30S ribosomal subunits with fragmented 16S RNA: a new approach for structure and function study of ribosomes.

A new approach for function and structure study of ribosomes based on oligodeoxyribonucleotide-directed cleavage of rRNA with RNase H and subsequent reconstitution of ribosomal subunits from fragmented RNA has been developed. The E coli 16S rRNA was cleaved at 9 regions belonging to different RNA domains. The deletion of 2 large regions was also produced by cleaving 16S rRNA in the presence of 2 or 3 oligonucleotides complementary to different RNA sites. Fragmented and deleted RNA were shown to be efficiently assembled with total ribosomal protein into 30S-like particles. The capacity to form 70S ribosomes and translate both synthetic and natural mRNA of 30S subunits reconstituted from intact and fragmented 16S mRNA was compared. All 30S subunits assembled with fragmented 16S rRNA revealed very different activity: the fragmentation of RNA at the 781-800 and 1392-1408 regions led to the complete inactivation of ribosomes, whereas the RNA fragmentation at the regions 296-305, 913-925, 990-998, 1043-1049, 1207-1215, 1499-1506, 1530-1539 did not significantly influence the ribosome protein synthesis activity, although it was also reduced. These findings are mainly in accordance with the data on the functional activity of some 16S rRNA sites obtained by other methods. The relations between different 16S RNA functional sites are discussed.     

Investigation of ribosomes using molecular dynamics simulation methods

The ribosome as a complex molecular machine undergoes significant conformational changes while synthesizing a protein molecule. Molecular dynamics simulations have been used as complementary approaches to X-ray crystallography and cryoelectron microscopy, as well as biochemical methods, to answer many questions that modern structural methods leave unsolved. In this review, we demonstrate that all-atom modeling of ribosome molecular dynamics is particularly useful in describing the process of tRNA translocation, atomic details of behavior of nascent peptides, antibiotics, and other small molecules in the ribosomal tunnel, and the putative mechanism of allosteric signal transmission to functional sites of the ribosome.     

The cholinolytic activity of the new anti-arrhythmia preparation Nibentan]

In the rabbit isolated right atrium and the rat atrial cells, a new class III antiarrhythmic drug Nibentan was shown to exert an anticholinergic effect contrary to Carbachol: the latter decreased the AP duration to 42 +/- 2% of the control whereas Nibentan restored it to 65 +/- 2%. The anticholinergic effect of the drug was found to be due to inhibition of the acetylcholine-activated potassium current: it was decreased by 79 +/- 3% in the rat isolated single atrial cells. In the rabbit isolated sino-atrial node, Nibentan prevented arrhythmogenic effects of vagal stimulation. The new drug may be quite efficient in treatment of flutter and atrial fibrillation.     

Synaptonemal complexes of the A- and B-chromosomes of the spermatocytes from the East Asian mouse Apodemus peninsulae

The analysis of whole-mount preparations of synaptonemal complexes (SCs) from surface-spread spermatocytes of A. peninsulae (2n = 48A + 1, 2, ... 12 B) had revealed SCs of 23 autosomal bivalents, sex bivalent XY, axial cores and SCs of the B-chromosomes. The intercellular and interindividual variability of the number of B-chromosomes varied from 1 to 12 per cell. The SCs of autosomal bivalents were shown to have a typical structure. The structure and behaviour of SCs of sex bivalent throughout meiotic prophase I appeared to be similar to those observed in other species of this order. Mainly B-univalents and less frequently B-bivalents containing SCs were found to be formed in meiotic prophase I. The full homologues appear to be rarely seen among B-chromosomes of the East-Asiatic mouse. A tendency of forming clusters of B-univalents near the sex bivalent was found, in addition to B-bivalents with lateral elements, having the form of bi- and tri-stranded elements with rare synaptic fragments. Besides this, the SCs of the autosomes of pachytene cells were found to contain structures resembling the recombination nodules.     

A carbon column-based liquid chromatography electrochemical approach to routine 8-hydroxy-2'-deoxyguanosine measurements in urine and other biologic matrices: a one-year evaluation of methods.

8-Hydroxy-2'-deoxyguanosine (8OH2'dG) is a principal stable marker of hydroxyl radical damage to DNA. It has been related to a wide variety of disorders and environmental insults, and has been proposed as a useful systematic marker of oxidative stress. Analytic procedures for 8OH2'dG in DNA digests are well established; however, routine measurement of free 8OH2'dG in other body fluids such as urine or plasma has been problematic. This has hindered its evaluation as a general clinical, therapeutic monitoring, or environmental assessment tool. Therefore, we developed a liquid chromatography electrochemical column-switching system based on the use of the unique purine selectivity of porous carbon columns that allows routine accurate measurement of 8OH2'dG in a variety of biologic matrices. This paper describes the rationale of the system design and the protocols developed for 8OH2'dG in urine, plasma, cerebrospinal fluid, tissue, DNA, saliva, sweat, kidney dialysis fluid, foods, feces, culture matrix, and microdialysates. Concentrations in both human and animal body fluids and tissues are reported. The system performance is discussed in the context of a 1-year evaluation of the methods applied to approximately 3600 samples, using internal quality control and external blind testing to determine long-term accuracy. The methods are reliable and accurate, and therefore should prove useful in assessing the role and utility of oxidative DNA damage in aging and human illness.     

Metabolomic Profiling in LRRK2-Related Parkinson's Disease

Background

Mutations in LRRK2 gene represent the most common known genetic cause of Parkinson''s disease (PD).

Methodology/Principal Findings

We used metabolomic profiling to identify biomarkers that are associated with idiopathic and LRRK2 PD. We compared plasma metabolomic profiles of patients with PD due to the G2019S LRRK2 mutation, to asymptomatic family members of these patients either with or without G2019S LRRK2 mutations, and to patients with idiopathic PD, as well as non-related control subjects. We found that metabolomic profiles of both idiopathic PD and LRRK2 PD subjects were clearly separated from controls. LRRK2 PD patients had metabolomic profiles distinguishable from those with idiopathic PD, and the profiles could predict whether the PD was secondary to LRRK2 mutations or idiopathic. Metabolomic profiles of LRRK2 PD patients were well separated from their family members, but there was a slight overlap between family members with and without LRRK2 mutations. Both LRRK2 and idiopathic PD patients showed significantly reduced uric acid levels. We also found a significant decrease in levels of hypoxanthine and in the ratios of major metabolites of the purine pathway in plasma of PD patients.

Conclusions/Significance

These findings show that LRRK2 patients with the G2019S mutation have unique metabolomic profiles that distinguish them from patients with idiopathic PD. Furthermore, asymptomatic LRRK2 carriers can be separated from gene negative family members, which raises the possibility that metabolomic profiles could be useful in predicting which LRRK2 carriers will eventually develop PD. The results also suggest that there are aberrations in the purine pathway in PD which may occur upstream from uric acid.