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The relationship between species diversity and sampled area is fundamental to ecology. Traditionally, theories of the species–area relationship have been dominated by random-placement models. Such models were used to formulate the canonical theory of species–area curves and species abundances. In this paper, however, armed with a detailed data set from a moist tropical forest, we investigate the validity of random placement and suggest improved models based upon spatial aggregation. By accounting for intraspecific, small-scale aggregation, we develop a cluster model which reproduces empirical species–area curves with high fidelity. We find that inter-specific aggregation patterns, on the other hand, do not affect the species–area curves significantly. We demonstrate that the tendency for a tree species to aggregate, as well as its average clump size, is not significantly correlated with the species' abundance. In addition, we investigate hierarchical clumping and the extent to which aggregation is driven by topography. We conclude that small-scale phenomena such as dispersal and gap recruitment determine individual tree placement more than adaptation to larger-scale topography.

A time-resolved photoacoustic technique has been applied to the study of dissolved and dispersed absorbers in aqueous systems. The temporal pressure profiles generated from colloidal graphite and glucose solutions were measured, and it was found that the amplitude of the photoacoustic signal of both the glucose and the colloidal graphite solutions increase linearly with concentration and that acoustic signal time delay yields the acoustic velocity. The logarithm of the photoacoustic signal amplitude changes linearly with the time delay, with a slope that is proportional to the product of the acoustic velocity and the optical absorption that can thus be determined.

A considerable volume of research has now been completed on the application of matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) to the analysis of bacteria; however, to date no definitive studies have been made using this technique on fungi. Preliminary studies on the application of the MALDI-MS methodology, previously developed for the analysis of bacteria, to the analysis of intact fungal spores are described here. MALDI-MS and electrospray mass spectrometry enable the high molecular weight analysis of proteins, glycoproteins, oligosaccharides and oligonucleotides. Using MALDI-MS with bacteria has demonstrated the ability to produce ‘fingerprints’ of the intact cells with the ions observed being associated with the proteinaceous components of the cell wall. This paper reports the adaptation of this technique to the direct analysis of fungal cells. The high percentage of carbohydrate in the fungal cell wall indicates that the ions observed in the mass spectrometric experiments may be of carbohydrate origin. Penicillium spp., Scytalidium dimidiatum and Trichophyton rubrum have been studied in this preliminary investigation and all show individually distinctive spectra which would appear to provide a profile of the cellular material with discrete peaks being observed over the mass range 2 to 13 kDa. The spectra obtained are reproducible within the method used but, as shown in our previous studies on bacteria, washing may selectively release components from the fungal cell wall. Copyright © 2000 John Wiley & Sons, Ltd.

The ability to rapidly identify the taxonomic class of the wide variety of microorganisms involved in human and animal disease is becoming increasingly important, especially with the increasing development of resistance to the antibiotics which form the main defence against them. A number of groups have recognised the utility of matrix-assisted laser desorption/ionisation time-of-flight mass spectrometry MALDI-TOF in the analysis of these microorganisms. However, no consistent methodology has been developed which is in general use. In particular the use of different solvent extraction systems and mass spectrometric matrices can have significant effects on the quality of the data obtained. We have now studied a number of the commonly used matrices and a range of solvent systems of widely varying polarity in an attempt to devise an optimum analytical strategy for the rapid characterisation of these organisms by MALDI-TOFMS. The E. coli ATCC 9637 organisms were initially washed to remove growth medium contaminants, followed by extraction with one of a range of solvents prior to admixing with a number of different single matrices or binary and ternary combinations of these matrices. The results obtained indicate that a binary combination of 2-(4-hydroxyphenylazo)benzoic acid and 2-mercaptobenzothiazole (1:1) as matrix provides the best data after the proteinaceous material from the organism cell surface was extracted with 17% formic acid, 33% isopropyl alcohol and 50% water, (solvent 2 in this work). Copyright © 1999 John Wiley & Sons, Ltd.

Dynamics of the Pasoh forest in Peninsular Malaysia were assessed by drawing a comparison with a forest in Panama, Central America, whose dynamics have been thoroughly described. Census plots of 50 ha were established at both sites using standard methods. Tree mortality at Pasoh over an eight–year interval was 1.46 yr−1for all stems greater than or equal to 10 mm diameter at breast height (dbh), and 1.48 yr−1for stems greater than or equal to 100 mm dbh. Comparable figures at the Barro Colorado Island site in Panama (BCI) were 2.55 and 2.03. Growth and recruitment rates were likewise considerably higher at BCI than at Pasoh. For example, in all trees 500 to 700 mm in dbh, mean BCI growth over the period 1985 to 1995 was 6 mm yr−1, whereas mean Pasoh growth was about 3.5 mm yr−1. Examining growth and mortality rates for individual species showed that the difference between the forests can be attributed to a few light–demanding pioneer species at BCI, which have very high growth and mortality; Pasoh is essentially lacking this guild. The bulk of the species in the two forests are shade–tolerant and have very similar mortality, growth and recruitment. The Pasoh forest is more stable than BCI's in another way as well: few of its tree populations changed much over the eight–year census interval. In contrast, at BCI, over 10 of the species had populations increasing or decreasing at a rate of > 0.05 yr−1(compared to just 2 of the species at Pasoh). The faster species turnover at BCI can probably be attributed to severe droughts that have plagued the forest periodically over the past 30 years; Pasoh has not suffered such extreme events recently. The dearth of pioneer species at Pasoh is associated with low–nutrient soil and slow litter breakdown, but the exact mechanisms behind this association remain poorly understood.

