The impact of genome evolution on the allotetraploid Nicotiana rustica - an intriguing story of enhanced alkaloid production.

BACKGROUND: Nicotiana rustica (Aztec tobacco), like common tobacco (Nicotiana tabacum), is an allotetraploid formed through a recent hybridization event; however, it originated from completely different progenitor species. Here, we report the comparative genome analysis of wild type N. rustica (5 Gb; 2n = 4x = 48) with its three putative diploid progenitors (2.3-3 Gb; 2n = 2x =24), Nicotiana undulata, Nicotiana paniculata and Nicotiana knightiana. RESULTS: In total, 41% of N. rustica genome originated from the paternal donor (N. undulata), while 59% originated from the maternal donor (N. paniculata/N. knightiana). Chloroplast genome and gene analyses indicated that N. knightiana is more closely related to N. rustica than N. paniculata. Gene clustering revealed 14,623 ortholog groups common to other Nicotiana species and 207 unique to N. rustica. Genome sequence analysis indicated that N. knightiana is more closely related to N. rustica than N. paniculata, and that the higher nicotine content of N. rustica leaves is the result of the progenitor genomes combination and of a more active transport of nicotine to the shoot. CONCLUSIONS: The availability of four new Nicotiana genome sequences provide insights into how speciation impacts plant metabolism, and in particular alkaloid transport and accumulation, and will contribute to better understanding the evolution of Nicotiana species.

Systems toxicology meta-analysis of in vitro assessment studies: biological impact of a candidate modified-risk tobacco product aerosol compared with cigarette smoke on human organotypic cultures of the aerodigestive tract.

Systems biology combines comprehensive molecular analyses with quantitative modeling to understand the characteristics of a biological system as a whole. Leveraging a similar approach, systems toxicology aims to decipher complex biological responses following exposures. This work reports a systems toxicology meta-analysis in the context of in vitro assessment of a candidate modified-risk tobacco product (MRTP) using three human organotypic cultures of the aerodigestive tract (buccal, bronchial, and nasal epithelia). Complementing a series of functional measures, a causal network enrichment analysis of transcriptomic data was used to compare quantitatively the biological impact of aerosol from the Tobacco Heating System (THS) 2.2, a candidate MRTP, with 3R4F cigarette smoke (CS) at similar nicotine concentrations. Lower toxicity was observed in all cultures following exposure to THS2.2 aerosol compared with 3R4F CS. Because of their morphological differences, a smaller exposure impact was observed in the buccal (stratified epithelium) compared with the bronchial and nasal (pseudostratified epithelium). However, the causal network enrichment approach supported a similar mechanistic impact of CS across the three cultures, including the impact on xenobiotic, oxidative stress, and inflammatory responses. At comparable nicotine concentrations, THS2.2 aerosol elicited reduced and more transient effects on these processes. To demonstrate the benefits of additional data modalities, we employed a newly established targeted mass-spectrometry marker panel to further confirm the reduced cellular stress responses elicited by THS2.2 aerosol compared with 3R4F CS in the nasal culture. Overall, this work demonstrates the applicability and robustness of the systems toxicology approach for in vitro inhalation toxicity assessment.

Genomic impact of cigarette smoke, with application to three smoking-related diseases.

There is considerable evidence that inhaled toxicants such as cigarette smoke can cause both irreversible changes to the genetic material (DNA mutations) and putatively reversible changes to the epigenetic landscape (changes in the DNA methylation and chromatin modification state). The diseases that are believed to involve genetic and epigenetic perturbations include lung cancer, chronic obstructive pulmonary disease (COPD), and cardiovascular disease (CVD), all of which are strongly linked epidemiologically to cigarette smoking. In this review, we highlight the significance of genomics and epigenomics in these major smoking-related diseases. We also summarize the in vitro and in vivo findings on the specific perturbations that smoke and its constituent compounds can inflict upon the genome, particularly on the pulmonary system. Finally, we review state-of-the-art genomics and new techniques such as high-throughput sequencing and genome-wide chromatin assays, rapidly evolving techniques which have allowed epigenetic changes to be characterized at the genome level. These techniques have the potential to significantly improve our understanding of the specific mechanisms by which exposure to environmental chemicals causes disease. Such mechanistic knowledge provides a variety of opportunities for enhanced product safety assessment and the discovery of novel therapeutic interventions.

[Spatial position of the cranium in craniofacial establishment of identity].

A total of 90 images of male cranes from different groups of horizontal profiling (120 +/- 10 degrees, 140 +/- 10 degrees, 160 +/- 10 degrees) were studied in experiment with the coordinate-controlled complex for turning angle (from the position full face to the right and left by 14 degrees with spacing 2 degrees). Each image was marked according to the system of 18 control points. Precision of the angle fixation was 0.1 degrees. Calculation of the angles of horizontal profiling and turning of the crane were made according to a specially devised program INPUTTING. Statistic processing of the computer data base made it possible to calculate precision rates of marking points and regression equation describing the pattern of cranial control points in turning. It is shown that presicion of the turning angle estimation with reference to horizontal profiling is much higher than without it. Basing on the data obtained a method of zeroing of coordinates of the control points (placing in position for correct scaling of the objects of craniofacial identification) was devised. The method allows greater reliability of the results of personal craniofacial identification.

