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The rapidly evolving stem cell field puts much stress on developing educational resources. The ISSCR Education Committee has created a flexible stem cell syllabus rooted in core concepts to facilitate stem cell literacy. The free syllabus will be updated regularly to maintain accuracy and relevance.

Over 100 years of studies in Drosophila melanogaster and related species in the genus Drosophila have facilitated key discoveries in genetics, genomics, and evolution. While high-quality genome assemblies exist for several species in this group, they only encompass a small fraction of the genus. Recent advances in long-read sequencing allow high-quality genome assemblies for tens or even hundreds of species to be efficiently generated. Here, we utilize Oxford Nanopore sequencing to build an open community resource of genome assemblies for 101 lines of 93 drosophilid species encompassing 14 species groups and 35 sub-groups. The genomes are highly contiguous and complete, with an average contig N50 of 10.5 Mb and greater than 97% BUSCO completeness in 97/101 assemblies. We show that Nanopore-based assemblies are highly accurate in coding regions, particularly with respect to coding insertions and deletions. These assemblies, along with a detailed laboratory protocol and assembly pipelines, are released as a public resource and will serve as a starting point for addressing broad questions of genetics, ecology, and evolution at the scale of hundreds of species.

Accurate and comprehensive characterization of genetic variation is essential for deciphering the genetic basis of diseases and other phenotypes. A vast amount of genetic variation stems from large-scale sequence changes arising from the duplication, deletion, inversion, and translocation of sequences. In the past 10 years, high-throughput short reads have greatly expanded our ability to assay sequence variation due to single nucleotide polymorphisms. However, a recent de novo assembly of a second Drosophila melanogaster reference genome has revealed that short read genotyping methods miss hundreds of structural variants, including those affecting phenotypes. While genomes assembled using high-coverage long reads can achieve high levels of contiguity and completeness, concerns about cost, errors, and low yield have limited widespread adoption of such sequencing approaches. Here we resequenced the reference strain of D. melanogaster (ISO1) on a single Oxford Nanopore MinION flow cell run for 24 hr. Using only reads longer than 1 kb or with at least 30x coverage, we assembled a highly contiguous de novo genome. The addition of inexpensive paired reads and subsequent scaffolding using an optical map technology achieved an assembly with completeness and contiguity comparable to the D. melanogaster reference assembly. Comparison of our assembly to the reference assembly of ISO1 uncovered a number of structural variants (SVs), including novel LTR transposable element insertions and duplications affecting genes with developmental, behavioral, and metabolic functions. Collectively, these SVs provide a snapshot of the dynamics of genome evolution. Furthermore, our assembly and comparison to the D. melanogaster reference genome demonstrates that high-quality de novo assembly of reference genomes and comprehensive variant discovery using such assemblies are now possible by a single lab for under $1,000 (USD).

Meiosis is a form of cell division that is essential to sexually reproducing organisms and is therefore highly regulated. Each event of meiosis must occur at the correct developmental stage to ensure that chromosomes are segregated properly during both meiotic divisions. One unique meiosis-specific structure that is tightly regulated in terms of timing of assembly and disassembly is the synaptonemal complex (SC). While the mechanism(s) for assembly and disassembly of the SC are poorly understood in Drosophila melanogaster, posttranslational modifications, including ubiquitination and phosphorylation, are known to play a role. Here, we identify a role for the deubiquitinase Usp7 in the maintenance of the SC in early prophase and show that its function in SC maintenance is independent of the meiotic recombination process. Using two usp7 shRNA constructs that result in different knockdown levels, we have shown that the presence of SC through early/mid-pachytene is critical for normal levels and placement of crossovers. [ABSTRACT FROM AUTHOR]

