ALBERT

Notes: Abstract. 15N labelled NH4NO3 (fertilizer N) was applied at a rate of 50 kg N ha–1 to an Ando-Humic Nitisol and two maize crops grown on it. About 20 months later, soil cores were taken to a depth of 2.5 m. Leached fertilizer N was found between 1.4 m and 1.8 m deep and was delayed relative to net drainage by between 4.2 and 4.9 pore volumes. Anion exchange capacity (AEC) increased ten-fold down the profile, up to 2.9 cmolckg–1. The delay to fertilizer N leaching was predicted to be between 4.1 and 5.3 pore volumes when calculated from the AEC and from an equation relating delay due to AEC in laboratory columns of repacked soil obtained by Wong et al. (1990b). It was concluded that the nitrate leaching delay equation was also valid in undisturbed field profiles. Two concentration maxima for mineral N were found, which did not usually coincide with the fertilizer N and were thought to result from mineralization of soil organic matter and plant residues at the end of each season. The delay equation overestimated their leaching delay but the results were considered close enough to support the hypothesis for their formation.

Notes: Abstract. Regions in the Po Valley, Northern Italy, are characterized by intensive crop-livestock farming systems. A simulation model has been chosen for an inter-regional project, which should help in defining groundwater vulnerability and pollution risk on a regional scale, in relation to agricultural land use, by allowing the prediction of nitrate leaching under different climate, soil, crop and management scenarios. The model derives from the coupling of a hydrological model, MACRO, simulating water flow and solute transport in structured soils, with a model simulating soil N dynamics, SOILN. The aim of this work was to test the model's ability to simulate nitrate leaching through soil after land spreading of pig slurries. A dataset obtained from lysimeter experiments which had been carried out in the period 1976–1981 was used for this purpose. Four soil types were compared (silty clay, sandy loam, loam and sand) in factorial combination with four rates of pig slurry (0, 142, 284, 426 g of N m–2, accumulated values from 1976 to 1979) for a seven crop sequence. The efficiency of the MACRO model ranged from 0.96, in the sandy-loam soil, to 0.81, in the sand. Percolation was usually under-estimated, the relative error ranging from 0.7 to 14.6, depending on the soil. The low efficiency of the SOILN model in simulating nitrate leaching is attributed to the lack of knowledge of the mechanisms regulating N transformation processes and especially the mineralization of pig slurry N. This lack of knowledge hampers the correct setting of the N transformation parameter values. A remarkable improvement of the model's performance was obtained by changing a few coefficients which control the mineralization-immobilization turnover of the faeces-organic N. The model efficiency, following this recalibration, ranged from –0.62 to 0.84, and the relative error ranged from –56 to 35, depending on soil and treatment. N leaching was under-estimated at the low pig slurry N application rates and over-estimated at the high ones.

Notes: Abstract. The effectiveness of contour grass strips in erosion control was investigated in a field experiment involving two grass treatments (Festuca ovina and Poa pratensis) and a bare soil control on an erodible sandy loam soil on a 5° slope using simulated rainstorms of 40 mm h–1 for 45 minutes duration. The grass strips resulted in significantly (P 〈 0.05) lower runoff and soil loss than the bare soil but there was no significant difference in the performance of the two grasses, despite their differences in density, height and leaf size. The effect of the lower density of the Poa pratensis was offset by its larger stem diameter so that the surface area facing the flow was similar for both grasses. Instead of acting as a filter with sedimentation occurring within the barrier, the grass strips operated by ponding water upslope of the barriers. Deposition then occurred in the ponded area above the barrier.

Notes: Abstract. Since the 1980s, land use in rural areas of China has changed greatly as the result of political initiatives. These changes have caused soil nutrient changes which are examined in this paper for Zunhua County, northern China from 1980 to 1999. The areas of farmland, grassland, and paddy decreased greatly and were replaced by increases in forest and residential land. The soils under forest in 1999 transformed from farmland in 1980 increased in organic matter by 21%, total nitrogen by 18%, available nitrogen by 65%, available phosphorus by 17% and available potassium by 17%. Similarly, in the area which was converted from farmland in 1980 to grassland in 1999, soil organic matter, total nitrogen, available nitrogen, available phosphorus, and available potassium increased by 38%, 37%, 71%, 2% and 28%, respectively. Changes from farmland to forest and grassland not only changed land cover but also improved soil fertility and probably reduced soil nutrient losses.

Notes: Abstract. Much of the low-lying farmland around the coastline of south-east England was once inter-tidal salt marsh, which was subsequently reclaimed from the sea and converted to farmland. It is becoming increasingly uneconomic to maintain the embankments which protect this land from the sea. ‘Managed retreat’ involves relocating the embankments further inland and recreating inter-tidal habitat in front of them. Salt marsh not only provides a protective buffer for these sea walls by dissipating wave energy, but is also important as a habitat for birds and as a source of organic matter for fish and inter-tidal fauna. When ‘managed retreat’ takes place, the creation of inter-tidal habitat occurs on soils that have undergone physical and chemical changes, some of which are irreversible. However, the indications are that rapid sedimentation creates conditions in which salt marsh plants germinate and become established; soil salinity rises quickly to a level which restricts competition from terrestrial plants, and deposited sediment is relatively rich in available phosphorus. The physical properties of the old agricultural soil influence the subsequent development of creeks.

Notes: Abstract. When the farmers of the Highlands of Tigray (northern Ethiopia) consider rock fragment cover in their fields to be excessive, they remove some of them. In addition, large amounts of rock fragments of all sizes are removed from fields for building stone bunds. Semi-structured interviews indicate that the farmers are often reluctant to take away the smaller rock fragments (i.e. 〈 5 cm across) from their fields, since they believe these benefit soil moisture conservation and protect topsoil from erosion. A field experiment was carried out on a Vertic Cambisol (average slope: 0.125 m m–1), 2 km east of Hagere Selam (subhumid climate). Rock fragments were totally, partially or not removed from the 12 runoff plots (5 m × 6 m) before the beginning of the 1999 cropping season, during which a local mixture of wheat varieties (Triticum spp.) was sown. After harvest, erosion rates were assessed by measuring deposited sediment volume in trenches at the lower side of each subplot, and grain and straw yields were assessed. We found a significant negative relationship between rock fragment cover and soil loss by water erosion. However, the resulting positive relationship between rock fragment cover and grain and straw yield was weak. This might be explained by the fact that the plot did not suffer from drought due to soil and climatic conditions. Detailed analysis showed that cover by medium and large rock fragments (〉 2 cm diameter) showed an optimum percentage cover above which crop yields decrease. A recommendation resulting from this study is to rely on the farmers’ experience: smaller rock fragments should never be removed from the surface of fields during soil and water conservation works; instead rock fragment rich soil can be used to top the stone bunds.

Notes: Abstract. The fertilizer nitrogen requirement of winter wheat was assessed in sixteen experiments on marine silt soils in Eastern England. Eight experimental sites followed potatoes (Solanum tuberosum), six vining peas (Pisum sativum) and two wheat (Triticum aestivum). The yield response to nitrogen fertilizer was much less following peas than potatoes or wheat, five sites following peas showed little response to more than 30 kg N ha–1. Previous crop explained some 79.7% of the variation in nitrogen optima. When autumn soil mineral nitrogen was also taken into account 81.9% of the variation in optimum nitrogen rate was explained (P〈0.001). The study revealed noticeably higher levels of autumn soil mineral nitrogen following vining peas on some sites than those found elsewhere in the UK and as assumed in the standard national fertilizer recommendation system.

Notes: Abstract. The aim of this study was to investigate the effects of water submergence depth on radial oxygen loss (ROL), soil solution chemistry and rice growth performance in acid sulphate soils in southern Vietnam. ROL was measured in a solution culture. In a separate pot experiment the impact of water submergence depth on rice growth and soil solution chemistry was studied. Three submergence depths were used in the two experiments (5, 10 and 15 cm). ROL declined with submergence depth and was significantly greater in young roots (with no root hairs) than in older roots. In the pot experiment rice growth and soil solution chemistry were clearly affected by the submergence depth. During the first crop at 5 cm submergence, there was a significantly higher yield and a higher oxidation state (pe+pH) compared to 10 or 15 cm submergence. The Fe concentration was significantly greater at the 5 cm depth compared to the 10 or 15 cm depth. SO42– reduction was delayed at the 5 cm depth. Rice yield was c. 25% less at the 15 cm than at the 5 cm depth. During a second crop, there was a substantial SO42- reduction and H2S formation and almost no significant effects of submergence depth on either soil solution chemistry or crop yield. In a field experiment with a dry-season rice crop, yield and Fe, Al and SO42– concentrations were higher at a shallow submergence depth than at greater depths in the same field, showing similar depth trends to those found during the first crop in the pot experiment. Farmers should be advised to use a shallow submergence depth and, if possible, avoid deep-rooted rice varieties. A conceptual model is suggested, which summarizes the relationships between ROL and soil solution chemistry.

Notes: Abstract. Tillage displaces large amounts of soil from upper slopes and deposits soil in lower landscape positions, greatly affecting productivity in these areas. The long-term effect of tillage on soil erosion was studied in four field sites growing mainly rainfed wheat. The soil loss from landscape positions with slopes, ranging from 3 to 28%, was estimated by: (a) comparing data of horizon thickness described at the same position at different times; and (b) using soil movement tracers added to the soil. Existing empirical relationships were used for estimating soil loss by tillage and runoff water, and loss in wheat biomass production. The experimental data showed soil losses of 0.4 to 1.4 cm yr–1 depending on slope gradient, plough depth, and tillage direction. In two of the sites, soil depth has been reduced by 24–30 cm in a period of 63 years. The mean soil displacement of the plough layer (30 cm thick), measured by soil movement tracers, ranged from 31 to 95 cm yr–1 depending mainly on slope gradient, corresponding to a rate of soil loss of 0.3 cm to 1.4 cm yr–1. Soil eroded from the upper slopes was deposited on the lower slopes increasing soil thickness by 0.4 cm to 1.4 cm yr–1. The application of empirical relationships, estimating soil loss by tillage and water runoff, showed that soil erosion at the field sites can be mainly attributed to tillage. The loss in wheat biomass production due to erosion was estimated at 26% on upper slopes for a period of 63 years, while a 14.5% increase in wheat production was estimated due to deposition of soil material in the lower landscape.

Notes: Abstract. The most common way of assessing soil organic matter content is by loss on ignition, which is both simple and inexpensive. This method tends to overestimate organic matter content because additional weight losses occur during ignition. An alternative, more expensive and time-consuming method for determining soil organic matter content is by an acid dichromate oxidation. This paper compares the results of applying these methods to soil on different parent materials in two arable fields. Summary statistics and correlation coefficients showed that there were consistent relationships between the two sets of values: the stronger was for the sandy soil and the weaker was for the clay loam. This relationship can be used to improve the accuracy with which soil organic matter content is known while using fewer of the expensive measurements and more of the inexpensive ones. Two approaches to prediction were compared: the geostatistical method of cokriging, and simple linear regression. These were used to predict organic matter determined by an acid dichromate oxidation from the loss on ignition. The estimates from cokriging were more accurate but the method requires the spatial correlation to be modelled reliably. The regression results showed it to be a valuable and practical approach. Using the information from nine carefully selected sampling sites a regression line could be fitted that was representative of the full data.

