Single molecule microscopy in 3D cell cultures and tissues

From the onset of the first microscopic visualization of single fluorescent molecules in living cells at the beginning of this century, to the present, almost routine application of single molecule microscopy, the method has well-proven its ability to contribute unmatched detailed insight into the heterogeneous and dynamic molecular world life is composed of. Except for investigations on bacteria and yeast, almost the entire story of success is based on studies on adherent mammalian 2D cell cultures. However, despite this continuous progress, the technique was not able to keep pace with the move of the cell biology community to adapt 3D cell culture models for basic research, regenerative medicine, or drug development and screening. In this review, we will summarize the progress, which only recently allowed for the application of single molecule microscopy to 3D cell systems and give an overview of the technical advances that led to it. While initially posing a challenge, we finally conclude that relevant 3D cell models will become an integral part of the on-going success of single molecule microscopy.

Separable spatiotemporal priors for convex reconstruction of time-varying 3D point clouds

Reconstructing 3D motion data is highly under-constrained due to several common sources of data loss during measurement, such as projection, occlusion, or miscorrespondence. We present a statistical model of 3D motion data, based on the Kronecker structure of the spatiotemporal covariance of natural motion, as a prior on 3D motion. This prior is expressed as a matrix normal distribution, composed of separable and compact row and column covariances. We relate the marginals of the distribution to the shape, trajectory, and shape-trajectory models of prior art. When the marginal shape distribution is not available from training data, we show how placing a hierarchical prior over shapes results in a convex MAP solution in terms of the trace-norm. The matrix normal distribution, fit to a single sequence, outperforms state-of-the-art methods at reconstructing 3D motion data in the presence of significant data loss, while providing covariance estimates of the imputed points.

Biomimicking natural nanopatterned topology by 3D laser lithography

Natural nanopatterned surfaces (nNPS) present on insect wings have demonstrated bactericidal activity [1, 2]. Fabricated nanopatterned surfaces (fNPS) derived by characterization of these wings have also shown superior bactericidal activity [2]. However bactericidal NPS topologies vary in both geometry and chemical characteristics of the individual features in different insects and fabricated surfaces, rendering it difficult to ascertain the optimum geometrical parameters underling bactericidal activity. This situation calls for the adaptation of new and emerging techniques, which are capable of fabricating and characterising comparable structures to nNPS from biocompatible materials. In this research, CAD drawn nNPS representing an area of 10 μm x10 μm was fabricated on a fused silica glass by Nanoscribe photonic professional GT 3D laser lithography system using two photon polymerization lithography. The glass was cleaned with acetone and isopropyl alcohol thrice and a drop of IP-DIP photoresist from Nanoscribe GmbH was cast onto the glass slide prior to patterning. Photosensitive IP-DIP resist was polymerized with high precision to make the surface nanopatterns using a 780 nm wavelength laser. Both moving-beam fixedsample (MBFS) and fixed-beam moving-sample (FBMS) fabrication approaches were tested during the fabrication process to determine the best approach for the precise fabrication of the required nanotopological pattern. Laser power was also optimized to fabricate the required fNPS, where this was changed from 3mW to 10mW to determine the optimum laser power for the polymerization of the photoresist for fabricating FNPS...

Supramolecular assembly of heterocirculenes in 2D and 3D

The results of a high-resolution ambient STM study of ‘sulflower’ (octathio[8]circulene) and ‘selenosulflower’ (sym-tetraselena-tetrathio[8]circulene) molecules, immobilized in a hydrogen-bonded matrix of trimesic acid (TMA) at the solid–liquid interface, are compared with the STM and X-ray structure of separate host and guest 2D and 3D crystals, respectively.

A 3D numerical study of the collateral capacity of the circle of Willis with anatomical variation in the posterior circulation

Background The Circle of Willis (CoW) is the most important collateral pathway of the cerebral artery. The present study aims to investigate the collateral capacity of CoW with anatomical variation when unilateral internalcarotid artery (ICA) is occluded. Methods Basing on MRI data, we have reconstructed eight 3D models with variations in the posterior circulation of the CoW and set four different degrees of stenosis in the right ICA, namely 24%, 43%, 64% and 79%, respectively. Finally, a total of 40 models are performed with computational fluid dynamics simulations. All of the simulations share the same boundary condition with static pressure and the volume flow rate (VFR) are obtained to evaluate their collateral capacity. Results As for the middle cerebral artery (MCA) and the anterior cerebral artery (ACA), the transitional-type model possesses the best collateral capacity. But for the posterior cerebral artery (PCA), unilateral stenosis of ICA has the weakest influence on the unilateral posterior communicating artery (PCoA) absent model. We also find that the full fetal-type posterior circle of Willis is an utmost dangerous variation which must be paid more attention. Conclusion The results demonstrate that different models have different collateral capacities in coping stenosis of unilateral ICA and these differences can be reflected by different outlets. The study could be used as a reference for neurosurgeon in choosing the best treatment strategy.

