A rapid and low-cost platform for detection of bacterial based on microchamber PCR microfluidic chip.

Polymerase chain reaction (PCR) has been considered as the gold standard for detecting nucleic acids. The simple PCR system is of great significance for medical applications in remote areas, especially for the developing countries. Herein, we proposed a low-cost self-assembled platform for microchamber PCR. The working principle is rotating the chamber PCR microfluidic chip between two heaters with fixed temperature to solve the problem of low temperature variation rate. The system consists of two temperature controllers, a screw slide rail, a chamber array microfluidic chip and a self-built software. Such a system can be constructed at a cost of about US$60. The micro chamber PCR can be finished by rotating the microfluidic chip between two heaters with fixed temperature. Results demonstrated that the sensitivity of the temperature controller is 0.1℃. The relative error of the duration for the microfluidic chip was 0.02 s. Finally, we successfully finished amplification of the target gene of Porphyromonas gingivalis in the chamber PCR microfluidic chip within 35 min and on-site detection of its PCR products by fluorescence. The chip consisted of 3200 cylindrical chambers. The volume of reagent in each volume is as low as 0.628 nL. This work provides an effective method to reduce the amplification time required for micro chamber PCR.

The Protective Effects of Sour Orange (Citrus aurantium L.) Polymethoxyflavones on Mice Irradiation-Induced Intestinal Injury.

Sour orange (Citrus aurantium L.) is one of the biological sources of polymethoxyflavones (PMFs), which are often used to deal with gastrointestinal diseases. The intestine is highly sensitive to irradiation damage. However, limited certain cures have been released for irradiation-induced gastrointestinal injury, and the potentials of sour orange PMFs as radio-resistance agents have not been fully discussed yet. The present study aims to (1) investigate the PMF components in 12 sour orange cultivars, (2) determine the protective effects of PMFs on irradiation-induced intestinal injury by treating mice that received 12 Gy abdominal irradiation with different doses of PMFs and observing the changes in organ indexes and pathological sections and (3) test cytotoxicity of PMFs by CCK-8 method. The results showed that sour orange PMFs appeared to have high intraspecies similarity. Besides, PMFs protected mice from irradiation-induced injury by alleviating body weight loss, reliving organ index changing and maintaining the intestinal structure. Finally, IC50 concentrations to cell line CCD 841 CoN of PMFs and nobiletin were calculated as 42.23 µg/mL and 51.58 µg/mL, respectively. Our study uncovered PMF contents in 12 sour orange materials and determined the protective effects on irradiation-induced intestinal injuries, providing guidance for the utilization of sour orange resources.

A portable instrument for on-site detection of heavy metal ions in water.

Based on differential pulse voltammetry technology, we developed a portable and affordable instrument for on-site detection of trace heavy metal pollutants in liquid through a disposable plastic pipette. It mainly consists of a six-electrode electrochemical sensor which is integrated in the instrument. The pipette chip is equipped with a pump valve, and thus, it can avoid contamination. We have analyzed the sensitivity and specificity of the electrochemical sensor for heavy metal detection. Experimental results demonstrated that the limit of detection for Pb, Hg, Cu, and Zn was 2.2 ng/mL, 2.5 ng/mL, 15.5 ng/mL, and 10 ng/mL, respectively. The limit of quantification for them was 10 ng/mL, 25 ng/mL, 25 ng/mL, and 14 ng/mL, respectively. The correlation coefficient between peak current and the target heavy metal concentration was above 0.96. Finally, we have tested the analytical performance of the self-build instrument by measuring heavy metal ions in industrial wastewater and rainwater, respectively. Such an instrument is user-friendly for all users even for the common people, and we can envision its wide application in future heavy metal pollutant detection in groundwater, tap water, and supernatant of soil solution.

Habitat heterogeneity mediates effects of individual variation on spatial species coexistence.

Numerous studies have documented the importance of individual variation (IV) in determining the outcome of competition between species. However, little is known about how the interplay between IV and habitat heterogeneity (i.e. variation and spatial autocorrelation in habitat quality) affects species coexistence at the landscape scale. Here, we incorporate habitat heterogeneity into a competition model with IV, in order to explore the mechanism of spatial species coexistence. We find that individual-level variation and habitat heterogeneity interact to promote species coexistence, more obviously at lower dispersal rates. This is in stark contrast to early non-spatial models, which predicted that IV reinforces competitive hierarchies and therefore speeds up species exclusion. In essence, increasing variation in patch quality and/or spatial habitat autocorrelation moderates differences in the competitive ability of species, thereby allowing species to coexist both locally and globally. Overall, our theoretical study offers a mechanistic explanation for emerging empirical evidence that both habitat heterogeneity and IV promote species coexistence and therefore biodiversity maintenance.

