| 1. |
- Klionsky, Daniel J., et al.
(author)
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Guidelines for the use and interpretation of assays for monitoring autophagy
- 2012
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In: Autophagy. - : Informa UK Limited. - 1554-8635 .- 1554-8627. ; 8:4, s. 445-544
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Research review (peer-reviewed)abstract
- In 2008 we published the first set of guidelines for standardizing research in autophagy. Since then, research on this topic has continued to accelerate, and many new scientists have entered the field. Our knowledge base and relevant new technologies have also been expanding. Accordingly, it is important to update these guidelines for monitoring autophagy in different organisms. Various reviews have described the range of assays that have been used for this purpose. Nevertheless, there continues to be confusion regarding acceptable methods to measure autophagy, especially in multicellular eukaryotes. A key point that needs to be emphasized is that there is a difference between measurements that monitor the numbers or volume of autophagic elements (e.g., autophagosomes or autolysosomes) at any stage of the autophagic process vs. those that measure flux through the autophagy pathway (i.e., the complete process); thus, a block in macroautophagy that results in autophagosome accumulation needs to be differentiated from stimuli that result in increased autophagic activity, defined as increased autophagy induction coupled with increased delivery to, and degradation within, lysosomes (in most higher eukaryotes and some protists such as Dictyostelium) or the vacuole (in plants and fungi). In other words, it is especially important that investigators new to the field understand that the appearance of more autophagosomes does not necessarily equate with more autophagy. In fact, in many cases, autophagosomes accumulate because of a block in trafficking to lysosomes without a concomitant change in autophagosome biogenesis, whereas an increase in autolysosomes may reflect a reduction in degradative activity. Here, we present a set of guidelines for the selection and interpretation of methods for use by investigators who aim to examine macroautophagy and related processes, as well as for reviewers who need to provide realistic and reasonable critiques of papers that are focused on these processes. These guidelines are not meant to be a formulaic set of rules, because the appropriate assays depend in part on the question being asked and the system being used. In addition, we emphasize that no individual assay is guaranteed to be the most appropriate one in every situation, and we strongly recommend the use of multiple assays to monitor autophagy. In these guidelines, we consider these various methods of assessing autophagy and what information can, or cannot, be obtained from them. Finally, by discussing the merits and limits of particular autophagy assays, we hope to encourage technical innovation in the field.
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| 2. |
- Lango Allen, Hana, et al.
(author)
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Hundreds of variants clustered in genomic loci and biological pathways affect human height.
- 2010
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In: Nature. - : Springer Science and Business Media LLC. - 1476-4687 .- 0028-0836. ; 467:7317, s. 832-8
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Journal article (peer-reviewed)abstract
- Most common human traits and diseases have a polygenic pattern of inheritance: DNA sequence variants at many genetic loci influence the phenotype. Genome-wide association (GWA) studies have identified more than 600 variants associated with human traits, but these typically explain small fractions of phenotypic variation, raising questions about the use of further studies. Here, using 183,727 individuals, we show that hundreds of genetic variants, in at least 180 loci, influence adult height, a highly heritable and classic polygenic trait. The large number of loci reveals patterns with important implications for genetic studies of common human diseases and traits. First, the 180 loci are not random, but instead are enriched for genes that are connected in biological pathways (P = 0.016) and that underlie skeletal growth defects (P<0.001). Second, the likely causal gene is often located near the most strongly associated variant: in 13 of 21 loci containing a known skeletal growth gene, that gene was closest to the associated variant. Third, at least 19 loci have multiple independently associated variants, suggesting that allelic heterogeneity is a frequent feature of polygenic traits, that comprehensive explorations of already-discovered loci should discover additional variants and that an appreciable fraction of associated loci may have been identified. Fourth, associated variants are enriched for likely functional effects on genes, being over-represented among variants that alter amino-acid structure of proteins and expression levels of nearby genes. Our data explain approximately 10% of the phenotypic variation in height, and we estimate that unidentified common variants of similar effect sizes would increase this figure to approximately 16% of phenotypic variation (approximately 20% of heritable variation). Although additional approaches are needed to dissect the genetic architecture of polygenic human traits fully, our findings indicate that GWA studies can identify large numbers of loci that implicate biologically relevant genes and pathways.
