Progressive erosion of genetic and epigenetic variation in callus-derived cocoa (Theobroma cacao) plants

Relatively little is known about the timing of genetic and epigenetic forms of somaclonal variation arising from callus growth. We surveyed for both types of change in cocoa (Theobroma cacao) plants regenerated from calli of various ages, and also between tissues from the source trees. For genetic change, we used 15 single sequence repeat (SSR) markers from four source trees and from 233 regenerated plants. For epigenetic change, we used 386 methylation-sensitive amplified polymorphism (MSAP) markers on leaf and explant (staminode) DNA from two source trees and on leaf DNA from 114 regenerants. Genetic variation within source trees was limited to one slippage mutation in one leaf. Regenerants were far more variable, with 35% exhibiting at least one mutation. Genetic variation initially accumulated with culture age but subsequently declined. MSAP (epigenetic) profiles diverged between leaf and staminode samples from source trees. Multivariate analysis revealed that leaves from regenerants occupied intermediate eigenspace between leaves and staminodes of source plants but became progressively more similar to source tree leaves with culture age. Statistical analysis confirmed this rather counterintuitive finding that leaves of ‘late regenerants’ exhibited significantly less genetic and epigenetic divergence from source leaves than those exposed to short periods of callus growth.

Assessing the spatial and temporal variation in the skill of precipitation forecasts from an NWP model

It is becoming increasingly important to be able to verify the spatial accuracy of precipitation forecasts, especially with the advent of high-resolution numerical weather prediction (NWP) models. In this article, the fractions skill score (FSS) approach has been used to perform a scale-selective evaluation of precipitation forecasts during 2003 from the Met Office mesoscale model (12 km grid length). The investigation shows how skill varies with spatial scale, the scales over which the data assimilation (DA) adds most skill, and how the loss of that skill is dependent on both the spatial scale and the rainfall coverage being examined. Although these results come from a specific model, they demonstrate how this verification approach can provide a quantitative assessment of the spatial behaviour of new finer-resolution models and DA techniques.

A geostatistical analysis of soil, vegetation, and image data characterizing land surface variation

The elucidation of spatial variation in the landscape can indicate potential wildlife habitats or breeding sites for vectors, such as ticks or mosquitoes, which cause a range of diseases. Information from remotely sensed data could aid the delineation of vegetation distribution on the ground in areas where local knowledge is limited. The data from digital images are often difficult to interpret because of pixel-to-pixel variation, that is, noise, and complex variation at more than one spatial scale. Landsat Thematic Mapper Plus (ETM+) and Satellite Pour l'Observation de La Terre (SPOT) image data were analyzed for an area close to Douna in Mali, West Africa. The variograms of the normalized difference vegetation index (NDVI) from both types of image data were nested. The parameters of the nested variogram function from the Landsat ETM+ data were used to design the sampling for a ground survey of soil and vegetation data. Variograms of the soil and vegetation data showed that their variation was anisotropic and their scales of variation were similar to those of NDVI from the SPOT data. The short- and long-range components of variation in the SPOT data were filtered out separately by factorial kriging. The map of the short-range component appears to represent the patterns of vegetation and associated shallow slopes and drainage channels of the tiger bush system. The map of the long-range component also appeared to relate to broader patterns in the tiger bush and to gentle undulations in the topography. The results suggest that the types of image data analyzed in this study could be used to identify areas with more moisture in semiarid regions that could support wildlife and also be potential vector breeding sites.

Genetic variation in GABRB3 is associated with Asperger syndrome and multiple endophenotypes relevant to autism.

