Juneteenth in STEMM and the barriers to equitable science.

We are 52 Black scientists. Here, we establish the context of Juneteenth in STEMM and discuss the barriers Black scientists face, the struggles they endure, and the lack of recognition they receive. We review racism's history in science and provide institutional-level solutions to reduce the burdens on Black scientists.

Amoeba predation of Cryptococcus: A quantitative and population genomic evaluation of the accidental pathogen hypothesis.

The "Amoeboid Predator-Fungal Animal Virulence Hypothesis" posits that interactions with environmental phagocytes shape the evolution of virulence traits in fungal pathogens. In this hypothesis, selection to avoid predation by amoeba inadvertently selects for traits that contribute to fungal escape from phagocytic immune cells. Here, we investigate this hypothesis in the human fungal pathogens Cryptococcus neoformans and Cryptococcus deneoformans. Applying quantitative trait locus (QTL) mapping and comparative genomics, we discovered a cross-species QTL region that is responsible for variation in resistance to amoeba predation. In C. neoformans, this same QTL was found to have pleiotropic effects on melanization, an established virulence factor. Through fine mapping and population genomic comparisons, we identified the gene encoding the transcription factor Bzp4 that underlies this pleiotropic QTL and we show that decreased expression of this gene reduces melanization and increases susceptibility to amoeba predation. Despite the joint effects of BZP4 on amoeba resistance and melanin production, we find no relationship between BZP4 genotype and escape from macrophages or virulence in murine models of disease. Our findings provide new perspectives on how microbial ecology shapes the genetic architecture of fungal virulence, and suggests the need for more nuanced models for the evolution of pathogenesis that account for the complexities of both microbe-microbe and microbe-host interactions.

The power of junior faculty mentoring committees.

Junior faculty mentoring committees have important roles in ensuring that faculty thrive and adjust to their new positions and institutions. Here, we describe the purpose, structure, and benefits of junior faculty mentoring committees, which can be a powerful tool for early-career academic investigators in science, technology, engineering, mathematics, and medical (STEMM) fields. There is a paucity of information about what mentoring committees are, how to use them effectively, what areas they should evaluate, and how they can most successfully help junior faculty progress in their careers. This work offers guidance for both junior faculty mentees and mentoring committee members on how to best structure and utilize mentoring committees to promote junior faculty success. A better understanding of the intricacies of the mentoring committee will allow junior faculty members to self-advocate and will equip committee mentors with tools to ensure that junior faculty are successful in thriving in academia.

Technology accountability groups: A novel form of technology learning and support for graduate students and faculty in STEM.

In academia, particularly in science, technology, engineering, and mathematics (STEM), writing accountability groups have emerged as an effective technique to enhance writing productivity by offering structure, increasing the commitment to write, and fostering social commitment. The rapid development of technology has introduced a new challenge across STEM fields: technostress, where individuals face heightened stress due to novel applications of technology. To address this, we introduce Technology Accountability Groups (TAGs), a novel form of community support for graduate students and faculty. TAGs are tailored to help individuals navigate technological innovations, alleviate technostress, acquire new skills, motivate, and connect with leaders in the field. This paper presents a framework for establishing, implementing, and sustaining TAGs in STEM.

Pleiotropy and epistasis within and between signaling pathways defines the genetic architecture of fungal virulence.

