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1.
Sci Total Environ ; 931: 172951, 2024 May 03.
Article in English | MEDLINE | ID: mdl-38703838

ABSTRACT

Micro-/nanoplastic contamination in agricultural soils raises concerns on agroecosystems and poses potential health risks. Some of agricultural soils have received significant amounts of micro-/nanoplastics (MNPs) through plastic mulch film and biosolid applications. However, a comprehensive understanding of the MNP impacts on soils and plants remains elusive. The interaction between soil particles and MNPs is an extremely complex issue due to the different properties and heterogeneity of soils and the diverse characteristics of MNPs. Moreover, MNPs are a class of relatively new anthropogenic pollutants that may negatively affect plants and food. Herein, we presented a comprehensive review of the impacts of MNPs on the properties of soil and the growth of plants. We also discussed different strategies for mitigating or eliminating MNP contamination. Moreover, perspectives for future research on MNP contamination in the agricultural soils are also highlighted.

3.
Cancers (Basel) ; 16(7)2024 Mar 24.
Article in English | MEDLINE | ID: mdl-38610947

ABSTRACT

Sperm-associated antigen 5 (SPAG5), also known as Astrin, was previously demonstrated as a biomarker for cellular resistance to major breast cancer therapies, including chemo-, endocrine- and targeted therapy. However, the contribution of SPAG5 to anthracycline- and taxane-based chemotherapy in triple-negative breast cancer (TNBC) remains controversial. In the present study, the SPAG5 knockout cell model was established by using clustered regularly interspaced palindromic repeats (CRISPR)-CRISPR-associated protein 9 (Cas9) system in MDA-MB-231 and BT549 TNBC cell lines. The knockout of SPAG5 was confirmed on both gene and protein levels using genomic PCR, DNA sequencing and western blotting. The functional loss of SPAG5 was determined by colony-formation assay. SPAG5-regulated doxorubicin- and docetaxel-resistance was assessed by MTT and apoptosis assays. The results indicated that all the SPAG5 knockout MDA-MB-231 and BT549 clones were biallelic, where one allele was replaced by the donor template, and the other allele had the same "T" insertion (indel) adjacent to the cutting sites of gRNAs at the exon 1 boundary, irrespective of the gRNAs and cell lines. The locus of indel interrupted the SPAG5 transcription by damaging the GT-AG mRNA processing rule. Deletion of SPAG5 decreased clonogenicity in both MDA-MB-231 and BT549 cells. SPAG5 was able to regulate the resistance and the drug-induced apoptosis of both doxorubicin and docetaxel. In conclusion, recombinant plasmid-based CRISPR-Cas9 technology can be used to delete the SPAG5 gene in the TNBC cell lines. SPAG5 has an important role in regulating cell proliferation and doxorubicin- and docetaxel-resistance in MDA-MB-231 and BT549 cells.

4.
Phys Med Biol ; 2024 Apr 26.
Article in English | MEDLINE | ID: mdl-38670137

ABSTRACT

PURPOSE: The dose hotspot areas in hypofractionated whole-breast irradiation greatly increase the risk of acute skin toxicity because of the anatomical peculiarities of the breast. In this study, we presented several novel planning strategies that integrate multiple sub-planning target volumes (sub-PTVs), field secondary placement, and RapidPlan models for right-sided hypofractionated whole-breast irradiation. Methods: A total of 35 cases of whole-breast irradiation with a dose of 42.5Gy for PTVs using tangential intensity-modulated radiotherapy(IMRT) were selected. Both PTVs were planned for simultaneous treatment using the original manual multiple sub-PTV plan (OMMP) and the original manual single-PTV plan (OMSP). The manual field secondary placement multiple sub-PTV plan (m-FSMP) with multiple objects on the original PTV and the manual field secondary placement single-objective plan (m-FSSP) were initially planned, which were distribution-based of V105(volume receiving 105% of the prescription dose). In addition, two RapidPlan-based plans were developed, including the RapidPlan-based multiple sub-PTVs plan (r-FSMP) and the RapidPlan-based single-PTV plan (r-FSSP). Dosimetric parameters of the plans were compared, and V105 was evaluated using multivariate analysis to determine how it was related to the volume of PTV and the interval of lateral beam angles (ILBA). Results: The lowest mean V105 (5.64±6.5%) of PTV was observed in m-FSMP compared to other manual plans. Upon validation, r-FSSP demonstrated superior dosimetric quality for OAR compared to the two other manual planning methods, except for V5(the volume of ipsilateral lung receiving 5 Gy) of the ipsilateral lung. While r-FSMP showed no significant difference (p=0.06) compared to r-FSSP, it achieved the lowest V105 value (4.3±4.5%), albeit with a slight increase in the dose to some OARs. Conclusions: m-FSMP and r-FSMP can substantially enhance the homogeneity index (HI) and reduce V105, thereby minimizing the risk of acute skin toxicities, even though there may be a slight dose compromise for certain OARs.

