Volatile communication in plants relies on a KAI2-mediated signaling pathway.

Plants are constantly exposed to volatile organic compounds (VOCs) that are released during plant-plant communication, within-plant self-signaling, and plant-microbe interactions. Therefore, understanding VOC perception and downstream signaling is vital for unraveling the mechanisms behind information exchange in plants, which remain largely unexplored. Using the hormone-like function of volatile terpenoids in reproductive organ development as a system with a visual marker for communication, we demonstrate that a petunia karrikin-insensitive receptor, PhKAI2ia, stereospecifically perceives the (-)-germacrene D signal, triggering a KAI2-mediated signaling cascade and affecting plant fitness. This study uncovers the role(s) of the intermediate clade of KAI2 receptors, illuminates the involvement of a KAI2ia-dependent signaling pathway in volatile communication, and provides new insights into plant olfaction and the long-standing question about the nature of potential endogenous KAI2 ligand(s).

Monitoring drug metabolic pathways through extracellular vesicles in mouse plasma.

The ability to monitor the response of metabolic enzymes to drug exposure in individuals is highly appealing and critical to personalized medicine. Although pharmacogenomics assesses genotypic differences, it does not report changes in metabolic enzyme activities due to environmental factors such as drug interactions. Here, we report a quantitative proteomics strategy to monitor drug metabolic pathways by profiling metabolic enzymes in circulating extracellular vesicles (EVs) upon drug exposure. Mass spectrometry (MS)-based measurement revealed that changes in metabolic enzyme abundance in EVs paralleled those in hepatic cells isolated from liver tissue. Coupling with multiplexed isotopic labeling, we temporally quantified 34 proteins involved in drug absorption, distribution, metabolism, and excretion (ADME) pathways. Out of 44 known ADME proteins in plasma EVs, previously annotated mouse cytochrome P450 3A11 (Cyp3a11), homolog to human CYP3A4, and uridine 5'-diphospho (UDP) glucuronosyltransferase 2A3 (Ugt2a3), increased upon daily rifampicin dosage. Dasatinib, a tyrosine kinase inhibitor to treat leukemia, also elevated Cyp3a11 levels in plasma EVs, but to a lesser extent. Altogether, this study demonstrates that measuring drug enzymes in circulating EVs as an effective surrogate is highly feasible and may transform today's drug discovery and development for personalized medicine.

Chemical Affinity-Based Isolation of Extracellular Vesicles from Biofluids for Proteomics and Phosphoproteomics Analysis.

Extracellular vesicles (EVs) from biofluids have recently gained significant attention in the field of liquid biopsy. Released by almost every type of cell, they provide a real-time snapshot of host cells and contain a wealth of molecular information, including proteins, in particular those with post-translational modifications (PTMs) such as phosphorylation, as the main player of cellular functions and disease onset and progression. However, the isolation of EVs from biofluids remains challenging due to low yields and impurities from current EV isolation methods, making the downstream analysis of EV cargo, such as EV phosphoproteins, difficult. Here, we describe a rapid and effective EV isolation method based on functionalized magnetic beads for EV isolation from biofluids such as human urine and downstream proteomics and phosphoproteomics analysis following EV isolation. The protocol enabled a high recovery yield of urinary EVs and sensitive profiles of EV proteome and phosphoproteome. Furthermore, the versatility of this protocol and relevant technical considerations are also addressed here.

One-Pot Analytical Pipeline for Efficient and Sensitive Proteomic Analysis of Extracellular Vesicles.

Extracellular vesicle (EV) proteomics emerges as an effective tool for discovering potential biomarkers for disease diagnosis, monitoring, and therapeutics. However, the current workflow of mass spectrometry-based EV proteome analysis is not fully compatible in a clinical setting due to inefficient EV isolation methods and a tedious sample preparation process. To streamline and improve the efficiency of EV proteome analysis, here we introduce a one-pot analytical pipeline integrating a robust EV isolation approach, EV total recovery and purification (EVtrap), with in situ protein sample preparation, to detect urinary EV proteome. By incorporating solvent-driven protein capture and fast on-bead digestion, the one-pot pipeline enabled the whole EV proteome analysis to be completed within one day. In comparison with the existing workflow, the one-pot pipeline was able to obtain better peptide yield and identify the equivalent number of unique EV proteins from 1 mL of urine. Finally, we applied the one-pot pipeline to profile proteomes in urinary EVs of bladder cancer patients. A total of 2774 unique proteins were identified in 53 urine samples using a 15 min gradient library-free data-independent acquisition method. Taken altogether, our novel one-pot analytical pipeline demonstrated its potential for routine and robust EV proteomics in biomedical applications.

