Data Integrity is a critical component of Data lifecycle management. Its importance increases even more in a complex and dynamic landscape. Actions like unauthorized access, unauthorized modifications, data manipulati...Data Integrity is a critical component of Data lifecycle management. Its importance increases even more in a complex and dynamic landscape. Actions like unauthorized access, unauthorized modifications, data manipulations, audit tampering, data backdating, data falsification, phishing and spoofing are no longer restricted to rogue individuals but in fact also prevalent in systematic organizations and states as well. Therefore, data security requires strong data integrity measures and associated technical controls in place. Without proper customized framework in place, organizations are prone to high risk of financial, reputational, revenue losses, bankruptcies, and legal penalties which we shall discuss further throughout this paper. We will also explore some of the improvised and innovative techniques in product development to better tackle the challenges and requirements of data security and integrity.展开更多
BACKGROUND Exosomes are 30-150 nm nanovesicles with sophisticated nucleic acids cargo,actively secreted by all cells within human body,and found in abundance in all body fluids,including urine.These extracellular vesi...BACKGROUND Exosomes are 30-150 nm nanovesicles with sophisticated nucleic acids cargo,actively secreted by all cells within human body,and found in abundance in all body fluids,including urine.These extracellular vesicles have tremendous potential for next generation diagnostics,theoretically enabling noninvasive assessment of organ and tissue function via liquid biopsy analysis.AIM Recently,feasibility of an exosomal molecular test was demonstrated for postorgan transplant monitoring:Analysis of urine-derived exosomal mRNA cargo allowed early detection of kidney allograft rejection.Here,we further studied urine-derived exosomes and their mRNA content as a highly promising diagnostic modality.This included stability studies of urine samples and exosomal mRNA upon transportation from the point of collection to a centralized testing facility,short-term storage of urine at different conditions upon receipt till the point molecular assay is performed,and effects of various potentially interfering substances on the downstream quantitative polymerase chain reaction(qPCR)assay.METHODS The urine specimens were stored at various conditions and pre-processed in different ways.Next,samples were passed through the columns to capture all extracellular vesicles,the vesicles were lysed to release their content and the exosomal RNA was purified on the mini-columns,reverse transcription was performed,next pre-amplification,followed by a qPCR analysis for a panel of RESULTS To ensure exosomal RNA integrity,the harvested urine specimens should be shipped refrigerated,by overnight delivery.Urine can next be stored at the test site for up to 1 wk at 4°C,and long term should be frozen at-80°C.Urine specimens must be centrifuge at low G-force to deplete cells and debris,to ensure consistent top results in downstream molecular assays.All commonly used medications(tacrolimus,cyclosporin A,mycophenolic acid,everolimus,sirolimus,ascomycin,teriflunomide)were tested and confirmed that they do not cause assay interference.CONCLUSION mRNA from urine-derived exosomes was shown to be stable across a broad range of conditions and produced accurate results when analyzed via qPCR assay for detection of kidney allograft rejection.We identified the most optimal conditions for every step of the process,ensuring pre-analytical sample integrity and robust qPCR results.展开更多
Stem cells are of global excitement for various diseases including heart diseases. It is worth to understand the mechanism or role of stem cells in the treatment of heart failure. Bone marrow derived stem cells are co...Stem cells are of global excitement for various diseases including heart diseases. It is worth to understand the mechanism or role of stem cells in the treatment of heart failure. Bone marrow derived stem cells are commonly practiced with an aim to improve the function of the heart. The majority of studies have been conducted with acute myocardial infarction and a few has been investigated with the use of stem cells for treating chronic or dilated cardiomyopathy. Heterogeneity in the treated group using stem cells has greatly emerged. Ever increasing demand for any alternative made is of at most priority for cardiomyopathy. Stem cells are of top priority with the current impact that has generated among physicians. However,meticulous selection of proper source is required since redundancy is clearly evident with the present survey. This review focuses on the methods adopted using stem cells for heart diseases and outcomes that are generated so far with an idea to determine the best therapeutic possibility in order to fulfill the present demand.展开更多
