GRAMPAL: A Morphological Processor for Spanish implemented in Prolog

A model for the full treatment of Spanish inflection for verbs, nouns and adjectives is presented. This model is based on feature unification and it relies upon a lexicon of allomorphs both for stems and morphemes. Word forms are built by the concatenation of allomorphs by means of special contextual features. We make use of standard Definite Clause Grammars (DCG) included in most Prolog implementations, instead of the typical finite-state approach. This allows us to take advantage of the declarativity and bidirectionality of Logic Programming for NLP. The most salient feature of this approach is simplicity: A really straightforward rule and lexical components. We have developed a very simple model for complex phenomena. Declarativity, bidirectionality, consistency and completeness of the model are discussed: all and only correct word forms are analysed or generated, even alternative ones and gaps in paradigms are preserved. A Prolog implementation has been developed for both analysis and generation of Spanish word forms. It consists of only six DCG rules, because our {\em lexicalist\/} approach --i.e. most information is in the dictionary. Although it is quite efficient, the current implementation could be improved for analysis by using the non logical features of Prolog, especially in word segmentation and dictionary access.Comment: 11 page

Arquitecturas de comunicaciones para la computacióon algorítmica en poblaciones de bacterias multi-cepa

Esta Tesis establece su desarrollo en el área interdisciplinar de la biología sintética y, más concretamente, la computación con bacterias. La unión entre la biología y las ciencias de la computación tiene su raíz a mediados del siglo XX, siendo la biología una importante fuente de inspiración para desarrollar diferentes paradigmas de cómputo en analogía directa a los seres vivos. Sin embargo, no ha sido hasta finales del mismo siglo y principios del XXI cuando el fujo de inspiración cambió de rumbo y se empezaron a construir dispositivos moleculares que actuaran como rudimentarios computadores desempeñando tareas de cálculo lógico definidas. La suma de otra disciplina, la ingeniería, ayuda a abordar el diseño de estos biosistemas como una tarea formalizada de conguración de componentes. Al observar y entender una bacteria como un sistema cuya maquinaria está formada por un conjunto de piezas funcionales diferentes, surge el objetivo de alterar los mecanismos naturales de las bacterias con el fin de construir sistemas vivos con funcionalidades no naturales. Los algoritmos aquí especificados están diseñados para llevarse a cabo en comunidades de bacterias formadas por más de una cepa, para lo cual la presente Tesis propone arquitecturas de comunicaciones diversas que ayuden a la sincronización necesaria entre bacterias distintas, basándose para ello en las capacidades y mecanismos de comunicación que las bacterias muestran en estado natural, como son la conjugación bacteriana y el quorum sensing. Esta Tesis propone la modificación y manipulación de estos mecanismos para conseguir computaciones con rudimentarios sistemas de toma de decisiones y que, en un futuro, puedan servir al desarrollo de aplicaciones en campos cientícos tan diversos como la medicina o la ecología. Entre los ejemplos de cóomputo a los que se someten las nuevas arquitecturas diseñadas caben destacar problemas complejos (TSP, SAT) y un oscilador poblacional en el que una comunidad heterogénea de bacterias muestra oscilación única. Es importante enfatizar que uno de los principales objetivos de la Tesis es la validación, tanto biológica (conocimiento experto) como computacional (simulación) de los modelos diseñados. Ya que la Tesis tiene carácter eminentemente teórico, se lleva a cabo un fuerte proceso de validación que asegure en un porcentaje muy alto el éxito de la -futura- experimentación en laboratorio con estos diseños

ZipN is an essential FtsZ membrane tether and contributes to the septal localization of SepJ in the flamentous cyanobacterium Anabaena

The organismic unit of heterocyst-forming cyanobacteria is a filament of communicating cells connected by septal junctions, proteinaceous structures bridging the cytoplasms of contiguous cells. This distinct bacterial organization is preserved during cell division. In Anabaena, deletion of the zipN gene could not be segregated. We generated strain CSL109 that expresses zipN from a synthetic regulatable promoter. Under conditions of ZipN depletion, cells progressively enlarged, reflecting restricted cell division, and showed drastic morphological alterations including cell detachment from the filaments, to finish lysing. In contrast to the wild-type localization in midcell Z-rings, FtsZ was found in delocalized aggregates in strain CSL109. Consistently, the proportion of membrane-associated to soluble FtsZ in fractionated cell extracts was lower in CSL109. Bacterial two-hybrid analysis showed that ZipN interacts with FtsZ and other cell-division proteins including cytoplasmic Ftn6 and SepF, and polytopic FtsW, FtsX, FtsQ and FtsI. Additionally, ZipN interacted with the septal protein SepJ, and in CSL109 depletion of ZipN was concomitant with a progressive loss of septal specificity of SepJ. Thus, in Anabaena ZipN represents an essential FtsZ membrane tether and an organizer of the divisome, and it contributes to the conformation of septal structures for filament integrity and intercellular communication.Agencia Estatal de Investigación BFU2013-44686-P, BFU2016-77097-

