Sensibilized dimer luminescence of singlet molecular oxygen in solutions

With the use of mechanical phosphoroscope the "universal" delayed emission has been found in aerobic solutions of different sensitizers in CCl4. The spectrum of this emission has the main maximum at 703 nm. The luminescence intensity is proportional to the square of the intensity of the exciting light. Removal of oxygen or addition of 10% of acetone led to disappearance of the luminescence. At equal intensities of singlet oxygen generation relative intensities of the 1272 and 703 nm bands differed by several orders of magnitude in solutions of different sensitizers. The energy migration from the molecules responsible for the luminescence to bacteriopheophytin and phtalocyanine has been observed. The luminescence is interpreted as dimol emission of solvated singlet molecular oxygen activated by sensitizer molecules.     

Base-Calling Algorithm with Vocabulary (BCV) Method for Analyzing Population Sequencing Chromatograms

Sanger sequencing is a common method of reading DNA sequences. It is less expensive than high-throughput methods, and it is appropriate for numerous applications including molecular diagnostics. However, sequencing mixtures of similar DNA of pathogens with this method is challenging. This is important because most clinical samples contain such mixtures, rather than pure single strains. The traditional solution is to sequence selected clones of PCR products, a complicated, time-consuming, and expensive procedure. Here, we propose the base-calling with vocabulary (BCV) method that computationally deciphers Sanger chromatograms obtained from mixed DNA samples. The inputs to the BCV algorithm are a chromatogram and a dictionary of sequences that are similar to those we expect to obtain. We apply the base-calling function on a test dataset of chromatograms without ambiguous positions, as well as one with 3–14% sequence degeneracy. Furthermore, we use BCV to assemble a consensus sequence for an HIV genome fragment in a sample containing a mixture of viral DNA variants and to determine the positions of the indels. Finally, we detect drug-resistant Mycobacterium tuberculosis strains carrying frameshift mutations mixed with wild-type bacteria in the pncA gene, and roughly characterize bacterial communities in clinical samples by direct 16S rRNA sequencing.     

Water Soluble Chlorophyll-Binding Proteins of Plants: Structure,Properties and Functions

Molecular Biology - Water soluble chlorophyll-binding proteins (WSCPs) of higher plants differ from most proteins containing chlorophyll or bacteriochlorophyll in that they are soluble in watr and...     

Oligonucleotide microarray for subtyping of influenza virus A neuraminidase

Microarray for influenza A neuraminidase subtyping was presented. Selection of oligoprobes proceeded in two steps. First step included selection of peptides specific for each subtype of neuraminidase. At the second step oligoprobes were calculated using found peptides structures with the subsequent additional selection of the most specific and representative probes. From 19 to 24 probes were used for determination of each subtype of neuraminidase. Microchip testing for 19 samples with the most widespread types (N1 and N2) specifies in unequivocal definition 18 of them and only one isolate has not been identified.     

Photoinhibition of photosystem II in vitro: Spectral and kinetic analyses

Two different preparations of photosystem II (PSII) (BBY-type membrane fragments and PSII core complexes) were isolated from 14-day-old pea seedlings (Pisum sativum L.) and used for spectral and kinetic study of photobleaching of chlorophyll (Chl) and amino acids under photoinhibitory conditions. A short-term (2–4 min) illumination of PSII preparations with high-intensity red light (λ > 610 nm, 800 W/m²) resulted in irreversible photobleaching of Chl at 672 and 682 nm under conditions of both acceptor- and donor-side photoinhibition. At longer illumination exposures (> 10 min) the photobleaching maximum at 682 nm was predominant. The calculated kinetic constants for Chl photobleaching in both absorption bands at temperatures of 20 and 4°C had similar values under different photoinhibitory conditions. The shape of action spectrum for Chl photooxidation indicates that photoinhibition of PSII was sensitized by two spectral forms of Chl with absorption maxima at 670 and 680 nm. The photobleaching of amino acids in PSII membrane fragments was only observed during acceptor-side photoinhibition and displayed the photobleaching peaks at 220 and 274 nm. The photogeneration of superoxide anion radical during donor-side photoinhibition was 4–6 times larger than during acceptor-side photoinhibition. Nevertheless, the kinetics of Chl and amino acid photobleaching in PSII preparations showed no appreciable differences. The activation energies for Chl photooxidation were estimated around 3.5 and 9 kcal/mol during acceptor- and donor-side photoinhibition, respectively, providing evidence for the involvement of biochemical stages in PSII photoinhibition. Based on the data obtained, it is proposed that the antenna Chl, rather than Chl of the reaction center, is the sensitizer for both acceptor- and donor-side photoinhibition of PSII in vitro.     

