On the History of Teaching Historical Disciplines in Russia: Projects of O. F. Waldhauer and V. V. Barthold

Поступила в редакцию 22.02.2019. Принята к печати 18.04.2019.Submitted on 22 February, 2019. Accepted on 18 April, 2019.Развитие науки и высшего, в том числе университетского, образования в России в течение XIX в. поставило вопрос о путях дальнейшего прогресса высшей школы, развитии методологии преподавания. Фактически, количественное накопление знаний, появление все новых дисциплин привели к следующей постановке вопроса: специализация (глубина) или общий курс (широта охвата). Ведущие ученые, занимавшиеся преподавательской деятельностью, уже на рубеже XIX–XX столетий осознавали остроту этой проблемы. Востоковед, историк науки академик В. В. Бартольд, преподававший в Санкт-Петербургском (Петроградском / Ленинградском) университете более 30 лет и историк античного искусства, сотрудник Эрмитажа и Института истории искусств О. Ф. Вальдгауер, обратившись независимо друг от друга к данной проблеме, пришли к схожему выводу. Во главу угла должна ставиться глубина специализации, практические занятия — семинары, работа с наглядным материалом, практическая работа с ведущими преподавателями по немецкому или британскому образцу (тьюторами). Выбор курсов для максимально глубокого преподавания должен обуславливаться не стремлением уравнять все предметы по количеству уделяемого им времени, а наибольшей актуальностью и наличием максимально подробных сведений. Остальные, менее разработанные, могут быть пройдены в рамках общих курсов. Архивные документы по истории высшего образования в России должны приниматься в расчет при составлении современных учебных планов, так как они отражают многолетний опыт преподавания ведущих специалистов.The development of science and higher education including universities in 19th-century Russia raised a question related to the ways of further progress of the higher school and methods of teaching. In fact, the quantitative accumulation of knowledge and emergence of new disciplines led to a dilemma concerning the need to choose between specialisation (depth) and more general courses (vast scope). The leading scholars who were engaged in teaching at the turn of the twentieth century realised the acute character of this problem. V. V. Barthold, an orientalist, historian of science, and academician who taught at St Petersburg (Petrograd / Leningrad) university for over 30 years and O. F. Waldhauer, a historian of classical art who worked at the Hermitage Museum and the Institute of the History of Arts independently paid attention to this problem and came to a similar conclusion. They maintain that the depth of specialisation and practical training, i.e. seminars, work with visual material, and practical work with the leading specialists according to the German and British models (tutors) are key factors to successful education. The choice of courses for in-depth teaching has to depend not on the desire to balance all disciplines according to the amount of time spent on them but on their relevance and availability of the most detailed information. Other less developed disciplines could be covered within the general courses. Consequently, it is essential to take archival documents on the history of higher education in Russia into consideration while drawing up modern curricula as they reflect long-term experience of teaching by leading scholars.Работа выполнена при поддержке гранта РНФ № 18-18-00367 «Всеобщая история в системе советской науки, культуры и образования в 1917–1947 гг.».The work was supported by the Russian Science Foundation; grant 18-18-00367 “General History in the System of Soviet Science, Culture, and Education in 1917–1947”

JunctionViewer: customizable annotation software for repeat-rich genomic regions

<p>Abstract</p> <p>Background</p> <p>Repeat-rich regions such as centromeres receive less attention than their gene-rich euchromatic counterparts because the former are difficult to assemble and analyze. Our objectives were to 1) map all ten centromeres onto the maize genetic map and 2) characterize the sequence features of maize centromeres, each of which spans several megabases of highly repetitive DNA. Repetitive sequences can be mapped using special molecular markers that are based on PCR with primers designed from two unique "repeat junctions". Efficient screening of large amounts of maize genome sequence data for repeat junctions, as well as key centromere sequence features required the development of specific annotation software.</p> <p>Results</p> <p>We developed JunctionViewer to automate the process of identifying and differentiating closely related centromere repeats and repeat junctions, and to generate graphical displays of these and other features within centromeric sequences. JunctionViewer generates NCBI BLAST, WU-BLAST, cross_match and MUMmer alignments, and displays the optimal alignments and additional annotation data as concise graphical representations that can be viewed directly through the graphical interface or as PostScript^®output.</p> <p>This software enabled us to quickly characterize millions of nucleotides of newly sequenced DNA ranging in size from single reads to assembled BACs and megabase-sized pseudochromosome regions. It expedited the process of generating repeat junction markers that were subsequently used to anchor all 10 centromeres to the maize map. It also enabled us to efficiently identify key features in large genomic regions, providing insight into the arrangement and evolution of maize centromeric DNA.</p> <p>Conclusions</p> <p>JunctionViewer will be useful to scientists who wish to automatically generate concise graphical summaries of repeat sequences. It is particularly valuable for those needing to efficiently identify unique repeat junctions. The scalability and ability to customize homology search parameters for different classes of closely related repeat sequences make this software ideal for recurring annotation (e.g., genome projects that are in progress) of genomic regions that contain well-defined repeats, such as those in centromeres. Although originally customized for maize centromere sequence, we anticipate this software to facilitate the analysis of centromere and other repeat-rich regions in other organisms.</p

