Land plants and DNA barcodes: short-term and long-term goals

Land plants have had the reputation of being problematic for DNA barcoding for two general reasons: (i) the standard DNA regions used in algae, animals and fungi have exceedingly low levels of variability and (ii) the typically used land plant plastid phylogenetic markers (e.g. rbcL, trnL-F, etc.) appear to have too little variation. However, no one has assessed how well current phylogenetic resources might work in the context of identification (versus phylogeny reconstruction). In this paper, we make such an assessment, particularly with two of the markers commonly sequenced in land plant phylogenetic studies, plastid rbcL and internal transcribed spacers of the large subunits of nuclear ribosomal DNA (ITS), and find that both of these DNA regions perform well even though the data currently available in GenBank/EBI were not produced to be used as barcodes and BLAST searches are not an ideal tool for this purpose. These results bode well for the use of even more variable regions of plastid DNA (such as, for example, psbA-trnH) as barcodes, once they have been widely sequenced. In the short term, efforts to bring land plant barcoding up to the standards being used now in other organisms should make swift progress. There are two categories of DNA barcode users, scientists in fields other than taxonomy and taxonomists. For the former, the use of mitochondrial and plastid DNA, the two most easily assessed genomes, is at least in the short term a useful tool that permits them to get on with their studies, which depend on knowing roughly which species or species groups they are dealing with, but these same DNA regions have important drawbacks for use in taxonomic studies (i.e. studies designed to elucidate species limits). For these purposes, DNA markers from uniparentally (usually maternally) inherited genomes can only provide half of the story required to improve taxonomic standards being used in DNA barcoding. In the long term, we will need to develop more sophisticated barcoding tools, which would be multiple, low-copy nuclear markers with sufficient genetic variability and PCR-reliability; these would permit the detection of hybrids and permit researchers to identify the 'genetic gaps' that are useful in assessing species limits.

Process planning methodology: dynamic short-term planning for off-site construction in Slovenia

Planning is a vital element of project management but it is still not recognized as a process variable. Its objective should be to outperform the initially defined processes, and foresee and overcome possible undesirable events. Detailed task-level master planning is unrealistic since one cannot accurately predict all the requirements and obstacles before work has even started. The process planning methodology (PPM) has thus been developed in order to overcome common problems of the overwhelming project complexity. The essential elements of the PPM are the process planning group (PPG), including a control team that dynamically links the production/site and management, and the planning algorithm embodied within two continuous-improvement loops. The methodology was tested on a factory project in Slovenia and in four successive projects of a similar nature. In addition to a number of improvement ideas and enhanced communication, the applied PPM resulted in 32% higher total productivity, 6% total savings and created a synergistic project environment.

Pea-barley intercropping and short-term subsequent crop effects across European organic cropping conditions

Grain legumes are known to increase the soil mineral nitrogen (N) content, reduce the infection pressure of soil borne pathogens, and hence enhance subsequent cereals yields. Replicated field experiments were performed throughout W. Europe (Denmark, United Kingdom, France, Germany and Italy) to asses the effect of intercropping pea and barley on the N supply to subsequent wheat in organic cropping systems. Pea and barley were grown either as sole crops at the recommended plant density (P100 and B100, respectively) or in replacement (P50B50) or additive (P100B50) intercropping designs. In the replacement design the total relative plant density is kept constant, while the additive design uses the optimal sole crop density for pea supplementing with 'extra' barley plants. The pea and barley crops were followed by winter wheat with and without N application. Additional experiments in Denmark and the United Kingdom included subsequent spring wheat with grass-clover as catch crops. The experiment was repeated over the three cropping seasons of 2003, 2004 and 2005. Irrespective of sites and intercrop design pea-barley intercropping improved the plant resource utilization (water, light, nutrients) to grain N yield with 25-30% using the Land Equivalent ratio. In terms of absolute quantities, sole cropped pea accumulated more N in the grains as compared to the additive design followed by the replacement design and then sole cropped barley. The post harvest soil mineral N content was unaffected by the preceding crops. Under the following winter wheat, the lowest mineral N content was generally found in early spring. Variation in soil mineral N content under the winter wheat between sites and seasons indicated a greater influence of regional climatic conditions and long-term cropping history than annual preceding crop and residue quality. Just as with the soil mineral N, the subsequent crop response to preceding crop was negligible. Soil N balances showed general negative values in the 2-year period, indicating depletion of N independent of preceding crop and cropping strategy. It is recommended to develop more rotational approaches to determine subsequent crop effects in organic cropping systems, since preceding crop effects, especially when including legumes, can occur over several years of cropping.

