A simple and effective method to enrich endogenous DNA from mammalian faeces.

Utilization of faeces has long been a popular approach for genetic and ecological studies of wildlife. However, the success of molecular marker genotyping and genome resequencing is often unpredictable due to insufficient enrichment of endogenous DNA in the total faecal DNA that is dominated by bacterial DNA. Here, we report a simple and cheap method named PEERS to predominantly lyse animal cells over bacteria by using sodium dodecyl sulphate so as to discharge endogenous DNA into liquid phase before bacterial DNA. By brief centrifugation, total DNA with enriched endogenous fraction can be extracted from the supernatant using routine methods. Our assessments showed that the endogenous DNA extracted by PEERS was significantly enriched for various types of faeces from different species, preservation time and conditions. It significantly improves the genotyping correctness and efficiency of genome resequencing with the total additional cost of $ 0.1 and a short incubation step to treat a faecal sample. We also provide methods to assess the enrichment efficiency of mitochondrial and nuclear DNA and models to predict the usability of faecal DNA for genotyping of short tandem repeat, single-nucleotide polymorphism and whole-genome resequencing.

Exosomal miRNA in early-stage hepatocellular carcinoma.

The incidence and mortality of hepatic carcinoma (HCC) remain high, and early diagnosis of HCC is seen as a key approach in improving clinical outcomes. However, the sensitivity and specificity of current early screening methods for HCC are not satisfactory. In recent years, research around exosomal miRNA has gradually increased, and these molecules have emerged as attractive candidates for early diagnosis and treatment of HCC. This review summarizes the feasibility of using miRNAs in peripheral blood exosomes as early diagnostic tools for HCC.

Synthesis of 1-substituted phenazines as novel antichlamydial agents.

A novel series of 1-substituted phenazines 4a-4l were designed and synthesized via Palladium-catalyzed reactions from 1-phenazine trifluoromethanesulfonate. These phenazines showed antichlamydial activity with IC50 values from 1 to 10 µM. Among them, compounds 4c and 4i exhibited the best antichlamydial activity with IC50 values from 2.06 to 2.74 µM without apparent cytotoxicity to host cells.

Clinicopathological features of neuronal intranuclear inclusion disease diagnosed by skin biopsy.

STUDY OBJECTIVES: Neuronal intranuclear inclusion disease (NIID) is a rare progressive neurodegenerative disorder, with complex and diverse of clinical manifestations characterized by eosinophilic hyaline inclusions in neurons and somatic cells. Due to the improvement in diagnostic methods, NIID is being increasingly diagnosed. METHODS: Herein, we reported three NIID cases, which were diagnosed by skin biopsy and FMR1 gene, after DWI showed the characteristic corticomedullary junction hyperintensity. Then we reviewed all the published cases of NIID in PubMed, which were diagnosed by the same method. RESULTS: We discussed 15 NIID cases, including three cases diagnosed by us. The average age was 63.4 ± 14.0 years. The average time from onset of symptom to diagnosis was 5.4 ± 7.9 years. Nine cases had dementia or cognitive impairment. Three cases presented with encephalitis. Three cases showed bladder dysfunction and two cases only presented with dizziness and headache. Two cases showed acute neurological deficit mimicking stroke. All cases were diagnosed by skin biopsy, after DWI showed abnormal corticomedullary junction hyperintensity. Ten cases showed inclusions in sweat gland cells, and seven cases in adipocytes, sweat gland cells, and fibroblasts. EMG was performed in five cases, four of whom had abnormal results, showing simultaneous involvement of motor and sensory nerves. CONCLUSIONS: The results indicated that inclusions were more easily detected in sweat gland cells in skin biopsy. The early stage of NIID could only characterized by autonomic nerve function involvement. Combined autonomic nerve dysfunction might be another relatively common manifestation in NIID.

Fatal and Rapid Progressive Isolated Cerebral Mucormycosis Involving the Bilateral Basal Ganglia: A Case Report.

