Publications by authors named "Zhimin Cao"

26 Publications

  • Page 1 of 1

Noninvasive detection of human dehydroepiandrosterone, progesterone and testosterone using LC-MS/MS revealed effects of birth control pills/devices and body weight on ovulatory prediction.

J Chromatogr B Analyt Technol Biomed Life Sci 2021 Apr 21;1174:122716. Epub 2021 Apr 21.

Wadsworth Center, New York State Department of Health, Albany, NY, United States; Department of Pathology, Upstate Medical University, Syracuse, NY, United States. Electronic address:

Liquid chromatography-tandem mass spectrometry (LC-MS/MS) has been increasingly used to measure steroids in human saliva. We studied the performance of a conventional LC-MS/MS for measuring dehydroepiandrosterone (DHEA), testosterone and progesterone in human saliva. These three steroids were co-extracted by liquid-liquid extraction and derivatized. Derivatives were resolved on a C18 column and quantified using an LC-MS/MS (AB Sciex API 2000) instrument. The assay's limits of quantification were 0.03 ng/mL for all three steroids. Inter-assay coefficients of variation were 16.6-18.8% (DHEA), 12.0-15.8% (testosterone), and 12.7-19.3% (progesterone). Assay linearity analysis showed R of 0.9926, 0.9750 and 0.9949 for DHEA, testosterone and progesterone, respectively. No carry-over between samplings was observed. An ion-enhancement effect of 11.6% for DHEA determination and ion-suppression effects of 13.9% and 20.7% for analysis of progesterone and testosterone, respectively, were determined. No interferences by 9 steroid analogs were detected. Spiked recoveries were 85.5% (DHEA), 86.5% (testosterone), and 92.6% (progesterone). Comparison with laboratory developed test (LDT)-LC-MS/MS methods by other New York State Department of Health certified laboratories revealed R = 0.9425 (DHEA, LC-MS/MS = 1.0267 LDT + 21.989), R = 0.9849 (testosterone, LC-MS/MS = 0.9447 LDT + 9.8037), and R = 0.9736 (progesterone, LC-MS/MS = 1.1196 LDT + 0.0985). Reference intervals for the 3 steroids in saliva for young males and females were estimated. Results of intra-individual salivary progesterone analysis indicated that caution should be exercised when using progesterone concentrations in predicting ovulation for females who are under treatment with birth control pills/devices or has body a weight of > 90 kg.
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http://dx.doi.org/10.1016/j.jchromb.2021.122716DOI Listing
April 2021

Resistance To First-Line Antituberculosis Drugs And Prevalence Of Mutations In Clinical Isolates Of From Zunyi, Guizhou Province Of China.

Infect Drug Resist 2019 30;12:3093-3102. Epub 2019 Sep 30.

Tuberculosis Division, Department of Respiratory and Critical Care Medicine, Affiliated Hospital of Zunyi Medical University, Zunyi, Guizhou 563003, People's Republic of China.

Background: China is one of the high-burden countries for multidrug-resistant tuberculosis (MDR-TB), and pyrazinamide is one of the anti-TB drugs used for the shorter MDR-TB treatment regimen. The aim of this study was to determine the correlation between gene mutations and resistance to four first-line anti-TB drugs as well as treatment history in clinical isolates of .

Patients And Methods: clinical isolates were collected from 318 in-patients with smear-positive TB between October 2008 and September 2016 at a major hospital in Zunyi, Guizhou Province of China, and used for drug susceptibility testing against four first-line anti-TB drugs. Genomic DNA extracted from clinical isolates was used for PCR amplification and DNA sequencing of the gene.

Results: Among 318 clinical isolates, 129 (40.6%), 170 (53.5%), 66 (20.8%) and 109 (34.3%) were resistant to rifampicin, isoniazid, ethambutol and streptomycin respectively. In addition, 124 clinical isolates were MDR-TB and 71.8% of them were previously treated cases. Sequencing results showed that 46.8% of MDR-TB and 2.2% of drug susceptible isolates harbored a mutation, and 52 types of mutations were detected from 64 isolates. The prevalence of mutations in isolates resistant to first-line anti-TB drugs and previously treated TB cases was significantly higher than that in drug-susceptible isolates and new cases of TB.

Conclusion: High prevalence of mutations in clinical isolates of from Zunyi, Guizhou Province of China, is correlated with resistance to four first-line anti-TB drugs, MDR-TB and previously treated TB cases.
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http://dx.doi.org/10.2147/IDR.S222943DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6777635PMC
September 2019

Fluctuations in progesterone moderate the relationship between daily mood and alcohol use in young adult women.

Addict Behav 2020 02 15;101:106146. Epub 2019 Oct 15.

University at Albany, State University of New York, Psychology Department, 1400 Washington Avenue, Albany, NY 12222, United States; Wadsworth Center, New York State Department of Health, Albany, NY 12201, United States.

Background: Research has demonstrated associations between hormonal fluctuations during the menstrual cycle and women's alcohol use. This association has been explained by mood changes that, for some women, accompany decreasing levels of progesterone during the menstrual cycle, particularly during the late luteal/premenstrual phase. The current study examined whether participants' daily ratings of mood interact with changing levels of progesterone to predict alcohol use.

Method: Young adult women attended two sessions scheduled two weeks apart, during which they completed questionnaires and provided salivary samples for the assay of progesterone levels. In the intervening two weeks, participants completed daily logs of their mood, alcohol use, and menses. Ordered Generalized Linear Mixed Models assessed the effects of daily mood (examined as both a within- and between-subject variable) on the likelihood of drinking, as a function of menstrual cycle phase and changes in progesterone across the two weeks.

Results: One standard deviation increase in progesterone corresponded to a 1.61 decrease in the odds of drinking. This main effect was moderated by daily mood. Women were more likely to drink during a decrease in progesterone on days they rated their mood as negative, whereas during an increase in progesterone they were more likely to drink on days they reported a positive mood. Between-subject analyses showed that women who reported lower overall mood during the two-week period were more likely to drink with an increase in progesterone and less likely with a decrease.

