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David J Miller

Publications and source records attributed to David J Miller.

At least 19 recordsLinked to original sources
PubMed2007

Dynamin 2 associates with complexins and is found in the acrosomal region of mammalian sperm.

Previous data showed that complexin I, a SNARE regulatory protein, is localized in and/or around the acrosome and is necessary for the acrosome reaction in sperm. To understand how complexin I regulates the acrosome reaction, we used complexin-GST pulldown assays to identify interacting proteins. We showed that both complexins I and II bound mouse sperm dynamin 2. Dynamin 2 is a 100 kDa GTPase essential to many aspects of endocytosis but its potential role in exocytosis is unknown. Dynamin 2 is expressed in rat testis and widely expressed in other tissues; however, the function of dynamin 2 in germ cells is uncertain. Dynamin 2 protein was detected in mouse testis and was most abundant in or around the developing acrosome of spermatids. In addition, dynamin 2 was co-localized with complexin I in the acrosomal region of mammalian sperm. Its co-localization and interaction with complexin I suggest that dynamin 2 may play a role during acrosome formation and/or acrosomal exocytosis.

Acrosome↗
PubMed2006

Sequence and expression of four coral G protein-coupled receptors distinct from all classifiable members of the rhodopsin family.

A measure of the functional importance of G protein-coupled receptors (GPCRs) as signalling molecules is that over seven hundred have been cloned and identified in the human genome alone. Yet few have been characterized in the lower metazoan phyla, especially in the phylum Cnidaria which is well positioned phylogenetically for tracing the early evolution of GPCRs owing to their possession of the first-evolved nervous systems. We report here the cloning and characterization of four novel rhodopsin-like GPCR cDNAs from the staghorn coral Acropora millepora that share significant similarity with each other but not with the majority of other members of the rhodopsin alpha subfamily. The deduced proteins lack many of the conserved residues and motifs that form the signature of the different groups of alpha rhodopsin receptors. Maximum likelihood phylogenetic analysis likewise implies that the coral receptors do not have a simple or close relationship with any of the major groups within the alpha rhodopsin subfamily. In situ hybridization revealed transcripts in endodermal cells of planula larvae of all ages and in post-settlement polyps. These GPCRs appear to belong to a alpha rhodopsin-like group unique to corals. Comparisons with other cnidarian GPCRs suggest also that GPCRs diverged early in metazoan evolution.

Amino Acid Sequence↗
PubMed2006

Phylogeny: the continuing classificatory conundrum of chaetognaths.

The phylogenetic conundrum posed by the Chaetognatha, a cryptic phylum consisting largely of planktonic predators, is the subject of two short papers in this issue of Current Biology. These analyses go some way towards defining the phylogenetic position of the chaetognaths, which possess features apparently spanning the protostome/deuterostome divide.

Animals↗
PubMed2006

Components of both major axial patterning systems of the Bilateria are differentially expressed along the primary axis of a 'radiate' animal, the anthozoan cnidarian Acropora millepora.

Cnidarians are animals with a single (oral/aboral) overt body axis and with origins that nominally predate bilaterality. To better understand the evolution of axial patterning mechanisms, we characterized genes from the coral, Acropora millepora (Class Anthozoa) that are considered to be unambiguous markers of the bilaterian anterior/posterior and dorsal/ventral axes. Homologs of Otx/otd and Emx/ems, definitive anterior markers across the Bilateria, are expressed at opposite ends of the Acropora larva; otxA-Am initially around the blastopore and later preferentially toward the oral end in the ectoderm, and emx-Am predominantly in putative neurons in the aboral half of the planula larva, in a domain overlapping that of cnox-2Am, a Gsh/ind gene. The Acropora homologs of Pax-3/7, NKX2.1/vnd and Msx/msh are expressed in axially restricted and largely non-overlapping patterns in larval ectoderm. In Acropora, components of both the D/V and A/P patterning systems of bilateral animals are therefore expressed in regionally restricted patterns along the single overt body axis of the planula larva, and two 'anterior' markers are expressed at opposite ends of the axis. Thus, although some specific gene functions appear to be conserved between cnidarians and higher animals, no simple relationship exists between axial patterning systems in the two groups.

Amino Acid Sequence↗
PubMed2006

Designed high affinity Cu2+-binding alpha-helical foldamer.

