Cryo-electron microscopy reveals a novel DNA-binding site on the MCM helicase

The eukaryotic MCM2-7 complex is recruited at origins of replication during the G1 phase and acts as the main helicase at the replication fork during the S phase of the cell cycle. To characterize the interplay between the MCM helicase and DNA prior to the melting of the double helix, we determined the structure of an archaeal MCM orthologue bound to a 5.6-kb double-stranded DNA segment, using cryo-electron microscopy. DNA wraps around the N-terminal face of a single hexameric ring. This interaction requires a conformational change within the outer belt of the MCM N-terminal domain, exposing a previously unrecognized helix-turn-helix DNA-binding motif. Our findings provide novel insights into the role of the MCM complex during the initiation step of DNA replication.     

Transmission photoemission electron microscopy for lateral mapping of the X-ray absorption structure of a metalloprotein in a liquid cell

We use photoemission electron microscopy in an X-ray transmission mode for full-field imaging of the X-ray absorption structure of copper in the respiratory metalloprotein hemocyanin KLH1. It contains 160 oxygen binding sites. Each site reversibly binds one molecule oxygen between two copper atoms. In our setup, hemocyanin is dissolved in aqueous solution and enclosed in an ultra-high vacuum compatible liquid sample cell with silicon nitride membranes. The local X-ray absorption structure of the liquid sample is converted into photoelectrons at the microscope side of the cell acting as a photocathode. In this way, different copper valencies are laterally distinguished under in vivo-like conditions, attributed to Cu(I) in the deoxy-state and Cu(II) in the oxy-state.     

Three-dimensional electron microscopy analysis of ndc10-1 mutant reveals an aberrant organization of the mitotic spindle and spindle pole body defects in Saccharomyces cerevisiae

Kinetochore components play a major role in regulating the transmission of genetic information during cell division. Ndc10p, a kinetochore component of the essential CBF3 complex in budding yeast is required for chromosome attachment to the mitotic spindle. ndc10-1 mutant was shown to display chromosome mis-segregation as well as an aberrant mitotic spindle (Goh and Kilmartin, 1993). In addition, Ndc10p localizes along the spindle microtubules (Muller-Reichert et al., 2003). To further understand the role of Ndc10p in the mitotic apparatus, we performed a three-dimensional electron microscopy (EM) reconstruction of mitotic spindles from serial sections of cryo-immobilized ndc10-1 mutant cells. This analysis reveals a dramatic reduction in the number of microtubules present in the half-spindle, which is connected to the newly formed spindle pole body (SPB) in ndc10-1 cells. Moreover, in contrast to wild-type (WT) cells, ndc10-1 cells showed a significantly lower signal intensity of the SPB components Spc42p and Spc110p fused with GFP, in mother cell bodies compared with buds. A subsequent EM analysis also showed clear defects in the newly formed SPB, which remains in the mother cell during anaphase. These results suggest that Ndc10p is required for maturation of the newly formed SPB. Intriguingly, mutations in other kinetochore components, ndc80-1 and spc24-1, showed kinetochore detachment from the spindle, similar to ndc10-1, but did not display defects in SPBs. This suggests that unattached kinetochores are not sufficient to cause SPB defects in ndc10-1 cells. We propose that Ndc10p, alongside its role in kinetochore–microtubule interaction, is also essential for SPB maturation and mitotic spindle integrity.     

The liquid crystalline nature of the cytoskeleton in epidermal cells of the chaetognath Sagitta

The chaetognaths have a multilayered epidermis, which is not covered by cuticle, except in the head region. Two kinds of cells are found in the epidermis: the filament-rich cells, adjacent to the basement membrane, and superficial cells, which are filament poor. The filament-rich cells, which are linked by gap junctions and columnar junctions, are highly developed in the collarette region, which joins the head and the trunk. As elsewhere in the epidermis these cells are covered by the filament poor cells which are linked by zonulae adhaerentes, gap junctions and septate junctions. The filaments present in the inner cells of the collarette form a twisted fibrous arrangement, which shows parallel series of nested arcs when observed in oblique section. Such systems are well known in numerous skeletal materials and correspond to polymerized analogues of certain liquid crystals. The amount of connective tissue is extremely reduced in Sagitta. One can hypothesize that filament-rich cells are abundant in regions which undergo strong deformations. This is the case in the collarette, in contact with the basement membrane of the epidermis (which in turn is in contact with a myotendinous system), in a region where ingested prey must go through the general cavity where there is high internal pressure.     

The effect of ethidium bromide on the liquid crystalline phases of aqueous DNA.

The influence of the intercalation of ethidium bromide (EB) on the characteristics of the DNA cholesteric and hexagonal mesophases is studied by optical microscopy, circular dichroism, and X-ray diffraction. The distance between DNA rods in the hexagonal phase is not modified by the presence of EB whereas the pitch of the cholesteric mesophase is considerably shortened by the dye. This seems to be related to the stereochemical effect of the intercalation rather than to the presence of a random distribution of the positive charge of the dye.     

