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Quantitative phase imaging has gained popularity in bioimaging because it can avoid the need for cell staining, which, in some cases, is difficult or impossible. However, as a result, quantitative phase imaging does not provide the labelling of various specific intracellular structures. Here we show a novel computational segmentation method based on statistical inference that makes it possible for quantitative phase imaging techniques to identify the cell nucleus. We demonstrate the approach with refractive index tomograms of stain-free cells reconstructed using tomographic phase microscopy in the flow cytometry mode. In particular, by means of numerical simulations and two cancer cell lines, we demonstrate that the nucleus can be accurately distinguished within the stain-free tomograms. We show that our experimental results are consistent with confocal fluorescence microscopy data and microfluidic cyto-fluorimeter outputs. This is a remarkable step towards directly extracting specific three-dimensional intracellular structures from the phase contrast data in a typical flow cytometry configuration.The accurate identification of the three-dimensional quantitative shape of a cell nucleus is now possible without fluorescent staining by applying computational segmentation to refractive index tomograms recorded in the flow cytometry mode.

Main conclusionETR/AN ratios should be in the range 7.5–10.5 for non-stressed C3 plants. Ratios extremely out of this range can be reflecting both uncontrolled plant status and technical mistakes during measurements. We urge users to explicitly refer to this ratio in future studies as a proof for internal data quality control.For the last few decades, the use of infra-red gas-exchange analysers (IRGAs) coupled with chlorophyll fluorometers that allow for measurements of net CO2 assimilation rate and estimates of electron transport rate over the same leaf area has been popularized. The evaluation of data from both instruments in an integrative manner can result in additional valuable information, such as the estimation of the light respiration, mesophyll conductance and the partitioning of the flux of electrons into carboxylation, oxygenation and alternative processes, among others. In this review, an additional and more ‘straight’ use of the combination of chlorophyll fluorescence and gas exchange-derived parameters is presented, namely using the direct ratio between two fully independently estimated parameters, electron transport rate (ETR)—determined by the fluorometer—and net CO2 assimilation rate (AN)—determined by the IRGA, i.e., the ETR/AN ratio, as a tool for fast detection of incongruencies in the data and potential technical problems associated with them, while checking for the study plant’s status. To illustrate this application, a compilation of 75 studies that reported both parameters for a total of 178 species under varying physiological status is presented. Values of ETR/AN between 7.5 and 10.5 were most frequently found for non-stressed C3 plants. C4 species showed an average ETR/AN ratio of 4.7. The observed ratios were larger for species with high leaf mass per area and for plants subjected to stressful factors like drought or nutritional deficit. Knowing the expected ETR/AN ratio projects this ratio as a routinary and rapid check point for guaranteeing both the correct performance of equipment and the optimal/stress status of studied plants. All known errors associated with the under- or overestimation of ETR or AN are summarized in a checklist that aims to be routinely used by any IRGA/fluorometer user to strength the validity of their data.

Background Photosynthetic efficiency might be a key factor determining plant resistance to abiotic stresses. Plants can sense when growing conditions are not favorable and trigger an internal response at an early stage before showing external symptoms. When a high amount of salt enters the plant cell, the membrane system and function of thylakoids in chloroplasts could be destroyed and affect photosynthetic performance if the salt concentration is not regulated to optimal values. Oryza species have salt-tolerant and salt-sensitive genotypes; however, very few studies have investigated the genetic architecture responsible for photosynthetic efficiency under salinity stress in cultivated rice. Results We used an imaging-based chlorophyll fluorometer to monitor eight rice varieties that showed different salt tolerance levels for four consecutive days under control and salt conditions. An analysis of the changes in chlorophyll fluorescence parameters clearly showed the maximum quantum efficiency of PSII in sensitive varieties was significantly reduced after NaCl treatment when compared to tolerant varieties. A panel of 232 diverse rice accessions was then analyzed for chlorophyll fluorescence under salt conditions, the results showed that chlorophyll fluorescence parameters such as F 0 and NPQ were higher in Japonica subspecies, ΦPSII of Indica varieties was higher than that in other subgroups, which suggested that the variation in photosynthetic efficiency was extensively regulated under salt treatment in diverse cultivated rice. Two significant regions on chromosome 5 were identified to associate with the fraction of open PSII centers (qL) and the minimum chlorophyll fluorescence (F 0 ). These regions harbored genes related to senescence, chloroplast biogenesis and response to salt stress are of interest for future functional characterization to determine their roles in regulating photosynthesis. Conclusions Rice plant is very sensitive to salinity stress, especially at young seedling stage. Our work identified the distribution pattern of chlorophyll fluorescence parameters in seedlings leaf and their correlations with salt tolerance level in a diverse gene pool. We also revealed the complexity of the genetic architecture regulating rice seedling photosynthetic performance under salinity stress, the germplasm analyzed in this study and the associated genetic information could be utilized in rice breeding program.

