An enigmatic fourth runt domain gene in the fugu genome: ancestral gene loss versus accelerated evolution

BACKGROUND: The runt domain transcription factors are key regulators of developmental processes in bilaterians, involved both in cell proliferation and differentiation, and their disruption usually leads to disease. Three runt domain genes have been described in each vertebrate genome (the RUNX gene family), but only one in other chordates. Therefore, the common ancestor of vertebrates has been thought to have had a single runt domain gene. RESULTS: Analysis of the genome draft of the fugu pufferfish (Takifugu rubripes) reveals the existence of a fourth runt domain gene, FrRUNT, in addition to the orthologs of human RUNX1, RUNX2 and RUNX3. The tiny FrRUNT packs six exons and two putative promoters in just 3 kb of genomic sequence. The first exon is located within an intron of FrSUPT3H, the ortholog of human SUPT3H, and the first exon of FrSUPT3H resides within the first intron of FrRUNT. The two gene structures are therefore "interlocked". In the human genome, SUPT3H is instead interlocked with RUNX2. FrRUNT has no detectable ortholog in the genomes of mammals, birds or amphibians. We consider alternative explanations for an apparent contradiction between the phylogenetic data and the comparison of the genomic neighborhoods of human and fugu runt domain genes. We hypothesize that an ancient RUNT locus was lost in the tetrapod lineage, together with FrFSTL6, a member of a novel family of follistatin-like genes. CONCLUSIONS: Our results suggest that the runt domain family may have started expanding in chordates much earlier than previously thought, and exemplify the importance of detailed analysis of whole-genome draft sequence to provide new insights into gene evolution

Genomic complexity of the variable region-containing chitin-binding proteins in amphioxus

<p>Abstract</p> <p>Background</p> <p>The variable region-containing chitin-binding proteins (VCBPs) are found in protochordates and consist of two tandem immunoglobulin variable (V)-type domains and a chitin-binding domain. We previously have shown that these polymorphic genes, which primarily are expressed in the gut, exhibit characteristics of immune genes. In this report, we describe VCBP genomic organization and characterize adjacent and intervening genetic features which may influence both their polymorphism and complex transcriptional repertoire.</p> <p>Results</p> <p>VCBP genes 1, 2, 4, and 5 are encoded in a single contiguous gene-rich chromosomal region and VCBP3 is encoded in a separate locus. The VCBPs exhibit extensive haplotype variation, including copy number variation (CNV), indel polymorphism and a markedly elevated variation in repeat type and density. In at least one haplotype, inverted repeats occur more frequently than elsewhere in the genome. Multi-animal cDNA screening, as well as transcriptional profilingusing a novel transfection system, suggests that haplotype-specific transcriptional variants may contribute to VCBP genetic diversity.</p> <p>Conclusion</p> <p>The availability of the <it>Branchiostoma floridae </it>genome (Joint Genome Institute, Brafl1), along with BAC and PAC screening and sequencing described here, reveal that the relatively limited number of VCBP genes present in the amphioxus genome exhibit exceptionally high haplotype variation. These VCBP haplotypes contribute a diverse pool of allelic variants, which includes gene copy number variation, pseudogenes, and other polymorphisms, while contributing secondary effects on gene transcription as well.</p

TRStalker: an efficient heuristic for finding fuzzy tandem repeats

Motivation: Genomes in higher eukaryotic organisms contain a substantial amount of repeated sequences. Tandem Repeats (TRs) constitute a large class of repetitive sequences that are originated via phenomena such as replication slippage and are characterized by close spatial contiguity. They play an important role in several molecular regulatory mechanisms, and also in several diseases (e.g. in the group of trinucleotide repeat disorders). While for TRs with a low or medium level of divergence the current methods are rather effective, the problem of detecting TRs with higher divergence (fuzzy TRs) is still open. The detection of fuzzy TRs is propaedeutic to enriching our view of their role in regulatory mechanisms and diseases. Fuzzy TRs are also important as tools to shed light on the evolutionary history of the genome, where higher divergence correlates with more remote duplication events

COOL-LAMPS. VII. Quantifying Strong-lens Scaling Relations with 177 Cluster-scale Gravitational Lenses in DECaLS

