Primary lowland dipterocarp forest at Danum Valley, Sabah, Malaysia. Species composition and patterns in the understorey

The spatial distributions of species of tree 10 cm gbh were examined in two 4 ha plots and related to the local variation in topography and soil chemistry. The plots were similar in their species composition, particularly in terms of the densities of small trees, and they showed very similar edaphic characteristics. Size class distributions varied little within and between plots. Ordination of 0.25 ha subplots highlighted parallel gradients in the vegetation of both plots when the densities of trees 10 cm gbh were considered. Focusing on understorey trees in the 10-<50 cm gbh class at the 0.04 ha subplot scale showed a similar vegetation gradient in both plots closely associated with change from lower slope to ridge. No relationship with soil chemistry was found. On the ridges a special group of understorey species formed clumps and these species contributed importantly to the ordinations. Borneo has a regional history of occasionally severe droughts. It is suggested here that the observed patterns in the understorey are due to differential responses to low soil water supply, the ridges probably tending to dryness more than the lower slopes. Within the large and diverse family Euphorbiaceae, which dominates the understorey at Danum, there may be ecophysiological groupings of species. The long-term effects of disturbance interacting with local edaphic factors on forest structure and composition are discussed.     

NMR solution structure of a dsRNA binding domain from Drosophila staufen protein reveals homology to the N-terminal domain of ribosomal protein S5.

The double-stranded RNA binding domain (dsRBD) is an approximately 65 amino acid motif that is found in a variety of proteins that interact with double-stranded (ds) RNA, such as Escherichia coli RNase III and the dsRNA-dependent kinase, PKR. Drosophila staufen protein contains five copies of this motif, and the third of these binds dsRNA in vitro. Using multinuclear/multidimensional NMR methods, we have determined that staufen dsRBD3 forms a compact protein domain with an alpha-beta-beta-beta-alpha structure in which the two alpha-helices lie on one face of a three-stranded anti-parallel beta-sheet. This structure is very similar to that of the N-terminal domain of a prokaryotic ribosomal protein S5. Furthermore, the consensus derived from all known S5p family sequences shares several conserved residues with the dsRBD consensus sequence, indicating that the two domains share a common evolutionary origin. Using in vitro mutagenesis, we have identified several surface residues which are important for the RNA binding of the dsRBD, and these all lie on the same side of the domain. Two residues that are essential for RNA binding, F32 and K50, are also conserved in the S5 protein family, suggesting that the two domains interact with RNA in a similar way.     

Skeletal muscle mass and the reduction of VO2 max in trained older subjects

Proctor, David N., and Michael J. Joyner. Skeletalmuscle mass and the reduction ofO_{2 max} in trainedolder subjects. J. Appl. Physiol.82(5): 1411-1415, 1997.The role of skeletal muscle mass in theage-associated decline in maximalO₂ uptake (O_{2 max}) is poorlydefined because of confounding changes in muscle oxidative capacity andin body fat and the difficulty of quantifying active muscle mass duringexercise. We attempted to clarify these issues byexamining the relationship between several indexes of muscle mass, asestimated by using dual-energy X-ray absorptiometry and treadmillO_{2 max} in 32 chronically endurance-trained subjects from four groups(n = 8/group): young men(20-30 yr), older men (56-72 yr), young women(19-31 yr), and older women (51-72 yr).O_{2 max} per kilogrambody mass was 26 and 22% lower in the older men (45.9 vs. 62.0 ml · kg¹ · min¹)and older women (40.0 vs. 51.5 ml · kg¹ · min¹).These age differences were reduced to 14 and 13%, respectively, whenO_{2 max} was expressedper kilogram of appendicular muscle. When appropriately adjusted forage and gender differences in appendicular muscle mass by analysis ofcovariance, whole body O_{2 max} was 0.50 ± 0.09 l/min less (P < 0.001) in theolder subjects. This effect was similar in both genders.These findings suggest that the reducedO_{2 max} seen in highlytrained older men and women relative to their younger counterparts isdue, in part, to a reduced aerobic capacity per kilogram of activemuscle independent of age-associated changes in body composition, i.e.,replacement of muscle tissue by fat. Because skeletal muscleadaptations to endurance training can be well maintained in oldersubjects, the reduced aerobic capacity per kilogram of muscle likelyresults from age-associated reductions in maximalO₂ delivery (cardiac outputand/or muscle blood flow).

     

Comparative trial of treatment with Prioderm lotion and Kwellada shampoo in children with head lice.

The safety and efficacy of treatment with a new pediculicide lotion, Prioderm (0.5% malathion in isopropanol), were compared with those of treatment with Kwellada (1% lindane) shampoo in a randomized trial of children with head lice. The children''s scalps were examined for live lice immediately, 7 days and 4 to 6 weeks following treatment. To determine the in-vitro ovicidal effect of treatment, samples of hair with nits were removed before and immediately following treatment; the subsequent rates of hatching were compared. No live lice were present immediately following either treatment. At 7 days after treatment 2 of the 29 children treated with Prioderm lotion and 4 of the 33 children treated with Kwellada shampoo were infested with live lice, whereas at 4 to 6 weeks after treatment 5 and 3 children respectively were infested. The initial effectiveness of treatment was 93% in the children treated with Prioderm lotion and 88% in those treated with Kwellada shampoo; however, a large difference in efficacy could have been missed owing to the small number of children in the study. Both preparations demonstrated in-vitro ovicidal activity, but neither totally abolished post-treatment hatching. No side effects were reported from either preparation. Because ovicidal activity was incomplete two treatments with the same pediculicides should be given about 7 days apart.     