Xiaoer-Feire-Kechuan(XFK) is an 11-herb Chinese medicine formula to treat cough and pulmonary inflammation.The complicated composition rendered its chemical analysis and effective-component elucidation.In this study,w...Xiaoer-Feire-Kechuan(XFK) is an 11-herb Chinese medicine formula to treat cough and pulmonary inflammation.The complicated composition rendered its chemical analysis and effective-component elucidation.In this study,we combined quantitative analysis and bioactivity test to reveal the antiinflammatory constituents of XFK.First,UPLC-DAD and UHPLC/Q-Orbitrap-MS methods were established and validated to quantify 35 analytes(covering 9 out of 11 herbs) in different XFK formulations.Parallel reaction monitoring mode built in Q-Orbitrap-MS was used to improve the sensitivity and selectivity.Then,anti-inflammatory activities of the 35 analytes were analyzed using in vitro COX-2 inhibition assay.Finally,major analytes forsythosides H,I,A(8-10),and baicalin(15)(total contents varied from 21.79 to 91.20 mg/dose in different formulations) with significant activities(inhibitory rate ≥ 80%) were proposed as the anti-inflammatory constituents of XFK.The present study provided an effective strategy to discover effective constituents of multi-herb formulas.展开更多
Unlike mammals with adaptive immunity,plants rely on their innate immunity based on pattern-triggered immunity(PTI)and effector-triggered immunity(ETI)for pathogen defense.Reactive oxygen species,known to play crucial...Unlike mammals with adaptive immunity,plants rely on their innate immunity based on pattern-triggered immunity(PTI)and effector-triggered immunity(ETI)for pathogen defense.Reactive oxygen species,known to play crucial roles in PTI and ETI,can perturb cellular redox homeostasis and lead to changes of redox-sensitive proteins through modification of cysteine sulfhydryl groups.Although redox regulation of protein functions has emerged as an important mechanism in several biological processes,little is known about redox proteins and how they function in PTI and ETI.In this study,cysTMT proteomics technology was used to identify similarities and differences of protein redox modifications in tomato resistant(PtoR)and susceptible(prf3)genotypes in response to Pseudomonas syringae pv tomato(Pst)infection.In addition,the results of the redox changes were compared and corrected with the protein level changes.A total of 90 potential redox-regulated proteins were identified with functions in carbohydrate and energy metabolism,biosynthesis of cysteine,sucrose and brassinosteroid,cell wall biogenesis,polysaccharide/starch biosynthesis,cuticle development,lipid metabolism,proteolysis,tricarboxylic acid cycle,protein targeting to vacuole,and oxidation–reduction.This inventory of previously unknown protein redox switches in tomato pathogen defense lays a foundation for future research toward understanding the biological significance of protein redox modifications in plant defense responses.展开更多
Time-series of chlorophyll-a(CHL),a proxy for phytoplankton biomass,and various satellite-derived climate indicators are compared in a region of the Subantarctic Southern Ocean(40°-60°S,110°-140°E)...Time-series of chlorophyll-a(CHL),a proxy for phytoplankton biomass,and various satellite-derived climate indicators are compared in a region of the Subantarctic Southern Ocean(40°-60°S,110°-140°E)for years 2012-2014.CHL reached a minimum in winter(June)and a maximum in late summer(early February).Zonal mean CHL decreased towards the south.Mean sea surface temperature(SST)ranged between 8℃and 15℃and peaked in late February.CHL and SST were positively correlated from March to June,negatively correlated from July to September.CHL and wind speed(WIND)were negatively correlated with peak WIND occurred in winter.Wind direction(WIRD)was mostly in the southwest to westerly direction.The Antarctic Oscillation index(AAO)and CHL were negatively correlated(R=−0.58),indicating that as synoptic wind systems move southwards,CHL increases,and conversely when wind systems move northwards,CHL decreases.A genetic algorithm is used to calibrate the biogeochemical DMS model’s key parameters.Under 4×CO2(after year 2100)Regional mean SST increases 12%-17%,WIND increases 1.2ms−1,Cloud Cover increases 4.8%and mixed layer depth(MLD)decreases 48m.The annual CHL increases 6.3%.The annual mean DMS flux increase 25.2%,increases 37%from day 1 to day 280 and decrease 3%from day 288 to day 360.The general increase of DMS flux under 4×CO2 conditions indicates the Subantarctic regional climate would be affected by changes in the DMS flux,with the potential for a cooling effect in the austral summer and autumn.展开更多
