Nanomechanical properties of molecular organic thin films

Using atomic force microscopy we have studied the nanomechanical response to nanoindentations of surfaces of highly oriented molecular organic thin films (thickness¿1000¿nm). The Young¿s modulus E can be estimated from the elastic deformation using Hertzian mechanics. For the quasi-one-dimensional metal tetrathiafulvalene tetracyanoquinodimethane E~20¿GPa and for the ¿ phase of the p-nitrophenyl nitronyl nitroxide radical E~2GPa. Above a few GPa, the surfaces deform plastically as evidenced by discrete discontinuities in the indentation curves associated to molecular layers being expelled by the penetrating tip.

Oligomerization and DNA binding of Ler, a master regulator of pathogenicity of enterohemorrhagic and enteropathogenic Escherichia coli

Ler is a DNA-binding, oligomerizable protein that regulates pathogenicity islands in enterohemorrhagic and enteropathogenic Escherichia coli strains. Ler counteracts the transcriptional silencing effect of H-NS, another oligomerizable nucleoid-associated protein. We studied the oligomerization of Ler in the absence and presence of DNA by atomic force microscopy. Ler forms compact particles with a multimodal size distribution corresponding to multiples of 35 units of Ler. DNA wraps around Ler particles that contain more than 1516 Ler monomers. The resulting shortening of the DNA contour length is in agreement with previous measurements of the length of DNA protected by Ler in footprinting assays. We propose that the repetition unit corresponds to the number of monomers per turn of a tight helical Ler oligomer. While the repressor (H-NS) and anti-repressor (Ler) have similar DNA-binding domains, their oligomerization domains are unrelated. We suggest that the different oligomerization behavior of the two proteins explains the opposite results of their interaction with the same or proximal regions of DNA.

Polymorphisms in fibronectin binding protein A of Staphylococcus aureus are associated with infection of cardiovascular devices.

Medical implants, like cardiovascular devices, improve the quality of life for countless individuals but may become infected with bacteria like Staphylococcus aureus. Such infections take the form of a biofilm, a structured community of bacterial cells adherent to the surface of a solid substrate. Every biofilm begins with an attractive force or bond between bacterium and substratum. We used atomic force microscopy to probe experimentally forces between a fibronectin-coated surface (i.e., proxy for an implanted cardiac device) and fibronectin-binding receptors on the surface of individual living bacteria from each of 80 clinical isolates of S. aureus. These isolates originated from humans with infected cardiac devices (CDI; n = 26), uninfected cardiac devices (n = 20), and the anterior nares of asymptomatic subjects (n = 34). CDI isolates exhibited a distinct binding-force signature and had specific single amino acid polymorphisms in fibronectin-binding protein A corresponding to E652D, H782Q, and K786N. In silico molecular dynamics simulations demonstrate that residues D652, Q782, and N786 in fibronectin-binding protein A form extra hydrogen bonds with fibronectin, complementing the higher binding force and energy measured by atomic force microscopy for the CDI isolates. This study is significant, because it links pathogenic bacteria biofilms from the length scale of bonds acting across a nanometer-scale space to the clinical presentation of disease at the human dimension.

Further ultrastructural evidence that spirochaetes may play a role in the aetiology of Alzheimer's disease

Recently it was reported that, at autopsy, in neuropathologically confirmed cases of Alzheimer's disease spirochaetes were found in blood and cerebrospinal fluid using dark-field microscopy. Moreover, the spirochaetes were isolated and cultured from brain tissue. We now show, using scanning electron microscopy and atomic force microscopy that the helically shaped microorganisms isolated and cultured from the Alzheimer brains possess axial filaments. This indicates that these microorganisms taxonomically indeed belong to the order Spirochaetales. A morphometric analysis reinforces this notion.

A role for septins in the interaction between the Listeria monocytogenes INVASION PROTEIN InlB and the Met receptor.

Septins are conserved GTPases that form filaments and are required for cell division. During interphase, septin filaments associate with cellular membrane and cytoskeleton networks, yet the functional significance of these associations have, to our knowledge, remained unknown. We recently discovered that different septins, SEPT2 and SEPT11, regulate the InlB-mediated entry of Listeria monocytogenes into host cells. Here we address the role of SEPT2 and SEPT11 in the InlB-Met interactions underlying Listeria invasion to explore how septins modulate surface receptor function. We observed that differences in InlB-mediated Listeria entry correlated with differences in Met surface expression caused by septin depletion. Using atomic force microscopy on living cells, we show that septin depletion significantly reduced the unbinding force of InlB-Met interaction and the viscosity of membrane tethers at locations where the InlB-Met interaction occurs. Strikingly, the same order of difference was observed for cells in which the actin cytoskeleton was disrupted. Consistent with a proposed role of septins in association with the actin cytoskeleton, we show that cell elasticity is decreased upon septin or actin inactivation. Septins are therefore likely to participate in anchorage of the Met receptor to the actin cytoskeleton, and represent a critical determinant in surface receptor function.

