Search results for "Palin"
showing 10 items of 79 documents
Efficient Control of raf Gene Expression by CAP and Two Raf Repressors that Bend DNA in Opposite Directions
1999
The plasmid-borne raf operon of Escherichia coli encodes proteins involved in the uptake and utilisation of the trisaccharide raffinose. The operon is subject to dual regulation; to negative control by the binding of RafR repressor to twin operators, O1 and O2, and to positive control by the cAMP-binding protein, CAP. We have identified the CAP binding site (CBS) as a 22 bp palindromic sequence with incomplete dyad symmetry by deletion analysis, DNasel footprinting and electrophoretic mobility shift assays (EMSA) of CAP-DNA complexes. The CBS is centred 60.5 bp upstream of the transcription start point and partially overlaps O1. In vivo, CAP increases rafA (alpha-galactosidase) gene express…
Hydro-mechanical behaviour of shallow Opalinus Clay shale
2019
In Switzerland, Opalinus Clay shale has been selected as the host formation for radioactive waste disposal. The minimum required depth of the repository is related to the long-lasting isolation required for the disposal (1 million years). During this period, possible erosion scenarios affecting the repository need to be analysed. Opalinus Clay from shallow depths (< 70 m) was sourced from a borehole in Northern Switzerland, where the formation was affected by a considerable exhumation process. This work aims to investigate the impact of the mentioned phenomenon on the hydro-mechanical behaviour of Opalinus Clay through one-dimensional consolidation and permeability measurements. Laboratory …
Balancing and clustering of words in the Burrows–Wheeler transform
2011
AbstractCompression algorithms based on Burrows–Wheeler transform (BWT) take advantage of the fact that the word output of BWT shows a local similarity and then turns out to be highly compressible. The aim of the present paper is to study such “clustering effect” by using notions and methods from Combinatorics on Words.The notion of balance of a word plays a central role in our investigation. Empirical observations suggest that balance is actually the combinatorial property of input word that ensure optimal BWT compression. Moreover, it is reasonable to assume that the more balanced the input word is, the more local similarity we have after BWT (and therefore the better the compression is).…
Fluorescence labels as sensors for oxygen binding of arthropod hemocyanins
2004
The molecular basis of high cooperativity in multi-subunit proteins is still unknown in most cases. Oxygen binding by multi-subunit hemocyanins produces two intrinsic spectroscopic signals which are, however, either limited to the UV or are very weak. Here we demonstrate that fluorescence labels emitting in the visible can be used as sensors for cooperative oxygen binding of hemocyanins. Fluorescence resonance energy transfer to the oxygenated active sites quenches the emission of the labels by roughly 50% upon oxygenation of the protein. The labels give strong and photo-stable emission, allowing imaging of single hemocyanin molecules. Therefore, this study opens up a new perspective for in…
Identification of proteolytic enzymes from Eriphia verrucosa and Palinurus elephas capable to degrade gliadin
2009
In small intestinal disease, coeliac sprue, proline-rich gluten peptides from wheat, rye and barley are relatively resistant to gastrointestinal digestion, and therefore remain in the intestinal lumen to elicit immunopathology in genetically susceptible individuals. Since most serine endopeptidases are unable to hydrolyse proline residues, proline specific proteases may be therapeutic keys in digestive diseases. Partial hydrolysis reduces the risk of allergenic sensitization while total hydrolysis ensures the elimination of the allergenicity of whey protein (Villad´oniga and others 2007). Kimoto and others (1998) reported that 18-, 31-, 37- and 58-kDa wheat allergens were recognized by the …
A subquadratic algorithm for minimum palindromic factorization
2014
We give an $\mathcal{O}(n \log n)$-time, $\mathcal{O}(n)$-space algorithm for factoring a string into the minimum number of palindromic substrings. That is, given a string $S [1..n]$, in $\mathcal{O}(n \log n)$ time our algorithm returns the minimum number of palindromes $S_1,\ldots, S_\ell$ such that $S = S_1 \cdots S_\ell$. We also show that the time complexity is $\mathcal{O}(n)$ on average and $\Omega(n\log n)$ in the worst case. The last result is based on a characterization of the palindromic structure of Zimin words.
Enumeration and Structure of Trapezoidal Words
2013
Trapezoidal words are words having at most $n+1$ distinct factors of length $n$ for every $n\ge 0$. They therefore encompass finite Sturmian words. We give combinatorial characterizations of trapezoidal words and exhibit a formula for their enumeration. We then separate trapezoidal words into two disjoint classes: open and closed. A trapezoidal word is closed if it has a factor that occurs only as a prefix and as a suffix; otherwise it is open. We investigate open and closed trapezoidal words, in relation with their special factors. We prove that Sturmian palindromes are closed trapezoidal words and that a closed trapezoidal word is a Sturmian palindrome if and only if its longest repeated …
A Classification of Trapezoidal Words
2011
Trapezoidal words are finite words having at most n+1 distinct factors of length n, for every n>=0. They encompass finite Sturmian words. We distinguish trapezoidal words into two disjoint subsets: open and closed trapezoidal words. A trapezoidal word is closed if its longest repeated prefix has exactly two occurrences in the word, the second one being a suffix of the word. Otherwise it is open. We show that open trapezoidal words are all primitive and that closed trapezoidal words are all Sturmian. We then show that trapezoidal palindromes are closed (and therefore Sturmian). This allows us to characterize the special factors of Sturmian palindromes. We end with several open problems.
On the least number of palindromes contained in an infinite word
2013
We investigate the least number of palindromic factors in an infinite word. We first consider general alphabets, and give answers to this problem for periodic and non-periodic words, closed or not under reversal of factors. We then investigate the same problem when the alphabet has size two.
On the Structure of Bispecial Sturmian Words
2013
A balanced word is one in which any two factors of the same length contain the same number of each letter of the alphabet up to one. Finite binary balanced words are called Sturmian words. A Sturmian word is bispecial if it can be extended to the left and to the right with both letters remaining a Sturmian word. There is a deep relation between bispecial Sturmian words and Christoffel words, that are the digital approximations of Euclidean segments in the plane. In 1997, J. Berstel and A. de Luca proved that \emph{palindromic} bispecial Sturmian words are precisely the maximal internal factors of \emph{primitive} Christoffel words. We extend this result by showing that bispecial Sturmian wo…