Foregrounding the Margins: A Dialogue about Literacy, Learning, and Social Annotation

Annotation, or the addition of a note to a text, enables readers-as-writers to make their thinking visible. This article, which is structured as a dialogue among four literacy educators, discusses the potential for social annotation to transform literacy learning, assessment, and teacher education. Collectively, the authors argue for social annotation as a vital and transformative practice in hybrid and post-pandemic education. The authors reflect on their personal and pedagogical uses of annotation, sharing related resources for educators across K-12 and higher education contexts

GHOSTS I: A New Faint very Isolated Dwarf Galaxy at D = 12 +/- 2 Mpc

We report the discovery of a new faint dwarf galaxy, GHOSTS I, using HST/ACS data from one of our GHOSTS (Galaxy Halos, Outer disks, Substructure, Thick disk, and Star clusters) fields. Its detected individual stars populate an approximately one magnitude range of its luminosity function (LF). Using synthetic color-magnitude diagrams (CMDs) to compare with the galaxy's CMD, we find that the colors and magnitudes of GHOSTS I's individual stars are most consistent with being young helium-burning and asymptotic giant branch stars at a distance of 12 +/- 2 Mpc. Morphologically, GHOSTS I appears to be actively forming stars, so we tentatively classify it as a dwarf irregular (dIrr) galaxy, although future HST observations deep enough to resolve a larger magnitude range in its LF are required to make a more secure classification. GHOSTS I's absolute magnitude is $M_V = -9.85^{+ 0.40}_{- 0.33}$, making it one of the least luminous dIrr galaxies known, and its metallicity is lower than [Fe/H] =-1.5 dex. The half-light radius of GHOSTS I is 226 +/- 38 pc and its ellipticity is 0.47 +/- 0.07, similar to Milky Way and M31 dwarf satellites at comparable luminosity. There are no luminous massive galaxies or galaxy clusters within ~ 4 Mpc from GHOSTS I that could be considered as its host, making it a very isolated dwarf galaxy in the Local Universe.Comment: 8 pages, 7 figures. Accepted for publication in Ap

Reconstruction and Validation of a Genome-Scale Metabolic Model for the Filamentous Fungus Neurospora crassa Using FARM

The filamentous fungus Neurospora crassa played a central role in the development of twentieth-century genetics, biochemistry and molecular biology, and continues to serve as a model organism for eukaryotic biology. Here, we have reconstructed a genome-scale model of its metabolism. This model consists of 836 metabolic genes, 257 pathways, 6 cellular compartments, and is supported by extensive manual curation of 491 literature citations. To aid our reconstruction, we developed three optimization-based algorithms, which together comprise Fast Automated Reconstruction of Metabolism (FARM). These algorithms are: LInear MEtabolite Dilution Flux Balance Analysis (limed-FBA), which predicts flux while linearly accounting for metabolite dilution; One-step functional Pruning (OnePrune), which removes blocked reactions with a single compact linear program; and Consistent Reproduction Of growth/no-growth Phenotype (CROP), which reconciles differences between in silico and experimental gene essentiality faster than previous approaches. Against an independent test set of more than 300 essential/non-essential genes that were not used to train the model, the model displays 93% sensitivity and specificity. We also used the model to simulate the biochemical genetics experiments originally performed on Neurospora by comprehensively predicting nutrient rescue of essential genes and synthetic lethal interactions, and we provide detailed pathway-based mechanistic explanations of our predictions. Our model provides a reliable computational framework for the integration and interpretation of ongoing experimental efforts in Neurospora, and we anticipate that our methods will substantially reduce the manual effort required to develop high-quality genome-scale metabolic models for other organisms

Halo orbits in cosmological disk galaxies : tracers of information history

We analyze the orbits of stars and dark matter particles in the halo of a disk galaxy formed in a cosmological hydrodynamical simulation. The halo is oblate within the inner ∼20 kpc and triaxial beyond this radius. About 43% of orbits are short axis tubes—the rest belong to orbit families that characterize triaxial potentials (boxes, long-axis tubes and chaotic orbits), but their shapes are close to axisymmetric. We find no evidence that the self-consistent distribution function of the nearly oblate inner halo is comprised primarily of axisymmetric short-axis tube orbits. Orbits of all families and both types of particles are highly eccentric, with mean eccentricity �0.6. We find that randomly selected samples of halo stars show no substructure in “integrals of motion” space. However, individual accretion events can clearly be identified in plots of metallicity versus formation time. Dynamically young tidal debris is found primarily on a single type of orbit. However, stars associated with older satellites become chaotically mixed during the formation process (possibly due to scattering by the central bulge and disk, and baryonic processes), and appear on all four types of orbits. We find that the tidal debris in cosmological hydrodynamical simulations experiences significantly more chaotic evolution than in collisionless simulations, making it much harder to identify individual progenitors using phase space coordinates alone. However, by combining information on stellar ages and chemical abundances with the orbital properties of halo stars in the underlying self-consistent potential, the identification of progenitors is likely to be possible

Patterns and Implications of Gene Gain and Loss in the Evolution of Prochlorococcus

