Characterisation of the Novel HLA-A*24:642 Allele Using New Next-Generation Sequencing Methods.
HLA-A*24:642 differs from HLA-A*24:02:01:01 by a single nucleotide substitution at position 76 T>C in exon 2.
Humans↗
Biomedical subjects
Xin Li
Publications and source records attributed to Xin Li.
Cr3a, a candidate gene conferring fruit cracking resistance, was fine-mapped in an introgression line of Solanum lycopersicum L.
In the cultivation and production of tomato (Solanum lycopersicum L.), fruit cracking is a prevalent and detrimental issue that significantly impacts the esthetic quality and commercial value of the fruit. The complexity of the trait has resulted in a slow advancement in research aimed at identifying genes that influence tomato fruit cracking and the underlying regulatory mechanisms. In this study, a sub-introgression population for tomato crack-resistant fruit has been constructed from the cross between S. lycopersicum 1052 and Solanum pennellii LA0716, followed by 11 generations of selfing. Utilizing specifically designed InDel markers, the tomato crack-resistant gene, Cr3a, was fine-mapped, cloned, and its functionality was confirmed through transgenic and gene-knockout approaches. The precise localization of Cr3a was delineated to a 30 kb genomic region on chromosome 3, corresponding to the gene Sopen03g034650 in S. pennellii and Solyc03g115660.3 in the Heinz1706 variety. An integrated transcriptomic and metabolomic analysis of fruits with and without the Cr3a gene was finally conducted to elucidate the intricate regulatory mechanisms associated with Cr3a. The findings revealed a molecular regulatory network for tomato fruit crack resistance, characterized by 7 key metabolites, 13 pivotal genes, and 4 critical pathways: the phenylpropanoid biosynthesis pathway, the phenylalanine, tyrosine, and tryptophan biosynthesis pathway, the linolenic acid metabolism pathway, and the cysteine and methionine metabolism pathway. In summary, this research provides novel insights into the molecular underpinnings of tomato fruit crack resistance and holds substantial promise for accelerating the molecular breeding of tomatoes with enhanced fruit crack resistance.
Solanum lycopersicum↗
Emergence of crucial evidence catalyzing the origin tracing of SARS-CoV-2.
Since the emergence of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), its genetic and geographical origins remain unclear, resulting in suspicions about its natural origin. In one of our previous studies, we reported the presence of a furin cleavage site RRAR in the junction region between S1 and S2 subunits of the spike protein, which was discovered as the first crucial clue for the origin tracing of SARS-CoV-2. In the present study, we conducted an integrative analysis of new genome data from bat Sarbecovirus strains reported after the COVID-19 outbreak. The primary results included the identification of BANAL-20-52, Rp22DB159, and S18CXBatR24 as three close relatives of SARS-CoV-2 and the successful detection of seven out of nine key genomic features (designated as RC0-7 and ORF8) observed in wild types of SARS-CoV-2 in the three close relatives from Laos, Vietnam, and Yunnan province of China, respectively. The most significant contribution of the present study lies in the detection of RC1 in wild genotype in a bat Sarbecovirus population BANAL-20-52 belonging to. Encoding a segment of the NSP3 protein, RC1 was discovered as the second crucial clue for the origin tracing of SARS-CoV-2. Although RC0, encoding the junction furin cleavage site, remains undetected outside of the SARS-CoV-2 genome, Feuang of Laos is the sole place where eight of the nine wild-type features (RC1-7 and ORF8) have been detected.
SARS-CoV-2↗
Assignment of polar states for protein amino acid residues using an interaction cluster decomposition algorithm and its application to high resolution protein structure modeling.
We have developed a new method (Independent Cluster Decomposition Algorithm, ICDA) for creating all-atom models of proteins given the heavy-atom coordinates, provided by X-ray crystallography, and the pH. In our method the ionization states of titratable residues, the crystallographic mis-assignment of amide orientations in Asn/Gln, and the orientations of OH/SH groups are addressed under the unified framework of polar states assignment. To address the large number of combinatorial possibilities for the polar hydrogen states of the protein, we have devised a novel algorithm to decompose the system into independent interacting clusters, based on the observation of the crucial interdependence between the short range hydrogen bonding network and polar residue states, thus significantly reducing the computational complexity of the problem and making our algorithm tractable using relatively modest computational resources. We utilize an all atom protein force field (OPLS) and a Generalized Born continuum solvation model, in contrast to the various empirical force fields adopted in most previous studies. We have compared our prediction results with a few well-documented methods in the literature (WHATIF, REDUCE). In addition, as a preliminary attempt to couple our polar state assignment method with real structure predictions, we further validate our method using single side chain prediction, which has been demonstrated to be an effective way of validating structure prediction methods without incurring sampling problems. Comparisons of single side chain prediction results after the application of our polar state prediction method with previous results with default polar state assignments indicate a significant improvement in the single side chain predictions for polar residues.
