Showing papers by "University of Tsukuba published in 2007"

A second generation human haplotype map of over 3.1 million SNPs

Abstract: We describe the Phase II HapMap, which characterizes over 3.1 million human single nucleotide polymorphisms (SNPs) genotyped in 270 individuals from four geographically diverse populations and includes 25-35% of common SNP variation in the populations surveyed. The map is estimated to capture untyped common variation with an average maximum r2 of between 0.9 and 0.96 depending on population. We demonstrate that the current generation of commercial genome-wide genotyping products captures common Phase II SNPs with an average maximum r2 of up to 0.8 in African and up to 0.95 in non-African populations, and that potential gains in power in association studies can be obtained through imputation. These data also reveal novel aspects of the structure of linkage disequilibrium. We show that 10-30% of pairs of individuals within a population share at least one region of extended genetic identity arising from recent ancestry and that up to 1% of all common variants are untaggable, primarily because they lie within recombination hotspots. We show that recombination rates vary systematically around genes and between genes of different function. Finally, we demonstrate increased differentiation at non-synonymous, compared to synonymous, SNPs, resulting from systematic differences in the strength or efficacy of natural selection between populations.

Genome-wide detection and characterization of positive selection in human populations

Abstract: With the advent of dense maps of human genetic variation, it is now possible to detect positive natural selection across the human genome. Here we report an analysis of over 3 million polymorphisms from the International HapMap Project Phase 2 (HapMap2). We used 'long-range haplotype' methods, which were developed to identify alleles segregating in a population that have undergone recent selection, and we also developed new methods that are based on cross-population comparisons to discover alleles that have swept to near-fixation within a population. The analysis reveals more than 300 strong candidate regions. Focusing on the strongest 22 regions, we develop a heuristic for scrutinizing these regions to identify candidate targets of selection. In a complementary analysis, we identify 26 non-synonymous, coding, single nucleotide polymorphisms showing regional evidence of positive selection. Examination of these candidates highlights three cases in which two genes in a common biological process have apparently undergone positive selection in the same population:LARGE and DMD, both related to infection by the Lassa virus, in West Africa;SLC24A5 and SLC45A2, both involved in skin pigmentation, in Europe; and EDAR and EDA2R, both involved in development of hair follicles, in Asia.

Targeted disruption of AdipoR1 and AdipoR2 causes abrogation of adiponectin binding and metabolic actions.

Abstract: Adiponectin plays a central role as an antidiabetic and antiatherogenic adipokine. AdipoR1 and AdipoR2 serve as receptors for adiponectin in vitro, and their reduction in obesity seems to be correlated with reduced adiponectin sensitivity. Here we show that adenovirus-mediated expression of AdipoR1 and R2 in the liver of Lepr(-/-) mice increased AMP-activated protein kinase (AMPK) activation and peroxisome proliferator-activated receptor (PPAR)-alpha signaling pathways, respectively. Activation of AMPK reduced gluconeogenesis, whereas expression of the receptors in both cases increased fatty acid oxidation and lead to an amelioration of diabetes. Alternatively, targeted disruption of AdipoR1 resulted in the abrogation of adiponectin-induced AMPK activation, whereas that of AdipoR2 resulted in decreased activity of PPAR-alpha signaling pathways. Simultaneous disruption of both AdipoR1 and R2 abolished adiponectin binding and actions, resulting in increased tissue triglyceride content, inflammation and oxidative stress, and thus leading to insulin resistance and marked glucose intolerance. Therefore, AdipoR1 and R2 serve as the predominant receptors for adiponectin in vivo and play important roles in the regulation of glucose and lipid metabolism, inflammation and oxidative stress in vivo.

The neural circuit of orexin (hypocretin): maintaining sleep and wakefulness

Abstract: Sleep and wakefulness are regulated to occur at appropriate times that are in accordance with our internal and external environments. Avoiding danger and finding food, which are life-essential activities that are regulated by emotion, reward and energy balance, require vigilance and therefore, by definition, wakefulness. The orexin (hypocretin) system regulates sleep and wakefulness through interactions with systems that regulate emotion, reward and energy homeostasis.

Emission of coherent THz radiation from superconductors.

