Identification of common carp innate immune genes with whole-genome sequencing and RNA-seq data

169Computer Systems, Imagery and MediaAnimal science

Fabrication of Atomically Precise Nanopores in Hexagonal Boron Nitride

We demonstrate the fabrication of individual nanopores in hexagonal boron nitride (hBN) with atomically precise control of the pore size. Previous methods of pore production in other 2D materials create pores of irregular geometry with imprecise diameters. By taking advantage of the preferential growth of boron vacancies in hBN under electron beam irradiation, we are able to observe the pore growth via transmission electron microscopy, and terminate the process when the pore has reached its desired size. Careful control of beam conditions allows us to nucleate and grow individual triangular and hexagonal pores with diameters ranging from subnanometer to 6nm over a large area of suspended hBN using a conventional TEM. These nanopores could find application in molecular sensing, DNA sequencing, water desalination, and molecular separation. Furthermore, the chemical edge-groups along the hBN pores can be made entirely nitrogen terminated or faceted with boron-terminated edges, opening avenues for tailored functionalization and extending the applications of these hBN nanopores.Comment: 5 pages, 6 figure

Deep sequencing of the innate immune transcriptomic response of zebrafish embryos to Salmonella infection

Animal science

First draft genome sequence of the Japanese eel, Anguilla japonica

The Japanese eel is a much appreciated research object and very important for Asian aquaculture; however, its genomic resources are still limited. We have used a streamlined bioinformatics pipeline for the de novo assembly of the genome sequence of the Japanese eel from raw Illumina sequence reads. The total assembled genome has a size of 1.15 Gbp, which is divided over 323,776 scaffolds with an N50 of 52,849 bp, a minimum scaffold size of 200 bp and a maximum scaffold size of 1.14 Mbp. Direct comparison of a representative set of scaffolds revealed that all the Hox genes and their intergenic distances are almost perfectly conserved between the European and the Japanese eel. The first draft genome sequence of an organism strongly catalyzes research progress in multiple fields. Therefore, the Japanese eel genome sequence will provide a rich resource of data for all scientists working on this important fish species.Microbial Biotechnolog

Comparison of the exomes of common carp (Cyprinus carpio) and zebrafish (Danio rerio)

Research on common carp, Cyprinus carpio, is beneficial for zebrafish research because of resources available owing to its large body size, such as the availability of sufficient organ material for transcriptomics, proteomics, and metabolomics. Here we describe the shot gun sequencing of a clonal double-haploid common carp line. The assembly consists of 511891 scaffolds with an N50 of 17¿kb, predicting a total genome size of 1.4–1.5¿Gb. A detailed analysis of the ten largest scaffolds indicates that the carp genome has a considerably lower repeat coverage than zebrafish, whilst the average intron size is significantly smaller, making it comparable to the fugu genome. The quality of the scaffolding was confirmed by comparisons with RNA deep sequencing data sets and a manual analysis for synteny with the zebrafish, especially the Hox gene clusters. In the ten largest scaffolds analyzed, the synteny of genes is almost complete. Comparisons of predicted exons of common carp with those of the zebrafish revealed only few genes specific for either zebrafish or carp, most of these being of unknown function. This supports the hypothesis of an additional genome duplication event in the carp evolutionary history, which—due to a higher degree of compactness—did not result in a genome larger than that of zebrafish

De novo whole-genome assembly of a wild type yeast isolate using nanopore sequencing

Microbial Biotechnolog

Changes in ovarian gene expression profiles and plasma hormone levels in maturing European eel (Anguilla anguilla); Biomarkers for broodstock selection.

Complete sexual maturation of European eels (Anguilla anguilla) in captivity can only be achieved via injections with gonadotropins. For female eels this procedure takes 4-6months and the response ranges from "unresponsive" to final maturation and ovulation. Reproductive success could be significantly increased via early selection of responders based on predictive markers and minimally invasive sampling methods. To get a better understanding of the genetic background of ovarian maturation of the European eel we performed a pilot deep-sequencing transcriptome analysis of ovarian tissue derived from a yellow eel, a prepubertal silver eel and a post-spawning matured eel. Two key players in steroidogenesis were strongly correlated with advanced sexual maturation, namely P450c17 and liver receptor homolog-1, suggesting that blood plasma steroids might qualify as minimally invasive markers for early detection of responders. Since the predictive value of plasma sex steroid levels for final maturation of the European eel had not yet been carefully examined, we performed an extensive artificial maturation trial. Farmed silver eels were treated with pituitary extracts and sampled at multiple time intervals. Expression of steroidogenesis-related genes in ovarian tissue of responding and non-responding eels after four weekly injections with pituitary extract was compared using a custom-built microarray and RNAseq. Increased expression of 17β-hsd1 was strongly linked to sexual maturation. Blood plasma levels of sex steroids were measured using ELISAs. We show that a 2.5-fold increase in blood-plasma estradiol level after 4 weekly pituitary extract injections is a strong predictor of final sexual maturation of female European eel.Animal science