Conclusions: Women's likelihood to drink increased when they experienced negative mood in the context of decreasing levels of progesterone, whereas the negative-mood/drinking association was mitigated among those with increasing levels of progesterone. However, compared to women who on average had an overall more positive mood, women with an overall lower mood (and corresponding higher levels of depression and anxiety at baseline) did not experience the protective effects of rising progesterone levels on drinking.
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http://dx.doi.org/10.1016/j.addbeh.2019.106146DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6876695PMC
February 2020

Impact of testosterone assay standardization efforts assessed via accuracy-based proficiency testing.

Clin Biochem 2019 Jun 28;68:37-43. Epub 2019 Mar 28.

Centers for Disease Control and Prevention, Atlanta, GA, United States of America. Electronic address:

Background: We reported observations on analytical performance in testosterone measurements of various methods/assays from the study carried out using accuracy-based proficiency testing (PT) during 2012-2013. In 2016, we re-evaluated analytical performance of testosterone assays using accuracy-based PT to assess effectiveness of CDC efforts toward standardization.

Methods: Five single-donor human serum samples from female and male adult donors were analyzed for testosterone by New York State Department of Health-certified clinical laboratories using 16 immunoassays and LC-MS/MS methods. Target values were determined using the CDC reference measurement procedure.

Results: Testosterone targets for the 5 samples were 43.5, 160, 294, 457, and 534 ng/dL. The biases of individual result of the 65 participant laboratories against the target for each sample were calculated. Of participants, 87.7% had ≥4 of the 5 results within the minimum allowable total error limits (± 25.1%), a 14.7% increase from the previous study. The improved PT scores were attributed to better analytical accuracy and precision, and laboratories' selection of more accurate assays/methods.

Conclusions: Improved analytical accuracy and precision for testosterone assays were demonstrated over a 3.5-year period after the first CDC-directed accuracy-based proficiency testing. Additional effort is needed to improve accuracy/precision of measurements, especially at low concentrations.
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http://dx.doi.org/10.1016/j.clinbiochem.2019.03.014DOI Listing
June 2019

Identification of novel miRNAs and their target genes from Populus szechuanica infected with Melampsora larici-populina.

Mol Biol Rep 2019 Jun 11;46(3):3083-3092. Epub 2019 Mar 11.

College of Forestry, Northwest A&F University, Yangling, Shaanxi, 712100, China.

Two novel miRNAs were selected from a pre-constructed RNA library of Populus szechuanica infected with the foliar rust fungus Melampsora larici-populina in order to detect the genes regulated as targets of the miRNAs novel_mir_11 and novel_mir_357. The novel miRNAs were identified from P. szechuanica using stem-loop methods and their precursors were able to fold into a complete stem loop structure. The predicted target genes of the novel miRNAs were verified with RNA ligase-mediated 5' rapid amplification of cDNA ends (RLM-5'RACE). The full-length sequences of target genes, RPM1 and RPS2/5, in P. szechuanica were obtained through rapid amplification of cDNA ends (RACE) and officially named PsRPM1 and PsRPS2/5. These genes contain nucleotide binding site-leucine-rich repeats (NBS-LRR) domains typical of resistance genes. The expression levels of miRNAs and their target genes in different periods post infection were analysed with quantitative real-time PCR (qRT-PCR). After infection with the foliar rust fungus, the expression levels of the novel miRNAs and their target genes were dynamic. Both novel_mir_11 and novel_mir_357 negatively regulated the expression of their target genes. In this study, the regulatory effects of two novel miRNAs through their target genes were characterized to provide further mechanistic information regarding the interaction between Populus and a foliar rust fungus. Results of this study improve our understanding of the defence response mechanisms of Populus and will stimulate future work to characterize strategies to prevent and control Populus diseases.
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http://dx.doi.org/10.1007/s11033-019-04746-2DOI Listing
June 2019

Noninvasive determination of human cortisol and dehydroepiandrosterone sulfate using liquid chromatography-tandem mass spectrometry.

Anal Bioanal Chem 2019 Feb 5;411(6):1203-1210. Epub 2019 Jan 5.

University at Albany, State University of New York, 1400 Washington Avenue, Albany, NY, 12222, USA.

Liquid chromatography-tandem mass spectrometry (LC-MS/MS) for measurements of steroids in human saliva has garnered increased interest in the area of clinical psychoneuroendocrinological research. However, performance characteristics of LC-MS/MS methods for the analysis of steroids in saliva are limited. Human saliva samples were collected via passive drool. Cortisol and dehydroepiandrosterone sulfate (DHEA-S) in the samples were extracted together, resolved on a C18-A column, and analyzed using tandem mass spectrometry. The LC-MS/MS method had limits of quantitation of 0.03 and 0.06 ng/mL for DHEA-S and cortisol, respectively. Method evaluations showed coefficient variation (%CV) of inter-assay ranging 4.6-17.9% for DHEA-S and cortisol, recoveries of 102.4-109.5% for DHEA-S and 94.6-98.3% for cortisol, and assay linearity with R = 0.9964 for DHEA-S (1.0-25.0 ng/mL) and R = 0.997 (1.0-25.0 ng/mL) for cortisol. No cross contamination among samples was observed. Human saliva showed 20% and 18% ion enhancement effect for DHEA-S and cortisol assay, respectively. No interference by ten common steroids was detected. Regression analysis of method comparisons with laboratory-developed test (LDT) method revealed R = 0.9688 (LC-MS/MS = 0.9665 LDT-LC-MS/MS - 0.7355) for cortisol, and R = 0.9039 (LC-MS/MS = 1.0173 LDT-LC-MS/MS + 3.6797) for DHEA-S. Reference ranges for young adults were determined to be 0.3-5.9 ng/mL for females and 0.1-5.6 ng/mL for males for salivary cortisol, and 0.6-7.4 ng/mL for females and 0.6-10.1 ng/mL for males for salivary DHEA-S. An LC-MS/MS method for quantifying cortisol and DHEA-S in human saliva was developed and validated for clinical and psychoneuroendocrinological research that require noninvasive means of measuring these hormones.
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http://dx.doi.org/10.1007/s00216-018-1549-xDOI Listing
February 2019

Liquid chromatography-tandem mass spectrometry analysis of 17-hydroxyprogesterone in dried blood spots revealed matrix effect on immunoassay.

