Relative Stabilities of C<Subscript>92</Subscript> IPR Fullerenes

The complete set of 86 isolated-pentagon-rule (IPR) isomers of C₉₂ has been described by the SAM1 quantum-chemical method, and their energetics checked by density functional theory at the B3LYP/6-31G* level. Although the lowest-energy cage is not identical in both approaches, it still exhibits D ₂ symmetry in both cases. As energetics themselves cannot produce reliable relative stabilities at high temperatures, entropy terms are also computed and the relative-stability problem is treated entirely in terms of the Gibbs function. The lowest-energy structure is not the most populated isomer at higher temperatures – it is replaced by a D ₃ structure. Further stability interchanges are possible at very high temperatures, when C ₃ and C ₁ structures are also important. There is a partial agreement of the computations with available observed data.     

Mechanisms of Interaction between DNA and Chemical Analogues of Microbial Anabiosis Autoinducers

The alkylhydroxybenzene (AHB) autoregulatory factors d₁ (fd₁) of microorganisms have been found to directly interact with highly polymeric DNA. This circumstance results in changes, related to alterations in the topology of this macromolecule, in DNA physicochemical properties. The physicochemical properties of DNA in the presence of chemical analogues of microbial AHBs (methylresorcinol; hexylresorcinol; and 2-(4-hydroxyphenyl)ethane-1-ol, also known as tyrosol) were investigated using adsorption spectrophotometry, fluorometry, heat denaturation, viscosimetry, and electrophoresis in agarose gel. A number of concordant effects pointing to DNA-AHB interactions were revealed that manifest themselves in the hypochromic properties of the resulting complexes, an increase in their melting temperature and viscosity, a decrease in their electrophoretic mobility, and a change in the fluorescent properties of AHBs upon complexation with DNA. Such alterations were particularly significant in the presence of hexylresorcinol, which possessed the maximum alkyl radical length among the fd₁ analogues tested. Using atomic force microscopy, we visualized the micellelike DNA structures forming in the presence of AHBs. The results obtained provided the basis for developing a hypothetical model of the interaction between the biopolymer macromolecule and low-molecular-weight AHBs that takes into account the differences in the hydrophobicity of individual AHB homologues functioning as ligands. In terms of our model, we discuss AHB involvement in the stabilization of DNA and alteration of its topology, i.e., in the process related to intragenomic rearrangements, which account for the intrapopulational variability of bacteria, including dissociation processes.     

Characteristics of a transverse RF discharge in Xe/Cl<Subscript>2</Subscript> mixtures

Results are presented from the study of the electrical and optical characteristics of a transverse RF discharge in Xe/Cl₂ mixtures at pressures of p≤400 Pa. The working mixture was excited by a modulated RF discharge (f=1.76 MHz) with a transverse electrode configuration (L≤17 cm). The emission spectrum in the spectral range of 210–600 nm and the waveforms of the discharge current, discharge voltage, and plasma emission intensity were investigated. The UV emission power from the discharge was studied as a function of the pressure and composition of a Xe/Cl₂ mixture. It is shown that a discharge in a xenon-chlorine mixture acts as planar excimer-halogen lamp operating in the spectral range of 220–450 nm, which contains a system of overlapping XeCl(D, B-X; B, C-A) and Cl₂(D′-A′) bands. Transverse RF discharges in Xe/Cl₂ mixtures can be used to create a wideband lamp with two 50-cm² planar apertures and the low circulation rate of the working mixture.     

Bacterial metabolites from intra- and inter-species influencing thermotolerance: the case of <Emphasis Type="Italic">Bacillus cereus</Emphasis> and <Emphasis Type="Italic">Geobacillus stearothermophilus</Emphasis>

Bacterial metabolites with communicative functions could provide protection against stress conditions to members of the same species. Yet, information remains limited about protection provided by metabolites in Bacillus cereus and inter-species. This study investigated the effect of extracellular compounds derived from heat shocked (HS) and non-HS cultures of B. cereus and Geobacillus stearothermophilus on the thermotolerance of non-HS vegetative and sporulating B. cereus. Cultures of B. cereus and G. stearothermophilus were subjected to HS (42 or 65 °C respectively for 30 min) or non-HS treatments. Cells and supernatants were separated, mixed in a combined array, and then exposed to 50 °C for 60 min and viable cells determined. For spores, D values (85 and 95 °C) were evaluated after 120 h. In most cases, supernatants from HS B. cereus cultures added to non-HS B. cereus cells caused their thermotolerance to increase (D ₅₀ 12.2–51.9) when compared to supernatants from non-HS cultures (D ₅₀ 7.4–21.7). While the addition of supernatants from HS and non-HS G. stearothermophilus cultures caused the thermotolerance of non-HS cells from B. cereus to decrease initially (D ₅₀ 3.7–7.1), a subsequent increase was detected in most cases (D ₅₀ 18–97.7). In most cases, supernatants from sporulating G. stearothermophilus added to sporulating cells of B. cereus caused the thermotolerance of B. cereus 4810 spores to decline, whereas that of B. cereus 14579 increased. This study clearly shows that metabolites in supernatants from either the same or different species (such as G. stearothermophilus) influence the thermotolerance of B. cereus.     

