scholarly journals Time-resolved quantitative proteomics implicates the core snRNP protein SmB together with SMN in neural trafficking

2013 ◽  
Vol 127 (4) ◽  
pp. 812-827 ◽  
Author(s):  
Alan R. Prescott ◽  
Alexandra Bales ◽  
John James ◽  
Laura Trinkle-Mulcahy ◽  
Judith E. Sleeman
Keyword(s):  
Quantitative Proteomics ◽  
Time Resolved ◽  
The Core ◽  
Snrnp Protein

Formation of Pt decorated Ni–Pt nanocubes through low temperature atomic diffusion – time-resolved elemental analysis of nanoparticle formation

Nanoscale ◽  
2015 ◽  
Vol 7 (21) ◽  
pp. 9927-9934 ◽  
Author(s):  
A. Nagao ◽  
K. Higashimine ◽  
J. L. Cuya Huaman ◽  
T. Iwamoto ◽  
T. Matsumoto ◽  
...  
Keyword(s):  
Low Temperature ◽  
Elemental Analysis ◽  
Diffusion Time ◽  
Atomic Diffusion ◽  
Pt Catalysts ◽  
Time Resolved ◽  
Nanoparticle Formation ◽  
The Core ◽  
Temperature Diffusion

Low temperature diffusion of Pt atoms from the core to the corners and edges of the Ni cube results in the preparation of potential novel cage-structured Pt catalysts.

scholarly journals Simultaneous Dual-mode Emission and Tunable Multicolor in the Time Domain from Lanthanide-doped Core-shell Microcrystals

Nanomaterials ◽  
2018 ◽  
Vol 8 (12) ◽  
pp. 1023 ◽  
Author(s):  
Dandan Ju ◽  
Feng Song ◽  
Adnan Khan ◽  
Feifei Song ◽  
Aihua Zhou ◽  
...  
Keyword(s):  
Time Domain ◽  
Near Infrared ◽  
Core Shell ◽  
Dual Mode ◽  
Time Resolved ◽  
Excitation Light ◽  
The Core ◽  
Surface Quenching ◽  
The Time Domain ◽  
High Level

The dual-mode emission and multicolor outputs in the time domain from core-shell microcrystals are presented. The core-shell microcrystals, with NaYF4:Yb/Er as the core and NaYF4:Ce/Tb/Eu as the shell, were successfully fabricated by employing the hydrothermal method, which confines the activator ions into a separate region and minimizes the effect of surface quenching. The material is capable of both upconversion and downshifting emission, and their multicolor outputs in response to 980 nm near-infrared (NIR) excitation laser and 252 nm, and 395 nm ultraviolet (UV) excitation light have been investigated. Furthermore, the tunable color emissions by controlling the Tb3+- Eu3+ ratio in shells and the energy transfer of Ce3+→Tb3+→ Eu3+ were discussed in details. In addition, color tuning of core-shell-structured microrods from green to red region in the time domain could be obtained by setting suitable delay time. Due to downshifting multicolor outputs (time-resolved and pump-wavelength-induced downshifting) coupled with the upconversion mode, the core-shell microrods can be potentially applied to displays and high-level security.

scholarly journals Design principles of autocatalytic cycles constrain enzyme kinetics and force low substrate saturation at flux branch points

2016 ◽  
Author(s):  
Uri Barenholz ◽  
Dan Davidi ◽  
Ed Reznik ◽  
Yinon Bar-On ◽  
Niv Antonovsky ◽  
...  
Keyword(s):  
Kinetic Parameters ◽  
Chemical Reactions ◽  
Carbon Metabolism ◽  
Quantitative Proteomics ◽  
Central Carbon Metabolism ◽  
Branch Points ◽  
The Core ◽  
Intermediate Metabolites ◽  
Central Carbon ◽  
Substrate Saturation

AbstractA set of chemical reactions that require a metabolite to synthesize more of that metabolite is an autocatalytic cycle. Here we show that most of the reactions in the core of central carbon metabolism are part of compact autocatalytic cycles. Such metabolic designs must meet specific conditions to support stable fluxes, hence avoiding depletion of intermediate metabolites. As such, they are subjected to constraints that may seem counter-intuitive: the enzymes of branch reactions out of the cycle must be overexpressed and the affinity of these enzymes to their substrates must be relatively weak. We use recent quantitative proteomics and fluxomics measurements to show that the above conditions hold for functioning cycles in central carbon metabolism of E.coli. This work demonstrates that the topology of a metabolic network can shape kinetic parameters of enzymes and lead to seemingly wasteful enzyme usage.

