PNA<Subscript>2</Subscript>/DNA Triplexes: Stability and Specificity

The review considers the properties and some applications of complexes formed by peptide nucleic acid (PNA) molecules with complementary DNA sites, with emphasis on the structure and properties of PNA₂/DNA triplexes.__________Translated from Genetika, Vol. 41, No. 7, 2005, pp. 869–883.Original Russian Text Copyright © 2005 by Krupnik, Lazurkin.     

Changes in the properties of oily gray forest soil during biological reclamation

Biological reclamation of gray forest soil severely contaminated by separator oil using Bacispecin was demonstrated. Agrophysical, agrochemical, physicochemical, and biological properties of the soil were restored in the plow layer during the reclamation.Translated from Izvestiya Akademii Nauk, Seriya Biologicheskaya, No. 1, 2005, pp. 109–115.Original Russian Text Copyright © 2005 by Suleimanov, Gabbasova, Sitdikov.     

Actinomycete complexes in the rhizosphere of winter rye on soddy podzolic soil

The structure of actinomycete complexes in the rhizosphere of winter rye (Secale cereale L.) varieties originating from different ecosystems and geographical zones was studied in field experiments on soddy podzolic soil. In addition to streptomycetes, the complexes studied contained actinomycetes of the genera Micromonospora and Streptosporangium, represented at high occurrence and comparable abundance rates. The rhizosphere of most of the studied rye varieties was dominated by micromonosporas. The antifungal potential of mycelial prokaryotes associated with winter rye was assessed. The taxonomic and functional structure of actinomycete complexes was shown to be similar in rye varieties originating from the nonchernozem zone of Russia. However, the actinomycete complex proved to be much different in the rye variety that developed in the steppe zone of the lower Volga region.__________Translated from Mikrobiologiya, Vol. 74, No. 2, 2005, pp. 271–277.Original Russian Text Copyright © 2005 by Shirokikh, Merzaeva.     

Enzymatic synthesis of a conducting complex of polyaniline and poly(2-acrylamido-2-methyl-1-propanesulfonic acid) using palm tree peroxidase and its properties

An enzymatic method of producing a conducting polyelectrolyte complex of polyaniline (PANI) and poly(2-acrylamido-2-methyl-1-propanesulfonic acid) (PAMPS) was developed. Acidic stable peroxidase isolated from royal palm tree (Roystonea regia L.) leaves was used as a catalyst in the oxidative polymerization of aniline at pH 2.8. The synthesis procedure was optimized. Spectroscopic and electrochemical characteristics of nanoparticles of obtained PANI/PAMPS complexes at different pH were studied. It was shown that the acidity of the medium affects their properties.__________Translated from Prikladnaya Biokhimiya i Mikrobiologiya, Vol. 41, No. 3, 2005, pp. 283–287.Original Russian Text Copyright © 2005 by Mazhugo, Caramyshev, Shleev, Sakharov, Yaropolov.     

Spectral properties and the number of photosynthetic reaction centers in chlorophyll-deficient mutants of <Emphasis Type="Italic">Pisum sativum</Emphasis>

Spectral and photochemical properties were analyzed on intact chloroplasts and pigment-protein complexes isolated with gel electrophoresis from pea (Pisum sativum L.) leaves of parental variety Torsdag and of chlorophyll-deficient mutants chlorotica 2004 and 2014. Measurements of chlorophyll absorption and fluorescence spectra and of second derivative low-temperature (–196°C) spectra clarified exact positions of fluorescence maxima and revealed the chlorophyll forms of individual complexes in samples investigated. The chlorotica 2004 mutant, whose hybrids yield the heterosis effect, was characterized by the decreased accumulation of chlorophyll forms absorbing at 690, 697, and 708 nm, known to constitute the core antenna in the vicinity of photosystem I (PSI) reaction center. In the chlorotica 2014 mutant, whose hybrids are low productive, the interaction between PSI and PSII complexes was weakened, but no other difference from the parental variety was observed. The analysis of PSI and PSII photochemical activities, as well as estimates of light-harvesting antenna size and the number of reaction centers revealed that the chlorotica 2004 mutant is deficient in the number of PSI reaction centers by a factor of 1.7. This deficiency resulted from the mutation-induced disorder in biosynthesis of chlorophyll a-protein complex of PSI. It appears that gene interactions between the 2004 mutant and the parental variety Torsdag enhance the functional and metabolic activity of leaves in their hybrids, thereby yielding the heterosis effect.Translated from Fiziologiya Rastenii, Vol. 52, No. 2, 2005, pp. 172–183.Original Russian Text Copyright © 2005 by Ladygin, Vaishlya.This revised version was published online in April 2005 with a corrected cover date.     