[Study of the skeleton of Admiral F. F. Ushakov]. / Issledovanie skeleta Admirala F. F. Ushakova.

Reports the results of examination of the skeleton of Admiral F. F. Ushakov, carried out in connection with canonization in the Russian Orthodox Church. Heretofore unknown data on the somatic characteristics of F. F. Ushakov and his diseases are presented. Special attention is paid to uneven age involution of the skeleton and the hypoergic aging velocity. A detailed morphological similarity between the skulls of F. F. Ushakov and monk Feodor (Admiral's uncle, I. I. Ushakov) evidenced common features inherited through the masculine line. Modern computer technologies showed that the appearance of F. F. Ushakov, determined by the skull and postcranial skeleton, agree with his appearance on the life-time portrait, in spite of Professor M. M. Gerasimov's opinion (1949). In this connection, the possibility of repeated reconstruction of Admiral Ushakov's appearance is proven.

[Does the computer act like the braine, or like any biological cell?]. / Rabotaet li komp'iuter kak mozg, ili kak liubaia biologicheskaia kletka?

A new conception of computer functioning is proposed, which suggests that a computer is a reactor in which a unique enzymic reaction at a single operation mode occurs. The analogy between informatics and enzymology is considered. In the context of the parallelism proposed, the work of the brain is analogous to the work of a global computer network. Not the brain as a network of neuron processors but a network of computers as the brain!

[Computer-aided personality identification by skull and life-time photography by POSKID 1.1 method]. / Komp'iuternaia identifikatsiia lichnosti po cherepu i prizhiznennoi fotografii metodom POSKID 1.1.

An improved method for computer-aided personality identification by the skull, based on the POSKID 1.1 software, consists in investigation of enlarged images of the skull and life-time photograph of the probable individual by coordinates of 49 anatomical points; independent quantitative evaluation of the aspect of each of the compared objects by the X, Y, and Z axes; formal evaluation of the results of comparative study of the skull-portrait by multidimensional discriminant analysis models. The proposed version differs from the POSKID 1.0 software in the method for evaluating the spatial position of the head on the portrait and adequate orientation of the skull in space, which necessitates the utilization of coordinate-regulated holder POSKID 1.1 method is based on multidimensional discriminant analysis and suggests a virtually reliable solution in 76.13-80.65% cases, a probable solution (positive and negative) in 11.61-18.06% cases, and motivated refusal from solution in 5.81-7.74% cases. In case of a probable or indefinite solution further investigations are recommended making use of life-time photographs with different aspects.

[Computer analysis of face and skull size by "quantitative verbal portrait" method]. / Komp'iuternoe issledovanie cherepno-litsevykh razmerov s pomoshch'iu metodiki "kolichestvennogo slovesnogo portreta".

The aim of this study was to develop a "quantitative verbal portrait" method on the basis of universal measured signs of the face and skull. The database includes 90 cases with expert evaluation of photocompatibility with proven identity. Four groups of signs were investigated: DX and DY--the width and height between accurately fixed concrete craniometrical (facial) points and the so-called RX and RY indices--the ratio between distances within the framework of the same direction. The proposed scheme of evaluation helps compare the photograph of a live human and the skull. For evaluating the degree of identity, one should have a summary characterization of all selected signs for the skull and compare it with the sum on the photograph; sometimes it is possible to rule out the identity of the photograph and the skull by the absolute size, e.g., a very large skull cannot belong to a human with a very little face. The score for each group of signs is used for analysis of the information for detecting the similarities. Accumulation and comparative analysis of two information flows are possible: database on portraits of lost subjects and database on graphic images of the skulls of unidentified corpses.

[The medical anthropological study of the bone remains from the Yekaterinburg burial]. / Mediko-antropologicheskoe issledovanie kostnykh ostankov iz Ekaterinburgskogo zakhoroneniia.

Results of medical anthropological expert studies of bone remains of Emperor Nicholas II, his family members, and persons in their attendance are presented. Craniological (including computer photoblending), odontological, osteometric, and spectral methods were sued. Numerous photographs, Imperial Family clothes from museums, soil specimens from Tsarskoe Selo and place of burial were used. Expert studies confirmed previous conclusions on personal identification of skeletons as Nicholas II and four Imperial Family members. Additional proofs of identification of skeleton No. 6 as Great Princess Anastasia Nikolaevna are presented. No remains which could be identified as Cesarevich Alexei Nikolaevich and Great Princess Maria Nikolaevna were found. The so-called "adolescent teeth" are upper teeth of a subject aged 17-18. Rare odontoglyphic characteristics of these teeth permit referring them only to skull No. 6 (Great Princess Anastasia Nikolaevna) but not to an adolescent, specifically, to Cesarevich Alexei Nikolaevich.

Specific cleavage of hybrid proteins by proteinase encoded by the KEX2 gene.