Notes: Abstract. In 1983, an annual Survey of Fertiliser Practice in England and Wales was extended to Scotland, to provide comprehensive information on inorganic fertilizer, lime and also organic manure use in mainland Britain. It was based on an annual sample of about 1500 farms, selected from the Agricultural Census and stratified by farm type and size. Results from the first fifteen years (1983–97) show that fertilizer nitrogen (N) rates on both tillage crops and grassland peaked at 157 and 132 kg ha–1, respectively, in the mid 1980s and subsequently decreased by c.10%. The majority of N was applied in straight form (without P or K) to tillage crops and in compound form (containing two or more nutrients e.g. NPK; NK) to grassland. Total N use on cereals showed little change but autumn-applied N decreased on both winter cereals and winter oilseed rape. Total N rates decreased on oilseed rape and, to a smaller extent, on maincrop potatoes and sugarbeet. Between 1983–87 and 1993–97, mean phosphate (P2O5) rates declined by almost 10% on both tillage crops (from 58 to 53 kg ha–1) and on grassland (from 25 to 23kg ha–1). The corresponding mean potash (K2O) rates decreased slightly on both tillage crops (from 64 to 62 kg ha–1), and on grassland (from 32 to 31 kg ha–1), although annual usage was more variable on grassland. Sulphur use increased appreciably on cereal and oilseed rape crops between 1993, when S data were first recorded in the survey, and 1997 when 13% and 30%, respectively, of these crop areas received S-fertilizer. However, on grassland, S use remained very low. Average lime use increased on both tillage crops and grassland between the mid 1980s and mid 1990s, from 10 to 12% and 4 to 7% of the total area, respectively. The proportion of land receiving organic manures remained at c. 16% for tillage cropping but increased slightly for grassland, from a mean of 40% in 1983–87 to 44% in 1993–97. Manures were applied throughout the year but about half the applications to tillage land, and a quarter of those to grassland, were made in autumn when the risk of subsequent nitrate leaching loss is greatest.

Notes: Abstract. A two year field experiment was carried out in a semiarid Mediterranean area in order to evaluate, the effect on soil erosion of adding different urban organic wastes: a stabilized municipal waste (compost), an unstabilized municipal waste, and an aerobic sewage sludge. All the treatments significantly reduced soil erosion, compared to the control soil. The soil amended with compost was the most effective treatment, reducing soil loss by 94% and runoff by 54%.

Notes: Abstract. Cashew soils of South Eastern Tanzania become acidified due to sulphur used for controlling powdery mildew disease (Oidium anacardii Noack). The buffering capacity of surface and subsurface horizons of 35 soil profiles of major cashew growing areas –- the Makonde plateau, its piedmont and inland plains –- was studied. The buffering capacity of surface and subsurface horizons was strongly correlated with clay content and weakly with organic carbon content. In addition, it was only weakly correlated with total exchangeable bases and available P of the surface horizon, but strongly with soil pH, base saturation and cation exchange capacity of the clay fraction of the subsurface horizon. Highly weathered sandy soils, dominant on the Makonde plateau and common on the Piedmont, had the lowest buffering capacity. Soils from the inland plains had better buffering capacities as they are generally more clayey or are less weathered. The risk of severe acidification and of a decline in productivity of cashew and of food crops is highest on the Makonde plateau. Further development and dissemination of methods which can reduce the use of sulphur are required.

Notes: Abstract. Biomass productivity and soil microbial responses to long-term CO2 enrichment have been investigated in a Mediterranean natural forest ecosystem. Several biochemical parameters have been measured on soil samples taken from six open top chambers (OTCs), enclosing clumps of natural Mediterranean woody vegetation including: Quercus ilex L., Phillyrea angustifolia L., Pistacia lentiscus L. and Myrtus communis L. The CO2 concentration of the air inside the OTCs was either ambient or ambient plus 350 μmol mol–1 (c. 710 ppm as mean daily value). Microbial C biomass, microbial respiration, dehydrogenase, β-glucosidase, acid phosphatase and protease activities, inorganic N and soluble P, were tested in order to evaluate soil microbial size and activity. Statistically correlated seasonal patterns have been identified in some biochemical parameters in response to climatic conditions, soil nutritional status and the physiology of the vegetative cover. In situ soil respiration and above- and below-ground productivity were also measured. Microbial responses to CO2 enrichment were observed only at the beginning of the study and a general progressive reduction of the CO2 effect was recorded as monitoring continued. These results are in agreement with data from literature regarding similar studies on natural complex communities.

Notes: Abstract. The Century model was used for estimating soil carbon levels under grassland at the regional scale in the Pampean Region of Argentina. Predicted values were compared with observed soil carbon contents obtained from soil surveys and the differences considered to be the results of cropping on soil organic matter. The Pampean Region was divided into five major sub-regions and carbon in the top 20 cm of each estimated by Century using aggregated soil and climatic data. In four of the sub-regions small differences between predicted and observed carbon contents were obtained which suggested little land use effect on soils. In the Rolling Pampa, a northern portion of the Pampean Region, observed carbon content was about half of Century prediction. In this sub-region, the main agricultural area of the country, cropping intensity, rainfall and temperature are higher than in the rest of the Pampas. A degradation index constructed by a multiplicative approach, taking into account percentage of surface cropped, rainfall and temperature was 2–5 times higher in the Rolling Pampa than in the other pampean sub-region. The difference between predicted C and observed C in the Rolling Pampa was attributed to carbon losses by cropping in a warm and wet climate.

Notes: Abstract. Recent developments in in situγ ray spectrometry offer a new approach to measuring the activity of radionuclides such as 137Cs and 40K in soils, and thus estimating erosion or deposition rates and field moist bulk density (ρm). Such estimates would be rapid and involve minimal site disturbance, especially important where archaeological remains are present. This paper presents the results of a pilot investigation of an eroded field in Scotland in which a portable hyper pure germanium (HPGe) detector was used to measure γ ray spectra in situ. The gamma (γ) photon flux observed at the soil surface is a function of the 137Cs inventory, its depth distribution characteristics and ρm. A coefficient, QCs, derived from the forward scattering of 137Cs γ ray photons within the soil profile relative to the 137Cs full energy peak (662 keV), was used to correct the in situ calibration for changes in the 137Cs vertical distribution in the ploughed field, a function of tillage, soil accumulation and ρm. Based on only 8 measurements, the agreement between in situγ ray spectrometry and soil sample measurements of 137Cs inventories improved from a non significant r2=0.05 to a significant r2=0.62 (P〈0.05). Erosion and deposition rates calculated from the corrected in situ137Cs measurements had a similarly good agreement with those calculated from soil cores. Mean soil bulk density was also calculated using a separate coefficient, QK, derived from the forward scattering γ photons from 40K within the soil relative to the 40K full energy peak (1460 keV). Again there was good agreement with soil core measurements (r2=0.64; P〈0.05). The precision of the in situ137Cs measurement was limited by the precision with which QCs can be estimated, a function of the low 137Cs deposition levels associated with the weapons testing fallout and relatively low detector efficiency (35%). In contrast, the precision of the in situ ρm determination was only limited by the spatial variability associated with soil sampling.

Notes: Books Reviewed in this Article: Fertiliser recommendations for agricultural and horticultural crops (RB209) Published with the permission of MAFF by HMSO, 7th edition 2000.

Notes: Abstract. Soil management studies show that intensive arable agriculture can lead to a decline in both organic matter levels and the stability of the soil structure. It is a priority to understand how soil structure responds when fresh organic materials are added to poor quality degraded arable soils. This is of particular interest because of its implication for carbon sequestration. We investigate whether the addition of organic materials can form stable aggregates in a degraded soil. Grass or peat residues were added to samples of soil obtained from the continuous grassland and arable plots of the long-term experiment at highfield, IACR-Rothamsted (UK) and incubated at 2° and 24°C, for upto 8 weeks at -5 kPa. At 1 day and at 2, 4 and 8 weeks the soil was slaked in de-ionised water and the aggregate size distributions were measured. The data was used to calculate mean weight diameters (MWD). The treatments with added grass showed increased aggregated relative to the control; the treatments with added peat did not. At 24°C the value of MWD increased with the incubation period, but at 2°C there was no further aggregation beyond week two. Respiration measurements were made and the samples that released the most CO2 were also those which re-aggregated the most. This suggests that the process of aggregation is microbiologically mediated. The results are discussed within the broader context of the implications of soil organic matter content on soil management.

Notes: Abstract. By comparing field measurements from 1989, 1997, and 1998, the differences between farmland (sloping farmland, sloping farmland with contour cultivation, terraced farmland) and orchard (terraced orchard, unterraced orchard), in the Three Gorges Reservoir Area, were significant for runoff (P〈0.01), erosion (P〈0.05) and nutrient loss (P〈0.05). Taking into account economic costs and environmental influences, reasonable and sustainable land use on slopes of 25° in the Three Gorges Reservoir Area should be unterraced orchard.

Notes: Abstract. Paper sludge composted or stored in static piles for six months was compared to raw and lime-stabilized sludge in a three-year pot experiment (loam) and a four-year field experiment (silt loam) at rates of up to 40 t DM ha-l. The original sludge contained equal amounts of fibre sludge and biological sludge, mixed with bark in 1:1 ratio to improve the structure. The N content in composted sludge (1.30%) was markedly lower than that of the uncomposted piles (1.98%), indicating significant loss during composting. The yield results were generally inversely proportionate to the C:N ratios of the sludges applied. Sludge from the uncomposted piles gave significant grain yield increases in the year following sludge application, while the other sludge types gave variable results. In the residual years there was, generally, a small but positive effect on yield from all the sludge types. The N and P content in grain generally increased with sludge application, but only the higher rates gave statistically significant increases. Sludge application also increased the Zn content in grain, while Mn, B and Cu was less affected. The increase in Cd content was very small. The 40 t ha-l sludge rate tended to increase the residual mineral N in soil at the field site and thus the risk of nitrate leaching.

Notes: Abstract. An increasing number of breeding sows is kept outdoors in Europe. Outdoor pig production has benefits in terms of animalwelfare but may have hidden costs through nutrient losses. We investigated the distribution of nutrients in sow paddocks and the consequence for losses and utilization in the succeeding crop. Significant correlation between soil inorganicNand the distance to feeding sites was observed after the paddocks had been used by lactating sows for 6 months (P〈0.01). Near to feeders inorganic N levels became extremely high whereas 30–40m from feeders some patches hadN levels in the topsoil corresponding to the levels in the reference area without sows. In the following spring only a minor part of inorganic N was still present in the top 0–40 cm. Similarly, extractable P and exchangeable K in topsoil were significantly affected by distance to feeders with the highest values close to the feeders (P〈0.001). In addition there were significant effects of the distance to huts with increasing nutrient content closer to huts. Although huge variations in dry matter production and nutrient content occurred in the succeeding potato crop, these were only weakly related to the distribution of nutrients (N, P and K) in the previous year, which explained 17%of the total variation in dry matter production. To increase nutrient efficiency in outdoor pig production a uniformdistribution of nutrients should be obtained by manipulating the excretory behaviour of the sows and stocking densities must be adjusted to locally acceptable nutrient surpluses.

