Analysis of plastid DNA-like sequences within the nuclear genomes of higher plants

A wide-ranging examination of plastid (pt)DNA sequence homologies within higher plant nuclear genomes (promiscuous DNA) was undertaken. Digestion with methylation-sensitive restriction enzymes and Southern analysis was used to distinguish plastid and nuclear DNA in order to assess the extent of variability of promiscuous sequences within and between plant species. Some species, such as Gossypium hirsutum (cotton), Nicotiana tabacum (tobacco), and Chenopodium quinoa, showed homogenity of these sequences, while intraspecific sequence variation was observed among different cultivars of Pisum sativum (pea), Hordeum vulgare (barley), and Triticum aestivum (wheat). Hypervariability of plastid sequence homologies was identified in the nuclear genomes of Spinacea oleracea (spinach) and Beta vulgaris (beet), in which individual plants were shown to possess a unique spectrum of nuclear sequences with ptDNA homology. This hypervariability apparently extended to somatic variation in B. vulgaris. No sequences with ptDNA homology were identified by this method in the nuclear genome of Arabidopsis thaliana.      

Incidence and levels of fumonisin contamination in Colombian corn and corn products

A survey was conducted to determine the levels of fumonisins B1 and B2 in corn and corn-based products available in Colombia for human and animal consumption. A total of 120 samples were analyzed by acetonitrile-water extraction, cleanup with a strong-anion-exchange column, and liquid chromatography with o-phthaldialdehyde-2-mercaptoethanol derivatization and fluorescence detection. The samples of corn and corn-based products for animal intake were taken at different feed manufacturing plants, whereas the samples used for human foods where purchased from local retail stores. The number of positive samples for fumonisin B1 was 20.0% higher in corn and corn-based products for animal intake (75.0%) than in corn and corn-based products for human consumption (55.0%). The levels of fumonisin B1 were also higher in corn and corn-based products for animal intake (mean = 694 μg/kg; range = 32–2964 μg/kg), than in corn and corn-based products for human intake (mean = 218 μg/kg; range = 24–2170 μg/ kg). The incidence and levels of fumonisin B2 were lower than those for fumonisin B1. Corn and corn-based products for animal consumption had an incidence of fumonisin B2 of 58.3%, with a mean value of 283 μg/kg, and a range of 44–987 μg/kg. The incidence of fumonisin B2 in corn-based products for human intake was 35.0%, with a mean value of 118 μg/kg and a range of 21–833 μg/kg. The highest incidence and levels of fumonisins were found in samples of hominy feed, with concentrations ranging from 86 to 2964 μg/kg fumonisin B1 and 57 to 987 μg/kg fumonisin B2.     

Plant structural changes due to herbivory: Do changes in <Emphasis Type="Italic">Aceria</Emphasis>-infested coconut fruits allow predatory mites to move under the perianth?

Being minute in size, eriophyoid mites can reach places that are small enough to be inaccessible to their predators. The coconut mite, Aceria guerreronis, is a typical example; it finds partial refuge under the perianth of the coconut fruit. However, some predators can move under the perianth of the coconut fruits and attack the coconut mite. In Sri Lanka, the phytoseiid mite Neoseiulus baraki, is the most common predatory mite found in association with the coconut mite. The cross-diameter of this predatory mite is c. 3 times larger than that of the coconut mite. Nevertheless, taking this predator’s flat body and elongated idiosoma into account, it is—relative to many other phytoseiid mites—better able to reach the narrow space under the perianth of infested coconut fruits. On uninfested coconut fruits, however, they are hardly ever observed under the perianth. Prompted by earlier work on the accessibility of tulip bulbs to another eriophyoid mite and its predators, we hypothesized that the structure of the coconut fruit perianth is changed in response to damage by eriophyoid mites and as a result predatory mites are better able to enter under the perianth of infested coconut fruits. This was tested in an experiment where we measured the gap between the rim of the perianth and the coconut fruit surface in three cultivars (‘Sri Lanka Tall’, ‘Sri Lanka Dwarf Green’ and ‘Sri Lanka Dwarf Green × Sri Lanka Tall’ hybrid) that are cultivated extensively in Sri Lanka. It was found that the perianth-fruit gap in uninfested coconut fruits was significantly different between cultivars: the cultivar ‘Sri Lanka Dwarf Green’ with its smaller and more elongated coconut fruits had a larger perianth-fruit gap. In the uninfested coconut fruits this gap was large enough for the coconut mite to creep under the perianth, yet too small for its predator N. baraki. However, when the coconut fruits were infested by coconut mites, the perianth-rim-fruit gap was not different among cultivars and had increased to such an extent that the space under the perianth became accessible to the predatory mites.     

