Sequencing of Aspergillus nidulans and comparative analysis with A. fumigatus and A. oryzae

The aspergilli comprise a diverse group of filamentous fungi spanning over 200 million years of evolution. Here we report the genome sequence of the model organism Aspergillus nidulans, and a comparative study with Aspergillus fumigatus, a serious human pathogen, and Aspergillus oryzae, used in the production of sake, miso and soy sauce. Our analysis of genome structure provided a quantitative evaluation of forces driving long-term eukaryotic genome evolution. It also led to an experimentally validated model of mating-type locus evolution, suggesting the potential for sexual reproduction in A. fumigatus and A. oryzae. Our analysis of sequence conservation revealed over 5,000 non-coding regions actively conserved across all three species. Within these regions, we identified potential functional elements including a previously uncharacterized TPP riboswitch and motifs suggesting regulation in filamentous fungi by Puf family genes. We further obtained comparative and experimental evidence indicating widespread translational regulation by upstream open reading frames. These results enhance our understanding of these widely studied fungi as well as provide new insight into eukaryotic genome evolution and gene regulation.     

The Collapse of Supertasks

A supertask consists in the performance of an infinite number of actions in a finite time. I show that any attempt to carry out a supertask will produce a divergence of the curvature of spacetime, resulting in the formation of a black hole. I maintain that supertaks, contrarily to a popular view among philosophers, are physically impossible. Supertasks, literally, collapse under their own weight.     

Prediction of central nervous system embryonal tumour outcome based on gene expression.

Embryonal tumours of the central nervous system (CNS) represent a heterogeneous group of tumours about which little is known biologically, and whose diagnosis, on the basis of morphologic appearance alone, is controversial. Medulloblastomas, for example, are the most common malignant brain tumour of childhood, but their pathogenesis is unknown, their relationship to other embryonal CNS tumours is debated, and patients' response to therapy is difficult to predict. We approached these problems by developing a classification system based on DNA microarray gene expression data derived from 99 patient samples. Here we demonstrate that medulloblastomas are molecularly distinct from other brain tumours including primitive neuroectodermal tumours (PNETs), atypical teratoid/rhabdoid tumours (AT/RTs) and malignant gliomas. Previously unrecognized evidence supporting the derivation of medulloblastomas from cerebellar granule cells through activation of the Sonic Hedgehog (SHH) pathway was also revealed. We show further that the clinical outcome of children with medulloblastomas is highly predictable on the basis of the gene expression profiles of their tumours at diagnosis.     

What does the tail of the distribution of current stock prices tell us about future economic activity?

This paper proposes three leading indicators of economic conditions estimated using current stock returns. The assumption underlying our approach is that current asset prices reflect all the available information about future states of economy. Each of the proposed indicators is related to the tail of the cross‐sectional distribution of stock returns. The results show that the leading indicators have strong correlation with future economic conditions and usually make better out‐of‐sample predictions than two traditional competitors (random walk and the average of previous observations). Furthermore, quantile regressions reveal that the leading indicators have strong connections with low future economic activity.     

Supernova--remnant origin of cosmic rays?

It is thought that Galactic cosmic-ray nuclei are gradually accelerated to high energies (up to about 300 TeV per nucleon, where 1 TeV is 10(12) eV) in the expanding shock waves connected with the remnants of powerful supernova explosions. However, this conjecture has eluded direct observational confirmation since it was first proposed in 1953 (ref. 3). Enomoto et al. claim to have finally found definitive evidence that corroborates this model, proposing that very-high-energy, TeV-range, gamma-rays from the supernova remnant (SNR) RX J1713.7-3946 are due to the interactions of energetic nuclei in this region. Here we argue that their claim is not supported by the existing multiwavelength spectrum of this source. The search for the origin(s) of Galactic cosmic-ray nuclei may be closing in on the long-suspected supernova-remnant sources, but it is not yet over.