Using community photography to investigate phenology: A case study of coat molt in the mountain goat (Oreamnos americanus) with missing data

Participatory approaches, such as community photography, can engage the public in questions of societal and scientific interest while helping advance understanding of ecological patterns and processes. We combined data extracted from community-sourced, spatially explicit photographs with research findings from 2018 fieldwork in the Yukon, Canada, to evaluate winter coat molt patterns and phenology in mountain goats (Oreamnos americanus), a cold-adapted, alpine mammal. Leveraging the community science portals iNaturalist and CitSci, in less than a year we amassed a database of almost seven hundred unique photographs spanning some 4,500 km between latitudes 37.6°N and 61.1°N from 0 to 4,333 m elevation. Using statistical methods accounting for incomplete data, a common issue in community science datasets, we identified the effects of intrinsic (sex and presence of offspring) and broad environmental (latitude and elevation) factors on molt onset and rate and compared our findings with published data. Shedding occurred over a 3-month period between 29 May and 6 September. Effects of sex and offspring on the timing of molt were consistent between the community-sourced and our Yukon data and with findings on wild mountain goats at a long-term research site in west-central Alberta, Canada. Males molted first, followed by females without offspring (4.4 days later in the coarse-grained, geographically wide community science sample; 29.2 days later in our fine-grained Yukon sample) and lastly females with new kids (6.2; 21.2 days later, respectively). Shedding was later at higher elevations and faster at northern latitudes. Our findings establish a basis for employing community photography to examine broad-scale questions about the timing of ecological events, as well as sex differences in response to possible climate drivers. In addition, community photography can help inspire public participation in environmental and outdoor activities specifically with reference to iconic wildlife.

Spatial and temporal analysis of litter in the Celtic Sea from Groundfish Survey data: Lessons for monitoring

The Marine Strategy Framework Directive requires EU Member States to sample and monitor marine litter. Criteria for sampling and detecting spatial and/or temporal variation in the amount of litter present have been developed and initiated throughout Europe. These include implementing standardised sampling and recording methods to enable cross-comparison and consistency between neighbours. Parameters of interest include; litter occurrence, composition, distribution and source. This paper highlights the litter-related initiatives occurring in Irish waters; presents an offshore benthic litter sampling series; provides a power analysis to determine trend detection thresholds; identifies areas and sources of litter; and proposes improvements to meet reporting obligations. Litter was found to be distributed throughout Irish waters with highest occurrences in the Celtic Sea. Over 50% of litter encountered was attributed to fishing activities: however only a small proportion of the variability in litter occurrence could be explained by spatial patterns in fishing effort. Issues in implementing standardised protocol were observed and addressed.

What factors determine cyclic amplitude in the snowshoe hare (Lepus americanus) cycle?

Snowshoe hares (Lepus americanus Erxleben, 1777) fluctuate in 9–10 year cycles throughout much of their North American range. These cycles show large variations in cyclic amplitude and we ask what factors could cause amplitude variation. We gathered data from 1976 to 2012 on hare numbers in the boreal forest of Alaska, Yukon, Northwest Territories, and northern British Columbia to describe the amplitude of hare fluctuations and to evaluate four possible causes. First, weather could cause variation in amplitude via hare reproduction or survival, but this mechanism does not fit our data. Second, bottom-up processes involving forest succession could explain amplitude variation through changes in winter forage availability, but succession is too slow a variable in our study areas. Third, plant defenses entrained by hare over-browsing in one cycle can produce variation in plant quality and quantity in subsequent cycles. A mathematical model suggests this is a possible explanation. Fourth, predator recovery following the cyclic low is inversely related to hare cyclic amplitude, and the existing data are consistent with this mechanism. A standardized regional monitoring program is needed to improve our understanding of cyclic amplitude variation in hares and the possible role of predators and winter foods in affecting amplitude.

Emerging asymmetric interactions between forage and predator fisheries impose management trade-offs

A size and trait-based marine community model was used to investigate interactions, with potential implications for yields, when a fishery targeting forage fish species (whose main adult diet is zooplankton) co-occurs with a fishery targeting larger-sized predator species. Predicted effects on the size structure of the fish community, growth and recruitment of fishes, and yield from the fisheries were used to identify management trade-offs among the different fisheries. Results showed that moderate fishing on forage fishes imposed only small effects on predator fisheries, whereas predator fisheries could enhance yield from forage fisheries under some circumstances.

Synchrony in the snowshoe hare (Lepus americanus) cycle in northwestern North America, 1970–2012

Snowshoe hares (Lepus americanus Erxleben, 1777) fluctuate in 9–10 year cycles throughout much of their North American range. Regional synchrony has been assumed to be the rule for these cycles, so that hare populations in virtually all of northwestern North America have been assumed to be in phase. We gathered qualitative and quantitative data on hare numbers and fur returns of Canada lynx (Lynx canadensis Kerr, 1792) in the boreal forest regions of Alaska, Yukon, Northwest Territories, and northern British Columbia to describe synchrony in the time window of 1970–2012. Broad-scale synchrony in lynx fur returns was strong from 1970 to about 1995 but then seemed to break down in different parts of this region. Hare populations at 20 sites in Alaska, the Yukon, and Northwest Territories showed peak populations that lagged by 1–4 years during the 1990s and 2000s cycles. The simplest hypothesis to explain these patterns of asynchrony in hare cycles is the movement of predators from British Columbia north into the Yukon and then east into the Northwest Territories and west into Alaska. A traveling wave of these cycles is clearly seen in the lynx fur returns from western Canada and Alaska from 1970 to 2009. One consequence of a failure of synchrony is that hare predators like Canada lynx and Great-horned Owls (Bubo virginianus (Gmelin, 1788)) can move from one adjacent area to the next within this region and survive long enough to prolong low densities in hare populations that have declined earlier.