Genetic analysis of housekeeping genes of members of the genus Acholeplasma: phylogeny and complementary molecular markers to the 16S rRNA gene

The partial nucleotide sequences of the rpoB and gyrB genes as well as the complete sequence of the 16S-23S rRNA intergenic transcribed spacer (ITS) were determined for all known Acholeplasma species. The same genes of Mesoplasma and Entomoplasma species were also sequenced and used to infer phylogenetic relationships among the species within the orders Entomoplasmatales and Acholeplasmatales. The comparison of the ITS, rpoB, and gyrB phylogenetic trees with the 16S rRNA phylogenetic tree revealed a similar branch topology suggesting that the ITS, rpoB, and gyrB could be useful complementary phylogenetic markers for investigation of evolutionary relationships among Acholeplasma species. Thus, the multilocus phylogenetic analysis of Acholeplasma multilocale sequence data (ATCC 49900 (T) = PN525 (NCTC 11723)) strongly indicated that this organism is most closely related to the genera Mesoplasma and Entomoplasma (family Entomoplasmataceae) and form the branch with Mesoplasma seiffertii, Mesoplasma syrphidae, and Mesoplasma photuris. The closest genetic relatedness of this species to the order Entomoplasmatales was additionally supported by the finding that A. multilocale uses UGA as the tryptophan codon in its gyrB and gyrA sequences. Use of the UGA codon for encoding tryptophan was previously reported as a unique genetic feature of Entomoplasmatales and Mycoplasmatales but not of Acholeplasmatales. These data, as well as previously published data on metabolic features of A. multilocale, leads to the proposal to reclassify A. multilocale as a member of the family Entomoplasmataceae.     

Conserved and species-specific alternative splicing in mammalian genomes

Background  

Alternative splicing has been shown to be one of the major evolutionary mechanisms for protein diversification and proteome expansion, since a considerable fraction of alternative splicing events appears to be species- or lineage-specific. However, most studies were restricted to the analysis of cassette exons in pairs of genomes and did not analyze functionality of the alternative variants.     

Photoreduction of Molecular Oxygen in Preparations of Photosystem II under Photoinhibitory Conditions

Preparations of photosystem II (PSII) from pea (Pisum sativum L.) leaves were used to study the evolution and reduction of molecular oxygen under photoinhibitory conditions. Under these conditions, the photoinduced oxygen uptake did not exceed 10% of the total oxygen-evolving activity in PSII preparations. Both the Hill and the Mehler reactions were found to occur simultaneously under long-term illumination of PSII preparations with high-intensity light in the presence of potassium ferricyanide. During this light treatment in the presence of potassium ferricyanide, the rate of oxygen uptake increased gradually reaching 30% of the oxygen-evolving activity. The photogeneration of superoxide anion radical at increasing light intensities followed a typical light-response curve with a light saturation at 800 W/m². The results provide evidence that the Mehler reaction is the major source for superoxide and hydrogen peroxide in PSII preparations under photoinhibitory conditions and that the Mehler reaction in PSII proceeds more effectively at high light intensities. The relatively low and sustained rate of oxygen photoreduction in PSII preparations under photoinhibitory conditions substantiates the hypothesis on the involvement of Mehler reaction in cell signaling and regulation.     

EDAS, databases of alternatively spliced human genes

EDAS, a database of alternatively spliced human genes, contains data on the alignment of proteins, mRNAs, and EST. It contains information on all exons and introns observed, as well as elementary alternatives formed from them. The database makes it possible to filter the output data by changing the cut-off threshold by the significance level. The database is accessible at http://www.gene-bee.msu.ru/edas/.