Detection of plastic debris degrading into micro particles across all oceanic environments and inside of marine organisms is no longer surprising news. Microplastic contamination now appears as one ...of the world's environmental main concerns. To determine the levels of microplastic pollution at sea, water samples were collected across a 4000 km-trajectory in the Tropical Eastern Pacific and the Galápagos archipelago, covering an area of 453,000 square kilometres. Furthermore, 240 specimens of 16 different species of fish, squid, and shrimp, all of human consumption, were collected along the continental coast. Microplastic particles were found in 100% of the water samples and marine organisms. Microplastic particles ranging from 150 to 500 µm in size were the most predominant. This is one of the first reports simultaneously detecting and quantifying microplastic particles abundance and their impact on marine organisms of this region.
Background
Today, scientists and academic researchers experience an enormous pressure to publish innovative and ground-breaking results in prestigious journals. This pressure may blight the general ...view concept of how scientific research needs to be done in terms of the general rules of transparency; duplication of data, and co-authorship rights might be compromised. As such, misconduct acts may occur more frequently than foreseen, as frequently these experiences are not openly shared or discussed among researchers.
Main body
While there are some concerns about the health and the transparency implications of such normalised pressure practices imposed on researchers in scientific research, there is a general acceptance that researchers must take and accept it in order to survive in the competitive world of science. This is even more the case for junior and mid-senior researchers who have recently started their adventure into the universe of independent researchers. Only the slightest fraction manages to endure, after many years of furious and cruel rivalry, to obtain a long-term, and even less probable, permanent position. There is an evil circle; excellent records of good publications are needed in order to obtain research funding, but how to produce pioneering research during these first years without funding? Many may argue this is a necessary process to ensure good quality scientific investigation, possibly, but perseverance and resilience may not be the only values needed when rejection is received consecutively for years.
Conclusion
There is a general culture that scientists rarely share previous bad experiences, in particular if they were associated to misconduct, as they may not be seen or considered as a relevant or hot topic to the scientific community readers. On next, a recent misconduct experience is shared, and a few additional reflections and suggestions on this topic were drafted in the hope other researchers might be spared unnecessary and unpleasant times.
During the current COVID‐19 pandemic, different methods have been used to evaluate patients with suspected SARS‐CoV‐2 infection. In this study, we experimentally evaluate the ability of spiked ...saliva‐moist swabs and spiked swabs without any transport medium to retain SARS‐CoV‐2 for storage and transport at different environmental settings during different incubation time periods. Our results show that at ambient temperature of 20°C, SARS‐CoV‐2 RNA remains stable for up to 9 days allowing a long‐time span for transport and storage without compromising clinical results. Additionally, this study demonstrates that saliva‐moist swabs can also be stored at −20°C and +4°C for up to 26 days without affecting RT‐qPCR results. Our data are relevant for low‐and middle‐income countries, which have limited access to rapid refrigerated transport and storage of samples representing an economical alternative. Finally, our study demonstrates the practical and economic advantage of using swabs without transport medium.
Severe acute respiratory syndrome coronavirus 2 has caused a pandemic in humans. Farmed mink (Neovison vison) are also susceptible. In Denmark, this virus has spread rapidly among farmed mink, ...resulting in some respiratory disease. Full-length virus genome sequencing revealed novel virus variants in mink. These variants subsequently appeared within the local human community.
In addition to humans, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) can transmit to animals that include hamsters, cats, dogs, mink, ferrets, tigers, lions, cynomolgus macaques, ...rhesus macaques, and treeshrew. Among these, mink are particularly susceptible. Indeed, 10 countries in Europe and North America reported SARS-CoV-2 infection among mink on fur farms. In Denmark, SARS-CoV-2 spread rapidly among mink farms and spilled-over back into humans, acquiring mutations/deletions with unknown consequences for virulence and antigenicity. Here we describe a mink-associated SARS-CoV-2 variant (Cluster 5) characterized by 11 amino acid substitutions and four amino acid deletions relative to Wuhan-Hu-1. Temporal virus titration, together with genomic and subgenomic viral RNA quantitation, demonstrated a modest
in vitro
fitness attenuation of the Cluster 5 virus in the Vero-E6 cell line. Potential alterations in antigenicity conferred by amino acid changes in the spike protein that include three substitutions (Y453F, I692V, and M1229I) and a loss of two amino acid residues 69 and 70 (ΔH69/V70), were evaluated in a virus microneutralization assay. Compared to a reference strain, the Cluster 5 variant showed reduced neutralization in a proportion of convalescent human COVID-19 samples. The findings underscore the need for active surveillance SARS-CoV-2 infection and virus evolution in susceptible animal hosts.
