Fine Structural Features Research Articles

Revealing the high-resolution three-dimensional network of chromatin and interchromatin space: A novel electron-microscopic approach to reconstructing nuclear architecture

The nuclear architecture is considered an important contributor to genome function. Although the fine structural features of the cell nucleus have been investigated extensively by means of ultrastructural cytochemistry, mainly on ultrathin sections in two dimensions (2D), there was a of lack routine methods for a rapid reconstruction of three-dimensional (3D) distribution of different structural constituents throughout the nuclear volume. We have now filled this gap by the application of a novel approach associating a pre-embedding selective visualization of nuclear components with a method making use of ultramicrotomy combined with scanning electron microscopy (microtome serial block face scanning electron microscopy--'3View'). We have been able to apply this method to the study of DNA distribution within the nuclear volume and reconstruction of 3D chromatin arrangement in nuclei of rat hepatocytes and endothelial cells. Our observations demonstrate that while chromatin appears to occupy the interior of nuclei rather sparsely on 2D images, once reconstructed in 3D from a series of sequential 2D images it gives the impression of considerably filling the nuclear volume. However, quantitative evaluation of the nuclear volume occupied by DNA in the above two types of nuclei leaves a significant part to the interchromatin space (66.2% for hepatic cells and 41.7% for endothelial cells, including nuclear space occupied by nucleoli). Detailed analysis of the reconstructed nuclei reveals a high degree of superposition of chromatin domains, giving rise to a false impression that they fill a much larger part of the nuclear volume than they really do. Our results show the importance of the contribution of such reconstruction techniques to our understanding of the nuclear architecture.

Fine Structural Features and Electronic Structure of Core-Shell Structured Fe Nanoparticles Probed using TEM/STEM and EELS

Extended abstract of a paper presented at Microscopy and Microanalysis 2009 in Richmond, Virginia, USA, July 26 – July 30, 2009

Perdeuteration, purification, crystallization and preliminary neutron diffraction of an ocean pout type III antifreeze protein.

The highly homologous type III antifreeze protein (AFP) subfamily share the capability to inhibit ice growth at subzero temperatures. Extensive studies by X-ray crystallography have been conducted, mostly on AFPs from polar fishes. Although interactions between a defined flat ice-binding surface and a particular lattice plane of an ice crystal have now been identified, the fine structural features underlying the antifreeze mechanism still remain unclear owing to the intrinsic difficulty in identifying H atoms using X-ray diffraction data alone. Here, successful perdeuteration (i.e. complete deuteration) for neutron crystallographic studies of the North Atlantic ocean pout (Macrozoarces americanus) AFP in Escherichia coli high-density cell cultures is reported. The perdeuterated protein (AFP D) was expressed in inclusion bodies, refolded in deuterated buffer and purified by cation-exchange chromatography. Well shaped perdeuterated AFP D crystals have been grown in D(2)O by the sitting-drop method. Preliminary neutron Laue diffraction at 293 K using LADI-III at ILL showed that with a few exposures of 24 h a very low background and clear small spots up to a resolution of 1.85 A were obtained using a ;radically small' perdeuterated AFP D crystal of dimensions 0.70 x 0.55 x 0.35 mm, corresponding to a volume of 0.13 mm(3).

Cellular organization of normal mouse liver: a histological, quantitative immunocytochemical, and fine structural analysis.

The cellular organization of normal mouse liver was studied using light and electron microscopy and quantitative immunocytochemical techniques. The general histological organization of the mouse liver is similar to livers of other mammalian species, with a lobular organization based on the distributions of portal areas and central venules. The parenchymal hepatocytes were detected with immunocytochemical techniques to recognize albumin or biotin containing cells. The macrophage Kupffer cells were identified with F4-80 immunocytochemistry, Ito stellate cells were identified with GFAP immunocytochemistry, and endothelial cells were labeled with the CD-34 antibody. Kupffer cells were labeled with intravascularly administered fluorescently labeled latex microspheres of both large (0.5 mum) and small (0.03 mum) diameters, while endothelial cells were labeled only with small diameter microspheres. Neither hepatocytes nor Ito stellate cells were labeled by intravascularly administered latex microspheres. The principal fine structural features of hepatocytes and non-parenchymal cells of mouse liver are similar to those reported for rat. Counts of immunocytochemically labeled cells with stained nuclei indicated that hepatocytes constituted approximately 52% of all labeled cells, Kupffer cells about 18%, Ito cells about 8%, and endothelial cells about 22% of all labeled cells. Approximately, 35% of the hepatocytes contained two nuclei; none of the Kupffer or Ito cells were double nucleated. The presence of canaliculi and a bile duct system appear similar to that reported for other species. The cellular organization of the mouse liver is quite similar to that of other mammalian species, confirming that the mouse presents a useful animal model for studies of liver structure and function.