Notes: Abstract. A survey of cattle manure management was undertaken in England and Wales, in 1997, by postal questionnaire sent out to a stratified sample (by unit size) of 1750 dairy and 1750 beef producers. The level of response obtained, with 471 dairy farmers (27%) and 515 beef farmers (29%) returning questionnaires, reflects well on the interest shown by the industry and on the survey design. The survey provided information on manure production and storage, when and how applied and nutrient value. Dairy farms are estimated to produce manures in the form of c. 65% slurry and 35% farmyard manures (FYM) and, beef units, 80%FYM and 20%slurry (based on survey response data, animal numbers and calculations of undiluted outputs of excreta). Slurry storage within both dairy and beef systems is typically up to 3–6 months capacity, although there is no storage for an estimated 16% of dairy and 25% of beef slurry. Autumn and winter spreading is common practice, with 40–50% of slurry and 50–60% of FYM applied at that time. Although some evidence suggests that farmers make little allowance for the nutrient content of manures in planning fertilizer inputs, the results of this survey suggest that many farmers do make some effort to utilize manure nutrients. However, they currently fail to be assured by the advice available to them or they lack confidence in manures as nutrient sources for a number of technical reasons. Information provided by the survey may be important to policy makers, researchers and consultants, as well as farmers.

Notes: Abstract. Demand for water from catchments dominated by upland peat as a source of drinking water supplies in the UK is likely to increase in the future as demand per capita continues to rise (Thomsen 1990) and/or summer droughts increase in frequency (Arnell 1992). Concern has been expressed in recent years over rising colour levels (related to dissolved organic carbon (DOC) and iron (Fe)) from such catchments (e.g. Kay et al. 1989) causing reduced drinking water quality. One of the major causes of increased DOC concentrations is rewetting following periods of relative drought (Mitchell & McDonald 1992). Experimental rewetting of a naturally drained wetland in Mid-Wales over four years was found to substantially increase the concentrations of DOC, and Fe in the pore-water, with peak values of 〉60 mg dm–3 (Fe) and 〉300 mg dm–3 (DOC) after rewetting, compared with typical values of 〈1 mgdm–3 (Fe) and 〈15 mg dm–3 (DOC) under the drained conditions. Seasonal peak concentrations of Fe and DOC have since remained at these higher levels. Rewetting produced a selective enrichment of the 〉5000 to 〈90 000 apparent molecular weight (AMW) material and this fraction was found to yield peak Fe concentrations. Two additional peaks of DOC were also found in the experimental wetland (not present in the control wetland), of 〉90 000 to 〈200 000 AMW and 〉200 000 AMW material. The AMW spectrum of DOC in the experimental wetland changed with season, and the 〉90 000 to 〈200 000 AMW fraction could only be seen in spring, representing a transient pool of carbon that is rapidly transformed in or transported from the wetland. These findings suggest that rewetting of peatland following drought (e.g. due to climate change) has the potential to reduce water quality. Moreover, recent interest in restoration (rewetting) of drained peatlands (Wheeler & Shaw 1995) could create an additional source of DOC rich water.

Notes: Abstract. The hierarchial concept of land use planning becomes less relevant in a society with continuous interactions between stakeholders, researchers, planners and politicians. In this context, land use negotiation rather than land use planning appears to be the most appropriate concept. In the negotiation process, good quality data about the land is important as land properties are, obviously, key elements to be considered. Case studies at farm and regional level have been analysed to explore answers to a number of questions. How can soil data be presented most effectively? What are the research needs? How can the large existing body of data be mobilized most effectively? Studies on regional land use in Costa Rica used methods in a logical sequence including projections, explorations and predictions of land use patterns. The work involved upscaling of data, obtained at farm level, to the regional level. Work at farm level focussed on prototyping procedures in which farming systems were ‘designed’ by close interaction between farmers and scientists, including applications of precision agriculture. Soil data demands were analysed, emphasizing the effects of using data with different degrees of detail together with the application of pedotransfer functions which effectively transform existing data into parameters that are difficult or expensive to measure directly. This not only facilitated interactions with stakeholders but also with colleague scientists in interdisciplinary teams. In addition, use of Geographical Information Systems allowed visual presentations of alternative geographical land use patterns that were associated with various scenarios, thereby facilitating the interaction processes. A plea is made to increase interaction of stakeholders and researchers by considering research programmes as vehicles for joint learning.

Notes: Abstract. Topsoil (0–15 cm) bulk density, aggregate stability, soil dispersibility, water retention and infiltration were measured between 1989 and 1996 on an Alfisol under rehabilitation in southwestern Nigeria. The planted leguminous species were Pueraria phaseoloides, Senna siamea, Leucaena leucocephala, Acacia leptocarpa and A. auriculiformis. Also, plots with natural fallow and maize/cassava intercropping were included. Level (minimum) and mound tillage with hoes was adopted for the cultivated areas under study after 4 and 6 year fallow periods. Under fallow, the soil bulk density decreased from1.56 to 1.11 t m73.The continuously cropped treatment (level tillage) had significantly higher bulk density than the fallowed subplots after 6 years. Mean soil penetrometer resistance ranged from 75 to 157 kPa for fallowed plots and from 192 to 295 kPa for the continuously cropped (level tillage) subplot. Surface soilwater contentswere similar for all the treatments during the soil strength measurements. Although soil aggregates were generally of low stability and not well formed, they were improved by fallowing.Soil structural improvement by planted fallows was similar to that by natural fallow, but the trees were more promising for long-term fallow (〉6 years) than the herbaceous P. phaseoloides. However, the improvement in soil structure after 4 or 6 year fallow could not be maintained in subsequent cropping. Furthermore, the significant improvement in soil bulk density caused by A. auriculiformis and natural fallow was more rapidly lost on the cultivated subplots compared with other fallow treatments. Thus, soil structure recovery under a fallow does not imply a sustained improvement when stress is applied to this soil. Post-fallow soil management options such as residue incorporation and tillage to ameliorate compaction or soil strength will be necessary to enhance the improvements by fallow species.

Notes: Abstract. Changes in particulate organic carbon (POC) relative to total organic carbon (TOC) were measured in soils from five agronomic trial sites in New South Wales, Australia. These sites covered a wide range of different land use and management practices. POC made up 42–74% of TOC and tended to be greater under pasture and more conservative management than traditional cropping regimes. It was the form of organic carbon preferentially lost when soils under long-term pasture were brought under cultivation. It was also the dominant form of organic carbon accumulating under more conservative management practices (direct drilling, stubble retained and organic farming). Across all sites, changes in POC accounted for 81.2% (range 69–94%) of the changes in total organic carbon caused by differences in land use and management. Significant differences were found between pasture and cropped soils in the carbon content in the 〈53 μm fraction, particularly for hardsetting soils. However, even with these, POC was a more sensitive indicator of change caused by land use and management practices than TOC. The current method for measuring POC involves dispersion using sodium hexametaphosphate. The dispersing agent was found to extract 4–19 % of the TOC, leading to a significant under-estimation of POC.

Notes: Abstract. An estimate of organic carbon stored in French soils to a depth of 30 cm was made using data from geo-referenced databases. We produced statistics on carbon stocks in soils according to land use, different land uses and soil type. Then, using a combination of maps of soil and land use we were able to estimate regional and national carbon stocks. This soil carbon map of France allowed us to identify the main controlling factors of the carbon distribution: land use, soil type in some cases, clay content, and elevation. Carbon stocks in French soils were found to be about 3.1 Pg (1015g).

Notes: Abstract. The problem of soil erosion is particularly evident in New Zealand, given the combination of coarse-textured soils, steep relief, high rainfall, and intensification of agriculture. A study was undertaken to assess the effects of land use change on soil erosion and sediment transport for the Ngongotaha catchment in New Zealand's North Island, using a GIS based decision support and modelling system. Model simulations considered the effect of increased catchment area under deer farming and forestry on the amount of sediment delivered to the catchment outlet, averaged over a period of six years. The simulations predicted that sediment loss from land under deer farming was considerably greater than from land under other livestock or forestry. Further model simulations testing best management practices demonstrated that sediment yield could be halved if deer farming was restricted to slopes under 20%.

Notes: Abstract. Measures to reduce ammonia (NH3) emissions by incorporating livestock manures into the soil may increase the potential for nitrate (NO3-) leaching. The Manure Evaluation Routine (MANNER) model estimates the amount of N available to crops following livestock manure applications after calculating losses due to NH3 volatilization and NO3- leaching. The main objective of this study was to use the MANNER model to quantify the impact on NO3- leaching of introducing measures to reduce NH3 emissions, following application of livestock manures. The data produced were also used to make preliminary estimates of the likely effect of selected NH3 abatement techniques on the potential for nitrous oxide (N2O) emissions. At typical UK rates of application, the potential for increased NO3- leaching following either injection of slurry or rapid incorporation of solid manures was greatest for broiler/turkey manure (22–58 kg N ha–1) and least for straw-based cattle manure (6–10 kg N ha–1). The results suggest that in order to avoid substantially increasing the potential for NO3- leaching as a consequence of NH3 abatement, livestock manures should not be applied by low NH3 emission techniques prior to autumn-sown crops in the UK. Instead, low-emission applications should be made from October onwards to grassland and where possible, late autumn-sown combinable crops or to arable land which will be planted in the spring. However, in several areas of England and Wales there is currently insufficient land planted to spring crops on which to incorporate the livestock manures produced in those areas.

Notes: Abstract. A survey of manure management practice was undertaken in 1996, by postal questionnaire submitted to a stratified sample of egg and broiler producers in England and Wales. Out of a target of 500 laying hen and 500 broiler (chickens produced for meat) production units in the survey sample, 356 (36%) returned questionnaires. The survey provided information on amount and type of manure production, manure storage and land application strategies (timing, techniques and awareness of nutrient content). Within the survey, no attempt was made to differentiate between organic and conventional production systems. About 45% of manure production was estimated to come from layer holdings, 55% from broiler litter. It was estimated that 70% of the national manure production is litter-based and about 30% are droppings collected without litter. Sawdust/shavings are the most popular bedding material, with an average final depth of 100 mm for broilers and 140 mm on litter-based layer units. Commonly, storage is available within housing for at least the length of the cropping cycle (6 weeks in broiler production, or 12 months in deep pit laying houses), around 60% of poultry manure is stored for a period following removal from the house, most commonly for 3-6 months. Overall, autumn was the peak period for manure spreading, with over 40% of laying hen manure and 50% of broiler manure applied at that time. On grassland, spreading was reasonably evenly distributed throughout the year but autumn application was favoured for arable crops, especially before the establishment of cereals and root crops, overall, almost 50% of layer and broiler manure was applied in the autumn. In the survey, up to 10% of manures were claimed to be incorporated within a day of application and about 60% within a week of application, presumably because of concern about odour nuisance. Around 25% of poultry manure was applied by contractors. A high proportion of farmers (c. 40% with layers, c. 60% with broilers) exported manures from their holdings, the proportion removed amounting to almost 90% on these farms. Although evidence elsewhere indicates that farmers make little allowance for manures in planning crop fertilizer inputs, the survey responses suggested that farmers do make an effort to allow for manures but that their confidence in the advice available to them is lacking, or they may have other technical reasons for not taking advantage of the manurial value. Information provided by the survey is of significant importance to policy makers (e.g. for the construction of environmental emissions inventories), researchers, consultants and farmers.

