Locomotion and brain gene expression exhibit sex-specific non-monotonic dose-response to HFPO-DA during Drosophila melanogaster lifespan.

BACKGROUND: Legacy per- and polyfluoroalkyl substances (PFAS), known for their environmental persistence and bio-accumulative properties, have been phased out in the U.S. due to public health concerns. A newer polymerization aid used in the manufacture of some fluoropolymers, hexafluoropropylene oxide-dimer acid (HFPO-DA), has lower reported bioaccumulation and toxicity, but is a potential neurotoxicant implicated in dopaminergic neurodegeneration. OBJECTIVE: We investigated HFPO-DA's bio-accumulative potential and sex-specific effects on lifespan, locomotion, and brain gene expression in fruit flies. METHODS: We quantified bioaccumulation of HFPO-DA in fruit flies exposed to 8.7 × 104 µg/L of HFPO-DA in the fly media for 14 days via UHPLC-MS. Long-term effect on lifespan was determined by exposing both sexes to 8.7 × 102 - 8.7 × 105 µg/L of HFPO-DA in media. Locomotion was measured following 3, 7, and 14 days of exposures at 8.7 × 101 - 8.7 × 105 µg/L of HFPO-DA in media, and high-throughput 3'-end RNA-sequencing was used to quantify gene expression in fly brains across the same time points. RESULTS: Bioaccumulation of HFPO-DA in fruit flies was not detected. HFPO-DA-induced effects on lifespan, locomotion, and brain gene expression, and lowest adverse effect level (LOAEL) showed sexually dimorphic patterns. Locomotion scores significantly decreased in at least one dose at all time points for females and only at 3-day exposure for males, while brain gene expression exhibited non-monotonic dose-response. Differentially expressed genes correlated to locomotion scores revealed sex-specific numbers of positively and negatively correlated genes per functional category. CONCLUSION: Although HFPO-DA effects on locomotion and survival were significant at doses higher than the US EPA reference dose, the brain transcriptomic profiling reveals sex-specific changes and neurological molecular targets; gene enrichments highlight disproportionately affected categories, including immune response: female-specific co-upregulation suggests potential neuroinflammation. Consistent sex-specific exposure effects necessitate blocking for sex in experimental design during HFPO-DA risk assessment.

Imagining, designing, and interpreting experiments: Using quantitative assessment to improve instruction in scientific reasoning.

Effectively teaching scientific reasoning requires an understanding of the challenges students face when learning these skills. We designed an assessment that measures undergraduate student abilities to form hypotheses, design experiments, and interpret data from experiments in cellular and molecular biology. The assessment uses intermediate-constraint free-response questions with a defined rubric to facilitate use with large classes, while identifying common reasoning errors that may prevent students from becoming proficient at designing and interpreting experiments. The assessment measured a statistically significant improvement in a senior-level biochemistry laboratory course, and a larger improvement between the biochemistry lab students and a separate cohort in a first-year introductory biology lab course. Two common errors were identified for forming hypotheses and using experimental controls. Students frequently constructed a hypothesis that was a restatement of the observation it was supposed to explain. They also often made comparisons to control conditions not included in an experiment. Both errors were most frequent among first-year students, and decreased in frequency as students completed the senior-level biochemistry lab. Further investigation of the absent controls error indicated that difficulties with reasoning about experimental controls may be widespread in undergraduate students. The assessment was a useful instrument for measuring improvement in scientific reasoning at different levels of instruction, and identified errors that can be targeted to improve instruction in the process of science.

Life Science Research Immersion Program Improves STEM-Specific Skills and Science Attitudes among Precollege Students.

