Digestive glycosidases from cannonball jellyfish (Stomolophus sp. 2): identification and temporal-spatial variability.

Jellyfish are economically important organisms in diverse countries, carnivorous organisms that consume various prey (crustaceans, mollusks, bivalves, etc.) and dissolved carbohydrates in marine waters. This study was focused on detecting and quantifying the activity of digestive glycosidases from the cannonball jellyfish (Stomolophus sp. 2) to understand carbohydrate digestion and its temporal-spatial variation. Twenty-three jellyfish gastric pouches were collected in 2015 and 2016 in the Gulf of California in three localities (Las Guásimas, Hermosillo, and Caborca). Nine samples were in intra-localities from Las Guásimas. Chitinase (Ch), ß-glucosidase (ß-glu), and ß-N-acetylhexosaminidase (ß-NAHA) were detected in the gastric pouches. However, cellulase, exoglucanase, α-amylase, polygalacturonase, xylanase, and κ-carrageenase were undetected. Detected enzymes showed halotolerant glycolytic activity (i = 0-4 M NaCl), optimal pH, and temperature at 5.0 and 30-50 °C, respectively. At least five ß-glucosidase and two ß-N-acetylhexosaminidase were detected using zymograms; however, the number of proteins with chitinase activity is not precise. The annual variation of cannonball jellyfish digestive glycosidases from Las Guásimas between 2015-2016 does not show significant differences despite the difference in phytoplankton measured as chlorophyll α (1.9 and 3.4 mg/m3, respectively). In the inter-localities, the glycosidase activity was statistically different in all localities, except for ß-N-acetylhexosaminidase activity between Caborca and Hermosillo (3,009.08 ± 87.95 and 3,101.81 ± 281.11 mU/g of the gastric pouch, respectively), with chlorophyll α concentrations of 2.6, 3.4 mg/m3, respectively. For intra-localities, the glycosidase activity did not show significant differences, with a mean chlorophyll α of 1.3 ± 0.1 mg/m3. These results suggest that digestive glycosidases from Stomolophus sp. 2 can hydrolyze several carbohydrates that may belong to their prey or carbohydrates dissolved in marine waters, with salinity over ≥ 0.6 M NaCl and diverse temperature (4-80 °C) conditions. Also, chlorophyll α is related to glycosidase activity in both seasons and inter-localities, except for chitinase activity in an intra-locality (Las Guásimas).

Viability of the vaquita, Phocoena sinus (Cetacea: Phocoenidae) population, threatened by poaching of Totoaba macdonaldi (Perciformes: Sciaenidae) / Viabilidad de la población de vaquita marina, Phocoena sinus (Cetacea: Phocoenidae), amenazada por la pesca ilegal de Totoaba macdonaldi (Perciformes: Sciaenidae)

Abstract Introduction: Despite extensive science-based conservation policy recommendations, with fewer than 20 individuals remaining, the vaquita (Phocoena sinus) -endemic to the Gulf of California- is the world's most endangered marine mammal due to incidental catch in fishing nets and whether it can recover is unclear. Objective: Assess expectations for vaquita over the next two decades. Methods: We identified factors affecting the vaquita, constructed life tables, derived demographic parameters for different scenarios and conducted a population viability analysis using stochastic age-structured matrix Leslie models. Results: Analytical results indicate that the vaquita net growth rate is particularly sensitive to juvenile survival. We find that intensive, ongoing bycatch in gillnets used to poach totoaba (Totoaba macdonaldi) over the past decade brought the vaquita population to its current critically low size. Currently this seems to be exacerbated by demographic stochasticity and a potential Allee effect. Conclusions: If totoaba poaching is eliminated immediately, demographically, vaquita can recover; its long-term survival will depend on its uncertain genetic status, although a recent study found encouraging results in this regard.

