Serum proteins differentially expressed in gestational diabetes mellitus assessed using isobaric tag for relative and absolute quantitation proteomics

BACKGROUND As a well-known fact to the public,gestational diabetes mellitus(GDM)could bring serious risks for both pregnant women and infants.During this important investigation into the linkage between GDM patients and their altered expression in the serum,proteomics techniques were deployed to detect the differentially expressed proteins(DEPs)of in the serum of GDM patients to further explore its pathogenesis,and find out possible biomarkers to forecast GDM occurrence.METHODS Subjects were divided into GDM and normal control groups according to the IADPSG diagnostic criteria.Serum samples were randomly selected from four cases in each group at 24-28 wk of gestation,and the blood samples were identified by applying iTRAQ technology combined with liquid chromatography-tandem mass spectrometry.Key proteins and signaling pathways associated with GDM were identified by bioinformatics analysis,and the expression of key proteins in serum from 12 wk to 16 wk of gestation was further verified using enzyme-linked immunosorbent assay (ELISA).RESULTS Forty-seven proteins were significantly differentially expressed by analyzing the serum samples between the GDMgravidas as well as the healthy ones. Among them, 31 proteins were found to be upregulated notably and the rest16 proteins were downregulated remarkably. Bioinformatic data report revealed abnormal expression of proteinsassociated with lipid metabolism, coagulation cascade activation, complement system and inflammatory responsein the GDM group. ELISA results showed that the contents of RBP4, as well as ANGPTL8, increased in the serumof GDM gravidas compared with the healthy ones, and this change was found to initiate from 12 wk to 16 wk ofgestation.CONCLUSION GDM symptoms may involve abnormalities in lipid metabolism, coagulation cascade activation, complementsystem and inflammatory response. RBP4 and ANGPTL8 are expected to be early predictors of GDM.

Quantitation of HBsAg predicts response to entecavir therapy in HBV genotype C patients

AIM： To analysis the factors that predict the response to entecavir therapy in chronic hepatitis patients with hepatitis B virus （HBV） genotype C. METHODS： Fifty patients [hepatitis B e antigen （HBeAg）- negative：HBeAg-positive = 26：24] with HBV genotype C, who received nalve entecavir therapy for 〉 2 years, were analyzed. Patients who showed HBV DNA levels ≥ 3.0 log viral copies/mL after 2 years of entecavir ther- apy were designated as slow-responders, while those that showed 〈 3.0 log copies/mL were termed rapid- responders. Quantitative hepatitis B surface antigen （HBsAg） levels （qHBsAg） were determined by the Archi- tect HBsAg QT immunoassay. Hepatitis B core-related antigen was detected by enzyme immunoassay. Pre-C and Core promoter mutations were determined using by polymerase chain reaction （PCR）. Drug-resistance muta- tions were detected by the PCR-Invader method. RESULTS： At year 2, HBV DNA levels in all patients in the HBeAg-negative group were 〈 3.0 log copies/mL. In contrast, in the HBeAg-positive group, 41.7% were slow-responders, while 58.3% were rapid-responders. No entecavir-resistant mutants were detected in the slow-responders. When the pretreatment factors were compared between the slow- and rapid-responders; the median qHBsAg in the slow-responders was 4.57 log IU/mL, compared with 3.63 log IU/mL in the rapid- responders （P 〈 0.01）. When the pretreatment factors predictive of HBV DNA-negative status at year 2 in all 50 patients were analyzed, HBeAg-negative status, low HBV DNA levels, and low qHBsAg levels were signifi- cant （P 〈 0.01）. Multivariate analysis revealed that the low qHBsAg level was the most significant predictive factor （P = 0.03）. CONCLUSION： Quantitation of HBsAg could be a use- ful indicator to predict response to entecavir therapy.