Anal Bioanal Chem 2019 Jan 20;411(2):395-402. Epub 2018 Nov 20.

New York State Department of Health, Wadsworth Center, Empire State Plaza, Albany, NY, USA.

Immunoassays for measuring 17-hydroxyprogesterone (17-OHP) produce high rates of false positives that impact the identification of congenital adrenal hyperplasia (CAH) in neonates. A confirmatory test with high analytical specificity employing liquid chromatography-tandem mass spectrometry (LC-MS/MS) methodology is needed in newborn screening for CAH. 17-OHP and cortisol were extracted from dried blood spot (DBS) samples, resolved on a C18 column, and measured using tandem mass spectrometry. The results were compared with those determined using the AutoDELFIA immunoassay. The LC-MS/MS method had a limit of quantitation of 10.0 and 5.0 ng/mL for 17-OHP and cortisol, respectively. The method characteristics showed coefficient variation (%CV) ≤ 11.9% for both 17-OHP and cortisol, recoveries ranging from 83.1 to 101.5% for 17-OHP and from 95.1 to 102.8% for cortisol, and linearity with R = 0.9994 for 17-OHP and R = 0.9996 for cortisol, clinical sensitivity of 100.0% and a specificity of 96.4% as obtained by receiver operating characteristic analysis on 45 patient samples when 17-OHP > 39.1 ng/mL was selected as the cutoff value. Comparison between the LC-MS/MS and the AutoDELFIA immunoassay methods revealed a poor correlation for patient DBS samples (R = 0.6784); however, an excellent correlation was obtained for QC and proficiency test (PT) DBS samples (R = 0.9797). The LC-MS/MS method produced reliable results for 17-OHP and cortisol for the diagnosis of CAH. The AutoDELFIA immunoassay appears to be subject to matrix effects in the analysis for 17-OHP in DBS patient samples. The DBS samples of non-patient origin may not be suitable for assessing analytical accuracy of immunoassays.
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http://dx.doi.org/10.1007/s00216-018-1449-0DOI Listing
January 2019

Stress responding and stress-related changes in cue reactivity in heavy smokers, problem gamblers, and healthy controls.

Addict Biol 2020 03 13;25(2):e12687. Epub 2018 Nov 13.

University at Albany, State University of New York, Albany, New York.

Addictions, both substance and behavioral, have been conceptualized as involving similar biopsychosocial processes with different opportunistic expressions. A maladaptive stress response in combination with craving or urges to engage in the addictive behavior may be among the underlying factors common to behavioral and substance addictions. The current study compared the neuroendocrine (cortisol) and subjective responses to stress of gamblers and smokers to healthy controls. We assessed if participants responded differently to smoking or gambling cues before and after a psychosocial stressor. To this end, the subjective urges/cravings of all participants were measured in response to smoking or gambling cues versus neutral cues, once under normal conditions and again after exposure to a stressor. Salivary cortisol was measured prior to, immediately following, and 10 minutes after conclusion of the stressor. Smokers and gamblers showed a similar blunted cortisol response to the acute stressor that differed from the control group's response. Following a stressor, subjective craving in smokers increased whereas gamblers' urges decreased. In smokers, a blunted cortisol and subjective stress response were related to increased urges. In contrast, for gamblers, changes in cortisol levels were unrelated to urges, and higher subjective stress was associated with decreased urges. In conclusion, individuals with a substance and a behavioral addiction share common patterns of reactivity to stress. However, while the stressor enhanced cue-related craving in smokers, it generally had the opposite effect on gamblers. Further research is necessary to elucidate the complicated patterns of similarities and differences that underlie substance and behavioral addictions.
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http://dx.doi.org/10.1111/adb.12687DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6513727PMC
March 2020

Measurement of human serum unconjugated estriol without derivatization using liquid chromatography-tandem mass spectrometry candidate reference method and compared with two immunoassays.

Anal Bioanal Chem 2018 Sep 14;410(24):6257-6267. Epub 2018 Jul 14.

Wadsworth Center, New York State Department of Health, Albany, NY, 12201-0509, USA.

A candidate reference measurement procedure (RMP) for measurement of unconjugated estriol in human serum has been developed and validated. The proposed method is highly reliable and uses isotope dilution coupled with liquid chromatography-tandem mass spectrometry (ID-LC-MS/MS) and requires no derivatization. An appropriate amount of serum was accurately weighed and spiked with an isotopically labeled internal standard. Unconjugated estriol and its internal standard were extracted from serum matrix using liquid-liquid extraction prior to reversed-phase LC-MS/MS. Calibrator bracketing was used to give higher specificity and accuracy for assigning serum level. The accuracy of the candidate RMP was validated by split-sample comparison to established RMPs. The lowest limit of detection (LLoD) and lowest limit of quantification (LLoQ) for developed RMP was estimated to be 0.14 nmol/L and 0.35 nmol/L, respectively. Both intra- and inter-assay imprecisions were ≤2.19% at 1.39, 17.34 and 69.35 nmol/L, respectively. Recoveries were 98.54% to 100.34% and linear response ranged from 0.35 to 173.38 nmol/L. No interference was observed. Biases were 5.6% and 2.8% against the targets of RELA2015A (3.87 nmol/L) and RELA2015B (40.62 nmol/L), respectively. Moreover, the candidate RMP was successfully applied to measure level of unconjugated estriol in serum samples of pregnant women (n = 3) and compared with two immunoassays in clinical laboratory. Our developed method is simple, accurate, and can be used as a candidate RMP to determine total unconjugated estriol level in human serum. Further improvement of certain immunoassays in accuracy and precision is needed. Graphical abstract Selected ion chromatograms by LC-MS/MS using a C18 column for uE from a serum sample.
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http://dx.doi.org/10.1007/s00216-018-1236-yDOI Listing
September 2018

Quantitative trait locus mapping under irrigated and drought treatments based on a novel genetic linkage map in mungbean (Vigna radiata L.).

