Data-driven guidelines for phylogenomic analyses using SNP data.

Premise: There is a general lack of consensus on the best practices for filtering of single-nucleotide polymorphisms (SNPs) and whether it is better to use SNPs or include flanking regions (full "locus") in phylogenomic analyses and subsequent comparative methods.

Methods: Using genotyping-by-sequencing data from 22 species, we assessed the effects of SNP vs. locus usage and SNP retention stringency.

Nuclear phylogenomics of Eperua (Leguminosae) highlights the role of habitat and morphological lability in dispersal and diversification across Amazonia and in the Caatinga-Cerrado ecotone.

Eperua is a genus of Neotropical trees that forms a major component of tropical lowland forests in Amazonia, especially in the Guiana Shield and on white-sand forests. One species occurs in the Cerrado-Caatinga ecotone, and the genus also inhabits riverine and terra firme forests. Species in Eperua exhibit one of two drastically different floral architectures and inflorescence types, each associated with distinct pollinators.

Preoperative Diagnosis of a Central Skull Base Giant Schwannoma From Tumoral Microhemorrhages Visualized on Susceptibility-Weighted Imaging.

A 64-year-old female presented with extensive osseous erosion of the central skull base from a large tumor, which was evaluated with a combination of CT and MRI. Susceptibility-weighted imaging (SWI) aided the correct preoperative diagnosis of giant skull base schwannoma by demonstrating intratumoral microhemorrhages, later confirmed on histology. Other imaging features on CT and MRI were not helpful to identify the schwannoma in this case.

Commonly used Bayesian diversification methods lead to biologically meaningful differences in branch-specific rates on empirical phylogenies.

Identifying along which lineages shifts in diversification rates occur is a central goal of comparative phylogenetics; these shifts may coincide with key evolutionary events such as the development of novel morphological characters, the acquisition of adaptive traits, polyploidization or other structural genomic changes, or dispersal to a new habitat and subsequent increase in environmental niche space. However, while multiple methods now exist to estimate diversification rates and identify shifts using phylogenetic topologies, the appropriate use and accuracy of these methods are hotly debated. Here we test whether five Bayesian methods-Bayesian Analysis of Macroevolutionary Mixtures (BAMM), two implementations of the Lineage-Specific Birth-Death-Shift model (LSBDS and PESTO), the approximate Multi-Type Birth-Death model (MTBD; implemented in BEAST2), and the Cladogenetic Diversification Rate Shift model (ClaDS2)-produce comparable results.

Immunological correlates of protection mediated by a whole organism, , vaccine deficient in chitosan.

Unlabelled: The global burden of infections due to the pathogenic fungus is substantial in persons with low CD4 T-cell counts. Previously, we deleted three chitin deacetylase genes from to create a chitosan-deficient, avirulent strain, designated as , which, when used as a vaccine, protected mice from challenge with virulent strain KN99. Here, we explored the immunological basis for protection.

Protection against experimental cryptococcosis elicited by Cationic Adjuvant Formulation 01-adjuvanted subunit vaccines.

The fungal infection, cryptococcosis, is responsible for >100,000 deaths annually. No licensed vaccines are available. We explored the efficacy and immune responses of subunit cryptococcal vaccines adjuvanted with Cationic Adjuvant Formulation 01 (CAF01).

Immunological correlates of protection mediated by a whole organism vaccine deficient in chitosan.

Unlabelled: The global burden of infections due to the pathogenic fungus is substantial in persons with low CD4 T cell counts. Previously, we deleted three chitin deacetylase genes from to create a chitosan-deficient, avirulent strain, designated which, when used as a vaccine, protected mice from challenge with virulent strain KN99. Here, we explored the immunological basis for protection.

Chitosan-Deficient Cryptococcus as Whole-Cell Vaccines.

Creating a safe and effective vaccine against infection by the fungal pathogen Cryptococcus neoformans is an appealing option that complements the discovery of new small molecule antifungals. Recent animal studies have yielded promising results for a variety of vaccines that include live-attenuated and heat-killed whole-cell vaccines, as well as subunit vaccines formulated around recombinant proteins. Some of the recombinantly engineered cryptococcal mutants in the chitosan biosynthesis pathway are avirulent and very effective at conferring protective immunity.

Fluorescence and Biochemical Assessment of the Chitin and Chitosan Content of Cryptococcus.

The cell wall of the fungal pathogens Cryptococcus neoformans and C. gattii is critical for cell wall integrity and signaling external threats to the cell, allowing it to adapt and grow in a variety of changing environments. Chitin is a polysaccharide found in the cell walls of fungi that is considered to be essential for fungal survival.

Protection against experimental cryptococcosis elicited by Cationic Adjuvant Formulation 01-adjuvanted subunit vaccines.

The fungal infection, cryptococcosis, is responsible for >100,000 deaths annually. No licensed vaccines are available. We explored the efficacy and immune responses of subunit cryptococcal vaccines adjuvanted with Cationic Adjuvant Formulation 01 (CAF01).

Immune evasion by in vaccinated mice coinfected with .

and , the etiologic agents of cryptococcosis, cause over 100,000 deaths worldwide every year, yet no cryptococcal vaccine has progressed to clinical trials. In preclinical studies, mice vaccinated with an attenuated strain of deleted of three cryptococcal chitin deacetylases (-ΔΔΔ) were protected against a lethal challenge with strain KN99. While ΔΔΔ extended the survival of mice infected with strain R265 compared to unvaccinated groups, we were unable to demonstrate fungal clearance as robust as that seen following KN99 challenge.

