RNA polymerase II clusters form in line with surface condensation on regulatory chromatin.

It is essential for cells to control which genes are transcribed into RNA. In eukaryotes, two major control points are recruitment of RNA polymerase II (Pol II) into a paused state, and subsequent pause release toward transcription. Pol II recruitment and pause release occur in association with macromolecular clusters, which were proposed to be formed by a liquid-liquid phase separation mechanism. How such a phase separation mechanism relates to the interaction of Pol II with DNA during recruitment and transcription, however, remains poorly understood. Here, we use live and super-resolution microscopy in zebrafish embryos to reveal Pol II clusters with a large variety of shapes, which can be explained by a theoretical model in which regulatory chromatin regions provide surfaces for liquid-phase condensation at concentrations that are too low for canonical liquid-liquid phase separation. Model simulations and chemical perturbation experiments indicate that recruited Pol II contributes to the formation of these surface-associated condensates, whereas elongating Pol II is excluded from these condensates and thereby drives their unfolding.

Application of ultraviolet-visible spectroscopy coupled with support vector regression for the quantitative detection of thiamethoxam in tea.

A model combining UV-visible (UV-Vis) spectroscopy and support vector regression (SVR) for the quantitative detection of thiamethoxam in tea is proposed. First, each original UV-Vis spectrum in the sample set is decomposed into some intrinsic mode functions (IMFs) and a residual via ensemble empirical mode decomposition. Next, the decomposed IMFs are reconstructed into high-frequency and low-frequency matrices, and the residuals are combined into a trend matrix. Then, the SVR is used to build regression sub-models between each matrix and the content of thiamethoxam in tea. Finally, the combination model is established by a weighted average of the sub-models. The prediction results are compared with SVR and SVR coupled with several preprocessing methods, and the results demonstrate the superiority of the proposed approach in the quantitative detection of thiamethoxam in tea.

Single-molecule fluorescence enhancement of a near-infrared dye by gold nanorods using DNA transient binding.

Fluorescence enhancement by plasmonic nanostructures enables the optical detection of single molecules with weak fluorescence, extending the scope of molecular fluorescence imaging to new materials and systems. In this work, we study single-molecule fluorescence enhancement by individual gold nanorods exploiting a DNA-based transient binding technique. Single molecules are attached to short DNA oligomers that can reversibly hybridize to their complementary docking DNA strands immobilized on the surface of gold nanorods or the glass substrate next to gold nanorods. This method continuously refreshes the single molecule in the near field of the gold nanorod, and enables a study of fluorescence enhancement at a well-defined position, with long dwell time and without limitation by photobleaching. Docking strands attached to the glass substrate are found to be more photo-stable. We find over 3000-fold fluorescence enhancement of single molecules of IRDye800CW, a near-infrared dye with a low quantum yield of 7%. This strong enhancement, consistent with numerical simulations, arises from the combined effect of local field enhancement and the competition between radiative and nonradiative decay rate enhancements.

Gold Nanorod Enhanced Fluorescence Enables Single-Molecule Electrochemistry of Methylene Blue.

Redox reactions are central to energy conversion and life metabolism. Herein we present electrochemical measurements with fluorescent readout of the redox-sensitive dye Methylene Blue (MB), at the single-molecule (SM) level. To overcome the low fluorescence quantum yield of MB we enhanced fluorescence by using individual gold nanorods to achieve the required sensitivity. By measuring the same molecule at different electrochemical potentials we determined the mid-point potential of each single molecule through its redox-induced fluorescence blinking dynamics.

A plasmon ruler based on nanoscale photothermal effect.

The determination of nanoscale distances or distance changes necessitates a nanoscale ruler. In the present paper, distance dependence of particle temperature in an optically heated gold nanoparticle pair is quantitatively investigated to explore the possibility of creating a plasmon ruler based on this effect. The two origins of the distance-dependence, i.e., electromagnetic coupling and thermal accumulative effect, are studied. For the particle temperature, a scaling behavior is found, and it suggests that the decay of particle temperature with the interparticle gap for different particle sizes follows a common exponential decay equation. This scaling behavior is qualitatively explained with a simple dipolar-coupling model combined with a point heat source interaction model. On the basis of this scaling behavior of absorption power, we further establish a plasmon ruler equation relating the particle temperature and the interparticle distance. Our findings can serve as an excellent guideline for designing and optimizing temperature-based plasmon rulers.