5.
Zhongguo Zhong Yao Za Zhi ; 49(6): 1526-1539, 2024 Mar.
Article in Chinese | MEDLINE | ID: mdl-38621936

ABSTRACT

This study aims to investigate the component variations and spatial distribution of ginsenosides in Panax quinquefolium roots during repeated steaming and drying. Ultra performance liquid chromatography quadrupole time-of-flight tandem mass spectrometry(UPLC-Q-TOF-MS/MS) was employed to identify the ginsenosides in the root extract. Matrix-assisted laser desorption/ionization mass spectrometry imaging(MALDI-MSI) was employed to visualize the spatial distribution and spatiotemporal changes of prototype ginsenosides and metabolites in P. quinquefolium roots. The UPLC results showed that 90 ginsenosides were identified during the steaming process of the roots, and polar ginsenosides were converted into low polar or non-polar ginsenosides. The content of prototype ginsenosides decreased, while that of rare ginsenosides increased, which included 20(S/R)-ginsenoside Rg_3, 20(S/R)-ginsenoside Rh_2, and ginsenosides Rk_1, Rg_5, Rs_5, and Rs_4. MALDI-MSI results showed that ginsenosides were mainly distributed in the epidermis and phloem. As the steaming times increased, ginsenosides were transported to the xylem and medulla. This study provides fundamental information for revealing the changes of biological activity and pharmacological effect of P. quinquefolium roots that are caused by repeated steaming and drying and gives a reference for expanding the application scope of this herbal medicine.


Subject(s)
Ginsenosides , Panax , Ginsenosides/analysis , Tandem Mass Spectrometry , Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization/methods , Panax/chemistry , Chromatography, High Pressure Liquid/methods , Plant Roots/chemistry
6.
mSystems ; 9(4): e0105523, 2024 Apr 16.
Article in English | MEDLINE | ID: mdl-38501864