Frasnian vertebrate taphonomy and sedimentology of macrofossil concentrations from the Langsēde Cliff,Latvia

Luk?evi?s, E., Ahlberg, P.E., Stinkulis, ?., Vasi?kova, J. & Zupi??, I. 2011: Frasnian vertebrate taphonomy and sedimentology of macrofossil concentrations from the Langsēde Cliff, Latvia. Lethaia, Vol. 45, pp. 356–370. The siliciclastic sequence of the Upper Devonian of Kurzeme, Western Latvia, is renowned for abundant vertebrate fossils, including the stem tetrapods Obruchevichthys gracilis and Ventastega curonica. During the first detailed taphonomic study of the vertebrate assemblage from the Ogre Formation cropping out at the Langsēde Cliff, Imula River, abundant vertebrate remains have been examined and identified as belonging to one psammosteid, two acanthodian and three sarcopterygian genera; the placoderm Bothriolepis maxima dominates the assemblage. Besides fully disarticulated placoderm and psammosteid plates, separate sarcopterygian scales and teeth, and acanthodian spines, partly articulated specimens including complete distal segments of Bothriolepis pectoral fins, Bothriolepis head shields and sarcopterygian lower jaws have been found. The size distribution of the placoderm bones demonstrates that the individuals within the assemblage are of approximately uniform age. Distinct zones have been traced within the horizontal distribution of the bones. These linear zones are almost perpendicular to the dominant dip azimuth of the cross‐beds and ripple‐laminae and most probably correspond to the depressions between subaqueous dunes. Concavity ratio varies significantly within the excavation area. The degree of fragmentation of the bones and disarticulation of the skeletons suggest that the carcasses were reworked and slightly transported before burial. Sedimentological data suggest deposition in a shallow marine environment under the influence of rapid currents. The fossiliferous bed consists of a basal bone conglomerate covered by a cross‐stratified sandstone with mud drapes, which is in turn overlain by ripple laminated sandstone, indicating the bones were buried by the gradual infilling of a tidal channel. All the Middle–Upper Devonian vertebrate bone‐beds from Latvia are associated with sandy to clayey deposits and have been formed in a sea‐coastal zone during rapid sedimentation episodes, but differ in fossil abundance and degree of preservation. □Agnathans, Devonian, facies analysis, fish, fossil assemblage, palaeoenvironment.     

Population dynamics of <Emphasis Type="Italic">Aceria guerreronis</Emphasis> (Acari: Eriophyidae) and its predatory mite, <Emphasis Type="Italic">Neoseiulus baraki</Emphasis> (Acari: Phytoseiidae) in two coconut growing areas in Sri Lanka

Densities of coconut mite, Aceria guerreronis Keifer (Acari: Eriophyidae) and its predatory mite, Neoseiulus baraki Athias-Henriot (Acari: Phytoseiidae) were monitored on coconut fruits in two coconut mite infested areas, Kalpitiya and Madurankuliya, in Sri Lanka, over a period of 3 years and were compared with local rainfall records. Significant differences in A. guerreronis densities were observed among years and months of the year. Rainfall (amount and frequency, i.e. the total number of days with rainfall of >5 mm) was not significantly correlated with the variation of A. guerreronis densities. But the drought length (i.e. the number of days without rainfall of >5 mm) significantly influenced A. guerreronis densities. Generally, peak densities of A. guerreronis were observed during February–March and June–September in both areas. The differences in the N. baraki densities were significantly different between the two areas and among the 3 years but not among months of the year. Although the amount of rainfall was not significantly correlated with the population densities of N. baraki, frequency of rainfall showed a negative significant correlation and drought length showed a positive significant correlation with the population densities. The results of this experiment indicated that the application of control methods for A. guerreronis may be more advantageous if they are carried out at the onset and during the dry seasons.     

A tree-based method for the rapid screening of chemical fingerprints

Background  

The fingerprint of a molecule is a bitstring based on its structure, constructed such that structurally similar molecules will have similar fingerprints. Molecular fingerprints can be used in an initial phase of drug development for identifying novel drug candidates by screening large databases for molecules with fingerprints similar to a query fingerprint.     

Recrafting the neighbor-joining method

Background  

The neighbor-joining method by Saitou and Nei is a widely used method for constructing phylogenetic trees. The formulation of the method gives rise to a canonical Θ(n ³) algorithm upon which all existing implementations are based.