Lemming winter habitat choice: a snow-fencing experiment

The insulative value of early and deep winter snow is thought to enhance winter reproduction and survival by arctic lemmings (Lemmus and Dicrostonyx spp). This leads to the general hypothesis that landscapes with persistently low lemming population densities, or low amplitude population fluctuations, have a low proportion of the land base with deep snow. We experimentally tested a component of this hypothesis, that snow depth influences habitat choice, at three Canadian Arctic sites: Bylot Island, Nunavut; Herschel Island, Yukon; Komakuk Beach, Yukon. We used snow fencing to enhance snow depth on 9-ha tundra habitats, and measured the intensity of winter use of these and control areas by counting rodent winter nests in spring. At all three sites, the density of winter nests increased in treated areas compared to control areas after the treatment, and remained higher on treated areas during the treatment. The treatment was relaxed at one site, and winter nest density returned to pre-treatment levels. The rodents' proportional use of treated areas compared to adjacent control areas increased and remained higher during the treatment. At two of three sites, lemmings and voles showed significant attraction to the areas of deepest snow accumulation closest to the fences. The strength of the treatment effect appeared to depend on how quickly the ground level temperature regime became stable in autumn, coincident with snow depths near the hiemal threshold. Our results provide strong support for the hypothesis that snow depth is a primary determinant of winter habitat choice by tundra lemmings and voles.

Global diversification of mangrove fauna: a molecular phylogeny of Littoraria (Gastropoda: Littorinidae)

The genus Littoraria is one of very few molluscan groups that are closely associated with mangroves. We document its global evolutionary radiation and compare biogeographic patterns with those of mangrove plants, based on phylogenetic and fossil evidence. Using sequences from three genes (nuclear 28S rRNA, mitochondrial 12S rRNA and COI) we reconstruct a phylogeny of 37 of the 39 living morphospecies. Six monophyletic subgenera are defined (Bulimilittorina, Lamellilitorina, Littoraria, Palustorina, Protolittoraria, Littorinopsis) and we synonymize L. coccinea and L. glabrata. A deep division between Palustorina from the Indo-West Pacific and Littoraria from the Atlantic and Eastern Pacific is estimated by a Bayesian relaxed-clock method to be of Middle Eocene to Palaeocene age (43.2-62.7 Ma), which far predates the Early Miocene (18 Ma) closure of the Tethyan Seaway; this, as in mangrove plants, may reflect vicariance by climatic cooling, rather than tectonic processes. The age of Littoraria angulifera in the Atlantic is, however, consistent with Early Miocene vicariance of a Tethyan ancestor. We infer that speciation events are mainly of Miocene or older age, and that diversification has not been driven by depletion of mangrove habitats during recent glacial intervals. Parsimonious reconstruction of ancestral habitats suggests that the genus has inhabited mangrove or wood substrates since its origin, while the rock-dwelling habit of the four members of Protolittoraria is derived. Three species span the Eastern Pacific Barrier, and one is amphi-Atlantic, consistent with a long larval phase of up to 10 weeks. Allopatric speciation is inferred, but usually with subsequent range overlap. Ovoviviparity (interpreted as an adaptation to life in mangroves) has arisen twice.

Correlating sideband patterns with powder patterns for accurate determination of chemical shift parameters in solid-state NMR

Powder patterns and sideband patterns have different strengths when it comes to using them to determine chemical shift parameters. Here, we show that chemical shift parameters can be determined with high accuracy by analysing the correlation pattern from a 2D experiment which correlates a powder pattern in the indirect dimension with a sideband pattern in the direct dimension. The chemical shift parameters so determined have greater accuracy than those obtained by analysing a sideband or powder pattern alone, for the same signal-to-noise ratio. This method can be applied for both resolved correlation patterns and to cases where two components share similar isotropic chemical shifts. The methodology is demonstrated in this paper, both theoretically and experimentally, on the (31)P signals of the bis-phosphonate drug, pamidronate.

Speciation and diversity on tropical rocky shores: a global phylogeny of snails of the genus Echinolittorina

A phylogenetic approach to the origin and maintenance of species diversity ideally requires the sampling of all species within a clade, confirmation that they are evolutionarily distinct entities, and knowledge of their geographical distributions. In the marine tropics such studies have mostly been of fish and reef-associated organisms, usually with high dispersal. In contrast, snails of the genus Echinolittorina (Littorinidae) are restricted to rocky shores, have a four-week pelagic development (and recorded dispersal up to 1400 km), and show different evolutionary patterns. We present a complete molecular phylogeny of Echinolittorina, derived from Bayesian analysis of sequences from nuclear 28S rRNA and mitochondrial 12S rRNA and COI genes (nodal support indicated by posterior probabilities, maximum likelihood, and neighbor-joining bootstrap). This consists of 59 evolutionarily significant units (ESUs), including all 50 known taxonomic species. The 26 ESUs found in the Indo-West Pacific region form a single clade, whereas the eastern Pacific and Atlantic species are basal. The earliest fossil occurred in the Tethys during the middle Eocene and we suggest that the Indo-West Pacific clade has been isolated since closure of the Tethyan seaway in the early Miocene. The geographical distributions of all species (based on more than 3700 locality records) appear to be circumscribed by barriers of low temperature, unsuitable sedimentary habitat, stretches of open water exceeding about 1400 km, and differences in oceanographic conditions on the continuum between oceanic and continental. The geographical ranges of sister species show little or no overlap, indicating that the speciation mode is predominantly allopatric. Furthermore, range expansion following speciation appears to have been limited, because a high degree of allopatry is maintained through three to five branching points of the phylogeny. This may be explained by infrequent long-distance colonization, habitat specialization on the oceanic/continental gradient, and perhaps by interspecific competition. In the eastern Pacific plus Atlantic we identify five cases of divergence on either side of the Isthmus of Panama, but our estimates of their ages pre-date the emergence of the Isthmus. There are three examples of sister relationships between species in the western Atlantic and eastern Atlantic, all resulting from dispersal to the east. Within the Indo-West Pacific, we find no geographical pattern of speciation events; narrowly endemic species of recent origin are present in both peripheral and central parts of the region. Evidence from estimated divergence times of sister species, and from a plot of the number of lineages over time, suggest that there has been no acceleration of diversification during the glacio-eustatic cycles of the Plio-Pleistocene. In comparison with reefal organisms, species of Echinolittorina on rocky shores may be less susceptible to extinction or isolation during sea-level fluctuations. The species richness of Echinolittorina in the classical biogeographic provinces conforms to the common pattern of highest diversity (11 species) in the central "East Indies Triangle" of the Indo-West Pacific, with a subsidiary focus in the eastern Pacific and western Atlantic, and lowest diversity in the eastern Atlantic. The diversity focus in the East Indies Triangle is produced by a mosaic of restricted allopatric species and overlap of a few widespread ones, and is the result of habitat specialization rather than historical vicariance. This study emphasizes the plurality of biogeographic histories and speciation patterns in the marine tropics.

