Macroarray for studying chloroplast gene expression profiles associated with the initial development of wheat

Item does not contain fulltextOBJECTIVES: Feedback should facilitate learning, but within medical education it often fails to deliver on its promise. To better understand why feedback is challenging, we explored the unique perspectives of doctors who had also trained extensively in sport or music, aiming to: (i) distinguish the elements of the response to feedback that are determined by the individual learner from those determined by the learning culture, and (ii) understand how these elements interact in order to make recommendations for improving feedback in medical education. METHODS: Using a constructivist grounded theory approach, we conducted semi-structured interviews with 27 doctors or medical students who had high-level training and competitive or performance experience in sport (n = 15) or music (n = 12). Data were analysed iteratively using constant comparison. Key themes were identified and their relationships critically examined to derive a conceptual understanding of feedback and its impact. RESULTS: We identified three essential sources of influence on the meaning that feedback assumed: the individual learner; the characteristics of the feedback, and the learning culture. Individual learner traits, such as motivation and orientation toward feedback, appeared stable across learning contexts. Similarly, certain feedback characteristics, including specificity, credibility and actionability, were valued in sport, music and medicine alike. Learning culture influenced feedback in three ways: (i) by defining expectations for teachers and teacher-learner relationships; (ii) by establishing norms for and expectations of feedback, and (iii) by directing teachers' and learners' attention toward certain dimensions of performance. Learning culture therefore neither creates motivated learners nor defines 'good feedback'; rather, it creates the conditions and opportunities that allow good feedback to occur and learners to respond. CONCLUSIONS: An adequate understanding of feedback requires an integrated approach incorporating both the individual and the learning culture. Our research offers a clear direction for medicine's learning culture: normalise feedback; promote trusting teacher-learner relationships; define clear performance goals, and ensure that the goals of learners and teachers align

THE GENERATION OF CODING SEQUENCES OF CELLULAR GENOME THROUGH COOPTION OF VIRAL GENES

This review attempts to summarize the available data concerning the influence of viruses on the generation of the cellular genome coding genes content. For a long time endogenous retroviruses have been considered as selfish elements of the organism genome. But now there is growing evidence that endogenous retroviruses are more than genome junk and can serve as source for new coding sequences allowing organism evolution. Many genes derived from retroviruses have been identified in eukaryote through comparative genomics and functional analyses. In particular, genes derived from gag structural protein and envelope (env) genes, as well as from the integrase-coding and protease-coding sequences, have been identified in humans and other vertebrates. It has been proved that a number of these genes fulfill essential functions for the development and survival of their host. One of the best known co-opted retroviral genes encoded syncytin plays a key role in the placenta development. It is interesting that during mammalian evolution retroviral envelope genes have been domesticated several times independently to generate syncytin. The activity-regulated cytoskeletal protein Arc is important for cognitive functions and memory formation. Arc was one of over 100 human proteins that have been ‘‘domesticated’’ from the retrotransposon remains of ancient viruses. A number of genes that code the transcription factors have emerged as a result of “taming” the viral genes by the host organism. Now growing evidence reveals that not only retroviruses but other RNA viruses are reverse-transcribed and integrated into the genome of infected cells. It has been recently demonstrated that all Homo sapiens bornavirus like nucleoproteins (EBLN) are expressed in at least one tissue and consequently may have function.The co-option of the viral sequences not only can lead to the major evolutionary innovations, but also is able to create interspecies polymorphism.What it has been described here is probably only the tip of the iceberg, and future genome analyses will certainly uncover new virus-derived genes

Antibacterial and fungicidal activities of ethanol extracts of 38 species of plants

