Establishing large mammal population trends from heterogeneous count data.

Monitoring population trends is pivotal to effective wildlife conservation and management. However, wildlife managers often face many challenges when analyzing time series of census data due to heterogeneities in sampling methodology, strategy, or frequency. We present a three-step method for modeling trends from time series of count data obtained through multiple census methods (aerial or ground census and expert estimates). First, we design a heuristic for constructing credible intervals for all types of animal counts including those which come with no precision measure. Then, we define conversion factors for rendering aerial and ground counts comparable and provide values for broad classes of animals from an extant series of parallel aerial and ground censuses. Lastly, we construct a Bayesian model that takes the reconciled counts as input and estimates the relative growth rates between successive dates while accounting for their precisions. Importantly, we bound the rate of increase to account for the demographic potential of a species. We propose a flow chart for constructing credible intervals for various types of animal counts. We provide estimates of conversion factors for 5 broad classes of species. We describe the Bayesian model for calculating trends, annual rates of population increase, and the associated credible intervals. We develop a bespoke R CRAN package, popbayes, for implementing all the calculations that take the raw counts as input. It produces consistent and reliable estimates of population trends and annual rates of increase. Several examples from real populations of large African mammals illustrate the different features of our method. The approach is well-suited for analyzing population trends for heterogeneous time series and allows a principled use of all the available historical census data. The method is general and flexible and applicable to various other animal species besides African large mammals. It can readily be adapted to test predictions of various hypotheses about drivers of rates of population increase.

Photoaffinity labeling of Torpedo nicotinic receptor with the agonist [3H]DCTA: identification of amino acid residues which contribute to the binding of the ester moiety of acetylcholine.

Torpedo marmorata acetylcholine binding sites were photolabeled using 360 nm light, at equilibrium in the desensitized state, with the agonist [3H]DCTA utilizing the CeIV/glutathione procedure described previously (Grutter, et al. (1999) Biochemistry 38, 7476-7484). Photoincorporation of [3H]DCTA was concentration-dependent with a maximum of 7.5% specific labeling on the alpha-subunit and 1.2% on the gamma-subunit. The apparent dissociation constants for labeling of the alpha- and gamma-subunits were 2.2 +/- 1.1 and 3.6 +/- 2.8 microM, respectively. The alpha-chains isolated from receptor-rich membranes photolabeled in the absence or in the presence of carbamylcholine were cleaved with CNBr using an efficient "in gel" procedure. The resulting peptide fragments were purified by HPLC and further submitted to trypsinolysis. The digest was analyzed by HPLC leading to a single radioactive peak which, by microsequencing, revealed two sequences extending from alpha Lys-179 and from alpha His-186, respectively. Radioactive signals could be unambiguously attributed to positions corresponding to residues alpha Tyr-190, alpha Cys-192, alpha Cys-193, and alpha Tyr-198. These four identified [3H]DCTA-labeled residues, which have been also labeled with other affinity and photoaffinity probes including the agonist [3H]nicotine, belong to loop C of the ACh binding site. The chemical structure of [3H]DCTA, together with its well-defined and powerful photochemical reactivity, provides convincing evidence that loop C-labeled residues are primarily involved in the interaction with the ester moiety of acetylcholine.

Molecular investigations on the nicotinic acetylcholine receptor: conformational mapping and dynamic exploration using photoaffinity labeling.

The nicotinic acetylcholine receptor (nAChR) is a well-understood member of the ligand-gated ion channels superfamily. The members of this signaling proteins group, including 5HT3, GABA(A), glycine, and ionotropic glutamate receptors, are thought to share common secondary, tertiary, and quaternary structures on the basis of a very high degree of sequence similarity. Despite the absence of X-ray crystallographic data, considerable progress on structural analysis of nAChR was achieved from biochemical, mutational, and electron microscopy data allowing the emergence of a three-dimensional image. Photoaffinity labeling and site-directed mutagenesis gave information on the tertiary structure with respect to the agonist/antagonist binding sites, the ion channel, and its selectivity filter. nAChR is an allosterical protein that undergoes interconversion among several conformational states. Time-resolved photolabeling was used in an attempt to elucidate the structural changes that occur in nAChR on neurotransmitter activation. Tertiary and quaternary rearrangements were found in the cholinergic binding pocket and in the channel lumen, but the structural determinant and the functional link between the binding of agonist and the channel gating remain unknown. Time-resolved photolabeling of the functional activated A state using photosensitive agonists might help in understanding the dynamic process leading to the interconversion of the different states.