A predicted rapid growth in science, technology, engineering, and math (STEM) careers demands a vast and talented workforce, but students most commonly abandon STEM majors within the first 2 years of college. Performance in introductory courses, scientific literacy, and the ability to critically reason are main predictors of retention in STEM, highlighting the importance of precollege and early college experience. The Life Science Research Immersion Program (LSRIP) is a novel science education model that focuses on the development of scientific research skills, thus preparing students for introductory college courses and beyond. To evaluate the efficacy of the LSRIP, pre- and postprogram assessments and surveys were administered to three precollege student cohorts. Scientific reasoning assessment scores improved by 4.70% in Summer 2019 (P < 0.01), 9.44% in Fall 2019 (P < 0.05), and 0.97% in Winter 2020 cohorts, with two of five questions showing statistically significant improvement. Surveyed attitudes toward science improved in 62.9% of questions across all cohorts. These results suggest that research immersion experiences are an effective educational instrument for improving and promoting scientific reasoning and attitudes among precollege students. To better prepare students for success in STEM higher education and careers, we recommend implementing LSRIPs to complement traditional precollege science curricula.

Toxicity assessment of hexafluoropropylene oxide-dimer acid on morphology, heart physiology, and gene expression during zebrafish (Danio rerio) development.

Hexafluoropropylene oxide-dimer acid (HFPO-DA) is one of the emerging replacements for the "forever" carcinogenic and toxic long-chain PFAS. HFPO-DA is a polymerization aid used for manufacturing fluoropolymers, whose global distribution and undetermined toxic properties are a concern regarding human and ecological health. To assess embryotoxic potential, zebrafish embryos were exposed to HFPO-DA at concentrations of 0.5-20,000 mg/L at 24-, 48-, and 72-h post-fertilization (hpf). Heart rate increased significantly in embryos exposed to 2 mg/L and 10 mg/L HFPO-DA across all time points. Spinal deformities and edema phenotypes were evident among embryos exposed to 1000-16,000 mg/L HFPO-DA at 72 hpf. A median lethal concentration (LC50) was derived as 7651 mg/L at 72 hpf. Shallow RNA sequencing analysis of 9465 transcripts identified 38 consistently differentially expressed genes at 0.5 mg/L, 1 mg/L, 2 mg/L, and 10 mg/L HFPO-DA exposures. Notably, seven downregulated genes were associated with visual response, and seven upregulated genes were expressed in or regulated the cardiovascular system. This study identifies biological targets and molecular pathways affected during animal development by an emerging, potentially problematic, and ubiquitous industrial chemical.

Physiological and transcriptomic effects of hexafluoropropylene oxide dimer acid in Caenorhabditis elegans during development.

Per- and polyfluoroalkyl substances (PFAS) are chemicals resistant to degradation. While such a feature is desirable in consumer and industrial products, some PFAS, including perfluorooctanoic acid (PFOA), are toxic and bioaccumulate. Hexafluoropropylene oxide dimer acid (HFPO-DA), an emerging PFAS developed to replace PFOA, has not been extensively studied. To evaluate the potential toxicity of HFPO-DA with a cost- and time-efficient approach, we exposed C. elegans larvae for 48 h to 4 × 10-9-4 g/L HFPO-DA in liquid media and measured developmental, behavioral, locomotor, and transcriptional effects at various exposure levels. Worms exposed to 1.5-4 g/L HFPO-DA were developmentally delayed, and progeny production was significantly delayed (p < 0.05) in worms exposed to 2-4 g/L HFPO-DA. Statistically significant differential gene expression was identified in all fourteen HFPO-DA exposure groups ranging from 1.25 × 10-5 to 4 g/L, except for 6.25 × 10-5 g/L. Among 10298 analyzed genes, 2624 differentially expressed genes (DEGs) were identified in the developmentally delayed 4 g/L group only, and 78 genes were differentially expressed in at least one of the thirteen groups testing 1.25 × 10-5-2 g/L HFPO-DA exposures. Genes encoding for detoxification enzymes including cytochrome P450 and UDP glucuronosyltransferases were upregulated in 0.25-4 g/L acute exposure groups. DEGs were also identified in lower exposure level groups, though they did not share biological functions except for six ribosomal protein-coding genes. While our transcriptional data is inconclusive to infer mechanisms of toxicity, the significant gene expression differences at 1.25 × 10-5 g/L, the lowest concentration tested for transcriptional changes, calls for further targeted analyses of low-dose HFPO-DA exposure effects.

Cardiac physiology and metabolic gene expression during late organogenesis among F. heteroclitus embryo families from crosses between pollution-sensitive and -resistant parents.

