Erratum: Corrigendum: Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution

International Chicken Genome Sequencing Consortium. The Original Article was published on 09 December 2004. Nature432, 695–716 (2004). In Table 5 of this Article, the last four values listed in the ‘Copy number’ column were incorrect. These should be: LTR elements, 30,000; DNA transposons, 20,000; simple repeats, 140,000; and satellites, 4,000. These errors do not affect any of the conclusions in our paper. Additional information. The online version of the original article can be found at 10.1038/nature0315

Regulatory Potential Scores From Genome-Wide Three-Way Alignments of Human, Mouse, and Rat

We generalize the computation of the Regulatory Potential (RP) score from two-way alignments of human and mouse to three-way alignments of human, mouse, and rat. This requires overcoming technical challenges that arise because the complexity of the models underlying the score increases exponentially with the number of species. Despite the close evolutionary proximity of rat to mouse, we find that adding the rat sequence increases our ability to predict genomic sites that regulate gene transcription. A variant of the RP scoring scheme that accounts for local variation in neutral mutational patterns further improves our predictions

Identification of members of the Wnt signaling pathway in the embryonic pituitary gland

Prop1 is one of several transcription factors important for the development of the pituitary gland. Downstream targets of PROP1 and other critical pituitary transcription factors remain largely unknown. We have generated a partial expression profile of the developing pituitary gland containing over 350 transcripts, using cDNA subtractive hybridization between Prop1 df/df and wild-type embryonic pituitary gland primordia. Numerous classes of genes including transcription factors, membrane associated molecules, and cell cycle regulators were identified in this study. Of the transcripts, 34% do not have sequence similarity to known genes, but are similar to ESTs, and 4% represent novel sequences. Pituitary gland expression of a number of clones was verified using in situ hybridization.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/42122/1/335-12-11-843_10120843.pd

Making Strides in Doctoral-Level Career Outcomes Reporting: Surveying the Landscape of Classification and Visualization Methodologies and Creating a Crosswalk Tool

Manuscript Abstract: The recent movement underscoring the importance of career taxonomies has helped usher in a new era of transparency in PhD career outcomes. The convergence of discipline-specific organizational movements, interdisciplinary collaborations, and federal initiatives have all helped to increase PhD career outcomes tracking and reporting. Transparent and publicly available PhD career outcomes are being used by institutions to attract top applicants, as prospective graduate students are factoring these in when deciding on the program and institution in which to enroll for their PhD studies. Given the increasing trend to track PhD career outcomes, the number of institutional efforts and supporting offices for these studies have increased, as has the variety of methods being used to classify and report/visualize outcomes. This report, therefore, aims to identify and summarize currently available PhD career taxonomy tools, resources, and visualization options to help catalyze and empower institutions to develop and publish their own PhD career outcomes. This work serves as an empirical review of the career outcome tracking systems available and highlights organizations, consortia, and funding agencies that are impacting policy change toward greater transparency in PhD career outcomes reporting. Project Description: We collated STEM and humanities career outcome taxonomies from 30 groups (universities, consortia, research institutions & professional societies) and mapped fields that were similar between these taxonomies. In mapping these fields, a number of challenges occurred. For example, some taxonomies were too comprehensive to fully map (e.g., there were nearly 1500 categories to choose from), and these omissions are noted within the headings. Some categories had a tally higher than the total number of taxonomies examined because they were present in multiple ways within a single taxonomy (e.g., tenure-track faculty may have appeared as a variety of different professor job titles). Additionally, some categories were repeated for the purposes of alignment; an asterisk (*) was used to depict when this "one-to-many" mapping occurred. Another key challenge is that no two taxonomies have categories that are 100% equivalent. This was especially apparent when examining employment categorization between different countries. Nevertheless, efforts were made to ascertain the fundamental meaning of each data field in order to best highlight approximate equivalencies between taxonomies. Furthermore, in order to prevent the loss of granularity when aligning taxonomies that are more complex, multiple rows are depicted back-to-back with the same color to highlight categories that are related. Some text is shown in a color other than black to indicate either multiple categories that align together, or to indicate that a category is out of place with respect to the parent taxonomy stratification. Not all of these occurrences are indicated for ease of illustration; one may refer to the original taxonomies to ascertain their structure

Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution

We present here a draft genome sequence of the red jungle fowl, Gallus gallus. Because the chicken is a modern descendant of the dinosaurs and the first non-mammalian amniote to have its genome sequenced, the draft sequence of its genome--composed of approximately one billion base pairs of sequence and an estimated 20,000-23,000 genes--provides a new perspective on vertebrate genome evolution, while also improving the annotation of mammalian genomes. For example, the evolutionary distance between chicken and human provides high specificity in detecting functional elements, both non-coding and coding. Notably, many conserved non-coding sequences are far from genes and cannot be assigned to defined functional classes. In coding regions the evolutionary dynamics of protein domains and orthologous groups illustrate processes that distinguish the lineages leading to birds and mammals. The distinctive properties of avian microchromosomes, together with the inferred patterns of conserved synteny, provide additional insights into vertebrate chromosome architecture

Genome Sequence of the Brown Norway Rat Yields Insights Into Mammalian Evolution

The laboratory rat (Rattus norvegicus) is an indispensable tool in experimental medicine and drug development, having made inestimable contributions to human health. We report here the genome sequence of the Brown Norway (BN) rat strain. The sequence represents a high-quality 'draft' covering over 90% of the genome. The BN rat sequence is the third complete mammalian genome to be deciphered, and three-way comparisons with the human and mouse genomes resolve details of mammalian evolution. This first comprehensive analysis includes genes and proteins and their relation to human disease, repeated sequences, comparative genome-wide studies of mammalian orthologous chromosomal regions and rearrangement breakpoints, reconstruction of ancestral karyotypes and the events leading to existing species, rates of variation, and lineage-specific and lineage-independent evolutionary events such as expansion of gene families, orthology relations and protein evolution