scholarly journals Two parallel pathways implement robust propionate catabolism and detoxification in mycobacteria

2018 ◽  
Author(s):  
Katja Tummler ◽  
Michael Zimmermann ◽  
Olga T. Schubert ◽  
Ruedi Aebersold ◽  
Clemens Kühn ◽  
...  
Keyword(s):  
Quantitative Proteomics ◽  
Drug Targets ◽  
High Capacity ◽  
Success Story ◽  
Time Resolved ◽  
Parallel Pathways ◽  
Control Distribution ◽  
Lower Capacity ◽  
Potential Drug Targets

AbstractTuberculosis remains a major global health threat with over 1.5 million deaths each year. Mycobacterium tuberculosis’ success story is related to a flexible metabolism, allowing growth despite restrictive conditions within the human host.Host lipids stores are a major carbon source in vivo. Their catabolism yields propionyl-CoA, which is processed by two parallel pathways, the methylmalonyl CoA pathway and the methylcitrate pathway. Both pathways are considered potential drug targets. The methylcitrate pathway is upregulated in the pathological context. However, intermediates of this pathway can be cytotoxic and Mtb’s preference for its usage remains unclear.We combine thermodynamic kinetic modeling, quantitative proteomics and time-resolved metabolomics to characterize the interplay between the two pathways and to show their functionalities in an efficient and fast propionate catabolism.We find that the methylcitrate pathway acts as a transcriptionally regulated, high capacity catabolic pathway due to its favorable thermodynamics and metabolic control distribution. In contrast, the methylmalonyl pathway is constitutively fulfilling biosynthetic tasks and can quickly detoxify propionate pulses, but is thermodynamically restricted to lower capacity.

Time-resolved X-ray diffraction of the core lipid transition of human low density lipoproteins

1999 ◽  
Vol 144 ◽  
pp. 42
Author(s):  
M. Pregetter ◽  
R. Prassl ◽  
H. Amenitsch ◽  
F. Nigon ◽  
J. Chapman ◽  
...  
Keyword(s):  
Low Density Lipoproteins ◽  
Low Density ◽  
X Ray Diffraction ◽  
Time Resolved ◽  
X Ray ◽  
The Core ◽  
Core Lipid

scholarly journals Recoil-induced ultrafast molecular rotation probed by dynamical rotational Doppler effect

2019 ◽  
Vol 116 (11) ◽  
pp. 4877-4882 ◽  
Author(s):  
Denis Céolin ◽  
Ji-Cai Liu ◽  
Vinícius Vaz da Cruz ◽  
Hans Ågren ◽  
Loïc Journel ◽  
...  
Keyword(s):  
Delay Time ◽  
Doppler Effect ◽  
Auger Electron ◽  
Molecular Motion ◽  
General Point ◽  
Core Hole ◽  
Time Resolved ◽  
Pump Probe ◽  
X Ray ◽  
The Core

Observing and controlling molecular motion and in particular rotation are fundamental topics in physics and chemistry. To initiate ultrafast rotation, one needs a way to transfer a large angular momentum to the molecule. As a showcase, this was performed by hard X-ray C1s ionization of carbon monoxide accompanied by spinning up the molecule via the recoil “kick” of the emitted fast photoelectron. To visualize this molecular motion, we use the dynamical rotational Doppler effect and an X-ray “pump-probe” device offered by nature itself: the recoil-induced ultrafast rotation is probed by subsequent Auger electron emission. The time information in our experiment originates from the natural delay between the C1s photoionization initiating the rotation and the ejection of the Auger electron. From a more general point of view, time-resolved measurements can be performed in two ways: either to vary the “delay” time as in conventional time-resolved pump-probe spectroscopy and use the dynamics given by the system, or to keep constant delay time and manipulate the dynamics. Since in our experiment we cannot change the delay time given by the core-hole lifetime τ, we use the second option and control the rotational speed by changing the kinetic energy of the photoelectron. The recoil-induced rotational dynamics controlled in such a way is observed as a photon energy-dependent asymmetry of the Auger line shape, in full agreement with theory. This asymmetry is explained by a significant change of the molecular orientation during the core-hole lifetime, which is comparable with the rotational period.

scholarly journals Time-resolved proteomics vs. ribosome profiling reveals translation dynamics under stress