ABSTRACT

Plant-associated diazotrophs strongly relate to plant nitrogen (N) supply and growth. However, our knowledge of diazotrophic community assembly and microbial N metabolism in plant microbiomes is largely limited. Here we examined the assembly and temporal dynamics of diazotrophic communities across multiple compartments (soils, epiphytic and endophytic niches of root and leaf, and grain) of three cereal crops (maize, wheat, and barley) and identified the potential N-cycling pathways in phylloplane microbiomes. Our results demonstrated that the microbial species pool, influenced by site-specific environmental factors (e.g., edaphic factors), had a stronger effect than host selection (i.e., plant species and developmental stage) in shaping diazotrophic communities across the soil-plant continuum. Crop diazotrophic communities were dominated by a few taxa (~0.7% of diazotrophic phylotypes) which were mainly affiliated with Methylobacterium, Azospirillum, Bradyrhizobium, and Rhizobium. Furthermore, eight dominant taxa belonging to Azospirillum and Methylobacterium were identified as keystone diazotrophic taxa for three crops and were potentially associated with microbial network stability and crop yields. Metagenomic binning recovered 58 metagenome-assembled genomes (MAGs) from the phylloplane, and the majority of them were identified as novel species (37 MAGs) and harbored genes potentially related to multiple N metabolism processes (e.g., nitrate reduction). Notably, for the first time, a high-quality MAG harboring genes involved in the complete denitrification process was recovered in the phylloplane and showed high identity to Pseudomonas mendocina. Overall, these findings significantly expand our understanding of ecological drivers of crop diazotrophs and provide new insights into the potential microbial N metabolism in the phyllosphere.IMPORTANCEPlants harbor diverse nitrogen-fixing microorganisms (i.e., diazotrophic communities) in both belowground and aboveground tissues, which play a vital role in plant nitrogen supply and growth promotion. Understanding the assembly and temporal dynamics of crop diazotrophic communities is a prerequisite for harnessing them to promote plant growth. In this study, we show that the site-specific microbial species pool largely shapes the structure of diazotrophic communities in the leaves and roots of three cereal crops. We further identify keystone diazotrophic taxa in crop microbiomes and characterize potential microbial N metabolism pathways in the phyllosphere, which provides essential information for developing microbiome-based tools in future sustainable agricultural production.


Subject(s)
Microbiota , Microbiota/genetics , Agriculture , Soil/chemistry , Nitrogen/analysis , Crops, Agricultural/metabolism , Plant Development
7.
Phys Rev E ; 109(2-2): 025205, 2024 Feb.
Article in English | MEDLINE | ID: mdl-38491683

ABSTRACT

In this study, the spatiotemporal evolution of full cycle of high-intensity dc argon arc discharge at atmospheric pressure is investigated by using a transferred arc device, which is easy to be directly observed in the experiment. Combining the voltage and current waveforms with high-speed images, the full cycle evolution process of high-intensity atmospheric dc arc can be divided into five different stages: breakdown pulse stage, cathode heating stage, current climbing stage, stable arc discharge stage, and finally arc extinguishing stage. The characteristics of each different stage are analyzed in detail through the electrical properties, high-speed pictures, and spectroscopic measurements. The results show that the strong luminescence region develops from the vicinity of cathode and anode to the middle in the breakdown pulse stage, which is explained from the spatiotemporal evolution of distributions of excited argon atom and ions. The development velocity of emission intensity of argon ions is mainly determined by the dominant stepwise ionization process. Then the cathode heating stage appears with many bright and nonuniformly distributed light spots on the cathode surface, and the electron emission mechanism of cathode gradually changes to the thermionic emission as the surface temperature rises. With the increase of arc current, the discharge channel significantly expands, then becomes stable due to the increment of the Lorentz force. The characteristics of arc extinguishing stage are clarified in terms of the decay of charged particles density.

8.
Eur J Obstet Gynecol Reprod Biol ; 296: 327-332, 2024 May.
Article in English | MEDLINE | ID: mdl-38520955

ABSTRACT

OBJECTIVE: To validate the accuracy of four early warning scores for early identification of women at risk. METHODS: This was a retrospective study of pregnant women admitted in obstetrics Critical Care Unit (ICU). Capacity of the Modified Obstetric Early Warning Score (MOEWS), ICNARC Obstetric Early Warning Score (OEWS), Maternal Early Obstetric Warning System (MEOWS chart), and Maternal Early Warning Trigger (MEWT) were compared in predicting severe maternal morbidity. Area under receiver operator characteristic (AUROC) curve was used to evaluate the predictive performance of scoring system. RESULTS: A total of 352 pregnant women were enrolled and 290 were identified with severe maternal morbidity. MOEWS was more sensitive than MEOWS chart, ICNARC OEWS and MEWT (96.9 % vs. 83.4 %, 66.6 % and 44.8 %). MEWT had the highest specificity (98.4 %), followed by MOEWS (83.9 %), ICNARC OEWS (75.8 %) and MEOWS chart (48.4 %). AUROC of MOEWS, ICNARC OEWS, MEOWS chart, and MEWT for prediction of maternal mortality were 0.91 (95 % CI: 0.874-0.945), 0.765(95 % CI: 0.71-0.82), 0.657(95 % CI: 0.577-0.738), and 0.716 (95 % CI, 0.659-0.773) respectively. MOEWS had the highest AUCs in the discrimination of serious complications in hypertensive disorders, cardiovascular disease, obstetric hemorrhage and infection. For individual vital signs, maximum diastolic blood pressure (DBP), maximum systolic blood pressure (SBP), maximum respiratory rate (RR) and peripheral oxygen saturation (SPO2) demonstrated greater predictive ability. CONCLUSION: MOEWS is more accurate than ICNARC OEWS, MEOWS chart, and MEWT in predicting the deterioration of women. The prediction ability of DBP, SBP, RR and SPO2 are more reliable.