Cryptococcal disease is estimated to affect nearly a quarter of a million people annually. Environmental isolates of Cryptococcus deneoformans, which make up 15 to 30% of clinical infections in temperate climates such as Europe, vary in their pathogenicity, ranging from benign to hyper-virulent. Key traits that contribute to virulence, such as the production of the pigment melanin, an extracellular polysaccharide capsule, and the ability to grow at human body temperature have been identified, yet little is known about the genetic basis of variation in such traits. Here we investigate the genetic basis of melanization, capsule size, thermal tolerance, oxidative stress resistance, and antifungal drug sensitivity using quantitative trait locus (QTL) mapping in progeny derived from a cross between two divergent C. deneoformans strains. Using a "function-valued" QTL analysis framework that exploits both time-series information and growth differences across multiple environments, we identified QTL for each of these virulence traits and drug susceptibility. For three QTL we identified the underlying genes and nucleotide differences that govern variation in virulence traits. One of these genes, RIC8, which encodes a regulator of cAMP-PKA signaling, contributes to variation in four virulence traits: melanization, capsule size, thermal tolerance, and resistance to oxidative stress. Two major effect QTL for amphotericin B resistance map to the genes SSK1 and SSK2, which encode key components of the HOG pathway, a fungal-specific signal transduction network that orchestrates cellular responses to osmotic and other stresses. We also discovered complex epistatic interactions within and between genes in the HOG and cAMP-PKA pathways that regulate antifungal drug resistance and resistance to oxidative stress. Our findings advance the understanding of virulence traits among diverse lineages of Cryptococcus, and highlight the role of genetic variation in key stress-responsive signaling pathways as a major contributor to phenotypic variation.

A switch to feeding on cycads generates parallel accelerated evolution of toxin tolerance in two clades of Eumaeus caterpillars (Lepidoptera: Lycaenidae).

We assembled a complete reference genome of Eumaeus atala, an aposematic cycad-eating hairstreak butterfly that suffered near extinction in the United States in the last century. Based on an analysis of genomic sequences of Eumaeus and 19 representative genera, the closest relatives of Eumaeus are Theorema and Mithras We report natural history information for Eumaeus, Theorema, and Mithras Using genomic sequences for each species of Eumaeus, Theorema, and Mithras (and three outgroups), we trace the evolution of cycad feeding, coloration, gregarious behavior, and other traits. The switch to feeding on cycads and to conspicuous coloration was accompanied by little genomic change. Soon after its origin, Eumaeus split into two fast evolving lineages, instead of forming a clump of close relatives in the phylogenetic tree. Significant overlap of the fast evolving proteins in both clades indicates parallel evolution. The functions of the fast evolving proteins suggest that the caterpillars developed tolerance to cycad toxins with a range of mechanisms including autophagy of damaged cells, removal of cell debris by macrophages, and more active cell proliferation.

Outcrossing, mitotic recombination, and life-history trade-offs shape genome evolution in Saccharomyces cerevisiae.

We carried out a population genomic survey of Saccharomyces cerevisiae diploid isolates and find that many budding yeast strains have high levels of genomic heterozygosity, much of which is likely due to outcrossing. We demonstrate that variation in heterozygosity among strains is correlated with a life-history trade-off that involves how readily yeast switch from asexual to sexual reproduction under nutrient stress. This trade-off is reflected in a negative relationship between sporulation efficiency and pseudohyphal development and correlates with variation in the expression of RME1, a transcription factor with pleiotropic effects on meiosis and filamentous growth. Selection for alternate life-history strategies in natural versus human-associated environments likely contributes to differential maintenance of genomic heterozygosity through its effect on the frequency that yeast lineages experience sexual cycles and hence the opportunity for inbreeding. In addition to elevated levels of heterozygosity, many strains exhibit large genomic regions of loss-of-heterozygosity (LOH), suggesting that mitotic recombination has a significant impact on genetic variation in this species. This study provides new insights into the roles that both outcrossing and mitotic recombination play in shaping the genome architecture of Saccharomyces cerevisiae. This study also provides a unique case where stark differences in the genomic distribution of genetic variation among individuals of the same species can be largely explained by a life-history trade-off.

Development and evaluation of a training curriculum to engage researchers on accessing and analyzing the All of Us data.