Theory of Wetting-Induced Fluid Entrainment by Advancing Contact Lines on Dry Surfaces

We report on the onset of fluid entrainment when a contact line is forced to advance over a dry solid of arbitrary wettability. We show that entrainment occurs at a critical advancing speed beyond which the balance between capillary, viscous, and contact-line forces sustaining the shape of the interface is no longer satisfied. Wetting couples to the hydrodynamics by setting both the morphology of the interface at small scales and the viscous friction of the front. We find that the critical deformation that the interface can sustain is controlled by the friction at the contact line and the viscosity contrast between the displacing and displaced fluids, leading to a rich variety of wetting-entrainment regimes. We discuss the potential use of our theory to measure contact-line forces using atomic force microscopy and to study entrainment under microfluidic conditions exploiting colloid-polymer fluids of ultralow surface tension.

Optoelectronic properties of CuPc thin films deposited at different substrate temperatures

Structural and optical characterization of copper phthalocyanine thin film thermally deposited at different substrate temperatures was the aim of this work. The morphology of the films shows strong dependence on temperature, as can be observed by atomic force microscopy and x-ray diffraction spectroscopy, specifically in the grain size and features of the grains. The increase in the crystal phase with substrate temperature is shown by x-ray diffractometry. Optical absorption coefficient measured by photothermal deflection spectroscopy and optical transmittance reveal a weak dependence on the substrate temperature. Besides, the electro-optical response measured by the external quantum efficiency of Schottky ITO/CuPc/Al diodes shows an optimized response for samples deposited at a substrate temperature of 60 °C, in correspondence to the I-V diode characteristics.

Characterization of the neuronal microtubule regulator SCG10 in transfected cells and " in vivo "

SUMMARY The ability of neuronal processes to find their way along complex paths and to establish appropriate connections depends on continual rearrangements of the cytoskeletal components. The regulation of microtubules plays an important role for morphological changes underlying nevrite outgrowth, axonal elongation, and growth cone steering. SCG10 (superior cervical ganglion clone 10) is a neuronal growthassociated protein developmentally regulated and highly enriched in the neuronal growth cones. SCG10 presents a microtubule destabilizing activity that could participate to the regulation of microtubule dynamics and thus explain microtubule behaviors in the growth cone during axonal elongation and turning. It is here suggested that a tight control of the opposite effects on microtubules of SCG10 and the stabilizing microtubule-associated protein MAP1B allows a fine tuning of cytoskeletal rearrangement and may provide the required microtubule dynamic instability to promote axonal growth. Moreover, antibodyblockade of SCG10 function, that leads to growth cone pauses similar as those triggered by the guidance molecule EphB, and the modulation of SCG10 activity by the Rho GTPase Rnd1 suggest a potential role for SCG10 in the signal transduction pathways of extracellular guidance cues. The identification of the active zone protein Bassoon as a potential interaction partner for the SCG10-related protein NPC2, using atomic force microscopy as well as COS-7 and neuronal cell cultures, also gives new insights for a role of this protein family into the processes of synapse genesis or plasticity. Finally, SCG10 mutant mice generated by gene targeting and expressing a soluble form of the protein have been characterized during early postnatal development and in the adulthood. Due to the deletion of its membrane binding domain, SCG10 specific subcellular targeting to growth cones is compromised and results in impairments of motor and coordination development. Further histological analysis in the sciatic nerve reveal that these symptoms are associated with neurodegenerative signs. RESUME Une navigation correcte des prolongements cellulaires neuronaux leur permettant de former des connections appropriées repose sur de continuels réarrangements des constituants de leur cytosquelette. La régulation des microtubules joue notamment un rôle important dans les changements morphologiques qui accompagnent la croissance axonale et les réorientations du cône de croissance. SCG10 (superior cervical ganglion clone 10) est une protéine étroitement associée à la croissance neuronale, hautement régulée durant le développement et abondante au niveau du cône de croissance. SCG10 présente une activité déstabilisatrice sur les microtubules qui pourrait permettre une régulation des paramètres dynamiques propres aux microtubules et ainsi expliquer leur comportement durant la navigation du cône de croissance. Il est ici proposé qu'un contrôle précis des effets opposés de SCG10 et d'une autre protéine stabilisante associée aux microtubules (MAP1 B) permette un réglage fin des réarrangements du cytosquelette et puisse ainsi produire l'instabilité dynamique nécessaire à la croissance anale. Par ailleurs, le blocage de la fonction de SCG10 par un anticorps spécifique, conduisant à des pauses du cônes de croissance similaires à celles provoquées par la molécule de guidage EphB, ainsi que la modulation de l'activité de SCG10 par la Rho GTPase Rnd1 suggèrent une potentielle implication de SCG10 dans les voies de transduction des signaux provenant de molécules de guidage extracellulaires. L'identification d'une interaction de la protéine synaptique Bassoon avec la protéine NPC2 apparentée à SCG10, au moyen de la microscopie à force atomique et dans des cultures de cellules neuronales et COS-7, ouvre des perspectives concernant ces protéines dans la formation et la plasticité synaptiques. Finalement, des souris mutantes pour SCG10 produites par ciblage de gène et exprimant une forme soluble de la protéine ont été caractérisées durant la phase précoce du développement et à l'âge adulte. La délétion du domaine permettant l'ancrage de SCG10 aux membranes compromet sa sub-localisation au niveau du cône de croissance et résulte en l'apparition de troubles moteurs et de la coordination. Des analyses histologiques complémentaires au niveau du nerf sciatique montrent que ces symptômes sont associés avec des signes neurodégénératifs.