Magnetophoretic harvesting of freshwater microalgae using polypyrrole/Fe<Subscript>3</Subscript>O<Subscript>4</Subscript> nanocomposite and its reusability

A magnetophoretic harvesting agent, a polypyrrole/Fe₃O₄ magnetic nanocomposite, is proposed as a cost and energy efficient alternative to recover biomass of the microalgae Botryococcus braunii, Chlorella protothecoides, and Chlorella vulgaris from their culture media. The maximal recovery efficiency reached almost 99 % for B. braunii, 92.4 % for C. protothecoides, and 90.8 % for C. vulgaris. The maximum adsorption capacity (Q ₀) of the magnetic nanocomposite for B. braunii (63.49 mg dry biomass mg^?1 PPy/Fe₃O₄) was higher than that for C. protothecoides (43.91 mg dry biomass mg^?1 PPy/Fe₃O₄) and C. vulgaris (39.98 mg dry biomass mg^?1 PPy/Fe₃O₄). The highest harvesting efficiency for all the studied microalgae were at pH 10.0, and measurement of zeta-potential confirmed that the flocculation was induced by charge neutralization. This study showed that polypyrrole/Fe₃O₄ can be a promising flocculant due to its high efficacy, low dose requirements, short settling time, its integrity with cells, and with great potential for saving energy because of its recyclability.     

Efficient inhibition of some multi-drug resistant pathogenic bacteria by bioactive metabolites from <Emphasis Type="Italic">Bacillus amyloliquefaciens</Emphasis> S<Subscript>5</Subscript>I<Subscript>4</Subscript> isolated from archaeological soil in Egypt

Sixty-eight bacterial cultures were isolated from 5 archaeological soils in Egypt. It is necessary to characterize bacteria from ancient temples to develop protection programs for such archaeological places. Purified bacterial cultures were then tested for their capability to inhibit some multi-drug resistant (MDR) pathogenic bacteria including Staphylococcus aureus, Listeria monocytogenes, Bacillus cereus, Escherichia coli and Klebsiella pneumoniae. Among the most active 10 antibacterial isolates, only one isolate designated as S₅I₄ was selected, characterized and identified as belonging to Bacillus amyloliquefaciens. The strain identification was confirmed by amplification of its 16S rRNA gene. The partial nucleotide sequence of the amplified 16S rRNA gene of the tested strain was submitted in GenBank with accession number AB813716. The physical and nutritional parameters were optimized to improve the production of antimicrobial agents by the B. amyloliquefaciens S₅I₄. The maximum antagonistic effect of this strain against the tested MDR pathogenic bacteria was achieved in presence of 1% galactose and 0.5% yeast extract at 37°C and pH 7.0 after 48 h incubation. The antibacterial compounds of B. amyloliquefaciens S₅I₄ were extracted, purified and characterized using spectroscopic analysis (IR, UV, proton NMR and MS). The compound having inhibitory activity was identified as butanedioic acid, octadecyl,1(1carboxy1methylethyl) 4octyl ester.     

Molecular and genetic characterization of the <Emphasis Type="Italic">Ry</Emphasis><Subscript><Emphasis Type="Italic">adg</Emphasis></Subscript> locus on chromosome XI from Andigena potatoes conferring extreme resistance to potato virus Y

Key message

We have elucidated the Andigena origin of the potato Ry_adg gene on chromosome XI of CIP breeding lines and developed two marker assays to facilitate its introgression in potato by marker-assisted selection.

