Computational and Experimental Approaches to Reveal the Effects of Single Nucleotide Polymorphisms with Respect to Disease Diagnostics

DNA mutations are the cause of many human diseases and they are the reason for natural differences among individuals by affecting the structure, function, interactions, and other properties of DNA and expressed proteins. The ability to predict whether a given mutation is disease-causing or harmless is of great importance for the early detection of patients with a high risk of developing a particular disease and would pave the way for personalized medicine and diagnostics. Here we review existing methods and techniques to study and predict the effects of DNA mutations from three different perspectives: in silico, in vitro and in vivo. It is emphasized that the problem is complicated and successful detection of a pathogenic mutation frequently requires a combination of several methods and a knowledge of the biological phenomena associated with the corresponding macromolecules

Discovery of genomic variations by whole-genome resequencing of the North American Araucana chicken

Gallus gallus (chicken) is phenotypically diverse, with over 60 recognized breeds, among the myriad species within the Aves lineage. Domestic chickens have been under artificial selection by humans for thousands of years for agricultural purposes. The North American Araucana (NAA) breed arose as a cross between the Chilean “Collonocas” that laid blue eggs and was rumpless and the “Quetros” that had unusual tufts but with tail. NAAs were introduced from South America in the 1940s and have been kept as show birds by enthusiasts since then due to several distinctive traits: laying eggs with blue eggshells, characteristic ear-tufts, a pea comb, and rumplessness. The population has maintained variants for clean-faced and tufted, as well as tailed and rumplessness traits making it advantageous for genetic studies. Genome resequencing of six NAA chickens with a mixture of these traits was done to 71-fold coverage using Illumina HiSeq 2000 paired-end reads. Trimmed and concordant reads were mapped to the Gallus_gallus-5.0 reference genome (galGal5), generated from a female Red Junglefowl (UCD001). To identify candidate genes that are associated with traits of the NAA, their genome was compared with the Korean Araucana, Korean Domestic and White Leghorn breeds. Genomic regions with significantly reduced levels of heterogeneity were detected on five different chromosomes in NAA. The sequence data generated confirm the identity of variants responsible for the blue eggshells, pea comb, and rumplessness traits of NAA and propose one for ear-tufts

Amplification of Earthquake Ground Motions in Washington, DC, and Implications for Hazard Assessments in Central and Eastern North America

The extent of damage in Washington, DC, from the 2011 MW 5.8 Mineral, VA, earthquake was surprising for an epicenter 130 km away; U.S. Geological Survey “Did-You-Feel-It” reports suggest that Atlantic Coastal Plain and other unconsolidated sediments amplified ground motions in the city. We measure this amplification relative to bedrock sites using earthquake signals recorded on a temporary seismometer array. The spectral ratios show strong amplification in the 0.7 to 4 Hz frequency range for sites on sediments. This range overlaps with resonant frequencies of buildings in the city as inferred from their heights, suggesting amplification at frequencies to which many buildings are vulnerable to damage. Our results emphasize that local amplification can raise moderate ground motions to damaging levels in stable continental regions, where low attenuation extends shaking levels over wide areas and unconsolidated deposits on crystalline metamorphic or igneous bedrock can result in strong contrasts in near-surface material properties

Nonpathological Inflammation Drives the Development of an Avian Flight Adaptation

The development of modern birds provides a window into the biology of their dinosaur ancestors. We investigated avian postnatal development and found that sterile inflammation drives formation of the pygostyle, a compound structure resulting from bone fusion in the tail. Inflammation is generally induced by compromised tissue integrity, but here is involved in normal bone development. Transcriptome profiling and immuno/histochemistry reveal a robust inflammatory response that resembles bone fracture healing. The data suggest the involvement of necroptosis and multiple immune cell types, notably heterophils (the avian equivalent of neutrophils). Additionally, nucleus pulposus structures, heretofore unknown in birds, are involved in disc remodeling. Anti-inflammatory corticosteroid treatment inhibited vertebral fusion, substantiating the crucial role of inflammation in the ankylosis process. This study shows that inflammation can drive developmental skeletogenesis, in this case leading to the formation of a flight-adapted tail structure on the evolutionary path to modern avians

Novel APC promoter and exon 1B deletion and allelic silencing in three mutation-negative classic familial adenomatous polyposis families

BACKGROUND: The overwhelming majority (approximately 80%) of individuals with classic familial adenomatous polyposis (FAP) exhibit mutations in the coding sequence of the adenomatous polyposis coli (APC) tumor suppressor gene. Families without detectable APC mutations are unable to benefit from the use of genetic testing for clinical management of this autosomal dominant syndrome. METHODS: We used exome sequencing and linkage analysis, coupled with second-generation sequencing of the APC locus including non-coding regions to investigate three APC mutation-negative classical FAP families. RESULTS: We identified a novel ~11 kb deletion localized 44 kb upstream of the transcription start site of APC that encompasses the APC 1B promoter and exon. This deletion was present only in affected family members of one kindred with classical FAP. Furthermore, this same deletion with identical breakpoints was found in the probands of two additional APC mutation-negative classical FAP kindreds. Phasing analysis of single nucleotide polymorphisms (SNPs) around the deletion site in the three probands showed evidence of a shared haplotype, suggesting a common founder deletion in the three kindreds. SNP analysis within the coding sequence of APC, revealed that this ~11 kb deletion was accompanied by silencing of one of the APC alleles in blood-derived RNA of affected individuals. CONCLUSIONS: These results support the causal role of a novel promoter deletion in FAP and suggest that non-coding deletions, identifiable using second-generation sequencing methods, may account for a significant fraction of APC mutation-negative classical FAP families