Mass spectrometry-based phosphoproteomics in clinical applications.

Protein phosphorylation is an essential post-translational modification that regulates many aspects of cellular physiology, and dysregulation of pivotal phosphorylation events is often responsible for disease onset and progression. Clinical analysis on disease-relevant phosphoproteins, while quite challenging, provides unique information for precision medicine and targeted therapy. Among various approaches, mass spectrometry (MS)-centered characterization features discovery-driven, high-throughput and in-depth identification of phosphorylation events. This review highlights advances in sample preparation and instrument in MS-based phosphoproteomics and recent clinical applications. We emphasize the preeminent data-independent acquisition method in MS as one of the most promising future directions and biofluid-derived extracellular vesicles as an intriguing source of the phosphoproteome for liquid biopsy.

Lower Bounds on Quantum Annealing Times.

The adiabatic theorem provides sufficient conditions for the time needed to prepare a target ground state. While it is possible to prepare a target state much faster with more general quantum annealing protocols, rigorous results beyond the adiabatic regime are rare. Here, we provide such a result, deriving lower bounds on the time needed to successfully perform quantum annealing. The bounds are asymptotically saturated by three toy models where fast annealing schedules are known: the Roland and Cerf unstructured search model, the Hamming spike problem, and the ferromagnetic p-spin model. Our bounds demonstrate that these schedules have optimal scaling. Our results also show that rapid annealing requires coherent superpositions of energy eigenstates, singling out quantum coherence as a computational resource.

Pharmacokinetics, optimal dosages and withdrawal time of florfenicol in Asian seabass (Lates calcarifer) after oral administration via medicated feed.

Asian seabass (Lates calcarifer) is an economically important fish in Asian and Australian markets, but few pharmacokinetic (PK) data of antimicrobial drugs in this species is available. The present study investigated the PK behaviour of florfenicol (FF) through medicated feed in Asian seabass cultured at 25°C. The serum and muscle/skin concentrations of FF and its metabolite florfenicol amine (FFA) were determined by the HPLC-FLD method and analysed by one-compartmental model. The optimal dosages were determined by pharmacokinetic-pharmacodynamic (PK-PD) approach and the linear regression analysis was used to determine the withdrawal time (WDT). The PK study following a single oral administration of 15 mg/kg FF via medicated feed revealed that the absorption half-life (t1/2Ka ), elimination half-life (t1/2K ), peak concentration (Cmax ), area under the concentration-time curve (AUC), volume of distribution (Vd/F) and clearance (CL/F) were 1.47 h, 8.07 h, 8.61 µg/ml, 146.41 h·µg/ml, 1.19 L/kg and 0.102 L/kg/h, respectively. The muscle/skin concentration-time profile was similar to that of the serum, suggesting well distribution but only a small fraction of FF was metabolized to FFA. The optimal dosage for a minimum inhibitory concentration of 2 µg/ml was calculated as 13.38 mg/kg/day. The appropriate WDT after multiple oral medications with 15 mg/kg FF once daily for 7 days was determined as 8 days. Information obtained from the current study can potentially be applied for the treatment of bacterial diseases in farming Asian seabass.

Combined Effects of Temperature and Salinity on the Pharmacokinetics of Florfenicol in Nile Tilapia (Oreochromis niloticus) Reared in Brackish Water.

Prudent antimicrobial use requires knowledge of pharmacokinetics (PK) in a specific fish species which in turn depends on water temperature and salinity. Although the influence of each individual factor is known, the combined effect is less clear. The objective of the current study was to investigate the effect of temperature and salinity concurrently on the PK of florfenicol (FF) in Nile tilapia reared in brackish water. Twenty-eight fish were divided into four groups and kept at one of two temperatures (24 vs. 32°C) and two salinity levels (5 vs. 15 ppt). The FF was administered at a single dose of 15 mg/kg body weight via oral gavage. The serum concentrations were analyzed by HPLC method and the PK parameters were analyzed by a 2-compartmental model. The result revealed that at 32°C, the elimination half-lives (t1/2ß), time to reach the peak concentration (Tmax), area under the serum concentration-time curve (AUC), and mean residence time (MRT) were significantly decreased, while the clearance relative to bioavailability (CL/F) significantly increased compared to those at 24°C. The extents of these PK changes were similar at the two salinity levels. On the contrary, increasing the salinity from 5 to 15 ppt at a given temperature level produced no significant change in the PK behavior. Our finding indicated that only water temperature, but not salinity, is the major determinant factor governing the FF fate in the fish body.