Resumen Introducción: Pese a las acciones de conservación basadas en la ciencia y las políticas recomendadas, con menos de 20 individuos sobrevivientes, la vaquita (Phocoena sinus) -endémica del Golfo de California- es el mamífero marino más amenazado del mundo debido a su muerte incidental en redes de pesca; una pregunta relevante es si su población se puede recuperar. Objetivo: Evaluar las expectativas para la vaquita marina durante los próximos 20 años. Métodos: Identificamos los factores que afectan a la vaquita marina, construimos tablas de vida, derivamos parámetros demográficos para diferentes escenarios y realizamos un análisis de viabilidad poblacional utilizando matrices estocásticas de Leslie, estructuradas por edad. Resultados: La tasa de crecimiento neto de la vaquita es muy sensible a la supervivencia de los juveniles. Encontramos que la captura incidental intensiva y continua en redes de enmalle para la pesca furtiva de totoaba (Totoaba macdonaldi) durante la última década llevó a la población de vaquitas a su actual estado crítico. Esto parece agravarse por la estocasticidad demográfica y un potencial efecto Allee. Conclusiones: Si la pesca furtiva de totoaba se elimina de inmediato, demográficamente la vaquita puede recuperarse; su supervivencia a largo plazo dependerá de su incierto estatus genético, aunque los resultados de un estudio reciente son alentadores en este sentido.

Illegal fisheries, environmental crime, and the conservation of marine resources.

The illegal harvest of marine species within exclusive economic zones can have a strong impact on the function of local ecosystems and livelihoods of coastal communities. The complexity of these problems is often overlooked in the development of solutions, leading to ineffective and sometimes harmful social and environmental outcomes. One-dimensional, oversimplified perspectives can lead to conservation prescriptions that exacerbate social stressors. This is particularly critical in the case of international illegal trade of endangered, high-value species, which generate a value chain in which artisanal fishers are the first operational and often the weakest link of an intricate web. We examined 2 illegal fisheries, totoaba (Totoaba macdonaldi) and sea cucumber (Isostichopus badionotus and Holothuria floridana), in Mexico. Although these are 2 separate and independent fisheries, important ecological (resource condition, fishery impacts at the ecosystem level) and social (governance, markets) similarities improve understanding of their complexity. Our findings are relevant globally and show the need for interdisciplinary decision-making groups, community engagement, and the development of demand reduction measures.

Pesquerías Ilegales, Crímenes Ambientales y la Conservación de los Recursos Marinos Resumen La cosecha ilegal de especies marinas dentro de las zonas económicas exclusivas puede tener un impacto serio sobre la función de los ecosistemas locales y el economia de las comunidades costeras. La complejidad de estos problemas generalmente se ignora durante el desarrollo de soluciones, lo que conlleva a resultados ambientales y sociales poco efectivos y algunas veces dañinos. Las perspectivas unidimensionales y sobresimplificadas pueden derivar en prescripciones de conservación que empeoran las condiciones sociales sociales. Lo anterior es particularmente crítico para el caso del mercado ilegal de especies en peligro y de alto valor, lo que genera una cadena de valores en la que los pescadores tradicionales son el primer eslabón operativo y con frecuencia el más débil de una red intrincada. Examinamos dos pesquerías ilegales, la de la totoaba (Totoaba macdonaldi) y la del pepino de mar (Isostichopus badionotus y Holothuria floridana), en México. Aunque estas dos pesquerías son diferentes e independientes, las importantes similitudes ecológicas (estado del recurso, impactos de la pesquería a nivel de ecosistema) y sociales (governancia, mercados) mejoran el conocimiento de su complejidad. Nuestros hallazgos son relevantes a escala global y muestran la necesidad de tener grupos interdisciplinarios para tomar decisiones, la participación de la comunidad y el desarrollo de medidas para reducir la demanda por el producto pesquero.

The future of food from the sea.

Global food demand is rising, and serious questions remain about whether supply can increase sustainably1. Land-based expansion is possible but may exacerbate climate change and biodiversity loss, and compromise the delivery of other ecosystem services2-6. As food from the sea represents only 17% of the current production of edible meat, we ask how much food we can expect the ocean to sustainably produce by 2050. Here we examine the main food-producing sectors in the ocean-wild fisheries, finfish mariculture and bivalve mariculture-to estimate 'sustainable supply curves' that account for ecological, economic, regulatory and technological constraints. We overlay these supply curves with demand scenarios to estimate future seafood production. We find that under our estimated demand shifts and supply scenarios (which account for policy reform and technology improvements), edible food from the sea could increase by 21-44 million tonnes by 2050, a 36-74% increase compared to current yields. This represents 12-25% of the estimated increase in all meat needed to feed 9.8 billion people by 2050. Increases in all three sectors are likely, but are most pronounced for mariculture. Whether these production potentials are realized sustainably will depend on factors such as policy reforms, technological innovation and the extent of future shifts in demand.

An RNA-centric dissection of host complexes controlling flavivirus infection.

