Survey of the genus Bursaphelenchus Fuchs, 1937 (Nematoda: Aphelenchoididae) in Romania

An overview of the occurrence of species of the genus Bursaphelenchus in Romania is presented. The data is based on recent surveys conducted for the first time throughout the country, to monitor and evaluate the potential entry of the pine wood nematode, Bursaphelenchus xylophilus. Wood samples were collected from declining trees, woodprocessing companies and imported wood packaging material. Of the 895 wood samples examined, 11 contained Bursaphelenchus specimens. Morphological and molecular analyses were carried out to characterize the species detected. With respect to the possible presence of B. xylophilus, all samples were negative, confirming the absence of this quarantine pest in Romania. Nevertheless, five Bursaphelenchus species were found: B. hofmanni, B. poligraphi, B. vallesianus, B. willibaldi, and one putative new species belonging to the sexdentati group, classified here as Bursaphelenchus sp. NR512. These results constitute the first report of the genus Bursaphelenchus in Romania

Transcriptional Rewiring of the Sex Determining dmrt1 Gene Duplicate by Transposable Elements

Control and coordination of eukaryotic gene expression rely on transcriptional and posttranscriptional regulatory networks. Evolutionary innovations and adaptations often require rapid changes of such networks. It has long been hypothesized that transposable elements (TE) might contribute to the rewiring of regulatory interactions. More recently it emerged that TEs might bring in ready-to-use transcription factor binding sites to create alterations to the promoters by which they were captured. A process where the gene regulatory architecture is of remarkable plasticity is sex determination. While the more downstream components of the sex determination cascades are evolutionary conserved, the master regulators can switch between groups of organisms even on the interspecies level or between populations. In the medaka fish (Oryzias latipes) a duplicated copy of dmrt1, designated dmrt1bY or DMY, on the Y chromosome was shown to be the master regulator of male development, similar to Sry in mammals. We found that the dmrt1bY gene has acquired a new feedback downregulation of its expression. Additionally, the autosomal dmrt1a gene is also able to regulate transcription of its duplicated paralog by binding to a unique target Dmrt1 site nested within the dmrt1bY proximal promoter region. We could trace back this novel regulatory element to a highly conserved sequence within a new type of TE that inserted into the upstream region of dmrt1bY shortly after the duplication event. Our data provide functional evidence for a role of TEs in transcriptional network rewiring for sub- and/or neo-functionalization of duplicated genes. In the particular case of dmrt1bY, this contributed to create new hierarchies of sex-determining genes

Acute-Phase CD8 T cell responses that select for escape variants are needed to control live attenuated simian immunodeficiency virus

The overall CD8 T cell response to human/simian immunodeficiency virus (HIV/SIV) targets a collection of discrete epitope specificities. Some of these epitope-specific CD8 T cells emerge in the weeks and months following infection and rapidly select forsequence variants, whereas other CD8 T cell responses develop during the chronic infection phase and rarely select for sequence variants. In this study, we tested the hypothesis that acute-phase CD8 T cell responses that do not rapidly select for escapevariants are unable to control viral replication in vivo as well as those that do rapidly select for escape variants. We created a derivative of live attenuated SIV (SIVmac239Δnef) in which we ablated five epitopes that elicit early CD8 T cell responses and rapidly accumulate sequence variants in SIVmac239-infected Mauritian cynomolgus macaques (MCMs) that are homozygous for the M3 major histocompatibility complex (MHC) haplotype. This live attenuated SIV variant was called m3KOΔnef. Viremia was significantly higher in M3 homozygous MCMs infected withm3KOΔnef than in either MHC-mismatched MCMs infected with m3KOΔ nef or MCMs infected with SIVmac239Δnef. Three CD8 T cell responses, including two that do not rapidly select for escape variants, predominated during earlym3KOΔnef infection in the M3 homozygous MCMs, but these animals were unable to control viral replication. These re-sults provide evidence that acute-phase CD8 T cell responses that have the potential to rapidly select for escape variants in the early phase ofinfection are needed to establish viral control in vivo