Separation of subcellular fluorescent microspheres by capillary electrophoresis.

Fluorescent microspheres (FMs) are widely employed in diagnostics and life sciences research; here, we investigated the effect of capillary coating, polymer concentration, electric field strength, and sample concentration on the separation performance of 1.0 µm FMs in hydroxyethyl cellulose (HEC) by capillary electrophoresis (CE). Results showed that (1) capillary coating could enhance the fluorescence signal. (2) For HEC with the same molecular weight, the higher HEC concentration is, the later the first peak appears in the electropherogram. (3) When FMs are diluted, increasing the electric field strength can enhance the migration speed and reduce the aggregation of FMs. (4) The number of FMs calculated is close to the theoretical value when it is diluted 10,000 times. The optimum conditions for CE were as follows: 6 cm/8 cm of effective length and total length of the coated capillary, 0.3% HEC (1300 k), and 300 V/cm of electric field strength. Such a study is helpful for the development of a FM counting system. Graphical abstract.

Design and fabrication of portable continuous flow PCR microfluidic chip for DNA replication.

The reasons for restricting continuous flow polymerase chain reaction (CF-PCR) microfluidic chip from lab to application are that it is not portable and requires costly external precision pumps for sample injection. Herein, we employed water as the substitute for PCR solution, and investigated the effect of the cross-section, width-to-depth ratio, and the length ratio for three temperature zones of the micro channel on the thermal and flow distribution of fluid in micro tube by finite element analysis. Results show that the central velocity is uniform and stable velocity occupies the most if the cross-section is rectangular. The deviation between predefined temperature and theoretical temperature is slight and the fluid flux is the most if width-to-depth ratio is 1:1. It is suitable for the short DNA replication if the high temperature zone Wh is larger than the low temperature zone Wl, and vice versa. Then a portable CF-PCR microfluidic chip was fabricated and an automatic sample injection system was developed. As an application, we have successfully amplified the DNA of Treponema denticola in the chip within 8 min. Such a study may offer new insight into the design of CF-PCR microfluidic chip and promote it from lab-scale research to full-scale application.

Deep Transcriptome Analysis Reveals Reactive Oxygen Species (ROS) Network Evolution, Response to Abiotic Stress, and Regulation of Fiber Development in Cotton.

Reactive oxygen species (ROS) are important molecules in the plant, which are involved in many biological processes, including fiber development and adaptation to abiotic stress in cotton. We carried out transcription analysis to determine the evolution of the ROS genes and analyzed their expression levels in various tissues of cotton plant under abiotic stress conditions. There were 515, 260, and 261 genes of ROS network that were identified in Gossypium hirsutum (AD1 genome), G. arboreum (A genome), and G. raimondii (D genome), respectively. The ROS network genes were found to be distributed in all the cotton chromosomes, but with a tendency of aggregating on either the lower or upper arms of the chromosomes. Moreover, all the cotton ROS network genes were grouped into 17 families as per the phylogenetic tress analysis. A total of 243 gene pairs were orthologous in G. arboreum and G. raimondii. There were 240 gene pairs that were orthologous in G. arboreum, G. raimondii, and G. hirsutum. The synonymous substitution value (Ks) peaks of orthologous gene pairs between the At subgenome and the A progenitor genome (G. arboreum), D subgenome and D progenitor genome (G. raimondii) were 0.004 and 0.015, respectively. The Ks peaks of ROS network orthologous gene pairs between the two progenitor genomes (A and D genomes) and two subgenomes (At and Dt subgenome) were 0.045. The majority of Ka/Ks value of orthologous gene pairs between the A, D genomes and two subgenomes of TM-1 were lower than 1.0. RNA seq. analysis and RT-qPCR validation, showed that, CSD1,2,3,5,6; FSD1,2; MSD1,2; APX3,11; FRO5.6; and RBOH6 played a major role in fiber development while CSD1, APX1, APX2, MDAR1, GPX4-6-7, FER2, RBOH6, RBOH11, and FRO5 were integral for enhancing salt stress in cotton. ROS network-mediated signal pathway enhances the mechanism of fiber development and regulation of abiotic stress in Gossypium. This study will enhance the understanding of ROS network and form the basic foundation in exploring the mechanism of ROS network-involving the fiber development and regulation of abiotic stress in cotton.

The effect of electrophoretic parameters on separation performance of short DNA fragments.

