Topochemical differences in the amount of RNA in the motoneurons of the spinal chord in hypoxia and hypokinesia

Reactions to hypoxia and hypoknesia were compared by measuring charges in the amount of ribonucleic acid (RNA) in the cytoplasm of neurons of the intumescentia cervicalis and lumbalis. Animals were subjected to hypoxia, hypokinesia and both combined and a control group to neither. A total of two groups of motoneurons were compared, one innervating the respiratory musculature, the other the musculature of the lower extremities, so that hypoxic hypoxia would probably affect the first group primarily and hypokinesia the second. Results indicate that neither affect the amount of RNA in the neurons of the first group but a significant increase is noted in neurons of the second group. Other significant results are reported

Comparison of Spectra in Unsequenced Species

International audienceWe introduce a new algorithm for the mass spectromet- ric identication of proteins. Experimental spectra obtained by tandem MS/MS are directly compared to theoretical spectra generated from pro- teins of evolutionarily closely related organisms. This work is motivated by the need of a method that allows the identication of proteins of unsequenced species against a database containing proteins of related organisms. The idea is that matching spectra of unknown peptides to very similar MS/MS spectra generated from this database of annotated proteins can lead to annotate unknown proteins. This process is similar to ortholog annotation in protein sequence databases. The difficulty with such an approach is that two similar peptides, even with just one mod- ication (i.e. insertion, deletion or substitution of one or several amino acid(s)) between them, usually generate very dissimilar spectra. In this paper, we present a new dynamic programming based algorithm: Packet- SpectralAlignment. Our algorithm is tolerant to modications and fully exploits two important properties that are usually not considered: the notion of inner symmetry, a relation linking pairs of spectrum peaks, and the notion of packet inside each spectrum to keep related peaks together. Our algorithm, PacketSpectralAlignment is then compared to SpectralAlignment [1] on a dataset of simulated spectra. Our tests show that PacketSpectralAlignment behaves better, in terms of results and execution tim

Expected length of the longest common subsequence for large alphabets

We consider the length L of the longest common subsequence of two randomly uniformly and independently chosen n character words over a k-ary alphabet. Subadditivity arguments yield that the expected value of L, when normalized by n, converges to a constant C_k. We prove a conjecture of Sankoff and Mainville from the early 80's claiming that C_k\sqrt{k} goes to 2 as k goes to infinity.Comment: 14 pages, 1 figure, LaTe

Thermodynamics of protein folding: a random matrix formulation

The process of protein folding from an unfolded state to a biologically active, folded conformation is governed by many parameters e.g the sequence of amino acids, intermolecular interactions, the solvent, temperature and chaperon molecules. Our study, based on random matrix modeling of the interactions, shows however that the evolution of the statistical measures e.g Gibbs free energy, heat capacity, entropy is single parametric. The information can explain the selection of specific folding pathways from an infinite number of possible ways as well as other folding characteristics observed in computer simulation studies.Comment: 21 Pages, no figure

Stationary Distribution and Eigenvalues for a de Bruijn Process

We define a de Bruijn process with parameters n and L as a certain continuous-time Markov chain on the de Bruijn graph with words of length L over an n-letter alphabet as vertices. We determine explicitly its steady state distribution and its characteristic polynomial, which turns out to decompose into linear factors. In addition, we examine the stationary state of two specializations in detail. In the first one, the de Bruijn-Bernoulli process, this is a product measure. In the second one, the Skin-deep de Bruin process, the distribution has constant density but nontrivial correlation functions. The two point correlation function is determined using generating function techniques.Comment: Dedicated to Herb Wilf on the occasion of his 80th birthda

Space-efficient merging of succinct de Bruijn graphs

We propose a new algorithm for merging succinct representations of de Bruijn graphs introduced in [Bowe et al. WABI 2012]. Our algorithm is based on the lightweight BWT merging approach by Holt and McMillan [Bionformatics 2014, ACM-BCB 2014]. Our algorithm has the same asymptotic cost of the state of the art tool for the same problem presented by Muggli et al. [bioRxiv 2017, Bioinformatics 2019], but it uses less than half of its working space. A novel important feature of our algorithm, not found in any of the existing tools, is that it can compute the Variable Order succinct representation of the union graph within the same asymptotic time/space bounds.Comment: Accepted to SPIRE'1

The initial appraisal of buried DAS system in CO2CRC Otway Project: the comparison of buried standard fibre-optic and helically wound cables using 2D imaging

This study aims to assess the ability of shallow distributed acoustic sensing (DAS) to serve as a cost-effective seismic sensor array for permanent monitoring applications. To this end, as part of the CO2CRC seismic monitoring program, a fibre-optic DAS array was deployed alongside a permanently buried geophone array at the Otway Project site (Victoria, Australia). The DAS array consisted of a standard commercially available tactical fibre-optic cable, which was deployed in 0.8 m deep trenches. A custom-designed helically wound (HW) cable was also deployed in one of the DAS trenches for comparison of the cable designs. Simultaneous acquisition of the seismic data was carried out using ~ 3000 vibroseis source points and geophones, DAS standard and HW cables. For initial assessment of the seismic images acquired with DAS and to compare different cable designs, preliminary 2D seismic reflection processing is conducted on both DAS cables and geophone data along a single 2D line. The geophone data processing guided processing of the DAS data. Several shallow structures (100–450 ms) and some important reflectors at 450–600 ms are observed on the final DAS images. Comparison of the two different DAS cable types demonstrated that seismic imaging would benefit DAS technology. However, the benefit of utilising HW cable is modest compared with the standard cable. The workflows and results of this study pave the way for processing of the 3D seismic data set acquired with the DAS array, as well as further detailed analysis of the DAS cables and the system itself

SEARCHPATTOOL: a new method for mining the most specific frequent patterns for binding sites with application to prokaryotic DNA sequences

<p>Abstract</p> <p>Background</p> <p>Computational methods to predict transcription factor binding sites (TFBS) based on exhaustive algorithms are guaranteed to find the best patterns but are often limited to short ones or impose some constraints on the pattern type. Many patterns for binding sites in prokaryotic species are not well characterized but are known to be large, between 16–30 base pairs (bp) and contain at least 2 conserved bases. The length of prokaryotic species promoters (about 400 bp) and our interest in studying a small set of genes that could be a cluster of co-regulated genes from microarray experiments led to the development of a new exhaustive algorithm targeting these large patterns.</p> <p>Results</p> <p>We present Searchpattool, a new method to search for and select the most specific (conservative) frequent patterns. This method does not impose restrictions on the density or the structure of the pattern. The best patterns (motifs) are selected using several statistics, including a new application of a z-score based on the number of matching sequences. We compared Searchpattool against other well known algorithms on a <it>Bacillus subtilis </it>group of 14 input sequences and found that in our experiments Searchpattool always performed the best based on performance scores.</p> <p>Conclusion</p> <p>Searchpattool is a new method for pattern discovery relative to transcription factor binding sites for species or genes with short promoters. It outputs the most specific significant patterns and helps the biologist to choose the best candidates.</p