Comparing environmental impacts of deep-seabed and land-based mining: A defensible framework

The crises of climate change and biodiversity loss are interlinked and must be addressed jointly. A proposed solution for reducing reliance on fossil fuels, and thus mitigating climate change, is the transition from conventional combustion-engine to electric vehicles. This transition currently requires additional mineral resources, such as nickel and cobalt used in car batteries, presently obtained from land-based mines. Most options to meet this demand are associated with some biodiversity loss. One proposal is to mine the deep seabed, a vast, relatively pristine and mostly unexplored region of our planet. Few comparisons of environmental impacts of solely expanding land-based mining versus extending mining to the deep seabed for the additional resources exist and for biodiversity only qualitative. Here, we present a framework that facilitates a holistic comparison of relative ecosystem impacts by mining, using empirical data from relevant environmental metrics. This framework (Environmental Impact Wheel) includes a suite of physicochemical and biological components, rather than a few selected metrics, surrogates, or proxies. It is modified from the "recovery wheel" presented in the International Standards for the Practice of Ecological Restoration to address impacts rather than recovery. The wheel includes six attributes (physical condition, community composition, structural diversity, ecosystem function, external exchanges and absence of threats). Each has 3-5 sub attributes, in turn measured with several indicators. The framework includes five steps: (1) identifying geographic scope; (2) identifying relevant spatiotemporal scales; (3) selecting relevant indicators for each sub-attribute; (4) aggregating changes in indicators to scores; and (5) generating Environmental Impact Wheels for targeted comparisons. To move forward comparisons of land-based with deep seabed mining, thresholds of the indicators that reflect the range in severity of environmental impacts are needed. Indicators should be based on clearly articulated environmental goals, with objectives and targets that are specific, measurable, achievable, relevant, and time bound.

Sexual dimorphism as a facilitator of worker caste evolution in ants

Ant societies are primarily composed of females, whereby labor is divided into reproductive, or queen, and non-reproductive, or worker, castes. Workers and reproductive queens can differ greatly in behavior, longevity, physiology, and morphology, but queen-worker differences are usually modest relative to the differences in males. Males are short-lived, typically do not provide the colony with labor, often look like a different species, and only occur seasonally. It is these differences that have historically led to their neglect in social insect research, but also why they may facilitate novel phenotypic variation - by increasing the phenotypic variability that is available for selection. In this study, worker variation in multivariate size-shape space paralleled male-queen variation. As worker variation increased within species, so did sexual variation. Across species in two independent genera, using head width as a proxy for body size, sexual size dimorphism correlated with worker polymorphism regardless of whether the ancestral condition was large or small worker/sexual dimorphism. Mounting molecular data support the hypothesis that queen-worker caste determination has co-opted many genes/pathways from sex determination. The molecular evidence, coupled with the observations from this study, leads to the hypothesis that sexual selection and selection on colony-level traits are non-independent, and that sexual dimorphism may even have facilitated the evolution of the distinct worker caste.

In Vivo Elongation Patterns of the Collateral Ligaments in Healthy Knees During Functional Activities

BACKGROUND

Improved knowledge of in vivo function of the collateral ligaments is essential for enhancing rehabilitation and guiding surgical reconstruction as well as soft-tissue balancing in total knee arthroplasty. The aim of this study was to quantify in vivo elongation patterns of the collateral ligaments throughout complete cycles of functional activities.

METHODS

Knee kinematics were measured using radiographic images captured with a mobile fluoroscope while healthy subjects performed level walking, downhill walking, and stair descent. The registered in vivo tibiofemoral kinematics were then used to drive subject-specific multibody knee models to track collateral ligament elongation.

RESULTS

The elongation patterns of the medial collateral ligament varied distinctly among its bundles, ranging from lengthening of the anterior fibers to shortening of the posterior bundle with increases in the knee flexion angle. The elongation patterns of the lateral collateral ligament varied considerably among subjects. It showed an average 4% shortening with increasing flexion until 60% to 70% of the gait cycle, and then recovered during the terminal-swing phase until reaching its reference length (defined at heel strike).

CONCLUSIONS

The observed nonuniform elongation of the medial collateral ligament bundles suggests that single-bundle reconstruction techniques may not fully restore healthy ligament function. Moreover, the observed ligament elongation patterns indicate greater varus than valgus laxity in the loaded knee.

CLINICAL RELEVANCE

Through providing key knowledge about the in vivo elongation patterns of the collateral ligaments throughout complete cycles of functional activities, this study offers in vivo evidence for benchmarking ligament reconstruction and soft-tissue balancing in total knee arthroplasty.

Comparison of LI-RADS with other non-invasive liver MRI criteria and radiological opinion for diagnosing hepatocellular carcinoma in cirrhotic livers using gadoxetic acid with histopathological explant correlation

AIM

To establish the diagnostic accuracy of the Liver Imaging Reporting and Data System (LI-RADS) for hepatocellular carcinoma (HCC) and compare its performance to that of international criteria from European Assofor the Study of the Liver (EASL), Japan Society of Hepatology (JSH), Asian Pacific Association for the Study of the Liver (APASL), and Organ Procurement and Transplantation Network (OPTN), and to the reporting radiologist's overall opinion regarding the probability of a nodule being a HCC by correlating with a histological diagnosis from whole liver explants.

MATERIALS AND METHODS

The present single-centre, retrospective review selected participants based on the following criteria: adults (≥18 years) listed for liver transplantation in 2014/2015, with liver cirrhosis at the time of magnetic resonance imaging (MRI) with hepatocyte specific contrast agent, and at least one liver lesion ≥10 mm on MRI with histology from subsequent liver explant for comparison. Each lesion was assessed against international criteria and given a "radiologist opinion" score of 1-5 (1 = definitely benign, 5 = definitely HCC).