A molecular phylogeny of the Littorininae (Gastropoda: Littorinidae): unequal evolutionary rates, morphological parallelism, and biogeography of the Southern Ocean

A molecular phylogeny is presented for the subfamily Littorininae (including representatives of all subgeneric taxa and all members of a group of southern-temperate species formerly classified as 'Nodilittorina'), based on sequence data from two nuclear (18S rRNA, 28S rRNA) and two mitochondrial (12S rRNA, CO1) genes. The phylogeny shows considerable disagreement with earlier hypotheses derived from morphological data. In particular, 'Nodilittorina' is polyphyletic and is here divided into four genera (Echinolittorina, Austrolittorina, Afrolittorina new genus, and the monotypic Nodilittorina s.s.). The phylogenetic relationships of 'Littorina' striata have been controversial and it is here transferred to the genus Tectarius, a surprising relationship for which there is little morphological support. The relationships of the enigmatic Mainwaringia remain poorly resolved, but it is not a basal member of the subfamily. The two living species of Mainwaringia are remarkable for a greatly elevated rate of evolution in all four genes examined; it is suggested that this may be connected with their protandrous hermaphroditism, which is unique in the family. The molecular phylogeny provides a new framework for the adaptive radiation of the Littorininae, showing more frequent shifts between habitats and climatic regimes than previously suspected, and striking parallelism of morphological characters. The fossil record of littorinids is poor, but ages of clades are estimated using a calibration based on a Lower Eocene age of the genus Littoraria. Using these estimates, the antitropical distribution of Littorina and Afrolittorina is an ancient pattern of possibly Cretaceous age. The five members of Austrolittorina show a Gondwanan distribution in Australia, New Zealand, and South America. Based on the morphological uniformity within this clade, relatively recent (Plio-Pleistocene) trans-Pacific dispersal events seemed a likely explanation, as proposed for numerous other congeneric marine taxa. However, molecular estimation of ages of divergence suggest an initial vicariance between Australian and South American lineages at 40-73Ma, contemporary with the later stages of fragmentation of the Gondwanan supercontinent, followed by more recent (but still mid-Cenozoic) dispersal events across the Tasman Sea and the Pacific Ocean. Afrolittorina is another Cretaceous clade, now restricted to southern Africa and southern Australia, but divergence between these lineages (29-55Ma) post-dates Gondwanan fragmentation. Within both Austrolittorina and Afrolittorina all sister-species divergences are estimated to fall in the range 10-47Ma, so that there is no evidence for speciation events in the Plio-Pleistocene.

Rapid reversal of hepatic steatosis, and reduction of muscle triglyceride, by rosiglitazone: MRI/S studies in Zucker fatty rats

AIM

This study aimed to chart the time course and durability of the effects of rosiglitazone, a potent thiazolidinedione-based peroxisome proliferator-activated receptor gamma agonist, on hepatic steatosis and intramyocellular lipid in an animal model of obesity, the Zucker Fatty (ZF) rat.

METHODS AND RESULTS

Rosiglitazone (3 mg/kg/day p.o.) significantly reduced both liver fat content (by 59%; p < 0.05) and size (11.5%; p < 0.05) in male ZF rats that received between 3 days and 1 week of treatment, and these reductions were maintained for at least 12 weeks. Liver fat content measured by magnetic resonance spectroscopy (MRS) correlated closely and positively with plasma insulin levels (reduced by 89% within a week, r = 0.8) and with postmortem histological fat fractional volume (r = 0.89). Similarly, liver volume measured by magnetic resonance imaging (MRI) correlated closely with postmortem wet weight (r = 0.99). MRS also showed, and numbers of lipid vacuoles counted in transmission electron micrographs confirmed, that rosiglitazone significantly reduced the elevated intramyocellular lipid seen in ZF rat skeletal muscle by at least 40% (p < 0.05).

CONCLUSIONS

Localized MRS and MRI showed that rosiglitazone reversed the hepatic steatosis, hepatomegaly and intramyocellular lipid, characteristic of the ZF rat, an animal model of obesity.

A longitudinal magnetic resonance imaging (MRI) study of differences in abdominal fat distribution between normal mice, and lean overexpressers of mitochondrial uncoupling protein-3 (UCP-3)

AIM

To characterize evolution and distribution of abdominal adipose fat between 6 and 18 weeks of age in an animal model of energy consumption based on mice overexpressing the mitochondrial uncoupler protein 3 (UCP-3).

METHODS

T2-weighted multislice MRI was performed six times during the 12 week study; visceral, subcutaneous and intermuscular fat depots were quantified.

RESULTS

The overexpressor (UCP-3tg) mice consistently have less subcutaneous, visceral, interskeletal muscle and total fat throughout the experiment. Mean (standard error) volumes (ml) of the three distinct depots change between week 6 and week 18 as follows: wild type: subcutaneous 1.93 (0.28) to 6.18 (0.47), visceral 2.15 (0.34) to 6.37 (0.64), intermuscular 0.23 (0.04) to 0.53 (0.03); UCP-3tg: subcutaneous 1.47 (0.17) to 4.07 (0.57), visceral 1.18 (0.04) to 3.69 (0.59), intermuscular 0.23 (0.01) to 0.32 (0.04). Although they eat more (4.3 g compared with 3.4 g per day) the UCP-3tg's always weigh less than controls. In wild-type control animals, increases of all fat pools between week 6 and week 18 is highly significant, as it is for subcutaneous, visceral and total pools in the UCP-3tg animals. The UCP-3tg mice, however, show no significant absolute or relative increase in intermuscular fat; UCP-3 is predominantly overexpressed in skeletal muscle.

