One-thousandth-level laser power stabilization based on optical feedback from a well-designed high-split-ratio and nonpolarized beam splitter.

Laser power stabilization plays a significant role in atomic and molecular physics, quantum precision measurement, and optical sensing and measurement. In the classical method of using a feedback control loop to stabilize the laser power, the beam splitter is the conjunction element to connect the feedback beam inside the loop and the output beam outside the loop. The stability of its split ratio will directly affect the result of power stabilization, especially in demand of high split ratios for high-efficiency output. For the compatibility of a high split ratio and high stability in a power-stabilized system, we designed and manufactured a high-split-ratio nonpolarized plate beam splitter, whose split ratio was insensitive to variations of beam intensity, polarization, and ambient temperature. Based on the optical feedback of the designed beam splitter, the light intensity was closed-loop controlled by an acousto-optic modulator; finally, the power outside the loop was stabilized as well. The output power was stabilized at 537 mW and a 6 h long-term test was performed. The relative stability of laser power outside the loop in terms of root mean square and peak to peak was 2.72×10-4 and 1.60×10-3, respectively. The relative Allan standard deviation reached 2.78×10-5 at an average time of 200 s. These results will greatly benefit many practical fields that require laser power stabilization with high split ratios and one-thousandth-level stability.

SlCAND1, encoding cullin-associated Nedd8-dissociated protein 1, regulates plant height, flowering time, seed germination, and root architecture in tomato.

KEY MESSAGE: Silencing of SlCAND1 expression resulted in dwarfish, loss of apical dominance, early flowering, suppression of seed germination, and abnormal root architecture in tomato Cullin-RING E3 ligases (CRLs)-dependent ubiquitin proteasome system mediates degradation of numerous proteins that controls a wide range of developmental and physiological processes in eukaryotes. Cullin-associated Nedd8-dissociated protein 1 (CAND1) acts as an exchange factor allowing substrate recognition part exchange and plays a vital role in reactivating CRLs. The present study reports on the identification of SlCAND1, the only one CAND gene in tomato. SlCAND1 expression is ubiquitous and positively regulated by multiple plant hormones. Silencing of SlCAND1 expression using RNAi strategy resulted in a pleiotropic and gibberellin/auxin-associated phenotypes, including dwarf plant with reduced internode length, loss of apical dominance, early flowering, low seed germination percentage, delayed seed germination speed, short primary root, and increased lateral root proliferation and elongation. Moreover, application of exogenous GA3 or IAA could partly rescue some SlCAND1-silenced phenotypes, and the expression levels of gibberellin/auxin-related genes were altered in SlCAND1-RNAi lines. These facts revealed that SlCAND1 is required for gibberellin/auxin-associated regulatory network in tomato. Although SlCAND1 is crucial for multiple developmental processes during vegetative growth stage, SlCAND1-RNAi lines didn't exhibit visible effect on fruit development and ripening. Meanwhile, we discussed that multiple physiological functions of SlCAND1 in tomato are different to previous report of its ortholog in Arabidopsis. Our study adds a new perspective on the functional roles of CAND1 in plants, and strongly supports the hypothesis that CAND1 and its regulated ubiquitin proteasome system are pivotal for plant vegetative growth but possibly have different roles in diverse plant species.

A novel microRNA, SlymiR208, promotes leaf senescence via regulating cytokinin biosynthesis in tomato.

Leaf senescence is a highly-programmed developmental process during the plant life cycle. Cytokinin (CK) has been widely acknowledged as a negative regulator to delay leaf senescence. MiRNAs play key roles in a variety of developmental and physiological processes through negatively regulating their target gene expression. However, to date, the roles of microRNAs (miRNAs) in CK biosynthesis remain unclear, and the knowledge on miRNA regulation of leaf senescence is still very limited. Isopentenyltransferases (IPTs) catalyze the initial and rate-limiting step of CK biosynthesis in higher plants. Our previous work uncovered that silencing of SlIPT4 expression in tomato resulted in premature leaf senescence. Here, we identified a novel tomato miRNA, SlymiR208, which regulates the expression of SlIPT2 and SlIPT4 at the post-transcriptional level. SlymiR208 expression is ubiquitous in tomato and exhibits an opposite transition to its target transcripts in aged leaf. SlymiR208 overexpression in tomato sharply reduced the transcript levels of SlIPT2 and SlIPT4, and the concentrations of endogenous CKs in leaves. The early leaf senescence caused by SlymiR208 overexpression was consistent with the phenotype of SlIPT4-silenced lines. The data demonstrated that SlymiR208 is a positive regulator in leaf senescence through negatively regulating CK biosynthesis via targeting SlIPT2 and SlIPT4 in tomato. This study indicated that post-transcriptional regulation via miRNA is a control point of CK biosynthesis and added a new layer to the understanding of the regulation of CK biosynthesis in tomato and a new factual proof to support that miRNAs are involved in leaf senescence.