Deciphering the genetic basis of plant secondary metabolism will provide useful insights for genetic improvement and enhance our fundamental understanding of plant biological processes.Although citrus plants are among...Deciphering the genetic basis of plant secondary metabolism will provide useful insights for genetic improvement and enhance our fundamental understanding of plant biological processes.Although citrus plants are among the most important fruit crops worldwide,the genetic basis of secondary metabolism in these plants is largely unknown.Here,we use a high-density linkage map to dissect large-scale flavonoid metabolic traits measured in different tissues(young leaf,old leaf,mature pericarp,and mature pulp)of an F_(1) pseudo-testcross citrus population.We detected 80 flavonoids in this population and identified 138 quantitative trait loci(QTLs)for 57 flavonoids in these four tissues.Based on transcriptional profiling and functional annotation,twenty-one candidate genes were identified,and one gene encoding flavanone 3-hydroxylase(F3H)was functionally verified to result in naturally occurring variation in dihydrokaempferol content through genetic variations in its promoter and coding regions.The abundant data resources collected for diverse citrus germplasms here lay the foundation for complete characterization of the citrus flavonoid biosynthetic pathway and will thereby promote efficient utilization of metabolites in citrus quality improvement.展开更多
Detection and quantification of transgenes are important in analyzing genetically modified organisms (GMOs). Quantitative polymerase chain reaction (qPCR) is commonly utilized for such purposes. However, qPCR has cert...Detection and quantification of transgenes are important in analyzing genetically modified organisms (GMOs). Quantitative polymerase chain reaction (qPCR) is commonly utilized for such purposes. However, qPCR has certain limitations in detecting and quantifying transgenes in GMOs, such as the need of certified reference materials, a standard curve, and possible affection by inhibitors. Therefore, alternative and possibly better methods are needed. Recent advances in digital PCR technologies have promised to allow accurate quantification of nucleic acids and therefore provided another useful technique to analyze GMOs. Thermo Fisher Scientific<sup>TM</sup> has recently commercialized the Applied Biosystems<sup>TM</sup> QuantStudio<sup>TM</sup> 3D digital PCR system that can be used for a wide range of applications involving nucleic acids. It will be beneficial to the scientific community to show the applicability of this digital PCR system in detecting and quantifying transgenes in GMOs. In the present study, the transgenes present in the Roundup Ready Soybean (RR1, event 40-3-2) and Roundup Ready Soybean 2 (RR2, event MON89788) developed by Monsanto Corporation were analyzed by using this digital PCR system. The qPCR analysis results were included for comparison. Using specifically designed TaqMan assays, as low as 1% of the RR1 or RR2 soybean material was reliably detected and quantified on the dPCR platform. Therefore, digital PCR is a sensitive and reliable method to analyze the RR transgenic soybeans, and should be another useful tool for analyzing other transgenic plants.展开更多
文摘Data Integrity is a critical component of Data lifecycle management. Its importance increases even more in a complex and dynamic landscape. Actions like unauthorized access, unauthorized modifications, data manipulations, audit tampering, data backdating, data falsification, phishing and spoofing are no longer restricted to rogue individuals but in fact also prevalent in systematic organizations and states as well. Therefore, data security requires strong data integrity measures and associated technical controls in place. Without proper customized framework in place, organizations are prone to high risk of financial, reputational, revenue losses, bankruptcies, and legal penalties which we shall discuss further throughout this paper. We will also explore some of the improvised and innovative techniques in product development to better tackle the challenges and requirements of data security and integrity.