Identification of protein targets for the antidepressant effects of Kai-Xin-San in Chinese medicine using isobaric tags for relative and absolute quantitation

Kai-Xin-San consists of Ginseng Radix, Polygalae Radix, Acori Tatarinowii Rhizoma, and Poria at a ratio of 3:3:2:2. Kai-Xin-San has been widely used for the treatment of emotional disorders in China. However, no studies have identified the key proteins implicated in response to Kai-Xin-San treatment. In this study, rat models of chronic mild stress were established using different stress methods over 28 days. After 14 days of stress stimulation, rats received daily intragastric administrations of 600 mg/kg Kai-Xin-San. The sucrose preference test was used to determine depression-like behavior in rats, while isobaric tags were used for relative and absolute quantitation-based proteomics to identify altered proteins following Kai-Xin-San treatment. Kai-Xin-San treatment for 2 weeks noticeably improved depression-like behaviors in rats with chronic mild stress. We identified 33 differentially expressed proteins: 7 were upregulated and 26 were downregulated. Functional analysis showed that these differentially expressed proteins participate in synaptic plasticity, neurodevelopment, and neurogenesis. Our results indicate that Kai-Xin-San has an important role in regulating the key node proteins in the synaptic signaling network, and are helpful to better understand the mechanism of the antidepressive effects of Kai-Xin-San and to provide objective theoretical support for its clinical application. The study was approved by the Ethics Committee for Animal Research from the Chinese PLA General Hospital(approval No. X5-2016-07) on March 5, 2016.

Different protein expression patterns in rat spinal nerves during wallerian degeneration assessed using isobaric tags for relative and absolute quantitation proteomics profiling

Sensory and motor nerve fibers of peripheral nerves have different anatomies and regeneration functions after injury. To gain a clear understanding of the biological processes behind these differences, we used a labeling technique termed isobaric tags for relative and absolute quantitation to investigate the protein profiles of spinal nerve tissues from Sprague-Dawley rats. In response to Wallerian degeneration, a total of 626 proteins were screened in sensory nerves, of which 368 were upregulated and 258 were downregulated. In addition, 637 proteins were screened in motor nerves, of which 372 were upregulated and 265 were downregulated. All identified proteins were analyzed using the Gene Ontology and Kyoto Encyclopedia of Genes and Genomes analysis of bioinformatics, and the presence of several key proteins closely related to Wallerian degeneration were tested and verified using quantitative real-time polymerase chain reaction analyses. The differentially expressed proteins only identified in the sensory nerves were mainly relevant to various biological processes that included cell-cell adhesion, carbohydrate metabolic processes and cell adhesion, whereas differentially expressed proteins only identified in the motor nerves were mainly relevant to biological processes associated with the glycolytic process, cell redox homeostasis, and protein folding. In the aspect of the cellular component, the differentially expressed proteins in the sensory and motor nerves were commonly related to extracellular exosomes, the myelin sheath, and focal adhesion. According to the Kyoto Encyclopedia of Genes and Genomes, the differentially expressed proteins identified are primarily related to various types of metabolic pathways. In conclusion, the present study screened differentially expressed proteins to reveal more about the differences and similarities between sensory and motor nerves during Wallerian degeneration. The present findings could provide a reference point for a future investigation into the differences between sensory and motor nerves in Wallerian degeneration and the characteristics of peripheral nerve regeneration. The study was approved by the Ethics Committee of the Chinese PLA General Hospital, China(approval No. 2016-x9-07) in September 2016.

Identification and Quantitation of Cashmere (Pashmina) Fiber and Wool Using Novel Microchip Based Real-Time PCR Technology

The textile industrial chain all over the world is facing a challenge of differentiating cashmere fiber from mixture of wool and other fibers in case cashmere stocks are adulterated with wool or other fibers. For identification of cashmere in such mixtures, the development of microchip based real-time PCR technology offers a very sensitive, specific, and accurate solution. The technology has been validated with cashmere and wool samples procured from distant farms, and from cashmere goats and sheep of different age and sex. Model samples with incremental raw cashmere or wool content were tested. The experimentally determined content was found to be comparable to the weighed content of the respective fibers in the samples. This technology may prove a cost cutter since it needs only 1.2 μl of the PCR reagent mix. It is substantially faster than traditional real-time PCR systems for being carried as miniature reaction volume in metal microchip. These features allow faster thermal equilibrium and thermal uniformity over the entire array of microreactors. For routine tests or in commercial set up, the microchips are available as ready-to-run with lyophilized reagents in its microreactors to which only 1 μl of the 10-fold diluted isolated DNA sample is added. The lyophilized microchips offer user-friendly handling in testing laboratories and help minimize human error.

