A collection of programs for one‐dimensional Ising analysis of linear repeat proteins with point substitutions

A collection of programs is presented to analyze the thermodynamics of folding of linear repeat proteins using a 1D Ising model to determine intrinsic folding and interfacial coupling free energies. Expressions for folding transitions are generated for a series of constructs with different repeat numbers and are globally fitted to transitions for these constructs. These programs are designed to analyze Ising parameters for capped homopolymeric consensus repeat constructs as well as heteropolymeric constructs that contain point substitutions, providing a rigorous framework for analysis of the effects of mutation on intrinsic and directional (i.e., N‐ vs. C‐terminal) interfacial coupling free‐energies. A bootstrap analysis is provided to estimate parameter uncertainty as well as correlations among fitted parameters. Rigorous statistical analysis is essential for interpreting fits using the complex models required for Ising analysis of repeat proteins, especially heteropolymeric repeat proteins. Programs described here are available at https://github.com/barricklab-at-jhu/Ising_programs .     

Effect of the duration of a reproducible interval on reaction time in man

The dependence of reaction time (RT) of reproduction of presented standard intervals on their duration (100-5000 ms) was studied on 30 subjects. The intervals were limited by two electrocutaneous stimuli or two clicks and were presented both at random and at a gradual increase or decrease, with a step of 100 ms. They were reproduced by pressing a button. The RTs duration depended on the presented interval within the range from 100 to 2000 ms. Such scatter of the upper limit is due to differences in the methods of presentation of the material and to individual features of the subjects. A presence of two mechanisms of time intervals reproduction is suggested for such experimental conditions: the image of the standard interval might be created either after its presentation or in the process of its presentation. Correspondingly, the RT dependence on the interval duration is manifest in the first case and is absent in the second.     

Characteristics of the leaf photosynthetic machinery in broad bean grown in zinc chloride aqueous solutions

The structural and functional characteristics of bean leaves (the content of chlorophyll, the rate of oxygen production, the slow fluorescence induction, and light-induced changes in the EPR signal I from oxidized reaction centers P700+) were investigated to obtain insight into the mechanism of influence of zinc chloride on the photosynthetic apparatus. Seedlings were grown on hydroponic medium containing ZnCl2 at concentrations from 10(-7) to 10(-3) M. At low concentrations of ZnCl2, a decrease in the content of chlorophyll per one unit of leaf mass was observed, while the rate of oxygen production per chlorophyll was increased. High concentrations of ZnCl2 in the hydroponic medium caused the slowed down the plant development and inhibited the light-induced production of oxygen. The changes in biophysical characteristics of leaves the parameter FM/FT of the slow fluorescence induction, and kinetics of redox transients of P700 induced by ZnCl2 were of similar character and correlated with the changes in photosynthetic activity. The data obtained demonstrate that structural and functional changes in the photosynthetic apparatus induced by the variations of growth conditions have adaptive character.     

Mitochondrial DNA variation in populations of the chum salmon Oncorhynchus keta (Walbaum) from rivers of the Prymorye and Sakhalin

Mitochondrial DNA (mtDNA) variation was studied using restriction fragment length polymorphism (RFLP) in chum salmon populations from three rivers in southern Primorye and one river in Sakhalin Island. Significant differences were detected between the samples from Primorye and Sakhalin Island. No differences were found between the samples from the rivers of Primorye, which can be explained by a high rate of gene flow due to transplantation of spawn from one river to another. The effect of fish breeding on the chum salmon populations correlated with the indices of haplotype and nucleotide diversity (h and pi, respectively). The lowest diversity was found in the completely artificial population from the Ryazanovka River; the highest, in natural populations from the Narva and Naiba rivers. Frequencies of haplotypes in consecutive generations were significantly different, which confirms the effects of genetic drift on the small-size chum salmon populations of Primorye.     

Evoked potentials in the brain of adolescents in norm and those with attention deficit during recognition of short-term acoustic stimuli

The effect of stimulus duration on auditory event-related potentials and performance of oddball task was studied in normal children and those with attention-deficit symptoms. Mismatch negativity was absent on presentation of short-term (11 ms) stimuli and present with longer stimuli (50 ms). The adolescents with deficit of attention performed much worse (errors of omission) with the short stimuli. The RT was significantly larger in subjects with attention-deficit with all types of tested stimulus duration. They also manifested a smaller P3b amplitude in response to task-relevant deviant stimuli and larger N2b peaks in response to the standard stimuli. It was possible to differentiate between the MMN and the N2b components owing to the fact that the MMN was absent with shorter stimuli. The findings suggest that there is a deficit in processing of sensory information at the cortical level in subjects with the attention-deficit symptoms.     

The role of antioxidative status in development of the consequences of biological action under low dose and low intensity irradiation

The scale and direction of changes of a number of biophysical, biochemical and physiological parameters in SHK mice (male) tissues were studied depending on their initial values for mice control groups within 1 day after low intensity gamma-irradiation (15 cGy). The reciprocal dependences between the scales of the lipid antioxidative activity (AOA) in brain or the spleen mass changes and their values for mice control groups were found. The external dependences were revealed between the amounts of lipid peroxidation secondary products in spleen, liver and blood plasma of the control mice and a scale of their change after irradiation. The most substantial changes of this parameter were observed in blood plasma and the changes of the phospholipid content within the total lipid composition were found in spleen and blood erythrocytes of the irradiated mice, that is in the lipids of tissues, which had the lowest level of AOA for mice control groups. The experimental data obtained indicate that the initial antioxidant status of animal tissues plays the important role for the development of consequences of the biological action under low dose and low intensity irradiation.     

The structure of the micromycete complexes of oligotrophic peat deposits in the southern taiga subzone of West Siberia

The analysis of the micromycete complexes of oligotrophic peat deposits in the Vasyugan Marsh by direct count and culture methods showed that the micromycete carbon comprises no more than 3% of the total peat carbon and that the microscopic fungal biomass varies from 2 to 13 tons/hectare, depending on the season and the peat deposit thickness. Fungal spores were found in all layers of the peat deposits, whereas the mycelium was found only in the active peat layer. The high abundance of eukaryotic cells in the peats was due to the presence of yeastlike cells rather than fungal spores. Analyses by culture methods showed that micromycetes were present in all peat layers and that their abundance tended to decrease with depth, except for yeasts, which were uniformly distributed in a vertical direction. The micromycete complexes of the peat deposits were similar in the diversity and abundance of dominant species but differed in the composition of minor species. Peat yeasts were dominated by ascomycetes.     

Functional topography of afferent projections of the horizontal division of the nucleus of the diagonal band in the dorsolateral neocortex of the cat

EPs recording under Nembutal anaesthesia during stimulation of the medial section of the horizontal part of the diagonal band nucleus (HNDB) shows a wide spreading of HNDB afferentation over the neocortex: from the frontal area to the medial and some posterior parts of the auditory, parietal areas and Ep zone, with the least activation of the latter three regions and activation increasing intensity correspondingly in the somatic zones II, I (SII, SI), motor and frontal cortex. Such reduction of signals flow intensity oriented both in caudal and ventral directions of the cortex goes with foci of maximal activity of these signals in the motor, parietal areas and zones of representation of various body parts in SI and SII. Traits of similarity and differences of signal's projections in the neocortex from HNDB and thalamic relay nuclei have been revealed. A hypothesis is substantiated on different mechanisms underlying peculiarities of influences of these subcortical nuclei on the cortex depending on the type of their afferent-neuronal links in the latter and their functional role in the brain activity.