On the origin of the stereoselective affinity of Nutlin-3 geometrical isomers for the MDM2 protein

The stereoselective affinity of small-molecule binding to proteins is typically broadly explained in terms of the thermodynamics of the final bound complex. Using Brownian dynamics simulations, we show that the preferential binding of the MDM2 protein to the geometrical isomers of Nutlin-3, an effective anticancer lead that works by inhibiting the interaction between the proteins p53 and MDM2, can be explained by kinetic arguments related to the formation of the MDM2:Nutlin-3 encounter complex. This is a diffusively bound state that forms prior to the final bound complex. We find that the MDM2 protein stereoselectivity for the Nutlin-3a enantiomer stems largely from the destabilization of the encounter complex of its mirror image enantiomer Nutlin-3b, by the K70 residue that is located away from the binding site. On the other hand, the trans-Nutlin-3a diastereoisomer exhibits a shorter residence time in the vicinity of MDM2 compared with Nutlin-3a due to destabilization of its encounter complex by the collective interaction of pairs of charged residues on either side of the binding site: Glu25 and Lys51 on one side, and Lys94 and Arg97 on the other side. This destabilization is largely due to the electrostatic potential of the trans-Nutlin-3a isomer being largely positive over extended continuous regions around its structure, which are otherwise well-identified into positive and negative regions in the case of the Nutlin-3a isomer. Such rich insight into the binding processes underlying biological selectivity complements the static view derived from the traditional thermodynamic analysis of the final bound complex. This approach, based on an explicit consideration of the dynamics of molecular association, suggests new avenues for kinetics-based anticancer drug development and discovery.     

Patterns of pollen removal and deposition in Polemonium brandegeei (Polemoniaceae): the role of floral visitors,floral design and sexual interference

The arrangement, colour, shape and size of floral parts (collectively floral design) have evolved primarily to promote mating success via animal‐mediated pollen transfer. Although numerous studies have examined variation in pollinator assemblages, relatively few have examined patterns of pollen removal and deposition in the presence of fluctuating pollinators and ineffective floral visitors; therefore, net pollen removal and deposition by entire visitor assemblages are unclear. We studied the timing (diurnal or nocturnal) and effects of floral traits on pollen removal and deposition under a dynamic visitor assemblage of Polemonium brandegeei. We quantified pollen grains remaining in anthers (pollen removal) and deposited on stigmas (pollen deposition) of plants visited during either the day (07:30–20:00 h) or night (20:30–07:30 h) in natural populations over two flowering seasons. Pollen removal and deposition occurred both diurnally and nocturnally during our study. Increased diurnal removal and deposition coincided with peak floral visitations in 2006. This increase in pollen removal and deposition may reflect increased visits by pollen consumers, effective hawkmoth pollinators and increased self‐pollen deposition due to hot, dry weather. Nonlinear effects of style length significantly affected pollen removal, with less pollen remaining in flowers with intermediate style lengths. Pollen deposition was more complex, with herkogamy and anther height affecting deposition. Further, close proximity of stigmas and anthers increased the potential for sexual interference between pollen removal and deposition. Overall, flower visitations and pollen removal and deposition varied between years and populations, but sex organ placement consistently influenced the removal and deposition of pollen.     

Tumor-induced STAT3 activation in monocytic myeloid-derived suppressor cells enhances stemness and mesenchymal properties in human pancreatic cancer

