Single-molecule kinetics of lambda exonuclease reveal base dependence and dynamic disorder

We used a multiplexed approach based on flow-stretched DNA to monitor the enzymatic digestion of lambda-phage DNA by individual bacteriophage lambda exonuclease molecules. Statistical analyses of multiple single-molecule trajectories observed simultaneously reveal that the catalytic rate is dependent on the local base content of the substrate DNA. By relating single-molecule kinetics to the free energies of hydrogen bonding and base stacking, we establish that the melting of a base from the DNA is the rate-limiting step in the catalytic cycle. The catalytic rate also exhibits large fluctuations independent of the sequence, which we attribute to conformational changes of the enzyme-DNA complex.     

Amplification of acetylcholine-binding catenanes from dynamic combinatorial libraries

Directed chemical synthesis can produce a vast range of molecular structures, but the intended product must be known at the outset. In contrast, evolution in nature can lead to efficient receptors and catalysts whose structures defy prediction. To access such unpredictable structures, we prepared dynamic combinatorial libraries in which reversibly binding building blocks assemble around a receptor target. We selected for an acetylcholine receptor by adding the neurotransmitter to solutions of dipeptide hydrazones [proline-phenylalanine or proline-(cyclohexyl)alanine], which reversibly combine through hydrazone linkages. At thermodynamic equilibrium, the dominant receptor structure was an elaborate [2]-catenane consisting of two interlocked macrocyclic trimers. This complex receptor with a 100 nM affinity for acetylcholine could be isolated on a preparative scale in 67% yield.     

A rapid and easy method of detecting levels of gene expression in intact tobacco plants using an Agrobacterium-mediated transient assay: Toward development of nutritional diagnosis based on gene expression

For the use of gene expression for nutritional diagnosis, a rapid and easy method of detecting levels of gene expression was proposed. Agrobacterium tumefaciens carrying the GUS reporter gene was injected into intact tobacco leaves with a plastic syringe, and transient GUS expression was determined. GUS activities were reproducible in young leaves.     

Technologies for the diagnosis and remediation of Fe deficiency

The objective of this paper is to review the developments in the last few years in two important issues related to Fe deficiency in plants. First, the current knowledge on the possible ways to carry out the diagnosis and prognosis of Fe deficiency in plants is discussed. This includes discussion on the best ways to carry out a meaningful analysis of Fe-containing compounds in different plant parts. We will also discuss other measurement techniques that can permit to assess the Fe nutritional status in plants, including leaf chlorophyll concentrations and others. Second, the new developments in management techniques to control and remediate iron deficiency are discussed. This includes possible improved ways to supply Fe compounds available to plants, both to the soil and to the irrigation water. We also discuss possible ways to supply directly the plant with Fe containing compounds, either to the foliage or to the stem. A particular emphasis is given throughout the paper to fruit tree crops growing in Mediterranean areas.     

Saliva chromogranin A in growing pigs: A study of circadian patterns during daytime and stability under different storage conditions

Salivary chromogranin A (CgA) is considered to be a biomarker of activation of the sympatho-adrenomedullary system, and has recently been proposed as a useful indicator of the acute stress response in pigs. The aim of the present study was to determinate whether salivary CgA concentrations in healthy growing pigs exhibits any circadian pattern during the daytime, and to evaluate its stability under different storage conditions. A total of 80 pigs (40 in spring and another 40 in autumn) of two different ages and genders were used. To establish the circadian pattern, saliva samples were collected at 07.00, 11.00, 15.00 and 19.00 h on two consecutive days. Pooled samples were used for the stability study and were measured on the day of sampling and periodically for up to 360 days later. Samples were stored at 4 °C, ?20 °C or ?80 °C and the effect of repeated freezing and thawing was also evaluated.No circadian pattern was detected for salivary CgA in either season and there were no significant effects of gender or age. However, mean salivary CgA concentrations were significantly higher (P < 0.0001) in the pigs sampled in autumn, compared to those sampled in the spring. Short term storage at 4 °C is recommended for up to 2 days, whereas frozen samples can be stored for 1 year at ?20 °C or ?80 °C, without substantial reduction in CgA values. In addition, samples can be frozen and thawed up to seven times without significant loss of the biomarker.     

Phytomedicines for Candida-associated denture stomatitis

Phytomedicines are becoming more popular all over the world. Denture stomatitis (DS) presents as an inflammatory reaction in denture-bearing patients, under maxillary prosthesis with Candida albicans being the principal etiological agent. Many different methods of treatment for DS have been observed. The effects of the main medicinal plants claimed to be useful as antifungal agents in the treatment of DS are reviewed. Herbal remedies that have shown potential promise are mentioned, although much research is still required.     

