A large scale temporal and spatial environmental DNA biodiversity survey of marine vertebrates in Brazil following the Fundão tailings dam failure

Seawater contains a wealth of genetic information, representing the biodiversity of numerous species residing within a particular marine habitat. Environmental DNA (eDNA) metabarcoding offers a cost effective, non-destructive method for large scale monitoring of environments, as diverse taxonomic groups are detected using metabarcoding assays. A large-scale eDNA monitoring program of marine vertebrates was conducted across three sampling seasons (Spring 2018, Autumn 2019; Spring 2019) in coastal waters of Brazil. The program was designed to investigate eDNA as a testing method for long term monitoring of marine vertebrates following the Fundão tailings dam failure in November 2015. While no baseline samples were available prior to the dam failure there is still value in profiling the taxa that use the impacted area and the trajectory of recovery. A total of 40 sites were sampled around the mouths of eight river systems, covering approximately 500 km of coastline. Metabarcoding assays targeting the mitochondrial genes 16S rRNA and COI were used to detect fish, marine mammals and elasmobranchs. We detected temporal differences between seasons and spatial differences between rivers/estuaries sampled. Overall, the largest eDNA survey in Brazil to date revealed 69 families from Class Actinopterygii (fish), 15 species from Class Chondrichthyes (sharks and rays), 4 species of marine and estuarine mammals and 23 species of conservation significance including 2 species of endangered dolphin. Our large-scale study reinforces the value eDNA metabarcoding can bring when monitoring the biodiversity of coastal environments and demonstrates the importance of collection of time-stamped environmental samples to better understand the impacts of anthropogenic activities.

eDNA metabarcoding of avocado flowers: 'Hass' it got potential to survey arthropods in food production systems?

In the face of global biodiversity declines, surveys of beneficial and antagonistic arthropod diversity as well as the ecological services that they provide are increasingly important in both natural and agro-ecosystems. Conventional survey methods used to monitor these communities often require extensive taxonomic expertise and are time-intensive, potentially limiting their application in industries such as agriculture, where arthropods often play a critical role in productivity (e.g. pollinators, pests and predators). Environmental DNA (eDNA) metabarcoding of a novel substrate, crop flowers, may offer an accurate and high throughput alternative to aid in the detection of these managed and unmanaged taxa. Here, we compared the arthropod communities detected with eDNA metabarcoding of flowers, from an agricultural species (Persea americana-'Hass' avocado), with two conventional survey techniques: digital video recording (DVR) devices and pan traps. In total, 80 eDNA flower samples, 96 h of DVRs and 48 pan trap samples were collected. Across the three methods, 49 arthropod families were identified, of which 12 were unique to the eDNA dataset. Environmental DNA metabarcoding from flowers revealed potential arthropod pollinators, as well as plant pests and parasites. Alpha diversity levels did not differ across the three survey methods although taxonomic composition varied significantly, with only 12% of arthropod families found to be common across all three methods. eDNA metabarcoding of flowers has the potential to revolutionize the way arthropod communities are monitored in natural and agro-ecosystems, potentially detecting the response of pollinators and pests to climate change, diseases, habitat loss and other disturbances.

Population genomics of Australian indigenous Mesorhizobium reveals diverse nonsymbiotic genospecies capable of nitrogen-fixing symbioses following horizontal gene transfer

