Cyanophages infecting the oceanic cyanobacterium Prochlorococcus

Prochlorococcus is the numerically dominant phototroph in the tropical and subtropical oceans, accounting for half of the photosynthetic biomass in some areas. Here we report the isolation of cyanophages that infect Prochlorococcus, and show that although some are host-strain-specific, others cross-infect with closely related marine Synechococcus as well as between high-light- and low-light-adapted Prochlorococcus isolates, suggesting a mechanism for horizontal gene transfer. High-light-adapted Prochlorococcus hosts yielded Podoviridae exclusively, which were extremely host-specific, whereas low-light-adapted Prochlorococcus and all strains of Synechococcus yielded primarily Myoviridae, which has a broad host range. Finally, both Prochlorococcus and Synechococcus strain-specific cyanophage titres were low (< 10(3) ml(-1)) in stratified oligotrophic waters even where total cyanobacterial abundances were high (> 10(5) cells x ml(-1)). These low titres in areas of high total host cell abundance seem to be a feature of open ocean ecosystems. We hypothesize that gradients in cyanobacterial population diversity, growth rates, and/or the incidence of lysogeny underlie these trends.     

Genome analysis of the platypus reveals unique signatures of evolution

We present a draft genome sequence of the platypus, Ornithorhynchus anatinus. This monotreme exhibits a fascinating combination of reptilian and mammalian characters. For example, platypuses have a coat of fur adapted to an aquatic lifestyle; platypus females lactate, yet lay eggs; and males are equipped with venom similar to that of reptiles. Analysis of the first monotreme genome aligned these features with genetic innovations. We find that reptile and platypus venom proteins have been co-opted independently from the same gene families; milk protein genes are conserved despite platypuses laying eggs; and immune gene family expansions are directly related to platypus biology. Expansions of protein, non-protein-coding RNA and microRNA families, as well as repeat elements, are identified. Sequencing of this genome now provides a valuable resource for deep mammalian comparative analyses, as well as for monotreme biology and conservation.     

The effect of millennial-scale changes in Arabian Sea denitrification on atmospheric CO2.

Most global biogeochemical processes are known to respond to climate change, some of which have the capacity to produce feedbacks through the regulation of atmospheric greenhouse gases. Marine denitrification-the reduction of nitrate to gaseous nitrogen-is an important process in this regard, affecting greenhouse gas concentrations directly through the incidental production of nitrous oxide, and indirectly through modification of the marine nitrogen inventory and hence the biological pump for CO2. Although denitrification has been shown to vary with glacial-interglacial cycles, its response to more rapid climate change has not yet been well characterized. Here we present nitrogen isotope ratio, nitrogen content and chlorin abundance data from sediment cores with high accumulation rates on the Oman continental margin that reveal substantial millennial-scale variability in Arabian Sea denitrification and productivity during the last glacial period. The detailed correspondence of these changes with Dansgaard-Oeschger events recorded in Greenland ice cores indicates rapid, century-scale reorganization of the Arabian Sea ecosystem in response to climate excursions, mediated through the intensity of summer monsoonal upwelling. Considering the several-thousand-year residence time of fixed nitrogen in the ocean, the response of global marine productivity to changes in denitrification would have occurred at lower frequency and appears to be related to climatic and atmospheric CO2 oscillations observed in Antarctic ice cores between 20 and 60 kyr ago.     

一种曲面网格优化的通用算法

提出了一种曲面网格优化的通用算法,该算法基于一些预先定义的优化准则,将给定的网格曲面优化成为单位网格曲面,定义了两种指导优化过程的优化标准。在优化过程中采用了三种优化算子（边分裂、边消除、边替换）,是一个简单的曲面网格优化的通用算法。     

Plant community patterns in unburned and burned blackbrush ( Coleogne ramosissima Torr.) shrublands in the Mojave Desert

The blackbrush vegetation type is dominated by Coleogyne ramossisima , which is thought to preclude the coexistence of many other plant species. Fire can remove blackbrush cover and possibly increase plant species richness and evenness. Fire also may increase the frequency and cover of alien annual grasses, thereby intensifying landscape flammability. We tested these predictions in unburned and burned (6-14 years postfire) blackbrush at 3 sites spanning the range of this vegetation type in the Mojave Desert. Species richness in unburned blackbrush was similar to published values for vegetation types in western North America, bur richness varied significantly among the 3 sites and 4 spatial scales (1, 10, 100, and 1000 m 2 ). Richness values declined in order from annual forbs, woody perennials, herbaceous perennials, annual grasses, cacti, to perennial grasses. Fire reduced Coleogyne cover, thus boosting species evenness. In contrast, species richness decreased after burning, although the results varied among spatial scales. Total cover was unaffected by fire because cover of wood perennials decreased, while cover of annual forbs, annual grasses, herbaceous perennials, and perennial grasses increased. Native species richness and cover decreased, whereas alien richness and cover increased after burning especially where the alien forb Erodium cicutarium was present. Fire had no effect on frequency and variable effects on cover of alien annual grasses. These results indicate that in blackbrush species richness can vary among sites and local spatial scales, and effects of fires can vary among plant life-forms and between natives and aliens.     

Aspects of Sacramento pikeminnow biology in nearshore habitats of the Sacramento-San Joaquin Delta, California

We documented distribution, relative abundance, diet composition, and body condition of Sacramento pikeminnow Ptychocheilus grandis during 2001 and 2003 at 5 sites in the Sacramento-San Joaquin Delta, California. Sacramento pikeminnow densities in nearshore habitats were higher in 2003 than 2001. In both years, spatial distribution of beach seine densities was similar. There were no significant differences in density among sampling sites except for the southernmost site where the catch was near zero. Based on rotary screw-trap data from a 6th site, we found relative abundance of Sacramento pikeminnow entering the Delta via an artificial floodplain was positively correlated with flow. Most individuals collected using all 3 gear types were age 1 or older, and appeared to grow quickly based on data from previous studies. Sacramento pikeminnow had diverse diets composed of freshwater and estuarine invertebrate and fish taxa. Incidence of piscivory was only 2% of the diet of individuals P. oregonensis , but in seeming contrast to endangered Colorado pikeminnow P. lucius , the present study showed that Sacramento pikeminnow can be successful in altered habitats. Sacramento pikeminnow; Ptychocheilus grandis; Sacramento-San Joaquin Delta; habitat use; diet composition; condition factor; Cyprinidae.     

Engineering microbes for targeted strikes against human pathogens

Lack of pathogen specificity in antimicrobial therapy causes non-discriminant microbial cell killing that disrupts the microflora present. As a result, potentially helpful microbial cells are killed along with the pathogen, altering the biodiversity and dynamic interactions within the population. Moreover, the unwarranted exposure of antibiotics to microbes increases the likelihood of developing resistance and perpetuates the emergence of multidrug resistance. Synthetic biology offers an alternative solution where specificity can be conferred to reduce the non-specific, non-targeted activity of currently available antibiotics, and instead provides targeted therapy against specific pathogens and minimising collateral damage to the host’s inherent microbiota. With a greater understanding of the microbiome and the available genetic engineering tools for microbial cells, it is possible to devise antimicrobial strategies for novel antimicrobial therapy that are able to precisely and selectively remove infectious pathogens. Herein, we review the strategies developed by unlocking some of the natural mechanisms used by the microbes and how these may be utilised in targeted antimicrobial therapy, with the promise of reducing the current global bane of multidrug antimicrobial resistance.