Potentiometric redox measurements in the environment: a novel perspective on method powers and limitations

Biogeochemistry - The South China Sea (SCS) is one of the largest marginal seas in the world, but the processes that control the silicon cycle are not well understood. Here, we analyse the factors...     

Marine bacterial exopolysaccharide EPS11 inhibits migration and invasion of liver cancer cells by directly targeting collagen I

Many natural polysaccharides have significant anticancer activity with low toxicity, but the complex chemical structures make in-depth studies of the involved mechanisms extremely difficult. The purpose of this study was to investigate the effect of the marine bacterial exopolysaccharide (exopolysaccharide 11 [EPS11]) on liver cancer metastasis to explore the underlying target protein and molecular mechanism. We found that EPS11 significantly suppressed cell adhesion, migration, and invasion in liver cancer cells. Proteomic analysis showed that EPS11 induced downregulation of proteins related to the extracellular matrix–receptor interaction signaling pathway. In addition, the direct pharmacological target of EPS11 was identified as collagen I using cellular thermal shift assays. Surface plasmon resonance and pull-down assays further confirmed the specific binding of EPS11 to collagen I. Moreover, EPS11 was shown to inhibit tumor metastasis by directly modulating collagen I activity via the β1-integrin–mediated signaling pathway. Collectively, our study demonstrated for the first time that collagen I could be a direct pharmacological target of polysaccharide drugs. Moreover, directly targeting collagen I may be a promising strategy for finding novel carbohydrate-based drugs.     

The Bari Manifesto: An interoperability framework for essential biodiversity variables

Essential Biodiversity Variables (EBV) are fundamental variables that can be used for assessing biodiversity change over time, for determining adherence to biodiversity policy, for monitoring progress towards sustainable development goals, and for tracking biodiversity responses to disturbances and management interventions. Data from observations or models that provide measured or estimated EBV values, which we refer to as EBV data products, can help to capture the above processes and trends and can serve as a coherent framework for documenting trends in biodiversity. Using primary biodiversity records and other raw data as sources to produce EBV data products depends on cooperation and interoperability among multiple stakeholders, including those collecting and mobilising data for EBVs and those producing, publishing and preserving EBV data products. Here, we encapsulate ten principles for the current best practice in EBV-focused biodiversity informatics as ‘The Bari Manifesto’, serving as implementation guidelines for data and research infrastructure providers to support the emerging EBV operational framework based on trans-national and cross-infrastructure scientific workflows. The principles provide guidance on how to contribute towards the production of EBV data products that are globally oriented, while remaining appropriate to the producer's own mission, vision and goals. These ten principles cover: data management planning; data structure; metadata; services; data quality; workflows; provenance; ontologies/vocabularies; data preservation; and accessibility. For each principle, desired outcomes and goals have been formulated. Some specific actions related to fulfilling the Bari Manifesto principles are highlighted in the context of each of four groups of organizations contributing to enabling data interoperability - data standards bodies, research data infrastructures, the pertinent research communities, and funders. The Bari Manifesto provides a roadmap enabling support for routine generation of EBV data products, and increases the likelihood of success for a global EBV framework.     

Spatial heterogeneity of ecosystem health and its sensitivity to pressure in the waters of nearshore archipelago

The ecosystem-based management of nearshore waters requires synthesis of spatial data on the distribution of ecological conditions and intensity of anthropogenic perturbations, and the overlay of their effects on the ecosystem health. An assessment framework for ecosystem health incorporating 4 components namely vigor, organization, resilience and maintenance was proposed in this paper, based on which an analytical approach was developed to quantify the integrated effects of island mass and anthropogenic pressures on the waters of nearshore archipelago. The southern waters of Miaodao Archipelago, which are located in the intersection of the Bohai Sea and the Yellow Sea, China, were taken as a typical example to acquire the spatial heterogeneity of the ecosystem health and its sensitivity to multiple anthropogenic pressures. Results indicated that there was a relatively significant performance of the spatial heterogeneity for the ecosystem health. It presented that the interisland waters were poorer health than the external waters, and the waters adjacent to the continent functioned less well than those in a relatively open area. This phenomenon was primarily determined by the performance of vigor as well as resilience of ecosystem. For the 4 components of ecosystem health, there were an obvious spatial heterogeneity of vigor as well as the resilience, a seasonal succession of organization, and a spatiotemporal uniformity of maintenance. Moreover, the ecosystem health was more sensitive to the stressors of inland activities and coastline exploitation especially in the waters of Miaodao Bay and Changdao Port. The analytical process and resulting maps provide flexible tools for regional efforts to implement ecosystem-based management in the waters of archipelago and further nearshore waters so as to promote their sustainable development.     