Physicochemical and biological factors affecting atmospheric methane oxidation in gray forest soils

The decline of methane oxidizing activities in gray forest soil upon its conversion into arable land was shown to be caused by major changes in biotic and physicochemical properties of soil. Using the method of immune serums, methane-oxidizing bacteria were detected in both forest and agricultural soils, but their populations differed significantly in both abundance and composition. In the forest soil, the number of methanotrophs was an order of magnitude higher than in arable soil, amounting to 3.5 × 10⁸ and 0.24 × 10⁸ cells/g soil, respectively. All methane-oxidizing bacteria identified in the forest soil belonged to the genus Methylocystis, and 94% of these were represented by a single species, M. parvus. The arable soil was dominated by type I methanotrophs (Methylobacter and Methylomonas, 67.6%), occurring along with bacteria of the genus Methylocystis. In addition, arable soil is characterized by a low content of microbial biomass, lower porosity and water resistance of soil aggregates, and the predominance of nitrogen mineralization processes over those of nitrogen immobilization. These factors can also contribute to lower rates of methane oxidation in arable soil as compared to forest soil.__________Translated from Mikrobiologiya, Vol. 74, No. 2, 2005, pp. 255–260.Original Russian Text Copyright © 2005 by Kravchenko, Semenov, Kuznetsova, Bykova, Dulov, Pardini, Gispert, Boeckx, Cleemput, Galchenko.     

Metal-humic complexes and plant micronutrient uptake: a study based on different plant species cultivated in diverse soil types

There are several studies in the literature dealing with the effect of metal-humic complexes on plant metal uptake, but none of them correlate the physicochemical properties of the complexes with agronomic results. Our study covers both aspects under various experimental conditions. A humic extract (SHE) obtained from a sapric peat was selected for preparing the metal–humic complexes used in plant experiments. Fe–, Zn– and Cu–humic complexes with a reaction stoichiometry of 2:0.25 (humic:metal, w/w) were chosen after studying their stability and solubility with respect to pH (6–9) and the humic:metal reaction stoichiometry. Wheat and alfalfa plants were greenhouse cultured in pots containing one of three model soils: an acid, sandy soil and two alkaline, calcareous soils. Treatments were: control (no additions), SHE (53 mg kg^–1 of SHE), and metal (Cu, Zn and Fe)–SHE complexes (2.5 and 5 mg kg^–1 of metal rate and a SHE concentration to make 53 mg kg ^–1). Cu- and Zn–humic complexes significantly (p0.05) increased the plant uptake and the DTPA-extractable soil fraction of complexed micronutrients in most plant–soil systems. However, these effects were associated with significant increases (p0.05) of shoot and root dry weight only in alfalfa plants. In wheat, significant increases of root and shoot dry matter were only observed in the Cu–humic treated plants growing in the acid soil, where Cu deficiency was more intense. The Fe–humic complex did not increase Fe plant assimilation in any plant–soil system, but SHE increased Fe-uptake and/or DTPA-extractable soil Fe in the wheat–calcareous soil systems. These results, taken together with those obtained from the study of the pH- and SHE:metal ratio-dependent SHE complex solubility and stability, highlight the importance of the humic:Fe complex stoichiometry on iron bioavailability as a result of its influence on complex solubility.     