BACKGROUND: The teleost fish Fundulus heteroclitus inhabit estuaries heavily polluted with persistent and bioaccumulative chemicals. While embryos of parents from polluted sites are remarkably resistant to toxic sediment and develop normally, embryos of parents from relatively clean estuaries, when treated with polluted sediment extracts, are developmentally delayed, displaying deformities characteristic of pollution-induced embryotoxicity. To gain insight into parental effects on sensitive and resistant phenotypes during late organogenesis, we established sensitive, resistant, and crossed embryo families using five female and five male parents from relatively clean and predominantly PAH-polluted estuaries each, measured heart rates, and quantified individual embryo expression of 179 metabolic genes. RESULTS: Pollution-induced embryotoxicity manifested as morphological deformities, significant developmental delays, and altered cardiac physiology was evident among sensitive embryos resulting from crosses between females and males from relatively clean estuaries. Significantly different heart rates among several geographically unrelated populations of sensitive, resistant, and crossed embryo families during late organogenesis and pre-hatching suggest site-specific adaptive cardiac physiology phenotypes relative to pollution exposure. Metabolic gene expression patterns (32 genes, 17.9%, at p < 0.05; 11 genes, 6.1%, at p < 0.01) among the embryo families indicate maternal pollutant deposition in the eggs and parental effects on gene expression and metabolic alterations. CONCLUSION: Heart rate differences among sensitive, resistant, and crossed embryos is a reliable phenotype for further explorations of adaptive mechanisms. While metabolic gene expression patterns among embryo families are suggestive of parental effects on several differentially expressed genes, a definitive adaptive signature and metabolic cost of resistant phenotypes is unclear and shows unexpected sensitive-resistant crossed embryo expression profiles. Our study highlights physiological and metabolic gene expression differences during a critical embryonic stage among pollution sensitive, resistant, and crossed embryo families, which may contribute to underlying resistance mechanisms observed in natural F. heteroclitus populations living in heavily contaminated estuaries.

U.S. national, regional, and state-specific socioeconomic factors correlate with child and adolescent ADHD diagnoses pre-COVID-19 pandemic.

Attention-deficit/hyperactivity disorder (ADHD), the most diagnosed emerging neurodevelopmental disorder in children, is a growing health crisis in the United States. Due to the potential increase in ADHD severity during and post the COVID-19 pandemic, we analyzed recent national and two state-specific ADHD data distribution among U.S. children and adolescents by investigating a broad range of socioeconomic status (SES) factors. Child and adolescent ADHD diagnosis and treatment data were parent-reported via National Survey of Children's Health (NSCH). The nationwide childhood prevalence of ADHD is 8.7%, and 62.1% of diagnosed children are taking medication. Louisiana (15.7%) has the highest percentage of children diagnosed with ADHD and California (5.6%) has the lowest, followed by Nevada (5.9%). Multiple correspondence analysis (MCA, n = 51,939) examining 30 factors highlights four areas of interest at the national and state level: race/ethnicity, financial status, family structure, and neighborhood characteristics. Positive correlations between ADHD diagnosis and unsafe school, unsafe neighborhood, and economic hardship are evident nationally and statewide, while the association between a lack of ADHD diagnosis and higher urban neighborhood amenities are evident nationally, but not in two opposing outlier states-Louisiana or Nevada. National and state-specific hierarchical analyses demonstrate significant correlations between the various SES factors and ADHD outcomes. Since the national analysis does not account for the demographic heterogeneity within regions or individual states, the U.S. should rely on comprehensive, county-specific, near real-time data reporting to effectively model and mitigate the ADHD epidemic and similar national health crises.

Reevaluate how to evaluate: Systemic assessment biases affect students' confidence in college upper-division biology laboratory courses.