Abstract: Compact solid-state sources of terahertz (THz) radiation are being sought for sensing, imaging, and spectroscopy applications across the physical and biological sciences. We demonstrate that coherent continuous-wave THz radiation of sizable power can be extracted from intrinsic Josephson junctions in the layered high-temperature superconductor Bi 2 Sr 2 CaCu 2 O 8 . In analogy to a laser cavity, the excitation of an electromagnetic cavity resonance inside the sample generates a macroscopic coherent state in which a large number of junctions are synchronized to oscillate in phase. The emission power is found to increase as the square of the number of junctions reaching values of 0.5 microwatt at frequencies up to 0.85 THz, and persists up to ∼50 kelvin. These results should stimulate the development of superconducting compact sources of THz radiation.

Six-rowed barley originated from a mutation in a homeodomain-leucine zipper I-class homeobox gene

Abstract: Increased seed production has been a common goal during the domestication of cereal crops, and early cultivators of barley (Hordeum vulgare ssp. vulgare) selected a phenotype with a six-rowed spike that stably produced three times the usual grain number. This improved yield established barley as a founder crop for the Near Eastern Neolithic civilization. The barley spike has one central and two lateral spikelets at each rachis node. The wild-type progenitor (H. vulgare ssp. spontaneum) has a two-rowed phenotype, with additional, strictly rudimentary, lateral rows; this natural adaptation is advantageous for seed dispersal after shattering. Until recently, the origin of the six-rowed phenotype remained unknown. In the present study, we isolated vrs1 (six-rowed spike 1), the gene responsible for the six-rowed spike in barley, by means of positional cloning. The wild-type Vrs1 allele (for two-rowed barley) encodes a transcription factor that includes a homeodomain with a closely linked leucine zipper motif. Expression of Vrs1 was strictly localized in the lateral-spikelet primordia of immature spikes, suggesting that the VRS1 protein suppresses development of the lateral rows. Loss of function of Vrs1 resulted in complete conversion of the rudimentary lateral spikelets in two-rowed barley into fully developed fertile spikelets in the six-rowed phenotype. Phylogenetic analysis demonstrated that the six-rowed phenotype originated repeatedly, at different times and in different regions, through independent mutations of Vrs1.

Dioxin receptor is a ligand-dependent E3 ubiquitin ligase

Abstract: Fat-soluble ligands, including sex steroid hormones and environmental toxins, activate ligand-dependent DNA-sequence-specific transcriptional factors that transduce signals through target-gene-selective transcriptional regulation However, the mechanisms of cellular perception of fat-soluble ligand signals through other target-selective systems remain unclear The ubiquitin-proteasome system regulates selective protein degradation, in which the E3 ubiquitin ligases determine target specificity Here we characterize a fat-soluble ligand-dependent ubiquitin ligase complex in human cell lines, in which dioxin receptor (AhR) is integrated as a component of a novel cullin 4B ubiquitin ligase complex, CUL4B(AhR) Complex assembly and ubiquitin ligase activity of CUL4B(AhR) in vitro and in vivo are dependent on the AhR ligand In the CUL4B(AhR) complex, ligand-activated AhR acts as a substrate-specific adaptor component that targets sex steroid receptors for degradation Thus, our findings uncover a function for AhR as an atypical component of the ubiquitin ligase complex and demonstrate a non-genomic signalling pathway in which fat-soluble ligands regulate target-protein-selective degradation through a ubiquitin ligase complex

Estimation of glomerular filtration rate by the MDRD study equation modified for Japanese patients with chronic kidney disease

Abstract: Background Accurate estimation of the glomerular filtration rate (GFR) is crucial for the detection of chronic kidney disease (CKD). In clinical practice, GFR is estimated from serum creatinine using the Modification of Diet in Renal Disease (MDRD) study equation or the Cockcroft-Gault (CG) equation instead of the time-consuming method of measured clearance for exogenous markers such as inulin. In the present study, the equations originally developed for a Caucasian population were tested in Japanese CKD patients, and modified with the Japanese coefficient determined by the data.

Sensitivity of the Enhanced Vegetation Index (EVI) and Normalized Difference Vegetation Index (NDVI) to Topographic Effects: A Case Study in High-Density Cypress Forest

Abstract: Vegetation indices play an important role in monitoring variations in vegetation.The Enhanced Vegetation Index (EVI) proposed by the MODIS Land Discipline Groupand the Normalized Difference Vegetation Index (NDVI) are both global-based vegetationindices aimed at providing consistent spatial and temporal information regarding globalvegetation. However, many environmental factors such as atmospheric conditions and soilbackground may produce errors in these indices. The topographic effect is another veryimportant factor, especially when the indices are used in areas of rough terrain. In thispaper, we theoretically analyzed differences in the topographic effect on the EVI and theNDVI based on a non-Lambertian model and two airborne-based images acquired from amountainous area covered by high-density Japanese cypress plantation were used as a casestudy. The results indicate that the soil adjustment factor "L" in the EVI makes it moresensitive to topographic conditions than is the NDVI. Based on these results, we stronglyrecommend that the topographic effect should be removed in the reflectance data beforethe EVI was calculated-as well as from other vegetation indices that similarly include a term without a band ratio format (e.g., the PVI and SAVI)-when these indices are used in the area of rough terrain, where the topographic effect on the vegetation indices having only a band ratio format (e.g., the NDVI) can usually be ignored.

