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  • 1
    Electronic Resource
    Electronic Resource
    TROUBLESHOOTING MOLECULAR PHYLOGENETIC ANALYSES (2002)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Ecology, Evolution, and Systematics 33 (2002), S. 49-72 
    Details
    ISSN: 0066-4162
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology
    Notes: Abstract The number, size, and scope of phylogenetic analyses using molecular data has increased steadily in recent years. This has simultaneously led to a dramatic improvement in our understanding of phylogenetic relationships and a better appreciation for an array of methodological problems that continue to hinder progress in phylogenetic studies of certain data sets and/or particular parts of the tree of life. This review focuses on several persistent problems, including rooting, conflict among data sets, weak support in trees, strong but evidently incorrect support, and the computational issues arising when methods are applied to the large data sets that are becoming increasingly commonplace. We frame each of these issues as a specific problem to be overcome, review the relevant theoretical and empirical literature, and suggest solutions, or at least strategies, for further investigation of the issues involved.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1146/annurev.ecolsys.33.010802.150509
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  • 2
    Electronic Resource
    Electronic Resource
    A versatile and quantitative computer-assisted photoelectronic technique used for the analysis of ciliary beat cycles (1985)
    New York, NY : Wiley-Blackwell
    Cell Motility and the Cytoskeleton 5 (1985), S. 267-292 
    Details
    ISSN: 0886-1544
    Keywords: mammalian cilia ; respiratory tract ; mucociliary clearance ; laterofrontal cirri ; Mytilus edulis ; beat cycle ; computer analysis ; Life and Medical Sciences ; Cell & Developmental Biology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Medicine
    Notes: The beat cycles of rabbit tracheal cilia in culture and Mytilus laterofrontal cirri were recorded using a phototransistor, transillumination, video, and phase-contrast microscopy. The photoelectronic signal and video image of the ciliary activity were simultaneously recorded as a composite image. The photoelectronic signal was converted into a digital signal by a data acquisition system for further computer processing.By the selection of a small detector area and accurate detector alignment, a simple, repetitive photoelectronic signal representing ciliary activity was obtained. This signal records the ciliary beat frequency and demonstrates the triphasic nature of the beat cycle. The photoelectronic signal can be precisely correlated with the ciliary activity by analysis of the composite video recordings to provide the duration of the effective, recovery, and rest phases of the beat cycle. The videophotoelectronic signal correlations were verified by high-speed cinematography. High-speed films of ciliary activity were digitized, and the image density of selected pixels was analyzed by computer with respect to time and ciliary motion.These studies indicate that duration of the phages of the beat cycle are differentially reduced with increased beat frequency; the effective phase duration was quickly reduced to a minimum. This was followed by the reduction of the duration of the recovery phase to a minimum. The rest phase continues to be reduced without reaching a minimum, over the range of beat frequencies observed. These results suggest that ciliary beat frequency may be regulated either by modifying the rates of dynein-microtubule interactions or the rate of transition from one beat phase to the next.
    Additional Material: 12 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/cm.970050402
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  • 3
    Electronic Resource
    Electronic Resource
    The effects of serum immunoglobulins on the metachronal coordination of the lateral cilia of Mytilus edulis (1984)
    New York, NY : Wiley-Blackwell
    Cell Motility and the Cytoskeleton 4 (1984), S. 103-119 
    Details
    ISSN: 0886-1544
    Keywords: cilia ; metachrony ; serum immunoglobulins ; IgM ; Mytilus edulis ; cystic fibrosis ; Life and Medical Sciences ; Cell & Developmental Biology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Medicine
    Notes: Human IgM and a bovine, IgM-enriched serum fraction isolated from normal adult serum at concentrations of 0.25-1 mg/ml protein induced a pronounced increase in the metachronal wavelength of the lateral (L) cilia of the sea mussel Mytilus edulis without altering their beat frequency. This change in activity was indistinguishable from that induced by 50% adult human or bovine serum. At protein concentrations ranging from 1-9 mg/ml, human IgG or a bovine, IgG-enriched serum fraction had no or little effect on the activity of the L cilia. Similarly, neither monomeric (8S) human IgM (0.25 mg/ml) nor monospecific pentameric IgM (1 mg/ml) isolated from Waldenström's macroglobulinemia patients altered the metachrony of the L cilia. Indirect immunofluorescence demonstrated that both bovine and human IgM became attached almost exclusively to the L cilia, while very little bovine or human IgG was found to associate with these cilia.The results of this study suggest that serum IgM specifically binds to the L cilia of Mytilus in an antigen-antibody manner and agglutinates adjacent cilia into blocks or bundles, thereby increasing the coupling between cilia. As a result, the wavelength of the metachronal coordination is increased. The origin of these ciliary antibodies and their significance to ciliary bioassays used to monitor serum for the detection of cystic fibrosis are discussed.
