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PubMed2026

Can't see the forest for the trees: The influence of marker type on inferred phylogenetic relationships in a cosmopolitan bat genus.

Fine-resolution information on species relationships and biological diversity is critically needed to guide conservation efforts amidst rapid environmental changes. Systematics, which forms the foundation of this knowledge, has been revolutionized by phylogenomics, utilizing genome-scale datasets. However, the use of diverse marker types, non-comparable taxon sampling, and outgroup selection can lead to conflicting phylogenetic hypotheses. These inconsistencies complicate study comparisons and hinder our ability to assess marker-specific impacts on phylogenetic resolution. The phylogenetic reconstruction of the bat genus Myotis, encompassing over 140 species and characterized by a rapid radiation in the last 20 million years, has been particularly influenced by these challenges. Achieving phylogenetic resolution in Myotis is particularly complex due to subtle interspecific differences in both morphological and molecular traits. Mitochondrial and nuclear markers often produce discordant trees, influenced by hybridization, introgression, and methodological variations. In this study, we employed a consistent taxonomic sample set of 44 Myotis taxa to evaluate the impact of five different genetic marker types on phylogenetic reconstruction. We observed significant discordance between topologies derived from conserved nuclear and mitochondrial markers and found that transposable elements were inadequate for resolving relationships across the entire genus. Our results also clarify the placement of previously problematic taxa within the genus. These findings emphasize the importance of aligning genetic marker choice with specific phylogenetic questions and highlight the influence of taxonomic and methodological variation on phylogenomic outcomes. This work provides a framework for improving phylogenetic inference in rapidly radiating groups and enhances our understanding of evolutionary history in Myotis.

Animals↗
PubMed2002

Molecular imaging of gene expression and protein function in vivo with PET and SPECT.

Molecular imaging is broadly defined as the characterization and measurement of biological processes in living animals, model systems, and humans at the cellular and molecular level using remote imaging detectors. One underlying premise of molecular imaging is that this emerging field is not defined by the imaging technologies that underpin acquisition of the final image per se, but rather is driven by the underlying biological questions. In practice, the choice of imaging modality and probe is usually reduced to choosing between high spatial resolution and high sensitivity to address a given biological system. Positron emission tomography (PET) and single-photon emission computed tomography (SPECT) inherently use image-enhancing agents (radiopharmaceuticals) that are synthesized at sufficiently high specific activity to enable use of tracer concentrations of the compound (picomolar to nanomolar) for detecting molecular signals while providing the desired levels of image contrast. The tracer technologies strategically provide high sensitivity for imaging small-capacity molecular systems in vivo (receptors, enzymes, transporters) at a cost of lower spatial resolution than other technologies. We review several significant PET and SPECT advances in imaging receptors (somatostatin receptor subtypes, neurotensin receptor subtypes, alpha(v)beta(3) integrin), enzymes (hexokinase, thymidine kinase), transporters (MDR1 P-glycoprotein, sodium-iodide symporter), and permeation peptides (human immunodeficiency virus type 1 (HIV-1) Tat conjugates), as well as innovative reporter gene constructs (herpes simplex virus 1 thymidine kinase, somatostatin receptor subtype 2, cytosine deaminase) for imaging gene promoter activation and repression, signal transduction pathways, and protein-protein interactions in vivo.

ATP Binding Cassette Transporter, Subfamily B↗
PubMed2003

Fitting of one ARMA model to multiple trials increases the time resolution of instantaneous coherence.

This study presents a least mean squares (LMS) algorithm for the ensemble modeling of a multivariate ARMA process. Generally, an LMS algorithm makes possible the tracking of parameters for nonstationary time series. Our estimation incorporates multiple process observations that improve the accuracy of the parameter estimation. As a consequence, the estimation sequences come close to the true model parameters with a fast adaptation speed. This advantage also holds true of spectral quantities (e.g., the momentary coherence), which are derived from the model parameters. Thus the extension of the ARMA fitting from one to multiple trajectories allows the investigation of nonstationary biological signals with an increased time resolution. The applicability of the algorithm is demonstrated for event-related EEG coherence analysis of the Sternberg task. The changing interaction between posterior association cortex and anterior brain area was shown for verbal and nonverbal stimuli by means of the time-variant theta coherence.

