Synthesis of 1-hydroxyalkyl-3-substituted ureas and thioureas as a substrates for alcohol dehydrogenase]

A series of 1-(2-hydroxyethyl)- and 1-(3-hydroxyethyl)-3-substituted ureas and thioureas were synthesized. 1-(3-Hydroxyethyl)-3-acylthioureas were shown to be specific substrates for alcohol dehydrogenase in vitro.     

Aryl–aryl interactions in designed peptide folds: Spectroscopic characteristics and optimal placement for structure stabilization

We have extended our studies of Trp/Trp to other Aryl/Aryl through‐space interactions that stabilize hairpins and other small polypeptide folds. Herein we detail the NMR and CD spectroscopic features of these types of interactions. NMR data remains the best diagnostic for characterizing the common T‐shape orientation. Designated as an edge‐to‐face (EtF or FtE) interaction, large ring current shifts are produced at the edge aryl ring hydrogens and, in most cases, large exciton couplets appear in the far UV circular dichroic (CD) spectrum. The preference for the face aryl in FtE clusters is W ? Y ≥ F (there are some exceptions in the Y/F order); this sequence corresponds to the order of fold stability enhancement and always predicts the amplitude of the lower energy feature of the exciton couplet in the CD spectrum. The CD spectra for FtE W/W, W/Y, Y/W, and Y/Y pairs all include an intense feature at 225–232 nm. An additional couplet feature seen for W/Y, W/F, Y/Y, and F/Y clusters, is a negative feature at 197–200 nm. Tyr/Tyr (as well as F/Y and F/F) interactions produce much smaller exciton couplet amplitudes. The Trp‐cage fold was employed to search for the CD effects of other Trp/Trp and Trp/Tyr cluster geometries: several were identified. In this account, we provide additional examples of the application of cross‐strand aryl/aryl clusters for the design of stable β‐sheet models and a scale of fold stability increments associated with all possible FtE Ar/Ar clusters in several structural contexts. © 2016 Wiley Periodicals, Inc. Biopolymers 105: 337–356, 2016.     

Genetic differentiation of the endemic Baikalian mollusk Baicalia carinata (Mollusca: Caenogastropoda)

In gastropod mollusk Baicalia carinata Dybowski, 1875, sampled in different sites of the Lake Baikal, comparison of 81 sequences of internal transcribed spacer 1 (ITS1) located between the genes for 18S rRNA and 5.8S rRNA, and of 100 sequences of the fragment of mitochondrial cytochrome-c-oxidase subunit 1 gene (CO1) was performed. Molecular phylogenetic analysis showed that the endemic mollusk species studied formed at least two distinct populations, Southwestern and Eastern. Statistical significance of the species subdivision into two populations was evaluated using the Mann-Whitney rank test.     

Effect of low above-zero temperature on the content of low-molecular antioxidants and activities of antioxidant enzymes in green barley leaves

We studied the effect of low above-zero temperature (2°C) on the content of low-molecular antioxidants (ascorbic acid, glutathione, and carotenoids) and also activities of antioxidant enzymes (ascorbate peroxidase, APO; catalase, CAT; glutathione reductase, GR; and superoxide dismutase, SOD) in green barley (Hordeum vulgare L.) seedlings. Under stress conditions, the content of low-molecular antioxidants, especially that of reduced ascorbate form, increased. Low-temperature stress activated APO, CAT, GR, and SOD. First enzymes responding to the action of stress factor were APO and CAT, i.e., enzymes neutralizing hydrogen peroxide in plant cells, which indicated H₂O₂ active generation at low temperature. Cytoplasmic SOD was more active than its chloroplast isoforms. This indicates that oxidative process initiation under low-temperature stress occurred more active in the cytosol. After termination of stress-factor action, the content of total ascorbate, glutathione, and carotenoids reduced rapidly to the level close to the initial one. During post-stress period, the amount of reduced ascorbate declined as well; however, it remained at the level higher than the initial one. Activities of APO and CAT dropped sharply; activities of GR and SOD reduced gradually. Thus, reduced ascorbate, APO, and CAT play an important role in plant cell defense against above-zero temperatures close to zero; reduced ascorbate, GR, and SOD are especially important during post-stress period.     

New planthoppers of the tribe Achilini (Homoptera,Fulgoroidea, Achilidae) from Baltic amber

New taxa of Achilini (Achilidae) are described from Baltic amber: Paratesum rasnitsyni gen. et sp. nov., Protomenocria notata gen. et sp. nov., Psycheona variegata gen. et sp. nov., P. striata sp. nov. Protepiptera kaweckii Usinger, 1939 (= Cixidia christinae Lefebvre, Bourgoin et Nel, 2007, syn. nov.) is redescribed with designation of a neotype. “Cixius” testudinarius Germar et Berendt, 1856, “C.” longirostris Germar et Berendt, 1856 and “Oliarus” oligocenus Cockerell, 1910 are transferred to Achilini. A key to the genera of Achilidae known from Baltic amber is provided.     