CONCLUSION

MRI provides an excellent approach to comparative studies of fat distribution in animal models of energy expenditure such as the UCP-3tg mouse.

Ischaemic preconditioning in the rat brain: a longitudinal magnetic resonance imaging (MRI) study

Ischaemic preconditioning in rats was studied using MRI. Ischaemic preconditioning was induced, using an intraluminal filament method, by 30 min middle cerebral artery occlusion (MCAO), and imaged 24 h later. The secondary insult of 100 min MCAO was induced 3 days following preconditioning and imaged 24 and 72 h later. Twenty-four hours following ischaemic preconditioning most rats showed small sub-cortical hyperintense regions not seen in sham-preconditioned rats. Twenty-four hours and 72 h following the secondary insult preconditioned animals showed significantly smaller lesions (24 h = 112 +/- 31 mm(3), mean +/- standard error; 72 h = 80 +/- 35 mm(3)), which were confined to the striatum, than controls (24 h = 234 +/- 32 mm(3), p = 0.026; 72 h = 275 +/- 37 mm(3), p = 0.003). In addition during lesion maturation from 24 to 72 h post-secondary MCAO, preconditioned rats displayed an average reduction in lesion size as measured by MRI whereas sham-preconditioned rats displayed increases in lesion size; this is the first report of such differential lesion volume evolution in cerebral ischaemic preconditioning.

A solid-state NMR study of the phospholamban transmembrane domain: local structure and interactions with Ca(2+)-ATPase

The structure and dynamics of a double (13)C-labelled 24-residue synthetic peptide ([(13)C(2)]CAPLB(29-52)), corresponding to the membrane-spanning sequence of phospholamban (PLB), were examined using (13)C cross-polarisation magic-angle spinning (CP-MAS) NMR spectroscopy. CP-MAS spectra of [(13)C(2)]CAPLB(29-52) reconstituted into unsaturated lipid membranes indicated that the peptide was mobile at temperatures down to -50 degrees C. The NMR spectra showed that peptide motion became constrained in the presence of the SERCA1 isoform of Ca(2+)-ATPase, and chemical cross-linking experiments indicated that [(13)C(2)]CAPLB(29-52) and Ca(2+)-ATPase came into close contact with one another. These results together suggested that the peptide and the 110-kDa calcium pump were interacting in the membrane. Rotational resonance CP-MAS (13)C-(13)C distance measurements on [(13)C(2)]CAPLB(29-52) reconstituted into lipid bilayers confirmed that the sequence spanning Phe-32 and Ala-36 was alpha-helical, and that this structure was not disrupted by interaction with Ca(2+)-ATPase. These results support the finding that the transmembrane domain of PLB is partially responsible for regulation of Ca(2+) transport through interactions with cardiac muscle Ca(2+)-ATPase in the lipid bilayer, and also demonstrate the feasibility of performing structural measurements on PLB peptides when bound to their physiological target.

Mice overexpressing human uncoupling protein-3 in skeletal muscle are hyperphagic and lean

Uncoupling protein-3 (UCP-3) is a recently identified member of the mitochondrial transporter superfamily that is expressed predominantly in skeletal muscle. However, its close relative UCP-1 is expressed exclusively in brown adipose tissue, a tissue whose main function is fat combustion and thermogenesis. Studies on the expression of UCP-3 in animals and humans in different physiological situations support a role for UCP-3 in energy balance and lipid metabolism. However, direct evidence for these roles is lacking. Here we describe the creation of transgenic mice that overexpress human UCP-3 in skeletal muscle. These mice are hyperphagic but weigh less than their wild-type littermates. Magnetic resonance imaging shows a striking reduction in adipose tissue mass. The mice also exhibit lower fasting plasma glucose and insulin levels and an increased glucose clearance rate. This provides evidence that skeletal muscle UCP-3 has the potential to influence metabolic rate and glucose homeostasis in the whole animal.

A molecular phylogeny of the patellid limpets (Gastropoda: Patellidae) and its implications for the origins of their antitropical distribution

The geographical distribution of the limpet family Patellidae is essentially antitropical, with 18 species in southern Africa, 10 in the northeastern Atlantic, and only 11 species elsewhere (although 4 of these do occur in the tropics). One possible explanation for this distribution is the suggestion of a recent, perhaps Early Pliocene, migration from southern Africa northward. We tested this hypothesis by constructing a molecular phylogeny, derived from partial sequences of the 12S and 16S mitochondrial genes, obtained from 34 of the 38 patellid species. Five species of Nacellidae and 3 of Lottiidae were included as potential outgroups. Analysis revealed that two patellid clades are represented in the northeastern Atlantic. The typical European patellids (Patella sensu stricto) form a single clade within which there is little molecular divergence, but are distant from all other patellids, thus refuting the idea of recent southern ancestry. From the limited fossil record and estimated rates of molecular divergence, we suggest that Patella s.s. may have originated at least as early as the Upper Cretaceous and that its northern distribution may have been achieved at the same time. The second patellid clade present in the northeastern Atlantic is the genus Cymbula, of which the single species Cymbula safiana extends from West Africa to the Mediterranean. In contrast to Patella s.s., C. safiana is indeed a member of an otherwise southern African clade and may have attained its present distribution more recently, during the Miocene. The geographical origin of the family remains unclear, but a Mesozoic radiation in southern Gondwana is possible. By optimizing morphological characters on our molecular tree, we consider the evolution of shell mineralogy and sperm ultrastructure. We also discuss the phylogenetic classification of the patellids and present some evidence that the family may not be monophyletic.