Mesorhizobia are soil bacteria that establish nitrogen-fixing symbioses with various legumes. Novel symbiotic mesorhizobia frequently evolve following horizontal transfer of symbiosis-gene-carrying integrative and conjugative elements (ICESyms) to indigenous mesorhizobia in soils. Evolved symbionts exhibit a wide range in symbiotic effectiveness, with some fixing nitrogen poorly or not at all. Little is known about the genetic diversity and symbiotic potential of indigenous soil mesorhizobia prior to ICESym acquisition. Here we sequenced genomes of 144 Mesorhizobium spp. strains cultured directly from cultivated and uncultivated Australian soils. Of these, 126 lacked symbiosis genes. The only isolated symbiotic strains were either exotic strains used previously as legume inoculants, or indigenous mesorhizobia that had acquired exotic ICESyms. No native symbiotic strains were identified. Indigenous nonsymbiotic strains formed 22 genospecies with phylogenomic diversity overlapping the diversity of internationally isolated symbiotic Mesorhizobium spp. The genomes of indigenous mesorhizobia exhibited no evidence of prior involvement in nitrogen-fixing symbiosis, yet their core genomes were similar to symbiotic strains and they generally lacked genes for synthesis of biotin, nicotinate and thiamine. Genomes of nonsymbiotic mesorhizobia harboured similar mobile elements to those of symbiotic mesorhizobia, including ICESym-like elements carrying aforementioned vitamin-synthesis genes but lacking symbiosis genes. Diverse indigenous isolates receiving ICESyms through horizontal gene transfer formed effective symbioses with Lotus and Biserrula legumes, indicating most nonsymbiotic mesorhizobia have an innate capacity for nitrogen-fixing symbiosis following ICESym acquisition. Non-fixing ICESym-harbouring strains were isolated sporadically within species alongside effective symbionts, indicating chromosomal lineage does not predict symbiotic potential. Our observations suggest previously observed genomic diversity amongst symbiotic Mesorhizobium spp. represents a fraction of the extant diversity of nonsymbiotic strains. The overlapping phylogeny of symbiotic and nonsymbiotic clades suggests major clades of Mesorhizobium diverged prior to introduction of symbiosis genes and therefore chromosomal genes involved in symbiosis have evolved largely independent of nitrogen-fixing symbiosis.

Pollen DNA metabarcoding identifies regional provenance and high plant diversity in Australian honey

Accurate identification of the botanical components of honey can be used to establish its geographical provenance, while also providing insights into honeybee (Apis mellifera L.) diet and foraging preferences. DNA metabarcoding has been demonstrated as a robust method to identify plant species from pollen and pollen-based products, including honey. We investigated the use of pollen metabarcoding to identify the floral sources and local foraging preferences of honeybees using 15 honey samples from six bioregions from eastern and western Australia. We used two plant metabarcoding markers, ITS2 and the trnL P6 loop. Both markers combined identified a total of 55 plant families, 67 genera, and 43 species. The trnL P6 loop marker provided significantly higher detection of taxa, detecting an average of 15.6 taxa per sample, compared to 4.6 with ITS2. Most honeys were dominated by Eucalyptus and other Myrtaceae species, with a few honeys dominated by Macadamia (Proteaceae) and Fabaceae. Metabarcoding detected the nominal primary source provided by beekeepers among the top five most abundant taxa for 85% of samples. We found that eastern and western honeys could be clearly differentiated by their floral composition, and clustered into bioregions with the trnL marker. Comparison with previous results obtained from melissopalynology shows that metabarcoding can detect similar numbers of plant families and genera, but provides significantly higher resolution at species level. Our results show that pollen DNA metabarcoding is a powerful and robust method for detecting honey provenance and examining the diet of honeybees. This is particularly relevant for hives foraging on the unique and diverse flora of the Australian continent, with the potential to be used as a novel monitoring tool for honeybee floral resources.

eDNAFlow, an automated, reproducible and scalable workflow for analysis of environmental DNA sequences exploiting Nextflow and Singularity

Metabarcoding of environmental DNA (eDNA) when coupled with high throughput sequencing is revolutionising the way biodiversity can be monitored across a wide range of applications. However, the large number of tools deployed in downstream bioinformatic analyses often places a challenge in configuration and maintenance of a workflow, and consequently limits the research reproducibility. Furthermore, scalability needs to be considered to handle the growing amount of data due to increase in sequence output and the scale of project. Here, we describe eDNAFlow, a fully automated workflow that employs a number of state-of-the-art applications to process eDNA data from raw sequences (single-end or paired-end) to generation of curated and noncurated zero-radius operational taxonomic units (ZOTUs) and their abundance tables. This pipeline is based on Nextflow and Singularity which enable a scalable, portable and reproducible workflow using software containers on a local computer, clouds and high-performance computing (HPC) clusters. Finally, we present an in-house Python script to assign taxonomy to ZOTUs based on user specified thresholds for assigning lowest common ancestor (LCA). We demonstrate the utility and efficiency of the pipeline using an example of a published coral diversity biomonitoring study. Our results were congruent with the aforementioned study. The scalability of the pipeline is also demonstrated through analysis of a large data set containing 154 samples. To our knowledge, this is the first automated bioinformatic pipeline for eDNA analysis using two powerful tools: Nextflow and Singularity. This pipeline addresses two major challenges in the analysis of eDNA data; scalability and reproducibility.

Irish prison guards call for expansion of methadone access

In many Western countries, including Canada, seroprevalence rates in prisons have reached epidemic levels, with infection rates among prisoners many times higher than among people outside prisons.