Grades influence students' confidence and decisions to complete STEM degrees and pursue relevant careers. What affects students' confidence and performance in college upper-division biology laboratory courses and how relevant are evaluation methods to career success? STEM laboratory courses are an excellent model to address these issues because of the hybrid environment, combining traditional lecture course format and the practical application of knowledge. We surveyed 567 students in two upper-division laboratory molecular biology courses at a major research university to compare course-content self-assessment, students' predicted grades, and actual grades received. By analyzing students' confidence and correlating them to grades assigned by the instructor, we identified biases including student and Instructor Assistant (IA) gender, IA experience, and academic quarter. Considering the systemic effect of identified biases, a correlation (R2  = 0.37, p < 0.01) between predicted and actual grades, and weak but statistically significant correlation (R2  = 0.10, p < 0.01) between students' comprehensive course-content self-assessment and their predicted grade are not surprising. Our analysis suggests that students' quantifiable self-assessment, a relatively simple and data-rich resource, helps identify evaluation bias. If administered periodically throughout the course, these assessments can help mitigate biases, improve student learning, evaluation, and retention in STEM fields.

PAH-pollution effects on sensitive and resistant embryos: Integrating structure and function with gene expression.

Polycyclic aromatic hydrocarbons (PAHs) are among the most widespread natural and anthropogenic pollutants, and some PAHs are proven developmental toxicants. We chemically characterized clean and heavily polluted sites and exposed fish embryos to PAH polluted sediment extracts during four critical developmental stages. Embryos were collected from Fundulus heteroclitus populations inhabiting the clean and heavily polluted Superfund estuary. Embryos of parents from the clean sites are sensitive to PAH pollutants while those of parents from the heavily polluted site are resistant. Chemical analysis of embryos suggests PAH accumulation and pollution-induced toxicity among sensitive embryos during development that ultimately kills all sensitive embryos before hatching, while remarkably, the resistant embryos develop normally. The adverse effects on sensitive embryos are manifested as developmental delays, reduced heart rates, and severe heart, liver, and kidney morphological abnormalities. Gene expression analysis of early somitogenesis, heartbeat initiation, late organogenesis, and pre-hatching developmental stages reveals genes whose expression significantly differs between sensitive and resistant embryo populations and helps to explain mechanisms of sensitivity and resistance to polluted environments during vertebrate animal development.

Relative genetic diversity of the rare and endangered Agave shawii ssp. shawii and associated soil microbes within a southern California ecological preserve.

Shaw's Agave (Agave shawii ssp. shawii) is an endangered maritime succulent growing along the coast of California and northern Baja California. The population inhabiting Point Loma Peninsula has a complicated history of transplantation without documentation. The low effective population size in California prompted agave transplanting from the U.S. Naval Base site (NB) to Cabrillo National Monument (CNM). Since 2008, there are no agave sprouts identified on the CNM site, and concerns have been raised about the genetic diversity of this population. We sequenced two barcoding loci, rbcL and matK, of 27 individual plants from 5 geographically distinct populations, including 12 individuals from California (NB and CNM). Phylogenetic analysis revealed the three US and two Mexican agave populations are closely related and have similar genetic variation at the two barcoding regions, suggesting the Point Loma agave population is not clonal. Agave-associated soil microbes used significantly more carbon sources in CNM soil samples than in NB soil likely due to higher pH and moisture content; meanwhile, soil type and soil chemistry analysis including phosphorus, nitrate nitrogen, organic matter, and metals revealed significant correlations between microbial diversity and base saturation (p < 0.05, r 2 = 0.3676), lime buffer capacity (p < 0.01, r 2 = 0.7055), equilibrium lime buffer capacity (p < 0.01, r 2 = 0.7142), and zinc (p < 0.01, r 2 = 0.7136). Soil microbiome analysis within the CNM population revealed overall expected richness (H' = 5.647-6.982) for Agave species, while the diversity range (1 - D = 0.003392-0.014108) suggests relatively low diversity marked by high individual variation. The most prominent remaining US population of this rare species is not clonal and does not seem to be threatened by a lack of genetic and microbial diversity. These results prompt further efforts to investigate factors affecting Agave's reproduction and fitness.

Plagiarism or not? investigation of Turnitin®-detected similarity hits in biology laboratory reports.

