Enigmatic persistence of dissolved organic matter in the ocean

Marine dissolved organic matter (DOM) contains more carbon than the combined stocks of Earth’s biota. Organisms in the ocean continuously release a myriad of molecules that become food for microheterotrophs, but, for unknown reasons, a residual fraction persists as DOM for millennia. In this Perspective, we discuss and compare two concepts that could explain this persistence. The long-standing ‘intrinsic recalcitrance’ paradigm attributes DOM stability to inherent molecular properties. In the ‘emergent recalcitrance’ concept, DOM is continuously transformed by marine microheterotrophs, with recalcitrance emerging on an ecosystems level. Both concepts are consistent with observations in the modern ocean, but they imply very different responses of the DOM pool to climate-related changes. To better understand DOM persistence, we propose a new overarching research strategy — the ecology of molecules — that integrates the concepts of intrinsic and emergent recalcitrance with the ecological and environmental context

Using Sequence Similarity Networks for Visualization of Relationships Across Diverse Protein Superfamilies

The dramatic increase in heterogeneous types of biological data—in particular, the abundance of new protein sequences—requires fast and user-friendly methods for organizing this information in a way that enables functional inference. The most widely used strategy to link sequence or structure to function, homology-based function prediction, relies on the fundamental assumption that sequence or structural similarity implies functional similarity. New tools that extend this approach are still urgently needed to associate sequence data with biological information in ways that accommodate the real complexity of the problem, while being accessible to experimental as well as computational biologists. To address this, we have examined the application of sequence similarity networks for visualizing functional trends across protein superfamilies from the context of sequence similarity. Using three large groups of homologous proteins of varying types of structural and functional diversity—GPCRs and kinases from humans, and the crotonase superfamily of enzymes—we show that overlaying networks with orthogonal information is a powerful approach for observing functional themes and revealing outliers. In comparison to other primary methods, networks provide both a good representation of group-wise sequence similarity relationships and a strong visual and quantitative correlation with phylogenetic trees, while enabling analysis and visualization of much larger sets of sequences than trees or multiple sequence alignments can easily accommodate. We also define important limitations and caveats in the application of these networks. As a broadly accessible and effective tool for the exploration of protein superfamilies, sequence similarity networks show great potential for generating testable hypotheses about protein structure-function relationships

Sample treatment for tissue proteomics in cancer, toxicology, and forensics

Since the birth of proteomics science in the 1990, the number of applications and of sample preparation methods has grown exponentially, making a huge contribution to the knowledge in life science disciplines. Continuous improvements in the sample treatment strategies unlock and reveal the fine details of disease mechanisms, drug potency, and toxicity as well as enable new disciplines to be investigated such as forensic science. This chapter will cover the most recent developments in sample preparation strategies for tissue proteomics in three areas, namely, cancer, toxicology, and forensics, thus also demonstrating breath of application within the domain of health and well-being, pharmaceuticals, and secure societies. In particular, in the area of cancer (human tumor biomarkers), the most efficient and multi-informative proteomic strategies will be covered in relation to the subsequent application of matrix-assisted laser desorption/ionization mass spectrometry imaging (MALDI-MSI) and liquid extraction surface analysis (LESA), due to their ability to provide molecular localization of tumor biomarkers albeit with different spatial resolution. With respect to toxicology, methodologies applied in toxicoproteomics will be illustrated with examples from its use in two important areas: the study of drug-induced liver injury (DILI) and studies of effects of chemical and environmental insults on skin, i.e., the effects of irritants, sensitizers, and ionizing radiation. Within this chapter, mainly tissue proteomics sample preparation methods for LC-MS/MS analysis will be discussed as (i) the use of LC-MS/MS is majorly represented in the research efforts of the bioanalytical community in this area and (ii) LC-MS/MS still is the gold standard for quantification studies. Finally, the use of proteomics will also be discussed in forensic science with respect to the information that can be recovered from blood and fingerprint evidence which are commonly encountered at the scene of the crime. The application of proteomic strategies for the analysis of blood and fingerprints is novel and proteomic preparation methods will be reported in relation to the subsequent use of mass spectrometry without any hyphenation. While generally yielding more information, hyphenated methods are often more laborious and time-consuming; since forensic investigations need quick turnaround, without compromising validity of the information, the prospect to develop methods for the application of quick forensic mass spectrometry techniques such as MALDI-MS (in imaging or profiling mode) is of great interest

Patterns in sexual reproduction of the dominant scleractinian corals at Rapa Nui (Easter Island): Pocillopora verrucosa and Porites lobata

Sexual reproduction is fundamental to the maintenance and recovery of coral-dominated communities in high-latitude and isolated locations, where replenishment often depends on local reproductive activity rather than recruitment from distant reefs. Rapa Nui (Easter Island) is one of the most remote islands in the Pacific, lying at the southern, subtropical edge of the range of reef-building scleractinians. Here, we describe the sexual reproduction and timing of the 2 dominant corals, Pocillopora verrucosa and Porites lobata. Reproductive activity was inferred from the identification and staging of gametes via histological analyses of monthly samples collected from December 2012 to May 2014 at 12 m depth at Motu Tautara (27∞6.6íS, 109∞25.5íW) with in situ temperature records. In P. verrucosa, the observed hermaphroditic activity spanned from December to January, resulting in mature oocytes of 117 µm mean diameter. In P. lobata, observed gonochoric activity spanned from December to March, resulting in mature oocytes of 180 µm mean diameter. The observed initiation of gametogenic cycles coincided with the onset of spring warming in both species. Inferred spawning of P. verrucosa followed a relatively calm period of daily variance reduction in local in situ temperature and wind speed prior to the peak in thermal conditions, whereas inferred spawning of P. lobata coincided with peak temperatures in one year but not the other. We suggest temporal restrictions of disruptive coastal activities such as dredging during coral spawning periods and mitigation of land-based sources of pollution and watershed discharge that may reduce water quality

Report and preliminary results of R/V POSEIDON cruise POS531, Las Palmas (Canary Islands) – Mindelo (Cape Verde), 18.01.2019 – 01.02.2019.