Isolated cerebral mucormycosis is a clinical type of mucormycosis that is estimated to account for 8% of all mucormycosis cases. The clinical symptoms of isolated cerebral mucormycosis are elusive, and thus conventional techniques often lake sensitivity and specificity. Moreover, cultures are often negative, even when direct microscopy examination is positive. Although histopathology will probably remain the gold standard for the diagnosis of mucormycosis, obtaining a biopsy specimen is not always feasible in most vulnerable populations. Thus, molecular approaches are currently used as an advantageous assistant examination method to improve the early identification of the causative agent and subsequently guide therapy to improve the prognosis of patients. Here, we report a case of isolated cerebral mucormycosis caused by Rhizopus microspores in a healthy young adult that was identified using next-generation sequencing technology.

RIPK4 promotes bladder urothelial carcinoma cell aggressiveness by upregulating VEGF-A through the NF-κB pathway.

BACKGROUND: Constitutively activated nuclear factor kappa B (NF-κB) signalling plays vital roles in bladder urothelial carcinoma (BC) progression. We investigate the effect of receptor-interacting protein kinase 4 (RIPK4) on NF-κB activation and BC progression. METHODS: The expression of RIPK4 was examined in 25 cryopreserved paired bladder samples and 112 paraffin BC specimens. In vivo and in vitro assays were performed to validate effect of RIPK4 on NF-κB pathway-mediated BC progression. RESULTS: High expression of RIPK4 was observed in BC tissues and was an independent predictor for poor overall survival. Up or downregulating the expression of RIPK4 enhanced or inhibited, respectively, the migration and invasion of BC cells in vitro and in vivo. Mechanistically, RIPK4 promoted K63-linked polyubiquitination of tumour necrosis factor receptor-associated factor 2 (TRAF2), receptor-interacting protein (RIP) and NF-κB essential modulator (NEMO). RIPK4 also promoted nuclear localisation of NF-κB-p65, and maintained activation of NF-κB substantially, leading to upregulation of VEGF-A, ultimately promoting BC cell aggressiveness. CONCLUSIONS: Our data highlighted the molecular aetiology and clinical significance of RIPK4 in BC: upregulation of RIPK4 contributes to NF-κB activation, and upregulates VEGF-A, and BC progression. Targeting RIPK4 might represent a new therapeutic strategy to improve survival for patients with BC.

Assessing the Risk of Hg Exposure Associated with Rice Consumption in a Typical City (Suzhou) in Eastern China.

Recent studies have revealed that not only fish but also rice consumption may significantly contribute to human exposure to mercury (Hg) in Asian countries. It is therefore essential to assess dietary exposure to Hg in rice and its associated health risk. However, risk assessments of Hg in rice in non-contaminated areas are generally lacking in Asian countries. In the present study, Hg concentrations were measured in rice samples collected from markets and supermarkets in Suzhou, a typical city in Eastern China. In addition, the rice ingestion rates (IR) were assessed via a questionnaire-based survey of Suzhou residents. The data were then used to assess the risk of Hg exposure associated with rice consumption, by calculating the hazard quotient (HQ). Hg contents in rice samples were well below the national standard (20 µg/kg), ranging from 1.46 to 8.48 ng/g. They were also significantly (p > 0.05) independent of the area of production and place of purchase (markets vs. supermarkets in the different districts). Our results indicate a low risk of Hg exposure from rice in Suzhou (HQ: 0.005-0.05), despite the generally high personal IR (0.05-0.4 kg/day). The risk of Hg associated with rice consumption for Suzhou residents was not significantly affected by the age or sex of the consumer (p > 0.05). Overall, our results provide a study of human exposure to Hg in rice in Chinese cities not known to be contaminated with Hg. Future studies should examine Hg exposure in different areas in China and in potentially vulnerable major food types.

Alterations and correlations of the gut microbiome, metabolism and immunity in patients with primary biliary cirrhosis.

