X-ray laser microscopy of rat sperm nuclei

A Genetically Encoded Two-Dimensional Infrared Probe for Enzyme Active-Site Dynamics

While two-dimensional infrared (2D-IR) spectroscopy is uniquely suitable for monitoring femtosecond (fs) to picosecond (ps) water dynamics around static protein structures, its utility for probing enzyme active-site dynamics is limited due to the lack of site-specific 2D-IR probes. We demonstrate the genetic incorporation of a novel 2D-IR probe, m-azido-L-tyrosine (N3Y) in the active-site of DddK, an iron-dependent enzyme that catalyzes the conversion of dimethylsulfoniopropionate to dimethylsulphide. Our results show that both the oxidation of active-site iron to Fe^III , and the addition of denaturation reagents, result in significant decrease in enzyme activity and active-site water motion confinement. As tyrosine residues play important roles, including as general acids and bases, and electron transfer agents in many key enzymes, the genetically encoded 2D-IR probe N3Y should be broadly applicable to investigate how the enzyme active-site motions at the fs-ps time scale direct reaction pathways to facilitating specific chemical reactions.

X-Ray Free-Electron Lasers for the Structure and Dynamics of Macromolecules

X-ray free-electron lasers provide femtosecond-duration pulses of hard X-rays with a peak brightness approximately one billion times greater than is available at synchrotron radiation facilities. One motivation for the development of such X-ray sources was the proposal to obtain structures of macromolecules, macromolecular complexes, and virus particles, without the need for crystallization, through diffraction measurements of single noncrystalline objects. Initial explorations of this idea and of outrunning radiation damage with femtosecond pulses led to the development of serial crystallography and the ability to obtain high-resolution structures of small crystals without the need for cryogenic cooling. This technique allows the understanding of conformational dynamics and enzymatics and the resolution of intermediate states in reactions over timescales of 100 fs to minutes. The promise of more photons per atom recorded in a diffraction pattern than electrons per atom contributing to an electron micrograph may enable diffraction measurements of single molecules, although challenges remain.

A Compact "Water Window" Microscope with 60 nm Spatial Resolution for Applications in Biology and Nanotechnology

Short illumination wavelength allows an extension of the diffraction limit toward nanometer scale; thus, improving spatial resolution in optical systems. Soft X-ray (SXR) radiation, from "water window" spectral range, λ=2.3-4.4 nm wavelength, which is particularly suitable for biological imaging due to natural optical contrast provides better spatial resolution than one obtained with visible light microscopes. The high contrast in the "water window" is obtained because of selective radiation absorption by carbon and water, which are constituents of the biological samples. The development of SXR microscopes permits the visualization of features on the nanometer scale, but often with a tradeoff, which can be seen between the exposure time and the size and complexity of the microscopes. Thus, herein, we present a desk-top system, which overcomes the already mentioned limitations and is capable of resolving 60 nm features with very short exposure time. Even though the system is in its initial stage of development, we present different applications of the system for biology and nanotechnology. Construction of the microscope with recently acquired images of various samples will be presented and discussed. Such a high resolution imaging system represents an interesting solution for biomedical, material science, and nanotechnology applications.

High numerical aperture tabletop soft x-ray diffraction microscopy with 70-nm resolution

Light microscopy has greatly advanced our understanding of nature. The achievable resolution, however, is limited by optical wavelengths to approximately 200 nm. By using imaging and labeling technologies, resolutions beyond the diffraction limit can be achieved for specialized specimens with techniques such as near-field scanning optical microscopy, stimulated emission depletion microscopy, and photoactivated localization microscopy. Here, we report a versatile soft x-ray diffraction microscope with 70- to 90-nm resolution by using two different tabletop coherent soft x-ray sources-a soft x-ray laser and a high-harmonic source. We also use field curvature correction that allows high numerical aperture imaging and near-diffraction-limited resolution of 1.5lambda. A tabletop soft x-ray diffraction microscope should find broad applications in biology, nanoscience, and materials science because of its simple optical design, high resolution, large depth of field, 3D imaging capability, scalability to shorter wavelengths, and ultrafast temporal resolution.

Compact soft x-ray transmission microscopy with sub-50 nm spatial resolution

In this paper, the development of compact transmission soft x-ray microscopy (XM) with sub-50 nm spatial resolution for biomedical applications is described. The compact transmission soft x-ray microscope operates at lambda = 2.88 nm (430 eV) and is based on a tabletop regenerative x-ray source in combination with a tandem ellipsoidal condenser mirror for sample illumination, an objective micro zone plate and a thinned back-illuminated charge coupled device to record an x-ray image. The new, compact x-ray microscope system requires the fabrication of proper x-ray optical devices in order to obtain high-quality images. For an application-oriented microscope, the alignment procedure is fully automated via computer control through a graphic user interface. In imaging studies using our compact XM system, a gold mesh image was obtained with 45 nm resolution at x580 magnification and 1 min exposure. Images of a biological sample (Coscinodiscus oculoides) were recorded.