Isogenic Pairs of Wild Type and Mutant Induced Pluripotent Stem Cell (iPSC) Lines from Rett Syndrome Patients as In Vitro Disease Model

Rett syndrome (RTT) is an autism spectrum developmental disorder caused by mutations in the X-linked methyl-CpG binding protein 2 (MECP2) gene. Excellent RTT mouse models have been created to study the disease mechanisms, leading to many important findings with potential therapeutic implications. These include the identification of many MeCP2 target genes, better understanding of the neurobiological consequences of the loss- or mis-function of MeCP2, and drug testing in RTT mice and clinical trials in human RTT patients. However, because of potential differences in the underlying biology between humans and common research animals, there is a need to establish cell culture-based human models for studying disease mechanisms to validate and expand the knowledge acquired in animal models. Taking advantage of the nonrandom pattern of X chromosome inactivation in female induced pluripotent stem cells (iPSC), we have generated isogenic pairs of wild type and mutant iPSC lines from several female RTT patients with common and rare RTT mutations. R294X (arginine 294 to stop codon) is a common mutation carried by 5–6% of RTT patients. iPSCs carrying the R294X mutation has not been studied. We differentiated three R294X iPSC lines and their isogenic wild type control iPSC into neurons with high efficiency and consistency, and observed characteristic RTT pathology in R294X neurons. These isogenic iPSC lines provide unique resources to the RTT research community for studying disease pathology, screening for novel drugs, and testing toxicology

On the Deformation of Dendrites During Directional Solidification of a Nickel-Based Superalloy

Abstract: Synchrotron X-ray imaging has been used to examine in situ the deformation of dendrites that takes place during the solidification of a nickel-based superalloy. By combining absorption and diffraction contrast imaging, deformation events could be classified by their localization and permanence. In particular, a deformation mechanism arising from thermal contraction in a temperature gradient was elucidated through digital image correlation. It was concluded that this mechanism may explain the small misorientations typically observed in single crystal castings

The Cotton Centromere Contains a Ty3-gypsy-like LTR Retroelement

The centromere is a repeat-rich structure essential for chromosome segregation; with the long-term aim of understanding centromere structure and function, we set out to identify cotton centromere sequences. To isolate centromere-associated sequences from cotton, (Gossypium hirsutum) we surveyed tandem and dispersed repetitive DNA in the genus. Centromere-associated elements in other plants include tandem repeats and, in some cases, centromere-specific retroelements. Examination of cotton genomic survey sequences for tandem repeats yielded sequences that did not localize to the centromere. However, among the repetitive sequences we also identified a gypsy-like LTR retrotransposon (Centromere Retroelement Gossypium, CRG) that localizes to the centromere region of all chromosomes in domestic upland cotton, Gossypium hirsutum, the major commercially grown cotton. The location of the functional centromere was confirmed by immunostaining with antiserum to the centromere-specific histone CENH3, which co-localizes with CRG hybridization on metaphase mitotic chromosomes. G. hirsutum is an allotetraploid composed of A and D genomes and CRG is also present in the centromere regions of other AD cotton species. Furthermore, FISH and genomic dot blot hybridization revealed that CRG is found in D-genome diploid cotton species, but not in A-genome diploid species, indicating that this retroelement may have invaded the A-genome centromeres during allopolyploid formation and amplified during evolutionary history. CRG is also found in other diploid Gossypium species, including B and E2 genome species, but not in the C, E1, F, and G genome species tested. Isolation of this centromere-specific retrotransposon from Gossypium provides a probe for further understanding of centromere structure, and a tool for future engineering of centromere mini-chromosomes in this important crop species

45S rDNA external transcribed spacer organization reveals new phylogenetic relationships in Avena genus

Research ArticleThe genus Avena comprises four distinct genomes organized in diploid (AA or CC), tetraploid (AABB or AACC) and hexaploid species (AACCDD), constituting an interesting model for phylogenetic analysis. The aim of this work was to characterize 45S rDNA intergenic spacer (IGS) variability in distinct species representative of Avena genome diversity±A. strigosa (AA), A. ventricosa (CvCv), A. eriantha (CpCp), A. barbata (AABB), A. murphyi (AACC), A. sativa (AACCDD) and A. sterilis (AACCDD) through the assessment of the 5' external transcribed spacer (5'-ETS), a promising IGS region for phylogenetic studies poorly studied in Avena genus. In this work, IGS length polymorphisms were detected mainly due to distinct 5'-ETS sequence types resulting from major differences in the number and organization of repeated motifs. Although species with A genome revealed a 5'-ETS organization (A-organization) similar to the one previously described in A. sativa, a distinct organization was unraveled in C genome diploid species (C-organization). Interestingly, such new organization presents a higher similarity with other Poaceae species than A-genome sequences, supporting the hypothesis of C-genome being the ancestral Avena genome. Additionally, polyploid species with both genomes mainly retain the A-genome 5'-ETS organization, confirming the preferential elimination of C-genome sequences in Avena polyploid species. Moreover, 5'-ETS sequences phylogenetic analysis consistently clustered the species studied according to ploidy and genomic constitution supporting the use of ribosomal genes to highlight Avena species evolutive pathways.info:eu-repo/semantics/publishedVersio