Preparation of recombinant tissue inhibitor of metalloproteinases-1 (TIMP-1) in high yield and identification of a hydrophobic surface feature

The work presented here describes an effective method for refolding recombinant tissue inhibitor of metalloproteinases-1 (TIMP-1), a 21-kDa protein with six disulphide bonds. A yield of 30 mg TIMP-1/l culture medium was obtained from a high level bacterial expression system, using a slow removal of denaturant in the presence of 0.5 M guanidine and a suitable redox buffer. This protein is identical to the wild-type species when specific activity and secondary structure (by CD) are compared. The fluorescent, hydrophobic compound 8-anilino 1-naphthalene sulphonate (ANS) was used to quantify hydrophobic binding sites on the surface of both wild-type and recombinant TIMP-1. The wild-type protein has 1 binding site with a mean Kd of 1.3 mM and the recombinant protein has 1.5 binding sites with a mean Kd of 0.39 mM. The presence of surface hydrophobic residues is confirmed by selective broadening of ethyl and aromatic signals in the 1H-NMR spectrum on the addition of the paramagnetic probe 4-hydroxy-2,2,6,6-tetramethylpiperidinyl-N-oxy, OH-TEMPO, to wild-type TIMP-1. When wild-type TIMP-1 is incubated with the N-terminal fragment of human fibroblast collagenase prior to the addition of ANS, the number of binding sites in the system decreases to 0.5 with a Kd of 0.15 mM.

Performance of 18S rRNA in littorinid phylogeny (Gastropoda: Caenogastropoda)

In the past, 18S rRNA sequences have proved to be very useful for tracing ancient divergences but were rarely used for resolving more recent ones. Moreover, it was suggested that the molecule does not contain useful information to resolve divergences which took place during less than 40 Myr. The present paper takes littorinid phylogeny as a case study to reevaluate the utility of the molecule for resolving recent divergences. Two data sets for nine species of the snail family Littorinidae were analyzed, both separately and combined. One data set comprised 7 new complete 18S rRNA sequences aligned with 2 published littorinid sequences; the other comprised 12 morphological, 1 biochemical, and 2 18S rRNA secondary structure characters. On the basis of its ability to confirm generally accepted relationships and the congruence of results derived from the different data sets, it is concluded that 18S rRNA sequences do contain information to resolve "rapid" cladogenetic events, provided that they occurred in the not too distant past. 18S rRNA sequences yielded support for (1) the branching order (L. littorea, (L. obtusata, (L. saxatilis, L. compressa))) and (2) the basal position of L. striata in the Littorina clade.

The effect of sample freezing on proton magic-angle spinning NMR spectra of biological tissue

Magic-angle spinning (MAS) has recently been shown to enhance spectral resolution in NMR examinations of intact biological tissue ex vivo. This work demonstrates that freezing certain tissue samples before examination by 1H MAS NMR can have a marked effect on their spectra. Spectra of rat kidney after freezing in liquid nitrogen, compared with spectra before freezing, showed a significant increase in signal intensities from alanine (>100%), glutamine (>40%), and glycine (>100%), and a decrease in signals assigned to lipids and other macromolecules. Some resonances--such as from leucine, valine, isoleucine, and aspartate--only became visible after freezing the tissue. These observations suggest that low temperature storage of tissue necropsies or biopsies might affect the results of a MAS NMR analysis, possibly resulting in the misinterpretation of metabolite changes to pathogen or disease effects.

A cross-polarization magic-angle spinning 13C NMR characterization of the stable solid-state forms of cimetidine

Proton decoupled, cross-polarization magic-angle spinning 13C NMR spectra of four polymorphic forms (A, B, C, and D) and a monohydrate form (M1) of the histamine H2 antagonist cimetidine were obtained, and the chemical shifts of the various forms were tabulated. A modified polarization inversion pulse sequence was used to distinguish quaternary, methine, methylene, and methyl carbon resonances and thereby assist spectral assignment. It is also shown that the solid-state form of cimetidine in a commercial formulation can be reliably ascertained by NMR, despite the presence in the spectrum of signals from organic excipients that are much more intense than those from the compound.

The conformation of an inhibitor bound to the gastric proton pump

Substituted imidazo[1,2-a]pyridines are pharmaceutically important small molecule inhibitors of the gastric H+/K+-ATPase, the membrane-bound therapeutic target for peptic ulcer disease. A non-perturbing analytical technique, rotational resonance NMR spectroscopy, was used to measure a precise (to +/-0.2 A) distance between atomic sites in a substituted imidazo[1,2-a]pyridine, TMPIP, bound to H+/K+-ATPase at its high-affinity site in the intact, native membrane. The structural analysis of the enzyme-inhibitor complex revealed that the flexible moiety of TMPIP adopts a 'syn-type' conformation at its site of action. Hence, the conformation of an inhibitor has been resolved directly under near-physiological conditions, providing a sound experimental basis for rational design of many active compounds of pharmaceutical interest. Chemically restraining the flexible moiety of compounds like TMPIP in the syn-type binding conformation was found to increase activity by over 2 orders of magnitude. Such information is normally only available after extensive synthesis of related compounds and multiple screening approaches.

DNA, morphology and fossils: phylogeny and evolutionary rates of the gastropod genus Littorina

Using data from the direct sequencing of fragments of three mitochondrial genes (12S and 16S ribosomal RNA, and cytochrome-b; total length 1469 b.p.) we have reconstructed a gene phylogeny for all 19 living species of the gastropod genus Littorina. Members of the closely related genera Nodilittorina, Littoraria and Mainwaringia have been used as outgroups, and it appears that Littorina is monophyletic. An earlier morphological phylogeny has been revised, and its topology found to be almost entirely consistent with that from the molecular data. The fossil record is sparse, but likewise consistent. A consensus tree is presented, showing clear resolution of basal and terminal branches, and a central unresolved polychotomy. We have used fossil evidence and geological events to estimate the ages of some clades, and thus to calculate average rates of molecular evolution, which in turn provide approximate dates for all branches of the molecular phylogeny. The central polychotomy may be explained by a burst of rapid speciation in the northwestern Pacific during the Middle Miocene, perhaps driven by climatic fluctuation. Our results support the hypothesis that the two clades of Littorina in the northern Atlantic originated from Pacific ancestors which took part in the Pliocene trans-Arctic migration of marine organisms.

