| 1. |
- Klionsky, Daniel J., et al.
(författare)
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Guidelines for the use and interpretation of assays for monitoring autophagy
- 2012
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Ingår i: Autophagy. - : Informa UK Limited. - 1554-8635 .- 1554-8627. ; 8:4, s. 445-544
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Forskningsöversikt (refereegranskat)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. |
- Foltynowicz, Aleksandra, 1981-, et al.
(författare)
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Measurement and assignment of double-resonance transitions to the 8900-9100- cm-1 levels of methane
- 2021
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Ingår i: Physical Review A: covering atomic, molecular, and optical physics and quantum information. - : American Physical Society. - 2469-9926 .- 2469-9934. ; 103:2
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Tidskriftsartikel (refereegranskat)abstract
- Optical-optical double-resonance spectroscopy with a continuous wave pump and frequency comb probe allows measurement of sub-Doppler transitions to highly excited molecular states over a wide spectral range with high frequency accuracy. We report on assessment and characterization of sub-Doppler double-resonance transitions in methane measured using a 3.3-μm continuous wave optical parametric oscillator as a pump and a 1.67-μm frequency comb as a probe. The comb spectra were recorded using a Fourier transform spectrometer with comb-mode-limited resolution. With the pump tuned to nine different transitions in the ν3 fundamental band, we detected 36 ladder-type transitions to the 3ν3 overtone band region, and 18 V-type transitions to the 2ν3 overtone band. We describe in detail the experimental approach and the pump stabilization scheme, which currently limits the frequency accuracy of the measurement. We present the data analysis procedure used to extract the frequencies and intensities of the probe transitions for parallel and perpendicular relative pump-probe polarization. We compare the center frequencies and relative intensities of the ladder-type transitions to theoretical predictions from the TheoReTS and ExoMol line lists, demonstrating good agreement with TheoReTS.
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| 3. |
- Foltynowicz, Aleksandra, 1981-, et al.
(författare)
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Sub-Doppler Double-Resonance Spectroscopy of Methane Using a Frequency Comb Probe
- 2021
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Ingår i: Physical Review Letters. - 0031-9007 .- 1079-7114. ; 126:6
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Tidskriftsartikel (refereegranskat)abstract
- We report the first measurement of sub-Doppler molecular response using a frequency comb by employing the comb as a probe in optical-optical double-resonance spectroscopy. We use a 3.3 μm continuous wave pump and a 1.67 μm comb probe to detect sub-Doppler transitions to the 2ν3 and 3ν3 bands of methane with ∼1.7 MHz center frequency accuracy. These measurements provide the first verification of the accuracy of theoretical predictions from highly vibrationally excited states, needed to model the high-temperature spectra of exoplanets. Transition frequencies to the 3ν3 band show good agreement with the TheoReTS line list.
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| 4. |
- Foltynowicz, Aleksandra, 1981-, et al.
(författare)
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Sub-doppler double-resonance spectroscopy of methane using a frequency comb probe
- 2020
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Ingår i: Conference on Lasers and Electro-Optics. - : Optica Publishing Group (formerly OSA). - 9781943580767 - 9781728144184
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Konferensbidrag (refereegranskat)abstract
- We use a 3.3 µm continuous wave optical parametric oscillator as a pump and a 1.67 µm frequency comb as a probe to record 36 sub-Doppler double-resonance transitions in the 3v3 band of methane (including 26 previously unreported) with ~1.5 MHz center frequency accuracy.
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| 5. |
- Hjältén, Adrian, 1988-, et al.
(författare)
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Accurate measurement and assignment of high rotational energy levels of the 3v3 ← v3 band of methane
- 2023
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Ingår i: 2023 conference on lasers and electro-optics, CLEO 2023. - : IEEE. - 9781957171258 - 9781665455688
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Konferensbidrag (refereegranskat)abstract
- We use optical-optical double-resonance spectroscopy with a high-power continuous wave pump and a cavity-enhanced comb probe to expand sub-Doppler measurements of the 3v3 ← v3 band of CH4 to higher rotational levels. We assign the final states using combination differences, i.e., by reaching the same state using different pump/probe combinations.
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| 6. |
- Silva de Oliveira, Vinicius, et al.
