How to determine sapling buckling risk with only a few measurements

Tree buckling risk (actual height/critical buckling height) is an important biomechanical trait of plant growth strategies, and one that contributes to species coexistence. To estimate the diversity of this trait among wide samples, a method that minimizes damage to the plants is necessary. On the basis of the rarely used, complete version of Greenhill's model (1881, Proceedings of the Cambridge Philosophical Society 4(2): 65-73), we precisely measured all the necessary parameters on a sample of 236 saplings of 16 species. Then, using sensitivity (variance) analysis, regressions between successive models for risk factors and species ranks and the use of these models on samples of self- and nonself-supporting saplings, we tested different degrees of simplification up to the most simple and widely used formula that assumes that the tree is a cylindrical homogeneous pole. The size factor had the greatest effect on buckling risk, followed by the form factor and the modulus of elasticity of the wood. Therefore, estimates of buckling risk must consider not only the wood properties but especially the form factor. Finally, we proposed a simple but accurate method of assessing tree buckling risk that is applicable to a wide range of samples and that requires mostly nondestructive measurements.     

The “sugar” coarse-grained DNA model

More than 20 coarse-grained (CG) DNA models have been developed for simulating the behavior of this molecule under various conditions, including those required for nanotechnology. However, none of these models reproduces the DNA polymorphism associated with conformational changes in the ribose rings of the DNA backbone. These changes make an essential contribution to the DNA local deformability and provide the possibility of the transition of the DNA double helix from the B-form to the A-form during interactions with biological molecules. We propose a CG representation of the ribose conformational flexibility. We substantiate the choice of the CG sites (six per nucleotide) needed for the ”sugar” GC DNA model, and obtain the potentials of the CG interactions between the sites by the ”bottom-up” approach using the all-atom AMBER force field. We show that the representation of the ribose flexibility requires one non-harmonic and one three-particle potential, the forms of both the potentials being different from the ones generally used. The model also includes (i) explicit representation of ions (in an implicit solvent) and (ii) sequence dependence. With these features, the sugar CG DNA model reproduces (with the same parameters) both the B- and A- stable forms under corresponding conditions and demonstrates both the A to B and the B to A phase transitions.

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Graphical Abstract The proposed coarse-grained DNA model allows to reproduce both the B- and A- DNA forms and the transitions between them under corresponding conditions.

     

Dinitrosyl iron complexes with thiol-containing ligands in plant tissues

The formation of dinitrosyl iron complexes with thiol-containing ligands in plant tissues (parsley and apple leaves) in the presence of nitric monoxide was demonstrated using electron paramagnetic resonance. In two types of tissues dinitrosyl iron complexes are predominantly represented by the binuclear diamagnetic form. This diamagnetic form can be transformed in EPR-detectable mononitrosyl iron complexes with diethyldithiocarbamate due to the ability of diethyldithiocarbamate to accept the iron-mononitrosyl groups from iron-dinitrosyl fragments of binuclear complexes. A similar transformation was observed under the effect of diethyldithiocarbamate on a mononuclear paramagnetic form of dinitrosyl iron complexes. The significant amount of binuclear dinitrosyl iron complexes found in plant tissues suggests that these complexes can be considered as a “working form” of nitric monoxide, which is recognized now as a universal regulator of metabolic processes in plants as well as in other organisms.     

Proteins that interact with GTP in Streptomyces griseus and its possible implication in morphogenesis

Abstract By cross-linking with [α-³²P]GTP or [γ-³²P]GTP with or without UV treatment, several proteins of Streptomyces griseus were shown to interact with GTP in specific ways. After gel electrophoresis, 19 bands of radioactivity were found; 12 bands were assigned as GTP-binding proteins and 6 bands as phosphorylated proteins. One band was assumed to be a guanylylated protein. The profile of radioactive bands was similar between cells prepared from liquid or solid culture, but markedly different between growth phases. A mutant (strain M-1) defective in aerial mycelium formation, which was originally found as a decoyinine-resistant isolate, was found to have a different profile of phosphorylated proteins.     

