A protocol for the rapid isolation of full geminivirus genomes from dried plant tissue

A high-throughput method of isolating and cloning geminivirus genomes from dried plant material, by combining an Extract-n-Amp™-based DNA isolation technique with rolling circle amplification (RCA) of viral DNA, is presented. Using this method an attempt was made to isolate and clone full geminivirus genomes/genome components from 102 plant samples, including dried leaves stored at room temperature for between 6 months and 10 years, with an average hands-on-time to RCA-ready DNA of 15 min per 20 samples. While storage of dried leaves for up to 6 months did not appreciably decrease cloning success rates relative to those achieved with fresh samples, efficiency of the method decreased with increasing storage time. However, it was still possible to clone virus genomes from 47% of 10-year-old samples. To illustrate the utility of this simple method for high-throughput geminivirus diversity studies, six Maize streak virus genomes, an Abutilon mosaic virus DNA-B component and the DNA-A component of a previously unidentified New Word begomovirus species were fully sequenced. Genomic clones of the 69 other viruses were verified as such by end sequencing. This method should be extremely useful for the study of any circular DNA plant viruses with genome component lengths smaller than the maximum size amplifiable by RCA. © 2008 Elsevier B.V. All rights reserved.

Cotton bunchy top virus and other relatives

Cotton bunchy top virus (CBTV) and the related Cotton leafroll dwarf virus (CLRDV) have caused sporadic disease outbreaks in most cotton regions of the world. Until recently, little was known about the diversity of CBTV or its natural host range. Seven natural field hosts and one experimental host of CBTV have now been identified. These include cotton, Malva parviflora (Marshmallow weed), Abutilon theophrasti (Velvetleaf), Anoda cristata (Spurred anoda), Hibiscus sabdariffa (Rosella), Sida rhombifolia (Paddy’s lucerne), Chamaesyce hirta (Asthma plant) and Gossypium australe. These are currently the only eight known hosts of CBTV. However the virus may have a wider host range than originally thought and include further non-Malvaceae species like asthma plant (family Euphorbiaceae). There are two distinct strains of CBTV in Australia, -A and -B, which have been detected in cotton from numerous locations across almost all growing regions. From 105 samples of cotton that have been positive for CBTV, 6 were infections of strain A only, 60 were strain B only and 64 were a mixed infection of strains A and B. These results indicate the symptoms of cotton bunchy top disease are closely associated with the presence of strain CBTV-B. A diagnostic assay for Cotton leafroll dwarf virus (CLRDV - cotton blue disease) is being developed and applied successfully for the detection of CLRDV samples from Brazil and Thailand. This is the first confirmation of CLRDV from SE-Asia, which may pose an increased biosecurity threat to the Australian industry.

Estudio preliminar de la relación mosca blanca virus-maleza en agroecosistema frijol común (Phaseolus vulgaris L) con riego en Nicaragua

En los diferentes agroecosistemas del frijol las malezas representan una de las amenazas más serias y constantes de pérdidas en el rendimiento por lo que se han sido estudiadas de el punto de vista de la competencia, pero estas puedes ser huéspedes alternos de insectos benéficos y dañinos y jugar otro papel de importancia. El frijol es atacado por diferentes patógenos virales siendo en su mayoría transmitidos por insectos entre los que se cuenta Mosca blanca para el caso del virus del mosaico dorado del frijol común Gámez (1971). Con el fin de estudiar la relación Mosca –Malezas virus se realizó un estudio en el centro de Granos Básicos San Cristóbal en el departamento de Managua entre los meses de Enero a Abril de 1987, en dicho centro se muestrearon tres áreas diferentes: cultivada (frijol común con riego), No cultivada (malezas). Ronda permanente (malezas). En las áreas se tomaron en cuenta diferente parámetros para determinar la composición florística, los huéspedes de mosca blanca, huéspedes de patógenos viral y preferencia de la mosca blanca entre malezas y frijol. Los resultados indican que el complejo de malezas predominantes las especies Abutilon crispum, Euphorbia heterpphylla, Baltimora recta y Sida sp. Se pueden considerar huéspedes de Mosca blanca. Existen preferencia de la mosca por especias de malezas como Abutilòn crispum, Eurphorbia heterophylla, chanmaesyce hisopifolìa más que por frijol y que especies como Abutilon crispum y Sida sp son huéspedes de patógenos virales. Estos resultados en conjunto sugieren una situación riesgosa para el futuro del frijol común con riego, ya que se presentan condiciones necesarias para la escorrentía de epifitorias virales en el campo encontramos el inóculo viral, el vector especies susceptibles y condiciones ambientales favorables que podrías llevar a una explosión de la enfermedad en términos mayores; hecho que no podemos asegurar sin estudios más detallados.

