PCR: una nueva herramienta para el estudio de hongos ectomicorrícicos

PCR: a new tool for the study of ectomycorrhizal fungi. PCR (Polymerase Chain Reaction) is a simple technique that allows the specific amplification of particular regions of the genome of living organisms to facilitate their study. In the last few years, this and other complementary techniques have opened the field of the molecular mycology, whose Applications in detection, identification and c1assification of fungi are increasing every day. In this article, the first of a series dealing with the Molecular Techniques that can be used in Mycology, we explain the basic principies of both the PCR and two other complementary techniques commonly used for the molecular analysis of the amplified regions: RFLPs (Restriction Fragment Length Polymorphisms) and sequencing (determination ofthe primary structure ofthe nucleic acids).La PCR (reacción en cadena de la polimerasa) es una técnica sencilla que permite sacar copias (amplificar) de una determinada región del genoma de los seres vivos con el fin de facilitar su estudio. Esta y otras técnicas complementarias se han abierto, en los últimos años, al ámbito de la micología molecular, cuyas aplicaciones a nivel de detección, identificación y clasificación de hongos se incrementan día a día. En este primer artículo de una serie dedicada a las técnicas moleculares aplicables en Micología, se exponen los principios básicos, tanto de la PCR como de las otras dos técnicas complementarias que se utilizan habitualmente para el análisis molecular de las regiones amplificadas: los RFLPs (polimorfismos del tamaño de los fragmentos de restricción) y la secuenciación (determinación de la estructura primaria de los ácidos nucleicos)

Benchmarking microbiome transformations favors experimental quantitative approaches to address compositionality and sampling depth biases

While metagenomic sequencing has become the tool of preference to study host-associated microbial communities, downstream analyses and clinical interpretation of microbiome data remains challenging due to the sparsity and compositionality of sequence matrices. Here, we evaluate both computational and experimental approaches proposed to mitigate the impact of these outstanding issues. Generating fecal metagenomes drawn from simulated microbial communities, we benchmark the performance of thirteen commonly used analytical approaches in terms of diversity estimation, identification of taxon-taxon associations, and assessment of taxon-metadata correlations under the challenge of varying microbial ecosystem loads. We find quantitative approaches including experimental procedures to incorporate microbial load variation in downstream analyses to perform significantly better than computational strategies designed to mitigate data compositionality and sparsity, not only improving the identification of true positive associations, but also reducing false positive detection. When analyzing simulated scenarios of low microbial load dysbiosis as observed in inflammatory pathologies, quantitative methods correcting for sampling depth show higher precision compared to uncorrected scaling. Overall, our findings advocate for a wider adoption of experimental quantitative approaches in microbiome research, yet also suggest preferred transformations for specific cases where determination of microbial load of samples is not feasible

