Scanning force microscopy in the applied biological sciences

Fifteen years after its invention, the scanning force microscope (SFM) is rooted deep in the biological sciences. Here we discuss the use of SFM in biotechnology and biomedical research. The spectrum of applications reviewed includes imaging, force spectroscopy and mapping, as well as sensor applications. It is our hope that this review will be useful for researchers considering the use of SFM in their studies but are uncertain about its scope of capabilities. For the benefit of readers unfamiliar with SFM technology, the fundamentals of SFM imaging and force measurement are also briefly introduced.     

Selective cleaning of the cell debris in human chromosome preparations studied by scanning force microscopy

The chromosome structure is one of most challenging biological structures to be discovered. Most evidence about the structure comes from optical microscopy. Scanning force microscopy (SFM) can achieve molecular resolution and allows imaging in liquids. However, little information about the chromosome structure has been revealed by SFM. In this work, a mild enzymatic treatment is applied to the chromosomes to remove selectively the RNA and proteins coming from the cell. The resulting SFM images indicate that a protein film with embedded RNA molecules covers chromosomes in standard cytogenetic preparations. The thickness of the protein layer is 15-35 nm and the RNA adheres preferentially to the chromosome surface. The cell material film results in a quite smooth chromosome surface without evidence of any structural detail. After treatment, the chromosome was cleaned from cell residues and individual chromatin fibers at the surface were resolved. Furthermore, insights about the higher order structure of the chromosome can be inferred.     

Investigating native coronary artery endothelium in situ and in cell culture by scanning force microscopy

The purpose of our studies is to better understand the morphology and functioning of the arteries and their changes in pathogenesis. The most frequently used imaging techniques are intravascular ultrasound, magnetic resonance imaging, and optical coherence tomography. These methods do not image cell-level structural details and only provide biomechanical properties indirectly. We present a new protocol for imaging the endothelial surface and measuring elastic properties of vascular tissue by scanning force microscopy. Full-thickness sections of native pig coronary arteries were prepared. In addition, cultured human umbilical vein endothelial cells were studied as an in vitro model system and for comparison. We encountered a variety of difficulties mostly due to the softness of vascular tissue which required significant adaptations of standard equipment: (i) a new specimen holder designed to stably immobilize the coronary arteries; (ii) a phase-contrast microscope incorporated for assessing the status of the cultured endothelial cells and positioning the scanning force microscope (SFM) tip at a site of interest; and (iii) a continuous exchange of the culture medium at 37 degrees C to assure viability of the cells in the SFM over extended times. We were thus able to investigate both fresh arterial tissue and living endothelial cells in a near-physiological environment. We present initial SFM images of vascular tissue at a spatial resolution similar to scanning electron microscopy, but which also provide a closer view of the bona fide structure of native tissue. Novel morphological features such as distinct granular particles were observed. Moreover, we report initial measurements of vascular tissue surface stiffness, obtained by indentation-type SFM.     

Assessment of the stability of TGFβ3 bioactivity for potential bioreactor applications

In order to develop suitable bioreactor systems and processes for automated and standardized cell cultures involving the use of bioactive factors, we determined the stability of transforming growth factor beta 3 (TGFβ3) over storage time and under conditions typically used for mammalian cell culture. Using a reporter gene assay with firefly luciferase as readout, significant reduction of TGFβ3 bioactivity was detected to occur both in serum containing medium (SCM) and serum free medium (SFM). The residual activity, quantified by parallel line assays, progressively decreased with time, down to 60% in SCM and 84% in SFM after 1 week at 37 °C, with no further decrease until 3 weeks, whereas such loss could not be predicted using a conventional ELISA method. The reduction of TGFβ3 bioactivity had a negligible influence in a typical biological assay (e.g., chondrocyte proliferation), supporting the possibility of prolonged storage of medium pre-supplemented with TGFβ3 for bioreactor-based chondrocyte expansion. With the ultimate goal of defining suitable operating protocols for automated cell culture bioreactors, the proposed approach should be extended to assessing the stability of other possibly labile medium supplements.     