OBJECTIVE: The All of Us Evenings with Genetics (EwG) Research Program at Baylor College of Medicine (BCM), funded to engage research scholars to work with the All of Us data, developed a training curriculum for the Researcher Workbench, the platform to access and analyze All of Us data. All of Us EwG developed the curriculum so that it could teach scholars regardless of their skills and background in programming languages and cloud computing. All of Us EwG delivered this curriculum at the first annual All of Us EwG Faculty Summit in May 2022. The curriculum was evaluated both during and after the Faculty Summit so that it could be improved for future training. MATERIALS AND METHODS: Surveys were administered to assess scholars' familiarity with the programming languages and computational tools required to use the Researcher Workbench. The curriculum was developed using backward design and was informed by the survey results, a review of available resources for training users on the Researcher Workbench, and All of Us EwG members' collective experience training students. The curriculum was evaluated using feedback surveys during the Faculty Summit as well as virtual meetings and emails following the Faculty Summit. RESULTS: The evaluation results demonstrated the success of the curriculum and identified areas for improvement. DISCUSSION AND CONCLUSION: The curriculum has been adapted and improved in response to evaluations and in response to changes to the All of Us data and infrastructure to train more researchers through this program and other scholarly programs.

Experiences in providing a community educational resource for the All of Us Researcher Workbench.

OBJECTIVE: Educational offerings to fill the bioinformatics knowledge gap are a key component to enhancing access and use of health data from the All of Us Research Program. We developed a Train the Trainer-based, innovative training series including project-based learning, modular on-demand demonstrations, and unstructured tutorial time as a model for educational engagement in the All of Us community. MATERIALS AND METHODS: We highlight our training modules and content, with training survey data informing cycles of development in the creation of a 6-module training series with modular demonstrations. RESULTS: We have conducted 2 public iterations of the Train the Trainer (Tx3) Series based on survey feedback while training over 300 registered researchers to access and analyze data on the All of Us Researcher Workbench. DISCUSSION AND CONCLUSION: Future directions of the Tx3 Series include enhanced focus on project-based learning and learner requests for modularity and asynchronous materials access.

A total-evidence approach to dating with fossils, applied to the early radiation of the hymenoptera.

Phylogenies are usually dated by calibrating interior nodes against the fossil record. This relies on indirect methods that, in the worst case, misrepresent the fossil information. Here, we contrast such node dating with an approach that includes fossils along with the extant taxa in a Bayesian total-evidence analysis. As a test case, we focus on the early radiation of the Hymenoptera, mostly documented by poorly preserved impression fossils that are difficult to place phylogenetically. Specifically, we compare node dating using nine calibration points derived from the fossil record with total-evidence dating based on 343 morphological characters scored for 45 fossil (4--20 complete) and 68 extant taxa. In both cases we use molecular data from seven markers (∼5 kb) for the extant taxa. Because it is difficult to model speciation, extinction, sampling, and fossil preservation realistically, we develop a simple uniform prior for clock trees with fossils, and we use relaxed clock models to accommodate rate variation across the tree. Despite considerable uncertainty in the placement of most fossils, we find that they contribute significantly to the estimation of divergence times in the total-evidence analysis. In particular, the posterior distributions on divergence times are less sensitive to prior assumptions and tend to be more precise than in node dating. The total-evidence analysis also shows that four of the seven Hymenoptera calibration points used in node dating are likely to be based on erroneous or doubtful assumptions about the fossil placement. With respect to the early radiation of Hymenoptera, our results suggest that the crown group dates back to the Carboniferous, ∼309 Ma (95% interval: 291--347 Ma), and diversified into major extant lineages much earlier than previously thought, well before the Triassic. [Bayesian inference; fossil dating; morphological evolution; relaxed clock; statistical phylogenetics.].

Phylogenetic relationships among superfamilies of Hymenoptera.