The livestock industry has been deeply affected by African swine fever virus (ASFV) and Capripoxvirus (CaPV), which caused an enormous economic damage. It is emergent to develop a reliable detection method. Here, we developed a rapid, ultra-sensitive, and one-pot DNA detection method combining recombinase polymerase amplification (RPA) and CRISPR/Cas12a for ASFV and CaPV, named one-pot-RPA-Cas12a (OpRCas) platform. It had the virtue of both RPA and CRISPR/Cas12a, such as high amplification efficiency, constant temperature reaction, and strict target selectivity, which made diagnosis simplified, accurate and easy to be operated without expensive equipment. Meanwhile, the reagents of RPA and CRISPR/Cas12a were added to the lid and bottom of tube in one go, which overcame the incompatibility of two reactions and aerosol contamination. To save cost, we only need a quarter of the amount of regular RPA per reaction which is enough to achieve clinical diagnosis. The OpRCas platform was 10 to 100 times more sensitive than qPCR; the limit of detection (LOD) was as low as 1.2 × 10 −6  ng/µL (3.07 copies/µL by ddPCR) of ASFV and 7.7 × 10 −5  ng/µL (1.02 copies/µL by ddPCR) of CaPV with the portable fluorometer in 40 min. In addition, the OpRCas platform combined with the lateral flow assay (LFA) strip to suit for point-of-care (POC) testing. It showed 93.3% consistency with qPCR for clinical sample analysis. Results prove that OpRCas platform is an easy-handling, ultra-sensitive, and rapid to achieve ASFV and CaPV POC testing. Key points • The platform realizes one-pot reaction of RPA and Cas12a. • Sensitivity is 100 times more than qPCR. • Three output modes are suitable to be used to quantitative test or POC testing.

A systematic study of the luminescence properties of monodisperse β-NaYF 4 : 20% Yb 3+ , 2% Er 3+ upconversion nanoparticles (UCNPs) with sizes ranging from 12–43 nm is presented utilizing steady-state and time-resolved fluorometry. Special emphasis was dedicated to the absolute quantification of size- and environment-induced quenching of upconversion luminescence (UCL) by high-energy O–H and C–H vibrations from solvent and ligand molecules at different excitation power densities ( P ). In this context, the still-debated population pathways of the 4 F 9/2 energy level of Er 3+ were examined. Our results highlight the potential of particle size and P value for color tuning based on the pronounced near-infrared emission of 12 nm UCNPs, which outweighs the red Er 3+ emission under “strongly quenched” conditions and accounts for over 50% of total UCL in water. Because current rate equation models do not include such emissions, the suitability of these models for accurately simulating all (de)population pathways of small UCNPs must be critically assessed. Furthermore, we postulate population pathways for the 4 F 9/2 energy level of Er 3+ , which correlate with the size-, environment-, and P-dependent quenching states of the higher Er 3+ energy levels.

The global COVID-19 pandemic has highlighted the need for rapid, accurate and accessible nucleic acid tests to enable timely identification of infected individuals. We optimized a sample-to-answer nucleic acid test for SARS-CoV-2 that provides results in <1 hour using inexpensive and readily available reagents. The test workflow includes a simple lysis and viral inactivation protocol followed by direct isothermal amplification of viral RNA using RT-LAMP. The assay was validated using two different instruments, a portable isothermal fluorimeter and a standard thermocycler. Results of the RT-LAMP assay were compared to traditional RT-qPCR for nasopharyngeal swabs, nasal swabs, and saliva collected from a cohort of patients hospitalized due to COVID-19. For all three sample types, positive agreement with RT-LAMP performed using the isothermal fluorimeter was 100% for samples with Ct <30 and 69–91% for samples with Ct <40. Following validation, the test was successfully scaled to test the saliva of up to 400 asymptomatic individuals per day as part of the campus surveillance program at Rice University. Successful development, validation, and scaling of this sample-to-answer, extraction-free real-time RT-LAMP test for SARS-CoV-2 adds a highly adaptable tool to efforts to control the COVID-19 pandemic, and can inform test development strategies for future infectious disease threats.

The integration of DNA methylation and transcriptional state within single cells is of broad interest. Several single-cell dual- and multi-omics approaches have been reported that enable further investigation into cellular heterogeneity, including the discovery and in-depth study of rare cell populations. Such analyses will continue to provide important mechanistic insights into the regulatory consequences of epigenetic modifications. We recently reported a new method for profiling the DNA methylome and transcriptome from the same single cells in a cancer research study. Here, we present details of the protocol and provide guidance on its utility. Our Smart-RRBS (reduced representation bisulfite sequencing) protocol combines Smart-seq2 and RRBS and entails physically separating mRNA from the genomic DNA. It generates paired epigenetic promoter and RNA-expression measurements for ~24% of protein-coding genes in a typical single cell. It also works for micro-dissected tissue samples comprising hundreds of cells. The protocol, excluding flow sorting of cells and sequencing, takes ~3 d to process up to 192 samples manually. It requires basic molecular biology expertise and laboratory equipment, including a PCR workstation with UV sterilization, a DNA fluorometer and a microfluidic electrophoresis system. This is a protocol for profiling the methylome and transcriptome of a single cell by using Smart-seq2 and reduced representation bisulfite sequencing.