We selected 42 early-stage primary biliary cirrhosis (PBC) patients and 30 healthy controls (HC). Metagenomic sequencing of the 16S rRNA gene was used to characterize the fecal microbiome. UPLC-MS/MS assaying of small molecules was used to characterize the metabolomes of the serum, urine and feces. Liquid chip assaying of serum cytokines was used to characterize the immune profiles. The gut of PBC patients were depleted of some potentially beneficial bacteria, such as Acidobacteria, Lachnobacterium sp., Bacteroides eggerthii and Ruminococcus bromii, but were enriched in some bacterial taxa containing opportunistic pathogens, such as γ-Proteobacteria, Enterobacteriaceae, Neisseriaceae, Spirochaetaceae, Veillonella, Streptococcus, Klebsiella, Actinobacillus pleuropneumoniae, Anaeroglobus geminatus, Enterobacter asburiae, Haemophilus parainfluenzae, Megasphaera micronuciformis and Paraprevotella clara. Several altered gut bacterial taxa exhibited potential interactions with PBC through their associations with altered metabolism, immunity and liver function indicators, such as those of Klebsiella with IL-2A and Neisseriaceae with urinary indoleacrylate. Many gut bacteria, such as some members of Bacteroides, were altered in their associations with the immunity and metabolism of PBC patients, although their relative abundances were unchanged. Consequently, the gut microbiome is altered and may be critical for the onset or development of PBC by interacting with metabolism and immunity.

Distinctive pathways characterize A. actinomycetemcomitans and P. gingivalis.

The study aimed to compare the molecular mechanism of Porphuromonas gingivalis (P. gingivalis) and Aggregatibacter actinomycetemcomitans (A. actinomycetemcomitans). With microarray dataset (GSE9723) from Gene Expression Omnibus, differentially expressed genes (DEGs) were identified comparing normal cell samples with A. actinomycetemcomitans-infected and P. gingivalis-infected periodontitis cell samples, respectively (|logFC| > 1, p value <0.01), followed by hierarchical cluster analysis using Cluster software. Network topological features of A. actinomycetemcomitans-related and P. gingivalis-related protein-protein interaction networks, and background network, which included average shortest path length (ASPL), degree, closeness centrality (CC), eccentricity (EC), betweenness centrality (BC) and topological coefficient (TC) were compared using network analysis plugin of Cytoscape, followed by pathway enrichment analysis (p value <0.05) using FISHER hyper-geometric algorithm and calculation of pathway alter scores using LIMMA. Totally, 839 DEGs and 251 DEGs were screened for A. actinomycetemcomitans and P. gingivalis, respectively. A. actinomycetemcomitans-related network had lower ASPL, degree and EC but higher CC and TC (p < 0.01), while P. gingivalis-related network had lower EC but higher CC and BC (p < 0.01) compared to background network. P. gingivalis-related network had lower ASPL, degree and EC, but higher CC than the A. actinomycetemcomitans-related network (p < 0.05). A. actinomycetemcomitans was associated with the pathways relating to endothelial cells function, while neuroactive ligand-receptor interaction and MAPK pathways were important for P. gingivalis, which had higher alter scores in hematopoietic cell lineage, hypertrophic cardiomyopathy and arrhythmogenic right ventricular cardiomyopathy pathways than A. actinomycetemcomitans. Genes and pathways of the two pathogens were distinctive. The findings aided in preventing and treating relevant diseases.

Viral genome and antiviral drug sensitivity analysis of two patients from a family cluster caused by the influenza A(H7N9) virus in Zhejiang, China, 2013.