The effects of a short-term increase in supplementation on the reproduction performance in lactating crossbred dairy cows

The hypothesis that dairy cows partially suckling their calves would ovulate following removal of calves when restored to positive energy balance by a short-term increase in supplementation was investigated in 65 crossbred cows. Five treatments (T1, T2, T3, T4, and T5) that differed in the amount of total concentrate fed from calving to week 24 were involved. Calves were allowed to suck residual milk to 12 weeks of age. Energy balance was estimated by measuring intake, milk yield and organic matter digestibility. The occurrence of ovulation was determined by the analysis of milk progesterone (P4) concentration. Four groups that were receiving additional supplementation were restored to positive energy balance, while the control group (T I) remained in negative energy balance. The percentage of cows ovulating was 36%, 58%, 92%, 90% and 60% for T1, T2, T3, T4 and T5, respectively (P = 0.026). Comparison of the timing of ovulation for combined results from T1+T2 and T3+T4+T5 estimated mean time to fail to ovulate as 110 +/- 9.0 and 87 +/- 7.6 days, respectively (p = 0.023). The percentage of the cows showing oestrus was 9%, 8%, 33%, 40% and 40% for T1, T2, T3, T4 and T5, respectively (P = 0.197). Short-term increases in supplementation are unlikely to be an attractive means of reducing calving intervals.

Temporal interval production and short-term memory

Interference with time estimation from concurrent nontemporal processing has been shown to depend on the short-term memory requirements of the concurrent task (Fortin Breton, 1995; Fortin, Rousseau, Bourque, & Kirouac, 1993). In particular, it has been claimed that active processing of information in short-term memory produces interference, whereas simply maintaining information does not. Here, four experiments are reported in which subjects were trained to produce a 2,500-msec interval and then perform concurrent memory tasks. Interference with timing was demonstrated for concurrent memory tasks involving only maintenance. In one experiment, increasing set size in a pitch memory task systematically lengthened temporal production. Two further experiments suggested that this was due to a specific interaction between the short-term memory requirements of the pitch task and those of temporal production. In the final experiment, subjects performed temporal production while concurrently remembering the durations of a set of tones. Interference with interval production was comparable to that produced by the pitch memory task. Results are discussed in terms of a pacemaker-counter model of temporal processing, in which the counter component is supported by short-term memory.

Short-term memory and the attentional blink: capacity versus content

When people monitor the rapid serial visual presentation (RSVP) of 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, a phenomenon known as the attentional blink (AB). We found that overall performance in an RSVP task was impaired by a concurrent short-term memory (STM) task and, furthermore, that this effect increased when STM load was higher and when its content was more task relevant. Loading visually defined stimuli and adding articulatory suppression further impaired performance on the RSVP task, but the size of the AB over time (i.e., T1-T2 lag) remained unaffected by load or content. This suggested that at least part of the performance in an RSVP task reflects interference between competing codes within STM, as interference models have held, whereas the AB proper reflects capacity limitations in the transfer to STM, as consolidation models have claimed.