Rheumatoid arthritis (RA) is an autoimmune inflammatory disorder. Reactive oxygen species (ROS) and pro-inflammatory cytokines have been believed to be involved in the etiopathogenesis of the disease. The aim of the study was to determine the correlation of inflammatory cytokines with 25-hydroxy vitamin D and ROS. 100 RA patients and 50 healthy age and sex matched individuals were included in the study. Patients were further divided on the basis of presence or absence of rheumatoid factor and disease severity. Serum 25-hydroxy vitamin D levels were monitored by chemiluminescent immunoassay. 10% hematocrit was used to detect the level of ROS by spectro fluorometer. The levels of inflammatory cytokines (TNF-α, IL-1β, IL-6, IL-10 and IL-17) were determined in plasma by ELISA. The level of 25-hydroxy vitamin D was found to be decreased in RA patients in comparison to the control group. However the level of ROS and inflammatory cytokines were found to be elevated in RA patients in comparison with the healthy controls, with the increase being more pronounced in seropositive and RA patients having high disease severity. Inflammatory cytokines showed negative correlation with 25-hydroxy vitamin D and positive correlation with ROS. This study for the first time shows the association of inflammatory cytokines with 25-hydroxy vitamin D and ROS in RA patients. The results suggest that 25-hydroxy vitamin D being an immune modulator is decreased in the serum of RA patients. Further ROS and cytokines play an important role in the pathogenesis of RA and are responsible for increasing the severity of disease.

Accurate DNA quantification is key for downstream application including library preparations for whole genome sequencing (WGS) and the quantification of standards for quantitative PCR. Two commonly used technologies for nucleic acid quantification are based on spectrometry, such as NanoDrop, and fluorometry, such as Qubit. The DS–11+ Series spectrophotometer/fluorometer (DeNovix) is a UV spectrophotometry-based instrument and is a relatively new spectrophotometric method but has not yet been compared to established platforms. Here, we compared three DNA quantification platforms, including two UV spectrophotometry-based techniques (DeNovix and NanoDrop) and one fluorometry-based approach (Qubit). We used genomic prokaryotic DNA extracted from Streptococcus pneumoniae using a Roche DNA extraction kit. We also evaluated purity assessment and effect of a single freeze-thaw cycle. Spectrophotometry-based methods reported 3 to 4-fold higher mean DNA concentrations compared to Qubit, both before and after freezing. The ratio of DNA concentrations assessed by spectrophotometry on the one hand, and Qubit on the other hand, was function of the A 260/280 . In case DNA was pure (A 260/280 between 1.7 and 2.0), the ratio DeNovix or Nanodrop vs. Qubit was close or equal to 2, while this ratio showed an incline for DNA with increasing A 260/280 values > 2.0. The A 260/280 and A 260/230 purity ratios exhibited negligible variation across spectrophotometric methods and freezing conditions. The comparison of DNA concentrations from before and after freezing revealed no statistically significant disparities for each technique. DeNovix exhibited the highest Spearman correlation coefficient (0.999), followed by NanoDrop (0.81), and Qubit (0.77). In summary, there is no difference between DeNovix and NanoDrop in estimated gDNA concentrations of S . pneumoniae , and the spectrophotometry methods estimated close or equal to 2 times higher concentrations compared to Qubit for pure DNA.

Retigabine (RTG) is a first-in-class antiepileptic drug that suppresses neuronal excitability through the activation of voltage-gated KCNQ2–5 potassium channels. Retigabine binds to the pore-forming domain, causing a hyperpolarizing shift in the voltage dependence of channel activation. To elucidate how the retigabine binding site is coupled to changes in voltage sensing, we used voltage-clamp fluorometry to track conformational changes of the KCNQ3 voltage-sensing domains (VSDs) in response to voltage, retigabine, and PIP2. Steady-state ionic conductance and voltage sensor fluorescence closely overlap under basal PIP2 conditions. Retigabine stabilizes the conducting conformation of the pore and the activated voltage sensor conformation, leading to dramatic deceleration of current and fluorescence deactivation, but these effects are attenuated upon disruption of channel:PIP2 interactions. These findings reveal an important role for PIP2 in coupling retigabine binding to altered VSD function. We identify a polybasic motif in the proximal C terminus of retigabine-sensitive KCNQ channels that contributes to VSD–pore coupling via PIP2, and thereby influences the unique gating effects of retigabine.