Multiplex conditional mutagenesis in zebrafish using the CRISPR/Cas system

The clustered regularly interspaced short palindromic repeat (CRISPR)/CRISPR-associated protein (Cas) system is a powerful tool for genome editing in numerous organisms. However, the system is typically used for gene editing throughout the entire organism. Tissue and temporal specific mutagenesis is often desirable to determine gene function in a specific stage or tissue and to bypass undesired consequences of global mutations. We have developed the CRISPR/Cas system for conditional mutagenesis in transgenic zebrafish using tissue-specific and/or inducible expression of Cas9 and U6-driven expression of sgRNA. To allow mutagenesis of multiple targets, we have isolated four distinct U6 promoters and designed Golden Gate vectors to easily assemble transgenes with multiple sgRNAs. We provide experimental details on the reagents and applications for multiplex conditional mutagenesis in zebrafish.

[Establishing a noninvasive prediction model for type 2 diabetes mellitus based on a rural Chinese population]

OBJECTIVE

To provide a noninvasive type 2 diabetes mellitus (T2DM) prediction model for a rural Chinese population.

METHODS

From July to August, 2007 and July to August, 2008, a total of 20 194 participants aged ≥18 years were selected by cluster sampling technique from a rural population in two townships of Henan province, China. Data were collected by questionnaire interview, anthropometric measurement, and fasting plasma glucose and lipid profile examination. A total 17 265 participants were followed up from July to August, 2013 and July to October, 2014. Finally, 12 285 participants were selected for analysis. Data for these participants were randomly divided into a derivation group (derivation dataset, n= 6 143) and validation group (validation dataset, n=6 142) by 1∶1, respectively. Randomization was carried out by the use of computer-generated random numbers. A Cox regression model was used to analyze risk factors of T2DM in the derivation dataset. A T2DM prediction model was established by multiplying β by 10 for each significant variable. After the total score was calculated by the model, analysis of the receiver operating characteristic (ROC) curve was performed. The area under the ROC curve (AUC) was used for evaluating model predictability. Furthermore, the model's predictability was validated in the validation dataset and compared with the Finnish Diabetes Risk Score (FINDRISC) model.

RESULTS

A total 779 of 12 285 participants developed T2DM during the 6-year study period. The incidence rate was 6.12% in the derivation dataset (n=376) and 6.56% in the validation dataset (n=403). The difference was not statistically significant (χ(2)=1.00, P=0.316). A total of four noninvasive T2DM prediction models were established using the Cox regression model. The ROCs of the risk score calculated by the prediction models indicated that the AUCs of these models were similar (0.67-0.70). The AUC and Youden index of model 4 was the highest. The optimal cut-off value, sensitivity, specificity, and Youden index were scores of 25, 65.96%, 66.47%, and 0.32, respectively. Age, sleep time, BMI, waist circumference, and hypertension were selected as predictive variables. Using age<30 years as reference, β values were 1.07, 1.58, and 1.67 and assigned scores were 11, 16, and 17 for age groups 30-44, 45-59, and ≥60 years, respectively. Using sleep time<8.0 h/d as reference, the β value and assigned score were 0.27 and 3, respectively, for sleep time ≥10.0 h/d. Using BMI 18.5-23.9 kg/m(2) as reference, β values were 0.53 and 1.00 and assigned scores 5 and 10, respectively, for BMI 24.0-27.9 kg/m(2), and ≥28.0 kg/m(2). Using waist circumference <85 cm for males/< 80 cm for females as reference, β values were 0.44 and 0.65 and assigned scores 4 and 7, respectively, for 85 cm ≤ waist circumference <90 cm for males/80 cm≤ waist circumference <85 cm for females, and waist circumference ≥90 cm for males/≥85 cm for females. Using nonhypertension as reference, the respective β value and assigned score were 0.34 and 3 for hypertension. The AUC performance of this model and the FINDRISC model was 0.66 and 0.64 (P=0.135), respectively, in the validation dataset.

CONCLUSION

Based on this cohort study, a noninvasive prediction model that included age, sleep time, BMI, waist circumference, and hypertension was established, which is equivalent to the FINDRISC model and applicable to a rural Chinese population.