Chromosomal evolution, environmental heterogeneity, and migration drive spatial patterns of species richness in (Liliaceae).

We used nuclear genomic data and statistical models to evaluate the ecological and evolutionary processes shaping spatial variation in species richness in (Liliaceae, 74 spp.). occupies diverse habitats in the western United States and Mexico and has a center of diversity in the California Floristic Province, marked by multiple orogenies, winter rainfall, and highly divergent climates and substrates (including serpentine).

Role of the Glycine Receptor β Subunit in Synaptic Localization and Pathogenicity in Severe Startle Disease.

Startle disease is due to the disruption of recurrent inhibition in the spinal cord. Most common causes are genetic variants in genes (, ) encoding inhibitory glycine receptor (GlyR) subunits. The adult GlyR is a heteropentameric complex composed of α1 and β subunits that localizes at postsynaptic sites and replaces embryonically expressed GlyRα2 homomers.

The rapid radiation of Bomarea (Alstroemeriaceae: Liliales), driven by the rise of the Andes.

Geological events such as mountain uplift affect how, when, and where species diversify, but measuring those effects is a longstanding challenge. Andean orogeny impacted the evolution of regional biota by creating barriers to gene flow, opening new habitats, and changing local climate. B⁢o⁢m⁢a⁢r⁢e⁢a (Alstroemeriaceae) are tropical plants with (often) small, isolated ranges; in total, B⁢o⁢m⁢a⁢r⁢e⁢a species occur from central Mexico to central Chile.

Dysregulated pulmonary inflammatory responses exacerbate the outcome of secondary aspergillosis following influenza.

Severe influenza is a risk factor for fatal invasive pulmonary aspergillosis; however, the mechanistic basis for the lethality is unclear. Utilizing an influenza-associated pulmonary aspergillosis (IAPA) model, we found that mice infected with influenza A virus followed by had 100% mortality when superinfected during the early stages of influenza but survived at later stages. While superinfected mice had dysregulated pulmonary inflammatory responses compared to controls, they had neither increased inflammation nor extensive fungal growth.

Dysregulated Pulmonary Inflammatory Responses Exacerbate the Outcome of Secondary Aspergillosis Following Influenza.

Unlabelled: Inhalation of airborne conidia of the ubiquitous fungus commonly occurs but invasive aspergillosis is rare except in profoundly immunocompromised persons. Severe influenza predisposes patients to invasive pulmonary aspergillosis by mechanisms that are poorly defined. Using a post-influenza aspergillosis model, we found that superinfected mice had 100% mortality when challenged with conidia on days 2 and 5 (early stages) of influenza A virus infection but 100% survival when challenged on days 8 and 14 (late stages).

Review of Shoreline Extraction Methods from Aerial Laser Scanning.

Autonomous technologies are increasingly used in various areas of science. The use of unmanned vehicles for hydrographic surveys in shallow coastal areas requires accurate estimation of shoreline position. This is a nontrivial task, which can be performed using a wide range of sensors and methods.

Eighteen new species of Neotropical Costaceae (Zingiberales).

In preparation for a full taxonomic revision of the Neotropical genera of Costaceae (i.e., , , , and ), we present the description of 17 new species of Neotropical and one new species of the Neotropic endemic genus with notes on their distribution and ecology, vernacular names (when known), and diagnostic characters for identification.

Putative adaptive loci show parallel clinal variation in a California-endemic wildflower.

As the global climate crisis continues, predictions concerning how wild populations will respond to changing climate conditions are informed by an understanding of how populations have responded and/or adapted to climate variables in the past. Changes in the local biotic and abiotic environment can drive differences in phenology, physiology, morphology and demography between populations leading to local adaptation, yet the molecular basis of adaptive evolution in wild non-model organisms is poorly understood. We leverage comparisons between two lineages of Calochortus venustus occurring along parallel transects that allow us to identify loci under selection and measure clinal variation in allele frequencies as evidence of population-specific responses to selection along climatic gradients.

One Step Purification-Vaccine Delivery System.

Glucan particles (GPs) are hollow, porous 3-5 µm microspheres derived from the cell walls of Baker's yeast (). Their 1,3-β-glucan outer shell allows for receptor-mediated uptake by macrophages and other phagocytic innate immune cells expressing β-glucan receptors. GPs have been used for the targeted delivery of a wide range of payloads, including vaccines and nanoparticles, encapsulated inside the hollow cavity of GPs.

A Wox3-patterning module organizes planar growth in grass leaves and ligules.

Grass leaves develop from a ring of primordial initial cells within the periphery of the shoot apical meristem, a pool of organogenic stem cells that generates all of the organs of the plant shoot. At maturity, the grass leaf is a flattened, strap-like organ comprising a proximal supportive sheath surrounding the stem and a distal photosynthetic blade. The sheath and blade are partitioned by a hinge-like auricle and the ligule, a fringe of epidermally derived tissue that grows from the adaxial (top) leaf surface.

Cone humidity is a strong attractant in an obligate cycad pollination system.

Studies of pollination biology often focus on visual and olfactory aspects of attraction, with few studies addressing behavioral responses and morphological adaptation to primary metabolic attributes. As part of an in-depth study of obligate nursery pollination of cycads, we find that Rhopalotria furfuracea weevils show a strong physiological response and behavioral orientation to the cone humidity of the host plant Zamia furfuracea in an equally sensitive manner to their responses to Z. furfuracea-produced cone volatiles.