Deciphering the Kinetic Binding Mechanism of Dimeric Ligands Using a Potent Plasma-stable Dimeric Inhibitor of Postsynaptic Density Protein-95 as an Example

Dimeric ligands can be potent inhibitors of protein-protein or enzyme-substrate interactions. They have increased affinity and specificity toward their targets due to their ability to bind two binding sites simultaneously and are therefore attractive in drug design. However, few studies have addressed the kinetic mechanism of interaction of such bivalent ligands. We have investigated the binding interaction of a recently identified potent plasma-stable dimeric pentapeptide and PDZ1–2 of postsynaptic density protein-95 (PSD-95) using protein engineering in combination with fluorescence polarization, isothermal titration calorimetry, and stopped-flow fluorimetry. We demonstrate that binding occurs via a two-step process, where an initial binding to either one of the two PDZ domains is followed by an intramolecular step, which produces the bidentate complex. We have determined all rate constants involved in the binding reaction and found evidence for a conformational transition of the complex. Our data demonstrate the importance of a slow dissociation for a successful dimeric ligand but also highlight the possibility of optimizing the intramolecular association rate. The results may therefore aid the design of dimeric inhibitors in general.     

Inhibition by 2,4-D of somatic embryogenesis in carrot as explored by its reversal by difluoromethylornithine

The development of somatic embryos is, in many plants, inhibited by 2,4-dichlorophenoxyacetic acid (2,4-D) and other auxins. The finding that difluoromethylornithine (DFMO) can counteract this inhibition has been used to test some of the hypotheses for the mechanism of inhibition.
Inhibition of somatic embryogenesis in carrot ( Daucus carota L.) by exogenous ethylene (from ethephon), antioxidants (ascorbic acid and glutathione), ethanol/acetaldehyde and abscisic acid was not counteracted by DFMO, indicating that the inhibitory effect of 2,4-D is not manifest through the formation of these compounds. Embryogenesis was abolished by micromolar concentrations of the polar auxin transport inhibitors 2, 3, 5-triiodobenzoic acid (TIBA), N-1-naphthylphthalamic acid (NPA) and 9-hydroxyfluorene-9-carboxylic acid (HFCA). This inhibition was counteracted to a considerable extent by DFMO. Inhibition by relatively high concentrations of the antiauxin 2-( p -chlorophenoxy)-isobutyric acid (CPIB), which does not affect polar auxin transport, was in contrast not counteracted by DFMO. These findings indicate that exogenous auxins may inhibit embryogenesis by interfering with the ability of postglobular embryos to set up internal auxin gradients necessary for polarized growth.     

Color pan traps often catch less when there are more flowers around

When assessing changes in populations of species, it is essential that the methods used to collect data have some level of precision and preferably also good accuracy. One commonly used method to collect pollinators is colour pan traps, but this method has been suggested to be biased by the abundance of surrounding flowers. The present study evaluated the relationship between pan trap catches and the frequency of flowers on small (25 m²) and large (2–6 ha) spatial scales. If pan traps work well, one should assume a positive relationship, that is, more insects caught when they have more food. However, in contrast, we found that catches in pan traps were often negatively affected by flower frequency. Among the six taxa evaluated, the negative bias was largest in Vespoidea and Lepturinae, while there was no bias in solitary Apoidea (Cetoniidae, Syrphidae and social Apoidea were intermediate). Furthermore, red flowers seemed to contribute most to the negative bias. There was also a tendency that the negative bias differed within the flight season and that it was higher when considering the large spatial scale compared to the small one. To conclude, pan trap catches may suffer from a negative bias due to surrounding flower frequency and color. The occurrence and magnitude of the negative bias were context and taxon dependent, and therefore difficult to adjust for. Thus, pan traps seem less suited to evaluate differences between sites and the effect of restoration, when gradients in flower density are large. Instead, it seems better suited to monitor population changes within sites, and when gradients are small.     

