Characterisation of two members of a macroschizont gene family, Tashat1 and Tashat2, from Theileria annulata

Theileria annulata is a protozoan parasite of cattle, that causes the disease tropical theileriosis throughout sub-tropical regions of the Old World. Theileria parasites have the ability to immortalise the host leukocyte they infect causing clonal expansion and dissemination of infected leukocytes throughout the host. This property has allowed the development of an in vitro system for the culture of bovine cells infected by the macroschizont stage of the parasite. In addition, differentiation of the parasite towards the next life cycle stage, the merozoite, can be induced in culture. The signals that cause the macroschizont to differentiate into merozoites are not fully understood, although it is known that this event is associated with a major elevation in merozoite gene expression (Shiels et al., 1994). Recently a small family of parasite genes that are negatively regulated early during differentiation to the merozoite were identified. One member, known as TashAT2 contained predicted AT hook DNA binding motifs and was shown to be localised to the host cell nucleus. It has been postulated that the TashAT2 polypeptide may play a role in the regulation of macroschizont or modulation of host cell gene expression (Swan et al., 1999). The focus of this project was to characterise TashAT1, a second member of the TashAT gene family. To this end, the TashAT1 gene was sub-cloned and sequenced and mapped to a region of the genome containing TashAT2 and a third Task AT gene, TashAT3. The 1.4kb open reading frame of TashAT1 was virtually identical to the five prime end of TashAT3, indicating that TashAT1 or TashAT3 (TashAT1/3) were derived from a recent duplication event. The predicted amino acid sequence of TashAT1/3 contained four AT hook motifs, a nuclear localisation signal and a signal sequence. Northern blot analysis revealed that TashAT1, TashAT2 and TashAT3 mRNA were down regulated early, during differentiation to the merozoite in vitro. However, no down regulation was observed for any of the TashAT transcripts in a cell line that was severely attenuated with respect to parasite differentiation. Sequence analysis of the upstream regions of TashAT1/3 identified a motif element (TashUM) located 43bp upstream of the putative transcription start site of TashAT1/3 that was highly related to a sequence upstream of TashAT1 and another, unrelated macroschizont gene, Tash1. Preliminary electromobility band shift analysis of TashUM revealed that it bound to a factor found in host and parasite enriched nuclear extract, which appeared to decrease in abundance as the parasite differentiated towards merogony. Antisera generated against a region of TashAT1 failed to recognise a TashAT1 polypeptide by Western blot analysis. However, a 180kDa polypeptide that was down regulated with respect to merogony and co-localised to the host nucleus was specifically recognised. The detected polypeptide was identified as TashAT3 on the basis of size, sequence identity and predicted expression profile. Immunofluorescence analysis showed that the anti-TashAT1 antisera reacted against both the host nucleus and parasite. This reactivity was lost as the parasite differentiated to the merozoite. The host reactivity was probably due to recognition of TashAT3, while it could not be concluded that the parasite reactivity was directed against TashAT1. Taken together, the results indicated that TashAT3 and possibly TashAT1 are additional candidates for parasite encoded factors that are translocated to the host nucleus, bind to DNA and alter host cell gene expression. This modulation of gene expression could directly or indirectly alter the phenotype of the host cell and be involved in parasite dependent regulation of leukocyte cell division

The Continuous Plankton Recorder survey: how can long-term phytoplankton datasets contribute to the assessment of Good Environmental Status?

Phytoplankton are crucial to marine ecosystem functioning and are important indicators of environmental change. Phytoplankton data are also essential for informing management and policy, particularly in supporting the new generation of marine legislative drivers, which take a holistic ecosystem approach to management. The Marine Strategy Framework Directive (MSFD) seeks to achieve Good Environmental Status (GES) of European seas through the implementation of such a management approach. This is a regional scale directive which recognises the importance of plankton communities in marine ecosystems; plankton data at the appropriate spatial, temporal and taxonomic scales are therefore required for implementation. The Continuous Plankton Recorder (CPR) survey is a multidecadal, North Atlantic–basin scale programme which routinely records approximately 300 phytoplankton taxa. Because of these attributes, the survey plays a key role in the implementation of the MSFD and the assessment of GES in the Northeast Atlantic region. This paper addresses the role of the CPR's phytoplankton time-series in delivering GES through the development and informing of MSFD indicators, the setting of targets against a background of climate change and the provision of supporting information used to interpret change in non-plankton indicators. We also discuss CPR data in the context of other phytoplankton data types that may contribute to GES, as well as explore future possibilities for the use of new and innovative applications of CPR phytoplankton datasets in delivering GES. Efforts must be made to preserve long-term time series, such as the CPR, which supply vital ecological information used to informed evidence-based environmental policy

mNCEA policy brief - Mind the Gap – The need to continue long-term plankton monitoring

