Energy landscape of a small peptide revealed by dihedral angle principal component analysis

A 100 ns molecular dynamics simulation of penta-alanine in explicit water is performed to study the reversible folding and unfolding of the peptide. Employing a standard principal component analysis (PCA) using Cartesian coordinates, the resulting free-energy landscape is found to have a single minimum, thus suggesting a simple, relatively smooth free-energy landscape. Introducing a novel PCA based on a transformation of the peptide dihedral angles, it is found, however, that there are numerous free energy minima of comparable energy (less than or approximately 1 kcal/mol), which correspond to well-defined structures with characteristic hydrogen-bonding patterns. That is, the true free-energy landscape is actually quite rugged and its smooth appearance in the Cartesian PCA represents an artifact of the mixing of internal and overall motion. Well-separated minima corresponding to specific conformational structures are also found in the unfolded part of the free energy landscape, revealing that the unfolded state of penta-alanine is structured rather than random. Performing a connectivity analysis, it is shown that neighboring states are connected by low barriers of similar height and that each state typically makes transitions to three or four neighbor states. Several principal pathways for helix nucleation are identified and discussed in some detail.     

Analysis of nucleotide sequence polymorphism of internal transcribed spacers of ribosomal genes in diploid <Emphasis Type="Italic">Aegilops</Emphasis> (L.) species

The nucleotide sequence of the fragment of the internal transcribed spacer (ITS) of rDNA comprising the full-length ITS1, the gene encoding 5.8S rRNA, and part of the ITS2 sequence was determined in 22 samples of five diploid Aegilops species. The full alignment length of compared sequences was 524 bp. Species-specific substitutions were found in the ITS nucleotide sequence of rDNA of different Aegilops species. Intraspecific differences in ITS structure in diploid Aegilops species were detected for the first time. Polymorphism of the ITS nucleotide sequence within the same sample was revealed, which might be due either to differences between the genomes of individual plants comprising the sample or to the presence of several types of ribosomal genes in the genome of one plant. In general, both interspecific and intraspecific variability of the ITS nucleotide sequences of rDNA is extremely low. In total, 26 variable sites, twelve of which were informative, were identified.__________Translated from Molekulyarnaya Biologiya, Vol. 39, No. 2, 2005, pp. 193–197.Original Russian Text Copyright © 2005 by Goryunova, Chikida, Gori, Kochieva.     

Anthraquinones from Hedyotis capitellata

Four new furanoanthraquinones, 2-hydroxymethyl-3,4-[2'-(1-hydroxy-1-methylethyl)-dihydrofurano]-8-hydroxyanthraquinone, 2-hydroxymethyl-3,4-[1'-hydroxy-2'-(1-hydroxy-1-methylethyl)-dihydrofurano]-8-hydroxyanthraquinone, 2-hydroxymethyl-3,4-[2'-1-hydroxy-1-methylethyl)-dihydrofurano]anthraquinone and 2-methyl-3,4-[2'-(1-hydroxy-1-methylethyl)-dihydrofurano] anthraquinone or capitellataquinone A-D and four known anthraquinones, rubiadin, anthragallol 2-methyl ether, alizarin 1-methyl ether and digiferruginol, together with scopoletin were isolated from the stems of Hedyotis capitellata Wall (Rubiaceae). Lucidin-3-O-beta-glucoside was isolated from the roots of the plant. Characterization of the new compounds was carried out by extensive NMR studies using FGCOSY, FGHMQC, FGHMBC and DEPT-135 in addition to other spectroscopic methods.     

Walker-256 tumor growth causes oxidative stress in rat brain

The elevated rate of oxygen consumption and high amount of polyunsaturated fatty acids make the central nervous system vulnerable to oxidative stress. The effect of Walker-256 tumor growth on oxi-reduction indexes in the hypothalamus (HT), cortex (CT), hippocampus (HC) and cerebellum (CB) of male Wistar rats was investigated. The presence of the tumor caused an increase in thiobarbituric acid reactant substances (TBARs) in the HT, CB and HC. Due to tumor growth, the activity of glucose-6-phosphate dehydrogenase increased in the HT and CB, whereas citrate synthase activity was reduced in the HT, CT and CB. Therefore, the potential for generation of reducing power is increased in the cytosol and decreased in the mitochondria of various brain regions of Walker-256 tumor-bearing rats. These changes occurred concomitantly with an unbalance in the brain enzymatic antioxidant system. The tumor decreased the activities of catalase in the HT and CB and of glutathione peroxidase in the HT, CB and HC, and raised the CuZn-superoxide dismutase activity in the HT, CB and HC. These combined findings indicate that Walker-256 tumor growth causes oxidative stress in the brain.     