MOCVD growth andproperties of GaN and AlGaN layers

In this work GaN and AlGaN layers were grown by metal-organic chemical vapor deposition (MOCVD) on sapphire substrates. The research was carried out at Micro and Nanoscience Laboratory of Helsinki University of Technology. The objective of this thesis is the study of MOCVD technique for the growth of GaN and AlGaN films and optimization of growth parameters in purpose to improve crystal quality of the films. The widely used two-step and the new multistep methods have been used for GaN, AlGaN MOCVD growth on c-plane sapphire. Properties of the GaN and AlGaN layers were studied using in-situ reflectance monitoring during MOCVD growth, atomic force microscopy and x-ray diffraction. Compared to the two step method, the multistep method has produced even better qualities of the GaN and AlGaN layers and significant reduction of threading dislocation density.

Functions of the human papillomavirus type 16 E4 protein

1. Abstract Cervical cancer is thought to be the consequence of infection by human papillomaviruses (HPV). In the majority of cases, DNA from HPV type 16 (HPV16) is found in malignant cervical lesions. The initial steps leading to transformation of an infected cell are not clearly understood but in most cases, disruption and integration of the episomal viral DNA must take place. As a consequence, the E2 and E4 genes are usually not expressed whereas the E6 and E7 oncogenes are highly expressed. However, in a normal infection in which the viral DNA is maintained as an episome, all viral genes are expressed. The pattern according to which the viral proteins are made, and therefore the life cycle of the virus, is tightly linked to the differentiation process of the host keratinocyte. The study of the viral oncogenes E6 and E7 has revealed crucial functions in the process of malignant transformation such as degradation of the p53 tumor suppressor protein, deregulation of the Retinoblastoma protein pathway and activation of the telomerase ribonucleoprotein. All these steps are necessary for cancerous lesions to develop. However, the loss of the E2 gene product seems to be necessary for sufficient expression of E6 and E7 in order to achieve such effects. In normal infections, the E4 protein is made abundantly in the later stages of the viral life cycle. Though extensive amounts of work have been carried out to define the function of E4, it still remains unclear. In this study, several approaches have been used to try and determine the functions of E4. First, a cell-penetrating fusion protein was designed and produced in order to circumvent the chronic difficulties of expressing E4 in mammalian cells. Unfortunately, this approach was not successful due to precipitation of the purified fusion protein. Second, the observation that E4 accumulates in cells having modified their adhesion properties led to the hypothesis that E4 might be involved in the differentiation process of keratinocytes. Preliminary results suggest that E4 triggers differentiation. Last, as E4 has been reported to collapse the cytokeratin network of keratinocytes, a direct approach using atomic force microscopy has allowed us to test the potential modification of mechanical properties of cells harboring reorganized cytokeratin networks. If so, a potential role for E4 in viral particle release could be hypothesized. 2. Résumé Il a été établi que le cancer du col de l'utérus se développe essentiellement à la suite d'une infection par le virus du papillome humain (HPV). Dans la majorité des cas analysés, de l'ADN du HPV de type 16 (HPV16) est détecté. Les étapes initiales de la transformation d'une cellule infectée sont mal connues mais il semble qu'une rupture du génome viral, normalement épisomal, suivi d'une intégration dans le génome de la cellule hôte soient des étapes nécessaires dans la plupart des cas. Or il semble qu'il y ait une sélection pour les cas où l'expression des oncogènes viraux E6 et E7 soit favorisée alors que l'expression des gènes E2 et E4 est en général impossible. Par contre, dans une infection dite normale où le génome viral n'est pas rompu, il n'y pas développement de cancer et tous les gènes viraux sont exprimés. L'ordre dans lequel les protéines virales sont produites, et donc le cycle de réplication du virus, est intimement lié au processus de différentiation de la cellule hôte. L'étude des protéines oncogènes E6 et E7 a révélé des fonctions clés dans le processus de transformation des cellules infectées telles que la dégradation du suppresseur de tumeur p53, la dérégulation de la voie de signalisation