Estimates of electronic coupling for excess electron transfer in DNA

Electronic coupling Vda is one of the key parameters that determine the rate of charge transfer through DNA. While there have been several computational studies of Vda for hole transfer, estimates of electronic couplings for excess electron transfer (ET) in DNA remain unavailable. In the paper, an efficient strategy is established for calculating the ET matrix elements between base pairs in a π stack. Two approaches are considered. First, we employ the diabatic-state (DS) method in which donor and acceptor are represented with radical anions of the canonical base pairs adenine-thymine (AT) and guanine-cytosine (GC). In this approach, similar values of Vda are obtained with the standard 6-31 G* and extended 6-31++ G* basis sets. Second, the electronic couplings are derived from lowest unoccupied molecular orbitals (LUMOs) of neutral systems by using the generalized Mulliken-Hush or fragment charge methods. Because the radical-anion states of AT and GC are well reproduced by LUMOs of the neutral base pairs calculated without diffuse functions, the estimated values of Vda are in good agreement with the couplings obtained for radical-anion states using the DS method. However, when the calculation of a neutral stack is carried out with diffuse functions, LUMOs of the system exhibit the dipole-bound character and cannot be used for estimating electronic couplings. Our calculations suggest that the ET matrix elements Vda for models containing intrastrand thymine and cytosine bases are essentially larger than the couplings in complexes with interstrand pyrimidine bases. The matrix elements for excess electron transfer are found to be considerably smaller than the corresponding values for hole transfer and to be very responsive to structural changes in a DNA stack

Charge transfer in DNA: hole charge is confined to a single base pair due to solvation effects

We include solvation effects in tight-binding Hamiltonians for hole states in DNA. The corresponding linear-response parameters are derived from accurate estimates of solvation energy calculated for several hole charge distributions in DNA stacks. Two models are considered: (A) the correction to a diagonal Hamiltonian matrix element depends only on the charge localized on the corresponding site and (B) in addition to this term, the reaction field due to adjacent base pairs is accounted for. We show that both schemes give very similar results. The effects of the polar medium on the hole distribution in DNA are studied. We conclude that the effects of polar surroundings essentially suppress charge delocalization in DNA, and hole states in (GC)n sequences are localized on individual guanines

Tandem chimeric transcription as a means to increase protein diversity in the human genome

The “one-gene, one-protein” rule, coined by Beadle and Tatum, has been fundamental to molecular biology. The rule implies that the genetic complexity of an organism depends essentially on its gene number. The discovery, however, that alternative gene splicing and transcription are widespread phenomena dramatically altered our understanding of the genetic complexity of higher eukaryotic organisms; in these, a limited number of genes may potentially encode a much larger number of proteins. Here we investigate yet another phenomenon that may contribute to generate additional protein diversity. Indeed, by relying on both computational and experimental analysis, we estimate that at least 4%–5% of the tandem gene pairs in the human genome can be eventually transcribed into a single RNA sequence encoding a putative chimeric protein. While the functional significance of most of these chimeric transcripts remains to be determined, we provide strong evidence that this phenomenon does not correspond to mere technical artifacts and that it is a common mechanism with the potential of generating hundreds of additional proteins in the human genome.

A comparison of random sequence reads versus 16S rDNA sequences for estimating the biodiversity of a metagenomic library

The construction of metagenomic libraries has permitted the study of microorganisms resistant to isolation and the analysis of 16S rDNA sequences has been used for over two decades to examine bacterial biodiversity. Here, we show that the analysis of random sequence reads (RSRs) instead of 16S is a suitable shortcut to estimate the biodiversity of a bacterial community from metagenomic libraries. We generated 10,010 RSRs from a metagenomic library of microorganisms found in human faecal samples. Then searched them using the program BLASTN against a prokaryotic sequence database to assign a taxon to each RSR. The results were compared with those obtained by screening and analysing the clones containing 16S rDNA sequences in the whole library. We found that the biodiversity observed by RSR analysis is consistent with that obtained by 16S rDNA. We also show that RSRs are suitable to compare the biodiversity between different metagenomic libraries. RSRs can thus provide a good estimate of the biodiversity of a metagenomic library and, as an alternative to 16S, this approach is both faster and cheaper.

