Food for all: designing sustainable and secure future seafood systems.

Food from the sea can make a larger contribution to healthy and sustainable diets, and to addressing hunger and malnutrition, through improvements in production, distribution and equitable access to wild harvest and mariculture resources and products. The supply and consumption of seafood is influenced by a range of 'drivers' including ecosystem change and ocean regulation, the influence of corporations and evolving consumer demand, as well as the growing focus on the importance of seafood for meeting nutritional needs. These drivers need to be examined in a holistic way to develop an informed understanding of the needs, potential impacts and solutions that align seafood production and consumption with relevant 2030 Sustainable Development Goals (SDGs). This paper uses an evidence-based narrative approach to examine how the anticipated global trends for seafood might be experienced by people in different social, geographical and economic situations over the next ten years. Key drivers influencing seafood within the global food system are identified and used to construct a future scenario based on our current trajectory (Business-as-usual 2030). Descriptive pathways and actions are then presented for a more sustainable future scenario that strives towards achieving the SDGs as far as technically possible (More sustainable 2030). Prioritising actions that not only sustainably produce more seafood, but consider aspects of access and utilisation, particularly for people affected by food insecurity and malnutrition, is an essential part of designing sustainable and secure future seafood systems. Supplementary Information: The online version contains supplementary material available at 10.1007/s11160-021-09663-x.

Complementary Metagenomic Approaches Improve Reconstruction of Microbial Diversity in a Forest Soil.

Soil ecosystems harbor diverse microorganisms and yet remain only partially characterized as neither single-cell sequencing nor whole-community sequencing offers a complete picture of these complex communities. Thus, the genetic and metabolic potential of this "uncultivated majority" remains underexplored. To address these challenges, we applied a pooled-cell-sorting-based mini-metagenomics approach and compared the results to bulk metagenomics. Informatic binning of these data produced 200 mini-metagenome assembled genomes (sorted-MAGs) and 29 bulk metagenome assembled genomes (MAGs). The sorted and bulk MAGs increased the known phylogenetic diversity of soil taxa by 7.2% with respect to the Joint Genome Institute IMG/M database and showed clade-specific sequence recruitment patterns across diverse terrestrial soil metagenomes. Additionally, sorted-MAGs expanded the rare biosphere not captured through MAGs from bulk sequences, exemplified through phylogenetic and functional analyses of members of the phylum Bacteroidetes Analysis of 67 Bacteroidetes sorted-MAGs showed conserved patterns of carbon metabolism across four clades. These results indicate that mini-metagenomics enables genome-resolved investigation of predicted metabolism and demonstrates the utility of combining metagenomics methods to tap into the diversity of heterogeneous microbial assemblages.IMPORTANCE Microbial ecologists have historically used cultivation-based approaches as well as amplicon sequencing and shotgun metagenomics to characterize microbial diversity in soil. However, challenges persist in the study of microbial diversity, including the recalcitrance of the majority of microorganisms to laboratory cultivation and limited sequence assembly from highly complex samples. The uncultivated majority thus remains a reservoir of untapped genetic diversity. To address some of the challenges associated with bulk metagenomics as well as low throughput of single-cell genomics, we applied flow cytometry-enabled mini-metagenomics to capture expanded microbial diversity from forest soil and compare it to soil bulk metagenomics. Our resulting data from this pooled-cell sorting approach combined with bulk metagenomics revealed increased phylogenetic diversity through novel soil taxa and rare biosphere members. In-depth analysis of genomes within the highly represented Bacteroidetes phylum provided insights into conserved and clade-specific patterns of carbon metabolism.

Impact of a sports project centered on scuba diving for adolescents with type 1 diabetes mellitus: New guidelines for adolescent recreational diving, a modification of the French regulations.