Algorithms↗
Preparation and evaluation of a molecularly imprinted polymer derivatized silica monolithic column for capillary electrochromatography and capillary liquid chromatography.
A method for preparation of molecularly imprinted polymer (MIP) derivatized onto the surface of a monolithic silica capillary column was successfully developed. The vinyl groups were first introduced onto the silica monolith by immobilization of gamma-methacryloxypropyltrimethoxysilane. Then the MIP coating was copolymerized and anchored onto the surface of the silica monolith. Acetonitrile was selected as porogen (solvent). The other preparation conditions, such as monomer concentration, temperature, and time of polymerization, were systematically studied. The obtained MIP-derivatized silica monolith using l-tetrahydropalmatine (l-THP) and (5S,11S)-(-)-Tröger's base (S-TB) as the imprinted template, respectively, was characterized in terms of the retention behavior of thiourea and toluene. Under the optimized CEC conditions, baseline enantioseparations of THP and TB were achieved in 4 min though the effective length of the columns was 8.5 cm. The result indicates that enough recognition sites were on the surface of silica monolith, resulting in strong recognition ability. Compared with a MIP organic monolith, the MIP-derivatized silica monolith exhibits better column efficiency and stability in CEC. Additionally, the comparison of these two kinds of monolithic columns was performed by capillary liquid chromatography. The separation on MIP-derivatized silica monolith was superior to that on the organic monolith.
Journal Article↗
The ubiquitin pathway is required for innate immunity in Arabidopsis.
Plant defences require a multitude of tightly regulated resistance responses. In Arabidopsis, the unique gain-of-function mutant suppressor of npr1-1 constitutive 1 (snc1) carries a point mutation in a Resistance (R)-gene, resulting in constitutive activation of defence responses without interaction with pathogens. This has allowed us to identify various downstream signalling components essential in multiple defence pathways. One mutant that suppresses snc1-mediated constitutive resistance is modifier of snc1 5 (mos5), which carries a 15-bp deletion in UBA1, one of two ubiquitin-activating enzyme genes in Arabidopsis. A mutation in UBA2 does not suppress snc1, suggesting that these two genes are not equally required in Arabidopsis disease resistance. On the other hand, a mos5 uba2 double mutant is lethal, implying partial redundancy of the two homologues. Apart from affecting snc1-mediated resistance, mos5 also exhibits enhanced disease susceptibility to a virulent pathogen and is impaired in response to infection with avirulent bacteria carrying the protease elicitor AvrRpt2. The mos5 mutation in the C-terminus of UBA1 might affect binding affinity of the downstream ubiquitin-conjugating enzymes, thus perturbing ubiquitination of target proteins. Furthermore, SGT1b and RAR1, which are necessary for resistance conferred by the SNC1-related R-genes RPP4 and RPP5, are dispensable in snc1-mediated resistance. Our data reveal the definite requirement for the ubiquitination pathway in the activation and downstream signalling of several R-proteins.
Amino Acid Sequence↗
Pancreatic islet cell therapy for type I diabetes: understanding the effects of glucose stimulation on islets in order to produce better islets for transplantation.
While insulin replacement remains the cornerstone treatment for type I diabetes mellitus (T1DM), the transplantation of pancreatic islets of Langerhans has the potential to become an important alternative. And yet, islet transplant therapy is limited by several factors, including far too few donor pancreases. Attempts to expand mature islets or to produce islets from stem cells are far from clinical application. The production and expansion of the insulin-producing cells within the islet (so called beta cells), or even creating cells that secrete insulin under appropriate physiological control, has proven difficult. The difficulty is explained, in part, because insulin synthesis and release is complex, unique, and not entirely characterized. Understanding beta-cell function at the molecular level will likely facilitate the development of techniques to manufacture beta-cells from stem cells. We will review islet transplantation, as well as the mechanisms underlying insulin transcription, translation and glucose stimulated insulin release.
Animals↗
Selective extraction of peptides from human plasma by highly ordered mesoporous silica particles for peptidome analysis.
Explore the source record for details and available documents.
