Small interfering RNA screens reveal enhanced cisplatin cytotoxicity in tumor cells having both BRCA network and TP53 disruptions

RNA interference technology allows the systematic genetic analysis of the molecular alterations in cancer cells and how these alterations affect response to therapies. Here we used small interfering RNA (siRNA) screens to identify genes that enhance the cytotoxicity (enhancers) of established anticancer chemotherapeutics. Hits identified in drug enhancer screens of cisplatin, gemcitabine, and paclitaxel were largely unique to the drug being tested and could be linked to the drug's mechanism of action. Hits identified by screening of a genome-scale siRNA library for cisplatin enhancers in TP53-deficient HeLa cells were significantly enriched for genes with annotated functions in DNA damage repair as well as poorly characterized genes likely having novel functions in this process. We followed up on a subset of the hits from the cisplatin enhancer screen and validated a number of enhancers whose products interact with BRCA1 and/or BRCA2. TP53(+/-) matched-pair cell lines were used to determine if knockdown of BRCA1, BRCA2, or validated hits that associate with BRCA1 and BRCA2 selectively enhances cisplatin cytotoxicity in TP53-deficient cells. Silencing of BRCA1, BRCA2, or BRCA1/2-associated genes enhanced cisplatin cytotoxicity approximately 4- to 7-fold more in TP53-deficient cells than in matched TP53 wild-type cells. Thus, tumor cells having disruptions in BRCA1/2 network genes and TP53 together are more sensitive to cisplatin than cells with either disruption alone.     

Enhanced isoprene-related tolerance of heat- and light-stressed photosynthesis at low, but not high, CO2 concentrations

The principal function of isoprene biosynthesis in plants remains unclear, but emission rates are positively correlated with temperature and light, supporting a role for isoprene in maintaining photosynthesis under transient heat and light stress from sunflecks. Isoprene production is also inversely correlated with CO(2) concentrations, implying that rising CO(2) may reduce the functional importance of isoprene. To understand the importance of isoprene in maintaining photosynthesis during sunflecks, we used RNAi technology to suppress isoprene production in poplar seedlings and compared the responses of these transgenic plants to wild-type and empty-vector control plants. We grew isoprene-emitting and non-emitting trees at low (190 ppm) and high (590 ppm) CO(2) concentrations and compared their photosynthetic responses to short, transient periods of high light and temperature, as well as their photosynthetic thermal response at constant light. While there was little difference between emitting and non-emitting plants in their photosynthetic responses to simulated sunflecks at high CO(2), isoprene-emitting trees grown at low CO(2) had significantly greater photosynthetic sunfleck tolerance than non-emitting plants. Net photosynthesis at 42°C was 50% lower in non-emitters than in isoprene-emitting trees at low CO(2), but only 22% lower at high CO(2). Dark respiration rates were significantly higher in non-emitting poplar from low CO(2), but there was no difference between isoprene-emitting and non-emitting lines at high CO(2). We propose that isoprene biosynthesis may have evolved at low CO(2) concentrations, where its physiological effect is greatest, and that rising CO(2) will reduce the functional benefit of isoprene in the near future.     

Stream detritus dynamics: Regulation by invertebrate consumers

Summary Insecticide treatment of a small, Appalachian forest stream caused massive downstream insect drift and reduced aquatic insect densities to <10% of an adjacent untreated reference stream. Reduction in breakdown rates of leaf detritus was accompanied by differences in quantity and composition of benthic organic matter between the two streams. Following treatment, transport of particulate organic matter was significantly lower in the treated stream than in the reference stream whereas no significant differences existed prior to treatment. Our results indicate that macroinvertebrate consumers, primarily insects, are important in regulating rates of detritus processing and availability to downstream communities.     

A survey of the year 2006 literature on applications of isothermal titration calorimetry

Isothermal titration calorimetry (ITC) is a fast and robust method to determine the energetics of association reactions in solution. The changes in enthalpy, entropy and heat capacity that accompany binding provide unique insights into the balance of forces driving association of molecular entities. ITC is used nowadays on a day-to-day basis in hundreds of laboratories. The method aids projects both in basic and practice-oriented research ranging from medicine and biochemistry to physical chemistry and material sciences. Not surprisingly, the range of studies utilizing ITC data is steadily expanding. In this review, we discuss selected results and ideas that have accumulated in the course of the year 2006, the focus being on biologically relevant systems. Theoretical developments, novel applications and studies that provide a deeper level of understanding of the energetic principles of biological function are primarily considered. Following the appearance of a new generation of titration calorimeters, recent papers provide instructive examples of the synergy between energetic and structural approaches in biomedical and biotechnological research.     