A Sexual Ornament in Chickens Is Affected by Pleiotropic Alleles at HAO1 and BMP2, Selected during Domestication

Domestication is one of the strongest forms of short-term, directional selection. Although selection is typically only exerted on one or a few target traits, domestication can lead to numerous changes in many seemingly unrelated phenotypes. It is unknown whether such correlated responses are due to pleiotropy or linkage between separate genetic architectures. Using three separate intercrosses between wild and domestic chickens, a locus affecting comb mass (a sexual ornament in the chicken) and several fitness traits (primarily medullary bone allocation and fecundity) was identified. This locus contains two tightly-linked genes, BMP2 and HAO1, which together produce the range of pleiotropic effects seen. This study demonstrates the importance of pleiotropy (or extremely close linkage) in domestication. The nature of this pleiotropy also provides insights into how this sexual ornament could be maintained in wild populations.     

Archaeal abundance in relation to root and fungal exudation rates

Archaea are ubiquitous in forest soils, but little is known about the factors regulating their abundance and distribution. Low molecular weight organic compounds represent an important energy source for archaea in marine environments, and it is reasonable to suspect that archaeal abundance is dependent on such compounds in soils as well, represented by, for example, plant and fungal exudates. To test this hypothesis, we designed a microcosm experiment in which we grew ponderosa pine, sitka spruce, and western hemlock in forest soil. Root and mycorrhizal exudation rates were estimated in a 13C pulse-chase experiment, and the number of archaeal and bacterial 16S rRNA genes was determined by qPCR. Archaeal abundance differed among plant species, and the number of archaeal 16S rRNA genes was generally lower in soil receiving high concentration of exudates. The mycorrhizal fungi of ponderosa pine seemed to favor archaea, while no such effect was found for mycorrhized sitka spruce or western hemlock. The low abundance of archaea in the proximity of roots and mycorrhiza may be a result of slow growth rates and poor competitive ability of archaea vs. bacteria and does not necessarily reflect a lack of heterotrophic abilities of the archaeal community.     

Comparison of gas chromatography-mass spectrometry,radioimmunoassay and bioassay for the quantification of gibberellin A9 in norway spruce (Picea abies (L.) Karst.)

Quantitative estimates of gibberellin A₉ in Norway spruce extracts obtained by gas chromatography-mass spectrometry, radioimmunoassay (RIA_ and bioassay were compared after successive purifications of the extracts. The extracts were assayed in several dilutions with and without the addition of standard gibberellin A₉, thus showing the effect of extract components on the response of the assays. Radioimmunoassay produced estimates comparable to gas chromatography-mass spectrometry after one purification step by high-performance liquid chromatography. Extracts purified by polyvinylpyrrolidone-column chromatography and solvent partitioning but not high-performance liquid chromatography resulted in inaccurate RIA estimates. The performance of the RIA could be monitored by logit-log transformations of the standard curve and extract dilution curve and by calculating the slope of the standard addition curve. It was, however, not possible to correct for the interference caused by extract components by the standard addition procedure. Quantifications by Tan-ginbozu dwarf-rice bioassay were accurate, but a large and unpredictable variation makes it unsuitable for quantitative determinations.Abbreviations FW fresh weight - GA₉ gibberellin A₉ - GA₉–Me methylated GA₉ - GC-MS gas chromatography-mass spectrometry - HPLC high performance liquid chromatography - MID multiple-ion detection - RIA radioimmunoassay     

Power and work produced in different leg muscle groups when rising from a chair

The aim of this study was to determine the power output and work done by different muscle groups at the hip and knee joints during a rising movement, to be able to tell the degree of activation of the muscle groups and the relationship between concentric and eccentric work. Nine healthy male subjects rose from a chair with the seat at knee level. The moments of force about the hip and knee joints were calculated semidynamically. The power output (P) and work in the different muscle groups surrounding the joints was calculated as moment of force times joint angular velocity. Work was calculated as: work = f Pdt. The mean peak concentric power output was for the hip extensors 49.9 W, hip flexors 7.9 W and knee extensor 89.5 W. This power output corresponded to a net concentric work of 20.7 J, 1.0 J and 55.6 J, respectively. There was no concentric power output from the knee flexor muscles. Energy absorption through eccentric muscle action was produced by the hip extensors and hip flexors with a mean peak power output of 4.8 W and 7.4 W, respectively. It was concluded that during rising, the hip and knee muscles mainly worked concentrically and that the greatest power output and work were produced during concentric contraction of the knee and hip extensor muscles. There was however also a demand for eccentric work by the hip extensors as well as both concentric and eccentric work by the hip flexors. The knee flexor muscles were unloaded.     

Food‐web structure and mercury dynamics in a large subarctic lake following multiple species introductions

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