Polylysine-coated mica can be used to observe systematic changes in the supercoiled DNA conformation by scanning force microscopy in solution

The conformations of supercoiled (sc) DNA and linear DNA bound to polylysine (PL)-coated mica were investigated by scanning force microscopy (SFM) in solution. From the polymer statistical analysis of linear DNA, we could distinguish between re-arrangements or trapping of the DNA on the surface. Conditions of re-arrangements to an almost equilibrated state can be achieved at appropriate PL surface concentrations. We could show that the ability of re-arrangements depends on the salt concentration of the adsorption/imaging buffer. Comparing the statistical analysis of the linear DNA with SFM images of scDNA suggested that irregular scDNA conformations are formed under conditions of trapping, whereas plectonemic structures are favoured under conditions of surface re-arrangements. Salt-dependent changes in the scDNA conformation over the range of 10–100 mM NaCl, as characterised by the parameters writhe and the superhelix radius r, are observable only under conditions that enable surface re-arrangements. The measured values of writhe suggest that the scDNA loses approximately one-half of the supercoils during the binding to the surface. At the same time r increases systematically with decreasing writhe, thus the scDNA topology remains determined by the constraints on supercoiling during the binding to PL-coated mica.     

Contributions of linker histones and histone H3 to chromatin structure: scanning force microscopy studies on trypsinized fibers.

Little is known about the mechanisms that organize linear arrays of nucleosomes into the three-dimensional structures of extended and condensed chromatin fibers. We have earlier defined, from scanning force microscopy (SFM) and mathematical modeling, a set of simple structural determinants of extended fiber morphology, the critical parameters being the entry-exit angle between consecutive linkers and linker length. Here we study the contributions of the structural domains of the linker histones (LHs) and of the N-terminus of histone H3 to extended fiber morphology by SFM imaging of progressively trypsinized chromatin fibers. We find that cleavage of LH tails is associated with a lengthening of the internucleosomal center-to-center distance, and that the somewhat later cleavage of the N-terminus of histone H3 is associated with a flattening of the fiber. The persistence of the "zigzag" fiber morphology, even at the latest stages of trypsin digestion, can be attributed to the retention of the globular domain of LH in the fiber.     

Physiological and nutritional features of Corynebacterium pyogenes

Growth and acid metabolic products were similar when Corynebacterium pyogenes was grown aerobically or anaerobically in a serum-free medium (SFM). This indicated that C. pyogenes obtains energy for growth primarily by fermentative metabolism even under aerobic growth conditions. Growth yield was reduced by 90% in SFM minus glucose, 50% in SFM minus NaHCO3, 90% in SFM minus yeast extract, 100% in SFM minus Trypticase and yeast extract, and 30% in SFM minus haemin or Trypticase. Growth was not detectable when a known mixture of amino acids, vitamins, and nucleic acid bases were substituted for Trypticase and yeast extract in SFM; addition to the latter medium of a peptide source such as Trypticase or casitone supported good growth of the organism. When NaHCO3 was omitted from SFM and dissolved CO2 in the medium was rigorously excluded, growth was undetectable indicating that C. pyogenes has an obligate requirement for CO2 for growth. Succinate, formate and acetate were the major fermentation products in SFM, whereas in SFM minus HCO-3 or haemin, lactate was the major product and only small quantities of other acids accumulated.     

Structure and activation dynamics of RBL-2H3 cells observed with scanning force microscopy.

Surface and subsurface dynamics of Rat Basophilic Leukemia cells, a model system of stimulated secretion, were imaged using Scanning Force Microscopy (SFM) at a rate of 50-60 s/image. Cytoskeletal elements and organelles were tracked within quiescent cells and those activated after IgE receptor crosslinking. In addition, surface waves were observed moving within the plasma membrane. The structures seen in quiescent and activated cells can be correlated with those seen in electron micrographs and topographic SFM images of fixed detergent-extracted cells. Furthermore, images of the detergent-extracted nuclei reveal the presence of numerous nuclear pore complexes. High-magnification images of the nuclear pore complexes show evidence of subunit structure and exhibit dimensions consistent with those reported previously using electron microscopy. The behavior and overall change in morphology of cells observed during activation was consistent with that observed under similar conditions with Differential Interference Contrast microscopy. This study demonstrates that SFM, unlike other techniques, can be used to provide high-resolution information in both fixed and living cells.     