Global Robustness and Identifiability of Random, Scale-Free, and Small-World Networks

We are interested in the relationships among network topology, robustness, and identifiability, and their implications in improving network reconstruction. We used three different types of artificial gene networks (AGNs) with distinct topologies: topologies random (RND), scale-free (SF), and small-world (SW), to investigate their robustness and identifiability. The robustness of a network is represented by structural reachability (existence of pathways between two nodes) and dynamic reachability (response on one node upon perturbation on another node). The identifiability of the network edges is assessed in silico with an established reverse-engineering algorithm. We found that (1) structural reachability does not always lead to dynamic reachability; (2) network robustness is high and identifiability is low in all surveyed AGNs; (3) robustness is more sensitive to network topologies than is identifiability. We also devised a method for network dissection in which three subnets (set of alternative pathways or feedbacks, referred to as pathnet) are related to each node pair. This method allows us to identify the fine structural features underlying the distinct behaviors of the networks. For example, pathnet of the edge tail negatively contributes to the edge identifiability, and it is likely that extra perturbation at this pathnet would improve edge identifiability. We provide a case study to prove that double perturbations decrease the edge robustness and increase structural identifiability with a T helper cell-differentiation network model.

Morphological and ultrastructural features of Iba1-immunolabeled microglial cells in the hippocampal dentate gyrus

Microglia are found throughout the central nervous system, respond rapidly to pathology and are involved in several components of the neuroinflammatory response. Iba1 is a marker for microglial cells and previous immunocytochemical studies have utilized this and other microglial-specific antibodies to demonstrate the morphological features of microglial cells at the light microscopic level. However, there is a paucity of studies that have used microglial-specific antibodies to describe the ultrastructural features of microglial cells and their processes. The goal of the present study is to use Iba1 immuno-electron microscopy to elucidate the fine structural features of microglial cells and their processes in the hilar region of the dentate gyrus of adult Sprague–Dawley rats. Iba1-labeled cell bodies were observed adjacent to neurons and capillaries, as well as dispersed in the neuropil. The nuclei of these cells had dense heterochromatin next to the nuclear envelope and lighter chromatin in their center. Iba1-immunolabeling was found within the thin shell of perikaryal cytoplasm that contained the usual organelles, including mitochondria, cisternae of endoplasmic reticulum and Golgi complexes. Iba1-labeled cell bodies also commonly displayed an inclusion body. Iba1-labeled cell bodies gave rise to processes that often had a small side branch arise within 5 μm of the microglial cell body. These data showing “resting” Iba-1 labeled microglial cells in the normal adult rat dentate gyrus provide a basis for comparison with the morphology of microglial cells in disease and injury models where they are activated or phagocytotic.

Atomic-resolution imaging of oxidation states in manganites

Aberration corrected electron optics allows routine acquisition of high spatial resolution spectroscopic images in the scanning transmission electron microscope, which is important when trying to understand the physics of transition-metal oxides such as manganites. The physical properties of these perovskites are intimately related to the occupancies of the partially filled $3d$ bands, which define their oxidation state. In this work, we review procedures to obtain this electronic property in ${\text{La}}_{x}{\text{Ca}}_{1\ensuremath{-}x}{\text{MnO}}_{3}$ from atomic-column-resolved electron energy-loss spectra measured in the aberration corrected scanning transmission electron microscope. In bulk samples, several features of both the average $\text{Mn}\text{ }{L}_{2,3}$ edge and the $\text{O}\text{ }K$ edge fine structure change linearly with Mn nominal valence. These linear correlations are extracted and used as a calibration to quantify oxidation states from atomic resolution spectroscopic images. In such images, the same fine-structure features exhibit further changes, commensurate with the underlying atomic lattice. Mn valence values calculated from those images show unexpected oscillations. The combination of experiment with density-functional theory and dynamical scattering simulations allows detailed interpretation of these maps, distinguishing dynamical scattering effects from actual changes in electronic properties related to the local atomic structure. Specifically, in ${\text{LaMnO}}_{3}$, the two nonequivalent O sites can be distinguished by these methods.