Subject(s)
Obstetrics , Pregnancy Complications , Pregnancy , Female , Humans , Retrospective Studies , Critical Illness , Pregnancy Complications/diagnosis , Blood Pressure
9.
ISME Commun ; 4(1): ycae017, 2024 Jan.
Article in English | MEDLINE | ID: mdl-38481578

ABSTRACT

Recent metagenomic advancements have offered unprecedented insights into soil viral ecology. However, it remains a challenge to select the suitable metagenomic method for investigating soil viruses under different environmental conditions. Here, we assessed the performance of viral size-fraction metagenomes (viromes) and total metagenomes in capturing viral diversity from hypersulfidic soils with neutral pH and sulfuric soils with pH <3.3. Viromes effectively enhanced the sequencing coverage of viral genomes in both soil types. Viomes of hypersulfidic soils outperformed total metagenomes by recovering a significantly higher number of viral operational taxonomic units (vOTUs). However, total metagenomes of sulfuric soils recovered ~4.5 times more vOTUs than viromes on average. Altogether, our findings suggest that the choice between viromes and total metagenomes for studying soil viruses should be carefully considered based on the specific environmental conditions.

10.
J Environ Manage ; 356: 120544, 2024 Apr.
Article in English | MEDLINE | ID: mdl-38471323

ABSTRACT

Biofilters are the important source and sink of antibiotic resistance genes (ARGs) and antibiotic resistance bacteria (ARB) in the drinking water. Current studies generally ascribed the prevalence of BAR in biofilter from the perspective of gene behavior, i.e. horizontal gene transfer (HGT), little attentions have been paid on the ARGs carrier- ARB. In this study, we proposed the hypothesis that ARB participating in pollutant metabolism processes and becoming dominant is an important way for the enrichment of ARGs. To verify this, the antibiotic resistome and bacterial functional metabolic pathways of a sand filter was profiled using heterotrophic bacterial plate counting method (HPC), high-throughput qPCR, Illumina Hiseq sequencing and PICRUSt2 functional prediction. The results illustrated a significant leakage of ARB in the effluent of the sand filter with an average absolute abundance of approximately 102-103 CFU/mL. Further contribution analysis revealed that the dominant genera, such as Acinetobacter spp., Aeromonas spp., Elizabethkingia spp., and Bacillus spp., were primary ARGs hosts, conferring resistance to multiple antibiotics including sulfamethoxazole, tetracycline and ß-lactams. Notably, these ARGs hosts were involved in nitrogen metabolism, including extracellular nitrate/nitrite transport and nitrite reduction, which are crucial in nitrification and denitrification in biofilters. For example, Acinetobacter spp., the dominant bacteria in the filter (relative abundance 69.97 %), contributed the majority of ARGs and 53.79 % of nitrite reduction function. That is, ARB can predominate by participating in the nitrogen metabolism pathways, facilitating the enrichment of ARGs. These findings provide insights into the stable presence of ARGs in biofilters from a functional metabolism perspective, offering a significant supplementary to the mechanisms of the emergence, maintenance, and transmission of BARin drinking water.