BACKGROUND: Recreational scuba diving has been authorized for type 1 diabetics over 18 years old - the age of majority in France - since 2004, but it remained forbidden for younger diabetics by the French underwater federation (FFESSM). Here, we present a study to evaluate: - the conditions under which diving could be authorized for 14- to 18 year olds with type 1 diabetes; - the value of continuous glucose monitoring (CGM) while diving. A secondary objective was to monitor the impact of diving on the teenagers' quality of life. SUBJECT AND METHODS: Sixteen adolescents (14-17.5 years old) were included. Diabetes was known for 6 years (range, 1-14) and Hb1Ac was 9.0% (range, 7.7-11.9). The study was conducted in Mayotte with both capillary glycemia (CG) and CGM measurements taken during five dives. RESULTS: The average CG prior to diving was 283mg/dL and decreased by 75±76mg/dL during the dive. No hypoglycemia occurred during the dives and four episodes occurred after. Glycemia variations during dives and for the overall duration of the study were greater than for adults, most likely due to the general adolescent behavior, notably regarding diet and diabetes management. CGM was greatly appreciated by the adolescents. They had an overall satisfactory quality of life. No significant variations were observed during the entire course of the study. CONCLUSIONS: Although in need of further studies, these preliminary results show that CGM can be used while diving. CGM records show a continuous decrease of glycemia during dives. Based on these results, the French underwater federation has now authorized diving for adolescent type 1 diabetics following a specific diving protocol that includes HbA1c<8.5%, autonomous management of diabetes by the adolescent, reduction of insulin doses, and target glycemia prior to the dive>250mg/dL.

Using an integral projection model to assess the effect of temperature on the growth of gilthead seabream Sparus aurata.

Accurate information on the growth rates of fish is crucial for fisheries stock assessment and management. Empirical life history parameters (von Bertalanffy growth) are widely fitted to cross-sectional size-at-age data sampled from fish populations. This method often assumes that environmental factors affecting growth remain constant over time. The current study utilized longitudinal life history information contained in otoliths from 412 juveniles and adults of gilthead seabream, Sparus aurata, a commercially important species fished and farmed throughout the Mediterranean. Historical annual growth rates over 11 consecutive years (2002-2012) in the Gulf of Lions (NW Mediterranean) were reconstructed to investigate the effect of temperature variations on the annual growth of this fish. S. aurata growth was modelled linearly as the relationship between otolith size at year t against otolith size at the previous year t-1. The effect of temperature on growth was modelled with linear mixed effects models and a simplified linear model to be implemented in a cohort Integral Projection Model (cIPM). The cIPM was used to project S. aurata growth, year to year, under different temperature scenarios. Our results determined current increasing summer temperatures to have a negative effect on S. aurata annual growth in the Gulf of Lions. They suggest that global warming already has and will further have a significant impact on S. aurata size-at-age, with important implications for age-structured stock assessments and reference points used in fisheries.

Gene transfer into the fetal primate: evidence for the secretion of transgene product.

In utero adenoviral-mediated transfer of genes via the amniotic fluid results in sustained high-efficiency expression in rodent lung and intestine. Rhesus macaque (Macaca mulatta) fetuses were injected with adenovirus vectors encoding reporter genes at different gestational ages to evaluate feasibility and timing in primates. The fetuses developed normally following gene transfer and no maternal adverse affects were noted. Highly efficient viral uptake and transgene protein expression occurred in the target organs. The lungs exhibited no immune response and transgenic protein was observed up to 30 days postinfection. Unexpectedly, large amounts of reporter gene protein were released, apparently from the lung, into the circulation and accumulated in the renal proximal tubules and bladder. PCR detection for adenovirus DNA was consistently negative in tissues not in contact with the amniotic fluid, such as kidneys, liver, gonads, and eyes. Treatment of primate fetuses at 110 days gestation with an adenovirus expressing the cystic fibrosis transmembrane conductance regulator (cftr) gene resulted in accelerated differentiation of the lung. These studies demonstrate the efficacy of in utero gene therapy in primates and its potential application to genetic diseases.

Organellar genes: why do they end up in the nucleus?

