A general mathematical framework for the analysis of spatiotemporal point processes

Spatial and stochastic models are often straightforward to simulate but difficult to analyze mathematically. Most of the mathematical methods available for nonlinear stochastic and spatial models are based on heuristic rather than mathematically justified assumptions, so that, e.g., the choice of the moment closure can be considered more of an art than a science. In this paper, we build on recent developments in specific branch of probability theory, Markov evolutions in the space of locally finite configurations, to develop a mathematically rigorous and practical framework that we expect to be widely applicable for theoretical ecology. In particular, we show how spatial moment equations of all orders can be systematically derived from the underlying individual-based assumptions. Further, as a new mathematical development, we go beyond mean-field theory by discussing how spatial moment equations can be perturbatively expanded around the mean-field model. While we have suggested such a perturbation expansion in our previous research, the present paper gives a rigorous mathematical justification. In addition to bringing mathematical rigor, the application of the mathematically well-established framework of Markov evolutions allows one to derive perturbation expansions in a transparent and systematic manner, which we hope will facilitate the application of the methods in theoretical ecology.     

A tethered bilayer sensor containing alamethicin channels and its detection of amiloride based inhibitors

Alamethicin, a small transmembrane peptide, inserts into a tethered bilayer membrane (tBLM) to form ion channels, which we have investigated using electrical impedance spectroscopy. The number of channels formed is dependent on the incubation time, concentration of the alamethicin and the application of DC voltage. The properties of the ion channels when formed in tethered bilayers are similar to those for such channels assembled into black lipid membranes (BLMs). Furthermore, amiloride and certain analogs can inhibit the channel pores, formed in the tBLMs. The potency and concentration of the inhibitors can be determined by measuring the change of impedance. Our work illustrates the possibility of using a synthetic tBLM for the study of small peptide voltage dependent ion channels. A potential application of such a device is as a screening tool in drug discovery processes.     

Navigating the multiple meanings of β diversity: a roadmap for the practicing ecologist

A recent increase in studies of β diversity has yielded a confusing array of concepts, measures and methods. Here, we provide a roadmap of the most widely used and ecologically relevant approaches for analysis through a series of mission statements. We distinguish two types of β diversity: directional turnover along a gradient vs. non-directional variation. Different measures emphasize different properties of ecological data. Such properties include the degree of emphasis on presence/absence vs. relative abundance information and the inclusion vs. exclusion of joint absences. Judicious use of multiple measures in concert can uncover the underlying nature of patterns in β diversity for a given dataset. A case study of Indonesian coral assemblages shows the utility of a multi-faceted approach. We advocate careful consideration of relevant questions, matched by appropriate analyses. The rigorous application of null models will also help to reveal potential processes driving observed patterns in β diversity.     

Characterization of the genetic diversity of <Emphasis Type="Italic">Mycobacterium tuberculosis</Emphasis> in São Paulo city,Brazil

Background

Tuberculosis is a major health problem in São Paulo, Brazil, which is the most populous and one of the most cosmopolitan cities in South America. To characterize the genetic diversity of Mycobacterium tuberculosis in the population of this city, the genotyping techniques of spoligotyping and MIRU were applied to 93 isolates collected in two consecutive years from 93 different tuberculosis patients residing in São Paulo city and attending the Clemente Ferreira Institute (the reference clinic for the treatment of tuberculosis).

Findings

Spoligotyping generated 53 different spoligotype patterns. Fifty-one isolates (54.8%) were grouped into 13 spoligotyping clusters. Seventy- two strains (77.4%) showed spoligotypes described in the international databases (SpolDB4, SITVIT), and 21 (22.6%) showed unidentified patterns. The most frequent spoligotype families were Latin American Mediterranean (LAM) (26 isolates), followed by the T family (24 isolates) and Haarlem (H) (11 isolates), which together accounted for 65.4% of all the isolates. These three families represent the major genotypes found in Africa, Central America, South America and Europe. Six Spoligo-International-types (designated SITs by the database) comprised 51.8% (37/72) of all the identified spoligotypes (SIT53, SIT50, SIT42, SIT60, SIT17 and SIT1). Other SITs found in this study indicated the great genetic diversity of M. tuberculosis, reflecting the remarkable ethnic diversity of São Paulo city inhabitants. The MIRU technique was more discriminatory and did not identify any genetic clusters with 100% similarity among the 93 isolates. The allelic analysis showed that MIRU loci 26, 40, 23 and 10 were the most discriminatory. When MIRU and spoligotyping techniques were combined, all isolates grouped in the 13 spoligotyping clusters were separated.

Conclusions

Our data indicated the genomic stability of over 50% of spoligotypes identified in São Paulo and the great genetic diversity of M. tuberculosis isolates in the remaining SITs, reflecting the large ethnic mix of the São Paulo city inhabitants. The results also indicated that in this city, M. tuberculosis isolates acquired drug resistance independently of genotype and that resistance was more dependent on the selective pressure of treatment failure and the environmental circumstances of patients.

