Novel high-resolution characterization of ancient DNA reveals C > U-type base modification events as the sole cause of post mortem miscoding lesions

Ancient DNA (aDNA) research has long depended on the power of PCR to amplify trace amounts of surviving genetic material from preserved specimens. While PCR permits specific loci to be targeted and amplified, in many ways it can be intrinsically unsuited to damaged and degraded aDNA templates. PCR amplification of aDNA can produce highly-skewed distributions with significant contributions from miscoding lesion damage and non-authentic sequence artefacts. As traditional PCR-based approaches have been unable to fully resolve the molecular nature of aDNA damage over many years, we have developed a novel single primer extension (SPEX)-based approach to generate more accurate sequence information. SPEX targets selected template strands at defined loci and can generate a quantifiable redundancy of coverage; providing new insights into the molecular nature of aDNA damage and fragmentation. SPEX sequence data reveals inherent limitations in both traditional and metagenomic PCR-based approaches to aDNA, which can make current damage analyses and correct genotyping of ancient specimens problematic. In contrast to previous aDNA studies, SPEX provides strong quantitative evidence that C U-type base modifications are the sole cause of authentic endogenous damage-derived miscoding lesions. This new approach could allow ancient specimens to be genotyped with unprecedented accuracy.

Duration from vine emergence to flowering suggests a long-day or rate of change of photoperiod response in white yam (Dioscorea rotundata Poir.)

The objective of this study was to quantify the effect of photoperiod on the duration from vine (shoot) emergence to flowering in white or Guinea yam (Dioscorea rotundata). The duration from vine emergence to flowering in two clonal varieties of yam (TDr 131 and TDr 99-9) was recorded at 10 different sowing dates/locations in Nigeria. Durations to flowering varied from 40 to > 88 days. Mean daily temperature and photoperiod between vine emergence and flowering varied from 25 to 27 degrees C and 13.1 to 13.4 h day(-1), respectively. Both clones had similar responses to temperature, with base and optimum temperatures of 12 and 25-27 degrees C, respectively. Thermal durations to flowering were strongly related (r(2) > 0.75-0.83) to absolute photoperiod (h) at vine emergence as well as to rate of change of photoperiod (s day(-1)) at vine emergence. The response to absolute photoperiod suggests that white yams are quantitative LDPs, flowering sooner in long than short days. Yams also flowered earlier when the rate of change of photoperiod was positive but small, or was negative. It is suggested that yams may use a combination of photoperiod and rate of change in order to fine tune flowering time. (c) 2006 Elsevier B.V. All rights reserved.

Far-red light filtering by plastic film, greenhouse-cladding materials: effects on growth and flowering in Petunia and Impatiens

Photoselective plastic films with low transmission to far-red (FR) light (700-800 nm) are now available so that plants grown in greenhouses clad with such plastics exhibit reduced stem extension and, consequently, plant height. Here we compare the action of three FR-absorbing polythene films on extension growth of Petunia (Petunia X hybrida) cv. 'Express Blue' and Impatiens walleriana cv. 'Accent Deep Pink' with plants grown under a control polythene film (standard UVI/EVA film). Half of the plants under the control film were treated with a chemical plant growth regulator (PGR; diaminozide, B-Nine) and half were sprayed with water alone. Possible negative effects of such film plastics on flowering, and on fresh and dry weight accumulation, were also quantified. Plants were harvested destructively when all plants in each treatment had reached the first open flower stage. In Petunia, plant height was reduced by all three FR-filtering films and by PGR-treatment. The FR-filtering films giving the highest R:FR ratios also reduced plant height in Impatiens. Leaf number, leaf area and total dry Weight in both species. were greatest in the controls and smallest under films with the lowest PAR transmission. The film giving the highest R:FR ratio and PAR transmission also produced the most compact Petunia plants;, while the film. with. the lowest PAR transmission produced the least compact plants in both species. There was no significant effect of treatments on time to first flower in Impatiens. However, Petunia plants under low PAR transmission films took longer to flower. Plastic-films which filter out FR light to increase the R:FR ratio, combined With high PAR transmission, can therefore be used as an alternative to conventional PGRs.