Genetic characterization of the ABO blood group in Neandertals

Background: The high polymorphism rate in the human ABO blood group gene seems to be related to susceptibility to different pathogens. It has been estimated that all genetic variation underlying the human ABO alleles appeared along the human lineage, after the divergence from the chimpanzee lineage. A paleogenetic analysis of the ABO blood group gene in Neandertals allows us to directly test for the presence of the ABO alleles in these extinct humans. Results: We have analysed two male Neandertals that were retrieved under controlled conditions at the El Sidron site in Asturias (Spain) and that appeared to be almost free of modern human DNA contamination. We find a human specific diagnostic deletion for blood group O (O01 haplotype) in both Neandertal individuals. Conclusion: These results suggest that the genetic change responsible for the O blood group in humans predates the human and Neandertal divergence. A potential selective event associated with the emergence of the O allele may have therefore occurred after humans separated from their common ancestor with chimpanzees and before the human-Neandertal population divergence.

Reassessing the role of mitochondrial DNA mutations in autism spectrum disorder

Background: There is increasing evidence that impairment of mitochondrial energy metabolism plays an important role in the pathophysiology of autism spectrum disorders (ASD; OMIM number: 209850). A significant proportion of ASD cases display biochemical alterations suggestive of mitochondrial dysfunction and several studies have reported that mutations in the mitochondrial DNA (mtDNA) molecule could be involved in the disease phenotype. Methods: We analysed a cohort of 148 patients with idiopathic ASD for a number of mutations proposed in the literature as pathogenic in ASD. We also carried out a case control association study for the most common European haplogroups (hgs) and their diagnostic single nucleotide polymorphisms (SNPs) by comparing cases with 753 healthy and ethnically matched controls.Results: We did not find statistical support for an association between mtDNA mutations or polymorphisms and ASD.Conclusions: Our results are compatible with the idea that mtDNA mutations are not a relevant cause of ASD and the frequent observation of concomitant mitochondrial dysfunction and ASD could be due to nuclear factors influencing mitochondrion functions or to a more complex interplay between the nucleus and the mitochondrion/mtDNA.

L'Impacte dels diaris gratuïts sobre els diaris de pagament

Com a manera d’analitzar l’efecte de les innovacions que contínuamentexperimenta el món actual, hem cregut interessant analitzar l’impacte deldiaris gratuïts o premsa gratuïta sobre els diaris de pagament o premsatradicional, ja que creiem que, tot i que tan sols representa un petit canvien un àmbit molt concret com és el de la premsa, pot significar un mirall enel que fixar-se per altres sectors d’àmbit tradicionalment privat.Avui dia, des de fa ja uns anys, quan agafes el metro o l’autobús cada matíper anar al treball o a la universitat veiem que gairebé tothom té und’aquests diaris gratuïts a la mà (Qué!, Metro, 20 Minutos, ADN...) que elshi acaben de donar a l’entrada de l’estació. Veient això s’ens van plantejaruna sèrie de preguntes: la gent que llegeix diaris gratuïts, llegeix també lapremsa tradicional? L’aparició dels diaris gratuïts, ha fet reduir el nombre delectors de premsa de pagament? El que volem esbrinar és si aquests noustipus de diaris són una amenaça o més aviat són complementaris als diarisde pagament. La pregunta que volem respondre és: Quin ha estat l’impactedels diaris gratuïts sobre els diaris de pagament.Al llarg del treball veurem que l’entrada al mercat d’aquest nou tipus depremsa no ha suposat una amenaça pels diaris tradicionals, com potsemblar en un principi. Podrem comprovar que pel que fa al nombre delectors l’impacte és gairebé nul, és a dir, és veritat que els diaris depagament han patit un estancament en quant a nombre de lectors però noha afectat quasi bé gens als beneficis d’aquests. Tambè veurem, que és enel terreny de la publicitat on realment competeixen els dos tipus de diarisaixí com tambè, que la situació és diferent al nostre entorn respecte a laresta del món.

