Synthesis of oligogalacturonates conjugated to BSA

The synthesis of three oligogalacturonates with an aldehyde spacer attached at the reducing end is described. Trigalacturonates alpha-d-GalpA-(1-->4)-alpha-d-GalpA-(1-->4)-alpha-d-GalpA-(1-->O(CH(2))(7)CHO and alpha-d-GalpA(Me)-(1-->4)-alpha-d-GalpA(Me)-(1-->4)-alpha-d-GalpA(Me)-(1-->O(CH(2))(7)CHO as well as hexagalacturonate alpha-d-GalpA-(1-->4)-[alpha-d-GalpA-(1-->4)](4)-alpha-d-GalpA-(1-->O(CH(2))(7)CHO are prepared by stepwise coupling of galactose units followed by oxidation of the 6-positions. The alpha-linkages are formed by employing n-pentenyl galactosides as glycosyl donors and N-iodosuccinimide/triethylsilyl triflate as the promoter. Deprotection furnishes the three target oligogalacturonates, which are subsequently linked to bovine serum albumin by reductive amination. These neoglycoproteins will serve as immunogens for generation of new antibodies that can be used for localization and characterization of pectin in plants.     

Control of chemical pattern formation by a clock-and-wavefront type mechanism

The segmentation of many animals ranging from insects to mammals involves the sequential formation of stationary stripes of gene expression that are perpendicular to the growth axis of the developing embryo. This process has been accounted for by a variety of theoretical “clock-and-wavefront” type models that involve the arrest of an oscillation (the clock) at a moving boundary (the wavefront). Here, we demonstrate experimentally that progressive arrest of a homogeneous oscillation can control the symmetry as well as the wavelength of spatial structures in a chemical system. We show how a spontaneously formed, labyrinthine pattern can be converted into a pattern composed of ordered, parallel stripes and confirm a previously predicted proportionality between the wavelength and the period of the homogeneous oscillation. Our experiments provide the first experimental demonstration of a general mechanism for the control of pattern formation that has been hypothesized to operate in the context of biological morphogenesis.     

Intercalator conjugates of pyrimidine locked nucleic acid-modified triplex-forming oligonucleotides: improving DNA binding properties and reaching cellular activities

Triplex-forming oligonucleotides (TFOs) are powerful tools to interfere sequence-specifically with DNA-associated biological functions. (A/T,G)-containing TFOs are more commonly used in cells than (T,C)-containing TFOs, especially C-rich sequences; indeed the low intracellular stability of the non-covalent pyrimidine triplexes make the latter less active. In this work we studied the possibility to enhance DNA binding of (T,C)-containing TFOs, aiming to reach cellular activities; to this end, we used locked nucleic acid-modified TFOs (TFO/LNAs) in association with 5′-conjugation of an intercalating agent, an acridine derivative. In vitro a stable triplex was formed with the TFO-acridine conjugate: by SPR measurements at 37°C and neutral pH, the dissociation equilibrium constant was found in the nanomolar range and the triplex half-life ~10 h (50-fold longer compared with the unconjugated TFO/LNA). Moreover to further understand DNA binding of (T,C)-containing TFO/LNAs, hybridization studies were performed at different pH values: triplex stabilization associated with pH decrease was mainly due to a slower dissociation process. Finally, biological activity of pyrimidine TFO/LNAs was evaluated in a cellular context: it occurred at concentrations ~0.1 μM for acridine-conjugated TFO/LNA (or ~2 μM for the unconjugated TFO/LNA) whereas the corresponding phosphodiester TFO was inactive, and it was demonstrated to be triplex-mediated.     

Foraging strategies and seasonal diet optimization of muskoxen in West Greenland

Various aspects of optimal foraging and seasonal diet composition of bulls (bachelor and dominant), cows, subadults, and yearlings of muskoxen Ovibos moschatus were investigated in West Greenland during the following seasons: calving, post-calving, summer, rut and mid-winter. The following hypotheses were tested: (1) muskoxen maximize daily energy intake during spring and summer, (2) dominant bulls monopolizing cows during the rutting season shift from an energy maximizing to a time minimizing foraging strategy in order to maximize the time available for reproductive activities, and (3) muskoxen employ a time minimizing foraging strategy during winter to conserve energy. As forage quality changed throughout the short Arctic growing season, muskoxen responded by changing the proportions of daily time spent feeding on graminoids (Cyperaceae, Poaceae) and dicots (Salix, Betula), respectively. This seasonal variation in the relative proportion of daily feeding time spent ingesting graminoids followed approximately the energy maximization prediction over the periods calving to rut. Neither time minimizing nor random foraging could explain the observed diets in this period, thus confirming hypothesis 1. Dominant bulls did not shift to the time minimizing strategy as predicted by hypothesis 2. However, during the pre-rutting and rutting seasons bulls deviated from the other sex/age classes by failing to obtain the daily maximum energy predicted by the model, as a result of a higher proportion of time allocated to agonistic and sexual behaviour. During winter, none of the sex/age classes employed a time minimizing strategy, so rejecting hypothesis 3. Instead, muskoxen were found to maximize Na intake, indicating that Na is of major importance for winter survival. The results emerging from a linear programming model with constraint settings varying over seasons confirm that the constraint parameters applied are indeed important limiting factors for muskoxen in natural populations.     