Humans↗
The mRNA expression of P450 aromatase, gonadotropin beta-subunits and FTZ-F1 in the orange-spotted grouper (Epinephelus Coioides) during 17alpha-methyltestosterone-induced precocious sex change.
The orange-spotted grouper Epinephelus coioides is a protogynous hermaphroditic fish, but the physiological basis of its sex change remains largely unknown. In the present study, the 2-year-old orange-spotted grouper was induced to change sex precociously by oral administration of 17alpha-methyltestosterone (MT, 50 mg/Kg diet, twice a day at daily ration of 5% bodyweight) for 60 days. The serum testosterone levels were significantly elevated after MT treatment for 20 and 40 days as compared to control, but the levels of serum estradiol (E(2)) remained unchanged. The expression of P450aromA in the gonad significantly decreased after MT treatment for 20, 40, and 60 days. Accordingly, the enzyme activity of gonadal aromatase was also lower. The expression of FSHbeta subunit in the pituitary was significantly decreased after MT treatment for 20 days, but returned to the control levels after 40 and 60 days; however, the expression of LHbeta subunit was not altered significantly by MT treatment. The expression of FTZ-F1 in the gonad also decreased significantly in response to MT treatment for 40 and 60 days, but its expression in the pituitary was not altered significantly. Interestingly, when tested in vitro on ovarian fragments, MT had no direct effect on the expression of P450aromA and FTZ-F1 as well as the activity of gonadal aromatase, suggesting that the inhibition of gonadal P450aromatase and FTZ-F1 by MT may be mediated at upper levels of the brain-pituitary-gonadal axis. Taken together, these results indicated that FSH, P450aromA, FTZ-F1, and serum testosterone are associated with the MT-induced sex change of the orange-spotted grouper, but the cause-effect relationship between these factors and sex change in this species remains to be characterized.
Animals↗
Determination of miglitol in human plasma by liquid chromatography/tandem mass spectrometry.
A rapid and sensitive method for the determination of miglitol in human plasma using voglibose as internal standard has been developed and validated. Samples of plasma were deproteinated with acetonitrile and washed with dichloromethane before being analyzed by reversed-phase high-performance liquid chromatography (HPLC). Separation was carried out on a short Nucleosil C(18) column (5 microm, 50 x 4.6 mm i.d.) using 10 mmol/L ammonium acetate at 1.0 mL/min as mobile phase. The detector was an Applied Biosystems Sciex API 4000 mass spectrometer using atmospheric pressure chemical ionization (APCI) for ion production. The instrument was operated at unit resolution in the multiple reaction monitoring mode. The assay was linear over the range 5.00-2000 ng/mL with a limit of detection of 1.00 ng/mL. Intra- and inter-day precision were <2.82% and <2.92%, respectively, with accuracy of 93.3-106%. The assay was successfully applied to a clinical pharmacokinetic study of miglitol given as a single oral dose (50 mg) to healthy volunteers.
1-Deoxynojirimycin↗
Identification of components in disease-resistance signaling in Arabidopsis by map-based cloning.
With the whole genome sequence and thousands of defined polymorphisms between ecotypes available, it has become much easier to clone a gene by position (map-based cloning) in Arabidopsis. Recent development of DNA-isolation methods in plants also dramatically facilitated large-scale processing of DNA samples. Here, we describe detailed protocols for each step on general scheme of map-based cloning, from mutagenesis to genetic analysis, from rough mapping to fine mapping, and at the end to cloning the gene. Not only can these methods be used to isolate genes that are involved in plant innate immunity, they can also be adapted for any forward genetics projects in Arabidopsis.
Arabidopsis↗
The Lyme disease agent Borrelia burgdorferi requires BB0690, a Dps homologue, to persist within ticks.
Borrelia burgdorferi survives in an enzootic cycle, and Dps proteins protect DNA against damage during starvation or oxidative stress. The role of a Dps homologue encoded by Borrelia in spirochaete survival was assessed. Dps-deficient spirochaetes were infectious in mice via needle-inoculation at the dose of 10(5) spirochaetes. Larval ticks successfully acquired Dps-deficient spirochaetes via a blood meal on mice. However, after extended periods within unfed nymphs, the Dps-deficient spirochaetes failed to be transmitted to a new host when nymphs fed. Our data suggest that Dps functions to protect the spirochaetes during dormancy in unfed ticks, and in its absence, the spirochaetes become susceptible during tick feeding. dps is differentially expressed in vivo- low in mice and high in ticks - but constitutively expressed in vitro, showing little change during growth or in response to oxidative stress. Borrelia Dps forms a dodecameric complex capable of sequestering iron. The Dps-deficient spirochaetes showed no defect in starvation and oxidative stress assays, perhaps due to the lack of iron in spirochaetes grown in vitro. Dps is critical for spirochaete persistence within ticks, and strategies to interfere with Dps could potentially reduce Borrelia populations in nature and thereby influence the incidence of Lyme disease.