In Silico Prediction of the Dissociation Rate Constants of Small Chemical Ligands by 3D-Grid-Based VolSurf Method.

Accumulated evidence suggests that binding kinetic properties-especially dissociation rate constant or drug-target residence time-are crucial factors affecting drug potency. However, quantitative prediction of kinetic properties has always been a challenging task in drug discovery. In this study, the VolSurf method was successfully applied to quantitatively predict the koff values of the small ligands of heat shock protein 90α (HSP90α), adenosine receptor (AR) and p38 mitogen-activated protein kinase (p38 MAPK). The results showed that few VolSurf descriptors can efficiently capture the key ligand surface properties related to dissociation rate; the resulting models demonstrated to be extremely simple, robust and predictive in comparison with available prediction methods. Therefore, it can be concluded that the VolSurf-based prediction method can be widely applied in the ligand-receptor binding kinetics and de novo drug design researches.

Computational Insights into Allosteric Conformational Modulation of P-Glycoprotein by Substrate and Inhibitor Binding.

The ATP-binding cassette (ABC) transporter P-glycoprotein (P-gp) is a physiologically essential membrane protein that protects many tissues against xenobiotic molecules, but limits the access of chemotherapeutics into tumor cells, thus contributing to multidrug resistance. The atomic-level mechanism of how substrates and inhibitors differentially affect the ATP hydrolysis by P-gp remains to be elucidated. In this work, atomistic molecular dynamics simulations in an explicit membrane/water environment were performed to explore the effects of substrate and inhibitor binding on the conformational dynamics of P-gp. Distinct differences in conformational changes that mainly occurred in the nucleotide-binding domains (NBDs) were observed from the substrate- and inhibitor-bound simulations. The binding of rhodamine-123 can increase the probability of the formation of an intermediate conformation, in which the NBDs were closer and better aligned, suggesting that substrate binding may prime the transporter for ATP hydrolysis. By contrast, the inhibitor QZ-Leu stabilized NBDs in a much more separated and misaligned conformation, which may result in the deficiency of ATP hydrolysis. The significant differences in conformational modulation of P-gp by substrate and inhibitor binding provided a molecular explanation of how these small molecules exert opposite effects on the ATPase activity. A further structural analysis suggested that the allosteric communication between transmembrane domains (TMDs) and NBDs was primarily mediated by two intracellular coupling helices. Our computational simulations provide not only valuable insights into the transport mechanism of P-gp substrates, but also for the molecular design of P-gp inhibitors.

SMD-Based Interaction-Energy Fingerprints Can Predict Accurately the Dissociation Rate Constants of HIV-1 Protease Inhibitors.

Recent research has increasingly suggested that the crucial factors affecting drug potencies are related not only to the thermodynamic properties but also to the kinetic properties. Therefore, in silico prediction of ligand-binding kinetic properties, especially the dissociation rate constant ( koff), has aroused more and more attention. However, there are still a lot of challenges that need to be addressed. In this paper, steered molecular dynamics (SMD) combined with residue-based energy decomposition was employed to predict the dissociation rate constants of 37 HIV-1 protease inhibitors (HIV-1 PIs). For the first time, a predictive model of the dissociation rate constant was established by using the interaction-energy fingerprints sampled along the ligand dissociation pathway. On the basis of the key fingerprints extracted it can be inferred that the dissociation rates of 37 HIV-1 PIs are basically determined in the first half of the dissociation processes and that the H-bond interactions with active-site Asp25 and van der Waals interactions with flap-region Ile47 and Ile50 have important influences on the dissociation processes. In general, the strategy established in this paper can provide an efficient way for the prediction of dissociation rate constants as well as the unbinding mechanism research.

