Development of eye phantom for mimicking the deformation of the human cornea accompanied by intraocular pressure alterations.

Comparative studies between artificial eyeball phantoms and in-vivo human subjects were carried out to better understanding the structural deformation of the cornea under varying intraocular pressure (IOP). The IOP-induced deformation and the tension of the cornea were measured by using an optical coherence tomography and noncontact tonometer readings, respectively. The dependence of the central cornea thickness (CCT) and corneal radius of curvature (CRC) on the IOP differed significantly between the full eyeball phantom (FEP) and cornea eyeball phantom (CEP) models. While the CCT changes were very similar between the two models, the relation between the CRC and the IOP was dependent on the type of eye phantom. For the CEP, the CRC drastically decreased as internal pressure increased. However, we found that the changes in the CRC of FEP was dependent on initial CCT under zero IOP (CCT0). When CCT0 was less than 460 µm, the CRC slightly decreased as IOP increased. Meanwhile, the CRC increased as IOP increased if CCT0 was 570 µm. A constitutive mechanical model was proposed to describe the response of the cornea accompanied by the changes in IOP. In vivo measurements on human subjects under both noninvasive and invasive conditions revealed that the relation between the CRC on the IOP is much closer to those observed from FEP. Considering the observed structural deformation of human cornea, we found that FEP mimics the human eye more accurately than the CEP. In addition, the tonometry readings of IOP show that the values from the CEP were overestimated, while those from the FEP were not. For these reasons, we expect that the FEP could be suitable for the estimation of true IOP and allow performance testing of tonometers for medical checkups and other clinical uses.

Biosynthesis of Commodity Chemicals From Oil Palm Empty Fruit Bunch Lignin.

Lignin is one of the most abundant natural resources that can be exploited for the bioproduction of value-added commodity chemicals. Oil palm empty fruit bunches (OPEFBs), byproducts of palm oil production, are abundant lignocellulosic biomass but largely used for energy and regarded as waste. Pretreatment of OPEFB lignin can yield a mixture of aromatic compounds that can potentially serve as substrates to produce commercially important chemicals. However, separation of the mixture into desired individual substrates is required, which involves expensive steps that undermine the utility of OPEFB lignin. Here, we report successful engineering of microbial hosts that can directly utilize heterogeneous mixtures derived from OPEFB lignin to produce commodity chemicals, adipic acid and levulinic acid. Furthermore, the corresponding bioconversion pathway was placed under a genetic controller to autonomously activate the conversion process as the cells are fed with a depolymerized OPEFB lignin mixture. This study demonstrates a simple, one-pot biosynthesis approach that directly utilizes derivatives of agricultural waste to produce commodity chemicals.

Single cardiac cycle three-dimensional intracoronary optical coherence tomography.

While high-speed intracoronary optical coherence tomography (OCT) provides three-dimensional (3D) visualization of coronary arteries in vivo, imaging speeds remain insufficient to avoid motion artifacts induced by heartbeat, limiting the clinical utility of OCT. In this paper, we demonstrate development of a high-speed intracoronary OCT system (frame rate: 500 frames/s, pullback speed: 100 mm/s) along with prospective electrocardiogram (ECG) triggering technology, which enabled volumetric imaging of long coronary segments within a single cardiac cycle (70 mm pullback in 0.7 s) with minimal cardiac motion artifact. This technology permitted detailed visualization of 3D architecture of the coronary arterial wall of a swine in vivo and fine structure of the implanted stent.

Genetic Engineering of an Unconventional Yeast for Renewable Biofuel and Biochemical Production.

