Integrative pathway and network analysis provide insights on flooding-tolerance genes in soybean.

Soybean is highly sensitive to flooding and extreme rainfall. The phenotypic variation of flooding tolerance is a complex quantitative trait controlled by many genes and their interaction with environmental factors. We previously constructed a gene-pool relevant to soybean flooding-tolerant responses from integrated multiple omics and non-omics databases, and selected 144 prioritized flooding tolerance genes (FTgenes). In this study, we proposed a comprehensive framework at the systems level, using competitive (hypergeometric test) and self-contained (sum-statistic, sum-square-statistic) pathway-based approaches to identify biologically enriched pathways through evaluating the joint effects of the FTgenes within annotated pathways. These FTgenes were significantly enriched in 36 pathways in the Gene Ontology database. These pathways were related to plant hormones, defense-related, primary metabolic process, and system development pathways, which plays key roles in soybean flooding-induced responses. We further identified nine key FTgenes from important subnetworks extracted from several gene networks of enriched pathways. The nine key FTgenes were significantly expressed in soybean root under flooding stress in a qRT-PCR analysis. We demonstrated that this systems biology framework is promising to uncover important key genes underlying the molecular mechanisms of flooding-tolerant responses in soybean. This result supplied a good foundation for gene function analysis in further work.

An advanced systems biology framework of feature engineering for cold tolerance genes discovery from integrated omics and non-omics data in soybean.

Soybean is sensitive to low temperatures during the crop growing season. An urgent demand for breeding cold-tolerant cultivars to alleviate the production loss is apparent to cope with this scenario. Cold-tolerant trait is a complex and quantitative trait controlled by multiple genes, environmental factors, and their interaction. In this study, we proposed an advanced systems biology framework of feature engineering for the discovery of cold tolerance genes (CTgenes) from integrated omics and non-omics (OnO) data in soybean. An integrative pipeline was introduced for feature selection and feature extraction from different layers in the integrated OnO data using data ensemble methods and the non-parameter random forest prioritization to minimize uncertainties and false positives for accuracy improvement of results. In total, 44, 143, and 45 CTgenes were identified in short-, mid-, and long-term cold treatment, respectively, from the corresponding gene-pool. These CTgenes outperformed the remaining genes, the random genes, and the other candidate genes identified by other approaches in an independent RNA-seq database. Furthermore, we applied pathway enrichment and crosstalk network analyses to uncover relevant physiological pathways with the discovery of underlying cold tolerance in hormone- and defense-related modules. Our CTgenes were validated by using 55 SNP genotype data of 56 soybean samples in cold tolerance experiments. This suggests that the CTgenes identified from our proposed systematic framework can effectively distinguish cold-resistant and cold-sensitive lines. It is an important advancement in the soybean cold-stress response. The proposed pipelines provide an alternative solution to biomarker discovery, module discovery, and sample classification underlying a particular trait in plants in a robust and efficient way.

Investigation of toxic heavy metals content and estimation of potential health risks in Chinese herbal medicine.

The content of toxic heavy metals (THMs), including lead (Pb), arsenic (As), cadmium (Cd), and mercury (Hg), was determined in a total of 10,245 samples for 279 types of Chinese herbal medicine (CHM) using a validated inductively coupled plasma mass spectrometry method. The exceeding rate (ER) for the four THMs were calculated based on diverse permissible limits (PLs) established by different organizations and national pharmacopeias. Cluster analysis was used to classify the degree risk of THMs contamination according to the calculated ER. Results revealed that Cibotii rhizome, Selaginellae herba, Morindae officinalis radix, Asprellae ilicis radix, and Toxicodendri resina exhibited high-degree risk of Pb contamination. Eckloniae/Laminariae thallus, Spirodelae herba, and Naturalis indigo possessed high-degree risk of As contamination. Tetrapanacis medulla, Centipedae herba, Cyathulae radix, Linderae radix, Meretricis/Cyclinae concha, and Tabanus displayed high-degree risk of Cd contamination. Toxicodendri resina has high-degree risk of Hg contamination. In addition, six types of CHM, including Asprellae ilicis radix, Toxicodendri resina, Eckloniae/Laminariae thallus, Fossilia Ossis Mastodi, Haematitum, and Hedyotidis diffusae herba, may have non-carcinogenic health risk after consumption of raw materials because the calculated hazard quotient and hazard index were over 1.0. In summary, these data provide useful information about THMs contamination in CHM.