The gene encoding the periplasmic cyclophilin homologue, PPlase A, in Escherichia coli, is expressed from four promoters, three of which are activated by the cAMP–CRP complex and negatively regulated by the CytR repressor

The rot gene in Escherichia coli encodes PPlase A, a periplasmic peptldyl-prolyl cis-trans isomerase with homology to the cyclophilin family of proteins. Here it is demonstrated that rot is expressed in a complex manner from four overlapping promoters and that the rot regulatory region is unusually compact, containing a close array of sites for DNA-binding proteins. The three most upstream rot promoters are activated by the global gene regulatory cAMP–CRP complex and negatively regulated by the CytR repressor protein. Activation of these three promoters occurs by binding of cAMP–CRP to two sites separated by 53 bp. Moreover, one of the cAMP–CRP complexes is involved in the activation of both a Class I and a Class II promoter. Repression takes place by the formation of a CytR/cAMP–CRP/DNA nucleoprotein complex consisting of the two cAMP–CRP molecules and CytR bound in between. The two regulators bind co-operatively to the DNA overlapping the three upstream promoters, simultaneously quenching the cAMP–CRP activator function. These results expand the CytR regulon to include a gene whose product has no known function in ribo- and deoxyribonucleoside catabolism or transport.     

Transient overexpression of DNA adenine methylase enables efficient and mobile genome engineering with reduced off-target effects

Homologous recombination of single-stranded oligonucleotides is a highly efficient process for introducing precise mutations into the genome of E. coli and other organisms when mismatch repair (MMR) is disabled. This can result in the rapid accumulation of off-target mutations that can mask desired phenotypes, especially when selections need to be employed following the generation of combinatorial libraries. While the use of inducible mutator phenotypes or other MMR evasion tactics have proven useful, reported methods either require non-mobile genetic modifications or costly oligonucleotides that also result in reduced efficiencies of replacement. Therefore a new system was developed, Transient Mutator Multiplex Automated Genome Engineering (TM-MAGE), that solves problems encountered in other methods for oligonucleotide-mediated recombination. TM-MAGE enables nearly equivalent efficiencies of allelic replacement to the use of strains with fully disabled MMR and with an approximately 12- to 33-fold lower off-target mutation rate. Furthermore, growth temperatures are not restricted and a version of the plasmid can be readily removed by sucrose counterselection. TM-MAGE was used to combinatorially reconstruct mutations found in evolved salt-tolerant strains, enabling the identification of causative mutations and isolation of strains with up to 75% increases in growth rate and greatly reduced lag times in 0.6 M NaCl.     

A sixth‐level habitat cascade increases biodiversity in an intertidal estuary

Many studies have documented habitat cascades where two co‐occurring habitat‐forming species control biodiversity. However, more than two habitat‐formers could theoretically co‐occur. We here documented a sixth‐level habitat cascade from the Avon‐Heathcote Estuary, New Zealand, by correlating counts of attached inhabitants to the size and accumulated biomass of their biogenic hosts. These data revealed predictable sequences of habitat‐formation (=attachment space). First, the bivalve Austrovenus provided habitat for green seaweeds (Ulva) that provided habitat for trochid snails in a typical estuarine habitat cascade. However, the trochids also provided habitat for the nonnative bryozoan Conopeum that provided habitat for the red seaweed Gigartina that provided habitat for more trochids, thereby resetting the sequence of the habitat cascade, theoretically in perpetuity. Austrovenus is here the basal habitat‐former that controls this “long” cascade. The strength of facilitation increased with seaweed frond size, accumulated seaweed biomass, accumulated shell biomass but less with shell size. We also found that Ulva attached to all habitat‐formers, trochids attached to Ulva and Gigartina, and Conopeum and Gigartina predominately attached to trochids. These “affinities” for different habitat‐forming species probably reflect species‐specific traits of juveniles and adults. Finally, manipulative experiments confirmed that the amount of seaweed and trochids was important and consistent regulators of the habitat cascade in different estuarine environments. We also interpreted this cascade as a habitat‐formation network that describes the likelihood of an inhabitant being found attached to a specific habitat‐former. We conclude that the strength of the cascade increased with the amount of higher‐order habitat‐formers, with differences in form and function between higher and lower‐order habitat‐formers, and with the affinity of inhabitants for higher‐order habitat‐formers. We suggest that long habitat cascades are common where species traits allow for physical attachment to other species, such as in marine benthic systems and old forest.