The Spitzer Survey of Interstellar Clouds in the Gould Belt. VI. The Auriga-California Molecular Cloud observed with IRAC and MIPS

We present observations of the Auriga-California Molecular Cloud (AMC) at 3.6, 4.5, 5.8, 8.0, 24, 70 and 160 micron observed with the IRAC and MIPS detectors as part of the Spitzer Gould Belt Legacy Survey. The total mapped areas are 2.5 sq-deg with IRAC and 10.47 sq-deg with MIPS. This giant molecular cloud is one of two in the nearby Gould Belt of star-forming regions, the other being the Orion A Molecular Cloud (OMC). We compare source counts, colors and magnitudes in our observed region to a subset of the SWIRE data that was processed through our pipeline. Using color-magnitude and color-color diagrams, we find evidence for a substantial population of 166 young stellar objects (YSOs) in the cloud, many of which were previously unknown. Most of this population is concentrated around the LkHalpha 101 cluster and the filament extending from it. We present a quantitative description of the degree of clustering and discuss the fraction of YSOs in the region with disks relative to an estimate of the diskless YSO population. Although the AMC is similar in mass, size and distance to the OMC, it is forming about 15 - 20 times fewer stars.Comment: (30 pages, 17 figures (2 multipage figures), accepted for publication in ApJ

Avian tail ontogeny, pygostyle formation, and interpretation of juvenile Mesozoic specimens

The avian tail played a critical role in the evolutionary transition from long- to short-tailed birds, yet its ontogeny in extant birds has largely been ignored. This deficit has hampered efforts to effectively identify intermediate species during the Mesozoic transition to short tails. Here we show that fusion of distal vertebrae into the pygostyle structure does not occur in extant birds until near skeletal maturity, and mineralization of vertebral processes also occurs long after hatching. Evidence for post-hatching pygostyle formation is also demonstrated in two Cretaceous specimens, a juvenile enantiornithine and a subadult basal ornithuromorph. These findings call for reinterpretations of Zhongornis haoae, a Cretaceous bird hypothesized to be an intermediate in the long- to short-tailed bird transition, and of the recently discovered coelurosaur tail embedded in amber. Zhongornis, as a juvenile, may not yet have formed a pygostyle, and the amber-embedded tail specimen is reinterpreted as possibly avian. Analyses of relative pygostyle lengths in extant and Cretaceous birds suggests the number of vertebrae incorporated into the pygostyle has varied considerably, further complicating the interpretation of potential transitional species. In addition, this analysis of avian tail development reveals the generation and loss of intervertebral discs in the pygostyle, vertebral bodies derived from different kinds of cartilage, and alternative modes of caudal vertebral process morphogenesis in birds. These findings demonstrate that avian tail ontogeny is a crucial parameter specifically for the interpretation of Mesozoic specimens, and generally for insights into vertebrae formation

Causality and the semantics of provenance

Provenance, or information about the sources, derivation, custody or history of data, has been studied recently in a number of contexts, including databases, scientific workflows and the Semantic Web. Many provenance mechanisms have been developed, motivated by informal notions such as influence, dependence, explanation and causality. However, there has been little study of whether these mechanisms formally satisfy appropriate policies or even how to formalize relevant motivating concepts such as causality. We contend that mathematical models of these concepts are needed to justify and compare provenance techniques. In this paper we review a theory of causality based on structural models that has been developed in artificial intelligence, and describe work in progress on a causal semantics for provenance graphs.Comment: Workshop submissio

High Titers of Transmissible Spongiform Encephalopathy Infectivity Associated with Extremely Low Levels of PrPSc in Vivo

Rona Barron - ORCID: 0000-0003-4512-9177 https://orcid.org/0000-0003-4512-9177Diagnosis of transmissible spongiform encephalopathy (TSE) disease in humans and ruminants relies on the detection in post-mortem brain tissue of the protease-resistant form of the host glycoprotein PrP. The presence of this abnormal isoform (PrPSc) in tissues is taken as indicative of the presence of TSE infectivity. Here we demonstrate conclusively that high titers of TSE infectivity can be present in brain tissue of animals that show clinical and vacuolar signs of TSE disease but contain low or undetectable levels of PrPSc. This work questions the correlation between PrPSc level and the titer of infectivity and shows that tissues containing little or no proteinase K-resistant PrP can be infectious and harbor high titers of TSE infectivity. Reliance on protease-resistant PrPSc as a sole measure of infectivity may therefore in some instances significantly underestimate biological properties of diagnostic samples, thereby undermining efforts to contain and eradicate TSEs.https://doi.org/10.1074/jbc.M704329200282pubpub4