Many mitochondrial and plastid proteins are derived from their bacterial endosymbiotic ancestors, but their genes now reside on nuclear chromosomes instead of remaining within the organelle. To become an active nuclear gene and return to the organelle as a functional protein, an organellar gene must first be assimilated into the nuclear genome. The gene must then be transcribed and acquire a transit sequence for targeting the protein back to the organelle. On reaching the organelle, the protein must be properly folded and modified, and in many cases assembled in an orderly manner into a larger protein complex. Finally, the nuclear copy must be properly regulated to achieve a fitness level comparable with the organellar gene. Given the complexity in establishing a nuclear copy, why do organellar genes end up in the nucleus? Recent data suggest that these genes are worse off than their nuclear and free-living counterparts because of a reduction in the efficiency of natural selection, but do these population-genetic processes drive the movement of genes to the nucleus? We are now at a stage where we can begin to discriminate between competing hypotheses using a combination of experimental, natural population, bioinformatic and theoretical approaches.

A method of video-assisted thoracoscopic surgery for collection of thymic biopsies in rhesus monkeys (Macaca mulatta).

To support an infectious disease study, we developed a surgical procedure to collect serial thymic biopsies in rhesus monkeys (Macaca mulatta). In many instances in which thymic tissue is required from living animals, open surgical approaches (thoracotomies) are used, which result in greater postoperative pain and longer recovery periods than those associated with thoracoscopic procedures. Our intent was to develop a surgical procedure that allowed serial biopsy of the thymus with minimal surgical morbidity. We modified a previously published experimental method of thoracoscopic total thymectomy in the dog to collect thymic biopsies in M. mulatta. Of the 15 animals evaluated, 8 underwent two biopsy procedures separated by a 5- to 6-week interoperative interval. The other seven animals underwent a single biopsy procedure. Thymic tissue was collected successfully during all procedures, with an average surgical time of 15 min. No significant intra- or postoperative complications were noted, and the animals recoveries from the surgical procedures were uneventful. Minimally invasive thoracoscopic surgical techniques can be used successfully to collect thymic tissue from adult and juvenile rhesus monkeys with minimal surgical morbidity.

Generation of an Ugi library of phosphate mimic-containing compounds and identification of novel dual specific phosphatase inhibitors.

The four-component Ugi reaction was utilized to prepare a library of dipeptidic compounds in order to explore the binding requirements of the key cell cycle phosphatase, Cdc25. Several phosphate surrogates were incorporated into the Ugi product to mimic either the mono- or bis-phosphorylated substrate.

Dysidiolide and related gamma-hydroxy butenolide compounds as inhibitors of the protein tyrosine phosphatase, CDC25.

Synthetic dysidiolide, as well as several related compounds containing a gamma-hydroxybutenolide moiety, were tested in in vitro Cdc25 assays against both synthetic and natural substrates. Contrary to literature values which are in the low micromolar range, we observe only millimolar inhibitory activity for these compounds versus Cdc25 phosphatase.

The non-photosynthetic plastid in malarial parasites and other apicomplexans is derived from outside the green plastid lineage.

The discovery of a non-photosynthetic plastid genome in Plasmodium falciparum and other apicomplexans has provided a new drug target, but the evolutionary origin of the plastid has been muddled by the lack of characters, that typically define major plastid lineages. To clarify the ancestry of the plastid, we undertook a comprehensive analysis of all genomic characters shared by completely sequenced plastid genomes. Cladistic analysis of the pattern of plastid gene loss and gene rearrangements suggests that the apicomplexan plastid is derived from an ancestor outside of the green plastid lineage. Phylogenetic analysis of primary sequence data (DNA and amino acid characters) produces results that are generally independent of the analytical method, but similar genes (i.e., rpoB and rpoC) give similar topologies. The conflicting phylogenies in primary sequence data sets make it difficult to determine the the exact origin of the apicomplexan plastid and the apparent artifactual association of apicomplexan and euglenoid sequences suggests that DNA sequence data may be an inappropriate set of characters to address this phylogenetic question. At present we cannot reject our null hypothesis that the apicomplexan plastid is derived from a shared common ancestor between apicomplexans and dinoflagellates. During the analysis, we noticed that the Plasmodium tRNA-Met is probably tRNA-fMet and the tRNA-fMet is probably tRNA-Ile. We suggest that P. falciparum has lost the elongator type tRNA-Met and that similar to metazoan mitochondria there is only one species of methionine tRNA. In P. falciparum, this has been accomplished by recruiting the fMet-type tRNA to dually function in initiation and elongation. The tRNA-Ile has an unusual stem-loop in the variable region. The insertion in this region appears to have occurred after the primary origin of the plastid and further supports the monophyletic ancestory of plastids.