Comparative studies of fresh and postmortem isolated rat cortical synaptosomes: uptake and potassium-evoked release of gamma-aminobutyric acid

Synaptosomal fractions were isolated from rat cerebral cortex immediately after decapitation and after 2 h and 4 h postmortem storage at room temperature. Uptake and release of [3H]GABA was compared between fresh and postmortem synaptosomal fractions. The results suggest that after a 2 h postmortem storage these functions are still comparable to those observed in fresh preparations, while a 4 h period of storage decreases them by about 50%. The present data are consistent with our previous findings that the 2 h postmortem fractions are comparable to freshly isolated fractions with respect to coupled respiration, potassium accumulation and capability of specific configurational changes.     

Mutating RBF Can Enhance Its Pro-Apoptotic Activity and Uncovers a New Role in Tissue Homeostasis

The tumor suppressor retinoblastoma protein (pRb) is inactivated in a wide variety of cancers. While its role during cell cycle is well characterized, little is known about its properties on apoptosis regulation and apoptosis-induced cell responses. pRb shorter forms that can modulate pRB apoptotic properties, resulting from cleavages at caspase specific sites are observed in several cellular contexts. A bioinformatics analysis showed that a putative caspase cleavage site (TELD) is found in the Drosophila homologue of pRb (RBF) at a position similar to the site generating the p76Rb form in mammals. Thus, we generated a punctual mutant form of RBF in which the aspartate of the TELD site is replaced by an alanine. This mutant form, RBF^D253A, conserved the JNK-dependent pro-apoptotic properties of RBF but gained the ability of inducing overgrowth phenotypes in adult wings. We show that this overgrowth is a consequence of an abnormal proliferation in wing imaginal discs, which depends on the JNK pathway activation but not on wingless (wg) ectopic expression. These results show for the first time that the TELD site of RBF could be important to control the function of RBF in tissue homeostasis in vivo.     

2D finite element ecological model for the Curonian lagoon

The results of application of 2D finite element model SHYFEM to the Curonian lagoon (Baltic Sea) are considered. SHYFEM consist of a physical processes module and an eutrophication module EUTRO adapted for the SHYFEM code from well known modelling system WASP. The SHYFEM/EUTRO model calibration results were compared with the performance of various biogeochemical models analysed in other studies (153 studies published from 1990 to 2002). The performance of all corresponding state variables—dissolved oxygen, NO₃, NH₄, PO₄, phyto- and zooplankton—was slightly lower than median model performance which could be considered satisfactory given the initial state of model formulation and calibration. Model underestimates phytoplankton autumn blooms, especially for the southern part of the lagoon, where fine sediments dominate and water residence time is high. It can be concluded that, in order to increase model performance, the eutrophication module should be improved to account for the dominance of different phytoplankton groups as well as for the exchanges between the sediments and the water column. The amount and quality of the data available for the model setup and calibration are unsatisfactory and should be improved for the development of the next enhanced model version. Guest editors: A. Razinkovas, Z. R. Gasiūnaitė, J. M. Zaldivar & P. Viaroli European Lagoons and their Watersheds: Function and Biodiversity     

Mechanical behavior of cellulose microfibrils in tension wood, in relation with maturation stress generation

A change in cellulose lattice spacing can be detected during the release of wood maturation stress by synchrotron x-ray diffraction experiment. The lattice strain was found to be the same order of magnitude as the macroscopic strain. The fiber repeat distance, 1.033 nm evaluated for tension wood after the release of maturation stress was equal to the conventional wood values, whereas the value before stress release was larger, corresponding to a fiber repeat of 1.035 nm, nearly equal to that of cotton and ramie. Interestingly, the fiber repeat varied from 1.033 nm for wood to 1.040 nm for algal cellulose, with an increasing order of lateral size of cellulose microfibrils so far reported. These lines of experiments demonstrate that, before the stress release, the cellulose was in a state of tension, which is, to our knowledge, the first experimental evidence supporting the assumption that tension is induced in cellulose microfibrils.