Nicotinic acetylcholine receptor probed with a photoactivatable agonist: improved labeling specificity by addition of CeIV/glutathione. Extension to laser flash photolabeling.

The molecular structure of Torpedo marmorata acetylcholine binding sites has been investigated previously by photoaffinity labeling. However, besides the nicotine molecule [Middleton et al. (1991) Biochemistry 30, 6987-6997], all other photosensitive probes used for this purpose interacted only with closed receptor states. In the perspective of mapping the functional activated state, we synthesized and developed a new photoactivatable agonist of nAChR capable of alkylation of the acetylcholine (ACh) binding sites, as reported previously [Kotzyba-Hibert et al. (1997) Bioconjugate Chem. 8, 472-480]. Here, we describe the setup of experimental conditions that were made in order to optimize the photolabeling reaction and in particular its specificity. We found that subsequent addition of the oxidant ceric ion (CeIV) and reduced glutathione before the photolabeling step lowered considerably nonspecific labeling (over 90% protection with d-tubocurarine) without affecting the binding properties of the ACh binding sites. As a consequence, irradiation at 360 nm for 20 min in these new conditions gave satisfactory coupling yields (7.5%). A general mechanism was proposed to explain the successive reactions occurring and their drastic effect on the specificity of the labeling reaction. Last, these incubation conditions can be extended to nanosecond pulsed laser photolysis leading to the same specific photoincorporation as for usual irradiations (8.5% coupling yield of ACh binding sites, 77% protection with carbamylcholine). Laser flash photocoupling of a diazocyclohexadienoyl probe on nAChR was achieved for the first time. Taken together, these data indicate that future investigation of the molecular dynamics of allosteric transitions occurring at the activated ACh binding sites should be possible.

Nicotinic acetylcholine receptor labeled with a tritiated, photoactivatable agonist: a new tool for investigating the functional, activated state.

Upon agonist activation, the nicotinic acetylcholine receptor undergoes allosteric transitions leading to channel opening and sodium ion influx. The molecular structure of the agonist binding site has been mapped previously by photoaffinity labeling, but most photosensitive probes used for this purpose interact only with closed receptor states (resting or desensitized). We have synthesized two novel photoactivatable 4-diazocyclohexa-2,5-dienone derivatives as cholinergic agonist candidates, with the objective of identifying structural changes at the acetylcholine binding site associated with receptor activation. One of these ligands, 9b, is a functional agonist at muscle acetylcholine receptors in human TE 671 cells. In photolabeling experiments with 9b, up to 35% inactivation of agonist binding sites was observed at Torpedo acetylcholine receptors. Tritiated 9b was synthesized, and photolabeling was found to occur mainly on the alpha-subunit in a partially protectable manner. This novel radiolabeled photoprobe appears to be suitable for future investigation of the molecular dynamics of allosteric transitions occurring at the active acetylcholine receptor binding site.

Novel photoactivatable agonist of the nicotinic acetylcholine receptor of potential use for exploring the functional activated state.

The nicotinic acetylcholine receptor (AChR) exhibits at least four different conformational states varying in affinity for agonists such as acetylcholine (ACh). Photoaffinity labeling has been previously used to elucidate the topography of the AChR. However, to date, the photosensitive probes used to explore the cholinergic binding site photolabeled only closed or desensitized states of the receptor. To identify the structural modifications occurring at the ACh binding site on allosteric transition associated with receptor activation, we have investigated novel photoactivatable 4-diazocyclohexa-2,5-dienone derivatives as putative cholinergic agonists. Such compounds are fairly stable in the dark and generate highly reactive carbenic species on irradiation. In binding experiments using AChRs from Torpedo marmorata, these ligands had affinities for the ACh binding site in the micromolar range and did not interact with the noncompetitive blocker site (greater than millimolar affinity). Irreversible photoinactivation of ACh binding sites was obtained with the ligand 1b (up to 42% at 500 microM) in a protectable manner. In patch-clamp studies, 1b was shown to be a functional agonist of peripheral AChR in TE 671 cells, with the interesting property of exhibiting no or very little desensitization even at high concentrations.

Photochemical labeling of membrane-associated and channel-forming domains of proteins directed by energy transfer.