In undergraduate biology laboratory courses, laboratory reports can be a useful tool for teaching scientific writing, integration of source material, and information literacy; however, these teaching objectives are at times undermined by students' plagiarism. Laboratory instructors often use similarity-matching software to detect plagiarism in laboratory reports, yet similarity hits detected with such software remain poorly characterized. In the upper division molecular biology laboratory course described here, Turnitin® routinely detected dozens of similarity hits in laboratory reports. To determine whether this abundance of similarity hits was indicative of widespread plagiarism, we analyzed similarity hits detected in 255 laboratory reports written by 135 students. Only a small minority of Turnitin® similarity matches were problematic, but over half of the laboratory reports contained at least one problem with incorporation of scientific sources (e.g., laboratory manual and scientific articles). We identified four common types of such writing problems: patchwriting, technical parroting, copying, and falsification of sources. In 18% of the laboratory reports, we detected an alarmingly superficial use of primary literature. Most of the source incorporation problems did not rise to the level of plagiarism. As a result of this study, we recommend changes in scientific writing instruction and a transition to laboratories providing more authentic research experiences. © 2019 International Union of Biochemistry and Molecular Biology, 47(4):370-379, 2019.

Genomic and physiological responses to strong selective pressure during late organogenesis: few gene expression changes found despite striking morphological differences.

BACKGROUND: Adaptations to a new environment, such as a polluted one, often involve large modifications of the existing phenotypes. Changes in gene expression and regulation during critical developmental stages may explain these phenotypic changes. Embryos from a population of the teleost fish, Fundulus heteroclitus, inhabiting a clean estuary do not survive when exposed to sediment extract from a site highly contaminated with polycyclic aromatic hydrocarbons (PAHs) while embryos derived from a population inhabiting a PAH polluted estuary are remarkably resistant to the polluted sediment extract. We exposed embryos from these two populations to surrogate model PAHs and analyzed changes in gene expression, morphology, and cardiac physiology in order to better understand sensitivity and adaptive resistance mechanisms mediating PAH exposure during development. RESULTS: The synergistic effects of two model PAHs, an aryl hydrocarbon receptor (AHR) agonist (ß-naphthoflavone) and a cytochrome P4501A (CYP1A) inhibitor (α-naphthoflavone), caused significant developmental delays, impaired cardiac function, severe morphological alterations and failure to hatch, leading to the deaths of reference embryos; resistant embryos were mostly unaffected. Unexpectedly, patterns of gene expression among normal and moderately deformed embryos were similar, and only severely deformed embryos showed a contrasting pattern of gene expression. Given the drastic morphological differences between reference and resistant embryos, a surprisingly low percentage of genes, 2.24% of 6,754 analyzed, show statistically significant differences in transcript levels during late organogenesis between the two embryo populations. CONCLUSIONS: Our study demonstrates important contrasts in responses between reference and resistant natural embryo populations to synergistic effects of surrogate model PAHs that may be important in adaptive mechanisms mediating PAH effects during fish embryo development. These results suggest that statistically significant changes in gene expression of relatively few genes contribute to the phenotypic changes and large morphological differences exhibited by reference and resistant populations upon exposure to PAH pollutants. By correlating cardiac physiology and morphology with changes in gene expression patterns of reference and resistant embryos, we provide additional evidence for acquired resistance among embryos whose parents live at heavily contaminated sites.

Dietary protein and sugar differentially affect development and metabolic pools in ecologically diverse Drosophila.

We examined the effects of 3 diets differing in their relative levels of sugar and protein on development and metabolic pools (protein, TG, and glycogen) among sets of isofemale lines of 2 ecologically distinct Drosophila species, D. melanogaster and D. mojavensis. Our high protein:sugar ratio diet contained 7.1% protein and 17.9% carbohydrate, the EPS diet was 4.3% protein and 21.2% carbohydrate, and the LPS was only 2.5% protein and 24.6% carbohydrate. Larvae of D. melanogaster, a generalist fruit breeder, were able to survive on all 3 diets, although all 3 metabolic pools responded with significant diet and diet × line interactions. Development was delayed by the diet with the most sugar relative to protein. The other species, D. mojavensis, a cactus breeder ecologically unaccustomed to encountering simple sugars, completely failed to survive when fed the diet with the highest sugar and showed very poor survival even with the diet with equal parts of protein and sugar. Furthermore, the D. mojavensis adult metabolic pools of protein, TG, and glycogen significantly differed from those of D. melanogaster adults fed the identical diet. Thus, considerable within- and between-species differences exist in how diets are metabolized. Given that the genomes of both of these Drosophila species have been sequenced, these differences and their genetic underpinnings hold promise for understanding human responses to nutrition and for developing strategies for dealing with metabolic disease.

