The CRISPR/Cas bacterial immune system cleaves bacteriophage and plasmid DNA

Bacteria and Archaea have developed several defence strategies against foreign nucleic acids such as viral genomes and plasmids. Among them, clustered regularly interspaced short palindromic repeats (CRISPR) loci together with cas (CRISPR-associated) genes form the CRISPR/Cas immune system, which involves partially palindromic repeats separated by short stretches of DNA called spacers, acquired from extrachromosomal elements. It was recently demonstrated that these variable loci can incorporate spacers from infecting bacteriophages and then provide immunity against subsequent bacteriophage infections in a sequence-specific manner. Here we show that the Streptococcus thermophilus CRISPR1/Cas system can also naturally acquire spacers from a self-replicating plasmid containing an antibiotic-resistance gene, leading to plasmid loss. Acquired spacers that match antibiotic-resistance genes provide a novel means to naturally select bacteria that cannot uptake and disseminate such genes. We also provide in vivo evidence that the CRISPR1/Cas system specifically cleaves plasmid and bacteriophage double-stranded DNA within the proto-spacer, at specific sites. Our data show that the CRISPR/Cas immune system is remarkably adapted to cleave invading DNA rapidly and has the potential for exploitation to generate safer microbial strains.     

Intraseasonal interaction between the Madden-Julian Oscillation and the North Atlantic Oscillation

Bridging the traditional gap between the spatio-temporal scales of weather and climate is a significant challenge facing the atmospheric community. In particular, progress in both medium-range and seasonal-to-interannual climate prediction relies on our understanding of recurrent weather patterns and the identification of specific causes responsible for their favoured occurrence, persistence or transition. Within this framework, I here present evidence that the main climate intra-seasonal oscillation in the tropics-the Madden-Julian Oscillation (MJO)-controls part of the distribution and sequences of the four daily weather regimes defined over the North Atlantic-European region in winter. North Atlantic Oscillation (NAO) regimes are the most affected, allowing for medium-range predictability of their phase far exceeding the limit of around one week that is usually quoted. The tropical-extratropical lagged relationship is asymmetrical. Positive NAO events mostly respond to a mid-latitude low-frequency wave train initiated by the MJO in the western-central tropical Pacific and propagating eastwards. Precursors for negative NAO events are found in the eastern tropical Pacific-western Atlantic, leading to changes along the North Atlantic storm track. Wave-breaking diagnostics tend to support the MJO preconditioning and the role of transient eddies in setting the phase of the NAO. I present a simple statistical model to quantitatively assess the potential predictability of the daily NAO index or the sign of the NAO regimes when they occur. Forecasts are successful in approximately 70 per cent of the cases based on the knowledge of the previous approximately 12-day MJO phase used as a predictor. This promising skill could be of importance considering the tight link between weather regimes and both mean conditions and the chances of extreme events occurring over Europe. These findings are useful for further stressing the need to better simulate and forecast the tropical coupled ocean-atmosphere dynamics, which is a source of medium-to-long range predictability and is the Achilles' heel of the current seamless prediction suites.     

Le Dosage Spectrométrique du Mercure dans l'Air vers 1930

In the 1930s, atomic absorption spectroscopy replaced chemical methods for determining the amount of mercury in atmospheric air. The overall state of chemical analysis was favourable: physical instruments were moving into the chemical laboratory. This new method emerged from work in quantitative physics, and it met a need arising from the risk encountered by those who handled mercury. The new spectrometer, which originally functioned as a detector, also made precise and rapid quantitative determinations possible. This in turn encouraged industrialists to take out patents and make commercial use of the method after various improvements. This method is considered to be the ancestor of modern atomic absorption spectroscopy, which developed independently after 1960. The method developed in the 1930s could only be used for gaseous mercury, and it was not generalized as a method for quantifying other elements. The determination of mercury in air by atomic absorption spectroscopy was the first application of this technique; indeed, it was the only example of a specific use of atomic absorption. It was also part of the instrumental revolution.     

Ultrastructural and quantitative analysis of the lipid droplet clustering induced by hepatitis C virus core protein

Hepatitis C virus (HCV) release is linked to the formation of lipid droplet (LD) clusters in the perinuclear area of infected cells, induced by the core protein. We used electron microscopy (EM) to monitor and compare the number and size of LD in cells producing the mature and immature forms of the HCV core protein, and 3D EM to reconstruct whole cells producing the mature core protein. Only the mature protein coated the LD and induced their clustering and emergence from endoplasmic reticulum membranes enriched in this protein. We found no particular association between LD clusters and the centrosome in reconstructed cells. The LD clustering induced by the mature core protein was associated with an increase in LD synthesis potentially due, at least in part, to the ability of this protein to coat the LD. These observations provide useful information for further studies of the mechanisms involved in HCV-induced steatosis.     

