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The impact of immunology on our daily lives is growing every year. From vaccines to immunotherapies, it's essential for our healthcare professionals (present and future) and the general public as patients or caregivers to be literate in immunology. One way to foster immune literacy in this rapidly advancing field is through Primary Scientific Literature (PSL). There are unique challenges with integrating PSL into immunology courses. First, the laboratory techniques used are often new and not things students have tried before or may have access to, such as flow cytometry. Second, the tools used in this literature can be confusing. For example, antibodies are often used as both part of the research method and as the research subject. Third, immunology literature is especially heavy in acronyms, jargon and abbreviations. In this manuscript, four instructors gathered to discuss the strategies that they have used in their classrooms to utilize PSL in immunology (PSL-I) and scaffold various activities around it. These teaching methods vary from highlighting immunology-specific techniques, interpreting figures, alignment with the 5E instructional model to guide an inquiry, jigsaw format learning, to in-depth journal-club style analysis. Finally, this paper discusses reflections from our experiences teaching PSL-I. We know that there are misconceptions about immunology and health in general. If we teach PSL and how to interpret it, we hope to prepare our students not just for their chosen field, but also to think critically and discern facts from fiction in society. 

ABSTRACT Bacteria and archaea employ a rudimentary immune system, CRISPR-Cas, to protect against foreign genetic elements such as bacteriophage. CRISPR-Cas systems are found inBombella apis.B. apisis an important honey bee symbiont, found primarily in larvae, queens, and hive compartments.B. apisis found in the worker bee gut but is not considered a core member of the bee microbiome and has therefore been understudied with regard to its importance in the honey bee colony. However,B. apisappears to play beneficial roles in the colony, by protecting developing brood from fungal pathogens and by bolstering their development under nutritional stress. Previously, we identified CRISPR-Cas systems as being acquired byB. apisin its transition to bee association, as they are absent in a sister clade. Here, we assess the variation and distribution of CRISPR-Cas types acrossB. apisstrains. We found multiple CRISPR-Cas types, some of which have multiple arrays, within the sameB. apisgenomes and also in the honey bee queen gut metagenomes. We analyzed the spacers between strains to identify the history of mobile element interaction for eachB. apisstrain. Finally, we predict interactions between viral sequences and CRISPR systems from different honey bee microbiome members. Our analyses show that theB. apisCRISPR-Cas systems are dynamic; that microbes in the same niche have unique spacers, which supports the functionality of these CRISPR-Cas systems; and that acquisition of new spacers may be occurring in multiple locations in the genome, allowing for a flexible antiviral arsenal for the microbe. IMPORTANCEHoney bee worker gut microbes have been implicated in everything from protection from pathogens to breakdown of complex polysaccharides in the diet. However, there are multiple niches within a honey bee colony that host different groups of microbes, including the acetic acid bacteriumBombella apis.B. apisis found in the colony food stores, in association with brood, in worker hypopharyngeal glands, and in the queen’s digestive tract. The roles thatB. apismay serve in these environments are just beginning to be discovered and include the production of a potent antifungal that protects developing bees and supplementation of dietary lysine to young larvae, bolstering their nutrition. Niche specificity inB. apismay be affected by the pressures of bacteriophage and other mobile elements, which may target different strains in each specific bee environment. Studying the interplay betweenB. apisand its mobile genetic elements (MGEs) may help us better understand microbial community dynamics within the colony and the potential ramifications for the honey bee host. 

Crystals of 10-bis((E)-2-(pyridin-4-yl)vinyl)anthracene (BP4VA) show heat-induced chromism and luminescence. Structural changes are described using variable-temperature synchrotron single-crystal X-ray diffraction, microscopy, and molecular modeling. 

ABSTRACT The opportunistic human pathogenPseudomonas aeruginosais naturally infected by a large class of temperate, transposable, Mu-like phages. We examined the genotypic and phenotypic diversity ofP. aeruginosaPA14 lysogen populations as they resolve clustered regularly interspaced short palindromic repeat(CRISPR) autoimmunity, mediated by an imperfect CRISPR match to the Mu-like DMS3 prophage. After 12 days of evolution, we measured a decrease in spontaneous induction in both exponential and stationary phase growth. Co-existing variation in spontaneous induction rates in the exponential phase depended on the way the coexisting strains resolved genetic conflict. Multiple mutational modes to resolve genetic conflict between host and phage resulted in coexistence in evolved populations of single lysogens that maintained CRISPR immunity to other phages and polylysogens that lost immunity completely. This work highlights a new dimension of the role of lysogenic phages in the evolution of their hosts.IMPORTANCEThe chronic opportunistic multi-drug-resistant pathogenPseudomonas aeruginosais persistently infected by temperate phages. We assess the contribution of temperate phage infection to the evolution of the clinically relevant strain UCBPP-PA14. We found that a low level of clustered regularly interspaced short palindromic repeat (CRISPR)-mediated self-targeting resulted in polylysogeny evolution and large genome rearrangements in lysogens; we also found extensive diversification in CRISPR spacers andcasgenes. These genomic modifications resulted in decreased spontaneous induction in both exponential and stationary phase growth, increasing lysogen fitness. This work shows the importance of considering latent phage infection in characterizing the evolution of bacterial populations. 