Rb ainsi que l'activation de la télomérase. Toutes ces activités sont nécessaires au développement de lésions cancéreuses. Toutefois, il semble que l'expression du gène E2 doit être empêchée afin que suffisamment des protéines E6 et E7 soient produites. Lorsque le gène E2 est exprimé, et donc lorsque le génome viral n'est pas rompu, les protéines E6 et E7 n'entraînent pas de telles conséquences. Le gène E4, qui se trouve dans la séquence codante de E2, a aussi besoin d'un génome viral intact pour être exprimé. Dans une infection normale, le gène E4 est exprimé abondamment dans les dernières étapes de la réplication du virus. Bien que de nombreuses études aient été menées afin de déterminer la fonction virale à E4, aucun résultat n'apparaît évident. Dans ce travail, plusieurs approches ont été utilisées afin d'adresser cette question. Premièrement, une protéine de fusion TAT-E4 a été produite et purifiée. Cette protéine, pouvant entrer dans les cellules vivantes par diffusion au travers de la membrane plasmique, aurait permis d'éviter ainsi les problèmes chroniques rencontrés lors de l'expression de E4 dans les cellules mammifères. Malheureusement, cette stratégie n'a pas pu être utilisée à cause de la précipitation de la protéine purifiée. Ensuite, l'observation que E4 s'accumule dans les cellules ayant modifié leurs propriétés d'adhésion a suggéré que E4 pourrait être impliqué dans le procédé de différentiation des kératinocytes. Des résultats préliminaires supportent cette possibilité. Enfin, il a été montré que E4 pouvait induire une réorganisation du réseau des cytokératines. Une approche directe utilisant le microscope à force atomique nous a ainsi permis de tester une potentielle modification des propriétés mécaniques de cellules ayant modifié leur réseau de cytokératines en présence de E4. Si tel est le cas, un rôle dans la libération de particules virales peut être proposé pour E4.

Comprehensive Study of Crystal Growth from Solution

Crystal growth is an essential phase in crystallization kinetics. The rate of crystal growth provides significant information for the design and control of crystallization processes; nevertheless, obtaining accurate growth rate data is still challenging due to a number of factors that prevail in crystal growth. In industrial crystallization, crystals are generally grown from multi-componentand multi-particle solutions under complicated hydrodynamic conditions; thus, it is crucial to increase the general understanding of the growth kinetics in these systems. The aim of this work is to develop a model of the crystal growth rate from solution. An extensive literature review of crystal growth focuses on themodelling of growth kinetics and thermodynamics, and new measuring techniques that have been introduced in the field of crystallization. The growth of a singlecrystal is investigated in binary and ternary systems. The binary system consists of potassium dihydrogen phosphate (KDP, crystallizing solute) and water (solvent), and the ternary system includes KDP, water and an organic admixture. The studied admixtures, urea, ethanol and 1-propanol, are employed at relatively highconcentrations (of up to 5.0 molal). The influence of the admixtures on the solution thermodynamics is studied using the Pitzer activity coefficient model. Theprediction method of the ternary solubility in the studied systems is introduced and verified. The growth rate of the KDP (101) face in the studied systems aremeasured in the growth cell as a function of supersaturation, the admixture concentration, the solution velocity over a crystal and temperature. In addition, the surface morphology of the KDP (101) face is studied using ex situ atomic force microscopy (AFM). The crystal growth rate in the ternary systems is modelled on the basis of the two-step growth model that contains the Maxwell-Stefan (MS) equations and a surface-reaction model. This model is used together with measuredcrystal growth rate data to develop a new method for the evaluation of the model parameters. The validation of the model is justified with experiments. The crystal growth rate in an imperfectly mixed suspension crystallizer is investigatedusing computational fluid dynamics (CFD). A solid-liquid suspension flow that includes multi-sized particles is described by the multi-fluid model as well as by a standard k-epsilon turbulence model and an interface momentum transfer model. The local crystal growth rate is determined from calculated flow information in a diffusion-controlled crystal growth regime. The calculated results are evaluated experimentally.