Diminishing returns from mutation supply rate in asexual populations.

Mutator genotypes with increased mutation rates may be especially important in microbial evolution if genetic adaptation is generally limited by the supply of mutations. In experimental populations of the bacterium Escherichia coli, the rate of evolutionary adaptation was proportional to the mutation supply rate only in particular circumstances of small or initially well-adapted populations. These experiments also demonstrate a "speed limit" on adaptive evolution in asexual populations, one that is independent of the mutation supply rate.

Clinical outcome of a protocol to produce immunosuppression in rhesus monkeys (Macaca mulatta): application to infectious disease and gene therapy studies.

Induced immunosuppression is required for a number of studies using rhesus monkeys (Macaca mulatta). This report describes the clinical outcome and safety of a dose-finding experiment that determined doses of cyclophosphamide and prednisone that could be used to induce a state of immunosuppression in rhesus monkeys. After determining the optimum dose of immunosuppressive agents, the protocol was then used on animals participating in infectious disease and gene therapy studies. Splenectomy was performed in some animals to increase the severity of immunosuppression. The onset, duration, and severity of lymphopenia and leukopenia were consistent in all animals. In most animals, physical examination findings and clinical serum chemistry profiles demonstrated only transient abnormalities. With proper clinical monitoring, combination treatment with cyclophosphamide and prednisone is an effective and safe method for inducing immunosuppression in rhesus monkeys.

Experimental leprosy in rhesus monkeys: transmission, susceptibility, clinical and immunological findings.

A total of 46 Rhesus monkeys (RM) was inoculated with Mycobacterium leprae (ML) and followed clinically and immunologically for extended periods. Twenty-one (45.7%) of the RM developed leprosy spanning the known leprosy spectrum, with six of 21 (28.6%) having disease in the borderline lepromatous to lepromatous area of the spectrum. RM with paucibacillary forms of leprosy produced predominantly IgG anti-phenolic glycolipid (PGL-I) antibodies and positive lepromin skin test and/or in vitro blastogenesis responses; IgM anti-PGL-I predominated in animals with BB-LL leprosy and correlated with negative immune responses to lepromin. IgG anti-PGL-I antibodies persisted in a number of RM for several years without histopathological evidence of leprosy, suggesting possible persisting subclinical infection. The data show that RM are a valuable model for the study of leprosy. Eleven of the 46 RM were inoculated with ML from sources infected with simian immunodeficiency virus (SIV), the monkey counterpart to the human immunodeficiency virus (HIV). The possible effect of SIV on the clinical outcome of ML infection could not be determined due to insufficient numbers of animals to yield statistically significant results.

Deleterious mutation accumulation in organelle genomes.

It is well established on theoretical grounds that the accumulation of mildly deleterious mutations in nonrecombining genomes is a major extinction risk in obligately asexual populations. Sexual populations can also incur mutational deterioration in genomic regions that experience little or no recombination, i.e., autosomal regions near centromeres, Y chromosomes, and organelle genomes. Our results suggest, for a wide array of genes (transfer RNAs, ribosomal RNAs, and proteins) in a diverse collection of species (animals, plants, and fungi), an almost universal increase in the fixation probabilities of mildly deleterious mutations arising in mitochondrial and chloroplast genomes relative to those arising in the recombining nuclear genome. This enhanced width of the selective sieve in organelle genomes does not appear to be a consequence of relaxed selection, but can be explained by the decline in the efficiency of selection that results from the reduction of effective population size induced by uniparental inheritance. Because of the very low mutation rates of organelle genomes (on the order of 10(-4) per genome per year), the reduction in fitness resulting from mutation accumulation in such genomes is a very long-term process, not likely to imperil many species on time scales of less than a million years, but perhaps playing some role in phylogenetic lineage sorting on time scales of 10 to 100 million years.