Abstract

Potato virus Y (PVY) is causing yield and quality losses forcing farmers to renew periodically their seeds from clean stocks. Two loci for extreme resistance to PVY, one on chromosome XI and the other on XII, have been identified and used in breeding. The latter corresponds to a well-known source of resistance (Solanum stoloniferum), whereas the one on chromosome XI was reported from S. stoloniferum and S. tuberosum group Andigena as well. To elucidate its taxonomic origin in our breeding lines, we analyzed the nucleotide sequences of tightly linked markers (M45, M6) and screened 251 landraces of S. tuberosum group Andigena for the presence of this gene. Our results indicate that the PVY resistance allele on chromosome XI in our breeding lines originated from S. tuberosum group Andigena. We have developed two marker assays to accelerate the introgression of Ry_adg gene into breeding lines by marker-assisted selection (MAS). First, we have multiplexed RYSC3, M6 and M45 DNA markers flanking the Ry_adg gene and validated it on potato varieties with known presence/absence of the Ry_adg gene and a progeny of 6,521 individuals. Secondly, we developed an allele-dosage assay particularly useful to identify multiplex Ry_adg progenitors. The assay based on high-resolution melting analysis at the M6 marker confirmed Ry_adg plex level as nulliplex, simplex and duplex progenitors and few triplex progenies. These marker assays have been validated and can be used to facilitate MAS in potato breeding.

     

Direct Inhibition of <Emphasis Type="Italic">Col</Emphasis> E<Subscript>1</Subscript> Plasmid DNA Replication in <Emphasis Type="Italic">Escherichia coli</Emphasis> by Rifampicin

COLICINOGENIC factor E₁ (Col E₁) is a small bacterial plasmid (4.2×10⁶ daltons) present in colicinogenic strains of Escherichia coli¹ to the extent of about twenty-four copies per cell (Clewell and Helinski, unpublished results), which continues to replicate in the presence of high levels of chloramphenicol, a specific inhibitor of protein synthesis, although the chromosome only completes current rounds of replication and ceases (Clewell and Helinski, unpublished results). The average rate of Col E₁ semiconservative replication in the absence of protein synthesis is, in certain conditions, faster than (as much as eight times) the normal rate of synthesis (Clewell, unpublished results). Replication continues for 10–15 h after the addition of chloramphenicol, resulting in nearly 3,000 copies of Col E¹ DNA per cell. We are taking advantage of this system to study the effects of a number of antibiotics on DNA replication and now report evidence that rifampicin (an active semisynthetic derivative of rifamycin B)², an antibiotic known specifically to inhibit bacterial DNA dependent RNA polymerase^3–6, has a dramatic inhibitory effect on Col E¹ DNA replication.     

Construction of flavocytochrome <Emphasis Type="Italic">b</Emphasis><Subscript>2</Subscript>-overproducing strains of the thermotolerant methylotrophic yeast <Emphasis Type="Italic">Hansenula polymorpha</Emphasis> (<Emphasis Type="Italic">Pichia angusta</Emphasis>)

L-Lactate cytochrome c oxidoreductase (flavocytochrome b ₂, FC b ₂) from the thermotolerant methylotrophic yeast Hansenula polymorpha (Pichia angusta) is, unlike the enzyme form baker’s yeast, a thermostable enzyme potentially important for bioanalytical technologies for highly selective assays of L-lactate in biological fluids and foods. This paper describes the construction of flavocytochrome b ₂ producers with over-expression of the H. polymorpha CYB2 gene, encoding FC b ₂. The HpCYB2 gene under the control of the strong H. polymorpha alcohol oxidase promoter in a plasmid for multicopy integration was transformed into the recipient strain H. polymorpha C-105 (grc1 catX), impaired in glucose repression and devoid of catalase activity. A method was developed for preliminary screening of the transformants with increased FC b ₂ activity in permeabilized yeast cells. The optimal cultivation conditions providing for the maximal yield of the target enzyme were found. The constructed strain is a promising FC b ₂ producer characterized by a sixfold increased (to 3 μmol min^?1 mg^?1 protein in cell-free extract) activity of the enzyme.     

Modeling zigzag CNT: dependence of structural and electronic properties on length,and application to encapsulation of HCN and C<Subscript>2</Subscript>H<Subscript>2</Subscript>

Density functional theory (B3LYP, B3LYP-D2 and wB97XD functionals) was used in finite models of zigzag carbon nanotubes (CNT), (n,0)×k with n?=?6–9 and k?=?2–4, to systematically investigate the effects of size on their structural and electronic properties. We found that the ratio between the length (L _t) and the diameter (d _t) of the pristine CNT has to be larger than 2, i.e., L _t/d _t?>?2, in order to provide the observed experimental trends of C=C bond distances, as well as to maintain the atomic charges nearly constant and zero around the center of the tube. Therefore, the concepts of useful length and volume were developed and tested for the encapsulation process of HCN and C₂H₂ into CNTs. The energies involved in these processes, as well as the changes in molecular structure and electronic properties of the dopants and the CNTs are discussed and rationalized by the amount of charge transferred between dopant and CNT.