Yarrowia lipolytica is a non-pathogenic, dimorphic and strictly aerobic yeast species. Owing to its distinctive physiological features and metabolic characteristics, this unconventional yeast is not only a good model for the study of the fundamental nature of fungal differentiation but is also a promising microbial platform for biochemical production and various biotechnological applications, which require extensive genetic manipulations. However, genetic manipulations of Y. lipolytica have been limited due to the lack of an efficient and stable genetic transformation system as well as very high rates of non-homologous recombination that can be mainly attributed to the KU70 gene. Here, we report an easy and rapid protocol for the efficient genetic transformation and for gene deletion in Y. lipolytica Po1g. First, a protocol for the efficient transformation of exogenous DNA into Y. lipolytica Po1g was established. Second, to achieve the enhanced double-crossover homologous recombination rate for further deletion of target genes, the KU70 gene was deleted by transforming a disruption cassette carrying 1 kb homology arms. Third, to demonstrate the enhanced gene deletion efficiency after deletion of the KU70 gene, we individually deleted 11 target genes encoding alcohol dehydrogenase and alcohol oxidase using the same procedures on the KU70 knockout platform strain. It was observed that the rate of precise homologous recombination increased substantially from less than 0.5% for deletion of the KU70 gene in Po1g to 33%-71% for the single gene deletion of the 11 target genes in Po1g KU70Δ. A replicative plasmid carrying the hygromycin B resistance marker and the Cre/LoxP system was constructed, and the selection marker gene in the yeast knockout strains was eventually removed by expression of Cre recombinase to facilitate multiple rounds of targeted genetic manipulations. The resulting single-gene deletion mutants have potential applications in biofuel and biochemical production.

A Two-Layer Gene Circuit for Decoupling Cell Growth from Metabolite Production.

We present a synthetic gene circuit for decoupling cell growth from metabolite production through autonomous regulation of enzymatic pathways by integrated modules that sense nutrient and substrate. The two-layer circuit allows Escherichia coli to selectively utilize target substrates in a mixed pool; channel metabolic resources to growth by delaying enzymatic conversion until nutrient depletion; and activate, terminate, and re-activate conversion upon substrate availability. We developed two versions of controller, both of which have glucose nutrient sensors but differ in their substrate-sensing modules. One controller is specific for hydroxycinnamic acid and the other for oleic acid. Our hydroxycinnamic acid controller lowered metabolic stress 2-fold and increased the growth rate 2-fold and productivity 5-fold, whereas our oleic acid controller lowered metabolic stress 2-fold and increased the growth rate 1.3-fold and productivity 2.4-fold. These results demonstrate the potential for engineering strategies that decouple growth and production to make bio-based production more economical and sustainable.

Intravascular optical imaging of high-risk plaques in vivo by targeting macrophage mannose receptors.

Macrophages mediate atheroma expansion and disruption, and denote high-risk arterial plaques. Therefore, they are substantially gaining importance as a diagnostic imaging target for the detection of rupture-prone plaques. Here, we developed an injectable near-infrared fluorescence (NIRF) probe by chemically conjugating thiolated glycol chitosan with cholesteryl chloroformate, NIRF dye (cyanine 5.5 or 7), and maleimide-polyethylene glycol-mannose as mannose receptor binding ligands to specifically target a subset of macrophages abundant in high-risk plaques. This probe showed high affinity to mannose receptors, low toxicity, and allowed the direct visualization of plaque macrophages in murine carotid atheroma. After the scale-up of the MMR-NIRF probe, the administration of the probe facilitated in vivo intravascular imaging of plaque inflammation in coronary-sized vessels of atheromatous rabbits using a custom-built dual-modal optical coherence tomography (OCT)-NIRF catheter-based imaging system. This novel imaging approach represents a potential imaging strategy enabling the identification of high-risk plaques in vivo and holds promise for future clinical implications.

Intracoronary dual-modal optical coherence tomography-near-infrared fluorescence structural-molecular imaging with a clinical dose of indocyanine green for the assessment of high-risk plaques and stent-associated inflammation in a beating coronary artery.

AIMS: Inflammation plays essential role in development of plaque disruption and coronary stent-associated complications. This study aimed to examine whether intracoronary dual-modal optical coherence tomography (OCT)-near-infrared fluorescence (NIRF) structural-molecular imaging with indocyanine green (ICG) can estimate inflammation in swine coronary artery. METHODS AND RESULTS: After administration of clinically approved NIRF-enhancing ICG (2.0 mg/kg) or saline, rapid coronary imaging (20 mm/s pullback speed) using a fully integrated OCT-NIRF catheter was safely performed in 12 atheromatous Yucatan minipigs and in 7 drug-eluting stent (DES)-implanted Yorkshire pigs. Stronger NIRF activity was identified in OCT-proven high-risk plaque compared to normal or saline-injected controls (P = 0.0016), which was validated on ex vivo fluorescence reflectance imaging. In vivo plaque target-to-background ratio (pTBR) was much higher in inflamed lipid-rich plaque compared to fibrous plaque (P < 0.0001). In vivo and ex vivo peak pTBRs correlated significantly (P < 0.0022). In vitro cellular ICG uptake and histological validations corroborated the OCT-NIRF findings in vivo. Indocyanine green colocalization with macrophages and lipids of human plaques was confirmed with autopsy atheroma specimens. Two weeks after DES deployment, OCT-NIRF imaging detected strong NIRF signals along stent struts, which was significantly higher than baseline (P = 0.0156). Histologically, NIRF signals in peri-strut tissue co-localized well with macrophages. CONCLUSION: The OCT-NIRF imaging with a clinical dose of ICG was feasible to accurately assess plaque inflammation and DES-related inflammation in a beating coronary artery. This highly translatable dual-modal molecular-structural imaging strategy could be relevant for clinical intracoronary estimation of high-risk plaques and DES biology.