     

Dispersal polymorphism and the speed of biological invasions

The speed at which biological range expansions occur has important consequences for the conservation management of species experiencing climate change and for invasion by exotic organisms. Rates of dispersal and population growth are known to affect the speed of invasion, but little is known about the effect of having a community of dispersal phenotypes on the rate of range expansion. We use reaction-diffusion equations to model the invasion of a species with two dispersal phenotypes into a previously unoccupied landscape. These phenotypes differ in both their dispersal rate and population growth rate. We find that the presence of both phenotypes can result in faster range expansions than if only a single phenotype were present in the landscape. For biologically realistic parameters, the invasion can occur up to twice as fast as a result of this polymorphism. This has implications for predicting the speed of biological invasions, suggesting that speeds cannot just be predicted from looking at a single phenotype and that the full community of phenotypes needs to be taken into consideration.     

Sphingosine inhibits the activity of rat liver CTP:phosphocholine cytidylyltransferase

We report CTP:phosphocholine cytidylyltransferase (CT) as another target enzyme of sphingosine actions in addition to the well-characterized protein kinase C. Effects of sphingosine and lysophingolipids were studied on the activity of purified cytidylyltransferase prepared by the method of Weinhold et al. (Weinhold, P. A., Rounsifer, M.E., and Feldman, D.A. (1986) J. Biol. Chem. 261, 5104-5110). The sphingolipids were tested as components of egg phosphatidylcholine (PC) vesicles, 25 mol% sphingosine inhibited the CT activity by about 50%. The inhibition of CT by sphingosine and lysosphingolipids was reversible. Sphingosine was found to be a reversible inhibitor of CT with respect to the activating lipids such as phosphatidylserine, phosphatidylinositol, phosphatidylglycerol, and fatty acid:phosphatidylcholine vesicles. Egg PC vesicles containing sphingosine, psychosine (galactosylsphingosine), glucopsychosine (glucosylsphingosine), and lysosphingomyelin (sphingosylphosphorylcholine) suppressed the activation by PC/oleic acid vesicles, whereas the parent sphingolipids did not. Egg PC vesicles containing oleylamine and hexadecyltrimethylamine inhibited CT activity, whereas egg PC-octylamine vesicles did not alter the enzyme activity. This indicates the importance of an amino group and long alkyl chain. LysoPC, a known detergent, did not inhibit the enzyme activity under the same assay conditions in which sphingosine inhibited. These results are the first report of a lipid inhibitor of purified CT.     

Seasonal changes in sodium transport and amiloride sensitivity in the isolated intestine of the earthworm, Lumbricus terrestris (L.)

Temporal changes in sodium flux rates and the electrical properties of two regions of the intestine appear to occur in a yearly cycle. In RIIIA, the anterior portion of the mid-intestine, the short-circuit current in January and April preparations is 60.2 and 10.2 microA cm-2, respectively and the net sodium fluxes are 1.50 and 1.24 mu Eq cm-2 hr-1, respectively. In RIIIB, the posterior portion of the mid-intestine, the short-circuit current in January and April preparations is 50.7 and 27.9 microA cm-2, respectively, while the net sodium fluxes are 1.78 and 0.59 mu Eq cm-2 hr-1, respectively. Sodium transport in RIIIB is inhibited by amiloride (10(-4)M) in January preparations but is refractory to amiloride (less than or equal to 10(-3)M) in April preparations.     

Preferential association of the insulin-like growth factors I and II with metabolically inactive and active carrier-bound complexes in serum.

Ion-exchange chromatography of serum on DEAE-Sephadex A-50 using a stepwise NaCl gradient showed that complexes enriched with insulin-like growth factors I and II (IGF-I and IGF-II) could be preferentially eluted. A fraction eluted with 0.075 M-NaCl preferentially contained immunoreactive IGF-I with peak levels appearing in fractions of Mr approx. 110,000. The IGF-I-binding protein complex itself had low bioactivity as measured in a non-suppressible insulin-like (NSILA) bioassay. On conversion to free IGF-I by gel-permeation chromatography on Sephadex G-75 in 1% formic acid, however, the IGF-I did express its intrinsic NSILA bioactivity. In contrast, an IGF-II-enriched complex was eluted from the DEAE-Sephadex with 0.15 M-NaCl. Practically all of the recovered NSILA of the original serum was present in this fraction, in the Mr range 70,000-300,000 with a peak of 150,000. Chromatography on Sephadex G-75 in 1% formic acid separated this high-Mr NSILA into low-Mr (less than 15000) IGF-II and high-Mr acid-stable NSILA-P. The high-Mr IGF-II complex bound to concanavalin A-Sepharose, suggesting that it was a glycoprotein. The results confirm previous reports that a large portion of the NSILA of whole serum can be accounted for by a biologically active acid-dissociable complex. These data show for the first time that this active complex consists of an IGF-II-preferring binding protein. In direct contrast, the IGF-I-preferring complex does not express NSILA bioactivity until the IGF-I is liberated through acidification. The presence of a metabolically active IGF-II complex in serum raises questions as to its possible biological role in the adult.