The design, synthesis, and characterization of a folded high-affinity metal-binding peptide is described. Based on the previously described folded peptide NTH-18, in which an alpha-helix was constrained through two disulfide bonds to a C-terminal extension of noncanonical secondary structure, a peptide (1) was designed to contain two histidine residues in positions 3 and 7. Air oxidation of 1 led to the formation of peptide 2, which contained two intramolecular disulfide bonds. The presence of the two histidines significantly destabilized the alpha-helical structure of 2 when compared to NTH-18. However, CD spectroscopy revealed that the addition of certain transition metal ions allowed the reformation of a stable alpha-helix. CD, NMR, and EPR spectroscopy as well as MALDI-TOF mass spectrometry indicated that 2 bound to Cu2+ to form a 1:1 complex via the imidazoles of the two histidine side chains. A glycine displacement assay revealed a dissociation constant for this complex of 5 nM at pH 8, which is the lowest reported value for a designed Cu2+-binding peptide. This peptide displayed more than 100-fold selectivity for Cu2+ over Zn2+, Ni2+, and Co2+. The 1.05 A crystal structure of the Cu(II)-complex of 2 revealed a square-pyramidal coordination geometry and confirmed that 2 bound to copper in an alpha-helical conformation via its two histidine side chains. The high affinity metal binding of peptide 2 demonstrates that metals can be used for the selective nucleation of alpha-helices.

Copper↗
PubMed2006

Axial patterning and diversification in the cnidaria predate the Hox system.

Across the animal kingdom, Hox genes are organized in clusters whose genomic organization reflects their central roles in patterning along the anterior/posterior (A/P) axis . While a cluster of Hox genes was present in the bilaterian common ancestor, the origins of this system remain unclear (cf. ). With new data for two representatives of the closest extant phylum to the Bilateria, the sea anemone Nematostella and the hydromedusa Eleutheria, we argue here that the Cnidaria predate the evolution of the Hox system. Although Hox-like genes are present in a range of cnidarians, many of these are paralogs and in neither Nematostella nor Eleutheria is an equivalent of the Hox cluster present. With the exception of independently duplicated genes, the cnidarian genes are unlinked and in several cases are flanked by non-Hox genes. Furthermore, the cnidarian genes are expressed in patterns that are inconsistent with the Hox paradigm. We conclude that the Cnidaria/Bilateria split occurred before a definitive Hox system developed. The spectacular variety in morphological and developmental characteristics shown by extant cnidarians demonstrates that there is no obligate link between the Hox system and morphological diversity in the animal kingdom and that a canonical Hox system is not mandatory for axial patterning.

Animals↗
PubMed2006

Gamete interaction: is it species-specific?

Reproductive isolation is pivotal to maintain species separation and it can be achieved through a plethora of mechanisms. In addition, the development of barriers to gamete interaction may drive speciation. Such barriers to interspecific gamete interaction can be prezygotic or postzygotic. Considering the great diversity in animal species, it is easy to assume that regulation of the early steps of fertilization is critical to maintain species identity. One prezygotic mechanism that is often mentioned in the literature is that gamete interaction is limited to gametes of the same species. But do gametes of all animals interact in a species-specific way? Are gamete interactions completely species-specific or perhaps just species-restricted? In species in which species-restrictions have been described, is the interspecies barrier at one major step in the fertilization process or is it a combination of partially restricted steps that together lead to a block in interspecific fertilization? Are the mechanisms used to avoid interspecific crosses different between free-spawning organisms and those with internal fertilization? This review will address these questions, focusing on prezygotic barriers, and will describe what is known about the molecular biology that may account for species-limited gamete recognition and fertilization.

Animals↗
PubMed2006

Measurement of total polycyclic aromatic hydrocarbon concentrations in sediments and toxic units used for estimating risk to benthic invertebrates at manufactured gas plant sites.