During the RV POSEIDON research cruise, POS531, from Las Palmas (Canary Islands) to Mindelo (Cape Verde), we studied organic matter transport in the Cape Blanc upwelling region. Cape Blanc upwelling is one of the coastal upwelling regimes of the Eastern Boundary Current Systems (EBUEs), which are the most productive ocean areas and key players in the global carbon cycle and climate change. Pelagic primary production drives the biological pump which, in coastal upwelling regions, is largely controlled by the sinking behaviour and lateral transport of marine snow aggregates and faecal pellets. We still lack a quantitative understanding about the role that zooplankton grazing, sediment processes, and lateral transport play in the transformation and export of particulate organic matter. Further gaps in knowledge exist about the distribution of particles, their size and density and the particle sinking velocities of various biogenic and lithogenic components. Even less is known about what happens when particles reach the sandy seafloor and the role that benthic primary production plays in shallow shelf systems. The sandy seabed is regularly reworked and resuspended and therefore biogeochemical processes in the sediment likely play an important role in nutrient and organic matter transformation. To study how the sandy shelf area is connected to open ocean carbon export and carbon sequestration, we deployed free-drifting sediment traps to study short term variability in mass fluxes and the decay and transformation of large, organic-rich marine snow particles. In addition, the water column was sampled and studied using in situ-pumps, Marine Snow Catchers, particle cameras, and vertical multi-net hauls. To link the pelagic processes with the benthic remineralization and production, we deployed benthic boundary layer samplers and benthic lander systems. This allowed us to study the physical environment near the seabed and elucidate its effects on the biogeochemistry of the sediment, which was quantified through in situ and on-board laboratory rate measurements. The major aim of the research cruise was to better quantify the carbon and nitrogen cycling in the sandy shelf region and to quantify the impact from this cycling on lateral transport to the open ocean

Discrimination of beta-1,4-and beta-1,3-Linkages in Native Oligosaccharides via Charge Transfer Dissociation Mass Spectrometry

The connection between monosaccharides influences the structure, solubility, and biological function of carbohydrates. Although tandem mass spectrometry (MS/MS) often enables the compositional identification of carbohydrates, traditional MS/MS fragmentation methods fail to generate abundant cross-ring fragments of intrachain monosaccharides that could reveal carbohydrate connectivity. We examined the potential of helium-charge transfer dissociation (He-CTD) as a method of MS/MS to decipher the connectivity of beta-1,4- and beta-1,3-linked oligosaccharides. In contrast to collision-induced dissociation (CID), He-CTD of isolated oligosaccharide precursors produced both glycosidic and cross-ring cleavages of each monosaccharide. The radical-driven dissociation in He-CTD induced single cleavage events, without consecutive fragmentations, which facilitated structural interpretation. He-CTD of various standards up to a degree of polymerization of 7 showed that beta-1,4- and beta-1,3-linked carbohydrates can be distinguished based on diagnostic 3,5A fragment ions that are characteristic for beta-1,4-linkages. Overall, fragment ion spectra from He-CTD contained sufficient information to infer the connectivity specifically for each glycosidic bond. When testing He-CTD to resolve the order of beta-1,4- and beta-1,3-linkages in mixed-linked oligosaccharide standards, He-CTD spectra sometimes provided less confident assignment of connectivity. Ion mobility spectrometry-mass spectrometry (IMS-MS) of the standards indicated that ambiguity in the He-CTD spectra was caused by isobaric impurities in the mixed-linked oligosaccharides. Radical-driven dissociation induced by He-CTD can thus expand MS/MS to carbohydrate linkage analysis, as demonstrated by the comprehensive fragment ion spectra on native oligosaccharides. The determination of connectivity in true unknowns would benefit from the separation of isobaric precursors, through UPLC or IMS, before linkage determination via He-CTD

Model-based identification of TNFα-induced IKKβ-mediated and IκBα-mediated regulation of NFκB signal transduction as a tool to quantify the impact of drug-induced liver injury compounds

Drug-induced liver injury (DILI) has become a major problem for patients and for clinicians, academics and the pharmaceutical industry. To date, existing hepatotoxicity test systems are only poorly predictive and the underlying mechanisms are still unclear. One of the factors known to amplify hepatotoxicity is the tumor necrosis factor alpha (TNFα), especially due to its synergy with commonly used drugs such as diclofenac. However, the exact mechanism of how diclofenac in combination with TNFα induces liver injury remains elusive. Here, we combined time-resolved immunoblotting and live-cell imaging data of HepG2 cells and primary human hepatocytes (PHH) with dynamic pathway modeling using ordinary differential equations (ODEs) to describe the complex structure of TNFα-induced NFκB signal transduction and integrated the perturbations of the pathway caused by diclofenac. The resulting mathematical model was used to systematically identify parameters affected by diclofenac. These analyses showed that more than one regulatory module of TNFα-induced NFκB signal transduction is affected by diclofenac, suggesting that hepatotoxicity is the integrated consequence of multiple changes in hepatocytes and that multiple factors define toxicity thresholds. Applying our mathematical modeling approach to other DILI-causing compounds representing different putative DILI mechanism classes enabled us to quantify their impact on pathway activation, highlighting the potential of the dynamic pathway model as a quantitative tool for the analysis of DILI compounds.Toxicolog