BACKGROUND: Autism spectrum conditions (ASC) are associated with deficits in social interaction and communication, alongside repetitive, restricted, and stereotyped behavior. ASC is highly heritable. The gamma-aminobutyric acid (GABA)-ergic system has been associated consistently with atypicalities in autism, in both genetic association and expression studies. A key component of the GABA-ergic system is encoded by the GABRB3 gene, which has been previously implicated both in ASC and in individual differences in empathy. METHODS: In this study, 45 genotyped single nucleotide polymorphisms (SNPs) within GABRB3 were tested for association with Asperger syndrome (AS), and related quantitative traits measured through the following tests: the Empathy Quotient (EQ), the Autism Spectrum Quotient (AQ), the Systemizing Quotient-Revised (SQ-R), the Embedded Figures Test (EFT), the Reading the Mind in the Eyes Test (RMET), and the Mental Rotation Test (MRT). Two-loci, three-loci, four-loci haplotype analyses, and one seven-loci haplotype analysis were also performed in the AS case--control sample. RESULTS: Three SNPs (rs7180158, rs7165604, rs12593579) were significantly associated with AS, and two SNPs (rs9806546, rs11636966) were significantly associated with EQ. Two SNP-SNP pairs, rs12438141-rs1035751 and rs12438141-rs7179514, showed significant association with variation in the EFT scores. One SNP-SNP pair, rs7174437-rs1863455, was significantly associated with variation in the MRT scores. Additionally, a few haplotypes, including a 19 kb genomic region that formed a linkage disequilibrium (LD) block in our sample and contained several nominally significant SNPs, were found to be significantly associated with AS. CONCLUSION: The current study confirms the role of GABRB3 as an important candidate gene in both ASC and normative variation in related endophenotypes.

ENSO related variation of equatorial MRG and Rossby waves and forcing from higher latitudes

The contrasting behaviour of westward-moving mixed Rossby-gravity (WMRG) and the first Rossby (R1) waves in El Niño (EN) and La Niña (LN) seasons is documented with a focus on the Northern Hemisphere winter. The eastward-moving variance in the upper troposphere is dominated by WMRG and R1 structures that appear to be Doppler-shifted by the flow and are referred to as WMRG-E and R1-E. In the East Pacific and Atlantic the years with stronger equatorial westerly winds have the stronger WMRG and WMRG- E. In the East Pacific, R1 is also a maximum in LN. However, R1-E exhibits an eastward-shift between LN and EN. The changes with ENSO phase provide a test-bed for the understanding of these waves. In the East Pacific and Atlantic, the stronger WMRG-E and WMRG with stronger westerlies are in accord with the dispersion relation with simple Doppler-shifting by the zonal flow. The possible existence of free waves can also explain stronger R1 in EN in the Eastern Hemisphere. 1-D free wave propagation theory based on wave activity conservation is also important for R1. However, this theory is unable to explain the amplitude maxima for other waves observed in the strong equatorial westerly regions in the Western Hemisphere, and certainly not their ENSO-related variation. The forcing of equatorial waves by higher latitude wave activity and its variation with ENSO phase is therefore examined. Propagation of extratropical eastward-moving Rossby wave activity through the westerly ducts into the equatorial region where it triggers WMRG-E is favoured in the stronger westerlies, in LN in the East Pacific and EN in the Atlantic. It is also found that WMRG is forced by Southern Hemisphere westward-moving wavetrains arching into the equatorial region where they are reflected. The most significant mechanism for both R1 and R1-E appear to be lateral forcing by subtropical wavetrains.

Granulometric characterization and evaluation of annually banded mid-Holocene estuarine silts, Welsh Severn Estuary (UK): coastal change, sea level and climate

Holocene silts (salt marshes) and highest intertidal-supratidal peats are superbly exposed on a 15 kin coastal transect which reveals two laterally extensive units of annually banded silts (Beds 3, 7) associated with three transgressive-regressive silt-peat cycles (early sixth-early fourth millennium BC). Bed 3 in places is concordantly and gradationally related to peats above and below, but in others transgresses older strata. Bed 7 also grades up into peat, but everywhere overlies a discordance. The banding in Bed 3 at three main and two minor sites was resolved and characterized texturally at high-resolution (2.5/5 mm contiguous slices) using laser granulometry (LS230 with PIDS) and a comprehensive scheme of data-assessment. Most of Bed 3 formed very rapidly, at peak values of several tens of millimetres annually, in accordance with modelled effects of sea-level fluctuations on mature marshes (bed concordant and gradational) and on marshes growing up after coastal erosion and retreat (bed with discordant base). Using data from the modern Severn Estuary, the textural contrast within bands, and its variation between bands, points to a variable but overall milder mid-Holocene climate than today. The inter-annual variability affected marsh dynamics, as shown by the behaviour of the finely divided plant tissues present. Given local calibration, the methodology is applicable to other tidal systems with banded silts in Britain and mainland northwest Europe. (c) 2006 Elsevier Ltd. All rights reserved.