Investigation of aflatoxins contamination in herbal materia medica in a Taiwan pharmaceutical factory.

During the years 2005-2016, a total of 1067 samples for 24 types of herbal materia medica were investigated for the presence of aflatoxins (AFs) using immunoaffinity column cleanup and HPLC-coupled to a fluorescence detector after post-column derivatization. AFs were detected in 373 (35%) out of the total samples. Among them, Platycladi Semen (65% for total AFs and 79% for AFB1), Corydalis Rhizoma (53% for total AFs and 32% for AFB1), Corni Fructus (3% for total AFs), Coicis Semen (3% for total AFs and AFB1), Nelumbinis Semen (6% for total AFs and 9% for AFB1), Arecae Semen (18% for AFB1), Polygalae Radix (5% for total AFs and AFB1), and Cassiae Semen (25% for total AFs and 38% for AFB1) exceeded the official limits of 5 and 10 µg/kg, for AFB1 and total AFs (the sum of AFB1, AFB2, AFG1, and AFG2), respectively, set by the Taiwan government. We concluded that Platycladi Semen, Corydalis Rhizoma, and Cassiae Semen are the most commonly contaminated by AFs.

Correlation between radioactivity and chemotherapeutics of the (111)In-VNB-liposome in pharmacokinetics and biodistribution in rats.

BACKGROUND: The combination of a radioisotope with a chemotherapeutic agent in a liposomal carrier (ie, Indium-111-labeled polyethylene glycol pegylated liposomal vinorelbine, [(111)In-VNB-liposome]) has been reported to show better therapeutic efficiency in tumor growth suppression. Nevertheless, the challenge remains as to whether this therapeutic effect is attributable to the combination of a radioisotope with chemotherapeutics. The goal of this study was to investigate the pharmacokinetics, biodistribution, and correlation of Indium-111 radioactivity and vinorelbine concentration in the (111)In-VNB-liposome. METHODS: The VNB-liposome and (111)In-VNB-liposome were administered to rats. Blood, liver, and spleen tissue were collected to determine the distribution profile of the (111)In-VNB-liposome. A liquid chromatography tandem mass spectrometry system and gamma counter were used to analyze the concentration of vinorelbine and radioactivity of Indium-111. RESULTS: High uptake of the (111)In-VNB-liposome in the liver and spleen demonstrated the properties of a nanosized drug delivery system. Linear regression showed a good correlation (r = 0.97) between Indium-111 radioactivity and vinorelbine concentration in the plasma of rats administered the (111)In-VNB-liposome. CONCLUSION: A significant positive correlation between the pharmacokinetics and biodistribution of (111)Indium radioactivity and vinorelbine in blood, spleen, and liver was found following administration of the (111)In-VNB-liposome. The liposome efficiently encapsulated both vinorelbine and Indium-111, and showed a similar concentration-radioactivity time profile, indicating the correlation between chemotherapy and radiotherapy could be identical in the liposomal formulation.

Investigation of the water purification efficiency of flood irrigation system by using flora succession as an index.

A flood irrigation system was constructed to remove nutrient-based water pollutants through the various natural treatment mechanisms of plants and microorganisms. Species of plants were allowed to proliferate naturally within the system. The succession of flora was then utilized as an index to evaluate the water purification efficiency of the flood irrigation system. The natural growth of plants during the test period indicated what part of the irrigation system would recover most efficiently from nutrient-based contamination. From the first stage of observation (50 days) to the second stage (50 days), the average processing efficiencies of Nitrate Nitrogen (NO3(-)-N) and Ortho-phosphate (PO4(3-)) were improved 1.7% and 70.3%, respectively. After the 60th day, the Compositae family flourished in the system. At the same time, removal rate of Nitrate Nitrogen was increased dramatically which may be related to prevalence of the Compositae family. Trends indicate that the Ortho-phosphate concentration of the irrigated water was low, and Brachiaria mutica of Poaceae were dominant which may have lead to the phenomenon of phosphorus released in the flood irrigation system.