This policy brief argues that while it is beneficial to explore novel plankton survey technology, it is essential that we also continue to maintain traditional long-term monitoring programmes to generate the necessary information to inform policy. Changes in plankton have important implications for the continued provision of ecosystem services, including supporting commercial fish stocks, carbon sequestration, and oxygen production. Such changes can only be detected by studying long-term, consistent plankton datasets which are needed to understand the pressures driving these changes and how we can manage them. Traditional long-term plankton monitoring relies on light microscopy to identify and count plankton taxa, with methods fully supported by national / international QA/QC standards and providing high quality trusted data. Novel technologies, including imaging and molecular methods, offer more efficient means of collecting some types of plankton data, filling targeted knowledge gaps left by traditional monitoring. However, these data are often semi-quantitative, lacking in QA/QC standards, and/or in taxonomic resolution. While these technologies are developed it remains critical to maintain the continuity of traditional plankton monitoring to inform policy assessments of important changes in biodiversity. Losing these time-series, many of which span multiple decades, would impair our ability to detect important change in pelagic habitats, as most changes cannot be detected from short-term data. This would also accelerate the loss of taxonomic expertise, already under threat globally, diminishing our UK skill-base. Novel technologies should be explored in parallel to traditional monitoring, as they can provide complementary data to support policy assessments and research, however, it is important that we do not attempt to replace traditional monitoring with new technology before it has been thoroughly integrated into long-term monitoring programmes. This project was funded by the Department for Environment, Food and Rural Affairs (Defra) as part of the marine arm of the Natural Capital and Ecosystem Assessment (NCEA) programme. The marine NCEA programme is leading the way in supporting Government ambition to integrate natural capital approaches into decision making for the marine environment. Find out more at https://www.gov.uk/government/publications/natural-capital-and-ecosystem-assessment-programme

From microscope to management: the critical value of plankton taxonomy to marine policy and biodiversity conservation

Taxonomic information provides a crucial understanding of the most basic component of biodiversity – which organisms are present in a region or ecosystem. Taxonomy, however, is a discipline in decline, at times perceived as ‘obsolete’ due to technical advances in science, and with fewer trained taxonomists and analysts emerging each year to replace the previous generation as it retires. Simultaneously, increasing focus is turned towards sustainable management of the marine environment using an ecosystem approach, and towards conserving biodiversity, key species, and habitats. Sensitive indicators derived from taxonomic data are instrumental to the successful delivery of these efforts. At the base of the marine food web and closely linked to their immediate environment, plankton are increasingly needed as indicators to support marine policy, inform conservation efforts for higher trophic organisms, and protect human health. Detailed taxonomic data, containing information on the presence/absence and abundance of individual plankton species, are required to underpin the development of sensitive species- and community-level indicators which are necessary to understand subtle changes in marine ecosystems and inform management and conservation efforts. Here the critical importance of plankton taxonomic data is illustrated, and therefore plankton taxonomic expertise, in informing marine policy and conservation and outline challenges, and potential solutions, facing this discipline

Mind the gap - The need to integrate novel plankton methods alongside ongoing long-term monitoring

Changes in plankton have important implications for ecosystem services, including supporting fish stocks, carbon sequestration, nutrient cycling, and oxygen production. Standard long-term plankton monitoring relies on light microscopy to identify and count plankton taxa, with methods fully supported by international standards, providing high quality trusted data. Novel methods, including imaging and molecular, offer means of collecting select types of plankton data efficiently, filling targeted knowledge gaps left by standard monitoring and generating a more complete picture of plankton dynamics. Standard and novel monitoring methods present different advantages and costs, positioning their suitability to address different management needs. Standard plankton monitoring time-series are unique in providing the long-term temporal coverage, and thus statistical power, needed to detect and understand climate change impacts. When explored in parallel with standard monitoring, novel methods open doors to observing our seas from complementary perspectives, but further work is necessary before data from standard and novel methods can be integrated to address policy needs. Marine management priorities are shifting, and novel methods are increasingly proposed as possible alternatives to standard monitoring. However, for a long-term taxonomic perspective it is still essential to retain the specialist skills and maintain standard monitoring time-series to inform policy assessments of important changes in pelagic biodiversity. This review aims to inform readers of the value of long-term data, the importance of retaining taxonomic skills and embracing novel methods for marine plankton monitoring to assess pelagic biodiversity. We recommend strategies to maintain long-term monitoring whilst incorporating novel methods

Molecular analyses of protists in long-term observation programmes—current status and future perspectives

Protists (microbial eukaryotes) are diverse, major components of marine ecosystems, and are fundamental to ecosystem services. In the last 10 years, molecular studies have highlighted substantial novel diversity in marine systems including sequences with no taxonomic context. At the same time, many known protists remain without a DNA identity. Since the majority of pelagic protists are too small to identify by light microscopy, most are neither comprehensively or regularly taken into account, particularly in Long-term Ecological Research Sites. This potentially undermines the quality of research and the accuracy of predictions about biological species shifts in a changing environment. The ICES Working Group for Phytoplankton and Microbial Ecology conducted a questionnaire survey in 2013–2014 on methods and identification of protists using molecular methods plus a literature review of protist molecular diversity studies. The results revealed an increased use of high-throughput sequencing methods and a recognition that sequence data enhance the overall datasets on protist species composition. However, we found only a few long-term molecular studies and noticed a lack of integration between microscopic and molecular methods. Here, we discuss and put forward recommendations to improve and make molecular methods more accessible to Long-term Ecological Research Site investigators

