Multidisciplinary teaching of Biotechnology and Omics sciences

In the last years, there was a great boom in the Omics fields that have developed as multidisciplinary sciences. They use laboratory techniques related to Biology and Chemistry but also Bioinformatics tools. However, the developmental progress of these disciplines has led that much of undergraduate studies related to Biology have curricula that become outdated. From this point of view, it is necessary to focus the students to the fundamentals and techniques of complementary disciplines that will be essentials for the understanding of the Omics sciences. In the present work, we have developed a new teaching approach for Biochemistry, Biology and Bioinformatics students. They formed interdisciplinary working groups. These groups have prepared and presented communications about different techniques or methods in Molecular Biology, Omics or Bioinformatics participating in a technical meeting. This learning strategy “I do and I learn” has enabled to the students a first contact with the scientific communication including the approach to the scientific literature to acquire technical knowledge. The cooperation between students from different disciplines has enriched their point of view and even has been used in some practical master’s works.Universidad de Málaga. Campus de Excelencia Internacional Andalucía Tech

Caracterización de la asparraginasa de pino: implicaciones en el desarrollo del sistema vascular

La asparragina es un metabolito clave en plantas para el transporte y reserva temporal de nitrógeno. La principal vía de movilización del nitrógeno contenido en el grupo amido de la asparragina implica a la enzima asparraginasa (ASPG, EC 3.5.1.1), especialmente en tejidos que demandan altas cantidades de este elemento, tales como semillas en desarrollo y hojas jóvenes. Durante el desarrollo y crecimiento del tronco de los árboles, éstos afrontan un consumo masivo de carbono y nitrógeno para proveer la síntesis de celulosa y lignina. Estudios previos han demostrado que la expresión del gen de asparraginasa en el pino está asociada al intensivo desarrollo del sistema vascular que se produce en el tallo de las plántulas una vez que ésta ha agotado las reservas de la semilla, y que su expresión está confinada a las células de la región del cambium (1). La observación de que este gen se expresa también en células de xilema secundario en diferenciación de árbol adulto sugiere que la ASPG podría jugar un papel importante en el desarrollo vascular y ser de gran relevancia en la producción de biomasa. Aunque conocemos, en líneas generales, la implicación de la asparraginasa en el transporte y movilización de nitrógeno, desconocemos los mecanismos moleculares que controlan espacial y temporalmente su actividad. En nuestro grupo seguimos diferentes aproximaciones para dilucidar el control transcripcional y post-transcripcional de esta enzima y su implicación en el desarrollo del sistema vascular. Nuestros objetivos específicos son determinar las características del procesado y activación de la asparraginasa de pino y los factores que regulan la expresión génica asociada al desarrollo vascular.Universidad de Málaga. Campus de Excelencia Internacional Andalucía Tech. BIO2012-33797, AGL9-12139C0202, AP2010-543

The status of redfish (S. mentella and S. fasciatus) in Divisions 3LN at present and the likelihood its follow up in the near future (under the ongoing the Management Strategy or a status quo TAC scenario)

There are two species of redfish in Divisions 3L and 3N, the deep-sea redfish (Sebastes mentella) and the Acadian redfish (Sebastes fasciatus) that have been commercially fished and reported collectively as redfish in fishery statistics. Both species, occurring on Div. 3LN and managed as a single stock, don’t belong to isolated local populations but, on the contrary, are part of a large Northwest Atlantic complex ranging from the Gulf of Maine to south of Baffin Island. The ASPIC assessment of this stock is based on the logistic form of a non-equilibrium surplus production model (Schaeffer, 1954; Prager, 1994), adjusted to a standardized catch rate series (Power, 1997) and to all stratified-random bottom trawl surveys conducted in various years and seasons in Div. 3L and Div. 3N from 1978 onwards. Both CPUE and surveys were used with all observations within each series. The 2018 assessment proceed on the threshold of the new 2014 approach, the main features of the previous input framework were kept, with MSY fixed at 1960-1985 average catch and the rest of the approved 2014 assessment framework updated. Despite its poor performance the 3L Spanish survey has been kept in the analysis due to its high correlation with the autumn 3LN Canadian survey, one of the two backbone series of the assessment. ASPIC results confirm a stable stock from the 1960’s to the first half of the 1980’s, sustaining an average yield of 21 000t. Stock declined with a sudden rise of the catch over the late 1980’s first half of the 1990’s, and started to gradually recover after catches fell to a residual level when the stock collapse. The maximum observed sustainable yield (MSY) of 21 000 t can be a long term sustainable yield if fishing mortality stands at 0.11/year, exploiting a correspondent Bmsy at 187 000 t. From assessment results there is a high probability (CL’s 80%) that the stock was at the beginning of 2018 above Bmsy, after crossing 2017 under a fishing mortality most likely below 34% Fmsy