ReverCSP: Time-Travelling in CSP Computations

[EN] This paper presents reverCSP, a tool to animate both forward and backward CSP computations. This ability to reverse computations can be done step by step or backtracking to a given desired state of interest. reverCSP allows us to reverse computations exactly in the same order in which they happened, or also in a causally-consistent way. Therefore, reverCSP is a tool that can be especially useful to comprehend, analyze, and debug computations. reverCSP is an open-source project publicly available for the community. We describe the tool and its functionality, and we provide implementation details so that it can be reimplemented for other languages.This work has been partially supported by the EU (FEDER) and the Spanish MCI/AEI under grants TIN2016-76843-C4-1-R and PID2019- 104735RB-C41, and by the Generalitat Valenciana under grant Prometeo/2019/098 (DeepTrust).Galindo-Jiménez, CS.; Nishida, N.; Silva, J.; Tamarit, S. (2020). ReverCSP: Time-Travelling in CSP Computations. Springer. 239-245. https://doi.org/10.1007/978-3-030-52482-1_14S239245Bernadet, A., Lanese, I.: A modular formalization of reversibility for concurrent models and languages. In: Proceedings of ICE 2016, EPTCS (2016)Brown, G., Sabry, A.: Reversible communicating processes. Electron. Proc. Theor. Comput. Sci. 203, 45–59 (2016)Conserva Filhoa, M., Oliveira, M., Sampaio, A., Cavalcanti, A.: Compositional and local livelock analysis for CSP. Inf. Process. Lett 133, 21–25 (2018)Danos, V., Krivine, J.: Reversible communicating systems. In: Gardner, P., Yoshida, N. (eds.) CONCUR 2004. LNCS, vol. 3170, pp. 292–307. Springer, Heidelberg (2004). https://doi.org/10.1007/978-3-540-28644-8_19Elnozahy, E.N.M., Alvisi, L., Wang, Y.-M., Johnson, D.B.: A survey of rollback- recovery protocols in message-passing systems. ACM Comput. Surv. 34(3), 375–408 (2002)Fang, Y., Zhu, H., Zeyda, F., Fei, Y.: Modeling and analysis of the disruptor framework in csp. In: Proceedings of CCWC 2018. IEEE Computer Society (2018)Ladkin, P.B., Simons, B.B.: Static deadlock analysis for CSP-type communications. In: Fussell, D.S., Malek, M. (eds.) Responsive Computer Systems: Steps Toward Fault-Tolerant Real-Time Systems. The Springer International Series in Engineering and Computer Science, vol. 297, pp. 89–102. Springer, Boston (1995). https://doi.org/10.1007/978-1-4615-2271-3_5Landauer, R.: Irreversibility and heat generation in the computing process. IBM J. Res. Dev. 5, 183–191 (1961)Lanese, I., Antares Mezzina, C., Tiezzi, F.: Causal-consistent reversibility. Bull. EATCS 114, 17 (2014)Lanese, I., Nishida, N., Palacios, A., Vidal, G.: CauDEr: a causal-consistent reversible debugger for erlang. In: Gallagher, J.P., Sulzmann, M. (eds.) FLOPS 2018. LNCS, vol. 10818, pp. 247–263. Springer, Cham (2018). https://doi.org/10.1007/978-3-319-90686-7_16Lanese, I., Palacios, A., Vidal, G.: Causal-consistent replay debugging for message passing programs. In: Pérez, J.A., Yoshida, N. (eds.) FORTE 2019. LNCS, vol. 11535, pp. 167–184. Springer, Cham (2019). https://doi.org/10.1007/978-3-030-21759-4_10Llorens, M., Oliver, J., Silva, J., Tamarit, S.: Dynamic slicing of concurrent specification languages. Parallel Comput. 53, 1–22 (2016)Llorens, M., Oliver, J., Silva, J., Tamarit, S.: Tracking CSP computations. J. Log. Algebr. Meth. Program. 102, 138–175 (2019)Perera, R., Garg, D., Cheney, J.: Causally consistent dynamic slicing. In Proceedings of CONCUR 2016, LIPIcs, vol. 59, pp. 18:1–18:15 (2016)Phillips, I., Ulidowski, I., Yuen, S.: A reversible process calculus and the modelling of the ERK signalling pathway. In: Glück, R., Yokoyama, T. (eds.) RC 2012. LNCS, vol. 7581, pp. 218–232. Springer, Heidelberg (2013). https://doi.org/10.1007/978-3-642-36315-3_18Roscoe, A.W.: The Theory and Practice of Concurrency. Prentice Hall PTR, Upper Saddle River (1997)Zhao, H., Zhu, H., Yucheng, F., Xiao, L.: Modeling and verifying storm using CSP. In: Proceedings of HASE 2019. IEEE Computer Society (2019

Study of association between Pre-Senile cataracts and the polymorphisms rs2228000 in XPC and rs1042522 in p53 in Spanish population

