Comparison of protein extraction methods suitable for proteomics analysis in seedling roots of Jerusalem artichoke under salt (NaCl) stress

An efficient protein extraction method is a prerequisite for successful implementation of proteomics. In this study, seedling roots of Jerusalem artichoke were treated with the concentration of 250 mM NaCl for 36 h. Subsequently, six different protocols of protein extraction were applied to seedling roots of Jerusalem artichoke for comparing extraction efficiency by conducting two-dimensional electrophoresis (2-DE). The first-dimensional electrophoresis was differently performed by using tube gel and immobilized pH gradient (IPG) strips, respectively. Sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) in the second dimension was equally carried out. The results indicated that precipitation of ammonium acetate in methanol after phenol extraction (Method 6) provided the best effect. Less impurity was contained in extracted proteins and the 2-DE gel images showed less horizontal and vertical stripes, the most proteineous spots were extracted on the basis of the protocol, up to 903. Trichloroacetic acid (TCA) method (Method 1) exhibited relative less quality gel images. 248 protein spots were only obtained according to the protocol and were the least among six protocols. Although, Mg/Nonidet P-40 (NP-40) methods (Methods 3 and 4) could extract a large number of proteins, it exhibited the worst quality gel images among all protocols and the horizontal and vertical stripes on the gel images were the most severe. It might be caused by a high salt content in extracted proteins.Key words: Proteomics, Jerusalem artichoke, roots, two-dimensional electrophoresis (2-DE), protocol, salt

The technology of large-scale pharmaceutical plasmid purification by cetyltrimethylammonium bromide and Tritonx-114

Many methods for plasmid purification have been developed, and the whole process must be designed to remove the host RNA, protein, genomic DNA and endotoxin. Currently, plasmid is mostly purified by time-consuming chromatographies. As an alternative, a new plasmid purification technology with cetyltrimethylammonium bromide (CTAB) is described. After lysis with alkali, the CTAB was directly titrated into the supernatant for plasmid precipitation, then the coprecipitated pellets were dealt with 3 M KAc and TritonX-114. Quality detection showed that the purified plasmids were free from the contamination of host RNA. In 1 mg purified plasmid, the bacterial genomic DNA, host endotoxin and protein were less than 10 g/ mg, 50 EU/ mg and 10 g/mg, respectively. The ratio of OD260/OD280 was between 1.75 - 1.85, more than 90% of the prepared plasmid presented in the supercoiled form. Further test demonstrated that the pcDNAlacZ purified with CTAB and authoritative endotoxin-free plasmid Kit had the similar transfection efficiency in vivo and in vitro. CTAB can be used for plasmid purification; the main advantages of the DNAs purified with CTAB include the avoidance of animal-derived enzymes, toxic substance like chloroform and phenol. More attractive is that the whole process has the predominance of low cost

Molecular characterisation of canine parvovirus strains circulating in China

Canine parvovirus (CPV) was first isolated at 1978 in the USA. Analysis of CPV isolates by monoclonal antibodies and restriction enzymes have shown that after the first emergence of CPV (CPV-2) it evolved to give rise to new antigenic types, which were designated CPV types 2a, 2b and 2c. These new types have replaced the original CPV type 2, although the proportions of each of the new antigenic types vary in different countries. In China, CPV infections were first observed in 1982, however, there has been no information concerning the antigenic types of CPV prevailing in China now. In this study, we designed a PCR assay to type canine parvovirus strains in fecal samples collected from symptomatic dogs from 2006 to 2009. Our data showed that the CPV prevalent strain is mostly 2b, the proportion of CPV-2a is very low, no CPV-2c and CPV-2 were observed

Deletion within the Src homology domain 3 of Bruton's tyrosine kinase resulting in X-linked agammaglobulinemia (XLA).

The gene responsible for X-linked agammaglobulinemia (XLA) has been recently identified to code for a cytoplasmic tyrosine kinase (Bruton's agammaglobulinemia tyrosine kinase, BTK), required for normal B cell development. BTK, like many other cytoplasmic tyrosine kinases, contains Src homology domains (SH2 and SH3), and catalytic kinase domain. SH3 domains are important for the targeting of signaling molecules to specific subcellular locations. We have identified a family with XLA whose affected members have a point mutation (g-->a) at the 5' splice site of intron 8, resulting in the skipping of coding exon 8 and loss of 21 amino acids forming the COOH-terminal portion of the BTK SH3 domain. The study of three generations within this kinship, using restriction fragment length polymorphism and DNA analysis, allowed identification of the mutant X chromosome responsible for XLA and the carrier status in this family. BTK mRNA was present in normal amounts in Epstein-Barr virus-induced B lymphoblastoid cell lines established from affected family members. Although the SH3 deletion did not alter BTK protein stability and kinase activity of the truncated BTK protein was normal, the affected patients nevertheless have a severe B cell defect characteristic for XLA. The mutant protein was modeled using the normal BTK SH3 domain. The deletion results in loss of two COOH-terminal beta strands containing several residues critical for the formation of the putative SH3 ligand-binding pocket. We predict that, as a result, one or more crucial SH3 binding proteins fail to interact with BTK, interrupting the cytoplasmic signal transduction process required for B cell differentiation