Hybrid photonic-plasmonic molecule based on metal/Si disks.

Optical properties of two identical coupled disks forming a "hybrid photonic-plasmonic molecule" are investigated. Each disk is a metal-dielectric structure supporting hybrid plasmonic-photonic whispering-gallery (WG) modes. The WG modes of a molecule split into two groups of nearly-degenerate modes, i.e., bonding and anti-bonding modes. The oscillation of quality factor (Q) with the inter-disk gap d and significant enhancement at certain inter-disk gaps can be observed. An enhanced Q factor of 1821 for a hybrid photonic-plasmonic molecule composed of two 1.2 µm-diameter disks, compared with that for a single disk, is achieved. The corresponding Purcell factor is 191, making the hybrid photonic-plasmonic molecule an optimal choice for subwavelength-scale device miniaturization and light-matter interactions. Moreover, the far-field emission pattern of the hybrid photonic-plasmonic molecule exhibits an enhanced directional light output by tuning the azimuthal mode number for both bonding and anti-bonding modes.

Horizontal and vertical variation of soil clay content and its controlling factors in China.

Detailed information on the variation of soil clay content at different soil depths are important for water repellency, management of soil fertility, and crop growth. However, studies on the variation of soil clay content at different depths at large scales are limited. In this study, 1446 soil profiles covering most areas of China were extracted from the World Soil Information Service (WoSIS) database and classified into 0-20, 20-60, and 60-100 cm depths using the equal-area quadratic splines. Random forest (RF) and Shapley additive explanations (SHAP) were used to investigate the relationship between soil clay content and environmental factors (climate, topography, land use, and soil types). The results showed that soil clay content and its variability increased with soil depth. The RF model predicted soil clay content at the three soil depths. The mean absolute error (MAE), root mean square error (RMSE), coefficient of determination (R2), and Lin's concordance correlation coefficient (CCC) ranged from 6.95 % to 8.74 %, 8.90 % to 11.30 %, 42 % to 46 %, and 56 % to 59 %, respectively. Mean annual temperature (MAT), mean annual precipitation (MAP), solar radiation (solarR), and elevation were the key factors that controlled the variation of soil clay content at depths of 0-20, 20-60, and 60-100 cm. In addition, the main effect values of SHAP can identify environmental thresholds consistent with significant areas by capturing the relationship between soil clay content and MAT, MAP, solarR, and elevation. Significant differences were found in soil clay content on both sides of the threshold at MAT of 15 °C, MAP of 800 mm, solarR of 15,000 Jm-2 yr-1, and elevation of 1200 m. The results provide clues to the management of national soil security under global and regional climate change.

Alterations of bacteriome, mycobiome and metabolome characteristics in PCOS patients with normal/overweight individuals.

To characterize the gut bacteriome, mycobiome and serum metabolome profiles in polycystic ovary syndrome (PCOS) patients with normal/overweight individuals and evaluate a potential microbiota-related diagnostic method development for PCOS, 16S rRNA and ITS2 gene sequencing using 88 fecal samples and 87 metabolome analysis from serum samples are conducted and PCOS classifiers based on multiomics markers are constructed. There are significant bacterial, fungal community and metabolite differences among PCOS patients and healthy volunteers with normal/overweight individuals. Healthy individuals with overweight/obesity display less abnormal metabolism than PCOS patients and uniquely higher abundance of the fungal genus Mortierella. Nine bacterial genera, 4 predicted pathways, 11 fungal genera and top 30 metabolites are screened out which distinguish PCOS from healthy controls, with AUCs of 0.84, 0.64, 0.85 and 1, respectively. The metabolite-derived model is more accurate than the microbe-based model in discriminating normal BMI PCOS (PCOS-LB) from normal BMI healthy (Healthy-LB), PCOS-HB from Healthy-HB. Featured bacteria, fungi, predicted pathways and serum metabolites display higher associations with free androgen index (FAI) in the cooccurrence network. In conclusion, our data reveal that hyperandrogenemia plays a central role in the dysbiosis of intestinal microecology and the change in metabolic status in patients with PCOS and that its effect exceeds the role of BMI. Healthy women with high BMI showed unique microbiota and metabolic features.The priority of predictive models in discriminating PCOS from healthy status in this study were serum metabolites, fungal taxa and bacterial taxa.

