Structured RNAs in the ENCODE selected regions of the human genome.

Functional RNA structures play an important role both in the context of noncoding RNA transcripts as well as regulatory elements in mRNAs. Here we present a computational study to detect functional RNA structures within the ENCODE regions of the human genome. Since structural RNAs in general lack characteristic signals in primary sequence, comparative approaches evaluating evolutionary conservation of structures are most promising. We have used three recently introduced programs based on either phylogenetic-stochastic context-free grammar (EvoFold) or energy directed folding (RNAz and AlifoldZ), yielding several thousand candidate structures (corresponding to approximately 2.7% of the ENCODE regions). EvoFold has its highest sensitivity in highly conserved and relatively AU-rich regions, while RNAz favors slightly GC-rich regions, resulting in a relatively small overlap between methods. Comparison with the GENCODE annotation points to functional RNAs in all genomic contexts, with a slightly increased density in 3'-UTRs. While we estimate a significant false discovery rate of approximately 50%-70% many of the predictions can be further substantiated by additional criteria: 248 loci are predicted by both RNAz and EvoFold, and an additional 239 RNAz or EvoFold predictions are supported by the (more stringent) AlifoldZ algorithm. Five hundred seventy RNAz structure predictions fall into regions that show signs of selection pressure also on the sequence level (i.e., conserved elements). More than 700 predictions overlap with noncoding transcripts detected by oligonucleotide tiling arrays. One hundred seventy-five selected candidates were tested by RT-PCR in six tissues, and expression could be verified in 43 cases (24.6%).

Nano-electro-mechanical in dynamical cellular processes

Report for the scientific sojourn carried out at the Department of Structure and Constituents of Matter during 2007.The main focus of the work was on phenomena related to nano-electromechanical processes that take place on a cellular level. Additionally, it has also been performed independent work related to charge and energy transfer in bio molecules, energy transfer in coupled spin systems as well as electrodynamics of nonlinear metamaterials.

On a size-structured two-phase population model with infinite states-at-birth

In this work we introduce and analyze a linear size-structured population model with infinite states-at-birth. We model the dynamics of a population in which individuals have two distinct life-stages: an “active” phase when individuals grow, reproduce and die and a second “resting” phase when individuals only grow. Transition between these two phases depends on individuals’ size. First we show that the problem is governed by a positive quasicontractive semigroup on the biologically relevant state space. Then we investigate, in the framework of the spectral theory of linear operators, the asymptotic behavior of solutions of the model. We prove that the associated semigroup has, under biologically plausible assumptions, the property of asynchronous exponential growth.

Asynchronous growth and competition in a two-sex age-structured population model

Asynchronous exponential growth has been extensively studied in population dynamics. In this paper we find out the asymptotic behaviour in a non-linear age-dependent model which takes into account sexual reproduction interactions. The main feature of our model is that the non-linear process converges to a linear one as the solution becomes large, so that the population undergoes asynchronous growth. The steady states analysis and the corresponding stability analysis are completely made and are summarized in a bifurcation diagram according to the parameter R0. Furthermore the effect of intraspecific competition is taken into account, leading to complex dynamics around steady states.

Structured and unstructured continuous models for Wolbachia infections

We introduce and investigate a series of models for an infection of a diplodiploid host species by the bacterial endosymbiont Wolbachia. The continuous models are characterized by partial vertical transmission, cytoplasmic incompatibility and fitness costs associated with the infection. A particular aspect of interest is competitions between mutually incompatible strains. We further introduce an age-structured model that takes into account different fertility and mortality rates at different stages of the life cycle of the individuals. With only a few parameters, the ordinary differential equation models exhibit already interesting dynamics and can be used to predict criteria under which a strain of bacteria is able to invade a population. Interestingly, but not surprisingly, the age-structured model shows significant differences concerning the existence and stability of equilibrium solutions compared to the unstructured model.

Semigroup analysis of structured populations with distributed states-at-birth arising in mathematical aquaculture

Motivated by the modelling of structured parasite populations in aquaculture we consider a class of physiologically structured population models, where individuals may be recruited into the population at different sizes in general. That is, we consider a size-structured population model with distributed states-at-birth. The mathematical model which describes the evolution of such a population is a first order nonlinear partial integro-differential equation of hyperbolic type. First, we use positive perturbation arguments and utilise results from the spectral theory of semigroups to establish conditions for the existence of a positive equilibrium solution of our model. Then we formulate conditions that guarantee that the linearised system is governed by a positive quasicontraction semigroup on the biologically relevant state space. We also show that the governing linear semigroup is eventually compact, hence growth properties of the semigroup are determined by the spectrum of its generator. In case of a separable fertility function we deduce a characteristic equation and investigate the stability of equilibrium solutions in the general case using positive perturbation arguments.

Optimal latent period in a bacteriophage population model structured by infection-age

We study the lysis timing of a bacteriophage population by means of a continuously infection-age-structured population dynamics model. The features of the model are the infection process of bacteria, the natural death process, and the lysis process which means the replication of bacteriophage viruses inside bacteria and the destruction of them. We consider that the length of the lysis timing (or latent period) is distributed according to a general probability distribution function. We have carried out an optimization procedure and we have found the latent period corresponding to the maximal fitness (i.e. maximal growth rate) of the bacteriophage population.

Stochastic demography and the neutral substitution rate in class-structured populations.