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Graphical Abstract Illustration of zigzag CNT length and diameter ratio in order to represent C=C bond experimental trend

     

On the nature of the domination of oligomeric (dA:dT)<Subscript><Emphasis Type="Italic">n</Emphasis></Subscript> tracts in the structure of eukaryotic genomes

The comparative analysis of the frequency of oligomeric W- and S-tracts was conducted in the genomes of different eukaryotic species that differ in their GC-composition. The domination of mononucleotide and mixed (A/T) _n -sequences compared with (G/C) _n -sequences was detected in the studied eukaryotic genomes, including Dictyostelium discoideum (GC ~ 25.7%), Caenorhabditis elegans (GC ~ 36.9%), Arabidopsis thaliana (GC ~ 38.0%), Drosophila melanogaster (GC ~ 38.8%), Homo sapiens (GC ~ 40.0%), Gallus gallus (GC ~ 50.0%), Leishmania major (GC ~ 59.1%). Using the results of quantum–chemical calculations, a theoretical rationale of the important role of existing differences in the initial hidden structural polymorphism of the hydrogen bonding of the Watson–Crick AT and GC pairs in the development of this phenomenon is given. It is concluded that a decreased structural polymorphism of AT pairs compared with the high fourfold polymorphism of the main state of GC pairs may be the most probable source of the preference and reliability of the “use” of AT pairs by nature in genomic DNA of many species.     

Bonding,aromaticity, and planar tetracoordinated carbon in Si<Subscript>2</Subscript>CH<Subscript>2</Subscript> and Ge<Subscript>2</Subscript>CH<Subscript>2</Subscript>

Natural bond orbital (NBO) analyses and dissected nucleus-independent chemical shifts (NICS _{π z z} ) were computed to evaluate the bonding (bond type, electron occupation, hybridization) and aromatic character of the three lowest-lying Si₂CH₂ (1-Si, 2-Si, 3-Si) and Ge₂CH₂ (1-Ge, 2-Ge, 3-Ge) isomers. While their carbon C₃H₂ analogs favor classical alkene, allene, and alkyne type bonding, these Si and Ge derivatives are more polarizable and can favor “highly electron delocalized”? and “non-classical”? structures. The lowest energy Si ₂CH₂ and Ge ₂CH₂ isomers, 1-Si and 1-Ge, exhibit two sets of 3–center 2–electron (3c-2e) bonding; a π-3c-2e bond involving the heavy atoms (C–Si–Si and C–Ge–Ge), and a σ-3c-2e bond (Si–H–Si, Ge–H–Ge). Both 3-Si and 3-Ge exhibit π and σ-3c-2e bonding involving a planar tetracoordinated carbon (ptC) center. Despite their highly electron delocalized nature, all of the Si₂CH₂ and Ge₂CH₂ isomers considered display only modest two π electron aromatic character (NICS(0) _{π z z} =--6.2 to –8.9 ppm, computed at the heavy atom ring center) compared to the cyclic-C ₃H₂ (–13.3 ppm).

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Graphical Abstract The three lowest Si2CH2 and Ge2CH2 isomers.

     

Simple generalisation of a mesophyll resistance model for various intracellular arrangements of chloroplasts and mitochondria in C<Subscript>3</Subscript> leaves

The classical definition of mesophyll conductance (g _m) represents an apparent parameter (g _m,app) as it places (photo)respired CO₂ at the same compartment where the carboxylation by Rubisco takes place. Recently, Tholen and co-workers developed a framework, in which g _m better describes a physical diffusional parameter (g _m,dif). They partitioned mesophyll resistance (r _m,dif = 1/g _m,dif) into two components, cell wall and plasmalemma resistance (r _wp) and chloroplast resistance (r _ch), and showed that g _m,app is sensitive to the ratio of photorespiratory (F) and respiratory (R _d) CO₂ release to net CO₂ uptake (A): g _m,app = g _m,dif/[1?+?ω(F?+?R _d)/A], where ω is the fraction of r _ch in r _m,dif. We herein extend the framework further by considering various scenarios for the intracellular arrangement of chloroplasts and mitochondria. We show that the formula of Tholen et al. implies either that mitochondria, where (photo)respired CO₂ is released, locate between the plasmalemma and the chloroplast continuum or that CO₂ in the cytosol is completely mixed. However, the model of Tholen et al. is still valid if ω is replaced by ω(1?σ), where σ is the fraction of (photo)respired CO₂ that experiences r _ch (in addition to r _wp and stomatal resistance) if this CO₂ is to escape from being refixed. Therefore, responses of g _m,app to (F?+?R _d)/A lie somewhere between no sensitivity in the classical method (σ =1) and high sensitivity in the model of Tholen et al. (σ =0).     