Fabrication of multilayer mirrors consisting of oxide and nitride layers for continual use across the K-absorption edge of carbon

The development of multilayer mirrors for continual use around the K-absorption edge of carbon (4.4 nm) has been begun. Cobalt oxide (Co3O4), silicon oxide (SiO2), and boron nitride (BN) are found to be suitable for multilayer mirrors on the basis of theoretical calculations for wavelengths around the carbon K-absorption edge region. X-ray reflectivity curves with CuKalpha1 x rays of the fabricated Co3O4/SiO2 multilayers have sharp Bragg peaks, and the layer structures evaluated from transmission electron microscopy (TEM) observations are uniform. On the other hand, the Bragg peaks of Co3O4/BN multilayers split, and aggregated Co3O4 is observed. To improve the Co3O4 layer structure, chromium oxide (Cr2O3) was mixed into Co3O4. The mixed oxide layer structure in the Mix/BN multilayer (Mix = Co3O4 + Cr2O3) is relatively uniform, and the Bragg peaks do not split.

Formation of native-like mammalian sperm cell chromatin with folded bull protamine

The DNA of most vertebrate sperm cells is packaged by protamines. The primary structure of mammalian protamine I can be divided into three domains, a central DNA binding domain that is arginine-rich and amino- and carboxyl-terminal domains that are rich in cysteine residues. In native bull sperm chromatin, intramolecular disulfide bonds hold the terminal domains of bull protamine folded back onto the central DNA binding domain, whereas intermolecular disulfide bonds between DNA-bound protamines help stabilize the chromatin of mature mammalian sperm cells. Folded bull protamine was used to condense DNA in vitro under various solution conditions. Using transmission electron microscopy and light scattering, we show that bull protamine forms particles with DNA that are morphologically similar to the subunits of native bull sperm chromatin. In addition, the stability provided by intermolecular disulfide bonds formed between bull protamine molecules within in vitro DNA condensates is comparable with that observed for native bull sperm chromatin. The importance of the bull protamine terminal domains in controlling the bull sperm chromatin morphology is indicated by our observation that DNA condensates formed under identical conditions with a fish protamine, which lacks cysteine-rich terminal domains, do not produce as uniform structures as bull protamine. A model is also presented for the bull protamine.DNA complex in native sperm cell chromatin that provides an explanation for the positions of the cysteine residues in bull protamine that form intermolecular disulfide bonds.

Application of X-ray microscopy in analysis of living hydrated cells

Because there is a limit for analysis of fine hydrophilic cell structures of living cells in medium by ordinary techniques, including electron microscopy, the development of a new technology to overcome such limitation is highly desirable. In this regard, soft X-ray microscopy (high-resolution X-ray imaging of structures), which does not require any special procedures for sample preparation, has been developed and applied to analyze structures of biological specimens. In this article, application of two types of X-ray microscopes, which use laser-produced plasma X-rays or synchrotron radiation to image the structure of macrophage cells, is introduced as an example of a novel approach to analysis of biological specimens. Both types of X-ray microscopy show the network of fine fibrillar surface structures on macrophages in medium. Ordinary transmission and scanning electron microscopy and light microscopy also show the presence of such structures, but electron microscopy showed alterations due to sample processing and light microscopy did not show a clear image due to low resolution. Thus, X-ray microscopy has the potential capability to analyze structures of live cells in a hydrated condition and may reveal a function-related structural alignment of cells in their natural form.

Significance of plasmalemma disruption in bovine and equine spermatozoa

We have investigated fresh and cryopreserved bovine and equine spermatozoa using light and transmission soft X-ray microscopy. Spermatozoa were examined, in the presence or absence of semen, after using Percoll gradient centrifugation and re-suspending in medium. X-ray microscopy provided high resolution (30 nm) transmission images of whole cells in solution with high contrast, while retaining the simple preparation techniques used in light microscopy. We demonstrated translucent, membrane-bound vesicles in the acrosomal and midpiece regions that were similar in size and we noted their incidence in both fresh and frozen-thawed material from both animals. The vesicles were formed by the separation and expansion of the plasmalemma away from the underlying structure but were not caused by the freeze-thaw process. We suggest that these structures form part of the normal ultrastructure of spermatozoa and are damaged during preparation of the samples for transmission electron microscopy, resulting in a structure previously and incorrectly identified as damaged by the freezing and thawing process.

