Synthesis and biological evaluation of disubstituted N6-cyclopentyladenine analogues: the search for a neutral antagonist with high affinity for the adenosine A1 receptor

Novel 3,8- and 8,9-disubstituted N(6)-cyclopentyladenine derivatives were synthesised in moderate overall yield from 6-chloropurine. The derivatives were made in an attempt to find a new neutral antagonist with high affinity for adenosine A(1) receptors. N(6)-Cyclopentyl-9-methyladenine (N-0840) was used as a lead compound. Binding affinities of the new analogues were determined for human adenosine A(1) and A(3) receptors. Their intrinsic activity was assessed in [35S]GTPgammaS binding experiments. Elongation of the 9-methyl of N-0840 to a 9-propyl substituent was very well tolerated. A 9-benzyl group, on the other hand, caused a decrease in adenosine A(1) receptor affinity. Next, the 8-position was examined in detail, and affinity was increased with appropriate substitution. Most derivatives were A(1)-selective and 20 of the new compounds (6-9, 15-21, 23-26, 28, 31, 33, 35, and 36) had higher adenosine A(1) receptor affinity than the reference substance, N-0840. Compound 31 (N(6)-cyclopentyl-8-(N-methylisopropylamino)-9-methyladenine, LUF 5608) had the highest adenosine A(1) receptor affinity, 7.7 nM. In the [35S]GTPgammaS binding experiments, derivatives 5, 14, 22, 23, 25, 26, 33 and 34 did not significantly change basal [35S]GTPgammaS binding, thus behaving as neutral antagonists. Moreover, four of these compounds (23, 25, 26, and 33) displayed a 4- to 10-fold increased adenosine A(1) receptor affinity (75-206 nM) compared to N-0840 (852 nM). In summary, we synthesised a range of N-0840 analogues with higher affinity for adenosine A(1) receptors. In addition, four new derivatives, LUF 5666 (23), LUF 5668 (25), LUF 5669 (26) and LUF 5674 (33), behaved as neutral antagonists when tested in [35S]GTPgammaS binding studies. Thus, these compounds have improved characteristics as neutral adenosine A(1) receptor antagonists.     

Comparing Allee effect-based and dispersal-based neutral models for species abundance distribution patterns

Dispersal is important for biodiversity maintenance in both neutral and niche theories. However, little is known about the potential role of Allee effect at the community level. In the present study, we developed neutral models for quantifying the separate and joint influences of the Allee effect and dispersal process, respectively, on species abundance distribution (SAD) patterns. Tree census data from Barro Colorado Island (BCI), Panama were used as the case to compare different neutral SAD models. Results showed that Allee effects were not detected in the BCI tree SAD curve. By contrast, the neutral models with the incorporation of dispersal process (including both immigration and emigration) can remarkably improve the fitting power of neutral models on the BCI tree SAD curve. Finally, even though the influence is not detectable, the Allee effect-based SAD models still might be alternative SAD models for model comparison and null hypothesis testing.     

Neutral theory and the species abundance distribution: recent developments and prospects for unifying niche and neutral perspectives

Published in 2001, The Unified Neutral Theory of Biodiversity and Biogeography (UNTB) emphasizes the importance of stochastic processes in ecological community structure, and has challenged the traditional niche‐based view of ecology. While neutral models have since been applied to a broad range of ecological and macroecological phenomena, the majority of research relating to neutral theory has focused exclusively on the species abundance distribution (SAD). Here, we synthesize the large body of work on neutral theory in the context of the species abundance distribution, with a particular focus on integrating ideas from neutral theory with traditional niche theory. First, we summarize the basic tenets of neutral theory; both in general and in the context of SADs. Second, we explore the issues associated with neutral theory and the SAD, such as complications with fitting and model comparison, the underlying assumptions of neutral models, and the difficultly of linking pattern to process. Third, we highlight the advances in understanding of SADs that have resulted from neutral theory and models. Finally, we focus consideration on recent developments aimed at unifying neutral‐ and niche‐based approaches to ecology, with a particular emphasis on what this means for SAD theory, embracing, for instance, ideas of emergent neutrality and stochastic niche theory. We put forward the argument that the prospect of the unification of niche and neutral perspectives represents one of the most promising future avenues of neutral theory research.     