Multicenter Prospective Trial of Stent Placement in Patients with Symptomatic High-Grade Intracranial Stenosis

BACKGROUND AND PURPOSE

On the basis of the high 1-month stroke and/or death (14.7%) rates associated with stent placement in the Stenting versus Aggressive Medical Management for Preventing Recurrent Stroke in Intracranial Stenosis trial, modifications in patient selection and procedural aspects for intracranial stent placement have been recommended. We performed a multicenter prospective single-arm trial to determine whether such modifications would result in lower rates of periprocedural stroke and/or death.

MATERIALS AND METHODS

The study enrolled patients with recent transient ischemic attack or ischemic stroke (excluding perforator ischemic events) related to high-grade (70%-99% in severity) stenosis of a major intracranial artery. Patients were treated by using angioplasty and self-expanding stents 3 weeks after the index ischemic event at 1 of the 10 high-volume centers in China. An independent neurologist ascertained the occurrence of any stroke and/or death within 1 month after the procedure.

RESULTS

A total of 100 consecutive patients were recruited. The target lesions were located in the middle cerebral artery (M1) (n = 38, 38%), intracranial internal carotid artery (n = 17, 17%), intradural vertebral artery (n = 18, 18%), and basilar artery (n = 27, 27%). The technical success rate of stent deployment with residual stenosis of <50% was 100%. The overall 1-month stroke and/or death rate was 2% (95% confidence interval, 0.2%-7.0%). Two ischemic strokes occurred in the pontine region (perforator distribution) in patients following angioplasty and stent placement for basilar artery stenosis.

CONCLUSIONS

The results of this prospective multicenter study demonstrated that modifications in patient selection and procedural aspects can substantially reduce the 1-month stroke and/or death rate following intracranial stent placement.

Brief Exercises Affect Gene Expression in Circulating Monocytes

We aimed to give a systematic hypothesis on the functions of exercise on circulating monocytes by identifying a discrete set of genes in circulating monocytes that were altered by exercise. The microarray expression profile of GSE51835 was downloaded from gene expression omnibus (GEO) database for the identification of differentially expressed genes (DEGs) using limma and affy packages in R language. Gene Ontology (GO) terms and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis were performed for DEGs, followed by the construction of co-expression network and protein-protein interaction (PPI) network. The top 10 nodes in PPI network were screened, and subnetwork was constructed for the key genes identification. Totally, 35 DEGs, including 2 upregulated genes and 33 downregulated genes, were identified. The enriched GO terms were mainly linked to immune response and defence response, and the enriched KEGG pathways were mainly associated with natural killer cell-mediated cytotoxicity and graft-versus-host disease. Dual-specificity phosphatase 2 (DUSP2) was identified as a key node in the co-expression network. In the PPI network, CD247 module (CD247), chemokine (C-X-C motif) receptor 4 (CXCR4), granzyme B (GZMB) and perforin 1 (PRF1) were identified as key nodes. An important interaction, GZMB/PRF1, was detected. Five key genes, including DUSP2, CD247, CXCR4, GZMB and PRF1, and an interaction of GZMB/PRF1, were significant factors in the immune processes of circulating monocytes, which might be regulated by brief exercises, leading to the enhancement of immune function.

Pharmacokinetic study of isatin in dog plasma by liquid chromatography tandem mass spectrometry

AIM

A sensitive and selective method was developed and validated to study the pharmacokinetics of isatin.

METHODS

The blood samples were pretreated by protein precipitation method using methanol. Quetiapine was used as an internal standard. After pretreatment, the samples were assayed by LC/MS/MS method and the pharmacokinetic parameters were calculated by WinNonlin 5.2 using non-compartment model. The separation was performed on a Venusil XBP PH column (5 µm, 2.0×100 mm) with an isocratic mobile phase consisted of methanol-water (containing 50 mM ammonium formate) (65:35, v/v) at a flow rate of 0.3 mL/min. The Agilent G6410B triple quadrupole LC/MS system was operated under the multiple reactions monitoring mode (MRM) using the electrospray ionization technique in positive mode.

RESULTS

The lower limits of quantification (LLOQ) of the analyte of the method was 10 ng/mL. The method was linear with correlation coefficient >0.995. The intraday and interday accuracy and precision of the assay were acceptable.

CONCLUSION

This method has been applied successfully to a pharmacokinetic study involving the oral and intravenous administration of isatin to beagle dogs.