The neutral rate of allelic substitution is analyzed for a class-structured population subject to a stationary stochastic demographic process. The substitution rate is shown to be generally equal to the effective mutation rate, and under overlapping generations it can be expressed as the effective mutation rate in newborns when measured in units of average generation time. With uniform mutation rate across classes the substitution rate reduces to the mutation rate.

Comparison of four embolic materials for portal vein embolization: experimental study in pigs.

Different embolic materials for portal vein embolization (PVE) were evaluated. Twenty pigs received left and median PVE. Hydrophilic phosphorylcholine, N-butyl cyanoacrylate, hydrophilic gel, and polyvinyl alcohol (PVA) particles measuring either 50-150 microm or 700-900 microm were used in five pigs each. Portography and portal vein pressure measurement were performed before, immediately after PVE, and before being euthanized at day 7. Tissue wedges from embolized, and non-embolized liver were obtained for pathology. After complete embolization, recanalization occurred at 7 days in one gel and one 700-900 PVA embolization. Post-PVE increase in portal pressure was found in all groups (p = 0.01). The area of the hepatic lobules in non-embolized liver was larger than in the embolized liver in all groups (p = 0.001). The ratios of the areas between non-embolized/embolized livers were 1.65, 2.19, 1.57, and 1.32 for gel, NBCA, 50-150 PVA and 700-900 PVA, respectively; the ratios of fibrosis between the embolized and non-embolized livers were 1.37, 3.01, 3.49, and 2.11 for gel, NBCA, 50-150 PVA and 700-900 PVA, respectively. Hepatic lobules in non-embolized liver were significantly larger with NBCA than in other groups (p = 0.01). Fibrosis in embolized liver was significantly higher for NBCA and 50-150 PVA (p = 0.002). The most severe changes in embolized and non-embolized liver were induced by 50-150 PVA and NCBA PVE.

Oscillations in a molecular structured cell population model

We consider a nonlinear cyclin content structured model of a cell population divided into proliferative and quiescent cells. We show, for particular values of the parameters, existence of solutions that do not depend on the cyclin content. We make numerical simulations for the general case obtaining, for some values of the parameters convergence to the steady state but also oscillations of the population for others.

Materials porosos per liofilització: els liogels

En aquest treball sobre materials porosos obtinguts per liofilització, s’ha demostrat que es poden produir materials anàlegs als aerogels de sílice mitjançant un procés de congelació i posterior sublimació. Malgrat les dificultats que es presenten en el procés de congelació, s’ha aconseguit un nou producte que hem denominat LIOGELS (per diferenciar-los dels aerogels) amb més o menys graus de monoliticitat segons la composició i el procés realitzat. S’han estudiat diversos sistemes de congelació, principalment amb nitrogen líquid i en la cambra del liofilitzador a -80ºC, però també s’han comparat els resultats de congelacions de gels amb tert-butanol a 12ºC (el tert-butanol fon a 25,69ºC). S’han sintetitzat diferents tipus de gels, de cara a la seva liofilització posterior. Alguns dels gels s’han deixat assecar amb molta cura i molt lentament per produir xerogels monolítics, amb l’objectiu de comparar les estructures dels aerogels, els xerogels i els nous liogels produïts en aquest treball. Per tal d’aconseguir líquids de rentat que al congelar no trenquessin l’estructura, s’han buscat les mescles idònies de dissolvents (que no canviessin de volum al congelar). S’ha instal·lat un equip de liofilització a l’Icmab, que s’ha utilitzat per elaborar les mostres estudiades. L’equip de liofilització té fonamentalment dos modes de funcionament: sublimació a través d’un "manifold" i dins d’una cambra amb safates. Per a la caracterització de les mostres dels nous materials obtinguts, s’ha utilitzat l’equip BET, i els equips de microscòpia electrònica SEM i TEM de l’ICMAB. S’han avaluat els resultats obtinguts amb l’equip de porosimetria (BET) i s’han analitzat les fotografies del SEM i del TEM, fent les oportunes comparacions entre aerogels i liogels, i entre aquests i els xerogels.

Internet com a laboratori virtual dins de l'ensenyament d'Enginyeria de Materials

L’objectiu principal d’aquest projecte és seleccionar i exposar una sèrie de recursos disponibles a Internet, que permetin complementar o facilitar l’aprenentatge dels continguts de la titulació d’Enginyeria de Materials. Al llarg del treball es presenten un total de 124 animacions de diferents temàtiques. La majoria d’elles provenen de pàgines web d’universitats i centres involucrats en l’estudi de materials. També s’exposa una animació d’elaboració pròpia, així com el fonament teòric en què es basa. Cal destacar que l’ús d’applets en l’ensenyament d’Enginyeria de Materials no implica una despesa econòmica extra, i que està d’acord amb les directrius de generar els mínims residus i de fomentar la reducció en origen, establertes en el Pla d’Acció Local per a la Sostenibilitat de la UAB. Gràcies també a la facilitat d’ús, els applets tenen un futur prometedor en l’ensenyament de moltes matèries.

DUGi, portal d'accés als materials en obert de la UdG

Desprès d'un cert temps de rodatge amb els tres repositoris institucionals de la UdG: DUGiDocs, DUGiMedia i DUGiFonsEspecials, haver-los migrat a la versió 1.5.2 de Dspace, i millorat les prestacions que ens permet el programari, ha arribat el moment de millorar l'eina que ens permet fer que el DUGi sigui un portal útil des del punt de vista de la usabilitat, visibilitat i difusió dels materials que es poden consultar als diferents repositoris.