miRNAs link metabolic reprogramming to oncogenesis

The most profound biochemical phenotype of cancer cells is their ability to metabolize glucose to lactate, even under aerobic conditions. This alternative metabolic circuitry is sufficient to support the biosynthetic and energy requirements for cancer cell proliferation and metastasis. Alterations in oncogenes and tumor suppressor genes are involved in the metabolic switch of cancer cells to aerobic glycolysis, increased glutaminolysis and fatty acid biosynthesis. MiRNAs mediate fine-tuning of genes involved directly or indirectly in cancer metabolism. In this review, we discuss the regulatory role of miRNAs on enzymes, signaling pathways and transcription factors involved in glucose and lipid metabolism. We further consider the therapeutic potential of metabolism-related miRNAs in cancer

Algorithms for Longest Common Abelian Factors

In this paper we consider the problem of computing the longest common abelian factor (LCAF) between two given strings. We present a simple $O(\sigma~ n^2)$ time algorithm, where $n$ is the length of the strings and $\sigma$ is the alphabet size, and a sub-quadratic running time solution for the binary string case, both having linear space requirement. Furthermore, we present a modified algorithm applying some interesting tricks and experimentally show that the resulting algorithm runs faster.Comment: 13 pages, 4 figure

The Swap Matching Problem Revisited

In this paper, we revisit the much studied problem of Pattern Matching with Swaps (Swap Matching problem, for short). We first present a graph-theoretic model, which opens a new and so far unexplored avenue to solve the problem. Then, using the model, we devise two efficient algorithms to solve the swap matching problem. The resulting algorithms are adaptations of the classic shift-and algorithm. For patterns having length similar to the word-size of the target machine, both the algorithms run in linear time considering a fixed alphabet.Comment: 23 pages, 3 Figures and 17 Table

Study of the Growth of Entropy Modes in MSSM Flat Directions Decay: Constraints on the Parameter Space

We study how the resonant decay of moduli fields arising in the Minimal Supersymmetric Standard Model (MSSM) could affect large scale curvature perturbations in the early universe. It has been known for some time that the presence of entropy perturbations in a multi-component system can act as seeds for the curvature perturbations on all scales. These entropy perturbations could be amplified exponentially if one of the moduli decays via stochastic resonance, affecting the curvature power spectrum in the process. By imposing the COBE normalization on this power spectrum, one could put constraints on the masses and couplings of the underlying particle physics model without having to rely on collider experiments. We discuss in detail the case of the MSSM but this method could be applied to other theories beyond the Standard Model.Comment: 6 pages, 1 figure, revtex4, comments added in section II, 1 reference adde

Faster algorithms for computing maximal multirepeats in multiple sequences

A repeat in a string is a substring that occurs more than once. A repeat is extendible if every occurrence of the repeat has an identical letter either on the left or on the right; otherwise, it is maximal. A multirepeat is a repeat that occurs at least mmin times (mmin greater than/equal to 2) in each of at least q greater than/equal to 1 strings in a given set of strings. In this paper, we describe a family of efficient algorithms based on suffix arrays to compute maximal multirepeats under various constraints. Our algorithms are faster, more flexible and much more space-efficient than algorithms recently proposed for this problem. The results extend recent work by two of the authors computing all maximal repeats in a single string

New complexity results for the k-covers problem

The k-covers problem (kCP) asks us to compute a minimum cardinality set of stringsof given length k > 1 that covers a given string. It was shown in a recent paper, by reduction to 3-SAT, that the k-covers problem is NP-complete. In this paper we introduce a new problem, that we call the k-Bounded Relaxed Vertex Cover Problem (RVCPk), which we show is equivalent to k-Bounded Set Cover (SCPk). We show further that kCP is a special case of RVCPk restricted to certain classes Gx,k of graphs that represent all strings x. Thus a minimum k-cover can be approximated to within a factor k in polynomial time. We discuss approximate solutions of kCP, and we state a number of conjectures and open problems related to kCP and Gx,k

Functional microRNA high throughput screening reveals miR-9 as a central regulator of liver oncogenesis by affecting the PPARA-CDH1 pathway