Flaviviruses, including dengue virus (DENV) and Zika virus (ZIKV), cause severe human disease. Co-opting cellular factors for viral translation and viral genome replication at the endoplasmic reticulum is a shared replication strategy, despite different clinical outcomes. Although the protein products of these viruses have been studied in depth, how the RNA genomes operate inside human cells is poorly understood. Using comprehensive identification of RNA-binding proteins by mass spectrometry (ChIRP-MS), we took an RNA-centric viewpoint of flaviviral infection and identified several hundred proteins associated with both DENV and ZIKV genomic RNA in human cells. Genome-scale knockout screens assigned putative functional relevance to the RNA-protein interactions observed by ChIRP-MS. The endoplasmic-reticulum-localized RNA-binding proteins vigilin and ribosome-binding protein 1 directly bound viral RNA and each acted at distinct stages in the life cycle of flaviviruses. Thus, this versatile strategy can elucidate features of human biology that control the pathogenesis of clinically relevant viruses.

A metadata approach to evaluate the state of ocean knowledge: Strengths, limitations, and application to Mexico.

Climate change, mismanaged resource extraction, and pollution are reshaping global marine ecosystems with direct consequences on human societies. Sustainable ocean development requires knowledge and data across disciplines, scales and knowledge types. Although several disciplines are generating large amounts of data on marine socio-ecological systems, such information is often underutilized due to fragmentation across institutions or stakeholders, limited standardization across scale, time or disciplines, and the fact that information is often not searchable within existing databases. Compiling metadata, the information which describes existing sets of data, is an effective tool that can address these challenges, particularly when metadata corresponding to multiple datasets can be combined to integrate, organize and classify multidisciplinary data. Here, using Mexico as a case study, we describe the compilation and analysis of a metadatabase of ocean knowledge that aims to improve access to information, facilitate multidisciplinary data sharing and integration, and foster collaboration among stakeholders. We also evaluate the knowledge trends and gaps for informing ocean management. Analysis of the metadatabase highlights that past and current research in Mexico focuses strongly on ecology and fisheries, with biological data more consistent over time and space compared to data on human dimensions. Regional imbalances in available information were also evident, with most available information corresponding to the Gulf of California, Campeche Bank and Caribbean and less available for the central and south Pacific and the western Gulf of Mexico. Despite existing knowledge gaps in Mexico and elsewhere, we argue that systematic efforts such as this can often reveal an abundance of information for decision-makers to develop policies that meet key commitments on ocean sustainability. Surmounting current cross-scale social and ecological challenges for sustainability requires transdisciplinary approaches. Metadatabases are critical tools to make efficient use of existing data, highlight and address strengths and deficiencies, and develop scenarios to inform policies for managing complex marine social-ecological systems.

Influenza virus differentially activates mTORC1 and mTORC2 signaling to maximize late stage replication.

Influenza A virus usurps host signaling factors to regulate its replication. One example is mTOR, a cellular regulator of protein synthesis, growth and motility. While the role of mTORC1 in viral infection has been studied, the mechanisms that induce mTORC1 activation and the substrates regulated by mTORC1 during influenza virus infection have not been established. In addition, the role of mTORC2 during influenza virus infection remains unknown. Here we show that mTORC2 and PDPK1 differentially phosphorylate AKT upon influenza virus infection. PDPK1-mediated phoshorylation of AKT at a distinct site is required for mTORC1 activation by influenza virus. On the other hand, the viral NS1 protein promotes phosphorylation of AKT at a different site via mTORC2, which is an activity dispensable for mTORC1 stimulation but known to regulate apoptosis. Influenza virus HA protein and down-regulation of the mTORC1 inhibitor REDD1 by the virus M2 protein promote mTORC1 activity. Systematic phosphoproteomics analysis performed in cells lacking the mTORC2 component Rictor in the absence or presence of Torin, an inhibitor of both mTORC1 and mTORC2, revealed mTORC1-dependent substrates regulated during infection. Members of pathways that regulate mTORC1 or are regulated by mTORC1 were identified, including constituents of the translation machinery that once activated can promote translation. mTORC1 activation supports viral protein expression and replication. As mTORC1 activation is optimal midway through the virus life cycle, the observed effects on viral protein expression likely support the late stages of influenza virus replication when infected cells undergo significant stress.

Genetic dissection of Flaviviridae host factors through genome-scale CRISPR screens.