Morphological variability of Atlantic salmon Salmo salar and brown trout Salmo trutta in different river environments

Abstract – The morphologies of sympatric juvenile Atlantic salmon Salmo salar parr and brown trout Salmo trutta parr were compared between Irish rivers with contrasting hydraulic environments – a high‐gradient and a low‐gradient tributary from the River Barrow catchment, south‐east Ireland and a high‐gradient river from the Burrishoole catchment, west of Ireland. The two catchments differ markedly in mean annual precipitation (849.0 mm year^?1 and 1370.3 mm year^?1 for the Barrow and Burrishoole catchments, respectively). Parr of both species demonstrated morphological variation between and within catchments. Changes in metrics such as pectoral fin length, body depth and body length between and within catchments suggest that hydraulic forces were a major determinant of morphological variation. Both species from the Burrishoole catchment had relatively larger pectoral fins, longer heads, larger eyes and shallower bodies than conspecifics from the Barrow catchment. In rivers subject to frequent rainfall‐driven high discharges, such as those in the Burrishoole catchment, a more fusiform body and head shape coupled with larger pectoral fins may reduce the energetic cost of maintaining position in the water column, as well as increase stability and manoeuvrability. The larger eyes in both parr species in the Burrishoole catchment could further be a response to the lower visibility of the more turbid and peat‐stained waters or to the reduced prey availability. The results of this study demonstrate that local adaptation to flow conditions can yield morphologically distinct populations and that multiple species can exhibit parallel phenotypic responses to changing environmental conditions.     

Parsimoniously modelling perennial vegetation suitability and identifying priority areas to support China's re-vegetation program in the Loess Plateau: Matching model complexity to data availability

The Chinese Central government's policy to re-vegetate large areas of the Loess Plateau is currently being rapidly implemented at the provincial, prefecture, county, township, and village levels of government. Managers at these five levels of government need access to information to assist them to plan the land use change prior to performing on-ground activities. To this end, the suitability of 38 predominately native species in the 113,000 km² Coarse Sandy Hilly Catchments (CSHC) has been mapped at a 100 m resolution. In this data-sparse region, this was achieved by using a five-variable spatial overlay approach as we were able to readily access the required environmental variables and rule-set defining the species’ requirements (or tolerances). As the rules did not consider optimal growth they were possibly ‘too inclusive’, so the spatial extent of areas suggested for re-planting was refined by defining ‘target areas’ for trees, shrubs and grasses based on precipitation, aspect, landform, and slope. In the land-use planning criteria developed here we suggest that hill-slopes and gullies with slopes greater than or equal to 15° (defined from a 100 m resolution DEM) be left for natural succession. Due to lateral flow of water, sediment and nutrients from these steep slope and gullies, further prioritising re-vegetation target areas to the zone adjacent to and down slope from these steep portions of the landscape reduces sediment entering the river network with a minimal decrease of regional stream flow. These two functions (mapping species suitability and locating where priority and target re-vegetation activities should be undertaken) are available at a 100 m resolution for the entire CSHC by accessing a bilingual decision support tool called ReVegIH (Re-Vegetation Impacts on Hydrology). Finally, an ecohydrological model was used to simulate changes in average annual stream flow originating from the CSHC based on implementing the ‘target’ and ‘priority’ area re-vegetation activities within the constraints of two land limits.     

Traders' preference for goat characteristics in selected markets of Pangasinan, Philippines

Preference for goat characteristics was determined from 42 traders in six markets in Pangasinan, an important trading center for goats in Luzon, the Philippines, and analyzed using a hedonic price model to determine whether these characteristics are important price determinants of goats. This information is important to goat raisers to respond to the needs of the local market, and thus to achieve a better price and higher income in goat raising. Meatiness, size, breed, sex and age (in descending order) were the dominant goat characteristics preferred by traders. Meatiness had the largest positive influence on price, with a price premium of US$6.24 (US$1.00 = PhP 53), whereas the age of the animal had the smallest influence at US$3.72. However, size and meatiness are manifestations of good breeds. Therefore, continued efforts to improve breeds in order to produce good quality goats are imperative to cater to market needs. Different characteristics implied different price premiums. Traders offered a higher price premium for better goat characteristics; thus, the improvement of these characteristics could result in higher returns for goat raisers.