RESULTS

Total 268 patient records were reviewed, with 105 eligible lesions identified from 47 patients. Median lesion size was 15.5 mm (range 10-68 mm). Sensitivity (%), specificity (%), and positive predictive value (PPV; %) for LI-RADS LR5 was 45, 89, and 89, for LI-RADS LR4+5 + TIV was 61, 80, and 86, for EASL was 44, 86 and 86, for JSH/APASL was 64, 81, and 87, for OPTN was 36, 90, and 88, and for "radiologist impression" of probably or definitely HCC was 79, 79, and 88 respectively.

CONCLUSIONS

MRI has moderate sensitivity and good specificity for the diagnosis of HCC with considerable variation depending on criteria used. OPTN criteria have the best specificity, but low sensitivity. "Radiologist opinion" gives highest overall accuracy with increases in sensitivity and reduction in specificity when compared to the imaging criteria.

Growth and survival of the superorganism: Ant colony macronutrient intake and investment

In this study, we used two common ant species (Lasius niger and Lasius neoniger) to assay how they translate variation in the diet (both in composition and frequency) into growth. We measured colony development for over 8 months and measured several phenotypic traits of the worker caste, and examined whether forager preference corresponded with diet quality. Optimal colony growth was a balance between survival and growth, and each of these was maximized with different nutrient regimes. Interestingly, forager preference was not totally aligned with the diet that maximized colony growth. Our results highlight that: (a) organism and superorganism size are controlled by the same nutrients, and this may reflect a common molecular basis for size across life's organizational levels, (b) there are nutrient trade-offs that are associated with life-history trade-offs, likely leading to selection for a balanced diet, and (c) the connection between the preference of foragers for different nutrients and how nutrient combinations affect colony success and demographics are complex and only beginning to be understood.

Functional insights from the GC-poor genomes of two aphid parasitoids, Aphidius ervi and Lysiphlebus fabarum

BACKGROUND

Parasitoid wasps have fascinating life cycles and play an important role in trophic networks, yet little is known about their genome content and function. Parasitoids that infect aphids are an important group with the potential for biological control. Their success depends on adapting to develop inside aphids and overcoming both host aphid defenses and their protective endosymbionts.

RESULTS

We present the de novo genome assemblies, detailed annotation, and comparative analysis of two closely related parasitoid wasps that target pest aphids: Aphidius ervi and Lysiphlebus fabarum (Hymenoptera: Braconidae: Aphidiinae). The genomes are small (139 and 141 Mbp) and the most AT-rich reported thus far for any arthropod (GC content: 25.8 and 23.8%). This nucleotide bias is accompanied by skewed codon usage and is stronger in genes with adult-biased expression. AT-richness may be the consequence of reduced genome size, a near absence of DNA methylation, and energy efficiency. We identify missing desaturase genes, whose absence may underlie mimicry in the cuticular hydrocarbon profile of L. fabarum. We highlight key gene groups including those underlying venom composition, chemosensory perception, and sex determination, as well as potential losses in immune pathway genes.

CONCLUSIONS

These findings are of fundamental interest for insect evolution and biological control applications. They provide a strong foundation for further functional studies into coevolution between parasitoids and their hosts. Both genomes are available at https://bipaa.genouest.org.

Conserved roles of Osiris genes in insect development, polymorphism and protection

Much of the variation among insects is derived from the different ways that chitin has been moulded to form rigid structures, both internal and external. In this study, we identify a highly conserved expression pattern in an insect-only gene family, the Osiris genes, that is essential for development, but also plays a significant role in phenotypic plasticity and in immunity/toxicity responses. The majority of Osiris genes exist in a highly syntenic cluster, and the cluster itself appears to have arisen very early in the evolution of insects. We used developmental gene expression in the fruit fly, Drosophila melanogaster, the bumble bee, Bombus terrestris, the harvester ant, Pogonomyrmex barbatus, and the wood ant, Formica exsecta, to compare patterns of Osiris gene expression both during development and between alternate caste phenotypes in the polymorphic social insects. Developmental gene expression of Osiris genes is highly conserved across species and correlated with gene location and evolutionary history. The social insect castes are highly divergent in pupal Osiris gene expression. Sets of co-expressed genes that include Osiris genes are enriched in gene ontology terms related to chitin/cuticle and peptidase activity. Osiris genes are essential for cuticle formation in both embryos and pupae, and genes co-expressed with Osiris genes affect wing development. Additionally, Osiris genes and those co-expressed seem to play a conserved role in insect toxicology defences and digestion. Given their role in development, plasticity, and protection, we propose that the Osiris genes play a central role in insect adaptive evolution.

