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HDPairFinder:A data processing platform for hydrogen/deuterium isotopic labeling-based nontargeted analysis of trace-level amino-containing chemicals in environmental water

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Journal of Environmental Sciences 2024年第2期136卷 583-593页

作者： Tingting Zhao Kristin Carroll caley b.craven Nicholas J.P.Wawryk Shipei Xing Jian Guo Xing-Fang Li Tao Huan Department of Chemistry Faculty of ScienceUniversity of British ColumbiaVancouver Campus2036 Main MallVancouverBritish ColumbiaV6T 1Z1Canada Division of Analytical and Environmental Toxicology Department of Laboratory Medicine and PathologyFaculty of Medicine and DentistryUniversity of AlbertaEdmontonAlberta T6G 2G3Canada

The combination of hydrogen/deuterium(H/D)formaldehyde-based isotopic methyl labeling with solid-phase extraction and high-performance liquid chromatography–high resolution mass spectrometry(HPLC-HRMS)is a powerful analytical solution for nontargeted analysis of trace-level amino-containing chemicals in water samples.Given the huge amount of chemical information generated in HPLC-HRMS analysis,identifying all possible H/Dlabeled amino chemicals presents a significant challenge in data processing.To address this,we designed a streamlined data processing pipeline that can automatically extract H/D-labeled amino chemicals from the raw HPLC-HRMS data with high accuracy and efficiency.First,we developed a cross-correlation algorithm to correct the retention time shift resulting from deuterium isotopic effects,which enables reliable pairing of H-and D-labeled peaks.Second,we implemented several bioinformatic solutions to remove false chemical features generated by in-source fragmentation,salt adduction,and natural13C isotopes.Third,we used a data mining strategy to construct the AMINES library that consists of over 38,000 structure-disjointed primary and secondary amines to facilitate putative compound annotation.Finally,we integrated these modules into a freely available R program,HDPairFinder.R.The rationale of each module was justified and its performance tested using experimental H/D-labeled chemical standards and authentic water samples.We further demonstrated the application of HDPairFinder to effectively extract N-containing contaminants,thus enabling the monitoring of changes of primary and secondary N-compounds in authentic water samples.HDPairFinder is a reliable bioinformatic tool for rapid processing of H/D isotopic methyl labeling-based nontargeted analysis of water samples,and will facilitate a better understanding of N-containing chemical compounds in water.

关键词： Isotope labeling Nontargeted analysis Reactive N-compounds HPLC-HRMS Source water

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Pesticides and trace elements in cannabis:Analytical and environmental challenges and opportunities

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Journal of Environmental Sciences 2019年第11期31卷 82-93页

作者： caley b.craven Nicholas Wawryk Ping Jiang Zhongshan Liu Xing-Fang Li Department of Chemistry Faculty of Science University of Alberta Edmonton AB T6G 2G2 Canada Division of Analytical and Environmental Toxicology Department of Laboratory Medicine and Pathology Faculty of Medicine and DentistryUniversity of Alberta Edmonton AB T6G 2G3 Canada

Cannabis is increasingly used for both medicinal and recreational purposes with an estimate of over 180 million users annually.Canada has recently legalized cannabis use in October 2018,joining several states,in the United States of America (e.g.,Colorado,California,and Oregon) and a few other countries.A variety of cannabis products including dry flowers,edibles,and oil products are widely consumed.With high demand for cannabis products worldwide,the quality of cannabis and its related products has become a major concern for consumer safety.Various guidelines have been set by different countries to ensure the quality,safety,and efficacy of cannabis products.In general,these guidelines require control of contaminants including pesticides,toxic elements,mycotoxins,and pathogens,as well as residual solvents in regard to cannabis oil.Accordingly,appropriate analytical methods are required to determine these contaminants in cannabis products for quality control.In this review,we focus on the current analytical challenges and method development for detection of pesticides and toxic elements in cannabis to meet various guidelines.

关键词： Cannabis QA/QC Contaminants Analytical testing Pesticides Heavy metals Regulations

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New methods for identification of disinfection byproducts of toxicological relevance: Progress and future directions

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Journal of Environmental Sciences 2021年第1期33卷 151-159页

作者： Nicholas J.P.Wawryk caley b.craven Lindsay K.Jmaiff blackstock Xing-Fang Li Division of Analytical and Environmental Toxicology Department of Laboratory Medicine and PathologyFaculty of Medicine and DentistryUniversity of AlbertaEdmontonABT6G 2G3Canada

