Genetic analysis reveals spatial structure in an expanding introduced rusa deer population

Context. Rusa deer (Cervus timorensis), originally introduced in the 1860s, are still spreading in eastern Australia. The expanding peri-urban rusa deer population in the Illawarra region of New South Wales, Australia is having undesirable impacts on human and ecological communities, but the spatial structure of this population has not been investigated. Genetic information on invasive species is potentially useful in identifying management units to mitigate undesirable impacts. Aims. The aim of this study was to investigate population structure, characterise dispersal, and determine if natural and human-made landscape features affected gene flow in rusa deer invading the Illawarra region of New South Wales. Methods. We used reduced representation sequencing (DArT-Seq) to analyse single nucleotide polymorphisms distributed throughout the genomic DNA of rusa deer culled during a management program. We used admixture and Principal Component Analyses to investigate population structure with respect to natural and human-made landscape features, and we investigated whether our genetic data supported the presence of sex-biased dispersal. Key results. Genetic diversity was highest in the north, near the original introduction site. A railway line demarcated restricted gene flow. Surprisingly, the Illawarra escarpment, a prominent landscape feature, did not restrict gene flow. There was no evidence of sex-biased dispersal and seven individuals were identified as genetic outliers. Conclusions. The genetic structure of the Illawarra rusa deer population is consistent with individuals spreading south from their introduction site in Royal National Park. The population is not panmictic, and a landscape feature associated with urbanisation was associated with increased spatial genetic structure. Outliers could indicate hybridisation or secondary incursion events. Implications. Rusa deer can be expected to continue invading southwards in the Illawarra region, but landscape features associated with urbanisation might reduce dispersal across the landscape. The genetic structuring of the population identified three potential management units on which to prioritise ground shooting operations

Transports and pathways of overflow water in the Rockall Trough

Water mass analysis reveals a persistent core of deep overflow water within the Rockall Trough which hugs the northern and western boundaries of the basin. Mean speeds within this overflow are 10–15 cm s−1 giving a transport time from the Wyville Thomson Ridge to the central basin of < 50 days. Analysis of the 40-year Extended Ellett Line record shows proportions of Norwegian Sea Deep Water associated with the deep core exceed 15% around one quarter of the time. We present the first transport estimates for overflow water in the Rockall Trough. This flux is for overflow water modified by mixing with a density greater than 27.65 kg m−3. Mean values calculated both from a newly deployed mooring array (OSNAP project) and indirectly from the Extended Ellett Line time-series are −0.3 ± 0.04 Sv. Although the flux is highly variable there is no long term trend. As some overflow appears to exit into the Iceland Basin via channels between the northern banks, we suggest that the volume transport will likely increase as the flow pathway is traced back around the boundary of the Rockall Trough towards the Wyville Thomson Ridge

Cytochrome oxidase subunit VI of Trypanosoma brucei is imported without a cleaved presequence and is developmentally regulated at both RNA and protein levels

Mitochondrial respiration in the African trypanosome undergoes dramatic developmental stage regulation. This requires co-ordinated control of components encoded by both the nuclear genome and the kinetoplast, the unusual mitochondrial genome of these parasites. As a model for understanding the co-ordination of these genomes, we have examined the regulation and mitochondrial import of a nuclear-encoded component of the cytochrome oxidase complex, cytochrome oxidase subunit VI (COXVI). By generating transgenic trypanosomes expressing intact or mutant forms of this protein, we demonstrate that COXVI is not imported using a conventional cleaved presequence and show that sequences at the N-terminus of the protein are necessary for correct mitochondrial sorting. Analyses of endogenous and transgenic COXVI mRNA and protein expression in parasites undergoing developmental stage differentiation demonstrates a temporal order of control involving regulation in the abundance of, first, mRNA and then protein. This represents the first dissection of the regulation and import of a nuclear-encoded protein into the cytochrome oxidase complex in these organisms, which were among the earliest eukaryotes to possess a mitochondrion