Subject(s)
Anti-Bacterial Agents , Drinking Water , Anti-Bacterial Agents/pharmacology , Anti-Bacterial Agents/analysis , Genes, Bacterial , Angiotensin Receptor Antagonists/analysis , Nitrites/analysis , Drug Resistance, Microbial/genetics , Angiotensin-Converting Enzyme Inhibitors/analysis , Nitrogen/analysis
11.
Environ Int ; 185: 108511, 2024 Mar.
Article in English | MEDLINE | ID: mdl-38382404

ABSTRACT

Fungal plant pathogens threaten crop production and sustainable agricultural development. However, the environmental factors driving their diversity and nationwide biogeographic model remain elusive, impacting our capacity to predict their changes under future climate scenarios. Here, we analyzed potential fungal plant pathogens from 563 samples collected from 57 agricultural fields across China. Over 28.0% of fungal taxa in the phyllosphere were identified as potential plant pathogens, compared to 22.3% in the rhizosphere. Dominant fungal plant pathogen groups were Cladosporium (in the phyllosphere) and Fusarium (in the rhizosphere), with higher diversity observed in the phyllosphere than in rhizosphere soil. Deterministic processes played an important role in shaping the potential fungal plant pathogen community assembly in both habitats. Mean annual precipitation and temperature were the most important factor influencing phyllosphere fungal plant pathogen richness. Significantly negative relationships were found between fungal pathogen diversity and sorghum yield. Notably, compared to the rhizosphere, the phyllosphere fungal plant pathogen diversity played a more crucial role in sorghum yield. Together, our work provides novel insights into the factors governing the spatial patterns of fungal plant pathogens in the crop microbiome, and highlights the potential significance of aboveground phyllosphere fungal plant pathogens in crop productivity.


Subject(s)
Microbiota , Sorghum , Soil Microbiology , Agriculture , Soil , Edible Grain
12.
BMC Public Health ; 24(1): 538, 2024 Feb 21.
Article in English | MEDLINE | ID: mdl-38383355

ABSTRACT

BACKGROUND: Large-scale outbreaks of scrub typhus combined with its emergence in new areas as a vector-borne rickettsiosis highlight the ongoing neglect of this disease. This study aims to explore the long-term changes and regional leading factors of scrub typhus in China, with the goal of providing valuable insights for disease prevention and control. METHODS: This study utilized a Bayesian space-time hierarchical model (BSTHM) to examine the spatiotemporal heterogeneity of scrub typhus and analyze the relationship between environmental factors and scrub typhus in southern and northern China from 2006 to 2018. Additionally, a GeoDetector model was employed to assess the predominant influences of geographical and socioeconomic factors in both regions. RESULTS: Scrub typhus exhibits a seasonal pattern, typically occurring during the summer and autumn months (June to November), with a peak in October. Geographically, the high-risk regions, or hot spots, are concentrated in the south, while the low-risk regions, or cold spots, are located in the north. Moreover, the distribution of scrub typhus is influenced by environment and socio-economic factors. In the north and south, the dominant factors are the monthly normalized vegetation index (NDVI) and temperature. An increase in NDVI per interquartile range (IQR) leads to a 7.580% decrease in scrub typhus risk in northern China, and a 19.180% increase in the southern. Similarly, of 1 IQR increase in temperature reduces the risk of scrub typhus by 10.720% in the north but increases it by 15.800% in the south. In terms of geographical and socio-economic factors, illiteracy rate and altitude are the key determinants in the respective areas, with q-values of 0.844 and 0.882. CONCLUSIONS: These results indicated that appropriate climate, environment, and social conditions would increase the risk of scrub typhus. This study provided helpful suggestions and a basis for reasonably allocating resources and controlling the occurrence of scrub typhus.


