The postdoctoral community is an essential component of the academic and scientific workforce, but a lack of data about this community has made it difficult to develop policies to address concerns about salaries, working conditions, diversity and career development, and to evaluate the impact of existing policies. Here we present comprehensive survey results from 7,603 postdocs based at 351 US academic and non-academic (e.g. hospital, industry and government lab) institutions in 2016. In addition to demographic and salary information, we present multivariate analyses on factors influencing postdoc career plans and satisfaction with mentorship. We further analyze gender dynamics and expose wage disparities. Academic research positions remain the predominant career choice, although women and US citizens are less likely than their male and non-US citizen counterparts to choose academic research positions. Receiving mentorship training has a significant positive effect on postdoc satisfaction with mentorship. Quality of and satisfaction with postdoc mentorship also appear to heavily influence career choice.

Antigen processing and presentation genes found within the MHC are among the most highly polymorphic genes of vertebrate genomes, providing populations with diverse immune responses to a wide array of pathogens. Here, we describe transcriptome, exome, and whole-genome sequencing of clonal zebrafish, uncovering the most extensive diversity within the antigen processing and presentation genes of any species yet examined. Our CG2 clonal zebrafish assembly provides genomic context within a remarkably divergent haplotype of the core MHC region on chromosome 19 for six expressed genes not found in the zebrafish reference genome: mhc1uga, proteasome-β 9b (psmb9b), psmb8f, and previously unknown genes psmb13b, tap2d, and tap2e. We identify ancient lineages for Psmb13 within a proteasome branch previously thought to be monomorphic and provide evidence of substantial lineage diversity within each of three major trifurcations of catalytic-type proteasome subunits in vertebrates: Psmb5/Psmb8/Psmb11, Psmb6/ Psmb9/Psmb12, and Psmb7/Psmb10/Psmb13. Strikingly, nearby tap2 and MHC class I genes also retain ancient sequence lineages, indicating that alternative lineages may have been preserved throughout the entire MHC pathway since early diversification of the adaptive immune system ∼500 Mya. Furthermore, polymorphisms within the three MHC pathway steps (antigen cleavage, transport, and presentation) are each predicted to alter peptide specificity. Lastly, comparative analysis shows that antigen processing gene diversity is far more extensive than previously realized (with ancient coelacanth psmb8 lineages, shark psmb13, and tap2t and psmb10 outside the teleost MHC), implying distinct immune functions and conserved roles in shaping MHC pathway evolution throughout vertebrates.comparative genomics | proteasome and TAP evolution | major histocompatibility | MHC class I pathway | CG2 clonal zebrafish

Heme oxygenase-1 is a highly inducible gene, the product of which catalyzes breakdown of the prooxidant heme. The purpose of this study was to investigate the regulation of the human heme oxygenase-1 gene in renal epithelial cells. DNase I hypersensitivity studies identified three distal sites (HS-2, -3, and -4) corresponding to approximately ؊4.0, ؊7.2, and ؊9.2 kb, respectively, of the heme oxygenase-1 promoter in addition to one proximal region, HS-1, which we have shown previously to be an E box. In vivo dimethyl sulfate footprinting of the HS-2 region revealed six individual protected guanines. Two mutations within HS-2 combined with a third mutation of the proximal E box abolished hemin-and cadmium-driven heme oxygenase-1 promoter activation, suggesting that these three sites synergized for maximal heme oxygenase-1 induction. Jun proteins bound to the antioxidant response element in the HS-2 region in vitro and associated with the heme oxygenase-1 promoter in vivo. JunB and JunD contribute opposing effects; JunB activated whereas JunD repressed heme oxygenase-1 expression in human renal epithelial cells, results that were corroborated in junB ؊/؊ and junD ؊/؊ cells. We propose that heme oxygenase-1 induction is controlled by a dynamic interplay of regulatory proteins, and we provide new insights into the molecular control of the human heme oxygenase-1 gene.

The zebrafish is an important animal model for stem cell biology, cancer, and immunology research. Histocompatibility represents a key intersection of these disciplines, however histocompatibility in zebrafish remains poorly understood. We examined a set of diverse zebrafish Class I major histocompatibility complex (MHC) genes that segregate with specific haplotypes at chromosome 19, and for which donor-recipient matching has been shown to improve engraftment after hematopoietic transplantation. Using flanking gene polymorphisms we identified six distinct chromosome 19 haplotypes. We describe several novel Class I U lineage genes and characterize their sequence properties, expression, and haplotype distribution. Altogether ten full-length zebrafish Class I genes were analyzed, mhc1uba through mhc1uka. Expression data and sequence properties indicate that most are candidate classical genes. Several substitutions in putative peptide anchor residues, often shared with deduced MHC molecules from additional teleost species, suggest flexibility in antigen binding. All ten zebrafish Class I genes were uniquely assigned among the six haplotypes, with dominant or co-dominant expression of one to three genes per haplotype. Interestingly, while the divergent MHC haplotypes display variable gene copy number and content, the different genes appear to have ancient origin, with extremely high levels of sequence diversity. Furthermore, haplotype variability extends beyond the MHC genes to include divergent forms of psmb8. The many disparate haplotypes at this locus therefore represent a remarkable form of genomic region configuration polymorphism. Defining the functional MHC genes within these divergent Class I haplotypes in zebrafish will provide an important foundation for future studies in immunology and transplantation.

A novel humanized mouse model of Cooley's Anemia (CA) was generated by targeted gene replacement in embryonic stem (ES) cells. Because the mouse does not have a true fetal hemoglobin, a delayed switching human ␥ to ␤ 0 globin gene cassette (␥␤ 0 ) was inserted directly into the murine ␤ globin locus replacing both adult mouse ␤ globin genes. The inserted human ␤ 0 globin allele has a mutation in the splice donor site that produces the same aberrant transcripts in mice as described in human cells. No functional human ␤ globin polypeptide chains are produced. Heterozygous ␥␤ 0 mice suffer from microcytic anemia. Unlike previously described animal models of ␤ thalassemia major, homozygous ␥␤ 0 mice switch from mouse embryonic globin chains to human fetal ␥ globin during fetal life. When bred with human ␣ globin knockin mice, homozygous CA mice survive solely upon human fetal hemoglobin at birth. This preclinical animal model of CA can be utilized to study the regulation of globin gene expression, synthesis, and switching; the reactivation of human fetal globin gene expression; and the testing of genetic and cell-based therapies for the correction of thalassemia.