The first comprehensive analysis of higher-level phylogeny of the order Hymenoptera is presented. The analysis includes representatives of all extant superfamilies, scored for 392 morphological characters, and sequence data for four loci (18S, 28S, COI and EF-1α). Including three outgroup taxa, 111 terminals were analyzed. Relationships within symphytans (sawflies) and Apocrita are mostly resolved. Well supported relationships include: Xyeloidea is monophyletic, Cephoidea is the sister group of Siricoidea + [Xiphydrioidea + (Orussoidea + Apocrita)]; Anaxyelidae is included in the Siricoidea, and together they are the sister group of Xiphydrioidea + (Orussoidea + Apocrita); Orussoidea is the sister group of Apocrita, Apocrita is monophyletic; Evanioidea is monophyletic; Aculeata is the sister group of Evanioidea; Proctotrupomorpha is monophyletic; Ichneumonoidea is the sister group of Proctotrupomorpha; Platygastroidea is sister group to Cynipoidea, and together they are sister group to the remaining Proctotrupomorpha; Proctotrupoidea s. str. is monophyletic; Mymarommatoidea is the sister group of Chalcidoidea; Mymarommatoidea + Chalcidoidea + Diaprioidea is monophyletic. Weakly supported relationships include: Stephanoidea is the sister group of the remaining Apocrita; Diaprioidea is monophyletic; Ceraphronoidea is the sister group of Megalyroidea, which together form the sister group of [Trigonaloidea (Aculeata + Evanioidea)]. Aside from paraphyly of Vespoidea within Aculeata, all currently recognized superfamilies are supported as monophyletic. The diapriid subfamily Ismarinae is raised to family status, Ismaridae stat. nov. © The Will Henning Society 2011.

Aquaporin (AQP) channels in the spiny dogfish, Squalus acanthias I: Characterization of AQP3 and AQP15 function and expression, and localization of the proteins in gill and spiral valve intestine.

Complementary DNAs (cDNAs) for two aquaporin water channel genes (AQP3 and AQP15) were amplified cloned and sequenced to initiate this study. Northern blot analysis was carried out to confirm the mRNA sizes of these AQP genes with AQP3 mRNA bands exhibiting sizes of 1.2 and 1.6 k bases and AQP15 had a mRNA band of 2.1 k bases. Northern blot analysis was also performed on kidney and esophagus total RNA samples from fish acclimated to 75%, 100% or 120% seawater (SW). The level of AQP15 mRNA expression was shown to significantly decrease following salinity acclimation from 100 to 120% SW. An opposite but non-significantly different trend was observed for AQP3 mRNA levels. Full length cDNAs were then used to generate AQP3 and AQP15 mRNAs for microinjection into Xenopus oocytes. Both AQP3- and AQP15- microinjected oocytes exhibited significantly elevated apparent water permeability compared to control oocytes at neutral pH. The apparent water permeability was mercury-inhibitable, significantly so in the case of AQP3. AQP3 microinjected oocytes showed pH sensitivity in their apparent water permeability, showing a lack of permeability at acidic pH values. The Carboxyl-terminal derived amino acid sequences of AQP3 and AQP15 were used to generate rabbit affinity-purified polyclonal antibodies. Western blots with the antibodies showed a band of 31.3 kDa for AQP3 in the kidney, with minor bands at 26, 24 and 21 kDa. For AQP15 a band of 26 kDa was seen in gill and kidney. Fainter bands at 28 and 24 kDa were also seen in the kidney. There was also some higher molecular weight banding. None of the bands were seen when the antibodies were pre- blocked with their peptide antigens. Immunohistochemical localization studies were also performed in the gill and spiral valve intestine. In the gill, AQP15 antibody staining was seen sporadically in the membranes of surface epithelial cells of the secondary lamellae. Tyramide amplification of signals was employed in the spiral valve intestine. Tyramide-amplified AQP3 antibody staining was observed in the basal membrane of the invaginated epithelial cell layer of secondary intestinal folds in luminal surface of either the side wall of the spiral valve intestine or in internal valve tissue 'flaps'. For the AQP15 antibody, tyramide-amplified staining was instead found on the apical and to a lesser extent the lateral membranes of the same invaginated epithelial cell layer. The localization of AQP3 and AQP15 in the spiral valve intestine suggests that a trans-cellular water absorption pathway may exist in this tissue.

Evolution of the hymenopteran megaradiation.