Wavelet-based background and noise subtraction for fluorescence microscopy images.

Fluorescence microscopy images are inevitably contaminated by background intensity contributions. Fluorescence from out-of-focus planes and scattered light are important sources of slowly varying, low spatial frequency background, whereas background varying from pixel to pixel (high frequency noise) is introduced by the detection system. Here we present a powerful, easy-to-use software, wavelet-based background and noise subtraction (WBNS), which effectively removes both of these components. To assess its performance, we apply WBNS to synthetic images and compare the results quantitatively with the ground truth and with images processed by other background removal algorithms. We further evaluate WBNS on real images taken with a light-sheet microscope and a super-resolution stimulated emission depletion microscope. For both cases, we compare the WBNS algorithm with hardware-based background removal techniques and present a quantitative assessment of the results. WBNS shows an excellent performance in all these applications and significantly enhances the visual appearance of fluorescence images. Moreover, it may serve as a pre-processing step for further quantitative analysis.

Evaluation of the Efficacy of Sex Hormone-Binding Globulin in Insulin Resistance Assessment Based on HOMA-IR in Patients with PCOS.

This study aimed to evaluate the efficacy of SHBG in predicting insulin resistance (IR) in newly diagnosed, untreated patients with polycystic ovary syndrome (PCOS). Hundred newly diagnosed, untreated patients with PCOS and 61 subjects without PCOS (41 healthy volunteers with normal BMI and 20 subjects with overweight/obese) were included in the study. Receiver-operating characteristic (ROC) analysis was used to assess the effectiveness of SHBG in predicting IR in overweight/obese and non-overweight PCOS patients and the optimal cut-off values of SHBG. The results showed negative correlations between log-SHBG and log-I0 (r = - 0.372, P < 0.001) and log-SHBG and log-Homeostatic Model Assessment of Insulin Resistance (HOMA-IR) (r = - 0.393, P < 0.001) after adjusting for blood pressure, serum lipid, age, and body mass index (BMI) in all of the PCOS patients. In patients with IR (defined as HOMA-IR ≥2.29), the area under the ROC curves (AUCs) of the SHBG for ROC analysis in the non-overweight group, overweight/obese group, and all PCOS patients were 0.774 (P = 0.0001), 0.922 (P = 0.0001), and 0.885 (P = 0.0001), respectively. The optimal cut-off value of SHBG was 37 nmol/L with a sensitivity of 97.62% and specificity of 80.85% in the overweight group. In patients with IR (HOMA-IR ≥2.5), the AUCs of SHBG for ROC analysis in the non-overweight group, overweight/obese group, and all PCOS patients were 0.741 (P = 0.0003), 0.928 (P = 0.0001), and 0.880 (P = 0.0001), respectively. The optimal cut-off value of SHBG was 30.2 nmol/L with a sensitivity of 97.44% and specificity of 82.69% in the overweight/obese group. In conclusion, this study observed a negative correlation between SHBG and HOMA-IR in PCOS patients after adjustment of confounding factors. SHBG was an independent influential factor of HOMA-IR and can be used as a positive predictive marker for IR in PCOS patients, especially in those who are overweight/obese.

Comparison of the efficacy of different androgens measured by LC-MS/MS in representing hyperandrogenemia and an evaluation of adrenal-origin androgens with a dexamethasone suppression test in patients with PCOS.

