| 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. |
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| 3. |
- Duarte, Fernanda, et al.
(författare)
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The Alkaline Hydrolysis of Sulfonate Esters : Challenges in Interpreting Experimental and Theoretical Data
- 2014
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Ingår i: Journal of Organic Chemistry. - : American Chemical Society (ACS). - 0022-3263 .- 1520-6904. ; 79:7, s. 2816-2828
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Tidskriftsartikel (refereegranskat)abstract
- Sulfonate ester hydrolysis has been the subject of recent debate, with experimental evidence interpreted in terms of both stepwise and concerted mechanisms. In particular, a recent study of the alkaline hydrolysis of a series of benzene arylsulfonates (Babtie et al., Org. Biomol. Chem. 10, 2012, 8095) presented a nonlinear Bronsted plot, which was explained in terms of a change from a stepwise mechanism involving a pentavalent intermediate for poorer leaving groups to a fully concerted mechanism for good leaving groups and supported by a theoretical study. In the present work, we have performed a detailed computational study of the hydrolysis of these compounds and find no computational evidence for a thermodynamically stable intermediate for any of these compounds. Additionally, we have extended the experimental data to include pyridine-3-yl benzene sulfonate and its N-oxide and N-methylpyridinium derivatives. Inclusion of these compounds converts the Bronsted plot to a moderately scattered but linear correlation and gives a very good Hammett correlation. These data suggest a concerted pathway for this reaction that proceeds via an early transition state with little bond cleavage to the leaving group, highlighting the care that needs to be taken with the interpretation of experimental and especially theoretical data.
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| 4. |
- Geng, Ting, et al.
(författare)
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Dynamics in higher lying excited states : Valence to Rydberg transitions in the relaxation paths of pyrrole and methylated derivatives
- 2017
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Ingår i: Journal of Chemical Physics. - : AIP Publishing. - 0021-9606 .- 1089-7690. ; 146:14
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Tidskriftsartikel (refereegranskat)abstract
- The involvement of intermediate Rydberg states in the relaxation dynamics of small organic molecules which, after excitation to the valence manifold, also return to the valence manifold is rarely observed. We report here that such a transiently populated Rydberg state may offer the possibility to modify the outcome of a photochemical reaction. In a time resolved photoelectron study on pyrrole and its methylated derivatives, N-methyl pyrrole and 2,5-dimethyl pyrrole, 6.2 eV photons (200 nm) are used to excite these molecules into a bright pi pi* state. In each case, a pi 3p-Rydberg state, either the B-1(pi 3p(y)) or the A(2)(pi 3p(z)) state, is populated within 20-50 fs after excitation. The wavepacket then proceeds to the lower lying A(2)(pi sigma*) state within a further 20 fs, at which point two competing reaction channels can be accessed: prompt N-H (N-CH3) bond cleavage or return to the ground state via a conical intersection accessed after ring puckering, the latter of which is predicted to require an additional 100-160 fs depending on the molecule.
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| 5. |
- Geng, Ting, 1987-
(författare)
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Excited-state dynamics of small organic molecules studied by time-resolved photoelectron spectroscopy
- 2017
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Ultra-violet and visible light induced processes in small organic molecules play very important roles in many fields, e.g., environmental sciences, biology, material development, chemistry, astrophysics and many others. Thus it is of great importance to better understand the mechanisms behind these processes. To achieve this, a bottom-up approach is most effective, where the photo-induced dynamics occurring in the simplest organic molecule (ethylene) are used as a starting point. Simple substituents and functional groups are added in a controlled manner to ethylene, and changes in the dynamics are investigated as a function of these modifications. In this manner, the dynamics occurring in more complex systems can be explored from a known base.In this thesis, the excited state dynamics of small organic molecules are studied by a combination of time-resolved photoelectron spectroscopy and various computational methods in order to determine the basic rules necessary to help understand and predict the dynamics of photo-induced processes.The dynamics occurring in ethylene involve a double bond torsion on the ππ* excited state, followed by the decay to the ground state coupled with pyramidalization and hydrogen migration. Several different routes of chemical modification are used as the basis to probe these dynamics as the molecular complexity is increased. (i) When ethylene is modified by the addition of an alkoxyl group (-OCnH2n+1), a new bond cleavage reaction is observed on the πσ* state. When modified by a cyano (-CN) group, a significant change in the carbon atom involved in pyramidalization is observed. (ii) When ethylene used to build up small cyclic polyenes, it is observed that the motifs of the ethylene dynamics persist, expressed as ring puckering and ring opening. (iii) In small heteroaromatic systems, i.e., an aromatic ring containing an ethylene-like sub-structure and one or two non-carbon atoms, the type of heteroatom (N: pyrrole, pyrazole O: furan) gives rise to different bond cleavage and ring puckering channels. Furthermore, adding an aldehyde group (-C=O) onto furan, as a way to lengthen the delocalised ring electron system, opens up additional reaction channels via a nπ* state.The results presented here are used to build up a more complete picture of the dynamics that occur in small molecular systems after they are excited by a visible or UV photon, and are used as a basis to motivate further investigations.