3D numerical simulation of avascular tumour growth: effect of hypoxic micro-environment in host tissue

A three-dimensional (3D) mathematical model of tumour growth at the avascular phase and vessel remodelling in host tissues is proposed with emphasis on the study of the interactions of tumour growth and hypoxic micro-environment in host tissues. The hybrid based model includes the continuum part, such as the distributions of oxygen and vascular endothelial growth factors (VEGFs), and the discrete part of tumour cells (TCs) and blood vessel networks. The simulation shows the dynamic process of avascular tumour growth from a few initial cells to an equilibrium state with varied vessel networks. After a phase of rapidly increasing numbers of the TCs, more and more host vessels collapse due to the stress caused by the growing tumour. In addition, the consumption of oxygen expands with the enlarged tumour region. The study also discusses the effects of certain factors on tumour growth, including the density and configuration of preexisting vessel networks and the blood oxygen content. The model enables us to examine the relationship between early tumour growth and hypoxic micro-environment in host tissues, which can be useful for further applications, such as tumour metastasis and the initialization of tumour angiogenesis.

Three-dimensional 3d-4f heterometallic polymers containing both azide and carboxylate as co-ligands

The hydrothermal reaction of Ln(NO3)(3), Ni(NO3)(2), NaN3, and isonicotinic acid (L) yielded two novel 3-D coordination frameworks (1 and 2) of general formula [Ni(2)Ln(L)(5)(N-3)(2)(H2O)(3)] center dot 2H(2)O (Ln = Pr(III) for 1 and Nd(III) for 2), containing Ni-Pr or Ni-Nd hybrid extended three-dimensional networks containing both azido and carboxylate as co-ligands. Both the compounds are found to be isostructural and crystallize in monoclinic system having P2(1)/n space group. Here the lanthanide ions are found to be nonacoordinated. Both bidentate and monodentate modes of binding of the carboxylate with the lanthanides have been observed in the above complexes. Variable temperature magnetic studies of the above two complexes have been investigated in the temperature range 2-300 K which showed dominant antiferromagnetic interaction in both the cases and these experimental results are analyzed with the theoretical models. (c) 2008 Elsevier B.V. All rights reserved.

Estimation of light interception in research environments: A joint approach using directional light sensors and 3D virtual plants applied to sunflower (Helianthus annuus) and Arabidopsis thaliana in natural and artificial conditions

Light interception is a major factor influencing plant development and biomass production. Several methods have been proposed to determine this variable, but its calculation remains difficult in artificial environments with heterogeneous light. We propose a method that uses 3D virtual plant modelling and directional light characterisation to estimate light interception in highly heterogeneous light environments such as growth chambers and glasshouses. Intercepted light was estimated by coupling an architectural model and a light model for different genotypes of the rosette species Arabidopsis thaliana (L.) Heynh and a sunflower crop. The model was applied to plants of contrasting architectures, cultivated in isolation or in canopy, in natural or artificial environments, and under contrasting light conditions. The model gave satisfactory results when compared with observed data and enabled calculation of light interception in situations where direct measurements or classical methods were inefficient, such as young crops, isolated plants or artificial conditions. Furthermore, the model revealed that A. thaliana increased its light interception efficiency when shaded. To conclude, the method can be used to calculate intercepted light at organ, plant and plot levels, in natural and artificial environments, and should be useful in the investigation of genotype-environment interactions for plant architecture and light interception efficiency. This paper originates from a presentation at the 5th International Workshop on Functional–Structural Plant Models, Napier, New Zealand, November 2007.

3d and 4d core level X-ray photoelectron spectroscopy of mixed-valence CePd3

3d and 4d core-level XPS spectra for CePd3, a mixed-valence system, have been measured. Each spectrum exhibits two sets of structures, each corresponding to one of the valence states of cerium. Thus the usefulness of XPS, which has so far not been used extensively to investigate the mixed-valence cerium systems, is pointed out.

Developing Queensland 3D Tropical Fruits and Nuts modelling capabilities

Development of 3D functional structural plant models for macadamias and other tropical fruit and nuts.