The U.S. Environmental Protection Agency's (U.S. EPA) narcosis model requires the measurement of 18 parent and 16 groups of alkyl polycyclic aromatic hydrocarbons (PAHs) (so-called 34 PAHs) in sediments to calculate the number of PAH toxic units (TU) available to benthic organisms. If data for the 34 PAHs are not available, the U.S. EPA proposes estimating the risk by multiplying the TU for 13 parent PAHs by 11.5 (95% confidence interval) based on data from 488 sediments. This estimate is overly conservative for PAHs from pyrogenic manufactured gas plant (MGP) processes based on the analysis of 45 sediments from six sites. Parent PAHs contributed approximately 40% of the total concentrations and TU for MGP sediments. In contrast, parent PAHs from diesel fuel and petroleum crude oil contributed only 2 and 1%, respectively, of the PAH concentrations and TU, compared to approximately 98 to 99% contributed by the alkyl PAHs. Statistical comparison of the TU based on the measured 34 alkyl and parent PAHs and those based on only 13 parent PAHs demonstrated that a factor of 4.2 (rather than 11.5) is sufficient to estimate total TU within a 95% confidence level for MGP sites. Similarly, measurement of parent PAHs is sufficient to accurately estimate the total 34 alkyl and parent PAH concentrations for MGP-impacted sediments.

Animals↗
PubMed2006

Measured partitioning coefficients for parent and alkyl polycyclic aromatic hydrocarbons in 114 historically contaminated sediments: part 1. K(OC) values.

Polycyclic aromatic hydrocarbon (PAH) partitioning coefficients between sediment organic carbon and water (K(OC)) values were determined using 114 historically contaminated and background sediments collected from eight different rural and urban waterways in the northeastern United States. More than 2100 individual K(OC) values were measured in quadruplicate for PAHs ranging from two to six rings, along with the first reported K(OC) values for alkyl PAHs included in the U.S. Environmental Protection Agency's (U.S. EPA) sediment narcosis model for the prediction of PAH toxicity to benthic organisms. Sediment PAH concentrations ranged from 0.2 to 8600 microg/g (U.S. EPA 16 parent PAHs), but no observable trends in K(OC) values with concentration were observed for any of the individual PAHs. Literature K(OC) values that are commonly used for environmental modeling are similar to the lowest measured values for a particular PAH, with actual measured values typically ranging up to two orders of magnitude higher for both background and contaminated sediments. For example, the median log K(OC) values we determined for naphthalene, pyrene, and benzo[a]pyrene were 4.3, 5.8, and 6.7, respectively, compared to typical literature K(OC) values for the same PAHs of 2.9, 4.8, and 5.8, respectively. Our results clearly demonstrate that the common practice of using PAH K(OC) values derived from spiked sediments and modeled values based on n-octanol-water coefficients can greatly overestimate the actual partitioning of PAHs into water from field sediments.

Carbon↗
PubMed2006

Physical therapist examination, evaluation, and intervention for a patient with West Nile virus paralysis.

BACKGROUND AND PURPOSE: The incidence of West Nile virus (WNV) has increased in the United States since 1999. A small percentage of people with WNV develop West Nile neuroinvasive disease (WNND) with encephalitis and flaccid paralysis. The purpose of this report is to describe the physical therapist management and outcomes for a patient with WNND and the therapist's efforts to use an evidence-based practice approach in the management of a patient with this disease. CASE DESCRIPTION: The patient was an active 55-year-old woman in excellent health who became acutely ill with asymmetrical lower-extremity weakness. The physical therapist reviewed the available literature, consulted with medical and physical therapist experts and the patient, and elected to use a poliovirus "period of recovery" approach combining intensive strengthening and monitoring of fatigue. OUTCOMES: The patient progressed from an initial nonambulatory status to ambulation with a single-point cane at week 18 after onset of symptoms. She began to ambulate without an assistive device by week 20. The patient returned to work part-time by week 22 and full-time by week 43. DISCUSSION: These outcomes demonstrate the recovery of a patient with WNND after an intensive strengthening program.

Evidence-Based Medicine↗
PubMed2005

An improved surrogate method for detecting the presence of chaos in gait.