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| 3. |
- Shen, Jian Qi
(author)
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A Three-Dimensionally Isotropic and Perfectly Vacuum-Impedance-Matched Negative-Index Material
- 2014
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In: Journal of the Physical Society of Japan. - 0031-9015 .- 1347-4073. ; 83:12, s. 124401-
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Journal article (peer-reviewed)abstract
- A new scenario for realizing a gain left-handed atomic vapor medium based on both dressed-state mixed-parity transitions (for simultaneous electric-and magnetic-dipole resonance) and incoherently-pumped population transfer (for high gain amplification) in a four-level atomic system is suggested. Dressed-state assisted simultaneous electric-and magnetic-dipole allowed transitions in such a four-level atomic system (of, e.g., neutral alkali-metal atoms such as lithium and potassium atoms) are utilized for achieving negative refractive index with impedance perfectly matched to vacuum. The attractive features of the present scenario include: i) three-dimensionally isotropic negative indices; ii) incoherent-gain wave amplification; iii) perfect impedance matching to vacuum. All these important properties of the double-negative medium would have potential applications in designing some optical and photonic devices, including particularly subwavelength focusing system and negative-index superlens for perfect imaging.
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| 4. |
- Shen, Jian Qi
(author)
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A three-level dark state and double-control single-photon logic gates via quantum coherent control
- 2012
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In: Annalen der Physik. - : Wiley-Blackwell. - 0003-3804 .- 1521-3889. ; 524:2, s. 85-96
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Journal article (peer-reviewed)abstract
- Multilevel quantum coherence and its quantum-vacuum counterpart, where a three-level dark state is involved, are suggested in order to achieve new photonic and quantum optical applications. It is shown that such a three-level dark state in a four-level tripod-configuration atomic system consists of three lower levels, where constructive and destructive quantum interference between two control transitions (driven by two control fields) arises. We point out that the controllable optical response due to the double-control tunable quantum interference can be utilized to design some fascinating new photonic devices such as logic gates, photonic transistors and switches at quantum level. A single-photon two-input XOR logic gate (in which the incident gate photons are the individual light quanta of the two control fields) based on such an effect of optical switching control with an EIT (electromagnetically induced transparency) microcavity is suggested as an illustrative example of the application of the dark-state manipulation via the double-control quantum interference. The present work would open up possibility of new applications in both fundamental physics (e.g., field quantization and relevant quantum optical effects in artificial systems that can mimic atomic energy levels) and applied physics (e.g., photonic devices such as integrated optical circuits at quantum level).
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| 5. |
- Shen, Jian Qi
(author)
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Coherent Manipulation of Optical Waves with Microwave Quantum Interference
- 2013
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In: Journal of the Physical Society of Japan. - 0031-9015 .- 1347-4073. ; 82:4, s. 044001-
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Journal article (peer-reviewed)abstract
- An experimentally feasible scheme of a four-level atomic system driven by two microwaves and one optical field is suggested in order to realize destructive and constructive quantum interference between the two microwave-driven transition pathways and hence to coherently manipulate the applied optical field. The destructive quantum interference can be switched to the constructive interference and vice versa if one tunes the intensity ratio of the two microwaves. Such an effect of tunable optical response based on microwave quantum interference may have some potential applications to the technique for designing new photonic and quantum optical devices, e. g., photonic logic gates, optical switches, and photonic transistors.
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| 6. |
- Shen, Jian Qi
(author)
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Dispersion-sensitive surface plasmon wave assisted by incoherent gain
- 2014
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In: Optics Communications. - : Elsevier BV. - 0030-4018 .- 1873-0310. ; 329, s. 15-22
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Journal article (peer-reviewed)abstract
- A three-level system with pumped electric-dipole allowed transition for incoherent-gain negative permittivity is suggested in order to realize dispersion-sensitive surface plasmon wave. The present surface wave modes occurring at an interface between an incoherent-gain negative-permittivity "plasmonic" medium (e.g., a semiconductor-quantum-dot material) and an ordinary dielectric can be amplified due to population transfer in the three-level system of the negative-permittivity medium. The issues of complex phase constant and the attenuation coefficients in the adjacent media are considered for addressing the problem of loss compensation of surface plasmon wave. The effect of incoherent-gain amplification exhibited by the dispersion-sensitive surface plasmon wave can be utilized for designing new quantum optical and photonic devices, e.g., photonic transistors and logic gates.
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| 7. |
- Shen, Jian Qi
(author)
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Double-negative atomic vapor assisted by two-photon quantum coherence
- 2012
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In: Journal of the Optical Society of America. B, Optical physics. - : The Optical Society. - 0740-3224 .- 1520-8540. ; 29:11, s. 3192-3200
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Journal article (peer-reviewed)abstract
- A scenario for realizing simultaneously negative permittivity and permeability of a two-photon quantum-coherent atomic vapor is suggested in order to achieve a left-handed atomic medium with a negative refractive index. One of the remarkable features of the present scheme is that it can lead to a controllable manipulation of the negative refractive index of the atomic vapor. Since the electric- and magnetic-dipole allowed transitions of atoms can be excited by visible and infrared lightwaves, the refractive index of the atomic vapor can exhibit its negative refractive index at optical and near-optical frequency bands. This may be a new scheme to fabricate a negatively refracting material based on the quantum optical approach. Such a three-dimensionally isotropic negative refractive index at visible and infrared wavelengths induced by the two-photon-resonant quantum coherence would find a potential application in fabrication of superlenses for perfect imaging and subwavelength focusing.