Non-destructive characterization of egg odor and fertilization status by SPME/GC-MS coupled with electronic nose.

BACKGROUND: Early and non-destructive identification of fertile (F) eggs is a difficult task in the process of breeding laying hens. The odors emitted from unfertilized (UF), infertile (IF), and fertile (F) eggs were characterized by solid-phase microextraction / gas chromatograph-mass spectrometry (SPME/GC-MS) and electronic nose (E-nose) to determine their differences by principal component, partial least squares, and canonical discriminant analyses. RESULTS: A total of 14 volatiles were identified in unhatched shell white Leghorn eggs, such as nonanal, decanal, 6-methyl-5-hepten-2-one, and 6,10-dimethyl-5,9-undecadien-2-one. Cedrene and decanal contributed greatly to the classification of UF and fertilized (Fd)/IF eggs; cedrene, decanal, 1-octanol and hexanal contributed greatly to the distinction between UF and IF eggs; heptanal might be the potential marker to determine F/IF eggs. P40/1, P10/2, P10/1, TA/2, T40/2 and T30/1, P30/1, P40/2, PA/2, T40/2 mostly contributed to the distinction between UF and Fd eggs and between F and IF eggs, respectively. Canonical discriminant analysis presented superior differentiating efficiency for almost all groups, and the odor differences between UF and Fd eggs were significantly larger than the differences between F and IF eggs. CONCLUSION: Solid-phase microextraction / gas chromatograph-mass spectrometer combined with E-nose may have the potential to non-destructively distinguish UF, F, and IF eggs, which will provide a new perspective to understand the differences among them. © 2018 Society of Chemical Industry.

Constructing Interconsistent, Reasonable, and Predictive Models for Both the Kinetic and Thermodynamic Properties of HIV-1 Protease Inhibitors.

Accumulated evidence suggests that the in vivo biological potency of a ligand is more strongly correlated with the binding/unbinding kinetics than the equilibrium thermodynamics of the protein-ligand interaction (PLI). However, the existing experimental and computational techniques are largely insufficient and limited in large-scale measurements or accurate predictions of the kinetic properties of PLI. In this work, elaborate efforts have been made to develop interconsistent, reasonable, and predictive models of the association rate constant (kon), dissociation rate constant (koff), and equilibrium dissociation constant (KD) of a series of HIV protease inhibitors with different structural skeletons. The results showed that nine Volsurf descriptors derived from water (OH2) and hydrophobic (DRY) probes are key molecular determinants for the kinetic and thermodynamic properties of HIV-1 protease inhibitors. To the best of our knowledge, this is the first time that interconsistent and reasonable models with strong prediction power have been established for both the kinetic and thermodynamic properties of HIV protease inhibitors.

Online Learners' Reading Ability Detection Based on Eye-Tracking Sensors.

The detection of university online learners' reading ability is generally problematic and time-consuming. Thus the eye-tracking sensors have been employed in this study, to record temporal and spatial human eye movements. Learners' pupils, blinks, fixation, saccade, and regression are recognized as primary indicators for detecting reading abilities. A computational model is established according to the empirical eye-tracking data, and applying the multi-feature regularization machine learning mechanism based on a Low-rank Constraint. The model presents good generalization ability with an error of only 4.9% when randomly running 100 times. It has obvious advantages in saving time and improving precision, with only 20 min of testing required for prediction of an individual learner's reading ability.

[Study on Non-Destructive Detection Method for Egg Freshness Based on LLE-SVR and Visible/Near-Infrared Spectrum].