Ecology of cryptic coral reef communities. III. Abundance and aggregation of encrusting organisms with particular reference to cheilostome bryozoa

The distribution and abundance of encrusting cheilostome bryozoans under foliaceous reef corals was studied at two depths at Rio Bueno, Jamaica. 46 species of cheilostomes were found, but most of these are rare. Only three species occupy, on average, > 5 % of the space available, and each of these is distributed differently. Steginoporella sp. nov. is most abundant at ? 10 m depth where it occasionally overgrows the entire edge zone (marginal 5 cm) of individual corals. Stylopoma spongites (Pallas) is most abundant at ? 21 m where it may also dominate coral edges. Abundance of both these species drops off sharply with distance from coral edges. The third species, Reptadeonella “plagiopora”, is more abundant at ? 10 m than ?21 m depth, but shows no significant variation in cover away from coral edges.Distributions of major groups of encrusting organisms and cheilostome species under corals are predictable enough for definition of spatially distinct assemblages by discriminant function analysis. Particularly distinct is the edge-zone community at ? 10 m where cheilostomes predominate. Nevertheless, variances in organism abundances are extremely high, especially for Steginoporella sp. nov. and Stylopoma spongites the great abundance of which results from relatively few, larger-than-average size colonies, rather than many smaller colonies. Edge-zone communities from replicate m² quadrats at the same depth were significantly different. The same was true within individual quadrats. Transects only 10 to 20 cm apart routinely differed as much as those 50 to 100 m apart. Edge-zone communities also varied significantly with coral size.Increase of Steginoporella sp. nov. and Stylopoma spongites abundance with increasing coral size and age suggests that larval recruitment and juvenile survival by these species is extremely slow and patchy. But once they have reached some critical size, colonies of these species may persist indefinitely by continued clonal growth onto newly grown coral undersurface as it becomes available. Communities under individual corals may develop largely independently, influenced by their unique histories (priority effects) and interactions between their particular inhabitants.     

Effects of Frequent Mowing on Survival and Persistence of Forbs Seeded into a Species-Poor Grassland

Many early attempts at tallgrass prairie reconstruction failed to achieve the high species diversity of remnant prairies, and instead consist primarily of C₄ grasses. We hypothesized that frequent mowing of established prairie grasses could create sufficient gaps in the aboveground and belowground environment to allow for the establishment of native forbs from seed. We studied forb seedling establishment in a 25‐year‐old prairie planting in northern Iowa that was dominated by native warm‐season grasses. In winter 1999, 23 species of native forbs were broadcast into the recently burned sod at a rate of 350 viable seeds/m². Treatment plots were mowed weekly for either one or two growing seasons, and control plots were unmowed. Mowed plots had greater light availability than controls, especially when warm‐season grasses began to flower. Overwinter seedling mortality was 3% in mowed treatments compared to 29% in the controls. Forbs in mowed plots had significantly greater root and shoot mass than those in control plots in the first and second growing seasons but were not significantly more abundant. By the fourth growing season, however, forbs were twice as abundant in the mowed treatments. No lasting negative impacts of frequent mowing on the grass population were observed. Mowing a second year influenced species composition but did not change total seedling establishment. Experimental evidence is consistent with the idea that mowing reduced competition for light from large established grasses, allowing forb seedlings the opportunity to reach sufficient size to establish, survive, and flower in the second and subsequent years.     

Phylogenetic analysis of the pPT23A plasmid family of Pseudomonas syringae

The pPT23A plasmid family of Pseudomonas syringae contains members that contribute to the ecological and pathogenic fitness of their P. syringae hosts. In an effort to understand the evolution of these plasmids and their hosts, we undertook a comparative analysis of the phylogeny of plasmid genes and that of conserved chromosomal genes from P. syringae. In total, comparative sequence and phylogenetic analyses were done utilizing 47 pPT23A family plasmids (PFPs) from 16 pathovars belonging to six genomospecies. Our results showed that the plasmid replication gene (repA), the only gene currently known to be distributed among all the PFPs, had a phylogeny that was distinct from that of the P. syringae hosts of these plasmids and from those of other individual genes on PFPs. The phylogenies of two housekeeping chromosomal genes, those for DNA gyrase B subunit (gyrB) and primary sigma factor (rpoD), however, were strongly associated with genomospecies of P. syringae. Based on the results from this study, we conclude that the pPT23A plasmid family represents a dynamic genome that is mobile among P. syringae pathovars.