It has been suggested that the intercycle variability present in the time series of biomechanical gait data is of chaotic nature. However, the proper methodology for the correct determination of whether intercycle fluctuations in the data are deterministic chaos or random noise has not been identified. Our goal was to evaluate the pseudoperiodic surrogation (PPS) [Small et al., 2001. Surrogate test for pseudoperiodic time series data. Physical Review Letters 87(18), 188,101-188,104], and the surrogation algorithms of Theiler et al. [1992. Testing for nonlinearity in time series: the method of surrogate data. Physica D 58(1-4), 77-94] and of Theiler and Rapp [1996. Re-examination of the evidence for low-dimensional, nonlinear structure in the human electroencephalogram. Electroencephalography and Clinical Neurophysiology 98, 213-222], to determine which is the more robust procedure for the verification of the presence of chaos in gait time series. The knee angle kinematic time series from six healthy subjects, generated from a 2-min walk, were processed with both algorithms. The Lyapunov exponent (LyE) and the approximate entropy (ApEn) were calculated from the original data and both surrogates. Paired t-tests that compared the LyE and the ApEn values revealed significant differences between both surrogated time series and the original data, indicating the presence of deterministic chaos in the original data. However, the Theiler algorithm affected the intracycle dynamics of the gait time series by changing their overall shape. This resulted in significantly higher LyE and ApEn values for the Theiler-surrogated data when compared with both the original and the PPS-generated data. Thus, the discovery of significant differences was a false positive because it was not based on differences in the intercycle dynamics but rather on the fact that the time series was of a completely different shape. The PPS algorithm, on the other hand, preserved the intracycle dynamics of the original time series, making it more suitable for the investigation of the intercycle dynamics and the identification of the presence of chaos in the gait time series.

Algorithms↗
PubMed2005

Maintenance of ancestral complexity and non-metazoan genes in two basal cnidarians.

Cnidarians are among the simplest extant animals; however EST analyses reveal that they have a remarkably high level of genetic complexity. In this article, we show that the full diversity of metazoan signaling pathways is represented in this phylum, as are antagonists previously known only in chordates. Many of the cnidarian ESTs match genes previously known only in non-animal kingdoms. At least some of these represent ancient genes lost by all bilaterians examined so far, rather than genes gained by recent lateral gene transfer.

Animals↗
PubMed2005

Comparative analysis of prothrombin activators from the venom of Australian elapids.

A key component of the venom of many Australian snakes belonging to the elapid family is a toxin that is structurally and functionally similar to that of the mammalian prothrombinase complex. In mammals, this complex is responsible for the cleavage of prothrombin to thrombin and is composed of factor Xa in association with its cofactors calcium, phospholipids, and factor Va. The snake prothrombin activators have been classified on the basis of their requirement for cofactors for activity. The two major subgroups described in Australian elapid snakes, groups C and D, are differentiated by their requirement for mammalian coagulation factor Va. In this study, we describe the cloning, characterization, and comparative analysis of the factor X- and factor V-like components of the prothrombin activators from the venom glands of snakes possessing either group C or D prothrombin activators. The overall domain arrangement in these proteins was highly conserved between all elapids and with the corresponding mammalian clotting factors. The deduced protein sequence for the factor X-like protease precursor, identified in elapids containing either group C or D prothrombin activators, demonstrated a remarkable degree of relatedness to each other (80%-97%). The factor V-like component of the prothrombin activator, present only in snakes containing group C complexes, also showed a very high degree of homology (96%-98%). Expression of both the factor X- and factor V-like proteins determined by immunoblotting provided an additional means of separating these two groups at the molecular level. The molecular phylogenetic analysis described here represents a new approach for distinguishing group C and D snake prothrombin activators and correlates well with previous classifications.

Amino Acid Sequence↗
PubMed2005

Persistence and biodegradation of monoethanolamine and 2-propanolamine at an abandoned industrial site.