Quantitation of Genital Herpes Virus DNA by Polymerase Chain Reaction and ELISA

Objective: To detect and quantitate genital herpes simplexvirus (HSV) DNA in specimens from 100 patients clinicallydiagnosed with genital herpes. Methods: Polymerase Chain Reaction (PCR) andenzyme-linked immunosorbent assay (ELISA) were used witha standard curve of DNA copies of HSV as quantitativecontrast. Results: Ninety-three cases were confirmed HSV positiveand 7 cases were found to be negative. There were 58 cases ofHSV-2 (62.4%) and 35 cases of HSV-1(37.6%) among the 93positive cases. The number of DNA plasmids ranged from 115to 1.1×10~5 per 250μL among the 93 positive samples (mean=7.1×10~4/250μL). The number of HSV DNA plasmids rangedfrom 136 to 1.1×10~5 copies per 250μL(mean=7.6×10~4) amongthose with HSV-2, and 115 to 9.4×10~4 per 250μL(mean=6.3×10~4) among those with HSV-1. Meanwhile 10μL ofextracted and dissolved DNA randomly taken from 8 each ofHSV-2 and HSV-1 samples were tested. The number of HSV-2DNA plasmids ranged from 35 copies to 2.7×10~4 (Mean=1.8×10~4) and the number of HSV-1 DNA ranged from 29 to2.5×10~4 (Mean=1.6×10~4). In the 7 negative cases, the quantityof HSV plasmids was zero. Conclusion: The sensitivity of ELISA quantitation (93%) isequal to that of Southern blot. The sensitivity of PCR fordiagnosis is 91%, and 88% for PCR typing.

Non-target Screening and Quantitation of Organic Chlorides in Oilfield Chemicals with Comprehensive Two Dimensional Gas Chromatography Coupled with Time of Flight Mass Spectrometry

Advanced analytical methodology based on comprehensive two-dimensional gas chromatography-time of flight mass spectrometry(GC×GC-TOFMS) is proposed for investigation of organic chlorides in different oilfield chemicals.The target screening was initially carried out on 8 suspected organic chlorides by evaluating the capability of the enhanced separation and reliable identification at a trace concentration. GC×GC-TOFMS allowed for the fast and automated analysis of organic chlorides at a level of 200 μg/L. This method was subsequently applied for non-target screening of organic chlorides in different oilfield chemicals at various locations across China. 22 organic chlorides were identified and verified by comparison with pure standards in the mixed sample. Finally, this method was used to determine the content of the organic chlorides in individual samples. The result showed that the organic chloride levels in 19 of the 39 tested oilfield chemicals were above the threshold limit of 1.0 mg/L.

Validation of Two Real-Time PCR Approaches for the Relative Quantitation of Pork and Horse DNA in Food Samples

Two real-time PCR methods for the relative quantitation of DNA from meat species in food samples are described: these methods are applicable for horse in processed beef meat products, and pork in raw/processed beef meat products. Test samples were prepared using raw meat admixtures or processed horse/pork in beef food products made to an industry-standard recipe. The methods were subjected to single laboratory method validation, evaluating the performance characteristics of specificity, PCR efficiency and r-squared (r2), Limit of Detection (LOD), Limit of Quantitation (LOQ), and precision and trueness. A limited UK-based inter-laboratory trial of the two methods was completed involving four participating laboratories. Full statistical analysis of the data qualified the applicability of the methods for accurate and sensitive trace-level analysis. The methods were deemed fit for purpose for reproducibly distinguishing between adventitious contamination at 0.1% (w/w), the level for further enforcement action at 1% (w/w), and a level representative of deliberate economically motivated adulteration (10% (w/w)). The data provided evidence that the precision of the two methods was applicable for qualitative and quantitative detection at topically important levels of adulteration. This work has added significant value to the current state of the art in quantitative determination of topical meat species adulteration, allowing analysts to distinguish between adventitious contamination and deliberate adulteration. The resulting methods described in this paper can easily be deployed and used by analytical laboratories for controls and due-diligence testing based on standard laboratory equipment.