Dietary cation-anion difference may explain why ammonium urate nephrolithiasis occurs more frequently in common bottlenose dolphins () under human care than in free-ranging common bottlenose dolphins

Ammonium urate nephrolithiasis frequently develops in common bottlenose dolphins () managed under human care but is rare in free-ranging common bottlenose dolphins. In other species, the dietary cation-anion difference (DCAD) can affect ammonium urate urolith formation by increasing proton excretion as ammonium ions. Therefore, differences in diet between the 2 dolphin populations could affect urolith formation, but the DCAD of most species consumed by free-ranging and managed dolphins is unknown. To compare the nutrient composition of diets consumed by free-ranging and managed bottlenose dolphins, samples ( = 5) of the 8 species of fish commonly consumed by free-ranging bottlenose dolphins in Sarasota Bay, FL, and the 7 species of fish and squid commonly fed to managed bottlenose dolphins were analyzed for nutrient content. Metabolizable energy was calculated using Atwater factors; the DCAD was calculated using 4 equations commonly used in people and animals that use different absorption coefficients. The nutrient composition of individual species was used to predict the DCAD of 2 model diets typically fed to managed common bottlenose dolphins and a model diet typically consumed by common bottlenose dolphins in Sarasota Bay. To mimic differences in postmortem handling of fish for the 2 populations of bottlenose dolphins, "free-ranging" samples were immediately frozen at -80°C and minimally thawed before analysis, whereas "managed" samples were frozen for 6 to 9 mo at -18°C and completely thawed. "Free-ranging" species contained more Ca and P and less Na and Cl than "managed" fish and squid species. As a consequence, the DCAD of both model managed dolphin diets obtained using 3 of the 4 equations was much more negative than the DCAD of the model free-ranging bottlenose dolphin diet ( < 0.05). The results imply that managed bottlenose dolphins must excrete more protons in urine than free-ranging bottlenose dolphins, which will promote nephrolith formation. The nutrient composition of the free-ranging bottlenose dolphin diet, determined for the first time here, can be used as a guide for feeding managed bottlenose dolphins, but research in vivo is warranted to determine whether adding more cations to the diet will prevent urolith formation in managed dolphins.

A Targeted Metabolomics Assay to Measure Eight Purines in the Diet of Common Bottlenose Dolphins, Tursiops truncatus

Bottlenose dolphins managed under human care, human beings and Dalmatian dogs are prone to forming urate uroliths. Limiting dietary purine intake limits urate urolith formation in people and dogs because purines are metabolized to uric acid, which is excreted in urine. Managed dolphins develop ammonium urate nephroliths, whereas free-ranging dolphins do not. Free-ranging dolphins consume live fish, whereas managed dolphins consume different species that have been stored frozen and thawed. Differences in the purine content of fish consumed by dolphins under human care versus in the wild may be responsible for the difference in urolith prevalence. Commercially available purine assays measure only four purines, but reported changes in purines during frozen storage suggest that a wider range of metabolites should be measured when comparing fresh and stored fish. A method using high performance liquid chromatography with tandem mass spectrometry was developed to quantify eight purine metabolites in whole fish and squid commonly consumed by dolphins. The coefficient of variation within and among days was sometimes high for purines present in small amounts but was acceptable (≤ 25%) for guanine, hypoxanthine, and inosine, which were present in high concentrations. This expanded assay identified a total purine content up to 2.5 times greater than the total that would be quantified if only four purines were measured. Assuming additional purines are absorbed, these results suggest that additional purine metabolites should be measured to better understand the associated risk when fish or other purine-rich foods are consumed by people or animals prone to developing uroliths.

Microbial community responses to soil tillage and crop rotation in a corn/soybean agroecosystem

The acreage planted in corn and soybean crops is vast, and these crops contribute substantially to the world economy. The agricultural practices employed for farming these crops have major effects on ecosystem health at a worldwide scale. The microbial communities living in agricultural soils significantly contribute to nutrient uptake and cycling and can have both positive and negative impacts on the crops growing with them. In this study, we examined the impact of the crop planted and soil tillage on nutrient levels, microbial communities, and the biochemical pathways present in the soil. We found that farming practice, that is conventional tillage versus no‐till, had a much greater impact on nearly everything measured compared to the crop planted. No‐till fields tended to have higher nutrient levels and distinct microbial communities. Moreover, no‐till fields had more DNA sequences associated with key nitrogen cycle processes, suggesting that the microbial communities were more active in cycling nitrogen. Our results indicate that tilling of agricultural soil may magnify the degree of nutrient waste and runoff by altering nutrient cycles through changes to microbial communities. Currently, a minority of acreage is maintained without tillage despite clear benefits to soil nutrient levels, and a decrease in nutrient runoff—both of which have ecosystem‐level effects and both direct and indirect effects on humans and other organisms.

A Targeted Metabolomics Assay to Measure Eight Purines in the Diet of Common Bottlenose Dolphins, Tursiops truncatus

Bottlenose dolphins managed under human care, human beings and Dalmatian dogs are prone to forming urate uroliths. Limiting dietary purine intake limits urate urolith formation in people and dogs because purines are metabolized to uric acid, which is excreted in urine. Managed dolphins develop ammonium urate nephroliths, whereas free-ranging dolphins do not. Free-ranging dolphins consume live fish, whereas managed dolphins consume different species that have been stored frozen and thawed. Differences in the purine content of fish consumed by dolphins under human care versus in the wild may be responsible for the difference in urolith prevalence. Commercially available purine assays measure only four purines, but reported changes in purines during frozen storage suggest that a wider range of metabolites should be measured when comparing fresh and stored fish. A method using high performance liquid chromatography with tandem mass spectrometry was developed to quantify eight purine metabolites in whole fish and squid commonly consumed by dolphins. The coefficient of variation within and among days was sometimes high for purines present in small amounts but was acceptable (≤ 25%) for guanine, hypoxanthine, and inosine, which were present in high concentrations. This expanded assay identified a total purine content up to 2.5 times greater than the total that would be quantified if only four purines were measured. Assuming additional purines are absorbed, these results suggest that additional purine metabolites should be measured to better understand the associated risk when fish or other purine-rich foods are consumed by people or animals prone to developing uroliths.

