Reconstructing mitochondrial genomes directly from genomic next-generation sequencing reads—a baiting and iterative mapping approach

We present an in silico approach for the reconstruction of complete mitochondrial genomes of non-model organisms directly from next-generation sequencing (NGS) data—mitochondrial baiting and iterative mapping (MITObim). The method is straightforward even if only (i) distantly related mitochondrial genomes or (ii) mitochondrial barcode sequences are available as starting-reference sequences or seeds, respectively. We demonstrate the efficiency of the approach in case studies using real NGS data sets of the two monogenean ectoparasites species Gyrodactylus thymalli and Gyrodactylus derjavinoides including their respective teleost hosts European grayling (Thymallus thymallus) and Rainbow trout (Oncorhynchus mykiss). MITObim appeared superior to existing tools in terms of accuracy, runtime and memory requirements and fully automatically recovered mitochondrial genomes exceeding 99.5% accuracy from total genomic DNA derived NGS data sets in <24 h using a standard desktop computer. The approach overcomes the limitations of traditional strategies for obtaining mitochondrial genomes for species with little or no mitochondrial sequence information at hand and represents a fast and highly efficient in silico alternative to laborious conventional strategies relying on initial long-range PCR. We furthermore demonstrate the applicability of MITObim for metagenomic/pooled data sets using simulated data. MITObim is an easy to use tool even for biologists with modest bioinformatics experience. The software is made available as open source pipeline under the MIT license at https://github.com/chrishah/MITObim.     

Chromatographic and immunological evidence for mammalian GnRH and chicken GnRH II in eel (Anguilla anguilla) brain and pituitary

Gonadotropin-releasing hormone (GnRH) peptides in the brain and pituitary of the European eel (Anguilla anguilla) were investigated by reverse phase high performance liquid chromatography (HPLC) and radioimmunoassay with region-specific antisera. Two GnRH molecular forms were demonstrated in brain and pituitary extracts. One form eluted in the same position as synthetic mammalian GnRH on HPLC and was recognized by antibodies directed against the NH2 and COOH termini of mammalian GnRH as well as by antibodies to the middle region. The second form eluted in the same position as synthetic chicken GnRH II and was recognized by specific antibodies to this molecule. Salmon GnRH and chicken GnRH I were not detected. The occurrence of mammalian GnRH in teleost fish suggests that this molecular form is more ancient than was previously suspected and arose earlier than in primitive tetrapods, or that it has arisen in the eel through random mutation of salmon GnRH. The lack of salmon GnRH in the eel brain indicates that this molecular form is not common to all teleost species. The finding in eel brain of chicken GnRH II, which has previously been described in species of Mammalia, Aves, Reptilia, Amphibia, Osteichthyes, and Chondrichthyes, supports our hypothesis that this widespread structural variant may represent an early evolved and conserved form of GnRH.     

Teaching animal habitat selection using wildlife tracking equipment

We present a hands-on outdoor activity coupled with classroom discussion to teach students about wildlife habitat selection, the process by which animals choose where to live. By selecting locations or habitats with many benefits (e.g., food, shelter, mates) and few costs (e.g., predators), animals improve their ability to survive and reproduce. Biologists track animal movement using radio telemetry technology to study habitat selection so they can better provide species with habitats that promote population growth. We present a curriculum in which students locate “animals” (transmitters) using radio telemetry equipment and apply math skills (use of fractions and percentages) to assess their “animal's” habitat selection by comparing the availability of habitat types with the proportion of “animals” they find in each habitat type.     

The oil of Adenanthera pavonina L. seeds and its emulsions

The oil of Adenanthera pavonina L. seeds was analysed by chromatographic and instrumental means. The oil was found to be rich in neutral lipids (86.2%), and low in polar lipids (13.8%). The neutral lipids consisted mainly of triacylglycerols (64.2%). Unsaturated fatty acids were found as high as 71%, while the percentage of saturated fatty acids was only 29%. GC and GC/MS analyses revealed linoleic, oleic and lignocerotic acid to be predominant among all fatty acids in the A. pavonina oil, whereas stigmasterol was the major steroid identified within this study. Subsequently, the oil was used for preparation of submicron oil-in-water (o/w) lipid emulsions. Lipid emulsions were formulated by using soybean lecithin (SL) to investigate their particle size, Zeta potential and stability at the different oil and SL ratios. The results obtained indicate possible applications of the tested oil in pharmaceutical and medical fields as drug and cosmetic active ingredient carriers.     

