Method for the characterization of size-exclusion chromatography media for preparative purification of DNA restriction fragments

A protocol has been developed to characterize the potential of size exclusion chromatography media for the separation of DNA fragments at a preparative scale. A standard DNA mixture composed of -DNA cut with the restriction enzymes, AluI and HaeIII, was chromatographed on a column packed with the gel of interest. Fractions were collected and examined by PAGE. A digitized image of the gel was analyzed with the aid of a computer software program to determine the DNA fractionation range and selectivity curve for each chromatography gel. Four gels were characterized using this protocol. The effect of the elution buffer ionic strength on the fractionation of DNA was also investigated.The US Government right to retain a non-exclusive royalty-freelicense in and to any copyright is acknowledged.     

Edge effect and species–area relationships in the gall-forming insect fauna of natural forest patches in the Brazilian Pantanal

The aim of this study was to (i) measure differences in species richness between edge habitats versus interior habitats, or more precisely the edge effect, and (ii) test the species–area relationship for gall-forming insects in natural forest patches in a Brazilian floodplain (Pantanal of Mato Grosso do Sul). These patches are regionally known as capões, basically composed of woody vegetation. Twenty-seven patches were surveyed. In each patch two transects were conducted for gall sampling. One transect encircled the patches while the other was conducted in the interior of the patch, totaling 54h of sampling. Host plant and galling insect species composition differed quite characteristically between the edge and the interior of patches, but galling insect richness did not. When insect gall richness was expressed as the ratio between insect gall and host plant richness (gall per plant ratio), a weak species–area relationship was found. Our results suggest that the number of galling insects per individual plant is not affected by the size of the patch. Despite these results, the natural forest patches found in this region seem well suited for long-term studies addressing species–area relationships. With regard to herbivorous insects, these studies should be combined with research on host plant dynamics during flooding and dry seasons.     

Reaction of peroxynitrite with hyaluronan and related saccharides

The effects of peroxynitrite on hyaluronan has been studied by using an integrated spectroscopical approach, namely electron paramagnetic resonance (EPR), nuclear magnetic resonance (NMR), and mass spectrometry (MS). The reaction has been performed with the polymer, the tetrasaccharide oligomer as well as with the monosaccharides N-acetylglucosamine and glucuronic acid. The outcome of the presence of molecular oxygen and carbon dioxide has been also evaluated. Although ₁H-NMR and ESI-MS experiments did not revealed peroxynitrite-mediated modification of hyaluronan as well as of related saccharides, from spin-trapping EPR experiments it was concluded that peroxynitrite induce the formation of C-centered carbon radicals, most probably by the way of its hydroxyl radical-like reactivity. These EPR data support the oxidative pathway involved in the degradation of hyaluronan, a probable event in the development and progression of rheumatoid arthritis.     

Protein fragment clustering and canonical local shapes

A novel clustering method is used to cluster protein fragments by shape. The centroids (mean fragments from each cluster) form a basis set of structural motifs. A database of 156,643 seven-residue fragments is used, and eight different basis sets with varying levels of resolution are generated. Coarse basis sets contain tens of centroids and provide meaningful local shapes, which are more detailed than the traditional secondary structure categories. High-resolution basis sets contain thousands of centroids and can be used to model tertiary structure of longer segments. The basis sets generated fit nontraining set proteins with the expected accuracy.     

A structure-based anatomy of the E.coli metabolome

The Escherichia coli metabolome has been characterised using the two-dimensional structures of 745 metabolites, obtained from the EcoCyc and KEGG databases. Physicochemical properties of the metabolome have been calculated to provide an overview of this set of cognate ligands. A library of fragments commonly found among these molecules has been employed to reveal the main constituents of metabolites, and to assist a broad classification of the metabolome into biochemically relevant classes. Fragment-based fingerprints reveal the metabolome as a continuum in the two-dimensional structural space, where clusters of molecules sharing similar scaffolds can be identified, but are generally overlapping. Nucleotide, carbohydrate and amino acid-like molecules are the most prominent, but at high levels of similarity, a more detailed classification is possible. Classification schemes for the metabolome are a promising tool for understanding the chemical diversity of the metabolome. When used in conjunction with existing classifications of the proteome, they can help to elucidate the binding preferences and promiscuity of proteins and their cognate substrates.     

Estimating the length of incomplete long bones: forensic standards from Guatemala

We report on new standards for estimating long bone length from incomplete bones for use in forensic and archaeological contexts in Central America. The measurements we use closely follow those defined by Steele ([1970] Personal Identification in Mass Disasters; Washington, DC: Smithsonian Institution), but we add several new landmarks. We measured the femur, humerus, tibia, and fibula of 100 Maya skeletons (68 males, 32 females) recovered from forensic exhumations. We derived the equations by regressing bone segment length on bone length, and solved for bone length to maximize the utility of the equations for taller populations. We generated equations for all segments that were significantly correlated with bone length for males, for females, and for both sexes combined, but accepted only regressions with r(2) > 0.85 as reliable. Landmarks defined by muscle attachment sites were more variable in location than landmarks on articular architecture; thus we retained few equations that use these landmarks. We tested the male and combined sex equations on 36 males of unknown ethnicity exhumed from a military base in Guatemala, and found that the equations performed satisfactorily. We also evaluated the performance of equations by Steele ([1970] Personal Identification in Mass Disasters; Washington, DC: Smithsonian Institution) and Jacobs ([1992] Am J Phys Anthropol 89:333-345) on the Maya bones, and conclude that significant population variation in long bone proportions hinders their application in Central America.     

