Contextualising the Last Survivors: Population Structure of Marine Turtles in the Dominican Republic

Nesting by three species of marine turtles persists in the Dominican Republic, despite historic threats and long-term population decline. We conducted a genetic survey of marine turtles in the Dominican Republic in order to link them with other rookeries around the Caribbean. We sequenced a 740_bp fragment of the control region of the mitochondrial DNA of 92 samples from three marine turtle species [hawksbill (n = 48), green (n = 2) and leatherback (n = 42)], and incorporated published data from other nesting populations and foraging grounds. The leatherback turtle (Dermochelys coriacea) in the Dominican Republic appeared to be isolated from Awala-Yalimapo, Cayenne, Trinidad and St. Croix but connected with other Caribbean populations. Two distinct nesting populations of hawksbill turtles (Eremochelys imbricata) were detected in the Dominican Republic and exhibited interesting patterns of connectivity with other nesting sites and juvenile and adult male foraging aggregations. The green sea turtle (Chelonia mydas) has almost been extirpated from the Dominican Republic and limited inference could be made from our samples. Finally, results were compared with Lagrangian drifting buoys and published Lagrangian virtual particles that travelled through the Dominican Republic and Caribbean waters. Conservation implications of sink-source effects or genetic isolation derived from these complex inter-connections are discussed for each species and population.     

Spatial distribution and aggregation of Xenobalanus globicipitis on the flukes of striped dolphins,Stenella coeruleoalba: An indicator of host hydrodynamics?

We analyzed patterns of aggregation and spatial distribution of the epizoic barnacle Xenobalanus globicipitis on the flukes of Mediterranean striped dolphins, Stenella coeruleoalba, assessing its potential use as an indicator of the host's hydrodynamics based on data from 55 dolphins. Barnacles occurred along the trailing edge with the cirri oriented towards the oncoming flow. Nearest neighbor analyses suggested that new recruits actively seek placement next to already settled barnacles, forming aggregations possibly to facilitate copulation. The probability of spanwise settlement strongly increased with fluke width (presumably enabling prolonged leading-edge vorticity), and with chordwise length where pressure is predicted to be positive. Consequently, clustering tended to increase nonlinearly towards the fluke notch. Furthermore, it was three times more likely for barnacles to occur on the dorsal vs. ventral side of flukes, at an average abundance ca. 12 times higher. This difference could result from a host's asymmetric oscillation of the tail, which would alter leading-edge vorticity, and/or an interaction between the wake produced by the dorsal fin and the flow associated with flukes. Both processes could primarily enhance cyprid contact and/or attachment on the dorsal side. This study offers a starting point for future comparison with other cetaceans.     

Weighted Interaction SNP Hub (WISH) network method for building genetic networks for complex diseases and traits using whole genome genotype data

Background

High-throughput genotype (HTG) data has been used primarily in genome-wide association (GWA) studies; however, GWA results explain only a limited part of the complete genetic variation of traits. In systems genetics, network approaches have been shown to be able to identify pathways and their underlying causal genes to unravel the biological and genetic background of complex diseases and traits, e.g., the Weighted Gene Co-expression Network Analysis (WGCNA) method based on microarray gene expression data. The main objective of this study was to develop a scale-free weighted genetic interaction network method using whole genome HTG data in order to detect biologically relevant pathways and potential genetic biomarkers for complex diseases and traits.

Results

We developed the Weighted Interaction SNP Hub (WISH) network method that uses HTG data to detect genome-wide interactions between single nucleotide polymorphism (SNPs) and its relationship with complex traits. Data dimensionality reduction was achieved by selecting SNPs based on its: 1) degree of genome-wide significance and 2) degree of genetic variation in a population. Network construction was based on pairwise Pearson's correlation between SNP genotypes or the epistatic interaction effect between SNP pairs. To identify modules the Topological Overlap Measure (TOM) was calculated, reflecting the degree of overlap in shared neighbours between SNP pairs. Modules, clusters of highly interconnected SNPs, were defined using a tree-cutting algorithm on the SNP dendrogram created from the dissimilarity TOM (1-TOM). Modules were selected for functional annotation based on their association with the trait of interest, defined by the Genome-wide Module Association Test (GMAT). We successfully tested the established WISH network method using simulated and real SNP interaction data and GWA study results for carcass weight in a pig resource population; this resulted in detecting modules and key functional and biological pathways related to carcass weight.

Conclusions

We developed the WISH network method which is a novel 'systems genetics' approach to study genetic networks underlying complex trait variation. The WISH network method reduces data dimensionality and statistical complexity in associating genotypes with phenotypes in GWA studies and enables researchers to identify biologically relevant pathways and potential genetic biomarkers for any complex trait of interest.