A method for isolation of the KEX2-gene-encoded membrane-bound proteinase from alpha-cells of Saccharomyces cerevisiae yeast has been modified. The isolated enzyme hydrolyzes peptides and proteins with basic amino acid pairs which are cleaved at the C-ends of their peptide bonds. Because KEX2 proteinase is located within the Golgi compartment, it may be isolated by differential centrifugation of broken cells at 7000g for 15 min and at 20,000g for 15 min. By extracting the fraction that contains the active enzyme by a detergent solution, a protein has been obtained with specific activity 30 times higher than that of the membrane extract prepared according to the standard technique. This protocol decreases the number of steps required to isolate the enzyme. The effects of pH and inhibitors on KEX2 proteinase-catalyzed hydrolysis of Ac-Leu-Lys-Arg-pNA were studied. KEX2 proteinase can participate in peptide hormone processing because it cleaves human proinsulin at the peptide bond between Arg32 and Glu33. The KEX2 proteinase can specifically cleave large recombinant proteins, for example, a protein consisting of a gamma-interferon fragment linked to HIV1-proteinase via a Lys-Arg-containing peptide.

[The craniometric individuality of the human skull]. / Kraniometricheskaia individual'nost' cherepa cheloveka.

Experimental findings indicate that if the basic position of the skull is assessed visually (as is usually done in expert photocombination), various video images of the same skull never fully conform to each other, the deviations reaching 1.5 and more degrees. As a result of this, the accuracy of determining the reference points on the video image varies from 1.-1.5 to 4.0-4.5 mm (en face) and 1.5-2.0 to 6.0-6.5 mm (profile). The task of identification of two images of the skull is reliably solved in 87.7% cases, and in 12.3% cases the results may be false-positive or false-negative. The individuality of the skull, that is, the impossibility of its replacement during computer-aided photocombination is realized in the absence of aspect distortions and minimal errors of measurements. Hence, a new technology of studies is to be introduced: coordination-monitored stable complex of video camera and computer with metric monitoring of all parameters liable to change.

[3'-(Tetrazol-2''-yl-3'-deoxythymidine and its 5''-substituted form: synthesis and conformation in the crystalline state. Substrate properties of 3'-(tetrazol-2''-yl)-3'-deoxythymidine-5'-triphosphate in relation to DNA polymerases]. / 3'-(Tetrazol-2''-il)-3'-dezoksitimidin i ego 5''-zameshchennye: sintez i konformatsiia v kristallicheskom sostoianii. Substratnye svoistva 3'-(tetrazol-2''-il)-3'-dezoksitimidin-5'-trifosfata po otnosheniiu k DNK-polimerazam.

5''-Derivatives of 3'-(tetrazole-2''-yl)-3'-deoxythymidines were synthesized by interaction of 5'-benzoyl-2',3'-anhydrothymidine with tetrazole or its 5-derivatives followed by debenzoylation. Structures of two of them, 3'-(tetrazole-2''-yl)-3'-deoxythymidine and 3'-(5''-methyltetrazole-2''-yl)-3'-deoxythymidine, elucidated by X-ray analysis, revealed anti conformation of thymine about the glycosidic bond and 2'-endo-3'-exo-conformation of the sugar residue with gauche+ orientation with respect to C4'-C5'-bond. 3'-(Tetrazole-2''-yl)-3'-deoxythymidine 5'-triphosphate demonstrated poor substrate properties for the avian myeloblastosis virus reverse transcriptase and none for several other DNA polymerases.

Reliability of quantal parameter estimates and their changes during long-term potentiation in guinea pig hippocampal slices.

Previously we found increases in quantal content (m) and smaller increases in quantal size (v) during long-term potentiation (LTP) in CA1 of hippocampal slices. However, the validity of the deconvolution technique was questioned recently because v estimates correlated with the noise standard deviation (Sn). In computer simulations we show a double-step dependence of v on Sn/v: correct v estimates (within +/- 20%) for Sn/v < or = 0.5 and overestimates (correlated with Sn) for Sn/v > 0.5. A novel 'noise addition' procedure is proposed for accepting reliable solutions on the basis of the double-step relationship between v and Sn. Quantal analysis of LTP for more reliable solutions confirmed previous conclusions.

[Analysis of the changes in the electrophysical and morphometric parameters in the growth and sporulation periods of Bacillus thuringiensis]. / Analiz izmenenii élektrofizicheskikh i morfometricheskikh parametrov v period rosta i sporuliatsii u Bacillus thuringiensis.

Changes in the electrophysical and morphometrical parameters of Bacillus thuringiensis cells were studied during their growth and differentiation using the electrophysical procedure with the frequency of an alternating electric field varying within a wide range. The appearing variations were interpreted on the basis of the data about changes in the concentration of vegetative cells and spores, the optical density and pH of the cultural broth, and the assimilation of glucose by the culture. The changes found in the electrophysical and morphometrical parameters were shown to accompany the main physiological processes in the cells. In principle, they can be used to control the process of cultivation.