Estudio morfológico y aplicaciones clínicas del nervio maseterino en la reconstrucción dinámica de la parálisis facial

La parálisis facial es una de las patologías más devastadoras para el ser humano debido a sus secuelas, no solamente por las alteraciones en el funcionamiento del nervio facial, sino por la importancia que tiene el rostro para nuestra identidad y habilidad para interactuar con otras personas. Las secuelas de la parálisis facial han sido siempre un reto para los cirujanos reconstructores. El término cirugía de reanimación facial engloba numerosos procedimientos quirúrgicos reconstructivos dirigidos a la restauración de la función, simetría y estética facial. En los casos donde es necesario realizar una transferencia muscular por atrofia de la musculatura facial intrínseca, la elección del nervio donante motor para el músculo trasplantado ha sido motivo de numerosas investigaciones. El nervio maseterino desempeña un papel destacado como nervio motor, por ello pretendemos realizar un estudio anatómico e histológico del mismo, y de las estructuras que se relacionan con él, para mejorar su eficacia en la cirugía de la parálisis facial..

Multicellular Computing Using Conjugation for Wiring

Recent efforts in synthetic biology have focussed on the implementation of logical functions within living cells. One aim is to facilitate both internal ‘‘re-programming’’ and external control of cells, with potential applications in a wide range of domains. However, fundamental limitations on the degree to which single cells may be re-engineered have led to a growth of interest in multicellular systems, in which a ‘‘computation’’ is distributed over a number of different cell types, in a manner analogous to modern computer networks. Within this model, individual cell type perform specific sub-tasks, the results of which are then communicated to other cell types for further processing. The manner in which outputs are communicated is therefore of great significance to the overall success of such a scheme. Previous experiments in distributed cellular computation have used global communication schemes, such as quorum sensing (QS), to implement the ‘‘wiring’’ between cell types. While useful, this method lacks specificity, and limits the amount of information that may be transferred at any one time. We propose an alternative scheme, based on specific cell-cell conjugation. This mechanism allows for the direct transfer of genetic information between bacteria, via circular DNA strands known as plasmids. We design a multicellular population that is able to compute, in a distributed fashion, a Boolean XOR function. Through this, we describe a general scheme for distributed logic that works by mixing different strains in a single population; this constitutes an important advantage of our novel approach. Importantly, the amount of genetic information exchanged through conjugation is significantly higher than the amount possible through QS-based communication. We provide full computational modelling and simulation results, using deterministic, stochastic and spatially-explicit methods. These simulations explore the behaviour of one possible conjugation-wired cellular computing system under different conditions, and provide baseline information for future laboratory implementations.This work was supported by the European Commission FP7 Future and Emerging Technologies Proactive initiative: Bio-chemistry-based Information Technology (CHEM-IT, ICT-2009.8.3), project reference 248919 (BACTOCOM). Work in FdlC lab was supported by Spanish Ministry of Education (BFU2011-26608), and European VII Framework Program grants num 248919/FP7-ICT-2009-4 and 282004/FP7-HEALTH.2001.2.3.1-2. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript

DiSCUS: A simulation platform for conjugation computing

© Springer International Publishing Switzerland 2015 In bacterial populations, cells are able to cooperate in order to yield complex collective functionalities. Interest in population-level cellular behaviour is increasing, due to both our expanding knowledge of the underlying biological principles, and the growing range of possible applications for engineered microbial consortia. The ability of cells to interact through small signalling molecules (a mechanism known as quorum sensing) is the basis for the majority of existing engineered systems. However, horizontal gene transfer (or conjugation) offers the possibility of cells exchanging messages (using DNA) that are much more information-rich. The potential of engineering this conjugation mechanism to suit specific goals will guide future developments in this area. Motivated by a lack of computational models for examining the specific dynamics of conjugation, we present a simulation framework for its further study. (This paper was first presented at the Spatial Computing Workshop of the 13th International Conference on Autonomous Agents and Multiagent Systems (AAMAS), Paris, France, May 5–9 2014. There were no published proceedings)