Histopathological, lymphoscintigraphical, and immunological changes in the inguinal lymph nodes of rhesus monkeys during the early course of infection with Brugia malayi.

The relationship of the early lymphatic pathophysiological alterations with those of tissue inflammatory and cellular responses in the inguinal lymph nodes of Brugia malayi-infected rhesus monkeys was examined. Each of five animals was inoculated subcutaneously in the right calf with 200 third stage larvae (L3) and 5 weeks later, before the onset of patency [10 to 12 weeks postinoculation (PI)], their right inguinal nodes began to show signs of enlargement, becoming most prominent between weeks 10 to 16 PI. Histopathologically, the right nodes had eosinophilic lymphadenitis, lymphoid hyperplasia, and pronounced germinal centers. Lymphoscintigraphy using 99mTc-antimony trisulfide colloid showed pathophysiological alterations of the lymph flow rate in the right leg but not in the left leg at weeks 7 and 15 PI. In vitro blastogenesis to B. malayi antigens at week 10 PI showed the inguinal lymph node cells proliferated more vigorously than did peripheral blood cells early in infection. However, at week 24 PI both lymph node and peripheral blood cells proliferated to antigens. Flow cytometry showed an upregulation of HLA-DR+ lymphocytes in right lymph node cells from infected animals when compared to those from control animals. No changes in CD2, CD4, CD8, CD20, CD29, and CD45R cell numbers in lymph node of infected animals were seen when compared to control animals. Our results show that lymphatic pathology occurs early before the onset of patency, correlating with a marked tissue inflammatory and cellular responses of lymph node cells in B. malayi-infected rhesus monkeys. The rhesus could be an extremely useful model for understanding the evolution of pathology and pathogenesis of the disease.

Polymyositis, arthritis, and uveitis in a macaque experimentally infected with human T lymphotropic virus type I.

OBJECTIVE: To establish a simian model of human T lymphotropic virus type I (HTLV-I) infection and disease. METHODS: Irradiated HTLV-I-producing cells were used to infect two 2-year-old rhesus macaque monkeys (Macaca mulatta). One monkey was also simultaneously inoculated with a cell-free suspension of simian immunodeficiency virus (SIV). Evidence of infection was monitored by serial clinical examinations and by serologic, molecular, and virologic assays. RESULTS: Both HTLV-I-inoculated monkeys became persistently infected following inoculation. Clinical disease was observed in the singly inoculated monkey, which developed arthritis (with synovial fluid positive for HTLV-I by culture and polymerase chain reaction), anterior chamber uveitis, and steroid-responsive polymyositis confirmed by electrophysiologic studies. The dually inoculated animal remained clinically healthy, despite high levels of SIV and HTLV-I virus expression and loss of HTLV-I-specific antibodies. CONCLUSION: These results indicate the utility of a nonhuman primate model for studying HTLV-I disease pathogenesis and the dynamics of SIV-1/HTLV-I retroviral coinfection.

Mitochondrial DNA migration events in yeast and humans: integration by a common end-joining mechanism and alternative perspectives on nucleotide substitution patterns.