To determine if the presence of certain polymorphisms in the DNA repair gene XPC and the apoptosis inductor gene p53 is associated with pre-senile cataract development. Methods We have performed a retrospective study over three groups of patients. The group with presenile cataract formed by 72 patients younger than 55 with cataract surgery. The group with senile cataract formed by 101 patients older than 55 with cataract surgery. The group without cataract was formed by 42 subjects older than 55 without lens opacities. We analyzed the presence of SNP rs2228000 from XPC and rs1042522 from p53; and the relationship between risk factors such as smoking, alcohol intake, hypertension or diabetes. Results The comparison of the genotype distribution in XPC, within the different groups, did not show any statistically significant association in any of our analysis (p>0, 05). The comparison of the genotype distribution in p53 within the different groups did not show any statistically significant association (p>0, 05); except for the comparison between the pre-senile cataract group and the group with senile cataract where the genotype Pro/Pro (C/C) in the recessive inheritance model showed a higher risk for developing pre-senile cataract (p = 0, 031; OR = 1.04-15.97). This association decreased when we performed the analysis adjusting by the studied risk factors (p = 0.056). Conclusions Allelic variants in the gene XPC are not associated with an increased risk for developing pre-senile cataract. The presence of the genotype Pro/Pro in p53 might be associated with a major risk for developing pre-senile cataract

Therapeutical Management for Ocular Rosacea

Purpose: The purpose of this study is to describe a case of ocular rosacea with a very complex evolution. Rosacea is a chronic dermatological disease that may affect the ocular structures up to 6-72% of all cases. This form is often misdiagnosed, which may lead to long inflammatory processes with important visual consequences for affected patients. Therefore, an early diagnosis and an adequate treatment are important. Methods: We report the case of a 43-year-old patient who had several relapses of what seemed an episode of acute bacterial conjunctivitis. Two weeks later, he developed a corneal ulcer with a torpid evolution including abundant intrastromal infiltrators and calcium deposits. He was diagnosed with ocular rosacea and treated with systemic doxycycline and topical protopic. Results: A coating with amniotic membrane was placed in order to heal the ulcer, but a deep anterior lamellar keratoplasty to restore the patient''s vision because of the corneal transparency loss was necessary. Conclusions: Ocular rosacea includes multiple ophthalmic manifestations ranging from inflammation of the eyelid margin and blepharitis to serious corneal affectations. A delayed diagnosis can result in chronic inflammatory conditions including keratinization and loss of corneal transparency, which lead to important visual sequelae for affected patients. (C) 2016 The Author(s) Published by S. Karger AG, Base

Factors that influence the quality of metabolomics data in in vitro cell toxicity studies: a systematic survey

REACH (Registration, Evaluation, Authorization and Restriction of Chemicals) is a global strategy and regulation policy of the EU that aims to improve the protection of human health and the environment through the better and earlier identification of the intrinsic properties of chemical substances. It entered into force on 1st June 2007 (EC 1907/2006). REACH and EU policies plead for the use of robust high-throughput 'omic' techniques for the in vitro investigation of the toxicity of chemicals that can provide an estimation of their hazards as well as information regarding the underlying mechanisms of toxicity. In agreement with the 3R's principles, cultured cells are nowadays widely used for this purpose, where metabolomics can provide a real-time picture of the metabolic effects caused by exposure of cells to xenobiotics, enabling the estimations about their toxicological hazards. High quality and robust metabolomics data sets are essential for precise and accurate hazard predictions. Currently, the acquisition of consistent and representative metabolomic data is hampered by experimental drawbacks that hinder reproducibility and difficult robust hazard interpretation. Using the differentiated human liver HepG2 cells as model system, and incubating with hepatotoxic (acetaminophen and valproic acid) and non-hepatotoxic compounds (citric acid), we evaluated in-depth the impact of several key experimental factors (namely, cell passage, processing day and storage time, and compound treatment) and instrumental factors (batch effect) on the outcome of an UPLC-MS metabolomic analysis data set. Results showed that processing day and storage time had a significant impact on the retrieved cell's metabolome, while the effect of cell passage was minor. Meta-analysis of results from pathway analysis showed that batch effect corrections and quality control (QC) measures are critical to enable consistent and meaningful estimations of the effects caused by compounds on cells. The quantitative analysis of the changes in metabolic pathways upon bioactive compound treatment remained consistent despite the concurrent causes of metabolomic data variation. Thus, upon appropriate data retrieval and correction and by an innovative metabolic pathway analysis, the metabolic alteration predictions remained conclusive despite the acknowledged sources of variability