A Site-Specific Phosphorylation of the Focal Adhesion Kinase Controls the Formation of Spheroid Cell Clusters

Human dental follicle cells (DFCs) are ectomesenchymal multipotent stem cells that form spheroid cell clusters (SCCs) under serum free medium cell culture conditions (SFM). Until today, molecular mechanisms for the formation of SCCs are unknown. In this study a quantitative phosphoproteomics approach revealed regulated phosphorylated proteins in SCCs, which were derived from DFCs after 24 and 48 h in SFM. These regulated proteins were categorized using the Kyoto encyclopedia of genes and genomes program. Here, cellular processes and signaling pathway were identified such as the focal adhesion kinase (FAK) signaling pathway. In addition to the phosphoproteomics approach we showed that a specific phosphorylation of FAK (Y397) was required for the formation of SCCs. In conclusion, this study disclosed the phosphoproteome of SCCs for the first time and showed that the FAK signaling pathway is required for the formation of SCCs.     

Yeast hydrolysate as a low-cost additive to serum-free medium for the production of human thrombopoietin in suspension cultures of Chinese hamster ovary cells

To enhance the performance of a serum-free medium (SFM) for human thrombopoietin (hTPO) production in suspension cultures of recombinant Chinese hamster ovary (rCHO) cells, several low-cost hydrolysates such as yeast hydrolysate (YH), soy hydrolysate, wheat gluten hydrolysate and rice hydrolysate were tested as medium additives. Among various hydrolysates tested, the positive effect of YH on hTPO production was most significant. When 5 g l^–1 YH was added to SFM, the maximum hTPO concentration in batch culture was 40.41 g ml^–1, which is 11.5 times higher than that in SFM without YH supplementation. This enhanced hTPO production in YH-supplemented SFM was obtained by the combined effect of enhanced q_hTPO (the specific rate of hTPO production). The supplementation of YH in SFM increased q_hTPO by 294% and extended culture longevity by >2 days if the culture was terminated at a cell viability of 50%. Furthermore, cell viability throughout the culture using YH-supplemented SFM was higher than that using any other hydrolysate-supplemented SFM tested, thereby minimizing degradation of hTPO susceptible to proteolytic degradation. In addition, YH supplementation did not affect in vivo biological activity of hTPO. Taken together, the results obtained demonstrate the potential of YH as a medium additive for hTPO production in serum-free suspension cultures of rCHO cells.     

Complementary visualization of mitotic barley chromatin by field-emission scanning electron microscopy and scanning force microscopy

The surface structure of mitotic barley chromatin was studied by field-emission scanning electron microscopy (FESEM) and scanning force microscopy (SFM). Different stages of the cell cycle were accessible after a cell suspension was dropped onto a glass surface, chemical fixed, and critically point dried. Imaging was carried out with metal-coated specimen or uncoated specimen (only for SFM). The spatial contour of the chromatin could be resolved by SFM correlating to FESEM data. The experimentally determined volume of the residue chromatin during mitosis was within the range of 65-85 microm(3). A comparison with the theoretically calculated volume indicated a contribution of about 40% of internal cavities. Decondensation of chromosomes by proteinase K led to a drastic decrease in the chromosome volume, and a 3-D netlike architecture of the residue nucleoprotein material, similar to that in the intact chromosome, was obvious. Incubation of metaphase chromosomes in citrate buffer permitted access to different levels of chromatin packing. We imaged intact chromosomes in liquid by SFM without any intermediate drying step. A granular surface was obvious but with an appreciably lower resolution. Under similar imaging conditions proteinase K-treated chromosomes exhibited low topographic contrast but were susceptible to plastic deformations.     