Physical Forces Shape Group Identity of Swimming Pseudomonas putida Cells

The often striking macroscopic patterns developed by motile bacterial populations on agar plates are a consequence of the environmental conditions where the cells grow and spread. Parameters such as medium stiffness and nutrient concentration have been reported to alter cell swimming behavior, while mutual interactions among populations shape collective patterns. One commonly observed occurrence is the mutual inhibition of clonal bacteria when moving toward each other, which results in a distinct halt at a finite distance on the agar matrix before having direct contact. The dynamics behind this phenomenon (i.e., intolerance to mix in time and space with otherwise identical others) has been traditionally explained in terms of cell-to-cell competition/cooperation regarding nutrient availability. In this work, the same scenario has been revisited from an alternative perspective: the effect of the physical mechanics that frame the process, in particular the consequences of collisions between moving bacteria and the semi-solid matrix of the swimming medium. To this end, we set up a simple experimental system in which the swimming patterns of Pseudomonas putida were tested with different geometries and agar concentrations. A computational analysis framework that highlights cell-to-medium interactions was developed to fit experimental observations. Simulated outputs suggested that the medium is compressed in the direction of the bacterial front motion. This phenomenon generates what was termed a compression wave that goes through the medium preceding the swimming population and that determines the visible high-level pattern. Taken together, the data suggested that the mechanical effects of the bacteria moving through the medium created a factual barrier that impedes to merge with neighboring cells swimming from a different site. The resulting divide between otherwise clonal bacteria is thus brought about by physical forces—not genetic or metabolic programs.This work was supported by the EVOPROG (FP7-ICT-610730), ARISYS (ERC-2012-ADG-322797), and EmPowerPutida (EU-H2020-BIOTEC-2014-2015-635536) Contracts of the European Union, and the CAMBIOS (RTC-2014-1777-3) and CONTIBUGS (PCIN-2013-040) Projects of the Spanish Ministry of Economy and Competitiveness.Peer Reviewe

Towards low-carbon conferencing : acceptance of virtual conferencing solutions and other sustainability measures in the ALIFE community

The latest report from the Intergovernmental Panel on Climate Change (IPCC) estimated that humanity has a time window of about 12 years in order to prevent anthropogenic climate change of catastrophic magnitude. Green house gas emission from air travel, which is currently rising, is possibly one of the factors that can be most readily reduced. Within this context, we advocate for the re-design of academic conferences in order to decrease their environmental footprint. Today, virtual technologies hold the promise to substitute many forms of physical interactions and increasingly make their way into conferences to reduce the number of travelling delegates. Here, we present the results of a survey in which we gathered the opinion on this topic of academics worldwide. Results suggest there is ample room for challenging the (dangerous) business-as-usual inertia of scientific lifestyle

High-Performance Biocomputing in Synthetic Biology–Integrated Transcriptional and Metabolic Circuits

Biocomputing uses molecular biology parts as the hardware to implement computational devices. By following pre-defined rules, often hard-coded into biological systems, these devices are able to process inputs and return outputs—thus computing information. Key to the success of any biocomputing endeavor is the availability of a wealth of molecular tools and biological motifs from which functional devices can be assembled. Synthetic biology is a fabulous playground for such purpose, offering numerous genetic parts that allow for the rational engineering of genetic circuits that mimic the behavior of electronic functions, such as logic gates. A grand challenge, as far as biocomputing is concerned, is to expand the molecular hardware available beyond the realm of genetic parts by tapping into the host metabolism. This objective requires the formalization of the interplay of genetic constructs with the rest of the cellular machinery. Furthermore, the field of metabolic engineering has had little intersection with biocomputing thus far, which has led to a lack of definition of metabolic dynamics as computing basics. In this perspective article, we advocate the conceptualization of metabolism and its motifs as the way forward to achieve whole-cell biocomputations. The design of merged transcriptional and metabolic circuits will not only increase the amount and type of information being processed by a synthetic construct, but will also provide fundamental control mechanisms for increased reliability