2016 ◽  
Author(s):  
Tzu-Yu Liu ◽  
Hector H. Huang ◽  
Diamond Wheeler ◽  
James A. Wells ◽  
Yun S. Song ◽  
...  
Keyword(s):  
Protein Synthesis ◽  
Quantitative Proteomics ◽  
Low Dose ◽  
Mrna Translation ◽  
Indirect Measurement ◽  
Ribosome Profiling ◽  
Response To Treatment ◽  
Time Resolved ◽  
Protein Synthesis And Degradation ◽  
Synthesis And Degradation

SummaryMany small molecule chemotherapeutics induce stresses that globally inhibit mRNA translation, remodeling the cancer proteome and governing response to treatment. Here we measured protein synthesis in multiple myeloma cells treated with low-dose bortezomib by coupling pulsed-SILAC (pSILAC) with high-accuracy targeted quantitative proteomics. We found that direct measurement of protein synthesis by pSILAC correlated well with the indirect measurement of protein synthesis by ribosome profiling under conditions of robust translation. By developing a statistical model integrating longitudinal proteomic and mRNA-seq measurements, we found that proteomics could directly detect global alterations in translational rate as a function of therapy-induced stress after prolonged bortezomib exposure. Finally, the model we develop here, in combination with our experimental data including both protein synthesis and degradation, predicts changes in proteome remodeling under a variety of cellular perturbations. pSILAC therefore provides an important complement to ribosome profiling in directly measuring proteome dynamics under conditions of cellular stress.

scholarly journals Proteomics of spatially identified tissues in whole organs

2021 ◽  
Author(s):  
Harsharan Singh Bhatia ◽  
Andreas-David Brunner ◽  
Zhouyi Rong ◽  
Hongcheng Mai ◽  
Marvin Thielert ◽  
...  
Keyword(s):  
Quantitative Proteomics ◽  
Proteome Analysis ◽  
High Sensitivity ◽  
Molecular Profiling ◽  
Compositional Heterogeneity ◽  
Proteomics Data ◽  
Qualitative And Quantitative ◽  
The Core ◽  
Core Proteome ◽  
Novel Biomarkers

Spatial molecular profiling of complex tissues is essential to investigate cellular function in physiological and pathological states. However, methods for molecular analysis of biological specimens imaged in 3D as a whole are lacking. Here, we present DISCO-MS, a technology combining whole-organ imaging, deep learning-based image analysis, and ultra-high sensitivity mass spectrometry. DISCO-MS yielded qualitative and quantitative proteomics data indistinguishable from uncleared samples in both rodent and human tissues. Using DISCO-MS, we investigated microglia activation locally along axonal tracts after brain injury and revealed known and novel biomarkers. Furthermore, we identified initial individual amyloid-beta plaques in the brains of a young familial Alzheimer's disease mouse model, characterized the core proteome of these aggregates, and highlighted their compositional heterogeneity. Thus, DISCO-MS enables quantitative, unbiased proteome analysis of target tissues following unbiased imaging of entire organs, providing new diagnostic and therapeutic opportunities for complex diseases, including neurodegeneration.

scholarly journals Effect of energy transfer on the optical properties of surface-passivated perovskite films with CdSe/ZnS quantum dots

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Il-Wook Cho ◽  
Mee-Yi Ryu
Keyword(s):  
Quantum Dots ◽  
Energy Transfer ◽  
Transfer Rate ◽  
Surface Passivation ◽  
Hybrid Structure ◽  
Core Diameter ◽  
Time Resolved ◽  
Size Dependent ◽  
The Core ◽  
Charge Transfer Rate

AbstractSurface passivation is an effective method to protect the surfaces and improve the luminescence properties of perovskite (PS) films. CdSe/ZnS core-shell quantum dots (QDs) have been employed for surface passivation of PS films because of their size-dependent tunable bandgaps. Herein, the energy transfer (ET) behavior of CH3NH3PbI2Br PS films covered with CdSe/ZnS QDs (QD/PS hybrid structures) is characterized by using photoluminescence (PL) and time-resolved PL spectroscopy. The PL decay time and the integrated PL intensity of the QD/PS hybrid structure increase compared with those of the bare PS films, owing to ET from the QDs to the PS and reduced charge traps. The ET efficiency increases from ~7% to 63% for the QD/PS hybrid structure when the core diameter of the QDs decreases from 6.5 to 2.7 nm, respectively. This can be explained by the charge transfer rate enhancement due to the control of energy level alignment of QDs. These results allow us to understand fundamental mechanisms such as ET from QDs to PS films as a function of the size of the QD.

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