"Preferred reading" of Legal Texts

In the 1970s, British cultural theorist Stuart Hall introduced a concept known as preferred reading. It combines the ideological influence of mass media and dominant ways of understanding any text. This article focuses on mass media as a source of ideological background or context of legal interpretation and of any reading of legal texts. Law operates in culture and culture represents limitations in the law, according to the needs of dominant ideology. Culture introduces structures of domination which manipulate law. An important role is also given to popular culture and mass culture. These parts of the culture industry create borders in which the recipients (audience) think of law. Through mass media – rather than through other channels – dominant ideology infiltrates law. Legal consciousness is formed by dominant cultural frames formed by dominant ideology. Through this formation of mass media, law becomes a commodity. It shares the same values or contents as that of cultural industry and is the place where the theory of preferred reading can be introduced. According to the aforementioned theory, there are methods of interpretation that are more accurate than others are. This is simply because they lead to a result that is more preferred by ‘common opinion’ disseminated by mass culture.V roce 1970, britský kulturní teoretik Stuart Hall představil koncept známý jako preferovaného čtení. Ten v sobě spojuje ideologický vliv masových médií a dominantní způsoby chápání jakéhokoli textu. Tento článek se zaměřuje masová média jako zdroj ideologického pozadí nebo kontextu právního výkladu. Právo působí v kultuře a kultura představuje omezení právo dle potřeb dominantní ideologie. Kultura vytváří struktury dominace, které manipulují právem. Důležitou roli také sehrává populární a masová kultura. Tyto části kulturního průmyslu vytváří hranice, ve kterých příjemci (publikum) uvažují o právu. Prostřednictvím masových médií - spíše než prostřednictvím jiných kanálů - dominantní ideologie infiltruje právo. Právní vědomí je tvořeno dominantními kulturními rámci vytvořenými dominantní ideologií. Prostřednictvím této formace vytvářené masovými médii se právo stává komoditou. Sdílí proto stejné hodnoty, nebo obsah jaké definuje kulturní průmysl. Proto lze i v právním kontextu uvažovat o tzv. preferovaném čtení. Proto lze identifikovat paradigmata výkladu, které jsou mnohem "použeitelnější" než jiné, protože vedou k očekávaným výsledkům. K výsledkům, které odpovídají očekávání masového publika.In the 1970s, British cultural theorist Stuart Hall introduced a concept known as preferred reading. It combines the ideological influence of mass media and dominant ways of understanding any text. This article focuses on mass media as a source of ideological background or context of legal interpretation and of any reading of legal texts. Law operates in culture and culture represents limitations in the law, according to the needs of dominant ideology. Culture introduces structures of domination which manipulate law. An important role is also given to popular culture and mass culture. These parts of the culture industry create borders in which the recipients (audience) think of law. Through mass media – rather than through other channels – dominant ideology infiltrates law. Legal consciousness is formed by dominant cultural frames formed by dominant ideology. Through this formation of mass media, law becomes a commodity. It shares the same values or contents as that of cultural industry and is the place where the theory of preferred reading can be introduced. According to the aforementioned theory, there are methods of interpretation that are more accurate than others are. This is simply because they lead to a result that is more preferred by ‘common opinion’ disseminated by mass culture

Population Pharmacokinetics of Olanzapine in Children

Aims The aim of this study was to evaluate the population pharmacokinetics (PopPK) of olanzapine in children and devise a model-informed paediatric dosing scheme. Methods The PopPK of olanzapine was characterized using opportunistically collected plasma samples from children receiving olanzapine per standard of care for any indication. A nonlinear mixed effect modelling approach was employed for model development using the software NONMEM (v7.4). Simulations from the developed PopPK model were used to devise a paediatric dosing scheme that targeted comparable plasma exposures to adolescents and adults. Results Forty-five participants contributed 83 plasma samples towards the analysis. The median (range) postnatal age and body weight of participants were 3.8 years (0.2–19.2) and 14.1 kg (4.2–111.7), respectively. The analysis was restricted to pharmacokinetic (PK) samples collected following enteral administration (oral and feeding tube). A one-compartment model with linear elimination provided an appropriate fit to the data. The final model included the covariates body weight and postmenstrual age (PMA) on apparent olanzapine clearance (CL/F). Typical CL/F and apparent volume of distribution (scaled to 70 kg) were 16.8 L/h (21% RSE) and 663 L (13% RSE), respectively. Developed dosing schemes used weight-normalized doses for children ≤6 months postnatal age or \u3c15 kg and fixed doses for children ≥15 kg. Conclusion We developed a paediatric PopPK model for enterally-administered olanzapine. To our knowledge, this analysis is the first study to characterize the PK of olanzapine in participants ranging from infants to adolescents. Body weight and PMA were identified as influential covariates for characterizing developmental changes in olanzapine apparent clearance

Concurrent invasions by European starlings (Sturnus vulgaris) suggest selection on shared genomic regions even after genetic bottlenecks