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| 6. |
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| 7. |
- Geng, Ting, et al.
(författare)
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Time-Resolved Photoelectron Spectroscopy Studies of Isoxazole and Oxazole
- 2020
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Ingår i: Journal of Physical Chemistry A. - : American Chemical Society (ACS). - 1089-5639 .- 1520-5215. ; 124:20, s. 3984-3992
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Tidskriftsartikel (refereegranskat)abstract
- The excited state relaxation pathways of isoxazole and oxazole upon excitation with UV-light were investigated by nonadiabatic ab initio dynamics simulations and time-resolved photoelectron spectroscopy. Excitation of the bright ππ*-state of isoxazole predominantly leads to ring-opening dynamics. Both the initially excited ππ*-state and the dissociative πσ*-state offer a combined barrier-free reaction pathway, such that ring-opening, defined as a distance of more than 2 Å between two neighboring atoms, occurs within 45 fs. For oxazole, in contrast, the excited state dynamics is about twice as slow (85 fs) and the quantum yield for ring-opening is lower. This is caused by a small barrier between the ππ*-state and the πσ*-state along the reaction path, which suppresses direct ring-opening. Theoretical findings are consistent with the measured time-resolved photoelectron spectra, confirming the timescales and the quantum yields for the ring-opening channel. The results indicate that a combination of time-resolved photoelectron spectroscopy and excited state dynamics simulations can explain the dominant reaction pathways for this class of molecules. As a general rule, we suggest that the antibonding σ*-orbital located between the oxygen atom and a neighboring atom of a five-membered heterocyclic system provides a driving force for ring-opening reactions, which is modified by the presence and position of additional nitrogen atoms.
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| 8. |
- Geng, Ting, et al.
(författare)
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Time-resolved photoelectron spectroscopy studies on pyrazole and several methylated derivatives
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Annan publikation (övrigt vetenskapligt/konstnärligt)abstract
- We present femtosecond time-resolved photoelectron spectra and ab initio studies on pyrazole andits methylated derivatives 1-, 3-, and 5-methylpyrazole. Excitation at 200 nm populates both the two lowest lying states, a 1ππ* state and a mixed 1πσ*/1π3s Rydberg state, from where three relaxation channels are observed: ring puckering, N-H bond cleavage, and ring opening via N-N bond breaking. The N-N bond breaking channel is the fastest process, occurring within one vibrational cycle of the Franc Condon active ring stretching mode. N-H bond cleavage is observed to be aminor channel, and occurs upon direct excitation to the mixed π3s/πσ* state. Finally, ring puckering occurs after a timescale of a few hundred fs because the molecules need time to find the gradient towards this conical intersection. However, this channel is accessed if the initially triggered processes are not successful. The quantum yields of the different channels were found to be very sensitive of the relative positioning of the excited states. In pyrazole and 5-methylpyrazole, N-Nbond cleavage dominates. In 1-, and 3-methylpyrazole, while the 1ππ* state drops in energy the dissociating 1πσ* valence state does not, and this leads to an increased barrier towards ring cleavage and a decreased the quantum yield for N-N bond cleavage. Upon excitation at 267 nm of 1- and 3-methylpyrazole, ring puckering is the only available pathway.
