with radiographic progression in ACPA-negative RA.

Electronic supplementary material

The online version of this article (doi:10.1186/s13075-014-0514-0) contains supplementary material, which is available to authorized users.