Pancreatic cancer (PC) mobilizes myeloid cells from the bone marrow to the tumor where they promote tumor growth and proliferation. Cancer stem cells (CSCs) are a population of tumor cells that are responsible for tumor initiation. Aldehyde dehydrogenase-1 activity in PC identifies CSCs, and its activity has been correlated with poor overall prognosis in human PC. Myeloid cells have been shown to impact tumor stemness, but the impact of immunosuppressive tumor-infiltrating granulocytic and monocytic myeloid-derived suppressor cells (Mo-MDSC) on ALDH1^Bright CSCs and epithelial to mesenchymal transition is not well understood. In this study, we demonstrate that Mo-MDSC (CD11b⁺/Gr1⁺/Ly6G^?/Ly6C^hi) significantly increase the frequency of ALDH1^Bright CSCs in a mouse model of PC. Additionally, there was significant upregulation of genes associated with epithelial to mesenchymal transition. We also found that human PC converts CD14⁺ peripheral blood monocytes into Mo-MDSC (CD14⁺/HLA-DR^low/?) in vitro, and this transformation is dependent on the activation of the STAT3 pathway. In turn, these Mo-MDSC increase the frequency of ALDH1^Bright CSCs and promote mesenchymal features of tumor cells. Finally, blockade of STAT3 activation reversed the increase in ALDH1^Bright CSCs. These data suggest that the PC tumor microenvironment transforms monocytes to Mo-MDSC by STAT3 activation, and these cells increase the frequency of ALDH1^Bright CSCs. Therefore, targeting STAT3 activation may be an effective therapeutic strategy in targeting CSCs in PC.     

Bactericidal properties of an organic N-chloramine formed in situ

Agent I (3-chloro-4,4-dimethyl-2-oxazolidinone) formed in situ was compared with pre-formed agent I as a disinfectant against Staphylococcus aureus. In situ formation involved combining the non-chlorinated oxazolidinone precursor with calcium hypochlorite to form 5 and 10 mg/l total chlorine concentrations of agent I. The variables included in the study were temperature, pH and concentration. Overall the bacteria were killed more rapidly at 22° than at 4°C. The in situ formation appeared to occur most rapidly at pH 7˙0, slightly slower at pH 9˙5, and very slowly at pH 4˙5 as evidenced by the presence of residual free chlorine. In the in situ experimental runs the 5 and 10 mg/l concentrations were equally effective in obtaining a six log decline in cfu/ml. This study indicates the potential for using the organic N-chloramine as a general purpose disinfectant while omitting the laboratory synthesis of the final product.     

SELECTION ON POLEMONIUM BRANDEGEEI (POLEMONIACEAE) FLOWERS UNDER HUMMINGBIRD POLLINATION: IN OPPOSITION,PARALLEL, OR INDEPENDENT OF SELECTION BY HAWKMOTHS?

Particular floral phenotypes are often associated with specific groups of pollinators. However, flowering plants are often visited, and may be effectively pollinated by more than one type of animal. Therefore, a major outstanding question in floral biology asks: what is the nature of selection on floral traits when pollinators are diverse? This study examined how hummingbirds selected on the floral traits of Polemonium brandegeei, a species pollinated by both hummingbirds and hawkmoths. In array populations of P. brandegeei, we measured pollen movement, and female (seeds set) and male (seeds sired) fitness under hummingbird pollination. We then compared the patterns of selection by hummingbirds with our previous study examining selection by hawkmoths. We documented contrasting selection on sex organ positioning through female function, with hummingbirds selecting for stigmas exserted beyond the anthers and hawkmoths selecting for stigmas recessed below the anthers. Furthermore, hummingbirds selected for longer and wider corolla tubes, and hawkmoths selected for narrower corolla tubes. Therefore, contrasting selection by hawkmoths and hummingbirds may account for variation in sex organ arrangements and corolla dimensions in P. brandegeei. We documented how floral traits under selection by multiple pollinators can result in either an intermediate “compromise” between selective pressures (sex organs) or apparent specialization (corolla tube length) to one pollinator.     

Effect of boundary type and season on predatory arthropods associated with field margins on New Zealand farmland