Theor Appl Genet 2017 Nov 22;130(11):2375-2393. Epub 2017 Aug 22.

Key Laboratory of Crop Germplasm Resources and Utilization, Ministry of Agriculture, The National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.

Key Message: A novel genetic linkage map was constructed using SSR markers and stable QTLs were identified for six drought tolerance related-traits using single-environment analysis under irrigation and drought treatments. Mungbean (Vigna radiata L.) is one of the most important leguminous food crops. However, mungbean production is seriously constrained by drought. Isolation of drought-responsive genetic elements and marker-assisted selection breeding will benefit from the detection of quantitative trait locus (QTLs) for traits related to drought tolerance. In this study, we developed a full-coverage genetic linkage map based on simple sequence repeat (SSR) markers using a recombinant inbred line (RIL) population derived from an intra-specific cross between two drought-resistant varieties. This novel map was anchored with 313 markers. The total map length was 1010.18 cM across 11 linkage groups, covering the entire genome of mungbean with a saturation of one marker every 3.23 cM. We subsequently detected 58 QTLs for plant height (PH), maximum leaf area (MLA), biomass (BM), relative water content, days to first flowering, and seed yield (Yield) and 5 for the drought tolerance index of 3 traits in irrigated and drought environments at 2 locations. Thirty-eight of these QTLs were consistently detected two or more times at similar linkage positions. Notably, qPH5A and qMLA2A were consistently identified in marker intervals from GMES5773 to MUS128 in LG05 and from Mchr11-34 to the HAAS_VR_1812 region in LG02 in four environments, contributing 6.40-20.06% and 6.97-7.94% of the observed phenotypic variation, respectively. None of these QTLs shared loci with previously identified drought-related loci from mungbean. The results of these analyses might facilitate the isolation of drought-related genes and help to clarify the mechanism of drought tolerance in mungbean.
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http://dx.doi.org/10.1007/s00122-017-2965-6DOI Listing
November 2017

Accuracy-based proficiency testing for testosterone measurements with immunoassays and liquid chromatography-mass spectrometry.

Clin Chim Acta 2017 Jun 10;469:31-36. Epub 2017 Mar 10.

Centers for Disease Control and Prevention, Atlanta, GA, United States. Electronic address:

Background: Accurate testosterone measurements are needed to correctly diagnose and treat patients. Proficiency Testing (PT) programs using modified specimens for testing can be limited because of matrix effects and usage of non-reference measurement procedure (RMP)-defined targets for evaluation. Accuracy-based PT can overcome such limitations; however, there is a lack of information on accuracy-based PT and feasibility of its implementation in evaluation for testosterone measurements.

Methods: Unaltered, single-donor human serum from 2 male and 2 female adult donors were analyzed for testosterone by 142 NYSDH-certified clinical laboratories using 16 immunoassays and LC-MS/MS methods. Testosterone target values were determined using an RMP.

Results: The testosterone target concentrations for the 4 specimens were 15.5, 30.0, 402 and 498ng/dl. The biases ranged from -17.8% to 73.1%, 3.1% to 21.3%, -24.8% to 8.6%, and -22.1% to 6.8% for the 4 specimens, respectively. Using a total error target of ±25.1%, which was calculated using the minimum allowable bias and imprecision, 73% of participating laboratories had ≥3 of the 4 results within these limits.

Conclusions: The variability in total testosterone measurements can affect clinical decisions. Accuracy-based PT can significantly contribute to improving testosterone testing by providing reliable data on accuracy in patient care to laboratories, assay manufacturers, and standardization programs.
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http://dx.doi.org/10.1016/j.cca.2017.03.010DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5695555PMC
June 2017

Development of a high-density genetic linkage map and identification of flowering time QTLs in adzuki bean (Vigna angularis).

Sci Rep 2016 12 23;6:39523. Epub 2016 Dec 23.

Key Laboratory of Crop Genetics and Breeding of Hebei Province; Institute of Cereal and Oil Crops, Hebei Academy of Agricultural and Forestry Sciences, Shijiazhuang 050035, China.

A high-density linkage map is crucial for the identification of quantitative trait loci (QTLs), positional cloning, and physical map assembly. Here, we report the development of a high-density linkage map based on specific length amplified fragment sequencing (SLAF-seq) for adzuki bean and the identification of flowering time-related QTLs. Through SLAF library construction and Illumina sequencing of a recombinant inbred line (RIL) population, a total of 4425 SLAF markers were developed and assigned to 11 linkage groups (LGs). After binning the SLAF markers that represented the same genotype, the final linkage map of 1628.15 cM contained 2032 markers, with an average marker density of 0.80 cM. Comparative analysis showed high collinearity with two adzuki bean physical maps and a high degree of synteny with the reference genome of common bean (Phaseolus vulgaris). Using this map, one major QTL on LG03 and two minor QTLs on LG05 associated with first flowering time (FLD) were consistently identified in tests over a two-year period. These results provide a foundation that will be useful for future genomic research, such as identifying QTLs for other important traits, positional cloning, and comparative mapping in legumes.
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http://dx.doi.org/10.1038/srep39523DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5180193PMC
December 2016

Structural Characterization of Oligochitosan Elicitor from Fusarium sambucinum and Its Elicitation of Defensive Responses in Zanthoxylum bungeanum.