Determination of Optimal Doses and Minimum Effective Concentrations of Tricaine Methanesulfonate, 2-Phenoxyethanol and Eugenol for Laboratory Managements in Nile Tilapia (Oreochromis niloticus).

Anesthetic agents are often used in fish experiments to reduce the stress and struggle and to improve animal welfare. The present study aimed to determine the optimal doses and serum minimum effective concentration (MEC) of tricaine methanesulfonate (MS-222), 2-phenoxyethanol (2-PE), and eugenol (EUG) in Nile tilapia. Twenty-one fish were immersed in three different doses of each anesthetic and the minimal dose that produce stage III anesthesia within 5 min, maintain anesthesia status for 3 min, and recover within 5 min was considered the optimal dose. The serum concentrations of anesthetics immediately after the fish reached stage III anesthesia was defined as the MEC. The results revealed that the anesthetics dose-dependently shorten the induction time while the effect of doses on the recovery times were variable. The determined optimal doses for MS-222, 2-PE, and EUG were 300, 900, and 90 ppm, respectively. The MECs were 70, 263, and 53 µg/mL, respectively, about two to four times lower than the optimal doses and were independent of the doses. After immersion stopped, the serum concentrations decreased by >90% within the first hour and >99% after 4 h. Our research provides useful information for a smooth fish handling and design for researches requiring stage III anesthesia.

Kinetic Characterization and Inhibitor Screening for the Proteases Leading to Identification of Drugs against SARS-CoV-2.

Coronavirus (CoV) disease 2019 (COVID-19), caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has claimed many lives worldwide and is still spreading since December 2019. The 3C-like protease (3CLpro) and papain-like protease (PLpro) are essential for maturation of viral polyproteins in SARS-CoV-2 life cycle and thus regarded as key drug targets for the disease. In this study, 3CLpro and PLpro assay platforms were established, and their substrate specificities were characterized. The assays were used to screen collections of 1,068 and 2,701 FDA-approved drugs. After excluding the externally used drugs which are too toxic, we totally identified 12 drugs as 3CLpro inhibitors and 36 drugs as PLpro inhibitors active at 10 µM. Among these inhibitors, six drugs were found to suppress SARS-CoV-2 with the half-maximal effective concentration (EC50) below or close to 10 µM. This study enhances our understanding on the proteases and provides FDA-approved drugs for prevention and/or treatment of COVID-19.

Single amino acid utilization for bacterial categorization.

Despite great advancement in genetic typing, phenotyping is still an indispensable tool for categorization of bacteria. Certain amino acids may be essential for bacterial survival, growth, pathogenicity or toxin production, which prompts the idea that the intrinsic ability to utilize single amino acid under live-or-die situation could be a basis for differentiation of bacteria species. In this study, we determined the single amino acid consumption profiles of 7 bacterial species, and demonstrated that most bacteria have species-specific pattern of amino acid consumption. We also discovered that bacterial strains from different hosts, toxigenicity, and antibiotic-resistance presented distinct preference for certain amino acids. Taken altogether, the amino acid consumption profiles showed potential to be a novel tool complementary to study not only bacterial categorization but also biochemical characteristics of the bacteria such that its phenotyping can be used to uncover strategies for nutritional, pharmaceutical, taxonomic, and evolutionary aspects of bacterial researches.

A one-pot analysis approach to simplify measurements of protein stability and folding kinetics.

To achieve a good understanding of the characteristics of a protein, it is important to study its stability and folding kinetics. Investigations of protein stability have been recently applied to drug-target identification, drug screening, and proteomic studies. The efficiency of the experiments performed to study protein stability and folding kinetics is now a crucial factor that needs to be optimized for these potential applications. However, the standard procedures used to carry out these experiments are usually complicated and time consuming. Large number of measurements is the bottleneck that limits the application of protein folding to large-scale experiments. To overcome this limitation, we developed a method denoted as "one-pot analysis" which is based on taking a single measurement from a mixture of samples rather than from every sample. We combined one-pot analysis with pulse proteolysis to determine the effects of the binding of maltose to maltose-binding protein on the protein folding properties. After carrying out a simple optimization, we demonstrated that protein stability or unfolding kinetics could be measured accurately with just one detection measurement. We then further applied the optimized conditions to cellular thermal shift assay (CETSA). Combining one-pot analysis with CETSA led to a successful determination of the effects of the binding of methotrexate to dihydrofolate reductase in HCT116 cancer cells. Our results demonstrated the applicability of one-pot analysis to energetics-based methods for studying protein folding. We expect the combination of one-pot analysis and energetics-based methods to significantly benefit studies such as drug-target identification, proteomic investigations, and drug screening.

