Molecular basis of xeroderma pigmentosum group C DNA recognition by engineered meganucleases

Xeroderma pigmentosum is a monogenic disease characterized by hypersensitivity to ultraviolet light. The cells of xeroderma pigmentosum patients are defective in nucleotide excision repair, limiting their capacity to eliminate ultraviolet-induced DNA damage, and resulting in a strong predisposition to develop skin cancers. The use of rare cutting DNA endonucleases-such as homing endonucleases, also known as meganucleases-constitutes one possible strategy for repairing DNA lesions. Homing endonucleases have emerged as highly specific molecular scalpels that recognize and cleave DNA sites, promoting efficient homologous gene targeting through double-strand-break-induced homologous recombination. Here we describe two engineered heterodimeric derivatives of the homing endonuclease I-CreI, produced by a semi-rational approach. These two molecules-Amel3-Amel4 and Ini3-Ini4-cleave DNA from the human XPC gene (xeroderma pigmentosum group C), in vitro and in vivo. Crystal structures of the I-CreI variants complexed with intact and cleaved XPC target DNA suggest that the mechanism of DNA recognition and cleavage by the engineered homing endonucleases is similar to that of the wild-type I-CreI. Furthermore, these derivatives induced high levels of specific gene targeting in mammalian cells while displaying no obvious genotoxicity. Thus, homing endonucleases can be designed to recognize and cleave the DNA sequences of specific genes, opening up new possibilities for genome engineering and gene therapy in xeroderma pigmentosum patients whose illness can be treated ex vivo.     

The genome of Theobroma cacao

We sequenced and assembled the draft genome of Theobroma cacao, an economically important tropical-fruit tree crop that is the source of chocolate. This assembly corresponds to 76% of the estimated genome size and contains almost all previously described genes, with 82% of these genes anchored on the 10 T. cacao chromosomes. Analysis of this sequence information highlighted specific expansion of some gene families during evolution, for example, flavonoid-related genes. It also provides a major source of candidate genes for T. cacao improvement. Based on the inferred paleohistory of the T. cacao genome, we propose an evolutionary scenario whereby the ten T. cacao chromosomes were shaped from an ancestor through eleven chromosome fusions.     

Inclusive fitness theory and eusociality

Arising from M. A. Nowak, C. E. Tarnita & E. O. Wilson 466, 1057-1062 (2010); Nowak et al. reply. Nowak et al. argue that inclusive fitness theory has been of little value in explaining the natural world, and that it has led to negligible progress in explaining the evolution of eusociality. However, we believe that their arguments are based upon a misunderstanding of evolutionary theory and a misrepresentation of the empirical literature. We will focus our comments on three general issues.     

DNA、字与模型：异常字统计学

大约在15年的时间里，生物学经历了巨大的变化。而这些变化中最重要的变化是DNA序列。计算生物学中一个重要的问题是鉴别短的DNA序列（它在数学上称为字），而这些短序列都具有生物学功能。一种鉴别方法就是决定一个特定的字是否纯粹是随机的，还是由于它出现的频率或所在的位置而具有统计学意义的。     

Glial versus melanocyte cell fate choice: Schwann cell precursors as a cellular origin of melanocytes

Melanocytes and Schwann cells are derived from the multipotent population of neural crest cells. Although both cell types were thought to be generated through completely distinct pathways and molecular processes, a recent study has revealed that these different cell types are intimately interconnected far beyond previously postulated limits in that they share a common post-neural crest progenitor, i.e. the Schwann cell precursor. This finding raises interesting questions about the lineage relationships of hitherto unrelated cell types such as melanocytes and Schwann cells, and may provide clinical insights into mechanisms of pigmentation disorders and for cancer involving Schwann cells and melanocytes.     

Early geochemical environment of Mars as determined from thermodynamics of phyllosilicates

Images of geomorphological features that seem to have been produced by the action of liquid water have been considered evidence for wet surface conditions on early Mars. Moreover, the recent identification of large deposits of phyllosilicates, associated with the ancient Noachian terrains suggests long-timescale weathering of the primary basaltic crust by liquid water. It has been proposed that a greenhouse effect resulting from a carbon-dioxide-rich atmosphere sustained the temperate climate required to maintain liquid water on the martian surface during the Noachian. The apparent absence of carbonates and the low escape rates of carbon dioxide, however, are indicative of an early martian atmosphere with low levels of carbon dioxide. Here we investigate the geochemical conditions prevailing on the surface of Mars during the Noachian period using calculations of the aqueous equilibria of phyllosilicates. Our results show that Fe3+-rich phyllosilicates probably precipitated under weakly acidic to alkaline pH, an environment different from that of the following period, which was dominated by strongly acid weathering that led to the sulphate deposits identified on Mars. Thermodynamic calculations demonstrate that the oxidation state of the martian surface was already high, supporting early escape of hydrogen. Finally, equilibrium with carbonates implies that phyllosilicate precipitation occurs preferentially at a very low partial pressure of carbon dioxide. We suggest that the possible absence of Noachian carbonates more probably resulted from low levels of atmospheric carbon dioxide, rather than primary acidic conditions. Other greenhouse gases may therefore have played a part in sustaining a warm and wet climate on the early Mars.     

Carbon dioxide release from the North Pacific abyss during the last deglaciation

Atmospheric carbon dioxide concentrations were significantly lower during glacial periods than during intervening interglacial periods, but the mechanisms responsible for this difference remain uncertain. Many recent explanations call on greater carbon storage in a poorly ventilated deep ocean during glacial periods, but direct evidence regarding the ventilation and respired carbon content of the glacial deep ocean is sparse and often equivocal. Here we present sedimentary geochemical records from sites spanning the deep subarctic Pacific that--together with previously published results--show that a poorly ventilated water mass containing a high concentration of respired carbon dioxide occupied the North Pacific abyss during the Last Glacial Maximum. Despite an inferred increase in deep Southern Ocean ventilation during the first step of the deglaciation (18,000-15,000 years ago), we find no evidence for improved ventilation in the abyssal subarctic Pacific until a rapid transition approximately 14,600 years ago: this change was accompanied by an acceleration of export production from the surface waters above but only a small increase in atmospheric carbon dioxide concentration. We speculate that these changes were mechanistically linked to a roughly coeval increase in deep water formation in the North Atlantic, which flushed respired carbon dioxide from northern abyssal waters, but also increased the supply of nutrients to the upper ocean, leading to greater carbon dioxide sequestration at mid-depths and stalling the rise of atmospheric carbon dioxide concentrations. Our findings are qualitatively consistent with hypotheses invoking a deglacial flushing of respired carbon dioxide from an isolated, deep ocean reservoir, but suggest that the reservoir may have been released in stages, as vigorous deep water ventilation switched between North Atlantic and Southern Ocean source regions.