Disinfection byproducts(DbPs)represent a ubiquitous source of chemical exposure in disinfected water.While over 700 DbPs have been identified,the drivers of toxicity remain poorly understood.Additionally,ever evolving water treatment practices have led to a continually growing list of DbPs.Advancement of analytical technologies have enabled the identification of new classes of DbPs and the quantification of these chemically diverse sets of DbPs.Here we summarize advances in new workflows for DbP analysis,including sample preparation,chromatographic separation with mass spectrometry(MS)detection,and data processing.To aid in the selection of techniques for future studies,we discuss necessary considerations for each step in the strategy.This review focuses on how each step of a workflow can be optimized to capture diverse classes of DbPs within a single method.Additionally,we highlight new MS-based approaches that can be powerful for identifying novel DbPs of toxicological relevance.We discuss current challenges and provide perspectives on future research directions with respect to studying new DbPs of toxicological relevance.As analytical technologies continue to advance,new strategies will be increasingly used to analyze complex DbPs produced in different treatment processes with the aim to identify potential drivers of toxicity.

关键词： Water disinfection byproducts(DbPs) Emerging contaminants Mass spectrometry Chromatography Nontargeted analysis Toxicity drivers

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Determination of eighty-two pesticides and application to screening pesticides in cannabis growing facilities

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Journal of Environmental Sciences 2021年第6期33卷 11-16页

作者： caley b.craven Afsoon Pajand birjandi brigette Simons Ping Jiang Xing-Fang Li Department of Chemistry Faculty of ScienceUniversity of AlbertaEdmonton T6G 2G3ABCanada Molecular Science Corp 120 Adelaide Street WestSuite 2500Toronto M5H 1T1ONCanada Division of Analytical and Environmental Toxicology Department of Laboratory Medicine and PathologyFaculty of Medicine and DentistryUniversity of AlbertaEdmonton T6G 2G3ABCanada

Determination of pesticides in cannabis facilities is increasingly important as medicinal and recreational uses of cannabis products expand rapidly. We report a method involving wipe sampling, liquid chromatography separation, and tandem mass spectrometry, which enables determination of 82 pesticides out of the 96 regulated by Health Canada. To demonstrate an application of the method, we sampled and measured pesticides in two cannabis growing facilities, representing a non-certified and a certified site. We detected 41 pesticides in surface wipe samples at the non-certified site and 6 at the certified site. This study provides the first evidence showing pesticide occurrence on common surfaces in cannabis growing facilities and points to a need for routine monitoring and strict control of pesticide use in cannabis facilities.

关键词： USA Determination of eighty-two pesticides and application to screening pesticides in cannabis growing facilities

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Integration of solid phase extraction with HILIC-MS/MS for analysis of free amino acids in source water

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Journal of Environmental Sciences 2022年第7期34卷 190-196页

作者： Junlang Qiu caley craven Nicholas Wawryk Kristin Carroll Xing-Fang Li Division of Analytical and Environmental Toxicology Department of Laboratory Medicine and PathologyUniversity of AlbertaEdmontonT6G 2G3Canada School of Environmental Science and Engineering Sun Yat-sen UniversityGuangzhou 510006China

Amino acids(AAs) are prevalent in source water, particularly during spring run-off. Monitoring of amino acids in source water is desirable for water treatment plants(WTP) to indicate changes in source water quality. The objective of this study was to establish analytical procedures for reliable monitoring of amino acids in source water. Therefore, we examined two different methods, large volume inject(LVI) and solid phase extraction(SPE), for sample preparation prior to HILIC-MS/MS. The LVI-HILIC-MS/MS method can provide fast and sensitive detection for clean samples, but suffers from matrix effects, resulting in irreproducible separation and shortening column lifetime. We have demonstrated that SPE was necessary prior to HILIC-MS/MS to achieve reproducible and reliable quantification of AAs in source water. A natural heterocyclic amine 1-methyl-1,2,3,4-tetrahydro-β-carboline-3-carboxylic acid(MTCCA) was also included in the method to indicate changes in other natural nitrogenous compounds in source water. The SPE-HILIC-MS/MS method was able to achieve limits of detection from 2.6-3400 ng/L for the amino acids and MTCCA with RSDs( n = 3) of 1.1%-4.8%. As well, retention times(RT) of the analytes were reproducible with variation less than 0.01 min( n = 3) through the entire project. We further applied the SPE-HILICMS/MS method to determine AAs in authentic source water samples collected from two drinking water treatment plants(WTPs) during the 2021 spring run-off season. The results support that the SPE-HILIC-MS/MS method does not require derivatization and can provide reliable, accurate, and robust analysis of AAs and MTCCA in source water, supporting future monitoring of source water quality.