Int J Mol Sci 2016 Dec 10;17(12). Epub 2016 Dec 10.

Department of Forest Pathology, College of Forestry, Northwest A&F University, Yangling 712100, Shaanxi, China.

Oligosaccharide elicitors from pathogens have been shown to play major roles in host plant defense responses involving plant-pathogen chemoperception and interaction. In the present study, chitosan and oligochitosan were prepared from pathogen , and their effects on infection of stems were investigated. Results showed that oligochitosan inhibited the infection of the pathogen, and that the oligochitosan fraction with a degree of polymerization (DP) between 5 and 6 showed the optimal effect. Oligochitosan DP5 was purified from fraction DP5-6 and was structurally characterized using electrospray ionization mass spectrometry, Fourier transform infrared spectroscopy, and nuclear magnetic resonance spectroscopy. Oligochitosan DP5 showed significant inhibition against the infection of the pathogenic fungi on host plant stems. An investigation of the mechanism underlying this effect showed that oligochitosan DP5 increased the activities of defensive enzymes and accumulation of phenolics in host . These results suggest that oligochitosan from pathogenic fungi can mediate the infection of host plants with a pathogen by acting as an elicitor that triggers the defense system of a plant. This information will be valuable for further exploration of the interactions between the pathogen and host plant .
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http://dx.doi.org/10.3390/ijms17122076DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5187876PMC
December 2016

A deep sequencing analysis of transcriptomes and the development of EST-SSR markers in mungbean (Vigna radiata).

J Genet 2016 Sep;95(3):527-35

Key Laboratory of Crop Genetics and Breeding of Hebei Province, Institute of Cereal and Oil Crops, Hebei Academy of Agricultural and Forestry Sciences, Shijiazhuang 050035, People's Republic of

Mungbean (Vigna radiata L. Wilczek) is one of the most important leguminous food crops in Asia. We employed Illumina paired-end sequencing to analyse transcriptomes of three different mungbean genotypes. A total of 38.3-39.8 million pairedend reads with 73 bp lengths were generated. The pooled reads from the three libraries were assembled into 56,471 transcripts. Following a cluster analysis, 43,293 unigenes were obtained with an average length of 739 bp and N50 length of 1176 bp. Of the unigenes, 34,903 (80.6%) had significant similarity to known proteins in the NCBI nonredundant protein database (Nr), while 21,450 (58.4%) had BLAST hits in the Swiss-Prot database (E-value<10⁻⁵). Further, 1245 differential expression genes were detected among three mungbean genotypes. In addition, we identified 3788 expressed sequence tag-simple sequence repeat (EST-SSR) motifs that could be used as potential molecular markers. Among 320 tested loci, 310 (96.5%) yielded amplification products, and 151 (47.0%) exhibited polymorphisms among six mungbean accessions. These transcriptome data and mungbean EST-SSRs could serve as a valuable resource for novel gene discovery and the marker-assisted selective breeding of this species.
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http://dx.doi.org/10.1007/s12041-016-0663-9DOI Listing
September 2016

The Effect and Action Mechanisms of Oligochitosan on Control of Stem Dry Rot of Zanthoxylum bungeanum.

Int J Mol Sci 2016 Jun 30;17(7). Epub 2016 Jun 30.

Department of Chemical Processing of Forest Products, College of Forestry, Northwest A&F University, Yangling 712100, China.

In this report, the effects of two oligochitosans, i.e., oligochitosan A (OCHA) and oligochitosan B (OCHB), on control of dry rot of Zanthoxylum bungeanum (Z. bungeanum) caused by Fusarium sambucinum (F. sambucinum) were evaluated. First, both oligochitosans show desirable ability to decrease the infection of F. sambucinum. Second, the oligochitosans strongly inhibit the radial colony and submerged biomass growth of F. sambucinum. Lastly, these oligochitosans are capable of increasing the activities of phenylalanine ammonia lyase (PAL), polyphenoloxidase (PPO) and peroxidase (POD) significantly, as well as enhancing the content of total phenolics in Z. bungeanum stems. These findings indicate that the protective effects of OCHA and OCHB on Z. bungeanum stems against dry rot may be associated with the direct fungitoxic function against pathogen and the elicitation of biochemical defensive responses in Z. bungeanum stems. The outcome of this report suggests that oligochitosans may serve as a promising natural fungicide to substitute, at least partially, for synthetic fungicides in the disease management of Z. bungeanum.
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http://dx.doi.org/10.3390/ijms17071044DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4964420PMC
June 2016

Spatial distribution and pollution assessment of heavy metals in the surface sediments of the Bohai and Yellow Seas.

Mar Pollut Bull 2016 Sep 4;110(1):596-602. Epub 2016 Jun 4.

Key Laboratory of Marine Hydrocarbon Resources and Environmental Geology, Ministry of Land and Resources, Qingdao Institute of Marine Geology, China Geological Survey, Qingdao 266071, China. Electronic address:

A total of 141 surface sediments were collected and analyzed for their geochemistry, total organic carbon, and grain size to assess the heavy metal pollution in the Bohai and Yellow Seas. The enrichment factor (EF) and geoaccumulation index (Igeo) of Cu, Pb, Zn, Cr, Cd, Ni, As, and Hg were calculated to assess anthropogenic contamination, and the results suggest that moderate Pb, Cd, and As contamination occurs in the study area. Sediment quality guidelines were applied to assess the adverse biological effects of these metals. The spatial distribution of the mean Effects Range-Median quotient for the vast majority of the study area is between 0.1 and 0.5, indicating low impact and potential negative biological effects. Multivariate analysis indicates that Cu, Pb, Zn, Cr, and Ni resulted primarily from lithogenic sources, whereas As, Cd, and Hg were mainly attributed to anthropogenic sources.
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http://dx.doi.org/10.1016/j.marpolbul.2016.05.079DOI Listing
September 2016

Genome-wide expression profiling of microRNAs in poplar upon infection with the foliar rust fungus Melampsora larici-populina.