The occasional westward transport of warm water of the Agulhas Current, "Agulhas leakage", around southern Africa has been suggested to facilitate tropical marine connectivity between the Atlantic ...and Indian oceans, but the "Agulhas leakage" hypothesis does not explain the signatures of eastward gene flow observed in many tropical marine fauna. We investigated an alternative hypothesis: the establishment of a warm-water corridor during comparatively warm interglacial periods. The "warm-water corridor" hypothesis was investigated by studying the population genomic structure of Atlantic and Southwest Indian Ocean green turtles (N = 27) using 12,035 genome-wide single nucleotide polymorphisms (SNPs) obtained via ddRAD sequencing. Model-based and multivariate clustering suggested a hierarchical population structure with two main Atlantic and Southwest Indian Ocean clusters, and a Caribbean and East Atlantic sub-cluster nested within the Atlantic cluster. Coalescent-based model selection supported a model where Southwest Indian Ocean and Caribbean populations diverged from the East Atlantic population during the transition from the last interglacial period (130-115 thousand years ago; kya) to the last glacial period (115-90 kya). The onset of the last glaciation appeared to isolate Atlantic and Southwest Indian Ocean green turtles into three refugia, which subsequently came into secondary contact in the Caribbean and Southwest Indian Ocean when global temperatures increased after the Last Glacial Maximum. Our findings support the establishment of a warm-water corridor facilitating tropical marine connectivity between the Atlantic and Southwest Indian Ocean during warm interglacials.
Fibropapillomatosis (FP) is a neoplastic disease characterized by cutaneous tumours that has been documented to infect all sea turtle species. Chelonid fibropapilloma-associated herpesvirus (CFPHV) ...is believed to be the aetiological agent of FP, based principally on consistent PCR-based detection of herpesvirus DNA sequences from FP tumours. We used a recently described PCR-based assay that targets 3 conserved CFPHV genes, to survey 208 green turtles (Chelonia mydas). This included both FP tumour exhibiting and clinically healthy individuals. An additional 129 globally distributed clinically healthy individual sea turtles; representing four other species were also screened.
CFPHV DNA sequences were obtained from 37/37 (100%) FP exhibiting green turtles, and 45/300 (15%) clinically healthy animals spanning all five species. Although the frequency of infected individuals per turtle population varied considerably, most global populations contained at least one CFPHV positive individual, with the exception of various turtle species from the Arabian Gulf, Northern Indian Ocean and Puerto Rico. Haplotype analysis of the different gene markers clustered the CFPHV DNA sequences for two of the markers (UL18 and UL22) in turtles from Turks and Caicos separate to all others, regardless of host species or geographic origin.
Presence of CFPHV DNA within globally distributed samples for all five species of sea turtle was confirmed. While 100% of the FP exhibiting green turtles yielded CFPHV sequences, surprisingly, so did 15% of the clinically healthy turtles. We hypothesize that turtle populations with zero (0%) CFPHV frequency may be attributed to possible environmental differences, diet and/or genetic resistance in these individuals. Our results provide first data on the prevalence of CFPHV among seemingly healthy turtles; a factor that may not be directly correlated to the disease incidence, but may suggest of a long-term co-evolutionary latent infection interaction between CFPHV and its turtle-host across species. Finally, computational analysis of amino acid variants within the Turks and Caicos samples suggest potential functional importance in a substitution for marker UL18 that encodes the major capsid protein gene, which potentially could explain differences in pathogenicity. Nevertheless, such a theory remains to be validated by further research.
Fast surveillance strategies are needed to control the spread of new emerging SARS-CoV-2 variants and gain time for evaluation of their pathogenic potential. This was essential for the Omicron ...variant (B.1.1.529) that replaced the Delta variant (B.1.617.2) and is currently the dominant SARS-CoV-2 variant circulating worldwide. RT-qPCR strategies complement whole genome sequencing, especially in resource lean countries, but mutations in the targeting primer and probe sequences of new emerging variants can lead to a failure of the existing RT-qPCRs. Here, we introduced an RT-qPCR platform for detecting the Delta- and the Omicron variant simultaneously using a degenerate probe targeting the key ΔH69/V70 mutation in the spike protein. By inclusion of the L452R mutation into the RT-qPCR platform, we could detect not only the Delta and the Omicron variants, but also the Omicron sub-lineages BA.1, BA.2 and BA.4/BA.5. The RT-qPCR platform was validated in small- and large-scale. It can easily be incorporated for continued monitoring of Omicron sub-lineages, and offers a fast adaption strategy of existing RT-qPCRs to detect new emerging SARS-CoV-2 variants using degenerate probes.
Abstract
Seaweed aquaculture has become a profitable and an attractive alternative of cultivation thanks to its quick biomass production for food, feed, and other non-food applications. In addition, ...the ecosystem services generated by seaweed cultivation towards carbon fixation represents a more sustainable solution to the ocean’s acidification. The growth of elkhorn sea moss (
Kappaphycus alvarezii
) was evaluated in three plots with 200 propagules during a period of 70 days in a floating raft system covered by a fishing net underneath. Initial weight of propagules was 159.3 ± 12.74 g in wet biomass and 15.3 ± 1.43 g in dry biomass and were sampled up to 19 days (in the lag growth phase; period I), up to 33 days (in the exponential growth phase; period II) and up to 70 days (in the stationarity growth phase; period III). The variations of sea surface water temperature, salinity, turbidity (Secchi depth), total ammonium, nitrites, nitrates, and phosphate were determined. The growth increase was more evident in the exponential phase II when a dry biomass of 28.0 ± 2.48 (1153.3 ± 6.25 g in wet mass) was reached, more than 7 times the biomass of propagules with an average daily growth rate of 15.2% g.day
–1
. The carrying capacity of the zone was estimated at 86.2% in the area where 53 cultivation units would be projected. The economic analysis presented a financial feasibility with a net profit of 19% over the projected income and an IRR of 16.5%, recovering the investment in an estimated period of 4.3 years. We recommend to continue with larger-scale studies to optimize the cultivation of
K. alvarezii
in the study area.
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