Focusing of a tabletop soft-x-ray laser beam and laser ablation

We focused the beam of a high-repetition-rate capillary-discharge tabletop laser operating at a wavelength of 46.9 nm, using a spherical Si/Sc multilayer mirror. The energy densities significantly exceeded the thresholds for the ablation of metals. Single-shot laser ablation patterns were used in combination with ray-tracing computations to characterize the focused beam. The radiation intensity within the 2-mum -diameter central region of the focal spot was estimated to be approximately 10(11)W/cm(2), with a corresponding energy density of ~100 J/cm(2).

Structure and normal incidence soft-x-ray reflectivity of Ni-Nb/C amorphous multilayers

Multilayers for the water window region of the soft x rays have been prepared by pulsed laser ablation with amorphous Ni(50) Nb(50) and amorphous C. The structural characterization of the multilayers, period d = 2.41 nm, shows that the interfaces are sharp with a roughness of only 0.4 nm that is chemical, not morphological, in origin. The interface roughness was found to be uncorrelated in the direction normal to the plane of the film. The normal incidence soft-x-ray reflectivity of the multilayer at 4.85-nm wavelength is 0.06%, 1 order of magnitude lower than the theoretically predicted value. However, the resolution limit lambda/Dlambda of the multilayer was found to be 16.7, close to the theoretically predicted value.

Kinesin force generation measured using a centrifuge microscope sperm-gliding motility assay

To measure force generation and characterize the relationship between force and velocity in kinesin-driven motility we have developed a centrifuge microscope sperm-gliding motility assay. The average (extrapolated) value of maximum isometric force at low kinesin density was 0.90 +/- 0.14 pN. Furthermore, in the experiments at low kinesin density, sperm pulled off before stall at forces between 0.40 and 0.75 pN. To further characterize our kinesin-demembranated sperm assay we estimated maximum isometric force using a laser trap-based assay. At low kinesin density, 4.34 +/- 1.5 pN was the maximum force. Using values of axoneme stiffness available from other studies, we concluded that, in our centrifuge microscope-based assay, a sperm axoneme functions as a lever arm, magnifying the centrifugal force and leading to pull-off before stall. In addition, drag of the distal portion of the axoneme is increased by the centrifugal force (because the axoneme is rotated into closer proximity to the glass surface) and represents an additional force that the kinesin motor must overcome.

Extent of sperm chromatin hydration determined by atomic force microscopy

Volume measurements were performed on intact bull and mouse sperm heads and amembranous sperm nuclei, both in the fully hydrated (fluid cell) and dehydrated (air-dried on glass coverslips) states by atomic force microscopy (AFM). Data were obtained by analyzing a small population of cells/nuclei, as well as by performing repeated measurements on single cells imaged following the addition of increasing concentrations of propanol. Results show that the volume of fully hydrated, intact sperm heads and amembranous sperm chromatin particles are at least twice the volume of their air-dried counterparts. Dehydration occurs rapidly in air, and the reduction in volume of chromatin induced by water loss appears to be completely reversible. These studies demonstrate that both mouse and bull sperm chromatin are extensively hydrated in the native state, and are not as compact as previous studies have suggested.

Simultaneous Measurement of Local Gain and Electron Density in X-ray Lasers

X-ray lasers (XRLs) have experimental average gains that are significantly less than calculated values and a persistently low level of spatial coherence. An XRL has been used both as an injected signal to a short XRL amplifier and as an interferometer beam to measure two-dimensional local gain and density profiles of the XRL plasma with a resolution near 1 micrometer. The measured local gain is in agreement with atomic models but is unexpectedly spatially inhomogeneous. This inhomogeneity is responsible for the low level of spatial coherence observed and helps explain the disparity between observed and simulated gains.

A characterisation of dark-field imaging of colloidal gold labels in a scanning transmission X-ray microscope

While X-ray microscopes provide images of biological specimens for which the contrast is mainly due to the difference in the absorption of carbon and oxygen when X-rays transmitted through the specimen are detected, signals other than absorption can also be used to form images. Using the Stony Brook scanning transmission X-ray microscope at the National Synchrotron Light Source, high-angle dark-field images have been formed of cells labelled with colloidal gold, with and without silver enhancement. The high density of the colloidal gold particles, or the silver particles seeded by the gold, leads to a large scattering signal, and the fact that the particle diameters are comparable to the width of the microscope point spread function results in good localisation of the label with high contrast. The dark-field images can have a greater signal to noise ratio than bright-field images acquired with the same incident X-ray dose. The theory of dark-and bright-field imaging is reviewed. Theoretical calculations of scattering from gold and silver particles are presented and good agreement is found between these and experimental dark-field images of 30 nm diameter gold particles. The signal to noise ratios of experimental bright-and dark-field images are measured and found to be in agreement with theory. Images are presented of cells labelled by immunolabelling and in situ hybridisation.

