Strategies to Eliminate Inherited Pigmentation in Australian Merino Sheep

The viability of eliminating inherited pigmentation from the Australian Merino flock by DNA technology was investigated as a means of reducing dark fibre contamination of white wool. Two genetically distinct forms of inherited pigmentation are known. Symmetrical patterns follow simple recessive inheritance. Meanwhile the inheritance of piebald spots is uncertain. Inheritance models for piebald were assessed against new and prior field records to resolve this point, but a clear-cut conclusion was not possible at this time - further field experimentation is required. Gene discovery for Mendelian characters by homozygosity mapping was reviewed and applied in simulation to livestock situations. The method was found to be efficient, powerful, robust, and readily adaptable to a wide range of gene discovery problems. In particular, modifications to the design of HM to suit livestock had a relatively small effect on experimental power in many cases. For a ram-breeding flock, paternal culling in addition to phenotypic culling was found to be a highly effective strategy to reduce the frequency of undesirable pigmentation alleles as well as being cost-effective through reduction in the incidence of pigmented phenotypes. Taking steps to minimise allele frequency prior to the commencement of DNA gene testing also gave large benefits. When DNA gene testing becomes available, early adoption and rapid elimination of pigmentation alleles were found to be preferable in most situations for ram breeding flocks. The costs of eliminating pigmentation alleles and the concomitant loss of selection intensity were found to be inversely proportional to the initial allele frequency. Across a spectrum of inheritance models (excluding simple dominance) the particular inheritance model had little additional effect. An efficient testing strategy could significantly reduce costs. Economic analysis at the industry level has revealed the key costs and sources of revenue which would be affected by eliminating inherited pigmentation. While many factors were difficult to specify, the cost of DNA testing emerged as the most critical factor. This study has demonstrated the technical potential of DNA technology to reveal many of the missing pieces of the puzzle of inherited pigmentation and its elimination from Merino flocks. DNA technology is vital to both gene discovery and gene testing for the presence of undesirable pigmentation alleles, and no practical alternatives exist. The economic viability of widespread DNA gene testing is subject to many uncertainties at this time. However many industry players are keen to adopt gene testing even at quite a high test cost and the trend for the cost of a new technology to decline over time would improve the financial outcome. Meanwhile, indirect benefits through enhancing the reputation of Australian apparel wool could be substantial. While the uncertainty over the eventual returns from investments in research should prompt some caution, continuation of research in this field is encouraged

Bulk Mediated Surface Diffusion: Non Markovian Desorption with Finite First Moment

Here we address a fundamental issue in surface physics: the dynamics of adsorbed molecules. We study this problem when the particle's desorption is characterized by a non Markovian process, while the particle's adsorption and its motion in the bulk are governed by a Markovian dynamics. We study the diffusion of particles in a semi-infinite cubic lattice, and focus on the effective diffusion process at the interface $z = 1$. We calculate analytically the conditional probability to find the particle on the $z=1$ plane as well as the surface dispersion as functions of time. The comparison of these results with Monte Carlo simulations show an excellent agreement.Comment: 16 pages, 7 figs. European Physical Journal B (in press

The DNA Damage Signal for Mdm2 Regulation, Trp53 Induction, and Sunburn Cell Formation In Vivo Originates from Actively Transcribed Genes

The stratum corneum and DNA repair do not completely protect keratinocytes from ultraviolet B. A third defense prevents cells with DNA photoproducts from becoming precancerous mutant cells: apoptosis of ultraviolet-damaged keratinocytes (“sunburn cells”). As signals for ultraviolet-induced apoptosis, some studies implicate DNA photoproducts in actively transcribed genes; other studies implicate non-nuclear signals. We traced and quantitated the in vivo DNA signal through several steps in the apoptosis-signaling pathway in haired mice. Homozygous inactivation of Xpa, Csb, or Xpc nucleotide excision repair genes directed the accumulation of DNA photoproducts to specific genome regions. Repair-defective Xpa−/− mice were 7–10-fold more sensitive to sunburn cell induction than wild-type mice, indicating that 86–90% of the ultraviolet B signal for keratinocyte apoptosis involved repairable photoproducts in DNA; the remainder involves unrepaired DNA lesions or nongenomic targets. Csb−/− mice, defective only in excising photoproducts from actively transcribed genes, were as sensitive as Xpa−/−, indicating that virtually all of the DNA signal originates from photoproducts in active genes. Conversely, Xpc−/− mice, defective in repairing the untranscribed majority of the genome, were as resistant to apoptosis as wild type. Sunburn cell formation requires the Trp53 tumor suppressor protein; 90–96% of the signal for its induction in vivo involved transcribed genes. Mdm2, which regulates the stability of Trp53 through degradation, was induced in vivo by low ultraviolet B doses but was suppressed at erythemal doses. DNA photoproducts in actively transcribed genes were involved in ≈ 89% of the Mdm2 response

Frontiers in Pigment Cell and Melanoma Research

We identify emerging frontiers in clinical and basic research of melanocyte biology and its associated biomedical disciplines. We describe challenges and opportunities in clinical and basic research of normal and diseased melanocytes that impact current approaches to research in melanoma and the dermatological sciences. We focus on four themes: (1) clinical melanoma research, (2) basic melanoma research, (3) clinical dermatology, and (4) basic pigment cell research, with the goal of outlining current highlights, challenges, and frontiers associated with pigmentation and melanocyte biology. Significantly, this document encapsulates important advances in melanocyte and melanoma research including emerging frontiers in melanoma immunotherapy, medical and surgical oncology, dermatology, vitiligo, albinism, genomics and systems biology, epidemiology, pigment biophysics and chemistry, and evolution