In contrast to extensive infiltration of plant nuclear genomes by mitochondrial and chloroplast DNA fragments, a computer assessment method could only detect seven mitochondrial DNA integration events in Saccharomyces cerevisiae chromosomes and five examples of DNA migration into mammalian nuclear genes. No evidence could be detected for mitochondrial DNA insertion into chromosome III of Caenorhabditis elegans or in nuclear DNA sequences of Drosophila sp. or Plasmodium falciparum. Thus, the quantity of organellar DNA in the nucleus appears to vary amongst organisms and is lower in Saccharomyces cerevisiae than suggested by experimental plasmid systems. As in plants, migratory mitochondrial DNA fragments in yeast and mammals are found in intergenic regions and introns. Although many of these insertions are located near retroelements, mitochondrial DNA incorporation appears to be independent of retroelement insertion. Comparison of the mitochondrial DNA fragments with mitochondrial transcription maps suggest that two fragments may have transposed through DNA-based and one through RNA-based mechanisms. Analyses of the integration sites indicate that organellar DNA sequences are incorporated by an end-joining mechanism common to yeast, mammals, and plants. The transferred sequences also provide a novel perspective on rates and patterns of nucleotide substitution. Analysis of the D-loop region including a nuclear copy of mitochondrial DNA supports a progressive reduction in D-loop length within both monkey and great apes mitochondrial lineages. Relative distance tests polarized with nuclear copies of the mitochondrial 12S/16S rRNA region suggest that a constant number of transversions has accumulated within the great ape clade, but the number of transitions in orangutan is elevated with respect to members of the human/chimp/gorilla clade. In addition to DNA migration events, 29 nuclear/mitochondrial genes were identified in GenBank that appear to result from inadvertent ligation of nuclear and mitochondrial mRNA transcripts during the cloning process.

Pervasive migration of organellar DNA to the nucleus in plants.

A surprisingly large number of plant nuclear DNA sequences inferred to be remnants of chloroplast and mitochondrial DNA migration events were detected through computer-assisted database searches. Nineteen independent organellar DNA insertions, with a median size of 117 bp (range of 38 to > 785 bp), occur in the proximity of 15 nuclear genes. One fragment appears to have been passed through a RNA intermediate, based on the presence of an edited version of the mitochondrial gene in the nucleus. Tandemly arranged fragments from disparate regions of organellar genomes and from different organellar genomes indicate that the fragments joined together from an intracellular pool of RNA and/or DNA before they integrated into the nuclear genome. Comparisons of integrated sequences to genes lacking the insertions, as well as the occurrence of coligated fragments, support a model of random integration by end joining. All transferred sequences were found in noncoding regions, but the positioning of organellar-derived DNA in introns, as well as regions 5' and 3' to nuclear genes, suggests that the random integration of organellar DNA has the potential to influence gene expression patterns. A semiquantitative estimate was performed on the amount of organellar DNA being transferred and assimilated into the nucleus. Based on this database survey, we estimate that 3-7% of the plant nuclear genomic sequence files contain organellar-derived DNA. The timing and the magnitude of genetic flux to the nuclear genome suggest that random integration is a substantial and ongoing process for creating sequence variation.

Immunogenicity of the recombinant serine rich Entamoeba histolytica protein (SREHP) amebiasis vaccine in the African green monkey.

We report the first study in non-human primates of the safety and immunogenicity of a recombinant vaccine designed to prevent amebic liver abscess. In a pilot study, a recombinant vaccine containing the serine rich Entamoeba histolytica protein (SREHP) attached to a maltose binding protein (SREHP/MBP), which has been shown to be effective in preventing amebic liver abscess in rodent models of infection, was used to immunize two African Green Monkeys. Vaccination with SREHP/MBP resulted in no systemic side-effects. The monkeys receiving the SREHP/MBP protein developed antibodies that recognized the recombinant SREHP/MBP molecule, the native SREHP protein, and the surface of amebic trophozoites. Antiserum from SREHP/MBP-vaccinated monkeys could block the adhesion of E. histolytica trophozoites to mammalian cells, a feature that may correlate with vaccine efficacy. Attempts to produce amebic liver abscess in naive African Green Monkeys by direct hepatic inoculation with virulent E. histolytica trophozoites was not successful, suggesting this species is probably not suitable for vaccine efficacy studies.