Soil property,CO2 emission and aridity index as agroecological indicators to assess the mineralization of cover crop green manure in a Mediterranean environment

In this study soil chemical and biochemical properties, cover crop biomass production and quality, and climatic factors (AI) have been taken into account in order to identify sensitive agroecological indicators suitable for an early assessment of green manuring outcomes, measured in terms of soil CO₂ emission and soil mineralization dynamics in a short term experiment in a Mediterranean environment. The field experiment was conducted over two cropping rotations during 2004–2005 in central Italy. A winter cover crop/sweet pepper sequence with the cover crop used as green manure was adopted. The cover crop treatments were common vetch (CV), rye grass (RG), and fallow soil as the control (Control). Soil enzyme activities (acid phosphatase. protease and β-glucosidase), CO₂ emission, and inorganic nitrogen concentrations were monitored from cover crop green manure incorporation to pepper harvesting in order to evaluate soil mineralization dynamics. The climatic conditions were summarized by the monthly aridity index (AI) calculated as the precipitation/temperature ratio. A group of mineralization indexes, calculated using values of available nitrogen and enzyme activities, was used to describe the soil process during crop cycle after green manure. The mineralization process dynamic results as a combined effect of climatic conditions and soil organic matter quality produced by different cover crop green manures. The common vetch green manuring was effective in lowering the soil C/N with respect to the control soil (5.7 vs. 8.3 and 8.5 vs. 12.1 in 2004 and 2005, respectively), promoting CO₂ emission (8.95 vs. 5.19 and 6.75 vs. 4.28 Mg CO₂-C ha⁻¹ in 2004 and 2005, respectively), enzyme activity, nitrogen release, and crop aboveground biomass (8.59 vs. 7.05 Mg ha⁻¹ dry matter). Among the selected agroecological indicators, the relationships between enzyme activities and the monthly aridity index may suggest a new approach for agronomists and soil scientists to understand the combined effect of temperature and precipitation on soil mineralization dynamic. The high aridity index at the time of green manuring may have caused a priming effect of SOM and promoted soil mineralization during the vegetable crop growing season in a Mediterranean environment. Finally, no evidence was found between soil CO₂ emission and the aridity index; soil respiration was mainly affected by cover crop biomass and the soil C/N ratio.     

Synthesis, spectroscopy, electrochemistry and thermal study of vanadyl unsymmetrical Schiff base complexes

The new tetradentate unsymmetrical N₂O₂ Schiff base ligands and VO(IV) complexes were synthesised and characterized by using IR, UV-Vis and elemental analysis. The electrochemical properties of the vanadyl complexes were investigated by means of cyclic voltammetry. The oxidation potentials are increased by increasing the electron-withdrawing properties of functional groups of the Schiff base ligands according to the trend of MeO < H < Br < NO₂. The thermogravimetry (TG) and differential thermoanalysis (DTA) of the VO(IV) complexes were carried out in the range of 20-700 °C. The complexes were decomposed in two stages. Also decomposition of synthesised complexes is related to the Schiff base characteristics. The thermal decomposition of the studied reactions was first order.     

Synthesis, X-ray crystal structures and linear and nonlinear optical characterization of a series of nickel(II) and copper(II) salicylaldiminato complexes

A series of nickel(II) and copper(II) salicylaldiminato complexes containing side arms with either potentially coordinating (OH) or non-coordinating (Cl) functional groups have been prepared and characterized by X-ray crystallography. The Cu(II) complexes are square planar, but the Ni(II) complexes prefer octahedral coordination. Linear absorption spectra depend on the metal and on its coordination geometry, with the octahedral Ni(II) complexes being the most weakly absorbing at 532 nm and the square planar Cu(II) complexes being the most strongly absorbing at 532 nm. The third-order nonlinear optical properties of the complexes have been characterized using degenerate four-wave mixing (DFWM) and Z-scan. Two different Z-scan experimental configurations were used, one of which employs a Gaussian beam in a tightly focused geometry while the other employs a top-hat beam and a more relaxed focus. The observed third-order optical nonlinearity is primarily due to transient thermal (photo-acoustic) effects associated with linear absorption in the samples. The dependence of the third-order nonlinear optical properties on the linear absorption means that the nonlinear optical properties vary substantially between the complexes even though they all contain the same chromophore. The hyperpolarizability of one of the complexes, γ = 1.3 × 10⁻³⁰ esu, rivals the nonlinearities measured at 532 nm in expanded porphyrin and phthalocyanine complexes.     

