Project description:MicroRNAs are important negative regulators of protein coding gene expression, and have been studied intensively over the last few years. To this purpose, different measurement platforms to determine their RNA abundance levels in biological samples have been developed. In this study, we have systematically compared 12 commercially available microRNA expression platforms by measuring an identical set of 20 standardized positive and negative control samples, including human universal reference RNA, human brain RNA and titrations thereof, human serum samples, and synthetic spikes from homologous microRNA family members. We developed novel quality metrics in order to objectively assess platform performance of very different technologies such as small RNA sequencing, RT-qPCR and (microarray) hybridization. We assessed reproducibility, sensitivity, quantitative performance, and specificity. The results indicate that each method has its strengths and weaknesses, which helps guiding informed selection of a quantitative microRNA gene expression platform in function of particular study goals.
Project description:Here we developed CapStarr-Seq, a novel high-throughput strategy to quantitatively assess enhancer activity in mammals. This approach couples capture of regions of interest to previously developed Starr-seq technique. Extensive assessment of CapStarr-seq demonstrated accurate quantification of enhancer activity. Furthermore, we found that enhancer strength correlates with binding complexity of tissue-specific transcription factors and super-enhancers, while additive enhancer activity isolates key genes involved in cell identity and function. CapStarr-seq analysis in P5424 cell line (2 replicates), 3T3 cell line and in the plasmid library before (Input) and after transfection
Project description:Goose circovirus (GoCV) is a recently identified pathogen in geese that is known to cause slow growth, feather disorder syndrome, and immunosuppression. Infection with GoCV may increase the risk of coinfections with multiple pathogens, leading to significant economic losses in the goose industry. However, due to a lack of serological detection methods, analysis of viral nucleic acids has been widely used in GoCV epidemiological surveys, which has limited accurate monitoring of the prevalence of GoCV. In this study, we developed and optimized an indirect ELISA method based on the prokaryotic-expressed recombinant GoCV capsid protein (△Cap-iELISA). The △Cap-iELISA was then used to test 349 goose serum samples collected from Guangdong, Shandong, and Fujian provinces during 2023 and 2024. The results showed that the positive rate of GoCV antibodies in the sampled geese was 71.06%. Further analysis indicated that the positive rate of GoCV antibodies increased with the age of the geese. In conclusion, we have developed a novel iELISA method that is well-suited for large-scale clinical detection and early diagnosis of GoCV infection. Notably, a significant correlation between age and the positive rate of GoCV antibodies among geese was observed based on this newly established method.
Project description:Studies evaluating xanthine oxidoreductase (XOR) activities in comprehensive liver diseases are scarce, and different etiologies have previously been combined in groups for comparison. To accurately evaluate XOR activities in liver diseases, the plasma XOR activities in etiology-based comprehensive liver diseases were measured using a novel, sensitive, and accurate assay that is a combination of liquid chromatography and triple quadrupole mass spectrometry to detect [13C2, 15N2]uric acid using [13C2, 15N2]xanthine as a substrate. We also mainly evaluated the association between the plasma XOR activities and parameters of liver tests, purine metabolism-associated markers, oxidative stress markers, and an inflammation marker. In total, 329 patients and 32 controls were enrolled in our study. Plasma XOR activities were generally increased in liver diseases, especially in the active phase, such as in patients with hepatitis C virus RNA positivity, those with abnormal alanine transaminase (ALT) levels in autoimmune liver diseases, and uncured hepatocellular carcinoma patients. Plasma XOR activities were numerically highest in patients with acute hepatitis B. Plasma XOR activities were closely correlated with parameters of liver tests, especially serum ALT levels, regardless of etiology and plasma xanthine levels. Our results indicated that plasma XOR activity might reflect the active phase in various liver diseases.
Project description:H. seropedicae wild-type or ntrC mutant were grown on three different nitrogen conditions: nitrogen limiting, ammonium shock and nitrate shock.
Project description:Naïve and activated T-cells has a different response to antigenic challenge. We examine whether a cytokine like IL-6 induces different responses through the Jak-STAT pathway to affect the functional characteristics of a given CD4 T‑cell subset. We isolated naïve and effector memory (Tem) CD4 T-cells to investigated STAT1 and STAT3 binding after 1-hour treatment with 20ng/ml IL-6 in the presence of anti-CD3/CD28.
Project description:In two recent articles a method has been described for calculating the total energy of large molecules. The method is called the kernel energy method (KEM) and requires knowledge of the crystal structure of interest. Calculations are simplified by adopting the approximation that a full molecule could be represented by smaller kernels of atoms. The KEM was illustrated with peptides ranging in size from 4 to 19 amino acid residues, and was found to deliver accurate results. The use of the KEM does not depend upon a particular choice of basis functions and is applicable across quantum computational methods of differing levels of accuracy. These earlier investigations suggested that the KEM could be used to calculate the ab initio quantum mechanical energy of proteins. An application has been made with the protein insulin, composed of 51 aa. Accurate KEM Hartree-Fock energies are obtained for the separate A and B chains of insulin and for their composite structure in the full insulin molecule. A limited basis is used to make possible calculation of the full insulin molecule, which can be used as a standard of accuracy for the KEM calculation. The KEM result obtained is E(KEM) = -21104.7656 a.u. It differs from a full molecule Hartree-Fock result by only 0.000002%. The solvent molecules can be treated effectively as a separate kernel. The KEM result for the fully solvated insulin molecule is E(KEM) = -26275.4127 a.u., differing from the full molecule Hartree-Fock result by as little as 0.000023%.
Project description:We have developed a mobile phone application for measuring the intake of dietary fiber and validated the ability of the application to accurately capture this intake against measurements registered by a dietary record. We also investigated what food groups contributed most to the total, soluble, and insoluble dietary fiber intake. Twenty-six randomly selected Swedish women aged 35-85 years were included and randomized to either start to register dietary intake in the application or by a dietary record, during three consecutive days. After a washout period of at least two weeks, the participants used the other method. We found that the difference in measured mean fiber intake between the dietary record and the application was two grams independent of the total intake per day. A statistically significant correlation between fiber intake as measured by the two methods was found (rho = 0.65, p < 0.001). Vegetables and roots were the predominantly contributing foods to total and soluble fiber intake. Bread and crackers contributed most to insoluble fiber intake. In conclusion, the application may be considered as a useful and easy-to-use method to measure dietary fiber intake.