Compound specific stable isotopes, BIT, pollen and spores of Miocene to Pliocene sediments of ODP Hole 175-1085A

Pollen and stable carbon (d13C) and hydrogen (dD) isotope ratios of terrestrial plant wax from the South Atlantic sediment core, ODP Site 1085, is used to reconstruct Miocene to Pliocene changes of vegetation and rainfall regime of western southern Africa. Our results reveal changes in the relative amount of precipitation and indicate a shift of the main moisture source from the Atlantic to the Indian Ocean during the onset of a major aridification 8 Ma ago. We emphasise the importance of declining precipitation during the expansion of C4 and CAM (mainly succulent) vegetation in South Africa. We suggest that the C4 plant expansion resulted from an increased equator-pole temperature gradient caused by the initiation of strong Atlantic Meridional Overturning Circulation following the shoaling of the Central American Seaway during the Late Miocene.

AMS radiocarbon dates and pollen analysis of ODP Hole 175-1078C

ODP Site 1078 situated under the coast of Angola provides the first record of the vegetation history for Angola. The upper 11 m of the core covers the past 30 thousand years, which has been analysed palynologically in decadal to centennial resolution. Alkenone sea surface temperature estimates were analysed in centennial resolution. We studied sea surface temperatures and vegetation development during full glacial, deglacial, and interglacial conditions. During the glacial the vegetation in Angola was very open consisting of grass and heath lands, deserts and semi-deserts, which suggests a cool and dry climate. A change to warmer and more humid conditions is indicated by forest expansion starting in step with the earliest temperature rise in Antarctica, 22 thousand years ago. We infer that around the period of Heinrich Event 1, a northward excursion of the Angola Benguela Front and the Congo Air Boundary resulted in cool sea surface temperatures but rain forest remained present in the northern lowlands of Angola. Rain forest and dry forest area increase 15 thousand years ago. During the Holocene, dry forests and Miombo woodlands expanded. Also in Angola globally recognised climate changes at 8 thousand and 4 thousand years ago had an impact on the vegetation. During the past 2 thousand years, savannah vegetation became dominant.

Distribution of pollen and spores in sediments of ODP Hole 175-1078C

The distribution of pollen in marine sediments is used to record vegetation change on the continent. Generally, a good latitudinal correspondence exists between the distribution patterns of pollen in the marine surface sediments and the occurrence of the source plants on the adjacent continent. To investigate land-sea interactions during deglaciation, we compare proxies for continental (pollen assemblages) and marine conditions (alkenone-derived sea surface temperatures) of two high-resolution, radiocarbon-dated sedimentary records from the tropical southeast Atlantic. The southern site is located West of the Cunene River mouth; the northern site is located West of the Angolan Huambe Mountains. It is inferred that the vegetation in Angola developed from Afroalpine and open savannah during the last Glacial maximum (LGM) via Afromontane Podocarpus forest during Heinrich Event 1 (H1), to an early increase of lowland forest after 14.5 ka. The vegetation record indicates dry and cold conditions during the LGM, cool and wet conditions during H1 and a gradual rise in temperature starting well before the Younger Dryas (YD) period. Terrestrial and oceanic climate developments seem largely running parallel, in contrast to the situation ca. 5° further South, where marine and terrestrial developments diverge during the YD. The cool and wet conditions in tropical West Africa, South of the equator, during H1 suggest that low-latitude insolation variation is more important than the slowdown of the thermohaline circulation for the climate in tropical Africa.

Bitumen and n-alkanes in organic matter from sedimentary rocks sampled in DSDP Holes 47-397A and 47-398

A study of samples from DSDP Leg 47 shows that transformation of organic matter in deep sea sediments is completly analogous to evolution of organic matter in sedimentary sequences on continents and depends on the same factors. Crucial among these factors are: genesis of organic matter, nature of its diagenetic changes, and current stage of catagenesis.