Increased eumelanin expression and tanning is induced by a superpotent melanotropin [Nle4-D-Phe7]-alpha-MSH in humans

Seven normal volunteers (six males and one female) with tanning skin types III or IV (Fitzpatrick scale) were given 10 daily subcutaneous injections of a superpotent synthetic analog of alpha-melanocyte stimulating hormone (alpha-MSH) over two weeks. This agent, [Nle4-D-Phe7]alpha-MSH, also called Melanotan-I (MT-I), was administered at a dose of 0.16 mg/kg/day (Monday-Friday), over a two week period. Tanning was measured serially using computerized light reflectance. This regimen induced tanning at 3 of 8 anatomic sites including the face, neck and forearm by comparison of baseline to (1) the end of the daily dosing period, (day 14), and (2) one week later, (day 21). Shave biopsies of the forearm taken at baseline and day 21 were analyzed by high performance liquid chromatography for eumelanin content which was measured as the permanganate oxidation product, pyrrole-2,3,5-tricarboxylic acid or PTCA. Pheomelanin content was measured as the hydroiodic acid digestion product, aminohydroxyphenylalanine (AHP). Eumelanin was also measured in the forehead skin samples of three subjects. The HPLC results show that mean (+/- SD) baseline eumelanin (PTCA) levels in forehead skin (n = 3) averaged 1.38 (+/- 0.87) ng/mg of wet skin tissue weight. Higher mean baseline levels of PTCA were detected in forearm skin (2.06 +/- 0.28 ng/mg wet weight, n = 7). One week after MT-I treatments ended, there was a mean (SD) 49% (+/- 17.6%) increase in forehead skin PTCA levels compared to baseline (P = 0.019, n = 3, by paired sample T-test). The mean (SD) increase in forearm skin PTCA levels was 98% (+/- 25.4%) over the same period (P = 0.003). In contrast, forearm pheomelanin expression following MT-I treatment did not significantly change from baseline. Overall, the MT-I regimen increased the eumelanin: pheomelanin ratio in forearm skin from 51:1 at baseline to 86:1 following MT-I (P = 0.054 by paired sample T-test). These results show that the tanning induced by MT-I in the face and forearm is associated with a significant increase in the eumelanin content of the human skin.

Evaluation of melanotan-II, a superpotent cyclic melanotropic peptide in a pilot phase-I clinical study

A pilot phase I study was conducted with a cyclic heptapeptide analog of alpha-melanocyte stimulating hormone (alpha-MSH). The lactam-bridged molecule, called Melanotan-II (MT-II), has the structure Ac-Nle4-Asp5-His6-D-Phe7-Arg8-Trp9-Lys10 alpha-MSH4-10-NH2 (MT-II) and has superpotent melanotropic activity in vitro. A single-blind, alternating day (saline or MT-II), placebo-controlled trial was conducted in 3 normal male volunteers at the starting dose of 0.01 mg/kg of MT-II. Subcutaneous injections of MT-II or saline were given daily (Monday-Friday) for 2 consecutive weeks. Two subjects were escalated by 0.005 mg/kg increments to 0.03 mg/kg and one to 0.025 mg/kg. The 0.03 mg/kg dose produced Grade II somnolence and fatigue in one of two subjects (WHO standards). Mild nausea, not requiring antiemetic treatment, was reported at most MT-II dose levels. A stretching and yawning complex appeared to correlate with the onset of spontaneous, penile erections which were intermittently experienced for 1-5 hours after MT-II dosing, depending on the MT-II dose. Two subjects had increased pigmentation in the face, upper body and buttock, as measured by quantitative reflectance and by visual perception 1 week after MT-II dosing ended. These results demonstrate that MT-II has tanning activity in humans given only 5 low doses every other day by subcutaneous injection. The recommended single MT-II dose for future Phase I studies is 0.025 mg/kg/day.

Handwriting as a Correlate of Extraversion

The validity of graphologists' claims that handwriting is a measure of extraversion was examined in this study. Three handwriting measures, line slope, letter slant, and letter width were chosen, and the relationship between these measures and extraversion as measured by the Eysenck Personality Inventory was studied. The subjects were 58 tertiary students. No significant correlations between the handwriting measures and extraversion were found, nor were there significant intercorrelations between the three handwriting measures. Thus the results did not support the claim that the three handwriting measures were valid indices of extraversion.