Background: Hepatocellular carcinoma (HCC) is the second leading cause of cancer-related deaths, reflecting the aggressiveness of this type of cancer and the absence of effective therapeutic regimens. MicroRNAs have been involved in the pathogenesis of different types of cancers, including liver cancer. Our aim was to identify microRNAs that have both functional and clinical relevance in HCC and examine their downstream signaling effectors. Methods: MicroRNA and gene expression levels were measured by quantitative real-time PCR in HCC tumors and controls. A TargetScan algorithm was used to identify miR-9 downstream direct targets. Results: A high-throughput screen of the human microRNAome revealed 28 microRNAs as regulators of liver cancer cell invasiveness. MiR-9, miR-21 and miR-224 were the top inducers of HCC invasiveness and also their expression was increased in HCC relative to control liver tissues. Integration of the microRNA screen and expression data revealed miR-9 as the top microRNA, having both functional and clinical significance. MiR-9 levels correlated with HCC tumor stage and miR-9 overexpression induced SNU-449 and HepG2 cell growth, invasiveness and their ability to form colonies in soft agar. Bioinformatics and 3’UTR luciferase analyses identified E-cadherin (CDH1) and peroxisome proliferator-activated receptor alpha (PPARA) as direct downstream effectors of miR-9 activity. Inhibition of PPARA suppressed CDH1 mRNA levels, suggesting that miR-9 regulates CDH1 expression directly through binding in its 3’UTR and indirectly through PPARA. On the other hand, miR-9 inhibition of overexpression suppressed HCC tumorigenicity and invasiveness. PPARA and CDH1 mRNA levels were decreased in HCC relative to controls and were inversely correlated with miR-9 levels. Conclusions: Taken together, this study revealed the involvement of the miR-9/PPARA/CDH1 signaling pathway in HCC oncogenesis

PRELIMINARY STUDIES ON SEDIMENT CORE FROM THE TYRO BASIN

Η παρούσα εργασία παρουσιάζει τα προκαταρκτικά αποτελέσματα της ορυκτολογικής και μικροπαλαιοντολογικής ανάλυσης που πραγματοποιήθηκε σε δείγματα ιζημάτων από τον πυρήνα TYR05 που συλλέχθηκε από την ανοξική και υπεράλμυρη λεκάνη Τύρου στην ανατολική Μεσόγειο. Ο πυρήνας αποτελεί μία σύνθετη λιθοστρωματογραφική ακολουθία που αποδίδεται στο ισχυρό γεωδυναμικό καθεστώς της περιοχής. Οι συγκεντρώσεις πλαγκτονικών τρηματοφόρων παρουσιάζουν διακυμάνσεις οι οποίες συμπίπτουν με αλλαγές στη λιθολογία του πυρήνα. Η ορυκτολογική σύσταση των ιζημάτων δείχνει επίδραση από τους εβαπορίτες που δημιουργούνται στον πυθμένα της λεκάνης. Τα ορυκτά συστατικά σε σχέση με τις συγκεντρώσεις της μικροπανίδας δείχνουν ότι τα ιζήματα περιλαμβάνουν σαπροπηλικά στρώματα. Χρειάζονται επιπλέον αναλύσεις για τον ασφαλή προσδιορισμό των σαπροπηλικών αποθέσεων.The present paper summarizes the preliminary results of the mineralogical and micropaleontological analysis conducted on sediment samples from core TYR05 retrieved from the anoxic and hypersaline Tyro basin in the eastern Mediterranean Sea. The core comprises a complex lithostratigraphic sequence attributed to the strong geodynamic regime of the area. The planktonic foraminifera associations present fluctuations which coincide with changes in the lithology of the core. The mineralogical composition of the sediments shows influence from the evaporites developed on the bottom of the basin. The mineral constituents in association to the microfauna assemblages suggest that the sediments include sapropelic layers. Further analyses are needed in order to determine safely the sapropelic deposits

Efficient Seeds Computation Revisited

The notion of the cover is a generalization of a period of a string, and there are linear time algorithms for finding the shortest cover. The seed is a more complicated generalization of periodicity, it is a cover of a superstring of a given string, and the shortest seed problem is of much higher algorithmic difficulty. The problem is not well understood, no linear time algorithm is known. In the paper we give linear time algorithms for some of its versions --- computing shortest left-seed array, longest left-seed array and checking for seeds of a given length. The algorithm for the last problem is used to compute the seed array of a string (i.e., the shortest seeds for all the prefixes of the string) in $O(n^2)$ time. We describe also a simpler alternative algorithm computing efficiently the shortest seeds. As a by-product we obtain an $O(n\log{(n/m)})$ time algorithm checking if the shortest seed has length at least $m$ and finding the corresponding seed. We also correct some important details missing in the previously known shortest-seed algorithm (Iliopoulos et al., 1996).Comment: 14 pages, accepted to CPM 201

Reversible recording medium based on optical storage of information, method of reversible recording on such a medium.

A reversible recording medium based on optical storage of at least one item ofinformation within a support material, includes at least one layer of support material having: base molecules able to take, in a local zone, a first collective state of molecules able to generate a first signal of second harmonic characteristic of this first collective state of molecules when excited by electromagnetic reading radiation; the base molecules having the first collective state of molecules able to transform, at least in part, into transformed molecules so as to pass to a second collective state of molecules when excited by electromagnetic writing radiation, the molecules having the second collective state of molecules able to generate a second signal of second harmonic characteristic of this second collective state of molecules when excited by the electromagnetic reading radiation. The molecules exhibit a molecular structure based on a coumarin skeleton of Formula (I)