An improved neutral landscape model for recreating real landscapes and generating landscape series for spatial ecological simulations

Many studies have assessed the effect of landscape patterns on spatial ecological processes by simulating these processes in computer‐generated landscapes with varying composition and configuration. To generate such landscapes, various neutral landscape models have been developed. However, the limited set of landscape‐level pattern variables included in these models is often inadequate to generate landscapes that reflect real landscapes. In order to achieve more flexibility and variability in the generated landscapes patterns, a more complete set of class‐ and patch‐level pattern variables should be implemented in these models. These enhancements have been implemented in Landscape Generator (LG), which is a software that uses optimization algorithms to generate landscapes that match user‐defined target values. Developed for participatory spatial planning at small scale, we enhanced the usability of LG and demonstrated how it can be used for larger scale ecological studies. First, we used LG to recreate landscape patterns from a real landscape (i.e., a mountainous region in Switzerland). Second, we generated landscape series with incrementally changing pattern variables, which could be used in ecological simulation studies. We found that LG was able to recreate landscape patterns that approximate those of real landscapes. Furthermore, we successfully generated landscape series that would not have been possible with traditional neutral landscape models. LG is a promising novel approach for generating neutral landscapes and enables testing of new hypotheses regarding the influence of landscape patterns on ecological processes. LG is freely available online.     

On the divergence of members of a transposable element family

Statistical properties of the amount of divergence of members of a transposable element family are studied. The analysis is based on the model proposed by Langley et al. [5], describing the evolution of a family of selectively neutral transposable elements in a finite haploid population of size 2N. By considering the time back to the most recent common ancestor of two copies, both the probability of identity and the moments of the number of sites that differ between two sampled copies are obtained. Our analytic results are consistent with the numerical results of Ohta [8] for a similar model. The effects of gene conversion are also examined. In agreement with Slatkin [9], we find that gene conversion has a minimal effect on the probability of identity providing that the rate of deletion is sufficiently large.     

Applying ecological models to communities of genetic elements: the case of neutral theory

A promising recent development in molecular biology involves viewing the genome as a mini‐ecosystem, where genetic elements are compared to organisms and the surrounding cellular and genomic structures are regarded as the local environment. Here, we critically evaluate the prospects of ecological neutral theory (ENT), a popular model in ecology, as it applies at the genomic level. This assessment requires an overview of the controversy surrounding neutral models in community ecology. In particular, we discuss the limitations of using ENT both as an explanation of community dynamics and as a null hypothesis. We then analyse a case study in which ENT has been applied to genomic data. Our central finding is that genetic elements do not conform to the requirements of ENT once its assumptions and limitations are made explicit. We further compare this genome‐level application of ENT to two other, more familiar approaches in genomics that rely on neutral mechanisms: Kimura's molecular neutral theory and Lynch's mutational‐hazard model. Interestingly, this comparison reveals that there are two distinct concepts of neutrality associated with these models, which we dub ‘fitness neutrality’ and ‘competitive neutrality’. This distinction helps to clarify the various roles for neutral models in genomics, for example in explaining the evolution of genome size.     

Relaxing the zero-sum assumption in neutral biodiversity theory

The zero-sum assumption is one of the ingredients of the standard neutral model of biodiversity by Hubbell. It states that the community is saturated all the time, which in this model means that the total number of individuals in the community is constant over time, and therefore introduces a coupling between species abundances. It was shown recently that a neutral model with independent species, and thus without any coupling between species abundances, has the same sampling formula (given a fixed number of individuals in the sample) as the standard model [Etienne, R.S., Alonso, D., McKane, A.J., 2007. The zero-sum assumption in neutral biodiversity theory. J. Theor. Biol. 248, 522-536]. The equilibria of both models are therefore equivalent from a practical point of view. Here we show that this equivalence can be extended to a class of neutral models with density-dependence on the community-level. This result can be interpreted as robustness of the model, i.e. insensitivity of the model to the precise interaction of the species in a neutral community. It can also be interpreted as a lack of resolution, as different mechanisms of interactions between neutral species cannot be distinguished using only a single snapshot of species abundance data.     