Notes: Abstract. The phosphorus (P) sorption and desorption dynamics of eleven major agricultural grassland soil types in Ireland were examined using laboratory techniques, so that soils vulnerable to P loss might be identified. Desorption of P from soil using the iron-oxide paper strip test (Pfeo), water extractable P (Pw) and calcium chloride extractable P (Pcacl2) depended on soil P status in all soils. However, soil types with high organic matter levels (OM), namely peat soils (%OM 〉30), had lower Pfeo and Pw but higher Pcacl2 values compared to mineral soils at similar soil test P levels. Phosphorus sorption capacity remaining (PSCr) was measured using a single addition of P to soils and used to calculate total P sorption capacities (PSCt) and degree of P saturation (DPS). Phosphorus sorption capacities correlated negatively with % OM in soils indicating that OM may inhibit P sorption from solution to soil. High organic matter soils exhibited low P sorption capacities and poor P reserves (total P, oxalate extractable P) compared to mineral soils. Low P sorption capacities (PSCt) in peat soils were attributed to OM, which blocked or eliminated sorption sites with organic acids, therefore, P remained in the soil solution phase (Pcacl2). In this work, peat and high organic matter soils exhibited P sorption and desorption characteristics which suggest that these soils may not be suitable for heavy applications of manure or fertilizer P owing to their low capacities for P sorption and storage.

Notes: Abstract. Field peas (Pisum sativum L.) were grown in sequence with winter wheat (Triticum aestivum L.) or spring barley (Hordeum vulgare L.) in large outdoor lysimeters. The pea crop was harvested either in a green immature state or at physiological maturity and residues returned to the lysimeters after pea harvest. After harvest of the pea crop in 1993, pea crop residues (pods and straw) were replaced with corresponding amounts of 15N-labelled pea residues grown in an adjacent field plot. Reference lysimeters grew sequences of cereals (spring barley/spring barley and spring barley/winter wheat) with the straw removed. Leaching and crop offtake of 15N and total N were measured for the following two years. These treatments were tested on two soils: a coarse sand and a sandy loam. Nitrate concentrations were greatest in percolate from lysimeters with immature peas. Peas harvested at maturity also raised the nitrate concentrations above those recorded for continuous cereal growing. The cumulative nitrate loss was 9–12 g NO3-N m–2 after immature peas and 5–7 g NO3-N m–2 after mature peas. Autumn sown winter wheat did not significantly reduce leaching losses after field peas compared with spring sown barley. 15N derived from above-ground pea residues accounted for 18–25% of the total nitrate leaching losses after immature peas and 12–17% after mature peas. When compared with leaching losses from the cereals, the extra leaching loss of N from roots and rhizodeposits of mature peas were estimated to be similar to losses of 15N from the above-ground pea residues. Only winter wheat yield on the coarse sand was increased by a previous crop of peas compared to wheat following barley. Differences between barley grown after peas and after barley were not statistically significant. 15N lost by leaching in the first winter after incorporation accounted for 11–19% of 15N applied in immature pea residues and 10–15% of 15N in mature residues. Another 2–5% were lost in the second winter. The 15N recovery in the two crops succeeding the peas was 3–6% in the first crop and 1–3% in the second crop. The winter wheat did not significantly improve the utilization of 15N from the pea residues compared with spring barley.

Notes: Abstract. In view of the increasing wheel loads of agricultural vehicles, the question arises as to whether soil can recover from the mechanical impact of traffic. The damage to soil quality depends also on the soils resilience. This paper presents a new approach to monitoring vertical soil movement in situ. We assessed the effects of trafficking the soil with excavators and sugarbeet harvesters by monitoring surface and subsurface levels. The caterpillar loads of the crawlers varied from 13 to 19 t, the wheel loads of the sugarbeet harvesters from 6 to 11 t. Classical geodetic levelling was used to record soil surface movement and a hydrostatic settlement meter measured deformation at three depths within the soil profile. The results of three field tests prove the importance of wheel load and soil moisture for soil compaction. Trafficking very dry soil with an excavator did not cause significant plastic deformation in 30 cm depth. Conversely, trafficking wet soil with a sugarbeet harvester led to soil sinkage of 1 to 2 cm even at 60 cm depth. Increased wheel load in subsequent passes led to greater subsidence than during the first pass. Settlement decreased from the soil surface to deeper layers, but it remained throughout the monitoring period of up to 12 days. No soil recovery from plastic deformation was recorded within this time. The measuring system has the potential for long-term monitoring of the mechanical recovery of the soil. Additionally, it can contribute to the validation of mechanical impact models, which are based on soil stresses.

Notes: Abstract. Two case studies on Danish sandy loams investigated the long-term effects of fertilization and crop rotation. Case Study 1 compared a diversely cropped organically farmed soil (DFG(1)) with a conventionally farmed soil predominantly growing annual crops (DFA), both receiving animal manure. In Case Study 2, a diversely cropped organically managed soil (DFG(2)) receiving animal manure was compared with an almost exclusively cereal cropped conventionally farmed soil receiving no animal manure (CCC). A multi-level experimental strategy was followed to compare integrating field methods with specialized laboratory methods. Ease of tillage was described in the field and characterized using a drop shatter field test and by measuring aggregate tensile strength. Fitness as a seedbed was characterised visually in the field and from the drop shatter test. Impedance to seedling emergence and root penetration was evaluated by measuring bulk soil shear strength. For Case Study 1, soil tilth was better for the DFA soil than for the DFG(1) soil (i.e. lower soil strength and higher ease of fragmentation and friability index for DFA). However, a crumbly structure and a moderate bulk density suggested that the DFG(1) soil was also a favourable medium for plant growth. For Case Study 2, the CCC soil had a lower organic matter content, higher bulk density, higher soil strength, and lower ease of fragmentation in comparison with the DFG(2) soil.

Notes: Abstract. A two year field study was conducted to evaluate the effects of straw management and tillage on the soil profile (1.5m) water storage, nature of the moisture profile, infiltration and sorptivity as influenced by rainfall, evaporativity (E0) and soil texture. The straw mulch treatment stored more moisture under low E0 rainy conditions in three coarse to medium textured soils. Straw incorporation treatment was better under low E0 rain free conditions, as well as under high E0 rainy conditions in the two coarser textured soils. In the coarsest textured soil, tillage and straw mulching were not effective in maintaining greater soil water storage under high E0 because of the very open nature of the soil. The soil moisture profiles showed a sharper increase in water content below the tilled layer in the tillage and straw- incorporation treatments than the untreated and straw mulch treatments. Tillage and straw incorporation treatments increased the sorptivity of the soil compared with untreated and straw mulch treatments respectively. The results of this study suggest that when selecting a suitable soil water conservation practice to increase water storage in the soil profile, information on soil texture and weather (rain and evaporativity) must be considered.

Notes: Abstract. Phosphorus (P) use in UK agriculture is reviewed and a P balance sheet presented. The productive grassland and arable area has accumulated an average P surplus of c. 1000 kg ha–1 over the last 65 years. Over the period 1935–1970, the annual P surplus more than doubled due to an increase in animal numbers and associated requirements for inorganic fertilizers and livestock feeds. Since 1970, surplus P has declined by c. 40% as crop yields and P offtake have continued to increase while fertilizer and manure P inputs have remained relatively constant. In 1993, P use efficiency (P imports/P exports) in UK agriculture was estimated at 25% leading to an average annual surplus of 15 kg P ha–1 yr–1, although the latter has since decreased slightly due to reduced fertilizer use. Intensification and specialization of agriculture has also increased the range in P surpluses that are likely between livestock and arable dominated systems. The largest P surpluses occur in the relatively limited areas of arable soils which receive manure from intensive pig and poultry units, whilst farms without manure inputs generate only small surpluses, or are in balance. The cumulative P surplus has led to a build-up of soil total and easily-exchangeable P, especially in areas receiving both fertilizers and manures. Fundamental differences in P use efficiency, surplus P accumulation and the potential for P loss to water, exist between arable and grassland farms and it is important to separate these, due to the marked regionalization of UK agriculture. More judicial use of feeds and fertilizers is required to further reduce the P surplus and minimize the long-term risk of water eutrophication.

Notes: Abstract. The ability of two nitrogen cycle models, of contrasting complexity, to predict N mineralization from a range of grassland soils in the UK, was evaluated. These were NCYCLE, a simple mass balance model of the N cycle in UK grasslands, and CENTURY, a more complex model simulating long-term C, N, P & S dynamics in grassland ecosystems. The models were tested using field measurements of net N mineralization from a range of grassland soils (differing in soil type, history & management practice), obtained over a 2 year period using a soil core incubation technique. This method was considered to measure the total net release of mineral N from the soil organic matter over a specified time, including N which may have been recycled several times. NCYCLE consistently under-estimated mineralization rates at all sites. By contrast, there was some correlation between CENTURY predictions of net N mineralization and field measurements. This may have reflected the different abilities of the two models to simulate N recycling. Neither model, however, was able to predict adequately the effect of cultivation and reseeding on net N mineralization.

Notes: Abstract. Nitrate leaching and soil mineral N status under grassland were measured on three contrasting soils, spanning winters 1995/96, 1996/97 and 1997/98, in Western England. The soils investigated were a freely draining silty clay loam (Rosemaund), a well drained loam (IGER 1) and a poorly drained clay loam (IGER 2). The effects of reseeding (ploughing and resowing grass) at IGER 1 and IGER 2 in autumn 1995 or 1996 were compared with undisturbed pasture. Reseeding at Rosemaund, in autumns 1995 or 1996, or spring 1996 was compared with undisturbed pasture of 3 sward ages (2, 5, 〉50 years).Nitrate-N leaching losses during the winter immediately following autumn reseeding ranged between 60 and 350 kg N ha–1 in 1995/96, depending on soil type, sward management history and rainfall. Losses were much less in the following winter when treatments were repeated (10–107 kg N ha–1).Reseeding in spring had little effect on soil mineral N content or leaching losses in the following autumn, compared with undisturbed pasture. Similarly, leaching losses from autumn reseeds in the second winter after cultivation were the same as undisturbed pasture (1-19 kg N ha–1). The effect of ploughing grassland for reseeding was relatively short-term, in contrast to the effect of repeated annual cultivation associated with arable rotations.

Notes: Abstract. Intensively managed grasslands are potentially a large source of N2O in the North Coast of Spain because of the large N input, the wet soil conditions and mild temperatures. To quantify the effect of fertilizer type and management practices carried out by farmers in this area, field N2O losses were measured over a year using the closed chamber technique. Plots received two types of fertilizer: cattle slurry (536 kg N ha–1) and calcium ammonium nitrate (140 kg N ha–1). N2O losses were less in the slurry treatment than after mineral fertilizer. This was probably due to high, short-lived peaks of N2O encountered immediately following mineral N addition. In contrast, the seasonal distribution of N2O losses from the slurry amended plot was more uniform over the year. The greater N2O losses in the mineral treatment might have been enhanced by the combined effect of mineral fertilizer and past organic residues present from previous organic amendments. Weak relationships were found between N2O emission rates and soil nitrate, soil ammonium, soil water content and temperature. Better relationships were obtained in the mineral treatment than in the slurry plots, because of the wider range in soil mineral N. Water filled pore space (WFPS) was a key factor controlling N2O emissions. In the 〉 90% WFPS range no relationships were found. The best regressions were found for the mineral treatment in the 40–65% WFPS range, 49% of the variance being explained by soil nitrate and ammonium content. In the 65–90% WFPS range, 43% of the variance was explained by nitrate only, but the inclusion of soil ammonium did not improve the model as it did in the 40–65% WFPS range. This fact indicates that nitrification is likely to be an important process involved in N2O emissions at the 40–65% WFPS.