How Do Genomes Create Novel Phenotypes? Insights from the Loss of the Worker Caste in Ant Social Parasites

A central goal of biology is to uncover the genetic basis for the origin of new phenotypes. A particularly effective approach is to examine the genomic architecture of species that have secondarily lost a phenotype with respect to their close relatives. In the eusocial Hymenoptera, queens and workers have divergent phenotypes that may be produced via either expression of alternative sets of caste-specific genes and pathways or differences in expression patterns of a shared set of multifunctional genes. To distinguish between these two hypotheses, we investigated how secondary loss of the worker phenotype in workerless ant social parasites impacted genome evolution across two independent origins of social parasitism in the ant genera Pogonomyrmex and Vollenhovia. We sequenced the genomes of three social parasites and their most-closely related eusocial host species and compared gene losses in social parasites with gene expression differences between host queens and workers. Virtually all annotated genes were expressed to some degree in both castes of the host, with most shifting in queen-worker bias across developmental stages. As a result, despite >1 My of divergence from the last common ancestor that had workers, the social parasites showed strikingly little evidence of gene loss, damaging mutations, or shifts in selection regime resulting from loss of the worker caste. This suggests that regulatory changes within a multifunctional genome, rather than sequence differences, have played a predominant role in the evolution of social parasitism, and perhaps also in the many gains and losses of phenotypes in the social insects.

Erratum: Seasonal dynamics of megafauna on the deep West Antarctic Peninsula shelf in response to variable phytodetrital influx

[This corrects the article DOI: 10.1098/rsos.140294.].

Volatile food attractants forOryzaephilus surinamensis (L.) from oats

The sawtoothed grain beetle,Oryzaephilus surinamensis (L.) (Coleoptera: Cucujidae), is attracted to certain volatile components that occur in whole and rolled oats as determined by a laboratory pitfall chamber bioassay. More than 100 components were detected in the attractive carbonyl-containing fractions; 14 of these, making up 60% of the total, were identified and bioassayed. Although hexanal, heptanal, octanal, (E)-2-heptenal, and 2-furaldehyde, at doses ranging variously from 1 to 100 μg, were all significantly attractive, only 1 /10 to 1 /100 as much (E)-2-nonenal or (E,E)-2,4-nonadienal was necessary to produce comparable insect response. In addition, propanal and formaldehyde (previously reported in oats but not detected by us) were bioassayed and found to be attractive.

Structure-activity relationships among maytansinoids in their effect on the European corn borer,Ostrinia nubilalis (Hübner)

Five maytansinoids fromMaytenus (Celastraceae) andPutterlickia (Rhamnaceae) species were tested for biological activity against the European corn borerOstrinia nubilalis. Maytanbutine, maytansine, and maytanvaline, all of which contain an amino acid residue at C-3, were active and comparable in their effect on larvae to trewiasine, a known active, amino acid-containing maytansinoid fromTrewia nudiflora. Maytanacine, which has an acetate group at C-3, was not as active as maytansine, maytanvaline, maytanbutine, or trewiasine, but significantly retarded the development of the larvae. Normaysine, which has no oxygen substituent at C-3, had no significant effect on mortality and only moderate effect on development of the larvae. The presence of the amino acid moiety at C-3 appears to be an important factor for the biological activity of maytansinoids.

From principles to practice: a spatial approach to systematic conservation planning in the deep sea

Increases in the demand and price for industrial metals, combined with advances in technological capabilities have now made deep-sea mining more feasible and economically viable. In order to balance economic interests with the conservation of abyssal plain ecosystems, it is becoming increasingly important to develop a systematic approach to spatial management and zoning of the deep sea. Here, we describe an expert-driven systematic conservation planning process applied to inform science-based recommendations to the International Seabed Authority for a system of deep-sea marine protected areas (MPAs) to safeguard biodiversity and ecosystem function in an abyssal Pacific region targeted for nodule mining (e.g. the Clarion-Clipperton fracture zone, CCZ). Our use of geospatial analysis and expert opinion in forming the recommendations allowed us to stratify the proposed network by biophysical gradients, maximize the number of biologically unique seamounts within each subregion, and minimize socioeconomic impacts. The resulting proposal for an MPA network (nine replicate 400 × 400 km MPAs) covers 24% (1 440 000 km(2)) of the total CCZ planning region and serves as example of swift and pre-emptive conservation planning across an unprecedented area in the deep sea. As pressure from resource extraction increases in the future, the scientific guiding principles outlined in this research can serve as a basis for collaborative international approaches to ocean management.

Video image analysis in the Australian meat industry - precision and accuracy of predicting lean meat yield in lamb carcasses

A wide selection of lamb types of mixed sex (ewes and wethers) were slaughtered at a commercial abattoir and during this process images of 360 carcasses were obtained online using the VIAScan® system developed by Meat and Livestock Australia. Soft tissue depth at the GR site (thickness of tissue over the 12th rib 110 mm from the midline) was measured by an abattoir employee using the AUS-MEAT sheep probe (PGR). Another measure of this thickness was taken in the chiller using a GR knife (NGR). Each carcass was subsequently broken down to a range of trimmed boneless retail cuts and the lean meat yield determined. The current industry model for predicting meat yield uses hot carcass weight (HCW) and tissue depth at the GR site. A low level of accuracy and precision was found when HCW and PGR were used to predict lean meat yield (R(2)=0.19, r.s.d.=2.80%), which could be improved markedly when PGR was replaced by NGR (R(2)=0.41, r.s.d.=2.39%). If the GR measures were replaced by 8 VIAScan® measures then greater prediction accuracy could be achieved (R(2)=0.52, r.s.d.=2.17%). A similar result was achieved when the model was based on principal components (PCs) computed from the 8 VIAScan® measures (R(2)=0.52, r.s.d.=2.17%). The use of PCs also improved the stability of the model compared to a regression model based on HCW and NGR. The transportability of the models was tested by randomly dividing the data set and comparing coefficients and the level of accuracy and precision. Those models based on PCs were superior to those based on regression. It is demonstrated that with the appropriate modeling the VIAScan® system offers a workable method for predicting lean meat yield automatically.