In the past three decades tropical rainforests of the Far East have been managed using systems based almost exclusively on cutting cycles. Much recent research concerning this management approach has focused on reducing logging impacts on the residual forest. Evidence from historical records and research suggests that in certain circumstances shelterwood systems and their variants that provide both structural and age-class diversity can be appropriate. We give examples of such systems in India, Sri Lanka, and Malaysia.

A variety of gram-positive and gram-negative intact bacterial cells have been analysed by matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) and shown to provide fingerprint mass spectra with discrete peaks being observed over the mass range from 3 to 40 kDa. The spectra show both more peaks and peaks at a higher mass/charge ratio than have hitherto been reported for these micro-organisms and would appear to provide a profile of cellular proteinaceous material. The spectra are shown to be reproducible over variable time periods of up to three months and factors affecting reproducibility are discussed. The procedure, which requires minimal sample preparation, yields results in 30–40 minutes and allows visual identification of species- and strain-specific biomarkers for the characterization of the organisms. The importance of accurately defining sample preparation methodologies is central to the ability of the technique to generate reliable and reproducible data. © 1998 John Wiley & Sons, Ltd.

Electrospray mass spectrometry has been used to measure the masses of the species present in solutions of three serine proteases (α-chymotrypsin, subtilisin Carlsberg and subtilisin BPN′) before, during and after completion of the hydrolytic reaction with cinnamoyl imidazole and indole acryloyl imidazole. The masses measured during the reaction demonstrated that covalent O-acyl enzyme intermediates had been formed.

The case is made that ecological characteristics can provide valuable evidence for species delimitation in complex floras such as those of tropical rain forests. Differences between sympatric populations of morphologically similar entities in such aspects as edaphic range, reproductive phenology, pollination biology, combined with evidence for outbreeding, and for interspecific hybridization in nature assist in evaluating whether such entities behave as biological species. Current evidence on the biological nature of rain forest tree species is discussed.

The influence of the operating parameters in capillary zone electrophoresis (CZE) on the separation of a human alpha-interferon has been investigated. The separation was characterised by the electrophoretic mobility of the first and last observed peaks, and the number of peaks on the electropherogram, whether visible as shoulders or adequately resolved. No peaks could be observed at lower pH values (below pH 4.7) due to capillary wall adsorption. The optimum pH (pH 6.1) for the CZE analysis of human alpha-interferon was close to the isoelectric points of the sample components (pI 5.5-6.5). The investigation of the effect of the borate, phosphate and Trizma buffer concentration on the separation showed that increasing buffer concentration generally decreases the electrophoretic mobility with increased resolution, up to a certain optimum. Longer capillary lengths and slightly higher voltages also increased the resolution. The maximum number of peaks (17) was observed by using 200 mM phosphate buffer (pH 6.1) with 50 cm effective length capillary applying 12 kV voltage.

The genus Pakaraimaeahas been restudied on the basis of new field collections. Evidence from data on habit, reproduction, and seed characters further supports its placement in the Dipterocarpaceae.

Nitric oxide (NO) released by vascular endothelial cells accounts for the relaxation of strips of vascular tissue1and for the inhibition of platelet aggregation2and platelet adhesion3attributed to endothelium-derived relaxing factor4. We now demonstrate that NO can be synthesized from L-arginine by porcine aortic endothelial cells in culture. Nitric oxide was detected by bioassay5, chemiluminescence1or by mass spectrometry. Release of NO from the endothelial cells induced by bradykinin and the calcium ionophore A23187 was reversibly enhanced by infusions of L-arginine and L-citrulline, but not D-arginine or other close structural analogues. Mass spectrometry studies using 15N-labelled L-arginine indicated that this enhancement was due to the formation of NO from the terminal guanidino nitrogen atom(s) of L-arginine. The strict substrate specificity of this reaction suggests that L-arginine is the precursor for NO synthesis in vascular endothelial cells.

IN the tropical rain forest, many tree species grow close together, and they are apparently equivalent in their edaphic requirements and spatially interchangeable. Most species occur at low density although they may be geographically widespread. No other plant community contains as many species of a single life form as do certain mixed dipterocarp forests of the aseasonal wet lowlands of Malesia1–3. Such a population structure and level of diversity makes it hard to see how speciation has occurred. Spatial isolation of individuals and the abundant, normally hermaphrodite flowers simultaneously available for fertilisation in the canopy of the dipterocarp emergents suggest the possibility of self-fertilisation, but many of the understorey species are dioecious. As part of a comparative study of the reproductive biology of rain forest tree species, intra-specific genetic variation of isozymes has been demonstrated for the first time in an emergent and an understorey species of rain forest trees. Polymorphism is common in both species and there is evidence for short-range spatial heterogeneity in gene frequency and also in leaf morphology.

Neuroepithelial stem cells (NSC) from different anatomical regions of the embryonic neural tube’s rostrocaudal axis can differentiate into diverse central nervous system tissues, but the transcriptional regulatory networks governing these processes are incompletely understood. Here, we measure region-specific NSC gene expression along the rostrocaudal axis in a human pluripotent stem cell model of early central nervous system development over a 72-h time course, spanning the hindbrain to cervical spinal cord. We introduce Escarole, a probabilistic clustering algorithm for non-stationary time series, and combine it with prior-based regulatory network inference to identify genes that are regulated dynamically and predict their upstream regulators. We identify known regulators of patterning and neural development, including the HOX genes, and predict a direct regulatory connection between the transcription factor POU3F2 and target gene STMN2. We demonstrate that POU3F2is required for expression of STMN2, suggesting that this regulatory connection is important for region specificity of NSCs.