Galenic preparations are broadly used against microorganisms pathogenic to humans, thought their poteintial in this aspect is not studied completely. In our in vitro experiment we studied the influence of alcohol tinctures from 38 species of plants on 15 species of bacteria and one species of fungus. Zones of growth inhibition of colonies measuring over 8 mm were observed during the use of ethanol extracts of Maclura pomifera against eight species of microorganisms (Escherichia сoli, Proteus mirabilis, Serratia marcescens, Yersinia enterocolitica, Salmonella typhimurium, Rhodococcus equi, Campylobacter jejuni and Corynebacterium xerosis), Ginkgo biloba – against eight species (Enterococcus faecalis, S. marcescens, Y. enterocolitica, Klebsiella pneumoniae, Listeria іnnocua, L. monocytogenes, Р. аeruginosa and C. jejuni), Genista tinctoria – against seven species (E. coli, Enterobacter aerogenes, Proteus mirabilis, K. pneumoniae, S. typhimurium, Р. аeruginosa and Rh. equi), Phellodendron amurense – against seven species (E. faecalis, S. marcescens, S. typhimurium, Rh. equi, C. jejunі, C. xerosis and Candida albicans), Berberis vulgaris – against seven species (P. mirabilis, S. marcescens, K. pneumoniae, S. typhimurium, C. jejuni, Р. аeruginosa and C. xerosis), Vitex negundo – against six species (E. faecalis, E. coli, P. mirabilis, K. pneumoniae, S. typhimurium and Rh. equi), Koelreuteria paniculata – against six species (E. faecalis, P. mirabilis, S. marcescens, S. typhimurium, C. jejunі and E. coli), Magnolia kobus – against six species (E. faecalis, E. coli, P. mirabilis, S. marcescens, S. typhimurium, C. jejunі and C. xerosis), Liriodendron tulipifera – against six species (K. pneumoniae, Listeria іnnocua, Р. аeruginosa, C. jejuni, Rh. equi and C. albicans), Clematis flammula – against six species (E. faecalis, P. mirabilis, L. monocytogenes, Р. аeruginosa, C. jejuni and C. xerosis), Wisteria sinensis – against five species (E. coli, S. typhimurium, L. monocytogenes, Rh. equi and C. albicans), Chimonanthus praecox – against five species (E. faecalis, S. marcescens, L. monocytogenes, C. jejuni and Rh. equi), Colchicum autumnale – against five species (S. marcescens, K. pneumoniae, L. ivanovi, L. monocytogenes and Р. аeruginosa). As a result of the study, these plants were found to be the most promising for further study of in vivo antibacterial activity. In the search of antibacterial and antifungal activities, the following plants were observed to be less promising: Ailanthus altissima, Aristolochia manshuriensis, Artemisia absinthium, Callicarpa bodinieri, Campsis radicans, Catalpa duclouxii, Celastrus scandens, Dictamnus alba, Eucommia ulmoides, Geranium sanguineum, Laburnum anagyroides, Nepeta racemosa, Parthenocissus tricuspidata, Polygonatum multiflorum, Prunus dulcis, P. laurocerasus, Ptelea trifoliata, Pteridium aquilinum, Quercus castaneifolia, Q. petraea iberica, Salvia officinalis, Securigera varia, Styphnolobium japonicum, Tamarix elongata and Vitex agnus-castus

A method for restoration of radio channel transfer function by chirp sounding of the ionosphere

[1] Analysis of both in-phase and quadrature components of received frequency-modulated continuous wave (FMCW) signal at the output of intermediate frequency (IF) band-pass filter of the chirp ionosonde demonstrates a new possibility of recovering the transfer function of the HF radio channel within the band of operating frequencies and the interval of time delays that are defined by the IF filter characteristics. The transfer function is determined by the parameters of all parts comprising the radio channel: transmitter, receiving-transmitting antenna-feeder devices, Earth surface, ionosphere, as well as the receiver circuitry participating in the signal processing. However, characteristics of all parts except the ionosphere can be considered stationary and well-known or controlled. It is the ionosphere that displays significant temporal variability. A new technique is proposed for recovering the transfer function of the ionospheric radio channel, together with its implementation as a signal preprocessing circuit containing a correcting digital filter that adapts to the current amplitude frequency and phase frequency characteristics of the channel

Expression of the chloroplast genome: modern concepts and experimental approaches

A unique feature of plants is the presence of two extranuclear genomes, chloroplasts and mitochondria. The chloroplast genome is relatively small, 100–120 genes, which encode less than 5 % of all proteins required for plastids to function. The cpDNA expression retains prokaryotic features, cotranscription in the operon, bacteria-like RNA polymerases and promoters, 70S ribosomes etc., also new characters appear such as uncoupling of transcription with translation, phage-type RNA polymerases, RNA editing, and splicing of primary transcripts. The interaction of the nucleus (nuclear genomes) and cytoplasm (plastid and mitochondrial genes) during plant development is necessary for proper development and adaptation to the environment. The aim of this review is to disclose the peculiarities of plastid genome expression. The way the genetic information in chloroplasts is used (transcription, editing, splicing, polyadenylation and translation) is consequently described. Furthermore, the importance of all expression machinery components in plant life is discussed. Modern approaches for RNA pool study are described and critical points of nuclear-cytoplasmic interaction in the functions of chloroplasts are revealed. The information about the most important factors of nuclear-cytoplasmic signaling in higher plants (sigma factors and PPR proteins encoded by the nucleus) are reviewed. Thus, the multilevelness and viability of plastid genome expression regula­tion in plant cells and interdependence of the pro­cesses in different compartments is proved. A summary of the latest studies of the expression of the plastid genome using genetic chips (microarrays, macroarrays) is provided. Original results are presented