Isolation and functional analysis of a MYB transcription factor gene that is a key regulator for the development of red coloration in apple skin

Abstract: Red coloration of apple (Malus x domestica) skin is an important determinant of consumer preference and marketability. Anthocyanins are responsible for this coloration, and their accumulation is positively correlated with the expression level of anthocyanin biosynthetic genes. Regulation of expression of these genes is believed to be controlled by MYB transcription factors, and the MYB transcription factors involved in the activation of anthocyanin biosynthetic genes have been isolated in various plants. In the present study, we isolated and characterized a MYB transcription factor gene (MdMYBA) from apple skin. Characterization of MdMYBA demonstrated that (i) MdMYBA expression was specifically regulated depending on the tissue and cultivar/species; (ii) its expression level was much higher in a deep-red cultivar ('Jonathan') than in a pale-red cultivar ('Tsugaru'); (iii) when cauliflower mosaic virus 35S::MdMYBA was introduced into the cotyledons of apple seedlings by means of a transient assay, reddish-purple spots were induced, and MdMYBA also induced anthocyanin accumulation in reproductive tissues of transgenic tobacco; (iv) the expression of MdMYBA was induced by UV-B irradiation and low-temperature treatment, both of which are known to be important in the promotion of anthocyanin accumulation in apple skin; (v) MdMYBA bound specifically to an anthocyanidin synthase (MdANS) promoter region in a gel-shift assay; and (vi) MdMYBA was mapped to the near region of the BC226-STS (a1) marker for the red skin color locus (R(f)). These results suggest that MdMYBA is a key regulatory gene in anthocyanin biosynthesis in apple skin.

Energy loss and flow of heavy quarks in Au+Au collisions at sNN=200GeV

Abstract: The PHENIX experiment at the BNL Relativistic Heavy Ion Collider (RHIC) has measured electrons with 0.3 < p(T) < 9 GeV/c at midrapidity (y < 0.35) from heavy-flavor (charm and bottom) decays in Au + Au collisions at root s(NN) = 200 GeV. The nuclear modification factor R-AA relative to p + p collisions shows a strong suppression in central Au + Au collisions, indicating substantial energy loss of heavy quarks in the medium produced at RHIC energies. A large azimuthal anisotropy v(2) with respect to the reaction plane is observed for 0.5 < p(T) < 5 GeV/c indicating substantial heavy-flavor elliptic flow. Both R-AA and v(2) show a p(T) dependence different from those of neutral pions. A comparison to transport models which simultaneously describe R-AA(p(T)) and v(2)(p(T)) suggests that the viscosity to entropy density ratio is close to the conjectured quantum lower bound, i.e., near a perfect fluid.

Crucial role of a long-chain fatty acid elongase, Elovl6, in obesity-induced insulin resistance

Abstract: Insulin resistance is often associated with obesity and can precipitate type 2 diabetes. To date, most known approaches that improve insulin resistance must be preceded by the amelioration of obesity and hepatosteatosis. Here, we show that this provision is not mandatory; insulin resistance and hyperglycemia are improved by the modification of hepatic fatty acid composition, even in the presence of persistent obesity and hepatosteatosis. Mice deficient for Elovl6, the gene encoding the elongase that catalyzes the conversion of palmitate to stearate, were generated and shown to become obese and develop hepatosteatosis when fed a high-fat diet or mated to leptin-deficient ob/ob mice. However, they showed marked protection from hyperinsulinemia, hyperglycemia and hyperleptinemia. Amelioration of insulin resistance was associated with restoration of hepatic insulin receptor substrate-2 and suppression of hepatic protein kinase C e activity resulting in restoration of Akt phosphorylation. Collectively, these data show that hepatic fatty acid composition is a new determinant for insulin sensitivity that acts independently of cellular energy balance and stress. Inhibition of this elongase could be a new therapeutic approach for ameliorating insulin resistance, diabetes and cardiovascular risks, even in the presence of a continuing state of obesity.