No BLUE among phylogenetic estimators

 Multivariate analysis is a branch of statistics that successfully exploits the powerful tools of linear algebra to obtain a fairly comprehensive theory of estimation. The purpose of this paper is to explore to what extent a linear theory of estimation can be developed in the context of coalescent models used in the analysis of DNA polymorphism. We consider a large class of coalescent models, of which the neutral infinite sites model is one example. In the process, we discover several limitations of linear estimators that are quite distinct from those in the classical theory. In particular, we prove that there does not exist a uniformly BLUE (best linear unbiased estimator) for the scaled mutation parameter, under the assumptions of the neutral model of evolution. In fact, we show that no linear estimator performs uniformly better than the Watterson (1975) method based on the total number of segregating sites. For certain coalescent models, the segregating-sites estimator is actually optimal. The general conclusion is the following. If genealogical information is useful for estimating the rate of evolution, then there is no optimal linear method. If there is an optimal linear method, then no information other than the total number of segregating sites is needed. Received: 29 July 1998 / Revised version: 9 October 1998     

On the utility of linkage disequilibrium as a statistic for identifying targets of positive selection in nonequilibrium populations

A critically important challenge in empirical population genetics is distinguishing neutral nonequilibrium processes from selective forces that produce similar patterns of variation. We here examine the extent to which linkage disequilibrium (i.e., nonrandom associations between markers) improves this discrimination. We show that patterns of linkage disequilibrium recently proposed to be unique to hitchhiking models are replicated under nonequilibrium neutral models. We also demonstrate that jointly considering spatial patterns of association among variants alongside the site-frequency spectrum is nonetheless of value. Through a comparison of models of equilibrium neutrality, nonequilibrium neutrality, equilibrium hitchhiking, nonequilibrium hitchhiking, and recurrent hitchhiking, we evaluate a linkage disequilibrium (LD) statistic (omega(max)) that appears to have power to identify regions recently shaped by positive selection. Most notably, for demographic parameters relevant to non-African populations of Drosophila melanogaster, we demonstrate that selected loci are distinguishable from neutral loci using this statistic.     

Are potential natural vegetation maps a meaningful alternative to neutral landscape models?

Abstract. In this paper, we present a short overview of neutral landscape models traditionally adopted in the landscape ecological literature to differentiate landscape patterns that are the result of simple random processes from patterns that are generated from more complex ecological processes. Then, we present another family of models based on Tuxen’ s definition of potential natural vegetation that play an important role, especially in Europe, for landscape planning and management. While neutral landscape models by their very nature do not take into account vegetation dynamics, nor abiotic constraints to vegetation distribution, the concept of potential natural vegetation includes the effects of vegetation dynamics in a spatially explicit manner. Therefore, we believe that distribution maps of potential natural vegetation may represent an ecological meaningful alternative to neutral landscape models for evaluating the effects of landscape structure on ecological processes.     

Computational studies of Cu(II)[peptide] binding motifs: Cu[HGGG] and Cu[HG] as models for Cu(II) binding to the prion protein octarepeat region

