Computed tomography for in vivo deep over‐1000 nm near‐infrared fluorescence imaging

This study aims to develop a novel cross‐sectional imaging of fluorescence in over‐1000 nm near‐infrared (OTN‐NIR), which allows in vivo deep imaging, using computed tomography (CT) system. Cylindrical specimens of composite of OTN‐NIR fluorophore, NaGdF₄ co‐doped with Yb³⁺ and Ho³⁺ (ex: 980 nm, em: 1150 nm), were embedded in cubic agar (10.5–12 mm) or in the peritoneal cavity of mice and placed on a rotatable stage. When the fluorescence from inside of the samples was serially captured from multiple angles, the images were disrupted by the reflection and refraction of emitted light on the sample‐air interface. Immersing the sample into water filled in a rectangular bath suppressed the disruption at the interface and successfully reconstructed the position and concentration of OTN‐NIR fluorophores on the cross‐sectional images using a CT technique. This is promising as a novel three‐dimensional imaging technique for OTN‐NIR fluorescent image projections of small animals captured from multiple angles.     

3D heart morphological changes in response to developmental temperature in zebrafish: More than ventricle roundness

A new, three‐dimensional geometric morphometric approach was assessed to study the effect of developmental temperature on fish heart shape utilizing geometric morphometrics of three‐dimensional landmarks captured on digitally reconstructed zebrafish hearts. This study reports the first three‐dimensional analysis of the fish heart and demonstrates significant shape modifications occurring after three developmental temperature treatments (T_D = 24, 28 or 32°C) at two distinct developmental stages (juvenile and adult fish). Elevation of T_D induced ventricle roundness in juveniles, males and females. Furthermore, significant differences that have not been described so far in heart morphometric indices (i.e., ventricle sphericity, bulbus arteriosus elongation and relative location, heart asymmetry) were identified. Sex proved to be a significant regulating factor of heart shape plasticity in response to T_D. This methodology offers unique benefits by providing a more precise representation of heart shape changes in response to developmental temperature that are otherwise not discernable with the previously described two‐dimensional methods. Our work provides the first evidence of three‐dimensional shape alterations of the zebrafish heart adding to the emerging rationale of temperature‐driven plastic responses of global warming and seasonal temperature disturbances in wild fish populations and in other ectothermic vertebrates as well (amphibians and reptiles).     

Comparison of Fat–Water MRI and Single‐voxel MRS in the Assessment of Hepatic and Pancreatic Fat Fractions in Humans

The ability to accurately and noninvasively quantify fatty infiltration in organs such as the liver and the pancreas remains a critical component in understanding the link between obesity and its comorbidities such as type 2 diabetes and fatty liver disease. Single‐voxel (¹H) proton magnetic resonance spectroscopy (MRS) has long been regarded as the gold‐standard noninvasive technique for such measurements. Recent advances in three‐dimensional fat–water magnetic resonance imaging (MRI) methods have led to the development of rapid, robust, and quantitative approaches that can accurately characterize the proportion of fat and water content in underlying tissues across the full imaging volume, and hence entire organs of interest. One such technique is called IDEAL (Iterative Decomposition with Echo Asymmetry and Least squares estimation). This article prospectively compares three‐dimensional (3D) IDEAL‐MRI and single‐voxel MRS in the assessment of hepatic (HFF) and pancreatic fat fraction (PFF) in 16 healthy subjects. MRS acquisitions took 3–4 min to complete whereas IDEAL acquisitions were completed in 20‐s breath‐holds. In the liver, there was a strong correlation (slope = 0.90, r² = 0.95, P < 0.001) between IDEAL and MRS‐based fat fractions. In the pancreas, a poorer agreement between IDEAL and MRS was observed (slope = 0.32, r² = 0.51, P < 0.02). The discrepancy of PFF is likely explained by MRS signal contamination from surrounding visceral fat, presumably during respiratory motion. We conclude that IDEAL is equally accurate in characterizing hepatic fat content as MRS, and is potentially better suited for fat quantification in smaller organs such as the pancreas.     

