STING Millennium Suite: integrated software for extensive analyses of 3d structures of proteins and their complexes

Background  

The integration of many aspects of protein/DNA structure analysis is an important requirement for software products in general area of structural bioinformatics. In fact, there are too few software packages on the internet which can be described as successful in this respect. We might say that what is still missing is publicly available, web based software for interactive analysis of the sequence/structure/function of proteins and their complexes with DNA and ligands. Some of existing software packages do have certain level of integration and do offer analysis of several structure related parameters, however not to the extent generally demanded by a user.     

Biomimetic oxidation of benzene by a polynuclear manganese complex [Mn12O12(CH3CO2)16(H2O)4] under mild conditions

The possibility of monooxygenase enzymes biomimetic construction models with the use of polynuclear manganese complexes was shown. It was demonstration that benzene is oxidized by polynuclear manganese complex [Mn12O12(CH3CO2)16(H2O)4] in acetonitrile solution at room temperature and atmospheric pressure yielding phenol with the selectivity more than 80%. It was determined that the addition of air oxygen as the reoxidizer to the reaction mixture didn't transfer the reaction into the catalytic mode.     

Genome-scale metabolic reconstruction and <Emphasis Type="Italic">in silico</Emphasis> analysis of methylotrophic yeast <Emphasis Type="Italic">Pichia pastoris</Emphasis> for strain improvement

Background  

Pichia pastoris has been recognized as an effective host for recombinant protein production. A number of studies have been reported for improving this expression system. However, its physiology and cellular metabolism still remained largely uncharacterized. Thus, it is highly desirable to establish a systems biotechnological framework, in which a comprehensive in silico model of P. pastoris can be employed together with high throughput experimental data analysis, for better understanding of the methylotrophic yeast's metabolism.     

Study of genetic diversity in potato cultivars using PCR analysis of organelle DNA

The genetic diversity of 98 potato cultivars of Russian and foreign breeding was studied using of PCR with organelle-specific primers. The polymorphism of both plastid (atpE, trnG/trnK) and mitochondrial (rps, atp6) loci was revealed. Eight different haplotypes were detected in the sample of cultivars studied. Comparatively low of polymorphism of organelle DNA in the potato cultivars was demonstrated: most cultivars (91 or 92.9%) possessed only two haplotypes (I and II); 62 cultivars of them had similar "cultural" cytoplasmic type (haplotype I). The breeding cultivars of the Russian and foreign origin did not differ from each other in frequency of basic haplotypes.     

Interaction of microwave radiation undergoing stochastic phase jumps with plasmas or gases

New types of beam-plasma devices generating intense stochastic microwave radiation in the interaction of electron beams with hybrid plasma waveguides were developed and put into operation at the National Science Center Kharkov Institute of Physics and Technology (Ukraine). The objective of the paper is to discuss the results of theoretical and experimental studies and numerical simulations of the normal and oblique incidence of linearly polarized electromagnetic waves on an interface between a vacuum and an overcritical plasma. The main results of the reported investigations are as follows: (i) for the parameter values under analysis, the transmission coefficient for microwaves with a stochastically jumping phase is one order of magnitude greater than that for a broadband regular electromagnetic wave with the same spectral density; (ii) the electrons are heated most efficiently by obliquely incident waves with a stochastically jumping phase and, in addition, the electron distribution function has a high-energy tail; and (iii) necessary conditions for gas breakdown and for the initiation of a microwave discharge in stochastic fields in a light source are determined. The anomalously large transmission coefficient for microwaves, the anomalous character of the breakdown conditions, the anomalous behavior of microwave gas discharges, and the anomalous nature of collisionless electron heating, are attributed to stochastic jumps in the phase of microwave radiation.     

Cytogenetic analysis of Lycopersicon esculentum (+) Solanum etuberosum somatic hybrids and their androgenetic regenerants

The aim of the study was to characterize genomic relationships among cultivated tomato (Lycopersicon esculentum Mill.) (2n=2x=24) and diploid (2n=2x=24) non-tuberous wild Solanum species (S. etuberosum Lindl.). Using genomic in situ hybridization (GISH) of mitotic and meiotic chromosomes, we analyzed intergeneric somatic hybrids between tomato and S. etuberosum. Of the five somatic hybrids, two plants were amphidiploids (2n=4x=48) mostly forming intragenomic bivalents in their microsporocytes, with a very low frequency of multivalents involving the chromosomes of tomato and S. etuberosum (less than 0.2 per meiocyte). Tomato chromosomes showed preferential elimination during subsequent meiotic divisions of the amphidiploids. Transmission of the parental chromosomes into microspores was also evaluated by GISH analysis of androgenic plants produced by direct embryogenesis from the amphidiploid somatic hybrids. Of the four androgenic regenerants, three were diploids (2n=2x=24 or 2n=2x+1=25) derived from reduced male gametes of the somatic hybrids, and one plant was a hypertetraploid (2n=4x+4=52). GISH revealed that each anther-derived plant had a unique chromosome composition. The prospects for introgression of desirable traits from S. etuberosum into the gene pool of cultivated tomato are discussed. Received: 2 August 2000 / Accepted: 4 December 2000     

Allopolyploid speciation of the Mexican tetraploid potato species Solanum stoloniferum and S. hjertingii revealed by genomic in situ hybridization

Thirty-six percent of the wild potato (Solanum L. section Petota Dumort.) species are polyploid, and about half of the polyploids are tetraploid species (2n = 4x = 48). Determination of the type of polyploidy and development of the genome concept for members of section Petota traditionally has been based on the analysis of chromosome pairing in species and their hybrids and, most recently, DNA sequence phylogenetics. Based on these data, the genome designation AABB was proposed for Mexican tetraploid species of series Longipedicellata Buk. We investigated this hypothesis with genomic in situ hybridization (GISH) for both representatives of the series, S. stoloniferum Schltdl. and S. hjertingii Hawkes. GISH analysis supports an AABB genome constitution for these species, with S. verrucosum Schltdl. (or its progenitor) supported as the A genome donor and another North or Central American diploid species (S. cardiophyllum Lindl., S. ehrenbergii (Bitter) Rydb., or S. jamesii Torrey) as the B genome donor. GISH analysis of chromosome pairing of S. stoloniferum also confirms the strict allopolyploid nature of this species. In addition, fluorescence in situ hybridization data suggest that 45S rDNA regions of the two genomes of S. stoloniferum were changed during coevolution of A and B genomes of this allotetraploid species.     

Polymer optoelectronic structures for retinal prosthesis

This commentary highlights the effectiveness of optoelectronic properties of polymer semiconductors based on recent results emerging from our laboratory, where these materials are explored as artificial receptors for interfacing with the visual systems. Organic semiconductors based polymer layers in contact with physiological media exhibit interesting photophysical features, which mimic certain natural photoreceptors, including those in the retina. The availability of such optoelectronic materials opens up a gateway to utilize these structures as neuronal interfaces for stimulating retinal ganglion cells. In a recently reported work entitled “A polymer optoelectronic interface provides visual cues to a blind retina,” we utilized a specific configuration of a polymer semiconductor device structure to elicit neuronal activity in a blind retina upon photoexcitation. The elicited neuronal signals were found to have several features that followed the optoelectronic response of the polymer film. More importantly, the polymer-induced retinal response resembled the natural response of the retina to photoexcitation. These observations open up a promising material alternative for artificial retina applications.