Authors:
Min Chen Zhimin Cao

BMC Genomics 2015 Sep 15;16:696. Epub 2015 Sep 15.

College of Forestry, Northwest A & F University, Yangling, Shaanxi, 712100, People's Republic of China.

Background: MicroRNAs (miRNAs) are small non-coding RNAs that regulate the gene expression of target mRNAs involved in plant growth, development, and abiotic stress and pathogen responses. Previous studies have reported miRNAs in Populus that respond to abiotic stresses, such as cold, heat, drought, flooding, high salt and mechanical stress. However, little is known about the regulatory roles of these molecules in the Populus response to the stress of foliar rust fungal infection. Here, we identified the miRNA profiles of Populus after inoculation with Melampsora larici-populina using high-throughput sequencing and bioinformatics analysis. Quantitative real-time PCR (qRT-PCR) was used to validate the expression levels of 10 miRNAs.

Results: A total of 90 known miRNAs belonging to 42 families and 378 novel miRNAs were identified from three small-RNA libraries of Populus szechuanica infected with M. larici-populina isolates Sb052 and Th053 and a control. Comparative analysis revealed that the expression of 38 known miRNAs and 92 novel miRNAs in P. szechuanica after infection with different rust fungus isolates showed significant differences, and more miRNAs were suppressed during rust infection. Among the differentially expressed miRNAs, 7 known and 20 novel miRNAs were relevant to the rust fungus infection, and according to KEGG (Kyoto Encyclopaedia of Genes and Genomes) pathway analysis, these miRNAs primarily regulate genes encoding disease-resistance proteins, serine/threonine protein kinases, transcription factors, and related proteins. QRT-PCR analysis indicated that most miRNAs were up-regulated in the Sb052 library and down-regulated in the Th053 library at 48 h post-inoculation (hpi).

Conclusions: These results demonstrate that the expression of miRNAs was altered in poplar under stress associated with M. larici-populina infection, and different temporal dynamics were observed in incompatible and compatible libraries. These findings suggest important roles for miRNA regulation in Populus upon infection with foliar rust fungus.
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http://dx.doi.org/10.1186/s12864-015-1891-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4570220PMC
September 2015

Measurement of unconjugated estriol in serum by liquid chromatography-tandem mass spectrometry and assessment of the accuracy of chemiluminescent immunoassays.

Clin Chem 2014 Jan 19;60(1):260-8. Epub 2013 Nov 19.

Department of Laboratory Medicine, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China;

Background: Unconjugated estriol (uE3) is routinely analyzed in clinical laboratories as risk assessment for Down syndrome. Immunoassays of various types are the most commonly used methods. The accuracies of RIAs and ELISAs for uE3 have been questioned, and to date there have been no independent studies investigating the accuracy of the relatively new chemiluminescent immunoassays. We developed and validated a liquid chromatography-tandem mass spectrometry (LC-MS/MS) method for uE3 measurements in serum.

Methods: Serum samples from patients in the second trimester of pregnancy were used, and uE3 concentrations were measured by LC-MS/MS and the Beckman Coulter Access® 2 and Siemens IMMULITE 2000 automatic chemiluminescent immunoassay analyzers.

Results: The LC-MS/MS method was validated and showed limit of detection 0.05 ng/mL; limit of quantification 0.2 ng/mL; linearity of response to 32 ng/mL; total imprecision of 16.2%, 10.4%, and 8.2% for uE3 at 1.10, 4.18, and 8.32 ng/mL, respectively; and analytical recoveries of 95.9%-104.2%. ANOVA of the correlation for LC-MS/MS results vs chemiluminescent immunoassays results showed R(2) = 0.9678 (Access 2 = 0.9305 LC-MS/MS + 0.2177, Sy|x = 0.1786, P < 0.0001), and R(2) = 0.9663 (IMMULITE 2000 = 0.8849 LC-MS/MS - 0.0403, Sy|x = 0.1738, P < 0.0001). Bland-Altman plots of uE3 results revealed concentration-dependent immunoassay biases. Mock risk analysis for Down syndrome showed no apparent difference in the risk assessment outcomes if the adjusted method-specific multiples of the median were used, and the assay imprecision was <10% CV.

Conclusions: Standardization of immunoassay methods for uE3 analysis is needed to improve the accuracy of the measurements.
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http://dx.doi.org/10.1373/clinchem.2013.212126DOI Listing
January 2014

Eighty-year sedimentary record of heavy metal inputs in the intertidal sediments from the Nanliu River estuary, Beibu Gulf of South China Sea.

Environ Pollut 2011 Jan 18;159(1):92-99. Epub 2010 Oct 18.

First Institute of Oceanography, State Oceanic Administration, Qingdao 266061, China.

210Pb analysis in the sediment core C11 was used to reconstruct the historical fluxes of Hg, Cu, Pb, Zn, Cd, Cr and As in the Nanliu River estuary during the last ∼81 year. The 210Pbxs-derived sedimentation rates, molar C/N ratios, enrichment factors and excess fluxes indicated that the natural inputs prevailed till the early 1990s. When the erosion related to land-use modifications enhanced, it promoted higher accumulation rates of the sedimentary material. In the recent sediments they were found a moderate enrichment of Cd and Hg (maximum 3.5- and 2.8-fold corresponding to the local background levels, respectively) and a slight enrichment of Cr, Zn, As and Pb (maximum 1.3-, 1.3-, 1.3- and 1.2-fold, respectively). The excess metal fluxes also showed a consistently increasing tread since the early 1990s, which could be associated with the intensive use of phosphate fertilizers and the combustion of fossil fuels derived from human activities.
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http://dx.doi.org/10.1016/j.envpol.2010.09.014DOI Listing
January 2011

Effects of resin or charcoal treatment on fetal bovine serum and bovine calf serum.

