Salt- and solvent-dependent conformational transitions of ribo-CGCGCG duplex

The conformational transition of r(CpG)₃ was investigated under different chemical conditions. It was found that NaCl at a high concentration induced a partial transformation of the duplex into another conformation of RNA, whereas MgCl₂ and LiCl at concentrations of 2.3 and 5.4 M, respectively, caused the complete transition from A-RNA to the new conformation. ³¹P-NMR spectra measured in 5.0 M LiCl confirmed the conclusion that A-RNA was transformed into another conformation which at 70°C was apparently melted to single-stranded RNA. An increase in MgCl₂ concentration to 0.5 M caused an apparent increase in the stability of the duplex. It was established that apolar alcohols did not influence the duplex conformation but, at 78% ($\text{v}\text{v}$), they caused the aggregation of the duplex. Trifluoroethanol and urea at 78% and 10 M, respectively, caused the melting of the duplex due to the breakage of the hydrogen bonds within the duplex. It was suggested that r(CpG)₃ formed a right-handed helix which under extreme conditions was transformed into another conformation and it was presumed that it might be a left-handed Z-RNA.     

A method for the study of N2O evolution in tropical wetlands

Simple gas handling equipment is presented and its use is described in biological denitrification potential measurements. Preliminary results are given for denitrification potentials at latitude 22° in South America. For the upper 5 cm of the sediment layer a first order kinetic process is found with a nitrate concentration decrement rate of 12% per day.     

The local impact of macrofauna and land-use intensity on soil nutrient concentration and exchangeability in lowland tropical Peru

Agricultural expansion is a major driver of deforestation which has negative consequences for biodiversity and habitat stability. While sustainable farming is known to be beneficial for biodiversity and crop resilience, little is known about the impact of macrofauna and land-use intensity on soil quality. In this study, we examine the relative effects of (a) soil macrofauna and (b) land use (primary forest, agroforestry, and annual crop) on element depletion rates, concentration, and exchangeability in standardized soil. We used microcosms with two different mesh sizes, 0.25 mm and 5 mm, to exclude and include macrofauna, respectively. The microcosms were incubated for up to a year throughout which samples were collected without replacement. Macrofauna did not have a significant impact on any of the soil parameters which is likely to be due to the low diversity of termites in the sites. Land-use intensity significantly affected cation depletion rates whose effects increased in order of primary forest<agroforestry<annual crop. At the end of the study, soil Mg⁺² concentration and Ca/Mg ratio in the agroforestry site differed from other land-use sites. Our results suggest that both bottom-up and top-down interactions have major effects on soil conditions, and the results should therefore be used to advise future research and policy around land-use management. Abstract in Spanish is available with online material.     

Cryo-electron microscopy targets in CASP13: Overview and evaluation of results

Structures of seven CASP13 targets were determined using cryo-electron microscopy (cryo-EM) technique with resolution between 3.0 and 4.0 Å. We provide an overview of the experimentally derived structures and describe results of the numerical evaluation of the submitted models. The evaluation is carried out by comparing coordinates of models to those of reference structures (CASP-style evaluation), as well as checking goodness-of-fit of modeled structures to the cryo-EM density maps. The performance of contributing research groups in the CASP-style evaluation is measured in terms of backbone accuracy, all-atom local geometry and similarity of inter-subunit interfaces. The results on the cryo-EM targets are compared with those on the whole set of eighty CASP13 targets. A posteriori refinement of the best models in their corresponding cryo-EM density maps resulted in structures that are very close to the reference structure, including some regions with better fit to the density.     

Inhibition of antigen trafficking through scavenger receptor A

B cell acquisition and presentation of specific autoantigens (auto-Ags) are thought to play an important and complex role in autoimmunity development. We previously identified scavenger receptor A (SR-A) as an early target in altering B cell-mediated autoimmunity. SR-A is highly expressed on professional antigen-presenting cells such as macrophages (MΦs) and dendritic cells (DCs). In this study, we demonstrate that SR-A is responsible for controlling B cell interactions with DCs/MΦs to promote Ag transfer from B cells to DCs/MΦs. We established a high-throughput ELISA-based screen to identify novel SR-A inhibitors, the specificity of which was determined by dose dependence and Biacore surface plasmon resonance testing. We identified small molecule inhibitors (SMIs) able to reduce SR-A-mediated Ag transfer in human cells. In particular, the SMIs prevented SR-A-positive cells from accumulating/loading Ag over time. Furthermore, we determined that one SMI, sennoside B, can reduce SR-A-mediated capture of B cells. Finally, SMI-mediated decreases in Ag transfer or accumulation reduced T cell proliferation in vitro and in vivo. These observations demonstrate that B cell-DC/MΦ interactions are conducive to promoting Ag trafficking between these cell types via SR-A. Inhibitors of SR-A may provide a novel therapeutic strategy in ameliorating autoimmune disease development.     

Diagnostic scintigraphy and effectiveness of 131I radioiodine therapy in differentiated thyroid carcinoma (DTC)

INTRODUCTION: Since the effect of pre-therapeutic scintigraphy on the outcome of DTC treatment is debated, we evaluated factors affecting the effectiveness of (131)I therapy with respect to the delay between diagnostic scintigraphy and the application of radioiodine. MATERIAL AND METHODS: In the studied group of 60 patients with DTC, mean age 54.6 +/- 13.0 years, four weeks prior to the planned diagnostics, L-thyroxine was withdrawn and the following tests performed: (131)I (4 MBq) uptake above the neck, thyroid volume by USG, TSH and hTg level. Wholebody scintigraphy (37 MBq) was performed. The time between this diagnostic scintigraphy and application of (131)I (3657 MBq) was calculated. Based on whole-body 131I scintigraphy (74 MBq) performed 1 year after radioiodine treatment, the patients were divided into: group I - 42 patients with no tracer accumulation, and group II--18 patients who continued to accumulate (131)I in the neck. RESULTS: The differences between the median values of (131)I uptake and of thyroid volumes, and between the TSH and hTg median values in the two groups of patients were found not to be statistically significant. The average times between diagnostic scintigraphy and (131)I treatment in group I and II (9.4 vs. 8.3 weeks, respectively) were not significantly different either. CONCLUSION: Despite the different effectiveness of supplementary (131)I treatment, patients in group I and group II showed no statistically significant differences in the studied parameters. It appears that the diagnostic (131)I activity of 37 MBq and the time between diagnostic scintigraphy and application of (131)I did not have any effect on the results of the treatment in our group of patients.     

Characterization and analysis of the regulatory network involved in control of lipomycin biosynthesis in Streptomyces aureofaciens Tü117

Analysis of the α-lipomycin biosynthesis gene cluster of Streptomyces aureofaciens Tü117 led to the identification of five putative regulatory genes, which are congregated into a subcluster. Analysis of the lipReg1–4 and lipX1 showed that they encode components of two-component signal transduction systems (LipReg1 and LipReg2), multiple antibiotics resistance-type regulator (LipReg3), large ATP-binding regulators of the LuxR family-type regulator (LipReg4), and small ribonuclease (LipRegX1), respectively. A combination of targeted gene disruptions, complementation experiments, lipomycin production studies, and gene expression analysis via RT-PCR suggests that all regulatory lip genes are involved in α-lipomycin production. On the basis of the obtained data, we propose that LipReg2 controls the activity of LipReg1, which in its turn govern the expression of the α-lipomycin pathway-specific regulatory gene lipReg4. The ribonuclease gene lipX1 and the transporter regulator lipReg3 appear to work independently of genes lipReg1, lipReg2, and lipReg4.