Notes: Abstract. Boreholes have been constructed at eight sites on the Permo-Triassic Sandstone and Chalk aquifers to assess the extent of chemical and microbiological contamination emanating from unlined farm manure stores. Slurry along fracture faces in the Chalk was found on cores taken from beneath two stores. Porewaters from the Chalk sites and one of the Sandstone sites were discoloured and showed high concentrations of nitrate, ammonium and organic carbon to depths in excess of 10 m. Although Cryptosporidia and Escherichia coli O157 were found in many of the cattle slurry lagoons, neither were found in the aquifer material beneath. The self-sealing of unlined slurry stores is seen as a crucial step in minimizing leakage. A simple mass balance shows farm boreholes near to contaminant sources are at greater risk than public supply wells. Contaminant modelling shows discontinuing use of an unlined farm manure store will lead to little difference in solute concentrations over the short to medium term. Groundwater is most at risk where the water table is shallow since direct hydraulic connection between the lagoon base and the water table considerably increases the rate of vertical migration. This is of greatest significance for pathogens that are thought to be relatively short lived in the subsurface. Under the majority of situations minimal threat is posed to potable groundwater drinking supplies.

Notes: Abstract NMR spin relaxation spectroscopy is a powerful approach for characterizing intramolecular and overall rotational motions in proteins. This review describes experimental methods for measuring laboratory frame spin relaxation rate constants by high-resolution solution-state NMR spectroscopy, together with theoretical approaches for interpreting spin relaxation data in order to quantify protein conformational dynamics on picosecond-nanosecond time scales. Recent applications of these techniques to proteins are surveyed, and investigations of the contribution of conformational chain entropy to protein function are highlighted. Insights into the dynamical properties of proteins obtained from NMR spin relaxation spectroscopy are compared with results derived from other experimental and theoretical techniques.

Notes: Abstract The fusion of vesicles with target membranes is controlled by a complex network of protein-protein and protein-lipid interactions. Structures of the SNARE complex, synaptotagmin III, nSec1, domains of the NSF chaperone and its adaptor SNAP, and Rab3 and some of its effectors provide the framework for developing molecular models of vesicle fusion and for designing experiments to test these models.

Notes: Abstract Considerable recent progress has been made in the field of ab initio protein structure prediction, as witnessed by the third Critical Assessment of Structure Prediction (CASP3). In spite of this progress, much work remains, for the field has yet to produce consistently reliable ab initio structure prediction protocols. In this work, we review the features of current ab initio protocols in an attempt to highlight the foundations of recent progress in the field and suggest promising directions for future work.

Notes: Abstract Species and tissue-specific isozymes of phosphorylase display differences in regulatory properties consistent with their distinct roles in particular organisms and tissues. In this review, we compare crystallographic structures of regulated and unregulated phosphorylases, including maltodextrin phosphorylase (MalP) from Escherichia coli, glycogen phosphorylase from yeast, and mammalian isozymes from muscle and liver tissues. Mutagenesis and functional studies supplement the structural work and provide insights into the structural basis for allosteric control mechanisms. MalP, a simple, unregulated enzyme, is contrasted with the more complicated yeast and mammalian phosphorylases that have evolved regulatory sites onto the basic catalytic architecture. The human liver and muscle isozymes show differences structurally in their means of invoking allosteric activation. Phosphorylation, though common to both the yeast and mammalian enzymes, occurs at different sites and activates the enzymes by surprisingly different mechanisms.

Notes: Abstract Computer modeling has been developed and widely applied in studying molecules of biological interest. The force field is the cornerstone of computer simulations, and many force fields have been developed and successfully applied in these simulations. Two interesting areas are (a) studying enzyme catalytic mechanisms using a combination of quantum mechanics and molecular mechanics, and (b) studying macromolecular dynamics and interactions using molecular dynamics (MD) and free energy (FE) calculation methods. Enzyme catalysis involves forming and breaking of covalent bonds and requires the use of quantum mechanics. Noncovalent interactions appear ubiquitously in biology, but here we confine ourselves to review only noncovalent interactions between protein and protein, protein and ligand, and protein and nucleic acids.

Notes: Abstract Molecular chaperones are required to assist folding of a subset of proteins in Escherichia coli. We describe a conceptual framework for understanding how the GroEL-GroES system assists misfolded proteins to reach their native states. The architecture of GroEL consists of double toroids stacked back-to-back. However, most of the fundamentals of the GroEL action can be described in terms of the single ring. A key idea in our framework is that, with coordinated ATP hydrolysis and GroES binding, GroEL participates actively by repeatedly unfolding the substrate protein (SP), provided that it is trapped in one of the misfolded states. We conjecture that the unfolding of SP becomes possible because a stretching force is transmitted to the SP when the GroEL particle undergoes allosteric transitions. Force-induced unfolding of the SP puts it on a higher free-energy point in the multidimensional energy landscape from which the SP can either reach the native conformation with some probability or be trapped in one of the competing basins of attraction (i.e., the SP undergoes kinetic partitioning). The model shows, in a natural way, that the time scales in the dynamics of the allosteric transitions are intimately coupled to folding rates of the SP. Several scenarios for chaperonin-assisted folding emerge depending on the interplay of the time scales governing the cycle. Further refinement of this framework may be necessary because single molecule experiments indicate that there is a great dispersion in the time scales governing the dynamics of the chaperonin cycle.

Notes: Abstract The mammalian thioredoxins are a family of small (approximately 12 kDa) redox proteins that undergo NADPH-dependent reduction by thioredoxin reductase and in turn reduce oxidized cysteine groups on proteins. The two main thioredoxins are thioredoxin-1, a cytosolic and nuclear form, and thioredoxin-2, a mitochondrial form. Thioredoxin-1 has been studied more. It performs many biological actions including the supply of reducing equivalents to thioredoxin peroxidases and ribonucleotide reductase, the regulation of transcription factor activity, and the regulation of enzyme activity by heterodimer formation. Thioredoxin-1 stimulates cell growth and is an inhibitor of apoptosis. Thioredoxins may play a role in a variety of human diseases including cancer. An increased level of thioredoxin-1 is found in many human tumors, where it is associated with aggressive tumor growth. Drugs are being developed that inhibit thioredoxin and that have antitumor activity.

Notes: Abstract Proteins are designed to function in environments crowded by cosolutes, but most studies of protein equilibria are conducted in dilute solution. While there is no doubt that crowding changes protein equilibria, interpretations of the changes remain controversial. This review combines experimental observations on the effect of small uncharged cosolutes (mostly sugars) on protein stability with a discussion of the thermodynamics of cosolute-induced nonideality and critical assessments of the most commonly applied interpretations. Despite the controversy surrounding the most appropriate manner for interpreting these effects of thermodynamic nonideality arising from the presence of small cosolutes, experimental advantage may still be taken of the ability of the cosolute effect to promote not only protein stabilization but also protein self-association and complex formation between dissimilar reactants. This phenomenon clearly has potential ramifications in the cell, where the crowded environment could well induce the same effects.

Notes: Abstract Nuclear receptors (NRs) form a superfamily of ligand-inducible transcription factors composed of several domains. Recent structural studies focused on domain E, which harbors the ligand-binding site and the ligand-dependent transcription activation function AF-2. Structures of single representatives in an increasing number of various complexes as well as new structures of further NRs addressed issues such as discrimination of ligands, superagonism, isotype specificity, and partial agonism. Until today, one unique transcriptionally active form of domain E was determined; however, divergent tertiary structures of apo-forms and transcriptionally inactive forms are known. Thus, recent results link the transformation of NRs upon ligand binding to principles of protein folding. Furthermore, the ensemble of NR structures, including those of DNA-binding domains, provides one of the foundations for the understanding of interactions with transcription intermediary factors up to the characterization of the link between NR complexes and the basal transcriptional machinery at the structural level.

Notes: Abstract Microtubules are polymers that are essential for, among other functions, cell transport and cell division in all eukaryotes. The regulation of the microtubule system includes transcription of different tubulin isotypes, folding of alpha/beta-tubulin heterodimers, post-translation modification of tubulin, and nucleotide-based microtubule dynamics, as well as interaction with numerous microtubule-associated proteins that are themselves regulated. The result is the precise temporal and spatial pattern of microtubules that is observed throughout the cell cycle. The recent high-resolution analysis of the structure of tubulin and the microtubule has brought new insight to the study of microtubule function and regulation, as well as the mode of action of antimitotic drugs that disrupt normal microtubule behavior. The combination of structural, genetic, biochemical, and biophysical data should soon give us a fuller understanding of the exquisite details in the regulation of the microtubule cytoskeleton.

Notes: Abstract The past few years have seen exciting advances in understanding the structure and function of catalytic RNA. Crystal structures of several ribozymes have provided detailed insight into the folds of RNA molecules. Models of other biologically important RNAs have been constructed based on structural, phylogenetic, and biochemical data. However, many questions regarding the catalytic mechanisms of ribozymes remain. This review compares the structures and possible catalytic mechanisms of four small self-cleaving RNAs: the hammerhead, hairpin, hepatitis delta virus, and in vitro-selected lead-dependent ribozymes. The organization of these small catalysts is contrasted to that of larger ribozymes, such as the group I intron.

Notes: Abstract The bacterial pathogen Salmonella enterica has evolved a very sophisticated functional interface with its vertebrate hosts. At the center of this interface is a specialized organelle, the type III secretion system, that directs the translocation of bacterial proteins into the host cell. Salmonella spp. encode two such systems that deliver a remarkable array of bacterial proteins capable of modulating a variety of cellular functions, including actin cytoskeleton dynamics, nuclear responses, and endocytic trafficking. Many of these bacterial proteins operate by faithful mimicry of host proteins, in some cases representing the result of extensive molecular tinkering and convergent evolution. The coordinated action of these type III secreted proteins secures the replication and survival of the bacteria avoiding overt damage to the host. The study of this remarkable pathogen is not only illuminating general paradigms in microbial pathogenesis but is also providing valuable insight into host cell functions.

Notes: Abstract Vertebrate limb buds are embryonic structures for which much molecular and cellular data are known regarding the mechanisms that control pattern formation during development. Specialized regions of the developing limb bud, such as the zone of polarizing activity (ZPA), the apical ectodermal ridge (AER), and the non-ridge ectoderm, direct and coordinate the development of the limb bud along the anterior-posterior (AP), dorsal-ventral (DV), and proximal-distal (PD) axes, giving rise to a stereotyped pattern of elements well conserved among tetrapods. In recent years, specific gene functions have been shown to mediate the organizing and patterning activities of the ZPA, the AER, and the non-ridge ectoderm. The analysis of these gene functions has revealed the existence of complex interactions between signaling pathways operated by secreted factors of the HH, TGF-beta/BMP, WNT, and FGF superfamilies, which interact with many other genetic networks to control limb positioning, outgrowth, and patterning. The study of limb development has helped to establish paradigms for the analysis of pattern formation in many other embryonic structures and organs.