关键词： Water analysis Disinfection byproducts Amino acids HPLC MS HILIC

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Acrylamide fragment inhibitors that induce unprecedented conformational distortions in enterovirus 713C and SARS-CoV-2 main protease

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Acta Pharmaceutica Sinica b 2022年第10期12卷 3924-3933页

作者： bo Qin Gregory b.craven Pengjiao Hou Julian Chesti Xinran Lu Emma S.Child Rhodri M.L.Morgan Wenchao Niu Lina Zhao Alan Armstrong David J.Mann Sheng Cui NHC Key Laboratory of Systems biology of Pathogens Institute of Pathogen BiologyChinese Academy of Medical Sciences&Peking Union Medical CollegeBeijing 100076China Department of Life Sciences Imperial College LondonSouth Kensington CampusLondon SW72AZUK Department of Chemistry Imperial College LondonMolecular Sciences Research HubWhite City CampusWood LaneLondon W120BZUK CAS Key Laboratory for biomedical Effects of Nanomaterials and Nanosafety Institute of High Energy PhysicsUniversity of Chinese Academy of SciencesBeijing 100049China

RNA viruses are critically dependent upon virally encoded proteases to cleave the viral polyproteins into functional proteins.Many of these proteases exhibit a similar fold and contain an essential catalytic cysteine,offering the opportunity to inhibit these enzymes with electrophilic small molecules.Here we describe the successful application of quantitative irreversible tethering(qIT)to identify acrylamide fragments that target the active site cysteine of the 3C protease(3Cpro)of Enterovirus 71,the causative agent of hand,foot and mouth disease in humans,altering the substrate binding region.Further,we re-purpose these hits towards the main protease(Mpro)of SARS-CoV-2 which shares the 3C-like fold and a similar active site.The hit fragments covalently link to the catalytic cysteine of Mpro to inhibit its activity.We demonstrate that targeting the active site cysteine of Mpro can have profound allosteric effects,distorting secondary structures to disrupt the active dimeric unit.

关键词： SARS-CoV-2 Protease inhibitors Covalent fragments Allosteric inhibition EV71

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PGRMC1 Elevation in Multiple Cancers and Essential Role in Stem Cell Survival

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Advances in Lung Cancer 2015年第3期4卷 37-51页

作者： Kaia K. Hampton Rachel Stewart Dana Napier Pier Paolo Claudio Rolf J. craven Department of Pharmacology and Nutritional Sciences University of Kentucky Lexington KY USA Department of Pathology and Laboratory Medicine University of Kentucky Lexington KY USA Markey Cancer Center University of Kentucky Lexington KY USA Department of biomolecular Sciences and National Center for Natural Products Research School of Pharmacy University of Mississippi Oxford MS USA Department of Radiation Oncology University of Mississippi Medical Center Jackson MS USA

Cancer is one of the leading causes of death in America, and there is an urgent need for new therapeutic approaches. The progesterone receptor membrane component 1 (PGRMC1) is a cytochrome b5 related protein that binds heme and is associated with signaling, apoptotic suppression and autophagy. PGRMC1 is essential for tumor formation, invasion and metastasis, and is upregulated in breast, colon, lung and thyroid tumors. In the present study, we have analyzed PGRMC1 levels in over 600 tumor sections, including a larger cohort of lung tumors than in previous studies, and report the first clinical analysis of PGRMC1 levels in human oral cavity and ovarian tumors compared to corresponding nonmalignant tissues. PGRMC1 was highly expressed in lung and ovarian cancers and correlated with patient survival. PGRMC1 has been previously associated with drug resistance, a characteristic of cancer stem cells. The stem cell theory proposes that a subset of cancerous stem cells contribute to drug resistance and tumor maintenance, and PGRMC1 was detected in lung-tumor derived stem cells. Drug treatment with a PGRMC1 inhibitor, AG-205, triggered stem cell death whereas treatment with erlotinib and the ERK inhibitor, PD98059, did not, suggesting a specific role for PGRMC1 in cancer stem cell viability. Together, our data demonstrate PGRMC1 as a potential tumor biomarker across a variety of tumors, as well as a therapeutic target for cancer stem cells.

关键词： Lung Cancer Oral Cancer Head and Neck Cancer Stem Cells PGRMC1

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Natural History, Outcomes and Antibiotic Treatment for Ventilator-Associated Tracheobronchitis in Critical Ill Patients

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Modern Research in Inflammation 2016年第1期5卷 1-11页

作者： Yuxiu Lei Jana Hudcova Jawad Rashid Akmal Sarwar Wendy Gillespie Carol Finn Marie Goggin Mohamed b. Omran Edward boroda Donald E. craven Pulmonary and Critical Care Medicine Lahey Hospital and Medical Center Burlington MA USA Center for Infectious Diseases and Prevention Lahey Clinic Hospital and Medical Center Burlington MA USA Surgical & Medical Critical Care Lahey Hospital and Medical Center Burlington MA USA Tufts University School of Medicine Boston MA USA Lab Medicine—Microbiology Lahey Hospital and Medical Center Burlington MA USA Respiratory Care Lahey Hospital and Medical Center Burlington MA USA