The Flaviviridae are a family of viruses that cause severe human diseases. For example, dengue virus (DENV) is a rapidly emerging pathogen causing an estimated 100 million symptomatic infections annually worldwide. No approved antivirals are available to date and clinical trials with a tetravalent dengue vaccine showed disappointingly low protection rates. Hepatitis C virus (HCV) also remains a major medical problem, with 160 million chronically infected patients worldwide and only expensive treatments available. Despite distinct differences in their pathogenesis and modes of transmission, the two viruses share common replication strategies. A detailed understanding of the host functions that determine viral infection is lacking. Here we use a pooled CRISPR genetic screening strategy to comprehensively dissect host factors required for these two highly important Flaviviridae members. For DENV, we identified endoplasmic-reticulum (ER)-associated multi-protein complexes involved in signal sequence recognition, N-linked glycosylation and ER-associated degradation. DENV replication was nearly completely abrogated in cells deficient in the oligosaccharyltransferase (OST) complex. Mechanistic studies pinpointed viral RNA replication and not entry or translation as the crucial step requiring the OST complex. Moreover, we show that viral non-structural proteins bind to the OST complex. The identified ER-associated protein complexes were also important for infection by other mosquito-borne flaviviruses including Zika virus, an emerging pathogen causing severe birth defects. By contrast, the most significant genes identified in the HCV screen were distinct and included viral receptors, RNA-binding proteins and enzymes involved in metabolism. We found an unexpected link between intracellular flavin adenine dinucleotide (FAD) levels and HCV replication. This study shows notable divergence in host-depenency factors between DENV and HCV, and illuminates new host targets for antiviral therapy.

Viral subversion of nucleocytoplasmic trafficking.

Trafficking of proteins and RNA into and out of the nucleus occurs through the nuclear pore complex (NPC). Because of its critical function in many cellular processes, the NPC and transport factors are common targets of several viruses that disrupt key constituents of the machinery to facilitate viral replication. Many viruses such as poliovirus and severe acute respiratory syndrome (SARS) virus inhibit protein import into the nucleus, whereas viruses such as influenza A virus target and disrupt host mRNA nuclear export. Current evidence indicates that these viruses may employ such strategies to avert the host immune response. Conversely, many viruses co-opt nucleocytoplasmic trafficking to facilitate transport of viral RNAs. As viral proteins interact with key regulators of the host nuclear transport machinery, viruses have served as invaluable tools of discovery that led to the identification of novel constituents of nuclear transport pathways. This review explores the importance of nucleocytoplasmic trafficking to viral pathogenesis as these studies revealed new antiviral therapeutic strategies and exposed previously unknown cellular mechanisms. Further understanding of nuclear transport pathways will determine whether such therapeutics will be useful treatments for important human pathogens.

Nuclear imprisonment: viral strategies to arrest host mRNA nuclear export.

Viruses possess many strategies to impair host cellular responses to infection. Nuclear export of host messenger RNAs (mRNA) that encode antiviral factors is critical for antiviral protein production and control of viral infections. Several viruses have evolved sophisticated strategies to inhibit nuclear export of host mRNAs, including targeting mRNA export factors and nucleoporins to compromise their roles in nucleo-cytoplasmic trafficking of cellular mRNA. Here, we present a review of research focused on suppression of host mRNA nuclear export by viruses, including influenza A virus and vesicular stomatitis virus, and the impact of this viral suppression on host antiviral responses.

Chemical inhibition of RNA viruses reveals REDD1 as a host defense factor.

A chemical genetics approach was taken to identify inhibitors of NS1, a major influenza A virus virulence factor that inhibits host gene expression. A high-throughput screen of 200,000 synthetic compounds identified small molecules that reversed NS1-mediated inhibition of host gene expression. A counterscreen for suppression of influenza virus cytotoxicity identified naphthalimides that inhibited replication of influenza virus and vesicular stomatitis virus (VSV). The mechanism of action occurs through activation of REDD1 expression and concomitant inhibition of mammalian target of rapamycin complex 1 (mTORC1) via TSC1-TSC2 complex. The antiviral activity of naphthalimides was abolished in REDD1(-/-) cells. Inhibition of REDD1 expression by viruses resulted in activation of the mTORC1 pathway. REDD1(-/-) cells prematurely upregulated viral proteins via mTORC1 activation and were permissive to virus replication. In contrast, cells conditionally expressing high concentrations of REDD1 downregulated the amount of viral protein. Thus, REDD1 is a new host defense factor, and chemical activation of REDD1 expression represents a potent antiviral intervention strategy.