Preparation and Application of Silica-based Perfusion Packing of Size Exclusion Chromatography for Quantitation of Polyacrylamide in Enhanced Oil Recovery Systems

The synthesis and characterization of a novel macroporous silica derived size exclusion chromatography （SEC） packing for quantitative analysis of high molecular weight （MW） polyacrylamide （PAM） are presented. Using this packing, a fast, sensitive and reproducible approach for quantitation of super high-MW PAM in demanding enhanced oil recovery （EOR） waters was developed and the effect of synthesis parameters on the properties of resultant materials was investigated. These parameters include salt addition, reaction temperature and duration, activation condition of functional groups on the silica surface, as well as the reaction cycles required for optimal silica modification. Moreover, SEC analysis conditions, such as mobile phase composition, flow rate, detection and sample preparation, were also explored and an optimal analysis protocol was developed. Under this optimized SEC analysis conditions, the synthesized macroporous materials proved satisfactory for quantification of PAM with average MW up to 22 million Daltons. An SEC analysis required less than few minutes with a detection limit of 1 ng, a linear response range of 0.1 to 75 mg/L with squared R value of 0.99 and reproducibility better than 9.2% RSD （relative standard deviation）. The analysis of PAM in highly saline oilfield production water containing interfering high MW polymeric surfactants indicated the recovery ranges from 92.5% to 110.1% for 1.0 mg/L PAM and 94.2% to 103.8% for 50 mg/L PAM solution. This study presented for the ftrst time that the reliable quantization of high MW PAM in highly demanding EOR waters can be achieved by SEC.

Quantitation of DNA by nuclease P1 digestion and UPLC-MS/MS to assess binding efficiency of pyrrolobenzodiazepine

Accurate DNA quantitation is a prerequisite in many biomedical and pharmaceutical studies.Here we established a new DNA quantitation method by nuclease P1 digestion and UPLC-MS/MS analysis.DNA fragments can be efficiently hydrolyzed to single deoxyribonucleotides by nuclease P1 in a short time.The decent stabilities of all the four deoxyribonucleotides were confirmed under different conditions.Deoxyadenosine monophosphate(dAMP)was selected as the surrogate for DNA quantitation because dAMP showed the highest sensitivity among the four deoxyribonucleotides in the UPLC-MS/MS analysis.The linear range in DNA quantitation by this method is 1.2-5000 ng/mL.In the validation,the inter-day and intra-day accuracies were within 90%-110%,and the inter-day and intra-day precision were acceptable(RSD<10%).The validated method was successfully applied to quantitate DNA isolated from tumors and organs of a mouse xenograft model.Compared to the quantitation methods using UV absorbance,the reported method provides an enhanced sensitivity,and it allows for the accurate quantitation of isolated DNA with contamination of RNA and ribonucleotide.

DETECTION AND QUANTITATION OF TRACE ETHYL CARBAMATE IN ALCOLLOLIC BEVERAGES BY GC/GC AND GC/GC/MS

Analytical difficulties encountered in the determination of ethyl carbamate, a known cancinogen, in a wide variety of wines and spirits have been overcome by spe- cific, sensitive GC/GC and CC/CC/MS methods with a relatively shorter extraction procedure. The lowest detection limits were estimated to be 0. 1 and 0. 01μg/L for GC/GC and GC/GC/MS respectively. The RSD of the GC/GC method was 2. 5%.