A species’ success during the invasion of new areas hinges on an interplay between the demographic processes common to invasions and the specific ecological context of the novel environment. Evolutionary genetic studies of invasive species can investigate how genetic bottlenecks and ecological conditions shape genetic variation in invasions, and our study pairs two invasive populations that are hypothesized to be from the same source population to compare how each population evolved during and after introduction. Invasive European Starlings (Sturnus vulgaris) established populations in both Australia and North America in the 19th century. Here, we compare whole-genome sequences among native and independently introduced European Starling populations to determine how demographic processes interact with rapid evolution to generate similar genetic patterns in these recent and replicated invasions. Demographic models indicate that both invasive populations experienced genetic bottlenecks as expected based on invasion history, and we find that specific genomic regions have differentiated even on this short evolutionary timescale. Despite genetic bottlenecks, we suggest that genetic drift alone cannot explain differentiation in at least two of these regions. The demographic boom intrinsic to many invasions as well as potential inversions may have led to high population-specific differentiation, although the patterns of genetic variation are also consistent with the hypothesis that this infamous and highly mobile invader adapted to novel selection (e.g., extrinsic factors). We use targeted sampling of replicated invasions to identify and evaluate support for multiple, interacting evolutionary mechanisms that lead to differentiation during the invasion process

Transcript- and annotation-guided genome assembly of the European starling

First published: 28 June 2022The European starling, Sturnus vulgaris, is an ecologically significant, globally invasive avian species that is also suffering from a major decline in its native range. Here, we present the genome assembly and long- read transcriptome of an Australian-sourced European starling (S. vulgaris vAU), and a second, North American, short- read genome assembly (S. vulgaris vNA), as complementary reference genomes for population genetic and evolutionary characterization. S. vulgaris vAU combined 10× genomics linked- reads, low-coverage Nanopore sequencing, and PacBio Iso-Seq full- length transcript scaffolding to generate a 1050 Mb assembly on 6222 scaffolds (7.6 Mb scaffold N50, 94.6% busco completeness). Further scaffolding against the high-quality zebra finch (Taeniopygia guttata) genome assigned 98.6% of the assembly to 32 puta-tive nuclear chromosome scaffolds. Species-specific transcript mapping and gene an-notation revealed good gene- level assembly and high functional completeness. Using S. vulgaris vAU, we demonstrate how the multifunctional use of PacBio Iso-Seq tran-script data and complementary homology-based annotation of sequential assembly steps (assessed using a new tool, saaga) can be used to assess, inform, and validate assembly workflow decisions. We also highlight some counterintuitive behaviour in traditional busco metrics, and present buscomp, a complementary tool for assembly comparison designed to be robust to differences in assembly size and base-calling quality. This work expands our knowledge of avian genomes and the available toolkit for assessing and improving genome quality. The new genomic resources presented will facilitate further global genomic and transcriptomic analysis on this ecologically important species.Katarina C. Stuart, Richard J. Edwards, Yuanyuan Cheng, Wesley C. Warren, David W. Burt, William B. Sherwin, Natalie R. Hofmeister, Scott J. Werner, Gregory F. Ball, Melissa Bateson, Matthew C. Brandley, Katherine L. Buchanan, Phillip Cassey, David F. Clayton, Tim De Meyer, Simone L. Meddle, Lee A. Rollin

The Cell Cycle Regulated Transcriptome of Trypanosoma brucei

Progression of the eukaryotic cell cycle requires the regulation of hundreds of genes to ensure that they are expressed at the required times. Integral to cell cycle progression in yeast and animal cells are temporally controlled, progressive waves of transcription mediated by cell cycle-regulated transcription factors. However, in the kinetoplastids, a group of early-branching eukaryotes including many important pathogens, transcriptional regulation is almost completely absent, raising questions about the extent of cell-cycle regulation in these organisms and the mechanisms whereby regulation is achieved. Here, we analyse gene expression over the Trypanosoma brucei cell cycle, measuring changes in mRNA abundance on a transcriptome-wide scale. We developed a “double-cut” elutriation procedure to select unperturbed, highly synchronous cell populations from log-phase cultures, and compared this to synchronization by starvation. Transcriptome profiling over the cell cycle revealed the regulation of at least 430 genes. While only a minority were homologous to known cell cycle regulated transcripts in yeast or human, their functions correlated with the cellular processes occurring at the time of peak expression. We searched for potential target sites of RNA-binding proteins in these transcripts, which might earmark them for selective degradation or stabilization. Over-represented sequence motifs were found in several co-regulated transcript groups and were conserved in other kinetoplastids. Furthermore, we found evidence for cell-cycle regulation of a flagellar protein regulon with a highly conserved sequence motif, bearing similarity to consensus PUF-protein binding motifs. RNA sequence motifs that are functional in cell-cycle regulation were more widespread than previously expected and conserved within kinetoplastids. These findings highlight the central importance of post-transcriptional regulation in the proliferation of parasitic kinetoplastids