Effective separation of short DNA fragments is important for the identification of PCR or LAMP products. We investigated the effect of electric field strength, sample plug width, effective length of the capillary, concentration and molecular weight of polymer on the separation performance of small DNA. Results demonstrated that the sample plug played a non-negligible role in the peak broadening. The migration time of DNA was exponentially decreased with the increase of electric field strength. Increasing effective length of capillary, concentration or molecular weight of HEC may improve the separation performance, but it was at the cost of long migration time.

Simultaneous Separation and Purification of Five Polymethoxylated Flavones from "Dahongpao" Tangerine (Citrus tangerina Tanaka) Using Macroporous Adsorptive Resins Combined with Prep-HPLC.

In this study, a preparative separation method was established to simultaneously isolate the polymethoxylated flavones (PMFs) from the peel of "Dahongpao" tangerine using macroporous adsorptive resins (MARs) combined with prep-HPLC. The total PMFs were enriched using MARs to remove most sugars, water-soluble pigments, and flavanones, and the eluents obtained were analyzed by ultra-performance liquid chromatography (UPLC) to determine the PMF composition. The separation and purification of PMFs were carried out by using a mass spectrometry-guided prep-HPLC with a gradient elution of acetonitrile-water (v/v), simultaneously. The purity of these PMFs was determined by UPLC, and their chemical structures were confirmed by electrospray ionization mass spectrometry (ESI-MS-MS), ultraviolet (UV), and nuclear magnetic resonance (NMR). Using the present method, five PMFs, including 5,6,7,4'-tetramethoxyflavone (1), nobiletin (2), tangeretin (3), sinensetin (4), and 5-hydroxy-6,7,8,3',4'-pentamethoxyflavone (5), can be purified simultaneously, and the purity of the compounds obtained were 95.3%, 99.7%, 99.5%, 98.9%, and 98.1%, respectively. The method reported here is simple, rapid, and efficient, and it can be used to separate PMFs from citrus fruit peels and, potentially, other plant materials.

Coexistence of species with different dispersal across landscapes: a critical role of spatial correlation in disturbance.

Disturbance is key to maintaining species diversity in plant communities. Although the effects of disturbance frequency and extent on species diversity have been studied, we do not yet have a mechanistic understanding of how these aspects of disturbance interact with spatial structure of disturbance to influence species diversity. Here we derive a novel pair approximation model to explore competitive outcomes in a two-species system subject to spatially correlated disturbance. Generally, spatial correlation in disturbance favoured long-range dispersers, while distance-limited dispersers were greatly suppressed. Interestingly, high levels of spatial aggregation of disturbance promoted long-term species coexistence that is not possible in the absence of disturbance, but only when the local disperser was intrinsically competitively superior. However, spatial correlation in disturbance led to different competitive outcomes, depending on the disturbed area. Concerning ecological conservation and management, we theoretically demonstrate that introducing a spatially correlated disturbance to the system or altering an existing disturbance regime can be a useful strategy either to control species invasion or to promote species coexistence. Disturbance pattern analysis may therefore provide new insights into biodiversity conservation.

Gene analysis of multiple oral bacteria by the polymerase chain reaction coupled with capillary polymer electrophoresis.

Capillary polymer electrophoresis is identified as a promising technology for the analysis of DNA from bacteria, virus and cell samples. In this paper, we propose an innovative capillary polymer electrophoresis protocol for the quantification of polymerase chain reaction products. The internal standard method was modified and applied to capillary polymer electrophoresis. The precision of our modified internal standard protocol was evaluated by measuring the relative standard deviation of intermediate capillary polymer electrophoresis experiments. Results showed that the relative standard deviation was reduced from 12.4-15.1 to 0.6-2.3%. Linear regression tests were also implemented to validate our protocol. The modified internal standard method showed good linearity and robust properties. Finally, the ease of our method was illustrated by analyzing a real clinical oral sample using a one-run capillary polymer electrophoresis experiment.

Analysis of small interfering RNA by capillary electrophoresis in hydroxyethylcellulose solutions.

The analysis of small interfering RNA (siRNA) is important for gene function studies and drug developments. We employed CE to study the separation of siRNA ladder marker, which were ten double-stranded RNA (dsRNA) fragments ranged from 20 to 1000 bp, in solutions of hydroxyethylcellulose (HEC) polymer with different concentrations and molecular weights (Mws). Migration mechanism of dsRNA during CE was studied by the mobility and resolution length (RL) plots. We found that the RL depended on not only the concentration of HEC, but also the Mw of HEC. For instance, RL of small dsRNA fragment was more influenced by concentration of high Mw HEC than large dsRNA fragment and RL of large dsRNA fragment was more influenced by concentration of low Mw HEC than small dsRNA fragment. In addition, we found electrophoretic evidence that the structure of dsRNA was more compact than dsDNA with the same length. In practice, we succeeded to separate the glyceraldehyde 3-phosphate dehydrogenase siRNA in the mixture of the siRNA ladder marker within 4 min.