Subject(s)
Scrub Typhus , Humans , Scrub Typhus/epidemiology , Bayes Theorem , China/epidemiology , Seasons , Economic Factors , Incidence
13.
Ren Fail ; 46(1): 2312533, 2024 Jan 30.
Article in English | MEDLINE | ID: mdl-38391179

ABSTRACT

OBJECTIVES: Currently, there is no consensus on the optimal timing for the initiation of peritoneal dialysis (PD) after catheter placement. DESIGN: Systematic review and meta-analysis. EXACT DATE OF DATA COLLECTION: From inception till July 31, 2023. MAIN OUTCOME MEASURES: To assess the outcomes and safety of unplanned PD initiation (<14/7 days after catheter insertion) in cohort studies. RESULTS: Fifteen studies involving 3054 participants were included. (1) The risk of unplanned initiation of leakage and Obstruction was no difference in both the break-in period (BI) <14 and BI < 7 groups. (2) Catheter displacement was more likely to occur in the emergency initiation group with BI < 7. (3) No significant differences were observed between the two groups regarding infectious complications. (4) There was no difference in transition to HD between patients with BI < 7 and BI < 14 d. CONCLUSION: Infectious complications of unplanned initiation of peritoneal dialysis did not differ from planned initiation. Emergency initiation in the BI < 7 group had higher catheter displacement, but heterogeneity was higher. There were no differences in leakage or obstruction in either group. Catheter survival was the same for emergency initiation of peritoneal dialysis compared with planned initiation of peritoneal dialysis and did not increase the risk of conversion to hemodialysis. REGISTRATION: This meta-analysis was registered on PROSPERO (https://www.crd.york.ac.uk/PROSPERO/, number: CRD42023431369).


Subject(s)
Kidney Failure, Chronic , Peritoneal Dialysis , Humans , Cohort Studies , Kidney Failure, Chronic/therapy , Prognosis , Renal Dialysis
14.
Sci Total Environ ; 921: 171227, 2024 Apr 15.
Article in English | MEDLINE | ID: mdl-38402820

ABSTRACT

Understanding the assembly mechanisms of microbial communities, particularly comammox Nitrospira, in agroecosystems is crucial for sustainable agriculture. However, the large-scale distribution and assembly processes of comammox Nitrospira in agricultural soils remain largely elusive. We investigated comammox Nitrospira abundance, community structure, and assembly processes in 16 paired upland peanuts and water-logged paddy soils in south China. Higher abundance, richness, and network complexity of comammox Nitrospira were observed in upland soils than in paddy soils, indicating a preference for upland soils over paddy soils among comammox Nitrospira taxa in agricultural environments. Clade A.2.1 and clade A.1 were the predominant comammox Nitrospira taxa in upland and paddy soils, respectively. Soil pH was the most crucial factor shaping comammox Nitrospira community structure. Stochastic processes were found to predominantly drive comammox Nitrospira community assembly in both upland and paddy soils, with deterministic processes playing a more important role in paddy soils than in upland soils. Overall, our findings demonstrate the higher stochasticity of comammox Nitrospira in upland soils than in the adjacent paddy soils, which may have implications for autotrophic nitrification in acidic agricultural soils.


Subject(s)
Ammonia , Soil , Soil/chemistry , Oxidation-Reduction , Bacteria , Nitrification , Phylogeny , Archaea
15.
Neurology ; 102(5): e208117, 2024 Mar 12.
Article in English | MEDLINE | ID: mdl-38350046

