Effect of irradiation and endogenous nucleases on rat liver chromatin

These assessment of the consequences of irradiation on chromatin is complicated by endogenous nucleases. Isolation and prolonged storage of rat liver nuclei in buffers containing divalent metal ions activates these enzymes and promotes the degradation of chromatin. Irradiation of rat liver nuclei to dose levels of 20,000 rad under conditions in which endogenous nucleases are inhibited and analysis of the irradiated chromatin by sucrose density gradient centrifugation gave no evidence for monosomes or oligosomes. When chromatin from irradiated nuclei was digested with micrococcal nuclease, the levels of monosomes and oligosomes were identical to those of micrococcal nuclease, the levels of monosomes and oligosomes are identical to suggest that irradiation results in neither a direct fragmentation of linkers nor the sensitization of linkers for subsequent cleavage by micrococcal nuclease. Histones isolated from monosomes of irradiated and unirradiated nuclei were intact, showing no fragmentation or loss of residues, as judged by sodium dodecyl sulfate-polyacrylamide electrophoresis.     

Soil Characteristics of Rehabilitating and Unmined Coastal Dunes at Richards Bay, KwaZulu-Natal, South Africa

The postmining rehabilitation of coastal sand dunes north of Richards Bay (28°43′S, 32°12′E), South Africa, is resulting in the development of a series of known-aged stands of vegetation dominated by Acacia karroo (sweet thorn). Other broad-leaved species are establishing themselves in rehabilitating areas more than 12 years of age. Soils from rehabilitating stands 3–5, 9–12, 13–15, and 16–18 years of age, from two disturbed, unmined stands 30 and 58 years of age, and from a mature unmined stand were examined to assess age-related trends in selected soil properties. Individually, these stands represent a series of different developmental stages of a coastal dune successional sere. Soil organic material, percentage organic carbon and concentrations of sodium, potassium, magnesium, calcium, and nitrogen increased with an increase in habitat regeneration age. Concentrations of most of these elements were lower than those recorded on the 58-year-old unmined and mature unmined stands. Multivariate analyses suggest, however, that the similarity of these values for rehabilitating stands to those for the unmined stands increased with an increase in regeneration age. The growth response of Raphanus sativus (radish) plants, based on mass attained under experimental growing conditions in soil collected from these stands, suggests an increase in soil fertility with an increase in regeneration age.     

Bioaccumulation of selected metals in the gill,liver and muscle tissue of rednose labeo Labeo rosae from two impoundments on the Olifants River,Limpopo river system,South Africa

Metal concentrations in the gill, muscle and liver tissues of Labeo rosae from two impoundments, Loskop and Flag Boshielo dams on the Olifants River, were evaluated in 2011 to detect patterns in metal associations between tissues and impoundments. Elevated concentrations of Ba, Zn, B, Al, Si and Fe, relative to a pristine site in the catchment, were found in the muscle, liver and gill tissues at both impoundments. Molybdenum concentrations were exceptionally high in all tissues at Loskop Dam and in liver at Flag Boshielo Dam. No definite pattern in the ratio metal concentrations within, or between, fish tissues was identified. The expected trend, liver > gills > muscle, was found at both impoundments, but was less prominent at Loskop Dam. Metal concentrations in muscle of Loskop Dam fish were significantly higher than in those at Flag Boshielo Dam. The inverse was true for liver. The long-term impact of elevated metal concentrations on fish health at both impoundments raises concern.     

A thrombelastographic study of the effect of stress on the blood coagulation in Cyprinus carpio (Cyprinidae) and Oreochromis mossambicus (Cichlidae)

The normal blood coagulation in Cyprinus carpio and Oreochromis mossambicus was investigated by thrombelastography and standard thrombelastographs were obtained for each species. The effect of stress on blood coagulation was thereafter determined. The thrombelastograms indicated hypercoagulability under stress conditions. A prominent observation is the differences in the elasticity of the clot under various conditions. Fibrinolysis occurred in all cases, except in the case of Cyprinus carpio after severe agitation for 30 min. Relevant values for various parameters are given.     

Two new species of the marine water mite family Pontarachnidae from Queensland,Australia (Acari: Hydrachnidia)

Two new species of the water mite family Pontarachnidae are described from Queensland, Australia: Pontarachna curvipalpis and Litarachna haleioides. Pontarachna curvipalpis can be distinguished from other members of the genus by its stocky leg segments, long apodemes of the fourth coxae, strongly bowed pre- and postgenital sclerite and wheel-like acetabula without radiating spokes. Litarachna haleoides is characterized by strongly bowed but not touching genital sclerites, relatively short apodemes of the fourth coxae, a slender palp and P2 with a ventral projection. A short discussion is provided on the occurrence of water mites on the Great Barrier Reef.     

RNA structure prediction from evolutionary patterns of nucleotide composition

Structural elements in RNA molecules have a distinct nucleotide composition, which changes gradually over evolutionary time. We discovered certain features of these compositional patterns that are shared between all RNA families. Based on this information, we developed a structure prediction method that evaluates candidate structures for a set of homologous RNAs on their ability to reproduce the patterns exhibited by biological structures. The method is named SPuNC for ‘Structure Prediction using Nucleotide Composition’. In a performance test on a diverse set of RNA families we demonstrate that the SPuNC algorithm succeeds in selecting the most realistic structures in an ensemble. The average accuracy of top-scoring structures is significantly higher than the average accuracy of all ensemble members (improvements of more than 20% observed). In addition, a consensus structure that includes the most reliable base pairs gleaned from a set of top-scoring structures is generally more accurate than a consensus derived from the full structural ensemble. Our method achieves better accuracy than existing methods on several RNA families, including novel riboswitches and ribozymes. The results clearly show that nucleotide composition can be used to reveal the quality of RNA structures and thus the presented technique should be added to the set of prediction tools.