GPU-accelerated framework for intracoronary optical coherence tomography imaging at the push of a button.

Frequency domain optical coherence tomography (FD-OCT) has become one of the important clinical tools for intracoronary imaging to diagnose and monitor coronary artery disease, which has been one of the leading causes of death. To help more accurate diagnosis and monitoring of the disease, many researchers have recently worked on visualization of various coronary microscopic features including stent struts by constructing three-dimensional (3D) volumetric rendering from series of cross-sectional intracoronary FD-OCT images. In this paper, we present the first, to our knowledge, "push-of-a-button" graphics processing unit (GPU)-accelerated framework for intracoronary OCT imaging. Our framework visualizes 3D microstructures of the vessel wall with stent struts from raw binary OCT data acquired by the system digitizer as one seamless process. The framework reports the state-of-the-art performance; from raw OCT data, it takes 4.7 seconds to provide 3D visualization of a 5-cm-long coronary artery (of size 1600 samples x 1024 A-lines x 260 frames) with stent struts and detection of malapposition automatically at the single push of a button.

Polarization-sensitive OFDI using polarization-multiplexed wavelength-swept laser.

We demonstrate a novel polarization-sensitive optical frequency domain imaging system employing passive polarization multiplexing. Simple modification of a fiber delay line in the wavelength-swept light source enables illumination with two perpendicular polarizations that are required for determination of the Stokes vector components of the light reflected from each depth of the tissue. This simple all-passive approach provides a robust and low-cost solution for PS imaging replacing relatively complex conventional schemes such as polarization modulation or frequency-encoded polarization multiplexing.

Fully integrated high-speed intravascular optical coherence tomography/near-infrared fluorescence structural/molecular imaging in vivo using a clinically available near-infrared fluorescence-emitting indocyanine green to detect inflamed lipid-rich atheromata in coronary-sized vessels.

BACKGROUND: Lipid-rich inflamed coronary plaques are prone to rupture. The purpose of this study was to assess lipid-rich inflamed plaques in vivo using fully integrated high-speed optical coherence tomography (OCT)/near-infrared fluorescence (NIRF) molecular imaging with a Food and Drug Administration-approved indocyanine green (ICG). METHODS AND RESULTS: An integrated high-speed intravascular OCT/NIRF imaging catheter and a dual-modal OCT/NIRF system were constructed based on a clinical OCT platform. For imaging lipid-rich inflamed plaques, the Food and Drug Administration-approved NIRF-emitting ICG (2.25 mg/kg) or saline was injected intravenously into rabbit models with experimental atheromata induced by balloon injury and 12- to 14-week high-cholesterol diets. Twenty minutes after injection, in vivo OCT/NIRF imaging of the infrarenal aorta and iliac arteries was acquired only under contrast flushing through catheter (pullback speed up to ≤20 mm/s). NIRF signals were strongly detected in the OCT-visualized atheromata of the ICG-injected rabbits. The in vivo NIRF target-to-background ratio was significantly larger in the ICG-injected rabbits than in the saline-injected controls (P<0.01). Ex vivo peak plaque target-to-background ratios were significantly higher in ICG-injected rabbits than in controls (P<0.01) on fluorescence reflectance imaging, which correlated well with the in vivo target-to-background ratios (P<0.01; r=0.85) without significant bias (0.41). Cellular ICG uptake, correlative fluorescence microscopy, and histopathology also corroborated the in vivo imaging findings. CONCLUSIONS: Integrated OCT/NIRF structural/molecular imaging with a Food and Drug Administration -approved ICG accurately identified lipid-rich inflamed atheromata in coronary-sized vessels. This highly translatable dual-modal imaging approach could enhance our capabilities to detect high-risk coronary plaques.