    Additional Material: 4 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/cm.970040204
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  • 4
    Electronic Resource
    Electronic Resource
    Multiple effects of ethanol and 5-hydroxytryptamine on the gill cilia of mytilus edulis (1982)
    New York, NY : Wiley-Blackwell
    Cell Motility and the Cytoskeleton 2 (1982), S. 215-224 
    Details
    ISSN: 0886-1544
    Keywords: Mytilus edulis ; 5-hydroxytryptamine ; cilia ; ethanol ; axoneme ; calcium ; filter feeding ; Life and Medical Sciences ; Cell & Developmental Biology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Medicine
    Notes: The lateral (L) cilia on an isolated filament from the gill of Mytilus edulis remain arrested at the end of their recovery stroke (hands up) when perfused with artificial sea water (ASW). The laterofrontal (LF) cilia continue to be active. The addition of 10% ethanol (ETOH) to the ASW perfusate arrests the LF cilia in a hands-up posture; the L cilia remain undisturbed. By contrast, 10-6 M 5-hydroxytryptamine (5HT) in ASW activates the L cilia and arrests the LF cilia at the end of their effective stroke (hands down). Continued perfusion with 10% ETOH (v/v) in ASW/5HT restores activity to the LF cilia but arrests the L cilia (hands up). These effects are reversible and independent of external Ca2+.Following the detergent extraction of the filament, all gill cilia are inactive. The addition of 0.2 mM ATP in the presence of low Ca2+ (〈 10-7 M) reactivates all model cilia. Under these conditions, 5HT can no longer inhibit the activity of LF cilia and is not required for the activation of the L cilia. This suggests that 5HT acts at a membrane level. An increase in free Ca2+ (〉 10-6 M) arrests the L cilia hands up; the LF cilia remain active. Further Ca2+ increase (〉 10-3 M) induces hands-up arrest of the LF cilia, confirming that the Ca2+ threshold of the two ciliary types is different by several orders of magnitude.The addition of 10% ETOH in low Ca2+ to demembranated reactivated cilia arrests the L cilia hands up while the LF cilia continue to beat. Ten percent ETOH appears to interact with the axoneme, mimicking the effect of high Ca2+ and with the membrane to increase Ca2+ permeability and possibly to inactivate 5HT receptors. These results are discussed in terms of axonemal switching mechanisms and the physiological control of filter feeding in the lamellibranch gill.
    Additional Material: 4 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/cm.970020303
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  • 5
    Electronic Resource
    Electronic Resource
    The antagonistic effects of 5-hydroxytryptamine and methylxanthine on the gill cilia of mytilus edulis (1985)
    New York, NY : Wiley-Blackwell
    Cell Motility and the Cytoskeleton 5 (1985), S. 293-309 
    Details
    ISSN: 0886-1544
    Keywords: Mytilus edulis ; 5-hydroxytryptamine ; lateral cilia ; laterofrontal cirri ; beat frequency ; methylxanthine ; filter-feeding ; Life and Medical Sciences ; Cell & Developmental Biology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Medicine
    Notes: The laterofrontal (LF) cirri on isolated gill filaments of Mytilus edulis, prepared in natural seawater, are active and initially beat with an average frequency of about 8 Hz (with a range of 6-14 Hz). However, the lateral (L) cilia on these filaments are arrested in a position at the end of their recovery stroke. Perfusion of the filament with artificial seawater (ASW), with or without 1% ethanol, has little or no biological effect on the activity of the LF cirri, although a transitory decrease in frequency often accompanies the perfusion process. The L cilia remain arrested during perfusion with ASW. The exposure of the gill to low levels of 5-hydroxytryptamine (5HT) (10-8 〈 5HT 〈 10-7 M) has no effect on the activity of the LF cirri but stimulates the L cilia to beat. Exposure to higher concentrations of 5HT (〉 10-7 M) elevates the beat frequency of the L cilia and simultaneously inhibits the activity of the LF cirri, leading to their arrest in a position at the end of the effective stroke. This arrest of the LF cirri occurs as the L cilia attain a 5HT-induced beat frequency between 12 to 14 Hz. The influence of 5HT on the L cilia and the LF cirri can be reversibly mimicked or enhanced by the phosphodiesterase inhibitor 3-isobutyl-1-methylxanthine (IBMX). A concentration of 0.5 mM IBMX mimics low 5HT concentrations (about 10-7 M) by stimulating the L cilia to beat without affecting the beat frequency of the LF cirri. A combimation of 10-7 M 5HT and 0.5 mM IBMX in ASW mimics high (〉 10-6 M) 5HT concentrations by arresting the LF cirri and increasing the beat frequency of the L cilia. Under these conditions, the threshold of the LF cirri arrest response is again found to occur as the L cilia attain a beat frequency of 12 - 14Hz. These results suggest that the mechanisms of LF cirri arrest and L cilia activation are mediated by 5HT -induced changes in intracellular cyclic AMP levels.