Neutron diffraction reveals the orientation of the headgroup of inositol lipids in model membranes

Neutron diffraction studies show that the inositol ring in the headgroup of phosphatidylinositol extends perpendicular to the membrane surface but that phosphorylation of the 4-position causes the ring to tilt over.

Synthesis and analysis of the enantiomers of calmidazolium, and a 1H NMR demonstration of a chiral interaction with calmodulin

Calmidazolium [R24571, 1-[bis(4-chlorophenyl)methyl]-3-[2-(2,4-dichlorophenyl)-2-[(2,4- dichlorophenyl)methoxy]ethyl]-1H-imidazolium chloride] is a potent calmodulin inhibitor. This paper describes the synthesis and properties of the enantiomers of calmidazolium from the enantiomers of miconazole [1(N)-(2-(2,4-dichlorobenzyloxy)-2-(2,4 dichlorophenyl))-ethyl imidazole], prepared from the racemate by chiral preparative scale high performance liquid chromatography. Overlap between ligand and protein resonances in the aromatic region of the 1H NMR spectrum of the calmidazolium-calmodulin complexes has been obviated by preparation of the protein with all of its nine phenylalanine rings deuterated (Phe-d5 calmodulin). This has been accomplished by the overexpression of calmodulin derived from Trypanosoma brucei rhodiesiense in E. coli in a medium supplemented with ring-deuterated phenylalanine. The kinetics of binding of each enantiomer are slow on the 1H NMR time scale as judged by the behaviour of the H2 resonance of Histidine-107, which is clearly visible under the sample conditions used. The aromatic spectral regions of the protein-bound (+) and (-) enantiomers contrast strikingly, reflecting differences in bound environment and/or conformation.

Correlation between high-field T2-weighted MR imaging and histology of ischemic lesions in gerbil brain

Global forebrain ischemia in the Mongolian gerbil is a common animal model for use in stroke research. We produced lesions of graded severity in gerbil brains (after prescreening by MR imaging) by performing 6-minute bilateral carotid artery occlusions while monitoring pericranial temperature with a temporalis muscle thermocouple probe and maintaining the temperature at 32 degrees C, 36 degrees C, or 40 degrees C. Lesion severity was scored 4 days after occlusion from findings on spin-echo images acquired at 7 T and from histologic scores. Statistically significant correlation was observed between the MR imaging score and brain temperature and between the MR imaging score and the area of the CA region of the hippocampus measured by histology. In addition, because prescreening with MR imaging revealed abnormalities in the hippocampus of some of the animals, and these animals were rejected from the study, the statistical significance of the result could be strengthened.

The conformations of a functional spin-labeled derivative of gastric H/K-ATPase investigated by EPR spectroscopy

A spin-labeled derivative of porcine gastric H/K-ATPase with high ATP hydrolyzing activity (77 mumol of Pi/(mg.h)) has been prepared. Over 65% of initial ATPase activity (115 mumol of Pi/(mg.h)) was preserved after complete reaction of the enzyme with the lysine reactive nitroxide spin-labeled TEMPO isothiocyanate (TITC). In contrast, rapid and complete loss of ATPase activity occurred after reaction of the enzyme with the lysine directed fluorescent probe FITC. Conventional EPR spectra of TITC labeled H/K-ATPase reflected mainly the slow rotational diffusion of the enzyme in the membrane. An upper limit enzyme intramembranous radius of 108 A was calculated on the basis of rotational correlation times estimated from saturation transfer (ST) EPR spectral lineshapes. Conventional EPR spectra exhibited two major components corresponding to at least two populations of strongly constrained spin-labels. Difference spectroscopy revealed that the proportion of these two components changed markedly with temperature. Moreover, the proportion of the components was sensitive to the presence of the activating ionic ligands Mg2+ and ATP, which induce enzyme conformational transitions, and to the reversible inhibitor SCH 28080, which binds to the K+ sensitive form of the enzyme. These findings show that EPR spectroscopy is able to report functionally coupled conformational changes of gastric H/K-ATPase and imply that the spin-labels are attached to lysines within functionally important regions of the enzyme.

Image directed proton spectroscopy of gerbil brain at 7 tesla

Image directed localized 1H NMR spectra were obtained at 7 T (300 MHz) from cubic volumes of less than 40 microL in the gerbil brain. Signals from cerebral metabolites commonly detected in other rodent species were easily assigned, and high resolution spectroscopy (360 MHz) of aqueous brain extracts assisted the tentative identification of partially overlapping resonances from lower concentration compounds like alanine, lysine, gamma-aminobutyrate, valine, leucine and isoleucine. Weak coupling at 7 T was manifest in the resolution of signals from the gamma-CH2 groups of glutamine and glutamate. Down-field of water, signals assigned to purine nucleotides were conspicuous in the extract spectra, but localized spectra acquired routinely in vivo, using selective excitation and gradient crushing (SUBMERGE) for water suppression, exhibited little or no signal from purines. When localized in vivo spectra were acquired without water suppression, however, or using a low power binomial excitation sequence rather than SUBMERGE, a broad signal appeared at the resonant frequency of purine aromatic protons. NMR experiments on the nucleotide adenosine 5'-monophosphate (AMP) in 90% glycerol/10% D2O solution demonstrated that pre-irradiation of the water signal even for less than 100 ms attenuated the nucleotide signal appreciably. This implies that the soft pulses required for selective excitation of water in sequences such as SUBMERGE induce spin-diffusion which eliminates or diminishes the signal from nucleotides in vivo.