Steroid-independent male sexual behavior in B6D2F2 male mice

It is well established that male sexual behavior (MSB) is regulated by gonadal steroids; however, individual differences in MSB, independent of gonadal steroids, are prevalent across a wide range of species, and further investigation is necessary to advance our understanding of steroid-independent MSB. Studies utilizing B6D2F1 hybrid male mice in which a significant proportion retain MSB after long-term orchidectomy, identified as steroid-independent-maters (SI-maters), have begun to unravel the genetic underpinnings of steroid-independent MSB. A recent study demonstrated that steroid-independent MSB is a heritable behavioral phenotype that is mainly passed down from B6D2F1 hybrid SI-maters when crossed with C57BL6J female mice. To begin to uncover whether the strain of the dam plays a role in the inheritance of steroid-independent MSB, B6D2F1 hybrid females were crossed with B6D2F1 hybrid males. While the present study confirms the finding that steroid-independent MSB is a heritable behavioral phenotype and that SI-mater sires are more likely to pass down some components of MSB than SI-non-maters to their offspring, it also reveals that the B6D2F2 male offspring that were identified as SI-maters that displayed the full repertoire of steroid-independent MSB had the same probability of being sired from either a B6D2F1 SI-mater or SI-non-mater. These results, in conjunction with previous findings, indicate that the specific chromosomal loci pattern that codes for steroid-independent MSB in the B6D2F2 male offspring may result regardless of whether the father was a SI-mater or SI-non-mater, and that the maternal strain may be an important factor in the inheritance of steroid-independent MSB.     

A novel variant of DNA polymerase ζ, Rev3ΔC,highlights differential regulation of Pol32 as a subunit of polymerase δ versus ζ in Saccharomyces cerevisiae

Unrepaired DNA lesions often stall replicative DNA polymerases and are bypassed by translesion synthesis (TLS) to prevent replication fork collapse. Mechanisms of TLS are lesion- and species-specific, with a prominent role of specialized DNA polymerases with relaxed active sites. After nucleotide(s) are incorporated across from the altered base(s), the aberrant primer termini are typically extended by DNA polymerase ζ (pol ζ). As a result, pol ζ is responsible for most DNA damage-induced mutations. The mechanisms of sequential DNA polymerase switches in vivo remain unclear. The major replicative DNA polymerase δ (pol δ) shares two accessory subunits, called Pol31/Pol32 in yeast, with pol ζ. Inclusion of Pol31/Pol32 in the pol δ/pol ζ holoenzymes requires a [4Fe–4S] cluster in C-termini of the catalytic subunits. Disruption of this cluster in Pol ζ or deletion of POL32 attenuates induced mutagenesis. Here we describe a novel mutation affecting the catalytic subunit of pol ζ, rev3ΔC, which provides insight into the regulation of pol switches. Strains with Rev3ΔC, lacking the entire C-terminal domain and therefore the platform for Pol31/Pol32 binding, are partially proficient in Pol32-dependent UV-induced mutagenesis. This suggests an additional role of Pol32 in TLS, beyond being a pol ζ subunit, related to pol δ. In search for members of this regulatory pathway, we examined the effects of Maintenance of Genome Stability 1 (Mgs1) protein on mutagenesis in the absence of Rev3–Pol31/Pol32 interaction. Mgs1 may compete with Pol32 for binding to PCNA. Mgs1 overproduction suppresses induced mutagenesis, but had no effect on UV-mutagenesis in the rev3ΔC strain, suggesting that Mgs1 exerts its inhibitory effect by acting specifically on Pol32 bound to pol ζ. The evidence for differential regulation of Pol32 in pol δ and pol ζ emphasizes the complexity of polymerase switches.     

Ecological dynamics and biotechnological implications of thraustochytrids from marine habitats

Thraustochytrids, a group of osmoheterotrophic marine protists, have recently gained increased attention owing to their spectacular biotechnological potentials. They possess enormous capability of producing omega-3 (ω-3) polyunsaturated fatty acids (PUFAs) such as docosahexaenoic acid (DHA), eicosapentaenoic acid (EPA), and several other bioactive metabolites, known to have nutritional implications in human health. They have emerged lately as an efficient economic alternative compared with other fish and algal oil sources by virtue of their simpler PUFA profiles and cost-effective culture conditions. This review is an attempt to summarize the ecological significance of thraustochytrids with an emphasis on their cultured and uncultured diversity from various marine habitats accounted during the last few decades. Moreover, improved technologies such as media optimization in conjugation with metabolic engineering, adopted for biotechnological advancement of ω-3 products of thraustochytrids are highlighted with particular concern on the respective fatty acid biosynthetic pathways. One of the future prospects focuses on utilization of thraustochytrids for biodiesel production owing to their tremendous potentiality of yielding low carbon monounsaturated fatty acids (LC-MUFAs). However, there is utmost need of in-depth diversity assessments from various oceanic ecosystems in order to gain insight on potential thraustochytrids for ameliorated employment toward biotechnological applications.