Electroencephalography↗
PubMed2005

Research strategies for safety evaluation of nanomaterials, Part III: nanoscale technologies for assessing risk and improving public health.

Risk assessment in the environmental health sciences focuses on understanding the nature of environmental exposures and the potential harm posed by those exposures which in turn is determined by the perturbation of biological pathways and the individual's susceptibility to damage. While there are extensive research efforts ongoing in these areas, progress in each is currently slowed by technological limitations including comprehensive assessment of multiple exposures in real time and dynamic assessment of biological response with high temporal and quantitative resolution. This Forum article discusses recent technological innovations capitalizing on the emergent properties of nanoscale materials and their potential adaptation to improving individual exposure assessment, determination of biological response, and environmental remediation. The ultimate goal is to raise the environmental health science community's awareness of these possibilities and encourage the development of improved strategies for assessing risk and improving public health.

Biomedical Research↗
PubMed1996

Quantitative analysis of the transcription factor AP2 binding to DNA by atomic force microscopy.

Atomic force microscopy (AFM) allows to study the molecular structure of biological macromolecules with nm to A resolutions without crystallization. We show here the applicability of AFM in the quantitative analysis of the molecular mechanisms of DNA/protein interaction: (i) Protein-binding sites can be mapped over a few kilobases of target DNA. (ii) Multimerization state of DNA-binding proteins can be determined simply by measuring the sizes of proteins bound to the DNA. These features are significant advantages over the capabilities provided by conventional techniques in biochemistry and molecular and structural biology.

Animals↗
PubMed1997

Atomic force microscope imaging of DNA and DNA repair proteins: applications in radiobiological research.

By using the atomic force microscope (AFM), three-dimensional structures of biological specimens may be imaged at nanometer resolution. Furthermore, samples can be imaged in air or in fluid environments. The tapping mode of AFM operation for imaging has offered a significant advance in visualizing soft biological structures, such as DNA, proteins, and membranes. Here, we review the principles underlying the application of this instrument to radiation biological investigations. We focus on examples of proteins involved in the processes of repair of damaged DNA, including poly(ADP-ribose) polymerase, Ku protein, and DNA protein kinase. Novel observations on the character of DNA damage and repair have been addressed by direct visualization of DNA and protein-DNA interactions, such as the observation that the Ku protein is capable of physically joining DNA fragments in vitro. The AFM offers a powerful tool for investigating biologically important molecular interactions that are relevant to DNA damage and repair processes.

Air↗
PubMed1992

Freeze-substitution of chemically stabilized samples for biological field emission scanning electron microscopy.

The high resolution imaging capabilities of modern field emission scanning electron microscopes require adequately improved tissue preparation procedures to prevent the collapse of macromolecular structures and the extraction of molecules. A routine cryo-stabilization technique is described which utilizes chemical crosslinking and cryo-dehydration for mechanical and chemical stabilization of protein and lipid structures and increase of electrical conductivity of the sample. Thiocarbohydrazide (TCH) serves as a general mordant for osmium tetroxide crosslinking. However, extensive washing after all impregnation steps is necessary to dissolve unspecific osmium black precipitations at the sample surface. Collagen I aggregates showed increased stability against collapse after TCH osmification alone, whereas pulmonary surfactant liposomes require additional freeze-substitution in methanol and Freon 113 for stabilization during critical point drying. Environmental scanning electron microscopy (at water vapor pressures of 5-10 torr within the specimen chamber) was used to control, in the wet phase, the stabilization procedure at the level of chemical crosslinkage. It could be confirmed that tannic acid, often used to stabilize lipids, leads to artificial rearrangement of bilayered liposomes into compact presumable multilayered bodies, whereas the TCH osmification preserved liposome structures and their aggregates. The increase of electrical conductivity of sliced tissue was demonstrated on kidney. Support technologies for the cryo-stabilization procedures are described in detail, as well as simple routines for first stabilization trials with new samples. On pulmonary tissue, the excellent preservation of alveolar shape and fine structures of intermediate forms of surfactant are described.