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| 9. |
- Geng, Yang, 1980-
(författare)
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Hybrid Integration of Active Bio-signal Cable with Intelligent Electrode : Steps toward Wearable Pervasive-Healthcare Applications
- 2012
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Personalized and pervasive healthcare help seamlessly integrate healthcare and wellness into people’s daily life, independent of time and space. With the developments in biomedical sensing technologies nowadays, silicon based integrated circuits have shown great advantages in terms of tiny physical size, and low power consumption. As a result, they have been found in many advanced medical applications. In the meanwhile, printed electronics is considered as a promising approach enabling cost-effective manufacturing of thin, flexible, and light-weight devices. A hybrid integration of integrated circuits and printed electronics provides a promising solution for the future wearable healthcare devices.This thesis first reviews the current approaches for bio-electric signal sensing and the state-of-the-art designs for biomedical circuit and systems. In the second part, the idea of Intelligent Electrode and Active Cable for wearable ECG monitoring systems is proposed. Based on this concept, we design and fabricate two customized IC chips to provide a single cable solution for long-term healthcare monitoring. The first chip is a digital ASIC with a serial communication protocol implemented on chip to support data and command packets transmission between different ASIC chips. Also, it has on-chip memory to buffer the digital bio-signal. An Intelligent Electrode is formed by embedding the ASIC chip into the conductive electrode. With the on-chip integrated communication protocol, a wired sensor network can be established enabling the single cable solution. The ASIC’s controlling logic is capable of making dynamic network management, thus endows the electrode with local intelligence. The second chip is a fully integrated mixed-signal SoC. In addition to the digital controller implemented and verified in the first chip, another 2 key modules are integrated: a tunable analog front end circuits, and a 6-input SAR ADC. The second chip works as a networked SoC sensor. The command-based network management is verified through functional tests using the fabricated SoCs. With the programmable analog front end circuits, the SoC sensor can be configured to detect a variety of bio-electric signals. EOG, EMG, ECG, and EEG signals are successfully recorded through in-vivo tests.This research also explores the potential of using high accurate inkjet printing technology as an inexpensive integration method and enabling technology to design and fabricate bio-sensing devices. Performance evaluation of printed electrodes and interconnections on flexible substrates is made to examine the feasibility of applying them in the fabrication of Bio-Patch. The reliability of the inkjet printed sliver traces is evaluated via static bending tests. The measurement results prove that the printed silver lines can offer a reliable interconnection. In-vivo test results show that the quality of ECG signal sensed by the printed electrodes is comparable with the one gained by commercial electrodes.Finally, two Bio-Patch prototypes are presented: one is based on photo paper substrate, the other on polyimide substrate. These two prototypes are implemented by heterogeneous integration of the silicon based SoC sensor with cost-effective printed electronics onto the flexible substrates. The measurement results indicate the SoC operates smoothly with the printed electronics. Clean ECG signal is successfully recorded from both of the implemented Bio-Patch prototypes. This versatile SoC sensor can be used in various applications according to specific requirements. And this heterogeneous system combining high-level integrated SoC technology and inkjet printing technique provides a promising solution for future personalized and pervasive healthcare applications.
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| 10. |
- MacDonell, R. J., et al.
(författare)
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Excited state dynamics of acrylonitrile: Substituent effects at conical intersections interrogated via time-resolved photoelectron spectroscopy and ab initio simulation
- 2016
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Ingår i: Journal of Chemical Physics. - : AIP Publishing. - 0021-9606 .- 1089-7690. ; 145:11
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Tidskriftsartikel (refereegranskat)abstract
- We report a joint experimental and theoretical study on the photoinitiated ultrafast dynamics of acrylonitrile (AN) and two methylated analogs: crotonitrile (CrN) and methacrylonitrile (MeAN). Time-resolved photoelectron spectroscopy (TRPES) and ab initio simulation are employed to discern the conical intersection mediated vibronic dynamics leading to relaxation to the ground electronic state. Each molecule is pumped with a femtosecond pulse at 200 nm and the ensuing wavepackets are probed by means of one and two photon ionization at 267 nm. The predominant vibrational motions involved in the de-excitation process, determined by ab initio trajectory simulations, are an initial twisting about the C=C axis followed by pyramidalization at a carbon atom. The decay of the time-resolved photoelectron signal for each molecule is characterized by exponential decay lifetimes for the passage back to the ground state of 60 +/- 10, 86 +/- 11, and 97 +/- 9 fs for AN, CrN, and MeAN, respectively. As these results show, the excited state dynamics are sensitive to the choice of methylation site and the explanation for the observed trend may be found in the trajectory simulations. Specifically, since the pyramidalization motion leading to the conical intersection with the ground state is accompanied by the development of a partial negative charge at the central atom of the pyramidal group, the electron donation of the cyano group ensures that this occurs exclusively at the medial carbon atom. In this way, the donated electron density from the cyano group "directs" the wavepacket to a particular region of the intersection seam. The excellent agreement between the experimental and simulated TRPES spectra, the latter determined by employing trajectory simulations, demonstrates that this mechanistic picture is consistent with the spectroscopic results.
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