     

Complex mixtures of antibodies generated from a single production qualitatively and quantitatively evaluated by native Orbitrap mass spectrometry

Composite antibody mixtures designed to combat diseases present a new, rapidly emerging technology in the field of biopharmaceuticals. The combination of multiple antibodies can lead to increased effector response and limit the effect of escape variants that can propagate the disease. However, parallel development of analytical technologies is required to provide fast, thorough, accurate, and robust characterization of these mixtures. Here, we evaluate the utility of native mass spectrometry on an Orbitrap platform with high mass resolving power to characterize composite mixtures of up to 15 separate antibodies. With this technique, unambiguous identification of each antibody in the mixtures was achieved. Mass measurements of the intact antibodies varied 7 ppm on average, allowing highly reproducible identification and quantitation of each compound in these complex mixtures. We show that with the high mass-resolving power and robustness of this technology, high-resolution native mass spectrometry can be used efficiently even for batch-to-batch characterization.     

Research into the (Cost-) effectiveness of the ketogenic diet among children and adolescents with intractable epilepsy: design of a randomized controlled trial

Background  

Epilepsy is a neurological disorder, characterized by recurrent unprovoked seizures which have a high impact on the individual as well as on society as a whole. In addition to the economic burden, epilepsy imposes a substantial burden on the patients and their surroundings. Patients with uncontrolled epilepsy depend heavily on informal care and on health care professionals. About 30% of patients suffer from drug-resistant epilepsy. The ketogenic diet can be a treatment of last resort, especially for children. The beneficial effect of the ketogenic diet has been proven, but information is lacking about its cost-effectiveness. In the current study we will evaluate the (cost-) effectiveness of the ketogenic diet in children and adolescents with intractable epilepsy.     

Segregation and linkage analyses in two complex populations derived from the citrus rootstock Cleopatra mandarin. Inheritance of seed reproductive traits

Two complex populations derived from the salt-tolerant citrus rootstock Cleopatra mandarin were used to investigate (1) the genomic regions affected by segregation distortion and (2) gene segregation heterogeneity and their causes and to obtain (3) a Citrus reshni linkage map to genetically analyze (4) the duration of the juvenility period and the seed embryony type. Both populations differed in the extent and origin of segregation distortion. The population derived from the cross between C. reshni and Poncirus trifoliata (R?×?Pr) showed 75?% of codominant markers with distorted segregation. The origin of this distortion was prezygotic in most cases. Meanwhile, 100?% of codominant markers in the self-pollinated population [F₂(R?×?Pr)] showed genotypic distortion, and the origin of such distortion was mostly postzygotic, with the heterozygote being the most frequent genotype in all cases. In the R?×?Pr population, where two pollinator varieties were used, allele segregation was significantly heterogeneous not only in P. trifoliata (28.6?% of markers) but also in C. reshni (19.5?%). The results on segregation heterogeneity in the F₂(R?×?Pr) suggest the presence at linkage group 4c of a postfertilization system of balanced lethal factors that reduces homozygosis in self-compatible hybrids. Four low to medium contributing quantitative trait loci (QTLs) were detected for the duration of juvenility period by both Kruskal?CWallis and interval mapping methodologies. For seed embryony type, three QTLs were detected by both methodologies, with the previously reported Apo2 being the QTL contributing the most. CR14,290 and TAA15 are good markers for early selection of polyembryonic rootstocks in progenies derived from C. reshni, Citrus aurantium, and Citrus volkameriana.     

Adults of European ant‐like stone beetles (Coleoptera: Staphylinidae: Scydmaeninae) Scydmaenus tarsatus Müller & Kunze and Scydmaenus hellwigii (Herbst) prey on soft‐bodied arthropods

Scydmaenine beetles are commonly described as predators specialized in capturing and feeding on armored mites of the order Oribatida, and documented cases of feeding on other live arthropods have not been known. Based on laboratory observations and a broad choice of Acari (armored and soft‐bodied) and other soil arthropods, food preferences and associated behavior of two scydmaenine species are clarified and described. Adults of Scydmaenus tarsatus ignored oribatid and mesostigmatan mites, but readily attacked and fed on a soft‐bodied Rhizoglyphus sp. (Acaridae), and on small springtails, especially on Ceratophysella denticulata (Hypogastruridae). A water drinking behavior was observed for this species, not reported previously in any Staphylinidae. Scydmaenus hellwigii ignored all tested Acari (including Rhizoglyphus) and scavenged on dead neanurine collembolans or freshly cut pieces of large springtails; a long term culture was maintained by feeding beetles with isotomid springtails. Previously reported strict specialization of Scydmaenus as a predator on Oribatida was not confirmed and it is concluded that the studied species feed on live soft‐bodied organisms and scavenge on dead arthropods.