The binding of Cu(II) to the prion protein is investigated by computations at the B3LYP level of theory on models of the octarepeat domain of the prion protein. The models incorporate the functionality of the glycine (G) and histidine (H) residues which occur in the octarepeat domain, PHGGGWGQ. The copper complexes are designated Cu[HG] and Cu[HGGG]. Coordination to the metal via the imidazole ring of the histidine, the amide carbonyl groups, and the backbone nitrogen atom of the amide groups were examined, as well as several protonation/deprotonation states of each structure. EPR and CD titration experiments suggest that the octarepeat segments of the unstructured N-terminal domain of prion protein can bind Cu(II) in a 1:1 Cu-to-octarepeat ratio. The results identify the extent to which the Cu(II) facilitates peptide backbone deprotonation, and the propensity of binding in the forward (toward the C-terminus) direction from the anchoring histidine residue. A plausible mechanism is suggested for changing from amide O-atom to deprotonated amide N-atom coordination, and for assembly of the observed species in solutions of Cu[PrP] and truncated models of it. A structure is proposed which has the N2O2 coordination pattern for the minor component observed experimentally by EPR spectroscopy for the Cu[HGGG] model. The most stable neutral Cu[HGGG] structure found, with coordination environment N3O1, corresponds to that observed for Cu[HGGGW] and Cu[HGGG] both in the solid state and as the major component in solution at neutral pH.     

Structure-activity relationship of the neurotransmitter alpha-bag cell peptide on Aplysia LUQ neurons: implications regarding its inactivation in the extracellular space.

Alpha-bag cell peptide [alpha-BCP (Ala-Pro-Arg-Leu-Arg-Phe-Tyr-Ser-Leu)] is a neurotransmitter that mediates bag cell-induced inhibition of left-upper-quadrant (LUQ) neurons L2, L3, L4, and L6 in the abdominal ganglion of Aplysia. Our recent biochemical studies have shown that alpha-BCP[1-9] is cleaved into alpha-BCP[1-2], [3-9], [1-5], [6-9], and [7-9] by a combination of three distinct peptidase activities located within the extracellular spaces of the CNS: A diaminopeptidase-IV (DAP-IV)-like enzyme cleaves alpha-BCP[1-9] at the 2-3 peptide bond; a neutral metalloendopeptidase (NEP)-like enzyme cleaves either alpha-BCP[1-9] or alpha-BCP[3-9] at the 5-6 bond; an aminopeptidase M-II (APM-II)-like enzyme cleaves alpha-BCP[6-9] at the 6-7 bond, but cleaves neither alpha-BCP[1-9], nor the other ganglionic peptidase products. To further understand the manner in which alpha-BCP is inactivated after release, that is loses its electrophysiological activity, we studied its structure-activity relationship by recording intracellularly from LUQ neurons in isolated abdominal ganglia that were arterially perfused with peptides dissolved in artificial sea water. The effects of alpha-BCP[1-9] and 15 of its fragments ([1-8], [1-7], [1-6], [1-5], [2-9], [3-9], [3-8], [6-9], [7-9], [8-9], [6-7], [6-8], [1-2], Phe, Tyr) indicated that the sequence Phe6-Tyr7 was both necessary and sufficient to produce LUQ inhibitory activity.(ABSTRACT TRUNCATED AT 250 WORDS)     

Deriving the probabilities of water loss and ammonia loss for amino acids from tandem mass spectra

In protein identification through tandem mass spectrometry, it is critical to accurately predict the theoretical spectrum for a peptide sequence. The widely used prediction models, such as SEQUEST and MASCOT, ignore the intensity of the ions with important neutral losses, including water loss and ammonia loss. However, ignoring these neutral losses results in a significant deviation between the predicted theoretical spectrum and its experimental counterpart. Here, based on the "one peak, multiple explanations" observation, we proposed an expectation-maximization (EM) method to automatically learn the probabilities of water loss and ammonia loss for each amino acid. Then we employed these probabilities to design an improved statistical model for theoretical spectrum prediction. We implemented these methods and tested them on practical data. On a training set containing 1803 spectra, the experimental results show a good agreement with some known knowledge about neutral losses, such as the tendency of water loss from Asp, Glu, Ser, and Thr. Furthermore, on a testing set containing 941 spectra, the improved similarity between the experimental and predicted spectra demonstrates that this method can generate more reasonable predictions relative to the model that ignores neutral losses. As an application of the derived probabilities, we implemented a database searching method adopting the improved theoretical spectrum model with neutral loss ions estimated. Experimental results on Keller's data set demonstrate that this method can identify peptides more accurately than SEQUEST. In another application to validate SEQUEST's results, the reported peptide-spectrum pairs are reranked with respect to the similarity between experimental and predicted spectra. Experimental results on both LTQ and QSTAR data sets suggest that this reranking strategy can effectively distinguish the false negative predictions reported by SEQUEST.     