Modelling the lava dome extruded at Soufrière Hills Volcano, Montserrat, August 2005–May 2006. Part II: Rockfall activity and talus deformation

During many lava dome-forming eruptions, persistent rockfalls and the concurrent development of a substantial talus apron around the foot of the dome are important aspects of the observed activity. An improved understanding of internal dome structure, including the shape and internal boundaries of the talus apron, is critical for determining when a lava dome is poised for a major collapse and how this collapse might ensue. We consider a period of lava dome growth at the Soufrière Hills Volcano, Montserrat, from August 2005 to May 2006, during which a 100 × 106 m3 lava dome developed that culminated in a major dome-collapse event on 20 May 2006. We use an axi-symmetrical Finite Element Method model to simulate the growth and evolution of the lava dome, including the development of the talus apron. We first test the generic behaviour of this continuum model, which has core lava and carapace/talus components. Our model describes the generation rate of talus, including its spatial and temporal variation, as well as its post-generation deformation, which is important for an improved understanding of the internal configuration and structure of the dome. We then use our model to simulate the 2005 to 2006 Soufrière Hills dome growth using measured dome volumes and extrusion rates to drive the model and generate the evolving configuration of the dome core and carapace/talus domains. The evolution of the model is compared with the observed rockfall seismicity using event counts and seismic energy parameters, which are used here as a measure of rockfall intensity and hence a first-order proxy for volumes. The range of model-derived volume increments of talus aggraded to the talus slope per recorded rockfall event, approximately 3 × 103–13 × 103 m3 per rockfall, is high with respect to estimates based on observed events. From this, it is inferred that some of the volumetric growth of the talus apron (perhaps up to 60–70%) might have occurred in the form of aseismic deformation of the talus, forced by an internal, laterally spreading core. Talus apron growth by this mechanism has not previously been identified, and this suggests that the core, hosting hot gas-rich lava, could have a greater lateral extent than previously considered.

Productivity and optimum plant density of pigeonpea in different environments in Tanzania

The objective of the present study was to determine the optimum plant density of four pigeonpea genotypes, representing early, medium and late maturing types, grown in five contrasting environments in Tanzania. ICPL 86005 (early), Kat 50/3 and QP 37 (medium) and Local (late) were grown at four plant densities (40 000-320 000 plants/ha) in irrigated and rainfed conditions at Ilonga and under rainfed conditions at Kibaha, Selian and Ismani. At maturity, total above-ground biomass and seed yield (SY) were measured. The highest yields were obtained in the irrigated experiment at Ilonga, where the medium/late genotypes produced 25 t biomass/ha and 5 center dot 6 t seed/ha. The lowest SY were at Kibaha, 0 58 to 1 center dot 76 t/ha, where a severe drought occurred. In nearly all cases the response to density was linear or asymptotic. The response of ICPL 86005 was significantly different from the other three genotypes. The optimum density for SY varied from 37 000 to 227 000 plants/ha in ICPL 86005, compared with 3000 to 101000 plants/ha in the medium/late genotypes. The highest optimum density was at Selian and Ismani and the lowest at Ilonga and Kibaha, where drought occurred. Optimum densities therefore varied greatly with genotype (duration) and environment, and this variation needs to be considered when planning trials.

Factors affecting biomass production and nutritive value of Calliandra calothyrsus leaf as fodder for ruminants