A forest typology for monitoring sustainable forest management: The case of European Forest Types

Abstract

Sustainable forest management (SFM) is presently widely accepted as the overriding objective for forest policy and practice. Regional processes are in progress all over the world to develop and implement criteria and indicators of SFM. In continental Europe, a set of 35 Pan-European indicators has been endorsed under the Ministerial Conference on the Protection of Forests in Europe (MCPFE) to measure progress towards SFM in the 44 countries of the region. The formulation of seven indicators (forest area, growing stock, age structure/diameter distribution, deadwood, tree species composition, damaging agents, naturalness) requires national data to be reported by forest types. Within the vast European forest area the values taken by these indicators show a considerable range of variation, due to variable natural conditions and anthropogenic influences. Given this variability, it is very difficult to grasp the meaning of these indicators when taken out of their ecological background. The paper discusses the concepts behind, and the requirements of, a classification more soundly ecologically framed and suitable for MCPFE reporting than the three (un-informative) classes adopted so far: broadleaved forest, coniferous forest, mixed broadleaved and coniferous forest. We propose a European Forest Types scheme structured into a reasonably higher number of classes, that would improve the specificity of the indicators reported under the MCPFE process and its understanding.     

Scanning force microscopy of DNA molecules elongated by convective fluid flow in an evaporating droplet.

Scanning force microscopy (SFM) was used to image intact, nearly fully elongated lambda bacteriophage DNA molecules, fixed onto freshly cleaved mica surfaces. Molecular elongation and fixation were accomplished using a newly characterized fixation technique, termed "fluid fixation." Here convective fluid flows generated within an evaporating droplet of DNA solution efficiently elongate DNA molecules for fixation onto suitably charged surfaces. SFM images of a very large bacteriophage genome, G, showed the presence of double-stranded bubbles. We speculate that these structures may contain putative replication forks. Overall, the experiments presented here demonstrate the viability of using fluid fixation for the preparation of DNA molecules for SFM imaging. The combination of largely automatable optically based techniques with the high-resolution SFM imaging presented here will likely produce a high-throughput system for detailed physical mapping of genomic DNA or clones.     

Effects of long- and short-term passage of insect cells in different culture media on baculovirus replication

Two insect cell lines that had been maintained in both serum-free (SFM) and serum-containing (SCM) media for over 5 years were each tested for their ability to replicate baculovirus. The gypsy moth cell line, IPLB-LdEIta (Ld), produced similar (not statistically different) amounts of gypsy moth nucleopolyhedrovirus (LdMNPV) occlusion bodies (OBs) in the two media (serum-free Ex-Cell 400 and TC-100 with 9% (v/v) fetal bovine serum, SCM(1)) but produced more of the Autographa californica nucleopolyhedrovirus (AcMNPV) OBs in SFM than in SCM(1). When Ld cells normally grown in SCM(1) were switched to SFM, production of OBs from both viruses improved and, after three passages, reached higher levels of AcMNPV production than in cells normally maintained in that medium. Alternatively, cells switched from SFM to SCM(1) initially produced as much (in the case of LdMNPV) or higher (in the case of AcMNPV) levels of virus OBs than cells normally maintained in SCM(1) but productivity dropped off over subsequent passages such that after five passages in SCM(1), cells produced substantially fewer OBs of both viruses. A fall armyworm cell line (IPLB-SF21AE; Sf) showed slightly different effects from long- and short-term passage in SFM (Ex-Cell 400) or SCM(2) (TMN-FH). Cells maintained in SFM produced about 20 times more AcMNPV OBs than cells maintained long-term in SCM. Sf cells switched from SFM to SCM maintained the level of production of that seen in SFM at the first passage, but quickly dropped off OB production levels to that normally seen in SCM. Alternatively, SCM-maintained Sf cells produced higher levels at the first passage in SFM and, within five passages in SFM, reached levels found in cells maintained for long term in this medium. Under the conditions in which these two cell lines were infected, the highest levels of AcMNPV OB production in Ld cells were about five times that of Sf cells. In a separate series of experiments, cells normally grown in SFM were passaged over five times in Ex-Cell 400 to which serum was added; both cell lines produced as much virus as that in SFM. These results suggest that it is not the serum per se but rather some other components which differ between the SFM and the SCM formulations that are responsible for the varied virus production obtained in these studies. The results of these studies suggest that a maintenance and virus production protocol can be developed with Ld cells which could improve overall efficiency of virus production. These studies also suggest that long-term maintenance of cells in SFM was not detrimental to their ability to produce baculoviruses.     

