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.     

Calf thymus composition: a comparison of differential centrifugation and chemical fractionation procedures

The extraction behavior of thymus and the composition of fractions prepared from this organ has been studied. Sequential extraction methods using 0.15 M NaCl followed by water gave information with respect to the weight fraction of cytoplasmic and nuclear constituents. Lipide, nucleic acid, and electrophoretic analysis of the extracts provided additional information. A less complex electrophoretic pattern was obtained from subsequent extracts in the sequence. Sucrose and saline dispersates obtained from tissue fragmented with either the Potter-Elvehjem homogenizer or in a Waring blendor were fractionated, using standard differential sedimentation methods. The fractions obtained by means of four different dispersion procedures were compared in terms of yield, chemical analysis, and electrophoretic composition. The quantity of material in thymus having the sedimentation characteristics of liver mitochondrial and microsomal fractions was remarkably small. Both the suspension medium employed and the method used to bring about a disruption of the cells in the tissue affected the yield of "particulate" material. The components present in the later extracts in the sequence, E(4) to E(7), in the case of sequential extraction study resembled with respect to chemical composition and electrophoretic characteristics, the microsome fraction prepared by differential sedimentation methods. About 76 per cent of the PNA in the tissue appeared to be in the cytoplasm. The remaining 24 per cent PNA was found in the nucleus and accounted for 1.7 per cent of nucleus on a dry weight basis. From 75 to 88 per cent of cytoplasmic PNA was extracted from the tissue and 76 to 94 per cent of the PNA in the extract was found in the final supernatant solutions, depending upon the dispersion methods and suspension medium used in the extraction procedure. The composition of the final supernatant fractions using differential sedimentation methods were comparable in terms of electrophoretic properties, protein concentration, nucleic acid content, and fractionation behavior to saline extracts E(1) to E(3), of thymus used in earlier studies.     

Heterogeneity of lipopolysaccharides from Yersinia pseudotuberculosis: chemical characterization of various molecular types

Prior studies have shown some unusual changes in the lipopolysaccharides (LPSs) from Yersinia pseudotuberculosis that occur when the microbe is grown at low temperature; the specific features of these LPSs in comparison with the LPSs from other enteropathogens may be due to unusual thermal adaptation mechanisms. To gain insight into this question, the chemical composition of Y. pseudotuberculosis LPS has been determined. The data indicate that two different S-form LPS species are produced in "cold"-grown bacteria. These have an identical set of bands after SDS-PAGE, similar elution profiles during gel-filtration on a Sephadex G-200 column in the presence of sodium deoxycholate, identical monosaccharide and fatty acid compositions, and similar polymerization degrees, but they have different acylation degree. On the whole, the macromolecularly different LPS populations, varying not only in their smooth or rough nature and hydrophobicity, but also in their localization in the outer membrane and, probably, their interactions with other cell components, are synthesized in "cold"-grown Y. pseudotuberculosis. The biological sense of the heterogeneity and its connection with psychrophilic and pathogenic properties of pseudotuberculosis organisms are discussed.     

Bovine aortic chondroitin sulphate- and dermatan sulphate-containing proteoglycans. Isolation, fractionation and chemical characterization.

1. Guanidinium chloride (4M) in the presence of proteinase inhibitors extracted 90% of bovine aorta galactosaminoglycans as proteoglycans that were subsequently purified by ion-exchange and gel chromatography. 2. Fractionation of the calcium salts of the purified proteoglycans with increasing concentration of ethanol yielded fractions PG-25 (28%), PG-35 (45%) and PG-50 (37%). 3. Fraction PG-50 contained proteochondroitin 6-sulphate, whereas fractions PG-25 and PG-35 were proteodermatan sulphates of greatly different carbohydrate composition; the molar proportions of L-iduronate-N-acetylgalactosamine 4-sulphate, D-glucuronate-N-acetyl-galactosamine 4-sulphate and D-glucuronate-N-acetylgalactosamine 6-sulphate were 75: 18 :7 in fraction PG-25 and 14 :46 :40 in fraction PG-35. 4. The presence of alternating or mixed sequences with L-iduronate- and D-glucuronate-containing repeating disaccharides was indicated by the formation of tetrasaccharides after chondroitinase AC digestion (single L-iduronate residues) and by the release of fragments containing four or five consecutive D-glucuronate-N-acetylgalactosamine repeats after periodate oxidation and alkaline elimination. 5. The amino acid compositions of fractions PG-25 and PG-35 were similar and markedly different from that of fraction PG-50, which also contained more side chains.     