Hyaluronan is an abundant constituent of the extracellular matrix of Xenopus embryos

The spatiotemporal distribution of hyaluronan (HA), a major constituent of the vertebrate extracellular matrix, was analyzed during early embryonic development of Xenopus laevis. This polysaccharide is abundantly present in ventricular structures such as the blastocoel, the archenteron as well as later on in the hepatic cavity, the brain ventricles and the developing heart. At the blastula stage, HA was detected in the extracellular matrix of the ecto- and mesodermal primordia. Shortly before gastrulation, it becomes enriched at the basal site of the superficial cell layer of the ectoderm. During gastrulation, enhanced synthesis of HA takes place in the involuting marginal zone, shortly before invagination starts, hence, resulting in a torus-like deposition in the deep layer of the equatorial mesodermal primordium. After gastrulation, HA appears to accumulate within the extracellular matrix demarcating the primary germ layers. During tailbud stages, it is found highly enriched in many mesodermal derivatives, e.g., in mesenchyme, the heart, precordal cartilage and the lung primordia. Furthermore, extracellular matrix of the ventral mesodermal cell layer in the trunk region and the immediate proximity of blood vessels contain high amounts of HA.     

Enzymes and chelating agent in cotton pretreatment

Desized cotton fabric and cotton seed-coat fragments (impurities) have been treated with commercial cellulase (Celluclast 1.5 L), hemicellulase–pectinase (Viscozyme 120 L) and xylanase (Pulpzyme HC) enzymes. Seed-coat fragments hydrolyzed much faster than the cotton fabric itself. This relative difference in hydrolysis rates makes possible a direct enzymatic removal of seed-coat fragments from desized cotton fabric. Addition of chelating agents such as ethylenediamine-tetra-acetic acid (EDTA) markedly enhanced the directed enzyme action. Pretreatments carried out in acidic solution at pH 5 increased the lightness of seed-coat fragments, contrary to the samples treated in neutral medium at pH 7. Alkaline scouring resulted in darker seed-coat fragments except for the samples pretreated with Pulpzyme HC plus EDTA. This effect is similar to that observed in the biobleaching process in pulp and paper industry.     

Isolation and cloning of Streptomyces terminal fragments

Streptomyces species have a linear chromosome of approximately 8 Mb in size. Many strains also carry linear plasmids. Most of these linear elements contain terminal proteins covalently bound to the 5 ends of the DNA. Using a method for the visualisation of terminal DNA fragments in agarose gels, it was possible to see three fragments in S. rimosus and five fragments in S. avermitilis. The method was also used to clone the 298 bp BamHI fragment carrying the left end of plasmid SLP2. Analysis of the sequence showed that the end resembled other Streptomyces chromosome and plasmid ends, but there were eight palindromes (instead of seven) and a tandem duplication of a 14 bp sequence.     

Photoinhibition as a function of the ambient redox potential in Tris-washed PS II membrane fragments

The mode of photoinhibition as a function of the ambient redox potential (E_ambient) in suspensions of Tris-washed PS II membrane fragments has been analyzed by monitoring flash-induced absorption changes at 830 nm. It was found: (a) the detectable initial amplitude, ΔA^total ₈₃₀, as a measure of the capacity to form the `stable' radical pair, P680^+ċ Q^−ċ _A, drastically decreases during a 10 min photoinhibition at E_ambient values below +350 mV; (b) conversely, the normalized extent of the 18 μs relaxation kinetics, ΔA^{18 μ s} ₈₃₀ as a measure of the electron transfer from Y_Z to P680^+ċ becomes highly susceptible to light stress when E_ambient exceeds values of about +350 mV; (c) effects of the ambient redox potentials are highly pronounced during light exposure under anaerobic conditions, while much smaller differences arise under aerobic conditions; (d) the extent of damage does not correlate with the total concentration of K₃[Fe(CN)₆] and K₄[Fe(CN)₆] in the suspension during photoinhibition but rather depends on the E_m-values; (e) qualitatively similar features are observed when the redox buffer system K₃[Fe(CN)₆]/Na₂S₂O₄ is replaced by K₂[IrCl₆]/Na₂S₂O₄; (f) the characteristic E_ambient-dependence of photoinhibition is observed only under anaerobic conditions. The results are discussed with respect to different redox components that might be involved, including brief comments on a possible role of Cyt b559. This revised version was published online in June 2006 with corrections to the Cover Date.