SFM studies of carbon ion induced damages in plasmid DNA

In this study we present for the first time detailed scanning force microscopy (SFM) investigations of carbon ion induced damages in plasmid DNA in order to obtain information about the biological effectiveness of particle radiation. For this purpose, we have combined SFM and gel electrophoresis measurements in a dose range between D = 0 Gy and 5000 Gy. After irradiation with C ions, the percentage of double-strand breaks (DSBs) increases drastically, i.e. from initially 0% for D = 0 Gy to 38% for D = 5000 Gy. Increasing the dose over the total range is accompanied by a shortening of the average fragment length from L = 1100 nm to L = 575 nm. In addition to our experiments, the average numbers of induced DSBs per irradiated plasmid and per broken plasmid have been calculated from the SFM measurements. The most important among the numerous results is that a significant amount of plasmids has suffered more than two DSBs for all applied doses, indicating multiple DSBs. The number of DSBs per broken plasmid increases from approximately 1.7 after irradiation with a dose of D = 250 Gy to 3.2 after exposure to the highest dose of D = 5000 Gy. The results provide experimental data for the spatially correlated production of DSBs after carbon irradiation, that are relevant to the understanding of its biological effectiveness.     

Approaches for recombinant human factor IX production in serum-free suspension cultures

Objective

To establish a serum-free suspension process for production of recombinant human factor IX (rhFIX) based on the human cell line HEK 293T by evaluating two approaches: (1) serum-free suspension adaptation of previously genetic modified cells (293T-FIX); and (2) genetic modification of cells already adapted to such conditions (293T/SF-FIX).

Results

After 10 months, 293T-FIX cells had become adapted to FreeStyle 293 serum-free medium (SFM) in Erlenmeyer flasks. After 48 and 72 h of culture, 2.1 µg rhFIX/ml and 3.3 µg rhFIX/ml were produced, respectively. However, no biological activity was detected. In the second approach, wild-type 293T cells were adapted to the same SFM (adaptation process took only 2 months) and then genetically modified for rhFIX production. After 48 h of culture, rhFIX reached 1.5 µg/ml with a biological activity of 0.2 IU/ml, while after 72 h, the production was 2.4 µg/ml with a biological activity of 0.3 IU/ml.

Conclusion

The findings demonstrate that the best approach to establish an rhFIX production process in suspension SFM involves the genetic modification of cells already adapted to the final conditions. This approach is time saving and may better ensure the quality of the produced protein.

     

Evaluation of swine fertilisation medium (SFM) efficiency in preserving spermatozoa quality during long-term storage in comparison to four commercial swine extenders

In pig production, artificial insemination is widely carried out and the use of fresh diluted semen is predominant. For this reason, there are increasing interests in developing new extenders and in establishing the optimal storage conditions for diluted spermatozoa. In the last few decades, we utilised a homemade diluent (swine fertilisation medium (SFM)) for spermatozoa manipulation and biotechnological application as the production of transgenic pigs utilising the sperm-mediated gene transfer technique. The purpose of the present study is therefore to analyse the ability of SFM, in comparison to four commercial extenders, in preserving the quality of diluted boar semen stored at 16.5°C till 15 days. We utilised some of the main predictive tests as objectively measured motility, acrosome and sperm membrane integrity, high mitochondrial membrane potential and pH. Based on our in vitro study, SFM could be declared as a good long-term extender, able to preserve spermatozoa quality as well as Androhep Enduraguard for up to 6 to 9 days and more.     