BRAFE600-associated senescence-like cell cycle arrest of human naevi

Most normal mammalian cells have a finite lifespan, thought to constitute a protective mechanism against unlimited proliferation. This phenomenon, called senescence, is driven by telomere attrition, which triggers the induction of tumour suppressors including p16(INK4a) (ref. 5). In cultured cells, senescence can be elicited prematurely by oncogenes; however, whether such oncogene-induced senescence represents a physiological process has long been debated. Human naevi (moles) are benign tumours of melanocytes that frequently harbour oncogenic mutations (predominantly V600E, where valine is substituted for glutamic acid) in BRAF, a protein kinase and downstream effector of Ras. Nonetheless, naevi typically remain in a growth-arrested state for decades and only rarely progress into malignancy (melanoma). This raises the question of whether naevi undergo BRAF(V600E)-induced senescence. Here we show that sustained BRAF(V600E) expression in human melanocytes induces cell cycle arrest, which is accompanied by the induction of both p16(INK4a) and senescence-associated acidic beta-galactosidase (SA-beta-Gal) activity, a commonly used senescence marker. Validating these results in vivo, congenital naevi are invariably positive for SA-beta-Gal, demonstrating the presence of this classical senescence-associated marker in a largely growth-arrested, neoplastic human lesion. In growth-arrested melanocytes, both in vitro and in situ, we observed a marked mosaic induction of p16(INK4a), suggesting that factors other than p16(INK4a) contribute to protection against BRAF(V600E)-driven proliferation. Naevi do not appear to suffer from telomere attrition, arguing in favour of an active oncogene-driven senescence process, rather than a loss of replicative potential. Thus, both in vitro and in vivo, BRAF(V600E)-expressing melanocytes display classical hallmarks of senescence, suggesting that oncogene-induced senescence represents a genuine protective physiological process.     

A high-resolution clay mineralogical record in the northern South China Sea since the Last Glacial Maximum,and its time series provenance analysis

High-resolution clay mineralogical analysis of Core MD05-2904 in the northern South China Sea (SCS) covering the period since the Last Glacial Maximum shows that illite (29%–48%), smectite (14%–45%), chlorite (17%–28%), and minor kaolinite (6%–14%) comprise the clay mineral assemblage, and that time series variation does not present glacial-interglacial cyclicity. Provenance analysis indicates three end-member sources: almost all smectite derives from Luzon, all kaolinite is sourced from the Pearl River, and illite and chlorite originate from both the Pearl River and Taiwan. By comparing clay mineral compositions in surface sediments from the three major source areas and of the SCS, we reconstructed a time series of clay mineral contribution from the major provenances to the northern slope of the SCS using the linear separation method for illite crystallinity. There were three stages of provenance change. (1) During 24.1–17.5 ka BP, contributions from Taiwan and Luzon were similar (30%–40%), while that from the Pearl River was only 25%. (2) During 17.5–14.0 ka BP, the contribution from Luzon decreased rapidly to 20%–25%, while that from Taiwan increased to 35% from an average of 25% at 18 ka BP, and that from the Pearl River increased largely to 40%. (3) During the Holocene, differences in contributions from the three major provenances increased: the contribution from Luzon increased slightly and then remained at 27%–35%, that from Taiwan increased rapidly and then remained at 55%–60%, and that from the Pearl River decreased to 15%. The change in clay mineral contributions from different provenances is influenced mainly by clay mineral production, monsoon rainfall denudation, oceanic current transport, and sea-level change.     

Constrained clustering and Kohonen Self-Organizing Maps

The Self-Organizing Feature Maps (SOFM; Kohonen 1984) algorithm is a well-known example of unsupervised learning in connectionism and is a clustering method closely related to the k-means. Generally the data set is available before running the algorithm and the clustering problem can be approached by an inertia criterion optimization. In this paper we consider the probabilistic approach to this problem. We propose a new algorithm based on the Expectation Maximization principle (EM; Dempster, Laird, and Rubin 1977). The new method can be viewed as a Kohonen type of EM and gives a better insight into the SOFM according to constrained clustering. We perform numerical experiments and compare our results with the standard Kohonen approach.     

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.     

Towards a proteome-scale map of the human protein-protein interaction network

Systematic mapping of protein-protein interactions, or 'interactome' mapping, was initiated in model organisms, starting with defined biological processes and then expanding to the scale of the proteome. Although far from complete, such maps have revealed global topological and dynamic features of interactome networks that relate to known biological properties, suggesting that a human interactome map will provide insight into development and disease mechanisms at a systems level. Here we describe an initial version of a proteome-scale map of human binary protein-protein interactions. Using a stringent, high-throughput yeast two-hybrid system, we tested pairwise interactions among the products of approximately 8,100 currently available Gateway-cloned open reading frames and detected approximately 2,800 interactions. This data set, called CCSB-HI1, has a verification rate of approximately 78% as revealed by an independent co-affinity purification assay, and correlates significantly with other biological attributes. The CCSB-HI1 data set increases by approximately 70% the set of available binary interactions within the tested space and reveals more than 300 new connections to over 100 disease-associated proteins. This work represents an important step towards a systematic and comprehensive human interactome project.