Potentiometric measurement of stability constants of complexes between fulvic acid carboxylate and Fe3+

The stability constants of complexes formed between iron (III) and fulvic acid extracted from organic manures and wastes such as urban domestic sewage sludge, farmyard manure, poultry manure and sulfitation pressmud were investigated by the potentiometric titration method in an ionic medium of 0.1 M KNO₃ at 25±1 °C. A modification of the Katchalsky's model was employed for the estimation of stability constants. The displacement of the titration curves due to presence of Fe³⁺ in FA solutions formed the basis of calculations. The weak acidic property of fulvic acids due to carboxyl groups resulted in buffering over a wide range of pH; fulvic acids were completely neutralized in the pH range of 7.00–8.85. Apparent dissociation constants (pK_APP) of weakly acidic carboxyl groups were a direct function of degree of dissociation (α_L) in the mid-range of titration curves but were non-linear at high and low α_L values. The stability constants for formation of Fe–FA complexes (log β_Fe) calculated from the titration data were in the range of 5.64–7.55, depending upon α_L and electrostatic properties of fulvic acids. The relatively high stability constants of Fe–FA complexes in comparison to those with other competing cations suggest that the Fe–FA complexes are relatively stable in a soil environment. This revised version was published online in June 2006 with corrections to the Cover Date.     

Artificial shiro formation of Tricholoma matsutake

One type of soil collected from Maoer-shan in Heilongjiang Province, China was selected to induce hyphal growth of Tricholoma matsutake by a soil screening experiment. It was confirmed that hyphal growth of all the tested T. matsutake isolates was significantly stimulated in soil by supplemented with 0.5%∼2.0% olive oil. The aggregation of hyphae and soil resembled natural Shiro. The biomass of hyphae in the soil increases with increasing olive oil concentrations. Moreover, seedlings of Pinus densiflora grew well in the soil containing 0.5%∼1.0% olive oil and were also successfully infected by T. matsutake isolate A in the soil containing 1.0% olive oil. This study established a culture system of artificial Shiro formation and also provided a premise for formulation of culture substratum for fruit body formation of T. matsutake. __________ Translated from Mycosystema 2005, 24(2): 267–276 [译自: 菌物学报, 2005, 24(2): 267–276]     

Physical and chemical characterization of soil and poultry litter humic and fulvic metal complexes

Summary Humic and fulvic-zinc complexes obtained from soil and poultry litter were characterized by I.R. spectroscopy, determination of stability constant and the free energy change associated with their formation. Infrared spectroscopy confirmed that both electrovalent, coordinate-covalent bonds of Zn²⁺ with the carboxylate, phenolic hydroxyl and amine groups lead to the formation of their stable complexes. This is evident from the changes in absorption bands at 1700 cm^–1, 1725 cm^–1, 1625 cm^–1 and 1400 cm^–1 of their infrared spectra.The stability constants of complexes are pH-dependent. Interaction of Zn with humic and fulvic acid involved the formation of mononuclear complexes. The values of stability constants of these complexes are lower than those reported earlier.The calculation of the free-energy change associated with salts and complex formation indicates the spontaneity of both reactions, although a higher probability of complex reaction than that of salt formation is evident. The implications of the complexation of metal ions by these naturally occurring polydisperse plyaanions in regulating the movement of metal ions from the ambient soil matrix to plant roots and biological system in terresterial and aquatic environments are indicated.Journal paper no. 2, Department of Soil Science and Agricultural Chemistry, Rajendra Agricultural University, Tirhut College of Agriculture, Dholi, Muzaffarpur, Bihar, India.     

Contribution of root respiration to soil respiration in a C3/C4 mixed grassland

The spatial and temporal variations of soil respiration were studied from May 2004 to June 2005 in a C₃/C₄ mixed grassland of Japan. The linear regression relationship between soil respiration and root biomass was used to determine the contribution of root respiration to soil respiration. The highest soil respiration rate of 11-54 Μmol m^-2 s^-1 was found in August 2004 and the lowest soil respiration rate of 4.99 Μmol m^-2 s^-1 was found in April 2005. Within-site variation was smaller than seasonal change in soil respiration. Root biomass varied from 0.71 kg m^-2 in August 2004 to 102 in May 2005. Within-site variation in root biomass was larger than seasonal variation. Root respiration rate was highest in August 2004 (5.7 Μmol m^-2 s^-1) and lowest in October 2004 (1.7 Μmol m^-2 s^-1). Microbial respiration rate was highest in August 2004 (5.8 Μmol m^-2 s^-1) and lowest in April 2005 (2.59 Μmol m^-2 s^-1). We estimated that the contribution of root respiration to soil respiration ranged from 31% in October to 51% in August of 2004, and from 45% to 49% from April to June 2005.     