Social insect genomes exhibit dramatic evolution in gene composition and regulation while preserving regulatory features linked to sociality

Genomes of eusocial insects code for dramatic examples of phenotypic plasticity and social organization. We compared the genomes of seven ants, the honeybee, and various solitary insects to examine whether eusocial lineages share distinct features of genomic organization. Each ant lineage contains ∼4000 novel genes, but only 64 of these genes are conserved among all seven ants. Many gene families have been expanded in ants, notably those involved in chemical communication (e.g., desaturases and odorant receptors). Alignment of the ant genomes revealed reduced purifying selection compared with Drosophila without significantly reduced synteny. Correspondingly, ant genomes exhibit dramatic divergence of noncoding regulatory elements; however, extant conserved regions are enriched for novel noncoding RNAs and transcription factor–binding sites. Comparison of orthologous gene promoters between eusocial and solitary species revealed significant regulatory evolution in both cis (e.g., Creb) and trans (e.g., fork head) for nearly 2000 genes, many of which exhibit phenotypic plasticity. Our results emphasize that genomic changes can occur remarkably fast in ants, because two recently diverged leaf-cutter ant species exhibit faster accumulation of species-specific genes and greater divergence in regulatory elements compared with other ants or Drosophila. Thus, while the “socio-genomes” of ants and the honeybee are broadly characterized by a pervasive pattern of divergence in gene composition and regulation, they preserve lineage-specific regulatory features linked to eusociality. We propose that changes in gene regulation played a key role in the origins of insect eusociality, whereas changes in gene composition were more relevant for lineage-specific eusocial adaptations.

cis-5,cis-9,cis-12-octadecatrienoic and some unusual oxygenated acids inXeranthemum annuum seed oil

Seed oil ofXeranthemum annuum (family Compositae) contains a number of unusual fatty acids in addition to palmitic, stearic, oleic, linoleic and linolenic. These acids includecis-5,cis-9,cis-12-octadecatrienoic, 5%;cis-9-L: ,10-L: -epoxyoctadecanoic, 3%;cis-9-L: ,10-L: -epoxy-cis-12-octadecenoic (coronaric), 8%; andcis-12-D: ,13-D: -epoxy-cis-9-octadecenoic (vernolic), 2%; as well as a mixture of two hydroxy acids, 11%. The absolute configurations of the two 9,10-epoxy acids are established for the first time.

Caltha palustris L. Seed Oil. A source of four fatty acids withcis-5-unsaturation

The seed oil ofCaltha palustris L. yields two unusual polyunsaturated components, all-cis-5,11,14-eicosatrienoic acid (23%) and all-cis-5,11,14,17-eicosatetraenoic acid (1%). The C(18) monoene fraction (26%) is a mixture ofcis-5- andcis-9-octadecenoic acids (2ratio1). The C(20) monoene fraction (12%) is a mixture ofcis-11- andcis-5-isomers (3ratio1).

Patterns of DNA methylation in development, division of labor and hybridization in an ant with genetic caste determination

BACKGROUND

DNA methylation is a common regulator of gene expression, including acting as a regulator of developmental events and behavioral changes in adults. Using the unique system of genetic caste determination in Pogonomyrmex barbatus, we were able to document changes in DNA methylation during development, and also across both ancient and contemporary hybridization events.

METHODOLOGY/PRINCIPAL FINDINGS

Sodium bisulfite sequencing demonstrated in vivo methylation of symmetric CG dinucleotides in P. barbatus. We also found methylation of non-CpG sequences. This validated two bioinformatics methods for predicting gene methylation, the bias in observed to expected ratio of CpG dinucleotides and the density of CpG/TpG single nucleotide polymorphisms (SNP). Frequencies of genomic DNA methylation were determined for different developmental stages and castes using ms-AFLP assays. The genetic caste determination system (GCD) is probably the product of an ancestral hybridization event between P. barbatus and P. rugosus. Two lineages obligately co-occur within a GCD population, and queens are derived from intra-lineage matings whereas workers are produced from inter-lineage matings. Relative DNA methylation levels of queens and workers from GCD lineages (contemporary hybrids) were not significantly different until adulthood. Virgin queens had significantly higher relative levels of DNA methylation compared to workers. Worker DNA methylation did not vary among developmental stages within each lineage, but was significantly different between the currently hybridizing lineages. Finally, workers of the two genetic caste determination lineages had half as many methylated cytosines as workers from the putative parental species, which have environmental caste determination.

CONCLUSIONS/SIGNIFICANCE

These results suggest that DNA methylation may be a conserved regulatory mechanism moderating division of labor in both bees and ants. Current and historic hybridization appear to have altered genomic methylation levels suggesting a possible link between changes in overall DNA methylation and the origin and regulation of genetic caste determination in P. barbatus.

Comparative safety of antiepileptic drugs during pregnancy

OBJECTIVE

To assess the safety of the newer antiepileptic drugs (AEDs) during pregnancy.