Dades epidemiològiques, clíniques i tractament de pacients amb infecció crònica pel virus hepatitis b en l’àrea barcelonès nord i maresme

Estudi observacional que analitza dades clínico-epidemiològiques, analítiques i tractament de pacients amb infecció crònica pel VHB en un Hospital de tercer nivell en l’àrea del Barcelonès Nord i Maresme durant 5 anys (2007-2012). La mostra (n=335), el 67% són homes caucàsics entre 40-60 anys i HBeAg negatiu. El 40% són immigrants. Els pacients HBeAg positiu s’associen a edat menor, transmissió vertical i nivells més elevats d’ALT i ADN-VHB. Els pacients HBeAg negatiu s’associen a edat > 40 anys, nivells més baixos d’ALT i ADN-VHB i fibrosi hepàtica avançada. El 45,1% rebien tractament antiviral. El 3,8% foren morts per carcinoma hepatocelul.lar.

Estudio Farmacogenético en Pacientes con Cáncer de Pulmón No Microcítico Avanzado tratados con Quimioterapia basada en Platino

a partir de ADN genómico obtenido de las células nucleadas de sangre periférica de 103 pacientes con Cáncer de Pulmón No Microcítico (CPNM) avanzado tratados con quimioterapia basada en platino, hemos analizado la asociación entre supervivencia y cinco SNPs (Single Nucleotide Polymorphism) pertenecientes a dos grupos de genes: i) de la via metabólica del ácido fólico (Timidilato Sintetasa (TS), Metil-tetrahidrofolato Reductasa (MTHFR) y, ii) de la vía de reparación del ADN (Excision repair cross-complemeting group 1 (ERCC1) y Xeroderma pigmentosum group D (XPD).

Assessment of microbial community structure changes by amplified ribosomal DNA restriction analysis (ARDRA)

Amplified ribosomal DNA restriction analysis (ARDRA) is a simple method based on restriction endonuclease digestion of the amplified bacterial 16S rDNA. In this study we have evaluated the suitability of this method to detect differences in activated sludge bacterial communities fed on domestic or industrial wastewater, and subject to different operational conditions. The ability of ARDRA to detect these differences has been tested in modified Ludzack-Ettinger (MLE) configurations. Samples from three activated sludge wastewater treatment plants (WWTPs) with the MLE configuration were collected for both oxic and anoxic reactors, and ARDRA patterns using double enzyme digestions AluI+MspI were obtained. A matrix of Dice similarity coefficients was calculated and used to compare these restriction patterns. Differences in the community structure due to influent characteristics and temperature could be observed, but not between the oxic and anoxic reactors of each of the three MLE configurations. Other possible applications of ARDRA for detecting and monitoring changes in activated sludge systems are also discussed

Disseny, implementació i avaluació d'un joc tangible basat en puzles per a l'aprenentatge d'arquitectura d'ordinadors

Actualment existeix una falta d'interès per part dels estudiants a l'àrea de les enginyeries en Tecnologies de la Informació i la Comunicació (TIC) que es pot veure reflectida en el descens de les matriculacions universitàries en aquest àmbit. Aquest fet està relacionat amb que la nova generació d‟estudiants està constantment en contacte amb tota mena d'aparells tecnològics estimulants i a l‟hora de l‟estudi poden sofrir una falta d‟interès per l‟ús d‟una metodologia d'aprenentatge més tradicional. En aquest sentit s'ha investigat que l‟ús de jocs com a eina educativa pot ser una bona solució per afrontar aquesta falta d'interès. No obstant això, actualment no existeixen gaires jocs destinats a aprendre conceptes relacionats amb les enginyeries TIC i que proporcionin als estudiants els mecanismes d'ajuda necessaris per donar-los suport durant l'aprenentatge d‟aquests nous conceptes. En aquest projecte es desenvoluparà un joc educatiu per a estudiants amb l‟objectiu de proporcionar uns primers coneixements sobre les TIC. Per una banda, per al disseny del joc s‟utilitzarà un model conceptual que defineix els elements necessaris per a dissenyar jocs basats en resoldre puzles. A més, aquest model conceptual permet el disseny no només de jocs per a PCs, sinó també de jocs tangibles i exploratius (mitjançant tecnologia mòbil). En el nostre cas, ens centrarem en la implementació d‟un joc tangible. Per altra banda, pel que fa a la implementació, tindrem en compte l‟estàndard educatiu d‟IMS Learning Design, demostrant d‟aquesta manera que aquest tipus de jocs es poden beneficiar dels avantatges que aporten els estàndards educatius. Per tant, en aquest PFC es dissenyarà i implementarà un joc tangible basat en puzles dintre de l‟àrea d‟arquitectura d‟ordinadors. El joc constarà de tres mini-jocs que es presentaran com jocs de realitat augmentada amb el suport d‟un ordinador i unes peces físiques amb les que interactuaran els usuaris. El sistema proporcionarà un sistema d‟ajuda i un sistema de puntuació. Per últim, avaluarem el joc en un centre escolar amb estudiants de 4t d‟ESO amb la finalitat d'analitzar les valoracions dels estudiants respecte el joc i les pistes proporcionades.