Determining crystal structures through crowdsourcing and coursework

We show here that computer game players can build high-quality crystal structures. Introduction of a new feature into the computer game Foldit allows players to build and real-space refine structures into electron density maps. To assess the usefulness of this feature, we held a crystallographic model-building competition between trained crystallographers, undergraduate students, Foldit players and automatic model-building algorithms. After removal of disordered residues, a team of Foldit players achieved the most accurate structure. Analysing the target protein of the competition, YPL067C, uncovered a new family of histidine triad proteins apparently involved in the prevention of amyloid toxicity. From this study, we conclude that crystallographers can utilize crowdsourcing to interpret electron density information and to produce structure solutions of the highest quality

Human telomeres are hypersensitive to UV-induced DNA damage and refractory to repair

Telomeric repeats preserve genome integrity by stabilizing chromosomes, a function that appears to be important for both cancer and aging. In view of this critical role in genomic integrity, the telomere’s own integrity should be of paramount importance to the cell. Ultraviolet light (UV), the preeminent risk factor in skin cancer development, induces mainly cyclobutane pyrimidine dimers (CPD) which are both mutagenic and lethal. The human telomeric repeat unit (59TTAGGG/ CCCTAA39) is nearly optimal for acquiring UV-induced CPD, which form at dipyrimidine sites. We developed a ChIP–based technique, immunoprecipitation of DNA damage (IPoD), to simultaneously study DNA damage and repair in the telomere and in the coding regions of p53, 28S rDNA, and mitochondrial DNA. We find that human telomeres in vivo are 7-fold hypersensitive to UV-induced DNA damage. In double-stranded oligonucleotides, this hypersensitivity is a property of both telomeric and non-telomeric repeats; in a series of telomeric repeat oligonucleotides, a phase change conferring UVsensitivity occurs above 4 repeats. Furthermore, CPD removal in the telomere is almost absent, matching the rate in mitochondria known to lack nucleotide excision repair. Cells containing persistent high levels of telomeric CPDs nevertheless proliferate, and chronic UV irradiation of cells does not accelerate telomere shortening. Telomeres are therefore unique in at least three respects: their biophysical UV sensitivity, their prevention of excision repair, and their tolerance of unrepaired lesions. Utilizing a lesion-tolerance strategy rather than repair would prevent double-strand break

Enhancing the detection of barcoded reads in high throughput DNA sequencing data by controlling the false discovery rate

Background: DNA barcodes are short unique sequences used to label DNA or RNA-derived samples in multiplexed deep sequencing experiments. During the demultiplexing step, barcodes must be detected and their position identified. In some cases (e. g., with PacBio SMRT), the position of the barcode and DNA context is not well defined. Many reads start inside the genomic insert so that adjacent primers might be missed. The matter is further complicated by coincidental similarities between barcode sequences and reference DNA. Therefore, a robust strategy is required in order to detect barcoded reads and avoid a large number of false positives or negatives. For mass inference problems such as this one, false discovery rate (FDR) methods are powerful and balanced solutions. Since existing FDR methods cannot be applied to this particular problem, we present an adapted FDR method that is suitable for the detection of barcoded reads as well as suggest possible improvements. Results: In our analysis, barcode sequences showed high rates of coincidental similarities with the Mus musculus reference DNA. This problem became more acute when the length of the barcode sequence decreased and the number of barcodes in the set increased. The method presented in this paper controls the tail area-based false discovery rate to distinguish between barcoded and unbarcoded reads. This method helps to establish the highest acceptable minimal distance between reads and barcode sequences. In a proof of concept experiment we correctly detected barcodes in 83% of the reads with a precision of 89%. Sensitivity improved to 99% at 99% precision when the adjacent primer sequence was incorporated in the analysis. The analysis was further improved using a paired end strategy. Following an analysis of the data for sequence variants induced in the Atp1a1 gene of C57BL/6 murine melanocytes by ultraviolet light and conferring resistance to ouabain, we found no evidence of cross-contamination of DNA material between samples. Conclusion: Our method offers a proper quantitative treatment of the problem of detecting barcoded reads in a noisy sequencing environment. It is based on the false discovery rate statistics that allows a proper trade-off between sensitivity and precision to be chosen

Common Contaminants in Next-Generation Sequencing That Hinder Discovery of Low-Abundance Microbes

<div><p>Unbiased high-throughput sequencing of whole metagenome shotgun DNA libraries is a promising new approach to identifying microbes in clinical specimens, which, unlike other techniques, is not limited to known sequences. Unlike most sequencing applications, it is highly sensitive to laboratory contaminants as these will appear to originate from the clinical specimens. To assess the extent and diversity of sequence contaminants, we aligned 57 “1000 Genomes Project” sequencing runs from six centers against the four largest NCBI BLAST databases, detecting reads of diverse contaminant species in all runs and identifying the most common of these contaminant genera (<i>Bradyrhizobium</i>) in assembled genomes from the NCBI Genome database. Many of these microorganisms have been reported as contaminants of ultrapure water systems. Studies aiming to identify novel microbes in clinical specimens will greatly benefit from not only preventive measures such as extensive UV irradiation of water and cross-validation using independent techniques, but also a concerted effort to sequence the complete genomes of common contaminants so that they may be subtracted computationally.</p></div