Aspectos estructurales y funcionales de la asparraginasa en pino

La asparragina es un metabolito clave en plantas para el transporte y reserva temporal de nitrógeno. La principal vía de movilización del nitrógeno contenido en el grupo amido de este aminoácido implica a la enzima asparraginasa (ASPG, EC 3.5.1.1), que cataliza la hidrólisis de asparragina a aspartato y amonio. Las asparraginasas de plantas, al igual que todas las enzimas de la familia Ntn-hidrolasas, son sintetizadas como precursores inactivos. La enzima activa es un heterotetrámero con dos tipos distintos de angiospermas se han identificado genes que codifican dos subtipos de asparraginasas (Bruneau et al. 2006), las K+-independientes y las K+-dependientes, con al menos un gen codificante para cada tipo en los genomas que han sido secuenciados. La caracterización de ambos subtipos indica que la forma K+-dependiente sería más eficiente en la movilización del nitrógeno amido de la asparragina bajo condiciones de alta demanda metabólica de nitrógeno (Bruneau et al. 2006), mientras que el papel de las K+-independientes estaría relacionado con su actividad isoaspartil dipeptidasa. Sin embargo, hasta la fecha no se ha realizado una caracterización de las distintas formas presentes y sus funciones en gimnospermas. Una búsqueda en el transcriptoma disponible de Pinus pinaster (Canales et al. 2014) nos permitió identificar un total de tres genes con similitud a asparraginasa. Sólo uno (PpASPG1), identificado previamente por nuestro grupo de investigación (Cañas et al. 2006), presenta mayor similitud con las asparraginasas K+-dependientes. El principal inconveniente para la caracterización de estas proteínas es su baja abundancia. Para soslayar este impedimento se expresaron transitoriamente los tres genes de pino en un sistema heterólogo, se purificaron las proteínas recombinantes y se compararon sus características. Por otro lado, esta aproximación nos ha permitido también estudiar cómo afecta al procesamiento del precursor y a la actividad de la enzima la presencia de una extensión de 70 aminoácidos proteínas ortólogas de especies angiospermas. Finalmente, con el objetivo de dilucidar posibles funciones, hemos realizado un análisis de expresión de los tres genes identificados, así como el aislamiento y análisis del promotor del gen PpASPG1. Referencias Bruneau L. et al (2006) Co-occurrence of both L-asparaginase subtypes in Arabidopsis: At3g16150 encodes a K+-dependent L-asparaginase. Planta, 224:668–679, doi: 10.1007/s00425-006-0245-9. Canales J. et al. (2014) De novo assembly of maritime pine transcriptome: implications for forest breeding and biotechnology. Plant Biotechnology Journal, 12:286–299. doi: 10.1111/pbi.12136. Cañas RA et al. (2006) Coordination of PsAS1 and PsASPG expression controls timing of re-allocated N utilization in hypocotyls of pine seedlings. Planta, 225:1205– 1219. doi: 10.1007/s00425-006-0431-9.Universidad de Málaga. Campus de Excelencia Internacional Andalucía Tech

A Revised Update of the 2014 ASPIC Assessment of Redfish (S. mentella and S. fasciatus) in Divisions 3LN (how the the stock is coping with the actual Management Strategy and its likely impact on the next coming years).