X‐ray computed tomography and its potential in ecological research: A review of studies and optimization of specimen preparation

Imaging techniques are a cornerstone of contemporary biology. Over the last decades, advances in microscale imaging techniques have allowed fascinating new insights into cell and tissue morphology and internal anatomy of organisms across kingdoms. However, most studies so far provided snapshots of given reference taxa, describing organs and tissues under “idealized” conditions. Surprisingly, there is an almost complete lack of studies investigating how an organism′s internal morphology changes in response to environmental drivers. Consequently, ecology as a scientific discipline has so far almost neglected the possibilities arising from modern microscale imaging techniques. Here, we provide an overview of recent developments of X‐ray computed tomography as an affordable, simple method of high spatial resolution, allowing insights into three‐dimensional anatomy both in vivo and ex vivo. We review ecological studies using this technique to investigate the three‐dimensional internal structure of organisms. In addition, we provide practical comparisons between different preparation techniques for maximum contrast and tissue differentiation. In particular, we consider the novel modality of phase contrast by self‐interference of the X‐ray wave behind an object (i.e., phase contrast by free space propagation). Using the cricket Acheta domesticus (L.) as model organism, we found that the combination of FAE fixative and iodine staining provided the best results across different tissues. The drying technique also affected contrast and prevented artifacts in specific cases. Overall, we found that for the interests of ecological studies, X‐ray computed tomography is useful when the tissue or structure of interest has sufficient contrast that allows for an automatic or semiautomatic segmentation. In particular, we show that reconstruction schemes which exploit phase contrast can yield enhanced image quality. Combined with suitable specimen preparation and automated analysis, X‐ray CT can therefore become a promising quantitative 3D imaging technique to study organisms′ responses to environmental drivers, in both ecology and evolution.     

Retracted: Single layer molybdenum disulfide as an optical nanoprobe for 2 photon luminescence and second harmonic generation cell imaging

More recently, tremendous progress has been achieved in the development of two‐dimensional semiconductor materials applied in catalyst, energy application, sensor device and bioengineering since the birth of graphene isolated from graphite. Layered molybdenum disulfide (MoS₂) as an indirect gap semiconductor can efficiently emit photoluminescence (PL) excited by visible light, which shows a great potential in adaptive biological imaging. However, 1 photon PL of MoS₂ for cell imaging purposes suffers from strong autofluorescence and ion‐induced PL quenching. Herein, we report single layer small chitosan decorated MoS₂ nanosheets as a nonbleaching, nonblinking optical nanoprobe under near infrared femtosecond laser excitation and their applications for strong 2 photon luminescence (TPL) and strong second harmonic generation (SHG) bioimaging. Furthermore, the TPL can resist the ion‐induced quenching on the cellular membrane. The proposed TPL and SHG of single‐layer MoS₂ show great potential for real‐time, deep, multiphoton and three‐dimensional bioimaging under low‐power laser excitation.      

Bioassembly of three‐dimensional embryonic stem cell‐scaffold complexes using compressed gases

Tissues are composed of multiple cell types in a well‐organized three‐dimensional (3D) microenvironment. To faithfully mimic the tissue in vivo, tissue‐engineered constructs should have well‐defined 3D chemical and spatial control over cell behavior to recapitulate developmental processes in tissue‐ and organ‐specific differentiation and morphogenesis. It is a challenge to build a 3D complex from two‐dimensional (2D) patterned structures with the presence of cells. In this study, embryonic stem (ES) cells grown on polymeric scaffolds with well‐defined microstructure were constructed into a multilayer cell‐scaffold complex using low pressure carbon dioxide (CO₂) and nitrogen (N₂). The mouse ES cells in the assembled constructs were viable, retained the ES cell‐specific gene expression of Oct‐4, and maintained the formation of embryoid bodies (EBs). In particular, cell viability was increased from 80% to 90% when CO₂ was replaced with N₂. The compressed gas‐assisted bioassembly of stem cell‐polymer constructs opens up a new avenue for tissue engineering and cell therapy. © 2009 American Institute of Chemical Engineers Biotechnol. Prog., 2009     

Unique spectral signature of human cutaneous squamous cell carcinoma by photoacoustic imaging

Cutaneous squamous cell carcinoma (cSCC) is a common skin cancer with metastatic potential. To reduce reoperations due to nonradical excision, there is a need to develop a technique for identification of tumor margins preoperatively. Photoacoustic (PA) imaging is a novel imaging technology that combines the strengths of laser optics and ultrasound. Our aim was to determine the spectral signature of cSCC using PA imaging and to use this signature to visualize tumor architecture and borders. Two‐dimensional PA images of 33 cSCCs and surrounding healthy skin were acquired ex vivo, using 59 excitation wavelengths from 680 to 970 nm. The spectral response of the cSCCs was compared to healthy tissue, and the difference was found to be greatest at wavelengths in the range 765 to 960 nm (P < .05). Three‐dimensional PA images were constructed from spectra obtained in the y‐z plane using a linear stepper motor moving along the x‐plane. Spectral unmixing was then performed which provided a clear three‐dimensional view of the distribution of tumor masses and their borders.     