Leafy, terminal flower1 and agamous are functionally conserved but do not regulate terminal flowering and floral determinacy in Impatiens balsamina

In Impatiens balsamina a lack of commitment of the meristem during floral development leads to the continuous requirement for a leaf-derived floral signal. In the absence of this signal the meristem reverts to leaf production. Current models for Arabidopsis state that LEAFY (LFY) is central to the integration of floral signals and regulates flowering partly via interactions with TERMINAL FLOWER1 (TFL1) and AGAMOUS (AG). Here we describe Impatiens homologues of LFY, TFL1 and AG (IbLFY, IbTFL1 and IbAG) that are highly conserved at a sequence level and demonstrate homologous functions when expressed ectopically in transgenic Arabidopsis. We relate the expression patterns of IbTFL1 and IbAG to the control of terminal flowering and floral determinacy in Impatiens. IbTFL1 is involved in controlling the phase of the axillary meristems and is expressed in axillary shoots and axillary meristems which produce inflorescences, but not in axillary flowers. It is not involved in maintaining the terminal meristem in either an inflorescence or indeterminate state. Terminal flowering in Impatiens appears therefore to be controlled by a pathway that uses a different integration system than that regulating the development of axillary flowers and branches. The pattern of ovule production in Impatiens requires the meristem to be maintained after the production of carpels. Consistent with this morphological feature IbAG appears to specify stamen and carpel identity, but is not sufficient to specify meristem determinacy in Impatiens.

The development of ISSR-derived SCAR markers around the Seasonal Flowering Locus (SFL) in fragaria vesca

Fragaria vesca is a short-lived perennial with a seasonal-flowering habit. Seasonality of flowering is widespread in the Rosaceae and is also found in the majority of temperate polycarpic perennials. Genetic analysis has shown that seasonal flowering is controlled by a single gene in F. vesca, the SEASONAL FLOWERING LOCUS (SFL). Here, we report progress towards the marker-assisted selection and positional cloning of SFL, in which three ISSR markers linked to SFL were converted to locus-specific sequence-characterized amplified region (SCAR1–SCAR3) markers to allow large-scale screening of mapping progenies. We believe this is the first study describing the development of SCAR markers from ISSR profiles. The work also provides useful insight into the nature of polymorphisms generated by the ISSR marker system. Our results indicate that the ISSR polymorphisms originally detected were probably caused by point mutations in the positions targeted by primer anchors (causing differential PCR failure), by indels within the amplicon (leading to variation in amplicon size) and by internal sequence differences (leading to variation in DNA folding and so in band mobility). The cause of the original ISSR polymorphism was important in the selection of appropriate strategies for SCAR-marker development. The SCAR markers produced were mapped using a F. vesca f. vesca × F. vesca f. semperflorens testcross population. Marker SCAR2 was inseparable from the SFL, whereas SCAR1 mapped 3.0 cM to the north of the gene and SCAR3 1.7 cM to its south.

The effect of temperature, photosynthetic photon flux density, and photoperiod on the vegetative growth and flowering of 'Autumn Bliss' raspberry

The effects of temperature, photosynthetic photon flux density (PPFD) and photoperiod on vegetative growth and flowering of the raspberry (Rubus idaeus L.) 'Autumn Bliss' were investigated. Increased temperature resulted in an increased rate of vegetative growth and a greater rate of progress to flowering. Optimum temperatures lay in the low to mid 20degreesC range. Above this the rate of plant development declined. Increased PPFD also advanced flowering. While photoperiod did not significantly affect the rate of vegetative growth, flowering occurred earliest at intermediate photoperiods and was delayed by extreme photoperiods. These responses suggest that there is potential for adjusting cropping times of raspberry grown under protection by manipulating the environment, especially temperature.

Lag-1 sparing in the attentional blink: benefits and costs of integrating two events into a single episode

When people monitor a visual stream of rapidly presented stimuli for two targets (T1 and T2), they often miss T2 if it falls into a time window of about half a second after T1 onset-the attentional blink. However, if T2 immediately follows T1, performance is often reported being as good as that at long lags-the so-called Lag-1 sparing effect. Two experiments investigated the mechanisms underlying this effect. Experiment 1 showed that, at Lag 1, requiring subjects to correctly report both identity and temporal order of targets produces relatively good performance on T2 but relatively bad performance on T1. Experiment 2 confirmed that subjects often confuse target order at short lags, especially if the two targets are equally easy to discriminate. Results suggest that, if two targets appear in close succession, they compete for attentional resources. If the two competitors are of unequal strength the stronger one is more likely to win and be reported at the expense of the other. If the two are equally strong, however, they will often be integrated into the same attentional episode and thus get both access to attentional resources. But this comes with a cost, as it eliminates information about the targets' temporal order.