The role of vitamin K3 in the hydroxylation of benz(a)pyrene in rat liver mitochondria after induction with 3-methylcholanthrene and phenobarbital

The "fast" phase reduction of microsomal cytochromes P-450 and P-448 and their benz(a)pyrene (BP) hydroxylase activity was investigated as a function of menadione concentrations. Within a narrow concentration range (1.5-3 microM) menadione activates cytochrome P-448 reduction and the BP hydroxylase activity. At higher concentrations menadione inhibits cytochromes P-450 and P-448 reduction and BP hydroxylation with participation of the both cytochromes. These data suggest that menadione molecules present in membrane lipids serve as an additional electron carrier to cytochrome P-448, the active site of which is embedded into lipids. The activating effect is unobserved is case of cytochrome P-450 with an active site localized in the aqueous phase. The number of different BP metabolites formed at low (3 microM) menadione concentrations in the microsomes of rats induced with 3-methylcholanthrene (MC) and phenobarbital (PB) was compared. In PB-induced microsomes the amount of 7,8-dihydrodiol rises whereas the total content of BP metabolites decreases. Contrariwise, in MC-induced microsomes the synthesis of all BP metabolites is augmented. Menadione has a very weak effect on the ratio of different BP metabolites in PB- and MC-microsomes, but strongly inhibits the formation of more polar metabolites. This results in a marked reduction of the number of "dangerous" BP diolepoxides.     

The role of the temporal areas in conditioned reflex activity following section of the brachia of the inferior colliculi]

The role of the neocortex temporal areas in the closing function was studied in chronic experiments on cats in the norm and after section of the posterior colliculi brachia. The techniques of functional elimination of the temporal neocortex by cold and section of the posterior colliculi brachia were used. Functional elimination of the cortical temporal areas prevents formation of a stable conditioned reflex in the first twenty sessions with cooling. Conditioned reflexes elaborated after section of the posterior colliculi brachia are not manifested in the case of cooling of the temporal areas throughout the period of observation (18 sessions). At the same time the conditioned reflexes elaborated before the section, are restored quite rapidly (five to six sessions). Hence, the neocortex temporal areas are more important for setting up conditioned connections than for their preservation and the use of connections previously elaborated.     

Estimation of the membrane potential of cultured macrophages from the fast potential transient upon microelectrode entry

Analysis of membrane potential recordings upon microelectrode impalement of four types of macrophages (cell lines P388D1 and PU5-1.8, cultured mouse peritoneal macrophages, and cultured human monocytes) reveals that these cells have membrane potentials at least two times more negative than sustained potential values (E(s)) frequently reported. Upon microelectrode entry into the cell (P388D1), the recorded potential drops to a peak value (E(p)) (mean -37 mV for 50 cells, range -15 to -70 mV) within 2 ms, after which it decays to a depolarized potential (E(n)) (mean -12 mV) in about 20 ms. Thereafter, the membrane develops one or a series of slow hyperpolarizations before a final sustained membrane potential (E(s)) (mean -14 mV, range -5 to -40) is established. The mean value of the peak of the first hyperpolarization (E(h)) is -30 mV (range -10 to -55 mV). The initial fast peak transient, measured upon microelectrode entry, was first described and analyzed by Lassen et al. (Lassen, U.V., A.M. T. Nielson, L. Pape, and L. O. Simonsen, 1971, J. Membr. Biol. 6:269-288 for other change in the membrane potential from its real value before impalement to a sustained depolarized value. This was shown to be true for macrophages by two-electrode impalements of single cells. Values of E(p), E(n), E(h), E(s), and membrane resistance (R(m)) measured for the other macrophages were similar to those of P388D1. From these results we conclude that E(p) is a better estimate of the true membrane potential of macrophages than E(s), and that the slow hyperpolarizations upon impalement should be regarded as transient repolarizations back to the original membrane potentials. Thus, analysis of the initial fast impalement transient can be a valuable aid in the estimation of the membrane potential of various sorts of small isolated cells by microelectrodes.     

Algorithms and software for support of gene identification experiments

MOTIVATION: Gene annotation is the final goal of gene prediction algorithms. However, these algorithms frequently make mistakes and therefore the use of gene predictions for sequence annotation is hardly possible. As a result, biologists are forced to conduct time-consuming gene identification experiments by designing appropriate PCR primers to test cDNA libraries or applying RT-PCR, exon trapping/amplification, or other techniques. This process frequently amounts to 'guessing' PCR primers on top of unreliable gene predictions and frequently leads to wasting of experimental efforts. RESULTS: The present paper proposes a simple and reliable algorithm for experimental gene identification which bypasses the unreliable gene prediction step. Studies of the performance of the algorithm on a sample of human genes indicate that an experimental protocol based on the algorithm's predictions achieves an accurate gene identification with relatively few PCR primers. Predictions of PCR primers may be used for exon amplification in preliminary mutation analysis during an attempt to identify a gene responsible for a disease. We propose a simple approach to find a short region from a genomic sequence that with high probability overlaps with some exon of the gene. The algorithm is enhanced to find one or more segments that are probably contained in the translated region of the gene and can be used as PCR primers to select appropriate clones in cDNA libraries by selective amplification. The algorithm is further extended to locate a set of PCR primers that uniformly cover all translated regions and can be used for RT-PCR and further sequencing of (unknown) mRNA.