In vivo coherent anti-Stokes Raman scattering microscopy reveals vitamin A distribution in the liver

Here we present a microscope setup for coherent anti-Stokes Raman scattering (CARS) imaging, devised to specifically address the challenges of in vivo experiments. We exemplify its capabilities by demonstrating how CARS microscopy can be used to identify vitamin A (VA) accumulations in the liver of a living mouse, marking the positions of hepatic stellate cells (HSCs). HSCs are the main source of extracellular matrix protein after hepatic injury and are therefore the main target of novel nanomedical strategies in the development of a treatment for liver fibrosis. Their role in the VA metabolism makes them an ideal target for a CARS-based approach as they store most of the body's VA, a class of compounds sharing a retinyl group as a structural motive, a moiety that is well known for its exceptionally high Raman cross section of the C═C stretching vibration of the conjugated backbone.     

A reevaluation of the epimeric and anomeric relationship of glucosides and galactosides in thermotropic liquid crystal self-assemblies

Anomers and epimers α- and β-gluco and -galactosides are expected to behave differently. However, recent results on a series of Guerbet glycosides have indicated similar liquid crystal clearing temperatures for pure β-glucosides and the corresponding α-galactosides. This observation has led to speculation on similarities in the self-assembly interactions between the two systems, attributed to the trans-configuration of the 4-OH group and the hydrophobic aglycon. Previous simulations on related bilayers systems support this hypothesis, by relating this clearing transition temperature to intralayer (sugar–sugar) hydrogen bonding. In order to confirm the hypothesis, the comparison was expanded to include the cis-configurated pair, that is, α-gluco/β-galactoside. A set of α-configurated Guerbet glucosides as well as octyl α-galactoside were prepared and their thermotropic phase behavior studied. The data obtained enabled a complete comparison of the isomers of interest. While the results in general are in line with a pairing of the stereo-isomers according to the indicated cis/trans-configuration, differences within the pairs can be explained based on the direction of hydrogen bonds from a simple modeling study.     

Three-dimensional organization of the collagen fibrils in the rat sciatic nerve as revealed by transmission- and scanning electron microscopy

Summary The organization of collagen fibrils in the rat sciatic nerve was studied by scanning electron microscopy after digestion of cellular elements by sodium hydroxide treatment, and by conventional transmission electron microscopy. The epineurium consisted mainly of thick bundles of collagen fibrils measuring about 10–20 m in width; they were wavy and ran slightly obliquely to the nerve axis. Between these collagen bundles, a very coarse meshwork of randomly oriented collagen fibrils was present. In the perineurium, collagen fibrils occupied the interspaces between the concentrically arranged perineurial cells; in each interspace, they formed a sheet of characteristic lacework elaborately interwoven by thin (about 3 m or less in width) bundles of collagen fibrils. In the subperineurial region, there was a distinct sheet of densely woven collagen fibrils between the perineurium and underlying endoneurial fibroblasts. In the endoneurium, collagen fibrils surrounded individual nerve fibers in two layers as scaffolds: the inner layer was made up of a delicate meshwork of very fine collagen fibrils, and the outer one consisted of longitudinally oriented bundles of about 1–3 m in width. The collagen fibril arrangement described above may protect the nerve fibers against external forces.     

Smartphone-integrated field microscopy (SPFM): a low-cost and portable tool to study live biological specimens in the wild

Abstract

Images and videos of organisms recorded in the wild have relevance for biodiversity studies. With the advent of smartphones and their potential integration with microscopy, scientific documentation and recording of organisms has surged to an unprecedented scale. Here we report a novel method, developed by integration of a portable smartphone with a handheld field microscope that we term Smartphone-integrated Field Microscopy (SPFM), to capture images and videos which can be highly useful in field-based biodiversity studies. We firstly describe the design of the method and equipment used, followed by successful field demonstration of the method using a case study of the gymnosperm Ephedra intermedia Schrenk & C. A. Meyer in the Kashmir Himalaya. We then discuss the novelty of our method and its potential applications in biodiversity studies.     