Els errors en les relacions assistencials: una aproximació des de la bioètica

De manera general, cal tenir present quel'error és habitual en els sistemes complexos, com la biologia ens ho ensenya ja a nivell cel·lular: els errors en la replicació de l'ADN els anomenem mutacions i pel que sabem han jugat i juguen un rol fonamental en l'evolució de les espècies vivents. L'error, per tant, és omnipresenten els organismes vivents; però, a diferènciade les màquines artificials, els organismesvivents poden funcionar amb l¿error i malgratl¿error.

SSCP-polymorphism in intron 12 of the CFTR gene recognized by BclI

Source/Description: SSCP analysis of intron 12 of the CFTR gene from PCR products showed an extra band in several DNA samples. Sequencing of the additional fragment extra band revealed a T- A change in the position 1898 + 152 of CFTR (Fig. 1). The change is a polymorphism which can be identified by SSCP or by BclI digestion...

Counter-ion effect on surfactant-DNA gel particles as controlled DNA delivery systems

The ability to entrap drugs within vehicles and subsequently release them has led to new treatments for a number of diseases. Based on an associative phase separation and interfacial diffusion approach, we developed a way to prepare DNA gel particles without adding any kind of cross-linker or organic solvent. Among the various agents studied, cationic surfactants offered particularly efficient control for encapsulation and DNA release from these DNA gel particles. The driving force for this strong association is the electrostatic interaction between the two components, as induced by the entropic increase due to the release of the respective counter-ions. However, little is known about the influence of the respective counter-ions on this surfactant-DNA interaction. Here we examined the effect of different counter-ions on the formation and properties of the DNA gel particles by mixing DNA (either single- (ssDNA) or double-stranded (dsDNA)) with the single chain surfactant dodecyltrimethylammonium (DTA). In particular, we used as counter-ions of this surfactant the hydrogen sulfate and trifluoromethane sulfonate anions and the two halides, chloride and bromide. Effects on the morphology of the particles obtained, the encapsulation of DNA and its release, as well as the haemocompatibility of these particles, are presented, using the counter-ion structure and the DNA conformation as controlling parameters. Analysis of the data indicates that the degree of counter-ion dissociation from the surfactant micelles and the polar/hydrophobic character of the counter-ion are important parameters in the final properties of the particles. The stronger interaction with amphiphiles for ssDNA than for dsDNA suggests the important role of hydrophobic interactions in DNA.

RPS4Y gene family evolution in primates

Background: The RPS4 gene codifies for ribosomal protein S4, a very well-conserved protein present in all kingdoms. In primates, RPS4 is codified by two functional genes located on both sex chromosomes: the RPS4X and RPS4Y genes. In humans, RPS4Y is duplicated and the Y chromosome therefore carries a third functional paralog: RPS4Y2, which presents a testis-specific expression pattern. Results: DNA sequence analysis of the intronic and cDNA regions of RPS4Y genes from species covering the entire primate phylogeny showed that the duplication event leading to the second Y-linked copy occurred after the divergence of New World monkeys, about 35 million years ago. Maximum likelihood analyses of the synonymous and non-synonymous substitutions revealed that positive selection was acting on RPS4Y2 gene in the human lineage, which represents the first evidence of positive selection on a ribosomal protein gene. Putative positive amino acid replacements affected the three domains of the protein: one of these changes is located in the KOW protein domain and affects the unique invariable position of this motif, and might thus have a dramatic effect on the protein function.Conclusion: Here, we shed new light on the evolutionary history of RPS4Y gene family, especially on that of RPS4Y2. The results point that the RPS4Y1 gene might be maintained to compensate gene dosage between sexes, while RPS4Y2 might have acquired a new function, at least in the lineage leading to humans.