GENETIC VARIABILITY OF BRAZILIAN STRAINS OF THE MICROCYSTIS AERUGINOSA COMPLEX (CYANOBACTERIA/CYANOPHYCEAE) USING THE PHYCOCYANIN INTERGENIC SPACER AND FLANKING REGIONS (cpcBA)

The genetic and morphological variability among 15 Brazilian strains of Microcystis aeruginosa (Kütz.) Kütz. collected from four locations was examined and compared with several reference strains of M. aeruginosa , M. viridis (A. Br.) Lemm. and M. wesenbergii (Kom.) Kom. in Kondr. Brazilian strains were classified by morphological features and by comparison of the nucleotide sequences of the cpc BA intergenic spacer and flanking regions. Our results indicate that Brazilian strains classified as M. aeruginosa are phylogenetically diverse compared with reference strains of M. aeruginosa and that the current taxonomy underestimates genetic diversity within M. aeruginosa. The data also demonstrate that morphological criteria alone are inadequate to characterize Microcystis species. Although colonial characters were shown to vary considerably in culture, some genetic lineages demonstrated consistent cellular diameter ranges, indicating that cell size has value as a taxonomic character. The detection of six M. aeruginosa genotypes in a single water body indicates that morphological approaches can also seriously underestimate the diversity of Microcystis bloom populations.     

Variation in Chromatin Structure of the rDNA Transcribed Region in Human Peripheral Blood Lymphocytes

The rDNA transcribed region (TR) was tested for its accessibility for RsaI recognizing 15 TR sites, DNase I, and photoinducible arylazide (N-(4-azido-2-hydroxybenzoyl)-N,N"-diaminoheptane acetate) in isolated nuclei, and for the arylazide in intact cells. Arylazide readily entered the cells and did not appreciably affect the chromatin structure. Its photolysis products efficiently modified DNA in accessible sites. Single-strand breaks made by DNase I were not transformed into two-strand ones in rDNA TR, suggesting the necessity of denaturing electrophoresis for such an analysis. About 70% of all rDNA copies proved poorly accessible for endonucleases and arylazide, the accessibility being higher in their 18S and 5.8S rRNA gene regions than in the regions of the external transcribed spacers (ETSs) and the 28S rRNA gene. Proteinase K disrupted this structure, and the corresponding copies were extracted from nuclei. This explained whyin situ hybridization occasionally fails to reveal rDNA in the nucleolar fibrillar center (FC) on electron microscopic preparations. In other rDNA copies, TR (excluding 5"-ETS) was accessible for nucleases and arylazide. These copies were not extracted from nuclei treated with proteinase K. Some of their RsaI sites were protected by tightly bound proteins. Seven such regions were identified in TR. Possible association of the molecular structure, nucleolar location, and functional state of rDNA is discussed.     

Evolutionary relationships of trichostrongyloid nematodes (Strongylida) inferred from ribosomal DNA sequence data

The evolutionary relationships of 21 species of trichostrongyloid nematodes were determined by use of sequence data of the second internal transcribed spacer of the ribosomal DNA aligned according to secondary structure information. Irrespective of the method of analysis used, the topologies of the phylogenetic trees derived from the molecular data differed with respect to all four hypotheses proposed previously for the evolutionary relationships of the different subfamilies within the Trichostrongylidae based on morphological data. Thus, the molecular data set did not resolve the conflict between the four previous proposals for the subfamilial relationships. Nonetheless, all trees derived from the molecular data showed strong support for the exclusion of the genera Filarinema and Amidostomum from the clade containing the species within the family Trichostrongylidae. This represents a major difference from the most recent proposal of the systematics of the Trichostrongyloidea in which these two genera were included within the Trichostrongylidae. Therefore, the molecular data support an earlier systematic framework in which Filarinema and Amidostomum were considered to be sister groups of the Trichostrongyloidea.     

Activated sludge encapsulation in gellan gum microbeads for gasoline biodegradation

A two-phase dispersion technique, termed emulsification–internal gelation, is proposed for encapsulation of activated sludge in gellan gum microbeads. The influence of emulsion parameters on size distribution of microbeads was investigated. Mean diameter of microbeads varied within a range of 34–265 µm as a descending function of emulsion stirring rate (1,000–5,000 rpm), emulsification time (10–40 min), and emulsifier concentration (0–0.1% w/w), and as an ascending function of disperse phase volume fraction (0.08–0.25). Encapsulated sludge expressed a high biodegradation activity compared with non-encapsulated sludge cultures even at 4.4 times lower level of overall biomass loading. Over 90% of gasoline at an initial concentration of 35 and 70 mg l^–1 was removed by both encapsulated and non-encapsulated sludge cultures in sealed serum bottles within 7 days. Encapsulation of activated sludge in gellan gum microbeads enhanced the biological activity of microbial populations in the removal of gasoline hydrocarbons. The results of this study demonstrated the feasibility of the production of size-controlled gellan gum-encapsulated sludge microbeads and their use in the biodegradation of gasoline.     

Molecular cytogenetics of Xeranthemum L. and related genera (Asteraceae, Cardueae)

Abstract: Seven representatives of the genera Amphoricarpus, Chardinia, Siebera, and Xeranthemum, all of them closely related as demonstraded by molecular phylogeny, have been studied from a cytogenetic perspective. Morphometrical karyotype parameters were calculated and idiograms obtained. Fluorochrome banding was performed with chromomycin A₃ to identify GC-rich regions in the chromosomes. Fluorescence in situ hybridization allowed us to locate the sites of 18S-5.8S-26S and 5S rDNA. Silver nitrate staining was used to count the number of nucleoli and to detect the active nucleolar organizing regions. Systematic and evolutionary issues are addressed in the light of these data.