Confocal microscopy as a tool to reveal the tridimensional organization of intracellular lumens and intercellular cysts in a human colon adenocarcinoma cell line

Adenocarcinoma cells often form intracellular lumens and intercellular cysts. In order to study the structural relationships between these lumens and the apical domain of normal enterocytes, we have applied electron microscopy and confocal microscopy to a cloned cell line derived from the human colon adenocarcinoma cell line LoVo which express a high number of intracellular lumens and intercellular cysts. Microvilli reminiscent of those detected in the brush border of small intestinal cells are formed in the two types of compartments. By immunofluorescence, we found that a 135 kDa membrane glycoprotein characterized by a monoclonal Ab and normally associated with the brush-border of enterocytes is expressed at the surface of the intracellular lumens and intercellular cysts present in the adenocarcinoma cells. Comparison of fluorescence and reflection contrast micrographs obtained by confocal microscopy demonstrate the presence of spherical intracellular lumens in the juxtanuclear region of single cells, and of more complex shaped intercellular cysts located within clusters of cells. The later cells form junctional complexes limiting an apical plasma membrane domain in contact with the intercellular cyst. It is suggested that the intracellular lumens may represent the abortive form of an apical plasma membrane due to the lack of components required to establish epithelial cell contacts. As opposed to conventional fluorescence microscopy, confocal microscopy allows rapid inspection of the tridimensional organization of intracellular lumens and intercellular cysts even when they are located in cell multilayers.     

Application of liquid chromatographic method with fluorescence detection for the determination of triclabendazole in tablets and biological fluids

A simple and rapid liquid chromatographic method was developed and validated for the determination of triclabendazole with high accuracy and precision within 6 min. Good chromatographic separation was achieved using a CLC Shim‐pack C₈ (250 × 4.6 mm, 5 µm particle size) using the mobile phase containing a mixture of 0.02 m phosphate buffer and methanol with a ratio of (20 : 80 v/v) at pH 4.0 was pumped at a flow rate of 1.2 mL/min with fluorescence detection for the first time at 338 nm after excitation at 298 nm. Losartan potassium was used as an internal standard. The method showed good linearity in the ranges of 0.05–2.0 µg/mL with limits of detection and quantification of 14.1 and 42.6 ng/mL, respectively. The suggested method was successfully applied for the analysis of triclabendazole in tablets. The high sensitivity of the method enabled the determination of the studied drug in spiked human plasma with mean percentage of recoveries of 99.79 ± 5.09. Statistical evaluation of the data was performed according to ICH Guidelines. Copyright © 2013 John Wiley & Sons, Ltd.     

The biological activities of protein/oleic acid complexes reside in the fatty acid

A complex formed by human α-lactalbumin (α-LA) and oleic acid (OA), named HAMLET, has been shown to have an apoptotic activity leading to the selective death of tumor cells. In numerous publications it has been reported that in the complex α-LA is monomeric and adopts a partly folded or “molten globule” state, leading to the idea that partly folded proteins can have “beneficial effects”. The protein/OA molar ratio initially has been reported to be 1:1, while recent data have indicated that the OA-complex is given by an oligomeric protein capable of binding numerous OA molecules per protein monomer. Proteolytic fragments of α-LA, as well as other proteins unrelated to α-LA, can form OA-complexes with biological activities similar to those of HAMLET, thus indicating that a generic protein can form a cytotoxic complex under suitable experimental conditions. Moreover, even the selective tumoricidal activity of HAMLET-like complexes has been questioned. There is recent evidence that the biological activity of long chain unsaturated fatty acids, including OA, can be ascribed to their effect of perturbing the structure of biological membranes and consequently the function of membrane-bound proteins. In general, it has been observed that the cytotoxic effects exerted by HAMLET-like complexes are similar to those reported for OA alone. Overall, these findings can be interpreted by considering that the protein moiety does not have a toxic effect on its own, but merely acts as a solubilising agent for the inherently toxic fatty acid.     

Folding Steps in the Fibrillation of Functional Amyloid: Denaturant Sensitivity Reveals Common Features in Nucleation and Elongation

Functional bacterial amyloids (FuBA) are intrinsically disordered proteins (IDPs) which rapidly and efficiently aggregate, forming extremely stable fibrils. The conversion from IDP to amyloid is evolutionarily optimized and likely couples folding to association. Many FuBA contain several imperfect repeat sequences which contribute to the stability of mature FuBA fibrils. Aggregation can be considered an intermolecular extension of the process of intramolecular protein folding which has traditionally been studied using chemical denaturants. Here we employ denaturants to investigate folding steps during fibrillation of CsgA and FapC. We quantify protein compactification (i.e. the extent of burial of otherwise exposed surface area upon association of proteins) during different stages of fibrillation based on the dependence of fibrillation rate constants on the denaturant concentration (m-values) determined from fibrillation curves. For both proteins, urea mainly affects nucleation and elongation (not fragmentation), consistent with the fact that these steps involve both intra- and intermolecular association. The two steps have similar m-values, indicating that activation steps in nucleation and elongation involve the same level of folding. Surprisingly, deletion of two or three repeats from FapC leads to larger m-values (i.e. higher compactification) during the activation step of fibril growth. This observation is extended by SAXS analysis of the fibrils which indicates that weakening of the amyloidogenic core caused by repeat deletions causes a larger portion of normally unstructured regions of the protein to be included into the amyloid backbone. We conclude that the sensitivity of fibrillation to denaturants can provide useful insight into molecular mechanisms of aggregation.