Electrophoresis of periodontal pathogens in poly(ethyleneoxide) solutions with uncoated capillary.

Periodontitis is a prevalent inflammatory disease caused by different species of anaerobic bacteria such as Porphyromonas gingivalis (P.g), Treponema denticola (T.d), and Tannerella forsythia (T.f). We compared the separation result of DNA ladders in hydroxyethyl cellulose, poly(ethyleneoxide) (PEO), and polyethylene glycol and analyzed the effect of polymer concentration, electric field, and temperature of the background electrolyte on the separation performance. Results demonstrated that there was a linear relationship (R=0.942) for 100 to 700bp of DNA and its migration time. Finally, the polymerase chain reaction products of P.g, T.d, and T.f were successfully identified within 8.5 min in 0.5% PEO with uncoated capillary.

Species coexistence in a lattice-structured habitat: effects of species dispersal and interactions.

Opinions differ on how the spatial distribution of species over space affects species coexistence. Here, we constructed both mean-field and pair approximation (PA) models to explore the effects of interspecific and intraspecific interactions and dispersal modes on species coexistence. We found that spatial structure resulting from species dispersal traits and neighboring interactions in PA model did not promote coexistence if two species had the same traits, though it might intensify the contact frequency of intraspecific competition. If two species adopt different dispersal modes, the spatial structure in PA would make the coexistence or founder control less likely since it alters the species effective birth rate. This suggests that the spatial distribution caused by neighboring interactions and local dispersal does not affect species coexistence unless it adequately alters the effective birth rate for two species. Besides, we modeled how the initial densities and patterns affected population dynamics and revealed how the final spatial pattern was generated.

Determination and quantification of Escherichia coli by capillary electrophoresis.

Capillary electrophoresis (CE) is widely employed for the separation of nucleic acids or protein, but it is rarely applied in the quantification of Escherichia coli (E. coli). Here, we have analysed E. coli by CE with mercury lamp induced fluorescence, and demonstrated the relationship between its fluorescence intensity with the concentration of E. coli for the first time. The gradient concentration of E. coli was obtained by polymerase chain reaction (PCR) with different amplification cycles and dilution certain PCR products of E. coli, respectively. Results show that the peak area was linearly related to the logarithm of the concentration of E. coli and the logarithm of PCR replication numbers. The correlation coefficients R(2) are 0.957 and 0.966, respectively. The limit of detection (LOD) was found to be about 8.913 × 10(-15) mol µl(-1). The reproducibility of capillary electrophoresis may make this technique possible for quantitative measurement of bacteria in bio-analytical science.

Deep causal speech enhancement and recognition using efficient long-short term memory Recurrent Neural Network.

Long short-term memory (LSTM) has been effectively used to represent sequential data in recent years. However, LSTM still struggles with capturing the long-term temporal dependencies. In this paper, we propose an hourglass-shaped LSTM that is able to capture long-term temporal correlations by reducing the feature resolutions without data loss. We have used skip connections in non-adjacent layers to avoid gradient decay. In addition, an attention process is incorporated into skip connections to emphasize the essential spectral features and spectral regions. The proposed LSTM model is applied to speech enhancement and recognition applications. The proposed LSTM model uses no future information, resulting in a causal system suitable for real-time processing. The combined spectral feature sets are used to train the LSTM model for improved performance. Using the proposed model, the ideal ratio mask (IRM) is estimated as a training objective. The experimental evaluations using short-time objective intelligibility (STOI) and perceptual evaluation of speech quality (PESQ) have demonstrated that the proposed model with robust feature representation obtained higher speech intelligibility and perceptual quality. With the TIMIT, LibriSpeech, and VoiceBank datasets, the proposed model improved STOI by 16.21%, 16.41%, and 18.33% over noisy speech, whereas PESQ is improved by 31.1%, 32.9%, and 32%. In seen and unseen noisy situations, the proposed model outperformed existing deep neural networks (DNNs), including baseline LSTM, feedforward neural network (FDNN), convolutional neural network (CNN), and generative adversarial network (GAN). With the Kaldi toolkit for automated speech recognition (ASR), the proposed model significantly reduced the word error rates (WERs) and reached an average WER of 15.13% in noisy backgrounds.

High-throughput 3D microfluidic chip for generation of concentration gradients and mixture combinations.

