Complex reorganization and predominant non-homologous repair following chromosomal breakage in karyotypically balanced germline rearrangements and transgenic integration

We defined the genetic landscape of balanced chromosomal rearrangements at nucleotide resolution by sequencing 141 breakpoints from cytogenetically interpreted translocations and inversions. We confirm that the recently described phenomenon of 'chromothripsis' (massive chromosomal shattering and reorganization) is not unique to cancer cells but also occurs in the germline, where it can resolve to a relatively balanced state with frequent inversions. We detected a high incidence of complex rearrangements (19.2%) and substantially less reliance on microhomology (31%) than previously observed in benign copy-number variants (CNVs). We compared these results to experimentally generated DNA breakage-repair by sequencing seven transgenic animals, revealing extensive rearrangement of the transgene and host genome with similar complexity to human germline alterations. Inversion was the most common rearrangement, suggesting that a combined mechanism involving template switching and non-homologous repair mediates the formation of balanced complex rearrangements that are viable, stably replicated and transmitted unaltered to subsequent generations.     

Temporal activity patterns of Dipodomys ordii population

Temporal activity patterns for Dipodomys ordii were generally bimodal during the summer, with the highest peak occurring during early predawn hours when conditions were optimum for water conservation. Removal of dominant members in the population resulted in a substantial shift in the activity pattern to increased activity during the evening hours.     

Economic and statistical measures of forecast accuracy

This paper argues in favour of a closer link between the decision and the forecast evaluation problems. Although the idea of using decision theory for forecast evaluation appears early in the dynamic stochastic programming literature, and has continued to be used with meteorological forecasts, it is hardly mentioned in standard academic texts on economic forecasting. Some of the main issues involved are illustrated in the context of a two‐state, two‐action decision problem as well as in a more general setting. Relationships between statistical and economic methods of forecast evaluation are discussed and links between the Kuipers score used as a measure of forecast accuracy in the meteorology literature and the market timing tests used in finance are established. An empirical application to the problem of stock market predictability is also provided, and the conditions under which such predictability could be explained in the presence of transaction costs are discussed. Copyright © 2000 John Wiley & Sons, Ltd.     

Accurate whole human genome sequencing using reversible terminator chemistry

DNA sequence information underpins genetic research, enabling discoveries of important biological or medical benefit. Sequencing projects have traditionally used long (400-800 base pair) reads, but the existence of reference sequences for the human and many other genomes makes it possible to develop new, fast approaches to re-sequencing, whereby shorter reads are compared to a reference to identify intraspecies genetic variation. Here we report an approach that generates several billion bases of accurate nucleotide sequence per experiment at low cost. Single molecules of DNA are attached to a flat surface, amplified in situ and used as templates for synthetic sequencing with fluorescent reversible terminator deoxyribonucleotides. Images of the surface are analysed to generate high-quality sequence. We demonstrate application of this approach to human genome sequencing on flow-sorted X chromosomes and then scale the approach to determine the genome sequence of a male Yoruba from Ibadan, Nigeria. We build an accurate consensus sequence from >30x average depth of paired 35-base reads. We characterize four million single-nucleotide polymorphisms and four hundred thousand structural variants, many of which were previously unknown. Our approach is effective for accurate, rapid and economical whole-genome re-sequencing and many other biomedical applications.     

Extrusion Freeforming of Millimeter-Wave Electromagnetic Bandgap (EBG) Photonic Crystals

Extrusion freeforming can be used for the rapid prototyping of millimeter-wave electromagnetic bandgap (EBG) structures. In this work, an alumina-polymer paste with a relatively high volatility solvent (propanol) was used and the characteristics of the ceramic paste, particularly the rheological features are described. The advantage of high volatility solvent is that the viscosity and elastic modulus of the paste are increased sharply as the solvent evaporates. Thus, the rigidity of the extruded filament is quickly increased as a small amount of solvent evaporates. Finally, by employing this procedure, different EBG structures such as 2-D, 3-D woodpile and aperiodic structures were fabricated and their bandgaps were measured. The experimental results show that extrusion freeforming is a relatively simple and easy method to fabricate these woodpile structures with a bandgap in the 90–110 GHz region.     

Mutations in LMF1 cause combined lipase deficiency and severe hypertriglyceridemia

Hypertriglyceridemia is a hallmark of many disorders, including metabolic syndrome, diabetes, atherosclerosis and obesity. A well-known cause is the deficiency of lipoprotein lipase (LPL), a key enzyme in plasma triglyceride hydrolysis. Mice carrying the combined lipase deficiency (cld) mutation show severe hypertriglyceridemia owing to a decrease in the activity of LPL and a related enzyme, hepatic lipase (HL), caused by impaired maturation of nascent LPL and hepatic lipase polypeptides in the endoplasmic reticulum (ER). Here we identify the gene containing the cld mutation as Tmem112 and rename it Lmf1 (Lipase maturation factor 1). Lmf1 encodes a transmembrane protein with an evolutionarily conserved domain of unknown function that localizes to the ER. A human subject homozygous for a deleterious mutation in LMF1 also shows combined lipase deficiency with concomitant hypertriglyceridemia and associated disorders. Thus, through its profound effect on lipase activity, LMF1 emerges as an important candidate gene in hypertriglyceridemia.     

Apple maggot ( Rhagoletis pomonella ) adaptation for cherries in Utah

The apple maggot, Rhagoletis pomonella (Walsh) is reported from Utah County, Utah, where it has adapted to sour cherries. It has been taken repeatedly from pheromone traps in the vicinity of hawthorn ( Crataegus douglassii ), but there are no Utah data that suggest it has adapted to apples.