Compact high-resolution soft-x-ray spectrograph design using two matched grazing-incidence gratings

A novel and simple soft-x-ray grating-spectrograph design for high-resolution plasma-spectroscopy applications is presented and analyzed. This design uses dual, matched, concave varied-groove-density gratings to provide high dispersion and slit magnification and can achieve a very high spectral resolution (λ/Δλ > 25,000) in an instrument that is less than 1 m in length while using detectors, such as microchannel plates, with relatively coarse spatial resolutions. The advantages of this design over other designs with a comparable spectral resolution include its simplicity and small size, whereas the disadvantages include a narrow useful spectral range (λ/Δλ ≈ 50). Potential applications include x-ray laser linewidth measurements.

Soft X-ray microscopes and their biological applications

In this review we propose to address the question: for the life-science researcher, what does X-ray microscopy have to offer that is not otherwise easily available?

We will see that the answer depends on a combination of resolution, penetrating power, analytical sensitivity, compatibility with wet specimens, and the ease of image interpretation.

Ultrahigh-Resolution X-ray Tomography

Ultrahigh-resolution three-dimensional images of a microscopic test object were made with soft x-rays collected with a scanning transmission x-ray microscope. The test object consisted of two different patterns of gold bars on silicon nitride windows that were separated by approximately 5 micrometers. Depth resolution comparable to the transverse resolution was achieved by recording nine two-dimensional images of the object at angles between -50 and +55 degrees with respect to the beam axis. The projections were then combined tomographically to form a three-dimensional image by means of an algorithm using an algebraic reconstruction technique. A transverse resolution of approximately 1000 angstroms was observed. Artifacts in the reconstruction limited the overall depth resolution to approximately 6000 angstroms; however, some features were clearly reconstructed with a depth resolution of approximately 1000 angstroms.

Stability of the mammalian sperm nucleus

The nuclei of spermatozoa leaving the testies are transcritionally inactivated and are structurally stabilised by extensive association of sperm DNA with protamines, highly basic proteins that replace somatic histones during spermiogenesis. During sperm matureation within teh epididymis, protamine–SH is oxidised to -SS-(Bedford & Calvin, 1974).

Probing chromatin with the scanning force microscope

With the scanning force microscope (SFM), one can image the topography of biological material adsorbed at air-solid or liquid-solid interfaces with up to nanometer resolution. In principle, fixation, contrast enhancement, and labeling are not required. We have adapted specimen preparation techniques of conventional electron microscopy for visualizing chromatin ultrastructures in the SFM. A beaded substructure of the nucleoprotein filament was obtained after hypotonic lysis of chicken erythrocytes and air drying. The beads-on-a-string morphology of the basic nucleosomal assembly was well delineated. The nucleosomes appeared as round protrusions with an apparent height of 4-6 nm. The histogram of center-to-center distances between adjacent nucleosome cores along the filament axis had a peak at approximately 30 nm. Reversible changes in the three-dimensional structure were observed upon exposure of air-dried samples of metaphase chromosomes to solutions of different ionic strengths.

Atomic force microscopy of mammalian sperm chromatin

We have used the atomic force microscope (AFM) to image the surfaces of intact bull, mouse and rat sperm chromatin and partially decondensed mouse sperm chromatin attached to coverglass. High resolution AFM imaging was performed in air and saline using uncoated, unfixed and unstained chromatin. Images of the surfaces of intact chromatin from all three species and of an AFM-dissected bull sperm nucleus have revealed that the DNA is organized into large nodular subunits, which vary in diameter between 50 and 100 nm. Other images of partially decondensed mouse sperm chromatin show that the nodules are arranged along thick fibers that loop out away from the nucleus upon decondensation. These fibers appear to stretch or unravel, generating narrow smooth fibers with thicknesses equivalent to a single DNA-protamine complex. High resolution AFM images of the nodular subunits suggest that they are discrete, ellipsoid-shaped DNA packaging units possibly only one level of packaging above the protamine-DNA complex.

Force-velocity relationships in kinesin-driven motility

Kinesin is a microtubule-based motor protein that uses energy released from Mg-ATP hydrolysis to generate force for the movement of intracellular membranes towards the fast-growing (plus) ends of microtubule tracks in cells. Kinesin-driven microtubule movement can be visualized and quantified using light microscope motility assays but our understanding of how kinesin generates force and motion is incomplete. Here we report the use of a centrifuge microscope to obtain force-velocity curves for kinesin-driven motility and to estimate that the maximal isometric force generated per kinesin is 0.12 +/- 0.03 pN per molecule.

Normal-incidence reflectance of W/B(4) C multilayer mirrors in the 34-50-A wavelength region

The measured normal-incidence reflectances of W/B(4)C multilayers mirrors are 2% in the 34-50-A wavelength region and are consistent with interfacial roughness in the range of 3-4 A.