We assessed incidence and outcomes of patients with ventilator-associated respiratory infections (VARI) due to tracheobronchitis (VAT) and pneumonia (VAP), including length of intensive care unit (ICU) stay and ventilator days. We also examined pathogens, rate of progression from VAT to VAP, and impact of antibiotic therapy for VAT. Data analysis included 234 patients, 100 patients (43%) had at least moderate (+++) bacterial growth in their semi-quantitative endotracheal aspirate (SQ-ETA) cultures. VAT and VAP were each diagnosed in 34 (15%) patients. Staphylococcus aureus was the most common pathogen isolated and had the highest rate of progression from VAT to VAP. Seven (21%) of the 34 patients were diagnosed with VAT that later progressed to VAP in averaged 3 days. Patients diagnosed with VAT had significantly more ventilator days (9 vs 6, p p bserved in the clinical outcomes of the 25 VAT patients with timely, appropriate antibiotics compared to the 9 VAT patients who did not receive timely appropriate antibiotics. VAT was a risk factor for increased ventilator days, longer length of ICU and hospital stay. The time window from VAT to VAP allowed physicians to identify the pathogens and sensitivity profile needed to treat VAT with appropriate antibiotics. Data from well-designed studies were needed to assess the impact of early, appropriate antibiotic therapy for VAT, the choice of antibiotics, as well as the duration and route of administration.

关键词： Ventilator-Associated Tracheobronchitis (VAT) and Pneumonia (VAP) bacterial Pathogens Semi-Quantitative Endotracheal Aspirate (SQ-ETA) Cultures Antibiotic Therapy

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阴道避孕环无意置入膀胱内导致的持续膀胱炎

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世界核心医学期刊文摘（妇产科学分册） 2006年第10期2卷 56-56页

作者： Teal S.b. craven W.M. 张旸 University of Colo-rado Health Sciences Center Box B-198 4200 East Ninth Avenue Denver CO 80262 United States Dr.

bACKGROUND: The NuvaRing is a soft, flexible, ring-shaped vaginal contraceptive device that is placed by the user herself. Incorrect placement has not been described, because any intravaginal position allows appropriate hormonal delivery through the vaginal mucosa. CASE: A 22-year-old otherwise healthy woman presented with 2 months of urinary urgency, frequency, and pelvic pain, which were unresponsive to antibiotic therapy. Her symptoms began immediately after placement of a NuvaRing vaginal contraceptive device, which she was subsequently unable to locate. Thorough evaluation revealed the ring in the urinary bladder. CONCLUSION: bladder or urethral foreign body should be considered in the evaluation of patients with chronic cystitis, especially if the patient uses vaginal medical devices. Intravesicular placement of a device may occur even without psychiatric or physical comorbidities.

关键词：阴道避孕环尿道异物阴道用避孕装置盆腔痛

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用核糖核酸(RNA)和脱氧核糖核酸(DNA)的合成率估测养殖池中微生物生产率和增长率

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水产科技情报 1989年第2期16卷 57-57页

作者： barry A.Costa-Pierce D.b.craven 周秀坤

由于缺少有效的方法,通常难以测定水产养殖池中微生物的总生产率。本研究以RNA和DNA的含成率对水体中微生物(藻类和细菌)的总生产作定量分析,同时对混养、单养、投饵或施肥各种条件下的养殖池作自养性生产过程中原初(藻类)生产率的定量... 详细信息

由于缺少有效的方法,通常难以测定水产养殖池中微生物的总生产率。本研究以RNA和DNA的含成率对水体中微生物(藻类和细菌)的总生产作定量分析,同时对混养、单养、投饵或施肥各种条件下的养殖池作自养性生产过程中原初(藻类)生产率的定量测定。根据DNA合成率所得的总生产率为218～6620微克碳/升·小时,其时异养性生产率35～3518微克碳/升·小时。以吸收^(14)C的碳酸氢盐得出的原初生产率4～336微克碳/升·小时。异养性生产率在8次观测资料中有7次占微生物总生产率的50％以上。RNA,DNA的合成率,微生物总生产率与三磷酸腺苷(ATP)生物量密切相关(P<0.01),而自养性生产率则与叶绿素—α或三磷酸腺苷生物量无显著相关。在此项研究中用DNA合成法测定微生物总生产率较之以往用常规方法估测的总生产率要高得多。

关键词：池塘养殖微生物 RNA DNA

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