Report from the Annual Meeting of Expert Group Chairs (WGCHAIRS)

The Annual Meeting of ICES Expert Group Chairs (WGCHAIRS) provides an opportunity for chairs of all ICES working groups to share experiences and ideas, co-ordinate work, meet with their steering group, Advisory Committee and Science Committee chairs, and highlight any support they need from the ICES network. The group also provides participants with updates on developments in the network and their implications, as well as opportunities to identify future science priorities and plans for advisory products. This 2023 meeting report contains advice-related, science-related and cross-cutting issues. The meeting in 2023 included an extra day for incoming chairs, covering an introduction on the responsibilities for chairs, an introduction to the guidelines for ICES groups and a forum to express expectations and ask questions for the Chairs of the Advisory and Science Committees. The advice topics that were addressed include conservation aspects in advice, challenges and solutions for advice-based working groups, guidelines for Benchmarks, exploring reference points, the Transparent Assessment Framework (TAF), online advice, and the Workplan for 2023. The science topics that were addressed include how we can make ICES science more visible, implementing the Science Plan, the next steps for the Ecosystem-Based Management (EBM) Framework, and breakout groups for steering group chair interaction. Cross-cutting topics included an update on the action items from the WGCHAIRS meeting 2022, gender and inclusivity in ICES, the Code of Ethics and Professional Conduct, developing and implementing methods for the knowledge that flows into advice, ICES Publications and the new ICES library, update from Overviews including the data profiling tool and pipeline, and a presentation and exercise on the role of scientists in ICES, as an applied science organisation Key actions resulting from the meeting are: The Secretariat, ACOM and SCICOM chairs develop an outline for chairs’ training in dialogue with chairs. An additional meeting in 2023 is needed to discuss the future and next steps on Diversity, Equity, and Inclusion (DEI) implementation together with WGCHAIRS. Secretariat, ACOM and SCICOM to work on a communication strategy: what is a feasible and meaningful way of communication and how can we use it most efficiently are the main questions. Communication needs to be focused, separating the signal from the noise. What kind of impact does ICES want to make, and who are the target groups

Environmental Barcoding Reveals Massive Dinoflagellate Diversity in Marine Environments

Rowena F. Stern is with University of British Columbia, Ales Horak is with University of British Columbia, Rose L. Andrew is with University of British Columbia, Mary-Alice Coffroth is with State University of New York at Buffalo, Robert A. Andersen is with the Bigelow Laboratory for Ocean Sciences, Frithjof C. Küpper is with the Scottish Marine Institute, Ian Jameson is with CSIRO Marine and Atmospheric Research, Mona Hoppenrath is with the German Center for Marine Biodiversity Research, Benoît Véron is with University of Caen Lower Normandy and the National Institute for Environmental Studies, Fumai Kasai is with the National Institute for Environmental Studies, Jerry Brand is with UT Austin, Erick R. James is with University of British Columbia, Patrick J. Keeling is with University of British Columbia.Background -- Dinoflagellates are an ecologically important group of protists with important functions as primary producers, coral symbionts and in toxic red tides. Although widely studied, the natural diversity of dinoflagellates is not well known. DNA barcoding has been utilized successfully for many protist groups. We used this approach to systematically sample known “species”, as a reference to measure the natural diversity in three marine environments. Methodology/Principal Findings -- In this study, we assembled a large cytochrome c oxidase 1 (COI) barcode database from 8 public algal culture collections plus 3 private collections worldwide resulting in 336 individual barcodes linked to specific cultures. We demonstrate that COI can identify to the species level in 15 dinoflagellate genera, generally in agreement with existing species names. Exceptions were found in species belonging to genera that were generally already known to be taxonomically challenging, such as Alexandrium or Symbiodinium. Using this barcode database as a baseline for cultured dinoflagellate diversity, we investigated the natural diversity in three diverse marine environments (Northeast Pacific, Northwest Atlantic, and Caribbean), including an evaluation of single-cell barcoding to identify uncultivated groups. From all three environments, the great majority of barcodes were not represented by any known cultured dinoflagellate, and we also observed an explosion in the diversity of genera that previously contained a modest number of known species, belonging to Kareniaceae. In total, 91.5% of non-identical environmental barcodes represent distinct species, but only 51 out of 603 unique environmental barcodes could be linked to cultured species using a conservative cut-off based on distances between cultured species. Conclusions/Significance -- COI barcoding was successful in identifying species from 70% of cultured genera. When applied to environmental samples, it revealed a massive amount of natural diversity in dinoflagellates. This highlights the extent to which we underestimate microbial diversity in the environment.This project was funded by Genome Canada and the Canadian Barcode of Life Network. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.Biological Sciences, School o