Experimentally generated randomness certified by the impossibility of superluminal signals.

From dice to modern electronic circuits, there have been many attempts to build better devices to generate random numbers. Randomness is fundamental to security and cryptographic systems and to safeguarding privacy. A key challenge with random-number generators is that it is hard to ensure that their outputs are unpredictable1-3. For a random-number generator based on a physical process, such as a noisy classical system or an elementary quantum measurement, a detailed model that describes the underlying physics is necessary to assert unpredictability. Imperfections in the model compromise the integrity of the device. However, it is possible to exploit the phenomenon of quantum non-locality with a loophole-free Bell test to build a random-number generator that can produce output that is unpredictable to any adversary that is limited only by general physical principles, such as special relativity1-11. With recent technological developments, it is now possible to carry out such a loophole-free Bell test12-14,22. Here we present certified randomness obtained from a photonic Bell experiment and extract 1,024 random bits that are uniformly distributed to within 10-12. These random bits could not have been predicted according to any physical theory that prohibits faster-than-light (superluminal) signalling and that allows independent measurement choices. To certify and quantify the randomness, we describe a protocol that is optimized for devices that are characterized by a low per-trial violation of Bell inequalities. Future random-number generators based on loophole-free Bell tests may have a role in increasing the security and trust of our cryptographic systems and infrastructure.

ATP alters protein folding and function of Escherichia coli uridine phosphorylase.

Uridine phosphorylase is one of the critical enzymes in the pyrimidine salvage pathway. Cells regenerate uridine for nucleotide metabolism by incorporating uracil with ribose-1-phosphate with this enzyme. Recent studies indicate that Escherichia coli uridine phosphorylase is destabilized in the presence of ATP. However, the mechanism underlying the destabilization process and its influence on uridine phosphorylase function remain to be established. Here, we comprehensively investigated the effects of ATP on protein folding and function of Escherichia coli uridine phosphorylase. Our results demonstrate that ATP apparently decreases the stability of uridine phosphorylase in a concentration-dependent manner. Additionally, simply increasing the level of ATP led to a reduction of enzymatic activity to complete inhibition. Further studies showed that uridine phosphorylase accumulates as a partially unfolded state in the presence of ATP. Moreover, ATP specifically accelerated the unfolding rate of uridine phosphorylase with no observable effects on the refolding process. Our preliminary findings suggest that ATP can alter the protein folding and function of enzymes via apparent destabilization. This mechanism may be significant for proteins functioning under conditions of high levels of ATP, such as cancer cell environments.

The Coupled Photothermal Reaction and Transport in a Laser Additive Metal Nanolayer Simultaneous Synthesis and Pattering for Flexible Electronics.

The Laser Direct Synthesis and Patterning (LDSP) technology has advantages in terms of processing time and cost compared to nanomaterials-based laser additive microfabrication processes. In LDSP, a scanning laser on the substrate surface induces chemical reactions in the reactive liquid solution and selectively deposits target material in a preselected pattern on the substrate. In this study, we experimentally investigated the effect of the processing parameters and type and concentration of the additive solvent on the properties and growth rate of the resulting metal film fabricated by this LDSP technology. It was shown that reactive metal ion solutions with substantial viscosity yield metal films with superior physical properties. A numerical analysis was also carried out the first time to investigate the coupled opto-thermo-fluidic transport phenomena and the effects on the metal film growth rate. To complete the simulation, the optical properties of the LDSP deposited metal film with a variety of thicknesses were measured. The characteristics of the temperature field and the thermally induced flow associated with the moving heat source are discussed. It was shown that the processing temperature range of the LDSP is from 330 to 390 K. A semi-empirical model for estimating the metal film growth rate using this process was developed based on these results. From the experimental and numerical results, it is seen that, owing to the increased reflectivity of the silver film as its thickness increases, the growth rate decreases gradually from about 40 nm at initial to 10 nm per laser scan after ten scans. This self-controlling effect of LDSP process controls the thickness and improves the uniformity of the fabricated metal film. The growth rate and resulting thickness of the metal film can also be regulated by adjustment of the processing parameters, and thus can be utilized for controllable additive nano/microfabrication.