Fatigue Mechanism of Internal Casting Defect-Originating Fracture of Aluminum Alloy Die Casting

The mechanism of internal casting defect-originating fracture of aluminum alloy die-casting in the ultra-high cycle regime was studied from the observation of fracture surface and cross section perpendicular to fracture surface. The main results were as follows : (1) Fine irregular fracture surface around the crack initiation point was clearly observed after 108 cycles, and the boundary between porosity and fine irregular fracture surface was not clear beyond 109 cycles, and a partial chip of spherical porosity was observed at crack initiation point. (2) From SIM observation of cross section perpendicular to fracture surface, fine structure of nanocrystalline was observed at fine irregular fracture surface and fine structure of nanocrystalline was not limited to fine irregular fracture surface. Fine structure of nanocrystalline was also observed at the vicinity of fine irregular fracture surface. (3) The boundary between fine structure of nanocrystalline and matrix structure was clear. This feature was similar to the feature of fine structure of nanocrystalline obtained from the severe plastic deformation process. (4) From the observation of fracture surface and cross section perpendicular to fracture surface, it seems to be that the contact between the fracture surface could occur at the crack initiation point and around the crack initiation point of the internal casting defect-originating fracture, and the repetition of the contact between the fracture surface seems to influence the formation of fine structure of nanocrystalline.

Silk spinning apparatuses in the cribellate spider nurscia albofasciata (Araneae: Titanoecidae)

The fine structural characteristics of the silk spinning apparatus in the titanoecid spiders Nurscia albofasciata have been examined by the field emission scanning electron microscopy (FESEM). This titanoecid spiders have a pair of medially divided cribella just in front of the anterior spinnerets, and the surface of the cribellum is covered by hundred of tiny spigots which produce numerous cribellate silk fibrils. The cribellar silks are produced from the spigots of the sieve‐like prate, and considered as a quite different sort of catching silk with dry‐adhesive properties. The other types of the silk spigots were identified as follows: ampullate, pyriform and aciniform glands. Two pairs of major ampullate glands send secretory ductules to the anterior spinnerets, and another 1–2 pairs of minor ampullate glands supply the middle spinnerets. In addition, the pyriform glands send ductules to the anterior spinnerets, and two kinds of the aciniform spigots feed silk into the middle (A type) and the posterior spinnerets (both of A & B types), respectively.

Fine structural analysis on the dry adhesion system of the jumping spider plexippus setipes (Araneae: Salticidae)

The cuticle of spider's exoskeleton is a hydrophobic and non‐adhesive material, but the jumping spiders have the distinctive attachment apparatus for adhesion on smooth dry surface without sticky fluids. We have examined the whole tarsal appendages of the jumping spider, Plexippus setipes with using scanning electron microscope to reveal the fine structural characteristics of the dry adhesion system. All eight legs have the scopulae with a pair of claws on the tip of feet. Each scopula is composed of two groups of setae that are capable of dry adhesion on smooth surface, and the hook structure of the claw is advanced to move on the rough surface. The setae toward the bottom of the tarsal segment are densely covered by numerous setules on the underside which broadened from middle to distal portion. It has been revealed by this research that the contact area of the setule is always a triangular shape, and these cuticular surfaces are connected by the elongated stalks from the underlying setae. It is likely that the nano‐scale structures including a triangular depression and a longitudinal groove on each setule could functionate when the spider detach its feet from the substrate.

Scaling turbulent dissipation and finestructure: The wave-propagation method.

In the 1980s the team of Flatté et al. developed a theory relating the turbulent kinetic energy dissipation rate in the open ocean to finestructure feature observations (1–100 m scale), building on work of Henyey and Pomphrey. Formulas derived from this work are now prevalently used for indirectly estimating cross‐isopycnal ocean mixing, a process of critical interest, using platforms and sensors unable to directly measure viscous‐scale dissipation and associated turbulent transport processes. The method originally involved the internal‐wave energy level. Revisions of the method introduced by follow‐on investigators involve internal‐wave shear and strain. The physics behind the method is that short‐wavelength shear‐rich internal waves propagate in a background of larger‐scale internal waves, with action conserved, and can have their energy concentrated spatially. The concentrated waves are inferred to break, and in doing so provide the energy to support diapycnal mixing. The approach is one of “wave propagation in random media,” a specialty of Flatté.

Structure and interactions of ulvan in the cell wall of the marine green algae Ulva rotundata (Ulvales, Chlorophyceae)

Ulvan, the sulfated cell-wall polysaccharides from green seaweeds ( Ulva species), presents structural and functional properties of interest for different applications. Its extraction yield in water varies depending on the species, the period of collect and the mode of conservation of algae. To identify limits of extraction, the structure and interactions of ulvan in the cell wall of Ulva were investigated following a sequential solvent extraction. Hot sodium oxalate and hot dilute HCl were the two major extracts. Other solvents affecting protein structure or low hydrogen bonded polymers yielded minor ulvan fractions but affected solid state 13C NMR spectra indicating that proteins likely contributed to cross-link and/or to entrap Ulva cell wall polysaccharides. Ulvan-lyase degradation showed that ulvan consisted in a wide continuum of related polysaccharides differing in the extent and type of fine structural characteristics. Besides solvent acidity, particle size of seaweeds was an important parameter controlling the ulvan extraction efficiency. Major ulvan cell wall interactions were discussed with regard to ionic interactions, covalent linkages and peculiar solution behavior of ulvan in various physicochemical environments.