Polyhydroxylated steroid compounds from the Far Eastern starfish <Emphasis Type="Italic">Distolasterias nipon</Emphasis>

Two new steroid glycosides: distolasteroside D₆, (24S)-24-O-(β-D-xylopyranosyl)-5α-cholestane-3β,6α,8,15β,16β,24-hexaol, and distolasteroside D₇, (22E,24R)-24-O-(β-D-xylopyranosyl)-5α-cholest-22-ene-3β,6α,8,15β,24-pentaol were isolated along with the previously known distolasterosides D₁, D₂, and D₃, echinasteroside C, and (25S)-5α-cholestane-3β4β,6α,7α,8,15α,16β,26-octaol from the Far Eastern starfish Distolasterias nipon. The structures of new compounds were elucidated by NMR spectroscopy and MALDI TOF mass spectrometry. Like neurotrophins, distolasterosides D₁, D₂, and D₃ were shown to induce neuroblast differentiation in a mouse neuroblastoma C1300 cell culture.     

Characterization of harpin<Subscript>Xoo</Subscript> induced hypersensitive responses in non host plant,tobacco

Harpin proteins encoded by hrp genes are bacterial protein elicitors that can stimulate hypersensitive response (HR) in non-host plants. HR-related pathogen resistance involves a complex form of programmed cell death (PCD). It is increasingly viewed as a key component of the hypersensitive disease response of plants. Currently, the evidence of harpin proteins-induced PCD is deficient though it exhibits phenotypic parallels with HR, and the mechanism of harpin proteins-induced PCD is not well understood. In this study, we demonstrate that harpin_Xoo protein from Xanthomonas oryzae pv. oryzae of rice bacterial blight expressed and isolated from bacterial cells acted as an agent to induce PCD in infiltrated tobacco plants. Treatment of tobacco leaves with harpin_Xoo induced typical PCD-related morphological and biochemical changes including cell shrinkage and nuclear DNA degradation. We further analyzed the expression of several genes in signal transduction pathway of PCD in tobacco plants by real-time qRT-PCR analysis using EF-1α as an endogenous control. Our results showed that the expression of NtDAD1 was down-regulated and the expression of BI-1, tpa1 and aox1 was up-regulated following the infiltration of harpin_Xoo into tobacco leaves. Our data suggest that harpin_Xoo can induce PCD with the coordination of PCD-related genes in infiltrated tobacco leaves, providing evidence to further investigate the signal transduction pathways of HR and PCD.     

Theoretical investigation on exciton-dissociation and charge-recombination processes of PC<Subscript>61</Subscript>BM-PTDPPSe interface

Designing and synthesizing novel electron-donor polymers with the high photovoltaic performances has remained a major challenge and hot issue in organic electronics. In this work, the exciton-dissociation (k _dis ) and charge-recombination (k _rec ) rates for the PC₆₁BM-PTDPPSe system as a promising polymer-based solar cell candidate have been theoretically investigated by means of density functional theory (DFT) calculations coupled with the non-adiabatic Marcus charge transfer model. Moreover, a series of regression analysis has been carried out to explore the rational structure–property relationship. Results reveal that the PC₆₁BM-PTDPPSe system possesses the large open-circuit voltage (0.77 V), middle-sized exiton binding energy (0.457 eV), and relatively small reorganization energies in exciton-dissociation (0.273 eV) and charge-recombination (0.530 eV) processes. With the Marcus model, the k _dis , k _rec , and the radiative decay rate (k _s ), are estimated to be 3.167×10¹¹ s^?1, 3.767×10¹⁰ s^?1, and 7.930×10⁸ s^?1 respectively in the PC₆₁BM-PTDPPSe interface. Comparably, the k _dis is as 1～3 orders of magnitude larger than the k _rec and the k _s , which indicates a fast and efficient photoinduced exciton-dissociation process in the PC₆₁BM-PTDPPSe interface.

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Graphical Abstract PTDPPSe is predicted to be a promising electron donor polymer, and the PC₆₁BM-PTDPPSe system is worthy of further device research by experiments.