The chemical fractionation of lymphatic organs

A method for chemically fractionating lymphatic organs has been described. The method has been shown to be applicable to bovine palatine tonsils, sheep palatine tonsils, and bovine thymus. Approximately 50 per cent of the dry weight of tonsils and about 30 per cent of thymus has been found to be soluble in the 0.15 M NaCl extract. Four components have been isolated which together account for 65 per cent by weight of the material in the extracts. Four other components have been identified and partially defined by means of electrophoretic mobility, solubility, or some other chemical or physical property.     

The polysaccharides of red wine: total fractionation and characterization

Ethanol-precipitated red wine polysaccharides were fractionated by a combination of anion-exchange, size-exclusion and affinity chromatography steps. This comprehensive fractionation allowed us to prepare a collection of wine polysaccharides in sufficient amount to permit the determination of their intrinsic properties. Glycosyl-residue composition of each polysaccharide fraction was determined by GC–EI–MS of the per-O-trimethylsilylated methyl glycoside derivatives (TMS), a method that has been recently developed and adapted to suit simultaneous determination of neutral and acidic glycosyl-residue compositions of polysaccharides present in plant-derived products. The results showed that mannoproteins released by yeast during fermentation, and grape derived arabinogalactan-proteins, rhamnogalacturonans I and II are the main wine polysaccharides and accounted for 35, 42, 4 and 19%, respectively, of the total polysaccharides. Structural characterization revealed that rhamnogalacturonan I fractions were linked with xyloglucan-like polysaccharides. This finding represents compelling evidence of the existence of cross-linking between pectin and hemicellulose domains in plant primary cell walls.     

Canine traceealis membrane fractionation and characterization

Canine trachealis was homogenized and the various membrane fractions isolated by differential centrifugation and discontinuous sucrose gradient centrifugation. A membrane fraction enriched in the plasma membrane marker enzymes 5′-nucleotidase (5-fold) and K⁺-activated ouabain sensitive p-nitrophenylphosphatase (3-fold) was obtained. The fraction contained very low levels of the inner mitochondrial marker succinate: cytochrome c oxidoreductase. These plasma membrane vesicles showed higher ATP-dependent Ca-uptake (20 μmoles/g protein) than any other submicrosomal fraction. The active Ca-uptake was enhanced by oxalate. The Ca taken up by the plasma membrane vesicles was released instantaneously by dilution in 5m$\text{M}$ EGTA and 10μ$\text{M}$ A23187 and more slowly by dilution only in 5m$\text{M}$ EGTA.     

Pharmacological characterization and chemical fractionation of the venom of the ponerine ant, Paraponera clavata (F.).

1. The neurotoxic action of the venom of the ponerine ant, Paraponera clavata, was studied using a cascade of mammalian smooth muscle preparations and a preparation for investigating transmission from fibres of the cercal nerve to a giant interneuron in the sixth abdominal ganglion of the cockroach. 2. The venom contains three toxic fractions that block synaptic transmission in the insect central nervous system. 3. Two of these fractions have agonistic action on mammalian smooth muscle preparations. 4. One of the later fractions was characterized pharmacologically as containing a kinin. 5. The other, and most active neurotoxic fraction, was rechromatographed, resulting in the purification of a peptide of 25 amino acids residues, called poneratoxin, PoTX: Phe-Leu-Pro-Leu-Leu-Ile-Leu-Gly-Ser-Leu-Leu-Met-Thr-Pro-Pro-Val-Ile-Gln- Ala-Ile-His-Asp-Ala-Gln-Arg-HN2.     

Flow field-flow fractionation as a methodology for protein separation and characterization

Flow field-flow fractionation is introduced as a new tool applicable to protein studies. Specific advantages of this method are discussed, including the capability for measuring diffusivities and Stokes radii directly, even for trace components. The theoretical equations of flow FFF are summarized and expanded to include an explicit dependence on the Stokes radius. Several native proteins are retained. The retention is shown to be systematically controllable by changes in cross flow and the results are in quantitative agreement with theory. Fractograms of different rat plasmas are then shown to produce coincident peaks, while human plasma exhibits several systematic peak shifts with respect to the fractogram of the rat plasma. Finally, changes in the Stokes radii of ferritin peaks are shown after various forms of treatment with SDS. Flow FFF in this study demonstrates a capability of working with a mass range of ∼ 10⁵ in a single run.     