UHPLC-ESI-HRMS Quantitation of Metabolites without Using Reference Standards: Impact of LC Flow Rate and Mobile Phase Composition on MS Responses

During LC-MS quantitation of drugs for pharmacokinetic assessment, usually metabolites are not quantified due to the unavailability of reference standards. If a metabolite is quantified without a reference standard, then it is assumed that the LC-MS response to a drug is similar to that of its metabolite and the standard curve, of the parent compound, is used to quantitate the metabolite. This approach could result in an over or underestimation of the metabolite. To evaluate the impact of mobile phase composition on LC-MS response, the mobile phases were interchanged between methanol, acetonitrile and a 50/50 mixture of methanol/acetonitrile. UHPLC flow rates were varied from 200-500 μL/min, with and without the addition of reverse composition of mobile phases, at the parent drug retention time. This change was necessary to achieve uniform MS responses for drugs and their metabolites. In this study, HRMS data, obtained using orbi-trap, resulted in a linear response over a wider dynamic range than that obtained using the linear ion trap. Overall, the parameters, required for achieving standard free quantitation, are dependent upon the mobile phase composition and LC flow rates.

Critical Considerations in the Immunochemical Detection and Quantitation of Antigenic Biomarkers

The formation of covalent adducts as a result of the interaction of metabolically activated chemicals with host macromolecules is a common critical event in mutagenic, carcinogenic, and immunologic phenomena. Because of their antigenicity and their immunogenicity, covalent adducts may be detected using sensitive immunochemical techniques. The immunochemical approaches to biomonitoring and molecular dosimetry of DNA damage are particularly attractive because they allow sensitive quantitation of specific DNA adducts present in small samples and do not rely on the use of radiolabeled adducts. Two examples of biomarker immunoassay development are presented: an avidin/biotin-amplified ELISA for the major DNA adduct of the human bladder carcinogen 4-aminobiphenyl (ABP), and a particle concentration fluorescent immunoassay (PCFIA) for the major protein adduct associated with toxicity by the prototype hepatotoxin acetaminophen. The examples illustrate critical steps in the development of biomarker immunoassays which include selection of the relevant adduct, preparation of an appropriate immunogen, immunization, characterization of antisera, and development of application-specific sample processing techniques for biomarker quantitation. Immunochemical procedures may be combined with other analytical techniques to form hybrid systems which take advantage of both the antigenicity and the physical or chemical properties of a biomarker to achieve greater specificity and/or sensitivity. The future usefulness of these new tools of molecular epidemiology will depend on a compound-by-compound validation of methods and critical evaluation of the biologic importance of the particular antigenic biomarker as an indicator of exposure and as an indicator of risk.

Protein quantitation using dyes obtained from plant materials

We present a preliminary report on the use of plant dyes in the quantitation of proteins in solution. We have used ethanol, acid, alkali and water to extract dyes from some plant materials, including flowers of Jungle flame (Izora coccinea), China rose (Hibiscus rosa-sinensis) and leaves of West African Indigo (Lonchocarpus cyanescens), Mimosa (Mimosa pudica), Roselle (Hibiscus sabdarifa), Jatropha (Jatropha curcas) and Henna (Lawsonia inermis). The dyes obtained were used in the protein-dye binding studies. The colour of the protein-dye complex of the ethanolic extracts was stable and increased linearly with increase in protein concentration. The extracts achieved linearity up to the following amount of proteins in the test samples: Hibiscus rosa-sinensis (60 mg), Ixora coccinea (120 mg), Hibiscus sabdarifa (80 - 100 mg), Jatropha curcas (80 mg), and Lawsonia inermis (100 mg). The sensitivity of the dyes especially at low protein concentrations indicate that they can provide suitable alternatives to other well known standard methods of protein determination.

Quantitation of PCR Products by Capillary Electrophoresis in a Single Run

A simple method was developed to quantify DNA fragments such as PCR (polymerase chain reaction) products by capillary electrophoresis. Restraint fragments with different lengths were employed as internal standards in the study, which makes it possible for the evaluation of the quantity of PCR product in a single run.