Predictive combinatorial design of mRNA translation initiation regions for systematic optimization of gene expression levels.

Balancing the amounts of enzymes is one of the important factors to achieve optimum performance of a designed metabolic pathway. However, the random mutagenesis approach is impractical since it requires searching an unnecessarily large number of variants and often results in searching a narrow range of expression levels which are out of optimal level. Here, we developed a predictive combinatorial design method, called UTR Library Designer, which systematically searches a large combinatorial space of expression levels. It accomplishes this by designing synthetic translation initiation region of mRNAs in a predictive way based on a thermodynamic model and genetic algorithm. Using this approach, we successfully enhanced lysine and hydrogen production in Escherichia coli. Our method significantly reduced the number of variants to be explored for covering large combinatorial space and efficiently enhanced pathway efficiency, thereby facilitating future efforts in metabolic engineering and synthetic biology.

High frame-rate intravascular optical frequency-domain imaging in vivo.

Intravascular optical frequency-domain imaging (OFDI), a second-generation optical coherence tomography (OCT) technology, enables imaging of the three-dimensional (3D) microstructure of the vessel wall following a short and nonocclusive clear liquid flush. Although 3D vascular visualization provides a greater appreciation of the vessel wall and intraluminal structures, a longitudinal imaging pitch that is several times bigger than the optical imaging resolution of the system has limited true high-resolution 3D imaging, mainly due to the slow scanning speed of previous imaging catheters. Here, we demonstrate high frame-rate intravascular OFDI in vivo, acquiring images at a rate of 350 frames per second. A custom-built, high-speed, and high-precision fiber-optic rotary junction provided uniform and high-speed beam scanning through a custom-made imaging catheter with an outer diameter of 0.87 mm. A 47-mm-long rabbit aorta was imaged in 3.7 seconds after a short contrast agent flush. The longitudinal imaging pitch was 34 µm, comparable to the transverse imaging resolution of the system. Three-dimensional volume-rendering showed greatly enhanced visualization of tissue microstructure and stent struts relative to what is provided by conventional intravascular imaging speeds.

Engineering glyceraldehyde-3-phosphate dehydrogenase for switching control of glycolysis in Escherichia coli.

Glycolysis has evolved to be a highly robust mechanism for maintaining the cellular metabolism of living organisms. However, relevant modifications of glycolytic activity are required to intentionally modulate cellular phenotypes. Here, we designed a platform that allows switching control of glycolysis in Escherichia coli in response to an environmental signal, in this case, temperature. This system functions by regulating the expression of gapA, which encodes glyceraldehyde-3-phosphate dehydrogenase (GAPDH), one of the key glycolytic enzymes. Because a very low level of gapA expression is capable of maintaining cellular physiology, we also modified GAPDH through directed evolution to provide sensitive regulation of glycolytic activity. The switching control of glycolysis was successfully demonstrated by regulating the expression of engineered gapA through changes in temperature. This system offers potential control over the cell's central carbon-metabolism switch, providing the ability to perform reprogrammed tasks with desired timing depending on environmental signals.

Engineering the pentose phosphate pathway to improve hydrogen yield in recombinant Escherichia coli.

Among various routes for the biological hydrogen production, the NAD(P)H-dependent pentose phosphate (PP) pathway is the most efficient for the dark fermentation. Few studies, however, have focused on the glucose-6-phosphate 1-dehydrogenase, encoded by zwf, as a key enzyme activating the PP pathway. Although the gluconeogenic activity is essential for activating the PP pathway, it is difficult to enhance the NADPH production by regulating only this activity because the gluconeogenesis is robust and highly sensitive to concentrations of glucose and AMP inside the cell. In this study, the FBPase II (encoded by glpX), a regulation-insensitive enzyme in the gluconeogenic pathway, was activated. Physiological studies of several recombinant, ferredoxin-dependent hydrogenase system-containing Escherichia coli BL21(DE3) strains showed that overexpression of glpX alone could increase the hydrogen yield by 1.48-fold compared to a strain with the ferredoxin-dependent hydrogenase system only; the co-overexpression of glpX with zwf increased the hydrogen yield further to 2.32-fold. These results indicate that activation of the PP pathway by glpX overexpression-enhanced gluconeogenic flux is crucial for the increase of NAD(P)H-dependent hydrogen production in E. coli BL21(DE3).