J/psi production versus centrality, transverse momentum, and rapidity in Au+Au collisions at root S-NN=200 GeV

Abstract: The PHENIX experiment at the BNL Relativistic Heavy Ion Collider (RHIC) has measured J/psi production for rapidities -2.2 < y < 2.2 in Au+Au collisions at root s(NN)=200 GeV. The J/psi invariant yield and nuclear modification factor R-AA as a function of centrality, transverse momentum, and rapidity are reported. A suppression of J/psi relative to binary collision scaling of proton-proton reaction yields is observed. Models which describe the lower energy J/psi data at the CERN Super Proton Synchrotron invoking only J/psi destruction based on the local medium density predict a significantly larger suppression at RHIC and more suppression at midrapidity than at forward rapidity. Both trends are contradicted by our data.

Intention-based walking support for paraplegia patients with Robot Suit HAL

Abstract: This paper proposes an algorithm to estimate human intentions related to walking in order to comfortably and safely support a paraplegia patient's walk. Robot Suit HAL (Hybrid Assistive Limb) has been developed for enhancement of a healthy person's activities and for support of a physically challenged person's daily life. The assisting method based on bioelectrical signals such as myoelectricity successfully supports a healthy person's walking. These bioelectrical signals, however, cannot be measured properly from a paraplegia patient. Therefore another interface that can estimate a patient's intentions without any manual controller is desired for robot control since a manual controller deprives a patient of his/her hand freedom. Estimation of a patient's intentions contributes to providing not only comfortable support but also safe support, because any inconformity between the robot suit motion and the patient motion results in his/her stumbling or falling. The proposed algorithm estimates a patient's in...

Rice NON-YELLOW COLORING1 Is Involved in Light-Harvesting Complex II and Grana Degradation during Leaf Senescence

Abstract: Chlorophyll degradation is an aspect of leaf senescence, which is an active process to salvage nutrients from old tissues. non-yellow coloring1 (nyc1) is a rice (Oryza sativa) stay-green mutant in which chlorophyll degradation during senescence is impaired. Pigment analysis revealed that degradation of not only chlorophylls but also light-harvesting complex II (LHCII)–bound carotenoids was repressed in nyc1, in which most LHCII isoforms were selectively retained during senescence. Ultrastructural analysis of nyc1 chloroplasts revealed that large and thick grana were present even in the late stage of senescence, suggesting that degradation of LHCII is required for the proper degeneration of thylakoid membranes. Map-based cloning of NYC1 revealed that it encodes a chloroplast-localized short-chain dehydrogenase/reductase (SDR) with three transmembrane domains. The predicted structure of the NYC1 protein and the phenotype of the nyc1 mutant suggest the possibility that NYC1 is a chlorophyll b reductase. Although we were unable to detect the chlorophyll b reductase activity of NYC1, NOL (for NYC1-like), a protein closely related to NYC1 in rice, showed chlorophyll b reductase activity in vitro. We suggest that NYC1 and NOL encode chlorophyll b reductases with divergent functions. Our data collectively suggest that the identified SDR protein NYC1 plays essential roles in the regulation of LHCII and thylakoid membrane degradation during senescence.

Nuclear force from lattice QCD.

Abstract: The nucleon-nucleon ($NN$) potential is studied by lattice QCD simulations in the quenched approximation, using the plaquette gauge action and the Wilson quark action on a ${32}^{4}$ [$\ensuremath{\simeq}(4.4\text{ }\text{ }\mathrm{fm}{)}^{4}$] lattice. A $NN$ potential ${V}_{NN}(r)$ is defined from the equal-time Bethe-Salpeter amplitude with a local interpolating operator for the nucleon. By studying the $NN$ interaction in the $^{1}S_{0}$ and $^{3}S_{1}$ channels, we show that the central part of ${V}_{NN}(r)$ has a strong repulsive core of a few hundred MeV at short distances ($r\ensuremath{\lesssim}0.5\text{ }\text{ }\mathrm{fm}$) surrounded by an attractive well at medium and long distances. These features are consistent with the known phenomenological features of the nuclear force.

Development of a novel systemic gene delivery system for cancer therapy with a tumor-specific cleavable PEG-lipid.