Animals↗
PubMed2005

Vibrational Dynamics of Biological Molecules: Multi-quantum Contributions.

High-resolution X-ray measurements near a nuclear resonance reveal the complete vibrational spectrum of the probe nucleus. Because of this, nuclear resonance vibrational spectroscopy (NRVS) is a uniquely quantitative probe of the vibrational dynamics of reactive iron sites in proteins and other complex molecules. Our measurements of vibrational fundamentals have revealed both frequencies and amplitudes of (57)Fe vibrations in proteins and model compounds. Information on the direction of Fe motion has also been obtained from measurements on oriented single crystals, and provides an essential test of normal mode predictions. Here, we report the observation of weaker two-quantum vibrational excitations (overtones and combinations) for compounds that mimic the active site of heme proteins. The predicted intensities depend strongly on the direction of Fe motion. We compare the observed features with predictions based on the observed fundamentals, using information on the direction of Fe motion obtained either from DFT predictions or from single crystal measurements. Two-quantum excitations may become a useful tool to identify the directions of the Fe oscillations when single crystals are not available.

Journal Article↗
PubMed1996

High-resolution diffusion and relaxation edited one- and two-dimensional 1H NMR spectroscopy of biological fluids.

A new approach to the characterization of biomolecules in whole biological fluids is presented based on simplification of 1H NMR spectra by utilizing differences in molecular diffusion coefficients alone and combinations of relaxation and diffusion parameters. New NMR pulse sequences incorporating both spectral editing features together with solvent water resonance elimination are presented. The methods are exemplified using whole human blood plasma, and it is shown that it is possible to obtain NMR spectra of the slowly diffusing species (generally large molecules) by diffusion editing, the slowly relaxing species (generally small molecules) by spin relaxation editing, or spectra showing any range of molecular mobility using a combination of the two methods. The diffusion-based editing methods are also applicable to the selection of resonances in two-dimensional NMR spectroscopy of biofluids, and we show this for the first time by the production of 1H-1H diffusion-edited TOCSY spectra of human blood plasma where the resonance intensities are weighted according to the molecular diffusion coefficient. In this case, by measuring a diffusion-edited 1H-1H TOCSY NMR spectrum of plasma, it is possible to obtain signals from only the macromolecular components, and this may be of benefit in the analysis of blood lipoproteins. In complex biofluids, the combination of diffusion and relaxation editing brings about considerable spectral simplification leading to an easier resonance assignment process. We also demonstrate the production of 1H NMR spectra with intensities corresponding to diffusion coefficient rather than number of protons, and this opens up new possibilities for pattern recognition classification of samples based on altered molecular mobility features of biofluid components.

Blood↗
PubMed1989

High-resolution low-temperature scanning electron microscopy for observing intracellular structures of quick frozen biological specimens.

Intracellular structures of rapidly frozen biological tissues were observed in 3-D under a low-temperature scanning electron microscope using a newly developed side-entry type cryo-holder. The present low-temperature SEM is simple, easy to operate and effective for observing biological materials at high magnification. Biological tissues (the pancreas, small intestine, brown adipose tissue and Harderian gland) freshly removed from the mouse were immediately frozen in liquid propane cooled with liquid nitrogen, and their surfaces were manually fractured using a precooled razor blade in liquid nitrogen before introducing the cryo-holder into the SEM. When intracellular structures were revealed after appropriate sublimation, the specimens were coated with gold using a metal evaporator fitted to the side of the microscope column at one of the specimen chamber ports. The cryo-holder was connected to a copper braid coming from a liquid nitrogen reservoir to maintain a low temperature. Using this method, intracellular structures such as the mitochondria and endoplasmic reticulum were demonstrated at high magnifications. Ribosomal granules were discerned on the rough endoplasmic reticulum of the pancreatic acinar cells. Granular substances, presumably elementary particles, were also recognized on the mitochondrial cristae of the brown adipose tissue. The method was particularly effective for studying the 3-D configuration of lipid droplets which had been difficult to preserve by chemical fixation.