Speech perception and phonological short-term memory capacity in language impairment: preliminary evidence from adolescents with specific language impairment (SLI) and autism spectrum disorders (ASD)

Background: The cognitive bases of language impairment in specific language impairment (SLI) and autism spectrum disorders (ASD) were investigated in a novel non-word comparison task which manipulated phonological short-term memory (PSTM) and speech perception, both implicated in poor non-word repetition. Aims: This study aimed to investigate the contributions of PSTM and speech perception in non-word processing and whether individuals with SLI and ASD plus language impairment (ALI) show similar or different patterns of deficit in these cognitive processes. Method & Procedures: Three groups of adolescents (aged 14–17 years), 14 with SLI, 16 with ALI, and 17 age and non-verbal IQ matched typically developing (TD) controls, made speeded discriminations between non-word pairs. Stimuli varied in PSTM load (two- or four-syllables) and speech perception load (mismatches on a word-initial or word-medial segment). Outcomes & Results: Reaction times showed effects of both non-word length and mismatch position and these factors interacted: four-syllable and word-initial mismatch stimuli resulted in the slowest decisions. Individuals with language impairment showed the same pattern of performance as those with typical development in the reaction time data. A marginal interaction between group and item length was driven by the SLI and ALI groups being less accurate with long items than short ones, a difference not found in the TD group. Conclusions & Implications: Non-word discrimination suggests that there are similarities and differences between adolescents with SLI and ALI and their TD peers. Reaction times appear to be affected by increasing PSTM and speech perception loads in a similar way. However, there was some, albeit weaker, evidence that adolescents with SLI and ALI are less accurate than TD individuals, with both showing an effect of PSTM load. This may indicate, at some level, the processing substrate supporting both PSTM and speech perception is intact in adolescents with SLI and ALI, but also in both there may be impaired access to PSTM resources.

An analysis of long-term trends, seasonality and short-term dynamics in water quality data from Plynlimon, Wales

This paper examines two hydrochemical time-series derived from stream samples taken in the Upper Hafren catchment, Plynlimon, Wales. One time-series comprises data collected at 7-hour intervals over 22 months (Neal et al., submitted, this issue), while the other is based on weekly sampling over 20 years. A subset of determinands: aluminium, calcium, chloride, conductivity, dissolved organic carbon, iron, nitrate, pH, silicon and sulphate are examined within a framework of non-stationary time-series analysis to identify determinand trends, seasonality and short-term dynamics. The results demonstrate that both long-term and high-frequency monitoring provide valuable and unique insights into the hydrochemistry of a catchment. The long-term data allowed analysis of long-termtrends, demonstrating continued increases in DOC concentrations accompanied by declining SO4 concentrations within the stream, and provided new insights into the changing amplitude and phase of the seasonality of the determinands such as DOC and Al. Additionally, these data proved invaluable for placing the short-term variability demonstrated within the high-frequency data within context. The 7-hour data highlighted complex diurnal cycles for NO3, Ca and Fe with cycles displaying changes in phase and amplitude on a seasonal basis. The high-frequency data also demonstrated the need to consider the impact that the time of sample collection can have on the summary statistics of the data and also that sampling during the hours of darkness provides additional hydrochemical information for determinands which exhibit pronounced diurnal variability. Moving forward, this research demonstrates the need for both long-term and high-frequency monitoring to facilitate a full and accurate understanding of catchment hydrochemical dynamics.

Moving the nanoscience and technology (NST) debate forwards: short-term impacts, long-term uncertainty and the social constitution

Nanoscience and technology (NST) are widely cited to be the defining technology for the 21st century. In recent years, the debate surrounding NST has become increasingly public, with much of this interest stemming from two radically opposing long-term visions of a NST-enabled future: ‘nano-optimism’ and ‘nano-pessimism’. This paper demonstrates that NST is a complex and wide-ranging discipline, the future of which is characterised by uncertainty. It argues that consideration of the present-day issues surrounding NST is essential if the public debate is to move forwards. In particular, the social constitution of an emerging technology is crucial if any meaningful discussion surrounding costs and benefits is to be realised. An exploration of the social constitution of NST raises a number of issues, of which unintended consequences and the interests of those who own and control new technologies are highlighted.