The freshness of egg is an important index to reflect the internal quality. In order to achieve non-destructive detection of freshness, micro fiber spectrometer was used to sample 550～950 nm transmittance spectra of eggs which performed quantitative analysis with haugh unit of eggs. Different pretreatment was combined with partial least squares regression(PLS) and support vector regression(SVR) respectively to find that first derivative combined with SVR predicted better than others through comparison, and it was better to model by SVR than by PLS. In order to improve efficiency and decrease adverse effects of useless information for modeling, the linear dimensionality reduction with principal component analysis (PCA) and the nonlinear dimensionality reduction with locally linear embedding(LLE) were used for the data of first derivative respectively. It indicated that LLE was better than PCA after comparison, and the correlation coefficient of calibration and prediction were 92.2%, 91.1%, and the root mean square error were 7.21, 8.80. The root mean square error of cross validation decreased 0.79.The experimental result illustrated that the nonlinear model of LLE combined with SVR improved predictive performance of egg freshness. It is feasible for the detection of visible/near-infrared spectrum of egg freshness to apply this method.

Drug hypersensitivity caused by alteration of the MHC-presented self-peptide repertoire.

Idiosyncratic adverse drug reactions are unpredictable, dose-independent and potentially life threatening; this makes them a major factor contributing to the cost and uncertainty of drug development. Clinical data suggest that many such reactions involve immune mechanisms, and genetic association studies have identified strong linkages between drug hypersensitivity reactions to several drugs and specific HLA alleles. One of the strongest such genetic associations found has been for the antiviral drug abacavir, which causes severe adverse reactions exclusively in patients expressing the HLA molecular variant B*57:01. Abacavir adverse reactions were recently shown to be driven by drug-specific activation of cytokine-producing, cytotoxic CD8(+) T cells that required HLA-B*57:01 molecules for their function; however, the mechanism by which abacavir induces this pathologic T-cell response remains unclear. Here we show that abacavir can bind within the F pocket of the peptide-binding groove of HLA-B*57:01, thereby altering its specificity. This provides an explanation for HLA-linked idiosyncratic adverse drug reactions, namely that drugs can alter the repertoire of self-peptides presented to T cells, thus causing the equivalent of an alloreactive T-cell response. Indeed, we identified specific self-peptides that are presented only in the presence of abacavir and that were recognized by T cells of hypersensitive patients. The assays that we have established can be applied to test additional compounds with suspected HLA-linked hypersensitivities in vitro. Where successful, these assays could speed up the discovery and mechanistic understanding of HLA-linked hypersensitivities, and guide the development of safer drugs.

[Quantitative Approach to Melamine Detection in Egg White with Surface-Enhanced Raman Spectroscopy].

Due to the harmfulness of melamine to human, the quantitative detection of melamine in egg is very necessary. In the present study, the surface enhanced Raman spectra technology combined with chemometric analysis method was used to conduct melamine quantitative detection in egg white. Firstly, the melamine egg sample could be got by the method of artificial feeding hens usingdifferent feeding formulation. Then the surface enhanced Raman spectra of egg white was determined using portable Raman spectroscopy (Opto Trace RamTracer-200) and Raman enhancement reagents, and the melamine content within the white eggs was measured with gas chromatography mass spectrometry technology. The software of Raman Analyzer was used for baseline correction of Raman spectra. The correlation coefficient method was used to choose 320 spectral variables from the surface enhanced Raman spectroscopy as input variables to establish partial least squares quantitative calibration model . And the peaks-decomposition method was used to establish peaks-decomposition quantitative calibration model. Both models selected 90 and 44 samples respectively as calibration sets and validation sets during model establishment, and both models achieved good prediction effect. The determination coefficient between predicted values of partial least squares quantitative calibration model and measured values of gas chromatography mass spectrometry was 0.856, and root mean square error of prediction was 1.547. The determination coefficient was 0.947 and RMSEP was 0.893 for the peaks-decomposition quantitative calibration model. This study demonstrated that the method can effectively quantitatively detect melamine in eggs. Testing a sample only takes 15 minutes, which can provide a new way for the melamine egg detection.

Subangstrom accuracy in pHLA-I modeling by Rosetta FlexPepDock refinement protocol.