Notes: Abstract Cells in the immune and nervous systems communicate through informational synapses. The two-dimensional chemistry underlying the process of synapse formation is beginning to be explored using fluorescence imaging and mechanical techniques. Early analysis of two-dimensional kinetic rates (kon and koff) and equilibrium constants (Kd) provides a number of biological insights. First, there are two regimes for adhesion-one disordered with slow kon and the other self-ordered with 104-fold faster kon. Despite huge variation in two-dimensional kon, the two-dimensional koff is like koff in solution, and two-dimensional koff is more closely related to intrinsic properties of the interaction than the two-dimensional kon. Thus difference in koff can be used to set signaling thresholds. Early signaling complexes are compartmentalized to generate synergistic signaling domains. Immune antigen receptor components have a role in neural synapse editing. This suggests significant parallels in informational synapse formation based on common two-dimensional chemistry and signaling strategies.

Notes: Abstract Pollen tubes and root hairs are highly elongated, cylindrically shaped cells whose polarized growth permits them to explore the environment for the benefit of the entire plant. Root hairs create an enormous surface area for the uptake of water and nutrients, whereas pollen tubes deliver the sperm cells to the ovule for fertilization. These cells grow exclusively at the apex and at prodigious rates (in excess of 200 nm/s for pollen tubes). Underlying this rapid growth are polarized ion gradients and fluxes, turnover of cytoskeletal elements (actin microfilaments), and exocytosis and endocytosis of membrane vesicles. Intracellular gradients of calcium and protons are spatially localized at the growing apex; inward fluxes of these ions are apically directed. These gradients and fluxes oscillate with the same frequency as the oscillations in growth rate but not with the same phase. Actin microfilaments, which together with myosin generate reverse fountain streaming, undergo rapid turnover in the apical domain, possibly being regulated by key actin-binding proteins, e.g., profilin, villin, and ADF/cofilin, in concert with the ion gradients. Exocytosis of vesicles at the apex, also dependent on the ion gradients, provides precursor material for the continuously expanding cell wall of the growing cell. Elucidation of the interactions and of the dynamics of these different components is providing unique insight into the mechanisms of polarized growth.

Notes: Abstract Developing organisms may contain billions of cells destined to differentiate in numerous different ways. One strategy organisms use to simplify the orchestration of development is the separation of cell populations into distinct functional units. Our expanding knowledge of boundary formation and function in different systems is beginning to reveal general principles of this process. Fields of cells are subdivided by the interpretation of morphogen gradients, and these subdivisions are then maintained and refined by local cell-cell interactions. Sharp and stable separation between cell populations requires special mechanisms to keep cells segregated, which in many cases appear to involve the regulation of cell affinity. Once cell populations become distinct, specialized cells are often induced along the borders between them. These boundary cells can then influence the patterning of surrounding cells, which can result in progressively finer subdivisions of a tissue. Much has been learned about the signaling pathways that establish boundaries, but a key challenge for the future remains to elucidate the cellular and molecular mechanisms that actually keep cell populations separated.

Notes: Abstract We focus on new observational capabilities (Yohkoh, SoHO, TRACE), observations, modeling approaches, and insights into physical processes of the solar corona. The most impressive new results and problems discussed in this article can be appreciated from the movies available on the Annual Reviews website and at http://www.lmsal.com/pub/araa/araa.html . "The Sun is new each day." Heraclites (ca 530-475 BC) "Everything flows." Heraclites (ca 530-475 BC)

Notes: Abstract This review takes a critical look at the cosmological scenario at the turn of the century by examining the available cosmological models in the light of the present observational evidence. The center stage is held by the big bang models, which are collectively referred to here as standard cosmology (SC) and its extensions. SC itself is characterized by a seven parameter set of models based on Einstein's general theory of relativity. The seven parameters are H0, OmegaB, OmegaDM, OmegaLambda, OmegaR (describing the background universe, and A, n (specifying the amplitude and power law index of initial fluctuation spectrum). The extended SC includes extrapolations of the SC to earlier epochs when the mean energies of the particles were greater than about 100 GeV. The strength of the SC is seen to lie in its successful prediction of the expansion of the universe, the abundance of light nuclei, and the spectrum and anisotropies of the cosmic microwave background (CMBR). The SC has led to a whole class of theories of structure formation, which are, in principle, testable observationally. The subject of twentieth century cosmology gained considerably from occasional ideas different from the SC; some of these are briefly outlined and placed in historical perspective. Currently there is only one alternative cosmology, the quasi steady state cosmology (QSSC), that has been developed to a stage where it can be compared with observations and also with the SC. Although the SC does appear quite successful, there are still many unresolved issues that keep the cosmological scene fairly open.

Notes: Abstract Fluid mechanics research related to fire is reviewed with a focus on canonical flows, multiphysics coupling aspects, and experimental and numerical techniques. Fire is a low-speed, chemically reacting flow in which buoyancy plays an important role. Fire research has focused on two canonical flows, the reacting boundary layer and the reacting free plume. There is rich, multilateral, bidirectional coupling among fluid mechanics and scalar transport, combustion, and radiation. There is only a limited experimental fluid mechanics database for fire owing to measurement difficulties in the harsh environment and to the focus within the fire community on thermal/chemical consequences. Increasingly, computational fluid dynamics techniques are being used to provide engineering guidance on thermal/chemical consequences and to study fire phenomenology.

Notes: Abstract Models are considered for rotating flows over sills, through straits, and along coasts where the variation in geometry in the flow direction is slow but otherwise unrestricted. In addition to the (rotation-modified) free surface waves of nonrotating open channel hydraulics, with their predominantly vertical signature, slow Rossby or vorticity waves are possible when the background potential vorticity varies. In all but the simplest cases the conservation of energy and momentum fluxes is no longer sufficient to determine the flow behavior. Various additional modeling assumptions are reviewed, and time-dependent finite-amplitude and weakly nonlinear theories that include long Rossby wave dynamics are summarized.

Notes: Abstract This review begins with the classical foundations of relative dispersion in Kolmogorov's similarity scaling. Analysis of the special cases of isotropic and homogeneous scalar fields is then used to establish most simply the connection with turbulent mixing. The importance of the two-particle acceleration covariance in relative dispersion is demonstrated from the kinematics of the motion of particle-pairs. A summary of the development of two-particle Lagrangian stochastic models is given, with emphasis on the assumptions and constraints involved, and on predictions of the scalar variance field for inhomogeneous sources. Two-point closures and kinematic simulation are also reviewed in the context of their prediction of the Richardson constant and other fundamental constants. In the absence of reliable field data, direct numerical simulations and laboratory measurements seem most likely to provide suitable data with which to test the assumptions and predictions of these theories.

Notes: Abstract The development of cancer requires multiple genetic alterations perturbing distinct cellular pathways. In human cancers, these alterations often arise owing to mutations in tumor-suppressor genes whose normal function is to either inhibit the proliferation, apoptosis, or differentiation of cells, or maintain their genomic integrity. Mouse models for tumor suppressors frequently provide definitive evidence for the antitumorigenic functions of these genes. In addition, animal models permit the identification of previously unsuspected roles of these genes in development and differentiation. The availability of null and tissue-specific mouse mutants for tumor-suppressor genes has greatly facilitated our understanding of the mechanisms leading to cancer. In this review, we describe mouse models for tumor-suppressor genes.

Notes: Abstract Chromatin boundaries and insulators are transcriptional regulatory elements that modulate interactions between enhancers and promoters and protect genes from silencing effects by the adjacent chromatin. Originally discovered in Drosophila, insulators have now been found in a variety of organisms, ranging from yeast to humans. They have been found interspersed with regulatory sequences in complex genes and at the boundaries between active and inactive chromatin. Insulators might modulate transcription by organizing the chromatin fiber within the nucleus through the establishment of higher-order domains of chromatin structure.

Notes: Abstract Double-strand breaks and other lesions in DNA can stimulate homologous genetic recombination in two quite different ways: by promoting recombination near the break (roughly within a kb) or far from the break. Recent emphasis on the repair aspect of recombination has focused attention on DNA interactions and recombination near breaks. Here I review evidence for recombination far from DNA breaks in bacteria and fungi and discuss mechanisms by which this can occur. These mechanisms include entry of a traveling entity ("recombination machine") at a break, formation of long heteroduplex DNA, priming of DNA replication by a broken end, and induction of recombination potential in trans. Special emphasis is placed on contrasting views of how the RecBCD enzyme of Escherichia coli promotes recombination far (tens of kb) from a double-strand break. The occurrence of recombination far from DNA breaks and of correlated recombination events far apart suggests that "action at a distance" during recombination is a widespread feature among diverse organisms.

Notes: Abstract Recombination is a major source of genetic variability in retroviruses. Each viral particle contains two single-stranded genomic RNAs. Recombination mostly results from a switch in template between these two RNAs during reverse transcription. Here we emphasize the main mechanisms underlying recombination that are emerging from recent advances in biochemical and cell culture techniques. Increasing evidence supporting the involvement of RNA secondary structures now complements the predominant role classically attributed to enzyme pausing during reverse transcription. Finally, the implications of recombination on the dynamics of emergence of genomic aberrations in retroviruses are discussed.

Notes: Abstract A central aspect of cellular function is the proper regulation of nucleocytoplasmic transport. In recent years, significant progress has been made in identifying and characterizing the essential components of the transport machinery. Despite these advances, some facets of this process are still unclear. Furthermore, recent work has uncovered novel molecules and mechanisms of nuclear transport. This review focuses on the unresolved and novel aspects of nuclear transport and explores issues in tRNA, snRNA, and mRNA export that highlight the diversity of nuclear transport mechanisms.

Notes: Abstract Phenotypic variation for quantitative traits results from the segregation of alleles at multiple quantitative trait loci (QTL) with effects that are sensitive to the genetic, sexual, and external environments. Major challenges for biology in the post-genome era are to map the molecular polymorphisms responsible for variation in medically, agriculturally, and evolutionarily important complex traits; and to determine their gene frequencies and their homozygous, heterozygous, epistatic, and pleiotropic effects in multiple environments. The ease with which QTL can be mapped to genomic intervals bounded by molecular markers belies the difficulty in matching the QTL to a genetic locus. The latter requires high-resolution recombination or linkage disequilibrium mapping to nominate putative candidate genes, followed by genetic and/or functional complementation and gene expression analyses. Complete genome sequences and improved technologies for polymorphism detection will greatly advance the genetic dissection of quantitative traits in model organisms, which will open avenues for exploration of homologous QTL in related taxa.

Notes: Abstract Translational control is a prevalent means of gene regulation during Drosophila oogenesis and embryogenesis. Multiple maternal mRNAs are localized within the oocyte, and this localization is often coupled to their translational regulation. Subsequently, translational control allows maternally deposited mRNAs to direct the early stages of embryonic development. In this review we outline some general mechanisms of translational regulation and mRNA localization that have been uncovered in various model systems. Then we focus on the posttranscriptional regulation of four maternal transcripts in Drosophila that are localized during oogenesis and are critical for embryonic patterning: bicoid (bcd), nanos (nos), oskar (osk), and gurken (grk). Cis- and trans-acting factors required for the localization and translational control of these mRNAs are discussed along with potential mechanisms for their regulation.