Amino Acid Sequence↗
Growth promoting effect of a transgenic Bacillus mucilaginosus on tobacco planting.
In this study, we have investigated the plant growth promoting effect of Bacillus mucilaginosus strain D(4)B(1), a rhizosphere soil organism, and its transgenic strain NKTS-3 on tobacco planting. The transgenic strain contains a phytase expression cassette that can express high active phytase extracellularly and hydrolyze phytate in the soil to liberate inorganic phosphorus for the growth of tobacco plants. Greenhouse study and field experiments showed that both wild-type B. mucilaginosus and the transgenic strain could promote tobacco plant growth. Moreover, the transgenic strain promoted tobacco plant growth (235% more than control in pot experiments and 125% more than control in field experiments) was higher than the wild-type B. mucilaginosus (183% more than control in pot experiments and 108% more than control in field experiments). In addition, the inoculation with transgenic rhizobacteria could significantly improve root acquisition of phosphorus and increase the phosphorus content of the plant.
6-Phytase↗
The impact of cost sharing of prescription drug expenditures on health care utilization by the elderly: own- and cross-price elasticities.
PURPOSE: To estimate healthcare demand elasticity and evaluate the impact of deductible/co-payment policy changes for prescription drugs on the use of drugs and physician visits among seniors with rheumatoid arthritis (RA) in British Columbia (BC), Canada. METHODS: According to the BC drug insurance program, prior to 2002, seniors co-paid the dispensing fee of each prescription to an annual maximum of CAN$ 200 (plan A). Starting in 2002, this plan was split into plan A and plan A1 (Premium Assistance) such that the co-payment amount equaled a maximum of CAN$ 25 and CAN$ 10 per prescription to an annual maximum of CAN$ 275 and CAN$ 200, respectively. Because of the endogeneity of the beneficiary price in the presence of a non-linear price schedule resulting from the cost-sharing policy, we implemented the method of instrumental variables to estimate price elasticities. The instrument was based on the price an individual would face under the new cost-sharing policy if their consumption remained at the pre-policy level. RESULTS: A total of 8017 patients were included. The estimated own-price elasticity of demand for prescription drugs and the cross-price elasticity of demand for physician visits were found to be negative and positive, respectively. The implications of our findings were that when cost sharing for prescription drugs increased, the demand for prescription drugs decreased and the demand for physician visits increased. CONCLUSIONS: In a predominantly publicly funded health care system, the selective introduction of market driven cost containment concepts such as patient cost-sharing might have the unintended impact of increasing overall health utilization for seniors with RA.
Aged↗
Non-muscle myosin-II-B filament regulation of paracellular resistance in cervical epithelial cells is associated with modulation of the cortical acto-myosin.
OBJECTIVE: To understand myosin regulation of epithelial permeability. METHODS: This was an experimental study, using human cervical epithelial cells CaSki. End points were paracellular permeability (determined in terms of transepithelial electrical resistance); non-muscle myosin-II-B (NMM-II-B) cellular localization; NMM-II-B phosphorylation status; NMM-II-B-actin interaction (determined in vitro by the immunoprecipitation-immunoreactivity method); and NMM-II-B filamentation (determined in vitro using purified NMM-II-B filaments in terms of filaments disassembly/assembly ratios. RESULTS: Treatment of cells with the Rho-associated kinase (ROCK) inhibitor Y-27632 or with the phosphatase inhibitor okadaic acid decreased the resistance of the lateral intercellular space (R(LIS)), and increased phosphorylation of NMM-II-B on threonine and serine residues. Y-27632 induced disorganization of the cortical acto-myosin and decreased co-immunoprecipitation of actin with NMM-II-B. Homodimerization assays using NMM-II-B filaments from cells treated with Y-27632 or okadaic acid revealed decreased filamentation compared to control cells. However, okadaic acid blocked Y-27632 decreased filamentation. Treatment with DRB, a casein kinase-II (CK2) inhibitor, induced opposing effects to those of Y-27632 and okadaic acid. Treatment with 5,6-dichloro-1-beta-(D)-ribofuranosylbenzimidazole (DRB) did not involve modulation of actin depolymerization, suggesting that NMM-II-B regulation of the R(LIS) was independent of actin polymerization status. Exposure of NMM-II-B filaments to CK2 increased filamentation, regardless of prior treatments in vivo with Y-27632, okadaic acid, or DRB. CONCLUSIONS: The results suggest that NMM-II-B filaments are in steady-state equilibrium of phosphorylation-dephosphorylation mediated by CK2 and by ROCK-regulated myosin heavy chain phosphatase, respectively. Increased phosphorylation would tend to inhibit assembly of NMM-II-B filaments and lead to decreased actin-myosin interaction, which would tend to decrease the R(LIS) and increase the paracellular permeability.