Flexible peptides binding to human leukocyte antigen (HLA) play a key role in mediating human immune responses and are also involved in idiosyncratic adverse drug reactions according to recent research. However, the structural determinations of pHLA complexes remain challenging under the present conditions. In this paper, the performance of a new peptide docking method, namely FlexPepDock, was systematically investigated by a benchmark of 30 crystallized structures of peptide-HLA class I complexes. The docking results showed that the near-native pHLA-I models with peptide bb-RMSD less than 2 Å were ranked in the top 1 model for 100% (70/70) docking cases, and the subangstrom models with peptide bb-RMSD less than 1 Å were ranked in the top 5 lowest-energy models for 65.7% (46/70) docking cases. Furthermore, 10 out of 70 docking cases ranked the subangstrom all-atom models in the top 5 lowest-energy models. The results showed that the FlexPepDock can generate high-quality models of pHLA-I complexes and can be widely applied to pHLA-I modeling and mechanism research of peptide-mediated immune responses.

Combined QSAR and molecule docking studies on predicting P-glycoprotein inhibitors.

P-glycoprotein (P-gp) is an ATP-binding cassette multidrug transporter. The over expression of P-gp leads to the development of multidrug resistance (MDR), which is a major obstacle to effective treatment of cancer. Thus, designing effective P-gp inhibitors has an extremely important role in the overcoming MDR. In this paper, both ligand-based quantitative structure-activity relationship (QSAR) and receptor-based molecular docking are used to predict P-gp inhibitors. The results show that each method achieves good prediction performance. According to the results of tenfold cross-validation, an optimal linear SVM model with only three descriptors is established on 857 training samples, of which the overall accuracy (Acc), sensitivity, specificity, and Matthews correlation coefficient are 0.840, 0.873, 0.813, and 0.683, respectively. The SVM model is further validated by 418 test samples with the overall Acc of 0.868. Based on a homology model of human P-gp established, Surflex-dock is also performed to give binding free energy-based evaluations with the overall accuracies of 0.823 for the test set. Furthermore, a consensus evaluation is also performed by using these two methods. Both QSAR and molecular docking studies indicate that molecular volume, hydrophobicity and aromaticity are three dominant factors influencing the inhibitory activities.

A supermolecular curcumin for enhanced antiproliferative and proapoptotic activities: molecular characteristics, computer modeling and in vivo pharmacokinetics.

The supermolecular curcumin (SMCCM) exhibiting remarkably improved solubility and release characteristics was fabricated to increase the oral bioavailability in rat as well as the antiproliferative and proapoptotic activities of curcumin (CCM) against human lung adenocarcinoma cell A549. SMCCM was characterized by differential scanning calorimetry, Fourier transform infrared spectroscopy, morphology and structure, aqueous solubility, and release behavior in vitro. Computer modeling of the supermolecular structure was performed. The pharmacokinetics, antiproliferative and proapoptotic activities of SMCCM were evaluated. The mechanisms by which SMCCM inhibited proliferation and induced apoptosis were identified. The formation of SMCCM was testified and the supermolecular structure was studied by a computer modeling technique. Compared to free CCM, SMCCM with much higher aqueous solubility exhibited obviously enhanced release and more favorable pharmacokinetic profiles, and, furthermore, SMCCM showed higher anticancer efficacy, enhanced induction of G2/M-phase arrest and apoptosis in A549 cells, which might be involved with the increases in reactive oxygen species production and intracellular Ca(2+) accumulation, and a decrease in mitochondrial membrane potential. SMCCM remarkably enhanced not only the oral bioavailability but also the antiproliferative and proapoptotic activities of CCM along with improved solubility and release characteristics of CCM.

[The associations between idiosyncratic adverse drug reactions and HLA alleles and their underlying mechanism].

With the advent of Twenty-First century, more and more genome-wide association studies (GWAS) showed that idiosyncratic adverse drug reactions (ADRs) were closely related with human leukocyte antigen (HLA) alleles, such as the associations of abacavir-HLA-B*5701, allopurinol-HLA-B*5801, and carbamazepine-HLA-B*1502, etc. To explore the mechanisms of these idiosyncratic drug reactions, hapten hypothesis, danger signal hypothesis, pharmacological interaction (P-I) concept and autoimmune mechanism are proposed. In this paper, recent GWAS studies on the HLA-mediated adverse drug reactions and underlying mechanism are reviewed in detail.

[Gene expressions of LOXs and MMPs of the ACL fibroblasts cells co-cultured with synovial cells].