ABSTRACT

BACKGROUND AND OBJECTIVES: Altered metabolism is observed in amyotrophic lateral sclerosis (ALS). However, without a standardized methodology to define metabolic changes, our understanding of factors contributing to and the clinical significance of altered metabolism in ALS is limited. METHODS: We aimed to determine how geographic variation in metabolic rates influences estimates and accuracy of predicted resting energy expenditure (REE) in patients with ALS and controls, while validating the effectiveness of cohort-specific approaches in predicting altered metabolic rate in ALS. Participants from 3 geographically distinct sites across Australia, China, and the Netherlands underwent REE assessments, and we considered 22 unique equations for estimating REE. Analyses evaluated equation performance and the influence of demographics on metabolic status. Comparisons were made using standardized and local reference values to identify metabolic alterations. RESULTS: 606 participants were included from Australia (patients with ALS: 140, controls: 154), the Netherlands (patients with ALS: 79, controls: 37) and China (patients with ALS: 67, controls: 129). Measured REE was variable across geographic cohorts, with fat-free mass contributing to this variation across all patients (p = 0.002 to p < 0.001). Of the 22 predication equations assessed, the Sabounchi Structure 4 (S4) equation performed relatively well across all control cohorts. Use of prediction thresholds generated using data from Australian controls generally increased the prevalence of hypermetabolism in Chinese (55%, [43%-67%]) and Dutch (44%, [33%-55%]) cases when compared with Australian cases (30%, [22%-38%]). Adjustment of prediction thresholds to consider geographically distinct characteristics from matched control cohorts resulted in a decrease in the proportion of hypermetabolic cases in Chinese and Dutch cohorts (25%-31% vs 55% and 20%-34% vs 43%-44%, respectively), and increased prevalence of hypometabolism in Dutch cases with ALS (1% to 8%-10%). DISCUSSION: The identification of hypermetabolism in ALS is influenced by the formulae and demographic-specific prediction thresholds used for defining alterations in metabolic rate. A consensus approach is needed for identification of metabolic changes in ALS and will facilitate improved understanding of the cause and clinical significance of this in ALS.


Subject(s)
Amyotrophic Lateral Sclerosis , Basal Metabolism , Humans , Energy Metabolism , Amyotrophic Lateral Sclerosis/epidemiology , Amyotrophic Lateral Sclerosis/metabolism , Australia/epidemiology , Body Composition
16.
Immunogenetics ; 76(2): 137-143, 2024 Apr.
Article in English | MEDLINE | ID: mdl-38206349

ABSTRACT

Killer cell immunoglobulin-like receptor (KIR) and human leukocyte antigen (HLA) play crucial roles in regulating NK cell activity. Here, we report a real-time quantitative PCR (qPCR) to genotype all KIR genes and their copy numbers simultaneously. With 18 pairs of locus-specific primers, we identified KIR genes by Ct values and determined KIR copy number using the 2-∆Ct method. Haplotypes were assigned based on KIR gene copy numbers. The real-time qPCR results were consistent with the NGS method, except for one sample with KIR2DL5 discrepancy. qPCR is a multiplex method that can identify KIR copy number, which helps obtain a relatively accurate haplotype structure, facilitating increased KIR research in laboratories where NGS or other high-resolution methods are not available.


Subject(s)
DNA Copy Number Variations , Receptors, KIR , Humans , DNA Copy Number Variations/genetics , Alleles , Genotype , Receptors, KIR/genetics , Haplotypes/genetics , Real-Time Polymerase Chain Reaction
17.
PLoS Genet ; 20(1): e1011037, 2024 Jan.
Article in English | MEDLINE | ID: mdl-38206971

ABSTRACT

Explicitly sharing individual level data in genomics studies has many merits comparing to sharing summary statistics, including more strict QCs, common statistical analyses, relative identification and improved statistical power in GWAS, but it is hampered by privacy or ethical constraints. In this study, we developed encG-reg, a regression approach that can detect relatives of various degrees based on encrypted genomic data, which is immune of ethical constraints. The encryption properties of encG-reg are based on the random matrix theory by masking the original genotypic matrix without sacrificing precision of individual-level genotype data. We established a connection between the dimension of a random matrix, which masked genotype matrices, and the required precision of a study for encrypted genotype data. encG-reg has false positive and false negative rates equivalent to sharing original individual level data, and is computationally efficient when searching relatives. We split the UK Biobank into their respective centers, and then encrypted the genotype data. We observed that the relatives estimated using encG-reg was equivalently accurate with the estimation by KING, which is a widely used software but requires original genotype data. In a more complex application, we launched a finely devised multi-center collaboration across 5 research institutes in China, covering 9 cohorts of 54,092 GWAS samples. encG-reg again identified true relatives existing across the cohorts with even different ethnic backgrounds and genotypic qualities. Our study clearly demonstrates that encrypted genomic data can be used for data sharing without loss of information or data sharing barrier.