Isobaric Tag for Relative and Absolute Quantitation-Based Proteomics for Investigating the Effect of Guasha on Lumbar Disc Herniation in Rats

Objective:The objective of the study is to examine the possible mechanism by which Guasha(scraping therapy)affects the expression profiles of proteins in a lumbar disc herniation(LDH)rat model using isobaric tags for relative and absolute quantitation(iTRAQ)-based proteomics.Methods:Thirty-six rats were used in this study.LDH rats were subjected to noncompressive LDH surgeries.Rats were randomly divided into the model and Guasha groups.Guasha was applied on alternate days for a total of nine times(three courses).At the end of each course,six rats were randomly selected from each group and their blood samples were collected.iTRAQ labeling was used to examine the mechanism of action of Guasha against LDH.The molecular functions,cellular components,and biological processes were analyzed using gene ontology analysis.The Ingenuity Pathway Analysis database was used to identify canonical pathways involving these proteins.Results:Compared to the model group,198,182,and 170 proteins were identified as differentially expressed at the three respective Guasha treatment courses.Pathways,including focal adhesion kinase signaling,acute-phase response signaling,and the LXR/RXR activation pathway,were closely related to the effects of Guasha in LDH rats.Furthermore,Rac1,Orm1,and Hpx were validated by western blotting,and the results were consistent with the protein expression levels observed using the iTRAQ method.Conclusion:Guasha could not only regulate the pathological changes related to LDH,but also achieve therapeutic effects by stimulating physiological changes.Our results offer a better understanding of the effects of Guasha on LDH.

Recursive Zero-COVID model and quantitation of control efforts of the Omicron epidemic in Jilin province

Since the beginning of March 2022,the epidemic due to the Omicron variant has developed rapidly in Jilin Province.To figure out the key controlling factors and validate the model to show the success of the Zero-COVID policy in the province,we constructed a Recursive Zero-COVID Model quantifying the strength of the control measures,and defined the control reproduction number as an index for describing the intensity of interventions.Parameter estimation and sensitivity analysis were employed to estimate and validate the impact of changes in the strength of different measures on the intensity of public health preventions qualitatively and quantitatively.The recursive Zero-COVID model predicted that the dates of elimination of cases at the community level of Changchun and Jilin Cities to be on April 8 and April 17,respectively,which are consistent with the real situation.Our results showed that the strict implementation of control measures and adherence of the public are crucial for controlling the epidemic.It is also essential to strengthen the control intensity even at the final stage to avoid the rebound of the epidemic.In addition,the control reproduction number we defined in the paper is a novel index to measure the intensity of the prevention and control measures of public health.

Circulating proteomic biomarkers for diagnosing sporadic amyotrophic lateral sclerosis:a cross-sectional study

Biomarke rs are required for the early detection,prognosis prediction,and monitoring of amyotrophic lateral sclerosis,a progressive disease.Proteomics is an unbiased and quantitative method that can be used to detect neurochemical signatures to aid in the identification of candidate biomarke rs.In this study,we used a label-free quantitative proteomics approach to screen for substantially differentially regulated proteins in ten patients with sporadic amyotrophic lateral scle rosis compared with five healthy controls.Su bstantial upregulation of serum proteins related to multiple functional clusters was observed in patients with spo radic amyotrophic lateral sclerosis.Potential biomarke rs were selected based on functionality and expression specificity.To validate the proteomics profiles,blood samples from an additional cohort comprising 100 patients with sporadic amyotrophic lateral sclerosis and 100 healthy controls were subjected to enzyme-linked immunosorbent assay.Eight substantially upregulated serum proteins in patients with spora dic amyotrophic lateral sclerosis were selected,of which the cathelicidin-related antimicrobial peptide demonstrated the best discriminative ability between patients with sporadic amyotrophic lateral sclerosis and healthy controls(area under the curve[AUC]=0.713,P<0.0001).To further enhance diagnostic accuracy,a multi-protein combined discriminant algorithm was developed incorporating five proteins(hemoglobin beta,cathelicidin-related antimicrobial peptide,talin-1,zyxin,and translationally-controlled tumor protein).The algo rithm achieved an AUC of 0.811 and a P-value of<0.0001,resulting in 79%sensitivity and 71%specificity for the diagnosis of sporadic amyotrophic lateral scle rosis.Subsequently,the ability of candidate biomarkers to discriminate between early-stage amyotrophic lateral sclerosis patients and controls,as well as patients with different disease severities,was examined.A two-protein panel comprising talin-1 and translationally-controlled tumor protein effectively distinguished early-stage amyotrophic lateral sclerosis patients from controls(AUC=0.766,P<0.0001).Moreove r,the expression of three proteins(FK506 binding protein 1A,cathelicidin-related antimicrobial peptide,and hemoglobin beta-1)was found to increase with disease progression.The proteomic signatures developed in this study may help facilitate early diagnosis and monitor the progression of sporadic amyotrophic lateral sclerosis when used in co mbination with curre nt clinical-based parameters.