SP1-induced upregulation of the long noncoding RNA TINCR regulates cell proliferation and apoptosis by affecting KLF2 mRNA stability in gastric cancer

The long noncoding RNA TINCR shows aberrant expression in human squamous carcinomas. However, its expression and function in gastric cancer remain unclear. We report that TINCR is strongly upregulated in human gastric carcinoma (GC), where it was found to contribute to oncogenesis and cancer progression. We also revealed that TINCR overexpression is induced by nuclear transcription factor SP1. Silencing TINCR expression inhibited cell proliferation, colony formation, tumorigenicity and apoptosis promotion, whereas TINCR overexpression promoted cell growth, as documented in the SGC7901 and BGC823 cell lines. Mechanistic analyses indicated that TINCR could bind to STAU1 (staufen1) protein, and influence KLF2 mRNA stability and expression, then KLF2 regulated cyclin-dependent kinase genes CDKN1A/P21 and CDKN2B/P15 transcription and expression, thereby affecting the proliferation and apoptosis of GC cells. Together, our findings suggest that TINCR contributes to the oncogenic potential of GC and may constitute a potential therapeutic target in this disease.

Prevalence of Metabolically Healthy Obese and Metabolically Obese but Normal Weight in Adults Worldwide: A Meta-Analysis

The objective of the present study was to summarize the prevalence and influencing factors of metabolically healthy obese (MHO) and metabolically obese but normal weight (MONW) among people ≥ 18 years old in the general population worldwide. We searched for studies of the prevalence of MHO and MONW published in English and Chinese up to October 2013. Pooled prevalence estimates were calculated by a random-effects model according to a Q test. The effects of gender, region, age, sample size, smoking, and alcohol consumption on MHO and MONW were analyzed. Differences between subgroups were assessed by chi-square test. Publication bias was estimated by Egger's test. Studies of MHO and MONW showed heterogeneity (I(2)=99.4% and I(2)=99.7%, respectively). The overall prevalence of MHO and MONW was 7.27% (95% CI 5.92-8.90%) and 19.98% (95% CI 16.54-23.94%), respectively. American populations had the highest MHO prevalence and European populations the highest MONW prevalence. Different patterns of MHO and MONW were observed in the subgroup analysis with respect to gender, age, sample size, smoking, alcohol consumption, and metabolically healthy criteria. The prevalence of both MHO and MONW were affected by gender, region, age, sample size, smoking, alcohol consumption, and metabolically healthy criteria, but studies showed high heterogeneity.

On local anomaly detection and analysis for clinical pathways

OBJECTIVE

Anomaly detection, as an imperative task for clinical pathway (CP) analysis and improvement, can provide useful and actionable knowledge of interest to clinical experts to be potentially exploited. Existing studies mainly focused on the detection of global anomalous inpatient traces of CPs using the similarity measures in a structured manner, which brings order in the chaos of CPs, may decline the accuracy of similarity measure between inpatient traces, and may distort the efficiency of anomaly detection. In addition, local anomalies that exist in some subsegments of events or behaviors in inpatient traces are easily overlooked by existing approaches since they are designed for detecting global or large anomalies.

METHOD

In this study, we employ a probabilistic topic model to discover underlying treatment patterns, and assume any significant unexplainable deviations from the normal behaviors surmised by the derived patterns are strongly correlated with anomalous behaviours. In this way, we can figure out the detailed local abnormal behaviors and the associations between these anomalies such that diagnostic information on local anomalies can be provided.

RESULTS

The proposed approach is evaluated via a clinical data-set, including 2954 unstable angina patient traces and 483,349 clinical events, extracted from a Chinese hospital. Using the proposed method, local anomalies are detected from the log. In addition, the identified associations between the detected local anomalies are derived from the log, which lead to clinical concern on the reason resulting in these anomalies in CPs. The correctness of the proposed approach has been evaluated by three experience cardiologists of the hospital. For four types of local anomalies (i.e., unexpected events, early events, delay events, and absent events), the proposed approach achieves 94%, 71% 77%, and 93.2% in terms of recall. This is quite remarkable as we do not use a prior knowledge.

CONCLUSION

Substantial experimental results show that the proposed approach can effectively detect local anomalies in CPs, and also provide diagnostic information on the detected anomalies in an informative manner.