Identification of unprecedented purine-containing compounds, the zingerines, from ginger rhizomes (Zingiber officinale Roscoe) using a phase-trafficking approach

Three unprecedented purine-containing compounds, named [6]-, [8]-, and [10]-zingerines as they are 5-(6-amino-9H-purin-9-yl) analogs of [6]-, [8]-, and [10]-gingerols, respectively, were isolated from a methanolic extract of ginger rhizomes using a phase trafficking-based method that utilizes solid phase reagents allowing for fast and selective simultaneous separation of basic, acidic, and neutral components of natural products extracts.     

Chelation of ThIV, EuIII and NdIII by dianionic N,N'-bis(pyridoxylideneiminato)ethylene, (Pyr2en)2-. On the search of feasible modelings for heavy metals damage inhibition in living beings

The neutral Schiff base N,N'-bis(pyridoxylideneiminato)ethylene {H(2)pyr(2)en} reacts with Th(NO(3))4.4H2O, NdCl3.6H2O and EuCl3.6H2O to give [Th(pyr(2)en)2(H2O)] (1), [Nd(pyr(2)en)(Hpyr(2)en)].12H2O (2) and [Eu(pyr(2)en)(Hpyr(2)en)] (3). In the three not yet reported bimolecular chelate systems the endo hydroxyl groups of the rings undergo deprotonation confirming the remarkable ability of the pyridoxal-containing ligand H(2)pyr(2)en to yield stable heavy metal chelates with unusual coordination polyhedra. Complexes 2 and 3 show a coordination number 8 for Nd and Eu, achieving a distorted quadratic antiprism. In complex 1 the additional water molecule increases the coordination number of Th to 9 producing a capped square antiprism. The synthesis and structural elucidation of the title complexes starting from a probably non-toxic metabolite like H(2)pyr(2)en should represent a useful contribution to the research on models of prevention and therapy of damage caused by radioactive and heavy elements.     

Niches versus neutrality: uncovering the drivers of diversity in a species-rich community

Ecological models suggest that high diversity can be generated by purely niche-based, purely neutral or by a mixture of niche-based and neutral ecological processes. Here, we compare the degree to which four contrasting hypotheses for coexistence, ranging from niche-based to neutral, explain species richness along a body mass niche axis. We derive predictions from these hypotheses and confront them with species body-mass patterns in a highly sampled marine phytoplankton community. We find that these patterns are consistent only with a mechanism that combines niche and neutral processes, such as the emergent neutrality mechanism. In this work, we provide the first empirical evidence that a niche-neutral model can explain niche space occupancy pattern in a natural species-rich community. We suggest this class of model may be a useful hypothesis for the generation and maintenance of species diversity in other size-structured communities.     

Neutral styrene divinylbenzene copolymers for adsorption of toxins in liver failure

In artificial extracorporeal liver support systems, albumin-bound toxins such as bilirubin, bile acids, or aromatic amino acids are removed by adsorption to polymer beads. To overcome the potential weaknesses of anion exchange polymers currently used in liver support, namely, binding of heparin and activation of coagulation, we prepared two series of neutral polystyrene divinylbenzene resins with average pore sizes of 5-6 and 8-9 nm, respectively. In in vitro experiments using human plasma spiked with bilirubin, cholic acid, tryptophan, and phenol, we found that only pores larger than 5-6 nm were accessible to strongly albumin-bound substances, such as bilirubin. On the other hand, less strongly albumin-bound substances, such as bile acids, were efficiently bound by polymers of the small pore size range due to a higher accessible surface area. None of the neutral resins bound significant amounts of heparin. To assess the influence of the polymers on activation of coagulation, generation of thrombin-antithrombin complexes (TAT) was measured at different citrate concentrations. While none of the neutral polymers induced TAT generation, TAT levels were significantly elevated after incubation of plasma with an anion exchange polymer that is in clinical use for extracorporeal liver support. Binding characteristics of the neutral resins for the natural anticoagulants protein C and antithrombin showed remarkable differences, with weak binding of antithrombin but strong removal of protein C, not only for the anion exchanger, but also for neutral polymers of the large pore size range. In conclusion, neutral polystyrene divinylbenzene polymers with a pore size larger than 5-6 nm are efficient adsorbents for albumin-bound toxins that do not induce generation of thrombin-antithrombin complexes.     