The Hymenoptera--ants, bees and wasps--represent one of the most successful but least understood insect radiations. We present the first comprehensive molecular study spanning the entire order Hymenoptera. It is based on approximately 7 kb of DNA sequence from 4 gene regions (18S, 28S, COI and EF-1α) for 116 species representing all superfamilies and 23 outgroup taxa from eight orders of Holometabola. Results are drawn from both parsimony and statistical (Bayesian and likelihood) analyses, and from both by-eye and secondary-structure alignments. Our analyses provide the first firm molecular evidence for monophyly of the Vespina (Orussoidea+Apocrita). Within Vespina, our results indicate a sister-group relationship between Ichneumonoidea and Proctotrupomorpha, while the stinging wasps (Aculeata) are monophyletic and nested inside Evaniomorpha. In Proctotrupomorpha, our results provide evidence for a novel core clade of proctotrupoids, and support for the recently proposed Diaprioidea. An unexpected result is the support for monophyly of a clade of wood-boring sawflies (Xiphydrioidea+Siricoidea). As in previous molecular studies, Orussidae remain difficult to place and are either sister group to a monophyletic Apocrita, or the sister group of Stephanidae within Apocrita. Both results support a single origin of parasitism, but the latter would propose a controversial reversal in the evolution of the wasp-waist. Generally our results support earlier hypotheses, primarily based on morphology, for a basal grade of phytophagous families giving rise to a single clade of parasitic Hymenoptera, the Vespina, from which predatory, pollen-feeding, gall-forming and eusocial forms evolved.

Genotypic and Phenotypic Characterization of Salmonella Isolated from Fresh Ground Meats Obtained from Retail Grocery Stores in the Brookings, South Dakota, Area.

Salmonella is one of the most common foodborne pathogens found in retail fresh meat products. The purpose of this study was to characterize the Salmonella that is found in common types of fresh ground meats available to consumers in grocery stores in the Brookings, South Dakota, area. Salmonella serotypes were detected in 50 (19%) of 261 retail fresh ground meat samples, with 2 (2%) of 115 ground turkey samples, 6 (14%) of 42 chicken samples, and 42 (40%) of 104 ground pork samples testing positive for Salmonella. The Salmonella isolates were sequenced using an Illumina MiSeq genome sequencer. The resulting genomic sequences were analyzed to determine the serotypes of the isolates and to detect the presence of virulence and antibiotic resistance genes. The Salmonella isolated from the ground meats belonged to 23 different serotypes. The predominant serotype isolated from ground chicken was Enteriditis (5 of 6, 83%). Among the ground pork isolates, the most common serotypes were the potential monophasic variant of Typhimurium (5 of 42, 12%), Uganda (5 of 42, 12%), Anatum (4 of 42, 10%), Derby (3 of 42, 7%), Infantis (3 of 42, 7%), and London (3 of 42, 7%). Among the 45 Salmonella isolates tested to determine their resistance to common veterinary antibiotics, 25 (56%) were found to be susceptible to all 14 antibiotics tested, 11 (24%) were resistant to 1 antibiotic, 4 (9%) were resistant to 2 antibiotics, 1 (2%) was resistant to 3 antibiotics, 2 (4%) were resistant to 4 antibiotics, 1 (2%) was resistant to 8 antibiotics, and 1 (2%) was resistant to 10 antibiotics. The most common antibiotic resistances observed in this study were to streptomycin (15 of 45, 33%), tetracycline (11 of 45, 24%), and sulfisoxazole (7 of 45, 16%). The results of phenotypic evaluation of antibiotic resistance profiles of Salmonella isolates correlated well with the antibiotic resistance genes detected in the genomic sequences of the isolates.

Revision of the Agathidinae (Hymenoptera: Braconidae) with comparisons of static and dynamic alignments.

The phylogeny of the Agathidinae (Insecta: Hymenoptera: Braconidae) is investigated based on morphological and sequence data from the D2-3 regions of 28S rDNA. Morphology and molecular data were run simultaneously and separately and the molecular and combined data sets were analyzed using both static, Clustal W, and dynamic, POY, alignments. Both alignments were conducted under a variety of gap costs and results are compared. Sixty-two ingroup exemplars representing 22 genera and six outgroup taxa representing two subfamilies and five genera were included. Numerous taxa at the generic and tribal levels were tested for monophyly and the evolutionary history of several characters is discussed. The tribe Agathidini s.s. is found to be a derived member of the Microdini and the two are synonymized under the older name, Agathidini s.l. Support is substantial for the tribes Cremnoptini and Disophrini and Earinini but equivocal for the Agathidini s.l. At the generic level, Bassus is found to be polyphyletic. Numerous new synonymies and combinations are proposed.