Abstract: For successful cancer gene therapy via intravenous (i.v.) administration, it is essential to optimize the stability of carriers in the systemic circulation and the cellular association after the accumulation of the carrier in tumor tissue. However, a dilemma exists regarding the use of poly(ethylene glycol) (PEG), which is useful for conferring stability in the systemic circulation, but is undesirable for the cellular uptake and the following processes. We report the development of a PEG-peptide-lipid ternary conjugate (PEG-Peptide-DOPE conjugate (PPD)). In this strategy, the PEG is removed from the carriers via cleavage by a matrix metalloproteinase (MMP), which is specifically expressed in tumor tissues. An in vitro study revealed that the PPD-modified gene carrier (Multifunctional Envelope-type Nano Device: MEND) exhibited pDNA expression activity that was dependent on the MMP expression level in the host cells. In vivo studies further revealed that the PPD was potent in stabilizing MEND in the systemic circulation and facilitating tumor accumulation. Moreover, the i.v. administration of PPD or PEG/PPD dually-modified MEND resulted in the stimulation of pDNA expression in tumor tissue, as compared with a conventional PEG-modified MEND. Thus, MEND modified with PPD is a promising device, which has the potential to make in vivo cancer gene therapy achievable.

Different electrostatic potentials define ETGE and DLG motifs as hinge and latch in oxidative stress response.

Abstract: Nrf2 is the regulator of the oxidative/electrophilic stress response. Its turnover is maintained by Keap1-mediated proteasomal degradation via a two-site substrate recognition mechanism in which two Nrf2-Keap1 binding sites form a hinge and latch. The E3 ligase adaptor Keap1 recognizes Nrf2 through its conserved ETGE and DLG motifs. In this study, we examined how the ETGE and DLG motifs bind to Keap1 in a very similar fashion but with different binding affinities by comparing the crystal complex of a Keap1-DC domain-DLG peptide with that of a Keap1-DC domain-ETGE peptide. We found that these two motifs interact with the same basic surface of either Keap1-DC domain of the Keap1 homodimer. The DLG motif works to correctly position the lysines within the Nrf2 Neh2 domain for efficient ubiquitination. Together with the results from calorimetric and functional studies, we conclude that different electrostatic potentials primarily define the ETGE and DLG motifs as a hinge and latch that senses the oxidative/electrophilic stress.

Extremely high stability of glutathionate-protected Au25 clusters against core etching.

Abstract: It is well known that so-called magic-numbered clusters can be preferentially populated by dissociative excitation of larger precursors, because the energy required for removal of a single atom from a magic-numbered cluster is higher than from a neighbor. Thus, if the Au atoms can be removed sequentially from preformed thiolated-protected gold (Au:SR) clusters, one can anticipate a population growth of certain stable Aun:SR clusters. Chemical etching by free thiols is one feasible method for core size reduction of the Au:SR clusters. The etching rate of Aun:SR clusters must be determined as a function of core size, in order to provide a synthesis for welldefined Aun(SR)m clusters in large quantity, as well as to provide information regarding the stability of Aun(SR)m. In the present paper, we studied etching reactions of Aun(SG)m clusters with (n,m) = (10,10), (15,13), (18,14), (22,16), (25,18), (29,20), (33,22), (39,24) by free glutathione (GSH). It was found that Au25:SG clusters show higher stability against etching than the others and as a result two different reaction modes are operative depending on the core size. The Aun(SG)m (n < 25) clusters are completely oxidized to Au(I):SG complexes while Aun(SG)m (n ≥ 25) clusters are etched into Au25: SG by free GSH molecules. On the basis of this observation, a model is proposed to explain our recent finding that Au25 (SG)18 clusters are selectively formed during the reaction of triphenylphosphine-stabilized Au11 clusters and an excess amount of GSH.

The Mitogen-Activated Protein Kinase Cascade MKK3–MPK6 Is an Important Part of the Jasmonate Signal Transduction Pathway in Arabidopsis

Abstract: The plant hormone jasmonic acid (JA) plays a key role in the environmental stress responses and developmental processes of plants. Although ATMYC2/JASMONATE-INSENSITIVE1 (JIN1) is a major positive regulator of JA-inducible gene expression and essential for JA-dependent developmental processes in Arabidopsis thaliana, molecular mechanisms underlying the control of ATMYC2/JIN1 expression remain largely unknown. Here, we identify a mitogen-activated protein kinase (MAPK) cascade, MAPK KINASE 3 (MKK3)–MAPK 6 (MPK6), which is activated by JA in Arabidopsis. We also show that JA negatively controls ATMYC2/JIN1 expression, based on quantitative RT-PCR and genetic analyses using gain-of-function and loss-of-function mutants of the MKK3–MPK6 cascade. These results indicate that this kinase unit plays a key role in JA-dependent negative regulation of ATMYC2/JIN1 expression. Both positive and negative regulation by JA may be used to fine-tune ATMYC2/JIN1 expression to control JA signaling. Moreover, JA-regulated root growth inhibition is affected by mutations in the MKK3–MPK6 cascade, which indicates important roles in JA signaling. We provide a model explaining how MPK6 can convert three distinct signals—JA, pathogen, and cold/salt stress—into three different sets of responses in Arabidopsis.