Concentration gradient generation and mixed combinations of multiple solutions are of great value in the field of biomedical research. However, existing concentration gradient generators for single or two-drug solutions cannot simultaneously achieve multiple concentration gradient formations and mixed solution combinations. Furthermore, the whole system was huge, and required expensive auxiliary equipment, which may lead to complex operations. To address this problem, we devised a novel 3D microchannel network design, which is capable of creating all the desired mixture combinations and concentration gradients of given small amounts of the input solutions. As a proof of concept, the device we presented was verified by both colorimetric and fluorescence detection methods to test the efficiency. This can enable the implementation of one to three solutions with no driving pump and facilitate unique multiple types of more concentration gradients and mixture combinations in a single operation. We envision that this will be a promising candidate for the development of simplified methods for screening of the appropriate concentration and combination, such as various drug screening applications.

Species persistence in landscapes with spatial variation in habitat quality: a pair approximation model.

Habitat degradation has become a major threat to species persistence. Although several models have explicitly integrated habitat quality into metapopulation dynamics, we still lack knowledge of the spatial variability of species persistence which may result from the clustering of habitat patches of differing quality. Here we construct both pair approximation (PA) and cellular automaton (CA) models for species persistence in homogeneous versus heterogeneous landscapes. Heterogeneous landscapes are generated by varying the orthogonal-neighbour correlation between two different-quality habitats. In our simulations, the PA model exhibits similar population dynamics to the CA model, though it overestimates species persistence due to the doublet approximation neglecting correlation beyond nearest neighbours. Generally, landscape heterogeneity enhances species persistence relative to landscape homogeneity, especially with enlarging habitat-quality difference. This indicates that models based on homogeneous landscapes may overestimate species extinction rate. In heterogeneous landscapes, habitat clumping does not influence global dispersers because of random establishment, although it does promote the persistence of local dispersers, especially under severe habitat degradation. However, habitat configurational fragmentation improves the persistence of global dispersers that are highly sensitive to local crowding, probably by reducing density dependence, but this positive fragmentation effect on local dispersers is overshadowed by the stronger negative border effect on impeding local extension. Furthermore, increasing density dependence promotes the extinction risk of local dispersers, while global dispersers are not influenced. For conservation and habitat management, our results suggest that minimising random anthropogenic disturbance should take priority over increasing the connectivity of good-quality habitat, as random habitat degradation poses a more serious threat to species persistence than clustered habitat degradation. Owing to species' diverse responses to habitat configurational fragmentation, landscapes with different properties may accommodate different species.

Correlation of continuous ryegrass regrowth with cytokinin induced by root nitrate absorption.

This study investigated the separate and combined effects of nitrate (NO3 (-)) and cytokinin additions on continuous ryegrass regrowth after defoliation and the underlying mechanisms. Our results showed that frequent defoliation reduced the biomass of newly grown leaves and roots, the root soluble carbohydrate contents, the root vitality (an indicator of root absorption capacity), and the leaf contents of NO3 (-), zeatin and zeatin riboside (Z + ZR), and isopentenyl adenine and isopentenyl adenosine (IP + IPA). NO3 (-)addition to the roots or leaves increased the biomass of newly grown leaves as well as the leaf contents of NO3 (-), Z + ZR, and IP + IPA without increasing the root-to-shoot delivery of endogenous cytokinin. Interestingly, cytokinin directly added to the leaves also increased the biomass of newly grown leaves and their Z + ZR and IP + IPA contents, suggesting that nitrate-induced leaf cytokinin production mediates the growth-promoting effects of nitrate. We also found that cytokinin had a direct whereas NO3 (-) had an indirect effect on the biomass of newly grown leaves. Taken together, our results indicate that leaf cytokinin production induced by NO3 (-) absorbed through the roots plays a key role in continuous ryegrass regrowth after defoliation.

Direct count of fluorescent microspheres in a microfluidic chip based on the capillary electrophoresis method.

Fluorescent microspheres (FMs) are tiny particles with special functions that are widely employed in biological research. Counting of microscale FMs is a great challenge by capillary electrophoresis. Herein we developed a method to count 2 µm FMs based on a microfluidic chip with a gradual change in inner size. Such a microfluidic chip can inhibit sample blocking at the inlet of the capillary. The results showed that FMs migrated in the wide part of the microchannel side by side, and then passed through the narrow part one by one. There was a linear relationship between the number of peaks in the electropherogram and concentration of FMs if they were running in the microchannel for more than 20 min. A high separation voltage may lead to aggregation of FMs in the microchannels, and about 2 × 104 FMs can be counted within 30 min by this microfluidic chip.