Scanning Force Microscopy at the Air-Water Interface of an Air Bubble Coated with Pulmonary Surfactant

To study the structure-function relationship of pulmonary surfactant under conditions close to nature, molecular films of a model system consisting of dipalmitoylphosphatidylcholine, dipalmitoylphosphatidylglycerol, and surfactant-associated protein C were prepared at the air-water interface of air bubbles about the size of human alveoli (diameter of 100 μm). The high mechanical stability as well as the absence of substantial film flow, inherent to small air bubbles, allowed for scanning force microscopy (SFM) directly at the air-water interface. The SFM topographical structure was correlated to the local distribution of fluorescent-labeled dipalmitoylphosphatidylcholine, as revealed from fluorescence light microscopy of the same bubbles. Although SFM has proven before to be exceptionally well suited to probe the structure of molecular films of pulmonary surfactant, the films so far had to be transferred onto a solid support from the air-water interface of a film balance, where they had been formed. This made them prone to artifacts imposed by the transfer. Moreover, the supported monolayers disallowed the direct observation of the structural dynamics associated with expansion and compression of the films as upon breathing. The current findings are compared in this respect to our earlier findings from films, transferred onto a solid support.     

Quasi-cubic magnetite/silica core-shell nanoparticles as enhanced MRI contrast agents for cancer imaging

Development of magnetic resonance imaging (MRI) contrast agents that can be readily applied for imaging of biological tissues under clinical settings is a challenging task. This is predominantly due to the expectation of an ideal MR agent being able to be synthesized in large quantities, possessing longer shelf life, reasonable biocompatibility, tolerance against its aggregation in biological fluids, and high relaxivity, resulting in better contrast during biological imaging. Although a repertoire of reports address various aforementioned issues, the previously reported results are far from optimal, which necessitates further efforts in this area. In this study, we demonstrate facile large-scale synthesis of sub-100 nm quasi-cubic magnetite and magnetite/silica core-shell (Mag@SiO2) nanoparticles and their applicability as a biocompatible T2 contrast agent for MRI of biological tissues. Our study suggests that silica-coated magnetite nanoparticles reported in this study can potentially act as improved MR contrast agents by addressing a number of aforementioned issues, including longer shelf life and stability in biological fluids. Additionally, our in vitro and in vivo studies clearly demonstrate the importance of silica coating towards improved applicability of T2 contrast agents for cancer imaging.     

Perovskite Oxyfluoride Electrode Enabling Direct Electrolyzing Carbon Dioxide with Excellent Electrochemical Performances

Solid oxide electrolysis cells (SOECs) can efficiently convert the greenhouse‐gas CO₂ to valuable fuel CO at the cathodes. Herein, fluorine is doped into mixed ionic–electronic conducting Sr₂Fe_1.5Mo_0.5O_6‐δ (SFM), to evaluate its potential use as a cathode for CO₂ reduction reaction (CO₂‐RR). SFM retains its cubic structure after doped with fluorine, forming perovskite oxyfluoride Sr₂Fe_1.5Mo_0.5O_6‐δF_0.1 (F‐SFM). The substitution of oxygen by fluorine increases CO₂ adsorption by a factor of ≈2, bulk oxygen vacancy concentration by 35–37% at 800 °C, and consequently enhances the surface reaction rate constant for CO₂‐RR and chemical bulk diffusion coefficient by factors of 2–3. The faster kinetics are also reflected by a lower polarization resistance of 0.656 Ω cm² for F‐SFM than 1.130 Ω cm² for SFM at 800 °C in symmetrical cells. Furthermore, the single cell with F‐SFM cathode exhibits the best CO₂ electrolysis performance among the reported perovskite electrodes, achieving current density of 1.36 A cm^?2 at 1.5 V and excellent stability over 120 h at 800 °C under harsh conditions. The theoretical computations confirm that fluorine doping is energetically favorable to CO₂ adsorption and dissociation. The present work provides a promising strategy for the design of robust cathodes for direct CO₂ electrolysis in SOECs.