Endocr Res 2009 ;34(4):101-8

Laboratory of Molecular Diagnostics, Wadsworth Center for Laboratories and Research, New York State Department of Health, Albany, New York, USA.

Introduction: Charcoal- or resin-stripping of fetal bovine serum (FBS) or bovine calf serum (BCS) intended for supplementation of cell culture media is widely practiced to remove a variety of endogenous compounds, including steroid, peptide, and thyroid hormones. The possibility that stripping removes other biologically relevant factors from serum may not be appreciated.

Methods: In this report, standardized clinical laboratory testing methods were used to assess the effects of resin- and charcoal-stripping on content in FBS and BCS of more than 25 analytes in the sera.

Results And Conclusion: In addition to hormones, the serum constituents affected by stripping are certain vitamins, electrolytes, enzyme activities, and metabolites.
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http://dx.doi.org/10.3109/07435800903204082DOI Listing
January 2010

Are laboratories reporting serum quantitative hCG results correctly?

Clin Chem 2008 Apr;54(4):761-4

Division of Molecular Medicine, Wadsworth Center for Laboratories and Research, New York State Department of Health, Albany, NY 12201-0509, USA.

Background: Human chorionic gonadotropin (hCG) is a heterodimeric glycoprotein hormone that exists in multiple forms. Immunoassays commonly used in clinical laboratories measure intact hCG, total beta hCG (intact hCG + hCG free beta-subunit), and/or hCG free beta-subunit. Measurement of serum concentrations of hCG is useful for confirmation and monitoring of pregnancy, diagnosis of trophoblastic diseases and monitoring of the efficacy of treatment, and prenatal screening. Correctly reporting results for the various forms of hCG is clinically important.

Method: We prepared samples by addition of intact hCG and hCG free beta-subunit to an essentially hCG-free human serum matrix. The samples were analyzed by participant laboratories using various immunoassay methods.

Results: We identified errors in participant reporting of intact hCG results as total beta hCG (9.3%; 22 of 235 laboratories) and total beta hCG as intact hCG (13.1%; 8 of 61 laboratories).

Conclusions: Many factors contribute to the erroneous reporting of hCG results, including (a) the complexity of hCG molecule and confusion of nomenclature on the various forms of hCG; (b) laboratory personnel's lack of awareness of the distinctions of the forms of hCG and failure to recognize the specificity of assays for their measurement; (c) lack of clarity and uniformity in manufacturers' reagent labeling; and (d) most product inserts' lack of information on the specificity of each method to the various forms of hCG.
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http://dx.doi.org/10.1373/clinchem.2007.098822DOI Listing
April 2008

[Genetic diversity of Melampsora larici-populina].

Ying Yong Sheng Tai Xue Bao 2006 Nov;17(11):2102-6

College of Forestry, Northwest Sci-Tech University of Agriculture and Forestry, Yangling 712100, China.

By using ITS - nrDNA-RELP, ITS sequencing, and RAPD molecular marker, this paper studied the genetic diversity of 11 isolates in 5 races of Melampsora larici-populina from different regions. The results indicated that the genetic differentiation of M. larici-populina was correlated to its geographical distribution, which could be grouped into northern and western geographic populations, and the latter could be grouped into high-mountain forest ecologic type (HMF) and western plain ecologic type (WPL). The genetic differentiation of the race was not always corresponded with the pathogenic one. T test manifested that the genetic diversity of the 5 races had no statistic difference in RAPD markers, and the diversity index of HMF was 0.5172, being slightly higher than that of WPL (0.5089). The ITS sequence of ribosome DNA was strictly conservative, and not suitable for the genetic diversity study of M. larici-populina intra-species populations.
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November 2006

Dss1 interaction with Brh2 as a regulatory mechanism for recombinational repair.

Mol Cell Biol 2007 Apr 29;27(7):2512-26. Epub 2007 Jan 29.

Department of Microbiology and Immunology, Cornell University Weill Medical College, 1300 York Avenue, New York, NY 10021, USA.

Brh2, the BRCA2 ortholog in Ustilago maydis, enables recombinational repair of DNA by controlling Rad51 and is in turn regulated by Dss1. Interplay with Rad51 is conducted via the BRC element located in the N-terminal region of the protein and through an unrelated domain, CRE, at the C terminus. Mutation in either BRC or CRE severely reduces functional activity, but repair deficiency of the brh2 mutant can be complemented by expressing BRC and CRE on different molecules. This intermolecular complementation is dependent upon the presence of Dss1. Brh2 molecules associate through the region overlapping with the Dss1-interacting domain to form at least dimer-sized complexes, which in turn, can be dissociated by Dss1 to monomer. We propose that cooperation between BRC and CRE domains and the Dss1-provoked dissociation of Brh2 complexes are requisite features of Brh2's molecular mechanism.
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http://dx.doi.org/10.1128/MCB.01907-06DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1899899PMC
April 2007

De novo biosynthesis and radiolabeling of mammalian digitalis-like factors.

Clin Chem 2004 Mar;50(3):612-20

Department of Pathology and Laboratory Medicine, University of Louisville School of Medicine, Louisville, KY 40292, USA.

Background: Digoxin-like immunoreactive factors (DLIFs) are endogenous mammalian cardenolides with structural features similar to those of the plant-derived digitalis compounds. DLIFs and their structurally related forms (Dh-DLIFs) may serve as effectors of ion-transport activity mediated by their interaction with Na,K-ATPase and thus play a role as a new hormonal axis. Although some evidence implicates the adrenal gland as a tissue source for the DLIFs, little is known about the biosynthetic pathway producing these compounds. We now demonstrate de novo biosynthesis of DLIF by incorporation of radioactive carbon ((14)C) into the structures of both DLIF and Dh-DLIF.

