A Comparison of Two Techniques for Wood Fibre Isolation - Evaluation by Tensile Tests on Single Fibres with Different Microfibril Angle

Abstract: Fibres (tracheids) of spruce ( Picea abies [L.] Karst.) were isolated by means of two isolation techniques. On the one hand, a soft chemical treatment with Jeffrey solution was used. The isolation was carried out with a reduced time of treatment (2 h), just to achieve the state where the fibres could be separated easily with tweezers. On the other hand, fibres were directly peeled out with tweezers, taking advantage of the low shear strength between them. Following this approach, a chemical treatment could be avoided completely. In order to compare the isolation techniques, single tracheids from tissue types with different microfibril angle (earlywood, latewood, juvenile wood, opposite wood, compression wood) were tested in the dry state. The microfibril angles were determined by X-ray diffraction. Single tracheids handled with both isolation techniques were strained in microtensile tests and load-strain diagrams were obtained. The chemically treated fibres were found to have much lower strength and stiffness compared to the mechanically isolated fibres, even though the influence of microfibril angle was still obvious for both kinds of treatment. The results clearly show the importance of single fibre extraction to preserve as much as possible the original properties.     

In-situ identification of major metabolites in the red alga Gracilariopsis lemaneiformis using high-resolution magic angle spinning nuclear magnetic resonance spectroscopy

The content of low-molecular-weight compounds in the red alga Gracilariopsis lemaneiformis [(Bory) Dawson, Acleto, et Foldvik] has been analysed in-situ using high-resolution magic angle spinning (HR-MAS) nuclear magnetic resonance (NMR) spectroscopy. The major heteroside was shown to be floridoside, but digeneaside and isofloridoside were also detected in the alga. Other major components were isethionic acid and the amino acids taurine and citrulline. The results from the HR-MAS NMR analysis were confirmed with high-resolution NMR spectroscopy, high-resolution fast atom bombardment mass spectrometry (FABMS) and GC-MS, on material isolated from the studied alga, but also on authentic samples. Received: 2 February 1998 / Accepted: 9 April 1998     

Torsion angle dynamics: Reduced variable conformational sampling enhances crystallographic structure refinement

A reduced variable conformational sampling strategy for macromolecules based on molecular dynamics in torsion angle space is evaluated using crystallographic refinement as a prototypical search problem. Bae and Haug's algorithm for constrained dynamics [Bae, D. S., Haug, E. J. A recursive formulation for constrained mechanical system dynamics. Mech. Struct. Mach. 15:359–382, 1987], originally developed for robotics, was used. Their formulation solves the equations of motion exactly for arbitrary holonomic constraints, and hence differs from commonly used approximation algorithms. It uses gradients calculated in Cartesian coordinates, and thus also differs from internal coordinate formulations. Molecular dynamics can be carried out at significantly higher temperatures due to the elimination of the high frequency bond and angle vibrations. The sampling strategy presented here combines high temperature torsion angle dynamics with repeated trajectories using different initial velocities. The best solutions can be identified by the free R value, or the R value if experimental phase information is appropriately included in the refinement. Applications to crystallographic refinement show a significantly increased radius of convergence over conventional techniques. For a test system with diffraction data to 2 Å resolution, slow-cooling protocols fail to converge if the backbone atom root mean square (rms) coordinate deviation from the crystal structure is greater than 1.25 Å, but torsion angle refinement can correct backbone atom rms coordinate deviations up to approximately 1.7 Å. © 1994 Wiley-Liss, Inc.     

Gypsophile vegetation patterns under a range of soil properties induced by topographical position

Iberian gypsophile plant communities are considered a priority for conservation by the European Community because of their highly specialized flora in gypsum outcrops in arid and semiarid regions. Despite the ecological importance of these ecosystems, the edaphic factors that constrain plant communities on gypsiferous soils remain unclear. It has been proposed that both the chemical and physical restrictive conditions of gypsum soils determine gypsophily in plants. Here we hypothesize that the rigors of the gypsum soil environment depends on topography, decreasing from flat areas on hilltops to south-oriented slopes and finally to slopes oriented to the north. We also hypothesized that the relaxation of the rigors of the gypsum soil environment with topography affects both to individual plant and community characteristics of gypsophile vegetation: we expect a reduction of gypsophyte abundance, an increase of diversity and the amelioration of facilitative interactions of plant species. We analysed the physical and chemical properties of gypsum soils that have been proposed that determine the rigors of the gypsum soil environment (i.e.: unbalanced ion concentrations and superficial soil crust). The predicted rigor gradient along topographical locations was confirmed and was mainly caused by superficial soil crust. The decreasing rigor gradient was accompanied by a fall in the abundance of gypsophytes. However, when gypsophytes were considered separately, several patterns were observed, indicating distinct tolerance to relaxation of rigor of the gypsum soil conditions and different competition abilities between gypsophytes. Plant species were more clumped, and gypsophile communities presented higher diversity, evenness and richness values where rigor of gypsum soil conditions were maximum (flat hilltop positions). Relaxation of rigor (north-oriented slopes) was characterized by loss of facilitative interaction between species and the dominance of the gypsovag Rosmarinus officinalis L., although richness was still very high, which can be attributed to the coexistence of gypsophytes and gypsovags. We conclude that the rigor of gypsum soil environment gradient with topography is mainly determined by superficial soil crust, and it is a crucial determinant of gypsophile plant communities.     