    Additional Material: 6 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/cm.970050403
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  • 6
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    Age and rate of diversification of the Hawaiian silversword alliance (Compositae) (1998)
    National Academy of Sciences
    Details
    Publication Date: 1998-08-04
    Description: Comparisons between insular and continental radiations have been hindered by a lack of reliable estimates of absolute diversification rates in island lineages. We took advantage of rate-constant rDNA sequence evolution and an “external” calibration using paleoclimatic and fossil data to determine the maximum age and minimum diversification rate of the Hawaiian silversword alliance (Compositae), a textbook example of insular adaptive radiation in plants. Our maximum-age estimate of 5.2 ± 0.8 million years ago for the most recent common ancestor of the silversword alliance is much younger than ages calculated by other means for the Hawaiian drosophilids, lobelioids, and honeycreepers and falls approximately within the history of the modern high islands (≤5.1 ± 0.2 million years ago). By using a statistically efficient estimator that reduces error variance by incorporating clock-based estimates of divergence times, a minimum diversification rate for the silversword alliance was estimated to be 0.56 ± 0.17 species per million years. This exceeds average rates of more ancient continental radiations and is comparable to peak rates in taxa with sufficiently rich fossil records that changes in diversification rate can be reconstructed.
    Print ISSN: 0027-8424
    Electronic ISSN: 1091-6490
    Topics: Biology , Medicine , Natural Sciences in General
    Published by National Academy of Sciences
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  • 7
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    On the dynamical structure of calcium oscillations (2017)
    National Academy of Sciences
    Details
    Publication Date: 2017-02-01
    Description: Oscillations in the concentration of free cytosolic Ca2+ are an important and ubiquitous control mechanism in many cell types. It is thus correspondingly important to understand the mechanisms that underlie the control of these oscillations and how their period is determined. We show that Class I Ca2+ oscillations (i.e., oscillations that can occur at a constant concentration of inositol trisphosphate) have a common dynamical structure, irrespective of the oscillation period. This commonality allows the construction of a simple canonical model that incorporates this underlying dynamical behavior. Predictions from the model are tested, and confirmed, in three different cell types, with oscillation periods ranging over an order of magnitude. The model also predicts that Ca2+ oscillation period can be controlled by modulation of the rate of activation by Ca2+ of the inositol trisphosphate receptor. Preliminary experimental evidence consistent with this hypothesis is presented. Our canonical model has a structure similar to, but not identical to, the classic FitzHugh–Nagumo model. The characterization of variables by speed of evolution, as either fast or slow variables, changes over the course of a typical oscillation, leading to a model without globally defined fast and slow variables.
    Print ISSN: 0027-8424
    Electronic ISSN: 1091-6490
    Topics: Biology , Medicine , Natural Sciences in General
    Published by National Academy of Sciences
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  • 8
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    Extensive gene tree discordance and hemiplasy shaped the genomes of North American columnar cacti (2017)
    National Academy of Sciences
    Details
    Publication Date: 2017-10-23
    Description: Few clades of plants have proven as difficult to classify as cacti. One explanation may be an unusually high level of convergent and parallel evolution (homoplasy). To evaluate support for this phylogenetic hypothesis at the molecular level, we sequenced the genomes of four cacti in the especially problematic tribe Pachycereeae, which contains most of the large columnar cacti of Mexico and adjacent areas, including the iconic saguaro cactus (Carnegiea gigantea) of the Sonoran Desert. We assembled a high-coverage draft genome for saguaro and lower coverage genomes for three other genera of tribe Pachycereeae (Pachycereus,Lophocereus, andStenocereus) and a more distant outgroup cactus,Pereskia. We used these to construct 4,436 orthologous gene alignments. Species tree inference consistently returned the same phylogeny, but gene tree discordance was high: 37% of gene trees having at least 90% bootstrap support conflicted with the species tree. Evidently, discordance is a product of long generation times and moderately large effective population sizes, leading to extensive incomplete lineage sorting (ILS). In the best supported gene trees, 58% of apparent homoplasy at amino sites in the species tree is due to gene tree-species tree discordance rather than parallel substitutions in the gene trees themselves, a phenomenon termed “hemiplasy.” The high rate of genomic hemiplasy may contribute to apparent parallelisms in phenotypic traits, which could confound understanding of species relationships and character evolution in cacti.
    Print ISSN: 0027-8424
    Electronic ISSN: 1091-6490
    Topics: Biology , Medicine , Natural Sciences in General
    Published by National Academy of Sciences
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  • 9
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    Genomes of 13 domesticated and wild rice relatives highlight genetic conservation, turnover and innovation across the genus Oryza (2018)
    Springer Nature
    Details
    Publication Date: 2018-01-22
    Print ISSN: 1061-4036
    Electronic ISSN: 1546-1718
    Topics: Biology , Medicine
    Published by Springer Nature
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  • 10
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    CD28 and ITK signals regulate autoreactive T cell trafficking (2013)
    Springer Nature
    Details
    Publication Date: 2013-11-24
    Print ISSN: 1078-8956
    Electronic ISSN: 1546-170X
    Topics: Biology , Medicine
    Published by Springer Nature
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