New resources for genetic studies in Populus nigra: genome‐wide SNP discovery and development of a 12k Infinium array

Whole genome resequencing of 51 Populus nigra (L.) individuals from across Western Europe was performed using Illumina platforms. A total number of 1 878 727 SNPs distributed along the P. nigra reference sequence were identified. The SNP calling accuracy was validated with Sanger sequencing. SNPs were selected within 14 previously identified QTL regions, 2916 expressional candidate genes related to rust resistance, wood properties, water‐use efficiency and bud phenology and 1732 genes randomly spread across the genome. Over 10 000 SNPs were selected for the construction of a 12k Infinium Bead‐Chip array dedicated to association mapping. The SNP genotyping assay was performed with 888 P. nigra individuals. The genotyping success rate was 91%. Our high success rate was due to the discovery panel design and the stringent parameters applied for SNP calling and selection. In the same set of P. nigra genotypes, linkage disequilibrium throughout the genome decayed on average within 5–7 kb to half of its maximum value. As an application test, ADMIXTURE analysis was performed with a selection of 600 SNPs spread throughout the genome and 706 individuals collected along 12 river basins. The admixture pattern was consistent with genetic diversity revealed by neutral markers and the geographical distribution of the populations. These newly developed SNP resources and genotyping array provide a valuable tool for population genetic studies and identification of QTLs through natural‐population based genetic association studies in P. nigra.     

Usefulness of linked DNA probes for prenatal diagnosis of cystic fibrosis: report of a case in a 1:4 risk pregnancy

Prenatal diagnosis of cystic fibrosis was performed with linked DNA probes in a couple with a 1:4 risk. The limits and the future of molecular prenatal diagnosis are discussed.     

Recolonizing native wildlife facilitates exotic plant invasion into Singapore's rain forests

Halting biological invasions and rewilding extirpated native fauna are conservation interventions to bolster biodiversity, species interactions, and ecosystems. These actions are often considered separately and the potential for reintroduced wildlife to facilitate invasive plants has been largely overlooked. Here, we investigated the role of Singapore's recolonizing native wild pigs (Sus scrofa) in facilitating an invasive weed Miconia crenata into tropical rainforests, which are normally highly resistant to invasion. We conducted line-transect surveys in 11 Singaporean rain forests and used generalized linear mixed models to consider the contribution of pigs' soil disturbances, human forest paths, and other environmental covariates, on the density of M. crenata. We found that M. crenata was more abundant at forest edges and invasion into forest interior was facilitated by pigs, paths, and canopy gaps, but that these effects were all additive, not synergistic (i.e., not multiplicative). These results highlight how modern invasions are driven by multiple disturbances as well as propagule pressure (e.g., urban birds dispersing seeds at forest edges where they establish in pig soil disturbances). Singapore's extensive native forest restoration efforts may have provided plentiful edge and secondary forests that are well suited to pigs and M. crenata, which in turn undermine the aims of fostering later-successional native plant communities. To prevent negative externalities, we suggest that plant restoration and rewilding projects consider the potential role of wildlife in facilitating non-native plants, and couple these actions with preliminary screening of unintended consequences and continued monitoring, as well as limiting human-mediated weed invasion to minimize propagule sources.     

Age-dependent changes in the in-vitro response of a pig Sertoli cell-enriched population to FSH

The response of pig Sertoli cell-enriched cultures to FSH was investigated by measuring plasminogen activator (PA) secretion in culture, throughout the nonpubertal and prepubertal periods. Sertoli cell-enriched populations could be isolated from birth until a testicular weight of 56 g. FSH elicited a dose-dependent increase in PA secretion by pig Sertoli cell-enriched cultures. The ED50 was minimal for cells coming from testes weighing 10-22 g, and increased more than 2-fold for cells from heavier testes. This suggests that, at the end of the non-pubertal period, an increased FSH sensitivity is important for initiation of spermatogenesis in this species, and that during the prepubertal period Sertoli cells become less sensitive to FSH. The FSH-stimulated PA secretion increased about 10-fold from a testicular weight of 25 g onwards, i.e. when primary spermatocytes appear in seminiferous tubules.     

The fast milk acidifying phenotype of Streptococcus thermophilus can be acquired by natural transformation of the genomic island encoding the cell-envelope proteinase PrtS

Background

FAD dependent glucose dehydrogenase (GDH) currently raises enormous interest in the field of glucose biosensors. Due to its superior properties such as high turnover rate, substrate specificity and oxygen independence, GDH makes its way into glucose biosensing. The recently discovered GDH from the ascomycete Glomerella cingulata is a novel candidate for such an electrochemical application, but also of interest to study the plant-pathogen interaction of a family of wide-spread, crop destroying fungi. Heterologous expression is a necessity to facilitate the production of GDH for biotechnological applications and to study its physiological role in the outbreak of anthracnose caused by Glomerella (anamorph Colletotrichum) spp.

Results

Heterologous expression of active G. cingulata GDH has been achieved in both Escherichia coli and Pichia pastoris, however, the expressed volumetric activity was about 4800-fold higher in P. pastoris. Expression in E. coli resulted mainly in the formation of inclusion bodies and only after co-expression with molecular chaperones enzymatic activity was detected. The fed-batch cultivation of a P. pastoris transformant resulted in an expression of 48,000 U L^-1 of GDH activity (57 mg L^-1). Recombinant GDH was purified by a two-step purification procedure with a yield of 71%. Comparative characterization of molecular and catalytic properties shows identical features for the GDH expressed in P. pastoris and the wild-type enzyme from its natural fungal source.

Conclusions

The heterologous expression of active GDH was greatly favoured in the eukaryotic host. The efficient expression in P. pastoris facilitates the production of genetically engineered GDH variants for electrochemical-, physiological- and structural studies.