A Computationally Efficient Method for Estimating Multi-Model Process Sensitivity Index

Identification of important processes of a hydrologic system is critical for improving process-based hydrologic modeling. To identify important processes while jointly considering parametric and model uncertainty, Dai et al. (2017), https://doi.org/10.1002/2016WR019715, developed a multi-model process sensitivity index. Numerical evaluation of the index using a brute force Monte Carlo (MC) simulation is computationally expensive, because it requires a nested structure of parameter sampling and the number of model simulations is on the order of N-2 (N being the number of parameter samples). To reduce computational cost, we develop a new method (here denoted as quasi-MC for brevity) that uses triple sets of parameter samples (generated using quasi-MC sequence) to remove the nested structure of parameter sampling in a theoretically rigorous way. The quasi-MC method reduces the number of model simulations from the order of N-2 to 2N. The performance of the method is assessed against the brute force MC approach and the recent binning method developed by Dai et al. (2017), https://doi.org/10.1002/2016WR019715, through two synthetic cases of groundwater flow and solute transport modeling. Due to its rigorous theoretical foundation, the quasi-MC method overcomes the limitations imposed by the inherently empirical nature of the binning method. We find that the quasi-MC method outperforms both the brute force MC and the binning method in terms of computational requirements and theoretical aspects, thus strengthening its potential for the assessment of process sensitivity indices subject to various sources of uncertainty

Study of transmission and reflection from a disordered lasing medium

A numerical study of the statistics of transmission ($t$) and reflection ($r$) of quasi-particles from a one-dimensional disordered lasing or amplifying medium is presented. The amplification is introduced via a uniform imaginary part in the site energies in the disordered segment of the single-band tight binding model. It is shown that $t$ is a non-self-averaging quantity. The cross-over length scale above which the amplification suppresses the transmittance is studied as a function of amplification strength. A new cross-over length scale is introduced in the regime of strong disorder and weak amplification. The stationary distribution of the backscattered reflection coefficient is shown to differ qualitatively from the earlier analytical results obtained within the random phase approximation.Comment: 5 pages RevTex (twocolumn format), 5 EPS figures, considerably modifie

Territory-Wide Chinese Cohort of Long QT Syndrome: Random Survival Forest and Cox Analyses

Introduction: Congenital long QT syndrome (LQTS) is a cardiac ion channelopathy that predisposes affected individuals to spontaneous ventricular tachycardia/fibrillation (VT/VF) and sudden cardiac death (SCD). The main aims of the study were to: (1) provide a description of the local epidemiology of LQTS, (2) identify significant risk factors of ventricular arrhythmias in this cohort, and (3) compare the performance of traditional Cox regression with that of random survival forests. / Methods: This was a territory-wide retrospective cohort study of patients diagnosed with congenital LQTS between 1997 and 2019. The primary outcome was spontaneous VT/VF. / Results: This study included 121 patients [median age of initial presentation: 20 (interquartile range: 8–44) years, 62% female] with a median follow-up of 88 (51–143) months. Genetic analysis identified novel mutations in KCNQ1, KCNH2, SCN5A, ANK2, CACNA1C, CAV3, and AKAP9. During follow-up, 23 patients developed VT/VF. Univariate Cox regression analysis revealed that age [hazard ratio (HR): 1.02 (1.01–1.04), P = 0.007; optimum cut-off: 19 years], presentation with syncope [HR: 3.86 (1.43–10.42), P = 0.008] or VT/VF [HR: 3.68 (1.62–8.37), P = 0.002] and the presence of PVCs [HR: 2.89 (1.22–6.83), P = 0.015] were significant predictors of spontaneous VT/VF. Only initial presentation with syncope remained significant after multivariate adjustment [HR: 3.58 (1.32–9.71), P = 0.011]. Random survival forest (RSF) model provided significant improvement in prediction performance over Cox regression (precision: 0.80 vs. 0.69; recall: 0.79 vs. 0.68; AUC: 0.77 vs. 0.68; c-statistic: 0.79 vs. 0.67). Decision rules were generated by RSF model to predict VT/VF post-diagnosis. / Conclusions: Effective risk stratification in congenital LQTS can be achieved by clinical history, electrocardiographic indices, and different investigation results, irrespective of underlying genetic defects. A machine learning approach using RSF can improve risk prediction over traditional Cox regression models