Notes: Abstract Although coevolution is complicated, in that the interacting species evolve in response to each other, such evolutionary dynamics are amenable to mathematical modeling. In this article, we briefly review models and data on coevolution between plants and the pathogens and herbivores that attack them. We focus on "arms races," in which trait values in the plant and its enemies escalate to more and more extreme values. Untested key assumptions in many of the models are the relationships between costs and benefits of resistance in the plant and the level of resistance, as well as how costs of virulence or detoxification ability in the enemy change with levels of these traits. A preliminary assessment of these assumptions finds only mixed support for the models. What is needed are models that are more closely tailored to particular plant-enemy interactions, as well as experiments that are expressly designed to test existing models.

Notes: Abstract Calmodulin, a small, ubiquitous Ca2+-binding protein, regulates a wide variety of proteins and processes in all eukaryotes. CMD1, the single gene encoding calmodulin in S. cerevisiae, is essential, and this review discusses studies that identified many of calmodulin's physiological targets and their functions in yeast cells. Calmodulin performs essential roles in mitosis, through its regulation of Nuf1p/Spc110p, a component of the spindle pole body, and in bud growth, by binding Myo2p, an unconventional class V myosin required for polarized secretion. Surprisingly, mutant calmodulins that fail to bind Ca2+ can perform these essential functions. Calmodulin is also required for endocytosis in yeast and participates in Ca2+-dependent, stress-activated signaling pathways through its regulation of a protein phosphatase, calcineurin, and the protein kinases, Cmk1p and Cmk2p. Thus, calmodulin performs important physiological functions in yeast cells in both its Ca2+-bound and Ca2+-free form.

Notes: Abstract The development of molecular markers and genomic resources has facilitated the isolation of genes responsible for rare monogenic epilepsies in human and mouse. Many of the identified genes encode ion channels or other components of neuronal signaling. The electrophysiological properties of mutant alleles indicate that neuronal hyperexcitability is one cellular mechanism underlying seizures. Genetic heterogeneity and allelic variability are hallmarks of human epilepsy. For example, mutations in three different sodium channel genes can produce the same syndrome, GEFS+, while individuals with the same allele can experience different types of seizures. Haploinsufficiency for the sodium channel SCN1A has been demonstrated by the severe infantile epilepsy and cognitive deficits in heterozygotes for de novo null mutations. Large-scale patient screening is in progress to determine whether less severe alleles of the genes responsible for monogenic epilepsy may contribute to the common types of epilepsy in the human population. The development of pharmaceuticals directed towards specific epilepsy genotypes can be anticipated, and the introduction of patient mutations into the mouse genome will provide models for testing these targeted therapies.

Notes: Abstract Hereditary isolated hearing loss is genetically highly heterogeneous. Over 100 genes are predicted to cause this disorder in humans. Sixty loci have been reported and 24 genes underlying 28 deafness forms have been identified. The present epistemic stage in the realm consists in a preliminary characterization of the encoded proteins and the associated defective biological processes. Since for several of the deafness forms we still only have fuzzy notions of their pathogenesis, we here adopt a presentation of the various deafness forms based on the site of the primary defect: hair cell defects, nonsensory cell defects, and tectorial membrane anomalies. The various deafness forms so far studied appear as monogenic disorders. They are all rare with the exception of one, caused by mutations in the gene encoding the gap junction protein connexin26, which accounts for between one third to one half of the cases of prelingual inherited deafness in Caucasian populations.

Notes: Abstract The separation of sister chromatids at the metaphase to anaphase transition is one of the most dramatic of all cellular events and is a crucial aspect of all sexual and asexual reproduction. The molecular basis for this process has until recently remained obscure. New research has identified proteins that hold sisters together while they are aligned on the metaphase plate. It has also shed insight into the mechanisms that dissolve sister chromatid cohesion during both mitosis and meiosis. These findings promise to provide insights into defects in chromosome segregation that occur in cancer cells and into the pathological pathways by which aneuploidy arises during meiosis.

Notes: Abstract The polarized architecture of epithelial cells and tissues is a fundamental determinant of animal anatomy and physiology. Recent progress made in the genetic and molecular analysis of epithelial polarity and cellular junctions in Drosophila has led to the most detailed understanding of these processes in a whole animal model system to date. Asymmetry of the plasma membrane and the differentiation of membrane domains and cellular junctions are controlled by protein complexes that assemble around transmembrane proteins such as DE-cadherin, Crumbs, and Neurexin IV, or other cytoplasmic protein complexes that associate with the plasma membrane. Much remains to be learned of how these complexes assemble, establish their polarized distribution, and contribute to the asymmetric organization of epithelial cells.

Notes: Abstract Human population genetics has entered a new era of public interest, of controversy, and of ethical problems. Population genetics raises novel ethical problems because both the individuals and the populations being studied are, in effect, "subjects" of the research. Those populations are collectively subject to possible benefits and harms from the research and have interests, somewhat different from those of the individuals, that must be considered from both ethical and practical standpoints. The chapter first describes the new setting for research in human population genetics. It then examines the most controversial ethical issue in population genetics-whether researchers must obtain the informed consent of both the individual subjects and the group as a collectivity. Other vexing issues, including special problems caused by researchers' commercial interests, confidentiality, control over research uses and materials, and return of information to the population are also considered.

Notes: Figure 1 G. LEDYARD STEBBINS Reproduction from Original Negative by Ansel Adams, Courtesy UCR/California Museum of Photography, Sweeney/Rubin Ansel Adams FIAT LUX Collection, University of California at Riverside. Figure 1 G. LEDYARD STEBBINS Reproduction from Original Negative by Ansel Adams, Courtesy UCR/Californ... More than any other individual, Stebbins synthesized knowledge from a disparate set of areas that included plant genetics, systematics, and evolution. This work culminated in 1950 with the appearance of his magnum opus, Variation and Evolution in Plants. This book gave plant evolution a coherent framework that was compatible with that emerging from the work of Theodosius Dobzhansky, Ernst Mayr, G. G. Simpson, and Julian Huxley, and others associated with establishing the synthetic theory of evolution. For this work he is regarded as the botanical "architect" of the evolutionary synthesis.

Notes: Abstract Genetic screens in Drosophila melanogaster have helped elucidate the process of axis formation during early embryogenesis. Axis formation in the D. melanogaster embryo involves the use of two fundamentally different mechanisms for generating morphogenetic activity: patterning the anteroposterior axis by diffusion of a transcription factor within the syncytial embryo and specification of the dorsoventral axis through a signal transduction cascade. Identification of Drosophila genes involved in axis formation provides a launch-pad for comparative studies that examine the evolution of axis specification in different insects. Additionally, there is similarity between axial patterning mechanisms elucidated genetically in Drosophila and those demonstrated for chordates such as Xenopus. In this review we examine the postfertilization mechanisms underlying axis specification in Drosophila. Comparative data are then used to ask whether aspects of axis formation might be derived or ancestral.

Notes: Abstract Quorum sensing is an example of community behavior prevalent among diverse bacterial species. The term "quorum sensing" describes the ability of a microorganism to perceive and respond to microbial population density, usually relying on the production and subsequent response to diffusible signal molecules. A significant number of gram-negative bacteria produce acylated homoserine lactones (acyl-HSLs) as signal molecules that function in quorum sensing. Bacteria that produce acyl-HSLs can respond to the local concentration of the signaling molecules, and high population densities foster the accumulation of inducing levels of acyl-HSLs. Depending upon the bacterial species, the physiological processes regulated by quorum sensing are extremely diverse, ranging from bioluminescence to swarming motility. Acyl-HSL quorum sensing has become a paradigm for intercellular signaling mechanisms. A flurry of research over the past decade has led to significant understanding of many aspects of quorum sensing including the synthesis of acyl-HSLs, the receptors that recognize the acyl-HSL signal and transduce this information to the level of gene expression, and the interaction of these receptors with the transcriptional machinery. Recent studies have begun to integrate acyl-HSL quorum sensing into global regulatory networks and establish its role in developing and maintaining the structure of bacterial communities.

Notes: Abstract L1 retrotransposons comprise 17% of the human genome. Although most L1s are inactive, some elements remain capable of retrotransposition. L1 elements have a long evolutionary history dating to the beginnings of eukaryotic existence. Although many aspects of their retrotransposition mechanism remain poorly understood, they likely integrate into genomic DNA by a process called target primed reverse transcription. L1s have shaped mammalian genomes through a number of mechanisms. First, they have greatly expanded the genome both by their own retrotransposition and by providing the machinery necessary for the retrotransposition of other mobile elements, such as Alus. Second, they have shuffled non-L1 sequence throughout the genome by a process termed transduction. Third, they have affected gene expression by a number of mechanisms. For instance, they occasionally insert into genes and cause disease both in humans and in mice. L1 elements have proven useful as phylogenetic markers and may find other practical applications in gene discovery following insertional mutagenesis in mice and in the delivery of therapeutic genes.

Notes: Abstract Early studies of animal mitochondrial DNA (mtDNA) assumed that nucleotide sequence variation was neutral. Recent analyses of sequences from a variety of taxa have brought the validity of this assumption into question. Here we review analytical methods used to test for neutrality and evidence for nonneutral evolution of animal mtDNA. Evaluations of mitochondrial haplotypes in different nuclear backgrounds identified differences in performance, typically favoring coevolved mitochondrial and nuclear genomes. Experimental manipulations also indicated that certain haplotypes have an advantage over others; however, biotic and historical effects and cyto-nuclear interactions make it difficult to assess the relative importance of nonneutral factors. Statistical analyses of sequences have been used to argue for nonneutrality of mtDNA; however, rejection of neutral patterns in the published literature is common but not predominant. Patterns of replacement and synonymous substitutions within and between species identified a trend toward an excess of replacement mutations within species. This pattern has been viewed as support for the existence of mildly deleterious mutations within species; however, other alternative explanations that can produce similar patterns cannot be eliminated.

Notes: Abstract Structural models of site-specific recombinases from the lambda integrase family of enzymes have in the last four years provided an important new perspective on the three-dimensional nature of the recombination pathway. Members of this family, which include the bacteriophage P1 Cre recombinase, bacteriophage lambda integrase, the yeast Flp recombinase, and the bacterial XerCD recombinases, exchange strands between DNA substrates in a stepwise process. One pair of strands is exchanged to form a Holliday junction intermediate, and the second pair of strands is exchanged during resolution of the junction to products. Crystal structures of reaction intermediates in the Cre-loxP site-specific recombination system, together with recent biochemical studies in the field, support a "strand swapping" model for recombination that does not require branch migration of the Holliday junction intermediate in order to test homology between recombining sites.