Improving liquid chromatography-tandem mass spectrometry determinations by modifying noise frequency spectrum between two consecutive wavelet-based low-pass filtering procedures.

This paper employs one chemometric technique to modify the noise spectrum of liquid chromatography-tandem mass spectrometry (LC-MS/MS) chromatogram between two consecutive wavelet-based low-pass filter procedures to improve the peak signal-to-noise (S/N) ratio enhancement. Although similar techniques of using other sets of low-pass procedures such as matched filters have been published, the procedures developed in this work are able to avoid peak broadening disadvantages inherent in matched filters. In addition, unlike Fourier transform-based low-pass filters, wavelet-based filters efficiently reject noises in the chromatograms directly in the time domain without distorting the original signals. In this work, the low-pass filtering procedures sequentially convolve the original chromatograms against each set of low pass filters to result in approximation coefficients, representing the low-frequency wavelets, of the first five resolution levels. The tedious trials of setting threshold values to properly shrink each wavelet are therefore no longer required. This noise modification technique is to multiply one wavelet-based low-pass filtered LC-MS/MS chromatogram with another artificial chromatogram added with thermal noises prior to the other wavelet-based low-pass filter. Because low-pass filter cannot eliminate frequency components below its cut-off frequency, more efficient peak S/N ratio improvement cannot be accomplished using consecutive low-pass filter procedures to process LC-MS/MS chromatograms. In contrast, when the low-pass filtered LC-MS/MS chromatogram is conditioned with the multiplication alteration prior to the other low-pass filter, much better ratio improvement is achieved. The noise frequency spectrum of low-pass filtered chromatogram, which originally contains frequency components below the filter cut-off frequency, is altered to span a broader range with multiplication operation. When the frequency range of this modified noise spectrum shifts toward the high frequency regimes, the other low-pass filter is able to provide better filtering efficiency to obtain higher peak S/N ratios. Real LC-MS/MS chromatograms, of which typically less than 6-fold peak S/N ratio improvement achieved with two consecutive wavelet-based low-pass filters remains the same S/N ratio improvement using one-step wavelet-based low-pass filter, are improved to accomplish much better ratio enhancement 25-folds to 40-folds typically when the noise frequency spectrum is modified between two low-pass filters. The linear standard curves using the filtered LC-MS/MS signals are validated. The filtered LC-MS/MS signals are also reproducible. The more accurate determinations of very low concentration samples (S/N ratio about 7-9) are obtained using the filtered signals than the determinations using the original signals.

Lymphatic absorption of quercetin and rutin in rat and their pharmacokinetics in systemic plasma.

Substances and macromolecules absorbed by the lymphatic system avoid hepatic first-pass effect and directly enter the blood circulation system. In this study, an anesthetized, mesenteric lymphatic/duodenum-cannulated rat model was used to investigate the role of lymphatic absorption with intraduodenally administered drugs. Quercetin and rutin were administered, respectively, at dosages of 30 and 300 mg/kg intraduodenally. Lymph and plasma samples were collected every 30 min. These samples were prepared by protein precipitation and then analyzed by high-performance liquid chromatography with a photodiode array detector (HPLC-PDA) and verified by LC tandem mass spectrometry (LC-MS/MS). Quercetin was separated by a C18 reversed-phase column, and rutin was separated by a phenyl reverse-phase column. Pharmacokinetic parameters were calculated using the software WinNonlin Standard Edition Version. The maximum concentration (Cmax) of quercetin recovered in lymph, 1.97+/-0.96 microg/mL, was about 5-fold higher than that in plasma, 0.41+/-0.08 microg/mL. The time to reach the highest concentration (Tmax) of quercetin in lymph was 30 min longer than that in plasma. The maximum concentration (Cmax) of rutin recovered in lymph, 0.86+/-0.13 microg/mL, was slightly lower than that in plasma, 1.35+/-0.37 microg/mL. The area under curve (AUC) of rutin recovered in lymph, 359+/-41 min microg/mL, was about 2-fold higher than the AUC of rutin in plasma, 150+/-22 min microg/mL. This phenomenon was due to the milder concentration decline of rutin in the lymphatic system. These results demonstrate the pharmacokinetic data of lymphatic and systemic absorption after intraduodenally administered quercetin and rutin. It is also the first report revealing the lymphatic absorption of rutin. Although both quercetin and rutin are absorbed and transported mainly via the blood circulation system, the AUC of these two drugs in lymph fluid appeared higher than their respective AUC in plasma.