The roles of perirhinal cortex, postrhinal cortex, and the fornix in memory for objects, contexts, and events in the rat

Investigation of the anatomical substructure of the medial temporal lobe has revealed a number of highly interconnected areas, which has led some to propose that the region operates as a unitary memory system. However, here we outline the results of a number of studies from our laboratories, which investigate the contributions of the rat's perirhinal cortex and postrhinal cortex to memory, concentrating particularly on their respective roles in memory for objects. By contrasting patterns of impairment and spared abilities on a number of related tasks, we suggest that perirhinal cortex and postrhinal cortex make distinctive contributions to learning and memory: for example, that postrhinal cortex is important in learning about within-scene position and context. We also provide evidence that despite the strong connectivity between these cortical regions and the hippocampus, the hippocampus, as evidenced by lesions of the fornix, has a distinct function of its own-combining information about objects, positions, and contexts.

A fuzzy multi-criteria decision approach for enhanced auto-tracking of seismic events

The main activity carried out by the geophysicist when interpreting seismic data, in terms of both importance and time spent is tracking (or picking) seismic events. in practice, this activity turns out to be rather challenging, particularly when the targeted event is interrupted by discontinuities such as geological faults or exhibits lateral changes in seismic character. In recent years, several automated schemes, known as auto-trackers, have been developed to assist the interpreter in this tedious and time-consuming task. The automatic tracking tool available in modem interpretation software packages often employs artificial neural networks (ANN's) to identify seismic picks belonging to target events through a pattern recognition process. The ability of ANNs to track horizons across discontinuities largely depends on how reliably data patterns characterise these horizons. While seismic attributes are commonly used to characterise amplitude peaks forming a seismic horizon, some researchers in the field claim that inherent seismic information is lost in the attribute extraction process and advocate instead the use of raw data (amplitude samples). This paper investigates the performance of ANNs using either characterisation methods, and demonstrates how the complementarity of both seismic attributes and raw data can be exploited in conjunction with other geological information in a fuzzy inference system (FIS) to achieve an enhanced auto-tracking performance.

Export of dissolved organic carbon from an upland peatland during storm events: implications for flux estimates

Most of the dissolved organic carbon (DOC) exported from catchments is transported during storm events. Accurate assessments of DOC fluxes are essential to understand long-term trends in the transport of DOC from terrestrial to aquatic systems, and also the loss of carbon from peatlands to determine changes in the source/sink status of peatland carbon stores. However, many long-term monitoring programmes collect water samples at a frequency (e.g. weekly/monthly) less than the time period of a typical storm event (typically <1–2 days). As widespread observations in catchments dominated by organo-mineral soils have shown that both concentration and flux of DOC increases during storm events, lower frequency monitoring could result in substantial underestimation of DOC flux as the most dynamic periods of transport are missed. However, our intensive monitoring study in a UK upland peatland catchment showed a contrasting response to these previous studies. Our results showed that (i) DOC concentrations decreased during autumn storm events and showed a poor relationship with flow during other seasons; and that (ii) this decrease in concentrations during autumn storms caused DOC flux estimates based on weekly monitoring data to be over-estimated, rather than under-estimated, because of over rather than under estimation of the flow-weighted mean concentration used in flux calculations. However, as DOC flux is ultimately controlled by discharge volume, and therefore rainfall, and the magnitude of change in discharge was greater than the magnitude of decline in concentrations, DOC flux increased during individual storm events. The implications for long-term DOC trends are therefore contradictory, as increased rainfall could increase flux but cause an overall decrease in DOC concentrations from peatland streams. Care needs to be taken when interpreting long-term trends in DOC flux rather than concentration; as flux is calculated from discharge estimates, and discharge is controlled by rainfall, DOC flux and rainfall/discharge will always be well correlated.

Transfer of conceptualisation patterns in bilinguals: the construal of motion events in Turkish and German

We test Slobin's (2003) Thinking-for-Speaking hypothesis on data from different groups of Turkish-German bilinguals, those living in Germany and those who have returned to Germany.