METHODS

The study population was pregnant women who enrolled in the North American AED Pregnancy Registry between 1997 and 2011. Data on AED use and maternal characteristics were collected through phone interviews at enrollment, at 7 months' gestation, and postpartum. Malformations were confirmed by medical records. The risk of major malformations was calculated among infants exposed to specific AEDs in monotherapy during the first trimester of pregnancy and among an unexposed group. Risk ratios (RRs) and 95% confidence intervals (CIs) were estimated with logistic regression.

RESULTS

The risk of major malformations was 9.3% (30 of 323) for valproate, 5.5% (11 of 199) for phenobarbital, 4.2% (15 of 359) for topiramate, 3.0% (31 of 1.033) for carbamazepine, 2.9% (12 of 416) for phenytoin, 2.4% (11 of 450) for levetiracetam, and 2.0% (31 of 1,562) for lamotrigine. Compared with lamotrigine, the RR was 5.1 (95% CI 3.0-8.5) for valproate, 2.9 (1.4-5.8) for phenobarbital, and 2.2 (1.2-4.0) for topiramate. The proportion of women with epilepsy who had seizures during pregnancy ranged from 23% for valproate to 31% for lamotrigine. Valproate was associated with a higher risk of neural tube defects, hypospadias, cardiac defects, and oral clefts and phenobarbital with a higher risk of cardiac defects and oral clefts; 5 infants exposed to topiramate (1.4%) had a cleft lip.

CONCLUSIONS

AEDs such as valproate and phenobarbital were associated with a higher risk of major malformations than newer AEDs such as lamotrigine and levetiracetam. Topiramate was associated with an increased risk of cleft lip compared with that of a reference population.

Nutritional asymmetries are related to division of labor in a queenless ant

Eusocial species exhibit pronounced division of labor, most notably between reproductive and non-reproductive castes, but also within non-reproductive castes via morphological specialization and temporal polyethism. For species with distinct worker and queen castes, age-related differences in behavior among workers (e.g. within-nest tasks versus foraging) appear to result from physiological changes such as decreased lipid content. However, we know little about how labor is divided among individuals in species that lack a distinct queen caste. In this study, we investigated how fat storage varied among individuals in a species of ant (Dinoponera australis) that lacks a distinct queen caste and in which all individuals are morphologically similar and capable of reproduction (totipotent at birth). We distinguish between two hypotheses, 1) all individuals are physiologically similar, consistent with the possibility that any non-reproductive may eventually become reproductive, and 2) non-reproductive individuals vary in stored fat, similar to highly eusocial species, where depletion is associated with foraging and non-reproductives have lower lipid stores than reproducing individuals. Our data support the latter hypothesis. Location in the nest, the probability of foraging, and foraging effort, were all associated with decreased fat storage.

The genome sequence of the leaf-cutter ant Atta cephalotes reveals insights into its obligate symbiotic lifestyle

Leaf-cutter ants are one of the most important herbivorous insects in the Neotropics, harvesting vast quantities of fresh leaf material. The ants use leaves to cultivate a fungus that serves as the colony's primary food source. This obligate ant-fungus mutualism is one of the few occurrences of farming by non-humans and likely facilitated the formation of their massive colonies. Mature leaf-cutter ant colonies contain millions of workers ranging in size from small garden tenders to large soldiers, resulting in one of the most complex polymorphic caste systems within ants. To begin uncovering the genomic underpinnings of this system, we sequenced the genome of Atta cephalotes using 454 pyrosequencing. One prediction from this ant's lifestyle is that it has undergone genetic modifications that reflect its obligate dependence on the fungus for nutrients. Analysis of this genome sequence is consistent with this hypothesis, as we find evidence for reductions in genes related to nutrient acquisition. These include extensive reductions in serine proteases (which are likely unnecessary because proteolysis is not a primary mechanism used to process nutrients obtained from the fungus), a loss of genes involved in arginine biosynthesis (suggesting that this amino acid is obtained from the fungus), and the absence of a hexamerin (which sequesters amino acids during larval development in other insects). Following recent reports of genome sequences from other insects that engage in symbioses with beneficial microbes, the A. cephalotes genome provides new insights into the symbiotic lifestyle of this ant and advances our understanding of host-microbe symbioses.

Functional proteomics of kallikrein-related peptidases in ovarian cancer ascites fluid

Kallikrein-related peptidases (KLKs) are secreted serine proteinases with trypsin or chymotrypsin-like activity. Several family members, such as KLKs 6 and 10, are potential ovarian cancer biomarkers. Recently, using a newly developed assay for active KLK6, we found that only a very small proportion of immunoreactive KLK6 in tumor-derived clinical samples (malignant ascites fluid), in cerebrospinal fluid, and in cancer cell line supernatants is enzymatically active. We therefore hypothesized that a proportion of other immunoreactive KLKs in such samples could be present, but might be partly complexed to endogenous serine proteinase inhibitors. Using a combination of immunological isolation of the enzymes, activity-based probe analysis and proteomics, we identified active KLK10 in ovarian cancer ascites and we provide preliminary data that the activity of other KLKs present in these samples can be decreased by known proteinase inhibitors (e.g., alpha2-macroglobulin, alpha1-antitrypsin). Our data suggest that the enzymatic activity of ovarian cancer-released KLKs that are detected by regular immunoassays is low in vivo and very likely regulated by proteinase inhibitors.