A spectroscopic study of the mitochondrial transit peptide of rat malate dehydrogenase

A peptide corresponding to the N-terminal sequence of the rat malate dehydrogenase, comprising the transit sequence and two residues of the mature protein (MLSALARPVGAALR-RSFSTSAQNNAK) has been chemically synthesized, and its structural characteristics investigated by Fourier-transform i.r. (FT-IR), c.d. and 1H-n.m.r. spectroscopy. FT-IR and c.d. spectra of the peptide were recorded in a variety of environments (aqueous solution, trifluoroethanol) and after incorporation into phospholipid bilayers. The peptide was found to be mainly in aperiodic or undefined conformation in aqueous solution. However, in trifluoroethanol a marked increase in alpha-helical content was observed. An increase in alpha-helical content was also observed in negatively charged lipids (dimyristoylphosphatidylglycerol and cardiolipin). However, when reconstituted in a zwitterionic phospholipid (dimyristoylphosphatidylcholine), no alpha-helical structure was observed. N.m.r. spectroscopy was used to characterize the helical structure in greater detail in trifluoroethanol. The 1H-n.m.r. spectrum of the peptide in this solvent was assigned using standard homonuclear two-dimensional methods. The observed patterns of nuclear Overhauser enhancements confirmed the deductions obtained from c.d. and FT-1R spectroscopy concerning the solution conformation, suggesting a region of flexible nascent helix between Ala-4 and Ser-18. This structure is discussed in terms of the possible function of the peptide.

Conformation of the cytoplasmic domain of phospholamban by NMR and CD

Nuclear magnetic resonance (NMR) and circular dichroism (CD) spectroscopy have been used to characterize the conformation of the putative cytoplasmic domain of phospholamban (PLB), an oligomeric membrane-bound protein which regulates the activity of the cardiac sarcoplasmic reticulum Ca(2+)-dependent ATPase. In aqueous solution the 25-residue peptide adopts a number of rapidly interconverting conformers with no secondary structural type obviously predominating. However, in trifluoroethanol (TFE) the conformation, while still highly dynamic, is characterized by a high proportion of helical structures. Evidence for this is provided by alpha CH chemical shifts and low NH chemical shift temperature coefficients, small NH-alpha CH intraresidue scalar coupling constants, a substantial number of distinctive interresidue nuclear Overhauser effects (NOEs) [dNN(i, i + 1), d alpha N(i, i + 3), d alpha beta(i, i + 3) and d alpha N(i, i + 4)] and characteristic CD bands at 190 (positive), 206 (negative) and 222 nm (negative). The helicity is interrupted around Pro-21. The activity of PLB is regulated by phosphorylation at either Ser-16 or Thr-17. CD shows that phosphorylation at Ser-16 by the cAMP-activated protein kinase causes about an 11% decrease in alpha-helical content in TFE.

Purification and secondary structural analysis of tissue inhibitor of metalloproteinases-1

In connective tissue diseases such as rheumatoid arthritis, the matrix metalloproteinases are the primary enzymes involved in tissue degradation. Tissue inhibitor metalloproteinases-1 (TIMP-1) is a specific inhibitor of these enzymes, which is thought to regulate their action in vivo. The structure and function of TIMP-1 may therefore be important as the basis for the rational design of therapeutic agents. This paper describes a simple and effective method for the purification of sufficient quantities of TIMP-1 for spectroscopic studies. Circular dichroism (CD) and Fourier transform infrared (FTIR) spectroscopy have, together, showed TIMP-1 to be mostly in a beta-sheet conformation, with significant amounts of alpha-helix and beta-turn. Two-dimensional nuclear magnetic resonance spectroscopy indicated a correspondingly high proportion of beta-sheet. CD and FTIR have also shown TIMP-1 to have high thermostability.

Polydeoxycholate in human and hamster feces: a major product of cholate metabolism

Fecal bile acid excretion is one of the two major routes by which cholesterol is eliminated from the body, fecal cholesterol being the other. During their enterohepatic circulation, bile acids are secreted into the duodenum, pass down the jejunum and into the ileum where more than 95% is reabsorbed by the gut. Bile acids that escape reabsorption in the small intestine are metabolized by microorganisms in the large intestine. The major routes of metabolism are reported to be deconjugation, dehydroxylation, especially at the 7 alpha-hydroxy position, and dehydrogenation of the hydroxyl moieties. There are also some reports that saponifiable metabolites containing mostly deoxycholic acid form a major component of the bile acids found in human feces. We have identified a novel metabolite of cholic acid, 3 alpha-hydroxy polydeoxycholate, in both human and hamster feces that is the major constituent of these saponifiable metabolites. Furthermore, we have shown in hamsters that the animals that excreted more bile acid were excreting the additional bile acid as polydeoxycholate. As expected, there was a negative correlation between bile acid excretion in the feces and plasma cholesterol concentrations in these animals. We speculate that polydeoxycholate is formed in the lower gut of both humans and hamsters and that, by its formation, bile acid will be sequestered in an insoluble form, thus inhibiting its reabsorption by the gut. This process may help to reduce plasma cholesterol concentrations and coronary heart disease in humans.

The conformational behaviour of phosphatidylinositol in model membranes: 2H-NMR studies

Dimyristoylphosphatidylinositol (DMPI) has been synthesized with the appropriate natural stereochemistry and labelled with deuterium at specific sites in the D-myo-inositol headgroup. 2H-NMR spectroscopy of DMPI in its lamellar phase at a molar ratio of water-to-lipid RW/L of 129 and at 70 degrees C reveals quadrupolar splittings delta v of 3.83 and 2.17 kHz, respectively, for the five axially oriented C-D bonds and the single equatorially oriented C-D bond of the D-myo-inositol headgroup. Between RW/L ratios of 129 and 210 and between 30 degrees C and 80 degrees C the value of the ratio of these splittings delta nu ax/delta nu eq varies significantly (between 1.17 and 4.38). If it is assumed that, at a particular temperature, there is a single preferred orientation of the inositol headgroup, and that motion of the DPMI molecule establishes axial symmetry with respect to the bilayer normal then the ratio of these quadrupolar splittings can be used to impose constraints on that orientation. For example, the data are inconsistent with a situation in which the inositol ring lies parallel to the membrane surface and are difficult to reconcile with an arrangement where the inositol ring lies perpendicular to the surface. Computational modelling identifies four possible 'tilted' orientations, all of which are consistent with the data, and two of these allow good intramolecular hydrogen bonds to be formed. In one there is hydrogen bonding between the inositol C2-OH and the phosphate pro-R oxygen. This is close to the conformation previously identified as being dominant in DMSO solution (Bushby, R.J., Byard, S.J., Hansbro, P.M. and Reid, D.G. (1990) Biochim. Biophys. Acta 1044, 231-236).