Comparative proteomic analysis reveals mite (Varroa destructor) resistance-related proteins in Eastern honeybees (Apis cerana)

The mite (Varroa destructor) has become the greatest threat to apiculture worldwide. As the original host of the mite, Apis cerana can effectively resist the mite. An increased understanding of the resistance mechanisms of Eastern honeybees against V. destructor may help researchers to protect other species against these parasites. In this study, the proteomes of 4 Apis cerana colonies were analyzed using an isobaric tag for relative and absolute quantitation technology. We determined the differences in gene and protein expression between susceptible and resistant colonies that were either unchallenged or challenged by V. destructor. The results showed that a total of 1532 proteins were identified. Gene Ontology enrichment analysis suggested that the transcription factors and basic metabolic and respiratory processes were efficient and feasible factors controlling this resistance, and 12 differentially expressed proteins were identified in Venn analysis. The results were validated by quantitative polymerase chain reaction. This study may provide insight into the genetic mechanisms underlying the resistance of honeybee to mites.

Effect of γ-Aminobutyric Acid-producing Lactobacillus Strain on Laying Performance, Egg Quality and Serum Enzyme Activity in Hy-Line Brown Hens under Heat Stress

Heat-stress remains a costly issue for animal production, especially for poultry as they lack sweat glands, and alleviating heat-stress is necessary for ensuring animal production in hot environment. A high γ-aminobutyric acid (GABA)-producer Lactobacillus strain was used to investigate the effect of dietary GABA-producer on laying performance and egg quality in heat-stressed Hy-line brown hens. Hy-Line brown hens (n = 1,164) at 280 days of age were randomly divided into 4 groups based on the amount of freeze-dried GABA-producer added to the basal diet as follows: i) 0 mg/kg, ii) 25 mg/kg, iii) 50 mg/kg, and iv) 100 mg/kg. All hens were subjected to heat-stress treatment through maintaining the temperature and the relative humidity at 28.83±3.85°C and 37% to 53.9%, respectively. During the experiment, laying rate, egg weight and feed intake of hens were recorded daily. At the 30th and 60th day after the start of the experiment, biochemical parameters, enzyme activity and immune activity in serum were measured. Egg production, average egg weight, average daily feed intake, feed conversion ratio and percentage of speckled egg, soft shell egg and misshaped egg were significantly improved (p<0.05) by the increasing supplementation of the dietary GABA-producer. Shape index, eggshell thickness, strength and weight were increased linearly with increasing GABA-producer supplementation. The level of calcium, phosphorus, glucose, total protein and albumin in serum of the hens fed GABA-producing strain supplemented diet was significantly higher (p<0.05) than that of the hens fed the basal diet, whereas cholesterol level was decreased. Compared with the basal diet, GABA-producer strain supplementation increased serum level of glutathione peroxidase (p = 0.009) and superoxide dismutase. In conclusion, GABA-producer played an important role in alleviating heat-stress, the isolated GABA-producer strain might be a potential natural and safe probiotic to use to improve laying performance and egg quality in heat-stressed hens.

Relationship between genetic polymorphisms of DNA ligase 1 and non-small cell lung cancer susceptibility and radiosensitivity

The aim of this study was to examine the relationship between genetic polymorphisms in DNA ligase 1 (LIG1) and non-small cell lung cancer (NSCLC) susceptibility and radiosensitivity in a Chinese population. This was a case-control study that included 352 NSCLC patients and 448 healthy controls. Polymerase chain reaction-restriction fragment length polymorphism analysis was conducted to detect HaeIII polymorphisms in exon 6 of the LIG1 gene in this popula-tion. This information was used to observe the effects of radiation in pa-tients with different genotypes in order to determine the genotypes as-sociated with radiosensitivity. The CC genotype and C allele frequency were significantly higher in the NSCLC group than in the control group (P = 0.012 and P = 0.023, respectively). The relative risk of experienc-ing NSCLC was 2.55 [95% confidence interval (CI), 1.12-3.98] for CC homozygous patients and 0.87 (95%CI, 0.46-1.88) for AA homozygous patients. Analysis of LIG1 genetic polymorphisms and radiosensitiv-ity of NSCLC patients showed that AA homozygous patients were sig-nificantly more radiosensitive than the control group (AA vs AC, P = 0.014; AA vs CC, P < 0.001; AC vs CC, P = 0.023). Therefore, the LIG1 CC genotype was associated with susceptibility to NSCLC, and the AA genotype demonstrated increased radiosensitivity compared to the AC and CC genotypes.