文摘BACKGROUND Exosomes are 30-150 nm nanovesicles with sophisticated nucleic acids cargo,actively secreted by all cells within human body,and found in abundance in all body fluids,including urine.These extracellular vesicles have tremendous potential for next generation diagnostics,theoretically enabling noninvasive assessment of organ and tissue function via liquid biopsy analysis.AIM Recently,feasibility of an exosomal molecular test was demonstrated for postorgan transplant monitoring:Analysis of urine-derived exosomal mRNA cargo allowed early detection of kidney allograft rejection.Here,we further studied urine-derived exosomes and their mRNA content as a highly promising diagnostic modality.This included stability studies of urine samples and exosomal mRNA upon transportation from the point of collection to a centralized testing facility,short-term storage of urine at different conditions upon receipt till the point molecular assay is performed,and effects of various potentially interfering substances on the downstream quantitative polymerase chain reaction(qPCR)assay.METHODS The urine specimens were stored at various conditions and pre-processed in different ways.Next,samples were passed through the columns to capture all extracellular vesicles,the vesicles were lysed to release their content and the exosomal RNA was purified on the mini-columns,reverse transcription was performed,next pre-amplification,followed by a qPCR analysis for a panel of RESULTS To ensure exosomal RNA integrity,the harvested urine specimens should be shipped refrigerated,by overnight delivery.Urine can next be stored at the test site for up to 1 wk at 4°C,and long term should be frozen at-80°C.Urine specimens must be centrifuge at low G-force to deplete cells and debris,to ensure consistent top results in downstream molecular assays.All commonly used medications(tacrolimus,cyclosporin A,mycophenolic acid,everolimus,sirolimus,ascomycin,teriflunomide)were tested and confirmed that they do not cause assay interference.CONCLUSION mRNA from urine-derived exosomes was shown to be stable across a broad range of conditions and produced accurate results when analyzed via qPCR assay for detection of kidney allograft rejection.We identified the most optimal conditions for every step of the process,ensuring pre-analytical sample integrity and robust qPCR results.
文摘Stem cells are of global excitement for various diseases including heart diseases. It is worth to understand the mechanism or role of stem cells in the treatment of heart failure. Bone marrow derived stem cells are commonly practiced with an aim to improve the function of the heart. The majority of studies have been conducted with acute myocardial infarction and a few has been investigated with the use of stem cells for treating chronic or dilated cardiomyopathy. Heterogeneity in the treated group using stem cells has greatly emerged. Ever increasing demand for any alternative made is of at most priority for cardiomyopathy. Stem cells are of top priority with the current impact that has generated among physicians. However,meticulous selection of proper source is required since redundancy is clearly evident with the present survey. This review focuses on the methods adopted using stem cells for heart diseases and outcomes that are generated so far with an idea to determine the best therapeutic possibility in order to fulfill the present demand.
基金supported by the National Key Research and Development Program of China (Grant No.: 2018YFC1707304, 2018YFC1707301)Beijing Natural Science Foundation (Grant No.: JQ18027)National Natural Science Foundation of China (Grant No.: 81725023)。
文摘Xiaoer-Feire-Kechuan(XFK) is an 11-herb Chinese medicine formula to treat cough and pulmonary inflammation.The complicated composition rendered its chemical analysis and effective-component elucidation.In this study,we combined quantitative analysis and bioactivity test to reveal the antiinflammatory constituents of XFK.First,UPLC-DAD and UHPLC/Q-Orbitrap-MS methods were established and validated to quantify 35 analytes(covering 9 out of 11 herbs) in different XFK formulations.Parallel reaction monitoring mode built in Q-Orbitrap-MS was used to improve the sensitivity and selectivity.Then,anti-inflammatory activities of the 35 analytes were analyzed using in vitro COX-2 inhibition assay.Finally,major analytes forsythosides H,I,A(8-10),and baicalin(15)(total contents varied from 21.79 to 91.20 mg/dose in different formulations) with significant activities(inhibitory rate ≥ 80%) were proposed as the anti-inflammatory constituents of XFK.The present study provided an effective strategy to discover effective constituents of multi-herb formulas.
基金The redox-proteomics work was partly supported by awards from the National Science Foundation(MCB 0818051 and MCB 1412547)to S.Chen.
文摘Unlike mammals with adaptive immunity,plants rely on their innate immunity based on pattern-triggered immunity(PTI)and effector-triggered immunity(ETI)for pathogen defense.Reactive oxygen species,known to play crucial roles in PTI and ETI,can perturb cellular redox homeostasis and lead to changes of redox-sensitive proteins through modification of cysteine sulfhydryl groups.Although redox regulation of protein functions has emerged as an important mechanism in several biological processes,little is known about redox proteins and how they function in PTI and ETI.In this study,cysTMT proteomics technology was used to identify similarities and differences of protein redox modifications in tomato resistant(PtoR)and susceptible(prf3)genotypes in response to Pseudomonas syringae pv tomato(Pst)infection.In addition,the results of the redox changes were compared and corrected with the protein level changes.A total of 90 potential redox-regulated proteins were identified with functions in carbohydrate and energy metabolism,biosynthesis of cysteine,sucrose and brassinosteroid,cell wall biogenesis,polysaccharide/starch biosynthesis,cuticle development,lipid metabolism,proteolysis,tricarboxylic acid cycle,protein targeting to vacuole,and oxidation–reduction.This inventory of previously unknown protein redox switches in tomato pathogen defense lays a foundation for future research toward understanding the biological significance of protein redox modifications in plant defense responses.