The study of organelle DNA variability in alloplasmic barley lines in the NGS era

Alloplasmic lines are a suitable model for studying molecular coevolution and interrelations between genetic systems of plant cells. Whole chloroplast (cp) and mitochondrial (mt) genome sequences were obtained by the MiSeq System (Illumina). Organelle DNA samples were prepared from a set of 12 alloplasmic barley lines with different cytoplasms of Hordeum vulgare ssp. spontaneum and H. vulgare ssp. vulgare, as well as from their paternal varieties. A bioinformatic approach for analysis of NGS data obtained on an organellar DNA mix has been developed and verified. A comparative study of Hordeum organelle genomes' variability and disposition of polymorphic loci was conducted. Eight types of chloroplast DNA and 5 types of mitochondrial DNA were distinguished for the barley sample set examined. These results were compared with the previous data of a restriction fragment length polymorphism (RFLP) study of organelle DNAs for the same material. Formerly established data about a field evaluation of alloplasmic barley lines were revised in the light of information about organelle genomes gained after NGS. Totally 17 polymorphic loci were found at exons of chloroplast genomes. Seven of the SNPs were located in the genes of the Ndh complex. The nonsynonymous changes of nucleotides were detected in the matK, rpoCI, ndhK, ndhG and infA genes. Some of the SNPs detected are very similar in codon position and in the type of amino acid substitution to the places where RNA editing can occur. Thus, these results outline new perspectives for the future study of nuclear-cytoplasmic interactions in alloplasmic lines

A multimodal transport chain choice model for container transport

A large part of freight transport movements are part of a multimodal transport chain, in particular for port-related containerized transport flows. Because data of multimodal transports are unavailable it is challenging to develop a multimodal transport chain models. This paper describes the development of a new module for multimodal transport chains for modelling container transport within the Dutch strategic freight transport model “BasGoed”. The choice model distinguishes unimodal, bi-modal or tri-modal transport chains, depending on whether the transport chain is port-related. A direct road chain is available between each production and consumption combination; direct barge or rail transport is only available between seaports. A route enumeration module generates a choice set for each observed uni- or multimodal container transport. Since no directly observed PC data are available, a synthetic dataset was constructed with container flows between locations of production and consumption, using uni-modal observed transport data. Main assumption is that each container transported by rail or barge requires a road leg at the side of destination and/or origin, to complete the multimodal transport chain. Discrete choice models were estimated with different model structures. The best choice model that was found was a multinomial logit model, segmented by port dependency. The results show that a choice model can be estimated with significant parameters, and with plausible model sensitivities

АНАЛИЗ ФРОНТА ЭЛЕКТРОМАГНИТНОЙ ВОЛНЫ, СОЗДАВАЕМОЙ КОГЕРЕНТНЫМИ ИСТОЧНИКАМИ ИЗЛУЧЕНИЯ ИЗ ДВУХ ТОЧЕК ПРОСТРАНСТВА

The front of electromagnetic wave generated by coherent sources of radiation from two points of space is analyzed in the article. General expressions are obtained that allow to estimate the directions of the arrival of the wave at a point in the space where the observer is situated (the angle-system), depending on the parameters of the radiators system. It is shown that the obtained relations for some particular cases coincide with the expressions presented in known publications on the subject under consideration.В статье рассматривается анализ фазового фронта электромагнитной волны, создаваемой когерентными источниками излучения из двух точек пространства. Получены общие выражения, позволяющие оценить направления прихода волны в некоторую точку пространства, где расположен наблюдатель (угломерная система), в зависимости от параметров системы излучателей. Показано, что полученные соотношения для некоторых частных случаев совпадают с выражениями, представленными в известных публикациях по рассматриваемой тематике