Gene expression throughout a vertebrate's embryogenesis.

BACKGROUND: Describing the patterns of gene expression during embryonic development has broadened our understanding of the processes and patterns that define morphogenesis. Yet gene expression patterns have not been described throughout vertebrate embryogenesis. This study presents statistical analyses of gene expression during all 40 developmental stages in the teleost Fundulus heteroclitus using four biological replicates per stage. RESULTS: Patterns of gene expression for 7,000 genes appear to be important as they recapitulate developmental timing. Among the 45% of genes with significant expression differences between pairs of temporally adjacent stages, significant differences in gene expression vary from as few as five to more than 660. Five adjacent stages have disproportionately more significant changes in gene expression (> 200 genes) relative to other stages: four to eight and eight to sixteen cell stages, onset of circulation, pre and post-hatch, and during complete yolk absorption. The fewest differences among adjacent stages occur during gastrulation. Yet, at stage 16, (pre-mid-gastrulation) the largest number of genes has peak expression. This stage has an over representation of genes in oxidative respiration and protein expression (ribosomes, translational genes and proteases). Unexpectedly, among all ribosomal genes, both strong positive and negative correlations occur. Similar correlated patterns of expression occur among all significant genes. CONCLUSIONS: These data provide statistical support for the temporal dynamics of developmental gene expression during all stages of vertebrate development.

Genomic approaches with natural fish populations from polluted environments.

Transcriptomics and population genomics are two complementary genomic approaches that can be used to gain insight into pollutant effects in natural populations. Transcriptomics identify altered gene expression pathways, and population genomics approaches more directly target the causative genomic polymorphisms. Neither approach is restricted to a predetermined set of genes or loci. Instead, both approaches allow a broad overview of genomic processes. Transcriptomics and population genomic approaches have been used to explore genomic responses in populations of fish from polluted environments and have identified sets of candidate genes and loci that appear biologically important in response to pollution. Often differences in gene expression or loci between polluted and reference populations are not conserved among polluted populations, suggesting a biological complexity that we do not yet fully understand. As genomic approaches become less expensive with the advent of new sequencing and genotyping technologies, they will be more widely used in complementary studies. However, although these genomic approaches are immensely powerful for identifying candidate genes and loci, the challenge of determining biological mechanisms that link genotypes and phenotypes remains.

Embryonic gene expression among pollutant resistant and sensitive Fundulus heteroclitus populations.

Changes in gene expression, coupled with biochemical, physiological, and behavioral alterations, play a critical role in adaptation to environmental stress. Our goal was to explore ways natural populations may have adapted to local, polluted environments. We took advantage of natural populations of Fundulus heteroclitus, one of the few studied fish species in North America that has established resistant populations in highly contaminated urban estuaries. We analyzed morphology, physiology, and gene expression of developing F. heteroclitus embryos during late organogenesis (stage 31); these embryos were from both resistant and sensitive populations and were raised in a common, unpolluted environment. While cardiac heart rates show significant differences between embryos of parents from clean and heavily contaminated Superfund sites, time-to-stage, embryo morphology, and gene expression profile analyses do not differ significantly between untreated embryos from resistant and sensitive populations. Further evaluation that includes tissue-specific approaches in gene expression analysis and larger sample sizes may be necessary to highlight important phenotypes associated with mechanisms of sensitivity and resistance among natural F. heteroclitus embryo populations. Alternatively, population differences may be masked by developmental canalization, and biologically important differences between sensitive and resistant embryos may only manifest with exposure (e.g., be dependent on gene by environment interactions).