Census books as a source for historical geography

AbstractCadastral books as a historical source: a new way of using the geographical information they provide.The article introduces an unconventional method for analyzing geographical data applicable to the study of historical sources containing systematically recurring place names. Establishing the geographical location of these toponyms not only allows the researcher to connect different elements of the text under study, but also to reveal spatial relationships which shed light on the composition and structure of the document under study. Geographical information is all the more precious as subsequent content changes have no effect on it. The author demonstrates his point with four cases drawn from his and N.V. Piotukh’s research on late fifteenth- and early sixteenth-century cadastral books of the Dereva piatina on the Novgorod land.RésuméL’article décrit une méthode inédite d’analyse des données géographiques, applicable chaque fois que l’on aborde des sources historiques où les toponymes sont employés systématiquement. La localisation de ces toponymes, en effet, permet non seulement de relier entre eux les différents éléments du texte étudié, mais encore de révéler les relations spatiales entre ces éléments. Celles-ci, à leur tour, éclairent la composition et la structure du document. Les informations géographiques sont d’autant plus précieuses que les remaniements ultérieurs du manuscrit sont sans effet sur elles. Quatre exemples, empruntés aux recherches de l’auteur et de N.V. Piotuh, sur le cadastre de la pjatina de Dereva, dans le pays de Novgorod, levé à la fin du xve et au début du xvie siècle, illustrent certaines possibilités de la méthode

Assembling nanostructures from DNA using a composite nanotweezers with a shape memory effect

The article demonstrates a technique for fabricating a structure with the inclusion of suspended DNA threads and manipulating them using composite nanotweezers with shape memory effect. This technique could be suitable for stretching of nanothin DNA-like conductive threads and for measuring their electrical conductivity, including the I-V characteristic directly in the electron microscope chamber, where the nanotweezers provide a two-sided clamping of the DNA tip, giving a stable nanocontact to the DNA bundle. Such contact, as a part of 1D nanostructure, is more reliable during manipulations with nanothreads than traditional measurements when a nanothread is touched by a thin needle, for example, in a scanning tunnel microscope.Comment: To be presented on IEEE 3M-NANO 201

Novgorodskie dorogi XVI veka kak prostranstvennyi instrument administrirovaniia

Dans cet article, l’auteur analyse les données d’une source historique unique, le «  Rôle des cantons ». Ce document, que l’auteur date du milieu du xvie siècle, est le plus ancien indicateur russe des routes. Les caractéristiques du calcul des distances séparant Novgorod de chaque centre urbain ou rural du territoire placé sous sa juridiction permettent de modéliser le réseau des routes et de visualiser une topographie administrative des terres de Novgorod dans les années 1540 sous la forme d’une carte anamorphique et d’un modèle tridimensionnel.The article analyzes data from a unique historical source called “List of Parishes.” The author dates it to the mid‑sixteenth century. It is a reference list, with a distance indicator, of the roads connecting Novgorod to each urban or rural center of the subordinated territory. This is the oldest Russian reference list of this kind. The author uses the specifics of distance calculation to model a network of roads and visualize an “administrative topography” of the Novgorod Land in the 1540s through an anamorphic map and a three‑dimensional model

SpCas9- and LbCas12a-Mediated DNA Editing Produce Different Gene Knockout Outcomes in Zebrafish Embryos

CRISPR/Cas (Clustered Regularly Interspaced Short Palindromic Repeats/CRISPR associated protein) genome editing is a powerful technology widely used in current genetic research. In the most simple and straightforward way it can be applied for a gene knockout resulting from repair errors, induced by dsDNA cleavage by Cas nuclease. For decades, zebrafish (Danio rerio) has been known as a convenient model object of developmental biology. Both commonly used nucleases SpCas9 (Streptococcus pyogenes Cas9) and LbCas12a (Lachnospiraceae bacterium Cas12a) are extensively used in this model. Among them, LbCas12a is featured with higher specificity and efficiency of homology-directed editing in human cells and mouse. But the editing outcomes for these two nucleases in zebrafish are still not compared quantitatively. Therefore, to reveal possible advantages of one nuclease in comparison to the other in the context of gene knockout generation, we compare here the outcomes of repair of the DNA breaks introduced by these two commonly used nucleases in zebrafish embryos. To address this question, we microinjected the ribonucleoprotein complexes of the both nucleases with the corresponding guide RNAs in zebrafish zygotes and sequenced the target gene regions after three days of development. We found that LbCas12a editing resulted in longer deletions and more rare inserts, in comparison to those generated by SpCas9, while the editing efficiencies (percentage of mutated copies of the target gene to all gene copies in the embryo) of both nucleases were the same. On the other hand, overlapping of protospacers resulted in similarities in repair outcome, although they were cut by two different nucleases. Thus, our results indicate that the repair outcome depends both on the nuclease mode of action and on protospacer sequence

A Comparison of Genome-Wide DNA Methylation Patterns between Different Vascular Tissues from Patients with Coronary Heart Disease

<div><p>Epigenetic mechanisms of gene regulation in context of cardiovascular diseases are of considerable interest. So far, our current knowledge of the DNA methylation profiles for atherosclerosis affected and healthy human vascular tissues is still limited. Using the Illumina Infinium Human Methylation27 BeadChip, we performed a genome-wide analysis of DNA methylation in right coronary artery in the area of advanced atherosclerotic plaques, atherosclerotic-resistant internal mammary arteries, and great saphenous veins obtained from same patients with coronary heart disease. The resulting DNA methylation patterns were markedly different between all the vascular tissues. The genes hypomethylated in athero-prone arteries to compare with atherosclerotic-resistant arteries were predominately involved in regulation of inflammation and immune processes, as well as development. The great saphenous veins exhibited an increase of the DNA methylation age in comparison to the internal mammary arteries. Gene ontology analysis for genes harboring hypermethylated CpG-sites in veins revealed the enrichment for biological processes associated with the development. Four CpG-sites located within the <i>MIR10B</i> gene sequence and about 1 kb upstream of the <i>HOXD4</i> gene were also confirmed as hypomethylated in the independent dataset of the right coronary arteries in the area of advanced atherosclerotic plaques in comparison with the other vascular tissues. The DNA methylation differences observed in vascular tissues of patients with coronary heart disease can provide new insights into the mechanisms underlying the development of pathology and explanation for the difference in graft patency after coronary artery bypass grafting surgery.</p></div

Flow chart describing experiment and analysis.

<p>Flow chart describing experiment and analysis.</p

Methylation level (mean ±SD) at the promoter of <i>HOXD4</i> gene in paired vascular tissues from twenty one patients with atherosclerosis.

<p>CAP indicates right coronary arteries in the area of advanced atherosclerotic plaques; IMA, internal mammary arteries; GSV, great saphenous veins.</p><p>Methylation level (mean ±SD) at the promoter of <i>HOXD4</i> gene in paired vascular tissues from twenty one patients with atherosclerosis.</p