Fine structure of the ventral nerve centre and interspecific identification of individual neurons in the enigmatic Chaetognatha

The enigmatic arrow worms (Chaetognatha) are marine carnivores and among the most abundant planktonic organisms. Their phylogenetic position has been heavily debated for a long time. Most recent molecular studies still provide a diverging picture and suggest arrow worms to be some kind of basal protostomes. In an effort to understand the organization of the nervous system in this clade for a broad comparison with other Metazoa we analysed the ultrastructure of the ventral nerve centre in Spadella cephaloptera by transmission electron microscopy. We were able to identify six different types of neurons in the bilateral somata clusters by means of the cytoplasmic composition (regarding the structure of the neurite and soma including the shape and eu-/heterochromatin ratio within the nucleus) as well as the size and position of these neurons. Furthermore, our study provides new insights into the neuropil composition of the ventral nerve centre and several other fine structural features. Our second goal was to examine if individually identifiable neurons are present in the ventral nerve centres of four chaetognath species, Sagitta setosa, Sagitta enflata, Pterosagitta draco, and Spadella cephaloptera. For that purpose, we processed whole mount specimens of these species for immunolocalization of RFamide-related neuropeptides and analysed them with confocal laser-scanning microscopy. Our experiments provide evidence for the interspecific homology of individual neurons in the ventral nerve centres of these four chaetognath species suggesting that the potential to generate serially arranged neurons with individual identities is part of their ground pattern.

Characteristics of thermal finestructure in the southern Yellow Sea and the East China Sea from airborne expendable bathythermograph measurements

Four surveys of airborne expendable bathythermograph with horizontal spacing of about 35 km and vertical spacing of 1 m extending from the surface down to 400 m deep are used to analyze thermal finestructures and their seasonality in frontal zones of the southern Yellow Sea and the East China Sea. Finestructure characteristics are different not only among fronts but also along the same front, implying different mixing mechanisms. Summer thermocline intrusions with thickness from few to 40 meters, generated by the vertically-sheared advection, are identified along the southern tongue of the Cheju-Yangtze Front (especially south of Cheju Island). The finestructures south of the Yangtze Bank (i.e. the western tip of the southern tongue) produced by strong along-frontal currents are not as rich as elsewhere in the southern tongue. The Cheju-Tsushima Front presents mixed finestructures due to confluent currents from various origins. The irregular-staircase finestructures in the Kuroshio region (below the seasonal thermocline), driven by double-diffusive mixing, show seasonal invariance and vertical/horizontal coherence. The strength of mixing related to finestructure is weaker in the Kuroshio region than in the Cheju-Tsushima Front or south of Cheju Island. The profiles in the Tsushima Warm Current branching area show large (∼50 m thick), irregular-staircase structures at the upper 230 m depth, which coincides roughly with the lower boundary of the maximum salinity layer. The finestructure at depths deeper 230 m is similar to that in the Kuroshio region. The possible mechanisms for generating the finestructures are also discussed.

INDIVIDUAL VARIATION AND LEK-BASED VOCAL DISTINCTIVENESS IN SONGS OF THE SCREAMING PIHA (LIPAUGUS VOCIFERANS), A SUBOSCINE SONGBIRD

One long-standing ornithological paradigm holds that song learning in oscine songbirds has a cultural component, whereas suboscine songbirds inherit songs genetically. Recent studies reveal that suboscine song may be more variable and complex than previously realized. Several suboscine species show marked individual variation in their songs—variation that may play a role in individual recognition and neighbor–stranger discrimination—and a few suboscine species show indications of song learning. We investigated individual variation in the vocalizations of a suboscine passerine, the Screaming Piha (Lipaugus vociferans), from recordings of 26 males at four lek sites along the Tambopata River in Peru. Male Screaming Piha songs consist of quiet introductory syllables followed by two explosively loud syllables that sound like an emphatic pee haw. We used three complementary methods to examine variation in song characteristics. Spectrogram cross-correlation revealed significant consistency within individual males and variability among males. Analysis of fine structural characteristics revealed that all measured song features were significantly less variable within individuals than among individuals. Canonical discriminant analysis based on these 13 song features correctly classified 93.2% of songs by individual and 76.4% of songs by lek site. Our results indicate that there is sufficient consistency in song features within males and sufficient variation among males for identification of individuals on the basis of songs and, to a lesser extent, that song features vary with the lek site of the singer. We conclude that Screaming Pihas sing songs that are individually distinctive and bear a lek signature.