An electrophysiological and spectroscopic study of the properties and structure of biological calcium channels. Investigations of a model ion channel

The N- and C-terminally protected peptide N-acetyl-Asp-Phe-Ala-Asn-Arg-Val-Leu-Leu-Ser-Leu-Phe-Thr-Ile-Glu-Met-Leu -Leu-Lys-Met-Leu-NH2, closely based on the sequence of the putative S2 membrane spanning helix of domain II of the dihydropyridine receptor calcium channel of the T-system of skeletal muscle, residues 465-486 (Tanabe et al. (1987) Nature 328, 313-318) has been synthesised. Conductance measurements in planar lipid bilayers show that the peptide is capable of inducing the transmembrane passage of calcium and barium ions, in preference to monovalent cations. No anion conductance is observed. 1H-NMR spectroscopy demonstrates that in an amphilic solvent, methanol, the peptide forms highly stable structures characterised by very slow exchange with solvent of peptide N-H protons. Double-quantum filtered phase-sensitive COSY shows that, on the basis of NH-CH alpha scalar coupling constants, most peptide torsion angles are appropriate to an overall alpha-helical conformation; the presence of some alpha-helix is also supported by CD measurements. Most side-chain connectivities have been identified in a DIPSI-TOCSY experiment. This evidence has been used to construct a low-resolution model of the ion-conducting channel of the muscle T-system dihydropyridine receptor from the sequences of the four homologous putative channel-lining stretches. It is characterised by an association of acidic residues at the putative extra-membranous face of the channel, followed by a predominantly hydrophobic band. The next prominent feature of the model is an ordered array of four acidic residues (glutamates 100, 478, 846 and 1164), followed by four lysines (104, 482, 850 and 1168) which may play a gating role.

Synthesis and evaluation of (+) and (-)-2,2-difluorocitrate as inhibitors of rat-liver ATP-citrate lyase and porcine-heart aconitase

The enantiomers (+) and (-)-2,2-difluorocitrate have been synthesized. Both are good inhibitors of ATP-citrate lyase, showing competitive inhibition against citrate, with Kis = 0.7 microM for (+)-2,2-difluorocitrate and 3.2 microM for (-)-2,2-difluorocitrate. The inhibition patterns with either ATP or CoA as the varied substrate were uncompetitive and mixed, respectively, but with much weaker inhibition constants. Neither isomer undergoes carbon-carbon bond cleavage as a substrate and there is no evidence of irreversible time-dependent inactivation. When ATP-citrate lyase is incubated with CoA and difluorocitrate, the maximal intrinsic ATPase rate is 10% of the citrate-induced rate for the (+)-enantiomer and 2% for the (-)-enantiomer. 19F-NMR studies confirm that only the (+)-enantiomer is chemically processed. The effects of the difluorocitrate enantiomers on the reaction catalysed by aconitase were examined. (-)-2,2-Difluorocitrate is a competitive inhibitor against citrate (Kis = 1.5 microM), whereas the (+)-enantiomer is a relatively poor mixed inhibitor (Ki greater than 300 microM). The (-)-enantiomer irreversibly inactivates aconitase at 1.1 min-1.mM-1 at 25 degrees C and pH 7.4, whereas no irreversible inhibition is seen with the (+)-enantiomer. Therefore, it would be expected that the (+)-enantiomer would slow the rate of acetyl-CoA synthesis in vivo, without inhibiting the citric acid cycle.

Precipitation and 13C-NMR relaxation enhancement measurements of the interactions of bile acids with synthetic cationic bile acid derivatives, and with spin labelled fatty acids

In an investigation of novel potential bile acid sequestrants, the affinities of the sodium salts of the glycine and taurine conjugates of naturally occurring bile acids (cholate, deoxycholate, chenodeoxycholate and lithocholate) for several cationic ammonium bile acid derivatives have been investigated by measurements of the extent to which the derivatives are able to precipitate the bile acids. This is roughly proportional to the lipophilicity of the interacting species. Thus, amino and ammonium derivatives of cholic acid do not precipitate taurocholate or glycocholate to any great extent, whereas ammonium derivatives of deoxycholate and lithocholate are much more effective. To complement the precipitation measurements, high resolution 13C-NMR has been applied to investigate the weaker interactions between the ammonium cholate derivative and glycocholate, glycodeoxycholate and glycochenodeoxycholate. Addition of either of the latter two bile acids to the cationic ammonium compound results in considerable broadening of the 13C resonances of both species, indicating the formation of relatively rigid structures. In addition, we have used T2 relaxation enhancement induced by spin-labelled fatty acids to examine the mechanism of interaction with bile acids of amphiphilic anions, which might compete with bile acids for sites on bile acid sequestrants. Low concentrations of 16-DOXY L-Stearate dramatically broaden the 13C-NMR resonances of deoxycholate carbons 19, 18 and 7 in particular, while 5-DOXY L-Stearate exerts much less specific effects. These results have been incorporated into a snapshot model of bile acid-fatty acid interactions.

Purification of cloned trypanosomal calmodulin and preliminary NMR studies

Cloned trypanosomal calmodulin was expressed in Escherichia coli and purified to homogeneity using hydrophobic interaction chromatography on phenyl-Sepharose. The purified protein was subjected to NMR analysis which allows detailed changes to be observed when, firstly, calcium, and secondly, the drug calmidazolium bind. These spectral changes are the result of conformational changes in the protein and proximity effects due to the drug.