An octadecatrienoic acid from Lamium purpureum L. seed oil containing 5,6-allenic and trans-16-olefinic unsaturation

1. Lamium purpureum L. (Labiatae) seed oil contains 16% of a new acid characterized as (-)-octadeca-5,6-trans-16-trienoic acid (proposed trivial name ;lamenallenic acid') (Ia). The acid was isolated as its methyl ester by countercurrent distribution by using a combination of recycle-single withdrawal techniques. Methyl lamenallenate (Ib) is strongly laevorotatory. 2. The structure was established by infrared spectroscopy, nuclear-magnetic-resonance spectroscopy, quantitative hydrogenation and oxidative cleavage data of the original acid and of hydrazine partial reduction products. 3. Other unsaturated esters identified by their cleavage products were oleate, linoleate and linolenate. 4. A very small amount (less than 1%) of methyl laballenate [(-)-methyl octadeca-5,6-dienoate] was also isolated and identified.

Ants (Formicidae): models for social complexity

The family Formicidae (ants) is composed of more than 12,000 described species that vary greatly in size, morphology, behavior, life history, ecology, and social organization. Ants occur in most terrestrial habitats and are the dominant animals in many of them. They have been used as models to address fundamental questions in ecology, evolution, behavior, and development. The literature on ants is extensive, and the natural history of many species is known in detail. Phylogenetic relationships for the family, as well as within many subfamilies, are known, enabling comparative studies. Their ease of sampling and ecological variation makes them attractive for studying populations and questions relating to communities. Their sociality and variation in social organization have contributed greatly to an understanding of complex systems, division of labor, and chemical communication. Ants occur in colonies composed of tens to millions of individuals that vary greatly in morphology, physiology, and behavior; this variation has been used to address proximate and ultimate mechanisms generating phenotypic plasticity. Relatedness asymmetries within colonies have been fundamental to the formulation and empirical testing of kin and group selection theories. Genomic resources have been developed for some species, and a whole-genome sequence for several species is likely to follow in the near future; comparative genomics in ants should provide new insights into the evolution of complexity and sociogenomics. Future studies using ants should help establish a more comprehensive understanding of social life, from molecules to colonies.

Collecting live ant specimens (colony sampling)

Because of the great diversity of ants, it is difficult to give a single protocol for the collection of live specimens. Ant body size can be very small or extremely large; the ants can be hard or soft, sting or spray toxic chemicals, live in the open or in hard-to-reach places; and colony size can range from tens of individuals to millions. Thus, collection techniques must be tailored to each particular species. In particular, caution must always be taken when dealing with stinging species, and symptoms and basic first-aid measures, especially for the treatment of anaphylactic shock, should be reviewed before beginning fieldwork. Nonetheless, many species are collectable as whole colonies. This protocol reviews some basic techniques for collecting ground-nesting species and describes how to collect whole live colonies (with queens), which are necessary for long-term laboratory studies and addressing questions of social organization and ecology.

Stable isotope and elemental analysis in ants

Over the past 20 yr, the use of stable isotopes to infer feeding ecology and the examination of how energetic and elemental exchanges are affected by and affect life (ecological stoichiometry) have gained momentum. The ecological diversity of ants makes them interesting models to explore dietary ecology and their role in food webs. Moreover, their ecological dominance in most habitats facilitates sampling. The protocol described here will produce samples adequate for submission to most labs that specialize in high-throughput analysis of stable isotopes; one should check with any particular lab for specific submission instructions. Note, however, that this protocol is designed specifically for the quantification of the natural abundance of stable isotopes; it does not cover the preparation of trace samples.

Ecological sampling of ants: competition and biodiversity

Ants are among the most dominant taxa in terrestrial ecosystems, despite their small individual size. Furthermore, they are a hyperdiverse family with an estimated 20,000 species. Together, these two properties make ants a model for ecological interactions (specifically competition) and biodiversity estimation. Although there are many means of measuring diversity, the two most common among myrmecologists are baiting and pitfall trapping. Pitfall traps provide an almost unbiased estimate of the ground foraging community, whereas baiting allows the estimation of ecological dominance and the competitive outcomes between species. This protocol describes an approach to assay both abundance (pitfall traps) and ecological interactions (baits) in the same community.

Identification of five candidate lung cancer biomarkers by proteomics analysis of conditioned media of four lung cancer cell lines

Detection of lung cancer at an early stage is necessary for successful therapy and improved survival rates. We performed a bottom-up proteomics analysis using a two-dimensional LC-MS/MS strategy on the conditioned media of four lung cancer cell lines of different histological backgrounds (non-small cell lung cancer: H23 (adenocarcinoma), H520 (squamous cell carcinoma), and H460 (large cell carcinoma); small cell lung cancer: H1688) to identify secreted or membrane-bound proteins that could be useful as novel lung cancer biomarkers. Proteomics analysis of the four conditioned media allowed identification of 1,830 different proteins (965, 871, 726, and 847 from H1688, H23, H460, and H520, respectively). All proteins were assigned a subcellular localization, and 38% were classified as extracellular or membrane-bound. We successfully identified the internal control proteins (also detected by ELISA), kallikrein-related peptidases 14 and 11, and IGFBP2. We also identified known or putative lung cancer tumor markers such as squamous cell carcinoma antigen, carcinoembryonic antigen, chromogranin A, creatine kinase BB, progastrin-releasing peptide, neural cell adhesion molecule, and tumor M2-PK. To select the most promising candidates for validation, we performed tissue specificity assays, functional classifications, literature searches for association to cancer, and a comparison of our proteome with the proteome of lung-related diseases and serum. Five novel lung cancer candidates, ADAM-17, osteoprotegerin, pentraxin 3, follistatin, and tumor necrosis factor receptor superfamily member 1A were preliminarily validated in the serum of patients with lung cancer and healthy controls. Our results demonstrate the utility of this cell culture proteomics approach to identify secreted and shed proteins that are potentially useful as serological markers for lung cancer.