Diagnostic value of aberrant gene methylation in stool samples for colorectal cancer or adenomas: a meta-analysis

AIM

Many studies have reported detection of aberrant methylation of genes in stool sample for early colorectal cancer (CRC) or adenomas had high sensitivity and specificity, but still remained controversial. We aimed to evaluate the diagnostic value of stool testing for markers of CRC and adenomas.

METHODS

Medline, EMbase, Web of Science, the Cochrane Library, and EMbase were systematically searched. Meta-analysis was performed using a random effects model with sensitivity, specificity, diagnostic OR (DOR), area under the summary ROC curves (SROC) and their 95% confidence interval (95% CI).

RESULTS

A total of 13 studies including 716 patients with CRC 220 cases of adenoma and 414 healthy controls were eligible for final analysis. The sensitivity, specificity, positive likelihood ratio, negative likelihood ratio, and DOR for the detection of CRC were 0.78 (95% CI: 0.75-0.82), 0.90 (95% CI: 0.91-0.96), 9.612 (95% CI: 6.761-13.666), 0.243 (95% CI: 0.176-0.336), and 48.21 (95% CI: 28.24-82.30), respectively. The sensitivity and specificity for the detection of adenoma were 0.63 (95% CI: 0.56-0.69) and 0.93 (95% CI: 0.90-0.96), respectively. The area under the SROC curve was 0.9438 and 0.9385 in CRC and adenoma detection, respectively.

CONCLUSION

Fecal gene methylation testing as a noninvasive method can be used as a screening measurement for CRC or colorectal adenoma with high sensitivity and specificity.

The Kinematics and Kinetics Analysis of the Lower Extremity in the Landing Phase of a Stop-jump Task

Large number of studies showed that landing with great impact forces may be a risk factor for knee injuries. The purpose of this study was to illustrate the different landing loads to lower extremity of both genders and examine the relationships among selected lower extremity kinematics and kinetics during the landing of a stop-jump task. A total of 35 male and 35 female healthy subjects were recruited in this study. Each subject executed five experiment actions. Lower extremity kinematics and kinetics were synchronously acquired. The comparison of lower extremity kinematics for different genders showed significant difference. The knee and hip maximum flexion angle, peak ground reaction force and peak knee extension moment have significantly decreased during the landing of the stop-jump task among the female subjects. The hip flexion angle at the initial foot contact phase showed significant correlation with peak ground reaction force during landing of the stop-jump task (r=-0.927, p<0.001). The knee flexion angle at the initial foot contact phase had significant correlation with peak ground reaction force and vertical ground reaction forces during landing of the stop-jump task (r=-0.908, p<0.001; r=0.812, P=0.002). A large hip and knee flexion angles at the initial foot contact with the ground did not necessarily reduce the impact force during landing, but active hip and knee flexion motions did. The hip and knee flexion motion of landing was an important technical factor that affects anterior cruciate ligament (ACL) loading during the landing of the stop-jump task.

Correlation between neuronal antibodies and limbic encephalitis in Chinese Han subjects

A variety of anti-neuronal cell membrane antibodies such as voltage-gated potassium channel antibody, N-methyl-D-aspartate-2B-antibody, and glutamic acid decarboxylase antibody, are correlated with limbic encephalitis (LE). In this study on patients with LE, the clinical manifestations, psychology Wechsler Adult Intelligence Scale, cerebrospinal fluid, electrophysiology, magnetic resonance imaging, and anti-immune therapy were studied and immunological determination was conducted; it was found that patients of Chinese Han nationality showed 2 types of clinical manifestations: simple and complex. Lesions could also be divided into focal and scalable lesions, and the clinical manifestations and lesions scopes were associated with various antibodies and antibody types. The prognosis may improve if early diagnosis is conducted and early anti-immune therapy is implemented in LE patients.

On the analysis of inhomogeneous magnetic field spectrometer for laser-driven ion acceleration

We present a detailed study of the use of a non-parallel, inhomogeneous magnetic field spectrometer for the investigation of laser-accelerated ion beams. Employing a wedged yoke design, we demonstrate the feasibility of an in-situ self-calibration technique of the non-uniform magnetic field and show that high-precision measurements of ion energies are possible in a wide-angle configuration. We also discuss the implications of a stacked detector system for unambiguous identification of different ion species present in the ion beam and explore the feasibility of detection of high energy particles beyond 100 MeV/amu in radiation harsh environments.