Adipose Tissue, Brown↗
PubMed2003

Compact, broad-bandwidth fiber laser for sub-2-microm axial resolution optical coherence tomography in the 1300-nm wavelength region.

A novel, compact, user friendly fiber laser with a broad emission bandwidth (MenloSystems, lambdac = 1375 nm, deltalambda = 470 nm, Pout = 4 mW) was used to achieve unprecedented sub-2-microm axial resolution optical coherence tomography (OCT) in nontransparent biological tissue in the 1300-nm wavelength region. Fresh human skin and arterial biopsies were imaged ex vivo with approximately 1.4-microm axial and approximately 3-microm lateral resolution and 95-dB sensitivity, demonstrating the great potential for clinical OCT applications of this stable, low-cost, and turn-on-key fiber laser.

Arteries↗
PubMed1980

[High resolution proton magnetic resonance study of a series of 9-substituted acridines: correlation with biological activities].

250 MHz 1H N.M.R. spectra of a set of 9-substituted derivatives of acridine as solutes in DMSO-d6 were studied. Because of ABCD coupling figures, magnetic parameters were determined by means of simulated spectra. Semi-empirical correlations were proposed for chemical shifts. Moreover, pi distribution in the heterocycle was investigated. Results are discussed in relation to some weak biological properties of the acridine drugs.

Acridines↗
PubMed2006

Refraction-angle resolution of diffraction enhanced imaging.

As a new method, x-ray diffraction enhanced imaging (DEI) has extremely high sensitivity for weakly absorbing low-Z samples in medical and biological fields. Conventional performance parameters, such as spatial resolution and low-contrast resolution, are not enough to describe the characteristics of a DEI system. This paper focuses on refraction-angle resolution which describes the ability of a DEI system to differentiate the x-rays refracted by the sample. The analysis of refraction-angle resolution is composed of two parts: the analysis of the single DEI image measured in a certain position of the rocking curve and the analysis of the refraction-angle image calculated by extraction methods. A 2D computer simulation experiment is performed to prove the results of the analyses. The limitations and conclusions of refraction-angle resolution are described in the end.

Algorithms↗
PubMedDate not supplied

Low-resolution density maps from atomic models: how stepping "back" can be a step "forward".

Atomic-resolution structures have had a tremendous impact on modern biological science. Much useful information also has been gleaned by merging and correlating atomic-resolution structural details with lower-resolution (15-40 A), three-dimensional (3D) reconstructions computed from images recorded with cryo-transmission electron microscopy (cryoTEM) procedures. One way to merge these structures involves reducing the resolution of an atomic model to a level comparable to a cryoTEM reconstruction. A low-resolution density map can be derived from an atomic-resolution structure by retrieving a set of atomic coordinates editing the coordinate file, computing structure factors from the model coordinates, and computing the inverse Fourier transform of the structure factors. This method is a useful tool for structural studies primarily in combination with 3D cryoTEM reconstructions. It has been used to assess the quality of 3D reconstructions, to determine corrections for the phase-contrast transfer function of the transmission electron microscope, to calibrate the dimensions and handedness of 3D reconstructions, to produce difference maps, to model features in macromolecules or macromolecular complexes, and to generate models to initiate model-based determination of particle orientation and origin parameters for 3D reconstruction.

Algorithms↗
PubMed1996

Striving for atomic resolution in biomolecular topography: the scanning force microscope (SFM).