Ant fat extraction with a Soxhlet extractor

Stored fat can be informative about the relative age of an ant, its nutritional status, and the nutritional status of the colony. Several methods are available for the quantification of stored fat. Before starting a project involving fat extraction, investigators should weigh the advantages and disadvantages of different methods in order to choose the one that is best suited to the question being addressed. This protocol, although not as accurate as some alternatives, facilitates the rapid quantification of many individuals.

Modeling the maintenance of a dependent lineage system: the influence of positive frequency-dependent selection on sex ratio

In insect societies, worker versus queen development (reproductive caste) is typically governed by environmental factors, but some Pogonomyrmex seed-harvester ants exhibit strict genetic caste determination, resulting in an obligate mutualism between two reproductively isolated lineages. Queens mate randomly with multiple males from each lineage and intralineage crosses produce new queens, whereas interlineage crosses produce workers. Early colony survival is negatively frequency dependent; when lineage frequencies are unequal, queens from the rarer lineage benefit because they acquire more interlineage sperm, and produce more workers. Here we examine theoretically and empirically the effect of relative lineage frequency on sex ratio. We predict that the ratio of inter- to intralineage sperm acquired by queens of each lineage will affect the sex ratio produced at colony maturity. Consistent with model predictions, we found that gyne production in mature colonies was positively frequency dependent, increasing significantly with increasing lineage frequency across 15 populations. Unequal lineage frequencies are common and likely maintained by a complex interplay between an ecological advantage specific to one lineage, and opposing frequency-dependent selection pressures experienced throughout the colonies life-cycle; rare lineage colonies benefit during early colony growth, and common lineage colonies benefit at reproductive maturity.

Field testing of a minimal record of disability in multiple sclerosis: the United States and Canada

The IFMSS Minimal Record of Disability (MRD) in Multiple Sclerosis was field tested at eight medical centers in the U.S. and Canada. The goals were to conduct a qualitative and quantitative evaluation of the MRD. Assessment were completed on 249 patients with definite MS by neurologists and allied health professionals. Effective administration required some study and practice. Refinement of some unclear wording and awkward format will improve ease of administration. The MRD fit well into clinic routines and was accepted by staff and patients. Scoring presented few problems and these were related to overlap among the MRD scales, poor wording, and content not appropriate to MS. Quantitative evaluation of the MRD indicated that Incapacity Status primarily reflects disability in mobility and self-care when used as a composite score. Heterogeneity of content in Incapacity Status suggests that summed scores be used cautiously. Both Incapacity and Environmental Status had high levels of reliability and high correlations with established measures of impairment in MS. Inter-rater agreement of the ISS and ESS were also high. Once some necessary revisions are made, the MRD should be well on its way to achieving the IFMSS goal of developing a brief, reliable, valid, and appropriate instrument acceptable to a wide variety of workers in MS.

Mining the ovarian cancer ascites proteome for potential ovarian cancer biomarkers

Current ovarian cancer biomarkers are inadequate because of their relatively low diagnostic sensitivity and specificity. There is a need to discover and validate novel ovarian cancer biomarkers that are suitable for early diagnosis, monitoring, and prediction of therapeutic response. We performed an in-depth proteomics analysis of ovarian cancer ascites fluid. Size exclusion chromatography and ultrafiltration were used to remove high abundance proteins with molecular mass >/=30 kDa. After trypsin digestion, the subproteome (</=30 kDa) of ascites fluid was determined by two-dimensional liquid chromatography-tandem mass spectrometry. Filtering criteria were used to select potential ovarian cancer biomarker candidates. By combining data from different size exclusion and ultrafiltration fractionation protocols, we identified 445 proteins from the soluble ascites fraction using a two-dimensional linear ion trap mass spectrometer. Among these were 25 proteins previously identified as ovarian cancer biomarkers. After applying a set of filtering criteria to reduce the number of potential biomarker candidates, we identified 52 proteins for which further clinical validation is warranted. Our proteomics approach for discovering novel ovarian cancer biomarkers appears to be highly efficient because it was able to identify 25 known biomarkers and 52 new candidate biomarkers that warrant further validation.

Caste determination in a polymorphic social insect: nutritional, social, and genetic factors

We examined how dietary, social, and genetic factors affect individual size and caste in the Florida harvester ant Pogonomyrmex badius, which has three discrete female castes. The diet that a larva consumed, as indicated by delta(13)C, delta(15)N, and C:N, varied with caste. Both N content and estimated trophic position of dietary input was higher for major than for minor workers and was highest for gynes (reproductive females). The size and resources of a colony affected the size of only minor workers, not that of gynes and major workers. Approximately 19% of patrilines showed a bias in which female caste they produced. There were significant genetic effects on female size, and the average sizes of a major worker and a gyne produced by a patriline were correlated, but neither was correlated with minor worker size. Thus, genetic factors influence both caste and size within caste. We conclude that environmental, social, and genetic variation interact to create morphological and physiological variation among females in P. badius. However, the relative importance of each type of factor affecting caste determination is caste specific.

Genetic and genomic analyses of the division of labour in insect societies

Division of labour--individuals specializing in different activities--features prominently in the spectacular success of the social insects. Until recently, genetic and genomic analyses of division of labour were limited to just a few species. However, research on an ever-increasing number of species has provided new insight, from which we highlight two results. First, heritable influences on division of labour are more pervasive than previously imagined. Second, different forms of division of labour, in lineages in which eusociality has arisen independently, have evolved through changes in the regulation of highly conserved molecular pathways associated with several basic life-history traits, including nutrition, metabolism and reproduction.