Cellular and Genomic Properties of Haloferax gibbonsii LR2-5, the Host of Euryarchaeal Virus HFTV1

Hypersaline environments are the source of many viruses infecting different species of halophilic euryarchaea. Information on infection mechanisms of archaeal viruses is scarce, due to the lack of genetically accessible virus-host models. Recently, a new archaeal siphovirus, Haloferax tailed virus 1 (HFTV1), was isolated together with its host belonging to the genus Haloferax, but it is not infectious on the widely used model euryarcheon Haloferax volcanii. To gain more insight into the biology of HFTV1 host strain LR2-5, we studied characteristics that might play a role in its virus susceptibility: growth-dependent motility, surface layer, filamentous surface structures, and cell shape. Its genome sequence showed that LR2-5 is a new strain of Haloferax gibbonsii. LR2-5 lacks obvious viral defense systems, such as CRISPR-Cas, and the composition of its cell surface is different from Hfx. volcanii, which might explain the different viral host range. This work provides first deep insights into the relationship between the host of halovirus HFTV1 and other members of the genus Haloferax. Given the close relationship to the genetically accessible Hfx. volcanii, LR2-5 has high potential as a new model for virus-host studies in euryarchaea

Electrochemical deposition of bismuth telluride thick layers onto nickel

Bismuth telluride (Bi2Te3) is the currently best performing thermoelectric (TE) material in commercial TE devices for refrigeration and waste heat recovery up to 200 °C. Up to 800 μm thick, compact, uniform and stoichiometric Bi2Te3 films were synthesized by pulsed electrodeposition from 2 M nitric acid baths containing bismuth and tellurium dioxide on 1 cm2 nickel (Ni) substrates at average film growth rates of ~ 50 μm/h. Pre-treatment of the Ni substrate was found to significantly enhance the adhesion of Bi2Te3 material onto Ni while pulsed electrodeposition was used to increase the compactness of the material. To maintain a homogeneous composition across the thickness of the films, a sacrificial Bi2Te3 anode was employed. All deposits produced were n-type with a Seebeck coefficient of up to − 80 μV/K and an electrical conductivity of ~ 330 S/cm at room temperature

Expanding the stdpopsim species catalog, and lessons learned for realistic genome simulations

Simulation is a key tool in population genetics for both methods development and empirical research, but producing simulations that recapitulate the main features of genomic datasets remains a major obstacle. Today, more realistic simulations are possible thanks to large increases in the quantity and quality of available genetic data, and the sophistication of inference and simulation software. However, implementing these simulations still requires substantial time and specialized knowledge. These challenges are especially pronounced for simulating genomes for species that are not well-studied, since it is not always clear what information is required to produce simulations with a level of realism sufficient to confidently answer a given question. The community-developed framework stdpopsim seeks to lower this barrier by facilitating the simulation of complex population genetic models using up-to-date information. The initial version of stdpopsim focused on establishing this framework using six well-characterized model species (Adrion et al., 2020). Here, we report on major improvements made in the new release of stdpopsim (version 0.2), which includes a significant expansion of the species catalog and substantial additions to simulation capabilities. Features added to improve the realism of the simulated genomes include non-crossover recombination and provision of species-specific genomic annotations. Through community-driven efforts, we expanded the number of species in the catalog more than threefold and broadened coverage across the tree of life. During the process of expanding the catalog, we have identified common sticking points and developed the best practices for setting up genome-scale simulations. We describe the input data required for generating a realistic simulation, suggest good practices for obtaining the relevant information from the literature, and discuss common pitfalls and major considerations. These improvements to stdpopsim aim to further promote the use of realistic whole-genome population genetic simulations, especially in non-model organisms, making them available, transparent, and accessible to everyone

Mycosis fungoides and Sézary syndrome.

Mycosis fungoides (MF) and Sézary syndrome (SS) are primary cutaneous T-cell lymphomas (CTCL) with not yet fully understood etiology and pathogenesis. Conceptually, MF and SS are classified as distinct entities arising from different T helper cell subsets. MF is the most common CTCL entity, while SS is very rare. MF presents clinically with patch, plaque and/or tumor stages, but can also evolve as erythroderma, which in turn is pathognomonic for SS. SS is characterized by a detectable tumor-cell burden (Sézary cells) in the peripheral blood consistent with advanced-stage disease and a poor prognosis. In early-stage disease of MF, which is the predominant form, the prognosis is generally favorable. However, in up to 30 % of patients, there is progression of skin lesions, which can ultimately lead to visceral involvement. The histological manifestation of MF can be subtle in early-stage disease and therefore a careful clinicopathological correlation is paramount. The treatment of MF/SS is dependent on the disease stage. Therapeutic options include both skin-directed and systemic regimens. Apart from allogeneic stem cell transplantation (alloSCT), there is as yet no curative therapy for MF/SS. Accordingly, the treatment approach is symptom oriented and aims to reduce the tumor burden and improve health-related quality of life. However, the therapeutic landscape for CTCL is constantly being expanded by the discovery of novel therapeutic targets

Posterior trees

Each line of the file contains a posterior phylogeny generated using BALi-Phy (Suchard and Redelings 2006

Name key

Name key matching growth chamber taxa and tree tip label

Data from: Grow where you thrive, or where only you can survive? An analysis of performance curve evolution in a clade with diverse habitat affinities

Performance curves are valuable tools for quantifying the fundamental niches of organisms and testing hypotheses about evolution, life history trade-offs, and the drivers of variation in species' distribution patterns. Here, we present a novel Bayesian method for characterizing performance curves that facilitates comparisons among species. We then use this model to quantify and compare the hydrological performance curves of 14 different taxa in the genus Lasthenia, an ecologically diverse clade of plants that collectively occupy a variety of habitats with unique hydrological features, including seasonally flooded wetlands called vernal pools. We conducted a growth chamber experiment to measure each taxon's fitness across five hydrological treatments that ranged from severe drought to extended flooding, and identified differences in hydrological performance curves that explain their associations with vernal pool and terrestrial habitats. Our analysis revealed that the distribution of vernal pool taxa in the field do not reflect their optimal hydrological environments: all taxa, regardless of habitat affinity, have highest fitness under similar hydrological conditions of saturated soil without submergence. We also found that a taxon's relative position across flood gradients within vernal pools is best predicted by the height of its performance curve. These results demonstrate the utility of our approach for generating insights into when and how performance curves evolve among taxa as they diversify into distinct environments. To facilitate its use, the modeling framework has been developed into an R package (https://github.com/silastittes/performr)

Lasthenia depths

Field measures for average depth (cm) of taxon occurring within vernal pools

Growth chamber data

Raw growth chamber data for fourteen Lasthenia taxa analyzed in manuscript. Response variable: Inflor_biomass. Treatment levels, D (drought = 1), MD (minor drought = 2), B (benign = 3), MF (minor flood = 4), F (flood = 5). See paper and GitHub repository for details on how this file was filtered and parsed for downstream analyses