Hanging drop: An in vitro air toxic exposure model using human lung cells in 2D and 3D structures

Using benzene as a candidate air toxicant and A549 cells as an in vitro cell model, we have developed and validated a hanging drop (HD) air exposure system that mimics an air liquid interface exposure to the lung for periods of 1 h to over 20 days. Dose response curves were highly reproducible for 2D cultures but more variable for 3D cultures. By comparing the HD exposure method with other classically used air exposure systems, we found that the HD exposure method is more sensitive, more reliable and cheaper to run than medium diffusion methods and the CULTEX (R) system. The concentration causing 50% of reduction of cell viability (EC50) for benzene, toluene, p-xylene, m-xylene and o-xylene to A549 cells for 1 h exposure in the HD system were similar to previous in vitro static air exposure. Not only cell viability could be assessed but also sub lethal biological endpoints such as DNA damage and interleukin expressions. An advantage of the HD exposure system is that bioavailability and cell concentrations can be derived from published physicochemical properties using a four compartment mass balance model. The modelled cellular effect concentrations EC50(cell) for 1 h exposure were very similar for benzene, toluene and three xylenes and ranged from 5 to 15 mmol/kg(dry weight) which corresponds to the intracellular concentration of narcotic chemicals in many aquatic species, confirming the high sensitivity of this exposure method. (C) 2013 Elsevier B.V. All rights reserved.

Save Left Shark: Katy Perry, Intellectual Property, and 3D Printing

There has been much interest in how intellectual property law, policy and practice will adapt to the emergence of 3D printing and the maker movement. Intellectual property lawyers will have to grapple with the impact of additive manufacturing upon a variety of forms of intellectual property — including copyright law, trade mark law, designs law, patent law and trade secrets. The disruptive technology of 3D printing will both pose opportunities and challenges for legal practitioners and policy makers.A performance by pop princess Katy Perry at the 2015 Super Bowl has sparked a public controversy over intellectual property, internet memes and 3D printing.

Inventing the Future: Intellectual Property and 3D Printing

A new technology – 3D printing – has the potential to make radical changes to aspects of the way in which we live. Put simply, it allows people to download designs and turn them into physical objects by laying down successive layers of material. Replacements or parts for household objects such as toys, utensils and gadgets could become available at the press of a button. With this innovation, however, comes the need to consider impacts on a wide range of forms of intellectual property, as Dr Matthew Rimmer explains. 3D Printing is the latest in a long line of disruptive technologies – including photocopiers, cassette recorders, MP3 players, personal computers, peer to peer networks, and wikis – which have challenged intellectual property laws, policies, practices, and norms. As The Economist has observed, ‘Tinkerers with machines that turn binary digits into molecules are pioneering a whole new way of making things—one that could well rewrite the rules of manufacturing in much the same way as the PC trashed the traditional world of computing.’

1-D hydrogen-bonded organization of hexanuclear {3d-4f-5d} complexes: evidence for slow relaxation of the magnetization for [{LMe2Ni(H2O)Ln(H2O)4.5}2{W(CN)8}2] with Ln = Tb and Dy

Heterometallic {3d-4f-5d} aggregates with formula [{LMe2Ni(H2O)Ln(H2O)4.5}2{W(CN)8}2]·15H2O, (LMe2 stands for N,N-2,2-dimethylpropylenedi(3-methoxysalicylideneiminato) Schiff-base ligand) with Ln = Gd, Tb, Dy, have been obtained by reacting bimetallic [LMe2Ni(H2O)2Ln(NO3)3] and Cs3{W(CN)8} in H2O. The hexanuclear complexes are organized in 1-D arrays by means of hydrogen bonds established between the solvent molecules coordinated to Ln and the CN ligands of an octacyanometallate moiety. The X-ray structure was solved for the Tb derivative. Magnetic behavior indicates ferromagnetic {W–Ni} and {Ni–Ln} interactions (JNiW = 18.5 cm-1, JNiGd = 1.85 cm-1) as well as ferromagnetic intermolecular interactions mediated by the H-bonds. Dynamic magnetic susceptibility studies reveal slow magnetic relaxation processes for the Tb and Dy derivatives, suggesting SMM type behavior for these compounds.

Three-component assembly of a metal-inorganic 3D Co(II) polymer containing bridging hydrazine

Three-component metal-inorganic assembly of a Co(II) network representing the first example of a 3D coordination polymer containing a hydrazine bridging ligand, has been synthesized and characterized.