Specific interactions of isoguanine with the neutral and deprotonated carboxylic group of amino acids: results of model quantum chemical calculations

The MNDO/H quantum chemical calculations performed in order to estimate energetic features of the isoguanine (isoGua) prototropic tautomers complexes with acetic acid and its carboxylate-ion (models of neutral and deprotonated forms of amino acid carboxylic group) demonstrate ability of the latter to induce the N9H-->N7H tautomeric transition in the base, being characteristic to other purine bases as well. By contrast, the neutral carboxylic group forms the most stable complex with the ground-state isoGua tautomer N3HN9H.     

Conformation-activity relations of des-Arg9-bradykinin. I. Conformation of molecules in solution

The spatial structure of [des-Arg9]bradykinin, a selective agonist of the B1 type kinin receptors, was studied by means of theoretical conformational analysis. In order to restrict the number of conformations under consideration, we used available data on 1H NMR in (CD3)2SO solution indicating the C-terminal carboxyl group to interact with the guanidine group of Arg1 and the hydroxyl group of Ser6. The calculated set of [des-Arg9]bradykinin low-energy conformations was compared with the 1H NMR data. Four types of conformations were selected, which are consistent with experimental data and serve as sterically reliable models for the preferable three-dimensional structure of [des-Arg9]bradykinin in solution.     

Time-resolved FTIR difference spectroscopy for the study of photosystem I particles with plastoquinone-9 occupying the A1 binding site

In photosystem I from plants and cyanobacteria a phylloquinone molecule, called A1, functions as the secondary electron acceptor. In cyanobacteria, genes that encode for proteins involved in phylloquinone biosynthesis can be deleted. Here, we have studied three different gene deletion mutants called menB, menD, and menE mutants. In these mutants, plastoquinone-9 occupies the A1 binding site. Using time-resolved, step-scan FTIR difference spectroscopy we have produced A1(-)/A1 FTIR difference spectra for menB, menD, and menE photosystem I particles at 77 K. These difference spectra show that the P700 triplet state ((3)P700) is formed in a large fraction of the particles. Infrared spectral signatures that are not due to (3)P700 are also observed in the spectra and are suggested to be associated with plastoquinone-9 anion formation in a portion of the particles. By subtracting the known (3)P700 spectral signatures, we produce an A1(-)/A1 FTIR difference spectrum for PS I particles with plastoquinone-9 occupying the binding site. This spectrum shows that a band that we have previously assigned to a C:-O mode of the phylloquinone anion in WT A1(-)/A1 FTIR DS down-shifts approximately 8 cm(-1) when plastoquinone-9 occupies the A1 binding site. Using density functional theory type calculations to produce anion minus neutral infrared difference spectra for both phylloquinone and plastoquinone-9, it is shown that such a downshift is reasonable. A1(-)/A1 FTIR difference spectra, obtained using menB mutant photosystem I particles that were incubated in the presence of phylloquinone, are found to be very similar to those obtained using normal WT photosystem I particles. This result indicates that we were able to reincorporate phylloquinone back into the A1 binding site and that the reincorporated phylloquinone and its immediate protein environment, in both the neutral and anion state, are very similar to that found in wild type photosystem I particles. For the reconstituted menB mutant photosystem I particles, no spectral signatures associated with (3)P700 are observed, indicating that phylloquinone occupies the A1 site in all of the reconstituted menB particles.