Charge disproportionation in quasi-one-dimensional vanadium oxides

The vanadium bronzes β ( β ′ )- A x V 2O 5 (A=Na +, Ag +, Ca 2+, Cu +) are investigated by electron energy-loss spectroscopy (EELS), X-ray absorption near edge spectroscopy and electronic structure calculations. We analysed the fine structural features of experimental spectra in the low-loss region and the vanadium L 2,3 and oxygen K ionization edges in correlation with electronic structure of this quasi-one-dimensional conducting system. The different energy separations on the fine structures of the vanadium L 3 edge and oxygen K edge arising from ligand field splitting suggest charge disproportionation occurring in β ( β ′ )- A x V 2O 5 materials at room temperature. Based on the analysis of the highly-damped valence electron plasmon peak for these materials, the charge distribution among different chains and ladders is briefly discussed.

Effect of shear deformation on the microstructure and mechanical properties of a steel St3

The effect of the methods of severe plastic shear deformation on the microstructure formation in a steel St3 has been studied. The shear deformation in hot and cold states allows one to obtain different levels of mechanical properties of the metal with different characteristic features of fine structure. It is shown that cold plastic shear deformation is accompanied by a rise in the level of internal stresses and a considerable increase in the fraction of low-angle boundaries, which is reflected in the enhancement of strength properties. Upon hot plastic shear deformation, numerous finely dispersed grains with high-angle boundaries and small density of dislocations are formed due to the concurrent development of fragmentation and recrystallization in situ. This results in a low level of stresses in the crystal lattice and favors enhancement in plasticity.

A comparative study of distortion-product-otoacoustic-emission fine structure in human newborns and adults with normal hearing

Distortion product otoacoustic emissions (DPOAE) measured in human newborns are not adult-like. More than a decade of work from various investigators has created a well-developed body of evidence describing these differences but the putative anatomy or physiology has only been partially explained. Recently, Abdala and Keefe [J. Acoust. Soc. Am. 120, 3832-3842 (2006)] have identified outer and middle ear immaturities that at least partially describe the differences observed between newborn and adult input-output functions and suppression tuning curves. DPOAE fine structure characteristics and their maturation have not been examined to any extent in the literature. Fine structure characteristics in two groups of ten newborns and young adults with normal hearing sensitivity are compared here. Consistent with previous reports, the newborns show higher DPOAE levels; greater fine structure depth and wider fine structure spacing is also observed in the newborns. Differences in fine structure morphology are also observed between the two age groups. While some of these findings are attributable to an immature outer and middle ear system in the newborns, it is argued that some observed differences in fine structure characteristics might be due to remnant immaturities in passive motion of the basilar membrane in the newborn cochlea.

Study of optical response near the absorption edge using vacuum ultra violet/soft X-ray reflectivity beamline on Indus-1

Fine structure features of energy dependent atomic scattering factor near the atomic absorption edge, is used for characterization of low Z containing hard-condensed matter thin films. Near the atomic absorption edge, reflectivity provides increased sensitivity to composition of the interface, due to tunable contrast of optical constants. This is illustrated through the characterization of molybdenum silicon X-ray multilayer and boron carbide (B4C) thin film.

Chondroitin sulphate proteoglycans in the vitreous gel of sheep and goat

In the present study, the amounts and the fine structural characteristics of chondroitin sulphate proteoglycans (CSPGs) present in sheep and goat vitreous gels were determined. The results showed that in both examined species hyaluronan was the predominant glycosaminoglycan (GAG), whereas CSPGs were present in minor amounts. CSPGs were identified as versican and collagen IX with versican being the predominant PG type. Fine structural characterization indicated that the CS chains of versican in both mammalian species were of smaller size than those found in collagen IX. The difference in the sulphation pattern of CS chains between versican and collagen IX was also of particular interest. The results indicated that the predominant disaccharide type in CS side chains of versican and collagen IX from both sheep and goat vitreous gels was the 4-sulphated disaccharide. CS chains of versican were found to be richer in 4-sulphated disaccharide units than those in collagen IX, which also contained a significant proportion of non-sulphated disaccharides. These findings showed that, firstly, the CS content and the hydrodynamic size of the CS chain and, secondly, the sulphation pattern of CS chains from versican and collagen IX in both sheep and goat vitreous gels are PG type-dependent.