基金the National Natural Science Foundation of China (Nos. 41276097 and 11701298) for providing research funding for this project
文摘Time-series of chlorophyll-a(CHL),a proxy for phytoplankton biomass,and various satellite-derived climate indicators are compared in a region of the Subantarctic Southern Ocean(40°-60°S,110°-140°E)for years 2012-2014.CHL reached a minimum in winter(June)and a maximum in late summer(early February).Zonal mean CHL decreased towards the south.Mean sea surface temperature(SST)ranged between 8℃and 15℃and peaked in late February.CHL and SST were positively correlated from March to June,negatively correlated from July to September.CHL and wind speed(WIND)were negatively correlated with peak WIND occurred in winter.Wind direction(WIRD)was mostly in the southwest to westerly direction.The Antarctic Oscillation index(AAO)and CHL were negatively correlated(R=−0.58),indicating that as synoptic wind systems move southwards,CHL increases,and conversely when wind systems move northwards,CHL decreases.A genetic algorithm is used to calibrate the biogeochemical DMS model’s key parameters.Under 4×CO2(after year 2100)Regional mean SST increases 12%-17%,WIND increases 1.2ms−1,Cloud Cover increases 4.8%and mixed layer depth(MLD)decreases 48m.The annual CHL increases 6.3%.The annual mean DMS flux increase 25.2%,increases 37%from day 1 to day 280 and decrease 3%from day 288 to day 360.The general increase of DMS flux under 4×CO2 conditions indicates the Subantarctic regional climate would be affected by changes in the DMS flux,with the potential for a cooling effect in the austral summer and autumn.
文摘Deciphering the genetic basis of plant secondary metabolism will provide useful insights for genetic improvement and enhance our fundamental understanding of plant biological processes.Although citrus plants are among the most important fruit crops worldwide,the genetic basis of secondary metabolism in these plants is largely unknown.Here,we use a high-density linkage map to dissect large-scale flavonoid metabolic traits measured in different tissues(young leaf,old leaf,mature pericarp,and mature pulp)of an F_(1) pseudo-testcross citrus population.We detected 80 flavonoids in this population and identified 138 quantitative trait loci(QTLs)for 57 flavonoids in these four tissues.Based on transcriptional profiling and functional annotation,twenty-one candidate genes were identified,and one gene encoding flavanone 3-hydroxylase(F3H)was functionally verified to result in naturally occurring variation in dihydrokaempferol content through genetic variations in its promoter and coding regions.The abundant data resources collected for diverse citrus germplasms here lay the foundation for complete characterization of the citrus flavonoid biosynthetic pathway and will thereby promote efficient utilization of metabolites in citrus quality improvement.
文摘Detection and quantification of transgenes are important in analyzing genetically modified organisms (GMOs). Quantitative polymerase chain reaction (qPCR) is commonly utilized for such purposes. However, qPCR has certain limitations in detecting and quantifying transgenes in GMOs, such as the need of certified reference materials, a standard curve, and possible affection by inhibitors. Therefore, alternative and possibly better methods are needed. Recent advances in digital PCR technologies have promised to allow accurate quantification of nucleic acids and therefore provided another useful technique to analyze GMOs. Thermo Fisher Scientific<sup>TM</sup> has recently commercialized the Applied Biosystems<sup>TM</sup> QuantStudio<sup>TM</sup> 3D digital PCR system that can be used for a wide range of applications involving nucleic acids. It will be beneficial to the scientific community to show the applicability of this digital PCR system in detecting and quantifying transgenes in GMOs. In the present study, the transgenes present in the Roundup Ready Soybean (RR1, event 40-3-2) and Roundup Ready Soybean 2 (RR2, event MON89788) developed by Monsanto Corporation were analyzed by using this digital PCR system. The qPCR analysis results were included for comparison. Using specifically designed TaqMan assays, as low as 1% of the RR1 or RR2 soybean material was reliably detected and quantified on the dPCR platform. Therefore, digital PCR is a sensitive and reliable method to analyze the RR transgenic soybeans, and should be another useful tool for analyzing other transgenic plants.