A Single Molecule Scaffold for the Maize Genome

About 85% of the maize genome consists of highly repetitive sequences that are interspersed by low-copy, gene-coding sequences. The maize community has dealt with this genomic complexity by the construction of an integrated genetic and physical map (iMap), but this resource alone was not sufficient for ensuring the quality of the current sequence build. For this purpose, we constructed a genome-wide, high-resolution optical map of the maize inbred line B73 genome containing >91,000 restriction sites (averaging 1 site/∼23 kb) accrued from mapping genomic DNA molecules. Our optical map comprises 66 contigs, averaging 31.88 Mb in size and spanning 91.5% (2,103.93 Mb/∼2,300 Mb) of the maize genome. A new algorithm was created that considered both optical map and unfinished BAC sequence data for placing 60/66 (2,032.42 Mb) optical map contigs onto the maize iMap. The alignment of optical maps against numerous data sources yielded comprehensive results that proved revealing and productive. For example, gaps were uncovered and characterized within the iMap, the FPC (fingerprinted contigs) map, and the chromosome-wide pseudomolecules. Such alignments also suggested amended placements of FPC contigs on the maize genetic map and proactively guided the assembly of chromosome-wide pseudomolecules, especially within complex genomic regions. Lastly, we think that the full integration of B73 optical maps with the maize iMap would greatly facilitate maize sequence finishing efforts that would make it a valuable reference for comparative studies among cereals, or other maize inbred lines and cultivars

Gene and genon concept: coding versus regulation: A conceptual and information-theoretic analysis of genetic storage and expression in the light of modern molecular biology

We analyse here the definition of the gene in order to distinguish, on the basis of modern insight in molecular biology, what the gene is coding for, namely a specific polypeptide, and how its expression is realized and controlled. Before the coding role of the DNA was discovered, a gene was identified with a specific phenotypic trait, from Mendel through Morgan up to Benzer. Subsequently, however, molecular biologists ventured to define a gene at the level of the DNA sequence in terms of coding. As is becoming ever more evident, the relations between information stored at DNA level and functional products are very intricate, and the regulatory aspects are as important and essential as the information coding for products. This approach led, thus, to a conceptual hybrid that confused coding, regulation and functional aspects. In this essay, we develop a definition of the gene that once again starts from the functional aspect. A cellular function can be represented by a polypeptide or an RNA. In the case of the polypeptide, its biochemical identity is determined by the mRNA prior to translation, and that is where we locate the gene. The steps from specific, but possibly separated sequence fragments at DNA level to that final mRNA then can be analysed in terms of regulation. For that purpose, we coin the new term “genon”. In that manner, we can clearly separate product and regulative information while keeping the fundamental relation between coding and function without the need to introduce a conceptual hybrid. In mRNA, the program regulating the expression of a gene is superimposed onto and added to the coding sequence in cis - we call it the genon. The complementary external control of a given mRNA by trans-acting factors is incorporated in its transgenon. A consequence of this definition is that, in eukaryotes, the gene is, in most cases, not yet present at DNA level. Rather, it is assembled by RNA processing, including differential splicing, from various pieces, as steered by the genon. It emerges finally as an uninterrupted nucleic acid sequence at mRNA level just prior to translation, in faithful correspondence with the amino acid sequence to be produced as a polypeptide. After translation, the genon has fulfilled its role and expires. The distinction between the protein coding information as materialised in the final polypeptide and the processing information represented by the genon allows us to set up a new information theoretic scheme. The standard sequence information determined by the genetic code expresses the relation between coding sequence and product. Backward analysis asks from which coding region in the DNA a given polypeptide originates. The (more interesting) forward analysis asks in how many polypeptides of how many different types a given DNA segment is expressed. This concerns the control of the expression process for which we have introduced the genon concept. Thus, the information theoretic analysis can capture the complementary aspects of coding and regulation, of gene and genon

Production of ϒ(nS) mesons in Pb + Pb and pp collisions at 5.02 TeV

A measurement of the production of vector bottomonium states, ϒ(1S), ϒ(2S), and ϒ(3S), in Pb + Pb and pp collisions at a center-of-mass energy per nucleon pair of 5.02 TeV is presented. The data correspond to integrated luminosities of 1.38 nb-1 of Pb + Pb data collected in 2018, 0.44 nb-1 of Pb + Pb data collected in 2015, and 0.26 fb-1 of pp data collected in 2017 by the ATLAS detector at the Large Hadron Collider. The measurements are performed in the dimuon decay channel for transverse momentum pμμT < 30 GeV, absolute rapidity |yμμ| < 1.5, and Pb + Pb event centrality 0-80%. The production rates of the three bottomonium states in Pb + Pb collisions are compared with those in pp collisions to extract the nuclear modification factors as functions of event centrality, pμμT, and |yμμ|. In addition, the suppression of the excited states relative to the ground state is studied. The results are compared with theoretical model calculations