We compute parametric measurements of the Einstein-radius-enclosed total mass for 177 cluster-scale strong gravitational lenses identified by the ChicagO Optically-selected Lenses Located At the Margins of Public Surveys (COOL-LAMPS) collaboration with lens redshifts ranging from $0.2 \lessapprox z \lessapprox 1.0$ using only two measured parameters in each lensing system: the Einstein radius, and the brightest-cluster-galaxy (BCG) redshift. We then constrain the Einstein-radius-enclosed luminosity and stellar mass by fitting parametric spectral energy distributions (SEDs) with aperture photometry from the Dark Energy Camera Legacy Survey (DECaLS) in the $g$, $r$, and $z$-band Dark Energy Camera (DECam) filters. We find that the BCG redshift, enclosed total mass, and enclosed luminosity are strongly correlated and well described by a planar relationship in 3D space. We also find that the enclosed total mass and stellar mass are correlated with a logarithmic slope of $0.443\pm0.035$, and the enclosed total mass and stellar-to-total mass fraction are correlated with a logarithmic slope of $-0.563\pm0.035$. The correlations described here can be used to validate strong lensing candidates in upcoming imaging surveys -- such as Rubin/Legacy Survey of Space and Time (LSST) -- in which an algorithmic treatment of lensing systems will be needed due to the sheer volume of data these surveys will produce.Comment: 17 pages, 5 figures, 2 tables. Submitted to The Astrophysical Journal. v3: updated authors, formatting, grammar, and reference

An international effort towards developing standards for best practices in analysis, interpretation and reporting of clinical genome sequencing results in the CLARITY Challenge

There is tremendous potential for genome sequencing to improve clinical diagnosis and care once it becomes routinely accessible, but this will require formalizing research methods into clinical best practices in the areas of sequence data generation, analysis, interpretation and reporting. The CLARITY Challenge was designed to spur convergence in methods for diagnosing genetic disease starting from clinical case history and genome sequencing data. DNA samples were obtained from three families with heritable genetic disorders and genomic sequence data were donated by sequencing platform vendors. The challenge was to analyze and interpret these data with the goals of identifying disease-causing variants and reporting the findings in a clinically useful format. Participating contestant groups were solicited broadly, and an independent panel of judges evaluated their performance. RESULTS: A total of 30 international groups were engaged. The entries reveal a general convergence of practices on most elements of the analysis and interpretation process. However, even given this commonality of approach, only two groups identified the consensus candidate variants in all disease cases, demonstrating a need for consistent fine-tuning of the generally accepted methods. There was greater diversity of the final clinical report content and in the patient consenting process, demonstrating that these areas require additional exploration and standardization. CONCLUSIONS: The CLARITY Challenge provides a comprehensive assessment of current practices for using genome sequencing to diagnose and report genetic diseases. There is remarkable convergence in bioinformatic techniques, but medical interpretation and reporting are areas that require further development by many groups

Astronomical data and derivations from historic photographic glass plate 10B-161 from Yerkes Observatory Glass Plate collection

Includes: - TIFF images of glass plate negative at full size, center 6”, and step wedge for calibration and associated README - Catalog of stars in center 6” and associated README - FITS images of center 6” and associated README - README of descriptions of file

Genetic Divergence of the Rhesus Macaque Major Histocompatibility Complex

The major histocompatibility complex (MHC) is comprised of the class I, class II, and class III regions, including the MHC class I and class II genes that play a primary role in the immune response and serve as an important model in studies of primate evolution. Although nonhuman primates contribute significantly to comparative human studies, relatively little is known about the genetic diversity and genomics underlying nonhuman primate immunity. To address this issue, we sequenced a complete rhesus macaque MHC spanning over 5.3 Mb, and obtained an additional 2.3 Mb from a second haplotype, including class II and portions of class I and class III. A major expansion of from six class I genes in humans to as many as 22 active MHC class I genes in rhesus and levels of sequence divergence some 10-fold higher than a similar human comparison were found, averaging from 2% to 6% throughout extended portions of class I and class II. These data pose new interpretations of the evolutionary constraints operating between MHC diversity and T-cell selection by contrasting with models predicting an optimal number of antigen presenting genes. For the clinical model, these data and derivative genetic tools can be implemented in ongoing genetic and disease studies that involve the rhesus macaque

Capturing the Stars: Early 20th Century Astronomical Photography and the Material Legacy of Yerkes Observatory

Presented at the 2022 History of Science Society conference, the poster features the labor being done at Yerkes Observatory in the early 20th century. It features the specific tasks of observing and astronomy, focusing on the women of Yerkes, and the ongoing research into this topic

Precise Photometric Measurements from a 1903 Photographic Plate Using a Commercial Scanner

Includes: README file and TIFF images of center 2.4” glass plate negative (3 repeated scans), 1 rotated center 2.4” glass plate negative, positive and negative step wedge for calibration and associated README Catalog of stars in center 2.4” and associated README Unchanged, inverted, and transformed FITS images of center 2.4” README of descriptions of file