Actins↗
Negative regulation of defense responses in Arabidopsis by two NPR1 paralogs.
NPR1 is required for systemic acquired resistance, and there are five NPR1 paralogs in Arabidopsis. Here we report knockout analysis of two of these, NPR3 and NPR4. npr3 single mutants have elevated basal PR-1 expression and the npr3 npr4 double mutant shows even higher expression. The double mutant plants also display enhanced resistance against virulent bacterial and oomycete pathogens. This enhanced disease resistance is partially dependent on NPR1, can be in part complemented by either wild-type NPR3 or NPR4, and is not associated with an elevated level of salicylic acid. NPR3 and NPR4 interact with TGA2, TGA3, TGA5 and TGA6 in yeast two-hybrid assays. Using bimolecular fluorescence complementation analysis, we show that NPR3 interacts with TGA2 in the nucleus of onion epidermal cells and Arabidopsis mesophyll protoplasts. Combined with our previous finding that basal PR-1 levels are also elevated in the tga2 tga5 tga6 triple mutant, we propose that NPR3 and NPR4 negatively regulate PR gene expression and pathogen resistance through their association with TGA2 and its paralogs.
Arabidopsis↗
Progress toward the total synthesis of frondosin C.
A straightforward approach toward the total synthesis of frondosin C is described. This strategy involves a key one-pot, microwave-assisted 5-exo cyclization-Claisen rearrangement sequence that was used for the expedient assembly of the frondosic C scaffold. Subsequent manipulation of the tetracyclic core allowed the synthesis of an advanced intermediate bearing the characteristic diene moiety in the B ring. [reaction: see text]
Animals↗
Highly active antiretroviral therapy and hospital readmission: comparison of a matched cohort.
BACKGROUND: Despite the known efficacy of highly active antiretroviral therapy (HAART), a large proportion of potentially-eligible HIV-infected patients do not access, and may stand to benefit from this treatment. In order to quantify these benefits in terms of reductions in hospitalizations and hospitalization costs, we sought to determine the impact of HAART on hospital readmission among HIV-infected patients hospitalized at St. Paul's Hospital (SPH) in Vancouver, BC, Canada. METHODS: All patients admitted to a specialized HIV/AIDS ward at SPH (Apr. 1997-Oct. 2002) were selected and classified as being on HAART or not on HAART based upon their initial admission. Patients were then matched by their propensity scores, which were calculated based on patients' sociodemographics such as age, gender, injection drug use (IDU) status, and AIDS indication, and followed up for one year. Multivariate logistic regression was used to estimate the difference in the odds of hospital readmission between patients on and not on HAART. RESULTS: Out of a total 1084 patients admitted to the HIV/AIDS ward between 1997 and 2002, 662 were matched according to their propensity score; 331 patients each on and not on HAART. Multivariate logistic regression revealed that patients on HAART had lower odds of AIDS hospital readmission (OR, 0.61; 95% CI, 0.42-0.89) compared to patients not on HAART. Odds of readmission among patients on HAART were also significantly lower for non-IDU related readmission (OR, 0.73; 95% CI, 0.53-0.99) and overall readmission (OR, 0.72; 95% CI, 0.53-0.98). CONCLUSION: Propensity score matching allowed us to reliably estimate the association between exposure (on or not on HAART) and outcome (readmitted to hospital). We found that HIV-infected patients who were potentially eligible for, but not on HAART had higher odds of being readmitted to hospital compared to those on HAART. Given the low level of uptake (31%) of HAART observed in our pre-matched hospitalized cohort, a large potential to achieve clinical benefits, reduce hospitalization costs and possibly slow disease progression from improved HAART uptake still exists.
Adult↗