The Rice Annotation Project Database (RAP-DB): 2008 update

Abstract: The Rice Annotation Project Database (RAP-DB) was created to provide the genome sequence assembly of the International Rice Genome Sequencing Project (IRGSP), manually curated annotation of the sequence, and other genomics information that could be useful for comprehensive understanding of the rice biology. Since the last publication of the RAP-DB, the IRGSP genome has been revised and reassembled. In addition, a large number of rice-expressed sequence tags have been released, and functional genomics resources have been produced worldwide. Thus, we have thoroughly updated our genome annotation by manual curation of all the functional descriptions of rice genes. The latest version of the RAP-DB contains a variety of annotation data as follows: clone positions, structures and functions of 31 439 genes validated by cDNAs, RNA genes detected by massively parallel signature sequencing (MPSS) technology and sequence similarity, flanking sequences of mutant lines, transposable elements, etc. Other annotation data such as Gnomon can be displayed along with those of RAP for comparison. We have also developed a new keyword search system to allow the user to access useful information. The RAP-DB is available at: http://rapdb.dna.affrc.go.jp/ and http://rapdb.lab.nig.ac.jp/.

Polyamines and their ability to provide environmental stress tolerance to plants

Abstract: The present review highlights some recent advances regarding the function of polyamines in the environmental stress tolerance of plants. When exposed to adverse environmental stresses, such as salt, drought, low temperature, and ozone, the complex dynamic kinetics of polyamine biosynthesis was observed. Polyamines titers altered in different manners dependent upon several factors, such as plant species, tolerance or sensitivity to stress, and duration of stress. The exogenous addition of polyamines to stress-treated cells or tissues could lead to injury alleviation and growth promotion in most cases, although the effects varied between polyamines and among plant species. Key genes responsible for polyamine biosynthesis have been cloned from a variety of plant species, whose expressions following stress have been investigated on a molecular basis. Overexpression of the genes caused the modification of polyamine biosynthesis in the transformants coupled with enhancement of stress tolerance. All of these results seem to indicate that polyamines are an important component in a plant's response to stress and that they play a significant role in counteracting stress.

Scaling properties of azimuthal anisotropy in Au+Au and Cu+Cu collisions at sNN=200GeV

Abstract: Differential measurements of elliptic flow (v(2)) for Au+Au and Cu+Cu collisions at root s(NN)=200 GeV are used to test and validate predictions from perfect fluid hydrodynamics for scaling of v(2) with eccentricity, system size, and transverse kinetic energy (KET). For KET equivalent to m(T)-m up to similar to 1 GeV the scaling is compatible with hydrodynamic expansion of a thermalized fluid. For large values of KET mesons and baryons scale separately. Quark number scaling reveals a universal scaling of v(2) for both mesons and baryons over the full KET range for Au+Au. For Au+Au and Cu+Cu the scaling is more pronounced in terms of KET, rather than transverse momentum.

In vivo high-contrast imaging of deep posterior eye by 1-microm swept source optical coherence tomography and scattering optical coherence angiography.

Abstract: Retinal, choroidal and scleral imaging by using swept-source optical coherence tomography (SS-OCT) with a 1-microm band probe light, and high-contrast and three-dimensional (3D) imaging of the choroidal vasculature are presented. This SS-OCT has a measurement speed of 28,000 A-lines/s, a depth resolution of 10.4 microm in tissue, and a sensitivity of 99.3 dB. Owing to the high penetration of the 1-microm probe light and the high sensitivity of the system, the in vivo sclera of a healthy volunteer can be observed. A software-based algorithm of scattering optical coherence angiography (S-OCA) is developed for the high-contrast and 3D imaging of the choroidal vessels. The S-OCA is used to visualize the 3D choroidal vasculature of the in vivo human macula and the optic nerve head. Comparisons of S-OCA with several other angiography techniques including Doppler OCA, Doppler OCT, fluorescein angiography, and indocyanine green angiography are also presented.