(författare)
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Double-Resonance Spectroscopy of Methane Using a Comb Probe
- 2021
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Ingår i: 2021 Conference on Lasers and Electro-Optics Europe and European Quantum Electronics Conference, CLEO/Europe-EQEC 2021. - : IEEE Lasers and Electro-Optics Society. - 9781665418768
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Konferensbidrag (refereegranskat)abstract
- Optical-optical double resonance (OODR) spectroscopy is a powerful tool for the experimental assignment of highly-excited molecular states, which in turn is needed for verification of the accuracy of theoretical predictions of high-temperature spectra observed in exoplanets and in combustion environments. Previous implementations of OODR used either continuous wave (cw) lasers, which limit the number of transitions that can be detected, or pulsed lasers, which limit the spectral resolution. Recently, we demonstrated OODR with a cw pump and a frequency comb probe and applied it to the detection and assignment of methane transitions in the 3ν 3 ← ν 3 range with sub-Doppler resolution over 200 cm -1 of bandwidth [1]. The pump [see Fig. 1(a) ] was a 1 W 3.3m idler of a cw optical parametric oscillator (cw-OPO), stabilized to the Lamb dip in a selected CH 4 transition in the ν 3 band using a signal from a reference cell. The probe was an amplified fully-stabilized Er:fiber comb ( f rep = 250 MHz), whose center wavelength was shifted to 1.67m using a soliton self-frequency shift fiber (SSSF). The sample of pure CH 4 was contained in an 80-cm-long single-pass cell cooled by liquid nitrogen. The probe spectra were detected using a Fourier transform spectrometer (FTS) with comb-mode-limited resolution [2] , and the final interleaved spectra had 2 MHz sampling point spacing. Figure 1(b) shows the 3ν 3 ← ν 3 R(1) transition at 6046.36008(5) cm -1 , detected with the pump on the ν 3 R(0) line. We measured, fit and assigned 36 probe transitions with the pump tuned to 9 different transitions. Figure 1(d) shows a comparison of the probe transition wavenumbers to predictions from the TheoReTS database [3] , demonstrating agreement within 1 cm -1.
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| 7. |
- Silva de Oliveira, Vinicius, et al.
(författare)
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Measurement and Assignment of Hot-Band Methane Transitions with Sub-MHz Accuracy
- 2022
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Ingår i: CLEO: 2022. - : Optica Publishing Group. - 9781557528209
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Konferensbidrag (refereegranskat)abstract
- We use double-resonance spectroscopy with cavity-enhanced comb probe to measure sub-Doppler transitions in the 3ν3←ν3 band of CH4. We assign the final states using different pump/probe combinations reaching the same state, and the dependence of line intensities on relative pump/probe polarization.
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| 8. |
- Silva de Oliveira, Vinicius, et al.
(författare)
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Optical-optical double-resonance spectroscopy of methane using a cavity-enhanced comb probe
- 2021
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Ingår i: OSA Technical Digest. - : Optical Society of America. - 9781557528209
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Konferensbidrag (refereegranskat)abstract
- We implement a cavity to enhance the absorption of a frequency comb probe in a double-resonance measurement of sub-Doppler 3ν3 ← ν3 methane transitions. This yields two orders of magnitude better sensitivity in 15 times shorter acquisition time compared to previous work using a single-pass cell.
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| 9. |
- Silva de Oliveira, Vinicius, et al.
(författare)
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Sub-doppler optical-optical double-resonance spectroscopy of methane using a frequency comb probe
- 2021
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Ingår i: OSA Optical Sensors and Sensing Congress 2021 (AIS, FTS, HISE, SENSORS, ES). - : Optical Society of America. - 9781557528209
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Konferensbidrag (refereegranskat)abstract
- We use a 3.3 µm high-power continuous wave pump and a 1.67 µm comb probe to detect transitions in the 3ν3 ← ν3 range of methane with sub-Doppler resolution over 6 THz of bandwidth. We achieve high absorption sensitivity for the comb probe using an enhancement cavity and a Fourier transform spectrometer with auto-balanced detection.
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| 10. |
- Silva de Oliveira, Vinicius, et al.
(författare)
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Sub-Doppler optical-optical double-resonance spectroscopy using a cavity-enhanced frequency comb probe
- 2024
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Ingår i: Nature Communications. - : Springer Nature. - 2041-1723. ; 15:1
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Tidskriftsartikel (refereegranskat)abstract
- Accurate parameters of molecular hot-band transitions, i.e., those starting from vibrationally excited levels, are needed to accurately model high-temperature spectra in astrophysics and combustion, yet laboratory spectra measured at high temperatures are often unresolved and difficult to assign. Optical-optical double-resonance (OODR) spectroscopy allows the measurement and assignment of individual hot-band transitions from selectively pumped energy levels without the need to heat the sample. However, previous demonstrations lacked either sufficient resolution, spectral coverage, absorption sensitivity, or frequency accuracy. Here we demonstrate OODR spectroscopy using a cavity-enhanced frequency comb probe that combines all these advantages. We detect and assign sub-Doppler transitions in the spectral range of the 3ν3 ← ν3 resonance of methane with frequency precision and sensitivity more than an order of magnitude better than before. This technique will provide high-accuracy data about excited states of a wide range of molecules that is urgently needed for theoretical modeling of high-temperature data and cannot be obtained using other methods.
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