Detailed imaging and genetic analysis reveal a secondary BRAFL505H resistance mutation and extensive intrapatient heterogeneity in metastatic BRAF mutant melanoma patients treated with vemurafenib

Resistance to treatment is the main problem of targeted treatment for cancer. We followed ten patients during treatment with vemurafenib, by three‐dimensional imaging. In all patients, only a subset of lesions progressed. Next‐generation DNA sequencing was performed on sequential biopsies in four patients to uncover mechanisms of resistance. In two patients, we identified mutations that explained resistance to vemurafenib; one of these patients had a secondary BRAF L505H mutation. This is the first observation of a secondary BRAF mutation in a vemurafenib‐resistant patient‐derived melanoma sample, which confirms the potential importance of the BRAF L505H mutation in the development of therapy resistance. Moreover, this study hints toward an important role for tumor heterogeneity in determining the outcome of targeted treatments.     

Mode‐coupling Smoluchowski dynamics of a double‐stranded DNA oligomer

The local dynamics of a double‐stranded DNA d(TpCpGpCpG)₂ is obtained to second order in the mode‐coupling expansion of the Smoluchowski diffusion theory. The time correlation functions of bond variables are derived and the ¹³C‐nmr spin–lattice relaxation times T₁ of different ¹³C along the chains are calculated and compared to experimental data from the literature at three frequencies. The DNA is considered as a fluctuating three‐dimensional structure undergoing rotational diffusion. The fluctuations are evaluated using molecular dynamics simulations, with the ensemble averages approximated by time averages along a trajectory of length 1 ns. Any technique for sampling the configurational space can be used as an alternative. For a fluctuating three‐dimensional (3D) structure using the three first‐order vector modes of lower rates, higher order basis sets of second‐rank tensor are built to give the required mode coupling dynamics. Second‐ and even first‐order theories are found to be in close agreement with the experimental results, especially at high frequency, where the differences in T₁ for ¹³C in the base pairs, sugar, and backbone are well described. These atomistic calculations are of general application for studying, on a molecular basis, the local dynamics of fluctuating 3D structures such as double‐helix DNA fragments, proteins, and protein–DNA complexes. © 1999 John Wiley & Sons, Inc. Biopoly 50: 613–629, 1999     

Two‐Photon polymerization for microfabrication of three‐dimensional scaffolds for tissue engineering application

In natural tissues cells are embedded in a three‐dimensional fibrous network of biopolymers like collagen, hyaluronic acid etc. This extracellular matrix (ECM) influences the cell fate, the differentiation status, metabolic processes and provides structural integrity. For a three‐dimensional or physiological cell cultivation that are required in biomedical applications (e.g. tissue engineering, BioMEMS) scaffolds are needed. These scaffolds mimic the ECM according to their biocompatibility which comprises aspects of surface compatibility and importantly for tissue engineering applications aspects of structural compatibility. We have evaluated scaffold design parameters for the three‐dimensional cultivation of chondrocytes for the tissue engineering of artificial cartilage. Two‐photon polymerization is a powerful technique for fabrication of polymeric three‐dimensional micro‐ and submicro‐structures. The photoinitiation system for two‐photon polymerization is excited by simultaneous absorption of two photons leading to chemical polymerization reactions. Due to a tight confinement of the excitation volume around the focal point, this method can produce micrometer sized objects maintaining a high spatial resolution down to 100 nm. Two‐photon processes require very high photon densities which are provided by pulsed femtosecond lasers. The potential of this approach for microfabrication of scaffolds for tissue engineering is demonstrated by investigation of the cell response to microstructures with complex three‐dimensional geometry and feature sizes in the range of few micrometers.     

Direct imaging electron microscopy (EM) methods in modern structural biology: Overview and comparison with X‐ray crystallography and single‐particle cryo‐EM reconstruction in the studies of large macromolecules

Determining the structure of macromolecules is important for understanding their function. The fine structure of large macromolecules is currently studied primarily by X‐ray crystallography and single‐particle cryo‐electron microscopy (EM) reconstruction. Before the development of these techniques, macromolecular structure was often examined by negative‐staining, rotary‐shadowing and freeze‐etching EM, which are categorised here as ‘direct imaging EM methods’. In this review, the results are summarised by each of the above techniques and compared with respect to four macromolecules: the ryanodine receptor, cadherin, rhodopsin and the ribosome–translocon complex (RTC). The results of structural analysis of the ryanodine receptor and cadherin are consistent between each technique. The results obtained for rhodopsin vary to some extent within each technique and between the different techniques. Finally, the results for RTC are inconsistent between direct imaging EM and other analytical techniques, especially with respect to the space within RTC, the reasons for which are discussed. Then, the role of direct imaging EM methods in modern structural biology is discussed. Direct imaging methods should support and verify the results obtained by other analytical methods capable of solving three‐dimensional molecular architecture, and they should still be used as a primary tool for studying macromolecule structure in vivo.     

