The banana (Musa acuminata) genome and the evolution of monocotyledonous plants

Bananas (Musa spp.), including dessert and cooking types, are giant perennial monocotyledonous herbs of the order Zingiberales, a sister group to the well-studied Poales, which include cereals. Bananas are vital for food security in many tropical and subtropical countries and the most popular fruit in industrialized countries. The Musa domestication process started some 7,000 years ago in Southeast Asia. It involved hybridizations between diverse species and subspecies, fostered by human migrations, and selection of diploid and triploid seedless, parthenocarpic hybrids thereafter widely dispersed by vegetative propagation. Half of the current production relies on somaclones derived from a single triploid genotype (Cavendish). Pests and diseases have gradually become adapted, representing an imminent danger for global banana production. Here we describe the draft sequence of the 523-megabase genome of a Musa acuminata doubled-haploid genotype, providing a crucial stepping-stone for genetic improvement of banana. We detected three rounds of whole-genome duplications in the Musa lineage, independently of those previously described in the Poales lineage and the one we detected in the Arecales lineage. This first monocotyledon high-continuity whole-genome sequence reported outside Poales represents an essential bridge for comparative genome analysis in plants. As such, it clarifies commelinid-monocotyledon phylogenetic relationships, reveals Poaceae-specific features and has led to the discovery of conserved non-coding sequences predating monocotyledon-eudicotyledon divergence.     

The causal structure of natural kinds

One primary goal for metaphysical theories of natural kinds is to account for their epistemic fruitfulness. According to cluster theories of natural kinds, this epistemic fruitfulness is grounded in the regular and stable co-occurrence of a broad set of properties. In this paper, I defend the view that such a cluster theory is insufficient to adequately account for the epistemic fruitfulness of kinds. I argue that cluster theories can indeed account for the projectibility of natural kinds, but not for several other epistemic operations that natural kinds support. Natural kinds also play a role in scientific explanations and categorizations. A theory of natural kinds can only account for these additional kind-based epistemic practices if it also analyzes their causal structure.     

Changing time scale for short-term forecasting in financial markets

A forecasting model based on high-frequency market makers quotes of financial instruments is presented. The statistical behaviour of these time series leads to discussion of the appropriate time scale for forecasting. We introduce variable time scales in a general way and define the new concept of intrinsic time. The latter reflects better the actual trading activity. Changing time scale means forecasting in two steps, first an intrinsic time forecast against physical time, then a price forecast against intrinsic time. The forecasting model consists, for both steps, of a linear combination of non-linear price-based indicators. The indicator weights are continuously re-optimized through a modified linear regression on a moving sample of past prices. The out-of-sample performance of this algorithm is reported on a set of important FX rates and interest rates over many years. It is remarkably consistent. Results for short horizons as well as techniques to measure this performance are discussed.     

A new subtype of bone sarcoma defined by BCOR-CCNB3 gene fusion

The identification of subtype-specific translocations has revolutionized the diagnostics of sarcoma and has provided new insight into oncogenesis. We used RNA-seq to investigate samples from individuals diagnosed with small round cell tumors of bone, possibly Ewing sarcoma, but which lacked the canonical EWSR1-ETS translocation. A new fusion was observed between BCOR (encoding the BCL6 co-repressor) and CCNB3 (encoding the testis-specific cyclin B3) on the X chromosome. RNA-seq results were confirmed by RT-PCR and through cloning of the tumor-specific genomic translocation breakpoints. In total, 24 BCOR-CCNB3-positive tumors were identified among a series of 594 sarcoma cases. Gene profiling experiments indicated that BCOR-CCNB3-positive cases are biologically distinct from other sarcomas, particularly Ewing sarcoma. Finally, we show that CCNB3 immunohistochemistry is a powerful diagnostic marker for this subgroup of sarcoma and that overexpression of BCOR-CCNB3 or of truncated CCNB3 activates S phase in NIH3T3 cells. Thus, the intrachromosomal X-chromosome fusion described here represents a new subtype of bone sarcoma caused by a newly identified gene fusion mechanism.     

Plectasin is a peptide antibiotic with therapeutic potential from a saprophytic fungus

Animals and higher plants express endogenous peptide antibiotics called defensins. These small cysteine-rich peptides are active against bacteria, fungi and viruses. Here we describe plectasin-the first defensin to be isolated from a fungus, the saprophytic ascomycete Pseudoplectania nigrella. Plectasin has primary, secondary and tertiary structures that closely resemble those of defensins found in spiders, scorpions, dragonflies and mussels. Recombinant plectasin was produced at a very high, and commercially viable, yield and purity. In vitro, the recombinant peptide was especially active against Streptococcus pneumoniae, including strains resistant to conventional antibiotics. Plectasin showed extremely low toxicity in mice, and cured them of experimental peritonitis and pneumonia caused by S. pneumoniae as efficaciously as vancomycin and penicillin. These findings identify fungi as a novel source of antimicrobial defensins, and show the therapeutic potential of plectasin. They also suggest that the defensins of insects, molluscs and fungi arose from a common ancestral gene.     

Can we trust Einstein’s accounts of the genesis of special relativity?

There are three kinds of sources available to reconstruct the reflections that led Einstein to special relativity: a few contemporary letters and documents, his impersonal accounts of the genesis of this theory, and recollections of his own path. At first glance, contradictions within and between these sources hamper the reliability of Einstein’s accounts. Yet, a closer analysis reveals much more consistency than foreseen and helps eliminate the dubious, contradictory elements. It then becomes possible to combine the three kinds of sources to produce a minimally speculative and yet fairly coherent account of the genesis of special relativity.     

斯里兰卡的总督列车

卡图那雅克距离斯里兰卡首都科伦坡有几千千米,铁轨一直延伸向天尽头。突然,大地开始颤抖起来,一列蒸汽火车头牵引的红色列车出现在我们面前：这就是路易·蒙巴顿公爵的列车,它像主人的名字一样长。路易·蒙巴顿公爵是大不列颠历史上赫赫有名的英雄之一,他与斯里兰卡的＂姻缘＂要从这列火车说起。