OBJECTIVES: In the winter of 2013, people were facing the risk of human-to-human transmission of the re-emerging influenza A(H7N9) virus. We report herein information on the clinical features of two patients from the same family infected with this virus, the genomic sequences of the viruses harbored, and antiviral drug sensitivity. METHODS: Clinical and epidemiological data of two patients from the same family were collected and analyzed. Sequencing was done for the viruses isolated from these two patients and one epidemiologically related chicken, and the sequences of the eight gene segments of the viruses were analyzed phylogenetically. The sensitivity of the viruses to antiviral drug treatment was determined by neuraminidase inhibitor susceptibility test. RESULTS: The two patients from one family cluster shared the same symptoms but had different outcomes, and had a strong epidemiological link. Three strains, two from these two patients and one from the chicken, were isolated. Genome sequencing and analyses of phylogenetic trees demonstrated that the two viruses were almost identical. We noted the presence of the PB2 E627K amino acid substitution that was not present in isolates from the first wave, as well as two new mutations in the NA gene and six in the PB2 gene. Drug sensitivity testing showed that the new isolates were resistant to oseltamivir but sensitive to peramivir. CONCLUSIONS: The two patients from one family cluster were probable human-to-human transmission cases. The new isolates were sensitive to peramivir but showed reduced sensitivity to oseltamivir.

[Fate of matrix-bound phosphine during acidification with anaerobic bacteria].

Matrix-bound phosphine of anaerobic granular sludge was studied during methanogenic and acidogenic stage of anaerobic reactors. Results showed that at methanogenic stage, the concentration of matrix-bound phosphine of anaerobic sludge decreased as the height of reactor increased. But during acidogenic stage, matrix-bound phosphine disappeared when pH of the solution declined to 4-5. Further anaerobic static experiments showed that increased acidification and lower pH value promoted the decrease of matrix-bound phosphine. After cultivation with 2 000 mg x L(-1) glucose synthetic wastewater for two days, the matrix-bound phosphine fell from 1.76 ng x kg(-1) to 0.09 ng x kg(-1); At the same time, the highest disappearing rate of phosphine was reached 0.84 ng x (kg x d)(-1). While the glucose synthetic wastewater was 400 mg x L(-1), the disappearing rate of phosphine was only 0.27 ng x (kg x d)(-1). With further cultivation under acidogenic stage, the phosphine decreasing rate slowed down.

Construction and characterization of chimeric BHIV (BIV/HIV-1) viruses carrying the bovine immunodeficiency virus gag gene.

AIM: To explore the possibility of the replacement of the gag gene between human immunodeficiency virus and bovine immunodeficiency virus, to achieve chimeric virions, and thereby gain a new kind of AIDS vaccine based on BHIV chimeric viruses. METHODS: A series of chimeric BHIV proviral DNAs differing in the replacement regions in gag gene were constructed, and then were transfected into 293T cells. The expression of chimeric viral genes was detected at the RNA and protein level. The supernatant of 293T cell was ultra centrifuged to detect the probable chimeric virion. Once the chimeric virion was detected, its biological activities were also assayed by infecting HIV-sensitive MT4 cells. RESULTS: Four chimeric BHIV proviral DNAs were constructed. Genes in chimeric viruses expressed correctly in transfected 293T cells. All four constructs assembled chimeric virions with different degrees of efficiency. These virions had complete structures common to retroviruses and packaged genomic RNAs, but the cleavages of the precursor Gag proteins were abnormal to some extent. Three of these virions tested could attach and enter into MT4 cells, and one of them could complete the course of reverse transcription. Yet none of them could replicate in MT4 cells. CONCLUSION: The replacement of partial gag gene of HIV with BIV gag gene is feasible. Genes in chimeric BHIVs are accurately expressed, and virions are assembled. These chimeric BHIVs (proviral DNA together with virus particles) have the potential to become a new kind of HIV/AIDS vaccine.

[A practical system for B-mode ultrasound image acquisition and patient's medical history management].

A practical system of B-ultrasonic is here introduced. By a special medical video card, the video image is digitized and captured dynamically or statically into computer. This system realizes a variety of functions such as the B-ultrasonic video image's acquisition and display, as well as the editing, processing, managing, storage, printing, It can build the database of patient's case history automatically. Together with other medical image workstation the system can be built as a PACS system of the hospital. And it can also act as an independent system.