NIST lipidomics workflow questionnaire: an assessment of community-wide methodologies and perspectives

Introduction

Efforts to harmonize lipidomic methodologies have been limited within the community. Here, we aimed to capitalize on the recent National Institute of Standards and Technology lipidomics interlaboratory comparison exercise by implementing a questionnaire that assessed current methodologies, quantitation strategies, standard operating procedures (SOPs), and quality control activities employed by the lipidomics community.

Objectives

Lipidomics is a rapidly developing field with diverse applications. At present, there are no community-vetted methods to assess measurement comparability or data quality. Thus, a major impetus of this questionnaire was to profile current efforts, highlight areas of need, and establish future objectives in an effort to harmonize lipidomics workflows.

Methods

The 54-question survey inquired about laboratory demographics, lipidomic methodologies and SOPs, analytical platforms, quantitation, reference materials, quality control procedures, and opinions regarding challenges existing within the community.

Results

A total of 125 laboratories participated in the questionnaire. A broad overview of results highlighted a wide methodological diversity within current lipidomic workflows. The impact of this diversity on lipid measurement and quantitation is currently unknown and needs to be explored further. While some laboratories do incorporate SOPs and quality control activities, these concepts have not been fully embraced by the community. The top five perceived challenges within the lipidomics community were a lack of standardization amongst methods/protocols, lack of lipid standards, software/data handling and quantification, and over-reporting/false positives.

Conclusion

The questionnaire provided an overview of current lipidomics methodologies and further promoted the need for community-accepted guidelines and protocols. The questionnaire also served as a platform to help determine and prioritize metrological issues to be investigated.

     

Is the Wild Coast in eastern South Africa a distinct marine bioregion?

The South African coastline can be divided into at least four temperature-defined marine bioregions, including the tropical north-east coast, the subtropical east coast, the warm-temperate south coast, and the cool-temperate west coast. There are also two biogeographical transition zones, the south-west coast and the south-east coast (or Wild Coast). The former is sometimes considered a distinct marine bioregion, but no such status has yet been suggested for the Wild Coast. Previous data on the distribution of a recently described but very common coastal crab, Hymenosoma longicrure, indicated that this species could be a Wild Coast endemic. If confirmed, this would be a first indication that this region harbours unique fauna, and that additional research is required to determine whether the Wild Coast constitutes a distinct bioregion that needs to be managed separately from other coastal regions. In the present study, we generated novel genetic data for H. longicrure and compared the species’ range with that of its southern African congeners. We found that H. longicrure occurs north of the Wild Coast, where its range overlaps with that of H. projectum. This finding rejects the idea that the Wild Coast harbours endemic fauna and suggests that the ranges of the two species may be linked to the subtropical and tropical bioregions, respectively, with some southward dispersal facilitated by the southward-flowing Agulhas Current. We conclude that there is as yet no compelling evidence that the Wild Coast is a distinct marine bioregion, and concur with previous biogeographical studies which have suggested that the Wild Coast is an area in which species from the subtropical and warm-temperate bioregions have overlapping ranges. Nonetheless, that fact that no biological information is available for the majority of the region’s estuaries highlights the necessity of comprehensively documenting the biodiversity of this understudied region to fully resolve this issue.     

Preliminary investigation of social interactions and feeding behavior in captive group-housed Tasmanian devils (Sarcophilus Harrisii)

As the number of Tasmanian devils (Sarcophilus harrisii) in captivity increases, an understanding of captive social dynamics and behavior is becoming increasingly important. In the wild, devils are solitary, although sometimes, they congregate to feed on a large carcass. However, it is common to house devils in groups as a form of social enrichment. This study investigated how behavior at feeding time of captive Tasmanian devils varied in groups of different sizes. Observations were made of individually housed devils and devils in groups of two, three, five, and six, when presented with a carcass on which to feed. Total feeding duration ranged from 6.5 to 47.4 minutes per observation period (70 minutes). There was no significant interaction between feeding duration and group size during the experiment. Feeding duration varied daily and depended on carcass size. Social housing of Tasmanian devils enabled them to display dyadic and agonistic behaviors during feeding. Observing behaviors and learning from the outcomes of these interactions can improve husbandry techniques. Creating a captive environment that encourages natural behaviors may enhance survival in the wild following translocation.     

Minimal organic medium for suspension cultures of Paul's scarlet rose

Summary Maximum growth of suspension cultures of Paul's Scarlet rose has been demonstrated in a minimal organic medium possessing only 4 organic compounds: napthaleneacetic acid, kinetin, myo-inositol, and sucrose. Myo-inositol was not essential for growth, but sustained growth was reduced by 90% when it was omitted. Maximum growth required nitrate plus a supplemental amount of either NH ₄ ⁺ or glutamine.     

Interactions of light and a temperature shift on seed germination

Germination of Rumex obtusifolius L. seeds is potentiated to an observable degree in 2 minutes by a single shift in temperature from 20 to 35 C. Half-maximal potentiation requires less than 32 minutes at the higher temperature. Similar sensitivities to shifts in temperature were observed for seeds of Barbarea vulgaris, R.Br. B. verna (Mill.) Asch., and Lepidium virginicum L. A shift in temperature interacts strongly with change in form of phytochrome induced by light on germination of the four kinds of seeds. The potentiated effects for R. obtusifolius are only moderately affected by 40 μm cycloheximide. Both the temperature shift and light actions are apparently independent of processes of synthesis necessary for growth.     

Promotion of seed germination by nitrate, nitrite, hydroxylamine, and ammonium salts

Action and uptake of azides, nitrates, nitrites, hydroxylamines, and ammonium salts were measured on germination of Amaranthus albus, Lactuca sativa, Phleum pratense, Barbarea vulgaris, B. verna, and Setaria glauca seeds. Nitrate and nitrite reductase activities were measured in vivo for each of these kinds of seeds. Activities were measured in vitro for catalase, peroxidase, glycolate oxidase, and pyridine nucleotide quinone reductase on extracts of A. albus and L. sativa seeds before and after germination. The enzymic activities measured and the responsiveness of the haemproteins to inhibition by the several compounds indicate that nitrites, azides, and hydroxylamines promote seed germination by inhibition of H₂O₂ decomposition by catalase. Ammonium salts showed pronounced promotive activity only for B. verna and B. vulgaris seeds, for which they served as metabolic substrates.     

Phytochrome Transformation and Action in Seeds of Rumex crispus L. during Secondary Dormancy

Promotion of germination by red light fails after prolonged dark imbibition of Rumex crispus L. seeds, indicative of a secondary dormancy. The degree and rate of inception of the dormancy increases with increasing temperature. Following establishment of the dormancy, germination response to red light can be restored by either prolonged cold treatment or brief high temperature shifts. Loss of phytochrome was not a factor in the initial establishment of the dormancy. When the seeds are in secondary dormancy, the chromophore of phytochrome can be transformed to the far red-absorbing form, but the far red-absorbing form cannot induce germination. The responses to changes in temperature suggested dependence of germination on order disorder transitions in components of the seeds.