Creating knowledge environment during lean product development process of jet engine

Organizations invest intense resources in their product development processes. This paper aims to create a knowledge environment using trade-off curves during the early stages of the set-based concurrent engineering (SBCE) process of an aircraft jet engine for a reduced noise level at takeoff. Data is collected from a range of products in the same family as the jet engine. Knowledge-based trade-off curves are used as a methodology to create and visualize knowledge from the collected data. Findings showed that this method provides designers with enough confidence to identify a set of design solutions during the SBCE application

Performance of ionospheric maps in support of long baseline GNSS kinematic positioning at low latitudes

Ionospheric scintillation occurs mainly at high and low latitude regions of the Earth and may impose serious degradation on GNSS (Global Navigation Satellite System) functionality. The Brazilian territory sits on one of the most affected areas of the globe, where the ionosphere behaves very unpredictably, with strong scintillation frequently occurring in the local postsunset hours. The correlation between scintillation occurrence and sharp variations in the ionospheric total electron content (TEC) in Brazil is demonstrated in Spogli et al. (2013). The compounded effect of these associated ionospheric disturbances on long baseline GNSS kinematic positioning is studied in this paper, in particular when ionospheric maps are used to aid the positioning solution. The experiments have been conducted using data from GNSS reference stations in Brazil. The use of a regional TEC map generated under the CALIBRA (Countering GNSS high-Accuracy applications Limitations due to Ionospheric disturbances in BRAzil) project, referred to as CALIBRA TEC map (CTM), was compared to the use of the Global Ionosphere Map (GIM), provided by the International GNSS Service (IGS). Results show that the use of the CTM greatly improves the kinematic positioning solution as compared with that using the GIM, especially under disturbed ionospheric conditions. Additionally, different hypotheses were tested regarding the precision of the TEC values obtained from ionospheric maps, and its effect on the long baseline kinematic solution evaluated. Finally, this study compares two interpolation methods for ionospheric maps, namely, the Inverse Distance Weight and the Natural Neighbor

The sterlet sturgeon genome sequence and the mechanisms of segmental rediploidization.

Sturgeons seem to be frozen in time. The archaic characteristics of this ancient fish lineage place it in a key phylogenetic position at the base of the ~30,000 modern teleost fish species. Moreover, sturgeons are notoriously polyploid, providing unique opportunities to investigate the evolution of polyploid genomes. We assembled a high-quality chromosome-level reference genome for the sterlet, Acipenser ruthenus. Our analysis revealed a very low protein evolution rate that is at least as slow as in other deep branches of the vertebrate tree, such as that of the coelacanth. We uncovered a whole-genome duplication that occurred in the Jurassic, early in the evolution of the entire sturgeon lineage. Following this polyploidization, the rediploidization of the genome included the loss of whole chromosomes in a segmental deduplication process. While known adaptive processes helped conserve a high degree of structural and functional tetraploidy over more than 180 million years, the reduction of redundancy of the polyploid genome seems to have been remarkably random

Chromosomal-level assembly of the Asian Seabass genome using long sequence reads and multi-layered scaffolding

We report here the ~670 Mb genome assembly of the Asian seabass (Lates calcarifer), a tropical marine teleost. We used long-read sequencing augmented by transcriptomics, optical and genetic mapping along with shared synteny from closely related fish species to derive a chromosome-level assembly with a contig N50 size over 1 Mb and scaffold N50 size over 25 Mb that span ~90% of the genome. The population structure of L. calcarifer species complex was analyzed by re-sequencing 61 individuals representing various regions across the species' native range. SNP analyses identified high levels of genetic diversity and confirmed earlier indications of a population stratification comprising three clades with signs of admixture apparent in the South-East Asian population. The quality of the Asian seabass genome assembly far exceeds that of any other fish species, and will serve as a new standard for fish genomics