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.     

Towards sustainability in world fisheries

Fisheries have rarely been 'sustainable'. Rather, fishing has induced serial depletions, long masked by improved technology, geographic expansion and exploitation of previously spurned species lower in the food web. With global catches declining since the late 1980s, continuation of present trends will lead to supply shortfall, for which aquaculture cannot be expected to compensate, and may well exacerbate. Reducing fishing capacity to appropriate levels will require strong reductions of subsidies. Zoning the oceans into unfished marine reserves and areas with limited levels of fishing effort would allow sustainable fisheries, based on resources embedded in functional, diverse ecosystems.     

Measures of effectiveness in medical research: Reporting both absolute and relative measures

Biomedical research, especially pharmaceutical research, has been criticised for engaging in practices that lead to over-estimations of the effectiveness of medical treatments. A central issue concerns the reporting of absolute and relative measures of medical effectiveness. In this paper we critically examine proposals made by Jacob Stegenga to (a) give priority to the reporting of absolute measures over relative measures, and (b) downgrade the measures of effectiveness (effect sizes) of the treatments tested in clinical trials (Stegenga, 2015a). After exposing significant flaws in a central case study used by Stegenga to bolster his first proposal (a), we go on to argue that neither of these proposals is defensible (a or b). We defend the practice, in line with the New England Journal of Medicine, of reporting both absolute and relative measures whenever feasible.     

Fourier analysis of vertebral shape change due to growth and selection for large and small body size

Summary Fourier analysis of videodigitised outlines of mouse vertebrae from two stocks, a pseudo-longitudinal series of mice aged 25–60 days and one selected for large or small body size over many generations shows that the shape changes due to normal growth are not similar to those produced by selection for body size.     

Magnetic resonance microscopy: in vivo sectioning of a developing insect

Summary The utility of magnetic resonance imaging vis-a-vis insect morphology and development was investigated. MRI is a noninvasive technique that distinguishes between tissues based on proton content and proton environment. At present a resolution of 100 m is achievable. The technique avoids fixation artifacts and allows the detection of motion within the organism.     

Light is a dominant mouse mutation resulting in premature cell death.

Light is a dominant mutant allele of the mouse brown locus which results in hairs pigmented only at their tips. The phenotype is due to premature melanocyte death. We have sequenced the tyrosinase-related protein-1 cDNA encoded at this locus from Light mice and found that it contains a single base alteration from wild-type, causing an Arg to Cys change in the protein. To further elucidate the mutant phenotype, we studied the expression of melanocyte specific genes in the skin of Light mice. We have demonstrated premature melanocyte death, but only in pigmented mice, indicating that the cell death is mediated through the inherent cytotoxicity of pigment production.     

Amyloid and the origin of life: self-replicating catalytic amyloids as prebiotic informational and protometabolic entities

A crucial stage in the origin of life was the emergence of the first molecular entity that was able to replicate, transmit information, and evolve on the early Earth. The amyloid world hypothesis posits that in the pre-RNA era, information processing was based on catalytic amyloids. The self-assembly of short peptides into β-sheet amyloid conformers leads to extraordinary structural stability and novel multifunctionality that cannot be achieved by the corresponding nonaggregated peptides. The new functions include self-replication, catalytic activities, and information transfer. The environmentally sensitive template-assisted replication cycles generate a variety of amyloid polymorphs on which evolutive forces can act, and the fibrillar assemblies can serve as scaffolds for the amyloids themselves and for ribonucleotides proteins and lipids. The role of amyloid in the putative transition process from an amyloid world to an amyloid–RNA–protein world is not limited to scaffolding and protection: the interactions between amyloid, RNA, and protein are both complex and cooperative, and the amyloid assemblages can function as protometabolic entities catalyzing the formation of simple metabolite precursors. The emergence of a pristine amyloid-based in-put sensitive, chiroselective, and error correcting information-processing system, and the evolvement of mutualistic networks were, arguably, of essential importance in the dynamic processes that led to increased complexity, organization, compartmentalization, and, eventually, the origin of life.