Gene expression throughout a vertebrate's embryogenesis

Abstract 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)

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

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

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

BackgroundThe 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.ResultsPollution-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.ConclusionHeart 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

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