Oral bioavailability, urinary excretion and organ distribution of melamine in Sprague-Dawley rats by high-performance liquid chromatography with tandem mass spectrometry.

High-performance liquid chromatography with tandem mass spectrometry (HPLC/MS/MS) was used to determine melamine oral bioavailability (BA) and urinary excretion. Organ distribution after a 14-day consecutive oral melamine administration (100 mg/kg/day, once a day) was also evaluated. A noncompartmental model was utilized to obtain pharmacokinetic parameters. According to the results, the BA of melamine was estimated to be 98.1%. Approximately 63% of administered melamine was recovered in urine within 96 h after a single oral administration (100 mg/kg). The bladder had the highest melamine concentration of all the organs after a 14-day consecutive oral administration of melamine, and almost no melamine was found in the rat brain. This result indicated that the oral absorption of melamine was almost complete and urinary excretion was the major route for its elimination. Repeated exposure to high-dose melamine may result in only slight accumulation in organs.

Determination of melamine in rat plasma, liver, kidney, spleen, bladder and brain by liquid chromatography-tandem mass spectrometry.

In this study, we describe a method for the analysis of melamine in rat plasma, liver, kidney, spleen, bladder, and brain using trichloroacetic acid precipitation with mixed-mode cation-exchange solid-phase extraction and hydrophilic interaction chromatography coupled to tandem mass spectrometry detection. Method validation was investigated completely, including linearity, precision, accuracy, matrix effect, extraction recovery, and carryover for the determination of melamine. The method exhibited a good linear range covering 20-500 ng/mL, and the overall precision ranged from 1.6 to 16.3%, with the accuracy varying from -7.9 to 15.1%. The mean matrix effects of melamine in rat plasma, liver, kidney, spleen, bladder, and brain ranged from 66.2+/-6.7 to 95.5+/-13.2%, and the mean recoveries for melamine varied from 79.8+/-8.2 to 113.0+/-9.6%. Rat kidney showed the highest level among the organs (192.5% of the plasma melamine level), and the average concentration of melamine in the brain was only 7.5% of the plasma melamine concentration. This work has pointed out that even with the application of two popular preparation procedures (acid precipitation and solid-phase extraction) of melamine, the matrix effect in analyzing biological samples still exists in certain kinds of matrices.

Using orthogonal array to obtain gradient liquid chromatography conditions of enhanced peak intensity to determine geniposide and genipin with electrospray tandem mass spectrometry.

The conditions to determine geniposide and genipin using gradient liquid chromatography-tandem mass spectrometry (LC-MS/MS) via electrospray ionization were obtained using fractional factorial experimental design approaches, guided with Taguchi orthogonal arrays to enhance peak intensity. Geniposide, the major iridoid glycoside component of Gardenia herbs, which has been recognized to have choleretic effects, is transformed to genipin in animals. In this paper, the gradient establishment times, ionization source temperatures, and the concentrations of volatile additive ammonium acetate were investigated under the guidance of experimental designs to obtain LC-MS/MS signals of the highest peak intensity. Using geniposide and genipin standards, the methods are validated at the concentration ranges of 0.5-1000ng/mL and 10-5000ng/mL using ammonium adducts. The correlation coefficients of geniposide and genipin standard curves are greater than 0.999. Compared with the sensitivities of previously published LC-MS/MS methods, the methods developed in this work provide 6-fold sensitivity improvement. The lowest concentrations of geniposide and genipin, 0.19 and 2ng/mL, respectively, to generate detectable LC-MS/MS signal peaks are one order of magnitude lower than the repoered values in previous publications. The measurement accuracy and precision of geniposide are within 23% and 15%, respectively. The accuracy and precision of genipin are within 16% and 12.5%, respectively. When the validated calibration curves of geniposide and genipin are used to determine spiked control samples in rat blood dialysates, the geniposide determination errors are within 15% accuracy and within 5.8% precision, respectively, and the genipin determination errors are within 23% accuracy and within 3.6% precision, respectively.