Notes: Abstract On laboratory time scales, the energy landscape of a weak bond along a dissociation pathway is fully explored through Brownian-thermal excitations, and energy barriers become encoded in a dissociation time that varies with applied force. Probed with ramps of force over an enormous range of rates (force/time), this kinetic profile is transformed into a dynamic spectrum of bond rupture force as a function of loading rate. On a logarithmic scale in loading rate, the force spectrum provides an easy-to-read map of the prominent energy barriers traversed along the force-driven pathway and exposes the differences in energy between barriers. In this way, the method of dynamic force spectroscopy (DFS) is being used to probe the complex relation between force-lifetime-and chemistry in single molecular bonds. Most important, DFS probes the inner world of molecular interactions to reveal barriers that are difficult or impossible to detect in assays of near equilibrium dissociation but that determine bond lifetime and strength under rapid detachment. To use an ultrasensitive force probe as a spectroscopic tool, we need to understand the physics of bond dissociation under force, the impact of experimental technique on the measurement of detachment force (bond strength), the consequences of complex interactions in macromolecular bonds, and effects of multiply-bonded attachments.

Notes: Abstract Understanding the mechanisms by which genetic information is replicated is important both to basic knowledge of biological organisms and to many useful applications in biomedical research and biotechnology. One of the main functions of a DNA polymerase enzyme is to help DNA recognize itself with high specificity when a strand is being copied. Recent studies have shed new light on the question of what physical forces cause a polymerase enzyme to insert a nucleotide into a strand of DNA and to choose the correct nucleotide over the incorrect ones. This is discussed in the light of three main forces that govern DNA recognition: base stacking, Watson-Crick hydrogen bonding, and steric interactions. These factors are studied with natural and structurally altered DNA nucleosides.

Notes: Abstract Enzymes of the mitochondrial respiratory chain serve as proton pumps, using the energy made available from electron transfer reactions to transport protons across the inner mitochondrial membrane and create an electrochemical gradient used for the production of ATP. The ATP synthase enzyme is reversible and can also serve as a proton pump by coupling ATP hydrolysis to proton translocation. Each of the respiratory enzymes uses a different strategy for performing proton pumping. In this work, the strategies are described and the structural bases for the action of these proteins are discussed in light of recent crystal structures of several respiratory enzymes. The mechanisms and efficiency of proton translocation are also analyzed in terms of the thermodynamics of the substrate transformations catalyzed by these enzymes.

Notes: Abstract Atomic resolution structure determinations of proteins by X-ray crystallography are formidable multidisciplinary undertakings, requiring protein construct design, expression and purification, crystallization trials, phase determination, and model building. Modern mass spectrometric methods can greatly facilitate these obligate tasks. Thus, mass spectrometry can be used to verify that the desired protein construct has been correctly expressed, to define compact domains in the target protein, to assess the components contained within the protein crystals, and to screen for successful incorporation of seleno-methionine and other heavy metal reagents used for phasing. In addition, mass spectrometry can be used to address issues of modeling, topology, and side-chain proximity. Here, we demonstrate how rational use of mass spectrometry assists and expedites high resolution X-ray structure determination through each stage of the process of protein crystallography.

Notes: Abstract Understanding the precise role of photosystem II as an element of oxygenic photosynthesis requires knowledge of the molecular structure of this membrane protein complex. The past few years have been particularly exciting because the structural era of the plant photosystem II has begun. Although the atomic structure has yet to be determined, the map obtained at 6 A resolution by electron crystallography allows assignment of the key reaction center subunits with their associated pigment molecules. In the following, we first review the structural details that have recently emerged and then discuss the primary and secondary photochemical reaction pathways. Finally, in an attempt to establish the evolutionary link between the oxygenic and the anoxygenic photosynthesis, a framework structure common to all photosynthetic reaction centers has been defined, and the implications have been described.

Notes: Abstract This review focuses on recent advances in understanding protein folding kinetics in the context of nucleation theory. We present basic concepts such as nucleation, folding nucleus, and transition state ensemble and then discuss recent advances and challenges in theoretical understanding of several key aspects of protein folding kinetics. We cover recent topology-based approaches as well as evolutionary studies and molecular dynamics approaches to determine protein folding nucleus and analyze other aspects of folding kinetics. Finally, we briefly discuss successful all-atom Monte-Carlo simulations of protein folding and conclude with a brief outlook for the future.

Notes: Abstract Oligosaccharides play a crucial role in many of the recognition, signaling, and adhesion events that take place at the surface of cells. Abnormalities in the synthesis or presentation of these carbohydrates can lead to misfolded and inactive proteins, as well as to several debilitating disease states. However, their diverse structures, which are the key to their function, have hampered studies by biologists and chemists alike. This review presents an overview of techniques for examining and manipulating cell surface oligosaccharides through genetic, enzymatic, and chemical strategies.

Notes: Abstract Thrombospondins are secreted, multidomain macromolecules that act as regulators of cell interactions in vertebrates. Gene knockout mice constructed for two members of this family demonstrate roles in the organization and homeostasis of multiple tissues, with particularly significant activities in the regulation of angiogenesis. This review discusses the functions of thrombospondins with regard to their cellular mechanisms of action and highlights recent advances in understanding how multifactorial molecular interactions, at the cell surface and within extracellular matrix, produce cell-type-specific effects on cell behavior and the organization of matrix and tissues.

Notes: Abstract Multipotent stem cells are clonal cells that self-renew as well as differentiate to regenerate adult tissues. Whereas stem cells and their fates are known by unique genetic marker studies, the fate and function of these cells are best studied by their prospective isolation. This review is about the properties of various highly purified tissue-specific multipotent stem cells and purified oligolineage progenitors. We contend that unless the stem or progenitor cells in question have been purified to near homogeneity, one cannot know whether their generation of expected (or unexpected) progeny is a property of a known cell type. It is interesting that in the hematopoietic system the only long-term self-renewing cells in the stem and progenitors pool are the hematopoietic stem cells. This fact is discussed in the context of normal and leukemic hematopoiesis.

Notes: Abstract Mouse embryonic stem cells are continuous cell lines derived directly from the fetal founder tissue of the preimplantation embryo. They can be expanded in culture while retaining the functional attributes of pluripotent early embryo cells. In particular, they can participate fully in fetal development when reintroduced into the embryo. The capacity for multilineage differentiation is reproduced in culture where embryonic stem cells can produce a wide range of well-defined cell types. This has stimulated interest in the isolation of analogous cells of human origin. Such human pluripotent stem cells could constitute a renewable source of more differentiated cells that could be employed to replace diseased or damaged tissue by cellular transplantation. In this review, the relationships between mouse embryonic stem cells, resident pluripotent cells in the embryo, and human embryo-derived cell lines are evaluated, and the prospects and challenges of embryo stem cell research are considered. This review is dedicated to Rosa Beddington FRS, a great developmental biologist, a wonderful colleague, and an inspirational advocate of human stem cell research.

Notes: Abstract The matrix metalloproteinases (MMPs) constitute a multigene family of over 25 secreted and cell surface enzymes that process or degrade numerous pericellular substrates. Their targets include other proteinases, proteinase inhibitors, clotting factors, chemotactic molecules, latent growth factors, growth factor-binding proteins, cell surface receptors, cell-cell adhesion molecules, and virtually all structural extracellular matrix proteins. Thus MMPs are able to regulate many biologic processes and are closely regulated themselves. We review recent advances that help to explain how MMPs work, how they are controlled, and how they influence biologic behavior. These advances shed light on how the structure and function of the MMPs are related and on how their transcription, secretion, activation, inhibition, localization, and clearance are controlled. MMPs participate in numerous normal and abnormal processes, and there are new insights into the key substrates and mechanisms responsible for regulating some of these processes in vivo. Our knowledge in the field of MMP biology is rapidly expanding, yet we still do not fully understand how these enzymes regulate most processes of development, homeostasis, and disease.

Notes: Abstract There has recently been considerable progress in understanding the regulation of clathrin-coated vesicle (CCV) formation and function. These advances are due to the determination of the structure of a number of CCV coat components at molecular resolution and the identification of novel regulatory proteins that control CCV formation in the cell. In addition, pathways of (a) phosphorylation, (b) receptor signaling, and (c) lipid modification that influence CCV formation, as well as the interaction between the cytoskeleton and CCV transport pathways are becoming better defined. It is evident that although clathrin coat assembly drives CCV formation, this fundamental reaction is modified by different regulatory proteins, depending on where CCVs are forming in the cell. This regulatory difference likely reflects the distinct biological roles of CCVs at the plasma membrane and trans-Golgi network, as well as the distinct properties of these membranes themselves. Tissue-specific functions of CCVs require even more-specialized regulation and defects in these pathways can now be correlated with human diseases.

Notes: Abstract A distinctive and essential feature of the vertebrate body is a pronounced left-right asymmetry of internal organs and the central nervous system. Remarkably, the direction of left-right asymmetry is consistent among all normal individuals in a species and, for many organs, is also conserved across species, despite the normal health of individuals with mirror-image anatomy. The mechanisms that determine stereotypic left-right asymmetry have fascinated biologists for over a century. Only recently, however, has our understanding of the left-right patterning been pushed forward by links to specific genes and proteins. Here we examine the molecular biology of the three principal steps in left-right determination: breaking bilateral symmetry, propagation and reinforcement of pattern, and the translation of pattern into asymmetric organ morphogenesis.

Notes: Abstract Circadian rhythms are found in most eukaryotes and some prokaryotes. The mechanism by which organisms maintain these roughly 24-h rhythms in the absence of environmental stimuli has long been a mystery and has recently been the subject of intense research. In the past few years, we have seen explosive progress in the understanding of the molecular basis of circadian rhythms in model systems ranging from cyanobacteria to mammals. This review attempts to outline these primarily genetic and biochemical findings and encompasses work done in cyanobacteria, Neurospora, higher plants, Drosophila, and rodents. Although actual clock components do not seem to be conserved between kingdoms, central clock mechanisms are conserved. Somewhat paradoxically, clock components that are conserved between species can be used in diverse ways. The different uses of common components may reflect the important role that the circadian clock plays in adaptation of species to particular environmental niches.

Notes: Abstract The synthesis of the two currently used superhard materials, diamond and cubic boron nitride, is briefly described with indications of the factors influencing the quality of the crystals obtained. The physics of hardness is discussed and the importance of covalent bonding and fixed atomic positions in the crystal structure, which determine high hardness values, is outlined. The materials investigated to date are described and new potentially superhard materials are presented. No material that is thermodynamically stable under ambient conditions and composed of light (small) atoms will have a hardness greater than that of diamond. Materials with hardness values similar to that of cubic boron nitride (cBN) can be obtained. However, increasing the capabilities of the high-pressure devices could lead to the production of better quality cBN compacts without binders.

Notes: Abstract A review of the field of photorefractive liquid crystals is presented. The first reports of photorefractive liquid crystals occurred in 1994, and the performance of these materials has dramatically improved since that time. Liquid crystalline materials have proven to be highly versatile, showing photorefractive character under a wide range of conditions. For example, new composites based on high-molar-mass liquid crystals are now capable of forming volume (Bragg) gratings with high photorefractive gain coefficients of 〉600 cm-1. Formation times for photorefractive Bragg gratings of 15 ms with applied fields of only 0.1 V/mum have been reported. Low-molar-mass liquid crystals continue to be developed and show their largest photorefractive character in the thin (Raman-Nath) grating regime. Composites of nonmesogenic polymers and liquid crystals are also discussed. The experiments and theoretical work that have been used to characterize these materials are reviewed.