Methods: We used a combination of reversed-phase HPLC techniques to separate the radioactive DLIF components after incorporation of (14)C into their structure by use of either [1,2-(14)C]acetic acid or [4-(14)C]cholesterol as precursors and a Y-1 mouse adrenocortical tumor cell line. We also stimulated and suppressed production of steroidogenesis by use of cAMP analogs and Mevastatin, respectively, to demonstrate the dependence of DLIF production on the cholesterol-dependent biosynthetic pathway. A combination of chromatographic mobility, immunoassays specific for digoxin and dihydrodigoxin, and deglycosylation using 5-sulfosalicylic acid were used to identify the DLIF and Dh-DLIF components.

Results: With cholesterol as precursor, the cells produced DLIF (7.5 mCi/mmol) with a labeling efficiency of 10%, whereas with acetate the cells produced DLIF (72.2 mCi/mmol) with a labeling efficiency of 0.08% of the total DLIF produced. The radiolabeled DLIF and Dh-DLIF molecules had identical chromatographic mobilities and stoichiometric removal of sugars as the previously characterized DLIFs isolated from different mammalian species and tissues. With radioactive cholesterol as precursor, the (14)C was incorporated into the DLIF-genin portion of the compounds and not the sugars. Interestingly, treatment of Y-1 cells with 8-bromoadenosine 3':5'-cAMP to stimulate steroidogenesis did not increase production of DLIF or Dh-DLIF but did increase production of progesterone. Mevastatin (5 micromol), an inhibitor of the enzyme hydroxymethylglutaryl-CoA reductase and thus of cholesterol biosynthesis, gave an 85% decrease in the production of (14)C-DLIF and progesterone, but only a modest 15% decrease in (14)C-Dh-DLIF production.

Conclusions: These data demonstrate that the adrenal cell has the cellular machinery necessary for de novo biosynthesis of DLIF and Dh-DLIF starting from a simple carbon pool and also support the concept that cholesterol is a major precursor of the DLIF compounds. This cell culture model provides a source of radiolabeled DLIF compounds for future experimental work.
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http://dx.doi.org/10.1373/clinchem.2003.022715DOI Listing
March 2004

Immunoassay of estradiol: unanticipated suppression by unconjugated estriol.

Clin Chem 2004 Jan;50(1):160-5

Laboratory of Molecular Diagnostics, Wadsworth Center for Laboratories and Research, New York State Department of Health, Albany, NY, USA.

Background: Accurate measurement of estradiol is important in clinical settings. The quality of laboratory estimations of estradiol may be assessed through external quality-assurance surveys.

Methods: Estradiol was measured by microparticle enzyme immunoassay (MEIA) and other immunoassays. Proficiency testing of medical laboratories was conducted using samples prepared from normal male human serum supplemented with exogenous estradiol and other steroid and nonsteroid hormones, and participant laboratories measured estradiol by a variety of commonly used immunoassay techniques.

Results: The imprecision (CV) for measurement of estradiol [100-300 ng/L (367-1102 pmol/L)] was 1.5 microg/L (>5.2 nmol/L) interfered with the MEIA method, leading to decreased recovery of added estradiol by up to 50%. This suppression in estradiol measurement was prevented by dilution of the specimen before measurement. Addition of unconjugated estriol gave a positive bias in some other immunoassay methods for estradiol. Poor comparability among the immunoassay methods for measurement of estradiol at clinically relevant concentrations [ approximately 60 ng/L (220 pmol/L)] was revealed.

Conclusions: A negative interference of unconjugated estriol with the MEIA method is a source of error for estradiol measurement. Lack of specificity and lack of comparability among immunoassay methods for estradiol may have detrimental effects on medical practice.
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http://dx.doi.org/10.1373/clinchem.2003.023325DOI Listing
January 2004

Estrogen regulates Ah responsiveness in MCF-7 breast cancer cells.

Carcinogenesis 2003 Dec 11;24(12):1941-50. Epub 2003 Sep 11.

Wadsworth Center, New York State Department of Health, Albany, NY 12201-0509, USA.

Cytochrome P450 (CYP)1A1 and CYP1B1, which are under the regulatory control of the aryl hydrocarbon (Ah) receptor (AhR), catalyze the metabolic activation of numerous procarcinogens and the hydroxylation of 17beta-estradiol (E2) at the C-2 and C-4 positions, respectively. There is evidence of cross-talk between estrogen receptor alpha (ERalpha)- and AhR-mediated signaling in breast and endometrial cells. To further examine these interactions, we investigated the short- and long-term effects of E2 exposure on Ah responsiveness in MCF-7 human breast cancer cells. Short-term exposure to 1 nM E2 elevated the ratio of the 4- to 2-hydroxylation pathways of 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD)-induced E2 metabolism and the ratio of the induced CYP1B1 to CYP1A1 mRNA levels, as determined by real-time PCR. Cells maintained long-term (9-12 months) in low-E2 medium progressively lost Ah responsiveness, as indicated by diminished rates of TCDD-induced E2 metabolism and ethoxyresorufin O-deethylase activity, and the reduced expression of the CYP1A1 and CYP1B1 mRNAs and proteins levels. These E2-deprived cells showed elevated levels of ERalpha mRNA, depressed levels of AhR mRNA, and unchanged levels of the AhR nuclear translocator mRNA. Transient transfection studies using a CYP1B1-promoter-luciferase reporter construct showed that reduced CYP1B1 promoter activity in E2-deprived cells could be restored by co-transfection with an AhR expression construct, indicating that AhR expression was limiting in these cells. The reduced Ah responsiveness of E2-deprived cells was reversed by culture for four passages in medium supplemented with 1 nM E2; ERalpha and AhR mRNAs returned to near-normal levels and the inducibility of the CYP1A1 and CYP1B1 mRNAs, proteins, and E2 metabolic activities by TCDD was restored. These studies indicate that the continued presence of estrogen is required to maintain high levels of AhR expression and inducibility of the procarcinogen-bioactivating enzymes, CYP1A1 and CYP1B1, in MCF-7 cells.
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http://dx.doi.org/10.1093/carcin/bgg162DOI Listing
December 2003