Pitfall traps were used to monitor predatory arthropod numbers along two types of field boundary, a post and wire fence line and a Cupressus macrocarpa hedge, along the same paddock margin in Canterbury, New Zealand, over 24 months. The seven most abundant predator groups recorded were: Araneae > Phalangiidae > Staphylinidae > Coccinellidae > Chilopoda > Hemerobiidae > Carabidae. Araneae, Phalangiidae, Staphylinidae, Chilopoda and Hemerobiidae were found in larger numbers at the wire fence than at the hedge site, whereas the numbers of Carabidae and Coccinellidae adults exhibited no field margin preference. However, more species of Araneae and Staphylinidae were caught at the hedge site, whereas species richness of carabid beetles was greatest at the wire fence. Principal component analysis clearly separated the samples collected from the two habitats based on the assemblages of Araneae, Staphylinidae and Carabidae, and certain species in each of these taxonomic groups appeared to be particularly associated with one boundary type or the other. All the main taxonomic groups exhibited clear seasonal patterns, with distinct peaks in abundance occurring at certain times of the year. The results of the study reinforce the idea that management of field boundaries can be used to manipulate the type and abundance of particular groups of predatory arthropods, and that seasonal patterns should be taken into account in schemes of integrated pest management so that any adverse effects of biocide application on these beneficial species may be minimised.     

Natural Variation for Nutrient Use and Remobilization Efficiencies in Switchgrass

Nutrient management in biomass production systems serves to maximize yield and minimize production costs and environmental impact. Loss of soil nutrients with harvested biomass can be reduced by the judicious choice of genotype and harvest time. Sustainable production of switchgrass for biofuel will depend, in part, on breeding of varieties that are conservative in their use of soil nutrients to produce biomass. To aid such breeding programs, we assessed the natural variation in nutrient-use and remobilization efficiencies of 31 accessions of Panicum virgatum by measuring the concentration of 20 elements (N, P, K, Li, B, Na, Mg, Ca, Mn, Fe, Co, Ni, Cu, Zn, As, Se, Rb, Sr, Mo, and Cd) in shoots of field-grown plants harvested at two different stages of development. Significant differences between accessions were found for elemental composition at maturity and after senescence. The concentration of several elements (N, P, K, and Rb) decreased in the shoots of all accessions during senescence, although the efficiency of remobilization ranged from 20% to 61% for N, 31% to 65% for P, 25% for 84% for K, and 33% to 84% for Rb. The accessions/cultivars with the greatest nutrient-use efficiency (smallest loss of nutrient per unit biomass) were BN-14668-65, Kanlow, Caddo from the point of view of N content, and Kanlow, Cave-in-Rock, and Blackwell from the point of view of P content in senescent shoots. Finally, differences in elemental composition between upland and lowland ecotypes were also found. The information presented here will help to guide future breeding programs and nutrient management practices.     

Isolation of two populations of sperm cells and microelectrophoresis of pairs of sperm cells from pollen tubes of tobacco (Nicotiana tabacum)

Prior research has indicated that the two sperm cells of Nicotiana tabacum are dimorphic, suggesting that they may participate in preferential fertilization during in vivo fusion with the egg and central cells. To probe the mechanism of potential preferential fertilization in this plant, it will be necessary to use modern sensitive molecular techniques. For this purpose, two individual populations of two sperm cells, constituting the Svn (associated with the vegetative nucleus) and Sua (unassociated with the vegetative nucleus), were isolated in the thousands from tobacco pollen tubes with a micromanipulator as a preliminary step toward research on gametic recognition using molecular techniques. Microelectrophoresis of paired sperm cells from a single pollen tube was conducted at different developmental stages. Sperm cells isolated from 1-, 2-, 3- and 4-cm stylar lengths migrated to the negative pole, with the Sua displaying significantly greater electrophoretic mobility than the Svn, reflecting a more positively charged cell surface on the Sua. The sperm cells isolated from 1-cm style are very sensitive to electron potential in an electrophoretic field, presumably reflecting that they are still in a young state. Differences in cell surface charge between the Sua and Svn may be related with cell fate during fertilization. Supported by National Natural Science Foundation of CHINA (30170060)     

Rats in the genomic era.

The rat genome project and the resources that it has generated are transforming the translation of rat biology to human medicine. The rat genome was sequenced to a high quality "draft," the structure and location of the genes were predicted, and a global assessment was published (Gibbs RA et al., Nature 428: 493-521, 2004). Since that time, researchers have made use of the genome sequence and annotations and related resources. We take this opportunity to review the currently available rat genome resources and to discuss the progress and future plans for the rat genome.