BACKGROUND: The aims of this study were to compare the efficacy of different androgens measured by liquid chromatography-mass spectrometry (LC-MS/MS) in representing hyperandrogenemia and to evaluate adrenal-origin androgens with a dexamethasone suppression test in patients with polycystic ovary syndrome (PCOS). METHODS: One hundred and two patients with PCOS and 41 healthy volunteers were recruited and total serum testosterone (TT), androstenedione (AD), dehydroepiandrosterone (DHEA) and dehydroepiandrosterone sulfate (DHEA-S) were measured by LC-MS/MS. ROC analysis was performed to compare the efficacy of different androgens in representing hyperandrogenemia. Dexamethasone suppression test was performed in 51 patients with PCOS and above indicators were measured after dexamethasone administration. The prediction efficacy of DHEA and DHEA-S at baseline in the dexamethasone suppression test was evaluated with ROC analysis. RESULTS: The AUCs of TT, AD, free androgen index (FAI) and DHEA-S in ROC analysis for representing hyperandrogenemia were 0.816, 0.842, 0.937 and 0.678, respectively. The optimal cutoff value of TT was 0.337 ng/ml, with a sensitivity of 72.0% and specificity of 82.93%. The optimal cutoff value for AD was 1.309 ng/ml, with a sensitivity of 81.0% and specificity of 73.17%. The optimal cutoff value of the FAI was 2.50, with a sensitivity of 87.0% and specificity of 92.68%. Alternatively, AD or FAI more than the optimal cutoff values as evidence of hyperandrogenemia had the highest sensitivity of 91.18%. The levels of cortisol, DHEA and DHEA-S were all suppressed to narrow ranges after dexamethasone administration. Nine and 8 of 51 patients with PCOS had significant decreases in TT and AD, respectively. DHEA can be used as a indicator for predicting significant decrease of TT in dexamethasone suppression test with cutoff value of 13.28 ng/ml. A total of 27.5% (14/51) of patients had DHEA-S excess, but only 1 of 9 patients who had a significant decrease in TT had elevated level of DHEA-S at baseline. CONCLUSIONS: AD measured by LC-MS/MS can represent hyperandrogenemia in PCOS patients and, combined with TT or FAI, can improve the screening efficiency of hyperandrogenemia. Seventeen percent of PCOS patients had adrenal-origin androgen dominance, with TT significantly decreasing after 2 days of dexamethasone administration. Adrenal-origin androgen dominance was not parallel with DHEA-S excess in patients with PCOS.

Reduced stress-associated FKBP5 DNA methylation together with gut microbiota dysbiosis is linked with the progression of obese PCOS patients.

Polycystic ovary syndrome (PCOS) is a common endocrine disease in females that is characterized by hyperandrogenemia, chronic anovulation, and polycystic ovaries. However, the exact etiology and pathogenesis of PCOS are still unknown. The aim of this study was to clarify the bacterial, stress status, and metabolic differences in the gut microbiomes of healthy individuals and patients with high body mass index (BMI) PCOS (PCOS-HB) and normal BMI PCOS (PCOS-LB), respectively. Here, we compared the gut microbiota characteristics of PCOS-HB, PCOS-LB, and healthy controls by 16S rRNA gene sequencing, FK506-binding protein 5 (FKBP5) DNA methylation and plasma metabolite determination. Clinical parameter comparisons indicated that PCOS patients had higher concentrations of total testosterone, androstenedione, dehydroepiandrosterone sulfate, luteinizing hormone, and HOMA-IR while lower FKBP5 DNA methylation. Significant differences in bacterial diversity and community were observed between the PCOS and healthy groups but not between the PCOS-HB and PCOS-LB groups. Bacterial species number was negatively correlated with insulin concentrations (both under fasting status and 120 min after glucose load) and HOMA-IR but positively related to FKBP5 DNA methylation. Compared to the healthy group, both PCOS groups had significant changes in bacterial genera, including Prevotella_9, Dorea, Maihella, and Slackia, and plasma metabolites, including estrone sulfate, lysophosphatidyl choline 18:2, and phosphatidylcholine (22:6e/19:1). The correlation network revealed the complicated interaction of the clinical index, bacterial genus, stress indices, and metabolites. Our work links the stress responses and gut microbiota characteristics of PCOS disease, which might afford perspectives to understand the progression of PCOS.

Plasmonic Enhancement of Two-Photon-Excited Luminescence of Single Quantum Dots by Individual Gold Nanorods.

Plasmonic enhancement of two-photon-excited fluorescence is not only of fundamental interest but also appealing for many bioimaging and photonic applications. The high peak intensity required for two-photon excitation may cause shape changes in plasmonic nanostructures, as well as transient plasmon broadening. Yet, in this work, we report on strong enhancement of the two-photon-excited photoluminescence of single colloidal quantum dots close to isolated chemically synthesized gold nanorods. Upon resonant excitation of the localized surface plasmon resonance, a gold nanorod can enhance the photoluminescence of a single quantum dot more than 10 000-fold. This strong enhancement arises from the combined effect of local field amplification and the competition between radiative and nonradiative decay rate enhancements, as is confirmed by time-resolved fluorescence measurements and numerical simulations.