Cationic oligopeptides modified with lipophilic fragments: Use for DNA delivery to cells

Cationic oligopeptides, including the amphipathic -helical peptides, are applied to the targeted delivery of DNA to eukaryotic cells due to their DNA-compacting properties and the ability to destabilize the cell lipid bilayer in some cases. We synthesized the peptides differing in the number and location of residues of decanoic acid covalently attached to Lys residues in order to combine the DNA-binding and the membrane activities in a single molecule. We chose peptide structures that assisted in the formation of helices. The DNA-binding ability of the peptides and the membrane activity of their complexes with DNA were shown to depend on the structure. The study of erythrocyte hemolysis by complexes with DNA of the pCMV LacZ plasmid and the peculiarities of transfection of these complexes revealed a correlation between the hemolytic activity and the expression level of the lacZ gene in cells.Translated from Bioorganicheskaya Khimiya, Vol. 31, No. 1, 2005, pp. 22–30.Original Russian Text Copyright © 2005 by Guryanov, Vlasov, Lesina, Kiselev, Baranov, Avdeeva, Vorobev.     

Ecosystem Properties of Urban Land Covers at the Aboveground–Belowground Interface

Understanding of ecological differences among urban land covers can guide the sustainable management of urbanized landscapes for conservation of ecosystem services. The objective of our study was to compare ecosystem properties at the aboveground–belowground interface of three land-cover types commonly found in residential landscapes: lawns, bark mulch, and gravel mulch. Using unmowed vegetation as a reference land cover, we measured surface soil variables (to 5 cm depth), CO₂ fluxes, and ground temperatures in experimental field plots within 3 years after their creation. Each land cover had a distinctive set of ecosystem properties. Mulched plots had significantly warmer soil and surface temperatures, wetter soils and faster surface litter decomposition than vegetated plots. Variables associated with soil C and earthworm numbers were consistently lowest in gravel-covered soils, whereas bark mulch plots had highest earthworm abundances, lowest soil bulk density, and temporally variable soil organic matter dynamics. Compared to unmowed plots, lawns had higher soil carbon, CO₂ fluxes, and temperatures but lower earthworm abundances especially during 2005 drought conditions. We conclude that ecosystem properties of the land covers were influenced by the composition, density, and arrangement of materials comprising their aboveground habitat structures. We discuss our results within an ecosystem services framework and suggest that interpretations of our findings depend on in situ urban environmental contexts and landscape management objectives. Future studies of urban land covers, their ecosystem properties and associated ecosystem services are needed to help provide a scientific basis for sustainable urban landscape management. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users. Loren B. Byrne conceived of the study, performed research, and analyzed data. Loren B. Byrne, M. A. Bruns and K. C. Kim designed the study and wrote the article.     

The Antibiotic-Aided Distinguishing of Fungal and Bacterial Substrate-Induced Respiration in Various Soil Ecosystems

Fungal and bacterial substrate-induced respiration have been distinguished in gray forest and chestnut soils in various ecosystems (forest, grassland, arable soil, fallow land, and shelterbelt) using the antibiotics cycloheximide and streptomycin. The optimal inhibitory concentrations of the antibiotics, added separately and in combination; the preincubation time of the antibiotics with the soil before glucose addition; and the mass of added inert material (talc) have been determined. The inhibitor additivity ratio (IAR) has been calculated for the antibiotics. With the IAR differing from 1.0 by a value of more than 5%, the fungal and bacterial substrate-induced respiration cannot be distinguished reliably. Respiration measurements show that the microbial communities of natural ecosystems are dominated by fungi (81–95% on average). The smallest amount of fungi (54–59%) is found in the arable soil ecosystem.__________Translated from Mikrobiologiya, Vol. 74, No. 3, 2005, pp. 394–400.Original Russian Text Copyright © 2005 by Susyan, Ananyeva, Blagodatskaya.     