Soil and groundwater samples were collected at the site of a former chemical processing plant in areas impacted by accidental releases of MEA (monoethanolamine) and IPA (2-propanolamine or isopropanolamine). Although their use had ceased ca. 10 years before sample collection, soils collected at contamination sites had MEA concentrations ranging from ca. 400 to 3000 mg/kg and IPA concentrations from ca. 30 to 120 mg/kg. Even though alkanolamines are miscible in water, transport to groundwater was slow, apparently because they are present in soil as bound cations. Only one groundwater sample (near the most highly contaminated soil)from wells directly adjacentto and down-gradient from the contaminated soils had detectable MEA, and none had detectable IPA. However, ammonia was found in the soil samples collected in the MEA-contaminated areas (ca. 500-1400 mg/kg) and the groundwater (80-120 mg/L), as would be consistent with bacterial degradation of MEA to ammonia, followed by transport of ammonia into the groundwater. Counts for bacteria capable of using MEA or IPA as a sole carbon source were ca. 5 x 106 and 1 x 106 (respectively) per gram in uncontaminated site soil, but no such organisms were found in highly contaminated soils. Similarly, bacterial degradation of MEA in slurries of highly contaminated soils was slow, with ca. 8-20 days required for half of the initial concentrations of MEA to be degraded at 20 degrees C and 30-60 days at 10 degrees C. In contrast, bacterial degradation studies using uncontaminated site soils spiked with ca. 1300 mg/L either MEA or IPA showed very rapid degradation of both compounds,with more than 99% degradation occurring in less than 3 days with quantitative conversion to ammonia, followed by slower conversion to nitrite and nitrate. The results obtained in the site soils, the groundwater samples, and from the biodegradation studies demonstrate that MEA and IPA can persist for decades on soil at high (hundreds of mg/kg) concentrations without significant migration into groundwater, despite the fact that they are miscible in water. Since MEA and IPA exist primarily as cations at the pH of site soils, their persistence apparently results from strong binding to soil, as well as inhibition of natural bioremediation in highly contaminated field soils.

Ammonia↗
PubMed2005

Solid-phase microextraction measurement of parent and alkyl polycyclic aromatic hydrocarbons in milliliter sediment pore water samples and determination of K(DOC) values.

The U.S. Environmental Protection Agency (EPA) narcosis model for benthic organisms in polycyclic aromatic hydrocarbon (PAH) contaminated sediments requires the measurement of 18 parent PAHs and 16 groups of alkyl PAHs ("34" PAHs) in pore water with desired detection limits as low as nanograms per liter. Solid-phase microextraction (SPME) with gas chromatographic/mass spectrometric (GC/ MS) analysis can achieve such detection limits in small water samples, which greatly reduces the quantity of sediment pore water that has to be collected, shipped, stored, and prepared for analysis. Four sediments that ranged from urban background levels (50 mg/kg total "34" PAHs) to highly contaminated (10 000 mg/kg total PAHs) were used to develop SPME methodology for the "34" PAH determinations with only 1.5 mL of pore water per analysis. Pore water was obtained by centrifuging the wet sediment, and alum flocculation was used to remove colloids. Quantitative calibration was simplified by adding 15 two- to six-ring perdeuterated PAHs as internal standards to the water calibration standards and the pore water samples. Response factors for SPME followed by GC/MS were measured for 22 alkyl PAHs compared to their parent PAHs and used to calibrate for the 18 groups of alkyl PAHs. Dissolved organic carbon (DOC) ranging from 4 to 27 mg/L had no measurable effect on the freely dissolved concentrations of two- and three-ring PAHs. In contrast, 5-80% of the total dissolved four- to six-ring PAHs were associated with the DOC rather than being freely dissolved, corresponding to DOC/water partitioning coefficients (K(DOC)) with log K(DOC) values ranging from 4.1 (for fluoranthene) to 5.6 (for benzo[ghi]perylene). However, DOC-associated versus freely dissolved PAHs had no significant effect on the total "34" PAH concentrations or the sum of the "toxic units" (calculated bythe EPA protocol), since virtually all (86-99%) of the dissolved PAH concentrations and toxic units were contributed by two- and three-ring PAHs.

Benzopyrenes↗
PubMed2005

Tandem organization of independently duplicated homeobox genes in the basal cnidarian Acropora millepora.

A number of examples of independently duplicated regulatory genes have been identified in cnidarians, but the extent of this phenomenon and organization of these duplicated genes are unknown. Here we describe the identification of three pairs of independently duplicated homeobox genes in the anthozoan cnidarian, Acropora millepora. In each case, the pairs of paralogous genes are tightly linked, but the extent of sequence divergence implies that these do not reflect recent duplication events. The phenomenon is likely to be more general, as the examples reported here represent most of the limited number of Acropora homeobox genes for which genomic data are yet available.

Amino Acid Sequence↗
PubMed2005

Animal evolution: the enigmatic phylum placozoa revisited.

A recent report of high levels of genetic variation between strains of Trichoplax adhaerens challenges the traditional view that the phylum Placozoa comprises only one species. At the morphological level, placozoans are amongst the simplest extant animals, but molecular evidence suggests that they may have more complex origins.

Animals↗