Mendel's genes: toward a full molecular characterization

The discipline of classical genetics is founded on the hereditary behavior of the seven genes studied by Gregor Mendel. The advent of molecular techniques has unveiled much about the identity of these genes. To date, four genes have been sequenced: A (flower color), LE (stem length), I (cotyledon color), and R (seed shape). Two of the other three genes, GP (pod color) and FA (fasciation), are amenable to candidate gene approaches on the basis of their function, linkage relationships, and synteny between the pea and Medicago genomes. However, even the gene (locus) identity is not known for certain for the seventh character, the pod form, although it is probably V. While the nature of the mutations used by Mendel cannot be determined with certainty, on the basis of the varieties available in Europe in the 1850s, we can speculate on their nature. It turns out that these mutations are attributable to a range of causes-from simple base substitutions and changes to splice sites to the insertion of a transposon-like element. These findings provide a fascinating connection between Mendelian genetics and molecular biology that can be used very effectively in teaching new generations of geneticists. Mendel's characters also provide novel insights into the nature of the genes responsible for characteristics of agronomic and consumer importance.     

Affinity fractionation and characterization of chick brain synaptosomes

Chick brain synaptosomes were fractionated by affinity chromatography on concanavalin A-Sepharose. Three subfractions were obtained. One, designated UBF, was not bound to the affinity adsorbent and represented 36% of the total synaptosomal protein treated with the beads. A second fraction, designated BF1, adhered to concanavalin A-Sepharose exclusively through its carbohydrate recognition site. The third fraction, called BF2, bound to the beads through hydrophobic interactions and represented about 20% of the total synaptosomal protein. About 20% of the total synaptosomal protein was found to be retarded on three ligand-less gels, with potential for only hydrophobic interactions. This binding can be reversed, however, by ethylene glycol, a result indicating hydrophobic binding sites on the synaptosomes. Enzyme marker studies and electron microscopy showed differences between UBF, BF1, and BF2, mainly with respect to mitochondrial contamination. Binding studies with [3H]-Con A show the absence of Con A-specific carbohydrates from the surface of UBF or BF2. As expected strong and specific binding between [3H]-Con A and [3H] BF1 was observed. These findings are discussed in relation to a model for the interior working of the synaptosomes.     

Isolation and chemical characterization of the phosphoproteins of chicken bone matrix: heterogeneity in molecular weight and composition

Ethylenediaminetetraacetic acid and HCl extracts of calcified chicken bone were fractionated by a variety of techniques, including molecular sieving in guanidinium chloride, ion-exchange chromatography on DEAE-cellulose, high-performance liquid chromatography (HPLC), reverse-phase HPLC, and preparative sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE). Using several different experimental schemas, we isolated 14 apparently homogeneous components varying in molecular weight from approximately 150K to approximately 4K-5K. The compositions of all of the phosphoproteins were characterized by high concentrations of Asp, Glu, Ser, Gly, and Ala. Seven of the components which were analyzed contained concentrations of carbohydrate varying from approximately 4% to approximately 17%. Three of the components containing O-phosphoserine which behaved as single bands on SDS-PAGE with molecular weights of approximately 150K, approximately 90K, and approximately 70K contained Hyp and Hyl or Hyl alone and may represent covalently bonded or strongly associated collagen-phosphoprotein complexes or hydroxylated Pro and/or Lys residues of the phosphoproteins. The findings that the amino acid compositions of several of the components were very similar and that N-terminal partial amino acid sequences of the approximately 90- and approximately 60-kilodalton (kDa) and of the approximately 150- and approximately 32-kDa components, respectively, were identical make it clear that some of the lower molecular weight components are derived by proteolysis from higher molecular weight species. In addition to proteolysis, we speculate that it is possible, from the N-terminal amino acid sequence data and preliminary cross-reaction studies of antibodies to four of the phosphoproteins, that the heterogeneity observed in the phosphoprotein components may also be due in part to there being more than one independent gene product for chicken bone phosphoproteins.     

International plant molecular biology: a bright future for green science

A new study in this issue of Genome Biology sheds light on why some pseudogenes persist in rodent, and other mammalian, genomes. Please see related Research article by Marques et al http://genomebiology.com/2012/13/11/R102     

Physical and chemical basis of carbon isotope fractionation in plants

Naturally-occurring variations in the abundances of the stable isotopes of carbon and other elements can be used to understand the dynamics of natural processes in chemistry, biochemistry, biology, medicine, ecology and other fields. The use of carbon-13 isotopic abundances as an indicator of photosynthetic function in plants has become common. The purpose of this article is to describe the physical and chemical processes that contribute to the abundances of carbon-13 in plant materials, and to provide a framework for understanding how those processes control the isotopic contents of natural materials.