There are two species of redfish in Divisions 3L and 3N, the deep-sea redfish (Sebastes mentella) and the Acadian redfish (Sebastes fasciatus) that have been commercially fished and reported collectively as redfish in fishery statistics. Both species, occurring on Div. 3LN and managed as a single stock, don’t belong to isolated local populations but, on the contrary, are part of a large Northwest Atlantic complex ranging from the Gulf of Maine to south of Baffin Island. The present ASPIC assessment of this stock is based on the logistic form of a non-equilibrium surplus production model (Schaeffer, 1954; Prager, 1994), adjusted to a standardized catch rate series (Power, 1997) and, for the first time, to all stratified-random bottom trawl surveys conducted in various years and seasons in Div. 3L and Div. 3N from 1978 onwards. Both CPUE and surveys were used with all observations within each series. In order to proceed on the threshold of the new 2014 approach, and taking into account that since then no substantial changes appear to have occurred on the state of the stock, the main features of the previous input framework were kept, with MSY fixed at 1960-1985 average catch and the rest of the approved 2014 assessment framework updated. The 3L Spanish survey, the only ongoing survey so far outside the analysis, has now been successfully included on this assessment framework (relative inter-quartile range from bootstrap analysis for the last two assessments highlight the higher consistence of most of the 2016 assessment results when compared with the ones from 2014). ASPIC assessment results confirm a stable stock from the 1960’s to the first half of the 1980’s, sustaining an average yield of 21 000t. Stock declined with a sudden rise of the catch over the late 1980’s first half of the 1990, and increased since then, after catches fell to a residual level with the stock collapse. Assessment results also confirm that the maximum observed sustainable yield (MSY) of 21 000 t can be a long term sustainable yield if fishing mortality stands at 0.11/year, exploiting a correspondent Bmsy at 190 000 t. 2 There is a very high probability that the stock was at the beginning of 2016 at or above Bmsy , after crossing 2015 under a fishing mortality most likely at or below 50% Fmsy. There is also a very high probability that catch on 2016 at 10 400 t TAC and on 2017 and 2018 at the predicted increases approved in the 2014 Risk‐Based Management Strategy for 3LN Redfish, will keep fishing mortality on 2018 below Fmsy and biomass at the beginning of 2019 above Bmsy.Postprint0,000

The status of redfish (S. mentella and S. fasciatus) in Divisions 3LN and two medium term scenarios (when recruitment is low, Risk Based Management Strategy or common sense?)

There are two species of redfish in Divisions 3L and 3N, the deep-sea redfish (Sebastes mentella) and the Acadian redfish (Sebastes fasciatus) that have been commercially fished and reported collectively as redfish in fishery statistics. Both species, occurring on Div. 3LN and managed as a single stock, don’t belong to isolated local populations but, on the contrary, are part of a large Northwest Atlantic complex ranging from the Gulf of Maine to south of Baffin Island. The ASPIC assessment of this stock is based on the logistic form of a non-equilibrium surplus production model (Schaeffer, 1954; Prager, 1994), adjusted to a standardized commercial catch rate series (Power, 1997) and to all stratified-random bottom trawl surveys conducted in various years and seasons in Div. 3L and Div. 3N from 1978 onwards. Both CPUE and surveys were used with all observations within each series. The 2020 assessment proceed on the threshold of the new 2014 approach, with MSY fixed at 1960- 1985 average catch and the rest of the approved 2014 assessment framework updated. ASPIC results present a stock stable from the 1960’s to the first half of the 1980’s while sustaining an average yield of 21 000t. Stock declined with a sudden rise of the catch over the late 1980’s first half of the 1990’s, and started to gradually recover after catches fell to a residual level in response to stock collapse. The maximum observed sustainable yield (MSY) of 21 000 t is linked to a Fmsy at 0.11/year and a Bmsy at 185 000 t. There is a high probability (>90%) that the stock was at least 38% above Bmsy at the beginning of 2020, after crossing 2019 under a fishing mortality not higher than 46% Fmsy

An assessment of beaked redfish (S. mentella and S. fasciatus) in NAFO Division 3M, from a biological based approach to recent levels of natural mortality (2011-2016)