Interactions between Seagrass Complexity, Hydrodynamic Flow and Biomixing Alter Food Availability for Associated Filter-Feeding Organisms

Seagrass shoots interact with hydrodynamic forces and thereby a positively or negatively influence the survival of associated species. The modification of these forces indirectly alters the physical transport and flux of edible particles within seagrass meadows, which will influence the growth and survivorship of associated filter-feeding organisms. The present work contributes to gaining insight into the mechanisms controlling the availability of resources for filter feeders inhabiting seagrass canopies, both from physical (influenced by seagrass density and patchiness) and biological (regulated by filter feeder density) perspectives. A factorial experiment was conducted in a large racetrack flume, which combined changes in hydrodynamic conditions, chlorophyll a concentration in the water and food intake rate (FIR) in a model active filter-feeding organism (the cockle). Results showed that seagrass density and patchiness modified both hydrodynamic forces and availability of resources for filter feeders. Chlorophyll a water content decreased to 50% of the initial value when densities of both seagrass shoots and cockles were high. Also, filter feeder density controlled resource availability within seagrass patches, depending on its spatial position within the racetrack flume. Under high density of filter-feeding organisms, chlorophyll a levels were lower between patches. This suggests that the pumping activity of cockles (i.e. biomixing) is an emergent key factor affecting both resource availability and FIR for filter feeders in dense canopies. Applying our results to natural conditions, we suggest the existence of a direct correlation between habitat complexity (i.e. shoot density and degree of patchiness) and filter feeders density. Fragmented and low-density patches seem to offer both greater protection from hydrodynamic forces and higher resource availability. In denser patches, however, resources are allocated mostly within the canopy, which would benefit filter feeders if they occurred at low densities, but would be limiting when filter feeder were at high densities

Relation of quality and sensory perception with changes in free amino acids of thawed seabream

[EN] This study aimed to investigate how the freshness before frozen storage affect the quality and sensory characteristics of seabream in different commercial presentations and to correlate the findings with free amino acids composition. The fish were slaughtered, allocated to three processing treatments (whole, gutted and filleted) and stored at refrigeration (0±1 °C) for different times (5, 9, 11 and 18 days) before one-month frozen storage (¿30 °C). After this time, physicochemical (pH, TVB-N, TBARS and free amino acids), bacterial count and sensory evaluation (Torry Index & Quality Descriptive Analysis -QDA-) were studied. Significant differences were found among treatments over time for TVB-N, TBARS and bacterial growth. The quality index (Torry) exhibited a gradual decrease. QDA showed that fillets had the lowest assessment. Free amino acids contents varied significantly during frozen storage with a particular behavior that depended on the previous treatment applied and the fish freshness degree (elapsed days before frozen)This study was financially supported by the Gobierno de Aragón (Grupo Consolidado de Calidad y Tecnología de la Carne, Ref: A04), Instituto Agroalimentario Mixto de Aragón (IA2) and Institute of Animal Science and Technology, Polytechnic University of Valencia.Calanche, J.; Tomas-Vidal, A.; Martínez-Llorens, S.; Jover Cerda, M.; Alonso, V.; Roncales, P.; Beltrán, J. (2019). Relation of quality and sensory perception with changes in free amino acids of thawed seabream. Food Research International. 119:126-134. https://doi.org/10.1016/j.foodres.2019.01.050S12613411