Prochlorococcus is a marine cyanobacterium that numerically dominates the mid-latitude oceans and is the smallest known oxygenic phototroph. Numerous isolates from diverse areas of the world's oceans have been studied and shown to be physiologically and genetically distinct. All isolates described thus far can be assigned to either a tightly clustered high-light (HL)-adapted clade, or a more divergent low-light (LL)-adapted group. The 16S rRNA sequences of the entire Prochlorococcus group differ by at most 3%, and the four initially published genomes revealed patterns of genetic differentiation that help explain physiological differences among the isolates. Here we describe the genomes of eight newly sequenced isolates and combine them with the first four genomes for a comprehensive analysis of the core (shared by all isolates) and flexible genes of the Prochlorococcus group, and the patterns of loss and gain of the flexible genes over the course of evolution. There are 1,273 genes that represent the core shared by all 12 genomes. They are apparently sufficient, according to metabolic reconstruction, to encode a functional cell. We describe a phylogeny for all 12 isolates by subjecting their complete proteomes to three different phylogenetic analyses. For each non-core gene, we used a maximum parsimony method to estimate which ancestor likely first acquired or lost each gene. Many of the genetic differences among isolates, especially for genes involved in outer membrane synthesis and nutrient transport, are found within the same clade. Nevertheless, we identified some genes defining HL and LL ecotypes, and clades within these broad ecotypes, helping to demonstrate the basis of HL and LL adaptations in Prochlorococcus. Furthermore, our estimates of gene gain events allow us to identify highly variable genomic islands that are not apparent through simple pairwise comparisons. These results emphasize the functional roles, especially those connected to outer membrane synthesis and transport that dominate the flexible genome and set it apart from the core. Besides identifying islands and demonstrating their role throughout the history of Prochlorococcus, reconstruction of past gene gains and losses shows that much of the variability exists at the “leaves of the tree,” between the most closely related strains. Finally, the identification of core and flexible genes from this 12-genome comparison is largely consistent with the relative frequency of Prochlorococcus genes found in global ocean metagenomic databases, further closing the gap between our understanding of these organisms in the lab and the wild

Patterns and Implications of Gene Gain and Loss in the Evolution of Prochlorococcus

Prochlorococcus is a marine cyanobacterium that numerically dominates the mid-latitude oceans and is the smallest known oxygenic phototroph. Numerous isolates from diverse areas of the world's oceans have been studied and shown to be physiologically and genetically distinct. All isolates described thus far can be assigned to either a tightly clustered high-light (HL)-adapted clade, or a more divergent low-light (LL)-adapted group. The 16S rRNA sequences of the entire Prochlorococcus group differ by at most 3%, and the four initially published genomes revealed patterns of genetic differentiation that help explain physiological differences among the isolates. Here we describe the genomes of eight newly sequenced isolates and combine them with the first four genomes for a comprehensive analysis of the core (shared by all isolates) and flexible genes of the Prochlorococcus group, and the patterns of loss and gain of the flexible genes over the course of evolution. There are 1,273 genes that represent the core shared by all 12 genomes. They are apparently sufficient, according to metabolic reconstruction, to encode a functional cell. We describe a phylogeny for all 12 isolates by subjecting their complete proteomes to three different phylogenetic analyses. For each non-core gene, we used a maximum parsimony method to estimate which ancestor likely first acquired or lost each gene. Many of the genetic differences among isolates, especially for genes involved in outer membrane synthesis and nutrient transport, are found within the same clade. Nevertheless, we identified some genes defining HL and LL ecotypes, and clades within these broad ecotypes, helping to demonstrate the basis of HL and LL adaptations in Prochlorococcus. Furthermore, our estimates of gene gain events allow us to identify highly variable genomic islands that are not apparent through simple pairwise comparisons. These results emphasize the functional roles, especially those connected to outer membrane synthesis and transport that dominate the flexible genome and set it apart from the core. Besides identifying islands and demonstrating their role throughout the history of Prochlorococcus, reconstruction of past gene gains and losses shows that much of the variability exists at the “leaves of the tree,” between the most closely related strains. Finally, the identification of core and flexible genes from this 12-genome comparison is largely consistent with the relative frequency of Prochlorococcus genes found in global ocean metagenomic databases, further closing the gap between our understanding of these organisms in the lab and the wild

Genomics of Loa loa, a Wolbachia-free filarial parasite of humans

Loa loa, the African eyeworm, is a major filarial pathogen of humans. Unlike most filariae, Loa loa does not contain the obligate intracellular Wolbachia endosymbiont. We describe the 91.4 Mb genome of Loa loa, and the genome of the related filarial parasite Wuchereria bancrofti, and predict 14,907 Loa loa genes based on microfilarial RNA sequencing. By comparing these genomes to that of another filarial parasite, Brugia malayi, and to several other nematode genomes, we demonstrate synteny among filariae but not with non-parasitic nematodes. The Loa loa genome encodes many immunologically relevant genes, as well as protein kinases targeted by drugs currently approved for humans. Despite lacking Wolbachia, Loa loa shows no new metabolic synthesis or transport capabilities compared to other filariae. These results suggest that the role played by Wolbachia in filarial biology is more subtle than previously thought and reveal marked differences between parasitic and non-parasitic nematodes