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| 8. |
- Shen, Jian Qi
(author)
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Electric and magnetic dipole allowed transitions of atoms for three-dimensionally isotropic left handedness in a mixed atomic vapor
- 2014
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In: Progress of Theoretical and Experimental Physics. - : Oxford University Press (OUP). - 2050-3911. ; :3, s. 033A01-
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Journal article (peer-reviewed)abstract
- Since previous negative-index atomic media based on quantum optical approaches are highly lossy, a proposal for realizing a three-dimensionally isotropic left-handed atomic vapor medium is suggested based on a mechanism of incoherent gain assisted atomic transitions. Two three-level atomic systems are utilized for producing simultaneously negative permittivity and negative permeability, respectively, in the same frequency band. We suggest that fine and hyperfine level transitions of atoms (e.g., a hyperfine level transition in a hydrogen atomic system and a fine level transition in an alkali-metal atomic system) would be applicable to realization of such a negatively refracting atomic vapor. The attractive features of the present scenario include: i) three-dimensionally isotropic negative indices; ii) incoherent gain wave amplification in the negative-index atomic vapor; iii) tunable negative indices depending upon external fields. Such a left-handed quantum optical medium can serve as a supporting substrate for lossy negative-index materials for loss compensation. It can also be used in designing new quantum optical and photonic devices (e.g., a subwavelength focusing system and a negative-index superlens for perfect imaging) because of its attractive properties of three-dimensional isotropy and high-gain wave amplification.
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| 9. |
- Shen, Jian Qi
(author)
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Electromagnetically-induced-transparency plasmonics : Quantum-interference-assisted tunable surface-plasmon-polariton resonance and excitation
- 2014
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In: Physical Review A. Atomic, Molecular, and Optical Physics. - : American Physical Society (APS). - 1050-2947 .- 1094-1622. ; 90:2, s. 023814-
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Journal article (peer-reviewed)abstract
- An experimentally feasible configuration of a prism coupler with an electromagnetically-induced-transparency (EIT) medium layer, e.g., a semiconductor-quantum-dot (SQD) medium, deposited upon its prism base is suggested for generating tunable surface-plasmon-polariton resonance. Such surface-plasmon-polariton resonance and optical excitation of a surface plasmon wave can be manipulated by switchable quantum interference among SQD multilevel transitions driven by two external control fields. When an incident probe field is coupled into a surface plasmon wave excitation mode, the surface-plasmon-polariton (SPP) resonance at the interface between the SQD medium layer and the substrate will arise, and the quantum-coherently controllable reflection spectrum of the probe field on the prism base can be achieved. In this process, destructive and constructive quantum interference (determined by the intensity ratio of the two external control fields) in the SQD multilevel system plays a key role for achieving the tunable reflection spectrum. The EIT-based surface-plasmon-polariton resonance presented here will have three characteristics (some of them would be attractive): (i) switchable quantum interference exhibited by surface plasmon wave excitation, (ii) quantum-coherently controllable surface plasmon polaritons by external optical fields, (iii) surface wave sensitive to dispersion of the SQD quantum coherent medium. Such an effect of controllable optical response based on the quantum-interference switchable surface-plasmon-polariton resonance in the EIT-prism coupler may find some potential applications in design of new photonic and quantum optical devices.
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| 10. |
- Shen, Jian Qi
(author)
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Fine-Structure Level Transition for Incoherent-Gain Isotropic Negative Permeability
- 2013
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In: Journal of the Physical Society of Japan. - 0031-9015 .- 1347-4073. ; 82:12, s. 124003-
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Journal article (peer-reviewed)abstract
- A three-dimensionally isotropic negative permeability of a neutral alkali-metal atomic medium, in which a fine-structure magnetic dipole-allowed transition in terahertz band is pumped for population transfer (and hence incoherent gain for negative permeability can be realized), is suggested based on quantum optical approach. The effects relevant to photonic resonance and quantum coherence are involved in the present quantum optical scheme of pumped magnetic-dipole allowed transition. The incoherent-gain assisted atomic medium (with fine-structure transition involved) may have some attractive features, e. g., three-dimensionally isotropic and homogeneous negative permeability for high-gain wave amplification at terahertz frequencies. Such a gain-assisted negative-permeability medium can be a candidate of magnetically resonant materials for artificial composite metamaterials, e.g., it may serve as a substrate of lossy negative-index materials for loss compensation or as a supporting medium for high-gain amplification of a TE-mode surface plasmon-like wave.
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