Laser direct synthesis and patterning of silver nano/microstructures on a polymer substrate.

This study presents a novel approach for the rapid fabrication of conductive nano/microscale metal structures on flexible polymer substrate (polyimide). Silver film is simultaneously synthesized and patterned on the polyimide substrate using an advanced continuous wave (CW) laser direct writing technology and a transparent, particle-free reactive silver ion ink. The location and shape of the resulting silver patterns are written by a laser beam from a digitally controlled micromirror array device. The silver patterns fabricated by this laser direct synthesis and patterning (LDSP) process exhibit the remarkably low electrical resistivity of 2.1 µΩ cm, which is compatible to the electrical resistivity of bulk silver. This novel LDSP process requires no vacuum chamber or photomasks, and the steps needed for preparation of the modified reactive silver ink are simple and straightforward. There is none of the complexity and instability associated with the synthesis of the nanoparticles that are encountered for the conventional laser direct writing technology which involves nanoparticle sintering process. This LDSP technology is an advanced method of nano/microscale selective metal patterning on flexible substrates that is fast and environmentally benign and shows potential as a feasible process for the roll-to-roll manufacturing of large area flexible electronic devices.

[Concentrations and distribution of organochlorine pesticides in the surface sediments of Jiaozhou Bay, Taozi Bay and Sishili Bay].

Forty-eight surface sediment samples collected from Jiaozhou Bay, Taozi Bay and Sishili Bay were analyzed for organochlorine pesticides (OCPs) by Gas Chromatography. Results showed that average concentrations of HCHs, HCB and DDTs in marine sediments were 0.33, 0.31 and 10.33 ng x g(-1) in Jiaozhou Bay and 0.26, 0.10 and 4.56 ng x g(-1) in Taozi Bay and Sishili Bay, respectively. Contamination status of OCPs was relatively higher in Jiaozhou Bay than in other inland coastal regions, especially for the levels of DDTs; however, OCPs concentrations were relatively low in Taozi Bay and Sishili Bay. The source of HCHs could be mainly attributed to the heavy historical application in agricultural areas and late transport to coastal region through surface runoff or riverine discharge, and DDTs were primarily originated from the use of technical DDTs. Fresh input of lindane and dicofol-type DDTs were found in several sites, such as Qingdao Port. High concentrations of DDTs in Jiaozhou Bay should arouse much attention.

Direct fidelity estimation from few Pauli measurements.

We describe a simple method for certifying that an experimental device prepares a desired quantum state ρ. Our method is applicable to any pure state ρ, and it provides an estimate of the fidelity between ρ and the actual (arbitrary) state in the lab, up to a constant additive error. The method requires measuring only a constant number of Pauli expectation values, selected at random according to an importance-weighting rule. Our method is faster than full tomography by a factor of d, the dimension of the state space, and extends easily and naturally to quantum channels.

Efficient quantum state tomography.

Quantum state tomography--deducing quantum states from measured data--is the gold standard for verification and benchmarking of quantum devices. It has been realized in systems with few components, but for larger systems it becomes unfeasible because the number of measurements and the amount of computation required to process them grows exponentially in the system size. Here, we present two tomography schemes that scale much more favourably than direct tomography with system size. One of them requires unitary operations on a constant number of subsystems, whereas the other requires only local measurements together with more elaborate post-processing. Both rely only on a linear number of experimental operations and post-processing that is polynomial in the system size. These schemes can be applied to a wide range of quantum states, in particular those that are well approximated by matrix product states. The accuracy of the reconstructed states can be rigorously certified without any a priori assumptions.

Quantum state tomography via compressed sensing.

We establish methods for quantum state tomography based on compressed sensing. These methods are specialized for quantum states that are fairly pure, and they offer a significant performance improvement on large quantum systems. In particular, they are able to reconstruct an unknown density matrix of dimension d and rank r using O(rdlog²d) measurement settings, compared to standard methods that require d² settings. Our methods have several features that make them amenable to experimental implementation: they require only simple Pauli measurements, use fast convex optimization, are stable against noise, and can be applied to states that are only approximately low rank. The acquired data can be used to certify that the state is indeed close to pure, so no a priori assumptions are needed.