Continuous-time modeling of cell fate determination in Arabidopsis flowers

Background  

The genetic control of floral organ specification is currently being investigated by various approaches, both experimentally and through modeling. Models and simulations have mostly involved boolean or related methods, and so far a quantitative, continuous-time approach has not been explored.     

Synthetic shuffling expands functional protein diversity by allowing amino acids to recombine independently

We describe synthetic shuffling, an evolutionary protein engineering technology in which every amino acid from a set of parents is allowed to recombine independently of every other amino acid. With the use of degenerate oligonucleotides, synthetic shuffling provides a direct route from database sequence information to functional libraries. Physical starting genes are unnecessary, and additional design criteria such as optimal codon usage or known beneficial mutations can also be incorporated. We performed synthetic shuffling of 15 subtilisin genes and obtained active and highly chimeric enzymes with desirable combinations of properties that we did not obtain by other directed-evolution methods.     

Modification of Vegetative Phenology in a Tropical Semi‐deciduous Forest by Abnormal Drought and Rain1

The control of vegetative phenology in tropical trees is not well understood. In dry forest trees, leaf abscission may be enhanced by advanced leaf age, increasing water stress, or declining photoperiod. Normally, it is impossible to dissect the effects of each of these variables because most leaves are shed during the early dry season when day length is near its minimum and leaves are relatively old. The 1997 El‐Niño Southern Oscillation caused a ten‐week long, severe abnormal drought from June to August in the semi‐deciduous forests of Guanacaste, Costa Rica. We monitored the effect of this drought on phenology and water status of trees with young leaves and compared modifications of phenology in trees of different functional types with the pattern observed during the regular dry season. Although deciduous trees at dry sites were severely water stressed (Ψstem < ‐7MPa) and their mesic leaves remained wilted for more than two months, these and all other trees retained all leaves during the abnormal drought. Many trees exchanged leaves three to four months earlier than normal during the wet period after the abnormal drought and shed leaves again during the regular dry season. Irrigation and an exceptional 70 mm rainfall during the mid‐dry season 1998/1999 caused bud break and flushing in all leafless trees except dormant stem succulents. The complex interactions between leaf age and water stress, the principal determinants of leaf abscission, were found to vary widely among trees of different functional types.     

The crystal structure of an engineered monomeric triosephosphate isomerase, monoTIM: the correct modelling of an eight-residue loop

BACKGROUND: The triosephosphate isomerase (TIM) fold is found in several different classes of enzymes, most of which are oligomers; TIM itself always functions as a very tight dimer. It has recently been shown that a monomeric form of TIM ('monoTIM') can be constructed by replacing a 15-residue interface loop, loop-3, with an eight-residue fragment; modelling suggests that this should result in a short strain-free turn, resulting in the subsequent helix, helix-A3, having an additional turn at its amino terminus. RESULTS: The crystal structure of monoTIM shows that it retains the characteristic TIM-barrel (betaalpha)8-fold and that the new loop has a structure very close to that predicted. Two other interface loops, loop-1 and loop-4, which contain the active site residues Lys13 and His95, respectively, show significant changes in structure in monoTIM compared with dimeric wild-type TIM. CONCLUSION: The observed structural differences between monoTIM and wild-type TIM indicate that the dimeric appearance of TIM determines the location and conformation of two of the four catalytic residues.     

Oriental fruit moth (Lepidoptera: Tortricidae) phenology and management with methoxyfenozide in North Carolina apples

The phenology of oriental fruit moth, Grapholita molesta (Busck), on apple (Malus spp.) in North Carolina was studied using pheromone traps and egg sampling in abandoned and commercial orchards in 2000 and 2001, with subsequent development of an oviposition degree-day model and management studies in relation to codling moth, Cydia pomonella (L.), phenology. Oriental fruit moth eggs were found in greater numbers on leaves early and on fruit later in the growing season, on the top versus the bottom of the leaf surface, and on the calyx area versus the side or stem end of the fruit. A degree-day (DD) model to predict oriental fruit moth oviposition was developed based on temperature accumulations from peak moth trap capture of the first (overwintering) generation, by using 7.2 and 32.2 degrees C as the temperature limits. The model predicted four ovipositing generations of oriental fruit moth with the second beginning 507 DD after peak moth catch. Using predictions of the oriental fruit moth and codling moth degree-day oviposition models, an experiment was conducted to determine the level of second generation oriental fruit moth control with methoxyfenozide applied under different scenarios for first generation codling moth. Methoxyfenozide was equally effective in managing codling moth and oriental fruit moth for all treatment timings.     

Phenology of temperate trees in tropical climates

Several North American broad-leaved tree species range from the northern United States at 47°N to moist tropical montane forests in Mexico and Central America at 15–20°N. Along this gradient the average minimum temperatures of the coldest month (T _Jan), which characterize annual variation in temperature, increase from –10 to 12°C and tree phenology changes from deciduous to leaf-exchanging or evergreen in the southern range with a year-long growing season. Between 30 and 45°N, the time of bud break is highly correlated with T _Jan and bud break can be reliably predicted for the week in which mean minimum temperature rises to 7°C. Temperature-dependent deciduous phenology—and hence the validity of temperature-driven phenology models—terminates in southern North America near 30°N, where T _Jan>7°C enables growth of tropical trees and cultivation of frost-sensitive citrus fruits. In tropical climates most temperate broad-leaved species exchange old for new leaves within a few weeks in January-February, i.e., their phenology becomes similar to that of tropical leaf-exchanging species. Leaf buds of the southern ecotypes of these temperate species are therefore not winter-dormant and have no chilling requirement. As in many tropical trees, bud break of Celtis, Quercus and Fagus growing in warm climates is induced in early spring by increasing daylength. In tropical climates vegetative phenology is determined mainly by leaf longevity, seasonal variation in water stress and day length. As water stress during the dry season varies widely with soil water storage, climate-driven models cannot predict tree phenology in the tropics and tropical tree phenology does not constitute a useful indicator of global warming.     

Protein engineering of bacterial alpha-amylases

alpha-Amylases constitute a very diverse family of glycosyl hydrolases that cleave alpha1-->4 linkages in amylose and related polymers. Recent structural and mutagenic studies of archeael, mammalian and bacterial alpha-amylases have resulted in a wealth of information on the catalytic mechanism and on the structural features of this enzyme class. Because of their high thermo-stability, the Bacillus alpha-amylases have found widespread use in industrial processes, and much attention has been devoted to optimising these enzymes for the very harsh conditions encountered there. Stability has been a major area of focus in this respect, and several remarkably stable bacterial alpha-amylases have been produced by bioengineering techniques. Protein engineering studies of pH-activity profiles and of substrate specificities have also been initiated, although without much success. In the coming years it is likely, however, that the focus of alpha-amylase engineering will shift from engineering stability to these new areas.