Direct Growth of Flower‐Like δ‐MnO2 on Three‐Dimensional Graphene for High‐Performance Rechargeable Li‐O2 Batteries

A challenge still remains to develop high‐performance and cost‐effective air electrode for Li‐O₂ batteries with high capacity, enhanced rate capability and long cycle life (100 times or above) despite recent advances in this field. In this work, a new design of binder‐free air electrode composed of three‐dimensional (3D) graphene (G) and flower‐like δ‐MnO₂ (3D‐G‐MnO₂) has been proposed. In this design, graphene and δ‐MnO₂ grow directly on the skeleton of Ni foam that inherits the interconnected 3D scaffold of Ni foam. Li‐O₂ batteries with 3D‐G‐MnO₂ electrode can yield a high discharge capacity of 3660 mAh g^?1 at 0.083 mA cm^?2. The battery can sustain 132 cycles at a capacity of 492 mAh g^?1 (1000 mAh g_carbon ^?1) with low overpotentials under a high current density of 0.333 mA cm^?2. A high average energy density of 1350 Wh Kg^?1 is maintained over 110 cycles at this high current density. The excellent catalytic activity of 3D‐G‐MnO₂ makes it an attractive air electrode for high‐performance Li‐O₂ batteries.     

Perspectives of data analysis of enzyme inhibition and activation,Part 1: Use of the three‐dimensional Km′ V′I coordinate system for data analysis of enzyme inhibition and activation

The possibility of construction of the three‐dimensional (unfolded and folded) K_m′ V′I rectangular coordinate systems convenient for vector representation of inhibited and activated enzymatic reactions as well as of a two‐dimensional K_m′ V′ scalar rectangular coordinate system convenient for diagrammatic representation of enzymatic reactions is considered. The perspectives of using the properties of the three‐dimensional L vectors and their scalar L projections for data analysis of enzyme inhibition and activation are analyzed. © 2009 Wiley Periodicals, Inc. J Biochem Mol Toxicol 23:97–100, 2009; Published online in Wiley InterScience ( www.interscience.wiley.com ). DOI 10.1002/jbt.20273     

Three‐dimensional mapping of the attenuation coefficient in optical coherence tomography to enhance breast tissue microarchitecture contrast

Effective intraoperative tumor margin assessment is needed to reduce re‐excision rates in breast‐conserving surgery (BCS). Mapping the attenuation coefficient in optical coherence tomography (OCT) throughout a sample to create an image (attenuation imaging) is one promising approach. For the first time, three‐dimensional OCT attenuation imaging of human breast tissue microarchitecture using a wide‐field (up to ~45 × 45 × 3.5 mm) imaging system is demonstrated. Representative results from three mastectomy and one BCS specimen (from 31 specimens) are presented with co‐registered postoperative histology. Attenuation imaging is shown to provide substantially improved contrast over OCT, delineating nuanced features within tumors (including necrosis and variations in tumor cell density and growth patterns) and benign features (such as sclerosing adenosis). Additionally, quantitative micro‐elastography (QME) images presented alongside OCT and attenuation images show that these techniques provide complementary contrast, suggesting that multimodal imaging could increase tissue identification accuracy and potentially improve tumor margin assessment.     

3D Porous γ‐Fe2O3@C Nanocomposite as High‐Performance Anode Material of Na‐Ion Batteries

A simple and template‐free method for preparing three‐dimensional (3D) porous γ‐Fe₂O₃@C nanocomposite is reported using an aerosol spray pyrolysis technology. The nanocomposite contains inner‐connected nanochannels and γ‐Fe₂O₃ nanoparticles (5 nm) uniformly embedded in a porous carbon matrix. The size of γ‐Fe₂O₃ nanograins and carbon content can be controlled by the concentration of the precursor solution. The unique structure of the 3D porous γ‐Fe₂O₃@C nanocomposite offers a synergistic effect to alleviate stress, accommodate large volume change, prevent nanoparticles aggregation, and facilitate the transfer of electrons and electrolyte during prolonged cycling. Consequently, the nanocomposite shows high‐rate capability and long‐term cyclability when applied as an anode material for Na‐ion batteries (SIBs). Due to the simple one‐pot synthesis technique and high electrochemical performance, 3D porous γ‐Fe₂O₃@C nanocomposites have a great potential as anode materials for rechargeable SIBs.     

