The microscopic structures of hydrogen-antimony, -tellurium, and -tin complexes in silicon have been studied using first-principles total-energy calculations, in order to obtain a more definitive... Show moreThe microscopic structures of hydrogen-antimony, -tellurium, and -tin complexes in silicon have been studied using first-principles total-energy calculations, in order to obtain a more definitive understanding of the various dopant-hydrogen complexes in n-type crystalline silicon. We find that for neutral SbH, TeH, and SnH complexes, the lowest-energy configurations are similar and of the type AB-Si (the H is located at the antibonding site of a Si atom that is adjacent to the impurity). The reaction SbH + H→SbH2 turns out to be exothermic. The results are consistent with recent experimental results using Mössbauer spectroscopy. For SbH2 various configurations are found that differ only slightly in energy. The lowest-energy configuration of SbH2 complexes exhibits electrical properties similar to those of substitutional Sb. This suggests that the formation of SbH2 not only competes with that of SbH and H*2, but may also electrically activate the sample. Show less
Bacteria belonging to the genera Rhizobium, Bradyrhizobium, and Azorhizobium, collectively known as rhizobia, penetrate the roots (or adventitious roots) of their leguminous host plants via tubular... Show moreBacteria belonging to the genera Rhizobium, Bradyrhizobium, and Azorhizobium, collectively known as rhizobia, penetrate the roots (or adventitious roots) of their leguminous host plants via tubular structures, the infection threads. During infection of the host plant they trigger the formation of a new organ, the root nodule, in which a differentiated form of rhizobia, the bacteroid, fixes nitrogen into ammonia, which can then be used by the plant. This review presents an update of the recent literature on the molecular biology of the infection and nodulation of plants by rhizobia, with special emphasis on results pertinent to other plant-microbe interactions. Particular attention is given to determinants of host specificity such as flavonoid and lipo-chitin oligosaccharide signal molecules. Show less
Saarloos, W. van; Hecke, M.L. van; Holyst, R. 1995
The fluorescence and fluorescence-excitation spectra of C-60 in a hydrocarbon glass at 1.2 K are reported. The fluorescence spectrum resembles that of a molecular X-trap in crystalline C-60. The... Show moreThe fluorescence and fluorescence-excitation spectra of C-60 in a hydrocarbon glass at 1.2 K are reported. The fluorescence spectrum resembles that of a molecular X-trap in crystalline C-60. The vibronic bands in these spectra are assigned, and the intensity distribution among the false origins points to vibronic coupling within the singlet manifold. The lowest excited singlet state of C-60 shows predominantly T-1g and G(g) character. Additionally, we show that a reduction of the symmetry of C-60 by either an intra- or an intermolecular perturbation leads to a fluorescence spectrum with a strong 0-0 transition and a different vibronic structure. Show less
A procedure for simulating the RNA folding process using the principles of genetic algorithm is proposed. The method allows one to simulate a folding pathway of RNA, including such processes as... Show moreA procedure for simulating the RNA folding process using the principles of genetic algorithm is proposed. The method allows one to simulate a folding pathway of RNA, including such processes as disruption of temporarily formed structures, the folding of a molecule during its synthesis and pseudoknot formation. The simulations are able to predict functional metastable foldings and kinetically driven transitions to more stable structures. The analysis of free energies for intermediate foldings allows estimation of the ranges of kinetic refolding barriers and suggests that in some RNAs the selective evolutionary pressure suppresses the possibilities for alternative structures that could form in the course of transcription. It is shown that the folding pathway simulation can result in structure predictions that are more consistent with phylogenetically proven structures than minimum energy solutions. This suggest that RNA folding kinetics is very important for the formation of functional RNA structures. Therefore, apart form its value for predictions of RNA structures, the proposed computer simulations ran be a powerful tool in the studies of RNA folding features. Show less
Bloemberg, G.V.; Kamst, E.; Harteveld, M.; Drift, K.M.G.M. van der; Haverkamp, J.; Thomas-Oates, J.E.; ... ; Spaink, H.P. 1995
Previously, we have shown that the nodE gene is a major determinant of the difference in host range between Rhizobium leguminosarum biovars viciae and trifolii. A new genetic test system for... Show morePreviously, we have shown that the nodE gene is a major determinant of the difference in host range between Rhizobium leguminosarum biovars viciae and trifolii. A new genetic test system for stringent functional analysis of nodE genes was constructed. By testing chimeric nodE genes constructed by the exchange of poiymerase chain reaction (PCR)-generated restriction cassettes, we show that a central domain, containing only 44 non-conserved amino acid residues, determines the host specificity of the NodE protein (401 amino acid residues). Mass spectrometric analysis of the lipo-chitin oligosaccharides (LCOs) produced by the new test strain containing the biovar viciae nodE gene shows that molecules containing a polyunsaturated C18:4 (trans-2. trans-4. trans-6. cis-11-octadecatetraenoic) fatty acyl moiety are produced, as is the case for wild-type R. leguminosarum bv. viciae. The LCOs determined by the biovar trifolii nodE gene, which was overproduced in our test strain, carry C1 8:2 and C18:3 fatty acyl chains containing two or three conjugated trans double bonds, respectively. Therefore, the main difference between the nodE-determined LCOs of biovar viviae and trifolii in this system is the presence or absence of one cis double bond, resulting in the very different hydrophobicity of the LCOs. Using a newly developed spot application assay, we show that the 18:2- and C18:3-containing LCOs are able to induce the formation of nodule primordia on roots of Trifolium pratense. On the basis of these and other recent results, we propose that the host range of nodulation of the R. leguminosarum biovars viciae and trifolii is determined by the degree of hydrophobicity of the poly-unsaturated fatty acyl moieties of their LCOs, which is mediated by the host-specific central domain of the NodE protein. Show less
An electron spin echo envelope modulation (ESEEM) study is performed on the reduced primary electron-accepting ubiquinone-10 (Q(A)(-.)) in Zn-substituted reaction centers of the photosynthetic... Show moreAn electron spin echo envelope modulation (ESEEM) study is performed on the reduced primary electron-accepting ubiquinone-10 (Q(A)(-.)) in Zn-substituted reaction centers of the photosynthetic bacterium Rhodobacter sphaeroides R26. The ESEEM spectra showed hyperfine and quadrupolar couplings of Q(A)(-.) to nitrogens in the protein matrix. Simulation of the spectra revealed the following N-14 coupling parameters: hyperfine interaction: A(iso)=1.85 MHz, T-11=0.32, alpha=0(0), beta=45(0); nuclear quadrupole interaction: e(2)qQ/h=1.52 MHz, eta=0.82. Comparison of the quadrupole values with data in the literature shows that Q(A)(-.) is coupled to the N-delta(1)-H group of the M219 heterocycle, most probably through a hydrogen bond with the 4-C carbonyl group of the quinone. Show less
Individual pentacene-d(14) molecules doped into a p-terphenyl-d(14) host crystal have been studied by optically detected electron paramagnetic resonance spectroscopy. The magnetic resonance... Show moreIndividual pentacene-d(14) molecules doped into a p-terphenyl-d(14) host crystal have been studied by optically detected electron paramagnetic resonance spectroscopy. The magnetic resonance transitions between the triplet sublevels of the pentacene molecule and the splitting of the resonance lines for a molecule that contains a carbon-13 nucleus have been observed in an edernal magnetic field. This splitting is caused by the hyperfine interaction of the triplet electron spin with the single carbon-13 nuclear spin. Show less
The possibilities of using a genetic algorithm for the prediction of RNA secondary structure were investigated. The algorithm, using the procedure of stepwise selection of the most fit structures ... Show moreThe possibilities of using a genetic algorithm for the prediction of RNA secondary structure were investigated. The algorithm, using the procedure of stepwise selection of the most fit structures (similarly to natural evolution), allows different models of fitness or driving forces determining RNA structure to be easily introduced. This can be used for simulation of the RNA folding process and for the investigation of possible folding pathways. Such an algorithm needs several modifications before it can predict RNA secondary structures. After modification, a fair number of correct stems are predicted, even when using computationally quick, but very crude, fitness criteria such as stem length and stacking energy, including elements of tertiary structure (pseudoknots). The fact that genetic algorithm simulation includes both stem formations and stem disruption allows one to observe intermediate structures that may be used in combination with phylogenetic or experimental research. Show less
Vos, R. van der; Franken, E.M.; Sexton, S.J.; Shochat, S.; Gast, P.; Hore, P.J.; Hoff, A.J. 1995
In this work, the magnetic field effects (MFE) on the triplet yield in reaction centers (RCs) of Rhodobacter (Rb.) sphaeroides 2.4.1 and its Tyr M210 --> Trp mutant are compared. The MFE is... Show moreIn this work, the magnetic field effects (MFE) on the triplet yield in reaction centers (RCs) of Rhodobacter (Rb.) sphaeroides 2.4.1 and its Tyr M210 --> Trp mutant are compared. The MFE is measured between 25 and 225 K by monitoring the absorbance. Using monochromatic polarised and unpolarised light, linear dichroic (LD-)MFE curves were obtained. Simulations of the (LD-) MFE measured at low temperatures (25 K) are presented, which suggest that the exchange interaction in the mutant and in the wild type have opposite sign. This is explained by considering the free energy differences between the excited primary donor state P-1* and the charge-separated state. The magnetic field dependence of the MFE of Q-depleted mutant RCs at low magnetic fields is similar for temperatures between 25 and 225 K, implying that k(T) is practically temperature independent. This suggests that the temperature dependence of the triplet yield is due to a change in radical pair singlet recombination rate k(s). The exchange interaction between the oxidised primary donor and reduced intermediary bacteriopheophytin acceptor of mutant RCs is twice as large as that of the wild type. This is attributed to an upward change of the energy level of the charge-separated state caused by the mutation. Show less