Integrin-Specific Mechanoresponses to Compression and Extension Probed by Cylindrical Flat-Ended AFM Tips in Lung Cells

Cells from lung and other tissues are subjected to forces of opposing directions that are largely transmitted through integrin-mediated adhesions. How cells respond to force bidirectionality remains ill defined. To address this question, we nanofabricated flat-ended cylindrical Atomic Force Microscopy (AFM) tips with ~1 µm2 cross-section area. Tips were uncoated or coated with either integrin-specific (RGD) or non-specific (RGE/BSA) molecules, brought into contact with lung epithelial cells or fibroblasts for 30 s to form focal adhesion precursors, and used to probe cell resistance to deformation in compression and extension. We found that cell resistance to compression was globally higher than to extension regardless of the tip coating. In contrast, both tip-cell adhesion strength and resistance to compression and extension were the highest when probed at integrin-specific adhesions. These integrin-specific mechanoresponses required an intact actin cytoskeleton, and were dependent on tyrosine phosphatases and Ca2+ signaling. Cell asymmetric mechanoresponse to compression and extension remained after 5 minutes of tip-cell adhesion, revealing that asymmetric resistance to force directionality is an intrinsic property of lung cells, as in most soft tissues. Our findings provide new insights on how lung cells probe the mechanochemical properties of the microenvironment, an important process for migration, repair and tissue homeostasis.

Nanocharacterization of Soft Biological Samples in Shear Mode with Quartz Tuning Fork Probes

Quartz tuning forks are extremely good resonators and their use is growing in scanning probe microscopy. Nevertheless, only a few studies on soft biological samples have been reported using these probes. In this work, we present the methodology to develop and use these nanosensors to properly work with biological samples. The working principles, fabrication and experimental setup are presented. The results in the nanocharacterization of different samples in different ambients are presented by using different working modes: amplitude modulation with and without the use of a Phase-Locked Loop (PLL) and frequency modulation. Pseudomonas aeruginosa bacteria are imaged in nitrogen using amplitude modulation. Microcontact printed antibodies are imaged in buffer using amplitude modulation with a PLL. Finally, metastatic cells are imaged in air using frequency modulation.

Bacterial adhesion efficiency on implant abutments: a comparative study

The attachment of Escherichia coli ATCC 25922 and Staphylococcus aureus ATCC 28213 onto six different materials used to manufacture dental implant abutments was quantitatively determined after 2 and 24 h of contact between the materials and the bacterial cultures. The materials were topographically characterized and their wettability determined, with both parameters subsequently related to bacterial adhesion. Atomic force microscopy, interferometry, and contact angle measurement were used to characterize the materials" surfaces. The results showed that neither roughness nor nano-roughness greatly influenced bacterial attachment whereas wettability strongly correlated with adhesion. After 2 h the degree of E. coli attachment markedly differed depending on the material whereas similar differences were not observed for S. aureus, which yielded consistently higher counts of adhered cells. Nevertheless, after 24 h the adhesion of the two species to the different test materials no longer significantly differed, although on all surfaces the numbers of finally adhered E. coli were higher than those of S. aureus

Diverse set of Turing nanopatterns coat corneae across insect lineages.

Nipple-like nanostructures covering the corneal surfaces of moths, butterflies, and Drosophila have been studied by electron and atomic force microscopy, and their antireflective properties have been described. In contrast, corneal nanostructures of the majority of other insect orders have either been unexamined or examined by methods that did not allow precise morphological characterization. Here we provide a comprehensive analysis of corneal surfaces in 23 insect orders, revealing a rich diversity of insect corneal nanocoatings. These nanocoatings are categorized into four major morphological patterns and various transitions between them, many, to our knowledge, never described before. Remarkably, this unexpectedly diverse range of the corneal nanostructures replicates the complete set of Turing patterns, thus likely being a result of processes similar to those modeled by Alan Turing in his famous reaction-diffusion system. These findings reveal a beautiful diversity of insect corneal nanostructures and shed light on their molecular origin and evolutionary diversification. They may also be the first-ever biological example of Turing nanopatterns.