Cryopreservation of embryonic stem cell‐derived multicellular neural aggregates labeled with micron‐sized particles of iron oxide for magnetic resonance imaging

Magnetic resonance imaging (MRI) provides an effective approach to track labeled pluripotent stem cell (PSC)‐derived neural progenitor cells (NPCs) for neurological disorder treatments after cell labeling with a contrast agent, such as an iron oxide derivative. Cryopreservation of pre‐labeled neural cells, especially in three‐dimensional (3D) structure, can provide a uniform cell population and preserve the stem cell niche for the subsequent applications. In this study, the effects of cryopreservation on PSC‐derived multicellular NPC aggregates labeled with micron‐sized particles of iron oxide (MPIO) were investigated. These NPC aggregates were labeled prior to cryopreservation because labeling thawed cells can be limited by inefficient intracellular uptake, variations in labeling efficiency, and increased culture time before use, minimizing their translation to clinical settings. The results indicated that intracellular MPIO incorporation was retained after cryopreservation (70–80% labeling efficiency), and MPIO labeling had little adverse effects on cell recovery, proliferation, cytotoxicity and neural lineage commitment post‐cryopreservation. MRI analysis showed comparable detectability for the MPIO‐labeled cells before and after cryopreservation indicated by T₂ and T₂* relaxation rates. Cryopreserving MPIO‐labeled 3D multicellular NPC aggregates can be applied in in vivo cell tracking studies and lead to more rapid translation from preservation to clinical implementation. © 2015 American Institute of Chemical Engineers Biotechnol. Prog., 31:510–521, 2015     

High‐speed X‐ray‐induced luminescence computed tomography

X‐ray‐induced luminescence computed tomography (XLCT) is an emerging molecular imaging. Challenges in improving spatial resolution and reducing the scan time in a whole‐body field of view (FOV) still remain for practical in vivo applications. In this study, we present a novel XLCT technique capable of obtaining three‐dimensional (3D) images from a single snapshot. Specifically, a customed two‐planar‐mirror component is integrated into a cone beam XLCT imaging system to obtain multiple optical views of an object simultaneously. Furthermore, a compressive sensing based algorithm is adopted to improve the efficiency of 3D XLCT image reconstruction. Numerical simulations and experiments were conducted to validate the single snapshot X‐ray‐induced luminescence computed tomography (SS‐XLCT). The results show that the 3D distribution of the nanophosphor targets can be visualized much faster than conventional cone beam XLCT imaging method that was used in our comparisons while maintaining comparable spatial resolution as in conventional XLCT imaging. SS‐XLCT has the potential to harness the power of XLCT for rapid whole‐body in vivo molecular imaging of small animals.     

A novel manual pooling system for preparing three-dimensional pools of a deep coverage soybean bacterial artificial chromosome library

Compared with hybridization‐based techniques, polymerase chain reaction‐based screening of large insert libraries has been used widely as it is fast, easy and sensitive. However, various pooling strategies are needed to ensure efficient screening. It is time‐consuming and labourious to prepare three‐dimensional pools for a deep coverage bacterial artificial chromosome (BAC) library of soybean (1.12 × 10⁹ bp) in the absence of robotic facility. In the present study, we describe a novel manual pooling system for preparing three‐dimensional pools of a soybean BAC library. This simple technique enables a single researcher to construct three‐dimensional pools for a deep‐coverage (12 haploid genome equivalents) BAC library of soybean in less than 2 months without any robotic manipulation. When the prepared three‐dimensional pools were screened with 29 polymerase chain reaction‐based markers, an average of 9.2 clones per marker were identified. These identified clones will be useful either in quantitative trait loci gene isolation or in synteny study between soybean and other legumes including Lotus japonicus. This efficient pooling system could be applied to any other BAC libraries without the need for robotic manipulation.     

Three-dimensional Raman imagery of precambrian microscopic organisms

Two major difficulties have long hindered studies of ancient permineralized micro‐organisms: (1) accurate documentation of their three‐dimensional morphology at micron‐scale resolution; and (2) direct characterization of their molecular‐structural composition. Here we introduce a technique new to palaeobiology, the three‐dimensional Raman imagery that meets both of these needs, which is a nonintrusive, nondestructive technique that can provide data by which to accurately and objectively characterize, in situ and at micron‐scale resolution, the morphology and molecular‐structural composition of permineralized micro‐organisms and their associated matrices. Application of this new technique can provide information about the morphology, taphonomy and fidelity of preservation of fossil micro‐organisms unavailable by any other means.