Teaching motivational interviewing to nurse practitioner students: a pilot study.

PURPOSE: This quasi-experimental study examined the outcomes of a brief educational module for graduate nursing students as to using motivational interviewing (MI)-consistent counseling skills. DATA SOURCES: Pre- and posttest narrative and video-taped data, surveys, and self-report. CONCLUSIONS: Significantly fewer closed questions, more open questions, and less advice-giving without permission were noted in the narratives completed after the education. Similarly, the second videotape revealed significantly more affirmations, use of reflections, and use of more summaries when ending patient sessions. Surveys and self-report indicated strong satisfaction with the opportunity to learn MI. IMPLICATIONS FOR PRACTICE: A core competency of nurse practitioner (NP) education involves helping persons adopt positive health behaviors. While research utilizing MI has evidenced substantial success in this regard, little has been published as to how to incorporate teaching this skill set within an already content-laden NP curriculum. Including at least minimal education in MI should occur in NP programs. Eight hours of education, including video-taped practice, followed by "booster sessions" to maintain skills and increase confidence is recommended. More research is necessary to elucidate best practices of teaching this skill set to NPs and its eventual outcomes on patients' health.

The genetic architecture of biofilm formation in a clinical isolate of Saccharomyces cerevisiae.

Biofilms are microbial communities that form on surfaces. They are the primary form of microbial growth in nature and can have detrimental impacts on human health. Some strains of the budding yeast Saccharomyces cerevisiae form colony biofilms, and there is substantial variation in colony architecture between biofilm-forming strains. To identify the genetic basis of biofilm variation, we developed a novel version of quantitative trait locus mapping, which leverages cryptic variation in a clinical isolate of S. cerevisiae. We mapped 13 loci linked to heterogeneity in biofilm architecture and identified the gene most closely associated with each locus. Of these candidate genes, six are members of the cyclic AMP-protein kinase A pathway, an evolutionarily conserved cell signaling network. Principal among these is CYR1, which encodes the enzyme that catalyzes production of cAMP. Through a combination of gene expression measurements, cell signaling assays, and gene overexpression, we determined the functional effects of allelic variation at CYR1. We found that increased pathway activity resulting from protein coding and expression variation of CYR1 enhances the formation of colony biofilms. Four other candidate genes encode kinases and transcription factors that are targets of this pathway. The protein products of several of these genes together regulate expression of the sixth candidate, FLO11, which encodes a cell adhesion protein. Our results indicate that epistatic interactions between alleles with both positive and negative effects on cyclic AMP-protein kinase A signaling underlie much of the architectural variation we observe in colony biofilms. They are also among the first to demonstrate genetic variation acting at multiple levels of an integrated signaling and regulatory network. Based on these results, we propose a mechanistic model that relates genetic variation to gene network function and phenotypic outcomes.

Molecular phylogenetics and evolutionary history of the neotropical Satyrine Subtribe Euptychiina (Nymphalidae: Satyrinae).

The Euptychiina is one of the more diverse lineages of satyrine butterflies, represented by over 300 species. The first phylogenetic analyses of the subtribe is presented based on 2506 aligned nucleotide sequences obtained from 69 individuals spanning 28 ingroup genera and nine outgroup genera. Two genes were used, the mitochondrial gene cytochrome oxidase 1 (1268 bp) and the nuclear gene elongation factor-1alpha (1238 bp). The subtribe is never recovered as monophyletic in analyses using parsimony, maximum likelihood, or Bayesian inference. Several euptychiine genera are placed basal to the ingroup, but support is found only for Euptychia and Oressinoma. Three main lineages within the ingroup were clearly defined and many taxonomic groupings within the clades strongly supported. The majority of genera tested were paraphyletic or polyphyletic. Based on results presented here and novel host use, a close relationship of Euptychia to the Indo-Australian tribe Ragadiini is hypothesized. Origins of the group remain unclear, but the basal position of most of the Nearctic genera is discussed.