Singlet-singlet energy transfer reactions from excited tryptophan residues to photoactivatable probes possessing a suitable chromophore, generate reactive species in the vicinity of the protein, leading to its covalent labeling. This delayed labeling process can be used to map the membrane-surrounded regions of proteins with improved efficiency when it is applied with appropriate photoactivatable phospholipids. The same principle could also be applied to the labeling of channel-forming transmembrane domains of ion channels, provided that suitable photoactivatable permeant ions were available. Both applications will be discussed with regard to their potential and feasibility.

Synthesis of an acetylcholine receptor-specific toxin derivative regioselectively labeled with an undecagold cluster.

The regioselective modification of a snake curaremimetic toxin is described. Toxin-alpha from Naja nigricollis was derivatized with an electron-dense maleimido undecagold cluster 5. The cluster-bound obtained toxin 8 has a very high affinity for the cholinergic binding site (Ki = 70 pM) of Torpedo marmorata nicotinic receptor. It is harboring a compact heavy atom core of about 8 A which makes it very useful for electron microscopy experiments.

Photoactivatable agonist of the nicotinic acetylcholine receptor: potential probe to characterize the structural transitions of the acetylcholine binding site in different states of the receptor.

The nicotinic acetylcholine receptor exhibits at least four different affinity states for agonists such as acetylcholine. In order to identify the structural changes occurring at or near the agonist binding site during the allosteric transitions, three photoactivatable compounds designed to display agonist activity were synthesized. Inhibition constants of these compounds for the cholinergic and the noncompetitive blocker binding sites were determined for the resting and the desensitized states of the receptor. Among these probes, two ligands, AC5 and AC7, displayed a high affinity for the agonist binding site and were poorly recognized by the binding site for noncompetitive blockers. Electrophysiological experiments revealed that these ligands behaved as agonists at low concentrations. We used these two compounds in photolabeling experiments and observed that they were able to inactivate the agonist binding site. Up to 50% of these sites were irreversibly inhibited, depending on the ligand, the irradiation conditions, and the selected receptor state. The compound with the most interesting properties (high affinity and selectivity for the acetylcholine binding site, as well as agonist activity and high photolabeling yield) is AC5, a structural analogue of the fluorescent agonist dansyl-C6-choline, which has been previously used to characterize the different states of the nicotinic receptor. After radioactive synthesis, [3H]AC5 was shown to label all four receptor subunits, in a protectable manner. This radioligand, thus, appears suitable for investigation of the dynamics of allosteric transitions occurring at the activated acetylcholine binding site.

Amino acids of the Torpedo marmorata acetylcholine receptor alpha subunit labeled by a photoaffinity ligand for the acetylcholine binding site.

The acetylcholine-binding sites on the native, membrane-bound acetylcholine receptor from Torpedo marmorata were covalently labeled with the photoaffinity reagent [3H]-p-(dimethylamino)-benzenediazonium fluoroborate (DDF) in the presence of phencyclidine by employing an energy-transfer photolysis procedure. The alpha-chains isolated from receptor-rich membranes photolabeled in the absence or presence of carbamoylcholine were cleaved with CNBr and the radiolabeled fragments purified by high-performance liquid chromatography. Amino acid and/or sequence analysis demonstrated that the alpha-chain residues Trp-149, Tyr-190, Cys-192, and Cys-193 and an unidentified residue(s) in the segment alpha 31-105 were all labeled by the photoaffinity reagent in an agonist-protectable manner. The labeled amino acids are located within three distinct regions of the large amino-terminal hydrophilic domain of the alpha-subunit primary structure and plausibly lie in proximity to one another at the level of the acetylcholine-binding sites in the native receptor. These findings are in accord with models proposed for the transmembrane topology of the alpha-chain that assign the amino-terminal segment alpha 1-210 to the synaptic cleft. Furthermore, the results suggest that the four identified [3H]DDF-labeled residues, which are conserved in muscle and neuronal alpha-chains but not in the other subunits, may be directly involved in agonist binding.

Aryldiazonium salts as photoaffinity labels of the nicotinic acetylcholine receptor PCP binding site.

Several aryldiazonium salts are described as irreversible blockers of the phencyclidine binding site of the nicotinic cholinergic receptor. A partial hydrophobic character increases the affinity of these salts for the phencyclidine binding site. Photoaffinity labelling with a tritiated diazonium salt in the presence of either carbamylcholine or alpha-bungarotoxin leads to incorporation of radioactivity into the 4 subunits of the receptor. Among these diazonium salts, an imidazole derivative is unique in that the photoinduced irreversible blocking in only effective when the receptor is in a desensitised state.