Knowledge-based protein secondary structure assignment

We have developed an automatic algorithm STRIDE for protein secondary structure assignment from atomic coordinates based on the combined use of hydrogen bond energy and statistically derived backbone torsional angle information. Parameters of the pattern recognition procedure were optimized using designations provided by the crystallographers as a standard-of-truth. Comparison to the currently most widely used technique DSSP by Kabsch and Sander (Biopolymers 22:2577-2637, 1983) shows that STRIDE and DSSP assign secondary structural states in 58 and 31% of 226 protein chains in our data sample, respectively, in greater agreement with the specific residue-by-residue definitions provided by the discoverers of the structures while in 11% of the chains, the assignments are the same. STRIDE delineates every 11th helix and every 32nd strand more in accord with published assignments. © 1995 Wiley-Liss, Inc.     

Ddhd1 knockout mouse as a model of locomotive and physiological abnormality in familial spastic paraplegia

We have previously reported a novel homozygous 4-bp deletion in DDHD1 as the responsible variant for spastic paraplegia type 28 (SPG28; OMIM#609340). The variant causes a frameshift, resulting in a functionally null allele in the patient. DDHD1 encodes phospholipase A₁ (PLA₁) catalyzing phosphatidylinositol to lysophosphatidylinositol (LPI). To clarify the pathogenic mechanism of SPG28, we established Ddhd1 knockout mice (Ddhd1[−/−]) carrying a 5-bp deletion in Ddhd1, resulting in a premature termination of translation at a position similar to that of the patient. We observed a significant decrease in foot–base angle (FBA) in aged Ddhd1(−/−) (24 months of age) and a significant decrease in LPI 20:4 (sn-2) in Ddhd1(−/−) cerebra (26 months of age). These changes in FBA were not observed in 14 months of age. We also observed significant changes of expression levels of 22 genes in the Ddhd1(−/−) cerebra (26 months of age). Gene Ontology (GO) terms relating to the nervous system and cell–cell communications were significantly enriched. We conclude that the reduced signaling of LPI 20:4 (sn-2) by PLA₁ dysfunction is responsible for the locomotive abnormality in SPG28, further suggesting that the reduction of downstream signaling such as GPR55 which is agonized by LPI is involved in the pathogenesis of SPG28.     

Ensemble structural analyses depict the regulatory mechanism of non-phosphorylated human MAP2K4

Mitogen-activated protein kinase kinase 4 (MAP2K4) plays a critical role in regulating the stress-activated protein kinase signaling cascade. A small angle X-ray scattering experiment, a powerful technique for analyzing a solution structure cleared from the structural artifacts due to crystal packing, provided the ensemble structures of human non-phosphorylated MAP2K4 in three states involving the apo form, the binary complex with an ATP analogue, and the ternary complex with the ATP analogue and substrate peptide. These ensemble structures provided more detailed mechanisms for regulating MAP2K4 in addition to those delineated only by the crystal structures in three states.     

Dynamic Solution Structures of Whole Human NAP1 Dimer Bound to One and Two Histone H2A-H2B Heterodimers Obtained by Integrative Methods

Nucleosome assembly protein 1 (NAP1) binds to histone H2A-H2B heterodimers, mediating their deposition on and eviction from the nucleosome. Human NAP1 (hNAP1) consists of a dimerization core domain and intrinsically disordered C-terminal acidic domain (CTAD), both of which are essential for H2A-H2B binding. Several structures of NAP1 proteins bound to H2A-H2B exhibit binding polymorphisms of the core domain, but the distinct structural roles of the core and CTAD domains remain elusive. Here, we have examined dynamic structures of the full-length hNAP1 dimer bound to one and two H2A-H2B heterodimers by integrative methods. Nuclear magnetic resonance (NMR) spectroscopy of full-length hNAP1 showed CTAD binding to H2A-H2B. Atomic force microscopy revealed that hNAP1 forms oligomers of tandem repeated dimers; therefore, we generated a stable dimeric hNAP1 mutant exhibiting the same H2A-H2B binding affinity as wild-type hNAP1. Size exclusion chromatography (SEC), multi-angle light scattering (MALS) and small angle X-ray scattering (SAXS), followed by modelling and molecular dynamics simulations, have been used to reveal the stepwise dynamic complex structures of hNAP1 binding to one and two H2A-H2B heterodimers. The first H2A-H2B dimer binds mainly to the core domain of hNAP1, while the second H2A-H2B binds dynamically to both CTADs. Based on our findings, we present a model of the eviction of H2A-H2B from nucleosomes by NAP1.     

Specificity of joint angle in isometric training

Six healthy women (21.8 +/- 0.4 y) did isometric strength training of the left plantarflexors at an ankle joint angle of 90 degrees. Training sessions, done 3 times per week for 6 weeks, consisted of 2 sets of ten 5 s maximal voluntary contractions. Prior to and following the training, and in random order, voluntary and evoked isometric contraction strength was measured at the training angle and at additional angles: 5 degrees, 10 degrees, 15 degrees, and 20 degrees intervals in the plantarflexion and dorsiflexion directions. Evoked contraction strength was measured as the peak torque of maximal twitch contractions of triceps surae. Training increased voluntary strength at the training angle and the two adjacent angles only (p less than 0.05). Time to peak twitch torque was not affected by training. Twitch half relaxation time increased after training (p = 0.013), but the increase was not specific to the training angle. There was a small (1.1%, p less than 0.05) increase in calf circumference after training. Evoked twitch torque did not increase significantly at any joint angle. It was therefore concluded that a neural mechanism is responsible for the specificity of joint angle observed in isometric training.