Calliandra calothyrsus is a tree legume native to Mexico and Central America. The species has attracted considerable attention for its capacity to produce both fuelwood and foliage for either green manure or fodder. Its high content of proanthocyanidins (condensed tannins) and associated low digestibility has, however, limited its use as a feed for ruminants, and there is also a widespread perception that wilting the leaves further reduces their nutritive value. Nevertheless, there has been increasing uptake of calliandra as fodder in certain regions, notably the Central Highlands of Kenya. The present study, conducted in Embu, Kenya, investigated effects of provenance, wilting, cutting frequency and seasonal variation both in the laboratory (in vitro digestibility, crude protein, neutral detergent fibre, extractable and bound proanthocyanidins) and in on-station animal production trials with growing lambs and lactating goats. The local Kenyan landrace of calliandra (Embu) and a closely-related Guatemalan provenance (Patulul) were found to be significantly different, and superior, to a provenance from Nicaragua (San Ramon) in most of the laboratory traits measured, as well as in animal production and feed efficiency. Cutting frequency had no important effect on quality; and although all quality traits displayed seasonal variation there was little discernible pattern to this variation. Wilting had a much less negative effect than expected, and for lambs fed calliandra as a supplement to a low quality basal feed (maize stover), wilting was actually found to give higher live-weight gain and feed efficiency. Conversely, with a high quality basal diet (Napier grass) wilting enhanced intake but not live-weight gain, so feed efficiency was greater for fresh material. The difference between fresh and wilted leaves was not great enough to justify the current widespread recommendation that calliandra should always be fed fresh.

Genotypic and phenotypic diversity of a baculovirus population within an individual insect host

It is becoming increasingly apparent that many pathogen populations, including those of insects, show high levels of genotypic variation. Baculoviruses are known to be highly variable, with isolates collected from the same species in different geographical locations frequently showing genetic variation and differences in their biology. More recent Studies at smaller scales have also shown that virus DNA profiles from individual larvae can show polymorphisms within and between populations of the same species. Here, we investigate the genotypic and phenotypic variation of an insect baculovirus infection within a single insect host. Twenty four genotypically distinct nucleopolyhedrovirus (NPV) variants were isolated from an individual pine beauty moth, Panolis flammea, caterpillar by in vivo cloning techniques. No variant appeared to be dominant in the population. The Pafl NPV variants have been mapped using three restriction endonucleases and shown to contain three hypervariable regions containing insertions of 70-750 bp. Comparison of seven of these variants in an alternative host, Mamestra brassicae, demonstrated that the variants differed significantly in both pathogenicity and speed of kill. The generation and maintenance of pathogen heterogeneity are discussed. (c) 2005 Elsevier Inc. All rights reserved.

Inter-simple sequence repeat and aggressiveness analyses revealed high genetic diversity, recombination and long-range dispersal in Fusarium culmorum

Inter-simple sequence repeat (ISSR) analysis and aggressiveness assays were used to investigate genetic variability within a global collection of Fusarium culmorum isolates. A set of four ISSR primers were tested, of which three primers amplified a total of 37 bands out of which 30 (81%) were polymorphic. The intraspecific diversity was high, ranging from four to 28 different ISSR genotypes for F. culmorum depending on the primer. The combined analysis of ISSR data revealed 59 different genotypes clustered into seven distinct clades amongst 75 isolates of F. culmorum examined. All the isolates were assayed to test their aggressiveness on a winter wheat cv. 'Armada'. A significant quantitative variation for aggressiveness was found among the isolates. The ISSR and aggressiveness variation existed on a macro- as well as micro-geographical scale. The data suggested a long-range dispersal of F. culmorum and indicated that this fungus may have been introduced into Canada from Europe. In addition to the high level of intraspecific diversity observed in F. culmorum, the index of multilocus association calculated using ISSR data indicated that reproduction in F. culmorum cannot be exclusively clonal and recombination is likely to occur.

Linking carbon and sulphur cycling during simulated drought cycles in peat from six sites across the UK

Water table draw-down is thought to increase peat decomposition and, therefore, DOC release. However, several studies have shown lower DOC concentrations during droughts relative to ‘normal’ periods with high water table. We carried out controlled incubation experiments at 10°C on 10x10 cm peat soil cores collected from six UK sites across a sulphur deposition gradient. Our aim was to quantify the balance between microbial consumption and chemical precipitation of DOC due to episodic acidification driven by sulphur redox reactions by comparing changes in soil water chemistry to microbial activity (i.e. soil respiration and trace gas fluxes). During dry periods, all sites showed a concurrent increase in SO4 and soil respiration and a decline in DOC. However, the magnitude of change in both DOC and SO4 varied considerably between sites according to historical sulphur deposition loads and the variation in acid/base chemistry.