The 3M redfish assessment is focused on the beaked redfish, regarded as a management unit composed of two populations from two very similar species: the Flemish Cap S. mentella and S. fasciatus. The reason for this approach is the historical dominance of this group in the 3M redfish commercial catch until 2005. However a new golden redfish fishery (S. marinus) started on September 2005 on shallower depths of the Flemish Cap bank above 300m, and the Flemish Cap cod fishery reopened in 2010. These new realities implied a revision of catch estimates, in order to split recent redfish commercial catch and by-catch from the major fleets on Div. 3M into golden (S. marinus) and beaked (S. mentella and S. faThe Extended Survivor Analysis assessment used as tuning file the 1989-2016 EU survey abundance at age matrix included in a revised input framework. Continuing pressure over Flemish Cap redfish stocks by cod predation, at levels higher, or much higher, than the levels prior to 2006 lead to higher natural mortalities since then. In order to include an independent approach to natural mortality in the sensitivity M framework, for the more recent years (2011-2016) natural mortality has been estimated from a number of different biological models, some size/age-independent and others size/age-dependent. These different estimates were arranged in two sets and tuned to survey at age data. A natural mortality of 0.1 on 2015-2016 and the natural mortalities adjusted on previous assessments were found to be the most suitable option to M input. A 2017-2013 retrospective XSA was performed, confirming the consistency of the present with preceding results as regards stock biomass, female spawning biomass and fishing mortality.sciatus) redfish catches. Above average year classes and high survival rates allowed a rapid growth of biomass and abundance 2003 onwards, pulling the stock to a 2008-2010 high. Since 2009 abundance went down for causes other than fishing, being still above the 1990’s low in 2016. By the turn of the decade stock biomass and female spawning biomass (SSB) shown marginal declines as well, but reversed on 2011-2012. Individual growth of survivors and low fishing mortalities sustained stock biomass and SSB at high levels till 2015-2016. Recruitment at age 4 increased from 2002 till 2006 and was maintained at a maximum level till 2009. Recruitment declined since then and is kept on 2015-2016 at the low of the weak year classes from the 1990’s, while SSB is still well above the size that originated the high 2002-2006 recruitments. Despite the significant decline so far natural mortality has not flattened yet. If natural mortality and fishing mortality stay at their most recent levels, the actual high of female spawning biomass can hold on 2018-2019. But on the long term it will be natural mortality, namely over pre recruited ages, to determine the future of beaked redfish as a fishery resource. On 2015 STACFIS remind that projections are based in the assumption that natural mortality stay at its most recent level on the present year and at least on the two next coming years. And that, taking into account the uncertainty on the present and future level of natural mortality, its impact on female spawning stock biomass at the end of any projection is unknown. On 2017 these constraints are still in place, and therefore short and medium term projections are not presented.Versión del edito

Potential Operating Models, Harvest Control Rules and Performance Statistics for the NAFO 3M Cod MSE.

This document presents a proposal of possible Operating Models (OMs), Harvest Control Rules (HCR) and Performance Statistics (PS) to carry out the Management Strategies Evaluation (MSE) for the 3M cod of NAFO. This proposal will have to be reviewed by the NAFO SC to decide the first set of OMs to test with the possible HCRs in the 3M Cod MSE

Potent Inhibition of Zika Virus Replication by Aurintricarboxylic Acid

Zika virus (ZIKV) is one of the recently emerging vector-borne viruses in humans and is responsible for severe congenital abnormalities such as microcephaly in the Western Hemisphere. Currently, only a few vaccine candidates and therapeutic drugs are being developed for the treatment of ZIKV infections, and as of yet none are commercially available. The polyanionic aromatic compound aurintricarboxylic acid (ATA) has been shown to have a broad-spectrum antimicrobial and antiviral activity. In this study, we evaluated ATA as a potential antiviral drug against ZIKV replication. The antiviral activity of ATA against ZIKV replication in vitro showed median inhibitory concentrations (IC50) of 13.87 ± 1.09 μM and 33.33 ± 1.13 μM in Vero and A549 cells, respectively; without showing any cytotoxic effect in both cell lines (median cytotoxic concentration (CC50) > 1,000 μM). Moreover, ATA protected both cell types from ZIKV-induced cytopathic effect (CPE) and apoptosis in a time- and concentration-dependent manner. In addition, pre-treatment of Vero cells with ATA for up to 72 h also resulted in effective suppression of ZIKV replication with similar IC50. Importantly, the inhibitory effect of ATA on ZIKV infection was effective against strains of the African and Asian/American lineages, indicating that this inhibitory effect was not strain dependent. Overall, these results demonstrate that ATA has potent inhibitory activity against ZIKV replication and may be considered as a potential anti-ZIKV therapy for future clinical evaluation