Many bacterial traits important to host-microbe symbiosis are determined by genes carried on extrachromosomal replicons such as plasmids, chromids, and integrative and conjugative elements. Multiple such replicons often coexist within a single cell and, due to horizontal mobility, have patterns of variation and evolutionary histories that are distinct from each other and from the bacterial chromosome. In nitrogen-fixing Rhizobium, genes carried on multiple plasmids make up almost 50% of the genome, are necessary for the formation of symbiosis, and underlie bacterial traits including host plant benefits. Thus the genomics and transmission of plasmids in Rhizobium underlie the ecology and evolution of this important model symbiont. Here we leverage a natural population of clover-associated Rhizobium in which partner quality has declined in response to long-term nitrogen fertilization. We use 62 novel, reference-quality genomes to characterize 257 replicons in the plasmidome and study their genomics and transmission patterns. We find that, of the four most frequent plasmid types, two (types II & III) have more stable size, larger core genomes, and track the chromosomal phylogeny (display more vertical transmission), while others (types I & IV – the symbiosis plasmid, or pSym) vary substantially in size, shared gene content, and have phylogenies consistent with frequent horizontal transmission. We also find differentiation in pSym subtypes driven by long-term nitrogen fertilization. Our results highlight the variation in plasmid transmission dynamics within a single symbiont and implicate plasmid horizontal transmission in the evolution of partner quality. 

Abstract Various metastable ice phases and their complicated transition pathways have been found by pressurization at low temperatures at which slow kinetics and high metastability are easily achieved. By contrast, such diversity is less expected at room or elevated temperatures. Here, using a combination of a dynamic diamond anvil cell and X-ray free electron laser techniques, we demonstrate that supercompressed water transforms into ice VI through multiple freezing–melting pathways at room temperature, hidden within the pressure region of ice VI. These multiple transition pathways occur via a metastable ice (more specifically, ice XXI with body-centred tetragonal structure ($$I\bar{4}2d$$ $I\overline{4}2d$)) discovered in this study and a metastable ice VII that exists within the pressure range of ice VI. We find that supercompressed water structurally evolves from high-density water to very-high-density water, causing multiple transition pathways. These findings provide an insight to find more metastable ice phases and their transition pathways at elevated temperatures. 

Abstract Horseshoe crabs, considered living fossils with a stable morphotype spanning ∼445 million years, are evolutionarily, ecologically, and biomedically important species experiencing rapid population decline. Of the four extant species of horseshoe crabs, the Atlantic horseshoe crab, Limulus polyphemus, has become an essential component of the modern medicine toolkit. Here, we present the first chromosome-level genome assembly, and the most contiguous and complete assembly to date, for L. polyphemus using nanopore long-read sequencing and chromatin conformation analysis. We find support for three horseshoe crab-specific whole-genome duplications, but none shared with Arachnopulmonata (spiders and scorpions). Moreover, we discovered tandem duplicates of endotoxin detection pathway components Factors C and G, identify candidate centromeres consisting of Gypsy retroelements, and classify the ZW sex chromosome system for this species and a sister taxon, Carcinoscorpius rotundicauda. Finally, we revealed this species has been experiencing a steep population decline over the last 5 million years, highlighting the need for international conservation interventions and fisheries-based management for this critical species. 

Methylmercury (MeHg) and, to a lesser extent, inorganic mercury (IHg) contamination of rice is a global public health concern, but little is known about how soil and grain Hg concentrations respond to elevated CO2 (ECO2), or how ECO2 alters movement of Hg through the soil-plant-grain system. To advance knowledge of how Hg contamination of rice will change in the future, this study explored the effect of elevated CO2 (ECO2, c. 800 ppm) on soil, iron plaque, root, stem/leaf, and grain concentrations of MeHg and IHg. We observed evidence that ECO2 increased accumulation of MeHg, but not IHg, in rice grain. For IHg, ECO2 did not alter its uptake from the soil, translocation through the plant, or concentration in rice grain. However, ECO2 did reduce uptake of IHg from the air into leaf tissues, likely as a result of the reduced stomatal conductivity and thus more limited direct uptake from the air. Methylmercury concentrations in the grain of plants grown at ECO2 were significantly higher than those of plants grown at ambient CO2. Moreover, MeHg concentrations were also elevated in stem/leaf (82 %) and root tissue (37 %) for ECO2 plants, although the root-tissue results were not statistically significant. In contrast, soil MeHg concentrations were virtually indistinguishable between treatments, indicating that higher rice grain MeHg concentrations were not likely due to higher microbial IHg methylation in soil. Plant uptake of MeHg into stem/leaves and grain from the soil was significantly greater in the ECO2 treatment; however, translocation patterns of MeHg within the plant itself did not differ between treatments. Notably, these patterns existed despite consistently lower transpiration in the ECO2 treatment, and thus less mass flow of solute towards and through the plant. Our results indicate that as CO2 concentrations rise, the human health risks related to MeHg in grain will likely increase. 

Abstract Humans and other primates have specialized visual pathways composed of interconnected cortical areas. The input area V1 contains neurons that encode basic visual features, whereas downstream in the lateral prefrontal cortex (LPFC) neurons acquire tuning for novel complex feature associations. It has been assumed that each cortical area is composed of repeatable neuronal subtypes, and variations in synaptic strength and connectivity patterns underlie functional specialization. Here we test the hypothesis that diversity in the intrinsic make-up of single neurons contributes to area specialization along the visual pathways. We measured morphological and electrophysiological properties of single neurons in areas V1 and LPFC of marmosets. Excitatory neurons in LPFC were larger, less excitable, and fired broader spikes than V1 neurons. Some inhibitory fast spiking interneurons in the LPFC had longer axons and fired spikes with longer latencies and a more depolarized action potential trough than in V1. Intrinsic bursting was found in subpopulations of both excitatory and inhibitory LPFC but not V1 neurons. The latter may favour temporal summation of spikes and therefore enhanced synaptic plasticity in LPFC relative to V1. Our results show that specialization within the primate visual system permeates the most basic processing level, the single neuron.