Improving signal-to-noise ratios of liquid chromatography-tandem mass spectrometry peaks using noise frequency spectrum modification between two consecutive matched-filtering procedures.

This paper reports a simple chemometric technique to alter the noise spectrum of liquid chromatography-tandem mass spectrometry (LC-MS-MS) chromatogram between two consecutive matched filter procedures to improve the peak signal-to-noise (S/N) ratio enhancement. This technique is to multiply one match-filtered LC-MS-MS chromatogram with another artificial chromatogram added with thermal noises prior to the second matched filter. Because matched filter cannot eliminate low-frequency components inherent in the flicker noises of spike-like sharp peaks randomly riding on LC-MS-MS chromatograms, efficient peak S/N ratio improvement cannot be accomplished using one-step or consecutive matched filter procedures to process LC-MS-MS chromatograms. In contrast, when the match-filtered LC-MS-MS chromatogram is conditioned with the multiplication alteration prior to the second matched filter, much better efficient ratio improvement is achieved. The noise frequency spectrum of match-filtered chromatogram, which originally contains only low-frequency components, is altered to span a boarder range with multiplication operation. When the frequency range of this modified noise spectrum shifts toward higher frequency regime, the second matched filter, working as a low-pass filter, is able to provide better filtering efficiency to obtain higher peak S/N ratios. Real LC-MS-MS chromatograms containing random spike-like peaks, of which peak S/N ratio improvement is less than four times with two consecutive matched filters typically, are remedied to accomplish much better ratio enhancement approximately 16-folds when the noise frequency spectrum is modified between two matched filters.

Parametric studies of matched filters to enhance the signal-to-noise ratios of LC-MS-MS peaks.

Chromatographic parameters of reference signals employed in matched filter methods have been studied using numerical experiments to improve the signal-to-noise (S/N) ratios of small liquid chromatography (LC) peaks obtained with electrospray tandem mass spectrometers (MS-MS). These parameters include the width, shape, and S/N ratios of chromatographic peaks used as the reference signal profiles. Our results show the effect of reference peak widths on improving the S/N ratio of chromatographic peaks; the influence of reference peak shapes is negligible. To verify simulation results, various reference signals, including analyte peaks of high concentration standards, internal standard peaks, and artificial Gaussian peaks of different widths, have been employed to enhance signal peaks on real liquid chromatography-tandem mass spectrometry (LC-MS-MS) chromatograms via matched filter methods. Our experimental results demonstrate that the S/N ratio enhancement of chromatographic peaks agree with the simulation predictions. These findings, therefore, suggest that regardless of peak shape, a well-smooth peak with a width close to that of the analyte peak is an adequate reference signal, when matched filter methods are used to improve LC-MS-MS chromatograms. Nevertheless, all methods processed LC-MS-MS peaks in this study do not achieve the ideal improvement ratios estimated with simulation results. We attribute this deficiency to spike-like noise, which have considerable low frequency components riding on LC-MS-MS chromatograms. Matched filtering, which works as a low-pass filter in the frequency domain, cannot effectively eliminate low frequency flicker noise contributed by these spikes. In addition, simple median filtering does not provide adequate improvement despite being able to smooth out most spikes in the chromatograms.

Gardenia herbal active constituents: applicable separation procedures.

Gardenia herb has been used as alternative drug for thousand years. They may provide therapeutic or cause toxic effect. Recently, large scale of biological screen, phytochemical separation, isolation, and identification were widely performed. Quality control of the active ingredients should be concern for the application of Gardenia herbs. Many systems have been developed for the determination of herbal ingredients. This article reviews some of the plants and their active constituents that have been used for medicinal applications. The sample preparation, separation, and determination of Gardenia herbal ingredients were discussed. Based on the separation, the method of gas chromatography, liquid chromatography, and capillary electrophoresis were also discussed.