Mining elite loci and candidate genes for root morphology-related traits at the seedling stage by genome-wide association studies in upland cotton(Gossypium hirsutum L.)

Root system architecture plays an essential role in water and nutrient acquisition in plants,and it is significantly involved in plant adaptations to various environmental stresses.In this study,a panel of 242 cotton accessions was collected to investigate six root morphological traits at the seedling stage,including main root length(MRL),root fresh weight(RFW),total root length(TRL),root surface area(RSA),root volume(RV),and root average diameter(AvgD).The correlation analysis of the six root morphological traits revealed strong positive correlations of TRL with RSA,as well as RV with RSA and AvgD,whereas a significant negative correlation was found between TRL and AvgD.Subsequently,a genome-wide association study(GWAS)was performed using the root phenotypic and genotypic data reported previously for the 242 accessions using 56,010 single nucleotide polymorphisms(SNPs)from the CottonSNP80K array.A total of 41 quantitative trait loci(QTLs)were identified,including nine for MRL,six for RFW,nine for TRL,12 for RSA,12 for RV and two for AvgD.Among them,eight QTLs were repeatedly detected in two or more traits.Integrating these results with a transcriptome analysis,we identified 17 candidate genes with high transcript values of transcripts per million(TPM)≥30 in the roots.Furthermore,we functionally verified the candidate gene GH_D05G2106,which encodes a WPP domain protein 2in root development.A virus-induced gene silencing(VIGS)assay showed that knocking down GH_D05G2106significantly inhibited root development in cotton,indicating its positive role in root system architecture formation.Collectively,these results provide a theoretical basis and candidate genes for future studies on cotton root developmental biology and root-related cotton breeding.

Simultaneously quantifying hundreds of acylcarnitines in multiple biological matrices within ten minutes using ultrahigh-performance liquid-chromatography and tandem mass spectrometry

Acylcarnitines are metabolic intermediates of fatty acids and branched-chain amino acids having vital biofunctions and pathophysiological significances. Here, we developed a high-throughput method for quantifying hundreds of acylcarnitines in one run using ultrahigh performance liquid chromatography and tandem mass spectrometry (UPLC-MS/MS). This enabled simultaneous quantification of 1136 acylcarnitines (C0–C26) within 10-min with good sensitivity (limit of detection < 0.7 fmol), linearity (correlation coefficient > 0.992), accuracy (relative error < 20%), precision (coefficient of variation (CV), CV < 15%), stability (CV < 15%), and inter-technician consistency (CV < 20%, n = 6). We also established a quantitative structure-retention relationship (goodness of fit > 0.998) for predicting retention time (tR) of acylcarnitines with no standards and built a database of their multiple reaction monitoring parameters (tR, ion-pairs, and collision energy). Furthermore, we quantified 514 acylcarnitines in human plasma and urine, mouse kidney, liver, heart, lung, and muscle. This provides a rapid method for quantifying acylcarnitines in multiple biological matrices.