The progress of research on the the anterior cruciate ligament (ACL) wound healing demonstrates that the synovial tissue in the knee joint plays a very important role in the healing process of injured ACL. Therefore, the molecular response mechanisms of lysyl oxidase (LOX) and matrix metalloproteina (MMP) in normal/injured ACL fibroblast cells could be considered to perform the major analysis function of injured ACL healing mechanism. The mRNA expressions of LOXs and MMPs and the activity expressions of MMP-2 in ACL fibroblasts co-cultured with synovial cells were analyzed by quantitative real-time PCR and zymography. The results showed that co-culture could regulate the mRNA expressions of LOXs and MMPs in the ACL fibroblasts cells. These results suggest that the differential expressions of LOXs and MMP-1, 2, 3 in co-cultured ACL indicate that interaction crosstalk do exist between ACL cells and synovial cells and provide a theoretical basis for subsequent exploration of the mechanisms and treatment of ACL injury and repair.

Existence of memory in membrane channels: analysis of ion current through a voltage-dependent potassium single channel.

Ion current fluctuation of voltage-dependent potassium channel in LßT2 cells has been investigated by autocorrelation function and DFA (detrended fluctuation analysis) methods. The calculation of the autocorrelation function exponent and DFA exponent of the sample was based on the digital signals or the 0-1 series corresponding to closing and opening of channels after routine evolution, rather than the sequence of sojourn times. The persistent character of the correlation of the time series was evident from the slow decay of the autocorrelation function. DFA exponent α was significantly greater than 0.5. The main outcome has been the demonstration of the existence of memory in this ion channel. Thus, the ion channel current fluctuation provided information about the kinetics of the channel protein. The result suggests the correlation character of the ion channel protein non-linear kinetics indicates whether the channel is open or not.

[Effect of heat treatment on the allergenicity and microstructure of ovomucoid].

The effect of heat treatment on the allergenicity and microstructure of ovomucoid was studied by enzyme-linked immunosorbent assay (ELISA), CD spectra, ANS fluorescence probe emission spectra and UV absorption spectra. The results showed that the allergenicity of ovomucoid decreased with increasing temperatures and time. CD spectra were used to examine the changes in the secondary structure of the ovomucoid treated by different temperatures. When treated by different temperatures, the mutual transformation between a-helix, b-sheet, b-turn and the random coil was observed, and the disorderliness of the secondary structure was increased with alpha-helix and beta-sheet decreasing, but the random coil increased correspondingly. The ANS fluorescence probe emission spectra analysis demonstrated that heat treatment induced reducing in surface hydrophobicity with the increase in heat temperatures. With the increase in heat temperatures, the amino acid residues with the UV-absorption were exposed gradually, and the UV-absorption maximum value increased. The results indicated that when treated by heating, the changes in the microstructure of ovomucoid can lead to the changes in the allergenicity of ovomucoid.

[Study on the stability of chicken egg yolk immunoglobulin (IgY) modified with mPEG].

The objective of the present paper was to study the effect of monomethoxypolyethlene glycol (mPEG) modification on the stability of chicken IgY and compare the stability of the modification products by Fourier transform infrared spectroscopy (FTIR), CD spectrooscopy and fluorescence spectroscopy. NHS-mPEG was used to modify IgY after mPEG was activated with N-hydroxysuccinimide (NHS). The optimal reaction condition for modification was 1:10 molar rate of IgY to mPEG at pH 7, reaction for 1 h, and the product was obtained with modification rate of 20.56% and activity reservation of 87. 62%. In addition, the thermal and pH stability of IgY and mPEG-IgY was compared by spectroscopic methods. The results showed that the alpha-helix, beta-sheet, beta-turn, and random content of IgY changed from 14.5%, 42.1%, 6.2% and 37.2% to 1.6%, 55.25%, 5.8% and 37.5%, while mPEG changed from 12.9%, 42.7%, 6.3% and 38. 1% to 3.1%, 50.5%, 7.2% and 39.2%, respectively, after incubating for 120 min at 70 degrees C. For the treatment with acid-base, similarly, the structure changes of mPEG-IgY were smaller than IgY. Thus, it is indicated that IgY modified by mPEG had greater stable properties.