Effects of long-range correlations in DNA on sequence alignment score statistics.

Long-range correlations in genomic base composition are a ubiquitous statistical feature among many eukaryotic genomes. In this article, these correlations are shown to substantially influence the statistics of sequence alignment scores. Using a Gaussian approximation to model the correlated score landscape, we calculate the corrections to the scale parameter lambda of the extreme value distribution of alignment scores. Our approximate analytic results are supported by a detailed numerical study based on a simple algorithm to efficiently generate long-range correlated random sequences. We find both, mean and exponential tail of the score distribution for long-range correlated sequences to be substantially shifted compared to random sequences with independent nucleotides. The significance of measured alignment scores will therefore change upon incorporation of the correlations in the null model. We discuss the magnitude of this effect in a biological context.     

TreeSnatcher: coding trees from images

TreeSnatcher is a GUI-driven JAVA application for the semi-automatic recognition of multifurcating phylogenetic trees in pixel images. The program accepts an image file as input and analyzes the topology and the metrics of a tree depicted. The analysis is carried out in a multiple-stage process using algorithms from image analysis. In the end, TreeSnatcher produces a Newick tree code that represents the tree structure optionally including branch lengths. TreeSnatcher can process trees with 100 leaves or more in a few seconds. AVAILABILITY: TreeSnatcher was developed in JAVA under Mac OS X and is executable on UNIX/Linux, Windows and Mac OS X systems. The application and its documentation can be freely downloaded from http://www.cibiv.at/software/treesnatcher.     

The tetratricopeptide repeats of receptors involved in protein translocation across membranes

Transport of polypeptides across membranes is a general and essential process in every cell. This process is utilized by molecular machines composed of soluble and membrane-inserted proteins. At least one component of the molecular transport machines present in different membranes contains a subunit with a domain composed of 3 tetratricopeptide repeat (TPR) motifs. These domains are important for protein-protein interaction, for example, recognition of chaperones. To understand the evolution of these TPR domain-containing receptors involved in protein translocation, we inferred their phylogenetic relationships. We show that the evolutionary rate of these TPR domains is reduced when compared with the remaining sequence. The reduction is explained by the interaction of the TPR domains with their substrates. Based on the TPR tree, we propose that Sec72 recognizes Hsp70 and that Tom34 recognizes Hsp90. The phylogeny can further be used to assign the localization of the Toc64 isoforms to mitochondria or chloroplasts. Our findings are discussed in the context of the evolutionary development of translocation systems with focus on the occurrence of Hsp70/Hsp90-recognizing TPR domains in these machineries.     

Development of hypothermia in rats at increase of [Ca2+] in the blood

In rats, data on influence of i. v. administration of calcium chloride on the level of [Ca2+] in the blood and on process of oppression ofthermoregulatory and respiratory functions in rats in hypothermia. 0.18 or 0.135 mmol Ca2+ on the 3rd minute from beginning of the administration increased [Ca2+] in the blood from 1.01 +/- 0.03 to 2.56 +/- 0.08 mM (or 2.27 +/- 0.06 mM). Then [Ca2+] was reduced gradually, in 20 minutes from administration, solution of CaCh [Ca2+] exceeded the initial level by 20-30 %. The increase of concentration of ionized calcium in the rat blood strengthened the cold oppression of breathing and cold shivering as compared with the control (administration of physiological solution). Arrest of breathing in rats after administration of CaCl2 solution occurred at higher rectal temperatures (21 +/- 0.03 degrees C) as compared with control experiments (18 +/- 0.4 degrees C), p < 0.05. It is suggested that increase of [Ca2+] in the blood strengthens effects of cold in the form of oppression of thermoregulatory and respiratory functions.     

The history of ranges of the great tit (<Emphasis Type="Italic">Parus major</Emphasis>) and Japanese tit (<Emphasis Type="Italic">Parus minor</Emphasis>) in the Amur Region

The history of ranges of the great tit (Parus major) and Japanese tit (P. minor) in the Amur River basin is described on the basis of original data collected between 1970 and 2010 and published data. The main factor accounting for the expansion of the great and Japanese tits to the Amur basin and neighboring territories in the 19th to 21st centuries is economic activity, primarily agriculture and timber harvesting. The approximate range boundaries and the sympatry zone of these two species have been determined for the second half of the 19th century; the beginning, middle, and third quarter of the 20th century; and the turn of the 21st century. Three different ecological channels consecutively played the main role in the eastward expansion of the great tit: the Amur River valley (from the mid-19th to the early 20th century), the Trans-Siberian Railroad (since the early 20th century), and the Baikal-Amur Railroad (since the 1970s). It is shown that the concept concerning the finding of great tits in Udskii Ostrog by Middendorff’s expedition is erroneous: according to dates on the labels, the corresponding two specimens were in fact collected in a different geographic locality. It has been found that Komsomolsk-on-Amur is a new locality jointly inhabited by both species, independent of the main zone of their sympatry. It has appeared very recently, at the turn of the 21st century.     

Quantitative and dynamic expression profile of premature and active forms of the regional ADAM proteins during chicken brain development

The ADAM (A Disintegrin and Metalloprotease) family of transmembrane proteins plays important roles in embryogenesis and tissue formation based on their multiple functional domains. In the present study, for the first time, the expression patterns of the premature and the active forms of six members of the ADAM proteins — ADAM9, ADAM10, ADAM12, ADAM17, ADAM22 and ADAM23 — in distinct parts of the developing chicken brain were investigated by quantitative Western blot analysis from embryonic incubation day (E) 10 to E20. The results show that the premature and the active forms of various ADAM proteins are spatiotemporally regulated in different parts of the brain during development, suggesting that the ADAMs play a very important role during embryonic development.