Interaction of two mechanisms regulating alkali cations in HeLa cells.

The alkali cation content of HeLa cells is independent of culture density and of whether the cells are grown in suspension or attached to the culture vessel. With a cell doubling time of 28 hours, the cell K content turns over approximately once per hour. Following partial blockade of the alkali-cation transport system with ouabain, two distinct but interrelated mechanisms operate in the cellular response: (a) an increase in intracellular Na stimulates the pump so that the short-term alteration in electrolyte compostition is less than would be expected from the fraction of pump sites inhibited, and (b) there is a cycloheximide-sensitive recovery in transport capacity reflecting a restoration of functional transport sites to their normal density on the cell surface. Experimental manipulations that mimic the effect of ouabain lead to a stimulation of transport, but they do not result in an increase in the number of ouabain-binding sites on the surface. The data are consistent with a four-to-six hour turn-over of transport sites at the surface, but there is no evidence for a speicific induction of the transport system within this short-term recovery period.     

Recovery rates of chlorophyll-fluorescence parameters in desiccation-tolerant plants: fitted logistic curves as a versatile and robust source of comparative data

Desiccation-tolerant plants vary greatly in the rate of recovery of chlorophyll-fluorescence parameters on re-wetting. This paper seeks general curves that will adequately describe the course of recovery, and quantify the variations in rate within and between species. Recovery of F _v /F _m is closely fitted in many species by a logistic curve, starting from zero, on a logarithmic time-scale (seconds to days). Such curves have three parameters, an asymptote at maximum F _v /F _m, a half-recovery time (T _0.5), and a slope constant (S). If F _v /F _m in dry material differs substantially from zero, four-parameter logistic curves can give a better fit. In either case, T _0.5 and S show wide ecologically-significant variation. Some species show anomalously high values of F _v /F _m in the early minutes of recovery, alongside low absolute values of F _m; these invite further investigation. Logistic curves give good fits to the recovery in light of Φ _PSII, q _P, and photosynthetic CO₂ fixation. The results provide the means to quantify ‘high-inertia’ versus ‘low-inertia’ strategies of desiccation tolerance, and to explore the factors influencing recovery time and rate, and the reasons for some discrepancies from the common course of recovery. There is substantial overlap in all parameters between the bryophytes and pteridophytes studied.     

Integrated evaluation of targeted and non-targeted therapies in a network meta-analysis

Individualized therapies for patients with biomarkers are moving more and more into the focus of research interest when developing new treatments. Hereby, the term individualized (or targeted) therapy denotes a treatment specifically developed for biomarker-positive patients. A network meta-analysis model for a binary endpoint combining the evidence for a targeted therapy from individual patient data with the evidence for a non-targeted therapy from aggregate data is presented and investigated. The biomarker status of the patients is either available at patient-level in individual patient data or at study-level in aggregate data. Both types of biomarker information have to be included. The evidence synthesis model follows a Bayesian approach and applies a meta-regression to the studies with aggregate data. In a simulation study, we address three treatment arms, one of them investigating a targeted therapy. The bias and the root-mean-square error of the treatment effect estimate for the subgroup of biomarker-positive patients based on studies with aggregate data are investigated. Thereby, the meta-regression approach is compared to approaches applying alternative solutions. The regression approach has a surprisingly small bias even in the presence of few studies. By contrast, the root-mean-square error is relatively greater. An illustrative example is provided demonstrating implementation of the presented network meta-analysis model in a clinical setting.     

Highly covarying residues have a functional role in antibody constant domains

The ability to generate and design antibodies recognizing specific targets has revolutionized the pharmaceutical industry and medical imaging. Engineering antibody therapeutics in some cases requires modifying their constant domains to enable new and altered interactions. Engineering novel specificities into antibody constant domains has proved challenging due to the complexity of inter‐domain interactions. Covarying networks of residues that tend to cluster on the protein surface and near binding sites have been identified in some proteins. However, the underlying role these networks play in the protein resulting in their conservation remains unclear in most cases. Resolving their role is crucial, because residues in these networks are not viable design targets if their role is to maintain the fold of the protein. Conversely, these networks of residues are ideal candidates for manipulating specificity if they are primarily involved in binding, such as the myriad interdomain interactions maintained within antibodies. Here, we identify networks of evolutionarily‐related residues in C‐class antibody domains by evaluating covariation, a measure of propensity with which residue pairs vary dependently during evolution. We computationally test whether mutation of residues in these networks affects stability of the folded antibody domain, determining their viability as design candidates. We find that members of covarying networks cluster at domain‐domain interfaces, and that mutations to these residues are diverse and frequent during evolution, precluding their importance to domain stability. These results indicate that networks of covarying residues exist in antibody domains for functional reasons unrelated to thermodynamic stability, making them ideal targets for antibody design. Proteins 2013. © 2012 Wiley Periodicals, Inc.