Systematic assessment of long-read RNA-seq methods for transcript identification and quantification

The Long-read RNA-Seq Genome Annotation Assessment Project (LRGASP) Consortium was formed to evaluate the effectiveness of long-read approaches for transcriptome analysis. The consortium generated over 427 million long-read sequences from cDNA and direct RNA datasets, encompassing human, mouse, and manatee species, using different protocols and sequencing platforms. These data were utilized by developers to address challenges in transcript isoform detection and quantification, as well as de novo transcript isoform identification. The study revealed that libraries with longer, more accurate sequences produce more accurate transcripts than those with increased read depth, whereas greater read depth improved quantification accuracy. In well-annotated genomes, tools based on reference sequences demonstrated the best performance. When aiming to detect rare and novel transcripts or when using reference-free approaches, incorporating additional orthogonal data and replicate samples are advised. This collaborative study offers a benchmark for current practices and provides direction for future method development in transcriptome analysis.

Chronic exposure to glyphosate in Florida manatee

Florida manatees depend on freshwater environments as a source of drinking water and as warm-water refuges. These freshwater environments are in direct contact with human activities where glyphosate-based herbicides are being used. Glyphosate is the most used herbicide worldwide and it is intensively used in Florida as a sugarcane ripener and to control invasive aquatic plants. The objective of the present study was to determine the concentration of glyphosate and its breakdown product, aminomethylphosphonic acid (AMPA), in Florida manatee plasma and assess their exposure to manatees seeking a warm-water refuge in Crystal River (west central Florida), and in South Florida. We analyzed glyphosate's and AMPA's concentrations in Florida manatee plasma (n = 105) collected during 2009-2019 using HPLC-MS/MS. We sampled eight Florida water bodies between 2019 and 2020, three times a year: before, during and after the sugarcane harvest using grab samples and molecular imprinted passive Polar Organic Chemical Integrative Samplers (MIP-POCIS). Glyphosate was present in 55.8% of the sampled Florida manatees' plasma. The concentration of glyphosate has significantly increased in Florida manatee samples from 2009 until 2019. Glyphosate and AMPA were ubiquitous in water bodies. The concentration of glyphosate and AMPA was higher in South Florida than in Crystal River, particularly before and during the sugarcane harvest when Florida manatees depend on warm water refuges. Based on our results, Florida manatees were chronically exposed to glyphosate and AMPA, during and beyond the glyphosate applications to sugarcane, possibly associated with multiple uses of glyphosate-based herbicides for other crops or to control aquatic weeds. This chronic exposure in Florida water bodies may have consequences for Florida manatees' immune and renal systems which may further be compounded by other environmental exposures such as red tide or cold stress.

Historic variation of trace elements in pinnipeds with spatially segregated trophic habits reveals differences in exposure to pollution

Marine mammals and the ecological functions they provide to coastal and pelagic ecosystems are increasingly threatened by the intensification of anthropogenic impacts. The Uruguayan coastline throughout the 20th century, like other coastal environments worldwide, has been the sink of a variety of trace metals derived from the rapid urbanization and industrialization of related land areas. This coastline is inhabited by two species of pinnipeds trophically and spatially segregated. Otaria byronia feeds in coastal environments while Arctocephalus australis preys mainly offshore. The present study aimed to analyze historic changes in concentrations of trace elements in teeth of both species from 1941 to the present day. We analyzed the dentin of 94 canine teeth using stable isotope analysis (δ¹³C) and ICP-MS to determine their feeding areas and the concentration of 10 trace elements (Al, As, Cd, Cr, Cu, Fe, Mn, Ni, Pb, and Zn) respectively. The concentration of Cr was significantly higher during '70-'80s, in both species coinciding with tannery industry development. Both species of pinnipeds have been differentially exposed to trace elements depending on their feeding area. A pelagic diet, possibly based on squid, increased the concentration of Cd in A. australis, while O. byronia has been more exposed to anthropogenic Pb and Cu associated to a costal and more benthic diet. Our results highlight dentin as a reliable matrix for historic studies on the exposure to trace elements. In light of our results, the O. byronia's declining population could be the result of the synergistic effects of trace elements together with other ecological pressures faced in their environment.

Antineoplastic Agents: Environmental Prevalence and Adverse Outcomes in Aquatic Organisms

Cancer is the second leading cause of death worldwide, with 9.6 million cancer-related deaths in 2018. Cancer incidence has increased over time, and so has the prescription rate of chemotherapeutic drugs. These pharmaceuticals, known as antineoplastic agents, enter the aquatic environment via human excretion and wastewater. The objectives of the present critical review were to investigate the risk of antineoplastics to aquatic species and to summarize the current state of knowledge regarding their levels in the environment, because many antineoplastics are not adequately removed during wastewater treatment. We conducted 2 separate literature reviews to synthesize data on the global environmental prevalence and toxicity of antineoplastics. The antineoplastics most frequently detected in the environment included cyclophosphamide, ifosfamide, tamoxifen, methotrexate, and 5-fluorouracil; all were detectable in multiple water sources, including effluent and surface waters. These antineoplastics span 3 different mechanistic classes, with cyclophosphamide and ifosfamide classified as alkylating agents, tamoxifen as a hormonal agent, and methotrexate and 5-fluorouracil as antimetabolites. Studies that characterize the risk of antineoplastics released into aquatic environments are scarce. We summarize the biological impacts of the most environmentally prevalent antineoplastics on aquatic organisms and propose an adverse outcome pathway for cyclophosphamide and ifosfamide, 2 widely prescribed drugs with a similar immunotoxic mode of action. Acute and chronic ecotoxicity studies using aquatic models are needed for risk characterization of antineoplastics. Environ Toxicol Chem 2020;39:967-985. © 2020 SETAC.

A historical perspective of niche differentiation between two top predators in the Uruguayan coastal area

Context As top predators, marine mammals play a key role consuming in different trophic levels and the trophic niche characterization may help to understand how species utilize and share resources . On the coast of the Río de la Plata and the South-west Atlantic, the South American sea lion (Otaria flavescens) and the franciscana dolphin (Pontoporia blainvillei) are two important predators. Aims The present study investigated potential trophic overlap of both species by measuring stable carbon (δ13C) and nitrogen (δ15N) isotopes over two periods: historical (1959–79) and recent (2002–15) on the Uruguayan coast. Methods Bone samples of P. blainvillei and O. flavescens were used to determine the isotopic niche using the Stable Isotope Bayesian Ellipses in R (SIBER) analysis. Key results The isotopic niche did not overlap between species in any period. δ15N was higher in O. flavescens in both periods (20.29‰±0.73 in the historical and 19.95‰±1.0 in the recent period), indicating that it feeds at a higher trophic level than P. blainvillei. The δ13C was also significantly higher in O. flavescens than in P. blainvillei during the two periods (O. flavescens: –11.43±0.6‰ historic, –12.72±0.4‰ recent, and P. blainvillei: –12.69±1.1‰ historic, –13.84±1.3‰ recent). The isotopic niche areas of P. blainvillei in recent and historic periods confirmed they forage in 2 distinct environments, marine and estuarine, with low isotopic overlap. This overlap was higher in the recent period. Conclusions and Implications O. flavescens and both P. blainvillei groups were segregated in both periods, with a higher overlap in the recent. These species appear to reduce competition by using different resources in the same coastal habitat. O. flavescens preferentially feeds on benthic fish and showed wider trophic amplitude in both periods, whereas P. blainvillei has a more coastal–pelagic diet and included a greater variability of resources in its diet. The differences between species trophic niches can still be detected after both marine mammals species abundance has declined and after the development of fisheries.