The invention in 1986 of scanning force microscopy (SFM) provided a new and powerful tool for the investigation of biological structures. SFM yields a three-dimensional view at nanometer resolution of the surface topography associated with biological objects. The potential for imaging either macromolecules or biomolecules and cells under native (physiological) conditions is currently being exploited to obtain functional information at the molecular level. In addition, the forces involved in individual bimolecular interactions are being assessed under static and dynamic conditions. In this report we focus on the imaging capability of the SFM. The rather broad spectrum of applications represented is intended to orient the prospective user of biological SFM.

Animals↗
PubMed2001

Development of an ICP-HRIDMS method for accurate determination of traces of silicon in biological and clinical samples.

An inductively coupled plasma-high resolution isotope dilution mass spectrometric (ICP-HRIDMS) method in combination with a microwave-assisted decomposition technique has been developed for the determination of traces of silicon in biological and clinical samples. A 30Si-enriched spike solution was used for the isotope dilution step. Decomposition of the samples was achieved by use either of HNO3 or a mixture of HNO3 and HF. By application of both methods of digestion to the same sample it was possible to differentiate between a poorly soluble silicate fraction and an HNO3-soluble silicon species. Traces of silicon were determined in different reference materials, which are not certified for this element, and in other biological and clinical samples. A concentration range of 1-600 microgram g(-1) was covered by the different samples. For homogeneous samples relative standard deviations of 2-4% were obtained. The detection limit was strongly affected by the blank. In this connection purification of water, used in the analytical procedure, was especially critical. The blank contribution of the ICP-MS instrument could be minimized by applying a nebulizer and a spray chamber made of PFA, a sapphire injection tube, and a silicon nitride torch. Under these conditions detection limits of 0.15 microgram g(-1) and 0.2 microgram g(-1) were obtained for the HNO3 and HNO3-HF digestion methods, respectively, when a sample weight of 0.5 g was used. With regard to expected silicon content this enables determination in almost all biological and clinical samples. The ICP-HRIDMS results were compared with those recently obtained in an interlaboratory study. This isotope-dilution method is an potential option for certification of silicon in reference materials, a method for which is still required.

Animals↗
PubMed1988

[Skeletal scintigraphy in hemangioma of the bones].

The results of scintigraphic investigations of the skeleton of 76 bone hemangioma patients were analyzed to study the informative value of this type of investigation and to determine the efficacy of its use during establishing diagnosis and dynamic observation. The probability of detection of bone hemangiomas using scintigraphy of the skeleton with 99m Tc labeled osteotropic agents was shown to be in direct relation to the biological activity of hemangioma, its site and resolution of radiodiagnostic apparatus. The utilization of scintigraphy of the skeleton in addition to x-ray investigation permits clarification of the nature of lesion (benign or malignant), the biological activity of hemangiomas, control of the time course of a pathological process and efficacy of therapy of biologically active hemangiomas.

Bone Neoplasms↗
PubMed1990

Chiral separation and determination of propranolol enantiomers in rat or mouse blood and tissue by column switching high performance liquid chromatography with ovomucoid bonded stationary phase.

Resolution of propranolol (PL) enantiomers in biological samples was accomplished by column switching high performance liquid chromatography using a short precolumn and an analytical column of ovomucoid chiral phase. Plasma, whole blood or tissue homogenate sample was directly injected into the precolumn, and PL was adsorbed on Butyl Toyopearl 650-M. After column switching, the PL was backflushed and transferred to the analytical column (Ultron ES-OVM) by the eluant. Fluorometric detection was carried out at lambda ex = 297 nm and lambda em = 340 nm with a detection limit of 0.5 pmol (signal to noise ratio = 2). The recovery (98.8-103%), reproducibility (coefficient of variance less than 3%) and enantiomer resolution (separation factor 1.15) were satisfactory using as eluant 50 mM sodium dihydrogenphosphate (pH 4.6) containing 12% ethanol. The time course of elimination of PL enantiomers in rat or mouse blood and tissues was also studied.

Animals↗