Modern Chinese Strategams as the Basis of the Training Program Using Artificial Intelligence

Artificial intelligence technologies are actively developing in areas that are consistent with commercial activities. We believe that the spiritual sphere also needs a new type of training programs. These programs should accumulate expressions that convey the spirit of the era. Chinese expressions are extremely important for understanding modernity, since China is a world leader in various fields of human activity. Using the two most popular expressions in China as an example, we focus on the current areas of Chinese domestic and foreign policy.Технологии искусственного интеллекта активно развиваются в сферах, соотносимых с коммерческой деятельностью. Мы полагаем, что и духовная сфера нуждается в обучающих программах нового типа. Данные программы должны аккумулировать выражения, передающие дух эпохи. Чрезвычайно важное значение для понимания современности имеют китайские выражения, поскольку Китай — мировой лидер в самых разных областях человеческой деятельности. На примере двух самых популярных в Китае выражений мы фокусируем внимание на актуальных направлениях китайской внутренней и внешней политики

Disparities and risks of sexually transmissible infections among men who have sex with men in China: a meta-analysis and data synthesis.

BACKGROUND: Sexually transmitted infections (STIs), including Hepatitis B and C virus, are emerging public health risks in China, especially among men who have sex with men (MSM). This study aims to assess the magnitude and risks of STIs among Chinese MSM. METHODS: Chinese and English peer-reviewed articles were searched in five electronic databases from January 2000 to February 2013. Pooled prevalence estimates for each STI infection were calculated using meta-analysis. Infection risks of STIs in MSM, HIV-positive MSM and male sex workers (MSW) were obtained. This review followed the PRISMA guidelines and was registered in PROSPERO. RESULTS: Eighty-eight articles (11 in English and 77 in Chinese) investigating 35,203 MSM in 28 provinces were included in this review. The prevalence levels of STIs among MSM were 6.3% (95% CI: 3.5-11.0%) for chlamydia, 1.5% (0.7-2.9%) for genital wart, 1.9% (1.3-2.7%) for gonorrhoea, 8.9% (7.8-10.2%) for hepatitis B (HBV), 1.2% (1.0-1.6%) for hepatitis C (HCV), 66.3% (57.4-74.1%) for human papillomavirus (HPV), 10.6% (6.2-17.6%) for herpes simplex virus (HSV-2) and 4.3% (3.2-5.8%) for Ureaplasma urealyticum. HIV-positive MSM have consistently higher odds of all these infections than the broader MSM population. As a subgroup of MSM, MSW were 2.5 (1.4-4.7), 5.7 (2.7-12.3), and 2.2 (1.4-3.7) times more likely to be infected with chlamydia, gonorrhoea and HCV than the broader MSM population, respectively. CONCLUSION: Prevalence levels of STIs among MSW were significantly higher than the broader MSM population. Co-infection of HIV and STIs were prevalent among Chinese MSM. Integration of HIV and STIs healthcare and surveillance systems is essential in providing effective HIV/STIs preventive measures and treatments. TRIAL REGISTRATION: PROSPERO NO: CRD42013003721

Association of NPAC score with survival after acute myocardial infarction

BACKGROUND AND AIMS: Risk stratification in acute myocardial infarction (AMI) is important for guiding clinical management. Current risk scores are mostly derived from clinical trials with stringent patient selection. We aimed to establish and evaluate a composite scoring system to improve short-term mortality classification after index episodes of AMI, independent of electrocardiography (ECG) pattern, in a large real-world cohort. METHODS: Using electronic health records, patients admitted to our regional teaching hospital (derivation cohort, n = 1747) and an independent tertiary care center (validation cohort, n = 1276), with index acute myocardial infarction between January 2013 and December 2017, as confirmed by principal diagnosis and laboratory findings, were identified retrospectively. RESULTS: Univariate logistic regression was used as the primary model to identify potential contributors to mortality. Stepwise forward likelihood ratio logistic regression revealed that neutrophil-to-lymphocyte ratio, peripheral vascular disease, age, and serum creatinine (NPAC) were significant for 90-day mortality (Hosmer- Lemeshow test, p = 0.21). Each component of the NPAC score was weighted by beta-coefficients in multivariate analysis. The C-statistic of the NPAC score was 0.75, which was higher than the conventional Charlson's score (C-statistic = 0.63). Judicious application of a deep learning model to our dataset improved the accuracy of classification with a C-statistic of 0.81. CONCLUSIONS: The NPAC score comprises four items from routine laboratory parameters to basic clinical information and can facilitate early identification of cases at risk of short-term mortality following index myocardial infarction. Deep learning model can serve as a gatekeeper to facilitate clinical decision-making