Pollen distribution in marine sediment samples along the south-western African coast

The distribution of pollen in marine sediments is used to reconstruct pathways of terrigenous input to the oceans and provides a record of vegetation change on adjacent continents. The wind transport routes of aeolian pollen is comprehensively illustrated by clusters of trajectories. Isobaric, 4-day backward trajectories are calculated using the modelled wind-field of ECHAM3, and are clustered on a seasonal basis to estimate the main pathways of aeolian particles to sites of marine cores in the south-eastern Atlantic. Trajectories and clusters based on the modelled wind-field of the Last Glacial Maximum hardly differ from those of the present-day. Trajectory clusters show three regional, and two seasonal patterns, determining the pathways of aeolian pollen transport into the south-eastern Atlantic ocean. Mainly, transport out of the continent occurs during austral fall and winter, when easterly and south-easterly winds prevail. South of 25°S, winds blow mostly from the west and southwest, and aeolian terrestrial input is very low. Generally, a good latitudinal correspondence exists between the distribution patterns of pollen in marine surface sediments and the occurrence of the source plants on the adjacent continent. The northern Angola Basin receives pollen and spores from the Congolian and Zambezian forests mainly through river discharge. The Zambezian vegetation zone is the main source area for wind-blown pollen in sediments of the Angola Basin, while the semi-desert and desert areas are the main sources for pollen in sediments of the Walvis Basin and on the Walvis Ridge. A transect of six marine pollen records along the south-western African coast indicates considerable changes in the vegetation of southern Africa between glacial and interglacial periods. Important changes in the vegetation are the decline of forests in equatorial Africa and the north of southern Africa and a northward shift of winter rain vegetation along the western escarpment.

Pollen analysis of sediment cores from the mouth of the river Congo to Walvis Bay and Lüderitz

The distribution of pollen in marine sediments is used to record vegetation changes over the past 30,000 years on the adjacent continent. A transect of marine pollen sequences from the mouth of the river Congo (~5°S) to Walvis Bay and Lüderitz (~25°S) shows vegetation changes in Congo, Angola and Namibia from the last glacial period into the Holocene. The comparison of pollen records from different latitudes provides information about the latitudinal shift of open forest and savannahs (Poaceae pollen), the extension of lowland forest (rain forest pollen) and Afromontane forest (Podocarpus pollen), and the position of the desert fringe (pollen of Caryophyllaceae, Chenopodiaceae and Amaranthaceae). High Cyperaceae pollen percentages in sediments from the last glacial period off the mouth of the river Congo suggest the presence of open swamps rather than savannah vegetation in the Congo Basin. Pollen from Restionaceae in combination with Stoebe-type pollen (probably from Elytropappus) indicates a possible northwards extension of winter rain vegetation during the last glacial period. The record of Rhizophora (mangrove) pollen is linked to erosion of the continental shelf and sea-level rise. Pollen influx is highest off river mouths (10-2000 grains year**-1 cm**-2), close to the coast (300-6000 grains year**-1 cm**-2), but is an order of magnitude lower at sites situated far from the continent (<10 grains year**-1 cm**-2).

Pollen analysis and age model of sediment core GIK-15856-2

Pollen and spores from a deep-sea core located west of the Niger Delta record an uninterrupted area of lowland rain forest in West Africa from Guinea to Cameroon during the last Interglacial and the early Holocene. During other periods of the last 150 ka, a savanna corridor between the western - Guinean - and the eastern - Congolian - part of the African lowland rain forest existed. This so-called Dahomey Gap had its largest extension during Glacial Stages 6, 4, 3, and 2. Reduced surface salinity in the eastern Gulf of Guinea as recorded by dinoflagellate cysts indicates sufficient precipitation for extensive forest growth during Stages 5 and 1. The large modern extension of dry forest and savanna in West Africa cannot be solely explained by climatic factors. Mangrove expansion in and west of the Niger Delta was largest during the phases of sea-level rise of Stages 5 and 1. During Stages 6, 4, 3, and 2, shelf areas were exposed and the area of the mangrove swamps was minimal.