STAT5 is a member of the signal transducers and activation of transcription (STAT) family of latent transcription factors activated in a variety of cytokine signaling pathways. We introduced alanine substitution mutations in highly conserved regions of murine STAT5A and studied the mutants for dimerization, DNA binding, transactivation, and dominant negative effects on erythropoietin-induced STAT5-dependent transcriptional activation. The mutations included two near the amino-terminus (W255KR-->AAA and R290QQ-->AAA), two in the DNA-binding domain (E437E-->AA and V466VV-->AAA), and a carboxy-terminal truncation of STAT5A (STAT5A/triangle up53C) analogous to a naturally occurring isoform of rat STAT5B. All of the STAT mutant proteins were tyrosine phosphorylated by JAK2 and heterodimerized with STAT5B except for the WKR mutant, suggesting an important role for this region in STAT5 for stabilizing dimerization. The WKR, EE, and VVV mutants had no detectable DNA-binding activity, and the WKR and VVV mutants, but not EE, were defective in transcriptional induction. The VVV mutant had a moderate dominant negative effect on erythropoietin-induced STAT5 transcriptional activation, which was likely due to the formation of heterodimers that are defective in DNA binding. Interestingly, the WKR mutant had a potent dominant negative effect, comparable to the transactivation domain deletion mutant, triangle up53C. Stable expression of either the WKR or triangle up53C STAT5 mutants in the murine myeloid cytokine-dependent cell line 32D inhibited both interleukin-3-dependent proliferation and granulocyte colony-stimulating factor (G-CSF)-dependent differentiation, without induction of apoptosis. Expression of these mutants in primary murine bone marrow inhibited G-CSF-dependent granulocyte colony formation in vitro. These results demonstrate that mutations in distinct regions of STAT5 exert dominant negative effects on cytokine signaling, likely through different mechanisms, and suggest a role for STAT5 in proliferation and differentiation of myeloid cells.

The martian North Polar layered deposits (NPLD) are composed of alternating water‐ice and dust‐rich layers resulting from atmospheric deposition and are key to understanding Mars climate cycles. Within these deposits are spiral troughs whose migration affects deposition signals. To understand the relationship between NPLD stratigraphy and Martian climate, we must identify modern‐day drivers of NPLD ice migration. Prevailing theory posits migration driven by upstream‐migrating bed undulations bounded by hydraulic jumps, caused by katabatic winds flowing over trough walls with asymmetric cross‐sectional relief. This is supported by trough‐parallel clouds, whose formation has been attributed to hydraulic jumps. We present a cloud atlas across the Martian north pole using ∼13,800 THEMIS images spanning ∼18 Earth years. We find trough‐parallel clouds in ∼400 images, with regions nearer to the pole having higher cloud frequency. We compare spiral trough geometry to our cloud atlas and find regions with trough‐parallel clouds often correlate with metrics associated with modern‐day sublimation‐deposition cycles (i.e., relief and asymmetry), but not always. In some regions, troughs with morphologies conducive to cloud formation have no clouds. Overall, trough geometry varies greatly across the deposits, both within and between troughs, suggesting localized differences in deposition relative to migration, varying katabatic wind intensities, differing past climatic states influencing the troughs, varying trough initiation properties, or the possibility of additional mechanisms for trough initiation and migration (e.g., in situ trough erosion). Understanding what controls trough shape variability across the NPLD and how these controls change through time and space is key when interpreting Martian paleoclimate. Plain Language Summary: The Martian North polar ice cap is composed of layers of water‐ice and dust deposited from the atmosphere, and differences in their thicknesses are thought to be the result of climate variations. Interpretations of the climate recorded in these layers can be affected by other processes that can deposit or erode ice. One process we need to understand is the migration history for the large spiraling troughs that occur across the ice cap, which tend to have asymmetric wall slopes and reliefs. The leading theory suggests that their migration is driven by ice ablation from winds that flow down the higher trough wall, and deposition (and cloud formation) when the wind hits the trough floor and decelerates. We present an updated record of cloud coverage across the ice cap using orbital images spanning ∼18 Earth years and analyze ∼3,000 trough cross‐sections to compare trough shape to cloud location. We find regions with clouds often correlate with trough shapes associated with modern‐day sublimation‐deposition cycles (wall asymmetry), but often asymmetric troughs have no clouds, or the troughs are symmetric. The fact that trough shape changes across the ice cap suggests that ice transport processes are variable and need to be considered when interpreting paleoclimate. Key Points: The spiral troughs on Mars' northern polar layered deposits (NPLD) have highly variable geometry, both within a trough and between troughsThe presence of trough‐parallel clouds, indicative of katabatic jumps and active trough migration, are regionally variable across the NPLDThe trough shape most conducive to the formation of katabatic jumps and generating clouds is not as widespread as previously suggested [ABSTRACT FROM AUTHOR]