Subject(s)
Genome-Wide Association Study , Privacy , Humans , Genome-Wide Association Study/methods , Genotype , Software , Genomics
18.
HLA ; 103(1): e15326, 2024 Jan.
Article in English | MEDLINE | ID: mdl-38180281

ABSTRACT

HLA-A*29:171 differs from HLA-A*29:01:01:01 by one nucleotide substitution at position 257T>G in exon 2.


Subject(s)
High-Throughput Nucleotide Sequencing , Humans , Alleles , Exons/genetics
19.
Acta Ophthalmol ; 102(1): e69-e77, 2024 Feb.
Article in English | MEDLINE | ID: mdl-37143398

ABSTRACT

PURPOSE: The morphological changes in the cornea and crystalline lens have not been closely evaluated after the administration of atropine 0.01%. This study aims to evaluate the radii of curvature and refractive power of the cornea and lens in myopic eyes during atropine 0.01% treatment. METHODS: Children aged 6-14 years with myopia <-6.0 D were randomized to receive atropine 0.01% once nightly with single vision lenses or simply wear single vision lenses. Ocular biometric parameters were measured using the IOLMaster 700 biometry and the radii of corneal and lenticular curvature were simulated using a customized program. RESULTS: At the 9-month visit, 69 atropine-treated eyes and 50 control eyes were included in the final analyses. In atropine-treated eyes, the posterior corneal surface steepened (-0.05 ± 0.13 mm) and the anterior lenticular surface flattened (0.20 ± 0.69 mm) significantly within 3-6 months, whereas the posterior corneal surface and anterior lenticular surface gradually flattened (0.07 ± 0.23 and 0.32 ± 0.80 mm respectively) in the control eyes over 9 months. The difference in the change of corneal refractive power was significant between groups (-0.03 ± 0.18 D vs. 0.11 ± 0.24 D, p = 0.001), while that in the change of lenticular refractive power was statistically insignificant (0.01 ± 0.92 D vs. -0.22 ± 0.86 D, p = 0.161). CONCLUSIONS: The administration of atropine 0.01% exhibited a clinically short and subtle impact on the cornea and lens, which may shed light on new targets of action for atropine in inhibiting myopia.


Subject(s)
Lens, Crystalline , Myopia , Child , Humans , Atropine , Cornea , Corneal Topography , Myopia/drug therapy , Ophthalmic Solutions , Radius , Refraction, Ocular , Adolescent
20.
Blood Transfus ; 22(2): 140-149, 2024 Mar.
Article in English | MEDLINE | ID: mdl-37458723

ABSTRACT

BACKGROUND: Emerging viruses in the blood of healthy/qualified donors can seriously affect transfusion safety. However, the virus characteristics in different healthy blood donors and blood components are still not fully understood. MATERIALS AND METHODS: Buffy coat (BC) and plasma specimens were collected from 32 whole blood donors, and platelet (PLT) and BC specimens from 30 apheresis platelet donors to explore the full annotation of viral metagenomics in different blood components from Chinese blood donors using next-generation sequencing technology. RESULTS: The study detected 56 viruses in the plasma and BC groups of whole blood donors. The plasma group had a significantly higher viral abundance and more types of viruses than the BC group. We detected 20 viruses in the PLT and BC groups of apheresis platelet donors. Viral abundance and types were significantly lower in the BC group than in the PLT group. According to ß-diversity analysis, the plasma group had a significantly different community structure and composition than the BC group. DISCUSSION: Viral nucleic acid is found in the blood of healthy Chinese blood donors, with the highest concentration in plasma, which could explain the distribution of viruses in the blood of healthy individuals.


Subject(s)
Blood Component Removal , Blood Donors , Humans , Blood Platelets , High-Throughput Nucleotide Sequencing , China
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