茂兰喀斯特森林不同地形植物多样性与土壤理化特征研究

为探讨不同地形植物群落物种多样性与土壤理化特征之间的相互关系。该文以茂兰喀斯特森林为研究对象,分析了不同地形植物多样性与土壤理化特征以及两者之间的相互关系。结果表明:(1)不同地形木本植物的物种组成存在差异,坡地木本植物有35科65属78种,槽谷木本植物有38科64属89种,漏斗木本植物有35科61属84种。同时,丰富度指数、多样性指数、均匀度指数大小表现为槽谷漏斗坡地;优势度指数大小表现为坡地漏斗槽谷。(2)不同地形土壤物理性质差异性显著(P0.05),其中土壤容重和非毛管孔隙度表现为坡地槽谷漏斗,自然含水量、田间持水量、总孔隙度、毛管孔隙度等指标均表现为漏斗槽谷坡地。(3)除全K外,大多数土壤养分指标表现为漏斗显著高于槽谷、坡地,即漏斗槽谷坡地。(4)冗余分析表明,植物多样性与土壤理化性质具有相关性,不同地形植物多样性指数受土壤理化性质的影响明显。以上结果旁证了茂兰喀斯特森林地形条件的复杂性和土壤理化性质的差异性是该区小生境多样、物种组成丰富的原因之一,为喀斯特森林物种多样性维持机制提供了科学依据。     

Some effects of plant ash on the chemical properties of soils and aqueous suspensions

Summary Laboratory studies indicate that percolation of water through accretions of plant ash will markedly increase the pH of solutions entering the underlying soil. Ash derived from graminaceous straws raised the pH of an aqueous suspension (1 g ash: 500 ml H₂O) to 10.6, compared to 9.3 for a saturated solution of CaCO₃. However, on a weight basis these ashes possess only approximately 5–15% of the alkalising power of CaCO₃ in terms of their ability to neutralise acid or elevate soil pH. The effect of ash on soil pH, and pH dependent soil properties, is determined by the amount and composition of the ash deposited and on the buffering capacity of the soil.High field rates (2480–6750 kg ha^–1) of ash added to a podzolic soil increased the pH of the soil solution by up to 3 units. A pH rise of 1 unit is sufficient to increase the solubility of native soil organic carbon (O.C.) in water (i.e. mobilize readily metabolizable microbial substrate) and stimulate respiration rate.In more strongly buffered krasnozem soil, maximum rise in pH of the soil solution did not exceed 0.7 unit. However, even such small pH shifts significantly reduced the solubility of soil O.C. in water; probably by changing the character (and hence solubility) of organo-mineral chelation complexes. High rates of ash application also slightly decreased respiration rate in this soil type.The application of neutralized ash, which added metal ions to the soil solution, had a similar but smaller effect to unneutralized ash on the solubility of soil O.C. in podzolic soil, but little effect in krasnozem soil.     

The processes of methane production and oxidation in the soils of the Russian Arctic tundra

Methane emission from the following types of tundra soils was studied: coarse humic gleyey loamy cryo soil, peaty gleyey soil, and peaty gleyey midloamy cryo soil of the arctic tundra. All the soils studied were found to be potential sources of atmospheric methane. The highest values of methane emission were recorded in August at a soil temperature of 8–10°C. Flooded parcels were the sources of atmospheric methane throughout the observation period. The rates of methane production and oxidation in tundra soils of various types were studied by the radioisotope method at 5 and 15°C. Methane oxidation was found to occur in bog water, in the green part of peat moss, and in all the soil horizons studied. Methane production was recorded in the horizons of peat, in clay with plant roots, and in peaty moss dust of the bogey parcels. At both temperatures, the methane oxidation rate exceeded the rate of methane production in all the horizons of the mossy-lichen tundra and of the hillock tundra with flat-bottom depressions. Methanogenesis prevailed only in a sedge-peat moss bog at 15°C. Bacterial enrichment cultures oxidizing methane at 5 and 15°C were obtained. Different types of methanotrophic bacteria were shown to be responsible for methane oxidation under these conditions. A representative of type I methylotrophs oxidized methane at 5°C, and Methylocella tundrae, a psychroactive representative of an acidophilic methanotrophic genus Methylocella, at 15°C.__________Translated from Mikrobiologiya, Vol. 74, No. 2, 2005, pp. 261–270.Original Russian Text Copyright © 2005 by Berestovskaya, Rusanov, Vasileva, Pimenov.